Merge pull request #22 from HaibingShao/react_trans_ops

taking in features from OPS branch.
adding one more benchmark case that is the sequential degradation of organic contaminants.
adding the reactions definition to this benchmark.
adding two more components, which are the microbial species into the chemical components list.
The x-z coordinate setting will cause trouble. Switch back to x-y direction.
changing the mesh to x-y direction.
removing the source term for GROUNDWATER_FLOW, using fixed head to control the flow rate.
fullfill the initial conditions and adding variables to the output.
adding the inhibition calculation to the kinetic reaction class.
changing output format to PVD and more frequent result print out.
This is a major mistake. When calculating Dispersion matrix,
we shall following the equation on page 219 of our benchmark book.
The equation reads,
D_{ij} = \alpha_T |v| \delta_{ij} + (\alpha_L - \alpha_T) \frac{v_i v_j}{|v|} + D^{d}_{ii}
Therefore, the first muliplication with the norm of velocity should be transverse dispersion, not the longitudinal one.

Now it is fixed in the FemKinReactGIA module. Other mass transport processes should be very careful about this.
1e-12 should be good enough.
This is a major mistake. When calculating Dispersion matrix,
we shall following the equation on page 219 of our benchmark book.
The equation reads,
D_{ij} = \alpha_T |v| \delta_{ij} + (\alpha_L - \alpha_T) \frac{v_i v_j}{|v|} + D^{d}_{ii}
Therefore, the first muliplication with the norm of velocity should be transverse dispersion, not the longitudinal one.

Now it is fixed in the FemKinReactGIA module. Other mass transport processes should be very careful about this.
Merge pull request #27 from HaibingShao/haibing_working

Haibing working