INSPHERE

	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:

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

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. In other words:

\[ r = sqrt{ ( x_i - x_0)^2 + ( y_i - y_0)^2 + ( z_i - z_0)^2} \]

In short this function, \(\sigma(r_{xy})\), measures whether or not the CV is within a sphere that is centered on the position of the atom specified using the keyword 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 sphere of radius 1.5 nm that is centered on the position of atom 101.

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

contract shortcuts

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}  The COORDINATIONNUMBER action with label c1 calculates a single scalar value
d2: INSPHERE 
ATOM
the atom whose vicinity we are interested in examining 
=101 
DATA
the label of an action that calculates multicolvars. 
=c1 
RADIUS
compulsory keyword 
the switching function that tells us the extent of the sphereical region of interest
={TANH R_0=1.5}  
MEAN
( default=off ) calculate the average value of the colvar inside the region of interest
 The INSPHERE action with label d2 calculates a single scalar value
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 The PRINT action with label 

c1_grp: GROUP 
ATOMS
the numerical indexes for the set of atoms in the group. 
=1-100 The GROUP action with label c1_grp defines a group of atoms so that they can be referred to later in the input
c1_mat: CONTACT_MATRIX 
GROUP
specifies the list of atoms that should be assumed indistinguishable. 
=1-100 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms.
=RATIONAL,R_0=0.1 The CONTACT_MATRIX action with label c1_mat
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   

Or alternatively by using



 ATOM  
the atom whose vicinity we are interested in examining   

Compulsory keywords



 KERNEL  
( default=gaussian ) the type of kernel function to be used   

 RADIUS  
the switching function that tells us the extent of the sphereical region of interest   

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  



 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