def __init__(self, symbols=['Si'], a0=5.431, cell_type='cubic'):
SimulationCell.__init__(self)
cell_initializers = {}
cell_initializers['cubic'] = self.initialize_cubic_cell
cell_initializers['primitive'] = self.initialize_primitive_cell
cell_initializers[cell_type](symbol=symbols[0], a0=a0)
def __init__(self, symbols=['Ni'], a=3.52):
assert isinstance(symbols, list)
assert len(symbols) == 1
SimulationCell.__init__(self)
self.H = np.array([[a, 0, 0], [0, a, 0], [0, 0, a]])
self.add_atom(symbol=symbols[0], position=[0.0, 0.0, 0.0])
self.add_atom(symbol=symbols[0], position=[0.5, 0.5, 0.5])
def __init__(self, symbols=['Pb'], a=5.8315, c=3.1814):
assert isinstance(symbols, list)
assert len(symbols) == 1
SimulationCell.__init__(self)
self.H = np.array([[a, 0, 0], [0, a, 0], [0, 0, c]])
self.add_atom(symbol=symbols[0], position=[0., 0., 0.])
self.add_atom(symbol=symbols[0], position=[0.5, 0.0, 0.75])
self.add_atom(symbol=symbols[0], position=[0.5, 0.5, 0.5])
self.add_atom(symbol=symbols[0], position=[0.0, 0.5, 0.25])
def make_fcc_stacking_fault(symbols, stacking_sequence):
# use ASE to make fcc 111 oriented cell
direction_x = [1, 2, -1]
direction_y = [1, -1, 0]
direction_z = [1, 1, 0]
ase_fcc_111 = FaceCenteredCubic(\
directions=[direction_x,direction_y,direction_z],
size=size,
symbol=symbols[0],
pbc=pbc)
ase_lattice = ase_fcc_111.get_cell()
for a in ase_fcc_111:
for i in range(3):
a.position[i] = round(a.position[i], 8)
z_layers = []
for a in ase_fcc_111:
if a.position[2] not in z_layers:
z_layers.append(a.position[2])
n_layers = len([v for v in stacking_sequence if v is not ','])
layer_spacing = ase_lattice[2, 2] / len(z_layers)
simulation_cell = SimulationCell()
simulation_cell.lattice_parameter = 1.0
simulation_cell.H = copy.deepcopy(ase_lattice)
simulation_cell.H[2, 2] = layer_spacing * n_layers
n_layers = len([v for v in stacking_sequence if v is not ','])
for n, c in enumerate([v for v in stacking_sequence if v != ',']):
if c == 'A':
layer = 'A'
z_layer = z_layers[0]
elif c == 'B':
layer = 'B'
z_layer = z_layers[1]
elif c == 'C':
layer = 'C'
z_layer = z_layers[2]
for a in ase_fcc_111:
if a.position[2] == z_layer:
s = a.symbol
x = copy.deepcopy(a.position)
x[0] = x[0] / simulation_cell.H[0, 0]
x[1] = x[1] / simulation_cell.H[1, 1]
x[2] = n * layer_spacing / simulation_cell.H[2, 2]
simulation_cell.add_atom(s, x)
return simulation_cell
_latticeconstant = {}
_latticeconstant['a'] = 5.022 # Angs
_latticeconstant['b'] = 5.022 # Angs
_latticeconstant['c'] = 5.511 # Angs
_latticeconstant['alpha'] = 90 #deg
_latticeconstant['beta'] = 90 # degrees
_latticeconstant['gamma'] = 120 # degrees
# make ASE structure
from ase import Atoms, Atom
SiO2_aq = SiO2_a_quartz(directions=_directions,
size=(1, 1, 1),
symbol=('Si', 'O'),
latticeconstant=_latticeconstant)
# convert to pypospack.crystal.SimulationCell
from pypospack.crystal import SimulationCell
SiO2_pyp = SimulationCell(SiO2_aq)
# write the poscar file
from pypospack.io.vasp import Poscar
SiO2_poscar = Poscar(SiO2_pyp)
SiO2_poscar.write('SiO2_aq_cubic.vasp')
# write lammps structure
from pypospack.io.lammps import LammpsStructure
SiO2_lammps = LammpsStructure(SiO2_pyp)
SiO2_lammps.write(filename='SiO2_aq_cubic.lammps',
symbol_list=['Si', 'O'],
atom_style='charge') #or 'atomic'
if os.path.exists(dst_structure_dir):
print('dst_structure_dir exists...')
print(
'...deleting directory and contents {}'.format(dst_structure_dir))
print('...recreating the directory {}'.format(dst_structure_dir))
shutil.rmtree(dst_structure_dir)
os.mkdir(dst_structure_dir)
else:
print('dst_structure_dir does not exist...')
print('...creating the directory {}'.format(dst_structure_dir))
os.mkdir(dst_structure_dir)
for k, v in structures.items():
# convert ase -> pypospack
v['pypospack_obj'] = SimulationCell(v['ase_obj'])
# convert pypospack -> VASP poscar
if is_write_vasp_structures:
v['vasp_obj'] = Poscar(v['pypospack_obj'])
v['vasp_fname'] = '{}.vasp'.format(k)
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'],
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)
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
system_name = "Fe-fccD"
# define simulation cell
cell = SimulationCell()
cell.a0 = 3.447
cell.H = [[1, 0, 0], [0, 1, 0], [0, 0, 2]]
cell.add_atom('Fe', [0.0, 0.0, 0.00], magmom=2.22)
cell.add_atom('Fe', [0.5, 0.5, 0.00], magmom=2.22)
cell.add_atom('Fe', [0.5, 0.0, 0.25], magmom=2.22)
cell.add_atom('Fe', [0.0, 0.5, 0.25], magmom=2.22)
cell.add_atom('Fe', [0.0, 0.0, 0.50], magmom=-2.22)
cell.add_atom('Fe', [0.5, 0.5, 0.50], magmom=-2.22)
cell.add_atom('Fe', [0.5, 0.0, 0.75], magmom=-2.22)
cell.add_atom('Fe', [0.0, 0.5, 0.75], magmom=-2.22)
poscar = vasp.Poscar(cell)
poscar.write('Fe_fcc_afm_D.init.vasp')
print(poscar.get_magmom_tag())