OUTPUT_CLUSTER

	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.

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
the switching function that it used in the construction of the contact matrix 
={CUBIC D_0=0.34 D_MAX=0.38}   You cannot view the components that are calculated by each action for this input file. Sorry 
cf: MFILTER_LESS 
DATA
compulsory keyword 
the vector you wish to transform 
=c1 
SWITCH
compulsory keyword 
the switching function that transform 
={CUBIC D_0=13 D_MAX=13.5}   You cannot view the components that are calculated by each action for this input file. Sorry 
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.
={CUBIC D_0=0.34 D_MAX=0.38}   You cannot view the components that are calculated by each action for this input file. Sorry 
dfs: DFSCLUSTERING 
MATRIX
the input matrix (can use ARG instead) 
=mat  You cannot view the components that are calculated by each action for this input file. Sorry 
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  You cannot view the components that are calculated by each action for this input file. Sorry 

Glossary of keywords and components

Compulsory keywords

ATOMS	the atoms for which clustering were performed
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