Coding Considerations

I found it useful to create a file with all the normal mode eigenvalues and eigenvectors generated from solving the linear problem. This file is then read by the code solving the nonlinear problem. I also created a file containing the initial displacements and velocities and wrote a similar file at the end of the integration process, so I could use it as input for further running if I wanted to. In that way standard input can be reserved for parameter values and filenames and standard output can be reserved for the time series of normal mode energies. However, you are welcome to arrange the data flow in any way you like.