Finding neighbors

sisl implements an algorithm to find neighbors in a geometry. It has two main properties:

It is very fast. It can compute all the neighbors for a system of 3 million atoms in around 6 seconds.

It scales linearly with the number of atoms in the system.

The algorithm is based on the partition of space into bins. This partition limits the search for neighbors of a certain atom only within the bins adjacent to the bin the atom is in.

Since the bins must be created only once, there is a NeighborFinder class which on initialization creates the bin grid. Once the finder is created, you can query it for neighbors as many times as you want. You can ask for all neighbors or only the neighbors of atoms that you are interested in.

NeighborFinder(geometry[, R, overlap, bin_size])	Fast and linear scaling finding of neighbors.
FullNeighborList(geometry, finder_results[, ...])	Full neighbors list of a system.
UniqueNeighborList(geometry, finder_results)	Full neighbors list of a system, but containing only the upper triangle of the adjacency matrix.
PartialNeighborList(geometry, ...[, ...])	Neighbors list containing only the neighbors of some atoms.
AtomNeighborList(geometry, finder_results, atom)	List of atoms that are close to a given atom.
PointsNeighborList(geometry, points, ...[, ...])	List of atoms that are close to a set of points in space.
PointNeighborList(geometry, point, ...)	List of atoms that are close to a point in space.

Neighbor lists

Once created, a neighbor finder can be queried to get the neighbors. It will return a neighbor list. Depending on which type of query you make to the neighbor finder, it will return a different type of neighbor list.

The following table summarizes the properties of each type of neighbor list:

Class	Neighbors for	i < j	Items
FullNeighborList	All atoms	No	AtomNeighborList
UniqueNeighborList	All atoms	Yes	N/A
PartialNeighborList	Selected atoms	No	AtomNeighborList
AtomNeighborList	One atom	No	N/A
PointsNeighborList	Points in space	No	PointNeighborList
PointNeighborList	One point in space	No	N/A

Where:

• i < j indicates whether the list only contains one direction of the interaction, i.e. by omitting the transposed interaction.

• Items indicates the type that you get when you iterate or index (e.g. neighbors[0]) the list.