def add_H(self):
self.get_free_coor_vector()
new_Hs = []
for atom in self.choosed_atoms:
if len(atom.coor_vec_free) > 0:
length = read_cov_rad(atom.nat, unit='a') + \
read_cov_rad('1', unit='a')
new_H = self.get_new_atom_according_to_vetor(
atom, atom.coor_vec_free[0], length, nat='1')
new_Hs.append(new_H)
final_cluster = self.choosed_atoms + new_Hs
return final_cluster
def cal_coor_no_of_all_atoms(self, atoms):
for i in range(len(atoms)):
coor = 0
coor_vec = []
for j in range(len(atoms)):
if i != j:
cor_rad = read_cov_rad(
atoms[i].nat, unit='a') + read_cov_rad(atoms[j].nat,
unit='a')
dis = self.cal_dis_two_atoms(atoms[i], atoms[j])
if dis <= cor_rad * 1.1 and dis > 0:
# print(atoms[i], atoms[j], cor_rad*1.2, dis)
vec = self.cal_vector_between_two_atoms(
atoms[i], atoms[j])
coor_vec.append(vec)
coor += 1
atoms[i].coor = coor
atoms[i].coor_vec = coor_vec
# for i in self.original_atoms:
# print(i.coor)
return atoms
def cal_coordinate_number_of_original_atoms(self):
"""
according to the distance between two atoms to judge if there is conectivity between these two atoms
afterwards calculate the coordniation number of each atom
and calculate the direction of each coordinated atom of each atom
:return:
"""
if self.dimensionality == 2:
vec = (1, 1)
else:
vec = (1, 1, 1)
new_atoms = self.gen_all_atoms(self.original_atoms, vec)
all_atoms = new_atoms + self.original_atoms
for i in range(len(self.original_atoms)):
coor = 0
coor_vec = []
for new_atom in all_atoms:
if new_atom != self.original_atoms[i]:
cov_rad = (
read_cov_rad(self.original_atoms[i].nat, unit='a') +
read_cov_rad(new_atom.nat, unit='a')) * 1.1
distance = self.cal_dis_two_atoms(self.original_atoms[i],
new_atom)
if distance <= cov_rad:
#print(self.original_atoms[i], new_atom.nat, distance, cov_rad)
vec = self.cal_vector_between_two_atoms(
self.original_atoms[i], new_atom)
coor_vec.append(vec)
coor += 1
self.original_atoms[i].coor = coor
# print(coor)
self.original_atoms[i].coor_vec = coor_vec
# print(coor_vec)
atoms_coor_dict, atoms_coor_vec_dict = {}, {}
for atom in self.original_atoms:
atoms_coor_dict[atom.no] = atom.coor
atoms_coor_vec_dict[atom.no] = atom.coor_vec
return atoms_coor_dict, atoms_coor_vec_dict