Action: CLUSTER_WEIGHTS

Module	clusters
Description	Usage
Setup 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.
output value	type
vector with elements that are one if the atom of interest is part of the required cluster and zero otherwise	vector

Input

The arguments that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword	Type	Description
CLUSTERS	vector	the label of the action that does the clustering

Further details and examples

Setup 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.

This method is designed to be used in tandem with the DFSCLUSTERING action. An example input that uses this action and that calculates the average coordination number for the atoms in the largest cluster in the system 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}
# Evaluate the coordination numbers of the 100 atoms with themselves
onesThe ONES action with label ones calculates the following quantities: Quantity    Type    Description  
ones vector a vector of ones with the required number of elements: ONESCreate a constant vector with all elements equal to one This action is a shortcut. More details SIZEthe number of ones that you would like to create=100
# PLUMED interprets the command:
# ones: ONES SIZE=100
# as follows (Click the red comment above to revert to the short version of the input):
onesThe CONSTANT action with label ones calculates the following quantities: Quantity    Type    Description  
ones vector the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details NOLOG do not report all the read in scalars in the log VALUESthe numbers that are in your constant value=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
# --- End of included input --- coordThe MATRIX_VECTOR_PRODUCT action with label coord calculates the following quantities: Quantity    Type    Description  
coord 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=cm,ones
# 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
# Returns a 100-dimensional vector that is 1 if the correpsonding atom index is in the largest cluster and is zero otherwise
c1The CLUSTER_WEIGHTS action with label c1 calculates the following quantities: Quantity    Type    Description  
c1 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
# Now evaluate the sum of the coordination numbers of the atoms in the larget cluster
numervThe CUSTOM action with label numerv calculates the following quantities: Quantity    Type    Description  
numerv 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=c1,coord 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
numerThe SUM action with label numer calculates the following quantities: Quantity    Type    Description  
numer 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=numerv PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# Evaluate the total number of atoms in the largest cluster
denomThe SUM action with label denom calculates the following quantities: Quantity    Type    Description  
denom 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 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# And finally calculate the average coordination number for the atoms in the largest cluster
fThe CUSTOM action with label f calculates the following quantities: Quantity    Type    Description  
f scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=numer,denom 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
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=f FILEthe name of the file on which to output these quantities=colvar

References

More information about how this action can be used is available in the following articles: - G. A. Tribello, F. Giberti, G. C. Sosso, M. Salvalaglio, M. Parrinello, Analyzing and Driving Cluster Formation in Atomistic Simulations. Journal of Chemical Theory and Computation. 13, 1317–1327 (2017)

Syntax

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

Keyword	Type	Default	Description
CLUSTERS	input	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
LOWMEM	optional	false	this flag does nothing and is present only to ensure back-compatibility

Keys	Action
`?`	Open this help
`n`	Next page
`p`	Previous page
`s`	Search

Quantity	Type	Description
cm	matrix	a matrix containing the weights for the bonds between each pair of atoms