TD_CHI

This is part of the ves module | |

It is only available if you configure PLUMED with ./configure –enable-modules=ves . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list. |

Chi distribution (static).

Employ a target distribution given by a chi distribution that is defined as

\[ p(s) = \frac {2^{1-\frac{k}{2}}} {\sigma \, \Gamma\left(\frac{k}{2}\right) } \, \left(\frac{s-a}{\sigma}\right)^{k-1} \, \exp\left(- \frac{1}{2} \left(\frac{s-a}{\sigma}\right)^2\right), \]

where \(a\) is the minimum of the distribution that is defined on the interval \([a,\infty)\), the parameter \(k\) (given as a positive integer larger than 1) determines how far the peak of the distribution is from the minimum (known as the "degrees of freedom"), and the parameter \(\sigma>0\) determines the broadness of the distribution.

The minimum \(a\) is given using the MINIMUM keyword, the parameter \(k\) is given using the KAPPA keyword, and the parameter \(\sigma\) is given using the SIGMA keyword.

This target distribution action is only defined for one dimension, for multiple dimensions it should be used in combination with the TD_PRODUCT_DISTRIBUTION action.

- Examples

Chi distribution with \(a=10.0\), \(\sigma=2.0\), and \(k=2\)

Click on the labels of the actions for more information on what each action computes

td:TD_CHIMINIMUM=10.0compulsory keywordThe minimum of the chi distribution.SIGMA=2.0compulsory keywordThe \f$\sigma\f$ parameter of the chi distribution given as a positive number.KAPPA=2compulsory keywordThe \f$k\f$ parameter of the chi distribution given as positive integer larger than 1.

The Chi distribution is only defined for one dimension so for multiple dimensions we have to use it in combination with the TD_PRODUCT_DISTRIBUTION action as shown in the following example where we have a uniform distribution for argument 1 and a Chi distribution for argument 1

Click on the labels of the actions for more information on what each action computes

td_uni:TD_UNIFORMtd_chi:TD_CHIMINIMUM=-10.0compulsory keywordThe minimum of the chi distribution.SIGMA=2.0compulsory keywordThe \f$\sigma\f$ parameter of the chi distribution given as a positive number.KAPPA=2compulsory keywordThe \f$k\f$ parameter of the chi distribution given as positive integer larger than 1.td_pd:TD_PRODUCT_DISTRIBUTIONDISTRIBUTIONS=compulsory keywordLabels of the one-dimensional target distribution actions for each argument to be used in the product distribution.td_uni,td_chi

- Glossary of keywords and components

- Compulsory keywords

MINIMUM | The minimum of the chi distribution. |

SIGMA | The \(\sigma\) parameter of the chi distribution given as a positive number. |

KAPPA | The \(k\) parameter of the chi distribution given as positive integer larger than 1. |

- Options

SHIFT_TO_ZERO | ( default=off ) Shift the minimum value of the target distribution to zero. This can for example be used to avoid negative values in the target distribution. If this option is active the distribution will be automatically normalized. |

NORMALIZE | ( default=off ) Renormalized the target distribution over the intervals on which it is defined to make sure that it is properly normalized to 1. In most cases this should not be needed as the target distributions should be normalized. The code will issue a warning (but still run) if this is needed for some reason. |

WELLTEMPERED_FACTOR | Broaden the target distribution such that it is taken as [p(s)]^(1/ \(\gamma\)) where \(\gamma\) is the well tempered factor given here. If this option is active the distribution will be automatically normalized. |