diff --git a/doc/pypolymlp.md b/doc/pypolymlp.md index 86e61f7c..39a4af60 100644 --- a/doc/pypolymlp.md +++ b/doc/pypolymlp.md @@ -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 ` 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]------------------------- _ ___ _ __ __| | / _ \ '_ \ / _` |