Computes the reorientation autocorrelation function for a list of multibodies. All multibodies in the list must consist of exactly 2 bodies so that they define a single vector (for example corresponding to a bond or other some intramolecular vector)
\[C(\Delta t) = P_n \left[\sum_{k=1}^{S} \frac{1}{N(s)} \sum_{i=1}^{M(s)} (\hat{r_i}(s_k+\Delta t) \cdot \hat{r_i}(s_k)) \right]\]where S is the number of start times employed, M is the number of multibodies, $\hat{r}_i(t)$ is the unit vector pointing from the first to second particle within the multibody at time $t$, $\Delta t$ is a timegap, and $P_n$ is the Legendre polynomial of the $n^{th}$ order.
As a few example of typical usage, this tool can be employed to compute bond vector autocorrelation functions by constructing multibodies out of each pair of bonded atoms. It can be employed to compute chain end to end vector autocorrelation functions by constructing multibodies out of the atoms at the ends of a polymer chain. Other intramolecular vector autocorrelation functions can be computed in an analagous manner.
raf <output filename> <name of multibody_list to analyze> <Legendre polynomial order to employ: either “1” or “2”> <optional: “xyz” or “xy” or “xz” or “yz” or “x” or “y” or “z”>
The optional argument specifies which spatial dimensions are including in the calculation (i.e. in the dot product). This defaults to “xyz” if not specified, in which case the full three-dimensional dot product is employed. If, for example, “xy” is specified, only the x and y dimensions of the unit vector are included in the dot product.