Shortcut: CLUSTER_NATOMS

Module	clusters
Description	Usage
Calculate the number of atoms in the cluster of interest
output value	type
the number of atoms in the cluster	scalar

Further details and examples

Calculate the number of atoms in the cluster of interest

An example input that determines the number of atoms in the second largest cluster that is identified by analysing the connected components of a CONTACT_MATRIX using DFSCLUSTERING is shown below:

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

# Calculate a contact matrix between the first 100 atoms in the configuration
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=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}
# Find the connected components from the contact matrix
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
# And determine the size of the second largest cluster that was identified
c1The CLUSTER_NATOMS action with label c1 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1
scalar
the number of atoms in the cluster: CLUSTER_NATOMSCalculate the number of atoms in the cluster of interest This action is a shortcut. 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=2
# PLUMED interprets the command:
# c1: CLUSTER_NATOMS CLUSTERS=dfs CLUSTER=2
# as follows (Click the red comment above to revert to the short version of the input):
c1_weightsThe CLUSTER_WEIGHTS action with label c1_weights calculates the following quantities:
 Quantity   
 Type   
 Description  
c1_weights
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=2
c1The SUM action with label c1 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1
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=c1_weights 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=c1 FILEthe name of the file on which to output these quantities=colvar

The output from this action is NOT differentiable

Syntax

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