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Adjustment to let both CUI and phno3py.load work nicely

This commit is contained in:
Atsushi Togo 2025-06-23 16:25:31 +09:00
parent 7f44ce3594
commit 072e195940
4 changed files with 104 additions and 89 deletions
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4
phono3py/api_phono3py.py
View File

@ -2241,7 +2241,7 @@ class Phono3py:
)
def save(
self, filename: str = "phono3py_params.yaml", settings: Optional[dict] = None
self, filename: str = "phono3py_params.yaml", settings: dict | None = None
):
"""Save parameters in Phono3py instants into file.
@ -2268,7 +2268,7 @@ class Phono3py:
def develop_mlp(
self,
params: Optional[Union[PypolymlpParams, dict, str]] = None,
params: PypolymlpParams | dict | str | None = None,
test_size: float = 0.1,
):
"""Develop machine learning potential.

137
phono3py/cui/load.py
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@ -38,7 +38,6 @@ from __future__ import annotations
import os
import pathlib
from collections.abc import Sequence
from typing import Optional, Union
import numpy as np
import phonopy.cui.load_helper as load_helper
@ -65,34 +64,34 @@ from phono3py.phonon3.fc3 import show_drift_fc3
def load(
phono3py_yaml: Optional[
Union[str, bytes, os.PathLike]
] = None, # phono3py.yaml-like must be the first argument.
supercell_matrix: Optional[Union[Sequence, np.ndarray]] = None,
primitive_matrix: Optional[Union[Sequence, np.ndarray]] = None,
phonon_supercell_matrix: Optional[Union[Sequence, np.ndarray]] = None,
phono3py_yaml: str
| os.PathLike
| None = None, # phono3py.yaml-like must be the first argument.
supercell_matrix: Sequence | NDArray | None = None,
primitive_matrix: Sequence | NDArray | None = None,
phonon_supercell_matrix: Sequence | NDArray | None = None,
is_nac: bool = True,
calculator: Optional[str] = None,
unitcell: Optional[PhonopyAtoms] = None,
supercell: Optional[PhonopyAtoms] = None,
nac_params: Optional[dict] = None,
unitcell_filename: Optional[Union[str, bytes, os.PathLike]] = None,
supercell_filename: Optional[Union[str, bytes, os.PathLike]] = None,
born_filename: Optional[Union[str, bytes, os.PathLike]] = None,
forces_fc3_filename: Optional[Union[str, bytes, os.PathLike]] = None,
forces_fc2_filename: Optional[Union[str, bytes, os.PathLike]] = None,
fc3_filename: Optional[Union[str, bytes, os.PathLike]] = None,
fc2_filename: Optional[Union[str, bytes, os.PathLike]] = None,
fc_calculator: Optional[str] = None,
fc_calculator_options: Optional[str] = None,
factor: Optional[float] = None,
calculator: str | None = None,
unitcell: PhonopyAtoms | None = None,
supercell: PhonopyAtoms | None = None,
nac_params: dict | None = None,
unitcell_filename: str | os.PathLike | None = None,
supercell_filename: str | os.PathLike | None = None,
born_filename: str | os.PathLike | None = None,
forces_fc3_filename: str | os.PathLike | None = None,
forces_fc2_filename: str | os.PathLike | None = None,
fc3_filename: str | os.PathLike | None = None,
fc2_filename: str | os.PathLike | None = None,
fc_calculator: str | None = None,
fc_calculator_options: str | None = None,
factor: float | None = None,
produce_fc: bool = True,
is_symmetry: bool = True,
symmetrize_fc: bool = True,
is_mesh_symmetry: bool = True,
is_compact_fc: bool = False,
use_pypolymlp: bool = False,
mlp_params: Optional[dict] = None,
mlp_params: dict | None = None,
use_grg: bool = False,
make_r0_average: bool = True,
symprec: float = 1e-5,
@ -347,15 +346,24 @@ def load(
load_fc2_and_fc3(
ph3py, fc3_filename=fc3_filename, fc2_filename=fc2_filename, log_level=log_level
)
load_dataset_and_phonon_dataset(
ph3py.dataset = select_and_load_dataset(
ph3py,
ph3py_yaml,
ph3py_yaml=ph3py_yaml,
forces_fc3_filename=forces_fc3_filename,
forces_fc2_filename=forces_fc2_filename,
phono3py_yaml_filename=phono3py_yaml,
calculator=_calculator,
log_level=log_level,
)
ph3py.phonon_dataset = select_and_load_phonon_dataset(
ph3py,
ph3py_yaml=ph3py_yaml,
forces_fc2_filename=forces_fc2_filename,
calculator=_calculator,
log_level=log_level,
)
if use_pypolymlp and ph3py.fc3 is None and forces_in_dataset(ph3py.dataset):
ph3py.mlp_dataset = ph3py.dataset
ph3py.dataset = None
@ -401,46 +409,6 @@ def load_fc2_and_fc3(
_load_fc2(ph3py, fc2_filename=fc2_filename, log_level=log_level)
def load_dataset_and_phonon_dataset(
ph3py: Phono3py,
ph3py_yaml: Phono3pyYaml | None = None,
forces_fc3_filename: str | os.PathLike | Sequence | None = None,
forces_fc2_filename: str | os.PathLike | Sequence | None = None,
phono3py_yaml_filename: str | os.PathLike | None = None,
cutoff_pair_distance: float | None = None,
calculator: str | None = None,
log_level: int = 0,
):
"""Set displacements, forces, and create force constants."""
if (
ph3py.fc3 is None
and ph3py.fc2 is None
and ph3py.phonon_supercell_matrix is None
):
dataset = _select_and_load_dataset(
ph3py,
ph3py_yaml=ph3py_yaml,
forces_fc3_filename=forces_fc3_filename,
phono3py_yaml_filename=phono3py_yaml_filename,
cutoff_pair_distance=cutoff_pair_distance,
calculator=calculator,
log_level=log_level,
)
if dataset is not None:
ph3py.dataset = dataset
if ph3py.fc2 is None:
phonon_dataset = _select_and_load_phonon_dataset(
ph3py,
ph3py_yaml=ph3py_yaml,
forces_fc2_filename=forces_fc2_filename,
calculator=calculator,
log_level=log_level,
)
if phonon_dataset is not None:
ph3py.phonon_dataset = phonon_dataset
def compute_force_constants_from_datasets(
ph3py: Phono3py,
fc_calculator: str | None = None,
@ -525,7 +493,7 @@ def _load_fc3(
print(f'fc3 was read from "{_fc3_filename}".')
def _select_and_load_dataset(
def select_and_load_dataset(
ph3py: Phono3py,
ph3py_yaml: Phono3pyYaml | None = None,
forces_fc3_filename: str | os.PathLike | Sequence | None = None,
@ -534,6 +502,7 @@ def _select_and_load_dataset(
calculator: str | None = None,
log_level: int = 0,
) -> dict | None:
"""Select and load dataset for fc3."""
# displacements and forces are in phono3py-yaml-like file
if (
ph3py_yaml is not None
@ -601,19 +570,18 @@ def _load_fc2(
ph3py.fc2 = fc2
def _select_and_load_phonon_dataset(
def select_and_load_phonon_dataset(
ph3py: Phono3py,
ph3py_yaml: Optional[Phono3pyYaml] = None,
forces_fc2_filename: Optional[Union[os.PathLike, Sequence]] = None,
calculator: Optional[str] = None,
ph3py_yaml: Phono3pyYaml | None = None,
forces_fc2_filename: str | os.PathLike | Sequence | None = None,
calculator: str | None = None,
log_level: int = 0,
) -> Optional[dict]:
phonon_dataset = None
if (
ph3py_yaml is not None
and ph3py_yaml.phonon_dataset is not None
and forces_in_dataset(ph3py_yaml.phonon_dataset)
):
) -> dict | None:
"""Select and load phonon dataset for fc2."""
if ph3py.phonon_supercell_matrix is None:
return None
if ph3py_yaml is not None and forces_in_dataset(ph3py_yaml.phonon_dataset):
phonon_dataset = _get_dataset_for_fc2(
ph3py,
ph3py_yaml,
@ -622,9 +590,9 @@ def _select_and_load_phonon_dataset(
calculator,
log_level,
)
elif (
forces_fc2_filename is not None or pathlib.Path("FORCES_FC2").exists()
) and ph3py.phonon_supercell_matrix is not None:
return phonon_dataset
if forces_fc2_filename is not None or pathlib.Path("FORCES_FC2").exists():
if forces_fc2_filename is None:
force_filename = "FORCES_FC2"
else:
@ -637,7 +605,9 @@ def _select_and_load_phonon_dataset(
calculator,
log_level,
)
elif ph3py_yaml is not None and ph3py_yaml.phonon_dataset is not None:
return phonon_dataset
if ph3py_yaml is not None:
# not forces_in_dataset(ph3py_yaml.dataset)
# but want to read displacement dataset.
phonon_dataset = _get_dataset_for_fc2(
@ -648,8 +618,9 @@ def _select_and_load_phonon_dataset(
calculator,
log_level,
)
return phonon_dataset
return phonon_dataset
return None
def _get_dataset_for_fc3(
@ -676,7 +647,7 @@ def _get_dataset_for_fc3(
def _get_dataset_for_fc2(
ph3py: Phono3py,
ph3py_yaml: Optional[Phono3pyYaml],
ph3py_yaml: Phono3pyYaml | None,
force_filename,
fc_type,
calculator,

44
phono3py/cui/phono3py_script.py
View File

@ -42,6 +42,7 @@ import os
import pathlib
import sys
import warnings
from collections.abc import Sequence
from typing import Optional, cast
import numpy as np
@ -82,8 +83,9 @@ from phono3py.cui.create_supercells import (
)
from phono3py.cui.load import (
compute_force_constants_from_datasets,
load_dataset_and_phonon_dataset,
load_fc2_and_fc3,
select_and_load_dataset,
select_and_load_phonon_dataset,
)
from phono3py.cui.phono3py_argparse import get_parser
from phono3py.cui.settings import Phono3pyConfParser, Phono3pySettings
@ -946,6 +948,44 @@ def _init_phph_interaction(
sys.exit(1)
def _load_dataset_and_phonon_dataset(
ph3py: Phono3py,
ph3py_yaml: Phono3pyYaml | None = None,
forces_fc3_filename: str | os.PathLike | Sequence | None = None,
forces_fc2_filename: str | os.PathLike | Sequence | None = None,
phono3py_yaml_filename: str | os.PathLike | None = None,
cutoff_pair_distance: float | None = None,
calculator: str | None = None,
log_level: int = 0,
):
"""Set displacements, forces, and create force constants."""
if ph3py.fc3 is None or (
ph3py.fc2 is None and ph3py.phonon_supercell_matrix is None
):
dataset = select_and_load_dataset(
ph3py,
ph3py_yaml=ph3py_yaml,
forces_fc3_filename=forces_fc3_filename,
phono3py_yaml_filename=phono3py_yaml_filename,
cutoff_pair_distance=cutoff_pair_distance,
calculator=calculator,
log_level=log_level,
)
if dataset is not None:
ph3py.dataset = dataset
if ph3py.fc2 is None and ph3py.phonon_supercell_matrix is not None:
phonon_dataset = select_and_load_phonon_dataset(
ph3py,
ph3py_yaml=ph3py_yaml,
forces_fc2_filename=forces_fc2_filename,
calculator=calculator,
log_level=log_level,
)
if phonon_dataset is not None:
ph3py.phonon_dataset = phonon_dataset
def main(**argparse_control):
"""Phono3py main part of command line interface."""
# import warnings
@ -1192,7 +1232,7 @@ def main(**argparse_control):
############
# Datasets #
############
load_dataset_and_phonon_dataset(
_load_dataset_and_phonon_dataset(
ph3py,
ph3py_yaml=cast(Phono3pyYaml, cell_info.phonopy_yaml),
phono3py_yaml_filename=unitcell_filename,

8
phono3py/interface/phono3py_yaml.py
View File

@ -298,7 +298,7 @@ class Phono3pyYamlDumper(PhonopyYamlDumperBase):
"dielectric_constant": True,
}
def __init__(self, data: Phono3pyYamlData, dumper_settings=None):
def __init__(self, data: Phono3pyYamlData, dumper_settings: dict | None = None):
"""Init method."""
self._data = data
self._init_dumper_settings(dumper_settings)
@ -405,7 +405,11 @@ class Phono3pyYaml(PhonopyYaml):
command_name = "phono3py"
def __init__(
self, configuration=None, calculator=None, physical_units=None, settings=None
self,
configuration: dict | None = None,
calculator: str | None = None,
physical_units: dict | None = None,
settings: dict | None = None,
):
"""Init method."""
self._data = Phono3pyYamlData(