add exclude option to make_ase_atoms

CHANGELOG.md

@@ -5,6 +5,12 @@ All notable changes to `casm-tools` will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unreleased]
+
+### Fixed
+
+- Exclude species from `casm.tools.shared.ase_utils.make_ase_atoms`.
+  Vacancies are excluded by default.
 
 ## [2.0a2] - 2024-08-07
 

casm/tools/shared/ase_utils.py

@@ -13,7 +13,9 @@
 import libcasm.xtal as xtal
 
 
-def make_ase_atoms(casm_structure: xtal.Structure) -> ase.Atoms:
+def make_ase_atoms(
+    casm_structure: xtal.Structure, exclude: list[str] = ["VA", "Va", "va"]
+) -> ase.Atoms:
     """Given a CASM Structure, convert it to an ASE Atoms
 
     .. attention::
@@ -33,6 +35,8 @@ def make_ase_atoms(casm_structure: xtal.Structure) -> ase.Atoms:
     Parameters
     ----------
     casm_structure : libcasm.xtal.Structure
+    exclude : list[str]
+        Species to exclude from the ASE Atoms.
 
     Returns
     -------
@@ -45,8 +49,14 @@ def make_ase_atoms(casm_structure: xtal.Structure) -> ase.Atoms:
             "to_ase_atoms"
         )
 
-    symbols = casm_structure.atom_type()
-    positions = casm_structure.atom_coordinate_cart().transpose()
+    initial_symbols = casm_structure.atom_type()
+    initial_positions = casm_structure.atom_coordinate_cart().transpose()
+    symbols = []
+    positions = []
+    for index, symbol in enumerate(initial_symbols):
+        if symbol not in exclude:
+            symbols.append(symbol)
+            positions.append(initial_positions[index])
     cell = casm_structure.lattice().column_vector_matrix().transpose()
 
     return ase.Atoms(

tests/shared/ase_utils/test_ase_utils.py

@@ -0,0 +1,7 @@
+from libcasm.xtal import structures
+from casm.tools.shared import ase_utils
+
+
+def test_make_ase_atoms_va():
+    test_structure = structures.BCC(r=1, atom_type="Va")
+    ase_utils.make_ase_atoms(test_structure)