Cluster#

Implementation of the Cluster class.

Represents a group of sites of a given lattice. These are the building blocks for a cluster basis of functions over configurational space.

class Cluster(site_spaces, frac_coords, lattice)[source]#

Bases: SiteCollection, MSONable

An undecorated (no occupancies) cluster.

Represented simply by a list of sites, its centroid, and the underlying lattice.

You probably never need to instantiate this class directly. Look at ClusterSubspace to create orbits and clusters necessary for a CE.

frac_coords#

fractional coordinates of each site.

Type:: ndarray

lattice#

Underlying lattice of cluster.

Type:: Lattice

centroid#

Geometric centroid of included sites.

Type:: float

id#

ID of cluster. Used to identify the Cluster in a given ClusterSubspace.

Type:: int

Initialize Cluster.

Parameters:

site_spaces (list of SiteSpace) – list of site spaces for the cluster
frac_coords (Sequence) – Sequence of frac coords for the site spaces
lattice (Lattice) – pymatgen Lattice object

as_dict()[source]#

Get json-serialization dict representation.

Returns:: MSONable dict

assign_ids(cluster_id)[source]#: Recursively assign IDs to clusters after initialization.

property centroid#: Return the centroid of cluster.

copy()[source]#: Return a copy of the cluster.

property diameter#: Get maximum distance between any 2 sites in the cluster.

property frac_coords#: Return the fractional coordinates of cluster w.r.t the underlying lattice.

classmethod from_dict(d)[source]#: Create a Cluster from serialized dict.

classmethod from_file(filename)[source]#

Read a cluster from a file. Supported formats are json and yaml only.

Parameters:: filename (str) – The filename to read from.
Returns:: Cluster

classmethod from_sites(sites, lattice)[source]#: Create a cluster from a list of sites and lattice object.

classmethod from_str(input_string, fmt)[source]#

Read a cluster from a string.

Parameters:

input_string (str) – String to parse.
fmt (str) – Format to output to. Defaults to JSON unless filename is provided. If fmt is specifies, it overrides whatever the filename is. Options include “yaml”, “json”. Non-case sensitive.

Returns:

Cluster

get_distance(i, j)[source]#

Return distance between sites at index i and j.

Parameters:

i (int) – Index of first site
j (int) – Index of second site

Return type:

float

Returns:

Distance between sites at index i and index j.

property lattice#: Return the underlying lattice.

property radius#: Get half the maximum distance between any 2 sites in the cluster.

property sites#: Return the list of sites.

to(fmt=None, filename=None)[source]#

Output the cluster to a file or string.

this is basically a watered down version of pymatgen.Molecule.to

Parameters:

fmt (str) –
Format to output to. Defaults to JSON unless filename is provided. If fmt is specifies, it overrides whatever the filename is. Options include “yaml” and “json” only.

Non-case sensitive.
filename (str) – If provided, output will be written to a file. If fmt is not specified, the format is determined from the filename. Defaults is None, i.e. string output.

Returns:

(str) if filename is None. None otherwise.