The main program calls initializations, runs through the main loop, and checks for exit conditions. There is a timing routine which can be uncommented to get information like the number of timesteps/second achieved.
There is also a small set of broad inputs and control parameters that affect an overall run, such as the timestep, some choices about normalizations, whether the run should be electrostatic or electromagnetic, etc. These are set in the run_parameters module.
At present, the documentation on this site consists mainly of source code (with comments) together with a higher-level description of the input parameters which the users control. A careful look at the input namelists will generally help to establish what the code can and cannot do for you. Please send questions to the webmaster (link in upper right corner).