Merge pull request #53 from zolfagha/react_trans_GIA

React trans gia
Merge pull request #54 from zolfagha/react_trans_GIA

solving xi kin bar with ode solver
Merge pull request #55 from zolfagha/react_trans_GIA

moving the ode solver to local problem
Merge pull request #56 from zolfagha/react_trans_GIA

update
adding one more mesh file, with about 3k nodes instead of 8k.
one should always do the ODE first, then calculate the residual. Not the other way around.
adding one more input argument to the calc_residual function.

Make it very clear that always use the xi_Kin_bar_old values as the starting values of ODE.
the variable n_unknowns is not necessary at all.
code cleaning. Remove a lot of redundent operations.
code cleaning.
giving more strict convergence criterias for both linear and non-linear problems.
mainly adding the DratesDxi terms to the Jacobian formulation.
changing the residual calculation so that the 1/dt * M + K form is taken.
turn off the comments. Attention the local problem is not correct yet.
create memory space to store drates_dxi.
set looser criteria for local problem.
add two coarser mesh files and switch current dense mesh to coarser one.
The new mesh is not working yet. Use the old mesh for now.
The calculated xi_kin_bar values need to be taken into account.
The number of unknowns in the local problem should be the same as number of components.