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Fix filter condition for warn msg of unphysical site occupancy in io.cif #3853

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merged 5 commits into from
Jun 3, 2024
Merged

Fix filter condition for warn msg of unphysical site occupancy in io.cif #3853

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87ed8f4
fix filter condition and to list
DanielYang59 Jun 1, 2024
54f7ade
update unit test for err msg
DanielYang59 Jun 1, 2024
e281fdf
increase monty version
DanielYang59 Jun 1, 2024
2c6da9a
Revert "increase monty version"
DanielYang59 Jun 3, 2024
2183779
Merge branch 'master' into fix-io-cif-err-msg
janosh Jun 3, 2024
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2 changes: 1 addition & 1 deletion pymatgen/io/cif.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1073,7 +1073,7 @@ def get_matching_coord(

if any(occu > 1 for occu in _sum_occupancies):
msg = (
f"Some occupancies ({filter(lambda x: x<=1, _sum_occupancies)}) sum to > 1! If they are within "
f"Some occupancies ({list(filter(lambda x: x>1, _sum_occupancies))}) sum to > 1! If they are within "
"the occupancy_tolerance, they will be rescaled. "
f"The current occupancy_tolerance is set to: {self._occupancy_tolerance}"
)
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5 changes: 4 additions & 1 deletion tests/io/test_cif.py
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Original file line number Diff line number Diff line change
Expand Up @@ -748,7 +748,10 @@ def test_not_check_occu(self):
cif_str = cif_file.read()
cif_str = cif_str.replace("Te Te 1.0000", "Te_label Te 10.0", 1)

structs = CifParser.from_str(cif_str).parse_structures(check_occu=False)
with pytest.warns(
UserWarning, match=r"Issues encountered while parsing CIF: Some occupancies \(\[10\.0\]\) sum to > 1!"
):
structs = CifParser.from_str(cif_str).parse_structures(check_occu=False)

assert len(structs) > 0
assert set(structs[0].labels) == {"Te_label", "Ge"}
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