Decide what is printed to screen and what is written to a log file
Created by: thopri
Right now most of the information that PyNEMO is outputting is saved to a log file. However other stuff is printed to the screen. It will be useful to decide what should be printed to console (e.g. some form of progress indication) and what should be printed to log (e.g. full diagnostic information, run time warnings and run time errors). Then apply this consistently to the module.