Merge pull request #532 from materialsproject/matpes

Add MatPES GGA and r2SCAN static makers

.github/workflows/testing.yml

@@ -43,6 +43,13 @@ jobs:
           cache-dependency-path: pyproject.toml
 
       - name: Install dependencies
+        # ERROR: Cannot install atomate2 and atomate2[strict,tests]==0.0.1 because these package versions have conflicting dependencies.
+        # The conflict is caused by:
+        #   atomate2[strict,tests] 0.0.1 depends on pymatgen>=2023.10.4
+        #   atomate2[strict,tests] 0.0.1 depends on pymatgen==2023.10.4; extra == "strict"
+        # ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/topics/dependency-resolution/#dealing-with-dependency-conflicts
+        #   chgnet 0.2.1 depends on pymatgen>=2023.5.31
+        #   emmet-core 0.70.0 depends on pymatgen>=2023.10.11
         run: |
           python -m pip install --upgrade pip
           pip install .[strict,tests]

ADMIN.md

@@ -2,6 +2,7 @@
 
 Version releases on Pypi and GitHub are handled automatically through GitHub
 actions. The steps to push a new release are:
+
 1. Update `CHANGELOG.md` with a new version and release notes.
 2. Create a tagged Git commit with the above changes: `git tag v0.0.1`
 3. Push the commit and tags to GitHub using: `git push origin --tags`

pyproject.toml

@@ -28,7 +28,7 @@ dependencies = [
     "PyYAML",
     "click",
     "custodian>=2023.3.10",
-    "emmet-core>=0.70.0",
+    "emmet-core>=0.70.5",
     "jobflow>=0.1.11",
     "monty>=2023.9.25",
     "numpy",
@@ -66,7 +66,7 @@ strict = [
     "click==8.1.7",
     "custodian==2023.10.9",
     "dscribe==2.1.0",
-    "emmet-core==0.70.4",
+    "emmet-core==0.70.5",
     "jobflow==0.1.14",
     "lobsterpy==0.3.2",
     "matgl==0.8.3",

src/atomate2/vasp/flows/matpes.py

@@ -0,0 +1,67 @@
+"""
+Module defining MatPES flows.
+
+In case of questions, consult @janosh or @esoteric-ephemera. Makes PBE + r2SCAN
+cheaper than running both separately.
+"""
+
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+from typing import TYPE_CHECKING
+
+from jobflow import Flow, Maker
+
+from atomate2.vasp.jobs.matpes import MatPesGGAStaticMaker, MatPesMetaGGAStaticMaker
+
+if TYPE_CHECKING:
+    from pathlib import Path
+
+    from pymatgen.core import Structure
+
+
+@dataclass
+class MatPesGGAPlusMetaGGAStaticMaker(Maker):
+    """MatPES flow doing a GGA static followed by meta-GGA static.
+
+    Uses the GGA WAVECAR to speed up electronic convergence on the meta-GGA static.
+
+    Parameters
+    ----------
+    name : str
+        Name of the flows produced by this maker.
+    static1 : .BaseVaspMaker
+        Maker to generate the first VASP static.
+    static2 : .BaseVaspMaker
+        Maker to generate the second VASP static.
+    """
+
+    name: str = "MatPES GGA plus meta-GGA static"
+    static1: Maker | None = field(default_factory=MatPesGGAStaticMaker)
+    static2: Maker = field(
+        default_factory=lambda: MatPesMetaGGAStaticMaker(
+            # could copy CHGCAR from GGA to meta-GGA directory too but is redundant
+            # since VASP can reconstruct it from WAVECAR
+            copy_vasp_kwargs={"additional_vasp_files": ("WAVECAR",)}
+        )
+    )
+
+    def make(self, structure: Structure, prev_vasp_dir: str | Path | None = None):
+        """
+        Create a flow with two chained statics.
+
+        Parameters
+        ----------
+        structure : .Structure
+            A pymatgen structure object.
+        prev_vasp_dir : str or Path or None
+            A previous VASP calculation directory to copy output files from.
+
+        Returns
+        -------
+        Flow
+            A flow containing two statics.
+        """
+        static1 = self.static1.make(structure, prev_vasp_dir=prev_vasp_dir)
+        static2 = self.static2.make(structure, prev_vasp_dir=static1.output.dir_name)
+        return Flow([static1, static2], output=static2.output, name=self.name)

src/atomate2/vasp/flows/mp.py

@@ -1,5 +1,5 @@
 """
-Module defining flows for Materials Project workflows.
+Module defining Materials Project workflows.
 
 Reference: https://doi.org/10.1103/PhysRevMaterials.6.013801
 

src/atomate2/vasp/jobs/matpes.py

@@ -0,0 +1,91 @@
+"""
+Module defining MatPES job makers.
+
+In case of questions, contact @janosh or @shyuep.
+"""
+
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+from typing import TYPE_CHECKING
+
+from atomate2.vasp.jobs.base import BaseVaspMaker
+from atomate2.vasp.sets.matpes import (
+    MatPesGGAStaticSetGenerator,
+    MatPesMetaGGAStaticSetGenerator,
+)
+
+if TYPE_CHECKING:
+    from atomate2.vasp.sets.base import VaspInputGenerator
+
+
+@dataclass
+class MatPesGGAStaticMaker(BaseVaspMaker):
+    """
+    Maker to create VASP static job using r2SCAN by default.
+
+    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 = "MatPES GGA static"
+    input_set_generator: VaspInputGenerator = field(
+        default_factory=MatPesGGAStaticSetGenerator
+    )
+    inherit_incar: bool = False
+
+
+@dataclass
+class MatPesMetaGGAStaticMaker(BaseVaspMaker):
+    """
+    Maker to create VASP static job using r2SCAN by default.
+
+    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 = "MatPES meta-GGA static"
+    input_set_generator: VaspInputGenerator = field(
+        default_factory=MatPesMetaGGAStaticSetGenerator
+    )
+    inherit_incar: bool = False

src/atomate2/vasp/jobs/mp.py

@@ -1,5 +1,5 @@
 """
-Module defining jobs for Materials Project r2SCAN workflows.
+Module defining Materials Project job makers.
 
 Reference: https://doi.org/10.1103/PhysRevMaterials.6.013801
 
@@ -22,14 +22,6 @@
 if TYPE_CHECKING:
     from atomate2.vasp.sets.base import VaspInputGenerator
 
-__all__ = [
-    "MPGGARelaxMaker",
-    "MPGGAStaticMaker",
-    "MPPreRelaxMaker",
-    "MPMetaGGARelaxMaker",
-    "MPMetaGGAStaticMaker",
-]
-
 
 @dataclass
 class MPGGARelaxMaker(BaseVaspMaker):

src/atomate2/vasp/sets/matpes.py

@@ -0,0 +1,87 @@
+"""
+Module defining MatPES input set generators.
+
+In case of questions, contact @janosh or @shyuep.
+"""
+
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+from typing import TYPE_CHECKING
+
+from monty.serialization import loadfn
+from pkg_resources import resource_filename
+
+from atomate2.vasp.sets.core import StaticSetGenerator
+
+if TYPE_CHECKING:
+    from pymatgen.core import Structure
+    from pymatgen.io.vasp import Outcar, Vasprun
+
+
+# POTCAR section comes from PARENT but atomate2 does not support inheritance yet
+_BASE_MATPES_PBE_STATIC_SET_NO_POTCAR = loadfn(
+    resource_filename("pymatgen.io.vasp", "MatPESStaticSet.yaml")
+)
+_BASE_PBE54_SET = loadfn(resource_filename("pymatgen.io.vasp", "PBE54Base.yaml"))
+_BASE_MATPES_PBE_STATIC_SET = {
+    **_BASE_PBE54_SET,
+    **_BASE_MATPES_PBE_STATIC_SET_NO_POTCAR,
+}
+
+
+@dataclass
+class MatPesGGAStaticSetGenerator(StaticSetGenerator):
+    """Class to generate MP-compatible VASP GGA static input sets."""
+
+    config_dict: dict = field(default_factory=lambda: _BASE_MATPES_PBE_STATIC_SET)
+    auto_ismear: bool = False
+    auto_kspacing: bool = True
+    user_incar_settings: dict = field(
+        # ensure _set_kspacing doesn't override input set ISMEAR
+        default_factory=lambda: {"ISMEAR": 0, "SIGMA": 0.05}
+    )
+
+
+@dataclass
+class MatPesMetaGGAStaticSetGenerator(StaticSetGenerator):
+    """Class to generate MP-compatible VASP GGA static input sets."""
+
+    config_dict: dict = field(default_factory=lambda: _BASE_MATPES_PBE_STATIC_SET)
+    auto_ismear: bool = False
+    auto_kspacing: bool = True
+    user_incar_settings: dict = field(
+        # ensure _set_kspacing doesn't override input set ISMEAR
+        default_factory=lambda: {"ISMEAR": 0, "SIGMA": 0.05}
+    )
+
+    def get_incar_updates(
+        self,
+        structure: Structure,
+        prev_incar: dict = None,
+        bandgap: float = None,
+        vasprun: Vasprun = None,
+        outcar: Outcar = None,
+    ) -> dict:
+        """
+        Get updates to the INCAR for this calculation type.
+
+        Parameters
+        ----------
+        structure
+            A structure.
+        prev_incar
+            An incar from a previous calculation.
+        bandgap
+            The band gap.
+        vasprun
+            A vasprun from a previous calculation.
+        outcar
+            An outcar from a previous calculation.
+
+        Returns
+        -------
+        dict
+            A dictionary of updates to apply.
+        """
+        return {"METAGGA": "R2SCAN", "ALGO": "ALL", "GGA": None}  # unset GGA

src/atomate2/vasp/sets/mp.py

@@ -1,5 +1,5 @@
 """
-Module defining jobs for Materials Project r2SCAN workflows.
+Module defining Materials Project input set generators.
 
 Reference: https://doi.org/10.1103/PhysRevMaterials.6.013801
 

tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/inputs/INCAR

@@ -0,0 +1,20 @@
+ALGO = Normal
+EDIFF = 1e-05
+ENAUG = 1360
+ENCUT = 680
+GGA = Pe
+ISMEAR = 0
+ISPIN = 2
+KSPACING = 0.22
+LAECHG = True
+LASPH = True
+LCHARG = True
+LMAXMIX = 6
+LMIXTAU = True
+LORBIT = 11
+LREAL = False
+LWAVE = False
+NELM = 200
+NSW = 0
+PREC = Accurate
+SIGMA = 0.05

tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/inputs/POSCAR

@@ -0,0 +1,10 @@
+Si2
+1.0
+   3.3488982826904379    0.0000000000000000    1.9334873250000004
+   1.1162994275634794    3.1573715802591895    1.9334873250000004
+   0.0000000000000000    0.0000000000000000    3.8669746500000000
+Si
+2
+direct
+   0.2500000000000000    0.2500000000000000    0.2500000000000000 Si
+   0.0000000000000000    0.0000000000000000    0.0000000000000000 Si

tests/test_data/vasp/matpes_pbe_r2scan_flow/pbe_static/inputs/POTCAR.spec

@@ -0,0 +1 @@
+Si

tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/inputs/INCAR

@@ -0,0 +1,20 @@
+ALGO = All
+EDIFF = 1e-05
+ENAUG = 1360.0
+ENCUT = 680
+ISMEAR = 0
+ISPIN = 2
+KSPACING = 0.28754316109307704
+LAECHG = True
+LASPH = True
+LCHARG = True
+LMAXMIX = 6
+LMIXTAU = True
+LORBIT = 11
+LREAL = False
+LWAVE = False
+METAGGA = R2scan
+NELM = 200
+NSW = 0
+PREC = Accurate
+SIGMA = 0.05

tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/inputs/POSCAR

@@ -0,0 +1,10 @@
+Si2
+1.0
+   3.3488982826904379    0.0000000000000000    1.9334873250000004
+   1.1162994275634794    3.1573715802591895    1.9334873250000004
+   0.0000000000000000    0.0000000000000000    3.8669746500000000
+Si
+2
+direct
+   0.2500000000000000    0.2500000000000000    0.2500000000000000 Si
+   0.0000000000000000    0.0000000000000000    0.0000000000000000 Si

tests/test_data/vasp/matpes_pbe_r2scan_flow/r2scan_static/inputs/POTCAR.spec

@@ -0,0 +1 @@
+Si