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
CENTER	the atom whose vicinity we are interested in examining. For more information on how to specify lists of atoms see Groups and Virtual Atoms

Compulsory keywords

KERNEL	( default=gaussian ) the type of kernel function to be used
DIRECTION	the direction of the long axis of the cylinder. Must be x, y or z
RADIUS	a switching function that gives the extent of the cylinder in the plane perpendicular to the direction
LOWER	( default=0.0 ) the lower boundary on the direction parallel to the long axis of the cylinder
UPPER	( default=0.0 ) the upper boundary on the direction parallel to the long axis of the cylinder

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

SIGMA

the width of the function to be used for kernel density estimation