Refactored main simulation routine and split into numerous subroutines, cleaned up image updating also.
Renamed functions, added margin to progress bars
Merge branch 'master' into cleanup
Fixed problem with rounding of stem area

Conflicts:
	GPU TEM-STEM Simulation/MainWindow.xaml.cs
Merge pull request #56 from ADyson/cleanup

Refactored main simulation routine and split into numerous subroutines, ...