Merge pull request #4 from phonopy/encut-differentiate

Add encut option to velph supercell differentiate

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

@@ -1,6 +1,7 @@
 """velph command line tool / velph-supercell."""
 
 import pathlib
+from typing import Optional
 
 import click
 import tomli
@@ -12,6 +13,7 @@
 from phelel.velph.cli.supercell.generate import write_supercell_input_files
 from phelel.velph.cli.supercell.init import run_init
 from phelel.velph.cli.supercell.phonopy import create_phonopy_yaml
+from phelel.velph.utils.vasp import CutoffToFFTMesh
 
 
 @cmd_root.group("supercell")
@@ -99,11 +101,19 @@ def cmd_generate(toml_filename: str, yaml_filename: str):
     type=click.Path(),
     default="supercell/phelel_params.hdf5",
 )
+@click.option(
+    "--encut",
+    nargs=1,
+    type=float,
+    default=None,
+    help=(
+        "Cutoff energy corresponding to FFT mesh of local potential grid. "
+        "(encut: float, default=None)"
+    ),
+)
 @click.help_option("-h", "--help")
 def cmd_differentiate(
-    toml_filename: str,
-    yaml_filename: str,
-    hdf5_filename: str,
+    toml_filename: str, yaml_filename: str, hdf5_filename: str, encut: Optional[float]
 ) -> None:
     """Calculate derivatives and write phelel_params.hdf5."""
     with open(toml_filename, "rb") as f:
@@ -131,6 +141,24 @@ def cmd_differentiate(
         is_symmetry=is_symmetry,
     )
 
+    if encut is not None:
+        try:
+            prec = toml_dict["vasp"]["selfenergy"]["incar"]["prec"]
+        except KeyError:
+            click.echo(f'[vasp.selfenergy.incar] not found in "{toml_filename}".')
+            click.echo('prec = "accurate" is assumed.')
+            prec = "accurate"
+        click.echo(f"FFT mesh is generated for encut={encut}.")
+        phe.fft_mesh = CutoffToFFTMesh.get_FFTMesh(encut, phe.primitive.cell, prec)
+
+    if phe.fft_mesh is None:
+        click.echo("FFT mesh is not specified.", err=True)
+    else:
+        if encut is None:
+            click.echo(f"FFT mesh: {phe.fft_mesh}.")
+        else:
+            click.echo(f"FFT mesh: {phe.fft_mesh} (encut={encut}).")
+
     run_derivatives(phe, hdf5_filename=hdf5_filename)
 
 

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

@@ -31,7 +31,11 @@ def run_derivatives(
         id_number = f"{i:0{nd}d}"
         filepath = pathlib.Path(f"{dir_name}/disp-{id_number}")
         if filepath.exists():
-            dir_names.append(filepath)
+            if _check_files_exist(filepath):
+                dir_names.append(filepath)
+            else:
+                click.echo(f'Necessary file not found in "{filepath}".', err=True)
+                return None
         else:
             click.echo(f'"{filepath}" does not exist.', err=True)
             return None
@@ -65,3 +69,53 @@ def run_derivatives(
     phe.save_hdf5(filename=hdf5_filename)
 
     click.echo(f'"{hdf5_filename}" has been made.')
+
+
+def _check_files_exist(filepath: pathlib.Path) -> bool:
+    if not _check_file_exists(filepath, "vasprun.xml"):
+        click.echo(f'"{filepath}/vasprun.xml" not found.', err=True)
+        return False
+    if _check_four_files_exist(filepath):
+        return True
+    else:
+        if (filepath / "vaspout.h5").exists():
+            click.echo(f'Found "{filepath}/vaspout.h5".', err=True)
+            return True
+        else:
+            for filename in (
+                "inwap.yaml",
+                "LOCAL-POTENTIAL.bin",
+                "PAW-STRENGTH.bin",
+                "PAW-OVERLAP.bin",
+            ):
+                if not _check_file_exists(filepath, filename):
+                    click.echo(f'"{filepath}/{filename}" not found.', err=True)
+            return False
+
+
+def _check_four_files_exist(filepath: pathlib.Path) -> bool:
+    for filename in (
+        "inwap.yaml",
+        "LOCAL-POTENTIAL.bin",
+        "PAW-STRENGTH.bin",
+        "PAW-OVERLAP.bin",
+    ):
+        if not _check_file_exists(filepath, filename):
+            return False
+    return True
+
+
+def _check_file_exists(filepath: pathlib.Path, filename: str) -> bool:
+    """Check if the necessary file exists.
+
+    The file can be compressed with xz, etc.
+
+    The file names that can be checked are:
+        inwap.yaml
+        LOCAL-POTENTIAL.bin
+        PAW-STRENGTH.bin
+        PAW-OVERLAP.bin
+        vasprun.xml
+
+    """
+    return bool(list(pathlib.Path(filepath).glob(f"{filename}*")))

src/phelel/velph/cli/transport/plot/plot_transport.py

@@ -135,15 +135,25 @@ def _show(transport: h5py._hl.group.Group, index: int):
             print(f"    {key[1]}: {transport[key[0]][()]}")
         else:
             print(f"    {key}: {transport[key][()]}")
-    print("  data_array_shapes:")
+
+    print("  data_array_diagonal:")
     for key in (
         "e_conductivity",
         "e_t_conductivity",
-        "energy",
-        ("lab", "Onsager_coefficients"),
         "mobility",
         "peltier",
         "seebeck",
+    ):
+        v = transport[key][:].ravel()
+        print(
+            f"    {key}: [{v[0]:.3e}, {v[4]:.3e}, {v[8]:.3e}, "
+            f"{v[5]:.3e}, {v[2]:.3e}, {v[1]:.3e}]"
+        )
+
+    print("  data_array_shapes:")
+    for key in (
+        "energy",
+        ("lab", "Onsager_coefficients"),
         "transport_function",
     ):
         if isinstance(key, tuple):

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

@@ -18,8 +18,11 @@ def test_run_derivatives():
     """
     phe = phelel.load(cwd / "C111" / "phelel_disp_C111.yaml", fft_mesh=[9, 9, 9])
     hdf5_filename = "phelel_params_test_run_derivatives.hdf5"
-    run_derivatives(phe, hdf5_filename=hdf5_filename, dir_name=cwd / "C111/supercell")
+    run_derivatives(
+        phe, hdf5_filename=hdf5_filename, dir_name=cwd / "C111" / "supercell"
+    )
     file_path = pathlib.Path(cwd_called / hdf5_filename)
+    print(file_path)
     assert file_path.exists()
     file_path.unlink()