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Preparationg for v3 release

This commit is contained in:
Atsushi Togo 2024-04-19 14:47:15 +09:00
parent 427e00463c
commit ac874d115f
16 changed files with 150 additions and 757 deletions
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13
doc/auxiliary-tools.md
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@ -39,21 +39,18 @@ Let's computer lattice thermal conductivity of Si using the `Si-PBEsol` example
found in the example directory.
```bash
% phono3py --dim="2 2 2" --pa="F" -c POSCAR-unitcell --mesh="11 11 11" --sym-fc --br
% phono3py --mesh="11 11 11" --sym-fc --br
```
Then using the output file, `kappa-m111111.hdf5`, run `phono3py-kaccum` as
follows:
```bash
% phono3py-kaccum --pa="F" -c POSCAR-unitcell kappa-m111111.hdf5 |tee kaccum.dat
% phono3py-kaccum kappa-m111111.hdf5 |tee kaccum.dat
```
Here `--pa` is optional. The definition of `--pa` option is same as
{ref}`pa_option`. `POSCAR-unitcell` is the unit cell filename that is specified
with `-c` option. `kappa-m111111.hdf5` is the output file of thermal
conductivity calculation, which is passed to `phono3py-kaccum` as the first
argument.
`kappa-m111111.hdf5` is the output file of thermal conductivity calculation,
which is passed to `phono3py-kaccum` as the first argument.
The format of the output is as follows: The first column gives frequency in THz,
and the second to seventh columns give the cumulative lattice thermal
@ -99,7 +96,7 @@ Let `phono3py-kaccum` read a QE (pw) unit cell file with `-c` option, for
example:
```bash
% phono3py-kaccum --qe --pa="F" -c Si.in kappa-m191919.hdf5
% phono3py-kaccum --qe kappa-m191919.hdf5
```
```{image} Si-kaccum-pwscf.png

20
doc/changelog.md
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@ -2,6 +2,24 @@
# Change Log
## Apr-19-2024: Version 3.0.0
This is a major version release. There are backward-incompatible changes.
- Method to transform supercell third-order force constants fc3 in real to
reciprocal space was changed as described at Version 2.9.0 changelog below.
This results in the change of results with respect to those obtained by
phono3py version 2. To emulate v2 behaviour, use `--v2` option in phono3py
command line script. For `Phono3py` class , `make_r0_average=True` (default)
when instantiating it, and similarly for `phono3py.load` function.
- Completely dropped support of `disp_fc3.yaml` and `disp_fc2.yaml`.
- Dropped support of old style usage of `phono3py-kaccum` script.
- Removed functions `write_fc3_dat`, `write_triplets`, `write_grid_address` in
`file_IO.py`.
- Removed methods marked by `DeprecationWarning`.
- Removed `masses`, `band_indices`, `sigmas`, `sigma_cutoff` parameters from
`Phono3py.__init__()`.
## Mar-20-2024: Version 2.10.0
- Maintenance release
@ -100,7 +118,7 @@
## Jul-22-2021: Version 2.0.0
This is a major version release. There are some backword-incompatible changes.
This is a major version release. There are some backward-incompatible changes.
1. Grid point indexing system to address grid points of q-points is changed.
2. Array data types of most of the integer arrays are changed to `dtype='int_'`

4
doc/conf.py
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@ -58,9 +58,9 @@ copyright = "2015, Atsushi Togo"
# built documents.
#
# The short X.Y version.
version = "2.10"
version = "3.0"
# The full version, including alpha/beta/rc tags.
release = "2.10.0"
release = "3.0.0"
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.

306
phono3py/api_phono3py.py
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@ -34,7 +34,6 @@
# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
import warnings
from collections.abc import Sequence
from typing import Optional, Union
@ -144,17 +143,13 @@ class Phono3py:
supercell_matrix=None,
primitive_matrix=None,
phonon_supercell_matrix=None,
masses=None,
band_indices=None,
sigmas=None,
sigma_cutoff=None,
cutoff_frequency=1e-4,
frequency_factor_to_THz=VaspToTHz,
is_symmetry=True,
is_mesh_symmetry=True,
use_grg=False,
SNF_coordinates="reciprocal",
make_r0_average: bool = False,
make_r0_average: bool = True,
symprec=1e-5,
calculator: Optional[str] = None,
log_level=0,
@ -185,14 +180,6 @@ class Phono3py:
than that of fc3. Unless setting this, supercell_matrix is used.
This is only valide when unitcell or unitcell_filename is given.
Default is None.
masses : Deprecated.
Use Phono3py.masses attribute after instanciation.
band_indices : Deprecated.
Use Phono3py.band_indices attribute after instanciation.
sigmas : Deprecated.
Use Phono3py.sigmas attribute after instanciation.
sigma_cutoff : Deprecated.
Use Phono3py.sigma_cutoff attribute after instanciation.
cutoff_frequency : float, optional
Phonon frequency below this value is ignored when the cutoff is
needed for the computation. Default is 1e-4.
@ -308,38 +295,6 @@ class Phono3py:
self._band_indices_flatten = None
self._set_band_indices()
if masses is not None:
warnings.warn(
"Phono3py init parameter of masses is deprecated. "
"Use Phono3py.masses attribute instead.",
DeprecationWarning,
)
self.masses = masses
if band_indices is not None:
warnings.warn(
"Phono3py init parameter of band_indices is deprecated. "
"Use Phono3py.band_indices attribute instead.",
DeprecationWarning,
)
self.band_indices = band_indices
if sigmas is not None:
warnings.warn(
"Phono3py init parameter of sigmas is deprecated. "
"Use Phono3py.sigmas attribute instead.",
DeprecationWarning,
)
self.sigmas = sigmas
if sigma_cutoff is not None:
warnings.warn(
"Phono3py init parameter of sigma_cutoff is deprecated. "
"Use Phono3py.sigma_cutoff attribute instead.",
DeprecationWarning,
)
self.sigma_cutoff = sigma_cutoff
@property
def version(self):
"""Return phono3py release version number.
@ -350,15 +305,6 @@ class Phono3py:
"""
return __version__
def get_version(self):
"""Return phono3py release version number."""
warnings.warn(
"Phono3py.get_version() is deprecated."
"Use Phono3py.version attribute instead.",
DeprecationWarning,
)
return self.version
@property
def calculator(self) -> Optional[str]:
"""Return calculator interface name.
@ -386,22 +332,6 @@ class Phono3py:
def fc3(self, fc3):
self._fc3 = fc3
def get_fc3(self):
"""Return third order force constants (fc3)."""
warnings.warn(
"Phono3py.get_fc3() is deprecated." "Use Phono3py.fc3 attribute instead.",
DeprecationWarning,
)
return self.fc3
def set_fc3(self, fc3):
"""Set fc3."""
warnings.warn(
"Phono3py.set_fc3() is deprecated." "Use Phono3py.fc3 attribute instead.",
DeprecationWarning,
)
self.fc3 = fc3
@property
def fc2(self):
"""Setter and getter of second order force constants (fc2).
@ -419,22 +349,6 @@ class Phono3py:
def fc2(self, fc2):
self._fc2 = fc2
def get_fc2(self):
"""Return second order force constants (fc2)."""
warnings.warn(
"Phono3py.get_fc2() is deprecated." "Use Phono3py.fc2 attribute instead.",
DeprecationWarning,
)
return self.fc2
def set_fc2(self, fc2):
"""Set fc2."""
warnings.warn(
"Phono3py.set_fc2() is deprecated." "Use Phono3py.fc2 attribute instead.",
DeprecationWarning,
)
self.fc2 = fc2
@property
def force_constants(self):
"""Return fc2. This is same as the getter attribute `fc2`."""
@ -511,24 +425,6 @@ class Phono3py:
if self._interaction is not None:
self._init_dynamical_matrix()
def get_nac_params(self):
"""Return NAC parameters."""
warnings.warn(
"Phono3py.get_nac_params() is deprecated."
"Use Phono3py.nac_params attribute instead.",
DeprecationWarning,
)
return self.nac_params
def set_nac_params(self, nac_params):
"""Set NAC parameters."""
warnings.warn(
"Phono3py.set_nac_params() is deprecated."
"Use Phono3py.nac_params attribute instead.",
DeprecationWarning,
)
self.nac_params = nac_params
@property
def dynamical_matrix(self):
"""Return DynamicalMatrix instance.
@ -552,15 +448,6 @@ class Phono3py:
"""
return self._primitive
def get_primitive(self):
"""Return primitive cell."""
warnings.warn(
"Phono3py.get_primitive() is deprecated."
"Use Phono3py.primitive attribute instead.",
DeprecationWarning,
)
return self.primitive
@property
def unitcell(self) -> PhonopyAtoms:
"""Return Unit cell.
@ -571,15 +458,6 @@ class Phono3py:
"""
return self._unitcell
def get_unitcell(self):
"""Return Unit cell."""
warnings.warn(
"Phono3py.get_unitcell() is deprecated."
"Use Phono3py.unitcell attribute instead.",
DeprecationWarning,
)
return self.unitcell
@property
def supercell(self) -> Supercell:
"""Return supercell.
@ -590,15 +468,6 @@ class Phono3py:
"""
return self._supercell
def get_supercell(self):
"""Return supercell."""
warnings.warn(
"Phono3py.get_supercell() is deprecated."
"Use Phono3py.supercell attribute instead.",
DeprecationWarning,
)
return self.supercell
@property
def phonon_supercell(self) -> Supercell:
"""Return supercell for fc2.
@ -609,15 +478,6 @@ class Phono3py:
"""
return self._phonon_supercell
def get_phonon_supercell(self):
"""Return supercell for fc2."""
warnings.warn(
"Phono3py.get_phonon_supercell() is deprecated."
"Use Phono3py.phonon_supercell attribute instead.",
DeprecationWarning,
)
return self.phonon_supercell
@property
def phonon_primitive(self) -> Primitive:
"""Return primitive cell for fc2.
@ -630,15 +490,6 @@ class Phono3py:
"""
return self._phonon_primitive
def get_phonon_primitive(self):
"""Return primitive cell for fc2."""
warnings.warn(
"Phono3py.get_phonon_primitive() is deprecated."
"Use Phono3py.phonon_primitive attribute instead.",
DeprecationWarning,
)
return self.phonon_primitive
@property
def symmetry(self) -> Symmetry:
"""Return symmetry of supercell.
@ -649,15 +500,6 @@ class Phono3py:
"""
return self._symmetry
def get_symmetry(self):
"""Return symmetry of supercell."""
warnings.warn(
"Phono3py.get_symmetry() is deprecated."
"Use Phono3py.symmetry attribute instead.",
DeprecationWarning,
)
return self.symmetry
@property
def primitive_symmetry(self) -> Symmetry:
"""Return symmetry of primitive cell.
@ -668,15 +510,6 @@ class Phono3py:
"""
return self._primitive_symmetry
def get_primitive_symmetry(self):
"""Return symmetry of primitive cell."""
warnings.warn(
"Phono3py.get_primitive_symmetry() is deprecated."
"Use Phono3py.primitive_symmetry attribute instead.",
DeprecationWarning,
)
return self.primitive_symmetry
@property
def phonon_supercell_symmetry(self) -> Symmetry:
"""Return symmetry of supercell for fc2.
@ -687,15 +520,6 @@ class Phono3py:
"""
return self._phonon_supercell_symmetry
def get_phonon_supercell_symmetry(self):
"""Return symmetry of supercell for fc2."""
warnings.warn(
"Phono3py.get_phonon_supercell_symmetry() is deprecated."
"Use Phono3py.phonon_supercell_symmetry attribute instead.",
DeprecationWarning,
)
return self.phonon_supercell_symmetry
@property
def supercell_matrix(self):
"""Return transformation matrix to supercell cell from unit cell.
@ -707,15 +531,6 @@ class Phono3py:
"""
return self._supercell_matrix
def get_supercell_matrix(self):
"""Return transformation matrix to supercell cell from unit cell."""
warnings.warn(
"Phono3py.get_supercell_matrix() is deprecated."
"Use Phono3py.supercell_matrix attribute instead.",
DeprecationWarning,
)
return self.supercell_matrix
@property
def phonon_supercell_matrix(self):
"""Return transformation matrix to phonon supercell from unit cell.
@ -727,15 +542,6 @@ class Phono3py:
"""
return self._phonon_supercell_matrix
def get_phonon_supercell_matrix(self):
"""Return transformation matrix to phonon supercell from unit cell."""
warnings.warn(
"Phono3py.get_phonon_supercell_matrix() is deprecated."
"Use Phono3py.phonon_supercell_matrix attribute instead.",
DeprecationWarning,
)
return self.phonon_supercell_matrix
@property
def primitive_matrix(self):
"""Return transformation matrix to primitive cell from unit cell.
@ -747,15 +553,6 @@ class Phono3py:
"""
return self._primitive_matrix
def get_primitive_matrix(self):
"""Return transformation matrix to primitive cell from unit cell."""
warnings.warn(
"Phono3py.get_primitive_matrix() is deprecated."
"Use Phono3py.primitive_matrix attribute instead.",
DeprecationWarning,
)
return self.primitive_matrix
@property
def unit_conversion_factor(self):
"""Return phonon frequency unit conversion factor.
@ -768,15 +565,6 @@ class Phono3py:
"""
return self._frequency_factor_to_THz
def set_displacement_dataset(self, dataset):
"""Set displacement-force dataset."""
warnings.warn(
"Phono3py.set_displacement_dataset() is deprecated."
"Use Phono3py.dataset attribute instead.",
DeprecationWarning,
)
self._dataset = dataset
@property
def dataset(self):
"""Setter and getter of displacement-force dataset.
@ -823,24 +611,6 @@ class Phono3py:
self._supercells_with_displacements = None
self._phonon_supercells_with_displacements = None
@property
def displacement_dataset(self):
"""Return displacement-force dataset."""
warnings.warn(
"Phono3py.displacement_dataset is deprecated." "Use Phono3py.dataset.",
DeprecationWarning,
)
return self.dataset
def get_displacement_dataset(self):
"""Return displacement-force dataset."""
warnings.warn(
"Phono3py.get_displacement_dataset() is deprecated."
"Use Phono3py.dataset.",
DeprecationWarning,
)
return self.displacement_dataset
@property
def phonon_dataset(self):
"""Setter and getter of displacement-force dataset for fc2.
@ -869,25 +639,6 @@ class Phono3py:
def phonon_dataset(self, dataset):
self._phonon_dataset = dataset
@property
def phonon_displacement_dataset(self):
"""Return phonon dispalcement-force dataset."""
warnings.warn(
"Phono3py.phonon_displacement_dataset is deprecated."
"Use Phono3py.phonon_dataset.",
DeprecationWarning,
)
return self._phonon_dataset
def get_phonon_displacement_dataset(self):
"""Return phonon dispalcement-force dataset."""
warnings.warn(
"Phono3py.get_phonon_displacement_dataset() is deprecated."
"Use Phono3py.phonon_dataset.",
DeprecationWarning,
)
return self.phonon_displacement_dataset
@property
def band_indices(self):
"""Setter and getter of band indices.
@ -903,15 +654,6 @@ class Phono3py:
def band_indices(self, band_indices):
self._set_band_indices(band_indices=band_indices)
def set_band_indices(self, band_indices):
"""Set band indices."""
warnings.warn(
"Phono3py.set_band_indices() is deprecated."
"Use Phono3py.band_indices attribute instead.",
DeprecationWarning,
)
self.band_indices = band_indices
def _set_band_indices(self, band_indices=None):
if band_indices is None:
num_band = len(self._primitive) * 3
@ -955,15 +697,6 @@ class Phono3py:
self._build_supercells_with_displacements()
return self._supercells_with_displacements
def get_supercells_with_displacements(self):
"""Return supercells with displacements."""
warnings.warn(
"Phono3py.get_supercells_with_displacements() is deprecated."
"Use Phono3py.supercells_with_displacements attribute instead.",
DeprecationWarning,
)
return self.supercells_with_displacements
@property
def phonon_supercells_with_displacements(self):
"""Return supercells with displacements for fc2.
@ -982,16 +715,6 @@ class Phono3py:
)
return self._phonon_supercells_with_displacements
def get_phonon_supercells_with_displacements(self):
"""Return supercells with displacements for fc2."""
warnings.warn(
"Phono3py.get_phonon_supercells_with_displacements() "
"is deprecated. Use Phono3py.phonon_supercells_with_displacements "
"attribute instead.",
DeprecationWarning,
)
return self.phonon_supercells_with_displacements
@property
def mesh_numbers(self):
"""Setter and getter of sampling mesh numbers in reciprocal space."""
@ -1009,15 +732,6 @@ class Phono3py:
"""Return thermal conductivity class instance."""
return self._thermal_conductivity
def get_thermal_conductivity(self):
"""Return thermal conductivity class instance."""
warnings.warn(
"Phono3py.get_thermal_conductivity() is deprecated."
"Use Phono3py.thermal_conductivity attribute instead.",
DeprecationWarning,
)
return self.thermal_conductivity
@property
def displacements(self):
"""Setter and getter displacements in supercells.
@ -1261,15 +975,6 @@ class Phono3py:
"""Return Interaction instance."""
return self._interaction
def get_phph_interaction(self):
"""Return Interaction instance."""
warnings.warn(
"Phono3py.get_phph_interaction() is deprecated."
"Use Phono3py.phph_interaction attribute instead.",
DeprecationWarning,
)
return self.phph_interaction
@property
def detailed_gammas(self):
"""Return detailed gamma."""
@ -1880,15 +1585,6 @@ class Phono3py:
return vals
def write_imag_self_energy(self, filename=None):
"""Write imaginary part of self energy to a file."""
warnings.warn(
"Phono3py.write_imag_self_energy is deprecated."
"Use Phono3py.run_imag_self_energy with write_txt=True.",
DeprecationWarning,
)
self._write_imag_self_energy(output_filename=filename)
def _write_imag_self_energy(self, output_filename=None):
write_imag_self_energy(
self._gammas,

104
phono3py/cui/create_force_constants.py
View File

@ -54,8 +54,6 @@ from phono3py import Phono3py
from phono3py.cui.show_log import show_phono3py_force_constants_settings
from phono3py.file_IO import (
get_length_of_first_line,
parse_disp_fc2_yaml,
parse_disp_fc3_yaml,
parse_FORCES_FC2,
parse_FORCES_FC3,
read_fc2_from_hdf5,
@ -117,7 +115,6 @@ def create_phono3py_force_constants(
ph3py_yaml,
phono3py_yaml_filename,
symmetrize_fc3r,
input_filename,
settings.is_compact_fc,
settings.cutoff_pair_distance,
fc_calculator,
@ -167,7 +164,6 @@ def create_phono3py_force_constants(
phono3py,
ph3py_yaml,
symmetrize_fc2,
input_filename,
settings.is_compact_fc,
fc_calculator,
fc_calculator_options,
@ -178,7 +174,6 @@ def create_phono3py_force_constants(
phono3py,
ph3py_yaml,
symmetrize_fc2,
input_filename,
settings.is_compact_fc,
fc_calculator,
fc_calculator_options,
@ -207,7 +202,6 @@ def parse_forces(
ph3py_yaml: Optional[Phono3pyYaml] = None,
cutoff_pair_distance=None,
force_filename: str = "FORCES_FC3",
disp_filename: Optional[str] = None,
phono3py_yaml_filename: Optional[str] = None,
fc_type=None,
log_level=0,
@ -269,32 +263,7 @@ def parse_forces(
force_to_eVperA=physical_units["force_to_eVperA"],
)
# No dataset is found. "disp_fc*.yaml" is read. But this is deprecated.
if dataset is None:
if disp_filename is None:
msg = (
"Displacement dataset corresponding to "
f'"{force_filename}" not found.'
)
raise RuntimeError(msg)
# Displacement dataset is obtained from disp_filename.
# can emit FileNotFoundError.
dataset = _read_disp_fc_yaml(disp_filename, fc_type)
filename_read_from = disp_filename
# No forces should exist. Therefore only unit of displacements is
# converted.
if calculator is None:
if log_level:
print(
f'Displacements are read from "{disp_filename}", but '
" the unit has not converted."
)
else:
_convert_unit_in_dataset(
dataset,
distance_to_A=physical_units["distance_to_A"],
)
assert dataset is not None
if "natom" in dataset and dataset["natom"] != natom:
msg = (
@ -369,15 +338,6 @@ def get_fc_calculator_params(settings):
return fc_calculator, fc_calculator_options
def _read_disp_fc_yaml(disp_filename, fc_type):
if fc_type == "phonon_fc2":
dataset = parse_disp_fc2_yaml(filename=disp_filename)
else:
dataset = parse_disp_fc3_yaml(filename=disp_filename)
return dataset
def _read_phono3py_fc3(phono3py, symmetrize_fc3r, input_filename, log_level):
if input_filename is None:
filename = "fc3.hdf5"
@ -469,13 +429,12 @@ def _create_phono3py_fc3(
phono3py: Phono3py,
ph3py_yaml: Optional[Phono3pyYaml],
phono3py_yaml_filename: Optional[str],
symmetrize_fc3r,
input_filename,
is_compact_fc,
cutoff_pair_distance,
fc_calculator,
fc_calculator_options,
log_level,
symmetrize_fc3r: bool,
is_compact_fc: bool,
cutoff_pair_distance: Optional[float],
fc_calculator: Optional[str],
fc_calculator_options: Optional[str],
log_level: int,
):
"""Read or calculate fc3.
@ -491,14 +450,7 @@ def _create_phono3py_fc3(
when the former value is smaller than the later.
"""
# disp_fc3.yaml is obsolete.
if input_filename is None:
disp_filename = "disp_fc3.yaml"
else:
disp_filename = "disp_fc3." + input_filename + ".yaml"
# If disp_fc3.yaml is not found, default phono3py.yaml file is
_ph3py_yaml = _get_ph3py_yaml(disp_filename, ph3py_yaml)
_ph3py_yaml = _get_default_ph3py_yaml(ph3py_yaml)
try:
dataset = parse_forces(
@ -506,7 +458,6 @@ def _create_phono3py_fc3(
ph3py_yaml=_ph3py_yaml,
cutoff_pair_distance=cutoff_pair_distance,
force_filename="FORCES_FC3",
disp_filename=disp_filename,
phono3py_yaml_filename=phono3py_yaml_filename,
fc_type="fc3",
log_level=log_level,
@ -534,25 +485,18 @@ def _create_phono3py_fc2(
phono3py: Phono3py,
ph3py_yaml: Optional[Phono3pyYaml],
symmetrize_fc2,
input_filename,
is_compact_fc,
fc_calculator,
fc_calculator_options,
log_level,
):
if input_filename is None:
disp_filename = "disp_fc3.yaml"
else:
disp_filename = "disp_fc3." + input_filename + ".yaml"
_ph3py_yaml = _get_ph3py_yaml(disp_filename, ph3py_yaml)
_ph3py_yaml = _get_default_ph3py_yaml(ph3py_yaml)
try:
dataset = parse_forces(
phono3py,
ph3py_yaml=_ph3py_yaml,
force_filename="FORCES_FC3",
disp_filename=disp_filename,
fc_type="fc2",
log_level=log_level,
)
@ -573,40 +517,30 @@ def _create_phono3py_fc2(
)
def _get_ph3py_yaml(disp_filename, ph3py_yaml: Optional[Phono3pyYaml]):
def _get_default_ph3py_yaml(ph3py_yaml: Optional[Phono3pyYaml]):
_ph3py_yaml = ph3py_yaml
# Try to use phono3py.phonon_dataset when the disp file not found
if not os.path.isfile(disp_filename):
disp_filename = None
if _ph3py_yaml is None and os.path.isfile("phono3py_disp.yaml"):
_ph3py_yaml = Phono3pyYaml()
_ph3py_yaml.read("phono3py_disp.yaml")
if _ph3py_yaml is None and os.path.isfile("phono3py_disp.yaml"):
_ph3py_yaml = Phono3pyYaml()
_ph3py_yaml.read("phono3py_disp.yaml")
return _ph3py_yaml
def _create_phono3py_phonon_fc2(
phono3py: Phono3py,
ph3py_yaml: Optional[Phono3pyYaml],
symmetrize_fc2,
input_filename,
is_compact_fc,
fc_calculator,
fc_calculator_options,
log_level,
symmetrize_fc2: bool,
is_compact_fc: bool,
fc_calculator: Optional[str],
fc_calculator_options: Optional[str],
log_level: int,
):
if input_filename is None:
disp_filename = "disp_fc2.yaml"
else:
disp_filename = "disp_fc2." + input_filename + ".yaml"
_ph3py_yaml = _get_ph3py_yaml(disp_filename, ph3py_yaml)
_ph3py_yaml = _get_default_ph3py_yaml(ph3py_yaml)
try:
dataset = parse_forces(
phono3py,
ph3py_yaml=_ph3py_yaml,
force_filename="FORCES_FC2",
disp_filename=disp_filename,
fc_type="phonon_fc2",
log_level=log_level,
)

25
phono3py/cui/create_supercells.py
View File

@ -37,7 +37,6 @@
from phonopy.interface.calculator import write_supercells_with_displacements
from phono3py import Phono3py
from phono3py.file_IO import write_disp_fc2_yaml, write_disp_fc3_yaml
from phono3py.interface.calculator import (
get_additional_info_to_write_fc2_supercells,
get_additional_info_to_write_supercells,
@ -52,18 +51,12 @@ def create_phono3py_supercells(
output_filename=None,
interface_mode="vasp",
log_level=1,
write_disp_yaml=False,
):
"""Create displacements and supercells.
Distance unit used is that for the calculator interface.
The default unit is Angstron.
Parameters
----------
write_disp_yaml : bool
Write old-style files of disp_fc3.yaml and disp_fc2.yaml. Default is False.
"""
optional_structure_info = cell_info["optional_structure_info"]
@ -92,15 +85,6 @@ def create_phono3py_supercells(
print('Unit cell was read from "%s".' % optional_structure_info[0])
print("Displacement distance: %s" % distance)
if write_disp_yaml:
if output_filename is None:
filename = "disp_fc3.yaml"
else:
filename = "disp_fc3." + output_filename + ".yaml"
num_disps, num_disp_files = write_disp_fc3_yaml(
phono3py.dataset, phono3py.supercell, filename=filename
)
ids = []
disp_cells = []
for i, cell in enumerate(phono3py.supercells_with_displacements):
@ -132,15 +116,6 @@ def create_phono3py_supercells(
print("Number of displacement supercell files created: %d" % num_disp_files)
if phono3py.phonon_supercell_matrix is not None:
if write_disp_yaml:
if output_filename is None:
filename = "disp_fc2.yaml"
else:
filename = "disp_fc2." + output_filename + ".yaml"
num_disps = write_disp_fc2_yaml(
phono3py.phonon_dataset, phono3py.phonon_supercell, filename=filename
)
additional_info = get_additional_info_to_write_fc2_supercells(
interface_mode, phono3py.phonon_supercell_matrix
)

7
phono3py/cui/kaccum_script.py
View File

@ -358,9 +358,10 @@ def main():
"""
args = _get_parser()
primitive = None
if len(args.filenames) > 1: # deprecated
cell, f_kappa = _read_files(args)
primitive_matrix = _analyze_primitive_matrix_option(args, unitcell=cell)
if len(args.filenames) > 1:
raise RuntimeError(
'Use of "phono3py-kaccum CRYSTAL_STRUCTURE_FILE" is not supported.'
)
else:
interface_mode = _get_calculator(args)
cell_info = _read_files_by_collect_cell_info(args.cell_filename, interface_mode)

70
phono3py/cui/load.py
View File

@ -94,17 +94,17 @@ def load(
can be overwritten.
'fc3.hdf5' is read if found in current directory. Unless 'fc3.hdf5' is found
and if 'FORCES_FC3' and 'disp_fc3.yaml" are found, these are read and fc3
and fc2 are produced.
and if 'FORCES_FC3' and 'phono3py_disp.yaml" are found, these are read and
fc3 and fc2 are produced.
if 'fc2.hdf5' is found, this is read. Unless 'fc2.hdf5' is found and if
'FORCES_FC2' and 'disp_fc2.yaml" are found, these are read and fc2 is
'FORCES_FC2' and 'phono3py_disp.yaml" are found, these are read and fc2 is
produced.
When force_sets_filename and force_constants_filename are not given,
'FORCES_FC3' and 'FORCES_FC2' are looked for in the current directory as the
default behaviour. When 'FORCES_FC3' ('FORCES_FC2') is given in the type-1
format, 'disp_fc3.yaml' ('disp_fc2.yaml') is also necessary and read.
format, 'phono3py_disp.yaml' is also necessary and read.
Crystal structure
-----------------
@ -121,12 +121,12 @@ def load(
priority:
1. fc3_filename (fc2_filename)
2. forces_fc3_filename (forces_fc2_filename). Do not forget that for
type-1 format, disp_fc3.yaml (disp_fc2.yaml) has to be given, too.
type-1 format, phono3py_disp.yaml has to be given, too.
3. 'fc3.hdf5' and 'fc2.hdf5' are searched in current directory.
4. 'FORCES_FC3' and 'FORCES_FC2' are searched in current directory.
'FORCES_FC2' is optional. For type-1 format, 'disp_fc3.yaml' and
optionally 'disp_fc2.yaml' are also searched in current directory.
When 'FORCES_FC2' is not found, 'FORCES_FC3' is used to create fc2.
'FORCES_FC2' is optional. For type-1 format, 'phono3py_disp.yaml' is
also searched in current directory. When 'FORCES_FC2' is not found,
'FORCES_FC3' is used to create fc2.
Parameters for non-analytical term correctiion (NAC)
----------------------------------------------------
@ -188,11 +188,11 @@ def load(
correction parameters.
forces_fc3_filename : sequence or os.PathLike, optional
A two-elemental sequence of filenames corresponding to ('FORCES_FC3',
'disp_fc3.yaml') in the type-1 format or a filename (os.PathLike)
'phono3py_disp.yaml') in the type-1 format or a filename (os.PathLike)
corresponding to 'FORCES_FC3' in the type-2 format. Default is None.
forces_fc2_filename : os.PathLike or sequence, optional
A two-elemental sequence of filenames corresponding to ('FORCES_FC2',
'disp_fc2.yaml') in the type-1 format or a filename (os.PathLike)
'phono3py_disp.yaml') in the type-1 format or a filename (os.PathLike)
corresponding to 'FORCES_FC2' in the type-2 format. Default is None.
fc3_filename : os.PathLike, optional
Filename of a file corresponding to 'fc3.hdf5', a file contains
@ -233,10 +233,10 @@ def load(
use_grg : bool, optional
Use generalized regular grid when True. Default is False.
make_r0_average : bool, optional
fc3 transformation from real to reciprocal space is done
around three atoms and averaged when True. Default is False, i.e.,
only around the first atom. Setting False is for rough compatibility
with v2.x. Default is True.
fc3 transformation from real to reciprocal space is done around three
atoms and averaged when True. Default is False, i.e., only around the
first atom. Setting False is for rough compatibility with v2.x. Default
is True.
symprec : float, optional
Tolerance used to find crystal symmetry. Default is 1e-5.
log_level : int, optional
@ -477,16 +477,11 @@ def _set_dataset_or_fc3(
if log_level:
print('fc3 was read from "%s".' % fc3_filename)
elif forces_fc3_filename is not None:
if isinstance(forces_fc3_filename, os.PathLike):
force_filename = forces_fc3_filename
disp_filename = None
else:
force_filename, disp_filename = forces_fc3_filename
force_filename = forces_fc3_filename
_set_dataset_for_fc3(
ph3py,
ph3py_yaml,
force_filename,
disp_filename,
phono3py_yaml_filename,
cutoff_pair_distance,
log_level,
@ -499,17 +494,10 @@ def _set_dataset_or_fc3(
if log_level:
print('fc3 was read from "fc3.hdf5".')
elif os.path.isfile("FORCES_FC3"):
disp_filename = None
if os.path.isfile("disp_fc3.yaml"):
if ph3py_yaml is None:
disp_filename = "disp_fc3.yaml"
elif ph3py_yaml.dataset is None:
disp_filename = "disp_fc3.yaml"
_set_dataset_for_fc3(
ph3py,
ph3py_yaml,
"FORCES_FC3",
disp_filename,
phono3py_yaml_filename,
cutoff_pair_distance,
log_level,
@ -523,7 +511,6 @@ def _set_dataset_or_fc3(
ph3py,
ph3py_yaml,
None,
None,
phono3py_yaml_filename,
cutoff_pair_distance,
log_level,
@ -548,16 +535,11 @@ def _set_dataset_phonon_dataset_or_fc2(
if log_level:
print('fc2 was read from "%s".' % fc2_filename)
elif forces_fc2_filename is not None:
if isinstance(forces_fc2_filename, os.PathLike):
force_filename = forces_fc2_filename
disp_filename = None
else:
force_filename, disp_filename = forces_fc2_filename
force_filename = forces_fc2_filename
_set_dataset_for_fc2(
ph3py,
ph3py_yaml,
force_filename,
disp_filename,
"phonon_fc2",
log_level,
)
@ -569,17 +551,10 @@ def _set_dataset_phonon_dataset_or_fc2(
if log_level:
print('fc2 was read from "fc2.hdf5".')
elif os.path.isfile("FORCES_FC2"):
disp_filename = None
if os.path.isfile("disp_fc2.yaml"):
if ph3py_yaml is None:
disp_filename = "disp_fc2.yaml"
elif ph3py_yaml.phonon_dataset is None:
disp_filename = "disp_fc2.yaml"
_set_dataset_for_fc2(
ph3py,
ph3py_yaml,
"FORCES_FC2",
disp_filename,
"phonon_fc2",
log_level,
)
@ -592,7 +567,6 @@ def _set_dataset_phonon_dataset_or_fc2(
ph3py,
ph3py_yaml,
None,
None,
"phonon_fc2",
log_level,
)
@ -605,23 +579,15 @@ def _set_dataset_phonon_dataset_or_fc2(
ph3py,
ph3py_yaml,
None,
None,
"fc2",
log_level,
)
elif os.path.isfile("FORCES_FC3"):
# suppose fc3.hdf5 is read but fc2.hdf5 doesn't exist.
disp_filename = None
if os.path.isfile("disp_fc3.yaml"):
if ph3py_yaml is None:
disp_filename = "disp_fc3.yaml"
elif ph3py_yaml.dataset is None:
disp_filename = "disp_fc3.yaml"
_set_dataset_for_fc2(
ph3py,
ph3py_yaml,
"FORCES_FC3",
disp_filename,
"fc2",
log_level,
)
@ -632,7 +598,6 @@ def _set_dataset_for_fc3(
ph3py: Phono3py,
ph3py_yaml: Optional[Phono3pyYaml],
force_filename,
disp_filename,
phono3py_yaml_filename,
cutoff_pair_distance,
log_level,
@ -642,7 +607,6 @@ def _set_dataset_for_fc3(
ph3py_yaml=ph3py_yaml,
cutoff_pair_distance=cutoff_pair_distance,
force_filename=force_filename,
disp_filename=disp_filename,
phono3py_yaml_filename=phono3py_yaml_filename,
fc_type="fc3",
log_level=log_level,
@ -653,7 +617,6 @@ def _set_dataset_for_fc2(
ph3py: Phono3py,
ph3py_yaml: Optional[Phono3pyYaml],
force_filename,
disp_filename,
fc_type,
log_level,
):
@ -661,7 +624,6 @@ def _set_dataset_for_fc2(
ph3py,
ph3py_yaml=ph3py_yaml,
force_filename=force_filename,
disp_filename=disp_filename,
fc_type=fc_type,
log_level=log_level,
)

55
phono3py/cui/phono3py_script.py
View File

@ -83,8 +83,6 @@ from phono3py.cui.show_log import (
from phono3py.cui.triplets_info import show_num_triplets, write_grid_points
from phono3py.file_IO import (
get_length_of_first_line,
parse_disp_fc2_yaml,
parse_disp_fc3_yaml,
parse_FORCES_FC2,
read_phonon_from_hdf5,
write_fc2_to_hdf5,
@ -385,7 +383,6 @@ def create_FORCE_SETS_from_FORCES_FCx_then_exit(
def create_FORCES_FC3_and_FORCES_FC2_then_exit(
settings,
input_filename: Optional[str],
cell_filename: Optional[str],
log_level: Union[bool, int],
):
@ -397,24 +394,18 @@ def create_FORCES_FC3_and_FORCES_FC2_then_exit(
# Create FORCES_FC3 #
#####################
if settings.create_forces_fc3 or settings.create_forces_fc3_file:
if input_filename is None:
disp_fc3_filename = "disp_fc3.yaml"
else:
disp_fc3_filename = "disp_fc3." + input_filename + ".yaml"
disp_filename_candidates = ["phono3py_disp.yaml", disp_fc3_filename]
disp_filename_candidates = [
"phono3py_disp.yaml",
]
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_filename = disp_filenames[0]
if disp_filename == disp_fc3_filename:
file_exists(disp_filename, log_level)
disp_dataset = parse_disp_fc3_yaml(filename=disp_filename)
else:
ph3py_yaml = Phono3pyYaml()
ph3py_yaml.read(disp_filename)
if ph3py_yaml.calculator is not None:
interface_mode = ph3py_yaml.calculator # overwrite
disp_dataset = ph3py_yaml.dataset
ph3py_yaml = Phono3pyYaml()
ph3py_yaml.read(disp_filename)
if ph3py_yaml.calculator is not None:
interface_mode = ph3py_yaml.calculator # overwrite
disp_dataset = ph3py_yaml.dataset
if log_level:
print("")
@ -488,27 +479,21 @@ def create_FORCES_FC3_and_FORCES_FC2_then_exit(
# Create FORCES_FC2 #
#####################
if settings.create_forces_fc2:
if input_filename is None:
disp_fc2_filename = "disp_fc2.yaml"
else:
disp_fc2_filename = "disp_fc2." + input_filename + ".yaml"
disp_filename_candidates = ["phono3py_disp.yaml", disp_fc2_filename]
disp_filename_candidates = [
"phono3py_disp.yaml",
]
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_filename = disp_filenames[0]
if disp_filename == disp_fc2_filename:
file_exists(disp_filename, log_level)
disp_dataset = parse_disp_fc2_yaml(filename=disp_filename)
else:
# ph3py_yaml is not None, phono3py_disp.yaml is already read.
if ph3py_yaml is None:
ph3py_yaml = Phono3pyYaml()
ph3py_yaml.read(disp_filename)
if ph3py_yaml.calculator is not None:
interface_mode = ph3py_yaml.calculator # overwrite
disp_dataset = ph3py_yaml.phonon_dataset
# ph3py_yaml is not None, phono3py_disp.yaml is already read.
if ph3py_yaml is None:
ph3py_yaml = Phono3pyYaml()
ph3py_yaml.read(disp_filename)
if ph3py_yaml.calculator is not None:
interface_mode = ph3py_yaml.calculator # overwrite
disp_dataset = ph3py_yaml.phonon_dataset
if log_level:
print('Displacement dataset was read from "%s".' % disp_filename)
@ -1138,9 +1123,7 @@ def main(**argparse_control):
####################################
# Create FORCES_FC3 and FORCES_FC2 #
####################################
create_FORCES_FC3_and_FORCES_FC2_then_exit(
settings, input_filename, cell_filename, log_level
)
create_FORCES_FC3_and_FORCES_FC2_then_exit(settings, cell_filename, log_level)
###########################################################
# Symmetry tolerance. Distance unit depends on interface. #

133
phono3py/file_IO.py
View File

@ -51,28 +51,12 @@ from phonopy.file_IO import check_force_constants_indices, get_cell_from_disp_ya
from phono3py.version import __version__
def write_cell_yaml(w, supercell):
"""Write cell info.
def write_disp_fc3_yaml(dataset, supercell, filename="disp_fc3.yaml"):
"""Write disp_fc3.yaml.
This is only used from write_disp_fc3_yaml and write_disp_fc2_yaml.
These methods are also deprecated.
This function should not be called from phono3py script from version 3.
"""
warnings.warn("write_cell_yaml() is deprecated.", DeprecationWarning)
w.write("lattice:\n")
for axis in supercell.get_cell():
w.write("- [ %20.15f,%20.15f,%20.15f ]\n" % tuple(axis))
symbols = supercell.get_chemical_symbols()
positions = supercell.get_scaled_positions()
w.write("atoms:\n")
for i, (s, v) in enumerate(zip(symbols, positions)):
w.write("- symbol: %-2s # %d\n" % (s, i + 1))
w.write(" position: [ %18.14f,%18.14f,%18.14f ]\n" % tuple(v))
def write_disp_fc3_yaml(dataset, supercell, filename="disp_fc3.yaml"):
"""Write disp_fc3.yaml."""
warnings.warn("write_disp_fc3_yaml() is deprecated.", DeprecationWarning)
w = open(filename, "w")
@ -158,7 +142,7 @@ def write_disp_fc3_yaml(dataset, supercell, filename="disp_fc3.yaml"):
ids = ["%d" % disp2["id"] for disp2 in disp2_list]
w.write(" displacement_ids: [ %s ]\n" % ", ".join(ids))
write_cell_yaml(w, supercell)
_write_cell_yaml(w, supercell)
w.close()
@ -166,7 +150,11 @@ def write_disp_fc3_yaml(dataset, supercell, filename="disp_fc3.yaml"):
def write_disp_fc2_yaml(dataset, supercell, filename="disp_fc2.yaml"):
"""Write disp_fc2.yaml."""
"""Write disp_fc2.yaml.
This function should not be called from phono3py script from version 3.
"""
warnings.warn("write_disp_fc2_yaml() is deprecated.", DeprecationWarning)
w = open(filename, "w")
@ -185,7 +173,7 @@ def write_disp_fc2_yaml(dataset, supercell, filename="disp_fc2.yaml"):
)
if supercell is not None:
write_cell_yaml(w, supercell)
_write_cell_yaml(w, supercell)
w.close()
@ -271,25 +259,6 @@ def write_FORCES_FC3(disp_dataset, forces_fc3=None, fp=None, filename="FORCES_FC
w.close()
def write_fc3_dat(force_constants_third, filename="fc3.dat"):
"""Write fc3.dat."""
warnings.warn("write_fc3_dat() is deprecated.", DeprecationWarning)
w = open(filename, "w")
for i in range(force_constants_third.shape[0]):
for j in range(force_constants_third.shape[1]):
for k in range(force_constants_third.shape[2]):
tensor3 = force_constants_third[i, j, k]
w.write(
" %d - %d - %d (%f)\n"
% (i + 1, j + 1, k + 1, np.abs(tensor3).sum())
)
for tensor2 in tensor3:
for vec in tensor2:
w.write("%20.14f %20.14f %20.14f\n" % tuple(vec))
w.write("\n")
def write_fc3_to_hdf5(fc3, filename="fc3.hdf5", p2s_map=None, compression="gzip"):
"""Write fc3 in fc3.hdf5.
@ -404,64 +373,6 @@ def read_fc2_from_hdf5(filename="fc2.hdf5", p2s_map=None):
)
def write_triplets(
triplets, weights, mesh, grid_address, grid_point=None, filename=None
):
"""Write triplets in triplets.dat."""
warnings.warn("write_triplets() is deprecated.", DeprecationWarning)
triplets_filename = "triplets"
suffix = "-m%d%d%d" % tuple(mesh)
if grid_point is not None:
suffix += "-g%d" % grid_point
if filename is not None:
suffix += "." + filename
suffix += ".dat"
triplets_filename += suffix
w = open(triplets_filename, "w")
for weight, g3 in zip(weights, triplets):
w.write("%4d " % weight)
for q3 in grid_address[g3]:
w.write("%4d %4d %4d " % tuple(q3))
w.write("\n")
w.close()
def write_grid_address(grid_address, mesh, filename=None):
"""Write grid addresses in grid_address.dat."""
warnings.warn("write_grid_address() is deprecated.", DeprecationWarning)
grid_address_filename = "grid_address"
suffix = "-m%d%d%d" % tuple(mesh)
if filename is not None:
suffix += "." + filename
suffix += ".dat"
grid_address_filename += suffix
w = open(grid_address_filename, "w")
w.write("# Grid addresses for %dx%dx%d mesh\n" % tuple(mesh))
w.write(
"#%9s %8s %8s %8s %8s %8s %8s\n"
% (
"index",
"a",
"b",
"c",
("a%%%d" % mesh[0]),
("b%%%d" % mesh[1]),
("c%%%d" % mesh[2]),
)
)
for i, bz_q in enumerate(grid_address):
if i == np.prod(mesh):
w.write("#" + "-" * 78 + "\n")
q = bz_q % mesh
w.write("%10d %8d %8d %8d " % (i, bz_q[0], bz_q[1], bz_q[2]))
w.write("%8d %8d %8d\n" % tuple(q))
return grid_address_filename
def write_grid_address_to_hdf5(
grid_address,
mesh,
@ -1566,7 +1477,7 @@ def write_ir_grid_points(bz_grid, grid_points, grid_weights, primitive_lattice):
def parse_disp_fc2_yaml(filename="disp_fc2.yaml", return_cell=False):
"""Parse disp_fc2.yaml file.
This is obsolete at v2 and later versions.
This function should not be called from phono3py script from version 3.
"""
warnings.warn("parse_disp_fc2_yaml() is deprecated.", DeprecationWarning)
@ -1593,7 +1504,7 @@ def parse_disp_fc2_yaml(filename="disp_fc2.yaml", return_cell=False):
def parse_disp_fc3_yaml(filename="disp_fc3.yaml", return_cell=False):
"""Parse disp_fc3.yaml file.
This is obsolete at v2 and later versions.
This function should not be called from phono3py script from version 3.
"""
warnings.warn("parse_disp_fc3_yaml() is deprecated.", DeprecationWarning)
@ -1800,3 +1711,23 @@ def _parse_force_lines(forcefile, num_atom):
return None
else:
return np.array(forces)
def _write_cell_yaml(w, supercell):
"""Write cell info.
This is only used from write_disp_fc3_yaml and write_disp_fc2_yaml.
These methods are also deprecated.
"""
warnings.warn("write_cell_yaml() is deprecated.", DeprecationWarning)
w.write("lattice:\n")
for axis in supercell.get_cell():
w.write("- [ %20.15f,%20.15f,%20.15f ]\n" % tuple(axis))
symbols = supercell.get_chemical_symbols()
positions = supercell.get_scaled_positions()
w.write("atoms:\n")
for i, (s, v) in enumerate(zip(symbols, positions)):
w.write("- symbol: %-2s # %d\n" % (s, i + 1))
w.write(" position: [ %18.14f,%18.14f,%18.14f ]\n" % tuple(v))

34
phono3py/other/isotope.py
View File

@ -34,8 +34,9 @@
# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
import warnings
from typing import Dict, List, Optional, Tuple, Union
from __future__ import annotations
from typing import Optional, Union
import numpy as np
from phonopy.harmonic.dynamical_matrix import get_dynamical_matrix
@ -58,8 +59,8 @@ from phono3py.phonon.solver import run_phonon_solver_c, run_phonon_solver_py
def get_mass_variances(
primitive: Optional[PhonopyAtoms] = None,
symbols: Optional[Union[List[str], Tuple[str]]] = None,
isotope_data: Optional[Dict] = None,
symbols: Optional[Union[list[str], tuple[str]]] = None,
isotope_data: Optional[dict] = None,
):
"""Calculate mass variances."""
if primitive is not None:
@ -176,14 +177,6 @@ class Isotope:
else:
self._sigma = float(sigma)
def set_sigma(self, sigma):
"""Set smearing width."""
warnings.warn(
"Isotope.set_sigma() is deprecated." "Use Isotope.sigma attribute.",
DeprecationWarning,
)
self.sigma = sigma
@property
def dynamical_matrix(self):
"""Return DynamicalMatrix* class instance."""
@ -199,14 +192,6 @@ class Isotope:
"""Return scattering strength."""
return self._gamma
def get_gamma(self):
"""Return scattering strength."""
warnings.warn(
"Isotope.get_gamma() is deprecated." "Use Isotope.gamma attribute.",
DeprecationWarning,
)
return self.gamma
@property
def bz_grid(self):
"""Return BZgrid class instance."""
@ -217,15 +202,6 @@ class Isotope:
"""Return mass variances."""
return self._mass_variances
def get_mass_variances(self):
"""Return mass variances."""
warnings.warn(
"Isotope.get_mass_variances() is deprecated."
"Use Isotope.mass_variances attribute.",
DeprecationWarning,
)
return self.mass_variances
def get_phonons(self):
"""Return phonons on grid."""
return self._frequencies, self._eigenvectors, self._phonon_done

36
phono3py/other/kaccum.py
View File

@ -2,7 +2,6 @@
from __future__ import annotations
import warnings
from collections.abc import Sequence
from typing import Optional, Union
@ -134,37 +133,6 @@ class KappaDOSTHM:
return bzgp2irgp_map
class KappaDOS(KappaDOSTHM):
"""Deprecated class to calculate DOS like spectram with tetrahedron method."""
def __init__(
self,
mode_kappa: np.ndarray,
frequencies: np.ndarray,
bz_grid: BZGrid,
ir_grid_points: np.ndarray,
ir_grid_map: Optional[np.ndarray] = None,
frequency_points: Optional[np.ndarray] = None,
num_sampling_points: int = 100,
):
"""Init method."""
warnings.warn(
"KappaDOS is deprecated."
"Use KappaDOSTHM instead with replacing ir_grid_points in BZ-grid "
"by ir_grid_points in GR-grid.",
DeprecationWarning,
)
super().__init__(
mode_kappa,
frequencies,
bz_grid,
bz_grid.bzg2grg[ir_grid_points],
ir_grid_map=ir_grid_map,
frequency_points=frequency_points,
num_sampling_points=num_sampling_points,
)
class GammaDOSsmearing:
"""Class to calculate Gamma spectram by smearing method."""
@ -245,7 +213,7 @@ def run_prop_dos(
bz_grid: BZGrid,
):
"""Run DOS-like calculation."""
kappa_dos = KappaDOS(
kappa_dos = KappaDOSTHM(
mode_prop,
frequencies,
bz_grid,
@ -270,7 +238,7 @@ def run_mfp_dos(
kdos = []
sampling_points = []
for i, _ in enumerate(mean_freepath):
kappa_dos = KappaDOS(
kappa_dos = KappaDOSTHM(
mode_prop[i : i + 1, :, :],
mean_freepath[i],
bz_grid,

3
phono3py/phonon3/dataset.py
View File

@ -47,8 +47,7 @@ def get_displacements_and_forces_fc3(disp_dataset):
Parameters
----------
disp_dataset : dict
Displacement dataset that may be obtained by
file_IO.parse_disp_fc3_yaml.
Displacement dataset.
Returns
-------

2
phono3py/phonon3/fc3.py
View File

@ -692,7 +692,7 @@ def _get_fc3_least_atoms(
first_atom_nums = []
for i in unique_first_atom_nums:
if i != s2p_map[i]:
print("Something wrong in disp_fc3.yaml")
print("Something wrong in displacement dataset.")
raise RuntimeError
else:
first_atom_nums.append(i)

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__ = "2.10.0"
__version__ = "3.0.0"

93
test/other/test_kaccum.py
View File

@ -5,15 +5,13 @@ from __future__ import annotations
from typing import Optional
import numpy as np
import pytest
from phono3py import Phono3py
from phono3py.other.kaccum import GammaDOSsmearing, KappaDOS, KappaDOSTHM, get_mfp
from phono3py.other.kaccum import GammaDOSsmearing, KappaDOSTHM, get_mfp
from phono3py.phonon.grid import get_ir_grid_points
@pytest.mark.parametrize("use_legacy_class", [False, True])
def test_kappados_si(si_pbesol: Phono3py, use_legacy_class: bool):
def test_kappados_si(si_pbesol: Phono3py):
"""Test KappaDOS class with Si.
* 3x3 tensor vs frequency
@ -110,7 +108,6 @@ def test_kappados_si(si_pbesol: Phono3py, use_legacy_class: bool):
ph3,
tc.mode_kappa[0],
freq_points=freq_points_in,
use_legacy_class=use_legacy_class,
)
# for f, (jval, ival) in zip(freq_points, kdos):
# print("[%.7f, %.7f, %.7f]," % (f, jval, ival))
@ -122,7 +119,6 @@ def test_kappados_si(si_pbesol: Phono3py, use_legacy_class: bool):
ph3,
tc.gamma[0, :, :, :, None],
freq_points=freq_points_in,
use_legacy_class=use_legacy_class,
)
# for f, (jval, ival) in zip(freq_points, kdos):
# print("[%.7f, %.7f, %.7f]," % (f, jval, ival))
@ -131,9 +127,7 @@ def test_kappados_si(si_pbesol: Phono3py, use_legacy_class: bool):
)
mfp_points_in = np.array(mfpdos_si).reshape(-1, 3)[:, 0]
mfp_points, mfpdos = _calculate_mfpdos(
ph3, mfp_points_in, use_legacy_class=use_legacy_class
)
mfp_points, mfpdos = _calculate_mfpdos(ph3, mfp_points_in)
# for f, (jval, ival) in zip(mfp_points, mfpdos):
# print("[%.7f, %.7f, %.7f]," % (f, jval, ival))
np.testing.assert_allclose(
@ -141,8 +135,7 @@ def test_kappados_si(si_pbesol: Phono3py, use_legacy_class: bool):
)
@pytest.mark.parametrize("use_legacy_class", [False, True])
def test_kappados_nacl(nacl_pbe: Phono3py, use_legacy_class: bool):
def test_kappados_nacl(nacl_pbe: Phono3py):
"""Test KappaDOS class with NaCl.
* 3x3 tensor vs frequency
@ -248,7 +241,6 @@ def test_kappados_nacl(nacl_pbe: Phono3py, use_legacy_class: bool):
ph3,
tc.gamma[0, :, :, :, None],
freq_points=freq_points_in,
use_legacy_class=use_legacy_class,
)
for f, (jval, ival) in zip(freq_points, kdos):
print("[%.7f, %.7f, %.7f]," % (f, jval, ival))
@ -257,9 +249,7 @@ def test_kappados_nacl(nacl_pbe: Phono3py, use_legacy_class: bool):
)
mfp_points_in = np.array(mfpdos_nacl).reshape(-1, 3)[:, 0]
mfp_points, mfpdos = _calculate_mfpdos(
ph3, mfp_points_in, use_legacy_class=use_legacy_class
)
mfp_points, mfpdos = _calculate_mfpdos(ph3, mfp_points_in)
# for f, (jval, ival) in zip(mfp_points, mfpdos):
# print("[%.7f, %.7f, %.7f]," % (f, jval, ival))
np.testing.assert_allclose(
@ -305,79 +295,42 @@ def _calculate_kappados(
ph3: Phono3py,
mode_prop: np.ndarray,
freq_points: Optional[np.ndarray] = None,
use_legacy_class: bool = False,
):
tc = ph3.thermal_conductivity
bz_grid = ph3.grid
frequencies, _, _ = ph3.get_phonon_data()
with pytest.deprecated_call():
kappados = KappaDOS(
mode_prop,
frequencies,
bz_grid,
tc.grid_points,
frequency_points=freq_points,
)
freq_points, kdos = kappados.get_kdos()
ir_grid_points, _, ir_grid_map = get_ir_grid_points(bz_grid)
if use_legacy_class:
with pytest.deprecated_call():
kappados = KappaDOS(
mode_prop,
tc.frequencies,
bz_grid,
tc.grid_points,
ir_grid_map=ir_grid_map,
frequency_points=freq_points,
)
else:
kappados = KappaDOSTHM(
mode_prop,
tc.frequencies,
bz_grid,
bz_grid.bzg2grg[tc.grid_points],
ir_grid_map=ir_grid_map,
frequency_points=freq_points,
)
kappados = KappaDOSTHM(
mode_prop,
tc.frequencies,
bz_grid,
bz_grid.bzg2grg[tc.grid_points],
ir_grid_map=ir_grid_map,
frequency_points=freq_points,
)
ir_freq_points, ir_kdos = kappados.get_kdos()
np.testing.assert_equal(bz_grid.bzg2grg[tc.grid_points], ir_grid_points)
np.testing.assert_allclose(ir_freq_points, freq_points, rtol=0, atol=1e-5)
np.testing.assert_allclose(ir_kdos, kdos, rtol=0, atol=1e-5)
return freq_points, kdos[0, :, :, 0]
return freq_points, ir_kdos[0, :, :, 0]
def _calculate_mfpdos(
ph3: Phono3py,
mfp_points=None,
use_legacy_class: bool = False,
):
tc = ph3.thermal_conductivity
bz_grid = ph3.grid
mean_freepath = get_mfp(tc.gamma[0], tc.group_velocities)
_, _, ir_grid_map = get_ir_grid_points(bz_grid)
if use_legacy_class:
with pytest.deprecated_call():
mfpdos = KappaDOS(
tc.mode_kappa[0],
mean_freepath[0],
bz_grid,
tc.grid_points,
ir_grid_map=ir_grid_map,
frequency_points=mfp_points,
num_sampling_points=10,
)
else:
mfpdos = KappaDOSTHM(
tc.mode_kappa[0],
mean_freepath[0],
bz_grid,
bz_grid.bzg2grg[tc.grid_points],
ir_grid_map=ir_grid_map,
frequency_points=mfp_points,
num_sampling_points=10,
)
mfpdos = KappaDOSTHM(
tc.mode_kappa[0],
mean_freepath[0],
bz_grid,
bz_grid.bzg2grg[tc.grid_points],
ir_grid_map=ir_grid_map,
frequency_points=mfp_points,
num_sampling_points=10,
)
freq_points, kdos = mfpdos.get_kdos()
return freq_points, kdos[0, :, :, 0]