Merge pull request #41 from phonopy/velph-phono3py

Improve velph-phono3py

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/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

test/velph/cli/phono3py/init/test_phono3py_init.py

@@ -10,31 +10,20 @@
 @pytest.mark.parametrize("distance", [0.03, 0.05])
 def test_phono3py_init_random_displacements(distance: float):
     """Test of plusminus and diagonal with Ti."""
-    toml_str = f"""title = "VASP el-ph settings"
+    phelel_str = f"""title = "VASP el-ph settings"
 
 [phelel]
 supercell_dimension = [4, 4, 2]
 amplitude = {distance}
 fft_mesh = [18, 18, 28]
+"""
 
-[vasp.phonopy.incar]
-lwap = true
-isym = 0
-kpar = 2
-ncore = 24
-ismear = 0
-sigma = 0.2
-ediff = 1e-08
-encut = 329.532
-prec = "accurate"
-lreal = false
-lwave = false
-lcharg = false
-addgrid = true
-lsorbit = true
-[vasp.phonopy.kpoints]
-mesh = [6, 6, 7]
+    phono3py_str = f"""[phono3py]
+supercell_dimension = [2, 2, 1]
+amplitude = {distance}
+"""
 
+    unitcell_str = """
 [unitcell]
 lattice = [
   [     2.930720886111760,     0.000000000000000,     0.000000000000000 ], # a
@@ -48,13 +37,25 @@ def test_phono3py_init_random_displacements(distance: float):
 [[unitcell.points]]  # 2
 symbol = "Ti"
 coordinates = [  0.666666666666664,  0.333333333333336,  0.750000000000000 ]
-magnetic_moment = [ 0.00000000, 0.00000000, 0.00000000 ]
-"""
+magnetic_moment = [ 0.00000000, 0.00000000, 0.00000000 ]"""
 
-    toml_dict = tomli.loads(toml_str)
+    toml_dict = tomli.loads(phelel_str + unitcell_str)
     ph3 = run_init(toml_dict, number_of_snapshots=10)
     np.testing.assert_array_equal(ph3.supercell_matrix, np.diag([4, 4, 2]))
-    natom = len(ph3.supercell)
-    assert natom == 64
-    assert ph3.displacements.shape == (10, natom, 3)
+    assert len(ph3.supercell) == 64
+    assert ph3.displacements.shape == (10, 64, 3)
+    np.testing.assert_allclose(np.linalg.norm(ph3.displacements, axis=2), distance)
+
+    toml_dict = tomli.loads(phelel_str + phono3py_str + unitcell_str)
+    ph3 = run_init(toml_dict, number_of_snapshots=10, number_of_snapshots_fc2=4)
+    np.testing.assert_array_equal(ph3.supercell_matrix, np.diag([2, 2, 1]))
+    np.testing.assert_array_equal(ph3.phonon_supercell_matrix, np.diag([4, 4, 2]))
+
+    assert len(ph3.supercell) == 8
+    assert ph3.displacements.shape == (10, 8, 3)
+    assert len(ph3.phonon_supercell) == 64
+    assert ph3.phonon_displacements.shape == (4, 64, 3)
     np.testing.assert_allclose(np.linalg.norm(ph3.displacements, axis=2), distance)
+    np.testing.assert_allclose(
+        np.linalg.norm(ph3.phonon_displacements, axis=2), distance
+    )