SMACOF_MDS
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 multidimensional scaling stress function using the SMACOF algorithm.

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

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

Quantity Keyword Description
gradient GRADIENT the gradient
vmean VMEAN the norm of the mean vector. The output component can be referred to elsewhere in the input file by using the label.vmean
vsum VSUM the norm of sum of vectors. The output component can be referred to elsewhere in the input file by using the label.vsum
spath SPATH the position on the path
gspath GPATH the position on the path calculated using trigonometry
gzpath GPATH the distance from the path calculated using trigonometry
zpath ZPATH the distance from the path
altmin ALT_MIN the minimum value. This is calculated using the formula described in the description of the keyword so as to make it continuous.
between BETWEEN the number/fraction of values within a certain range. This is calculated using one of the formula described in the description of the keyword so as to make it continuous. You can calculate this quantity multiple times using different parameters.
highest HIGHEST the highest of the quantities calculated by this action
lessthan LESS_THAN the number of values less than a target value. This is calculated using one of the formula described in the description of the keyword so as to make it continuous. You can calculate this quantity multiple times using different parameters.
lowest LOWEST the lowest of the quantities calculated by this action
max MAX the maximum value. This is calculated using the formula described in the description of the keyword so as to make it continuous.
mean MEAN the mean value. The output component can be referred to elsewhere in the input file by using the label.mean
min MIN the minimum value. This is calculated using the formula described in the description of the keyword so as to make it continuous.
moment MOMENTS the central moments of the distribution of values. The second moment would be referenced elsewhere in the input file using label.moment-2, the third as label.moment-3, etc.
morethan MORE_THAN the number of values more than a target value. This is calculated using one of the formula described in the description of the keyword so as to make it continuous. You can calculate this quantity multiple times using different parameters.
sum SUM the sum of values
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
SMACOF_TOL ( default=1E-4 ) tolerance for the SMACOF optimization algorithm
SMACOF_MAXCYC ( default=1000 ) maximum number of optimization cycles for SMACOF algorithm
Options
SERIAL ( default=off ) do the calculation in serial. Do not use MPI
LOWMEM

( default=off ) lower the memory requirements

Examples