KDE

This is part of the gridtools module |

Create a histogram from the input scalar/vector/matrix using KDE

- 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 |

.#!value | a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments |

- Compulsory keywords

GRID_MIN | ( default=auto ) the lower bounds for the grid |

GRID_MAX | ( default=auto ) the upper bounds for the grid |

METRIC | the inverse covariance to use for the kernels that are added to the grid |

CUTOFF | ( default=6.25 ) the cutoff at which to stop evaluating the kernel functions is set equal to sqrt(2*x)*bandwidth in each direction where x is this number |

KERNEL | ( default=GAUSSIAN ) the kernel function you are using. More details on the kernels available in plumed plumed can be found in kernelfunctions. |

CONCENTRATION | the concentration parameter for Von Mises-Fisher distributions (only required for SPHERICAL_KDE) |

- Options

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

IGNORE_IF_OUT_OF_RANGE | ( default=off ) if a kernel is outside of the range of the grid it is safe to ignore |

ARG | the input for this action is the scalar output from one or more other actions. The particular scalars that you will use are referenced using the label of the action. If the label appears on its own then it is assumed that the Action calculates a single scalar value. The value of this scalar is thus used as the input to this new action. If * or *.* appears the scalars calculated by all the proceeding actions in the input file are taken. Some actions have multi-component outputs and each component of the output has a specific label. For example a DISTANCE action labelled dist may have three components x, y and z. To take just the x component you should use dist.x, if you wish to take all three components then use dist.*.More information on the referencing of Actions can be found in the section of the manual on the PLUMED Getting Started. Scalar values can also be referenced using POSIX regular expressions as detailed in the section on Regular Expressions. To use this feature you you must compile PLUMED with the appropriate flag.. You can use multiple instances of this keyword i.e. ARG1, ARG2, ARG3... |

HEIGHTS | this keyword takes the label of an action that calculates a vector of values. The elements of this vector are used as weights for the Gaussians. |

VOLUMES | this keyword take the label of an action that calculates a vector of values. The elements of this vector divided by the volume of the Gaussian are used as weights for the Gaussians |

BANDWIDTH | the bandwidths for kernel density esimtation |

GRID_BIN | the number of bins for the grid |

GRID_SPACING | the approximate grid spacing (to be used as an alternative or together with GRID_BIN) |