DENSITY

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.

Examples

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

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

d: DENSITY 
SPECIES
this keyword is used for colvars such as coordination number. 
=1-100 The DENSITY action with label d
d1: AROUND 
ATOM
the atom whose vicinity we are interested in examining. 
=101 
DATA
compulsory keyword 
The multicolvar that calculates the set of base quantities that we are interested
in 
=d 
SIGMA
compulsory keyword 
the width of the function to be used for kernel density estimation 
=0.1 
XLOWER
compulsory keyword ( default=0.0 )
the lower boundary in x relative to the x coordinate of the atom (0 indicates use
full extent of box). 
=0.0 
XUPPER
compulsory keyword ( default=0.0 )
the upper boundary in x relative to the x coordinate of the atom (0 indicates use
full extent of box). 
=0.5 The AROUND action with label d1 calculates a single scalar value
PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=d1.* 
FILE
the name of the file on which to output these quantities 
=colvar1 
FMT
the format that should be used to output real numbers 
=%8.4f The PRINT action with label 

Glossary of keywords and components

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 use MPI
LOWMEM	( default=off ) lower the memory requirements
TIMINGS	( default=off ) output information on the timings of the various parts of the calculation