Fixed an issue with -s -e commandline flags.  It wasn't actaully
stopping with the -e flag, or more specifically it was still reserving
Nt - start_time places in the matrix container even though it was only
writing a small number of times.  It has been corrected to only reserve,
and store, end - start data structures for the sensor mask in the matrixcontainer.

TO DO:
- Commandline flags still don't work properly.  It depends on the order
  in which they are given for correct behavior.  Fix this.
- Currently if you specify --refractive_x, for instance, on the commandline
  and don't specify any other attributes to save there is an error because
  StoreSensorData() tries to store data if any of the flags are given (logical OR'ing).
  This should be changed to only store (and compute) what is specified.