| 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
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