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Fix atom type consistency #10

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Merged
chaibhave merged 3 commits into from
Apr 13, 2026
Merged

Fix atom type consistency #10

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fcf5df7
Fix atom type consistency across generations/iterations. Closes #9
jarinfrench Apr 7, 2026
4a97561
Improve GA robustness against failed energy evaluations
jarinfrench Apr 7, 2026
11ec56b
Add initial_structure support and mutation tracking to minimizers
jarinfrench Apr 7, 2026
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3 changes: 2 additions & 1 deletion GBOpt/Atom.py
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Original file line number Diff line number Diff line change
Expand Up @@ -192,7 +192,8 @@ def as_array(atoms: np.ndarray, *, type_map: dict[str, int] = None) -> np.ndarra
converted = np.empty((len(atoms), 4))
names = atoms["name"]
if type_map is None:
type_map = {name: idx + 1 for idx, name in enumerate(set(names))}
unique_names = list(dict.fromkeys(names))
type_map = {name: idx + 1 for idx, name in enumerate(unique_names)}
else:
if not isinstance(type_map, dict):
return AtomTypeError(
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10 changes: 9 additions & 1 deletion GBOpt/GBMaker.py
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Original file line number Diff line number Diff line change
Expand Up @@ -596,7 +596,15 @@ def write_lammps(
"'atoms' and 'box_sizes' must be specified together."
)

name_to_int = {name: i + 1 for i, name in enumerate(np.unique(atoms["name"]))}
atom_names = np.unique(atoms["name"])
if set(atom_names).issubset(self.__unit_cell.type_map.keys()):
name_to_int = {
name: self.__unit_cell.type_map[name]
for name in self.__unit_cell.type_map
if name in atom_names
}
else:
name_to_int = {name: i + 1 for i, name in enumerate(atom_names)}

if charges is not None:
if not all([isinstance(i, int) or isinstance(i, str) for i in charges.keys()]):
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