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: v0.7.3
+  rev: v0.8.1
   hooks:
   - id: ruff
     args: [ "--fix", "--show-fixes" ]

doc/changelog.md

@@ -0,0 +1,7 @@
+(changelog)=
+
+# Change Log
+
+## Dec-9-2024: Version 0.6.6
+
+- Collection of minor updates of velph command.

doc/conf.py

@@ -11,7 +11,7 @@
 author = "Atsushi Togo"
 
 version = "0.6"
-release = "0.6.1"
+release = "0.6.5"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

doc/index.md

@@ -21,4 +21,5 @@ BSD-3-Clause.
 :hidden:
 install
 velph
+changelog
 ```

src/phelel/cui/create_supercells.py

@@ -12,15 +12,17 @@
 from phonopy.interface.calculator import write_supercells_with_displacements
 
 from phelel.api_phelel import Phelel
+from phelel.cui.settings import PhelelSettings
+from phelel.interface.phelel_yaml import PhelelYaml
 
 
 def create_phelel_supercells(
-    cell_info,
-    settings,
-    symprec,
-    interface_mode="vasp",
-    load_phelel_yaml=False,
-    log_level=1,
+    cell_info: dict,
+    settings: PhelelSettings,
+    symprec: float,
+    interface_mode: Optional[str] = "vasp",
+    load_phelel_yaml: bool = False,
+    log_level: int = 1,
 ):
     """Create displacements and supercells.
 
@@ -30,7 +32,7 @@ def create_phelel_supercells(
     """
     optional_structure_info = cell_info["optional_structure_info"]
     unitcell_filename = cell_info["optional_structure_info"][0]
-    phe_yml = cell_info["phonopy_yaml"]
+    phe_yml: Optional[PhelelYaml] = cell_info["phonopy_yaml"]
 
     phelel = Phelel(
         cell_info["unitcell"],

src/phelel/velph/cli/el_bands/plot.py

@@ -6,6 +6,7 @@
 
 import click
 import h5py
+import numpy as np
 
 from phelel.velph.cli.utils import (
     get_distances_along_BZ_path,
@@ -38,13 +39,31 @@ def plot_el_bandstructures(
 
     f_h5py_bands = h5py.File(vaspout_filename_bands)
     f_h5py_dos = h5py.File(vaspout_filename_dos)
-    efermi = f_h5py_dos["results"]["electron_dos_kpoints_opt"]["efermi"][()]
+    if "results" not in f_h5py_bands:
+        raise ValueError(
+            f"No electronic band structure results found in {vaspout_filename_bands}."
+        )
+    if "results" not in f_h5py_dos:
+        raise ValueError(f"No electronic DOS results found in {vaspout_filename_dos}.")
+    if "electron_dos_kpoints_opt" in f_h5py_dos["results"]:
+        f_h5py_dos_results = f_h5py_dos["results/electron_dos_kpoints_opt"]
+    elif "electron_dos" in f_h5py_dos["results"]:
+        f_h5py_dos_results = f_h5py_dos["results/electron_dos"]
+    else:
+        raise ValueError("No electron DOS data found in vaspout.h5.")
+
+    efermi = f_h5py_dos_results["efermi"][()]
     emin = window[0]
     emax = window[1]
     _, axs = plt.subplots(1, 2, gridspec_kw={"width_ratios": [3, 1]})
     ax0, ax1 = axs
 
-    distances, eigvals, points, labels_at_points = _get_bands_data(f_h5py_bands)
+    reclat = get_reclat_from_vaspout(f_h5py_bands)
+    distances, eigvals, points, labels_at_points = _get_bands_data(
+        reclat,
+        f_h5py_bands["results/electron_eigenvalues_kpoints_opt"],
+        f_h5py_bands["input/kpoints_opt"],
+    )
 
     ax0.plot(distances, eigvals[0, :, :], "ok", markersize=1)
     ax0.hlines(efermi, distances[0], distances[-1], "r", linewidth=1)
@@ -57,7 +76,7 @@ def plot_el_bandstructures(
     ax0.set_ylabel("E[eV]", fontsize=14)
     ymin, ymax = ax0.get_ylim()
 
-    dos, energies, xmax = _get_dos_data(f_h5py_dos, ymin, ymax)
+    dos, energies, xmax = _get_dos_data(f_h5py_dos_results, ymin, ymax)
 
     ax1.plot(dos, energies, "-k", linewidth=1)
     ax1.hlines(efermi, 0, xmax, "r", linewidth=1)
@@ -73,20 +92,18 @@ def plot_el_bandstructures(
     click.echo(f'Electronic band structure plot was saved in "{plot_filename}".')
 
 
-def _get_bands_data(f_h5py: h5py.File):
-    eigvals = f_h5py["results"]["electron_eigenvalues_kpoints_opt"]["eigenvalues"]
+def _get_bands_data(
+    reclat: np.ndarray, f_h5py_bands_results: h5py.Group, f_h5py_bands_input: h5py.Group
+):
+    eigvals = f_h5py_bands_results["eigenvalues"]
 
-    reclat = get_reclat_from_vaspout(f_h5py)
     # k-points in reduced coordinates
-    kpoint_coords = f_h5py["results"]["electron_eigenvalues_kpoints_opt"][
-        "kpoint_coords"
-    ]
+    kpoint_coords = f_h5py_bands_results["kpoint_coords"]
     # Special point labels
     labels = [
-        label.decode("utf-8")
-        for label in f_h5py["input"]["kpoints_opt"]["labels_kpoints"][:]
+        label.decode("utf-8") for label in f_h5py_bands_input["labels_kpoints"][:]
     ]
-    nk_per_seg = f_h5py["input"]["kpoints_opt"]["number_kpoints"][()]
+    nk_per_seg = f_h5py_bands_input["number_kpoints"][()]
     nk_total = len(kpoint_coords)
     k_cart = kpoint_coords @ reclat
     n_segments = nk_total // nk_per_seg
@@ -99,9 +116,9 @@ def _get_bands_data(f_h5py: h5py.File):
     return distances, eigvals, points, labels_at_points
 
 
-def _get_dos_data(f_h5py: h5py.File, ymin: float, ymax: float):
-    dos = f_h5py["results"]["electron_dos_kpoints_opt"]["dos"][0, :]
-    energies = f_h5py["results"]["electron_dos_kpoints_opt"]["energies"][:]
+def _get_dos_data(f_h5py_dos_results: h5py.Group, ymin: float, ymax: float):
+    dos = f_h5py_dos_results["dos"][0, :]
+    energies = f_h5py_dos_results["energies"][:]
     i_min = 0
     i_max = len(energies)
     for i, val in enumerate(energies):

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

@@ -54,12 +54,12 @@
     ),
 )
 @click.option(
-    "--diagonal/--parallel-to-axes",
+    "--diagonal",
     "diagonal",
     type=bool,
     default=None,
     help=(
-        "Generate displacements only along axes or not."
+        "Generate displacements in diagonal directions or only along axes."
         f"(diagonal: bool, default={VelphInitParams.diagonal})"
     ),
 )
@@ -146,16 +146,17 @@
     ),
 )
 @click.option(
-    "--phonon-max-num-atoms",
-    "phonon_max_num_atoms",
+    "--phono3py-max-num-atoms",
+    "phono3py_max_num_atoms",
     nargs=1,
     default=None,
     type=int,
     help=(
-        "Determine phonon supercell dimension so that number of atoms in supercell "
-        "for phonon is less than this number if different one from electron-phonon "
-        "(phelel) or phonon-phonon (phono3py) is expected. "
-        f"(phonon_max_num_atoms: int, default={VelphInitParams.phonon_max_num_atoms})"
+        "Determine phono3py supercell dimension so that number of atoms in supercell "
+        "for phono3py is less than this number if different dimension from "
+        "that of electron-phonon (phelel) is expected. "
+        "(phono3py_max_num_atoms: int, "
+        f"default={VelphInitParams.phono3py_max_num_atoms})"
     ),
 )
 @click.option(
@@ -245,7 +246,7 @@ def cmd_init(
     max_num_atoms: Optional[int],
     phelel_dir_name: str,
     phelel_nosym: Optional[bool],
-    phonon_max_num_atoms: Optional[int],
+    phono3py_max_num_atoms: Optional[int],
     primitive_cell_choice: Optional[str],
     project_folder: str,
     symmetrize_cell: Optional[bool],
@@ -286,7 +287,7 @@ def cmd_init(
         "magmom": magmom,
         "max_num_atoms": max_num_atoms,
         "phelel_nosym": phelel_nosym,
-        "phonon_max_num_atoms": phonon_max_num_atoms,
+        "phono3py_max_num_atoms": phono3py_max_num_atoms,
         "primitive_cell_choice": primitive_cell_choice,
         "symmetrize_cell": symmetrize_cell,
         "tolerance": tolerance,

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

@@ -629,19 +629,19 @@ def _get_toml_lines(
         )
         return None
 
-    phonon_supercell_dimension = _get_supercell_dimension(
-        velph_dict.get("phonopy", {}),
-        vip.phonon_max_num_atoms,
+    phono3py_supercell_dimension = _get_supercell_dimension(
+        velph_dict.get("phono3py", {}),
+        vip.phono3py_max_num_atoms,
         sym_dataset,
         vip.find_primitive,
     )
 
     click.echo("[phelel]")
     _show_supercell_dimension(supercell_dimension)
 
-    if phonon_supercell_dimension is not None:
-        click.echo("[phonopy]")
-        _show_supercell_dimension(phonon_supercell_dimension)
+    if phono3py_supercell_dimension is not None:
+        click.echo("[phono3py]")
+        _show_supercell_dimension(phono3py_supercell_dimension)
 
     (
         kpoints_dict,
@@ -657,7 +657,7 @@ def _get_toml_lines(
         primitive,
         sym_dataset,
         supercell_dimension,
-        phonon_supercell_dimension,
+        phono3py_supercell_dimension,
         cell_choices["nac"],
         cell_choices["relax"],
         phelel_dir_name=phelel_dir_name,
@@ -696,12 +696,12 @@ def _get_toml_lines(
             vip.phelel_nosym,
         )
 
-    # [phonopy]
-    if phonon_supercell_dimension is not None:
-        lines += ["[phonopy]"]
-        lines += _get_supercell_dimension_lines(phonon_supercell_dimension)
+    # [phono3py]
+    if phono3py_supercell_dimension is not None:
+        lines += ["[phono3py]"]
+        lines += _get_supercell_dimension_lines(phono3py_supercell_dimension)
         lines += _get_displacement_settings_lines(
-            velph_dict, "phonopy", vip.amplitude, vip.diagonal, vip.plusminus
+            velph_dict, "phono3py", vip.amplitude, vip.diagonal, vip.plusminus
         )
         lines.append("")
 
@@ -1333,7 +1333,7 @@ def _get_supercell_dimension_lines(
 
 def _get_displacement_settings_lines(
     velph_dict: dict,
-    calc_type: Literal["phelel", "phonopy"],
+    calc_type: Literal["phelel", "phono3py"],
     amplitude: Optional[float],
     diagonal: Optional[bool],
     plusminus: Optional[bool],

src/phelel/velph/cli/phono3py/__init__.py

@@ -38,13 +38,32 @@ def cmd_phono3py():
     type=int,
     help="Number of snapshots of supercells with random directional displacement.",
 )
+@click.option(
+    "--rd-fc2",
+    "random_displacements_fc2",
+    nargs=1,
+    default=None,
+    type=int,
+    help=(
+        "Number of snapshots of phonon supercells "
+        "with random directional displacement."
+    ),
+)
 @click.help_option("-h", "--help")
-def cmd_init(toml_filename: str, random_displacements: Optional[int]):
+def cmd_init(
+    toml_filename: str,
+    random_displacements: Optional[int],
+    random_displacements_fc2: Optional[int],
+):
     """Generate displacements and write phelel_disp.yaml."""
     with open(toml_filename, "rb") as f:
         toml_dict = tomli.load(f)
 
-    ph3py = run_init(toml_dict, number_of_snapshots=random_displacements)
+    ph3py = run_init(
+        toml_dict,
+        number_of_snapshots=random_displacements,
+        number_of_snapshots_fc2=random_displacements_fc2,
+    )
 
     phono3py_yaml_filename = pathlib.Path("phono3py/phono3py_disp.yaml")
     phono3py_yaml_filename.parent.mkdir(parents=True, exist_ok=True)

src/phelel/velph/cli/phono3py/init.py

@@ -18,6 +18,7 @@ def run_init(
     toml_dict: dict,
     current_directory: pathlib.Path = pathlib.Path(""),
     number_of_snapshots: Optional[int] = None,
+    number_of_snapshots_fc2: Optional[int] = None,
 ) -> Optional[Phono3py]:
     """Generate displacements and write phono3py_disp.yaml.
 
@@ -27,8 +28,9 @@ def run_init(
     """
     convcell = parse_cell_dict(toml_dict["unitcell"])
     supercell_matrix = toml_dict["phelel"].get("supercell_dimension", None)
-    if "phonopy" in toml_dict:
-        phonon_supercell_matrix = toml_dict["phonopy"].get("supercell_dimension", None)
+    if "phono3py" in toml_dict:
+        phonon_supercell_matrix = supercell_matrix
+        supercell_matrix = toml_dict["phono3py"].get("supercell_dimension", None)
     else:
         phonon_supercell_matrix = None
     if "primitive_cell" in toml_dict:
@@ -70,6 +72,7 @@ def run_init(
         is_plusminus=is_plusminus,
         is_diagonal=is_diagonal,
         number_of_snapshots=number_of_snapshots,
+        number_of_snapshots_fc2=number_of_snapshots_fc2,
     )
 
     nac_directory = current_directory / "nac"
@@ -99,6 +102,7 @@ def _generate_phono3py_supercells(
     is_plusminus: Union[str, bool] = "auto",
     is_diagonal: bool = True,
     number_of_snapshots: Optional[int] = None,
+    number_of_snapshots_fc2: Optional[int] = None,
 ):
     """Generate phelel supercells."""
     if distance is None:
@@ -119,12 +123,14 @@ def _generate_phono3py_supercells(
 
     if phono3py.phonon_supercell_matrix is not None:
         # For estimating number of displacements for harmonic phonon
-        phono3py.generate_fc2_displacements(
-            distance=distance, is_plusminus=False, is_diagonal=False
-        )
-        n_disps = len(phono3py.phonon_supercells_with_displacements)
-        phono3py.generate_fc2_displacements(
-            distance=distance, number_of_snapshots=n_disps, is_plusminus=True
-        )
+        if number_of_snapshots_fc2 is None:
+            phono3py.generate_fc2_displacements(
+                distance=distance, is_plusminus="auto", is_diagonal=False
+            )
+        else:
+            phono3py.generate_fc2_displacements(
+                distance=distance,
+                number_of_snapshots=number_of_snapshots_fc2,
+            )
         n_snapshots = len(phono3py.phonon_supercells_with_displacements)
         click.echo(f"Number of displacements for phonon: {n_snapshots}")

src/phelel/velph/cli/utils.py

@@ -78,13 +78,13 @@ class VelphInitParams:
     cell_for_nac: Optional[CellChoice] = CellChoice.UNSPECIFIED
     cell_for_relax: Optional[CellChoice] = CellChoice.UNSPECIFIED
     find_primitive: Optional[bool] = True
-    diagonal: Optional[bool] = True
+    diagonal: Optional[bool] = False
     plusminus: Optional[bool] = True
     kspacing: Optional[float] = 0.1
     kspacing_dense: Optional[float] = 0.05
     magmom: Optional[str] = None
     max_num_atoms: Optional[int] = None
-    phonon_max_num_atoms: Optional[int] = None
+    phono3py_max_num_atoms: Optional[int] = None
     phelel_nosym: Optional[bool] = False
     primitive_cell_choice: Optional[PrimitiveCellChoice] = (
         PrimitiveCellChoice.STANDARDIZED

src/phelel/version.py

@@ -1,3 +1,3 @@
 """Version number."""
 
-__version__ = "0.6.4"
+__version__ = "0.6.5"