VES_OUTPUT_BASISFUNCTIONS

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. |

Output basis functions to file.

This action can be used to write out to a grid file the values and derivatives of given basis functions. This is normally used for debugging when programming new types of basis functions. For example, it is possible to calculate the derivatives numerically and compare to the analytically calculated derivatives.

This action is normally used through the driver.

- Examples

In the following input we define a Legendre polynomials basis functions of order 14 over the interval -4.0 to 4.0 and output their values and derivatives to files called bfL.values.data and bfL.derivs.data.

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

bfL:BF_LEGENDRE ...ORDER=14compulsory keywordThe order of the basis function expansion.MINIMUM=-4.0compulsory keywordThe minimum of the interval on which the basis functions are defined.MAXIMUM=4.0 ... VES_OUTPUT_BASISFUNCTIONS ...compulsory keywordThe maximum of the interval on which the basis functions are defined.BASIS_FUNCTIONS=compulsory keywordthe label of the basis functions that you want to usebfLGRID_BINS=200the number of bins used for the grid for writing the basis function values and derivatives.FORMAT_VALUES_DERIVS=%13.6f ...the numerical format of the basis function values and derivatives written to file.

This input should be run through the driver by using a command similar to the following one where the trajectory/configuration file configuration.gro is needed to trick the code to exit correctly.

plumed driver --plumed plumed.dat --igro configuration.gro

- Glossary of keywords and components

- Compulsory keywords

BASIS_FUNCTIONS | the label of the basis functions that you want to use |

- Options

IGNORE_PERIODICITY | ( default=off ) if the periodicity of the basis functions should be ignored. |

NUMERICAL_DERIVATIVES | ( default=off ) if the derivatives of the basis functions should be calculated numerically. |

GRID_BINS | the number of bins used for the grid for writing the basis function values and derivatives. The default value is 1000. |

GRID_MIN | the minimum of the grid for writing the basis function values and derivatives. By default it is the minimum of the interval on which the basis functions are defined. |

GRID_MAX | the maximum of the grid for writing the basis function values and derivatives. By default it is the maximum of the interval on which the basis functions are defined. |

FILE_VALUES | filename of the file on which the basis function values are written. By default it is BF_LABEL.values.data. |

FILE_DERIVS | filename of the file on which the basis function derivatives are written. By default it is BF_LABEL.derivs.data. |

FORMAT_VALUES_DERIVS | the numerical format of the basis function values and derivatives written to file. By default it is %15.8f. . You can also use FORMAT_VALUES and FORMAT_DERIVS to give the numerical formats separately. |

FORMAT_VALUES | the numerical format of the basis function derivatives written to file. By default it is %15.8f. |

FORMAT_DERIVS | the numerical format of the basis function values written to file. By default it is %15.8f. |

FILE_TARGETDIST_AVERAGES | filename of the file on which the averages over the target distributions are written. By default it is BF_LABEL.targetdist-averages.data. |

FORMAT_TARGETDIST_AVERAGES | the numerical format of the target distribution averages written to file. By default it is %15.8f. |

FILE_TARGETDIST | filename of the files on which the target distributions are written. By default it is BF_LABEL.targetdist-#.data. |

TARGET_DISTRIBUTION | the target distribution to be used. You can use multiple instances of this keyword i.e. TARGET_DISTRIBUTION1, TARGET_DISTRIBUTION2, TARGET_DISTRIBUTION3... |