GRADIENT

	This is part of the crystallization module
	It is only available if you configure PLUMED with ./configure –enable-modules=crystallization . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list.

Calculate the gradient of the average value of a multicolvar value

This command allows you to calculate the collective variable discussed in [53].

Examples

The input below calculates the gradient of the density of atoms in the manner described in [53] in order to detect whether or not atoms are distributed uniformly along the x-axis of the simulation cell.

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. 
=1-50 The DENSITY action with label d1
s1: GRADIENT 
ORIGIN
we will use the position of this atom as the origin in our calculation. 
=1 
DATA
compulsory keyword 
The multicolvar that calculates the set of base quantities that we are interested
in 
=d1 
DIR
compulsory keyword ( default=xyz )
the directions in which we are calculating the gradient. 
=x 
NBINS
compulsory keyword 
number of bins to use in each direction for the calculation of the gradient 
=4 
SIGMA
compulsory keyword ( default=1.0 )
the width of the function to be used for kernel density estimation 
=1.0 The GRADIENT action with label s1 calculates a single scalar value
PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=s1 
FILE
the name of the file on which to output these quantities 
=colvar The PRINT action with label 

The input below calculates the coordination numbers of the 50 atoms in the simulation cell. The gradient of this quantity is then evaluated in the manner described using the equation above to detect whether the average values of the coordination number are uniformly distributed along the x-axis of the simulation cell.

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

d2: COORDINATIONNUMBER 
SPECIES
this keyword is used for colvars such as coordination number. 
=1-50 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching
function defined above. 
={RATIONAL R_0=2.0}  
MORE_THAN
calculate the number of variables more than a certain target value. 
={EXP R_0=4.0}  The COORDINATIONNUMBER action with label d2 calculates a single scalar value
s2: GRADIENT 
ORIGIN
we will use the position of this atom as the origin in our calculation. 
=1 
DATA
compulsory keyword 
The multicolvar that calculates the set of base quantities that we are interested
in 
=d2 
DIR
compulsory keyword ( default=xyz )
the directions in which we are calculating the gradient. 
=x 
NBINS
compulsory keyword 
number of bins to use in each direction for the calculation of the gradient 
=4 
SIGMA
compulsory keyword ( default=1.0 )
the width of the function to be used for kernel density estimation 
=1.0 The GRADIENT action with label s2 calculates a single scalar value
PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=s2 
FILE
the name of the file on which to output these quantities 
=colvar The PRINT action with label 

Glossary of keywords and components

The atoms involved can be specified using

ORIGIN

we will use the position of this atom as the origin in our calculation. 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
DIR	( default=xyz ) the directions in which we are calculating the gradient. Should be x, y, z, xy, xz, yz or xyz
NBINS	number of bins to use in each direction for the calculation of the gradient
SIGMA	( default=1.0 ) the width of the function to be used for kernel density estimation
KERNEL	( default=gaussian ) the type of kernel function to be used

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