Removed direct access to timeloop->loop variable
Removed all public variables from timeloop and made them private.
Added accessor functions in order to retrieve the values
Renamed the setTimeLimit function to setTimeStepLimit
Cleaned up the main loop and added better comments
Renamed the setTimeDep function to updateTimeDep
Renamed the precompiler statements
Keep the underscore in the  precompiler identifiers
Only write files serial mode if they don't exist
Merge branch 'master' of https://github.com/microhh/microhh into masterupstream