createFolder('%02d_%s' % (idx + 1.0, formula))
struc_ini.replace(0, TM_list[idx])
struc_ini.replace(1, TM_list[idx])
struc_ini.replace(2, TM_list[idx])
struc_ini.replace(3, TM_list[idx])
# getting conventional unit cell
sga = SpacegroupAnalyzer(struc_ini)
conv_struc = sga.get_conventional_standard_structure()
poscar = Poscar(conv_struc)
poscar.write_file('%02d_%s/POSCAR' % (idx + 1.0, formula))
poscar_ase = read_vasp('%02d_%s/POSCAR' % (idx + 1.0, formula))
write_xsd('models/poscar_%02d_%s.xsd' % (idx + 1.0, formula),
poscar_ase)
for k in range(len(df)):
if formula == df['pretty_formula'][k]:
struc = df['structure'][k]
sga = SpacegroupAnalyzer(struc)
# print(idx+1.0," ",formula," ",len(sga.get_conventional_standard_structure()))
if len(sga.get_conventional_standard_structure()) != 30:
print('Error for conv. struc. of %s' % formula)
f.writelines('Error for conv. struc. of %s\n' % formula)
break
conv_struc = sga.get_conventional_standard_structure()
poscar = Poscar(conv_struc)
poscar.write_file('%02d_%s/POSCAR' % (idx + 1.0, formula))
c1 = zwitter_AA.cell[2][0] / cell_params[2]
c2 = zwitter_AA.cell[2][1] / cell_params[2]
c3 = zwitter_AA.cell[2][2] / cell_params[2]
print('cell vector C: %4.5f %4.5f %4.5f ' % (c1,c2,c3))
for a_int in range(0,11):
for c_int in range(0,11):
createFolder('%02d_%02d_shift' % (a_int, c_int))
createFolder('xsd')
for i in range(tot_num):
if i in idx_list:
# count = count + 1
# print(i," ",zwitter_temp[i]," ",count)
zwitter_temp[i].x = x_data[i] + a_int*cell_params[0]*a1*0.1 - c_int*cell_params[2]*c1*0.1
zwitter_temp[i].z = z_data[i] + a_int*cell_params[0]*a3*0.1 - c_int*cell_params[2]*c3*0.1
INCAR.write_file('%02d_%02d_shift/INCAR' % (a_int, c_int))
KPOINTS.write_file('%02d_%02d_shift/KPOINTS' % (a_int, c_int))
write_vasp('%02d_%02d_shift/POSCAR' % (a_int, c_int), zwitter_temp)
write_xsd('xsd/%02d_%02d.xsd' % (a_int, c_int), zwitter_temp)
# jobscript copy
destination = '%02d_%02d_shift' % (a_int, c_int)
job_file = os.getcwd() + '/jobscript_vasp.sh'
shutil.copy(job_file, destination)
from ase.io.vasp import read_vasp
from ase.io.xsd import write_xsd
contcar = read_vasp('CONTCAR')
write_xsd('contcar.xsd', contcar)
from pymatgen import Structure
struc = Structure.from_file('CONTCAR')
from pymatgen.io.vasp.inputs import Poscar
poscar = Poscar.from_file('CONTCAR')
poscar.structure
del atoms[atoms.numbers == 6]
del atoms[[atom.index for atom in atoms if atom.symbol == 'C']]
del atoms[[atom.symbol == 'C' for atom in atoms]]
del surf_2x2[[atom.position[2] / z_param < 0.35 for atom in surf_2x2]]
elements = list(set(slab.get_chemical_symbols()))