Merge branch 'develop' into rc

.github/workflows/wheels.yml

@@ -12,8 +12,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, ubuntu-24.04-arm, macos-latest]
-        # os: [ubuntu-latest, ubuntu-24.04-arm, windows-latest, macos-latest]
+        os: [ubuntu-latest, ubuntu-24.04-arm, macos-latest, windows-latest]
 
     steps:
     - uses: actions/checkout@v4

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
     exclude: ^example/AlN-LDA/
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.9.3
+  rev: v0.9.4
   hooks:
   - id: ruff
     args: [ "--fix", "--show-fixes" ]

doc/changelog.md

@@ -2,6 +2,10 @@
 
 # Change Log
 
+## Feb-5-2025: Version 3.13.0
+
+- Release to follow the change of phonopy
+
 ## Feb-1-2025: Version 3.12.2
 
 - Fix an openmp related bug in computing collision matrix in C

doc/conf.py

@@ -58,9 +58,9 @@ copyright = "2015, Atsushi Togo"
 # built documents.
 #
 # The short X.Y version.
-version = "3.12"
+version = "3.13"
 # The full version, including alpha/beta/rc tags.
-release = "3.12.2"
+release = "3.13.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

phono3py/cui/load.py

@@ -54,7 +54,10 @@ from phono3py.cui.create_force_constants import (
     run_pypolymlp_to_compute_forces,
 )
 from phono3py.file_IO import read_fc2_from_hdf5, read_fc3_from_hdf5
-from phono3py.interface.fc_calculator import extract_fc2_fc3_calculators
+from phono3py.interface.fc_calculator import (
+    extract_fc2_fc3_calculators,
+    update_cutoff_fc_calculator_options,
+)
 from phono3py.interface.phono3py_yaml import Phono3pyYaml
 from phono3py.phonon3.dataset import forces_in_dataset
 from phono3py.phonon3.fc3 import show_drift_fc3
@@ -435,6 +438,7 @@ def compute_force_constants_from_datasets(
     ph3py: Phono3py,
     fc_calculator: Optional[str] = None,
     fc_calculator_options: Optional[Union[dict, str]] = None,
+    cutoff_pair_distance: Optional[float] = None,
     symmetrize_fc: bool = True,
     is_compact_fc: bool = True,
     log_level: int = 0,
@@ -453,13 +457,18 @@ def compute_force_constants_from_datasets(
     """
     fc3_calculator = extract_fc2_fc3_calculators(fc_calculator, 3)
     fc2_calculator = extract_fc2_fc3_calculators(fc_calculator, 2)
+    fc3_calc_opts = extract_fc2_fc3_calculators(fc_calculator_options, 3)
+    fc3_calc_opts = update_cutoff_fc_calculator_options(
+        fc3_calc_opts, cutoff_pair_distance
+    )
+    fc2_calc_opts = extract_fc2_fc3_calculators(fc_calculator_options, 2)
     exist_fc2 = ph3py.fc2 is not None
     if ph3py.fc3 is None and forces_in_dataset(ph3py.dataset):
         ph3py.produce_fc3(
             symmetrize_fc3r=symmetrize_fc,
             is_compact_fc=is_compact_fc,
             fc_calculator=fc3_calculator,
-            fc_calculator_options=extract_fc2_fc3_calculators(fc_calculator_options, 3),
+            fc_calculator_options=fc3_calc_opts,
         )
 
         if log_level and symmetrize_fc and fc_calculator is None:
@@ -476,9 +485,7 @@ def compute_force_constants_from_datasets(
                 symmetrize_fc2=symmetrize_fc,
                 is_compact_fc=is_compact_fc,
                 fc_calculator=fc2_calculator,
-                fc_calculator_options=extract_fc2_fc3_calculators(
-                    fc_calculator_options, 2
-                ),
+                fc_calculator_options=fc2_calc_opts,
             )
             if log_level and symmetrize_fc and fc_calculator is None:
                 print("fc2 was symmetrized.")

phono3py/cui/phono3py_script.py

@@ -158,12 +158,6 @@ def finalize_phono3py(
     else:
         yaml_filename = filename
 
-    if phono3py.mlp is not None and phono3py.dataset is not None:
-        mlp_eval_filename = "phono3py_mlp_eval_dataset.yaml"
-        if log_level:
-            print(f'Dataset generated using MLPs was written in "{mlp_eval_filename}".')
-        phono3py.save(mlp_eval_filename)
-
     _physical_units = get_default_physical_units(phono3py.calculator)
 
     ph3py_yaml = Phono3pyYaml(
@@ -603,6 +597,7 @@ def _store_force_constants(ph3py: Phono3py, settings: Phono3pySettings, log_leve
 
     load_fc2_and_fc3(ph3py, log_level=log_level)
 
+    cutoff_pair_distance = get_cutoff_pair_distance(settings)
     (fc_calculator, fc_calculator_options) = get_fc_calculator_params(
         settings, log_level=(not read_fc3) * 1
     )
@@ -611,6 +606,7 @@ def _store_force_constants(ph3py: Phono3py, settings: Phono3pySettings, log_leve
             ph3py,
             fc_calculator=fc_calculator,
             fc_calculator_options=fc_calculator_options,
+            cutoff_pair_distance=cutoff_pair_distance,
             symmetrize_fc=settings.fc_symmetry,
             is_compact_fc=settings.is_compact_fc,
             log_level=log_level,
@@ -623,6 +619,7 @@ def _store_force_constants(ph3py: Phono3py, settings: Phono3pySettings, log_leve
             ph3py,
             fc_calculator="symfc",
             fc_calculator_options=fc_calculator_options,
+            cutoff_pair_distance=cutoff_pair_distance,
             symmetrize_fc=settings.fc_symmetry,
             is_compact_fc=settings.is_compact_fc,
             log_level=log_level,
@@ -1169,6 +1166,15 @@ def main(**argparse_control):
             log_level=log_level,
         )
 
+        if ph3py.dataset is not None:
+            mlp_eval_filename = "phono3py_mlp_eval_dataset.yaml"
+            if log_level:
+                print(
+                    "Dataset generated using MLPs was written in "
+                    f'"{mlp_eval_filename}".'
+                )
+            ph3py.save(mlp_eval_filename)
+
         # pypolymlp dataset is stored in "phono3py.pmlp" and stop here.
         if not prepare_dataset:
             if log_level:

phono3py/interface/fc_calculator.py

@@ -118,7 +118,10 @@ def get_fc3(
         raise RuntimeError(msg)
 
 
-def extract_fc2_fc3_calculators(fc_calculator: Optional[Union[str, dict]], order: int):
+def extract_fc2_fc3_calculators(
+    fc_calculator: Optional[Union[str, dict]],
+    order: int,
+) -> Optional[Union[str, dict]]:
     """Extract fc_calculator and fc_calculator_options for fc2 and fc3.
 
     fc_calculator : str
@@ -141,4 +144,32 @@ def extract_fc2_fc3_calculators(fc_calculator: Optional[Union[str, dict]], order
                 return None
             return fc_calculator
     else:
-        raise RuntimeError("fc_calculator should be str or dict.")
+        raise RuntimeError("fc_calculator should be str, dict, or None.")
+
+
+def update_cutoff_fc_calculator_options(
+    fc_calc_opts: Optional[Union[str, dict]],
+    cutoff_pair_distance: Optional[float],
+) -> Optional[Union[str, dict]]:
+    """Update fc_calculator_options with cutoff distances.
+
+    Parameters
+    ----------
+    fc_calc_opts : str or dict
+        FC calculator options.
+    cutoff_pair_distance : float, optional
+        Cutoff distance for pair interaction.
+
+    """
+    if cutoff_pair_distance is not None:
+        if not isinstance(fc_calc_opts, (str, dict)) and fc_calc_opts is not None:
+            raise RuntimeError("fc_calculator_options should be str, dict, or None.")
+
+        if isinstance(fc_calc_opts, dict) and "cutoff" not in fc_calc_opts:
+            fc_calc_opts["cutoff"] = float(cutoff_pair_distance)
+        elif isinstance(fc_calc_opts, str) and "cutoff" not in fc_calc_opts:
+            fc_calc_opts = f"{fc_calc_opts}, cutoff = {cutoff_pair_distance}"
+        elif fc_calc_opts is None:
+            fc_calc_opts = f"cutoff = {cutoff_pair_distance}"
+
+    return fc_calc_opts

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__ = "3.12.2"
+__version__ = "3.13.0"

pyproject.toml

@@ -16,7 +16,7 @@ dependencies = [
     "matplotlib",
     "h5py",
     "spglib",
-    "phonopy>=2.35,<2.36",
+    "phonopy>=2.36,<2.37",
 ]
 license = { file = "LICENSE" }
 

test/phonon3/test_displacements.py

@@ -105,7 +105,7 @@ def test_random_disps_agno2(
         is_plusminus=is_plusminus,
     )
 
-    for d, n_d in zip((ph3.displacements, ph3.phonon_displacements), (92, 4)):
+    for d, n_d in zip((ph3.displacements, ph3.phonon_displacements), (96, 4)):
         if number_of_snapshots == "auto":
             assert len(d) == n_d * (is_plusminus + 1)
         else: