def __init__(self, simulation_path="."):
self.simulation_path = simulation_path
self.poscar = Poscar()
self.incar = Incar()
self.kpoints = Kpoints()
self.potcar = Potcar()
self.submission_script = SlurmSubmissionScript()
def test__no_charges():
filename = os.path.join(
'test__simulation_cell_to_phonts_string',
'Si_dia_unit.relax.gga.vasp')
poscar = Poscar()
poscar.read(filename=filename)
from pypospack.io.phonts import simulation_cell_to_phonts_string
simulation_cell_to_phonts_string(
simulation_cell=poscar)
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)
import argparse
from pypospack.io.vasp import Poscar
_description = 'Normalizes the H-matrix'
_parser = argparse.ArgumentParser(description=_description)
_parser.add_argument('--in', action='store', dest='filename_in', type=str)
_parser.add_argument('--out', action='store', dest='filename_out', type=str)
_args = _parser.parse_args()
_filename_in = _args.filename_in
_filename_out = _args.filename_out
print('filename_in:{}'.format(_filename_in))
_poscar = Poscar()
_poscar.read(_filename_in)
print('a0:{}'.format(_poscar.a0))
print('H:\n{}'.format(_poscar.H))
print('filename_out:{}'.format(_filename_out))
_poscar.normalize_h_matrix()
print(80 * '-')
print('a0:{}'.format(_poscar.a0))
print('H:\n{}'.format(_poscar.H))
_poscar.write(_filename_out)
_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'
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'],
atom_style=v['lmps_atom_style'])
print('{}->{}'.format(k, v['lammps_fname']))
import ase.build
import numpy as np
from pypospack.crystal import SimulationCell
class DiamondStructure(SimulationCell):
def __init__(self, symbols=['Si'], a=5.43):
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=[0.25, 0.25, 0.25])
self.add_atom(symbol=symbols[0], position=[0.00, 0.50, 0.50])
self.add_atom(symbol=symbols[0], position=[0.25, 0.75, 0.75])
self.add_atom(symbol=symbols[0], position=[0.50, 0.00, 0.50])
self.add_atom(symbol=symbols[0], position=[0.75, 0.25, 0.75])
self.add_atom(symbol=symbols[0], position=[0.50, 0.50, 0.00])
self.add_atom(symbol=symbols[0], position=[0.75, 0.75, 0.25])
if __name__ == "__main__":
from pypospack.io.vasp import Poscar
filename = "Si_dia_unit.vasp"
cell = DiamondStructure(symbols=['Si'], a=5.43)
poscar = Poscar(obj_cell=DiamondStructure(symbols=['Si'], a=5.43))
poscar.write(filename=filename)
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
if __name__ == "__main__":
from pypospack.io.vasp import Poscar
# INTRINSIC STACKING FAULT
symbols = ['Ni']
stacking_sequence = "ABC,ABC,AC,ABC,ABC"
simulation_cell = make_fcc_stacking_fault(symbols, stacking_sequence)
simulation_cell.normalize_h_matrix()
poscar = Poscar(simulation_cell)
poscar.write('Ni_fcc_isf.vasp')
symbols = ['Ni']
stacking_sequence = "ABC,ABC,ABAC,ABC,ABC"
simulation_cell = make_fcc_stacking_fault(symbols, stacking_sequence)
simulation_cell.normalize_h_matrix()
poscar = Poscar(simulation_cell)
poscar.write('Ni_fcc_esf.vasp')
symbols = ['Ni']
stacking_sequence = "ABC,ABC,AABC,ABC,ABC"
simulation_cell = make_fcc_stacking_fault(symbols, stacking_sequence)
simulation_cell.normalize_h_matrix()
poscar = Poscar(simulation_cell)
poscar.write('Ni_fcc_usf.vasp')
""" make FCC structure for silicon """
from pypospack.crystal import SimulationCell
import numpy as np
class BodyCenteredCubicStructure(SimulationCell):
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])
if __name__ == "__main__":
from pypospack.io.vasp import Poscar
# For Si, in fcc phase
# Pizzagalli
# LDA calculations
a = 3.42
filename = 'Si_bcc.vasp'
poscar = Poscar(obj_cell=BodyCenteredCubicStructure(symbols=['Si'], a=a))
poscar.write(filename=filename)
class VaspSimulation():
def __init__(self, simulation_path="."):
self.simulation_path = simulation_path
self.poscar = Poscar()
self.incar = Incar()
self.kpoints = Kpoints()
self.potcar = Potcar()
self.submission_script = SlurmSubmissionScript()
@property
def symbols(self):
return self.incar.symbols
@property
def xc(self):
return self.potcar.xc
@xc.setter
def xc(self, xc):
self.potcar.xc = xc
def read_incar(self, filename=None):
if filename is None:
filename_ = os.path.join(self.simulation_path, "INCAR")
else:
filename_ = filename
self.incar.read(filename=filename_)
def write_incar(self, filename=None):
if filename is None:
filename_ = os.path.join(self.simulation_path, "INCAR")
else:
filename_ = filename
self.incar.write(filename=filename_)
def write_poscar(self, filename=None):
if filename is None:
filename_ = os.path.join(self.simulation_path, "POSCAR")
else:
filename_ = filename
self.poscar.write(filename=filename_)
def write_potcar(self, xc='GGA', filename=None):
self.xc = xc
if filename is None:
filename_ = os.path.join(self.simulation_path, 'POTCAR')
else:
filename_ = filename
self.potcar.symbols = self.symbols
self.potcar.write(filename=filename_)
def write_kpoints(self, filename=None):
if filename is None:
filename_ = os.path.join(self.simulation_path, "KPOINTS")
else:
fiename_ = filename
self.kpoints.write(filename_)
def write_submission_script(self, filename=None):
if filename is None:
filename_ = os.path.join(self.simulation_path, "runjob.slurm")
else:
filename_ = filename
self.simulation_script.write(filename=filename_)
def write(self, path, is_clobber=False):
self.simulation_path = path
try:
os.path.mkdir(path)
except FileExistsError as e:
if is_clobber:
shutil.rmthree(path)
os.path.mkdir(path)
else:
raise
self.write_poscar()
self.write_potcar()
self.write_incar()
self.write_kpoints()
self.write_submission_script()
import numpy as np
class BetaTinStructure(SimulationCell):
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])
if __name__ == "__main__":
from pypospack.io.vasp import Poscar
# For Si, in beta-pb phase
#
# 10.1103/PhysRevB.83.075119
a = 4.81
c_over_a = 0.552
c = a * c_over_a
filename = 'Si_betaPb.vasp'
poscar = Poscar(obj_cell=BetaTinStructure(symbols=['Si'], a=a, c=c))
poscar.write(filename=filename)
self.add_atom(symbol=symbol, position=[0.500000, 0.000000, 0.500000])
self.add_atom(symbol=symbol, position=[0.000000, 0.500000, 0.500000])
self.add_atom(symbol=symbol, position=[0.500000, 0.500000, 0.000000])
self.add_atom(symbol=symbol, position=[0.750000, 0.250000, 0.750000])
self.add_atom(symbol=symbol, position=[0.750000, 0.750000, 0.250000])
def initialize_primitive_cell(self, symbol='Si', a0=5.431):
self.a0 = a0
a1 = 1 / 2 * np.array([0, 1, 1])
a2 = 1 / 2 * np.array([1, 0, 1])
a3 = 1 / 2 * np.array([1, 1, 0])
self.H = np.stack((a1, a2, a3))
self.add_atom(symbol=symbol, position=[0.7500, 0.75000, 0.75000])
self.add_atom(symbol=symbol, position=[0.5000, 0.50000, 0.50000])
if __name__ == "__main__":
from pypospack.io.vasp import Poscar
o = Poscar(obj_cell=Diamond(symbols=['Si'], a0=5.431, cell_type='cubic'))
o.write(filename="Si_dia_unit.vasp")
o = Poscar(
obj_cell=Diamond(symbols=['Si'], a0=5.431, cell_type='primitive'))
o.write(filename='Si_dia_prim.vasp')
o = Diamond(symbols=['Si'], a0=5.431, cell_type='primitive')
print(o.b1)
print(o.b2)
print(o.b3)
def test__setup__can_read_poscar_file():
filename = os.path.join(
'test__simulation_cell_to_phonts_string',
'Si_dia_unit.relax.gga.vasp')
poscar = Poscar()
poscar.read(filename=filename)
def test__setup__can_read_poscar_file():
filename = os.path.join(
'test__simulation_cell_to_phonts_string',
'Si_dia_unit.relax.gga.vasp')
poscar = Poscar()
poscar.read(filename=filename)
def test__no_charges():
filename = os.path.join(
'test__simulation_cell_to_phonts_string',
'Si_dia_unit.relax.gga.vasp')
poscar = Poscar()
poscar.read(filename=filename)
from pypospack.io.phonts import simulation_cell_to_phonts_string
simulation_cell_to_phonts_string(
simulation_cell=poscar)
if __name__ == "__main__":
# creating tests for formatting is difficult.
# it's better to do integration tests later to determine if
# file created is valid.
from pypospack.io.phonts import simulation_cell_to_phonts_string
poscar = Poscar()
poscar.read(filename='Si_dia_unit.relax.gga.vasp')
cell_str= simulation_cell_to_phonts_string(
simulation_cell=poscar)
print(cell_str)
# Basic idea = triple loop over all nearby image, pick shortest relative vector.
# This is horribly slow, and for very skewed cells, n has to become very large.
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(
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)
latticeconstant=_lattice_constants)
else:
raise
return atoms
if __name__ == "__main__":
Ni_fcc_100_unit = OrderedDict()
Ni_fcc_100_unit['name'] = 'Ni_fcc_100'
Ni_fcc_100_unit['symbols'] = ['Ni']
Ni_fcc_100_unit['filename_prefix'] = 'Ni_fcc_100_unit'
Ni_fcc_100_unit['ase'] = make_fcc_100_cell(
symbols=Ni_fcc_100_unit['symbols'])
Ni_fcc_100_unit['poscar_filename'] = '{}.vasp'.format(
Ni_fcc_100_unit['filename_prefix'])
Ni_fcc_100_unit['poscar'] = Poscar(Ni_fcc_100_unit['ase'])
Ni_fcc_100_unit['poscar'].normalize_h_matrix()
Ni_fcc_100_unit['poscar'].write(
filename=Ni_fcc_100_unit['poscar_filename'])
Ni_fcc_110_unit = OrderedDict()
Ni_fcc_110_unit['name'] = 'Ni_fcc_110'
Ni_fcc_110_unit['symbols'] = ['Ni']
Ni_fcc_110_unit['filename_prefix'] = 'Ni_fcc_110_unit'
Ni_fcc_110_unit['ase'] = make_fcc_110_cell(
symbols=Ni_fcc_110_unit['symbols'])
Ni_fcc_110_unit['poscar_filename'] = '{}.vasp'.format(
Ni_fcc_110_unit['filename_prefix'])
Ni_fcc_110_unit['poscar'] = Poscar(Ni_fcc_110_unit['ase'])
Ni_fcc_100_unit['poscar'].normalize_h_matrix()
Ni_fcc_110_unit['poscar'].write(