This is part of the multicolvar module

Calculate number of pairs of atoms/molecules that are "linked"

In its simplest guise this coordinate calculates a coordination number. Each pair of atoms is assumed "linked" if they are within some cutoff of each other. In more complex applications each entity is a vector and this quantity measures whether pairs of vectors are (a) within a certain cutoff and (b) if the two vectors have similar orientations. The vectors on individual atoms could be Steinhardt parameters (see Q3, Q4 and Q6) or they could describe some internal vector in a molecule.

Compulsory keywords
 DATA the labels of the action that calculates the multicolvars we are interested in NN ( default=6 ) The n parameter of the switching function MM ( default=12 ) The m parameter of the switching function D_0 ( default=0.0 ) The d_0 parameter of the switching function R_0 The r_0 parameter of the switching function
Options
 NOPBC ( default=off ) ignore the periodic boundary conditions when calculating distances SERIAL ( default=off ) do the calculation in serial. Do not parallelize TIMINGS ( default=off ) output information on the timings of the various parts of the calculation LOWMEM ( default=off ) lower the memory requirements
 SWITCH This keyword is used if you want to employ an alternative to the continuous swiching function defined above. The following provides information on the switchingfunction that are available. When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords.
Examples

The following calculates how many bonds there are in a system containing 64 atoms and outputs this quantity to a file.

DENSITY SPECIES=1-64 LABEL=d1
NLINKS ARG=d1 SWITCH={RATIONAL D_0=1.3 R_0=0.2} LABEL=dd
PRINT ARG=dd FILE=colvar


The following calculates how many pairs of neighbouring atoms in a system containg 64 atoms have similar dispositions for the atoms in their coordination sphere. This calculation uses the dot product of the Q6 vectors on adjacent atoms to measure whether or not two atoms have the same orientation"

Q6 SPECIES=1-64 SWITCH={RATIONAL D_0=1.3 R_0=0.2} LABEL=q6
NLINKS ARG=q6 SWITCH={RATIONAL D_0=1.3 R_0=0.2} LABEL=dd
PRINT ARG=dd FILE=colvar