SPRINT
This is part of the adjmat module
It is only available if you configure PLUMED with ./configure –enable-modules=adjmat . 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 [109] 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 v2.9
d1: DENSITY 
SPECIES
this keyword is used for colvars such as coordination number.
=1-7 mat: CONTACT_MATRIX
ATOMS
The list of atoms for which you would like to calculate the contact matrix.
=d1
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above.
={RATIONAL R_0=0.1} ss: SPRINT
MATRIX
compulsory keyword the action that calculates the adjacency matrix vessel we would like to analyze
=mat PRINT
ARG
the input for this action is the scalar output from one or more other actions.
=ss.*
FILE
the 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 v2.9
c: DENSITY 
SPECIES
this keyword is used for colvars such as coordination number.
=1-7 h: DENSITY
SPECIES
this keyword is used for colvars such as coordination number.
=8-14 mat: CONTACT_MATRIX ...
ATOMS
The list of atoms for which you would like to calculate the contact matrix.
=c,h
SWITCH11
This keyword is used if you want to employ an alternative to the continuous switching function defined above.
={RATIONAL R_0=2.6 NN=6 MM=12}
SWITCH12
This keyword is used if you want to employ an alternative to the continuous switching function defined above.
={RATIONAL R_0=2.2 NN=6 MM=12}
SWITCH22
This keyword is used if you want to employ an alternative to the continuous switching function defined above.
={RATIONAL R_0=2.2 NN=6 MM=12} ... ss: SPRINT
MATRIX
compulsory keyword the action that calculates the adjacency matrix vessel we would like to analyze
=mat PRINT
ARG
the input for this action is the scalar output from one or more other actions.
=ss.*
FILE
the name of the file on which to output these quantities
=colvar
Glossary of keywords and components
Description of components

By default this Action calculates the following quantities. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.

Quantity Description
coord all \(n\) sprint coordinates are calculated and then stored in increasing order. the smallest sprint coordinate will be labeled label.coord-0, the second smallest will be labelled label.coord-1 and so on

In addition the following quantities can be calculated by employing the keywords listed below

Quantity Keyword Description
gradient GRADIENT the gradient
vmean VMEAN the norm of the mean vector. The output component can be referred to elsewhere in the input file by using the label.vmean
vsum VSUM the norm of sum of vectors. The output component can be referred to elsewhere in the input file by using the label.vsum
spath SPATH the position on the path
gspath GPATH the position on the path calculated using trigonometry
gzpath GPATH the distance from the path calculated using trigonometry
zpath ZPATH the distance from the path
altmin ALT_MIN the minimum value. This is calculated using the formula described in the description of the keyword so as to make it continuous.
between BETWEEN the number/fraction of values within a certain range. This is calculated using one of the formula described in the description of the keyword so as to make it continuous. You can calculate this quantity multiple times using different parameters.
highest HIGHEST the highest of the quantities calculated by this action
lessthan LESS_THAN the number of values less than a target value. This is calculated using one of the formula described in the description of the keyword so as to make it continuous. You can calculate this quantity multiple times using different parameters.
lowest LOWEST the lowest of the quantities calculated by this action
max MAX the maximum value. This is calculated using the formula described in the description of the keyword so as to make it continuous.
mean MEAN the mean value. The output component can be referred to elsewhere in the input file by using the label.mean
min MIN the minimum value. This is calculated using the formula described in the description of the keyword so as to make it continuous.
moment MOMENTS the central moments of the distribution of values. The second moment would be referenced elsewhere in the input file using label.moment-2, the third as label.moment-3, etc.
morethan MORE_THAN the number of values more than a target value. This is calculated using one of the formula described in the description of the keyword so as to make it continuous. You can calculate this quantity multiple times using different parameters.
sum SUM the sum of values
Compulsory keywords
MATRIX the action that calculates the adjacency matrix vessel we would like to analyze
Options
NUMERICAL_DERIVATIVES ( default=off ) calculate the derivatives for these quantities numerically
NOPBC ( default=off ) ignore the periodic boundary conditions when calculating distances
SERIAL ( default=off ) do the calculation in serial. Do not use MPI
LOWMEM ( default=off ) lower the memory requirements
TIMINGS

( default=off ) output information on the timings of the various parts of the calculation