Merge branch 'develop' into rc

.github/workflows/phono3py-pytest-conda-mkl-phphmtblas.yml

@@ -24,7 +24,7 @@ jobs:
       run: |
         conda activate test
         conda install --yes python=${{ matrix.python-version }}
-        conda install --yes matplotlib-base pyyaml "libblas=*=*mkl" mkl-include h5py scipy pytest spglib alm cmake c-compiler cxx-compiler
+        conda install --yes matplotlib-base pyyaml "libblas=*=*mkl" mkl-include h5py scipy pytest spglib alm cmake c-compiler cxx-compiler pypolymlp
     - name: Install symfc develop branch
       run: |
         conda activate test

.github/workflows/phono3py-pytest-conda-mkl-v2.yml

@@ -24,7 +24,7 @@ jobs:
       run: |
         conda activate test
         conda install --yes python=${{ matrix.python-version }}
-        conda install --yes matplotlib-base pyyaml "libblas=*=*mkl" mkl-include h5py scipy pytest spglib alm cmake c-compiler cxx-compiler
+        conda install --yes matplotlib-base pyyaml "libblas=*=*mkl" mkl-include h5py scipy pytest spglib alm cmake c-compiler cxx-compiler pypolymlp
     - name: Install symfc develop branch
       run: |
         conda activate test

.github/workflows/phono3py-pytest-conda-mkl.yml

@@ -24,7 +24,7 @@ jobs:
       run: |
         conda activate test
         conda install --yes python=${{ matrix.python-version }}
-        conda install --yes matplotlib-base pyyaml "libblas=*=*mkl" mkl-include h5py scipy pytest codecov pytest-cov spglib alm cmake c-compiler cxx-compiler
+        conda install --yes matplotlib-base pyyaml "libblas=*=*mkl" mkl-include h5py scipy pytest codecov pytest-cov spglib alm cmake c-compiler cxx-compiler pypolymlp
     - name: Install symfc develop branch
       run: |
         conda activate test

.github/workflows/phono3py-pytest-conda-numpy2.yml

@@ -24,7 +24,7 @@ jobs:
       run: |
         conda activate test
         conda install --yes python=${{ matrix.python-version }}
-        conda install --yes matplotlib-base pyyaml "libblas=*=*openblas" openblas h5py "numpy=2" scipy pytest cmake c-compiler cxx-compiler
+        conda install --yes matplotlib-base pyyaml "libblas=*=*openblas" openblas h5py "numpy=2" scipy pytest cmake c-compiler cxx-compiler pypolymlp
     - name: Install spglib develop branch
       run: |
         conda activate test

.github/workflows/phono3py-pytest-conda-phphmtblas.yml

@@ -24,7 +24,7 @@ jobs:
       run: |
         conda activate test
         conda install --yes python=${{ matrix.python-version }}
-        conda install --yes matplotlib-base pyyaml "libblas=*=*openblas" openblas h5py scipy pytest spglib alm cmake c-compiler cxx-compiler
+        conda install --yes matplotlib-base pyyaml "libblas=*=*openblas" openblas h5py scipy pytest spglib alm cmake c-compiler cxx-compiler pypolymlp
     - name: Install symfc develop branch
       run: |
         conda activate test

.github/workflows/phono3py-pytest-conda.yml

@@ -20,11 +20,25 @@ jobs:
     - uses: conda-incubator/setup-miniconda@v3
       with:
         miniforge-version: latest
-    - name: Install dependent packages
+    - name: Install dependent packages for python > 3.9
+      if: ${{ matrix.python-version != 3.9 }}
+      run: |
+        conda activate test
+        conda install --yes python=${{ matrix.python-version }}
+        conda install --yes matplotlib-base pyyaml "libblas=*=*openblas" openblas h5py "numpy>=2.1" scipy pytest spglib alm cmake c-compiler cxx-compiler pypolymlp
+    - name: Install dependent packages for python == 3.9
+      if: ${{ matrix.python-version == 3.9 }}
       run: |
         conda activate test
         conda install --yes python=${{ matrix.python-version }}
         conda install --yes matplotlib-base pyyaml "libblas=*=*openblas" openblas h5py scipy pytest spglib alm cmake c-compiler cxx-compiler
+    - name: Install symfc develop branch
+      run: |
+        conda activate test
+        git clone --depth 1 https://github.com/symfc/symfc.git
+        cd symfc
+        pip install -e . -vvv
+        cd ..
     - name: Install phonopy develop branch
       run: |
         conda activate test

.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: v4.6.0
+  rev: v5.0.0
   hooks:
   - id: trailing-whitespace
   - id: end-of-file-fixer
@@ -11,7 +11,7 @@ repos:
     exclude: ^example/AlN-LDA/
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.6.7
+  rev: v0.7.0
   hooks:
   - id: ruff
     args: [ "--fix", "--show-fixes" ]

doc/changelog.md

@@ -2,6 +2,10 @@
 
 # Change Log
 
+## Nov-3-2024: Version 3.6.0
+
+- Maintenance release.
+
 ## Sep-24-2024: Version 3.5.2
 
 - Fix a memory leak.

doc/command-options.md

@@ -626,9 +626,9 @@ $$
  \bigl|\Phi_{-\lambda\lambda'\lambda''}\bigl|^2
  \left\{(n_{\lambda'}+ n_{\lambda''}+1)
   \delta(\omega-\omega_{\lambda'}-\omega_{\lambda''}) \right.
-  * (n_{\lambda'}-n_{\lambda''})
+  + (n_{\lambda'}-n_{\lambda''})
  \left[\delta(\omega+\omega_{\lambda'}-\omega_{\lambda''})
-* \left. \delta(\omega-\omega_{\lambda'}+\omega_{\lambda''})
+- \left. \delta(\omega-\omega_{\lambda'}+\omega_{\lambda''})
 \right]\right\}.
 $$
 
@@ -858,7 +858,7 @@ $$
  \bigl|\Phi_{-\lambda\lambda_1\lambda_2}\bigl|^2
  (n_{\lambda_1}-n_{\lambda_2})
  \left[\delta(\omega+\omega_{\lambda_1}-\omega_{\lambda_2})
- *  \delta(\omega-\omega_{\lambda_1}+\omega_{\lambda_2})
+ - \delta(\omega-\omega_{\lambda_1}+\omega_{\lambda_2})
  \right]
  \end{align*}
 $$
@@ -872,7 +872,7 @@ $$
  \bigl|\Phi_{-\lambda\lambda_1\lambda_2}\bigl|^2
 (n_{\lambda_1}+ n_{\lambda_2}+1)
  \left[ \delta(\omega-\omega_{\lambda_1}-\omega_{\lambda_2})
- * \delta(\omega + \omega_{\lambda_1} + \omega_{\lambda_2}) \right]
+ - \delta(\omega + \omega_{\lambda_1} + \omega_{\lambda_2}) \right]
  \end{align*},
 $$
 
@@ -940,11 +940,11 @@ $$
  \bigl|\Phi_{-\lambda\lambda_1\lambda_2}\bigl|^2 &
  \left\{(n_{\lambda_1}+ n_{\lambda_2}+1)
  \left[ \delta(\omega-\omega_{\lambda_1}-\omega_{\lambda_2})
- * \delta(\omega+\omega_{\lambda_1}+\omega_{\lambda_2}) \right] \right.
+ - \delta(\omega+\omega_{\lambda_1}+\omega_{\lambda_2}) \right] \right.
  \\
  & + (n_{\lambda_1}-n_{\lambda_2})
  \left[\delta(\omega+\omega_{\lambda_1}-\omega_{\lambda_2})
- * \left. \delta(\omega-\omega_{\lambda_1}+\omega_{\lambda_2})
+ - \left. \delta(\omega-\omega_{\lambda_1}+\omega_{\lambda_2})
  \right]\right\},
 \end{align*}
 $$
@@ -959,14 +959,14 @@ $$
  \left\{
  \left[ \frac{(n_{\lambda_1}+ n_{\lambda_2}+1)}{
  (\omega-\omega_{\lambda_1}-\omega_{\lambda_2})_\mathrm{p}}
- * \frac{(n_{\lambda_1}+ n_{\lambda_2}+1)}{
+ - \frac{(n_{\lambda_1}+ n_{\lambda_2}+1)}{
  (\omega+\omega_{\lambda_1}+\omega_{\lambda_2})_\mathrm{p}}
  \right]
  \right. \\
   & + \left[
  \frac{(n_{\lambda_1}-n_{\lambda_2})}{(\omega +
  \omega_{\lambda_1} - \omega_{\lambda_2})_\mathrm{p}}
- * \left. \frac{(n_{\lambda_1}-n_{\lambda_2})}{(\omega -
+ - \left. \frac{(n_{\lambda_1}-n_{\lambda_2})}{(\omega -
  \omega_{\lambda_1} + \omega_{\lambda_2})_\mathrm{p}}
  \right]\right\},
 \end{align*}
@@ -1030,7 +1030,7 @@ A_\lambda(\omega) = \frac{1}{\pi} \frac{4\Omega^2_\lambda
  \Gamma_\lambda(\omega)}
  {\left[\omega^2 - \Omega^2_\lambda -
  2\Omega_\lambda \Delta_\lambda(\omega) \right]^2
- * \left[ 2\Omega_\lambda
+ - \left[ 2\Omega_\lambda
  \Gamma_\lambda(\omega) \right]^2},
 $$
 

doc/conf.py

@@ -58,9 +58,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = "3.5"
+version = "3.6"
 # The full version, including alpha/beta/rc tags.
-release = "3.5.2"
+release = "3.6.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/pypolymlp.md

@@ -23,12 +23,38 @@ For further details on combining phono3py calculations with pypolymlp, refer to
 An example of its usage can be found in the `example/NaCl-pypolymlp` directory
 in the distribution from GitHub or PyPI.
 
+## Citation of pypolymlp
+
+"Tutorial: Systematic development of polynomial machine learning potentials for elemental and alloy systems", A. Seko, J. Appl. Phys. **133**, 011101 (2023).
+
+```
+@article{pypolymlp,
+    author = {Seko, Atsuto},
+    title = "{"Tutorial: Systematic development of polynomial machine learning potentials for elemental and alloy systems"}",
+    journal = {J. Appl. Phys.},
+    volume = {133},
+    number = {1},
+    pages = {011101},
+    year = {2023},
+    month = {01},
+}
+```
+
 ## Requirements
 
 - [pypolymlp](https://github.com/sekocha/pypolymlp)
+
+  For linux (x86-64), a compiled package of pypolymlp can be installed via
+  conda-forge (recommended). Otherwise, pypolymlp can be installed from
+  source-code.
+
 - [symfc](https://github.com/symfc/symfc)
 
-## Workflow
+  Installed via pip, conda-forge, or source code.
+
+## How to calculate
+
+### Workflow
 
 1. Generate random displacements in supercells. Use {ref}`--rd
    <random_displacements_option>` option.