Removed normalization, it is more convenient to do this on the caller side so that the proper mass labels can be created first

Added a phase inclusion tolerance, i.e. for  below this tolerance, the phase fraction will be set to zero. The value was set to be the same as that in pseudoBinaryPhaseDiagramFunctions.py

Must specify fuzzy stochiometry when generating input script, not when running it, as there is no such argument