	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.

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 [135].

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 [135] 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 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching
function defined above. ={GAUSSIAN D_0=5.29 R_0=0.01 D_MAX=5.3}  LOWMEM( default=off ) lower the memory requirements  The Q6 action with label q6
lq6: LOCAL_Q6 SPECIESthis keyword is used for colvars such as coordination number. =q6 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching
function defined above. ={GAUSSIAN D_0=5.29 R_0=0.01 D_MAX=5.3}  LOWMEM( default=off ) lower the memory requirements  The LOCAL_Q6 action with label lq6
flq6: MFILTER_MORE DATAcompulsory keyword 
The multicolvar that calculates the set of base quantities that we are interested
in =lq6 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching
function defined above. ={GAUSSIAN D_0=0.19 R_0=0.01 D_MAX=0.2}  The MFILTER_MORE action with label flq6
cc: COORDINATIONNUMBER SPECIESthis keyword is used for colvars such as coordination number. =flq6 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching
function defined above. ={GAUSSIAN D_0=3.59 R_0=0.01 D_MAX=3.6}  The COORDINATIONNUMBER action with label cc
fcc: MFILTER_MORE DATAcompulsory keyword 
The multicolvar that calculates the set of base quantities that we are interested
in =cc SWITCHThis keyword is used if you want to employ an alternative to the continuous switching
function defined above. ={GAUSSIAN D_0=5.99 R_0=0.01 D_MAX=6.0}  The MFILTER_MORE action with label fcc
mat: CONTACT_MATRIX ATOMSThe list of atoms for which you would like to calculate the contact matrix. =fcc SWITCHThis keyword is used if you want to employ an alternative to the continuous switching
function defined above. ={GAUSSIAN D_0=3.59 R_0=0.01 D_MAX=3.6}  The CONTACT_MATRIX action with label mat
dfs: DFSCLUSTERING MATRIXcompulsory keyword 
the action that calculates the adjacency matrix vessel we would like to analyze =mat The DFSCLUSTERING action with label dfs
nclust: CLUSTER_DISTRIBUTION CLUSTERScompulsory keyword 
the label of the action that does the clustering =dfs TRANSFORMcompulsory keyword ( default=none )
the switching function to use to convert the crystallinity parameter to a number
between zero and one ={GAUSSIAN D_0=5.99 R_0=0.01 D_MAX=6.0}  MORE_THANcalculate the number of variables more than a certain target value. ={GAUSSIAN D_0=26.99 R_0=0.01 D_MAX=27}  The CLUSTER_DISTRIBUTION action with label nclust calculates a single scalar value
PRINT ARGthe input for this action is the scalar output from one or more other actions. =nclust.* FILEthe name of the file on which to output these quantities =colvar The PRINT action with label

Glossary of keywords and components

Description of components

When the label of this action is used as the input for a second you are not referring to a scalar quantity as you are in regular collective variables. The label is used to reference the full set of quantities calculated by the action. This is usual when using MultiColvar functions. Generally when doing this the previously calculated multicolvar will be referenced using the DATA keyword rather than ARG.

This Action can be used to calculate the following scalar quantities directly. These quantities are calculated by employing the keywords listed below. These quantities can then be referenced elsewhere in the input file by using this Action's label followed by a dot and the name of the quantity. Some of them can be calculated multiple times with different parameters. In this case the quantities calculated can be referenced elsewhere in the input by using the name of the quantity followed by a numerical identifier e.g. label.lessthan-1, label.lessthan-2 etc. When doing this and, for clarity we have made it so that the user can set a particular label for each of the components. As such by using the LABEL keyword in the description of the keyword input you can customize the component name

Quantity	Keyword	Description
altmin	ALT_MIN	the minimum value. This is calculated using the formula described in the description of the keyword so as to make it continuous.
between	BETWEEN	the number/fraction of values within a certain range. This is calculated using one of the formula described in the description of the keyword so as to make it continuous. You can calculate this quantity multiple times using different parameters.
lessthan	LESS_THAN	the number of values less than a target value. This is calculated using one of the formula described in the description of the keyword so as to make it continuous. You can calculate this quantity multiple times using different parameters.
max	MAX	the maximum value. This is calculated using the formula described in the description of the keyword so as to make it continuous.
min	MIN	the minimum value. This is calculated using the formula described in the description of the keyword so as to make it continuous.
morethan	MORE_THAN	the number of values more than a target value. This is calculated using one of the formula described in the description of the keyword so as to make it continuous. You can calculate this quantity multiple times using different parameters.

Compulsory keywords

CLUSTERS	the label of the action that does the clustering
TRANSFORM	( default=none ) the switching function to use to convert the crystallinity parameter to a number between zero and one

Options

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 use MPI
LOWMEM	( default=off ) lower the memory requirements
TIMINGS	( default=off ) output information on the timings of the various parts of the calculation
INVERSE_TRANSFORM	( 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.
MORE_THAN	calculate the number of variables more than a certain target value. This quantity is calculated using \(\sum_i 1.0 - \sigma(s_i)\), where \(\sigma(s)\) is a switchingfunction. The final value can be referenced using label.morethan. You can use multiple instances of this keyword i.e. MORE_THAN1, MORE_THAN2, MORE_THAN3... The corresponding values are then referenced using label.morethan-1, label.morethan-2, label.morethan-3...
LESS_THAN	calculate the number of variables less than a certain target value. This quantity is calculated using \(\sum_i \sigma(s_i)\), where \(\sigma(s)\) is a switchingfunction. The final value can be referenced using label.lessthan. You can use multiple instances of this keyword i.e. LESS_THAN1, LESS_THAN2, LESS_THAN3... The corresponding values are then referenced using label.lessthan-1, label.lessthan-2, label.lessthan-3...
BETWEEN	calculate the number of values that are within a certain range. These quantities are calculated using kernel density estimation as described on histogrambead. The final value can be referenced using label.between. You can use multiple instances of this keyword i.e. BETWEEN1, BETWEEN2, BETWEEN3... The corresponding values are then referenced using label.between-1, label.between-2, label.between-3...
HISTOGRAM	calculate how many of the values fall in each of the bins of a histogram. This shortcut allows you to calculates NBIN quantities like BETWEEN. The final value can be referenced using label.histogram. You can use multiple instances of this keyword i.e. HISTOGRAM1, HISTOGRAM2, HISTOGRAM3... The corresponding values are then referenced using label.histogram-1, label.histogram-2, label.histogram-3...
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= \(\beta\)). The final value can be referenced using label.altmin. You can use multiple instances of this keyword i.e. ALT_MIN1, ALT_MIN2, ALT_MIN3... The corresponding values are then referenced using label.altmin-1, label.altmin-2, label.altmin-3...
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= \(\beta\)) The final value can be referenced using label.min. You can use multiple instances of this keyword i.e. MIN1, MIN2, MIN3... The corresponding values are then referenced using label.min-1, label.min-2, label.min-3...
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= \(\beta\)) The final value can be referenced using label.max. You can use multiple instances of this keyword i.e. MAX1, MAX2, MAX3... The corresponding values are then referenced using label.max-1, label.max-2, label.max-3...