feat: Single-phase reactive transport combined with HPCReact

[frankfeifan]

This branch aims to implement the single-phase reactive transport model into GEOS. The following tasks are listed for completion:

• A SinglePhaseReactiveTransport solver (derived from SinglePhaseBase) that contains all needed functions to solve the problem and SinglePhaseReactiveTransportFields.hpp to store all necessary fields
• AccumulationKernel and FluxComputeKernel to assemble the local rhs and matrix
• Make everything work for both isothermal and thermal
• Plug in the chemistry module from this repo through a ReactiveSinglePhaseFluid constitutive model
• A unit test testSinglePhaseReactiveTransport to verify the implementation of Jacobian matrix
• Examples for representative reaction systems
• A porosity model that updates the solid porosity with chemical reaction
• Update surfaceArea (added but need test)
• MoMaS verification (transport + all equilibrium) and generic chain reaction verification (transport + all kinetic)

[paveltomin]

@frankfeifan is this ready for review?

yes. I think it's ready for review.

can you fix the build?

yes, I think I fix it now.

thanks @frankfeifan but there are still build and unit test failures, could you please have another look?

Sorry, I forgot to update new unit tests for some new changes I did recently and looks like there is an error in CUDA build. I'll look into this later this week.

I think I figured out the CUDA build error. For unit tests in HPCReact, I think we need to update reference solutions, but for some tests like the mixed reaction one, we don't have a true reference solution for now to compare... I will work with @rrsettgast to address that.

several cpu builds in CI still fail to compile, could you please have a look and fix it?

[frankfeifan]

@frankfeifan is this ready for review?

yes. I think it's ready for review.

can you fix the build?

yes, I think I fix it now.

thanks @frankfeifan but there are still build and unit test failures, could you please have another look?

Sorry, I forgot to update new unit tests for some new changes I did recently and looks like there is an error in CUDA build. I'll look into this later this week.

I think I figured out the CUDA build error. For unit tests in HPCReact, I think we need to update reference solutions, but for some tests like the mixed reaction one, we don't have a true reference solution for now to compare... I will work with @rrsettgast to address that.

several cpu builds in CI still fail to compile, could you please have a look and fix it?

Yes. I will fix it together with those cuda errors today or tomorrow.

[frankfeifan]

@frankfeifan is this ready for review?

yes. I think it's ready for review.

can you fix the build?

yes, I think I fix it now.

thanks @frankfeifan but there are still build and unit test failures, could you please have another look?

Sorry, I forgot to update new unit tests for some new changes I did recently and looks like there is an error in CUDA build. I'll look into this later this week.

I think I figured out the CUDA build error. For unit tests in HPCReact, I think we need to update reference solutions, but for some tests like the mixed reaction one, we don't have a true reference solution for now to compare... I will work with @rrsettgast to address that.

several cpu builds in CI still fail to compile, could you please have a look and fix it?

CPU builds should work now, although unit tests in HPCReact still fail because we need to update the reference solutions and clean up the codes there.

For CUDA builds, I fixed some issues in data layouts but some other issues remain. I'll need more time and some help if any to pass the compile on CUDA.

[frankfeifan]

This test is expected to fail now until this PR: GEOS-DEV/HPCReact#9 is merged in HPCReact