def test_redf(self):
d = ElectronicRadialDistributionFunction().featurize(
self.diamond)[0]
self.assertAlmostEqual(int(1000 * d["distances"][0]), 25)
self.assertAlmostEqual(int(1000 * d["distribution"][0]), 0)
self.assertAlmostEqual(int(1000 * d["distances"][len(
d["distances"]) - 1]), 6175)
self.assertAlmostEqual(int(1000 * d["distribution"][len(
d["distances"]) - 1]), 0)
d = ElectronicRadialDistributionFunction().featurize(
self.nacl)[0]
self.assertAlmostEqual(int(1000 * d["distances"][0]), 25)
self.assertAlmostEqual(int(1000 * d["distribution"][0]), 0)
self.assertAlmostEqual(int(1000 * d["distances"][56]), 2825)
self.assertAlmostEqual(int(1000 * d["distribution"][56]), -2108)
self.assertAlmostEqual(int(1000 * d["distances"][len(
d["distances"]) - 1]), 9875)
d = ElectronicRadialDistributionFunction().featurize(
self.cscl)[0]
self.assertAlmostEqual(int(1000 * d["distances"][0]), 25)
self.assertAlmostEqual(int(1000 * d["distribution"][0]), 0)
self.assertAlmostEqual(int(1000 * d["distances"][72]), 3625)
self.assertAlmostEqual(int(1000 * d["distribution"][72]), -2194)
self.assertAlmostEqual(int(1000 * d["distances"][len(
d["distances"]) - 1]), 7275)
from matminer.featurizers.structure import ElectronicRadialDistributionFunction
import numpy as np
cen_structures=np.load('centrosymmetric_insulators.npy',allow_pickle=True)
cen_redf=[]
non_cen_structures=np.load('non_centrosymmetric_insulators.npy',allow_pickle=True)
non_cen_redf=[]
#create redf representations
redf = ElectronicRadialDistributionFunction()
redf.set_n_jobs(28)
redf.fit(cen_structures)
for item in cen_structures:
cen_redf.append(redf.featurize(item))
np.save('centrosymmetric_redf_representation.npy',cen_redf)
redf.fit(non_cen_structures)
for item in non_cen_structures:
non_cen_redf.append(redf.featurize(item))
np.save('non_centrosymmetric_redf_representation.npy',non_cen_redf)
namecolumns = ['structure']
for i in CIFfiles:
structlist.append([Structure.from_file(directoryname + i)
]) #Converts CIF to pymatgen structure object
namelist.append(os.path.splitext(i)[0]) #Collects all the structure names
structs.append(Structure.from_file(directoryname + i))
#Creates Pandas dataframe with data being a list of structures and the row name being the structure name
dftest = pd.DataFrame(data=structlist, index=namelist, columns=namecolumns)
p = PartialRadialDistributionFunction()
p.fit(np.asarray(structs))
c = CoulombMatrix()
c.fit(np.asarray(structs))
erdf = ElectronicRadialDistributionFunction()
erdf.cutoff = 10 #longest diagonal of lattice...I picked a number semi-arbitrarily
#Featurizes the structures
featurizer = MultipleFeaturizer([
ElementProperty.from_preset('magpie'),
OxidationStates(),
AtomicOrbitals(),
BandCenter(),
ElectronegativityDiff(),
DensityFeatures(),
RadialDistributionFunction(), p, c, erdf
])
r = (featurizer.featurize_many(dftest, ['structure'])
) #Featurizes entire Pandas Dataframe