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. You can specify the atoms here as another multicolvar action or using a MultiColvarFilter or ActionVolume action. When you do so the quantity is calculated for those atoms specified in the previous multicolvar. This is useful if you would like to calculate the Steinhardt parameter for those atoms that have a coordination number more than four for example

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

Examples

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

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