def process_item(self, item):
"""
Process the tasks and materials into a magnetism collection
Args:
item dict: a dict of material_id, structure, and tasks
Returns:
dict: a magnetism dictionary
"""
struct = Structure.from_dict(item["structure"])
total_magnetization = item["magnetism"].get(
"total_magnetization", 0) # not necessarily == sum(magmoms)
msa = CollinearMagneticStructureAnalyzer(struct)
sign = np.sign(total_magnetization)
total_magnetization = abs(total_magnetization)
magmoms = list(sign * np.array(msa.magmoms))
magnetism = {
self.magnetism.key: item[self.materials.key],
"magnetism": {
'ordering':
msa.ordering.value,
'is_magnetic':
msa.is_magnetic,
'exchange_symmetry':
msa.get_exchange_group_info()[1],
'num_magnetic_sites':
msa.number_of_magnetic_sites,
'num_unique_magnetic_sites':
msa.number_of_unique_magnetic_sites(),
'types_of_magnetic_species':
[str(t) for t in msa.types_of_magnetic_specie],
'magmoms':
magmoms,
'total_magnetization_normalized_vol':
total_magnetization / struct.volume,
'total_magnetization_normalized_formula_units':
total_magnetization /
(struct.composition.get_reduced_composition_and_factor()[1])
},
"pymatgen_version": pymatgen_version
}
return magnetism
def calc(self, item):
"""
Process the tasks and materials into a magnetism collection
Args:
item dict: a dict of material_id, structure, and tasks
Returns:
dict: a magnetism dictionary
"""
struct = Structure.from_dict(get(item, "output.structure"))
struct_has_magmoms = 'magmom' in struct.site_properties
total_magnetization = abs(
get(item, "calcs_reversed.0.output.outcar.total_magnetization", 0))
msa = CollinearMagneticStructureAnalyzer(struct)
magmoms = msa.magmoms
magnetism = {
"magnetism": {
'ordering':
msa.ordering.value if struct_has_magmoms else "Unknown",
'is_magnetic':
msa.is_magnetic,
'exchange_symmetry':
msa.get_exchange_group_info()[1],
'num_magnetic_sites':
msa.number_of_magnetic_sites,
'num_unique_magnetic_sites':
msa.number_of_unique_magnetic_sites(),
'types_of_magnetic_species':
[str(t) for t in msa.types_of_magnetic_specie],
'magmoms':
magmoms,
'total_magnetization':
total_magnetization,
'total_magnetization_normalized_vol':
total_magnetization / struct.volume,
'total_magnetization_normalized_formula_units':
total_magnetization /
(struct.composition.get_reduced_composition_and_factor()[1])
},
"pymatgen_version": pymatgen_version
}
return magnetism
def test_magnetic_properties(self):
msa = CollinearMagneticStructureAnalyzer(self.GdB4)
self.assertFalse(msa.is_collinear)
msa = CollinearMagneticStructureAnalyzer(self.Fe)
self.assertFalse(msa.is_magnetic)
self.Fe.add_site_property("magmom", [5])
msa = CollinearMagneticStructureAnalyzer(self.Fe)
self.assertTrue(msa.is_magnetic)
self.assertTrue(msa.is_collinear)
self.assertEqual(msa.ordering, Ordering.FM)
msa = CollinearMagneticStructureAnalyzer(
self.NiO,
make_primitive=False,
overwrite_magmom_mode="replace_all_if_undefined",
)
self.assertEqual(msa.number_of_magnetic_sites, 4)
self.assertEqual(msa.number_of_unique_magnetic_sites(), 1)
self.assertEqual(msa.types_of_magnetic_species, (Element.Ni, ))
self.assertEqual(msa.get_exchange_group_info(), ("Fm-3m", 225))