Merge pull request #634 from JaGeo/add_lobster_mp_workflow

Add lobster mp workflow

docs/user/codes/vasp.md

@@ -258,6 +258,13 @@ VASP_CMD: <<VASP_CMD>>
 LOBSTER_CMD: <<LOBSTER_CMD>>
 ```
 
+```{note}
+A LOBSTER workflow with settings compatible to LOBSTER database (Naik, A.A., et al. Sci Data 10, 610 (2023). https://doi.org/10.1038/s41597-023-02477-5 , currently being integrated into Materials Project) is also available now,
+which could be used by simply importing from atomate2.vasp.flows.mp > MPVaspLobsterMaker
+instead of VaspLobsterMaker. Rest of the things to execute the workflow stays same as
+shown below.
+```
+
 The corresponding flow could, for example, be started with the following code:
 
 ```py

src/atomate2/lobster/schemas.py

@@ -596,7 +596,7 @@ class StrongestBonds(BaseModel):
     )
 
 
-class LobsterTaskDocument(StructureMetadata):
+class LobsterTaskDocument(StructureMetadata, extra="allow"):  # type: ignore[call-arg]
     """Definition of LOBSTER task document."""
 
     structure: Structure = Field(description="The structure used in this task")
@@ -742,7 +742,7 @@ def from_directory(
         LobsterTaskDocument
             A task document for the lobster calculation.
         """
-        additional_fields = additional_fields or {}
+        additional_fields = {} if additional_fields is None else additional_fields
         dir_name = Path(dir_name)
 
         # Read in lobsterout and lobsterin

src/atomate2/vasp/flows/mp.py

@@ -13,20 +13,25 @@
 
 from jobflow import Flow, Maker
 
+from atomate2.lobster.jobs import LobsterMaker
 from atomate2.vasp.flows.core import DoubleRelaxMaker
+from atomate2.vasp.flows.lobster import VaspLobsterMaker
 from atomate2.vasp.jobs.mp import (
     MPGGARelaxMaker,
     MPGGAStaticMaker,
     MPMetaGGARelaxMaker,
     MPMetaGGAStaticMaker,
     MPPreRelaxMaker,
 )
+from atomate2.vasp.sets.mp import MPGGAStaticSetGenerator
 
 if TYPE_CHECKING:
     from pathlib import Path
 
     from pymatgen.core.structure import Structure
 
+    from atomate2.vasp.jobs.base import BaseVaspMaker
+
 
 @dataclass
 class MPGGADoubleRelaxMaker(DoubleRelaxMaker):
@@ -185,3 +190,71 @@ def make(self, structure: Structure, prev_dir: str | Path | None = None) -> Flow
             jobs += [static_job]
 
         return Flow(jobs=jobs, output=output, name=self.name)
+
+
+# update potcars to 54, use correct W potcar
+# use staticmaker for compatibility
+
+
+@dataclass
+class MPVaspLobsterMaker(VaspLobsterMaker):
+    """
+    Maker to perform a Lobster computation.
+
+    The calculations performed are:
+
+    1. Optional optimization.
+    2. Static calculation with ISYM=0.
+    3. Several Lobster computations testing several basis sets are performed.
+
+    .. Note::
+
+        The basis sets can only be changed with yaml files.
+
+    Parameters
+    ----------
+    name : str
+        Name of the flows produced by this maker.
+    relax_maker : .BaseVaspMaker or None
+        A maker to perform a relaxation on the bulk. Set to ``None`` to skip the
+        bulk relaxation.
+    lobster_static_maker : .BaseVaspMaker
+        A maker to perform the computation of the wavefunction before the static run.
+        Cannot be skipped. It can be LOBSTERUNIFORM or LobsterStaticMaker()
+    lobster_maker : .LobsterMaker
+        A maker to perform the Lobster run.
+    delete_wavecars : bool
+        If true, all WAVECARs will be deleted after the run.
+    address_min_basis : str
+        A path to a yaml file including basis set information.
+    address_max_basis : str
+       A path to a yaml file including basis set information.
+    """
+
+    name: str = "lobster"
+    relax_maker: BaseVaspMaker | None = field(
+        default_factory=lambda: MPGGADoubleRelaxMaker()
+    )
+    lobster_static_maker: BaseVaspMaker = field(
+        default_factory=lambda: MPGGAStaticMaker(
+            input_set_generator=MPGGAStaticSetGenerator(
+                user_potcar_functional="PBE_54",
+                user_potcar_settings={"W": "W_sv"},
+                user_kpoints_settings={"reciprocal_density": 310},
+                user_incar_settings={
+                    "EDIFF": 1e-6,
+                    "NSW": 0,
+                    "LWAVE": True,
+                    "ISYM": 0,
+                    "IBRION": -1,
+                    "ISMEAR": -5,
+                    "LORBIT": 11,
+                    "ALGO": "Normal",
+                },
+            )
+        )
+    )
+    lobster_maker: LobsterMaker | None = field(default_factory=lambda: LobsterMaker())
+    delete_wavecars: bool = True
+    address_min_basis: str | None = None
+    address_max_basis: str | None = None

tests/test_data/lobster/Fe_lobster/lobster_0/inputs/INCAR

@@ -0,0 +1,19 @@
+ALGO = Normal
+EDIFF = 1e-06
+ENCUT = 520
+IBRION = -1
+ISMEAR = -5
+ISPIN = 2
+ISYM = 0
+LASPH = True
+LCHARG = True
+LMAXMIX = 4
+LORBIT = 11
+LREAL = False
+LWAVE = True
+MAGMOM = 2*2.758
+NBANDS = 18
+NELM = 100
+NSW = 0
+PREC = Accurate
+SIGMA = 0.05

tests/test_data/lobster/Fe_lobster/lobster_0/inputs/lobsterin

@@ -0,0 +1,6 @@
+COHPstartEnergy -5.0
+COHPendEnergy 5.0
+basisSet pbeVaspFit2015
+cohpGenerator from 0.1 to 3.0 orbitalwise
+saveProjectionToFile
+basisfunctions Fe 3d 3p 4s

tests/test_data/lobster/Fe_lobster/lobster_0/outputs/POTCAR.spec

@@ -0,0 +1 @@
+Fe_pv

tests/test_data/vasp/Fe_lobster_mp/GGA_relax_1/inputs/INCAR

@@ -0,0 +1,18 @@
+ALGO = Fast
+EDIFF = 0.0001
+ENCUT = 520
+IBRION = 2
+ISIF = 3
+ISMEAR = -5
+ISPIN = 2
+LASPH = True
+LCHARG = False
+LMAXMIX = 4
+LORBIT = 11
+LREAL = Auto
+LWAVE = False
+MAGMOM = 2*2.758
+NELM = 100
+NSW = 99
+PREC = Accurate
+SIGMA = 0.05

tests/test_data/vasp/Fe_lobster_mp/GGA_relax_1/inputs/KPOINTS

@@ -0,0 +1,4 @@
+pymatgen with grid density = 211 / number of atoms
+0
+Gamma
+5 5 3

tests/test_data/vasp/Fe_lobster_mp/GGA_relax_1/inputs/POSCAR

@@ -0,0 +1,10 @@
+Fe2
+1.0
+   2.3361450900000000    0.0001116700000000   -0.8258229300000000
+  -1.1680779800000001    2.0230472399999999   -0.8260822000000000
+   1.1700738700000000    2.0273050000000001    3.3103279600000000
+Fe
+2
+direct
+   0.5000000200000000    0.5000000800000000    0.4999999900000000 Fe
+   0.9999999800000000    0.9999999200000000    0.0000000100000000 Fe

tests/test_data/vasp/Fe_lobster_mp/GGA_relax_1/inputs/POTCAR.spec

@@ -0,0 +1 @@
+Fe_pv

tests/test_data/vasp/Fe_lobster_mp/GGA_relax_1/outputs/POTCAR.spec

@@ -0,0 +1 @@
+Fe_pv

tests/test_data/vasp/Fe_lobster_mp/GGA_relax_2/inputs/INCAR

@@ -0,0 +1,18 @@
+ALGO = Fast
+EDIFF = 0.0001
+ENCUT = 520
+IBRION = 2
+ISIF = 3
+ISMEAR = -5
+ISPIN = 2
+LASPH = True
+LCHARG = False
+LMAXMIX = 4
+LORBIT = 11
+LREAL = Auto
+LWAVE = False
+MAGMOM = 1*2.106 1*2.107
+NELM = 100
+NSW = 99
+PREC = Accurate
+SIGMA = 0.05

tests/test_data/vasp/Fe_lobster_mp/GGA_relax_2/inputs/KPOINTS

@@ -0,0 +1,4 @@
+pymatgen with grid density = 220 / number of atoms
+0
+Gamma
+5 5 3

tests/test_data/vasp/Fe_lobster_mp/GGA_relax_2/inputs/POSCAR

@@ -0,0 +1,10 @@
+Fe2
+1.0
+   2.3247697431142709    0.0011158394059855   -0.8224083286119700
+  -1.1615226345878924    2.0137000999124477   -0.8226732920954348
+   1.1372826593766157    1.9704788611038830    3.2175225091681869
+Fe
+2
+direct
+   0.4999999975681003    0.5000000220874210    0.5000000028567035 Fe
+   0.0000000024318998    0.9999999779125790   -0.0000000028567036 Fe

tests/test_data/vasp/Fe_lobster_mp/GGA_relax_2/inputs/POTCAR.spec

@@ -0,0 +1 @@
+Fe_pv

tests/test_data/vasp/Fe_lobster_mp/GGA_relax_2/outputs/POTCAR.spec

@@ -0,0 +1 @@
+Fe_pv

tests/test_data/vasp/Fe_lobster_mp/GGA_static/inputs/INCAR

@@ -0,0 +1,19 @@
+ALGO = Normal
+EDIFF = 1e-06
+ENCUT = 520
+IBRION = -1
+ISMEAR = -5
+ISPIN = 2
+ISYM = 0
+LASPH = True
+LCHARG = True
+LMAXMIX = 4
+LORBIT = 11
+LREAL = False
+LWAVE = True
+MAGMOM = 2*2.105
+NBANDS = 18
+NELM = 100
+NSW = 0
+PREC = Accurate
+SIGMA = 0.05

tests/test_data/vasp/Fe_lobster_mp/GGA_static/inputs/KPOINTS

@@ -0,0 +1,4 @@
+pymatgen with grid density = 221 / number of atoms
+0
+Gamma
+5 5 3

tests/test_data/vasp/Fe_lobster_mp/GGA_static/inputs/POSCAR

@@ -0,0 +1,10 @@
+Fe2
+1.0
+   2.3191222174320663    0.0022375575036685   -0.8210990887096972
+  -1.1577271585521238    2.0093705129625041   -0.8213633337288552
+   1.1366928212633334    1.9694568925378289    3.2158537811988110
+Fe
+2
+direct
+   0.4999999975681035    0.5000000220874199    0.5000000028567015 Fe
+   0.0000000024318965    0.9999999779125801    0.9999999971432985 Fe

tests/test_data/vasp/Fe_lobster_mp/GGA_static/inputs/POTCAR.spec

@@ -0,0 +1 @@
+Fe_pv

tests/test_data/vasp/Fe_lobster_mp/GGA_static/outputs/POTCAR.spec

@@ -0,0 +1 @@
+Fe_pv

tests/vasp/lobster/flows/test_lobster.py

@@ -4,6 +4,7 @@
 from atomate2.lobster.jobs import LobsterMaker
 from atomate2.lobster.schemas import LobsterTaskDocument
 from atomate2.vasp.flows.lobster import VaspLobsterMaker
+from atomate2.vasp.flows.mp import MPVaspLobsterMaker
 from atomate2.vasp.jobs.lobster import LobsterStaticMaker
 from atomate2.vasp.powerups import update_user_incar_settings
 
@@ -246,3 +247,88 @@ def test_lobstermaker_delete(mock_vasp, mock_lobster, clean_dir, memory_jobstore
         .resolve(memory_jobstore),
         LobsterTaskDocument,
     )
+
+
+def test_mp_vasp_lobstermaker(
+    mock_vasp, mock_lobster, clean_dir, memory_jobstore, vasp_test_dir
+):
+    # mapping from job name to directory containing test files
+    ref_paths = {
+        "MP GGA relax 1": "Fe_lobster_mp/GGA_relax_1",
+        "MP GGA relax 2": "Fe_lobster_mp/GGA_relax_2",
+        "MP GGA static": "Fe_lobster_mp/GGA_static",
+    }
+
+    # settings passed to fake_run_vasp; adjust these to check for certain INCAR settings
+    fake_run_vasp_kwargs = {
+        "MP GGA relax 1": {
+            "incar_settings": ["NSW", "ISMEAR"],
+            "check_inputs": ["poscar", "potcar", "kpoints", "incar"],
+        },
+        "MP GGA relax 2": {
+            "incar_settings": ["NSW", "ISMEAR"],
+            "check_inputs": ["poscar", "potcar", "kpoints", "incar"],
+        },
+        "MP GGA static": {
+            "incar_settings": ["NSW", "LWAVE", "ISMEAR", "ISYM", "NBANDS", "ISPIN"],
+            "check_inputs": ["poscar", "potcar", "kpoints", "incar"],
+        },
+    }
+
+    ref_paths_lobster = {
+        "lobster_run_0": "Fe_lobster/lobster_0",
+        "delete_lobster_wavecar": "Fe_lobster/lobster_0",
+    }
+
+    # settings passed to fake_run_vasp; adjust these to check for certain INCAR settings
+    fake_run_lobster_kwargs = {
+        "lobster_run_0": {"lobsterin_settings": ["basisfunctions"]},
+    }
+
+    # automatically use fake VASP and write POTCAR.spec during the test
+    mock_vasp(ref_paths, fake_run_vasp_kwargs)
+    mock_lobster(ref_paths_lobster, fake_run_lobster_kwargs)
+
+    fe_structure = Structure(
+        lattice=[
+            [2.33614509e00, 1.11670000e-04, -8.25822930e-01],
+            [-1.16807798e00, 2.02304724e00, -8.26082200e-01],
+            [1.17007387e00, 2.02730500e00, 3.31032796e00],
+        ],
+        species=["Fe", "Fe"],
+        coords=[
+            [5.0000002e-01, 5.0000008e-01, 4.9999999e-01],
+            [9.9999998e-01, 9.9999992e-01, 1.0000000e-08],
+        ],
+    )
+
+    job = MPVaspLobsterMaker(
+        lobster_maker=LobsterMaker(
+            task_document_kwargs={
+                "calc_quality_kwargs": {"potcar_symbols": ["Fe_pv"], "n_bins": 10},
+                "save_computational_data_jsons": False,
+                "save_cba_jsons": False,
+            },
+            user_lobsterin_settings={
+                "COHPstartEnergy": -5.0,
+                "COHPEndEnergy": 5.0,
+                "cohpGenerator": "from 0.1 to 3.0 orbitalwise",
+            },
+        ),
+    ).make(fe_structure)
+
+    # run the flow or job and ensure that it finished running successfully
+    responses = run_locally(
+        job,
+        create_folders=True,
+        ensure_success=True,
+        store=memory_jobstore,
+    )
+
+    task_doc = (
+        responses[job.jobs[-2].uuid][1]
+        .replace.output["lobster_task_documents"][0]
+        .resolve(memory_jobstore)
+    )
+
+    assert isinstance(task_doc, LobsterTaskDocument)