SPRINT
This is part of the sprint module
It is only available if you configure PLUMED with ./configure –enable-modules=sprint . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list.

Calculate SPRINT topological variables from an adjacency matrix.

The SPRINT topological variables are calculated from the largest eigenvalue, \(\lambda\) of an \(n\times n\) adjacency matrix and its corresponding eigenvector, \(\mathbf{V}\), using:

\[ s_i = \sqrt{n} \lambda v_i \]

You can use different quantities to measure whether or not two given atoms/molecules are adjacent or not in the adjacency matrix. The simplest measure of adjacency is is whether two atoms/molecules are within some cutoff of each other. Further complexity can be added by insisting that two molecules are adjacent if they are within a certain distance of each other and if they have similar orientations.

Examples

This example input calculates the 7 SPRINT coordinates for a 7 atom cluster of Lennard-Jones atoms and prints their values to a file. In this input the SPRINT coordinates are calculated in the manner described in ?? so two atoms are adjacent if they are within a cutoff:

Click on the labels of the actions for more information on what each action computes
tested on master
d1: DENSITY SPECIEScompulsory keyword 
the atoms in the group =1-7 
mat: CONTACT_MATRIX ATOMSthe atoms for which you would like to calculate the adjacency matrix. =d1 SWITCHspecify the switching function to use between two sets of indistinguishable atoms.
={RATIONAL R_0=0.1}  
ss: SPRINT MATRIXthe matrix that you would like to perform SPRINT on =mat 
PRINT ARGcompulsory keyword 
the labels of the values that you would like to print to the file =ss.* FILEthe name of the file on which to output these quantities =colvar 

This example input calculates the 14 SPRINT coordinates for a molecule composed of 7 hydrogen and 7 carbon atoms. Once again two atoms are adjacent if they are within a cutoff:

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