Re-organizing VASP I/O code

.pre-commit-config.yaml

@@ -25,6 +25,7 @@ repos:
     rev: v1.11.1
     hooks:
       - id: mypy
+        entry: env MYPYPATH=src mypy
 
   - repo: https://github.com/codespell-project/codespell
     rev: v2.3.0

pyproject.toml

@@ -174,6 +174,7 @@ repair-wheel-command = "delocate-wheel --require-archs {delocate_archs} -w {dest
 [tool.ruff]
 target-version = "py39"
 line-length = 120
+output-format = "concise"
 
 [tool.ruff.lint]
 select = ["ALL"]

src/pymatgen/io/vasp/sets/__init__.py

@@ -0,0 +1,44 @@
+"""Re-export all VASP input sets, for more convenient imports and to maintain backwards compatible imports
+following the split up of sets.py into submodules in #3865.
+"""
+
+from __future__ import annotations
+
+from pymatgen.io.vasp.sets.base import (
+    MODULE_DIR,
+    BadInputSetWarning,
+    DictSet,
+    UserPotcarFunctional,
+    VaspInputGenerator,
+    VaspInputSet,
+    _load_yaml_config,
+    batch_write_input,
+    get_structure_from_prev_run,
+    get_valid_magmom_struct,
+)
+from pymatgen.io.vasp.sets.lobster import LobsterSet
+from pymatgen.io.vasp.sets.matpes import MatPESStaticSet
+from pymatgen.io.vasp.sets.mit import MITMDSet, MITNEBSet, MITRelaxSet
+from pymatgen.io.vasp.sets.mp import (
+    MPAbsorptionSet,
+    MPHSEBSSet,
+    MPHSERelaxSet,
+    MPMDSet,
+    MPMetalRelaxSet,
+    MPNMRSet,
+    MPNonSCFSet,
+    MPRelaxSet,
+    MPScanRelaxSet,
+    MPScanStaticSet,
+    MPSOCSet,
+    MPStaticSet,
+)
+from pymatgen.io.vasp.sets.mvl import (
+    MVLElasticSet,
+    MVLGBSet,
+    MVLGWSet,
+    MVLNPTMDSet,
+    MVLRelax52Set,
+    MVLScanRelaxSet,
+    MVLSlabSet,
+)

src/pymatgen/io/vasp/sets/lobster.py

@@ -0,0 +1,107 @@
+# ruff: noqa: PGH003
+
+from __future__ import annotations
+
+import warnings
+from dataclasses import dataclass
+from typing import TYPE_CHECKING
+
+from pymatgen.io.vasp.sets.base import UserPotcarFunctional, VaspInputSet
+from pymatgen.io.vasp.sets.mp import MPRelaxSet
+
+if TYPE_CHECKING:
+    from collections.abc import Sequence
+
+    from pymatgen.io.vasp.inputs import Kpoints
+
+
+@dataclass
+class LobsterSet(VaspInputSet):
+    """Input set to prepare VASP runs that can be digested by Lobster (See cohp.de).
+
+    Args:
+        structure (Structure): input structure.
+        isym (int): ISYM entry for INCAR, only isym=-1 and isym=0 are allowed
+        ismear (int): ISMEAR entry for INCAR, only ismear=-5 and ismear=0 are allowed
+        reciprocal_density (int): density of k-mesh by reciprocal volume
+        user_supplied_basis (dict): dict including basis functions for all elements in
+            structure, e.g. {"Fe": "3d 3p 4s", "O": "2s 2p"}; if not supplied, a
+            standard basis is used
+        address_basis_file (str): address to a file similar to
+            "BASIS_PBE_54_standard.yaml" in pymatgen.io.lobster.lobster_basis
+        user_potcar_settings (dict): dict including potcar settings for all elements in
+            structure, e.g. {"Fe": "Fe_pv", "O": "O"}; if not supplied, a standard basis
+            is used.
+        **kwargs: Other kwargs supported by VaspInputSet.
+    """
+
+    isym: int = 0
+    ismear: int = -5
+    reciprocal_density: int | None = None
+    address_basis_file: str | None = None
+    user_supplied_basis: dict | None = None
+
+    # newest potcars are preferred
+    # Choose PBE_54 unless the user specifies a different potcar_functional
+    user_potcar_functional: UserPotcarFunctional = "PBE_54"
+
+    CONFIG = MPRelaxSet.CONFIG
+    _valid_potcars: Sequence[str] | None = ("PBE_52", "PBE_54")
+
+    def __post_init__(self):
+        super().__post_init__()
+        warnings.warn("Make sure that all parameters are okay! This is a brand new implementation.")
+
+        if self.isym not in (-1, 0):
+            raise ValueError("Lobster cannot digest WAVEFUNCTIONS with symmetry. isym must be -1 or 0")
+        if self.ismear not in (-5, 0):
+            raise ValueError("Lobster usually works with ismear=-5 or ismear=0")
+
+        self._config_dict["POTCAR"]["W"] = "W_sv"
+
+    @property
+    def kpoints_updates(self) -> dict | Kpoints:
+        """Updates to the kpoints configuration for this calculation type."""
+        # test, if this is okay
+        return {"reciprocal_density": self.reciprocal_density or 310}
+
+    @property
+    def incar_updates(self) -> dict:
+        """Updates to the INCAR config for this calculation type."""
+        from pymatgen.io.lobster import Lobsterin
+
+        potcar_symbols = self.potcar_symbols
+
+        # predefined basis! Check if the basis is okay! (charge spilling and bandoverlaps!)
+        if self.user_supplied_basis is None and self.address_basis_file is None:
+            basis = Lobsterin.get_basis(structure=self.structure, potcar_symbols=potcar_symbols)  # type: ignore
+        elif self.address_basis_file is not None:
+            basis = Lobsterin.get_basis(
+                structure=self.structure,  # type: ignore
+                potcar_symbols=potcar_symbols,
+                address_basis_file=self.address_basis_file,
+            )
+        elif self.user_supplied_basis is not None:
+            # test if all elements from structure are in user_supplied_basis
+            for atom_type in self.structure.symbol_set:  # type: ignore
+                if atom_type not in self.user_supplied_basis:
+                    raise ValueError(f"There are no basis functions for the atom type {atom_type}")
+            basis = [f"{key} {value}" for key, value in self.user_supplied_basis.items()]
+        else:
+            basis = None
+
+        lobsterin = Lobsterin(settingsdict={"basisfunctions": basis})
+        nbands = lobsterin._get_nbands(structure=self.structure)  # type: ignore
+
+        return {
+            "EDIFF": 1e-6,
+            "NSW": 0,
+            "LWAVE": True,
+            "ISYM": self.isym,
+            "NBANDS": nbands,
+            "IBRION": -1,
+            "ISMEAR": self.ismear,
+            "LORBIT": 11,
+            "ICHARG": 0,
+            "ALGO": "Normal",
+        }

src/pymatgen/io/vasp/sets/matpes.py

@@ -0,0 +1,84 @@
+from __future__ import annotations
+
+import warnings
+from dataclasses import dataclass
+from typing import TYPE_CHECKING
+
+from pymatgen.io.vasp.sets.base import VaspInputSet, _load_yaml_config
+
+if TYPE_CHECKING:
+    from typing import Literal
+
+
+@dataclass
+class MatPESStaticSet(VaspInputSet):
+    """Create input files for a MatPES static calculation.
+
+    The goal of MatPES is to generate potential energy surface data. This is a distinctly different
+    from the objectives of the MP static calculations, which aims to obtain primarily accurate
+    energies and also electronic structure (DOS). For PES data, force accuracy (and to some extent,
+    stress accuracy) is of paramount importance.
+
+    The default POTCAR versions have been updated to PBE_54 from the old PBE set used in the
+    MPStaticSet. However, **U values** are still based on PBE. The implicit assumption here is that
+    the PBE_54 and PBE POTCARs are sufficiently similar that the U values fitted to the old PBE
+    functional still applies.
+
+    Args:
+        structure (Structure): The Structure to create inputs for. If None, the input
+            set is initialized without a Structure but one must be set separately before
+            the inputs are generated.
+        xc_functional ('R2SCAN'|'PBE'): Exchange-correlation functional to use. Defaults to 'PBE'.
+        **kwargs: Keywords supported by VaspInputSet.
+    """
+
+    xc_functional: Literal["R2SCAN", "PBE", "PBE+U"] = "PBE"
+    prev_incar: dict | str | None = None
+    # These are parameters that we will inherit from any previous INCAR supplied. They are mostly parameters related
+    # to symmetry and convergence set by Custodian when errors are encountered in a previous run. Given that our goal
+    # is to have a strictly homogeneous PES data, all other parameters (e.g., ISMEAR, ALGO, etc.) are not inherited.
+    inherit_incar: list[str] | bool = (  # type: ignore  # noqa: PGH003
+        "LPEAD",
+        "NGX",
+        "NGY",
+        "NGZ",
+        "SYMPREC",
+        "IMIX",
+        "LMAXMIX",
+        "KGAMMA",
+        "ISYM",
+        "NCORE",
+        "NPAR",
+        "NELMIN",
+        "IOPT",
+        "NBANDS",
+        "KPAR",
+        "AMIN",
+        "NELMDL",
+        "BMIX",
+        "AMIX_MAG",
+        "BMIX_MAG",
+    )
+    CONFIG = _load_yaml_config("MatPESStaticSet")
+
+    def __post_init__(self):
+        """Validate inputs."""
+        super().__post_init__()
+        valid_xc_functionals = ("R2SCAN", "PBE", "PBE+U")
+        if self.xc_functional.upper() not in valid_xc_functionals:
+            raise ValueError(
+                f"Unrecognized xc_functional='{self.xc_functional}'. "
+                f"Supported exchange-correlation functionals are {valid_xc_functionals}"
+            )
+
+        default_potcars = self.CONFIG["PARENT"].replace("PBE", "PBE_").replace("Base", "")  # PBE64Base -> PBE_64
+        self.user_potcar_functional = self.user_potcar_functional or default_potcars
+        if self.user_potcar_functional.upper() != default_potcars:
+            warnings.warn(
+                f"{self.user_potcar_functional=} is inconsistent with the recommended {default_potcars}.", UserWarning
+            )
+
+        if self.xc_functional.upper() == "R2SCAN":
+            self._config_dict["INCAR"].update({"METAGGA": "R2SCAN", "ALGO": "ALL", "GGA": None})
+        if self.xc_functional.upper().endswith("+U"):
+            self._config_dict["INCAR"]["LDAU"] = True