Shortcut: CLUSTER_DIAMETER

Module	clusters
Description	Usage
Print out the diameter of one of the connected components.
output value	type
the largest of all the distances between the pairs of atom in the cluster	scalar

Further details and examples

Print out the diameter of one of the connected components.

An example input that determines the diameter of 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
# Returns a 100-dimensional vector that is 1 if the correpsonding atom index is in the largest cluster and is zero otherwise
clustThe CLUSTER_WEIGHTS action with label clust calculates the following quantities:
 Quantity   
 Type   
 Description  
clust
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
# And determine the size of the largest cluster that was identified
c1The CLUSTER_DIAMETER action with label c1 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1
scalar
the largest of all the distances between the pairs of atom in the cluster: CLUSTER_DIAMETERPrint out the diameter of one of the connected components. This action is a shortcut. More details ARGcalculate ths radius of the cluster that are in this particular cluster=clust ATOMSthe atoms that were used to calculate the matrix that was clustered=1-100
# PLUMED interprets the command:
# c1: CLUSTER_DIAMETER ARG=clust ATOMS=1-100
# as follows (Click the red comment above to revert to the short version of the input):
c1_dmatThe DISTANCE_MATRIX action with label c1_dmat calculates the following quantities:
 Quantity   
 Type   
 Description  
c1_dmat
matrix
a matrix containing the weights for the bonds between each pair of atoms: DISTANCE_MATRIXCalculate a matrix of distances between atoms. More details GROUPthe atoms for which you would like to calculate the adjacency matrix=1-100
c1_bmatThe OUTER_PRODUCT action with label c1_bmat calculates the following quantities:
 Quantity   
 Type   
 Description  
c1_bmat
matrix
a matrix containing the outer product of the two input vectors that was obtained using the function that was input: OUTER_PRODUCTCalculate the outer product matrix of two vectors More details FUNC the function of the input vectors that should be put in the elements of the outer product=x*y ARGthe labels of the two vectors from which the outer product is being computed=clust,clust
c1_dclsThe CUSTOM action with label c1_dcls calculates the following quantities:
 Quantity   
 Type   
 Description  
c1_dcls
matrix
the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=c1_dmat,c1_bmat 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
c1_vdclsThe FLATTEN action with label c1_vdcls calculates the following quantities:
 Quantity   
 Type   
 Description  
c1_vdcls
vector
a vector containing all the elements of the input matrix: FLATTENConvert a matrix into a vector More details ARGthe label for the matrix that you would like to flatten to a vector=c1_dcls
c1The HIGHEST action with label c1 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1
scalar
the largest element of the input vector if one vector specified.  If multiple vectors of the same size specified the largest elements of these vector computed elementwise.: HIGHESTThis function can be used to find the highest colvar by magnitude in a set. More details ARGthe values input to this function=c1_vdcls
# --- 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 diameter here is defined as the largest of all the distances between the pairs of atom in the cluster

The output from this action is NOT differentiable

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