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Merge branch 'develop' into publish-gh-pages

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Atsushi Togo 2025-07-26 14:52:44 +09:00
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17
doc/command-options.md
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@ -330,13 +330,13 @@ information about primitive cell (`primitive_matrix` key) in
(random_displacements_option)=
### `--rd` (`RANDOM_DISPLACEMENTS`), `--rd-fc2` (`RANDOM_DISPLACEMENTS_FC2`) and `--random-seed` (`RANDOM_SEED`)
**`phono3py-load` doesn't have this option.**
See also {ref}`random-displacements`.
Random directional displacements are generated for fc3 and fc2 supercells by
`--rd` and `--rd-fc2`, respectively. `--amplitude` and `--random-seed` options
may be used together. These are used in the equivalent way to [`--rd` of
`--rd` and `--rd-fc2`, respectively. `--rd auto` can estimate a possible number
of supercells required (see {ref}`rd_number_estimation_factor_option`).
`--amplitude` and `--random-seed` options may be used together. These are used
in the equivalent way to [`--rd` of
phonopy](https://phonopy.github.io/phonopy/setting-tags.html#random-displacements).
Like `-d` option, it is recommended to specify `--pa auto` together with `--rd`
@ -346,6 +346,15 @@ and/or `--rd-fc2`,
% phono3py -c POSCAR-unitcell --dim 2 2 2 --dim-fc2 4 4 4 --rd 100 --rd-fc2 2 --pa auto
```
(rd_number_estimation_factor_option)=
### `--rd-auto-factor` (`RD_NUMBER_ESTIMATION_FACTOR`)
This scales the number of supercells generated by `--rd auto` by the specified
factor.
See
[RD_NUMBER_ESTIMATION_FACTOR](https://phonopy.github.io/phonopy/setting-tags.html#rd-number-estimation-factor).
(amplitude_option)=
### `--amplitude` (`DISPLACEMENT_DISTANCE`)

269
doc/pypolymlp.md
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@ -20,8 +20,8 @@ For further details on combining phono3py calculations with pypolymlp, refer to
[[doi](https://doi.org/10.1063/5.0211296)]
[[arxiv](https://arxiv.org/abs/2401.17531)].
An example of its usage can be found in the `example/NaCl-pypolymlp` directory
in the distribution from GitHub or PyPI.
Examples of its usage can be found in the `example/NaCl-pypolymlp` and
`example/AlN-rd` directories in the distribution from GitHub or PyPI.
## Citation of pypolymlp
@ -42,15 +42,12 @@ in the distribution from GitHub or PyPI.
## Requirements
- [pypolymlp](https://github.com/sekocha/pypolymlp) < 0.9
- [pypolymlp](https://github.com/sekocha/pypolymlp)
For linux (x86-64), a compiled package of pypolymlp can be installed via
conda-forge (recommended). Otherwise, pypolymlp can be installed from
source-code.
From pypolymlp 0.9, its file format was changed. This will be taken care of
by the future version of phonopy and phono3py.
## How to calculate
### Workflow
@ -156,28 +153,28 @@ obtained by
```
``````
### Step 4: Development of MLPs
The `phono3py_params.yaml` file contains the training data required for
developing polynomial MLPs when running with the `--pypolymlp` option.
```
% phono3py-load --pypolymlp phono3py_params.yaml
phono3py-load --pypolymlp phono3py_params.yaml
_ _____
_ __ | |__ ___ _ __ ___|___ / _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ |_ \| '_ \| | | |
| |_) | | | | (_) | | | | (_) |__) | |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___/____/| .__/ \__, |
|_| |_| |___/
3.11.3
3.18.0
-------------------------[time 2025-01-19 18:02:40]-------------------------
-------------------------[time 2025-07-26 13:59:10]-------------------------
Compiled with OpenMP support (max 10 threads).
Running in phono3py.load mode.
Python version 3.12.6
Spglib version 2.5.0
Python version 3.13.3
Spglib version 2.6.1
----------------------------- General settings -----------------------------
Run mode: pypolymlp
HDF5 data compression filter: gzip
Crystal structure was read from "phono3py_params.yaml".
Supercell (dim): [2 2 2]
@ -190,6 +187,7 @@ Use -v option to watch primitive cell, unit cell, and supercell structures.
NAC parameters were read from "phono3py_params.yaml".
Displacement dataset for fc3 was read from "phono3py_params.yaml".
----------------------------- pypolymlp start ------------------------------
Pypolymlp version 0.12.9
Pypolymlp is a generator of polynomial machine learning potentials.
Please cite the paper: A. Seko, J. Appl. Phys. 133, 011101 (2023).
Pypolymlp is developed at https://github.com/sekocha/pypolymlp.
@ -202,26 +200,11 @@ Parameters:
gaussian_params1: (1.0, 1.0, 1)
gaussian_params2: (0.0, 7.0, 10)
Developing MLPs by pypolymlp...
Regression: cholesky decomposition ...
- alpha: 0.001
- alpha: 0.01
- alpha: 0.1
- alpha: 1.0
- alpha: 10.0
Clear training X.T @ X
Calculate X.T @ X for test data
Clear test X.T @ X
Regression: model selection ...
- alpha = 1.000e-03 : rmse (train, test) = 1.12211e+15 1.12211e+15
- alpha = 1.000e-02 : rmse (train, test) = 1.12211e+15 1.12211e+15
- alpha = 1.000e-01 : rmse (train, test) = 0.00002 0.00002
- alpha = 1.000e+00 : rmse (train, test) = 0.00002 0.00002
- alpha = 1.000e+01 : rmse (train, test) = 0.00002 0.00002
MLPs were written into "polymlp.yaml"
------------------------------ pypolymlp end -------------------------------
Generate displacements (--rd or -d) for proceeding to phonon calculations.
Summary of calculation was written in "phono3py.yaml".
-------------------------[time 2025-01-19 18:03:44]-------------------------
-------------------------[time 2025-07-26 14:00:12]-------------------------
_
___ _ __ __| |
/ _ \ '_ \ / _` |
@ -252,14 +235,15 @@ structure file.
| |_) | | | | (_) | | | | (_) |__) | |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___/____/| .__/ \__, |
|_| |_| |___/
3.11.3
3.18.0
-------------------------[time 2025-01-19 18:06:46]-------------------------
-------------------------[time 2025-07-26 14:00:49]-------------------------
Compiled with OpenMP support (max 10 threads).
Running in phono3py.load mode.
Python version 3.12.6
Spglib version 2.5.0
Python version 3.13.3
Spglib version 2.6.1
----------------------------- General settings -----------------------------
Run mode: pypolymlp + force constants
HDF5 data compression filter: gzip
Crystal structure was read from "phono3py.yaml".
Supercell (dim): [2 2 2]
@ -271,6 +255,7 @@ Spacegroup: Fm-3m (225)
Use -v option to watch primitive cell, unit cell, and supercell structures.
NAC parameters were read from "phono3py.yaml".
----------------------------- pypolymlp start ------------------------------
Pypolymlp version 0.12.9
Pypolymlp is a generator of polynomial machine learning potentials.
Please cite the paper: A. Seko, J. Appl. Phys. 133, 011101 (2023).
Pypolymlp is developed at https://github.com/sekocha/pypolymlp.
@ -279,6 +264,7 @@ Load MLPs from "polymlp.yaml".
Generate displacements
Displacement distance: 0.01
Evaluate forces in 292 supercells by pypolymlp
Dataset generated using MLPs was written in "phono3py_mlp_eval_dataset.yaml".
----------------------------- Force constants ------------------------------
Computing fc3[ 1, x, x ] using numpy.linalg.pinv.
Displacements (in Angstrom):
@ -289,16 +275,26 @@ Displacements (in Angstrom):
[ 0.0100 0.0000 0.0000]
[-0.0100 0.0000 0.0000]
Expanding fc3.
fc3 was symmetrized.
fc2 was symmetrized.
Max drift of fc3: 0.000000 (zzz) 0.000000 (zzz) 0.000000 (zzz)
Max drift of fc2: 0.000000 (zz) 0.000000 (zz)
Symmetrizing fc3 by symfc projector.
Symfc version 1.5.3 (https://github.com/symfc/symfc)
Citation: A. Seko and A. Togo, Phys. Rev. B, 110, 214302 (2024)
Symmetrizing fc2 by symfc projector.
Symfc version 1.5.3 (https://github.com/symfc/symfc)
Citation: A. Seko and A. Togo, Phys. Rev. B, 110, 214302 (2024)
Max drift of fc3: 0.00000000 (zyz) 0.00000000 (yzz) 0.00000000 (yzz)
Max drift of fc2: -0.00000000 (yy) -0.00000000 (yy)
fc3 was written into "fc3.hdf5".
fc2 was written into "fc2.hdf5".
--------------------------- Calculation settings ---------------------------
Non-analytical term correction (NAC): True
NAC unit conversion factor: 14.39965
BZ integration: Tetrahedron-method
Temperatures: 0.0 300.0
Cutoff frequency: 0.01
Frequency conversion factor to THz: 15.63330
----------- None of ph-ph interaction calculation was performed. -----------
Dataset generated using MLPs was written in "phono3py_mlp_eval_dataset.yaml".
Summary of calculation was written in "phono3py.yaml".
-------------------------[time 2025-01-19 18:06:55]-------------------------
-------------------------[time 2025-07-26 14:00:58]-------------------------
_
___ _ __ __| |
/ _ \ '_ \ / _` |
@ -315,29 +311,28 @@ corresponding forces are stored in the `phono3py_mlp_eval_dataset.yaml` file.
### Steps 5-7: Force constants calculation (random displacements in step 5)
Random displacements are generated by specifying {ref}`--rd
<random_displacements_option>` option. To compute force constants with random
displacements, an external force constants calculator is necessary. By default,
symfc is used unless another force constants solver is explicitly specified.
When running with the `--pypolymlp` option, MLPs are read from `polymlp.yaml`
if the file exists. In this case, training data is no longer required, and files
such as `phono3py.yaml` can be used as the input structure file.
<random_displacements_option>` option. When running with the `--pypolymlp`
option, MLPs are read from `polymlp.yaml` if the file exists. In this case,
training data is no longer required, and files such as `phono3py.yaml` can be
used as the input structure file.
```
% phono3py-load --pypolymlp --rd 200 phono3py.yaml
% phono3py-load --pypolymlp --rd auto phono3py.yaml
_ _____
_ __ | |__ ___ _ __ ___|___ / _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ |_ \| '_ \| | | |
| |_) | | | | (_) | | | | (_) |__) | |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___/____/| .__/ \__, |
|_| |_| |___/
3.11.3
3.18.0
-------------------------[time 2025-01-19 18:13:21]-------------------------
-------------------------[time 2025-07-26 14:02:24]-------------------------
Compiled with OpenMP support (max 10 threads).
Running in phono3py.load mode.
Python version 3.12.6
Spglib version 2.5.0
Python version 3.13.3
Spglib version 2.6.1
----------------------------- General settings -----------------------------
Run mode: pypolymlp + force constants
HDF5 data compression filter: gzip
Crystal structure was read from "phono3py.yaml".
Supercell (dim): [2 2 2]
@ -349,6 +344,7 @@ Spacegroup: Fm-3m (225)
Use -v option to watch primitive cell, unit cell, and supercell structures.
NAC parameters were read from "phono3py.yaml".
----------------------------- pypolymlp start ------------------------------
Pypolymlp version 0.12.9
Pypolymlp is a generator of polynomial machine learning potentials.
Please cite the paper: A. Seko, J. Appl. Phys. 133, 011101 (2023).
Pypolymlp is developed at https://github.com/sekocha/pypolymlp.
@ -357,31 +353,34 @@ Load MLPs from "polymlp.yaml".
Generate random displacements
Twice of number of snapshots will be generated for plus-minus displacements.
Displacement distance: 0.01
Evaluate forces in 400 supercells by pypolymlp
Evaluate forces in 32 supercells by pypolymlp
Dataset generated using MLPs was written in "phono3py_mlp_eval_dataset.yaml".
----------------------------- Force constants ------------------------------
Symfc will be used to handle general (or random) displacements.
Type-II dataset for displacements and forces was provided,
but the selected force constants calculator cannot process it.
Use another force constants calculator, e.g., symfc,
to generate force constants.
Try symfc to handle general (or random) displacements.
-------------------------------- Symfc start -------------------------------
Symfc is a force constants calculator. See the following paper:
A. Seko and A. Togo, Phys. Rev. B, 110, 214302 (2024).
Symfc is developed at https://github.com/symfc/symfc.
Symfc version 1.5.3 (https://github.com/symfc/symfc)
Citation: A. Seko and A. Togo, Phys. Rev. B, 110, 214302 (2024)
Computing [2, 3] order force constants.
Increase log-level to watch detailed symfc log.
--------------------------------- Symfc end --------------------------------
-------------------------------- Symfc start -------------------------------
Symfc is a force constants calculator. See the following paper:
A. Seko and A. Togo, Phys. Rev. B, 110, 214302 (2024).
Symfc is developed at https://github.com/symfc/symfc.
Computing [2] order force constants.
Increase log-level to watch detailed symfc log.
--------------------------------- Symfc end --------------------------------
Max drift of fc3: -0.000000 (zxz) -0.000000 (xzz) -0.000000 (xzz)
Max drift of fc2: -0.000000 (yy) -0.000000 (yy)
Max drift of fc3: -0.00000000 (xyx) -0.00000000 (yxx) -0.00000000 (yxx)
Max drift of fc2: -0.00000000 (yy) -0.00000000 (yy)
fc3 was written into "fc3.hdf5".
fc2 was written into "fc2.hdf5".
--------------------------- Calculation settings ---------------------------
Non-analytical term correction (NAC): True
NAC unit conversion factor: 14.39965
BZ integration: Tetrahedron-method
Temperatures: 0.0 300.0
Cutoff frequency: 0.01
Frequency conversion factor to THz: 15.63330
----------- None of ph-ph interaction calculation was performed. -----------
Dataset generated using MLPs was written in "phono3py_mlp_eval_dataset.yaml".
Summary of calculation was written in "phono3py.yaml".
-------------------------[time 2025-01-19 18:13:34]-------------------------
-------------------------[time 2025-07-26 14:02:29]-------------------------
_
___ _ __ __| |
/ _ \ '_ \ / _` |
@ -389,88 +388,121 @@ Summary of calculation was written in "phono3py.yaml".
\___|_| |_|\__,_|
```
After the MLPs are read, 200 supercells with random directional displacements
are generated. These displacements are then inverted (such as $\Delta
\mathbf{u}_i$ and $-\Delta \mathbf{u}_i$ of all atoms $i$ in each supercell),
resulting in an additional 200 supercells. In total, 400 supercells are created.
The forces for these supercells are then evaluated. Finally, the force constants
are calculated using symfc.
After the MLPs are read, 16 supercells with random directional displacements are
generated by the option `--rd auto`. These displacements are then inverted (such
as $\Delta \mathbf{u}_i$ and $-\Delta \mathbf{u}_i$ of all atoms $i$ in each
supercell), resulting in an additional 16 supercells. In total, 32 supercells
are created. The forces for these supercells are then evaluated. Finally, the
force constants are calculated using symfc. The `--rd-auto-factor` option can
change the number of supercells generated.
### Command options for force constants calculation
## Command options for force constants calculation
After obtaining the MLPs, displacements are generated using those MLPs, and the
resulting forces are computed accordingly. The displacement distance is set by
the `--amplitude` option, whose default value is 0.01 Angstrom. When the `--rd`
option is used, it specifies the number of supercells with random directional
displacements. Note that to achieve accurate force constants, the actual number
of generated supercells is twice the specified number. If `--rd` is omitted,
systematic displacements are introduced.
After obtaining the MLPs, displacements are generated using these MLPs, and the
resulting forces are computed. The displacement distance is controlled by the
`--amplitude` option, with a default value of 0.01 Angstrom. When `-d` is
specified, systematic displacements are introduced. When the `--rd` option is
used, it specifies the number of supercells with random directional
displacements. To ensure accurate force constants, the actual number of
generated supercells is twice the specified value.
Once the file `polymlp.yaml` is obtained, force constants can be calculated
using MLPs from `polymlp.yaml`. After removing the `fc3.hdf5` and `fc2.hdf5`
files, `phono3py-load` will detect `polymlp.yaml` and then compute the force
constants by loading the MLPs from `polymlp.yaml` as follows:
When atoms in the unit cell have positional degrees of freedom within the
crystal symmetry, the `--relax-atomic-positions` option can relax their
positions using MLPs. In the `example/AlN-rd` case, the following command
develops polynomial MLPs and then relaxes atomic positions using these MLPs. The
force constants are calculated using supercells with 0.005 Angstrom systematic
displacements.
```
% phono3py-load --pypolymlp --rd 100 --amplitude 0.005 phono3py.yaml
% phono3py-load phonopy_params_mp-661.yaml.xz --pypolymlp --relax-atomic-positions -d
_ _____
_ __ | |__ ___ _ __ ___|___ / _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ |_ \| '_ \| | | |
| |_) | | | | (_) | | | | (_) |__) | |_) | |_| |
| .__/|_| |_|\___/|_| |_|\___/____/| .__/ \__, |
|_| |_| |___/
3.11.3
3.18.0-dev21+ge26f3ecb
-------------------------[time 2025-01-19 18:19:02]-------------------------
-------------------------[time 2025-07-26 14:29:16]-------------------------
Compiled with OpenMP support (max 10 threads).
Running in phono3py.load mode.
Python version 3.12.6
Spglib version 2.5.0
Python version 3.13.3
Spglib version 2.6.1
----------------------------- General settings -----------------------------
Run mode: pypolymlp + force constants
HDF5 data compression filter: gzip
Crystal structure was read from "phono3py.yaml".
Supercell (dim): [2 2 2]
Crystal structure was read from "phonopy_params_mp-661.yaml.xz".
Supercell (dim): [4 4 2]
Primitive matrix:
[0. 0.5 0.5]
[0.5 0. 0.5]
[0.5 0.5 0. ]
Spacegroup: Fm-3m (225)
[1. 0. 0.]
[0. 1. 0.]
[0. 0. 1.]
Spacegroup: P6_3mc (186)
Use -v option to watch primitive cell, unit cell, and supercell structures.
NAC parameters were read from "phono3py.yaml".
NAC parameters were read from "phonopy_params_mp-661.yaml.xz".
Displacement dataset for fc3 was read from "phonopy_params_mp-661.yaml.xz".
----------------------------- pypolymlp start ------------------------------
Pypolymlp version 0.12.9.post0
Pypolymlp is a generator of polynomial machine learning potentials.
Please cite the paper: A. Seko, J. Appl. Phys. 133, 011101 (2023).
Pypolymlp is developed at https://github.com/sekocha/pypolymlp.
Load MLPs from "polymlp.yaml".
Parameters:
cutoff: 8.0
model_type: 3
max_p: 2
gtinv_order: 3
gtinv_maxl: (8, 8)
gaussian_params1: (1.0, 1.0, 1)
gaussian_params2: (0.0, 7.0, 10)
Developing MLPs by pypolymlp...
MLPs were written into "polymlp.yaml"
------------------------------ pypolymlp end -------------------------------
Generate random displacements
Twice of number of snapshots will be generated for plus-minus displacements.
Relaxing atomic positions using polynomial MLPs...
Change in fractional position and in distance:
1 N : 0.00000000 0.00000000 -0.00000021 (|d|=0.00000105)
2 N : 0.00000000 0.00000000 -0.00000021 (|d|=0.00000105)
3 Al: 0.00000000 0.00000000 0.00000021 (|d|=0.00000105)
4 Al: 0.00000000 0.00000000 0.00000021 (|d|=0.00000105)
----------------------------------------------------------------------------
Generate displacements
Displacement distance: 0.005
Evaluate forces in 200 supercells by pypolymlp
Evaluate forces in 3720 supercells by pypolymlp
Dataset generated using MLPs was written in "phono3py_mlp_eval_dataset.yaml".
----------------------------- Force constants ------------------------------
Symfc will be used to handle general (or random) displacements.
-------------------------------- Symfc start -------------------------------
Symfc is a force constants calculator. See the following paper:
A. Seko and A. Togo, Phys. Rev. B, 110, 214302 (2024).
Symfc is developed at https://github.com/symfc/symfc.
Computing [2, 3] order force constants.
Increase log-level to watch detailed symfc log.
--------------------------------- Symfc end --------------------------------
-------------------------------- Symfc start -------------------------------
Symfc is a force constants calculator. See the following paper:
A. Seko and A. Togo, Phys. Rev. B, 110, 214302 (2024).
Symfc is developed at https://github.com/symfc/symfc.
Computing [2] order force constants.
Increase log-level to watch detailed symfc log.
--------------------------------- Symfc end --------------------------------
Max drift of fc3: -0.000000 (zxz) -0.000000 (xzz) -0.000000 (xzz)
Max drift of fc2: -0.000000 (yy) -0.000000 (yy)
Computing fc3[ 1, x, x ] using numpy.linalg.pinv.
Displacements (in Angstrom):
[ 0.0050 0.0000 0.0000]
[-0.0050 0.0000 0.0000]
[ 0.0000 0.0000 0.0050]
[ 0.0000 0.0000 -0.0050]
Computing fc3[ 65, x, x ] using numpy.linalg.pinv.
Displacements (in Angstrom):
[ 0.0050 0.0000 0.0000]
[-0.0050 0.0000 0.0000]
[ 0.0000 0.0000 0.0050]
[ 0.0000 0.0000 -0.0050]
Expanding fc3.
Symmetrizing fc3 by symfc projector.
Symfc version 1.5.3 (https://github.com/symfc/symfc)
Citation: A. Seko and A. Togo, Phys. Rev. B, 110, 214302 (2024)
Symmetrizing fc2 by symfc projector.
Symfc version 1.5.3 (https://github.com/symfc/symfc)
Citation: A. Seko and A. Togo, Phys. Rev. B, 110, 214302 (2024)
Max drift of fc3: -0.00000000 (xxz) -0.00000000 (xxz) -0.00000000 (xzx)
Max drift of fc2: -0.00000000 (xx) -0.00000000 (xx)
fc3 was written into "fc3.hdf5".
fc2 was written into "fc2.hdf5".
--------------------------- Calculation settings ---------------------------
Non-analytical term correction (NAC): True
NAC unit conversion factor: 14.39965
BZ integration: Tetrahedron-method
Temperatures: 0.0 300.0
Cutoff frequency: 0.01
Frequency conversion factor to THz: 15.63330
----------- None of ph-ph interaction calculation was performed. -----------
Dataset generated using MLPs was written in "phono3py_mlp_eval_dataset.yaml".
Summary of calculation was written in "phono3py.yaml".
-------------------------[time 2025-01-19 18:19:09]-------------------------
-------------------------[time 2025-07-26 14:39:11]-------------------------
_
___ _ __ __| |
/ _ \ '_ \ / _` |
@ -478,7 +510,6 @@ Summary of calculation was written in "phono3py.yaml".
\___|_| |_|\__,_|
```
## Parameters for developing MLPs
A few parameters can be specified using the `--mlp-params` option for the

5
phono3py/cui/phono3py_script.py
View File

@ -634,11 +634,6 @@ def _run_pypolymlp(
print("-" * 76)
if relaxed_unitcell is not None:
if log_level:
print(
"Relaxed crystal structures will be stored in "
f'"{output_yaml_filename}".'
)
_ph3py, _, _ = _init_phono3py(
settings,
relaxed_unitcell.copy(),