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
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.
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: COORDINATIONNUMBERSPECIES=1-1996this keyword is used for colvars such as coordination number.SWITCH={CUBIC D_0=0.34 D_MAX=0.38} cf: MFILTER_LESSthe switching function that it used in the construction of the contact matrixDATA=c1compulsory keyword the vector you wish to transformSWITCH={CUBIC D_0=13 D_MAX=13.5} mat: CONTACT_MATRIXcompulsory keyword the switching function that transformATOMS=cfthe atoms for which you would like to calculate the adjacency matrix (basically equivalent to GROUP)SWITCH={CUBIC D_0=0.34 D_MAX=0.38} dfs: DFSCLUSTERINGspecify the switching function to use between two sets of indistinguishable atoms.MATRIX=mat OUTPUT_CLUSTERthe input matrix (can use ARG instead)CLUSTERS=dfscompulsory keyword the action that performed the clusteringCLUSTER=1compulsory 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 onFILE=dfs.datcompulsory keyword the name of the file on which to output the details of the cluster
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 |