Back to the software engineering process side of things - as mentioned in previous post the plan is to build the document set around;
and the functional, data and physical models outlined in;
References for two of these models are;
Functional Model = http://en.wikipedia.org/wiki/Function_model specifically Functional perspective section.
Data Model = http://en.wikipedia.org/wiki/Data_model
Now the job is to figure out exactly which elements of these can be best used to help represent the code. Not all of these models are appropriate for this form of scientific programming. Especially when the coding uses an ODE solver which for me feels like the code operates in more of an Object Oriented mode - where the objects are based around the physical forces acting on the ship. More on this later.