	This is part of the volumes module
	It is only available if you configure PLUMED with ./configure –enable-modules=volumes . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list.

Calculate a vector from the input positions with elements equal to one when the positions are in a particular part of the cell and elements equal to zero otherwise

Examples

Glossary of keywords and components

Description of components

By default the value of the calculated quantity can be referenced elsewhere in the input file by using the label of the action. Alternatively this Action can be used to calculate the following quantities by employing the keywords listed below. 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
.#!value	vector of numbers between 0 and 1 that measure the degree to which each atom is within the volume of interest

The atoms involved can be specified using

ATOMS	the group of atoms that you would like to investigate. For more information on how to specify lists of atoms see Groups and Virtual Atoms
ORIGIN	the atom whose vicinity we are interested in examining. For more information on how to specify lists of atoms see Groups and Virtual Atoms

Or alternatively by using

ATOM

an alternative to ORIGIN

Compulsory keywords

SIGMA	the width of the function to be used for kernel density estimation
KERNEL	( default=gaussian ) the type of kernel function to be used
XLOWER	( default=0.0 ) the lower boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box).
XUPPER	( default=0.0 ) the upper boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box).
YLOWER	( default=0.0 ) the lower boundary in y relative to the y coordinate of the atom (0 indicates use full extent of box).
YUPPER	( default=0.0 ) the upper boundary in y relative to the y coordinate of the atom (0 indicates use full extent of box).
ZLOWER	( default=0.0 ) the lower boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box).
ZUPPER	( default=0.0 ) the upper boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box).

Options

SERIAL

( default=off ) do the calculation in serial. Do not parallelize

OUTSIDE

( default=off ) calculate quantities for colvars that are on atoms outside the region of interest