	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 functions of the distribution of properties in your connected components.

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 distribution of the sizes of the clusters in your system. A detailed description of this CV can be found in [107].

Examples

The input provided below calculates the local q6 Steinhardt parameter on each atom. The coordination number that atoms with a high value for the local q6 Steinhardt parameter have with other atoms that have a high value for the local q6 Steinhardt parameter is then computed. A contact matrix is then computed that measures whether atoms atoms \(i\) and \(j\) have a high value for this coordination number and if they are within 3.6 nm of each other. The connected components of this matrix are then found using a depth first clustering algorithm on the corresponding graph. The number of components in this graph that contain more than 27 atoms is then computed. As discussed in [107] an input similar to this one was used to analyze the formation of a polycrystal of GeTe from amorphous GeTe.

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

q6: Q6 SPECIESthis keyword is used for colvars such as coordination number. 
=1-300 SWITCHthe switching function that it used in the construction of the contact matrix 
={GAUSSIAN D_0=5.29 R_0=0.01 D_MAX=5.3}  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 
lq6: LOCAL_Q6 SPECIES
=q6 SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching
function defined above. 
={GAUSSIAN D_0=5.29 R_0=0.01 D_MAX=5.3}  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 
flq6: MFILTER_MORE DATAcompulsory keyword 
the vector you wish to transform 
=lq6 SWITCHcompulsory keyword 
the switching function that transform 
={GAUSSIAN D_0=0.19 R_0=0.01 D_MAX=0.2}   You cannot view the components that are calculated by each action for this input file. Sorry 
cc: COORDINATIONNUMBER SPECIESthis keyword is used for colvars such as coordination number. 
=flq6 SWITCHthe switching function that it used in the construction of the contact matrix 
={GAUSSIAN D_0=3.59 R_0=0.01 D_MAX=3.6}   You cannot view the components that are calculated by each action for this input file. Sorry 
fcc: MFILTER_MORE DATAcompulsory keyword 
the vector you wish to transform 
=cc SWITCHcompulsory keyword 
the switching function that transform 
={GAUSSIAN D_0=5.99 R_0=0.01 D_MAX=6.0}   You cannot view the components that are calculated by each action for this input file. Sorry 
mat: CONTACT_MATRIX ATOMSthe atoms for which you would like to calculate the adjacency matrix. 
=fcc SWITCHspecify the switching function to use between two sets of indistinguishable atoms.
={GAUSSIAN D_0=3.59 R_0=0.01 D_MAX=3.6}   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) 
=mat  You cannot view the components that are calculated by each action for this input file. Sorry 
nclust: CLUSTER_DISTRIBUTION CLUSTERScompulsory keyword 
the label of the action that does the clustering 
=dfs TRANSFORM could not find this keyword 
={GAUSSIAN D_0=5.99 R_0=0.01 D_MAX=6.0}  MORE_THANcalculate the number of variables that are more than a certain target value. 
={GAUSSIAN D_0=26.99 R_0=0.01 D_MAX=27}   You cannot view the components that are calculated by each action for this input file. Sorry 
PRINT ARGcompulsory keyword 
the labels of the values that you would like to print to the file 
=nclust.* 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

CLUSTERS

the label of the action that does the clustering

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.
WEIGHTS	use the vector of values calculated by this action as weights rather than giving each atom a unit weight
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.