def test_kappa_RTA_si_nomeshsym(si_pbesol: Phono3py, si_pbesol_nomeshsym: Phono3py):
"""Test RTA without considering mesh symmetry by Si."""
si_pbesol_nomeshsym.fc2 = si_pbesol.fc2
si_pbesol_nomeshsym.fc3 = si_pbesol.fc3
kappa = _get_kappa(si_pbesol_nomeshsym, [7, 7, 7]).ravel()
kappa_ref = si_pbesol_kappa_RTA_si_nomeshsym
np.testing.assert_allclose(kappa_ref, kappa, atol=0.5)
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