def run_isotope_then_exit(phono3py, settings, updated_settings, log_level):
mass_variances = settings.mass_variances
if settings.band_indices is not None:
band_indices = np.hstack(settings.band_indices).astype('intc')
else:
band_indices = None
iso = Phono3pyIsotope(
phono3py.mesh_numbers,
phono3py.phonon_primitive,
mass_variances=mass_variances,
band_indices=band_indices,
sigmas=updated_settings['sigmas'],
frequency_factor_to_THz=updated_settings['frequency_factor_to_THz'],
symprec=phono3py.symmetry.tolerance,
cutoff_frequency=settings.cutoff_frequency,
lapack_zheev_uplo=settings.lapack_zheev_uplo)
iso.init_dynamical_matrix(
phono3py.fc2,
phono3py.phonon_supercell,
phono3py.phonon_primitive,
nac_params=phono3py.nac_params,
frequency_scale_factor=updated_settings['frequency_scale_factor'])
if log_level > 0:
dm = iso.dynamical_matrix
if (dm.is_nac() and dm.nac_method == 'gonze'):
dm.show_Gonze_nac_message()
iso.run(updated_settings['grid_points'])
if log_level:
print_end()
sys.exit(0)
def run_jdos_then_exit(phono3py, settings, updated_settings, output_filename,
log_level):
joint_dos = Phono3pyJointDos(
phono3py.phonon_supercell,
phono3py.phonon_primitive,
phono3py.mesh_numbers,
phono3py.fc2,
nac_params=phono3py.nac_params,
nac_q_direction=settings.nac_q_direction,
sigmas=updated_settings['sigmas'],
cutoff_frequency=updated_settings['cutoff_frequency'],
frequency_step=updated_settings['frequency_step'],
num_frequency_points=updated_settings['num_frequency_points'],
temperatures=updated_settings['temperature_points'],
frequency_factor_to_THz=updated_settings['frequency_factor_to_THz'],
frequency_scale_factor=updated_settings['frequency_scale_factor'],
is_mesh_symmetry=settings.is_mesh_symmetry,
symprec=phono3py.symmetry.tolerance,
output_filename=output_filename,
log_level=log_level)
if log_level > 0:
dm = joint_dos.dynamical_matrix
if (dm.is_nac() and dm.nac_method == 'gonze'):
dm.show_Gonze_nac_message()
joint_dos.run(updated_settings['grid_points'], write_jdos=True)
if log_level:
print_end()
sys.exit(0)
def create_FORCE_SETS_from_FORCES_FCx_then_exit(phonon_smat,
input_filename: Optional[str],
cell_filename: Optional[str],
log_level):
"""Convert FORCES_FC3 or FORCES_FC2 to FORCE_SETS."""
if cell_filename is not None:
disp_filename = cell_filename
elif input_filename is None:
disp_filename = "phono3py_disp.yaml"
else:
disp_filename = f"phono3py_disp.{input_filename}.yaml"
if phonon_smat is not None:
forces_filename = "FORCES_FC2"
else:
forces_filename = "FORCES_FC3"
if log_level:
print(f'Displacement dataset is read from "{disp_filename}".')
print(f'Forces are read from "{forces_filename}"')
with open(forces_filename, "r") as f:
len_first_line = get_length_of_first_line(f)
if len_first_line == 3:
file_exists(disp_filename, log_level)
file_exists(forces_filename, log_level)
ph3yml = Phono3pyYaml()
ph3yml.read(disp_filename)
if phonon_smat is None:
dataset = copy.deepcopy(ph3yml.dataset)
smat = ph3yml.supercell_matrix
else:
dataset = copy.deepcopy(ph3yml.phonon_dataset)
smat = ph3yml.phonon_supercell_matrix
if smat is None or (phonon_smat is not None and
(phonon_smat != smat).any()):
if log_level:
print("")
print("Supercell matrix is inconsistent.")
print(f'Supercell matrix read from "{disp_filename}":')
print(smat)
print("Supercell matrix given by --dim-fc2:")
print(phonon_smat)
print_error()
sys.exit(1)
parse_FORCES_FC2(dataset, filename=forces_filename)
write_FORCE_SETS(dataset)
if log_level:
print("FORCE_SETS has been created.")
print_end()
else:
if log_level:
print("The file format of %s is already readable by phonopy." %
forces_filename)
print_end()
sys.exit(0)
def finalize_phono3py(
phono3py: Phono3py,
confs_dict,
log_level,
displacements_mode=False,
filename=None,
):
"""Write phono3py.yaml and then exit.
Parameters
----------
phono3py : Phono3py
Phono3py instance.
confs_dict : dict
This contains the settings and command options that the user set.
log_level : int
Log level. 0 means quiet.
displacements_mode : Bool
When True, crystal structure is written in the length unit of
calculator interface in phono3py_disp.yaml. Otherwise, the
default unit (angstrom) is used.
filename : str, optional
phono3py.yaml is written in this filename.
"""
if filename is None:
yaml_filename = "phono3py.yaml"
else:
yaml_filename = filename
if displacements_mode:
_calculator = phono3py.calculator
else:
_calculator = None
_physical_units = get_default_physical_units(_calculator)
yaml_settings = {"force_sets": False, "displacements": displacements_mode}
ph3py_yaml = Phono3pyYaml(configuration=confs_dict,
physical_units=_physical_units,
settings=yaml_settings)
ph3py_yaml.set_phonon_info(phono3py)
ph3py_yaml.calculator = _calculator
with open(yaml_filename, "w") as w:
w.write(str(ph3py_yaml))
if log_level > 0:
print("")
if displacements_mode:
print(f'Displacement dataset was written in "{yaml_filename}".')
else:
print(f'Summary of calculation was written in "{yaml_filename}".')
print_end()
sys.exit(0)
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 run_gruneisen_then_exit(phono3py, settings, output_filename, log_level):
"""Run mode Grueneisen parameter calculation from fc3."""
if (settings.mesh_numbers is None and settings.band_paths is None
and settings.qpoints is None):
print("An option of --mesh, --band, or --qpoints has to be specified.")
if log_level:
print_error()
sys.exit(1)
if len(phono3py.fc2) != len(phono3py.fc3):
print("Supercells used for fc2 and fc3 have to be same.")
if log_level:
print_error()
sys.exit(1)
if settings.band_paths is not None:
if settings.band_points is None:
npoints = 51
else:
npoints = settings.band_points
band_paths = settings.band_paths
bands = get_band_qpoints(band_paths, npoints=npoints)
else:
bands = None
rotations = phono3py.primitive_symmetry.pointgroup_operations
run_gruneisen_parameters(
phono3py.fc2,
phono3py.fc3,
phono3py.supercell,
phono3py.primitive,
bands,
settings.mesh_numbers,
rotations,
settings.qpoints,
nac_params=phono3py.nac_params,
nac_q_direction=settings.nac_q_direction,
ion_clamped=settings.ion_clamped,
factor=VaspToTHz,
symprec=phono3py.symmetry.tolerance,
output_filename=output_filename,
log_level=log_level,
)
if log_level:
print_end()
sys.exit(0)
def create_FORCES_FC2_from_FORCE_SETS_then_exit(log_level):
"""Convert FORCE_SETS to FORCES_FC2."""
filename = "FORCE_SETS"
file_exists(filename, log_level)
disp_dataset = parse_FORCE_SETS(filename=filename)
write_FORCES_FC2(disp_dataset)
if log_level:
print("")
print("FORCES_FC2 has been created from FORCE_SETS.")
print("The following yaml lines should replace respective part of")
print("phono3py_disp.yaml made with --dim-fc2=dim_of_FORCE_SETS.")
print("")
print("\n".join(displacements_yaml_lines_type1(disp_dataset)))
if log_level:
print_end()
sys.exit(0)
def run_isotope_then_exit(phono3py, settings, updated_settings, log_level):
"""Run isotope scattering calculation."""
mass_variances = settings.mass_variances
if settings.band_indices is not None:
band_indices = np.hstack(settings.band_indices).astype("intc")
else:
band_indices = None
iso = Phono3pyIsotope(
settings.mesh_numbers,
phono3py.phonon_primitive,
mass_variances=mass_variances,
band_indices=band_indices,
sigmas=updated_settings["sigmas"],
frequency_factor_to_THz=updated_settings["frequency_factor_to_THz"],
use_grg=settings.use_grg,
store_dense_gp_map=(not settings.emulate_v1),
symprec=phono3py.symmetry.tolerance,
cutoff_frequency=settings.cutoff_frequency,
lapack_zheev_uplo=settings.lapack_zheev_uplo,
)
iso.init_dynamical_matrix(
phono3py.fc2,
phono3py.phonon_supercell,
phono3py.phonon_primitive,
nac_params=phono3py.nac_params,
frequency_scale_factor=updated_settings["frequency_scale_factor"],
)
if log_level > 0:
dm = iso.dynamical_matrix
if dm.is_nac() and dm.nac_method == "gonze":
dm.show_Gonze_nac_message()
grid_points = settings_to_grid_points(settings, iso.grid)
iso.run(grid_points)
if log_level:
print_end()
sys.exit(0)
def run_jdos_then_exit(phono3py: Phono3py, settings, updated_settings,
output_filename, log_level):
"""Run joint-DOS calculation."""
joint_dos = Phono3pyJointDos(
phono3py.phonon_supercell,
phono3py.phonon_primitive,
phono3py.fc2,
mesh=settings.mesh_numbers,
nac_params=phono3py.nac_params,
nac_q_direction=settings.nac_q_direction,
sigmas=updated_settings["sigmas"],
cutoff_frequency=updated_settings["cutoff_frequency"],
frequency_step=updated_settings["frequency_step"],
num_frequency_points=updated_settings["num_frequency_points"],
num_points_in_batch=updated_settings["num_points_in_batch"],
temperatures=updated_settings["temperature_points"],
frequency_factor_to_THz=updated_settings["frequency_factor_to_THz"],
frequency_scale_factor=updated_settings["frequency_scale_factor"],
use_grg=settings.use_grg,
is_mesh_symmetry=settings.is_mesh_symmetry,
store_dense_gp_map=(not settings.emulate_v1),
symprec=phono3py.symmetry.tolerance,
output_filename=output_filename,
log_level=log_level,
)
if log_level > 0:
dm = joint_dos.dynamical_matrix
if dm.is_nac() and dm.nac_method == "gonze":
dm.show_Gonze_nac_message()
grid_points = settings_to_grid_points(settings, joint_dos.grid)
joint_dos.run(grid_points, write_jdos=True)
if log_level:
print_end()
sys.exit(0)
def create_FORCE_SETS_from_FORCES_FCx_then_exit(phonon_smat, input_filename,
log_level):
if phonon_smat is not None:
if input_filename is None:
disp_filename = 'disp_fc2.yaml'
else:
disp_filename = 'disp_fc2.' + input_filename + '.yaml'
forces_filename = "FORCES_FC2"
else:
if input_filename is None:
disp_filename = 'disp_fc3.yaml'
else:
disp_filename = 'disp_fc3.' + input_filename + '.yaml'
forces_filename = "FORCES_FC3"
with open(forces_filename, 'r') as f:
len_first_line = get_length_of_first_line(f)
if len_first_line == 3:
file_exists(disp_filename, log_level)
disp_dataset = parse_disp_fc2_yaml(filename=disp_filename)
file_exists(forces_filename, log_level)
parse_FORCES_FC2(disp_dataset, filename=forces_filename)
if log_level:
print("Displacement dataset was read from \"%s\"." % disp_filename)
write_FORCE_SETS(disp_dataset)
if log_level:
print("FORCE_SETS has been created.")
print_end()
else:
if log_level:
print("The file format of %s is already readable by phonopy." %
forces_filename)
print_end()
sys.exit(0)
def main(**argparse_control):
load_phono3py_yaml = argparse_control.get('load_phono3py_yaml', False)
args, log_level = start_phono3py(**argparse_control)
physical_units = get_default_physical_units(get_interface_mode(vars(args)))
if load_phono3py_yaml:
input_filename = None
output_filename = None
else:
(input_filename,
output_filename) = get_input_output_filenames_from_args(args)
settings, confs, cell_filename = read_phono3py_settings(
args, argparse_control, log_level)
if args.force_sets_to_forces_fc2_mode:
create_FORCES_FC2_from_FORCE_SETS_then_exit(log_level)
if args.force_sets_mode:
create_FORCE_SETS_from_FORCES_FCx_then_exit(
settings.phonon_supercell_matrix, input_filename, log_level)
if args.write_grid_points:
run_mode = "write_grid_info"
elif args.show_num_triplets:
run_mode = "show_triplets_info"
else:
run_mode = None
# -----------------------------------------------------------------------
# ----------------- 'args' should not be used below. --------------------
# -----------------------------------------------------------------------
####################################
# Create FORCES_FC3 and FORCES_FC2 #
####################################
create_FORCES_FC3_and_FORCES_FC2_then_exit(settings, input_filename,
output_filename, log_level)
###########################################################
# Symmetry tolerance. Distance unit depends on interface. #
###########################################################
if settings.symmetry_tolerance is None:
symprec = 1e-5
else:
symprec = settings.symmetry_tolerance
cell_info = get_cell_info(settings, cell_filename, symprec, log_level)
unitcell_filename = cell_info['optional_structure_info'][0]
interface_mode = cell_info['interface_mode']
# ph3py_yaml = cell_info['phonopy_yaml']
if run_mode is None:
run_mode = get_run_mode(settings)
######################################################
# Create supercells with displacements and then exit #
######################################################
if settings.create_displacements:
phono3py = create_phono3py_supercells(cell_info,
settings,
symprec,
output_filename=output_filename,
interface_mode=interface_mode,
log_level=log_level)
finalize_phono3py(phono3py,
confs,
log_level,
displacements_mode=True,
filename="phono3py_disp.yaml")
#######################
# Initialize phono3py #
#######################
# updated_settings keys
# ('grid_points', 'sigmas', 'temperature_points', 'temperatures',
# 'frequency_factor_to_THz', 'num_frequency_points',
# 'frequency_step', 'frequency_scale_factor',
# 'cutoff_frequency')
phono3py, updated_settings = init_phono3py(settings, cell_info,
interface_mode, output_filename,
symprec, log_level)
#################################################
# Show phono3py settings and crystal structures #
#################################################
if log_level:
show_general_settings(settings, run_mode, phono3py, unitcell_filename,
input_filename, output_filename)
if log_level > 1:
show_phono3py_cells(phono3py, settings)
else:
print("Spacegroup: %s" % phono3py.symmetry.get_international_table())
print("Use -v option to watch primitive cell, unit cell, "
"and supercell structures.")
##################
# Check settings #
##################
run_modes_with_mesh = ("conductivity-RTA", "conductivity-LBTE",
"imag_self_energy", "jdos", "isotope",
"write_grid_info", "show_triplets_info")
run_modes_with_gp = ("imag_self_energy", "jdos", "isotope")
if phono3py.mesh_numbers is None and run_mode in run_modes_with_mesh:
print("")
print("Mesh numbers have to be specified.")
print("")
if log_level:
print_error()
sys.exit(1)
if (run_mode in run_modes_with_gp
and updated_settings['grid_points'] is None):
print("")
print("Grid point(s) has to be specified.")
print("")
if log_level:
print_error()
sys.exit(1)
#########################################################
# Write ir-grid points and grid addresses and then exit #
#########################################################
if run_mode == "write_grid_info":
write_grid_points(phono3py.primitive,
phono3py.mesh_numbers,
mesh_divs=settings.mesh_divisors,
band_indices=settings.band_indices,
sigmas=updated_settings['sigmas'],
temperatures=updated_settings['temperatures'],
coarse_mesh_shifts=settings.coarse_mesh_shifts,
is_kappa_star=settings.is_kappa_star,
is_lbte=(settings.write_collision
or settings.is_lbte),
compression=settings.hdf5_compression,
symprec=symprec)
if log_level:
print_end()
sys.exit(0)
################################################################
# Show reduced number of triplets at grid points and then exit #
################################################################
if run_mode == "show_triplets_info":
show_num_triplets(phono3py.primitive,
phono3py.mesh_numbers,
mesh_divs=settings.mesh_divisors,
band_indices=settings.band_indices,
grid_points=updated_settings['grid_points'],
coarse_mesh_shifts=settings.coarse_mesh_shifts,
is_kappa_star=settings.is_kappa_star,
symprec=symprec)
if log_level:
print_end()
sys.exit(0)
##################################
# Non-analytical term correction #
##################################
store_nac_params(phono3py,
settings,
cell_info['phonopy_yaml'],
unitcell_filename,
log_level,
nac_factor=Hartree * Bohr,
load_phonopy_yaml=load_phono3py_yaml)
###################
# Force constants #
###################
store_force_constants(phono3py, settings, cell_info['phonopy_yaml'],
physical_units, input_filename, output_filename,
load_phono3py_yaml, log_level)
############################################
# Phonon Gruneisen parameter and then exit #
############################################
if settings.is_gruneisen:
run_gruneisen_then_exit(phono3py, settings, output_filename, log_level)
#################
# Show settings #
#################
if log_level and run_mode is not None:
show_phono3py_settings(phono3py, settings, updated_settings, log_level)
###########################
# Joint DOS and then exit #
###########################
if run_mode == "jdos":
run_jdos_then_exit(phono3py, settings, updated_settings,
output_filename, log_level)
################################################
# Mass variances for phonon-isotope scattering #
################################################
if settings.is_isotope and settings.mass_variances is None:
from phonopy.structure.atoms import isotope_data
symbols = phono3py.phonon_primitive.symbols
in_database = True
for s in set(symbols):
if s not in isotope_data:
print("%s is not in the list of isotope databese" % s)
print("(not implemented).")
print("Use --mass_variances option.")
in_database = False
if not in_database:
if log_level:
print_end()
sys.exit(0)
#########################################
# Phonon-isotope lifetime and then exit #
#########################################
if run_mode == "isotope":
run_isotope_then_exit(phono3py, settings, updated_settings, log_level)
########################################
# Initialize phonon-phonon interaction #
########################################
if run_mode is not None:
init_phph_interaction(phono3py, settings, updated_settings,
input_filename, output_filename, log_level)
#######################################################
# Run imaginary part of self energy of bubble diagram #
#######################################################
if run_mode == "imag_self_energy":
phono3py.run_imag_self_energy(
updated_settings['grid_points'],
updated_settings['temperature_points'],
frequency_step=updated_settings['frequency_step'],
num_frequency_points=updated_settings['num_frequency_points'],
scattering_event_class=settings.scattering_event_class,
write_txt=True,
write_gamma_detail=settings.write_gamma_detail,
output_filename=output_filename)
#####################################################
# Run frequency shift calculation of bubble diagram #
#####################################################
elif run_mode == "real_self_energy":
phono3py.run_real_self_energy(
updated_settings['grid_points'],
updated_settings['temperature_points'],
frequency_step=updated_settings['frequency_step'],
num_frequency_points=updated_settings['num_frequency_points'],
write_txt=True,
output_filename=output_filename)
#######################################################
# Run spectral function calculation of bubble diagram #
#######################################################
elif run_mode == "spectral_function":
phono3py.run_spectral_function(
updated_settings['grid_points'],
updated_settings['temperature_points'],
frequency_step=updated_settings['frequency_step'],
num_frequency_points=updated_settings['num_frequency_points'],
num_points_in_batch=updated_settings['num_points_in_batch'],
write_txt=True,
write_hdf5=True,
output_filename=output_filename)
####################################
# Run lattice thermal conductivity #
####################################
elif run_mode == "conductivity-RTA" or run_mode == "conductivity-LBTE":
phono3py.run_thermal_conductivity(
is_LBTE=settings.is_lbte,
temperatures=updated_settings['temperatures'],
is_isotope=settings.is_isotope,
mass_variances=settings.mass_variances,
grid_points=updated_settings['grid_points'],
boundary_mfp=settings.boundary_mfp,
solve_collective_phonon=settings.solve_collective_phonon,
use_ave_pp=settings.use_ave_pp,
gamma_unit_conversion=settings.gamma_conversion_factor,
mesh_divisors=settings.mesh_divisors,
coarse_mesh_shifts=settings.coarse_mesh_shifts,
is_reducible_collision_matrix=settings.
is_reducible_collision_matrix,
is_kappa_star=settings.is_kappa_star,
gv_delta_q=settings.group_velocity_delta_q,
is_full_pp=settings.is_full_pp,
pinv_cutoff=settings.pinv_cutoff,
pinv_solver=settings.pinv_solver,
write_gamma=settings.write_gamma,
read_gamma=settings.read_gamma,
write_kappa=True,
is_N_U=settings.is_N_U,
write_gamma_detail=settings.write_gamma_detail,
write_collision=settings.write_collision,
read_collision=settings.read_collision,
write_pp=settings.write_pp,
read_pp=settings.read_pp,
write_LBTE_solution=settings.write_LBTE_solution,
compression=settings.hdf5_compression,
input_filename=input_filename,
output_filename=output_filename)
else:
if log_level:
print("-" * 11 +
" None of ph-ph interaction calculation was performed. " +
"-" * 11)
finalize_phono3py(phono3py, confs, log_level)
def create_FORCES_FC3_and_FORCES_FC2_then_exit(settings, input_filename,
output_filename, log_level):
interface_mode = settings.calculator
#####################
# Create FORCES_FC3 #
#####################
if settings.create_forces_fc3 or settings.create_forces_fc3_file:
if input_filename is None:
disp_fc3_filename = 'disp_fc3.yaml'
else:
disp_fc3_filename = 'disp_fc3.' + input_filename + '.yaml'
ph3py_yaml = None
disp_filenames = files_exist(['phono3py_disp.yaml', disp_fc3_filename],
log_level,
is_any=True)
if disp_filenames[0] == 'phono3py_disp.yaml':
try:
ph3py_yaml = Phono3pyYaml()
ph3py_yaml.read('phono3py_disp.yaml')
if ph3py_yaml.calculator is not None:
interface_mode = ph3py_yaml.calculator # overwrite
disp_filename = 'phono3py_disp.yaml'
except KeyError:
file_exists('disp_fc3.yaml', log_level)
if log_level > 0:
print("\"phono3py_disp.yaml\" was found but wasn't used.")
disp_filename = disp_fc3_filename
else:
disp_filename = disp_filenames[0]
if ph3py_yaml is None:
file_exists(disp_filename, log_level)
disp_dataset = parse_disp_fc3_yaml(filename=disp_filename)
else:
disp_dataset = ph3py_yaml.dataset
if log_level:
print('')
print("Displacement dataset was read from \"%s\"." % disp_filename)
num_atoms = disp_dataset['natom']
num_disps = len(disp_dataset['first_atoms'])
for d1 in disp_dataset['first_atoms']:
for d2 in d1['second_atoms']:
if 'included' not in d2 or d2['included']:
num_disps += 1
if settings.create_forces_fc3_file:
file_exists(settings.create_forces_fc3_file, log_level)
force_filenames = [
x.strip() for x in open(settings.create_forces_fc3_file)
]
else:
force_filenames = settings.create_forces_fc3
for filename in force_filenames:
file_exists(filename, log_level)
if log_level > 0:
print("Number of displacements: %d" % num_disps)
print("Number of supercell files: %d" % len(force_filenames))
if not check_number_of_force_files(num_disps, force_filenames,
disp_filename):
force_sets = []
else:
force_sets = get_force_sets(interface_mode,
num_atoms,
num_disps,
force_filenames,
disp_filename=disp_filename,
verbose=(log_level > 0))
if settings.subtract_forces:
force_filename = settings.subtract_forces
file_exists(force_filename, log_level)
force_set_zero = get_force_sets(interface_mode,
num_atoms,
1, [
force_filename,
],
verbose=(log_level > 0))[0]
for fs in force_sets:
fs -= force_set_zero
if log_level > 0:
print(
"Forces in \'%s\' were subtracted from supercell forces." %
force_filename)
if force_sets:
write_FORCES_FC3(disp_dataset, force_sets, filename="FORCES_FC3")
if log_level:
print("")
print("%s has been created." % "FORCES_FC3")
print_end()
sys.exit(0)
else:
if log_level:
print("")
print("%s could not be created." % "FORCES_FC3")
print_error()
sys.exit(1)
#####################
# Create FORCES_FC2 #
#####################
if settings.create_forces_fc2:
if input_filename is None:
disp_filename = 'disp_fc2.yaml'
else:
disp_filename = 'disp_fc2.' + input_filename + '.yaml'
file_exists(disp_filename, log_level)
disp_dataset = parse_disp_fc2_yaml(filename=disp_filename)
if log_level:
print("Displacement dataset was read from \"%s\"." % disp_filename)
num_atoms = disp_dataset['natom']
num_disps = len(disp_dataset['first_atoms'])
force_filenames = settings.create_forces_fc2
for filename in force_filenames:
file_exists(filename, log_level)
if log_level > 0:
print("Number of displacements: %d" % num_disps)
print("Number of supercell files: %d" % len(force_filenames))
force_sets = get_force_sets(interface_mode,
num_atoms,
num_disps,
force_filenames,
disp_filename,
verbose=(log_level > 0))
if settings.subtract_forces:
force_filename = settings.subtract_forces
file_exists(force_filename, log_level)
force_set_zero = get_force_sets(interface_mode,
num_atoms,
1, [
force_filename,
],
verbose=(log_level > 0))[0]
for fs in force_sets:
fs -= force_set_zero
if log_level > 0:
print(
"Forces in \'%s\' were subtracted from supercell forces." %
force_filename)
if force_sets:
write_FORCES_FC2(disp_dataset,
forces_fc2=force_sets,
filename="FORCES_FC2")
if log_level:
print("")
print("%s has been created." % "FORCES_FC2")
print_end()
sys.exit(0)
else:
if log_level:
print("")
print("%s could not be created." % "FORCES_FC2")
print_error()
sys.exit(1)
def create_FORCES_FC3_and_FORCES_FC2_then_exit(settings, input_filename,
log_level):
"""Create FORCES_FC3 and FORCES_FC2 from files."""
interface_mode = settings.calculator
ph3py_yaml = None
#####################
# Create FORCES_FC3 #
#####################
if settings.create_forces_fc3 or settings.create_forces_fc3_file:
if input_filename is None:
disp_fc3_filename = "disp_fc3.yaml"
else:
disp_fc3_filename = "disp_fc3." + input_filename + ".yaml"
disp_filenames = files_exist(["phono3py_disp.yaml", disp_fc3_filename],
log_level,
is_any=True)
disp_filename = disp_filenames[0]
if "phono3py_disp.yaml" in disp_filename:
ph3py_yaml = Phono3pyYaml()
ph3py_yaml.read(disp_filename)
if ph3py_yaml.calculator is not None:
interface_mode = ph3py_yaml.calculator # overwrite
disp_dataset = ph3py_yaml.dataset
else:
file_exists(disp_filename, log_level)
disp_dataset = parse_disp_fc3_yaml(filename=disp_filename)
if log_level:
print("")
print('Displacement dataset was read from "%s".' % disp_filename)
num_atoms = disp_dataset["natom"]
num_disps = len(disp_dataset["first_atoms"])
for d1 in disp_dataset["first_atoms"]:
for d2 in d1["second_atoms"]:
if "included" not in d2 or d2["included"]:
num_disps += 1
if settings.create_forces_fc3_file:
file_exists(settings.create_forces_fc3_file, log_level)
force_filenames = [
x.strip() for x in open(settings.create_forces_fc3_file)
]
else:
force_filenames = settings.create_forces_fc3
for filename in force_filenames:
file_exists(filename, log_level)
if log_level > 0:
print("Number of displacements: %d" % num_disps)
print("Number of supercell files: %d" % len(force_filenames))
if not check_number_of_force_files(num_disps, force_filenames,
disp_filename):
force_sets = []
else:
force_sets = get_force_sets(
interface_mode,
num_atoms,
force_filenames,
verbose=(log_level > 0),
)
if settings.subtract_forces:
force_filename = settings.subtract_forces
file_exists(force_filename, log_level)
force_set_zero = get_force_sets(
interface_mode,
num_atoms,
[
force_filename,
],
verbose=(log_level > 0),
)[0]
for fs in force_sets:
fs -= force_set_zero
if log_level > 0:
print("Forces in '%s' were subtracted from supercell forces." %
force_filename)
if force_sets:
write_FORCES_FC3(disp_dataset,
forces_fc3=force_sets,
filename="FORCES_FC3")
if log_level:
print("")
print("%s has been created." % "FORCES_FC3")
print_end()
sys.exit(0)
else:
if log_level:
print("")
print("%s could not be created." % "FORCES_FC3")
print_error()
sys.exit(1)
#####################
# Create FORCES_FC2 #
#####################
if settings.create_forces_fc2:
if input_filename is None:
disp_fc2_filename = "disp_fc2.yaml"
else:
disp_fc2_filename = "disp_fc2." + input_filename + ".yaml"
disp_filenames = files_exist(["phono3py_disp.yaml", disp_fc2_filename],
log_level,
is_any=True)
if "phono3py_disp.yaml" in disp_filenames[0]:
# ph3py_yaml is not None, phono3py_disp.yaml is already read.
if ph3py_yaml is None:
disp_filename = disp_filenames[0]
ph3py_yaml = Phono3pyYaml()
ph3py_yaml.read(disp_filename)
if ph3py_yaml.calculator is not None:
interface_mode = ph3py_yaml.calculator # overwrite
disp_dataset = ph3py_yaml.phonon_dataset
else:
disp_filename = disp_filenames[0]
file_exists(disp_filename, log_level)
disp_dataset = parse_disp_fc2_yaml(filename=disp_filename)
if log_level:
print('Displacement dataset was read from "%s".' % disp_filename)
num_atoms = disp_dataset["natom"]
num_disps = len(disp_dataset["first_atoms"])
force_filenames = settings.create_forces_fc2
for filename in force_filenames:
file_exists(filename, log_level)
if log_level > 0:
print("Number of displacements: %d" % num_disps)
print("Number of supercell files: %d" % len(force_filenames))
force_sets = get_force_sets(
interface_mode,
num_atoms,
force_filenames,
verbose=(log_level > 0),
)
if settings.subtract_forces:
force_filename = settings.subtract_forces
file_exists(force_filename, log_level)
force_set_zero = get_force_sets(
interface_mode,
num_atoms,
[
force_filename,
],
verbose=(log_level > 0),
)[0]
for fs in force_sets:
fs -= force_set_zero
if log_level > 0:
print("Forces in '%s' were subtracted from supercell forces." %
force_filename)
if force_sets:
write_FORCES_FC2(disp_dataset,
forces_fc2=force_sets,
filename="FORCES_FC2")
if log_level:
print("")
print("%s has been created." % "FORCES_FC2")
print_end()
sys.exit(0)
else:
if log_level:
print("")
print("%s could not be created." % "FORCES_FC2")
print_error()
sys.exit(1)
