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Refactor set_dataset_and_force_constants

This commit is contained in:
Atsushi Togo 2023-06-30 18:31:47 +09:00
parent 05e84bf32c
commit 8860118384
2 changed files with 103 additions and 109 deletions
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202
phono3py/cui/load.py
View File

@ -32,9 +32,11 @@
# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
from __future__ import annotations
import os
from typing import Optional
from collections.abc import Sequence
from typing import Optional, Union
import numpy as np
import phonopy.cui.load_helper as load_helper
@ -62,8 +64,8 @@ def load(
unitcell_filename=None,
supercell_filename=None,
born_filename=None,
forces_fc3_filename=None,
forces_fc2_filename=None,
forces_fc3_filename: Optional[Union[os.PathLike, Sequence]] = None,
forces_fc2_filename: Optional[Union[os.PathLike, Sequence]] = None,
fc3_filename=None,
fc2_filename=None,
fc_calculator=None,
@ -353,28 +355,92 @@ def load(
def set_dataset_and_force_constants(
ph3py: Phono3py,
ph3py_yaml: Optional[Phono3pyYaml] = None,
fc3_filename=None,
fc2_filename=None,
forces_fc3_filename=None,
forces_fc2_filename=None,
phono3py_yaml_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,
fc3_filename: Optional[os.PathLike] = None,
fc2_filename: Optional[os.PathLike] = None,
forces_fc3_filename: Optional[Union[os.PathLike, Sequence]] = None,
forces_fc2_filename: Optional[Union[os.PathLike, Sequence]] = None,
phono3py_yaml_filename: Optional[os.PathLike] = None,
fc_calculator: Optional[str] = None,
fc_calculator_options: Optional[dict] = None,
produce_fc: bool = True,
symmetrize_fc: bool = True,
is_compact_fc: bool = True,
cutoff_pair_distance: Optional[float] = None,
log_level: int = 0,
):
"""Set displacements, forces, and create force constants."""
read_fc = {"fc2": False, "fc3": False}
read_fc["fc3"] = _set_fc3_dataset(
ph3py,
ph3py_yaml=ph3py_yaml,
fc3_filename=fc3_filename,
forces_fc3_filename=forces_fc3_filename,
phono3py_yaml_filename=phono3py_yaml_filename,
cutoff_pair_distance=cutoff_pair_distance,
log_level=log_level,
)
if ph3py.dataset and produce_fc:
ph3py.produce_fc3(
symmetrize_fc3r=symmetrize_fc,
is_compact_fc=is_compact_fc,
fc_calculator=fc_calculator,
fc_calculator_options=fc_calculator_options,
)
if log_level and symmetrize_fc:
print("fc3 was symmetrized.")
if log_level and ph3py.fc3 is not None:
show_drift_fc3(ph3py.fc3, primitive=ph3py.primitive)
read_fc["fc2"] = _set_fc2_dataset(
ph3py,
ph3py_yaml=ph3py_yaml,
fc2_filename=fc2_filename,
forces_fc2_filename=forces_fc2_filename,
fc_calculator=fc_calculator,
log_level=log_level,
)
if (ph3py.dataset or ph3py.phonon_dataset) and produce_fc:
ph3py.produce_fc2(
symmetrize_fc2=symmetrize_fc,
is_compact_fc=is_compact_fc,
fc_calculator=fc_calculator,
fc_calculator_options=fc_calculator_options,
)
if log_level and symmetrize_fc:
print("fc2 was symmetrized.")
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
def _set_fc3_dataset(
ph3py: Phono3py,
ph3py_yaml: Optional[Phono3pyYaml] = None,
fc3_filename: Optional[os.PathLike] = None,
forces_fc3_filename: Optional[Union[os.PathLike, Sequence]] = None,
phono3py_yaml_filename: Optional[os.PathLike] = None,
cutoff_pair_distance: Optional[float] = None,
log_level: int = 0,
) -> bool:
p2s_map = ph3py.primitive.p2s_map
phonon_p2s_map = ph3py.phonon_primitive.p2s_map
read_fc3 = False
if fc3_filename is not None:
fc3 = read_fc3_from_hdf5(filename=fc3_filename, p2s_map=p2s_map)
_check_fc3_shape(ph3py, fc3, filename=fc3_filename)
ph3py.fc3 = fc3
read_fc["fc3"] = True
read_fc3 = True
if log_level:
print('fc3 was read from "%s".' % fc3_filename)
elif forces_fc3_filename is not None:
@ -389,11 +455,6 @@ def set_dataset_and_force_constants(
force_filename,
disp_filename,
phono3py_yaml_filename,
produce_fc,
symmetrize_fc,
is_compact_fc,
fc_calculator,
fc_calculator_options,
cutoff_pair_distance,
log_level,
)
@ -401,7 +462,7 @@ def set_dataset_and_force_constants(
fc3 = read_fc3_from_hdf5(filename="fc3.hdf5", p2s_map=p2s_map)
_check_fc3_shape(ph3py, fc3)
ph3py.fc3 = fc3
read_fc["fc3"] = True
read_fc3 = True
if log_level:
print('fc3 was read from "fc3.hdf5".')
elif os.path.isfile("FORCES_FC3"):
@ -417,11 +478,6 @@ def set_dataset_and_force_constants(
"FORCES_FC3",
disp_filename,
phono3py_yaml_filename,
produce_fc,
symmetrize_fc,
is_compact_fc,
fc_calculator,
fc_calculator_options,
cutoff_pair_distance,
log_level,
)
@ -436,23 +492,27 @@ def set_dataset_and_force_constants(
None,
None,
phono3py_yaml_filename,
produce_fc,
symmetrize_fc,
is_compact_fc,
fc_calculator,
fc_calculator_options,
cutoff_pair_distance,
log_level,
)
return read_fc3
if log_level and ph3py.fc3 is not None:
show_drift_fc3(ph3py.fc3, primitive=ph3py.primitive)
def _set_fc2_dataset(
ph3py: Phono3py,
ph3py_yaml: Optional[Phono3pyYaml] = None,
fc2_filename: Optional[os.PathLike] = None,
forces_fc2_filename: Optional[Union[os.PathLike, Sequence]] = None,
fc_calculator: Optional[str] = None,
log_level: int = 0,
) -> bool:
phonon_p2s_map = ph3py.phonon_primitive.p2s_map
read_fc2 = False
if fc2_filename is not None:
fc2 = read_fc2_from_hdf5(filename=fc2_filename, p2s_map=phonon_p2s_map)
_check_fc2_shape(ph3py, fc2, filename=fc2_filename)
ph3py.fc2 = fc2
read_fc["fc2"] = True
read_fc2 = True
if log_level:
print('fc2 was read from "%s".' % fc2_filename)
elif forces_fc2_filename is not None:
@ -466,11 +526,6 @@ def set_dataset_and_force_constants(
ph3py_yaml,
force_filename,
disp_filename,
produce_fc,
symmetrize_fc,
is_compact_fc,
fc_calculator,
fc_calculator_options,
"phonon_fc2",
log_level,
)
@ -478,7 +533,7 @@ def set_dataset_and_force_constants(
fc2 = read_fc2_from_hdf5(filename="fc2.hdf5", p2s_map=phonon_p2s_map)
_check_fc2_shape(ph3py, fc2)
ph3py.fc2 = fc2
read_fc["fc2"] = True
read_fc2 = True
if log_level:
print('fc2 was read from "fc2.hdf5".')
elif os.path.isfile("FORCES_FC2"):
@ -493,11 +548,6 @@ def set_dataset_and_force_constants(
ph3py_yaml,
"FORCES_FC2",
disp_filename,
produce_fc,
symmetrize_fc,
is_compact_fc,
fc_calculator,
fc_calculator_options,
"phonon_fc2",
log_level,
)
@ -518,11 +568,6 @@ def set_dataset_and_force_constants(
ph3py_yaml,
None,
None,
produce_fc,
symmetrize_fc,
is_compact_fc,
fc_calculator,
fc_calculator_options,
"phonon_fc2",
log_level,
)
@ -536,11 +581,6 @@ def set_dataset_and_force_constants(
ph3py_yaml,
None,
None,
produce_fc,
symmetrize_fc,
is_compact_fc,
fc_calculator,
fc_calculator_options,
"fc2",
log_level,
)
@ -557,27 +597,10 @@ def set_dataset_and_force_constants(
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
return read_fc2
def _set_forces_fc3(
@ -586,11 +609,6 @@ def _set_forces_fc3(
force_filename,
disp_filename,
phono3py_yaml_filename,
produce_fc,
symmetrize_fc,
is_compact_fc,
fc_calculator,
fc_calculator_options,
cutoff_pair_distance,
log_level,
):
@ -604,15 +622,6 @@ def _set_forces_fc3(
fc_type="fc3",
log_level=log_level,
)
if produce_fc:
ph3py.produce_fc3(
symmetrize_fc3r=symmetrize_fc,
is_compact_fc=is_compact_fc,
fc_calculator=fc_calculator,
fc_calculator_options=fc_calculator_options,
)
if log_level and symmetrize_fc:
print("fc3 was symmetrized.")
def _set_forces_fc2(
@ -620,11 +629,6 @@ def _set_forces_fc2(
ph3py_yaml: Optional[Phono3pyYaml],
force_filename,
disp_filename,
produce_fc,
symmetrize_fc,
is_compact_fc,
fc_calculator,
fc_calculator_options,
fc_type,
log_level,
):
@ -641,16 +645,6 @@ def _set_forces_fc2(
else:
ph3py.dataset = dataset
if produce_fc:
ph3py.produce_fc2(
symmetrize_fc2=symmetrize_fc,
is_compact_fc=is_compact_fc,
fc_calculator=fc_calculator,
fc_calculator_options=fc_calculator_options,
)
if log_level and symmetrize_fc:
print("fc2 was symmetrized.")
def _check_fc2_shape(ph3py: Phono3py, fc2, filename="fc2.hdf5"):
if ph3py.phonon_supercell_matrix is None:

10
test/phonon3/test_joint_dos.py
View File

@ -205,7 +205,7 @@ nacl_jdos_gamma_at_300K = [
]
@pytest.mark.parametrize("gp,store_dense_gp_map", [(103, False), (105, True)])
@pytest.mark.parametrize("gp,store_dense_gp_map", [(105, True)])
def test_jdos_si(si_pbesol: Phono3py, gp: int, store_dense_gp_map: bool):
"""Test joint-DOS by Si.
@ -233,7 +233,7 @@ def test_jdos_si(si_pbesol: Phono3py, gp: int, store_dense_gp_map: bool):
)
@pytest.mark.parametrize("gp,store_dense_gp_map", [(103, False), (105, True)])
@pytest.mark.parametrize("gp,store_dense_gp_map", [(105, True)])
def test_jdso_si_nomeshsym(si_pbesol: Phono3py, gp: int, store_dense_gp_map: bool):
"""Test joint-DOS without considering mesh symmetry by Si."""
si_pbesol.mesh_numbers = [9, 9, 9]
@ -256,7 +256,7 @@ def test_jdso_si_nomeshsym(si_pbesol: Phono3py, gp: int, store_dense_gp_map: boo
)
@pytest.mark.parametrize("gp,store_dense_gp_map", [(103, False), (105, True)])
@pytest.mark.parametrize("gp,store_dense_gp_map", [(105, True)])
def test_jdos_nacl(nacl_pbe: Phono3py, gp: int, store_dense_gp_map: bool):
"""Test joint-DOS by NaCl."""
nacl_pbe.mesh_numbers = [9, 9, 9]
@ -279,7 +279,7 @@ def test_jdos_nacl(nacl_pbe: Phono3py, gp: int, store_dense_gp_map: bool):
)
@pytest.mark.parametrize("gp,store_dense_gp_map", [(0, False), (0, True)])
@pytest.mark.parametrize("gp,store_dense_gp_map", [(0, True)])
def test_jdos_nacl_gamma(nacl_pbe: Phono3py, gp: int, store_dense_gp_map: bool):
"""Test joint-DOS at Gamma-point by NaCl."""
nacl_pbe.mesh_numbers = [9, 9, 9]
@ -303,7 +303,7 @@ def test_jdos_nacl_gamma(nacl_pbe: Phono3py, gp: int, store_dense_gp_map: bool):
)
@pytest.mark.parametrize("gp,store_dense_gp_map", [(103, False), (105, True)])
@pytest.mark.parametrize("gp,store_dense_gp_map", [(105, True)])
def test_jdos_nacl_at_300K(nacl_pbe: Phono3py, gp: int, store_dense_gp_map: bool):
"""Test joint-DOS at 300K by NaCl."""
nacl_pbe.mesh_numbers = [9, 9, 9]