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get_all_permutation.py
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get_all_permutation.py
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import numpy as np
import itertools
import os
from pymatgen.core.structure import Structure
import pymatgen.io.vasp.inputs as inputs
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer, SpacegroupOperations
from more_itertools import distinct_permutations
potentials = {'Mn':'Mn_pv', 'V':'V_sv', 'Sb':'Sb', 'Ni':'Ni','Cr':'Cr_pv','Sc':'Sc_sv','As':'As','Ti':'Ti_sv','Fe':'Fe','Ru':'Ru_pv','Co':'Co', 'Ge':'Ge_d', 'Rh':'Rh_pv', 'Si':'Si', 'Ni':'Ni','P':'P', 'Ga':'Ga_d','Sn':'Sn_d'}
structure_0 = Structure.from_file('POSCAR')
position_for_permutation = [8, 9, 10, 11, 12, 13, 14, 15]
magmom = [0,0,0,0,0,0,0,0,1, 2, 3, 4, 5, 6, 7, 8]
species_for_permutation = []
species_constant = []
for i in range(len(structure_0.species)):
if i in position_for_permutation:
species_for_permutation += [structure_0.species[i]]
else:
species_constant += [structure_0.species[i]]
sg = SpacegroupAnalyzer(structure_0)
operations = sg.get_space_group_operations()
unique_structures = []
for n, p in enumerate(distinct_permutations(species_for_permutation)):
print(p)
species_new = species_constant + list(p)
structure = Structure(structure_0.lattice, species_new, structure_0.frac_coords)
flag = False
for us in unique_structures:
if operations.are_symmetrically_equivalent(structure, us):
flag = True
break
if flag == False:
unique_structures += [structure]
for n, s in enumerate(unique_structures):
if not os.path.isdir('unique_structures'):
os.makedirs('unique_structures')
poscar = inputs.Poscar(s, sort_structure = True)
paw = [potentials[i.symbol] for i in s.types_of_species]
potcar = inputs.Potcar(symbols=paw, functional="PBE_54")
kpoints = inputs.Kpoints.automatic_density(s, 5000)
incar = inputs.Incar({#'METAGGA': 'SCAN',
'LCHARG': False,
'LWAVE': False,
'ICHARG': 1,
'IBRION': 2,
'ISIF': 3,
'POTIM': 0.005,
'PREC': 'Accurate',
'EDIFF': 1e-7,
'EDIFFG': 1e-3,
'ISMEAR': 1,
'SIGMA': 0.1,
'ISPIN': 2,
'LMAXMIX': 6,
'ADDGRID': True,
'LORBIT': 11,
'LASPH': True,
'NSW ': 100,
'NEDOS': 1000,
'NELM': 101,
'ALGO': 'Fast',
'NCORE': 6,
'KPAR': 2,
'MAGMOM': })
VaspInput = inputs.VaspInput(incar, kpoints, poscar, potcar)
VaspInput.write_input('unique_structures/{}'.format(n))