Molecular dynamics job

src/atomate2/vasp/jobs/core.py

@@ -21,6 +21,7 @@
     RelaxSetGenerator,
     StaticSetGenerator,
     TightRelaxSetGenerator,
+    MDSetGenerator,
 )
 
 logger = logging.getLogger(__name__)
@@ -36,6 +37,7 @@
     "TightRelaxMaker",
     "HSETightRelaxMaker",
     "TransmuterMaker",
+    "MDMaker",
 ]
 
 
@@ -529,6 +531,40 @@ def make(
         return super().make.original(self, structure, prev_vasp_dir)
 
 
+@dataclass
+class MDMaker(BaseVaspMaker):
+    """
+    Maker to create VASP molecular dynamics jobs.
+
+    Parameters
+    ----------
+    name : str
+        The job name.
+    input_set_generator : .VaspInputSetGenerator
+        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:`.TaskDocument.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"}``.
+    """
+
+    # TODO expose basic setting of INCAR parameters to user
+    name: str = "molecular dynamics"
+    input_set_generator: VaspInputSetGenerator = field(default_factory=MDSetGenerator)
+
+
 def _get_transformations(
     transformations: tuple[str, ...], params: tuple[dict, ...] | None
 ):

src/atomate2/vasp/sets/core.py

@@ -6,6 +6,7 @@
 
 import numpy as np
 from pymatgen.core import Structure
+from pymatgen.core.periodic_table import Element
 from pymatgen.io.vasp import Outcar, Vasprun
 
 from atomate2.common.schemas.math import Vector3D
@@ -21,6 +22,7 @@
     "HSEBSSetGenerator",
     "HSETightRelaxSetGenerator",
     "ElectronPhononSetGenerator",
+    "MDSetGenerator",
 ]
 
 
@@ -775,6 +777,86 @@ def get_kpoints_updates(
         return {"reciprocal_density": self.reciprocal_density}
 
 
+@dataclass
+class MDSetGenerator(VaspInputSetGenerator):
+    """Class to generate VASP molecular dynamics input sets."""
+
+    def get_incar_updates(
+        self,
+        structure: Structure,
+        prev_incar: dict = None,
+        bandgap: float = 0,
+        vasprun: Vasprun = None,
+        outcar: Outcar = None,
+    ) -> dict:
+        """
+        Get updates to the INCAR for a molecular dynamics job.
+
+        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.
+        """
+        # TODO is is copied and changed based on pymatgen.io.vasp.sets.MPMDSet,
+        #  dobule check and discuss with others
+        updates = {
+            # expect to be changed by user
+            "NSW": 1000,
+            "ISIF": 0,
+            "MDALGO": 0,
+            "SMASS": 0,
+            "TEBEG": 300,
+            "TEEND": 300,
+            "POTIM": 2,
+            # exepct to be fixed
+            "PREC": "Normal",
+            "IBRION": 0,
+            "LREAL": "Auto",
+            "NELM": 500,
+            "NELMIN": 4,
+            "ISYM": 0,
+            "NBLOCK": 1,
+            "KBLOCK": 100,
+            "LSCALU": False,
+            "LCHARG": False,
+            "LPLANE": False,
+            "LWAVE": True,
+            "LDAU": False,
+            # "ISMEAR": 0,
+            # "EDIFF_PER_ATOM": 0.00001, # TODO deprecated?
+            # "MAXMIX": 20,
+            # "BMIX": 1,
+            # "NSIM": 4,
+            # "ADDGRID": True,
+        }
+
+        # use VASP default ENCUT
+        update["ENCUT"] = None
+
+        if defaults["ISPIN"] == 1:
+            update["MAGMOM"] = None
+
+        # smaller steps for H containing structrue
+        if Element("H") in structure.species:
+            updates["POTIM"] = 0.5
+            # updates["NSW"] = defaults["NSW"] * 4  # TODO not a big deal
+
+        return updates
+
+
 def _get_nedos(vasprun: Optional[Vasprun], dedos: float):
     """Automatic setting of nedos using the energy range and the energy step."""
     if vasprun is None:

tests/test_data/vasp/Si_md/inputs/INCAR

@@ -0,0 +1,23 @@
+ALGO = Normal
+EDIFF = 1e-07
+EDIFFG = -0.001
+ENAUG = 1360.0
+IBRION = 0
+ISIF = 2
+ISMEAR = -5
+ISPIN = 2
+KSPACING = 0.2925287784072645
+LAECHG = False
+LASPH = True
+LCHARG = True
+LELF = True
+LMIXTAU = True
+LORBIT = 11
+LREAL = False
+LVTOT = True
+LWAVE = False
+MAGMOM = 2*-0.0
+NELM = 200
+NSW = 99
+PREC = Normal
+SIGMA = 0.05

tests/test_data/vasp/Si_md/inputs/KPOINTS

@@ -0,0 +1,4 @@
+pymatgen with grid density = 100 / number of atoms
+0
+Gamma
+3 3 3

tests/test_data/vasp/Si_md/inputs/POSCAR

@@ -0,0 +1,10 @@
+Si2
+1.0
+0.000000 2.752777 2.752777
+2.725110 0.000000 2.752777
+2.725110 2.752777 0.000000
+Si
+2
+direct
+0.750000 0.750000 0.750000 Si
+0.500000 0.500000 0.500000 Si

tests/test_data/vasp/Si_md/inputs/POTCAR.spec

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

tests/vasp/jobs/test_core.py

@@ -193,3 +193,29 @@ def test_transmuter(mock_vasp, clean_dir, si_structure):
     np.testing.assert_allclose(
         output1.structure.lattice.abc, [3.866974, 3.866975, 7.733949]
     )
+
+
+def test_md(mock_vasp, clean_dir, si_structure):
+    from jobflow import run_locally
+
+    from atomate2.vasp.jobs.core import MDMaker
+    from atomate2.vasp.schemas.task import TaskDocument
+
+    # mapping from job name to directory containing test files
+    ref_paths = {"molecular dynamics": "Si_md"}
+
+    # settings passed to fake_run_vasp; adjust these to check for certain INCAR settings
+    fake_run_vasp_kwargs = {"transmuter": {"incar_settings": ["ISMEAR", "NSW"]}}
+
+    # automatically use fake VASP and write POTCAR.spec during the test
+    mock_vasp(ref_paths, fake_run_vasp_kwargs)
+
+    # generate transmuter job
+    job = MDMaker(
+        transformations=["SupercellTransformation"],
+        transformation_params=[{"scaling_matrix": ((1, 0, 0), (0, 1, 0), (0, 0, 2))}],
+    ).make(si_structure)
+    job.maker.input_set_generator.user_incar_settings["KSPACING"] = 0.5
+
+    # run the job and ensure that it finished running successfully
+    responses = run_locally(job, create_folders=True, ensure_success=True)