INENVELOPE

This is part of the multicolvar 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
this keyword is used for colvars such as coordination number. 
=14401-74134:3 
LOWMEM
( default=off ) lower the memory requirements 
 The DENSITY action with label d1
fi: INENVELOPE 
DATA
compulsory keyword 
The multicolvar that calculates the set of base quantities that we are interested
in 
=d1 
ATOMS
the atom whose positions we are constructing a field from. 
=1-14400 
CONTOUR
compulsory keyword 
a switching function 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 estimation 
=0.1,0.1,0.1 
LOWMEM
( default=off ) lower the memory requirements 
 The INENVELOPE action with label fi calculates a single scalar value
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 The PRINT action with label 

Glossary of keywords and components

Description of components

When the label of this action is used as the input for a second you are not referring to a scalar quantity as you are in regular collective variables. The label is used to reference the full set of quantities calculated by the action. This is usual when using MultiColvar functions. Generally when doing this the previously calculated multicolvar will be referenced using the DATA keyword rather than ARG.

This Action can be used to calculate the following scalar quantities directly. These quantities are calculated by employing the keywords listed below. These quantities can then be referenced elsewhere in the input file by using this Action's label followed by a dot and the name of the quantity. Some of them can be calculated multiple times with different parameters. In this case the quantities calculated can be referenced elsewhere in the input by using the name of the quantity followed by a numerical identifier e.g. label.lessthan-1, label.lessthan-2 etc. When doing this and, for clarity we have made it so that the user can set a particular label for each of the components. As such by using the LABEL keyword in the description of the keyword input you can customize the component name

Quantity	Keyword	Description
vmean	VMEAN	the norm of the mean vector. The output component can be referred to elsewhere in the input file by using the label.vmean
between	BETWEEN	the number/fraction of values within a certain range. This is calculated using one of the formula described in the description of the keyword so as to make it continuous. You can calculate this quantity multiple times using different parameters.
lessthan	LESS_THAN	the number of values less than a target value. This is calculated using one of the formula described in the description of the keyword so as to make it continuous. You can calculate this quantity multiple times using different parameters.
mean	MEAN	the mean value. The output component can be referred to elsewhere in the input file by using the label.mean
morethan	MORE_THAN	the number of values more than a target value. This is calculated using one of the formula described in the description of the keyword so as to make it continuous. You can calculate this quantity multiple times using different parameters.
sum	SUM	the sum of values

The atoms involved can be specified using

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

DATA	The multicolvar that calculates the set of base quantities that we are interested in
KERNEL	( default=gaussian ) the type of kernel function to be used
BANDWIDTH	the bandwidths for kernel density estimation
CONTOUR	a switching function that tells PLUMED how large the density should be

Options

NUMERICAL_DERIVATIVES	( default=off ) calculate the derivatives for these quantities numerically
NOPBC	( default=off ) ignore the periodic boundary conditions when calculating distances
SERIAL	( default=off ) do the calculation in serial. Do not use MPI
LOWMEM	( default=off ) lower the memory requirements
TIMINGS	( default=off ) output information on the timings of the various parts of the calculation
OUTSIDE	( default=off ) calculate quantities for colvars that are on atoms outside the region of interest
VMEAN	calculate the norm of the mean vector. The final value can be referenced using label.vmean. You can use multiple instances of this keyword i.e. VMEAN1, VMEAN2, VMEAN3... The corresponding values are then referenced using label.vmean-1, label.vmean-2, label.vmean-3...
MEAN	take the mean of these variables. The final value can be referenced using label.mean. You can use multiple instances of this keyword i.e. MEAN1, MEAN2, MEAN3... The corresponding values are then referenced using label.mean-1, label.mean-2, label.mean-3...
LESS_THAN	calculate the number of variables less than a certain target value. This quantity is calculated using \(\sum_i \sigma(s_i)\), where \(\sigma(s)\) is a switchingfunction. The final value can be referenced using label.lessthan. You can use multiple instances of this keyword i.e. LESS_THAN1, LESS_THAN2, LESS_THAN3... The corresponding values are then referenced using label.lessthan-1, label.lessthan-2, label.lessthan-3...
MORE_THAN	calculate the number of variables more than a certain target value. This quantity is calculated using \(\sum_i 1.0 - \sigma(s_i)\), where \(\sigma(s)\) is a switchingfunction. The final value can be referenced using label.morethan. You can use multiple instances of this keyword i.e. MORE_THAN1, MORE_THAN2, MORE_THAN3... The corresponding values are then referenced using label.morethan-1, label.morethan-2, label.morethan-3...
BETWEEN	calculate the number of values that are within a certain range. These quantities are calculated using kernel density estimation as described on histogrambead. The final value can be referenced using label.between. You can use multiple instances of this keyword i.e. BETWEEN1, BETWEEN2, BETWEEN3... The corresponding values are then referenced using label.between-1, label.between-2, label.between-3...
HISTOGRAM	calculate how many of the values fall in each of the bins of a histogram. This shortcut allows you to calculates NBIN quantities like BETWEEN. The final value can be referenced using label.histogram. You can use multiple instances of this keyword i.e. HISTOGRAM1, HISTOGRAM2, HISTOGRAM3... The corresponding values are then referenced using label.histogram-1, label.histogram-2, label.histogram-3...
SUM	calculate the sum of all the quantities. The final value can be referenced using label.sum. You can use multiple instances of this keyword i.e. SUM1, SUM2, SUM3... The corresponding values are then referenced using label.sum-1, label.sum-2, label.sum-3...