Action: DFSCLUSTERING

Module	clusters
Description	Usage
Find the connected components of the matrix using the depth first search clustering algorithm.
output value	type
vector with length that is equal to the number of rows in the input matrix	vector

Input

The arguments that serve as the input for this action are specified using one or more of the keywords in the following table.

Further details and examples

Find the connected components of the matrix using the depth first search clustering algorithm.

This action 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 and is used in conjustion with tools from the adjmat module. The adjmat modlule contains a number of different methods that can be used to calculate adjacency matrices. An adjacency matrix is an $N \times N$ matrix in which the $i$th, $j$th element tells you whether or not the $i$th and $j$th atoms/molecules from a set of $N$ atoms/molecules are adjacent or not. The simplest of these adjcency matrix methods is the one for calculating a CONTACT_MATRIX. All adjacency matrices provide a representation of a graph and can thus can be analyzed using tools from graph theory. This particular action thus performs a depth first search clustering to find the connected components of this graph.

The input below calculates a CONTACT_MATRIX for 100 atoms. In the graph that is created from this CONTACT_MATRIX atoms are connected if they are within a distance of D_MAX of each other and are disconnected otherwise. The DFSCLUSTERING method is used to find the connected components in this graph. This method outputs a 100-dimensional vector. The 1st element in this vector tells you which cluster the first atom is within, the second element tells you which cluster the second atom is in and so on. If an atom is in the largest cluster its corresponding element in the vector dfs will be one. We can thus print the positions of the atoms in the largest cluster by using a DUMPATOMS command like the one shown below:

Click on the labels of the actions for more information on what each action computes

cmThe CONTACT_MATRIX action with label cm calculates the following quantities:
 Quantity   
 Type   
 Description  
cm
matrix
a matrix containing the weights for the bonds between each pair of atoms: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-100 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=0.45  D_MAX=0.55}
dfsThe DFSCLUSTERING action with label dfs calculates the following quantities:
 Quantity   
 Type   
 Description  
dfs
vector
vector with length that is equal to the number of rows in the input matrix.  Elements of this vector are equal to the cluster that each node is a part of: DFSCLUSTERINGFind the connected components of the matrix using the depth first search clustering algorithm. More details ARGthe input matrix=cm
DUMPATOMSDump selected atoms on a file. More details FILEfile on which to output coordinates; extension is automatically detected=cluster.xyz ATOMSthe atom indices whose positions you would like to print out=1-100 ARGthe labels of vectors that should be output in the xyz file=dfs LESS_THAN_OR_EQUALwhen printing with arguments that are vectors only print components of vectors have a value less than or equal to this value=1.5 GREATER_THAN_OR_EQUALwhen printing with arguments that are vectors only print components of vectors have a value greater than or equal to this value=0.5

References

More information about how this action can be used is available in the following articles: - G. A. Tribello, F. Giberti, G. C. Sosso, M. Salvalaglio, M. Parrinello, Analyzing and Driving Cluster Formation in Atomistic Simulations. Journal of Chemical Theory and Computation. 13, 1317–1327 (2017)

Syntax

The following table describes the keywords and options that can be used with this action