def make_bulk_structure(filename_poscar_in,
filename_outcar_in=None,
supercell=None):
poscar_in = vasp.Poscar()
poscar_in.read(filename=filename_poscar_in)
if filename_outcar_in is not None:
# add magnetic moments to the structure
outcar_in = vasp.Outcar()
outcar_in.read(filename=filename_outcar_in)
magnetic_moments = outcar_in.get_magnetic_moments()
for i, atom in enumerate(poscar_in.atomic_basis):
atom.magmom = magnetic_moments[i][-1]
z_distances = [k.position[2] for k in poscar_in.atomic_basis]
min_z_distance = min(z_distances)
for atom in poscar_in.atomic_basis:
atom.position[2] = atom.position[2] - min_z_distance
# make supercell
if supercell is not None:
poscar_out = vasp.Poscar(
crystal.make_super_cell(structure=poscar_in, sc=supercell))
else:
poscar_out = poscar_in
# sort by z_axis
new_atomic_basis = []
while len(poscar_out.atomic_basis) > 0:
z_distances = [k.position[2] for k in poscar_out.atomic_basis]
idx_min = z_distances.index(min(z_distances))
new_atomic_basis.append(copy.deepcopy(
poscar_out.atomic_basis[idx_min]))
del poscar_out.atomic_basis[idx_min]
poscar_out.atomic_basis = new_atomic_basis
return poscar_out
def write_lammps_structure_filename(self):
_supercell = self.supercell
_structure_filename_src \
= self.configuration['structure']['structure_filename']
_structure = vasp.Poscar()
_structure.read(_structure_filename_src)
self.structure = crystal.make_super_cell(structure=_structure,
sc=_supercell)
self.lammps_structure = lammps.LammpsStructure(\
obj=self.structure)
_str_out = self.lammps_input_file_to_string()
_lammps_filename = os.path.join(self.task_directory, filename)
with open(_lammps_filename, 'w') as f:
f.write(_str_out)
from pypospack.io.vasp import Poscar
from pypospack.crystal import make_super_cell
_bulk_filename = "Ni_fcc_111_unit.gga.relaxed.vasp"
_bulk_poscar = Poscar()
_bulk_poscar.read(_bulk_filename)
_isf_filename = "Ni_fcc_isf.vasp"
print('a1', _bulk_poscar.a1)
print('a1', _bulk_poscar.a2)
print('a1', _bulk_poscar.a3)
_isf_sc = [1, 1, 5]
_isf_sc = Poscar(make_super_cell(_bulk_poscar, _isf_sc))
import numpy as np
_isf_sc.H[2, 2] = _isf_sc.H[2, 2] * 0.933333
for a in _isf_sc.atomic_basis:
a.position[2] = a.position[2] / 0.933333
_isf_sc.write(_isf_filename)
result = None
n = 2
for i0 in range(-n, n+1):
for i1 in range(-n, n+1):
for i2 in range(-n, n+1):
rp = r+np.dot(a0*H.T, [i0,i1,i2])
d = np.linalg.norm(rp)
if (result is None) or (result[1] > d):
result = (rp, d)
return result[0]
poscar_filename = 'Ni_fcc_unit.gga.relaxed.vasp'
cell_poscar = Poscar()
cell_poscar.read(poscar_filename)
cell_poscar.normalize_h_matrix()
cell_sc = make_super_cell(structure=cell_poscar,sc=[3,3,3])
_positions = [a.position for a in cell_sc.atomic_basis]
_n_atoms = len(_positions)
min_distances = []
for i in range(1,_n_atoms):
r1 = np.array(_positions[0])
r2 = np.array(_positions[i])
r = r2-r1
r_min = brute_minimum_image_convention(r=r,H=cell_sc.H,a0=cell_sc.a0)
d = np.linalg.norm(r_min)
min_distances.append(d*cell_poscar.a0*cell_poscar.a1)
min_distances = np.array(min_distances)
distances = np.linspace(
np.min(min_distances),
np.max(min_distances),
100)
from pypospack.io.vasp import Poscar
from pypospack.crystal import make_super_cell
_bulk_filename = "Ni_fcc_110_unit.gga.relaxed.vasp"
_bulk_poscar = Poscar()
_bulk_poscar.read(_bulk_filename)
_surface_filename = "Ni_fcc_110_surf.vasp"
_surface_sc = [1, 1, 10]
_surface_sc = Poscar(make_super_cell(_bulk_poscar, _surface_sc))
_surface_slab_pct_of_z = 0.5
_surface_slab_thickness = _surface_sc.a3 * _surface_slab_pct_of_z
atoms_to_remove = []
for a in _surface_sc.atomic_basis:
print(a.position, a.position[2] < _surface_slab_pct_of_z)
if not a.position[2] < _surface_slab_pct_of_z:
atoms_to_remove.append([a.symbol, list(a.position)])
for a in atoms_to_remove:
symbol = a[0]
position = a[1]
print('removing {} atom @ {}'.format(str(a[0]), str(a[1])))
_surface_sc.remove_atom(symbol=symbol, position=position)
for a in _surface_sc.atomic_basis:
print(a.symbol, a.position)
_surface_sc.write(_surface_filename)
v['vasp_obj'].write(
os.path.join(dst_structure_dir, v['vasp_fname']))
print('{}->{}'.format(k, v['vasp_fname']))
# convert pypospack -> LAMMPS structure
if is_write_lammps_structures:
v['lammps_obj'] = LammpsStructure(v['pypospack_obj'])
v['lammps_fname'] = '{}.structure'.format(k)
v['lammps_obj'].write(filename=os.path.join(
dst_structure_dir, v['lammps_fname']),
symbol_list=v['symbol_list'],
atom_style=v['lmps_atom_style'])
print('{}->{}'.format(k, v['lammps_fname']))
structures['Si_dia_333'] = OrderedDict()
structures['Si_dia_333']['pypospack_obj'] = crystal.make_super_cell(
structure=structures['Si_dia_unit']['pypospack_obj'], sc=[3, 3, 3])
poscar = Poscar(structures['Si_dia_333']['pypospack_obj'])
poscar.write(os.path.join(dst_structure_dir, 'Si_dia_333.vasp'))
lammps_structure = LammpsStructure(
structures['Si_dia_333']['pypospack_obj'])
lammps_structure.write(filename=os.path.join(dst_structure_dir,
'Si_dia_333.structure'),
symbol_list=['Si'],
atom_style='atomic')
structures['Si_dia_333_vac'] = OrderedDict()
structures['Si_dia_333_vac']['pypospack_obj'] = SimulationCell(
structures['Si_dia_333']['pypospack_obj'])
structures['Si_dia_333_vac']['pypospack_obj'].add_vacancy(
symbol='Si', position=[0.0000, 0.0000, 0.0000])
poscar = Poscar(structures['Si_dia_333_vac']['pypospack_obj'])
import os, shutil, subprocess
from pypospack.crystal import SimulationCell
import pypospack.io.vasp as vasp
import pypospack.crystal as crystal
import pypospack.io.slurm as minimize_init_slurm
# define simulation cell
cell = SimulationCell()
cell.a0 = 3.447
cell.add_atom('Fe', [0.0, 0.0, 0.0], magmom=3.00)
cell.add_atom('Fe', [0.5, 0.5, 0.0], magmom=3.00)
cell.add_atom('Fe', [0.5, 0.0, 0.5], magmom=-3.00)
cell.add_atom('Fe', [0.0, 0.5, 0.5], magmom=-3.00)
from pypospack.crystal import make_super_cell
poscar = vasp.Poscar(make_super_cell(structure=cell, sc=[3, 3, 3]))
poscar.add_atom('Fe', [1. / 6., 0.0, 0.0])
poscar.write("POSCAR")
s_out = ""
for atom in poscar.atomic_basis:
s_out += "{:<4}{:10.6f}{:10.6f}{:10.6f}\n".format(atom.symbol,
atom.position[0],
atom.position[1],
atom.position[2])
with open('Fe_defect.gulp.structure', 'w') as f:
f.write(s_out)