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Merge pull request #408 from phonopy/fix-407 

Fix issue 407
This commit is contained in:
Atsushi Togo 2025-07-04 16:01:15 +09:00 committed by GitHub
parent 8eeb09d934 617a6e9162
commit 48105c5f52
No known key found for this signature in database
GPG Key ID: B5690EEEBB952194
3 changed files with 162 additions and 16 deletions
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4
phono3py/conductivity/base.py
View File

@ -303,7 +303,7 @@ class ConductivityComponents(ConductivityComponentsBase):
log_level=log_level,
)
self._gv_by_gv: np.ndarray
self._gv_by_gv: NDArray
if self._pp.dynamical_matrix is None:
raise RuntimeError("Interaction.init_dynamical_matrix() has to be called.")
@ -318,7 +318,7 @@ class ConductivityComponents(ConductivityComponentsBase):
self._allocate_values()
@property
def gv_by_gv(self):
def gv_by_gv(self) -> NDArray:
"""Return gv_by_gv at grid points where mode kappa are calculated."""
return self._gv_by_gv

11
phono3py/conductivity/direct_solution.py
View File

@ -79,7 +79,6 @@ class ConductivityLBTE(ConductivityLBTEBase):
self._kappa_RTA = None
self._mode_kappa = None
self._mode_kappa_RTA = None
self._gv_by_gv = None
super().__init__(
interaction,
@ -103,7 +102,7 @@ class ConductivityLBTE(ConductivityLBTEBase):
lang=lang,
)
self._conductivity_components = ConductivityComponents(
self._conductivity_components: ConductivityComponents = ConductivityComponents(
self._pp,
self._grid_points,
self._grid_weights,
@ -137,6 +136,11 @@ class ConductivityLBTE(ConductivityLBTEBase):
"""Return RTA mode lattice thermal conductivities."""
return self._mode_kappa_RTA
@property
def gv_by_gv(self):
"""Return gv_by_gv at grid points where mode kappa are calculated."""
return self._conductivity_components.gv_by_gv
def _set_cv(self, i_gp, i_data):
"""Set cv for conductivity components."""
self._conductivity_components.set_heat_capacities(i_gp, i_data)
@ -169,9 +173,6 @@ class ConductivityLBTE(ConductivityLBTEBase):
self._kappa_RTA = np.zeros(
(len(self._sigmas), num_temp, 6), dtype="double", order="C"
)
self._gv_by_gv = np.zeros(
(num_grid_points, num_band0, 6), dtype="double", order="C"
)
self._mode_kappa = np.zeros(
(len(self._sigmas), num_temp, num_grid_points, num_band0, 6), dtype="double"
)

163
test/cui/test_phono3py_load_script.py
View File

@ -22,23 +22,25 @@ cwd = pathlib.Path(__file__).parent
class MockArgs:
"""Mock args of ArgumentParser."""
cell_filename: str | None = None
conf_filename: os.PathLike | None = None
cell_filename: str | os.PathLike | None = None
conf_filename: str | os.PathLike | None = None
fc_calculator: str | None = None
fc_calculator_options: str | None = None
fc_symmetry: bool = True
filename: Sequence[os.PathLike] | None = None
filename: Sequence[str | os.PathLike] | None = None
force_sets_mode: bool = False
force_sets_to_forces_fc2_mode: bool = False
input_filename = None
input_output_filename = None
log_level: int | None = None
is_bterta: bool | None = None
is_lbte: bool | None = None
is_wigner_kappa: bool | None = None
mesh_numbers: Sequence | None = None
mlp_params: str | None = None
rd_number_estimation_factor: float | None = None
output_filename = None
output_yaml_filename: os.PathLike | None = None
output_yaml_filename: str | os.PathLike | None = None
random_displacements: int | str | None = None
show_num_triplets: bool = False
temperatures: Sequence | None = None
@ -89,8 +91,144 @@ def test_phono3py_load():
"kappa-m555.hdf5",
):
file_path = pathlib.Path(created_filename)
if file_path.exists():
file_path.unlink()
assert file_path.exists()
file_path.unlink()
finally:
os.chdir(original_cwd)
def test_phono3py_load_lbte():
"""Test phono3py-load script running direct solution."""
with tempfile.TemporaryDirectory() as temp_dir:
original_cwd = pathlib.Path.cwd()
os.chdir(temp_dir)
try:
# Check sys.exit(0)
argparse_control = _get_phono3py_load_args(
cwd / ".." / "phono3py_params_Si-111-222.yaml",
)
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
argparse_control = _get_phono3py_load_args(
"phono3py.yaml",
is_lbte=True,
temperatures=[
"300",
],
mesh_numbers=["5", "5", "5"],
)
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
# Clean files created by phono3py-load script.
for created_filename in (
"phono3py.yaml",
"fc2.hdf5",
"fc3.hdf5",
"kappa-m555.hdf5",
"coleigs-m555.hdf5",
):
file_path = pathlib.Path(created_filename)
assert file_path.exists()
file_path.unlink()
finally:
os.chdir(original_cwd)
def test_phono3py_load_wigner_rta():
"""Test phono3py-load script running wigner rta."""
with tempfile.TemporaryDirectory() as temp_dir:
original_cwd = pathlib.Path.cwd()
os.chdir(temp_dir)
try:
# Check sys.exit(0)
argparse_control = _get_phono3py_load_args(
cwd / ".." / "phono3py_params_Si-111-222.yaml",
)
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
argparse_control = _get_phono3py_load_args(
"phono3py.yaml",
is_bterta=True,
is_wigner_kappa=True,
temperatures=[
"300",
],
mesh_numbers=["5", "5", "5"],
)
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
# for filename in pathlib.Path.cwd().iterdir():
# print(filename)
# Clean files created by phono3py-load script.
for created_filename in (
"phono3py.yaml",
"fc2.hdf5",
"fc3.hdf5",
"kappa-m555.hdf5",
):
file_path = pathlib.Path(created_filename)
assert file_path.exists()
file_path.unlink()
finally:
os.chdir(original_cwd)
def test_phono3py_load_wigner_lbte():
"""Test phono3py-load script running wigner rta."""
with tempfile.TemporaryDirectory() as temp_dir:
original_cwd = pathlib.Path.cwd()
os.chdir(temp_dir)
try:
# Check sys.exit(0)
argparse_control = _get_phono3py_load_args(
cwd / ".." / "phono3py_params_Si-111-222.yaml",
)
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
argparse_control = _get_phono3py_load_args(
"phono3py.yaml",
is_lbte=True,
is_wigner_kappa=True,
temperatures=[
"300",
],
mesh_numbers=["5", "5", "5"],
)
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
# for filename in pathlib.Path.cwd().iterdir():
# print(filename)
# Clean files created by phono3py-load script.
for created_filename in (
"phono3py.yaml",
"fc2.hdf5",
"fc3.hdf5",
"kappa-m555.hdf5",
"coleigs-m555.hdf5",
):
file_path = pathlib.Path(created_filename)
assert file_path.exists()
file_path.unlink()
finally:
os.chdir(original_cwd)
@ -181,8 +319,8 @@ def test_phono3py_with_QE_calculator(load_phono3py_yaml):
"kappa-m111111.hdf5",
):
file_path = pathlib.Path(created_filename)
if file_path.exists():
file_path.unlink()
assert file_path.exists()
file_path.unlink()
finally:
os.chdir(original_cwd)
@ -404,11 +542,13 @@ def test_phono3py_load_with_pypolymlp_nacl():
def _get_phono3py_load_args(
phono3py_yaml_filepath: str | pathlib.Path,
phono3py_yaml_filepath: str | os.PathLike | None,
fc_calculator: str | None = None,
fc_calculator_options: str | None = None,
load_phono3py_yaml: bool = True,
is_bterta: bool = False,
is_lbte: bool = False,
is_wigner_kappa: bool = False,
mesh_numbers: Sequence | None = None,
mlp_params: str | None = None,
rd_number_estimation_factor: float | None = None,
@ -418,11 +558,14 @@ def _get_phono3py_load_args(
):
# Mock of ArgumentParser.args.
if load_phono3py_yaml:
assert phono3py_yaml_filepath is not None
mockargs = MockArgs(
filename=[phono3py_yaml_filepath],
fc_calculator=fc_calculator,
fc_calculator_options=fc_calculator_options,
is_bterta=is_bterta,
is_lbte=is_lbte,
is_wigner_kappa=is_wigner_kappa,
log_level=1,
mesh_numbers=mesh_numbers,
mlp_params=mlp_params,
@ -439,6 +582,8 @@ def _get_phono3py_load_args(
log_level=1,
cell_filename=phono3py_yaml_filepath,
is_bterta=is_bterta,
is_lbte=is_lbte,
is_wigner_kappa=is_wigner_kappa,
mesh_numbers=mesh_numbers,
mlp_params=mlp_params,
rd_number_estimation_factor=rd_number_estimation_factor,