Initial version of adding in the saving of seeds, reading them
back in and using them has been implemented.

To Do:
- Verify this works on the server with differing number of cores
  (i.e. 2,4,6,8,10,12, etc).
- Verify that it doesn't change the results of the acousto-optic
  simulation.
- Come up with command line parameters for saving and using seeds.
- If everything is correct and/or implemented above, merge into
  master.
Small changes to process_speckles.m
Committing changes to run on server.
- Generate seeds using 1 core
- Run AO_sim with seeds
Merge branch 'reimplemt_seeds' of https://github.com/jacobwjs/AO-KWave-MCBoost into reimplemt_seeds
Commenting out the detector bounds check in AO_Sim::
This needs to be fixed, but it uncorrectly says the detector
does not fit in the medium.
Added a change in MC_Boost::Run_MC_time_step() to check if
the seeds have already been loaded.  They are not cleared
after each run, so the vector containing the seeds was
being loaded with duplicate seeds, effectively doubling
the amount of photons each run during an acousto-optic
simulation without adding any statistical benefit.
Small fix to the logical operator on the previous commit.
Small changes to makefile
Changes made to specify the use of RNG seeds, or saving seeds, via
the commandline. See commandlineparameters.h(cpp) for details.
Committing latest changes for using seeds. There is an issue however
that the total number of seeds loaded does not produce the total
number of detected photons when running the AO_sim. It's almost
as if the RNG starts in a different state by the time photon
propagation begins when compared to the MC_sim (produced the seeds)
and the AO_sim (using the seeds). Need to verify this. This only
impacts the number of photons we detect in the end, which for the
brief testing that has been made, it results in about half of the
seeds photons generated being detected in the AO_sim.
Added changes to AOsim, medium, and maps for inverting phase via
the new command line option 'phase_inversion'. Also changed
the injection point of photons to be over a diameter (3mm)
instead of a perfect point source.

To do:
- Run a battery of tests to ensure that phase inversion works
- Merge changes into developement branch and start beginnings
  of ensuring it's ready to be pulled into master.
Added lots of formatting changes in the output that is displayed
to the user. Much cleaner presentation of what is happening in the
simulations.
Small changes
Adding small changes, nothing to mention.
Small changes for cleaning up code and enabling refractive index AO mechanism.
Committing working version that will be tagged. These changes should
be merged into developement branch, and eventually into master.
Small changes as to where the detected photons are saved.
Now saved to 'Data/Detected_photons' directory.

TO DO:
 - Apply a current time to the end of the file and create it on each run,
   therefore bypassing the possibility of blowing away data from a previous run
Committing latest changes for merging and debugging to figure
out what is going on with problem of saving raw pressures.
Adding a file for generating a debugging scheme for the AO simulation. Basically
a smaller grid with less memory requirements. Nice for using on OS X with
X-code.

This commit is only for updating everything to the latest and pulling onto my
mac machine for debugging.
Small changes to timing and makefile to build properly on OS X.