Today following some guidance I was given by a Java expert, I finally managed to get methods in the main class of the simulation to take in arguments passed from the command line, set variables to equal these using setter methods, and then return them using getter methods. This is a large breakthrough which has taken me literally months to get to. In my next coding session, the task will be to start automating simulation so that it can run on its own, using some sort of scripting to kick it off with appropriate input values. In the meanwhile, gone to celebrate!