Including VASP surface adsorption flow (#691)

* [WIP] adding surface adsorption calculation flow * [WIP] adding surface adsorption calculation flow * [WIP] adding surface adsorption calculation flow * [WIP] adding surface adsorption calculation flow * [WIP] adding surface adsorption calculation flow * [WIP] adding surface adsorption calculation flow * [WIP] adding surface adsorption calculation flow * [wip] implementing more of jobs and flow in surface adsorption function * [wip] implementing more of jobs and flow in surface adsorption function * [wip] implementing more of jobs and flow in surface adsorption function * [wip] implementing more of jobs and flow in surface adsorption function * [wip] implementing more of jobs and flow in surface adsorption function * [wip] implementing more of jobs and flow in surface adsorption function * [wip] implementing more of jobs and flow in surface adsorption function * [wip] implementing more of jobs and flow in surface adsorption function * [wip] implementing more of jobs and flow in surface adsorption function * temp test on push * fix adsorption in flows and jobs * add document in adsorption of jobs and flows * check format * [wip] implementing test for adsorption workflow * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] bug fixing * [wip] updating VASP database * fixes to the input structures 1. using the DFT relaxed structures for molecule & bulk slab instead of raw MP structures. * Using a Molecule object instead of a Structure object for molecule_structure * Add files via upload * Delete tests/test_data/vasp/Au_adsorption/ads_relax_1_3/inputs directory * Delete tests/test_data/vasp/Au_adsorption/ads_relax_2_3/inputs directory * Delete tests/test_data/vasp/Au_adsorption/ads_relax_3_3/inputs directory * Delete tests/test_data/vasp/Au_adsorption/bulk directory * Delete tests/test_data/vasp/Au_adsorption/mol directory * Add files via upload * Add files via upload * [wip] updating the test file * [wip] updating the test file * [wip] updating the test file * [wip] updating the test file * [wip] updating the test file * [wip] updating the test file * [wip] updating the test file * [wip] updating the test file * [wip] updating the test file * [wip] updating the test file * [wip] updating the test file * [wip] updating the test file * [wip] updating the test file * [wip] updating the test_adsorption file * [wip] updating the test_adsorption file * [wip] updating the test_adsorption file * [wip] updating the test_adsorption file * fixing K point mesh * fixing K point mesh * fixing K point mesh * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * fixing K point mesh * fixing K point mesh * fixing K point mesh * fixing K point mesh * fixing K point mesh * fixing K point mesh * fixing K point mesh * fixing K point mesh * fixing k points and creating a schema * fixing k points and creating a schema * creating a schema * creating a schema * creating a schema --------- Co-authored-by: Xin_Chen <[email protected]> Co-authored-by: Xin Chen <[email protected]> Co-authored-by: Hrushikesh Sahasrabuddhe <[email protected]>
materialsproject · Sep 24, 2024 · 2513903 · 2513903
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diff --git a/src/atomate2/vasp/flows/adsorption.py b/src/atomate2/vasp/flows/adsorption.py
@@ -0,0 +1,191 @@
+"""Flow for calculating surface adsorption energies."""
+
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+from typing import TYPE_CHECKING
+
+from jobflow import Flow, Job, Maker
+
+from atomate2.vasp.jobs.adsorption import (
+    BulkRelaxMaker,
+    MolRelaxMaker,
+    MolStaticMaker,
+    SlabRelaxMaker,
+    SlabStaticMaker,
+    adsorption_calculations,
+    generate_adslabs,
+    generate_slab,
+    run_adslabs_job,
+)
+
+if TYPE_CHECKING:
+    from pathlib import Path
+
+    from pymatgen.core.structure import Molecule, Structure
+
+
+@dataclass
+class AdsorptionMaker(Maker):
+    """
+    Workflow that calculates the adsorption energy of a molecule on a surface.
+
+    The flow consists of the following steps:
+    1. Optimize the molecule structure and calculate its static energy.
+    2. Optimize the bulk structure.
+    3. Generate a slab structure using the optimized bulk structure and calculate its static energy.
+    4. Generate adsorption sites on the slab and calculate corresponding static energy.
+    5. Calculate the adsorption energy by calculating the energy difference between the slab with
+    adsorbed molecule and the sum of the slab without the adsorbed molecule and the molecule.
+
+    Parameters
+    ----------
+    name: str
+        Name of the flow.
+    bulk_relax_maker: BaseVaspMaker
+        Maker for bulk relaxation.
+    mol_relax_maker: BaseVaspMaker
+        Maker for molecule relaxation.
+    slab_relax_maker: BaseVaspMaker
+        Maker for slab relaxation with adsorption.
+    slab_static_maker: BaseVaspMaker
+        Maker for slab static energy calculation.
+    mol_static_maker: BaseVaspMaker
+        Maker for molecule static energy calculation.
+    min_vacuum: float
+        The minimum size of the vacuum region. In Angstroms or number of hkl planes.
+    min_slab_size: float
+        The minimum size of layers of the slab. In Angstroms or number of hkl planes.
+    min_lw: float
+        Minimum length and width of the slab
+    surface_idx: tuple
+        Miller index [h, k, l] of plane parallel to surface.
+    """  # noqa: E501
+
+    name: str = "adsorption workflow"
+    mol_relax_maker: Maker | None = field(default_factory=MolRelaxMaker)
+    mol_static_maker: Maker | None = field(default_factory=MolStaticMaker)
+    bulk_relax_maker: Maker | None = field(default_factory=BulkRelaxMaker)
+    slab_relax_maker: Maker | None = field(default_factory=SlabRelaxMaker)
+    slab_static_maker: Maker | None = field(default_factory=SlabStaticMaker)
+    min_vacuum: float = 20.0
+    min_slab_size: float = 10.0
+    min_lw: float = 10.0
+    surface_idx: tuple[int, int, int] = (0, 0, 1)
+
+    def make(
+        self,
+        molecule: Molecule,
+        structure: Structure,
+        prev_dir_mol: str | Path | None = None,
+        prev_dir_bulk: str | Path | None = None,
+    ) -> Flow:
+        """
+        Generate a flow for calculating adsorption energies.
+
+        Parameters
+        ----------
+        molecule: Molecule
+            A pymatgen molecule object. The molecule to be adsorbed.
+        structure: Structure
+            A pymatgen structure object. The bulk structure to be used for slab generation.
+        prev_dir_mol: str or Path or None
+            A previous VASP calculation directory to copy output files from.
+        prev_dir_bulk: str or Path or None
+            A previous VASP calculation directory to copy output files from.
+
+        Returns
+        -------
+        Flow
+            A flow object for calculating adsorption energies.
+        """  # noqa: E501
+        molecule_structure = molecule.get_boxed_structure(10, 10, 10)
+
+        jobs: list[Job] = []
+
+        if self.mol_relax_maker:
+            mol_optimize_job = self.mol_relax_maker.make(
+                molecule_structure, prev_dir=prev_dir_mol
+            )
+            mol_optimize_job.append_name("mol_relax_job")
+            jobs += [mol_optimize_job]
+
+        mol_static_job = self.mol_static_maker.make(
+            mol_optimize_job.output.structure, prev_dir=prev_dir_mol
+        )  # updated
+        mol_static_job.append_name("mol_static_job")
+        jobs += [mol_static_job]
+
+        molecule_dft_energy = mol_static_job.output.output.energy
+
+        if self.bulk_relax_maker:
+            bulk_optimize_job = self.bulk_relax_maker.make(
+                structure, prev_dir=prev_dir_bulk
+            )
+            bulk_optimize_job.append_name("bulk_relax_job")
+            jobs += [bulk_optimize_job]
+
+            optimized_bulk = bulk_optimize_job.output.structure
+
+        else:
+            optimized_bulk = structure
+
+        generate_slab_structure = generate_slab(
+            bulk_structure=optimized_bulk,
+            min_slab_size=self.min_slab_size,
+            surface_idx=self.surface_idx,
+            min_vacuum_size=self.min_vacuum,
+            min_lw=self.min_lw,
+        )
+
+        jobs += [generate_slab_structure]
+        slab_structure = generate_slab_structure.output
+
+        generate_adslabs_structures = generate_adslabs(
+            bulk_structure=optimized_bulk,
+            molecule_structure=molecule,
+            min_slab_size=self.min_slab_size,
+            surface_idx=self.surface_idx,
+            min_vacuum_size=self.min_vacuum,
+            min_lw=self.min_lw,
+        )
+        jobs += [generate_adslabs_structures]
+        adslab_structures = generate_adslabs_structures.output
+
+        # slab relaxation without adsorption
+        slab_optimize_job = self.slab_relax_maker.make(slab_structure, prev_dir=None)
+        slab_optimize_job.append_name("slab_relax_job")
+        jobs += [slab_optimize_job]
+
+        optimized_slab = slab_optimize_job.output.structure
+        prev_dir_slab = slab_optimize_job.output.dir_name
+
+        slab_static_job = self.slab_static_maker.make(
+            optimized_slab, prev_dir=prev_dir_slab
+        )
+        slab_static_job.append_name("slab_static_job")
+        jobs += [slab_static_job]
+
+        slab_dft_energy = slab_static_job.output.output.energy
+
+        run_ads_calculation = run_adslabs_job(
+            adslab_structures=adslab_structures,
+            relax_maker=self.slab_relax_maker,
+            static_maker=self.slab_static_maker,
+        )
+        jobs += [run_ads_calculation]
+        ads_outputs = run_ads_calculation.output
+
+        adsorption_calc = adsorption_calculations(
+            adslab_structures=adslab_structures,
+            adslabs_data=ads_outputs,
+            molecule_dft_energy=molecule_dft_energy,
+            slab_dft_energy=slab_dft_energy,
+        )
+        jobs += [adsorption_calc]
+
+        return Flow(
+            jobs=jobs,
+            output=adsorption_calc.output,
+            name=self.name,
+        )