Covariance Analysis

The dynamics covariance statement computes the covariances of the spatial atom displacements of a dynamics trajectory for selected pairs of atoms. The function

$$s_{1,2}= {{<x[1]*x[2]>}\over{\sqrt{<x[1]**2><x[2]**2>}}}$$ (12.1)

is calculated for all atoms #1 in SET1 and #2 in SET2 where $x[\cdot ]$ is the coordinate displacement with respect to the average, and the corresponding covariance matrix is written to a file.