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Cluster Class

Contains information about a cluster, i.e. a part of some bigger original atomistic system.

This class is a simple data container where every attribute should be set only once, but does not have to be set in one go and can be insted built gradually.

__init__​

def __init__(indices=None,
             species=None,
             region=None,
             dimensionality=None,
             cell=None,
             system=None,
             distances=None,
             radii=None,
             bond_threshold=None)

Arguments:

  • indices(Iterable) - Contains the indices of atoms belonging to this cluster.
  • species(set) - Contains the species of atoms belonging to this cluster. Each unique species should be include only once.
  • region(Region) - The Region instance from which this cluster was exracted from.
  • dimensionality(int) - The dimensionality of the cluster. Can be set initially here or calculated through the get_dimensionality-function.
  • cell(ase.Atoms) - The unit cell from which this cluster is constructed from.
  • system(ase.Atoms) - Reference to the original system which this cluster is a part of.
  • distances(Distances) - Contains cached distance information about this cluster.
  • radii(ndarray) - Contains the radii for each atom in the cluster as floating point numbers.

get_cell​

def get_cell() -> Atoms

Used to fetch the prototypical cell for this cluster if one exists.

get_atoms​

def get_atoms() -> Atoms

Returns the ase.Atoms object for this cluster.

get_dimensionality​

def get_dimensionality() -> int

Shortcut for fetching the dimensionality of the cluster using matid.geometry.get_dimensionality and the radii + bond thresholds that were used during the clustering.