def test_matches(self):
self.assertTrue(self.NiO.matches(self.NiO_AFM_111))
self.assertTrue(self.NiO.matches(self.NiO_AFM_001))
# MSA adds magmoms to Structure, so not equal
msa = CollinearMagneticStructureAnalyzer(
self.NiO, overwrite_magmom_mode="replace_all")
self.assertFalse(msa.matches_ordering(self.NiO))
self.assertFalse(msa.matches_ordering(self.NiO_AFM_111))
self.assertFalse(msa.matches_ordering(self.NiO_AFM_001))
msa = CollinearMagneticStructureAnalyzer(
self.NiO_AFM_001, overwrite_magmom_mode="respect_sign")
self.assertFalse(msa.matches_ordering(self.NiO))
self.assertFalse(msa.matches_ordering(self.NiO_AFM_111))
self.assertTrue(msa.matches_ordering(self.NiO_AFM_001))
self.assertTrue(msa.matches_ordering(self.NiO_AFM_001_opposite))
msa = CollinearMagneticStructureAnalyzer(
self.NiO_AFM_111, overwrite_magmom_mode="respect_sign")
self.assertFalse(msa.matches_ordering(self.NiO))
self.assertTrue(msa.matches_ordering(self.NiO_AFM_111))
self.assertFalse(msa.matches_ordering(self.NiO_AFM_001))
self.assertFalse(msa.matches_ordering(self.NiO_AFM_001_opposite))
def collate_mp_data(struct):
mag_tasks = {}
min_energy = 0
ordering_labels = {
"Unknown": "Unknown",
"FM": "Ferromagnetic",
"AFM": "Antiferromagnetic",
"FiM": "Ferrimagnetic",
"NM": "Non-magnetic",
}
with MPRester(endpoint="https://zola.lbl.gov/rest/v2") as mpr:
# find similar structures in Materials Project
mpids = mpr.find_structure(struct)
# and all tasks for those materials, specifically their structures
# and total energy per atom
for d in mpr.query({"task_id": {"$in": mpids}}, ["task_ids"]):
for task_id in d["task_ids"]:
add_task = True
task_struct = mpr.get_task_data(
task_id, prop="structure")[0]["structure"]
have_magmoms = "magmom" in task_struct.site_properties
task_energy = mpr.get_task_data(
task_id, prop="energy_per_atom")[0]["energy_per_atom"]
min_energy = min([min_energy, task_energy])
msa = CollinearMagneticStructureAnalyzer(task_struct)
if not have_magmoms:
ordering = "Unknown"
else:
ordering = msa.ordering.value
# group together similar orderings, only display lowest
# energy task for each ordering
mag_tasks_to_remove = []
for mag_task_id, mag_task in mag_tasks.items():
struct_to_compare = mag_task["struct"]
if msa.matches_ordering(struct_to_compare):
# if existing task is lower in energy, keep that one
if mag_task["energy"] < task_energy:
add_task = False
# else remove existing task and add this one
else:
mag_tasks_to_remove.append(mag_task_id)
# remove higher energy duplicate tasks
for mag_task_id in mag_tasks_to_remove:
del mag_tasks[mag_task_id]
if add_task:
mag_tasks[task_id] = {
"struct": task_struct,
"ordering": ordering_labels[ordering],
"energy": task_energy,
}
for k, v in mag_tasks.items():
v["energy"] = 1000 * (v["energy"] - min_energy)
mag_tasks[k] = v
return mag_tasks