def anion_inter(x, *args):
cations = args[0]
anions = args[1]
lattice = args[2]
Species_list = args[3]
num_atoms = args[4]
cutoff_distance = args[5]
BVpara = args[6]
Formal_Valence = args[7]
wycks = args[8]
space_group = args[9]
b0 = args[10]
center_atom_in_regular_poly = args[11]
max_angle = args[12]
nearest_neighbor_distance = args[13]
Shannon_anion_anion = args[14]
pymat_structure = Structure(lattice, Species_list, x.reshape(num_atoms, 3))
anions_indx = pymat_structure.indices_from_symbol(anions[0])
logic = 0
for anion in anions_indx:
NN = pymat_structure.get_neighbors(pymat_structure.sites[anion],
4,
include_index=True)
#print len(NN)
for neigh in NN:
if str(neigh[0].specie.symbol) in anions:
#print neigh[1]
logic += 0.25 / (1 + np.exp(50 *
(neigh[1] - Shannon_anion_anion)))
#print logic
return logic / 10
def check_hydrogens(s: Structure,
neighbor_threshold: float = 2.0,
strictness: str = 'CH') -> bool:
"""
checks if there are any hydrogens in a structure object.
Args:
s (pymatgen structure object): structure to be checked
neighbor_threshold (float): threshold for distance that is still considered to be bonded
strictness (str): available levels: 'tight': returns false if there is no H at all, 'medium'
returns false if there are carbons but no hydrogens, 'CH' (default) checks if there are
carbons with less or equal 2 non-hydrogen neighbors (e.g. the most common case for aromatic rings).
If those have also no hydrogen bonded to them, it will return False
Returns:
"""
symbols = s.symbol_set
return_val = True
if strictness == 'tight':
logger.debug('running H check with tight strictness')
if not 'H' in symbols:
return False
elif strictness == 'medium':
logger.debug('running H check with medium strictness')
if 'C' in symbols:
if not 'H' in symbols:
return False
elif strictness == 'CH':
logger.debug('running H check with CH strictness')
if 'C' in symbols:
c_sites = s.indices_from_symbol('C')
for c_site in c_sites:
neighbors = s.get_neighbors(s[c_site], neighbor_threshold)
neighbors_symbol_list = [
neighbor_site[0].species_string
for neighbor_site in neighbors
]
neighbors_no_h = [
neighbor_site for neighbor_site in neighbors
if neighbor_site[0].species_string != 'H'
]
if len(neighbors_symbol_list) == 0:
return False
if len(neighbors_no_h) <= 2:
if len(neighbors) - len(neighbors_no_h) == 0:
return False
return return_val
def calc_orbital_character(orbitals,
structure: Structure,
spin: Spin,
kpt_index: int,
band_index: int):
""" Consider the two pattern of orbitals.
LORBIT 10 -> consider only "s", "p", "d" orbitals
LORBIT >=11 -> consider "s", "px", "py", "pz",.. orbitals
"""
def projection_sum(atom_indices: tuple, first: int, last: int):
end = last + 1
procar_sum = np.sum(orbitals[spin]
[kpt_index, band_index, atom_indices, first:end])
return float(procar_sum)
orbital_components = {}
azimuthal = len(orbitals[Spin.up][0, 0, 0]) > 5
for element in structure.symbol_set:
# get list of index
indices = structure.indices_from_symbol(element)
if azimuthal:
orbital_components[element] = \
[round(projection_sum(indices, 0, 0), 3),
round(projection_sum(indices, 1, 3), 3),
round(projection_sum(indices, 4, 8), 3)]
try:
orbital_components[element].append(round(projection_sum(indices, 9, 16), 3))
except KeyError:
pass
else:
orbital_components[element] = \
[round(projection_sum(indices, 0, 0), 3),
round(projection_sum(indices, 1, 1), 3),
round(projection_sum(indices, 2, 2), 3)]
return orbital_components
