NeighborList

class atomman.NeighborList(**kwargs)

Bases: object

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

build(system, cutoff, initialsize=20, deltasize=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

The atomic coordination numbers

dump(fname)

Saves the neighbor list to a file.

Parameters

fname (str) – The file name to save the content to.

load(model)

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

The underlying numpy array of coord + neighbor ids

Type

numpy.ndarray