Merge branch 'develop'

.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 pypolymlp
+        conda install --yes matplotlib-base pyyaml "libblas=*=*mkl" mkl-include h5py scipy pytest spglib alm cmake c-compiler cxx-compiler "pypolymlp<0.9"
     - 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 pypolymlp
+        conda install --yes matplotlib-base pyyaml "libblas=*=*mkl" mkl-include h5py scipy pytest spglib alm cmake c-compiler cxx-compiler "pypolymlp<0.9"
     - 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 pypolymlp
+        conda install --yes matplotlib-base pyyaml "libblas=*=*mkl" mkl-include h5py scipy pytest codecov pytest-cov spglib alm cmake c-compiler cxx-compiler "pypolymlp<0.9"
     - name: Install symfc 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 pypolymlp
+        conda install --yes matplotlib-base pyyaml "libblas=*=*openblas" openblas h5py scipy pytest spglib alm cmake c-compiler cxx-compiler "pypolymlp<0.9"
     - name: Install symfc develop branch
       run: |
         conda activate test

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

@@ -25,7 +25,7 @@ jobs:
       run: |
         conda activate test
         conda install --yes python=${{ matrix.python-version }}
-        conda install --yes matplotlib-base pyyaml h5py "numpy>=2.1" scipy pytest spglib alm cmake c-compiler cxx-compiler pypolymlp
+        conda install --yes matplotlib-base pyyaml h5py "numpy>=2.1" scipy pytest spglib alm cmake c-compiler cxx-compiler "pypolymlp<0.9"
     - name: Install dependent packages for python == 3.9
       if: ${{ matrix.python-version == 3.9 }}
       run: |

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
         exclude: ^example/AlN-LDA/
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.4
+    rev: v0.9.7
     hooks:
       - id: ruff
         args: [ "--fix", "--show-fixes" ]

doc/changelog.md

@@ -2,6 +2,10 @@
 
 # Change Log
 
+## Mar-1-2025: Version 3.14.1
+
+- Release to follow the change of phonopy
+
 ## Feb-7-2025: Version 3.14.0
 
 - Release to follow the change of phonopy

doc/conf.py

@@ -60,7 +60,7 @@
 # The short X.Y version.
 version = "3.14"
 # The full version, including alpha/beta/rc tags.
-release = "3.14.0"
+release = "3.14.1"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/pypolymlp.md

@@ -42,12 +42,15 @@ in the distribution from GitHub or PyPI.
 
 ## Requirements
 
-- [pypolymlp](https://github.com/sekocha/pypolymlp)
+- [pypolymlp](https://github.com/sekocha/pypolymlp) < 0.9
 
   For linux (x86-64), a compiled package of pypolymlp can be installed via
   conda-forge (recommended). Otherwise, pypolymlp can be installed from
   source-code.
 
+  From pypolymlp 0.9, its file format was changed. This will be taken care of
+  by the future version of phonopy and phono3py.
+
 ## How to calculate
 
 ### Workflow

phono3py/api_phono3py.py

@@ -41,7 +41,6 @@
 from typing import Literal, Optional, Union
 
 import numpy as np
-from phonopy.exception import ForceCalculatorRequiredError
 from phonopy.harmonic.displacement import (
     directions_to_displacement_dataset,
     get_least_displacements,
@@ -74,10 +73,10 @@
 
 from phono3py.conductivity.direct_solution import get_thermal_conductivity_LBTE
 from phono3py.conductivity.rta import get_thermal_conductivity_RTA
-from phono3py.interface.fc_calculator import get_fc3
+from phono3py.interface.fc_calculator import get_fc3_solver
 from phono3py.interface.phono3py_yaml import Phono3pyYaml
 from phono3py.phonon.grid import BZGrid
-from phono3py.phonon3.dataset import forces_in_dataset, get_displacements_and_forces_fc3
+from phono3py.phonon3.dataset import forces_in_dataset
 from phono3py.phonon3.displacement_fc3 import (
     direction_to_displacement,
     get_third_order_displacements,
@@ -89,7 +88,6 @@
     set_translational_invariance_compact_fc3,
     set_translational_invariance_fc3,
 )
-from phono3py.phonon3.fc3 import get_fc3 as get_phono3py_fc3
 from phono3py.phonon3.imag_self_energy import (
     get_imag_self_energy,
     write_imag_self_energy,
@@ -1485,33 +1483,20 @@ def produce_fc3(
             Options for external force constants calculator.
 
         """
-        if fc_calculator is not None:
-            disps, forces = get_displacements_and_forces_fc3(self._dataset)
-            fc2, fc3 = get_fc3(
-                self._supercell,
-                self._primitive,
-                disps,
-                forces,
-                fc_calculator=fc_calculator,
-                fc_calculator_options=fc_calculator_options,
-                is_compact_fc=is_compact_fc,
-                symmetry=self._symmetry,
-                log_level=self._log_level,
-            )
-        else:
-            if "displacements" in self._dataset:
-                raise ForceCalculatorRequiredError(
-                    "fc_calculator has to be set to produce force constants from this "
-                    "dataset."
-                )
-            fc2, fc3 = get_phono3py_fc3(
-                self._supercell,
-                self._primitive,
-                self._dataset,
-                self._symmetry,
-                is_compact_fc=is_compact_fc,
-                verbose=self._log_level,
-            )
+        fc_solver = get_fc3_solver(
+            self._supercell,
+            self._primitive,
+            self._dataset,
+            fc_calculator=fc_calculator,
+            fc_calculator_options=fc_calculator_options,
+            is_compact_fc=is_compact_fc,
+            symmetry=self._symmetry,
+            log_level=self._log_level,
+        )
+        fc2 = fc_solver.force_constants[2]
+        fc3 = fc_solver.force_constants[3]
+
+        if fc_calculator is None or fc_calculator == "traditional":
             if symmetrize_fc3r:
                 if is_compact_fc:
                     set_translational_invariance_compact_fc3(fc3, self._primitive)

phono3py/interface/fc_calculator.py

@@ -39,84 +39,70 @@
 from typing import Optional, Union
 
 import numpy as np
+from phonopy.interface.fc_calculator import FCSolver
 from phonopy.interface.symfc import SymfcFCSolver
 from phonopy.structure.atoms import PhonopyAtoms
 from phonopy.structure.cells import Primitive
 from phonopy.structure.symmetry import Symmetry
 
+from phono3py.phonon3.dataset import get_displacements_and_forces_fc3
+from phono3py.phonon3.fc3 import get_fc3
 
-def get_fc3(
+
+def get_fc3_solver(
     supercell: PhonopyAtoms,
     primitive: Primitive,
-    displacements: np.ndarray,
-    forces: np.ndarray,
+    dataset: dict,
     fc_calculator: Optional[str] = None,
     fc_calculator_options: Optional[str] = None,
     is_compact_fc: bool = False,
     symmetry: Optional[Symmetry] = None,
     log_level: int = 0,
-):
-    """Calculate 2upercell 2nd and 3rd order force constants.
+) -> FC3Solver:
+    """Return force constants solver for fc3.
 
     Parameters
     ----------
     supercell : PhonopyAtoms
         Supercell
     primitive : Primitive
         Primitive cell
-    displacements : array_like
-        Displacements of atoms in supercell.
-        shape=(num_snapshots, num_atoms, 3), dtype='double', order='C'
-    forces : array_like
-        Forces of atoms in supercell.
-        shape=(num_snapshots, num_atoms, 3), dtype='double', order='C'
+    dataset : dict, optional
+        Dataset that contains displacements, forces, and optionally
+        energies. Default is None.
     fc_calculator : str, optional
         Currently only 'alm' is supported. Default is None, meaning invoking
         'alm'.
     fc_calculator_options : str, optional
         This is arbitrary string.
+    is_compact_fc : bool, optional
+        If True, force constants are returned in the compact form.
+    symmetry : Symmetry, optional
+        Symmetry of supercell. This is used for the traditional and symfc FC
+        solver. Default is None.
     log_level : integer or bool, optional
         Verbosity level. False or 0 means quiet. True or 1 means normal level
         of log to stdout. 2 gives verbose mode.
 
     Returns
     -------
-    (fc2, fc3) : tuple[ndarray]
-        2nd and 3rd order force constants.
+    FC3Solver
+        Force constants solver for fc3.
 
     """
-    if fc_calculator == "alm":
-        from phonopy.interface.alm import run_alm
-
-        fc = run_alm(
-            supercell,
-            primitive,
-            displacements,
-            forces,
-            2,
-            options=fc_calculator_options,
-            is_compact_fc=is_compact_fc,
-            log_level=log_level,
-        )
-        return fc[2], fc[3]
-    elif fc_calculator == "symfc":
-        from phonopy.interface.symfc import run_symfc
-
-        fc = run_symfc(
-            supercell,
-            primitive,
-            displacements,
-            forces,
-            orders=[2, 3],
-            is_compact_fc=is_compact_fc,
-            symmetry=symmetry,
-            options=fc_calculator_options,
-            log_level=log_level,
-        )
-        return fc[2], fc[3]
-    else:
-        msg = "Force constants calculator of %s was not found ." % fc_calculator
-        raise RuntimeError(msg)
+    fc_solver_name = fc_calculator if fc_calculator is not None else "traditional"
+    fc_solver = FC3Solver(
+        fc_solver_name,
+        supercell,
+        symmetry=symmetry,
+        dataset=dataset,
+        is_compact_fc=is_compact_fc,
+        primitive=primitive,
+        orders=[2, 3],
+        options=fc_calculator_options,
+        log_level=log_level,
+    )
+    return fc_solver
 
 
 def extract_fc2_fc3_calculators(
@@ -192,3 +178,70 @@ def estimate_symfc_memory_usage(
     memsize = basis_size**2 * 3 * 8 / 10**9
     memsize2 = len(supercell) * 3 * batch_size * basis_size * 8 / 10**9
     return memsize, memsize2
+
+
+class FDFC3Solver:
+    """Finite difference type force constants calculator.
+
+    This is phono3py's traditional force constants calculator.
+
+    """
+
+    def __init__(
+        self,
+        supercell: PhonopyAtoms,
+        primitive: Primitive,
+        symmetry: Symmetry,
+        dataset: dict,
+        is_compact_fc: bool = False,
+        log_level: int = 0,  # currently not used
+    ):
+        self._fc2, self._fc3 = self._run(
+            supercell,
+            primitive,
+            symmetry,
+            dataset,
+            is_compact_fc,
+            log_level,
+        )
+
+    @property
+    def force_constants(self) -> dict[int, np.ndarray]:
+        """Return force constants.
+
+        Returns
+        -------
+        dict[int, np.ndarray]
+            Force constants with order as key.
+
+        """
+        return {2: self._fc2, 3: self._fc3}
+
+    def _run(
+        self,
+        supercell: PhonopyAtoms,
+        primitive: Primitive,
+        symmetry: Symmetry,
+        dataset: dict,
+        is_compact_fc: bool,
+        log_level: int,
+    ):
+        return get_fc3(
+            supercell,
+            primitive,
+            dataset,
+            symmetry,
+            is_compact_fc=is_compact_fc,
+            verbose=log_level > 0,
+        )
+
+
+class FC3Solver(FCSolver):
+    """Force constants solver for fc3."""
+
+    def _set_traditional_solver(self, solver_class: Optional[type] = FDFC3Solver):
+        return super()._set_traditional_solver(solver_class=solver_class)
+
+    def _get_displacements_and_forces(self):
+        """Return displacements and forces for fc3."""
+        return get_displacements_and_forces_fc3(self._dataset)

phono3py/phonon3/fc3.py

@@ -40,13 +40,13 @@
 import numpy as np
 from phonopy.harmonic.force_constants import (
     distribute_force_constants,
-    get_fc2,
     get_nsym_list_and_s2pp,
     get_positions_sent_by_rot_inv,
     get_rotated_displacement,
     similarity_transformation,
     solve_force_constants,
 )
+from phonopy.interface.fc_calculator import get_fc2
 from phonopy.structure.atoms import PhonopyAtoms
 from phonopy.structure.cells import Primitive, compute_all_sg_permutations
 from phonopy.structure.symmetry import Symmetry
@@ -84,7 +84,13 @@ def get_fc3(
     """
     # fc2 has to be full matrix to compute delta-fc2
     # p2s_map elements are extracted if is_compact_fc=True at the last part.
-    fc2 = get_fc2(supercell, symmetry, disp_dataset)
+    fc2 = get_fc2(
+        supercell,
+        disp_dataset,
+        primitive=primitive,
+        is_compact_fc=False,
+        symmetry=symmetry,
+    )
     fc3 = _get_fc3_least_atoms(
         supercell,
         primitive,

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__ = "3.14.0"
+__version__ = "3.14.1"

pyproject.toml

@@ -16,7 +16,7 @@ dependencies = [
     "matplotlib",
     "h5py",
     "spglib",
-    "phonopy>=2.37,<2.38",
+    "phonopy>=2.37.1,<2.38",
 ]
 license = { file = "LICENSE" }