SKETCHMAP_SMACOF
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.

Optimize the sketch-map stress function using the SMACOF algorithm.

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
coord the low-dimensional projections of the various input configurations
The data to analyze can be the output from another analysis algorithm
USE_OUTPUT_DATA_FROM use the output of the analysis performed by this object as input to your new analysis object
Compulsory keywords
HIGH_DIM_FUNCTION ( default=as in input action ) the parameters of the switching function in the high dimensional space
LOW_DIM_FUNCTION ( default=as in input action ) the parameters of the switching function in the low dimensional space
MIXPARAM ( default=0.0 ) the amount of the pure distances to mix into the stress function
SMACOF_TOL ( default=1E-4 ) the tolerance for each SMACOF cycle
SMACOF_MAXCYC ( default=1000 ) maximum number of optimization cycles for SMACOF algorithm
SMAP_TOL ( default=1E-4 ) the tolerance for sketch-map
SMAP_MAXCYC ( default=100 ) maximum number of optimization cycles for iterative sketch-map algorithm
REGULARISE_PARAM ( default=0.001 ) this is used to ensure that we don't divide by zero when updating weights
Options
SERIAL ( default=off ) do the calculation in serial. Do not use MPI
LOWMEM

( default=off ) lower the memory requirements