Feature/radiation vode#1975
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…ariables WIP: Add reduced speed of light to burn state and some missing radiation variables WIP: Add reduced speed of light to burn state and some missing radiation variables
Minor fixes WIP: Minor fixes WIP: Minor fixes Cleanup
Simplify photoionization eos implementation, change species masses Simplify photoionization eos implementation, change species masses
…n EOS The EOS was incorrectly normalizing the total heat capacity sum_ni_fi_over_2 by dividing by the particle count before using it for internal energy and temperature calculations. This made the internal energy per unit mass ~1/n_total times too small, causing the ionized gas temperature to be ~140x too low for the DTypeFront test (n_H=139.9), giving an expansion speed of ~750 m/s instead of the expected ~10 km/s. Fix: separate the unnormalized sum_ni_fi_over_2 (total heat capacity, used for e, T, dedT) from fi_over_2_avg = sum_ni_fi_over_2 / sum_Abarinv (per-particle average, used for pressure, cs, G). Also fix electron mass: spmasses[Electron] was set to proton mass; now correctly set to C::m_e = 9.109e-28 g. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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The radiation loop had two bugs: the upper bound `NumRadEqs` should be `net_ienuc + NumRadEqs` (the loop never executed since net_ienuc+1 > NumRadEqs), and `state.rn[i-1]` / `state.rn[j-1]` should be indexed relative to net_ienuc to correctly map VODE 1-based indices to the rn[] array. The inner loop upper bound was also off by one (`<= i + N` → `<= i + N - 1`). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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@zingale This is something that is critical for our simulation in the second half of this year. We'd like to merge this in the next week or two if possible. Let us know if there's any additional context or review guidance we can provide. A follow-up PR will make analogous changes to the Rosenbrock integrator to add support for radiation variables. |
fix: correct loop bounds and rn[] indexing in numerical_jacobian.H
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A description of the physics for the photoionization network is here: quokka-astro/quokka#1800 |
Meowwish
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Jun 15, 2026
### 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:_ - [x] I have added a description (see above). - [x] I have added a link to any related issues (if applicable; see above). - [x] I have read the [Contributing Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md). - [x] 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`. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: ChongChong He <chongchonghe99@gmail.com> Co-authored-by: Ben Wibking <ben@wibking.com>
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The PR adds radiation number densities and fluxes and reduced speed of light in burn state. It also makes changes to the VODE integrator to handle photochemical reactions. The PR also fixes a bug that causes the last character of eos file to not be read if the files doesn't end with a newline character.