Module: volumes

Description	Usage
tools for calculating whether atoms are within a certain part of the simulation cell or not
Authors: Gareth Tribello

Details

The actions in this module take a vector of $n$ atomic positions in input. These actions then return an $n$-dimensional vector. The elements of this vector are one if the correpsonding input atom is in a particular part of the box and zero otherwise. These actions were implemented so that you can calculate functions with the following functional form:

$$s = \sum_i w(\{X\}_i) g[f(\{X\}_i)]$$

In this expression, $g$ is a function with one argument and $g$ is a function of a set of atomic positions, $\{X\}_i$.
Meanwhile, \f$w\f$ is a weight that is also a function of the set of atomic positions. This weight varies between zero and one. You can thus use expressions like the one above to determine the average value of a quanitty in a particular part of the simulation box.

Actions

The following actions are part of this module

Tags

MCOLVAR VOLUMES

MCOLVAR: actions for calculating a vector of colvars VOLUMES: actions for calculating whether atoms are within a certain part of the simulation cell or not

Name	Description	Tags
AROUND	This quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell.	VOLUMES
CAVITY	This quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a box defined by the positions of four atoms.	VOLUMES
DENSITY	Depreciated command that is bascially equivalant to GROUP.	MCOLVAR
INCYLINDER	This quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell.	VOLUMES
INENVELOPE	This quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a region where the density of a certain type of atom is high.	VOLUMES
INSPHERE	This quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell.	VOLUMES
TETRAHEDRALPORE	This quantity can be used to calculate functions of the distribution of collective variables for the atoms lie that lie in a box defined by the positions of four atoms at the corners of a tetrahedron.	VOLUMES