The analysis facility provides the means for analyzing the trajectory of a dynamics calculation. Since there is a wealth of information in these runs, one must be able to look at the information at various levels of detail. Two methods are provided for such analysis: one can look at numerical measures such as the average or various moments of the time distribution of all internal coordinates or atoms at once or one can calculate correlation functions on a few atoms or internal coordinates. In this chapter we shall discuss the methods used to look at all the properties simultaneously, and in the next chapter, we shall look at correlation functions, see Correlation Functions.
To analyze the dynamical properties of the system en masse, the table, see Tables, is used. This allows one to use the table manipulation commands to massage the information in the most appropriate way.
In order to perform the analysis successfully, one must understand the flow of data. The coordinates and/or velocities output during the dynamics runs are summed in various ways to provide the basis for calculating various moments of the time distribution. This information is put into one of several averaging data structures which are described below. One can read or write these averages using the analysis facility's I/O commands, see I/O in Analysis. One can combine two averaging data structures to get long time averages, and one can add more points from other trajectories to an existing average. The flow of data is diagrammed below:
Dynamics Trajectory | v Accumulation Command | v Averaging Data Structures<----+ | | | Combination Command | | +------------------+ | v Build Command | v Table