NEIGHBORS

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

Build a matrix with ones in for the N nearest neighbours of an atom

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 matrix in which the ij element is one if the ij-element of the input matrix is one of the NLOWEST/NHIGHEST elements on that row of the input matrix and zero otherwise

Compulsory keywords

ARG	the label of an adjacency/distance matrix that will be used to find the nearest neighbors
NLOWEST	( default=0 ) in each row of the output matrix set the elements that correspond to the n lowest elements in each row of the input matrix equal to one
NHIGHEST	( default=0 ) in each row of the output matrix set the elements that correspond to the n highest elements in each row of the input matrix equal to one

Options

SERIAL

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