From 9b230fe4136cdbc5a45e0f6dfe72ef0c4e5e945a Mon Sep 17 00:00:00 2001
From: Rohit Goswami <rog32@hi.is>
Date: Wed, 20 Mar 2024 15:45:09 +0000
Subject: [PATCH 01/12] MAINT: Use the cmcrameri color scheme

---
 pypotlib/systems/cu_slab_h2.py | 12 ++++++------
 pyproject.toml                 |  1 +
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/pypotlib/systems/cu_slab_h2.py b/pypotlib/systems/cu_slab_h2.py
index 792d006..90e06e1 100644
--- a/pypotlib/systems/cu_slab_h2.py
+++ b/pypotlib/systems/cu_slab_h2.py
@@ -8,23 +8,22 @@
 import numpy as np
 import matplotlib.pyplot as plt
 from ase.calculators.calculator import Calculator, all_changes
+import cmcrameri.cm as cmc
 
 from pypotlib import cpot
 from pypotlib.aux import reshape_data
 
 FuncVal = namedtuple("FuncVal", ["x", "y", "energy"])
 PltRange = namedtuple("PltRange", ["low", "high"])
-PlotPtPosData = namedtuple('PlotPtPosData', ['h2pos', 'pltpts'])
-PlotPoints = namedtuple('PlotPoints', ['x_npt', 'y_npt'])
+PlotPtPosData = namedtuple("PlotPtPosData", ["h2pos", "pltpts"])
+PlotPoints = namedtuple("PlotPoints", ["x_npt", "y_npt"])
+
 
 class CuH2PotSlab(Calculator):
     implemented_properties = ["energy", "forces"]
     discard_results_on_any_change = True
 
-    def __init__(self,
-                 e_zero=FuncVal(x=0.752542,
-                                y=5.0,
-                                energy=-697.311695)):
+    def __init__(self, e_zero=FuncVal(x=0.752542, y=5.0, energy=-697.311695)):
         Calculator.__init__(self)
         self.cpot = cpot.CuH2Pot()
         self._ezero = e_zero
@@ -88,6 +87,7 @@ def contour_plot(data, _max_val = 5, _nlvls=500):
         energy,
         levels=np.linspace(0, _max_val, _nlvls),
         extend="max",
+        cmap=cmc.batlow,
     )
     # Add labels and title to the plot
     ax.set_xlabel("H-H distance")
diff --git a/pyproject.toml b/pyproject.toml
index 61727a4..09fe735 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,6 +11,7 @@ authors = [
 dependencies = [
     "numpy>=1.24.3",
     "ase>=3.22.1",
+    "cmcrameri>=1.8",
 ]
 requires-python = ">=3.8"
 readme = "README.md"

From d70f70b985b6adcb9978193a1b9ab7de00c78f0c Mon Sep 17 00:00:00 2001
From: Rohit Goswami <rog32@hi.is>
Date: Wed, 20 Mar 2024 15:46:29 +0000
Subject: [PATCH 02/12] ENH: Add the option of scattering points

---
 pypotlib/systems/cu_slab_h2.py | 44 +++++++++++++++++++++++++---------
 1 file changed, 33 insertions(+), 11 deletions(-)

diff --git a/pypotlib/systems/cu_slab_h2.py b/pypotlib/systems/cu_slab_h2.py
index 90e06e1..9c62d3e 100644
--- a/pypotlib/systems/cu_slab_h2.py
+++ b/pypotlib/systems/cu_slab_h2.py
@@ -1,6 +1,12 @@
-__all__ = ["CuH2PotSlab", "FuncVal", "PltRange",
-           "PlotPtPos", "contour_plot", "plt_data",
-           "set_slab_dist"]
+__all__ = [
+    "CuH2PotSlab",
+    "FuncVal",
+    "PltRange",
+    "PlotPtPos",
+    "contour_plot",
+    "plt_data",
+    "set_slab_dist",
+]
 
 import warnings
 from collections import namedtuple
@@ -42,6 +48,7 @@ def calculate(
         self.results["energy"] = energy - self._ezero.energy
         self.results["forces"] = forces
 
+
 def set_slab_dist(atoms, dist):
     h_ind = np.where(np.asarray(atoms.get_chemical_symbols()) == "H")[0]
     n_hatoms = len(h_ind)
@@ -50,12 +57,14 @@ def set_slab_dist(atoms, dist):
     cpos[-n_hatoms:, 2] = np.repeat(max_slab_z + dist, n_hatoms)
     atoms.set_positions(cpos)
 
-def plt_data(_atms, hh_range=PltRange(low=0.4, high=3),
-                  h2slab_range = PltRange(low=-0.05, high=5),
-                  n_points=PlotPoints(x_npt=60, y_npt=60)):
-    h_dists = np.linspace(
-        hh_range.low, hh_range.high, n_points.x_npt
-    )
+
+def plt_data(
+    _atms,
+    hh_range=PltRange(low=0.4, high=3),
+    h2slab_range=PltRange(low=-0.05, high=5),
+    n_points=PlotPoints(x_npt=60, y_npt=60),
+):
+    h_dists = np.linspace(hh_range.low, hh_range.high, n_points.x_npt)
     slab_dists = np.linspace(
         h2slab_range.low, h2slab_range.high, n_points.y_npt
     )
@@ -76,7 +85,8 @@ def plt_data(_atms, hh_range=PltRange(low=0.4, high=3),
             )
     return PlotPtPosData(h2pos=plt_h2pos, pltpts=plt_data)
 
-def contour_plot(data, _max_val = 5, _nlvls=500):
+
+def contour_plot(data, _max_val=5, _nlvls=500, scatter_points=None):
     x, y, energy = reshape_data(data)
     # Create a contour plot of the energy surface
     fig, ax = plt.subplots()
@@ -89,10 +99,22 @@ def contour_plot(data, _max_val = 5, _nlvls=500):
         extend="max",
         cmap=cmc.batlow,
     )
+    # Scatter
+    if scatter_points is not None:
+        scatter_points = np.array(scatter_points)
+        ax.scatter(
+            scatter_points[:, 0],
+            scatter_points[:, 1],
+            marker="+",
+            color="gray",
+        )
+
     # Add labels and title to the plot
     ax.set_xlabel("H-H distance")
     ax.set_ylabel("Slab distance")
-    ax.set_title('Energy Surface Contour Plot\nShifted by the zero of the energy')
+    ax.set_title(
+        "Energy Surface Contour Plot\nShifted by the zero of the energy"
+    )
     # Add a colorbar to the plot
     cbar = fig.colorbar(cs)
     # Show the plot

From 03fe04b17318e1c52f67b978df02360580ccc7e5 Mon Sep 17 00:00:00 2001
From: Rohit Goswami <rog32@hi.is>
Date: Wed, 20 Mar 2024 15:47:42 +0000
Subject: [PATCH 03/12] ENH: Add an function to get distances from a slab

Given the HH and HCu distances along with the baseline configuration
---
 pypotlib/systems/cu_slab_h2.py | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/pypotlib/systems/cu_slab_h2.py b/pypotlib/systems/cu_slab_h2.py
index 9c62d3e..60dbbb5 100644
--- a/pypotlib/systems/cu_slab_h2.py
+++ b/pypotlib/systems/cu_slab_h2.py
@@ -58,6 +58,37 @@ def set_slab_dist(atoms, dist):
     atoms.set_positions(cpos)
 
 
+def calculate_hh_and_hcu_distances(h_positions, ref_atoms):
+    """
+    Calculate the H-H distance and the specific H(midpoint)-slab distance based on the reference configuration.
+
+    Parameters:
+    - h_positions: A 6-element list or array with the coordinates of the H atoms [x1, y1, z1, x2, y2, z2].
+    - ref_atoms: An ASE Atoms object containing the reference configuration, including H and Cu atoms.
+
+    Returns:
+    - hh_distance: Distance between the two H atoms.
+    - hcu_distance: Distance from the H-H midpoint to the slab, considering the reference configuration.
+    """
+    # Reshape h_positions to a 2x3 matrix for easier manipulation
+    h_positions_matrix = np.array(h_positions).reshape(2, 3)
+
+    # Calculate H-H midpoint
+    midpoint = np.mean(h_positions_matrix, axis=0)
+
+    # Calculate H-H distance
+    hh_distance = np.linalg.norm(h_positions_matrix[0] - h_positions_matrix[1])
+
+    # Determine the maximum Z position of Cu atoms in the reference configuration as the reference slab surface
+    cu_positions = ref_atoms.positions[ref_atoms.numbers == 29]
+    max_cu_z = np.max(cu_positions[:, 2])
+
+    # Calculate the distance from the H-H midpoint to the reference slab surface
+    hcu_distance = midpoint[2] - max_cu_z
+
+    return hh_distance, hcu_distance
+
+
 def plt_data(
     _atms,
     hh_range=PltRange(low=0.4, high=3),

From 0a4ca2bf84e51b6dda0eba0f1e72bb9d2b4bdc33 Mon Sep 17 00:00:00 2001
From: Rohit Goswami <rog32@hi.is>
Date: Wed, 20 Mar 2024 15:48:21 +0000
Subject: [PATCH 04/12] DOC: Minor reword

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index cb9621a..c361544 100644
--- a/README.md
+++ b/README.md
@@ -25,8 +25,8 @@ The easiest way is to use the environment file, compatible with `conda`,
 `mamba`, `micromamba` etc.
 
 ```bash
-mamba env create -f environment.yml
-mamba activate rgpotpy
+micromamba env create -f environment.yml
+micromamba activate rgpotpy
 pdm install
 ```
 

From b568a6604ee66b73808573bb5994cb3d3101ae9e Mon Sep 17 00:00:00 2001
From: Rohit Goswami <rog32@hi.is>
Date: Wed, 20 Mar 2024 16:35:51 +0000
Subject: [PATCH 05/12] MAINT: Bump to 3.9 and nightly numpy / scipy

---
 pyproject.toml | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 09fe735..4978578 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,11 +9,11 @@ authors = [
 ]
 # These are only if ase integration is requested, consider a group
 dependencies = [
-    "numpy>=1.24.3",
+    "numpy>=2.0",
     "ase>=3.22.1",
     "cmcrameri>=1.8",
 ]
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 readme = "README.md"
 license = {text = "MIT"}
 
@@ -50,3 +50,10 @@ all = {composite = ["lint pypotlib/"]}
 [tool.black]
 line-length = 80
 target-version = ['py310']
+
+[[tool.pdm.source]]
+name = "nightly-scientific-python"
+url = "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple/"
+verify_ssl = true
+include_packages = ["scipy", "scipy-*", "numpy", "numpy-*"]
+exclude_packages = ["*"]

From 690625041ae53a8f2cacd9cf9dbc5776572c170a Mon Sep 17 00:00:00 2001
From: Rohit Goswami <rog32@hi.is>
Date: Wed, 20 Mar 2024 17:58:10 +0000
Subject: [PATCH 06/12] MAINT: Add dev matplotlib

---
 pyproject.toml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 4978578..b19e008 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,6 +12,7 @@ dependencies = [
     "numpy>=2.0",
     "ase>=3.22.1",
     "cmcrameri>=1.8",
+    "matplotlib>=3.9.0.dev0",
 ]
 requires-python = ">=3.9"
 readme = "README.md"
@@ -55,5 +56,5 @@ target-version = ['py310']
 name = "nightly-scientific-python"
 url = "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple/"
 verify_ssl = true
-include_packages = ["scipy", "scipy-*", "numpy", "numpy-*"]
+include_packages = ["scipy", "scipy-*", "numpy", "numpy-*", "matplotlib", "matplotlib-*"]
 exclude_packages = ["*"]

From 956c90cb2a3c22dbf5bacac53be6fe6cf3840637 Mon Sep 17 00:00:00 2001
From: Rohit Goswami <rog32@hi.is>
Date: Thu, 11 Apr 2024 13:53:33 +0000
Subject: [PATCH 07/12] BUG: Fix the windows aux issue

Closes gh-1
---
 meson.build                    | 2 +-
 pypotlib/{aux.py => _aux.py}   | 0
 pypotlib/systems/cu_slab_h2.py | 2 +-
 3 files changed, 2 insertions(+), 2 deletions(-)
 rename pypotlib/{aux.py => _aux.py} (100%)

diff --git a/meson.build b/meson.build
index 5fbe894..c6530f1 100644
--- a/meson.build
+++ b/meson.build
@@ -61,7 +61,7 @@ py.install_sources([
 # Adapters
 py.install_sources([
     'pypotlib/ase_adapters.py',
-    'pypotlib/aux.py',
+    'pypotlib/_aux.py',
   ],
   pure: false,
   subdir: 'pypotlib'
diff --git a/pypotlib/aux.py b/pypotlib/_aux.py
similarity index 100%
rename from pypotlib/aux.py
rename to pypotlib/_aux.py
diff --git a/pypotlib/systems/cu_slab_h2.py b/pypotlib/systems/cu_slab_h2.py
index 60dbbb5..5735c6f 100644
--- a/pypotlib/systems/cu_slab_h2.py
+++ b/pypotlib/systems/cu_slab_h2.py
@@ -17,7 +17,7 @@
 import cmcrameri.cm as cmc
 
 from pypotlib import cpot
-from pypotlib.aux import reshape_data
+from pypotlib._aux import reshape_data
 
 FuncVal = namedtuple("FuncVal", ["x", "y", "energy"])
 PltRange = namedtuple("PltRange", ["low", "high"])

From a313bef64da9c0360e47c035184848b510ea475d Mon Sep 17 00:00:00 2001
From: Rohit Goswami <rog32@hi.is>
Date: Thu, 11 Apr 2024 13:56:32 +0000
Subject: [PATCH 08/12] MAINT: Export the new function

---
 pypotlib/systems/cu_slab_h2.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pypotlib/systems/cu_slab_h2.py b/pypotlib/systems/cu_slab_h2.py
index 5735c6f..aeb257f 100644
--- a/pypotlib/systems/cu_slab_h2.py
+++ b/pypotlib/systems/cu_slab_h2.py
@@ -6,6 +6,7 @@
     "contour_plot",
     "plt_data",
     "set_slab_dist",
+    "calculate_hh_and_hcu_distances",
 ]
 
 import warnings

From 2f83d783ba54b19377aa4daca380a3becafae237 Mon Sep 17 00:00:00 2001
From: Rohit Goswami <rog32@hi.is>
Date: Tue, 16 Apr 2024 22:23:55 +0000
Subject: [PATCH 09/12] MAINT: Add a title

---
 pypotlib/systems/cu_slab_h2.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/pypotlib/systems/cu_slab_h2.py b/pypotlib/systems/cu_slab_h2.py
index aeb257f..c7c74c5 100644
--- a/pypotlib/systems/cu_slab_h2.py
+++ b/pypotlib/systems/cu_slab_h2.py
@@ -118,7 +118,7 @@ def plt_data(
     return PlotPtPosData(h2pos=plt_h2pos, pltpts=plt_data)
 
 
-def contour_plot(data, _max_val=5, _nlvls=500, scatter_points=None):
+def contour_plot(data, _max_val=5, _nlvls=500, scatter_points=None, title=None):
     x, y, energy = reshape_data(data)
     # Create a contour plot of the energy surface
     fig, ax = plt.subplots()
@@ -144,9 +144,12 @@ def contour_plot(data, _max_val=5, _nlvls=500, scatter_points=None):
     # Add labels and title to the plot
     ax.set_xlabel("H-H distance")
     ax.set_ylabel("Slab distance")
-    ax.set_title(
-        "Energy Surface Contour Plot\nShifted by the zero of the energy"
-    )
+    if title:
+        ax.set_title(title)
+    else:
+        ax.set_title(
+            "Energy Surface Contour Plot\nShifted by the zero of the energy"
+        )
     # Add a colorbar to the plot
     cbar = fig.colorbar(cs)
     # Show the plot

From f121b8d9b694f7dd22ef5a7838bc6ba253834b8f Mon Sep 17 00:00:00 2001
From: Rohit Goswami <rog32@hi.is>
Date: Tue, 16 Apr 2024 22:24:01 +0000
Subject: [PATCH 10/12] BLD: Stay with numpy<2.x

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index b19e008..d1b39a6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,7 +9,7 @@ authors = [
 ]
 # These are only if ase integration is requested, consider a group
 dependencies = [
-    "numpy>=2.0",
+    "numpy",
     "ase>=3.22.1",
     "cmcrameri>=1.8",
     "matplotlib>=3.9.0.dev0",

From 7b3ee8c606eab15972ed883c28c92c192bccd2b8 Mon Sep 17 00:00:00 2001
From: Rohit Goswami <rog32@hi.is>
Date: Fri, 19 Apr 2024 18:12:26 +0000
Subject: [PATCH 11/12] MAINT: Don't move input atoms, cleanup

---
 pypotlib/systems/cu_slab_h2.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/pypotlib/systems/cu_slab_h2.py b/pypotlib/systems/cu_slab_h2.py
index c7c74c5..92b2205 100644
--- a/pypotlib/systems/cu_slab_h2.py
+++ b/pypotlib/systems/cu_slab_h2.py
@@ -91,8 +91,8 @@ def calculate_hh_and_hcu_distances(h_positions, ref_atoms):
 
 
 def plt_data(
-    _atms,
-    hh_range=PltRange(low=0.4, high=3),
+    atms,
+    hh_range=PltRange(low=0.4, high=3.8),
     h2slab_range=PltRange(low=-0.05, high=5),
     n_points=PlotPoints(x_npt=60, y_npt=60),
 ):
@@ -100,6 +100,8 @@ def plt_data(
     slab_dists = np.linspace(
         h2slab_range.low, h2slab_range.high, n_points.y_npt
     )
+    _atms = atms.copy()
+    _atms.calc = atms.calc
     h_ind = np.where(np.asarray(_atms.get_chemical_symbols()) == "H")[0]
     plt_data = []  # x, y, energy
     plt_h2pos = []  # h2 positions
@@ -138,7 +140,7 @@ def contour_plot(data, _max_val=5, _nlvls=500, scatter_points=None, title=None):
             scatter_points[:, 0],
             scatter_points[:, 1],
             marker="+",
-            color="gray",
+            color="lightgray",
         )
 
     # Add labels and title to the plot

From 6d73bda179bd37abdcc77c3bdf9c32c85c73cad6 Mon Sep 17 00:00:00 2001
From: Rohit Goswami <rog32@hi.is>
Date: Thu, 26 Sep 2024 20:15:03 +0000
Subject: [PATCH 12/12] MAINT: Use both

---
 pypotlib/systems/cu_slab_h2.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pypotlib/systems/cu_slab_h2.py b/pypotlib/systems/cu_slab_h2.py
index 92b2205..352ddb3 100644
--- a/pypotlib/systems/cu_slab_h2.py
+++ b/pypotlib/systems/cu_slab_h2.py
@@ -130,7 +130,7 @@ def contour_plot(data, _max_val=5, _nlvls=500, scatter_points=None, title=None):
         y,
         energy,
         levels=np.linspace(0, _max_val, _nlvls),
-        extend="max",
+        extend="both",
         cmap=cmc.batlow,
     )
     # Scatter