Merge pull request #5 from phonopy/velph-phono3py

Experimental implementation of velph-phono3py

src/phelel/velph/cli/__init__.py

@@ -14,11 +14,10 @@ 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.ph_bands import cmd_ph_bands  # noqa F401
 from phelel.velph.cli.relax import cmd_relax  # noqa F401
-
-# The followings are written here to avoid ciclic import but needed.
 from phelel.velph.cli.selfenergy import cmd_selfenergy  # noqa F401
 from phelel.velph.cli.supercell import cmd_supercell  # noqa F401
 from phelel.velph.cli.transport import cmd_transport  # noqa F401

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

@@ -0,0 +1,73 @@
+"""velph command line tool / velph-supercell."""
+
+from __future__ import annotations
+
+import pathlib
+
+import click
+import tomli
+
+from phelel.velph.cli import cmd_root
+from phelel.velph.cli.phono3py.generate import write_supercell_input_files
+from phelel.velph.cli.phono3py.init import run_init
+
+
+@cmd_root.group("phono3py")
+@click.help_option("-h", "--help")
+def cmd_phono3py():
+    """Choose phono3py options."""
+    pass
+
+
+#
+# velph phono3py init
+#
+@cmd_phono3py.command("init")
+@click.argument(
+    "toml_filename",
+    nargs=1,
+    type=click.Path(),
+    default="velph.toml",
+)
+@click.help_option("-h", "--help")
+def cmd_init(toml_filename: str):
+    """Generate displacements and write phelel_disp.yaml."""
+    with open(toml_filename, "rb") as f:
+        toml_dict = tomli.load(f)
+
+    ph3py = run_init(toml_dict)
+
+    phono3py_yaml_filename = pathlib.Path("phono3py/phono3py_disp.yaml")
+    phono3py_yaml_filename.parent.mkdir(parents=True, exist_ok=True)
+    ph3py.save(phono3py_yaml_filename)
+
+    click.echo(f'"{phono3py_yaml_filename}" was generated. ')
+    click.echo('VASP input files will be generated by "velph phono3py generate".')
+
+
+#
+# velph phono3py generate
+#
+@cmd_phono3py.command("generate")
+@click.argument(
+    "toml_filename",
+    nargs=1,
+    type=click.Path(),
+    default="velph.toml",
+)
+@click.option(
+    "--yaml-filename",
+    "yaml_filename",
+    nargs=1,
+    type=click.Path(),
+    default="phono3py/phono3py_disp.yaml",
+)
+@click.help_option("-h", "--help")
+def cmd_generate(toml_filename: str, yaml_filename: str):
+    """Generate phono3py input files."""
+    if not pathlib.Path("POTCAR").exists():
+        click.echo('"POTCAR" not found in current directory.')
+
+    write_supercell_input_files(
+        pathlib.Path(toml_filename), pathlib.Path(yaml_filename)
+    )

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

@@ -0,0 +1,36 @@
+"""Implementation of velph-phono3py-generate."""
+
+from __future__ import annotations
+
+import pathlib
+
+import click
+import phono3py
+import tomli
+
+from phelel.velph.cli.supercell.generate import (
+    write_phonon_supercells,
+    write_supercells,
+)
+
+
+def write_supercell_input_files(
+    toml_filename: pathlib.Path,
+    phono3py_yaml_filename: pathlib.Path,
+) -> None:
+    """Generate supercells."""
+    if not phono3py_yaml_filename.exists():
+        click.echo(f'File "{phono3py_yaml_filename}" not found.', err=True)
+        click.echo('Run "velph phono3py init" if necessary.', err=True)
+        return None
+
+    ph3py = phono3py.load(phono3py_yaml_filename)
+    with open(toml_filename, "rb") as f:
+        toml_dict = tomli.load(f)
+
+    write_supercells(ph3py, toml_dict, dir_name="phono3py")
+    if ph3py.phonon_supercell_matrix is not None:
+        if "phonon" in toml_dict["vasp"]["supercell"]:
+            write_phonon_supercells(ph3py, toml_dict, dir_name="phono3py")
+        else:
+            print(f'[vasp.supercell.phonon.*] not found in "{toml_filename}"')

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

@@ -0,0 +1,136 @@
+"""Implementation of velph-phono3py-init."""
+
+from __future__ import annotations
+
+import pathlib
+from typing import Optional, Union
+
+import click
+import numpy as np
+from phono3py import Phono3py
+from phono3py.interface.calculator import get_default_displacement_distance
+from phonopy.structure.atoms import parse_cell_dict
+
+from phelel.velph.cli.utils import get_nac_params
+
+
+def run_init(
+    toml_dict: dict,
+    current_directory: pathlib.Path = pathlib.Path(""),
+    number_of_snapshots: Optional[int] = None,
+) -> Optional[Phono3py]:
+    """Generate displacements and write phono3py_disp.yaml.
+
+    current_directory : Path
+        Used for test.
+
+    """
+    convcell = parse_cell_dict(toml_dict["unitcell"])
+    supercell_matrix = toml_dict["phelel"].get("supercell_dimension", None)
+    phonon_supercell_matrix = toml_dict["phelel"].get(
+        "phonon_supercell_dimension", None
+    )
+    if "primitive_cell" in toml_dict:
+        primitive = parse_cell_dict(toml_dict["primitive_cell"])
+        primitive_matrix = np.dot(np.linalg.inv(convcell.cell.T), primitive.cell.T)
+    else:
+        primitive = convcell
+        primitive_matrix = None
+
+    is_symmetry = True
+    try:
+        if toml_dict["phelel"]["nosym"] is True:
+            is_symmetry = False
+    except KeyError:
+        pass
+
+    ph3py = Phono3py(
+        convcell,
+        supercell_matrix=supercell_matrix,
+        phonon_supercell_matrix=phonon_supercell_matrix,
+        primitive_matrix=primitive_matrix,
+        is_symmetry=is_symmetry,
+        calculator="vasp",
+    )
+
+    amplitude = toml_dict["phelel"].get("amplitude", None)
+
+    if number_of_snapshots is None:
+        is_diagonal = toml_dict["phelel"].get("diagonal", True)
+        is_plusminus = toml_dict["phelel"].get("plusminus", "auto")
+    else:
+        is_diagonal = False
+        is_plusminus = False
+
+    _generate_phono3py_supercells(
+        ph3py,
+        interface_mode="vasp",
+        distance=amplitude,
+        is_plusminus=is_plusminus,
+        is_diagonal=is_diagonal,
+        number_of_snapshots=number_of_snapshots,
+    )
+
+    nac_directory = current_directory / "nac"
+    if nac_directory.exists():
+        click.echo('Found "nac" directory. Read NAC params.')
+        vasprun_path = nac_directory / "vasprun.xml"
+        if vasprun_path.exists():
+            nac_params = get_nac_params(
+                toml_dict,
+                vasprun_path,
+                primitive,
+                convcell,
+                is_symmetry,
+            )
+            if nac_params is not None:
+                ph3py.nac_params = nac_params
+        else:
+            click.echo('Not found "nac/vasprun.xml". NAC params were not included.')
+            return None
+
+    return ph3py
+
+
+def _generate_phono3py_supercells(
+    phono3py: Phono3py,
+    interface_mode: str = "vasp",
+    distance: Optional[float] = None,
+    is_plusminus: Union[str, bool] = "auto",
+    is_diagonal: bool = True,
+    number_of_snapshots: Optional[int] = None,
+    log_level: int = 0,
+):
+    """Generate phelel supercells."""
+    if distance is None:
+        _distance = get_default_displacement_distance(interface_mode)
+    else:
+        _distance = distance
+
+    phono3py.generate_displacements(
+        distance=distance,
+        is_plusminus=is_plusminus,
+        is_diagonal=is_diagonal,
+        number_of_snapshots=number_of_snapshots,
+    )
+    if log_level:
+        print("Displacement distance: %s" % _distance)
+        print(
+            "Number of displacements: %d" % len(phono3py.supercells_with_displacements)
+        )
+
+    if phono3py.phonon_supercell_matrix is not None:
+        phono3py.generate_fc2_displacements(
+            distance=distance, is_plusminus=is_plusminus, is_diagonal=is_diagonal
+        )
+        n_snapshots = len(phono3py.phonon_supercells_with_displacements)
+        if number_of_snapshots is not None:
+            phono3py.generate_fc2_displacements(
+                distance=distance, number_of_snapshots=n_snapshots
+            )
+
+        if log_level:
+            print(
+                "Number of displacements for phonon: %d"
+                % len(phono3py.phonon_supercells_with_displacements)
+            )

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

@@ -1,5 +1,7 @@
 """velph command line tool / velph-supercell."""
 
+from __future__ import annotations
+
 import pathlib
 from typing import Optional
 
@@ -50,7 +52,7 @@ def cmd_init(toml_filename: str):
         sys_exit_after_finalize=False,
     )
 
-    click.echo(f'"{phelel_yaml_filename}" was generated by phelel. ')
+    click.echo(f'"{phelel_yaml_filename}" was generated. ')
     click.echo('VASP input files will be generated by "velph supercell generate".')
 
 

src/phelel/velph/cli/supercell/generate.py

@@ -4,9 +4,11 @@
 
 import pathlib
 import shutil
+from typing import Union
 
 import click
 import tomli
+from phono3py import Phono3py
 from phonopy.interface.calculator import write_crystal_structure
 
 import phelel
@@ -35,15 +37,22 @@ def write_supercell_input_files(
     with open(toml_filename, "rb") as f:
         toml_dict = tomli.load(f)
 
-    _write_supercells(phe, toml_dict)
+    write_supercells(phe, toml_dict)
     if phe.phonon_supercell_matrix is not None:
         if "phonon" in toml_dict["vasp"]["supercell"]:
-            _write_phonon_supercells(phe, toml_dict)
+            write_phonon_supercells(phe, toml_dict)
         else:
             print(f'[vasp.supercell.phonon.*] not found in "{toml_filename}"')
 
 
-def _write_supercells(phe: Phelel, toml_dict: dict):
+def write_supercells(
+    phe: Union[Phelel, Phono3py], toml_dict: dict, dir_name: str = "supercell"
+):
+    """Write VASP input for supercells.
+
+    This is alos used by velph-phono3py-generate.
+
+    """
     kpoints_dict = toml_dict["vasp"]["supercell"]["kpoints"]
     if "kspacing" in kpoints_dict:
         symmetry_dataset = kspacing_to_mesh(kpoints_dict, phe.supercell)
@@ -61,8 +70,8 @@ def _write_supercells(phe: Phelel, toml_dict: dict):
         + phe.supercells_with_displacements
     ):
         id_number = f"{i:0{nd}d}"
-        dir_name = f"supercell/disp-{id_number}"
-        directory = pathlib.Path(dir_name)
+        disp_dir_name = f"{dir_name}/disp-{id_number}"
+        directory = pathlib.Path(disp_dir_name)
         directory.mkdir(parents=True, exist_ok=True)
 
         # POSCAR
@@ -89,10 +98,17 @@ def _write_supercells(phe: Phelel, toml_dict: dict):
             scheduler_dict = get_scheduler_dict(toml_dict, "supercell")
             write_launch_script(scheduler_dict, directory, job_id=id_number)
 
-        click.echo(f'VASP input files were generated in "{dir_name}".')
+        click.echo(f'VASP input files were generated in "{disp_dir_name}".')
+
+
+def write_phonon_supercells(
+    phe: Union[Phelel, Phono3py], toml_dict: dict, dir_name: str = "supercell"
+):
+    """Write VASP input for phonon supercells.
 
+    This is alos used by velph-phono3py-generate.
 
-def _write_phonon_supercells(phe: Phelel, toml_dict: dict):
+    """
     kpoints_dict = toml_dict["vasp"]["supercell"]["phonon"]["kpoints"]
     nd = get_num_digits(phe.phonon_supercells_with_displacements)
 
@@ -103,8 +119,8 @@ def _write_phonon_supercells(phe: Phelel, toml_dict: dict):
         + phe.phonon_supercells_with_displacements
     ):
         id_number = f"{i:0{nd}d}"
-        dir_name = f"supercell/ph-disp-{id_number}"
-        directory = pathlib.Path(dir_name)
+        disp_dir_name = f"{dir_name}/ph-disp-{id_number}"
+        directory = pathlib.Path(disp_dir_name)
         directory.mkdir(parents=True, exist_ok=True)
 
         # POSCAR
@@ -133,4 +149,4 @@ def _write_phonon_supercells(phe: Phelel, toml_dict: dict):
             scheduler_dict = get_scheduler_dict(toml_dict, ["supercell", "phonon"])
             write_launch_script(scheduler_dict, directory, job_id=id_number)
 
-        click.echo(f'VASP input files were generated in "{dir_name}".')
+        click.echo(f'VASP input files were generated in "{disp_dir_name}".')