Merge branch 'develop' into rc

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

@@ -35,7 +35,7 @@ jobs:
     - name: Install phonopy develop branch
       run: |
         conda activate test
-        git clone --depth 1 https://github.com/phonopy/phonopy.git
+        git clone https://github.com/phonopy/phonopy.git
         cd phonopy
         pip install -e . -vvv
         cd ..

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

@@ -35,7 +35,7 @@ jobs:
     - name: Install phonopy develop branch
       run: |
         conda activate test
-        git clone --depth 1 https://github.com/phonopy/phonopy.git
+        git clone https://github.com/phonopy/phonopy.git
         cd phonopy
         pip install -e . -vvv
         cd ..

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

@@ -35,7 +35,7 @@ jobs:
     - name: Install phonopy develop branch
       run: |
         conda activate test
-        git clone --depth 1 https://github.com/phonopy/phonopy.git
+        git clone https://github.com/phonopy/phonopy.git
         cd phonopy
         pip install -e . -vvv
         cd ..

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

@@ -35,14 +35,14 @@ jobs:
     - name: Install symfc develop branch
       run: |
         conda activate test
-        git clone --depth 1 https://github.com/symfc/symfc.git
+        git clone https://github.com/symfc/symfc.git
         cd symfc
         pip install -e . -vvv
         cd ..
     - name: Install phonopy develop branch
       run: |
         conda activate test
-        git clone --depth 1 https://github.com/phonopy/phonopy.git
+        git clone https://github.com/phonopy/phonopy.git
         cd phonopy
         pip install -e . -vvv
         cd ..

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

@@ -28,14 +28,14 @@ jobs:
     - name: Install symfc develop branch
       run: |
         conda activate test
-        git clone --depth 1 https://github.com/symfc/symfc.git
+        git clone https://github.com/symfc/symfc.git
         cd symfc
         pip install -e . -vvv
         cd ..
     - name: Install phonopy develop branch
       run: |
         conda activate test
-        git clone --depth 1 https://github.com/phonopy/phonopy.git
+        git clone https://github.com/phonopy/phonopy.git
         cd phonopy
         pip install -e . -vvv
         cd ..

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

@@ -28,7 +28,7 @@ jobs:
     - name: Install phonopy develop branch
       run: |
         conda activate test
-        git clone --depth 1 https://github.com/phonopy/phonopy.git
+        git clone https://github.com/phonopy/phonopy.git
         cd phonopy
         pip install -e . -vvv
         cd ..

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
     exclude: ^example/AlN-LDA/
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.6.1
+  rev: v0.6.4
   hooks:
   - id: ruff
     args: [ "--fix", "--show-fixes" ]

doc/changelog.md

@@ -2,6 +2,10 @@
 
 # Change Log
 
+## Sep-13-2024: Version 3.5
+
+- Maintenance release.
+
 ## Aug-23-2024: Version 3.4
 
 - Update for spglib v2.5 and for following the change in phonopy.

doc/command-options.md

@@ -86,8 +86,7 @@ These options have no respective configuration file tags.
 
 This is used to create `FORCES_FC3` from `phono3py_disp.yaml` and force
 calculator outputs containing forces in supercells. `phono3py_disp.yaml` has to
-be located at the current directory. Calculator interface has to be specified
-except for VASP (default) case.
+be located at the current directory.
 
 ```bash
 % phono3py --cf3 disp-{00001..00755}/vasprun.xml
@@ -97,14 +96,26 @@ except for VASP (default) case.
 % phono3py --cf3 supercell_out/disp-{00001..00111}/Si.out
 ```
 
+````{note}
+The calculator interface should be stored in `phono3py_disp.yaml`, so it is not
+needed to set it manually. Command-line-options like `--qe` will be ignored. If
+the calculator interface is missing from `phono3py_disp.yaml` but needed, please
+update the `phono3py` section in the file as follows:
+
+```yaml
+phono3py:
+  calculator: qe
+```
+````
+
 (cf3_file_option)=
 
 ### `--cf3-file` (command option only)
 
 This is used to create `FORCES_FC3` from a text file containing a list of
 calculator output file names. `phono3py_disp.yaml` has to be located at the
-current directory. Calculator interface has to be specified except for VASP
-(default) case.
+current directory. The calculator interface is unnecessary to specify, see the
+note at {ref}`--cf3 <cf3_option>`.
 
 ```bash
 % phono3py --cf3-file file_list.dat
@@ -130,8 +141,9 @@ together with `--cutoff-pair` option.
 
 This is used to create `FORCES_FC2` similarly to `--cf3` option.
 `phono3py_disp.yaml` has to be located at the current directory. This is
-optional. Calculator interface has to be specified except for VASP (default)
-case. `FORCES_FC2` is necessary to run with `--dim-fc2` option.
+optional. `FORCES_FC2` is necessary to run with `--dim-fc2` option. The
+calculator interface is unnecessary to specify, see the note at {ref}`--cf3
+<cf3_option>`.
 
 ```bash
 % phono3py --cf2 disp_fc2-{00001..00002}/vasprun.xml
@@ -142,8 +154,8 @@ case. `FORCES_FC2` is necessary to run with `--dim-fc2` option.
 ### `--cfz` (command option only)
 
 This is used to create `FORCES_FC3` and `FORCES_FC2` subtracting residual forces
-combined with `--cf3` and `--cf2`, respectively. Calculator interface has to be
-specified except for VASP (default) case.
+combined with `--cf3` and `--cf2`, respectively. The calculator interface is
+unnecessary to specify, see the note at {ref}`--cf3 <cf3_option>`.
 
 In the following example, it is supposed that `disp3-00000/vasprun.xml` and
 `disp2-00000/vasprun.xml` contain the forces of the perfect supercells. In ideal
@@ -204,7 +216,6 @@ When using with `--cf2`, `--cf3` has to be specified simultaneously as below,
 % phono3py --cf3 disp-{00001..00755}/vasprun.xml --cf2 disp_fc2-{00001..00002}/vasprun.xml --sp
 ```
 
-
 ## Supercell, primitive cell, masses, magnetic moments
 
 (dim_option)=
@@ -299,6 +310,7 @@ web page](https://phonopy.github.io/phonopy/setting-tags.html#magmom).
 ## Displacement creation
 
 (create_displacements_option)=
+
 ### `-d` (`CREATE_DISPLACEMENTS = .TRUE.`)
 
 **`phono3py-load` doesn't have this option.**
@@ -317,6 +329,7 @@ information about primitive cell (`primitive_matrix` key) in
 ```
 
 (random_displacements_option)=
+
 ### `--rd` (`RANDOM_DISPLACEMENTS`), `--rd-fc2` (`RANDOM_DISPLACEMENTS_FC2`) and `--random-seed` (`RANDOM_SEED`)
 
 **`phono3py-load` doesn't have this option.**
@@ -336,6 +349,7 @@ and/or `--rd-fc2`,
 ```
 
 (amplitude_option)=
+
 ### `--amplitude` (`DISPLACEMENT_DISTANCE`)
 
 **`phono3py-load` doesn't have this option.**
@@ -348,6 +362,7 @@ The default value depends on calculator. See
 {ref}`default_displacement_distance_for_calculator`.
 
 (fc_calculator_option)=
+
 ### `--fc-calc`, `--fc-calculator` (`FC_CALCULATOR`)
 
 Choice of force constants calculator.
@@ -357,14 +372,17 @@ Choice of force constants calculator.
 ```
 
 To use different force constants calculators for fc2 and fc3
+
 ```bash
 % phono3py-load --fc-calc "symfc|" ...
 ```
+
 Those for fc2 and fc3 are seprated by `|` such as `symfc|` . Blank means to
 employ the finite difference method for systematic displacements generated by
 the option `-d`.
 
 (fc_calculator_options_option)=
+
 ### `--fc-calc-opt`, `--fc-calculator-options` (`FC_CALCULATOR_OPTIONS`)
 
 Special options for force constants calculators.
@@ -608,9 +626,9 @@ $$
  \bigl|\Phi_{-\lambda\lambda'\lambda''}\bigl|^2
  \left\{(n_{\lambda'}+ n_{\lambda''}+1)
   \delta(\omega-\omega_{\lambda'}-\omega_{\lambda''}) \right.
-  + (n_{\lambda'}-n_{\lambda''})
+  * (n_{\lambda'}-n_{\lambda''})
  \left[\delta(\omega+\omega_{\lambda'}-\omega_{\lambda''})
-+ \left. \delta(\omega-\omega_{\lambda'}+\omega_{\lambda''})
+* \left. \delta(\omega-\omega_{\lambda'}+\omega_{\lambda''})
 \right]\right\}.
 $$
 
@@ -840,7 +858,7 @@ $$
  \bigl|\Phi_{-\lambda\lambda_1\lambda_2}\bigl|^2
  (n_{\lambda_1}-n_{\lambda_2})
  \left[\delta(\omega+\omega_{\lambda_1}-\omega_{\lambda_2})
- +  \delta(\omega-\omega_{\lambda_1}+\omega_{\lambda_2})
+ *  \delta(\omega-\omega_{\lambda_1}+\omega_{\lambda_2})
  \right]
  \end{align*}
 $$
@@ -854,7 +872,7 @@ $$
  \bigl|\Phi_{-\lambda\lambda_1\lambda_2}\bigl|^2
 (n_{\lambda_1}+ n_{\lambda_2}+1)
  \left[ \delta(\omega-\omega_{\lambda_1}-\omega_{\lambda_2})
- + \delta(\omega + \omega_{\lambda_1} + \omega_{\lambda_2}) \right]
+ * \delta(\omega + \omega_{\lambda_1} + \omega_{\lambda_2}) \right]
  \end{align*},
 $$
 
@@ -922,11 +940,11 @@ $$
  \bigl|\Phi_{-\lambda\lambda_1\lambda_2}\bigl|^2 &
  \left\{(n_{\lambda_1}+ n_{\lambda_2}+1)
  \left[ \delta(\omega-\omega_{\lambda_1}-\omega_{\lambda_2})
- + \delta(\omega+\omega_{\lambda_1}+\omega_{\lambda_2}) \right] \right.
+ * \delta(\omega+\omega_{\lambda_1}+\omega_{\lambda_2}) \right] \right.
  \\
  & + (n_{\lambda_1}-n_{\lambda_2})
  \left[\delta(\omega+\omega_{\lambda_1}-\omega_{\lambda_2})
- + \left. \delta(\omega-\omega_{\lambda_1}+\omega_{\lambda_2})
+ * \left. \delta(\omega-\omega_{\lambda_1}+\omega_{\lambda_2})
  \right]\right\},
 \end{align*}
 $$
@@ -941,14 +959,14 @@ $$
  \left\{
  \left[ \frac{(n_{\lambda_1}+ n_{\lambda_2}+1)}{
  (\omega-\omega_{\lambda_1}-\omega_{\lambda_2})_\mathrm{p}}
- + \frac{(n_{\lambda_1}+ n_{\lambda_2}+1)}{
+ * \frac{(n_{\lambda_1}+ n_{\lambda_2}+1)}{
  (\omega+\omega_{\lambda_1}+\omega_{\lambda_2})_\mathrm{p}}
  \right]
  \right. \\
   & + \left[
  \frac{(n_{\lambda_1}-n_{\lambda_2})}{(\omega +
  \omega_{\lambda_1} - \omega_{\lambda_2})_\mathrm{p}}
- + \left. \frac{(n_{\lambda_1}-n_{\lambda_2})}{(\omega -
+ * \left. \frac{(n_{\lambda_1}-n_{\lambda_2})}{(\omega -
  \omega_{\lambda_1} + \omega_{\lambda_2})_\mathrm{p}}
  \right]\right\},
 \end{align*}
@@ -1012,7 +1030,7 @@ A_\lambda(\omega) = \frac{1}{\pi} \frac{4\Omega^2_\lambda
  \Gamma_\lambda(\omega)}
  {\left[\omega^2 - \Omega^2_\lambda -
  2\Omega_\lambda \Delta_\lambda(\omega) \right]^2
- + \left[ 2\Omega_\lambda
+ * \left[ 2\Omega_\lambda
  \Gamma_\lambda(\omega) \right]^2},
 $$
 
@@ -1348,12 +1366,12 @@ Using this option, output file names are slightly modified. For example, with
 
 This rule is applied to
 
-+ `fc3.hdf5`
-+ `fc2.hdf5`
-+ `kappa-xxx.hdf5`
-+ `phonon-xxx.hdf5`
-+ `pp-xxx.hdf5`
-+ `gamma_detail-xxx.hdf5` (write only)
+* `fc3.hdf5`
+* `fc2.hdf5`
+* `kappa-xxx.hdf5`
+* `phonon-xxx.hdf5`
+* `pp-xxx.hdf5`
+* `gamma_detail-xxx.hdf5` (write only)
 
 (input_filename_option)=
 
@@ -1367,11 +1385,11 @@ specifying `-i iso --fc3`, a file name `fc3.iso.hdf5` is read instead of
 
 This rule is applied to
 
-+ `fc3.hdf5`
-+ `fc2.hdf5`
-+ `kappa-xxx.hdf5`
-+ `phonon-xxx.hdf5`
-+ `pp-xxx.hdf5`
+* `fc3.hdf5`
+* `fc2.hdf5`
+* `kappa-xxx.hdf5`
+* `phonon-xxx.hdf5`
+* `pp-xxx.hdf5`
 
 ### `--io` (command option only)
 

doc/conf.py

@@ -58,9 +58,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = "3.3"
+version = "3.5"
 # The full version, including alpha/beta/rc tags.
-release = "3.3.4"
+release = "3.5.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/index.md

@@ -30,11 +30,8 @@ Papers that may introduce phono3py:
   [JPCM.35.353001](https://iopscience.iop.org/article/10.1088/1361-648X/acd831)
   (open access)
 
-
-## Documentation
-
 ```{toctree}
-:maxdepth: 1
+:hidden:
 install
 workflow
 examples

phono3py/api_phono3py.py

@@ -58,8 +58,10 @@
 from phonopy.interface.pypolymlp import (
     PypolymlpData,
     PypolymlpParams,
+    develop_mlp_by_pypolymlp,
     develop_polymlp,
     evalulate_polymlp,
+    load_polymlp,
     parse_mlp_params,
 )
 from phonopy.structure.atoms import PhonopyAtoms
@@ -2203,31 +2205,20 @@ def develop_mlp(
         if self._mlp_dataset is None:
             raise RuntimeError("MLP dataset is not set.")
 
-        if params is not None:
-            _params = parse_mlp_params(params)
-        else:
-            _params = params
-
-        disps = self._mlp_dataset["displacements"]
-        forces = self._mlp_dataset["forces"]
-        energies = self._mlp_dataset["supercell_energies"]
-        n = int(len(disps) * (1 - test_size))
-        train_data = PypolymlpData(
-            displacements=disps[:n], forces=forces[:n], supercell_energies=energies[:n]
-        )
-        test_data = PypolymlpData(
-            displacements=disps[n:], forces=forces[n:], supercell_energies=energies[n:]
-        )
-        self._mlp = develop_polymlp(
+        self._mlp = develop_mlp_by_pypolymlp(
+            self._mlp_dataset,
             self._supercell,
-            train_data,
-            test_data,
-            params=_params,
-            verbose=self._log_level - 1 > 0,
+            params=params,
+            test_size=test_size,
+            log_level=self._log_level,
         )
 
+    def load_mlp(self, filename: str = "phono3py.pmlp"):
+        """Load machine learning potential of pypolymlp."""
+        self._mlp = load_polymlp(filename=filename)
+
     def evaluate_mlp(self):
-        """Evaluate the machine learning potential of pypolymlp.
+        """Evaluate machine learning potential of pypolymlp.
 
         This method calculates the supercell energies and forces from the MLP
         for the displacements in self._dataset of type 2. The results are stored