	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.

Calculate properties of the distribution of some quantities that are part of a connected component

This collective variable was developed for looking at nucleation phenomena, where you are interested in using studying the behavior of atoms in small aggregates or nuclei. In these sorts of problems you might be interested in the degree the atoms in a nucleus have adopted their crystalline structure or (in the case of heterogeneous nucleation of a solute from a solvent) you might be interested in how many atoms are present in the largest cluster [107].

Examples

The input below calculates the coordination numbers of atoms 1-100 and then computes the an adjacency matrix whose elements measures whether atoms \(i\) and \(j\) are within 0.55 nm of each other. The action labelled dfs then treats the elements of this matrix as zero or ones and thus thinks of the matrix as defining a graph. This dfs action then finds the largest connected component in this graph. The sum of the coordination numbers for the atoms in this largest connected component are then computed and this quantity is output to a colvar file. The way this input can be used is described in detail in [107].

Click on the labels of the actions for more information on what each action computes

lq: COORDINATIONNUMBER SPECIESthis keyword is used for colvars such as coordination number. 
=1-100 SWITCHthe switching function that it used in the construction of the contact matrix 
={CUBIC D_0=0.45  D_MAX=0.55}  LOWMEM( default=off ) this flag does nothing and is present only to ensure back-compatibility
  You cannot view the components that are calculated by each action for this input file. Sorry 
cm: CONTACT_MATRIX ATOMSthe atoms for which you would like to calculate the adjacency matrix (basically equivalent
to GROUP) 
=lq SWITCHspecify the switching function to use between two sets of indistinguishable atoms.
={CUBIC D_0=0.45  D_MAX=0.55}   You cannot view the components that are calculated by each action for this input file. Sorry 
dfs: DFSCLUSTERING MATRIXthe input matrix (can use ARG instead) 
=cm  You cannot view the components that are calculated by each action for this input file. Sorry 
clust1: CLUSTER_PROPERTIES CLUSTERScompulsory keyword 
the label of the action that does the clustering 
=dfs CLUSTERcompulsory 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 on. 
=1 SUM( default=off ) calculate the sum of all the quantities. 
  You cannot view the components that are calculated by each action for this input file. Sorry 
PRINT ARGthe input for this action is the scalar output from one or more other actions. 
=clust1.* FILEthe name of the file on which to output these quantities 
=colvar  You cannot view the components that are calculated by each action for this input file. Sorry

Glossary of keywords and components

Description of components

Quantity	Keyword	Description
lessthan	LESS_THAN	the number of colvars that have a value less than a threshold
morethan	MORE_THAN	the number of colvars that have a value more than a threshold
altmin	ALT_MIN	the minimum value of the cv
min	MIN	the minimum colvar
max	MAX	the maximum colvar
between	BETWEEN	the number of colvars that have a value that lies in a particular interval
highest	HIGHEST	the largest of the colvars
lowest	LOWEST	the smallest of the colvars
sum	SUM	the sum of the colvars
mean	MEAN	the mean of the colvars

Compulsory keywords

ARG	calculate the sum of the arguments calculated by this action for the cluster
CLUSTERS	the label of the action that does 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.

Options

HIGHEST	( default=off ) this flag allows you to recover the highest of these variables.
LOWEST	( default=off ) this flag allows you to recover the lowest of these variables.
SUM	( default=off ) calculate the sum of all the quantities.
MEAN	( default=off ) calculate the mean of all the quantities.
LESS_THAN	calculate the number of variables that are less than a certain target value. This quantity is calculated using \(\sum_i \sigma(s_i)\), where \(\sigma(s)\) is a switchingfunction.. You can use multiple instances of this keyword i.e. LESS_THAN1, LESS_THAN2, LESS_THAN3...
MORE_THAN	calculate the number of variables that are more than a certain target value. This quantity is calculated using \(\sum_i 1 - \sigma(s_i)\), where \(\sigma(s)\) is a switchingfunction.. You can use multiple instances of this keyword i.e. MORE_THAN1, MORE_THAN2, MORE_THAN3...
ALT_MIN	calculate the minimum value. To make this quantity continuous the minimum is calculated using \( \textrm{min} = -\frac{1}{\beta} \log \sum_i \exp\left( -\beta s_i \right) \) The value of \(\beta\) in this function is specified using (BETA= \(\beta\)).
MIN	calculate the minimum value. To make this quantity continuous the minimum is calculated using \( \textrm{min} = \frac{\beta}{ \log \sum_i \exp\left( \frac{\beta}{s_i} \right) } \) The value of \(\beta\) in this function is specified using (BETA= \(\beta\))
MAX	calculate the maximum value. To make this quantity continuous the maximum is calculated using \( \textrm{max} = \beta \log \sum_i \exp\left( \frac{s_i}{\beta}\right) \) The value of \(\beta\) in this function is specified using (BETA= \(\beta\))
BETWEEN	calculate the number of values that are within a certain range. These quantities are calculated using kernel density estimation as described on histogrambead.. You can use multiple instances of this keyword i.e. BETWEEN1, BETWEEN2, BETWEEN3...
HISTOGRAM	calculate a discretized histogram of the distribution of values. This shortcut allows you to calculates NBIN quantites like BETWEEN.