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Do not introduce zero magmoms in SpacegroupAnalyzer #2727

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merged 3 commits into from
Nov 8, 2022
Merged

Do not introduce zero magmoms in SpacegroupAnalyzer #2727

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d39aa9f
do not introduce zero magmoms in SpacegroupAnalyzer
lbluque Nov 8, 2022
ba08bc0
fix mypy error
janosh Nov 8, 2022
803d750
fix test_get_symmetry()
janosh Nov 8, 2022
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10 changes: 6 additions & 4 deletions pymatgen/symmetry/analyzer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@
from collections import defaultdict
from fractions import Fraction
from math import cos, sin
from typing import Literal
from typing import Any, Literal

import numpy as np
import spglib
Expand Down Expand Up @@ -76,12 +76,14 @@ def __init__(self, structure: Structure, symprec: float = 0.01, angle_tolerance=
magmoms.append(site.magmom)
elif site.is_ordered and hasattr(site.specie, "spin"):
magmoms.append(site.specie.spin)
else:
magmoms.append(0) # needed for spglib

self._unique_species = unique_species
self._numbers = zs
self._cell = structure.lattice.matrix, structure.frac_coords, zs, magmoms

if len(magmoms) > 0:
self._cell: tuple[Any, ...] = structure.lattice.matrix, structure.frac_coords, zs, magmoms
else: # if no magmoms given do not add to cell
self._cell = structure.lattice.matrix, structure.frac_coords, zs

self._space_group_data = spglib.get_symmetry_dataset(
self._cell, symprec=self._symprec, angle_tolerance=angle_tolerance
Expand Down
5 changes: 4 additions & 1 deletion pymatgen/symmetry/tests/test_analyzer.py
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Expand Up @@ -134,7 +134,10 @@ def test_get_symmetry(self):
match=f"Symmetry detection failed for structure with formula {Co8.formula}. "
f"Try setting {symprec=} to a different value.",
):
SpacegroupAnalyzer(Co8, symprec=symprec)._get_symmetry()
sga = SpacegroupAnalyzer(Co8, symprec=symprec)
magmoms = [0] * len(Co8) # bad magmoms, see https://github.com/materialsproject/pymatgen/pull/2727
sga._cell = (*sga._cell, magmoms)
sga._get_symmetry()

def test_get_crystal_system(self):
crystal_system = self.sg.get_crystal_system()
Expand Down