deploy: e5da0c5

.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: c60c004ec093e9dddcdf4d3db6ee3da0
+config: 038eb0d6d22c3802bd330298771c653a
 tags: 645f666f9bcd5a90fca523b33c5a78b7

README.html

@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>How to write phono3py documentation &#8212; Phono3py v.3.11.0</title>
+    <title>How to write phono3py documentation &#8212; Phono3py v.3.11.1</title>
 
 
 
@@ -30,7 +30,7 @@
   <link href="_static/styles/theme.css?digest=8878045cc6db502f8baf" rel="stylesheet" />
 <link href="_static/styles/pydata-sphinx-theme.css?digest=8878045cc6db502f8baf" rel="stylesheet" />
 
-    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
+    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="_static/styles/sphinx-book-theme.css?v=a3416100" />
 
   <!-- So that users can add custom icons -->
@@ -39,7 +39,7 @@
   <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=8878045cc6db502f8baf" />
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf" />
 
-    <script src="_static/documentation_options.js?v=9aac1449"></script>
+    <script src="_static/documentation_options.js?v=21509654"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
@@ -125,7 +125,7 @@
 
 
 
-    <p class="title logo__title">Phono3py v.3.11.0</p>
+    <p class="title logo__title">Phono3py v.3.11.1</p>
 
 </a></div>
         <div class="sidebar-primary-item">

_sources/changelog.md

@@ -2,6 +2,12 @@
 
 # Change Log
 
+## Jan-12-2024: Version 3.11.1
+
+- `-i`, `-o`, `--io` options have been deprecated.
+- The `--amplitude` option can now be used to specify the displacement distance
+  for `phono3py-load --pypolymlp`.
+
 ## Jan-2-2024: Version 3.11.0
 
 - Release to follow the change of phonopy

_sources/command-options.md

@@ -1358,8 +1358,11 @@ set. Other filters (`lzf` or integer values of 0 to 9) may be used, see h5py
 documentation
 (<http://docs.h5py.org/en/stable/high/dataset.html#filter-pipeline>).
 
-(output_filename_option)=
+### `-o`, `-i`, `--io`
 
+These options are deprecated.
+
+<!-- (output_filename_option)=
 ### `-o` (command option only)
 
 This modifies default output file names to write.
@@ -1378,7 +1381,6 @@ This rule is applied to
 * `gamma_detail-xxx.hdf5` (write only)
 
 (input_filename_option)=
-
 ### `-i` (command option only)
 
 This modifies default input file names to read.
@@ -1399,7 +1401,7 @@ This rule is applied to
 
 This modifies default input and output file names.
 
-This is equivalent to setting `-i` and `-o` simultaneously.
+This is equivalent to setting `-i` and `-o` simultaneously. -->
 
 <!-- ## References
 

_sources/install.md

@@ -41,7 +41,6 @@ removed.
 If phono3py is compiled with a special compiler or special options, manual
 modification of `CMakeLists.txt` may be needed.
 
-- {ref}`OpenMP library <install_openmp>`: For the multithreding support.
 - {ref}`Linear algebra library <install_lapacke>`: BLAS, LAPACK, and LAPACKE
   (optional, see {ref}`install_with_lapacke`)
 

_sources/pypolymlp.md

@@ -230,7 +230,7 @@ Max drift of fc2: -0.000000 (zz) -0.000000 (zz)
 fc3 was written into "fc3.hdf5".
 fc2 was written into "fc2.hdf5".
 ----------- None of ph-ph interaction calculation was performed. -----------
-Dataset generated using MMLPs was written in "phono3py_mlp_eval_dataset.yaml".
+Dataset generated using MLPs was written in "phono3py_mlp_eval_dataset.yaml".
 Summary of calculation was written in "phono3py.yaml".
 -------------------------[time 2024-09-19 15:21:41]-------------------------
                  _
@@ -334,7 +334,7 @@ Max drift of fc2: 0.000000 (xx) 0.000000 (xx)
 fc3 was written into "fc3.hdf5".
 fc2 was written into "fc2.hdf5".
 ----------- None of ph-ph interaction calculation was performed. -----------
-Dataset generated using MMLPs was written in "phono3py_mlp_eval_dataset.yaml".
+Dataset generated using MLPs was written in "phono3py_mlp_eval_dataset.yaml".
 Summary of calculation was written in "phono3py.yaml".
 -------------------------[time 2024-09-19 15:34:41]-------------------------
                  _
@@ -353,6 +353,89 @@ 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.
 
+### 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 0.001 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.
+
+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`
+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
+        _                      _____
+  _ __ | |__   ___  _ __   ___|___ / _ __  _   _
+ | '_ \| '_ \ / _ \| '_ \ / _ \ |_ \| '_ \| | | |
+ | |_) | | | | (_) | | | | (_) |__) | |_) | |_| |
+ | .__/|_| |_|\___/|_| |_|\___/____/| .__/ \__, |
+ |_|                                |_|    |___/
+                      3.11.1-dev14+g5f281b65
+
+-------------------------[time 2025-01-12 10:08:31]-------------------------
+Compiled with OpenMP support (max 10 threads).
+Running in phono3py.load mode.
+Python version 3.12.3
+Spglib version 2.5.0
+----------------------------- General settings -----------------------------
+HDF5 data compression filter: gzip
+Crystal structure was read from "phono3py.yaml".
+Supercell (dim): [2 2 2]
+Primitive matrix:
+  [0.  0.5 0.5]
+  [0.5 0.  0.5]
+  [0.5 0.5 0. ]
+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).
+Pypolymlp is developed at https://github.com/sekocha/pypolymlp.
+Load MLPs from "phono3py.pmlp".
+------------------------------ pypolymlp end -------------------------------
+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
+-------------------------------- 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)
+fc3 was written into "fc3.hdf5".
+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]-------------------------
+                 _
+   ___ _ __   __| |
+  / _ \ '_ \ / _` |
+ |  __/ | | | (_| |
+  \___|_| |_|\__,_|
+```
+
+
 ## Parameters for developing MLPs
 
 A few parameters can be specified using the `--mlp-params` option for the

_sources/workload-distribution.md

@@ -54,13 +54,11 @@ indices are chosen and executed as follows:
 % phono3py-load --mesh 19 19 19 --br --gp "0,1,2,3,4,5,6,7,8,9,20,21,22,23,24,25" --write-gamma
 ```
 
-Then many `kappa-m191919-gx.hdf5` files are generated. These file
-names should not be altered because in reading the data by phono3py,
-those file names are supposed to be so, though there is a little
-freedom to arrange those file names, for which see {ref}`-o <output_filename_option>` and {ref}`-i <input_filename_option>`
-options. After completing calculations for all irreducible grid-point
-indices, the RTA thermal conductivity is computed by another run in a
-short time from the stored data:
+Then many `kappa-m191919-gx.hdf5` files are generated. These file names should
+not be altered because in reading the data by phono3py, those file names are
+supposed to be so. After completing calculations for all irreducible grid-point
+indices, the RTA thermal conductivity is computed by another run in a short time
+from the stored data:
 
 ```bash
 % phono3py-load --mesh 19 19 19 --br --read-gamma

_static/documentation_options.js

@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '3.11.0',
+    VERSION: '3.11.1',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',