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velph: vasp.calc_type.kpoints is preferred than kspacing #11

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Aug 6, 2024
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velph: vasp.calc_type.kpoints is preferred than kspacing #11

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136 changes: 63 additions & 73 deletions src/phelel/velph/cli/init/init.py
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Original file line number Diff line number Diff line change
Expand Up @@ -591,6 +591,23 @@ def _get_toml_lines(
cell_choices["relax"],
)

if "vasp" in velph_dict:
_update_kpoints_by_vasp_dict(
kpoints_dict,
kpoints_dense_dict,
qpoints_dict,
kpoints_opt_dict,
velph_dict["vasp"],
)
_show_kpoints_lines(
kpoints_dict,
kpoints_dense_dict,
kpoints_opt_dict,
velph_dict["vasp"],
vip.kspacing,
vip.kspacing_dense,
)

#
# velph.toml
#
Expand Down Expand Up @@ -708,30 +725,20 @@ def _get_kpoints_dict(
cell_for_relax: CellChoice,
) -> tuple[dict, dict, dict, dict]:
"""Return kpoints dicts."""
if vip_kspacing:
_kspacing = vip_kspacing
else:
_kspacing = 0.3

if vip_kspacing_dense:
_kspacing_dense = vip_kspacing_dense
else:
_kspacing_dense = 0.3
use_grg_unitcell = vip_use_grg and (len(unitcell) == len(primitive))

sym_dataset_prim = get_symmetry_dataset(primitive, tolerance=vip_tolerance)

# Grid matrix for unitcell
gm = GridMatrix(
2 * np.pi / _kspacing,
2 * np.pi / vip_kspacing,
lattice=unitcell.cell,
symmetry_dataset=sym_dataset,
use_grg=use_grg_unitcell,
)

# Grid matrix for primitive cell
gm_prim = GridMatrix(
2 * np.pi / _kspacing,
2 * np.pi / vip_kspacing,
lattice=primitive.cell,
symmetry_dataset=sym_dataset_prim,
use_grg=vip_use_grg,
Expand All @@ -741,15 +748,15 @@ def _get_kpoints_dict(
supercell = get_supercell(unitcell, supercell_dimension)
sym_dataset_super = get_symmetry_dataset(supercell, tolerance=vip_tolerance)
gm_super = GridMatrix(
2 * np.pi / _kspacing,
2 * np.pi / vip_kspacing,
lattice=supercell.cell,
symmetry_dataset=sym_dataset_super,
use_grg=False,
)

# Dense grid matrix for primitive cell
gm_dense_prim = GridMatrix(
2 * np.pi / _kspacing_dense,
2 * np.pi / vip_kspacing_dense,
lattice=primitive.cell,
symmetry_dataset=sym_dataset_prim,
use_grg=vip_use_grg,
Expand All @@ -763,42 +770,6 @@ def _get_kpoints_dict(
qpoints_dict: dict = {}
kpoints_opt_dict: dict = {}

if "vasp" in velph_dict:
_update_kpoints_by_vasp_dict(
kpoints_dict,
kpoints_dense_dict,
qpoints_dict,
kpoints_opt_dict,
velph_dict["vasp"],
vip_kspacing,
vip_kspacing_dense,
)

k_mesh_lines = ["[vasp.*.kpoints(_dense).mesh]"]
if "supercell" in kpoints_dict:
k_mesh_lines.append(
" supercell: {mesh}".format(mesh=kpoints_dict["supercell"]["mesh"])
)
if "selfenergy" in kpoints_dict:
k_mesh_lines.append(
" primitive: {mesh}".format(mesh=kpoints_dict["selfenergy"]["mesh"])
)
if "selfenergy" in kpoints_dense_dict:
k_mesh_lines.append(
" primitive(dense): {mesh}".format(
mesh=kpoints_dense_dict["selfenergy"]["mesh"]
)
)
if "relax" in kpoints_dict:
k_mesh_lines.append(
" relax: {mesh}".format(mesh=kpoints_dict["relax"]["mesh"])
)
if "nac" in kpoints_dict:
k_mesh_lines.append(" nac: {mesh}".format(mesh=kpoints_dict["nac"]["mesh"]))

if k_mesh_lines:
click.echo("\n".join(k_mesh_lines))

return kpoints_dict, kpoints_dense_dict, qpoints_dict, kpoints_opt_dict


Expand All @@ -808,32 +779,51 @@ def _update_kpoints_by_vasp_dict(
qpoints_dict: dict,
kpoints_opt_dict: dict,
vasp_dict: dict,
kspacing: Optional[float],
kspacing_dense: Optional[float],
) -> None:
for key in (
"supercell",
"selfenergy",
"relax",
"nac",
"el_bands",
"ph_bands",
):
if not kspacing:
if key in vasp_dict and "kpoints" in vasp_dict[key]:
kpoints_dict[key] = vasp_dict[key]["kpoints"]

if not kspacing_dense:
for key in ("selfenergy", "el_bands"):
if key in vasp_dict and "kpoints_dense" in vasp_dict[key]:
kpoints_dense_dict[key] = vasp_dict[key]["kpoints_dense"]

for key in ("ph_bands",):
if key in vasp_dict and "qpoints" in vasp_dict[key]:
"""Overwrite kpoints_(dense_)dict if kpoints are defined in vasp_dict."""
for key in vasp_dict:
if "kpoints" in vasp_dict[key]:
kpoints_dict[key] = vasp_dict[key]["kpoints"]
if "kpoints_dense" in vasp_dict[key]:
kpoints_dense_dict[key] = vasp_dict[key]["kpoints_dense"]
if "qpoints" in vasp_dict[key]:
qpoints_dict[key] = vasp_dict[key]["qpoints"]
if "kpoints_opt" in vasp_dict[key]:
kpoints_opt_dict[key] = vasp_dict[key]["kpoints_opt"]


if "el_bands" in vasp_dict and "kpoints_opt" in vasp_dict["el_bands"]:
kpoints_opt_dict["el_bands"] = vasp_dict["el_bands"]["kpoints_opt"]
def _show_kpoints_lines(
kpoints_dict: dict,
kpoints_dense_dict: dict,
kpoints_opt_dict: dict,
vasp_dict: dict,
vip_kspacing: float,
vip_kspacing_dense: float,
):
k_mesh_lines = [f"[vasp.*.kpoints.mesh] (*kspacing={vip_kspacing})"]
for key in vasp_dict:
if key == "ph_bands":
continue
if key in kpoints_dict:
mesh = kpoints_dict[key].get("mesh")
if mesh is not None:
line = f" {key}: {mesh}"
if "kpoints" not in vasp_dict[key]:
line += "*"
k_mesh_lines.append(line)
k_mesh_lines.append(
f"[vasp.*.kpoints_dense.mesh] (*kspacing_dense={vip_kspacing_dense})"
)
for key in vasp_dict:
if key in kpoints_dense_dict:
mesh = kpoints_dense_dict[key].get("mesh")
if mesh is not None:
line = f" {key}: {mesh}"
if "kpoints_dense" not in vasp_dict[key]:
line += "*"
k_mesh_lines.append(line)
if k_mesh_lines:
click.echo("\n".join(k_mesh_lines))


def _get_kpoints_by_kspacing(
Expand Down