Do not introduce zero magmoms in SpacegroupAnalyzer (#2727)

* do not introduce zero magmoms in SpacegroupAnalyzer * fix mypy error * fix test_get_symmetry() modify sga._cell in place to make sure ValueError is raised Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>
materialsproject · Nov 8, 2022 · 6b520e3 · 6b520e3
1 parent c70a590
commit 6b520e3
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Showing 2 changed files with 10 additions and 5 deletions.
diff --git a/pymatgen/symmetry/analyzer.py b/pymatgen/symmetry/analyzer.py
@@ -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
@@ -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

diff --git a/pymatgen/symmetry/tests/test_analyzer.py b/pymatgen/symmetry/tests/test_analyzer.py
@@ -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()