A new git repo.

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Added the ability to factor the number of SMLs to
determine optimal layout
Also replaced loops over all faces with loops over incoming
and outgoing faces
Forgot to add this file in the last commit.
Changed send and receive tag to include info about
angleset and groupset. Added multiple sweeps for averaging.
Fixed index math in single and polar angle aggregations.
Changed Problem destructor to virtual so it calls Quadature
and Subdomain destructors.
Add a function to write the flux solution to boundary buffers
when a cellset is on a global boundary
Fixed the send buffer storage. Now there are X,Y, and Z buffers as well
as X,Y, and Z Send buffers.
Fixed a bug in the translation step of the transport sweep.
Now the sweep gives a flat solution like it should.
Took out some allocations and declarations from the inner
loops of the sweep.
Replaced Blocking Receives with Nonblocking Receives and a
Waitall. Hopefully this will reduce the wait time at
the Receive if check
Cleaned up the comments in the code and changed cout statements
to have rank 0 write to an output file
Replaced Blocking Receives and Waits with Probes so that
messages not yet needed can still be transmitted
Bug fix. Iprobe update should work now
Changed clock() calls to MPI_Wtime(). This gives more significant
digits for the timing.
Added a Waitall to enforce all communication takes place before
work is done.
Reduced the Received buffer size. Added a queue to determine next
available spot in Received buffer
Fixed Cosmea compiler warnings and removed multi-threaded input parameter.
Resized Received buffer, took out not used variables from the input
and added a case for when downstream neighbors are owned by the same SML.
Made sure the options for blocked and round robin were consistent
throughout the code. Now 1=blocked and 2=round robin.
Committing changes to add to github
Merge branch 'master' of https://github.com/cnmcgraw/DFEComm