Initial attempt at MP workflows

src/atomate2/vasp/flows/mp.py

@@ -0,0 +1,12 @@
+"""
+Module defining flows for Materials Project r2SCAN workflows
+
+Reference: https://doi.org/10.1103/PhysRevMaterials.6.013801
+"""
+
+from __future__ import annotations
+
+from copy import deepcopy
+from dataclasses import dataclass, field
+
+from jobflow import Flow, Maker

src/atomate2/vasp/jobs/mp.py

@@ -0,0 +1,149 @@
+"""
+Module defining jobs for Materials Project r2SCAN workflows
+
+Reference: https://doi.org/10.1103/PhysRevMaterials.6.013801
+"""
+
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+from typing import TYPE_CHECKING
+
+import numpy as np
+from monty.serialization import loadfn
+from pkg_resources import resource_filename
+
+from atomate2.vasp.jobs.base import BaseVaspMaker
+from atomate2.vasp.sets.base import VaspInputGenerator
+from atomate2.vasp.sets.core import RelaxSetGenerator, StaticSetGenerator
+
+__all__ = ["MPPrelaxMaker", "MPRelaxMaker", "MPStaticMaker"]
+
+_BASE_MP_R2SCAN_RELAX_SET = loadfn(
+    resource_filename("atomate2.vasp.sets", "BaseMPr2SCANRelaxSet.yaml")
+)
+
+
+class MPRelaxR2SCANGenerator(VaspInputGenerator):
+    config_dict: dict = field(lambda: _BASE_MP_R2SCAN_RELAX_SET)
+
+
+@dataclass
+class MPPreRelaxMaker(BaseVaspMaker):
+    """
+    Maker to create VASP pre-relaxation job using PBEsol 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 = "MP-PreRelax"
+    input_set_generator: VaspInputGenerator = field(
+        default_factory=lambda: MPRelaxR2SCANGenerator(
+            {"user_incar_settings": {"EDIFFG": -0.05, "METAGGA": None, "GGA": "PS"}}
+        )
+    )
+
+
+@dataclass
+class MPRelaxMaker(BaseVaspMaker):
+    """
+    Maker to create VASP relaxation job using r2SCAN by default.
+
+    Parameters
+    ----------
+    name : str
+        The job name.
+    bandgap : float
+        The bandgap of the material in eV. Used to determine the k-point density.
+    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 = "MP-Relax"
+    bandgap: float = 0.0
+    input_set_generator: VaspInputGenerator = field(
+        default_factory=MPRelaxR2SCANGenerator
+    )
+
+    def __post_init__(self):
+        if self.bandgap < 1e-4:
+            kspacing = 0.22
+        else:
+            rmin = 25.22 - 2.87 * self.bandgap
+            kspacing = 2 * np.pi * 1.0265 / (rmin - 1.0183)
+
+        self.input_set_generator.config_dict["user_incar_settings"].update(
+            KSPACING=kspacing if 0.22 < kspacing < 0.44 else 0.44, ISMEAR=0.05, SIGMA=-5
+        )
+
+
+@dataclass
+class MPStaticMaker(MPRelaxMaker):
+    """
+    Maker to create VASP static job using r2SCAN by default.
+
+    Parameters
+    ----------
+    name : str
+        The job name.
+    bandgap : float
+        The bandgap of the material in eV. Used to determine the k-point density.
+    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 = "MP-Static"
+    input_set_generator: VaspInputGenerator = field(StaticSetGenerator)

src/atomate2/vasp/sets/BaseMPR2SCANRelaxSet.yaml

@@ -0,0 +1,160 @@
+# Default VASP settings for calculations in the Materials Project
+# using the Regularized-Restored Strongly Constrained and Appropriately
+# Normed functional (r2SCAN).
+INCAR:
+  ALGO: ALL
+  EDIFF: 1.e-05
+  EDIFFG: -0.02
+  ENAUG: 1360
+  ENCUT: 680
+  IBRION: 2
+  ISIF: 3
+  ISMEAR: 2
+  ISPIN: 2
+  KSPACING: 0.22
+  LAECHG: True # Output AECCAR
+  LASPH: True
+  LCHARG: True # Output CHGCAR
+  LELF: True # Output ELFCAR
+  LMIXTAU: True
+  LORBIT: 11
+  LREAL: Auto
+  LVTOT: True # Output LOCPOT
+  LWAVE: False # Don't output WAVECAR
+  METAGGA: R2SCAN
+  NELM: 200
+  NSW: 99
+  PREC: Accurate
+  SIGMA: 0.2
+  MAGMOM:
+    Ce: 5
+    Ce3+: 1
+    Co: 0.6
+    Co3+: 0.6
+    Co4+: 1
+    Cr: 5
+    Dy3+: 5
+    Er3+: 3
+    Eu: 10
+    Eu2+: 7
+    Eu3+: 6
+    Fe: 5
+    Gd3+: 7
+    Ho3+: 4
+    La3+: 0.6
+    Lu3+: 0.6
+    Mn: 5
+    Mn3+: 4
+    Mn4+: 3
+    Mo: 5
+    Nd3+: 3
+    Ni: 5
+    Pm3+: 4
+    Pr3+: 2
+    Sm3+: 5
+    Tb3+: 6
+    Tm3+: 2
+    V: 5
+    W: 5
+    Yb3+: 1
+POTCAR_FUNCTIONAL: PBE_54
+POTCAR:
+  Ac: Ac
+  Ag: Ag
+  Al: Al
+  Am: Am
+  Ar: Ar
+  As: As
+  At: At
+  Au: Au
+  B: B
+  Ba: Ba_sv
+  Be: Be_sv
+  Bi: Bi
+  Br: Br
+  C: C
+  Ca: Ca_sv
+  Cd: Cd
+  Ce: Ce
+  Cf: Cf
+  Cl: Cl
+  Cm: Cm
+  Co: Co
+  Cr: Cr_pv
+  Cs: Cs_sv
+  Cu: Cu_pv
+  Dy: Dy_3
+  Er: Er_3
+  Eu: Eu
+  F: F
+  Fe: Fe_pv
+  Fr: Fr_sv
+  Ga: Ga_d
+  Gd: Gd
+  Ge: Ge_d
+  H: H
+  He: He
+  Hf: Hf_pv
+  Hg: Hg
+  Ho: Ho_3
+  I: I
+  In: In_d
+  Ir: Ir
+  K: K_sv
+  Kr: Kr
+  La: La
+  Li: Li_sv
+  Lu: Lu_3
+  Mg: Mg_pv
+  Mn: Mn_pv
+  Mo: Mo_pv
+  N: N
+  Na: Na_pv
+  Nb: Nb_pv
+  Nd: Nd_3
+  Ne: Ne
+  Ni: Ni_pv
+  Np: Np
+  O: O
+  Os: Os_pv
+  P: P
+  Pa: Pa
+  Pb: Pb_d
+  Pd: Pd
+  Pm: Pm_3
+  Po: Po_d
+  Pr: Pr_3
+  Pt: Pt
+  Pu: Pu
+  Ra: Ra_sv
+  Rb: Rb_sv
+  Re: Re_pv
+  Rh: Rh_pv
+  Rn: Rn
+  Ru: Ru_pv
+  S: S
+  Sb: Sb
+  Sc: Sc_sv
+  Se: Se
+  Si: Si
+  Sm: Sm_3
+  Sn: Sn_d
+  Sr: Sr_sv
+  Ta: Ta_pv
+  Tb: Tb_3
+  Tc: Tc_pv
+  Te: Te
+  Th: Th
+  Ti: Ti_pv
+  Tl: Tl_d
+  Tm: Tm_3
+  U: U
+  V: V_pv
+  W: W_sv
+  Xe: Xe
+  Y: Y_sv
+  # 2023-05-02: change Yb_2 to Yb_3 as Yb_2 gives incorrect thermodynamics for most systems with Yb3+
+  # https://github.com/materialsproject/pymatgen/issues/2968
+  Yb: Yb_3
+  Zn: Zn
+  Zr: Zr_sv

src/atomate2/vasp/sets/BaseVaspSet.yaml

@@ -12,7 +12,7 @@ INCAR:
   ISMEAR: 0
   LORBIT: 11
   LASPH: True
-  LDAU: true
+  LDAU: True
   LDAUJ:
     F:
       Co: 0

src/atomate2/vasp/sets/MPMAGMOM.yaml

@@ -0,0 +1,32 @@
+INCAR:
+  MAGMOM:
+    Ce: 5
+    Ce3+: 1
+    Co: 0.6
+    Co3+: 0.6
+    Co4+: 1
+    Cr: 5
+    Dy3+: 5
+    Er3+: 3
+    Eu: 10
+    Eu2+: 7
+    Eu3+: 6
+    Fe: 5
+    Gd3+: 7
+    Ho3+: 4
+    La3+: 0.6
+    Lu3+: 0.6
+    Mn: 5
+    Mn3+: 4
+    Mn4+: 3
+    Mo: 5
+    Nd3+: 3
+    Ni: 5
+    Pm3+: 4
+    Pr3+: 2
+    Sm3+: 5
+    Tb3+: 6
+    Tm3+: 2
+    V: 5
+    W: 5
+    Yb3+: 1

src/atomate2/vasp/sets/core.py

@@ -46,6 +46,7 @@ def get_incar_updates(
         bandgap: float = None,
         vasprun: Vasprun = None,
         outcar: Outcar = None,
+        **kwargs: Any,
     ) -> dict:
         """
         Get updates to the INCAR for a relaxation job.
@@ -68,7 +69,7 @@ def get_incar_updates(
         dict
             A dictionary of updates to apply.
         """
-        return {"NSW": 99, "LCHARG": False, "ISIF": 3, "IBRION": 2}
+        return {"NSW": 99, "LCHARG": False, "ISIF": 3, "IBRION": 2, **kwargs}
 
 
 @dataclass