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phono3py
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Merge branch 'develop' into publish-gh-pages

This commit is contained in:
Atsushi Togo 2024-05-04 09:42:45 +02:00
parent 78e94a4a5b d57feb3e90
commit 4132db5eca
19 changed files with 895 additions and 380 deletions
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2
.pre-commit-config.yaml
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@ -19,7 +19,7 @@ repos:
- "--ignore=E203,W503"
- repo: https://github.com/psf/black
rev: 24.4.0
rev: 24.4.2
hooks:
- id: black
args:

4
doc/changelog.md
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@ -2,6 +2,10 @@
# Change Log
## May-4-2024: Version 3.0.3
- Release to follow the update of phonopy.
## Apr-21-2024: Version 3.0.2
- New way of ph-ph interaction calculation (see {ref}`changelog_v290`) is used as

2
doc/conf.py
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@ -60,7 +60,7 @@ copyright = "2015, Atsushi Togo"
# The short X.Y version.
version = "3.0"
# The full version, including alpha/beta/rc tags.
release = "3.0.2"
release = "3.0.3"
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.

277
phono3py/api_phono3py.py
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@ -34,8 +34,9 @@
# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
import copy
from collections.abc import Sequence
from typing import Optional, Union
from typing import Literal, Optional, Union
import numpy as np
from phonopy.exception import ForceCalculatorRequiredError
@ -582,6 +583,7 @@ class Phono3py:
{'number': atom index of second displaced atom,
'displacement': displacement in Cartesian coordinates},
'forces': forces on atoms in supercell,
'supercell_energy': energy of supercell,
'pair_distance': distance between paired atoms,
'included': with cutoff pair distance in displacement
pair generation, this indicates if this
@ -591,9 +593,11 @@ class Phono3py:
... ] }, ... ] }
Type 2. All atomic displacements in each supercell:
{'displacements': ndarray, dtype='double', order='C',
shape=(supercells, atoms in supercell, 3)
shape=(supercells, atoms in supercell, 3),
'forces': ndarray, dtype='double',, order='C',
shape=(supercells, atoms in supercell, 3)}
shape=(supercells, atoms in supercell, 3),
'supercell_energies': ndarray, dtype='double',
shape=(supercells,)}
In type 2, displacements and forces can be given by numpy array
with different shape but that can be reshaped to
(supercells, natom, 3).
@ -607,7 +611,20 @@ class Phono3py:
@dataset.setter
def dataset(self, dataset):
self._dataset = dataset
if dataset is None:
self._dataset = None
elif "first_atoms" in dataset:
self._dataset = copy.deepcopy(dataset)
elif "displacements" in dataset:
self._dataset = {}
self.displacements = dataset["displacements"]
if "forces" in dataset:
self.forces = dataset["forces"]
if "supercell_energies" in dataset:
self.supercell_energies = dataset["supercell_energies"]
else:
raise RuntimeError("Data format of dataset is wrong.")
self._supercells_with_displacements = None
self._phonon_supercells_with_displacements = None
@ -622,12 +639,15 @@ class Phono3py:
'first_atoms': [
{'number': atom index of first displaced atom,
'displacement': displacement in Cartesian coordinates,
'forces': forces on atoms in supercell} ... ]}
'forces': forces on atoms in supercell,
'supercell_energy': energy of supercell}, ... ]}
Type 2. All atomic displacements in each supercell:
{'displacements': ndarray, dtype='double', order='C',
shape=(supercells, atoms in supercell, 3)
shape=(supercells, atoms in supercell, 3),
'forces': ndarray, dtype='double',, order='C',
shape=(supercells, atoms in supercell, 3)}
shape=(supercells, atoms in supercell, 3),
'supercell_energies': ndarray, dtype='double',
shape=(supercells,)}
In type 2, displacements and forces can be given by numpy array
with different shape but that can be reshaped to
(supercells, natom, 3).
@ -637,7 +657,21 @@ class Phono3py:
@phonon_dataset.setter
def phonon_dataset(self, dataset):
self._phonon_dataset = dataset
if dataset is None:
self._phonon_dataset = None
elif "first_atoms" in dataset:
self._phonon_dataset = copy.deepcopy(dataset)
elif "displacements" in dataset:
self._phonon_dataset = {}
self.phonon_displacements = dataset["displacements"]
if "forces" in dataset:
self.phonon_forces = dataset["forces"]
if "supercell_energies" in dataset:
self.phonon_supercell_energies = dataset["supercell_energies"]
else:
raise RuntimeError("Data format of dataset is wrong.")
self._phonon_supercells_with_displacements = None
@property
def band_indices(self):
@ -816,45 +850,32 @@ class Phono3py:
be the same order of supercells_with_displacements.
"""
dataset = self._dataset
if "forces" in dataset:
return dataset["forces"]
elif "first_atoms" in dataset:
num_scells = len(dataset["first_atoms"])
for disp1 in dataset["first_atoms"]:
num_scells += len(disp1["second_atoms"])
forces = np.zeros(
(num_scells, self._supercell.get_number_of_atoms(), 3),
dtype="double",
order="C",
)
i = 0
for disp1 in dataset["first_atoms"]:
forces[i] = disp1["forces"]
i += 1
for disp1 in dataset["first_atoms"]:
for disp2 in disp1["second_atoms"]:
forces[i] = disp2["forces"]
i += 1
return forces
else:
raise RuntimeError("displacement dataset has wrong format.")
return self._get_forces_energies(target="forces")
@forces.setter
def forces(self, forces_fc3):
forces = np.array(forces_fc3, dtype="double", order="C")
dataset = self._dataset
if "first_atoms" in dataset:
i = 0
for disp1 in dataset["first_atoms"]:
disp1["forces"] = forces[i]
i += 1
for disp1 in dataset["first_atoms"]:
for disp2 in disp1["second_atoms"]:
disp2["forces"] = forces[i]
i += 1
elif "displacements" in dataset or "forces" in dataset:
dataset["forces"] = forces
def forces(self, values):
self._set_forces_energies(values, target="forces")
@property
def supercell_energies(self):
"""Setter and getter of supercell energies in displacement dataset.
A set of supercell energies of displaced supercells. The order of
displaced supercells has to match with that in displacement dataset.
shape=(displaced supercells,)
getter : ndarray
setter : array_like
The order of supercells used for calculating supercell energies has
to be the same order of supercells_with_displacements.
"""
return self._get_forces_energies(target="supercell_energies")
@supercell_energies.setter
def supercell_energies(self, values):
self._set_forces_energies(values, target="supercell_energies")
@property
def phonon_displacements(self):
@ -922,7 +943,7 @@ class Phono3py:
@property
def phonon_forces(self):
"""Setter and getter of forces in displacement dataset for fc2.
"""Setter and getter of forces in fc2 displacement dataset.
A set of atomic forces in displaced supercells. The order of
displaced supercells has to match with that in phonon displacement
@ -936,39 +957,30 @@ class Phono3py:
be the same order of phonon_supercells_with_displacements.
"""
if self._phonon_dataset is None:
raise RuntimeError("phonon_displacement_dataset does not exist.")
dataset = self._phonon_dataset
if "forces" in dataset:
return dataset["forces"]
elif "first_atoms" in dataset:
num_scells = len(dataset["first_atoms"])
forces = np.zeros(
(num_scells, self._phonon_supercell.get_number_of_atoms(), 3),
dtype="double",
order="C",
)
for i, disp1 in enumerate(dataset["first_atoms"]):
forces[i] = disp1["forces"]
return forces
else:
raise RuntimeError("displacement dataset has wrong format.")
return self._get_phonon_forces_energies(target="forces")
@phonon_forces.setter
def phonon_forces(self, forces_fc2):
if self._phonon_dataset is None:
raise RuntimeError("phonon_displacement_dataset does not exist.")
def phonon_forces(self, values):
self._set_phonon_forces_energies(values, target="forces")
forces = np.array(forces_fc2, dtype="double", order="C")
dataset = self._phonon_dataset
if "first_atoms" in dataset:
i = 0
for i, disp1 in enumerate(dataset["first_atoms"]):
disp1["forces"] = forces[i]
i += 1
elif "displacements" in dataset or "forces" in dataset:
dataset["forces"] = forces
@property
def phonon_supercell_energies(self):
"""Setter and getter of supercell energies in fc2 displacement dataset.
shape=(displaced supercells,)
getter : ndarray
setter : array_like
The order of supercells used for calculating supercell energies has
to be the same order of phonon_supercells_with_displacements.
"""
return self._get_phonon_forces_energies(target="supercell_energies")
@phonon_supercell_energies.setter
def phonon_supercell_energies(self, values):
self._set_phonon_forces_energies(values, target="supercell_energies")
@property
def phph_interaction(self):
@ -2274,3 +2286,116 @@ class Phono3py:
_fc_calculator_options = None
return _fc_calculator, _fc_calculator_options
def _get_forces_energies(
self, target: Literal["forces", "supercell_energies"]
) -> Optional[np.ndarray]:
"""Return fc3 forces and supercell energies.
Return None if tagert data is not found rather than raising exception.
"""
if target in self._dataset: # type-2
return self._dataset[target]
elif "first_atoms" in self._dataset: # type-1
num_scells = len(self._dataset["first_atoms"])
for disp1 in self._dataset["first_atoms"]:
num_scells += len(disp1["second_atoms"])
if target == "forces":
values = np.zeros(
(num_scells, len(self._supercell), 3),
dtype="double",
order="C",
)
type1_target = "forces"
elif target == "supercell_energies":
values = np.zeros(num_scells, dtype="double")
type1_target = "supercell_energy"
count = 0
for disp1 in self._dataset["first_atoms"]:
values[count] = disp1[type1_target]
count += 1
for disp1 in self._dataset["first_atoms"]:
for disp2 in disp1["second_atoms"]:
values[count] = disp2[type1_target]
count += 1
return values
return None
def _set_forces_energies(
self, values, target: Literal["forces", "supercell_energies"]
):
if "first_atoms" in self._dataset: # type-1
count = 0
for disp1 in self._dataset["first_atoms"]:
if target == "forces":
disp1[target] = np.array(values[count], dtype="double", order="C")
elif target == "supercell_energies":
disp1["supercell_energy"] = float(values[count])
count += 1
for disp1 in self._dataset["first_atoms"]:
for disp2 in disp1["second_atoms"]:
if target == "forces":
disp2[target] = np.array(
values[count], dtype="double", order="C"
)
elif target == "supercell_energies":
disp2["supercell_energy"] = float(values[count])
count += 1
elif "displacements" in self._dataset or "forces" in self._dataset: # type-2
self._dataset[target] = np.array(values, dtype="double", order="C")
else:
raise RuntimeError("Set of FC3 displacements is not available.")
def _get_phonon_forces_energies(
self, target: Literal["forces", "supercell_energies"]
) -> Optional[np.ndarray]:
"""Return fc2 forces and supercell energies.
Return None if tagert data is not found rather than raising exception.
"""
if self._phonon_dataset is None:
raise RuntimeError("Dataset for fc2does not exist.")
if target in self._phonon_dataset: # type-2
return self._phonon_dataset[target]
elif "first_atoms" in self._phonon_dataset: # type-1
values = []
for disp in self._phonon_dataset["first_atoms"]:
if target == "forces":
if target in disp:
values.append(disp[target])
elif target == "supercell_energies":
if "supercell_energy" in disp:
values.append(disp["supercell_energy"])
if values:
return np.array(values, dtype="double", order="C")
return None
def _set_phonon_forces_energies(
self, values, target: Literal["forces", "supercell_energies"]
):
if self._phonon_dataset is None:
raise RuntimeError("Dataset for fc2 does not exist.")
if "first_atoms" in self._phonon_dataset:
for disp, v in zip(self._phonon_dataset["first_atoms"], values):
if target == "forces":
disp[target] = np.array(v, dtype="double", order="C")
elif target == "supercell_energies":
disp["supercell_energy"] = float(v)
elif "displacements" in self._phonon_dataset:
_values = np.array(values, dtype="double", order="C")
natom = len(self._phonon_supercell)
ndisps = len(self._phonon_dataset["displacements"])
if target == "forces" and (
_values.ndim != 3 or _values.shape != (ndisps, natom, 3)
):
raise RuntimeError(f"Array shape of input {target} is incorrect.")
elif target == "supercell_energies":
if _values.ndim != 1 or _values.shape != (ndisps,):
raise RuntimeError(f"Array shape of input {target} is incorrect.")
self._phonon_dataset[target] = _values
else:
raise RuntimeError("Set of FC2 displacements is not available.")

396
phono3py/cui/create_force_sets.py Normal file
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@ -0,0 +1,396 @@
"""Command line user interface to create force sets files."""
# Copyright (C) 2024 Atsushi Togo
# All rights reserved.
#
# This file is part of phono3py.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in
# the documentation and/or other materials provided with the
# distribution.
#
# * Neither the name of the phonopy project nor the names of its
# contributors may be used to endorse or promote products derived
# from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
# FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
# COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
from __future__ import annotations
import copy
import sys
from typing import Optional
import numpy as np
from phonopy.cui.create_force_sets import check_number_of_force_files
from phonopy.cui.load_helper import get_nac_params
from phonopy.cui.phonopy_script import file_exists, files_exist, print_error
from phonopy.file_IO import parse_FORCE_SETS, write_FORCE_SETS
from phonopy.interface.calculator import get_calc_dataset
from phono3py.file_IO import (
get_length_of_first_line,
parse_FORCES_FC2,
write_FORCES_FC2,
write_FORCES_FC3,
)
from phono3py.interface.phono3py_yaml import (
Phono3pyYaml,
displacements_yaml_lines_type1,
)
def create_FORCES_FC3_and_FORCES_FC2(
settings,
cell_filename: Optional[str],
log_level: int = 0,
):
"""Create FORCES_FC3 and FORCES_FC2 or phono3py_params.yaml from files.
With settings.save_params=True, phono3py_params.yaml is created instead of
FORCES_FC3 and FORCES_FC2. To create phono3py_params.yaml, at least fc3
forces have to be collected.
"""
interface_mode = settings.calculator
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]
ph3py_yaml = Phono3pyYaml(settings={"force_sets": True})
ph3py_yaml.read(disp_filename)
if ph3py_yaml.calculator is not None:
interface_mode = ph3py_yaml.calculator # overwrite
if settings.create_forces_fc3 or settings.create_forces_fc3_file:
calc_dataset_fc3 = _get_force_sets_fc3(
settings, ph3py_yaml.dataset, disp_filename, interface_mode, log_level
)
if not calc_dataset_fc3["forces"]:
if log_level:
print("%s could not be created." % "FORCES_FC3")
print_error()
sys.exit(1)
if settings.create_forces_fc2:
calc_dataset_fc2 = _get_force_sets_fc2(
settings,
ph3py_yaml.phonon_dataset,
disp_filename,
interface_mode,
log_level,
)
if not calc_dataset_fc2["forces"]:
if log_level:
print("%s could not be created." % "FORCES_FC2")
print_error()
sys.exit(1)
if settings.save_params:
fc3_yaml_filename = "phono3py_params.yaml"
if not (settings.create_forces_fc3 or settings.create_forces_fc3_file):
if log_level:
print(f'When creating "{fc3_yaml_filename}" with force sets for fc2, ')
print("force sets for fc3 have to be collected simultaneously.")
print(f'"{fc3_yaml_filename}" could not be created.')
print("")
print_error()
sys.exit(1)
_set_forces_and_nac_params(
ph3py_yaml, settings, calc_dataset_fc3, calc_dataset_fc2
)
with open(fc3_yaml_filename, "w") as w:
w.write(str(ph3py_yaml))
if log_level:
print(f'"{fc3_yaml_filename}" has been created.')
else:
if settings.create_forces_fc3 or settings.create_forces_fc3_file:
write_FORCES_FC3(
ph3py_yaml.dataset,
forces_fc3=calc_dataset_fc3["forces"],
filename="FORCES_FC3",
)
if log_level:
print("%s has been created." % "FORCES_FC3")
if settings.create_forces_fc2:
write_FORCES_FC2(
ph3py_yaml.phonon_dataset,
forces_fc2=calc_dataset_fc2["forces"],
filename="FORCES_FC2",
)
if log_level:
print("%s has been created." % "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)
disp_dataset = parse_FORCE_SETS(filename=filename)
write_FORCES_FC2(disp_dataset)
if log_level:
print("")
print("FORCES_FC2 has been created from FORCE_SETS.")
print("The following yaml lines should replace respective part of")
print("phono3py_disp.yaml made with --dim-fc2=dim_of_FORCE_SETS.")
print("")
print("\n".join(displacements_yaml_lines_type1(disp_dataset)))
def create_FORCE_SETS_from_FORCES_FCx(
phonon_smat, input_filename: Optional[str], cell_filename: Optional[str], log_level
):
"""Convert FORCES_FC3 or FORCES_FC2 to FORCE_SETS."""
if cell_filename is not None:
disp_filename = cell_filename
elif input_filename is None:
disp_filename = "phono3py_disp.yaml"
else:
disp_filename = f"phono3py_disp.{input_filename}.yaml"
if phonon_smat is not None:
forces_filename = "FORCES_FC2"
else:
forces_filename = "FORCES_FC3"
if log_level:
print(f'Displacement dataset is read from "{disp_filename}".')
print(f'Forces are read from "{forces_filename}"')
with open(forces_filename, "r") as f:
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)
ph3yml = Phono3pyYaml()
ph3yml.read(disp_filename)
if phonon_smat is None:
dataset = copy.deepcopy(ph3yml.dataset)
smat = ph3yml.supercell_matrix
else:
dataset = copy.deepcopy(ph3yml.phonon_dataset)
smat = ph3yml.phonon_supercell_matrix
if smat is None or (phonon_smat is not None and (phonon_smat != smat).any()):
if log_level:
print("")
print("Supercell matrix is inconsistent.")
print(f'Supercell matrix read from "{disp_filename}":')
print(smat)
print("Supercell matrix given by --dim-fc2:")
print(phonon_smat)
print_error()
sys.exit(1)
parse_FORCES_FC2(dataset, filename=forces_filename)
write_FORCE_SETS(dataset)
if log_level:
print("FORCE_SETS has been created.")
else:
if log_level:
print(
"The file format of %s is already readable by phonopy."
% forces_filename
)
def _get_force_sets_fc2(
settings, disp_dataset, disp_filename, interface_mode, log_level
) -> dict:
interface_mode = settings.calculator
if log_level:
print(f'FC2 displacement dataset was read from "{disp_filename}".')
if "first_atoms" in disp_dataset: # type-1
num_atoms = disp_dataset["natom"]
num_disps = len(disp_dataset["first_atoms"])
elif "displacements" in disp_dataset: # type-2:
num_disps = len(disp_dataset["displacements"])
num_atoms = len(disp_dataset["displacements"][0])
else:
raise RuntimeError("FC2 displacement dataset is broken.")
force_filenames = settings.create_forces_fc2
for filename in force_filenames:
file_exists(filename, log_level)
if log_level > 0:
print(f" Number of displacements: {num_disps}")
print(f" Number of supercell files: {len(force_filenames)}")
calc_dataset = get_calc_dataset(
interface_mode,
num_atoms,
force_filenames,
verbose=(log_level > 0),
)
force_sets = calc_dataset["forces"]
if settings.subtract_forces:
force_filename = settings.subtract_forces
file_exists(force_filename, log_level)
calc_dataset_zero = get_calc_dataset(
interface_mode,
num_atoms,
[
force_filename,
],
verbose=(log_level > 0),
)
force_set_zero = calc_dataset_zero["forces"][0]
for fs in force_sets:
fs -= force_set_zero
if log_level > 0:
print("Forces in '{force_filename}' were subtracted from supercell forces.")
if log_level > 0:
print("")
return calc_dataset
def _get_force_sets_fc3(
settings, disp_dataset, disp_filename, interface_mode, log_level
) -> dict:
if log_level:
print("")
print(f'FC3 Displacement dataset was read from "{disp_filename}".')
if "first_atoms" in disp_dataset: # type-1
num_atoms = disp_dataset["natom"]
num_disps = len(disp_dataset["first_atoms"])
for d1 in disp_dataset["first_atoms"]:
for d2 in d1["second_atoms"]:
if "included" not in d2 or d2["included"]:
num_disps += 1
elif "displacements" in disp_dataset: # type-2:
num_disps = len(disp_dataset["displacements"])
num_atoms = len(disp_dataset["displacements"][0])
else:
raise RuntimeError("FC3 displacement dataset is broken.")
if settings.create_forces_fc3_file:
file_exists(settings.create_forces_fc3_file, 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)
if log_level > 0:
print(f" Number of displacements: {num_disps}")
print(f" Number of supercell files: {len(force_filenames)}")
if not check_number_of_force_files(num_disps, force_filenames, disp_filename):
calc_dataset = {"forces": []}
else:
calc_dataset = get_calc_dataset(
interface_mode,
num_atoms,
force_filenames,
verbose=(log_level > 0),
)
force_sets = calc_dataset["forces"]
if settings.subtract_forces:
force_filename = settings.subtract_forces
file_exists(force_filename, log_level)
calc_dataset = get_calc_dataset(
interface_mode,
num_atoms,
[
force_filename,
],
verbose=(log_level > 0),
)
force_set_zero = calc_dataset["forces"][0]
for fs in force_sets:
fs -= force_set_zero
if log_level > 0:
print(
f"Forces in '{force_filename}' were subtracted from supercell forces."
)
if log_level > 0:
print("")
return calc_dataset
def _set_forces_and_nac_params(
ph3py_yaml: Phono3pyYaml, settings, calc_dataset_fc3: dict, calc_dataset_fc2: dict
):
if "first_atoms" in ph3py_yaml.dataset:
count = len(ph3py_yaml.dataset["first_atoms"])
for i, d1 in enumerate(ph3py_yaml.dataset["first_atoms"]):
d1["forces"] = calc_dataset_fc3["forces"][i]
if "supercell_energies" in calc_dataset_fc3:
d1["supercell_energy"] = float(
calc_dataset_fc3["supercell_energies"][i]
)
for d2 in d1["second_atoms"]:
if "included" not in d2 or d2["included"]:
d2["forces"] = calc_dataset_fc3["forces"][count]
if "supercell_energies" in calc_dataset_fc3:
d2["supercell_energy"] = float(
calc_dataset_fc3["supercell_energies"][count]
)
count += 1
else:
ph3py_yaml.dataset["forces"] = np.array(
calc_dataset_fc3["forces"], dtype="double", order="C"
)
ph3py_yaml.dataset["supercell_energies"] = np.array(
calc_dataset_fc3["supercell_energies"], dtype="double"
)
if settings.create_forces_fc2:
if "first_atoms" in ph3py_yaml.phonon_dataset:
for i, d in enumerate(ph3py_yaml.phonon_dataset["first_atoms"]):
d["forces"] = calc_dataset_fc2["forces"][i]
if "supercell_energies" in calc_dataset_fc2:
d["supercell_energy"] = float(
calc_dataset_fc2["supercell_energies"][i]
)
else:
ph3py_yaml.phonon_dataset["forces"] = np.array(
calc_dataset_fc2["forces"], dtype="double", order="C"
)
ph3py_yaml.phonon_dataset["supercell_energies"] = np.array(
calc_dataset_fc2["supercell_energies"], dtype="double"
)
nac_params = get_nac_params(primitive=ph3py_yaml.primitive)
if nac_params:
ph3py_yaml.nac_params = nac_params

5
phono3py/cui/create_supercells.py
View File

@ -1,4 +1,4 @@
"""Utilities of main CUI script."""
"""Command line user interface to create supercells."""
# Copyright (C) 2015 Atsushi Togo
# All rights reserved.
@ -48,7 +48,6 @@ def create_phono3py_supercells(
cell_info,
settings,
symprec,
output_filename=None,
interface_mode="vasp",
log_level=1,
):
@ -121,7 +120,7 @@ def create_phono3py_supercells(
)
write_supercells_with_displacements(
interface_mode,
phono3py.supercell,
phono3py.phonon_supercell,
phono3py.phonon_supercells_with_displacements,
optional_structure_info,
zfill_width=5,

15
phono3py/cui/load.py
View File

@ -390,13 +390,14 @@ def set_dataset_and_force_constants(
cutoff_pair_distance=cutoff_pair_distance,
log_level=log_level,
)
read_fc["fc2"] = _set_dataset_phonon_dataset_or_fc2(
ph3py,
ph3py_yaml=ph3py_yaml,
fc2_filename=fc2_filename,
forces_fc2_filename=forces_fc2_filename,
log_level=log_level,
)
if ph3py.phonon_supercell_matrix is not None:
read_fc["fc2"] = _set_dataset_phonon_dataset_or_fc2(
ph3py,
ph3py_yaml=ph3py_yaml,
fc2_filename=fc2_filename,
forces_fc2_filename=forces_fc2_filename,
log_level=log_level,
)
# Cases that dataset is in phono3py.yaml but not forces.
if ph3py.dataset is None:

8
phono3py/cui/phono3py_argparse.py
View File

@ -681,6 +681,14 @@ def get_parser(fc_symmetry=False, is_nac=False, load_phono3py_yaml=False):
default=False,
help="Calculate real part of self energy",
)
parser.add_argument(
"--sp",
"--save-params",
dest="save_params",
action="store_true",
default=None,
help="Save parameters that can run phono3py in phono3py_params.yaml.",
)
parser.add_argument(
"--scattering-event-class",
dest="scattering_event_class",

292
phono3py/cui/phono3py_script.py
View File

@ -36,18 +36,14 @@
from __future__ import annotations
import copy
import datetime
import sys
from typing import Optional, Union
import numpy as np
from phonopy.cui.collect_cell_info import collect_cell_info
from phonopy.cui.create_force_sets import check_number_of_force_files
from phonopy.cui.phonopy_argparse import show_deprecated_option_warnings
from phonopy.cui.phonopy_script import (
file_exists,
files_exist,
print_end,
print_error,
print_error_message,
@ -56,9 +52,9 @@ from phonopy.cui.phonopy_script import (
store_nac_params,
)
from phonopy.exception import ForceCalculatorRequiredError
from phonopy.file_IO import is_file_phonopy_yaml, parse_FORCE_SETS, write_FORCE_SETS
from phonopy.file_IO import is_file_phonopy_yaml
from phonopy.harmonic.force_constants import show_drift_force_constants
from phonopy.interface.calculator import get_default_physical_units, get_force_sets
from phonopy.interface.calculator import get_default_physical_units
from phonopy.phonon.band_structure import get_band_qpoints
from phonopy.structure.cells import isclose as cells_isclose
from phonopy.units import Bohr, Hartree, VaspToTHz
@ -68,6 +64,11 @@ from phono3py.cui.create_force_constants import (
create_phono3py_force_constants,
get_fc_calculator_params,
)
from phono3py.cui.create_force_sets import (
create_FORCE_SETS_from_FORCES_FCx,
create_FORCES_FC2_from_FORCE_SETS,
create_FORCES_FC3_and_FORCES_FC2,
)
from phono3py.cui.create_supercells import create_phono3py_supercells
from phono3py.cui.load import (
compute_force_constants_from_datasets,
@ -82,19 +83,12 @@ 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_FORCES_FC2,
read_phonon_from_hdf5,
write_fc2_to_hdf5,
write_fc3_to_hdf5,
write_FORCES_FC2,
write_FORCES_FC3,
write_phonon_to_hdf5,
)
from phono3py.interface.phono3py_yaml import (
Phono3pyYaml,
displacements_yaml_lines_type1,
)
from phono3py.interface.phono3py_yaml import Phono3pyYaml
from phono3py.phonon3.fc3 import show_drift_fc3
from phono3py.phonon3.gruneisen import run_gruneisen_parameters
from phono3py.phonon.grid import get_grid_point_from_address, get_ir_grid_points
@ -299,255 +293,6 @@ def read_phono3py_settings(args, argparse_control, log_level):
return settings, confs_dict, cell_filename
def create_FORCES_FC2_from_FORCE_SETS_then_exit(log_level):
"""Convert FORCE_SETS to FORCES_FC2."""
filename = "FORCE_SETS"
file_exists(filename, log_level)
disp_dataset = parse_FORCE_SETS(filename=filename)
write_FORCES_FC2(disp_dataset)
if log_level:
print("")
print("FORCES_FC2 has been created from FORCE_SETS.")
print("The following yaml lines should replace respective part of")
print("phono3py_disp.yaml made with --dim-fc2=dim_of_FORCE_SETS.")
print("")
print("\n".join(displacements_yaml_lines_type1(disp_dataset)))
if log_level:
print_end_phono3py()
sys.exit(0)
def create_FORCE_SETS_from_FORCES_FCx_then_exit(
phonon_smat, input_filename: Optional[str], cell_filename: Optional[str], log_level
):
"""Convert FORCES_FC3 or FORCES_FC2 to FORCE_SETS."""
if cell_filename is not None:
disp_filename = cell_filename
elif input_filename is None:
disp_filename = "phono3py_disp.yaml"
else:
disp_filename = f"phono3py_disp.{input_filename}.yaml"
if phonon_smat is not None:
forces_filename = "FORCES_FC2"
else:
forces_filename = "FORCES_FC3"
if log_level:
print(f'Displacement dataset is read from "{disp_filename}".')
print(f'Forces are read from "{forces_filename}"')
with open(forces_filename, "r") as f:
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)
ph3yml = Phono3pyYaml()
ph3yml.read(disp_filename)
if phonon_smat is None:
dataset = copy.deepcopy(ph3yml.dataset)
smat = ph3yml.supercell_matrix
else:
dataset = copy.deepcopy(ph3yml.phonon_dataset)
smat = ph3yml.phonon_supercell_matrix
if smat is None or (phonon_smat is not None and (phonon_smat != smat).any()):
if log_level:
print("")
print("Supercell matrix is inconsistent.")
print(f'Supercell matrix read from "{disp_filename}":')
print(smat)
print("Supercell matrix given by --dim-fc2:")
print(phonon_smat)
print_error()
sys.exit(1)
parse_FORCES_FC2(dataset, filename=forces_filename)
write_FORCE_SETS(dataset)
if log_level:
print("FORCE_SETS has been created.")
print_end_phono3py()
else:
if log_level:
print(
"The file format of %s is already readable by phonopy."
% forces_filename
)
print_end_phono3py()
sys.exit(0)
def create_FORCES_FC3_and_FORCES_FC2_then_exit(
settings,
cell_filename: Optional[str],
log_level: Union[bool, int],
):
"""Create FORCES_FC3 and FORCES_FC2 from files."""
interface_mode = settings.calculator
ph3py_yaml = None
#####################
# Create FORCES_FC3 #
#####################
if settings.create_forces_fc3 or settings.create_forces_fc3_file:
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]
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("")
print('Displacement dataset was read from "%s".' % disp_filename)
num_atoms = disp_dataset["natom"]
num_disps = len(disp_dataset["first_atoms"])
for d1 in disp_dataset["first_atoms"]:
for d2 in d1["second_atoms"]:
if "included" not in d2 or d2["included"]:
num_disps += 1
if settings.create_forces_fc3_file:
file_exists(settings.create_forces_fc3_file, 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)
if log_level > 0:
print("Number of displacements: %d" % num_disps)
print("Number of supercell files: %d" % len(force_filenames))
if not check_number_of_force_files(num_disps, force_filenames, disp_filename):
force_sets = []
else:
force_sets = get_force_sets(
interface_mode,
num_atoms,
force_filenames,
verbose=(log_level > 0),
)
if settings.subtract_forces:
force_filename = settings.subtract_forces
file_exists(force_filename, log_level)
force_set_zero = get_force_sets(
interface_mode,
num_atoms,
[
force_filename,
],
verbose=(log_level > 0),
)[0]
for fs in force_sets:
fs -= force_set_zero
if log_level > 0:
print(
"Forces in '%s' were subtracted from supercell forces."
% force_filename
)
if force_sets:
write_FORCES_FC3(disp_dataset, forces_fc3=force_sets, filename="FORCES_FC3")
if log_level:
print("")
print("%s has been created." % "FORCES_FC3")
print_end_phono3py()
sys.exit(0)
else:
if log_level:
print("")
print("%s could not be created." % "FORCES_FC3")
print_error()
sys.exit(1)
#####################
# Create FORCES_FC2 #
#####################
if settings.create_forces_fc2:
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]
# 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)
num_atoms = disp_dataset["natom"]
num_disps = len(disp_dataset["first_atoms"])
force_filenames = settings.create_forces_fc2
for filename in force_filenames:
file_exists(filename, log_level)
if log_level > 0:
print("Number of displacements: %d" % num_disps)
print("Number of supercell files: %d" % len(force_filenames))
force_sets = get_force_sets(
interface_mode,
num_atoms,
force_filenames,
verbose=(log_level > 0),
)
if settings.subtract_forces:
force_filename = settings.subtract_forces
file_exists(force_filename, log_level)
force_set_zero = get_force_sets(
interface_mode,
num_atoms,
[
force_filename,
],
verbose=(log_level > 0),
)[0]
for fs in force_sets:
fs -= force_set_zero
if log_level > 0:
print(
"Forces in '%s' were subtracted from supercell forces."
% force_filename
)
if force_sets:
write_FORCES_FC2(disp_dataset, forces_fc2=force_sets, filename="FORCES_FC2")
if log_level:
print("")
print("%s has been created." % "FORCES_FC2")
print_end_phono3py()
sys.exit(0)
else:
if log_level:
print("")
print("%s could not be created." % "FORCES_FC2")
print_error()
sys.exit(1)
def get_input_output_filenames_from_args(args):
"""Return strings inserted to input and output filenames."""
input_filename = args.input_filename
@ -1104,11 +849,17 @@ def main(**argparse_control):
)
if args.force_sets_to_forces_fc2_mode:
create_FORCES_FC2_from_FORCE_SETS_then_exit(log_level)
create_FORCES_FC2_from_FORCE_SETS(log_level)
if log_level:
print_end_phono3py()
sys.exit(0)
if args.force_sets_mode:
create_FORCE_SETS_from_FORCES_FCx_then_exit(
create_FORCE_SETS_from_FORCES_FCx(
settings.phonon_supercell_matrix, input_filename, cell_filename, log_level
)
if log_level:
print_end_phono3py()
sys.exit(0)
if args.write_grid_points:
run_mode = "write_grid_info"
elif args.show_num_triplets:
@ -1123,7 +874,15 @@ def main(**argparse_control):
####################################
# Create FORCES_FC3 and FORCES_FC2 #
####################################
create_FORCES_FC3_and_FORCES_FC2_then_exit(settings, cell_filename, log_level)
if (
settings.create_forces_fc3
or settings.create_forces_fc3_file
or settings.create_forces_fc2
):
create_FORCES_FC3_and_FORCES_FC2(settings, cell_filename, log_level=log_level)
if log_level:
print_end_phono3py()
sys.exit(0)
###########################################################
# Symmetry tolerance. Distance unit depends on interface. #
@ -1149,7 +908,6 @@ def main(**argparse_control):
cell_info,
settings,
symprec,
output_filename=output_filename,
interface_mode=interface_mode,
log_level=log_level,
)

54
phono3py/interface/phono3py_yaml.py
View File

@ -133,14 +133,11 @@ class Phono3pyYamlLoader(PhonopyYamlLoader):
This method override PhonopyYaml._parse_dataset.
key="phonon_displacements" at v2.2 or later.
key="displacements" at older version than v2.2.
"""
self._data.phonon_dataset = self._get_dataset(
self._data.phonon_supercell, key="phonon_displacements"
self._data.phonon_supercell, key_prefix="phonon_"
)
if self._data.phonon_dataset is None: # key="displacements"
if self._data.phonon_dataset is None:
self._data.phonon_dataset = self._get_dataset(self._data.phonon_supercell)
def _parse_fc3_dataset(self):
@ -192,6 +189,8 @@ class Phono3pyYamlLoader(PhonopyYamlLoader):
data1["id"] = d1_id
if "forces" in d1:
data1["forces"] = np.array(d1["forces"], dtype="double", order="C")
if "supercell_energy" in d1:
data1["supercell_energy"] = d1["supercell_energy"]
d2_list = d1.get("paired_with")
if d2_list is None: # backward compatibility
d2_list = d1.get("second_atoms")
@ -226,6 +225,8 @@ class Phono3pyYamlLoader(PhonopyYamlLoader):
second_atom_dict["id"] = d2_id
if "pair_distance" in d2:
second_atom_dict["pair_distance"] = d2["pair_distance"]
if "supercell_energy" in d2:
second_atom_dict["supercell_energy"] = d2["supercell_energy"]
disp2_id += 1
data1["second_atoms"].append(second_atom_dict)
return disp2_id
@ -294,15 +295,6 @@ class Phono3pyYamlDumper(PhonopyYamlDumper):
lines += self._phonon_supercell_yaml_lines()
return lines
def _phonon_supercell_matrix_yaml_lines(self):
lines = []
if self._data.phonon_supercell_matrix is not None:
lines.append("phonon_supercell_matrix:")
for v in self._data.supercell_matrix:
lines.append("- [ %3d, %3d, %3d ]" % tuple(v))
lines.append("")
return lines
def _phonon_supercell_yaml_lines(self):
lines = []
if self._data.phonon_supercell is not None:
@ -326,7 +318,7 @@ class Phono3pyYamlDumper(PhonopyYamlDumper):
else:
return self._nac_yaml_lines_given_symbols(self._data.primitive.symbols)
def _displacements_yaml_lines(self, with_forces=False, key="displacements"):
def _displacements_yaml_lines(self, with_forces: bool = False) -> list:
"""Get YAML lines for phonon_dataset and dataset.
This method override PhonopyYaml._displacements_yaml_lines.
@ -337,16 +329,18 @@ class Phono3pyYamlDumper(PhonopyYamlDumper):
lines = []
if self._data.phonon_supercell_matrix is not None:
lines += self._displacements_yaml_lines_2types(
self._data.phonon_dataset, with_forces=with_forces, key=f"phonon_{key}"
self._data.phonon_dataset,
with_forces=with_forces,
key_prefix="phonon_",
)
lines += self._displacements_yaml_lines_2types(
self._data.dataset, with_forces=with_forces, key=key
self._data.dataset, with_forces=with_forces
)
return lines
def _displacements_yaml_lines_type1(
self, dataset, with_forces=False, key="displacements"
):
self, dataset: dict, with_forces: bool = False, key_prefix: str = ""
) -> list:
"""Get YAML lines for type1 phonon_dataset and dataset.
This method override PhonopyYaml._displacements_yaml_lines_type1.
@ -354,7 +348,9 @@ class Phono3pyYamlDumper(PhonopyYamlDumper):
Phono3pyYaml._displacements_yaml_lines_type1.
"""
return displacements_yaml_lines_type1(dataset, with_forces=with_forces, key=key)
return displacements_yaml_lines_type1(
dataset, with_forces=with_forces, key_prefix=key_prefix
)
class Phono3pyYaml(PhonopyYaml):
@ -441,7 +437,9 @@ class Phono3pyYaml(PhonopyYaml):
self._data.phonon_supercell = phono3py.phonon_supercell
def displacements_yaml_lines_type1(dataset, with_forces=False, key="displacements"):
def displacements_yaml_lines_type1(
dataset: dict, with_forces: bool = False, key_prefix: str = ""
) -> list:
"""Get YAML lines for type1 phonon_dataset and dataset.
This is a function but not class method because used by other function.
@ -452,7 +450,7 @@ def displacements_yaml_lines_type1(dataset, with_forces=False, key="displacement
if "second_atoms" in dataset["first_atoms"][0]:
lines = ["displacement_pairs:"]
else:
lines = [f"{key}:"]
lines = [f"{key_prefix}displacements:"]
for disp1_id, d1 in enumerate(dataset["first_atoms"]):
lines.append("- atom: %4d" % (d1["number"] + 1))
lines.append(" displacement:")
@ -464,6 +462,12 @@ def displacements_yaml_lines_type1(dataset, with_forces=False, key="displacement
lines.append(" forces:")
for v in d1["forces"]:
lines.append(" - [ %19.16f, %19.16f, %19.16f ]" % tuple(v))
if "supercell_energy" in d1:
lines.append(
" supercell_energy: {energy:.8f}".format(
energy=d1["supercell_energy"]
)
)
if "second_atoms" in d1:
ret_lines, id_offset = _second_displacements_yaml_lines(
d1["second_atoms"], id_offset, with_forces=with_forces
@ -542,6 +546,12 @@ def _second_displacements_yaml_lines(dataset2, id_offset, with_forces=False):
lines.append(" forces:")
for v in dataset2[j]["forces"]:
lines.append(" - [ %19.16f, %19.16f, %19.16f ]" % tuple(v))
if "supercell_energy" in dataset2[j]:
lines.append(
" supercell_energy: {energy:.8f}".format(
energy=dataset2[j]["supercell_energy"]
)
)
else:
lines.append(" - atom: %4d" % (i + 1))
lines.append(

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__ = "3.0.2"
__version__ = "3.0.3"

2
requirements.txt
View File

@ -2,4 +2,4 @@ numpy >= 1.17.0
PyYAML >= 5.3
matplotlib >= 2.2.2
h5py >= 3.0
phonopy >=2.22,<2.23
phonopy >=2.23,<2.24

2
setup.py
View File

@ -326,7 +326,7 @@ def main(build_dir):
"matplotlib>=2.2.2",
"h5py>=3.0",
"spglib>=2.0",
"phonopy>=2.22,<2.23",
"phonopy>=2.23,<2.24",
],
provides=["phono3py"],
scripts=scripts_phono3py,

BIN
test/Si-111-222-fd.tar.xz Normal file
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test/Si-111-222-rd.tar.xz Normal file
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126
test/api/test_api_phono3py.py
View File

@ -1,7 +1,11 @@
"""Tests of Phono3py API."""
from __future__ import annotations
from pathlib import Path
import numpy as np
from phono3py import Phono3py
cwd = Path(__file__).parent
@ -40,3 +44,125 @@ def test_displacements_setter_Si(si_pbesol_111_222_fd: Phono3py):
)
ph3.displacements = displacements
ph3.phonon_displacements = phonon_displacements
def test_type1_forces_energies_setter_Si(si_111_222_fd: Phono3py):
"""Test type1 supercell_energies, phonon_supercell_energies attributes."""
ph3_in = si_111_222_fd
ref_ph_supercell_energies = [-346.85204143]
ref_supercell_energies = [
-43.3509760,
-43.33608775,
-43.35352904,
-43.34370672,
-43.34590849,
-43.34540162,
-43.34421408,
-43.34481089,
-43.34703607,
-43.34241924,
-43.34786243,
-43.34168203,
-43.34274245,
-43.34703607,
-43.34786243,
-43.34184454,
]
np.testing.assert_allclose(ph3_in.supercell_energies, ref_supercell_energies)
np.testing.assert_allclose(
ph3_in.phonon_supercell_energies, ref_ph_supercell_energies
)
ref_force00 = [-0.4109520800000000, 0.0000000100000000, 0.0000000300000000]
ref_force_last = [0.1521426300000000, 0.0715600600000000, -0.0715600700000000]
ref_ph_force00 = [-0.4027479600000000, 0.0000000200000000, 0.0000001000000000]
np.testing.assert_allclose(ph3_in.forces[0, 0], ref_force00)
np.testing.assert_allclose(ph3_in.forces[-1, -1], ref_force_last)
np.testing.assert_allclose(ph3_in.phonon_forces[0, 0], ref_ph_force00)
ph3 = Phono3py(
ph3_in.unitcell,
supercell_matrix=ph3_in.supercell_matrix,
phonon_supercell_matrix=ph3_in.phonon_supercell_matrix,
primitive_matrix=ph3_in.primitive_matrix,
)
ph3.dataset = ph3_in.dataset
ph3.phonon_dataset = ph3_in.phonon_dataset
ph3.supercell_energies = ph3_in.supercell_energies + 1
ph3.phonon_supercell_energies = ph3_in.phonon_supercell_energies + 1
np.testing.assert_allclose(ph3_in.supercell_energies + 1, ph3.supercell_energies)
np.testing.assert_allclose(
ph3_in.phonon_supercell_energies + 1, ph3.phonon_supercell_energies
)
ph3.forces = ph3_in.forces + 1
ph3.phonon_forces = ph3_in.phonon_forces + 1
np.testing.assert_allclose(ph3_in.forces + 1, ph3.forces)
np.testing.assert_allclose(ph3_in.phonon_forces + 1, ph3.phonon_forces)
def test_type2_forces_energies_setter_Si(si_111_222_rd: Phono3py):
"""Test type2 supercell_energies, phonon_supercell_energies attributes."""
ph3_in = si_111_222_rd
ref_ph_supercell_energies = [
-346.81061270, # 1
-346.81263617, # 2
]
ref_supercell_energies = [
-43.35270268, # 1
-43.35211687, # 2
-43.35122776, # 3
-43.35226673, # 4
-43.35146358, # 5
-43.35133209, # 6
-43.35042212, # 7
-43.35008442, # 8
-43.34968796, # 9
-43.35348999, # 10
-43.35134937, # 11
-43.35335251, # 12
-43.35160892, # 13
-43.35009115, # 14
-43.35202797, # 15
-43.35076370, # 16
-43.35174477, # 17
-43.35107001, # 18
-43.35037949, # 19
-43.35126123, # 20
]
np.testing.assert_allclose(ph3_in.supercell_energies, ref_supercell_energies)
np.testing.assert_allclose(
ph3_in.phonon_supercell_energies, ref_ph_supercell_energies
)
ref_force00 = [0.0445647800000000, 0.1702929900000000, 0.0913398200000000]
ref_force_last = [-0.1749668700000000, 0.0146997300000000, -0.1336066300000000]
ref_ph_force00 = [-0.0161598900000000, -0.1161657500000000, 0.1399128100000000]
ref_ph_force_last = [0.1049486700000000, 0.0795870900000000, 0.1062164600000000]
np.testing.assert_allclose(ph3_in.forces[0, 0], ref_force00)
np.testing.assert_allclose(ph3_in.forces[-1, -1], ref_force_last)
np.testing.assert_allclose(ph3_in.phonon_forces[0, 0], ref_ph_force00)
np.testing.assert_allclose(ph3_in.phonon_forces[-1, -1], ref_ph_force_last)
ph3 = Phono3py(
ph3_in.unitcell,
supercell_matrix=ph3_in.supercell_matrix,
phonon_supercell_matrix=ph3_in.phonon_supercell_matrix,
primitive_matrix=ph3_in.primitive_matrix,
)
ph3.dataset = ph3_in.dataset
ph3.phonon_dataset = ph3_in.phonon_dataset
ph3.supercell_energies = ph3_in.supercell_energies + 1
ph3.phonon_supercell_energies = ph3_in.phonon_supercell_energies + 1
np.testing.assert_allclose(ph3_in.supercell_energies + 1, ph3.supercell_energies)
np.testing.assert_allclose(
ph3_in.phonon_supercell_energies + 1, ph3.phonon_supercell_energies
)
ph3.forces = ph3_in.forces + 1
ph3.phonon_forces = ph3_in.phonon_forces + 1
np.testing.assert_allclose(ph3_in.forces + 1, ph3.forces)
np.testing.assert_allclose(ph3_in.phonon_forces + 1, ph3.phonon_forces)

88
test/conftest.py
View File

@ -1,5 +1,6 @@
"""Pytest conftest.py."""
import tarfile
from pathlib import Path
import numpy as np
@ -482,6 +483,20 @@ def aln_lda(request) -> Phono3py:
)
@pytest.fixture(scope="session")
def si_111_222_fd() -> Phono3py:
"""Return Phono3py class instance of Si-1x1x1-2x2x2 FD."""
yaml_filename = cwd / "phono3py_params_Si-111-222-fd.yaml.xz"
return phono3py.load(yaml_filename, produce_fc=False, log_level=1)
@pytest.fixture(scope="session")
def si_111_222_rd() -> Phono3py:
"""Return Phono3py class instance of Si-1x1x1-2x2x2 RD."""
yaml_filename = cwd / "phono3py_params_Si-111-222-rd.yaml.xz"
return phono3py.load(yaml_filename, produce_fc=False, log_level=1)
@pytest.fixture(scope="session")
def ph_nacl() -> Phonopy:
"""Return Phonopy class instance of NaCl 2x2x2."""
@ -508,3 +523,76 @@ def ph_si() -> Phonopy:
log_level=1,
produce_fc=True,
)
@pytest.fixture(scope="session")
def si_111_222_fd_raw_data() -> tarfile.TarFile:
"""Return Si fc3 111 fc2 222 vasp inputs.
tar.getnames()
['Si-111-222-fd',
'Si-111-222-fd/vasprun-001.xml',
'Si-111-222-fd/vasprun-015.xml',
'Si-111-222-fd/vasprun-014.xml',
'Si-111-222-fd/vasprun-000.xml',
'Si-111-222-fd/vasprun-016.xml',
'Si-111-222-fd/vasprun-002.xml',
'Si-111-222-fd/vasprun-003.xml',
'Si-111-222-fd/vasprun-013.xml',
'Si-111-222-fd/vasprun-007.xml',
'Si-111-222-fd/vasprun-fc2-000.xml',
'Si-111-222-fd/vasprun-fc2-001.xml',
'Si-111-222-fd/vasprun-006.xml',
'Si-111-222-fd/vasprun-012.xml',
'Si-111-222-fd/vasprun-004.xml',
'Si-111-222-fd/vasprun-010.xml',
'Si-111-222-fd/vasprun-011.xml',
'Si-111-222-fd/vasprun-005.xml',
'Si-111-222-fd/phono3py_disp.yaml',
'Si-111-222-fd/vasprun-008.xml',
'Si-111-222-fd/vasprun-009.xml']
member = tar.getmember("Si-111-222-fd/phono3py_disp.yaml")
tar.extractfile(member) -> byte file object
"""
tar = tarfile.open(cwd / "Si-111-222-fd.tar.xz")
return tar
@pytest.fixture(scope="session")
def si_111_222_rd_raw_data() -> tarfile.TarFile:
"""Return Si fc3 111 fc2 222 vasp inputs.
tar.getnames()
['Si-111-222-rd',
'Si-111-222-rd/vasprun-001.xml',
'Si-111-222-rd/vasprun-015.xml',
'Si-111-222-rd/vasprun-014.xml',
'Si-111-222-rd/vasprun-000.xml',
'Si-111-222-rd/vasprun-016.xml',
'Si-111-222-rd/vasprun-002.xml',
'Si-111-222-rd/vasprun-003.xml',
'Si-111-222-rd/vasprun-017.xml',
'Si-111-222-rd/vasprun-013.xml',
'Si-111-222-rd/vasprun-007.xml',
'Si-111-222-rd/vasprun-fc2-000.xml',
'Si-111-222-rd/vasprun-fc2-001.xml',
'Si-111-222-rd/vasprun-006.xml',
'Si-111-222-rd/vasprun-012.xml',
'Si-111-222-rd/vasprun-004.xml',
'Si-111-222-rd/vasprun-010.xml',
'Si-111-222-rd/vasprun-fc2-002.xml',
'Si-111-222-rd/vasprun-011.xml',
'Si-111-222-rd/vasprun-005.xml',
'Si-111-222-rd/phono3py_disp.yaml',
'Si-111-222-rd/vasprun-020.xml',
'Si-111-222-rd/vasprun-008.xml',
'Si-111-222-rd/vasprun-009.xml',
'Si-111-222-rd/vasprun-019.xml',
'Si-111-222-rd/vasprun-018.xml']
member = tar.getmember("Si-111-222-rd/phono3py_disp.yaml")
tar.extractfile(member) -> byte file object
"""
tar = tarfile.open(cwd / "Si-111-222-fd.tar.xz")
return tar

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