CLUSTER_DIAMETER
This is part of the clusters module
It is only available if you configure PLUMED with ./configure –enable-modules=clusters . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list.

Print out the diameter of one of the connected components

As discussed in the section of the manual on Exploiting contact matrices a useful tool for developing complex collective variables is the notion of the so called adjacency matrix. 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. When analyzing these matrix we can treat them as a graph and find connected components using some clustering algorithm. This action is used in tandem with this form of analysis to output the largest of the distances between the pairs of atoms that are connected together in a particular connected component. It is important to note that the quantity that is output by this action cannot be differentiated. As such it cannot be used as a collective variable in a biased simulation.

Examples

The following input uses PLUMED to calculate a adjacency matrix that connects a pair of atoms if they both have a coordination number that is greater than 2.0 and if they are within 6.0 nm of each other. Depth first search clustering is used to find the connected components in this matrix. The distance between every pair of atoms that are within the largest of the clusters found is then calculated and the largest of these distances is output to a file named colvar.

Click on the labels of the actions for more information on what each action computes
tested on master
# Calculate coordination numbers
c1: COORDINATIONNUMBER 
SPECIES
this keyword is used for colvars such as coordination number. 
=1-512 
SWITCH
the switching function that it used in the construction of the contact matrix 
={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}  
# Select coordination numbers that are more than 2.0
cf: MFILTER_MORE 
DATA
compulsory keyword 
the vector you wish to transform 
=c1 
SWITCH
compulsory keyword 
the switching function that transform 
={RATIONAL D_0=2.0 R_0=0.1}  
LOWMEM
( default=off ) this flag does nothing and is present only to ensure back-compatibility

 
# Build a contact matrix
mat: CONTACT_MATRIX 
ATOMS
the atoms for which you would like to calculate the adjacency matrix (basically equivalent
to GROUP) 
=cf 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms.

={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}  
# Find largest cluster
dfs: DFSCLUSTERING 
MATRIX
the input matrix (can use ARG instead) 
=mat 
clust1: CLUSTER_PROPERTIES 
CLUSTERS
compulsory keyword 
the label of the action that does the clustering 
=dfs 
CLUSTER
compulsory keyword ( default=1 )
which cluster would you like to look at 1 is the largest cluster, 2 is the second
largest, 3 is the the third largest and so on. 
=1 
dia: CLUSTER_DIAMETER 
CLUSTERS
 could not find this keyword 
=dfs 
CLUSTER
 could not find this keyword 
=1 
PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=dia 
FILE
the name of the file on which to output these quantities 
=colvar
Glossary of keywords and components
Compulsory keywords
ATOMS the atoms that were used to calculate the matrix that was clustered
Options
ARG calculate ths radius of the cluster that are in this particular cluster