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Update pypolymlp interface documentation

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Atsushi Togo 2025-01-15 19:36:24 +09:00
parent 394e7e0601
commit c64aefd726
1 changed files with 14 additions and 12 deletions
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doc/pypolymlp.md
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@ -257,12 +257,13 @@ corresponding forces are stored in the `phono3py_mlp_eval_dataset` file.
After developing MLPs, 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.
For this, symfc is used which is invoked by `--symfc` option.
By default, symfc is used unless another force constants solver is explicitly
specified.
Having `phono3py_params.yaml`, phono3py is executed with `--pypolymlp` option,
```
% phono3py-load --pypolymlp --rd 200 --symfc phono3py_params.yaml
% phono3py-load --pypolymlp --rd 200 phono3py_params.yaml
_ _____
_ __ | |__ ___ _ __ ___|___ / _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ |_ \| '_ \| | | |
@ -271,10 +272,10 @@ Having `phono3py_params.yaml`, phono3py is executed with `--pypolymlp` option,
|_| |_| |___/
3.11.2
-------------------------[time 2025-01-15 16:43:57]-------------------------
-------------------------[time 2025-01-15 19:30:47]-------------------------
Compiled with OpenMP support (max 10 threads).
Running in phono3py.load mode.
Python version 3.12.6
Python version 3.12.3
Spglib version 2.5.0
----------------------------- General settings -----------------------------
HDF5 data compression filter: gzip
@ -315,6 +316,7 @@ Generate random displacements
Displacement distance: 0.001
Evaluate forces in 400 supercells by pypolymlp
----------------------------- 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).
@ -336,7 +338,7 @@ fc2 was written into "fc2.hdf5".
----------- 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 2025-01-15 16:45:15]-------------------------
-------------------------[time 2025-01-15 19:32:04]-------------------------
_
___ _ __ __| |
/ _ \ '_ \ / _` |
@ -360,9 +362,8 @@ resulting forces are computed accordingly. The displacement distance is set by
the `--amplitude` option, whose default value is 0.001 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. Additionally, when using
`--rd`, the `--symfc` option must be used together. If `--rd` is omitted,
systematic displacements are introduced, and thus `--symfc` is not required.
of generated supercells is twice the specified number. If `--rd` is omitted,
systematic displacements are introduced.
Once the file `phono3py.pmlp` is obtained, force constants can be calculated
using MLPs from `phono3py.pmlp`. After removing the `fc3.hdf5` and `fc2.hdf5`
@ -370,7 +371,7 @@ files, `phono3py-load` will detect `phono3py.pmlp` and then compute the force
constants by loading the MLPs from `phono3py.pmlp` as follows:
```
% phono3py-load --pypolymlp --rd 100 --symfc --amplitude 0.01 phono3py.yaml
% phono3py-load --pypolymlp --rd 100 --amplitude 0.01 phono3py.yaml
_ _____
_ __ | |__ ___ _ __ ___|___ / _ __ _ _
| '_ \| '_ \ / _ \| '_ \ / _ \ |_ \| '_ \| | | |
@ -379,7 +380,7 @@ constants by loading the MLPs from `phono3py.pmlp` as follows:
|_| |_| |___/
3.11.2
-------------------------[time 2025-01-12 10:08:31]-------------------------
-------------------------[time 2025-01-15 19:28:22]-------------------------
Compiled with OpenMP support (max 10 threads).
Running in phono3py.load mode.
Python version 3.12.3
@ -395,7 +396,6 @@ Primitive matrix:
Spacegroup: Fm-3m (225)
Use -v option to watch primitive cell, unit cell, and supercell structures.
NAC parameters were read from "phono3py.yaml".
----------------------------- Force constants ------------------------------
----------------------------- pypolymlp start ------------------------------
Pypolymlp is a generator of polynomial machine learning potentials.
Please cite the paper: A. Seko, J. Appl. Phys. 133, 011101 (2023).
@ -406,6 +406,8 @@ Generate random displacements
Twice of number of snapshots will be generated for plus-minus displacements.
Displacement distance: 0.01
Evaluate forces in 200 supercells by pypolymlp
----------------------------- 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).
@ -427,7 +429,7 @@ fc2 was written into "fc2.hdf5".
----------- 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 2025-01-12 10:08:40]-------------------------
-------------------------[time 2025-01-15 19:28:30]-------------------------
_
___ _ __ __| |
/ _ \ '_ \ / _` |