Module_Number, Situation_Number))
for Diffusion_Atom in Diffusion_Atoms:
for Diffusion_Position in Diffusion_Positions:
Substitutional_Number = Diffusion_Position[1] - 1
Substitutional_structure = deepcopy(Structure_Poscar.structure)
Substitutional_Coord = deepcopy(Substitutional_structure[Substitutional_Number].coords)
Substitutional_structure.remove_sites(range(Substitutional_Number, Substitutional_Number + 1))
Substitutional_structure.append(Diffusion_Atom, Substitutional_Coord, coords_are_cartesian=True)
sd_init = np.ones((Substitutional_structure.num_sites, 3))
for number_atom in range(0,Substitutional_structure.num_sites):
atom_position_z = Substitutional_structure[number_atom].z
if atom_position_z<bottom_limit or atom_position_z >upper_limit:
sd_init[number_atom]=np.zeros((1,3))
sd_atoms = sd_init
Neb_Path = '/mnt/c/Users/jackx/OneDrive/Calculation_Data/TC17_TI80/NEB_Files/M{0}_S{1}/Substitutional/{2}/Optimistic/{3}'.format(
Module_Number,
Situation_Number,
Diffusion_Atom,
Diffusion_Position[
0])
if os.path.exists(Neb_Path):
shutil.rmtree(Neb_Path)
os.makedirs(Neb_Path)
Poscar_write = Poscar(Substitutional_structure)
Poscar_write.selective_dynamics = sd_atoms
Poscar_write.write_file('{}/POSCAR'.format(Neb_Path))
Poscar_write.structure.to(filename='{}/POSCAR.cif'.format(Neb_Path))
