sisl.geom.CoordsNeighborList

class sisl.geom.CoordsNeighborList

Bases: Neighbors

List of atoms that are close to a set of coordinates in space.

Examples

You can get a coordinates neighbors list from the find_close method of a NeighborFinder object. Then, you can retrieve the neighbors from it:

import sisl

# Build a graphene supercell with a vacancy
graphene = sisl.geom.graphene().tile(2, 0).tile(2, 1)
graphene = graphene.remove(2).translate2uc()

# Initialize a finder for neighbors that are within 1.5 Angstrom
finder = sisl.geom.NeighborFinder(graphene, R=1.5)

# Get the full neighbors list
coords = [[0, 0, 0], [2, 0, 0]]
neighbors = finder.find_close(coords)

# You can loop through coordinates to get their neighbors
for coord_neighs in neighbors:
    print()
    print(f"NEIGHBORS OF COORDINATE {coord_neighs.xyz} ({coord_neighs.n_neighbors} neighbors): ")
    print("J", coord_neighs.J)
    print("ISC", coord_neighs.isc)

# Or get the neighbors of a particular coordinate:
neighbors[0].J

See also

CoordNeighborList

The object returned by this list when iterating or indexing.

Attributes

I

For each neighbor pair (I, J), the first index.

J

For each neighbor pair (I, J), the second index.

i

Same as I, provided for backwards compatibility, may be deprecated later

isc

For each neighbor pair (I, J), the supercell indices of \(J\).

j

Same as J, provided for backwards compatibility, may be deprecated later

min_nsc

The minimum nsc for an auxiliary supercell to contain all neighbors in this object.

n_neighbors

Number of atoms that are close to each coordinate

split_indices

Indices to split the interactions of each atom.
property I: ndarray

For each neighbor pair (I, J), the first index.

property J: ndarray

For each neighbor pair (I, J), the second index.

property i: ndarray

Same as I, provided for backwards compatibility, may be deprecated later

property isc: ndarray

For each neighbor pair (I, J), the supercell indices of \(J\).

property j: ndarray

Same as J, provided for backwards compatibility, may be deprecated later

property min_nsc: ndarray

The minimum nsc for an auxiliary supercell to contain all neighbors in this object.

property n_neighbors: ndarray

Number of atoms that are close to each coordinate

property split_indices: ndarray

Indices to split the interactions of each atom.