Added dedicated file for constants.
Created files for managing simulation statistics.
Moved constants to dedicated file.
Updates to test system.
Added vector magnitude function.
Updated file read.
Fixed error in particle data printing.
Updates fixing some errors.
Fixed error in mass update of root node.
Complete refactor of top-level simulation management.

Dedicated simulation struct added with (actual) methods for managing
the simulation.
Added total cpu time tracker for simulation.