INENVELOPE

This is part of the volumes module

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.

This collective variable can be used to determine whether colvars are within region where the density of a particular atom is high. This is achieved by calculating the following function at the point where the atom is located \((x,y,z)\):

\[ w_j = 1 - \sigma\left[ \sum_{i=1}^N K\left( \frac{x-x_i}{\sigma_x},\frac{y-y_i}{\sigma_y},\frac{z-z_i}{\sigma_z} \right) \right] \]

Here \(\sigma\) is a switchingfunction and \(K\) is a kernelfunctions. The sum runs over the atoms specified using the ATOMS keyword and a \(w_j\) value is calculated for each of the central atoms of the input multicolvar.

Examples

The input below calculates a density field from the positions of atoms 1-14400. The number of the atoms that are specified in the DENSITY action that are within a region where the density field is greater than 2.0 is then calculated.

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

d1: DENSITY 
SPECIES
compulsory keyword 
the atoms in the group 
=14401-74134:3 
LOWMEM
 could not find this keyword 
  You cannot view the components that are calculated by each action for this input file. Sorry 
fi: INENVELOPE 
DATA
the label of an action that calculates multicolvars. 
=d1 
ATOMS
the group of atoms that you would like to investigate. 
=1-14400 
CONTOUR
compulsory keyword 
a switching funciton that tells PLUMED how large the density should be 
={RATIONAL D_0=2.0 R_0=1.0}  
BANDWIDTH
compulsory keyword 
the bandwidths for kernel density esimtation 
=0.1,0.1,0.1 
LOWMEM
 could not find this keyword 
  You cannot view the components that are calculated by each action for this input file. Sorry 
PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=fi 
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	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
FIELD_ATOMS	the atom whose positions we are constructing a field from. 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
BANDWIDTH	the bandwidths for kernel density esimtation
CONTOUR	a switching funciton that tells PLUMED how large the density should be
CUTOFF	( default=6.25 ) the cutoff at which to stop evaluating the kernel functions is set equal to sqrt(2*x)*bandwidth in each direction where x is this number

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