def run_thermal_conductivity(phono3py):
# Create fc3 and fc2 from disp_fc3.yaml and FORCES_FC3
disp_dataset = parse_disp_fc3_yaml(filename="disp_fc3.yaml")
forces_fc3 = parse_FORCES_FC3(disp_dataset, filename="FORCES_FC3")
phono3py.produce_fc3(forces_fc3,
displacement_dataset=disp_dataset,
is_translational_symmetry=True,
is_permutation_symmetry=True,
is_permutation_symmetry_fc2=True)
fc3 = phono3py.get_fc3()
fc2 = phono3py.get_fc2()
# # Create fc2 from disp_fc2.yaml and FORCES_FC2
# disp_dataset2 = parse_disp_fc2_yaml(filename="disp_fc2.yaml")
# forces_fc2 = parse_FORCES_FC2(disp_dataset2, filename="FORCES_FC2")
# phono3py.produce_fc2(
# forces_fc2,
# displacement_dataset=disp_dataset2,
# is_translational_symmetry=True,
# is_permutation_symmetry=True)
# # Read fc3 and fc2 from c3.hdf5 and fc2.hdf5
# fc3 = read_fc3_from_hdf5(filename="fc3.hdf5")
# fc2 = read_fc2_from_hdf5(filename="fc2.hdf5")
# phono3py.set_fc3(fc3)
# phono3py.set_fc2(fc2)
show_drift_fc3(fc3)
show_drift_force_constants(fc2, name='fc2')
# # For special cases like NAC
# primitive = phono3py.get_phonon_primitive()
# nac_params = parse_BORN(primitive, filename="BORN")
# nac_params['factor'] = Hartree * Bohr
# phono3py.set_phph_interaction(nac_params=nac_params)
phono3py.run_thermal_conductivity(
temperatures=range(0, 1001, 10),
boundary_mfp=1e6, # This is to avoid divergence of phonon life time.
write_kappa=True)
# Conductivity_RTA object (https://git.io/vVRUW)
cond_rta = phono3py.get_thermal_conductivity()
def create_phono3py_force_constants(phono3py,
phonon_supercell_matrix,
settings,
force_to_eVperA=None,
distance_to_A=None,
compression=None,
input_filename=None,
output_filename=None,
log_level=1):
if settings.get_fc_calculator() is None:
symmetrize_fc3r = (settings.get_is_symmetrize_fc3_r()
or settings.get_fc_symmetry())
symmetrize_fc2 = (settings.get_is_symmetrize_fc2()
or settings.get_fc_symmetry())
else: # Rely on fc calculator the symmetrization of fc.
symmetrize_fc2 = False
symmetrize_fc3r = False
if log_level:
show_phono3py_force_constants_settings(settings)
#######
# fc3 #
#######
if (settings.get_is_joint_dos()
or (settings.get_is_isotope()
and not (settings.get_is_bterta() or settings.get_is_lbte()))
or settings.get_read_gamma() or settings.get_read_pp()
or settings.get_write_phonon()
or settings.get_constant_averaged_pp_interaction() is not None):
pass
else:
if settings.get_read_fc3(): # Read fc3.hdf5
_read_phono3py_fc3(phono3py, symmetrize_fc3r, input_filename,
log_level)
else: # fc3 from FORCES_FC3
if not _create_phono3py_fc3(
phono3py, force_to_eVperA, distance_to_A, symmetrize_fc3r,
symmetrize_fc2, input_filename, output_filename,
settings.get_is_compact_fc(),
settings.get_cutoff_pair_distance(),
settings.get_fc_calculator(),
settings.get_fc_calculator_options(), compression,
log_level):
print("fc3 was not created properly.")
if log_level:
print_error()
sys.exit(1)
cutoff_distance = settings.get_cutoff_fc3_distance()
if cutoff_distance is not None and cutoff_distance > 0:
if log_level:
print("Cutting-off fc3 by zero (cut-off distance: %f)" %
cutoff_distance)
phono3py.cutoff_fc3_by_zero(cutoff_distance)
if log_level:
show_drift_fc3(phono3py.get_fc3(),
primitive=phono3py.get_primitive())
#######
# fc2 #
#######
phonon_primitive = phono3py.get_phonon_primitive()
p2s_map = phonon_primitive.p2s_map
if settings.get_read_fc2():
_read_phono3py_fc2(phono3py, symmetrize_fc2, input_filename, log_level)
else:
if phonon_supercell_matrix is None:
if settings.get_fc_calculator() is not None:
pass
elif not _create_phono3py_fc2(
phono3py, force_to_eVperA, distance_to_A, symmetrize_fc2,
input_filename, settings.get_is_compact_fc(),
settings.get_fc_calculator(),
settings.get_fc_calculator_options(), log_level):
print("fc2 was not created properly.")
if log_level:
print_error()
sys.exit(1)
else:
if not _create_phono3py_phonon_fc2(
phono3py, force_to_eVperA, distance_to_A, symmetrize_fc2,
input_filename, settings.get_is_compact_fc(),
settings.get_fc_calculator(),
settings.get_fc_calculator_options(), log_level):
print("fc2 was not created properly.")
if log_level:
print_error()
sys.exit(1)
if output_filename is None:
filename = 'fc2.hdf5'
else:
filename = 'fc2.' + output_filename + '.hdf5'
if log_level:
print("Writing fc2 to %s" % filename)
write_fc2_to_hdf5(phono3py.get_fc2(),
filename=filename,
p2s_map=p2s_map,
physical_unit='eV/Angstrom^2',
compression=compression)
if log_level:
show_drift_force_constants(phono3py.get_fc2(),
primitive=phonon_primitive,
name='fc2')
def create_phono3py_force_constants(
phono3py,
settings,
ph3py_yaml=None,
input_filename=None,
output_filename=None,
log_level=1,
):
"""Read or calculate force constants."""
if settings.fc_calculator is None:
symmetrize_fc3r = settings.is_symmetrize_fc3_r or settings.fc_symmetry
symmetrize_fc2 = settings.is_symmetrize_fc2 or settings.fc_symmetry
else: # Rely on fc calculator the symmetrization of fc.
symmetrize_fc2 = False
symmetrize_fc3r = False
if log_level:
show_phono3py_force_constants_settings(settings)
#######
# fc3 #
#######
if (settings.is_joint_dos or
(settings.is_isotope and not (settings.is_bterta or settings.is_lbte))
or settings.read_gamma or settings.read_pp
or (not settings.is_bterta and settings.write_phonon)
or settings.constant_averaged_pp_interaction is not None):
pass
else:
if settings.read_fc3:
_read_phono3py_fc3(phono3py, symmetrize_fc3r, input_filename,
log_level)
else: # fc3 from FORCES_FC3 or ph3py_yaml
_create_phono3py_fc3(
phono3py,
ph3py_yaml,
symmetrize_fc3r,
input_filename,
settings.is_compact_fc,
settings.cutoff_pair_distance,
settings.fc_calculator,
settings.fc_calculator_options,
log_level,
)
if output_filename is None:
filename = "fc3.hdf5"
else:
filename = "fc3." + output_filename + ".hdf5"
if log_level:
print('Writing fc3 to "%s".' % filename)
write_fc3_to_hdf5(
phono3py.fc3,
filename=filename,
p2s_map=phono3py.primitive.p2s_map,
compression=settings.hdf5_compression,
)
cutoff_distance = settings.cutoff_fc3_distance
if cutoff_distance is not None and cutoff_distance > 0:
if log_level:
print("Cutting-off fc3 by zero (cut-off distance: %f)" %
cutoff_distance)
phono3py.cutoff_fc3_by_zero(cutoff_distance)
if log_level:
show_drift_fc3(phono3py.fc3, primitive=phono3py.primitive)
#######
# fc2 #
#######
phonon_primitive = phono3py.phonon_primitive
p2s_map = phonon_primitive.p2s_map
if settings.read_fc2:
_read_phono3py_fc2(phono3py, symmetrize_fc2, input_filename, log_level)
else:
if phono3py.phonon_supercell_matrix is None:
if settings.fc_calculator == "alm" and phono3py.fc2 is not None:
if log_level:
print("fc2 that was fit simultaneously with fc3 "
"by ALM is used.")
else:
_create_phono3py_fc2(
phono3py,
ph3py_yaml,
symmetrize_fc2,
input_filename,
settings.is_compact_fc,
settings.fc_calculator,
settings.fc_calculator_options,
log_level,
)
else:
_create_phono3py_phonon_fc2(
phono3py,
ph3py_yaml,
symmetrize_fc2,
input_filename,
settings.is_compact_fc,
settings.fc_calculator,
settings.fc_calculator_options,
log_level,
)
if output_filename is None:
filename = "fc2.hdf5"
else:
filename = "fc2." + output_filename + ".hdf5"
if log_level:
print('Writing fc2 to "%s".' % filename)
write_fc2_to_hdf5(
phono3py.fc2,
filename=filename,
p2s_map=p2s_map,
physical_unit="eV/angstrom^2",
compression=settings.hdf5_compression,
)
if log_level:
show_drift_force_constants(phono3py.fc2,
primitive=phonon_primitive,
name="fc2")
def create_phono3py_force_constants(phono3py, phonon_supercell_matrix,
settings, read_fc3, read_fc2, tsym_type,
symmetrize_fc3_r, symmetrize_fc3_q,
symmetrize_fc2, input_filename,
output_filename, log_level):
if log_level:
show_phono3py_force_constants_settings(read_fc3, read_fc2, tsym_type,
symmetrize_fc3_r,
symmetrize_fc3_q,
symmetrize_fc2, settings)
# fc3
if (settings.get_is_joint_dos()
or (settings.get_is_isotope()
and not (settings.get_is_bterta() or settings.get_is_lbte()))
or settings.get_read_gamma() or settings.get_read_amplitude()
or settings.get_constant_averaged_pp_interaction() is not None):
pass
else:
if read_fc3: # Read fc3.hdf5
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)
fc3 = read_fc3_from_hdf5(filename=filename)
phono3py.set_fc3(fc3)
else: # fc3 from FORCES_THIRD and FORCES_SECOND
_create_phono3py_fc3(phono3py, tsym_type, symmetrize_fc3_r,
symmetrize_fc2,
settings.get_cutoff_fc3_distance(),
input_filename, output_filename, log_level)
if log_level:
show_drift_fc3(phono3py.get_fc3())
# fc2
if read_fc2:
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)
phonon_supercell = phono3py.get_phonon_supercell()
phonon_fc2 = read_fc2_from_hdf5(filename=filename)
if phonon_fc2.shape[0] != phonon_supercell.get_number_of_atoms():
print("Matrix shape of fc2 doesn't agree with supercell.")
if log_level:
print_error()
sys.exit(1)
phono3py.set_fc2(phonon_fc2)
else:
if log_level:
print("Solving fc2")
if phonon_supercell_matrix is None:
if phono3py.get_fc2() is None:
_create_phono3py_fc2(phono3py, tsym_type, symmetrize_fc2,
input_filename, log_level)
else:
_create_phono3py_phonon_fc2(phono3py, tsym_type, symmetrize_fc2,
input_filename, log_level)
if output_filename is None:
filename = 'fc2.hdf5'
else:
filename = 'fc2.' + output_filename + '.hdf5'
if log_level:
print("Writing fc2 to %s" % filename)
write_fc2_to_hdf5(phono3py.get_fc2(), filename=filename)
if log_level:
show_drift_force_constants(phono3py.get_fc2(), name='fc2')
def create_phono3py_force_constants(phono3py,
phonon_supercell_matrix,
settings,
energy_to_eV=None,
distance_to_A=None,
input_filename=None,
output_filename=None,
log_level=1):
read_fc3 = settings.get_read_fc3()
read_fc2 = settings.get_read_fc2()
symmetrize_fc3_r = settings.get_is_symmetrize_fc3_r()
symmetrize_fc3_q = settings.get_is_symmetrize_fc3_q()
symmetrize_fc2 = settings.get_is_symmetrize_fc2()
if settings.get_is_translational_symmetry():
tsym_type = 1
elif settings.get_tsym_type() > 0:
tsym_type = settings.get_tsym_type()
else:
tsym_type = 0
if log_level:
show_phono3py_force_constants_settings(read_fc3, read_fc2, tsym_type,
symmetrize_fc3_r,
symmetrize_fc3_q,
symmetrize_fc2, settings)
# fc3
if (settings.get_is_joint_dos()
or (settings.get_is_isotope()
and not (settings.get_is_bterta() or settings.get_is_lbte()))
or settings.get_read_gamma() or settings.get_read_amplitude()
or settings.get_constant_averaged_pp_interaction() is not None):
pass
else:
if read_fc3: # Read fc3.hdf5
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)
fc3 = read_fc3_from_hdf5(filename=filename)
num_atom = phono3py.get_supercell().get_number_of_atoms()
if fc3.shape[0] != num_atom:
print("Matrix shape of fc3 doesn't agree with supercell size.")
if log_level:
print_error()
sys.exit(1)
phono3py.set_fc3(fc3)
else: # fc3 from FORCES_FC3
if not _create_phono3py_fc3(
phono3py, energy_to_eV, distance_to_A, tsym_type,
symmetrize_fc3_r, symmetrize_fc2,
settings.get_cutoff_fc3_distance(), input_filename,
output_filename, log_level):
print("fc3 was not created properly.")
if log_level:
print_error()
sys.exit(1)
if log_level:
show_drift_fc3(phono3py.get_fc3())
# fc2
if read_fc2:
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.get_phonon_supercell().get_number_of_atoms()
phonon_fc2 = read_fc2_from_hdf5(filename=filename)
if phonon_fc2.shape[0] != num_atom:
print("Matrix shape of fc2 doesn't agree with supercell size.")
if log_level:
print_error()
sys.exit(1)
phono3py.set_fc2(phonon_fc2)
else:
if log_level:
print("Solving fc2")
if phonon_supercell_matrix is None:
if phono3py.get_fc2() is None:
if not _create_phono3py_fc2(
phono3py, energy_to_eV, distance_to_A, tsym_type,
symmetrize_fc2, input_filename, log_level):
print("fc2 was not created properly.")
if log_level:
print_error()
sys.exit(1)
else:
if not _create_phono3py_phonon_fc2(
phono3py, energy_to_eV, distance_to_A, tsym_type,
symmetrize_fc2, input_filename, log_level):
print("fc2 was not created properly.")
if log_level:
print_error()
sys.exit(1)
if output_filename is None:
filename = 'fc2.hdf5'
else:
filename = 'fc2.' + output_filename + '.hdf5'
if log_level:
print("Writing fc2 to %s" % filename)
write_fc2_to_hdf5(phono3py.get_fc2(), filename=filename)
if log_level:
show_drift_force_constants(phono3py.get_fc2(), name='fc2')
# # Create fc2 from disp_fc2.yaml and FORCES_FC2
# disp_dataset2 = parse_disp_fc2_yaml(filename="disp_fc2.yaml")
# forces_fc2 = parse_FORCES_FC2(disp_dataset2, filename="FORCES_FC2")
# phono3py.produce_fc2(
# forces_fc2,
# displacement_dataset=disp_dataset2,
# is_translational_symmetry=True,
# is_permutation_symmetry=True)
# # Read fc3 and fc2 from c3.hdf5 and fc2.hdf5
# fc3 = read_fc3_from_hdf5(filename="fc3.hdf5")
# fc2 = read_fc2_from_hdf5(filename="fc2.hdf5")
# phono3py.set_fc3(fc3)
# phono3py.set_fc2(fc2)
show_drift_fc3(fc3)
show_drift_force_constants(fc2, name='fc2')
# # For special cases like NAC
# primitive = phono3py.get_phonon_primitive()
# nac_params = parse_BORN(primitive, filename="BORN")
# nac_params['factor'] = Hartree * Bohr
# phono3py.set_phph_interaction(nac_params=nac_params)
phono3py.run_thermal_conductivity(temperatures=range(0, 1001, 10),
write_kappa=True)
# Conductivity_RTA object (https://git.io/vVRUW)
cond_rta = phono3py.get_thermal_conductivity()
# # Create fc2 from disp_fc2.yaml and FORCES_FC2
# disp_dataset2 = parse_disp_fc2_yaml(filename="disp_fc2.yaml")
# forces_fc2 = parse_FORCES_FC2(disp_dataset2, filename="FORCES_FC2")
# phono3py.produce_fc2(
# forces_fc2,
# displacement_dataset=disp_dataset2,
# is_translational_symmetry=True,
# is_permutation_symmetry=True)
# # Read fc3 and fc2 from c3.hdf5 and fc2.hdf5
# fc3 = read_fc3_from_hdf5(filename="fc3.hdf5")
# fc2 = read_fc2_from_hdf5(filename="fc2.hdf5")
# phono3py.set_fc3(fc3)
# phono3py.set_fc2(fc2)
show_drift_fc3(fc3)
show_drift_force_constants(fc2, name='fc2')
# # For special cases like NAC
# primitive = phono3py.get_phonon_primitive()
# nac_params = parse_BORN(primitive, filename="BORN")
# nac_params['factor'] = Hartree * Bohr
# phono3py.set_phph_interaction(nac_params=nac_params)
phono3py.run_thermal_conductivity(temperatures=range(0, 1001, 10),
write_kappa=True)
# Conductivity_RTA object (https://git.io/vVRUW)
cond_rta = phono3py.get_thermal_conductivity()
def _set_force_constants(
ph3py,
units,
dataset=None,
fc3_filename=None,
fc2_filename=None,
forces_fc3_filename=None,
forces_fc2_filename=None,
fc_calculator=None,
fc_calculator_options=None,
symmetrize_fc=True,
is_compact_fc=False,
log_level=0):
p2s_map = ph3py.primitive.p2s_map
if fc3_filename is not None:
fc3 = read_fc3_from_hdf5(filename=fc3_filename, p2s_map=p2s_map)
ph3py.fc3 = fc3
elif forces_fc3_filename is not None:
if type(forces_fc3_filename) is str:
force_filename = forces_fc3_filename
disp_filename = None
else:
force_filename, disp_filename = forces_fc3_filename
_set_fc3(ph3py,
units,
force_filename,
disp_filename,
symmetrize_fc,
is_compact_fc,
fc_calculator,
fc_calculator_options,
log_level)
elif os.path.isfile("fc3.hdf5"):
ph3py.fc3 = read_fc3_from_hdf5(filename="fc3.hdf5", p2s_map=p2s_map)
if log_level:
print("fc3 was loaded from \"fc3.hdf5\".")
elif os.path.isfile("FORCES_FC3") and os.path.isfile("disp_fc3.yaml"):
_set_fc3(ph3py,
units,
"FORCES_FC3",
"disp_fc3.yaml",
symmetrize_fc,
is_compact_fc,
fc_calculator,
fc_calculator_options,
log_level)
if log_level and ph3py.fc3 is not None:
show_drift_fc3(ph3py.fc3, primitive=ph3py.primitive)
if fc2_filename is not None:
fc2 = read_fc2_from_hdf5(filename=fc2_filename, p2s_map=p2s_map)
ph3py.fc2 = fc2
elif forces_fc2_filename is not None:
if type(forces_fc2_filename) == str:
force_filename = forces_fc2_filename
disp_filename = None
else:
force_filename, disp_filename = forces_fc2_filename
_set_fc2(ph3py,
units,
force_filename,
disp_filename,
symmetrize_fc,
is_compact_fc,
fc_calculator,
fc_calculator_options,
log_level)
elif os.path.isfile("fc2.hdf5"):
ph3py.fc2 = read_fc2_from_hdf5(filename="fc2.hdf5", p2s_map=p2s_map)
if log_level:
print("fc2 was loaded from \"fc2.hdf5\".")
elif os.path.isfile("FORCES_FC2") and os.path.isfile("disp_fc2.yaml"):
_set_fc2(ph3py,
units,
"FORCES_FC2",
"disp_fc2.yaml",
symmetrize_fc,
is_compact_fc,
fc_calculator,
fc_calculator_options,
log_level)
if log_level and ph3py.fc2 is not None:
show_drift_force_constants(ph3py.fc2,
primitive=ph3py.phonon_primitive,
name='fc2')
def create_phono3py_force_constants(phono3py,
phonon_supercell_matrix,
settings,
force_to_eVperA=None,
distance_to_A=None,
compression=None,
input_filename=None,
output_filename=None,
log_level=1):
read_fc3 = settings.get_read_fc3()
read_fc2 = settings.get_read_fc2()
symmetrize_fc3r = (settings.get_is_symmetrize_fc3_r() or
settings.get_fc_symmetry())
symmetrize_fc3q = settings.get_is_symmetrize_fc3_q()
symmetrize_fc2 = (settings.get_is_symmetrize_fc2() or
settings.get_fc_symmetry())
if settings.get_use_alm_fc2():
symmetrize_fc2 = False
if settings.get_use_alm_fc3():
symmetrize_fc3r = False
alm_options = None
if settings.get_use_alm_fc3() or settings.get_use_alm_fc2():
if settings.get_alm_options() is not None:
alm_option_types = {'solver': str,
'cutoff_distance': float}
alm_options = {}
for option_str in settings.get_alm_options().split(","):
key, val = [x.strip() for x in option_str.split('=')[:2]]
if key.lower() in alm_option_types:
option_value = alm_option_types[key.lower()](val)
alm_options[key.lower()] = option_value
if log_level:
show_phono3py_force_constants_settings(read_fc3,
read_fc2,
symmetrize_fc3r,
symmetrize_fc3q,
symmetrize_fc2,
settings)
# fc3
if (settings.get_is_joint_dos() or
(settings.get_is_isotope() and
not (settings.get_is_bterta() or settings.get_is_lbte())) or
settings.get_read_gamma() or
settings.get_read_pp() or
settings.get_write_phonon() or
settings.get_constant_averaged_pp_interaction() is not None):
pass
else:
if read_fc3: # Read fc3.hdf5
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.get_primitive().get_primitive_to_supercell_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.get_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.set_fc3(fc3)
else: # fc3 from FORCES_FC3
if not _create_phono3py_fc3(phono3py,
force_to_eVperA,
distance_to_A,
symmetrize_fc3r,
symmetrize_fc2,
input_filename,
output_filename,
settings.get_is_compact_fc(),
settings.get_use_alm_fc3(),
alm_options,
compression,
log_level):
print("fc3 was not created properly.")
if log_level:
print_error()
sys.exit(1)
cutoff_distance = settings.get_cutoff_fc3_distance()
if cutoff_distance is not None and cutoff_distance > 0:
if log_level:
print("Cutting-off fc3 by zero (cut-off distance: %f)" %
cutoff_distance)
phono3py.cutoff_fc3_by_zero(cutoff_distance)
if log_level:
show_drift_fc3(phono3py.get_fc3(),
primitive=phono3py.get_primitive())
# fc2
phonon_primitive = phono3py.get_phonon_primitive()
phonon_supercell = phono3py.get_phonon_supercell()
p2s_map = phonon_primitive.get_primitive_to_supercell_map()
if read_fc2:
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 = phonon_supercell.get_number_of_atoms()
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,
phonon_primitive)
phono3py.set_fc2(phonon_fc2)
else:
if phonon_supercell_matrix is None:
if not _create_phono3py_fc2(phono3py,
force_to_eVperA,
distance_to_A,
symmetrize_fc2,
input_filename,
settings.get_is_compact_fc(),
settings.get_use_alm_fc2(),
alm_options,
log_level):
print("fc2 was not created properly.")
if log_level:
print_error()
sys.exit(1)
else:
if not _create_phono3py_phonon_fc2(phono3py,
force_to_eVperA,
distance_to_A,
symmetrize_fc2,
input_filename,
settings.get_is_compact_fc(),
settings.get_use_alm_fc2(),
alm_options,
log_level):
print("fc2 was not created properly.")
if log_level:
print_error()
sys.exit(1)
if output_filename is None:
filename = 'fc2.hdf5'
else:
filename = 'fc2.' + output_filename + '.hdf5'
if log_level:
print("Writing fc2 to %s" % filename)
write_fc2_to_hdf5(phono3py.get_fc2(),
filename=filename,
p2s_map=p2s_map,
compression=compression)
if log_level:
show_drift_force_constants(phono3py.get_fc2(),
primitive=phonon_primitive,
name='fc2')
def set_dataset_and_force_constants(ph3py,
ph3py_yaml=None,
fc3_filename=None,
fc2_filename=None,
forces_fc3_filename=None,
forces_fc2_filename=None,
fc_calculator=None,
fc_calculator_options=None,
produce_fc=True,
symmetrize_fc=True,
is_compact_fc=False,
cutoff_pair_distance=None,
log_level=0):
read_fc = {'fc2': False, 'fc3': False}
p2s_map = ph3py.primitive.p2s_map
if fc3_filename is not None:
fc3 = read_fc3_from_hdf5(filename=fc3_filename, p2s_map=p2s_map)
ph3py.fc3 = fc3
read_fc['fc3'] = True
if log_level:
print("fc3 was read from \"%s\"." % fc3_filename)
elif forces_fc3_filename is not None:
if type(forces_fc3_filename) is str:
force_filename = forces_fc3_filename
disp_filename = None
else:
force_filename, disp_filename = forces_fc3_filename
_set_forces_fc3(ph3py, ph3py_yaml, force_filename, disp_filename,
produce_fc, symmetrize_fc, is_compact_fc,
fc_calculator, fc_calculator_options,
cutoff_pair_distance, log_level)
elif os.path.isfile("fc3.hdf5"):
ph3py.fc3 = read_fc3_from_hdf5(filename="fc3.hdf5", p2s_map=p2s_map)
read_fc['fc3'] = True
if log_level:
print("fc3 was read from \"fc3.hdf5\".")
elif os.path.isfile("FORCES_FC3"):
disp_filename = None
if os.path.isfile("disp_fc3.yaml"):
if ph3py_yaml is None:
disp_filename = "disp_fc3.yaml"
elif ph3py_yaml.dataset is None:
disp_filename = "disp_fc3.yaml"
_set_forces_fc3(ph3py, ph3py_yaml, "FORCES_FC3", disp_filename,
produce_fc, symmetrize_fc, is_compact_fc,
fc_calculator, fc_calculator_options,
cutoff_pair_distance, log_level)
elif (ph3py_yaml is not None and ph3py_yaml.dataset is not None
and forces_in_dataset(ph3py_yaml.dataset)):
_set_forces_fc3(ph3py, ph3py_yaml, None, None, produce_fc,
symmetrize_fc, is_compact_fc, fc_calculator,
fc_calculator_options, cutoff_pair_distance, log_level)
if log_level and ph3py.fc3 is not None:
show_drift_fc3(ph3py.fc3, primitive=ph3py.primitive)
if fc2_filename is not None:
fc2 = read_fc2_from_hdf5(filename=fc2_filename, p2s_map=p2s_map)
ph3py.fc2 = fc2
read_fc['fc2'] = True
if log_level:
print("fc2 was read from \"%s\"." % fc2_filename)
elif forces_fc2_filename is not None:
if type(forces_fc2_filename) is str:
force_filename = forces_fc2_filename
disp_filename = None
else:
force_filename, disp_filename = forces_fc2_filename
_set_forces_fc2(ph3py, ph3py_yaml, force_filename, disp_filename,
produce_fc, symmetrize_fc, is_compact_fc,
fc_calculator, fc_calculator_options, "phonon_fc2",
log_level)
elif os.path.isfile("fc2.hdf5"):
ph3py.fc2 = read_fc2_from_hdf5(filename="fc2.hdf5", p2s_map=p2s_map)
read_fc['fc2'] = True
if log_level:
print("fc2 was read from \"fc2.hdf5\".")
elif os.path.isfile("FORCES_FC2"):
disp_filename = None
if os.path.isfile("disp_fc2.yaml"):
if ph3py_yaml is None:
disp_filename = "disp_fc2.yaml"
elif ph3py_yaml.dataset is None:
disp_filename = "disp_fc2.yaml"
_set_forces_fc2(ph3py, ph3py_yaml, "FORCES_FC2", disp_filename,
produce_fc, symmetrize_fc, is_compact_fc,
fc_calculator, fc_calculator_options, "phonon_fc2",
log_level)
elif (ph3py.phonon_supercell_matrix is None and fc_calculator == 'alm'
and ph3py.fc2 is not None):
if log_level:
print("fc2 that was fit simultaneously with fc3 by ALM is used.")
elif (ph3py_yaml is not None and ph3py_yaml.phonon_dataset is not None
and forces_in_dataset(ph3py_yaml.phonon_dataset)):
_set_forces_fc2(ph3py, ph3py_yaml, None, None, produce_fc,
symmetrize_fc, is_compact_fc, fc_calculator,
fc_calculator_options, "phonon_fc2", log_level)
elif (ph3py_yaml is not None and ph3py_yaml.dataset is not None
and forces_in_dataset(ph3py_yaml.dataset)):
_set_forces_fc2(ph3py, ph3py_yaml, None, None, produce_fc,
symmetrize_fc, is_compact_fc, fc_calculator,
fc_calculator_options, "fc2", log_level)
elif os.path.isfile("FORCES_FC3"):
# suppose fc3.hdf5 is read but fc2.hdf5 doesn't exist.
disp_filename = None
if os.path.isfile("disp_fc3.yaml"):
if ph3py_yaml is None:
disp_filename = "disp_fc3.yaml"
elif ph3py_yaml.dataset is None:
disp_filename = "disp_fc3.yaml"
_set_forces_fc2(ph3py, ph3py_yaml, "FORCES_FC3", disp_filename,
produce_fc, symmetrize_fc, is_compact_fc,
fc_calculator, fc_calculator_options, "fc2", log_level)
if log_level and ph3py.fc2 is not None:
show_drift_force_constants(ph3py.fc2,
primitive=ph3py.phonon_primitive,
name='fc2')
# Cases that dataset is in phono3py.yaml but not forces.
if (ph3py_yaml is not None and ph3py_yaml.dataset is not None):
ph3py.dataset = ph3py_yaml.dataset
if (ph3py_yaml is not None and ph3py_yaml.phonon_dataset is not None):
ph3py.phonon_dataset = ph3py_yaml.phonon_dataset
return read_fc
def set_dataset_and_force_constants(
ph3py: Phono3py,
ph3py_yaml: typing.Union[Phono3pyYaml, None] = None,
fc3_filename=None,
fc2_filename=None,
forces_fc3_filename=None,
forces_fc2_filename=None,
fc_calculator=None,
fc_calculator_options=None,
produce_fc=True,
symmetrize_fc=True,
is_compact_fc=False,
cutoff_pair_distance=None,
log_level=0,
):
"""Set displacements, forces, and create force constants."""
read_fc = {"fc2": False, "fc3": False}
p2s_map = ph3py.primitive.p2s_map
phonon_p2s_map = ph3py.phonon_primitive.p2s_map
if fc3_filename is not None:
fc3 = read_fc3_from_hdf5(filename=fc3_filename, p2s_map=p2s_map)
ph3py.fc3 = fc3
read_fc["fc3"] = True
if log_level:
print('fc3 was read from "%s".' % fc3_filename)
elif forces_fc3_filename is not None:
if type(forces_fc3_filename) is str:
force_filename = forces_fc3_filename
disp_filename = None
else:
force_filename, disp_filename = forces_fc3_filename
_set_forces_fc3(
ph3py,
ph3py_yaml,
force_filename,
disp_filename,
produce_fc,
symmetrize_fc,
is_compact_fc,
fc_calculator,
fc_calculator_options,
cutoff_pair_distance,
log_level,
)
elif os.path.isfile("fc3.hdf5"):
ph3py.fc3 = read_fc3_from_hdf5(filename="fc3.hdf5", p2s_map=p2s_map)
read_fc["fc3"] = True
if log_level:
print('fc3 was read from "fc3.hdf5".')
elif os.path.isfile("FORCES_FC3"):
disp_filename = None
if os.path.isfile("disp_fc3.yaml"):
if ph3py_yaml is None:
disp_filename = "disp_fc3.yaml"
elif ph3py_yaml.dataset is None:
disp_filename = "disp_fc3.yaml"
_set_forces_fc3(
ph3py,
ph3py_yaml,
"FORCES_FC3",
disp_filename,
produce_fc,
symmetrize_fc,
is_compact_fc,
fc_calculator,
fc_calculator_options,
cutoff_pair_distance,
log_level,
)
elif (
ph3py_yaml is not None
and ph3py_yaml.dataset is not None
and forces_in_dataset(ph3py_yaml.dataset)
):
_set_forces_fc3(
ph3py,
ph3py_yaml,
None,
None,
produce_fc,
symmetrize_fc,
is_compact_fc,
fc_calculator,
fc_calculator_options,
cutoff_pair_distance,
log_level,
)
if log_level and ph3py.fc3 is not None:
show_drift_fc3(ph3py.fc3, primitive=ph3py.primitive)
if fc2_filename is not None:
fc2 = read_fc2_from_hdf5(filename=fc2_filename, p2s_map=phonon_p2s_map)
ph3py.fc2 = fc2
read_fc["fc2"] = True
if log_level:
print('fc2 was read from "%s".' % fc2_filename)
elif forces_fc2_filename is not None:
if type(forces_fc2_filename) is str:
force_filename = forces_fc2_filename
disp_filename = None
else:
force_filename, disp_filename = forces_fc2_filename
_set_forces_fc2(
ph3py,
ph3py_yaml,
force_filename,
disp_filename,
produce_fc,
symmetrize_fc,
is_compact_fc,
fc_calculator,
fc_calculator_options,
"phonon_fc2",
log_level,
)
elif os.path.isfile("fc2.hdf5"):
ph3py.fc2 = read_fc2_from_hdf5(filename="fc2.hdf5", p2s_map=phonon_p2s_map)
read_fc["fc2"] = True
if log_level:
print('fc2 was read from "fc2.hdf5".')
elif os.path.isfile("FORCES_FC2"):
disp_filename = None
if os.path.isfile("disp_fc2.yaml"):
if ph3py_yaml is None:
disp_filename = "disp_fc2.yaml"
elif ph3py_yaml.phonon_dataset is None:
disp_filename = "disp_fc2.yaml"
if (
disp_filename is None
and ph3py_yaml is not None
and ph3py_yaml.phonon_dataset is None
):
msg = (
'"FORCES_FC2" was found. But phonon displacement dataset '
f'was not found in "{ph3py_yaml.yaml_filename}".'
)
raise RuntimeError(msg)
_set_forces_fc2(
ph3py,
ph3py_yaml,
"FORCES_FC2",
disp_filename,
produce_fc,
symmetrize_fc,
is_compact_fc,
fc_calculator,
fc_calculator_options,
"phonon_fc2",
log_level,
)
elif (
ph3py.phonon_supercell_matrix is None
and fc_calculator == "alm"
and ph3py.fc2 is not None
):
if log_level:
print("fc2 that was fit simultaneously with fc3 by ALM is used.")
elif (
ph3py_yaml is not None
and ph3py_yaml.phonon_dataset is not None
and forces_in_dataset(ph3py_yaml.phonon_dataset)
):
_set_forces_fc2(
ph3py,
ph3py_yaml,
None,
None,
produce_fc,
symmetrize_fc,
is_compact_fc,
fc_calculator,
fc_calculator_options,
"phonon_fc2",
log_level,
)
elif (
ph3py_yaml is not None
and ph3py_yaml.dataset is not None
and forces_in_dataset(ph3py_yaml.dataset)
):
_set_forces_fc2(
ph3py,
ph3py_yaml,
None,
None,
produce_fc,
symmetrize_fc,
is_compact_fc,
fc_calculator,
fc_calculator_options,
"fc2",
log_level,
)
elif os.path.isfile("FORCES_FC3"):
# suppose fc3.hdf5 is read but fc2.hdf5 doesn't exist.
disp_filename = None
if os.path.isfile("disp_fc3.yaml"):
if ph3py_yaml is None:
disp_filename = "disp_fc3.yaml"
elif ph3py_yaml.dataset is None:
disp_filename = "disp_fc3.yaml"
_set_forces_fc2(
ph3py,
ph3py_yaml,
"FORCES_FC3",
disp_filename,
produce_fc,
symmetrize_fc,
is_compact_fc,
fc_calculator,
fc_calculator_options,
"fc2",
log_level,
)
if log_level and ph3py.fc2 is not None:
show_drift_force_constants(
ph3py.fc2, primitive=ph3py.phonon_primitive, name="fc2"
)
# Cases that dataset is in phono3py.yaml but not forces.
if ph3py.dataset is None:
if ph3py_yaml is not None and ph3py_yaml.dataset is not None:
ph3py.dataset = ph3py_yaml.dataset
if ph3py_yaml is not None and ph3py_yaml.phonon_dataset is not None:
ph3py.phonon_dataset = ph3py_yaml.phonon_dataset
return read_fc
def create_phono3py_force_constants(phono3py,
phonon_supercell_matrix,
settings,
energy_to_eV=None,
distance_to_A=None,
input_filename=None,
output_filename=None,
log_level=1):
read_fc3 = settings.get_read_fc3()
read_fc2 = settings.get_read_fc2()
symmetrize_fc3_r = settings.get_is_symmetrize_fc3_r()
symmetrize_fc3_q = settings.get_is_symmetrize_fc3_q()
symmetrize_fc2 = settings.get_is_symmetrize_fc2()
if settings.get_is_translational_symmetry():
tsym_type = 1
elif settings.get_tsym_type() > 0:
tsym_type = settings.get_tsym_type()
else:
tsym_type = 0
if log_level:
show_phono3py_force_constants_settings(read_fc3,
read_fc2,
tsym_type,
symmetrize_fc3_r,
symmetrize_fc3_q,
symmetrize_fc2,
settings)
# fc3
if (settings.get_is_joint_dos() or
(settings.get_is_isotope() and
not (settings.get_is_bterta() or settings.get_is_lbte())) or
settings.get_read_gamma() or
settings.get_read_amplitude() or
settings.get_constant_averaged_pp_interaction() is not None):
pass
else:
if read_fc3: # Read fc3.hdf5
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)
fc3 = read_fc3_from_hdf5(filename=filename)
num_atom = phono3py.get_supercell().get_number_of_atoms()
if fc3.shape[0] != num_atom:
print("Matrix shape of fc3 doesn't agree with supercell size.")
if log_level:
print_error()
sys.exit(1)
phono3py.set_fc3(fc3)
else: # fc3 from FORCES_FC3
if not _create_phono3py_fc3(phono3py,
energy_to_eV,
distance_to_A,
tsym_type,
symmetrize_fc3_r,
symmetrize_fc2,
settings.get_cutoff_fc3_distance(),
input_filename,
output_filename,
log_level):
print("fc3 was not created properly.")
if log_level:
print_error()
sys.exit(1)
if log_level:
show_drift_fc3(phono3py.get_fc3())
# fc2
if read_fc2:
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.get_phonon_supercell().get_number_of_atoms()
phonon_fc2 = read_fc2_from_hdf5(filename=filename)
if phonon_fc2.shape[0] != num_atom:
print("Matrix shape of fc2 doesn't agree with supercell size.")
if log_level:
print_error()
sys.exit(1)
phono3py.set_fc2(phonon_fc2)
else:
if log_level:
print("Solving fc2")
if phonon_supercell_matrix is None:
if phono3py.get_fc2() is None:
if not _create_phono3py_fc2(phono3py,
energy_to_eV,
distance_to_A,
tsym_type,
symmetrize_fc2,
input_filename,
log_level):
print("fc2 was not created properly.")
if log_level:
print_error()
sys.exit(1)
else:
if not _create_phono3py_phonon_fc2(phono3py,
energy_to_eV,
distance_to_A,
tsym_type,
symmetrize_fc2,
input_filename,
log_level):
print("fc2 was not created properly.")
if log_level:
print_error()
sys.exit(1)
if output_filename is None:
filename = 'fc2.hdf5'
else:
filename = 'fc2.' + output_filename + '.hdf5'
if log_level:
print("Writing fc2 to %s" % filename)
write_fc2_to_hdf5(phono3py.get_fc2(), filename=filename)
if log_level:
show_drift_force_constants(phono3py.get_fc2(), name='fc2')
