Shortcut: INCYLINDER

Module	volumes
Description	Usage
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.
output value	type
sum of values of input CVs in regin of interest	scalar

Output components

This action can calculate the values in the following table when the associated keyword is included in the input for the action. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.

Input

The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.

Further details and examples

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.

This action can be used to calculate whether each of the atoms are within a particular part of the simulation box or not as illustrated by the following example:

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

fThe FIXEDATOM action with label f calculates the following quantities:
 Quantity   
 Type   
 Description  
f
atoms
virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=0,0,0
f: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=0,0,0  SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0
aThe INCYLINDER action with label a calculates the following quantities:
 Quantity   
 Type   
 Description  
a
vector
vector of numbers between 0 and 1 that measure the degree to which each atom is within the volume of interest: INCYLINDERThis 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. More details ATOMSthe group of atoms that you would like to investigate=1-100 CENTERthe atom whose vicinity we are interested in examining=f DIRECTIONthe direction of the long axis of the cylinder=Z RADIUSa switching function that gives the extent of the cylinder in the plane perpendicular to the direction. Options for this keyword are explained in the documentation for LESS_THAN.={TANH R_0=1.5} SIGMAthe width of the function to be used for kernel density estimation=0.1 LOWER the lower boundary on the direction parallel to the long axis of the cylinder=-1.0 UPPER the upper boundary on the direction parallel to the long axis of the cylinder=1.0
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=a FILEthe name of the file on which to output these quantities=colvar

The 100 elements of the vector a that is returned from the INCYLINDER action in the above input are calculated using:

$$w(x_i,y_i,z_i) = s\left( r_{xy} \right) \int_{zl}^{zu} \textrm{d}z K\left( \frac{z - z_i}{\sigma} \right)$$

where

$$r_{xy} = \sqrt{ x_i^2 + y_i^2 }$$

In these expressions $K$ is one of the kernel functions described in the documentation for the function BETWEEN, $\sigma$ is a bandwidth parameter and the limits for the integrals are the values specified using the keywords LOWER and UPPER. $x_i$, $y_i$ and $z_i$ are then the components of the vector that connects the $i$th atom that was specified using the ATOMS keyword to the atom that was specified using the CENTER keyword. In other words, $w(x_i,y_i,z_i)$ is 1 if the atom is within a cylinder that is centered on the $z$ axis that has an extent along the $z$ direction around the position of atom f that is determined by the values specified by LOWER and UPPER keywords. The radial extent of this cylinder is determined by the parameters of the switching function that is specified using the RADIUS keyword.

If you want to caluclate and print the number of atoms in the cylinder of interest you can use an input like the one shown below:

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

fThe FIXEDATOM action with label f calculates the following quantities:
 Quantity   
 Type   
 Description  
f
atoms
virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=0,0,0
f: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=0,0,0  SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0
aThe INCYLINDER action with label a calculates the following quantities:
 Quantity   
 Type   
 Description  
a
vector
vector of numbers between 0 and 1 that measure the degree to which each atom is within the volume of interest: INCYLINDERThis 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. More details ATOMSthe group of atoms that you would like to investigate=1-100 CENTERthe atom whose vicinity we are interested in examining=f DIRECTIONthe direction of the long axis of the cylinder=X RADIUSa switching function that gives the extent of the cylinder in the plane perpendicular to the direction. Options for this keyword are explained in the documentation for LESS_THAN.={TANH R_0=1.5} SIGMAthe width of the function to be used for kernel density estimation=0.1 LOWER the lower boundary on the direction parallel to the long axis of the cylinder=-1.0 UPPER the upper boundary on the direction parallel to the long axis of the cylinder=1.0
sThe SUM action with label s calculates the following quantities:
 Quantity   
 Type   
 Description  
s
scalar
the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=a PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=s FILEthe name of the file on which to output these quantities=colvar

Notice that now the cylinder is centered on the x axis rather than the z axis as we have changed the input for the DIRECTION keyword.

You can also calculate the average values of symmetry functions in the cylinder of interest by using inputs similar to those described the documentation for the AROUND action. In other words, you can swap out AROUND actions for an INCLYLINDER actions. Also as with AROUND, earlier versions of PLUMED used a different syntax for doing these types of calculations, which can still be used with this new version of the command. However, we strongly recommend using the newer syntax.

Syntax

The following table describes the keywords and options that can be used with this action