Surface Binding Energy¶

SBEAnalyzer ¶

SBEAnalyzer(
    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,
    calculator: BaseCalculator | None = None,
    sbe_transformation: SBETransformation | None = None,
)

A class used to compute surface binding energies (SBE) for a bulk structure.

Initializes the SBEAnalyzer 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. Defaults to 1.0.	`1.0`
`supercell_size`	`list[int] \| None`	Supercell replication factors used when building the slab supercell for vacancy calculations. Defaults to `[4, 4, 1]`.	`None`
`calculator`	`BaseCalculator \| None`	The calculator used for energy calculations. Defaults to a lazily constructed default calculator.	`None`
`sbe_transformation`	`SBETransformation \| None`	The transformation object used to generate slabs, supercells, vacancy structures, and isolated-atom references. If not provided, a new instance is initialized from `max_index`, `min_slab_size`, `min_vacuum_size`, `height`, and `supercell_size`.	`None`

calculate ¶

calculate(
    structure: Structure | Atoms, is_relaxed: bool = False
) -> dict[str, Any]

Calculates the surface binding energy (SBE) for a given bulk structure.

Every energy/metadata collection below is a flat list of uniform dicts, joinable on miller_index/termination_index/site_index. Structure objects are kept out of these records and returned separately under structures, keyed the same way, so the main result stays small and easy to hand to e.g. pandas.DataFrame.

Parameters:

Name	Type	Description	Default
`structure`	`Structure \| Atoms`	The bulk structure to be analyzed.	required
`is_relaxed`	`bool`	Whether the input structure is already relaxed. Defaults to False.	`False`

Returns:

Type Description

dict[str, Any]

dict[str, Any]: A dictionary with the following keys: - bulk_energy_per_atom: The energy per atom of the (relaxed) bulk structure. - best_miller_index: The Miller index containing the single lowest-surface-energy termination. - best_surface_energy: That termination's surface_energy (the minimum across every entry in surface_energies). - surface_energies: One entry per screened slab termination (every Miller index up to max_index), each a dict with keys miller_index, termination_index, slab_area, slab_energy, and surface_energy. - isolated_atom_energies: A dict mapping each element symbol to its isolated-atom energy. - terminations: One entry per termination of best_miller_index, each a dict with keys miller_index, termination_index, supercell_slab_energy (E_s), and avg_surface_binding_energy_by_element (mean SBE per element for that termination alone). - vacancy_results: One entry per surface site of every termination of best_miller_index, each a dict with keys miller_index, termination_index, site_index, element, vacancy_energy (E_{s+v}), and surface_binding_energy. - avg_surface_binding_energy_by_element: Mean, across terminations, of each termination's per-element average SBE (each termination weighted equally, not each site). - avg_surface_binding_energy: Mean, across terminations and elements, of the per-termination per-element averages above. - structures: A dict with keys bulk_structure (the relaxed bulk Structure), slabs (parallel to surface_energies, each with slab and relaxed_slab), supercells (parallel to terminations, each with supercell_slab), and vacancies (parallel to vacancy_results, each with structure (unrelaxed) and relaxed_structure).

Raises:

Type	Description
`ValueError`	If the calculator does not implement the 'energy' property, or if no slabs were generated for the given structure and parameters.

sbe_transformation ¶

sbe_transformation() -> SBETransformation

Returns the transformation object used to generate slabs, supercells, and vacancy structures.

Returns:

Name	Type	Description
`SBETransformation`	`SBETransformation`	The transformation object used to generate structures.