KDE

This is part of the gridtools module

Create a histogram from the input scalar/vector/matrix using KDE

Examples

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	a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments

Compulsory keywords

ARG	the label for the value that should be used to construct the histogram
GRID_MIN	( default=auto ) the lower bounds for the grid
GRID_MAX	( default=auto ) the upper bounds for the grid
METRIC	the inverse covariance to use for the kernels that are added to the grid
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
KERNEL	( default=GAUSSIAN ) the kernel function you are using. More details on the kernels available in plumed plumed can be found in kernelfunctions.
CONCENTRATION	the concentration parameter for Von Mises-Fisher distributions (only required for SPHERICAL_KDE)

Options

SERIAL	( default=off ) do the calculation in serial. Do not parallelize
IGNORE_IF_OUT_OF_RANGE	( default=off ) if a kernel is outside of the range of the grid it is safe to ignore
HEIGHTS	this keyword takes the label of an action that calculates a vector of values. The elements of this vector are used as weights for the Gaussians.
VOLUMES	this keyword take the label of an action that calculates a vector of values. The elements of this vector divided by the volume of the Gaussian are used as weights for the Gaussians
BANDWIDTH	the bandwidths for kernel density esimtation
GRID_BIN	the number of bins for the grid
GRID_SPACING	the approximate grid spacing (to be used as an alternative or together with GRID_BIN)