Module: matrixtools

Description	Usage
tools for constructing and manipulating matrices
Authors: Gareth Tribello

Details

Each line in a PLUMED input file defines and action. The actions in the input file communicate through the passing of values. In early versions of PLUMED these values were scalars. However, from PLUMED 2.10 onwards you can pass values that are scalars, vectors, matrices or functions on grids.

The tools in this module all you to construct or manipulate matrices. Please note that you can also use the tools in the adjmat module to construct matrices that might be used in the input to the actions in this module.

Actions

The following actions are part of this module

Tags

ANALYSIS MCOLVAR REWEIGHTING COLVAR

ANALYSIS: tools for analysing trajectories MCOLVAR: actions for calculating a vector of colvars REWEIGHTING: actions for computing weights that can be used when calculating the unbiased distribution COLVAR: a function of a set of atomic positions that returns a scalar

Name	Description	Tags
COVARIANCE_MATRIX	Calculate a covariance matix	REWEIGHTING
DETERMINANT	Calculate the determinant of a matrix	MCOLVAR
DIAGONALIZE	Calculate the eigenvalues and eigenvectors of a square matrix	ANALYSIS
DISSIMILARITIES	Calculate the matrix of dissimilarities between a trajectory of atomic configurations.	ANALYSIS
INVERT_MATRIX	Calculate the inverse of the input matrix	MCOLVAR
MATRIX_PRODUCT	Calculate the product of two matrices	MCOLVAR
MATRIX_VECTOR_PRODUCT	Calculate the product of the matrix and the vector	MCOLVAR
OUTER_PRODUCT	Calculate the outer product matrix of two vectors	COLVAR
TRANSPOSE	Calculate the transpose of a matrix	MCOLVAR
VORONOI	Do a voronoi analysis	MCOLVAR