Fix velph-selfenergy-generate (issue #28)

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

@@ -56,10 +56,10 @@ def _show_hints(toml_filename: str):
     click.echo("3. Run VASP.")
     click.echo()
     click.echo("# Supercell calculation")
-    click.echo(f'1. Modify [vasp.supercell] section in "{toml_filename}".')
-    click.echo('2. "velph supercell init": Prepare finite displacement calculation. ')
+    click.echo(f'1. Modify [vasp.phelel] section in "{toml_filename}".')
+    click.echo('2. "velph phelel init": Prepare finite displacement calculation. ')
     click.echo("   NAC parameters are read when NAC calculation is available.")
-    click.echo('3. "velph supercell generate": Generate input files.')
+    click.echo('3. "velph phelel generate": Generate input files.')
     click.echo("4. Run VASP.")
     click.echo()
     click.echo("# Phonon band structure calculation")
@@ -72,31 +72,29 @@ def _show_hints(toml_filename: str):
     click.echo("3. Run VASP in ph_bands directories.")
     click.echo('4. "velph ph_bands plot" to plot the phonon bands')
     click.echo()
-    click.echo(
-        '# Electron self-energy calculation (optional, default for "velph selfenergy")'
-    )
+    click.echo("# Electron transport calculation")
+    click.echo(f'1. Write [vasp.transport] section in "{toml_filename}".')
+    click.echo('2. (optioanl) "velph transport generate": ' "Dry-run to find FFT-mesh.")
+    click.echo("3. (optioanl) Run VASP.")
+    click.echo('4. (optioanl) "velph transport check-fft": Check FFT grid.')
+    click.echo('5. (optioanl) Modify "fft_mesh" in [phelel] section manually.')
+    click.echo('6. "velph supercell differentiate": Generate derivatives hdf5 file')
+    click.echo('7. "velph transport generate": Generate input files')
+    click.echo()
+    click.echo("# Electron self-energy calculation")
     click.echo(f'1. Modify [vasp.selfenergy] section in "{toml_filename}".')
     click.echo(
         '2. (optional) "velph selfenergy generate -d": ' "Dry-run to find FFT-mesh."
     )
     click.echo("3. (optional) Run VASP.")
     click.echo('4. (optioanl) "velph selfenergy check-fft": Check FFT grid.')
     click.echo('5. (optioanl) Modify "fft_mesh" in [phelel] section manually.')
-    click.echo('6. "velph supercell differentiate": Generate derivatives hdf5 file')
+    click.echo('6. "velph phelel differentiate": Generate derivatives hdf5 file')
     click.echo('7. "velph selfenergy generate": Generate input files')
     click.echo()
-    click.echo("# Other electron-phonon calculation, e.g., transport")
-    click.echo(f'1. Write [vasp.transport] section in "{toml_filename}".')
-    click.echo('2. (optioanl) "velph transport generate": ' "Dry-run to find FFT-mesh.")
-    click.echo("3. (optioanl) Run VASP.")
-    click.echo('4. (optioanl) "velph transport check-fft": Check FFT grid.')
-    click.echo('5. (optioanl) Modify "fft_mesh" in [phelel] section manually.')
-    click.echo('6. "velph supercell differentiate": Generate derivatives hdf5 file')
-    click.echo('7. "velph transport generate": Generate input files')
-    click.echo()
     click.echo("# Different supercell size for phonon")
-    click.echo('1. Write "phonon_supercell_dimension" in [phelel] section and')
-    click.echo("2. Write [vasp.supercell.phonon.*] entry.")
+    click.echo('1. Write "supercell_dimension" in [phonopy] section and')
+    click.echo("2. Write [vasp.phelel.phonon.*] entry.")
     click.echo(
         "------------------------------- velph hints -------------------------------"
     )

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

@@ -9,7 +9,7 @@
 from phelel.velph.cli.utils import check_fft
 
 
-@cmd_root.group("elph")
+@cmd_root.group("selfenergy")
 @click.help_option("-h", "--help")
 def cmd_selfenergy():
     """Choose selfenergy options."""
@@ -23,23 +23,6 @@ def cmd_selfenergy():
     type=click.Path(),
     default="velph.toml",
 )
-@click.option(
-    "--hdf5-filename",
-    "hdf5_filename",
-    nargs=1,
-    type=click.Path(),
-    default="supercell/phelel_params.hdf5",
-    show_default=True,
-)
-@click.option(
-    "-c",
-    "--calculation",
-    "calculation_name",
-    nargs=1,
-    type=str,
-    default="selfenergy",
-    show_default=True,
-)
 @click.option(
     "--dry-run/--no-dry-run",
     "-d",
@@ -49,19 +32,12 @@ def cmd_selfenergy():
     show_default=True,
 )
 @click.help_option("-h", "--help")
-def cmd_generate(
-    toml_filename: str, hdf5_filename: str, calculation_name: str, dry_run: bool
-):
+def cmd_generate(toml_filename: str, dry_run: bool):
     """Generate elph input files."""
     if not pathlib.Path("POTCAR").exists():
         click.echo('"POTCAR" not found in current directory.')
 
-    write_input_files(
-        pathlib.Path(toml_filename),
-        pathlib.Path(hdf5_filename),
-        calculation_name,
-        dry_run,
-    )
+    write_input_files(pathlib.Path(toml_filename), dry_run)
 
 
 @cmd_selfenergy.command("check-fft")
@@ -71,16 +47,7 @@ def cmd_generate(
     type=click.Path(),
     default="velph.toml",
 )
-@click.option(
-    "-c",
-    "--calculation",
-    "calculation_name",
-    nargs=1,
-    type=click.Path(),
-    default="selfenergy",
-    show_default=True,
-)
 @click.help_option("-h", "--help")
-def cmd_check_fft(toml_filename: str, calculation_name: str):
+def cmd_check_fft(toml_filename: str):
     """Show [NGX, NGY, NGZ] in vasprun.xml."""
-    check_fft(toml_filename, calculation_name)
+    check_fft(toml_filename, "selfenergy")

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

@@ -20,24 +20,15 @@
 )
 
 
-def write_input_files(
-    toml_filepath: pathlib.Path,
-    hdf5_filepath: pathlib.Path,
-    calculation_name: str,
-    dry_run: bool,
-):
+def write_input_files(toml_filepath: pathlib.Path, dry_run: bool):
     """Generate el-ph input files."""
-    write_selfenergy_input_files(
-        toml_filepath, hdf5_filepath, calculation_name, dry_run
-    )
+    write_selfenergy_input_files(toml_filepath, dry_run, calc_type="selfenergy")
 
 
 def write_selfenergy_input_files(
     toml_filepath: pathlib.Path,
-    hdf5_filepath: pathlib.Path,
-    calculation_name: str,
     dry_run: bool,
-    calc_type: Optional[Literal["transport"]] = None,
+    calc_type: Optional[Literal["transport", "selfenergy"]] = None,
     current_directory: pathlib.Path = pathlib.Path(""),
     energy_threshold: float = 0.5,
 ) -> None:
@@ -50,29 +41,44 @@ def write_selfenergy_input_files(
         calc_type="transport".
 
     """
-    directory_path = pathlib.Path(calculation_name)
+    directory_path = pathlib.Path(calc_type)
 
     with open(toml_filepath, "rb") as f:
         toml_dict = tomli.load(f)
 
-    if calculation_name not in toml_dict["vasp"]:
+    if "vasp" not in toml_dict:
+        click.echo(f"[vasp] section not found in {toml_filepath}.", err=True)
+        return None
+
+    if "phelel" in toml_dict["vasp"]:
+        hdf5_filepath = pathlib.Path("phelel/phelel_params.hdf5")
+    elif "supercell" in toml_dict["vasp"]:
+        hdf5_filepath = pathlib.Path("supercell/phelel_params.hdf5")
+    else:
+        click.echo(
+            f'[vasp.phelel] section not found in "{toml_filepath}".',
+            err=True,
+        )
+        return None
+
+    if calc_type not in toml_dict["vasp"]:
         click.echo(
-            f'[vasp.{calculation_name}.*] section not found in "{toml_filepath}".',
+            f'[vasp.{calc_type}] section not found in "{toml_filepath}".',
             err=True,
         )
         return None
 
     # Check phelel_params.hdf5
     if not dry_run and not hdf5_filepath.exists():
         click.echo(f'"{hdf5_filepath}" not found.', err=True)
-        click.echo('Run "velph supercell differentiate" if necessary.')
+        click.echo('Run "velph phelel differentiate" if necessary.', err=True)
         return None
 
     # mkdir, e.g., selfenergy
     directory_path.mkdir(parents=True, exist_ok=True)
 
     # Dry run
-    toml_incar_dict = toml_dict["vasp"][calculation_name]["incar"]
+    toml_incar_dict = toml_dict["vasp"][calc_type]["incar"]
     if dry_run:
         toml_incar_dict["nelm"] = 0
         toml_incar_dict["elph_run"] = False
@@ -93,22 +99,22 @@ def write_selfenergy_input_files(
     write_incar(toml_incar_dict, directory_path, cell=primitive)
 
     # KPOINTS
-    kpoints_dict = toml_dict["vasp"][calculation_name]["kpoints"]
+    kpoints_dict = toml_dict["vasp"][calc_type]["kpoints"]
     assert_kpoints_mesh_symmetry(toml_dict, kpoints_dict, primitive)
     write_kpoints_mesh_mode(
         toml_incar_dict,
         directory_path,
-        f"vasp.{calculation_name}.kpoints",
+        f"vasp.{calc_type}.kpoints",
         kpoints_dict,
     )
 
     # KPOINTS_DENSE
-    kpoints_dense_dict = toml_dict["vasp"][calculation_name]["kpoints_dense"]
+    kpoints_dense_dict = toml_dict["vasp"][calc_type]["kpoints_dense"]
     assert_kpoints_mesh_symmetry(toml_dict, kpoints_dense_dict, primitive)
     write_kpoints_mesh_mode(
         toml_incar_dict,
         directory_path,
-        f"vasp.{calculation_name}.kpoints_dense",
+        f"vasp.{calc_type}.kpoints_dense",
         kpoints_dense_dict,
         kpoints_filename="KPOINTS_DENSE",
         kspacing_name="elph_kspacing",
@@ -125,7 +131,7 @@ def write_selfenergy_input_files(
 
     # Scheduler launch script
     if "scheduler" in toml_dict:
-        scheduler_dict = get_scheduler_dict(toml_dict, calculation_name)
+        scheduler_dict = get_scheduler_dict(toml_dict, calc_type)
         write_launch_script(scheduler_dict, directory_path)
 
     click.echo(f'VASP input files were generated in "{directory_path}".')

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

@@ -23,14 +23,6 @@ def cmd_transport():
     type=click.Path(),
     default="velph.toml",
 )
-@click.option(
-    "--hdf5-filename",
-    "hdf5_filename",
-    nargs=1,
-    type=click.Path(),
-    default="supercell/phelel_params.hdf5",
-    show_default=True,
-)
 @click.option(
     "--dry-run/--no-dry-run",
     "-d",
@@ -40,16 +32,12 @@ def cmd_transport():
     show_default=True,
 )
 @click.help_option("-h", "--help")
-def cmd_generate(toml_filename: str, hdf5_filename: str, dry_run: bool):
+def cmd_generate(toml_filename: str, dry_run: bool):
     """Generate transport input files."""
     if not pathlib.Path("POTCAR").exists():
         click.echo('"POTCAR" not found in current directory.')
 
-    write_input_files(
-        pathlib.Path(toml_filename),
-        pathlib.Path(hdf5_filename),
-        dry_run,
-    )
+    write_input_files(pathlib.Path(toml_filename), dry_run)
 
 
 @cmd_transport.command("check-fft")

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

@@ -5,12 +5,6 @@
 from phelel.velph.cli.selfenergy.generate import write_selfenergy_input_files
 
 
-def write_input_files(
-    toml_filepath: pathlib.Path,
-    hdf5_filepath: pathlib.Path,
-    dry_run: bool,
-):
+def write_input_files(toml_filepath: pathlib.Path, dry_run: bool):
     """Generate transport input files."""
-    write_selfenergy_input_files(
-        toml_filepath, hdf5_filepath, "transport", dry_run, calc_type="transport"
-    )
+    write_selfenergy_input_files(toml_filepath, dry_run, calc_type="transport")

test/velph/cli/phelel/differentiate/test_differentiate.py

@@ -18,7 +18,7 @@ def test_run_derivatives():
 
     """
     phe = phelel.load(cwd / "C111" / "phelel_disp_C111.yaml", fft_mesh=[9, 9, 9])
-    assert run_derivatives(phe, dir_name=cwd / "C111" / "supercell")
+    assert run_derivatives(phe, dir_name=cwd / "C111" / "phelel")
 
 
 def test_run_derivatives_with_wrong_supercell_matrix():
@@ -30,7 +30,7 @@ def test_run_derivatives_with_wrong_supercell_matrix():
     """
     phe = phelel.load(cwd / "phelel_disp_C222.yaml", fft_mesh=[9, 9, 9])
     with pytest.raises(ValueError):
-        run_derivatives(phe, dir_name=cwd / "C111/supercell")
+        run_derivatives(phe, dir_name=cwd / "C111" / "phelel")
 
 
 def test_run_derivatives_with_wrong_phonon_supercell_matrix():
@@ -40,4 +40,4 @@ def test_run_derivatives_with_wrong_phonon_supercell_matrix():
 
     """
     phe = phelel.load(cwd / "phelel_disp_C111-222.yaml", fft_mesh=[9, 9, 9])
-    assert not run_derivatives(phe, dir_name=cwd / "C111/supercell")
+    assert not run_derivatives(phe, dir_name=cwd / "C111" / "phelel")