Added tubers and glucose to the state
Gave variables more meaningful names
Moved file open closer to its usage
Added tubers to grain_system and simulator.cpp
Shoved R, K, Q, M variables into states
Added set_all() method to grain_state
Used grain_state::set_all() to clean up grain_system init
Added Tuber line
Eliminated tuber from the grain system in order to facilitate merging of changes back to dev
Fixed grain system of equations to fit new variables.
Eliminated glucose from system
Finished rolling back tuber from grain system.
Minor formatting improvements to mathematics