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Merge pull request #396 from phonopy/number-estimation-factor 

Add number_estimation_factor parameter for rd displacement generation
This commit is contained in:
Atsushi Togo 2025-06-13 14:01:49 +09:00 committed by GitHub
parent dd60053a74 788fab3cdf
commit 200e1b92a9
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GPG Key ID: B5690EEEBB952194
8 changed files with 371 additions and 259 deletions
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52
phono3py/api_phono3py.py
View File

@ -1253,13 +1253,14 @@ class Phono3py:
def generate_displacements(
self,
distance: Optional[float] = None,
cutoff_pair_distance: Optional[float] = None,
is_plusminus: Union[bool, str] = "auto",
distance: float | None = None,
cutoff_pair_distance: float | None = None,
is_plusminus: bool | str = "auto",
is_diagonal: bool = True,
number_of_snapshots: Optional[Union[int, Literal["auto"]]] = None,
random_seed: Optional[int] = None,
max_distance: Optional[float] = None,
number_of_snapshots: int | Literal["auto"] | None = None,
random_seed: int | None = None,
max_distance: float | None = None,
number_estimation_factor: float | None = None,
):
"""Generate displacement dataset in supercell for fc3.
@ -1307,7 +1308,7 @@ class Phono3py:
pair of displacements is considered to calculate fc3 or not. Default
is None, which means cutoff is not used.
is_plusminus : True, False, or 'auto', optional
With True, atomis are displaced in both positive and negative
With True, atoms are displaced in both positive and negative
directions. With False, only one direction. With 'auto', mostly
equivalent to is_plusminus=True, but only one direction is chosen
when the displacements in both directions are symmetrically
@ -1328,9 +1329,15 @@ class Phono3py:
random_seed : int or None, optional
Random seed for random displacements generation. Default is None.
max_distance : float or None, optional
In random direction and distance displacements generation, this
value is specified. In random direction and random distance
displacements generation, this value is used as `max_distance`.
When specified, displacements are generated with random direction
and random distance. This value serves as the maximum distance,
while the `distance` parameter sets the minimum distance. The
displacement distance is randomly sampled from a uniform
distribution between these two bounds.
number_estimation_factor : float, optional
This factor multiplies the number of snapshots estimated by symfc
when `number_of_snapshots` is set to "auto". Default is None, which
sets this factor to 8 when `max_distance` is specified, otherwise 4.
"""
if distance is None:
@ -1346,14 +1353,19 @@ class Phono3py:
options = None
else:
options = {"cutoff": {3: cutoff_pair_distance}}
_number_of_snapshots = (
SymfcFCSolver(
self._supercell,
symmetry=self._symmetry,
options=options,
).estimate_numbers_of_supercells(orders=[3])[3]
* 2
)
_number_of_snapshots = SymfcFCSolver(
self._supercell,
symmetry=self._symmetry,
options=options,
).estimate_numbers_of_supercells(orders=[3])[3]
if number_estimation_factor is None:
if max_distance is None:
_number_of_snapshots *= 4
else:
_number_of_snapshots *= 8
else:
_number_of_snapshots *= number_estimation_factor
_number_of_snapshots = int(_number_of_snapshots)
else:
_number_of_snapshots = number_of_snapshots
self._dataset = self._generate_random_displacements(
@ -2733,8 +2745,8 @@ class Phono3py:
number_of_atoms: int,
distance: float = 0.03,
is_plusminus: bool = False,
random_seed: Optional[int] = None,
max_distance: Optional[float] = None,
random_seed: int | None = None,
max_distance: float | None = None,
):
if random_seed is not None and random_seed >= 0 and random_seed < 2**32:
_random_seed = random_seed

20
phono3py/cui/create_force_constants.py
View File

@ -452,16 +452,17 @@ def _read_dataset_fc3(
def run_pypolymlp_to_compute_forces(
ph3py: Phono3py,
mlp_params: Union[str, dict, PypolymlpParams],
displacement_distance: Optional[float] = None,
number_of_snapshots: Optional[int] = None,
random_seed: Optional[int] = None,
mlp_params: str | dict | PypolymlpParams | None = None,
displacement_distance: float | None = None,
number_of_snapshots: int | None = None,
number_estimation_factor: int | None = None,
random_seed: int | None = None,
prepare_dataset: bool = False,
fc_calculator: Optional[str] = None,
fc_calculator_options: Optional[str] = None,
cutoff_pair_distance: Optional[float] = None,
symfc_memory_size: Optional[float] = None,
mlp_filename: Optional[str] = None,
fc_calculator: str | None = None,
fc_calculator_options: str | None = None,
cutoff_pair_distance: float | None = None,
symfc_memory_size: float | None = None,
mlp_filename: str | None = None,
log_level: int = 0,
):
"""Run pypolymlp to compute forces."""
@ -557,6 +558,7 @@ def run_pypolymlp_to_compute_forces(
is_plusminus=True,
number_of_snapshots=number_of_snapshots,
random_seed=random_seed,
number_estimation_factor=number_estimation_factor,
)
if log_level:

1
phono3py/cui/create_supercells.py
View File

@ -108,6 +108,7 @@ def create_phono3py_supercells(
is_diagonal=settings.is_diagonal_displacement,
number_of_snapshots=settings.random_displacements,
random_seed=settings.random_seed,
number_estimation_factor=settings.rd_number_estimation_factor,
)
if (

7
phono3py/cui/phono3py_argparse.py
View File

@ -676,6 +676,13 @@ def get_parser(fc_symmetry=False, is_nac=False, load_phono3py_yaml=False):
default=None,
help='Number of supercells with random displacements or "auto"',
)
parser.add_argument(
"--rd-auto-factor",
dest="rd_number_estimation_factor",
type=float,
default=None,
help="Factor to estimate number of supercells with random displacements",
)
parser.add_argument(
"--rd-fc2",
"--random-displacements-fc2",

1
phono3py/cui/phono3py_script.py
View File

@ -1196,6 +1196,7 @@ def main(**argparse_control):
mlp_params=settings.mlp_params,
displacement_distance=settings.displacement_distance,
number_of_snapshots=settings.random_displacements,
number_estimation_factor=settings.rd_number_estimation_factor,
random_seed=settings.random_seed,
fc_calculator=settings.fc_calculator,
fc_calculator_options=settings.fc_calculator_options,

518
test/cui/test_phono3py_load_script.py
View File

@ -4,9 +4,9 @@ from __future__ import annotations
import os
import pathlib
import tempfile
from collections.abc import Sequence
from dataclasses import dataclass, fields
from typing import Optional, Union
import h5py
import numpy as np
@ -16,32 +16,32 @@ import phono3py
from phono3py.cui.phono3py_script import main
cwd = pathlib.Path(__file__).parent
cwd_called = pathlib.Path.cwd()
@dataclass
class MockArgs:
"""Mock args of ArgumentParser."""
cell_filename: Optional[str] = None
conf_filename: Optional[os.PathLike] = None
fc_calculator: Optional[str] = None
fc_calculator_options: Optional[str] = None
cell_filename: str | None = None
conf_filename: os.PathLike | None = None
fc_calculator: str | None = None
fc_calculator_options: str | None = None
fc_symmetry: bool = True
filename: Optional[Sequence[os.PathLike]] = None
filename: Sequence[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: Optional[int] = None
is_bterta: Optional[bool] = None
mesh_numbers: Optional[Sequence] = None
mlp_params: Optional[str] = None
log_level: int | None = None
is_bterta: 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: Optional[os.PathLike] = None
random_displacements: Optional[Union[int, str]] = None
output_yaml_filename: os.PathLike | None = None
random_displacements: int | str | None = None
show_num_triplets: bool = False
temperatures: Optional[Sequence] = None
temperatures: Sequence | None = None
use_pypolymlp: bool = False
write_grid_points: bool = False
@ -56,36 +56,44 @@ class MockArgs:
def test_phono3py_load():
"""Test phono3py-load script."""
# 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
with tempfile.TemporaryDirectory() as temp_dir:
original_cwd = pathlib.Path.cwd()
os.chdir(temp_dir)
argparse_control = _get_phono3py_load_args(
cwd_called / "phono3py.yaml",
is_bterta=True,
temperatures=[
"300",
],
mesh_numbers=["5", "5", "5"],
)
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
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
# Clean files created by phono3py-load script.
for created_filename in (
"phono3py.yaml",
"fc2.hdf5",
"fc3.hdf5",
"kappa-m555.hdf5",
):
file_path = cwd_called / created_filename
if file_path.exists():
file_path.unlink()
argparse_control = _get_phono3py_load_args(
"phono3py.yaml",
is_bterta=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",
):
file_path = pathlib.Path(created_filename)
if file_path.exists():
file_path.unlink()
finally:
os.chdir(original_cwd)
@pytest.mark.parametrize(
@ -108,59 +116,76 @@ def test_phono3py_load_with_typeII_dataset(
"""
pytest.importorskip("symfc")
argparse_control = _get_phono3py_load_args(
cwd / ".." / "phono3py_params-Si111-rd.yaml.xz",
load_phono3py_yaml=load_phono3py_yaml,
fc_calculator=fc_calculator,
fc_calculator_options=fc_calculator_options,
)
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"):
file_path = pathlib.Path(cwd_called / created_filename)
if file_path.exists():
if created_filename == "fc3.hdf5":
with h5py.File(file_path, "r") as f:
if fc_calculator_options is None:
assert "fc3_nonzero_indices" not in f
else:
assert "fc3_nonzero_indices" in f
assert "fc3_cutoff" in f
assert f["fc3_cutoff"][()] == pytest.approx(4.0)
file_path.unlink()
with tempfile.TemporaryDirectory() as temp_dir:
original_cwd = pathlib.Path.cwd()
os.chdir(temp_dir)
try:
argparse_control = _get_phono3py_load_args(
cwd / ".." / "phono3py_params-Si111-rd.yaml.xz",
load_phono3py_yaml=load_phono3py_yaml,
fc_calculator=fc_calculator,
fc_calculator_options=fc_calculator_options,
)
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"):
file_path = pathlib.Path(created_filename)
if file_path.exists():
if created_filename == "fc3.hdf5":
with h5py.File(file_path, "r") as f:
if fc_calculator_options is None:
assert "fc3_nonzero_indices" not in f
else:
assert "fc3_nonzero_indices" in f
assert "fc3_cutoff" in f
assert f["fc3_cutoff"][()] == pytest.approx(4.0)
file_path.unlink()
finally:
os.chdir(original_cwd)
@pytest.mark.parametrize("load_phono3py_yaml", [True, False])
def test_phono3py_with_QE_calculator(load_phono3py_yaml):
"""Test phono3py-load script with QE calculator."""
argparse_control = _get_phono3py_load_args(
cwd / "phono3py_params-qe-Si222.yaml.xz",
load_phono3py_yaml=load_phono3py_yaml,
is_bterta=True,
temperatures=[
"300",
],
mesh_numbers=["11", "11", "11"],
)
with pytest.raises(SystemExit):
main(**argparse_control)
with tempfile.TemporaryDirectory() as temp_dir:
original_cwd = pathlib.Path.cwd()
os.chdir(temp_dir)
with h5py.File(cwd_called / "kappa-m111111.hdf5", "r") as f:
np.testing.assert_almost_equal(f["kappa"][0, 0], 118.93, decimal=1)
try:
argparse_control = _get_phono3py_load_args(
cwd / "phono3py_params-qe-Si222.yaml.xz",
load_phono3py_yaml=load_phono3py_yaml,
is_bterta=True,
temperatures=[
"300",
],
mesh_numbers=["11", "11", "11"],
)
with pytest.raises(SystemExit):
main(**argparse_control)
# Clean files created by phono3py/phono3py-load script.
for created_filename in (
"phono3py.yaml",
"fc2.hdf5",
"fc3.hdf5",
"kappa-m111111.hdf5",
):
file_path = pathlib.Path(cwd_called / created_filename)
if file_path.exists():
file_path.unlink()
with h5py.File("kappa-m111111.hdf5", "r") as f:
np.testing.assert_almost_equal(f["kappa"][0, 0], 118.93, decimal=1)
# Clean files created by phono3py/phono3py-load script.
for created_filename in (
"phono3py.yaml",
"fc2.hdf5",
"fc3.hdf5",
"kappa-m111111.hdf5",
):
file_path = pathlib.Path(created_filename)
if file_path.exists():
file_path.unlink()
finally:
os.chdir(original_cwd)
def test_phono3py_load_with_pypolymlp_si():
@ -173,56 +198,64 @@ def test_phono3py_load_with_pypolymlp_si():
pytest.importorskip("pypolymlp", minversion="0.9.2")
pytest.importorskip("symfc")
# Create fc2.hdf5
argparse_control = _get_phono3py_load_args(
cwd / ".." / "phono3py_params_Si-111-222-rd.yaml.xz",
fc_calculator="symfc",
)
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
for created_filename in ("phono3py.yaml", "fc2.hdf5", "fc3.hdf5"):
file_path = pathlib.Path(cwd_called / created_filename)
assert file_path.exists()
pathlib.Path(cwd_called / "fc3.hdf5").unlink()
with tempfile.TemporaryDirectory() as temp_dir:
original_cwd = pathlib.Path.cwd()
os.chdir(temp_dir)
# Create MLP (polymlp.yaml)
argparse_control = _get_phono3py_load_args(
cwd / ".." / "phono3py_params_Si-111-222-rd.yaml.xz",
use_pypolymlp=True,
)
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
for created_filename in ("phono3py.yaml", "polymlp.yaml"):
file_path = pathlib.Path(cwd_called / created_filename)
assert file_path.exists()
try:
# Create fc2.hdf5
argparse_control = _get_phono3py_load_args(
cwd / ".." / "phono3py_params_Si-111-222-rd.yaml.xz",
fc_calculator="symfc",
)
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
for created_filename in ("phono3py.yaml", "fc2.hdf5", "fc3.hdf5"):
file_path = pathlib.Path(created_filename)
assert file_path.exists()
pathlib.Path("fc3.hdf5").unlink()
# Create phono3py_mlp_eval_dataset.yaml
argparse_control = _get_phono3py_load_args(
cwd_called / "phono3py.yaml",
fc_calculator="symfc",
random_displacements="auto",
use_pypolymlp=True,
)
# Create MLP (polymlp.yaml)
argparse_control = _get_phono3py_load_args(
cwd / ".." / "phono3py_params_Si-111-222-rd.yaml.xz",
use_pypolymlp=True,
)
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
for created_filename in ("phono3py.yaml", "polymlp.yaml"):
file_path = pathlib.Path(created_filename)
assert file_path.exists()
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
# Create phono3py_mlp_eval_dataset.yaml
argparse_control = _get_phono3py_load_args(
"phono3py.yaml",
fc_calculator="symfc",
random_displacements="auto",
use_pypolymlp=True,
)
ph3 = phono3py.load(cwd_called / "phono3py_mlp_eval_dataset.yaml")
assert len(ph3.displacements) == 4
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
for created_filename in (
"phono3py.yaml",
"fc2.hdf5",
"fc3.hdf5",
"polymlp.yaml",
"phono3py_mlp_eval_dataset.yaml",
):
file_path = pathlib.Path(cwd_called / created_filename)
assert file_path.exists()
file_path.unlink()
ph3 = phono3py.load("phono3py_mlp_eval_dataset.yaml")
assert len(ph3.displacements) == 8
for created_filename in (
"phono3py.yaml",
"fc2.hdf5",
"fc3.hdf5",
"polymlp.yaml",
"phono3py_mlp_eval_dataset.yaml",
):
file_path = pathlib.Path(created_filename)
assert file_path.exists()
file_path.unlink()
finally:
os.chdir(original_cwd)
def test_phono3py_load_with_pypolymlp_nacl():
@ -235,109 +268,152 @@ def test_phono3py_load_with_pypolymlp_nacl():
pytest.importorskip("pypolymlp", minversion="0.9.2")
pytest.importorskip("symfc")
# Stage1 (preparation)
argparse_control = _get_phono3py_load_args(
cwd / ".." / "phono3py_params_MgO-222rd-444rd.yaml.xz",
mlp_params="cutoff=4.0,gtinv_maxl=4 4,max_p=1,gtinv_order=2",
fc_calculator="symfc",
random_displacements="auto",
use_pypolymlp=True,
)
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
with tempfile.TemporaryDirectory() as temp_dir:
original_cwd = pathlib.Path.cwd()
os.chdir(temp_dir)
ph3 = phono3py.load(cwd_called / "phono3py_mlp_eval_dataset.yaml")
assert len(ph3.displacements) == 16
try:
# Stage1 (preparation)
argparse_control = _get_phono3py_load_args(
cwd / ".." / "phono3py_params_MgO-222rd-444rd.yaml.xz",
mlp_params="cutoff=4.0,gtinv_maxl=4 4,max_p=1,gtinv_order=2",
fc_calculator="symfc",
random_displacements="auto",
use_pypolymlp=True,
)
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
for created_filename in (
"phono3py.yaml",
"fc2.hdf5",
"fc3.hdf5",
"polymlp.yaml",
"phono3py_mlp_eval_dataset.yaml",
):
file_path = pathlib.Path(cwd_called / created_filename)
assert file_path.exists()
ph3 = phono3py.load("phono3py_mlp_eval_dataset.yaml")
assert len(ph3.displacements) == 32
for created_filename in (
"fc3.hdf5",
"phono3py_mlp_eval_dataset.yaml",
):
file_path = pathlib.Path(cwd_called / created_filename)
assert file_path.exists()
file_path.unlink()
for created_filename in (
"phono3py.yaml",
"fc2.hdf5",
"fc3.hdf5",
"polymlp.yaml",
"phono3py_mlp_eval_dataset.yaml",
):
file_path = pathlib.Path(created_filename)
assert file_path.exists()
# Stage2 (cutoff test)
argparse_control = _get_phono3py_load_args(
cwd_called / "phono3py.yaml",
fc_calculator="symfc",
fc_calculator_options="|cutoff=4.0",
random_displacements="auto",
use_pypolymlp=True,
)
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
for created_filename in (
"fc3.hdf5",
"phono3py_mlp_eval_dataset.yaml",
):
file_path = pathlib.Path(created_filename)
assert file_path.exists()
file_path.unlink()
ph3 = phono3py.load(cwd_called / "phono3py_mlp_eval_dataset.yaml")
assert len(ph3.displacements) == 4
# Stage2 (cutoff test)
argparse_control = _get_phono3py_load_args(
"phono3py.yaml",
fc_calculator="symfc",
fc_calculator_options="|cutoff=4.0",
random_displacements="auto",
use_pypolymlp=True,
)
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
for created_filename in (
"phono3py.yaml",
"fc2.hdf5",
"fc3.hdf5",
"polymlp.yaml",
"phono3py_mlp_eval_dataset.yaml",
):
file_path = pathlib.Path(cwd_called / created_filename)
assert file_path.exists()
ph3 = phono3py.load("phono3py_mlp_eval_dataset.yaml")
assert len(ph3.displacements) == 8
for created_filename in (
"fc3.hdf5",
"phono3py_mlp_eval_dataset.yaml",
):
file_path = pathlib.Path(cwd_called / created_filename)
assert file_path.exists()
file_path.unlink()
for created_filename in (
"phono3py.yaml",
"fc2.hdf5",
"fc3.hdf5",
"polymlp.yaml",
"phono3py_mlp_eval_dataset.yaml",
):
file_path = pathlib.Path(created_filename)
assert file_path.exists()
# Stage3 (memsize test)
argparse_control = _get_phono3py_load_args(
cwd_called / "phono3py.yaml",
fc_calculator="symfc",
fc_calculator_options="|memsize=0.05",
random_displacements="auto",
use_pypolymlp=True,
)
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
for created_filename in (
"fc3.hdf5",
"phono3py_mlp_eval_dataset.yaml",
):
file_path = pathlib.Path(created_filename)
assert file_path.exists()
file_path.unlink()
ph3 = phono3py.load(cwd_called / "phono3py_mlp_eval_dataset.yaml")
assert len(ph3.displacements) == 8
# Stage3 (memsize test)
argparse_control = _get_phono3py_load_args(
"phono3py.yaml",
fc_calculator="symfc",
fc_calculator_options="|memsize=0.05",
random_displacements="auto",
use_pypolymlp=True,
)
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
for created_filename in (
"phono3py.yaml",
"fc2.hdf5",
"fc3.hdf5",
"polymlp.yaml",
"phono3py_mlp_eval_dataset.yaml",
):
file_path = pathlib.Path(cwd_called / created_filename)
assert file_path.exists()
file_path.unlink()
ph3 = phono3py.load("phono3py_mlp_eval_dataset.yaml")
assert len(ph3.displacements) == 16
for created_filename in (
"phono3py.yaml",
"fc2.hdf5",
"fc3.hdf5",
"polymlp.yaml",
"phono3py_mlp_eval_dataset.yaml",
):
file_path = pathlib.Path(created_filename)
assert file_path.exists()
for created_filename in (
"fc3.hdf5",
"phono3py_mlp_eval_dataset.yaml",
):
file_path = pathlib.Path(created_filename)
assert file_path.exists()
file_path.unlink()
# Stage4 (number_estimation_factor)
argparse_control = _get_phono3py_load_args(
"phono3py.yaml",
fc_calculator="symfc",
fc_calculator_options="|cutoff=4.0",
random_displacements="auto",
rd_number_estimation_factor=2.0,
use_pypolymlp=True,
)
with pytest.raises(SystemExit) as excinfo:
main(**argparse_control)
assert excinfo.value.code == 0
ph3 = phono3py.load("phono3py_mlp_eval_dataset.yaml")
assert len(ph3.displacements) == 4
for created_filename in (
"phono3py.yaml",
"fc2.hdf5",
"fc3.hdf5",
"polymlp.yaml",
"phono3py_mlp_eval_dataset.yaml",
):
file_path = pathlib.Path(created_filename)
assert file_path.exists()
file_path.unlink()
finally:
os.chdir(original_cwd)
def _get_phono3py_load_args(
phono3py_yaml_filepath: Union[str, pathlib.Path],
fc_calculator: Optional[str] = None,
fc_calculator_options: Optional[str] = None,
phono3py_yaml_filepath: str | pathlib.Path,
fc_calculator: str | None = None,
fc_calculator_options: str | None = None,
load_phono3py_yaml: bool = True,
is_bterta: bool = False,
mesh_numbers: Optional[Sequence] = None,
mlp_params: Optional[str] = None,
random_displacements: Optional[Union[int, str]] = None,
temperatures: Optional[Sequence] = None,
mesh_numbers: Sequence | None = None,
mlp_params: str | None = None,
rd_number_estimation_factor: float | None = None,
random_displacements: int | str | None = None,
temperatures: Sequence | None = None,
use_pypolymlp: bool = False,
):
# Mock of ArgumentParser.args.
@ -350,6 +426,7 @@ def _get_phono3py_load_args(
log_level=1,
mesh_numbers=mesh_numbers,
mlp_params=mlp_params,
rd_number_estimation_factor=rd_number_estimation_factor,
random_displacements=random_displacements,
temperatures=temperatures,
use_pypolymlp=use_pypolymlp,
@ -364,6 +441,7 @@ def _get_phono3py_load_args(
is_bterta=is_bterta,
mesh_numbers=mesh_numbers,
mlp_params=mlp_params,
rd_number_estimation_factor=rd_number_estimation_factor,
random_displacements=random_displacements,
temperatures=temperatures,
use_pypolymlp=use_pypolymlp,

30
test/file_IO/test_file_IO.py
View File

@ -1,6 +1,8 @@
"""Tests of Phono3py API."""
import os
import pathlib
import tempfile
from collections.abc import Sequence
from typing import Optional
@ -11,7 +13,6 @@ from phono3py import Phono3py
from phono3py.file_IO import _get_filename_suffix
cwd = pathlib.Path(__file__).parent
cwd_called = pathlib.Path.cwd()
def test_kappa_filename():
@ -60,16 +61,25 @@ def test_kappa_hdf5_with_boundary_mpf(si_pbesol: Phono3py):
]
boundary_mfp = 10000.0
kappa_filename = _set_kappa(
si_pbesol, [4, 4, 4], write_kappa=True, boundary_mfp=boundary_mfp
)
file_path = pathlib.Path(cwd_called / kappa_filename)
with h5py.File(file_path, "r") as f:
np.testing.assert_almost_equal(f["boundary_mfp"][()], boundary_mfp)
assert set(list(f)) == set(key_ref)
if file_path.exists():
file_path.unlink()
with tempfile.TemporaryDirectory() as temp_dir:
original_cwd = pathlib.Path.cwd()
os.chdir(temp_dir)
try:
kappa_filename = _set_kappa(
si_pbesol, [4, 4, 4], write_kappa=True, boundary_mfp=boundary_mfp
)
file_path = pathlib.Path(kappa_filename)
with h5py.File(file_path, "r") as f:
np.testing.assert_almost_equal(f["boundary_mfp"][()], boundary_mfp)
assert set(list(f)) == set(key_ref)
if file_path.exists():
file_path.unlink()
finally:
os.chdir(original_cwd)
def _set_kappa(

1
test/phonon3/test_displacements.py
View File

@ -97,6 +97,7 @@ def test_random_disps_agno2(
number_of_snapshots=number_of_snapshots,
distance=distance,
is_plusminus=is_plusminus,
number_estimation_factor=2,
)
ph3.generate_fc2_displacements(