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

Construct a sketch map projection of the input data

Examples
Glossary of keywords and components
Description of components
Quantity Description
.#!value the sketch-map projection of the input points

In addition the following quantities can be calculated by employing the keywords listed below

Quantity Keyword Description
osample PROJECT_ALL the out-of-sample projections
Compulsory keywords
NLOW_DIM number of low-dimensional coordinates required
ARG the matrix of high dimensional coordinates that you want to project in the low dimensional space
HIGH_DIM_FUNCTION the parameters of the switching function in the high dimensional space
LOW_DIM_FUNCTION the parameters of the switching function in the low dimensional space
CGTOL ( default=1E-6 ) The tolerance for the conjugate gradient minimization that finds the projection of the landmarks
MAXITER ( default=1000 ) maximum number of optimization cycles for optimisation algorithms
NCYCLES ( default=0 ) The number of cycles of pointwise global optimisation that are required
BUFFER ( default=1.1 ) grid extent for search is (max projection - minimum projection) multiplied by this value
CGRID_SIZE ( default=10 ) number of points to use in each grid direction
FGRID_SIZE ( default=0 ) interpolate the grid onto this number of points – only works in 2D
OS_CGTOL ( default=1E-6 ) The tolerance for the conjugate gradient minimization that finds the out of sample projections
SMACTOL ( default=1E-4 ) the tolerance for the smacof algorithm
SMACREG ( default=0.001 ) this is used to ensure that we don't divide by zero when updating weights for SMACOF algorithm
Options
PROJECT_ALL ( default=off ) if the input are landmark coordinates then project the out of sample configurations
USE_SMACOF

( default=off ) find the projection in the low dimensional space using the SMACOF algorithm

WEIGHTS a vector containing the weights of the points