Shortcut: CLUSTER_PROPERTIES

Module	clusters
Description	Usage
Calculate properties of the distribution of some quantities that are part of a connected component
output value	type
a vector that is one if the atom is part of the cluster or interest and zero otherwise	vector

Output components

This action can calculate the values in the following table when the associated keyword is included in the input for the action. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.

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

Further details and examples

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

This shortcut action is present to ensure that inputs for older PLUMED versions remain compatible. We STRONGLY encourage you to use the newer (and simpler) syntax for clustering calculations Look at the documentation for CLUSTER_WEIGHTS and the expanded version of the input below to see how this new input syntax operates.

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.

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.

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

lqThe COORDINATIONNUMBER action with label lq calculates the following quantities: Quantity    Type    Description  
lq vector the coordination numbers of the specified atoms: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-100 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=0.45  D_MAX=0.55}
# PLUMED interprets the command:
# lq: COORDINATIONNUMBER SPECIES=1-100 SWITCH={CUBIC D_0=0.45  D_MAX=0.55}
# as follows (Click the red comment above to revert to the short version of the input):
lq_grpThe GROUP action with label lq_grp calculates the following quantities: Quantity    Type    Description  
lq_grp atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-100
lq_matThe CONTACT_MATRIX action with label lq_mat calculates the following quantities: Quantity    Type    Description  
lq_mat matrix a matrix containing the weights for the bonds between each pair of atoms: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-100 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=0.45  D_MAX=0.55}
lq_onesThe CONSTANT action with label lq_ones calculates the following quantities: Quantity    Type    Description  
lq_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=100
lqThe MATRIX_VECTOR_PRODUCT action with label lq calculates the following quantities: Quantity    Type    Description  
lq vector the vector that is obtained by taking the product between the matrix and the vector that were input: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details  ARGthe label for the matrix and the vector/scalar that are being multiplied=lq_mat,lq_ones
lq_caverageThe MEAN action with label lq_caverage calculates the following quantities: Quantity    Type    Description  
lq_caverage scalar the mean of all the elements in the input vector: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=lq PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- cmThe CONTACT_MATRIX action with label cm calculates the following quantities: Quantity    Type    Description  
cm matrix a matrix containing the weights for the bonds between each pair of atoms: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=lq  SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=0.45  D_MAX=0.55}
dfsThe DFSCLUSTERING action with label dfs calculates the following quantities: Quantity    Type    Description  
dfs vector vector with length that is equal to the number of rows in the input matrix.  Elements of this vector are equal to the cluster that each node is a part of: DFSCLUSTERINGFind the connected components of the matrix using the depth first search clustering algorithm. More details ARGthe input matrix=cm
clust1The CLUSTER_PROPERTIES action with label clust1 calculates the following quantities: Quantity    Type    Description  
clust1 vector a vector that is one if the atom is part of the cluster or interest and zero otherwise
clust1_sum scalar the sum of the colvars: CLUSTER_PROPERTIESCalculate properties of the distribution of some quantities that are part of a connected component This action is a shortcut. More details ARGcalculate the sum of the arguments calculated by this action for the cluster=lq CLUSTERSthe label of the action that does the clustering=dfs CLUSTER 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 calculate the sum of all the quantities
# PLUMED interprets the command:
# clust1: CLUSTER_PROPERTIES ARG=lq CLUSTERS=dfs CLUSTER=1 SUM
# as follows (Click the red comment above to revert to the short version of the input):
clust1The CLUSTER_WEIGHTS action with label clust1 calculates the following quantities: Quantity    Type    Description  
clust1 vector vector with elements that are one if the atom of interest is part of the required cluster and zero otherwise: CLUSTER_WEIGHTSSetup a vector that has one for all the atoms that form part of the cluster of interest and that has zero for all other atoms. More details  CLUSTERSthe label of the action that does the clustering=dfs CLUSTER 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
clust1_wsumThe CUSTOM action with label clust1_wsum calculates the following quantities: Quantity    Type    Description  
clust1_wsum vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=clust1,lq FUNCthe function you wish to evaluate=x*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
clust1_sumThe SUM action with label clust1_sum calculates the following quantities: Quantity    Type    Description  
clust1_sum scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=clust1_wsum PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=clust1.sum FILEthe name of the file on which to output these quantities=colvar

Syntax

The following table describes the keywords and options that can be used with this action

Keyword	Type	Default	Description
ARG	compulsory	none	calculate the sum of the arguments calculated by this action for the cluster
CLUSTERS	compulsory	none	the label of the action that does the clustering
CLUSTER	compulsory	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
LESS_THAN	optional	not used	calculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.
MORE_THAN	optional	not used	calculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.
ALT_MIN	optional	not used	calculate the minimum value
MIN	optional	not used	calculate the minimum value
MAX	optional	not used	calculate the maximum value
BETWEEN	optional	not used	calculate the number of values that are within a certain range. Options for this keyword are explained in the documentation for BETWEEN.
HIGHEST	optional	false	this flag allows you to recover the highest of these variables
HISTOGRAM	optional	not used	calculate a discretized histogram of the distribution of values
LOWEST	optional	false	this flag allows you to recover the lowest of these variables
SUM	optional	false	calculate the sum of all the quantities
MEAN	optional	false	calculate the mean of all the quantities

Keys	Action
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Quantity	Type	Description
lq	vector	the coordination numbers of the specified atoms