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slabs

Recipes for slabs.

bulk_to_slabs_flow 

bulk_to_slabs_flow(
    atoms: Atoms,
    make_slabs_kwargs: dict[str, Any] | None = None,
    run_static: bool = True,
    job_params: dict[str, dict[str, Any]] | None = None,
    job_decorators: (
        dict[str, Callable | None] | None
    ) = None,
) -> list[VaspSchema]

Workflow consisting of:

  1. Slab generation

  2. Slab relaxations

  3. Optional slab statics

Parameters:

  • atoms (Atoms) –

    Atoms object

  • make_slabs_kwargs (dict[str, Any] | None, default: None ) –

    Additional keyword arguments to pass to quacc.atoms.slabs.make_slabs_from_bulk

  • run_static (bool, default: True ) –

    Whether to run static calculations.

  • job_params (dict[str, dict[str, Any]] | None, default: None ) –

    Custom parameters to pass to each Job in the Flow. This is a dictionary where the keys are the names of the jobs and the values are dictionaries of parameters.

  • job_decorators (dict[str, Callable | None] | None, default: None ) –

    Custom decorators to apply to each Job in the Flow. This is a dictionary where the keys are the names of the jobs and the values are decorators.

Returns:

Source code in quacc/recipes/vasp/slabs.py 
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@flow
def bulk_to_slabs_flow(
    atoms: Atoms,
    make_slabs_kwargs: dict[str, Any] | None = None,
    run_static: bool = True,
    job_params: dict[str, dict[str, Any]] | None = None,
    job_decorators: dict[str, Callable | None] | None = None,
) -> list[VaspSchema]:
    """
    Workflow consisting of:

    1. Slab generation

    2. Slab relaxations
        - name: "relax_job"
        - job: [quacc.recipes.vasp.slabs.relax_job][]

    3. Optional slab statics
        - name: "static_job"
        - job: [quacc.recipes.vasp.slabs.static_job][]

    Parameters
    ----------
    atoms
        Atoms object
    make_slabs_kwargs
        Additional keyword arguments to pass to [quacc.atoms.slabs.make_slabs_from_bulk][]
    run_static
        Whether to run static calculations.
    job_params
        Custom parameters to pass to each Job in the Flow. This is a dictionary where
        the keys are the names of the jobs and the values are dictionaries of parameters.
    job_decorators
        Custom decorators to apply to each Job in the Flow. This is a dictionary where
        the keys are the names of the jobs and the values are decorators.

    Returns
    -------
    list[VaspSchema]
        List of dictionary results from [quacc.schemas.vasp.VaspSummarize.run][].
        See the type-hint for the data structure.
    """
    relax_job_, static_job_ = customize_funcs(
        ["relax_job", "static_job"],
        [relax_job, static_job],
        param_swaps=job_params,
        decorators=job_decorators,
    )

    return bulk_to_slabs_subflow(
        atoms,
        relax_job_,
        static_job=static_job_ if run_static else None,
        make_slabs_kwargs=make_slabs_kwargs,
    )

relax_job 

relax_job(
    atoms: Atoms,
    preset: str | None = "SlabSet",
    copy_files: (
        SourceDirectory
        | dict[SourceDirectory, Filenames]
        | None
    ) = None,
    additional_fields: dict[str, Any] | None = None,
    **calc_kwargs
) -> VaspSchema

Function to relax a slab.

Parameters:

  • atoms (Atoms) –

    Atoms object

  • preset (str | None, default: 'SlabSet' ) –

    Preset to use from quacc.calculators.vasp.presets.

  • copy_files (SourceDirectory | dict[SourceDirectory, Filenames] | None, default: None ) –

    Files to copy (and decompress) from source to the runtime directory.

  • additional_fields (dict[str, Any] | None, default: None ) –

    Additional fields to add to the results dictionary.

  • **calc_kwargs –

    Custom kwargs for the Vasp calculator. Set a value to None to remove a pre-existing key entirely. For a list of available keys, refer to quacc.calculators.vasp.vasp.Vasp.

Returns:

Source code in quacc/recipes/vasp/slabs.py 
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@job
def relax_job(
    atoms: Atoms,
    preset: str | None = "SlabSet",
    copy_files: SourceDirectory | dict[SourceDirectory, Filenames] | None = None,
    additional_fields: dict[str, Any] | None = None,
    **calc_kwargs,
) -> VaspSchema:
    """
    Function to relax a slab.

    Parameters
    ----------
    atoms
        Atoms object
    preset
        Preset to use from `quacc.calculators.vasp.presets`.
    copy_files
        Files to copy (and decompress) from source to the runtime directory.
    additional_fields
        Additional fields to add to the results dictionary.
    **calc_kwargs
        Custom kwargs for the Vasp calculator. Set a value to
        `None` to remove a pre-existing key entirely. For a list of available
        keys, refer to [quacc.calculators.vasp.vasp.Vasp][].

    Returns
    -------
    VaspSchema
        Dictionary of results from [quacc.schemas.vasp.VaspSummarize.run][].
        See the type-hint for the data structure.
    """
    calc_defaults = {
        "auto_dipole": True,
        "ediffg": -0.02,
        "isif": 2,
        "ibrion": 2,
        "isym": 0,
        "lcharg": False,
        "lwave": False,
        "nsw": 200,
        "symprec": 1e-8,
    }
    return run_and_summarize(
        atoms,
        preset=preset,
        calc_defaults=calc_defaults,
        calc_swaps=calc_kwargs,
        additional_fields={"name": "VASP Slab Relax"} | (additional_fields or {}),
        copy_files=copy_files,
    )

slab_to_ads_flow 

slab_to_ads_flow(
    slab: Atoms,
    adsorbate: Atoms,
    run_static: bool = True,
    make_ads_kwargs: dict[str, Any] | None = None,
    job_params: dict[str, dict[str, Any]] | None = None,
    job_decorators: (
        dict[str, Callable | None] | None
    ) = None,
) -> list[VaspSchema]

Workflow consisting of:

  1. Slab-adsorbate generation

  2. Slab-adsorbate relaxations

  3. Optional slab-adsorbate statics

Parameters:

  • slab (Atoms) –

    Atoms object for the slab structure.

  • adsorbate (Atoms) –

    Atoms object for the adsorbate.

  • run_static (bool, default: True ) –

    Whether to run static calculations.

  • make_ads_kwargs (dict[str, Any] | None, default: None ) –

    Additional keyword arguments to pass to quacc.atoms.slabs.make_adsorbate_structures

  • job_params (dict[str, dict[str, Any]] | None, default: None ) –

    Custom parameters to pass to each Job in the Flow. This is a dictionary where the keys are the names of the jobs and the values are dictionaries of parameters.

  • job_decorators (dict[str, Callable | None] | None, default: None ) –

    Custom decorators to apply to each Job in the Flow. This is a dictionary where the keys are the names of the jobs and the values are decorators.

Returns:

Source code in quacc/recipes/vasp/slabs.py 
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@flow
def slab_to_ads_flow(
    slab: Atoms,
    adsorbate: Atoms,
    run_static: bool = True,
    make_ads_kwargs: dict[str, Any] | None = None,
    job_params: dict[str, dict[str, Any]] | None = None,
    job_decorators: dict[str, Callable | None] | None = None,
) -> list[VaspSchema]:
    """
    Workflow consisting of:

    1. Slab-adsorbate generation

    2. Slab-adsorbate relaxations
        - name: "relax_job"
        - job: [quacc.recipes.vasp.slabs.relax_job][]

    3. Optional slab-adsorbate statics
        - name: "static_job"
        - job: [quacc.recipes.vasp.slabs.static_job][]

    Parameters
    ----------
    slab
        Atoms object for the slab structure.
    adsorbate
        Atoms object for the adsorbate.
    run_static
        Whether to run static calculations.
    make_ads_kwargs
        Additional keyword arguments to pass to [quacc.atoms.slabs.make_adsorbate_structures][]
    job_params
        Custom parameters to pass to each Job in the Flow. This is a dictionary where
        the keys are the names of the jobs and the values are dictionaries of parameters.
    job_decorators
        Custom decorators to apply to each Job in the Flow. This is a dictionary where
        the keys are the names of the jobs and the values are decorators.

    Returns
    -------
    list[VaspSchema]
        List of dictionaries of results from [quacc.schemas.vasp.VaspSummarize.run][].
        See the type-hint for the data structure.
    """
    relax_job_, static_job_ = customize_funcs(
        ["relax_job", "static_job"],
        [relax_job, static_job],
        param_swaps=job_params,
        decorators=job_decorators,
    )

    return slab_to_ads_subflow(
        slab,
        adsorbate,
        relax_job_,
        static_job=static_job_ if run_static else None,
        make_ads_kwargs=make_ads_kwargs,
    )

static_job 

static_job(
    atoms: Atoms,
    preset: str | None = "SlabSet",
    copy_files: (
        SourceDirectory
        | dict[SourceDirectory, Filenames]
        | None
    ) = None,
    additional_fields: dict[str, Any] | None = None,
    **calc_kwargs
) -> VaspSchema

Function to carry out a single-point calculation on a slab.

Parameters:

  • atoms (Atoms) –

    Atoms object

  • preset (str | None, default: 'SlabSet' ) –

    Preset to use from quacc.calculators.vasp.presets.

  • copy_files (SourceDirectory | dict[SourceDirectory, Filenames] | None, default: None ) –

    Files to copy (and decompress) from source to the runtime directory.

  • additional_fields (dict[str, Any] | None, default: None ) –

    Additional fields to add to the results dictionary.

  • **calc_kwargs –

    Custom kwargs for the Vasp calculator. Set a value to None to remove a pre-existing key entirely. For a list of available keys, refer to quacc.calculators.vasp.vasp.Vasp.

Returns:

Source code in quacc/recipes/vasp/slabs.py 
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@job
def static_job(
    atoms: Atoms,
    preset: str | None = "SlabSet",
    copy_files: SourceDirectory | dict[SourceDirectory, Filenames] | None = None,
    additional_fields: dict[str, Any] | None = None,
    **calc_kwargs,
) -> VaspSchema:
    """
    Function to carry out a single-point calculation on a slab.

    Parameters
    ----------
    atoms
        Atoms object
    preset
        Preset to use from `quacc.calculators.vasp.presets`.
    copy_files
        Files to copy (and decompress) from source to the runtime directory.
    additional_fields
        Additional fields to add to the results dictionary.
    **calc_kwargs
        Custom kwargs for the Vasp calculator. Set a value to
        `None` to remove a pre-existing key entirely. For a list of available
        keys, refer to [quacc.calculators.vasp.vasp.Vasp][].

    Returns
    -------
    VaspSchema
        Dictionary of results from [quacc.schemas.vasp.VaspSummarize.run][].
        See the type-hint for the data structure.
    """
    calc_defaults = {
        "auto_dipole": True,
        "ismear": -5,
        "laechg": True,
        "lcharg": True,
        "lreal": False,
        "lvhar": True,
        "lwave": True,
        "nedos": 3001,
        "nsw": 0,
    }
    return run_and_summarize(
        atoms,
        preset=preset,
        calc_defaults=calc_defaults,
        calc_swaps=calc_kwargs,
        additional_fields={"name": "VASP Slab Static"} | (additional_fields or {}),
        copy_files=copy_files,
    )