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

Author: yanghan234

pyproject.toml

@@ -28,7 +28,7 @@ dependencies = [
     "PyYAML",
     "click",
     "custodian>=2024.4.18",
-    "emmet-core>=0.82.2",
+    "emmet-core>=0.84.3rc3",
     "jobflow>=0.1.11",
     "monty>=2024.7.30",
     "numpy",
@@ -98,7 +98,7 @@ strict = [
     "click==8.1.7",
     "custodian==2024.10.16",
     "dscribe==2.1.1",
-    "emmet-core==0.84.2",
+    "emmet-core==0.84.3rc3",
     "ijson==3.3.0",
     "jobflow==0.1.18",
     "lobsterpy==0.4.9",

src/atomate2/vasp/flows/mvl.py

@@ -0,0 +1,73 @@
+"""Materials Virtual Lab (MVL) VASP flows."""
+
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+from typing import TYPE_CHECKING
+
+from jobflow import Flow, Maker
+
+from atomate2.vasp.jobs.mvl import MVLGWMaker, MVLNonSCFMaker, MVLStaticMaker
+
+if TYPE_CHECKING:
+    from pathlib import Path
+
+    from pymatgen.core.structure import Structure
+
+    from atomate2.vasp.jobs.base import BaseVaspMaker
+
+
+@dataclass
+class MVLGWBandStructureMaker(Maker):
+    """
+    Maker to generate VASP band structures with Materials Virtual Lab GW setup.
+
+    .. warning::
+        This workflow is only compatible with the Materials Virtual Lab GW setup,
+        and it may require additional benchmarks. Please use with caution.
+
+    Parameters
+    ----------
+    name : str
+        Name of the flows produced by this maker.
+    gw_maker : .BaseVaspMaker
+        The maker to use for the GW calculation.
+    """
+
+    name: str = "MVL G0W0 band structure"
+    static_maker: BaseVaspMaker = field(default_factory=MVLStaticMaker)
+    nscf_maker: BaseVaspMaker = field(default_factory=MVLNonSCFMaker)
+    gw_maker: BaseVaspMaker = field(default_factory=MVLGWMaker)
+
+    def make(self, structure: Structure, prev_dir: str | Path | None = None) -> Flow:
+        """
+        Create a band structure flow.
+
+        Parameters
+        ----------
+        structure : Structure
+            A pymatgen structure object.
+        prev_dir : str or Path or None
+            A previous VASP calculation directory to copy output files from.
+
+        Returns
+        -------
+        Flow
+            A band structure flow.
+        """
+        static_job = self.static_maker.make(structure, prev_dir=prev_dir)
+        nscf_job = self.nscf_maker.make(
+            static_job.output.structure, prev_dir=static_job.output.dir_name
+        )
+        gw_job = self.gw_maker.make(
+            nscf_job.output.structure, prev_dir=nscf_job.output.dir_name
+        )
+        jobs = [static_job, nscf_job, gw_job]
+
+        outputs = {
+            "static": static_job.output,
+            "nscf": nscf_job.output,
+            "gw": gw_job.output,
+        }
+
+        return Flow(jobs, outputs, name=self.name)

src/atomate2/vasp/jobs/mvl.py

@@ -0,0 +1,189 @@
+"""Core jobs for running VASP calculations."""
+
+from __future__ import annotations
+
+import logging
+from dataclasses import dataclass, field
+from typing import TYPE_CHECKING
+
+from pymatgen.io.vasp.sets import MVLGWSet
+
+from atomate2.vasp.jobs.base import BaseVaspMaker, vasp_job
+
+if TYPE_CHECKING:
+    from pathlib import Path
+
+    from jobflow import Response
+    from pymatgen.core.structure import Structure
+
+    from atomate2.vasp.sets.base import VaspInputGenerator
+
+
+logger = logging.getLogger(__name__)
+
+
+@dataclass
+class MVLStaticMaker(BaseVaspMaker):
+    """
+    Maker to create a static calculation compatible with Materials Virtual Lab GW jobs.
+
+    Parameters
+    ----------
+    name : str
+        The job name.
+    input_set_generator : .VaspInputGenerator
+        A generator used to make the input set.
+    write_input_set_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.write_vasp_input_set`.
+    copy_vasp_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`.
+    run_vasp_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.run_vasp`.
+    task_document_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`.
+    stop_children_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.should_stop_children`.
+    write_additional_data : dict
+        Additional data to write to the current directory. Given as a dict of
+        {filename: data}. Note that if using FireWorks, dictionary keys cannot contain
+        the "." character which is typically used to denote file extensions. To avoid
+        this, use the ":" character, which will automatically be converted to ".". E.g.
+        ``{"my_file:txt": "contents of the file"}``.
+    """
+
+    name: str = "MVL static"
+    input_set_generator: VaspInputGenerator = field(
+        default_factory=lambda: MVLGWSet(mode="STATIC")
+    )
+
+    @vasp_job
+    def make(
+        self,
+        structure: Structure,
+        prev_dir: str | Path | None = None,
+    ) -> Response:
+        """
+        Run a static calculation compatible with later Materials Virtual Lab GW jobs.
+
+        Parameters
+        ----------
+        structure : .Structure
+            A pymatgen structure object.
+        prev_dir : str or Path or None
+            A previous VASP calculation directory to copy output files from.
+        """
+        return super().make.original(self, structure, prev_dir)
+
+
+@dataclass
+class MVLNonSCFMaker(BaseVaspMaker):
+    """
+    Maker to create a non-scf calculation compatible with Materials Virtual Lab GW jobs.
+
+    Parameters
+    ----------
+    name : str
+        The job name.
+    input_set_generator : .VaspInputGenerator
+        A generator used to make the input set.
+    write_input_set_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.write_vasp_input_set`.
+    copy_vasp_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`.
+    run_vasp_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.run_vasp`.
+    task_document_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`.
+    stop_children_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.should_stop_children`.
+    write_additional_data : dict
+        Additional data to write to the current directory. Given as a dict of
+        {filename: data}. Note that if using FireWorks, dictionary keys cannot contain
+        the "." character which is typically used to denote file extensions. To avoid
+        this, use the ":" character, which will automatically be converted to ".". E.g.
+        ``{"my_file:txt": "contents of the file"}``.
+    """
+
+    name: str = "MVL nscf"
+    input_set_generator: VaspInputGenerator = field(
+        default_factory=lambda: MVLGWSet(mode="DIAG")
+    )
+
+    @vasp_job
+    def make(
+        self,
+        structure: Structure,
+        prev_dir: str | Path | None = None,
+    ) -> Response:
+        """
+        Run a static calculation compatible with later Materials Virtual Lab GW jobs.
+
+        Parameters
+        ----------
+        structure : .Structure
+            A pymatgen structure object.
+        prev_dir : str or Path or None
+            A previous VASP calculation directory to copy output files from.
+        """
+        self.copy_vasp_kwargs.setdefault("additional_vasp_files", ("CHGCAR",))
+
+        return super().make.original(self, structure, prev_dir)
+
+
+@dataclass
+class MVLGWMaker(BaseVaspMaker):
+    """
+    Maker to create Materials Virtual Lab GW jobs.
+
+    This class can make the jobs for the typical three stapes of the GW calculation.
+
+    Parameters
+    ----------
+    name : str
+        The job name.
+    input_set_generator : .VaspInputGenerator
+        A generator used to make the input set.
+    write_input_set_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.write_vasp_input_set`.
+    copy_vasp_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.copy_vasp_outputs`.
+    run_vasp_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.run_vasp`.
+    task_document_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.TaskDoc.from_directory`.
+    stop_children_kwargs : dict
+        Keyword arguments that will get passed to :obj:`.should_stop_children`.
+    write_additional_data : dict
+        Additional data to write to the current directory. Given as a dict of
+        {filename: data}. Note that if using FireWorks, dictionary keys cannot contain
+        the "." character which is typically used to denote file extensions. To avoid
+        this, use the ":" character, which will automatically be converted to ".". E.g.
+        ``{"my_file:txt": "contents of the file"}``.
+    """
+
+    name: str = "MVL G0W0"
+    input_set_generator: VaspInputGenerator = field(
+        default_factory=lambda: MVLGWSet(mode="GW")
+    )
+
+    @vasp_job
+    def make(
+        self,
+        structure: Structure,
+        prev_dir: str | Path | None = None,
+    ) -> Response:
+        """
+        Run a Materials Virtual Lab GW band structure VASP job.
+
+        Parameters
+        ----------
+        structure : .Structure
+            A pymatgen structure object.
+        prev_dir : str or Path or None
+            A previous VASP calculation directory to copy output files from.
+        """
+        self.copy_vasp_kwargs.setdefault(
+            "additional_vasp_files", ("CHGCAR", "WAVECAR", "WAVEDER")
+        )
+
+        return super().make.original(self, structure, prev_dir)

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

@@ -0,0 +1,13 @@
+ALGO = Gw0
+ENCUTGW = 250
+ICHARG = 1
+ISMEAR = 0
+ISPIN = 1
+LORBIT = 11
+LREAL = Auto
+LWAVE = True
+NBANDS = 48
+NELM = 1
+NOMEGA = 80
+PREC = Accurate
+SIGMA = 0.01

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

@@ -0,0 +1,4 @@
+pymatgen with grid density = 61 / number of atoms
+0
+Gamma
+3 3 3

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

@@ -0,0 +1,10 @@
+Si2
+1.0
+   0.0000000000000000    2.7300000000000000    2.7300000000000000
+   2.7300000000000000    0.0000000000000000    2.7300000000000000
+   2.7300000000000000    2.7300000000000000    0.0000000000000000
+Si
+2
+direct
+   0.0000000000000000    0.0000000000000000    0.0000000000000000 Si
+   0.2500000000000000    0.2500000000000000    0.2500000000000000 Si

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

@@ -0,0 +1 @@
+Si_GW

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

@@ -0,0 +1 @@
+Si_GW

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

@@ -0,0 +1,14 @@
+ALGO = Exact
+EDIFF = 1e-08
+ICHARG = 1
+ISMEAR = 0
+ISPIN = 1
+LOPTICS = True
+LORBIT = 11
+LPEAD = True
+LREAL = Auto
+LWAVE = True
+NBANDS = 48
+NELM = 1
+PREC = Accurate
+SIGMA = 0.01

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

@@ -0,0 +1,4 @@
+pymatgen with grid density = 61 / number of atoms
+0
+Gamma
+3 3 3

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

@@ -0,0 +1,10 @@
+Si2
+1.0
+   0.0000000000000000    2.7300000000000000    2.7300000000000000
+   2.7300000000000000    0.0000000000000000    2.7300000000000000
+   2.7300000000000000    2.7300000000000000    0.0000000000000000
+Si
+2
+direct
+   0.0000000000000000    0.0000000000000000    0.0000000000000000 Si
+   0.2500000000000000    0.2500000000000000    0.2500000000000000 Si

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

@@ -0,0 +1 @@
+Si_GW

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

@@ -0,0 +1 @@
+Si_GW

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

@@ -0,0 +1,11 @@
+ALGO = Normal
+EDIFF = 1e-08
+ICHARG = 1
+ISMEAR = 0
+ISPIN = 1
+LORBIT = 11
+LREAL = Auto
+LWAVE = True
+NELM = 100
+PREC = Accurate
+SIGMA = 0.01

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

@@ -0,0 +1,4 @@
+pymatgen with grid density = 61 / number of atoms
+0
+Gamma
+3 3 3

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

@@ -0,0 +1,10 @@
+Si2
+1.0
+   0.0000000000000000    2.7300000000000000    2.7300000000000000
+   2.7300000000000000    0.0000000000000000    2.7300000000000000
+   2.7300000000000000    2.7300000000000000    0.0000000000000000
+Si
+2
+direct
+   0.0000000000000000    0.0000000000000000    0.0000000000000000 Si
+   0.2500000000000000    0.2500000000000000    0.2500000000000000 Si

tests/test_data/vasp/Si_G0W0/MVL_G0W0/outputs/custodian.json.gz

@@ -0,0 +1 @@
+Si_GW

tests/test_data/vasp/Si_G0W0/MVL_G0W0/outputs/vasprun.xml.gz

@@ -0,0 +1 @@
+Si_GW