saturate

sisl.geom.saturate(geometry, rules)

Saturate missing bonds of atoms with other atoms

Each rule is a pair (selector, saturation). An atom gets the saturation of the first rule that selects it. All rules use the input geometry, thus the added atoms do not change the selection of other rules.

Parameters:

geometry (Geometry) – the geometry to saturate
rules (Sequence[tuple[SelectorLike, SaturateLike]]) – pairs of (selector, saturation). A selector is a category, a dict for AtomCategory, or atomic indices. A saturation is a Saturate, or an atom ("H" equals Saturate("H")).

Returns:

the input geometry with the added atoms at the end, in the order of the rules

Return type:

Geometry

Examples

Saturate the edges of a zigzag nanoribbon with hydrogen:

>>> ribbon = sisl.geom.zgnr(4)
>>> edge = AtomNeighbors(max=2, R=1.5)
>>> saturated = saturate(ribbon, [(edge, Saturate("H", bond=1.09, R=1.5))])
>>> saturated.na - ribbon.na
2

The first rule that selects an atom is used:

>>> rules = [
...     (edge & AtomOdd(), Saturate("F", bond=1.35, R=1.5)),
...     (edge, Saturate("H", bond=1.09, R=1.5)),
... ]
>>> saturate(ribbon, rules).atoms.Z[ribbon.na:].tolist()
[9, 1]