sisl.geom.FullNeighborList

class sisl.geom.FullNeighborList(geometry: Geometry, finder_results: ndarray, split_indices: ndarray | None = None)

Bases: AtomsNeighborList

Full neighbors list of a system.

This class, contrary to UniqueNeighborList, (possibly) contains the two directions of an interaction between two given atoms. Notice that it is possible that there is a connection from atom i to atom j but not the other way around.

Examples

You can get a full neighbors list from the find_neighbors method of a NeighborFinder object. Then, you can retreive 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
neighbors = finder.find_neighbors()

# You can loop through atoms to get their neighbors
for at_neighs in neighbors:
    print()
    print(f"NEIGHBORS OF ATOM {at_neighs.atom} ({at_neighs.n_neighbors} neighbors): ")
    print("J", at_neighs.j)
    print("ISC", at_neighs.isc)

# Or get the neighbors of a particular atom:
neighbors[0].j

See also

AtomNeighborList

The object returned by this list when iterating or indexing.

Methods

to_unique()

Converts the full neighbors list to a unique neighbors list.

i

For each neighbor pair (i, j), the first index.

isc

For each neighbor pair (i, j), the supercell indices of j.

j

For each neighbor pair (i, j), the second index.

min_nsc

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

n_neighbors

Number of neighbors that each atom has.

split_indices

Indices to split the interactions of each atom.
Parameters:

  • geometry (Geometry)

  • finder_results (np.ndarray)

  • split_indices (Optional[np.ndarray])

__init__(geometry: Geometry, finder_results: ndarray, split_indices: ndarray | None = None)
Parameters:
property i: ndarray

For each neighbor pair (i, j), the first index.

property isc: ndarray

For each neighbor pair (i, j), the supercell indices of j.

property j: ndarray

For each neighbor pair (i, j), the second index.

property min_nsc: ndarray

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

property n_neighbors: ndarray

Number of neighbors that each atom has.

property split_indices: ndarray

Indices to split the interactions of each atom.

to_unique() → UniqueNeighborList[source]

Converts the full neighbors list to a unique neighbors list.

Return type:

UniqueNeighborList