Add VASP input set MatPESStaticSet (#3254)

* add MatPESStaticSet to sets.py

* pre-commit auto-fixes

* add MatPESStaticSet type hints

* simplify to Incar(self.prev_incar or parent_incar)

prev:
incar = Incar(self.prev_incar) if self.prev_incar is not None else Incar(parent_incar)

* handle functional="PBE" with no U correctly

* fix MatPESStaticSet.incar() not returning anything

* add return type hint def incar(self) -> Incar:

same for def kpoint()

* change formats

* add pymatgen/io/vasp/PBE54Base.yaml

* add pymatgen/io/vasp/PBE54Base.yaml

* pre-commit auto-fixes

* change Normal=All for R2SCAN

* add PARENT to MatPESStaticSet PBE54Base

* add test for MatPESStaticSet, fix typo in sets.py

* remove setup() in TestMatPESStaticSet, remove unnecessary incar key checks

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Janosh Riebesell <[email protected]>
Co-authored-by: Shyue Ping Ong <[email protected]>

Author: 4 people

pymatgen/io/vasp/MatPESStaticSet.yaml

@@ -0,0 +1,26 @@
+# Default VASP settings for static calculations in the MatPES Project
+# using the Regularized-Restored Strongly Constrained and Appropriately
+# Normed functional (default PBE, PBE+U or R2SCAN or R2SCAN+U).
+PARENT: PBE54Base
+INCAR:
+  ALGO: Normal # Normal for PBE, ALL for R2SCAN, included to have some reasonable default
+  EDIFF: 1.e-05
+  ENAUG: 1360
+  ENCUT: 680
+  ISMEAR: 0 # change from 2 to 0, included to have some reasonable default
+  ISPIN: 2
+  KSPACING: 0.22 # included to have some reasonable default
+  LAECHG: True
+  LASPH: True
+  LCHARG: True
+  LELF: False # LELF = True restricts calculation to KPAR = 1
+  LMIXTAU: True
+  LORBIT: 11
+  LREAL: Auto
+  LVTOT: True
+  LWAVE: False
+  GGA: PE # change R2SCAN to PBE as default
+  NELM: 200
+  NSW: 0 # static calculation
+  PREC: Accurate
+  SIGMA: 0.05 # change from 0.02 to 0.05, included to have some reasonable default

pymatgen/io/vasp/PBE54Base.yaml

@@ -0,0 +1,103 @@
+# POTCARs for PBE_54
+PARENT: VASPIncarBase
+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

pymatgen/io/vasp/sets.py

@@ -1084,10 +1084,10 @@ def __init__(
         self.small_gap_multiply = small_gap_multiply
 
     @property
-    def incar(self):
+    def incar(self) -> Incar:
         """Incar"""
         parent_incar = super().incar
-        incar = Incar(self.prev_incar) if self.prev_incar is not None else Incar(parent_incar)
+        incar = Incar(self.prev_incar or parent_incar)
 
         incar.update(
             {
@@ -1215,6 +1215,43 @@ def from_prev_calc(cls, prev_calc_dir, **kwargs):
         return input_set.override_from_prev_calc(prev_calc_dir=prev_calc_dir)
 
 
+class MatPESStaticSet(MPStaticSet):
+    """Creates input files for a MatPES static calculation."""
+
+    CONFIG = _load_yaml_config("MatPESStaticSet")
+
+    def __init__(
+        self,
+        structure: str,
+        functional: Literal["R2SCAN", "R2SCAN+U", "PBE", "PBE+U"] = "PBE",
+        **kwargs: Any,
+    ) -> None:
+        """
+        Args:
+            structure (Structure): Structure from previous run.
+            functional ('R2SCAN' | 'R2SCAN+U' | 'PBE' | 'PBE+U'): Which functional to use and whether to include
+                Hubbard U corrections. Defaults to 'PBE'.
+            **kwargs: Passed to MPStaticSet.
+        """
+        super().__init__(structure, MatPESStaticSet.CONFIG, **kwargs)
+        if functional.startswith("R2SCAN"):
+            self.user_incar_settings.setdefault("METAGGA", "R2SCAN")
+            self.user_incar_settings.setdefault("ALGO", "ALL")
+        if functional.startswith("PBE"):
+            self.user_incar_settings.setdefault("GGA", "PE")
+        if functional.endswith("+U"):
+            self.user_incar_settings.setdefault("LDAU", True)
+
+        self.kwargs = kwargs
+        self.functional = functional
+
+    @property
+    def incar(self) -> Incar:
+        """Incar"""
+        parent_incar = super().incar
+        return Incar(self.prev_incar or parent_incar)
+
+
 class MPScanStaticSet(MPScanRelaxSet):
     """
     Creates input files for a static calculation using the accurate and numerically
@@ -1245,10 +1282,10 @@ def __init__(self, structure: Structure, bandgap=0, prev_incar=None, lepsilon=Fa
         self.lcalcpol = lcalcpol
 
     @property
-    def incar(self):
+    def incar(self) -> Incar:
         """Incar"""
         parent_incar = super().incar
-        incar = Incar(self.prev_incar) if self.prev_incar is not None else Incar(parent_incar)
+        incar = Incar(self.prev_incar or parent_incar)
 
         incar.update({"LREAL": False, "NSW": 0, "LORBIT": 11, "LVHAR": True, "ISMEAR": -5})
 
@@ -1892,7 +1929,7 @@ def __init__(
         super().__init__(structure, prev_incar=prev_incar, reciprocal_density=reciprocal_density, **kwargs)
 
     @property
-    def incar(self):
+    def incar(self) -> Incar:
         """Incar"""
         incar = super().incar
 
@@ -2037,18 +2074,18 @@ def __init__(
         self.ncores = ncores
 
     @property
-    def kpoints(self):
+    def kpoints(self) -> Kpoints:
         """
         Generate gamma center k-points mesh grid for GW calc,
         which is requested by GW calculation.
         """
         return Kpoints.automatic_density_by_vol(self.structure, self.reciprocal_density, force_gamma=True)
 
     @property
-    def incar(self):
+    def incar(self) -> Incar:
         """Incar"""
         parent_incar = super().incar
-        incar = Incar(self.prev_incar) if self.prev_incar is not None else Incar(parent_incar)
+        incar = Incar(self.prev_incar or parent_incar)
 
         if self.mode == "DIAG":
             # Default parameters for diagonalization calculation.
@@ -2303,7 +2340,7 @@ def kpoints(self):
         return kpt
 
     @property
-    def incar(self):
+    def incar(self) -> Incar:
         """Incar"""
         incar = super().incar
 
@@ -2531,7 +2568,7 @@ def __init__(self, structure: Structure, start_temp, end_temp, nsteps, time_step
         self._config_dict["INCAR"].update(defaults)
 
     @property
-    def kpoints(self):
+    def kpoints(self) -> Kpoints:
         """Kpoints"""
         return Kpoints.gamma_automatic()
 
@@ -2613,7 +2650,7 @@ def __init__(self, structure: Structure, start_temp, end_temp, nsteps, spin_pola
         self._config_dict["INCAR"].update(defaults)
 
     @property
-    def kpoints(self):
+    def kpoints(self) -> Kpoints:
         """Kpoints"""
         return Kpoints.gamma_automatic()
 
@@ -3106,15 +3143,15 @@ def __init__(
         self.kwargs = kwargs
 
     @property
-    def kpoints(self):
+    def kpoints(self) -> Kpoints:
         """
         Generate gamma center k-points mesh grid for optical calculation. It is not mandatory for 'ALGO = Exact',
         but is requested by 'ALGO = CHI' calculation.
         """
         return Kpoints.automatic_density_by_vol(self.structure, self.reciprocal_density, force_gamma=True)
 
     @property
-    def incar(self):
+    def incar(self) -> Incar:
         """Incar"""
         parent_incar = super().incar
         absorption_incar = {
@@ -3147,7 +3184,7 @@ def incar(self):
         elif self.mode == "RPA":
             # Default parameters for the response function calculation. NELM has to be set to 1.
             # NOMEGA is set to 1000 in order to get smooth spectrum
-            incar = Incar(self.prev_incar) if self.prev_incar is not None else Incar(parent_incar)
+            incar = Incar(self.prev_incar or parent_incar)
             incar.update({"ALGO": "CHI", "NELM": 1, "NOMEGA": 1000})
 
             if self.nkred is not None:

tests/io/vasp/test_sets.py

@@ -25,6 +25,7 @@
     BadInputSetWarning,
     DictSet,
     LobsterSet,
+    MatPESStaticSet,
     MITMDSet,
     MITNEBSet,
     MITRelaxSet,
@@ -47,6 +48,7 @@
     MVLScanRelaxSet,
     MVLSlabSet,
     VaspInputSet,
+    _load_yaml_config,
     batch_write_input,
     get_structure_from_prev_run,
     get_valid_magmom_struct,
@@ -743,6 +745,71 @@ def test_grid_size_from_struct(self):
             assert matched
 
 
+class TestMatPESStaticSet(PymatgenTest):
+    def test_init(self):
+        prev_run = f"{TEST_FILES_DIR}/relaxation"
+
+        vis = MatPESStaticSet.from_prev_calc(prev_calc_dir=prev_run)
+        # Check that INCAR settings were load from yaml, check the default functional is PBE.
+        CONFIG = _load_yaml_config("MatPESStaticSet")
+        assert vis.incar == CONFIG["INCAR"]
+        assert vis.kpoints.style == Kpoints.supported_modes.Monkhorst
+
+        # Check as from dict.
+        vis = MatPESStaticSet.from_dict(vis.as_dict())
+        # Check that INCAR settings were load from yaml.
+        assert vis.incar == CONFIG["INCAR"]
+
+        prev_run_scan = f"{TEST_FILES_DIR}/scan_relaxation"
+
+        vis_scan = MatPESStaticSet.from_prev_calc(prev_calc_dir=prev_run_scan, functional="R2SCAN")
+        # Check that INCAR settings were load from yaml, check the functional "R2SCAN".
+        assert vis_scan.incar["METAGGA"] == "R2SCAN"
+        assert vis_scan.incar["ALGO"] == "ALL"
+
+        # Check as from dict.
+        vis_scan = MatPESStaticSet.from_dict(vis_scan.as_dict())
+        # Check that INCAR settings were load from yaml.
+        assert vis_scan.incar["METAGGA"] == "R2SCAN"
+        assert vis_scan.incar["ALGO"] == "ALL"
+
+        # test with changed user_incar_settings
+        non_prev_vis = MatPESStaticSet(vis.structure, user_incar_settings={"ENCUT": 800, "LORBIT": 12, "LWAVE": True})
+        # Check that the ENCUT and Kpoints style has NOT been inherited.
+        assert non_prev_vis.incar["ENCUT"] == 800
+        # Check that user incar settings are applied.
+        assert non_prev_vis.incar["LORBIT"] == 12
+        assert non_prev_vis.incar["LWAVE"]
+
+        non_prev_vis = MatPESStaticSet.from_dict(non_prev_vis.as_dict())
+        assert non_prev_vis.incar["ENCUT"] == 800
+        # Check that user incar settings are applied.
+        assert non_prev_vis.incar["LORBIT"] == 12
+        assert non_prev_vis.incar["LWAVE"]
+
+        # test R2SCAN with changed user_incar_settings
+        non_prev_vis_scan = MatPESStaticSet(
+            vis_scan.structure, functional="R2SCAN", user_incar_settings={"ENCUT": 800, "LORBIT": 12, "LWAVE": True}
+        )
+        # Check functional has been changed to R2SCAN
+        assert vis_scan.incar["METAGGA"] == "R2SCAN"
+        assert vis_scan.incar["ALGO"] == "ALL"
+        # Check that the ENCUT and Kpoints style has NOT been inherited.
+        assert non_prev_vis_scan.incar["ENCUT"] == 800
+        # Check that user incar settings are applied.
+        assert non_prev_vis_scan.incar["LORBIT"] == 12
+        assert non_prev_vis_scan.incar["LWAVE"]
+
+        non_prev_vis_scan = MatPESStaticSet.from_dict(non_prev_vis_scan.as_dict())
+        # Check functional has been changed to R2SCAN
+        assert vis_scan.incar["METAGGA"] == "R2SCAN"
+        assert vis_scan.incar["ALGO"] == "ALL"
+        assert non_prev_vis_scan.incar["ENCUT"] == 800
+        # Check that user incar settings are applied.
+        assert non_prev_vis_scan.incar["LORBIT"] == 12
+        assert non_prev_vis_scan.incar["LWAVE"]
+
+
 class TestMPNonSCFSet(PymatgenTest):
     def setUp(self):
         self.set = MPNonSCFSet