Merge pull request #23 from zolfagha/react_trans_GIA

Merge pull request #1 from HaibingShao/react_trans_GIA
Merge pull request #24 from zolfagha/react_trans_GIA

local problem
In this commit, the old parameter _J_kin is removed. Instead, we use _J_kin_tot referring to the number of kinetic reactions. This will remove the problem that uninitialized values were used.
The _concentrations vector was twice initialized. That is the reason why we could not get the right concentration values. Now it is fixed.
Merge pull request #2 from HaibingShao/react_trans_GIA

Fixing the concentration bug