def run(self):
logger.info("MaterialsDescriptorBuilder starting...")
self._build_indexes()
q = {}
if not self.update_all:
q["descriptors.density"] = {"$exists": False}
mats = [
m for m in self._materials.find(q, {
"structure": 1,
"material_id": 1
})
]
pbar = tqdm(mats)
for m in pbar:
pbar.set_description("Processing materials_id: {}".format(
m['material_id']))
struct = Structure.from_dict(m["structure"])
d = {"descriptors": {}}
d["descriptors"]["dimensionality"] = get_dimensionality(struct)
d["descriptors"]["density"] = struct.density
d["descriptors"]["nsites"] = len(struct)
d["descriptors"]["volume"] = struct.volume
self._materials.update_one({"material_id": m["material_id"]},
{"$set": d})
def list_dimensionality(list_struc):
get_list = []
for structure in list_struc:
print(structure.formula)
try:
get_list.append(
get_dimensionality(structure,
max_hkl=2,
el_radius_updates=None,
min_slab_size=5,
min_vacuum_size=5,
standardize=True,
bonds=None))
except:
get_list.append("N/A")
continue
return get_list
def run(self):
logger.info("MaterialsDescriptorBuilder starting...")
self._build_indexes()
q = {}
if not self.update_all:
q["descriptors.density"] = {"$exists": False}
mats = [m for m in self._materials.find(q, {"structure": 1, "material_id": 1})]
pbar = tqdm(mats)
for m in pbar:
pbar.set_description("Processing materials_id: {}".format(m['material_id']))
struct = Structure.from_dict(m["structure"])
d = {"descriptors": {}}
d["descriptors"]["dimensionality"] = get_dimensionality(struct)
d["descriptors"]["density"] = struct.density
d["descriptors"]["nsites"] = len(struct)
d["descriptors"]["volume"] = struct.volume
self._materials.update_one({"material_id": m["material_id"]}, {"$set": d})
def test_get_dimensionality_with_bonds(self):
s = self.get_structure('CsCl')
self.assertEqual(get_dimensionality(s), 1)
self.assertEqual(get_dimensionality(s, bonds={("Cs", "Cl"): 3.7}), 3)
def test_get_dimensionality(self):
s = self.get_structure('LiFePO4')
self.assertEqual(get_dimensionality(s), 3)
s = self.get_structure('Graphite')
self.assertEqual(get_dimensionality(s), 2)
def test_get_dimensionality_with_bonds(self):
s = self.get_structure('CsCl')
self.assertEqual(get_dimensionality(s), 1)
self.assertEqual(get_dimensionality(s, bonds={("Cs", "Cl"): 3.7}), 3)
def test_get_dimensionality(self):
s = self.get_structure('LiFePO4')
self.assertEqual(get_dimensionality(s), 3)
s = self.get_structure('Graphite')
self.assertEqual(get_dimensionality(s), 2)
def plug_in(symbol_values):
structure = symbol_values['structure']
return {'dimensionality': get_dimensionality(structure)}
