#!/usr/bin/env python
import numpy as np
from ase.io import read, write
backbone = read('wrapped-POSCAR_1_Kooi-wo-vdw-12x12x3.vasp')
# posi = backbone.get_positions()
# fix_ind = []
# for i in range(len(backbone)):
# if posi[i][1] < 28.7:
# fix_ind.append(i)
# from ase.visualize import view
# view(backbone[fix_ind])
# np.save('fix_inds.npy', fix_ind)
from ss_util import random_atoms_gen as RAG
atoms = RAG(
backbone,
fix_ind_dict = {'Te':list(range(12*12*3*4, 12*12*3*9))},
cutoff_frac = 0.80,
random_radi = 0.0,
pin_the_fixed = True,
)
write('matsunaga-w-rag-kooi-layer-12x12x3.traj', atoms)
#!/usr/bin/env python
import numpy as np
from ase.io import read, write
backbone = read('wrapped-POSCAR_1_Kooi-wo-vdw-16x8x4.vasp')
# from ase.visualize import view
# view(backbone[fix_ind])
# np.save('fix_inds.npy', fix_ind)
from ss_util import random_atoms_gen as RAG
atoms = RAG(
backbone,
# fix_ind_dict = fix_ind,
cutoff_frac=0.80,
random_radi=0.6,
# pin_the_fixed = True,
)
write('init-liquid.traj', atoms)
from ase.io import read, write
backbone = read('cubic-backbone-64.vasp-4x4x4.vasp')
# posi = backbone.get_positions()
# fix_ind = []
# for i in range(len(backbone)):
# if posi[i][1] < 28.7:
# fix_ind.append(i)
# from ase.visualize import view
# view(backbone[fix_ind])
# np.save('fix_inds.npy', fix_ind)
from ss_util import random_atoms_gen as RAG
atoms = RAG(
backbone,
num_spec_dict={
'Ge': 819,
'Sb': 819,
'Te': 2048,
'V': 410
},
fix_ind_dict={'Te': list(range(2048, 4096))},
cutoff_frac=0.80,
random_radi=0.0,
pin_the_fixed=True,
)
write('cubic-w-rag.vasp', atoms)