def create_FORCES_FC2_from_FORCE_SETS_then_exit(log_level):
filename = 'FORCE_SETS'
file_exists(filename, log_level)
disp_dataset = parse_FORCE_SETS(filename=filename)
write_FORCES_FC2(disp_dataset)
write_disp_fc2_yaml(disp_dataset, None)
if log_level:
print("FORCES_FC2 and disp_fc2.yaml have been created from "
"FORCE_SETS.")
print_end()
sys.exit(0)
def create_phono3py_supercells(unitcell,
supercell_matrix,
phonon_supercell_matrix,
displacement_distance,
is_plusminus,
is_diagonal,
cutoff_pair_distance,
write_supercells_with_displacements,
optional_structure_file_information,
symprec,
interface_mode='vasp',
output_filename=None,
log_level=1):
if displacement_distance is None:
if interface_mode in ('pwscf', 'abinit'):
distance = 0.06
elif interface_mode == 'crystal':
distance = 0.03
else:
distance = 0.03
else:
distance = displacement_distance
phono3py = Phono3py(unitcell,
supercell_matrix,
phonon_supercell_matrix=phonon_supercell_matrix,
symprec=symprec)
supercell = phono3py.get_supercell()
phono3py.generate_displacements(distance=distance,
cutoff_pair_distance=cutoff_pair_distance,
is_plusminus=is_plusminus,
is_diagonal=is_diagonal)
dds = phono3py.get_displacement_dataset()
if log_level:
print('')
print("Displacement distance: %s" % distance)
if output_filename is None:
filename = 'disp_fc3.yaml'
else:
filename = 'disp_fc3.' + output_filename + '.yaml'
num_disps, num_disp_files = write_disp_fc3_yaml(dds,
supercell,
filename=filename)
cells_with_disps = phono3py.get_supercells_with_displacements()
if interface_mode == 'pwscf':
pp_filenames = optional_structure_file_information[1]
write_supercells_with_displacements(supercell,
cells_with_disps,
pp_filenames,
width=5)
elif interface_mode == 'crystal':
conv_numbers = optional_structure_file_information[1]
write_supercells_with_displacements(supercell,
cells_with_disps,
conv_numbers,
supercell_matrix,
width=5,
template_file="TEMPLATE3")
elif interface_mode == 'abinit':
write_supercells_with_displacements(supercell,
cells_with_disps,
width=5)
else: # VASP
write_supercells_with_displacements(supercell,
cells_with_disps,
width=5)
if log_level:
print("Number of displacements: %d" % num_disps)
if cutoff_pair_distance is not None:
print("Cutoff distance for displacements: %s" %
cutoff_pair_distance)
print("Number of displacement supercell files created: %d" %
num_disp_files)
if phonon_supercell_matrix is not None:
phonon_dds = phono3py.get_phonon_displacement_dataset()
phonon_supercell = phono3py.get_phonon_supercell()
if output_filename is None:
filename = 'disp_fc2.yaml'
else:
filename = 'disp_fc2.' + output_filename + '.yaml'
num_disps = write_disp_fc2_yaml(phonon_dds,
phonon_supercell,
filename=filename)
cells_with_disps = phono3py.get_phonon_supercells_with_displacements()
if interface_mode == 'pwscf':
pp_filenames = optional_structure_file_information[1]
write_supercells_with_displacements(phonon_supercell,
cells_with_disps,
pp_filenames,
pre_filename="supercell_fc2",
width=5)
elif interface_mode == 'crystal':
conv_numbers = optional_structure_file_information[1]
write_supercells_with_displacements(phonon_supercell,
cells_with_disps,
conv_numbers,
phonon_supercell_matrix,
pre_filename="supercell_fc2",
width=5,
template_file="TEMPLATE")
elif interface_mode == 'abinit':
write_supercells_with_displacements(phonon_supercell,
cells_with_disps,
pre_filename="supercell_fc2",
width=5)
else:
write_supercells_with_displacements(phonon_supercell,
cells_with_disps,
pre_filename="POSCAR_FC2",
width=5)
if log_level:
print("Number of displacements for special fc2: %d" % num_disps)
return phono3py
def create_phono3py_supercells(unitcell,
supercell_matrix,
phonon_supercell_matrix,
displacement_distance,
is_plusminus,
is_diagonal,
cutoff_pair_distance,
optional_structure_info,
is_symmetry,
symprec,
interface_mode='vasp',
output_filename=None,
log_level=1):
if displacement_distance is None:
distance = get_default_displacement_distance(interface_mode)
else:
distance = displacement_distance
phono3py = Phono3py(unitcell,
supercell_matrix,
phonon_supercell_matrix=phonon_supercell_matrix,
is_symmetry=is_symmetry,
symprec=symprec)
supercell = phono3py.get_supercell()
phono3py.generate_displacements(distance=distance,
cutoff_pair_distance=cutoff_pair_distance,
is_plusminus=is_plusminus,
is_diagonal=is_diagonal)
dds = phono3py.get_displacement_dataset()
if log_level:
print('')
print("Displacement distance: %s" % distance)
if output_filename is None:
filename = 'disp_fc3.yaml'
else:
filename = 'disp_fc3.' + output_filename + '.yaml'
num_disps, num_disp_files = write_disp_fc3_yaml(dds,
supercell,
filename=filename)
cells_with_disps = phono3py.supercells_with_displacements
ids = []
disp_cells = []
for i, cell in enumerate(cells_with_disps):
if cell is not None:
ids.append(i + 1)
disp_cells.append(cell)
additional_info = get_additional_info_to_write_supercells(
interface_mode, phono3py)
write_supercells_with_displacements(interface_mode,
supercell,
disp_cells,
optional_structure_info,
displacement_ids=ids,
zfill_width=5,
additional_info=additional_info)
if log_level:
print("Number of displacements: %d" % num_disps)
if cutoff_pair_distance is not None:
print("Cutoff distance for displacements: %s" %
cutoff_pair_distance)
print("Number of displacement supercell files created: %d" %
num_disp_files)
if phonon_supercell_matrix is not None:
phonon_dds = phono3py.phonon_dataset
phonon_supercell = phono3py.phonon_supercell
phonon_supercell_matrix = phono3py.phonon_supercell_matrix
if output_filename is None:
filename = 'disp_fc2.yaml'
else:
filename = 'disp_fc2.' + output_filename + '.yaml'
num_disps = write_disp_fc2_yaml(phonon_dds,
phonon_supercell,
filename=filename)
cells_with_disps = phono3py.phonon_supercells_with_displacements
additional_info = get_additional_info_to_write_fc2_supercells(
interface_mode, phono3py)
write_supercells_with_displacements(interface_mode,
supercell,
cells_with_disps,
optional_structure_info,
zfill_width=5,
additional_info=additional_info)
if log_level:
print("Number of displacements for special fc2: %d" % num_disps)
return phono3py
def create_phono3py_supercells(cell_info,
settings,
symprec,
output_filename=None,
interface_mode='vasp',
log_level=1):
"""create displacements and supercells
Distance unit used is that for the calculator interface.
The default unit is Angstron.
"""
optional_structure_info = cell_info['optional_structure_info']
if settings.displacement_distance is None:
distance = get_default_displacement_distance(interface_mode)
else:
distance = settings.displacement_distance
phono3py = Phono3py(
cell_info['unitcell'],
cell_info['supercell_matrix'],
primitive_matrix=cell_info['primitive_matrix'],
phonon_supercell_matrix=cell_info['phonon_supercell_matrix'],
is_symmetry=settings.is_symmetry,
symprec=symprec,
calculator=interface_mode)
phono3py.generate_displacements(
distance=distance,
cutoff_pair_distance=settings.cutoff_pair_distance,
is_plusminus=settings.is_plusminus_displacement,
is_diagonal=settings.is_diagonal_displacement)
if log_level:
print('')
print("Unit cell was read from \"%s\"." %
optional_structure_info[0])
print("Displacement distance: %s" % distance)
if output_filename is None:
filename = 'disp_fc3.yaml'
else:
filename = 'disp_fc3.' + output_filename + '.yaml'
num_disps, num_disp_files = write_disp_fc3_yaml(phono3py.dataset,
phono3py.supercell,
filename=filename)
ids = []
disp_cells = []
for i, cell in enumerate(phono3py.supercells_with_displacements):
if cell is not None:
ids.append(i + 1)
disp_cells.append(cell)
additional_info = get_additional_info_to_write_supercells(
interface_mode, phono3py.supercell_matrix)
write_supercells_with_displacements(interface_mode,
phono3py.supercell,
disp_cells,
optional_structure_info,
displacement_ids=ids,
zfill_width=5,
additional_info=additional_info)
if log_level:
print("Number of displacements: %d" % num_disps)
if settings.cutoff_pair_distance is not None:
print("Cutoff distance for displacements: %s" %
settings.cutoff_pair_distance)
print("Number of displacement supercell files created: %d" %
num_disp_files)
if phono3py.phonon_supercell_matrix is not None:
if output_filename is None:
filename = 'disp_fc2.yaml'
else:
filename = 'disp_fc2.' + output_filename + '.yaml'
num_disps = write_disp_fc2_yaml(phono3py.phonon_dataset,
phono3py.phonon_supercell,
filename=filename)
additional_info = get_additional_info_to_write_fc2_supercells(
interface_mode, phono3py.phonon_supercell_matrix)
write_supercells_with_displacements(
interface_mode,
phono3py.supercell,
phono3py.phonon_supercells_with_displacements,
optional_structure_info,
zfill_width=5,
additional_info=additional_info)
if log_level:
print("Number of displacements for special fc2: %d" % num_disps)
return phono3py
def create_phono3py_supercells(
cell_info,
settings,
symprec,
output_filename=None,
interface_mode="vasp",
log_level=1,
write_disp_yaml=False,
):
"""Create displacements and supercells.
Distance unit used is that for the calculator interface.
The default unit is Angstron.
Parameters
----------
write_disp_yaml : bool
Write old-style files of disp_fc3.yaml and disp_fc2.yaml. Default is False.
"""
optional_structure_info = cell_info["optional_structure_info"]
if settings.displacement_distance is None:
distance = get_default_displacement_distance(interface_mode)
else:
distance = settings.displacement_distance
phono3py = Phono3py(
cell_info["unitcell"],
cell_info["supercell_matrix"],
primitive_matrix=cell_info["primitive_matrix"],
phonon_supercell_matrix=cell_info["phonon_supercell_matrix"],
is_symmetry=settings.is_symmetry,
symprec=symprec,
calculator=interface_mode,
)
phono3py.generate_displacements(
distance=distance,
cutoff_pair_distance=settings.cutoff_pair_distance,
is_plusminus=settings.is_plusminus_displacement,
is_diagonal=settings.is_diagonal_displacement,
)
if log_level:
print("")
print('Unit cell was read from "%s".' % optional_structure_info[0])
print("Displacement distance: %s" % distance)
if write_disp_yaml:
if output_filename is None:
filename = "disp_fc3.yaml"
else:
filename = "disp_fc3." + output_filename + ".yaml"
num_disps, num_disp_files = write_disp_fc3_yaml(
phono3py.dataset, phono3py.supercell, filename=filename
)
ids = []
disp_cells = []
for i, cell in enumerate(phono3py.supercells_with_displacements):
if cell is not None:
ids.append(i + 1)
disp_cells.append(cell)
additional_info = get_additional_info_to_write_supercells(
interface_mode, phono3py.supercell_matrix
)
write_supercells_with_displacements(
interface_mode,
phono3py.supercell,
disp_cells,
optional_structure_info,
displacement_ids=ids,
zfill_width=5,
additional_info=additional_info,
)
if log_level:
num_disps = len(phono3py.supercells_with_displacements)
num_disp_files = len(disp_cells)
print("Number of displacements: %d" % num_disps)
if settings.cutoff_pair_distance is not None:
print(
"Cutoff distance for displacements: %s" % settings.cutoff_pair_distance
)
print("Number of displacement supercell files created: %d" % num_disp_files)
if phono3py.phonon_supercell_matrix is not None:
if write_disp_yaml:
if output_filename is None:
filename = "disp_fc2.yaml"
else:
filename = "disp_fc2." + output_filename + ".yaml"
num_disps = write_disp_fc2_yaml(
phono3py.phonon_dataset, phono3py.phonon_supercell, filename=filename
)
additional_info = get_additional_info_to_write_fc2_supercells(
interface_mode, phono3py.phonon_supercell_matrix
)
write_supercells_with_displacements(
interface_mode,
phono3py.supercell,
phono3py.phonon_supercells_with_displacements,
optional_structure_info,
zfill_width=5,
additional_info=additional_info,
)
if log_level:
print("Number of displacements for special fc2: %d" % num_disps)
return phono3py