Module: clusters
| Description | Usage |
|---|---|
| tools for using depth first search clustering to find the largest connected component in an adjacency matrix | |
| Authors: Gareth Tribello, Federico Giberti, Matteo Salvalaglio and Gabriele Sosso |   |
Details
To use the actions in this module you have to construct an adjacency matrix using one of the methods from the adjmat module. The DFSCLUSTERING takes an adjacency matrix in input and finds the various connected components in the graph that is represented by that adjacency matrix. This form analysis is useful if you are looking at a phenomenon such as nucleation where the aim is to detect the sizes of the crystalline nuclei that have formed in your simulation cell.
Actions
The following actions are part of this module
| Name | Description | Tags |
|---|---|---|
| CLUSTER_DIAMETER | Print out the diameter of one of the connected components. | CONCOMP |
| CLUSTER_DISTRIBUTION | Calculate functions of the distribution of properties in your connected components. | CONCOMP |
| CLUSTER_NATOMS | Calculate the number of atoms in the cluster of interest | CONCOMP |
| CLUSTER_PROPERTIES | Calculate properties of the distribution of some quantities that are part of a connected component | CONCOMP |
| CLUSTER_WEIGHTS | Setup a vector that has one for all the atoms that form part of the cluster of interest and that has zero for all other atoms. | CONCOMP |
| CLUSTER_WITHSURFACE | Determine the atoms that are within a certain cutoff of the atoms in a cluster. | CONCOMP |
| DFSCLUSTERING | Find the connected components of the matrix using the depth first search clustering algorithm. | MATRIXF |
| OUTPUT_CLUSTER | Output the indices of the atoms in one of the clusters identified by a clustering object | CONCOMP |
References
More information about this module is available in the following articles: