Congratulations, you have just written your first useful MATSim controler. You can now start to extend it, add your own re-planning modules or implement your own mobility simulation. A good starting point may be to improve your current controler by eliminating some of the flaws. As an example, currently the events of each iteration overwrite the previous iteration’s events. You may want to create a new eventWriter for every iteration. In that case, do not forget to remove the old eventWriter with events.removeHandler(eventWriter). Or you may just re-init the eventWriter with a new filename: eventWriter.init(newFilename).
Another possibility is to move some hard coded settings to the configuration file and using config.getParam(moduleName, paramName) to access the values. The number of iterations may be a good example of a value that could be specified in the configuration file.
You can find additional documentation on our website in the developer’s guide at www.matsim.org.

If you plan to set up your own scenario, you need a network and a description of a population. Have a look at the provided example files to get a better understanding of the file formats.  The creation of the population can be based on a variety of data (census, commuter matrices, …), whatever is available. The page “Building a new Scenario” (http://matsim.org/docs/new-scenario) gives further information about that topic.
If you want to customize your analysis, reading the Event and Controler Programming tutorials is highly recommended.

Have fun with MATSim! We would be happy to hear from you what for you are using MATSim.