| 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. |
This can be used to output the data that has been stored in an Analysis object.
- Compulsory keywords
NLOW_DIM | the dimension of the low dimensional space in which the projections will be constructed |
MATRIX | the matrix of distances between points that you want to reproduce in your sketch-map projection |
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 |
ANNEAL_RATE | ( default=0.5 ) the rate at which to do the annealing |
ANNEAL_STEPS | ( default=10 ) the number of steps of annealing to do |
CGTOL | ( default=1E-6 ) the tolerance for the conjugate gradient minimization |
NCYCLES | ( default=5 ) the number of cycles of global optimization to attempt |
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 |
- Examples