Merging branch parallel

This was originally a branch that was created to test the parallel R file that gbass had requested to pull. After tests passed, the code has been updated with E only depending on nearest neighbour distribution and axial distance distributions. Some variables were moved to the settings.R file. 

The merge also reflects the completely updated input and output files to the latest version. The tomography image stack simulation of RyR cluster distributions are also included in the branch.