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Recreate structure fresh during get_primitive_cell #144

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708a643
Recreate structure fresh during get_primitive_cell
pmrv Feb 14, 2024
354d825
Format black
pyiron-runner Feb 14, 2024
4942144
Adapt tests
pmrv Feb 14, 2024
bfc42f0
Remove array copies and add warning
pmrv Feb 14, 2024
b1d1f46
Merge remote-tracking branch 'refs/remotes/origin/main' into standardize
jan-janssen Jul 18, 2024
8f5fbab
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 18, 2024
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30 changes: 23 additions & 7 deletions structuretoolkit/analyse/symmetry.py
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Original file line number Diff line number Diff line change
Expand Up @@ -384,26 +384,42 @@ def get_primitive_cell(
>>> symmetry = Symmetry(structure)
>>> len(symmetry.get_primitive_cell()) == len(basis)
True

.. warning::
Custom arrays defined in the base structures
:attr:`ase.atoms.Atoms.arrays` are not copied to the new structure!
"""
if not all(self._structure.pbc):
raise ValueError("Can only symmetrize periodic structures.")
ret = spglib.standardize_cell(
self._get_spglib_cell(use_elements=use_elements, use_magmoms=use_magmoms),
to_primitive=not standardize,
)
if ret is None:
raise SymmetryError(spglib.spglib.spglib_error.message)
cell, positions, indices = ret
positions = (cell.T @ positions.T).T
new_structure = self._structure.copy()
new_structure.cell = cell
new_structure = new_structure[: len(indices)]
cell, scaled_positions, indices = ret
indices_dict = {
v: k
for k, v in structuretoolkit.common.helper.get_species_indices_dict(
structure=self._structure
).items()
}
new_structure.symbols = [indices_dict[i] for i in indices]
new_structure.positions = positions
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!")
Comment on lines +407 to +421
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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

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
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)


return new_structure

def get_ir_reciprocal_mesh(
Expand Down
6 changes: 4 additions & 2 deletions tests/test_symmetry.py
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Original file line number Diff line number Diff line change
Expand Up @@ -173,7 +173,9 @@ def test_get_ir_reciprocal_mesh(self):

def test_get_primitive_cell(self):
cell = 2.2 * np.identity(3)
basis = Atoms("AlFe", scaled_positions=[(0, 0, 0), (0.5, 0.5, 0.5)], cell=cell)
basis = Atoms(
"AlFe", scaled_positions=[(0, 0, 0), (0.5, 0.5, 0.5)], cell=cell, pbc=True
)
structure = basis.repeat([2, 2, 2])
sym = stk.analyse.get_symmetry(structure=structure)
self.assertEqual(len(basis), len(sym.get_primitive_cell(standardize=True)))
Expand All @@ -199,7 +201,7 @@ def test_get_primitive_cell_hex(self):
[0.77, 1.57, 5.74],
]
cell = [[2.519, 1.454, 4.590], [-2.519, 1.454, 4.590], [0.0, -2.909, 4.590]]
structure = Atoms(symbols=elements, positions=positions, cell=cell)
structure = Atoms(symbols=elements, positions=positions, cell=cell, pbc=True)
structure_repeat = structure.repeat([2, 2, 2])
sym = stk.analyse.get_symmetry(structure=structure_repeat)
structure_prim_base = sym.get_primitive_cell()
Expand Down