SKETCHMAP_READ

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. |

Read in a sketch-map projection from an input file

- Examples

- Glossary of keywords and components

- Description of components

The names of the components in this action can be customized by the user in the actions input file. However, in addition to the components that can be customized the following quantities will always be output

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 |

- 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 |

TYPE | ( default=OPTIMAL-FAST ) the manner in which distances are calculated. More information on the different metrics that are available in PLUMED can be found in the section of the manual on Distances from reference configurations |

REFERENCE | the file containing the sketch-map projection |

PROPERTY | the property to be used in the index. This should be in the REMARK of the reference |

- Options

SERIAL | ( default=off ) do the calculation in serial. Do not use MPI |

LOWMEM | ( default=off ) lower the memory requirements |

DISABLE_CHECKS | ( default=off ) disable checks on reference input structures. |