Implemented logging using Log4cxx library:
- added loggers and replaced cout with LOG4CXX_* calls.
- implemented configuration of Log4cxx by property file.
- added basic logging configuration file "MolSim.logging.conf".

In MolSim.cpp: moved code for commandline parsing from main() function to a new function parseParameters() to make code easier to read.

Updated Doxygen documentation.