def test_orbital_field_matrix(self):
ofm_maker = OrbitalFieldMatrix()
ofm = ofm_maker.featurize(self.diamond)[0]
mtarget = np.zeros((32, 32))
mtarget[1][1] = 1.4789015 # 1.3675444
mtarget[1][3] = 1.4789015 # 1.3675444
mtarget[3][1] = 1.4789015 # 1.3675444
mtarget[3][3] = 1.4789015 # 1.3675444 if for a coord# of exactly 4
for i in range(32):
for j in range(32):
if not i in [1, 3] and not j in [1, 3]:
self.assertEqual(ofm[i, j], 0.0)
mtarget = np.matrix(mtarget)
self.assertAlmostEqual(np.linalg.norm(ofm - mtarget), 0.0, places=4)
ofm_maker = OrbitalFieldMatrix(True)
ofm = ofm_maker.featurize(self.diamond)[0]
mtarget = np.zeros((39, 39))
mtarget[1][1] = 1.4789015
mtarget[1][3] = 1.4789015
mtarget[3][1] = 1.4789015
mtarget[3][3] = 1.4789015
mtarget[1][33] = 1.4789015
mtarget[3][33] = 1.4789015
mtarget[33][1] = 1.4789015
mtarget[33][3] = 1.4789015
mtarget[33][33] = 1.4789015
mtarget = np.matrix(mtarget)
self.assertAlmostEqual(np.linalg.norm(ofm - mtarget), 0.0, places=4)
def test_orbital_field_matrix(self):
ofm_maker = OrbitalFieldMatrix()
ofm = ofm_maker.featurize(self.diamond)[0]
mtarget = np.zeros((32, 32))
mtarget[1][1] = 1.4789015 # 1.3675444
mtarget[1][3] = 1.4789015 # 1.3675444
mtarget[3][1] = 1.4789015 # 1.3675444
mtarget[3][3] = 1.4789015 # 1.3675444 if for a coord# of exactly 4
for i in range(32):
for j in range(32):
if not i in [1, 3] and not j in [1, 3]:
self.assertEqual(ofm[i, j], 0.0)
mtarget = np.matrix(mtarget)
self.assertAlmostEqual(
np.linalg.norm(ofm - mtarget), 0.0, places=4)
ofm_maker = OrbitalFieldMatrix(True)
ofm = ofm_maker.featurize(self.diamond)[0]
mtarget = np.zeros((39, 39))
mtarget[1][1] = 1.4789015
mtarget[1][3] = 1.4789015
mtarget[3][1] = 1.4789015
mtarget[3][3] = 1.4789015
mtarget[1][33] = 1.4789015
mtarget[3][33] = 1.4789015
mtarget[33][1] = 1.4789015
mtarget[33][3] = 1.4789015
mtarget[33][33] = 1.4789015
mtarget = np.matrix(mtarget)
self.assertAlmostEqual(
np.linalg.norm(ofm - mtarget), 0.0, places=4)
ofm_flat = OrbitalFieldMatrix(period_tag=False, flatten=True)
self.assertEqual(len(ofm_flat.feature_labels()), 1024)
ofm_flat = OrbitalFieldMatrix(period_tag=True, flatten=True)
self.assertEqual(len(ofm_flat.feature_labels()), 1521)
ofm_vector = ofm_flat.featurize(self.diamond)
for ix in [40, 42, 72, 118, 120, 150, 1288, 1320]:
self.assertAlmostEqual(ofm_vector[ix], 1.4789015345821415)
def test_orbital_field_matrix(self):
ofm_maker = OrbitalFieldMatrix(flatten=False)
ofm = ofm_maker.featurize(self.diamond)[0]
mtarget = np.zeros((32, 32))
mtarget[1][1] = 1.4789015 # 1.3675444
mtarget[1][3] = 1.4789015 # 1.3675444
mtarget[3][1] = 1.4789015 # 1.3675444
mtarget[3][3] = 1.4789015 # 1.3675444 if for a coord# of exactly 4
for i in range(32):
for j in range(32):
if not i in [1, 3] and not j in [1, 3]:
self.assertEqual(ofm[i, j], 0.0)
mtarget = np.matrix(mtarget)
self.assertAlmostEqual(
np.linalg.norm(ofm - mtarget), 0.0, places=4)
ofm_maker = OrbitalFieldMatrix(True, flatten=False)
ofm = ofm_maker.featurize(self.diamond)[0]
mtarget = np.zeros((39, 39))
mtarget[1][1] = 1.4789015
mtarget[1][3] = 1.4789015
mtarget[3][1] = 1.4789015
mtarget[3][3] = 1.4789015
mtarget[1][33] = 1.4789015
mtarget[3][33] = 1.4789015
mtarget[33][1] = 1.4789015
mtarget[33][3] = 1.4789015
mtarget[33][33] = 1.4789015
mtarget = np.matrix(mtarget)
self.assertAlmostEqual(
np.linalg.norm(ofm - mtarget), 0.0, places=4)
ofm_flat = OrbitalFieldMatrix(period_tag=False, flatten=True)
self.assertEqual(len(ofm_flat.feature_labels()), 1024)
ofm_flat = OrbitalFieldMatrix(period_tag=True, flatten=True)
self.assertEqual(len(ofm_flat.feature_labels()), 1521)
ofm_vector = ofm_flat.featurize(self.diamond)
for ix in [40, 42, 72, 118, 120, 150, 1288, 1320]:
self.assertAlmostEqual(ofm_vector[ix], 1.4789015345821415)
import numpy as np
from matminer.featurizers.structure import OrbitalFieldMatrix
cen_structures = np.load(
'/home/dennis/Dropbox/mp_share_dt_ag/structs/centrosymmetric_insulators.npy',
allow_pickle=True)
print(len(cen_structures))
#create ofm representations
ofm = OrbitalFieldMatrix()
cen_ofm = []
for item in cen_structures:
cen_ofm.append(ofm.featurize(item))
np.save('centrosymmetric_ofm_representation.npy', cen_ofm)
non_cen_structures = np.load(
'/home/dennis/Dropbox/mp_share_dt_ag/structs/non_centrosymmetric_insulators.npy',
allow_pickle=True)
print(len(non_cen_structures))
non_cen_ofm = []
for item in non_cen_structures:
non_cen_ofm.append(ofm.featurize(item))
np.save('non_centrosymmetric_ofm_representation.npy', non_cen_ofm)