This is part of the volumes module

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

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