Merge pull request #1 from HaibingShao/react_trans_GIA

React trans gia
reduction function
chemReductionGIA.cpp
chemReductionGIA.cpp
calcite_GIA example
SingleStepGIAReduction
update
update the nonlinear part
finished the initialization
Merge pull request #23 from zolfagha/react_trans_GIA

Merge pull request #1 from HaibingShao/react_trans_GIA
local problem
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.
initialize num_phases in MMP
fix compiling errors with releaseObject
Merge pull request #2 from HaibingShao/react_trans_GIA

Fixing the concentration bug
Merge pull request #3 from norihiro-w/react_trans_GIA

fix minor bugs
update
update