NeighborList

class atomman.NeighborList(**kwargs)

Class that finds and stores the neighbor atoms for a system.

build(system, cutoff: float, initialsize: int = 20, deltasize: int = 10)

Builds the neighbor list for a system.

Parameters:

system (atomman.System) – The system to calculate the neighbor list for.
cutoff (float) – Radial cutoff distance for identifying neighbors.
initialsize (int, optional) – The number of neighbor positions to initially assign to each atom. Default value is 20.
deltasize (int, optional) – Specifies the number of extra neighbor positions to allow each atom when the number of neighbors exceeds the underlying array size. Default value is 10.

property coord: ndarray

The atomic coordination numbers

dump(fname: str)

Saves the neighbor list to a file.

load(model: str | IOBase)

Read in a neighbor list from a file.

Parameters:: model (str or file-like object) – Gives the file path or content to load.

property nlist: ndarray

The underlying numpy array of coord + neighbor ids