SKETCH_MAP

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.

- Examples

- Glossary of keywords and components

- 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 |