Merge branch 'develop' into publish-gh-pages

.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: v0.6.3
+  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/conf.py

@@ -58,9 +58,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = "3.4"
+version = "3.5"
 # The full version, including alpha/beta/rc tags.
-release = "3.4.0"
+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

@@ -58,6 +58,7 @@
 from phonopy.interface.pypolymlp import (
     PypolymlpData,
     PypolymlpParams,
+    develop_mlp_by_pypolymlp,
     develop_polymlp,
     evalulate_polymlp,
     load_polymlp,
@@ -2204,30 +2205,15 @@ 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 = "pypolymlp.mlp"):
+    def load_mlp(self, filename: str = "phono3py.pmlp"):
         """Load machine learning potential of pypolymlp."""
         self._mlp = load_polymlp(filename=filename)
 

phono3py/cui/create_force_constants.py

@@ -118,19 +118,28 @@ def create_phono3py_force_constants(
         if settings.read_fc3:
             _read_phono3py_fc3(phono3py, symmetrize_fc3r, input_filename, log_level)
         else:  # fc3 from FORCES_FC3 or ph3py_yaml
-            _read_dataset_fc3(
+            dataset = _read_dataset_fc3(
                 phono3py,
                 ph3py_yaml,
                 phono3py_yaml_filename,
                 settings.cutoff_pair_distance,
                 calculator,
-                settings.use_pypolymlp,
-                settings.mlp_params,
-                settings.displacement_distance,
-                settings.random_displacements,
-                settings.random_seed,
                 log_level,
             )
+
+            if settings.use_pypolymlp:
+                phono3py.mlp_dataset = dataset
+                run_pypolymlp_to_compute_forces(
+                    phono3py,
+                    settings.mlp_params,
+                    displacement_distance=settings.displacement_distance,
+                    number_of_snapshots=settings.random_displacements,
+                    random_seed=settings.random_seed,
+                    log_level=log_level,
+                )
+            else:
+                phono3py.dataset = dataset
+
             phono3py.produce_fc3(
                 symmetrize_fc3r=symmetrize_fc3r,
                 is_compact_fc=settings.is_compact_fc,
@@ -214,7 +223,7 @@ def parse_forces(
     fc_type: Literal["fc3", "phonon_fc2"] = "fc3",
     calculator: Optional[str] = None,
     log_level=0,
-):
+) -> dict:
     """Read displacements and forces.
 
     Physical units of displacements and forces are converted following the
@@ -459,13 +468,8 @@ def _read_dataset_fc3(
     phono3py_yaml_filename: Optional[str],
     cutoff_pair_distance: Optional[float],
     calculator: Optional[str],
-    use_pypolymlp: bool,
-    mlp_params: Union[str, dict, PypolymlpParams],
-    displacement_distance: Optional[float],
-    number_of_snapshots: Optional[int],
-    random_seed: Optional[int],
     log_level: int,
-):
+) -> dict:
     """Read or calculate fc3.
 
     Note
@@ -501,19 +505,7 @@ def _read_dataset_fc3(
         # from _get_type2_dataset
         file_exists(e.filename, log_level=log_level)
 
-    if use_pypolymlp:
-        if forces_in_dataset(dataset):
-            phono3py.mlp_dataset = dataset
-        run_pypolymlp_to_compute_forces(
-            phono3py,
-            mlp_params,
-            displacement_distance=displacement_distance,
-            number_of_snapshots=number_of_snapshots,
-            random_seed=random_seed,
-            log_level=log_level,
-        )
-    else:
-        phono3py.dataset = dataset
+    return dataset
 
 
 def run_pypolymlp_to_compute_forces(
@@ -522,7 +514,7 @@ def run_pypolymlp_to_compute_forces(
     displacement_distance: Optional[float] = None,
     number_of_snapshots: Optional[int] = None,
     random_seed: Optional[int] = None,
-    mlp_filename: str = "pypolymlp.mlp",
+    mlp_filename: str = "phono3py.pmlp",
     log_level: int = 0,
 ):
     """Run pypolymlp to compute forces."""
@@ -536,13 +528,14 @@ def run_pypolymlp_to_compute_forces(
             for k, v in asdict(parse_mlp_params(mlp_params)).items():
                 if v is not None:
                     print(f"  {k}: {v}")
-    if log_level > 1:
-        print("")
 
     if forces_in_dataset(ph3py.mlp_dataset):
         if log_level:
             print("Developing MLPs by pypolymlp...", flush=True)
         ph3py.develop_mlp(params=mlp_params)
+        ph3py.mlp.save_mlp(filename=mlp_filename)
+        if log_level:
+            print(f'MLPs were written into "{mlp_filename}"', flush=True)
     else:
         if pathlib.Path(mlp_filename).exists():
             if log_level:
@@ -613,8 +606,6 @@ def run_pypolymlp_to_compute_phonon_forces(
                 for k, v in asdict(parse_mlp_params(mlp_params)).items():
                     if v is not None:
                         print(f"  {k}: {v}")
-        if log_level > 1:
-            print("")
         if log_level:
             print("Developing MLPs by pypolymlp...", flush=True)
 

phono3py/cui/phono3py_script.py

@@ -163,18 +163,23 @@ def finalize_phono3py(
     else:
         yaml_filename = filename
 
-    _physical_units = get_default_physical_units(phono3py.calculator)
+    if phono3py.mlp_dataset is not None:
+        mlp_eval_filename = "phono3py_mlp_eval_dataset.yaml"
+        if log_level:
+            print(
+                f'Dataset generated using MMLPs was written in "{mlp_eval_filename}".'
+            )
+        phono3py.save(mlp_eval_filename)
 
-    write_force_sets = phono3py.mlp is not None
-    _write_displacements = write_displacements or phono3py.mlp is not None
+    _physical_units = get_default_physical_units(phono3py.calculator)
 
     ph3py_yaml = Phono3pyYaml(
         configuration=confs_dict,
         calculator=phono3py.calculator,
         physical_units=_physical_units,
         settings={
-            "force_sets": write_force_sets,
-            "displacements": _write_displacements,
+            "force_sets": False,
+            "displacements": write_displacements,
         },
     )
     ph3py_yaml.set_phonon_info(phono3py)

phono3py/version.py

@@ -34,4 +34,4 @@
 # ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
 
-__version__ = "3.4.0"
+__version__ = "3.5.0"

pyproject.toml

@@ -16,7 +16,7 @@ dependencies = [
     "matplotlib>=2.2.2",
     "h5py>=3.0",
     "spglib>=2.3",
-    "phonopy>=2.27,<2.28",
+    "phonopy>=2.28,<2.29",
 ]
 license = { file = "LICENSE" }