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.

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

c1: COORDINATIONNUMBER SPECIES=1-1996 SWITCH={CUBIC D_0=0.34 D_MAX=0.38}
cf: MFILTER_LESS DATA=c1 SWITCH={CUBIC D_0=13 D_MAX=13.5}
mat: CONTACT_MATRIX ATOMS=cf SWITCH={CUBIC D_0=0.34 D_MAX=0.38}
dfs: DFSCLUSTERING MATRIX=mat
OUTPUT_CLUSTER CLUSTERS=dfs CLUSTER=1 FILE=dfs.dat