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.

- 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 |

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 |