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.

Find the number of clusters that have a size larger than a certain cutoff

Compulsory keywords
DATA the labels of the action that calculates the multicolvars we are interested in
TRANSFORM ( default=none ) the switching function to use to convert the crystallinity parameter to a number between zero and one
THRESHOLD a switching function that defines how large the clusters should be in order to be counted
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
HIGHMEM ( default=off ) use a more memory intensive version of this collective variable

( default=off ) when TRANSFORM appears alone the input symmetry functions, \(x\) are transformed used \(1-s(x)\) where \(s(x)\) is a switching function. When this option is used you instead transform using \(s(x)\) only.


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...