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Update README.md in examples and fix CLI bugs

This commit is contained in:
Atsushi Togo 2024-08-07 18:51:13 +09:00
parent 95d2e4f4f8
commit 8e13167f0a
14 changed files with 176 additions and 142 deletions
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2
.pre-commit-config.yaml
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@ -7,8 +7,8 @@ repos:
- id: trailing-whitespace
- id: end-of-file-fixer
- id: check-yaml
exclude: ^conda/
- id: check-added-large-files
exclude: ^example/AlN-LDA/
- repo: https://github.com/astral-sh/ruff-pre-commit
rev: v0.5.6

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example/AlN-LDA/FORCES_FC3.lzma
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62
example/AlN-LDA/README.md
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@ -14,52 +14,56 @@ from all displaced supercell forces.
Perfect and displaced supercells were created by
```
```bash
% phono3py --dim 3 3 2 -c POSCAR-unitcell -d
```
In the example directory, `FORCES_FC3` is compressed to `FORCES_FC3.lzma`. After
unzipping `FORCES_FC3.lzma` (e.g., using `tar xvfz` or `tar xvfa`), to obtain
`fc3.hdf5` and normal `fc2.hdf5`,
In the example directory, `FORCES_FC3` is compressed to `FORCES_FC3.xz`. After
unzipping `FORCES_FC3.xz` (e.g., using `xz -d`), to obtain `fc3.hdf5` and
`fc2.hdf5` using symfc (the results without using symfc, i.e., finite difference
method, are shown at the bottom of this README)
```
% phono3py --sym-fc
```bash
% phono3py-load --symfc -v
```
Using 13x13x9 sampling mesh, lattice thermal conductivity is calculated by
Lattice thermal conductivity is calculated by
```
% phono3py --mesh 13 13 9 --fc3 --fc2 --br
```bash
% phono3py-load --mesh 40 --br --ts 300
```
`kappa-m13139.hdf5` is written as the result. The lattice thermal conductivity
is calculated as k_xx=228.2 and k_zz=224.1 W/m-K at 300 K.
`kappa-m15158.hdf5` is written as the result. Parameters for non-analytical term
correction (NAC) is automatically read from those stored in `phono3py_disp.yaml` or
`BORN` file. The lattice thermal conductivity is calculated as k_xx=242.8 and
k_zz=226.5 W/m-K at 300 K. Without NAC, k_xx=233.6 and k_zz=222.2.
With `--nac` option, non-analytical term correction is applied reading the Born
effective charges and dielectric constant from `BORN` file:
Use of larger supercell for fc2 may change the shape of phonon band structure.
To see it, first regenerate `phono3py_disp.yaml` with `--dim-fc2` option,
```
% phono3py --mesh 13 13 9 --fc3 --fc2 --br --nac
```
This changes thermal conductivity at 300 K to k_xx=235.7 and k_zz=219.1. The
shape of phonon band structure is important to fullfil energy and momentum
conservations.
Use of larger supercell of fc2 may change the shape of phonon band structure. To
see it, first regenerate `phono3py_disp.yaml` with `--dim-fc2` option,
```
```bash
% phono3py --dim 3 3 2 --dim-fc2 5 5 3 -c POSCAR-unitcell -d
```
Then re-create force constants and calculate thermal conductivity,
```
% phono3py --sym-fc
% phono3py --mesh="13 13 9" --fc3 --fc2 --br --nac
```bash
% phono3py-load --symfc -v
% phono3py-load --br --mesh=40 --ts 300
```
k_xx=236.0 and k_zz=222.2 are obtained. In the case of this example, we can see
If `phono3py_disp.yaml` is renamed to `phono3py_disp_dimfc2.yaml`, it can be
specified at the first argument of `phono3py-load` command:
```bash
% phono3py-load phono3py_disp_dimfc2.yaml --symfc -v
% phono3py-load phono3py_disp_dimfc2.yaml --br --mesh=40 --ts 300
```
k_xx=240.2 and k_zz=230.1 are obtained. In the case of this example, we can see
that the larger fc2 supercell contributes little, which means that the 3x3x2
supercell was good enough to obtain a good shape of phonon band structure.
Using the finite difference method implemented in phono3py, lattice thermal
conductivities are obtained as k_xx=251.2 and k_zz=233,4 without using the large
fc2 supercell and k_xx=249.4 k_zz=236.9 using the large fc2 supercell.

2
example/NaCl-alm/README.md
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@ -29,4 +29,4 @@ lattice thermal conductivity at 300 K is calculated by
% phono3py-load phono3py_params_NaCl222.yaml.xz --mesh 50 --ts 300 --br
```
The result is ~7.2 W/m-K at 300 K.
The result is ~7.3 W/m-K at 300 K.

8
example/Si-LDA/README.md
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@ -13,18 +13,18 @@ conventional unit cell to the primitive cell.
To create `fc3.hdf5` and `fc2.hdf5`,
```
% phono3py --sym-fc
% phono3py-load
```
Using 11x11x11 sampling mesh, lattice thermal conductivity is calculated by
```
% phono3py --mesh 11 11 11 --fc3 --fc2 --br
% phono3py-load --mesh 11 11 11 --br --ts 300
```
`kappa-m111111.hdf5` is written as the result. The lattice thermal conductivity
is calculated as 112.5 W/m-K at 300 K. This becomes, with 19x19x19 sampling
mesh, 127.0 W/m-K.
is calculated as 112.4 W/m-K at 300 K. This becomes, with 19x19x19 sampling
mesh, 128.2 W/m-K.
Accumulated lattice thermal conductivity is calculated using `phono3py-kaccum`
script.

8
example/Si-PBE/README.md
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@ -13,18 +13,18 @@ conventional unit cell to the primitive cell.
To create `fc3.hdf5` and `fc2.hdf5`,
```
% phono3py --sym-fc
% phono3py-load
```
Using 11x11x11 sampling mesh, lattice thermal conductivity is calculated by
```
% phono3py --mesh 11 11 11 --fc3 --fc2 --br
% phono3py-load --mesh 11 11 11 --fc3 --fc2 --br
```
`kappa-m111111.hdf5` is written as the result. The lattice thermal conductivity
is calculated as 119.3 W/m-K at 300 K. This becomes, with 19x19x19 sampling
mesh, 132.4 W/m-K.
is calculated as 119.5 W/m-K at 300 K. This becomes, with 19x19x19 sampling
mesh, 130.1 W/m-K.
Accumulated lattice thermal conductivity is calculated using `phono3py-kaccum`
script.

12
example/Si-PBEsol/README.md
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@ -13,18 +13,18 @@ the conventional unit cell to the primitive cell.
To create `fc3.hdf5` and `fc2.hdf5`,
```
% phono3py --sym-fc
% phono3py-load
```
Using 11x11x11 sampling mesh, lattice thermal conductivity is calculated by
```
% phono3py --mesh 11 11 11 --fc3 --fc2 --br
% phono3py-load --mesh 11 11 11 --br
```
`kappa-m111111.hdf5` is written as the result. The lattice thermal conductivity
is calculated as 109.0 W/m-K at 300 K. This becomes, with 19x19x19 sampling
mesh, 123.2 W/m-K.
is calculated as 109.1 W/m-K at 300 K. This becomes, with 19x19x19 sampling
mesh, 124.4 W/m-K.
Accumulated lattice thermal conductivity is calculated using `phono3py-kaccum`
script.
@ -80,11 +80,11 @@ In this example directory, the dataset is renamed to
at `vasprun_xml_fc2/disp-fc2-00001/vasprun.xml`. `FORCES_FC2` is generated by
```
% phono3py phono3py_disp_dimfc2.yaml --cf2 vasprun_xml_fc2/disp-fc2-00001/vasprun.xml
% phono3py -c phono3py_disp_dimfc2.yaml --cf2 vasprun_xml_fc2/disp-fc2-00001/vasprun.xml
```
A lattice thermal conductivity calculation is performed by, e.g.,
```
% phono3py-load phono3py_disp_dimfc2.yaml --mesh 11 11 11 --br --ts 300
```
The result is 108.0 W/m-K, and with the 19x19x19 mesh, 125.4 W/m-K.
The result is 107.9 W/m-K, and with the 19x19x19 mesh, 125.4 W/m-K.

8
example/Si-QE/README.md
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@ -13,18 +13,18 @@ the conventional unit cell to the primitive cell.
To create `fc3.hdf5` and `fc2.hdf5`,
```
% phono3py --sym-fc
% phono3py-load
```
Using 11x11x11 sampling mesh, lattice thermal conductivity is calculated by
```
% phono3py --mesh 11 11 11 --fc3 --fc2 --br
% phono3py-load --mesh 11 11 11 --br --ts 300
```
`kappa-m111111.hdf5` is written as the result. The lattice thermal conductivity
is calculated as 118.9 W/m-K at 300 K. This becomes, with 19x19x19 sampling
mesh, 129.9 W/m-K.
is calculated as 121.3 W/m-K at 300 K. This becomes, with 19x19x19 sampling
mesh, 135.4 W/m-K.
The .out files for supercells are found in `supercell_out.tar.lzma`. If phono3py
is properly installed, the following command should work.

11
phono3py/api_phono3py.py
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@ -1487,6 +1487,9 @@ class Phono3py:
fc2 = None
if fc_calculator_options is not None and "|" in fc_calculator_options:
fc2 = None
# fc2 should not be set if phonon_supercell_matrix is available.
if self._phonon_supercell_matrix is not None:
fc2 = None
# Normally self._fc2 is overwritten in produce_fc2
if self._fc2 is None:
@ -1527,6 +1530,9 @@ class Phono3py:
else:
disp_dataset = self._phonon_dataset
if not forces_in_dataset(disp_dataset):
raise RuntimeError("Forces are not set in the dataset.")
if is_compact_fc:
p2s_map = self._phonon_primitive.p2s_map
else:
@ -1548,10 +1554,7 @@ class Phono3py:
)
else:
if "displacements" in disp_dataset:
msg = (
"fc_calculator has to be set to produce force "
"constans from this dataset for fc2."
)
msg = "fc_calculator to solve fc2 has to be set."
raise RuntimeError(msg)
self._fc2 = get_phonopy_fc2(
self._phonon_supercell,

118
phono3py/cui/create_force_constants.py
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@ -217,51 +217,40 @@ def parse_forces(
dataset = 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.
if 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 phono3py.phonon_supercell is None or fc_type == "fc3":
natom = len(phono3py.supercell)
else:
natom = len(phono3py.phonon_supercell)
if dataset:
filename_read_from = phono3py_yaml_filename
# Get dataset from ph3py_yaml. dataset can be None.
# physical_units can be overwritten if calculator is found in ph3py_yaml.
if ph3py_yaml:
dataset = _extract_dataset_from_ph3py_yaml(ph3py_yaml, fc_type)
if dataset:
filename_read_from = phono3py_yaml_filename
if ph3py_yaml.calculator:
calculator = ph3py_yaml.calculator
# 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"],
physical_units = get_default_physical_units(calculator)
# Forces are not yet found in dataset. Then try to read from FORCES_FC3 or
# FORCES_FC2.
if force_filename is not None:
if dataset is None or (dataset is not None and not forces_in_dataset(dataset)):
dataset = _read_FORCES_FC3_or_FC2(
natom, dataset, fc_type, filename=force_filename, log_level=log_level
)
if dataset:
filename_read_from = force_filename
# Try to read FORCES_FC* if type-2 and return dataset.
# None is returned unless type-2.
# can emit FileNotFoundError.
if dataset is None or (dataset is not None and not forces_in_dataset(dataset)):
_dataset = read_type2_dataset(
natom, filename=force_filename, log_level=log_level
# 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"],
)
# Do not overwrite dataset when _dataset is None.
if _dataset:
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"],
)
assert dataset is not None
@ -286,29 +275,6 @@ def parse_forces(
if log_level:
print("Cutoff-pair-distance: %f" % cutoff_pair_distance)
# Type-1 FORCES_FC*.
# dataset comes either from disp_fc*.yaml or phono3py*.yaml.
if not forces_in_dataset(dataset):
if force_filename is not None:
if fc_type == "fc3":
parse_FORCES_FC3(dataset, filename=force_filename)
else:
parse_FORCES_FC2(dataset, filename=force_filename)
if log_level:
print(
f'Sets of supercell forces were read from "{force_filename}".',
flush=True,
)
# 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"],
)
return dataset
@ -437,20 +403,40 @@ def _read_phono3py_fc2(phono3py, symmetrize_fc2, input_filename, log_level):
phono3py.fc2 = phonon_fc2
def read_type2_dataset(natom, filename="FORCES_FC3", log_level=0) -> Optional[dict]:
"""Read type-2 FORCES_FC3."""
def _read_FORCES_FC3_or_FC2(
natom: int,
dataset: Optional[dict],
fc_type: str,
filename: str = "FORCES_FC3",
log_level: int = 0,
) -> Optional[dict]:
"""Read FORCES_FC3 or FORCES_FC2.
Read the first line of forces file to determine the type of the file.
"""
if filename is None or not pathlib.Path(filename).exists():
return None
with open(filename, "r") as f:
len_first_line = get_length_of_first_line(f)
if len_first_line == 6:
dataset = get_dataset_type2(f, natom)
if len_first_line == 6: # Type-2
_dataset = get_dataset_type2(f, natom)
if log_level:
n_disp = len(dataset["displacements"])
n_disp = len(_dataset["displacements"])
print(f'{n_disp} snapshots were found in "{filename}".')
else:
dataset = None
return _dataset
# Type-1
if fc_type == "fc3":
parse_FORCES_FC3(dataset, filename)
else:
parse_FORCES_FC2(dataset, filename)
if log_level:
print(
f'Sets of supercell forces were read from "{filename}".',
flush=True,
)
return dataset

28
phono3py/cui/load.py
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@ -475,17 +475,23 @@ def compute_force_constants_from_datasets(
if log_level and symmetrize_fc and fc_calculator is None:
print("fc3 was symmetrized.")
if not read_fc["fc2"] and (
forces_in_dataset(ph3py.dataset) or forces_in_dataset(ph3py.phonon_dataset)
):
ph3py.produce_fc2(
symmetrize_fc2=symmetrize_fc,
is_compact_fc=is_compact_fc,
fc_calculator=fc2_calculator,
fc_calculator_options=extract_fc2_fc3_calculators(fc_calculator_options, 2),
)
if log_level and symmetrize_fc and fc_calculator is None:
print("fc2 was symmetrized.")
if not read_fc["fc2"]:
if (
ph3py.phonon_supercell_matrix is None and forces_in_dataset(ph3py.dataset)
) or (
ph3py.phonon_supercell_matrix is not None
and forces_in_dataset(ph3py.phonon_dataset)
):
ph3py.produce_fc2(
symmetrize_fc2=symmetrize_fc,
is_compact_fc=is_compact_fc,
fc_calculator=fc2_calculator,
fc_calculator_options=extract_fc2_fc3_calculators(
fc_calculator_options, 2
),
)
if log_level and symmetrize_fc and fc_calculator is None:
print("fc2 was symmetrized.")
def _get_dataset_or_fc3(

29
phono3py/cui/phono3py_script.py
View File

@ -38,6 +38,7 @@ from __future__ import annotations
import argparse
import datetime
import pathlib
import sys
from typing import Optional
@ -92,6 +93,7 @@ from phono3py.file_IO import (
)
from phono3py.interface.phono3py_yaml import Phono3pyYaml
from phono3py.phonon.grid import get_grid_point_from_address, get_ir_grid_points
from phono3py.phonon3.dataset import forces_in_dataset
from phono3py.phonon3.fc3 import show_drift_fc3
from phono3py.phonon3.gruneisen import run_gruneisen_parameters
from phono3py.version import __version__
@ -541,15 +543,16 @@ def create_supercells_with_displacements(
log_level=log_level,
)
store_nac_params(
phono3py,
settings,
cell_info["phonopy_yaml"],
unitcell_filename,
log_level,
nac_factor=Hartree * Bohr,
load_phonopy_yaml=load_phono3py_yaml,
)
if pathlib.Path("BORN").exists():
store_nac_params(
phono3py,
settings,
cell_info["phonopy_yaml"],
unitcell_filename,
log_level,
nac_factor=Hartree * Bohr,
load_phonopy_yaml=load_phono3py_yaml,
)
if log_level:
if phono3py.supercell.magnetic_moments is None:
@ -616,10 +619,18 @@ def store_force_constants(
if log_level:
if phono3py.fc3 is None:
print("fc3 could not be obtained.")
if not forces_in_dataset(phono3py.dataset):
print("Forces were not found.")
else:
show_drift_fc3(phono3py.fc3, primitive=phono3py.primitive)
if phono3py.fc2 is None:
print("fc2 could not be obtained.")
if phono3py.phonon_supercell_matrix is None:
if not forces_in_dataset(phono3py.dataset):
print("Forces were not found.")
else:
if not forces_in_dataset(phono3py.phonon_dataset):
print("Forces for dim-fc2 were not found.")
else:
show_drift_force_constants(
phono3py.fc2, primitive=phono3py.phonon_primitive, name="fc2"

30
phono3py/interface/phono3py_yaml.py
View File

@ -133,10 +133,34 @@ class Phono3pyYamlLoader(PhonopyYamlLoaderBase):
This method override PhonopyYaml._parse_dataset.
Phonon_displacements in type1 in old format is represented in yaml by
displacements:
But displacements (for fc3) in type2 in old format is also represented
by
displacements:
Therefore, these have to be distinguished by phonon_supercell_matrix.
In new format of type1
displacements: -> phonon_displacements:
and displacements: of type2 is put under phonon_dataset: block.
"""
self._data.phonon_dataset = self._get_dataset(
self._data.phonon_supercell, key_prefix="phonon_"
)
if (
self._data.phonon_supercell_matrix is not None
and "phonon_displacements" not in self._yaml
and "displacements" in self._yaml
): # old type1
self._data.phonon_dataset = self._get_dataset(self._data.phonon_supercell)
else:
self._data.phonon_dataset = self._get_dataset(
self._data.phonon_supercell, key_prefix="phonon_"
)
def _parse_fc3_dataset(self):
"""Parse force dataset for fc3.