Merge branch 'rc'

.github/workflows/phonopy-pytest-conda-openmp-site-cfg.yml

@@ -1,6 +1,11 @@
 name: phonopy test using conda-forge environment with openmp triggered by site.cfg
 
-on: [push]
+on:
+  push:
+    branches-ignore:
+    - publish-gh-pages
+    - master
+    - rc
 
 jobs:
   build-linux:

.github/workflows/phonopy-pytest-conda-openmp.yml

@@ -1,6 +1,11 @@
 name: phonopy test using conda-forge environment with openmp
 
-on: [push]
+on:
+  push:
+    branches-ignore:
+    - publish-gh-pages
+    - master
+    - rc
 
 jobs:
   build-linux:

.github/workflows/phonopy-pytest-conda.yml

@@ -1,6 +1,11 @@
 name: phonopy test using conda-forge environment
 
-on: [push]
+on:
+  push:
+    branches-ignore:
+    - publish-gh-pages
+    - master
+    - rc
 
 jobs:
   build-linux:

.github/workflows/publish-gh-pages.yml

@@ -0,0 +1,41 @@
+name: publish phonopy gh-pages
+
+on:
+  push:
+    branches: [publish-gh-pages]
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      matrix:
+        python-version: ["3.9"]
+
+    steps:
+    - uses: actions/checkout@v2
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        auto-update-conda: true
+        channels: conda-forge
+        channel-priority: strict
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        conda activate test
+        conda install --yes -c conda-forge python=${{ matrix.python-version }}
+        conda install --yes -c conda-forge sphinx-book-theme linkify-it-py "myst-parser=0.17.2" sphinxcontrib-bibtex
+    - name: Build
+      run: |
+        conda activate test
+        sphinx-build doc docs_build
+
+    - name: Deploy docs at develop branch
+      if: ${{ github.ref == 'refs/heads/publish-gh-pages' }}
+      uses: peaceiris/actions-gh-pages@v3
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./docs_build
+        # deploy_key: ${{ secrets.ACTIONS_DEPLOY_KEY }}

.pre-commit-config.yaml

@@ -35,19 +35,19 @@ repos:
     - "--ignore=E203,W503,E501"
 
 - repo: https://github.com/psf/black
-  rev: 22.12.0
+  rev: 23.1.0
   hooks:
   - id: black
     args:
     - --line-length=88
 
 - repo: https://github.com/pycqa/pydocstyle
-  rev: 6.1.1
+  rev: 6.3.0
   hooks:
   - id: pydocstyle
 
 - repo: https://github.com/pycqa/isort
-  rev: 5.11.4
+  rev: 5.12.0
   hooks:
     - id: isort
       name: isort (python)

doc/changelog.md

@@ -2,6 +2,10 @@
 
 # Change Log
 
+## Mar-6-2023: Version 2.17.2
+
+- Bug fixes of user interface.
+
 ## Dec-29-2022: Version 2.17.1
 
 - Maintenance release.

doc/citation.md

@@ -2,7 +2,8 @@
 
 ## Citation of phonopy
 
-If you have used phonopy, please cite the following article:
+If you have used phonopy, please cite the following articles, which
+indeed helps the phonopy project to continue:
 
 - "First principles phonon calculations in materials science",
 
@@ -11,7 +12,7 @@ If you have used phonopy, please cite the following article:
   http://dx.doi.org/10.1016/j.scriptamat.2015.07.021 (Open access)
 
   ```
-  @article {phonopy,
+  @article{phonopy,
      Journal = {Scr. Mater.},
      Year = {2015},
      Title = {First principles phonon calculations in materials science},
@@ -22,6 +23,25 @@ If you have used phonopy, please cite the following article:
   }
   ```
 
+- "First-principles Phonon Calculations with Phonopy and Phono3py",
+
+  Atsushi Togo, J. Phys. Soc. Jpn., **92**, 012001-1-21 (2023)
+
+  https://doi.org/10.7566/JPSJ.92.012001 (Open access)
+
+  ```
+  @article{phonopy-phono3py-JPSJ,
+    author  = {Togo ,Atsushi},
+    title   = {First-principles Phonon Calculations with Phonopy and Phono3py},
+    journal = {J. Phys. Soc. Jpn.},
+    volume  = {92},
+    number  = {1},
+    pages   = {012001},
+    year    = {2023},
+    doi     = {10.7566/JPSJ.92.012001}
+  }
+  ```
+
 ## Some papers where phonopy was used
 
 ### `phonopy-qha`: Thermal properties, quasi-harmonic approximation used for thermal expansion

doc/conf.py

@@ -49,7 +49,7 @@
 # The short X.Y version.
 version = "2.17"
 # The full version, including alpha/beta/rc tags.
-release = "2.17.1"
+release = "2.17.2"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/setting-tags.md

@@ -271,6 +271,7 @@ distribution functions of phonon modes.
 
 An example of configure file for 2x2x2 supercell of NaCl conventional unit cell
 is as follows.
+
 ```
 CREATE_DISPLACEMENTS = .TRUE.
 DIM = 2 2 2
@@ -285,6 +286,7 @@ calculation, therefore a set of data for the phonon calculation is necessary. In
 the following example, `POSCAR-unitcell` and `FORCE_SETS` of NaCl example is
 copied to an empty directory. Running following command, `phonopy_disp.yaml` is
 generated.
+
 ```bash
 mkdir rd && cd rd
 cp <somewhere>/example/NaCl/POSCAR-unitcell .
@@ -304,7 +306,7 @@ See also {ref}`f_force_sets_option` for creating `FORCE_SETS` from a series of
 sueprcell calculation. Be careful that if `FORCE_SETS` exists in the current
 directory, it will be overwritten by creating new `FORCE_SETS`.
 
- To obtain force constants with random displacements and
+To obtain force constants with random displacements and
 respective forces, an external force constants calculator is necessary. See
 {ref}`fc_calculator_tag`.
 
@@ -319,6 +321,7 @@ imaginary modes are treated as their absolute values.
 
 Distribution of displacement distances may be visualized and checked by a python
 script like below.
+
 ```python
 import matplotlib.pyplot as plt
 import numpy as np
@@ -333,6 +336,41 @@ plt.show()
 :scale: 50
 ```
 
+An example case using this tag is as follows.
+
+1. Compute supercell force sets in the usual manner with small displacements.
+   Generate `FORCE_SETS` in the current directory.
+2. Create new directory and copy `FORCE_SETS` and input crystal structure, or
+   `phonopy_disp.yaml` to the new directory, then change to the new directory.
+3. Using `FORCE_SETS`, generate supercells with random displacements at finite
+   temperature using this tag. `phonopy_disp.yaml` is generated at this step.
+   Therefore, if `phonopy_disp.yaml` already exists in this directory, it is
+   overwritten. The required number of supercells depends on your system and
+   also the purpose. It can be 10, or can be 1000.
+4. Using those supercells with random displacements, calculate supercell forces
+   with some force calculator with VASP, QE, etc.
+5. Generate `FORCE_SETS` in this directory, which overwrites previous
+   `FORCE_SETS`.
+6. Run the force constants calculation, e.g., with ALM. ALM does the fitting
+   force constants using the dataset of displacements and forces stored in
+   `FORCE_SETS`. Run also phonon calculation. This is done for example,
+
+   ```
+   phonopy -v --alm --mesh 10 10 10 -p
+   ```
+
+   or
+
+   ```bash
+   phonopy -v --alm --writefc
+   phonopy --readfc --mesh 10 10 10 -p
+   ```
+
+   Normally the force constants calculation with ALM will not take much time,
+   but for some cases it can be. So it may be a good idea to store force constants like the second example.
+
+To perform above procedure more systematically, it is recommended to write a
+python script using phonopy API.
 
 (random_seed_tag)=
 

example/Al2O3/Al2O3.py

@@ -38,10 +38,9 @@
 frequencies = bs["frequencies"]
 qpoints = bs["qpoints"]
 
-for (qs_at_segments, dists_at_segments, freqs_at_segments) in zip(
+for qs_at_segments, dists_at_segments, freqs_at_segments in zip(
     qpoints, distances, frequencies
 ):
-
     for q, d, f in zip(qs_at_segments, dists_at_segments, freqs_at_segments):
         print("# %f %f %f" % tuple(q))
         print(("%s " + "%f " * len(f)) % ((d,) + tuple(f)))