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. |
Take a connected component that was found using a clustering algorithm and create a new cluster that contains those atoms that are in the cluster together with those atoms that are within a certain cutoff of the cluster.
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 analysing 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 and takes one of the connected components that was found during this analysis and creates a new cluster that includes all the atoms within the connected component that was found together that were within a certain cutoff distance of the atoms in the connected component. This form of analysis has been used sucessfully in the forward flux sampling simulations described in this paper [78]
CLUSTERS | the label of the action that does the clustering |
RCUT_SURF | you also have the option to find the atoms on the surface of the cluster. An atom must be within this distance of one of the atoms of the cluster in order to be considered a surface atom |
NUMERICAL_DERIVATIVES | ( default=off ) calculate the derivatives for these quantities numerically |
NOPBC | ( default=off ) ignore the periodic boundary conditions when calculating distances |
SERIAL | ( default=off ) do the calculation in serial. Do not parallelize |
LOWMEM | ( default=off ) lower the memory requirements |
TIMINGS | ( default=off ) output information on the timings of the various parts of the calculation |
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 less than 13.5 and if they are within 0.38 nm of each other. Depth first search clustering is used to find the connected components in this matrix. The number of atoms with indices that are between 1 and 1996 and that are either in the second largest cluster or that are within within 0.3 nm of one of the atoms within the the second largest cluster are then counted and this number of atoms is output to a file called size. In addition the indices of the atoms that were counted are output to a file called dfs2.dat.
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 clust2a: CLUSTER_WITHSURFACE CLUSTERS=dfs RCUT_SURF=0.3 size2a: CLUSTER_NATOMS CLUSTERS=clust2a CLUSTER=2 PRINT ARG=size2a FILE=size FMT=%8.4f OUTPUT_CLUSTER CLUSTERS=clust2a CLUSTER=2 FILE=dfs2.dat