Merge pull request #60 from zolfagha/react_trans_GIA

React trans gia
This commit will fix the transport issue. Now the aqueous components are flushing into the column.
printing each time step result.
the old code does not take into account the amount of minerals. Thus corrected it.
changing back the original structure. It is fine.
changing the back calculation function so that it includes the mineral concentration.
clean the code.
using the _I_NMin_bar instead.
merg Reza's pull request.
Merge remote-tracking branch 'origin/react_trans_GIA' into react_trans_GIA

Conflicts:
	UserModules/FemReactGIAReduct/LocalProblem.cpp
add a non-negativity protection here, otherwise the activity model will break down.
clean unused code.
remove the local vec_AI data structure in the local problem.
The current code will not compile.
The plan is, to store the current vec_AI for each node in the ReductConc data structure, and passing the address of local vectors into the LocalProblem.
This will faciliate the use of vec_AI elsewhere.
adding the declaration of nodal AI vector in the ReductConc class.
initialization of the _nodal_vec_AI vector.
reclaim the memory of _nodal_vec_AI vector.
using pointers instead.
passing on the vec_AI for particular node.
1) Here, instead of using the real-time calculated mineral status, we directly use the stored vec_AI vector from the local problem.
2) Based on the stored vec_AI values, we decide the size of mat_S1minA (for active mineral reactions), and mat_S1minI (for inactive mineral reactions).
3) Then the corresponding stoichiometry values are added into the two seperate matrixes.
4) Test shows that this change will prevent the "not a number" value to apprear in the Jacobi matrix and now the global non-linear iterations are going forward.
switch off the print out function.