mirror of https://github.com/phonopy/phono3py.git
Merge branch 'develop' into publish-gh-pages
This commit is contained in:
Atsushi Togo
commit
2888f818a2
|
|
@ -19,7 +19,7 @@ repos:
|
|||
- "--ignore=E203,W503"
|
||||
|
||||
- repo: https://github.com/psf/black
|
||||
rev: 23.9.1
|
||||
rev: 23.10.1
|
||||
hooks:
|
||||
- id: black
|
||||
args:
|
||||
|
|
|
|||
|
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@ -2,6 +2,11 @@
|
|||
|
||||
# Change Log
|
||||
|
||||
## Dec-4-2023: Version 2.8.0
|
||||
|
||||
- Maintenance release
|
||||
- Fix unit conversion for non-VASP calculators
|
||||
|
||||
## Jul-3-2023: Version 2.7.0
|
||||
|
||||
- Drop python 3.7 support
|
||||
|
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@ -47,7 +52,7 @@
|
|||
|
||||
- Maintenance release to follow the change of phonopy at v2.12.1.
|
||||
- Installation using `setup.py` now requires creating `site.cfg` file. See
|
||||
https://phonopy.github.io/phono3py/install.html and
|
||||
<https://phonopy.github.io/phono3py/install.html> and
|
||||
[PR #59](https://github.com/phonopy/phono3py/pull/59).
|
||||
- Dorp python 3.6 support, and dependencies of numpy and matplotlib versions are
|
||||
updated:
|
||||
|
|
|
|||
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@ -57,7 +57,7 @@ copyright = "2015, Atsushi Togo"
|
|||
# built documents.
|
||||
#
|
||||
# The short X.Y version.
|
||||
version = "2.7"
|
||||
version = "2.8"
|
||||
# The full version, including alpha/beta/rc tags.
|
||||
release = "2.7.0"
|
||||
|
||||
|
|
|
|||
|
|
@ -1,330 +0,0 @@
|
|||
natom: 64
|
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first_atoms:
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
||||
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|
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|
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|
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|
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|
||||
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|
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|
||||
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|
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|
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|
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|
||||
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|
||||
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|
||||
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|
||||
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|
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|
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|
||||
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|
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|
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|
||||
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|
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|
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|
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|
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|
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|
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|
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
position: [ 0.93750000000000, 0.68750000000000, 0.18750000000000 ]
|
||||
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|
||||
position: [ 0.43750000000000, 0.18750000000000, 0.68750000000000 ]
|
||||
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|
||||
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|
||||
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|
||||
position: [ 0.43750000000000, 0.68750000000000, 0.68750000000000 ]
|
||||
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|
||||
position: [ 0.93750000000000, 0.68750000000000, 0.68750000000000 ]
|
||||
- symbol: Si # 17
|
||||
position: [ 0.18750000000000, 0.43750000000000, 0.18750000000000 ]
|
||||
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|
||||
position: [ 0.68750000000000, 0.43750000000000, 0.18750000000000 ]
|
||||
- symbol: Si # 19
|
||||
position: [ 0.18750000000000, 0.93750000000000, 0.18750000000000 ]
|
||||
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|
||||
position: [ 0.68750000000000, 0.93750000000000, 0.18750000000000 ]
|
||||
- symbol: Si # 21
|
||||
position: [ 0.18750000000000, 0.43750000000000, 0.68750000000000 ]
|
||||
- symbol: Si # 22
|
||||
position: [ 0.68750000000000, 0.43750000000000, 0.68750000000000 ]
|
||||
- symbol: Si # 23
|
||||
position: [ 0.18750000000000, 0.93750000000000, 0.68750000000000 ]
|
||||
- symbol: Si # 24
|
||||
position: [ 0.68750000000000, 0.93750000000000, 0.68750000000000 ]
|
||||
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|
||||
position: [ 0.18750000000000, 0.18750000000000, 0.43750000000000 ]
|
||||
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|
||||
position: [ 0.68750000000000, 0.18750000000000, 0.43750000000000 ]
|
||||
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|
||||
position: [ 0.18750000000000, 0.68750000000000, 0.43750000000000 ]
|
||||
- symbol: Si # 28
|
||||
position: [ 0.68750000000000, 0.68750000000000, 0.43750000000000 ]
|
||||
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|
||||
position: [ 0.18750000000000, 0.18750000000000, 0.93750000000000 ]
|
||||
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|
||||
position: [ 0.68750000000000, 0.18750000000000, 0.93750000000000 ]
|
||||
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|
||||
position: [ 0.18750000000000, 0.68750000000000, 0.93750000000000 ]
|
||||
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|
||||
position: [ 0.68750000000000, 0.68750000000000, 0.93750000000000 ]
|
||||
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|
||||
position: [ 0.06250000000000, 0.06250000000000, 0.06250000000000 ]
|
||||
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|
||||
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|
||||
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|
||||
position: [ 0.06250000000000, 0.56250000000000, 0.06250000000000 ]
|
||||
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|
||||
position: [ 0.56250000000000, 0.56250000000000, 0.06250000000000 ]
|
||||
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|
||||
position: [ 0.06250000000000, 0.06250000000000, 0.56250000000000 ]
|
||||
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|
||||
position: [ 0.56250000000000, 0.06250000000000, 0.56250000000000 ]
|
||||
- symbol: Si # 39
|
||||
position: [ 0.06250000000000, 0.56250000000000, 0.56250000000000 ]
|
||||
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|
||||
position: [ 0.56250000000000, 0.56250000000000, 0.56250000000000 ]
|
||||
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|
||||
position: [ 0.06250000000000, 0.31250000000000, 0.31250000000000 ]
|
||||
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|
||||
position: [ 0.56250000000000, 0.31250000000000, 0.31250000000000 ]
|
||||
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|
||||
position: [ 0.06250000000000, 0.81250000000000, 0.31250000000000 ]
|
||||
- symbol: Si # 44
|
||||
position: [ 0.56250000000000, 0.81250000000000, 0.31250000000000 ]
|
||||
- symbol: Si # 45
|
||||
position: [ 0.06250000000000, 0.31250000000000, 0.81250000000000 ]
|
||||
- symbol: Si # 46
|
||||
position: [ 0.56250000000000, 0.31250000000000, 0.81250000000000 ]
|
||||
- symbol: Si # 47
|
||||
position: [ 0.06250000000000, 0.81250000000000, 0.81250000000000 ]
|
||||
- symbol: Si # 48
|
||||
position: [ 0.56250000000000, 0.81250000000000, 0.81250000000000 ]
|
||||
- symbol: Si # 49
|
||||
position: [ 0.31250000000000, 0.06250000000000, 0.31250000000000 ]
|
||||
- symbol: Si # 50
|
||||
position: [ 0.81250000000000, 0.06250000000000, 0.31250000000000 ]
|
||||
- symbol: Si # 51
|
||||
position: [ 0.31250000000000, 0.56250000000000, 0.31250000000000 ]
|
||||
- symbol: Si # 52
|
||||
position: [ 0.81250000000000, 0.56250000000000, 0.31250000000000 ]
|
||||
- symbol: Si # 53
|
||||
position: [ 0.31250000000000, 0.06250000000000, 0.81250000000000 ]
|
||||
- symbol: Si # 54
|
||||
position: [ 0.81250000000000, 0.06250000000000, 0.81250000000000 ]
|
||||
- symbol: Si # 55
|
||||
position: [ 0.31250000000000, 0.56250000000000, 0.81250000000000 ]
|
||||
- symbol: Si # 56
|
||||
position: [ 0.81250000000000, 0.56250000000000, 0.81250000000000 ]
|
||||
- symbol: Si # 57
|
||||
position: [ 0.31250000000000, 0.31250000000000, 0.06250000000000 ]
|
||||
- symbol: Si # 58
|
||||
position: [ 0.81250000000000, 0.31250000000000, 0.06250000000000 ]
|
||||
- symbol: Si # 59
|
||||
position: [ 0.31250000000000, 0.81250000000000, 0.06250000000000 ]
|
||||
- symbol: Si # 60
|
||||
position: [ 0.81250000000000, 0.81250000000000, 0.06250000000000 ]
|
||||
- symbol: Si # 61
|
||||
position: [ 0.31250000000000, 0.31250000000000, 0.56250000000000 ]
|
||||
- symbol: Si # 62
|
||||
position: [ 0.81250000000000, 0.31250000000000, 0.56250000000000 ]
|
||||
- symbol: Si # 63
|
||||
position: [ 0.31250000000000, 0.81250000000000, 0.56250000000000 ]
|
||||
- symbol: Si # 64
|
||||
position: [ 0.81250000000000, 0.81250000000000, 0.56250000000000 ]
|
||||
|
|
@ -34,6 +34,7 @@
|
|||
# POSSIBILITY OF SUCH DAMAGE.
|
||||
|
||||
import warnings
|
||||
from typing import Optional
|
||||
|
||||
import numpy as np
|
||||
from phonopy.exception import ForceCalculatorRequiredError
|
||||
|
|
@ -155,7 +156,7 @@ class Phono3py:
|
|||
store_dense_gp_map=True,
|
||||
store_dense_svecs=True,
|
||||
symprec=1e-5,
|
||||
calculator=None,
|
||||
calculator: Optional[str] = None,
|
||||
log_level=0,
|
||||
lapack_zheev_uplo=None,
|
||||
):
|
||||
|
|
@ -254,7 +255,7 @@ class Phono3py:
|
|||
self._store_dense_svecs = store_dense_svecs
|
||||
|
||||
self._cutoff_frequency = cutoff_frequency
|
||||
self._calculator = calculator
|
||||
self._calculator: Optional[str] = calculator
|
||||
self._log_level = log_level
|
||||
|
||||
# Create supercell and primitive cell
|
||||
|
|
@ -399,7 +400,7 @@ class Phono3py:
|
|||
return self.version
|
||||
|
||||
@property
|
||||
def calculator(self):
|
||||
def calculator(self) -> Optional[str]:
|
||||
"""Return calculator interface name.
|
||||
|
||||
str
|
||||
|
|
|
|||
|
|
@ -33,6 +33,7 @@
|
|||
# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
|
||||
# POSSIBILITY OF SUCH DAMAGE.
|
||||
|
||||
import copy
|
||||
import os
|
||||
import sys
|
||||
from typing import Optional
|
||||
|
|
@ -78,7 +79,12 @@ def create_phono3py_force_constants(
|
|||
output_filename: Optional[str] = None,
|
||||
log_level=1,
|
||||
):
|
||||
"""Read or calculate force constants."""
|
||||
"""Read or calculate force constants.
|
||||
|
||||
This function is for the 'phonopy' command only and not for the
|
||||
'phonopy-load' command.
|
||||
|
||||
"""
|
||||
# Only for build-in fc calculator.
|
||||
# These are not applied to external fc calculators.
|
||||
symmetrize_fc3r = settings.is_symmetrize_fc3_r or settings.fc_symmetry
|
||||
|
|
@ -205,19 +211,43 @@ def parse_forces(
|
|||
fc_type=None,
|
||||
log_level=0,
|
||||
):
|
||||
"""Read displacements and forces."""
|
||||
filename_read_from = None
|
||||
"""Read displacements and forces.
|
||||
|
||||
Physical units of displacements and forces are converted following the
|
||||
calculator name. The calculator name may be given as the user input or found
|
||||
in phono3py-yaml file. When dumping to phono3py-yaml file, it is assumed
|
||||
that displacements and forces are written in the default units (A and eV/A)
|
||||
without writing calculator name in it.
|
||||
|
||||
"""
|
||||
filename_read_from: Optional[str] = None
|
||||
|
||||
calculator = phono3py.calculator
|
||||
# Get dataset from ph3py_yaml. dataset can be None.
|
||||
# physical_units can be overwritten if calculator is found in ph3py_yaml.
|
||||
dataset = _extract_dataset_from_ph3py_yaml(ph3py_yaml, fc_type)
|
||||
if dataset and ph3py_yaml.calculator:
|
||||
calculator = ph3py_yaml.calculator
|
||||
|
||||
physical_units = get_default_physical_units(calculator)
|
||||
|
||||
if fc_type == "phonon_fc2":
|
||||
natom = len(phono3py.phonon_supercell)
|
||||
else:
|
||||
natom = len(phono3py.supercell)
|
||||
|
||||
# Get dataset from ph3py_yaml. dataset can be None.
|
||||
dataset = _extract_dataset_from_ph3py_yaml(ph3py_yaml, fc_type)
|
||||
if dataset:
|
||||
filename_read_from = phono3py_yaml_filename
|
||||
|
||||
# Units of displacements and forces are converted. If forces don't
|
||||
# exist, the convesion will not be performed for forces.
|
||||
if calculator is not None:
|
||||
_convert_unit_in_dataset(
|
||||
dataset,
|
||||
distance_to_A=physical_units["distance_to_A"],
|
||||
force_to_eVperA=physical_units["force_to_eVperA"],
|
||||
)
|
||||
|
||||
# Try to read FORCES_FC* if type-2 and return dataset.
|
||||
# None is returned unless type-2.
|
||||
# can emit FileNotFoundError.
|
||||
|
|
@ -230,6 +260,15 @@ def parse_forces(
|
|||
filename_read_from = force_filename
|
||||
dataset = _dataset
|
||||
|
||||
# Units of displacements and forces are converted.
|
||||
if calculator is not None:
|
||||
_convert_unit_in_dataset(
|
||||
dataset,
|
||||
distance_to_A=physical_units["distance_to_A"],
|
||||
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 = (
|
||||
|
|
@ -242,6 +281,20 @@ def parse_forces(
|
|||
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"],
|
||||
)
|
||||
|
||||
if "natom" in dataset and dataset["natom"] != natom:
|
||||
msg = (
|
||||
"Number of atoms in supercell is not consistent with "
|
||||
|
|
@ -273,12 +326,18 @@ def parse_forces(
|
|||
else:
|
||||
parse_FORCES_FC3(dataset, filename=force_filename)
|
||||
|
||||
# Unit of displacements is already converted.
|
||||
# Therefore, only unit of forces is converted.
|
||||
if calculator is not None:
|
||||
_convert_unit_in_dataset(
|
||||
dataset,
|
||||
force_to_eVperA=physical_units["force_to_eVperA"],
|
||||
)
|
||||
|
||||
if log_level:
|
||||
print('Sets of supercell forces were read from "%s".' % force_filename)
|
||||
sys.stdout.flush()
|
||||
|
||||
_convert_unit_in_dataset(dataset, phono3py.calculator)
|
||||
|
||||
return dataset
|
||||
|
||||
|
||||
|
|
@ -567,11 +626,16 @@ def _create_phono3py_phonon_fc2(
|
|||
)
|
||||
|
||||
|
||||
def _convert_unit_in_dataset(dataset, calculator):
|
||||
physical_units = get_default_physical_units(calculator)
|
||||
force_to_eVperA = physical_units["force_to_eVperA"]
|
||||
distance_to_A = physical_units["distance_to_A"]
|
||||
def _convert_unit_in_dataset(
|
||||
dataset: dict,
|
||||
distance_to_A: Optional[float] = None,
|
||||
force_to_eVperA: Optional[float] = None,
|
||||
) -> None:
|
||||
"""Convert physical units of displacements and forces in dataset.
|
||||
|
||||
dataset is overwritten.
|
||||
|
||||
"""
|
||||
if "first_atoms" in dataset:
|
||||
for d1 in dataset["first_atoms"]:
|
||||
if distance_to_A is not None:
|
||||
|
|
@ -608,8 +672,8 @@ def _extract_dataset_from_ph3py_yaml(ph3py_yaml: Optional[Phono3pyYaml], fc_type
|
|||
dataset = None
|
||||
if fc_type == "phonon_fc2":
|
||||
if ph3py_yaml and ph3py_yaml.phonon_dataset is not None:
|
||||
dataset = ph3py_yaml.phonon_dataset
|
||||
dataset = copy.deepcopy(ph3py_yaml.phonon_dataset)
|
||||
else:
|
||||
if ph3py_yaml and ph3py_yaml.dataset is not None:
|
||||
dataset = ph3py_yaml.dataset
|
||||
dataset = copy.deepcopy(ph3py_yaml.dataset)
|
||||
return dataset
|
||||
|
|
|
|||
|
|
@ -84,25 +84,24 @@ def load(
|
|||
) -> Phono3py:
|
||||
"""Create Phono3py instance from parameters and/or input files.
|
||||
|
||||
"phono3py_yaml"-like file is parsed unless crystal structure information
|
||||
is given by unitcell_filename, supercell_filename, unitcell
|
||||
(PhonopyAtoms-like), or supercell (PhonopyAtoms-like).
|
||||
Even when "phono3py_yaml"-like file is parse, parameters except for
|
||||
crystal structure can be overwritten.
|
||||
"phono3py_yaml"-like file is parsed unless crystal structure information is
|
||||
given by unitcell_filename, supercell_filename, unitcell
|
||||
(PhonopyAtoms-like), or supercell (PhonopyAtoms-like). Even when
|
||||
"phono3py_yaml"-like file is parse, parameters except for crystal structure
|
||||
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.
|
||||
'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.
|
||||
|
||||
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 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
|
||||
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.
|
||||
'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.
|
||||
|
||||
Crystal structure
|
||||
-----------------
|
||||
|
|
@ -115,18 +114,16 @@ def load(
|
|||
|
||||
Force sets or force constants
|
||||
-----------------------------
|
||||
Optional. Means to provide information to generate force constants
|
||||
and their priority:
|
||||
Optional. Means to provide information to generate force constants and their
|
||||
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.
|
||||
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.
|
||||
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.
|
||||
optionally 'disp_fc2.yaml' are 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)
|
||||
----------------------------------------------------
|
||||
|
|
@ -139,45 +136,40 @@ def load(
|
|||
Parameters
|
||||
----------
|
||||
phono3py_yaml : str, optional
|
||||
Filename of "phono3py.yaml"-like file. If this is given, the data
|
||||
in the file are parsed. Default is None.
|
||||
Filename of "phono3py.yaml"-like file. If this is given, the data in the
|
||||
file are parsed. Default is None.
|
||||
supercell_matrix : array_like, optional
|
||||
Supercell matrix multiplied to input cell basis vectors.
|
||||
shape=(3, ) or (3, 3), where the former is considered a diagonal
|
||||
matrix. Default is the unit matrix.
|
||||
dtype=int
|
||||
Supercell matrix multiplied to input cell basis vectors. shape=(3, ) or
|
||||
(3, 3), where the former is considered a diagonal matrix. Default is the
|
||||
unit matrix. dtype=int
|
||||
primitive_matrix : array_like or str, optional
|
||||
Primitive matrix multiplied to input cell basis vectors. Default is
|
||||
the identity matrix.
|
||||
When given as array_like, shape=(3, 3), dtype=float.
|
||||
When 'F', 'I', 'A', 'C', or 'R' is given instead of a 3x3 matrix,
|
||||
the primitive matrix defined at
|
||||
https://spglib.github.io/spglib/definition.html
|
||||
is used.
|
||||
When 'auto' is given, the centring type ('F', 'I', 'A', 'C', 'R', or
|
||||
primitive 'P') is automatically chosen.
|
||||
Default is 'auto'.
|
||||
Primitive matrix multiplied to input cell basis vectors. Default is the
|
||||
identity matrix. When given as array_like, shape=(3, 3), dtype=float.
|
||||
When 'F', 'I', 'A', 'C', or 'R' is given instead of a 3x3 matrix, the
|
||||
primitive matrix defined at
|
||||
https://spglib.github.io/spglib/definition.html is used. When 'auto' is
|
||||
given, the centring type ('F', 'I', 'A', 'C', 'R', or primitive 'P') is
|
||||
automatically chosen. Default is 'auto'.
|
||||
phonon_supercell_matrix : array_like, optional
|
||||
Supercell matrix used for fc2. In phono3py, supercell matrix for fc3
|
||||
and fc2 can be different to support longer range interaction of fc2
|
||||
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.
|
||||
Supercell matrix used for fc2. In phono3py, supercell matrix for fc3 and
|
||||
fc2 can be different to support longer range interaction of fc2 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.
|
||||
is_nac : bool, optional
|
||||
If True, look for 'BORN' file. If False, NAS is turned off.
|
||||
Default is True.
|
||||
If True, look for 'BORN' file. If False, NAS is turned off. Default is
|
||||
True.
|
||||
calculator : str, optional.
|
||||
Calculator used for computing forces. This is used to switch the set
|
||||
of physical units. Default is None, which is equivalent to "vasp".
|
||||
Calculator used for computing forces. This is used to switch the set of
|
||||
physical units when parsing calculator input/output files. Default is
|
||||
None, which is equivalent to "vasp".
|
||||
unitcell : PhonopyAtoms, optional
|
||||
Input unit cell. Default is None.
|
||||
supercell : PhonopyAtoms, optional
|
||||
Input supercell. With given, default value of primitive_matrix is set
|
||||
to 'auto' (can be overwitten). supercell_matrix is ignored. Default is
|
||||
Input supercell. With given, default value of primitive_matrix is set to
|
||||
'auto' (can be overwitten). supercell_matrix is ignored. Default is
|
||||
None.
|
||||
nac_params : dict, optional
|
||||
Parameters required for non-analytical term correction. Default is
|
||||
None.
|
||||
Parameters required for non-analytical term correction. Default is None.
|
||||
{'born': Born effective charges
|
||||
(array_like, shape=(primitive cell atoms, 3, 3), dtype=float),
|
||||
'dielectric': Dielectric constant matrix
|
||||
|
|
@ -192,15 +184,13 @@ def load(
|
|||
Filename corresponding to 'BORN', a file contains non-analytical term
|
||||
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) corresponding to 'FORCES_FC3' in the type-2 format.
|
||||
Default is None.
|
||||
A two-elemental sequence of filenames corresponding to ('FORCES_FC3',
|
||||
'disp_fc3.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) corresponding to 'FORCES_FC2' in the type-2 format.
|
||||
Default is None.
|
||||
A two-elemental sequence of filenames corresponding to ('FORCES_FC2',
|
||||
'disp_fc2.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
|
||||
third-order force constants. Default is None.
|
||||
|
|
@ -210,32 +200,31 @@ def load(
|
|||
fc_calculator : str, optional
|
||||
Force constants calculator. Currently only 'alm'. Default is None.
|
||||
fc_calculator_options : str, optional
|
||||
Optional parameters that are passed to the external fc-calculator.
|
||||
This is given as one text string. How to parse this depends on the
|
||||
fc-calculator. For alm, each parameter is splitted by comma ',',
|
||||
and each set of key and value pair is written in 'key = value'.
|
||||
Optional parameters that are passed to the external fc-calculator. This
|
||||
is given as one text string. How to parse this depends on the
|
||||
fc-calculator. For alm, each parameter is splitted by comma ',', and
|
||||
each set of key and value pair is written in 'key = value'.
|
||||
factor : float, optional
|
||||
Phonon frequency unit conversion factor. Unless specified, default
|
||||
unit conversion factor for each calculator is used.
|
||||
Phonon frequency unit conversion factor. Unless specified, default unit
|
||||
conversion factor for each calculator is used.
|
||||
produce_fc : bool, optional
|
||||
Setting False, force constants are not calculated from displacements
|
||||
and forces. Default is True.
|
||||
Setting False, force constants are not calculated from displacements and
|
||||
forces. Default is True.
|
||||
is_symmetry : bool, optional
|
||||
Setting False, crystal symmetry except for lattice translation is not
|
||||
considered. Default is True.
|
||||
symmetrize_fc : bool, optional
|
||||
Setting False, force constants are not symmetrized when creating
|
||||
force constants from displacements and forces. Default is True.
|
||||
Setting False, force constants are not symmetrized when creating force
|
||||
constants from displacements and forces. Default is True.
|
||||
is_mesh_symmetry : bool, optional
|
||||
Setting False, reciprocal mesh symmetry is not considered.
|
||||
Default is True.
|
||||
Setting False, reciprocal mesh symmetry is not considered. Default is
|
||||
True.
|
||||
is_compact_fc : bool, optional
|
||||
fc3 are created in the array whose shape is
|
||||
True: (primitive, supercell, supecell, 3, 3, 3)
|
||||
False: (supercell, supercell, supecell, 3, 3, 3)
|
||||
True: (primitive, supercell, supecell, 3, 3, 3) False: (supercell,
|
||||
supercell, supecell, 3, 3, 3)
|
||||
and for fc2
|
||||
True: (primitive, supecell, 3, 3)
|
||||
False: (supercell, supecell, 3, 3)
|
||||
True: (primitive, supecell, 3, 3) False: (supercell, supecell, 3, 3)
|
||||
where 'supercell' and 'primitive' indicate number of atoms in these
|
||||
cells. Default is False.
|
||||
use_grg : bool, optional
|
||||
|
|
@ -243,9 +232,9 @@ def load(
|
|||
store_dense_gp_map : bool, optional, Deprecated
|
||||
Use new format of BZ grid system. Default is True.
|
||||
store_dense_svecs : bool, optional, Deprecated
|
||||
Shortest vectors are stored in the dense array format. This is
|
||||
expected to be always True. Setting False is for rough
|
||||
compatibility with v1.x. Default is True.
|
||||
Shortest vectors are stored in the dense array format. This is expected
|
||||
to be always True. Setting False is for rough compatibility with v1.x.
|
||||
Default is True.
|
||||
symprec : float, optional
|
||||
Tolerance used to find crystal symmetry. Default is 1e-5.
|
||||
log_level : int, optional
|
||||
|
|
@ -257,7 +246,7 @@ def load(
|
|||
or supercell_filename is not None
|
||||
or unitcell is not None
|
||||
or unitcell_filename is not None
|
||||
): # noqa E129
|
||||
):
|
||||
cell, smat, pmat = load_helper.get_cell_settings(
|
||||
supercell_matrix=supercell_matrix,
|
||||
primitive_matrix=primitive_matrix,
|
||||
|
|
|
|||
|
|
@ -490,7 +490,7 @@ def get_parser(fc_symmetry=False, is_nac=False, load_phono3py_yaml=False):
|
|||
"--nac-method",
|
||||
dest="nac_method",
|
||||
default=None,
|
||||
help="Non-analytical term correction method: Wang (default) or Gonze",
|
||||
help="Non-analytical term correction method: Gonze (default) or Wang",
|
||||
)
|
||||
if fc_symmetry:
|
||||
parser.add_argument(
|
||||
|
|
|
|||
|
|
@ -59,9 +59,9 @@ from phonopy.structure.symmetry import Symmetry
|
|||
class Phono3pyYamlData:
|
||||
"""PhonopyYaml data structure."""
|
||||
|
||||
configuration: dict
|
||||
calculator: str
|
||||
physical_units: dict
|
||||
configuration: Optional[dict] = None
|
||||
calculator: Optional[str] = None
|
||||
physical_units: Optional[dict] = None
|
||||
unitcell: Optional[PhonopyAtoms] = None
|
||||
primitive: Optional[Primitive] = None
|
||||
supercell: Optional[Supercell] = None
|
||||
|
|
|
|||
|
|
@ -459,12 +459,11 @@ def _solve_fc3(
|
|||
solver = "numpy.linalg.pinv"
|
||||
|
||||
if verbose:
|
||||
text = "Computing fc3[ %d, x, x ] using %s with " % (first_atom_num + 1, solver)
|
||||
print(f"Computing fc3[ {first_atom_num + 1}, x, x ] using {solver}.")
|
||||
if len(displacements_first) > 1:
|
||||
text += "displacements:"
|
||||
print("Displacements (in Angstrom):")
|
||||
else:
|
||||
text += "a displacement:"
|
||||
print(text)
|
||||
print("One displacement (in Angstrom):")
|
||||
for i, v in enumerate(displacements_first):
|
||||
print(" [%7.4f %7.4f %7.4f]" % tuple(v))
|
||||
sys.stdout.flush()
|
||||
|
|
|
|||
|
|
@ -33,4 +33,4 @@
|
|||
# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
|
||||
# POSSIBILITY OF SUCH DAMAGE.
|
||||
|
||||
__version__ = "2.7.0"
|
||||
__version__ = "2.8.0"
|
||||
|
|
|
|||
|
|
@ -2,4 +2,4 @@ numpy >= 1.17.0
|
|||
PyYAML >= 5.3
|
||||
matplotlib >= 2.2.2
|
||||
h5py >= 3.0
|
||||
phonopy >=2.20,<2.21
|
||||
phonopy >=2.21,<2.22
|
||||
|
|
|
|||
2
setup.py
2
setup.py
|
|
@ -319,7 +319,7 @@ def main(build_dir):
|
|||
"matplotlib>=2.2.2",
|
||||
"h5py>=3.0",
|
||||
"spglib>=2.0",
|
||||
"phonopy>=2.20,<2.21",
|
||||
"phonopy>=2.21,<2.22",
|
||||
],
|
||||
provides=["phono3py"],
|
||||
scripts=scripts_phono3py,
|
||||
|
|
|
|||
Binary file not shown.
|
|
@ -5,8 +5,10 @@ import os
|
|||
import pathlib
|
||||
from collections.abc import Sequence
|
||||
from dataclasses import dataclass, fields
|
||||
from typing import Optional
|
||||
from typing import Optional, Union
|
||||
|
||||
import h5py
|
||||
import numpy as np
|
||||
import pytest
|
||||
|
||||
from phono3py.cui.phono3py_script import main
|
||||
|
|
@ -19,7 +21,7 @@ cwd_called = pathlib.Path.cwd()
|
|||
class MockArgs:
|
||||
"""Mock args of ArgumentParser."""
|
||||
|
||||
filename: Sequence[os.PathLike]
|
||||
filename: Optional[Sequence[os.PathLike]] = None
|
||||
conf_filename: Optional[os.PathLike] = None
|
||||
fc_calculator: Optional[str] = None
|
||||
force_sets_mode: bool = False
|
||||
|
|
@ -28,11 +30,22 @@ class MockArgs:
|
|||
output_yaml_filename: Optional[os.PathLike] = None
|
||||
show_num_triplets: bool = False
|
||||
write_grid_points: bool = False
|
||||
fc_symmetry: bool = True
|
||||
cell_filename: Optional[str] = None
|
||||
is_bterta: Optional[bool] = None
|
||||
mesh_numbers: Optional[Sequence] = None
|
||||
temperatures: Optional[Sequence] = None
|
||||
input_filename = None
|
||||
output_filename = None
|
||||
input_output_filename = None
|
||||
|
||||
def __iter__(self):
|
||||
"""Make self iterable to support in."""
|
||||
return (getattr(self, field.name) for field in fields(self))
|
||||
|
||||
def __contains__(self, item):
|
||||
return item in (field.name for field in fields(self))
|
||||
|
||||
|
||||
def test_phono3py_load():
|
||||
"""Test phono3py-load script."""
|
||||
|
|
@ -71,19 +84,70 @@ def test_phono3py_load_with_typeII_dataset(fc_calculator, exit_code):
|
|||
file_path.unlink()
|
||||
|
||||
|
||||
def _get_phono3py_load_args(phono3py_yaml_filepath, fc_calculator=None):
|
||||
# Mock of ArgumentParser.args.
|
||||
mockargs = MockArgs(
|
||||
filename=[phono3py_yaml_filepath],
|
||||
fc_calculator=fc_calculator,
|
||||
log_level=1,
|
||||
@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 h5py.File(cwd_called / "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(cwd_called / created_filename)
|
||||
if file_path.exists():
|
||||
file_path.unlink()
|
||||
|
||||
|
||||
def _get_phono3py_load_args(
|
||||
phono3py_yaml_filepath: Union[str, pathlib.Path],
|
||||
fc_calculator: Optional[str] = None,
|
||||
load_phono3py_yaml: bool = True,
|
||||
is_bterta: bool = False,
|
||||
temperatures: Optional[Sequence] = None,
|
||||
mesh_numbers: Optional[Sequence] = None,
|
||||
):
|
||||
# Mock of ArgumentParser.args.
|
||||
if load_phono3py_yaml:
|
||||
mockargs = MockArgs(
|
||||
filename=[phono3py_yaml_filepath],
|
||||
fc_calculator=fc_calculator,
|
||||
is_bterta=is_bterta,
|
||||
temperatures=temperatures,
|
||||
mesh_numbers=mesh_numbers,
|
||||
log_level=1,
|
||||
)
|
||||
else:
|
||||
mockargs = MockArgs(
|
||||
filename=[],
|
||||
fc_calculator=fc_calculator,
|
||||
log_level=1,
|
||||
cell_filename=phono3py_yaml_filepath,
|
||||
is_bterta=is_bterta,
|
||||
temperatures=temperatures,
|
||||
mesh_numbers=mesh_numbers,
|
||||
)
|
||||
|
||||
# See phono3py-load script.
|
||||
argparse_control = {
|
||||
"fc_symmetry": True,
|
||||
"is_nac": True,
|
||||
"load_phono3py_yaml": True,
|
||||
"fc_symmetry": load_phono3py_yaml,
|
||||
"is_nac": load_phono3py_yaml,
|
||||
"load_phono3py_yaml": load_phono3py_yaml,
|
||||
"args": mockargs,
|
||||
}
|
||||
return argparse_control
|
||||
|
|
|
|||
Loading…
Reference in New Issue