Quick optimization to avoid copying of the TotalPopulation object

Now functions in output.h/.cpp take a pointer to the
TotalPopulation rather than itself. The runtime is restored back
to the value corresponding to no file writing. Values:

                            Time per reaction, s     Measurements
No file io, prev commit        4.2e-3                   4
With file io, prev commit      3.0e-1                   5
With file io, cur commit       4.7e-3                   1

	modified:   main.cpp
	modified:   output.cpp
	modified:   output.h