I am using openflower for some academic work, so it is important for me to understand what exactly the program is doing. In the reference manual, I do not understand how equation 4.4 relates to the previous equations, or how the last term of 4.1 relates to 2.2. I have the book that you referenced later on, but I have not been able to find the connecting information. Any additional references or insights on your thought processes would be helpful.
On another note, does there exist a summary of the function of the various components of the program? I built the doxygen documentation, but I did not find it very helpful when trying to understand what peices of the software performed what function. I would eventually like to modify the program to model different problems, but before I can change it, I need to know how it works!