Surface Binding Energy¶

SBETransformation ¶

SBETransformation(
    max_index: int = 1,
    min_slab_size: float = 10.0,
    min_vacuum_size: float = 10.0,
    height: float = 1.0,
    supercell_size: list[int] | None = None,
    isolated_atom_box_size: float = 20.0,
)

Generates slab, supercell, vacancy, and isolated-atom structures for SBE calculations.

apply_transformation is the sole public method. Exactly one of its structure, slab, supercell_slab, or element arguments should be given; which one selects the structure generated, since each is built from the previous step's (calculator-relaxed) output rather than from the original bulk structure.

Initializes the SBETransformation object.

Parameters:

Name	Type	Description	Default
`max_index`	`int`	Maximum Miller index to consider when generating slabs. Defaults to 1.	`1`
`min_slab_size`	`float`	Minimum slab thickness in Angstroms for slab generation. Defaults to 10.0.	`10.0`
`min_vacuum_size`	`float`	Minimum vacuum size in Angstroms for slab generation. Defaults to 10.0.	`10.0`
`height`	`float`	Height above the surface, in Angstroms, used to identify surface atoms via `pymatgen.analysis.adsorption.AdsorbateSiteFinder`. Defaults to 1.0.	`1.0`
`supercell_size`	`list[int] \| None`	Supercell replication factors applied to a slab termination before vacancy generation. Defaults to `[4, 4, 1]`.	`None`
`isolated_atom_box_size`	`float`	Side length, in Angstroms, of the cubic cell used to approximate a non-interacting isolated atom. Defaults to 20.0.	`20.0`

apply_transformation ¶

apply_transformation(
    structure: Structure | None = None,
    slab: Structure | None = None,
    supercell_slab: Structure | None = None,
    element: str | None = None,
) -> (
    list[Slab]
    | Structure
    | list[dict[str, int | str | Structure]]
)

Generates one of the SBE pipeline structures from exactly one of the given inputs.

Parameters:

Name	Type	Description	Default
`structure`	`Structure \| None`	The (relaxed) bulk structure to generate slab terminations from.	`None`
`slab`	`Structure \| None`	The slab termination, typically already relaxed, to replicate into a supercell.	`None`
`supercell_slab`	`Structure \| None`	The slab supercell to generate one single-atom vacancy structure from per identified surface site.	`None`
`element`	`str \| None`	The chemical symbol to build an isolated single-atom reference structure for.	`None`

Returns:

Type Description

list[Slab] | Structure | list[dict[str, int | str | Structure]]

list[Slab] | Structure | list[dict[str, int | str | Structure]]: Depending on which argument was given: - structure: The generated slab terminations, repaired to remove broken bonds at the surface. Each slab's miller_index attribute identifies which Miller index it belongs to. - slab: The replicated supercell, independent of slab. - supercell_slab: One entry per surface site, each a dictionary with keys site_index (the removed site's index in supercell_slab), element (its species string), and structure (a copy of supercell_slab with that site removed). - element: A single atom of element in a cubic cell of side self.isolated_atom_box_size Angstroms, large enough to make periodic-image interactions negligible.

Raises:

Type	Description
`ValueError`	If zero, or more than one, of `structure`, `slab`, `supercell_slab`, and `element` is given.