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phono3py
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Merge branch 'develop'

This commit is contained in:
Atsushi Togo 2024-08-23 22:37:53 +09:00
parent b828d78241 372f7cadde
commit 20d7c86621
11 changed files with 73 additions and 67 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: v0.5.6
rev: v0.6.1
hooks:
- id: ruff
args: [ "--fix", "--show-fixes" ]

4
doc/changelog.md
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@ -2,6 +2,10 @@
# Change Log
## Aug-23-2024: Version 3.4
- Update for spglib v2.5 and for following the change in phonopy.
## Aug-8-2024: Version 3.3.4
- Fix of command line user interface.

17
get_nanoversion.sh
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@ -1,17 +0,0 @@
#!/bin/bash
br=`git rev-parse HEAD`
echo $br
read o u f <<< `git remote -v |grep origin |grep fetch`
echo "Repo: $o $u $br"
git describe --tags --dirty
TD=`mktemp -d`
WD=`pwd`
git branch
git clone $u $TD
cd $TD
git checkout $br
echo $u $br
git describe --tags --dirty | sed -e 's/\([.0-9]*\)-\(.*\)-g.*/\2/' -e 's/^[vr]//g' -e 's/rc-//g' > $WD/__nanoversion__.txt
cd $WD
rm -rf "$TD"

8
phono3py/cui/create_force_constants.py
View File

@ -347,7 +347,7 @@ def _read_phono3py_fc3(phono3py: Phono3py, symmetrize_fc3r, input_filename, log_
filename = "fc3.hdf5"
else:
filename = "fc3." + input_filename + ".hdf5"
file_exists(filename, log_level)
file_exists(filename, log_level=log_level)
if log_level:
print('Reading fc3 from "%s".' % filename)
@ -380,7 +380,7 @@ def _read_phono3py_fc2(phono3py, symmetrize_fc2, input_filename, log_level):
filename = "fc2.hdf5"
else:
filename = "fc2." + input_filename + ".hdf5"
file_exists(filename, log_level)
file_exists(filename, log_level=log_level)
if log_level:
print('Reading fc2 from "%s".' % filename)
@ -494,7 +494,7 @@ def _read_dataset_fc3(
sys.exit(1)
except FileNotFoundError as e:
# from _get_type2_dataset
file_exists(e.filename, log_level)
file_exists(e.filename, log_level=log_level)
if use_pypolymlp:
phono3py.mlp_dataset = dataset
@ -672,7 +672,7 @@ def _read_dataset_fc2(
print_error()
sys.exit(1)
except FileNotFoundError as e:
file_exists(e.filename, log_level)
file_exists(e.filename, log_level=log_level)
if phono3py.phonon_supercell_matrix is not None:
phono3py.phonon_dataset = dataset

20
phono3py/cui/create_force_sets.py
View File

@ -77,7 +77,9 @@ def create_FORCES_FC3_and_FORCES_FC2(
]
if cell_filename is not None:
disp_filename_candidates.insert(0, cell_filename)
disp_filenames = files_exist(disp_filename_candidates, log_level, is_any=True)
disp_filenames = files_exist(
disp_filename_candidates, log_level=log_level, is_any=True
)
disp_filename = disp_filenames[0]
ph3py_yaml = Phono3pyYaml(settings={"force_sets": True})
ph3py_yaml.read(disp_filename)
@ -152,7 +154,7 @@ def create_FORCES_FC3_and_FORCES_FC2(
def create_FORCES_FC2_from_FORCE_SETS(log_level):
"""Convert FORCE_SETS to FORCES_FC2."""
filename = "FORCE_SETS"
file_exists(filename, log_level)
file_exists(filename, log_level=log_level)
disp_dataset = parse_FORCE_SETS(filename=filename)
write_FORCES_FC2(disp_dataset)
@ -189,8 +191,8 @@ def create_FORCE_SETS_from_FORCES_FCx(
len_first_line = get_length_of_first_line(f)
if len_first_line == 3:
file_exists(disp_filename, log_level)
file_exists(forces_filename, log_level)
file_exists(disp_filename, log_level=log_level)
file_exists(forces_filename, log_level=log_level)
ph3yml = Phono3pyYaml()
ph3yml.read(disp_filename)
if phonon_smat is None:
@ -242,7 +244,7 @@ def _get_force_sets_fc2(
force_filenames = settings.create_forces_fc2
for filename in force_filenames:
file_exists(filename, log_level)
file_exists(filename, log_level=log_level)
if log_level > 0:
print(f" Number of displacements: {num_disps}")
@ -258,7 +260,7 @@ def _get_force_sets_fc2(
if settings.subtract_forces:
force_filename = settings.subtract_forces
file_exists(force_filename, log_level)
file_exists(force_filename, log_level=log_level)
calc_dataset_zero = get_calc_dataset(
interface_mode,
num_atoms,
@ -301,13 +303,13 @@ def _get_force_sets_fc3(
raise RuntimeError("FC3 displacement dataset is broken.")
if settings.create_forces_fc3_file:
file_exists(settings.create_forces_fc3_file, log_level)
file_exists(settings.create_forces_fc3_file, log_level=log_level)
force_filenames = [x.strip() for x in open(settings.create_forces_fc3_file)]
else:
force_filenames = settings.create_forces_fc3
for filename in force_filenames:
file_exists(filename, log_level)
file_exists(filename, log_level=log_level)
if log_level > 0:
print(f" Number of displacements: {num_disps}")
@ -326,7 +328,7 @@ def _get_force_sets_fc3(
if settings.subtract_forces:
force_filename = settings.subtract_forces
file_exists(force_filename, log_level)
file_exists(force_filename, log_level=log_level)
calc_dataset = get_calc_dataset(
interface_mode,
num_atoms,

9
phono3py/cui/phono3py_script.py
View File

@ -114,7 +114,7 @@ def print_phono3py():
| .__/|_| |_|\___/|_| |_|\___/____/| .__/ \__, |
|_| |_| |___/ """
)
print_version(__version__)
print_version(__version__, package_name="phono3py")
print_time()
@ -244,7 +244,10 @@ def start_phono3py(**argparse_control) -> tuple[argparse.Namespace, int]:
print("Python version %d.%d.%d" % sys.version_info[:3])
import spglib
print("Spglib version %d.%d.%d" % spglib.get_version())
try: # spglib.get_version() is deprecated.
print(f"Spglib version {spglib.spg_get_version()}")
except AttributeError:
print("Spglib version %d.%d.%d" % spglib.get_version())
if deprecated:
show_deprecated_option_warnings(deprecated)
@ -264,7 +267,7 @@ def read_phono3py_settings(args, argparse_control, log_level):
load_phono3py_yaml = argparse_control.get("load_phono3py_yaml", False)
if len(args.filename) > 0:
file_exists(args.filename[0], log_level)
file_exists(args.filename[0], log_level=log_level)
if load_phono3py_yaml:
phono3py_conf_parser = Phono3pyConfParser(
filename=args.conf_filename,

62
phono3py/phonon/grid.py
View File

@ -38,6 +38,13 @@ from __future__ import annotations
import warnings
from collections.abc import Sequence
try:
from spglib import SpglibDataset
except ImportError:
from types import SimpleNamespace as SpglibDataset
from typing import Optional, Union
import numpy as np
@ -137,7 +144,7 @@ class BZGrid:
mesh: Union[int, float, Sequence, np.ndarray],
reciprocal_lattice=None,
lattice=None,
symmetry_dataset: Optional[dict] = None,
symmetry_dataset: Optional[Union[SpglibDataset]] = None,
transformation_matrix: Optional[Union[Sequence, np.ndarray]] = None,
is_shift: Optional[Union[list, np.ndarray]] = None,
is_time_reversal: bool = True,
@ -156,9 +163,10 @@ class BZGrid:
lattice : array_like
Direct primitive basis vectors given as row vectors shape=(3, 3),
dtype='double', order='C'
symmetry_dataset : dict, optional
symmetry_dataset : SpglibDataset, optional
Symmetry dataset (Symmetry.dataset) searched for the primitive cell
corresponding to ``reciprocal_lattice`` or ``lattice``.
corresponding to ``reciprocal_lattice`` or ``lattice``. For spglib <
v2.5, SimpleNamespace is used instead of SpglibDataset.
transformation_matrix : array_like, optional
Transformation matrix equivalent to ``transformation_matrix`` in
spglib-dataset. This is only used when ``use_grg=True`` and
@ -384,7 +392,7 @@ class BZGrid:
return self._reciprocal_operations
@property
def symmetry_dataset(self):
def symmetry_dataset(self) -> SpglibDataset:
"""Return Symmetry.dataset."""
return self._symmetry_dataset
@ -472,7 +480,7 @@ class BZGrid:
direct_rotations = np.eye(3, dtype="int_", order="C").reshape(1, 3, 3)
else:
direct_rotations = np.array(
self._symmetry_dataset["rotations"], dtype="int_", order="C"
self._symmetry_dataset.rotations, dtype="int_", order="C"
)
rec_rotations = np.zeros((48, 3, 3), dtype="int_", order="C")
num_rec_rot = recgrid.reciprocal_rotations(
@ -530,7 +538,7 @@ class GridMatrix:
self,
mesh: Union[int, float, Sequence, np.ndarray],
lattice: Union[Sequence, np.ndarray],
symmetry_dataset: Optional[dict] = None,
symmetry_dataset: Optional[SpglibDataset] = None,
transformation_matrix: Optional[Union[list, np.ndarray]] = None,
use_grg: bool = True,
force_SNF: bool = False,
@ -547,9 +555,10 @@ class GridMatrix:
lattice : array_like
Primitive basis vectors in direct space given as row vectors.
shape=(3, 3), dtype='double', order='C'
symmetry_dataset : dict, optional
symmetry_dataset : SpglibDataset, optional
Symmetry dataset of spglib (Symmetry.dataset) of primitive cell that
has `lattice`. Default is None.
has `lattice`. Default is None. For spglib <
v2.5, SimpleNamespace is used instead of SpglibDataset.
transformation_matrix : array_like, optional
Transformation matrix equivalent to ``transformation_matrix`` in
spglib-dataset. This is only used when ``use_grg=True`` and
@ -627,7 +636,7 @@ class GridMatrix:
self,
mesh: Union[int, float, Sequence, np.ndarray],
use_grg: bool = False,
symmetry_dataset: Optional[dict] = None,
symmetry_dataset: Optional[SpglibDataset] = None,
transformation_matrix: Optional[Union[list, np.ndarray]] = None,
force_SNF=False,
coordinates="reciprocal",
@ -673,7 +682,7 @@ class GridMatrix:
self._D_diag = length2mesh(length, self._lattice)
else:
self._D_diag = length2mesh(
length, self._lattice, rotations=symmetry_dataset["rotations"]
length, self._lattice, rotations=symmetry_dataset.rotations
)
if num_values == 9:
self._run_grg(
@ -703,7 +712,7 @@ class GridMatrix:
sym_dataset = symmetry_dataset
else: # transformation_matrix is not None
sym_dataset = self._get_mock_symmetry_dataset(transformation_matrix)
if is_primitive_cell(sym_dataset["rotations"]):
if is_primitive_cell(sym_dataset.rotations):
self._set_GRG_mesh(
sym_dataset,
length=length,
@ -742,18 +751,23 @@ class GridMatrix:
"be equal to or larger than 1."
)
raise RuntimeError(msg)
sym_dataset = {
"rotations": np.eye(3, dtype="intc", order="C").reshape(1, 3, 3),
"transformation_matrix": transformation_matrix,
"std_lattice": self._lattice,
"std_types": np.array([1], dtype="intc"),
"number": 1,
}
from types import SimpleNamespace
sym_dataset = SimpleNamespace(
**{
"rotations": np.eye(3, dtype="intc", order="C").reshape(1, 3, 3),
"transformation_matrix": transformation_matrix,
"std_lattice": self._lattice,
"std_types": np.array([1], dtype="intc"),
"number": 1,
}
)
return sym_dataset
def _set_GRG_mesh(
self,
sym_dataset: dict,
sym_dataset: SpglibDataset,
length: Optional[float] = None,
grid_matrix=None,
force_SNF=False,
@ -807,22 +821,22 @@ class GridMatrix:
`reciprocal` (default) or `direct`.
"""
tmat = sym_dataset["transformation_matrix"]
tmat = sym_dataset.transformation_matrix
conv_lat = np.dot(np.linalg.inv(tmat).T, self._lattice)
# GRG is wanted to be generated with respect to std_lattice if possible.
if _can_use_std_lattice(
conv_lat,
tmat,
sym_dataset["std_lattice"],
sym_dataset["rotations"],
sym_dataset.std_lattice,
sym_dataset.rotations,
):
conv_lat = sym_dataset["std_lattice"]
conv_lat = sym_dataset.std_lattice
tmat = np.dot(self._lattice, np.linalg.inv(conv_lat)).T
if coordinates == "direct":
num_cells = int(np.prod(length2mesh(length, conv_lat)))
max_num_atoms = num_cells * len(sym_dataset["std_types"])
max_num_atoms = num_cells * len(sym_dataset.std_types)
conv_mesh_numbers = estimate_supercell_matrix(
sym_dataset, max_num_atoms=max_num_atoms, max_iter=200
)

10
phono3py/phonon3/interaction.py
View File

@ -772,8 +772,8 @@ class Interaction:
# perms.shape = (len(spg_ops), len(primitive)), dtype='intc'
perms = compute_all_sg_permutations(
self._primitive.scaled_positions,
self._bz_grid.symmetry_dataset["rotations"],
self._bz_grid.symmetry_dataset["translations"],
self._bz_grid.symmetry_dataset.rotations,
self._bz_grid.symmetry_dataset.translations,
np.array(self._primitive.cell.T, dtype="double", order="C"),
symprec=self._symprec,
)
@ -821,13 +821,13 @@ class Interaction:
"""
d2r_map = []
for r in self._bz_grid.symmetry_dataset["rotations"]:
for r in self._bz_grid.symmetry_dataset.rotations:
for i, rec_r in enumerate(self._bz_grid.reciprocal_operations):
if (rec_r.T == r).all():
d2r_map.append(i)
break
assert len(d2r_map) == len(self._bz_grid.symmetry_dataset["rotations"])
assert len(d2r_map) == len(self._bz_grid.symmetry_dataset.rotations)
return d2r_map
@ -838,7 +838,7 @@ class Interaction:
"""
Rq = np.dot(self._bz_grid.QDinv, self._bz_grid.addresses[bzgp])
tau = self._bz_grid.symmetry_dataset["translations"][t_i]
tau = self._bz_grid.symmetry_dataset.translations[t_i]
phase_factor = np.exp(-2j * np.pi * np.dot(Rq, tau))
self._phonon_done[bzgp] = 1
self._frequencies[bzgp, :] = self._frequencies[orig_gp, :]

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__ = "3.3.4"
__version__ = "3.4.0"

2
pyproject.toml
View File

@ -16,7 +16,7 @@ dependencies = [
"matplotlib>=2.2.2",
"h5py>=3.0",
"spglib>=2.3",
"phonopy>=2.26,<2.27",
"phonopy>=2.27,<2.28",
]
license = { file = "LICENSE" }

4
test/phonon/test_grid.py
View File

@ -2425,7 +2425,7 @@ def test_GridMatrix_with_grid_matrix(ph_nacl: Phonopy):
np.testing.assert_array_equal(gm.grid_matrix, mesh)
np.testing.assert_array_equal(gm.D_diag, [9, 18, 18])
tmat = ph_nacl.primitive_symmetry.dataset["transformation_matrix"]
tmat = ph_nacl.primitive_symmetry.dataset.transformation_matrix
gm = GridMatrix(mesh, ph_nacl.primitive.cell, transformation_matrix=tmat)
np.testing.assert_array_equal(gm.grid_matrix, mesh)
np.testing.assert_array_equal(gm.D_diag, [9, 18, 18])
@ -2439,7 +2439,7 @@ def test_GridMatrix_with_transformation_matrix(ph_nacl: Phonopy):
"""
mesh = 50.0
tmat = ph_nacl.primitive_symmetry.dataset["transformation_matrix"]
tmat = ph_nacl.primitive_symmetry.dataset.transformation_matrix
gm = GridMatrix(
mesh,
ph_nacl.primitive.cell,