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.
Merge pull request #25 from zolfagha/react_trans_GIA

React trans gia
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 #26 from HaibingShao/haibing_working

Haibing working
Merge pull request #27 from HaibingShao/haibing_working

Haibing working
change the input files to better fit the specified benchmark case
Merge branch 'react_trans_ops' of github.com:HaibingShao/ogs into haibing_working
We change the input concentrations so that they exactly fits the ogs-PhreeqC input concentrations.
The way of writing the reactions and the corresponding K values are also changed. The K values are according to the Nagra-PSI database.
We tune all the input files to be the same as the benchmark case.
1) every 10 steps one output.
2) 210 steps with dt = 100 sec.
3) reactions written in a way that basis on the left, secondary on the right.
relax the relative tolerance from 1e-16 to 1e-12.