This is part of the multicolvar module

Calculate functions of the density of atoms as a function of the box. This allows one to calculate the number of atoms in half the box.

The atoms involved can be specified using

SPECIES

this keyword is used for colvars such as coordination number. In that context it specifies that plumed should calculate one coordination number for each of the atoms specified. Each of these coordination numbers specifies how many of the other specified atoms are within a certain cutoff of the central atom.

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 parallelize
LOWMEM	( default=off ) lower the memory requirements
VERBOSE	( default=off ) write a more detailed output

TOL

this keyword can be used to speed up your calculation. When accumulating sums in which the individual terms are numbers inbetween zero and one it is assumed that terms less than a certain tolerance make only a small contribution to the sum. They can thus be safely ignored as can the the derivatives wrt these small quantities.

Examples

The following example calculates the number of atoms in one half of the simulation box.

DENSITY SPECIES=1-100 LABEL=d
SUBCELL ARG=d XLOWER=0.0 XUPPER=0.5 LABEL=d1
PRINT ARG=d1.* FILE=colvar1 FMT=%8.4f