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Fix broken data structure related to phonon_supercell_matrix etc #231

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merged 1 commit into from
Jun 6, 2024
Merged

Fix broken data structure related to phonon_supercell_matrix etc #231

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32 changes: 19 additions & 13 deletions phono3py/cui/load.py
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,7 @@
from __future__ import annotations

import os
import pathlib
from collections.abc import Sequence
from typing import Optional, Union

Expand Down Expand Up @@ -390,14 +391,13 @@ def set_dataset_and_force_constants(
cutoff_pair_distance=cutoff_pair_distance,
log_level=log_level,
)
if ph3py.phonon_supercell_matrix is not None:
read_fc["fc2"] = _set_dataset_phonon_dataset_or_fc2(
ph3py,
ph3py_yaml=ph3py_yaml,
fc2_filename=fc2_filename,
forces_fc2_filename=forces_fc2_filename,
log_level=log_level,
)
read_fc["fc2"] = _set_dataset_phonon_dataset_or_fc2(
ph3py,
ph3py_yaml=ph3py_yaml,
fc2_filename=fc2_filename,
forces_fc2_filename=forces_fc2_filename,
log_level=log_level,
)

# Cases that dataset is in phono3py.yaml but not forces.
if ph3py.dataset is None:
Expand Down Expand Up @@ -487,14 +487,14 @@ def _set_dataset_or_fc3(
cutoff_pair_distance,
log_level,
)
elif os.path.isfile("fc3.hdf5"):
elif pathlib.Path("fc3.hdf5").exists():
fc3 = read_fc3_from_hdf5(filename="fc3.hdf5", p2s_map=p2s_map)
_check_fc3_shape(ph3py, fc3)
ph3py.fc3 = fc3
read_fc3 = True
if log_level:
print('fc3 was read from "fc3.hdf5".')
elif os.path.isfile("FORCES_FC3"):
elif pathlib.Path("FORCES_FC3").exists():
_set_dataset_for_fc3(
ph3py,
ph3py_yaml,
Expand Down Expand Up @@ -544,14 +544,17 @@ def _set_dataset_phonon_dataset_or_fc2(
"phonon_fc2",
log_level,
)
elif os.path.isfile("fc2.hdf5"):
elif pathlib.Path("fc2.hdf5").exists():
fc2 = read_fc2_from_hdf5(filename="fc2.hdf5", p2s_map=phonon_p2s_map)
_check_fc2_shape(ph3py, fc2)
ph3py.fc2 = fc2
read_fc2 = True
if log_level:
print('fc2 was read from "fc2.hdf5".')
elif os.path.isfile("FORCES_FC2"):
elif (
pathlib.Path("FORCES_FC2").exists()
and ph3py.phonon_supercell_matrix is not None
):
_set_dataset_for_fc2(
ph3py,
ph3py_yaml,
Expand Down Expand Up @@ -583,7 +586,10 @@ def _set_dataset_phonon_dataset_or_fc2(
"fc2",
log_level,
)
elif os.path.isfile("FORCES_FC3"):
elif (
pathlib.Path("FORCES_FC3").exists()
and ph3py.phonon_supercell_matrix is not None
):
# suppose fc3.hdf5 is read but fc2.hdf5 doesn't exist.
_set_dataset_for_fc2(
ph3py,
Expand Down
33 changes: 16 additions & 17 deletions phono3py/interface/phono3py_yaml.py
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Original file line number Diff line number Diff line change
Expand Up @@ -115,18 +115,18 @@ def _parse_all_cells(self):

"""
super()._parse_all_cells()
if "phonon_primitive_cell" in self._yaml:
self._data.phonon_primitive = self._parse_cell(
self._yaml["phonon_primitive_cell"]
)
if "phonon_supercell" in self._yaml:
self._data.phonon_supercell = self._parse_cell(
self._yaml["phonon_supercell"]
)
if "phonon_supercell_matrix" in self._yaml:
self._data.phonon_supercell_matrix = np.array(
self._yaml["phonon_supercell_matrix"], dtype="intc", order="C"
)
if "phonon_primitive_cell" in self._yaml:
self._data.phonon_primitive = self._parse_cell(
self._yaml["phonon_primitive_cell"]
)
if "phonon_supercell" in self._yaml:
self._data.phonon_supercell = self._parse_cell(
self._yaml["phonon_supercell"]
)

def _parse_dataset(self):
"""Parse phonon_dataset.
Expand All @@ -137,8 +137,6 @@ def _parse_dataset(self):
self._data.phonon_dataset = self._get_dataset(
self._data.phonon_supercell, key_prefix="phonon_"
)
if self._data.phonon_dataset is None:
self._data.phonon_dataset = self._get_dataset(self._data.phonon_supercell)

def _parse_fc3_dataset(self):
"""Parse force dataset for fc3.
Expand Down Expand Up @@ -286,13 +284,14 @@ def _cell_info_yaml_lines(self):

"""
lines = super()._cell_info_yaml_lines()
lines += self._supercell_matrix_yaml_lines(
self._data.phonon_supercell_matrix, "phonon_supercell_matrix"
)
lines += self._primitive_yaml_lines(
self._data.phonon_primitive, "phonon_primitive_cell"
)
lines += self._phonon_supercell_yaml_lines()
if self._data.phonon_supercell_matrix is not None:
lines += self._supercell_matrix_yaml_lines(
self._data.phonon_supercell_matrix, "phonon_supercell_matrix"
)
lines += self._primitive_yaml_lines(
self._data.phonon_primitive, "phonon_primitive_cell"
)
lines += self._phonon_supercell_yaml_lines()
return lines

def _phonon_supercell_yaml_lines(self):
Expand Down
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