INCYLINDER

	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.

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.

Each of the base quantities calculated by a multicolvar can can be assigned to a particular point in three dimensional space. For example, if we have the coordination numbers for all the atoms in the system each coordination number can be assumed to lie on the position of the central atom. Because each base quantity can be assigned to a particular point in space we can calculate functions of the distribution of base quantities in a particular part of the box by using:

\[ \overline{s}_{\tau} = \frac{ \sum_i f(s_i) \sigma(r_{xy}) }{ \sum_i \sigma(r_{xy}) } \]

where the sum is over the collective variables, \(s_i\), each of which can be thought to be at \( (x_i,y_i,z_i)\). The function \(\sigma\) is a switchingfunction that acts on the distance between the point at which the collective is located \((x_i,y_i,z_i)\) and the position of the atom that was specified using the ORIGIN keyword projected in the xy plane if DIRECTION=z is used. In other words:

\[ r_{xy} = sqrt{ ( x_i - x_0)^2 + ( y_i - y_0)^2 } \]

In short this function, \(\sigma(r_{xy})\), measures whether or not the CV is within a cylinder that runs along the axis specified using the DIRECTION keyword and that is centered on the position of the atom specified using ORIGIN.

The function \((s_i)\) can be any of the usual LESS_THAN, MORE_THAN, WITHIN etc that are used in all other multicolvars.

When INCYLINDER is used with the DENSITY action the number of atoms in the specified region is calculated

Examples

The input below can be use to calculate the average coordination numbers for those atoms that are within a cylindrical tube of radius 1.5 nm that is centered on the position of atom 101 and that has its long axis parallel to the z-axis.

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

c1: COORDINATIONNUMBER 
SPECIES
this keyword is used for colvars such as coordination number. 
=1-100 
SWITCH
the switching function that it used in the construction of the contact matrix 
={RATIONAL R_0=0.1}   You cannot view the components that are calculated by each action for this input file. Sorry 
d2: INCYLINDER 
ATOM
 could not find this keyword 
=101 
DATA
the label of an action that calculates multicolvars. 
=c1 
DIRECTION
compulsory keyword 
the direction of the long axis of the cylinder. 
=Z 
RADIUS
compulsory keyword 
a switching function that gives the extent of the cylinder in the plane perpendicular
to the direction 
={TANH R_0=1.5}  
SIGMA
the width of the function to be used for kernel density estimation 
=0.1 
LOWER
compulsory keyword ( default=0.0 )
the lower boundary on the direction parallel to the long axis of the cylinder 
=-0.1 
UPPER
compulsory keyword ( default=0.0 )
the upper boundary on the direction parallel to the long axis of the cylinder 
=0.1 
MEAN
( default=off ) calculate the average value of the colvar inside the region of interest
  You cannot view the components that are calculated by each action for this input file. Sorry 
PRINT 
ARG
compulsory keyword 
the labels of the values that you would like to print to the file 
=d2.* 
FILE
the name of the file on which to output these quantities 
=colvar  You cannot view the components that are calculated by each action for this input file. Sorry 

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	sum of values of input CVs in regin of interest

In addition the following quantities can be calculated by employing the keywords listed below

Quantity	Keyword	Description
lessthan	LESS_THAN	the number of cvs in the region of interest that are less than a certain threshold
morethan	MORE_THAN	the number of cvs in the region of interest that are more than a certain threshold
between	BETWEEN	the number of cvs in the region of interest that are within a certain range
sum	SUM	the sum of all the colvars weighted by the function that determines if we are in the region
mean	MEAN	the average values of the colvar in the region 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
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
SUM	( default=off ) calculate the sum of all the quantities.
MEAN	( default=off ) calculate the average value of the colvar inside the region of interest
SIGMA	the width of the function to be used for kernel density estimation
DATA	the label of an action that calculates multicolvars. Weighted sums based on the location of the colvars calculated by this action will be calcualted
LESS_THAN	calcualte the number of colvars that are inside the region of interest and that are less than a certain threshold
MORE_THAN	calcualte the number of colvars that are inside the region of interest and that are greater that a certain threshold
BETWEEN	calculate the number of colvars that are inside the region of interest and that have a CV value that is between a particular set of bounds