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

Retrieve the size of a cluster. This quantity is NOT differentiable.

This action uses the DFS clustering algorithm described in DFSCLUSTERING to find a set of connected components based on the configuration of the atoms in your system. Once again this can be used to find crystalline nuclei or bubble of atoms. Once these connected components you can then find the sizes of the connected components by measuring the distance between the two most widely separated atoms in the connected component. This is what is done by this action.

Compulsory keywords
DATA the labels of the action that calculates the multicolvars we are interested in
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.
WTOL if the base multicolvars have weights then you must define a hard cutoff on those you want to consider explicitally
NOPBC ( default=off ) ignore the periodic boundary conditions when calculating distances
SERIAL ( default=off ) do the calculation in serial. Do not parallelize
TIMINGS ( default=off ) output information on the timings of the various parts of the calculation
USE_ORIENTATION ( default=off ) When computing whether two atoms/molecules are adjacent also take their orientations into account

( default=off ) use a more memory intensive version of this collective variable


This keyword is used if you want to employ an alternative to the continuous swiching function defined above. The following provides information on the switchingfunction that are available. When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords. You can use multiple instances of this keyword i.e. SWITCH1, SWITCH2, SWITCH3...