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phono3py
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Merge branch 'develop' into publish-gh-pages

This commit is contained in:
Atsushi Togo 2025-07-05 10:47:47 +09:00
parent ddd01f6ae4 7e6e2ce628
commit c88ff7bac5
9 changed files with 249 additions and 86 deletions
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2
.pre-commit-config.yaml
View File

@ -11,7 +11,7 @@ repos:
exclude: ^example/AlN-LDA/
- repo: https://github.com/astral-sh/ruff-pre-commit
rev: v0.11.13
rev: v0.12.1
hooks:
- id: ruff
args: [ "--fix", "--show-fixes" ]

4
doc/changelog.md
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@ -2,6 +2,10 @@
# Change Log
## Jul-5-2025: Version 3.17.1
- Fix direct-solution crashing when executed via command line
## Jun-26-2025: Version 3.17.0
- Major refactoring of command-user interface. Most of routines behind the

2
doc/conf.py
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@ -60,7 +60,7 @@ copyright = "2015, Atsushi Togo"
# The short X.Y version.
version = "3.17"
# The full version, including alpha/beta/rc tags.
release = "3.17.0"
release = "3.17.1"
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.

145
phono3py/api_phono3py.py
View File

@ -1536,49 +1536,15 @@ class Phono3py:
fc2 = fc_solver.force_constants[2]
fc3 = fc_solver.force_constants[3]
if symmetrize_fc3r:
if use_symfc_projector and fc_calculator is None:
if self._log_level:
print("Symmetrizing fc3 by symfc projector.", flush=True)
fc3 = symmetrize_by_projector(
self._supercell,
fc3,
3,
primitive=self._primitive,
log_level=self._log_level,
show_credit=True,
)
if self._fc2 is None:
if self._log_level:
print("Symmetrizing fc2 by symfc projector.", flush=True)
fc2 = symmetrize_by_projector(
self._supercell,
fc2,
2,
primitive=self._primitive,
log_level=self._log_level,
)
elif fc_calculator is None or fc_calculator == "traditional":
if self._log_level:
print("Symmetrizing fc3 by traditional approach.", flush=True)
if is_compact_fc:
set_translational_invariance_compact_fc3(fc3, self._primitive)
set_permutation_symmetry_compact_fc3(fc3, self._primitive)
else:
set_translational_invariance_fc3(fc3)
set_permutation_symmetry_fc3(fc3)
if self._fc2 is None:
if self._log_level:
print("Symmetrizing fc2 by traditional approach.", flush=True)
if is_compact_fc:
symmetrize_compact_force_constants(fc2, self._primitive)
else:
symmetrize_force_constants(fc2)
self._fc3 = fc3
self._fc3_nonzero_indices = None
if fc_calculator == "symfc":
if fc_calculator == "traditional" or fc_calculator is None:
if symmetrize_fc3r:
self.symmetrize_fc3(
use_symfc_projector=use_symfc_projector and fc_calculator is None
)
elif fc_calculator == "symfc":
symfc_solver = cast(SymfcFCSolver, fc_solver.fc_solver)
fc3_nonzero_elems = symfc_solver.get_nonzero_atomic_indices_fc3()
options = symfc_solver.options
@ -1596,18 +1562,40 @@ class Phono3py:
fc3_nonzero_elems, dtype="byte", order="C"
)
# fc2 as obtained above will not be set when "|" in fc-calculator setting.
if fc_calculator is not None and "|" in fc_calculator:
fc2 = None
if fc_calculator_options is not None and "|" in fc_calculator_options:
fc2 = None
# fc2 should not be set if phonon_supercell_matrix is available.
if self._phonon_supercell_matrix is not None:
fc2 = None
# Normally self._fc2 is overwritten in produce_fc2
if self._fc2 is None:
if self._phonon_supercell_matrix is None:
self._fc2 = fc2
if fc_calculator == "traditional" or fc_calculator is None:
if symmetrize_fc3r:
self.symmetrize_fc2(
use_symfc_projector=use_symfc_projector
and fc_calculator is None
)
def symmetrize_fc3(self, use_symfc_projector: bool = False):
"""Symmetrize fc3 by symfc projector or traditional approach."""
if self._fc3 is None:
raise RuntimeError("fc3 is not set. Call produce_fc3 first.")
if use_symfc_projector:
if self._log_level:
print("Symmetrizing fc3 by symfc projector.", flush=True)
self._fc3 = symmetrize_by_projector(
self._supercell,
self._fc3,
3,
primitive=self._primitive,
log_level=self._log_level,
show_credit=True,
)
else:
if self._log_level:
print("Symmetrizing fc3 by traditional approach.", flush=True)
if self._fc3.shape[0] == self._fc3.shape[1]:
set_translational_invariance_fc3(self._fc3)
set_permutation_symmetry_fc3(self._fc3)
else:
set_translational_invariance_compact_fc3(self._fc3, self._primitive)
set_permutation_symmetry_compact_fc3(self._fc3, self._primitive)
def produce_fc2(
self,
@ -1653,6 +1641,9 @@ class Phono3py:
if not forces_in_dataset(disp_dataset):
raise RuntimeError("Forces are not set in the dataset.")
if self._log_level:
print("Computing phonon fc2.", flush=True)
self._fc2 = get_fc2(
self._phonon_supercell,
disp_dataset,
@ -1665,21 +1656,43 @@ class Phono3py:
)
if symmetrize_fc2 and (fc_calculator is None or fc_calculator == "traditional"):
if use_symfc_projector:
self._fc2 = symmetrize_by_projector(
self._phonon_supercell,
self._fc2,
2,
primitive=self._primitive,
log_level=self._log_level,
)
self.symmetrize_fc2(
use_symfc_projector=use_symfc_projector and fc_calculator is None
)
def symmetrize_fc2(self, use_symfc_projector: bool = False):
"""Symmetrize fc2 by symfc projector or traditional approach."""
if self._fc2 is None:
raise RuntimeError(
"fc2 is not set. Call produce_fc3 or produce_fc2 (phonon_fc2) first."
)
if self._phonon_supercell_matrix is None:
supercell = self._supercell
primitive = self._primitive
else:
supercell = self._phonon_supercell
primitive = self._phonon_primitive
assert self._fc2.shape[1] == len(supercell)
if use_symfc_projector:
if self._log_level:
print("Symmetrizing fc2 by symfc projector.", flush=True)
self._fc2 = symmetrize_by_projector(
supercell,
self._fc2,
2,
primitive=primitive,
log_level=self._log_level,
show_credit=True,
)
else:
if self._log_level:
print("Symmetrizing fc2 by traditional approach.", flush=True)
if self._fc2.shape[0] == self._fc2.shape[1]:
symmetrize_force_constants(self._fc2)
else:
if is_compact_fc:
symmetrize_compact_force_constants(
self._fc2, self._phonon_primitive
)
else:
symmetrize_force_constants(self._fc2)
symmetrize_compact_force_constants(self._fc2, primitive)
def cutoff_fc3_by_zero(self, cutoff_distance, fc3=None):
"""Set zero to fc3 elements out of cutoff distance.

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"
)

2
phono3py/cui/phono3py_script.py
View File

@ -1195,7 +1195,7 @@ def main(**argparse_control):
if settings.is_nac:
store_nac_params(
cast(Phonopy, ph3py),
cast(PhonopySettings, settings),
settings,
cell_info.phono3py_yaml,
unitcell_filename,
log_level,

2
phono3py/version.py
View File

@ -34,4 +34,4 @@
# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
__version__ = "3.17.0"
__version__ = "3.17.1"

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,