def get_motiff_distribution(atoms, nn_info):
"""
"""
atoms_i = atoms
struct_i = AseAtomsAdaptor.get_structure(atoms_i)
metal_species_index_list = []
for j_cnt, site_j in enumerate(struct_i):
if site_j.species_string == "Ir":
metal_species_index_list.append(j_cnt)
coord_data_i = nn_info
motiff_list_i = []
for metal_index_j in metal_species_index_list:
coord_data_j = coord_data_i[coord_data_i["structure_index"] == metal_index_j]
nn_info_list = coord_data_j["nn_info"].iloc[0]
nn_info_list = [i["site"] for i in nn_info_list]
print(nn_info_list)
motiff_j = site_is_of_motif_type(
struct_i,
metal_index_j,
neighbors_list=nn_info_list,
# "min_dist", "voronoi", "min_OKeeffe", "min_VIRE"
approach="min_dist",
delta=0.1,
# delta=0.3,
cutoff=10.0,
thresh=thresh_dict,
)
motiff_list_i.append(motiff_j)
motiff_count_dict = {}
list_i = motiff_list_i
for items in list(set(list_i)):
motiff_count_dict[items] = list_i.count(items)
num_motiffs = len(motiff_list_i)
motiff_frac_dict = {}
for key, val in motiff_count_dict.items():
motiff_frac_i = val / num_motiffs
motiff_frac_dict[key] = motiff_frac_i
return(motiff_frac_dict)
def test_site_is_of_motif_type(self):
for i in range(self.diamond.num_sites):
self.assertEqual(site_is_of_motif_type(self.diamond, i),
"tetrahedral")
for i in range(self.nacl.num_sites):
self.assertEqual(site_is_of_motif_type(self.nacl, i), "octahedral")
for i in range(self.cscl.num_sites):
self.assertEqual(site_is_of_motif_type(self.cscl, i), "bcc")
self.assertEqual(site_is_of_motif_type(self.square_pyramid, 0),
"square pyramidal")
for i in range(1, self.square_pyramid.num_sites):
self.assertEqual(site_is_of_motif_type(self.square_pyramid, i),
"unrecognized")
self.assertEqual(site_is_of_motif_type(self.trigonal_bipyramid, 0),
"trigonal bipyramidal")
for i in range(1, self.trigonal_bipyramid.num_sites):
self.assertEqual(site_is_of_motif_type(self.trigonal_bipyramid, i),
"unrecognized")
def test_site_is_of_motif_type(self):
for i in range(self.diamond.num_sites):
self.assertEqual(site_is_of_motif_type(
self.diamond, i), "tetrahedral")
for i in range(self.nacl.num_sites):
self.assertEqual(site_is_of_motif_type(
self.nacl, i), "octahedral")
for i in range(self.cscl.num_sites):
self.assertEqual(site_is_of_motif_type(
self.cscl, i), "bcc")
self.assertEqual(site_is_of_motif_type(
self.square_pyramid, 0), "square pyramidal")
for i in range(1, self.square_pyramid.num_sites):
self.assertEqual(site_is_of_motif_type(
self.square_pyramid, i), "unrecognized")
self.assertEqual(site_is_of_motif_type(
self.trigonal_bipyramid, 0), "trigonal bipyramidal")
for i in range(1, self.trigonal_bipyramid.num_sites):
self.assertEqual(site_is_of_motif_type(
self.trigonal_bipyramid, i), "unrecognized")
