Recreate structure fresh during get_primitive_cell #144
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This avoids a problem, when you pass standardize=True and the resulting cell would be larger than the original.
I mark this pull request as draft until the tests pass. |
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I made tests pass by passing |
The trouble is that when spglib returns the symmetrized cell, it may permute, add or remove atoms so that we cannot tell anymore which values from the original arrays we would need to copy or remove.
# Conflicts: # structuretoolkit/analyse/symmetry.py
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Actionable comments posted: 1
Outside diff range, codebase verification and nitpick comments (1)
structuretoolkit/analyse/symmetry.py (1)
388-390: Add a period at the end of the warning message.The warning message should end with a period for consistency.
- Custom arrays defined in the base structures - :attr:`ase.atoms.Atoms.arrays` are not copied to the new structure! + Custom arrays defined in the base structures + :attr:`ase.atoms.Atoms.arrays` are not copied to the new structure!.
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Files selected for processing (2)
- structuretoolkit/analyse/symmetry.py (1 hunks)
- tests/test_symmetry.py (2 hunks)
Additional context used
Ruff
structuretoolkit/analyse/symmetry.py
421-421: Undefined name
warning(F821)
Additional comments not posted (3)
tests/test_symmetry.py (2)
176-178: LGTM! The addition ofpbc=Trueis correct.The change ensures that the structure is treated as periodic, which is necessary for the
get_primitive_cellfunction to work correctly.
204-204: LGTM! The addition ofpbc=Trueis correct.The change ensures that the structure is treated as periodic, which is necessary for the
get_primitive_cellfunction to work correctly.structuretoolkit/analyse/symmetry.py (1)
392-393: Good check for periodic structures.The check ensures that the function only operates on periodic structures, which is necessary for symmetrization.
| symbols = [indices_dict[i] for i in indices] | ||
| arrays = { | ||
| k: self._structure.arrays[k] | ||
| for k in self._structure.arrays | ||
| if k not in ("numbers", "positions") | ||
| } | ||
| new_structure = type(self._structure)( | ||
| symbols=symbols, | ||
| scaled_positions=scaled_positions, | ||
| cell=cell, | ||
| pbc=[True, True, True], | ||
| ) | ||
| keys = set(arrays) - {"numbers", "positions"} | ||
| if len(keys) > 0: | ||
| warning(f"Custom arrays {keys} do not carry over to new structure!") |
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Fix the undefined name warning.
The warning function is not defined. Use the warnings.warn function instead.
- if len(keys) > 0:
- warning(f"Custom arrays {keys} do not carry over to new structure!")
+ if len(keys) > 0:
+ import warnings
+ warnings.warn(f"Custom arrays {keys} do not carry over to new structure!")Committable suggestion
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| symbols = [indices_dict[i] for i in indices] | |
| arrays = { | |
| k: self._structure.arrays[k] | |
| for k in self._structure.arrays | |
| if k not in ("numbers", "positions") | |
| } | |
| new_structure = type(self._structure)( | |
| symbols=symbols, | |
| scaled_positions=scaled_positions, | |
| cell=cell, | |
| pbc=[True, True, True], | |
| ) | |
| keys = set(arrays) - {"numbers", "positions"} | |
| if len(keys) > 0: | |
| warning(f"Custom arrays {keys} do not carry over to new structure!") | |
| symbols = [indices_dict[i] for i in indices] | |
| arrays = { | |
| k: self._structure.arrays[k] | |
| for k in self._structure.arrays | |
| if k not in ("numbers", "positions") | |
| } | |
| new_structure = type(self._structure)( | |
| symbols=symbols, | |
| scaled_positions=scaled_positions, | |
| cell=cell, | |
| pbc=[True, True, True], | |
| ) | |
| keys = set(arrays) - {"numbers", "positions"} | |
| if len(keys) > 0: | |
| import warnings | |
| warnings.warn(f"Custom arrays {keys} do not carry over to new structure!") |
Tools
Ruff
421-421: Undefined name
warning(F821)
This avoids a problem, when you pass standardize=True and the resulting cell would be larger than the original.
Summary by CodeRabbit
New Features
Bug Fixes
Tests