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Feat: GW workflow with VASP (#808)
* Added the Materials Virtual Lab GW Set to the repo and implemented the MVLGWSetGenerator * add a Materials Virtual Lab GW band structure maker * fix bug * rename MVLGWMaker * created a Flow that does all three stages (static, diag, gw) for a GW band structure calculation * fixed bug * update the mvl gw yaml file and explicity copy the magmon in it * update the gw workflow * Revert line 37 to original state and fixed a typo * update the class doc of MVLGWSetGenerator * rewrite job name * rewrite job name * make job and flow names short * update job name * change the method names to adjust for recent updates on the main branch * explicitly specify files to copy * copied all data files for gw test case * add testcase for running MVL GW workflow * modified the files needed to copy between jobs * fixed wrong assertation * added missing data files to run the tests * add a warning in the GW workflow * removed MVL GW set yaml file, instead, import from pymatgen * reorganize the mvl jobs * reorganize the mvl gw workflow * update test case for mvl gw workflow and update the test data * update the mvl gw workflow * update test case for mvl gw workflow and corresponding test data * Bump emmet-core from 0.84.2 to 0.84.3rc3 * updated test data for mvl g0w0 * removed MVLGWSetGenerator class; use MVLGWSet directly instead * removed deprecate comments * remove CONTCAR.gz, use CONTCAR instead
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‎pyproject.toml

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@@ -28,7 +28,7 @@ dependencies = [
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"PyYAML",
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"click",
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"custodian>=2024.4.18",
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"emmet-core>=0.82.2",
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"emmet-core>=0.84.3rc3",
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"jobflow>=0.1.11",
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"monty>=2024.7.30",
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"numpy",
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"click==8.1.7",
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"custodian==2024.10.16",
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"dscribe==2.1.1",
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"emmet-core==0.84.2",
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"emmet-core==0.84.3rc3",
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"ijson==3.3.0",
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"jobflow==0.1.18",
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"lobsterpy==0.4.9",

‎src/atomate2/vasp/flows/mvl.py

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"""Materials Virtual Lab (MVL) VASP flows."""
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from __future__ import annotations
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from dataclasses import dataclass, field
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from typing import TYPE_CHECKING
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from jobflow import Flow, Maker
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from atomate2.vasp.jobs.mvl import MVLGWMaker, MVLNonSCFMaker, MVLStaticMaker
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if TYPE_CHECKING:
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from pathlib import Path
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from pymatgen.core.structure import Structure
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from atomate2.vasp.jobs.base import BaseVaspMaker
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@dataclass
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class MVLGWBandStructureMaker(Maker):
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"""
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Maker to generate VASP band structures with Materials Virtual Lab GW setup.
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.. warning::
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This workflow is only compatible with the Materials Virtual Lab GW setup,
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and it may require additional benchmarks. Please use with caution.
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Parameters
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----------
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name : str
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Name of the flows produced by this maker.
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gw_maker : .BaseVaspMaker
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The maker to use for the GW calculation.
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"""
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name: str = "MVL G0W0 band structure"
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static_maker: BaseVaspMaker = field(default_factory=MVLStaticMaker)
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nscf_maker: BaseVaspMaker = field(default_factory=MVLNonSCFMaker)
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gw_maker: BaseVaspMaker = field(default_factory=MVLGWMaker)
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def make(self, structure: Structure, prev_dir: str | Path | None = None) -> Flow:
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"""
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Create a band structure flow.
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Parameters
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----------
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structure : Structure
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A pymatgen structure object.
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prev_dir : str or Path or None
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A previous VASP calculation directory to copy output files from.
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Returns
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-------
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Flow
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A band structure flow.
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"""
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static_job = self.static_maker.make(structure, prev_dir=prev_dir)
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nscf_job = self.nscf_maker.make(
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static_job.output.structure, prev_dir=static_job.output.dir_name
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)
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gw_job = self.gw_maker.make(
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nscf_job.output.structure, prev_dir=nscf_job.output.dir_name
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)
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jobs = [static_job, nscf_job, gw_job]
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outputs = {
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"static": static_job.output,
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"nscf": nscf_job.output,
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"gw": gw_job.output,
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}
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return Flow(jobs, outputs, name=self.name)

‎src/atomate2/vasp/jobs/mvl.py

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"""Core jobs for running VASP calculations."""
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from __future__ import annotations
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import logging
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from dataclasses import dataclass, field
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from typing import TYPE_CHECKING
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from pymatgen.io.vasp.sets import MVLGWSet
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from atomate2.vasp.jobs.base import BaseVaspMaker, vasp_job
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if TYPE_CHECKING:
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from pathlib import Path
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from jobflow import Response
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from pymatgen.core.structure import Structure
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from atomate2.vasp.sets.base import VaspInputGenerator
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logger = logging.getLogger(__name__)
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@dataclass
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class MVLStaticMaker(BaseVaspMaker):
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"""
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Maker to create a static calculation compatible with Materials Virtual Lab GW jobs.
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Parameters
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----------
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name : str
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The job name.
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input_set_generator : .VaspInputGenerator
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A generator used to make the input set.
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write_input_set_kwargs : dict
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Keyword arguments that will get passed to :obj:`.write_vasp_input_set`.
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copy_vasp_kwargs : dict
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Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`.
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run_vasp_kwargs : dict
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Keyword arguments that will get passed to :obj:`.run_vasp`.
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task_document_kwargs : dict
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Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`.
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stop_children_kwargs : dict
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Keyword arguments that will get passed to :obj:`.should_stop_children`.
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write_additional_data : dict
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Additional data to write to the current directory. Given as a dict of
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{filename: data}. Note that if using FireWorks, dictionary keys cannot contain
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the "." character which is typically used to denote file extensions. To avoid
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this, use the ":" character, which will automatically be converted to ".". E.g.
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``{"my_file:txt": "contents of the file"}``.
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"""
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name: str = "MVL static"
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input_set_generator: VaspInputGenerator = field(
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default_factory=lambda: MVLGWSet(mode="STATIC")
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)
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@vasp_job
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def make(
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self,
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structure: Structure,
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prev_dir: str | Path | None = None,
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) -> Response:
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"""
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Run a static calculation compatible with later Materials Virtual Lab GW jobs.
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Parameters
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----------
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structure : .Structure
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A pymatgen structure object.
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prev_dir : str or Path or None
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A previous VASP calculation directory to copy output files from.
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"""
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return super().make.original(self, structure, prev_dir)
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@dataclass
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class MVLNonSCFMaker(BaseVaspMaker):
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"""
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Maker to create a non-scf calculation compatible with Materials Virtual Lab GW jobs.
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Parameters
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----------
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name : str
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The job name.
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input_set_generator : .VaspInputGenerator
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A generator used to make the input set.
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write_input_set_kwargs : dict
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Keyword arguments that will get passed to :obj:`.write_vasp_input_set`.
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copy_vasp_kwargs : dict
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Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`.
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run_vasp_kwargs : dict
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Keyword arguments that will get passed to :obj:`.run_vasp`.
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task_document_kwargs : dict
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Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`.
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stop_children_kwargs : dict
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Keyword arguments that will get passed to :obj:`.should_stop_children`.
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write_additional_data : dict
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Additional data to write to the current directory. Given as a dict of
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{filename: data}. Note that if using FireWorks, dictionary keys cannot contain
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the "." character which is typically used to denote file extensions. To avoid
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this, use the ":" character, which will automatically be converted to ".". E.g.
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``{"my_file:txt": "contents of the file"}``.
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"""
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name: str = "MVL nscf"
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input_set_generator: VaspInputGenerator = field(
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default_factory=lambda: MVLGWSet(mode="DIAG")
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)
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@vasp_job
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def make(
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self,
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structure: Structure,
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prev_dir: str | Path | None = None,
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) -> Response:
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"""
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Run a static calculation compatible with later Materials Virtual Lab GW jobs.
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Parameters
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----------
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structure : .Structure
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A pymatgen structure object.
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prev_dir : str or Path or None
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A previous VASP calculation directory to copy output files from.
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"""
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self.copy_vasp_kwargs.setdefault("additional_vasp_files", ("CHGCAR",))
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return super().make.original(self, structure, prev_dir)
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@dataclass
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class MVLGWMaker(BaseVaspMaker):
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"""
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Maker to create Materials Virtual Lab GW jobs.
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This class can make the jobs for the typical three stapes of the GW calculation.
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Parameters
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----------
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name : str
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The job name.
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input_set_generator : .VaspInputGenerator
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A generator used to make the input set.
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write_input_set_kwargs : dict
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Keyword arguments that will get passed to :obj:`.write_vasp_input_set`.
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copy_vasp_kwargs : dict
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Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`.
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run_vasp_kwargs : dict
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Keyword arguments that will get passed to :obj:`.run_vasp`.
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task_document_kwargs : dict
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Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`.
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stop_children_kwargs : dict
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Keyword arguments that will get passed to :obj:`.should_stop_children`.
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write_additional_data : dict
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Additional data to write to the current directory. Given as a dict of
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{filename: data}. Note that if using FireWorks, dictionary keys cannot contain
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the "." character which is typically used to denote file extensions. To avoid
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this, use the ":" character, which will automatically be converted to ".". E.g.
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``{"my_file:txt": "contents of the file"}``.
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"""
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name: str = "MVL G0W0"
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input_set_generator: VaspInputGenerator = field(
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default_factory=lambda: MVLGWSet(mode="GW")
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)
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@vasp_job
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def make(
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self,
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structure: Structure,
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prev_dir: str | Path | None = None,
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) -> Response:
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"""
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Run a Materials Virtual Lab GW band structure VASP job.
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Parameters
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----------
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structure : .Structure
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A pymatgen structure object.
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prev_dir : str or Path or None
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A previous VASP calculation directory to copy output files from.
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"""
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self.copy_vasp_kwargs.setdefault(
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"additional_vasp_files", ("CHGCAR", "WAVECAR", "WAVEDER")
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)
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return super().make.original(self, structure, prev_dir)

‎tests/test_data/vasp/Si_G0W0/MVL_G0W0/inputs/INCAR

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ALGO = Gw0
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ENCUTGW = 250
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ICHARG = 1
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ISMEAR = 0
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ISPIN = 1
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LORBIT = 11
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LREAL = Auto
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LWAVE = True
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NBANDS = 48
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NELM = 1
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NOMEGA = 80
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PREC = Accurate
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SIGMA = 0.01

‎tests/test_data/vasp/Si_G0W0/MVL_G0W0/inputs/KPOINTS

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pymatgen with grid density = 61 / number of atoms
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0
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Gamma
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3 3 3

‎tests/test_data/vasp/Si_G0W0/MVL_G0W0/inputs/POSCAR

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Si2
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1.0
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0.0000000000000000 2.7300000000000000 2.7300000000000000
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2.7300000000000000 0.0000000000000000 2.7300000000000000
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2.7300000000000000 2.7300000000000000 0.0000000000000000
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Si
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2
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direct
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0.0000000000000000 0.0000000000000000 0.0000000000000000 Si
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0.2500000000000000 0.2500000000000000 0.2500000000000000 Si

‎tests/test_data/vasp/Si_G0W0/MVL_G0W0/inputs/POTCAR.spec

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Si_GW

‎tests/test_data/vasp/Si_G0W0/MVL_G0W0/outputs/CONTCAR

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‎tests/test_data/vasp/Si_G0W0/MVL_G0W0/outputs/INCAR.gz

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‎tests/test_data/vasp/Si_G0W0/MVL_G0W0/outputs/INCAR.orig.gz

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