sisl.geom.PartialNeighborList

class sisl.geom.PartialNeighborList(geometry: Geometry, finder_results, atoms: ndarray, split_indices=None)

Bases: AtomsNeighborList

Neighbors list containing only the neighbors of some atoms.

Examples

You can get a partial neighbors list from the find_neighbors method of a NeighborFinder object if you pass the atoms argument. 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 a partial neighbors list
neighbors = finder.find_neighbors(atoms=[2, 4])

# You can loop through atoms to get their neighbors
# In this case, the loop will go through atoms 2 and 4
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].atom # This will be 2
neighbors[0].j

See also

AtomNeighborList

The object returned by this list when iterating or indexing.

Methods

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)

  • atoms (np.ndarray)

__init__(geometry: Geometry, finder_results, atoms: ndarray, split_indices=None)[source]
Parameters:
atoms: np.ndarray
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.