"""Flows for Lobster computations."""
from __future__ import annotations
from dataclasses import dataclass, field
from typing import TYPE_CHECKING
from jobflow import Flow, Maker
from monty.dev import requires
from atomate2.lobster.jobs import LobsterMaker
from atomate2.vasp.flows.core import DoubleRelaxMaker, UniformBandStructureMaker
from atomate2.vasp.jobs.core import NonSCFMaker, RelaxMaker, StaticMaker
from atomate2.vasp.jobs.lobster import (
delete_lobster_wavecar,
get_basis_infos,
get_lobster_jobs,
update_user_incar_settings_maker,
)
from atomate2.vasp.sets.core import NonSCFSetGenerator, StaticSetGenerator
try:
import ijson
from lobsterpy.cohp.analyze import Analysis
from lobsterpy.cohp.describe import Description
except ImportError:
ijson = None
Analysis = None
Description = None
if TYPE_CHECKING:
from pathlib import Path
from pymatgen.core import Structure
from atomate2.vasp.jobs.base import BaseVaspMaker
LOBSTER_UNIFORM_MAKER = UniformBandStructureMaker(
name="uniform lobster structure",
static_maker=StaticMaker(
input_set_generator=StaticSetGenerator(
user_kpoints_settings={"reciprocal_density": 100},
user_incar_settings={
"EDIFF": 1e-7,
"LAECHG": False,
"LVTOT": False,
"LREAL": False,
"ALGO": "Normal",
"LWAVE": False,
},
)
),
bs_maker=NonSCFMaker(
input_set_generator=NonSCFSetGenerator(
user_kpoints_settings={"reciprocal_density": 400},
user_incar_settings={
"LWAVE": True,
"ISYM": 0,
},
),
task_document_kwargs={"parse_dos": False, "parse_bandstructure": False},
),
)
[docs]
@dataclass
class VaspLobsterMaker(Maker):
"""
Maker to perform a Lobster computation.
The calculations performed are:
1. Optional optimization.
2. Static calculation with ISYM=0.
3. Several Lobster computations testing several basis sets are performed.
.. Note::
The basis sets can only be changed with yaml files.
Parameters
----------
name : str
Name of the flows produced by this maker.
relax_maker : .BaseVaspMaker or None
A maker to perform a relaxation on the bulk. Set to ``None`` to skip the
bulk relaxation.
lobster_static_maker : .BaseVaspMaker
A maker to perform the computation of the wavefunction before the static run.
Cannot be skipped. It can be LOBSTERUNIFORM or LobsterStaticMaker()
lobster_maker : .LobsterMaker
A maker to perform the Lobster run.
delete_wavecars : bool
If true, all WAVECARs will be deleted after the run.
address_min_basis : str
A path to a yaml file including basis set information.
address_max_basis : str
A path to a yaml file including basis set information.
"""
name: str = "lobster"
relax_maker: BaseVaspMaker | None = field(
default_factory=lambda: DoubleRelaxMaker.from_relax_maker(RelaxMaker())
)
lobster_static_maker: BaseVaspMaker = field(
default_factory=lambda: LOBSTER_UNIFORM_MAKER
)
lobster_maker: LobsterMaker | None = field(default_factory=LobsterMaker)
delete_wavecars: bool = True
address_min_basis: str | None = None
address_max_basis: str | None = None
[docs]
@requires(
Analysis,
"This flow requires lobsterpy and ijson to function properly. "
"Please reinstall atomate2 using atomate2[lobster]",
)
def make(
self,
structure: Structure,
prev_dir: str | Path | None = None,
) -> Flow:
"""
Make flow to calculate bonding properties.
Parameters
----------
structure : .Structure
A pymatgen structure. Please start with a structure
that is nearly fully optimized as the internal optimizers
have very strict settings!
prev_dir : str or Path or None
A previous vasp calculation directory to use for copying outputs.
"""
jobs = []
# optionally relax the structure
optimization_dir = None
optimization_uuid = None
if self.relax_maker is not None:
optimization = self.relax_maker.make(structure, prev_dir=prev_dir)
jobs.append(optimization)
structure = optimization.output.structure
optimization_dir = optimization.output.dir_name
optimization_uuid = optimization.output.uuid
prev_dir = optimization_dir
# Information about the basis is collected
basis_infos = get_basis_infos(
structure=structure,
vasp_maker=self.lobster_static_maker,
address_min_basis=self.address_min_basis,
address_max_basis=self.address_max_basis,
)
jobs.append(basis_infos)
# Maker needs to be updated here. If the job itself is updated, no further
# updates on the job are possible
lobster_static = update_user_incar_settings_maker(
self.lobster_static_maker,
basis_infos.output["nbands"],
structure,
prev_dir,
)
jobs.append(lobster_static)
lobster_static_dir = lobster_static.output.dir_name
lobster_static_uuid = lobster_static.output.uuid
lobster_jobs = get_lobster_jobs(
lobster_maker=self.lobster_maker,
basis_dict=basis_infos.output["basis_dict"],
optimization_dir=optimization_dir,
optimization_uuid=optimization_uuid,
static_dir=lobster_static_dir,
static_uuid=lobster_static_uuid,
)
jobs.append(lobster_jobs)
# delete all WAVECARs that have been copied
# TODO: this has to be adapted as well
if self.delete_wavecars:
delete_wavecars = delete_lobster_wavecar(
dirs=lobster_jobs.output["lobster_dirs"],
lobster_static_dir=lobster_static.output.dir_name,
)
jobs.append(delete_wavecars)
return Flow(jobs, output=lobster_jobs.output)