def _read_phono3py_fc3(phono3py, symmetrize_fc3r, input_filename, log_level):
if input_filename is None:
filename = "fc3.hdf5"
else:
filename = "fc3." + input_filename + ".hdf5"
file_exists(filename, log_level)
if log_level:
print('Reading fc3 from "%s".' % filename)
p2s_map = phono3py.primitive.p2s_map
try:
fc3 = read_fc3_from_hdf5(filename=filename, p2s_map=p2s_map)
except RuntimeError:
import traceback
traceback.print_exc()
if log_level:
print_error()
sys.exit(1)
num_atom = phono3py.supercell.get_number_of_atoms()
if fc3.shape[1] != num_atom:
print("Matrix shape of fc3 doesn't agree with supercell size.")
if log_level:
print_error()
sys.exit(1)
if symmetrize_fc3r:
set_translational_invariance_fc3(fc3)
set_permutation_symmetry_fc3(fc3)
phono3py.fc3 = fc3
def _read_phono3py_fc2(phono3py, symmetrize_fc2, input_filename, log_level):
if input_filename is None:
filename = "fc2.hdf5"
else:
filename = "fc2." + input_filename + ".hdf5"
file_exists(filename, log_level)
if log_level:
print('Reading fc2 from "%s".' % filename)
num_atom = phono3py.phonon_supercell.get_number_of_atoms()
p2s_map = phono3py.phonon_primitive.p2s_map
try:
phonon_fc2 = read_fc2_from_hdf5(filename=filename, p2s_map=p2s_map)
except RuntimeError:
import traceback
traceback.print_exc()
if log_level:
print_error()
sys.exit(1)
if phonon_fc2.shape[1] != num_atom:
print("Matrix shape of fc2 doesn't agree with supercell size.")
if log_level:
print_error()
sys.exit(1)
if symmetrize_fc2:
if phonon_fc2.shape[0] == phonon_fc2.shape[1]:
symmetrize_force_constants(phonon_fc2)
else:
symmetrize_compact_force_constants(phonon_fc2,
phono3py.phonon_primitive)
phono3py.fc2 = phonon_fc2
def check_supercell_in_yaml(cell_info, ph3, distance_to_A, log_level):
"""Check consistency between generated cells and cells in yaml."""
if cell_info["phonopy_yaml"] is not None:
if distance_to_A is None:
d2A = 1.0
else:
d2A = distance_to_A
if (cell_info["phonopy_yaml"].supercell is not None
and ph3.supercell is not None): # noqa E129
yaml_cell = cell_info["phonopy_yaml"].supercell.copy()
yaml_cell.cell = yaml_cell.cell * d2A
if not cells_isclose(yaml_cell, ph3.supercell):
if log_level:
print("Generated supercell is inconsistent with "
'that in "%s".' %
cell_info["optional_structure_info"][0])
print_error()
sys.exit(1)
if (cell_info["phonopy_yaml"].phonon_supercell is not None
and ph3.phonon_supercell is not None): # noqa E129
yaml_cell = cell_info["phonopy_yaml"].phonon_supercell.copy()
yaml_cell.cell = yaml_cell.cell * d2A
if not cells_isclose(yaml_cell, ph3.phonon_supercell):
if log_level:
print("Generated phonon supercell is inconsistent with "
'that in "%s".' %
cell_info["optional_structure_info"][0])
print_error()
sys.exit(1)
def get_cell_info(settings, cell_filename, log_level):
"""Return calculator interface and crystal structure information."""
cell_info = collect_cell_info(
supercell_matrix=settings.supercell_matrix,
primitive_matrix=settings.primitive_matrix,
interface_mode=settings.calculator,
cell_filename=cell_filename,
chemical_symbols=settings.chemical_symbols,
phonopy_yaml_cls=Phono3pyYaml,
)
if "error_message" in cell_info:
print_error_message(cell_info["error_message"])
if log_level > 0:
print_error()
sys.exit(1)
set_magnetic_moments(cell_info, settings, log_level)
cell_info["phonon_supercell_matrix"] = settings.phonon_supercell_matrix
ph3py_yaml: Phono3pyYaml = cell_info["phonopy_yaml"]
if cell_info["phonon_supercell_matrix"] is None and ph3py_yaml:
ph_smat = ph3py_yaml.phonon_supercell_matrix
cell_info["phonon_supercell_matrix"] = ph_smat
return cell_info
def _create_phono3py_phonon_fc2(phono3py, ph3py_yaml, symmetrize_fc2,
input_filename, is_compact_fc, fc_calculator,
fc_calculator_options, log_level):
if input_filename is None:
disp_filename = 'disp_fc2.yaml'
else:
disp_filename = 'disp_fc2.' + input_filename + '.yaml'
_ph3py_yaml = _get_ph3py_yaml(disp_filename, ph3py_yaml)
try:
dataset = parse_forces(phono3py,
ph3py_yaml=_ph3py_yaml,
force_filename="FORCES_FC2",
disp_filename=disp_filename,
fc_type='phonon_fc2',
log_level=log_level)
except RuntimeError as e:
if log_level:
print(str(e))
print_error()
sys.exit(1)
except FileNotFoundError as e:
file_exists(e.filename, log_level)
phono3py.phonon_dataset = dataset
phono3py.produce_fc2(symmetrize_fc2=symmetrize_fc2,
is_compact_fc=is_compact_fc,
fc_calculator=fc_calculator,
fc_calculator_options=fc_calculator_options)
def get_cell_info(settings, cell_filename, symprec, log_level):
"""calculator interface and crystal structure information"""
cell_info = collect_cell_info(supercell_matrix=settings.supercell_matrix,
primitive_matrix=settings.primitive_matrix,
interface_mode=settings.calculator,
cell_filename=cell_filename,
chemical_symbols=settings.chemical_symbols,
phonopy_yaml_cls=Phono3pyYaml,
symprec=symprec,
return_dict=True)
if type(cell_info) is str:
print_error_message(cell_info)
if log_level > 0:
print_error()
sys.exit(1)
# cell_info keys
# ('unitcell', 'supercell_matrix', 'primitive_matrix',
# 'optional_structure_info', 'interface_mode', 'phonopy_yaml')
cell_info['phonon_supercell_matrix'] = settings.phonon_supercell_matrix
ph3py_yaml = cell_info['phonopy_yaml']
if cell_info['phonon_supercell_matrix'] is None and ph3py_yaml:
ph_smat = ph3py_yaml.phonon_supercell_matrix
cell_info['phonon_supercell_matrix'] = ph_smat
return cell_info
def _create_phono3py_fc3(
phono3py,
ph3py_yaml,
symmetrize_fc3r,
input_filename,
is_compact_fc,
cutoff_pair_distance,
fc_calculator,
fc_calculator_options,
log_level,
):
"""Read or calculate fc3.
Note
----
cutoff_pair_distance is the parameter to determine each displaced
supercell is included to the computation of fc3. It is assumed that
cutoff_pair_distance is stored in the step to create sets of
displacements and the value is stored n the displacement dataset and
also as the parameter 'included': True or False for each displacement.
The parameter cutoff_pair_distance here can be used in the step to
create fc3 by overwriting original cutoff_pair_distance value only
when the former value is smaller than the later.
"""
if input_filename is None:
disp_filename = "disp_fc3.yaml"
else:
disp_filename = "disp_fc3." + input_filename + ".yaml"
_ph3py_yaml = _get_ph3py_yaml(disp_filename, ph3py_yaml)
try:
dataset = parse_forces(
phono3py,
ph3py_yaml=_ph3py_yaml,
cutoff_pair_distance=cutoff_pair_distance,
force_filename="FORCES_FC3",
disp_filename=disp_filename,
fc_type="fc3",
log_level=log_level,
)
except RuntimeError as e:
# from _parse_forces_type1
if log_level:
print(str(e))
print_error()
sys.exit(1)
except FileNotFoundError as e:
# from _get_type2_dataset
file_exists(e.filename, log_level)
phono3py.dataset = dataset
phono3py.produce_fc3(
symmetrize_fc3r=symmetrize_fc3r,
is_compact_fc=is_compact_fc,
fc_calculator=fc_calculator,
fc_calculator_options=fc_calculator_options,
)
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 init_phono3py(settings, cell_info, interface_mode, output_filename,
symprec, log_level):
physical_units = get_default_physical_units(interface_mode)
distance_to_A = physical_units['distance_to_A']
# Change unit of lattice parameters to angstrom
unitcell = cell_info['unitcell'].copy()
if distance_to_A is not None:
lattice = unitcell.cell
lattice *= distance_to_A
unitcell.cell = lattice
# updated_settings keys
# ('grid_points', 'sigmas', 'temperature_points', 'temperatures',
# 'frequency_factor_to_THz', 'num_frequency_points',
# 'frequency_step', 'frequency_scale_factor',
# 'cutoff_frequency')
updated_settings = get_default_values(settings)
phono3py = Phono3py(
unitcell,
cell_info['supercell_matrix'],
primitive_matrix=cell_info['primitive_matrix'],
phonon_supercell_matrix=cell_info['phonon_supercell_matrix'],
masses=settings.masses,
mesh=settings.mesh_numbers,
band_indices=settings.band_indices,
sigmas=updated_settings['sigmas'],
sigma_cutoff=settings.sigma_cutoff_width,
cutoff_frequency=updated_settings['cutoff_frequency'],
frequency_factor_to_THz=updated_settings['frequency_factor_to_THz'],
is_symmetry=settings.is_symmetry,
is_mesh_symmetry=settings.is_mesh_symmetry,
symmetrize_fc3q=settings.is_symmetrize_fc3_q,
symprec=symprec,
calculator=interface_mode,
log_level=log_level,
lapack_zheev_uplo=settings.lapack_zheev_uplo)
check_supercell_in_yaml(cell_info, phono3py, log_level)
if cell_info['phonopy_yaml'] is not None:
if (cell_info['phonopy_yaml'].phonon_supercell is not None
and phono3py.phonon_supercell is not None):
if not cells_isclose(cell_info['phonopy_yaml'].phonon_supercell,
phono3py.phonon_supercell):
if log_level:
print("Generated phonon supercell is inconsistent with "
"that in \"%s\"." %
cell_info['optional_structure_info'][0])
print_error()
sys.exit(1)
return phono3py, updated_settings
def store_force_constants(phono3py, settings, ph3py_yaml, physical_units,
input_filename, output_filename, load_phono3py_yaml,
log_level):
if load_phono3py_yaml:
if log_level:
print("-" * 29 + " Force constants " + "-" * 30)
(fc_calculator,
fc_calculator_options) = get_fc_calculator_params(settings)
read_fc = set_dataset_and_force_constants(
phono3py,
ph3py_yaml=ph3py_yaml,
fc_calculator=fc_calculator,
fc_calculator_options=fc_calculator_options,
symmetrize_fc=settings.fc_symmetry,
is_compact_fc=settings.is_compact_fc,
log_level=log_level)
if log_level:
if phono3py.fc3 is None:
print("fc3 could not be obtained.")
if phono3py.fc2 is None:
print("fc2 could not be obtained.")
if phono3py.fc3 is None or phono3py.fc2 is None:
print_error()
sys.exit(1)
if not read_fc['fc3']:
write_fc3_to_hdf5(phono3py.fc3,
p2s_map=phono3py.primitive.p2s_map,
compression=settings.hdf5_compression)
if log_level:
print("fc3 was written into \"fc3.hdf5\".")
if not read_fc['fc2']:
write_fc2_to_hdf5(phono3py.fc2,
p2s_map=phono3py.primitive.p2s_map,
physical_unit='eV/angstrom^2',
compression=settings.hdf5_compression)
if log_level:
print("fc2 was written into \"fc2.hdf5\".")
else:
create_phono3py_force_constants(phono3py,
settings,
ph3py_yaml=ph3py_yaml,
input_filename=input_filename,
output_filename=output_filename,
log_level=log_level)
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 init_phph_interaction(phono3py, settings, updated_settings, input_filename,
output_filename, log_level):
ave_pp = settings.constant_averaged_pp_interaction
phono3py.init_phph_interaction(
nac_q_direction=settings.nac_q_direction,
constant_averaged_interaction=ave_pp,
frequency_scale_factor=updated_settings['frequency_scale_factor'],
solve_dynamical_matrices=(not settings.read_phonon))
if log_level > 0:
dm = phono3py.dynamical_matrix
if (dm.is_nac() and dm.nac_method == 'gonze'):
dm.show_Gonze_nac_message()
if settings.write_phonon:
freqs, eigvecs, grid_address = phono3py.get_phonon_data()
filename = write_phonon_to_hdf5(freqs,
eigvecs,
grid_address,
phono3py.mesh_numbers,
compression=settings.hdf5_compression,
filename=output_filename)
if filename:
if log_level:
print("Phonons are written into \"%s\"." % filename)
else:
print("Writing phonons failed.")
if log_level:
print_error()
sys.exit(1)
if settings.read_phonon:
phonons = read_phonon_from_hdf5(phono3py.mesh_numbers,
filename=input_filename,
verbose=(log_level > 0))
if phonons is None:
print("Reading phonons failed.")
if log_level:
print_error()
sys.exit(1)
try:
phono3py.set_phonon_data(*phonons)
except RuntimeError:
if log_level:
print_error()
sys.exit(1)
def store_force_constants(
phono3py,
settings,
ph3py_yaml,
input_filename,
output_filename,
load_phono3py_yaml,
log_level,
):
"""Calculate, read, and write force constants."""
if load_phono3py_yaml:
if log_level:
print("-" * 29 + " Force constants " + "-" * 30)
(fc_calculator,
fc_calculator_options) = get_fc_calculator_params(settings)
read_fc = set_dataset_and_force_constants(
phono3py,
ph3py_yaml=ph3py_yaml,
fc_calculator=fc_calculator,
fc_calculator_options=fc_calculator_options,
symmetrize_fc=settings.fc_symmetry,
is_compact_fc=settings.is_compact_fc,
cutoff_pair_distance=settings.cutoff_pair_distance,
log_level=log_level,
)
if log_level:
if phono3py.fc3 is None:
print("fc3 could not be obtained.")
if phono3py.fc2 is None:
print("fc2 could not be obtained.")
if phono3py.fc3 is None or phono3py.fc2 is None:
print_error()
sys.exit(1)
if not read_fc["fc3"]:
write_fc3_to_hdf5(
phono3py.fc3,
p2s_map=phono3py.primitive.p2s_map,
compression=settings.hdf5_compression,
)
if log_level:
print('fc3 was written into "fc3.hdf5".')
if not read_fc["fc2"]:
write_fc2_to_hdf5(
phono3py.fc2,
p2s_map=phono3py.primitive.p2s_map,
physical_unit="eV/angstrom^2",
compression=settings.hdf5_compression,
)
if log_level:
print('fc2 was written into "fc2.hdf5".')
else:
create_phono3py_force_constants(
phono3py,
settings,
ph3py_yaml=ph3py_yaml,
input_filename=input_filename,
output_filename=output_filename,
log_level=log_level,
)
def init_phph_interaction(
phono3py: Phono3py,
settings,
updated_settings,
input_filename,
output_filename,
log_level,
):
"""Initialize ph-ph interaction and phonons on grid."""
if log_level:
print("Generating grid system ... ", end="", flush=True)
phono3py.mesh_numbers = settings.mesh_numbers
bz_grid = phono3py.grid
if log_level:
if bz_grid.grid_matrix is None:
print("[ %d %d %d ]" % tuple(phono3py.mesh_numbers))
else:
print("")
print("Generalized regular grid: [ %d %d %d ]" %
tuple(bz_grid.D_diag))
print("Grid generation matrix:")
print(" [ %d %d %d ]" % tuple(bz_grid.grid_matrix[0]))
print(" [ %d %d %d ]" % tuple(bz_grid.grid_matrix[1]))
print(" [ %d %d %d ]" % tuple(bz_grid.grid_matrix[2]))
if settings.is_symmetrize_fc3_q:
print("Permutation symmetry of ph-ph interaction strengths: True")
ave_pp = settings.constant_averaged_pp_interaction
phono3py.init_phph_interaction(
nac_q_direction=settings.nac_q_direction,
constant_averaged_interaction=ave_pp,
frequency_scale_factor=updated_settings["frequency_scale_factor"],
symmetrize_fc3q=settings.is_symmetrize_fc3_q,
lapack_zheev_uplo=settings.lapack_zheev_uplo,
)
if not settings.read_phonon:
if log_level:
print("-" * 27 + " Phonon calculations " + "-" * 28)
dm = phono3py.dynamical_matrix
if dm.is_nac() and dm.nac_method == "gonze":
dm.show_nac_message()
print("Running harmonic phonon calculations...")
sys.stdout.flush()
phono3py.run_phonon_solver()
if settings.write_phonon:
freqs, eigvecs, grid_address = phono3py.get_phonon_data()
ir_grid_points, ir_grid_weights, _ = get_ir_grid_points(bz_grid)
ir_grid_points = np.array(bz_grid.grg2bzg[ir_grid_points],
dtype="int_")
filename = write_phonon_to_hdf5(
freqs,
eigvecs,
grid_address,
phono3py.mesh_numbers,
bz_grid=bz_grid,
ir_grid_points=ir_grid_points,
ir_grid_weights=ir_grid_weights,
compression=settings.hdf5_compression,
filename=output_filename,
)
if filename:
if log_level:
print('Phonons are written into "%s".' % filename)
else:
print("Writing phonons failed.")
if log_level:
print_error()
sys.exit(1)
if settings.read_phonon:
phonons = read_phonon_from_hdf5(phono3py.mesh_numbers,
filename=input_filename,
verbose=(log_level > 0))
if phonons is None:
print("Reading phonons failed.")
if log_level:
print_error()
sys.exit(1)
try:
phono3py.set_phonon_data(*phonons)
except RuntimeError:
if log_level:
print_error()
sys.exit(1)
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,
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)
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)