def write_twinboundary_shear_cells(self,
is_original_frame: bool = True,
is_relax: bool = True,
header: str = 'twinboundary_shear'):
"""
write twinboundary shear cells to POSCAR.
Args:
is_original_frame: If True, returns cells in original frame.
is_relax: If True, return relax cells.
header: File header.
"""
cells = self.get_twinboundary_shear_cells(
is_original_frame=is_original_frame, is_relax=is_relax)
for i, cell in enumerate(cells):
ratio = self._twinboundary_shear_analyzer.shear_strain_ratios[i]
filename = header + '_%1.2f.poscar' % ratio
write_poscar(cell=cell, filename=filename)
def write_shear_cells(self,
is_original_frame: bool = True,
is_relax: bool = True,
header: str = 'shear'):
"""
Write shear cells to POSCAR.
Args:
is_original_frame: If True, returns cells in original frame.
is_relax: If True, return relax cells.
header: File header.
"""
cells = self.get_shear_cells(is_original_frame=is_original_frame,
is_relax=is_relax)
ratios = self._shear_analyzer.shear_strain_ratios
for cell, ratio in zip(cells, ratios):
filename = header + '_%1.2f.poscar' % ratio
write_poscar(cell=cell, filename=filename)
def write(self,
filename="MPOSCAR",
multiply: float = 1.,
origin_shift=[0, 0, 0]):
"""
Write modulated cells.
Args:
filename: Cell filename header.
multiply: Displacements are multiplied.
"""
num = len(self._modulation._u)
deltas = []
for i, u in enumerate(self._modulation._u):
cell = get_cell_from_phonopy_structure(
self._modulation._get_cell_with_modulation(u * multiply))
cell = list(cell)
cell[1] = (cell[1] + np.array(origin_shift)) % 1
filename_ = filename + "-%03d" % (i + 1)
write_poscar(cell=cell, filename=filename_)
def main(
twinboundary_relax_pk: int,
additional_relax_pks: list = None,
twinboundary_phonon_pk: int = None,
hexagonal_relax_pk: int = None,
hexagonal_phonon_pk: int = None,
plot_plane_diff: bool = False,
plot_band: bool = False,
show_band_points: bool = False,
write_cell_in_original_frame: bool = False,
):
twinpy = Twinpy.initialize_from_aiida_twinboundary(
twinboundary_relax_pk=twinboundary_relax_pk,
additional_relax_pks=additional_relax_pks,
twinboundary_phonon_pk=twinboundary_phonon_pk,
hexagonal_relax_pk=hexagonal_relax_pk,
hexagonal_phonon_pk=hexagonal_phonon_pk,
)
# plot plane interval
if plot_plane_diff:
fig = twinpy.twinboundary_analyzer.plot_plane_diff()
plt.show()
# show band points
if show_band_points:
twinpy.show_twinboundary_reciprocal_high_symmetry_points()
# plot band structure
if plot_band:
twinpy.plot_twinboundary_shear_bandstructure()
# write out relax cell in original frame
if write_cell_in_original_frame:
rlx_analyzer = twinpy.twinboundary_analyzer.relax_analyzer
rlx_cell_orig = rlx_analyzer.final_cell_in_original_frame
write_poscar(cell=rlx_cell_orig, filename='rlx_cell_orig.poscar')
def main(
a: float,
c: float,
symbol: str,
twinmode: str,
layers: float,
expansion_ratios: np.array,
make_tb_flat: bool,
xshifts: list,
yshifts: list,
pair_style: str,
pot_file: str,
twintype: int = 1,
is_run_hexagonal_relax: bool = True,
is_relax_lattice: bool = False,
):
lattice = get_hexagonal_lattice_from_a_c(a=a, c=c)
scaled_positions = get_hcp_atom_positions(wyckoff='c')
symbols = [symbol] * 2
hex_cell = (lattice, scaled_positions, symbols)
hex_lmp_stc = get_lammps_relax(
cell=hex_cell,
pair_style=pair_style,
pot_file=pot_file,
is_relax_lattice=is_run_hexagonal_relax,
)
hex_rlx_analyzer = get_relax_analyzer_from_lammps_static(
lammps_static=hex_lmp_stc,
no_standardize=True,
)
itr = itertools.product(xshifts, yshifts)
data = []
os.makedirs("./poscar")
os.makedirs("./joblib")
for i, xy in enumerate(itr):
xshift, yshift = xy
twinpy = Twinpy(lattice=lattice,
twinmode=twinmode,
symbol=symbol,
wyckoff='c')
twinpy.set_twinboundary(
layers=layers,
twintype=twintype,
xshift=xshift,
yshift=yshift,
shear_strain_ratio=0.,
expansion_ratios=expansion_ratios,
make_tb_flat=make_tb_flat,
)
twinpy.set_twinboundary_analyzer_from_lammps(
pair_style=pair_style,
pot_file=pot_file,
is_relax_lattice=is_relax_lattice,
is_run_phonon=False,
hexagonal_relax_analyzer=hex_rlx_analyzer,
)
num = "%03d" % i
filename = "./joblib/{}_xshift-{}_yshift-{}.joblib".format(
num, xshift, yshift)
joblib.dump(twinpy, filename)
rlx_cell = twinpy.twinboundary_analyzer.relax_analyzer.final_cell
posname = "./poscar/{}_xshift-{}_yshift-{}.poscar".format(
num, xshift, yshift)
write_poscar(rlx_cell, posname)
formation_energy = twinpy.twinboundary_analyzer.get_formation_energy()
data.append([xshift, yshift, formation_energy])
data = np.array(data)
print(data)
# plot plane interval
im = plt.scatter(data[:, 0], data[:, 1], c=data[:, 2], cmap=cm.jet)
plt.colorbar(im)
plt.show()
def main(
structure,
shear_strain_ratio,
twinmode,
twintype,
xshift,
yshift,
dim,
layers,
delta,
expansion_ratios,
no_make_tb_flat,
posfile,
get_poscar,
get_lattice,
output,
is_primitive,
get_primitive_standardized,
get_conventional_standardized,
dump,
show_nearest_distance,
):
move_atoms_into_unitcell = True
symprec = 1e-5
no_idealize = False
no_sort = True
get_sort_list = False
if posfile is None:
print("Warning:")
print(" POSCAR file did not specify")
print(" Set automatically, a=2.93, c=4.65, symbol='Ti', "
"wyckoff='c'")
lattice = get_hexagonal_lattice_from_a_c(a=2.93, c=4.65)
symbol = 'Ti'
wyckoff = 'c'
else:
poscar = Poscar.from_file(posfile)
pmgstructure = poscar.structure
cell = get_cell_from_pymatgen_structure(pmgstructure)
lattice = cell[0]
symbol = cell[2][0]
wyckoff = get_wyckoff_from_hcp(cell)
twinpy = Twinpy(lattice=lattice,
twinmode=twinmode,
symbol=symbol,
wyckoff=wyckoff)
if get_poscar:
if output is None:
output = _get_output_name(structure=structure,
get_lattice=get_lattice,
shear_strain_ratio=shear_strain_ratio,
twinmode=twinmode)
if structure == 'shear':
twinpy.set_shear(xshift=xshift,
yshift=yshift,
dim=dim,
shear_strain_ratio=shear_strain_ratio,
expansion_ratios=expansion_ratios,
is_primitive=is_primitive)
std = twinpy.get_shear_standardize(
get_lattice=get_lattice,
move_atoms_into_unitcell=move_atoms_into_unitcell,
)
else:
make_tb_flat = not no_make_tb_flat
twinpy.set_twinboundary(twintype=twintype,
xshift=xshift,
yshift=yshift,
layers=layers,
delta=delta,
shear_strain_ratio=shear_strain_ratio,
expansion_ratios=expansion_ratios,
make_tb_flat=make_tb_flat)
std = twinpy.get_twinboundary_standardize(
get_lattice=get_lattice,
move_atoms_into_unitcell=move_atoms_into_unitcell,
)
if show_nearest_distance:
from twinpy.structure.twinboundary \
import plot_nearest_atomic_distance_of_twinboundary
plot_nearest_atomic_distance_of_twinboundary(
lattice=lattice,
symbol=symbol,
twinmode=twinmode,
layers=layers,
wyckoff=wyckoff,
delta=delta,
twintype=twintype,
shear_strain_ratio=shear_strain_ratio,
expansion_ratios=expansion_ratios,
make_tb_flat=make_tb_flat,
)
if get_primitive_standardized:
to_primitive = True
elif get_conventional_standardized:
to_primitive = False
else:
to_primitive = None
if to_primitive is None:
out_cell = std.cell
else:
out_cell = std.get_standardized_cell(
to_primitive=to_primitive,
no_idealize=no_idealize,
symprec=symprec,
no_sort=no_sort,
get_sort_list=get_sort_list,
)
if output is not None:
write_poscar(cell=out_cell, filename=output)
if dump:
twinpy.dump_yaml()