Merge pull request #59 from zolfagha/react_trans_GIA

Using activities instead of concentrations and constant K values.
cleaning the unnecessary comments.
logK values are constants. Therefore, it is absolutely not correct to change logK values during the simulation.

I remove all data structure related to this practice and it is never allowed.
need the intermediate output in debug mode.

and clean the code.
Merge pull request #19 from HaibingShao/react_trans_GIA

React trans gia