def test_all_nn_classes(self):
self.assertEqual(MinimumDistanceNN(cutoff=5, get_all_sites=True).get_cn(
self.cscl, 0), 14)
self.assertEqual(MinimumDistanceNN().get_cn(self.diamond, 0), 4)
self.assertEqual(MinimumDistanceNN().get_cn(self.nacl, 0), 6)
self.assertEqual(MinimumDistanceNN().get_cn(self.lifepo4, 0), 6)
self.assertEqual(MinimumDistanceNN(tol=0.01).get_cn(self.cscl, 0), 8)
self.assertEqual(MinimumDistanceNN(tol=0.1).get_cn(self.mos2, 0), 6)
for image in MinimumDistanceNN(tol=0.1).get_nn_images(self.mos2, 0):
self.assertTrue(image in [(0, 0, 0), (0, 1, 0), (-1, 0, 0),
(0, 0, 0), (0, 1, 0), (-1, 0, 0)])
okeeffe = MinimumOKeeffeNN(tol=0.01)
self.assertEqual(okeeffe.get_cn(self.diamond, 0), 4)
self.assertEqual(okeeffe.get_cn(self.nacl, 0), 6)
self.assertEqual(okeeffe.get_cn(self.cscl, 0), 8)
self.assertEqual(okeeffe.get_cn(self.lifepo4, 0), 2)
virenn = MinimumVIRENN(tol=0.01)
self.assertEqual(virenn.get_cn(self.diamond, 0), 4)
self.assertEqual(virenn.get_cn(self.nacl, 0), 6)
self.assertEqual(virenn.get_cn(self.cscl, 0), 8)
self.assertEqual(virenn.get_cn(self.lifepo4, 0), 2)
brunner_recip = BrunnerNN_reciprocal(tol=0.01)
self.assertEqual(brunner_recip.get_cn(self.diamond, 0), 4)
self.assertEqual(brunner_recip.get_cn(self.nacl, 0), 6)
self.assertEqual(brunner_recip.get_cn(self.cscl, 0), 14)
self.assertEqual(brunner_recip.get_cn(self.lifepo4, 0), 6)
brunner_rel = BrunnerNN_relative(tol=0.01)
self.assertEqual(brunner_rel.get_cn(self.diamond, 0), 4)
self.assertEqual(brunner_rel.get_cn(self.nacl, 0), 6)
self.assertEqual(brunner_rel.get_cn(self.cscl, 0), 14)
self.assertEqual(brunner_rel.get_cn(self.lifepo4, 0), 6)
brunner_real = BrunnerNN_real(tol=0.01)
self.assertEqual(brunner_real.get_cn(self.diamond, 0), 4)
self.assertEqual(brunner_real.get_cn(self.nacl, 0), 6)
self.assertEqual(brunner_real.get_cn(self.cscl, 0), 14)
self.assertEqual(brunner_real.get_cn(self.lifepo4, 0), 30)
econn = EconNN()
self.assertEqual(econn.get_cn(self.diamond, 0), 4)
self.assertEqual(econn.get_cn(self.nacl, 0), 6)
self.assertEqual(econn.get_cn(self.cscl, 0), 14)
self.assertEqual(econn.get_cn(self.lifepo4, 0), 6)
voroinn = VoronoiNN(tol=0.5)
self.assertEqual(voroinn.get_cn(self.diamond, 0), 4)
self.assertEqual(voroinn.get_cn(self.nacl, 0), 6)
self.assertEqual(voroinn.get_cn(self.cscl, 0), 8)
self.assertEqual(voroinn.get_cn(self.lifepo4, 0), 6)
crystalnn = CrystalNN()
self.assertEqual(crystalnn.get_cn(self.diamond, 0), 4)
self.assertEqual(crystalnn.get_cn(self.nacl, 0), 6)
self.assertEqual(crystalnn.get_cn(self.cscl, 0), 8)
self.assertEqual(crystalnn.get_cn(self.lifepo4, 0), 6)
def test_noble_gas_material(self):
cnn = CrystalNN()
self.assertEqual(cnn.get_cn(self.he_bcc, 0, use_weights=False), 0)
cnn = CrystalNN(distance_cutoffs=(1.25, 5))
self.assertEqual(cnn.get_cn(self.he_bcc, 0, use_weights=False), 8)
def test_noble_gas_material(self):
cnn = CrystalNN()
self.assertEqual(cnn.get_cn(self.he_bcc, 0, use_weights=False), 0)
cnn = CrystalNN(distance_cutoffs=(1.25, 5))
self.assertEqual(cnn.get_cn(self.he_bcc, 0, use_weights=False), 8)
def test_sanity(self):
with self.assertRaises(ValueError):
cnn = CrystalNN()
cnn.get_cn(self.lifepo4, 0, use_weights=True)
with self.assertRaises(ValueError):
cnn = CrystalNN(weighted_cn=True)
cnn.get_cn(self.lifepo4, 0, use_weights=False)
def test_sanity(self):
with self.assertRaises(ValueError):
cnn = CrystalNN()
cnn.get_cn(self.lifepo4, 0, use_weights=True)
with self.assertRaises(ValueError):
cnn = CrystalNN(weighted_cn=True)
cnn.get_cn(self.lifepo4, 0, use_weights=False)
def test_noble_gas_material(self):
cnn = CrystalNN()
with self.assertRaises(RuntimeError):
cnn.get_cn(self.he_bcc, 0, use_weights=False)
cnn = CrystalNN(distance_cutoffs=(1.25, 5))
self.assertAlmostEqual(cnn.get_cn(self.he_bcc, 0, use_weights=False),
8)
def get_coordinations(self):
"""
Inputs
struct: a pymatgen structure object
Returns
coordination_numbers: a dictionary containing each species' name and average coordination
number rounded to nearest integer
"""
struct = self.structure
vnn = CrystalNN()
coordination_numbers = {}
stoich = defaultdict(int)
for site in struct.as_dict()['sites']:
elem = site['species'][0]['element']
stoich[elem] += 1
for spec in stoich.keys():
coordination_numbers[spec] = 0.0
for atom in range(len(struct)):
try:
cn = vnn.get_cn(struct, atom, use_weights=False)
coordination_numbers[
struct[atom].species.elements[0].element.symbol] += cn
except:
return None
for spec in coordination_numbers:
coordination_numbers[
spec] = coordination_numbers[spec] / stoich[spec]
coordination_numbers[spec] = int(round(coordination_numbers[spec]))
return coordination_numbers
def test_discrete_cn(self):
cnn = CrystalNN()
cn_array = []
expected_array = [6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4]
for idx, _ in enumerate(self.lifepo4):
cn_array.append(cnn.get_cn(self.lifepo4, idx))
self.assertSequenceEqual(cn_array, expected_array)
def test_discrete_cn(self):
cnn = CrystalNN()
cn_array = []
expected_array = [6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4]
for idx, _ in enumerate(self.lifepo4):
cn_array.append(cnn.get_cn(self.lifepo4, idx))
self.assertSequenceEqual(cn_array, expected_array)
def test_weighted_cn(self):
cnn = CrystalNN(weighted_cn=True)
cn_array = []
expected_array = [6.0449, 6.0431, 6.0449, 6.0431, 5.6262, 5.6253,
5.6258, 5.6258, 3.9936, 3.9936, 3.9936, 3.9936,
3.9183, 3.7318, 3.7259, 3.781, 3.781, 3.7259,
3.7318, 3.9183, 3.9183, 3.7318, 3.7248, 3.7819,
3.7819, 3.7248, 3.7318, 3.9183]
for idx, _ in enumerate(self.lifepo4):
cn_array.append(cnn.get_cn(self.lifepo4, idx, use_weights=True))
self.assertArrayAlmostEqual(expected_array, cn_array, 2)
def test_weighted_cn(self):
cnn = CrystalNN(weighted_cn=True)
cn_array = []
expected_array = [5.863, 5.8716, 5.863, 5.8716, 5.7182, 5.7182, 5.719,
5.7181, 3.991, 3.991, 3.991, 3.9907, 3.5997, 3.525,
3.4133, 3.4714, 3.4727, 3.4133, 3.525, 3.5997,
3.5997, 3.525, 3.4122, 3.4738, 3.4728, 3.4109,
3.5259, 3.5997]
for idx, _ in enumerate(self.lifepo4):
cn_array.append(cnn.get_cn(self.lifepo4, idx, use_weights=True))
self.assertArrayAlmostEqual(expected_array, cn_array, 2)
def test_weighted_cn(self):
cnn = CrystalNN(weighted_cn=True)
cn_array = []
expected_array = [5.8962, 5.8996, 5.8962, 5.8996, 5.7195, 5.7195,
5.7202, 5.7194, 4.0012, 4.0012, 4.0012, 4.0009,
3.3897, 3.2589, 3.1218, 3.1914, 3.1914, 3.1218,
3.2589, 3.3897, 3.3897, 3.2589, 3.1207, 3.1924,
3.1915, 3.1207, 3.2598, 3.3897]
for idx, _ in enumerate(self.lifepo4):
cn_array.append(cnn.get_cn(self.lifepo4, idx, use_weights=True))
self.assertArrayAlmostEqual(expected_array, cn_array, 2)
def test_weighted_cn(self):
cnn = CrystalNN(weighted_cn=True)
cn_array = []
expected_array = [5.863, 5.8716, 5.863 , 5.8716, 5.7182, 5.7182, 5.719,
5.7181, 3.991 , 3.991 , 3.991 , 3.9907, 3.5997, 3.525,
3.4133, 3.4714, 3.4727, 3.4133, 3.525 , 3.5997,
3.5997, 3.525 , 3.4122, 3.4738, 3.4728, 3.4109,
3.5259, 3.5997]
for idx, _ in enumerate(self.lifepo4):
cn_array.append(cnn.get_cn(self.lifepo4, idx, use_weights=True))
self.assertArrayAlmostEqual(expected_array, cn_array, 2)
def test_weighted_cn(self):
cnn = CrystalNN(weighted_cn=True)
cn_array = []
expected_array = [
6.0449, 6.0431, 6.0449, 6.0431, 5.6262, 5.6253, 5.6258, 5.6258,
3.9936, 3.9936, 3.9936, 3.9936, 3.9183, 3.7318, 3.7259, 3.781,
3.781, 3.7259, 3.7318, 3.9183, 3.9183, 3.7318, 3.7248, 3.7819,
3.7819, 3.7248, 3.7318, 3.9183
]
for idx, _ in enumerate(self.lifepo4):
cn_array.append(cnn.get_cn(self.lifepo4, idx, use_weights=True))
self.assertArrayAlmostEqual(expected_array, cn_array, 2)
def get_Species_Substitution_Order(structure, dummies, species, to_ignore):
els_removed = species.copy()
for element in to_ignore:
els_removed.remove(Element(element))
subs = [list(p) for p in permutations(els_removed)]
diff_coords = []
struct_copies = []
for sub in subs:
copy = structure.copy()
for dummy_ind in range(len(dummies)):
copy[dummies[dummy_ind].symbol] = sub[dummy_ind]
struct_copies.append(copy)
coordination_numbers = []
CN = CrystalNN(weighted_cn=True)
for element_ind in range(len(copy.species)):
cn = CN.get_cn(copy, element_ind, use_weights=True)
coordination_numbers.append((copy.species[element_ind], cn))
diff_coords.append(coordination_numbers)
unique_cn_els = []
for cn in diff_coords:
cns = []
for i in range(len(cn)):
if cn[i] not in cns:
cns.append(cn[i])
unique_cn_els.append(cns)
substitution_ind = None
check_len = 300 # arbitrarily high number to start, used to get substitution scheme with lowest number of unique sites
for unique_cn_el_ind in range(len(unique_cn_els)):
if len(unique_cn_els[unique_cn_el_ind]) < check_len:
substitution_ind = unique_cn_el_ind
check_len = len(unique_cn_els[unique_cn_el_ind])
else:
continue
ox_transform = AutoOxiStateDecorationTransformation()
ox_species = ox_transform.apply_transformation(
struct_copies[substitution_ind]).types_of_specie
for specie in ox_species:
for element in to_ignore:
if specie.symbol == Element(element).symbol:
ox_species.remove(specie)
return subs[substitution_ind], ox_species
def test_x_diff_weight(self):
cnn = CrystalNN(weighted_cn=True, x_diff_weight=0)
self.assertAlmostEqual(cnn.get_cn(self.lifepo4, 0, use_weights=True),
5.9522, 2)
def test_cation_anion(self):
cnn = CrystalNN(weighted_cn=True, cation_anion=True)
self.assertAlmostEqual(cnn.get_cn(self.lifepo4, 0, use_weights=True),
5.8630, 2)
def test_x_diff_weight(self):
cnn = CrystalNN(weighted_cn=True, x_diff_weight=0)
self.assertAlmostEqual(cnn.get_cn(self.lifepo4, 0, use_weights=True),
5.9522, 2)
def test_cation_anion(self):
cnn = CrystalNN(weighted_cn=True, cation_anion=True)
self.assertAlmostEqual(cnn.get_cn(self.lifepo4, 0, use_weights=True),
5.8630, 2)