Implement photoionization and add tests

[James471]

Description

Implements photochemistry in quokka and changes the Microphysics hash to a compatible version. Also adds the one zone test and the stromgren sphere test problem

Related issues

Depends on AMReX-Astro/Microphysics#1975

Checklist

Before this pull request can be reviewed, all of these tasks should be completed. Denote completed tasks with an x inside the square brackets [ ] in the Markdown source below:

• I have added a description (see above).
• I have added a link to any related issues (if applicable; see above).
• I have read the Contributing Guide.
• I have added tests for any new physics that this PR adds to the code.
• (For quokka-astro org members) I have manually triggered the GPU tests with the magic comment /azp run.

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[gemini-code-assist]

Summary of Changes

Hello, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request implements photoionization in Quokka, updates the Microphysics hash, and adds one-zone and Stromgren sphere test problems. The changes introduce a new photochemistry module, enhancing Quokka's ability to simulate astrophysical phenomena involving radiation and matter interactions. The included tests help ensure the correctness and stability of the new features.

Highlights

• Photoionization Implementation: This PR introduces a new photochemistry module to Quokka, enabling simulations that model the interaction of radiation with matter.
• Microphysics Compatibility: The Microphysics submodule has been updated to a compatible version, ensuring proper interaction with the new photochemistry routines.
• Test Cases: Two new test problems, the one-zone test and the Stromgren sphere test, have been added to validate the implementation of the photochemistry module.

Activity

• The pull request includes a description and a checklist of completed tasks.
• The author has manually triggered the GPU tests.

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[gemini-code-assist]

Code Review

This pull request implements photochemistry and adds corresponding tests. The changes include modifications to the main simulation loop and EOS to support a new PHOTOCHEMISTRY flag, and adds new networks for photoionization. The implementation of the photochemistry step as an operator-split source term seems correct. My main feedback is regarding code duplication in the new network definitions, which could be refactored for better maintainability. I've also pointed out several places with commented-out code that should be cleaned up before merging.

_{Note: Security Review did not run due to the size of the PR.}

[James471]

/gemini review

[gemini-code-assist]

Code Review

This pull request implements a major update to the project's development infrastructure, including a new quokka CLI tool, a complete migration of input files to TOML format, and extensive documentation updates. Feedback points out syntax errors in several new TOML files regarding array formatting and missing required parameters. Furthermore, portability issues were identified in the regression scripts due to hardcoded absolute paths and local directory references.

[BenWibking]

Ok, something went wrong with a merge into this branch. Essentially the last several weeks of PRs have somehow been included here as new commits.

[James471]

Is it fine now? I had performed a merge from dev to my branch for some tests to pass, since I had branched from a very old commit of dev, and after that format.h had been removed causing tests to fail. I have now rebased, so the commit history should look normal.

[BenWibking]

Is it fine now? I had performed a merge from dev to my branch for some tests to pass, since I had branched from a very old commit of dev, and after that format.h had been removed causing tests to fail. I have now rebased, so the commit history should look normal.

Yeah, it looks fine now.

[chongchonghe]

This looks really good in general! I made some quick comments and will continue to review tomorrow.

[James471]

Thanks ChongChong! I'll make the changes suggested by you and Ben towards the end collectively once you have finished reviewing.

[chongchonghe]

@claude review

[chongchonghe]

/azp run

[azure-pipelines]

Azure Pipelines successfully started running 2 pipeline(s).

[BenWibking]

This is what Codex says:

• The patch has runtime correctness issues for default photochemistry energy handling and reduced-speed radiation, and it registers a
  3D-only problem in 2D builds. These should be addressed before considering the change correct.

  Full review comments:

  - [P2] Avoid treating generated energy as final energy — /Users/benwibking/amrex_codes/quokka/src/radiation/photochemistry.hpp:112-
    112
    When a photochemistry input omits integrator.subtract_internal_energy = 0, Microphysics uses its default of returning only the
    generated energy after burner(). This eos_input_re call interprets that delta as the final specific energy, so the later dEint =
    photochemstate.e * rho - Eint subtracts the initial internal energy again (or zeroes it for energy_switch=0); force that parameter
    for photochemistry or reconstruct from the final temperature as the chemistry path does.

  - [P2] Use the reduced light speed in the chemistry RHS — /Users/benwibking/amrex_codes/quokka/src/networks/photoionization/
    actual_rhs.H:82-82
    For PHOTOCHEMISTRY problems that set RadSystem_Traits::c_hat_over_c < 1, computePhotoChemistry stores the reduced speed in
    state.c_hat, but the RHS and Jacobian hard-code C::c_light. Those runs will absorb photons and heat gas on a full-c timescale
    while radiation transport/source terms use the reduced speed, making ionization fronts too fast; use state.c_hat consistently here
    and in the Jacobian.

  - [P2] Restrict StromgrenSphere target to 3D — /Users/benwibking/amrex_codes/quokka/src/problems/StromgrenSphere/CMakeLists.txt:1-1
    With the documented 2d preset this block still adds and registers StromgrenSphere, but the problem implementation unconditionally
    uses z coordinates (prob_lo[2], dx[2]) and 3D source normalization/inputs. The 2D target is therefore invalid; guard it with
    AMReX_SPACEDIM EQUAL 3 unless the problem is made dimension-aware.

[James471]

/azp run

[azure-pipelines]

Azure Pipelines successfully started running 2 pipeline(s).