Merge branch 'rc'

phonopy · Dec 4, 2023 · 2e004db · 2e004db
2 parents f5fb5a0 + bd4250e
commit 2e004db
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diff --git a/.github/workflows/publish-gh-pages.yml b/.github/workflows/publish-gh-pages.yml
@@ -12,7 +12,7 @@ jobs:
         shell: bash -l {0}
     strategy:
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.11"]
 
     steps:
     - uses: actions/checkout@v2
@@ -26,7 +26,7 @@ jobs:
       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
+        conda install --yes -c conda-forge sphinx-book-theme linkify-it-py myst-parser sphinxcontrib-bibtex ipython
     - name: Build
       run: |
         conda activate test

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.5.0
   hooks:
   - id: trailing-whitespace
   - id: end-of-file-fixer
@@ -11,15 +11,15 @@ repos:
   - id: check-added-large-files
 
 - repo: https://github.com/pycqa/flake8
-  rev: 6.0.0
+  rev: 6.1.0
   hooks:
   - id: flake8
     args:
     - "--max-line-length=88"
     - "--ignore=E203,W503"
 
 - repo: https://github.com/psf/black
-  rev: 23.3.0
+  rev: 23.10.1
   hooks:
   - id: black
     args:
@@ -37,7 +37,7 @@ repos:
       name: isort (python)
 
 - repo: https://github.com/Takishima/cmake-pre-commit-hooks
-  rev: v1.9.1
+  rev: v1.9.4
   hooks:
     - id: clang-format
       args:

diff --git a/doc/changelog.md b/doc/changelog.md
@@ -2,6 +2,11 @@
 
 # Change Log
 
+## Dec-4-2023: Version 2.8.0
+
+- Maintenance release
+- Fix unit conversion for non-VASP calculators
+
 ## Jul-3-2023: Version 2.7.0
 
 - Drop python 3.7 support
@@ -47,7 +52,7 @@
 
 - Maintenance release to follow the change of phonopy at v2.12.1.
 - Installation using `setup.py` now requires creating `site.cfg` file. See
-  https://phonopy.github.io/phono3py/install.html and
+  <https://phonopy.github.io/phono3py/install.html> and
   [PR #59](https://github.com/phonopy/phono3py/pull/59).
 - Dorp python 3.6 support, and dependencies of numpy and matplotlib versions are
   updated:

diff --git a/doc/conf.py b/doc/conf.py
@@ -57,9 +57,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = "2.7"
+version = "2.8"
 # The full version, including alpha/beta/rc tags.
-release = "2.7.0"
+release = "2.8.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/doc/vasp.md b/doc/vasp.md
@@ -1,15 +1,17 @@
 (vasp_interface)=
+
 # VASP & phono3py calculation
 
 (vasp_workflow)=
+
 ## Workflow
 
 1. Create POSCARs with displacements
 
    This is the same way as usual phonopy:
 
    ```bash
-   % phono3py -d --dim="2 2 2" --pa="F" -c POSCAR-unitcell
+   % phono3py -d --dim 2 2 2 --pa F -c POSCAR-unitcell
    ```
 
    `phono3py_disp.yaml` and `POSCAR-xxxxx` files are created.
@@ -19,7 +21,7 @@
    for third-order force constants (fc3) calculation:
 
    ```bash
-   % phono3py -d --dim-fc2="4 4 4" --dim="2 2 2" --pa="F" -c POSCAR-unitcell
+   % phono3py -d --dim-fc2 4 4 4 --dim 2 2 2 --pa F -c POSCAR-unitcell
    ```
 
    In this case, `POSCAR_FC2-xxxxx` files are also created.
@@ -52,6 +54,7 @@
    ```bash
    % phono3py --cf2 disp_fc2-{00001..00002}/vasprun.xml
    ```
+
    `phono3py_displ.yaml` is necessary in this case and `FORCES_FC2` is
    created.
 
@@ -73,7 +76,7 @@
    An example of thermal conductivity calculation is:
 
    ```
-   % phono3py --mesh="11 11 11" --br
+   % phono3py --mesh 11 11 11 --br
    ```
 
    This calculation may take very long time. `--thm` invokes a
@@ -90,22 +93,30 @@
    First run the same command with the addition option of `--wgp`:
 
    ```
-   % phono3py --fc3 --fc2 --mesh="11 11 11" --br --wgp
+   % phono3py --fc3 --fc2 --mesh 11 11 11 --br --wgp
+   ```
+
+   `ir_grid_points.yaml` is obtained. Irreducible q-points are found in this
+   file. For example, the grid point indices of the irreducible q-points are
+   printed by
+
+   ```
+   % grep grid_point: ir_grid_points.yaml|awk '{printf("%d ", $3)}'
+   0 1 2 3 4 5 12 13 14 15 16 17 18 19 20 21 24 25 26 27 28 29 30 31 36 37 38 39 40 41 48 49 50 51 60 61 148 149 150 151 160 161 162 163 164 165 172 173 174 175 184 185 297 298 309 310
    ```
 
-   `ir_grid_points.yaml` is obtained. In this file, irreducible
-   q-points are shown. Then distribute calculations of phonon
-   lifetimes on grid points with `--write-gamma` option by:
+   Phonon lifetimes on the first ten irreducible grid points are calculated and
+   stored in files with `--write-gamma` option by:
 
    ```
-   % phono3py --mesh="11 11 11" --br --write-gamma --gp="[grid ponit(s)]"
+   % phono3py --mesh 11 11 11 --br --write-gamma --gp 0 1 2 3 4 5 12 13 14 15
    ```
 
-   After finishing all distributed calculations, run with
-   `--read-gamma` option:
+   After finishing distributed calculations at all irreducible grid points
+   (0, 1, ..., 310), run with `--read-gamma` option:
 
    ```
-   % phono3py --fc3 --fc2 --mesh="11 11 11" --br --read-gamma
+   % phono3py --fc3 --fc2 --mesh 11 11 11 --br --read-gamma
    ```
 
    Once this calculation runs without problem, separately calculated