Merge branch 'develop' into publish-gh-pages

.pre-commit-config.yaml

@@ -10,7 +10,7 @@ repos:
   - id: check-added-large-files
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.8.1
+  rev: v0.8.4
   hooks:
   - id: ruff
     args: [ "--fix", "--show-fixes" ]

doc/changelog.md

@@ -2,6 +2,12 @@
 
 # Change Log
 
+## Dec-31-2024: Version 0.7.0
+
+- Maintenance release to follow the change of phonopy.
+- `elph_selfen_band_stop` is estimated from el-DOS instead of `elph_nbands` for
+  transport mode in velph.
+
 ## Dec-9-2024: Version 0.6.6
 
 - Collection of minor updates of velph command.

doc/conf.py

@@ -10,8 +10,8 @@
 copyright = "2024, Atsushi Togo"
 author = "Atsushi Togo"
 
-version = "0.6"
-release = "0.6.5"
+version = "0.7"
+release = "0.7.0"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

doc/velph.md

@@ -208,7 +208,7 @@ source /opt/intel/oneapi/setvars.sh --config="/home/togo/.oneapi-config"
 pe = "paris 24"
 
 ...
-[vasp.phono3py.phonon.scheduler]
+[vasp.phonopy.scheduler]
 scheduler_template = '''#!/bin/bash
 #QSUB2 core 192
 #QSUB2 mpi 192

pyproject.toml

@@ -12,6 +12,7 @@ authors = [
 ]
 requires-python = ">=3.9"
 dependencies = [
+    "phonopy >= 2.33.4",
     "phono3py >= 3.6.0",
     "finufft",
     "click",

src/phelel/api_phelel.py

@@ -495,20 +495,13 @@ def _get_phonopy(
         supercell_matrix: Optional[Union[int, float, Sequence, np.ndarray]],
         primitive_matrix: Optional[Union[str, Sequence, np.ndarray]],
     ) -> Phonopy:
-        """Return Phonopy instance.
-
-        Note
-        ----
-        store_dense_svecs=False is necessary to be compatible with code in VASP.
-
-        """
+        """Return Phonopy instance."""
         return Phonopy(
             self._unitcell,
             supercell_matrix=supercell_matrix,
             primitive_matrix=primitive_matrix,
             symprec=self._symprec,
             is_symmetry=self._is_symmetry,
-            store_dense_svecs=False,
             calculator=self._calculator,
             log_level=self._log_level,
         )

src/phelel/file_IO.py

@@ -10,7 +10,7 @@
 import h5py
 import numpy as np
 from phonopy.structure.atoms import PhonopyAtoms, atom_data
-from phonopy.structure.cells import Primitive
+from phonopy.structure.cells import Primitive, dense_to_sparse_svecs
 from phonopy.structure.symmetry import Symmetry
 
 from phelel.base.Dij_qij import DDijQij
@@ -244,7 +244,7 @@ def _add_datasets(
         w.create_dataset(
             "primitive_masses", data=np.array(primitive.masses, dtype="double")
         )
-        p2s_vectors, p2s_multiplicities = primitive.get_smallest_vectors()
+        p2s_vectors, p2s_multiplicities = _get_smallest_vectors(primitive)
         w.create_dataset("p2s_map", data=np.array(primitive.p2s_map, dtype="int_"))
         w.create_dataset("s2p_map", data=np.array(primitive.s2p_map, dtype="int_"))
         w.create_dataset("shortest_vectors", data=np.array(p2s_vectors, dtype="double"))
@@ -308,7 +308,7 @@ def _add_datasets(
             data=np.array(phonon_supercell_matrix, dtype="int_", order="C"),
         )
     if phonon_primitive is not None:
-        p2s_vectors, p2s_multiplicities = phonon_primitive.get_smallest_vectors()
+        p2s_vectors, p2s_multiplicities = _get_smallest_vectors(phonon_primitive)
         w.create_dataset(
             "phonon_p2s_map", data=np.array(phonon_primitive.p2s_map, dtype="int_")
         )
@@ -375,3 +375,11 @@ def _add_datasets(
                 data=int(symmetry_dataset.uni_number),
                 dtype="int_",
             )
+
+
+def _get_smallest_vectors(primitive: Primitive) -> tuple[np.ndarray, np.ndarray]:
+    """Get smallest vectors."""
+    svecs, multi = primitive.get_smallest_vectors()
+    if primitive.store_dense_svecs:
+        svecs, multi = dense_to_sparse_svecs(svecs, multi)
+    return svecs, multi

src/phelel/velph/cli/__init__.py

@@ -14,10 +14,11 @@ def cmd_root():
 from phelel.velph.cli.generate import cmd_generate  # noqa F401
 from phelel.velph.cli.hints import cmd_hints  # noqa F401
 from phelel.velph.cli.init import cmd_init  # noqa F401
-from phelel.velph.cli.phono3py import cmd_phono3py  # noqa F401
 from phelel.velph.cli.nac import cmd_nac  # noqa F401
+from phelel.velph.cli.phelel import cmd_phelel  # noqa F401
+from phelel.velph.cli.phonopy import cmd_phonopy  # noqa F401
+from phelel.velph.cli.phono3py import cmd_phono3py  # noqa F401
 from phelel.velph.cli.ph_bands import cmd_ph_bands  # noqa F401
 from phelel.velph.cli.relax import cmd_relax  # noqa F401
 from phelel.velph.cli.selfenergy import cmd_selfenergy  # noqa F401
-from phelel.velph.cli.phelel import cmd_phelel  # noqa F401
 from phelel.velph.cli.transport import cmd_transport  # noqa F401

src/phelel/velph/cli/init/__init__.py

@@ -145,6 +145,20 @@
         f"(phelel_nosym: bool, default={VelphInitParams.phelel_nosym})"
     ),
 )
+@click.option(
+    "--phonopy-max-num-atoms",
+    "phonopy_max_num_atoms",
+    nargs=1,
+    default=None,
+    type=int,
+    help=(
+        "Determine phonopy supercell dimension so that number of atoms in supercell "
+        "for phonopy is less than this number if different dimension from "
+        "that of electron-phonon (phelel) is expected. "
+        "(phonopy_max_num_atoms: int, "
+        f"default={VelphInitParams.phono3py_max_num_atoms})"
+    ),
+)
 @click.option(
     "--phono3py-max-num-atoms",
     "phono3py_max_num_atoms",
@@ -246,6 +260,7 @@ def cmd_init(
     max_num_atoms: Optional[int],
     phelel_dir_name: str,
     phelel_nosym: Optional[bool],
+    phonopy_max_num_atoms: Optional[int],
     phono3py_max_num_atoms: Optional[int],
     primitive_cell_choice: Optional[str],
     project_folder: str,
@@ -287,6 +302,7 @@ def cmd_init(
         "magmom": magmom,
         "max_num_atoms": max_num_atoms,
         "phelel_nosym": phelel_nosym,
+        "phonopy_max_num_atoms": phonopy_max_num_atoms,
         "phono3py_max_num_atoms": phono3py_max_num_atoms,
         "primitive_cell_choice": primitive_cell_choice,
         "symmetrize_cell": symmetrize_cell,