React trans gia

Dear Reza, 

Please merge my changes tonight. 

The first commit should fix your dt = 0 issue. 
In the second one, I have changed your residual calculation to the form that dt has been multiplied on both sides of the equation. This is in line with what you have been using in the matlab script and also your J formulation. 

The first Newton linear equation J*dx = -r still can not converge yet. Please first change your matlab script so that we have the same transport operator. Then compare each values in your J matrix and r vector. If they are the same, then make sure you use the same pre-conditioner in your linear solver. 

Have fun. 
Haibing