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Bugfix for Interstitial Oxidation States #208

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Merged
merged 3 commits into from
Nov 4, 2024
Merged

Bugfix for Interstitial Oxidation States #208

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11ddf46
Update `core.py`
kavanase Nov 3, 2024
409e168
Update core.py
kavanase Nov 3, 2024
ab8c9b9
Update test_core.py
kavanase Nov 3, 2024
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4 changes: 2 additions & 2 deletions pymatgen/analysis/defects/core.py
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Expand Up @@ -706,9 +706,9 @@ def name(self) -> str:
def defect_structure(self) -> Structure:
"""Returns the defect structure."""
struct: Structure = self.structure.copy()
# use the highest value oxidation state among the two most popular ones
# use the highest value oxidation state among the most popular ones
# found in the ICSD
inter_states = self.site.specie.icsd_oxidation_states[:2]
inter_states = self.site.specie.common_oxidation_states
if len(inter_states) == 0:
_logger.warning(
"No oxidation states found for %s. "
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4 changes: 2 additions & 2 deletions tests/test_core.py
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Expand Up @@ -119,8 +119,8 @@ def test_interstitial(gan_struct) -> None:
inter_fpos = [0, 0, 0.75]
n_site = PeriodicSite(Specie("N"), inter_fpos, s.lattice)
inter = Interstitial(s, n_site)
assert inter.oxi_state == 3
assert inter.get_charge_states() == [-1, 0, 1, 2, 3, 4]
assert inter.oxi_state == 5
assert inter.get_charge_states() == [-1, 0, 1, 2, 3, 4, 5, 6]
assert np.allclose(inter.defect_structure[0].frac_coords, inter_fpos)
sc = inter.get_supercell_structure()
assert sc.formula == "Ga64 N65"
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