Fix XML output of impropers and dihedrals

fixes #2702
Omitted unnecessary duplicate statement in DPD pair force kernel
Removed unnecessary statement in DPD GPU class
Removed automatic enabling of GPUDirect RDMA for MVAPICH2

This enables benchmarking GDR against cuda-aware MPI
Move nlist from __main__ to a module wrapper

refs #1688
Move sorter from __main__ to a module

refs #1688
Update mac build script

- Now builds against booost 1.52
- Now updloads builds to petry
Update icons to new UMich colors

For future reference, I got the icns and various sized png files by feeding a pdf file into http://iconverticons.com/beta/
Remove no longer applicable comment

MPI_init is now called in the module load.
Use known compute capability

Instead of querying for the compute capability of a function, use the known compute capability from ExecutionConfiguration.