My take as a mentor on this project:

• This is a research project with a large scientific and numerical analysis scope.
  • I see it is a PhD level research with lots of unknowns.
• It was a very ambitious undertaking to program and produce simulations within 12 days.
• I basically decided to run that project as a "computer science project", not as a scientific one.
• We did not have time to gather and document all target (of possible) combinations of types of fluids, species, chemistry between species, and transport parameters.
• At this stage we have a tool to simulate underground flows around different configurations of convex or concave rocks.
  • See the three panel Manipulate interface in post.
• Based on my previous work in large scale air pollution simulations, I proposed the separation of "physics" and "chemistry".
  • It is very hard to apply classical methods to this kind of processes.
  • The splitting allows for "separation of duties" -- different researchers, with different expertise, can work on corresponding parts.