Merge pull request #3157 from mattmcdermott/magnetic-analyzer-fix

Bug fix: `CollinearMagneticAnalyzer` should not fail when `Species.spin = None`

Author: mkhorton

pymatgen/analysis/magnetism/analyzer.py

@@ -187,7 +187,7 @@ def __init__(
                 )
             magmoms = [m or 0 for m in structure.site_properties["magmom"]]
         elif has_spin:
-            magmoms = [getattr(sp, "spin", 0) for sp in structure.species]
+            magmoms = [sp.spin or 0 for sp in structure.species]
             structure.remove_spin()
         else:
             # no magmoms present, add zero magmoms for now

pymatgen/analysis/magnetism/tests/test_analyzer.py

@@ -237,6 +237,18 @@ def test_round_magmoms(self):
         assert msa.magnetic_species_and_magmoms["Ni"][1] == approx(5.0143)
         assert msa.magnetic_species_and_magmoms["O"] == approx(0.1465)
 
+    def test_missing_spin(self):
+        # This test catches the case where a structure has some species with
+        # Species.spin=None. This previously raised an error upon construction
+        # of the analyzer).
+        latt = Lattice([[2.085, 2.085, 0.0], [0.0, -2.085, -2.085], [-2.085, 2.085, -4.17]])
+        species = [Species("Ni", spin=-5), Species("Ni", spin=5), Species("O", spin=None), Species("O", spin=None)]
+        coords = [[0.5, 0, 0.5], [0, 0, 0], [0.25, 0.5, 0.25], [0.75, 0.5, 0.75]]
+        struct = Structure(latt, species, coords)
+
+        msa = CollinearMagneticStructureAnalyzer(struct, round_magmoms=0.001, make_primitive=False)
+        assert msa.structure.site_properties["magmom"] == [-5, 5, 0, 0]
+
 
 class MagneticStructureEnumeratorTest(unittest.TestCase):
     @unittest.skipIf(not enumlib_present, "enumlib not present")