OUTPUT_CLUSTER

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

Output the indices of the atoms in one of the clusters identified by a clustering object

This action provides one way of getting output from a DFSCLUSTERING calculation. The output in question here is either

• a file that contains a list of the atom indices that form part of one of the clusters that was identified using DFSCLUSTERING
• an xyz file containing the positions of the atoms in one of the the clusters that was identified using DFSCLUSTERING

Notice also that if you choose to output an xyz file you can ask PLUMED to try to reconstruct the cluster taking the periodic boundary conditions into account by using the MAKE_WHOLE flag.

Examples

The input shown below identifies those atoms with a coordination number less than 13 and then constructs a contact matrix that describes the connectivity between the atoms that satisfy this criteria. The DFS algorithm is then used to find the connected components in this matrix and the indices of the atoms in the largest connected component are then output to a file.

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

c1: COORDINATIONNUMBER 
SPECIES
this keyword is used for colvars such as coordination number. 
=1-1996 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching
function defined above. 
={CUBIC D_0=0.34 D_MAX=0.38}  The COORDINATIONNUMBER action with label c1
cf: MFILTER_LESS 
DATA
compulsory keyword 
The multicolvar that calculates the set of base quantities that we are interested
in 
=c1 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching
function defined above. 
={CUBIC D_0=13 D_MAX=13.5}  The MFILTER_LESS action with label cf
mat: CONTACT_MATRIX 
ATOMS
The list of atoms for which you would like to calculate the contact matrix. 
=cf 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching
function defined above. 
={CUBIC D_0=0.34 D_MAX=0.38}  The CONTACT_MATRIX action with label mat
dfs: DFSCLUSTERING 
MATRIX
compulsory keyword 
the action that calculates the adjacency matrix vessel we would like to analyze 
=mat The DFSCLUSTERING action with label dfs
OUTPUT_CLUSTER 
CLUSTERS
compulsory keyword 
the action that performed 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 
FILE
compulsory keyword 
the name of the file on which to output the details of the cluster 
=dfs.dat The OUTPUT_CLUSTER action with label 

Glossary of keywords and components

Compulsory keywords

CLUSTERS	the action that performed the clustering
CLUSTER	( 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
STRIDE	( default=1 ) the frequency with which you would like to output the atoms in the cluster
FILE	the name of the file on which to output the details of the cluster
MAXDEPTH	( default=6 ) maximum depth for searches over paths to reconstruct clusters for PBC
MAXGOES	( default=200 ) number of times to run searches to reconstruct clusters

Options

MAKE_WHOLE

( default=off ) reconstruct the clusters and remove all periodic boundary conditions.