commit 94dad22e5d335f39660af808438fd372e7d04811
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Jun 16 10:47:43 2025 -0400

    Bump github/codeql-action from 3.28.19 to 3.29.0 (#1144)
    
    Bumps [github/codeql-action](https://github.com/github/codeql-action)
    from 3.28.19 to 3.29.0.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
    href="https://github.com/github/codeql-action/releases">github/codeql-action's
    releases</a>.</em></p>
    <blockquote>
    <h2>v3.29.0</h2>
    <h1>CodeQL Action Changelog</h1>
    <p>See the <a
    href="https://github.com/github/codeql-action/releases">releases
    page</a> for the relevant changes to the CodeQL CLI and language
    packs.</p>
    <h2>3.29.0 - 11 Jun 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.22.0. <a
    href="https://redirect.github.com/github/codeql-action/pull/2925">#2925</a></li>
    <li>Bump minimum CodeQL bundle version to 2.16.6. <a
    href="https://redirect.github.com/github/codeql-action/pull/2912">#2912</a></li>
    </ul>
    <p>See the full <a
    href="https://github.com/github/codeql-action/blob/v3.29.0/CHANGELOG.md">CHANGELOG.md</a>
    for more information.</p>
    </blockquote>
    </details>
    <details>
    <summary>Changelog</summary>
    <p><em>Sourced from <a
    href="https://github.com/github/codeql-action/blob/main/CHANGELOG.md">github/codeql-action's
    changelog</a>.</em></p>
    <blockquote>
    <h1>CodeQL Action Changelog</h1>
    <p>See the <a
    href="https://github.com/github/codeql-action/releases">releases
    page</a> for the relevant changes to the CodeQL CLI and language
    packs.</p>
    <h2>[UNRELEASED]</h2>
    <p>No user facing changes.</p>
    <h2>3.29.0 - 11 Jun 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.22.0. <a
    href="https://redirect.github.com/github/codeql-action/pull/2925">#2925</a></li>
    <li>Bump minimum CodeQL bundle version to 2.16.6. <a
    href="https://redirect.github.com/github/codeql-action/pull/2912">#2912</a></li>
    </ul>
    <h2>3.28.19 - 03 Jun 2025</h2>
    <ul>
    <li>The CodeQL Action no longer includes its own copy of the extractor
    for the <code>actions</code> language, which is currently in public
    preview.
    The <code>actions</code> extractor has been included in the CodeQL CLI
    since v2.20.6. If your workflow has enabled the <code>actions</code>
    language <em>and</em> you have pinned
    your <code>tools:</code> property to a specific version of the CodeQL
    CLI earlier than v2.20.6, you will need to update to at least CodeQL
    v2.20.6 or disable
    <code>actions</code> analysis.</li>
    <li>Update default CodeQL bundle version to 2.21.4. <a
    href="https://redirect.github.com/github/codeql-action/pull/2910">#2910</a></li>
    </ul>
    <h2>3.28.18 - 16 May 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.21.3. <a
    href="https://redirect.github.com/github/codeql-action/pull/2893">#2893</a></li>
    <li>Skip validating SARIF produced by CodeQL for improved performance.
    <a
    href="https://redirect.github.com/github/codeql-action/pull/2894">#2894</a></li>
    <li>The number of threads and amount of RAM used by CodeQL can now be
    set via the <code>CODEQL_THREADS</code> and <code>CODEQL_RAM</code>
    runner environment variables. If set, these environment variables
    override the <code>threads</code> and <code>ram</code> inputs
    respectively. <a
    href="https://redirect.github.com/github/codeql-action/pull/2891">#2891</a></li>
    </ul>
    <h2>3.28.17 - 02 May 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.21.2. <a
    href="https://redirect.github.com/github/codeql-action/pull/2872">#2872</a></li>
    </ul>
    <h2>3.28.16 - 23 Apr 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.21.1. <a
    href="https://redirect.github.com/github/codeql-action/pull/2863">#2863</a></li>
    </ul>
    <h2>3.28.15 - 07 Apr 2025</h2>
    <ul>
    <li>Fix bug where the action would fail if it tried to produce a debug
    artifact with more than 65535 files. <a
    href="https://redirect.github.com/github/codeql-action/pull/2842">#2842</a></li>
    </ul>
    <h2>3.28.14 - 07 Apr 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.21.0. <a
    href="https://redirect.github.com/github/codeql-action/pull/2838">#2838</a></li>
    </ul>
    <h2>3.28.13 - 24 Mar 2025</h2>
    <p>No user facing changes.</p>
    <h2>3.28.12 - 19 Mar 2025</h2>
    <ul>
    <li>Dependency caching should now cache more dependencies for Java
    <code>build-mode: none</code> extractions. This should speed up
    workflows and avoid inconsistent alerts in some cases.</li>
    </ul>
    <!-- raw HTML omitted -->
    </blockquote>
    <p>... (truncated)</p>
    </details>
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/github/codeql-action/commit/ce28f5bb42b7a9f2c824e633a3f6ee835bab6858"><code>ce28f5b</code></a>
    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2926">#2926</a>
    from github/update-v3.29.0-e8799281c</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/bc251b7932638a7881a8db15d1aaf0151642af99"><code>bc251b7</code></a>
    Update changelog for v3.29.0</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/e8799281c8dee3b2e1aaed2c059e530fcfdc2d6d"><code>e879928</code></a>
    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2925">#2925</a>
    from github/update-bundle/codeql-bundle-v2.22.0</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/efd43b3097c094d883d91934155f0a32af09dff7"><code>efd43b3</code></a>
    Merge branch 'main' into update-bundle/codeql-bundle-v2.22.0</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/7cb9b16051842e6c23c8b9fbcf92481f92d0644a"><code>7cb9b16</code></a>
    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2912">#2912</a>
    from github/henrymercer/bump-minimum-codeql-2.16.6</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/3855117ba18b27e082b12e3e92e00d1b52aaa605"><code>3855117</code></a>
    Add changelog note</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/f5d4e2a7ca2a5826357748bb8743390a4775946f"><code>f5d4e2a</code></a>
    Update default bundle to codeql-bundle-v2.22.0</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/22deae890c55a1dc3ffba1aa20ad4148284e72d1"><code>22deae8</code></a>
    Update package-lock.json</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/df2a830ca4348a013f4804b56f41795f408f1e4e"><code>df2a830</code></a>
    Merge branch 'main' into henrymercer/bump-minimum-codeql-2.16.6</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/b1e4dc3db58c9601794e22a9f6d28d45461b9dbf"><code>b1e4dc3</code></a>
    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2916">#2916</a>
    from github/dependabot/npm_and_yarn/npm-5cdccdc43f</li>
    <li>Additional commits viewable in <a
    href="https://github.com/github/codeql-action/compare/fca7ace96b7d713c7035871441bd52efbe39e27e...ce28f5bb42b7a9f2c824e633a3f6ee835bab6858">compare
    view</a></li>
    </ul>
    </details>
    <br />
    
    
    [![Dependabot compatibility
    score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=github/codeql-action&package-manager=github_actions&previous-version=3.28.19&new-version=3.29.0)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
    
    Dependabot will resolve any conflicts with this PR as long as you don't
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    <details>
    <summary>Dependabot commands and options</summary>
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.github/workflows/codeql.yml
.github/workflows/scorecard.yml

commit 2954c3119caab0a431de4e9f90e90f3929ad0b5c
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Mon Jun 16 04:27:11 2025 +1000

    Optimize github pipelines (#1105)
    
    ### Description
    
    Attempts to optimize github CI pipelines by doing smart test selection
    to skip unnecessary compilation and testing.
    
    Now, a PR that does not modify any of the following files/folders will
    ignore most pipelines and the CIs would take ~1 minute to finish.
    
    ```
    - 'src/**'
    - 'tests/**'
    - 'CMakeLists.txt'
    - '**/*.cpp'
    - '**/*.c'
    - '**/*.hpp'
    - '**/*.h'
    ```
    
    General rules are:
    1. `build` and `run` pipelines will run only if any of the code files
    listed above were modified.
    2. `docs` CI runs only if docs folders has been changed.
    3. `clange-tidy` will run only if any code files or scripts folder were
    changed.
    
    Built upon this, we can add more sophisticated filters for precision CI
    test, e.g.
    
    ### Related issues
    
    Closes #1043
    
    ### 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](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] 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`.

.circleci/config.yml
.circleci/continue-config.yml
.github/workflows/check_changes.yml
.github/workflows/checkpoint-restart.yml
.github/workflows/clang-tidy.yml
.github/workflows/cmake-macos.yml
.github/workflows/cmake.yml
.github/workflows/codeql.yml
.github/workflows/docs.yml
.github/workflows/hip.yml
.github/workflows/openpmd.yml
.github/workflows/warnings.yml

commit 6f5ea5d7069fe9fdb930467ef6f059f1d34b074f
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Jun 10 10:38:56 2025 -0400

    Reimplement cooling with resampled tables (#1126)
    
    ### Description
    Adds the `quokka::ResampledCooling` cooling module that reads and uses
    cooling tables tabulated in terms of density and specific internal
    energy.
    
    Updates the ShockCloud problem to work with the new cooling module.
    
    (Includes https://github.com/quokka-astro/quokka/pull/1140 for I/O
    scaling runs on Frontier.)
    
    ### Related issues
    N/A
    
    ### 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.
    - [x] *(For quokka-astro org members)* I have manually triggered the GPU
    tests with the magic comment `/azp run`.
    
    ---------
    
    Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com>
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
    Co-authored-by: Claude <noreply@anthropic.com>

extern/cooling/CloudyData_UVB=HM2012_resampled.h5
extern/cooling/Koyama_Inutsuka_cooling.py
extern/cooling/README.md
extern/cooling/cct_cooling_reference_solution.csv
extern/cooling/cloudy_cooling_tools_tables.py
extern/cooling/fast_log_round_trip_error_analysis.md
extern/cooling/grackle_reference_solution.csv
extern/cooling/grackle_tables.py
extern/cooling/integrate_cooling_zone.py
extern/cooling/isrf_1000Go_grains_resampled.h5
extern/cooling/resample_cloudy_cooling_tables.py
extern/cooling/resample_grackle_cooling_tables.py
extern/cooling/test_cloudy_cooling_onezone.py
extern/cooling/test_cooling_onezone.py
scripts/tidy.sh
src/.clang-tidy
src/CMakeLists.txt
src/QuokkaSimulation.hpp
src/cooling/ResampledCooling.cpp
src/cooling/ResampledCooling.hpp
src/problems/CMakeLists.txt
src/problems/DiskGalaxy/galaxy.cpp
src/problems/ResampledCoolingTest/CMakeLists.txt
src/problems/ResampledCoolingTest/test_resampled_cooling.cpp
src/problems/ShockCloud/cloud.cpp
tests/DiskGalaxy.in
tests/ResampledCooling.in
tests/ShockCloud_32.in
tests/TabulatedCooling.in

commit 4efc35b07a1d1dcb20ed3cc33c773ca1a8631171
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Jun 10 09:29:03 2025 -0400

    Delete .github/workflows/intel.yml (#1141)
    
    ### Description
    Removes the Intel compiler from the CI tests.
    
    ### Related issues
    Closes https://github.com/quokka-astro/quokka/issues/1139.
    
    ### 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).
    - [ ] 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`.

.github/workflows/intel.yml

commit f88e5d9c4cfd79686f18cf0959182116e2ccecfb
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Jun 9 21:59:12 2025 -0400

    Add skip_initial_plotfile runtime parameter (#1140)
    
    ## Summary
    - Added `skip_initial_plotfile` boolean runtime parameter to allow
    skipping the initial plotfile at t=0
    - Updated documentation to include the new parameter
    
    ## Test plan
    - [ ] Build the code with the changes
    - [ ] Run a test with `skip_initial_plotfile = 1` and verify no plt00000
    is created
    - [ ] Run a test without the parameter (or with `skip_initial_plotfile =
    0`) and verify plt00000 is created as before
    - [ ] Verify existing tests still pass
    
    🤖 Generated with [Claude Code](https://claude.ai/code)
    
    ---------
    
    Co-authored-by: Claude <noreply@anthropic.com>

docs/markdown/parameters.md
src/simulation.hpp

commit ba5252a0366a98baa3cc753b3756e82c94be696e
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Jun 9 03:57:57 2025 +0000

    Bump github/codeql-action from 3.28.18 to 3.28.19 (#1138)
    
    Bumps [github/codeql-action](https://github.com/github/codeql-action)
    from 3.28.18 to 3.28.19.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
    href="https://github.com/github/codeql-action/releases">github/codeql-action's
    releases</a>.</em></p>
    <blockquote>
    <h2>v3.28.19</h2>
    <h1>CodeQL Action Changelog</h1>
    <p>See the <a
    href="https://github.com/github/codeql-action/releases">releases
    page</a> for the relevant changes to the CodeQL CLI and language
    packs.</p>
    <h2>3.28.19 - 03 Jun 2025</h2>
    <ul>
    <li>The CodeQL Action no longer includes its own copy of the extractor
    for the <code>actions</code> language, which is currently in public
    preview.
    The <code>actions</code> extractor has been included in the CodeQL CLI
    since v2.20.6. If your workflow has enabled the <code>actions</code>
    language <em>and</em> you have pinned
    your <code>tools:</code> property to a specific version of the CodeQL
    CLI earlier than v2.20.6, you will need to update to at least CodeQL
    v2.20.6 or disable
    <code>actions</code> analysis.</li>
    <li>Update default CodeQL bundle version to 2.21.4. <a
    href="https://redirect.github.com/github/codeql-action/pull/2910">#2910</a></li>
    </ul>
    <p>See the full <a
    href="https://github.com/github/codeql-action/blob/v3.28.19/CHANGELOG.md">CHANGELOG.md</a>
    for more information.</p>
    </blockquote>
    </details>
    <details>
    <summary>Changelog</summary>
    <p><em>Sourced from <a
    href="https://github.com/github/codeql-action/blob/main/CHANGELOG.md">github/codeql-action's
    changelog</a>.</em></p>
    <blockquote>
    <h1>CodeQL Action Changelog</h1>
    <p>See the <a
    href="https://github.com/github/codeql-action/releases">releases
    page</a> for the relevant changes to the CodeQL CLI and language
    packs.</p>
    <h2>[UNRELEASED]</h2>
    <p>No user facing changes.</p>
    <h2>3.28.19 - 03 Jun 2025</h2>
    <ul>
    <li>The CodeQL Action no longer includes its own copy of the extractor
    for the <code>actions</code> language, which is currently in public
    preview.
    The <code>actions</code> extractor has been included in the CodeQL CLI
    since v2.20.6. If your workflow has enabled the <code>actions</code>
    language <em>and</em> you have pinned
    your <code>tools:</code> property to a specific version of the CodeQL
    CLI earlier than v2.20.6, you will need to update to at least CodeQL
    v2.20.6 or disable
    <code>actions</code> analysis.</li>
    <li>Update default CodeQL bundle version to 2.21.4. <a
    href="https://redirect.github.com/github/codeql-action/pull/2910">#2910</a></li>
    </ul>
    <h2>3.28.18 - 16 May 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.21.3. <a
    href="https://redirect.github.com/github/codeql-action/pull/2893">#2893</a></li>
    <li>Skip validating SARIF produced by CodeQL for improved performance.
    <a
    href="https://redirect.github.com/github/codeql-action/pull/2894">#2894</a></li>
    <li>The number of threads and amount of RAM used by CodeQL can now be
    set via the <code>CODEQL_THREADS</code> and <code>CODEQL_RAM</code>
    runner environment variables. If set, these environment variables
    override the <code>threads</code> and <code>ram</code> inputs
    respectively. <a
    href="https://redirect.github.com/github/codeql-action/pull/2891">#2891</a></li>
    </ul>
    <h2>3.28.17 - 02 May 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.21.2. <a
    href="https://redirect.github.com/github/codeql-action/pull/2872">#2872</a></li>
    </ul>
    <h2>3.28.16 - 23 Apr 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.21.1. <a
    href="https://redirect.github.com/github/codeql-action/pull/2863">#2863</a></li>
    </ul>
    <h2>3.28.15 - 07 Apr 2025</h2>
    <ul>
    <li>Fix bug where the action would fail if it tried to produce a debug
    artifact with more than 65535 files. <a
    href="https://redirect.github.com/github/codeql-action/pull/2842">#2842</a></li>
    </ul>
    <h2>3.28.14 - 07 Apr 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.21.0. <a
    href="https://redirect.github.com/github/codeql-action/pull/2838">#2838</a></li>
    </ul>
    <h2>3.28.13 - 24 Mar 2025</h2>
    <p>No user facing changes.</p>
    <h2>3.28.12 - 19 Mar 2025</h2>
    <ul>
    <li>Dependency caching should now cache more dependencies for Java
    <code>build-mode: none</code> extractions. This should speed up
    workflows and avoid inconsistent alerts in some cases.</li>
    <li>Update default CodeQL bundle version to 2.20.7. <a
    href="https://redirect.github.com/github/codeql-action/pull/2810">#2810</a></li>
    </ul>
    <h2>3.28.11 - 07 Mar 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.20.6. <a
    href="https://redirect.github.com/github/codeql-action/pull/2793">#2793</a></li>
    </ul>
    <!-- raw HTML omitted -->
    </blockquote>
    <p>... (truncated)</p>
    </details>
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
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commit 687de7bf699706c6e726edbc04576bdf0e41e6c2
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Sun Jun 8 17:38:03 2025 +1000

    Fix bugs in SF and SN prescriptions (#1137)
    
    ### Description
    
    This PR fixes one fatal bug in the SF prescription and one (potentially)
    fatal bug in the SN prescription.
    
    Bug fix in SF: The turbulent velocity in a star-forming cell could be
    zero, causing a call of RandomNormal with sigma = 0, which is illegal. I
    set a floor of `sigma_sq = cs * cs`, which reflects that star-forming
    regions typically have turbulent and thermal energies in equipartition.
    
    Bug fix in SN: During the limiter step, I added a special case for `a =
    0` in the solution of `a x^2 + b x + c = 0`. I don't see it happen in
    the test problem, and it could potentially happen somewhere.
    
    Also updated the SF test problem:
    - Add more checks at step 1: check the total mass in high-mass stars,
    the number of high-mass stars, and the number of low-mass stars. Fail
    the test if those numbers are not within tolerance.
    - Let the problem run to step 10 and check mass conservation in the end.
    
    ### Related issues
    None.
    
    ### 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
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    above).
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
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    code.
    - [x] *(For quokka-astro org members)* I have manually triggered the GPU
    tests with the magic comment `/azp run`.
    
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src/particles/particle_creation.hpp
src/particles/particle_deposition.hpp
src/problems/ParticleSF/test_particle_SF.cpp
src/problems/ParticleSF/test_particle_SF.hpp
tests/ParticleSF.in

commit a36e71b02c7b75605ce4060d62b600f8105d8d3b
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Sun Jun 8 03:47:12 2025 +1000

    Disable FPE on AppleClang (#1134)
    
    ### Description
    
    FPE behaves spuriously on macOS with Apple chips, so we'd better turn it
    off for all compilers on macOS.
    
    ### Related issues
    None.
    
    ### 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:_
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    above).
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] 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`.

CMakeLists.txt

commit fa35f79c3fe1aab1b6dfbc81ed53de2ffb1f7ee2
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Jun 7 12:41:25 2025 -0400

    Cooling: use functors instead of function pointers (#1131)
    
    ### Description
    Converts the cooling modules to use functors instead of function
    pointers when calling the integrator in `math/ODEIntegrate.hpp`.
    
    ### Related issues
    N/A
    
    ### 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:_
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    above).
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] *(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>
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src/cooling/GrackleLikeCooling.hpp
src/cooling/TabulatedCooling.hpp
src/math/ODEIntegrate.hpp
src/problems/ODEIntegration/test_ode.cpp

commit 50bfeaac40e357d8710c544aa9e739bd2a4b37f9
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Jun 6 22:31:08 2025 -0400

    Reduce communication in kickParticlesAllLevels (#1133)
    
    ### Description
    kickParticlesAllLevels is currently a performance bottleneck at scale.
    The appears to be related to my previous sub-optimal implementation for
    communicating the acceleration fields. This version is much faster.
    
    ### Related issues
    N/A
    
    ### 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:_
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    above).
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] *(For quokka-astro org members)* I have manually triggered the GPU
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src/simulation.hpp

commit e3cd77d36c0523962ef78136a4f8bde999522281
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Jun 5 19:05:13 2025 -0400

    update Dockerfiles to use Clang 20 (#1130)
    
    ### Description
    Updates Dockerfiles to use Clang 20 instead of Clang 19.
    
    ### Related issues
    Closes https://github.com/quokka-astro/quokka/issues/1129.
    
    ### 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).
    - [ ] 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`.

.devcontainer/cuda-container/Dockerfile
.devcontainer/gcc-container/Dockerfile

commit a241f133f7fece752ff48c0e1c442e65d34f9e9e
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Jun 4 22:41:46 2025 -0400

    Allow specifying which variables to include in plotfiles (#1111)
    
    ### Description
    Allows the user to specify which variables are included as cell-centered
    outputs in plotfiles. By default, all variables are included except for
    RiemannVelocity variables (which are only useful in their raw,
    face-centered form).
    
    ### Related issues
    Fixes https://github.com/quokka-astro/quokka/issues/735.
    
    ### 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:_
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    above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] *(For quokka-astro org members)* I have manually triggered the GPU
    tests with the magic comment `/azp run`.
    
    ---------
    
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src/.clang-tidy
src/QuokkaSimulation.hpp
src/simulation.hpp

commit e480215e73987c1a04501281359db52ae0407bab
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Jun 4 21:02:05 2025 -0400

    update amrex to include Lustre I/O workarounds (#1127)
    
    ### Description
    Updates the AMReX submodule to include my PR that adds workarounds for
    Lustre I/O issues.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] *(For quokka-astro org members)* I have manually triggered the GPU
    tests with the magic comment `/azp run`.

extern/amrex

commit 3a2ead969ffb7df6e5dfd90565f56e35cdc24648
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Jun 2 21:42:48 2025 -0400

    Isolated disk galaxy (#506)
    
    ### Description
    Initializes a isolated disk galaxy simulation with collisionless
    particles and gas for a user-specified disk scale height, disk scale
    length, and disk mass.
    
    Static mesh refinement is specified in terms of a maximum cylindrical
    radius $R_{max}$ and a maximum height $z_{max}$. The user must also
    provide i) an ASCII file with the particle initial conditions and ii) an
    ASCII file with the circular velocity tabulated as a function of radius
    (used to initialize the gas velocities).
    
    _Caveat:_ These initial conditions do not have a realistic CGM (it is at
    a constant density and temperature).
    
    This problem is added to the nightly regression tests.
    
    ### Related issues
    N/A
    
    ### 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
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    
    ---------
    
    Co-authored-by: ChongChong He <chongchong.he@anu.edu.au>
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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.gitignore
extern/agora_data/AgoraGalaxy_particles_LOW.tar.gz
extern/agora_data/README.txt
extern/agora_data/create_amrex_particles.py
extern/agora_data/filter_particles.py
extern/agora_data/vcirc.tar.gz
regression/quokka-tests.ini
src/problems/CMakeLists.txt
src/problems/DiskGalaxy/CMakeLists.txt
src/problems/DiskGalaxy/ascent_actions.yaml
src/problems/DiskGalaxy/galaxy.cpp
src/problems/DiskGalaxy/plot_disk.py
src/problems/DiskGalaxy/plot_faceon.py
src/problems/DiskGalaxy/plot_phase.py
tests/DiskGalaxy.in

commit 2e9fa17d22d98952ba518a5411f0510983c34d9b
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Jun 2 11:57:44 2025 -0400

    Refactor restart code and add universal refinement option (#1100)
    
    ### Description
    Refactors the entire checkpoint reading code, and on restart:
    * Optionally, universally refines all levels with piecewise constant
    interpolation
    * Chops grids on all levels in order to better load balance across all
    MPI ranks
    * Splits particles (except for tracer particles) by a factor of
    `pow(refine_factor, AMREX_SPACEDIM)`
    
    The user can adjust `amr.n_cell` to be an integer multiple of the
    previous simulation. Then, the restart code will check that the new base
    grid size is the same integer multiple of the original grid in all
    dimensions, and then interpolate each level onto new refined grids.
    
    Adds a new `CheckpointRestartRefine` test, which tests multi-level
    restarts with universal refinement using the HydroBlast3D problem with
    tracer particles.
    
    *Warning:* **AMReX PC->Restart() does not work if there are more levels
    than in the checkpoint.** This is a bug in AMReX. For now, we detect
    this situation and abort.
    
    ### Related issues
    N/A
    
    ### Checklist
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    completed. Denote completed tasks with an `x` inside the square brackets
    `[ ]` in the Markdown source below:_
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
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    code.
    - [x] *(For quokka-astro org members)* I have manually triggered the GPU
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.github/workflows/checkpoint-restart-refine.yml
CLAUDE.md
src/problems/BinaryOrbitCIC/CMakeLists.txt
src/problems/BinaryOrbitCIC/binary_orbit.cpp
src/problems/HydroBlast3D/test_hydro3d_blast.cpp
src/simulation.hpp
tests/BinaryOrbit_refactor.in
tests/BinaryOrbit_refactor_init.in
tests/blast_32.in
tests/blast_64.in
tests/checkpoint_restart_refine_test.sh

commit 327e99738da0b474fd8117ad21e72f15b74da26c
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Jun 2 08:13:00 2025 -0400

    Support setting the maximum number of binary output files (#1013)
    
    ### Description
    Support the ParmParse options `amr.plot_nfiles` and
    `amr.checkpoint_nfiles`. These set the maximum number of binary files
    written on disk per MultiFab.
    
    This is necessary to optimize I/O performance on some Lustre
    filesystems. These should usually be set to either:
     * the number of MPI ranks, or, for extreme scale simulations, or
     * the number of nodes.
    
    A value of `-1` sets it to the number of MPI ranks (which is the
    default).
    
    The striping on Lustre filesystems should usually be set using the
    command:
    ```
    lfs setstripe -c 1 -S 16M my_sim_working_dir
    ```
    where `my_sim_working_dir` is the directory where the simulation is
    running and will write plotfiles and checkpoints.
    
    ### Related issues
    N/A
    
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
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    code.
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src/io/io_utils.hpp
src/simulation.hpp
tests/checkpoint_restart_test.sh

commit e60db615724afb4ec5973cd805adc402dd8bf5e4
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Jun 2 08:08:03 2025 -0400

    Bump devcontainers/cpp from `a74f174` to `a7cddc1` in /.devcontainer/gcc-container (#1122)
    
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.devcontainer/gcc-container/Dockerfile

commit f75592294c6d9be375588a6ea8215c255f963b80
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Jun 2 08:07:53 2025 -0400

    Bump ossf/scorecard-action from 2.4.1 to 2.4.2 (#1123)
    
    Bumps [ossf/scorecard-action](https://github.com/ossf/scorecard-action)
    from 2.4.1 to 2.4.2.
    <details>
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    <p><em>Sourced from <a
    href="https://github.com/ossf/scorecard-action/releases">ossf/scorecard-action's
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    release notes.</p>
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    href="https://github.com/ossf/scorecard-action/compare/v2.4.1...v2.4.2">https://github.com/ossf/scorecard-action/compare/v2.4.1...v2.4.2</a></p>
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    <li><a
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    :seedling: bump docker to ghcr v2.4.2 (<a
    href="https://redirect.github.com/ossf/scorecard-action/issues/1548">#1548</a>)</li>
    <li><a
    href="https://github.com/ossf/scorecard-action/commit/b225da6b2b97811a123bb34532642f3ad6a4f011"><code>b225da6</code></a>
    Bump github.com/ossf/scorecard/v5 from v5.2.0 to v5.2.1 (<a
    href="https://redirect.github.com/ossf/scorecard-action/issues/1550">#1550</a>)</li>
    <li><a
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    :seedling: Bump the docker-images group across 1 directory with 2
    updates (<a
    href="https://redirect.github.com/ossf/scorecard-action/issues/1">#1</a>...</li>
    <li><a
    href="https://github.com/ossf/scorecard-action/commit/e1daa8c5c7ed469dbb0167e261ed1c9fa673a9ae"><code>e1daa8c</code></a>
    :seedling: Bump the github-actions group across 1 directory with 5
    updates (#...</li>
    <li><a
    href="https://github.com/ossf/scorecard-action/commit/9fe6511b9b36af3b03200e49cf8fb09d261b5402"><code>9fe6511</code></a>
    :seedling: Bump golang.org/x/net from 0.39.0 to 0.40.0 (<a
    href="https://redirect.github.com/ossf/scorecard-action/issues/1542">#1542</a>)</li>
    <li><a
    href="https://github.com/ossf/scorecard-action/commit/25b9cd9cd11610dcac11e59afed9910714b12129"><code>25b9cd9</code></a>
    :seedling: Bump github.com/ossf/scorecard/v5 from v5.1.1 to v5.2.0 (<a
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    <li><a
    href="https://github.com/ossf/scorecard-action/commit/18cc9b81307fc5ab3c2cd7092955f06dcfdf8c42"><code>18cc9b8</code></a>
    :seedling: Bump golang.org/x/net from 0.38.0 to 0.39.0 (<a
    href="https://redirect.github.com/ossf/scorecard-action/issues/1536">#1536</a>)</li>
    <li><a
    href="https://github.com/ossf/scorecard-action/commit/db7814227b097a902957aa24d989c6e473613a8e"><code>db78142</code></a>
    :seedling: Bump the github-actions group with 2 updates (<a
    href="https://redirect.github.com/ossf/scorecard-action/issues/1538">#1538</a>)</li>
    <li><a
    href="https://github.com/ossf/scorecard-action/commit/de386ed459e2f85111697f50fe076d0ea617a32f"><code>de386ed</code></a>
    :seedling: Bump golang from 1.24.1 to 1.24.2 in the docker-images group
    (<a
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.github/workflows/scorecard.yml

commit 25ae72a9b1f584d6047020f84a6b1a460cc1d7a5
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Jun 1 22:05:13 2025 -0400

    add BL_PROFILE annotations to particle functions (#1120)
    
    ### Description
    Adds `BL_PROFILE("FunctionName()")` to particle-related functions.
    
    ### Related issues
    N/A
    
    ### 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
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    above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
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src/QuokkaSimulation.hpp
src/particles/PhysicsParticles.hpp
src/particles/particle_accretion.hpp
src/particles/particle_creation.hpp
src/particles/particle_deposition.hpp
src/particles/particle_destruction.hpp
src/simulation.hpp

commit ba9326ba58642d71c8610c02a23c41ce4e9da508
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sun Jun 1 14:01:42 2025 -0400

    Bump extern/amrex from `d49d229` to `5181c27` (#1117)
    
    Bumps [extern/amrex](https://github.com/AMReX-Codes/amrex) from
    `d49d229` to `5181c27`.
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/5181c2798f821033351caebcd66e1b50228eb139"><code>5181c27</code></a>
    ParallelCopy: Fix a launch region issue (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4481">#4481</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/78268f16d62624ae69968e6510403397e2e61c52"><code>78268f1</code></a>
    Reuse MLEBNodeFDLaplacian and MLCurlCurl (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4480">#4480</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/fc469a32d34d320cca5d2e96758757952066075a"><code>fc469a3</code></a>
    Add new amrex::Initialize (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4476">#4476</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/8ea01a1c925a5fd5dcac0ddf8c9ce76ae4123a80"><code>8ea01a1</code></a>
    GNU Make: Use -g1 for optimized builds with GCC and Clang (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4475">#4475</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/d70dd73e3aa564a00c6d7ce268c104da55f54223"><code>d70dd73</code></a>
    Update rules of check-changes (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4474">#4474</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/390ed35b26bca69aa5e1dabed81cc64a5cd009e7"><code>390ed35</code></a>
    Fix compilation of PlotfileToMatLab (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4471">#4471</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/d3798de0bd81b76ed148af042b4656bd271ed2c7"><code>d3798de</code></a>
    Print max CArena usage (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4468">#4468</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/69363b24e8f8e11a2808f4b33920642182276e35"><code>69363b2</code></a>
    Put MPI datatypes in separate namespace (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4470">#4470</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/9d5f111259df6a5005ce74ddba64d98e9e44cb6c"><code>9d5f111</code></a>
    Fix incorrect static_cast in amrex::cast (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4465">#4465</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/1fbc66798140479a59ecd16796079984cc0370c0"><code>1fbc667</code></a>
    Avoid polluting global namespace with MPI types for non-MPI builds (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4463">#4463</a>)</li>
    <li>Additional commits viewable in <a
    href="https://github.com/AMReX-Codes/amrex/compare/d49d22968b403bc978749b5e2feb7c94a7710158...5181c2798f821033351caebcd66e1b50228eb139">compare
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extern/amrex

commit 9c23b69fceb2bda6f852415a41afbca6aa35e9f2
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sun Jun 1 15:15:17 2025 +0000

    Bump extern/fmt from `505ee05` to `02de29e` (#1118)
    
    Bumps [extern/fmt](https://github.com/fmtlib/fmt) from `505ee05` to
    `02de29e`.
    <details>
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    <li><a
    href="https://github.com/fmtlib/fmt/commit/02de29e00321787fa515ca60f0f5911e61892dc6"><code>02de29e</code></a>
    Remove a reference to a compromised account</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/6d51c78c1e35650602a33d73cbd4af3900b1cfae"><code>6d51c78</code></a>
    Cleanup FP formatting</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/0f4e9d0bde3ba83369dd1e249e8eafaa47535240"><code>0f4e9d0</code></a>
    Cleanup FP formatting</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/d9d50495ac72fcb961807a5b21d039c339b7181c"><code>d9d5049</code></a>
    Optimize the default FP formatting</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/befbc5fdb838040b3721d13b59e32edb122f224d"><code>befbc5f</code></a>
    Fix ADL lookup for memory_buffer</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/8aa1d6a9fbf0dd8b44b400e79c74c6aec9e1c1d9"><code>8aa1d6a</code></a>
    Minor cleanup</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/6d79757a3804658f692e21fb57d32972a1371c13"><code>6d79757</code></a>
    Interpret precision as display width (<a
    href="https://redirect.github.com/fmtlib/fmt/issues/4443">#4443</a>)</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/1ff0b7f5e1d1ff36ade3fe714b47a861db41ef9f"><code>1ff0b7f</code></a>
    Cleanup warning suppression</li>
    <li><a
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    Remove some implicit conversions (<a
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    <li><a
    href="https://github.com/fmtlib/fmt/commit/f7033da09e8ca2932ee2f5c40ae8277cad3e1958"><code>f7033da</code></a>
    Avoid include locale inline if C++20 modules are enabled (<a
    href="https://redirect.github.com/fmtlib/fmt/issues/4451">#4451</a>)</li>
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extern/fmt

commit e16d5867fb35272732bb884ccf968a5fca8cbdf7
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sun Jun 1 11:14:41 2025 -0400

    Bump extern/openPMD-api from `aa2cc99` to `257cf87` (#1119)
    
    Bumps [extern/openPMD-api](https://github.com/openPMD/openPMD-api) from
    `aa2cc99` to `257cf87`.
    <details>
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    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/257cf875fd24b46ee670fbcb36080f5340754623"><code>257cf87</code></a>
    Workaround for Hipcc error (reference to host function in host device
    functio...</li>
    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/1ff5cf78682731b34e676ea9a625bce92b156838"><code>1ff5cf7</code></a>
    Safeguards for READ_LINEAR mode (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1753">#1753</a>)</li>
    <li>See full diff in <a
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extern/openPMD-api

commit aa5a958a47c26d3a13a185ef09a2a48b85ae6dee
Author: Ben Wibking <ben@wibking.com>
Date:   Sat May 31 21:32:13 2025 -0400

    Add citation badge (#1093)
    
    ### Description
    Add a citation badge that links to the [Software Citation
    Station](https://www.tomwagg.com/software-citation-station/).
    
    ### Related issues
    Depends on
    https://github.com/TomWagg/software-citation-station/issues/73.
    
    ### 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).
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    above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] 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`.

README.md

commit fe8040b5f39274d9b999fc9390fd4d1a353f6b4c
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Sat May 31 20:02:36 2025 +1000

    Validate stochastic star formation algorithm (#1035)
    
    ### Description
    
    Add a test for the stochastic star formation algorithm. Fixed a few
    fatal bugs in the implementation on CPU. Fixed the bug related to RNG on
    GPU ( #1032 ). Also added a new evolution stage named `LowMassComposite`
    to address #1033 . Now, high-mass stars (>8 Msun) are labeled as either
    `SNProgenitor`, if they go SN, or `LowMassStar` (confusing name, sorry,
    should fix later), if they don't go SN. Low-mass stellar composites are
    labeled as `LowMassComposite`.
    
    Test problem: uniform background: n = 1 cm-3, T = 10 K. A single cell at
    the center with n = 1e6 cm-3. At first timestep, a large number of stars
    form in the center cell. We run the sim for 2 timesteps (< 1 Myr) and
    check for the mass distribution of the stars created. This test problem
    runs on GPU and the output looks good.
    
    After fixing a few math errors in the SF creation routine, the massive
    star mass fraction in the output agrees with what's coded (`contexpr
    fstar_high = 3.638945e-01` is computed at compile time), although the
    `constexpr fstar_high` is set wrong (should be 0.22). We can choose to
    hard-code this number in, but I'll leave it there and deal with it
    later.
    
    ```
    Total particle mass = 12326914.47 Msun
    Number of high mass stars = 231137
    Number of all stars = 231138
    Mstar_high_mean = 19.50259074 Msun
    fstar_high = 0.3656852108
    
    Expected values:
    Mstar_high_mean = 19.39 Msun
    fstar_high = 0.22
    
    Relative error:
    rel_err(Mstar_high_mean) = 0.00580663974
    rel_err(fstar_high) = 0.6622055034
    ```
    
    Code checks:
    1. Compiles and runs successfully on CPU
    2. The test problem compiles in ROCm container.
    3. The test problem compiles and runs successfully on moth GPU.
    
    Physics checks:
    1. `Mstar_high_mean`, `fstar_high`. Everything is fine now, except that
    `fstar_high` is set wrong (at compile time).
    4. Stars are indeed visible at the domain center
    5. The density of the SF cell goes from 1e6 to ~1e4 after SF, which
    means gas are consumed.
    
    Not checked:
    1. Mass and momentum conservation
    2. SFR.
    3. Mass function
    
    ### Related issues
    Fixes https://github.com/quokka-astro/quokka/issues/1032 and fixes
    https://github.com/quokka-astro/quokka/issues/1033.
    
    ### 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](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] 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: Aditi Vijayan <aditi.vijayan@anu.edu.au>
    Co-authored-by: Aditi <45175933+aditivijayan@users.noreply.github.com>
    Co-authored-by: Ben Wibking <ben@wibking.com>

docs/markdown/star_formation.md
docs/mkdocs.yml
extern/ChabrierIMFCalculations.nb
src/math/interpolate.cpp
src/particles/PhysicsParticles.hpp
src/particles/particle_creation.hpp
src/particles/particle_types.hpp
src/particles/stellarpop_data.hpp
src/problems/CMakeLists.txt
src/problems/ParticleCreation/particle_creation_from_cell.cpp
src/problems/ParticleSF/CMakeLists.txt
src/problems/ParticleSF/test_particle_SF.cpp
src/problems/ParticleSF/test_particle_SF.hpp
src/simulation.hpp
tests/ParticleSF.in

commit d9e1cd426b22e2976a44fdc1e060277780150e01
Author: lizmcole <lizmcole@users.noreply.github.com>
Date:   Fri May 30 17:15:05 2025 +1000

    Update simulation.hpp to fix plotfileMF_fc bug (#1108)
    
    Fix bug plotfileMF_fc
    
    ### Description
    One line change to plotMF_fc so that the grid sizes are for the faces
    and not cell centers
    
    ### Related issues
    Are there any GitHub issues that are fixed by this pull request? Add a
    link to them here.
    
    ### 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).
    - [ ] I have added a link to any related issues (if applicable; see
    above).
    - [ ] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] *(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>

src/problems/CMakeLists.txt
src/problems/HydroWave/CMakeLists.txt
src/problems/HydroWave/test_hydro_wave.cpp
src/problems/HydroWaveFC/CMakeLists.txt
src/problems/HydroWaveFC/test_hydro_wave_fc.cpp
src/simulation.hpp
tests/hydro_wave.in

commit 6770fc268383441b428c1601afc7a008a2b14cae
Author: Ben Wibking <ben@wibking.com>
Date:   Fri May 30 00:03:45 2025 -0400

    Ensure runtime parameters override compile-time settings (#1114)
    
    ### Description
    This pull request ensures that runtime parameters specified in input
    files always take precedence over compile-time values set in
    `problem_main()` functions. Previously, parameters directly assigned in
    problem code (before calling `sim.evolve()`) would override user input,
    which was counterintuitive and limited flexibility. The fix adds a
    `rereadRuntimeParameters()` method that is called at the beginning of
    evolve() to re-read all runtime parameters, ensuring that user-specified
    values take precedence over any compile-time assignments made earlier in
    `problem_main()`.
    
    ### Related issues
    No related issues.
    
    ### 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).
    - [ ] 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>

src/QuokkaSimulation.hpp
src/simulation.hpp
tests/hydro_wave_fc.in

commit 850b7c392993269e9f5d9ac0b9177526a6600b40
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Fri May 30 00:59:33 2025 +1000

    Remove RadPulse test (#1109)
    
    ### Description
    Remove the RadPulse test. This is an old test before IMEX where the
    pulse does not diffuse at all over the course of the simulation and we
    can remove it.
    
    ### Related issues
    Are there any GitHub issues that are fixed by this pull request? Add a
    link to them here.
    
    ### 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](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] 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`.

src/problems/CMakeLists.txt
src/problems/RadPulse/CMakeLists.txt
src/problems/RadPulse/test_radiation_pulse.cpp
tests/RadPulse.in

commit 0bd5f7180ae8557151c4a9db267ebab5161ae6d4
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Thu May 29 03:38:54 2025 +1000

    Add the ability to split massive particles (#1104)
    
    ### Description
    This adds the ability to split each massive particle into an integer
    number `splitFactor` new particles of equal mass.
    
    This is needed in order to scale the disk galaxy problem to higher
    resolutions.
    
    ### Related issues
    Replace #996
    
    ### 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.
    - [x] *(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>

src/particles/PhysicsParticles.hpp
src/problems/BinaryOrbitCIC/CMakeLists.txt
src/problems/BinaryOrbitCIC/binary_orbit.cpp
tests/BinaryOrbit.in
tests/BinaryOrbitAMR.in
tests/BinaryOrbit_split.in

commit 895fb57841627f32ee3d377947204f76f05050d2
Author: Ben Wibking <ben@wibking.com>
Date:   Wed May 28 12:01:39 2025 -0400

    update CLAUDE.md (#1102)
    
    ### Description
    This updates the `CLAUDE.md` file used to provide guidance to AI coding
    tools.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] 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`.

CLAUDE.md

commit 16bb3ea96b6ab13a335e93f37671a302059714c2
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Tue May 27 23:03:30 2025 +1000

    Remove all hpp files from problem generators (#1095)
    
    ### Description
    
    Since the header files in the `src/problems` folder are not actually
    helpful, we'd better just remove all of them to keep the code clean.
    This makes duplicating a test problem easier.
    
    ### Related issues
    Are there any GitHub issues that are fixed by this pull request? Add a
    link to them here.
    
    ### 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).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] *(For quokka-astro org members)* I have manually triggered the GPU
    tests with the magic comment `/azp run`.

src/problems/Advection/test_advection.cpp
src/problems/Advection/test_advection.hpp
src/problems/Advection2D/test_advection2d.cpp
src/problems/Advection2D/test_advection2d.hpp
src/problems/AdvectionSemiellipse/test_advection_semiellipse.cpp
src/problems/AdvectionSemiellipse/test_advection_semiellipse.hpp
src/problems/BinaryOrbitCIC/binary_orbit.cpp
src/problems/BinaryOrbitCIC/binary_orbit.hpp
src/problems/Cooling/test_cooling.cpp
src/problems/Cooling/test_cooling.hpp
src/problems/FCQuantities/test_fc_quantities.cpp
src/problems/FCQuantities/test_fc_quantities.hpp
src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp
src/problems/GravRadParticle3D/test_grav_rad_particle_3D.hpp
src/problems/HydroBlast2D/test_hydro2d_blast.cpp
src/problems/HydroBlast2D/test_hydro2d_blast.hpp
src/problems/HydroBlast3D/test_hydro3d_blast.cpp
src/problems/HydroBlast3D/test_hydro3d_blast.hpp
src/problems/HydroContact/test_hydro_contact.cpp
src/problems/HydroContact/test_hydro_contact.hpp
src/problems/HydroHighMach/test_hydro_highmach.cpp
src/problems/HydroHighMach/test_hydro_highmach.hpp
src/problems/HydroKelvinHelmholz/test_hydro2d_kh.cpp
src/problems/HydroKelvinHelmholz/test_hydro2d_kh.hpp
src/problems/HydroLeblanc/test_hydro_leblanc.cpp
src/problems/HydroLeblanc/test_hydro_leblanc.hpp
src/problems/HydroQuirk/test_quirk.cpp
src/problems/HydroQuirk/test_quirk.hpp
src/problems/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
src/problems/HydroRichtmeyerMeshkov/test_hydro2d_rm.hpp
src/problems/HydroSMS/test_hydro_sms.cpp
src/problems/HydroSMS/test_hydro_sms.hpp
src/problems/HydroShocktube/test_hydro_shocktube.cpp
src/problems/HydroShocktube/test_hydro_shocktube.hpp
src/problems/HydroShocktubeCMA/test_hydro_shocktube_cma.cpp
src/problems/HydroShocktubeCMA/test_hydro_shocktube_cma.hpp
src/problems/HydroShuOsher/test_hydro_shuosher.cpp
src/problems/HydroShuOsher/test_hydro_shuosher.hpp
src/problems/HydroVacuum/test_hydro_vacuum.cpp
src/problems/HydroVacuum/test_hydro_vacuum.hpp
src/problems/HydroWave/test_hydro_wave.cpp
src/problems/HydroWave/test_hydro_wave.hpp
src/problems/HydroWaveFC/test_hydro_wave_fc.cpp
src/problems/HydroWaveFC/test_hydro_wave_fc.hpp
src/problems/NSCBC/channel.cpp
src/problems/NSCBC/channel.hpp
src/problems/NSCBC/vortex.cpp
src/problems/NSCBC/vortex.hpp
src/problems/ODEIntegration/test_ode.cpp
src/problems/ODEIntegration/test_ode.hpp
src/problems/ParticleAccretion/test_particle_accretion.cpp
src/problems/ParticleAccretion/test_particle_accretion.hpp
src/problems/ParticleCreation/particle_creation_from_cell.cpp
src/problems/ParticleCreation/particle_creation_from_cell.hpp
src/problems/ParticleSink/test_particle_sink.cpp
src/problems/ParticleSink/test_particle_sink.hpp
src/problems/PassiveScalar/test_scalars.cpp
src/problems/PassiveScalar/test_scalars.hpp
src/problems/PopIII/popiii.cpp
src/problems/PopIII/popiii.hpp
src/problems/PrimordialChem/test_primordial_chem.cpp
src/problems/PrimordialChem/test_primordial_chem.hpp
src/problems/RadBeam/test_radiation_beam.cpp
src/problems/RadBeam/test_radiation_beam.hpp
src/problems/RadDust/test_rad_dust.cpp
src/problems/RadDust/test_rad_dust.hpp
src/problems/RadDustMG/test_rad_dust_MG.cpp
src/problems/RadDustMG/test_rad_dust_MG.hpp
src/problems/RadForce/test_radiation_force.cpp
src/problems/RadForce/test_radiation_force.hpp
src/problems/RadLineCooling/test_rad_line_cooling.cpp
src/problems/RadLineCooling/test_rad_line_cooling.hpp
src/problems/RadLineCoolingMG/test_rad_line_cooling_MG.cpp
src/problems/RadLineCoolingMG/test_rad_line_cooling_MG.hpp
src/problems/RadMarshak/test_radiation_marshak.cpp
src/problems/RadMarshak/test_radiation_marshak.hpp
src/problems/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/problems/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.hpp
src/problems/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/problems/RadMarshakCGS/test_radiation_marshak_cgs.hpp
src/problems/RadMarshakDust/test_radiation_marshak_dust.cpp
src/problems/RadMarshakDust/test_radiation_marshak_dust.hpp
src/problems/RadMarshakDustPE/test_radiation_marshak_dust_and_PE.cpp
src/problems/RadMarshakDustPE/test_radiation_marshak_dust_and_PE.hpp
src/problems/RadMarshakVaytet/test_radiation_marshak_Vaytet.cpp
src/problems/RadMarshakVaytet/test_radiation_marshak_Vaytet.hpp
src/problems/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/problems/RadMatterCoupling/test_radiation_matter_coupling.hpp
src/problems/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/problems/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.hpp
src/problems/RadParticle/test_radparticle.cpp
src/problems/RadParticle/test_radparticle.hpp
src/problems/RadParticle2D/test_radparticle_2D.cpp
src/problems/RadParticle2D/test_radparticle_2D.hpp
src/problems/RadPulse/test_radiation_pulse.cpp
src/problems/RadPulse/test_radiation_pulse.hpp
src/problems/RadShadow/test_radiation_shadow.cpp
src/problems/RadShadow/test_radiation_shadow.hpp
src/problems/RadStreaming/test_radiation_streaming.cpp
src/problems/RadStreaming/test_radiation_streaming.hpp
src/problems/RadStreamingY/test_radiation_streaming_y.cpp
src/problems/RadStreamingY/test_radiation_streaming_y.hpp
src/problems/RadSuOlson/test_radiation_SuOlson.cpp
src/problems/RadSuOlson/test_radiation_SuOlson.hpp
src/problems/RadTophat/test_radiation_tophat.cpp
src/problems/RadTophat/test_radiation_tophat.hpp
src/problems/RadTube/test_radiation_tube.cpp
src/problems/RadTube/test_radiation_tube.hpp
src/problems/RadhydroBB/test_radhydro_bb.cpp
src/problems/RadhydroBB/test_radhydro_bb.hpp
src/problems/RadhydroPulse/test_radhydro_pulse.cpp
src/problems/RadhydroPulse/test_radhydro_pulse.hpp
src/problems/RadhydroPulseDyn/test_radhydro_pulse_dyn.cpp
src/problems/RadhydroPulseDyn/test_radhydro_pulse_dyn.hpp
src/problems/RadhydroPulseGrey/test_radhydro_pulse_grey.cpp
src/problems/RadhydroPulseGrey/test_radhydro_pulse_grey.hpp
src/problems/RadhydroPulseMGconst/test_radhydro_pulse_MG_const_kappa.cpp
src/problems/RadhydroPulseMGconst/test_radhydro_pulse_MG_const_kappa.hpp
src/problems/RadhydroPulseMGint/test_radhydro_pulse_MG_int.cpp
src/problems/RadhydroPulseMGint/test_radhydro_pulse_MG_int.hpp
src/problems/RadhydroShell/test_radhydro_shell.cpp
src/problems/RadhydroShell/test_radhydro_shell.hpp
src/problems/RadhydroShock/test_radhydro_shock.cpp
src/problems/RadhydroShock/test_radhydro_shock.hpp
src/problems/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/problems/RadhydroShockCGS/test_radhydro_shock_cgs.hpp
src/problems/RadhydroShockMultigroup/test_radhydro_shock_multigroup.cpp
src/problems/RadhydroShockMultigroup/test_radhydro_shock_multigroup.hpp
src/problems/RadhydroUniformAdvecting/test_radhydro_uniform_advecting.cpp
src/problems/RadhydroUniformAdvecting/test_radhydro_uniform_advecting.hpp
src/problems/RandomBlast/blast.cpp
src/problems/RandomBlast/blast.hpp
src/problems/RayleighTaylor2D/test_hydro2d_rt.cpp
src/problems/RayleighTaylor2D/test_hydro2d_rt.hpp
src/problems/RayleighTaylor3D/test_hydro3d_rt.cpp
src/problems/RayleighTaylor3D/test_hydro3d_rt.hpp
src/problems/SN/test_SN.hpp
src/problems/ShockCloud/cloud.cpp
src/problems/ShockCloud/cloud.hpp
src/problems/SphericalCollapse/spherical_collapse.cpp
src/problems/SphericalCollapse/spherical_collapse.hpp
src/problems/StarCluster/star_cluster.cpp
src/problems/StarCluster/star_cluster.hpp

commit 0e69dc461ac089e4439e804299530df1efe277cb
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon May 26 18:03:58 2025 +0000

    [pre-commit.ci] pre-commit autoupdate (#1098)
    
    <!--pre-commit.ci start-->
    updates:
    - [github.com/pre-commit/mirrors-clang-format: v20.1.4 →
    v20.1.5](https://github.com/pre-commit/mirrors-clang-format/compare/v20.1.4...v20.1.5)
    <!--pre-commit.ci end-->
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

commit 1b66df1a11bcf72539fb5212df20a1bdab6b43ff
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Tue May 27 01:44:43 2025 +1000

    Keep all problem cpp files tidy (#1096)
    
    ### Description
    
    I tried to get rid of as many `clang-tidy` warnings as possible from all
    cpp files in `src/problems` by doing both `clang-tidy -fix` and manual
    fix.
    
    These are the changes I made:
    
    `clang-tidy` auto fixes:
    - Add missing `const`
    - Replace `std::endl` with `\n`
    - Replace `amrex::Real` with `static_cast<amrex::Real>`
    
    Manual fixes:
    
    - Add `NOLINT` to static mutable variables.
    - Rename `T0` and `T1` with `T_lo` and `T_hi`. `clang-tidy` complains
    `T1` is confusable with `TI`
    - Replace `if (AMREX_SPACEDIM == 3)` with `#if (AMREX_SPACEDIM == 3)`
    
    I also added `-cppcoreguidelines-pro-bounds-pointer-arithmetic` to the
    `.clang-tidy` file: #1097
    
    ### Related issues
    Are there any GitHub issues that are fixed by this pull request? Add a
    link to them here.
    
    ### 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).
    - [ ] 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>

src/problems/Advection/test_advection.cpp
src/problems/Advection2D/test_advection2d.cpp
src/problems/AdvectionSemiellipse/test_advection_semiellipse.cpp
src/problems/Cooling/test_cooling.cpp
src/problems/FCQuantities/test_fc_quantities.cpp
src/problems/HydroBlast2D/test_hydro2d_blast.cpp
src/problems/HydroBlast3D/test_hydro3d_blast.cpp
src/problems/HydroContact/test_hydro_contact.cpp
src/problems/HydroHighMach/test_hydro_highmach.cpp
src/problems/HydroKelvinHelmholz/test_hydro2d_kh.cpp
src/problems/HydroLeblanc/test_hydro_leblanc.cpp
src/problems/HydroQuirk/test_quirk.cpp
src/problems/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
src/problems/HydroSMS/test_hydro_sms.cpp
src/problems/HydroShocktube/test_hydro_shocktube.cpp
src/problems/HydroShocktubeCMA/test_hydro_shocktube_cma.cpp
src/problems/HydroShuOsher/test_hydro_shuosher.cpp
src/problems/HydroVacuum/test_hydro_vacuum.cpp
src/problems/HydroWave/test_hydro_wave.cpp
src/problems/NSCBC/channel.cpp
src/problems/NSCBC/vortex.cpp
src/problems/ODEIntegration/test_ode.cpp
src/problems/PassiveScalar/test_scalars.cpp
src/problems/PrimordialChem/test_primordial_chem.cpp
src/problems/RadBeam/test_radiation_beam.cpp
src/problems/RadDust/test_rad_dust.cpp
src/problems/RadDustMG/test_rad_dust_MG.cpp
src/problems/RadForce/test_radiation_force.cpp
src/problems/RadLineCooling/test_rad_line_cooling.cpp
src/problems/RadLineCoolingMG/test_rad_line_cooling_MG.cpp
src/problems/RadMarshak/test_radiation_marshak.cpp
src/problems/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/problems/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/problems/RadMarshakDust/test_radiation_marshak_dust.cpp
src/problems/RadMarshakDustPE/test_radiation_marshak_dust_and_PE.cpp
src/problems/RadMarshakVaytet/test_radiation_marshak_Vaytet.cpp
src/problems/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/problems/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/problems/RadPulse/test_radiation_pulse.cpp
src/problems/RadShadow/test_radiation_shadow.cpp
src/problems/RadStreaming/test_radiation_streaming.cpp
src/problems/RadStreamingY/test_radiation_streaming_y.cpp
src/problems/RadSuOlson/test_radiation_SuOlson.cpp
src/problems/RadTophat/test_radiation_tophat.cpp
src/problems/RadTube/test_radiation_tube.cpp
src/problems/RadhydroBB/test_radhydro_bb.cpp
src/problems/RadhydroPulse/test_radhydro_pulse.cpp
src/problems/RadhydroPulseDyn/test_radhydro_pulse_dyn.cpp
src/problems/RadhydroPulseGrey/test_radhydro_pulse_grey.cpp
src/problems/RadhydroPulseMGconst/test_radhydro_pulse_MG_const_kappa.cpp
src/problems/RadhydroPulseMGint/test_radhydro_pulse_MG_int.cpp
src/problems/RadhydroShell/test_radhydro_shell.cpp
src/problems/RadhydroShock/test_radhydro_shock.cpp
src/problems/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/problems/RadhydroShockMultigroup/test_radhydro_shock_multigroup.cpp
src/problems/RadhydroUniformAdvecting/test_radhydro_uniform_advecting.cpp
src/problems/RayleighTaylor2D/test_hydro2d_rt.cpp
src/problems/RayleighTaylor3D/test_hydro3d_rt.cpp
src/problems/SphericalCollapse/spherical_collapse.cpp
src/problems/StarCluster/star_cluster.cpp

commit 37aaced678913447c14e3c4383caf9f4b51a5337
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Tue May 27 00:33:37 2025 +1000

    remove tidy check: pointer-arithmetic (#1097)
    
    ### Description
    
    The codebase makes extensive use of pointer arithmetic, and a good
    fraction of them are suppressed by `NOLINT`. We may just ignore it
    globally.
    
    ### Related issues
    
    ### 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).
    - [ ] 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`.

src/.clang-tidy

commit d93b690742738d714887698e421e3fa6c8b859a3
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Sun May 25 11:27:38 2025 +1000

    Fix bug: FillBoundary before computing accretion rate (#1092)
    
    ### Description
    
    Fixed a bug: need to `FillBoundary` before computing sink particle
    accretion rates. Failing to do so causes the two stages of the sink
    accretion scheme to calculate the accretion rate differently because
    somehow (?) `state_new_cc_` has boundaries filled in the second stage.
    
    This has been bugging me for a little while. I found that the total mass
    (gas + particle) is not conserved to machine precision when testing the
    sink formation PR #1045; the relative error can be as large as 1e-5.
    This happens when a particle is at a box boundary.
    
    This PR fixed this problem. I also updated the `test_particle_sink` test
    to validate that the total mass is conserved to machine precision in our
    sink accretion scheme (#1017 and #1055)
    
    ### Related issues
    
    None.
    
    ### 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)](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.
    - [x] *(For quokka-astro org members)* I have manually triggered the GPU
    tests with the magic comment `/azp run`.

src/problems/ParticleSink/test_particle_sink.cpp
src/simulation.hpp
tests/ParticleSink.in

commit e09a312aa90cf4d4df1cb8f5cc6011eb61ef4827
Author: Ben Wibking <ben@wibking.com>
Date:   Thu May 22 20:57:29 2025 -0400

    Frontier-like docker container (#1088)
    
    ### Description
    This changes the ROCm container to be as close as possible to the
    environment on Frontier and Setonix:
    * **OpenSUSE Leap 15.6** (Frontier uses the commerical SLES 15.6).
    * **MPICH 3.4.3** (from which Cray MPI is derived and which which it is
    binary compatible). This lets us compile against MPICH in the container
    and then, when running on Frontier, bind-mount the Cray MPI libraries
    and use them at runtime.
    * **ROCm 6.4.0** Should be the same everywhere, in principle, but OLCF
    rebuilds this from source. We can just use the version in the container.
    
    Things that will not be identical:
    * Cray MPI vs MPICH: Cray MPI has optimizations and bugs that aren't in
    open-source MPICH. For testing purposes only, we can run with
    open-source MPICH across multiple systems (this will be slow and should
    never be done for production sims). Usually, the bugs we've seen aren't
    in MPI itself, but in the network layer.
    * Network: Setonix and Frontier have HPE Slingshot with different driver
    and firmware versions installed. It's buggy and behaves differently
    across versions, and we can't do anything about it.
    * GPU driver: different systems have different driver versions
    installed. We can't do anything about this.
    
    ### Related issues
    https://github.com/quokka-astro/quokka/issues/1087
    
    ### 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).
    - [ ] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] 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`.

.devcontainer/rocm-container/Dockerfile
.devcontainer/rocm-container/rocm_so.conf

commit 82bdf261d1f9930abb1cb997637fe5c655b0e054
Author: Ben Wibking <ben@wibking.com>
Date:   Thu May 22 00:20:14 2025 -0400

    Fix bug caused by function rename in #1071 (#1091)
    
    ### Description
    Fixes a bug introduced by renaming `PlotFileMF` to `PlotFileMF_cc` in
    https://github.com/quokka-astro/quokka/pull/1071.
    
    ### Related issues
    N/A
    
    ### 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:_
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    above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] 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
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src/simulation.hpp

commit 9bc762b7df513d3effabfce8a72f4fa1a9d06df7
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Wed May 21 20:34:49 2025 +1000

    Add Bondi accretion test from Krumholz 2004 (#1072)
    
    ### Description
    
    Add the Bondi accretion test from Krumholz 2004.
    
    ### Related issues
    Are there any GitHub issues that are fixed by this pull request? Add a
    link to them here.
    
    ### Checklist
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    code.
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    tests with the magic comment `/azp run`.
    
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    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/particles/particle_accretion.hpp
src/problems/CMakeLists.txt
src/problems/ParticleAccretion/CMakeLists.txt
src/problems/ParticleAccretion/test_particle_accretion.cpp
src/problems/ParticleAccretion/test_particle_accretion.hpp
src/problems/ParticleSink/test_particle_sink.cpp
tests/ParticleAccretion.in
tests/sink.txt

commit 8d3d2e4433230dd3dbda3431c942bfb129b3ed56
Author: lizmcole <lizmcole@users.noreply.github.com>
Date:   Tue May 20 07:43:41 2025 +1000

    Add plotfilemf_fc (#1071)
    
    ### Description
    Adds data files for face-centered variables in subdirectories to
    pltNNNNN files. The regular plotfileMF and associated functions are
    appended with _cc, and the new functions use _fc.
    
    New files:
    src/problems/HydroWaveFC/hydro_wave_fc_.cpp, hydro_wave_fc.hpp,
    CMakeLists.txt
    tests/hydro_wave_fc.in
    
    Modified files:
    src/simulation.hpp
    src/QuokkaSimulation.hpp
    src/problems/CMakeLists.txt
    
    ### Related issues
    N/A
    
    
    ### Checklist
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    above).
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    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.
    - [x] *(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>

src/QuokkaSimulation.hpp
src/problems/CMakeLists.txt
src/problems/HydroWaveFC/CMakeLists.txt
src/problems/HydroWaveFC/test_hydro_wave_fc.cpp
src/problems/HydroWaveFC/test_hydro_wave_fc.hpp
src/simulation.hpp
tests/hydro_wave_fc.in

commit 2c7d89f45f98f265cf20d7cf81d5ded73b83f12e
Author: Ben Wibking <ben@wibking.com>
Date:   Sun May 18 23:50:42 2025 -0400

    change default SNScheme to hybrid thermal/momentum and use AMREX_ENUM (#1083)
    
    ### Description
    This uses the `AMREX_ENUM` macro for `SNScheme`, so users can specify
    the SN scheme using the full string corresponding to each enum entry:
    ```
    particles.SN_scheme = SN_pure_kinetic_or_thermal_momentum
    ```
    
    The full set of options is:
    ```
    AMREX_ENUM(SNScheme,
            SN_thermal_only,                        // pure thermal
            SN_thermal_or_thermal_momentum,         // pure thermal (RM<1) or thermal+momentum (RM>=1)
            SN_thermal_kinetic_or_thermal_momentum, // thermal+kinetic (RM<1) or thermal+momentum (RM>=1)
            SN_pure_kinetic_or_thermal_momentum     // pure kinetic (RM<1) or thermal+momentum (RM>=1)
    );
    ```
    
    ### Related issues
    Closes https://github.com/quokka-astro/quokka/issues/713.
    
    ### 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
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    above).
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] *(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>

src/particles/particle_types.hpp
tests/ParticleSink.in
tests/SN.in

commit 52dee09ea18f9d4ef91b11b19e2f917e38962bd6
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commit 9eb53a5e1f07944377437e9088394dc87242f383
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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    Bump github/codeql-action from 3.28.17 to 3.28.18 (#1085)
    
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    <ul>
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    href="https://redirect.github.com/github/codeql-action/pull/2872">#2872</a></li>
    </ul>
    <h2>3.28.16 - 23 Apr 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.21.1. <a
    href="https://redirect.github.com/github/codeql-action/pull/2863">#2863</a></li>
    </ul>
    <h2>3.28.15 - 07 Apr 2025</h2>
    <ul>
    <li>Fix bug where the action would fail if it tried to produce a debug
    artifact with more than 65535 files. <a
    href="https://redirect.github.com/github/codeql-action/pull/2842">#2842</a></li>
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    href="https://redirect.github.com/github/codeql-action/pull/2838">#2838</a></li>
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    <h2>3.28.13 - 24 Mar 2025</h2>
    <p>No user facing changes.</p>
    <h2>3.28.12 - 19 Mar 2025</h2>
    <ul>
    <li>Dependency caching should now cache more dependencies for Java
    <code>build-mode: none</code> extractions. This should speed up
    workflows and avoid inconsistent alerts in some cases.</li>
    <li>Update default CodeQL bundle version to 2.20.7. <a
    href="https://redirect.github.com/github/codeql-action/pull/2810">#2810</a></li>
    </ul>
    <h2>3.28.11 - 07 Mar 2025</h2>
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    href="https://redirect.github.com/github/codeql-action/pull/2793">#2793</a></li>
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    <h2>3.28.10 - 21 Feb 2025</h2>
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    <li>Update default CodeQL bundle version to 2.20.5. <a
    href="https://redirect.github.com/github/codeql-action/pull/2772">#2772</a></li>
    <li>Address an issue where the CodeQL Bundle would occasionally fail to
    decompress on macOS. <a
    href="https://redirect.github.com/github/codeql-action/pull/2768">#2768</a></li>
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    <h2>3.28.9 - 07 Feb 2025</h2>
    <!-- raw HTML omitted -->
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    href="https://github.com/github/codeql-action/commit/ff0a06e83cb2de871e5a09832bc6a81e7276941f"><code>ff0a06e</code></a>
    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2896">#2896</a>
    from github/update-v3.28.18-b86edfc27</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/a41e0844be4d25fcef7ce7fa536f3e30275a9a1c"><code>a41e084</code></a>
    Update changelog for v3.28.18</li>
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    href="https://github.com/github/codeql-action/commit/b86edfc27a1e0d3b55127a7496a1c770a02b2f84"><code>b86edfc</code></a>
    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2893">#2893</a>
    from github/update-bundle/codeql-bundle-v2.21.3</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/e93b90025f7c49dccc3ee640c4155b63eb9a6b39"><code>e93b900</code></a>
    Merge branch 'main' into update-bundle/codeql-bundle-v2.21.3</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/510dfa3460b15b34a807ab5609b4691aed5ebbee"><code>510dfa3</code></a>
    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2894">#2894</a>
    from github/henrymercer/skip-validating-codeql-sarif</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/492d7832457da825a964331d860789f3f19d105b"><code>492d783</code></a>
    Merge branch 'main' into henrymercer/skip-validating-codeql-sarif</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/83bdf3b7f92061d2f6d74e2a4555ecf719adad68"><code>83bdf3b</code></a>
    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2859">#2859</a>
    from github/update-supported-enterprise-server-versions</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/cffc916774454a5ead1c8fb7925abad20cda85e4"><code>cffc916</code></a>
    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2891">#2891</a>
    from austinpray-mixpanel/patch-1</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/4420887272f1c68c7c58ca2970bdfb5eb657cf08"><code>4420887</code></a>
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.github/workflows/codeql.yml
.github/workflows/scorecard.yml

commit 7acda273ac4e5db0295a220c5f815b267ab22f3d
Author: Ben Wibking <ben@wibking.com>
Date:   Sun May 18 22:21:58 2025 -0400

    set FPE strict mode to avoid spurious FPEs with AppleClang (#1084)
    
    ### Description
    This prevents AppleClang from vectorizing code in a way that causes
    spurious FPEs. This has a performance cost, but when AppleClang is used,
    the user is probably running the code on their laptop and running the
    test suite (which turns on FPEs by default).
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] *(For quokka-astro org members)* I have manually triggered the GPU
    tests with the magic comment `/azp run`.

CMakeLists.txt

commit e748b3bb04a9b848d085ac700e801390c795afb2
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Sun May 18 11:54:07 2025 +1000

    Add a DeepWiki badge to README to allow auto-refreshing deepwiki page  (#1082)
    
    ### Description
    
    This adds a DeepWiki badge to the README page, which allows the user to
    click on it and jump to the DeepWiki page of Quokka. More importantly,
    this enables auto-refreshing the wiki weekly with the latest code.
    
    DeepWiki provides an AI-generated website with up-to-date documentation
    you can talk to.
    
    ### Related issues
    Are there any GitHub issues that are fixed by this pull request? Add a
    link to them here.
    
    ### 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).
    - [ ] 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`.

README.md

commit 9354de162fb096588de64fa6ff12fa42f3a2aca7
Author: Ben Wibking <ben@wibking.com>
Date:   Sat May 17 20:56:55 2025 -0400

    Fix volume rendering (#1080)
    
    ### Description
    Convexify the MultiFabs (https://github.com/AMReX-Codes/amrex/pull/4013)
    before sending them to Ascent for volume rendering.
    
    This fixes the volume rendering bugs. It works now. This is the
    SphericalCollapse test:
    
    <img
    src=https://github.com/user-attachments/assets/84638873-514a-4a9a-9cbc-843d448e62a4
    width=384 height=384 />
    
    ### Related issues
    Closes https://github.com/quokka-astro/quokka/issues/1078.
    
    ### 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).
    - [ ] I have added a link to any related issues (if applicable; see
    above).
    - [ ] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] 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>

docs/markdown/insitu_analysis.md
docs/markdown/volume_render_sphere.png
src/simulation.hpp
tests/ascent_actions.yaml

commit 9a17b0e81f8d72c557ed57af4e473f94fcb466d1
Author: Ben Wibking <ben@wibking.com>
Date:   Fri May 16 20:40:58 2025 -0400

    add Viskores build to dev containers (#1018)
    
    ### Description
    Adds [Viskores](https://github.com/Viskores/viskores) (with GPU support,
    if applicable) to the dev container images.
    
    This will let us do CI tests for in-situ volume rendering and isosurface
    contouring.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] 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`.

.devcontainer/cuda-container/Dockerfile
.devcontainer/gcc-container/Dockerfile
.devcontainer/rocm-container/Dockerfile

commit 40a71d79a8ac4d8b380fd86ad323f2da014e2d2d
Author: Ben Wibking <ben@wibking.com>
Date:   Fri May 16 19:46:14 2025 -0400

    add MPI_Barrier after writing each level in checkpoint files (#1079)
    
    ### Description
    This adds an `MPI_Barrier()` after writing each level in the checkpoint
    files. This seems to be necessary to avoid hangs while writing
    checkpoint files on Frontier.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] 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`.

src/simulation.hpp

commit 853b8e43a50117a0a92694cd87ae8d2fa0623049
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Fri May 16 22:16:35 2025 +1000

    Fix all clang-tidy warnings in simulation.hpp (#1075)
    
    ### Description
    
    `simulation.hpp` is tidy-free now. Any future edits to `simulation.hpp`
    will not trigger a clangt-tidy warning unless it's new in that change.
    
    Also updated `tidy.sh` to support `--fix` option to apply automatic fix.
    
    ### Related issues
    Are there any GitHub issues that are fixed by this pull request? Add a
    link to them here.
    
    ### 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).
    - [ ] 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>

scripts/tidy.sh
src/simulation.hpp

commit 9dab33a33cd058a76ac37ddd91d7a32f8044a37c
Author: Ben Wibking <ben@wibking.com>
Date:   Wed May 14 01:59:42 2025 -0400

    add example SLURM script to cancel job when I/O hangs (#1057)
    
    ### Description
    This SLURM script provides an example of how to automatically kill batch
    jobs that stop writing output to stdout/stderr after 5 minutes. This is
    useful when the filesystem is semi-broken and there are stochastic hangs
    when writing output files.
    
    I have manually tested this on DeltaAI.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] 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`.

scripts/slurm_job_monitor.sh

commit 8e1d11cb0cefd5adb9cffed8956e511e47dc29be
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Tue May 13 16:23:05 2025 +1000

    Add `using Real = amrex::Real;` (#1070)
    
    ### Description
    
    Add `using Real = amrex::Real;` in physics_info.hpp. Since
    physics_info.hpp is included in almost all source files in Quokka, this
    allows you to use Real to replace `double` or `amrex::Real` everywhere.
    
    We will gradually make this switch from double to Real and support
    single precision, but this change brings immediate convenience that we
    can replace the long `amrex::Real` with the short `Real`.
    
    ### Related issues
    #666 and #1003
    
    ### 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).
    - [ ] 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`.

src/physics_info.hpp

commit 2e2975e16bc2d0174232dfd13ac01ef54ff75514
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon May 12 18:01:08 2025 +0000

    [pre-commit.ci] pre-commit autoupdate (#1068)
    
    <!--pre-commit.ci start-->
    updates:
    - [github.com/pre-commit/mirrors-clang-format: v20.1.3 →
    v20.1.4](https://github.com/pre-commit/mirrors-clang-format/compare/v20.1.3...v20.1.4)
    <!--pre-commit.ci end-->
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

commit 4f888b34a3c3611242fe14f8f9016ef7f2a43c85
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Tue May 13 01:35:30 2025 +1000

    Change output behaviour  (#1066)
    
    ### Description
    
    As an example, let's run the ParticleCreation test, which has these time
    stamps: 0, 0.001, 0.002, 0.003, 0.004.
    
    If we set `plotfile_interval = 3` and `plottime_interval = 0.003`
    1. Previously: `plt00003` will be written twice, because both
    `plotfile_interval` and `plottime_interval` checks will result in
    writing a plotfile.
       2. Now: `plt00003` will be written once.
    
    If we set `plottime_interval = 0.003`
       1. Previously: Will write the following outputs: 1, 3
    2. Now: Will write the following outputs: 0, 3, 4, i.e. will write the
    first (0) and last steps along with steps whose time is a multiple of
    `plottime_interval`. 
    
    ### Related issues
    Are there any GitHub issues that are fixed by this pull request? Add a
    link to them here.
    
    ### 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).
    - [ ] 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`.

src/simulation.hpp
tests/ParticleCreation.in

commit b13ab7d14b5820529816a9c801c7e8396e52154e
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon May 12 00:05:43 2025 -0400

    Bump actions/dependency-review-action from 4.6.0 to 4.7.0 (#1065)
    
    Bumps
    [actions/dependency-review-action](https://github.com/actions/dependency-review-action)
    from 4.6.0 to 4.7.0.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
    href="https://github.com/actions/dependency-review-action/releases">actions/dependency-review-action's
    releases</a>.</em></p>
    <blockquote>
    <h2>v4.7.0</h2>
    <ul>
    <li>Handle complex license expressions (e.g. <code>MIT AND
    GPL-2.0</code>) in allow lists (fixes <a
    href="https://redirect.github.com/actions/dependency-review-action/issues/809">#809</a>
    and probably others)</li>
    <li>Replace <code>OTHER</code> in package licenses with
    <code>LicenseRef-clearlydefined-OTHER</code> so that parsing passes</li>
    </ul>
    </blockquote>
    </details>
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/actions/dependency-review-action/commit/38ecb5b593bf0eb19e335c03f97670f792489a8b"><code>38ecb5b</code></a>
    Merge pull request <a
    href="https://redirect.github.com/actions/dependency-review-action/issues/929">#929</a>
    from actions/dangoor/4.7-release</li>
    <li><a
    href="https://github.com/actions/dependency-review-action/commit/0e9e935cc870609b60e95f0ca9c5439df6c5a001"><code>0e9e935</code></a>
    Version 4.7.0 release</li>
    <li><a
    href="https://github.com/actions/dependency-review-action/commit/69d2faa36575aaf6f3b6e83344dccafd1434b31e"><code>69d2faa</code></a>
    Merge pull request <a
    href="https://redirect.github.com/actions/dependency-review-action/issues/926">#926</a>
    from dangoor/dangoor/replace-other</li>
    <li><a
    href="https://github.com/actions/dependency-review-action/commit/7e14978e0e6d56c5c368d665cfe64859530ae43e"><code>7e14978</code></a>
    Merge branch 'actions:main' into dangoor/replace-other</li>
    <li><a
    href="https://github.com/actions/dependency-review-action/commit/8477905b0e5eb937fce8d6d92309aee88f4a4295"><code>8477905</code></a>
    Merge pull request <a
    href="https://redirect.github.com/actions/dependency-review-action/issues/927">#927</a>
    from dangoor/dangoor/multilicense</li>
    <li><a
    href="https://github.com/actions/dependency-review-action/commit/f3ff3564fad5f71b84386e8dd99dcdd5f25b6e9e"><code>f3ff356</code></a>
    Update dist</li>
    <li><a
    href="https://github.com/actions/dependency-review-action/commit/c7565d44ece013dd49742989a6bd8f2042aed16a"><code>c7565d4</code></a>
    Fix tests and respond to review feedback</li>
    <li><a
    href="https://github.com/actions/dependency-review-action/commit/82299c3bbe54c01331889c2b0f62af249dfb0ee8"><code>82299c3</code></a>
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commit 4112f66fc8cf24d219b76f41a7cbd69305c5ff8a
Author: Ben Wibking <ben@wibking.com>
Date:   Sun May 11 19:57:03 2025 -0400

    allow supercycling of Poisson solves (#1063)
    
    ### Description
    This adds a user-defined parameter for supercycling Poisson solves,
    redoing the Poisson solve only every $N$ coarse steps. (Whether this is
    appropriate is problem-dependent.) Because AMR interpolation would be
    required otherwise, we only allow this for static meshes for now.
    
    The gravitational acceleration is still always applied to the hydro and
    to the particles every step.
    
    ### Related issues
    Closes https://github.com/quokka-astro/quokka/issues/1040.
    
    ### 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).
    - [ ] 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`.

src/simulation.hpp

commit 791c12be1a4f464c438ff55823cb14dc99b268ff
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Sun May 11 16:07:58 2025 +1000

    Implement the Krumholz 2004 model for sink particle accretion (#1055)
    
    ### Description
    
    We first compute the particle's Bondi-Hoyle radius,
    
    $$
    r_{\mathrm{BH}}=\frac{G M}{v_{\infty}^2+c_{\infty}^2},
    $$
    
    where $M$ is the particle's mass and $v_{\infty}$ and $c_{\infty}$ are
    the velocity and sound speed of the gas far from the sink particle. We
    compute `v_infty` as the mass-weighted mean velocity relative to the
    particle inside the accretion zone and `c_infty` as the mass-weighted
    mean sound speed inside the accretion zone.
    
    Then, we compute the Bondi-Hoyle-Lyttleton accretion rate:
    
    $$
    \dot{M}=4 \pi \rho_{\infty} G^2 M^2\left[\frac{\lambda^2
    c_{\infty}^2+v_{\infty}^2}{\left(c_{\infty}^2+v_{\infty}^2\right)^4}\right]^{1
    / 2}=4 \pi \rho_{\infty} r_{\mathrm{BH}}^2\left(\lambda^2
    c_{\infty}^2+v_{\infty}^2\right)^{1 / 2}
    $$
    
    where $\rho_{\infty}$ is the the gas density far from the sink particle.
    We compute `rho_infty` as the mean density inside the accretion zone.
    
    Last, we apply an accretion kernel on the accretion rate from each cell.
    We assign each cell a weight
    
    $$
    w = \exp \left(-r^2 / r_K^2\right),
    $$
    
    where $r$ is the distance from the particle to the cell center; cells
    outside of the accretion zone have a weight of 0. $r_K$ is the kernel
    radius
    
    $$
    r_K= \begin{cases}\Delta x / 4 & r_{\mathrm{BH}}<\Delta x / 4, \\
    r_{\mathrm{BH}} & \Delta x / 4 \leq r_{\mathrm{BH}} \leq
    r_{\mathrm{acc}} / 2, \\ r_{\mathrm{acc}} / 2 &
    r_{\mathrm{BH}}>r_{\mathrm{acc}} / 2\end{cases}
    $$
    
    The accretion rate from each cell is $\dot{M} w_i / \sum_i w_i$.
    
    We further apply two limitations/corrections to the accretion rate in
    each cell, in the following order:
    1. We set a cap that no more than 25% (Krumholz 2004) of the mass may be
    removed from a cell in any single time step.
    2. If the density of a cell is above Jeans density, $\rho_{\mathrm{J}} =
    J^2 \frac{\pi c_s^2}{G \Delta x^2}$ where $J=0.25$, we bring down the
    density to $\rho_J$.
    
    #### Test problem
    
    Based on the test problem introduced in #1017 . It's simple to derive an
    exact solution for the Bondi-Hoyle accretion from four particles in one
    step, if we use a uniform, cubic accretion kernel (only for testing
    purpose). The numerical result is in perfect agreement with the analytic
    one:
    
    <img
    src="https://github.com/user-attachments/assets/2bc9e60e-c42e-4398-b4e9-d80e2f72082d"
    width=400></img>
    
    
    
    
    ### Related issues
    Are there any GitHub issues that are fixed by this pull request? Add a
    link to them here.
    
    ### 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>

src/particles/PhysicsParticles.hpp
src/particles/particle_accretion.hpp
src/particles/particle_types.hpp
src/particles/particle_utils.hpp
src/problems/ParticleSink/test_particle_sink.cpp
src/simulation.hpp
tests/ParticleSink.in
tests/Sink_4.txt

commit b8ba66c78ee6092b701602ac1479c4ae1f2a0b42
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Sun May 11 11:49:55 2025 +1000

    Add a simple script to run clang-tidy on modified files (#1056)
    
    ### Description
    
    This will run `clang-tidy` on all the files that have been modified:
    ```bash
    ./scripts/tidy.sh ./build
    ```
    where `./build` is the directory to the build folder.
    
    This will run `clang-tidy` on all the files that have been modified in
    the last commit:
    ```bash
    ./scripts/tidy.sh ./build previous
    ```
    
    This will run `clang-tidy` on all the files that have been modified with
    respect to the remote branch:
    ```bash
    ./scripts/tidy.sh ./build origin
    ```
    
    This will run `clang-tidy` on all the files that have been modified with
    respect to the local development branch:
    ```bash
    ./scripts/tidy.sh ./build dev
    ```
    
    Also update the documentation on how to use tidy. The python script Ben
    originally recommended is too complicated and I couldn't make it work
    the way I wanted. The new bash script is a lot simpler and easy to use.
    
    ### Related issues
    Are there any GitHub issues that are fixed by this pull request? Add a
    link to them here.
    
    ### 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](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] 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`.

docs/markdown/howto_clang_tidy.md
scripts/tidy.sh

commit efbc8622a2c5c40e09182759fa4b37075b93eac8
Author: Ben Wibking <ben@wibking.com>
Date:   Sat May 10 20:28:08 2025 -0400

    Update gallery with AGORA sim (#1059)
    
    ### Description
    Adds a movie of the AGORA disk galaxy simulation to the Gallery in the
    docs.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] 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`.

docs/markdown/gallery.md

commit 169436b87759ea3c13ce5bdbfc10fd43c6c80f46
Author: Ben Wibking <ben@wibking.com>
Date:   Sat May 10 20:27:59 2025 -0400

    Move contributing guide to docs (#1060)
    
    ### Description
    Move `CONTRIBUTING.md` to the MkDocs documentation.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] 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`.

CONTRIBUTING.md
docs/markdown/contributing.md
docs/mkdocs.yml

commit 62bc0091457ba0992e6a50f393ae2a427bd840a5
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Fri May 9 00:31:21 2025 +1000

    Bump nvidia/cuda from `d14f269` to `632c7db` in /.devcontainer/cuda-container (#1053)
    
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commit ac03814db8b2ce3a57114fe8ff266e0c42c637a0
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Wed May 7 16:48:41 2025 +1000

    Bump nvidia/cuda from 12.8.1-devel-ubuntu24.04 to 12.9.0-devel-ubuntu24.04 in /.devcontainer/cuda-container (#1050)
    
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.devcontainer/cuda-container/Dockerfile

commit f1b04002d4c72eef15de99f6f5bd1d87675847f7
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Wed May 7 13:49:08 2025 +1000

    Include interpolate.cpp and fextract.cpp in src/CMakeLists (#1048)
    
    ### Description
    
    Include interpolate.cpp and fextract.cpp in src/CMakeLists.txt so that
    we can remove them from all problem CMakeLists.txt
    
    ### Related issues
    Closes https://github.com/quokka-astro/quokka/issues/1023.
    
    ### 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).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] *(For quokka-astro org members)* I have manually triggered the GPU
    tests with the magic comment `/azp run`.

src/CMakeLists.txt
src/problems/Advection/CMakeLists.txt
src/problems/AdvectionSemiellipse/CMakeLists.txt
src/problems/FCQuantities/CMakeLists.txt
src/problems/GravRadParticle3D/CMakeLists.txt
src/problems/HydroContact/CMakeLists.txt
src/problems/HydroHighMach/CMakeLists.txt
src/problems/HydroLeblanc/CMakeLists.txt
src/problems/HydroSMS/CMakeLists.txt
src/problems/HydroShocktube/CMakeLists.txt
src/problems/HydroShocktubeCMA/CMakeLists.txt
src/problems/HydroShuOsher/CMakeLists.txt
src/problems/HydroVacuum/CMakeLists.txt
src/problems/HydroWave/CMakeLists.txt
src/problems/NSCBC/CMakeLists.txt
src/problems/ParticleCreation/CMakeLists.txt
src/problems/ParticleSink/CMakeLists.txt
src/problems/PassiveScalar/CMakeLists.txt
src/problems/RadDust/CMakeLists.txt
src/problems/RadDustMG/CMakeLists.txt
src/problems/RadForce/CMakeLists.txt
src/problems/RadLineCooling/CMakeLists.txt
src/problems/RadLineCoolingMG/CMakeLists.txt
src/problems/RadMarshak/CMakeLists.txt
src/problems/RadMarshakAsymptotic/CMakeLists.txt
src/problems/RadMarshakCGS/CMakeLists.txt
src/problems/RadMarshakDust/CMakeLists.txt
src/problems/RadMarshakDustPE/CMakeLists.txt
src/problems/RadMarshakVaytet/CMakeLists.txt
src/problems/RadMatterCoupling/CMakeLists.txt
src/problems/RadMatterCouplingRSLA/CMakeLists.txt
src/problems/RadParticle/CMakeLists.txt
src/problems/RadParticle2D/CMakeLists.txt
src/problems/RadPulse/CMakeLists.txt
src/problems/RadStreaming/CMakeLists.txt
src/problems/RadStreamingY/CMakeLists.txt
src/problems/RadSuOlson/CMakeLists.txt
src/problems/RadTube/CMakeLists.txt
src/problems/RadhydroBB/CMakeLists.txt
src/problems/RadhydroPulse/CMakeLists.txt
src/problems/RadhydroPulseDyn/CMakeLists.txt
src/problems/RadhydroPulseGrey/CMakeLists.txt
src/problems/RadhydroPulseMGconst/CMakeLists.txt
src/problems/RadhydroPulseMGint/CMakeLists.txt
src/problems/RadhydroShell/CMakeLists.txt
src/problems/RadhydroShock/CMakeLists.txt
src/problems/RadhydroShockCGS/CMakeLists.txt
src/problems/RadhydroShockMultigroup/CMakeLists.txt
src/problems/RadhydroUniformAdvecting/CMakeLists.txt
src/problems/SN/CMakeLists.txt

commit 0c1849cb792bdab7843bd58183eb7f108f47a5df
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Wed May 7 03:42:31 2025 +0000

    Bump devcontainers/cpp from `165d17c` to `a74f174` in /.devcontainer/gcc-container (#1049)
    
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.devcontainer/gcc-container/Dockerfile

commit c74a4afa3eb71c5d842daa6d8adc06405db7e908
Author: Ben Wibking <ben@wibking.com>
Date:   Tue May 6 21:39:22 2025 -0400

    Fix restarts when using `plottime_interval` (#1047)
    
    ### Description
    Sets the correct output cadence when restarting from a run that sets
    `plottime_interval`.
    
    ### Related issues
    Fixes https://github.com/quokka-astro/quokka/issues/1041.
    
    ### 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:_
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    above).
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] 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`.

src/simulation.hpp

commit 9e6da51ecbe791e1afa524324a5a7f1694dd8067
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon May 5 18:05:32 2025 +0000

    [pre-commit.ci] pre-commit autoupdate (#1044)
    
    <!--pre-commit.ci start-->
    updates:
    - [github.com/pre-commit/mirrors-clang-format: v20.1.0 →
    v20.1.3](https://github.com/pre-commit/mirrors-clang-format/compare/v20.1.0...v20.1.3)
    <!--pre-commit.ci end-->
    
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.pre-commit-config.yaml

commit 110e4881c250b98af739d3080c9327dc264c9374
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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    Bump github/codeql-action from 3.28.16 to 3.28.17 (#1039)
    
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    from 3.28.16 to 3.28.17.
    <details>
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    href="https://github.com/github/codeql-action/releases">github/codeql-action's
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    <p>No user facing changes.</p>
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    <h2>3.28.11 - 07 Mar 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.20.6. <a
    href="https://redirect.github.com/github/codeql-action/pull/2793">#2793</a></li>
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    <ul>
    <li>Update default CodeQL bundle version to 2.20.5. <a
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    <li>Update default CodeQL bundle version to 2.20.4. <a
    href="https://redirect.github.com/github/codeql-action/pull/2753">#2753</a></li>
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    <h2>3.28.8 - 29 Jan 2025</h2>
    <ul>
    <li>Enable support for Kotlin 2.1.10 when running with CodeQL CLI
    v2.20.3. <a
    href="https://redirect.github.com/github/codeql-action/pull/2744">#2744</a></li>
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    <!-- raw HTML omitted -->
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    Merge pull request <a
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    href="https://github.com/github/codeql-action/commit/0d5a3115da6459f8ab4333164184f8292c0c7a7f"><code>0d5a311</code></a>
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    href="https://github.com/github/codeql-action/commit/97a2bfd2a3d26d458da69e548f7f859d6fca634d"><code>97a2bfd</code></a>
    Merge pull request <a
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    from github/update-bundle/codeql-bundle-v2.21.2</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/9aba20e4c91fd8c3a71d5ab2bdeba0da11713864"><code>9aba20e</code></a>
    Merge branch 'main' into update-bundle/codeql-bundle-v2.21.2</li>
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    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2876">#2876</a>
    from github/henrymercer/fix-diff-informed-multiple-a...</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/1569f4c145413fbce7d6573c6ee9212d2612d27f"><code>1569f4c</code></a>
    Disable diff-informed queries in code scanning config tests</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/62fbeb66b359bfbdec7d4d96af8f68aece59b4db"><code>62fbeb6</code></a>
    Merge branch 'main' into
    henrymercer/fix-diff-informed-multiple-analyze</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/f122d1dc9eb83b12dc16b38495b667a2dddfa6f9"><code>f122d1d</code></a>
    Address test failures from computing temporary directory too early</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/083772aae48a3be5654921bb6e6ccb00e0e1d563"><code>083772a</code></a>
    Do not fail diff informed analyses when <code>analyze</code> is run
    twice in the same job</li>
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    Merge branch 'main' into update-bundle/codeql-bundle-v2.21.2</li>
    <li>Additional commits viewable in <a
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.github/workflows/codeql.yml
.github/workflows/scorecard.yml

commit f39f1e73018ec8203a724f70f62d4f0f9770d309
Author: Aditi <45175933+aditivijayan@users.noreply.github.com>
Date:   Fri May 2 00:22:42 2025 +1000

    Stochastic Stellar Population (#966)
    
    ### Description
    This branch includes a specialisation for the particles. We check cells
    for Jeans stability condition and if it is Jeans unstable, we add a
    population of particles. The population comprises one particle
    representing low mass star and a random number of high mass particles.
    The number of high mass particles is determined using the Chabrier IMF,
    which is log normal for M<Msun and a power law with a slope of -2.35
    above that. It is assumed that the IMF covers a mass range 0.08-120
    Msun. The fate and lifetime of the high mass particles are interpolated
    using tables from SLUG.
    
    Once added, the high mass stars gain a momentum weighted over
    neighbouring particles while the low mass particle gains an opposite
    momentum. At the end of particle updates, the density, total energy and
    the internal energy density of the gas cell.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] 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).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] *(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: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
    Co-authored-by: Ben Wibking <ben@wibking.com>
    Co-authored-by: ChongChong He <chongchong.he@anu.edu.au>

docs/markdown/star_formation.md
src/particles/PhysicsParticles.hpp
src/particles/particle_creation.hpp
src/particles/stellarpop_data.hpp
src/problems/ParticleCreation/CMakeLists.txt
src/problems/ParticleCreation/particle_creation_from_cell.cpp
src/problems/ParticleCreation/particle_creation_from_cell.hpp
src/problems/ParticleSink/CMakeLists.txt
src/problems/ParticleSink/test_particle_sink.hpp
src/problems/SN/CMakeLists.txt
src/problems/SN/test_SN.cpp

commit bb7e7c3cb934ef3fcc78944d9c017f0aa2f486f1
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Thu May 1 12:34:34 2025 +0000

    Bump extern/amrex from `d3540b9` to `d49d229` (#1030)
    
    Bumps [extern/amrex](https://github.com/AMReX-Codes/amrex) from
    `d3540b9` to `d49d229`.
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/d49d22968b403bc978749b5e2feb7c94a7710158"><code>d49d229</code></a>
    SYCL on Windows workaround (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4436">#4436</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/eb137e3644c452707549abd04fa502b822590b08"><code>eb137e3</code></a>
    Fix MF ParallelFor&lt;MT&gt; (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4414">#4414</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/2acedfe0b358e4127816806f92766a73b573d7b9"><code>2acedfe</code></a>
    Avoid calling bisection in MFParallelFor (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4392">#4392</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/1a97b969996b3057778fb953aed264d0c7a04dcb"><code>1a97b96</code></a>
    SYCL: Update link flag for huge device code in GNU Make file (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4421">#4421</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/6d6e519870cb50b214740e86796a5845db00a8c7"><code>6d6e519</code></a>
    Hypre &amp; PETSc: Fix compilation when MLMG's MF type is not FabArray
    (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4422">#4422</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/3541264af85a82455f95ffe589c4812122e5f2a3"><code>3541264</code></a>
    Intel CI: Update warning flags (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4412">#4412</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/06bc76cff1807ff80a09658251ef13d79d744a0d"><code>06bc76c</code></a>
    iMulitFab: Add more methods (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4410">#4410</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/f1cfe3bbb353ea917e2afb6ea7939237d2b9a82b"><code>f1cfe3b</code></a>
    HIP Debug Build (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4408">#4408</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/5e3a7a372f5e3f647ad65ea0e3e9111b2b679b00"><code>5e3a7a3</code></a>
    ReduceToPlaneMF (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4384">#4384</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/2343e4f07d59fcf2830a30b1ed7f878645b20606"><code>2343e4f</code></a>
    Periodicity boundary support for multi-ghost communication (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4405">#4405</a>)</li>
    <li>Additional commits viewable in <a
    href="https://github.com/AMReX-Codes/amrex/compare/d3540b92d574148722bebe315ca50dd027e11aa0...d49d22968b403bc978749b5e2feb7c94a7710158">compare
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extern/amrex

commit 2353352e32cab4f56b34010f5bff898b200b769f
Author: Ben Wibking <ben@wibking.com>
Date:   Thu May 1 08:51:22 2025 -0400

    Update CODEOWNERS (#1031)
    
    ### Description
    Adds @chongchonghe as a CODEOWNER for the whole code.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] 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`.

.github/CODEOWNERS

commit 34259ff07127163bc93ef16032ef7cbb2448db79
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Thu May 1 03:59:57 2025 +0000

    Bump extern/yaml-cpp from `28f93bd` to `2f86d13` (#1029)
    
    Bumps [extern/yaml-cpp](https://github.com/jbeder/yaml-cpp) from
    `28f93bd` to `2f86d13`.
    <details>
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    href="https://github.com/jbeder/yaml-cpp/commit/2f86d13775d119edbb69af52e5f566fd65c6953b"><code>2f86d13</code></a>
    Update googletest to 1.13</li>
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    href="https://github.com/jbeder/yaml-cpp/commit/c9371de7836d113c0b14bfa15ca70f00ebb3ac6f"><code>c9371de</code></a>
    [cmake] Require minimum CMake version 3.5</li>
    <li>See full diff in <a
    href="https://github.com/jbeder/yaml-cpp/compare/28f93bdec6387d42332220afa9558060c8016795...2f86d13775d119edbb69af52e5f566fd65c6953b">compare
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extern/yaml-cpp

commit e8c35e949bf864744545beeed29d439e610f5f3e
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Thu May 1 03:57:49 2025 +0000

    Bump extern/fmt from `5199e0f` to `505ee05` (#1028)
    
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    `505ee05`.
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extern/fmt

commit fef73ee050f89a80df0ef60a034665c153c7e9a0
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Thu May 1 03:57:42 2025 +0000

    Bump extern/openPMD-api from `53c0512` to `aa2cc99` (#1027)
    
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    <li><a
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extern/openPMD-api

commit 02cef5a85396a7ad1cc5faa7f94457f3454ee2f1
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Apr 30 20:37:15 2025 -0400

    Update Dockerfile to use ROCm 6.4 (#1025)
    
    ### Description
    This updates the Dockerfile to use this [ROCm 6.4 base
    image](https://hub.docker.com/layers/rocm/dev-ubuntu-24.04/6.4/images/sha256-4fbcf879d22aaca65b756c7c6c3586ee75090ae55953c4e44e7e88960fbb1e1c).
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] 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`.

.devcontainer/rocm-container/Dockerfile

commit 200da519514fee2ef5115ae53125a52c0ead5e84
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Tue Apr 29 22:31:40 2025 +1000

    A novel scheme for sink particle accretion -- framework (#1017)
    
    ### Description
    
    A novel scheme for sink particle accretion. We use a buffer to store the
    accretion rate on cells, and apply a limiter to prevent negative mass in
    hydro cells before we apply the accretion rate to particles and the
    hydro state. This scheme eliminates the need for communication between
    particles and the need to find neighboring particles. We support an
    accretion radius of 3 dx with 4 ghost cells (since a particle can move
    one box size in a time step.)
    
    We conduct two stages of accretion. In stage one, we compute the raw
    accretion rate on each cell from all particles and store it in a
    MultiFab `accretion_rate`. A `accretion_rate.SumBoundary` is called to
    sum the boundary values to the real cells.
    
    In stage two, we do the following steps:
    1. Apply a limiter to prevent negative mass in hydro cells by computing
    a `scale_factor` MultiFab. At the same time, we apply the rescaling to
    `accretion_rate`. Then, a `scale_down.FillBoundary` is called to fill
    the real values to the boundary cells.
    2. Loop through all particles again to compute the accretion rate on
    each particle. For each particle, we loop through all cells in the
    accretion zone and add the accreted mass and momentum multiplied by the
    `scale_factor` to the particle.
    3. Subtract `accretion_rate` from hydro state.
    
    In between stage one and stage two, we can apply sink particle formation
    subject to limitation by the accretion rate.
    
    I've implemented a very simple threshold-based accretion method, similar
    to Federrath (2010). In every time step, a sink particle accretes $0.5
    (\rho - \rho_{\rm th}) \Delta x$ amount of mass from each cell in its
    fixed accretion zone. A limiter is applied to prevent cell density from
    dropping by more than 90%.
    
    I have added a new test, `test_particle_sink`, to demonstrate the
    accretion scheme. The following figure shows the accretion zones of 40
    sink particles randomly distributed in the box. I use the simplest
    threshold accretion scheme for this test, and the accretion zone is set
    to a cube for better visualization. The white lines are MPI box
    boundaries. As we can see, sink particle accretion zones can overlap
    through Fab boundaries or periodic domain boundaries.
    
    
    ![40sink-lev1-plt00001_Slice_z_n_H](https://github.com/user-attachments/assets/8cf48002-204c-4fca-8289-5c2572ecb557)
    
    The `test_particle_sink` test includes quantitative validation of both
    mass conservation and accretion rates. The test compares simulation
    results against analytical solutions. A plot of the gas density along
    the central horizontal line of the box after one accretion step shows
    that the numerical solution matches the analytical solution to machine
    precision, validating the accuracy of the accretion implementation.
    
    <img
    src="https://github.com/user-attachments/assets/91160ca5-cafb-47b3-84e4-c66a2a128dd3"
    width=420></img><img
    src="https://github.com/user-attachments/assets/be417c35-70d6-417c-a24c-35525c8a74d2"
    width=350></img>
    
    
    
    ### Related issues
    Are there any GitHub issues that are fixed by this pull request? Add a
    link to them here.
    
    ### 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.
    - [x] *(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>

.codespell-ignore-words
src/QuokkaSimulation.hpp
src/linear_advection/AdvectionSimulation.hpp
src/particles/PhysicsParticles.hpp
src/particles/particle_accretion.hpp
src/particles/particle_types.hpp
src/particles/particle_utils.hpp
src/problems/CMakeLists.txt
src/problems/ParticleSink/CMakeLists.txt
src/problems/ParticleSink/test_particle_sink.cpp
src/problems/ParticleSink/test_particle_sink.hpp
src/simulation.hpp
tests/ParticleSink.in
tests/Sink_2.txt
tests/Sink_4.txt
tests/Sink_40.txt

commit 191b7b00ee1375c0c71c38e123b0a4f7be62dc58
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Apr 28 09:56:18 2025 -0400

    Bump actions/setup-python from 5.5.0 to 5.6.0 (#1021)
    
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    from 5.5.0 to 5.6.0.
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    Remove Ubuntu 20.04 from workflows due to deprecation from 2025-04-15
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.github/workflows/cmake-macos.yml
.github/workflows/codespell.yml

commit 4a7bf78c868981180ee6bb9981c76c0856c92e9d
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Apr 28 09:55:58 2025 -0400

    Bump github/codeql-action from 3.28.15 to 3.28.16 (#1022)
    
    Bumps [github/codeql-action](https://github.com/github/codeql-action)
    from 3.28.15 to 3.28.16.
    <details>
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    <p><em>Sourced from <a
    href="https://github.com/github/codeql-action/releases">github/codeql-action's
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    <blockquote>
    <h2>v3.28.16</h2>
    <h1>CodeQL Action Changelog</h1>
    <p>See the <a
    href="https://github.com/github/codeql-action/releases">releases
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    <h2>3.28.16 - 23 Apr 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.21.1. <a
    href="https://redirect.github.com/github/codeql-action/pull/2863">#2863</a></li>
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    <h2>[UNRELEASED]</h2>
    <p>No user facing changes.</p>
    <h2>3.28.16 - 23 Apr 2025</h2>
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    href="https://redirect.github.com/github/codeql-action/pull/2863">#2863</a></li>
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    artifact with more than 65535 files. <a
    href="https://redirect.github.com/github/codeql-action/pull/2842">#2842</a></li>
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    <h2>3.28.14 - 07 Apr 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.21.0. <a
    href="https://redirect.github.com/github/codeql-action/pull/2838">#2838</a></li>
    </ul>
    <h2>3.28.13 - 24 Mar 2025</h2>
    <p>No user facing changes.</p>
    <h2>3.28.12 - 19 Mar 2025</h2>
    <ul>
    <li>Dependency caching should now cache more dependencies for Java
    <code>build-mode: none</code> extractions. This should speed up
    workflows and avoid inconsistent alerts in some cases.</li>
    <li>Update default CodeQL bundle version to 2.20.7. <a
    href="https://redirect.github.com/github/codeql-action/pull/2810">#2810</a></li>
    </ul>
    <h2>3.28.11 - 07 Mar 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.20.6. <a
    href="https://redirect.github.com/github/codeql-action/pull/2793">#2793</a></li>
    </ul>
    <h2>3.28.10 - 21 Feb 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.20.5. <a
    href="https://redirect.github.com/github/codeql-action/pull/2772">#2772</a></li>
    <li>Address an issue where the CodeQL Bundle would occasionally fail to
    decompress on macOS. <a
    href="https://redirect.github.com/github/codeql-action/pull/2768">#2768</a></li>
    </ul>
    <h2>3.28.9 - 07 Feb 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.20.4. <a
    href="https://redirect.github.com/github/codeql-action/pull/2753">#2753</a></li>
    </ul>
    <h2>3.28.8 - 29 Jan 2025</h2>
    <ul>
    <li>Enable support for Kotlin 2.1.10 when running with CodeQL CLI
    v2.20.3. <a
    href="https://redirect.github.com/github/codeql-action/pull/2744">#2744</a></li>
    </ul>
    <h2>3.28.7 - 29 Jan 2025</h2>
    <p>No user facing changes.</p>
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    from github/dependabot/github_actions/actions-457587...</li>
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commit 7558060de069dc49773d03c638ab301fc069aa50
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Mon Apr 28 13:16:41 2025 +1000

    Modularize SNDeposition (#1020)
    
    ### Description
    
    Modularize `SNDeposition` function. This would make the code more
    readable and maintainable.
    
    ### Related issues
    None.
    
    ### 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).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] *(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>

src/particles/PhysicsParticles.hpp
src/particles/particle_deposition.hpp

commit afacfda49fb11add336af8ce7dbae50f01de51ff
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Mon Apr 28 11:18:33 2025 +1000

    Allow to force some particles to always live in finest cells (#1009)
    
    ### Description
    We want to force some particles to always live on the finest cells.
    Those particles could be sink particles that need to accrete, or
    `SNProgenitor` particles that can go SN explosion at any time. This is
    also important for getting around the issue with the gravity solver on
    refinment boundaries.
    
    The user can turn on manually turn on this feature for a specific
    particle type by running the following line of code in `problem_main()`
    
    ```cpp
    sim.particleRegister_.getParticleDescriptor(quokka::ParticleType::Test)->setForceFinestLevel(true);
    ```
    
    Here is a demonstration with the `ParticleCreation` test. It seems that
    by tagging a single cell at the particle location, the code actually
    refines at least 4+ cells around it. This happens to be the desired
    behaviour. Lovely.
    
    
    ![plt00004_Slice_z_density](https://github.com/user-attachments/assets/a31caa63-51da-45ea-b403-a830e1576c57)
    
    
    Note: This branch is set to merge to #1005 because it's based on that
    branch. This is just for showing the actual changes made in this PR.
    Once we merge #1005 , I'll update this PR to merge to dev branch.
    
    ### Related issues
    None.
    
    ### 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 see (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.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
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src/QuokkaSimulation.hpp
src/linear_advection/AdvectionSimulation.hpp
src/particles/PhysicsParticles.hpp
src/problems/Advection2D/test_advection2d.cpp
src/problems/BinaryOrbitCIC/binary_orbit.cpp
src/problems/HydroBlast2D/test_hydro2d_blast.cpp
src/problems/HydroBlast3D/test_hydro3d_blast.cpp
src/problems/HydroKelvinHelmholz/test_hydro2d_kh.cpp
src/problems/HydroShocktube/test_hydro_shocktube.cpp
src/problems/HydroShocktubeCMA/test_hydro_shocktube_cma.cpp
src/problems/ParticleCreation/particle_creation_from_cell.cpp
src/problems/PassiveScalar/test_scalars.cpp
src/problems/PopIII/popiii.cpp
src/problems/RadBeam/test_radiation_beam.cpp
src/problems/RadShadow/test_radiation_shadow.cpp
src/problems/RadhydroShell/test_radhydro_shell.cpp
src/problems/RandomBlast/blast.cpp
src/problems/RayleighTaylor2D/test_hydro2d_rt.cpp
src/problems/RayleighTaylor3D/test_hydro3d_rt.cpp
src/problems/ShockCloud/cloud.cpp
src/problems/SphericalCollapse/spherical_collapse.cpp
src/problems/StarCluster/star_cluster.cpp
src/simulation.hpp
tests/ParticleCreationAMR.in
tests/TestParticles.txt

commit 50c179cfdaa4d4fa018e994ef921ab5c9efea646
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Sun Apr 27 00:44:03 2025 +1000

    A new SN feedback model (#995)
    
    ### Description
    
    In this PR I implement a new SNe feedback model that smoothly
    transitions between thermal feedback, kinetic feedback, and momentum
    feedback, depending on how well the cooling/shell formation phase of the
    SNR evolution is resolved. An innovation of this scheme is that we do a
    two stage deposition scheme to account for SNR overlapping and get rid
    of depedence on the order that SNe events occur.
    
    I have tested three models:
    1. Model 0: Pure thermal deposition (for comparison only, not for
    production)
    2. Model 1: Thermal energy deposition in the resolved regime, thermal +
    kinetic in the intermediate regime, and terminal momentum in the
    unresolved regime.
    3. Model 2: Kinetic energy deposition in the resolved regime, thermal +
    kinetic in the intermediate regime, and terminal momentum in the
    unresolved regime.
    
    At a SN event, we distribute mass, momentum, and energy uniformly among
    the cells that intercect with s sphere of radius `3 dx` centered at the
    center of the cell that the SN is located in. No background smoothing is
    conducted before deposition.
    
    The results looks great! See figure below. Both model 1 and 2 produces
    'correct' and almost identical results. The only difference is the
    maximum temperature (defined as the maximum temperature in any cell
    throughout the simulation) in model 2 is slightly lower than that in
    model 1. In model 2, right after SN explosion, the gas is cool but moves
    fast, and the shock wave immediately heat the gas to comparable
    temperature to that in the thermal model. After some experiments, I am
    convinced that the thermal model and kinetic model (in the resolved
    regime) has no difference in accuracy or performance related to
    timestep. This is because, imagine a star explodes into vacuum, q simple
    calculation will show that the sound speed of the hot SNR in the pure
    thermal model is about $1/\sqrt{3}$ times the bulk velocity of the cool
    SNR in the pure kinetic model (microscopic thermal motion has three
    degrees of freedom while kinetic motion has one). The thermal model
    turns out to have slightly longer timestep overall. In the TIGRESS model
    they advocate thermal model because they have over cooling issue, but we
    don't have this issue at all (thanks to Ben's awesome Grackle cooling
    module which has a robust ODE solver).
    
    
    ![compare](https://github.com/user-attachments/assets/23895e3d-e00a-46a5-af30-a62d70509a02)
    
    > Reproducing Figure 6 of Kim & Ostriker 2017. The spacial resolution
    and SN ejecta mass/energy/momentum in our simulations are the same as
    theirs.
    
    ### 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>

src/particles/PhysicsParticles.hpp
src/particles/particle_deposition.hpp
src/particles/particle_types.hpp
src/problems/CMakeLists.txt
src/problems/SN/CMakeLists.txt
src/problems/SN/test_SN.cpp
src/problems/SN/test_SN.hpp
src/simulation.hpp
tests/SN.in
tests/SN.txt

commit 57306bdc6a6e91c34611c722261782f580344a0c
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Apr 25 22:51:27 2025 -0400

    Update copyright year in docs (#999)
    
    ### Description
    Update the copyright year in the documentation.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] 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`.

docs/mkdocs.yml

commit 48fbe7f5aee411fedbe88c3b4a0e15ec2ed41714
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Sat Apr 26 04:34:11 2025 +1000

    Update Dockerfile (#1012)
    
    ### Description
    
    This PR updates the image used in the CUDA Dockerfile from a nvhpc image
    to a smaller base CUDA image. Two images, built by
    cuda-container/Dockerfile and rocm-container/Dockerfile, are uploaded to
    `ghcr.io/quokka-astro/quokka-linux-amd64-cuda:development` and
    `ghcr.io/quokka-astro/quokka-linux-amd64-rocm:development`,
    respectively. Additionally, the `devcontainer.json` files have been
    updated to utilize those images from the ghcr.io server. Users can
    employ those pre-built images by either using Docker/singularityCE to
    pull them in the command line, or by initiating `Dev Containers: Reopen
    in Container` in VSCode.
    
    ### Related issues
    None.
    
    ### 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).
    - [ ] NOT NEEDED. I have added tests for any new physics that this PR
    adds to the code.
    - [ ] NOT NEEDED. *(For quokka-astro org members)* I have manually
    triggered the GPU tests with the magic comment `/azp run`.

.devcontainer/cuda-container/Dockerfile
.devcontainer/cuda-container/devcontainer.json
.devcontainer/rocm-container/Dockerfile
.devcontainer/rocm-container/devcontainer.json
.gitignore

commit 58191707715f41c6686c4d8149fa5addebea0428
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Fri Apr 25 13:03:39 2025 +1000

    Move particle parameter specialization into PhysicsParticleRegister (#1015)
    
    ### Description
    
    Since the parameter specialization for a given particle type is not
    meant to be customizable (e.g. Rad_particles always have massIndex_ = -1
    and allowsCreation_ = false), we don't have to pass those parameters
    from simulation.hpp. Instead, we can hard-code those parameters inside
    `registerParticleType` and `registerStarParticleType`. This cleans up
    `registerParticleType` in simulation.hpp.
    
    I also cleaned up and reordered the particle paramters. Now, the base
    particle type (registered in `PhysicsParticleDescriptor`) has the
    following parameters:
    ```
    mass_idx, lum_idx, birth_time_idx, allows_creation, allows_destruction
    ```
    and the derived `StarParticleDescriptor` has the following parameters:
    ```
    mass_idx, lum_idx, birth_time_idx, allows_creation, allows_destruction, evolution_stage_idx, allows_accretion
    ```
    
    All particles that belong to `PhysicsParticleDescriptor` have only 5
    relavent parameters listed above, and all particles that belong to
    `StarParticleDescriptor` have those 5 mandatory parameters plus 2 extra
    parameters. In the future, we can define other derived classes (e.g.
    `DustParticleDescriptor`) with 5 + n parameters.
    
    Note that all parameters have to present in the base class
    `ParticleDescriptorBase` because all particles actions are casted to
    `ParticleDescriptorBase` and the compiler will not be able to resolve
    the correct overload if the parameters are not in the base class.
    
    ### Related issues
    None.
    
    ### 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).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] *(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>

src/particles/PhysicsParticles.hpp
src/simulation.hpp

commit 60356a3e50f852083f5f0df68253f9608f3dd67e
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Apr 23 12:50:42 2025 -0400

    Remove default CUDA GPU architectures (#1011)
    
    ### Description
    This removes the default settings for CUDA GPU architectures. (We have
    never set a default for AMD GPUs.)
    
    This is done to reduce the compile time, since the default was set to 2
    GPU architectures, which made the build time almost twice as large as it
    would be compared to setting only one GPU arch. This makes the GPU tests
    on avatargpu take significantly longer.
    
    Users will need to specify which CUDA GPU architecture they want to
    build for explicitly using either `-DAMReX_CUDA_ARCH` or the
    `AMREX_CUDA_ARCH` environment variable. If a GPU is present on the
    machine used to build, CMake should (in principle) autodetect the
    correct GPU arch:
    ```
    -- Autodetected CUDA architecture(s):  7.0
    ```
    
    Documentation:
    https://amrex-codes.github.io/amrex/docs_html/GPU.html#enabling-cuda-support
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] 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`.

CMakeLists.txt

commit b1d3f4f3e504d0743409bf627c966344f97688cd
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Thu Apr 24 01:15:37 2025 +1000

    New ParticleCreation test to replace Gravity3D (#1005)
    
    ### Description
    
    The previous `Gravity3D` problem tested too many things simultaneously,
    making it hard to track specific module functions. Consequently, I have
    replaced it with a new test called `ParticleCreation`, which tests
    particle creation from cell, stellar evolution, and particle
    destruction. It's unnecessary to test gravity in this problem because
    gravity is tested in `BinaryOrbit`. Similarly, SN feedback is tested in
    the `SN` test in #995. Additionally, `Gravity3D` is badly named.
    
    More changes:
    
    - Add logging of the number of particles created inside
    `createParticlesImpl`
    - Add logging of the number of particles removed at each level inside
    `destroyParticlesImpl`
    - `updateEvolutionStage` updates a particle's stage based on its
    `deathtime`.
    - Add an extra evolution stage: `Removed`. Only those particles will be
    removed.
    - Updated the format of `printParticleStatistics`
    
    ### 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.
    - [x] *(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>

src/particles/PhysicsParticles.hpp
src/particles/particle_creation.hpp
src/particles/particle_deposition.hpp
src/particles/particle_destruction.hpp
src/particles/particle_types.hpp
src/problems/CMakeLists.txt
src/problems/Gravity3D/CMakeLists.txt
src/problems/Gravity3D/gravity_3d.hpp
src/problems/ParticleCreation/CMakeLists.txt
src/problems/ParticleCreation/particle_creation_from_cell.cpp
src/problems/ParticleCreation/particle_creation_from_cell.hpp
src/simulation.hpp
tests/Gravity3D.txt
tests/ParticleCreation.in
tests/ParticleCreationAMR.in
tests/TestParticles.txt

commit af4a22f5210e9919dfbdc3fb63efacec1c75e3dd
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Thu Apr 24 01:13:36 2025 +1000

    Use getParticleDataAtLevel in binary_orbit.cpp (#1004)
    
    ### Description
    Use the existing `getParticleDataAtLevel()` function in binary_orbit.cpp
    
    ### 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
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    above).
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
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    code.
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src/problems/BinaryOrbitCIC/binary_orbit.cpp

commit 382fe1ab525f59ccf430240776073e5949e4ac26
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Apr 18 18:06:43 2025 -0400

    Update .clang-tidy again (#998)
    
    ### Description
    Suppress Boost-related warnings (e.g.,
    https://clang.llvm.org/extra/clang-tidy/checks/boost/use-ranges.html).
    
    While a nice library, we don't want to add Boost as a dependency.
    
    ### Related issues
    N/A
    
    ### 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:_
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    above).
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
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    code.
    - [ ] *(For quokka-astro org members)* I have manually triggered the GPU
    tests with the magic comment `/azp run`.

src/.clang-tidy

commit 04923e86a63851b9bcc11b5f9be2ed3c3133cf17
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Sat Apr 19 00:33:09 2025 +1000

    Make getParticleDataAtLevel work on multiple ranks (#1001)
    
    ### Description
    
    This PR adds `analysisPC.Redistribute();` to copy particles from all
    ranks to Rank 0. Now, calling `getParticleDataAtLevel()` with MPI should
    work properly.
    
    I also updated the Gravity3D problem to test `getParticleDataAtLevel()`
    on multiple ranks. Now, `TestParticles.txt` contains 8 extra particles,
    one in each octant of the domain. `amr.blocking_factor` is set to 16
    while `amr.n_cell = 32`, so when you run the test with 8 processes, each
    process will contain at least one particle.
    
    Haven't tested on GPU + MPI yet.
    
    ### Related issues
    
    Fixes #1000
    
    ### Checklist
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    completed. Denote completed tasks with an `x` inside the square brackets
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    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.
    - [x] *(For quokka-astro org members)* I have manually triggered the GPU
    tests with the magic comment `/azp run`.
    
    ---------
    
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src/particles/PhysicsParticles.hpp
src/problems/Gravity3D/gravity_3d.cpp
tests/Gravity3D.in
tests/TestParticles.txt

commit 371117febb8446c280efe5b18060fc64e981c0b4
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Thu Apr 17 12:52:32 2025 +1000

    Add tests of SNR deposition on multiple levels (#964)
    
    ### Description
    
    In this PR, all particle operations (creation, destruction and SNR
    deposition) are fully tested on multiple levels. Assuming particles
    always live in the finest level, SNR deposition is accurate to machine
    accuracy even if they are near the coarse-fine boundary. Particles in
    coarser grids near coarse-fine boundary might work just fine, although I
    haven't tested it because the gravity solver doesn't work in this
    situation.
    
    Now we have two problems to test particle operations:
    
    1. `Gravity3D`. This problem tests particle creation from fluid cells,
    stellar evolution (from SNProgenitor to SNRemnant), supernova
    deposition, and stellar destruction with fully refined grids (lev=1 in
    all domain). In the end of the simulation, we check (1) the number of
    Test particles, (2) the SNR mass, and (3) the orbit of the CIC particles
    (binary star in circular orbit), which is checked agains analytic
    solution. The Test particles are located at the corners of MultiFab
    boxes where eight boxes intersect. SNR mass is accurate to machine
    accuracy.
    2. `Gravity3DAMR`. This is the same test problem but with half of the
    domain refined to lev=1 and the other half in lev=0. The CIC particle is
    also removed due to the failure of the gravity solver when a particle
    crosses a coarse-fine boundary. The Test particles are located at the
    intersections between MultiFab boxes, and also at the coarse-fine
    boundary. SNR deposition is accurate to machine accuracy at the step
    right after deposition, but the relative error increases to ~1e-6
    several steps after. Is mass a conserved quantity when AMR is turned on?
    2. Rewrite `getParticleData()` (now named `getParticleDataAtLevel()`) to
    make it work on any AMR level.
    4. Removed `getParticlePositions()` since `getParticleDataAtLevel()`
    provides the same (and more) functionality.
    
    ### 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:_
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    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.
    - [x] *(For quokka-astro org members)* I have manually triggered the GPU
    tests with the magic comment `/azp run`.
    
    ---------
    
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src/particles/PhysicsParticles.hpp
src/particles/particle_deposition.hpp
src/particles/particle_destruction.hpp
src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp
src/problems/Gravity3D/CMakeLists.txt
src/problems/Gravity3D/gravity_3d.cpp
src/simulation.hpp
tests/Gravity3D.in
tests/Gravity3D.txt
tests/Gravity3DAMR.in

commit 321c9f1425d66ffde0d2ecdace7879f1e03839ff
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Apr 16 18:04:29 2025 -0400

    Use FaceLinear AMR interpolation for particle accelerations (#985)
    
    ### Description
    This extends the ghost cells in the particle acceleration MultiFab, and
    uses `amrex::FaceLinear` AMR interpolation (linear in the normal
    component, constant for the transverse components) for the face-centered
    accelerations, which are then averaged to cell centers before kicking
    particles.
    
    We also extend the ghost cells in the `rhs` MultiFab when solving the
    Poisson equation (in order to allow for particle drift since the last
    redistribute).
    
    ### Related issues
    Fixes https://github.com/quokka-astro/quokka/issues/984.
    
    ### Checklist
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    completed. Denote completed tasks with an `x` inside the square brackets
    `[ ]` in the Markdown source below:_
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    above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] *(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>

src/problems/BinaryOrbitCIC/binary_orbit.cpp
src/simulation.hpp

commit bf38110471803b708b4e3b722d25b453e61cd2e5
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Apr 16 10:58:31 2025 -0400

    Print the cell that sets the timestep on each level (#990)
    
    ### Description
    When `amr.v = 1`, this will print the cell that sets the candidate
    timestep for hydro (and also for particles, if applicable) for each
    level, as well as which level sets the overall coarse timestep.
    
    Example output:
    ```
    Coarse STEP 74 at t = 638990.8046 (1.277981609%) starts ...
    ...[level 0] estimated hydro timestep: 1.009208e+04
    ...[level 0]    hydro timestep limited at cell [16, 17, 15] with signal speed = 4.644731e+07
    ...[level 0]    cell density = 9.641857e-22, |v| = 3.344731e+07, cs = nan
    ...[level 0] estimated particle timestep: 7.274247e+04
    ...[level 0]    max particle velocity: 1.073994e+07
    ...[level 0]    particle timestep limited at position [1.724770e+12, -2.473514e+12, -9.395845e+03]
    ...[level 0] timestep limited by HYDRO
    ...coarse timestep set by level 0
    ```
    
    **Note that for Cray MPICH, standard output is not ordered with respect
    to different ranks, so the cell density, velocity and sound speed may be
    printed later in the output.** (We could copy the cell to rank 0 and
    then print, but that will incur a performance cost.)
    
    This PR also gets rid of old timestepping code that was used when the
    hydro update was insufficiently stable to take timesteps longer than the
    cooling time for some problems. Since that is no longer necessary, that
    code is removed.
    
    ### Related issues
    Implementation based on https://github.com/AMReX-Astro/Castro/pull/2273.
    
    ### Checklist
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    completed. Denote completed tasks with an `x` inside the square brackets
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    above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] 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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extern/amrex
src/QuokkaSimulation.hpp
src/linear_advection/AdvectionSimulation.hpp
src/particles/PhysicsParticles.hpp
src/simulation.hpp

commit 9ec31f0d49038e5865c1c5e1f27d73a8ff36074e
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Apr 16 10:54:20 2025 -0400

    Update .clang-tidy (#997)
    
    ### Description
    This suppresses some irrelevant warnings from clang-tidy.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] 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`.

src/.clang-tidy

commit 7bc602f45ac47d1d419a0379b0452dda296a566c
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Wed Apr 16 06:15:59 2025 +1000

    Fix GPU-related error in createInitialTestParticles() (#994)
    
    ### Description
    
    That was an obvious mistake. I forgot to use GPU function in
    `createInitialTestParticles()` in gravity_3d.cpp.
    
    ### Related issues
    Are there any GitHub issues that are fixed by this pull request? Add a
    link to them here.
    
    ### Checklist
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    completed. Denote completed tasks with an `x` inside the square brackets
    `[ ]` in the Markdown source below:_
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    above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] *(For quokka-astro org members)* I have manually triggered the GPU
    tests with the magic comment `/azp run`.
    
    ---------
    
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src/problems/Gravity3D/gravity_3d.cpp

commit 765dea35ea76e349c46c4c5555b224f759689fa3
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Apr 14 12:21:41 2025 +0000

    Bump ZedThree/clang-tidy-review from 0.20.1 to 0.21.0 (#991)
    
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    href="https://redirect.github.com/ZedThree/clang-tidy-review/pull/142">ZedThree/clang-tidy-review#142</a></li>
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    href="https://redirect.github.com/ZedThree/clang-tidy-review/pull/141">ZedThree/clang-tidy-review#141</a></li>
    <li>[install_commands] add option to inject install commands by <a
    href="https://github.com/akallabeth"><code>@​akallabeth</code></a> in <a
    href="https://redirect.github.com/ZedThree/clang-tidy-review/pull/146">ZedThree/clang-tidy-review#146</a></li>
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    Apply black changes</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/237487fd8d6c1efb36cd4074a00ff79e9f361b30"><code>237487f</code></a>
    Merge pull request <a
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    from akallabeth/master</li>
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    strip enclosing quotes</li>
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    href="https://github.com/ZedThree/clang-tidy-review/commit/27c845211e51b551b64373e40e2e5ddce1d452cb"><code>27c8452</code></a>
    quote install commands</li>
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    href="https://github.com/ZedThree/clang-tidy-review/commit/5714de4825666426c57f1b857e73cb407ad6a53d"><code>5714de4</code></a>
    Merge pull request <a
    href="https://redirect.github.com/zedthree/clang-tidy-review/issues/141">#141</a>
    from aobolensk/v0.20.1-patch-clang-tidy-19</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/187ce1c8b00151983ec9ee66301f5a415d5b5165"><code>187ce1c</code></a>
    Merge pull request <a
    href="https://redirect.github.com/zedthree/clang-tidy-review/issues/142">#142</a>
    from Nerixyz/fix/pr-comments</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/a6a03166cb988f1e8e2bfb07d698661f1177e50d"><code>a6a0316</code></a>
    [install_commands] add option to inject install commands</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/b9e7f522c310886afd30489da268d91499b53197"><code>b9e7f52</code></a>
    fix: use pygithub to get PR comments directly</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/ba7a1be1fadaadc4473666a2aa33ce8243c2e34b"><code>ba7a1be</code></a>
    Add support for clang-tidy-19</li>
    <li>See full diff in <a
    href="https://github.com/zedthree/clang-tidy-review/compare/e005a6ddf5cc4884b4bcab9930df255438183fd1...4ea7f7b72e7e039588ef5e64de9a845e5a3f8db5">compare
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.github/workflows/clang-tidy-comments.yml
.github/workflows/clang-tidy.yml

commit 033e1e10957a9188c1293db8abde0d744786530c
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Apr 14 08:21:04 2025 -0400

    Bump github/codeql-action from 3.28.13 to 3.28.15 (#992)
    
    Bumps [github/codeql-action](https://github.com/github/codeql-action)
    from 3.28.13 to 3.28.15.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
    href="https://github.com/github/codeql-action/releases">github/codeql-action's
    releases</a>.</em></p>
    <blockquote>
    <h2>v3.28.15</h2>
    <h1>CodeQL Action Changelog</h1>
    <p>See the <a
    href="https://github.com/github/codeql-action/releases">releases
    page</a> for the relevant changes to the CodeQL CLI and language
    packs.</p>
    <h2>3.28.15 - 07 Apr 2025</h2>
    <ul>
    <li>Fix bug where the action would fail if it tried to produce a debug
    artifact with more than 65535 files. <a
    href="https://redirect.github.com/github/codeql-action/pull/2842">#2842</a></li>
    </ul>
    <p>See the full <a
    href="https://github.com/github/codeql-action/blob/v3.28.15/CHANGELOG.md">CHANGELOG.md</a>
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    <h2>v3.28.14</h2>
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    <p>See the <a
    href="https://github.com/github/codeql-action/releases">releases
    page</a> for the relevant changes to the CodeQL CLI and language
    packs.</p>
    <h2>3.28.14 - 07 Apr 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.21.0. <a
    href="https://redirect.github.com/github/codeql-action/pull/2838">#2838</a></li>
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    <p>See the full <a
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    for more information.</p>
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    href="https://github.com/github/codeql-action/releases">releases
    page</a> for the relevant changes to the CodeQL CLI and language
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    <h2>[UNRELEASED]</h2>
    <p>No user facing changes.</p>
    <h2>3.28.15 - 07 Apr 2025</h2>
    <ul>
    <li>Fix bug where the action would fail if it tried to produce a debug
    artifact with more than 65535 files. <a
    href="https://redirect.github.com/github/codeql-action/pull/2842">#2842</a></li>
    </ul>
    <h2>3.28.14 - 07 Apr 2025</h2>
    <ul>
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    <p>No user facing changes.</p>
    <h2>3.28.12 - 19 Mar 2025</h2>
    <ul>
    <li>Dependency caching should now cache more dependencies for Java
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    <ul>
    <li>Enable support for Kotlin 2.1.10 when running with CodeQL CLI
    v2.20.3. <a
    href="https://redirect.github.com/github/codeql-action/pull/2744">#2744</a></li>
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    <p>No user facing changes.</p>
    <h2>3.28.6 - 27 Jan 2025</h2>
    <ul>
    <li>Re-enable debug artifact upload for CLI versions 2.20.3 or greater.
    <a
    href="https://redirect.github.com/github/codeql-action/pull/2726">#2726</a></li>
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commit 450e62a0071be3353d02fb40fe311d2e2e1ba673
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Fri Apr 11 12:50:04 2025 +1000

    Add an example of manually setting particles' integer components (#988)
    
    ### Description
    
    `InitFromAsciiFile` does not support integer components (see
    [here](https://github.com/AMReX-Codes/amrex/blob/e24e4a8c4df84ed71f961efe7637f86ba1c2ce62/Src/Particle/AMReX_ParticleInit.H#L24)).
    In this PR, I added an example showing how to initialize the integer
    components of particles in the `createInitialTestParticles` function in
    `gravity_3d.cpp`. We loop over all Test particles and set the integer
    component manually. This is helpful, for example, when the user want to
    initialize StachasticStellerPop particles from file and set all of them
    to `LowMassStar`, or assign their StellarEvolutionStage according to
    their mass and age.
    
    More changes:
    - Defined `createInitialTestParticles`
    - Added `StochasticStellarPopParticleDeathTimeIdx` and
    `TestParticleDeathTimeIdx`
    
    I also created an
    [issue](https://github.com/AMReX-Codes/amrex/issues/4415) on AMReX repo
    to request adding the functionality to initialize particles with integer
    components from file.
    
    ### 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:_
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    above).
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    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.
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    tests with the magic comment `/azp run`.
    
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src/QuokkaSimulation.hpp
src/linear_advection/AdvectionSimulation.hpp
src/particles/particle_types.hpp
src/problems/Gravity3D/gravity_3d.cpp
src/simulation.hpp
tests/TestParticles.txt

commit 45d05ffb6969c6b828a98b383bb6a351882b49d7
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Fri Apr 11 10:09:16 2025 +1000

    Define a virtual function to tell if a particle type belongs to the Star particle class (#987)
    
    ### Description
    We have `PhysicsParticleDescriptor` for most particle types and
    `StarParticleDescriptor` for star-like particle types, and some
    operations like `depositSN` only exists in the latter. However, the code
    does not know which of these two classes a `descriptor` belongs to. In
    this PR, I define a virtual function `isStarParticle()` that returns
    whether or not a particle type belongs to `StarParticleDescriptor` so
    that we can call `depositSN` on it. This makes `depositSN` in
    `PhysicsParticleRegister` very clean.
    
    This design can generalize to more particle classes , in which case I
    will change `isStarParticle()` to `getParticleClass` which returns the
    particle class: base_particles, star_particles, DM_particles, etc.
    
    ### Related issues
    Are there any GitHub issues that are fixed by this pull request? Add a
    link to them here.
    
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    completed. Denote completed tasks with an `x` inside the square brackets
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    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.
    - [x] *(For quokka-astro org members)* I have manually triggered the GPU
    tests with the magic comment `/azp run`.

src/particles/PhysicsParticles.hpp
src/particles/particle_types.hpp

commit f6efa3db1dd4f25219a66aa6934551ab20890729
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Fri Apr 11 02:54:08 2025 +1000

    only kick particles when Poisson solver is turned on (#989)
    
    ### Description
    
    We should only kick particles when Poisson solver is turned on.
    Otherwise, if we have massive particles in a sim and forget to turn on
    gravity, the code will complain that `phi` is not defined.
    
    ### 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:_
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    above).
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] 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`.

src/simulation.hpp

commit 33669446682dd7696367a6dbd3d9bdf24982dd66
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Wed Apr 9 23:49:06 2025 -0400

    Bump devcontainers/cpp from `53f5af4` to `165d17c` in /.devcontainer/gcc-container (#986)
    
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.devcontainer/gcc-container/Dockerfile

commit 2aa89067717d149545f1791954070f4ae02a35fb
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Wed Apr 9 10:08:13 2025 +1000

    binary orbit test on multilevel grids (#983)
    
    ### Description
    
    Previously the binary_orbit test runs on uniform grid. This PR add a new
    test with the whole domain refined to `lev=1`. The orbit separation is
    checked against the expected value and the error is within 6%. Note that
    the orbit radius is resolved by only 4 cells. In the uniform-grid test,
    the orbit radius is resolved by 2 (!!!) cells and the the error is
    confined in 16%.
    
    More changes:
    - I also updated `computeAfterTimestep` in `binary_orbit.cpp` to copy
    all particles from the finest level to the IO processor and validate the
    answer on the go. Previously `computeAfterTimestep` only works when AMR
    is disabled (`lev_max = 0`).
    
    ### Related issues
    Are there any GitHub issues that are fixed by this pull request? Add a
    link to them here.
    
    ### Checklist
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    completed. Denote completed tasks with an `x` inside the square brackets
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    above).
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
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src/problems/BinaryOrbitCIC/CMakeLists.txt
src/problems/BinaryOrbitCIC/binary_orbit.cpp
src/problems/BinaryOrbitCIC/particle_orbit_plot.py
tests/BinaryOrbit.in
tests/BinaryOrbitAMR.in

commit a30891d669fb51afa61194afaa825ce88d37767f
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Apr 8 00:36:12 2025 -0400

    Fix bug in particle acceleration field for refined levels (#982)
    
    ### Description
    The particle acceleration field was not filled correctly for levels > 0.
    
    (A binary orbit test problem with AMR to will be done in a future PR
    from @chongchonghe.)
    
    ### Related issues
    Fixes https://github.com/quokka-astro/quokka/issues/979.
    
    ### 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:_
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    above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
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    code.
    - [ ] *(For quokka-astro org members)* I have manually triggered the GPU
    tests with the magic comment `/azp run`.
    
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src/simulation.hpp

commit 6911b6260abcdc48e5e95faed1cdcbabdda1c8e3
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Apr 7 09:00:07 2025 -0400

    Bump actions/dependency-review-action from 4.5.0 to 4.6.0 (#981)
    
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    <li>Clarify comment-summary-in-pr behaviour by <a
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    in <a
    href="https://redirect.github.com/actions/dependency-review-action/pull/902">actions/dependency-review-action#902</a></li>
    <li>Prepare 4.6.0 Release candidate by <a
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    <h2>New Contributors</h2>
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    made their first contribution in <a
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commit a5c1eda577eff5a4381ea430f9875661c60f716d
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Apr 7 08:59:40 2025 -0400

    update Frontier modules (#980)
    
    ### Description
    Updates modules loaded on Frontier following the April 1, 2025 system
    update.
    
    ### Related issues
    N/A
    
    ### 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
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    above).
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] 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`.

scripts/frontier.profile

commit 17c18433b0fc8b88ef54a5db966962b2a572039d
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Apr 6 22:52:31 2025 -0400

    Fix typo in comment about particleCfl (#970)
    
    ### Description
    Fixes typo in comment about the default value of the particle CFL. The
    actual default value is 0.5 (line 161).
    
    ### Related issues
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src/simulation.hpp

commit bbc589e02ecb3b247d0222927b7992c76062ecd3
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Sun Apr 6 02:29:23 2025 +1100

    rename docs/docs to docs/markdown (#976)
    
    ### Description
    
    Rename docs/docs to docs/markdown.
    
    ### Related issues
    Addresses #972
    
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    completed. Denote completed tasks with an `x` inside the square brackets
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    code.
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    tests with the magic comment `/azp run`.

.gitignore
docs/docs/requirements.txt
docs/markdown/about.md
docs/markdown/citation.md
docs/markdown/debugging.md
docs/markdown/equations.md
docs/markdown/error_checking.md
docs/markdown/extra.css
docs/markdown/flowchart.md
docs/markdown/gallery.md
docs/markdown/howto_clang_tidy.md
docs/markdown/index.md
docs/markdown/insitu_analysis.md
docs/markdown/instability.md
docs/markdown/installation.md
docs/markdown/javascripts/mathjax.js
docs/markdown/parameters.md
docs/markdown/performance.md
docs/markdown/postprocessing.md
docs/markdown/references.bib
docs/markdown/running_on_hpc_clusters.md
docs/markdown/tests/attach/hydro_shuosher.png
docs/markdown/tests/attach/hydro_sms.png
docs/markdown/tests/attach/radcoupling.png
docs/markdown/tests/attach/radcoupling_rsla.png
docs/markdown/tests/attach/radhydro_pulse_density-1.png
docs/markdown/tests/attach/radhydro_pulse_density.png
docs/markdown/tests/attach/radhydro_pulse_temperature-1.png
docs/markdown/tests/attach/radhydro_pulse_temperature.png
docs/markdown/tests/attach/radhydro_pulse_velocity-1.png
docs/markdown/tests/attach/radhydro_pulse_velocity.png
docs/markdown/tests/attach/radhydro_uniform_advecting_temperature-nobeta.png
docs/markdown/tests/attach/radhydro_uniform_advecting_temperature.png
docs/markdown/tests/attach/radhydro_uniform_advecting_velocity-nobeta.png
docs/markdown/tests/attach/radhydro_uniform_advecting_velocity.png
docs/markdown/tests/attach/radshock_cgs_temperature.png
docs/markdown/tests/energy_exchange.md
docs/markdown/tests/index.md
docs/markdown/tests/radhydro_pulse.md
docs/markdown/tests/radhydro_uniform_adv.md
docs/markdown/tests/radshock.md
docs/markdown/tests/shu_osher.md
docs/markdown/tests/sms.md
docs/mkdocs.yml

commit 8bdd5cb074fd3dfd5364a676d83889792cee6047
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Fri Apr 4 22:23:06 2025 -0400

    Bump extern/amrex from `7626a3f` to `728688d` (#974)
    
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extern/amrex

commit 384291dc27541b6a209efacbe077246dc018d00f
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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    Bump extern/openPMD-api from `12e1bb6` to `53c0512` (#973)
    
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extern/openPMD-api

commit 81637e2d1121f3c121638acb97c58639602343f1
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Sat Apr 5 03:28:58 2025 +1100

    add chongchonghe to CODEOWNERS for particles (#971)
    
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.github/CODEOWNERS

commit c5cba08b8781913c64642d4f42fd9e3262ebc9ff
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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    Bump mkdocs-bibtex from 4.2.3 to 4.2.5 in /docs/docs (#968)
    
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commit fe6ed5c48522cfc4c8ec3b42d8d1f98dd1330803
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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    Bump mkdocs-bibtex from 4.2.3 to 4.2.5 in /docs (#967)
    
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docs/docs/requirements.txt
docs/requirements.txt

commit 3639a5df7cebee3004b224554cbb4dd9e9161c1b
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Tue Apr 1 11:18:43 2025 -0400

    Bump extern/amrex from `06b4a5b` to `7626a3f` (#963)
    
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    <li><a
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extern/amrex

commit 17bf797609e583994a82828f759afdb4c1e3ca60
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Wed Apr 2 02:10:14 2025 +1100

    add metadata.yaml to slice outputs (#965)
    
    ### Description
    
    This adds a metadata.yaml file to slicez_pltxxxxx folders. This is
    helpful because when yt loads that folder (it can, very sweet), yt will
    recognize it as a Quokka simulation output and do all the customization
    for Quokka.
    
    Note that this yt customization for Quokka is implemented and tested in
    [my yt fork](https://github.com/chongchonghe/yt) and we are in the
    process of publishing it before the next yt release. Demo of using the
    new YT frontend is here:
    https://github.com/Rongjun-ANU/README-of-yt-frontend-for-QUOKKA/blob/main/README.ipynb
    
    Other changes:
    - this also adds `tests/slice*` to .gitignore
    
    ### Related issues
    None.
    
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    _Before this pull request can be reviewed, all of these tasks should be
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
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    ---------
    
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.gitignore
src/io/DiagBase.H
src/io/DiagFramePlane.H
src/io/DiagFramePlane.cpp
src/io/DiagPDF.H
src/io/DiagPDF.cpp
src/simulation.hpp

commit 7520abc34d87802c6767beed08da8dc24e400d99
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Tue Apr 1 09:43:09 2025 -0400

    Bump extern/openPMD-api from `ff52a8d` to `12e1bb6` (#962)
    
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    Dataset-specific JSON/TOML configuration (<a
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    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/c48408835a29432045da7e687e9f6a0eb1b7be19"><code>c484088</code></a>
    Attribute preparsing for variable-encoded files in ReadRandomAccess
    mode: Sup...</li>
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    Fix zero-sized storeChunk for Span API in Python (<a
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    WarpX: Repo Moved (<a
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    BP5+groupbased: allow only up to 100 steps (<a
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    Followup: Bug fixes for random-access in variable encoding (<a
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extern/openPMD-api

commit f1486632386686eaa669e46db9776ae180cff17f
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Tue Apr 1 13:41:57 2025 +0000

    Bump extern/yaml-cpp from `39f7374` to `28f93bd` (#961)
    
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    docs: Fix link in README</li>
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extern/yaml-cpp

commit 97796a3692d1fcf1b37aeeac9efb84fe1a6b1dbf
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Tue Apr 1 09:41:16 2025 -0400

    Bump extern/fmt from `577fd3b` to `5199e0f` (#960)
    
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    Fix a flush issue on libstdc++</li>
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    href="https://github.com/fmtlib/fmt/commit/2f58430573c2b543fbafee63fefa72de05e03115"><code>2f58430</code></a>
    Move buffering tests to os-test</li>
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    href="https://github.com/fmtlib/fmt/commit/d5d32c1e81cb5a3bd2ba7225e38478142ebee904"><code>d5d32c1</code></a>
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    href="https://github.com/fmtlib/fmt/commit/204661287b9af5c5045e5cd6f4fa4a6467a4dbea"><code>2046612</code></a>
    Improve local_time test</li>
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    href="https://github.com/fmtlib/fmt/commit/e1ab38336130a805e3ef20861f00a761f2af22ea"><code>e1ab383</code></a>
    Report an error when timezone is not available</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/b9e0e94a016b0f93c1bf8d7b0d609b346ab16959"><code>b9e0e94</code></a>
    Enable more chrono tests on Windows</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/a81842428d8bce9d66a1da74a6edd3bb85efea9e"><code>a818424</code></a>
    Update changelog</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/f53055efe0dc14fe90278e75c8eed73ba6cbe1b2"><code>f53055e</code></a>
    Revert &quot;Workaround an ABI issue in spdlog&quot;</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/b2dfcb2b805f8670d5a1fa4ed0a70b3c92c6a94e"><code>b2dfcb2</code></a>
    Fix local_time test</li>
    <li><a
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    Enable some local_time tests and make them deterministic</li>
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commit f009ffa1004bba45b850c09698fec28f5d53868a
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Mar 31 09:00:32 2025 -0400

    Bump github/codeql-action from 3.28.12 to 3.28.13 (#957)
    
    Bumps [github/codeql-action](https://github.com/github/codeql-action)
    from 3.28.12 to 3.28.13.
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    <h2>3.28.13 - 24 Mar 2025</h2>
    <p>No user facing changes.</p>
    <h2>3.28.12 - 19 Mar 2025</h2>
    <ul>
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    href="https://redirect.github.com/github/codeql-action/pull/2793">#2793</a></li>
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    <li>Update default CodeQL bundle version to 2.20.5. <a
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    decompress on macOS. <a
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    <h2>3.28.9 - 07 Feb 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.20.4. <a
    href="https://redirect.github.com/github/codeql-action/pull/2753">#2753</a></li>
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    <ul>
    <li>Enable support for Kotlin 2.1.10 when running with CodeQL CLI
    v2.20.3. <a
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    <p>No user facing changes.</p>
    <h2>3.28.6 - 27 Jan 2025</h2>
    <ul>
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    <a
    href="https://redirect.github.com/github/codeql-action/pull/2726">#2726</a></li>
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    <h2>3.28.4 - 23 Jan 2025</h2>
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    <!-- raw HTML omitted -->
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    Update changelog for v3.28.13</li>
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    from github/cklin/empty-pr-diff-range</li>
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    href="https://github.com/github/codeql-action/commit/b361a915088c90790a0c458a63a4b63108a9ab0a"><code>b361a91</code></a>
    Diff-informed analysis: fix empty PR handling</li>
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    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2816">#2816</a>
    from github/cklin/overlay-file-list</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/b98ae6ca52694a727f4a03c9bf7a52df66492f23"><code>b98ae6c</code></a>
    Add overlay-database-utils tests</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/9825184a0aec625d59c8e5bcc122734a77e38e7b"><code>9825184</code></a>
    Add getFileOidsUnderPath() tests</li>
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    href="https://github.com/github/codeql-action/commit/ac67cffe5c20e84b598930c8453336a7404b2786"><code>ac67cff</code></a>
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    href="https://github.com/github/codeql-action/commit/9c674ba4f548f8b6a6f1a7990756e80453894f56"><code>9c674ba</code></a>
    build: refresh js files</li>
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    Detect PR branches for Default Setup</li>
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.github/workflows/codeql.yml
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commit 89af6093926e0af514b329bd3bfa5a566a66371c
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Mar 31 09:00:08 2025 -0400

    Bump actions/setup-python from 5.4.0 to 5.5.0 (#956)
    
    Bumps [actions/setup-python](https://github.com/actions/setup-python)
    from 5.4.0 to 5.5.0.
    <details>
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    <p><em>Sourced from <a
    href="https://github.com/actions/setup-python/releases">actions/setup-python's
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    <h2>v5.5.0</h2>
    <h2>What's Changed</h2>
    <h3>Enhancements:</h3>
    <ul>
    <li>Support free threaded Python versions like '3.13t' by <a
    href="https://github.com/colesbury"><code>@​colesbury</code></a> in <a
    href="https://redirect.github.com/actions/setup-python/pull/973">actions/setup-python#973</a></li>
    <li>Enhance Workflows: Include ubuntu-arm runners, Add e2e Testing for
    free threaded and Upgrade <code>@​action/cache</code> from 4.0.0 to
    4.0.3 by <a
    href="https://github.com/priya-kinthali"><code>@​priya-kinthali</code></a>
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    href="https://github.com/mahabaleshwars"><code>@​mahabaleshwars</code></a>
    in <a
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    <h3>Bug fixes:</h3>
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    href="https://github.com/mayeut"><code>@​mayeut</code></a> in <a
    href="https://redirect.github.com/actions/setup-python/pull/1011">actions/setup-python#1011</a>
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    installations.</li>
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    href="https://github.com/dependabot"><code>@​dependabot</code></a> in <a
    href="https://redirect.github.com/actions/setup-python/pull/1016">actions/setup-python#1016</a></li>
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    href="https://github.com/dependabot"><code>@​dependabot</code></a> in <a
    href="https://redirect.github.com/actions/setup-python/pull/1015">actions/setup-python#1015</a></li>
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    <h2>New Contributors</h2>
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    <li><a href="https://github.com/colesbury"><code>@​colesbury</code></a>
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    href="https://redirect.github.com/actions/setup-python/pull/973">actions/setup-python#973</a></li>
    <li><a
    href="https://github.com/mahabaleshwars"><code>@​mahabaleshwars</code></a>
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    href="https://redirect.github.com/actions/setup-python/pull/1043">actions/setup-python#1043</a></li>
    </ul>
    <p><strong>Full Changelog</strong>: <a
    href="https://github.com/actions/setup-python/compare/v5...v5.5.0">https://github.com/actions/setup-python/compare/v5...v5.5.0</a></p>
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    <li><a
    href="https://github.com/actions/setup-python/commit/8d9ed9ac5c53483de85588cdf95a591a75ab9f55"><code>8d9ed9a</code></a>
    Add e2e Testing for free threaded and Bump <code>@​action/cache</code>
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    <li><a
    href="https://github.com/actions/setup-python/commit/19e4675e06535f6b54e894da5c1f044400bb4996"><code>19e4675</code></a>
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    fix: install PyPy on Linux ARM64 (<a
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    <li>See full diff in <a
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.github/workflows/cmake-macos.yml
.github/workflows/codespell.yml

commit 8ad389586c6e358e7832d4a685bfa9398a28af8f
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Mar 26 09:59:02 2025 -0400

    update ROCm version on Frontier (#944)
    
    ### Description
    Updates SLURM scripts and Bash profile for Frontier to use ROCm 6.3
    (same as Setonix).
    
    Also, we no longer need any workarounds for Slingshot network issues.
    
    Scaling plot:
    
    ![frontier_weak_scaling_quokka](https://github.com/user-attachments/assets/2dd776cf-60b0-45b7-a9bd-e7422ed6401d)
    
    Depends on:
    * https://github.com/quokka-astro/quokka/pull/946
    
    ### Related issues
    N/A
    
    ### 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:_
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    above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] 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
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    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

scripts/frontier-1node.submit
scripts/frontier-4096node.submit
scripts/frontier-512node.submit
scripts/frontier-64node.submit
scripts/frontier-8node.submit
scripts/frontier.profile

commit 978203852163b75c2a024935694b7787af324b2e
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Wed Mar 26 11:46:36 2025 +1100

    Create StellarPop particle type for Aditi's outflow simulations (#954)
    
    ### Description
    
    This PR creates a new particle type, StellarPop, for Aditi's outflow
    simulations. StellarPop is nearly identical to Test particle, but I
    define it here for Aditi's convenience and it won't grow like the Test
    particle will in the future. In Aditi's simulations, she has to write a
    specialization of ParticleCreationTraits for StellarPop particles in
    particle_creation.hpp .
    
    ### Related issues
    Are there any GitHub issues that are fixed by this pull request? Add a
    link to them here.
    
    ### Checklist
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    above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
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src/QuokkaSimulation.hpp
src/linear_advection/AdvectionSimulation.hpp
src/particles/PhysicsParticles.hpp
src/particles/particle_types.hpp
src/simulation.hpp

commit b2f4531e3b724c62bd6b506e956d90157c76ae20
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Mar 25 19:28:34 2025 -0400

    ignore FPE in YAML I/O (#946)
    
    ### Description
    This turns off floating point exceptions when reading YAML files.
    
    This should avoid stochastic CI failures due to FPEs in the yaml-cpp
    library. They do not appear to affect Quokka in any way.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] 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`.

src/simulation.hpp

commit cad8b4ecf2c73b489cf79c8e159052179df85ec6
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Mar 25 19:27:57 2025 -0400

    add DeltaAI scripts (#947)
    
    ### Description
    Add build and SLURM scripts for the DeltaAI (NVIDIA Grace Hopper)
    machine at NCSA.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] 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`.

scripts/delta_ai.profile
scripts/dtai-1node.submit
scripts/dtai-64node.submit
scripts/dtai-8node.submit
src/QuokkaSimulation.hpp

commit b0ad271c49f407072d3237ca8adcaf64a1cfe79f
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Mar 25 01:01:13 2025 -0400

    add ROCm dev container (#953)
    
    ### Description
    Adds a Docker container to build Quokka with the AMD ROCm software stack
    for AMD GPUs. Note that using this on a recent Mac will be slow, since
    it runs under emulation (AMD only supports its software stack on x86_64
    host CPUs).
    
    In the near future, I am planning to run the CI tests on moth inside
    this container.
    
    ### Related issues
    Closes https://github.com/quokka-astro/quokka/issues/768.
    
    ### 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).
    - [ ] 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`.

.devcontainer/rocm-container/Dockerfile
.devcontainer/rocm-container/devcontainer.json

commit b443ffe3f498424015e2a0d8d70dad4795c07ffd
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Mar 24 03:28:55 2025 +0000

    Bump actions/upload-artifact from 4.6.1 to 4.6.2 (#952)
    
    Bumps
    [actions/upload-artifact](https://github.com/actions/upload-artifact)
    from 4.6.1 to 4.6.2.
    <details>
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    <p><em>Sourced from <a
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    <blockquote>
    <h2>v4.6.2</h2>
    <h2>What's Changed</h2>
    <ul>
    <li>Update to use artifact 2.3.2 package &amp; prepare for new
    upload-artifact release by <a
    href="https://github.com/salmanmkc"><code>@​salmanmkc</code></a> in <a
    href="https://redirect.github.com/actions/upload-artifact/pull/685">actions/upload-artifact#685</a></li>
    </ul>
    <h2>New Contributors</h2>
    <ul>
    <li><a href="https://github.com/salmanmkc"><code>@​salmanmkc</code></a>
    made their first contribution in <a
    href="https://redirect.github.com/actions/upload-artifact/pull/685">actions/upload-artifact#685</a></li>
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    <p><strong>Full Changelog</strong>: <a
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    <li><a
    href="https://github.com/actions/upload-artifact/commit/ea165f8d65b6e75b540449e92b4886f43607fa02"><code>ea165f8</code></a>
    Merge pull request <a
    href="https://redirect.github.com/actions/upload-artifact/issues/685">#685</a>
    from salmanmkc/salmanmkc/3-new-upload-artifacts-release</li>
    <li><a
    href="https://github.com/actions/upload-artifact/commit/08396203c179e13c71b9754ce3472ed71842eec0"><code>0839620</code></a>
    Prepare for new release of actions/upload-artifact with new toolkit
    cache ver...</li>
    <li>See full diff in <a
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.github/workflows/checkpoint-restart.yml
.github/workflows/cmake-macos.yml
.github/workflows/cmake.yml
.github/workflows/codeql.yml
.github/workflows/docs.yml
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commit 2da9307777cf0d9e15812f7338ad31fa5c527829
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Mar 24 03:28:00 2025 +0000

    Bump github/codeql-action from 3.28.11 to 3.28.12 (#950)
    
    Bumps [github/codeql-action](https://github.com/github/codeql-action)
    from 3.28.11 to 3.28.12.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
    href="https://github.com/github/codeql-action/releases">github/codeql-action's
    releases</a>.</em></p>
    <blockquote>
    <h2>v3.28.12</h2>
    <h1>CodeQL Action Changelog</h1>
    <p>See the <a
    href="https://github.com/github/codeql-action/releases">releases
    page</a> for the relevant changes to the CodeQL CLI and language
    packs.</p>
    <h2>3.28.12 - 19 Mar 2025</h2>
    <ul>
    <li>Dependency caching should now cache more dependencies for Java
    <code>build-mode: none</code> extractions. This should speed up
    workflows and avoid inconsistent alerts in some cases.</li>
    <li>Update default CodeQL bundle version to 2.20.7. <a
    href="https://redirect.github.com/github/codeql-action/pull/2810">#2810</a></li>
    </ul>
    <p>See the full <a
    href="https://github.com/github/codeql-action/blob/v3.28.12/CHANGELOG.md">CHANGELOG.md</a>
    for more information.</p>
    </blockquote>
    </details>
    <details>
    <summary>Changelog</summary>
    <p><em>Sourced from <a
    href="https://github.com/github/codeql-action/blob/main/CHANGELOG.md">github/codeql-action's
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    <blockquote>
    <h1>CodeQL Action Changelog</h1>
    <p>See the <a
    href="https://github.com/github/codeql-action/releases">releases
    page</a> for the relevant changes to the CodeQL CLI and language
    packs.</p>
    <h2>[UNRELEASED]</h2>
    <p>No user facing changes.</p>
    <h2>3.28.12 - 19 Mar 2025</h2>
    <ul>
    <li>Dependency caching should now cache more dependencies for Java
    <code>build-mode: none</code> extractions. This should speed up
    workflows and avoid inconsistent alerts in some cases.</li>
    <li>Update default CodeQL bundle version to 2.20.7. <a
    href="https://redirect.github.com/github/codeql-action/pull/2810">#2810</a></li>
    </ul>
    <h2>3.28.11 - 07 Mar 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.20.6. <a
    href="https://redirect.github.com/github/codeql-action/pull/2793">#2793</a></li>
    </ul>
    <h2>3.28.10 - 21 Feb 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.20.5. <a
    href="https://redirect.github.com/github/codeql-action/pull/2772">#2772</a></li>
    <li>Address an issue where the CodeQL Bundle would occasionally fail to
    decompress on macOS. <a
    href="https://redirect.github.com/github/codeql-action/pull/2768">#2768</a></li>
    </ul>
    <h2>3.28.9 - 07 Feb 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.20.4. <a
    href="https://redirect.github.com/github/codeql-action/pull/2753">#2753</a></li>
    </ul>
    <h2>3.28.8 - 29 Jan 2025</h2>
    <ul>
    <li>Enable support for Kotlin 2.1.10 when running with CodeQL CLI
    v2.20.3. <a
    href="https://redirect.github.com/github/codeql-action/pull/2744">#2744</a></li>
    </ul>
    <h2>3.28.7 - 29 Jan 2025</h2>
    <p>No user facing changes.</p>
    <h2>3.28.6 - 27 Jan 2025</h2>
    <ul>
    <li>Re-enable debug artifact upload for CLI versions 2.20.3 or greater.
    <a
    href="https://redirect.github.com/github/codeql-action/pull/2726">#2726</a></li>
    </ul>
    <h2>3.28.5 - 24 Jan 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.20.3. <a
    href="https://redirect.github.com/github/codeql-action/pull/2717">#2717</a></li>
    </ul>
    <h2>3.28.4 - 23 Jan 2025</h2>
    <p>No user facing changes.</p>
    <h2>3.28.3 - 22 Jan 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.20.2. <a
    href="https://redirect.github.com/github/codeql-action/pull/2707">#2707</a></li>
    <li>Fix an issue downloading the CodeQL Bundle from a GitHub Enterprise
    Server instance which occurred when the CodeQL Bundle had been synced to
    the instance using the <a
    href="https://github.com/github/codeql-action-sync-tool">CodeQL Action
    sync tool</a> and the Actions runner did not have Zstandard installed.
    <a
    href="https://redirect.github.com/github/codeql-action/pull/2710">#2710</a></li>
    </ul>
    <!-- raw HTML omitted -->
    </blockquote>
    <p>... (truncated)</p>
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    <li><a
    href="https://github.com/github/codeql-action/commit/5f8171a638ada777af81d42b55959a643bb29017"><code>5f8171a</code></a>
    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2814">#2814</a>
    from github/update-v3.28.12-6349095d1</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/bb59f7707d836b040802dbdf2ad1a16482d319da"><code>bb59f77</code></a>
    Update changelog for v3.28.12</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/6349095d19ec30397ffb02a63b7aa4f867deb563"><code>6349095</code></a>
    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2810">#2810</a>
    from github/update-bundle/codeql-bundle-v2.20.7</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/d7d03fda1241f6b0b3fae460c9f19c6e887158ad"><code>d7d03fd</code></a>
    Add changelog note</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/4e3a5342c5e8e627915b9a29b363f49da8c4a32e"><code>4e3a534</code></a>
    Update default bundle to codeql-bundle-v2.20.7</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/55f023701cfc1e7d11ef2ae0c5ec3193dae4fce4"><code>55f0237</code></a>
    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2802">#2802</a>
    from github/mbg/dependency-caching/java-buildless</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/6a151cd77488e58567da1dcf953e7aeeaca4950c"><code>6a151cd</code></a>
    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2811">#2811</a>
    from github/dependabot/github_actions/actions-c2c311...</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/7866bcdb1b15b5d5cba0021b87f36d9f6d977156"><code>7866bcd</code></a>
    Manually bump workflow to match autogenerated file</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/611289e0b0ce1f6fc14820f1b72edaed2de4ba2c"><code>611289e</code></a>
    build(deps): bump ruby/setup-ruby in the actions group</li>
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    href="https://github.com/github/codeql-action/commit/4c409a5b664afa7d5b12cd8487e310f286487472"><code>4c409a5</code></a>
    Remove temporary dependency directory in <code>analyze</code> post
    action</li>
    <li>Additional commits viewable in <a
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commit 602680d349923e3f2bb391e11a1b6f01086776cd
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Mar 24 03:26:22 2025 +0000

    Bump actions/cache from 4.2.2 to 4.2.3 (#951)
    
    Bumps [actions/cache](https://github.com/actions/cache) from 4.2.2 to
    4.2.3.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
    href="https://github.com/actions/cache/releases">actions/cache's
    releases</a>.</em></p>
    <blockquote>
    <h2>v4.2.3</h2>
    <h2>What's Changed</h2>
    <ul>
    <li>Update to use <code>@​actions/cache</code> 4.0.3 package &amp;
    prepare for new release by <a
    href="https://github.com/salmanmkc"><code>@​salmanmkc</code></a> in <a
    href="https://redirect.github.com/actions/cache/pull/1577">actions/cache#1577</a>
    (SAS tokens for cache entries are now masked in debug logs)</li>
    </ul>
    <h2>New Contributors</h2>
    <ul>
    <li><a href="https://github.com/salmanmkc"><code>@​salmanmkc</code></a>
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    <h1>Releases</h1>
    <h3>4.2.3</h3>
    <ul>
    <li>Bump <code>@actions/cache</code> to v4.0.3 (obfuscates SAS token in
    debug logs for cache entries)</li>
    </ul>
    <h3>4.2.2</h3>
    <ul>
    <li>Bump <code>@actions/cache</code> to v4.0.2</li>
    </ul>
    <h3>4.2.1</h3>
    <ul>
    <li>Bump <code>@actions/cache</code> to v4.0.1</li>
    </ul>
    <h3>4.2.0</h3>
    <p>TLDR; The cache backend service has been rewritten from the ground up
    for improved performance and reliability. <a
    href="https://github.com/actions/cache">actions/cache</a> now integrates
    with the new cache service (v2) APIs.</p>
    <p>The new service will gradually roll out as of <strong>February 1st,
    2025</strong>. The legacy service will also be sunset on the same date.
    Changes in these release are <strong>fully backward
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    <p><strong>We are deprecating some versions of this action</strong>. We
    recommend upgrading to version <code>v4</code> or <code>v3</code> as
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    instructions below).</p>
    <p>If you are using pinned SHAs, please use the SHAs of versions
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    <p>If you do not upgrade, all workflow runs using any of the deprecated
    <a href="https://github.com/actions/cache">actions/cache</a> will
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    <p>Upgrading to the recommended versions will not break your
    workflows.</p>
    <h3>4.1.2</h3>
    <ul>
    <li>Add GitHub Enterprise Cloud instances hostname filters to inform API
    endpoint choices - <a
    href="https://redirect.github.com/actions/cache/pull/1474">#1474</a></li>
    <li>Security fix: Bump braces from 3.0.2 to 3.0.3 - <a
    href="https://redirect.github.com/actions/cache/pull/1475">#1475</a></li>
    </ul>
    <h3>4.1.1</h3>
    <ul>
    <li>Restore original behavior of <code>cache-hit</code> output - <a
    href="https://redirect.github.com/actions/cache/pull/1467">#1467</a></li>
    </ul>
    <h3>4.1.0</h3>
    <ul>
    <li>Ensure <code>cache-hit</code> output is set when a cache is missed -
    <a
    href="https://redirect.github.com/actions/cache/pull/1404">#1404</a></li>
    <li>Deprecate <code>save-always</code> input - <a
    href="https://redirect.github.com/actions/cache/pull/1452">#1452</a></li>
    </ul>
    <h3>4.0.2</h3>
    <ul>
    <li>Fixed restore <code>fail-on-cache-miss</code> not working.</li>
    </ul>
    <h3>4.0.1</h3>
    <ul>
    <li>Updated <code>isGhes</code> check</li>
    </ul>
    <!-- raw HTML omitted -->
    </blockquote>
    <p>... (truncated)</p>
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.github/workflows/codeql.yml
.github/workflows/codespell.yml
.github/workflows/hip.yml
.github/workflows/intel.yml

commit 3194f9d154a5fa565b749fa5768b1e74cd07e6d9
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Fri Mar 21 00:25:32 2025 +1100

    add QUOKKA_VERSION in metadata.yaml (#945)
    
    ### Description
    
    Add `QUOKKA_VERSION` variable into metadata.yaml. `QUOKKA_VERSION` will
    be used in YT to perform version checks and determine the corresponding
    data structure.
    
    I recommend we update `QUOKKA_VERSION` under the following
    circumstances:
    (1) before a release,
    (2) when modifying the structure of the simulation outputs, especially
    if such changes require elaborate scripting in post-processing tools
    like YT.
    
    ### Related issues
    None.
    
    ### 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).
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    above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] 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`.

src/simulation.hpp

commit 03ee145062f40af77189efe7bdb7405fe31ed06e
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Tue Mar 18 09:59:43 2025 -0400

    Bump devcontainers/cpp from `6493de2` to `53f5af4` in /.devcontainer/gcc-container (#943)
    
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.devcontainer/gcc-container/Dockerfile

commit ef6e9437c384933c50788d72431479edf607e3ee
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon Mar 17 18:03:26 2025 +0000

    [pre-commit.ci] pre-commit autoupdate (#942)
    
    <!--pre-commit.ci start-->
    updates:
    - [github.com/pre-commit/mirrors-clang-format: v19.1.7 →
    v20.1.0](https://github.com/pre-commit/mirrors-clang-format/compare/v19.1.7...v20.1.0)
    <!--pre-commit.ci end-->
    
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.pre-commit-config.yaml

commit b15dcfa2e007b82ccbd0249d7a90d34b4dd27dcc
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Sun Mar 16 15:36:43 2025 +1100

    Add Stellar Evolution attribute and SNDeposition (#938)
    
    ### Description
    
    This PR adds a new attribute `evolutionStage` to the particle data and a
    new function `SNDeposition` to deposit mass, momentum, and energy from
    particles to the grid.
    
    Changes:
    
    1. Add `Test` particle type for testing all particle features.
    
    2. Define an integer component `evolutionStage` to Test_particles. It is
    used to track the evolution stage of the particle. The evolution stage
    is defined as an enum class as listed below. For particle types that
    support stellar evolution (`evolutionStageIndex_ >= 0`), each star is
    created either as a low mass star or as a SN progenitor. When a SN
    progenitor reaches the end of its life, it executes `SNDeposition()` and
    evolves into a SN remnant.
    
    ```cpp
    enum class StellarEvolutionStage {
            LowMassStar,  // Low mass star stage
            SNProgenitor,  // Supernova progenitor stage
            SNRemnant     // Supernova remnant stage
    };
    ```
    
    3. Defined `SNDeposition` to deposit mass, momentum, and energy from
    particles to the grid. At each time step, we find the particle types
    that support stellar evolution, and check if each particle is a SN
    progenitor and if it has reached the end of its life. If so, we run
    `SNDeposition()` and update the particle's evolution stage to SNRemnant.
    This also works as a framework for other interact-with-mesh operations.
    Unlike `interp.ParticleToMesh` which uses linear interpolation to
    deposit N particle components to N mesh components on a one-to-one
    basis, `SNDeposition` calculates the exact position of the particle in
    the mesh and deposit particle properties to arbitrary components of
    neighboring cells, using any interpolation kernel. Note that the maximum
    number of cells allowed to use in SNDeposition (the `stencil_width`) is
    `nghost_cc_ = 4`.
    
    The new code is fully tested via the gravity_3d test on CPU, GPU, and
    MPI, where we check the creation, stellar evolution, and destruction of
    the particles, as well as the total mass in SN ejecta.
    
    ### 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
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    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>

src/particles/PhysicsParticles.hpp
src/particles/particle_creation.hpp
src/particles/particle_deposition.hpp
src/particles/particle_destruction.hpp
src/particles/particle_types.hpp
src/problems/Gravity3D/gravity_3d.cpp
src/simulation.hpp
tests/Gravity3D.in

commit d1d7a6fac94bd217c080eec33364a42088fb5bed
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Sat Mar 15 14:30:33 2025 +1100

    Remove all unused const variables (#941)
    
    ### Description
    
    This PR removes all unused const variables so that we can successfully
    build the code with `-DWARNINGS_AS_ERRORS=ON` on moth. This helps to
    reproduce the warning github action locally.
    
    When I compile Quokka on moth with warnings_as_errors on, I got millions
    of `-Wunused-const-variable` errors. I don't know why we don't see that
    kind of warnings in the github action, but in order to avoid that on
    moth, I have to remove all unused const variables.
    
    ### Related issues
    Are there any GitHub issues that are fixed by this pull request? Add a
    link to them here.
    
    ### 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).
    - [ ] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] 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`.

src/problems/RadLineCooling/test_rad_line_cooling.cpp
src/problems/RadMarshak/test_radiation_marshak.cpp
src/problems/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/problems/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/problems/RadMarshakDustPE/test_radiation_marshak_dust_and_PE.cpp
src/problems/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/problems/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/problems/RadSuOlson/test_radiation_SuOlson.cpp
src/problems/RadTophat/test_radiation_tophat.cpp
src/problems/RadhydroPulseMGconst/test_radhydro_pulse_MG_const_kappa.cpp
src/problems/RadhydroPulseMGint/test_radhydro_pulse_MG_int.cpp
src/problems/RandomBlast/blast.cpp
src/simulation.hpp

commit e494c57860cf205f86ec6ab3090763b8696a0f72
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Mar 13 16:56:44 2025 -0400

    add OpenPMD CI action (#937)
    
    ### Description
    This adds a Github action to test and run with OpenPMD plotfile output
    for the HydroBlast3D problem. This is just to ensure that we don't
    inadvertently break the OpenPMD output code path.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] 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`.

.github/workflows/openpmd.yml

commit b111a719ab947cf3692dc595ad8bc577c0100c9f
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Fri Mar 14 01:14:57 2025 +1100

    Make metadata.yaml structured and add Fields.yaml in particle plotfile (#935)
    
    ### Description
    
    Changes:
    
    1. The metadata.yaml file now has nested structure for better
    readability. e.g.
    
    ```yaml
    git_hash_quokka: bc8f153da813c76784fac37a91002d631e5dc3c1-dirty
    git_hash_amrex: 06b4a5b105f5aebe66b987194fc9b5c207fae5ff
    units:
      unit_length: .nan
      unit_mass: .nan
      unit_time: .nan
      unit_temperature: .nan
    constants:
      k_B: 1
      G: 1
    ```
    
    2. Added a `Fields.yaml` file in each particle folder inside the
    checkpoint and plotfile directories. This gives the field names and
    their units. e.g., chk00003/CIC_particles/Fields.yaml:
    
    ```yaml
    # field: [M, L, T, Θ]
    mass: [1, 0, 0, 0]
    vx: [0, 1, -1, 0]
    vy: [0, 1, -1, 0]
    vz: [0, 1, -1, 0]
    ```
    
    The numbers in the bracket give the powers of the unit mass, length,
    time, and temperature. For instance, the unit of`vx` would be
    `unit_length * unit_time^-1` in the example above. This will be used by
    the yt Quokka frontend that Rongjun and I wrote (releasing soon).
    
    ### Related issues
    None.
    
    ### 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).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] *(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>

src/QuokkaSimulation.hpp
src/particles/PhysicsParticles.hpp
src/particles/particle_types.hpp
src/problems/ShockCloud/cloud.cpp
src/simulation.hpp
tests/Gravity3D.in

commit 25099128c23402e9267dc6d23aaae50ad44d11e9
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Mar 10 10:06:58 2025 -0400

    Bump mkdocs-bibtex from 4.2.2 to 4.2.3 in /docs/docs (#934)
    
    Bumps [mkdocs-bibtex](https://github.com/shyamd/mkdocs-bibtex) from
    4.2.2 to 4.2.3.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
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    <blockquote>
    <h2>v4.2.3</h2>
    <p>Version 4.2.3</p>
    <h3>Commits</h3>
    <ul>
    <li>[43c16f26] Minor improvements to pandoc registry (<a
    href="https://redirect.github.com/shyamd/mkdocs-bibtex/issues/303">#303</a>)</li>
    <li>[fea4a568] Bump mypy from 1.14.1 to 1.15.0</li>
    <li>[cddff5aa] Bump ruff from 0.9.4 to 0.9.9</li>
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    Minor improvements to pandoc registry (<a
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    <li><a
    href="https://github.com/shyamd/mkdocs-bibtex/commit/fea4a568a5822f5a41998137f20e5093c0fe27f7"><code>fea4a56</code></a>
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commit 2af6ddabaccaf88aa019018a39e7631c4fdf20de
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Mar 10 10:06:39 2025 -0400

    Bump github/codeql-action from 3.28.10 to 3.28.11 (#932)
    
    Bumps [github/codeql-action](https://github.com/github/codeql-action)
    from 3.28.10 to 3.28.11.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
    href="https://github.com/github/codeql-action/releases">github/codeql-action's
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    <h2>v3.28.11</h2>
    <h1>CodeQL Action Changelog</h1>
    <p>See the <a
    href="https://github.com/github/codeql-action/releases">releases
    page</a> for the relevant changes to the CodeQL CLI and language
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    <h2>3.28.11 - 07 Mar 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.20.6. <a
    href="https://redirect.github.com/github/codeql-action/pull/2793">#2793</a></li>
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    href="https://github.com/github/codeql-action/blob/v3.28.11/CHANGELOG.md">CHANGELOG.md</a>
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    <h2>3.28.11 - 07 Mar 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.20.6. <a
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    <li>Enable support for Kotlin 2.1.10 when running with CodeQL CLI
    v2.20.3. <a
    href="https://redirect.github.com/github/codeql-action/pull/2744">#2744</a></li>
    </ul>
    <h2>3.28.7 - 29 Jan 2025</h2>
    <p>No user facing changes.</p>
    <h2>3.28.6 - 27 Jan 2025</h2>
    <ul>
    <li>Re-enable debug artifact upload for CLI versions 2.20.3 or greater.
    <a
    href="https://redirect.github.com/github/codeql-action/pull/2726">#2726</a></li>
    </ul>
    <h2>3.28.5 - 24 Jan 2025</h2>
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    <li>Update default CodeQL bundle version to 2.20.3. <a
    href="https://redirect.github.com/github/codeql-action/pull/2717">#2717</a></li>
    </ul>
    <h2>3.28.4 - 23 Jan 2025</h2>
    <p>No user facing changes.</p>
    <h2>3.28.3 - 22 Jan 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.20.2. <a
    href="https://redirect.github.com/github/codeql-action/pull/2707">#2707</a></li>
    <li>Fix an issue downloading the CodeQL Bundle from a GitHub Enterprise
    Server instance which occurred when the CodeQL Bundle had been synced to
    the instance using the <a
    href="https://github.com/github/codeql-action-sync-tool">CodeQL Action
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    <h2>3.28.2 - 21 Jan 2025</h2>
    <p>No user facing changes.</p>
    <!-- raw HTML omitted -->
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.github/workflows/codeql.yml
.github/workflows/scorecard.yml

commit 1c9f8e63568335d5575a4189d6aaf9e16379dcc3
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Mar 10 10:06:14 2025 -0400

    Bump mkdocs-bibtex from 4.2.2 to 4.2.3 in /docs (#933)
    
    Bumps [mkdocs-bibtex](https://github.com/shyamd/mkdocs-bibtex) from
    4.2.2 to 4.2.3.
    <details>
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    <li>[43c16f26] Minor improvements to pandoc registry (<a
    href="https://redirect.github.com/shyamd/mkdocs-bibtex/issues/303">#303</a>)</li>
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    <li><a
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docs/docs/requirements.txt
docs/requirements.txt

commit 26fcfe266fedf54d4b93d2b6c45c580027c360a7
Author: Aditi <45175933+aditivijayan@users.noreply.github.com>
Date:   Tue Mar 11 01:05:21 2025 +1100

    Movie from QED I paper (#928)
    
    ### Description
    Adding movie for QED I paper.
    
    
    ### Related issues
    Are there any GitHub issues that are fixed by this pull request? Add a
    link to them here.
    
    ### 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).
    - [ ] I have added a link to any related issues (if applicable; see
    above).
    - [ ] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] 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: Ben Wibking <ben@wibking.com>

docs/docs/gallery.md

commit 52736cf07b0f3bc8ea1ad68e54797b7b76106fec
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Mar 9 19:15:49 2025 -0400

    remove workarounds from Setonix job scripts (#931)
    
    ### Description
    Setonix does not appear to need any workarounds for bugs anymore! So
    I've removed them from the job scripts. These scripts have been tested
    and work as of March 2025.
    
    ### Related issues
    Closes https://github.com/quokka-astro/quokka/issues/353.
    
    ### 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).
    - [ ] 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`.

scripts/setonix-1node.submit
scripts/setonix-64nodes.submit
scripts/setonix-8nodes.submit

commit 13029a249b855585ced50c693487918911983eb0
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Fri Mar 7 10:04:27 2025 -0500

    Bump mkdocs-bibtex from 2.15.0 to 4.2.2 in /docs (#929)
    
    Bumps [mkdocs-bibtex](https://github.com/shyamd/mkdocs-bibtex) from
    2.15.0 to 4.2.2.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
    href="https://github.com/shyamd/mkdocs-bibtex/releases">mkdocs-bibtex's
    releases</a>.</em></p>
    <blockquote>
    <h2>v4.2.2</h2>
    <p>Version 4.2.2</p>
    <h3>Commits</h3>
    <h2>v4.2.1</h2>
    <p>Version 4.2.1</p>
    <h3>Commits</h3>
    <ul>
    <li>[c39da111] fixed typo with new option (<a
    href="https://redirect.github.com/shyamd/mkdocs-bibtex/issues/300">#300</a>)</li>
    <li>[8e562dcf] update README</li>
    </ul>
    <h2>v4.2.0</h2>
    <p>Version 4.2.0</p>
    <h3>Commits</h3>
    <ul>
    <li>[c0bb2bba] Add option to disable inline citations all together (<a
    href="https://redirect.github.com/shyamd/mkdocs-bibtex/issues/298">#298</a>)</li>
    </ul>
    <h2>v4.1.4</h2>
    <p>Version 4.1.4</p>
    <h3>Commits</h3>
    <h2>v4.1.3</h2>
    <p>Version 4.1.3</p>
    <h3>Commits</h3>
    <ul>
    <li>[d4866d4a] only process new blocks (<a
    href="https://redirect.github.com/shyamd/mkdocs-bibtex/issues/297">#297</a>)</li>
    </ul>
    <h2>v4.1.2</h2>
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    <h2>v4.1.1</h2>
    <p>Version 4.1.1</p>
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    <ul>
    <li>[be7620bb] Fix inline citations capturing emails (<a
    href="https://redirect.github.com/shyamd/mkdocs-bibtex/issues/296">#296</a>)</li>
    <li>[91fdfd99] Bump ruff from 0.9.1 to 0.9.4</li>
    <li>[0e51f179] Bump pypandoc from 1.14 to 1.15</li>
    <li>[7d52ebe6] update readme</li>
    </ul>
    <h2>v4.1.0</h2>
    <p>Version 4.1.0</p>
    <!-- raw HTML omitted -->
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    <li><a
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    fixed typo with new option (<a
    href="https://redirect.github.com/shyamd/mkdocs-bibtex/issues/300">#300</a>)</li>
    <li><a
    href="https://github.com/shyamd/mkdocs-bibtex/commit/8e562dcfabbd88d6d4cb2c8c82b2c4e2326155bb"><code>8e562dc</code></a>
    update README</li>
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    href="https://github.com/shyamd/mkdocs-bibtex/commit/c0bb2bba3b5662610a7caabc2115d9f70cc79b26"><code>c0bb2bb</code></a>
    Add option to disable inline citations all together (<a
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    href="https://github.com/shyamd/mkdocs-bibtex/commit/d4866d4a070b111b4219bbfd4627523b38fb7780"><code>d4866d4</code></a>
    only process new blocks (<a
    href="https://redirect.github.com/shyamd/mkdocs-bibtex/issues/297">#297</a>)</li>
    <li><a
    href="https://github.com/shyamd/mkdocs-bibtex/commit/be7620bb132abd9411ba2b006a12383b5eb571e5"><code>be7620b</code></a>
    Fix inline citations capturing emails (<a
    href="https://redirect.github.com/shyamd/mkdocs-bibtex/issues/296">#296</a>)</li>
    <li><a
    href="https://github.com/shyamd/mkdocs-bibtex/commit/91fdfd99b1c957de3a617b24a4738c7b1b58593e"><code>91fdfd9</code></a>
    Bump ruff from 0.9.1 to 0.9.4</li>
    <li><a
    href="https://github.com/shyamd/mkdocs-bibtex/commit/0e51f17927329b85af3b0256e05ed993acaba7ce"><code>0e51f17</code></a>
    Bump pypandoc from 1.14 to 1.15</li>
    <li><a
    href="https://github.com/shyamd/mkdocs-bibtex/commit/7d52ebe63592cca5e06d8f0ef76750f708afa170"><code>7d52ebe</code></a>
    update readme</li>
    <li><a
    href="https://github.com/shyamd/mkdocs-bibtex/commit/17ffee3f33f6886bf3cf209b2e3db31dab7089eb"><code>17ffee3</code></a>
    Inline References (<a
    href="https://redirect.github.com/shyamd/mkdocs-bibtex/issues/291">#291</a>)</li>
    <li><a
    href="https://github.com/shyamd/mkdocs-bibtex/commit/26da33389b83166c18a33fa58c2a9f5818440576"><code>26da333</code></a>
    FIX: Not invalidating citation blocks with 0 citations (<a
    href="https://redirect.github.com/shyamd/mkdocs-bibtex/issues/290">#290</a>)</li>
    <li>Additional commits viewable in <a
    href="https://github.com/shyamd/mkdocs-bibtex/compare/v2.15.0...v4.2.2">compare
    view</a></li>
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docs/requirements.txt

commit 306cf35a6500b718255a953fa66304a4f628e810
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Fri Mar 7 12:34:06 2025 +1100

    Particle destructor (#927)
    
    ### Description
    Support particle destruction.
    
    Changes:
    - Define `ParticleDestructionTraits`. The user define their own particle
    destructor by specializing the `ParticleChecker` method in
    `ParticleDestructionTraits`, which return true or false to mark a
    particle for destruction. As a placeholder, `particles.param3` is used
    in particle destructor.
    - Define `ParticleDestructionImpl`, which loops over all particles at a
    level and mark particles for destruction.
    - Add a `getNumParticles` function to `PhysicsParticleDescriptor` to get
    the total number of *valid* particles of that type.
    - Add a new particle parameter `particles.verbose` to turn on printing
    particle logistics at each time step. Currently, it prints the number of
    particles of each type.
    
    The new particle destructor feature is tested in gravity_3d.cpp.
    
    Next, I'll add a `particleDestruction` method in
    `ParticleDestructionTraits`, which modifies the hydro state while
    removing a particle.
    
    ### Related issues
    None.
    
    ### 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>

src/particles/PhysicsParticles.hpp
src/particles/particle_creation.hpp
src/particles/particle_destruction.hpp
src/particles/particle_types.hpp
src/problems/Gravity3D/gravity_3d.cpp
src/simulation.hpp
tests/Gravity3D.in

commit 824c6c7e5acec8bca09706249b3f61bd46f8c88f
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Thu Mar 6 17:56:17 2025 +1100

    Allow creating multiple particle from one cell.  (#926)
    
    ### Description
    
    Previously, `particle_checker` returns a boolean, which means each cell
    creates 0 or 1 particle at a time. This PR allows creating multiple
    particles from a cell at a time.
    
    Changes:
    - `particle_checker` now returns an integer instead of a bool.
    - `particle_creator` now takes a pointer to particles and
    `num_particles`, and create `num_particles` particles at one call.
    - Updated `gravity_3d.cpp` problem to test this. Two particles are
    created from each cell at a timestep and the total number of particles
    is compared to the expect one in the end of the simulation.
    
    #### Alternatives
    
    Keep the original `createParticlesImpl` (or rename it to
    `createSingleParticleImpl`) and add a new `createMultiParticlesImpl` to
    allow creating multiple particles from a cell. Then, depending on the
    particle types, you use the proper implementation. For example,
    StellarParticle would use `createSingleParticleImpl` and
    StellarPopulationParticle would use `createSingleParticleImpl`.
    
    ### 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>

src/particles/particle_creation.hpp
src/problems/Gravity3D/gravity_3d.cpp

commit 5f60784bb29137266de4ba38bfd882c587d8b1c5
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Thu Mar 6 13:16:20 2025 +1100

    Mermaid flowchart (#924)
    
    ### Description
    
    1. Add mermaid plugin to mkdocs.
    2. Replace the old PDF flowchart with a new Mermaid flowchart. This
    change enables easy editing of the flowchart as the code evolves.
    
    ### Related issues
    Are there any GitHub issues that are fixed by this pull request? Add a
    link to them here.
    
    ### 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).
    - [ ] 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`.

.github/workflows/docs.yml
.pre-commit-config.yaml
docs/docs/flowchart-v2.jpg
docs/docs/flowchart-v2.pdf
docs/docs/flowchart.md
docs/docs/flowchart.svg
docs/mkdocs.yml
docs/requirements.txt

commit 9f89fe9d8d095f1ca17d93187cbc7d85f32d5da5
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Thu Mar 6 01:37:45 2025 +1100

    A clean fix of the FPE issue on moth  (#923)
    
    ### Description
    Clang might have changed its FPE behaviour recently and triggers an FPE
    on unused vector lanes. A clean solution is applied in this PR: add
    `-ffp-exception-behavior=strict` to `CMAKE_CXX_FLAGS` for Clang, just
    like what we did on macOS. See discussions in #921 . This reverts the
    previous change in calculation the radiation pressure and also bring
    back the SphericalCollapse test with FPE checks on moth.
    
    ### Related issues
    This PR reverts #921 .
    
    ### 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](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] 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`.

.ci/azure-pipelines-amdgpu.yml
.github/workflows/hip.yml
src/problems/SphericalCollapse/CMakeLists.txt
src/radiation/radiation_system.hpp

commit 2f1e1703ded0bef621467a6d8aa2387de8c957bb
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Wed Mar 5 16:27:06 2025 +1100

    Compile-time particle switch with Bitwise Operations (#911)
    
    ### Description
    
    This PR introduces a flexible architecture for particle creation,
    implementing a type-specific framework for handling multiple particle
    types with specialized behaviors.
    
    #### Key Features
    
    ##### Type-Safe Particle Switching
    
    - Implemented a type-safe bitwise operation system for controlling
    particle types
    - Added `ParticleSwitch` enum class with proper bitflag operations
    - Enables combining multiple particle types in a type-safe manner
    
    ```cpp
    enum class ParticleSwitch : unsigned int {
        None = 0U,           // No particles, = 0b0000
        CIC = bitflag<1>(),  // Cloud-In-Cell (gravitating) particles, = 0b0001
        Rad = bitflag<2>(),  // Radiation particles, = 0b0010
        CICRad = bitflag<3>() // Combined gravitating-radiating particles, = 0b0100
    };
    ```
    
    ##### Improved Particle Traits System
    
    - Added `Particle_Traits` template for configuring particle types per
    problem
    - Simple interface for enabling multiple particle types:
    
    ```cpp
    template <> struct Particle_Traits<BinaryOrbit> {
        static constexpr ParticleSwitch particle_switch = ParticleSwitch::CIC | ParticleSwitch::Rad;
    };
    ```
    
    - Type checking prevents common errors like using wrong enum types or
    raw integers
    
    ##### Flexible Particle Creation Framework
    
    - Introduced `ParticleCreationTraits` to solve C++ partial template
    specialization limitations
    - Each particle type can now have specialized creation behavior while
    maintaining the problem_t template
    - Modular design with separate checker and creator components per
    particle type
    
    #### Implementation Details about particle creation
    
    The architecture uses a traits-based approach with specialized
    components:
    
    1. **ParticleCreationTraits**: Template class for particle creation
    specialized for each particle type
    2. **ParticleChecker & ParticleCreator**: Problem-specific
    implementations
    3. **ParticleCreationImpl**: Common implementation logic for particle
    creation, including CPU, GPU, and MPI-related operations
    4. **PhysicsParticleDescriptor::createParticlesFromState**: Interface
    for particle creation from simulation state for a specific particle type
    5. **PhysicsParticleRegister::createParticlesFromState**: Registry of
    all particle types and their creation methods
    
    #### Usage Example
    
    To enable particle types in your problem:
    
    ```cpp
    // Enable multiple particle types in your problem
    template <> struct Particle_Traits<MyProblem> {
        static constexpr ParticleSwitch particle_switch = ParticleSwitch::CIC | ParticleSwitch::Rad;
    };
    ```
    
    To define creation routine for the particle types that support creation:
    
    ```cpp
    namespace quokka
    {
    // Specialization for CIC particles
    template <> struct ParticleCreationTraits<ParticleType::CIC> {
            // Specialized nested ParticleChecker for CIC particles
            template <typename problem_t> struct ParticleChecker {
                    amrex::Real param1 = particle_param1;
                    amrex::Real param2 = particle_param2;
    
                    AMREX_GPU_DEVICE auto operator()(amrex::Array4<const amrex::Real> const &state_arr, int i, int j, int k,
                                                     amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> const &dx, amrex::Real current_time, amrex::Real dt) const -> bool
                    {
                            // Check if we should create a particle at this location and time
                    }
            };
    
            // Specialized nested ParticleCreator for CIC particles
            template <typename problem_t> struct ParticleCreator {
                    int mass_idx;
                    int cpu_id;
                    amrex::Long pid_start;
                    amrex::Real param1 = particle_param1;
                    amrex::Real param2 = particle_param2;
    
                    AMREX_GPU_HOST_DEVICE
                    ParticleCreator(int mass_index, int processor_id, amrex::Long particle_id_start)
                        : mass_idx(mass_index), cpu_id(processor_id), pid_start(particle_id_start)
                    {
                    }
    
                    template <typename ParticleType, typename StateArray>
                    AMREX_GPU_DEVICE void operator()(ParticleType &p, StateArray const &state_arr, int i, int j, int k,
                                                     amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> const &dx,
                                                     amrex::GpuArray<amrex::Real, AMREX_SPACEDIM> const &plo, amrex::Long particle_offset) const
                    {
                            // Create a particle at the given location and time
                    }
            };
    
            // Main method to create particles - uses the helper implementation
            template <typename problem_t, typename ContainerType>
            static void createParticles(ContainerType *container, int mass_idx, amrex::MultiFab &state, int lev, amrex::Real current_time, amrex::Real dt)
            {
                    // Use the common implementation with our checker and creator types
                    ParticleCreationImpl::createParticlesImpl<problem_t, ContainerType, ParticleCreationTraits<ParticleType::CIC>::template ParticleChecker,
                                                              ParticleCreationTraits<ParticleType::CIC>::template ParticleCreator>(container, mass_idx, state, lev,
                                                                                                                                   current_time, dt);
            }
    };
    } // namespace quokka
    ```
    
    
    ### Related issues
    Closes https://github.com/quokka-astro/quokka/issues/815.
    
    ### 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.
    - [x] *(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: Ben Wibking <ben@wibking.com>

src/particles/PhysicsParticles.hpp
src/particles/particle_creation.hpp
src/particles/particle_deposition.hpp
src/particles/particle_types.hpp
src/physics_info.hpp
src/problems/BinaryOrbitCIC/binary_orbit.cpp
src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp
src/problems/Gravity3D/gravity_3d.cpp
src/problems/RadParticle/test_radparticle.cpp
src/problems/RadParticle2D/test_radparticle_2D.cpp
src/problems/SphericalCollapse/spherical_collapse.cpp
src/simulation.hpp
tests/BinaryOrbit.in
tests/Gravity3D.in
tests/RadParticles1D.in
tests/RadParticles2D.in
tests/SphericalCollapse.in

commit cae5aa7ee3c97a6574fb24a27fcfd32e83c2e2d4
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Wed Mar 5 14:11:12 2025 +1100

    Particle CFL condition (#912)
    
    ### Description
    Add particle speed to the calculation of hydro CFL condition.
    
    1. Defined a function `computeMaxParticleSpeed` in
    `PhysicsParticleRegister` to compute the maximum speed of all particles
    of all particle types that have velocity components.
    2. Defined particle CFL number `particleCflNumber_`, which can be
    specified via runtime parameter `particle_cfl`. The default value is
    0.99
    3. Run `computeMaxParticleSpeed` every timestep to compute the maximum
    particle speed. Then, `particle_dt` is calculated: `particle_dt =
    particleCflNumber_ * (dx_min / max_particle_speed)`, where
    `particleCflNumber_` is the particle CFL number and is a runtime
    parameter.
    
    ### Related issues
    Replace #833 and resolve #884 .
    
    ### 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.
    - [x] *(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: Ben Wibking <ben@wibking.com>

src/particles/PhysicsParticles.hpp
src/problems/Gravity3D/gravity_3d.cpp
src/problems/SphericalCollapse/CMakeLists.txt
src/simulation.hpp
tests/Gravity3D.in

commit 8852ff326a05748bbcaed1e408f1b06d6519eba4
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Mar 4 17:52:01 2025 -0500

    update Setonix script to use ROCm 6.3 (#922)
    
    ### Description
    This updates the Setonix configuration to use rocm/6.3.2, which avoids
    the compiler bugs that caused all the problems we saw on AMD GPUs
    before.
    
    Example build:
    ```
    source scripts/setonix-gpu.profile
    mkdir build && cd build
    cmake .. -DAMReX_SPACEDIM=3 -DAMReX_GPU_BACKEND=HIP
    make -j32 my_favorite_problem
    ```
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] 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`.

scripts/setonix-1node.submit
scripts/setonix-64nodes.submit
scripts/setonix-8nodes.submit
scripts/setonix-gpu.profile

commit 3dfa9dbda1550ebd42a6d4f8ef5abe42f5fe25ed
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Wed Mar 5 09:47:53 2025 +1100

    add safety check in ComputeEddingtonTensor to avoid FPE error (#921)
    
    ### Description
    Add safety check in ComputeEddingtonTensor to avoid FPE error:
    1. Check for large flux limiting violation: `if (fvec[ii] > 2.0) { # set
    n = 0.0 }`
    2. set `f_floor = 1e-10` and `if (f <= f_floor) { # set n = 0.0 }`
    
    ### Related issues
    Are there any GitHub issues that are fixed by this pull request? Add a
    link to them here.
    
    ### 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](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] 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`.

src/radiation/radiation_system.hpp

commit 8ae2ff73e3c77845a26064eb5c42a73b1ca7282c
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Mar 3 09:51:17 2025 -0500

    Bump mkdocs-bibtex from 4.2.1 to 4.2.2 in /docs (#919)
    
    Bumps [mkdocs-bibtex](https://github.com/shyamd/mkdocs-bibtex) from
    4.2.1 to 4.2.2.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
    href="https://github.com/shyamd/mkdocs-bibtex/releases">mkdocs-bibtex's
    releases</a>.</em></p>
    <blockquote>
    <h2>v4.2.2</h2>
    <p>Version 4.2.2</p>
    <h3>Commits</h3>
    </blockquote>
    </details>
    <details>
    <summary>Commits</summary>
    <ul>
    <li>See full diff in <a
    href="https://github.com/shyamd/mkdocs-bibtex/compare/v4.2.1...v4.2.2">compare
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    </ul>
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docs/requirements.txt

commit c955e71fa95e7bd79d345b16be9caea773ac186b
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Mar 3 03:54:54 2025 +0000

    Bump mkdocs-bibtex from 4.2.1 to 4.2.2 in /docs/docs (#918)
    
    Bumps [mkdocs-bibtex](https://github.com/shyamd/mkdocs-bibtex) from
    4.2.1 to 4.2.2.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
    href="https://github.com/shyamd/mkdocs-bibtex/releases">mkdocs-bibtex's
    releases</a>.</em></p>
    <blockquote>
    <h2>v4.2.2</h2>
    <p>Version 4.2.2</p>
    <h3>Commits</h3>
    </blockquote>
    </details>
    <details>
    <summary>Commits</summary>
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    <li>See full diff in <a
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docs/docs/requirements.txt

commit 07e15d6ce472e28583ff6bcd83317e287db7fe02
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Mar 3 03:41:10 2025 +0000

    Bump actions/cache from 4.2.1 to 4.2.2 (#917)
    
    Bumps [actions/cache](https://github.com/actions/cache) from 4.2.1 to
    4.2.2.
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.github/workflows/codeql.yml
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commit 1499d7f83825ec95e17da4910ad64a5bf3b88b4f
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sat Mar 1 10:01:45 2025 -0500

    Bump extern/amrex from `69f1ac8` to `06b4a5b` (#914)
    
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extern/amrex

commit 3032121eefcd5590d96b76061544c161f872d7c4
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sat Mar 1 10:01:22 2025 -0500

    Bump extern/Microphysics from `397d3d2` to `05b09dc` (#916)
    
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    document eos_cell.H (<a
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extern/Microphysics

commit b624bb97990ab2a435f8c072b16e07253fe3317b
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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    Bump extern/fmt from `c9267da` to `577fd3b` (#915)
    
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extern/fmt

commit 865f38d1a71030813cb1278e9cea4f52b9eaf050
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sat Mar 1 03:12:35 2025 +0000

    Bump extern/openPMD-api from `e6628c3` to `ff52a8d` (#913)
    
    Bumps [extern/openPMD-api](https://github.com/openPMD/openPMD-api) from
    `e6628c3` to `ff52a8d`.
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/ff52a8d18c29e8d7e463a966dc5a25c023ae7f3c"><code>ff52a8d</code></a>
    Random-access for variable-based encoding (i.e. use SetStepSelection for
    ADIO...</li>
    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/a4d66cc72b2771fc34756d246f32d06400344982"><code>a4d66cc</code></a>
    JSON: Selectively suppress unknown key warnings (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1700">#1700</a>)</li>
    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/d5b42ed58f1d99a9b09e6f8e275d83a6315c459b"><code>d5b42ed</code></a>
    [pre-commit.ci] pre-commit autoupdate (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1714">#1714</a>)</li>
    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/8cace7e03ece8c5e9b2c898565fa59ef83f9c9b3"><code>8cace7e</code></a>
    ADIOS2: Require v2.9 as minimum (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1711">#1711</a>)</li>
    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/df6cc717a40dff648694b6a4cef3ff32faa71990"><code>df6cc71</code></a>
    Fix source/documentation CI run (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1719">#1719</a>)</li>
    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/cb7ffe141276f463d1ad6321090b11fd644b5c91"><code>cb7ffe1</code></a>
    Remove venv Python workarounds in our CI workflows (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1717">#1717</a>)</li>
    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/d95d3a3a67db9fde2d6f41afb86b02964df8bd67"><code>d95d3a3</code></a>
    RTD: Fix GA Integration (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1718">#1718</a>)</li>
    <li>See full diff in <a
    href="https://github.com/openPMD/openPMD-api/compare/e6628c3e705891051bcf381e275d4a47cdddf618...ff52a8d18c29e8d7e463a966dc5a25c023ae7f3c">compare
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extern/openPMD-api

commit 9e3a4210042a2f3a4118da28be3da9d490ddf370
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Thu Feb 27 14:15:28 2025 +1100

    Particle creator (#896)
    
    ### Description
    
    The `createCICParticles` method in `PhysicsParticles.hpp` provides a
    framework for particle creation on the fly from fluid cells. We run
    `createCICParticles` in the end of each hydro timestep. It uses two key
    components:
    
    1. `CICParticleChecker`: A functor that determines whether a particle
    should be created in a given cell based on:
    - State-based conditions (can be customized to check fluid properties)
       - Time conditions
       - Spatial conditions (grid spacing)
    
    2. `CICParticleCreator`: A functor that handles the actual particle
    creation and initialization, including:
       - Setting particle position (e.g. cell-centered)
       - Assigning particle properties (mass, velocities)
       - Conserving mass and momentum between fluid and particles
       - Updating the fluid state after particle creation
    
    This separation of checker and creator allows for easy customization of
    both when/where particles are created and how they are initialized.
    Currently, `CICParticleChecker` is set to return false, meaning no
    particles are created. `CICParticleCreator` is left empty. In
    `gravity_3d.cpp`, I showed an example of how to override the default
    checker and creator.
    
    This implementation is validated by the `gravity_3d` test on CPU, GPU,
    and MPI, which demonstrates:
    1. correct orbital dynamics of the CIC particles under self-gravity.
    2. gravitational interaction between fluid, CIC particles, and
    CICRadParticles.
    3. energy conservation of radiation energy in the presence of
    RadParticles.
    4. creation of CICParticles from fluid cells on the fly.
    
    #### Future
    
    1. Particle creation with access to neighbor cells can be supported by
    adding ghost cells to the multi-fab.
    2. Particle-fluid interaction can be implemented similarly with very
    little extra work.
    3. More work needs to be done to add non-gravitational particle-particle
    interaction. `NeighborParticleContainer` does not have a AMR
    implementation, as far as I know.
    
    ### Related issues
    None.
    
    ### 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>

src/particles/PhysicsParticles.hpp
src/physics_info.hpp
src/problems/Gravity3D/gravity_3d.cpp
src/simulation.hpp
tests/Gravity3D.in

commit 08fc5f7ad9f7cf992d701ba94f7ed1e4c2127493
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Thu Feb 27 12:42:00 2025 +1100

    Clean up operatorSplitSourceTerms() (#909)
    
    ### Description
    After implementing RadParticles, `operatorSplitSourceTerms` becomes a
    single call to `AddSourceTermsSingleGroup`, so I removed it to simplify
    the code.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] *(For quokka-astro org members)* I have manually triggered the GPU
    tests with the magic comment `/azp run`.

src/QuokkaSimulation.hpp

commit aad7bf871e8456679b5a6a89bd9066a443f5d288
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Feb 26 19:51:08 2025 -0500

    Add CLAUDE.md with build instructions and coding guidelines (#910)
    
    ## Summary
    - Add CLAUDE.md file to document build/test commands and code style
    guidelines
    - Intended for use with agentic coding tools ([Claude
    Code](https://docs.anthropic.com/en/docs/agents-and-tools/claude-code/overview),
    etc.)
    - Summarizes key project conventions in a compact reference format
    
    ## Test plan
    - N/A - Documentation only change
    
    🤖 Generated with Claude Code

CLAUDE.md

commit 126dcb56da43a1f470139ff28ef1da1ada36bc99
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Feb 24 04:05:53 2025 +0000

    Bump ossf/scorecard-action from 2.4.0 to 2.4.1 (#907)
    
    Bumps [ossf/scorecard-action](https://github.com/ossf/scorecard-action)
    from 2.4.0 to 2.4.1.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
    href="https://github.com/ossf/scorecard-action/releases">ossf/scorecard-action's
    releases</a>.</em></p>
    <blockquote>
    <h2>v2.4.1</h2>
    <h2>What's Changed</h2>
    <ul>
    <li>This update bumps the Scorecard version to the v5.1.1 release. For a
    complete list of changes, please refer to the <a
    href="https://github.com/ossf/scorecard/releases/tag/v5.1.0">v5.1.0</a>
    and <a
    href="https://github.com/ossf/scorecard/releases/tag/v5.1.1">v5.1.1</a>
    release notes.</li>
    <li>Publishing results now uses half the API quota as before. The exact
    savings depends on the repository in question.
    <ul>
    <li>use Scorecard library entrypoint instead of Cobra hooking by <a
    href="https://github.com/spencerschrock"><code>@​spencerschrock</code></a>
    in <a
    href="https://redirect.github.com/ossf/scorecard-action/pull/1423">ossf/scorecard-action#1423</a></li>
    </ul>
    </li>
    <li>Some errors were made into annotations to make them more visible
    <ul>
    <li>Make default branch error more prominent by <a
    href="https://github.com/jsoref"><code>@​jsoref</code></a> in <a
    href="https://redirect.github.com/ossf/scorecard-action/pull/1459">ossf/scorecard-action#1459</a></li>
    </ul>
    </li>
    <li>There is now an optional <code>file_mode</code> input which controls
    how repository files are fetched from GitHub. The default is
    <code>archive</code>, but <code>git</code> produces the most accurate
    results for repositories with <code>.gitattributes</code> files at the
    cost of analysis speed.
    <ul>
    <li>add input for specifying <code>--file-mode</code> by <a
    href="https://github.com/spencerschrock"><code>@​spencerschrock</code></a>
    in <a
    href="https://redirect.github.com/ossf/scorecard-action/pull/1509">ossf/scorecard-action#1509</a></li>
    </ul>
    </li>
    <li>The underlying container for the action is now <a
    href="https://github.com/ossf/scorecard-action/pkgs/container/scorecard-action">hosted
    on GitHub Container Registry</a>. There should be no functional changes.
    <ul>
    <li>:seedling: publish docker images to GitHub Container Registry by <a
    href="https://github.com/spencerschrock"><code>@​spencerschrock</code></a>
    in <a
    href="https://redirect.github.com/ossf/scorecard-action/pull/1453">ossf/scorecard-action#1453</a></li>
    </ul>
    </li>
    </ul>
    <h3>Docs</h3>
    <ul>
    <li>Installation docs update by <a
    href="https://github.com/JeremiahAHoward"><code>@​JeremiahAHoward</code></a>
    in <a
    href="https://redirect.github.com/ossf/scorecard-action/pull/1416">ossf/scorecard-action#1416</a></li>
    </ul>
    <h2>New Contributors</h2>
    <ul>
    <li><a
    href="https://github.com/JeremiahAHoward"><code>@​JeremiahAHoward</code></a>
    made their first contribution in <a
    href="https://redirect.github.com/ossf/scorecard-action/pull/1416">ossf/scorecard-action#1416</a></li>
    <li><a href="https://github.com/jsoref"><code>@​jsoref</code></a> made
    their first contribution in <a
    href="https://redirect.github.com/ossf/scorecard-action/pull/1459">ossf/scorecard-action#1459</a>
    <strong>Full Changelog</strong>: <a
    href="https://github.com/ossf/scorecard-action/compare/v2.4.0...v2.4.1">https://github.com/ossf/scorecard-action/compare/v2.4.0...v2.4.1</a></li>
    </ul>
    </blockquote>
    </details>
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/ossf/scorecard-action/commit/f49aabe0b5af0936a0987cfb85d86b75731b0186"><code>f49aabe</code></a>
    bump docker to ghcr v2.4.1 (<a
    href="https://redirect.github.com/ossf/scorecard-action/issues/1478">#1478</a>)</li>
    <li><a
    href="https://github.com/ossf/scorecard-action/commit/30a595ba8670f7bd5e2d33119dfeeb6ab2f64991"><code>30a595b</code></a>
    :seedling: Bump github.com/sigstore/cosign/v2 from 2.4.2 to 2.4.3 (<a
    href="https://redirect.github.com/ossf/scorecard-action/issues/1515">#1515</a>)</li>
    <li><a
    href="https://github.com/ossf/scorecard-action/commit/69ae593b7addfd5241b46c43c7ed6abbd7203d55"><code>69ae593</code></a>
    omit vcs info from build (<a
    href="https://redirect.github.com/ossf/scorecard-action/issues/1514">#1514</a>)</li>
    <li><a
    href="https://github.com/ossf/scorecard-action/commit/6a62a1cbf28018bd61197d0c2852b94b046fe1a4"><code>6a62a1c</code></a>
    add input for specifying <code>--file-mode</code> (<a
    href="https://redirect.github.com/ossf/scorecard-action/issues/1509">#1509</a>)</li>
    <li><a
    href="https://github.com/ossf/scorecard-action/commit/2722664778d49161a69d42f8e82e15ed38fea8d1"><code>2722664</code></a>
    :seedling: Bump the github-actions group with 2 updates (<a
    href="https://redirect.github.com/ossf/scorecard-action/issues/1510">#1510</a>)</li>
    <li><a
    href="https://github.com/ossf/scorecard-action/commit/ae0ef3171a81cb48c3fdaaf34cba323d0c51fefb"><code>ae0ef31</code></a>
    :seedling: Bump github.com/spf13/cobra from 1.8.1 to 1.9.1 (<a
    href="https://redirect.github.com/ossf/scorecard-action/issues/1512">#1512</a>)</li>
    <li><a
    href="https://github.com/ossf/scorecard-action/commit/3676bbc29082184ac34a84d1573c0419f81c4a68"><code>3676bbc</code></a>
    :seedling: Bump golang from 1.23.6 to 1.24.0 in the docker-images group
    (<a
    href="https://redirect.github.com/ossf/scorecard-action/issues/1513">#1513</a>)</li>
    <li><a
    href="https://github.com/ossf/scorecard-action/commit/ae7548a0ff1b94dda3a89eeda8f59c031874f035"><code>ae7548a</code></a>
    Limit codeQL push trigger to main branch (<a
    href="https://redirect.github.com/ossf/scorecard-action/issues/1507">#1507</a>)</li>
    <li><a
    href="https://github.com/ossf/scorecard-action/commit/9165624e75f0c73d13a9db2d4d920bcc5fc3a801"><code>9165624</code></a>
    upgrade scorecard to v5.1.0 (<a
    href="https://redirect.github.com/ossf/scorecard-action/issues/1508">#1508</a>)</li>
    <li><a
    href="https://github.com/ossf/scorecard-action/commit/620fd28d6b2ba01c1d70cf63dfb4bdf868e19d6f"><code>620fd28</code></a>
    :seedling: Bump the github-actions group with 2 updates (<a
    href="https://redirect.github.com/ossf/scorecard-action/issues/1505">#1505</a>)</li>
    <li>Additional commits viewable in <a
    href="https://github.com/ossf/scorecard-action/compare/62b2cac7ed8198b15735ed49ab1e5cf35480ba46...f49aabe0b5af0936a0987cfb85d86b75731b0186">compare
    view</a></li>
    </ul>
    </details>
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.github/workflows/scorecard.yml

commit c58c8d0869f5979f48b117b9ba453dce0cbe5119
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Feb 24 03:53:40 2025 +0000

    Bump actions/upload-artifact from 4.6.0 to 4.6.1 (#906)
    
    Bumps
    [actions/upload-artifact](https://github.com/actions/upload-artifact)
    from 4.6.0 to 4.6.1.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
    href="https://github.com/actions/upload-artifact/releases">actions/upload-artifact's
    releases</a>.</em></p>
    <blockquote>
    <h2>v4.6.1</h2>
    <h2>What's Changed</h2>
    <ul>
    <li>Update to use artifact 2.2.2 package by <a
    href="https://github.com/yacaovsnc"><code>@​yacaovsnc</code></a> in <a
    href="https://redirect.github.com/actions/upload-artifact/pull/673">actions/upload-artifact#673</a></li>
    </ul>
    <p><strong>Full Changelog</strong>: <a
    href="https://github.com/actions/upload-artifact/compare/v4...v4.6.1">https://github.com/actions/upload-artifact/compare/v4...v4.6.1</a></p>
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    <summary>Commits</summary>
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    <li><a
    href="https://github.com/actions/upload-artifact/commit/4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1"><code>4cec3d8</code></a>
    Merge pull request <a
    href="https://redirect.github.com/actions/upload-artifact/issues/673">#673</a>
    from actions/yacaovsnc/artifact_2.2.2</li>
    <li><a
    href="https://github.com/actions/upload-artifact/commit/e9fad966ccdffceea5de0445882c9455934bcf8e"><code>e9fad96</code></a>
    license cache update for artifact</li>
    <li><a
    href="https://github.com/actions/upload-artifact/commit/b26fd06e9da88a61ada55f23d7863325b1f115d3"><code>b26fd06</code></a>
    Update to use artifact 2.2.2 package</li>
    <li>See full diff in <a
    href="https://github.com/actions/upload-artifact/compare/v4.6.0...4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1">compare
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.github/workflows/checkpoint-restart.yml
.github/workflows/cmake-macos.yml
.github/workflows/cmake.yml
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.github/workflows/docs.yml
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commit ce9f7a00c8f179ff86c8016703353a93a6502090
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Feb 24 03:52:28 2025 +0000

    Bump github/codeql-action from 3.28.9 to 3.28.10 (#904)
    
    Bumps [github/codeql-action](https://github.com/github/codeql-action)
    from 3.28.9 to 3.28.10.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
    href="https://github.com/github/codeql-action/releases">github/codeql-action's
    releases</a>.</em></p>
    <blockquote>
    <h2>v3.28.10</h2>
    <h1>CodeQL Action Changelog</h1>
    <p>See the <a
    href="https://github.com/github/codeql-action/releases">releases
    page</a> for the relevant changes to the CodeQL CLI and language
    packs.</p>
    <h2>3.28.10 - 21 Feb 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.20.5. <a
    href="https://redirect.github.com/github/codeql-action/pull/2772">#2772</a></li>
    <li>Address an issue where the CodeQL Bundle would occasionally fail to
    decompress on macOS. <a
    href="https://redirect.github.com/github/codeql-action/pull/2768">#2768</a></li>
    </ul>
    <p>See the full <a
    href="https://github.com/github/codeql-action/blob/v3.28.10/CHANGELOG.md">CHANGELOG.md</a>
    for more information.</p>
    </blockquote>
    </details>
    <details>
    <summary>Changelog</summary>
    <p><em>Sourced from <a
    href="https://github.com/github/codeql-action/blob/main/CHANGELOG.md">github/codeql-action's
    changelog</a>.</em></p>
    <blockquote>
    <h1>CodeQL Action Changelog</h1>
    <p>See the <a
    href="https://github.com/github/codeql-action/releases">releases
    page</a> for the relevant changes to the CodeQL CLI and language
    packs.</p>
    <h2>[UNRELEASED]</h2>
    <p>No user facing changes.</p>
    <h2>3.28.10 - 21 Feb 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.20.5. <a
    href="https://redirect.github.com/github/codeql-action/pull/2772">#2772</a></li>
    <li>Address an issue where the CodeQL Bundle would occasionally fail to
    decompress on macOS. <a
    href="https://redirect.github.com/github/codeql-action/pull/2768">#2768</a></li>
    </ul>
    <h2>3.28.9 - 07 Feb 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.20.4. <a
    href="https://redirect.github.com/github/codeql-action/pull/2753">#2753</a></li>
    </ul>
    <h2>3.28.8 - 29 Jan 2025</h2>
    <ul>
    <li>Enable support for Kotlin 2.1.10 when running with CodeQL CLI
    v2.20.3. <a
    href="https://redirect.github.com/github/codeql-action/pull/2744">#2744</a></li>
    </ul>
    <h2>3.28.7 - 29 Jan 2025</h2>
    <p>No user facing changes.</p>
    <h2>3.28.6 - 27 Jan 2025</h2>
    <ul>
    <li>Re-enable debug artifact upload for CLI versions 2.20.3 or greater.
    <a
    href="https://redirect.github.com/github/codeql-action/pull/2726">#2726</a></li>
    </ul>
    <h2>3.28.5 - 24 Jan 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.20.3. <a
    href="https://redirect.github.com/github/codeql-action/pull/2717">#2717</a></li>
    </ul>
    <h2>3.28.4 - 23 Jan 2025</h2>
    <p>No user facing changes.</p>
    <h2>3.28.3 - 22 Jan 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.20.2. <a
    href="https://redirect.github.com/github/codeql-action/pull/2707">#2707</a></li>
    <li>Fix an issue downloading the CodeQL Bundle from a GitHub Enterprise
    Server instance which occurred when the CodeQL Bundle had been synced to
    the instance using the <a
    href="https://github.com/github/codeql-action-sync-tool">CodeQL Action
    sync tool</a> and the Actions runner did not have Zstandard installed.
    <a
    href="https://redirect.github.com/github/codeql-action/pull/2710">#2710</a></li>
    <li>Uploading debug artifacts for CodeQL analysis is temporarily
    disabled. <a
    href="https://redirect.github.com/github/codeql-action/pull/2712">#2712</a></li>
    </ul>
    <h2>3.28.2 - 21 Jan 2025</h2>
    <p>No user facing changes.</p>
    <h2>3.28.1 - 10 Jan 2025</h2>
    <ul>
    <li>CodeQL Action v2 is now deprecated, and is no longer updated or
    supported. For better performance, improved security, and new features,
    upgrade to v3. For more information, see <a
    href="https://github.blog/changelog/2025-01-10-code-scanning-codeql-action-v2-is-now-deprecated/">this
    changelog post</a>. <a
    href="https://redirect.github.com/github/codeql-action/pull/2677">#2677</a></li>
    </ul>
    <!-- raw HTML omitted -->
    </blockquote>
    <p>... (truncated)</p>
    </details>
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/github/codeql-action/commit/b56ba49b26e50535fa1e7f7db0f4f7b4bf65d80d"><code>b56ba49</code></a>
    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2778">#2778</a>
    from github/update-v3.28.10-9856c48b1</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/60c9c77c33f2cd66390a3778d54de88b735b2526"><code>60c9c77</code></a>
    Update changelog for v3.28.10</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/9856c48b1a54789454314b4c32ef2354fe213208"><code>9856c48</code></a>
    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2773">#2773</a>
    from github/redsun82/rust</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/9572e09da430b4c71f7488e4195b4ca6ce1c6ef0"><code>9572e09</code></a>
    Rust: fix log string</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/1a529366ac3620317d953e2d4018eafa7459cb1c"><code>1a52936</code></a>
    Rust: special case default setup</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/cf7e90952bcceaebd4a548c2809ea6a5d461a1bc"><code>cf7e909</code></a>
    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2772">#2772</a>
    from github/update-bundle/codeql-bundle-v2.20.5</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/b7006aab6d38638d18e38a27c18f67138529c2f8"><code>b7006aa</code></a>
    Merge branch 'main' into update-bundle/codeql-bundle-v2.20.5</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/cfedae723eaced5e13052b529375e7b00d49a9cd"><code>cfedae7</code></a>
    Rust: throw configuration errors if requested and not correctly
    enabled</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/3971ed2a74ede0669fa7f4f5af4292030280dbfd"><code>3971ed2</code></a>
    Merge branch 'main' into redsun82/rust</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/d38c6e60dfb0232f85e388dd416559ed07da5f3a"><code>d38c6e6</code></a>
    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2775">#2775</a>
    from github/angelapwen/bump-octokit</li>
    <li>Additional commits viewable in <a
    href="https://github.com/github/codeql-action/compare/9e8d0789d4a0fa9ceb6b1738f7e269594bdd67f0...b56ba49b26e50535fa1e7f7db0f4f7b4bf65d80d">compare
    view</a></li>
    </ul>
    </details>
    <br />
    
    
    [![Dependabot compatibility
    score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=github/codeql-action&package-manager=github_actions&previous-version=3.28.9&new-version=3.28.10)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
    
    Dependabot will resolve any conflicts with this PR as long as you don't
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commit 3e7f16c2719fdb3afc113e31a485e964b4ffabac
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Feb 24 03:51:26 2025 +0000

    Bump actions/cache from 4.2.0 to 4.2.1 (#905)
    
    Bumps [actions/cache](https://github.com/actions/cache) from 4.2.0 to
    4.2.1.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
    href="https://github.com/actions/cache/releases">actions/cache's
    releases</a>.</em></p>
    <blockquote>
    <h2>v4.2.1</h2>
    <h2>What's Changed</h2>
    <blockquote>
    <p>[!IMPORTANT]
    As a reminder, there were important backend changes to release v4.2.0,
    see <a href="https://github.com/actions/cache/releases/tag/v4.2.0">those
    release notes</a> and <a
    href="https://github.com/actions/cache/discussions/1510">the
    announcement</a> for more details.</p>
    </blockquote>
    <ul>
    <li>docs: GitHub is spelled incorrectly in caching-strategies.md by <a
    href="https://github.com/janco-absa"><code>@​janco-absa</code></a> in <a
    href="https://redirect.github.com/actions/cache/pull/1526">actions/cache#1526</a></li>
    <li>docs: Make the &quot;always save prime numbers&quot; example more
    clear by <a href="https://github.com/Tobbe"><code>@​Tobbe</code></a> in
    <a
    href="https://redirect.github.com/actions/cache/pull/1525">actions/cache#1525</a></li>
    <li>Update force deletion docs due a recent deprecation by <a
    href="https://github.com/sebbalex"><code>@​sebbalex</code></a> in <a
    href="https://redirect.github.com/actions/cache/pull/1500">actions/cache#1500</a></li>
    <li>Bump <code>@​actions/cache</code> to v4.0.1 by <a
    href="https://github.com/robherley"><code>@​robherley</code></a> in <a
    href="https://redirect.github.com/actions/cache/pull/1554">actions/cache#1554</a></li>
    </ul>
    <h2>New Contributors</h2>
    <ul>
    <li><a
    href="https://github.com/janco-absa"><code>@​janco-absa</code></a> made
    their first contribution in <a
    href="https://redirect.github.com/actions/cache/pull/1526">actions/cache#1526</a></li>
    <li><a href="https://github.com/Tobbe"><code>@​Tobbe</code></a> made
    their first contribution in <a
    href="https://redirect.github.com/actions/cache/pull/1525">actions/cache#1525</a></li>
    <li><a href="https://github.com/sebbalex"><code>@​sebbalex</code></a>
    made their first contribution in <a
    href="https://redirect.github.com/actions/cache/pull/1500">actions/cache#1500</a></li>
    </ul>
    <p><strong>Full Changelog</strong>: <a
    href="https://github.com/actions/cache/compare/v4.2.0...v4.2.1">https://github.com/actions/cache/compare/v4.2.0...v4.2.1</a></p>
    </blockquote>
    </details>
    <details>
    <summary>Changelog</summary>
    <p><em>Sourced from <a
    href="https://github.com/actions/cache/blob/main/RELEASES.md">actions/cache's
    changelog</a>.</em></p>
    <blockquote>
    <h1>Releases</h1>
    <h3>4.2.1</h3>
    <ul>
    <li>Bump <code>@actions/cache</code> to v4.0.1</li>
    </ul>
    <h3>4.2.0</h3>
    <p>TLDR; The cache backend service has been rewritten from the ground up
    for improved performance and reliability. <a
    href="https://github.com/actions/cache">actions/cache</a> now integrates
    with the new cache service (v2) APIs.</p>
    <p>The new service will gradually roll out as of <strong>February 1st,
    2025</strong>. The legacy service will also be sunset on the same date.
    Changes in these release are <strong>fully backward
    compatible</strong>.</p>
    <p><strong>We are deprecating some versions of this action</strong>. We
    recommend upgrading to version <code>v4</code> or <code>v3</code> as
    soon as possible before <strong>February 1st, 2025.</strong> (Upgrade
    instructions below).</p>
    <p>If you are using pinned SHAs, please use the SHAs of versions
    <code>v4.2.0</code> or <code>v3.4.0</code></p>
    <p>If you do not upgrade, all workflow runs using any of the deprecated
    <a href="https://github.com/actions/cache">actions/cache</a> will
    fail.</p>
    <p>Upgrading to the recommended versions will not break your
    workflows.</p>
    <h3>4.1.2</h3>
    <ul>
    <li>Add GitHub Enterprise Cloud instances hostname filters to inform API
    endpoint choices - <a
    href="https://redirect.github.com/actions/cache/pull/1474">#1474</a></li>
    <li>Security fix: Bump braces from 3.0.2 to 3.0.3 - <a
    href="https://redirect.github.com/actions/cache/pull/1475">#1475</a></li>
    </ul>
    <h3>4.1.1</h3>
    <ul>
    <li>Restore original behavior of <code>cache-hit</code> output - <a
    href="https://redirect.github.com/actions/cache/pull/1467">#1467</a></li>
    </ul>
    <h3>4.1.0</h3>
    <ul>
    <li>Ensure <code>cache-hit</code> output is set when a cache is missed -
    <a
    href="https://redirect.github.com/actions/cache/pull/1404">#1404</a></li>
    <li>Deprecate <code>save-always</code> input - <a
    href="https://redirect.github.com/actions/cache/pull/1452">#1452</a></li>
    </ul>
    <h3>4.0.2</h3>
    <ul>
    <li>Fixed restore <code>fail-on-cache-miss</code> not working.</li>
    </ul>
    <h3>4.0.1</h3>
    <ul>
    <li>Updated <code>isGhes</code> check</li>
    </ul>
    <h3>4.0.0</h3>
    <ul>
    <li>Updated minimum runner version support from node 12 -&gt; node
    20</li>
    </ul>
    <h3>3.4.0</h3>
    <ul>
    <li>Integrated with the new cache service (v2) APIs</li>
    </ul>
    <!-- raw HTML omitted -->
    </blockquote>
    <p>... (truncated)</p>
    </details>
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/actions/cache/commit/0c907a75c2c80ebcb7f088228285e798b750cf8f"><code>0c907a7</code></a>
    Merge pull request <a
    href="https://redirect.github.com/actions/cache/issues/1554">#1554</a>
    from actions/robherley/v4.2.1</li>
    <li><a
    href="https://github.com/actions/cache/commit/710893c2369beb60748049b671f18c43a3656fce"><code>710893c</code></a>
    bump <code>@​actions/cache</code> to v4.0.1</li>
    <li><a
    href="https://github.com/actions/cache/commit/9fa7e61ec7e1f44ac75218e7aaea81da8856fd11"><code>9fa7e61</code></a>
    Update force deletion docs due a recent deprecation (<a
    href="https://redirect.github.com/actions/cache/issues/1500">#1500</a>)</li>
    <li><a
    href="https://github.com/actions/cache/commit/36f1e144e1c8edb0a652766b484448563d8baf46"><code>36f1e14</code></a>
    docs: Make the &quot;always save prime numbers&quot; example more clear
    (<a
    href="https://redirect.github.com/actions/cache/issues/1525">#1525</a>)</li>
    <li><a
    href="https://github.com/actions/cache/commit/53aa38c736a561b9c17b62df3fe885a17b78ee6d"><code>53aa38c</code></a>
    Correct GitHub Spelling in caching-strategies.md (<a
    href="https://redirect.github.com/actions/cache/issues/1526">#1526</a>)</li>
    <li>See full diff in <a
    href="https://github.com/actions/cache/compare/1bd1e32a3bdc45362d1e726936510720a7c30a57...0c907a75c2c80ebcb7f088228285e798b750cf8f">compare
    view</a></li>
    </ul>
    </details>
    <br />
    
    
    [![Dependabot compatibility
    score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=actions/cache&package-manager=github_actions&previous-version=4.2.0&new-version=4.2.1)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
    
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.github/workflows/codeql.yml
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commit b3f357df28e2c016a8f50dbc194844f18ab93289
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Sun Feb 23 12:19:01 2025 +1100

    Fix RadhydroShell failure: SetRadEnergySource should return erg.cm^-3.s^-1 (#901)
    
    ### Description
    This should fix the RadhydroShell-GPU regression test failure.
    
    After PR #891, the radiation source term (SetRadEnergySource) should
    return radiation energy density rate (erg.cm^-3.s^-1). The `1/c` from
    the original definition is removed.
    
    ### Related issues
    #898 is no longer required.
    
    ### 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).
    - [ ] 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>

src/problems/RadParticle/test_radparticle.cpp
src/problems/RadSuOlson/test_radiation_SuOlson.cpp
src/problems/RadhydroShell/test_radhydro_shell.cpp

commit adbf913a7dd361bbf33522fdfe66b6be16f845a7
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Fri Feb 21 15:21:40 2025 +1100

    Extensible particle architecture based on templated polymorphism (#891)
    
    ### Description
    
    This PR introduces a flexible and extensible particle architecture that
    supports multiple particle types with different physical properties.
    
    #### Architecture Components
    
    ##### 1. Base Classes and Interfaces
    
    - `PhysicsParticleDescriptorBase`: Abstract base class defining the
    interface for any given particle type
    - `PhysicsParticleDescriptor<ContainerType>`: Template class
    implementing the interface for specific particle containers
    - `PhysicsParticleRegister<problem_t>`: Registry managing all particle
    container types in a simulation and their corresponding operations
    
    ##### 2. Particle Types
    
    Each particle type has predefined properties and data components (with
    predefined indices):
    
    - `CICParticleDataIdx`: Massive particles that interact through gravity.
    Components:
      - `mass`: Particle mass in simulation units
      - `vx`, `vy`, `vz`: Velocity components in each dimension
    
    - `RadParticleDataIdx`: Massless particles that emit radiation.
    Components:
      - `birth_time`: Time when the particle starts emitting radiation
      - `death_time`: Time when the particle stops emitting radiation
    - `luminosity[nGroups]`: Array of luminosity values for each radiation
    group
    
    - `CICRadParticleDataIdx`: massive particles that also emit radiation.
    Components:
      - `mass`: Particle mass in simulation units
      - `vx`, `vy`, `vz`: Velocity components in each dimension
      - `birth_time`: Time when the particle starts emitting radiation
      - `death_time`: Time when the particle stops emitting radiation
    - `luminosity[nGroups]`: Array of luminosity values for each radiation
    group
    
    #### How to Use
    
    ##### 1. Enable Particle Types
    
    In your problem's input file, enable the desired particle types:
    
    ```
    do_cic_particles = 1        # Enable gravitational particles
    do_rad_particles = 1        # Enable radiating particles
    do_cic_rad_particles = 1    # Enable combined particles
    ```
    
    ##### 2. Initialize Particles
    
    For each particle type you want to use, implement the corresponding
    initialization function in your problem class. In this implementation,
    particles are created only at the beginning of the simulation. They
    can't be created or destroyed during the simulation (although their
    radiation can be turned off by setting `death_time`)
    
    ```cpp
    template <> void QuokkaSimulation<ParticleProblem>::createInitialCICRadParticles()
    {
            // read particles from ASCII file
            const int nreal_extra = 6 + nGroups_; // mass vx vy vz birth_time death_time lum1
            CICRadParticles->SetVerbose(1);
            CICRadParticles->InitFromAsciiFile("GravRadParticles3D.txt", nreal_extra, nullptr);
    }
    ```
    
    ##### 3. Access particle data in the end of the simulation
    
    Use the particle register to access particle data:
    
    ```cpp
    // Get particle positions
    auto positions = sim.particleRegister_.getParticleDescriptor("CIC_particles")->getParticlePositions(lev=0);
    ```
    
    #### For developers
    
    ##### adding a new particle type
    
    To add a new particle type:
    
    1. Define the particle data layout in `PhysicsParticles.hpp`:
    
    ```cpp
    // Indices for the new particle type
    enum NewParticleDataIdx {
        NewParticleProperty1Idx = 0,
        NewParticleProperty2Idx,
        // ... additional properties
    };
    // Number of real components for the new particle type
    template <typename problem_t>
    constexpr int NewParticleRealComps = N; // N = number of components
    ```
    
    2. Create the container type:
    
    ```cpp
    template <typename problem_t>
    using NewParticleContainer = amrex::AmrParticleContainer<NewParticleRealComps<problem_t>>;
    ```
    
    3. Add container member to `AMRSimulation` class:
    
    ```cpp
        public:
    int do_new_particles = 0;
    virtual void createInitialNewParticles() = 0;
        protected:
    std::unique_ptr<NewParticleContainer<problem_t>> NewParticles;
    ```
    
    4. Add initialization flag to `AMRSimulation` constructor:
    
    ```cpp
    pp.query("do_new_particles", do_new_particles);
    ```
    
    5. Implement initialization in `InitPhyParticles()`:
    
    ```cpp
    if (do_new_particles != 0) {
        NewParticles = std::make_unique<NewParticleContainer<problem_t>>(this);
        particleRegister_.registerParticleType("New_particles", mass_idx, lum_idx, birth_time_idx, hydro_interact, NewParticles.get());
        createInitialNewParticles();
    }
    ```
    
    6. Implement initialization in `ReadCheckpointFile()`:
    
    ```cpp
    if (do_new_particles != 0) {
        NewParticles = std::make_unique<NewParticleContainer<problem_t>>(this);
        particleRegister_.registerParticleType("New_particles", mass_idx, lum_idx, birth_time_idx, hydro_interact, NewParticles.get());
        NewParticles->Restart(restart_chkfile, "New_particles");
    }
    ```
    
    7. Override `createInitialNewParticles` in `QuokkaSimulation` class:
    
    ```cpp
    void createInitialNewParticles() override;
    ```
    
    8. Implement an empty `createInitialNewParticles()` in
    `QuokkaSimulation.hpp`:
    
    ```cpp
    template <typename problem_t> void QuokkaSimulation<problem_t>::createInitialNewParticles()
    {
            // default empty implementation
            // user should implement using problem-specific template specialization
            // note: an implementation is only required if New_particles are used
    }
    ```
    
    #### Testing
    
    Includes comprehensive tests in `test_grav_rad_particle_3D.cpp`.
    
    
    
    ### Related issues
    None.
    
    ### 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.
    - [x] *(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>

.github/workflows/warnings.yml
src/.clang-tidy
src/QuokkaSimulation.hpp
src/linear_advection/AdvectionSimulation.hpp
src/particles/CICParticles.hpp
src/particles/PhysicsParticles.hpp
src/problems/BinaryOrbitCIC/binary_orbit.cpp
src/problems/CMakeLists.txt
src/problems/GravRadParticle3D/CMakeLists.txt
src/problems/GravRadParticle3D/test_grav_rad_particle_3D.cpp
src/problems/GravRadParticle3D/test_grav_rad_particle_3D.hpp
src/problems/Gravity3D/CMakeLists.txt
src/problems/Gravity3D/gravity_3d.cpp
src/problems/Gravity3D/gravity_3d.hpp
src/problems/HydroBlast3D/test_hydro3d_blast.cpp
src/problems/RadParticle/CMakeLists.txt
src/problems/RadParticle/test_radparticle.cpp
src/problems/RadParticle/test_radparticle.hpp
src/problems/RadParticle2D/CMakeLists.txt
src/problems/RadParticle2D/test_radparticle_2D.cpp
src/problems/RadParticle2D/test_radparticle_2D.hpp
src/problems/RadhydroShell/test_radhydro_shell.cpp
src/problems/SphericalCollapse/spherical_collapse.cpp
src/radiation/source_terms_multi_group.hpp
src/radiation/source_terms_single_group.hpp
src/simulation.hpp
tests/GravRadParticle3D.in
tests/GravRadParticles3D.txt
tests/GravRadParticles3D_cic_only.txt
tests/GravRadParticles3D_rad_only.txt
tests/Gravity3D.in
tests/Gravity3D.txt
tests/RadParticles1D.in
tests/RadParticles1D.txt
tests/RadParticles2D.in
tests/RadParticles2D.txt

commit 229f561b30ced2f6f0fe4dab0f7fc3a421482622
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Feb 17 11:52:38 2025 -0500

    Bump mkdocs-bibtex from 4.1.0 to 4.2.1 in /docs/docs (#893)
    
    Bumps [mkdocs-bibtex](https://github.com/shyamd/mkdocs-bibtex) from
    4.1.0 to 4.2.1.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
    href="https://github.com/shyamd/mkdocs-bibtex/releases">mkdocs-bibtex's
    releases</a>.</em></p>
    <blockquote>
    <h2>v4.2.1</h2>
    <p>Version 4.2.1</p>
    <h3>Commits</h3>
    <ul>
    <li>[c39da111] fixed typo with new option (<a
    href="https://redirect.github.com/shyamd/mkdocs-bibtex/issues/300">#300</a>)</li>
    <li>[8e562dcf] update README</li>
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    <h2>v4.2.0</h2>
    <p>Version 4.2.0</p>
    <h3>Commits</h3>
    <ul>
    <li>[c0bb2bba] Add option to disable inline citations all together (<a
    href="https://redirect.github.com/shyamd/mkdocs-bibtex/issues/298">#298</a>)</li>
    </ul>
    <h2>v4.1.4</h2>
    <p>Version 4.1.4</p>
    <h3>Commits</h3>
    <h2>v4.1.3</h2>
    <p>Version 4.1.3</p>
    <h3>Commits</h3>
    <ul>
    <li>[d4866d4a] only process new blocks (<a
    href="https://redirect.github.com/shyamd/mkdocs-bibtex/issues/297">#297</a>)</li>
    </ul>
    <h2>v4.1.2</h2>
    <p>Version 4.1.2</p>
    <h3>Commits</h3>
    <h2>v4.1.1</h2>
    <p>Version 4.1.1</p>
    <h3>Commits</h3>
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    <li>[be7620bb] Fix inline citations capturing emails (<a
    href="https://redirect.github.com/shyamd/mkdocs-bibtex/issues/296">#296</a>)</li>
    <li>[91fdfd99] Bump ruff from 0.9.1 to 0.9.4</li>
    <li>[0e51f179] Bump pypandoc from 1.14 to 1.15</li>
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    Bump ruff from 0.9.1 to 0.9.4</li>
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    update readme</li>
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commit 5413c5aff0831dbb6911e7a7c547659bbf20836c
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Feb 17 11:52:31 2025 -0500

    Bump mkdocs-bibtex from 4.1.0 to 4.2.1 in /docs (#892)
    
    Bumps [mkdocs-bibtex](https://github.com/shyamd/mkdocs-bibtex) from
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docs/docs/requirements.txt
docs/requirements.txt

commit a4705288e3c315220fe9f201eef40f3a259bfc23
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Feb 12 19:01:59 2025 -0500

    Revert "Reduce regression testing disk space usage" (#890)
    
    Reverts quokka-astro/quokka#889.
    
    This exposes a bug that I introduced into the regression testing script,
    and it currently causes the nightly regression tests to fail, so we go
    back to the prior working state.

.ci/azure-pipelines-regression.yml

commit 1ac7ce2bd295340dc0ac495ff11fd8330c3ee798
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Feb 10 20:42:34 2025 -0500

    Reduce regression testing disk space usage (#889)
    
    ### Description
    This enables the option in the nightly regression tests that deletes the
    compiled binary for each test after it runs.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] 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`.

.ci/azure-pipelines-regression.yml

commit a1413ac2262766594c360351fbc7efeb48dca6b9
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Feb 10 19:17:12 2025 -0500

    add git hash to metadata output (#888)
    
    ### Description
    This adds the git commit hash to `metadata.yaml` for plotfiles and
    checkpoints. This allows users to track the exact provenance of
    simulation outputs.
    
    ### Related issues
    Closes https://github.com/quokka-astro/quokka/issues/852.
    
    ### 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).
    - [ ] 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`.

CMakeLists.txt
src/simulation.hpp

commit 3e60b70c0b1f9cabff4f816a6490c6947d48b44f
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Feb 10 04:01:43 2025 +0000

    Bump github/codeql-action from 3.28.8 to 3.28.9 (#887)
    
    Bumps [github/codeql-action](https://github.com/github/codeql-action)
    from 3.28.8 to 3.28.9.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
    href="https://github.com/github/codeql-action/releases">github/codeql-action's
    releases</a>.</em></p>
    <blockquote>
    <h2>v3.28.9</h2>
    <h1>CodeQL Action Changelog</h1>
    <p>See the <a
    href="https://github.com/github/codeql-action/releases">releases
    page</a> for the relevant changes to the CodeQL CLI and language
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    <h2>3.28.9 - 07 Feb 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.20.4. <a
    href="https://redirect.github.com/github/codeql-action/pull/2753">#2753</a></li>
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    for more information.</p>
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    href="https://github.com/github/codeql-action/blob/main/CHANGELOG.md">github/codeql-action's
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    <p>See the <a
    href="https://github.com/github/codeql-action/releases">releases
    page</a> for the relevant changes to the CodeQL CLI and language
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    <h2>[UNRELEASED]</h2>
    <p>No user facing changes.</p>
    <h2>3.28.9 - 07 Feb 2025</h2>
    <ul>
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    href="https://redirect.github.com/github/codeql-action/pull/2753">#2753</a></li>
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    <h2>3.28.8 - 29 Jan 2025</h2>
    <ul>
    <li>Enable support for Kotlin 2.1.10 when running with CodeQL CLI
    v2.20.3. <a
    href="https://redirect.github.com/github/codeql-action/pull/2744">#2744</a></li>
    </ul>
    <h2>3.28.7 - 29 Jan 2025</h2>
    <p>No user facing changes.</p>
    <h2>3.28.6 - 27 Jan 2025</h2>
    <ul>
    <li>Re-enable debug artifact upload for CLI versions 2.20.3 or greater.
    <a
    href="https://redirect.github.com/github/codeql-action/pull/2726">#2726</a></li>
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    <h2>3.28.5 - 24 Jan 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.20.3. <a
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    </ul>
    <h2>3.28.4 - 23 Jan 2025</h2>
    <p>No user facing changes.</p>
    <h2>3.28.3 - 22 Jan 2025</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.20.2. <a
    href="https://redirect.github.com/github/codeql-action/pull/2707">#2707</a></li>
    <li>Fix an issue downloading the CodeQL Bundle from a GitHub Enterprise
    Server instance which occurred when the CodeQL Bundle had been synced to
    the instance using the <a
    href="https://github.com/github/codeql-action-sync-tool">CodeQL Action
    sync tool</a> and the Actions runner did not have Zstandard installed.
    <a
    href="https://redirect.github.com/github/codeql-action/pull/2710">#2710</a></li>
    <li>Uploading debug artifacts for CodeQL analysis is temporarily
    disabled. <a
    href="https://redirect.github.com/github/codeql-action/pull/2712">#2712</a></li>
    </ul>
    <h2>3.28.2 - 21 Jan 2025</h2>
    <p>No user facing changes.</p>
    <h2>3.28.1 - 10 Jan 2025</h2>
    <ul>
    <li>CodeQL Action v2 is now deprecated, and is no longer updated or
    supported. For better performance, improved security, and new features,
    upgrade to v3. For more information, see <a
    href="https://github.blog/changelog/2025-01-10-code-scanning-codeql-action-v2-is-now-deprecated/">this
    changelog post</a>. <a
    href="https://redirect.github.com/github/codeql-action/pull/2677">#2677</a></li>
    <li>Update default CodeQL bundle version to 2.20.1. <a
    href="https://redirect.github.com/github/codeql-action/pull/2678">#2678</a></li>
    </ul>
    <h2>3.28.0 - 20 Dec 2024</h2>
    <ul>
    <li>Bump the minimum CodeQL bundle version to 2.15.5. <a
    href="https://redirect.github.com/github/codeql-action/pull/2655">#2655</a></li>
    </ul>
    <!-- raw HTML omitted -->
    </blockquote>
    <p>... (truncated)</p>
    </details>
    <details>
    <summary>Commits</summary>
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    <li><a
    href="https://github.com/github/codeql-action/commit/9e8d0789d4a0fa9ceb6b1738f7e269594bdd67f0"><code>9e8d078</code></a>
    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2757">#2757</a>
    from github/update-v3.28.9-24e1c2d33</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/43d9be670147092b305c63cf69481e8923af83b7"><code>43d9be6</code></a>
    Update changelog for v3.28.9</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/24e1c2d337459cce262cbca8d69998e56cd5eb8e"><code>24e1c2d</code></a>
    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2753">#2753</a>
    from github/update-bundle/codeql-bundle-v2.20.4</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/57a08c0c7f05d4d8251162c9658ddd7cc7782198"><code>57a08c0</code></a>
    Add changelog note</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/52189d23af4e071445f59d2e6fbbac566e49f15b"><code>52189d2</code></a>
    Update default bundle to codeql-bundle-v2.20.4</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/08bc0cf022445eacafaa248bf48da20f26b8fd40"><code>08bc0cf</code></a>
    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2751">#2751</a>
    from github/henrymercer/fix-init-post-without-config</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/cf7c6879199cf6eb2a002d3b2530ea1e4ce99610"><code>cf7c687</code></a>
    Send <code>init-post</code> status report in absence of config</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/ad42dbd32d472b6fe380130655e27089c7eac343"><code>ad42dbd</code></a>
    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2750">#2750</a>
    from github/dependabot/npm_and_yarn/npm-768bd9b555</li>
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    href="https://github.com/github/codeql-action/commit/a8f5935da08829e657dfc18d887df9385685a20a"><code>a8f5935</code></a>
    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2749">#2749</a>
    from github/dependabot/github_actions/actions-29d379...</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/9660df3fccdf5b20ab86e041325c17a2204cc1ae"><code>9660df3</code></a>
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.github/workflows/codeql.yml
.github/workflows/scorecard.yml

commit 60909c69b8efe38d1a917eec0e89242181372a84
Author: Aditi <45175933+aditivijayan@users.noreply.github.com>
Date:   Thu Feb 6 14:22:14 2025 +1100

    Quokka movies (#886)
    
    ### Description
    Adding the arxiv link to gallery.
    
    ### Related issues
    Are there any GitHub issues that are fixed by this pull request? Add a
    link to them here.
    
    ### 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](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] 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: Ben Wibking <ben@wibking.com>

docs/docs/gallery.md

commit e52a0ed5e3afc4d952c58a00558834e03e1f70e6
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Feb 3 16:32:16 2025 -0500

    Bump extern/amrex from `d4d9214` to `69f1ac8` (#881)
    
    Bumps [extern/amrex](https://github.com/AMReX-Codes/amrex) from
    `d4d9214` to `69f1ac8`.
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/69f1ac884c6aba4d9881260819ade3bb25ed8aad"><code>69f1ac8</code></a>
    SpMatrix: Add constructor for CSR format (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4316">#4316</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/12d0882ab98dff922edd804704207daf56feb86a"><code>12d0882</code></a>
    Modify warning messages about number of GPUs (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4315">#4315</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/2f3a8c7d914c2e8c75d68b5332e6b3f21753a0b2"><code>2f3a8c7</code></a>
    Fix Doxygen with default void std::enable_if_t (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4314">#4314</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/4b34f9c89476795ced8114b04d45539ca1d52954"><code>4b34f9c</code></a>
    CUDA On Windows (MSVC) (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4309">#4309</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/0f46a1615c17f0bbeaedb20c27a97c9f6e439781"><code>0f46a16</code></a>
    Fix includes (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4308">#4308</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/59693539f4be3c1e159d5bea622d2f85aab570af"><code>5969353</code></a>
    Fix CMake Compiler Flag Summary: ID Regex Matching (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4272">#4272</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/e2146822d2af7afe6123147e7d245bf10798cb05"><code>e214682</code></a>
    Use std::move (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4307">#4307</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/b15bbd3a34d9434ffdc9e440b2047a4c42bbe11b"><code>b15bbd3</code></a>
    ParaView: AnyLocation -&gt; Any Location (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4306">#4306</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/bd2d730d925bf2b3dc5911b821deb52501d30890"><code>bd2d730</code></a>
    Documentation: Fix malformed table (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4305">#4305</a>)</li>
    <li>See full diff in <a
    href="https://github.com/AMReX-Codes/amrex/compare/d4d9214f68b7450a9041259f11a9c4b4d417d5aa...69f1ac884c6aba4d9881260819ade3bb25ed8aad">compare
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extern/amrex

commit 023084389bfa445e8ed771653573ebaf6fea9675
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Feb 3 20:52:34 2025 +1100

    fix username for gcc devcontainer (#885)
    
    ### Description
    This changes the username used inside the Docker container from "ubuntu"
    to "vscode". This is required to get it working again.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] 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`.

.devcontainer/gcc-container/Dockerfile
.devcontainer/gcc-container/devcontainer.json

commit da60d08dd922cffae3a2727251f26a78db838373
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sun Feb 2 23:59:27 2025 -0500

    Bump actions/setup-python from 5.3.0 to 5.4.0 (#882)
    
    Bumps [actions/setup-python](https://github.com/actions/setup-python)
    from 5.3.0 to 5.4.0.
    <details>
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    <p><em>Sourced from <a
    href="https://github.com/actions/setup-python/releases">actions/setup-python's
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    <h2>v5.4.0</h2>
    <h2>What's Changed</h2>
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    <li>Update cache error message by <a
    href="https://github.com/aparnajyothi-y"><code>@​aparnajyothi-y</code></a>
    in <a
    href="https://redirect.github.com/actions/setup-python/pull/968">actions/setup-python#968</a></li>
    <li>Enhance Workflows: Add Ubuntu-24, Remove Python 3.8 by <a
    href="https://github.com/priya-kinthali"><code>@​priya-kinthali</code></a>
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    href="https://github.com/benwells"><code>@​benwells</code></a> in <a
    href="https://redirect.github.com/actions/setup-python/pull/1009">actions/setup-python#1009</a></li>
    <li>Improve Advanced Usage examples by <a
    href="https://github.com/lrq3000"><code>@​lrq3000</code></a> in <a
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    <h2>New Contributors</h2>
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    made their first contribution in <a
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    <li><a
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    made their first contribution in <a
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.github/workflows/cmake-macos.yml
.github/workflows/codespell.yml

commit 0c7087c7b7ec79d8941ee20be82ef0648f90ef7c
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sun Feb 2 23:59:02 2025 -0500

    Bump github/codeql-action from 3.28.5 to 3.28.8 (#883)
    
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    from 3.28.5 to 3.28.8.
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    page</a> for the relevant changes to the CodeQL CLI and language
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    <ul>
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    <h2>3.28.3 - 22 Jan 2025</h2>
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    <li>Update default CodeQL bundle version to 2.20.2. <a
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    supported. For better performance, improved security, and new features,
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    changelog post</a>. <a
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    href="https://redirect.github.com/github/codeql-action/pull/2678">#2678</a></li>
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    <h2>3.28.0 - 20 Dec 2024</h2>
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    <li>Bump the minimum CodeQL bundle version to 2.15.5. <a
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    href="https://redirect.github.com/github/codeql-action/pull/2660">#2660</a>.</li>
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    <h2>3.27.9 - 12 Dec 2024</h2>
    <!-- raw HTML omitted -->
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    <summary>Commits</summary>
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    <li><a
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    Update changelog for v3.28.8</li>
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    Merge pull request <a
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    <li><a
    href="https://github.com/github/codeql-action/commit/3879c5766041d8b2b7504c5c4b2d6dbd289f7634"><code>3879c57</code></a>
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.github/workflows/codeql.yml
.github/workflows/scorecard.yml

commit 6145933d84823f1a5d93a446f721d491c62dff1f
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sat Feb 1 04:21:08 2025 -0500

    Bump extern/openPMD-api from `654bc90` to `e6628c3` (#879)
    
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extern/openPMD-api

commit f9d6a8d6165b8c2ed8973c8200354cf28fcd6bc6
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sat Feb 1 04:20:47 2025 -0500

    Bump extern/yaml-cpp from `73ef006` to `39f7374` (#878)
    
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    `73ef006` to `39f7374`.
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    href="https://github.com/jbeder/yaml-cpp/commit/39f737443b05e4135e697cb91c2b7b18095acd53"><code>39f7374</code></a>
    Update README.md</li>
    <li>See full diff in <a
    href="https://github.com/jbeder/yaml-cpp/compare/73ef0060aaa1a9dc742c1d8a36fa336b35e94035...39f737443b05e4135e697cb91c2b7b18095acd53">compare
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extern/yaml-cpp

commit d045e77a11a923d1e978b56c59de25ee10e155e5
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sat Feb 1 04:20:23 2025 -0500

    Bump extern/fmt from `aabe639` to `c9267da` (#880)
    
    Bumps [extern/fmt](https://github.com/fmtlib/fmt) from `aabe639` to
    `c9267da`.
    <details>
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    <li><a
    href="https://github.com/fmtlib/fmt/commit/c9267da4dfec806e6137ce68a2ce50d833a27bc6"><code>c9267da</code></a>
    Fix typo in <code>FMT_HAS_BUILTIN</code> check</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/373855c1b0ec3e5e66003e94aa65344bf53078a8"><code>373855c</code></a>
    Clarify difference in FP representation</li>
    <li><a
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    Make exponent threshold depend on representation (<a
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    <li><a
    href="https://github.com/fmtlib/fmt/commit/cb6fdf2191c7dcac1b4c0b8c7abcc8b488e6919f"><code>cb6fdf2</code></a>
    Restore constraint on map formatter (<a
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    <li><a
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    <li><a
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    Workaround a bug in gcc 6 (<a
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    <li>See full diff in <a
    href="https://github.com/fmtlib/fmt/compare/aabe63910c953469a39bda4be631fdc365d5365e...c9267da4dfec806e6137ce68a2ce50d833a27bc6">compare
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extern/fmt

commit f46ef19e302d011076592f77f1d40e4a0174e281
Author: Aditi <45175933+aditivijayan@users.noreply.github.com>
Date:   Thu Jan 30 16:07:21 2025 +1100

    Movie for R8 (#874)
    
    ### Description
    This is a test to make sure movies are uploaded correctly.
    
    ### Related issues
    Are there any GitHub issues that are fixed by this pull request? Add a
    link to them here.
    
    ### 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:_
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    above).
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] 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
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docs/docs/gallery.md
docs/mkdocs.yml

commit 34391c4387ffb84128a745e3023fe9e1c9ba8e87
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Jan 30 14:10:40 2025 +1100

    allow disabling energy check in Sedov problem (#875)
    
    ### Description
    Add a runtime option to disable the energy check for the Sedov problem.
    It is only useful for the test suite, so users running the blast problem
    to learn how to use the code should be able to disable it.
    
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    N/A
    
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src/problems/HydroBlast3D/test_hydro3d_blast.cpp
tests/blast_32.in

commit 39b806ffae8c7548054de34a0cab48bd8bf3f5e5
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Jan 30 14:06:51 2025 +1100

    set default max_timesteps to INT_MAX (#876)
    
    ### Description
    Set the default maximum number of timesteps to `INT_MAX`. The previous
    default was rather arbitrary and confusing.
    
    ### Related issues
    N/A
    
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    completed. Denote completed tasks with an `x` inside the square brackets
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    above).
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
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src/simulation.hpp

commit bc4dba35d9b2955c1bca181d546a7244a59c3a89
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Tue Jan 28 03:43:57 2025 +0000

    Bump nvidia/nvhpc from 24.11-devel-cuda12.6-ubuntu24.04 to 25.1-devel-cuda12.6-ubuntu24.04 in /.devcontainer/cuda-container (#871)
    
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    25.1-devel-cuda12.6-ubuntu24.04.
    
    
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.devcontainer/cuda-container/Dockerfile

commit 6bf064caf1b6358ae9cc8a48398d4bedfcab5f9c
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Date:   Mon Jan 27 03:46:00 2025 +0000

    Bump mkdocs-bibtex from 4.0.1 to 4.1.0 in /docs/docs (#870)
    
    Bumps [mkdocs-bibtex](https://github.com/shyamd/mkdocs-bibtex) from
    4.0.1 to 4.1.0.
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    <li>[17ffee3f] Inline References (<a
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commit 4800e92fab841c73ac16270a1a9aadd41754b8d2
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Jan 27 03:41:30 2025 +0000

    Bump mkdocs-bibtex from 4.0.1 to 4.1.0 in /docs (#869)
    
    Bumps [mkdocs-bibtex](https://github.com/shyamd/mkdocs-bibtex) from
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docs/docs/requirements.txt
docs/requirements.txt

commit 1a070d448c648e069145290bddcc7ec5f1bcecdc
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Jan 27 03:33:43 2025 +0000

    Bump github/codeql-action from 3.28.2 to 3.28.5 (#868)
    
    Bumps [github/codeql-action](https://github.com/github/codeql-action)
    from 3.28.2 to 3.28.5.
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    href="https://redirect.github.com/github/codeql-action/pull/2717">#2717</a></li>
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    </ul>
    <h2>3.28.2 - 21 Jan 2025</h2>
    <p>No user facing changes.</p>
    <h2>3.28.1 - 10 Jan 2025</h2>
    <ul>
    <li>CodeQL Action v2 is now deprecated, and is no longer updated or
    supported. For better performance, improved security, and new features,
    upgrade to v3. For more information, see <a
    href="https://github.blog/changelog/2025-01-10-code-scanning-codeql-action-v2-is-now-deprecated/">this
    changelog post</a>. <a
    href="https://redirect.github.com/github/codeql-action/pull/2677">#2677</a></li>
    <li>Update default CodeQL bundle version to 2.20.1. <a
    href="https://redirect.github.com/github/codeql-action/pull/2678">#2678</a></li>
    </ul>
    <h2>3.28.0 - 20 Dec 2024</h2>
    <ul>
    <li>Bump the minimum CodeQL bundle version to 2.15.5. <a
    href="https://redirect.github.com/github/codeql-action/pull/2655">#2655</a></li>
    <li>Don't fail in the unusual case that a file is on the search path. <a
    href="https://redirect.github.com/github/codeql-action/pull/2660">#2660</a>.</li>
    </ul>
    <h2>3.27.9 - 12 Dec 2024</h2>
    <p>No user facing changes.</p>
    <h2>3.27.8 - 12 Dec 2024</h2>
    <ul>
    <li>Fixed an issue where streaming the download and extraction of the
    CodeQL bundle did not respect proxy settings. <a
    href="https://redirect.github.com/github/codeql-action/pull/2624">#2624</a></li>
    </ul>
    <h2>3.27.7 - 10 Dec 2024</h2>
    <ul>
    <li>We are rolling out a change in December 2024 that will extract the
    CodeQL bundle directly to the toolcache to improve performance. <a
    href="https://redirect.github.com/github/codeql-action/pull/2631">#2631</a></li>
    <li>Update default CodeQL bundle version to 2.20.0. <a
    href="https://redirect.github.com/github/codeql-action/pull/2636">#2636</a></li>
    </ul>
    <h2>3.27.6 - 03 Dec 2024</h2>
    <!-- raw HTML omitted -->
    </blockquote>
    <p>... (truncated)</p>
    </details>
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/github/codeql-action/commit/f6091c0113d1dcf9b98e269ee48e8a7e51b7bdd4"><code>f6091c0</code></a>
    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2721">#2721</a>
    from github/update-v3.28.5-01f001931</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/064af10f0de41995b41632364b4bfb00a34df047"><code>064af10</code></a>
    Update changelog for v3.28.5</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/01f0019310ce544d1cf748667a69f8fd6e26e48a"><code>01f0019</code></a>
    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2717">#2717</a>
    from github/update-bundle/codeql-bundle-v2.20.3</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/573ad887cd5b527e9baef02653bd455e1ff5181c"><code>573ad88</code></a>
    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2718">#2718</a>
    from github/kaeluka/4779-1</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/d7f39764f685cbe3764f763469a0d72383d7b9c8"><code>d7f3976</code></a>
    permissions block in query-filters.yml</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/428975ce2cf327a0e919004c63e734eddd0e6255"><code>428975c</code></a>
    Add changelog note</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/208091da0a1069394981cdf5e7a91a8ee3f10709"><code>208091d</code></a>
    Update default bundle to codeql-bundle-v2.20.3</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/7e3036b9cd87fc26dd06747b7aa4b96c27aaef3a"><code>7e3036b</code></a>
    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2716">#2716</a>
    from github/mergeback/v3.28.4-to-main-ee117c90</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/e32a0d62d44ac06377953bfaf3ffd43618be076a"><code>e32a0d6</code></a>
    Update checked-in dependencies</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/67c21e4084d5e020fbc969b839d42911b87fb8b5"><code>67c21e4</code></a>
    Update changelog and version after v3.28.4</li>
    <li>Additional commits viewable in <a
    href="https://github.com/github/codeql-action/compare/d68b2d4edb4189fd2a5366ac14e72027bd4b37dd...f6091c0113d1dcf9b98e269ee48e8a7e51b7bdd4">compare
    view</a></li>
    </ul>
    </details>
    <br />
    
    
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.github/workflows/codeql.yml
.github/workflows/scorecard.yml

commit f747b82095e5f2935a568ec4185261232c942a17
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Wed Jan 22 10:11:30 2025 -0500

    Bump extern/amrex from `b3f6738` to `d4d9214` (#860)
    
    Bumps [extern/amrex](https://github.com/AMReX-Codes/amrex) from
    `b3f6738` to `d4d9214`.
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/d4d9214f68b7450a9041259f11a9c4b4d417d5aa"><code>d4d9214</code></a>
    PC: SoA Name Helpers (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4300">#4300</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/afa9510684d1d26daf42668d467d6301d8dc1cdc"><code>afa9510</code></a>
    Fix Codespell Warnings (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4304">#4304</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/66e83eaa80e94db9060cc7ffec63fe77855206c0"><code>66e83ea</code></a>
    PC: Ensure Uniqueness of SoA Names (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4299">#4299</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/20eb1ab1eeb28337fbe847a86af77ec7c78cec65"><code>20eb1ab</code></a>
    PC Names: Same Type, Multiple Vars/Instances (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4302">#4302</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/92d35c2c816363d592020b42e126de7619aa9412"><code>92d35c2</code></a>
    Use bigint in HypreSolver test (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4297">#4297</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/1803a94e310c5daa708106853f9d05ca079fd5c6"><code>1803a94</code></a>
    Fix new coverity scan warnings (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4295">#4295</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/59fb60357692fcb073b364e9bb0021cb34beb939"><code>59fb603</code></a>
    Use PETSc 3.22.2 in CI (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4301">#4301</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/90373e71b7bde364c322b4d699e137cf3c65fcbe"><code>90373e7</code></a>
    CI: Remove ICC/ICPC (Compiler Classic) (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4303">#4303</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/0233b8e67675c43211b27f789e16926e86f86138"><code>0233b8e</code></a>
    Fix: PC Tile Copy w/ Names (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4298">#4298</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/e6828ed4604eb843adab6874bd852b567bab68ea"><code>e6828ed</code></a>
    misspelling in a profiler (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4296">#4296</a>)</li>
    <li>Additional commits viewable in <a
    href="https://github.com/AMReX-Codes/amrex/compare/b3f67385e62f387b548389222840486c0fffca57...d4d9214f68b7450a9041259f11a9c4b4d417d5aa">compare
    view</a></li>
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extern/amrex

commit a3c3b6292738a65e805c06b476ea9c0c9e56abe2
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Wed Jan 22 00:56:35 2025 -0500

    Bump actions/checkout from 4.1.1 to 4.2.2 (#863)
    
    Bumps [actions/checkout](https://github.com/actions/checkout) from 4.1.1
    to 4.2.2.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
    href="https://github.com/actions/checkout/releases">actions/checkout's
    releases</a>.</em></p>
    <blockquote>
    <h2>v4.2.2</h2>
    <h2>What's Changed</h2>
    <ul>
    <li><code>url-helper.ts</code> now leverages well-known environment
    variables by <a href="https://github.com/jww3"><code>@​jww3</code></a>
    in <a
    href="https://redirect.github.com/actions/checkout/pull/1941">actions/checkout#1941</a></li>
    <li>Expand unit test coverage for <code>isGhes</code> by <a
    href="https://github.com/jww3"><code>@​jww3</code></a> in <a
    href="https://redirect.github.com/actions/checkout/pull/1946">actions/checkout#1946</a></li>
    </ul>
    <p><strong>Full Changelog</strong>: <a
    href="https://github.com/actions/checkout/compare/v4.2.1...v4.2.2">https://github.com/actions/checkout/compare/v4.2.1...v4.2.2</a></p>
    <h2>v4.2.1</h2>
    <h2>What's Changed</h2>
    <ul>
    <li>Check out other refs/* by commit if provided, fall back to ref by <a
    href="https://github.com/orhantoy"><code>@​orhantoy</code></a> in <a
    href="https://redirect.github.com/actions/checkout/pull/1924">actions/checkout#1924</a></li>
    </ul>
    <h2>New Contributors</h2>
    <ul>
    <li><a href="https://github.com/Jcambass"><code>@​Jcambass</code></a>
    made their first contribution in <a
    href="https://redirect.github.com/actions/checkout/pull/1919">actions/checkout#1919</a></li>
    </ul>
    <p><strong>Full Changelog</strong>: <a
    href="https://github.com/actions/checkout/compare/v4.2.0...v4.2.1">https://github.com/actions/checkout/compare/v4.2.0...v4.2.1</a></p>
    <h2>v4.2.0</h2>
    <h2>What's Changed</h2>
    <ul>
    <li>Add Ref and Commit outputs by <a
    href="https://github.com/lucacome"><code>@​lucacome</code></a> in <a
    href="https://redirect.github.com/actions/checkout/pull/1180">actions/checkout#1180</a></li>
    <li>Dependabot updates in <a
    href="https://redirect.github.com/actions/checkout/pull/1777">actions/checkout#1777</a>
    &amp; <a
    href="https://redirect.github.com/actions/checkout/pull/1872">actions/checkout#1872</a></li>
    </ul>
    <h2>New Contributors</h2>
    <ul>
    <li><a href="https://github.com/yasonk"><code>@​yasonk</code></a> made
    their first contribution in <a
    href="https://redirect.github.com/actions/checkout/pull/1869">actions/checkout#1869</a></li>
    <li><a href="https://github.com/lucacome"><code>@​lucacome</code></a>
    made their first contribution in <a
    href="https://redirect.github.com/actions/checkout/pull/1180">actions/checkout#1180</a></li>
    </ul>
    <p><strong>Full Changelog</strong>: <a
    href="https://github.com/actions/checkout/compare/v4.1.7...v4.2.0">https://github.com/actions/checkout/compare/v4.1.7...v4.2.0</a></p>
    <h2>v4.1.7</h2>
    <h2>What's Changed</h2>
    <ul>
    <li>Bump the minor-npm-dependencies group across 1 directory with 4
    updates by <a
    href="https://github.com/dependabot"><code>@​dependabot</code></a> in <a
    href="https://redirect.github.com/actions/checkout/pull/1739">actions/checkout#1739</a></li>
    <li>Bump actions/checkout from 3 to 4 by <a
    href="https://github.com/dependabot"><code>@​dependabot</code></a> in <a
    href="https://redirect.github.com/actions/checkout/pull/1697">actions/checkout#1697</a></li>
    <li>Check out other refs/* by commit by <a
    href="https://github.com/orhantoy"><code>@​orhantoy</code></a> in <a
    href="https://redirect.github.com/actions/checkout/pull/1774">actions/checkout#1774</a></li>
    <li>Pin actions/checkout's own workflows to a known, good, stable
    version. by <a href="https://github.com/jww3"><code>@​jww3</code></a> in
    <a
    href="https://redirect.github.com/actions/checkout/pull/1776">actions/checkout#1776</a></li>
    </ul>
    <h2>New Contributors</h2>
    <ul>
    <li><a href="https://github.com/orhantoy"><code>@​orhantoy</code></a>
    made their first contribution in <a
    href="https://redirect.github.com/actions/checkout/pull/1774">actions/checkout#1774</a></li>
    </ul>
    <p><strong>Full Changelog</strong>: <a
    href="https://github.com/actions/checkout/compare/v4.1.6...v4.1.7">https://github.com/actions/checkout/compare/v4.1.6...v4.1.7</a></p>
    <h2>v4.1.6</h2>
    <h2>What's Changed</h2>
    <ul>
    <li>Check platform to set archive extension appropriately by <a
    href="https://github.com/cory-miller"><code>@​cory-miller</code></a> in
    <a
    href="https://redirect.github.com/actions/checkout/pull/1732">actions/checkout#1732</a></li>
    <li>Update for 4.1.6 release by <a
    href="https://github.com/cory-miller"><code>@​cory-miller</code></a> in
    <a
    href="https://redirect.github.com/actions/checkout/pull/1733">actions/checkout#1733</a></li>
    </ul>
    <p><strong>Full Changelog</strong>: <a
    href="https://github.com/actions/checkout/compare/v4.1.5...v4.1.6">https://github.com/actions/checkout/compare/v4.1.5...v4.1.6</a></p>
    <h2>v4.1.5</h2>
    <h2>What's Changed</h2>
    <!-- raw HTML omitted -->
    </blockquote>
    <p>... (truncated)</p>
    </details>
    <details>
    <summary>Changelog</summary>
    <p><em>Sourced from <a
    href="https://github.com/actions/checkout/blob/main/CHANGELOG.md">actions/checkout's
    changelog</a>.</em></p>
    <blockquote>
    <h1>Changelog</h1>
    <h2>v4.2.2</h2>
    <ul>
    <li><code>url-helper.ts</code> now leverages well-known environment
    variables by <a href="https://github.com/jww3"><code>@​jww3</code></a>
    in <a
    href="https://redirect.github.com/actions/checkout/pull/1941">actions/checkout#1941</a></li>
    <li>Expand unit test coverage for <code>isGhes</code> by <a
    href="https://github.com/jww3"><code>@​jww3</code></a> in <a
    href="https://redirect.github.com/actions/checkout/pull/1946">actions/checkout#1946</a></li>
    </ul>
    <h2>v4.2.1</h2>
    <ul>
    <li>Check out other refs/* by commit if provided, fall back to ref by <a
    href="https://github.com/orhantoy"><code>@​orhantoy</code></a> in <a
    href="https://redirect.github.com/actions/checkout/pull/1924">actions/checkout#1924</a></li>
    </ul>
    <h2>v4.2.0</h2>
    <ul>
    <li>Add Ref and Commit outputs by <a
    href="https://github.com/lucacome"><code>@​lucacome</code></a> in <a
    href="https://redirect.github.com/actions/checkout/pull/1180">actions/checkout#1180</a></li>
    <li>Dependency updates by <a
    href="https://github.com/dependabot"><code>@​dependabot</code></a>- <a
    href="https://redirect.github.com/actions/checkout/pull/1777">actions/checkout#1777</a>,
    <a
    href="https://redirect.github.com/actions/checkout/pull/1872">actions/checkout#1872</a></li>
    </ul>
    <h2>v4.1.7</h2>
    <ul>
    <li>Bump the minor-npm-dependencies group across 1 directory with 4
    updates by <a
    href="https://github.com/dependabot"><code>@​dependabot</code></a> in <a
    href="https://redirect.github.com/actions/checkout/pull/1739">actions/checkout#1739</a></li>
    <li>Bump actions/checkout from 3 to 4 by <a
    href="https://github.com/dependabot"><code>@​dependabot</code></a> in <a
    href="https://redirect.github.com/actions/checkout/pull/1697">actions/checkout#1697</a></li>
    <li>Check out other refs/* by commit by <a
    href="https://github.com/orhantoy"><code>@​orhantoy</code></a> in <a
    href="https://redirect.github.com/actions/checkout/pull/1774">actions/checkout#1774</a></li>
    <li>Pin actions/checkout's own workflows to a known, good, stable
    version. by <a href="https://github.com/jww3"><code>@​jww3</code></a> in
    <a
    href="https://redirect.github.com/actions/checkout/pull/1776">actions/checkout#1776</a></li>
    </ul>
    <h2>v4.1.6</h2>
    <ul>
    <li>Check platform to set archive extension appropriately by <a
    href="https://github.com/cory-miller"><code>@​cory-miller</code></a> in
    <a
    href="https://redirect.github.com/actions/checkout/pull/1732">actions/checkout#1732</a></li>
    </ul>
    <h2>v4.1.5</h2>
    <ul>
    <li>Update NPM dependencies by <a
    href="https://github.com/cory-miller"><code>@​cory-miller</code></a> in
    <a
    href="https://redirect.github.com/actions/checkout/pull/1703">actions/checkout#1703</a></li>
    <li>Bump github/codeql-action from 2 to 3 by <a
    href="https://github.com/dependabot"><code>@​dependabot</code></a> in <a
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    <a
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    <ul>
    <li>Disable <code>extensions.worktreeConfig</code> when disabling
    <code>sparse-checkout</code> by <a
    href="https://github.com/jww3"><code>@​jww3</code></a> in <a
    href="https://redirect.github.com/actions/checkout/pull/1692">actions/checkout#1692</a></li>
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    <h2>v4.1.3</h2>
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    href="https://redirect.github.com/actions/checkout/pull/1656">actions/checkout#1656</a></li>
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    href="https://redirect.github.com/actions/checkout/pull/1650">actions/checkout#1650</a></li>
    </ul>
    <h2>v4.1.2</h2>
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    <li>Fix: Disable sparse checkout whenever <code>sparse-checkout</code>
    option is not present <a
    href="https://github.com/dscho"><code>@​dscho</code></a> in <a
    href="https://redirect.github.com/actions/checkout/pull/1598">actions/checkout#1598</a></li>
    </ul>
    <h2>v4.1.1</h2>
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    <li>Correct link to GitHub Docs by <a
    href="https://github.com/peterbe"><code>@​peterbe</code></a> in <a
    href="https://redirect.github.com/actions/checkout/pull/1511">actions/checkout#1511</a></li>
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    <!-- raw HTML omitted -->
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    Prepare 4.2.0 release (<a
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    <li><a
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.github/workflows/scorecard.yml

commit 38a76955023f703b1d7b69a622d9e9bb8a5ad7dc
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Wed Jan 22 04:25:38 2025 +0000

    Bump extern/fmt from `e3ddede` to `aabe639` (#858)
    
    Bumps [extern/fmt](https://github.com/fmtlib/fmt) from `e3ddede` to
    `aabe639`.
    <details>
    <summary>Commits</summary>
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    <li><a
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    Tweak changelog</li>
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    Update changelog</li>
    <li><a
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    Bump version</li>
    <li><a
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    Update changelog</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/5f0572acdca120e11f6d810765d7a6a3c593fcbb"><code>5f0572a</code></a>
    Workaround a compilation error on gcc 9.4</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/898d43857139bd2522b547eef6859753af5dc535"><code>898d438</code></a>
    Fix formatting into std::ostreambuf_iterator using a compiled format (<a
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    <li><a
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    <li><a
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    Reduce size of basic_specs</li>
    <li><a
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    Workaround an ICE when using modules with gcc 14.2 and earlier</li>
    <li><a
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    Update version</li>
    <li>Additional commits viewable in <a
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extern/fmt

commit 0c519b6acaa94d98d8f0170c3a09ec459b174fae
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Wed Jan 22 03:55:37 2025 +0000

    Bump github/codeql-action from 3.28.1 to 3.28.2 (#866)
    
    Bumps [github/codeql-action](https://github.com/github/codeql-action)
    from 3.28.1 to 3.28.2.
    <details>
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    <p><em>Sourced from <a
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    <h2>v3.28.2</h2>
    <h1>CodeQL Action Changelog</h1>
    <p>See the <a
    href="https://github.com/github/codeql-action/releases">releases
    page</a> for the relevant changes to the CodeQL CLI and language
    packs.</p>
    <h2>3.28.2 - 21 Jan 2025</h2>
    <p>No user facing changes.</p>
    <p>See the full <a
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    for more information.</p>
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    <p>See the <a
    href="https://github.com/github/codeql-action/releases">releases
    page</a> for the relevant changes to the CodeQL CLI and language
    packs.</p>
    <h2>[UNRELEASED]</h2>
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    <h2>3.28.2 - 21 Jan 2025</h2>
    <p>No user facing changes.</p>
    <h2>3.28.1 - 10 Jan 2025</h2>
    <ul>
    <li>CodeQL Action v2 is now deprecated, and is no longer updated or
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    changelog post</a>. <a
    href="https://redirect.github.com/github/codeql-action/pull/2677">#2677</a></li>
    <li>Update default CodeQL bundle version to 2.20.1. <a
    href="https://redirect.github.com/github/codeql-action/pull/2678">#2678</a></li>
    </ul>
    <h2>3.28.0 - 20 Dec 2024</h2>
    <ul>
    <li>Bump the minimum CodeQL bundle version to 2.15.5. <a
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    href="https://redirect.github.com/github/codeql-action/pull/2660">#2660</a>.</li>
    </ul>
    <h2>3.27.9 - 12 Dec 2024</h2>
    <p>No user facing changes.</p>
    <h2>3.27.8 - 12 Dec 2024</h2>
    <ul>
    <li>Fixed an issue where streaming the download and extraction of the
    CodeQL bundle did not respect proxy settings. <a
    href="https://redirect.github.com/github/codeql-action/pull/2624">#2624</a></li>
    </ul>
    <h2>3.27.7 - 10 Dec 2024</h2>
    <ul>
    <li>We are rolling out a change in December 2024 that will extract the
    CodeQL bundle directly to the toolcache to improve performance. <a
    href="https://redirect.github.com/github/codeql-action/pull/2631">#2631</a></li>
    <li>Update default CodeQL bundle version to 2.20.0. <a
    href="https://redirect.github.com/github/codeql-action/pull/2636">#2636</a></li>
    </ul>
    <h2>3.27.6 - 03 Dec 2024</h2>
    <ul>
    <li>Update default CodeQL bundle version to 2.19.4. <a
    href="https://redirect.github.com/github/codeql-action/pull/2626">#2626</a></li>
    </ul>
    <h2>3.27.5 - 19 Nov 2024</h2>
    <p>No user facing changes.</p>
    <h2>3.27.4 - 14 Nov 2024</h2>
    <p>No user facing changes.</p>
    <h2>3.27.3 - 12 Nov 2024</h2>
    <p>No user facing changes.</p>
    <!-- raw HTML omitted -->
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    <li><a
    href="https://github.com/github/codeql-action/commit/d68b2d4edb4189fd2a5366ac14e72027bd4b37dd"><code>d68b2d4</code></a>
    Merge pull request <a
    href="https://redirect.github.com/github/codeql-action/issues/2708">#2708</a>
    from github/update-v3.28.2-d90e07f32</li>
    <li><a
    href="https://github.com/github/codeql-action/commit/ea237964450673c10ad7b678a6aab37176b787a3"><code>ea23796</code></a>
    Update changelog for v3.28.2</li>
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    from github/dependabot/npm_and_yarn/npm-cd3f77644b</li>
    <li><a
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    Update checked-in dependencies</li>
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    build(deps): bump the npm group with 3 updates</li>
    <li><a
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    Merge pull request <a
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    from github/cklin/diff-informed-file-fallback</li>
    <li><a
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    Merge pull request <a
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    getDiffRanges: better fallback for absent patch</li>
    <li><a
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    Add analysis_is_diff_informed to status report</li>
    <li>Additional commits viewable in <a
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.github/workflows/codeql.yml
.github/workflows/scorecard.yml

commit 70702d2697984d338ebe6a41cd5a5aec58757db2
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Wed Jan 22 03:51:36 2025 +0000

    Bump mkdocs-bibtex from 2.15.0 to 4.0.1 in /docs/docs (#864)
    
    Bumps [mkdocs-bibtex](https://github.com/shyamd/mkdocs-bibtex) from
    2.15.0 to 4.0.1.
    <details>
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    <h2>v4.0.1</h2>
    <p>Version 4.0.1</p>
    <h3>Commits</h3>
    <ul>
    <li>[26da3338] FIX: Not invalidating citation blocks with 0 citations
    (<a
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    <h2>v4.0.0</h2>
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    <h2>v3.0.0</h2>
    <p>Version 3.0.0</p>
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    <li>[fddf1c20] Refactor for easier updating (<a
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    </ul>
    <h2>v2.21.0</h2>
    <p>Version 2.21.0</p>
    <h3>Commits</h3>
    <h2>v2.20.0</h2>
    <p>Version 2.20.0</p>
    <h3>Commits</h3>
    <h2>v2.19.0</h2>
    <p>Version 2.19.0</p>
    <h3>Commits</h3>
    <h2>v2.18.0</h2>
    <p>Version 2.18.0</p>
    <h3>Commits</h3>
    <h2>v2.17.0</h2>
    <p>Version 2.17.0</p>
    <h3>Commits</h3>
    <ul>
    <li>[dd0695f5] Zotero pagination (<a
    href="https://redirect.github.com/shyamd/mkdocs-bibtex/issues/288">#288</a>)</li>
    <li>[632ad7aa] remove branching for unsupported python versions</li>
    <li>[b14bf151] Bump validators from 0.20.0 to 0.34.0</li>
    <li>[acef152e] Bump pytest-cov from 4.1.0 to 6.0.0</li>
    <li>[e90c2e7c] Bump mkdocs from 1.5.3 to 1.6.1</li>
    <li>[ceeb742b] Bump requests from 2.31.0 to 2.32.3</li>
    </ul>
    <!-- raw HTML omitted -->
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    <p>... (truncated)</p>
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    <li><a
    href="https://github.com/shyamd/mkdocs-bibtex/commit/26da33389b83166c18a33fa58c2a9f5818440576"><code>26da333</code></a>
    FIX: Not invalidating citation blocks with 0 citations (<a
    href="https://redirect.github.com/shyamd/mkdocs-bibtex/issues/290">#290</a>)</li>
    <li><a
    href="https://github.com/shyamd/mkdocs-bibtex/commit/fddf1c204d13fc32fbc444381746d0751d516af2"><code>fddf1c2</code></a>
    Refactor for easier updating (<a
    href="https://redirect.github.com/shyamd/mkdocs-bibtex/issues/285">#285</a>)</li>
    <li><a
    href="https://github.com/shyamd/mkdocs-bibtex/commit/dd0695f52c319a9ba47416da3ad4cbec81470b0f"><code>dd0695f</code></a>
    Zotero pagination (<a
    href="https://redirect.github.com/shyamd/mkdocs-bibtex/issues/288">#288</a>)</li>
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    href="https://github.com/shyamd/mkdocs-bibtex/commit/632ad7aabdcf4f7354e567febf06c8aa8f905c95"><code>632ad7a</code></a>
    remove branching for unsupported python versions</li>
    <li><a
    href="https://github.com/shyamd/mkdocs-bibtex/commit/b14bf15171ae3eb88249e4c8e9461e84e65a7f97"><code>b14bf15</code></a>
    Bump validators from 0.20.0 to 0.34.0</li>
    <li><a
    href="https://github.com/shyamd/mkdocs-bibtex/commit/acef152ed0cdd16065b07b74d17cea629433ed60"><code>acef152</code></a>
    Bump pytest-cov from 4.1.0 to 6.0.0</li>
    <li><a
    href="https://github.com/shyamd/mkdocs-bibtex/commit/e90c2e7ca7d354bbd211a81862102b24b9c9ef43"><code>e90c2e7</code></a>
    Bump mkdocs from 1.5.3 to 1.6.1</li>
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    href="https://github.com/shyamd/mkdocs-bibtex/commit/ceeb742b7ead497c6fee6843feceff1486390dcd"><code>ceeb742</code></a>
    Bump requests from 2.31.0 to 2.32.3</li>
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    Bump pytest from 7.4.4 to 8.3.4</li>
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    Bump ruff from 0.4.7 to 0.9.1 (<a
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commit 82f639ade5fa80f897a43c32edd0d28056b240cc
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Wed Jan 22 03:24:01 2025 +0000

    Bump extern/regression_testing from `d1e0aef` to `d8849ba` (#862)
    
    Bumps
    [extern/regression_testing](https://github.com/AMReX-Codes/regression_testing)
    from `d1e0aef` to `d8849ba`.
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    Merge pull request <a
    href="https://redirect.github.com/AMReX-Codes/regression_testing/issues/151">#151</a>
    from BenWibking/delete-exe</li>
    <li><a
    href="https://github.com/AMReX-Codes/regression_testing/commit/28c7277770acde45d26ce618836d923a50122ad7"><code>28c7277</code></a>
    Merge branch 'main' into delete-exe</li>
    <li><a
    href="https://github.com/AMReX-Codes/regression_testing/commit/6e28c54e5975901fc41ba53b7f03aa63e726401e"><code>6e28c54</code></a>
    Merge pull request <a
    href="https://redirect.github.com/AMReX-Codes/regression_testing/issues/149">#149</a>
    from BenWibking/update-submodules</li>
    <li><a
    href="https://github.com/AMReX-Codes/regression_testing/commit/eebd3e3ebb9630a8a7b8f6408ade5b48477a1911"><code>eebd3e3</code></a>
    Merge branch 'main' into update-submodules</li>
    <li><a
    href="https://github.com/AMReX-Codes/regression_testing/commit/9d33cdd7dc85cddf8c939ee4f763e735cdf6a8f8"><code>9d33cdd</code></a>
    Merge branch 'main' into delete-exe</li>
    <li><a
    href="https://github.com/AMReX-Codes/regression_testing/commit/3387dbdd674ba28caf5a4a28993bf710a6df9470"><code>3387dbd</code></a>
    add option to delete executable if test passes</li>
    <li><a
    href="https://github.com/AMReX-Codes/regression_testing/commit/b735d418e9b69ccd6f4b80461d2b8265bedcc3e3"><code>b735d41</code></a>
    fix bug</li>
    <li><a
    href="https://github.com/AMReX-Codes/regression_testing/commit/e09d992401d461e736083acaac9cee144ccc60be"><code>e09d992</code></a>
    add log message</li>
    <li><a
    href="https://github.com/AMReX-Codes/regression_testing/commit/691854b54386ec0195f590d547db558579126890"><code>691854b</code></a>
    add option to update git submodules</li>
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    href="https://github.com/AMReX-Codes/regression_testing/commit/cba71d3e55343a3c17ed0c3f08b8064bccaa3f26"><code>cba71d3</code></a>
    update submodules when doing git fetch</li>
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extern/regression_testing

commit 3740d985984922df2343367af679b1b0ed901984
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Wed Jan 22 03:23:04 2025 +0000

    Bump nvidia/nvhpc from 24.9-devel-cuda12.6-ubuntu24.04 to 24.11-devel-cuda12.6-ubuntu24.04 in /.devcontainer/cuda-container (#861)
    
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    24.11-devel-cuda12.6-ubuntu24.04.
    
    
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.devcontainer/cuda-container/Dockerfile

commit 5ecdda5190bf18e886cf0d503b02d334db418522
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Wed Jan 22 03:06:10 2025 +0000

    Bump SonarSource/sonarcloud-github-c-cpp from 3.1.0 to 3.2.0 (#867)
    
    Bumps
    [SonarSource/sonarcloud-github-c-cpp](https://github.com/sonarsource/sonarcloud-github-c-cpp)
    from 3.1.0 to 3.2.0.
    <details>
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    <p><em>Sourced from <a
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    <blockquote>
    <h2>v3.2.0</h2>
    <blockquote>
    <p>[!WARNING]
    <strong>This new version of the GitHub action for C, C++, and
    Objective-C with SonarQube Cloud (<code>sonarcloud-github-c-cpp</code>)
    is going to be the last one specifically designed for these
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    <p>If the action is used to install the SonarScanner CLI, and the Build
    Wrapper is not required:</p>
    <ul>
    <li>remove the <code>sonarcloud-github-c-cpp</code> step altogether</li>
    <li>replace the step calling <code>sonar-scanner</code> with a step
    using <code>SonarSource/sonarqube-scan-action</code></li>
    <li>the arguments passed to <code>sonar-scanner</code> should be passed
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    <h2>What's Changed</h2>
    <ul>
    <li>SCCPPGHA-9 Upgrade all recommended GitHub Action versions by <a
    href="https://github.com/7PH"><code>@​7PH</code></a> in <a
    href="https://redirect.github.com/SonarSource/sonarcloud-github-c-cpp/pull/61">SonarSource/sonarcloud-github-c-cpp#61</a></li>
    <li>SCCPPGHA-13 Add Jira integration by <a
    href="https://github.com/pavel-mikula-sonarsource"><code>@​pavel-mikula-sonarsource</code></a>
    in <a
    href="https://redirect.github.com/SonarSource/sonarcloud-github-c-cpp/pull/62">SonarSource/sonarcloud-github-c-cpp#62</a></li>
    <li>SCCPPGHA-10 Rebrand and forward to the C and C++ action for SQS by
    <a
    href="https://github.com/antonioaversa"><code>@​antonioaversa</code></a>
    in <a
    href="https://redirect.github.com/SonarSource/sonarcloud-github-c-cpp/pull/64">SonarSource/sonarcloud-github-c-cpp#64</a></li>
    <li>SCCPPGHA-16 Deprecate in favor of sonarqube-scan-action by <a
    href="https://github.com/antonioaversa"><code>@​antonioaversa</code></a>
    in <a
    href="https://redirect.github.com/SonarSource/sonarcloud-github-c-cpp/pull/66">SonarSource/sonarcloud-github-c-cpp#66</a></li>
    <li>SCCPPGHA-21 Change title back to SonarCloud Scan for C and C++ by <a
    href="https://github.com/antonioaversa"><code>@​antonioaversa</code></a>
    in <a
    href="https://redirect.github.com/SonarSource/sonarcloud-github-c-cpp/pull/65">SonarSource/sonarcloud-github-c-cpp#65</a></li>
    </ul>
    <h2>New Contributors</h2>
    <ul>
    <li><a href="https://github.com/7PH"><code>@​7PH</code></a> made their
    first contribution in <a
    href="https://redirect.github.com/SonarSource/sonarcloud-github-c-cpp/pull/61">SonarSource/sonarcloud-github-c-cpp#61</a></li>
    <li><a
    href="https://github.com/pavel-mikula-sonarsource"><code>@​pavel-mikula-sonarsource</code></a>
    made their first contribution in <a
    href="https://redirect.github.com/SonarSource/sonarcloud-github-c-cpp/pull/62">SonarSource/sonarcloud-github-c-cpp#62</a></li>
    <li><a
    href="https://github.com/antonioaversa"><code>@​antonioaversa</code></a>
    made their first contribution in <a
    href="https://redirect.github.com/SonarSource/sonarcloud-github-c-cpp/pull/64">SonarSource/sonarcloud-github-c-cpp#64</a></li>
    </ul>
    <p><strong>Full Changelog</strong>: <a
    href="https://github.com/SonarSource/sonarcloud-github-c-cpp/compare/v3.1.0...v3.2.0">https://github.com/SonarSource/sonarcloud-github-c-cpp/compare/v3.1.0...v3.2.0</a></p>
    </blockquote>
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    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/SonarSource/sonarcloud-github-c-cpp/commit/44cc4d3d487fbc35e5c29b0a9d717be218d3a0e8"><code>44cc4d3</code></a>
    SCCPPGHA-21 Change title back to SonarCloud Scan for C and C++ (<a
    href="https://redirect.github.com/sonarsource/sonarcloud-github-c-cpp/issues/65">#65</a>)</li>
    <li><a
    href="https://github.com/SonarSource/sonarcloud-github-c-cpp/commit/211a45f5dc6a920e7a5ee05643fa179255220894"><code>211a45f</code></a>
    SCCPPGHA-16 Deprecate in favor of sonarqube-scan-action (<a
    href="https://redirect.github.com/sonarsource/sonarcloud-github-c-cpp/issues/66">#66</a>)</li>
    <li><a
    href="https://github.com/SonarSource/sonarcloud-github-c-cpp/commit/166e6d6bc1425019fa106c0eb3b113c699f548a4"><code>166e6d6</code></a>
    SCCPPGHA-10 Rebrand and forward to the C and C++ action for SQS (<a
    href="https://redirect.github.com/sonarsource/sonarcloud-github-c-cpp/issues/64">#64</a>)</li>
    <li><a
    href="https://github.com/SonarSource/sonarcloud-github-c-cpp/commit/0aed73788d6243216a10ac66c1a2d13111d3ab99"><code>0aed737</code></a>
    Add Jira integration</li>
    <li><a
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    SCCPPGHA-9 Upgrade all recommended GitHub Action versions (<a
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commit da4d2aaf59ff209541a1a903255e0a5118759ca3
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Wed Jan 22 03:05:10 2025 +0000

    Bump mkdocs-bibtex from 2.15.0 to 4.0.1 in /docs (#865)
    
    Bumps [mkdocs-bibtex](https://github.com/shyamd/mkdocs-bibtex) from
    2.15.0 to 4.0.1.
    <details>
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    <p><em>Sourced from <a
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    <p>Version 4.0.1</p>
    <h3>Commits</h3>
    <ul>
    <li>[26da3338] FIX: Not invalidating citation blocks with 0 citations
    (<a
    href="https://redirect.github.com/shyamd/mkdocs-bibtex/issues/290">#290</a>)</li>
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    <h2>v4.0.0</h2>
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    <h2>v3.0.0</h2>
    <p>Version 3.0.0</p>
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    <li>[fddf1c20] Refactor for easier updating (<a
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    <h2>v2.21.0</h2>
    <p>Version 2.21.0</p>
    <h3>Commits</h3>
    <h2>v2.20.0</h2>
    <p>Version 2.20.0</p>
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    <p>Version 2.19.0</p>
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    <p>Version 2.18.0</p>
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    <li>[dd0695f5] Zotero pagination (<a
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    <li>[632ad7aa] remove branching for unsupported python versions</li>
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    <li>[acef152e] Bump pytest-cov from 4.1.0 to 6.0.0</li>
    <li>[e90c2e7c] Bump mkdocs from 1.5.3 to 1.6.1</li>
    <li>[ceeb742b] Bump requests from 2.31.0 to 2.32.3</li>
    </ul>
    <!-- raw HTML omitted -->
    </blockquote>
    <p>... (truncated)</p>
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    <li><a
    href="https://github.com/shyamd/mkdocs-bibtex/commit/26da33389b83166c18a33fa58c2a9f5818440576"><code>26da333</code></a>
    FIX: Not invalidating citation blocks with 0 citations (<a
    href="https://redirect.github.com/shyamd/mkdocs-bibtex/issues/290">#290</a>)</li>
    <li><a
    href="https://github.com/shyamd/mkdocs-bibtex/commit/fddf1c204d13fc32fbc444381746d0751d516af2"><code>fddf1c2</code></a>
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    href="https://github.com/shyamd/mkdocs-bibtex/commit/dd0695f52c319a9ba47416da3ad4cbec81470b0f"><code>dd0695f</code></a>
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    remove branching for unsupported python versions</li>
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    Bump validators from 0.20.0 to 0.34.0</li>
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    Bump ruff from 0.4.7 to 0.9.1 (<a
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docs/docs/requirements.txt
docs/requirements.txt

commit 4ce732a0dacb062855a22d969a40d463418e0724
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Wed Jan 22 02:36:09 2025 +0000

    Bump extern/openPMD-api from `2e246cc` to `654bc90` (#859)
    
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    <details>
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extern/openPMD-api

commit 4857f3a525506606acf64007f67ea978e19821a8
Author: StepSecurity Bot <bot@stepsecurity.io>
Date:   Tue Jan 21 16:26:19 2025 -0800

    [StepSecurity] Apply security best practices (#850)
    
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.devcontainer/cuda-container/Dockerfile
.devcontainer/gcc-container/Dockerfile
.github/dependabot.yml
.github/workflows/checkpoint-restart.yml
.github/workflows/clang-tidy.yml
.github/workflows/cmake-macos.yml
.github/workflows/cmake.yml
.github/workflows/codeql.yml
.github/workflows/codespell.yml
.github/workflows/dependency-review.yml
.github/workflows/docs.yml
.github/workflows/hip.yml
.github/workflows/intel.yml
.github/workflows/scorecard.yml
.github/workflows/sonarcloud.yml
.github/workflows/warnings.yml

commit bc8aebab16b3d296690c6fc49b2828e3c81db64d
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Wed Jan 22 00:23:12 2025 +0000

    [pre-commit.ci] pre-commit autoupdate (#855)
    
    <!--pre-commit.ci start-->
    updates:
    - [github.com/pre-commit/mirrors-clang-format: v19.1.6 →
    v19.1.7](https://github.com/pre-commit/mirrors-clang-format/compare/v19.1.6...v19.1.7)
    <!--pre-commit.ci end-->
    
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    Co-authored-by: Ben Wibking <ben@wibking.com>

.pre-commit-config.yaml

commit b5335403b18485a67f036dc71516e683a08a6e46
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Jan 21 16:18:48 2025 -0500

    Temporary workaround for gcc 14 libstdc++ incompatibility with HIP (#857)
    
    ### Description
    Temporarily workaround incompatibilities between the C++ standard
    library headers shipped with GCC 14 and HIP by switching to using the
    C++ standard library headers shipped with Clang (an independent
    implementation).
    
    This may not be viable in production, since (in principle) any
    third-party libraries that use C++ should be complied against the same
    C++ standard library in order to ensure compatibility, but it will at
    least allow the CI to pass again and unblock several PRs. Currently, the
    only C++ library dependency that is not built simultaneously alongside
    Quokka is ADIOS2, which is optional.
    
    ### Related issues
    Fixes https://github.com/quokka-astro/quokka/issues/856.
    
    ### 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).
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    above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] 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`.

.github/workflows/dependencies/dependencies_hip.sh
.github/workflows/hip.yml

commit be31ca33f1b728d3175bb331f0c5c4baffa7fb13
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Mon Jan 13 13:37:33 2025 +1100

    exclude misc-include-cleaner in clang-tidy  (#848)
    
    ### Description
    add `misc-include-cleaner` to exclusion list of .clang-tidy. This will
    get rid of warnings like `warning: no header providing
    "AMREX_GPU_HOST_DEVICE" is directly included` in clang-tidy-review.
    
    ### Related issues
    Should get rid of the `clang-tidy-review` failure in PR #827 .
    
    ### Checklist
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    completed. Denote completed tasks with an `x` inside the square brackets
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    above).
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
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    code.
    - [ ] *(For quokka-astro org members)* I have manually triggered the GPU
    tests with the magic comment `/azp run`.

src/.clang-tidy

commit 900b0ff1e0f3678d30ac6a2d3db777ab5576790e
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Jan 12 17:34:43 2025 -0500

    Update docs for AMD GPUs (#845)
    
    ### Description
    Update docs to reflect minimum ROCm version.
    
    ### Related issues
    https://github.com/quokka-astro/quokka/pull/843
    
    ### 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).
    - [ ] 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`.

README.md
docs/docs/installation.md

commit 5d46ac3a292dc6809648e04e7050950db9238736
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Jan 9 17:38:02 2025 -0500

    Enforce minimum ROCm version >= 6.3 (#843)
    
    ### Description
    Require ROCm 6.3 or newer to compile Quokka for AMD GPUs.
    
    ### Related issues
    Closes https://github.com/quokka-astro/quokka/issues/394.
    
    ### 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).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] *(For quokka-astro org members)* I have manually triggered the GPU
    tests with the magic comment `/azp run`.

.github/workflows/dependencies/dependencies_hip.sh
CMakeLists.txt

commit 7fc222042bf64f5a377eef0f4fe4317e2ccb195f
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Tue Jan 7 09:39:13 2025 +1100

    Bump extern/amrex from `c35aad2` to `b3f6738` (#839)
    
    Bumps [extern/amrex](https://github.com/AMReX-Codes/amrex) from
    `c35aad2` to `b3f6738`.
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/b3f67385e62f387b548389222840486c0fffca57"><code>b3f6738</code></a>
    Make FFT safe for slabs (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4268">#4268</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/bdb4be3decff29d3228c4071ffe6bce1ee4c5800"><code>bdb4be3</code></a>
    Fix sumToLine for multiple components (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4266">#4266</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/7111355437dbf5f8968607f63ea2e656b311d3f9"><code>7111355</code></a>
    Fix WarpX CI (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4267">#4267</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/3fcfcce263bdfdb80297336284b3e9c07c85060d"><code>3fcfcce</code></a>
    Add version of PC::Checkpoint that allows toggling off certain
    components. (#...</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/9643da4522f955767ab78bc03abe206d238f8949"><code>9643da4</code></a>
    Use async sends in particle communication (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4257">#4257</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/8024e3a362ed1dcfd059ce14fcc1316b0b27be00"><code>8024e3a</code></a>
    Fix OMP bug in <a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4238">#4238</a>
    (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4260">#4260</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/50e25ec7ff2175a6377b777a5dcc060b7ad1c4d6"><code>50e25ec</code></a>
    AMReX Algebra: AlgVector and SpMatrix (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4259">#4259</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/96db0a665ff1e6bbe638490fd02d3aafb9188f6b"><code>96db0a6</code></a>
    EBData: New class containing Array4's for all EB data (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4238">#4238</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/6aa80dfba6df10f3e711153ea63fd7169df97da8"><code>6aa80df</code></a>
    FFT::OpenBCSolver: Fix batch mode (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4255">#4255</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/2f10b41e39747e1c38e01c39e08251e20be11309"><code>2f10b41</code></a>
    use abs for spherical 2d area (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4256">#4256</a>)</li>
    <li>Additional commits viewable in <a
    href="https://github.com/AMReX-Codes/amrex/compare/c35aad273352c2526801f7c987fa4b3c551207f6...b3f67385e62f387b548389222840486c0fffca57">compare
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.github/workflows/dependencies/dependencies_hip.sh
extern/amrex

commit 4ae3edefb9823eda8301e768ab1673979c679613
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon Jan 6 18:25:08 2025 +0000

    [pre-commit.ci] pre-commit autoupdate (#841)
    
    <!--pre-commit.ci start-->
    updates:
    - [github.com/pre-commit/mirrors-clang-format: v19.1.5 →
    v19.1.6](https://github.com/pre-commit/mirrors-clang-format/compare/v19.1.5...v19.1.6)
    <!--pre-commit.ci end-->
    
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.pre-commit-config.yaml

commit 3184aa6f595823a89fd6e246287edf5ff0fb8b90
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Wed Jan 1 10:56:41 2025 -0500

    Bump extern/openPMD-api from `269c5e2` to `2e246cc` (#838)
    
    Bumps [extern/openPMD-api](https://github.com/openPMD/openPMD-api) from
    `269c5e2` to `2e246cc`.
    <details>
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    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/2e246cc8be8003071a3aece734ad4e632bd87fd7"><code>2e246cc</code></a>
    JSON/TOML backend: introduce abbreviated IO modes (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1493">#1493</a>)</li>
    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/c639257322dc15a459fc89107f091a81868e4356"><code>c639257</code></a>
    TOUCH IOTask: Avoid setting files as dirty in non-write modes (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1704">#1704</a>)</li>
    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/b8ce8a09cd9715b7cd72462bd030df9b58d1c913"><code>b8ce8a0</code></a>
    Unify Random-Access API and Streaming API into Series::snapshots() (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1592">#1592</a>)</li>
    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/77a55a39ebf1d774997e01429d7bbbab4a98e252"><code>77a55a3</code></a>
    HDF5: Delete and re-create attribute when overwriting with diff. type
    (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1697">#1697</a>)</li>
    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/1bd63c7014f9f331427174e878d97e22b0eed535"><code>1bd63c7</code></a>
    Properly check for empty HDF5_VERSION in CMake (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1702">#1702</a>)</li>
    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/bb45720aeb1c155598b0b8429b98e857bb61b9ff"><code>bb45720</code></a>
    Upgrade appleclang14 build to MacOS 13 (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1703">#1703</a>)</li>
    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/1628567cacf611d563cbfe4937e2b76515a9a1e2"><code>1628567</code></a>
    Conda: Pin HDF5 to 1.14.1 in CI workflow (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1701">#1701</a>)</li>
    <li>See full diff in <a
    href="https://github.com/openPMD/openPMD-api/compare/269c5e22de1bdcb6296896c060eb6b8777af7ae9...2e246cc8be8003071a3aece734ad4e632bd87fd7">compare
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extern/openPMD-api

commit e73ae77f031fb0b2c585cdaf9f74cdeb521e7393
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Wed Jan 1 10:56:16 2025 -0500

    Bump extern/yaml-cpp from `9ce5a25` to `73ef006` (#840)
    
    Bumps [extern/yaml-cpp](https://github.com/jbeder/yaml-cpp) from
    `9ce5a25` to `73ef006`.
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/jbeder/yaml-cpp/commit/73ef0060aaa1a9dc742c1d8a36fa336b35e94035"><code>73ef006</code></a>
    Avoid including &lt;iostream&gt; in library code</li>
    <li><a
    href="https://github.com/jbeder/yaml-cpp/commit/7470c2d871464aa2350dd8eb63ee4d21c1048dec"><code>7470c2d</code></a>
    emitter: Support std::string_view</li>
    <li><a
    href="https://github.com/jbeder/yaml-cpp/commit/8a9a7b74efe41399437a94bcd05f66fcd96f839e"><code>8a9a7b7</code></a>
    Update CONTRIBUTING.md</li>
    <li><a
    href="https://github.com/jbeder/yaml-cpp/commit/d45c4fba3eccb318441ceeccca67345b0dd21a80"><code>d45c4fb</code></a>
    Update README.md</li>
    <li><a
    href="https://github.com/jbeder/yaml-cpp/commit/61db89741d11322751c9e7c98376df17008bc4e9"><code>61db897</code></a>
    Exclude ubuntu/C++ 11/googletest system from the test matrix since it
    doesn't...</li>
    <li><a
    href="https://github.com/jbeder/yaml-cpp/commit/7def2046ffc17535a4581573838d8dc86a89b3b5"><code>7def204</code></a>
    Fix bazel build, and commit module lock file.</li>
    <li><a
    href="https://github.com/jbeder/yaml-cpp/commit/1da813f56aaed91b0bb1f38d770ab4d9cc1776fb"><code>1da813f</code></a>
    ensuring local tags are retained after loading a node + test</li>
    <li><a
    href="https://github.com/jbeder/yaml-cpp/commit/f878043f12a9434a2ef72de3992ec92e6845c889"><code>f878043</code></a>
    Don't install embedded copy of GTest</li>
    <li>See full diff in <a
    href="https://github.com/jbeder/yaml-cpp/compare/9ce5a25188d83b43dd5cd633f2975be10f5d6608...73ef0060aaa1a9dc742c1d8a36fa336b35e94035">compare
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extern/yaml-cpp

commit eac74cdad196d02e6ee69826dad7ae31b2119b1d
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Wed Jan 1 10:55:51 2025 -0500

    Bump extern/regression_testing from `b735d41` to `d1e0aef` (#837)
    
    Bumps
    [extern/regression_testing](https://github.com/AMReX-Codes/regression_testing)
    from `b735d41` to `d1e0aef`.
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    <li><a
    href="https://github.com/AMReX-Codes/regression_testing/commit/d1e0aefc861f6fe589cf6f6c9b714f823429ee6f"><code>d1e0aef</code></a>
    Merge pull request <a
    href="https://redirect.github.com/AMReX-Codes/regression_testing/issues/148">#148</a>
    from BenWibking/delete-compressed-plotfiles</li>
    <li><a
    href="https://github.com/AMReX-Codes/regression_testing/commit/6ab39e5c9959a782f8c302678d4dffe9a5d4d841"><code>6ab39e5</code></a>
    remove delete exe</li>
    <li><a
    href="https://github.com/AMReX-Codes/regression_testing/commit/d76cf24383063427c03789922c0134f9f3894389"><code>d76cf24</code></a>
    Merge pull request <a
    href="https://redirect.github.com/AMReX-Codes/regression_testing/issues/150">#150</a>
    from BenWibking/patch-1</li>
    <li><a
    href="https://github.com/AMReX-Codes/regression_testing/commit/be6d77baf285e7547e6b732f14b6bbc7a0e8a3e0"><code>be6d77b</code></a>
    add bokeh to requirements.txt</li>
    <li><a
    href="https://github.com/AMReX-Codes/regression_testing/commit/e9a20b84be32c83e45fcddad3f49227ecf840eb1"><code>e9a20b8</code></a>
    delete compressed plotfiles, executable</li>
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extern/regression_testing

commit d7de1e8f0dd4b2cda578690774601089d65b9c38
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Wed Jan 1 10:54:59 2025 -0500

    Bump extern/fmt from `385c01d` to `e3ddede` (#836)
    
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    `e3ddede`.
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    <li><a
    href="https://github.com/fmtlib/fmt/commit/e3ddede6c4ee818825c4e5a6dfa1d384860c27d9"><code>e3ddede</code></a>
    Update version</li>
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    href="https://github.com/fmtlib/fmt/commit/e9ec4fdc88f1bc8e91edf1567f8ac7ba0d1d81d5"><code>e9ec4fd</code></a>
    Bump version</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/feb72126b438e670e7f6474b9f211b6114ed68ba"><code>feb7212</code></a>
    Readd FMT_NO_UNIQUE_ADDRESS</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/8d517e54c99b6e87117bd0864d3ba9cd06f6efb7"><code>8d517e5</code></a>
    Update changelog</li>
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    href="https://github.com/fmtlib/fmt/commit/563fc74ae491a7d24f3636643ee018375de9191a"><code>563fc74</code></a>
    Update changelog</li>
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    href="https://github.com/fmtlib/fmt/commit/3e04222d53e683f60a4ad79016a9c6d82186bbb5"><code>3e04222</code></a>
    Restore ABI compatibility with 11.0.2</li>
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    href="https://github.com/fmtlib/fmt/commit/853df39d0a1f5b0f8c584c856f84ed3c553fa464"><code>853df39</code></a>
    Mention compile-time formatting</li>
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    href="https://github.com/fmtlib/fmt/commit/11742a09c7e575393ae482b3219030caadb34743"><code>11742a0</code></a>
    Clarify that format_string should be used instead of fstring</li>
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    Document fstring</li>
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    href="https://github.com/fmtlib/fmt/commit/5fa4bdd758073ad64619fc53d345255b5abed5ec"><code>5fa4bdd</code></a>
    Define CMake components to allow docs to be installed separately (<a
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extern/fmt

commit fb24ba35f6bcc5ed62b627a8fbd456e0a578409c
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Dec 19 17:28:20 2024 -0500

    Update .clang-tidy (#828)
    
    ### Description
    Avoid using the
    [`llvm-header-guard`](https://clang.llvm.org/extra/clang-tidy/checks/llvm/header-guard.html)
    check. It doesn't work correctly with the GitHub action we use to run
    clang-tidy.
    
    Also disable the
    [`performance-enum-size`](https://clang.llvm.org/extra/clang-tidy/checks/performance/enum-size.html)
    check. It doesn't appear to be useful.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] 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`.

src/.clang-tidy

commit fb5587535e31aa1039e6da34bdf32b337907a5b7
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Dec 16 20:16:54 2024 -0500

    Update quokka-tests.ini (#825)
    
    ### Description
    Updates the configuration file for the nightly regression tests. This
    should prevent the disk quota from being hit as quickly. This also
    updates git submodules when checking out new versions of Quokka before
    running the tests (this was not done previously).
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] 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`.

extern/regression_testing
regression/quokka-tests.ini

commit 3805dfb1b984ff19b60e31c0da90b36871431264
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon Dec 16 18:15:05 2024 +0000

    [pre-commit.ci] pre-commit autoupdate (#824)
    
    <!--pre-commit.ci start-->
    updates:
    - [github.com/pre-commit/mirrors-clang-format: v19.1.4 →
    v19.1.5](https://github.com/pre-commit/mirrors-clang-format/compare/v19.1.4...v19.1.5)
    <!--pre-commit.ci end-->
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

commit 79e99cbc31b2b8ceceb818e89715ca1fd3b3d25e
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Dec 13 20:15:35 2024 -0500

    Update cron schedule for regression tests (#823)
    
    ### Description
    The cron job schedule is in UTC, not local timezone. This changes the
    nightly regression tests to run at 14:00 UTC (1am Australian Eastern
    Daylight Time).
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] 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`.

.ci/azure-pipelines-regression.yml

commit 8d8735f3a8d33cb273818e8fcfd86d62f6f003b4
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Dec 13 20:07:41 2024 -0500

    Update .clang-tidy (#821)
    
    ### Description
    Due to a change in configuration file format, clang-tidy had stopped
    working. This should fix it.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] 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`.

src/.clang-tidy

commit 8235b079dc91f905e58e438573900dea75319e13
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Dec 13 20:07:22 2024 -0500

    Reduce walltime for RandomBlast regression test (#822)
    
    ### Description
    It takes about 1 hour to run, which is too long. This changes the max
    simulation time to 1e5 yr (instead of 1e6 yr), so the regression test
    should complete about 10x faster.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] 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`.

tests/RandomBlast_regression.in

commit 01c5186695cc3c8911f706f322209baad459c9bc
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Dec 13 14:03:36 2024 +1100

    add print_cycle_timing runtime option (#819)
    
    ### Description
    Adds the runtime option `print_cycle_timing = 1` to output the elapsed
    walltime (in seconds) of each coarse timestep.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] *(For quokka-astro org members)* I have manually triggered the GPU
    tests with the magic comment `/azp run`.

src/simulation.hpp
tests/benchmark_unigrid_1024.in
tests/benchmark_unigrid_2048.in
tests/benchmark_unigrid_4096.in
tests/benchmark_unigrid_512.in
tests/benchmark_unigrid_8192.in

commit a4a1d4696981f7a59fab2cc7902e2ffb96a6e6bb
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Dec 13 09:47:10 2024 +1100

    rename {x,y,z}-velocity to {x,y,z}-RiemannSolverVelocity in plotfiles (#818)
    
    ### Description
    Renames the plotfile variables for the cell-centered averages of the
    face-centered velocities from the Riemann solver to:
    `x-RiemannSolverVelocity`, `y-RiemannSolverVelocity`, and
    `z-RiemannSolverVelocity`.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] *(For quokka-astro org members)* I have manually triggered the GPU
    tests with the magic comment `/azp run`.

src/QuokkaSimulation.hpp

commit 993f0bc4830b68cccc24170b906166723632d794
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Dec 12 13:18:48 2024 +1100

    Fixes for Setonix (#817)
    
    ### Description
    Uses `amrex::` math functions instead of `std::` math functions in some
    cases. This is due to problems with the GCC 14 C++ standard library
    headers.
    
    Adds new `setonix.profile` and job scripts. 64-node jobs appear to work
    now.
    
    Scaling test:
    ![Screenshot 2024-12-11 at 2 25
    37 PM](https://github.com/user-attachments/assets/b55451a8-7aff-4e2c-a616-0361b84004dd)
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] 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`.

scripts/setonix-1node.submit
scripts/setonix-64nodes.submit
scripts/setonix-8nodes.submit
scripts/setonix-gpu.profile
src/cooling/GrackleLikeCooling.hpp
src/cooling/TabulatedCooling.hpp
src/hydro/NSCBC_inflow.hpp
src/hydro/NSCBC_outflow.hpp
src/math/Interpolate2D.hpp
src/math/ODEIntegrate.hpp

commit e45f4e79448099fba12495ad1604258d9fddee8b
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Dec 12 09:28:21 2024 +1100

    Update ROCm version in dependencies_hip.sh (#816)
    
    ### Description
    For GitHub actions CI tests, compile the code using ROCm 5.7.1 (the
    latest version available on Setonix).
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] 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`.

.github/workflows/dependencies/dependencies_hip.sh

commit 1d9d0786aa231e4a85105bcd5825f4dbc7506b60
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Dec 12 09:24:57 2024 +1100

    add scripts to run on Frontier (#813)
    
    ### Description
    Adds scripts to run on OLCF Frontier. Changes one instance of
    `std::array` to `amrex::GpuArray` to get it to compile on Frontier.
    
    Weak scaling numbers:
    ![chart
    (1)](https://github.com/user-attachments/assets/8f6bc67f-99dc-4ff7-ad3c-a78791b032f9)
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] 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>

scripts/frontier-1node.submit
scripts/frontier-4096node.submit
scripts/frontier-512node.submit
scripts/frontier-64node.submit
scripts/frontier-8node.submit
scripts/frontier.profile
src/hydro/HydroState.hpp
tests/benchmark_unigrid_8192.in

commit 83150cf76a3225313ad1838d0a415431c8d1f5eb
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Wed Dec 11 15:01:00 2024 +1100

    Use RSLA in all dust tests (#811)
    
    ### Description
    Since in all practical runs we will use RSLA, it's important to test
    that our RSLA method gives the exacted result. In this PR, I update
    RadDust, RadMarshakDust, and RadMarshakDustPE tests to use RSLA. The
    analytical solutions are updated to include RSLA as well. In all these
    tests, RSLA changes the results significantly because 1) in the Marshak
    tests, the problem is in the optically thin limit, so the propagation
    speed is reduced, or 2) in the RadDust test, the gas has an initial
    temperature of $T_0$ and cools to a temperature $T_1$ through thermal
    emission: $T_0$ $C_V T_0 = C_V T_1 + (\hat{c} / c) a_R T_1^4$ .
    
    This also prepares for the variable RSLA method I'm working on.
    
    ### Related issues
    None.
    
    ### 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>

extern/data/dust/rad_dust_exact.csv
extern/data/dust/rad_dust_exact_chat0.1.csv
extern/data/dust/rad_dust_exact_chat0.8.csv
src/problems/RadDust/test_rad_dust.cpp
src/problems/RadDustMG/test_rad_dust_MG.cpp
src/problems/RadMarshakDust/test_radiation_marshak_dust.cpp
src/problems/RadMarshakDustPE/test_radiation_marshak_dust_and_PE.cpp
src/radiation/radiation_dust_system.hpp
tests/RadDust.in
tests/RadMarshakDust.in
tests/RadMarshakDustPEcoupled.in
tests/RadMarshakDustPEdecoupled.in

commit 5835ef88049b3625adb68790852be78b050bc6cc
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Dec 11 09:21:53 2024 +1100

    Add radiation-driven shell to regression tests (#810)
    
    ### Description
    Adds this problem to the nightly regression test suite. There was also a
    bug in the initial conditions in the radiation flux in converting from
    spherical to Cartesian flux components (now fixed).
    
    At late times, the simulation still has a slightly discrepancy w.r.t.
    the semi-analytic solution (similar to that shown in the original code
    paper). This is most likely due to initial shell thickness being quite
    significant. (There is not an easy solution to this, since there is no
    steady-state solution that satisfies the M1 closure for sufficiently
    thin shells.)
    
    
    ![shell_velocity](https://github.com/user-attachments/assets/0473f97c-3506-4d40-94c5-a9b84e2900f0)
    
    
    https://github.com/user-attachments/assets/8851d7cd-9d92-4de6-ac7e-ab5fef035af5
    
    ### Related issues
    Closes https://github.com/quokka-astro/quokka/issues/743.
    
    ### 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).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] *(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>

extern/dust_shell/initial_conditions.txt
extern/dust_shell/matplotlibrc
extern/dust_shell/solution.py
regression/quokka-tests.ini
src/problems/RadhydroShell/CMakeLists.txt
src/problems/RadhydroShell/test_radhydro_shell.cpp
tests/radhydro_shell.in
tests/radhydro_shell_regression.in

commit ba0007690237e1bcd0c6e9668e1bd09b248fd03b
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Dec 11 09:20:01 2024 +1100

    use upload-artifact@v4 (#812)
    
    ### Description
    GitHub is disabling older versions of this action. See
    https://github.com/actions/upload-artifact?tab=readme-ov-file#actionsupload-artifact.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] 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`.

.github/workflows/docs.yml
.github/workflows/scorecard.yml

commit 214de9d5e9ff811e564230f3fd694b8cf8902d09
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Dec 9 11:27:20 2024 +1100

    fix openPMD plotfile output (#804)
    
    ### Description
    Fixes a segmentation fault during openPMD plotfile output when
    face-centered variables are enabled.
    
    There was an implicit assumption in
    `AMRSimulation<problem_t>::AverageFCToCC()` that the number of
    face-centered ghost zones was the same as the number of cell-centered
    ghost zones. This PR allows the number of ghosts to differ.
    
    I manually tested that this works inside the CUDA dev container by
    compiling Quokka with `-DQUOKKA_OPENPMD=ON`, running the HydroBlast3D
    problem, and then examining the output files with
    [openPMD-viewer](https://github.com/openPMD/openPMD-viewer).
    
    ### Related issues
    Fixes https://github.com/quokka-astro/quokka/issues/742.
    
    ### 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).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] *(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>

src/simulation.hpp

commit e8a181b1fa51cea0feeb7ede21a5623d1bda7b44
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Sat Dec 7 16:22:16 2024 +1100

    add 'cellUpdates_ > 0' check (#808)
    
    ### Description
    Add checks `if (step == 0)` and `cellUpdates_ == 0` in the end of a
    simulation to prevent 'division by zero' error when max_time = 0.0 or
    max_timesteps = 0.
    
    ### Related issues
    Closes #721
    
    ### 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.
    - [x] *(For quokka-astro org members)* I have manually triggered the GPU
    tests with the magic comment `/azp run`.

src/QuokkaSimulation.hpp
src/simulation.hpp

commit 06470346e6b642008582dd6612e14d558c106d8e
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sun Dec 1 12:27:40 2024 -0500

    Bump extern/amrex from `b9d549b` to `c35aad2` (#802)
    
    Bumps [extern/amrex](https://github.com/AMReX-Codes/amrex) from
    `b9d549b` to `c35aad2`.
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/c35aad273352c2526801f7c987fa4b3c551207f6"><code>c35aad2</code></a>
    FFT::PoissonHybrid: Add solve() needed by ERF (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4250">#4250</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/4a3a5ff9052afb70bcacc3ac5e7ed557653bf11a"><code>4a3a5ff</code></a>
    Add CMake option: AMReX_CUDA_OBJDIR_AS_TEMPDIR (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4246">#4246</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/1c8b5453023acb66bf65580b56e2f2f1dfd40c8e"><code>1c8b545</code></a>
    FFT::PoissonHybrid: Support non-periodic boundaries in x &amp; y
    directions (<a
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    Fix dangling-reference warnings for particle functions. (<a
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    Parser: Use malloc if Arena is not ready (<a
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    Add portable implementation of random numbers drawn from the Gamma
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    Fix warning and undefined behavior (<a
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    Implementation of Bessel functions of second kind (yn) (<a
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extern/amrex

commit 8cd876f38880c141dc154ef63fe28a4e05452698
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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    Bump extern/yaml-cpp from `c2bec4c` to `9ce5a25` (#800)
    
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    fix: spell fix</li>
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    patch: move dragonbox.h from 'include' folder to 'src' folder</li>
    <li><a
    href="https://github.com/jbeder/yaml-cpp/commit/5d9e4b6251b3cfc9fff41a8d980c1a3bfdfaf019"><code>5d9e4b6</code></a>
    patch: split fp_to_string.h into fptostring.h and fptostring.cpp</li>
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extern/yaml-cpp

commit 5d574f92a5de54f676625f89f6e71c9a8fed341c
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sun Dec 1 10:48:13 2024 -0500

    Bump extern/fmt from `4b8e283` to `385c01d` (#801)
    
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    Allow bit_cast to work for 80bit long double (<a
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    Remove an old workaround</li>
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    <li><a
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    <li><a
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    Sort specifiers</li>
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extern/fmt

commit 2f1fda0168063e71baf09ad349e0342012c414dd
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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    Bump extern/openPMD-api from `94a3a8f` to `269c5e2` (#803)
    
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extern/openPMD-api

commit 09f158915e6a72e3bcc1c6200d680f5cb1baaa8d
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Nov 30 13:49:33 2024 +1100

    fix flags for NVHPC compiler (#799)
    
    ### Description
    Adds the correct flags for the NVHPC compiler to disable fused
    multiply-add instructions (FMA).
    
    ### Related issues
    Fixes https://github.com/quokka-astro/quokka/issues/758
    
    ### 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
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    above).
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] *(For quokka-astro org members)* I have manually triggered the GPU
    tests with the magic comment `/azp run`.

src/CMakeLists.txt

commit d8509736807a3c96a85674b1b3c1e295e370790d
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon Nov 25 18:15:02 2024 +0000

    [pre-commit.ci] pre-commit autoupdate (#798)
    
    <!--pre-commit.ci start-->
    updates:
    - [github.com/pre-commit/mirrors-clang-format: v19.1.3 →
    v19.1.4](https://github.com/pre-commit/mirrors-clang-format/compare/v19.1.3...v19.1.4)
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.pre-commit-config.yaml

commit 727f6031e894fe3003957971785046e17e542a12
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Tue Nov 26 01:45:26 2024 +1100

    update yt: replace AMReXDataset with yt.load (#797)
    
    ### Description
    Since yt version 4.4.0 (or perhaps 4.3.0), you can read Quokka outputs
    with `yt.load`. It returns a `QuokkaDataset`, which inherits from
    `AMReXDataset`. This PR modifies `particle_orbit_plot.py` to reflect
    this update. I have tested running ``particle_orbit_plot.py` on my own
    computer and it works.
    
    ### Related issues
    N/A
    
    ### Checklist
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    completed. Denote completed tasks with an `x` inside the square brackets
    `[ ]` in the Markdown source below:_
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    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`.

src/problems/BinaryOrbitCIC/particle_orbit_plot.py

commit 0ee3ebc059abc1e6a9930e53b768f02771b60dab
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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    Bump ZedThree/clang-tidy-review from 0.20.0 to 0.20.1 (#796)
    
    Bumps
    [ZedThree/clang-tidy-review](https://github.com/zedthree/clang-tidy-review)
    from 0.20.0 to 0.20.1.
    <details>
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    <p><em>Sourced from <a
    href="https://github.com/zedthree/clang-tidy-review/releases">ZedThree/clang-tidy-review's
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    <blockquote>
    <h2>v0.20.1</h2>
    <h2>What's Changed</h2>
    <ul>
    <li>fix(split-review): search by string in names by <a
    href="https://github.com/Nerixyz"><code>@​Nerixyz</code></a> in <a
    href="https://redirect.github.com/ZedThree/clang-tidy-review/pull/140">ZedThree/clang-tidy-review#140</a></li>
    </ul>
    <p><strong>Full Changelog</strong>: <a
    href="https://github.com/ZedThree/clang-tidy-review/compare/v0.20.0...v0.20.1">https://github.com/ZedThree/clang-tidy-review/compare/v0.20.0...v0.20.1</a></p>
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    <ul>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/e005a6ddf5cc4884b4bcab9930df255438183fd1"><code>e005a6d</code></a>
    Merge pull request <a
    href="https://redirect.github.com/zedthree/clang-tidy-review/issues/140">#140</a>
    from Nerixyz/fix/split-review</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/94e005676729057253668afe4b4fddeb3344e162"><code>94e0056</code></a>
    chore: remove redundant <code>Path(..)</code></li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/74d6cb58ff54aa71227d67c6df34b86cec0a7fb3"><code>74d6cb5</code></a>
    fix: search by string in names</li>
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commit 83d3bf95b155a4a3cc9c9b5ac970619ffad91420
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Nov 21 18:21:03 2024 -0500

    Update pull request template (#795)
    
    ### Description
    This removes some items from the pull request checklist that probably
    aren't necessary anymore:
    * GitHub will auto-assign a reviewer to all PRs now that we have code
    owners defined.
    * The testing infrastructure is robust enough that's not strictly
    necessary to test on one's own local computer before creating a PR
    (although still recommended).
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] 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).
    - [ ] 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`.

.github/pull_request_template.md

commit bda41562ee293fde97970a10f5766571a1d0f5cb
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Nov 21 18:20:25 2024 -0500

    Disable building unused linear solvers from AMReX (#794)
    
    ### Description
    This disables building the specialized linear solvers included in AMReX
    that are typically used for incompressible and/or electromagnetic codes.
    This has no effect on the code, but it should make compiling Quokka
    faster.
    
    ### Related issues
    Closes https://github.com/quokka-astro/quokka/issues/770.
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [ ] I have requested a reviewer for this PR.

CMakeLists.txt

commit 3f282b4d9b6ad999c4ace9d1bdd84fbd5af3cf28
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Nov 15 19:52:00 2024 -0500

    remove scripts to run on Summit (#793)
    
    ### Description
    Summit was decommissioned today, November 15, 2024. It was a nice
    machine. RIP.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] I have added a link to any related issues see (see above).
    - [ ] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [ ] I have requested a reviewer for this PR.

scripts/summit-1node.bsub
scripts/summit-4096node.bsub
scripts/summit-512node.bsub
scripts/summit-64node.bsub
scripts/summit-8node.bsub
scripts/summit.profile

commit ec76a04b6ed61db228917cb4724bfc3d2e01d474
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Nov 11 09:56:27 2024 -0500

    Bump ZedThree/clang-tidy-review from 0.19.0 to 0.20.0 (#792)
    
    Bumps
    [ZedThree/clang-tidy-review](https://github.com/zedthree/clang-tidy-review)
    from 0.19.0 to 0.20.0.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
    href="https://github.com/zedthree/clang-tidy-review/releases">ZedThree/clang-tidy-review's
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    <h2>v0.20.0</h2>
    <h2>What's Changed</h2>
    <ul>
    <li>ensure diff paths are the same on all platforms by <a
    href="https://github.com/bwrsandman"><code>@​bwrsandman</code></a> in <a
    href="https://redirect.github.com/ZedThree/clang-tidy-review/pull/130">ZedThree/clang-tidy-review#130</a></li>
    <li>Fix regression to cull_comments by <a
    href="https://github.com/bwrsandman"><code>@​bwrsandman</code></a> in <a
    href="https://redirect.github.com/ZedThree/clang-tidy-review/pull/128">ZedThree/clang-tidy-review#128</a></li>
    <li>fix: support empty commits/PRs by <a
    href="https://github.com/Nerixyz"><code>@​Nerixyz</code></a> in <a
    href="https://redirect.github.com/ZedThree/clang-tidy-review/pull/132">ZedThree/clang-tidy-review#132</a></li>
    <li>Add a run time profile report by <a
    href="https://github.com/bwrsandman"><code>@​bwrsandman</code></a> in <a
    href="https://redirect.github.com/ZedThree/clang-tidy-review/pull/127">ZedThree/clang-tidy-review#127</a></li>
    <li>Use task queue to spawn multiple processes of tidy by <a
    href="https://github.com/bwrsandman"><code>@​bwrsandman</code></a> in <a
    href="https://redirect.github.com/ZedThree/clang-tidy-review/pull/126">ZedThree/clang-tidy-review#126</a></li>
    <li>Fix remaining Ruff lints and (most) type errors by <a
    href="https://github.com/Nerixyz"><code>@​Nerixyz</code></a> in <a
    href="https://redirect.github.com/ZedThree/clang-tidy-review/pull/137">ZedThree/clang-tidy-review#137</a></li>
    <li>Fix a bunch of ruff issues by <a
    href="https://github.com/ZedThree"><code>@​ZedThree</code></a> in <a
    href="https://redirect.github.com/ZedThree/clang-tidy-review/pull/133">ZedThree/clang-tidy-review#133</a></li>
    </ul>
    <p><strong>Full Changelog</strong>: <a
    href="https://github.com/ZedThree/clang-tidy-review/compare/v0.19.0...v0.20.0">https://github.com/ZedThree/clang-tidy-review/compare/v0.19.0...v0.20.0</a></p>
    </blockquote>
    </details>
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/95398232f4a8b8b8d7cd3191370f4ac077ca2046"><code>9539823</code></a>
    Merge pull request <a
    href="https://redirect.github.com/zedthree/clang-tidy-review/issues/133">#133</a>
    from ZedThree/linting</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/3aea09f3850d4fc1cd1aaff9aa99dbdf2613679b"><code>3aea09f</code></a>
    Use <code>Path</code> in more places</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/30fd7040161543f122ea880de9f0d3dc68149d3c"><code>30fd704</code></a>
    Merge branch 'master' into linting</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/1ad1991d59519a3afeea71210ccadbf87a52573d"><code>1ad1991</code></a>
    Merge pull request <a
    href="https://redirect.github.com/zedthree/clang-tidy-review/issues/137">#137</a>
    from Nerixyz/chore/more-linting</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/87a563ce94ff56fa79e055f3d503352b1b2c14e7"><code>87a563c</code></a>
    fix: correct various types</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/5e9fb02cd82bf6494d4beb0b131af93e0d3e1fa3"><code>5e9fb02</code></a>
    fix: use positional args for regex (<code>B034</code>)</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/71fa1583db3d7f4ec226ef3d6c87b57be3a687e1"><code>71fa158</code></a>
    fix: merge <code>with</code> (<code>SIM117</code>)</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/afd3a850fa8d6b9bcaec39c2905dab421a54938b"><code>afd3a85</code></a>
    fix: resolve <code>PTH*</code> lints</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/88d4e32f25ec19477e003e775780c4bce42c5ce4"><code>88d4e32</code></a>
    Merge pull request <a
    href="https://redirect.github.com/zedthree/clang-tidy-review/issues/126">#126</a>
    from bwrsandman/multiprocess</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/02da2438af97cc01290bba072e379bd77f9aaa75"><code>02da243</code></a>
    Use task queue to spawn multiple processes of tidy</li>
    <li>Additional commits viewable in <a
    href="https://github.com/zedthree/clang-tidy-review/compare/v0.19.0...v0.20.0">compare
    view</a></li>
    </ul>
    </details>
    <br />
    
    
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commit e470861fa518d8a9d2c86d1109aa210c19449040
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Nov 8 09:45:52 2024 -0500

    Write 2D plotfiles for projections (#791)
    
    ### Description
    Writes projections as 2D plotfiles, rather than as 3D plotfiles with one
    cell in the 3rd dimension.
    
    ### Related issues
    Fixes https://github.com/quokka-astro/quokka/issues/685.
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/CMakeLists.txt
src/QuokkaSimulation.hpp
src/io/projection.cpp
src/io/projection.hpp
src/linear_advection/AdvectionSimulation.hpp
src/problems/NSCBC/channel.cpp
src/problems/ShockCloud/cloud.cpp
src/simulation.hpp

commit 89c5ad23aa9da5854e355afa216da597b44cd034
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Tue Nov 5 11:29:26 2024 -0500

    Bump extern/Microphysics from `fb8b008` to `397d3d2` (#787)
    
    Bumps [extern/Microphysics](https://github.com/psharda/Microphysics)
    from `fb8b008` to `397d3d2`.
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/397d3d206d0de0f494a728279f448ba6485c37d5"><code>397d3d2</code></a>
    Add cosmic rays to metal chemistry (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1651">#1651</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/ca10c3ead328230f1844f70eb7aac6bacfebd137"><code>ca10c3e</code></a>
    Update README to mention ISM chemistry (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1652">#1652</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/01cc637f10e8b2079059514f609d244152b18eca"><code>01cc637</code></a>
    Correctly handle ices in metal chemistry (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1650">#1650</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/1e1dc1440489abf82c55247b72507bb9bf15740d"><code>1e1dc14</code></a>
    Remove unused param (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1648">#1648</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/d98d39bd2f0d97ac2ad0dba554b9ffc787001253"><code>d98d39b</code></a>
    Define Tdust as aux var (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1649">#1649</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/3961b439ba5c8193975018300e4c23a09b533206"><code>3961b43</code></a>
    update changes for 24.09</li>
    <li>See full diff in <a
    href="https://github.com/psharda/Microphysics/compare/fb8b0080c25fba6b224fc188ece89f962a34cc7f...397d3d206d0de0f494a728279f448ba6485c37d5">compare
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extern/Microphysics

commit 69cf0409187248be3f28c04cfea184adff5843b6
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon Nov 4 18:19:35 2024 +0000

    [pre-commit.ci] pre-commit autoupdate (#790)
    
    <!--pre-commit.ci start-->
    updates:
    - [github.com/pre-commit/mirrors-clang-format: v19.1.2 →
    v19.1.3](https://github.com/pre-commit/mirrors-clang-format/compare/v19.1.2...v19.1.3)
    <!--pre-commit.ci end-->
    
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.pre-commit-config.yaml

commit 4fa830c2efac48aa56fb2083f137cba5cf07cf92
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Mon Nov 4 10:59:51 2024 +1100

    Add support for unit systems: CGS, CONSTANTS, CUSTOM (#782)
    
    ### Description
    
    In this PR we add the ability to allow the user to choose from one of
    the three unit systems: `CGS`, `CUSTOM`, and `CONSTANTS`.
    
    **CGS:**
    By setting `unit_system = UnitSystem::CGS`, the user opt to use the CGS
    units and no constants definition are required. If `is_radiation_enabled
    = true`, the user need to also specify `c_hat_over_c`. See examples in
    HydroShuOsher and RadTube tests.
    ```C++
    template <> struct Physics_Traits<TubeProblem> {
            static constexpr UnitSystem unit_system = UnitSystem::CGS;
            ...
    };
    
    template <> struct RadSystem_Traits<TubeProblem> {
            static constexpr double c_hat_over_c = 0.1;
            ...
    };
    ```
    
    **CONSTANTS:**
    By setting `unit_system = UnitSystem::CONSTANTS`, the user need to
    define `boltzmann_constant` and `gravitational_constant` for hydro
    simulations. If `is_radiation_enabled = true`, the user need to also
    define `c_light`, `c_hat_over_c`, and `radiation_constant`. See examples
    in the `RadhydroShock` test.
    ```C++
    template <> struct Physics_Traits<problem_t> {
            static constexpr UnitSystem unit_system = UnitSystem::CONSTANTS;
            static constexpr double gravitational_constant = 1.0;
            static constexpr double boltzmann_constant = 1.0;
            static constexpr double c_light = 1.0;
            static constexpr double radiation_constant = 1.0;
            ...
    };
    
    template <> struct RadSystem_Traits<problem_t> {
            static constexpr double c_hat_over_c = 1.0;
            ...
    };
    ```
    
    **CUSTOM:**
    By setting `unit_system = UnitSystem::CUSTOM`, the user opt to use a
    custom unit system. The values of the following variables need to be
    given in cgs units: `unit_length, unit_mass, unit_time,
    unit_temperature`. If `is_radiation_enabled = true`, the user need to
    also define `c_hat` in code units. See examples in the `RadLineCooling`
    and `RadhydroShockCGS` tests.
    ```C++
    template <> struct Physics_Traits<problem_t> {
            // A custom unit system is used here to replicate a dimentionless unit system (c = k_B = a_rad = G = 1), for testing units conversion. This is similar to, but not exact, the Planck unit system.
            static constexpr UnitSystem unit_system = UnitSystem::CUSTOM;
            static constexpr double unit_length = 1.733039549e-33;
            static constexpr double unit_mass = 2.333695323e-05;
            static constexpr double unit_time = 5.780797690e-44;
            static constexpr double unit_temperature = 1.519155670e+32;
            ...
    };
    
    template <> struct RadSystem_Traits<problem_t> {
            static constexpr double c_hat_over_c = 0.1;
            ...
    };
    ```
    
    Other changes include:
    1. The following variables are available in `AMRSimulation` class:
    `unit_length, unit_mass, unit_time, unit_temperature`. They give the
    unit length, mass, time, and temperature in CGS units (cm, g, s, and K).
    2. The code will write the following variables into `metadata.yaml`
    located inside every plotfile and checkpoint outputs: `unit_length,
    unit_mass, unit_time, unit_temperature, c, c_hat, k_B, a_rad, G`. The
    values of `unit_xxx` are given in CGS units and the values of `c, c_hat,
    k_B, a_rad, G` are given in code units.
    3. The gravitational constant is no longer a runtime parameter. It's
    defined by the unit system the user specifies or by
    `Physics_Traits::gravitational_constant`.
    
    A typical `metadata.yaml` file looks like this:
    
    ```
    a_rad: 7.5657313567241239e-15
    c_hat: 402955198.55200708
    c: 29979245800
    G: 6.6742800000000007e-08
    unit_length: 1
    unit_time: 1
    k_B: 1.3806488e-16
    unit_temperature: 1
    unit_mass: 1
    ```
    
    Footnote: When `CONSTANTS` is chosen, I set `unit_xxx` to `NAN` for two
    reasons. First, when radiation is turned off, the units are
    unconstrained because it's not possible to derive `unit_xxx` from only
    two constants, `boltzmann_constant` and `gravitational_constant`.
    Second, the `CONSTANTS` unit system is only used for testing purpose and
    we don't care about the physical dimensions of the variables.
    
    ### Related issues
    Resolves #780
    
    ### 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). ✅ 2024-10-27
    - [x] I have added a link to any related issues see (see above). ✅
    2024-10-27
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    ✅ 2024-10-27
    - [x] I have added tests for any new physics that this PR adds to the
    code. ✅ 2024-10-27
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR. ✅ 2024-10-27
    
    
    
    ### Appendix: Units conversion
    
    Here I show how to convert between CGS, CONSTANTS, and CUSTOM unit
    system.
    
    Let the code units of length, mass, time, and temperature expressed in
    CGS units be $u_l, u_m, u_t, u_T$. Let $G$, $k_B$, $c$, and $a_R$ be the
    values of the gravitational constant, Boltzmann constant, speed of
    light, and radiation constant in CGS units, respectively. Assume the
    values of those constants in code units are $\hat{G}, \hat{k}_B,
    \hat{c}, \hat{a}_R$. The following relations apply:
    
    $$
    \begin{aligned}
    \bar{G} & \equiv G / \hat{G} = u_l^3 u_m^{-1} u_t^{-2}  \\
    \bar{k}_B & \equiv k_B / \hat{k}_B = u_l^2 u_m u_t^{-2} u_T^{-1} \\
    \bar{c} & \equiv c / \hat{c} = u_l  u_t^{-1} \\
    \bar{a}_R & \equiv a_R/\hat{a}_R = u_l^{-1} u_m u_t^{-2} u_T^{-4}
    \end{aligned}
    $$
    
    To convert from $\hat{G}$ etc into $u_l$ etc, we want to solve for $u_l$
    etc from this set of four equations. By taking logarithm on both sides
    of the equations, we can turn them into a system of linear equations:
    
    $$
    \begin{aligned}
    & \left(\begin{array}{cccc}
    3 & -1 & -2 & 0 \\
    2 & 1 & -2 & -1 \\
    1 & 0 & -1 & 0 \\
    -1 & 1 & -2 & -4
    \end{array}\right)\left(\begin{array}{l}
    \log u_l \\
    \log u_m \\
    \log u_t \\
    \log u_T
    \end{array}\right)=\left(\begin{array}{l}
    \log \bar{G} \\
    \log \bar{k}_B \\
    \log \bar{c} \\
    \log \bar{a}_R
    \end{array}\right)
    \end{aligned}
    $$
    
    A simple matrix inversion gives
    
    $$
    \begin{aligned}
    \left(\begin{array}{l}
    \log u_l \\
    \log u_m \\
    \log u_t \\
    \log u_T
    \end{array}\right)=\left(\begin{array}{cccc}
    1 / 2 & 2 / 3 & -2 & -1 / 6 \\
    -1 / 2 & 2 / 3 & 0 & -1 / 6 \\
    1 / 2 & 2 / 3 & -3 & -1 / 6 \\
    -1 / 2 & -1 / 3 & 2 & -1 / 6
    \end{array}\right)\left(\begin{array}{c}
    \log \bar{G} \\
    \log \bar{k}_B \\
    \log \bar{c} \\
    \log \bar{a}_R
    \end{array}\right)
    \end{aligned}
    $$
    
    or, expressing explicitly,
    
    $$
    \begin{aligned}
    u_l&=\bar{G}^{1/2} \bar{c}^{-2} \bar{d} \\
    u_r&=\bar{G}^{-1/2} \bar{d} \\
    u_t&=\bar{G}^{1/2} \bar{c}^{-3} \bar{d} \\
    u_T&=\bar{G}^{-1/2} \bar{c}^2\left(\bar{k}^2 \bar{a}_R\right)^{-1 / 6}
    \end{aligned}
    $$
    
    where $\bar{d} \equiv \left(\bar{k}^4 / \bar{a}_R\right)^{1 / 6}$. These
    equations are used to derive `unit_length` etc in the `RadLineCooling`
    test.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/QuokkaSimulation.hpp
src/hydro/EOS.hpp
src/hydro/NSCBC_inflow.hpp
src/physics_info.hpp
src/problems/Advection/test_advection.cpp
src/problems/Advection2D/test_advection2d.cpp
src/problems/AdvectionSemiellipse/test_advection_semiellipse.cpp
src/problems/BinaryOrbitCIC/binary_orbit.cpp
src/problems/Cooling/test_cooling.cpp
src/problems/FCQuantities/test_fc_quantities.cpp
src/problems/HydroBlast2D/test_hydro2d_blast.cpp
src/problems/HydroBlast3D/test_hydro3d_blast.cpp
src/problems/HydroContact/test_hydro_contact.cpp
src/problems/HydroHighMach/test_hydro_highmach.cpp
src/problems/HydroKelvinHelmholz/test_hydro2d_kh.cpp
src/problems/HydroLeblanc/test_hydro_leblanc.cpp
src/problems/HydroQuirk/test_quirk.cpp
src/problems/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
src/problems/HydroSMS/test_hydro_sms.cpp
src/problems/HydroShocktube/test_hydro_shocktube.cpp
src/problems/HydroShocktubeCMA/test_hydro_shocktube_cma.cpp
src/problems/HydroShuOsher/test_hydro_shuosher.cpp
src/problems/HydroVacuum/test_hydro_vacuum.cpp
src/problems/HydroWave/test_hydro_wave.cpp
src/problems/NSCBC/channel.cpp
src/problems/NSCBC/vortex.cpp
src/problems/ODEIntegration/test_ode.cpp
src/problems/PassiveScalar/test_scalars.cpp
src/problems/PopIII/popiii.cpp
src/problems/PrimordialChem/test_primordial_chem.cpp
src/problems/RadBeam/test_radiation_beam.cpp
src/problems/RadDust/test_rad_dust.cpp
src/problems/RadDustMG/test_rad_dust_MG.cpp
src/problems/RadForce/test_radiation_force.cpp
src/problems/RadLineCooling/test_rad_line_cooling.cpp
src/problems/RadLineCoolingMG/test_rad_line_cooling_MG.cpp
src/problems/RadMarshak/test_radiation_marshak.cpp
src/problems/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/problems/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/problems/RadMarshakDust/test_radiation_marshak_dust.cpp
src/problems/RadMarshakDustPE/test_radiation_marshak_dust_and_PE.cpp
src/problems/RadMarshakVaytet/test_radiation_marshak_Vaytet.cpp
src/problems/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/problems/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/problems/RadPulse/test_radiation_pulse.cpp
src/problems/RadShadow/test_radiation_shadow.cpp
src/problems/RadStreaming/test_radiation_streaming.cpp
src/problems/RadStreamingY/test_radiation_streaming_y.cpp
src/problems/RadSuOlson/test_radiation_SuOlson.cpp
src/problems/RadTophat/test_radiation_tophat.cpp
src/problems/RadTube/test_radiation_tube.cpp
src/problems/RadhydroBB/test_radhydro_bb.cpp
src/problems/RadhydroPulse/test_radhydro_pulse.cpp
src/problems/RadhydroPulseDyn/test_radhydro_pulse_dyn.cpp
src/problems/RadhydroPulseGrey/test_radhydro_pulse_grey.cpp
src/problems/RadhydroPulseMGconst/test_radhydro_pulse_MG_const_kappa.cpp
src/problems/RadhydroPulseMGint/test_radhydro_pulse_MG_int.cpp
src/problems/RadhydroShell/test_radhydro_shell.cpp
src/problems/RadhydroShock/test_radhydro_shock.cpp
src/problems/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/problems/RadhydroShockMultigroup/test_radhydro_shock_multigroup.cpp
src/problems/RadhydroUniformAdvecting/test_radhydro_uniform_advecting.cpp
src/problems/RandomBlast/blast.cpp
src/problems/RayleighTaylor2D/test_hydro2d_rt.cpp
src/problems/RayleighTaylor3D/test_hydro3d_rt.cpp
src/problems/ShockCloud/cloud.cpp
src/problems/SphericalCollapse/spherical_collapse.cpp
src/problems/StarCluster/star_cluster.cpp
src/radiation/radiation_system.hpp
src/simulation.hpp
tests/RadStreamingY.in
tests/RadTube.in
tests/SphericalCollapse.in
tests/radshock.in
tests/radshock_dimensionless.in

commit 2e9e166a577f60446d67e60c2ce22d4ba7c94daf
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Fri Nov 1 22:47:52 2024 -0400

    Bump extern/amrex from `6d9c25b` to `b9d549b` (#786)
    
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    Fix typo in documentation of Tensor Linear Solver (<a
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    <li><a
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commit 4ac04cdc47a2c3826d2d42f217bc35735dcf9e9a
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Fri Nov 1 19:27:54 2024 -0400

    Bump extern/yaml-cpp from `da82fd9` to `c2bec4c` (#785)
    
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commit 828e4961780e42fe856da9799cd2422ef333e71d
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Fri Nov 1 19:27:33 2024 -0400

    Bump extern/fmt from `c95722a` to `4b8e283` (#788)
    
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extern/fmt

commit 756c520b1e2fddce8c990d022e29d7d5b763aa35
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Fri Nov 1 19:27:15 2024 -0400

    Bump extern/openPMD-api from `d2d8f40` to `94a3a8f` (#789)
    
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    <details>
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extern/openPMD-api

commit d3e2ca29c7cc4f538fa821943427e3f357687cdb
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Nov 1 11:01:01 2024 -0400

    Add script to make a movie from simulation images (#779)
    
    ### Description
    This adds a Bash script to process a sequence of image files (`*.png`)
    in the current working directory into a H.264-encoded `*.mov` movie,
    with a text annotation for consistent branding of Quokka simulation
    movies.
    
    ### Related issues
    N/A
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

scripts/make_movie.sh

commit 7a8dc754e30658c1c3c85a8173feb0baf8e692d0
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Tue Oct 29 13:21:09 2024 +1100

    Speed up unit tests by running ctest in parallel (#784)
    
    ### Description
    Speed up CPU unit tests by running ctest on parallel, e.g. `ctest -j4`.
    
    ### Related issues
    #783
    
    ### 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 see (see above).
    - [ ] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [ ] I have requested a reviewer for this PR.

.github/workflows/cmake-macos.yml
.github/workflows/cmake.yml
.github/workflows/intel.yml

commit 781f834da0640dd6851dc9b6a54e51ac74033437
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Thu Oct 24 22:05:52 2024 +1100

    Line cooling and cosmic ray heating (#773)
    
    ### Description
    This pull request implements line cooling and cosmic ray heating. The
    key changes include:
    - Added line cooling to the single-group and multi-group radiation
    solvers when `enable_dust_gas_thermal_coupling_model = true` . Line
    cooling is enabled by defining `DefineNetCoolingRate` and
    `DefineNetCoolingRateTempDerivative` in the problem file.
    - Implemented cosmic ray heating in all solvers, which is enabled by
    defining `DefineCosmicRayHeatingRate` in the problem file.
    - Added tests for the new line cooling and cosmic ray heating
    functionality.
    - RadLineCooling: test line cooling + CR heating + PE heating for
    single-group radiation system.
    - RadLineCoolingMG: test line cooling + CR heating + PE heating for
    multi-group radiation system, for both well-coupled and decoupled
    gas-dust systems.
    
    This is the last feature I have finished implementing a while ago and I
    want to merge into the development branch before we move to
    Microphysics. In the next PR, I'll try to structure the code in the
    format of `actual_rhs()`, `actual_jac()`,
    and`backward_euler_integrator()` so that we can readily start to use
    Microphysics API.
    
    #### Test problems
    
    ##### RadLineCooling
    
    Initial conditions: uniform static gas with a temperature $T_0 = 1$ and
    $C_V = 1$; the radiation energy density is 0. The dust opacity is 0. The
    line cooling rate is $\Lambda_{\rm line} = C_{\Lambda} T$, where
    $C_{\Lambda} = 0.1$, and the CR heating rate is $\Gamma_{\rm cr} =
    0.03$. As the gas cools down, its temperature follows the following ODE:
    
    $$
    C_V \frac{d T}{d t} = - C_{\Lambda} T + \Gamma_{\rm cr}
    $$
    
    The solution is
    ```math
    \begin{gather}
    T(t) = C_{\Lambda}^{-1} e^{-\frac{C_{\Lambda
       }}{C_V} t} \left(\Gamma
       _{\text{cr}} e^{\frac{C_{\Lambda}}{C_V} t}+ T_0
       C_{\Lambda }-\Gamma_{\text{cr}}\right) \\
       E_{\rm rad}(t) = -(C_V T(t) - C_V T_0 - \Gamma_{\rm cr} t)
    \end{gather}
    ```
    
    In the end of the test, the numerical results of $T(t)$ and $E_{\rm
    rad}(t)$ are checked against the exact analytical solution.
    
    ##### RadLineCoolingMG
    
    The initial condition is the same as that of RadLineCooling, except
    1. There are four radiation bins. The first bin is the line emission and
    the last bin is photoelectric heating (FUV).
    2. The initial radiation energy density is 1 in the last bin and 0 in
    all other bins. The opacity is 0 in all bins.
    3. PE heating is enabled and $\Gamma_{\rm pe} = 0.02 E_{\rm FUV} =
    0.02$.
    The ODE is
    
    $$
    C_V \frac{d T}{d t} = - C_{\Lambda} T + \Gamma_{\rm cr} + \Gamma_{\rm
    pe}
    $$
    
    and the solution is the same as the previous one with two differences:
    (1) $\Gamma_{\rm cr}$ is replaced with $\Gamma_{\rm cr} + \Gamma_{\rm
    pe}$; (2) $E_{\rm rad}$ represents the energy density of the first bin.
    
    This test is run twice, one with well-coupled gas-dust model and one
    with decoupled gas-dust model.
    
    ### Related issues
    Are there any GitHub issues that are fixed by this pull request? Add a
    link to them here.
    
    ### 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 see (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.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/math/interpolate.cpp
src/problems/CMakeLists.txt
src/problems/RadLineCooling/CMakeLists.txt
src/problems/RadLineCooling/test_rad_line_cooling.cpp
src/problems/RadLineCooling/test_rad_line_cooling.hpp
src/problems/RadLineCoolingMG/CMakeLists.txt
src/problems/RadLineCoolingMG/test_rad_line_cooling_MG.cpp
src/problems/RadLineCoolingMG/test_rad_line_cooling_MG.hpp
src/problems/RadMarshakDust/test_radiation_marshak_dust.cpp
src/problems/RadhydroBB/test_radhydro_bb.cpp
src/problems/RadhydroPulseMGconst/test_radhydro_pulse_MG_const_kappa.cpp
src/radiation/radiation_dust_system.hpp
src/radiation/radiation_system.hpp
src/radiation/source_terms_multi_group.hpp
src/radiation/source_terms_single_group.hpp
tests/RadLineCooling.in
tests/RadLineCoolingCoupled.in

commit 18f6997cd3d50653e6cdc3d96f053b6b1f38e234
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon Oct 21 15:05:18 2024 -0400

    [pre-commit.ci] pre-commit autoupdate (#778)
    
    <!--pre-commit.ci start-->
    updates:
    - [github.com/pre-commit/mirrors-clang-format: v19.1.1 →
    v19.1.2](https://github.com/pre-commit/mirrors-clang-format/compare/v19.1.1...v19.1.2)
    <!--pre-commit.ci end-->
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

commit 30bc6945597800bb72a348f1e9c2c19f8178052c
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Mon Oct 14 13:08:37 2024 +1100

    fix 'pure virtual method called' error (#774)
    
    ### Description
    Move `DeviceVector` inside `setInitialConditionsOnGrid` to avoid the
    `pure virtual method called` error, first seen in #761 .
    
    This branch is based on dependabot/submodules/extern/amrex-6d9c25b .
    
    ### Related issues
    Fix issues in PR #761
    
    ### 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 see (see above).
    - [ ] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [ ] I have requested a reviewer for this PR.
    
    ---------
    
    Signed-off-by: dependabot[bot] <support@github.com>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

extern/amrex
src/problems/RadTube/test_radiation_tube.cpp

commit 5f84397ede8fddc087985c8fe701ad6afe24c6bb
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon Oct 7 18:46:17 2024 +0000

    [pre-commit.ci] pre-commit autoupdate (#772)
    
    <!--pre-commit.ci start-->
    updates:
    - [github.com/pre-commit/pre-commit-hooks: v4.6.0 →
    v5.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.6.0...v5.0.0)
    - [github.com/pre-commit/mirrors-clang-format: v19.1.0 →
    v19.1.1](https://github.com/pre-commit/mirrors-clang-format/compare/v19.1.0...v19.1.1)
    <!--pre-commit.ci end-->
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

commit 45cdad37d61aacf710980eba9d78e0901eedd17f
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Mon Oct 7 15:59:41 2024 +1100

    Move enable_dust_gas_thermal_coupling_model to ISM_Traits (#771)
    
    ### Description
    Move the dust model switch `enable_dust_gas_thermal_coupling_model` from
    RadSystem_Traits to ISM_Traits so that the RadSystem_Traits is free of
    dust/non-LTE parameters.
    
    ### Related issues
    None.
    
    ### 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).
    - [ ] I have added a link to any related issues see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/QuokkaSimulation.hpp
src/problems/RadBeam/test_radiation_beam.cpp
src/problems/RadDust/test_rad_dust.cpp
src/problems/RadDustMG/test_rad_dust_MG.cpp
src/problems/RadForce/test_radiation_force.cpp
src/problems/RadMarshak/test_radiation_marshak.cpp
src/problems/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/problems/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/problems/RadMarshakDust/test_radiation_marshak_dust.cpp
src/problems/RadMarshakDustPE/test_radiation_marshak_dust_and_PE.cpp
src/problems/RadMarshakVaytet/test_radiation_marshak_Vaytet.cpp
src/problems/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/problems/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/problems/RadPulse/test_radiation_pulse.cpp
src/problems/RadShadow/test_radiation_shadow.cpp
src/problems/RadStreaming/test_radiation_streaming.cpp
src/problems/RadStreamingY/test_radiation_streaming_y.cpp
src/problems/RadSuOlson/test_radiation_SuOlson.cpp
src/problems/RadTophat/test_radiation_tophat.cpp
src/problems/RadTube/test_radiation_tube.cpp
src/problems/RadhydroBB/test_radhydro_bb.cpp
src/problems/RadhydroPulse/test_radhydro_pulse.cpp
src/problems/RadhydroPulseDyn/test_radhydro_pulse_dyn.cpp
src/problems/RadhydroPulseGrey/test_radhydro_pulse_grey.cpp
src/problems/RadhydroPulseMGconst/test_radhydro_pulse_MG_const_kappa.cpp
src/problems/RadhydroPulseMGint/test_radhydro_pulse_MG_int.cpp
src/problems/RadhydroShell/test_radhydro_shell.cpp
src/problems/RadhydroShock/test_radhydro_shock.cpp
src/problems/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/problems/RadhydroShockMultigroup/test_radhydro_shock_multigroup.cpp
src/problems/RadhydroUniformAdvecting/test_radhydro_uniform_advecting.cpp
src/radiation/radiation_system.hpp

commit e69f403dd0ee5550d23204fa7f956ca2cde6bcdf
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Sat Oct 5 02:18:45 2024 +1000

    photoelectric heating (#766)
    
    ### Description
    In this PR, I implement photoelectric heating within the current
    gas-radiation-dust interaction framework. PE can be enabled by setting
    `enable_photoelectric_heating = true` in `ISM_Traits`. The prerequisite
    is `nGroups > 1` and `enable_dust_gas_thermal_coupling_model = true`.
    
    Added two test problems, `RadiationMarshakDustPE-coupled` and
    `RadiationMarshakDustPE-decoupled`, to test photoelectric heating in
    cases where gas and dust are well coupled and decoupled. These two tests
    share the same problem code `test_radiation_marshak_dust_and_PE.cpp` but
    use different runtime parameters.
    
    Here is the code structure:
    
    ```
    - AddSourceTermsMultiGroup
      - outer loop:
        - compute `v_times_F_term`
        - solve gas-dust-radiation energy exchange:
          - if constexpr (!enable_dust_gas_thermal_coupling_model_)
            - `SolveGasRadiationEnergyExchange`:
              - The matter-radiation coupling scheme from the multigroup paper
          - else if constexpr (!enable_photoelectric_heating_)
            - `SolveGasDustRadiationEnergyExchange()`:
              - The gas-dust-radiation coupling scheme proposed in #733, which has two cases: the well-coupled case and decoupled case
          - else
            - `SolveGasDustRadiationEnergyExchangeWithPE()`:
              - Based on the gas-dust-radiation coupling scheme, but with modified Jacobian in the well-coupled case to include PE heating. In the decoupled case, PE heating is added via a forward-Euler update using the updated radiation energy density after the gas-dust-radiation step.
        - compute updated `v_times_F_term`
        - if `v_times_F_term` has converged, break
      - `UpdateFlux()`
    ```
    
    ### Related issues
    A modification to #733 to include PE heating.
    
    ### 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 see (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.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/QuokkaSimulation.hpp
src/problems/CMakeLists.txt
src/problems/RadDustMG/test_rad_dust_MG.hpp
src/problems/RadMarshakDust/test_radiation_marshak_dust.cpp
src/problems/RadMarshakDust/test_radiation_marshak_dust.hpp
src/problems/RadMarshakDustPE/CMakeLists.txt
src/problems/RadMarshakDustPE/test_radiation_marshak_dust_and_PE.cpp
src/problems/RadMarshakDustPE/test_radiation_marshak_dust_and_PE.hpp
src/radiation/radiation_dust_system.hpp
src/radiation/radiation_system.hpp
src/radiation/source_terms_multi_group.hpp
src/util/valarray.hpp
tests/RadMarshakDust.in
tests/RadMarshakDustPEcoupled.in
tests/RadMarshakDustPEdecoupled.in

commit 8671c5ea4d94c82f21abc22ec39ea004e3a54806
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Fri Oct 4 01:10:32 2024 +0000

    Bump extern/grackle_data_files from `83c2929` to `9286964` (#760)
    
    Bumps
    [extern/grackle_data_files](https://github.com/grackle-project/grackle_data_files)
    from `83c2929` to `9286964`.
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/grackle-project/grackle_data_files/commit/928696482fbe15d9bac4382de6134d95568f099c"><code>9286964</code></a>
    Merge pull request <a
    href="https://redirect.github.com/grackle-project/grackle_data_files/issues/11">#11</a>
    from brittonsmith/update</li>
    <li><a
    href="https://github.com/grackle-project/grackle_data_files/commit/737009c1566bb72d0c53f02fe0d4ca7c063673ae"><code>737009c</code></a>
    Remove rate coefficients testing file after transitioning test to gold
    standa...</li>
    <li><a
    href="https://github.com/grackle-project/grackle_data_files/commit/7499abbc6c7e4b9d629d55d9f21b1c8166529b75"><code>7499abb</code></a>
    Merge pull request <a
    href="https://redirect.github.com/grackle-project/grackle_data_files/issues/10">#10</a>
    from brittonsmith/gtest</li>
    <li><a
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    Remove obsolete testing answer files.</li>
    <li><a
    href="https://github.com/grackle-project/grackle_data_files/commit/9a63dbefeb1410483df0071eefcbff666f40816d"><code>9a63dbe</code></a>
    Merge pull request <a
    href="https://redirect.github.com/grackle-project/grackle_data_files/issues/9">#9</a>
    from brittonsmith/issue6</li>
    <li><a
    href="https://github.com/grackle-project/grackle_data_files/commit/ee5ff1c6eee544d76ce26b5dcfc6b4ac795bea9f"><code>ee5ff1c</code></a>
    Add missing redshift dataset to cooling table.</li>
    <li><a
    href="https://github.com/grackle-project/grackle_data_files/commit/5d73d81c657a9f0795b1058774eccc49787e2f62"><code>5d73d81</code></a>
    Merge pull request <a
    href="https://redirect.github.com/grackle-project/grackle_data_files/issues/8">#8</a>
    from brittonsmith/PR126</li>
    <li><a
    href="https://github.com/grackle-project/grackle_data_files/commit/9084536dbffff9ce2f1fd347c083a632062797a8"><code>9084536</code></a>
    Update answers for PR <a
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    <li><a
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    Merge pull request <a
    href="https://redirect.github.com/grackle-project/grackle_data_files/issues/5">#5</a>
    from brittonsmith/PR97</li>
    <li><a
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    Update answers for PR <a
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extern/grackle_data_files

commit 80d38c034229685931a4a1d2948ebc199f62fea3
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Fri Oct 4 09:52:35 2024 +1000

    Restructure: define ComputeModelBasedKappaEAndKappaP (#767)
    
    ### Description
    Another PR to restructure the code to increase readability.
    
    This PR defines two functions: `ComputeModelDependentKappaEAndKappaP`
    and `ComputeModelDependentKappaFAndDeltaTerms`. They are used to replace
    the chunk of code that computes `kappaE` and `kappaP`, and `kappaF`
    based on the opacity model, controlled by constant if.
    
    ### Related issues
    This will simplify a large chunk of code in #766, where the same code is
    repeatedly used in all three energy exchange functions. I would like to
    merge in this PR before #766 .
    
    ### 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:_
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
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src/radiation/radiation_system.hpp
src/radiation/source_terms_multi_group.hpp

commit 4210608ae643dea542a5375e03eb4d657f38428a
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Oct 3 19:50:00 2024 -0400

    Avoid running out of disk space for regression testing (#769)
    
    ### Description
    This runs the regression testing Python script with the
    `--clean_testdir` option, which deletes the test output directory after
    a given test passes.
    
    ### Related issues
    https://github.com/quokka-astro/quokka/issues/764
    
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.ci/azure-pipelines-regression.yml

commit 4f4d128e1cfb4c30a07d083d2f4b4ae754b08b42
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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    Bump extern/fmt from `621e9c1` to `c95722a` (#759)
    
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    <li><a
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    Improve naming consistency</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/db06b0df875856968c562d564b595a4e2861144e"><code>db06b0d</code></a>
    Use countl_zero in bigint</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/b9ec48d9ca60253ca295910e9078566090d98135"><code>b9ec48d</code></a>
    Cleanup bigint</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/3faf6f181e4b277868578dd97034aada145aee8c"><code>3faf6f1</code></a>
    Add min_of/max_of</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/d64b100a30f5e3df9f7fe08cfdf3d89ed755ad6d"><code>d64b100</code></a>
    Relax constexpr</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/ff9ee0461a8dd02cbaf9458aa13301aa1099c0f7"><code>ff9ee04</code></a>
    Fix handling FMT_BUILTIN_TYPES</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/1c5883bef081a5cce75bdc4dab0ce922d3bb600f"><code>1c5883b</code></a>
    Test nondeterministic conversion to format string</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/cacc3108c5b74020dba7bf3c6d3a7e58cdc085b2"><code>cacc310</code></a>
    Don't assume repeated evaluation of string literal produce the same
    pointer</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/fade652ade6e9ba4b16e7484cbda5ee4c9178918"><code>fade652</code></a>
    Require clang &gt;=15 for _BitInt support (<a
    href="https://redirect.github.com/fmtlib/fmt/issues/4176">#4176</a>)</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/96dca569a1251ea77f434c2773d4db55c4b8a488"><code>96dca56</code></a>
    Module linkage fixes for shared build (<a
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extern/fmt

commit 5cf950e5926df59d4df929bc1879df6aacb31a0f
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Tue Oct 1 09:22:35 2024 -0400

    Bump extern/openPMD-api from `1c7d7ff` to `d2d8f40` (#762)
    
    Bumps [extern/openPMD-api](https://github.com/openPMD/openPMD-api) from
    `1c7d7ff` to `d2d8f40`.
    <details>
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    Script: New Version (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1467">#1467</a>)</li>
    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/88089bcc0edef65d9d5a566a13aeb3a78346de43"><code>88089bc</code></a>
    CMake Superbuild: Tarball (<a
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    Independent writes: Make workaround more flexible (<a
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    href="https://github.com/openPMD/openPMD-api/commit/016bb8ade2a7440daeaed28acea00ffb208a3bad"><code>016bb8a</code></a>
    Allow numpy 2.0 in requirements.txt (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1669">#1669</a>)</li>
    <li><a
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    Python Series/Iteration: Fix Length (<a
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    Remove ThirdParty Directories (<a
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    Replace internal dependencies by FetchContent (<a
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extern/openPMD-api

commit eaf7d30d7f15ccc470277f5b4e8b393bd3cce26d
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Tue Oct 1 09:22:11 2024 -0400

    Bump extern/yaml-cpp from `47cd272` to `da82fd9` (#763)
    
    Bumps [extern/yaml-cpp](https://github.com/jbeder/yaml-cpp) from
    `47cd272` to `da82fd9`.
    <details>
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    href="https://github.com/jbeder/yaml-cpp/commit/da82fd982c260e7f335ce5acbceff24b270544d1"><code>da82fd9</code></a>
    chore(test/integration): refactor some test cases to their own
    test.</li>
    <li><a
    href="https://github.com/jbeder/yaml-cpp/commit/1f2b841949de53366508d44e59a6d5bbac562fa3"><code>1f2b841</code></a>
    fix(src,include,test): fixed multiple cases where a bad yaml was
    accepted.</li>
    <li>See full diff in <a
    href="https://github.com/jbeder/yaml-cpp/compare/47cd2725d61e54719933b83ea51c64ad60c24066...da82fd982c260e7f335ce5acbceff24b270544d1">compare
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extern/yaml-cpp

commit d23330a361c4ac885f07662d9f0d30dde71a1661
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Tue Oct 1 08:05:39 2024 -0400

    [pre-commit.ci] pre-commit autoupdate (#757)
    
    <!--pre-commit.ci start-->
    updates:
    - [github.com/pre-commit/mirrors-clang-format: v18.1.8 →
    v19.1.0](https://github.com/pre-commit/mirrors-clang-format/compare/v18.1.8...v19.1.0)
    <!--pre-commit.ci end-->
    
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.pre-commit-config.yaml
extern/sedov/sedov.ipynb
src/QuokkaSimulation.hpp
src/hydro/EOS.hpp
src/hydro/LLF.hpp
src/hydro/NSCBC_inflow.hpp
src/hydro/NSCBC_outflow.hpp
src/hydro/hydro_system.hpp
src/hyperbolic_system.hpp
src/linear_advection/AdvectionSimulation.hpp
src/linear_advection/linear_advection.hpp
src/math/quadrature.hpp
src/problems/NSCBC/dQ_dx_inflow.ipynb
src/problems/NSCBC/dQ_dx_outflow.ipynb
src/problems/RadDustMG/test_rad_dust_MG.cpp
src/problems/RadMarshak/test_radiation_marshak.cpp
src/problems/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/problems/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/problems/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/problems/RadSuOlson/test_radiation_SuOlson.cpp
src/problems/RadhydroPulseMGint/test_radhydro_pulse_MG_int.cpp
src/problems/RadhydroShockMultigroup/test_radhydro_shock_multigroup.cpp
src/problems/ShockCloud/boundary_conditions.ipynb
src/radiation/radiation_system.hpp
src/radiation/source_terms_multi_group.hpp
src/util/CheckNaN.hpp
src/util/fextract.cpp
src/util/fextract.hpp

commit bb67d4508d03fc94c6b0934704bd5e93b26638e7
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Sep 30 03:18:34 2024 +0000

    Bump ossf/scorecard-action from 2.3.1 to 2.4.0 (#756)
    
    Bumps [ossf/scorecard-action](https://github.com/ossf/scorecard-action)
    from 2.3.1 to 2.4.0.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
    href="https://github.com/ossf/scorecard-action/releases">ossf/scorecard-action's
    releases</a>.</em></p>
    <blockquote>
    <h2>v2.4.0</h2>
    <h2>What's Changed</h2>
    <p>This update bumps the Scorecard version to the v5 release. For a
    complete list of changes, please refer to the <a
    href="https://github.com/ossf/scorecard/releases/tag/v5.0.0">v5.0.0
    release notes</a>. Of special note to Scorecard Action is the Maintainer
    Annotation feature, which can be used to suppress some Code Scanning
    false positives. Alerts will not be generated for any Scorecard Check
    with an annotation.</p>
    <ul>
    <li>:seedling: Bump github.com/ossf/scorecard/v5 from v5.0.0-rc2 to
    v5.0.0 by <a
    href="https://github.com/spencerschrock"><code>@​spencerschrock</code></a>
    in <a
    href="https://redirect.github.com/ossf/scorecard-action/pull/1410">ossf/scorecard-action#1410</a></li>
    <li>:bug: lower license sarif alert threshold to 9 by <a
    href="https://github.com/spencerschrock"><code>@​spencerschrock</code></a>
    in <a
    href="https://redirect.github.com/ossf/scorecard-action/pull/1411">ossf/scorecard-action#1411</a></li>
    </ul>
    <h3>Documentation</h3>
    <ul>
    <li>docs: dogfooding badge by <a
    href="https://github.com/jkowalleck"><code>@​jkowalleck</code></a> in <a
    href="https://redirect.github.com/ossf/scorecard-action/pull/1399">ossf/scorecard-action#1399</a></li>
    </ul>
    <h2>New Contributors</h2>
    <ul>
    <li><a
    href="https://github.com/jkowalleck"><code>@​jkowalleck</code></a> made
    their first contribution in <a
    href="https://redirect.github.com/ossf/scorecard-action/pull/1399">ossf/scorecard-action#1399</a></li>
    </ul>
    <p><strong>Full Changelog</strong>: <a
    href="https://github.com/ossf/scorecard-action/compare/v2.3.3...v2.4.0">https://github.com/ossf/scorecard-action/compare/v2.3.3...v2.4.0</a></p>
    <h2>v2.3.3</h2>
    <blockquote>
    <p>[!NOTE]<br />
    There is no v2.3.2 release as a step was skipped in the release process.
    This was fixed and re-released under the v2.3.3 tag</p>
    </blockquote>
    <h2>What's Changed</h2>
    <ul>
    <li>:seedling: Bump github.com/ossf/scorecard/v4 (v4.13.1) to
    github.com/ossf/scorecard/v5 (v5.0.0-rc1) by <a
    href="https://github.com/spencerschrock"><code>@​spencerschrock</code></a>
    in <a
    href="https://redirect.github.com/ossf/scorecard-action/pull/1366">ossf/scorecard-action#1366</a></li>
    <li>:seedling: Bump github.com/ossf/scorecard/v5 from v5.0.0-rc1 to
    v5.0.0-rc2 by <a
    href="https://github.com/spencerschrock"><code>@​spencerschrock</code></a>
    in <a
    href="https://redirect.github.com/ossf/scorecard-action/pull/1374">ossf/scorecard-action#1374</a></li>
    <li>:seedling: Bump github.com/ossf/scorecard/v5 from v5.0.0-rc2 to
    v5.0.0-rc2.0.20240509182734-7ce860946928 by <a
    href="https://github.com/spencerschrock"><code>@​spencerschrock</code></a>
    in <a
    href="https://redirect.github.com/ossf/scorecard-action/pull/1377">ossf/scorecard-action#1377</a></li>
    </ul>
    <p>For a full changelist of what these include, see the <a
    href="https://github.com/ossf/scorecard/releases/tag/v5.0.0-rc1">v5.0.0-rc1</a>
    and <a
    href="https://github.com/ossf/scorecard/releases/tag/v5.0.0-rc2">v5.0.0-rc2</a>
    release notes.</p>
    <h3>Documentation</h3>
    <ul>
    <li>:book: Move token discussion out of main README. by <a
    href="https://github.com/spencerschrock"><code>@​spencerschrock</code></a>
    in <a
    href="https://redirect.github.com/ossf/scorecard-action/pull/1279">ossf/scorecard-action#1279</a></li>
    <li>:book: link to <code>ossf/scorecard</code> workflow instead of
    maintaining an example by <a
    href="https://github.com/spencerschrock"><code>@​spencerschrock</code></a>
    in <a
    href="https://redirect.github.com/ossf/scorecard-action/pull/1352">ossf/scorecard-action#1352</a></li>
    <li>:book: update api links to new scorecard.dev site by <a
    href="https://github.com/spencerschrock"><code>@​spencerschrock</code></a>
    in <a
    href="https://redirect.github.com/ossf/scorecard-action/pull/1376">ossf/scorecard-action#1376</a></li>
    </ul>
    <p><strong>Full Changelog</strong>: <a
    href="https://github.com/ossf/scorecard-action/compare/v2.3.1...v2.3.3">https://github.com/ossf/scorecard-action/compare/v2.3.1...v2.3.3</a></p>
    </blockquote>
    </details>
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/ossf/scorecard-action/commit/62b2cac7ed8198b15735ed49ab1e5cf35480ba46"><code>62b2cac</code></a>
    bump docker tag to v2.4.0 for release (<a
    href="https://redirect.github.com/ossf/scorecard-action/issues/1414">#1414</a>)</li>
    <li><a
    href="https://github.com/ossf/scorecard-action/commit/c09630c42e97d04c7cd8f69735ddf0ec53f0e189"><code>c09630c</code></a>
    lower license score alert threshold to 9 (<a
    href="https://redirect.github.com/ossf/scorecard-action/issues/1411">#1411</a>)</li>
    <li><a
    href="https://github.com/ossf/scorecard-action/commit/cf8594c5485256008de4ec57c936bd4a1a381a0b"><code>cf8594c</code></a>
    :seedling: Bump github.com/sigstore/cosign/v2 from 2.2.4 to 2.3.0 (<a
    href="https://redirect.github.com/ossf/scorecard-action/issues/1413">#1413</a>)</li>
    <li><a
    href="https://github.com/ossf/scorecard-action/commit/de5fcb95b9d8f899bc5dc11b4e202eb6a2fd67e9"><code>de5fcb9</code></a>
    :seedling: Bump the github-actions group with 2 updates (<a
    href="https://redirect.github.com/ossf/scorecard-action/issues/1412">#1412</a>)</li>
    <li><a
    href="https://github.com/ossf/scorecard-action/commit/a46b90b4caca61e2298cc4a9bd4c90d3dfe7f09d"><code>a46b90b</code></a>
    bump scorecard to v5.0.0 release (<a
    href="https://redirect.github.com/ossf/scorecard-action/issues/1410">#1410</a>)</li>
    <li><a
    href="https://github.com/ossf/scorecard-action/commit/9fc518d5249b2564cbeb11d029b87d7d1ba55396"><code>9fc518d</code></a>
    :seedling: Bump golang in the docker-images group (<a
    href="https://redirect.github.com/ossf/scorecard-action/issues/1407">#1407</a>)</li>
    <li><a
    href="https://github.com/ossf/scorecard-action/commit/a8eaa1b46e3fd7e003f79fd39dff99ca53bbe732"><code>a8eaa1b</code></a>
    :seedling: Bump the github-actions group with 2 updates (<a
    href="https://redirect.github.com/ossf/scorecard-action/issues/1408">#1408</a>)</li>
    <li><a
    href="https://github.com/ossf/scorecard-action/commit/873d5fdf63bc863d140f57ed481e6a297324030b"><code>873d5fd</code></a>
    :seedling: Bump the github-actions group across 1 directory with 2
    updates (#...</li>
    <li><a
    href="https://github.com/ossf/scorecard-action/commit/54cc1fe4e2c7bc69051a267c8e183497ca7d8da7"><code>54cc1fe</code></a>
    :seedling: Bump the docker-images group with 2 updates (<a
    href="https://redirect.github.com/ossf/scorecard-action/issues/1401">#1401</a>)</li>
    <li><a
    href="https://github.com/ossf/scorecard-action/commit/82bcb91c5d3f72aaf692a0d3e399c425a29ac512"><code>82bcb91</code></a>
    :seedling: Bump golang.org/x/net from 0.26.0 to 0.27.0 (<a
    href="https://redirect.github.com/ossf/scorecard-action/issues/1400">#1400</a>)</li>
    <li>Additional commits viewable in <a
    href="https://github.com/ossf/scorecard-action/compare/0864cf19026789058feabb7e87baa5f140aac736...62b2cac7ed8198b15735ed49ab1e5cf35480ba46">compare
    view</a></li>
    </ul>
    </details>
    <br />
    
    
    [![Dependabot compatibility
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    Dependabot will resolve any conflicts with this PR as long as you don't
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    [//]: # (dependabot-automerge-start)
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    <summary>Dependabot commands and options</summary>
    <br />
    
    You can trigger Dependabot actions by commenting on this PR:
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.github/workflows/scorecard.yml

commit bb00fce0e1a4157e39db74f014e32272befe73e9
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Sep 28 23:38:20 2024 -0400

    Add OpenSSF Security Scorecard action (#736)
    
    ### Description
    Runs the OpenSSF Security Scorecard on the Quokka repository. For
    details, see: https://scorecard.dev/#what-is-openssf-scorecard.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] I have added a link to any related issues see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

.github/workflows/scorecard.yml
README.md

commit c7c6d7ce077f198f995f02b63ccfd562a8c99d46
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Sep 28 23:37:42 2024 -0400

    fix bug in make_tarball.py (#755)
    
    ### Description
    Sonarcloud complained about a bug in `paper/make_tarball.py`. This was
    only ever used to submit the paper, so it is not relevant to users, but
    it should be fixed so that we have a clean report from Sonarcloud.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] I have added a link to any related issues see (see above).
    - [ ] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [ ] I have requested a reviewer for this PR.

paper/make_tarball.py

commit c77f80c09755eb837b6d9188a2102b71c021aa7e
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Sun Sep 29 13:36:54 2024 +1000

    Add a CUDA devcontainer  (#751)
    
    ### Description
    Adds a new CUDA devcontainer. Now you can choose from `gcc-container`
    and `cuda-container`.
    
    When using the default compiler and MPI library in the CUDA container,
    it is necessary to add these options to the CMake configuration flags
    when building Quokka:
    ```console
    $ export PATH=$PATH:/workspaces/quokka/scripts
    $ cmake .. -DCMAKE_TEST_LAUNCHER=mpirun-singleton-wrapper -DDISABLE_FMAD=OFF
    ```
    For details on `CMAKE_TEST_LAUNCHER`, see:
    *
    https://cmake.org/cmake/help/latest/variable/CMAKE_TEST_LAUNCHER.html#variable:CMAKE_TEST_LAUNCHER
    * https://www.scivision.dev/ctest-test-launcher/
    
    ### Related issues
    Closes https://github.com/quokka-astro/quokka/issues/745.
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: Ben Wibking <ben@wibking.com>

.devcontainer/cuda-container/Dockerfile
.devcontainer/cuda-container/devcontainer.json
.devcontainer/gcc-container/Dockerfile
.devcontainer/gcc-container/devcontainer.json
scripts/mpirun-singleton-wrapper
src/CMakeLists.txt

commit f42de31d1f227349fbb3c72edb33b509698f7f39
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Sep 26 22:17:43 2024 -0400

    Update README.md to list Python as required (#753)
    
    ### Description
    Python is required to compile Quokka, since we need to run a Python
    script in Microphysics to generate some header files.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] I have added a link to any related issues see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

README.md

commit aa2a618eee026556abe540c935f236c16ae858be
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Thu Sep 26 11:17:31 2024 +1000

    Restructure: put radiation flux update into a function (#750)
    
    ### Description
    
    This PR wraps the radiation flux update in source_terms_multi_group.hpp
    into a single function `UpdateFlux`. A new struct `FluxUpdateResult` is
    created to store the results from `UpdateFlux`.
    
    ### Related issues
    None.
    
    ### 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).
    - [ ] I have added a link to any related issues see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/radiation/radiation_system.hpp
src/radiation/source_terms_multi_group.hpp
src/radiation/source_terms_single_group.hpp

commit a1632ff25f46968d860a61b50497fd3bb5f2fd74
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Sep 25 09:59:19 2024 -0400

    Create CODEOWNERS (#749)
    
    ### Description
    Adds a `CODEOWNERS` file.
    
    Subdirectories and files are listed alongside users and PRs that modify
    files that match these patterns (either subdirectories or individual
    files) have to be approved by _one of_ the listed GitHub users in order
    to be merged. It is necessary to have more than one person listed for
    any given set of files, since users cannot approve their own pull
    requests, and in case someone is unavailable or at a conference, etc.
    
    See docs:
    https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners#codeowners-and-branch-protection
    
    ### Related issues
    Closes https://github.com/quokka-astro/quokka/issues/747.
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

.github/CODEOWNERS

commit 5e5176c01a7eeb165b7060740fb7c3a06da33e86
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Sep 18 23:21:01 2024 -0400

    Update Dockerfile (#741)
    
    ### Description
    This removes Sphinx dependencies from the included Dockerfile, since we
    no longer use Sphinx. ADIOS2 is also added to the Dockerfile (needed for
    OpenPMD I/O support).
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] I have added a link to any related issues see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

.devcontainer/Dockerfile
.devcontainer/devcontainer.json
src/simulation.hpp

commit 2d273a2595dc6f59f7fa9bb5ed20129fc33d97a0
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Mon Sep 9 14:32:14 2024 +1000

    A robust numerical scheme for the dust-gas coupling model (#733)
    
    ### Description
    In this PR, we solve the dust coupling to the gas and radiation in two
    different regimes: the well-coupled regime and the low-density,
    poorly-coupled regime.
    
    #### Changes to the code
    
    - Defined `ComputeJacobianForGasAndDustDecoupled` to compute the
    Jacobian for the gas-dust-radiation system in the regime where gas and
    dust are decoupled.
    - Added a new parameter `lambda_gd_times_dt` to
    `SolveMatterRadiationEnergyExchange`. `lambda_gd_times_dt` is
    $\Lambda_{\rm gd} \Delta t$, which is used to update gas energy as well
    as constraining the sum of $R_g$.
    - Added a new parameter `dust_model` to
    `SolveMatterRadiationEnergyExchange`. Unfortunately, the energy-exchange
    system becomes complicated and you can't deal with all three dust models
    by passing functions to `SolveMatterRadiationEnergyExchange`.
    `dust_model` takes three values, representing a gas-dust-radiation
    system in different regimes:
    - 0: dust and gas are perfectly coupled. In this case, `T_d = T_gas`,
    and we solve a system that involves T_gas and Erad. This is the model
    used in Wibking & Krumholz (2022), He, Wibking & Krumholz (2024a) and
    He, Wibking & Krumholz (2024b).
    - 1: dust and gas are well coupled. In this case, we solve a system that
    involves T_gas, T_d, and Erad, where T_d is used as an implicit,
    dependent variable.
    - 2: dust and gas are poorly coupled. In this case, we solve a system
    that involves only T_d and Erad.
    - `dust_model = 0` is enabled by setting
    `enable_dust_gas_thermal_coupling_model_ = false`. Otherwise,
    `dust_model = 1` or `dust_model = 2` is determined automatically in the
    code on a cell-by-cell basis. See the description below.
    
    #### Alternative things to do
    
    - Make `threshold_for_dust_gas_coupling` a runtime parameter. This is
    the parameter to control when to switch between dust model 1 and 2.
    
    #### Physics
    
    In the well-coupled regime, we solve the following equations:
    
    $$
    \begin{split}
    \frac{\partial E_{\rm gas}}{\partial t} = - \Lambda_{{\rm gd}} \\
    \frac{\partial E_g}{\partial t} = \hat{c} \left[ \chi_B \frac{4 \pi}{c}
    B_g(T_d) - \chi_E E_g \right]
    \end{split}
    $$
    
    where $\Lambda_{\mathrm{gd}}$ is the thermal interaction rate due to
    collisions between the gas and the dust, which we take the rate of Keto
    & Field (2005)
    
    $$
    \Lambda_{{\rm gd}} = \Theta_{{\rm gd}} ~n_{\mathrm{H}}^2 T^{1 /
    2}\left(T-T_{{d}}\right) \quad{} (1)
    $$
    
    where $\Theta_{\mathrm{gd}} = 2.5 \times 10^{-34} \mathrm{erg \ cm^3 \
    s^{-1} \ K^{-3/2}}$. This parameter can be specified in arbitrary units
    by the user. As in most literature, we assume that the dust is in LTE
    with the total radiation field (e.g. Bate & Keto 2015):
    
    $$
    c \sum_g \left[ \chi_B \frac{4 \pi}{c} B_g(T_d) - \chi_E E_g \right] =
    \Lambda_{{\rm gd}}. \quad{} (2)
    $$
    
    We can then define a similar set of independent variables as in the IMEX
    paper, $(E_{\rm gas}, R_g), g = 1, 2, ..., N_g$, where
    
    $$
    R_g \equiv \hat{c} \Delta t \left[ \chi_B \frac{4 \pi}{c} B_g(T_d) -
    \chi_E E_g \right], \quad{} (3)
    $$
    
    and solve for the following set of equations using Newton-Raphson
    iteration:
    
    $$
    \begin{split}
    0 = F_G \equiv E_{\rm gas} - E_{\rm gas}^0 + \frac{c}{\hat{c}} \sum_g
    R_g,\\
    0 = F_{R,g} \equiv E_g - E_g^0 - R_g
    \end{split}
    $$
    
    This is similar to the original gas-only scheme, except that the gas
    temperature $T$ is replaced with $T_d$.
    
    We still need to calculate the dust temperature $T_d$. In the first step
    of the iteration, we solve for $T_d$ given $T$ and $E_g$ via combining
    Equation (1) and (2). Then, later in the iteration, we solve for $T_d$
    via a simple relation:
    
    $$
    \sum_g R_g = \frac{\hat{c}}{c} \Delta t \ \Lambda_{\rm gd} =
    \frac{\hat{c}}{c} \Delta t \ \Theta_{{\rm gd}} ~n_{\mathrm{H}}^2 T^{1 /
    2}\left(T-T_{{d}}\right) = N_{\rm gd} T^{1/2}(T - T_d) \quad{} (4)
    $$
    
    where we have defined $N_{\rm gd} \equiv (\hat{c}/c) \Delta t
    \Theta_{\rm gd} n_H^2$. Apparently,
    
    $$
    T_d = T - \frac{\sum_g R_g}{N_{\rm gd} \sqrt{T}}. \quad{} (5)
    $$
    
    Equation (4) also gives a simple formula for $d T_d / d T$, which is
    used in the computation of the Jacobian. Further, the Jacobian is no
    longer sparse. However, I did a trick to analytically simplify the
    Jacobian matrix via Gauss-Jordan elimination to make it sparse so that
    we can use the numerical scheme in the multigroup paper. More details in
    Overleaf document "quokka-thermochemistry".
    
    In the decoupled regime where $N_{\rm gd}$ is small, however, this
    scheme failed. This is obvious from Equation (5): even a small value of
    $\sum_g R_g$ will result in a large, negative $T_d$. This is unavoidable
    in the Newton-Raphson step; the valid domain for $\sum_g R_g$ is tiny:
    $[0, N_{\rm gd} T^{3/2})$. Here I'm considering the case where the
    radiation temperature is well below the gas temperature, so $T \gg T_r
    \approx T_d$, therefore $\Lambda_{\rm gd} \ge 0$.
    
    After extensive exploration, I constructed the following scheme for the
    decoupled regime. First, we define the decoupled regime as when
    $\max(N_{\rm gd} T^{3/2}, N_{\rm gd} T_d^{3/2}) < 10^{-6} \max(E_{\rm
    gas}, \sum_g R_g)$. Since the gas temperature won't change much, it can
    be updated via a simple forward Euler step of the following equation:
    
    $$
    C_V \frac{d T}{dt} = - \Lambda_{\rm gd} = - \Theta_{{\rm gd}}
    ~n_{\mathrm{H}}^2 \ T^{1 / 2}\left(T-T_{{d}}\right) \quad{} (6)
    $$
    
    One can also choose to solve this analytically. Thus we have obtained
    $\Lambda_{\rm gd} \Delta t$.
    
    Then, we want to deal with energy exchange between radiation groups, to
    capture dust absorbing UV radiation and re-emitting in IR. At first, I
    tried to update $E_g$ with fixed $T_d$, by solving
    
    $$
    E_g - E_g^0 = c \Delta t \ \chi_g (B_g(T_d) - E_g).
    $$
    
    This can be solved with simple algebra. However, I have shown that the
    resulting $\sum_g R_g$ (the sum of the RHS over groups) does not
    necessarily equal to the $\Lambda_{\rm gd} \Delta t$ used previously to
    update gas temperature. This results in the failure of energy
    conservation. To enforce $\sum_g R_g = \Lambda_{\rm gd} \Delta t$, we
    have to include $T_d$ as an independent variable; otherwise, the system
    is over-determined.
    
    Then, here is the new scheme that I have shown to be very robust. After
    updating $T$ via Equation (6), we solve the updated $T_d$ and $E_g$ via
    the following set of equations:
    
    $$
    \begin{split}
    \sum_g R_g = \Lambda_{\rm gd} \Delta t, \\
    E_g - E_g^0 = R_g.
    \end{split}
    $$
    
    We solve this equation via Newton-Raphson iteration on the base variable
    $(T_d, R_g)$.
    
    $$
    \begin{split}
    0 = F_0 = \sum_g R_g - \Lambda_{\rm gd} \Delta t \\
    0 = F_g = E_g - E_g^0 - R_g
    \end{split}
    $$
    
    and the Jacobian is
    
    $$
    \begin{split}
    J_{00} = 0 \\
    J_{0g} = 1 \\
    J_{g0} = \frac{\partial E_g}{\partial T_d} =
    \frac{\chi_{B,g}}{\chi_{E,g}} \frac{\partial B_g(T_d)}{\partial T_d} \\
    J_{gg} = \frac{\partial E_g}{\partial R_g} - 1 = -
    \frac{\chi_{B,g}}{\chi_{E,g}} \frac{1}{\hat{c} \chi_{\rm B,g} \Delta t}
    - 1
    \end{split}
    $$
    
    This set of equations is very similar to the previous ones, so we can
    use the same routine with some switches to reset different Jacobian for
    different regimes. After this system is converged, the whole iteration
    is done and energy is guaranteed to be conserved (to the degree of how
    well the Newton-Raphson iteration converges).
    
    #### Tests
    
    `RadMarshakDust` is a Marshak wave problem where FUV radiation is
    streaming from the left boundary, gets absorbed by dust which then
    radiates in IR. The IR opacity is set to a large number so that
    diffusion is extremely slow. I compare the (semi-)exact analytic
    solution with the numerical calculation and find perfect agreement.
    Figure shown below:
    
    ![CleanShot 2024-09-02 at 17 03
    24](https://github.com/user-attachments/assets/cbc2b4d8-ea5f-45c8-8647-37fc69f54a8e)
    
    
    ### Related issues
    None.
    
    ### 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 see (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.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/problems/RadMarshakDust/test_radiation_marshak_dust.cpp
src/radiation/planck_integral.hpp
src/radiation/radiation_system.hpp
src/radiation/source_terms_multi_group.hpp
tests/RadMarshakDust.in

commit 4a7057f464636f64f58275c61ef7e0fb284580f9
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Sat Sep 7 11:44:39 2024 +1000

    Restructure AddSourceTermsMultiGroup (#734)
    
    ### Description
    
    In this PR I attempt to make the `AddSourceTermsMultiGroup` function
    more structured.
    
    Now, `AddSourceTermsMultiGroup` looks like this:
    
    
    ```c++
    AddSourceTermsMultiGroup()
    {
      // declare variables
      ...
    
      for outer loop {
        // declare variables
        ...
    
        // Compute the gas and radiation energy update. This also updates the opacities. When ite == 0, this also computes the work term.
        if (enable_dust_gas_thermal_coupling_model_) {
          updated_energy = SolveMatterRadiationEnergyExchange(..., &ComputeJacobianForGasAndDust, &ComputeDustTemperatureBateKeto);
        } else {
          updated_energy = SolveMatterRadiationEnergyExchange(..., &ComputeJacobianForGas, &ComputeDustTemperatureGasOnly);
        }
    
        // Compute radiation flux update
        ...
    
        // Deal with the work term.
        ...
      }
    }
    ```
    
    and this is the only place where
    `enable_dust_gas_thermal_coupling_model_` is used.
    
    Next, hopefully, I can implement more complex dust models and
    cooling/heating by defining new `ComputeJacobian` and new
    `ComputeDustTemperature`.
    
    ### Related issues
    
    N/A
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/QuokkaSimulation.hpp
src/radiation/radiation_system.cpp
src/radiation/radiation_system.hpp
src/radiation/source_terms_multi_group.hpp
src/radiation/source_terms_single_group.hpp
tests/RadDust.in

commit f145580eae845f8a3063fdab1324fe72d037426a
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Thu Sep 5 09:50:25 2024 +1000

    Separate single- and multi-group radiation modules (#731)
    
    ### Description
    
    The single-group radiation scheme has complex high-order terms, while
    the multi-group scheme has complexy opacity functions and Jacobian
    matrix. Previously, these two schemes are mixed together. It's a mess.
    In this PR, I splitted `AddSourceTerms` into
    `AddSourceTermsSingleGroup` and `AddSourceTermsMultiGroup`. In
    `AddSourceTermsSingleGroup`, whether or not the dust model is enabled,
    the Jacobian is a 2x2 matrix and can be inverted with a simple
    analytical expression. Second or higher order terms are supported. In
    `AddSourceTermsMultiGroup`, complexy multigroup opacity models are
    included but only 0th and 1st order terms are supported. The Jacobian is
    a (Ng + 1) by (Ng + 1) sparse matrix.
    
    ### Related issues
    
    None.
    
    ### 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 see (see above).
    - [x] I have read the [[Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md)](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/QuokkaSimulation.hpp
src/problems/RadDust/test_rad_dust.cpp
src/problems/RadDustMG/test_rad_dust_MG.cpp
src/problems/RadMarshakVaytet/test_radiation_marshak_Vaytet.cpp
src/problems/RadhydroPulseMGconst/test_radhydro_pulse_MG_const_kappa.cpp
src/problems/RadhydroPulseMGint/test_radhydro_pulse_MG_int.cpp
src/problems/RadhydroShockMultigroup/test_radhydro_shock_multigroup.cpp
src/radiation/radiation_system.hpp
src/radiation/source_terms_multi_group.hpp
src/radiation/source_terms_single_group.hpp
tests/radshock_dimensionless.in

commit 384d62d652ea147a9612a4cb3c0516f7e3efff67
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sun Sep 1 13:03:25 2024 -0400

    Bump extern/amrex from `6f039ae` to `74127d6` (#729)
    
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    `6f039ae` to `74127d6`.
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/74127d6d8fa83f922069a25e7ef9f153aa73f68c"><code>74127d6</code></a>
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    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/d06504acea6847f9c5aace1d3e0ecba193d47c69"><code>d06504a</code></a>
    Simplify cache cleanup actions (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4121">#4121</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/7c2ef81fc14dcabcb5791137b52ff368c4d7acfc"><code>7c2ef81</code></a>
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    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/df0d594a6a243db711dce732909ea427a93eca26"><code>df0d594</code></a>
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    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3812">#3812</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/12002e7283284281503ed4ae5e79ae02e006b897"><code>12002e7</code></a>
    Support for multiple periods in FillBoundary and ParallelCopy (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4106">#4106</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/b05f69fe3748012a69aa61a87989f73214c58a4e"><code>b05f69f</code></a>
    ParmParse::prettyPrintTable (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4101">#4101</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/dea243266d54b570ef4b48936fd0fdf5b66e55c2"><code>dea2432</code></a>
    TinyProfiler:: Add more runtime parameters (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4100">#4100</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/baec46e7baebb315bd82fb3057ba7a9e4385d676"><code>baec46e</code></a>
    Fix start_comp offset in tracer particle routines (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4098">#4098</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/0e97bad41a577c32b40bbe853bdb6a507964d70d"><code>0e97bad</code></a>
    ParmParse: queryarrWithParser (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4073">#4073</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/68e3741c6f985025ee23e0734a771c1f2b17a227"><code>68e3741</code></a>
    Add Geometry::RoundoffLo and RoundoffHi functions (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4097">#4097</a>)</li>
    <li>Additional commits viewable in <a
    href="https://github.com/AMReX-Codes/amrex/compare/6f039ae18e892c606c06fab7111bf11b57c8975a...74127d6d8fa83f922069a25e7ef9f153aa73f68c">compare
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extern/amrex

commit c95bc55246f147042c84d159e722e5162255fd08
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sun Sep 1 10:01:30 2024 -0400

    Bump extern/regression_testing from `466b340` to `4789924` (#730)
    
    Bumps
    [extern/regression_testing](https://github.com/AMReX-Codes/regression_testing)
    from `466b340` to `4789924`.
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    <li><a
    href="https://github.com/AMReX-Codes/regression_testing/commit/4789924db7db82346baf57c8a583e0cf2712a972"><code>4789924</code></a>
    Merge pull request <a
    href="https://redirect.github.com/AMReX-Codes/regression_testing/issues/146">#146</a>
    from EZoni/EZoni_rm_testdir</li>
    <li><a
    href="https://github.com/AMReX-Codes/regression_testing/commit/715ea85009f9a685b7255d9a831d3280aaef9df0"><code>715ea85</code></a>
    Rename option <code>rm_testdir</code> to <code>clean_testdir</code></li>
    <li><a
    href="https://github.com/AMReX-Codes/regression_testing/commit/5bd6a57c8d485a618190c7a4baffba8b2fd1c270"><code>5bd6a57</code></a>
    Check test run, analysis, and comparison</li>
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    href="https://github.com/AMReX-Codes/regression_testing/commit/2b047a69023c0ddcad59abc0d8859a731d24d572"><code>2b047a6</code></a>
    Add <code>rm_testdir</code> option</li>
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    href="https://github.com/AMReX-Codes/regression_testing/commit/21c052c7df471e3765f6d4408e328772c60b1b58"><code>21c052c</code></a>
    Merge pull request <a
    href="https://redirect.github.com/AMReX-Codes/regression_testing/issues/147">#147</a>
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extern/regression_testing

commit a475eedc722f0cdbffd38cf3fcd2774db3a0c7c0
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sun Sep 1 10:00:14 2024 -0400

    Bump extern/openPMD-api from `4f83a7e` to `1c7d7ff` (#728)
    
    Bumps [extern/openPMD-api](https://github.com/openPMD/openPMD-api) from
    `4f83a7e` to `1c7d7ff`.
    <details>
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    href="https://github.com/openPMD/openPMD-api/commit/1c7d7ffc5ef501e1d2dcbd5169b3e5eff677b399"><code>1c7d7ff</code></a>
    Fix memory leak (<a
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    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/ff21bbcf45f01e60ec3c2d9ea01eb26fa1bc75f8"><code>ff21bbc</code></a>
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    href="https://redirect.github.com/openPMD/openPMD-api/issues/1652">#1652</a>)</li>
    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/e9dd0e395c1f7512f194c035aa68b9a83ada4354"><code>e9dd0e3</code></a>
    HDF5 independent flush config (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1634">#1634</a>)</li>
    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/6956b0123b5d2cb65fc25551e6bcf10a065e4f7c"><code>6956b01</code></a>
    setup.py: Transitive ZLIB Static (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1522">#1522</a>)</li>
    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/443fdef7d369b12b2dcc727db5ffaa9ccc11c815"><code>443fdef</code></a>
    Use a shared pointer to bool to check if destructor ran (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1657">#1657</a>)</li>
    <li>See full diff in <a
    href="https://github.com/openPMD/openPMD-api/compare/4f83a7e91f7a841eaee741e0dc0729625e0b11f5...1c7d7ffc5ef501e1d2dcbd5169b3e5eff677b399">compare
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commit 5a2375a7a5ba2e6045223fdf3e13b7dcc8dd7bbf
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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    Bump extern/fmt from `d326c72` to `621e9c1` (#727)
    
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    Clarify why we have TYPE in native_formatter</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/bca70405569efa2e43768efea25ac7499e17b35e"><code>bca7040</code></a>
    Simplify compile-time checks</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/8c4b17fe648073bd5fc9aa76db907bec71babcb0"><code>8c4b17f</code></a>
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    href="https://github.com/fmtlib/fmt/commit/6797f0c39a4ef13061cbc3bb850c35af7428fdc4"><code>6797f0c</code></a>
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    href="https://github.com/fmtlib/fmt/commit/db496b47c1c5abe963f1dddcd52e26aff7b5910b"><code>db496b4</code></a>
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    <li><a
    href="https://github.com/fmtlib/fmt/commit/8eda3c8e900a205056ba58779f1ef0d43acec747"><code>8eda3c8</code></a>
    Cleanup compile-time check</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/53316903e64116cf0d53a7ab0ed17e8a76be7858"><code>5331690</code></a>
    Move string_literal to format.h</li>
    <li><a
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extern/fmt

commit a36586007903a0c76f6f5494a01765ca4cfd9e2a
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sun Sep 1 09:59:14 2024 -0400

    Bump extern/yaml-cpp from `b95aa14` to `47cd272` (#726)
    
    Bumps [extern/yaml-cpp](https://github.com/jbeder/yaml-cpp) from
    `b95aa14` to `47cd272`.
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    doc, fix: invalid liquid '{{...}}' tags</li>
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    href="https://redirect.github.com/jbeder/yaml-cpp/issues/1305">#1305</a>)(Issues
    <a
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extern/yaml-cpp

commit 76eff2f67c70e6804ce86f626d56b24a648e7884
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Sat Aug 31 04:13:19 2024 +1000

    improve convergence rate of the radiation Newton-Raphson solver (#720)
    
    ### Description
    
    Changes:
    
    1. Added a trick to make the Newton-Raphson iteration converge faster in
    some situations: when $\Delta T > \max(T_{\rm gas}, T_{\rm rad})$, set
    $T_{\rm gas}$ to $T_{\rm rad}$ and $R$ to 0. The motivation for doing
    this trick is explained below.
    2. Added `radiation.print_iteration_counts` parameter to enable counting
    the mean and max number of Newton-Raphson iterations in each radiation
    step. When set to `true`, the log file would look like:
    
    ```log
    Coarse STEP 1 at t = 0 (0%) starts ...
    time_subcycle = 0, total number of Newton-Raphson solvings is 128, (mean, max) number of Newton-Raphson iterations are 1, 1
    
    Coarse STEP 2 at t = 0.0046875 (0.9375%) starts ...
    time_subcycle = 0.0046875, total number of Newton-Raphson solvings is 128, (mean, max) number of Newton-Raphson iterations are 1, 1
    
    ```
    
    3. Defined a new radiation problem, `RadMarshakDust`. Initially, the gas
    is set with a density and temperature of 1, and the initial radiation
    energy density is 0. Radiation with a temperature $T_r = 0.01$ streams
    in from the left boundary. Before the dust model was introduced, we
    assumed gas and dust were perfectly coupled, and the gas would be heated
    by radiation where it could penetrate, and in regions without radiation,
    the gas temperature would cool to 0.003159 (solution of $1 = a_R T^4 +
    T$). In this test, however, we turned on the dust model and set the
    dust-gas interaction coefficient to a very small number. As a result,
    the dust and gas are decoupled: the dust temperature will reach the
    radiation temperature and stay in equilibrium, while the gas remains at
    its initial temperature.
    
    
    In a future PR, I will extend this test by incorporating a multigroup
    model. This will demonstrate how FUV radiation from the left boundary is
    absorbed by the dust, which then re-radiates in IR.
    
    ### Related issues
    
    None.
    
    ### 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:_
    
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    - [x] I have read the [[Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md)](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.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
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src/QuokkaSimulation.hpp
src/problems/CMakeLists.txt
src/problems/RadMarshakDust/CMakeLists.txt
src/problems/RadMarshakDust/test_radiation_marshak_dust.cpp
src/problems/RadMarshakDust/test_radiation_marshak_dust.hpp
src/radiation/radiation_system.hpp
tests/RadMarshakDust.in

commit 198cd1a7248f184e9fbd5f264c2d9f0db49d8ba9
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Thu Aug 29 22:38:33 2024 +0200

    Update microphysics to include metal chemistry (#725)
    
    ### Description
    Important updates to microphysics now enables using chemistry at all
    metallicities.
    
    ### Related issues
    Will be used in #723
    
    ### 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:_
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
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extern/Microphysics

commit e7ced4473637508c0e5eb27436e005b1e4c377a0
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Thu Aug 29 21:24:00 2024 +0200

    Redefine PRIMORDIAL_CHEM preprocessor as CHEMISTRY (#724)
    
    ### Description
    Now that we are going to have metal+dust chemistry, redefine the ifdef
    to CHEMISTRY
    
    ### Related issues
    Will be useful for #723
    
    ### 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).
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: Piyush Sharda <psharda@RSAA-43608.local>

src/QuokkaSimulation.hpp
src/chemistry/Chemistry.hpp
src/hydro/EOS.hpp
src/problems/PopIII/CMakeLists.txt
src/problems/PrimordialChem/CMakeLists.txt
tests/PopIII.in
tests/primordial_chem.in

commit 86686408835cf731c5792151bb890f6c6f78b2fc
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Tue Aug 20 02:04:57 2024 +1000

    Make assertion work in the exchange step and dust temperature solution step  (#716)
    
    ### Description
    
    A fix to #543 : make the Newton-Raphson iteration return a flag and
    check it on host.
    
    More changes:
    - Change `maxIter` from 400 to 50. 50 iterations should be more than
    enough. If it doesn't converge in less than 50 steps, it probably never
    will.
    
    ### Related issues
    Fixes #543
    
    ### 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
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
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src/QuokkaSimulation.hpp
src/radiation/radiation_system.hpp

commit 21ba4c2bdd8f552abc27f8e23fdfe029d97af57f
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Fri Aug 16 17:29:17 2024 +1000

    Dust temperature coupled to gas and radiation (#715)
    
    ### Description
    Add support for dust temperature coupled to radiation and gas, following
    [Bate & Keto
    (2015)](https://ui.adsabs.harvard.edu/abs/2015MNRAS.449.2643B).
    
    The dust is assumed to be in thermal equilibrium all the time:
    
    $$
    \Lambda_{{\rm gd},g} = - c \left[ \chi_{0,g} E_g - \chi_{0,g} \frac{4
    \pi}{c} B_g(T_d) \right]
    $$
    
    where $\sum_g \Lambda_{{\rm gd},g} = \Lambda_{{\rm gd}}$ is the dust-gas
    interaction rate:
    
    $$
    \Lambda_{\mathrm{gd}} = \Lambda_{{\mathrm{gd}}}^0 n_{\mathrm{H}}^2 T^{1
    / 2}\left(T-T_{{d}}\right)
    $$
    
    and $\Lambda_{\mathrm{gd}}^0 = 2.5 \times 10^{-34} \ {\rm erg \ cm^3 \
    s^{-1} \ K^{-3/2}}$.
    
    In the matter-radiation coupling step, we ignore the opacity of the gas
    and the coupling equations become:
    
    $$
    \begin{align}
    \frac{\partial E_{\rm gas}}{\partial t} &= - \sum_g \Lambda_{{\rm gd},g}
    \\
    \frac{\partial E_g}{\partial t} &= \frac{\hat{c}}{c} \Lambda_{{\rm
    gd},g}
    \end{align}
    $$
    
    
    At high density, the dust and gas are thermally coupled to each other,
    so $T_d = T_{\rm gas}$, and the original recipe is retrieved. In the
    low-density regime, however, the dust temperature is significantly lower
    than the gas temperature, therefore the thermal emission of the gas is
    very low and the gas relies on line emission to cool.
    
    This PR only implements dust temperature and I will implement line
    cooling, photoelectric heating and cosmic ray heating in the next PR.
    
    More changes:
    
    - Added a new parameter `enable_dust` in `RadSystem_Traits` to control
    enabling dust.
    - Added two tests, RadDust and RadDustMG, to test the new dust physics.
    The simulation results are compared to the reference results obtained
    from solving the above equations using an ODE integrator.
    
    ### Related issues
    
    None.
    
    ### 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).
    - [ ] I have added a link to any related issues see (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.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [ ] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.gitignore
extern/data/dust/rad_dust_exact.csv
src/QuokkaSimulation.hpp
src/problems/CMakeLists.txt
src/problems/RadBeam/test_radiation_beam.cpp
src/problems/RadDust/CMakeLists.txt
src/problems/RadDust/test_rad_dust.cpp
src/problems/RadDust/test_rad_dust.hpp
src/problems/RadDustMG/CMakeLists.txt
src/problems/RadDustMG/test_rad_dust_MG.cpp
src/problems/RadDustMG/test_rad_dust_MG.hpp
src/problems/RadForce/test_radiation_force.cpp
src/problems/RadMarshak/test_radiation_marshak.cpp
src/problems/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/problems/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/problems/RadMarshakVaytet/test_radiation_marshak_Vaytet.cpp
src/problems/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/problems/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/problems/RadPulse/test_radiation_pulse.cpp
src/problems/RadShadow/test_radiation_shadow.cpp
src/problems/RadStreaming/test_radiation_streaming.cpp
src/problems/RadStreamingY/test_radiation_streaming_y.cpp
src/problems/RadSuOlson/test_radiation_SuOlson.cpp
src/problems/RadTophat/test_radiation_tophat.cpp
src/problems/RadTube/test_radiation_tube.cpp
src/problems/RadhydroBB/test_radhydro_bb.cpp
src/problems/RadhydroPulse/test_radhydro_pulse.cpp
src/problems/RadhydroPulseDyn/test_radhydro_pulse_dyn.cpp
src/problems/RadhydroPulseGrey/test_radhydro_pulse_grey.cpp
src/problems/RadhydroPulseMGconst/test_radhydro_pulse_MG_const_kappa.cpp
src/problems/RadhydroPulseMGint/test_radhydro_pulse_MG_int.cpp
src/problems/RadhydroShell/test_radhydro_shell.cpp
src/problems/RadhydroShock/test_radhydro_shock.cpp
src/problems/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/problems/RadhydroShockMultigroup/test_radhydro_shock_multigroup.cpp
src/problems/RadhydroUniformAdvecting/test_radhydro_uniform_advecting.cpp
src/radiation/radiation_system.hpp
tests/RadDust.in

commit 9d7699713ce3edc64536f04729180a423d7a3e2e
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Thu Aug 15 22:43:40 2024 +1000

    Cleanup: remove repeating calculation of kappa (#714)
    
    ### Description
    
    In this PR I removed repeating calculation of kappa_E and kappa_B to
    make the code a lot cleaner. Nothing particularly interesting.
    
    ### Related issues
    None.
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/radiation/radiation_system.hpp

commit bea14af0ca26d5fbdfc3f3c3989740dc14ba96ba
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Aug 9 11:05:24 2024 -0400

    Upload results even if regression tests fail (#711)
    
    ### Description
    Upload the test results even if a test fails. Currently, the pipeline is
    canceled if any of the tests fail, and the results aren't available on
    the website
    (https://quokka-astro.github.io/regression-testing-results/).
    
    Documentation:
    https://learn.microsoft.com/en-us/azure/devops/pipelines/process/conditions?view=azure-devops
    
    ### Related issues
    N/A
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

.ci/azure-pipelines-regression.yml

commit 58eb97ef5ea07be7b5b93558565d7abc68159d7a
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Aug 9 11:04:59 2024 -0400

    fix Setonix compiler version (#709)
    
    ### Description
    This uses ROCm version 5.5.3, which is actually able to compile the
    metal advection problem.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] I have added a link to any related issues see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [ ] I have requested a reviewer for this PR.

scripts/setonix-gpu.profile

commit c5c6a879c47f4f7ae60dbc6239e1fa78b14ab788
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Aug 8 19:52:08 2024 -0400

    Revert "Metal Advection Problem" (#710)
    
    Reverts quokka-astro/quokka#704.
    
    It wasn't quite ready yet.

regression/quokka-tests.ini
src/problems/CMakeLists.txt
src/problems/MetalAdvectionProblem/CMakeLists.txt
src/problems/MetalAdvectionProblem/data_sets.dat
src/problems/MetalAdvectionProblem/test_sne.cpp
src/problems/MetalAdvectionProblem/test_sne.hpp
tests/metal_problem_regression.in

commit 2c7f17dec5e848d48882b7292f4d25df4762e617
Author: Aditi <45175933+aditivijayan@users.noreply.github.com>
Date:   Fri Aug 9 05:05:30 2024 +1000

    Metal Advection Problem (#704)
    
    ### Description
    This is the version of the Metal Advection problem that compiles on
    Setonix. It add four new files to the problem folder- test_sne.hpp/cpp,
    an input file, and data set file containing parameters for various
    Galactic environments.
    
    ### Related issues
    N/A
    
    ### 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 see (see above).
    - [ ] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [ ] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: Aditi Vijayan <aditi@setonix-03.pawsey.org.au>
    Co-authored-by: Aditi Vijayan <aditi@setonix-01.pawsey.org.au>
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    Co-authored-by: Ben Wibking <ben@wibking.com>
    Co-authored-by: Ben Wibking <wibkingb@msu.edu>

regression/quokka-tests.ini
src/problems/CMakeLists.txt
src/problems/MetalAdvectionProblem/CMakeLists.txt
src/problems/MetalAdvectionProblem/data_sets.dat
src/problems/MetalAdvectionProblem/test_sne.cpp
src/problems/MetalAdvectionProblem/test_sne.hpp
tests/metal_problem_regression.in

commit b2f3e2fc058c66de14d443acb2e8980632d1e08d
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Thu Aug 8 13:09:40 2024 +1000

    Use MkDocs to generate documentation (#705)
    
    ### Description
    
    Use MkDocs to generate the documentation page, replacing Sphinx.
    
    I tested it on my computer with the following steps and it worked
    perfectly fine. Not guaranteed to work on github. May need your help
    @BenWibking to update the docs.yml properly.
    
    ```sh
    cd docs2
    python -m pip install -r requirements.txt
    mkdocs build && mkdocs serve
    ```
    
    Currently all the new docs are in docs2. Once everything works fine,
    I'll use it to replace docs.
    
    ### Related issues
    Closes #542
    
    ### 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 see (see above).
    - [ ] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [ ] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    Co-authored-by: Ben Wibking <ben@wibking.com>

.github/workflows/dependencies/documentation.sh
.github/workflows/docs.yml
.gitignore
build_docs.sh
docs/Doxyfile
docs/Makefile
docs/about.rst
docs/apa-6th-edition.csl
docs/bibliography.rst
docs/citation.rst
docs/conf.py
docs/debugging.rst
docs/docs/about.md
docs/docs/citation.md
docs/docs/debugging.md
docs/docs/equations.md
docs/docs/error_checking.md
docs/docs/extra.css
docs/docs/flowchart-v2.jpg
docs/docs/flowchart-v2.pdf
docs/docs/flowchart.md
docs/docs/flowchart.svg
docs/docs/howto_clang_tidy.md
docs/docs/index.md
docs/docs/insitu_analysis.md
docs/docs/instability.md
docs/docs/installation.md
docs/docs/javascripts/mathjax.js
docs/docs/parameters.md
docs/docs/performance.md
docs/docs/postprocessing.md
docs/docs/references.bib
docs/docs/requirements.txt
docs/docs/running_on_hpc_clusters.md
docs/docs/tests/attach/hydro_shuosher.png
docs/docs/tests/attach/hydro_sms.png
docs/docs/tests/attach/radcoupling.png
docs/docs/tests/attach/radcoupling_rsla.png
docs/docs/tests/attach/radhydro_pulse_density-1.png
docs/docs/tests/attach/radhydro_pulse_density.png
docs/docs/tests/attach/radhydro_pulse_temperature-1.png
docs/docs/tests/attach/radhydro_pulse_temperature.png
docs/docs/tests/attach/radhydro_pulse_velocity-1.png
docs/docs/tests/attach/radhydro_pulse_velocity.png
docs/docs/tests/attach/radhydro_uniform_advecting_temperature-nobeta.png
docs/docs/tests/attach/radhydro_uniform_advecting_temperature.png
docs/docs/tests/attach/radhydro_uniform_advecting_velocity-nobeta.png
docs/docs/tests/attach/radhydro_uniform_advecting_velocity.png
docs/docs/tests/attach/radshock_cgs_temperature.png
docs/docs/tests/energy_exchange.md
docs/docs/tests/index.md
docs/docs/tests/radhydro_pulse.md
docs/docs/tests/radhydro_uniform_adv.md
docs/docs/tests/radshock.md
docs/docs/tests/shu_osher.md
docs/docs/tests/sms.md
docs/equations.rst
docs/error_checking.rst
docs/flowchart.rst
docs/howto_clang_tidy.rst
docs/index.rst
docs/insitu_analysis.rst
docs/instability.rst
docs/installation.rst
docs/mkdocs.yml
docs/parameters.rst
docs/performance.rst
docs/postprocessing.rst
docs/requirements.txt
docs/running_on_hpc_clusters.rst
docs/tests/energy_exchange.rst
docs/tests/index.rst
docs/tests/radhydro_pulse.rst
docs/tests/radhydro_uniform_adv.rst
docs/tests/radshock.rst
docs/tests/shu_osher.rst
docs/tests/sms.rst

commit d68f360a527430e562ed8de06c1081a2e3a204b3
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Aug 7 19:16:15 2024 -0400

    CUDA 12.6 hotfix (#708)
    
    ### Description
    Update AMReX to fix a bug so we can compile with CUDA 12.6.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] I have added a link to any related issues see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

extern/amrex

commit fe6215e0ebbf4ae1d3d75125c005a750f8a691da
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Tue Aug 6 04:04:36 2024 +1000

    Rename RadhydroSimulation class to QuokkaSimulation (#702)
    
    ### Description
    
    What's changed in the PR:
    - Renamed `RadhydroSimulation` class to `QuokkaSimulation` in all
    occurances inside src/.
    - Renamed `RadhydroSimulation.cpp/.hpp` to `QuokkaSimulation.cpp/.hpp`
    
    Why? This is the main simulation class that does all of the physics,
    including HD, gravity, radiation, MHD, etc. It should be given a more
    general and inclusive name to avoid the confusion caused by the name
    `RadhydroSimulation`. See #428
    
    ### Related issues
    
    Addressed issue #428
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/QuokkaSimulation.cpp
src/QuokkaSimulation.hpp
src/RadhydroSimulation.cpp
src/linear_advection/AdvectionSimulation.hpp
src/problems/Advection/test_advection.cpp
src/problems/Advection2D/test_advection2d.cpp
src/problems/AdvectionSemiellipse/test_advection_semiellipse.cpp
src/problems/BinaryOrbitCIC/binary_orbit.cpp
src/problems/Cooling/test_cooling.cpp
src/problems/FCQuantities/test_fc_quantities.cpp
src/problems/HydroBlast2D/test_hydro2d_blast.cpp
src/problems/HydroBlast3D/test_hydro3d_blast.cpp
src/problems/HydroContact/test_hydro_contact.cpp
src/problems/HydroHighMach/test_hydro_highmach.cpp
src/problems/HydroKelvinHelmholz/test_hydro2d_kh.cpp
src/problems/HydroLeblanc/test_hydro_leblanc.cpp
src/problems/HydroQuirk/test_quirk.cpp
src/problems/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
src/problems/HydroSMS/test_hydro_sms.cpp
src/problems/HydroShocktube/test_hydro_shocktube.cpp
src/problems/HydroShocktubeCMA/test_hydro_shocktube_cma.cpp
src/problems/HydroShuOsher/test_hydro_shuosher.cpp
src/problems/HydroVacuum/test_hydro_vacuum.cpp
src/problems/HydroWave/test_hydro_wave.cpp
src/problems/NSCBC/channel.cpp
src/problems/NSCBC/vortex.cpp
src/problems/PassiveScalar/test_scalars.cpp
src/problems/PopIII/popiii.cpp
src/problems/PrimordialChem/test_primordial_chem.cpp
src/problems/RadBeam/test_radiation_beam.cpp
src/problems/RadBeam/test_radiation_beam.hpp
src/problems/RadForce/test_radiation_force.cpp
src/problems/RadMarshak/test_radiation_marshak.cpp
src/problems/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/problems/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/problems/RadMarshakCGS/test_radiation_marshak_cgs.hpp
src/problems/RadMarshakVaytet/test_radiation_marshak_Vaytet.cpp
src/problems/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/problems/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/problems/RadPulse/test_radiation_pulse.cpp
src/problems/RadShadow/test_radiation_shadow.cpp
src/problems/RadShadow/test_radiation_shadow.hpp
src/problems/RadStreaming/test_radiation_streaming.cpp
src/problems/RadStreamingY/test_radiation_streaming_y.cpp
src/problems/RadSuOlson/test_radiation_SuOlson.cpp
src/problems/RadSuOlson/test_radiation_SuOlson.hpp
src/problems/RadTophat/test_radiation_tophat.cpp
src/problems/RadTophat/test_radiation_tophat.hpp
src/problems/RadTube/test_radiation_tube.cpp
src/problems/RadhydroBB/test_radhydro_bb.cpp
src/problems/RadhydroBB/test_radhydro_bb.hpp
src/problems/RadhydroPulse/test_radhydro_pulse.cpp
src/problems/RadhydroPulseDyn/test_radhydro_pulse_dyn.cpp
src/problems/RadhydroPulseGrey/test_radhydro_pulse_grey.cpp
src/problems/RadhydroPulseMGconst/test_radhydro_pulse_MG_const_kappa.cpp
src/problems/RadhydroPulseMGint/test_radhydro_pulse_MG_int.cpp
src/problems/RadhydroShell/test_radhydro_shell.cpp
src/problems/RadhydroShock/test_radhydro_shock.cpp
src/problems/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/problems/RadhydroShockCGS/test_radhydro_shock_cgs.hpp
src/problems/RadhydroShockMultigroup/test_radhydro_shock_multigroup.cpp
src/problems/RadhydroShockMultigroup/test_radhydro_shock_multigroup.hpp
src/problems/RadhydroUniformAdvecting/test_radhydro_uniform_advecting.cpp
src/problems/RandomBlast/blast.cpp
src/problems/RayleighTaylor2D/test_hydro2d_rt.cpp
src/problems/RayleighTaylor3D/test_hydro3d_rt.cpp
src/problems/ShockCloud/cloud.cpp
src/problems/SphericalCollapse/spherical_collapse.cpp
src/problems/StarCluster/star_cluster.cpp
src/simulation.hpp

commit 9e20d50a921dbc9e6c3c4a24152cb9aa2cd9076f
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Aug 1 14:07:55 2024 -0400

    update docs for runtime parameters (#697)
    
    ### Description
    This add `temperature_floor` to the list of runtime parameters in the
    documentation and removes the `*_ceiling` parameters, since those have
    been removed.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] I have added a link to any related issues see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

docs/parameters.rst

commit 2cc68d8eeaa43decaf8dd5b791c34981df46445a
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Thu Aug 1 10:50:05 2024 -0400

    Bump extern/amrex from `7418556` to `83ecf62` (#694)
    
    Bumps [extern/amrex](https://github.com/AMReX-Codes/amrex) from
    `7418556` to `83ecf62`.
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/83ecf62e0b4363e1fa8dd83f3e68e9046d329496"><code>83ecf62</code></a>
    Catalyst support (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4011">#4011</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/a8c525572b33024f316562aded96f5a81f905409"><code>a8c5255</code></a>
    Fix typos in FaceDivFree interior interpolation. (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4048">#4048</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/20e6f2eadf0c297517588ba38973ec7c7084fa31"><code>20e6f2e</code></a>
    ParmParse: Fix assertion in new queryarr for IntVect &amp; RealVect (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4051">#4051</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/6975ae0ed5ca51ec95268f323bdc705dab4fe571"><code>6975ae0</code></a>
    ParmParse: Read IntVect &amp; RealVect from array (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4050">#4050</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/80b0c7ea3dbc097fc0ddd263f544aacf812e4b13"><code>80b0c7e</code></a>
    IParser: Use long long int (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4046">#4046</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/fd1633e4be1146206ebcee6aed03933135ea960a"><code>fd1633e</code></a>
    ParmParse: Math expression support (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4032">#4032</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/11d31e5f787d9357f1c153e8cbd55462bffd7e41"><code>11d31e5</code></a>
    AmrData: remove dependency on Fortran (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4049">#4049</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/d9dec56e2201e25fd36324a4788ed64c943e1045"><code>d9dec56</code></a>
    Remove reliance on managed memory in HDF5 mesh IO (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4047">#4047</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/3cb7f1555494ce443922d66e31fba94bead52fe6"><code>3cb7f15</code></a>
    New Feature in MLEBNodeFDLaplacian: MultiFab sigma coefficient (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3968">#3968</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/930e75ea9d02a46278a802ea886d950f4c8d1a90"><code>930e75e</code></a>
    Nodal Solver: Use multi-color Gauss-Seidel on GPU (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/4043">#4043</a>)</li>
    <li>Additional commits viewable in <a
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extern/amrex

commit 6b438504cb8653a275822004cecdfea83b15eb77
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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    Bump extern/Microphysics from `a3bc246` to `24fc854` (#695)
    
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    from `a3bc246` to `24fc854`.
    <details>
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    <li><a
    href="https://github.com/psharda/Microphysics/commit/24fc8547090297bacdefe30f14bc2c37e53069f4"><code>24fc854</code></a>
    include higher taylor terms for fast_atan (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1611">#1611</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/a5408bad445e49e4b8c0622843905a4c08b1ed6d"><code>a5408ba</code></a>
    update self-consistent NSE SDC update with Tabular NSE (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1569">#1569</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/b413290def9550c8fac7035ec614f90f68c12ba4"><code>b413290</code></a>
    remove some more Fortran comments (<a
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    href="https://github.com/psharda/Microphysics/commit/448132f96834e1958e5fe38a10f08610ec665981"><code>448132f</code></a>
    remove test_nse and rename test_ase -&gt; test_nse_net (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1610">#1610</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/963ff00371ca38c271b82c96ccde9fbd17bb4952"><code>963ff00</code></a>
    remove the old test_screening (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1608">#1608</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/d791e67c65f623e0ee05b7458f6e6fae19668704"><code>d791e67</code></a>
    Remove strang nse (<a
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    href="https://github.com/psharda/Microphysics/commit/4142d4fbff132040a405d0bc3759b5c99099334c"><code>4142d4f</code></a>
    Update rhoX for nse_solver for SDC and discard strang (<a
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    <li><a
    href="https://github.com/psharda/Microphysics/commit/0b1a2310392f83adfee33c5a50da9fd90a2b5a7c"><code>0b1a231</code></a>
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extern/Microphysics

commit 3a754c548847a4d84c02b21955f0ca0e6d5bf572
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    Bump extern/fmt from `686339f` to `d326c72` (#696)
    
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extern/fmt

commit d1b5764ca47f2be4e35c80c51ef22e01efe450b8
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    Bump extern/yaml-cpp from `1d8ca1f` to `b95aa14` (#692)
    
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    fix: use C locale by default</li>
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extern/yaml-cpp

commit b978c16d28747795463dc387df51bde5ff15a272
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Thu Aug 1 04:13:08 2024 +0000

    Bump extern/openPMD-api from `9184c2e` to `4f83a7e` (#693)
    
    Bumps [extern/openPMD-api](https://github.com/openPMD/openPMD-api) from
    `9184c2e` to `4f83a7e`.
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    href="https://github.com/openPMD/openPMD-api/commit/4f83a7e91f7a841eaee741e0dc0729625e0b11f5"><code>4f83a7e</code></a>
    ADIOS2: Override access mode (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1638">#1638</a>)</li>
    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/74fdc479a1008fd0d848ad123006c74f47fc6232"><code>74fdc47</code></a>
    Pickle API: Avoid static Series hack, allow multiple Series (<a
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extern/openPMD-api

commit e6e23a9e6fab5d8c4174b882c8feda82a32bada7
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Jul 31 00:39:04 2024 -0400

    add equations to docs (#691)
    
    ### Description
    This adds the complete set of equations that are solved by Quokka to the
    documentation.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] I have added a link to any related issues see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

docs/equations.rst

commit 725c343e537527c75aafdf15d94ec3ada2497968
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Wed Jul 31 02:23:38 2024 +1000

    Update citations (#690)
    
    ### Description
    
    Update citation for the newly published multigroup RHD paper on arxiv.
    
    ### 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:_
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    - [ ] I have added a link to any related issues see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
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docs/citation.rst
docs/references.bib

commit 8d855a16461fbd926450b274f9010c7f50f05b3c
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Tue Jul 30 13:29:45 2024 +1000

    Clean up code for single-group radiation  (#684)
    
    ### Description
    
    This PR updates the code structure for single-group radiation so that
    functions like `ComputePlanckOpacity` return a `double`. This change
    enforces the use of the correct opacity models (i.e.,
    `piecewise_constant_opacity` or `PPL_opacity_fixed_slope_spectrum`, or
    `PPL_opacity_full_spectrum`) when dealing with multiple radiation
    groups. The previous code provides an option to naively extend the
    single-group formulation in the IMEX paper to the multigroup case, i.e.
    replacing $\kappa_P$ and $\kappa_F$ with $\kappa_g$. However, that
    method does not correctly describe multigroup radiation transport and
    should be removed, because it misses the important delta term in the
    flux equation. See Equation 16 of the multigroup paper and the
    discussion thereafter.
    
    In summary, here's how you should define gas opacity in a problem:
    - Single-group opacity definition:
    - Define `ComputePlanckOpacity` and optionally `ComputeFluxMeanOpacity`
    and `ComputeEnergyMeanOpacity`. By default, the latter two are set equal
    to the first.
    - Multigroup opacity definition:
    - Choose an opacity model by setting `opacity_model` in
    `RadSystem_Traits` to one of the following:
    `piecewise_constant_opacity`, `PPL_opacity_fixed_slope_spectrum`, or
    `PPL_opacity_full_spectrum`
    - Define `DefineOpacityExponentsAndLowerValues`. See the example in
    RadhydroShockMultigroup.
    
    Bug fix:
    - fixed bug related to multigroup opacity in `ComputeCellOpticalDepth`.
    This function is only used when you turn on wave speed correction by
    hand and is not turned on by default. We can't have a regression test
    for this because it is controlled by `use_wavespeed_correction` inside
    `radiation_system.hpp` and we don't have a way to turn it on for a
    specific problem. I tested it on my computer and it worked as expected.
    
    ### 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 see (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.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    Co-authored-by: Ben Wibking <ben@wibking.com>

src/RadhydroSimulation.hpp
src/problems/RadBeam/test_radiation_beam.cpp
src/problems/RadForce/test_radiation_force.cpp
src/problems/RadMarshak/test_radiation_marshak.cpp
src/problems/RadMarshakAsymptotic/CMakeLists.txt
src/problems/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/problems/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/problems/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/problems/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/problems/RadPulse/test_radiation_pulse.cpp
src/problems/RadShadow/test_radiation_shadow.cpp
src/problems/RadStreaming/test_radiation_streaming.cpp
src/problems/RadStreamingY/test_radiation_streaming_y.cpp
src/problems/RadSuOlson/test_radiation_SuOlson.cpp
src/problems/RadTophat/test_radiation_tophat.cpp
src/problems/RadTube/test_radiation_tube.cpp
src/problems/RadhydroBB/test_radhydro_bb.cpp
src/problems/RadhydroPulse/test_radhydro_pulse.cpp
src/problems/RadhydroPulseDyn/test_radhydro_pulse_dyn.cpp
src/problems/RadhydroPulseGrey/test_radhydro_pulse_grey.cpp
src/problems/RadhydroPulseMGconst/test_radhydro_pulse_MG_const_kappa.cpp
src/problems/RadhydroPulseMGint/test_radhydro_pulse_MG_int.cpp
src/problems/RadhydroShell/test_radhydro_shell.cpp
src/problems/RadhydroShock/test_radhydro_shock.cpp
src/problems/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/problems/RadhydroShockMultigroup/test_radhydro_shock_multigroup.cpp
src/problems/RadhydroUniformAdvecting/test_radhydro_uniform_advecting.cpp
src/radiation/radiation_system.hpp
tests/MarshakAsymptoticCorr.in

commit c37cfb21266fb793d2ff39d865a3f2174a3912e9
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Jul 29 00:16:28 2024 -0400

    reorganize source code into subdirectories (#689)
    
    ### Description
    The code used to be simple, but now it's not. I've reorganized all of
    the source code files under `src/` into subdirectories (one level only).
    
    Unfortunately, virtually every file had to be changed in order to update
    header include paths. No other changes were made to the code (other than
    file renaming).
    
    The new `src/` directory layout is as follows:
    ```console
    $ tree -d .
    .
    ├── chemistry
    ├── cooling
    ├── hydro
    ├── io
    ├── linear_advection
    ├── math
    ├── particles
    ├── problems
    │   ├── Advection
    │   ├── Advection2D
    │   ├── AdvectionSemiellipse
    │   ├── BinaryOrbitCIC
    │   ├── Cooling
    │   ├── FCQuantities
    │   ├── HydroBlast2D
    │   ├── HydroBlast3D
    │   ├── HydroContact
    │   ├── HydroHighMach
    │   ├── HydroKelvinHelmholz
    │   ├── HydroLeblanc
    │   ├── HydroQuirk
    │   ├── HydroRichtmeyerMeshkov
    │   ├── HydroShocktube
    │   ├── HydroShocktubeCMA
    │   ├── HydroShuOsher
    │   ├── HydroSMS
    │   ├── HydroVacuum
    │   ├── HydroWave
    │   ├── NSCBC
    │   ├── ODEIntegration
    │   ├── PassiveScalar
    │   ├── PopIII
    │   ├── PrimordialChem
    │   ├── RadBeam
    │   ├── RadForce
    │   ├── RadhydroBB
    │   ├── RadhydroPulse
    │   ├── RadhydroPulseDyn
    │   ├── RadhydroPulseGrey
    │   ├── RadhydroPulseMGconst
    │   ├── RadhydroPulseMGint
    │   ├── RadhydroShell
    │   ├── RadhydroShock
    │   ├── RadhydroShockCGS
    │   ├── RadhydroShockMultigroup
    │   ├── RadhydroUniformAdvecting
    │   ├── RadMarshak
    │   ├── RadMarshakAsymptotic
    │   ├── RadMarshakCGS
    │   ├── RadMarshakVaytet
    │   ├── RadMatterCoupling
    │   ├── RadMatterCouplingRSLA
    │   ├── RadPulse
    │   ├── RadShadow
    │   ├── RadStreaming
    │   ├── RadStreamingY
    │   ├── RadSuOlson
    │   ├── RadTophat
    │   ├── RadTube
    │   ├── RandomBlast
    │   ├── RayleighTaylor2D
    │   ├── RayleighTaylor3D
    │   ├── ShockCloud
    │   ├── SphericalCollapse
    │   └── StarCluster
    ├── radiation
    ├── turbulence
    └── util
    ```
    
    ### Related issues
    N/A
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/AdvectionSimulation.cpp
src/CMakeLists.txt
src/RadhydroSimulation.hpp
src/chemistry/Chemistry.cpp
src/chemistry/Chemistry.hpp
src/cooling/CloudyDataReader.cpp
src/cooling/CloudyDataReader.hpp
src/cooling/GrackleDataReader.cpp
src/cooling/GrackleDataReader.hpp
src/cooling/GrackleLikeCooling.cpp
src/cooling/GrackleLikeCooling.hpp
src/cooling/TabulatedCooling.cpp
src/cooling/TabulatedCooling.hpp
src/hydro/EOS.hpp
src/hydro/HLLC.hpp
src/hydro/HLLD.hpp
src/hydro/HydroState.hpp
src/hydro/LLF.hpp
src/hydro/NSCBC_inflow.hpp
src/hydro/NSCBC_outflow.hpp
src/hydro/hydro_system.cpp
src/hydro/hydro_system.hpp
src/hydro/mhd_system.cpp
src/hydro/mhd_system.hpp
src/hyperbolic_system.hpp
src/io/DiagBase.H
src/io/DiagBase.cpp
src/io/DiagFilter.H
src/io/DiagFilter.cpp
src/io/DiagFramePlane.H
src/io/DiagFramePlane.cpp
src/io/DiagPDF.H
src/io/DiagPDF.cpp
src/io/openPMD.cpp
src/io/openPMD.hpp
src/linear_advection/AdvectionSimulation.cpp
src/linear_advection/AdvectionSimulation.hpp
src/linear_advection/linear_advection.cpp
src/linear_advection/linear_advection.hpp
src/math/FastMath.hpp
src/math/Interpolate2D.cpp
src/math/Interpolate2D.hpp
src/math/ODEIntegrate.hpp
src/math/gauss.hpp
src/math/interpolate.cpp
src/math/interpolate.hpp
src/math/math_impl.hpp
src/math/quadrature.hpp
src/math/root_finding.hpp
src/particles/CICParticles.hpp
src/problems/Advection/CMakeLists.txt
src/problems/Advection/test_advection.cpp
src/problems/Advection/test_advection.hpp
src/problems/Advection2D/CMakeLists.txt
src/problems/Advection2D/test_advection2d.cpp
src/problems/Advection2D/test_advection2d.hpp
src/problems/AdvectionSemiellipse/CMakeLists.txt
src/problems/AdvectionSemiellipse/test_advection_semiellipse.cpp
src/problems/AdvectionSemiellipse/test_advection_semiellipse.hpp
src/problems/BinaryOrbitCIC/CMakeLists.txt
src/problems/BinaryOrbitCIC/binary_orbit.cpp
src/problems/BinaryOrbitCIC/binary_orbit.hpp
src/problems/BinaryOrbitCIC/particle_orbit_plot.py
src/problems/CMakeLists.txt
src/problems/Cooling/CMakeLists.txt
src/problems/Cooling/test_cooling.cpp
src/problems/Cooling/test_cooling.hpp
src/problems/FCQuantities/CMakeLists.txt
src/problems/FCQuantities/test_fc_quantities.cpp
src/problems/FCQuantities/test_fc_quantities.hpp
src/problems/HydroBlast2D/CMakeLists.txt
src/problems/HydroBlast2D/test_hydro2d_blast.cpp
src/problems/HydroBlast2D/test_hydro2d_blast.hpp
src/problems/HydroBlast3D/CMakeLists.txt
src/problems/HydroBlast3D/test_hydro3d_blast.cpp
src/problems/HydroBlast3D/test_hydro3d_blast.hpp
src/problems/HydroContact/CMakeLists.txt
src/problems/HydroContact/test_hydro_contact.cpp
src/problems/HydroContact/test_hydro_contact.hpp
src/problems/HydroHighMach/CMakeLists.txt
src/problems/HydroHighMach/test_hydro_highmach.cpp
src/problems/HydroHighMach/test_hydro_highmach.hpp
src/problems/HydroKelvinHelmholz/CMakeLists.txt
src/problems/HydroKelvinHelmholz/test_hydro2d_kh.cpp
src/problems/HydroKelvinHelmholz/test_hydro2d_kh.hpp
src/problems/HydroLeblanc/CMakeLists.txt
src/problems/HydroLeblanc/test_hydro_leblanc.cpp
src/problems/HydroLeblanc/test_hydro_leblanc.hpp
src/problems/HydroQuirk/CMakeLists.txt
src/problems/HydroQuirk/test_quirk.cpp
src/problems/HydroQuirk/test_quirk.hpp
src/problems/HydroRichtmeyerMeshkov/CMakeLists.txt
src/problems/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
src/problems/HydroRichtmeyerMeshkov/test_hydro2d_rm.hpp
src/problems/HydroSMS/CMakeLists.txt
src/problems/HydroSMS/test_hydro_sms.cpp
src/problems/HydroSMS/test_hydro_sms.hpp
src/problems/HydroShocktube/CMakeLists.txt
src/problems/HydroShocktube/test_hydro_shocktube.cpp
src/problems/HydroShocktube/test_hydro_shocktube.hpp
src/problems/HydroShocktubeCMA/CMakeLists.txt
src/problems/HydroShocktubeCMA/test_hydro_shocktube_cma.cpp
src/problems/HydroShocktubeCMA/test_hydro_shocktube_cma.hpp
src/problems/HydroShuOsher/CMakeLists.txt
src/problems/HydroShuOsher/test_hydro_shuosher.cpp
src/problems/HydroShuOsher/test_hydro_shuosher.hpp
src/problems/HydroVacuum/CMakeLists.txt
src/problems/HydroVacuum/test_hydro_vacuum.cpp
src/problems/HydroVacuum/test_hydro_vacuum.hpp
src/problems/HydroWave/CMakeLists.txt
src/problems/HydroWave/test_hydro_wave.cpp
src/problems/HydroWave/test_hydro_wave.hpp
src/problems/NSCBC/CMakeLists.txt
src/problems/NSCBC/channel.cpp
src/problems/NSCBC/channel.hpp
src/problems/NSCBC/dQ_dx_inflow.ipynb
src/problems/NSCBC/dQ_dx_outflow.ipynb
src/problems/NSCBC/vortex.cpp
src/problems/NSCBC/vortex.hpp
src/problems/ODEIntegration/CMakeLists.txt
src/problems/ODEIntegration/test_ode.cpp
src/problems/ODEIntegration/test_ode.hpp
src/problems/PassiveScalar/CMakeLists.txt
src/problems/PassiveScalar/test_scalars.cpp
src/problems/PassiveScalar/test_scalars.hpp
src/problems/PopIII/CMakeLists.txt
src/problems/PopIII/ascent_actions.yaml
src/problems/PopIII/popiii.cpp
src/problems/PopIII/popiii.hpp
src/problems/PrimordialChem/CMakeLists.txt
src/problems/PrimordialChem/test_primordial_chem.cpp
src/problems/PrimordialChem/test_primordial_chem.hpp
src/problems/RadBeam/CMakeLists.txt
src/problems/RadBeam/test_radiation_beam.cpp
src/problems/RadBeam/test_radiation_beam.hpp
src/problems/RadForce/CMakeLists.txt
src/problems/RadForce/test_radiation_force.cpp
src/problems/RadForce/test_radiation_force.hpp
src/problems/RadMarshak/CMakeLists.txt
src/problems/RadMarshak/test_radiation_marshak.cpp
src/problems/RadMarshak/test_radiation_marshak.hpp
src/problems/RadMarshakAsymptotic/CMakeLists.txt
src/problems/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/problems/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.hpp
src/problems/RadMarshakCGS/CMakeLists.txt
src/problems/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/problems/RadMarshakCGS/test_radiation_marshak_cgs.hpp
src/problems/RadMarshakVaytet/CMakeLists.txt
src/problems/RadMarshakVaytet/test_radiation_marshak_Vaytet.cpp
src/problems/RadMarshakVaytet/test_radiation_marshak_Vaytet.hpp
src/problems/RadMatterCoupling/CMakeLists.txt
src/problems/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/problems/RadMatterCoupling/test_radiation_matter_coupling.hpp
src/problems/RadMatterCouplingRSLA/CMakeLists.txt
src/problems/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/problems/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.hpp
src/problems/RadPulse/CMakeLists.txt
src/problems/RadPulse/test_radiation_pulse.cpp
src/problems/RadPulse/test_radiation_pulse.hpp
src/problems/RadShadow/CMakeLists.txt
src/problems/RadShadow/test_radiation_shadow.cpp
src/problems/RadShadow/test_radiation_shadow.hpp
src/problems/RadStreaming/CMakeLists.txt
src/problems/RadStreaming/test_radiation_streaming.cpp
src/problems/RadStreaming/test_radiation_streaming.hpp
src/problems/RadStreamingY/CMakeLists.txt
src/problems/RadStreamingY/test_radiation_streaming_y.cpp
src/problems/RadStreamingY/test_radiation_streaming_y.hpp
src/problems/RadSuOlson/CMakeLists.txt
src/problems/RadSuOlson/test_radiation_SuOlson.cpp
src/problems/RadSuOlson/test_radiation_SuOlson.hpp
src/problems/RadTophat/CMakeLists.txt
src/problems/RadTophat/test_radiation_tophat.cpp
src/problems/RadTophat/test_radiation_tophat.hpp
src/problems/RadTube/CMakeLists.txt
src/problems/RadTube/test_radiation_tube.cpp
src/problems/RadTube/test_radiation_tube.hpp
src/problems/RadhydroBB/CMakeLists.txt
src/problems/RadhydroBB/test_radhydro_bb.cpp
src/problems/RadhydroBB/test_radhydro_bb.hpp
src/problems/RadhydroPulse/CMakeLists.txt
src/problems/RadhydroPulse/test_radhydro_pulse.cpp
src/problems/RadhydroPulse/test_radhydro_pulse.hpp
src/problems/RadhydroPulseDyn/CMakeLists.txt
src/problems/RadhydroPulseDyn/test_radhydro_pulse_dyn.cpp
src/problems/RadhydroPulseDyn/test_radhydro_pulse_dyn.hpp
src/problems/RadhydroPulseGrey/CMakeLists.txt
src/problems/RadhydroPulseGrey/test_radhydro_pulse_grey.cpp
src/problems/RadhydroPulseGrey/test_radhydro_pulse_grey.hpp
src/problems/RadhydroPulseMGconst/CMakeLists.txt
src/problems/RadhydroPulseMGconst/test_radhydro_pulse_MG_const_kappa.cpp
src/problems/RadhydroPulseMGconst/test_radhydro_pulse_MG_const_kappa.hpp
src/problems/RadhydroPulseMGint/CMakeLists.txt
src/problems/RadhydroPulseMGint/test_radhydro_pulse_MG_int.cpp
src/problems/RadhydroPulseMGint/test_radhydro_pulse_MG_int.hpp
src/problems/RadhydroShell/CMakeLists.txt
src/problems/RadhydroShell/test_radhydro_shell.cpp
src/problems/RadhydroShell/test_radhydro_shell.hpp
src/problems/RadhydroShock/CMakeLists.txt
src/problems/RadhydroShock/test_radhydro_shock.cpp
src/problems/RadhydroShock/test_radhydro_shock.hpp
src/problems/RadhydroShockCGS/CMakeLists.txt
src/problems/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/problems/RadhydroShockCGS/test_radhydro_shock_cgs.hpp
src/problems/RadhydroShockMultigroup/CMakeLists.txt
src/problems/RadhydroShockMultigroup/test_radhydro_shock_multigroup.cpp
src/problems/RadhydroShockMultigroup/test_radhydro_shock_multigroup.hpp
src/problems/RadhydroUniformAdvecting/CMakeLists.txt
src/problems/RadhydroUniformAdvecting/test_radhydro_uniform_advecting.cpp
src/problems/RadhydroUniformAdvecting/test_radhydro_uniform_advecting.hpp
src/problems/RandomBlast/CMakeLists.txt
src/problems/RandomBlast/blast.cpp
src/problems/RandomBlast/blast.hpp
src/problems/RayleighTaylor2D/CMakeLists.txt
src/problems/RayleighTaylor2D/test_hydro2d_rt.cpp
src/problems/RayleighTaylor2D/test_hydro2d_rt.hpp
src/problems/RayleighTaylor3D/CMakeLists.txt
src/problems/RayleighTaylor3D/ascent_actions.yaml
src/problems/RayleighTaylor3D/test_hydro3d_rt.cpp
src/problems/RayleighTaylor3D/test_hydro3d_rt.hpp
src/problems/ShockCloud/CMakeLists.txt
src/problems/ShockCloud/boundary_conditions.ipynb
src/problems/ShockCloud/cloud.cpp
src/problems/ShockCloud/cloud.hpp
src/problems/SphericalCollapse/CMakeLists.txt
src/problems/SphericalCollapse/spherical_collapse.cpp
src/problems/SphericalCollapse/spherical_collapse.hpp
src/problems/StarCluster/CMakeLists.txt
src/problems/StarCluster/ascent_actions.yaml
src/problems/StarCluster/star_cluster.cpp
src/problems/StarCluster/star_cluster.hpp
src/radiation/planck_integral.hpp
src/radiation/radiation_system.cpp
src/radiation/radiation_system.hpp
src/simulation.hpp
src/turbulence/TurbDataReader.cpp
src/turbulence/TurbDataReader.hpp
src/turbulence/perturbation.py
src/util/ArrayUtil.hpp
src/util/ArrayView.hpp
src/util/ArrayView_2d.hpp
src/util/ArrayView_3d.hpp
src/util/CheckNaN.hpp
src/util/fextract.cpp
src/util/fextract.hpp
src/util/matplotlibcpp.h
src/util/valarray.hpp
tests/checkpoint_restart_test.sh

commit da1931a37fa9e21d9ec8fbd9f8f952baabbfd730
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Jul 27 22:23:58 2024 -0400

    fix Sphinx warnings (#688)
    
    ### Description
    Fixes Sphinx warnings. The documentation now compiles without warnings.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] I have added a link to any related issues see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

docs/api.rst
docs/conf.py
docs/debugging.rst
docs/error_checking.rst
docs/howto_clang_tidy.rst
docs/index.rst
docs/insitu_analysis.rst
docs/instability.rst
docs/performance.rst
docs/postprocessing.rst
docs/running_on_hpc_clusters.rst
docs/tests/radhydro_pulse.rst

commit 514e5a73dfb9e0a4b973c62242820fab2a716fc2
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Jul 27 20:09:08 2024 -0400

    Add VSCode/Codespaces Dev Container settings (#687)
    
    ### Description
    This adds `.devcontainer/devcontainer.json` so that VSCode will
    automatically download and start a Docker container and load a
    development environment for Quokka inside this container.
    
    For more information, see:
    https://code.visualstudio.com/docs/devcontainers/containers#_quick-start-open-a-git-repository-or-github-pr-in-an-isolated-container-volume.
    
    This will also enable GitHub Codespaces:
    https://docs.github.com/en/codespaces/overview#what-is-a-codespace.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] I have added a link to any related issues see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.devcontainer/Dockerfile
.devcontainer/devcontainer.json

commit 78894d56c8c19e5585a6f69f976c72acb52dcb4d
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Thu Jul 25 02:09:14 2024 +1000

    remove unused function ComputeSourceTermsExplicit (#682)
    
    ### Description
    
    Removed unused function ComputeSourceTermsExplicit in
    radiation_system.hpp
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
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src/radiation_system.hpp

commit 4686c6ae13457126e792fde190127905491ee0f5
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Wed Jul 24 17:41:02 2024 +1000

    PPL opacity models (#678)
    
    ### Description
    
    Main updates:
    
    - Defined three opacity models described in Paper III: piecewise
    constant (`piecewise_constant_opacity`), piecewise powerlaw with fixed
    slope (`PPL_opacity_fixed_slope_spectrum`), piecewise powerlaw with full
    spectrum fitting (`PPL_opacity_full_spectrum`).
    
    - Added tests for each of these methods.
    - RadhydroBB tests the PC method's ability to resolve the
    Doppler-shifted spectrum in a moving blackbody.
    - RadMarshakVaytet tests the ability of all three methods (by default
    `PPL_opacity_full_spectrum`) to deal with frequency-dependent velocities
    within an energy bin.
    - RadTube tests that in the special case of opacity being independent of
    frequency, the `PPL_opacity_fixed_slope_spectrum` method provides the
    same result as the single-group method.
    - RadhydroShockMultigroup tests `PPL_opacity_full_spectrum` in the
    special case of constant opacity.
    
    More updates:
    
    - Removed `ComputePlanckOpacityTempDerivative`
    - Defined `ComputeDiffusionFluxMeanOpacity` and removed the calculation
    of component-specific flux-mean opacity. See Paper III.
    - Defined `ComputeBinCenterOpacity` to use when `opacity_model_ ==
    OpacityModel::PPL_opacity_full_spectrum` and
    `use_diffuse_flux_mean_opacity = false`.
    - Changed the structure of the Newton-Raphson iteration loop. We check
    the residuals first, then calculate opacities and the Jacobian.
    - Fixed a bug in the Newton iteration where the calculation of alpha_E
    uses `Erad0Vec` but `EradVec_guess` should be used.
    - More robust break condition for the Newton iteration.
    - Stop updating `alpha_E` and `alpha_B` after
    `max_ite_to_update_alpha_E` steps in the Newton iteration.
    - Set `reconstructionOrder_=3` in the RadTube and
    RadhydroShockMultigroup tests to avoid "erroneous arithmetic" error
    after using `-DCMAKE_CXX_FLAGS=-ffp-exception-behavior=strict`.
    
    
    
    ### Checklist
    
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    completed. Denote completed tasks with an `x` inside the square brackets
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    - [x] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
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extern/Doppler-spectrum/exact_flux_density.csv
src/CMakeLists.txt
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/RadMarshakVaytet/CMakeLists.txt
src/RadMarshakVaytet/test_radiation_marshak_Vaytet.cpp
src/RadMarshakVaytet/test_radiation_marshak_Vaytet.hpp
src/RadPulse/test_radiation_pulse.cpp
src/RadTube/test_radiation_tube.cpp
src/RadhydroBB/CMakeLists.txt
src/RadhydroBB/test_radhydro_bb.cpp
src/RadhydroBB/test_radhydro_bb.hpp
src/RadhydroPulseMG/CMakeLists.txt
src/RadhydroPulseMGconst/CMakeLists.txt
src/RadhydroPulseMGconst/test_radhydro_pulse_MG_const_kappa.cpp
src/RadhydroPulseMGconst/test_radhydro_pulse_MG_const_kappa.hpp
src/RadhydroPulseMGint/test_radhydro_pulse_MG_int.cpp
src/RadhydroShockMultigroup/test_radhydro_shock_multigroup.cpp
src/radiation_system.hpp
tests/MarshakVaytet.in
tests/RadhydroBB.in
tests/radshockMG.in

commit d5210ff4b118272d67cd5a7c38a99eaf0fa88ee0
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Jul 13 10:16:35 2024 -0400

    update Setonix job scripts (#677)
    
    ### Description
    This updates the Setonix job scripts so that they work again after the
    June 2024 software update.
    
    However, 64 node jobs do not work. They either hang or fail with an
    error in Cray MPI.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] I have added a link to any related issues see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

scripts/setonix-1node.submit
scripts/setonix-64nodes.submit
scripts/setonix-8nodes.submit

commit 1731a9291c9baf94edcc94e02fc8f03a8de6d6fa
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Jul 11 19:45:15 2024 -0400

    update Setonix config (#676)
    
    ### Description
    This updates the Setonix profile to use the latest module versions that
    are available. Pawsey updated the software stack in mid-June 2024 to
    Cray PE 23.09.
    
    I've compiled and tested the ShockCloud problem on Setonix GPUs. It
    appears to work.
    
    ### Related issues
    https://github.com/quokka-astro/quokka/issues/569
    
    ### 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:_
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
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scripts/setonix-cpu.profile
scripts/setonix-gpu.profile
src/ShockCloud/cloud.cpp

commit d719a59626ff55d65bdb1aea5cfc770e399a9220
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Jul 11 19:05:13 2024 -0400

    Fix Intel CI (#675)
    
    ### Description
    Removes unused CMake option whose behavior changed in version 3.30.0.
    Thanks to Weiqun for the fix.
    
    ### Related issues
    Fixes https://github.com/quokka-astro/quokka/issues/674.
    
    ### 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).
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    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
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    `/azp run`.
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.github/workflows/intel.yml

commit 14469c023b4c254811e01c20a53c5866d7781ee8
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Jul 10 19:34:02 2024 -0400

    enable FPE traps in CI (#611)
    
    ### Description
    Enables signal handling and floating-point exception (FPE) traps for
    NANs when running the test suite, so it will stop and report an error
    when NANs are encountered. (This only works on CPUs.)
    
    In order for this to work, we change the signal handling settings back
    to AMReX defaults. We also have to suppress FPEs when importing `numpy`
    (see https://github.com/numpy/numpy/issues/20504).
    
    By default, many compilers perform optimizations that assume that
    floating-point exceptions are disabled, and will often produce spurious
    FPEs for vectorized code (however, this does not affect the results in
    any way). There are compiler-specific options to disable this behavior
    for Intel and Clang.
    
    Note that `AMReX_FPE=ON` only sets the compiler option `-ftrapv` (or
    similar). We instead add the runtime options `amrex.fpe_trap_invalid=1`,
    `amrex.fpe_trap_zero=1`, and `amrex.fpe_trap_overflow=1` to the
    command-line arguments for each test. These options can also be added to
    the input file (or command line) to debug individual problems.
    
    **Depends on:**
    * https://github.com/quokka-astro/quokka/pull/667
    * https://github.com/quokka-astro/quokka/pull/668
    * https://github.com/quokka-astro/quokka/pull/671
    
    ### Related issues
    Partially resolves https://github.com/quokka-astro/quokka/issues/556.
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: Piyush Sharda <34922596+psharda@users.noreply.github.com>
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/workflows/cmake-macos.yml
.github/workflows/intel.yml
CMakeLists.txt
src/Advection/CMakeLists.txt
src/Advection2D/CMakeLists.txt
src/AdvectionSemiellipse/CMakeLists.txt
src/AdvectionSimulation.hpp
src/BinaryOrbitCIC/CMakeLists.txt
src/CMakeLists.txt
src/FCQuantities/CMakeLists.txt
src/HydroBlast3D/CMakeLists.txt
src/HydroContact/CMakeLists.txt
src/HydroHighMach/CMakeLists.txt
src/HydroLeblanc/CMakeLists.txt
src/HydroQuirk/CMakeLists.txt
src/HydroSMS/CMakeLists.txt
src/HydroShocktube/CMakeLists.txt
src/HydroShocktubeCMA/CMakeLists.txt
src/HydroShuOsher/CMakeLists.txt
src/HydroVacuum/CMakeLists.txt
src/HydroWave/CMakeLists.txt
src/NSCBC/CMakeLists.txt
src/ODEIntegration/CMakeLists.txt
src/PassiveScalar/CMakeLists.txt
src/PopIII/CMakeLists.txt
src/PrimordialChem/CMakeLists.txt
src/RadForce/CMakeLists.txt
src/RadMarshak/CMakeLists.txt
src/RadMarshakAsymptotic/CMakeLists.txt
src/RadMarshakCGS/CMakeLists.txt
src/RadMatterCoupling/CMakeLists.txt
src/RadMatterCouplingRSLA/CMakeLists.txt
src/RadPulse/CMakeLists.txt
src/RadStreaming/CMakeLists.txt
src/RadStreamingY/CMakeLists.txt
src/RadSuOlson/CMakeLists.txt
src/RadSuOlson/test_radiation_SuOlson.cpp
src/RadTube/CMakeLists.txt
src/RadTube/test_radiation_tube.cpp
src/RadhydroPulse/CMakeLists.txt
src/RadhydroPulseDyn/CMakeLists.txt
src/RadhydroPulseGrey/CMakeLists.txt
src/RadhydroPulseMG/CMakeLists.txt
src/RadhydroPulseMGint/CMakeLists.txt
src/RadhydroShock/CMakeLists.txt
src/RadhydroShockCGS/CMakeLists.txt
src/RadhydroShockMultigroup/CMakeLists.txt
src/RadhydroSimulation.hpp
src/RadhydroUniformAdvecting/CMakeLists.txt
src/SphericalCollapse/CMakeLists.txt
src/StarCluster/CMakeLists.txt
src/main.cpp
src/matplotlibcpp.h

commit fda0b4a5c67e6dc7eccd4db3b91a95b82136444f
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Jul 10 17:05:47 2024 -0400

    simplify EnforceLimits (#667)
    
    ### Description
    This removes the ceilings from EnforceLimits. Now, we only have a
    density floor, a mass scalar floor, and a temperature floor.
    
    The density floor also no longer adjusts the internal energy and total
    energy.
    
    In the previous version, there were several corner cases that could
    cause a divide by zero. In this version, there are no FPEs when running
    the test suite.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] I have added a link to any related issues see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/RadhydroSimulation.hpp
src/hydro_system.hpp
src/simulation.hpp

commit 0c4645004cc970c3275a3c18ac0bf6678f19f459
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Jul 10 01:11:03 2024 -0400

    random blast ISM problem (#179)
    
    This simulates the explosion of supernovae in a homogeneous ISM.
    
    This problem is also added to the nightly regression test suite.
    
    ---------
    
    Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.gitignore
extern/quadrature/quad.py
regression/quokka-tests.ini
src/AdvectionSimulation.hpp
src/CMakeLists.txt
src/RadhydroSimulation.hpp
src/RandomBlast/CMakeLists.txt
src/RandomBlast/blast.cpp
src/RandomBlast/blast.hpp
src/gauss.hpp
src/quadrature.hpp
src/simulation.hpp
tests/RandomBlast.in
tests/RandomBlast_regression.in

commit 3a2f8934a87fbbfdf72b107cd8e5e2c8d388638b
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Tue Jul 9 15:21:03 2024 +0200

    Update microphysics: primordial chemistry actual_rhs updated to speedup chemistry (#673)
    
    ### Description
    This PR will update microphysics. Among several other changes, the key
    change that matters for quokka is the speedup of primordial chemistry.
    
    ### Related issues
    https://github.com/AMReX-Astro/Microphysics/pull/1605
    
    ### 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:_
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
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    `/azp run`.
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    Co-authored-by: Piyush Sharda <psharda@RSAA-043527.local>

extern/Microphysics

commit d616a63e7a483785f954682ce7ef233ba71d3464
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Jul 7 21:27:18 2024 -0400

    no ghost cells in reference solution multifab (#671)
    
    ### Description
    The reference solution multifab does not need to have ghost cells (they
    often weren't filled, and left as NaNs).
    
    ### Related issues
    N/A
    
    ### 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).
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    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

src/RadhydroSimulation.hpp

commit 080145d32d3664eb99f460a3b7f919ceb85a0c8f
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Jul 7 06:46:25 2024 -0400

    remove unnecessary EnforceLimits on old state (#668)
    
    ### Description
    Immediately after a regrid, the old state `state_old_cc_` is
    uninitialized (and unused, because all of the times of the regridded
    levels are synchronized at that moment). Therefore, `EnforceLimits` does
    not need to be called on it.
    
    Since the old state is unused, this PR doesn't affect the simulation
    evolution in any way. However, this avoids spurious FPEs from trying to
    process zero or NaN values in the old state array.
    
    ### Related issues
    Fixes https://github.com/quokka-astro/quokka/issues/401.
    
    ### 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:_
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
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src/RadhydroSimulation.hpp

commit f3955190df06cb9b77981b8ff010837b08210630
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Jul 1 16:13:28 2024 -0400

    Bump extern/amrex from `a65f0a5` to `7418556` (#659)
    
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    HDF5: Correctly handle writing only some components when writing
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    href="https://github.com/AMReX-Codes/amrex/commit/2f93525639dae966ee41e1f36f37ee6693a72ba0"><code>2f93525</code></a>
    Fix L2 norms in C_util/Convergence codes (<a
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    GNU Make: try nvidia-smi for CUDA arch if deviceQuery fails (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3997">#3997</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/259db7cfb99e7d1d2ab4bec9b1587fdf624a138a"><code>259db7c</code></a>
    Sundials Update (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3984">#3984</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/adfc227334daa769f1a783adb2ae2253ae44d7cf"><code>adfc227</code></a>
    Derive: Add MultiFab version of DeriveFunc (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3990">#3990</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/85bef47dc69bcd7f1940d62c4deae6eb8ece7dbd"><code>85bef47</code></a>
    GNU Make: Add support for CUDA LTO (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3993">#3993</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/0e3e39b5ed9115401dec0a76e62ae2eeee23ab6f"><code>0e3e39b</code></a>
    Bottom Solver: Keep the unconverged result if it's an improvement (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3991">#3991</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/36f111b2c9687a187229f01c04738755edf6e5e4"><code>36f111b</code></a>
    Workaround std::exclusive_scan issue with old compilers (<a
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extern/amrex

commit 5b4b95af45939e866fb3b51d98f4fca13bb88d48
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon Jul 1 18:32:52 2024 +0000

    [pre-commit.ci] pre-commit autoupdate (#665)
    
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    v18.1.8](https://github.com/pre-commit/mirrors-clang-format/compare/v18.1.7...v18.1.8)
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.pre-commit-config.yaml

commit bb1da3c90dcc5015b60bc2c4d7b7b616e3aeef53
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Jul 1 04:11:53 2024 +0000

    Bump SonarSource/sonarcloud-github-c-cpp from 2 to 3 (#662)
    
    Bumps
    [SonarSource/sonarcloud-github-c-cpp](https://github.com/sonarsource/sonarcloud-github-c-cpp)
    from 2 to 3.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
    href="https://github.com/sonarsource/sonarcloud-github-c-cpp/releases">SonarSource/sonarcloud-github-c-cpp's
    releases</a>.</em></p>
    <blockquote>
    <h2>v3.0.0</h2>
    <h2>What's Changed</h2>
    <ul>
    <li>SC-12362 Improve the SonarCloud Intro in README.md by <a
    href="https://github.com/claire-villard-sonarsource"><code>@​claire-villard-sonarsource</code></a>
    in <a
    href="https://redirect.github.com/SonarSource/sonarcloud-github-c-cpp/pull/50">SonarSource/sonarcloud-github-c-cpp#50</a></li>
    <li>Update actions/cache to v4 by <a
    href="https://github.com/N-Coder"><code>@​N-Coder</code></a> in <a
    href="https://redirect.github.com/SonarSource/sonarcloud-github-c-cpp/pull/48">SonarSource/sonarcloud-github-c-cpp#48</a></li>
    <li>SCCPPGHA-2 Support macOS ARM runners by <a
    href="https://github.com/enzo-pellegrini"><code>@​enzo-pellegrini</code></a>
    in <a
    href="https://redirect.github.com/SonarSource/sonarcloud-github-c-cpp/pull/55">SonarSource/sonarcloud-github-c-cpp#55</a></li>
    <li>CPP-5241 Migrate github action from build-wrapper-output to
    compilation-database by <a
    href="https://github.com/enzo-pellegrini"><code>@​enzo-pellegrini</code></a>
    in <a
    href="https://redirect.github.com/SonarSource/sonarcloud-github-c-cpp/pull/54">SonarSource/sonarcloud-github-c-cpp#54</a></li>
    <li>SCCPPGHA-6 Support Running on Linux ARM64 by <a
    href="https://github.com/enzo-pellegrini"><code>@​enzo-pellegrini</code></a>
    in <a
    href="https://redirect.github.com/SonarSource/sonarcloud-github-c-cpp/pull/57">SonarSource/sonarcloud-github-c-cpp#57</a></li>
    <li>Update sonar-scanner-version to 6.0.0.4432 by <a
    href="https://github.com/github-actions"><code>@​github-actions</code></a>
    in <a
    href="https://redirect.github.com/SonarSource/sonarcloud-github-c-cpp/pull/58">SonarSource/sonarcloud-github-c-cpp#58</a></li>
    </ul>
    <p><strong>Full Changelog</strong>: <a
    href="https://github.com/SonarSource/sonarcloud-github-c-cpp/compare/v2.0.2...v3.0.0">https://github.com/SonarSource/sonarcloud-github-c-cpp/compare/v2.0.2...v3.0.0</a></p>
    <h2>New Contributors</h2>
    <ul>
    <li><a
    href="https://github.com/claire-villard-sonarsource"><code>@​claire-villard-sonarsource</code></a>
    made their first contribution in <a
    href="https://redirect.github.com/SonarSource/sonarcloud-github-c-cpp/pull/50">SonarSource/sonarcloud-github-c-cpp#50</a></li>
    <li><a href="https://github.com/N-Coder"><code>@​N-Coder</code></a> made
    their first contribution in <a
    href="https://redirect.github.com/SonarSource/sonarcloud-github-c-cpp/pull/48">SonarSource/sonarcloud-github-c-cpp#48</a></li>
    <li><a href="https://github.com/vil02"><code>@​vil02</code></a> made
    their first contribution in <a
    href="https://redirect.github.com/SonarSource/sonarcloud-github-c-cpp/pull/38">SonarSource/sonarcloud-github-c-cpp#38</a></li>
    <li><a
    href="https://github.com/enzo-pellegrini"><code>@​enzo-pellegrini</code></a>
    made their first contribution in <a
    href="https://redirect.github.com/SonarSource/sonarcloud-github-c-cpp/pull/55">SonarSource/sonarcloud-github-c-cpp#55</a></li>
    </ul>
    <h2>Update README</h2>
    <p>No release notes provided.</p>
    </blockquote>
    </details>
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/SonarSource/sonarcloud-github-c-cpp/commit/e25edaefff1e076daf6517d462ed86f8c99fec70"><code>e25edae</code></a>
    SCCPPGHA-6 Support Running on Linux ARM64 (<a
    href="https://redirect.github.com/sonarsource/sonarcloud-github-c-cpp/issues/57">#57</a>)</li>
    <li><a
    href="https://github.com/SonarSource/sonarcloud-github-c-cpp/commit/905f4e38a15b0572ba5d41a30ecee2c0ac76a2b7"><code>905f4e3</code></a>
    Update sonar-scanner-version to 6.0.0.4432 (<a
    href="https://redirect.github.com/sonarsource/sonarcloud-github-c-cpp/issues/58">#58</a>)</li>
    <li><a
    href="https://github.com/SonarSource/sonarcloud-github-c-cpp/commit/5c3c39143e381909307f6903f13774b275ed956d"><code>5c3c391</code></a>
    CPP-5241 Migrate github action from build-wrapper-output to
    compilation-datab...</li>
    <li><a
    href="https://github.com/SonarSource/sonarcloud-github-c-cpp/commit/8a10879c4e21507b8f735be384830dd9d55212b5"><code>8a10879</code></a>
    SCCPPGHA-2 Support macOS ARM runners (<a
    href="https://redirect.github.com/sonarsource/sonarcloud-github-c-cpp/issues/55">#55</a>)</li>
    <li><a
    href="https://github.com/SonarSource/sonarcloud-github-c-cpp/commit/bc8c8629118e5b8d796b3cb628339cc6473fde1a"><code>bc8c862</code></a>
    NO-JIRA Remove duplicated space in README</li>
    <li><a
    href="https://github.com/SonarSource/sonarcloud-github-c-cpp/commit/16022088a235701bc540d0e7987bc6a7f5cf1898"><code>1602208</code></a>
    This repository is owned by the Analysis Experience squad</li>
    <li><a
    href="https://github.com/SonarSource/sonarcloud-github-c-cpp/commit/388d75036688c49bcb622bb0d0935282b16fd02b"><code>388d750</code></a>
    Update actions/cache to v4 (<a
    href="https://redirect.github.com/sonarsource/sonarcloud-github-c-cpp/issues/48">#48</a>)</li>
    <li><a
    href="https://github.com/SonarSource/sonarcloud-github-c-cpp/commit/0f2dd7bc7d8810b9d5b33e8971e10111b89fcbd5"><code>0f2dd7b</code></a>
    Update the SonarCloud intro in README.md (<a
    href="https://redirect.github.com/sonarsource/sonarcloud-github-c-cpp/issues/51">#51</a>)</li>
    <li><a
    href="https://github.com/SonarSource/sonarcloud-github-c-cpp/commit/a5e1e96807ea578deae644594146e29faddc6f41"><code>a5e1e96</code></a>
    SC-12362 Improve the SonarCloud intro in README.md (<a
    href="https://redirect.github.com/sonarsource/sonarcloud-github-c-cpp/issues/50">#50</a>)</li>
    <li>See full diff in <a
    href="https://github.com/sonarsource/sonarcloud-github-c-cpp/compare/v2...v3">compare
    view</a></li>
    </ul>
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.github/workflows/sonarcloud.yml

commit 6755507666dbc78e78d44624ba1019b3688d508e
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Jul 1 03:56:26 2024 +0000

    Bump extern/fmt from `fcd3e1e` to `686339f` (#660)
    
    Bumps [extern/fmt](https://github.com/fmtlib/fmt) from `fcd3e1e` to
    `686339f`.
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    <li><a
    href="https://github.com/fmtlib/fmt/commit/686339f7c12967975af0381eec7ca1a90af6bfcc"><code>686339f</code></a>
    Minor cleanup</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/e355c116f94d9150c4d9da5ad20c5218335ccec0"><code>e355c11</code></a>
    Tweak wording in the changelog</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/707bb5b369b998728980b9e781016a8427681c99"><code>707bb5b</code></a>
    Fix grammar</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/6f68c62cb5d1bbf661fbde28224f1067b6b27e41"><code>6f68c62</code></a>
    Ignore doxygen files</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/d059fe42a87a45a5ca337fecbbcbe10b0bcf5ca5"><code>d059fe4</code></a>
    Ignore vagrant files</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/43c5b34749d338be15dac11d3039c0266097a28a"><code>43c5b34</code></a>
    Fix package build</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/e89568e6cba4e456f587206fb1ecb20cdb478745"><code>e89568e</code></a>
    Update vagrant config</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/f5bf6f778120278f19995e64a102243e38c10ee0"><code>f5bf6f7</code></a>
    Update build script</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/bd9af9a9f1477ed125b0b27192ce54278fc04b9d"><code>bd9af9a</code></a>
    Update changelog</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/165210890546bfcc843aa144e6fc27a6c3ea52cc"><code>1652108</code></a>
    Fix typo</li>
    <li>Additional commits viewable in <a
    href="https://github.com/fmtlib/fmt/compare/fcd3e1e19c8d2df94bb6cb40d7f1c97a9872cf2b...686339f7c12967975af0381eec7ca1a90af6bfcc">compare
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extern/fmt

commit 9bcef23b3b3ec7e5c4d9179bb4eb9946298148c0
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Jul 1 03:54:25 2024 +0000

    Bump extern/openPMD-api from `2c1dbc9` to `9184c2e` (#661)
    
    Bumps [extern/openPMD-api](https://github.com/openPMD/openPMD-api) from
    `2c1dbc9` to `9184c2e`.
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/9184c2e8b8d069ee16915bb7b4eaf2f662eaf813"><code>9184c2e</code></a>
    Fix wrong logging of TOUCH task (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1643">#1643</a>)</li>
    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/7f5c33d98beb6b9eb4794c1021da94a5ae4d6a65"><code>7f5c33d</code></a>
    Fix: Add back iteration.close() call (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1641">#1641</a>)</li>
    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/3daaa140985a7f6647022979ef8503fe5454846b"><code>3daaa14</code></a>
    CI fixes and documentation for Pybind v2.12.0 and Numpy 2.0 (<a
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    Update Pybind to v2.12.0 (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1640">#1640</a>)</li>
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    href="https://github.com/openPMD/openPMD-api/commit/a2071184cfae03854939c8d72d865f492b6a2b5e"><code>a207118</code></a>
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    Fix particle patches flush api (<a
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    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/87cdc965b7b0b97da39ef8d176833ef3077aa576"><code>87cdc96</code></a>
    Fix Python container and pickle API (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1627">#1627</a>)</li>
    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/5d9fb34c2d35b1a88a78db0d071033e8afc392b4"><code>5d9fb34</code></a>
    Workaround for independent writes to Iterations in parallel, better
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    href="https://github.com/openPMD/openPMD-api/commit/51caab374db5298c25999c960dfc35bab1058ea2"><code>51caab3</code></a>
    Seems we need the MPI workaround for Conda now too..... (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1628">#1628</a>)</li>
    <li>See full diff in <a
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extern/openPMD-api

commit d6728ef5914a409a9f15d436277f32dc29aae93e
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Jun 30 20:54:24 2024 -0400

    update shock-cloud problem (#350)
    
    This updates the shock-cloud problem to use a new setup that:
    
    - tracks the cloud center-of-mass frame
    - refines so that the cooling length $l_{\text{cool}} = c_s
    t_{\text{cool}}$ is resolved with at least 10 cells
    - adds derived fields for temperature, entropy, pressure, etc. to the
    outputs
    - uses the (simplified) Navier-Stokes Characteristic Boundary Conditions
    for inflow/outflow on the left/right sides of the box
    - adds shock-cloud problem to nightly regression testing
    
    **This PR depends on:**
    * https://github.com/quokka-astro/quokka/pull/352
    * https://github.com/quokka-astro/quokka/pull/360
    * https://github.com/quokka-astro/quokka/pull/363
    * https://github.com/quokka-astro/quokka/pull/364
    * https://github.com/quokka-astro/quokka/pull/365
    * https://github.com/quokka-astro/quokka/pull/366
    * https://github.com/quokka-astro/quokka/pull/367
    * https://github.com/quokka-astro/quokka/pull/430
    * https://github.com/quokka-astro/quokka/pull/581
    * https://github.com/quokka-astro/quokka/pull/596
    * https://github.com/quokka-astro/quokka/pull/597
    * https://github.com/quokka-astro/quokka/pull/598
    * https://github.com/quokka-astro/quokka/pull/599
    * https://github.com/quokka-astro/quokka/pull/616
    * https://github.com/quokka-astro/quokka/pull/645

extern/cooling/isrf_1000Go_grains.h5
regression/quokka-tests.ini
src/NSCBC_inflow.hpp
src/NSCBC_outflow.hpp
src/ShockCloud/CMakeLists.txt
src/ShockCloud/boundary_conditions.ipynb
src/ShockCloud/cloud.cpp
src/ShockCloud/test_grackle_cooling.cpp
tests/ShockCloud_128.in
tests/ShockCloud_32.in
tests/ShockCloud_512.in
tests/ShockCloud_64.in
tests/ShockCloud_64_regression.in
tests/ascent_actions.yaml

commit cd6cdb69ab21ae834b981dc1a2b7b5a9e0d247b8
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Jun 30 19:36:37 2024 -0400

    Use specific Intel compiler version in CI (#658)
    
    ### Description
    This is a temporary workaround to avoid overly-aggressive floating-point
    optimizations in newer Intel compilers.
    
    ### Related issues
    Temporary workaround for
    https://github.com/quokka-astro/quokka/issues/649.
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

.github/workflows/dependencies/dependencies_dpcpp.sh

commit 899592edf6d5d95daf6e1b8676a2fcb4ac8354de
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Thu Jun 27 09:15:33 2024 -0400

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.pre-commit-config.yaml
src/DiagPDF.cpp

commit 8191640ae0629f0916b85be85ba6826a87a35005
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Jun 24 07:19:21 2024 -0400

    Delete perfdata directory (#655)
    
    ### Description
    Delete the `perfdata` directory. All of the performance timings are
    out-of-date from the current version of the code. For historical
    reference, they can still be accessed from the git history.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] I have added a link to any related issues see (see above).
    - [ ] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

perfdata/gpu_performance.txt
perfdata/gpu_profiling.txt
perfdata/gpu_profiling_unigrid.txt
perfdata/unigrid_cpu/bw0729.1629090348.145871.ipm.xml
perfdata/unigrid_cpu/bw0729.1629091661.837884.ipm.xml
perfdata/unigrid_cpu/bw0729.1629092733.31126.ipm.xml
perfdata/unigrid_cpu/sedov_1node.log
perfdata/unigrid_cpu/sedov_64nodes.log
perfdata/unigrid_cpu/sedov_8nodes.log

commit 349ef20eccaa88198977567e050512794e049a59
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Jun 24 07:19:09 2024 -0400

    update docs re Intel GPUs (#654)
    
    ### Description
    Updates the documentation to note that Quokka cannot currently be
    compiled for Intel GPUs due to design limitations in Intel's GPU
    programming model.
    
    ### Related issues
    https://github.com/quokka-astro/quokka/issues/619
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

docs/installation.rst

commit a33e6383f79bea11f4176e46e8a6f7c062252a79
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Jun 23 22:35:46 2024 -0400

    Update perturbation.py for NumPy 2.0 compatibility (#656)
    
    ### Description
    This changes `perturbation.py` to work with NumPy 2.0.
    
    ### Related issues
    Fixes https://github.com/quokka-astro/quokka/issues/653.
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

src/perturbation.py

commit 157ac7027f827984f1cb2a8b55256dacded162bc
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Jun 23 22:34:47 2024 -0400

    upload regression testing results to GitHub pages (#650)
    
    ### Description
    This uploads the regression testing results to GitHub Pages, so it can
    be viewed here:
    https://quokka-astro.github.io/regression-testing-results/
    
    Also, this turns on checks for the particle outputs, so they are checked
    against the reference plotfile.
    
    ### Related issues
    Also fixes https://github.com/quokka-astro/quokka/issues/651.
    
    ### 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).
    - [ ] I have added a link to any related issues see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

.ci/azure-pipelines-regression.yml
regression/quokka-tests.ini

commit 7333fa5f067e06de04d6c9dab6533bc943eb2471
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Jun 20 20:03:11 2024 -0400

    add nightly regression testing infrastructure (#647)
    
    ### Description
    Adds nightly regression testing infrastructure to compare outputs for
    science problems with "known good" solutions.
    
    This also adds the ability to specify the plotfile prefix and the
    checkpoint file prefix with ParmParse parameters `plotfile_prefix` and
    `checkpoint_prefix`.
    
    If the "correct" answers (i.e., plotfile outputs) change and need to be
    updated, then it is necessary to run
    ```
    ./extern/regression_testing/regtest.py --make_benchmarks "<some useful comment>" regression/quokka-tests.ini
    ```
    on avatargpue.
    
    ### Related issues
    Closes https://github.com/quokka-astro/quokka/issues/346.
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

.ci/azure-pipelines-regression.yml
.gitmodules
extern/regression_testing
regression/quokka-tests.ini
src/simulation.hpp
tests/blast_32.in
tests/blast_unigrid_128_cpu.in
tests/blast_unigrid_128_regression.in

commit 79d6328878f4a7b9020203515dc3dcf431f09b0a
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Jun 11 07:06:39 2024 -0400

    remove old debugging code from ODE integrator (#645)
    
    ### Description
    This removes old debugging `printf`s from the ODE integrator. They are
    not necessary anymore, and each `printf` has a performance penalty on
    GPU.
    
    Error handling has already been fully integrated into hydro retries
    mechanism for some time already.
    
    ### Related issues
    N/A
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

src/ODEIntegrate.hpp

commit 1b07ade7dbc631c5b1ddb25927ff0fc39d0d905a
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon Jun 10 18:24:20 2024 +0000

    [pre-commit.ci] pre-commit autoupdate (#644)
    
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    updates:
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    v18.1.6](https://github.com/pre-commit/mirrors-clang-format/compare/v17.0.6...v18.1.6)
    <!--pre-commit.ci end-->
    
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    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml
src/AdvectionSimulation.hpp
src/CheckNaN.hpp
src/EOS.hpp
src/LLF.hpp
src/NSCBC/vortex.cpp
src/NSCBC_inflow.hpp
src/NSCBC_outflow.hpp
src/RadForce/test_radiation_force.cpp
src/RadMarshak/test_radiation_marshak.cpp
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadPulse/test_radiation_pulse.cpp
src/RadStreaming/test_radiation_streaming.cpp
src/RadStreamingY/test_radiation_streaming_y.cpp
src/RadSuOlson/test_radiation_SuOlson.cpp
src/RadTophat/test_radiation_tophat.cpp
src/RadhydroPulseMG/test_radhydro_pulse_MG.cpp
src/RadhydroPulseMGint/test_radhydro_pulse_MG_int.cpp
src/RadhydroShock/test_radhydro_shock.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/RadhydroShockMultigroup/test_radhydro_shock_multigroup.cpp
src/RadhydroSimulation.hpp
src/fextract.cpp
src/fextract.hpp
src/hydro_system.hpp
src/hyperbolic_system.hpp
src/linear_advection.hpp
src/radiation_system.hpp

commit c52d071483c295bcf2f12ce585bce7bd442bea7f
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Jun 10 06:39:12 2024 -0400

    quokka::EOS code linting (#578)
    
    ### Description
    This fixes some clang-tidy and CodeQL warnings for EOS.hpp. All of the
    changes convert pass-by-value to pass-by-reference for large objects in
    EOS function calls.
    
    ### Related issues
    https://github.com/quokka-astro/quokka/security/code-scanning/2609
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/EOS.hpp
src/RadMarshak/test_radiation_marshak.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadSuOlson/test_radiation_SuOlson.cpp
src/RadTophat/test_radiation_tophat.cpp

commit 2938a275f67041112573e550155a5970bef4c135
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Fri Jun 7 22:11:25 2024 +0200

    Add citation to quokka paper (#577)
    
    ### Description
    Updating the docs to add the citation to the Quokka paper.
    
    ### 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).
    - [ ] I have added a link to any related issues see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: Piyush Sharda <psharda@RSAA-043527.local>
    Co-authored-by: Ben Wibking <ben@wibking.com>

docs/citation.rst
docs/conf.py
docs/index.rst
docs/references.bib

commit ad81f3117a85eb2fb719b32ef3e762fbc4301175
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sat Jun 1 15:43:00 2024 -0400

    Bump extern/amrex from `95a92e2` to `a65f0a5` (#636)
    
    Bumps [extern/amrex](https://github.com/AMReX-Codes/amrex) from
    `95a92e2` to `a65f0a5`.
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/a65f0a5811443430e33867662c0e739942a9799b"><code>a65f0a5</code></a>
    add missing AMReX_SUNDIALS in AMReXConfig.cmake (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3962">#3962</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/14d56ef18ac30db85a523a58ffa84e6e71953125"><code>14d56ef</code></a>
    Linear Solver: Fix semicoarsening issues with multiple AMR levels (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3961">#3961</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/28b010126a1b39297d8a496ba81f171d8563953b"><code>28b0101</code></a>
    add DEBUG_LIBSTDCXX option to GNU Make gcc for libstdc++ debug (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3945">#3945</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/f4749636ce66f7315cc6699602b5cab088af2f54"><code>f474963</code></a>
    Fix bug introduced in <a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3959">#3959</a>
    (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3960">#3960</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/8e67cc99f07949f07ced3711d15e21f6d1e9af1c"><code>8e67cc9</code></a>
    InterpBndryData: Make changes for multi-level hypre (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3959">#3959</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/74ab0719f697cbf6ec9af55d97c5e35611b13e02"><code>74ab071</code></a>
    FabArray: Make some functions static (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3958">#3958</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/345cb887096e28c5ed67d336489acb5ab0b3c8f2"><code>345cb88</code></a>
    MultiArray4: add conversion operator to bool (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3957">#3957</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/523c11ed2f1ea2b48fb8671aa2af64951fa4c997"><code>523c11e</code></a>
    Overloading <code>Array4::operator()</code>, <code>ptr</code> and
    <code>contains</code> (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3956">#3956</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/e6c93bf22695585282ffedfeeb576f5e5450a47b"><code>e6c93bf</code></a>
    Fix block size in PermutationForDeposition (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3953">#3953</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/fed4bc1b98a0f7c2d4f8596356ab65832e758464"><code>fed4bc1</code></a>
    Tune PermutationForDeposition for MI250X (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3925">#3925</a>)</li>
    <li>Additional commits viewable in <a
    href="https://github.com/AMReX-Codes/amrex/compare/95a92e2f82227a8a4a2144bac06813f4ca1632c9...a65f0a5811443430e33867662c0e739942a9799b">compare
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commit de70849421db1194a4310d0bf33e9ae90be906b7
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sat Jun 1 10:47:00 2024 -0400

    Bump extern/yaml-cpp from `76dc671` to `1d8ca1f` (#637)
    
    Bumps [extern/yaml-cpp](https://github.com/jbeder/yaml-cpp) from
    `76dc671` to `1d8ca1f`.
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/jbeder/yaml-cpp/commit/1d8ca1f35eb3a9c9142462b28282a848e5d29a91"><code>1d8ca1f</code></a>
    Avoid static reference to temporary</li>
    <li>See full diff in <a
    href="https://github.com/jbeder/yaml-cpp/compare/76dc6715734295ff1866bfc32872ff2278258fc8...1d8ca1f35eb3a9c9142462b28282a848e5d29a91">compare
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extern/yaml-cpp

commit fb2811219c005d34ab311aa7c83332ace58cf1ed
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sat Jun 1 10:46:41 2024 -0400

    Bump extern/fmt from `48c9084` to `fcd3e1e` (#638)
    
    Bumps [extern/fmt](https://github.com/fmtlib/fmt) from `48c9084` to
    `fcd3e1e`.
    <details>
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    <li><a
    href="https://github.com/fmtlib/fmt/commit/fcd3e1e19c8d2df94bb6cb40d7f1c97a9872cf2b"><code>fcd3e1e</code></a>
    is_convertible_v -&gt; is_convertible::value (<a
    href="https://redirect.github.com/fmtlib/fmt/issues/3983">#3983</a>)</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/dc401b1c285a04a5942a593f67fee8f57236f811"><code>dc401b1</code></a>
    Move handlers outside of the docs</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/f7c5588c46df2f246985ed544fe2564621a9da06"><code>f7c5588</code></a>
    Cleanup syntax doc</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/a4e40677af50bb4035b85c607c8aad70f0332696"><code>a4e4067</code></a>
    Fix markdown</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/3479828e1d26ada250c3b5227d832ae643c5e9b2"><code>3479828</code></a>
    Fix markdown</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/191b0cb486ae24744d2f39dbfd9971d7833a6c75"><code>191b0cb</code></a>
    Fix markdown</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/e80f4a9b72405fae20acf807613534180140bce6"><code>e80f4a9</code></a>
    Cleanup syntax doc</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/022d8efec96ff1744af502259b4909281d77614f"><code>022d8ef</code></a>
    Update doc.yml</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/ca8eeb09eed72e4bef26fb1d3d8e89b46a15bbba"><code>ca8eeb0</code></a>
    Add glibc ext for day of month and week of year (<a
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    <li><a
    href="https://github.com/fmtlib/fmt/commit/cddb41f63321fba890b713e555fbdf93d8b47335"><code>cddb41f</code></a>
    Fix markdown</li>
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extern/fmt

commit 6a476ca8bdf891c85f1bd1bb341dd365be13f51f
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sat Jun 1 10:46:23 2024 -0400

    Bump extern/openPMD-api from `805c760` to `2c1dbc9` (#639)
    
    Bumps [extern/openPMD-api](https://github.com/openPMD/openPMD-api) from
    `805c760` to `2c1dbc9`.
    <details>
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    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/2c1dbc92b8914a7d889009a8afd330b1a33b745b"><code>2c1dbc9</code></a>
    [pre-commit.ci] pre-commit autoupdate (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1613">#1613</a>)</li>
    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/4d77fadf75fe38ea9ac40e30445be456bdd9b1d3"><code>4d77fad</code></a>
    Bump s-weigand/setup-conda from 1.2.1 to 1.2.2 (<a
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    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/8c57285160c679151520bdfff80ec2a6897ae973"><code>8c57285</code></a>
    Span API: Set dirty flag (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1615">#1615</a>)</li>
    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/95cbcb6dad0c6a2e607af0cbf008de0c2a9a4d40"><code>95cbcb6</code></a>
    Fix CI issues for ADIOS2 v2.10: Add openPMD_HAVE_ADIOS2_BP5, datatype
    fixes i...</li>
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extern/openPMD-api

commit 7a597a57579780a8e0e25ee0220296de479ff4ea
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Wed May 29 03:23:51 2024 +1000

    Fix radiation transport error in Y and Z directions.  (#633)
    
    ### Description
    Fix bug #632 . This is a dumb mistake I made on using `AMREX_D_TERM` in
    `AddFluxesRK2`, causing a wrong calculation of the HLL flux in 2D/3D
    cases. The mistake was introduced in the "Use IMEX PD-ARS ..." commit
    (78c5970857430e155885555bdfaa30a6ef4946e4) 6 months ago. Because of this
    mistake, all 2D/3D simulations since then with non-zero y/z-component
    radiation fluxes are wrong.
    
    To avoid mistakes like this in the future, I added a new test of
    radiation streaming in the Y direction. I plan to add a better test
    (say, the RadShock test) in both Y and Z direction, with the following
    grid configuration: [4, 128, 4] and [4, 4, 128]. Or, alternatively, we
    should have a non-trivial 3D test with an exact solution.
    
    ### Related issues
    Fixed #632
    
    ### 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
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
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src/CMakeLists.txt
src/RadStreamingY/CMakeLists.txt
src/RadStreamingY/test_radiation_streaming_y.cpp
src/RadStreamingY/test_radiation_streaming_y.hpp
src/radiation_system.hpp
tests/RadStreamingY.in

commit ba387405a46e267b4add6ff1b7e779727d632849
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Wed May 29 03:14:54 2024 +1000

    Add "copy" button to the sphinx documentation page. (#609)
    
    ### Description
    
    Following https://sphinx-copybutton.readthedocs.io/en/latest/ to add a
    little “copy” button to the right of the code blocks. Added
    `sphinx_copybutton` extension in conf.py.
    
    Tested in local build (`make html`) and it works fine, but I'm not sure
    if the `sphinx_copybutton` extension is available on the server where
    the website HTML is built.
    
    ### 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:_
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
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.github/workflows/docs.yml
build_docs.sh
docs/conf.py
docs/requirements.txt

commit 4c1a57659490ef59a5034602e5b9d6acaca070db
Author: Ben Wibking <ben@wibking.com>
Date:   Sun May 26 19:25:30 2024 -0400

    migrate ARM64 testing to CircleCI (#583)
    
    ### Description
    This sets up ARM64 CI testing on CircleCI. Removes the ARM64 CI testing
    currently on Oracle Cloud, which is harder to maintain and configure.
    
    ### Related issues
    N/A
    
    ### Checklist
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    completed. Denote completed tasks with an `x` inside the square brackets
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
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    code.
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    `/azp run`.
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.ci/azure-pipelines-aarch64-debug.yml
.ci/azure-pipelines-aarch64-hwasan.yml
.ci/azure-pipelines-aarch64.yml
.circleci/config.yml
.github/workflows/codespell.yml
.github/workflows/codespell_ignore.txt

commit 88bdc181ed6a348e4bf4ff636b0bb8624725a690
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Tue May 21 23:29:26 2024 -0400

    Bump ZedThree/clang-tidy-review from 0.18.0 to 0.19.0 (#630)
    
    Bumps
    [ZedThree/clang-tidy-review](https://github.com/zedthree/clang-tidy-review)
    from 0.18.0 to 0.19.0.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
    href="https://github.com/zedthree/clang-tidy-review/releases">ZedThree/clang-tidy-review's
    releases</a>.</em></p>
    <blockquote>
    <h2>v0.19.0</h2>
    <h2>What's Changed</h2>
    <ul>
    <li>Add links to check documentation in review by <a
    href="https://github.com/bwrsandman"><code>@​bwrsandman</code></a> in <a
    href="https://redirect.github.com/ZedThree/clang-tidy-review/pull/123">ZedThree/clang-tidy-review#123</a></li>
    <li>Add clang-tidy 18 by <a
    href="https://github.com/daljit46"><code>@​daljit46</code></a> in <a
    href="https://redirect.github.com/ZedThree/clang-tidy-review/pull/121">ZedThree/clang-tidy-review#121</a></li>
    <li>Add a hint for generating the compile command outside the container
    by <a href="https://github.com/m-kuhn"><code>@​m-kuhn</code></a> in <a
    href="https://redirect.github.com/ZedThree/clang-tidy-review/pull/120">ZedThree/clang-tidy-review#120</a></li>
    </ul>
    <h2>New Contributors</h2>
    <ul>
    <li><a href="https://github.com/daljit46"><code>@​daljit46</code></a>
    made their first contribution in <a
    href="https://redirect.github.com/ZedThree/clang-tidy-review/pull/121">ZedThree/clang-tidy-review#121</a></li>
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    href="https://github.com/ZedThree/clang-tidy-review/compare/v0.18.0...v0.19.0">https://github.com/ZedThree/clang-tidy-review/compare/v0.18.0...v0.19.0</a></p>
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    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/85799d63d217e8d0686b7735fb923acc986d8043"><code>85799d6</code></a>
    Merge pull request <a
    href="https://redirect.github.com/zedthree/clang-tidy-review/issues/120">#120</a>
    from m-kuhn/patch-1</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/b719737efab14c01d5db685a87925e18e2d0f2b8"><code>b719737</code></a>
    Merge pull request <a
    href="https://redirect.github.com/zedthree/clang-tidy-review/issues/121">#121</a>
    from daljit46/clang_tidy_18</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/3ff13b4112a16890a3eafedbce1213ef805f10b0"><code>3ff13b4</code></a>
    Merge pull request <a
    href="https://redirect.github.com/zedthree/clang-tidy-review/issues/123">#123</a>
    from bwrsandman/links-in-comments</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/dbe658e1a07ca18043459c3faeab6d6376974ac4"><code>dbe658e</code></a>
    Add links to check documentation in review</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/9bde8c5e4faea4dcd1290ec8a16558384bdcaf1b"><code>9bde8c5</code></a>
    Add clang-tidy 18</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/65fbe78c4af1b8c809b1c68e729ca57ef7b77679"><code>65fbe78</code></a>
    Add a hint for generating the compile command outside</li>
    <li>See full diff in <a
    href="https://github.com/zedthree/clang-tidy-review/compare/v0.18.0...v0.19.0">compare
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commit 734ce9bbcd933a193f3c9e4d3d4f398bcf59d3c7
Author: Ben Wibking <ben@wibking.com>
Date:   Tue May 21 20:55:54 2024 -0400

    update GitHub actions VMs to ubuntu-latest (#631)
    
    ### Description
    This updates the virtual machines used to run the test suite on GitHub's
    cloud infrastructure to use `ubuntu-latest` (currently Ubuntu 22.04).
    
    See:
    https://github.com/actions/runner-images?tab=readme-ov-file#available-images
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] I have added a link to any related issues see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
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.github/workflows/checkpoint-restart.yml
.github/workflows/cmake.yml
.github/workflows/hip.yml
.github/workflows/warnings.yml

commit 314debb80aca086b4808a806d6245a6ca9cb7d2d
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Wed May 15 11:49:23 2024 +1000

    Fix GPU problems in pulse_MG.cpp  (#629)
    
    ### Description
    
    I discovered some GPU-related issues in radhydro_pulse_MG.cpp and fixed
    it. In the previous PR, I turned if off for 3D problems because it is
    too expensive. As a result, it didn't get to compile and run on nvcc or
    ROCm. I fixed some first-capture and undefined on device issues and
    turned this test (and radhydro_pulse_MG_int.cpp) on. I set
    `max_timesteps=10` in these tests in order to let them finish fast. We
    are not comparing with exact solutions any way (because there isn't
    one), so it's okay to run only a small number of time steps and show
    that the architecture is working. The accuracy of the multigroup
    implementation is tested by hand, and I will include it in a planned
    nightly unit test.
    
    ### Checklist
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    completed. Denote completed tasks with an `x` inside the square brackets
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
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    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/RadhydroPulseMG/CMakeLists.txt
src/RadhydroPulseMG/test_radhydro_pulse_MG.cpp
src/RadhydroPulseMGint/CMakeLists.txt
src/RadhydroPulseMGint/test_radhydro_pulse_MG_int.cpp

commit 66da9804101d281edee00bb0ca010f7d3c832f32
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Tue May 14 03:23:39 2024 +1000

    Mean opacity for variable kappa based on piecewise-power-law approximation (#626)
    
    ### Description
    
    This PR implements piecewise-power-law approximation for multigroup
    radiation transfer. We calculate Planck-mean, energy-mean, and flux-mean
    opacity given an arbitrary function kappa(nu, T, rho) based on
    piecewise-power-law fitting to kappa(nu), E(nu), and F(nu). The user can
    enable this routine by setting `OpacityModel` to
    `OpacityModel::piecewisePowerLaw`. See examples in
    test_radhydro_shock_multigroup.cpp and test_radhydro_pulse_MG_int.hpp.
    The original approach that the opacities are defined via
    `ComputePlanckOpacity`, `ComputeFluxMeanOpacity`, etc are retained by
    setting `OpacityModel` to `OpacityModel::user`, which is the default.
    
    We calculate the power-law slope of a radiation quantity via the
    following relations:
    
    $$
    \alpha_{i} = {\rm minmod}(s_{i-1/2}, s_{i+1/2})
    $$
    
    where
    
    $$
    s_{i+1/2} = \frac{\ln \frac{X_{i+1}}{\nu_{i+3/2} - \nu_{i+1/2}} - \ln
    \frac{X_i}{\nu_{i+1/2} - \nu_{i-1/2}}}{\ln \sqrt{\nu_{i+1/2}
    \nu_{i+3/2}} - \ln \sqrt{\nu_{i-1/2} \nu_{i+1/2}}}
    $$
    
    I will try to construct a better estimate of the power-law slope in a
    separate PR. The user can choose to overwrite this by defining your own
    `RadSystem<problem_t>::ComputeRadQuantityExponents`; see example in
    test_radhydro_pulse_MG_int.cpp.
    
    The power-law fitting of $\kappa(\nu)$ can be specified in two ways. The
    first method is to specify its power-law slope and lower-bound value for
    every photon bin, given $T$ and $\rho$. The second method is to specify
    a precise definition of $\kappa(\nu, T, \rho)$. Then, a power-law
    fitting to $\kappa(\nu)$ is done on the fly in the following way:
    
    $$
    \begin{gather}
    \kappa_{L}^i = \kappa(\nu_{i-1/2}, T, \rho) \\
    \alpha^i_{\kappa} = \frac{\ln(\kappa(\nu_{i+1/2}, T, \rho) /
    \kappa(\nu_{i-1/2},T,\rho))}{\ln(\nu_{i+1/2} / \nu_{i-1/2})} \\
    \kappa_{{\rm fit}}^i(\nu) = \kappa_{L}^i \left( \frac{\nu}{\nu_{i-1/2}}
    \right)^{\alpha_{\kappa}^i}
    \end{gather}
    $$
    
    This is definitely not the most accurate way to do this as it is not
    volume conservative, but it's simple and this is important since it's
    done for every cell. An alternative is to construct $\kappa_{L,i}$ and
    $\alpha_{\kappa,i}$ in the beginning if $\kappa$ does not depend on $T$
    or $\rho$.
    
    ### Related issues
    
    N/A
    
    ### 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
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
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src/CMakeLists.txt
src/RadTube/test_radiation_tube.cpp
src/RadhydroPulseMGint/CMakeLists.txt
src/RadhydroPulseMGint/test_radhydro_pulse_MG_int.cpp
src/RadhydroPulseMGint/test_radhydro_pulse_MG_int.hpp
src/RadhydroShockMultigroup/test_radhydro_shock_multigroup.cpp
src/radiation_system.hpp

commit d7f4b43f4519a2c662de1d725db40833b52dde9c
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Mon May 13 04:00:42 2024 +1000

    change initial condition of RadForce (#627)
    
    ### Description
    
    The RadForce test can be improved to be more realistic and less `ad
    hoc`. Instead of initializing with the exact solution and letting the
    simulation maintain a static state, we start the simulation with a
    uniform density of rho0 and zero velocity. The left boundary condition
    is kept the same as before, but the right boundary is set to be
    foextrap. The end result is exactly the same as before: the radiation
    blows away the gas and the system comes to the static state given by the
    differential equation.
    
    ### 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:_
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    - [ ] I have added a link to any related issues see (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.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/RadForce/test_radiation_force.cpp
tests/RadForce.in

commit 4ab068ebda59e45ab21eccb05aae17985d570548
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Thu May 2 18:42:01 2024 -0400

    Bump extern/amrex from `47347f7` to `95a92e2` (#621)
    
    Bumps [extern/amrex](https://github.com/AMReX-Codes/amrex) from
    `47347f7` to `95a92e2`.
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/95a92e2f82227a8a4a2144bac06813f4ca1632c9"><code>95a92e2</code></a>
    cleanup of latest changes for 3D EB (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3912">#3912</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/ddf15b965da63bbd160d62a7b16d5bef2467c584"><code>ddf15b9</code></a>
    3d anisotropic eb (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3907">#3907</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/d857968968ae2cdf18f39ee50df96529e326ff39"><code>d857968</code></a>
    Fix compiler warnings in Parser (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3908">#3908</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/b029e4f335b09c2992b2e4017db277aa9c293781"><code>b029e4f</code></a>
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    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3898">#3898</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/aba9891ec5edbf4c6fbd23fb072662c3bb33223e"><code>aba9891</code></a>
    clarify comment about EnforcePeriodicity (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3903">#3903</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/b752027c1aebdfb4be339b1e30932b4108286a7a"><code>b752027</code></a>
    fix a HIP/Frontier issue (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3902">#3902</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/2c9e432ddf8e2b02d0b4f4855ae93cbfe1f58611"><code>2c9e432</code></a>
    Update HIP CIs for rocm 6.1.0 (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3897">#3897</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/64d2360b209c1e625bfc9a6feeb7501a618f7ed5"><code>64d2360</code></a>
    Set AMD wavefront size according to AMReX_AMD_ARCH (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3881">#3881</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/96f6d669d1bb2622346663a2b7cb58624866fcc3"><code>96f6d66</code></a>
    Fix offset in recv buffer of single precision particle communication (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3896">#3896</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/2780fa8147bd7e992e77a703db93fe36e7458362"><code>2780fa8</code></a>
    Fix Assertion (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3894">#3894</a>)</li>
    <li>Additional commits viewable in <a
    href="https://github.com/AMReX-Codes/amrex/compare/47347f785f5c26f1f9e65bef8e10f2d383406ef7...95a92e2f82227a8a4a2144bac06813f4ca1632c9">compare
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extern/amrex

commit f7d0e904180a403aff46fbdcf5316c354319215c
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Fri May 3 07:29:21 2024 +1000

    Changed parameters in pulse_grey test to reduce runtime (#625)
    
    ### Description
    
    Address issue #624 . I reduced `max_time` of the
    test_radhydro_pulse_grey test by ~5. Now the runtime of this test on my
    Mac Studio reduced from 28 s to 6 s.
    
    ### Related issues
    
    Fixes #624.
    
    ### 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:_
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
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    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
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src/RadhydroPulseGrey/CMakeLists.txt
src/RadhydroPulseGrey/test_radhydro_pulse_grey.cpp
tests/RadhydroPulseGrey.in

commit f97d823468118298d726d31e2f96bec1555097e3
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Tue Apr 30 23:38:23 2024 -0400

    Bump extern/fmt from `f5ec5ad` to `48c9084` (#622)
    
    Bumps [extern/fmt](https://github.com/fmtlib/fmt) from `f5ec5ad` to
    `48c9084`.
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/48c908453d8fe2a78610b523dfd88c54d4192252"><code>48c9084</code></a>
    Fix CodeQL alert (<a
    href="https://redirect.github.com/fmtlib/fmt/issues/3945">#3945</a>)</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/cf1f55f7985c4dd53f32f07a34d8fad5cdb2dc61"><code>cf1f55f</code></a>
    Specialize <code>formatter</code> for all <code>std::basic_string</code>
    types (<a
    href="https://redirect.github.com/fmtlib/fmt/issues/3943">#3943</a>)</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/400f6a8ee289a862c035d82eaf340a27952d1ae7"><code>400f6a8</code></a>
    Dedup ADL begin/end lookup</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/a3e0931ea2296b516bfda47c901eefa5ecb3f046"><code>a3e0931</code></a>
    Update signature in the doc</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/51eeccd0fbfcb197afbf45881a7f81f2ee12c13e"><code>51eeccd</code></a>
    const void* is neither a fundamental nor string type</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/f30f1fd5141dd22afdcd32fafaa1f58f10bae8fc"><code>f30f1fd</code></a>
    Document formatter specializations provided by base.h</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/f4b256c6676280dff9a9573c9b295414fd3e6861"><code>f4b256c</code></a>
    Fix warning C26439</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/f746a59a5c41ce1c8c2ee889fb38c95f898c3a95"><code>f746a59</code></a>
    Cleanup FMT_ASSERT</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/ee0c3351a4d47ca89090b8a7458846288b18efca"><code>ee0c335</code></a>
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extern/fmt

commit 53f5501fa890790664853d2e14e8e06966324dac
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Tue Apr 30 23:38:00 2024 -0400

    Bump extern/openPMD-api from `3feb5c5` to `805c760` (#623)
    
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extern/openPMD-api

commit 2e7c3aa0a8940943bdd270994e6359e6f66294c3
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Apr 23 19:36:16 2024 -0400

    run test suite with Intel oneAPI compiler on CPU (#618)
    
    ### Description
    This adds a GitHub action that compiles Quokka and runs the test suite
    with the Intel oneAPI compiler on CPU. This is needed in order to use a
    compute allocation on Stampede3.
    
    Note that this compiler is LLVM-based and is *not* the old Intel `icc`
    compiler (which cannot compile Quokka).
    
    ### Related issues
    N/A
    
    ### 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
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.github/workflows/dependencies/dependencies_dpcpp.sh
.github/workflows/intel.yml

commit deabc66dc2c040ae3a2ffce4e2577b4a7970d593
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Apr 22 16:42:43 2024 -0400

    retry hydro update if cooling solve fails (#616)
    
    ### Description
    This triggers the retry mechanism for the hydro update if the cooling
    solve fails. This mirrors the behavior for the chemistry solve (#615).
    
    ### Related issues
    Closes https://github.com/quokka-astro/quokka/issues/372.
    
    ### Checklist
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    completed. Denote completed tasks with an `x` inside the square brackets
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src/GrackleLikeCooling.hpp
src/RadhydroSimulation.hpp
src/TabulatedCooling.hpp

commit 525d025edc0eee2a232fa1ae3e0ea176d3a9de99
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Sun Apr 21 20:58:20 2024 +0200

    If microphysics burn fails, retry hydro (#615)
    
    ### Description
    If the (VODE) burn fails in microphysics, we should retry hydro with a
    reduced timestep, just like we retry hydro with a reduced timestep if
    the CFL is violated.
    
    These changes have been successfully tested on CPUs and GPUs.
    
    ### Related issues
    PopIII test on NVIDIA GPUs crashes due to a burn failure in VODE. This
    did not occur on AMD GPUs at the same timestep.
    
    Resolves #372 for chemistry
    
    ### 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:_
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    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: Piyush Sharda <psharda@RSAA-043527.local>
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/Chemistry.hpp
src/RadhydroSimulation.hpp

commit bb121de2927701ba2f4b1142419e4f69ad7f31c7
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Sat Apr 20 02:55:04 2024 +0200

    Print timestep info in scientific notation (#614)
    
    ### Description
    This change ensures the timestep info is printed in scientific notation
    in the output logfile.
    
    ### Related issues
    By default, it only prints in scientific notation if the number is
    greater than 1e10.
    
    ### 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).
    - [ ] I have added a link to any related issues see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
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src/simulation.hpp

commit 7778c4c68118f064f1e78eb32d7047ef3e81d677
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Fri Apr 19 17:57:21 2024 +0200

    Use mass scalars while computing EOS quantities in NSCBC (#610)
    
    ### Description
    We currently do not pass mass scalars as an input to the
    `ComputeSoundSpeed` function in NSCBC.
    
    ### 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:_
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    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: Piyush Sharda <psharda@RSAA-043527.local>
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/NSCBC_inflow.hpp
src/NSCBC_outflow.hpp

commit cab810d0b292f5c32a4e604e16c56cb1dcce13f7
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Fri Apr 19 17:06:26 2024 +0200

    Update some default values for the PopIII test (#613)
    
    ### Description
    Slightly lowering the jeans density refinement threshold and raising the
    density threshold for chemistry avoids a crash due to VODE in the
    background region.
    
    ### Related issues
    
    ### 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).
    - [ ] I have added a link to any related issues see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
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tests/PopIII.in

commit 9d44f9156beba9a5e4b91ce460b4323f2e1663c0
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Apr 14 10:47:57 2024 -0400

    fix typo in TabulatedCooling (#606)
    
    ### Description
    PR https://github.com/quokka-astro/quokka/pull/599 had a typo that
    causes simulations with `cloudy_cooling_tools` cooling to fail.
    
    ### Related issues
    N/A
    
    ### 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:_
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
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src/TabulatedCooling.cpp

commit f4784d23815c1510a71badfc750ab71e48ad5c1f
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Sun Apr 14 23:22:55 2024 +1000

    Move installation instructions to docs (#607)
    
    ### Description
    
    Moved installation instructions from README to docs and added a link to
    the docs in README.md
    
    ### Related issues
    #605
    
    ### 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:_
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
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README.md
docs/installation.rst

commit a49bfe1819b849846c6451003403321b8e3ceae1
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Apr 13 20:32:48 2024 -0400

    read cloudy-cooling-tools tables (#599)
    
    ### Description
    Reads tables created by `cloudy-cooling-tools` and adds corresponding
    source terms.
    
    Users must generate their own tables using cloudy-cooling-tools in order
    to use this feature. No tables are included in the repository.
    
    Unlike the Grackle tables, these tables do not split the cooling and
    heating rates into separate contributions from primordial species and
    metals, and in the implementation of the source terms, no additional
    terms are added "by hand" to the tabulated rates.
    
    ***User-breaking changes and how to fix them:***
    * The name of the `cooling.grackle_data_file` parameter is changed to
    `cooling.hdf5_data_file`.
    * The `cooling.cooling_table_type` parameter is added. It can be set to
    `grackle` or `cloudy_cooling_tools`. *(In order to migrate existing
    problems with cooling, this parameter must be set to `grackle`.)*
    
    ### Related issues
    N/A
    
    ### 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).
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    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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src/CMakeLists.txt
src/CloudyDataReader.cpp
src/CloudyDataReader.hpp
src/GrackleDataReader.cpp
src/GrackleDataReader.hpp
src/GrackleLikeCooling.cpp
src/GrackleLikeCooling.hpp
src/ODEIntegration/test_ode.hpp
src/PopIII/CMakeLists.txt
src/RadhydroSimulation.hpp
src/ShockCloud/CMakeLists.txt
src/ShockCloud/cloud.cpp
src/ShockCloud/test_grackle_cooling.cpp
src/TabulatedCooling.cpp
src/TabulatedCooling.hpp
tests/ShockCloud_128.in
tests/ShockCloud_512.in

commit c6c2637f12765c02bfebbbb466c059ded3e720f9
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Thu Apr 11 21:04:18 2024 +1000

    Fix Newton-Rasphon convergence bug when tau = 0 (#603)
    
    ### Description
    
    This is a replacement of #595 .
    
    Since we base our Newton-Rasphon iteration on (E_gas, R), where R = tau
    (4 pi B / c - E), when tau = 0, E is not deducible from R. This causes
    division-by-zero error and E = NAN, which causes the iteration fail to
    converge. In this PR, I fixed this issue by enforcing d E_g = 0 when
    tau_g = 0. Here E_g is the radiation energy of the g'th photon group.
    
    To validate this fix, I modified the ShockMultigroup test to include an
    extra redundant photon bin where kappa is set to 0.
    
    ### 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 see (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.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
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src/RadhydroShockMultigroup/test_radhydro_shock_multigroup.cpp
src/radiation_system.hpp

commit a210782b115b7ab19314c105fb6b1051dd35c800
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Apr 10 21:39:01 2024 -0400

    add "experimental" warning for AMD and Intel GPUs (#602)
    
    ### Description
    There are known issues for AMD GPUs, so this is noted in the README.
    
    Intel GPUs remain untested. Based on the other two GPU platforms, it is
    extremely likely that there are as-yet-undiscovered issues that will
    affect the code.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] I have added a link to any related issues see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [ ] I have requested a reviewer for this PR.

README.md

commit f8ed5f91dc70d97e98b0a69c1453fa601900e4a0
Author: Neco Kriel <43261821+AstroKriel@users.noreply.github.com>
Date:   Thu Apr 11 01:56:08 2024 +1000

    Refactor Reconstruction Functions (#570)
    
    ### Description
    I have relocated the reconstruction functions to all sit within the
    HyperbolicSystem class, and tried to minimise code duplication.
    
    ### Checklist
    - [x] I have added a description (see above).
    - [ ] (Not Applicable) I have added a link to any related issues see
    (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] (Not Applicable) I have added tests for any new physics that this
    PR adds to the code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/RadhydroSimulation.hpp
src/hyperbolic_system.hpp
src/radiation_system.hpp

commit 54519af15fc1e323045cc9c1017195a3b2e452ff
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Wed Apr 10 17:08:28 2024 +1000

    Update test parameters to produce all the figures in the IMEX paper (#600)
    
    ### Description
    
    Under the reproducible research philosophy which I believe in, I would
    like the reader to be able to reproduce all the figures and data from a
    paper with little effort. Therefore, I updated the tests used in the
    IMEX paper, setting some of the physical parameters as runtime
    parameters, so that the reader can reproduce the exact result in the
    paper by simply changing the config.in files, while the default
    parameters are kept moderate so that the automatic tests can run in a
    reasonable time.
    
    ### Checklist
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    completed. Denote completed tasks with an `x` inside the square brackets
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    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.
    - [x] I have tested this PR on my local computer and all tests pass.
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    `/azp run`.
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    ---------
    
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src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/RadhydroPulse/test_radhydro_pulse.cpp
src/RadhydroPulseDyn/test_radhydro_pulse_dyn.cpp
src/RadhydroUniformAdvecting/test_radhydro_uniform_advecting.cpp
tests/MarshakAsymptotic.in
tests/RadhydroPulse.in
tests/RadhydroPulseDyn.in

commit 40c8f7248de1a7e9f7a26a5de1e4d6ddde72751e
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Wed Apr 10 01:59:43 2024 +1000

    Remove wavespeed correction in radiation flux (#582)
    
    ### Description
    
    The wavespeed adjustment, $S = c \sqrt{f/\tau}$, in the HLL flux of
    radiation energy (e.g.
    [Jiang+2013](https://ui.adsabs.harvard.edu/abs/2013ApJ...767..148J/abstract),
    [Skinner+2019](https://ui.adsabs.harvard.edu/abs/2019ApJS..241....7S/abstract))
    is not necessary any more since we implemented the IMEX PD-ARS scheme.
    All previous tests passed after this change. Two of the tests get
    slightly worse results but still within the error tolerance. The fact
    that it passed all the tests seems to suggest that this correction at
    diffusion limit is no longer required. In fact, I have shown in the IMEX
    paper that, at diffusion limit, the wavespeed is roughly $c
    \sqrt{f/\tau}$.
    
    Our numerical scheme gives the following discretization:
    
    $$
    \frac{\partial}{\partial t} E = \frac{\cal C}{3 \cal L}
    \frac{\partial^2}{\partial x^2} \frac{E}{3}
    $$
    
    which is a diffusion equation with the correct diffusion coefficient.
    The diffusion speed in time interval $t$ is approximated
    
    $$
    C_{\rm eff} \equiv \frac{\sqrt{D t}}{t} = \sqrt{\frac{\cal C}{3 {\cal L}
    t}}
    $$
    
    In dimensional terms,
    
    $$
    C_{\rm eff,\ with \ dim} =
        \frac{c}{\sqrt{3}} \frac{1}{\sqrt{{\rm CFL} ~\tau_{\rm cell}}}
    $$
    
    The $1/\tau$ correction is a natural result of the IMEX scheme.
    
    A side note: it might be possible to remove the 0.1 c floor of the
    wavespeeds S_L and S_R while not causing any issues. Simply removing it
    causes S_L = S_R = 0 and F = NAN in the 3D RadForce test *only*. I'll
    take a second look at this in a future PR.
    
    ### Related issues
    Odd-even instability #541
    
    ### 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:_
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    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.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
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    ---------
    
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src/RadTube/test_radiation_tube.cpp
src/RadhydroPulse/test_radhydro_pulse.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/radiation_system.hpp

commit 3fa255d833aa2fdd04755911d9d61466d0b90fe4
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Apr 7 22:09:59 2024 -0400

    add computeVolumeIntegral function (#597)
    
    ### Description
    Adds a function that can be used to a compute a volume integral of a
    user-defined function that takes an Array4 for a box of the
    `state_new_cc_` MultiFab as input.
    
    ### Related issues
    N/A
    
    ### 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 see (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.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [ ] I have requested a reviewer for this PR.

src/simulation.hpp

commit 62b82a6eedfb6ecee38159d73fd4864c13c7f4fe
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Apr 7 20:14:59 2024 -0400

    fix tracer particle handling in hydro retries (#596)
    
    ### Description
    This fixes a bug in handling tracer particles in the hydro update retry
    code.
    
    This only affects you if you were using tracer particles and hydro
    retries were triggered. In that case, all of the tracer particles would
    disappear.
    
    ### Related issues
    N/A
    
    ### 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).
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    - [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.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [ ] I have requested a reviewer for this PR.
    
    ---------
    
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src/RadhydroSimulation.hpp

commit dd5c2fd31c7f28e4444df4caf9eef33194050d98
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Apr 7 20:14:51 2024 -0400

    add simple subsonic inflow/outflow BCs (#598)
    
    ### Description
    This adds simplified subsonic inflow and outflow boundary conditions.
    For outflows, it specifies the pressure at the outflow and extrapolates
    the other primitive variables (while turning into a reflecting boundary
    if the normal velocity is inflowing). For inflows, it specifies the
    velocity components, the temperature, and the passive scalars, while
    extrapolating the density.
    
    Unlike the naive boundary conditions, these boundary conditions are
    well-posed, since they specify the correct number of quantities required
    for the steady-state solution to be unique. The amplitude of reflected
    waves is greater than for the NSCBC boundary conditions, but these
    boundary conditions are much more stable in the presence of supersonic
    turbulent flow near the boundary.
    
    ### Related issues
    Workaround for https://github.com/quokka-astro/quokka/issues/532.
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [ ] I have requested a reviewer for this PR.

src/NSCBC_inflow.hpp
src/NSCBC_outflow.hpp

commit d13e3bc6dbdb44151397cea6d12ad2e515a888d8
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Apr 3 21:49:35 2024 -0400

    docs: add in-situ analysis (#586)
    
    ### Description
    Adds documentation for enabling *in-situ* analysis of simulations.
    
    Also: updates the documentation on how to read a time series of
    plotfiles with VisIt.
    
    ### Related issues
    N/A
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

docs/index.rst
docs/insitu_analysis.rst
docs/postprocessing.rst

commit 04fc0c87358379f9f96da9871d5bdd255e9f0499
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Apr 2 08:41:29 2024 -0400

    update histogram plotting script (#588)
    
    ### Description
    Updates the histogram plotting script to read the variables, time, and
    timestep from the header.
    
    ### Related issues
    N/A
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

scripts/plot_PDF_2D_outputs.py
scripts/plot_PDF_outputs.py

commit 79ef0e6eb2b6083f913d3bd32810461523eb60e5
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Apr 1 13:41:54 2024 -0400

    Bump extern/Microphysics from `e587300` to `124b71b` (#590)
    
    Bumps [extern/Microphysics](https://github.com/psharda/Microphysics)
    from `e587300` to `124b71b`.
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/124b71becfb95e1a0c7cdbc9b3a15e0e4be1096b"><code>124b71b</code></a>
    use a helper function to get the index into the NSE tables (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1495">#1495</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/95cb860c0cda929b91b883ce00e7c15189a4fd86"><code>95cb860</code></a>
    remove redundant rhs and ydot for NSE_NET (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1507">#1507</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/886498d0db40396c5989e3b5815ba2894b7e156a"><code>886498d</code></a>
    Optimize fill_merge_indices/nse_grouping for NSE_NET (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1506">#1506</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/3169bfed5c07804b91f541b7637d68954f4eec62"><code>3169bfe</code></a>
    remove the is_jacobian_term_used logic in the linear algebra (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1502">#1502</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/d7e5b848b5e0f86cc746e632ac08371b6db7d478"><code>d7e5b84</code></a>
    remove fast reaction cycle check for NSE_NET check. (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1503">#1503</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/9dd9dbb619da9a210e5d453db502994cb844a846"><code>9dd9dbb</code></a>
    add more unit test for testing NSE_NET (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1504">#1504</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/ce331bc849de71dafa0d32e7f2ba0c09527ba1d5"><code>ce331bc</code></a>
    update test_linear_algebra to output the Jacobian mask (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1501">#1501</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/02d46a67cf5852509cc35db7850e5f87da495679"><code>02d46a6</code></a>
    updated changelog for 24.03 (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1498">#1498</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/2359fab66cfb9a2cf2749a4c89005c5d5527bf54"><code>2359fab</code></a>
    fix RKC integration with SDC (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1497">#1497</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/695b7118aa20023c7baa9b34fa0cba1049011fd2"><code>695b711</code></a>
    update test_linear_algebra to reflect pivot templating (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1496">#1496</a>)</li>
    <li>See full diff in <a
    href="https://github.com/psharda/Microphysics/compare/e587300c654f9dc8a4be111a30b384dc269fab52...124b71becfb95e1a0c7cdbc9b3a15e0e4be1096b">compare
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extern/Microphysics

commit 782643a39a2f0a5edba93a0a4dba734fa46ebe21
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Apr 1 13:41:36 2024 -0400

    Bump extern/amrex from `2ecafcf` to `47347f7` (#591)
    
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    href="https://github.com/AMReX-Codes/amrex/commit/47347f785f5c26f1f9e65bef8e10f2d383406ef7"><code>47347f7</code></a>
    Fix: Resize Component on Add (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3861">#3861</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/fe6f3de74333ccf7e4babb4832602cf6c108ce52"><code>fe6f3de</code></a>
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    href="https://github.com/AMReX-Codes/amrex/commit/f264290e4d6ec13a2697d7c1112f3b3fd98505ea"><code>f264290</code></a>
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    href="https://github.com/AMReX-Codes/amrex/commit/1be7257928eb5b553905a482e3a3d608272d22f0"><code>1be7257</code></a>
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    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3857">#3857</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/67523bb7b0d5661db6c5f53ef3818d4dea834669"><code>67523bb</code></a>
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    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3860">#3860</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/41df2a586666728280b8215e47b5c28eb041d2f2"><code>41df2a5</code></a>
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    href="https://github.com/AMReX-Codes/amrex/commit/7437aa17d36ff7f7538b664c2ba49498dc001503"><code>7437aa1</code></a>
    <code>MultiFab::deepCopy()</code> (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3848">#3848</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/dffdeac6f45fe7ccbe8178ff17bfe7046dbc5784"><code>dffdeac</code></a>
    <code>FabArray\&lt;FAB&gt;::copy</code> Argument Name (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3856">#3856</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/8d57ebc0139705f208cb1f6f6a699ad534eb2bb8"><code>8d57ebc</code></a>
    AMReX_FLATTEN_FOR (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3855">#3855</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/21a7a66f775b65a1e669fd1f2f068c7ac9dd1af7"><code>21a7a66</code></a>
    Use Clang-Tidy 17 in GitHub CI (<a
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extern/amrex

commit 441434afd98208be69daff372538fb1a5d17f41d
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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    Bump extern/openPMD-api from `c2e0e83` to `3feb5c5` (#592)
    
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    [pre-commit.ci] pre-commit autoupdate (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1602">#1602</a>)</li>
    <li><a
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    Fix dirtyRecursive() performance for Series with many steps (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1598">#1598</a>)</li>
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    Fix hdf5 dataset specific config (<a
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extern/openPMD-api

commit 9b11bcb61c7355f1044eb5950248e5fd19babc00
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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    Bump ZedThree/clang-tidy-review from 0.17.2 to 0.18.0 (#593)
    
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    fix: download artifact as blob and follow redirects</li>
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commit a56e5727d7df74815e8e2556b55562c3c4657a2a
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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    Bump extern/fmt from `ae1e93d` to `f5ec5ad` (#589)
    
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    href="https://github.com/fmtlib/fmt/commit/3b5f3de3b57505c7f1a60ee40ef3448c623b1326"><code>3b5f3de</code></a>
    Make CMake version message less confusing (<a
    href="https://redirect.github.com/fmtlib/fmt/issues/3907">#3907</a>)</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/ca9193983bdfa5cd3351d7801f31925f4dee8e2e"><code>ca91939</code></a>
    Replace std::fill_n with fmt::detail::fill_n (<a
    href="https://redirect.github.com/fmtlib/fmt/issues/3909">#3909</a>)</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/74a187288bbf10e2eb7bd6282715530392e8a2a2"><code>74a1872</code></a>
    Implemented fmt::day, fmt::month, fmt::year and related unit tests (<a
    href="https://redirect.github.com/fmtlib/fmt/issues/3906">#3906</a>)</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/88620e53a4ffe4cb02af02fc13d6618ff9727f94"><code>88620e5</code></a>
    Range formatting documentation (<a
    href="https://redirect.github.com/fmtlib/fmt/issues/3905">#3905</a>)</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/5d63e87d235b86341f8d87f79ed8eb9825f34c44"><code>5d63e87</code></a>
    Add a formatter for float128</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/aecec01b34aa3d1bb3fb991d4f75b0750508f9a0"><code>aecec01</code></a>
    Initial support for extended FP types</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/5af88653eb9c57940cecad748e1192de1a1a0bb3"><code>5af8865</code></a>
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    href="https://github.com/fmtlib/fmt/commit/45b772f85c0c8ef95cdee73a2f33ed5d69739e28"><code>45b772f</code></a>
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extern/fmt

commit e275647a7d0a5e42b6c6b7404336a15e6a2fda52
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Mar 31 05:08:52 2024 -0400

    add histogram (PDF) output (#581)
    
    ### Description
    This adds histogram / probability density function (PDF) outputs (as
    fixed-width text files) at timestep intervals as the simulation runs.
    
    Bins can be optionally log-spaced. Normalization of the output is left
    up to the user, with bin volumes calculated (for convenience) in both
    original variable coordinates and optionally-log-transformed
    coordinates.
    
    *Example usage:*
    ```
    quokka.hist_temp.type = DiagPDF                         # Diagnostic type
    quokka.hist_temp.file = PDFTempDens                     # Output file prefix
    quokka.hist_temp.int  = 10                              # Output cadence (in number of coarse steps)
    quokka.hist_temp.weight_by = mass                       # (Optional) Weight by: mass, volume, cell_counts
    quokka.hist_temp.var_names = temperature gasDensity     # Variable(s) of interest (compute a N-D histogram)
    
    quokka.hist_temp.temperature.nBins = 20                 # temperature: Number of bins
    quokka.hist_temp.temperature.log_spaced_bins = 1        # temperature: (Optional, default: 0) Use log-spaced bins
    quokka.hist_temp.temperature.range = 1e3 1e7            # temperature: (Optional) Specify the min/max of the bins
    
    quokka.hist_temp.gasDensity.nBins = 5                   # gasDensity: Number of bins
    quokka.hist_temp.gasDensity.log_spaced_bins = 1         # gasDensity: (Optional, default: 0) Use log-spaced bins
    quokka.hist_temp.gasDensity.range = 1e-29 1e-23         # gasDensity: (Optional) Specify the min/max of the bins
    ```
    
    *Filters (based on any variables, not necessary those used for the
    histogram) can be optionally added:*
    ```
    quokka.hist_temp.filters = dense                       # (Optional) List of filters
    quokka.hist_temp.dense.field_name = gasDensity         # Filter field
    quokka.hist_temp.dense.value_greater = 1e-25           # Filters: value_greater, value_less, value_inrange
    ```
    
    *Output snippet:*
    ```
    #                     time:   0.00000000000000000e+00
    #                    cycle:                         0
    #                variables:               temperature                gasDensity
    #            is_log_spaced:                         1                         1
              temperature_idx           temperature_min           temperature_max           gasDensity_idx            gasDensity_min            gasDensity_max                  mass_sum
                            0   1.00000000000000000e+03   1.58489319246111404e+03                         0   9.99999999999999943e-30   1.58489319246111091e-28   0.00000000000000000e+00
                            0   1.00000000000000000e+03   1.58489319246111404e+03                         1   1.58489319246111091e-28   2.51188643150957179e-27   0.00000000000000000e+00
                            0   1.00000000000000000e+03   1.58489319246111404e+03                         2   2.51188643150957179e-27   3.98107170553495291e-26   0.00000000000000000e+00
                            0   1.00000000000000000e+03   1.58489319246111404e+03                         3   3.98107170553498563e-26   6.30957344480194281e-25   0.00000000000000000e+00
                            0   1.00000000000000000e+03   1.58489319246111404e+03                         4   6.30957344480194281e-25   9.99999999999999960e-24   0.00000000000000000e+00
    ```
    
    Based on the [PeleLMeX
    implementation](https://amrex-combustion.github.io/PeleLMeX/manual/html/LMeXControls.html#run-time-diagnostics)
    with extensions to N-D histograms, log binning, and mass weighting.
    
    ### Related issues
    N/A
    
    ### 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).
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    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

scripts/plot_PDF_outputs.py
src/CMakeLists.txt
src/DiagBase.H
src/DiagBase.cpp
src/DiagPDF.H
src/DiagPDF.cpp
tests/ShockCloud_128.in
tests/ShockCloud_512.in

commit 80a8aef5b95f1dde499bbe1912963cdb137890fe
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Mar 29 09:19:46 2024 -0400

    fix face-centered BCs for refined levels (#584)
    
    ### Description
    Face-centered boundary conditions weren't using the correct physical
    boundary functor for refined levels.
    
    Since we currently don't evolve any face-centered vars with AMR, this
    bug should not have affected anyone.
    
    ### Related issues
    N/A
    
    ### 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:_
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    - [x] I have added a link to any related issues see (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.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/simulation.hpp

commit 4f2e993a655cd34dde9098ee2bb39fb44a400547
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Thu Mar 28 04:58:27 2024 +1100

    Remove redundant parameter compute_v_over_c_terms (#579)
    
    ### Description
    
    I removed the redundant parameter `compute_v_over_c_terms` since now by
    setting `beta_order = 0` we achieve exactly the same effect as
    `compute_v_over_c_terms = false`.
    
    ### 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 see (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.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/RadBeam/test_radiation_beam.cpp
src/RadForce/test_radiation_force.cpp
src/RadMarshak/test_radiation_marshak.cpp
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadPulse/test_radiation_pulse.cpp
src/RadShadow/test_radiation_shadow.cpp
src/RadStreaming/test_radiation_streaming.cpp
src/RadSuOlson/test_radiation_SuOlson.cpp
src/RadTophat/test_radiation_tophat.cpp
src/RadTube/test_radiation_tube.cpp
src/RadhydroPulse/test_radhydro_pulse.cpp
src/RadhydroPulseDyn/test_radhydro_pulse_dyn.cpp
src/RadhydroPulseGrey/test_radhydro_pulse_grey.cpp
src/RadhydroPulseMG/test_radhydro_pulse_MG.cpp
src/RadhydroShell/test_radhydro_shell.cpp
src/RadhydroShock/test_radhydro_shock.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/RadhydroShockMultigroup/test_radhydro_shock_multigroup.cpp
src/RadhydroUniformAdvecting/test_radhydro_uniform_advecting.cpp
src/radiation_system.hpp

commit 188b7cc0c21a368d6849288fb61c907b4966da92
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Mar 25 10:42:41 2024 -0400

    Bump ZedThree/clang-tidy-review from 0.17.1 to 0.17.2 (#580)
    
    Bumps
    [ZedThree/clang-tidy-review](https://github.com/zedthree/clang-tidy-review)
    from 0.17.1 to 0.17.2.
    <details>
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    href="https://github.com/zedthree/clang-tidy-review/releases">ZedThree/clang-tidy-review's
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    <h2>v0.17.2</h2>
    <h2>What's Changed</h2>
    <ul>
    <li>fix: artifact download by <a
    href="https://github.com/Nerixyz"><code>@​Nerixyz</code></a> in <a
    href="https://redirect.github.com/ZedThree/clang-tidy-review/pull/115">ZedThree/clang-tidy-review#115</a></li>
    </ul>
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    href="https://github.com/ZedThree/clang-tidy-review/compare/v0.17.1...v0.17.2">https://github.com/ZedThree/clang-tidy-review/compare/v0.17.1...v0.17.2</a></p>
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    href="https://github.com/ZedThree/clang-tidy-review/commit/9a32adc734e10e4d84baa60f2b7d7c021568c527"><code>9a32adc</code></a>
    Merge pull request <a
    href="https://redirect.github.com/zedthree/clang-tidy-review/issues/115">#115</a>
    from Nerixyz/fix/pr-stuff</li>
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commit b52d74ce7c47f0f69fd33efcd21bc9c9bcd842b4
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Fri Mar 22 03:37:00 2024 +0100

    Fix amrex::abort not aborting unconditionally on GPUs (for primordial chem and popiii problems) (#575)
    
    ### Description
    As described in #543 , `amrex::Abort()` does not unconditionally abort
    on GPUs. Following the workaround proposed in #543, I have implemented a
    way to circumvent this issue for problems using microphysics' `burn`
    (PrimordialChem and PopIIII).
    
    ### Related issues
    #543
    
    ### 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:_
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
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src/Chemistry.hpp

commit aa95d0cde2c3ed186d0071004c4ee63b1031b76d
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Wed Mar 20 15:07:33 2024 +1100

    New source terms that include the work term (#552)
    
    ### Description
    
    A new scheme for radiation-matter coupling that includes the work term
    in the source terms and also includes up to $\beta^2$ terms in the flux
    update.
    
    - A new parameter `beta_order` is introduced in RadSystem_Traits. It's
    used to control the order of the $\beta$ terms to include in the
    radiation four-force. Available options are 1, 2, and 3.
    - The user can set `include_work_term_in_source = false` in
    radiation_system.hpp to restore the old scheme. I didn't add this to
    RadSystem_Traits, so you have to do it in the source file.
    
    The radiation-matter coupling is done in three steps:
    
    ##### Step 1: Energy exchange
    
    The motivation to include the work term in the source terms is as
    fellows. The energy equations excluding the transport part are:
    
    $$
    \begin{gather}
    \frac{\partial}{\partial t} E = c G^0 \\
    \frac{\partial}{\partial t} E_r = -\hat{c} G^0
    \end{gather}
    $$
    
    where E is the gas **total** energy. The fully relativistic expression
    of the time-like component of the four-force is (there are extra terms
    if $\kappa_F \ne \kappa_E$):
    
    $$
    -cG^0 = \hat{c} \gamma (\kappa_P B - \kappa_E E_r) + \hat{c} c^{-2}
    \gamma_3 \kappa_F v^i F^i
    $$
    
    where I denote $4 \pi B/c$ as $B$. In the scheme presented in the Quokka
    paper, only the $B-E$ term is included in the source function, and it's
    okay to assume the $E$ in the above RHD equation is the internal energy.
    However, this simplification breaks down in the advecting diffusive
    uniform medium test. Imagine a test problem where the radiation (with
    uniform energy density $E_0$) is in thermal equilibrium with a uniform
    medium and you boost it to a moving frame with velocity $v$. In the lab
    frame, $B = E_0$ but $E_r > E_0$ due to Lorentz transformation.
    Therefore, in this scheme the source term is non-zero and the radiation
    is out of equilibrium with matter. The matter temperature will increase
    in the energy exchange step. In the next steps, the gas internal energy
    is not touched, so it's off from the correct equilibrium forever.
    
    This issue goes away if you include the work ($v^i F^i$) in the source
    term. We can show that the source $G^0$ in the lab frame vanishes
    precisely in the aforementioned test problem.
    
    ##### Step 2: Flux update
    
    The momentum and flux equations (excluding the transport part) are
    
    $$
    \begin{gather}
    \frac{\partial}{\partial t} \rho v^i = G^i, \\
    \frac{\partial}{\partial t} F^i = - \hat{c} c G^i
    \end{gather}
    $$
    
    and
    
    $$
    \begin{align}
    -c \hat{c} G^i = &- \hat{c} \kappa_F \gamma ~F^i + \hat{c} \kappa_P B
    \gamma ~v^i + \hat{c} \kappa_F \gamma ~v^j P^{ji} \\
    & + \hat{c} (\kappa_F - \kappa_E)(E \gamma^3 - 2 \frac{v^j F^j}{c^2}
    \gamma^3) ~v^i
    \end{align}
    $$
    
    We use the backward Euler scheme for flux update:
    
    $$
    \frac{F^i - F_0^i}{\Delta t} = - \hat{c} c G^i
    $$
    
    where the subscript $0$ indicates the old state and the variables
    without subscript $0$ are in the new state. In $G^i$, the following two
    terms are lagged: the velocity $v^i$ and Edington tensor $T^{ij}$. We
    take a valid assumption that the Eddington tensor is unchanged, because
    the regime where the flux could have significant variable, which is the
    diffusion regime, is when the Eddington tensor is nearly constant at 1/3
    I. The lagged velocity can cause huge error when the radiation force is
    stronge. We eliminate this lag in velocity via iterations in the next
    step.
    
    Assuming $F^i$ is the only implicit quantity in the equation, it's
    straight forward to solve $F^i$. In the case of $\kappa_F - \kappa_E =
    0$​, the solution is
    
    
    $$
    F_i = \frac{F_0^i + \hat{c} \Delta t (\kappa_P B \gamma v^i + \kappa_F
    \gamma v^j P^{ji})}{1 + \hat{c} \Delta t \kappa_F \gamma}
    $$
    
    In the case of $\kappa_F - \kappa_E \ne 0$, $G^i$ would contain all
    three components of $F$, therefore we need to solve for $F^i$​ by
    inverting a 3x3 matrix. This is done by the hand-crafted
    `Solve3x3matrix` function that avoids dividing any of the off-diagonal
    elements which could be zero.
    
    The value of $\gamma$ is controled by the `beta_order` parameter.
    $\gamma = 1$ when `beta_order = 0` or `beta_order = 1`, and $\gamma = 1
    + \beta^2/2$ when `beta_order = 2`. When `beta_order >= 3`, we use the
    fully relativistic formula $\gamma = 1/\sqrt{1 - \beta^2}$. Furthermore,
    the $\beta^2$ term in $G^i$ is ignored when `beta_order < 2`.
    
    ##### Step 3: Perform iteration to ensure the gas velocity is up to date
    
    To complete radiation-matter coupling, we iteration step 1 and step 2 to
    make sure the gas velocity is up to date and the energy is conserved.
    
    1. Use the new source term, $S = \Delta t \hat{c} \gamma (\kappa_{P} B -
    \kappa_E E) + \Delta t \hat{c} c^{-2} \gamma \kappa_F v_i F_i$, to
    update the gas internal energy $E_g$ and radiation energy $E_r$. In this
    step, the total energy is conserved. We record the (lagged) work term as
    $W^\star \sim v_i F_i$.
    2. Update flux using backward Euler scheme.
    3. Update gas momentum following $(\rho v_i)^{(t+1)} = (\rho
    v_i)^{\star} - \Delta F_i / (c \hat{c})$.
    4. $E_g^{(t+1)} \leftarrow E_g^{(t+1)} - \Delta K$ where $\Delta K$ is
    the change in kinetic energy. In this and previous step, the gas total
    energy is conserved.
    5. Calculate the updated work term: $W \sim v_i F_i$.
    6. Check if $W$ converges to $W^\star$ with the criteria listed below.
    If yes, break; otherwise, restart from step 1 with $W^\star \leftarrow
    W$. The convergence criteria I use are: $(c/\hat{c}) |W -
    W^{\star}|/E_{\rm tot} < 10^{-13}$, or $|W - W^{\star}|/W^{\star} <
    10^{-13}$, or $|W - W^{\star}|/S < 10^{-13}$.
    
    This scheme passed all the tests, and at most 5 iterations is used. The
    results from all the tests are nearly identical to the previous results.
    
    ### Related issues
    
    I adjusted the parameters in the `RadhydroUniformAdvecting` test problem
    so that it's in the dynamic diffusion regime. The old scheme failed at
    this test but the new scheme passed.
    
    ### Alternative Approaches
    
    We can also set the old scheme to default and optionally turn on this
    new scheme. But since this new scheme passes tests that the old scheme
    failed, and it is ONLY more expensive in the diffusion regime where it
    gives more accurate result, we should probably keep it as default.
    
    We can remove `compute_v_over_c_terms` in RadSystem_Traits and replace
    it with `beta_order = 0`.
    
    ### 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:_
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    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.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
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src/RadBeam/test_radiation_beam.cpp
src/RadForce/test_radiation_force.cpp
src/RadMarshak/test_radiation_marshak.cpp
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadPulse/test_radiation_pulse.cpp
src/RadShadow/test_radiation_shadow.cpp
src/RadStreaming/test_radiation_streaming.cpp
src/RadSuOlson/test_radiation_SuOlson.cpp
src/RadTophat/test_radiation_tophat.cpp
src/RadTube/test_radiation_tube.cpp
src/RadhydroPulse/test_radhydro_pulse.cpp
src/RadhydroPulseDyn/test_radhydro_pulse_dyn.cpp
src/RadhydroPulseGrey/test_radhydro_pulse_grey.cpp
src/RadhydroPulseMG/test_radhydro_pulse_MG.cpp
src/RadhydroShell/test_radhydro_shell.cpp
src/RadhydroShock/test_radhydro_shock.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/RadhydroShockMultigroup/test_radhydro_shock_multigroup.cpp
src/RadhydroUniformAdvecting/test_radhydro_uniform_advecting.cpp
src/radiation_system.hpp
tests/RadhydroUniformAdvecting.in

commit 0d97954dc2de806f867571877939228c6e5136cd
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Tue Mar 19 21:45:50 2024 +0100

    Fixed bug in PopIII refinement (#574)
    
    ### Description
    Fixed a bug in the name of the refinement runtime parameter for PopIII.
    The simulation wasn't refining because of the mismatch in the name.
    
    ### Related issues
    No
    
    ### 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:_
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    - [ ] I have added a link to any related issues see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
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tests/PopIII.in

commit 8e37d528d3a3afda242cd6030e05f6e24e9cfe1b
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Tue Mar 19 21:45:14 2024 +0100

    Avoid imaginary roe average sound speed (#572)
    
    ### Description
    There can be instances when the Roe-averaged sound speed (`cs_tilde` in
    `HLLC.hpp`) can be negative. In such cases, the current implementation
    will generate a NAN cs_tilde, which is handled differently by different
    compilers (e.g., GCC versus HIPCC). This was one of the causes of
    StarCluster and PopIII problems failing on HIPCC-based CPUs and AMD
    GPUs.
    
    ### Related issues
    Fixes #555.
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/HLLC.hpp

commit 199f93d9c84220062601d3ee3045abb6217d84fa
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Tue Mar 19 21:44:42 2024 +0100

    Define K_S for isothermal gamma (#573)
    
    ### Description
    Currently, `K_S` is undefined in the `computeFlatenningCoefficients`
    function for the case of isothermal gamma, because the function to
    compute sound speed within `EOS.hpp` that it calls only works if gamma
    != 1.
    
    ### Related issues
    Fixes #553 for now. In the long run, this wont be needed because we will
    move all EOS calculations (including for gamma=1) to EOS.hpp. But for
    now, we should apply this patch so that the gamma=1 case is correctly
    handled while computing flattening coefficients.
    
    ### 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).
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
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    ---------
    
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src/hydro_system.hpp

commit 9f9c30054d3fbb156c05625a1727e78dfe481af8
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Mar 18 22:12:23 2024 -0400

    Update Factory.H to use std::move (#576)
    
    ### Description
    Sonarcloud complained about the last PR using `std::forward` instead of
    `std::move`. It appears that `std::move` should be used instead.
    
    ### Related issues
    [Sonarcloud
    issue](https://sonarcloud.io/project/issues?resolved=false&severities=BLOCKER%2CCRITICAL%2CMAJOR%2CMINOR&sinceLeakPeriod=true&types=BUG&id=BenWibking_TwoMomentRad&open=AY5UChgLLdUsq9L5VHlt&tab=code)
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

src/Factory.H

commit c564770e25628c16f2cc36b5a5bce6c6db01fe93
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Mar 18 18:23:55 2024 -0400

    output 2D slice plotfiles (#562)
    
    ### Description
    Output 2D slices of the simulation as AMReX plotfiles. The
    implementation is adaped from PeleLMeX
    ([documentation](https://amrex-combustion.github.io/PeleLMeX/manual/html/LMeXControls.html#run-time-diagnostics)).
    
    It can be turned on for any variables (including derived variables) with
    runtime parameters, e.g.:
    ```
    quokka.diagnostics = slice_z           # Space-separated name(s) of diagnostics (arbitrary)
    quokka.slice_z.type = DiagFramePlane   # Diagnostic type (others may be added in the future)
    quokka.slice_z.file = slicez_plt       # Output file prefix (should end in "plt")
    quokka.slice_z.normal = 2              # Plane normal (0 == x, 1 == y, 2 == z)
    quokka.slice_z.center = 2.4688e20      # Coordinate in the normal direction
    quokka.slice_z.int    = 10             # Output interval (in number of coarse steps)
    quokka.slice_z.interpolation = Linear  # Interpolation type: Linear or Quadratic (default: Linear)
    
    # The problem must output these derived variable(s)
    derived_vars = temperature
    # List of variables to include in output
    quokka.slice_z.field_names = gasDensity gasInternalEnergy temperature
    ```
    
    ### Related issues
    Closes https://github.com/quokka-astro/quokka/issues/237.
    
    ### 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
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/CMakeLists.txt
src/DiagBase.H
src/DiagBase.cpp
src/DiagFilter.H
src/DiagFilter.cpp
src/DiagFramePlane.H
src/DiagFramePlane.cpp
src/Factory.H
src/HydroBlast3D/test_hydro3d_blast.cpp
src/PrimordialChem/CMakeLists.txt
src/ShockCloud/cloud.cpp
src/simulation.hpp
tests/ShockCloud_128.in
tests/ShockCloud_512.in
tests/blast_unigrid_128.in

commit a2acbb741a282be88b48ad52279196c3d421aaeb
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Mar 17 20:56:37 2024 -0400

    run CodeQL analysis with AMREX_SPACEDIM=3 (#568)
    
    ### Description
    This changes the CodeQL action so that it compiles Quokka with
    `AMREX_SPACEDIM=3`. This enables code analysis of 3D-only problems,
    which were not analyzed before.
    
    ### Related issues
    N/A
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

.github/workflows/codeql.yml

commit 3f390682cdc8c33689baa2817ae0157debf8a7e6
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Mar 17 20:50:55 2024 -0400

    Fix clang-tidy-review comment posting (#567)
    
    ### Description
    This updates the clang-tidy-review comment-posting action in order to
    fix https://github.com/ZedThree/clang-tidy-review/issues/117.
    
    ### Related issues
    https://github.com/ZedThree/clang-tidy-review/issues/117
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
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.github/workflows/clang-tidy-comments.yml

commit e22ce71ab858c68f639aa7ebd4da518db4404d2d
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Mar 17 19:05:55 2024 -0400

    compile warnings with AMREX_SPACEDIM=3 (#564)
    
    ### Description
    This adds `-DAMReX_SPACEDIM=3` to the CMake flags for the GitHub action
    that emits compiler warnings. This will allow us to catch compiler
    warnings for problems that are only built in 3D.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] I have added a link to any related issues see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

.github/workflows/warnings.yml
src/Cooling/test_cooling.cpp
src/HydroBlast3D/test_hydro3d_blast.cpp
src/HydroQuirk/test_quirk.cpp
src/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
src/PopIII/popiii.cpp
src/RadBeam/test_radiation_beam.cpp
src/RadShadow/test_radiation_shadow.cpp
src/RadTophat/test_radiation_tophat.cpp
src/RayleighTaylor2D/test_hydro2d_rt.cpp
src/RayleighTaylor3D/test_hydro3d_rt.cpp
src/ShockCloud/cloud.cpp
src/TurbDataReader.cpp

commit 91e52b0f64978b52a254a2d9eecd634fe4522f21
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Fri Mar 15 18:30:24 2024 +0000

    Bump extern/amrex from `689144d` to `2ecafcf` (#547)
    
    Bumps [extern/amrex](https://github.com/AMReX-Codes/amrex) from
    `689144d` to `2ecafcf`.
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/2ecafcff40132f56eb2b494e1a374684ff97117a"><code>2ecafcf</code></a>
    assert wavefront size (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3777">#3777</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/f924a1d380a3222dd2697cddc5753a5b7d6b4170"><code>f924a1d</code></a>
    Curl of Curl solver: Tweak restriction (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3765">#3765</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/c3e70604cb76cbc9a9d634a1de2a7e4ca92f4d1e"><code>c3e7060</code></a>
    Adjust debug info argument for HIP compiler (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3761">#3761</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/d8d4828b04df948972613983b18a9dd32c555cfa"><code>d8d4828</code></a>
    fixed bug in MLCurlCurL::xdoty() to prevent doing MPI sum twice. (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3774">#3774</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/1959b1f7026f69d352bc6a025380881578fe92ee"><code>1959b1f</code></a>
    Fix bug in AMREX_ASSUME (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3773">#3773</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/2230caa24c7d4bd07edb08b54e9368f9c73eae6e"><code>2230caa</code></a>
    Pure SoA: <code>NextID</code> as <code>Long</code> (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3772">#3772</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/3003edb3b5bd58ce5c460f09ac78c5ab8a6c4b92"><code>3003edb</code></a>
    GNU Make: set COMP_VERSION for hipcc and nvcc (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3771">#3771</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/4ebd5e0c0a709e215e8edfea09830261219dd568"><code>4ebd5e0</code></a>
    Make MFParallelFor safer from int overflow (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3768">#3768</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/398b20bddfa63ec1792de6c199c98dfb73be22c3"><code>398b20b</code></a>
    Implement portable assumptions with AMREX_ASSUME (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3770">#3770</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/99b47cb58a3c734ff9292226b952d7a79b351b72"><code>99b47cb</code></a>
    getParticleTileData: HostVector must be initialized during resize (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3769">#3769</a>)</li>
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    view</a></li>
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extern/amrex

commit 2494796a4327c2f198a7ae2c72aca78db8c7bd99
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Fri Mar 15 14:29:45 2024 -0400

    Bump extern/Microphysics from `348ca2f` to `e587300` (#546)
    
    Bumps [extern/Microphysics](https://github.com/psharda/Microphysics)
    from `348ca2f` to `e587300`.
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/e587300c654f9dc8a4be111a30b384dc269fab52"><code>e587300</code></a>
    some more cleaning of the runtime_parameters.py (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1448">#1448</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/8fc4cfeef47d78b056f7f1b3bcffb86a60f030b1"><code>8fc4cfe</code></a>
    template pivoting in the linear algebra (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1454">#1454</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/adb26008165aecf183466ac9b1a2be19861689ef"><code>adb2600</code></a>
    work on addressing some issues with the Jacobian scaling (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1479">#1479</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/48bf41c51a9da8dc9c654cfc4b9f461bf5b8e23b"><code>48bf41c</code></a>
    remove some unused includes in test_nse_interp (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1494">#1494</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/f336cab4e612f032a60042e503dc571bfc38a182"><code>f336cab</code></a>
    create a linear algebra unit test (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1493">#1493</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/9a8c260b7af05cf09478d589e04f3c60f53e1ce2"><code>9a8c260</code></a>
    clean up some unused vars in unit tests (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1492">#1492</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/348dad9c7326fe14e9becec2ec5cd0584d20bee0"><code>348dad9</code></a>
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    <li><a
    href="https://github.com/psharda/Microphysics/commit/86807d6ba1bb4bc731cb7d7efb9518d56d6b8969"><code>86807d6</code></a>
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extern/Microphysics

commit bbf934a551e490da802257c89c999dfc30ce12f9
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Fri Mar 15 13:26:53 2024 +1100

    Defined advecting pulse test in dynamic diffusion regime (#551)
    
    1. Defined advecting pulse test in the dynamic diffusion regime.
    2. Use a new odd-even correction: S_corr = (1/tau, 1, 1, 1) at high tau
    and (1, 1, 1, 1) otherwise.
    3. Increased error_tol in some tests as we use a new odd-even correction
    
    ### Related issues
    None.
    
    ### 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:_
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src/CMakeLists.txt
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.hpp
src/RadPulse/test_radiation_pulse.cpp
src/RadhydroPulse/test_radhydro_pulse.cpp
src/RadhydroPulse/test_radhydro_pulse.hpp
src/RadhydroPulseDyn/CMakeLists.txt
src/RadhydroPulseDyn/test_radhydro_pulse_dyn.cpp
src/RadhydroPulseDyn/test_radhydro_pulse_dyn.hpp
src/radiation_system.hpp
tests/RadhydroPulseDyn.in

commit 66d3b80a1fc66631c54dc7525245ff31dc5319dd
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Mar 13 08:33:51 2024 -0400

    fix final checkpoint file write (#558)
    
    ### Description
    This fixes the checkpoint/restart failure identified in
    https://github.com/quokka-astro/quokka/issues/554 and adds a GitHub
    action to test that checkpoint/restart works correctly for the
    HydroBlast3D test.
    
    ### Related issues
    Fixes https://github.com/quokka-astro/quokka/issues/554.
    
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.github/workflows/checkpoint-restart.yml
src/simulation.hpp
tests/blast_32.in
tests/checkpoint_restart_test.sh

commit fcde1aa11205ed64365e42ce7e084a9964aa7e9f
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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    Bump extern/openPMD-api from `d9fce66` to `c2e0e83` (#549)
    
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commit 30b2b7b345c730cf50db847c3d99a2886b746cf6
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Thu Feb 29 22:22:34 2024 -0500

    Bump extern/fmt from `6321a97` to `ae1e93d` (#545)
    
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    href="https://redirect.github.com/fmtlib/fmt/issues/3856">#3856</a>)</li>
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extern/fmt

commit 401ad01824f74f430567e345b1d1ad1cee91e413
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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    Bump extern/yaml-cpp from `4afd53b` to `76dc671` (#548)
    
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extern/yaml-cpp

commit 6aca86475ce95a8e9cec545e01dfae1edd52639c
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Sat Feb 17 16:06:05 2024 +1100

    Define the grey-radiation advecting pulse test (#538)
    
    ### Description
    Define the advecting pulse test (Krumholz2017) under grey-radiation
    approximation. The setup of the test is exactly the same as Sec. 4.1.6
    of CASTRO III
    ([Zhang+2013](https://ui.adsabs.harvard.edu/abs/2013ApJS..204....7Z/abstract)).
    
    ### Related issues
    This PR corrected the formula of the v/c terms in the radiation flux
    update. The correct formula for the space-like component of the
    radiation four-force to order $\beta$ is
    
    ```math
    -\boldsymbol{G} =-\rho \kappa_F \frac{\boldsymbol{F}_r}{c} + \rho \kappa_P\left(\frac{4 \pi B}{c} - E\right) \frac{\boldsymbol{v}}{c}+\rho \kappa_F \left (\frac{\boldsymbol{v}}{c} E + \frac{\boldsymbol{v} :\boldsymbol{P}_r}{c} \right).
    ```
    
    instead of Eq. (8) of the Quokka paper, i.e.
    
    ```math
    -\boldsymbol{G} =-\rho \kappa_F \frac{\boldsymbol{F}_r}{c} + \rho \kappa_P\left(\frac{4 \pi B}{c} \right) \frac{\boldsymbol{v}}{c}+\rho \kappa_F  \frac{\boldsymbol{v} :\boldsymbol{P}_r}{c} .
    ```
    
    
    ### Checklist
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src/CMakeLists.txt
src/RadhydroPulseGrey/CMakeLists.txt
src/RadhydroPulseGrey/test_radhydro_pulse_grey.cpp
src/RadhydroPulseGrey/test_radhydro_pulse_grey.hpp
src/radiation_system.hpp

commit 3db769b126d2e8d6e0e54635bda5d314a26e43fc
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Fri Feb 16 09:17:05 2024 +1100

    Newton iteration on new basis (Egas, R / tau0) (#535)
    
    ### Description
    Use a new basis in the Newton-Raphson iteration for the radiation-matter
    exchange. Instead of (Egas, Erad), we use the new basis (Egas, D), where
    D = R / tau0 and tau0 = c dt rho kappa^(t). This makes the iteration
    converge SO much faster. The code is also much simpler. The basis (Egas,
    R) may work equally well, but the 1/tau0 factor scales the second
    coordinate to the same scale as the first coordinate and should speed up
    the convergence rate and improve stability.
    
    The Jacobian of $F$ with respect to (Egas, R) is
    
    ```math
    \begin{aligned}
        \frac{\partial F_G}{\partial E_g} &= 1 \\
        \frac{\partial F_G}{\partial R_i} &= \frac{c}{\hat{c}} \\
        \frac{\partial F_{R,i}}{\partial E_g} &= \frac{\partial E_{r,i}}{\partial E_g} |_{R_i = {\rm const.}} = \frac{1}{\hat{c}} \frac{1}{C_v} \frac{\partial}{\partial T} \left( \frac{\kappa_{P,i}}{\kappa_{E,i}} 4 \pi B_i \right) \\
        \frac{\partial F_{R,i}}{\partial R_i} &= \frac{\partial E_{r,i}}{\partial R_i}|_{T = {\rm const.}} - 1 = - \frac{1}{\hat{c} \Delta t \rho \kappa_{E,i}} - 1
    \end{aligned}
    ```
    
    For (Egas, D), simply multiple the second and fourth lines by
    $\tau_i^{(t)}$.
    
    If we assume $\kappa_{P, i} / \kappa_{E, i} = $ const., we can take this
    term out of the derivative, and we don't need to compute the derivative
    of opacity with respect to temperature at all.
    
    ### Related issues
    Should solve most 'Newton iteration fail to converge' error, even when
    error_tol = 1e-13. No extra break condition is required other than the
    one used in the original version of QUOKKA.
    
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src/radiation_system.hpp
src/valarray.hpp

commit 2d863d655ec1e1f684f55ea745021b9c97a03c60
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Feb 9 15:07:46 2024 -0500

    fix clang-tidy warnings (#468)
    
    ### Description
    This fixes many `clang-tidy` warnings thoughout the code. Most of them
    had to do with unnecessary header includes or const issues. No outputs
    should change at the bitwise level.
    
    ### Related issues
    N/A
    
    ### Checklist
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    completed. Denote completed tasks with an `x` inside the square brackets
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extern/Microphysics
src/AdvectionSimulation.hpp
src/Chemistry.hpp
src/CloudyCooling.cpp
src/CloudyCooling.hpp
src/EOS.hpp
src/FCQuantities/test_fc_quantities.cpp
src/GrackleDataReader.cpp
src/GrackleDataReader.hpp
src/LLF.hpp
src/NSCBC/channel.cpp
src/NSCBC/vortex.cpp
src/NSCBC_inflow.hpp
src/NSCBC_outflow.hpp
src/ODEIntegrate.hpp
src/RadhydroSimulation.hpp
src/ShockCloud/test_cloudy.cpp
src/fextract.cpp
src/fextract.hpp
src/grid.hpp
src/hydro_system.hpp
src/hyperbolic_system.hpp
src/interpolate.cpp
src/interpolate.hpp
src/linear_advection.hpp
src/mhd_system.hpp
src/planck_integral.hpp
src/radiation_system.hpp
src/simulation.hpp
src/valarray.hpp

commit a16b88fb0f810691d9bf3421671d88c50fee0cf7
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Feb 7 17:51:52 2024 -0500

    fix copies to rank zero for correctness tests (#531)
    
    ### Description
    This fixes parallel copies of particles and/or MultiFabs to rank zero so
    that they actually work. In this case, constructing a
    `amrex::DistributionMapping` must be done by explicitly setting it equal
    to `{0}`.
    
    This is used when testing the correctness of the results for the
    `HydroRichtmyerMeshkov` and `BinaryOrbitCIC` tests.
    
    Thanks to Andrew Myers for the fix.
    
    ### Related issues
    N/A
    
    ### Checklist
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    completed. Denote completed tasks with an `x` inside the square brackets
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src/BinaryOrbitCIC/binary_orbit.cpp
src/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp

commit edc1dbcf2e22ae47dc2d78aa9b0b6d0966671bb6
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Mon Feb 5 22:46:03 2024 +0100

    Fix bug in perturbation.py (#525)
    
    ### Description
    Fix the bug in perturbation.py to compare `f.solenoidal` to both `None`
    and `"None"`
    
    ### Related issues
    Pointed out by sonarcloud
    
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src/perturbation.py

commit 93686aaf9c84f4babf5a6c14310315cdc4b5b18a
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Mon Feb 5 18:43:43 2024 +0100

    PopIII Simulation (#368)
    
    This PR will add a PopIII simulation to quokka. It will only test that
    the simulation starts successfully and runs for a few timesteps - it's
    not meant to be a _production_ simulation.
    
    ---------
    
    Co-authored-by: Piyush Sharda <psharda@RSAA-043527.local>
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.github/workflows/clang-tidy.yml
.pre-commit-config.yaml
src/CMakeLists.txt
src/Chemistry.hpp
src/PopIII/CMakeLists.txt
src/PopIII/ascent_actions.yaml
src/PopIII/popiii.cpp
src/PopIII/popiii.hpp
src/RadhydroSimulation.hpp
src/StarCluster/CMakeLists.txt
src/TurbDataReader.cpp
src/TurbDataReader.hpp
src/perturbation.py
tests/PopIII.in

commit ae42169d912724ee3642b79ac1d493964a87e801
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Feb 4 05:30:39 2024 -0500

    change projection plotfile names (#523)
    
    ### Description
    This changes the filename for projection plotfiles to `proj_x_plt00000`,
    `proj_y_plt00001`, etc.
    
    ### Related issues
    Fixes https://github.com/quokka-astro/quokka/issues/521.
    
    ### 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:_
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    code.
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    `/azp run`.
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src/simulation.hpp

commit 185770745bc365a1c5953c947ac11ecb3f393fc1
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Feb 3 20:24:46 2024 -0500

    Fix RadShadow test problem (#476)
    
    ### Description
    Updates `RadShadow` to use `Physics_Traits`. This test problem had not
    been updated to use `Physics_Traits`, so the variable indexing was wrong
    and caused it to crash.
    
    Now it crashes at runtime due to the Newton-Raphson iteration failing to
    converge about ~40% of the way through the simulation.
    
    ### Related issues
    N/A
    
    ### Checklist
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    completed. Denote completed tasks with an `x` inside the square brackets
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src/RadShadow/test_radiation_shadow.cpp

commit 3455fc8ef2ce93033df9d7be11651e427a1f49a1
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Sat Feb 3 07:54:24 2024 +1100

    Multigroup advecting pulse test (#486)
    
    ### Description
    Define the multigroup, variable opacity advecting pulse test. See Sec.
    4.1.6 of the CASTRO III paper (Zhang et al. 2013). The code perfectly
    reproduces Figure 6 of the paper. We use the original Newton-Raphson
    method on the (Egas, Erad) basis.
    
    ### Related issues
    N/A
    
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    code.
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.ci/azure-pipelines-aarch64-debug.yml
src/CMakeLists.txt
src/RadhydroPulse/CMakeLists.txt
src/RadhydroPulseMG/CMakeLists.txt
src/RadhydroPulseMG/test_radhydro_pulse_MG.cpp
src/RadhydroPulseMG/test_radhydro_pulse_MG.hpp
src/RadhydroShockMultigroup/test_radhydro_shock_multigroup.cpp
src/planck_integral.hpp
src/radiation_system.hpp

commit 4e15bbc51b442a9462f3d98ce70f3a384b789014
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Thu Feb 1 19:27:52 2024 -0500

    Bump extern/Microphysics from `7de2124` to `fbeddb3` (#517)
    
    Bumps [extern/Microphysics](https://github.com/psharda/Microphysics)
    from `7de2124` to `fbeddb3`.
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/fbeddb367c6ef7d71052e23c20deda164243e643"><code>fbeddb3</code></a>
    update pynucastro nets to have bion/mion constexpr (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1437">#1437</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/3700590cd0dfb4c8e85c0814f97f69d38534c303"><code>3700590</code></a>
    constexpr some helm EOS table parameters (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1440">#1440</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/6fceeecf5fffcb28334790159cfaee93852be307"><code>6fceeec</code></a>
    update tols for Urca test_react so it runs (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1438">#1438</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/6dc51ad9e22e3c6e8ae2d26e6c84e1bca4819a8c"><code>6dc51ad</code></a>
    fix NSE+SDC when we are doing drive_initial_convection (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1431">#1431</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/d99cee07ad28935a9d061d685bed08afc76ca0a4"><code>d99cee0</code></a>
    update github actions to latest versions (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1429">#1429</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/a0deaaed6397a83598f1096bbe414e828917f169"><code>a0deaae</code></a>
    add struct support for runtime_parameters.py (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1422">#1422</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/9d0655b75c2d7c0690fe637f8491fa572227a1dc"><code>9d0655b</code></a>
    update for 24.01</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/3185974142008f9504ebeca06dd9d37f3ff4dddc"><code>3185974</code></a>
    optional quantum correction terms for chabrier1998 (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1428">#1428</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/a83fe0040339307ee0a358b1c403a076a4f9eba6"><code>a83fe00</code></a>
    [WIP] fix powi script and bug in chugunov2009 screening (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1432">#1432</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/32fa759848dab6e7314ed69ce9c04ba8de11b858"><code>32fa759</code></a>
    Replace std::pow with integer powers to amrex::Math::powi (<a
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extern/Microphysics

commit 16395247a9eb6330f6ed9e619ac8ef696475e7d7
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Thu Feb 1 17:01:08 2024 +0000

    Bump extern/amrex from `b96b731` to `689144d` (#519)
    
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    `b96b731` to `689144d`.
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    Update AoS Restrict (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3738">#3738</a>)</li>
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    href="https://github.com/AMReX-Codes/amrex/commit/d861bdff6ab7b31ada277f87c3b4a57b5883a0b0"><code>d861bdf</code></a>
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    Particle Copy Plan: Default Vals (<a
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extern/amrex

commit d96715f1e9318e412c0d2aac9e23958ea2a7112d
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Thu Feb 1 12:00:26 2024 -0500

    Bump extern/yaml-cpp from `94710bb` to `4afd53b` (#516)
    
    Bumps [extern/yaml-cpp](https://github.com/jbeder/yaml-cpp) from
    `94710bb` to `4afd53b`.
    <details>
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    <li><a
    href="https://github.com/jbeder/yaml-cpp/commit/4afd53b0d3140ba2eb85816bfced209cf37ff096"><code>4afd53b</code></a>
    Bump the github-actions group with 1 update</li>
    <li><a
    href="https://github.com/jbeder/yaml-cpp/commit/96f5c887f373ac483844c51cfc9a3621002314f0"><code>96f5c88</code></a>
    assign fallback value</li>
    <li><a
    href="https://github.com/jbeder/yaml-cpp/commit/c67d701ad81da65a576efd3341634f8cd3892c9b"><code>c67d701</code></a>
    Fix indentation of empty sequences and add test</li>
    <li><a
    href="https://github.com/jbeder/yaml-cpp/commit/9eb1142900096b9115ba2db2a521c76c117cacd9"><code>9eb1142</code></a>
    Fix GIT_TAG field in cmake integration example</li>
    <li><a
    href="https://github.com/jbeder/yaml-cpp/commit/c28295bda489422e4b5928aa0b978eb51dbdcbb1"><code>c28295b</code></a>
    Add CMake integration example</li>
    <li>See full diff in <a
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extern/yaml-cpp

commit 2479420183b2c756d89c2b14eccc293fb3c032e0
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Thu Feb 1 12:00:14 2024 -0500

    Bump extern/fmt from `a5bacf3` to `6321a97` (#518)
    
    Bumps [extern/fmt](https://github.com/fmtlib/fmt) from `a5bacf3` to
    `6321a97`.
    <details>
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    <li><a
    href="https://github.com/fmtlib/fmt/commit/6321a97d6bd1096274b4e1b22f6210cc9031cab4"><code>6321a97</code></a>
    Simplify color formatting</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/4b6b32f3884b41c9e13467bf9b0e3022a4d84f1e"><code>4b6b32f</code></a>
    Deprecate wide stream function</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/1b54ba4b9d9f722302343cf409ae7a7b3fe91553"><code>1b54ba4</code></a>
    Fix UB in format_arg_store implementation. (<a
    href="https://redirect.github.com/fmtlib/fmt/issues/3833">#3833</a>)</li>
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    href="https://github.com/fmtlib/fmt/commit/71a4a8d47999e95f5e460eaf8cec894f60354a13"><code>71a4a8d</code></a>
    Really fix MSVC warning about &lt;bit&gt; only being available in C++20.
    (<a
    href="https://redirect.github.com/fmtlib/fmt/issues/3832">#3832</a>)</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/8e62172ab6742c0e399d906456f54c927ebd4f3a"><code>8e62172</code></a>
    Fix a warning</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/28afff363c8ff21f80f235abaab1702394a326fb"><code>28afff3</code></a>
    Improve buffering</li>
    <li><a
    href="https://github.com/fmtlib/fmt/commit/af44c29744e623a6583ba5d05ad5140c6c751f58"><code>af44c29</code></a>
    Separate buffer initialization from flush</li>
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    Minor cleanup</li>
    <li><a
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    Add glibc stream support</li>
    <li><a
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extern/fmt

commit d03f52ad638516d77b4a4de02ea767dd842a9104
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Thu Feb 1 12:00:01 2024 -0500

    Bump extern/openPMD-api from `a3fe9b7` to `d9fce66` (#520)
    
    Bumps [extern/openPMD-api](https://github.com/openPMD/openPMD-api) from
    `a3fe9b7` to `d9fce66`.
    <details>
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    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/d9fce66ddf256beb527c3d3e98e212725dae7f47"><code>d9fce66</code></a>
    Don't allow Container insertion in READ_LINEAR (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1590">#1590</a>)</li>
    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/8faadde42af0bfc56304e020717de22b07c70336"><code>8faadde</code></a>
    Initial support for HDF5 subfiling (<a
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    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/17e757f9f0d0ad4cf006d422636d660efedf30df"><code>17e757f</code></a>
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    ADIOS2...</li>
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    Fix: Strings with a single char in Python (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1585">#1585</a>)</li>
    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/d5524ec16a170173d7b19e72c6b4b4fdb6caa022"><code>d5524ec</code></a>
    Fix availableChunks for READ_LINEAR in ADIOS2 (<a
    href="https://redirect.github.com/openPMD/openPMD-api/issues/1586">#1586</a>)</li>
    <li><a
    href="https://github.com/openPMD/openPMD-api/commit/7bb2948bb9ce0473bae9b6c8cc776c1285e35a8f"><code>7bb2948</code></a>
    Fix docstring for MyPath (<a
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    <li>See full diff in <a
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extern/openPMD-api

commit b4222b7e92d41231fc115e0298c75faf7d6300ca
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Feb 1 03:53:48 2024 -0500

    re-enable CodeQL (#514)
    
    ### Description
    This re-enables CodeQL static analysis based on the settings used by
    AMReX.
    
    ### Related issues
    Closes https://github.com/quokka-astro/quokka/issues/508.
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [ ] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: Piyush Sharda <34922596+psharda@users.noreply.github.com>

.github/workflows/codeql.yml
.github/workflows/codeql/codeql-config.yml

commit c0344d5e07a19dcce207ddf29be2a06898c99598
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Feb 1 03:53:08 2024 -0500

    add HWASAN CI run (#510)
    
    ### Description
    This adds a CI run on Oracle Cloud Infrastructure (with Ampere aarch64
    processors) with HWASAN enabled.
    
    Processor info:
    ```
    Architecture:           aarch64
      CPU op-mode(s):       32-bit, 64-bit
      Byte Order:           Little Endian
    CPU(s):                 4
      On-line CPU(s) list:  0-3
    Vendor ID:              ARM
      Model name:           Neoverse-N1
        Model:              1
        Thread(s) per core: 1
        Core(s) per socket: 4
        Socket(s):          1
        Stepping:           r3p1
        BogoMIPS:           50.00
        Flags:              fp asimd evtstrm aes pmull sha1 sha2 crc32 atomics fphp asimdhp cpuid asimdrdm lrcpc dcpop asimddp ssbs
    ```
    
    ### Related issues
    Closes https://github.com/quokka-astro/quokka/issues/509.
    
    ### Checklist
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    completed. Denote completed tasks with an `x` inside the square brackets
    `[ ]` in the Markdown source below:_
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    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.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [ ] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: Piyush Sharda <34922596+psharda@users.noreply.github.com>

.ci/azure-pipelines-aarch64-hwasan.yml
.ci/azure-pipelines-asan.yml
.ci/azure-pipelines-build-llvm.yml
.ci/azure-pipelines-debug.yml
CMakeLists.txt
src/CMakeLists.txt

commit 11d743650c45629029aa86b30d30fc7dff79d023
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Jan 31 14:33:59 2024 -0500

    update macOS CI to use M1 runner (#513)
    
    ### Description
    macOS GitHub actions can now run on M1
    (https://github.blog/changelog/2024-01-30-github-actions-introducing-the-new-m1-macos-runner-available-to-open-source/),
    so we update it to do so.
    
    ### Related issues
    N/A
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

.github/workflows/cmake-macos.yml

commit 089ba268926590db08c30b5242941b7e3de99b21
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Thu Feb 1 03:10:31 2024 +1100

    Make ComputeRadPressure return F and S (#512)
    
    ### Description
    Make ComputeRadPressure in radiation_system.hpp return F and S instead
    of modifying them at place.
    
    ### 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).
    - [ ] I have added a link to any related issues see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
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    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/radiation_system.hpp

commit 4f319f8919ab52baed5f02c78862659e179823d4
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Jan 29 03:45:16 2024 +0000

    Bump ZedThree/clang-tidy-review from 0.17.0 to 0.17.1 (#511)
    
    Bumps
    [ZedThree/clang-tidy-review](https://github.com/zedthree/clang-tidy-review)
    from 0.17.0 to 0.17.1.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
    href="https://github.com/zedthree/clang-tidy-review/releases">ZedThree/clang-tidy-review's
    releases</a>.</em></p>
    <blockquote>
    <h2>v0.17.1</h2>
    <h2>What's Changed</h2>
    <ul>
    <li>auth: Allow private key for apps to be base64 by <a
    href="https://github.com/bwrsandman"><code>@​bwrsandman</code></a> in <a
    href="https://redirect.github.com/ZedThree/clang-tidy-review/pull/112">ZedThree/clang-tidy-review#112</a></li>
    <li>Use PyGithub to reuse auth headers to do requests by <a
    href="https://github.com/bwrsandman"><code>@​bwrsandman</code></a> in <a
    href="https://redirect.github.com/ZedThree/clang-tidy-review/pull/113">ZedThree/clang-tidy-review#113</a></li>
    </ul>
    <p><strong>Full Changelog</strong>: <a
    href="https://github.com/ZedThree/clang-tidy-review/compare/v0.17.0...v0.17.1">https://github.com/ZedThree/clang-tidy-review/compare/v0.17.0...v0.17.1</a></p>
    </blockquote>
    </details>
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/4923dc7cbb13a291cecc8507a89f70ed25ac9ce9"><code>4923dc7</code></a>
    Merge pull request <a
    href="https://redirect.github.com/zedthree/clang-tidy-review/issues/113">#113</a>
    from bwrsandman/authenticated-requests</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/baadf424d2af3b418e4c7de25989570fded55e34"><code>baadf42</code></a>
    Use set difference to cull comments</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/40e754e569e9aad0183712b96b3da37de04a961f"><code>40e754e</code></a>
    Reuse auth headers to do requests</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/f5273417752b89feb2903b47a72352b5d2ac4b41"><code>f527341</code></a>
    Merge pull request <a
    href="https://redirect.github.com/zedthree/clang-tidy-review/issues/112">#112</a>
    from bwrsandman/base64-private-key</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/d51789bde871d26e75c895ef69b3c3b11e39b38e"><code>d51789b</code></a>
    auth: Allow private key for apps to be base64</li>
    <li>See full diff in <a
    href="https://github.com/zedthree/clang-tidy-review/compare/v0.17.0...v0.17.1">compare
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commit 97cbab3ed80f75fa73750869ff82c7c870d092ec
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Jan 24 22:31:53 2024 -0500

    add CIC particles (#502)
    
    ### Description
    This adds cloud-in-cell particles that interact with the gravitational
    field and are integrated in time using a kick-drift-kick leapfrog
    assuming a global simulation timestep (i.e., no AMR subcycling).
    
    ### Related issues
    Closes https://github.com/quokka-astro/quokka/issues/491.
    
    ### 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 see (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.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
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src/AdvectionSimulation.hpp
src/BinaryOrbitCIC/CMakeLists.txt
src/BinaryOrbitCIC/binary_orbit.cpp
src/BinaryOrbitCIC/binary_orbit.hpp
src/BinaryOrbitCIC/particle_orbit_plot.py
src/CICParticles.hpp
src/CMakeLists.txt
src/RadhydroSimulation.hpp
src/SphericalCollapse/spherical_collapse.cpp
src/simulation.hpp
tests/BinaryOrbit.in
tests/BinaryOrbit_particles.txt
tests/SphericalCollapse.in

commit 8b023955528f28486b6cda1c7fb482ad97758a6d
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Jan 22 02:52:19 2024 +0000

    Bump actions/cache from 3 to 4 (#503)
    
    Bumps [actions/cache](https://github.com/actions/cache) from 3 to 4.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
    href="https://github.com/actions/cache/releases">actions/cache's
    releases</a>.</em></p>
    <blockquote>
    <h2>v4.0.0</h2>
    <h2>What's Changed</h2>
    <ul>
    <li>Update action to node20 by <a
    href="https://github.com/takost"><code>@​takost</code></a> in <a
    href="https://redirect.github.com/actions/cache/pull/1284">actions/cache#1284</a></li>
    <li>feat: save-always flag by <a
    href="https://github.com/to-s"><code>@​to-s</code></a> in <a
    href="https://redirect.github.com/actions/cache/pull/1242">actions/cache#1242</a></li>
    </ul>
    <h2>New Contributors</h2>
    <ul>
    <li><a href="https://github.com/takost"><code>@​takost</code></a> made
    their first contribution in <a
    href="https://redirect.github.com/actions/cache/pull/1284">actions/cache#1284</a></li>
    <li><a href="https://github.com/to-s"><code>@​to-s</code></a> made their
    first contribution in <a
    href="https://redirect.github.com/actions/cache/pull/1242">actions/cache#1242</a></li>
    </ul>
    <p><strong>Full Changelog</strong>: <a
    href="https://github.com/actions/cache/compare/v3...v4.0.0">https://github.com/actions/cache/compare/v3...v4.0.0</a></p>
    <h2>v3.3.3</h2>
    <h2>What's Changed</h2>
    <ul>
    <li>Cache v3.3.3 by <a
    href="https://github.com/robherley"><code>@​robherley</code></a> in <a
    href="https://redirect.github.com/actions/cache/pull/1302">actions/cache#1302</a></li>
    </ul>
    <h2>New Contributors</h2>
    <ul>
    <li><a href="https://github.com/robherley"><code>@​robherley</code></a>
    made their first contribution in <a
    href="https://redirect.github.com/actions/cache/pull/1302">actions/cache#1302</a></li>
    </ul>
    <p><strong>Full Changelog</strong>: <a
    href="https://github.com/actions/cache/compare/v3...v3.3.3">https://github.com/actions/cache/compare/v3...v3.3.3</a></p>
    <h2>v3.3.2</h2>
    <h2>What's Changed</h2>
    <ul>
    <li>Fixed readme with new segment timeout values by <a
    href="https://github.com/kotewar"><code>@​kotewar</code></a> in <a
    href="https://redirect.github.com/actions/cache/pull/1133">actions/cache#1133</a></li>
    <li>Readme fixes by <a
    href="https://github.com/kotewar"><code>@​kotewar</code></a> in <a
    href="https://redirect.github.com/actions/cache/pull/1134">actions/cache#1134</a></li>
    <li>Updated description of the lookup-only input for main action by <a
    href="https://github.com/kotewar"><code>@​kotewar</code></a> in <a
    href="https://redirect.github.com/actions/cache/pull/1130">actions/cache#1130</a></li>
    <li>Change two new actions mention as quoted text by <a
    href="https://github.com/bishal-pdMSFT"><code>@​bishal-pdMSFT</code></a>
    in <a
    href="https://redirect.github.com/actions/cache/pull/1131">actions/cache#1131</a></li>
    <li>Update Cross-OS Caching tips by <a
    href="https://github.com/pdotl"><code>@​pdotl</code></a> in <a
    href="https://redirect.github.com/actions/cache/pull/1122">actions/cache#1122</a></li>
    <li>Bazel example (Take <a
    href="https://redirect.github.com/actions/cache/issues/2">#2</a>️⃣) by
    <a href="https://github.com/vorburger"><code>@​vorburger</code></a> in
    <a
    href="https://redirect.github.com/actions/cache/pull/1132">actions/cache#1132</a></li>
    <li>Remove actions to add new PRs and issues to a project board by <a
    href="https://github.com/jorendorff"><code>@​jorendorff</code></a> in <a
    href="https://redirect.github.com/actions/cache/pull/1187">actions/cache#1187</a></li>
    <li>Consume latest toolkit and fix dangling promise bug by <a
    href="https://github.com/chkimes"><code>@​chkimes</code></a> in <a
    href="https://redirect.github.com/actions/cache/pull/1217">actions/cache#1217</a></li>
    <li>Bump action version to 3.3.2 by <a
    href="https://github.com/bethanyj28"><code>@​bethanyj28</code></a> in <a
    href="https://redirect.github.com/actions/cache/pull/1236">actions/cache#1236</a></li>
    </ul>
    <h2>New Contributors</h2>
    <ul>
    <li><a href="https://github.com/vorburger"><code>@​vorburger</code></a>
    made their first contribution in <a
    href="https://redirect.github.com/actions/cache/pull/1132">actions/cache#1132</a></li>
    <li><a
    href="https://github.com/jorendorff"><code>@​jorendorff</code></a> made
    their first contribution in <a
    href="https://redirect.github.com/actions/cache/pull/1187">actions/cache#1187</a></li>
    <li><a href="https://github.com/chkimes"><code>@​chkimes</code></a> made
    their first contribution in <a
    href="https://redirect.github.com/actions/cache/pull/1217">actions/cache#1217</a></li>
    <li><a
    href="https://github.com/bethanyj28"><code>@​bethanyj28</code></a> made
    their first contribution in <a
    href="https://redirect.github.com/actions/cache/pull/1236">actions/cache#1236</a></li>
    </ul>
    <p><strong>Full Changelog</strong>: <a
    href="https://github.com/actions/cache/compare/v3...v3.3.2">https://github.com/actions/cache/compare/v3...v3.3.2</a></p>
    <h2>v3.3.1</h2>
    <h2>What's Changed</h2>
    <ul>
    <li>Reduced download segment size to 128 MB and timeout to 10 minutes by
    <a href="https://github.com/kotewar"><code>@​kotewar</code></a> in <a
    href="https://redirect.github.com/actions/cache/pull/1129">actions/cache#1129</a></li>
    </ul>
    <p><strong>Full Changelog</strong>: <a
    href="https://github.com/actions/cache/compare/v3...v3.3.1">https://github.com/actions/cache/compare/v3...v3.3.1</a></p>
    <h2>v3.3.0</h2>
    <h2>What's Changed</h2>
    <ul>
    <li>Bug: Permission is missing in cache delete example by <a
    href="https://github.com/kotokaze"><code>@​kotokaze</code></a> in <a
    href="https://redirect.github.com/actions/cache/pull/1123">actions/cache#1123</a></li>
    </ul>
    <!-- raw HTML omitted -->
    </blockquote>
    <p>... (truncated)</p>
    </details>
    <details>
    <summary>Changelog</summary>
    <p><em>Sourced from <a
    href="https://github.com/actions/cache/blob/main/RELEASES.md">actions/cache's
    changelog</a>.</em></p>
    <blockquote>
    <h1>Releases</h1>
    <h3>3.0.0</h3>
    <ul>
    <li>Updated minimum runner version support from node 12 -&gt; node
    16</li>
    </ul>
    <h3>3.0.1</h3>
    <ul>
    <li>Added support for caching from GHES 3.5.</li>
    <li>Fixed download issue for files &gt; 2GB during restore.</li>
    </ul>
    <h3>3.0.2</h3>
    <ul>
    <li>Added support for dynamic cache size cap on GHES.</li>
    </ul>
    <h3>3.0.3</h3>
    <ul>
    <li>Fixed avoiding empty cache save when no files are available for
    caching. (<a
    href="https://redirect.github.com/actions/cache/issues/624">issue</a>)</li>
    </ul>
    <h3>3.0.4</h3>
    <ul>
    <li>Fixed tar creation error while trying to create tar with path as
    <code>~/</code> home folder on <code>ubuntu-latest</code>. (<a
    href="https://redirect.github.com/actions/cache/issues/689">issue</a>)</li>
    </ul>
    <h3>3.0.5</h3>
    <ul>
    <li>Removed error handling by consuming actions/cache 3.0 toolkit, Now
    cache server error handling will be done by toolkit. (<a
    href="https://redirect.github.com/actions/cache/pull/834">PR</a>)</li>
    </ul>
    <h3>3.0.6</h3>
    <ul>
    <li>Fixed <a
    href="https://redirect.github.com/actions/cache/issues/809">#809</a> -
    zstd -d: no such file or directory error</li>
    <li>Fixed <a
    href="https://redirect.github.com/actions/cache/issues/833">#833</a> -
    cache doesn't work with github workspace directory</li>
    </ul>
    <h3>3.0.7</h3>
    <ul>
    <li>Fixed <a
    href="https://redirect.github.com/actions/cache/issues/810">#810</a> -
    download stuck issue. A new timeout is introduced in the download
    process to abort the download if it gets stuck and doesn't finish within
    an hour.</li>
    </ul>
    <h3>3.0.8</h3>
    <ul>
    <li>Fix zstd not working for windows on gnu tar in issues <a
    href="https://redirect.github.com/actions/cache/issues/888">#888</a> and
    <a
    href="https://redirect.github.com/actions/cache/issues/891">#891</a>.</li>
    <li>Allowing users to provide a custom timeout as input for aborting
    download of a cache segment using an environment variable
    <code>SEGMENT_DOWNLOAD_TIMEOUT_MINS</code>. Default is 60 minutes.</li>
    </ul>
    <h3>3.0.9</h3>
    <ul>
    <li>Enhanced the warning message for cache unavailablity in case of
    GHES.</li>
    </ul>
    <h3>3.0.10</h3>
    <ul>
    <li>Fix a bug with sorting inputs.</li>
    <li>Update definition for restore-keys in README.md</li>
    </ul>
    <!-- raw HTML omitted -->
    </blockquote>
    <p>... (truncated)</p>
    </details>
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/actions/cache/commit/13aacd865c20de90d75de3b17ebe84f7a17d57d2"><code>13aacd8</code></a>
    Merge pull request <a
    href="https://redirect.github.com/actions/cache/issues/1242">#1242</a>
    from to-s/main</li>
    <li><a
    href="https://github.com/actions/cache/commit/53b35c543921fe2e8b288765ff817de9de8d906f"><code>53b35c5</code></a>
    Merge branch 'main' into main</li>
    <li><a
    href="https://github.com/actions/cache/commit/65b8989fab3bb394817bdb845a453dff480c2b51"><code>65b8989</code></a>
    Merge pull request <a
    href="https://redirect.github.com/actions/cache/issues/1284">#1284</a>
    from takost/update-to-node-20</li>
    <li><a
    href="https://github.com/actions/cache/commit/d0be34d54485f31ca2ccbe66e6ea3d96544a807b"><code>d0be34d</code></a>
    Fix dist</li>
    <li><a
    href="https://github.com/actions/cache/commit/66cf064d47313d2cccf392d01bd10925da2bd072"><code>66cf064</code></a>
    Merge branch 'main' into update-to-node-20</li>
    <li><a
    href="https://github.com/actions/cache/commit/1326563738ddb735c5f2ce85cba8c79f33b728cd"><code>1326563</code></a>
    Merge branch 'main' into main</li>
    <li><a
    href="https://github.com/actions/cache/commit/e71876755e268d6cc25a5d3e3c46ae447e35290a"><code>e718767</code></a>
    Fix format</li>
    <li><a
    href="https://github.com/actions/cache/commit/01229828ffa049a8dee4db27bcb23ed33f2b451f"><code>0122982</code></a>
    Apply workaround for earlyExit</li>
    <li><a
    href="https://github.com/actions/cache/commit/3185ecfd6135856ca6d904ae032cff4f39b8b365"><code>3185ecf</code></a>
    Update &quot;only-&quot; actions to node20</li>
    <li><a
    href="https://github.com/actions/cache/commit/25618a0a675e8447e5ffc8ed9b7ddb2aaf927f65"><code>25618a0</code></a>
    Bump version</li>
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commit b9e1be5b7d6b7c014a3c7f3530e088879683f616
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Jan 22 02:51:42 2024 +0000

    Bump ZedThree/clang-tidy-review from 0.15.1 to 0.17.0 (#504)
    
    Bumps
    [ZedThree/clang-tidy-review](https://github.com/zedthree/clang-tidy-review)
    from 0.15.1 to 0.17.0.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
    href="https://github.com/zedthree/clang-tidy-review/releases">ZedThree/clang-tidy-review's
    releases</a>.</em></p>
    <blockquote>
    <h2>v0.17.0</h2>
    <h2>What's Changed</h2>
    <ul>
    <li>Don't override original env variables by <a
    href="https://github.com/bwrsandman"><code>@​bwrsandman</code></a> in <a
    href="https://redirect.github.com/ZedThree/clang-tidy-review/pull/111">ZedThree/clang-tidy-review#111</a></li>
    <li>Fix default <code>REVIEW_FILES</code> in split workflow post by <a
    href="https://github.com/bwrsandman"><code>@​bwrsandman</code></a> in <a
    href="https://redirect.github.com/ZedThree/clang-tidy-review/pull/110">ZedThree/clang-tidy-review#110</a></li>
    <li>Add Github App authentication method by <a
    href="https://github.com/bwrsandman"><code>@​bwrsandman</code></a> in <a
    href="https://redirect.github.com/ZedThree/clang-tidy-review/pull/109">ZedThree/clang-tidy-review#109</a></li>
    <li>Fix line filter on for clang compiler on windows by <a
    href="https://github.com/bwrsandman"><code>@​bwrsandman</code></a> in <a
    href="https://redirect.github.com/ZedThree/clang-tidy-review/pull/108">ZedThree/clang-tidy-review#108</a></li>
    </ul>
    <p><strong>Full Changelog</strong>: <a
    href="https://github.com/ZedThree/clang-tidy-review/compare/v0.16.0...v0.17.0">https://github.com/ZedThree/clang-tidy-review/compare/v0.16.0...v0.17.0</a></p>
    <h2>v0.16.0</h2>
    <h2>What's Changed</h2>
    <ul>
    <li>Bump PyGithub to 2.1 by <a
    href="https://github.com/bwrsandman"><code>@​bwrsandman</code></a> in <a
    href="https://redirect.github.com/ZedThree/clang-tidy-review/pull/107">ZedThree/clang-tidy-review#107</a></li>
    <li>Get username from PR to use in <code>google-readability-todo</code>
    by <a href="https://github.com/bwrsandman"><code>@​bwrsandman</code></a>
    in <a
    href="https://redirect.github.com/ZedThree/clang-tidy-review/pull/106">ZedThree/clang-tidy-review#106</a></li>
    <li>Fix split workflow when no comments can be posted by <a
    href="https://github.com/bwrsandman"><code>@​bwrsandman</code></a> in <a
    href="https://redirect.github.com/ZedThree/clang-tidy-review/pull/105">ZedThree/clang-tidy-review#105</a></li>
    </ul>
    <p><strong>Full Changelog</strong>: <a
    href="https://github.com/ZedThree/clang-tidy-review/compare/v0.15.1...v0.16.0">https://github.com/ZedThree/clang-tidy-review/compare/v0.15.1...v0.16.0</a></p>
    </blockquote>
    </details>
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/5d848bcdce74e046c72a7addedbb13293f5e5605"><code>5d848bc</code></a>
    Merge pull request <a
    href="https://redirect.github.com/zedthree/clang-tidy-review/issues/108">#108</a>
    from bwrsandman/clang-on-windows</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/27e81787888376c9626b7efd74e86917f0927896"><code>27e8178</code></a>
    Merge pull request <a
    href="https://redirect.github.com/zedthree/clang-tidy-review/issues/109">#109</a>
    from bwrsandman/app-auth</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/3977392e4cbf917ffa38bb0ff49760c57a4bdadf"><code>3977392</code></a>
    Merge pull request <a
    href="https://redirect.github.com/zedthree/clang-tidy-review/issues/110">#110</a>
    from bwrsandman/default-post</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/a7710544a34bbb1b98b61d933d8fdbbef5d77abc"><code>a771054</code></a>
    Merge pull request <a
    href="https://redirect.github.com/zedthree/clang-tidy-review/issues/111">#111</a>
    from bwrsandman/env</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/d8b8a3ca6dfed93e0dbf757ffe0546da79dfda12"><code>d8b8a3c</code></a>
    Apply black changes</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/882160cc9c5a89f2bcb844f40083d49013d0298d"><code>882160c</code></a>
    Don't override original env variables</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/4a4f63039c48ba31312092ee0eca358b406532c2"><code>4a4f630</code></a>
    Fix default <code>REVIEW_FILES</code> in split workflow post</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/72b3a12d9bb044aa6b6b610a98333ef6e3bd70e9"><code>72b3a12</code></a>
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    Add github app authentication arguments</li>
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    github wrapper: Use Auth class to encapsulate token</li>
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commit 08219f8863b24521501f3ef2d7e594d7e91e6a86
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Jan 20 11:27:46 2024 -0500

    build GitHub actions in parallel (#501)
    
    ### Description
    This changes the Github actions builds to build in parallel with 4
    processes, since the Github actions VMs are now more powerful:
    https://github.blog/2024-01-17-github-hosted-runners-double-the-power-for-open-source/
    
    The macOS actions runners are the same as before, so those should not be
    changed.
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [ ] I have requested a reviewer for this PR.

.github/workflows/cmake.yml

commit bf376942ea67fb2473aa7fbbdb5964478c2aa080
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Jan 17 18:08:51 2024 -0500

    add tracer particles (#490)
    
    ### Description
    This adds tracer particles. Particles are created one-per-cell in the
    initial conditions, then they advect with the fluid using the
    face-centered velocities returned from the Riemann solver. Particles are
    included in plotfiles and checkpoints. *(Particles will be added to
    openPMD outputs in a subsequent PR.)*
    
    The method adopted here for particle advection with face-centered
    velocities is the ["marker-and-cell method" (Harlow & Welch
    1965)](https://ui.adsabs.harvard.edu/abs/1965PhFl....8.2182H/abstract).
    
    Tracer particles are turned on for the `HydroBlast3D` and
    `SphericalCollapse` problems, so tracer particle functionality is
    included in the test suite.
    
    *Significant code infrastructure changes:*
    * This removes the old AMR level subcycling code taken from Chombo and
    replaces it with the cleaner version from the AMReX code examples.
    However, it should behave identically as before. This is necessary for
    particle redistribution to work with subcycling.
    * This adds the face-centered velocities to `state_new_fc_` and
    `state_old_fc_`. Some changes to the machinery for face-centered
    variables was necessary to get this to work, such as implementing AMR
    interpolation for face-centered variables using the `amrex::FaceLinear`
    interpolator (*caution: this interpolator does NOT preserve the
    divergence of the field!*). This is necessary because ghost faces are
    needed in order to handle particles that cross coarse-fine boundaries
    during a timestep. (In the future, this machinery can be modified so
    that it creates alias MultiFabs for separate face-centered components
    and then uses a different AMR interpolator for each component.)
    * In order to avoid modifying the initial conditions for every problem
    when tracer particles are enabled, this separates the initial conditions
    set-up function into `setInitialConditionsOnGrid` (cell-centered
    variables) and `setInitialConditionsOnGridFaceVars` (face-centered
    variables). This only affects the `FCQuantities` test problem.
    
    ### Related issues
    Closes https://github.com/quokka-astro/quokka/issues/489 and
    https://github.com/quokka-astro/quokka/issues/498.
    
    ### 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 see (see above).
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    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.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
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docs/parameters.rst
extern/amrex
src/AdvectionSimulation.hpp
src/FCQuantities/test_fc_quantities.cpp
src/RadhydroSimulation.hpp
src/physics_info.hpp
src/physics_numVars.hpp
src/simulation.hpp
tests/KelvinHelmholz_tracer.in
tests/SphericalCollapse.in
tests/blast2d.in
tests/blast_unigrid_128.in

commit 5479bca3d9ffb0787bec0237af8396d7d6b0fc70
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Jan 15 10:32:20 2024 -0500

    Bump ZedThree/clang-tidy-review from 0.14.0 to 0.15.1 (#500)
    
    Bumps
    [ZedThree/clang-tidy-review](https://github.com/zedthree/clang-tidy-review)
    from 0.14.0 to 0.15.1.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
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    <ul>
    <li>Fix Recursive source clang-tidy by <a
    href="https://github.com/bwrsandman"><code>@​bwrsandman</code></a> in <a
    href="https://redirect.github.com/ZedThree/clang-tidy-review/pull/104">ZedThree/clang-tidy-review#104</a></li>
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    <h2>v0.15.0</h2>
    <h2>What's Changed</h2>
    <ul>
    <li>Python fixes for running on multiple platforms and outside of docker
    by <a href="https://github.com/bwrsandman"><code>@​bwrsandman</code></a>
    in <a
    href="https://redirect.github.com/ZedThree/clang-tidy-review/pull/103">ZedThree/clang-tidy-review#103</a></li>
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    <li><a
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    Merge pull request <a
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    from bwrsandman/recursive-source-config</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/7765f56c9ababbd5264eb65ad4c7f811b5cc75ad"><code>7765f56</code></a>
    Fix Recursive source clang-tidy</li>
    <li><a
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    Merge pull request <a
    href="https://redirect.github.com/zedthree/clang-tidy-review/issues/103">#103</a>
    from bwrsandman/windows_shell_fix</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/406fab7d45c5f8c72c1f02d8f8a78fd9211e8d96"><code>406fab7</code></a>
    Apply black changes</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/e2610c9474fddc1ee2e6b7f343a0d9c0a0a06e8b"><code>e2610c9</code></a>
    Use pathlib for clang_tidy_binary and args list for version</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/e78c0b171597e2ca74b44011e4f5c830682639c9"><code>e78c0b1</code></a>
    Add an option to merge multiple comments</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/a09d6ab33b3fb2f84c40f8d67a5dfd1b4e2a5a67"><code>a09d6ab</code></a>
    Split workflow: return the number of comments</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/df2e12122b01447d8beb7eb5ed41e85b59ab588d"><code>df2e121</code></a>
    Fix review command line to run on windows</li>
    <li><a
    href="https://github.com/ZedThree/clang-tidy-review/commit/828c9a45e1b47ef2e14dc865cf76fa7e719fef05"><code>828c9a4</code></a>
    Bump versions of actions in README</li>
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    href="https://github.com/zedthree/clang-tidy-review/compare/v0.14.0...v0.15.1">compare
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.github/workflows/clang-tidy.yml

commit 26bb807a7576b07e601bc7b52613ff16185c68cd
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Sun Jan 14 22:09:23 2024 +0100

    Save gravitational potential gpot as a derived var in pltfiles (#406)
    
    Will fix #357 (when it actually works).
    
    Testing it out on the SphericalCollapse test. The code compiles but
    gives a segfault after writing chk00000
    
    I'm sure there are bugs in what I did.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    Co-authored-by: Ben Wibking <ben@wibking.com>
    Co-authored-by: Piyush Sharda <psharda@RSAA-043527.local>

src/SphericalCollapse/spherical_collapse.cpp
src/simulation.hpp
tests/SphericalCollapse.in

commit ad85a5820bdfed0646460db8cc5c06d3a9bd1a57
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Fri Jan 12 12:10:35 2024 +0100

    Use correct units for mean molecular weight (#494)
    
    ### Description
    Bug fix to use consistent units and dimensions for EOS_Traits
    
    ### Related issues
    Resolves #493
    
    ### 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:_
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    - [x ] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x ] I have requested a reviewer for this PR.

src/HydroBlast2D/test_hydro2d_blast.cpp
src/HydroBlast3D/test_hydro3d_blast.cpp
src/HydroHighMach/test_hydro_highmach.cpp
src/HydroKelvinHelmholz/test_hydro2d_kh.cpp
src/HydroQuirk/test_quirk.cpp
src/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
src/HydroShocktube/test_hydro_shocktube.cpp
src/HydroShocktubeCMA/test_hydro_shocktube_cma.cpp
src/HydroVacuum/test_hydro_vacuum.cpp
src/RayleighTaylor2D/test_hydro2d_rt.cpp
src/SphericalCollapse/spherical_collapse.cpp
src/StarCluster/star_cluster.cpp

commit ceee9df0a3156533b5e9897db130a6918d674798
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Jan 12 04:11:47 2024 -0500

    fix macOS CI (#496)
    
    ### Description
    The macOS GitHub runner is broken once again due to broken Homebrew
    packages.
    
    We fix this by installing a specific version of Python using
    `actions/setup-python` instead of `brew install python3` and by
    specifying `brew install hdf5@1.10` (since the Homebrew `hdf5@1.14`
    package is broken due to
    https://github.com/Homebrew/homebrew-core/pull/159165).
    
    ### 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).
    - [ ] I have added a link to any related issues see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [ ] I have requested a reviewer for this PR.

.github/workflows/cmake-macos.yml

commit 50ed0d4eb14f71ceda56bb72368addfd01e219b2
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Jan 11 10:51:53 2024 -0500

    document hydro, rad, and cooling runtime parameters (#488)
    
    ### Description
    Adds the hydrodynamics, radiation, and cooling runtime parameters to the
    documentation.
    
    ### Related issues
    Closes https://github.com/quokka-astro/quokka/issues/485.
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

docs/parameters.rst

commit 54514129450e4c9788024fcfbf63248eabe5ea96
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Sun Jan 7 03:59:49 2024 +1100

    Define advecting pulse test problem. (#463)
    
    ### Description
    Defined the advecting pulse test problem (Krumholz+2007). This test
    gives exactly the same result (visually) as in CASTRO II paper and
    consistent result between non-advecting and advecting case,
    demonstrating the code's ability to resolve diffusion limit as well as
    capture radiation advection in this limit.
    
    Notes:
    - Based on Add-O(beta-tau)-terms branch
    
    ### Checklist
    
    - [x] I have added a description (see above).
    - [x] I have added a link to any related issues see (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.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/CMakeLists.txt
src/RadhydroPulse/CMakeLists.txt
src/RadhydroPulse/test_radhydro_pulse.cpp
src/RadhydroPulse/test_radhydro_pulse.hpp
tests/RadhydroPulse.in

commit ec55fffd1a328a9e53ab6d4551a18e46a6aa1e5d
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Fri Jan 5 15:57:45 2024 +1100

    add tests to sphinx docs (#483)
    
    ### Description
    Add a few pages to the Sphinx docs under the tests section.
    
    ### Related issues
    N/A
    
    ### 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).
    - [ ] I have added a link to any related issues see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

docs/references.bib
docs/tests/attach/hydro_shuosher.png
docs/tests/attach/hydro_sms.png
docs/tests/attach/radcoupling.png
docs/tests/attach/radcoupling_rsla.png
docs/tests/attach/radhydro_pulse_density-1.png
docs/tests/attach/radhydro_pulse_density.png
docs/tests/attach/radhydro_pulse_temperature-1.png
docs/tests/attach/radhydro_pulse_temperature.png
docs/tests/attach/radhydro_pulse_velocity-1.png
docs/tests/attach/radhydro_pulse_velocity.png
docs/tests/attach/radhydro_uniform_advecting_temperature-nobeta.png
docs/tests/attach/radhydro_uniform_advecting_temperature.png
docs/tests/attach/radhydro_uniform_advecting_velocity-nobeta.png
docs/tests/attach/radhydro_uniform_advecting_velocity.png
docs/tests/attach/radshock_cgs_temperature.png
docs/tests/energy_exchange.rst
docs/tests/index.rst
docs/tests/radhydro_pulse.rst
docs/tests/radhydro_uniform_adv.rst
docs/tests/radshock.rst
docs/tests/shu_osher.rst
docs/tests/sms.rst

commit a3a5948c1122b061d855af70117c468e2a534970
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Thu Jan 4 09:34:43 2024 +1100

    Multigroup radiative shock test (#467)
    
    ### Description
    Extending the original single-group radiation shock test to multigroup
    gray-opacity radiation shock, following Sec 9.5 of Skinner et al. 2019.
    We use 8 radiation groups logarithmically spaced over [1e15, 1e19] Hz.
    The run time increases from 22.0 s in the single-group case to 122 s in
    the 8-group case, so I have to reduce Nx from 512 to 128 and increase
    `error_tol` from 0.005 to 0.008. Note that with Nx=512, the multigroup
    test has an error within 0.005, similar to the single-group test.
    
    ### Checklist
    - [x] I have added a description (see above).
    - [ ] I have added a link to any related issues see (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.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/CMakeLists.txt
src/RadhydroShockMultigroup/CMakeLists.txt
src/RadhydroShockMultigroup/test_radhydro_shock_multigroup.cpp
src/RadhydroShockMultigroup/test_radhydro_shock_multigroup.hpp
tests/radshockMG.in

commit 54b3d606fda28175f6486c01aef035bdd8dfee6d
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Tue Jan 2 19:12:03 2024 -0500

    Bump extern/Microphysics from `657406d` to `7de2124` (#480)
    
    Bumps [extern/Microphysics](https://github.com/psharda/Microphysics)
    from `657406d` to `7de2124`.
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/7de212422501a88c1c1f536b93217721e3dc6701"><code>7de2124</code></a>
    an EOS interface with NSE (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1405">#1405</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/4a44497fa0e72e0135ea28b0a246aa6d788ed654"><code>4a44497</code></a>
    initialize nse_table_t members (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1418">#1418</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/925e0ce0f99140121954cad98b71398292f47b67"><code>925e0ce</code></a>
    fix concurrency for castro-development (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1423">#1423</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/d7428160359fb550276a80b51d2fa425b499b348"><code>d742816</code></a>
    add another Castro action that tests against AMReX development (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1421">#1421</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/8a61b961d953ea1c54c2e01a1556ac13481deed2"><code>8a61b96</code></a>
    a simpler fix for constexpr_for in amrex (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1420">#1420</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/4d7d0299fb39281eaac7c4d66bca1976d62c07b3"><code>4d7d029</code></a>
    add a script to test network compatibility with NSE_NET (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1416">#1416</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/5757fb59a11e4a53dcabe71f0fadc9c221fb5af6"><code>5757fb5</code></a>
    make sure const T evolution (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1408">#1408</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/01577f32112fc8ad4c6ccc509c222d0e41fee062"><code>01577f3</code></a>
    Revert &quot;Start moving towards zero-based indexing with linpack (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/536">#536</a>)&quot;
    (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1412">#1412</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/43b5138dcecd92aa919a26afca9ef15f6937b22d"><code>43b5138</code></a>
    add a method to compute the T derivative of an NSE table quantity (<a
    href="https://redirect.github.com/psharda/Microphysics/issues/1407">#1407</a>)</li>
    <li><a
    href="https://github.com/psharda/Microphysics/commit/96f4c7efb1adbc6e653ed6966580b6e947735f1a"><code>96f4c7e</code></a>
    update hip install for ROCm 6.0 (<a
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extern/Microphysics

commit 079aad2fcdd0461d8dbc3353c81abf4c92fe239d
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Jan 1 15:00:48 2024 -0500

    Bump extern/amrex from `9b733ec` to `75571e2` (#482)
    
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    MLMG: Use free functions instead of MF member functions (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3681">#3681</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/3407e877a7b219546c0ef12bef287845f5cb9f05"><code>3407e87</code></a>
    Add a few free functions for MLMG (<a
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    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3674">#3674</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/d1e55fbab7c5d5cb72d3c448a91430a568628b9e"><code>d1e55fb</code></a>
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    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/78c4fdaf95175f992b87e670780f5cf0d01d0783"><code>78c4fda</code></a>
    Improve ParIter docs (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3676">#3676</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/3497f016d9204adf2b406659100adb2803118468"><code>3497f01</code></a>
    Fix CI for ROCm 6.0 (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3673">#3673</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/554b1ca3b00c3a56cbed4861bfa16c8074a78fc5"><code>554b1ca</code></a>
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    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3671">#3671</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/0c6f2b4ad81178a6e14f26ebb5f2ad6c642c785c"><code>0c6f2b4</code></a>
    CMake: AMReX_PARALLEL_LINK_JOBS (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3628">#3628</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/0a208bbc4635abacd9f087b62aa3cdffc25db113"><code>0a208bb</code></a>
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extern/amrex

commit 6bd8b63fe10c2e05b9f896a9db8bde2f1003f732
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commit 38d195cd849613834f3afec9cacd2d3430f87ff4
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    Bump extern/yaml-cpp from `eaf7205` to `94710bb` (#481)
    
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extern/yaml-cpp

commit bd6c18a979f81a62e6579c045ac1fb44c50d6ff1
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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    Bump extern/fmt from `99b9fbf` to `a5bacf3` (#478)
    
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    Remove custom_formatter</li>
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    Implement scan argument access</li>
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    href="https://github.com/fmtlib/fmt/commit/23826669cf1fa8c6b60e4c6497aff9be36bf48ae"><code>2382666</code></a>
    Cleanup error handling</li>
    <li><a
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    Apply coding conventions</li>
    <li><a
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    Cleanup scripts</li>
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    Update release script</li>
    <li><a
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    Improve scripts</li>
    <li><a
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    Workaround github markdown mess</li>
    <li><a
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extern/fmt

commit aa18236ba8a0138f246627152bd39dbc4a0b5277
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Thu Dec 28 18:13:21 2023 +1100

    radiation advection (#462)
    
    ### Description
    Add support for advection on grey radiation.
    
    - Add the O(beta tau) terms to the matter-radiation exchange.
    - Add the RadhydroUniformAdvecting test for this new physics. Without
    O(beta tau), the relative error is about 1e-8 (v = 100 km/s, rho = 1.2,
    kappa = 100 cm2 g-1). With this update, this test is accurate to machine
    accuracy.
    - Modified boundary condition in RadhydroShock problem
    - Passed all tests
    
    ### Related issues
    N/A
    
    ### Checklist
    
    - [x] I have added a description (see above).
    - [x] I have added a link to any related issues see (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.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    Co-authored-by: Ben Wibking <ben@wibking.com>

.ci/azure-pipelines.yml
src/CMakeLists.txt
src/RadhydroShock/test_radhydro_shock.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/RadhydroSimulation.hpp
src/RadhydroUniformAdvecting/CMakeLists.txt
src/RadhydroUniformAdvecting/test_radhydro_uniform_advecting.cpp
src/RadhydroUniformAdvecting/test_radhydro_uniform_advecting.hpp
src/planck_integral.hpp
src/radiation_system.hpp
tests/RadForce.in
tests/RadhydroUniformAdvecting.in
tests/radshock_dimensionless.in

commit 098d170af84dea5219c3c3917c70c32490f80b21
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Dec 25 12:41:41 2023 -0500

    Bump actions/deploy-pages from 3 to 4 (#477)
    
    Bumps [actions/deploy-pages](https://github.com/actions/deploy-pages)
    from 3 to 4.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
    href="https://github.com/actions/deploy-pages/releases">actions/deploy-pages's
    releases</a>.</em></p>
    <blockquote>
    <h2>v4.0.0</h2>
    <h1>Changelog</h1>
    <ul>
    <li>Deploy pages using artifact IDs <a
    href="https://github.com/konradpabjan"><code>@​konradpabjan</code></a>
    (<a
    href="https://redirect.github.com/actions/deploy-pages/issues/251">#251</a>)</li>
    <li>This version requires the permission <code>actions: read</code> in
    the workflows which use it.</li>
    </ul>
    <hr />
    <p>ℹ️ This version of <code>actions/deploy-pages</code> is
    <strong>ONLY</strong> compatible with artifacts uploaded by either:</p>
    <ul>
    <li><a
    href="https://github.com/actions/upload-pages-artifact/releases/tag/v3.0.0"><code>actions/upload-pages-artifact@v3</code></a>
    or newer</li>
    <li><a
    href="https://github.com/actions/upload-artifact/releases/tag/v4.0.0"><code>actions/upload-artifact@v4</code></a>
    or newer.</li>
    </ul>
    <p>See details of <a
    href="https://github.com/actions/deploy-pages/compare/v3.0.1...v4.0.0">all
    code changes</a> since previous release.</p>
    <p>:warning: For use with products other than GitHub.com, such as GitHub
    Enterprise Server, please consult the <a
    href="https://github.com/actions/deploy-pages/#compatibilty">compatibility
    table</a>.</p>
    <h2>v3.0.1</h2>
    <h1>Changelog</h1>
    <ul>
    <li>Bump eslint from 8.54.0 to 8.55.0 <a
    href="https://github.com/dependabot"><code>@​dependabot</code></a> (<a
    href="https://redirect.github.com/actions/deploy-pages/issues/266">#266</a>)</li>
    <li>Bump nock from 13.3.8 to 13.4.0 <a
    href="https://github.com/dependabot"><code>@​dependabot</code></a> (<a
    href="https://redirect.github.com/actions/deploy-pages/issues/267">#267</a>)</li>
    <li>Bump eslint-config-prettier from 9.0.0 to 9.1.0 <a
    href="https://github.com/dependabot"><code>@​dependabot</code></a> (<a
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    <li>Update compatibility table for v3 <a
    href="https://github.com/JamesMGreene"><code>@​JamesMGreene</code></a>
    (<a
    href="https://redirect.github.com/actions/deploy-pages/issues/270">#270</a>)</li>
    </ul>
    <h2>🧰 Maintenance</h2>
    <ul>
    <li>chore/docs: update version, fix typos <a
    href="https://github.com/kbdharun"><code>@​kbdharun</code></a> (<a
    href="https://redirect.github.com/actions/deploy-pages/issues/272">#272</a>)</li>
    </ul>
    <hr />
    <p>See details of <a
    href="https://github.com/actions/deploy-pages/compare/v3.0.0...v3.0.1">all
    code changes</a> since previous release.</p>
    <p>:warning: For use with products other than GitHub.com, such as GitHub
    Enterprise Server, please consult the <a
    href="https://github.com/actions/deploy-pages/#compatibilty">compatibility
    table</a>.</p>
    </blockquote>
    </details>
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/actions/deploy-pages/commit/7a9bd943aa5e5175aeb8502edcc6c1c02d398e10"><code>7a9bd94</code></a>
    Merge pull request <a
    href="https://redirect.github.com/actions/deploy-pages/issues/290">#290</a>
    from actions/dependabot/npm_and_yarn/undici-6.2.1</li>
    <li><a
    href="https://github.com/actions/deploy-pages/commit/eee8a27158326d4a4993574decb74691422aa9ff"><code>eee8a27</code></a>
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    <li><a
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    Bump undici from 6.0.1 to 6.2.1</li>
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    Merge pull request <a
    href="https://redirect.github.com/actions/deploy-pages/issues/282">#282</a>
    from actions/dependabot/github_actions/github/codeql-...</li>
    <li><a
    href="https://github.com/actions/deploy-pages/commit/53d1eac7fd4d43bdb78c7492d45ce17598a8fbf6"><code>53d1eac</code></a>
    Bump github/codeql-action from 2 to 3</li>
    <li><a
    href="https://github.com/actions/deploy-pages/commit/3f0ef9d75df3fc372f78051e41dfa694bb50f83f"><code>3f0ef9d</code></a>
    Merge pull request <a
    href="https://redirect.github.com/actions/deploy-pages/issues/281">#281</a>
    from actions/dependabot/github_actions/actions/upload...</li>
    <li><a
    href="https://github.com/actions/deploy-pages/commit/82751044df20afbd0ae563fb79e45eb19524ed36"><code>8275104</code></a>
    Bump actions/upload-artifact from 3 to 4</li>
    <li><a
    href="https://github.com/actions/deploy-pages/commit/9be9d731c91469d80c7cee3e565a1b54220def07"><code>9be9d73</code></a>
    Merge pull request <a
    href="https://redirect.github.com/actions/deploy-pages/issues/280">#280</a>
    from actions/dependabot/npm_and_yarn/eslint-8.56.0</li>
    <li><a
    href="https://github.com/actions/deploy-pages/commit/d8afefafec56df80907efefd0d5fc75007540533"><code>d8afefa</code></a>
    Bump eslint from 8.55.0 to 8.56.0</li>
    <li><a
    href="https://github.com/actions/deploy-pages/commit/304d0b77f8ce8509118d3d01565a9ac8dc244104"><code>304d0b7</code></a>
    Merge pull request <a
    href="https://redirect.github.com/actions/deploy-pages/issues/277">#277</a>
    from actions/dependabot/github_actions/actions/publis...</li>
    <li>Additional commits viewable in <a
    href="https://github.com/actions/deploy-pages/compare/v3...v4">compare
    view</a></li>
    </ul>
    </details>
    <br />
    
    
    [![Dependabot compatibility
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.github/workflows/docs.yml

commit d34f253c8e37660d925a55e03c8adcba9f16e0ae
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Dec 21 23:25:37 2023 -0500

    add additional metadata to openPMD outputs (#473)
    
    ### Description
    openPMD expects additional metadata to be compliant with its standard
    that wasn't included in the initial implementation of openPMD support.
    
    ### Related issues
    N/A
    
    ### 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 see (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.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

src/openPMD.cpp
src/simulation.hpp

commit 433e681e87f1188ad59b83db8996c23ae7ab045c
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Dec 20 15:15:32 2023 -0500

    update moth profile for ROCm 6.0 (#475)
    
    ### Description
    This updates the build profile for moth.anu.edu.au to use ROCm 6.0.
    
    ### Related issues
    N/A
    
    ### 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 see (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.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

.ci/azure-pipelines-amdgpu.yml
scripts/moth-sanitizer.profile
scripts/moth.profile

commit bfe2c73548d9e06d90fe66a3e5162ef77fcc9d38
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Dec 18 03:54:35 2023 +0000

    Bump actions/upload-artifact from 3 to 4 (#474)
    
    Bumps
    [actions/upload-artifact](https://github.com/actions/upload-artifact)
    from 3 to 4.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
    href="https://github.com/actions/upload-artifact/releases">actions/upload-artifact's
    releases</a>.</em></p>
    <blockquote>
    <h2>v4.0.0</h2>
    <h2>What's Changed</h2>
    <p>The release of upload-artifact@v4 and download-artifact@v4 are major
    changes to the backend architecture of Artifacts. They have numerous
    performance and behavioral improvements.</p>
    <p>For more information, see the <a
    href="https://github.com/actions/toolkit/tree/main/packages/artifact"><code>@​actions/artifact</code></a>
    documentation.</p>
    <h2>New Contributors</h2>
    <ul>
    <li><a href="https://github.com/vmjoseph"><code>@​vmjoseph</code></a>
    made their first contribution in <a
    href="https://redirect.github.com/actions/upload-artifact/pull/464">actions/upload-artifact#464</a></li>
    </ul>
    <p><strong>Full Changelog</strong>: <a
    href="https://github.com/actions/upload-artifact/compare/v3...v4.0.0">https://github.com/actions/upload-artifact/compare/v3...v4.0.0</a></p>
    <h2>v3.1.3</h2>
    <h2>What's Changed</h2>
    <ul>
    <li>chore(github): remove trailing whitespaces by <a
    href="https://github.com/ljmf00"><code>@​ljmf00</code></a> in <a
    href="https://redirect.github.com/actions/upload-artifact/pull/313">actions/upload-artifact#313</a></li>
    <li>Bump <code>@​actions/artifact</code> version to v1.1.2 by <a
    href="https://github.com/bethanyj28"><code>@​bethanyj28</code></a> in <a
    href="https://redirect.github.com/actions/upload-artifact/pull/436">actions/upload-artifact#436</a></li>
    </ul>
    <p><strong>Full Changelog</strong>: <a
    href="https://github.com/actions/upload-artifact/compare/v3...v3.1.3">https://github.com/actions/upload-artifact/compare/v3...v3.1.3</a></p>
    <h2>v3.1.2</h2>
    <ul>
    <li>Update all <code>@actions/*</code> NPM packages to their latest
    versions- <a
    href="https://redirect.github.com/actions/upload-artifact/issues/374">#374</a></li>
    <li>Update all dev dependencies to their most recent versions - <a
    href="https://redirect.github.com/actions/upload-artifact/issues/375">#375</a></li>
    </ul>
    <h2>v3.1.1</h2>
    <ul>
    <li>Update actions/core package to latest version to remove
    <code>set-output</code> deprecation warning <a
    href="https://redirect.github.com/actions/upload-artifact/issues/351">#351</a></li>
    </ul>
    <h2>v3.1.0</h2>
    <h2>What's Changed</h2>
    <ul>
    <li>Bump <code>@​actions/artifact</code> to v1.1.0 (<a
    href="https://redirect.github.com/actions/upload-artifact/pull/327">actions/upload-artifact#327</a>)
    <ul>
    <li>Adds checksum headers on artifact upload (<a
    href="https://redirect.github.com/actions/toolkit/pull/1095">actions/toolkit#1095</a>)
    (<a
    href="https://redirect.github.com/actions/toolkit/pull/1063">actions/toolkit#1063</a>)</li>
    </ul>
    </li>
    </ul>
    </blockquote>
    </details>
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/actions/upload-artifact/commit/c7d193f32edcb7bfad88892161225aeda64e9392"><code>c7d193f</code></a>
    Merge pull request <a
    href="https://redirect.github.com/actions/upload-artifact/issues/466">#466</a>
    from actions/v4-beta</li>
    <li><a
    href="https://github.com/actions/upload-artifact/commit/13131bb095770b4070a7477c3cd2d96e1c16d9f4"><code>13131bb</code></a>
    licensed cache</li>
    <li><a
    href="https://github.com/actions/upload-artifact/commit/4a6c273b9834f66a1d05c170dc3f80f9cdb9def1"><code>4a6c273</code></a>
    Merge branch 'main' into v4-beta</li>
    <li><a
    href="https://github.com/actions/upload-artifact/commit/f391bb91a3d3118aeca171c365bb319ece276b37"><code>f391bb9</code></a>
    Merge pull request <a
    href="https://redirect.github.com/actions/upload-artifact/issues/465">#465</a>
    from actions/robherley/v4-documentation</li>
    <li><a
    href="https://github.com/actions/upload-artifact/commit/9653d03c4b74c32144e02dae644fea70e079d4b3"><code>9653d03</code></a>
    Apply suggestions from code review</li>
    <li><a
    href="https://github.com/actions/upload-artifact/commit/875b63076402f25ef9d52c294c86ba4f97810575"><code>875b630</code></a>
    add limitations section</li>
    <li><a
    href="https://github.com/actions/upload-artifact/commit/ecb21463e93740a6be75c3116242169bfdbcb15a"><code>ecb2146</code></a>
    add compression example</li>
    <li><a
    href="https://github.com/actions/upload-artifact/commit/5e7604f84a055838f64ed68bb9904751523081ae"><code>5e7604f</code></a>
    trim some repeated info</li>
    <li><a
    href="https://github.com/actions/upload-artifact/commit/d6437d07581fe318a364512e6cf6b1dca6b4f92c"><code>d6437d0</code></a>
    naming</li>
    <li><a
    href="https://github.com/actions/upload-artifact/commit/1b561557037b4957d7d184e9aac02bec86c771eb"><code>1b56155</code></a>
    s/v4-beta/v4/g</li>
    <li>Additional commits viewable in <a
    href="https://github.com/actions/upload-artifact/compare/v3...v4">compare
    view</a></li>
    </ul>
    </details>
    <br />
    
    
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.github/workflows/cmake-macos.yml
.github/workflows/cmake.yml

commit ed906519115c0836d293812dfe6749b4e2eb8d8b
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Dec 17 00:28:45 2023 -0500

    use frexp and ldexp in FastMath (#471)
    
    ### Description
    This avoids `reinterpret_cast` in FastMath.hpp, which is undefined
    behavior. Instead, we use `ldexp` and `frexp` to manipulate the
    floating-point mantissa and exponent for the fast approximate log
    functions.
    
    ### Related issues
    Fixes https://github.com/quokka-astro/quokka/issues/333.
    
    ### 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 see (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.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
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src/FastMath.hpp

commit ed51d0d4985895a8a2a793ad7fdbf32bcfc3454c
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Dec 17 00:27:08 2023 -0500

    Fallback to zero-gradient extrapolation when NSCBC fails (#472)
    
    ### Description
    This implemented a fallback to zero-gradient extrapolation when the
    NSCBC outflow boundary condition produces ghost cells with negative
    density or pressure.
    
    This is necessary to prevent the simulation from crashing when NSCBC
    outflow is used for the cloud acceleration problem. There does not
    appear to be anything better that can be done when this happens
    (Zingale, personal communication). This only is needed for an extremely
    small fraction of ghost cells.
    
    ### Related issues
    N/A
    
    ### 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).
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    - [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.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.

src/NSCBC_outflow.hpp

commit f7f34fcb073484da96b1503612227724a0d30dd6
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Dec 12 19:01:28 2023 -0500

    add support for writing openPMD/ADIOS2 plotfiles (#466)
    
    ### Description
    This adds support for writing ADIOS2 format plotfiles using openPMD-api
    (https://github.com/openPMD/openPMD-api). This is the file format used
    by WarpX for its large-scale runs, and it is the fastest option for
    large-scale I/O (~Terabytes or larger).
    
    This adds support for cell-centered variables only. (However, it does
    include cell-centered averages of the face-centered variables, and all
    of the other derived variables.)
    
    openPMD currently does not support ghost cells, so we exclude them when
    writing the plotfile in openPMD/ADIOS2 format.
    
    There is no support for checkpoints or restarts with this format (nor is
    there in WarpX, or any other code that I'm aware of).
    
    ### Related issues
    N/A
    
    ### 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).
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    - [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.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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.github/workflows/clang-tidy.yml
.gitmodules
CMakeLists.txt
README.md
extern/openPMD-api
src/CMakeLists.txt
src/PrimordialChem/CMakeLists.txt
src/openPMD.cpp
src/openPMD.hpp
src/simulation.hpp

commit 12a3a48a4bfcfe14d40e63a515d1f5650d07c855
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Dec 11 03:25:37 2023 +0000

    Bump actions/setup-python from 4 to 5 (#470)
    
    Bumps [actions/setup-python](https://github.com/actions/setup-python)
    from 4 to 5.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
    href="https://github.com/actions/setup-python/releases">actions/setup-python's
    releases</a>.</em></p>
    <blockquote>
    <h2>v5.0.0</h2>
    <h2>What's Changed</h2>
    <p>In scope of this release, we update node version runtime from node16
    to node20 (<a
    href="https://redirect.github.com/actions/setup-python/pull/772">actions/setup-python#772</a>).
    Besides, we update dependencies to the latest versions.</p>
    <p><strong>Full Changelog</strong>: <a
    href="https://github.com/actions/setup-python/compare/v4.8.0...v5.0.0">https://github.com/actions/setup-python/compare/v4.8.0...v5.0.0</a></p>
    <h2>v4.8.0</h2>
    <h2>What's Changed</h2>
    <p>In scope of this release we added support for GraalPy (<a
    href="https://redirect.github.com/actions/setup-python/pull/694">actions/setup-python#694</a>).
    You can use this snippet to set up GraalPy:</p>
    <pre lang="yaml"><code>steps:
    - uses: actions/checkout@v4
    - uses: actions/setup-python@v4
      with:
        python-version: 'graalpy-22.3'
    - run: python my_script.py
    </code></pre>
    <p>Besides, the release contains such changes as:</p>
    <ul>
    <li>Trim python version when reading from file by <a
    href="https://github.com/FerranPares"><code>@​FerranPares</code></a> in
    <a
    href="https://redirect.github.com/actions/setup-python/pull/628">actions/setup-python#628</a></li>
    <li>Use non-deprecated versions in examples by <a
    href="https://github.com/jeffwidman"><code>@​jeffwidman</code></a> in <a
    href="https://redirect.github.com/actions/setup-python/pull/724">actions/setup-python#724</a></li>
    <li>Change deprecation comment to past tense by <a
    href="https://github.com/jeffwidman"><code>@​jeffwidman</code></a> in <a
    href="https://redirect.github.com/actions/setup-python/pull/723">actions/setup-python#723</a></li>
    <li>Bump <code>@​babel/traverse</code> from 7.9.0 to 7.23.2 by <a
    href="https://github.com/dependabot"><code>@​dependabot</code></a> in <a
    href="https://redirect.github.com/actions/setup-python/pull/743">actions/setup-python#743</a></li>
    <li>advanced-usage.md: Encourage the use actions/checkout@v4 by <a
    href="https://github.com/cclauss"><code>@​cclauss</code></a> in <a
    href="https://redirect.github.com/actions/setup-python/pull/729">actions/setup-python#729</a></li>
    <li>Examples now use checkout@v4 by <a
    href="https://github.com/simonw"><code>@​simonw</code></a> in <a
    href="https://redirect.github.com/actions/setup-python/pull/738">actions/setup-python#738</a></li>
    <li>Update actions/checkout to v4 by <a
    href="https://github.com/dmitry-shibanov"><code>@​dmitry-shibanov</code></a>
    in <a
    href="https://redirect.github.com/actions/setup-python/pull/761">actions/setup-python#761</a></li>
    </ul>
    <h2>New Contributors</h2>
    <ul>
    <li><a
    href="https://github.com/FerranPares"><code>@​FerranPares</code></a>
    made their first contribution in <a
    href="https://redirect.github.com/actions/setup-python/pull/628">actions/setup-python#628</a></li>
    <li><a href="https://github.com/timfel"><code>@​timfel</code></a> made
    their first contribution in <a
    href="https://redirect.github.com/actions/setup-python/pull/694">actions/setup-python#694</a></li>
    <li><a
    href="https://github.com/jeffwidman"><code>@​jeffwidman</code></a> made
    their first contribution in <a
    href="https://redirect.github.com/actions/setup-python/pull/724">actions/setup-python#724</a></li>
    </ul>
    <p><strong>Full Changelog</strong>: <a
    href="https://github.com/actions/setup-python/compare/v4...v4.8.0">https://github.com/actions/setup-python/compare/v4...v4.8.0</a></p>
    <h2>v4.7.1</h2>
    <h2>What's Changed</h2>
    <ul>
    <li>Bump word-wrap from 1.2.3 to 1.2.4 by <a
    href="https://github.com/dependabot"><code>@​dependabot</code></a> in <a
    href="https://redirect.github.com/actions/setup-python/pull/702">actions/setup-python#702</a></li>
    <li>Add range validation for toml files by <a
    href="https://github.com/dmitry-shibanov"><code>@​dmitry-shibanov</code></a>
    in <a
    href="https://redirect.github.com/actions/setup-python/pull/726">actions/setup-python#726</a></li>
    </ul>
    <p><strong>Full Changelog</strong>: <a
    href="https://github.com/actions/setup-python/compare/v4...v4.7.1">https://github.com/actions/setup-python/compare/v4...v4.7.1</a></p>
    <h2>v4.7.0</h2>
    <p>In scope of this release, the support for reading python version from
    pyproject.toml was added (<a
    href="https://redirect.github.com/actions/setup-python/pull/669">actions/setup-python#669</a>).</p>
    <pre lang="yaml"><code>      - name: Setup Python
            uses: actions/setup-python@v4
    &lt;/tr&gt;&lt;/table&gt;
    </code></pre>
    </blockquote>
    <p>... (truncated)</p>
    </details>
    <details>
    <summary>Commits</summary>
    <ul>
    <li><a
    href="https://github.com/actions/setup-python/commit/0a5c61591373683505ea898e09a3ea4f39ef2b9c"><code>0a5c615</code></a>
    Update action to node20 (<a
    href="https://redirect.github.com/actions/setup-python/issues/772">#772</a>)</li>
    <li><a
    href="https://github.com/actions/setup-python/commit/0ae58361cdfd39e2950bed97a1e26aa20c3d8955"><code>0ae5836</code></a>
    Add example of GraalPy to docs (<a
    href="https://redirect.github.com/actions/setup-python/issues/773">#773</a>)</li>
    <li><a
    href="https://github.com/actions/setup-python/commit/b64ffcaf5b410884ad320a9cfac8866006a109aa"><code>b64ffca</code></a>
    update actions/checkout to v4 (<a
    href="https://redirect.github.com/actions/setup-python/issues/761">#761</a>)</li>
    <li><a
    href="https://github.com/actions/setup-python/commit/8d2896179abf658742de432b3f203d2c2d86a587"><code>8d28961</code></a>
    Examples now use checkout@v4 (<a
    href="https://redirect.github.com/actions/setup-python/issues/738">#738</a>)</li>
    <li><a
    href="https://github.com/actions/setup-python/commit/7bc6abb01e0555719edc2dbca70a2fde309e5e56"><code>7bc6abb</code></a>
    advanced-usage.md: Encourage the use actions/checkout@v4 (<a
    href="https://redirect.github.com/actions/setup-python/issues/729">#729</a>)</li>
    <li><a
    href="https://github.com/actions/setup-python/commit/e8111cec9d3dc15220d8a3b638f08419f57b906a"><code>e8111ce</code></a>
    Bump <code>@​babel/traverse</code> from 7.9.0 to 7.23.2 (<a
    href="https://redirect.github.com/actions/setup-python/issues/743">#743</a>)</li>
    <li><a
    href="https://github.com/actions/setup-python/commit/a00ea43da65e7c04d2bdae58b3afecd77057eb9e"><code>a00ea43</code></a>
    add fix for graalpy ci (<a
    href="https://redirect.github.com/actions/setup-python/issues/741">#741</a>)</li>
    <li><a
    href="https://github.com/actions/setup-python/commit/8635b1ccc5934e73ed3510980fd2e7790b85839b"><code>8635b1c</code></a>
    Change deprecation comment to past tense (<a
    href="https://redirect.github.com/actions/setup-python/issues/723">#723</a>)</li>
    <li><a
    href="https://github.com/actions/setup-python/commit/f6cc428f535856f9c23558d01765a42a4d6cf758"><code>f6cc428</code></a>
    Use non-deprecated versions in examples (<a
    href="https://redirect.github.com/actions/setup-python/issues/724">#724</a>)</li>
    <li><a
    href="https://github.com/actions/setup-python/commit/5f2af211d616f86005883b44826180b21abb4060"><code>5f2af21</code></a>
    Add GraalPy support (<a
    href="https://redirect.github.com/actions/setup-python/issues/694">#694</a>)</li>
    <li>Additional commits viewable in <a
    href="https://github.com/actions/setup-python/compare/v4...v5">compare
    view</a></li>
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.github/workflows/codespell.yml

commit 4484b720c7248f77dfa9b77bebe3fa002158fb3b
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Dec 11 03:24:22 2023 +0000

    Bump actions/deploy-pages from 2 to 3 (#469)
    
    Bumps [actions/deploy-pages](https://github.com/actions/deploy-pages)
    from 2 to 3.
    <details>
    <summary>Release notes</summary>
    <p><em>Sourced from <a
    href="https://github.com/actions/deploy-pages/releases">actions/deploy-pages's
    releases</a>.</em></p>
    <blockquote>
    <h2>v3.0.0</h2>
    <h1>Changelog</h1>
    <ul>
    <li>Update action to node20 <a
    href="https://github.com/takost"><code>@​takost</code></a> (<a
    href="https://redirect.github.com/actions/deploy-pages/issues/256">#256</a>)</li>
    </ul>
    <hr />
    <p>See details of <a
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    code changes</a> since previous release.</p>
    <p>:warning: For use with products other than GitHub.com, such as GitHub
    Enterprise Server, please consult the <a
    href="https://github.com/actions/deploy-pages/#compatibilty">compatibility
    table</a>.</p>
    <h2>v2.0.5</h2>
    <h1>Changelog</h1>
    <ul>
    <li>Bump prettier from 3.0.0 to 3.1.0 <a
    href="https://github.com/dependabot"><code>@​dependabot</code></a> (<a
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    href="https://redirect.github.com/actions/deploy-pages/issues/232">#232</a>)</li>
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    <li>Fix cosmetic error by replacing comma with period <a
    href="https://github.com/JamesMGreene"><code>@​JamesMGreene</code></a>
    (<a
    href="https://redirect.github.com/actions/deploy-pages/issues/210">#210</a>)</li>
    <li>Bump actions/checkout from 3 to 4 <a
    href="https://github.com/dependabot"><code>@​dependabot</code></a> (<a
    href="https://redirect.github.com/actions/deploy-pages/issues/220">#220</a>)</li>
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    <p>:warning: For use with products other than GitHub.com, such as GitHub
    Enterprise Server, please consult the <a
    href="https://github.com/actions/deploy-pages/#compatibilty">compatibility
    table</a>.</p>
    <h2>v2.0.4</h2>
    <h1>Changelog</h1>
    <ul>
    <li>Update GHES compatibility table after verifying with
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    href="https://github.com/JamesMGreene"><code>@​JamesMGreene</code></a>
    (<a
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commit 1bbc41f6e22c5c7af6b8e2880f18d58968a65fbb
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Dec 9 07:07:54 2023 -0500

    move numerical stability page from wiki to Sphinx docs (#460)
    
    ### Description
    This moves the content on the GitHub wiki page about numerical stability
    to the Sphinx documentation for better visibility.
    
    ### Related issues
    N/A
    
    ### 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
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
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    code.
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docs/index.rst
docs/instability.rst

commit add3105a5575c6f55796bdb4b671b50c4fb61e01
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Dec 8 00:57:57 2023 -0500

    add chapter headings and developer guide to Sphinx docs (#465)
    
    ### Description
    This is a major update to the Sphinx documentation that rewrites the
    introduction to be more consistent with `README.md`, adds chapter
    headings for the User Guide and the Developer Guide, and moves the
    developer-oriented content from the GitHub wiki to the Sphinx
    documentation.
    
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    N/A
    
    ### Checklist
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    completed. Denote completed tasks with an `x` inside the square brackets
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docs/api.rst
docs/conf.py
docs/debugging.rst
docs/error_checking.rst
docs/howto_clang_tidy.rst
docs/index.rst
docs/performance.rst

commit 78c5970857430e155885555bdfaa30a6ef4946e4
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Thu Dec 7 17:13:55 2023 +1100

    Use IMEX PD-ARS scheme for radiation update (#448)
    
    ### Description
    Replace SSP-RK2 + implicit exchange solver with IMEX PD-ARS scheme. Also
    removed diffusive fluxes in PredictStep and AddFluxesRK2. These two
    changes fixed the Asymptotic Marshak test.
    
    Notes:
    - You can restore the original SSP-RK2 scheme by setting `IMEX_a22 =
    0.0; IMEX_a32 = 0.0;` in radiation_system.hpp.
    - Also changed the criteria for odd-even instability fix to `i+j+k`
    being odd.
    
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src/RadMarshakAsymptotic/CMakeLists.txt
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/RadhydroSimulation.hpp
src/radiation_system.hpp

commit dab9342403faa82d06f6071a78b9482dfc0f28a8
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Dec 6 23:30:41 2023 -0500

    move cluster-specific instructions from wiki to Sphinx docs (#461)
    
    ### Description
    This moves the content of the GitHub wiki pages on running on Gadi and
    Setonix to the Sphinx documentation for greater visibility.
    
    ### Related issues
    N/A
    
    ### Checklist
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    completed. Denote completed tasks with an `x` inside the square brackets
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    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
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docs/index.rst
docs/running_on_hpc_clusters.rst

commit 6f9863af11f1fc40f34b1f3df0e5ab274b064f34
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Dec 6 23:26:18 2023 -0500

    move analysis pages from GitHub wiki to Sphinx docs (#459)
    
    ### Description
    This moves the content about simulation analysis from the GitHub wiki to
    the Sphinx documentation for greater visibility.
    
    ### Related issues
    N/A
    
    ### 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 see (see above).
    - [x] I have read the [Contributing
    Guide](https://github.com/quokka-astro/quokka/blob/development/CONTRIBUTING.md).
    - [ ] I have added tests for any new physics that this PR adds to the
    code.
    - [ ] I have tested this PR on my local computer and all tests pass.
    - [ ] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
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docs/analysis.rst
docs/index.rst

commit 5f7ba7d926cae7a140c96962cf41ef7ddc9b810a
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon Dec 4 12:56:30 2023 -0500

    [pre-commit.ci] pre-commit autoupdate (#464)
    
    <!--pre-commit.ci start-->
    updates:
    - [github.com/pre-commit/mirrors-clang-format: v17.0.5 →
    v17.0.6](https://github.com/pre-commit/mirrors-clang-format/compare/v17.0.5...v17.0.6)
    <!--pre-commit.ci end-->
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

commit 44b11c718b9416c84c5001a03552f176a2c850f4
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Dec 2 12:55:52 2023 -0500

    Add pull_request_template.md (#452)
    
    This creates a pull request template with a checklist for future PRs to
    use.
    
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.github/pull_request_template.md

commit 67d9f84ad7542168bf1dded1b00bcd77f3c6107d
Author: Aditi <45175933+aditivijayan@users.noreply.github.com>
Date:   Sun Dec 3 04:48:21 2023 +1100

    adding parameters.rst to docs (#432)
    
    New push from freshly repo-ed quokka!
    
    ---------
    
    Co-authored-by: Ben Wibking <ben@wibking.com>

docs/index.rst
docs/parameters.rst

commit ead817cc0bfa69363208c2bd3afcbb3526101eec
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Fri Dec 1 08:57:48 2023 -0500

    Bump extern/amrex from `601cc4e` to `9b733ec` (#457)
    
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    `601cc4e` to `9b733ec`.
    <details>
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    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/9b733ec45cd93a80234a7c98248b6eb4816589d5"><code>9b733ec</code></a>
    solve_cg: avoid use of MF <code>z</code> (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3637">#3637</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/0cd1385bde604099e5822d636f85d724d74d756e"><code>0cd1385</code></a>
    Fix: nosmt OMP Threads Default (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3647">#3647</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/44c5c7a5da23c1a5e7e899612b1df696cea7e4fe"><code>44c5c7a</code></a>
    When checking for periodic outs on GPU, copy full particle data (<a
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    href="https://github.com/AMReX-Codes/amrex/commit/4b8dd0373188ca6505e3a9dfaaafbaf4b7fe5ffe"><code>4b8dd03</code></a>
    Comments on FAB-related classes and methods (<a
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    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/60b45bc19b691c1187f4cfd9cd39b2744bf7e35a"><code>60b45bc</code></a>
    MLEBABecLap: Support Robin BC at Domain Boundaries (<a
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    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/9e35dc19489dc5d312e92781cb0471d282cf8370"><code>9e35dc1</code></a>
    Ascent: SoA Particle Support (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3350">#3350</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/c51e0a3071f3f1d2a11b6c339bff58d4ba5e30e8"><code>c51e0a3</code></a>
    CI: Ascent + Conduit (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3639">#3639</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/d75c04b422dae567c9d3c74482b5be84d002ee57"><code>d75c04b</code></a>
    solve_bicgstab: use fewer MFs (<a
    href="https://redirect.github.com/AMReX-Codes/amrex/issues/3635">#3635</a>)</li>
    <li><a
    href="https://github.com/AMReX-Codes/amrex/commit/175b99d913dc2748e43c53192737170c770fe0e8"><code>175b99d</code></a>
    solve_bicgstab: cut use of <code>s</code> (<a
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commit e1de98f249a01a8dbbaaec9387b2c01f5d548a7e
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Fri Dec 1 03:16:50 2023 +0000

    Bump extern/yaml-cpp from `db03655` to `eaf7205` (#458)
    
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    href="https://github.com/jbeder/yaml-cpp/commit/eaf72053724814be3b99d38e292fca5797a57b7b"><code>eaf7205</code></a>
    README.md: Describe building with debug libstdc++ mode</li>
    <li><a
    href="https://github.com/jbeder/yaml-cpp/commit/1c5a38eef3fafea9f796b04d16d1c27874f70a02"><code>1c5a38e</code></a>
    workflows/build.yml: Use debug std C++ library on Ubuntu</li>
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extern/yaml-cpp

commit a59dec9d8d0f35c04ecebe922a8ed62663b6c845
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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    Bump extern/fmt from `e0d3e34` to `99b9fbf` (#456)
    
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    href="https://github.com/fmtlib/fmt/commit/99b9fbf8eff2fc63e639260bd96e22f058f4f818"><code>99b9fbf</code></a>
    Add formatter for std::source_location (<a
    href="https://redirect.github.com/fmtlib/fmt/issues/3730">#3730</a>)</li>
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    href="https://github.com/fmtlib/fmt/commit/8f83ee2ad1ec5508434a4570063154465f31d492"><code>8f83ee2</code></a>
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    href="https://github.com/fmtlib/fmt/commit/2a8a694466076eeb69ed5030545409d6bcaeb85b"><code>2a8a694</code></a>
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    Add native and generic representation for filesystem::path format spec
    (<a
    href="https://redirect.github.com/fmtlib/fmt/issues/3729">#3729</a>)</li>
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    href="https://github.com/fmtlib/fmt/commit/5cfd28d476c6859617878f951931b8ce7d36b9df"><code>5cfd28d</code></a>
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extern/fmt

commit f38533bb9e7020c49bf3b159285ac742f7ace185
Author: Neco Kriel <43261821+AstroKriel@users.noreply.github.com>
Date:   Thu Nov 30 01:41:56 2023 +1100

    Extend HydroState to include MHD-vars for HLLD solver (#420)
    
    I have updated the HLLD solver to make reference to the HydroState
    struct, rather than the MHDState struct (which I have deleted). I have
    added the two transverse components of b-field to HydroState, and have
    also added static_assert's to make sure MHD problems only ever use the
    HLLD solver.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    Co-authored-by: Ben Wibking <ben@wibking.com>

src/HLLD.hpp
src/HydroState.hpp
src/MHDState.hpp
src/RadhydroSimulation.hpp
src/hydro_system.hpp

commit 545acfaa0530dd65227daf3a1c16daa79f3b690b
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Thu Nov 30 01:41:00 2023 +1100

    Fix the convergence problem of the Newton-Raphson (#454)
    
    ### Description
    
    Fix the convergence problem of the Newton-Raphson iteration at high
    opatical depth by adding relative and absolute checks of Erad. This
    solves the problem of the Newton-Raphson iteration fails to converge
    when `c dt kappa rho >~ 10^4`. Now, all tests pass even with `resid_tol
    = 1e-13` while originally the RadTube test will fail with this
    resid_tol.
    
    ### Related issues
    
    Fix #451
    
    ### 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 see (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.
    - [x] I have tested this PR on my local computer and all tests pass.
    - [x] I have manually triggered the GPU tests with the magic comment
    `/azp run`.
    - [x] I have requested a reviewer for this PR.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/RadPulse/test_radiation_pulse.cpp
src/radiation_system.hpp

commit 0fb0c56c587bab53c9bce023cab2b2cf8777dc13
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Nov 28 00:49:56 2023 -0500

    fix odd-even decoupling in radiation diffusion limit (#453)
    
    This modifies the radiation Riemann solver in order to suppress the
    odd-even instability that appears in the asymptotic diffusion limit.
    
    A modified equation analysis that explains why the problem occurs is
    given in section 3.1 of [Radice et al.
    (2022)](https://ui.adsabs.harvard.edu/abs/2022MNRAS.512.1499R/abstract).
    
    Fixes https://github.com/quokka-astro/quokka/issues/34.
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/radiation_system.hpp

commit f0b8e39c4bdc0e82a344431295d93f3dfa44891e
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon Nov 20 17:54:41 2023 +0000

    [pre-commit.ci] pre-commit autoupdate (#450)
    
    updates:
    - [github.com/pre-commit/mirrors-clang-format: v17.0.4 → v17.0.5](https://github.com/pre-commit/mirrors-clang-format/compare/v17.0.4...v17.0.5)
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

commit 06113a3db88695505a120619198f55e6b04ed2f5
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Nov 12 21:17:28 2023 -0500

    add profile for AMDGPU ASAN (#446)

scripts/moth-sanitizer.profile

commit 779d51b9cac970fbc1c0863de7889873a3eca5e6
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon Nov 6 12:58:29 2023 -0500

    [pre-commit.ci] pre-commit autoupdate (#444)
    
    updates:
    - [github.com/pre-commit/mirrors-clang-format: v17.0.3 → v17.0.4](https://github.com/pre-commit/mirrors-clang-format/compare/v17.0.3...v17.0.4)
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

commit 0dcd03bc239b6c5a5741065c53065e377802e457
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Nov 5 11:47:25 2023 -0500

    Add build configuration for Moth (#440)
    
    * Add build configuration for Moth
    
    This adds build settings for the AMD GPU node moth.anu.edu.au.
    
    To load these settings, run `source scripts/moth.profile`.
    Then build with `cd build; cmake -DAMReX_GPU_BACKEND=HIP`.
    
    * workaround ROCm compiler bug
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

scripts/moth.profile
src/NSCBC/channel.cpp

commit 07bde3295a179537c380120fb929e63e67a13387
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Nov 5 11:47:13 2023 -0500

    Fix GPU CI config (#443)
    
    * Fix avatargpu CI config
    
    * Update azure-pipelines.yml
    
    * fix typo
    
    * Update azure-pipelines-amdgpu.yml

.ci/azure-pipelines-amdgpu.yml
.ci/azure-pipelines.yml

commit 0eeb3c53f5ff6a19b0f2c2d77b2342aa80712daf
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Nov 3 15:15:17 2023 -0400

    add CI pipeline for AMDGPU (#442)
    
    Co-authored-by: Piyush Sharda <34922596+psharda@users.noreply.github.com>

.ci/azure-pipelines-amdgpu.yml

commit da000f0c5fe1d36c3b538cf508f07d902075452e
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Fri Nov 3 12:40:45 2023 -0400

    Bump extern/Microphysics from `9c08d80` to `657406d` (#439)
    
    Bumps [extern/Microphysics](https://github.com/psharda/Microphysics) from `9c08d80` to `657406d`.
    - [Commits](https://github.com/psharda/Microphysics/compare/9c08d809b6798df9798691174e2fc3a64c41360c...657406dcaf546a5601c8388ef1a2b34a0016edb5)
    
    ---
    updated-dependencies:
    - dependency-name: extern/Microphysics
      dependency-type: direct:production
    ...
    
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extern/Microphysics

commit fda9b7ba885e91dcc91dc0ca3478e2f619c7d5d4
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Thu Nov 2 01:18:11 2023 +1100

    fix src/CMakeLists for macOS with Clang (#395)
    
    * fix src/CMakeLists for macOS with Clang
    
    It's called Clang instead of AppleClang. I have to change this
    in order to make the compiler skip stdc++fs on my Mac
    with apple silicon
    
    * improved check to skip stdc++fs on macOS
    
    * Add AppleClang and Clang check to CMakeLists.txt
    
    * New criterial for including stdc++fs
    
    Do not include stdc++fs if the system is macOS AND
    the compiler is either AppleClang or Clang.
    
    ---------
    
    Co-authored-by: Ben Wibking <ben@wibking.com>

src/CMakeLists.txt

commit 665e4ec8f5675e499457c39d4cba4227755abb30
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Wed Nov 1 14:16:20 2023 +0000

    Bump extern/amrex from `b95482d` to `601cc4e` (#436)
    
    Bumps [extern/amrex](https://github.com/AMReX-Codes/amrex) from `b95482d` to `601cc4e`.
    - [Release notes](https://github.com/AMReX-Codes/amrex/releases)
    - [Commits](https://github.com/AMReX-Codes/amrex/compare/b95482d3b2ad6cab8318c867eb3b71b4f9ee11ac...601cc4ee80e0d7435a5b099202459bbb1f16b7a6)
    
    ---
    updated-dependencies:
    - dependency-name: extern/amrex
      dependency-type: direct:production
    ...
    
    Signed-off-by: dependabot[bot] <support@github.com>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

extern/amrex

commit 5ee5cc0d2b49d8cb698b5092ac98c05efab02ca4
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Wed Nov 1 10:15:09 2023 -0400

    Bump extern/fmt from `349e1c4` to `e0d3e34` (#437)
    
    Bumps [extern/fmt](https://github.com/fmtlib/fmt) from `349e1c4` to `e0d3e34`.
    - [Release notes](https://github.com/fmtlib/fmt/releases)
    - [Commits](https://github.com/fmtlib/fmt/compare/349e1c48d14524c761cc8a72c75abb0d33c237a3...e0d3e346d2308ba581457efb024c88c7a6ed5fe1)
    
    ---
    updated-dependencies:
    - dependency-name: extern/fmt
      dependency-type: direct:production
    ...
    
    Signed-off-by: dependabot[bot] <support@github.com>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

extern/fmt

commit 0dd39aac36d82868677140a3dfc3da4651de2a06
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Wed Nov 1 10:14:53 2023 -0400

    Bump extern/yaml-cpp from `37f1b8b` to `db03655` (#438)
    
    Bumps [extern/yaml-cpp](https://github.com/jbeder/yaml-cpp) from `37f1b8b` to `db03655`.
    - [Release notes](https://github.com/jbeder/yaml-cpp/releases)
    - [Commits](https://github.com/jbeder/yaml-cpp/compare/37f1b8b8c9e5172ff3a79a3d5fdbb87f2994842b...db03655d58c66f31952c772718d0394eac2e5481)
    
    ---
    updated-dependencies:
    - dependency-name: extern/yaml-cpp
      dependency-type: direct:production
    ...
    
    Signed-off-by: dependabot[bot] <support@github.com>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

extern/yaml-cpp

commit daf01c124de3bd2c9eb0fa433f338e8b23827c0d
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Nov 1 07:29:33 2023 -0400

    add Summit (OLCF) config (#435)
    
    * add Summit (OLCF) config
    
    * use bandwidth-optimized MPI settings
    
    * Update summit.profile

cmake/summit.cmake
scripts/summit-1node.bsub
scripts/summit-4096node.bsub
scripts/summit-512node.bsub
scripts/summit-64node.bsub
scripts/summit-8node.bsub
scripts/summit.profile
tests/benchmark_unigrid_256.in
tests/benchmark_unigrid_4096.in

commit 6e190d05fa7ab38dfe4887e99f3cdb59ec3ce8e9
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Nov 1 07:29:17 2023 -0400

    fix out-of-bounds bug in NSCBC outflow (#430)

src/NSCBC_outflow.hpp

commit 306e64497b291c8ff83f297a89df9384b4664f3d
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon Oct 23 18:40:20 2023 +0000

    [pre-commit.ci] pre-commit autoupdate (#433)
    
    updates:
    - [github.com/pre-commit/mirrors-clang-format: v17.0.2 → v17.0.3](https://github.com/pre-commit/mirrors-clang-format/compare/v17.0.2...v17.0.3)
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

commit 1e9ed88bd91f147fd9ccb1d9900b8bd835d3b451
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon Oct 16 18:20:47 2023 +0000

    [pre-commit.ci] pre-commit autoupdate (#427)
    
    updates:
    - [github.com/pre-commit/mirrors-clang-format: v16.0.6 → v17.0.2](https://github.com/pre-commit/mirrors-clang-format/compare/v16.0.6...v17.0.2)
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

commit 10f1350ed51d0ec55dab84b5a505ea78ece7dba8
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Oct 16 08:46:22 2023 -0400

    Bump ZedThree/clang-tidy-review from 0.13.4 to 0.14.0 (#426)
    
    Bumps [ZedThree/clang-tidy-review](https://github.com/zedthree/clang-tidy-review) from 0.13.4 to 0.14.0.
    - [Release notes](https://github.com/zedthree/clang-tidy-review/releases)
    - [Changelog](https://github.com/ZedThree/clang-tidy-review/blob/master/CHANGELOG.md)
    - [Commits](https://github.com/zedthree/clang-tidy-review/compare/v0.13.4...v0.14.0)
    
    ---
    updated-dependencies:
    - dependency-name: ZedThree/clang-tidy-review
      dependency-type: direct:production
      update-type: version-update:semver-minor
    ...
    
    Signed-off-by: dependabot[bot] <support@github.com>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

.github/workflows/clang-tidy-comments.yml
.github/workflows/clang-tidy.yml

commit 323b25eb38a3e0e8a27edd1f716e4d78b33006c7
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Sat Oct 14 18:11:58 2023 +0000

    [pre-commit.ci] pre-commit autoupdate (#423)
    
    updates:
    - [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v4.5.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.4.0...v4.5.0)
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    Co-authored-by: Ben Wibking <ben@wibking.com>

.pre-commit-config.yaml

commit cf5bcda3b235dbedfc0350d261bf6713c5f097dc
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Oct 14 02:54:59 2023 -0400

    workaround macOS GitHub actions bug (#425)
    
    Fixes https://github.com/quokka-astro/quokka/issues/424.

.github/workflows/cmake-macos.yml

commit bd9046b6cbedc4e25e2456e1033e695202df204d
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Fri Oct 6 22:56:43 2023 +0200

    Renormalize mass scalars post enforcing floor (#405)
    
    * renormalize mass scalars post enforcing limit
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci
    
    ---------
    
    Co-authored-by: Piyush Sharda <psharda@RSAA-043527.local>
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/hydro_system.hpp

commit 35b17f20657b0a5cd5a959876dbe70416696d84d
Author: ChongChong He <chongchonghe99@gmail.com>
Date:   Sat Oct 7 01:57:52 2023 +1100

    Multigroup radiation transport implementation (#388)
    
    * first commit: fix CMakeLists for macOS
    
    * multigroup branch, first try, with bugs
    
    * on macOS, at 2023-09-06 22:02:53
    
    * multigrou photon, second commit, fixed bug
    
    Added multigroup photon support for radiation only.
    The matter-radiation coupling is not added yet.
    
    test_radiation_streaming: fully passed
    test_radiation_force: produce the same result. The error caused by
    ignoring matter-radiation coupling is negligible.
    test_radiation_SuOlson: simulation runs but failed at logging stage.
    
    * Add radiation-matter coupling and radiation
    energy update
    
    - radiation_streaming is working
    - SuOlson is kind of working
    
    * Multigropu RT, passed RadForce test
    
    * Multigroup RT, passed RadTube test
    
    * Multigroup: clean up
    
    * tmp commit
    
    * some minor fixes
    
    1. moved nGroups to Physics_Traits and put lower and upper bounds into radBoundaries
    2. Renamed ComputePlanckOpacityForGroup to ComputePlanckOpacity.
    
    * renamed fillin in valarray
    
    * Implementing suggestions from Ben and Mark.
    Two more major things to be done before ready to merge to
    main branch after review:
    1. update all tests to apply to multigroup (most of them are trivial)
    2. update integrate_planck function following Mark's suggestion
    - removing array_x.
    
    * define valarray.fillin and fixed radiation_tube
    
    * Ready to merge to main branch.
    Passed 100% of the tests for 1D problems
    
    * Fixed compiling errors of the 2D and 3D problems
    on multigroup branch
    
    * try to fix HIP errors and clang-tidy warnings
    
    * fix a few tidy warnings
    
    * fix ifndef bug
    
    * fix warning in SuOlson.cpp
    
    * fix a few tidy warnings
    
    * fixed "radBoundaries not on device" error
    for radiation_system.hpp and SuOlson test
    
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src/CloudyCooling.hpp
src/Cooling/test_cooling.cpp
src/FCQuantities/test_fc_quantities.cpp
src/HydroBlast2D/test_hydro2d_blast.cpp
src/HydroBlast3D/test_hydro3d_blast.cpp
src/HydroContact/test_hydro_contact.cpp
src/HydroHighMach/test_hydro_highmach.cpp
src/HydroKelvinHelmholz/test_hydro2d_kh.cpp
src/HydroLeblanc/test_hydro_leblanc.cpp
src/HydroQuirk/test_quirk.cpp
src/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
src/HydroSMS/test_hydro_sms.cpp
src/HydroShocktube/test_hydro_shocktube.cpp
src/HydroShocktubeCMA/test_hydro_shocktube_cma.cpp
src/HydroShuOsher/test_hydro_shuosher.cpp
src/HydroVacuum/test_hydro_vacuum.cpp
src/HydroWave/test_hydro_wave.cpp
src/NSCBC/channel.cpp
src/NSCBC/vortex.cpp
src/PassiveScalar/test_scalars.cpp
src/PrimordialChem/test_primordial_chem.cpp
src/RadBeam/test_radiation_beam.cpp
src/RadForce/test_radiation_force.cpp
src/RadMarshak/test_radiation_marshak.cpp
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadPulse/test_radiation_pulse.cpp
src/RadShadow/test_radiation_shadow.cpp
src/RadStreaming/test_radiation_streaming.cpp
src/RadSuOlson/test_radiation_SuOlson.cpp
src/RadTophat/test_radiation_tophat.cpp
src/RadTube/test_radiation_tube.cpp
src/RadhydroShell/test_radhydro_shell.cpp
src/RadhydroShock/test_radhydro_shock.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/RadhydroSimulation.hpp
src/RayleighTaylor2D/test_hydro2d_rt.cpp
src/RayleighTaylor3D/test_hydro3d_rt.cpp
src/ShockCloud/cloud.cpp
src/SphericalCollapse/spherical_collapse.cpp
src/StarCluster/star_cluster.cpp
src/physics_info.hpp
src/planck_integral.hpp
src/radiation_system.hpp

commit 7d9ab28218d32c163ddcf20ec86165f78e6a517a
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Oct 4 11:27:30 2023 -0400

    Update GPU CI timeout (#417)
    
    * Update GPU CI timeout
    
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    * Update azure-pipelines.yml
    
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.ci/azure-pipelines.yml

commit cb0c1151c5baa510c1c45282d8373431b9d1896b
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Oct 3 12:52:45 2023 -0400

    Fix typos found by codespell (#416)
    
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src/AdvectionSimulation.hpp
src/StarCluster/perturbation.py

commit c374406310a277c4e178df4ddc196c2ff58253ac
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Oct 2 22:23:23 2023 -0400

    Update issue templates (#414)
    
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    1. bug reports, and
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.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/feature-proposal.md

commit 7767642c624ac8ea3765e7ba8107b19078bb2052
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sun Oct 1 08:21:10 2023 -0400

    Bump extern/amrex from `1aea95c` to `b95482d` (#409)
    
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extern/amrex

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Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sun Oct 1 08:20:49 2023 -0400

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extern/Microphysics

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Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sun Oct 1 08:20:28 2023 -0400

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extern/yaml-cpp

commit 10afd87980675499bb57207748e049919273b651
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sun Oct 1 08:20:18 2023 -0400

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extern/fmt

commit 22ffc1b4f2c8cf56784b1fb21039ab275cbcca53
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Fri Sep 29 00:11:07 2023 +0200

    Fix indentations  (#407)
    
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src/AdvectionSimulation.hpp
src/RadhydroSimulation.hpp
src/hydro_system.hpp
src/simulation.hpp
src/valarray.hpp

commit a37934f74c6de738321d6898906afd4a054f26bd
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Mon Sep 25 20:50:10 2023 +0200

    Add sample Setonix scripts (#399)
    
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    Co-authored-by: Piyush Sharda <psharda@RSAA-043527.local>

scripts/cpu-setonix.sh
scripts/setonix-cpu.profile
scripts/setonix-gpu.profile

commit a97b927aa0130743bc6c195dba7f6b72fa642ddf
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Mon Sep 25 16:22:46 2023 +0200

    Update README (#398)
    
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README.md

commit 033e4f3e98b20243922d1e4407a62209f8282cee
Author: ChongChong He <che1234@umd.edu>
Date:   Thu Sep 21 23:11:15 2023 +1000

    Valarray extended (#391)
    
    * first commit: fix CMakeLists for macOS
    
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src/valarray.hpp

commit 1cebf4bf5dfc5a676e70e004649e627637d40e77
Author: ChongChong He <che1234@umd.edu>
Date:   Thu Sep 21 23:11:02 2023 +1000

    update the flowchart on the website (#392)
    
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docs/flowchart-v2.jpg
docs/flowchart-v2.pdf
docs/flowchart.rst

commit 2eb8d6c980c2c3e12bf7facd012d4f8306685275
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Sep 19 08:05:35 2023 -0400

    update amrex (#387)

extern/amrex

commit ba35f265efa5eb010b252a520fad7a6384806ac7
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Sep 19 08:02:48 2023 -0400

    output multifab to disk if hydro update fails (#385)
    
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src/RadhydroSimulation.hpp

commit ab9ca8b937bcc65126b18150934618276a806045
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Tue Sep 19 13:59:41 2023 +0200

    Print coordinates of cells where flux correction is needed (#383)
    
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src/RadhydroSimulation.hpp

commit 5a4276394416a10b994262955c257bc4a6caedcf
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Sep 19 07:59:28 2023 -0400

    use minmod limiting for PLM (#384)

src/hyperbolic_system.hpp

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Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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    Bump ZedThree/clang-tidy-review from 0.13.3 to 0.13.4 (#389)
    
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.github/workflows/clang-tidy-comments.yml
.github/workflows/clang-tidy.yml

commit a3fc85cc318b1738cfb42431546cf167fe4848a9
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Thu Sep 14 03:04:52 2023 +0200

    Enforce checks and limits on mass scalars (#378)
    
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src/hydro_system.hpp

commit 16d57370dd346603f54d5977aa65c823b26eeec5
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Sep 13 19:05:31 2023 -0500

    add LLF fallback solver (#380)
    
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src/LLF.hpp
src/RadhydroSimulation.hpp
src/hydro_system.hpp

commit ca3f360580ba184058ac696aadeedb600e94ec72
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Sep 12 20:05:26 2023 -0500

    ensure first-order flux correction is consistent at box boundaries (#376)
    
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src/RadhydroSimulation.hpp

commit 6b0e0c8e37888f7cdbc6f207c8c8b385e3def035
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Sep 12 06:37:03 2023 -0500

    revert to first-order space+time flux when RK2 flux fails (#221)
    
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extern/highmach_reference.txt
src/HydroHighMach/test_hydro_highmach.cpp
src/RadhydroSimulation.hpp

commit e513022b5f0b0ca7caf5fd0f0f3851e75c52b861
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Sep 11 11:55:11 2023 -0400

    Bump actions/checkout from 3 to 4 (#370)
    
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.github/workflows/clang-tidy.yml
.github/workflows/cmake-macos.yml
.github/workflows/cmake.yml
.github/workflows/codespell.yml
.github/workflows/docs.yml
.github/workflows/hip.yml
.github/workflows/sonarcloud.yml
.github/workflows/warnings.yml

commit d17b5e4b742e3b9b1401c0418edaf4c625503ea4
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Sep 9 17:42:41 2023 -0400

    update setonix configuration (#362)
    
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cmake/setonix.cmake
scripts/setonix-1node.submit
scripts/setonix-64nodes.submit
scripts/setonix-8nodes.submit
scripts/setonix-rocm5.3.0.profile
scripts/setonix-rocm5.4.3.profile
scripts/setonix.profile

commit 7ffd65fd08eece9c3e5e8c6db61b835d9e410fd4
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Sep 9 07:40:19 2023 -0400

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src/simulation.hpp

commit b169a30c59d57e80eb83fcad77d3fb76d4350334
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Sep 9 07:38:50 2023 -0400

    add axis-aligned projection outputs (#367)
    
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src/AdvectionSimulation.hpp
src/RadhydroSimulation.hpp
src/simulation.hpp

commit bce9c28d5353073552e273093983c3111cd21242
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Fri Sep 8 18:58:28 2023 -0600

    Remove is_chemistry_enabled (#369)
    
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src/Advection/test_advection.cpp
src/Advection2D/test_advection2d.cpp
src/AdvectionSemiellipse/test_advection_semiellipse.cpp
src/Cooling/test_cooling.cpp
src/FCQuantities/test_fc_quantities.cpp
src/HydroBlast2D/test_hydro2d_blast.cpp
src/HydroBlast3D/test_hydro3d_blast.cpp
src/HydroContact/test_hydro_contact.cpp
src/HydroHighMach/test_hydro_highmach.cpp
src/HydroKelvinHelmholz/test_hydro2d_kh.cpp
src/HydroLeblanc/test_hydro_leblanc.cpp
src/HydroQuirk/test_quirk.cpp
src/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
src/HydroSMS/test_hydro_sms.cpp
src/HydroShocktube/test_hydro_shocktube.cpp
src/HydroShocktubeCMA/test_hydro_shocktube_cma.cpp
src/HydroShuOsher/test_hydro_shuosher.cpp
src/HydroVacuum/test_hydro_vacuum.cpp
src/HydroWave/test_hydro_wave.cpp
src/NSCBC/channel.cpp
src/NSCBC/vortex.cpp
src/PassiveScalar/test_scalars.cpp
src/PrimordialChem/test_primordial_chem.cpp
src/RadBeam/test_radiation_beam.cpp
src/RadForce/test_radiation_force.cpp
src/RadMarshak/test_radiation_marshak.cpp
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadPulse/test_radiation_pulse.cpp
src/RadStreaming/test_radiation_streaming.cpp
src/RadSuOlson/test_radiation_SuOlson.cpp
src/RadTophat/test_radiation_tophat.cpp
src/RadTube/test_radiation_tube.cpp
src/RadhydroShell/test_radhydro_shell.cpp
src/RadhydroShock/test_radhydro_shock.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/RadhydroSimulation.hpp
src/RayleighTaylor2D/test_hydro2d_rt.cpp
src/RayleighTaylor3D/test_hydro3d_rt.cpp
src/ShockCloud/cloud.cpp
src/SphericalCollapse/spherical_collapse.cpp
src/StarCluster/star_cluster.cpp
src/physics_info.hpp

commit 2704e30ca6322e9bb543a9512f5c32ca7a5c57c2
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Sep 7 22:29:29 2023 -0400

    add history file output (#366)
    
    * add history file output
    
    * code linting
    
    * note user responsibility for MPI reductions

src/AdvectionSimulation.hpp
src/RadhydroSimulation.hpp
src/simulation.hpp

commit 048e8ad0575ad7a78f793f0cc959f277c37fbd0c
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Sep 7 20:00:56 2023 -0400

    fill ghost cells before output (#363)
    
    * fill ghost cells before output
    
    * also fill face-centered vars
    
    * use FillPatchType::fillpatch_function
    
    * check if fc vars exist

src/simulation.hpp

commit a292e791014e40e81e15d2fc8dad747a3e23cfa9
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Sep 7 19:59:45 2023 -0400

    copy Blueprint mesh to host (#365)

src/simulation.hpp

commit 50b22e1781bbe8e26548347f5738d5916784463d
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Sep 5 19:41:20 2023 -0400

    add yaml-cpp as a submodule (#360)
    
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.gitmodules
CMakeLists.txt
extern/sedov/sedov.ipynb
extern/yaml-cpp
src/CMakeLists.txt
src/NSCBC/dQ_dx_inflow.ipynb
src/NSCBC/dQ_dx_outflow.ipynb

commit 1b5d55dc15b46b56cc4722543230db32aa42c97f
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Fri Sep 1 09:23:21 2023 -0400

    Bump extern/amrex from `cf8d9f8` to `de7c618` (#354)
    
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    - [Release notes](https://github.com/AMReX-Codes/amrex/releases)
    - [Commits](https://github.com/AMReX-Codes/amrex/compare/cf8d9f8e233be2ac68aeb65a95e992adfb483939...de7c6189623bc3ba178a380e703e3173f33f78ef)
    
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    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

extern/amrex

commit d063f3932bb8ee61cee54f366778aba010f68960
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Fri Sep 1 09:22:56 2023 -0400

    Bump extern/fmt from `8a4bec5` to `e8259c5` (#355)
    
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extern/fmt

commit 9e804e6615c6ed3977710751402bd6715ec63505
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Fri Sep 1 09:22:36 2023 -0400

    Bump extern/Microphysics from `9ecfd8d` to `ced7cc4` (#356)
    
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extern/Microphysics

commit 13be468b4ccfe13090d5aa515c026cd2cf482fac
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Aug 31 19:52:52 2023 -0400

    add Navier-Stokes Characteristic Boundary Conditions (#352)
    
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src/CMakeLists.txt
src/NSCBC/CMakeLists.txt
src/NSCBC/channel.cpp
src/NSCBC/channel.hpp
src/NSCBC/dQ_dx_inflow.ipynb
src/NSCBC/dQ_dx_outflow.ipynb
src/NSCBC/vortex.cpp
src/NSCBC/vortex.hpp
src/NSCBC_inflow.hpp
src/NSCBC_outflow.hpp
src/RadhydroSimulation.hpp
src/hydro_system.hpp
src/simulation.hpp
tests/NSCBC_Channel.in
tests/NSCBC_Vortex.in

commit 21e95ca8f252296c4666c62828edcada86d91894
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Thu Aug 17 09:26:16 2023 -0700

    updated microphysics (#351)

extern/Microphysics

commit 6959b0edd0d3ffd1c8ab2e37491a0a356f377b0c
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Aug 14 04:19:29 2023 +0000

    Bump ZedThree/clang-tidy-review from 0.13.2 to 0.13.3 (#348)
    
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.github/workflows/clang-tidy-comments.yml
.github/workflows/clang-tidy.yml

commit fb96683045919a9b574b2329d59039605e9e6cf6
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Wed Aug 9 10:35:49 2023 -0700

    Starcluster example problem (#342)
    
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    Co-authored-by: Ben Wibking <ben@wibking.com>
    Co-authored-by: Ben Wibking <wibkingb@msu.edu>
    Co-authored-by: Piyush Sharda <psharda@RSAA-043527.local>
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.gitmodules
cmake/crusher.cmake
extern/Microphysics
src/CMakeLists.txt
src/RadhydroSimulation.hpp
src/SphericalCollapse/spherical_collapse.hpp
src/StarCluster/CMakeLists.txt
src/StarCluster/TurbDataReader.cpp
src/StarCluster/TurbDataReader.hpp
src/StarCluster/ascent_actions.yaml
src/StarCluster/perturbation.py
src/StarCluster/star_cluster.cpp
src/StarCluster/star_cluster.hpp
src/simulation.hpp
tests/SphericalCollapse.in
tests/StarCluster.in
tests/StarCluster_AMR.in

commit add2204f6e89a10d2dda5544a3d3d3d15f0565d8
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Aug 7 12:24:05 2023 -0400

    Bump ZedThree/clang-tidy-review from 0.13.1 to 0.13.2 (#343)
    
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.github/workflows/clang-tidy-comments.yml
.github/workflows/clang-tidy.yml

commit eb3bdf8a78c5ded4cbc285c240d9054334929c1f
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Aug 7 12:23:34 2023 -0400

    Bump SonarSource/sonarcloud-github-c-cpp from 1 to 2 (#344)
    
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.github/workflows/sonarcloud.yml

commit 685110f04c9f4dc9b1139a85e74c2cc9c0588e00
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Wed Aug 2 19:28:19 2023 +0200

    Implement general EOS equations in Riemann Solver (#338)
    
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extern/Microphysics
src/EOS.hpp
src/HLLC.hpp
src/HydroContact/test_hydro_contact.cpp
src/HydroSMS/test_hydro_sms.cpp
src/HydroState.hpp
src/hydro_system.hpp

commit 842ddf9428ebc194f03baf00d68746441ff39cc6
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Tue Aug 1 10:12:46 2023 -0400

    Bump extern/amrex from `9c256b1` to `cf8d9f8` (#340)
    
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extern/amrex

commit 1310040afdee7d9c441760b6d560c592e7f10d21
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Tue Aug 1 09:01:33 2023 -0400

    Bump extern/fmt from `e4c8cfe` to `8a4bec5` (#341)
    
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extern/fmt

commit efc47cf90657e1eee74bb4da01e5b3c0f0597c3a
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Mon Jul 31 00:02:10 2023 +0200

    Compute pressure from microphysics eos (#335)
    
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.gitmodules
extern/Microphysics
src/EOS.hpp
src/HydroBlast2D/test_hydro2d_blast.cpp
src/HydroBlast3D/test_hydro3d_blast.cpp
src/HydroContact/test_hydro_contact.cpp
src/HydroHighMach/test_hydro_highmach.cpp
src/HydroKelvinHelmholz/test_hydro2d_kh.cpp
src/HydroQuirk/test_quirk.cpp
src/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
src/HydroShocktube/test_hydro_shocktube.cpp
src/HydroShocktubeCMA/test_hydro_shocktube_cma.cpp
src/HydroVacuum/test_hydro_vacuum.cpp
src/PassiveScalar/test_scalars.cpp
src/RadMarshak/test_radiation_marshak.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadhydroSimulation.hpp
src/RayleighTaylor2D/test_hydro2d_rt.cpp
src/ShockCloud/cloud.cpp
src/SphericalCollapse/spherical_collapse.cpp
src/hydro_system.hpp

commit aa288b57d2dda961815af7f986ebbb8fc30b9234
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Wed Jul 26 18:51:00 2023 +0200

    Use microphysics EOS in Quokka's EOS.hpp for all quokka tests + use amu instead of hydrogen mass throughout Quokka (#324)
    
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.gitmodules
extern/Microphysics
src/CMakeLists.txt
src/CloudyCooling.hpp
src/Cooling/test_cooling.cpp
src/EOS.hpp
src/FCQuantities/test_fc_quantities.cpp
src/HydroBlast2D/test_hydro2d_blast.cpp
src/HydroBlast3D/test_hydro3d_blast.cpp
src/HydroContact/test_hydro_contact.cpp
src/HydroHighMach/test_hydro_highmach.cpp
src/HydroKelvinHelmholz/test_hydro2d_kh.cpp
src/HydroLeblanc/test_hydro_leblanc.cpp
src/HydroQuirk/test_quirk.cpp
src/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
src/HydroSMS/test_hydro_sms.cpp
src/HydroShocktube/test_hydro_shocktube.cpp
src/HydroShocktubeCMA/test_hydro_shocktube_cma.cpp
src/HydroShuOsher/test_hydro_shuosher.cpp
src/HydroVacuum/test_hydro_vacuum.cpp
src/HydroWave/test_hydro_wave.cpp
src/ODEIntegration/test_ode.cpp
src/PassiveScalar/test_scalars.cpp
src/PrimordialChem/test_primordial_chem.cpp
src/RadBeam/test_radiation_beam.cpp
src/RadForce/test_radiation_force.cpp
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadPulse/test_radiation_pulse.cpp
src/RadShadow/test_radiation_shadow.cpp
src/RadTophat/test_radiation_tophat.cpp
src/RadTube/test_radiation_tube.cpp
src/RadhydroShell/test_radhydro_shell.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/RadhydroSimulation.hpp
src/RayleighTaylor2D/test_hydro2d_rt.cpp
src/RayleighTaylor3D/test_hydro3d_rt.cpp
src/ShockCloud/cloud.cpp
src/ShockCloud/test_cloudy.cpp
src/SphericalCollapse/spherical_collapse.cpp

commit 1b572e70c1ab71d40e8c7f8650d9c90f4fcbe0df
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Jul 5 05:06:40 2023 +1000

    updated libfabric settings on Setonix (#331)

scripts/setonix-1node.submit
scripts/setonix-64nodes.submit
scripts/setonix-8nodes.submit

commit 4826207bed55969c35893df8c77f7251d70258d0
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sun Jul 2 10:26:57 2023 +1000

    Bump extern/amrex from `2e1106e` to `9c256b1` (#329)
    
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extern/amrex

commit e95c02f34c7ca51f1944ca0674b7e7707f1dc664
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Sun Jul 2 00:34:57 2023 +1000

    Bump extern/fmt from `b2106f3` to `e4c8cfe` (#330)
    
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extern/fmt

commit 158a3e6c02b1f809429cf9759321554afa7a8d52
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Thu Jun 22 15:00:57 2023 +0200

    Two EOS compilation for Quokka + fix build on cray systems (#311)
    
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.gitmodules
extern/Microphysics
src/Advection/CMakeLists.txt
src/Advection2D/CMakeLists.txt
src/AdvectionSemiellipse/CMakeLists.txt
src/CMakeLists.txt
src/Chemistry.hpp
src/Cooling/CMakeLists.txt
src/EOS.hpp
src/FCQuantities/CMakeLists.txt
src/HydroBlast2D/CMakeLists.txt
src/HydroBlast3D/CMakeLists.txt
src/HydroContact/CMakeLists.txt
src/HydroHighMach/CMakeLists.txt
src/HydroKelvinHelmholz/CMakeLists.txt
src/HydroLeblanc/CMakeLists.txt
src/HydroQuirk/CMakeLists.txt
src/HydroRichtmeyerMeshkov/CMakeLists.txt
src/HydroSMS/CMakeLists.txt
src/HydroShocktube/CMakeLists.txt
src/HydroShocktubeCMA/CMakeLists.txt
src/HydroShuOsher/CMakeLists.txt
src/HydroVacuum/CMakeLists.txt
src/HydroWave/CMakeLists.txt
src/ODEIntegration/CMakeLists.txt
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src/RadMatterCouplingRSLA/CMakeLists.txt
src/RadPulse/CMakeLists.txt
src/RadShadow/CMakeLists.txt
src/RadStreaming/CMakeLists.txt
src/RadSuOlson/CMakeLists.txt
src/RadTophat/CMakeLists.txt
src/RadTube/CMakeLists.txt
src/RadhydroShell/CMakeLists.txt
src/RadhydroShock/CMakeLists.txt
src/RadhydroShockCGS/CMakeLists.txt
src/RayleighTaylor2D/CMakeLists.txt
src/RayleighTaylor3D/CMakeLists.txt
src/ShockCloud/CMakeLists.txt
src/SphericalCollapse/CMakeLists.txt

commit 761f4b6f92675ab7ce25a79eafbd260624993619
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Jun 22 05:39:12 2023 +1000

    Update dependencies_hip.sh to use ROCm 5.4.3 (#318)
    
    * Update dependencies_hip.sh to use ROCm 5.4.3
    
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.github/workflows/dependencies/dependencies_hip.sh

commit d6828f8b1e1408040ba1b757071ce70c46309fe4
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Jun 21 16:44:20 2023 +1000

    update Setonix CMake settings (#321)
    
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    * add script for ROCm 5.3.0

cmake/setonix.cmake
scripts/setonix-rocm5.3.0.profile
scripts/setonix-rocm5.4.3.profile
src/simulation.hpp

commit 6c2a334a82343403129cac96849d4ef5c57291e5
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Tue Jun 20 00:13:20 2023 +0000

    [pre-commit.ci] pre-commit autoupdate (#322)
    
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.pre-commit-config.yaml

commit 6194feb05750602233433f6e051616b0ee2b29e6
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Thu Jun 15 14:23:58 2023 +0200

    use two cores to run arm64 debug pipeline (#317)
    
    * use two cores to ctest debug pipeline
    
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.ci/azure-pipelines-aarch64-debug.yml
.ci/azure-pipelines-aarch64.yml

commit 3f0e55b363d050f61132884608b5986f5a9938a4
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Sun Jun 11 23:21:55 2023 +0200

    Ensure EOS.hpp compiles on AMD GPUs (#310)
    
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.github/workflows/dependencies/dependencies_ccache.sh
.github/workflows/dependencies/dependencies_hip.sh
.github/workflows/hip.yml
src/EOS.hpp

commit e28914a74882802caec19203a434d45ca062da58
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Fri Jun 2 12:29:36 2023 +0000

    Bump extern/amrex from `cf6b46b` to `2e1106e` (#305)
    
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extern/amrex

commit 0cf84a1af8d81d9740f04531fcd2096511219408
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Thu Jun 1 03:24:41 2023 -0400

    Bump extern/fmt from `02cae7e` to `b2106f3` (#302)
    
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extern/fmt

commit cdc0c8b80f6ba3aa5812b8e06471bb032e209999
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Thu Jun 1 03:24:12 2023 -0400

    Bump extern/Microphysics from `7fd6094` to `bf80346` (#303)
    
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    ---
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extern/Microphysics

commit 9514ffcd78794d26b695e7f80e2683fa058b6d83
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon May 29 20:07:20 2023 +1000

    Bump ZedThree/clang-tidy-review from 0.13.0 to 0.13.1 (#301)
    
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    - [Changelog](https://github.com/ZedThree/clang-tidy-review/blob/master/CHANGELOG.md)
    - [Commits](https://github.com/ZedThree/clang-tidy-review/compare/v0.13.0...v0.13.1)
    
    ---
    updated-dependencies:
    - dependency-name: ZedThree/clang-tidy-review
      dependency-type: direct:production
      update-type: version-update:semver-patch
    ...
    
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.github/workflows/clang-tidy-comments.yml
.github/workflows/clang-tidy.yml

commit 5fefc19578e6a19a192a5c6fd13349550d0eddf2
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Thu May 25 23:59:49 2023 +0200

    include massScalars in call to EOS functions in hydro and radiation (#298)
    
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src/hydro_system.hpp
src/radiation_system.hpp

commit 4baa62394d42a35c4000c5912258317baa2ccd43
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Wed May 24 20:31:27 2023 +0200

    Compute massScalars and use them in EOS routines (#296)
    
    * defined a new function to retrieve mass scalars
    
    * use microphysics EOS for primordial chem
    
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    * rename massFractions --> massScalars
    
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    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/EOS.hpp
src/RadMarshak/test_radiation_marshak.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadSuOlson/test_radiation_SuOlson.cpp
src/RadTophat/test_radiation_tophat.cpp
src/hydro_system.hpp

commit 79748f5745f0d2ab549fb30e1cfe30dcbb82f282
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Tue May 23 21:28:04 2023 +0200

    Using CMake object library to compile files needed by all tests (#295)
    
    * updated microphysics
    
    * using object library to compile CloudyCooling, main and GrackleReader
    
    * added comment

src/Advection/CMakeLists.txt
src/Advection2D/CMakeLists.txt
src/AdvectionSemiellipse/CMakeLists.txt
src/CMakeLists.txt
src/Cooling/CMakeLists.txt
src/FCQuantities/CMakeLists.txt
src/HydroBlast2D/CMakeLists.txt
src/HydroBlast3D/CMakeLists.txt
src/HydroContact/CMakeLists.txt
src/HydroHighMach/CMakeLists.txt
src/HydroKelvinHelmholz/CMakeLists.txt
src/HydroLeblanc/CMakeLists.txt
src/HydroQuirk/CMakeLists.txt
src/HydroRichtmeyerMeshkov/CMakeLists.txt
src/HydroSMS/CMakeLists.txt
src/HydroShocktube/CMakeLists.txt
src/HydroShocktubeCMA/CMakeLists.txt
src/HydroShuOsher/CMakeLists.txt
src/HydroVacuum/CMakeLists.txt
src/HydroWave/CMakeLists.txt
src/ODEIntegration/CMakeLists.txt
src/PassiveScalar/CMakeLists.txt
src/PrimordialChem/CMakeLists.txt
src/RadBeam/CMakeLists.txt
src/RadForce/CMakeLists.txt
src/RadMarshak/CMakeLists.txt
src/RadMarshakAsymptotic/CMakeLists.txt
src/RadMarshakCGS/CMakeLists.txt
src/RadMatterCoupling/CMakeLists.txt
src/RadMatterCouplingRSLA/CMakeLists.txt
src/RadPulse/CMakeLists.txt
src/RadShadow/CMakeLists.txt
src/RadStreaming/CMakeLists.txt
src/RadSuOlson/CMakeLists.txt
src/RadTophat/CMakeLists.txt
src/RadTube/CMakeLists.txt
src/RadhydroShell/CMakeLists.txt
src/RadhydroShock/CMakeLists.txt
src/RadhydroShockCGS/CMakeLists.txt
src/RayleighTaylor2D/CMakeLists.txt
src/RayleighTaylor3D/CMakeLists.txt
src/ShockCloud/CMakeLists.txt
src/SphericalCollapse/CMakeLists.txt

commit 780d65110fe0bf051dbdf803965217f8b41a6fa2
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Tue May 23 21:27:42 2023 +0200

    Add massFractions as an optional argument to EOS routines (#291)
    
    * updated eos
    
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    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.gitmodules
extern/Microphysics
src/EOS.hpp
src/RadBeam/test_radiation_beam.cpp
src/RadMarshak/test_radiation_marshak.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadSuOlson/test_radiation_SuOlson.cpp
src/RadTophat/test_radiation_tophat.cpp

commit d123a518eb51f401ad5127e40f99164a81ed7a8e
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon May 22 23:25:37 2023 +0000

    [pre-commit.ci] pre-commit autoupdate (#294)
    
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.pre-commit-config.yaml

commit 7d6c8b7ccd616347e5443b37aeb17ed8c1032da2
Author: Ben Wibking <ben@wibking.com>
Date:   Tue May 23 04:13:32 2023 +1000

    create new GitHub action for compiler warnings (#293)

.ci/azure-pipelines-aarch64-debug.yml
.ci/azure-pipelines-aarch64.yml
.github/workflows/cmake-macos.yml
.github/workflows/cmake.yml
.github/workflows/warnings.yml

commit 0e24f9d2b246ae683bab319dd49c4176013dae7d
Author: Ben Wibking <ben@wibking.com>
Date:   Sat May 20 00:33:43 2023 +1000

    simplify Setonix SLURM scripts (#289)
    
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scripts/setonix-1node.submit
scripts/setonix-64nodes.pbs
scripts/setonix-64nodes.submit
scripts/setonix-8nodes.pbs
scripts/setonix-8nodes.submit

commit 3db8ac6d5bf2e2405a1a0a69491047113b72b21e
Author: Ben Wibking <ben@wibking.com>
Date:   Fri May 19 16:33:38 2023 +1000

    treat all compiler warnings as errors (#283)
    
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    Co-authored-by: Ben Wibking <benwibking@gmail.com>
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.ci/azure-pipelines-aarch64-debug.yml
.ci/azure-pipelines-aarch64.yml
.github/workflows/cmake-macos.yml
.github/workflows/cmake.yml
CMakeLists.txt
extern/Microphysics
src/CMakeLists.txt
src/CloudyCooling.hpp
src/HydroShocktube/test_hydro_shocktube.cpp
src/ODEIntegrate.hpp
src/PrimordialChem/test_primordial_chem.cpp
src/RadMarshak/test_radiation_marshak.cpp
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadPulse/test_radiation_pulse.cpp
src/RadSuOlson/test_radiation_SuOlson.cpp
src/RadhydroShock/test_radhydro_shock.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/RadhydroSimulation.hpp
src/hydro_system.hpp
src/radiation_system.hpp
src/valarray.hpp

commit 09e5d4e1501d9f90d6048013d1d4849f792b5f5f
Author: Aditi <45175933+aditivijayan@users.noreply.github.com>
Date:   Wed May 17 03:31:42 2023 +1000

    optimise load (#287)
    
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src/simulation.hpp

commit 5e6c3e0ea770cd3452228139ffa80c1780cad7bb
Author: Ben Wibking <ben@wibking.com>
Date:   Tue May 16 13:47:11 2023 +1000

    Remove ReadTheDocs badge from README (#288)
    
    We no longer use ReadTheDocs to host documentation, so this shouldn't be in the README.

README.md

commit 1ae79e62ba64dc2f9bdc39a8a55323dddc9f93a9
Author: Ben Wibking <ben@wibking.com>
Date:   Mon May 15 16:29:58 2023 +1000

    update Setonix SLURM script (#284)
    
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    * update SLURM script
    
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    * working slurm script using wrapper script
    
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    Co-authored-by: Benjamin Wibking <bwibking@setonix-01.pawsey.org.au>
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scripts/setonix-1node.submit
scripts/setonix-64nodes.pbs
scripts/setonix-8nodes.pbs
scripts/setonix.profile

commit 5564aa534cee2bd613a38a17d4fe851cd7317882
Author: Ben Wibking <ben@wibking.com>
Date:   Tue May 9 23:51:56 2023 +1000

    added Setonix scripts (#282)
    
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cmake/setonix.cmake
scripts/setonix-1node.submit
scripts/setonix.profile

commit a14eabe13d50d025cf033855102ccab2331bf3be
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon May 8 23:59:24 2023 +0000

    [pre-commit.ci] pre-commit autoupdate (#281)
    
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commit 9db4a05e75d80bc6197d365a71af80aaf8386256
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Mon May 8 19:39:34 2023 +0200

    Added mass scalars and consistent multi-fluid advection (CMA) (#273)
    
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    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    Co-authored-by: Piyush Sharda <psharda@RSAA-043527.local>
    Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

extern/Microphysics
src/Advection/test_advection.cpp
src/Advection2D/test_advection2d.cpp
src/AdvectionSemiellipse/test_advection_semiellipse.cpp
src/CMakeLists.txt
src/Chemistry.hpp
src/Cooling/test_cooling.cpp
src/FCQuantities/test_fc_quantities.cpp
src/HydroBlast2D/test_hydro2d_blast.cpp
src/HydroBlast3D/test_hydro3d_blast.cpp
src/HydroContact/test_hydro_contact.cpp
src/HydroHighMach/test_hydro_highmach.cpp
src/HydroKelvinHelmholz/test_hydro2d_kh.cpp
src/HydroLeblanc/test_hydro_leblanc.cpp
src/HydroQuirk/test_quirk.cpp
src/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
src/HydroSMS/test_hydro_sms.cpp
src/HydroShocktube/test_hydro_shocktube.cpp
src/HydroShocktubeCMA/CMakeLists.txt
src/HydroShocktubeCMA/test_hydro_shocktube_cma.cpp
src/HydroShocktubeCMA/test_hydro_shocktube_cma.hpp
src/HydroShuOsher/test_hydro_shuosher.cpp
src/HydroVacuum/test_hydro_vacuum.cpp
src/HydroWave/test_hydro_wave.cpp
src/PassiveScalar/test_scalars.cpp
src/PrimordialChem/test_primordial_chem.cpp
src/RadForce/test_radiation_force.cpp
src/RadMarshak/test_radiation_marshak.cpp
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadPulse/test_radiation_pulse.cpp
src/RadStreaming/test_radiation_streaming.cpp
src/RadSuOlson/test_radiation_SuOlson.cpp
src/RadTophat/test_radiation_tophat.cpp
src/RadTube/test_radiation_tube.cpp
src/RadhydroShell/test_radhydro_shell.cpp
src/RadhydroShock/test_radhydro_shock.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/RayleighTaylor2D/test_hydro2d_rt.cpp
src/RayleighTaylor3D/test_hydro3d_rt.cpp
src/ShockCloud/cloud.cpp
src/SphericalCollapse/spherical_collapse.cpp
src/hydro_system.hpp
src/physics_info.hpp
tests/shocktube_cma.in

commit de6c07b61aa54b0b5ef76a70502fffb4533eb144
Author: Ben Wibking <ben@wibking.com>
Date:   Tue May 2 22:55:10 2023 +1000

    check spelling in source code (#277)
    
    * add codespell action
    
    * fix spelling
    
    ---------
    
    Co-authored-by: Ben Wibking <benwibking@gmail.com>

.codespell-ignore-words
.codespellrc
.github/workflows/codespell.yml
.github/workflows/dependencies/requirements.txt
src/FCQuantities/test_fc_quantities.cpp
src/HLLD.hpp
src/RadhydroSimulation.hpp
src/matplotlibcpp.h
src/simulation.hpp

commit 19c49a2609c2e495804d3adf08baabdc0233c375
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon May 1 23:01:35 2023 +1000

    Bump extern/Microphysics from `4300ac4` to `dcbe5d6` (#274)
    
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extern/Microphysics

commit d498fae32aac2721779c0856efca8d45465e7a35
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon May 1 03:52:26 2023 +0000

    Bump extern/fmt from `8ec94ac` to `02cae7e` (#276)
    
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    Signed-off-by: dependabot[bot] <support@github.com>
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extern/fmt

commit 0a2c1c374cbdde8ce46aed0c0d97705a1b2c2ea3
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon May 1 03:47:09 2023 +0000

    Bump extern/amrex from `c1e8e73` to `cf6b46b` (#275)
    
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    ...
    
    Signed-off-by: dependabot[bot] <support@github.com>
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extern/amrex

commit 80dfe77c8bc09c9739ea8628a7f371e8a626c8a1
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Wed Apr 26 17:59:24 2023 +0200

    Patched microphysics to quokka, and added primordial chem test (#263)
    
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    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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.ci/azure-pipelines-aarch64-debug.yml
.ci/azure-pipelines-aarch64.yml
.ci/azure-pipelines-asan.yml
.ci/azure-pipelines.yml
CMakeLists.txt
extern/Microphysics
src/CMakeLists.txt
src/Chemistry.cpp
src/Chemistry.hpp
src/PrimordialChem/CMakeLists.txt
src/PrimordialChem/test_primordial_chem.cpp
src/PrimordialChem/test_primordial_chem.hpp
src/RadhydroSimulation.hpp
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commit f002cea8e50388637852e978864848383b526da8
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Apr 26 09:40:57 2023 +1000

    Update sonarcloud.yml (#264)
    
    * Update sonarcloud.yml
    
    Use the Sonarcloud GitHub Action. Allows Sonarcloud analysis to run on PRs.
    
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.github/workflows/sonarcloud.yml

commit 4a74efa67340c3bb076475934b2031449a73c65f
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Apr 26 09:40:22 2023 +1000

    Use macOS 13 on GitHub Actions (#266)
    
    * Use macOS 13 on GitHub Actions
    
    Use the 12-core virtual machine running macOS 13 for macOS testing.
    
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.github/workflows/cmake-macos.yml

commit c972a51d8ba6383bc984288318a84a54f95655e5
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Apr 26 09:39:52 2023 +1000

    cancel in-progress CI builds on new push (#268)

.ci/azure-pipelines-aarch64-debug.yml
.ci/azure-pipelines-aarch64.yml
.ci/azure-pipelines-asan.yml
.ci/azure-pipelines-build-llvm.yml
.ci/azure-pipelines-debug.yml
.ci/azure-pipelines.yml
.github/workflows/clang-tidy.yml
.github/workflows/cmake-macos.yml
.github/workflows/cmake.yml

commit eb935c48193c5785c30de31c867af899f5b189b3
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon Apr 24 23:33:05 2023 +0000

    [pre-commit.ci] pre-commit autoupdate (#267)
    
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    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml
src/CloudyCooling.hpp
src/Cooling/test_cooling.cpp
src/ODEIntegrate.hpp
src/RadBeam/test_radiation_beam.cpp
src/RadForce/test_radiation_force.cpp
src/RadMarshak/test_radiation_marshak.cpp
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadPulse/test_radiation_pulse.cpp
src/RadShadow/test_radiation_shadow.cpp
src/RadStreaming/test_radiation_streaming.cpp
src/RadTophat/test_radiation_tophat.cpp
src/RadTube/test_radiation_tube.cpp
src/RadhydroShell/test_radhydro_shell.cpp
src/RadhydroShock/test_radhydro_shock.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/RadhydroSimulation.hpp
src/ShockCloud/cloud.cpp
src/hyperbolic_system.hpp
src/main.hpp
src/matplotlibcpp.h
src/radiation_system.hpp
src/simulation.hpp

commit f818a946c664ba84fe3750a6374913fda35965f4
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Apr 24 03:53:27 2023 +0000

    Bump ZedThree/clang-tidy-review from 0.12.3 to 0.13.0 (#265)
    
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.github/workflows/clang-tidy-comments.yml
.github/workflows/clang-tidy.yml

commit da74a4e6c569b4a3513eeaa4164af5ffa5023501
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Tue Apr 18 13:58:28 2023 +0000

    Bump actions/upload-artifact from 2 to 3 (#260)
    
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.github/workflows/cmake-macos.yml
.github/workflows/cmake.yml

commit e56eb4917da9764b01e2d840e223424fbc5e1fa3
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Tue Apr 18 09:44:22 2023 -0400

    Bump actions/deploy-pages from 1 to 2 (#258)
    
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.github/workflows/docs.yml

commit 0d43d5ab295a4e814938bf359fc7fdfdafa7452d
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Tue Apr 18 09:08:35 2023 -0400

    Bump extern/amrex from `1e73fa8` to `c1e8e73` (#257)
    
    Bumps [extern/amrex](https://github.com/AMReX-Codes/amrex) from `1e73fa8` to `c1e8e73`.
    - [Release notes](https://github.com/AMReX-Codes/amrex/releases)
    - [Commits](https://github.com/AMReX-Codes/amrex/compare/1e73fa8ec7c31fbaf994fbb4f59792b90ae78433...c1e8e73b63dc8b6732c6cdfe51914f7ae144575b)
    
    ---
    updated-dependencies:
    - dependency-name: extern/amrex
      dependency-type: direct:production
    ...
    
    Signed-off-by: dependabot[bot] <support@github.com>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

extern/amrex

commit 4e46ecfd1978edd87e3501198b178126c54b77d4
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Tue Apr 18 09:07:28 2023 -0400

    Bump extern/fmt from `b00a1ea` to `8ec94ac` (#261)
    
    Bumps [extern/fmt](https://github.com/fmtlib/fmt) from `b00a1ea` to `8ec94ac`.
    - [Release notes](https://github.com/fmtlib/fmt/releases)
    - [Commits](https://github.com/fmtlib/fmt/compare/b00a1eac7519cf0b0053818116bd25e3144f4280...8ec94ac6a5cb1a7f8ee8a86bebc1100fd7b212ca)
    
    ---
    updated-dependencies:
    - dependency-name: extern/fmt
      dependency-type: direct:production
    ...
    
    Signed-off-by: dependabot[bot] <support@github.com>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

extern/fmt

commit b4a86f3b766443c170d6e3d905662a915db5a0dd
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Apr 18 22:09:22 2023 +1000

    fix clang-tidy-review from forks (#255)

.github/workflows/clang-tidy-comments.yml
.github/workflows/clang-tidy.yml

commit bb80d27329f30039c211baf00420ea7bf01db33b
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Apr 18 21:29:45 2023 +1000

    Create dependabot.yml (#254)
    
    This activates GitHub's Dependabot, which will automatically create PRs to update GitHub Actions and submodules that are out of date.

.github/dependabot.yml

commit 34fe2452d9033569694d87ecd7af880be46b67af
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon Apr 17 22:44:54 2023 +0000

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    updates:
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.pre-commit-config.yaml

commit 6d2691bb5c1d050269d48c53ece9ba427f229630
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Apr 13 12:27:14 2023 +1000

    remove CodeQL CI (#250)
    
    This removes the CodeQL analysis from the automated tests run on each commit.
    
    It is not very useful, it is very slow, and it causes an out-of-memory failure when trying to analyze the chemistry network. So we just remove it.

.github/workflows/codeql-analysis.yml

commit c76f3e26e69a7ea24310417f149421bc971e45b3
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Apr 13 12:26:40 2023 +1000

    increase azure-pipelines CI time limit (#249)
    
    * Update azure-pipelines timeout
    
    * increase job timeout to 120 minutes

.ci/azure-pipelines-aarch64-debug.yml
.ci/azure-pipelines-aarch64.yml

commit 894ed52858d3f9e45c14a9d5d1fb7127f462716d
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Apr 12 11:25:41 2023 +1000

    Disable parallel builds in CI (#248)
    
    * Update cmake.yml
    
    Only build 1 file at a time to avoid OOM kills.
    
    * update all CI pipelines
    
    * update clang-tidy config
    
    * re-enable parallel CUDA builds
    
    * update clang-tidy-review version
    
    * attempt to fix clang-tidy action
    
    * add trigger for merge queue

.ci/azure-pipelines-aarch64-debug.yml
.ci/azure-pipelines-aarch64.yml
.ci/azure-pipelines-asan.yml
.github/workflows/clang-tidy-comments.yml
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.github/workflows/cmake-macos.yml
.github/workflows/cmake.yml
.github/workflows/codeql-analysis.yml
.github/workflows/docs.yml
.github/workflows/sonarcloud.yml

commit ca3d1dbb3a88459f9cd4e7ed8c78239540280090
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Apr 6 01:50:58 2023 -0400

    update amrex submodule (#246)

extern/amrex

commit 9c9d2b2b9bc38fab09c1498024a2e8b3b90654da
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Apr 6 01:50:20 2023 -0400

    avoid deprecated Python API call (#247)

src/matplotlibcpp.h

commit cade0e18d91e4b5e626fd67365a32add25bdc8cf
Author: Neco Kriel <43261821+AstroKriel@users.noreply.github.com>
Date:   Sun Apr 2 22:31:53 2023 +1000

    Add ability to specify which quantities to PPM reconstruct (#244)
    
    * add input arguments to PPM reconstruct to read / write from a particular index
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
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    * relocate optional indexing arguments to the end of the arguments list
    
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    * remove const-qualifier; only has an affect in defns
    
    * explicitly comment out input arg since it is unused
    
    * rename input args in func declr to be consistent with func defn
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
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    * update arg-names in func decl to be consistent with func defn
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
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    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/hyperbolic_system.hpp
src/radiation_system.hpp

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Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon Mar 27 19:03:15 2023 -0400

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    * [pre-commit.ci] pre-commit autoupdate
    
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    ---------
    
    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml
src/CloudyCooling.hpp
src/Cooling/test_cooling.cpp
src/ODEIntegrate.hpp
src/RadBeam/test_radiation_beam.cpp
src/RadForce/test_radiation_force.cpp
src/RadMarshak/test_radiation_marshak.cpp
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadPulse/test_radiation_pulse.cpp
src/RadShadow/test_radiation_shadow.cpp
src/RadStreaming/test_radiation_streaming.cpp
src/RadTophat/test_radiation_tophat.cpp
src/RadTube/test_radiation_tube.cpp
src/RadhydroShell/test_radhydro_shell.cpp
src/RadhydroShock/test_radhydro_shock.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/RadhydroSimulation.hpp
src/ShockCloud/cloud.cpp
src/hyperbolic_system.hpp
src/main.hpp
src/matplotlibcpp.h
src/radiation_system.hpp
src/simulation.hpp

commit 0840a562d5e1e09f8039dca41b80b9739e23c66a
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Sun Mar 26 01:17:07 2023 +0100

    Updating cmakelists in quokka to include microphysics (#240)
    
    * added Microphysics as a submodule for Quokka
    
    * adding microphysics as a submodule from PS
    
    * added specific branch that has cmake
    
    * added cmake branch of microphysics
    
    * updated Microphysics with cmake
    
    * updated to include Microphysics
    
    * changed microphysics path to psharda while in development
    
    * added flags to build amrex and unit test in microphysics
    
    * set amrex build flag in microphysics to false
    
    * updated default value for unit test flag

.gitmodules
CMakeLists.txt
extern/Microphysics

commit 8a314f10ae37f2cc894a20ecaa5e08aa82943b46
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Fri Mar 24 19:23:46 2023 +0100

    added Microphysics as a submodule for Quokka (#216)
    
    * added Microphysics as a submodule for Quokka
    
    * adding microphysics as a submodule from PS
    
    * added specific branch that has cmake
    
    * added cmake branch of microphysics
    
    * updated Microphysics with cmake

.gitmodules
extern/Microphysics

commit d3c82bf84cbd962ec01f6563595304b4c0271608
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Feb 14 19:53:59 2023 -0500

    updated Delta (NCSA) config (#235)
    
    Co-authored-by: Benjamin Wibking <wibkingb@msu.edu>

cmake/delta_gcc_cuda.cmake
scripts/blast_1gpu.submit
scripts/blast_1node.submit

commit 6be736419c0921ef9eb0a4397b21e9108c66a656
Author: Neco Kriel <43261821+AstroKriel@users.noreply.github.com>
Date:   Wed Feb 15 11:52:40 2023 +1100

    Fix typos in the HLLD implementation (#236)
    
    * fix typos in the HLLD implementation
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
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    * add headerfile defining quantities conserved in the Riemann solver
    
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    ---------
    
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src/HLLD.hpp
src/MHDState.hpp

commit 4c34ac8fd1299192ef8934b7959eb73f83b27bea
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Feb 13 07:44:07 2023 -0500

    update amrex submodule (#234)

extern/amrex

commit da42a8c1043d1112569bfa6ac1908884beb5e9c3
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Feb 7 19:57:46 2023 -0500

    add GitHub CI for macOS (#233)

.github/workflows/cmake-macos.yml

commit 9e472af9744e94ffcae6267ed90dd65e6b976862
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Feb 7 00:54:12 2023 -0500

    update amrex to fix sincos on macOS (#232)

extern/amrex

commit 64b087d30576f3b8c84d0eb1bf127924d076f28d
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Feb 6 16:20:41 2023 -0500

    adjust multigrid parameters for gravity solve (#223)
    
    * adjust multigrid parameters for gravity solve
    
    * reduce reltol for poisson solve
    
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    ---------
    
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src/simulation.hpp
tests/SphericalCollapse.in

commit b167d9b70b5a06216917c8e5842352875b8dcc04
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Jan 31 23:22:37 2023 -0500

    enable cooling with a runtime parameter (#225)
    
    * consolidate cooling solver into quokka::cooling
    
    * add cooling runtime parameters
    
    * add temperature floor
    
    ---------

src/Advection/CMakeLists.txt
src/Advection2D/CMakeLists.txt
src/AdvectionSemiellipse/CMakeLists.txt
src/CloudyCooling.cpp
src/CloudyCooling.hpp
src/Cooling/CMakeLists.txt
src/Cooling/test_cooling.cpp
src/FCQuantities/CMakeLists.txt
src/HydroBlast2D/CMakeLists.txt
src/HydroBlast3D/CMakeLists.txt
src/HydroContact/CMakeLists.txt
src/HydroHighMach/CMakeLists.txt
src/HydroKelvinHelmholz/CMakeLists.txt
src/HydroLeblanc/CMakeLists.txt
src/HydroQuirk/CMakeLists.txt
src/HydroRichtmeyerMeshkov/CMakeLists.txt
src/HydroSMS/CMakeLists.txt
src/HydroShocktube/CMakeLists.txt
src/HydroShuOsher/CMakeLists.txt
src/HydroVacuum/CMakeLists.txt
src/HydroWave/CMakeLists.txt
src/ODEIntegration/CMakeLists.txt
src/PassiveScalar/CMakeLists.txt
src/RadBeam/CMakeLists.txt
src/RadForce/CMakeLists.txt
src/RadMarshak/CMakeLists.txt
src/RadMarshakAsymptotic/CMakeLists.txt
src/RadMarshakCGS/CMakeLists.txt
src/RadMatterCoupling/CMakeLists.txt
src/RadMatterCouplingRSLA/CMakeLists.txt
src/RadPulse/CMakeLists.txt
src/RadShadow/CMakeLists.txt
src/RadStreaming/CMakeLists.txt
src/RadSuOlson/CMakeLists.txt
src/RadTophat/CMakeLists.txt
src/RadTube/CMakeLists.txt
src/RadhydroShell/CMakeLists.txt
src/RadhydroShock/CMakeLists.txt
src/RadhydroShockCGS/CMakeLists.txt
src/RadhydroSimulation.hpp
src/RayleighTaylor2D/CMakeLists.txt
src/RayleighTaylor3D/CMakeLists.txt
src/ShockCloud/CMakeLists.txt
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tests/Cooling.in
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tests/ShockCloud_128.in
tests/ShockCloud_512.in

commit c6b9b88cddaccb58ab4b816402e6bda6c48aa450
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Jan 31 21:59:54 2023 -0500

    update SLURM script for crusher (#226)

scripts/crusher-1node.submit

commit a6bff7fdad536a87ae09a517119758964de67b88
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Jan 31 20:40:10 2023 -0500

    add multidimensional artificial viscosity (#228)
    
    * add multidimensional artificial viscosity
    
    * add runtime parameter for artificial viscosity
    
    ---------
    
    Co-authored-by: Mark Krumholz <mark.krumholz@gmail.com>

src/RadhydroSimulation.hpp
src/hydro_system.hpp
tests/blast_unigrid_128.in

commit e2d19c502a43fa7d7113bd125523b897227a5914
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Jan 31 18:25:30 2023 -0500

    fix AppleClang build (#229)

src/CMakeLists.txt

commit af42820a16bdfd9d9532d8a9c0fa10df7345959b
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Jan 31 18:14:27 2023 -0500

    fix constexpr-related error on Clang-based compilers (#222)

src/EOS.hpp

commit 3dab565e6a088398304a49189fe46847c601c3d9
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon Jan 23 20:04:37 2023 -0500

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    updates:
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commit a94366d88e308fffc7d37f421a48bccff24c5e91
Author: Aditi <45175933+aditivijayan@users.noreply.github.com>
Date:   Tue Jan 24 11:00:57 2023 +1100

    Timed output (#227)
    
    * including provision for checkpoint time interval

src/simulation.hpp

commit 4ef464db0695137420036eff07a8af0e8fbff81a
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Jan 2 18:51:53 2023 -0500

    allow simulation to continue if retries exceed max (#209)
    
    * use fallback stencil for PdV term
    
    * add hydro.abort_on_fofc_failure option
    
    Add hydro.abort_on_fofc_failure = 0 to the input params file to continue running even if first-order flux correction does not succeed in producing a positive density everywhere. This will require using a density floor.

src/RadhydroSimulation.hpp
src/hydro_system.hpp

commit 8693ba5d31946250094981689296bab062edc1ff
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Jan 1 21:00:56 2023 -0500

    use Roe-average wavespeeds for HLLC (#217)
    
    * use Roe-average wavespeeds
    
    * fix bug in roe-averaged sound speed
    
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src/HLLC.hpp

commit 03483a97eb30b5336a65d353f5d502603178e736
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Dec 28 10:48:55 2022 -0500

    update SphericalCollapse parameters (#219)
    
    * update SphericalCollapse parameters
    
    Use a larger blocking_factor and max_grid_size to improve GPU performance on the SphericalCollapse test.
    
    * set max_level=0

tests/SphericalCollapse.in

commit c9ba653b18bfe8b4bfe5f1479eec08b8db87359c
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Thu Dec 22 04:44:18 2022 +1100

    Increased pressure for spherical collapse gravity test (#215)
    
    * increased pressure for gravity test
    
    * increased nsteps

src/SphericalCollapse/spherical_collapse.cpp
tests/SphericalCollapse.in

commit 4719a7dfe9370ae590cb3f4803064bcdceb9264b
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Dec 22 02:28:22 2022 +1100

    update amrex submodule (#213)

extern/amrex

commit e1f306ca519e2b0aa92049a81dda6e8332070524
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Dec 21 11:49:28 2022 +1100

    fix branch name in docs.yml (#212)
    
    The branch name must be hard-coded in GitHub Actions workflows.

.github/workflows/docs.yml

commit 70bf58315736b2353dab5026eaa0458ead4a8f0a
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Dec 21 10:29:50 2022 +1100

    avoid using inf for limits (#210)
    
    * avoid using inf for limits
    
    * fix comments

src/simulation.hpp

commit 19012b4b98b30d5402eb85b3b26d3896ad9fe133
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Dec 21 09:29:06 2022 +1100

    fix publish docs action (#211)
    
    * fix deployment of docs to GitHub Pages
    
    This will hopefully fix deployment to GitHub Pages, which is currently broken.
    
    * only deploy when pushed to development
    
    * move conditional to job 'deploy'

.github/workflows/docs.yml

commit 88c882fbf6d462a11fed8f3c35377b463ca2a824
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Dec 21 04:07:09 2022 +1100

    add flowchart to docs (#203)
    
    Co-authored-by: Mark Krumholz <mark.krumholz@gmail.com>

docs/flowchart.rst
docs/flowchart.svg
docs/index.rst

commit 7857e358ff44f8d7930eb8a488b23b6f7dfa0128
Author: Piyush Sharda <34922596+psharda@users.noreply.github.com>
Date:   Wed Dec 21 02:45:10 2022 +1100

    changed box dimensions to center at 0,0,0 (#206)

tests/SphericalCollapse.in

commit 245264bf2c733bcf85e2a5720e3e3889c0e05c71
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Dec 20 13:02:49 2022 +1100

    create GitHub Action for docs (#205)
    
    * create GitHub Action for docs
    
    Deploy docs to quokka-astro.github.io on push to development branch.
    
    * add dependencies.sh
    
    * update permissions
    
    * fix docs build

.github/workflows/dependencies/documentation.sh
.github/workflows/docs.yml
build_docs.sh
docs/conf.py

commit 2312ebb15876e05d287ca1b1d997c9b793cd9b5e
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Dec 20 11:45:06 2022 +1100

    avoid clang-tidy-review post on merged PRs (#208)
    
    This avoids trying to post code style comments on PRs that have already been merged.

.github/workflows/clang-tidy-comments.yml

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Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon Dec 19 17:16:40 2022 -0500

    [pre-commit.ci] pre-commit autoupdate (#207)
    
    updates:
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    Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

commit 12e9dd97b2943dcb65ef1243a7132c9b858d8abe
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Dec 19 09:41:12 2022 +1100

    disable readability-function-cognitive-complexity warning (#201)

src/.clang-tidy

commit ea9d27850b349a3f7440d631fb8b34f73b4cf06e
Author: Aditi <45175933+aditivijayan@users.noreply.github.com>
Date:   Mon Dec 19 08:13:20 2022 +1100

    Enforcing upper/lower limits to density, temperature and speed. (#192)
    
    * Adding Fixed potential and enforcing limiits on physical quantities
    
    * Remove extra lines
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
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    * remove enforce density
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
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    * Fixing bug in the enforcelimit function
    
    * removing bugged line from radhydro
    
    * minor changes
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
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    * Moving EnforceLimit to hydrosystem and modifying to include EOS traits
    
    * Fixing radhydro
    
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    * putting mean molecular wght=NAN in test problem files
    
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    * Setting mean molecular weight to NAN in tests
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
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    * Update src/hydro_system.hpp
    
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    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
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    * Formatting and changing ceilings to INFs
    
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    * Update src/hydro_system.hpp
    
    Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
    
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    Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
    
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    * Minor changes to EnforceLimits to ensure tests don't fail
    
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    * minor changes to hydrosys
    
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    * addressing float to bool conversion and removing extra line
    
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src/HydroBlast2D/test_hydro2d_blast.cpp
src/HydroBlast3D/test_hydro3d_blast.cpp
src/HydroHighMach/test_hydro_highmach.cpp
src/HydroKelvinHelmholz/test_hydro2d_kh.cpp
src/HydroQuirk/test_quirk.cpp
src/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
src/HydroShocktube/test_hydro_shocktube.cpp
src/HydroVacuum/test_hydro_vacuum.cpp
src/RadhydroSimulation.hpp
src/RayleighTaylor2D/test_hydro2d_rt.cpp
src/RayleighTaylor3D/test_hydro3d_rt.cpp
src/ShockCloud/cloud.cpp
src/SphericalCollapse/spherical_collapse.cpp
src/hydro_system.hpp
src/simulation.hpp

commit 3f151d93702c3e762dca8658ba6f235acb7735d0
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Dec 14 23:51:44 2022 +1100

    fix build error with CUDA 12 (#200)

src/AdvectionSimulation.hpp

commit 0c15764a35a5ee991d9cf1c57ef1d38dbec5939b
Author: Neco Kriel <43261821+AstroKriel@users.noreply.github.com>
Date:   Wed Dec 14 03:58:37 2022 +1000

    Add HLLD solver for ideal MHD (#195)
    
    * ported most of the HLLD Riemann solver implemented in Athena++
    
    * add input reference arguments to hydro and bfield (electric-field) flux
    
    * Remove comp of weights for calculating EMF req by GS05. We are now implementing the FS17's 4th order accurate UCT scheme.
    
    * remove electric field components
    
    * update how HLLD returns hydro-fluxes (for consistency with HLLC method).

src/HLLD.hpp

commit ae82a53cd4f6e1ca956cc899ae33f9e9236c02e2
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Dec 8 12:56:35 2022 +1100

    create EOS and EOS_Traits classes (#196)
    
    * create EOS and EOS_Traits classes
    
    * replace references to HydroSystem::gamma_
    
    * update test problems
    
    * fix radshock and radpulse tests
    
    * add execution space annotations for GPU
    
    * fix annotations
    
    * fix 2d tests
    
    * fix 3d tests
    
    * default mean mol weight is NaN
    
    * fix tests
    
    * add function annotations

src/CloudyCooling.hpp
src/Cooling/test_cooling.cpp
src/EOS.hpp
src/FCQuantities/test_fc_quantities.cpp
src/HydroBlast2D/test_hydro2d_blast.cpp
src/HydroBlast3D/test_hydro3d_blast.cpp
src/HydroContact/test_hydro_contact.cpp
src/HydroHighMach/test_hydro_highmach.cpp
src/HydroKelvinHelmholz/test_hydro2d_kh.cpp
src/HydroLeblanc/test_hydro_leblanc.cpp
src/HydroQuirk/test_quirk.cpp
src/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
src/HydroSMS/test_hydro_sms.cpp
src/HydroShocktube/test_hydro_shocktube.cpp
src/HydroShuOsher/test_hydro_shuosher.cpp
src/HydroVacuum/test_hydro_vacuum.cpp
src/HydroWave/test_hydro_wave.cpp
src/ODEIntegration/test_ode.cpp
src/PassiveScalar/test_scalars.cpp
src/RadBeam/test_radiation_beam.cpp
src/RadForce/test_radiation_force.cpp
src/RadMarshak/test_radiation_marshak.cpp
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadPulse/test_radiation_pulse.cpp
src/RadShadow/test_radiation_shadow.cpp
src/RadStreaming/test_radiation_streaming.cpp
src/RadSuOlson/test_radiation_SuOlson.cpp
src/RadTophat/test_radiation_tophat.cpp
src/RadTube/test_radiation_tube.cpp
src/RadhydroShell/test_radhydro_shell.cpp
src/RadhydroShock/test_radhydro_shock.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/RayleighTaylor2D/test_hydro2d_rt.cpp
src/RayleighTaylor3D/test_hydro3d_rt.cpp
src/ShockCloud/cloud.cpp
src/ShockCloud/test_cloudy.cpp
src/SphericalCollapse/spherical_collapse.cpp
src/hydro_system.hpp
src/radiation_system.hpp

commit 8e3b929e949d03a71487e8a6761e8fc86be833be
Author: Neco Kriel <43261821+AstroKriel@users.noreply.github.com>
Date:   Thu Dec 8 02:43:56 2022 +1100

    Read cc and fc ncomp from Physics_Indices (#197)
    
    * update: reference compile time calculation of the number of cc-states (via physics_indices)
    
    * remove global variable tracking the number of cc quantities
    
    * updated to determine the numper of cc quantities, whether advection or rad+hydro problem
    
    * get the number of components from physics_indices
    
    * define required physics_traits for advection problem
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci

src/Advection/test_advection.cpp
src/Advection2D/test_advection2d.cpp
src/AdvectionSemiellipse/test_advection_semiellipse.cpp
src/AdvectionSimulation.hpp
src/Cooling/test_cooling.cpp
src/FCQuantities/test_fc_quantities.cpp
src/HydroBlast2D/test_hydro2d_blast.cpp
src/HydroBlast3D/test_hydro3d_blast.cpp
src/HydroContact/test_hydro_contact.cpp
src/HydroHighMach/test_hydro_highmach.cpp
src/HydroKelvinHelmholz/test_hydro2d_kh.cpp
src/HydroLeblanc/test_hydro_leblanc.cpp
src/HydroQuirk/test_quirk.cpp
src/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
src/HydroSMS/test_hydro_sms.cpp
src/HydroShocktube/test_hydro_shocktube.cpp
src/HydroShuOsher/test_hydro_shuosher.cpp
src/HydroVacuum/test_hydro_vacuum.cpp
src/HydroWave/test_hydro_wave.cpp
src/PassiveScalar/test_scalars.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadTophat/test_radiation_tophat.cpp
src/RadhydroShell/test_radhydro_shell.cpp
src/RadhydroSimulation.hpp
src/RayleighTaylor2D/test_hydro2d_rt.cpp
src/RayleighTaylor3D/test_hydro3d_rt.cpp
src/ShockCloud/cloud.cpp
src/SphericalCollapse/spherical_collapse.cpp
src/physics_info.hpp
src/simulation.hpp

commit 09959b8ae3f4eeb0fd7e05ef783ced7520569aba
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Tue Dec 6 23:29:59 2022 -0500

    [pre-commit.ci] pre-commit autoupdate (#194)
    
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.pre-commit-config.yaml

commit 11ef47b84810acedd667f68c6ae8a47497c6d355
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Dec 3 02:10:44 2022 +1100

    enforce code formatting (#191)
    
    * add pre-commit enforcement of code formatting
    
    * [pre-commit.ci] auto fixes from pre-commit.com hooks
    
    for more information, see https://pre-commit.ci

.pre-commit-config.yaml
src/Advection/test_advection.cpp
src/Advection2D/test_advection2d.cpp
src/AdvectionSemiellipse/test_advection_semiellipse.cpp
src/AdvectionSemiellipse/test_advection_semiellipse.hpp
src/AdvectionSimulation.hpp
src/ArrayUtil.hpp
src/ArrayView_2d.hpp
src/ArrayView_3d.hpp
src/CheckNaN.hpp
src/CloudyCooling.cpp
src/CloudyCooling.hpp
src/Cooling/test_cooling.cpp
src/FCQuantities/test_fc_quantities.cpp
src/FastMath.hpp
src/GrackleDataReader.cpp
src/GrackleDataReader.hpp
src/HydroBlast2D/test_hydro2d_blast.cpp
src/HydroBlast3D/test_hydro3d_blast.cpp
src/HydroContact/test_hydro_contact.cpp
src/HydroHighMach/test_hydro_highmach.cpp
src/HydroHighMach/test_hydro_highmach.hpp
src/HydroKelvinHelmholz/test_hydro2d_kh.cpp
src/HydroLeblanc/test_hydro_leblanc.cpp
src/HydroLeblanc/test_hydro_leblanc.hpp
src/HydroQuirk/test_quirk.cpp
src/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
src/HydroSMS/test_hydro_sms.cpp
src/HydroSMS/test_hydro_sms.hpp
src/HydroShocktube/test_hydro_shocktube.cpp
src/HydroShocktube/test_hydro_shocktube.hpp
src/HydroShuOsher/test_hydro_shuosher.cpp
src/HydroShuOsher/test_hydro_shuosher.hpp
src/HydroState.hpp
src/HydroVacuum/test_hydro_vacuum.cpp
src/HydroWave/test_hydro_wave.cpp
src/Interpolate2D.cpp
src/Interpolate2D.hpp
src/ODEIntegrate.hpp
src/ODEIntegration/test_ode.cpp
src/ODEIntegration/test_ode.hpp
src/PassiveScalar/test_scalars.cpp
src/PassiveScalar/test_scalars.hpp
src/RadBeam/test_radiation_beam.cpp
src/RadBeam/test_radiation_beam.hpp
src/RadForce/test_radiation_force.cpp
src/RadMarshak/test_radiation_marshak.cpp
src/RadMarshak/test_radiation_marshak.hpp
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.hpp
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.hpp
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.hpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.hpp
src/RadPulse/test_radiation_pulse.cpp
src/RadPulse/test_radiation_pulse.hpp
src/RadShadow/test_radiation_shadow.cpp
src/RadShadow/test_radiation_shadow.hpp
src/RadStreaming/test_radiation_streaming.cpp
src/RadSuOlson/test_radiation_SuOlson.cpp
src/RadSuOlson/test_radiation_SuOlson.hpp
src/RadTophat/test_radiation_tophat.cpp
src/RadTophat/test_radiation_tophat.hpp
src/RadTube/test_radiation_tube.cpp
src/RadhydroShell/test_radhydro_shell.cpp
src/RadhydroShock/test_radhydro_shock.cpp
src/RadhydroShock/test_radhydro_shock.hpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.hpp
src/RadhydroSimulation.hpp
src/RayleighTaylor2D/test_hydro2d_rt.cpp
src/RayleighTaylor3D/test_hydro3d_rt.cpp
src/ShockCloud/cloud.cpp
src/ShockCloud/test_cloudy.cpp
src/SimulationData.hpp
src/SphericalCollapse/spherical_collapse.cpp
src/fextract.cpp
src/fextract.hpp
src/grid.hpp
src/hydro_system.hpp
src/hyperbolic_system.hpp
src/interpolate.cpp
src/interpolate.hpp
src/linear_advection.cpp
src/linear_advection.hpp
src/main.cpp
src/main.hpp
src/math_impl.hpp
src/matplotlibcpp.h
src/mhd_system.cpp
src/mhd_system.hpp
src/physics_info.hpp
src/physics_numVars.hpp
src/radiation_system.hpp
src/root_finding.hpp
src/simulation.hpp
src/valarray.hpp

commit 5cab157a613863c19f3b8bc149f66ea218dfceee
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Dec 2 15:07:12 2022 +1100

    refactor hydro Riemann solver in canonical form (#190)
    
    * refactor hydro Riemann solver in canonical form
    
    * fix formatting

src/HLLC.hpp
src/HydroState.hpp
src/hydro_system.hpp

commit 953bdf23d7bdb07e2b6d6fec9756ab36a704e84b
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Dec 2 00:27:43 2022 +1100

    Add more notes about GPU-aware MPI to README (#189)

README.md

commit d73f1c76a079ff84ec82dca20af51a87697724d7
Author: Neco Kriel <43261821+AstroKriel@users.noreply.github.com>
Date:   Thu Dec 1 15:25:27 2022 +1100

    Add ability to create and work with face-centred quantities (#125)
    
    * rename state variables to indicate they store cell-centred quantities
    
    * fix bug: indexRange should store a copy, rather than a reference.
    
    * update: pass single grid element to user-init func, instead of a vector of grid elems
    
    * update init func in all test problems to init the single grid elem passed
    
    * set ICs flag to true after user-init complete.
    
    * add: compile-time calc. num. of cc quantities used in sim.
    
    * refer to ct calc. num. cc quantities.
    
    * update reference to total num. (now specify) cc vars.
    
    * update: the num. quantities for each physics module should not be ct determined / template-able.
    
    * update: physics num. vars. is not template-able.
    
    * rename BCs to indicate centering
    
    * rename vars to indicate the centering of quantities stored.
    
    * add vars required to store face-centred quanatities
    
    * add ability to track the number of face-centred qunatities
    
    * turn mhd off for sim
    
    * turn mhd off for sim
    
    * update fillBCs func: pass cc BCs
    
    * add preliminary bits of code to create and initialise fc vars
    
    * update: only create fc vars if required
    
    * minor syntax update
    
    * add place-holder mhd module
    
    * add sim to test that fc quantities are being created and initialised correctly.
    
    * created prelim bits of code to test fc vars being init properly
    
    * minor format changes
    
    * generalise FillCoarsePatch so that it will work for face-centred quantities, also
    
    * add funcs to fill fc quantities
    
    * add funcs to fill fc quantities
    
    * removed unused + outdated constructor
    
    * extend constructors to also define fc BCs
    
    * extend constructor to accept fc BCs also
    
    * minor changes to make testing more tractable.
    
    * add string to index for creating fc quantity names.
    
    * add functionality to output fc quanitities to plt and chk files.
    
    * remove unused copy
    
    * extend average func to also copy ghost zones
    
    * resolve bugs introduced in merge
    
    * remove residual (bug) FillCoarsePatch-call introduced from merge.
    
    * introduce test problem to check that writing/reading fc quantities works correctly
    
    * remove unused test problem
    
    * add fc-test problem to CMakeLists
    
    * init cc quantities to value = their index
    
    * fix call to fillBCs in rk2 step (introduced in merge)
    
    * add hdyro-wave init to fc-test problem
    
    * run a second simulation instance to check that chk-files can be read successfully
    
    * comment out buggy function
    
    * enquire physics traits for the num. of cc vars.
    
    * fix references to grid_elem member variables
    
    * add ../MFInterpolater.cpp to CMakeLists
    
    * remove duplicate func defn (indroduced by git merge)
    
    * updated C-style casting to use preffered modern C++ static_cast-ing
    
    * update order of included libraries in src/mhd_system.hpp
    
    * update order of imported libraries in src/simulation.hpp
    
    * update from C-style casting to the preffered modern C++ static_cast-ing
    
    * create input param file to test creation/writing of fc vars
    
    * update reference to file-name
    
    * update reference to file-name
    
    * the quantity being stored is the magnitude component of the magnetic field
    
    * reintroduce hydro check (func has been fixed in another PR)
    
    * redefine string storing xyz chars
    
    * redefine mhd var name. quantity is not an energy, it is the amplitude of the bfield vector.
    
    * get number of components for each centering from state variables. also, allow fc variables to have different number of ghost cells.
    
    * ignore clang-tidy suggestion
    
    * fixed averaging fc array to cc array
    
    * fc quantities are defined in each space-dimension
    
    * fc quantities are defined in each space-dimension
    
    * give each fc quantity a name in each dim.
    
    * rename var. to reflect centering
    
    * update argument passed to problem (use amrex interpolator)
    
    * Physics_NumVars is no longer a template.
    
    * remove interpolator header (now using amrex's interpolator)
    
    * remove duplicate library import
    
    * fix getting fc quantity names
    
    * specify plt and chk file output rate.
    
    * update name of magnetic field quantity
    
    * removed ncomp_fc_: details about the number of components should now be looked up in physic_indices
    
    * keep track of num of fc vars in each dim, as well as total num vars across dims
    
    * keep track of num of fc vars in each dim, as well as total num vars across dims
    
    * keep track of num of fc vars in each dim, as well as total num vars across dims
    
    * removed ncomp_fc_; instead look-up num of fc vars in physic_indices struct (determined at compile time)
    
    * ignore extraneous files created when restarting test simulations (i.e., last_chk folder)
    
    * compartmentalise setICs of cc and fc vars into seperate func calls
    
    * Update src/mhd_system.hpp
    
    * no need to pass BCs when already passing centering
    
    * Revert "updated C-style casting to use preffered modern C++ static_cast-ing"
    
    * added flag to problem to turn bfields off
    
    * widen simulation domain
    
    * fix which dimension bfield ICs are modulus wrt
    
    * add test to check that FC quantities are read-in correctly from chk-file.
    
    * add func to set chk-file to read from
    
    * remove print func for debugging

.gitignore
src/AdvectionSimulation.hpp
src/CMakeLists.txt
src/FCQuantities/CMakeLists.txt
src/FCQuantities/test_fc_quantities.cpp
src/FCQuantities/test_fc_quantities.hpp
src/HydroLeblanc/test_hydro_leblanc.cpp
src/PassiveScalar/test_scalars.cpp
src/RadhydroSimulation.hpp
src/SphericalCollapse/spherical_collapse.cpp
src/grid.hpp
src/hydro_system.hpp
src/mhd_system.cpp
src/mhd_system.hpp
src/physics_info.hpp
src/physics_numVars.hpp
src/radiation_system.hpp
src/simulation.hpp
tests/fc_hydro_wave.in

commit 26a28c830f5951f014d746f3e551c3a2def4e769
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Nov 29 13:20:48 2022 +1100

    update build instructions in README (#188)
    
    * cleanup GPU build notes
    
    * add intel gpu build instructions
    
    * explicitly specify dependencies
    
    * clarify CMake usage

README.md

commit a0b17e11dfcb3e647f8ea62220857b483b9324c2
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Nov 21 14:49:32 2022 -0500

    remove unneeded MFs from RemakeLevel (#187)

src/simulation.hpp

commit e757b7c2b648766a9c647004785578fd183e1623
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Nov 21 13:54:30 2022 -0500

    self-gravity for non-subcycling-in-time AMR (#167)
    
    * self-gravity for non-subcycling-in-time AMR
    
    * add spherical collapse problem
    
    * refine on density threshold
    
    * update amrex
    
    Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

CMakeLists.txt
extern/amrex
src/AdvectionSimulation.hpp
src/CMakeLists.txt
src/RadhydroSimulation.hpp
src/SphericalCollapse/CMakeLists.txt
src/SphericalCollapse/spherical_collapse.cpp
src/SphericalCollapse/spherical_collapse.hpp
src/simulation.hpp
tests/SphericalCollapse.in
tests/ascent_actions.yaml

commit 2646fd3f14062787061bc8e9b1a16a7f99fa275b
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Nov 17 15:22:26 2022 -0500

    refactor hydro riemann solver (#185)
    
    * refactor hydro riemann solver
    
    * compute du, dw in ComputeFluxes
    
    * remove meaningless const

src/HLLC.hpp
src/HydroState.hpp
src/hydro_system.hpp

commit aaf20c68b32e8d0d89f94183dfec04b7fbf26974
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Nov 16 14:44:09 2022 -0500

    fix cooling failure at high densities (#184)

src/CloudyCooling.hpp

commit 723a5d961850373e24a949c2e6e5de1059799874
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Nov 15 22:58:15 2022 -0500

    use adaptive wavespeed estimates (#183)

src/hydro_system.hpp

commit 9e1aff6f2e855be45a5f54cbde7086498a3ddc69
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Nov 14 17:12:58 2022 -0500

    reduce memory usage in hydro retries (#182)
    
    * reduce memory usage in hydro retries
    
    * fix YAFluxRegister fine data copy

src/RadhydroSimulation.hpp

commit ce885aa2fc97a32db0e0c6c068cb74d20757fd5e
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Nov 14 13:25:58 2022 -0500

    use the amrex version of the new interpolater (#181)

extern/amrex
src/Advection/CMakeLists.txt
src/Advection2D/CMakeLists.txt
src/AdvectionSemiellipse/CMakeLists.txt
src/Cooling/CMakeLists.txt
src/HydroBlast2D/CMakeLists.txt
src/HydroBlast3D/CMakeLists.txt
src/HydroContact/CMakeLists.txt
src/HydroHighMach/CMakeLists.txt
src/HydroKelvinHelmholz/CMakeLists.txt
src/HydroLeblanc/CMakeLists.txt
src/HydroQuirk/CMakeLists.txt
src/HydroRichtmeyerMeshkov/CMakeLists.txt
src/HydroSMS/CMakeLists.txt
src/HydroShocktube/CMakeLists.txt
src/HydroShuOsher/CMakeLists.txt
src/HydroVacuum/CMakeLists.txt
src/HydroWave/CMakeLists.txt
src/MFInterp_1D_C.H
src/MFInterp_2D_C.H
src/MFInterp_3D_C.H
src/MFInterpolater.H
src/MFInterpolater.cpp
src/ODEIntegration/CMakeLists.txt
src/PassiveScalar/CMakeLists.txt
src/RadBeam/CMakeLists.txt
src/RadForce/CMakeLists.txt
src/RadMarshak/CMakeLists.txt
src/RadMarshakAsymptotic/CMakeLists.txt
src/RadMarshakCGS/CMakeLists.txt
src/RadMatterCoupling/CMakeLists.txt
src/RadMatterCouplingRSLA/CMakeLists.txt
src/RadPulse/CMakeLists.txt
src/RadShadow/CMakeLists.txt
src/RadStreaming/CMakeLists.txt
src/RadSuOlson/CMakeLists.txt
src/RadTophat/CMakeLists.txt
src/RadTube/CMakeLists.txt
src/RadhydroShell/CMakeLists.txt
src/RadhydroShock/CMakeLists.txt
src/RadhydroShockCGS/CMakeLists.txt
src/RayleighTaylor2D/CMakeLists.txt
src/RayleighTaylor3D/CMakeLists.txt
src/ShockCloud/CMakeLists.txt
src/simulation.hpp

commit 44c496486846635dbb352c73b8a1063147841823
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Nov 13 18:29:29 2022 -0500

    use SimulationData for problem-specific data (#180)
    
    * add SimulationData member variable
    
    * use SimulationData instead of problem-specific member variables
    
    * update ShockCloud
    
    * update cooling test

src/Cooling/test_cooling.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadhydroSimulation.hpp
src/ShockCloud/cloud.cpp
src/SimulationData.hpp
src/hydro_system.hpp

commit 19a890e302322d95873e979590303f408d4e3c0e
Author: Neco Kriel <43261821+AstroKriel@users.noreply.github.com>
Date:   Fri Nov 11 06:56:05 2022 +1100

    turn fc vars off (not implemented yet) (#177)
    
    Co-authored-by: Ben Wibking <ben@wibking.com>

src/Cooling/test_cooling.cpp
src/HydroBlast2D/test_hydro2d_blast.cpp
src/HydroBlast3D/test_hydro3d_blast.cpp
src/HydroContact/test_hydro_contact.cpp
src/HydroHighMach/test_hydro_highmach.cpp
src/HydroKelvinHelmholz/test_hydro2d_kh.cpp
src/HydroLeblanc/test_hydro_leblanc.cpp
src/HydroQuirk/test_quirk.cpp
src/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
src/HydroSMS/test_hydro_sms.cpp
src/HydroShocktube/test_hydro_shocktube.cpp
src/HydroShuOsher/test_hydro_shuosher.cpp
src/HydroVacuum/test_hydro_vacuum.cpp
src/HydroWave/test_hydro_wave.cpp
src/PassiveScalar/test_scalars.cpp
src/RadBeam/test_radiation_beam.cpp
src/RadForce/test_radiation_force.cpp
src/RadMarshak/test_radiation_marshak.cpp
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadPulse/test_radiation_pulse.cpp
src/RadStreaming/test_radiation_streaming.cpp
src/RadSuOlson/test_radiation_SuOlson.cpp
src/RadTophat/test_radiation_tophat.cpp
src/RadTube/test_radiation_tube.cpp
src/RadhydroShell/test_radhydro_shell.cpp
src/RadhydroShock/test_radhydro_shock.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/RayleighTaylor2D/test_hydro2d_rt.cpp
src/RayleighTaylor3D/test_hydro3d_rt.cpp
src/ShockCloud/cloud.cpp
src/physics_info.hpp

commit b8acd6b1af161769ec56e37a4d5f56959b97460a
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Nov 10 13:27:36 2022 -0500

    Update README.md with CUDA version requirement (#178)
    
    CUDA >= 11.7 is now required. Note this in the README.

README.md

commit fa8ef98d618c5c151a53e9e049b249fcce872087
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Nov 7 10:15:40 2022 -0500

    ignore clang-tidy array index warning (#175)

src/.clang-tidy

commit 3f9c1673e28e27ce894bd82d47de316255139997
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Nov 7 08:59:41 2022 -0500

    update .clang-tidy config file (#174)

src/.clang-tidy

commit 06b8f28bd2b6b4869067c9c8f6b26078fb08fd2a
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Nov 7 08:45:30 2022 -0500

    fix clang-tidy-review GitHub action (#173)
    
    * clang-tidy should run CMake and read compile_commands.json
    
    * trigger comments from a separate action

.github/workflows/clang-tidy-comments.yml
.github/workflows/clang-tidy.yml

commit 9c84c8c0a4117ec4e6dcbe06550e0958d38bf097
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Nov 6 21:16:47 2022 -0500

    clang-tidy should read compile_commands.json (#172)

.github/workflows/clang-tidy.yml

commit e47bf77d0c05da8f198f599b26b2f0acc317dee0
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Nov 6 20:58:40 2022 -0500

    use .clang-tidy file with clang-tidy-review (#171)

.github/workflows/clang-tidy.yml

commit 6d0c53b546ef58874a0e8c9b072e658f5df2d60d
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Nov 6 16:43:52 2022 -0500

    run clang-tidy on PRs (#170)

.github/workflows/clang-tidy.yml

commit e7c6041d39a4748122c4a26cb1feaab0217928d0
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Nov 6 16:16:20 2022 -0500

    update .clang-format (#169)

src/.clang-format

commit d5b4fe92a3b01c4047a46b9e757aa0eea1795f70
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Nov 6 13:21:40 2022 -0500

    require CUDA 11.7 or newer (#168)

CMakeLists.txt

commit a4de9cf3db8953a0cafe27811a0420495309b944
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Nov 4 14:44:37 2022 -0400

    use GPU reduction for checkHydroStates (#166)

src/RadhydroSimulation.hpp
src/hydro_system.hpp

commit f48ec18f794d96475b98d40b03309e03a4a9a331
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Nov 4 13:27:32 2022 -0400

    fix FOFC (#164)

src/RadhydroSimulation.hpp

commit bb0634e05bd5541f503dd8bfda393e08553a7d40
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Nov 4 12:09:06 2022 -0400

    use custom AMR interpolation method (#163)
    
    * switch to amrex::MFInterpolater
    
    * add new interpolater
    
    * prevent new extrema in AMR interp
    
    * add MFInterpolate.cpp to CMakeLists.txt
    
    * add 1D and 2D interpolaters
    
    * replace lincc_interp with mf_linear_slope_minmax_interp

src/Advection/CMakeLists.txt
src/Advection2D/CMakeLists.txt
src/AdvectionSemiellipse/CMakeLists.txt
src/Cooling/CMakeLists.txt
src/HydroBlast2D/CMakeLists.txt
src/HydroBlast3D/CMakeLists.txt
src/HydroContact/CMakeLists.txt
src/HydroHighMach/CMakeLists.txt
src/HydroKelvinHelmholz/CMakeLists.txt
src/HydroLeblanc/CMakeLists.txt
src/HydroQuirk/CMakeLists.txt
src/HydroRichtmeyerMeshkov/CMakeLists.txt
src/HydroSMS/CMakeLists.txt
src/HydroShocktube/CMakeLists.txt
src/HydroShuOsher/CMakeLists.txt
src/HydroVacuum/CMakeLists.txt
src/HydroWave/CMakeLists.txt
src/MFInterp_1D_C.H
src/MFInterp_2D_C.H
src/MFInterp_3D_C.H
src/MFInterpolater.H
src/MFInterpolater.cpp
src/ODEIntegration/CMakeLists.txt
src/PassiveScalar/CMakeLists.txt
src/RadBeam/CMakeLists.txt
src/RadForce/CMakeLists.txt
src/RadMarshak/CMakeLists.txt
src/RadMarshakAsymptotic/CMakeLists.txt
src/RadMarshakCGS/CMakeLists.txt
src/RadMatterCoupling/CMakeLists.txt
src/RadMatterCouplingRSLA/CMakeLists.txt
src/RadPulse/CMakeLists.txt
src/RadShadow/CMakeLists.txt
src/RadStreaming/CMakeLists.txt
src/RadSuOlson/CMakeLists.txt
src/RadTophat/CMakeLists.txt
src/RadTube/CMakeLists.txt
src/RadhydroShell/CMakeLists.txt
src/RadhydroShock/CMakeLists.txt
src/RadhydroShockCGS/CMakeLists.txt
src/RayleighTaylor2D/CMakeLists.txt
src/RayleighTaylor3D/CMakeLists.txt
src/ShockCloud/CMakeLists.txt
src/simulation.hpp

commit 014467b0e5d365dadd8990ceb0feaab9eeb9b808
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Nov 2 13:17:13 2022 -0400

    update amrex submodule (#161)

extern/amrex

commit fe52af0b908bdbb6ae899b56007526df2be24cec
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Nov 1 12:48:07 2022 -0400

    update settings for Crusher (OLCF) (#159)
    
    * fix GPU-to-NIC binding on Crusher (OLCF)
    
    * update cmake settings

cmake/crusher.cmake
scripts/crusher-1node.submit

commit 507775e19cd4c1429e132424b87e08b0a31d4499
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Oct 31 16:25:29 2022 -0400

    use lincc_interp AMR interpolation method by default (#157)
    
    * add runtime parameter for AMR interpolation method
    
    * comment on mathematical properties of interpolater
    
    * use lincc_interp when amrInterpMethod_ == 1

src/simulation.hpp

commit 9842c66899661e51ee9ab9ffa64e57d643cf13dc
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Oct 30 21:46:47 2022 -0400

    use CellConservativeProtected in 2D and 3D (#156)
    
    * use CellConservativeProtected in 2D and 3D

src/simulation.hpp

commit faee4696021e662d86b17c1355792e0ec2c75ac6
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Oct 30 19:09:53 2022 -0400

    add refinement to passive scalar test (#155)
    
    * add refinement to passive scalar test
    
    * add explicit check for passive scalar conservation

src/PassiveScalar/test_scalars.cpp
tests/PassiveScalar.in

commit cae78ad2293ab71b190a6ad02dbbf676063cb317
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Oct 30 17:06:10 2022 -0400

    disable additional subcycling code (#154)

src/simulation.hpp

commit 56f999d1d72a58ec8028480c4ad385c0ee15df90
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Oct 29 12:07:30 2022 -0400

    Fix bug in additional subcycling (#151)
    
    * reset reductionFactor when recomputing timesteps
    
    * add assertion to ensure the subcycles are working

src/simulation.hpp

commit 45867247877a503ff3d85b76763f5b965c39504d
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Oct 28 10:08:19 2022 -0400

    fix reflux when timestep retries are used (#150)
    
    * fix flux registers when doing timestep retries
    
    * scale flux register values properly
    
    * remove flux regs from advanceHydroAtLevel args
    
    * do not increment flux registers if hydro advance failed

src/RadhydroSimulation.hpp

commit 98b94de094aaa22bc04dd021e9542b26bafdfb8c
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Oct 27 09:57:55 2022 -0400

    retry hydro step on post-hoc CFL violation (#149)
    
    * retry hydro step if CFL is violated post-hoc
    
    * add debugging output

src/RadhydroSimulation.hpp
src/hydro_system.hpp

commit 5a2c39227384707aaabfb83dfdd36940594d9636
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Oct 26 19:14:07 2022 -0400

    use FillPatcher class for ghost cell filling when using AMR (#133)
    
    * use FillPatcher class, update InterpHooks
    
    * update amrex submodule

extern/amrex
src/RadhydroSimulation.hpp
src/simulation.hpp

commit 687d9096d5eceab2eafacddabba13c318d28dc32
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Oct 26 14:18:32 2022 -0400

    add ability to retry hydro advance with smaller dt (#148)
    
    * add ability to retry hydro with smaller dt
    
    * initialize tmp multifab to zero

src/RadhydroSimulation.hpp

commit b539541e01078fb889e522eb6ea2a21f2d1c8ecd
Author: Neco Kriel <43261821+AstroKriel@users.noreply.github.com>
Date:   Wed Oct 26 12:13:42 2022 +1100

    Rename BCs-variable to indicate centering (#146)
    
    * rename BCs to indicate quantity centering
    
    * rename varaible that stores the total number of cc quantities

src/Advection/test_advection.cpp
src/Advection2D/test_advection2d.cpp
src/AdvectionSemiellipse/test_advection_semiellipse.cpp
src/Cooling/test_cooling.cpp
src/HydroBlast2D/test_hydro2d_blast.cpp
src/HydroBlast3D/test_hydro3d_blast.cpp
src/HydroContact/test_hydro_contact.cpp
src/HydroHighMach/test_hydro_highmach.cpp
src/HydroKelvinHelmholz/test_hydro2d_kh.cpp
src/HydroLeblanc/test_hydro_leblanc.cpp
src/HydroQuirk/test_quirk.cpp
src/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
src/HydroSMS/test_hydro_sms.cpp
src/HydroShocktube/test_hydro_shocktube.cpp
src/HydroShuOsher/test_hydro_shuosher.cpp
src/HydroVacuum/test_hydro_vacuum.cpp
src/HydroWave/test_hydro_wave.cpp
src/PassiveScalar/test_scalars.cpp
src/RadBeam/test_radiation_beam.cpp
src/RadForce/test_radiation_force.cpp
src/RadMarshak/test_radiation_marshak.cpp
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadPulse/test_radiation_pulse.cpp
src/RadShadow/test_radiation_shadow.cpp
src/RadStreaming/test_radiation_streaming.cpp
src/RadSuOlson/test_radiation_SuOlson.cpp
src/RadTophat/test_radiation_tophat.cpp
src/RadTube/test_radiation_tube.cpp
src/RadhydroShell/test_radhydro_shell.cpp
src/RadhydroShock/test_radhydro_shock.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/RadhydroSimulation.hpp
src/RayleighTaylor2D/test_hydro2d_rt.cpp
src/RayleighTaylor3D/test_hydro3d_rt.cpp
src/ShockCloud/cloud.cpp

commit 9afc1aaa90131dd4a20a2cce2567892543366d08
Author: Neco Kriel <43261821+AstroKriel@users.noreply.github.com>
Date:   Wed Oct 26 11:07:51 2022 +1100

    Rename grid member variables (#147)
    
    * add underscore to grid member vars

src/Advection/test_advection.cpp
src/Advection2D/test_advection2d.cpp
src/AdvectionSemiellipse/test_advection_semiellipse.cpp
src/Cooling/test_cooling.cpp
src/HydroBlast2D/test_hydro2d_blast.cpp
src/HydroBlast3D/test_hydro3d_blast.cpp
src/HydroContact/test_hydro_contact.cpp
src/HydroHighMach/test_hydro_highmach.cpp
src/HydroKelvinHelmholz/test_hydro2d_kh.cpp
src/HydroLeblanc/test_hydro_leblanc.cpp
src/HydroQuirk/test_quirk.cpp
src/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
src/HydroSMS/test_hydro_sms.cpp
src/HydroShocktube/test_hydro_shocktube.cpp
src/HydroShuOsher/test_hydro_shuosher.cpp
src/HydroVacuum/test_hydro_vacuum.cpp
src/HydroWave/test_hydro_wave.cpp
src/PassiveScalar/test_scalars.cpp
src/RadBeam/test_radiation_beam.cpp
src/RadForce/test_radiation_force.cpp
src/RadMarshak/test_radiation_marshak.cpp
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadPulse/test_radiation_pulse.cpp
src/RadShadow/test_radiation_shadow.cpp
src/RadStreaming/test_radiation_streaming.cpp
src/RadSuOlson/test_radiation_SuOlson.cpp
src/RadTophat/test_radiation_tophat.cpp
src/RadTube/test_radiation_tube.cpp
src/RadhydroShell/test_radhydro_shell.cpp
src/RadhydroShock/test_radhydro_shock.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/RayleighTaylor2D/test_hydro2d_rt.cpp
src/RayleighTaylor3D/test_hydro3d_rt.cpp
src/ShockCloud/cloud.cpp
src/grid.hpp

commit ad6c0dc8f1175b0ae290031f6dc6aa2f95cd2b95
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Oct 24 18:33:51 2022 -0400

    use MultiFab ParallelFor for hydro (#135)
    
    * partial refactor for MF ParFor in hydro
    
    * add stream synchronize after each stage
    
    * use MF ParallelFor for AdvectionSimulation
    
    * fix flux register usage
    
    * add PLM and constant reconstruction with MFParFor
    
    * add FOFC to MFParFor hydro
    
    * use iMultiFab for redoFlags

src/AdvectionSimulation.hpp
src/ArrayView_2d.hpp
src/ArrayView_3d.hpp
src/RadhydroSimulation.hpp
src/hydro_system.hpp
src/hyperbolic_system.hpp
src/linear_advection.hpp
src/radiation_system.hpp
src/simulation.hpp

commit 38c6191ec6535af9816d139a5cc84ea33dac878a
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Oct 24 11:33:03 2022 -0400

    decide whether to subcycle based on cost (#145)
    
    * decide whether to subcycle based on cost
    
    * add verbose output

src/simulation.hpp

commit 74e524985eea03daa575dec23e3a944d4b9dd609
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Oct 20 16:15:56 2022 -0400

    remove dt assert in ODEIntegrate (#143)

src/ODEIntegrate.hpp

commit 131065f2c08c295a68380d3e7a5d5b96d7557aa8
Author: Neco Kriel <43261821+AstroKriel@users.noreply.github.com>
Date:   Fri Oct 21 04:47:51 2022 +1100

    Update input argument to user initialisation function (#129)
    
    * fix init-ing bug: now init-ing all state varaibles (for running in debug mode)
    
    * Delete highmach_output.csv
    
    * update gitignore to ignore extraneous (output or testing) files
    
    * remove testing files
    
    * remove debugging code
    
    * update: only pass single grid element to user-initialisation function.
    
    * remove unused vector
    
    * update: refer directly to grid elem passed to func.
    
    * remove extra git ignore line
    
    * revert git ignore to original version
    
    * undo edits to gitignore (reitroduce duplicate entry)
    
    * add empty line in gitignore as in ben/quokka/development/gitignore
    
    * remove init. of (unused) vector of grid elems

src/Advection/test_advection.cpp
src/Advection2D/test_advection2d.cpp
src/AdvectionSemiellipse/test_advection_semiellipse.cpp
src/AdvectionSimulation.hpp
src/Cooling/test_cooling.cpp
src/HydroBlast2D/test_hydro2d_blast.cpp
src/HydroBlast3D/test_hydro3d_blast.cpp
src/HydroContact/test_hydro_contact.cpp
src/HydroHighMach/test_hydro_highmach.cpp
src/HydroKelvinHelmholz/test_hydro2d_kh.cpp
src/HydroLeblanc/test_hydro_leblanc.cpp
src/HydroQuirk/test_quirk.cpp
src/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
src/HydroSMS/test_hydro_sms.cpp
src/HydroShocktube/test_hydro_shocktube.cpp
src/HydroShuOsher/test_hydro_shuosher.cpp
src/HydroVacuum/test_hydro_vacuum.cpp
src/HydroWave/test_hydro_wave.cpp
src/PassiveScalar/test_scalars.cpp
src/RadBeam/test_radiation_beam.cpp
src/RadForce/test_radiation_force.cpp
src/RadMarshak/test_radiation_marshak.cpp
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadPulse/test_radiation_pulse.cpp
src/RadShadow/test_radiation_shadow.cpp
src/RadStreaming/test_radiation_streaming.cpp
src/RadSuOlson/test_radiation_SuOlson.cpp
src/RadTophat/test_radiation_tophat.cpp
src/RadTube/test_radiation_tube.cpp
src/RadhydroShell/test_radhydro_shell.cpp
src/RadhydroShock/test_radhydro_shock.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/RadhydroSimulation.hpp
src/RayleighTaylor2D/test_hydro2d_rt.cpp
src/RayleighTaylor3D/test_hydro3d_rt.cpp
src/ShockCloud/cloud.cpp
src/simulation.hpp

commit 92475faed82b397e759f4d12824309b78f9d5252
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Oct 20 09:36:02 2022 -0400

    update GitHub actions (#142)
    
    * Update cmake.yml
    
    * update CodeQL and Sonarcloud actions

.github/workflows/cmake.yml
.github/workflows/codeql-analysis.yml
.github/workflows/sonarcloud.yml

commit cc319c980caf0e8f14eafe7a4903bb6e80dac3ce
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Oct 20 09:14:46 2022 -0400

    fix memory issue in ShockCloud initial conditions (#140)
    
    * fix memory issue in ShockCloud initial conditions
    
    * fix cooling problem
    
    * don't initialize rad variables

src/Cooling/test_cooling.cpp
src/ShockCloud/cloud.cpp

commit 2b0b2c536a77927563fc1473517f854a7db2abc9
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Oct 20 08:28:43 2022 -0400

    run CI with ENABLE_ASAN=ON (#141)

.github/workflows/cmake.yml

commit 63596d213f835c4bf841b6683ca76646bdbd09eb
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Oct 19 20:21:32 2022 -0400

    fix memory errors in setInitialConditionsOnGrid (#139)

src/grid.hpp
src/simulation.hpp

commit a9a245a6302bd8badc213024937767a73e68f6e9
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Oct 19 17:43:47 2022 -0400

    fix undefined behavior in ComputeRhsFromFluxes (#138)

src/hydro_system.hpp

commit 4f288b40ef90403af54353776f729107ee7d77a9
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Oct 18 09:45:35 2022 -0400

    suppress gcc warnings about ARM ABI change (#137)

CMakeLists.txt

commit c644c1ba8597c29d23c9658a76d77e76be8b7035
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Oct 18 09:06:20 2022 -0400

    fix undefined behavior in AddInternalEnergyPdV (#136)

src/hydro_system.hpp

commit 7eb1b752becd81dffc560c7b27f153937933607f
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Oct 14 15:46:47 2022 -0400

    allow limiting timesteps based on extra physics (#134)
    
    * allow limiting dt based on cooling time
    
    * output min tcool

src/AdvectionSimulation.hpp
src/RadhydroSimulation.hpp
src/ShockCloud/cloud.cpp
src/simulation.hpp

commit 103a46d9a0742f26f58db7d858837ff6a4df9546
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Oct 14 13:23:39 2022 -0400

    avoid filling old_state when regridding (#131)
    
    * don't fill old_state when regridding
    
    * avoid filling state_old in MakeNewLevelFromCoarse
    
    * apply FixUpState only to state_new

src/RadhydroSimulation.hpp
src/simulation.hpp

commit 51aab4835ecc7533e60537a5970c251dfd4557ba
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Oct 14 11:32:22 2022 -0400

    apply density floor after regrid (#132)

src/RadhydroSimulation.hpp

commit 032948c2a1bd40e5120c8e783f96f4f25dd972da
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Oct 10 14:56:09 2022 -0400

    add benchmark parameter files for Crusher (#130)

scripts/crusher-1node.submit
tests/benchmark_unigrid_1024.in
tests/benchmark_unigrid_2048.in
tests/benchmark_unigrid_512.in

commit 5b72d6295969defd7f6e0c9945d0f377ff563210
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Oct 9 20:59:10 2022 -0400

    disable pltfile output for shocktube test (#128)

tests/shocktube.in

commit 6a85cb9dc8773da4cdb8e7a5816af6df72c52a50
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Oct 9 18:14:00 2022 -0400

    add CMake settings for Crusher (OLCF) (#127)

cmake/crusher.cmake

commit 5ab273f859fe1b75d2dfa032145d0d03869c6d44
Author: Neco Kriel <43261821+AstroKriel@users.noreply.github.com>
Date:   Fri Oct 7 23:54:38 2022 +1000

    Rename variables to indicate they store cell-centred quantities (#126)
    
    * rename cc vars
    
    * fix variable name (bug)

src/Advection/test_advection.cpp
src/Advection2D/test_advection2d.cpp
src/AdvectionSemiellipse/test_advection_semiellipse.cpp
src/AdvectionSimulation.hpp
src/Cooling/test_cooling.cpp
src/HydroBlast2D/test_hydro2d_blast.cpp
src/HydroBlast3D/test_hydro3d_blast.cpp
src/HydroContact/test_hydro_contact.cpp
src/HydroHighMach/test_hydro_highmach.cpp
src/HydroKelvinHelmholz/test_hydro2d_kh.cpp
src/HydroLeblanc/test_hydro_leblanc.cpp
src/HydroQuirk/test_quirk.cpp
src/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
src/HydroSMS/test_hydro_sms.cpp
src/HydroShocktube/test_hydro_shocktube.cpp
src/HydroShuOsher/test_hydro_shuosher.cpp
src/HydroVacuum/test_hydro_vacuum.cpp
src/HydroWave/test_hydro_wave.cpp
src/PassiveScalar/test_scalars.cpp
src/RadBeam/test_radiation_beam.cpp
src/RadForce/test_radiation_force.cpp
src/RadMarshak/test_radiation_marshak.cpp
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadPulse/test_radiation_pulse.cpp
src/RadShadow/test_radiation_shadow.cpp
src/RadStreaming/test_radiation_streaming.cpp
src/RadSuOlson/test_radiation_SuOlson.cpp
src/RadTube/test_radiation_tube.cpp
src/RadhydroShell/test_radhydro_shell.cpp
src/RadhydroShock/test_radhydro_shock.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/RadhydroSimulation.hpp
src/RayleighTaylor2D/test_hydro2d_rt.cpp
src/RayleighTaylor3D/test_hydro3d_rt.cpp
src/ShockCloud/cloud.cpp
src/simulation.hpp

commit cfec18274dcc73a8260649f29b1ded718db077ed
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Oct 4 14:56:48 2022 -0400

    update amrex (#123)

extern/amrex

commit 6ea0c9a028d34a9c943327c37ee45af59109ae64
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Oct 3 15:47:23 2022 -0400

    update MI100 build settings (#122)

cmake/delta_gcc_hip.cmake

commit 851cbddae54f9f89763e112939cc9cb545d48423
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Oct 1 12:37:35 2022 -0400

    enable gpu-aware MPI by default (#121)
    
    * enable gpu-aware MPI by default
    
    * updated README for GPU-aware MPI
    
    * updated batch scripts
    
    * change fextract to use device-allocated data
    
    * copy reference solution to device when needed
    
    * interpolate.h -> interpolate.hpp
    
    * initialize on device
    
    * avoid LoopConcurrentOnCpu

README.md
cmake/delta_gcc_cuda.cmake
scripts/blast_1gpu.submit
scripts/blast_1node.submit
scripts/delta-1node.submit
scripts/gpu_wrapper_amr_shell.sh
scripts/gpu_wrapper_amr_shell_stream.sh
scripts/gpu_wrapper_cooling_1024.sh
scripts/gpu_wrapper_sedov_1024.sh
scripts/gpu_wrapper_sedov_2048.sh
scripts/gpu_wrapper_sedov_256.sh
scripts/gpu_wrapper_sedov_256_gpuaware.sh
scripts/gpu_wrapper_sedov_512.sh
scripts/gpu_wrapper_shell_1024.sh
scripts/gpu_wrapper_shell_2048.sh
scripts/gpu_wrapper_shell_256.sh
scripts/gpu_wrapper_shell_512.sh
src/Advection/test_advection.cpp
src/AdvectionSemiellipse/test_advection_semiellipse.cpp
src/HydroBlast2D/test_hydro2d_blast.hpp
src/HydroBlast3D/test_hydro3d_blast.hpp
src/HydroContact/test_hydro_contact.cpp
src/HydroContact/test_hydro_contact.hpp
src/HydroHighMach/CMakeLists.txt
src/HydroHighMach/test_hydro_highmach.cpp
src/HydroHighMach/test_hydro_highmach.hpp
src/HydroKelvinHelmholz/test_hydro2d_kh.hpp
src/HydroLeblanc/CMakeLists.txt
src/HydroLeblanc/test_hydro_leblanc.cpp
src/HydroLeblanc/test_hydro_leblanc.hpp
src/HydroQuirk/test_quirk.hpp
src/HydroRichtmeyerMeshkov/test_hydro2d_rm.hpp
src/HydroSMS/test_hydro_sms.cpp
src/HydroSMS/test_hydro_sms.hpp
src/HydroShocktube/CMakeLists.txt
src/HydroShocktube/test_hydro_shocktube.cpp
src/HydroShocktube/test_hydro_shocktube.hpp
src/HydroShuOsher/CMakeLists.txt
src/HydroShuOsher/test_hydro_shuosher.cpp
src/HydroShuOsher/test_hydro_shuosher.hpp
src/HydroVacuum/CMakeLists.txt
src/HydroVacuum/test_hydro_vacuum.cpp
src/HydroVacuum/test_hydro_vacuum.hpp
src/HydroWave/test_hydro_wave.cpp
src/PassiveScalar/test_scalars.cpp
src/PassiveScalar/test_scalars.hpp
src/RadForce/CMakeLists.txt
src/RadForce/test_radiation_force.cpp
src/RadMarshak/CMakeLists.txt
src/RadMarshak/test_radiation_marshak.cpp
src/RadMarshak/test_radiation_marshak.hpp
src/RadMarshakAsymptotic/CMakeLists.txt
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.hpp
src/RadMarshakCGS/CMakeLists.txt
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.hpp
src/RadMatterCoupling/CMakeLists.txt
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.hpp
src/RadMatterCouplingRSLA/CMakeLists.txt
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.hpp
src/RadPulse/test_radiation_pulse.cpp
src/RadPulse/test_radiation_pulse.hpp
src/RadStreaming/test_radiation_streaming.cpp
src/RadSuOlson/CMakeLists.txt
src/RadSuOlson/test_radiation_SuOlson.cpp
src/RadSuOlson/test_radiation_SuOlson.hpp
src/RadTophat/test_radiation_tophat.hpp
src/RadTube/CMakeLists.txt
src/RadTube/test_radiation_tube.cpp
src/RadhydroShell/CMakeLists.txt
src/RadhydroShell/test_radhydro_shell.cpp
src/RadhydroShell/test_radhydro_shell.hpp
src/RadhydroShock/CMakeLists.txt
src/RadhydroShock/test_radhydro_shock.cpp
src/RadhydroShock/test_radhydro_shock.hpp
src/RadhydroShockCGS/CMakeLists.txt
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.hpp
src/RayleighTaylor2D/test_hydro2d_rt.hpp
src/RayleighTaylor3D/test_hydro3d_rt.hpp
src/fextract.cpp
src/fextract.hpp
src/interpolate.cpp
src/interpolate.h
src/interpolate.hpp
src/main.cpp

commit 5b3c9df9b57ae4db0eec623ba264b5bf6b954fb9
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Sep 18 19:33:23 2022 -0400

    use MultiFab ParallelFor for RT2D/3D problems (#120)
    
    * use MultiFab ParallelFor
    
    * added Gpu::streamSynchronize()

src/RayleighTaylor2D/test_hydro2d_rt.cpp
src/RayleighTaylor3D/ascent_actions.yaml
src/RayleighTaylor3D/test_hydro3d_rt.cpp

commit 448fe5a82c3dbe21d74b0c1f6410130d04f81022
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Sep 16 16:07:00 2022 -0400

    Update NCSA Delta config (#119)
    
    * update delta config

cmake/delta_gcc_cuda.cmake
scripts/delta-1gpu.submit
scripts/delta-1node.submit
scripts/mi100-1gpu.submit
scripts/mi100-1node.submit

commit 1d9f8568074d3ff97555620530af694a1e782c3c
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Sep 12 13:06:25 2022 -0400

    added CMake config for NCSA Delta (#116)
    
    Co-authored-by: Benjamin Wibking <wibkingb@msu.edu>

cmake/delta_gcc_cuda.cmake
cmake/delta_gcc_hip.cmake

commit 2f81cec9ddb851a9f13e107367d6a98d449431a6
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Sep 10 20:09:34 2022 -0400

    compute 1D averages of user-specified quantities (#115)

src/RadhydroSimulation.hpp
src/RayleighTaylor3D/test_hydro3d_rt.cpp

commit 6f99778829125b1223518b09c332d0fad86cdfcb
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Sep 9 22:21:18 2022 -0400

    use internal energy for AMR interpolation (#113)
    
    * use specific internal energy for AMR interpolation using pre_interp and post_interp hooks

src/AdvectionSimulation.hpp
src/RadhydroSimulation.hpp
src/simulation.hpp

commit 3079df0bbbbda7d58ad4eae9eb04e4cf5d9a1ec4
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Sep 9 14:43:02 2022 -0400

    fix shock-cloud initialization (#114)

src/ShockCloud/cloud.cpp

commit 293766fea74a4c7167024aa8e6756e83607601d3
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Sep 4 18:42:03 2022 -0400

    add image of RT3D simulation to README.md (#111)
    
    * add image of RT3D simulation to README.md

README.md
extern/rt3d_visit.png

commit ecf5582a9e60ab01729a757d846ce3d2a1bf8bfc
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Sep 2 20:33:11 2022 -0400

    add Rayleigh-Taylor test problems (#110)

src/CMakeLists.txt
src/RayleighTaylor2D/CMakeLists.txt
src/RayleighTaylor2D/test_hydro2d_rt.cpp
src/RayleighTaylor2D/test_hydro2d_rt.hpp
src/RayleighTaylor3D/CMakeLists.txt
src/RayleighTaylor3D/test_hydro3d_rt.cpp
src/RayleighTaylor3D/test_hydro3d_rt.hpp
tests/RT2D.in
tests/RT3D.in

commit 711e90a0007e4fef6ec5d05455344b9ed6ca32de
Author: Neco Kriel <43261821+AstroKriel@users.noreply.github.com>
Date:   Mon Aug 15 11:41:04 2022 +1000

    Remove dimension dependent (3D) import of ArrayView (#108)
    
    * removed the import of the dimension-dependent arrayview header file (i.e., ArrayView_3d.hpp)

src/hydro_system.hpp

commit c485d8f033444bcd2a6b1d8ff66e322076b052ec
Author: Neco Kriel <43261821+AstroKriel@users.noreply.github.com>
Date:   Fri Aug 12 20:32:51 2022 +1000

    Refactor simulation initialisation (#106)
    
    * fix init-ing bug: now init-ing all state varaibles (for running in debug mode)
    
    * created a container for storing information relevant when initialising different grids (i.e., cell- or face-centred)
    
    * provide empty implementations for funcs evaluated in the init step. the user should provide an implementation for each in the problem file if required.
    
    * relocate boiler-plate code for simulation initialisation to the parent simulation class, with calls to user-defined funcs.
    
    * implement ini funcs for each problem file (in progress)
    
    * put grid struct and grid enums in a quokka namespace
    
    * add quokka namespace call for grid in problem files
    
    * move access of state variables outside of func (i.e., computeWaveSolution) which is potentially evaluated on GPU, but grid_vec[0].array lives on CPU.
    
    * move access of state variables reference outside of ParFor.
    
    * create a copy of global variables so  if the program is compiled to run on the GPU, then the GPU  will be able to access variables.
    
    Co-authored-by: Ben Wibking <benjamin.wibking@anu.edu.au>
    Co-authored-by: Neco Kriel <necoturb@avatargpue.anu.edu.au>

.gitignore
src/Advection/test_advection.cpp
src/Advection2D/test_advection2d.cpp
src/AdvectionSemiellipse/test_advection_semiellipse.cpp
src/AdvectionSimulation.hpp
src/Cooling/test_cooling.cpp
src/HydroBlast2D/test_hydro2d_blast.cpp
src/HydroBlast3D/test_hydro3d_blast.cpp
src/HydroContact/test_hydro_contact.cpp
src/HydroHighMach/test_hydro_highmach.cpp
src/HydroKelvinHelmholz/test_hydro2d_kh.cpp
src/HydroLeblanc/test_hydro_leblanc.cpp
src/HydroQuirk/test_quirk.cpp
src/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
src/HydroSMS/test_hydro_sms.cpp
src/HydroShocktube/test_hydro_shocktube.cpp
src/HydroShuOsher/test_hydro_shuosher.cpp
src/HydroVacuum/test_hydro_vacuum.cpp
src/HydroWave/test_hydro_wave.cpp
src/PassiveScalar/test_scalars.cpp
src/RadBeam/test_radiation_beam.cpp
src/RadForce/test_radiation_force.cpp
src/RadMarshak/test_radiation_marshak.cpp
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadPulse/test_radiation_pulse.cpp
src/RadShadow/test_radiation_shadow.cpp
src/RadStreaming/test_radiation_streaming.cpp
src/RadSuOlson/test_radiation_SuOlson.cpp
src/RadTophat/test_radiation_tophat.cpp
src/RadTube/test_radiation_tube.cpp
src/RadhydroShell/test_radhydro_shell.cpp
src/RadhydroShock/test_radhydro_shock.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/RadhydroSimulation.hpp
src/ShockCloud/cloud.cpp
src/grid.hpp
src/simulation.hpp

commit 86601860703bb9e598f4ba1afa02508ca3d7692f
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Aug 9 16:52:48 2022 +1000

    Fix bug in P dV term in dual energy update (#107)
    
    * fix dual energy bugs

src/Cooling/test_cooling.cpp
src/RadhydroSimulation.hpp
src/ShockCloud/cloud.cpp
src/hydro_system.hpp

commit 177b5b9720c456e9d45d49d74f4d365f12ef9fdf
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Aug 8 19:35:57 2022 +1000

    add CI debug build on arm64 (#105)
    
    [skip ci]

.ci/azure-pipelines-aarch64-debug.yml

commit 41aa7147c95be5875693c368009c748981b4f2d0
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Aug 8 17:01:37 2022 +1000

    Fix P -> Pgas in Hydro_System assert (#103)

src/hydro_system.hpp

commit bd60b4ba71d7438cb31e94d31ccaa8ea68bea8b6
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Aug 3 12:13:24 2022 +1000

    reconstruct SIE for internal energy variable (#100)

src/hydro_system.hpp

commit 0efb41bcd499f9383ca5d885631ec5101761d7ea
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Aug 2 19:00:23 2022 +1000

    compute internalEnergy P dV with face-centered velocities (#95)
    
    * save face-centered velocities from Riemann solver
    
    * use unsplit cell-centered P dV term

extern/highmach_reference.txt
src/RadhydroSimulation.hpp
src/hydro_system.hpp

commit 923ae6b714a0e18c77af1bb733527baf8cd48977
Author: Neco Kriel <43261821+AstroKriel@users.noreply.github.com>
Date:   Tue Aug 2 17:07:47 2022 +1000

    Fix periodicity bug in the rad-hydro-shell simulation (#98)
    
    * fixed periodicity flag in the shell-simulation parameter file
    
    * removed duplicate and incorrect state variable initialisation

src/RadhydroShell/test_radhydro_shell.cpp
tests/radhydro_shell.in

commit 7b5e68d3a2751a169e539085638ea58848e397a1
Author: Neco Kriel <43261821+AstroKriel@users.noreply.github.com>
Date:   Tue Aug 2 15:58:43 2022 +1000

    Added include guards for the physics-trait header files (#99)
    
    * added include guards to physics-trait header files

src/physics_info.hpp
src/physics_numVars.hpp

commit c5c572e8b0ef9e74a3c812c4f5c375275975e5b2
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Aug 2 14:33:10 2022 +1000

    Update CONTRIBUTING.md (#97)

CONTRIBUTING.md

commit bc930da3b7b1174749e5f17427b1e62a6c6d64f2
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Aug 1 14:24:00 2022 +1000

    add Strang-split sources to hydro update (#94)
    
    * add calls to Strang-split sources

src/RadhydroSimulation.hpp

commit 1e921c798304f43c1dc09a10cc5155b1e7e906ca
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Jul 30 20:09:51 2022 +1000

    add AMREX_GPUS_PER_NODE to Gadi host config (#91)

cmake/gadi_gcc_cuda.cmake

commit 03e4bad1d5c47c28a663cbe96c255e6b15fb799e
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Jul 30 18:51:13 2022 +1000

    specify max_timesteps at runtime for blast test (#90)

scripts/gpu_wrapper_sedov_256_gpuaware.sh
src/HydroBlast3D/test_hydro3d_blast.cpp
tests/blast_unigrid_256.in

commit 4ed87774a2ffe65d164a2afd2b7df825b8a3a7af
Author: Neco Kriel <43261821+AstroKriel@users.noreply.github.com>
Date:   Thu Jul 28 11:51:03 2022 +1000

    add Physics_Traits compile-time options (#88)
    
    * make quokka uppercase in README.md
    
    * add physics-trait booleans
    
    * num. passive scalars is now defined in physics-traits
    
    * move naming of state variables to child-classes
    
    * add minor bits of code. not integrated with the simulation code yet.
    
    * state variable indices are defined in physics-indices struct
    
    * remove MHD-module flag (not implemented yet; causes confusion)
    
    * rename chemistry-module flag to is_chemistry_enabled
    
    * removed unnecessary physics-trait flags + added check that modules cannot be enabled if they are not implemented.

README.md
src/Advection2D/test_advection2d.cpp
src/AdvectionSimulation.hpp
src/Cooling/test_cooling.cpp
src/HydroBlast2D/test_hydro2d_blast.cpp
src/HydroBlast3D/test_hydro3d_blast.cpp
src/HydroContact/test_hydro_contact.cpp
src/HydroHighMach/test_hydro_highmach.cpp
src/HydroKelvinHelmholz/test_hydro2d_kh.cpp
src/HydroLeblanc/test_hydro_leblanc.cpp
src/HydroQuirk/test_quirk.cpp
src/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
src/HydroSMS/test_hydro_sms.cpp
src/HydroShocktube/test_hydro_shocktube.cpp
src/HydroShuOsher/test_hydro_shuosher.cpp
src/HydroVacuum/test_hydro_vacuum.cpp
src/HydroWave/test_hydro_wave.cpp
src/PassiveScalar/test_scalars.cpp
src/RadBeam/test_radiation_beam.cpp
src/RadForce/test_radiation_force.cpp
src/RadMarshak/test_radiation_marshak.cpp
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadPulse/test_radiation_pulse.cpp
src/RadStreaming/test_radiation_streaming.cpp
src/RadSuOlson/test_radiation_SuOlson.cpp
src/RadTophat/test_radiation_tophat.cpp
src/RadTube/test_radiation_tube.cpp
src/RadhydroShell/test_radhydro_shell.cpp
src/RadhydroShock/test_radhydro_shock.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/RadhydroSimulation.hpp
src/ShockCloud/cloud.cpp
src/ShockCloud/test_cloudy.cpp
src/hydro_system.hpp
src/physics_info.hpp
src/physics_numVars.hpp
src/radiation_system.hpp
src/simulation.hpp

commit 4098e13a8741e5c5f546a859d39ffe508978caac
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Jul 27 14:48:00 2022 +1000

    move sonarcloud analysis to separate CI action (#89)
    
    * Create sonarcloud.yml
    
    * update cmake build action

.github/workflows/cmake.yml
.github/workflows/sonarcloud.yml

commit d62c19caacc4037c242f91eae88db7f4daa4dceb
Author: Neco Kriel <43261821+AstroKriel@users.noreply.github.com>
Date:   Wed Jul 27 10:37:35 2022 +1000

    initialise auxiliary gas internal energy in test problems (#83)
    
    * fix init-ing bug: now init-ing all state varaibles (for running in debug mode)
    
    * changed the initial value of the gas internal energy: Eint = Etot - Ekin, where Ekin = (px*px + py*py + pz*pz)/(2*rho).
    
    Co-authored-by: Ben Wibking <benjamin.wibking@anu.edu.au>

src/RadBeam/test_radiation_beam.cpp
src/RadForce/test_radiation_force.cpp
src/RadMarshak/test_radiation_marshak.cpp
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadPulse/test_radiation_pulse.cpp
src/RadShadow/test_radiation_shadow.cpp
src/RadStreaming/test_radiation_streaming.cpp
src/RadSuOlson/test_radiation_SuOlson.cpp
src/RadTophat/test_radiation_tophat.cpp
src/RadTube/test_radiation_tube.cpp
src/RadhydroShell/test_radhydro_shell.cpp
src/RadhydroShock/test_radhydro_shock.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp

commit 3a2e3da8bc0660c18e03719203b15c41f752af7b
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jul 26 19:33:08 2022 +1000

    Update cmake.yml (#85)

.github/workflows/cmake.yml

commit 8206f4b911c8f410c1d776002f6c955a7164c0ad
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jul 26 12:38:20 2022 +1000

    run CI on pull requests (#84)

.github/workflows/cmake.yml

commit 9802b89523f61fcbb7c2e261c31479c8b9dd676a
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jul 24 17:50:11 2022 +1000

    add use_dual_energy parameter (#81)

src/RadhydroSimulation.hpp
tests/HighMach.in

commit d999b61c44bd664194c105f6a512eba4674c760a
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jul 24 17:01:54 2022 +1000

    fix cmake python support (#82)

src/CMakeLists.txt

commit 1f95732b7e71ff132ba76af2d1bce4ebc355204b
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jul 24 14:39:06 2022 +1000

    add reconstruction order input params (#80)

src/RadhydroSimulation.hpp
tests/shocktube.in

commit 151ae70cb369441bc34ad21b4c367cf163757322
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Jul 23 16:35:02 2022 +1000

    change the way CMake finds Python headers (#79)

CMakeLists.txt
README.md
src/CMakeLists.txt

commit 64f16e2c33b199b41386529dc44a323f474c913b
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Jul 23 12:48:46 2022 +1000

    Update README.md
    
    use https git url rather than ssh url to make it easier for new git users

README.md

commit 5b031988965dbe497f391e391339de12c2274b6c
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jul 19 16:01:45 2022 +1000

    fix buffer overlap, uninitialized vars (#76)

src/HydroQuirk/test_quirk.cpp

commit 56904c697e3a6e8b9f0a5317e8ba379e70bcf972
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jul 19 15:39:23 2022 +1000

    make functions accessed in initializer list static (#77)

src/RadhydroSimulation.hpp

commit 9fbcfefedd725205fe03abfda9a94dd3fb27507d
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jul 18 12:12:56 2022 +1000

    Update azure-pipelines-aarch64.yml for Azure Pipelines

.ci/azure-pipelines-aarch64.yml

commit b6aabf0f5f41ef3c6ed783ccc623504557250077
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jul 18 11:28:09 2022 +1000

    add aarch64 CI
    
    [skip ci]

.ci/azure-pipelines-aarch64.yml

commit dcdd88769314b878b5a8fa7230153fb1d07a07b9
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jul 17 23:50:46 2022 +1000

    arm64 build fix (#72)
    
    * add cmake config for arm64
    
    * add include guard for matplotlibcpp header
    
    * guard x86-specific function attributes
    
    Co-authored-by: Ben Wibking <ben.wibking@gmail.com>

cmake/altra_gcc.cmake
src/CMakeLists.txt
src/HydroHighMach/test_hydro_highmach.cpp
src/hyperbolic_system.hpp

commit 0beb484ce6760b4c1682af4319fb562f7824168e
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Jun 30 16:10:48 2022 +1000

    use fast scaled interpolation of cooling tables (#66)
    
    * use FastMath functions to do scaled interpolation
    
    * add execution space annotations
    
    * add USE_FASTMATH ifdef

src/CloudyCooling.hpp
src/FastMath.hpp
src/GrackleDataReader.cpp

commit 36b5485dc979e6d079e105cc5c508d621027d21c
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Jun 29 17:52:53 2022 +1000

    add ascent_interval runtime parameter (#65)
    
    * add ascent_interval runtime parameter
    
    * add ifdefs

src/simulation.hpp

commit c3871ad2aa67e4db55b0470c944f7a37f8e5aae9
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Jun 29 12:59:51 2022 +1000

    avoid allocating radiation variables for hydro-only problems (#64)
    
    * allow hydro-only sims to avoid allocating rad vars
    
    * avoid allocating rad vars in hydro-only tests
    
    * don't try to use radEnergy if it doesn't exist
    
    * fix edge case in expandFluxArrays assert

src/Cooling/test_cooling.cpp
src/HydroBlast2D/test_hydro2d_blast.cpp
src/HydroBlast3D/test_hydro3d_blast.cpp
src/HydroContact/test_hydro_contact.cpp
src/HydroHighMach/test_hydro_highmach.cpp
src/HydroKelvinHelmholz/test_hydro2d_kh.cpp
src/HydroLeblanc/test_hydro_leblanc.cpp
src/HydroQuirk/test_quirk.cpp
src/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
src/HydroSMS/test_hydro_sms.cpp
src/HydroShocktube/test_hydro_shocktube.cpp
src/HydroShuOsher/test_hydro_shuosher.cpp
src/HydroVacuum/test_hydro_vacuum.cpp
src/HydroWave/test_hydro_wave.cpp
src/PassiveScalar/test_scalars.cpp
src/RadhydroSimulation.hpp
src/ShockCloud/cloud.cpp
src/simulation.hpp

commit e93f63828bb539e9fcb5e7535e8ce3f184a6228b
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jun 27 21:39:37 2022 +1000

    set dual energy eta = 1e-3 (#59)

src/hydro_system.hpp
tests/HighMach.in

commit 35f2165516342101064fc4678315f616850e5902
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jun 27 16:44:07 2022 +1000

    add passive scalar test problem (#62)
    
    * add passive scalar test problem
    
    * fix undefined behavior in valarray
    
    * update comments in riemann solver

src/CMakeLists.txt
src/PassiveScalar/CMakeLists.txt
src/PassiveScalar/test_scalars.cpp
src/PassiveScalar/test_scalars.hpp
src/hydro_system.hpp
src/valarray.hpp
tests/PassiveScalar.in

commit 398932686e49b5d50a208c9ede9ee12c5bc91031
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jun 26 18:55:33 2022 +1000

    add passive scalars (#61)
    
    * add indexing machinery for passive scalars
    
    * add passive scalars to test problems (HydroContact)
    
    * use new RadhydroSimulation ctor in HydroBlast2D
    
    * add [[nodiscard]]
    
    * fix header circular inclusion problem

src/Cooling/test_cooling.cpp
src/HydroBlast2D/test_hydro2d_blast.cpp
src/HydroBlast3D/test_hydro3d_blast.cpp
src/HydroContact/test_hydro_contact.cpp
src/HydroHighMach/test_hydro_highmach.cpp
src/HydroKelvinHelmholz/test_hydro2d_kh.cpp
src/HydroLeblanc/test_hydro_leblanc.cpp
src/HydroQuirk/test_quirk.cpp
src/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
src/HydroRichtmeyerMeshkov/test_hydro2d_rm.hpp
src/HydroSMS/test_hydro_sms.cpp
src/HydroShocktube/test_hydro_shocktube.cpp
src/HydroShuOsher/test_hydro_shuosher.cpp
src/HydroVacuum/test_hydro_vacuum.cpp
src/HydroWave/test_hydro_wave.cpp
src/RadForce/test_radiation_force.cpp
src/RadhydroShell/test_radhydro_shell.cpp
src/RadhydroShock/test_radhydro_shock.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/RadhydroSimulation.hpp
src/ShockCloud/cloud.cpp
src/ShockCloud/test_cloudy.cpp
src/hydro_system.hpp
src/radiation_system.hpp

commit 6c5eecb22f30ada55d2a3e5016bdacfa8e68e1eb
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jun 26 14:22:58 2022 +1000

    rename EOS_Traits to HydroSystem_Traits (#60)

src/Cooling/test_cooling.cpp
src/HydroBlast2D/test_hydro2d_blast.cpp
src/HydroBlast3D/test_hydro3d_blast.cpp
src/HydroContact/test_hydro_contact.cpp
src/HydroHighMach/test_hydro_highmach.cpp
src/HydroKelvinHelmholz/test_hydro2d_kh.cpp
src/HydroLeblanc/test_hydro_leblanc.cpp
src/HydroQuirk/test_quirk.cpp
src/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
src/HydroSMS/test_hydro_sms.cpp
src/HydroShocktube/test_hydro_shocktube.cpp
src/HydroShuOsher/test_hydro_shuosher.cpp
src/HydroVacuum/test_hydro_vacuum.cpp
src/HydroWave/test_hydro_wave.cpp
src/RadForce/test_radiation_force.cpp
src/RadhydroShell/test_radhydro_shell.cpp
src/RadhydroShock/test_radhydro_shock.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/ShockCloud/cloud.cpp
src/ShockCloud/test_cloudy.cpp
src/hydro_system.hpp

commit c09d5881ea24a07a288eb91e15319448c6b4da25
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Jun 23 10:10:49 2022 +1000

    allow arbitrary number of scalars in riemann solver (#56)

src/hydro_system.hpp
src/valarray.hpp

commit 407d165a955cab079059549cdc705701621b2946
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jun 21 19:28:44 2022 +1000

    include ghost cells in plotfiles and ascent renders (#55)

src/simulation.hpp

commit f8375c26c4d17200123fb169de52d75666bd5f51
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jun 21 14:02:13 2022 +1000

    add auxiliary internal energy equation for high-Mach flows (#27)
    
    * add HydroSystem::AddInternalEnergyPressureTerm
    
    * add internal energy var to test problems
    
    * add cooling source terms to internal energy var
    
    * add Ryu et al. (1993) test problem
    
    * add reference solution for Ryu high-mach test
    
    *update auxiliary eint in radiation-matter exchange
    
    Co-authored-by: Ben Wibking <benwibking@gmail.com>

extern/highmach_reference.txt
src/CMakeLists.txt
src/Cooling/test_cooling.cpp
src/HydroContact/test_hydro_contact.cpp
src/HydroHighMach/CMakeLists.txt
src/HydroHighMach/test_hydro_highmach.cpp
src/HydroHighMach/test_hydro_highmach.hpp
src/HydroLeblanc/test_hydro_leblanc.cpp
src/HydroSMS/test_hydro_sms.cpp
src/HydroShocktube/test_hydro_shocktube.cpp
src/HydroShuOsher/test_hydro_shuosher.cpp
src/HydroVacuum/test_hydro_vacuum.cpp
src/HydroWave/test_hydro_wave.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadhydroSimulation.hpp
src/ShockCloud/cloud.cpp
src/hydro_system.hpp
src/radiation_system.hpp
tests/HighMach.in
tests/HighMach_reference.in

commit fe76e0e8cc90440f8da84a58d74ebcc1ab8bc036
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jun 19 10:48:17 2022 +1000

    add CONTRIBUTING.md based on AMReX's version (#54)

CONTRIBUTING.md

commit 6510f1a39095a155ef21b7f13ff5580f9e31147e
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Jun 18 16:21:59 2022 +1000

    update avatar cmake settings

cmake/avatar_gcc_cuda.cmake

commit c671a5f088582cd5b2b64b559b9c65f7ecae0a2b
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Jun 16 16:53:12 2022 +1000

    add CFL-respecting AMR subcycling (#52)
    
    * add cfl-respecting subcycling
    
    * update HydroShocktube to test subcycling
    
    * disable ptxas output
    
    * update specializations of computeAfterLevelAdvance

src/Advection2D/CMakeLists.txt
src/Advection2D/test_advection2d.cpp
src/AdvectionSimulation.hpp
src/CMakeLists.txt
src/Cooling/test_cooling.cpp
src/HydroShocktube/test_hydro_shocktube.cpp
src/RadhydroSimulation.hpp
src/ShockCloud/cloud.cpp
src/simulation.hpp
tests/advection2d_amr.in
tests/shocktube.in

commit 709605a3631f90f706153cd5081cc42e2eef7cd5
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Jun 15 14:35:35 2022 +1000

    add stop_time, plotfile_interval, and checkpoint_interval (#51)

src/simulation.hpp

commit 53778ddcc24edc0b254b40a0aefb11e479dbeda4
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jun 7 17:10:12 2022 +1000

    add Sedov verification scripts and notebook (#49)
    
    * add exact solution for Sedov test
    
    * update Sedov verification notebook

extern/sedov/README
extern/sedov/sedov.ipynb
extern/sedov/sedov3_qp.dek
extern/sedov/sedov3_qp.f90
extern/sedov/sedov_library_qp.f90
extern/sedov/spherical_standard_omega0p00.dat

commit b4963e7c512866f5995af70f4d46b5c28832cece
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jun 5 11:16:45 2022 +1000

    Update README.md

README.md

commit 2d00e3f639a88a1dee9d7b2179a194b37074c3d0
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jun 5 11:13:35 2022 +1000

    Update README.md

README.md

commit fcc9c582eae2215ab703f7f3ade04afd5feafd4e
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Jun 2 09:08:31 2022 +1000

    update amrex submodule

extern/amrex

commit cb62916799c751a9b97afe654c7ed3fa1cfc24ff
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon May 30 09:44:04 2022 +1000

    Revert "implement xsPPM7"
    
    This reverts commit d8a1dd73d9cf2afff122934abf0183e4f82d1c06.

extern/weno_weights.ipynb
src/ArrayUtil.hpp
src/CMakeLists.txt
src/HydroContact/test_hydro_contact.cpp
src/HydroHighMach/CMakeLists.txt
src/HydroHighMach/test_hydro_highmach.cpp
src/HydroHighMach/test_hydro_highmach.hpp
src/RadPulse/test_radiation_pulse.cpp
src/RadhydroSimulation.hpp
src/hydro_system.hpp
src/hyperbolic_system.hpp
src/simulation.hpp
tests/HighMach.in

commit 020a93a68008cceb409a89346dd049432926b6b1
Merge: d81a3fdf a29b5150
Author: Ben Wibking <ben@wibking.com>
Date:   Sun May 29 18:51:18 2022 +1000

    Merge branch 'development' of github.com:BenWibking/quokka into hybrid-ppm-weno

commit a29b51504be674f2573510255e14a02dbce70b68
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat May 28 12:43:38 2022 +1000

    Update README.md

README.md

commit d81a3fdff3b5d1fcb177a8be37c6d9b800f0a18e
Merge: 12f02e03 095d5d22
Author: Ben Wibking <ben@wibking.com>
Date:   Fri May 27 07:46:38 2022 +1000

    Merge branch 'development' of github.com:BenWibking/quokka into hybrid-ppm-weno

commit 095d5d220a3bfec04c15fa873932dff01ce1c53d
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu May 26 13:45:05 2022 +1000

    fix 2d carbuncle fix (#48)

src/ArrayView.hpp
src/ArrayView_2d.hpp
src/ArrayView_3d.hpp
src/HydroQuirk/test_quirk.cpp
src/hydro_system.hpp

commit 12f02e0397ed3bcedf6e688aa8a79b69722863ff
Author: Ben Wibking <ben@wibking.com>
Date:   Tue May 24 20:15:02 2022 -0400

    add 4th-order conservative to primitive

extern/weno_weights.ipynb
src/ArrayUtil.hpp
src/CMakeLists.txt
src/HydroHighMach/CMakeLists.txt
src/HydroHighMach/test_hydro_highmach.cpp
src/HydroHighMach/test_hydro_highmach.hpp
src/RadhydroSimulation.hpp
src/hydro_system.hpp
src/hyperbolic_system.hpp
src/simulation.hpp
tests/HighMach.in

commit f8c4db3f26fde6935ab96f063305f6cade9dfea5
Author: Ben Wibking <ben@wibking.com>
Date:   Sun May 15 15:34:55 2022 -0500

    adjust HydroContact tolerance

src/HydroContact/test_hydro_contact.cpp

commit 91f768e6dc626d7aa5b537788767f150307bbdda
Author: Ben Wibking <ben@wibking.com>
Date:   Sun May 15 15:34:39 2022 -0500

    use 5th-order stencil

src/hyperbolic_system.hpp
src/simulation.hpp

commit d8a1dd73d9cf2afff122934abf0183e4f82d1c06
Author: Ben Wibking <ben@wibking.com>
Date:   Sat May 14 17:46:55 2022 -0500

    implement xsPPM7

src/HydroContact/test_hydro_contact.cpp
src/RadPulse/test_radiation_pulse.cpp
src/hyperbolic_system.hpp
src/simulation.hpp

commit 9a79a2dc1ebfba60bf843c425adc8cccd3ba614a
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon May 2 20:40:53 2022 +1000

    only create symlink on IO processor

src/simulation.hpp

commit 3d766ba480b2adf2bc9985bc017a0791b2e93e6a
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon May 2 15:33:23 2022 +1000

    add max_walltime parameter (#46)
    
    * add max_walltime parameter
    
    * fix link issues for std::filesystem
    
    * add sanity check
    
    * fix walltime parser
    
    * check for existing symlink
    
    * symlink check should succeed even if target does not exist
    
    * fix existing symlink check

cmake/avatar_gcc_cuda.cmake
src/CMakeLists.txt
src/simulation.hpp

commit 2e993716f3aad3f5be75ce6c6bf44d7cf62c6644
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun May 1 22:33:40 2022 +1000

    add support for Ascent (#29)
    
    * build AMReX with ascent + blueprint
    
    * initialize MPI in ascent
    
    * add vtk paths to cmake cache files
    
    * change ascent output filenames
    
    * rescale geometry for ascent
    
    * add ascent actions file
    
    * move ascent stuff behind ifdefs

CMakeLists.txt
cmake/avatar_gcc_cuda.cmake
cmake/avatar_nvhpc_cuda.cmake
cmake/gadi_gcc_cuda.cmake
scripts/gpu_wrapper_sedov_256.sh
src/simulation.hpp
tests/ShockCloud_512.in
tests/ascent_actions.yaml

commit 8b7071850643a68eb16eb5014a8e9351e441bb5c
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Apr 26 11:25:54 2022 +1000

    Delete codacy.yml

.github/workflows/codacy.yml

commit 820dffc6c1773986f30a190861eb36b06f816389
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Apr 20 17:54:09 2022 +1000

    Delete cmake-cuda.yml

.github/workflows/cmake-cuda.yml

commit 2a58feb2a2c0ec4550ecfe7623a51938081979ad
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Apr 20 17:06:55 2022 +1000

    force-disable HDF5 plotfile outputs

CMakeLists.txt

commit a8562b5242ac4c46d0451fa7af1e1262aa7178f0
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Apr 19 22:25:46 2022 +1000

    Create codacy.yml

.github/workflows/codacy.yml

commit a32f9fcb79d6e3789ee24beb537c9c2977c29ec6
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Apr 19 20:39:12 2022 +1000

    update amrex submodule

extern/amrex

commit 8795fb7ed725b958145337603f815eec98d2dae0
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Apr 19 19:12:46 2022 +1000

    add debug CI builds

.ci/azure-pipelines-asan.yml
.ci/azure-pipelines-debug.yml

commit e074d677801b355b349e1d8bae6aaff81b0f16f9
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Apr 16 17:18:06 2022 +1000

    Update azure-pipelines-build-llvm.yml

.ci/azure-pipelines-build-llvm.yml

commit e0dc45cfc43b112131d5c83a7c38e725a32b2090
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Apr 16 16:35:37 2022 +1000

    allow building device code with Clang (#42)
    
    * disable -Wno-unknown-pragmas
    
    * fixes to allow building with CUDA Clang
    
    * add CMake options file for building on Avatar with Clang
    
    * update CMake build settings files
    
    * add option to disable/enable FMAD on device
    
    * add -ffp-contract to host options
    
    * avoid __managed__ variables
    
    * move azure pipelines to .ci/

.ci/azure-pipelines-build-llvm.yml
.ci/azure-pipelines.yml
.github/workflows/cmake.yml
CMakeLists.txt
cmake/avatar_gcc_cuda.cmake
cmake/avatar_llvm_cuda.cmake
cmake/avatar_nvhpc_cuda.cmake
cmake/avatar_oneapi_cuda.cmake
cmake/gadi_llvm_cuda.cmake
cmake/gadi_oneapi_cuda.cmake
src/CMakeLists.txt
src/HydroQuirk/test_quirk.cpp
src/RadMarshak/test_radiation_marshak.cpp
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/RadhydroShell/test_radhydro_shell.cpp
src/RadhydroShock/test_radhydro_shock.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/ShockCloud/CMakeLists.txt
src/hyperbolic_system.hpp
src/radiation_system.hpp

commit 94c5d00f5291a5769d02788d327e233543a5125c
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Apr 16 16:34:38 2022 +1000

    add support for Chombo-format HDF5 plotfile outputs (#44)
    
    * add support for Chombo-format HDF5 plotfile outputs
    
    * enable AMReX_HDF5

CMakeLists.txt
src/simulation.hpp

commit 388c0bcd52d5a97febf830a6e5dcb56ace03bb4b
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Apr 15 21:31:13 2022 +1000

    refuse to run with async_out=1 (currently broken)

src/simulation.hpp

commit 52b6c67d6c6343fb0e0a56b24b047df7f2d1cc88
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Apr 15 10:51:26 2022 +1000

    pause simulation to flush async outputs if needed (#43)

src/simulation.hpp

commit da63db21c17c292fb891395cf1ccce3d0a4befd4
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Apr 15 10:49:48 2022 +1000

    adjust sedov energy conservation tolerance

src/HydroBlast3D/test_hydro3d_blast.cpp

commit 67d7d4f769d7d4fc490bc93215cc83cc763a8f35
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Apr 14 23:10:42 2022 +1000

    fix typo in low-dissipation pressure correction

src/hydro_system.hpp

commit a4c1fad5d3e20b201c1240efcc9ea20716ec485c
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Apr 14 15:18:31 2022 +1000

    fix HydroBlast3D test

src/HydroBlast3D/test_hydro3d_blast.cpp
tests/blast_amr.in
tests/blast_amr_1024.in
tests/blast_amr_2048.in
tests/blast_amr_512.in
tests/blast_amr_maxlev2.in
tests/blast_unigrid_1024.in
tests/blast_unigrid_128.in
tests/blast_unigrid_2048.in
tests/blast_unigrid_256.in
tests/blast_unigrid_256_cpu.in
tests/blast_unigrid_512.in
tests/blast_unigrid_512_cpu.in

commit a306c2ca29bc09227d5df14a45026d4a2b16093b
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Apr 14 12:51:59 2022 +1000

    Update README with git clone --recursive

README.md

commit 1b3f2c8e216c212e3890699407b4c0431428da7d
Merge: c7afae73 32b24f45
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Apr 13 21:06:15 2022 +1000

    Merge branch 'development' of github.com:BenWibking/TwoMomentRad into development

commit c7afae739c8b9bf8c7a2a75c83a4f3199e89db41
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Apr 13 21:06:04 2022 +1000

    update amrex submodule

extern/amrex

commit 32b24f4503a3382af7eff15c359a23b7e7c0462e
Author: Conrad Chan <8309215+conradtchan@users.noreply.github.com>
Date:   Wed Apr 13 18:53:42 2022 +1000

    Fuse PPM reconstruction kernels (#36)
    
    * fuse PPM reconstruction kernels into one kernel
    
    * tidy formatting

src/hyperbolic_system.hpp

commit 375ded5bcdbe0da9e983f7359eca37d6d2552696
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Apr 13 18:14:01 2022 +1000

    add energy checks to Sedov test (#41)
    
    * add energy checks
    
    * add CTest test for HydroBlast3D

src/HydroBlast3D/CMakeLists.txt
src/HydroBlast3D/test_hydro3d_blast.cpp
tests/blast_unigrid_128.in

commit 2fb4ac8163da90dc2dec9fafa14619c72a55c3f2
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Apr 12 18:48:53 2022 +1000

    output on test failure for azure-pipeline CI

azure-pipelines.yml

commit ed1782c0559cfcc6cf48026bd27ada3358837721
Author: Conrad Chan <8309215+conradtchan@users.noreply.github.com>
Date:   Tue Apr 12 17:51:54 2022 +1000

    inline ComputeVelocityDifferences into ComputeFluxes (#35)
    
    dvn and dvt are only used for carbuncle correction, so the results can be used directly without storing in an array.

src/RadhydroSimulation.hpp
src/hydro_system.hpp

commit af105c77dd80be4dcde7b4b0b58291689cd8849b
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Apr 12 17:51:26 2022 +1000

    add automated test for carbuncle instability (#40)
    
    * add automated test for carbuncle instability
    
    * fix test on GPU

src/HydroQuirk/CMakeLists.txt
src/HydroQuirk/test_quirk.cpp
tests/quirk.in

commit 7b2c9c3ecef00d32d0d169ea0c16c67f075fc78e
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Apr 11 22:06:18 2022 +1000

    export CTest results in azure-pipelines

azure-pipelines.yml

commit 7691cdeaf5687da60bd48304900f21a9194f32a8
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Apr 11 21:42:47 2022 +1000

    disable python in azure-pipelines

azure-pipelines.yml

commit 83b32e646ebb8e80fac9c08bae0a0df90986457d
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Apr 11 21:34:09 2022 +1000

    enable ninja build in azure-pipelines

azure-pipelines.yml

commit 37b38958d9c4716bbeb1062d8764c9b8527bb9d2
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Apr 11 20:55:51 2022 +1000

    Update azure-pipelines.yml

azure-pipelines.yml

commit afdbf25e0f00aae8e98c03448a8db0f7d37dff60
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Apr 11 20:54:10 2022 +1000

    Add CUDA build to Azure Pipelines

azure-pipelines.yml

commit bf2c4132cf76a6f65ad80dabfc0f68e5288c120a
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Apr 11 15:59:38 2022 +1000

    Add performance hints (#39)
    
    * add PerformanceHints, default abort when out of GPU memory
    
    * fix GPU lambda-capture issues

src/CMakeLists.txt
src/hydro_system.hpp
src/main.cpp
src/radiation_system.hpp
src/simulation.hpp

commit b37d4ead0d6e91548303a09ea8a0ae317a0b961c
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Apr 11 13:59:20 2022 +1000

    Update sonarcloud CLI version

.github/workflows/cmake.yml

commit 557af3667649878d64a740cc1fc3c15011c7c038
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Apr 9 14:58:54 2022 +1000

    set build type to RelWithDebInfo for CI

.github/workflows/cmake.yml

commit 4e1e4106cc053c4d4ff8b1619a495370f739e1e0
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Apr 7 19:35:23 2022 +1000

    fix build in azure-pipelines.yml

azure-pipelines.yml

commit 2349c9d46626f8e7e1a60c7288fbcc3cbac4d78a
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Apr 7 19:33:20 2022 +1000

    Add CMake build to azure-pipelines.yml

azure-pipelines.yml

commit fd1b1fde3cae5e4ccdf1e0c405400c55e701d30c
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Apr 7 19:27:01 2022 +1000

    Update azure-pipelines.yml for Azure Pipelines

azure-pipelines.yml

commit d11b18806ea379b98fbfcfbee0aec7ce29198e3b
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Apr 7 18:57:48 2022 +1000

    Set up CI with Azure Pipelines
    
    [skip ci]

azure-pipelines.yml

commit 1bc928d0da550f3aa75f26b8704a8fb993eff515
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Mar 21 14:33:15 2022 +1100

    Enable Debug + ASAN in CI (#32)
    
    * various fixes for warnings in gcc 11.2; add leak suppresion file
    
    * update CI to use gcc-11
    
    * use leak suppression file in CI
    
    * fix division-by-zero bugs
    
    * fix isothermal case in ComputeCellOpticalDepth
    
    * zero-fill radiation variables when using custom Dirichlet BCs

.github/workflows/cmake.yml
src/ArrayUtil.hpp
src/CMakeLists.txt
src/Cooling/test_cooling.cpp
src/HydroLeblanc/test_hydro_leblanc.cpp
src/HydroSMS/test_hydro_sms.cpp
src/HydroShocktube/test_hydro_shocktube.cpp
src/HydroVacuum/test_hydro_vacuum.cpp
src/RadForce/test_radiation_force.cpp
src/hydro_system.hpp
src/radiation_system.hpp
src/simulation.hpp
tests/leak_suppress.txt

commit d2b17ab5194e6559d245f1cf38ada402d00207b9
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Mar 20 16:33:47 2022 +1100

    enable ASAN when debugging

CMakeLists.txt
src/CMakeLists.txt

commit 12ebe217645bed6cdd59033cbfb2f10cbdd7e002
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Mar 20 10:11:15 2022 +1100

    add CUDA version check to CMakeLists.txt

CMakeLists.txt

commit 6c98562dd9ac6e9546f3a7e67d4b435f68a4788b
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Mar 19 15:12:27 2022 +1100

    output CUDA kernel register use when compiling

src/CMakeLists.txt

commit e9825fc04153eb8c04febbab36c5a5b90fb59c6e
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Mar 19 14:56:03 2022 +1100

    remove HDF5 plotfile support (buggy)

CMakeLists.txt
src/simulation.hpp

commit 5a054e30f49f1e829cad91e5c92faf092b0c5822
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Mar 18 17:01:38 2022 +1100

    fix case-insensitive filename collision

extern/Toro/E1RPEX_old.INI

commit 45830c82bc11975130539386135d9a7d514181f0
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Mar 18 16:40:53 2022 +1100

    update .clang-format to work with new clang-format version

src/.clang-format

commit 9580b6c26c455bd12d03a43c21bde5d1e7696a92
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Mar 7 14:06:51 2022 +1100

    Enable regridding on AMR subcycles (#31)
    
    * add regrids on AMR subcycles
    
    * fix typos in regrid code
    
    * no need to output message on regrid

src/RadhydroSimulation.hpp
src/simulation.hpp
tests/CoolingCloud.in

commit 32f99ee970370a7bfb7bc72fc0c486a2e0df98d7
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Mar 7 11:16:10 2022 +1100

    More cooling solver fixes (#30)
    
    * increase debugging output
    
    * fix electron number density calculation

src/CloudyCooling.hpp
src/ODEIntegrate.hpp
src/ShockCloud/cloud.cpp
src/ShockCloud/test_cloudy.cpp
tests/ODE.in

commit 206448536a9f44062d462641b0e71125cb6fc215
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Mar 6 18:47:06 2022 +1100

    Robustness fixes for cooling + AMR (#28)
    
    * add check if maxStepsODEIntegrate is hit
    
    * add debugging for failed cooling solve
    
    * tweak format strings
    
    * fix off-by-one error in Interpolate2D
    
    * add fix-up after reflux
    
    * add profiling to FixupState()
    
    * add robustness checks to cooling, hydro states
    
    * clean up error messages
    
    * add FixupState to AdvectionSimulation
    
    * handle isothermal case in CheckStatesValid
    
    * add error handling to cooling ODE solve
    
    * add debugging to cooling solve
    
    * fix corner cases in interpolate2D

src/AdvectionSimulation.hpp
src/CloudyCooling.hpp
src/Interpolate2D.hpp
src/ODEIntegrate.hpp
src/RadhydroSimulation.hpp
src/ShockCloud/CMakeLists.txt
src/ShockCloud/cloud.cpp
src/ShockCloud/test_cloudy.cpp
src/hydro_system.hpp
src/simulation.hpp
tests/CoolingCloud.in
tests/ShockCloud_512.in

commit 014c3f32928ffaab0d10d805f68eb3e009e5d458
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Mar 4 17:37:22 2022 +1100

    fix off-by-one error in Interpolate2D

src/Interpolate2D.hpp

commit 23957e2c1a86dc0cde64a9ef226978afd7668116
Merge: f242abd8 7dd73417
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Mar 4 11:22:44 2022 +1100

    Merge branch 'development' of github.com:BenWibking/TwoMomentRad into development

commit f242abd8025af29c18ed0c844c027b2157e6ed2b
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Mar 4 11:22:39 2022 +1100

    update test_cloudy

src/ShockCloud/test_cloudy.cpp

commit 7dd73417f9888835538db1d8d97ed29eda4a6e39
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Mar 3 21:13:39 2022 +1100

    update for rk_adaptive_integrate API

src/Cooling/test_cooling.cpp
src/ODEIntegration/test_ode.cpp
src/ShockCloud/test_cloudy.cpp

commit 2ac6355c33d0d76ef460962d55cd6d960a2d4e71
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Mar 3 17:41:35 2022 +1100

    print num of cooling substeps

src/ODEIntegrate.hpp
src/ShockCloud/cloud.cpp

commit 9beb43018fc6f3a9168936a608af88847442cc27
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Mar 2 15:26:58 2022 +1100

    adjust cloud refinement

src/ShockCloud/cloud.cpp

commit 4e6a310488fe98f4443e9a8f7be8b7065ea3e881
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Mar 2 13:33:17 2022 +1100

    adjust cloud refinement

src/ShockCloud/cloud.cpp

commit 8235f37e9512f2db7eae3bf901529e94f4a4d44b
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Mar 2 12:03:38 2022 +1100

    add optically-thin cooling (radiative, collisional, etc.) (#24)
    
    * use amrex::Interpolater instead of MFInterpolater
    
    * update amrex submodule
    
    * fix memory leak; initialize with perturbations
    
    * add first-order flux correction (FOFC)
    
    * revert to 1D CI
    
    * add temperature floor
    
    * fix MULTIDIM_EXTREMA_CHECK in 2D
    
    * add 3D to cooling test
    
    * reconstruct temperature when using PPM
    
    * reconstruct T instead of pressure for all tests
    
    * set reconstruct_eint = false for some tests
    
    * add basic cell-by-cell RK4 integrator
    
    * update RK4 integrator
    
    * fix test_ode on GPU
    
    * use cell-by-cell integrator for cooling test
    
    * use RK2 to integrate cooling
    
    * add gpu wrapper script
    
    * use RK2 integration for cooling by default
    
    * add Cloudy table reader (using Grackle tables)
    
    * add 2D bilinear interpolation utility functinos
    
    * fix uninitialized value in valarray min(); lots of cloudy fixes
    
    * fix C-ordering/Fortran-ordering issue; do not use binary search; many fixes
    
    * AMREX_FORCE_INLINE all cooling-related functions
    
    * add Compton cooling
    
    * add photoelectric heating term
    
    * use consistent temperature floor
    
    * fix ODETest
    
    * add shock-cloud problem
    
    * set boundary conditions based on shock jump conditions
    
    * fix out of bounds issue in interpolate2d
    
    * fix PPM race condition -- do not fuse kernels
    
    * use more robust root-finding for T(rho, Eint) solve
    
    * adjust root-finding tolerance for temperature
    
    * move root finding to quokka::math
    
    * add cloudy debugging code
    
    * adjust temperature tolerance, error messages
    
    * output temperature in plotfiles
    
    * add ComputeDerivedVar to AdvectionSimulation
    
    * clean up GrackleDataReader
    
    * add refinement criteria to ShockCloud
    
    Co-authored-by: Ben Wibking <benwibking@gmail.com>

.github/workflows/cmake-cuda.yml
.github/workflows/cmake.yml
.github/workflows/codeql-analysis.yml
.gitmodules
CMakeLists.txt
extern/grackle_data_files
extern/sundials
scripts/gpu_wrapper_cooling_1024.sh
src/AdvectionSimulation.hpp
src/ArrayView.hpp
src/CMakeLists.txt
src/CheckNaN.hpp
src/CloudyCooling.cpp
src/CloudyCooling.hpp
src/Cooling/CMakeLists.txt
src/Cooling/test_cooling.cpp
src/Cooling/test_cooling.hpp
src/GrackleDataReader.cpp
src/GrackleDataReader.hpp
src/HydroBlast2D/test_hydro2d_blast.cpp
src/HydroBlast3D/test_hydro3d_blast.cpp
src/HydroContact/test_hydro_contact.cpp
src/HydroKelvinHelmholz/test_hydro2d_kh.cpp
src/HydroLeblanc/test_hydro_leblanc.cpp
src/HydroQuirk/test_quirk.cpp
src/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
src/HydroSMS/test_hydro_sms.cpp
src/HydroShocktube/test_hydro_shocktube.cpp
src/HydroShuOsher/test_hydro_shuosher.cpp
src/HydroVacuum/test_hydro_vacuum.cpp
src/HydroWave/test_hydro_wave.cpp
src/Interpolate2D.cpp
src/Interpolate2D.hpp
src/ODEIntegrate.hpp
src/ODEIntegration/CMakeLists.txt
src/ODEIntegration/test_ode.cpp
src/ODEIntegration/test_ode.hpp
src/RadForce/test_radiation_force.cpp
src/RadhydroShell/test_radhydro_shell.cpp
src/RadhydroShock/test_radhydro_shock.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/RadhydroSimulation.hpp
src/ShockCloud/CMakeLists.txt
src/ShockCloud/cloud.cpp
src/ShockCloud/cloud.hpp
src/ShockCloud/test_cloudy.cpp
src/hydro_system.hpp
src/hyperbolic_system.hpp
src/math_impl.hpp
src/root_finding.hpp
src/simulation.hpp
src/valarray.hpp
tests/Cooling.in
tests/CoolingCloud.in
tests/Cooling_1024.in
tests/Cooling_2048.in
tests/ODE.in

commit 2759062fbad58263733018ec3f3cd2cb12891a54
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Feb 15 20:47:11 2022 +1100

    updated manuscript with acceptance details

paper/quokka.pdf
paper/quokka.tex

commit 60e8808d3bb2dee19f3d471ecb915213111354cc
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Feb 9 16:08:07 2022 +1100

    implement first-order flux correction (FOFC) for hydro (#25)
    
    * add first-order flux correction (FOFC)
    
    * gpu fixes
    
    * fix advection test
    
    * debug FOFC bug
    
    * move FOFC code from cooling branch here
    
    * working FOFC; fix isValidState for isothermal
    
    * compile in 1D for CI
    
    * avoid template argument functions
    
    * workaround nvcc bug (const vars in outer function parameters used from inside lambda)
    
    Co-authored-by: Ben Wibking <benwibking@gmail.com>

.gitmodules
CMakeLists.txt
extern/amrex
extern/cooling/cooling.py
extern/sundials
src/AdvectionSimulation.hpp
src/RadhydroSimulation.hpp
src/hydro_system.hpp
src/hyperbolic_system.hpp
src/linear_advection.hpp
src/simulation.hpp
tests/Cooling.in
tests/Cooling_1024.in
tests/matplotlibrc

commit 5edc184a2f85fe0715f4e99d2d6f3b63756e2dbb
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun Jan 30 18:53:30 2022 +1100

    updated abstract

paper/abstract.txt

commit 1776c73976dad21e032e9f516e19e26883c4374b
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Jan 29 17:34:17 2022 +1100

    add discussion for Tables 2 and 4 in paper

paper/quokka.pdf
paper/quokka.tex
paper/quokka_diff.pdf
paper/quokka_diff.tex

commit 729f559e044d498e933caba4022a25018f955cc8
Merge: 0ad1a05b 7ba702d9
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Jan 28 16:24:36 2022 +1100

    Merge branch 'development' of github.com:BenWibking/TwoMomentRad into development

commit 0ad1a05b07739ec95ba113712063635edbd72203
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Jan 28 16:24:32 2022 +1100

    update performance numbers

paper/performance_a100.csv
paper/quokka.pdf
paper/quokka.tex
paper/quokka_diff.pdf
paper/quokka_diff.tex
paper/strong_scaling.csv
paper/weak_scaling_hydro.csv
paper/weak_scaling_hydro_plm.csv
paper/weak_scaling_radhydro.csv

commit 7ba702d99e4946d1c09bdf97f80e4158ce5bacd8
Merge: 88e0b449 7e1b7d60
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Jan 28 14:20:13 2022 +1100

    Merge branch 'development' of github.com:BenWibking/quokka-code into development

commit 88e0b4490e8e7ff99294ac88e701b906f56b3435
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Jan 28 14:19:49 2022 +1100

    disable async output for 64-node scaling test

scripts/gpu_wrapper_shell_2048.sh

commit 7e1b7d60480a792028611633a551686087c8ff34
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Jan 27 18:03:54 2022 +1100

    move long footnotes to main text

paper/quokka.pdf
paper/quokka.tex
paper/quokka_diff.pdf
paper/quokka_diff.tex

commit 4ef3b1f1006445bfb4958599c321f5328994014f
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Jan 27 16:02:39 2022 +1100

    added cmake cache file for Gadi

cmake/gadi_oneapi_cuda.cmake

commit 494eb7cd0ca60c73198d388b8a0ba0071aa93de9
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Jan 27 14:25:31 2022 +1100

    updated fmt submodule

extern/fmt

commit 41ee6145abd9b30e204fd6f3fdf85c3d2f320374
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Jan 27 14:19:33 2022 +1100

    add cmake cache file for oneapi compilers on avatar

cmake/avatar_oneapi_cuda.cmake
src/HydroBlast3D/test_hydro3d_blast.cpp

commit 3b3a315c55fe92421b7673af79e78ca829abc097
Merge: 4079b5d2 a738bab8
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Jan 27 14:01:40 2022 +1100

    Merge branch 'development' of github.com:BenWibking/TwoMomentRad into development

commit 4079b5d257b781f65f9a61712ee982bd3e6e9d52
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Jan 27 14:01:23 2022 +1100

    add cmake machine-specific files for avatar

CMakeLists.txt
cmake/avatar_gcc_cuda.cmake
cmake/avatar_nvhpc_cuda.cmake
src/interpolate.h

commit a738bab8f77e614e428b412bba8d853eda02709e
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Jan 27 13:48:51 2022 +1100

    Add warning about CUDA 11.6 to README.md

README.md

commit bf3058decf08024f8ec086212955e2db9a396513
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Jan 25 20:46:19 2022 +1100

    added machine-specific cmake configuration files

cmake/ubuntu_aocc.cmake
cmake/ubuntu_aocc_cuda.cmake

commit ccb8ed35fb2d141af8760b80da5e4c2434b60b00
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Jan 25 15:06:31 2022 +1100

    update manuscript text, add citation to Leblanc & Wilson (1970)

paper/quokka.bib
paper/quokka.pdf
paper/quokka.tex
paper/quokka_diff.pdf
paper/quokka_diff.tex

commit 213b8fb51c675d9da6e2c9b325539046a3711ca6
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Jan 24 17:40:30 2022 +1100

    revise manuscript text

paper/quokka.pdf
paper/quokka.tex
paper/quokka_v1.tex

commit 50dbb88ae6b9b2d77df517727b4aaf91d5f4e008
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun Jan 9 16:17:04 2022 +1100

    fix Quirk test on GPU

src/HydroQuirk/test_quirk.cpp

commit e7de52276e14abb82c66aa57cb77fc588862a5e1
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Jan 9 16:06:50 2022 +1100

    implement carbuncle-free low-dissipation HLLC solver (#18)
    
    * implement pressure correction from low-dissipation HLLC solver
    
    * draft version of carbuncle correction
    
    * pragma diag_disable -> pragma nv_diag_disable
    
    * pragma diag_suppress -> pragma nv_diag_suppress
    
    * add comments to ReconstructStatesPPM
    
    * add ComputeVelocityDifferences kernel (not yet implemented)
    
    * update amrex
    
    * update PBS script
    
    * fuse PPM kernels
    
    * combine cell-centered PPM kernels
    
    * tune max_grid_size on CPU
    
    * add carbuncle correction
    
    * re-enable low-dissipation pressure correction
    
    * implement pressure correction from low-dissipation HLLC solver
    
    * draft version of carbuncle correction
    
    * add ComputeVelocityDifferences kernel (not yet implemented)
    
    * add carbuncle correction
    
    * re-enable low-dissipation pressure correction
    
    * add Quirk (1994) test problem
    
    * add ref
    
    Co-authored-by: Ben Wibking <benwibking@gmail.com>

src/CMakeLists.txt
src/HydroQuirk/CMakeLists.txt
src/HydroQuirk/test_quirk.cpp
src/HydroQuirk/test_quirk.hpp
src/HydroWave/test_hydro_wave.cpp
src/RadhydroSimulation.hpp
src/hydro_system.hpp
tests/blast2d.in
tests/blast_unigrid_256_cpu.in
tests/quirk.in

commit 9f0bb3177151740302b1d483550f40c18075a192
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Jan 5 23:28:59 2022 +1100

    tune max_grid_size on CPU

scripts/cpu-sedov-1node.pbs
tests/blast_unigrid_512_cpu.in

commit 9fce3955a372afb119067991ed882cf6f779eafe
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Jan 4 12:35:01 2022 +1100

    combine cell-centered PPM kernels

src/hyperbolic_system.hpp

commit 43186110124d09a5b9dfaede57032b0db3dc263d
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Jan 4 12:20:47 2022 +1100

    fuse PPM kernels

src/hyperbolic_system.hpp

commit 6eb28fd10968ebd5584fe3a0d987c38b80b2f535
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jan 4 12:01:13 2022 +1100

    update PBS script

scripts/cpu-sedov-1node.pbs

commit 26f1b816cd3ad42c7a866ae73cecc1cbed62e030
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jan 3 21:08:37 2022 +1100

    update amrex

extern/amrex

commit c8f778854bb5f89146bca813b04c27759b3b9fbb
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Dec 28 13:42:36 2021 +1100

    add comments to ReconstructStatesPPM

src/hyperbolic_system.hpp

commit 18efd49c997e145507902366f72c4ef9c5687029
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Dec 24 17:37:33 2021 +1100

    pragma diag_suppress -> pragma nv_diag_suppress

src/hydro_system.hpp
src/radiation_system.hpp

commit 65c1b4a7dbd584cd6734b224c8f7403044ad892e
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Dec 13 13:55:38 2021 +1100

    Update README.md to mention QUOKKA_PYTHON option

README.md

commit 534cc4a4706768101985cce059525160648b2a38
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Dec 13 13:29:05 2021 +1100

    add CMake option to enable/disable Python support

CMakeLists.txt
src/CMakeLists.txt

commit efbd0a019a3c2cc6777453c0250cd813837ba281
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Dec 13 11:58:47 2021 +1100

    suppress spurious warnings produced by nvcc/EDG frontend

src/hydro_system.hpp
src/radiation_system.hpp

commit 6fb14de27e68a211a0b5dee030e7fb559598b234
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Dec 13 11:36:18 2021 +1100

    prevent compiling with the EDG-based (buggy) Intel compiler

CMakeLists.txt
src/main.hpp

commit 9d945d1936f74d31b21344c2ce89e1f6899aeb84
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Nov 26 13:49:16 2021 +1100

    add scripts for MPICH usage

scripts/sedov-1node-mpich.pbs
scripts/sedov-64nodes-mpich.pbs
scripts/sedov-8nodes-mpich.pbs

commit 4592c529b0e7e06989a2b20d6528dbe717df1627
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Nov 26 13:48:07 2021 +1100

    revert change to FillBoundary

src/simulation.hpp

commit f67b98abd2a1917906026338ece49966fa309ebc
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Nov 26 10:04:27 2021 +1100

    disable CUDA-aware MPI by default (about 1.7x slower if used)

scripts/gpu_wrapper_sedov_512.sh

commit f20f47f308b28692676d682e6216b53165684cb2
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Nov 26 09:44:37 2021 +1100

    set use_gpu_aware_mpi=1 for 1 node test

scripts/gpu_wrapper_sedov_512.sh

commit 9957231cb38bae830af204cf10874e5715e175bf
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Nov 26 09:41:28 2021 +1100

    avoid communicating corner cells on level=0

src/simulation.hpp

commit c8732a3971c9e56e3b228d54af4e4ac19c47a604
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Nov 19 14:55:30 2021 +1100

    add MULTIDIM_EXTREMA_CHECK option

src/hyperbolic_system.hpp

commit cd9da9237853e9858f7a5e4cbdfd7703a4472a3f
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Nov 19 14:40:09 2021 +1100

    gpu fix for ppm code

src/hyperbolic_system.hpp

commit bf361a48eb2b284a8b685fae90200a112478e58a
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Nov 19 14:22:25 2021 +1100

    workaround another nvcc bug

src/hyperbolic_system.hpp

commit cabc8c7aab5794078ff16be05a65a031c1b858df
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Nov 18 15:34:50 2021 +1100

    update paper

paper/quokka.pdf
paper/quokka.tex
paper/quokka_diff.tex

commit e0a0677f6a43b101b77a3713523963a7aa0dae35
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Nov 18 15:09:36 2021 +1100

    update paper

paper/latexdiff.cfg
paper/quokka.pdf
paper/quokka.tex
paper/weak_scaling_hydro_plm.csv

commit 65c9304e5889e627845312f135ee8ae7853364ec
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Nov 17 18:34:50 2021 +1100

    fix shock flattening and monotonicity in 2D/3D

src/RadhydroSimulation.hpp
src/hydro_system.hpp
src/hyperbolic_system.hpp

commit e4c0ef51c45b478fd97588690f8d770cce7bda57
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Nov 17 15:14:04 2021 +1100

    edits to manuscript

paper/quokka.bib
paper/quokka.pdf
paper/quokka.tex
paper/quokka_diff.tex

commit ca1d59a7f25b7ab30e96ff28ac2e942da428e072
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Nov 17 14:34:12 2021 +1100

    update manuscript

paper/quokka_diff.tex

commit 18548257b63a1229b436bac6d89390798f9e774a
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Nov 17 14:23:18 2021 +1100

    more edits to paper

paper/quokka.bib
paper/quokka.pdf
paper/quokka.tex
paper/quokka_diff.tex

commit a2f7155cb970af104daa609661af91a61fbb3f04
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Nov 15 18:58:21 2021 +1100

    edit 2.2.1

paper/quokka.bib
paper/quokka.pdf
paper/quokka.tex
paper/quokka_diff.tex

commit 09d3671eadb16e57c2944403c9d40ed61f7e214a
Merge: b5b88a84 e5ccfb07
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Nov 15 17:35:36 2021 +1100

    Merge branch 'development' of github.com:BenWibking/TwoMomentRad into development

commit b5b88a8438f35e3dfd8cb95046a1f9c9648d69db
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Nov 15 17:35:07 2021 +1100

    add option to use PLM for Sedov test

src/HydroBlast3D/test_hydro3d_blast.cpp

commit e5ccfb072f61e31bf400592b1107d4fd0aee5959
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Nov 15 15:22:10 2021 +1100

    add details re stability in 2.2.1

paper/quokka.bib
paper/quokka.pdf
paper/quokka.tex
paper/quokka_diff.tex

commit ae600de1740e66c2013402a1f89ea1bc5198c495
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Nov 11 13:40:38 2021 +1100

    fix unused var warning

src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp

commit e64030c605244240fb16a2cf5699aae1ac92ae9d
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Nov 11 13:40:09 2021 +1100

    add scripts to test turning GPU streams on/off

scripts/amr-shell-1node-1stream.pbs
scripts/gpu_wrapper_amr_shell_stream.sh

commit 57cf426a72a96bc88eb831a0798374f7f297d1d1
Merge: 4379ed87 f853b5e3
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Nov 11 12:08:51 2021 +1100

    Merge branch 'development' of github.com:BenWibking/TwoMomentRad into development

commit 4379ed87a6d6ddce88a20f227377955d2b946b18
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Nov 11 12:08:08 2021 +1100

    abort on out-of-memory on GPU

scripts/gpu_wrapper_amr_shell.sh

commit f853b5e307063b02a317787079024ae743458ccc
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Nov 11 11:42:39 2021 +1100

    Update README.md

README.md

commit 235913c5c0377f82bc3f9625fe54cd2c9942abbf
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Nov 8 20:10:10 2021 +1100

    fix (more) unused var warnings

src/fextract.cpp

commit 75975b8460b1cce7f44434df0e0a7a5cc73d8da0
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Nov 8 19:59:42 2021 +1100

    fix unused var warnings in fextract

src/fextract.cpp

commit ed276cd5007ca6d4b533df653d91e68bad0a4aac
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Nov 8 12:56:22 2021 +1100

    fix author names in CITATION.cff

CITATION.cff

commit fae1d2a588dc8420a3118e353448a6a86c3c74df
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Nov 8 12:54:04 2021 +1100

    add CITATION.cff

CITATION.cff

commit 77dc03e56fa3c2d410145f2541dc386a66fc32e4
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Nov 8 10:26:37 2021 +1100

    fix codeql warnings

.gitignore
run-codeql.sh
src/AdvectionSemiellipse/test_advection_semiellipse.hpp
src/HydroContact/test_hydro_contact.hpp
src/HydroSMS/test_hydro_sms.hpp
src/HydroShuOsher/test_hydro_shuosher.hpp
src/HydroVacuum/test_hydro_vacuum.hpp
src/RadMarshak/test_radiation_marshak.cpp
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.hpp
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.hpp
src/RadPulse/test_radiation_pulse.cpp
src/RadSuOlson/test_radiation_SuOlson.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.hpp
src/RadhydroSimulation.hpp

commit 308d09a61db2e67906700e8dedf638ef56e6d6cb
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Nov 8 09:13:31 2021 +1100

    add script to run CodeQL static analysis

run-codeql.sh

commit 37a7119e05243c493b85482931b4162a40f24382
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Nov 7 21:29:31 2021 +1100

    fix build on gcc 11 (size_t -> std::size_t)

src/ArrayUtil.hpp

commit bab81a9f83db486f961be4347c272450339f29c3
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Nov 5 16:11:15 2021 +1100

    fix RadForce test when AMREX_SPACEDIM=3

tests/RadForce.in

commit 9f8f7f0b2091e75414fad95c91066c5ba82a7904
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Nov 2 20:52:37 2021 +1100

    no default opacities

src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/radiation_system.hpp

commit 0d990afb1a9d143c121419565972a9b271a2d157
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Nov 2 20:31:21 2021 +1100

    fix unused var warnings

src/hydro_system.hpp
src/radiation_system.hpp

commit 845aa1ff40ea5f10e7090b2e8cf0212bce14218b
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Nov 2 10:52:22 2021 +1100

    add link to Doxygen docs

docs/api.rst
docs/index.rst

commit e5ee4f14b3c227cb0d0a34ee29a1b02b0d928d0a
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Nov 2 10:42:11 2021 +1100

    add doxygen to rtd

.gitignore
docs/Doxyfile
docs/conf.py

commit b8c0134bfec19d14709597043911b675ca16c833
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Oct 27 19:26:53 2021 +1100

    Update README.md

README.md

commit 5dfcd572f463e95aeea0e1e4927b34324e23c5fe
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Oct 27 19:01:11 2021 +1100

    update CodeQL config

.github/workflows/codeql-analysis.yml

commit 5d66b78800cad42a1f3bb2be3ed50ce574b5d156
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Oct 27 18:51:23 2021 +1100

    clean up semi-analytic radshock code

extern/LowrieEdwards/radshock.py
extern/LowrieEdwards/shock_Mach_30.0.txt

commit 4eac036394880b4c6416789012e897814fd174a3
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Oct 27 18:12:53 2021 +1100

    cleean up documentation

docs/equations.rst
docs/index.rst
docs/tests/index.rst

commit 0df9c00db56e88a5366ce55039fbb1a9917038b1
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Oct 21 20:43:21 2021 +1100

    fix build without python

src/HydroLeblanc/test_hydro_leblanc.cpp
src/HydroSMS/test_hydro_sms.cpp
src/HydroShocktube/test_hydro_shocktube.cpp
src/HydroShuOsher/test_hydro_shuosher.cpp
src/HydroVacuum/test_hydro_vacuum.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadSuOlson/test_radiation_SuOlson.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp

commit 33b550eb6c13116cb3b12a1e197ecd9b301b5da9
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Oct 16 14:47:07 2021 +1100

    Update README.md

README.md

commit e59a8ee7212a4575fd58a7e9fe3ec384dbcb1caf
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Oct 14 21:00:29 2021 +1100

    update docs

docs/about.rst
docs/index.rst
docs/installation.rst

commit 09bea02abb27b66307db9fc4847ed625de88f994
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Oct 14 20:51:26 2021 +1100

    add ReadTheDocs badge to README

README.md

commit a35dd54da612bc2721d10f88ffde8f97c3a600b8
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Oct 14 20:49:05 2021 +1100

    update docs metadata

docs/conf.py

commit ce0358cbcd61040ba6d0eab9bda4536cf7c6448c
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Oct 14 20:46:43 2021 +1100

    update docs

docs/about.rst
docs/references.bib

commit 2733c6acd3cbd9bc574862a72c6e9ed82112b315
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Oct 14 20:39:50 2021 +1100

    update docs for rtd

docs/Doxyfile
docs/about.rst
docs/index.rst
docs/installation.rst
docs/requirements.txt

commit 3f54101831564267cfffe748656be52c0d29e448
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Oct 13 22:00:14 2021 +1100

    update amrex version

.gitmodules
extern/amrex

commit 36a2ae0df0cd98338c5d52bfb23b7a5b958316d0
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Oct 12 15:43:08 2021 +1100

    add dependencies to CodeQL build

.github/workflows/codeql-analysis.yml

commit a96092892c0fd1f77dfef7ed4486aea68e32a13a
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Oct 12 15:39:47 2021 +1100

    checkout submodules when doing CodeQL build

.github/workflows/codeql-analysis.yml

commit e665af47ab56e583d6450d054107ccdde02eabf7
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Oct 12 15:36:10 2021 +1100

    fix CodeQL analysis (again)

.github/workflows/codeql-analysis.yml

commit 257fff2e2bfd31a8056b3ce6baf3b7e8a142544f
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Oct 12 15:33:39 2021 +1100

    attempt to fix CodeQL CI

.github/workflows/codeql-analysis.yml

commit 472424aa3d4bdd0e22d60e1d17695003567e20ba
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Oct 12 15:32:11 2021 +1100

    Update codeql-analysis.yml

.github/workflows/codeql-analysis.yml

commit f803cf20fb4b05133d3c15be0b915f11f27220ca
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Oct 11 20:39:45 2021 +1100

    fix include guard

src/ArrayUtil.hpp

commit 34a81bd32b1aa3d879159ac0f36ff5a6cd273d63
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Oct 7 12:46:14 2021 +1100

    update KH figure caption

paper/quokka.pdf
paper/quokka.tex

commit 5ec497df58302a6e5de30724c46886a567bf2d8e
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Oct 6 14:59:24 2021 +1100

    add installation notes to README

README.md

commit 2489afeaf39090a8a80b86ac0929c13e52d32d95
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Oct 5 22:19:18 2021 +1100

    Create codeql-analysis.yml

.github/workflows/codeql-analysis.yml

commit f50bf7dcb8a10013a91cfbe7418101bb048c84ad
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Oct 5 13:28:20 2021 +1100

    fix make_tarball script

paper/make_tarball.py

commit ab6a7eba591e08b3e14b4e29962d7b652b5daff2
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Oct 5 13:14:31 2021 +1100

    add abstract.txt

paper/abstract.txt

commit b113e5f314b31302d23bf21653320b44e66e72e3
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Oct 5 12:55:43 2021 +1100

    update data availability statement

paper/quokka.pdf
paper/quokka.tex

commit 384e9f890f6ce3e93ba6058d58d017323c87e684
Merge: 2b3836cf b21246ff
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Oct 5 12:49:31 2021 +1100

    Merge branch 'master' of github.com:BenWibking/TwoMomentRad

commit 2b3836cfcfb14de3b1e96e931260bac6dd96278e
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Oct 5 12:45:52 2021 +1100

    added additional strong scaling discussion

paper/quokka.pdf
paper/quokka.tex
paper/strong_scaling.csv

commit b21246ff8308353e09ee110d294b1555b21ac2c3
Author: Mark Krumholz <mark.krumholz@anu.edu.au>
Date:   Tue Oct 5 12:21:30 2021 +1100

    More edits.

paper/quokka.pdf
paper/quokka.tex

commit 25ee02fda5f392a11a4eab3f83362e5b2c2679d4
Merge: 564d1744 7be93755
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Oct 5 09:45:29 2021 +1100

    Merge branch 'master' of github.com:BenWibking/TwoMomentRad

commit 564d1744c10697228f79f72d7b41da0350237909
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Oct 5 09:44:40 2021 +1100

    update figure formatting

README.md
paper/SuOlsonTest.pdf
paper/hydro_leblanc_6.0000.pdf
paper/hydro_leblanc_eint_6.0000.pdf
paper/hydro_shocktube_0.4000.pdf
paper/hydro_shuosher.pdf
paper/hydro_sms_1.0000.pdf
paper/hydro_vacuum_0.1500.pdf
paper/hydro_vacuum_eint_0.1500.pdf
paper/marshak_wave_cgs_gastemperature.pdf
paper/quokka.pdf
paper/quokka.tex
paper/radcoupling_rsla.pdf
paper/radiation_force_tube_vel.pdf
paper/radiation_pressure_tube.pdf
paper/radshock_cgs_temperature.pdf
src/ArrayUtil.hpp
src/HydroLeblanc/test_hydro_leblanc.cpp
src/HydroSMS/test_hydro_sms.cpp
src/HydroShocktube/test_hydro_shocktube.cpp
src/HydroShuOsher/test_hydro_shuosher.cpp
src/HydroVacuum/test_hydro_vacuum.cpp
src/RadForce/test_radiation_force.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadSuOlson/test_radiation_SuOlson.cpp
src/RadTube/test_radiation_tube.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp

commit 7be9375503808ac883fda5f79991547b1d728b92
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Oct 4 20:56:26 2021 +1100

    minor wording change

paper/quokka.pdf
paper/quokka.tex

commit 3dafc8141a912a0ce389a7d133ac8f167158369f
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Oct 4 19:27:43 2021 +1100

    add AMReX and yt buttons to README

README.md

commit de8715340f5124f612655c4f2b9840160a7c8736
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Oct 4 19:18:52 2021 +1100

    update README

README.md
compile_commands.json
default.in
vscode-workspace.code-workspace

commit 5a417bce449ce7c4a7ebb42321668e47ebea6a78
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Oct 4 19:03:34 2021 +1100

    clarify rad-matter coupling figure

paper/quokka.pdf
paper/quokka.tex

commit c0373fdcd7a088c23ba97729ca8c86a757dab5ac
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Oct 4 18:55:10 2021 +1100

    update scaling numbers used in introduction

paper/quokka.pdf
paper/quokka.tex

commit 632b00609d75fc3ab3fe870dd476d74f1cef95e8
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Oct 4 18:51:33 2021 +1100

    update acknowledgements

paper/quokka.pdf
paper/quokka.tex

commit cc7b9f2b3e142e8e5e02e99e26a8b51537284812
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Oct 4 18:44:13 2021 +1100

    recompile paper

paper/quokka.pdf

commit 56ae4899cd3ee8504679cc7d0bdad970ec3563ad
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Oct 4 18:42:05 2021 +1100

    update radiation-driven shell figure

extern/dust_shell/shell_velocity.pdf
paper/shell_velocity.pdf

commit c8445d44c09bae802b197b9b5b49ba3230d5ec1d
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Oct 4 18:33:42 2021 +1100

    homogenize figures

extern/dust_shell/analyze.py
paper/SuOlsonTest.pdf
paper/hydro_leblanc_6.0000.pdf
paper/hydro_leblanc_eint_6.0000.pdf
paper/hydro_shocktube_0.4000.pdf
paper/hydro_shuosher.pdf
paper/hydro_sms_1.0000.pdf
paper/hydro_vacuum_0.1500.pdf
paper/hydro_vacuum_eint_0.1500.pdf
paper/marshak_wave_cgs_gastemperature.pdf
paper/quokka.pdf
paper/quokka.tex
paper/radcoupling_rsla.pdf
paper/radiation_force_tube_vel.pdf
paper/radiation_pressure_tube.pdf
paper/radshock_cgs_temperature.pdf
src/HydroLeblanc/test_hydro_leblanc.cpp
src/HydroSMS/test_hydro_sms.cpp
src/HydroShocktube/test_hydro_shocktube.cpp
src/HydroShuOsher/test_hydro_shuosher.cpp
src/HydroVacuum/test_hydro_vacuum.cpp
src/RadForce/test_radiation_force.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadSuOlson/test_radiation_SuOlson.cpp
src/RadTube/test_radiation_tube.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp

commit 8aabf91316765987e4597ac4c9e9bbba0473f4bb
Merge: d2204509 46686e50
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Oct 4 15:51:28 2021 +1100

    Merge branch 'master' of github.com:BenWibking/TwoMomentRad

commit d220450910fbd090de4fda118cc0368ff3c5853c
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Oct 4 15:51:24 2021 +1100

    update scaling numbers

paper/quokka.pdf
paper/quokka.tex
paper/strong_scaling.csv
paper/weak_scaling_hydro.csv
paper/weak_scaling_radhydro.csv

commit 46686e5007580ebe255ffdf983f1beb8a7add123
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Oct 4 15:21:33 2021 +1100

    added new AMR scaling test

tests/radhydro_shell_amr_512.in

commit 624cf8e33ac9a451e1a1871b45ff92bd806d447e
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Oct 4 13:11:41 2021 +1100

    rename pbs scripts

scripts/codecov.sh
scripts/sedov-1gpu.pbs
scripts/sedov-1node.pbs
scripts/sedov-64nodes.pbs
scripts/sedov-8nodes.pbs

commit 3831c5360422561bb72c047e26ea7de12bfbdecf
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Oct 4 13:05:34 2021 +1100

    update paths for scaling test scripts

scripts/gpu_wrapper_amr_shell.sh
scripts/gpu_wrapper_sedov_1024.sh
scripts/gpu_wrapper_sedov_2048.sh
scripts/gpu_wrapper_sedov_256.sh
scripts/gpu_wrapper_sedov_512.sh

commit 8a2319cdeb17269a104afc65c323efac7800ca69
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Oct 4 12:48:01 2021 +1100

    update gridding parameters for scaling tests

src/RadhydroShell/test_radhydro_shell.cpp
tests/blast_unigrid_1024.in
tests/blast_unigrid_2048.in
tests/blast_unigrid_256.in
tests/blast_unigrid_512.in
tests/radhydro_shell.in
tests/radhydro_shell_1024.in
tests/radhydro_shell_2048.in
tests/radhydro_shell_256.in
tests/radhydro_shell_512.in
tests/radhydro_shell_amr.in

commit ce95456c07fcc0e4da2c633d76d4d86b0b9e1017
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Oct 4 10:34:50 2021 +1100

    fix Sedov refinement criteria

src/HydroBlast3D/test_hydro3d_blast.cpp

commit cf666101fa018f60b7c014ea95e53ad8232fac79
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Oct 4 09:52:07 2021 +1100

    update text on dust shell

paper/quokka.pdf
paper/quokka.tex

commit fa0a87c27af76bc653408161277da3f8d2994d07
Author: Mark Krumholz <mark.krumholz@anu.edu.au>
Date:   Sun Oct 3 21:55:21 2021 +1100

    More edits.

paper/quokka.pdf
paper/quokka.tex

commit d1b9d36524b0b941db4bb235545c76018f4fd57b
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun Oct 3 20:55:18 2021 +1100

    update shell test subsection

paper/quokka.pdf
paper/quokka.tex

commit a3039b453aff239e78a18f562354ec3aff2d5f27
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Oct 3 20:39:01 2021 +1100

    fixed radhydro shell test

extern/dust_shell/analyze.py
extern/dust_shell/initial_conditions.txt
extern/dust_shell/matplotlibrc
extern/dust_shell/shell_velocity.pdf
extern/dust_shell/solution.py
paper/shell_velocity.pdf
src/RadhydroShell/test_radhydro_shell.cpp
tests/radhydro_shell.in

commit ea67c0f2397d4d4486c560adb33b0d8bb70dc2a9
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun Oct 3 16:52:55 2021 +1100

    fixes for isothermal problems

paper/quokka.pdf
paper/quokka.tex
paper/radiation_force_tube_vel.pdf
src/RadForce/test_radiation_force.cpp
src/RadhydroShell/test_radhydro_shell.cpp
src/hydro_system.hpp
src/radiation_system.hpp

commit 860da25ebd8767e8f285446189752fc1f3c03829
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Oct 2 15:41:30 2021 +1000

    another typo fix

paper/quokka.pdf
paper/quokka.tex

commit 25989ce10260b5e68e2d1640c801b06e8180eaa7
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Oct 2 15:34:43 2021 +1000

    fix typo

paper/quokka.pdf
paper/quokka.tex

commit a72d1455cdff64bc48a5e61a4c68d812e650b05c
Author: Mark Krumholz <mark.krumholz@anu.edu.au>
Date:   Sat Oct 2 14:53:24 2021 +1000

    Minor edits to beam test.

paper/quokka.pdf
paper/quokka.tex

commit 58da493276ba59d1570d6785e4245639ae10e8de
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Oct 2 14:34:22 2021 +1000

    re-ran beam test, added time

paper/beam1.png
paper/beam2.png
paper/quokka.pdf
paper/quokka.tex

commit d661df4c94a43b41110b365ede55ab3bcd8d8bf0
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Oct 2 14:27:07 2021 +1000

    fix beam test

src/RadBeam/test_radiation_beam.cpp

commit 6aeddbbdc7949927461289f72ac53129520f1294
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Oct 2 14:07:11 2021 +1000

    add beam test subsection

paper/quokka.bib
paper/quokka.pdf
paper/quokka.tex
src/RadBeam/test_radiation_beam.cpp
src/radiation_system.hpp

commit 329bbaef26bbbc8dc7f897a1e84f402be05ba7f4
Author: Mark Krumholz <mark.krumholz@anu.edu.au>
Date:   Sat Oct 2 11:53:28 2021 +1000

    Minor edits to shadowing test, and throughout intro and methods.

paper/quokka.pdf
paper/quokka.tex

commit 64b4b256d7da9cc691f16ab6554fcdf37a055ff6
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Oct 2 09:00:07 2021 +1000

    added figures for beam/shadow tests

paper/beam1.png
paper/beam2.png
paper/quokka.pdf
paper/shadow1.png
paper/shadow2.png

commit 1eb764fd64cb8521c3bb725882a8d3bc9bfa8830
Author: Mark Krumholz <mark.krumholz@anu.edu.au>
Date:   Fri Oct 1 21:01:55 2021 +1000

    Edits to the Liska-Wendroff problem section.

paper/quokka.pdf
paper/quokka.tex

commit 4400cfe010fc7589bbcba09440e6d46e0f782185
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Oct 1 20:31:27 2021 +1000

    add text for shadow test

paper/quokka.pdf
paper/quokka.tex
src/RadShadow/test_radiation_shadow.cpp

commit 689e0ff61ab3009986129618f4e3034b6ba56ba8
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Oct 1 18:29:53 2021 +1000

    update shadow and beam tests

src/RadBeam/test_radiation_beam.cpp
src/RadShadow/test_radiation_shadow.cpp
src/radiation_system.hpp

commit 0874a5af5e4deead5d377ecbab6ef91607a67004
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Oct 1 16:38:15 2021 +1000

    fix typo

paper/quokka.pdf
paper/quokka.tex

commit 2e1868e8c2226c67cf849408f8334a87a76c5a23
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Oct 1 16:08:21 2021 +1000

    add implosion test

paper/implosion.png
paper/quokka.bib
paper/quokka.pdf
paper/quokka.tex

commit 18ed4a1a2cf7526dec6105db58e346f1bf52d18b
Author: Mark Krumholz <mark.krumholz@anu.edu.au>
Date:   Thu Sep 30 22:09:04 2021 +1000

    More edits.

paper/quokka.pdf
paper/quokka.tex

commit a23eab5a92ae9e1b7feeacc831e851777e923cb0
Author: Mark Krumholz <mark.krumholz@anu.edu.au>
Date:   Thu Sep 30 22:01:51 2021 +1000

    More edits.

paper/quokka.bib
paper/quokka.pdf
paper/quokka.tex

commit 6005c187de0356e49600a0f7931c5976291611dd
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Sep 30 18:24:18 2021 +1000

    add Kelvin-Helmholz subsection

paper/quokka.bib
paper/quokka.pdf
paper/quokka.tex

commit 59b814ae9078484d0544559b2cf797b78bfdb67c
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Sep 30 15:40:39 2021 +1000

    more references

paper/quokka.bib
paper/quokka.pdf
paper/quokka.tex

commit 7bf89934869a7b7ce9755d0bc782edd84c3e0d67
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Sep 30 14:43:12 2021 +1000

    add references

paper/quokka.bib
paper/quokka.pdf
paper/quokka.tex

commit eabd899d3c37477784cbfef58497bced7958ea9a
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Sep 30 13:48:56 2021 +1000

    add conclusion

paper/quokka.bib
paper/quokka.pdf
paper/quokka.tex

commit 9cee0fcf60a3f8d112ce826ed4208d0597759134
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Sep 30 11:44:53 2021 +1000

    added strong scaling section

paper/quokka.pdf
paper/quokka.tex

commit 607f982d23f2dab528dd5b9dd4defd5a1451b7da
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Sep 30 10:35:02 2021 +1000

    added missing info

paper/quokka.pdf
paper/quokka.tex
paper/radiation_force_tube_vel.pdf

commit 66603ef90f6fde5a81291a788e864f84abe9508c
Author: Mark Krumholz <mark.krumholz@anu.edu.au>
Date:   Wed Sep 29 20:02:52 2021 +1000

    Edits

paper/quokka.pdf
paper/quokka.tex

commit 958263c7a48cc56309fc7103eaa886d86eb348c7
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Sep 29 17:48:28 2021 +1000

    re-word wind test. add weak scaling text

paper/quokka.pdf
paper/quokka.tex

commit bbbc39a8916db92dd6273f6ba35be81f55d7fb88
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Sep 29 17:09:47 2021 +1000

    add weak scaling text

paper/quokka.bib
paper/quokka.pdf
paper/quokka.tex

commit e020074e79bf320dfcb30e048624dccf88e43dbe
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Sep 29 15:58:54 2021 +1000

    add text for optically-thin wind test

paper/quokka.bib
paper/quokka.pdf
paper/quokka.tex

commit 69a48d4fdbacd6bff76f091d17ca0d9ee7bb70e9
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Sep 29 12:44:21 2021 +1000

    updated paths in pbs scripts

scripts/gpu_wrapper_shell_1024.sh
scripts/gpu_wrapper_shell_2048.sh
scripts/gpu_wrapper_shell_256.sh
scripts/gpu_wrapper_shell_512.sh

commit e7ea44f96de3673438b9faf541bfd5af43954ec3
Merge: 153a2555 690b4d98
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Sep 29 12:27:20 2021 +1000

    Merge branch 'master' of github.com:BenWibking/quokka-code

commit 690b4d98cd12a245b88b9d39d0731565c22985a6
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Sep 29 12:26:47 2021 +1000

    enable tests to build without python

src/RadForce/test_radiation_force.cpp
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/RadPulse/test_radiation_pulse.cpp
src/RadStreaming/test_radiation_streaming.cpp
src/RadTube/test_radiation_tube.cpp

commit 153a2555590b4ae4c33d7a74ca5825c11ca3f757
Merge: 37a258a1 74be9e2c
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Sep 29 12:13:47 2021 +1000

    Merge branch 'master' of github.com:BenWibking/quokka-code

commit 37a258a16f5a89684552887af5ff00856b4f28f7
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Sep 29 12:13:28 2021 +1000

    merge radshell changes

src/test_radhydro_shell.cpp

commit 74be9e2cc083c9943cd2aa79503e869069395225
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Sep 29 12:09:47 2021 +1000

    add radiation-driven optically-thin wind

extern/pressure_tube/optically_thin.py
extern/pressure_tube/optically_thin_wind.txt
paper/quokka.pdf
paper/quokka.tex
src/RadForce/CMakeLists.txt
src/RadForce/test_radiation_force.cpp
src/hydro_system.hpp
src/radiation_system.hpp
tests/RadForce.in

commit b9f46ea5272e806f2c5441dd60646965b55c669c
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Sep 28 09:03:51 2021 +1000

    add scaling tables

paper/quokka.pdf
paper/quokka.tex
paper/strong_scaling.csv
paper/weak_scaling_radhydro.csv

commit 6773276e47f322807e18909db43ee21bc8f6551b
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Sep 27 22:04:06 2021 +1000

    added hydro weak scaling

CMakeLists.txt
paper/quokka.pdf
paper/quokka.tex
paper/weak_scaling_hydro.csv

commit ec0f8bbeb265161f4a515561d5fd80eda78a2392
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Sep 27 17:38:23 2021 +1000

    add number of cells for rad tube test

paper/quokka.pdf
paper/quokka.tex

commit cd593cbf839cc2e721daa5af7922bbada59295d2
Author: Mark Krumholz <mark.krumholz@anu.edu.au>
Date:   Mon Sep 27 15:29:47 2021 +1000

    More edits.

paper/quokka.pdf
paper/quokka.tex

commit d085b877251652a8fc934f2cd29eac97ce579f4b
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Sep 27 13:51:11 2021 +1000

    minor wording change

paper/quokka.pdf
paper/quokka.tex

commit a132c9e1cdf5d6fba1658e35c57f715a0131155f
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Sep 27 13:41:41 2021 +1000

    added more details

paper/quokka.pdf
paper/quokka.tex
paper/radcoupling_rsla.pdf
paper/radiation_pressure_tube.pdf
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadTube/test_radiation_tube.cpp

commit 3355f004869bad467e7c451e83b730995b03b92a
Author: Mark Krumholz <mark.krumholz@anu.edu.au>
Date:   Sat Sep 25 23:30:11 2021 +1000

    Edits and comments.

paper/quokka.pdf
paper/quokka.tex

commit 1e05c76ccaf5a23b1d3d8b87f6dd7edf792c8846
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Sep 25 15:32:38 2021 +1000

    more text

paper/quokka.pdf
paper/quokka.tex

commit 174b9f326e6919ec329ba96dbdb2ceecac6ceb9f
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Sep 25 14:50:57 2021 +1000

    write Teq explicitly

paper/quokka.pdf
paper/quokka.tex

commit bbe7af667013bd29e5d7b59c5721881796263c43
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Sep 25 14:36:40 2021 +1000

    fix typos

paper/quokka.pdf
paper/quokka.tex

commit df550b84a0849a447039939027a1103ca511fb44
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Sep 25 14:23:12 2021 +1000

    more test problems!

paper/quokka.bib
paper/quokka.pdf
paper/quokka.tex

commit c6cf2a0b1a08fce14a16a524af234931dc760828
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Sep 24 14:59:48 2021 +1000

    more text

paper/quokka.pdf
paper/quokka.tex

commit ec35c7114bc2700ef6328300ae85aa0f55d84a32
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Sep 24 13:04:27 2021 +1000

    more text

paper/quokka.bib
paper/quokka.pdf
paper/quokka.tex

commit cd114761a2955e08c47a14e54de8803ab9731cb0
Merge: 4c0ad371 d0eda88d
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Sep 24 08:06:18 2021 +1000

    Merge branch 'master' of github.com:BenWibking/TwoMomentRad

commit 4c0ad37183021d29688a4cc2de57447ff7cbd7fe
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Sep 24 07:55:51 2021 +1000

    add discussion of vacuum test

paper/quokka.bib
paper/quokka.pdf
paper/quokka.tex

commit d0eda88d516b7f7cb1910c8280f1ba2f8fc69286
Author: Mark Krumholz <mark.krumholz@anu.edu.au>
Date:   Thu Sep 23 23:44:58 2021 +1000

    More edits to paper text.

paper/quokka.bib
paper/quokka.pdf
paper/quokka.tex

commit 51cfe89751c6303d8f66dc93055bd82c620b029f
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Sep 23 18:57:51 2021 +1000

    add slow-moving shock description + refs

paper/quokka.bib
paper/quokka.pdf
paper/quokka.tex

commit 53c0c7b1e6e12efb2ea47c6af4e6cbbb2606e8bb
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Sep 23 17:57:47 2021 +1000

    add descriptions of test problems

paper/quokka.bib
paper/quokka.pdf
paper/quokka.tex

commit 8310c6c4349388b5508b3440cf5c82609b42169f
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Sep 23 14:17:37 2021 +1000

    add references; change title

paper/quokka.bib
paper/quokka.pdf
paper/quokka.tex

commit c77aa1c4ee6ae69f3d9433dc49fd240ea97254cc
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Sep 23 10:57:16 2021 +1000

    added references to additional codes

paper/quokka.bib
paper/quokka.pdf
paper/quokka.tex

commit c6ff6793c111aba2c5cf16d679e7a6909ebbe4c5
Author: Mark Krumholz <mark.krumholz@anu.edu.au>
Date:   Wed Sep 22 21:56:56 2021 +1000

    Finished draft of intro, did some cleanup of references.

paper/quokka.bib
paper/quokka.pdf
paper/quokka.tex

commit a40f27ec3d43d83713db1d70bcef2b5613efc566
Merge: 6fadd442 9d0aab58
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Sep 22 19:39:56 2021 +1000

    Merge branch 'master' of github.com:BenWibking/TwoMomentRad

commit 6fadd4422c1c17db30296f9ae88b22c911d0cb96
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Sep 22 19:35:55 2021 +1000

    add contact wave test

paper/quokka.bib
paper/quokka.pdf
paper/quokka.tex

commit 9d0aab5843c09c361359afb912d1bb45198e0bf6
Merge: 8aab01c7 2fbc9305
Author: Mark Krumholz <mark.krumholz@anu.edu.au>
Date:   Wed Sep 22 17:43:22 2021 +1000

    Merge branch 'master' of github.com:BenWibking/quokka-code

commit 8aab01c7be325eb6bd88fc44cae5e18e809d1c8c
Author: Mark Krumholz <mark.krumholz@anu.edu.au>
Date:   Wed Sep 22 17:42:52 2021 +1000

    Added a lot of intro. Not quite done, but getting there.

paper/quokka.bib
paper/quokka.tex

commit 2fbc9305e484acdb84de4d0ef40aeefe458a16e8
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Sep 22 17:37:44 2021 +1000

    clearer wording

paper/quokka.pdf
paper/quokka.tex

commit 87d5d808b5c2fac84c55a686fa77ea265bbbf3f6
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Sep 22 17:14:34 2021 +1000

    add linear convergence plot

paper/matplotlibrc
paper/plot_convergence.py
paper/quokka.pdf
paper/quokka.tex
paper/wave_convergence.pdf

commit 9749aecd1bbff25fceb3bb732af1edbd8d05df22
Merge: ead8899b 8f384dd3
Author: Mark Krumholz <mark.krumholz@anu.edu.au>
Date:   Wed Sep 22 16:31:28 2021 +1000

    Merge branch 'master' of github.com:BenWibking/quokka-code

commit ead8899b405212310778c72287127e1193175928
Author: Mark Krumholz <mark.krumholz@anu.edu.au>
Date:   Wed Sep 22 16:31:06 2021 +1000

    Adding references for intro.

paper/quokka.bib

commit 0e5a7875854c1cba64ba0401ad191f0ae3d85bed
Author: Mark Krumholz <mark.krumholz@anu.edu.au>
Date:   Wed Sep 22 16:30:42 2021 +1000

    Started rewrite of intro.

paper/quokka.tex

commit 8f384dd33cd94795b9587722c92fb1ac66fb4a1f
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Sep 22 16:04:35 2021 +1000

    add figures to repo

paper/SuOlsonTest.pdf
paper/density_1.0000.pdf
paper/hydro_contact.pdf
paper/hydro_leblanc_6.0000.pdf
paper/hydro_leblanc_eint_6.0000.pdf
paper/hydro_shocktube_0.4000.pdf
paper/hydro_shuosher.pdf
paper/hydro_sms_1.0000.pdf
paper/hydro_vacuum_0.1500.pdf
paper/hydro_vacuum_eint_0.1500.pdf
paper/marshak_wave_cgs_gastemperature.pdf
paper/pressure_1.0000.pdf
paper/quokka.pdf
paper/quokka.tex
paper/radcoupling.pdf
paper/radiation_pressure_tube.pdf
paper/radshock_cgs_temperature.pdf
tests/matplotlibrc

commit e1c0f1e21f12743df184c3cb527b76682f59088f
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Sep 22 14:02:04 2021 +1000

    added sound wave test to manuscript

paper/linear_wave.csv
paper/quokka.bib
paper/quokka.pdf
paper/quokka.tex
src/HydroWave/test_hydro_wave.cpp

commit 00de6933025aeb9be29b36b163fa88bb42731376
Author: Mark Krumholz <mark.krumholz@anu.edu.au>
Date:   Mon Sep 20 22:34:41 2021 +1000

    More edits. Also commented out the test figures for now, since they don't appear to be in the repo yet.

paper/quokka.tex

commit 180d732a13d258f1df86637aa8a8c6c4ba89ae9c
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Sep 20 20:01:12 2021 +1000

    minor edits

paper/quokka.pdf
paper/quokka.tex

commit 25853eeb5e62a17350a2908506d346bea76e5290
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Sep 20 18:43:00 2021 +1000

    added references

paper/quokka.bib
paper/quokka.pdf
paper/quokka.tex

commit 1330d30fe6911949a46d294ba833970badf295c6
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Sep 20 18:06:50 2021 +1000

    add figures for 1D test problems

paper/quokka.pdf
paper/quokka.tex

commit b70f82e09116bfcd1f044626808cd5539251091e
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Sep 20 17:37:39 2021 +1000

    minor edit

paper/quokka.pdf
paper/quokka.tex

commit 51ce69972342408da12abfde11d61a0170202a4f
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Sep 20 17:31:48 2021 +1000

    added level sync subsection

paper/quokka.pdf
paper/quokka.tex

commit 40567103d774a49034938e2bd6ce25f89b20b4ff
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Sep 20 16:06:36 2021 +1000

    add KH zoom-in figure

paper/quokka.pdf
paper/quokka.tex
paper/quokka_full.pdf
paper/quokka_zoom.pdf
paper/quokka_zoom2.pdf

commit 4d8db0bcce1ad519ecd89dbe3fae56575ed58569
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Sep 20 15:54:12 2021 +1000

    added section matter-radiation coupling

paper/quokka.tex

commit 0d93489767080559d32665afb3a8b5f9a2eb8c09
Merge: 576ddee9 352ae14b
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Sep 20 10:30:04 2021 +1000

    Merge branch 'master' of github.com:BenWibking/TwoMomentRad

commit 576ddee9210c8bdd246f09dba70546bf851fd836
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Sep 20 10:30:00 2021 +1000

    added references

paper/quokka.bib
paper/quokka.tex

commit 352ae14bebbb990324e1df8f4a8b1f07524f2083
Author: Mark Krumholz <mark.krumholz@anu.edu.au>
Date:   Sun Sep 19 21:39:15 2021 +1000

    Minor edit.

paper/quokka.tex

commit 6c38733e2c39647a750eda43e4df0a9162541e35
Merge: 096d4546 dbd80a2f
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Sep 17 21:36:19 2021 +1000

    Merge branch 'master' of github.com:BenWibking/TwoMomentRad

commit 096d4546c5c7e892bc710be644ea37be67058d91
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Sep 17 20:25:09 2021 +1000

    added reference for MOL hydro

paper/quokka.bib
paper/quokka.tex

commit dbd80a2f52e5d90aa88bd7093450c92874125b7b
Author: Mark Krumholz <mark.krumholz@anu.edu.au>
Date:   Fri Sep 17 19:30:42 2021 +1000

    Edits to paper text.

paper/quokka.bib
paper/quokka.tex

commit 55e369dcb284fed9bcd441272e8b4f2a74c45f28
Merge: 20c75764 bf798b10
Author: Mark Krumholz <mark.krumholz@anu.edu.au>
Date:   Fri Sep 17 18:31:32 2021 +1000

    Merge branch 'master' of github.com:BenWibking/quokka-code

commit 20c757646657f174be5a2eac0c6823a2a49467ea
Author: Mark Krumholz <mark.krumholz@anu.edu.au>
Date:   Fri Sep 17 18:31:15 2021 +1000

    Edits

paper/quokka.tex

commit bf798b10b39968eac1f69da2303fd5363edb94f8
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Sep 17 18:01:01 2021 +1000

    add radiation methods section

paper/quokka.bib
paper/quokka.tex

commit 0c0449968675bc7ac5c311d8d76f9e77cd0e70b9
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Sep 16 21:46:04 2021 +1000

    update title

paper/quokka.tex

commit f5ffc2625c01340197571788ea8933f5c5f07b30
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Sep 16 21:28:19 2021 +1000

    mention PLM option in paper

paper/quokka.tex

commit 463fa1482439aeb0c8a5c14a56da00725b495804
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Sep 16 21:19:48 2021 +1000

    added section 2.2 ('hydrodynamics')

README.md
extern/quokka2.png
paper/quokka.bib
paper/quokka.tex

commit 229e72d652d8c7bd6e04e085cf197f6bdc188b72
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Sep 16 15:49:40 2021 +1000

    fix equations

paper/quokka.tex

commit a915e3703331804ac90334c301c33377faaa9402
Merge: 92522d35 1d3f7185
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Sep 15 17:28:19 2021 +1000

    Merge branch 'master' of github.com:BenWibking/TwoMomentRad

commit 92522d35cec86408c75d180305561b6f47e22f80
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Sep 15 17:28:15 2021 +1000

    modify outline

paper/quokka.tex

commit 1d3f7185de4e7a664d48ea2a54b9d4bfaa109c6c
Author: Mark Krumholz <mark.krumholz@anu.edu.au>
Date:   Wed Sep 15 17:24:42 2021 +1000

    Edited the text. Main changes are to somewhat alter the discussion about how to treat the averaged opacities.

paper/quokka.tex

commit 93ceeeebec4f6022d7d2a8e47dabfa1c90a3db26
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Sep 14 21:43:38 2021 +1000

    update equations

paper/quokka.tex

commit 922bc2da39836e4f31d370741c30e8d5c0650291
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Sep 14 16:50:42 2021 +1000

    moar equations

paper/quokka.tex

commit fe827c260392faa3fd79714e51b6d8ce51350ada
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Sep 14 14:25:44 2021 +1000

    added equations section to manuscript

paper/quokka.bib
paper/quokka.tex

commit 279ec78668e9f69bdaa9780e1499b644d587b740
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Sep 13 17:55:30 2021 +1000

    added outline to manuscript

paper/quokka.bib
paper/quokka.tex

commit 431f56713f89cc6cc2baa061337f1f878b2a2556
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Sep 13 16:03:20 2021 +1000

    updated manuscript

paper/quokka.bib
paper/quokka.tex

commit 97435d00f61da11c3348e677eef1b756d056f403
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Sep 13 12:55:50 2021 +1000

    Rename CUDA workflow on Github CI

.github/workflows/cmake-cuda.yml

commit c54699d964fa848c96ca4a31ef314706f3881013
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Sep 13 12:30:23 2021 +1000

    many CUDA fixes for test problems

src/Advection/CMakeLists.txt
src/Advection/test_advection.cpp
src/Advection/test_advection.hpp
src/Advection2D/CMakeLists.txt
src/Advection2D/test_advection2d.cpp
src/Advection2D/test_advection2d.hpp
src/AdvectionSemiellipse/CMakeLists.txt
src/AdvectionSemiellipse/test_advection_semiellipse.cpp
src/AdvectionSemiellipse/test_advection_semiellipse.hpp
src/CMakeLists.txt
src/HydroBlast2D/CMakeLists.txt
src/HydroBlast2D/test_hydro2d_blast.cpp
src/HydroBlast2D/test_hydro2d_blast.hpp
src/HydroBlast3D/CMakeLists.txt
src/HydroBlast3D/test_hydro3d_blast.cpp
src/HydroBlast3D/test_hydro3d_blast.hpp
src/HydroContact/CMakeLists.txt
src/HydroContact/test_hydro_contact.cpp
src/HydroContact/test_hydro_contact.hpp
src/HydroKelvinHelmholz/CMakeLists.txt
src/HydroKelvinHelmholz/test_hydro2d_kh.cpp
src/HydroKelvinHelmholz/test_hydro2d_kh.hpp
src/HydroLeblanc/CMakeLists.txt
src/HydroLeblanc/test_hydro_leblanc.cpp
src/HydroLeblanc/test_hydro_leblanc.hpp
src/HydroRichtmeyerMeshkov/CMakeLists.txt
src/HydroRichtmeyerMeshkov/test_hydro2d_rm.cpp
src/HydroRichtmeyerMeshkov/test_hydro2d_rm.hpp
src/HydroSMS/CMakeLists.txt
src/HydroSMS/test_hydro_sms.cpp
src/HydroSMS/test_hydro_sms.hpp
src/HydroShocktube/CMakeLists.txt
src/HydroShocktube/test_hydro_shocktube.cpp
src/HydroShocktube/test_hydro_shocktube.hpp
src/HydroShuOsher/CMakeLists.txt
src/HydroShuOsher/test_hydro_shuosher.cpp
src/HydroShuOsher/test_hydro_shuosher.hpp
src/HydroVacuum/CMakeLists.txt
src/HydroVacuum/test_hydro_vacuum.cpp
src/HydroVacuum/test_hydro_vacuum.hpp
src/HydroWave/CMakeLists.txt
src/HydroWave/test_hydro_wave.cpp
src/HydroWave/test_hydro_wave.hpp
src/RadBeam/CMakeLists.txt
src/RadBeam/test_radiation_beam.cpp
src/RadBeam/test_radiation_beam.hpp
src/RadForce/CMakeLists.txt
src/RadForce/test_radiation_force.cpp
src/RadForce/test_radiation_force.hpp
src/RadMarshak/CMakeLists.txt
src/RadMarshak/test_radiation_marshak.cpp
src/RadMarshak/test_radiation_marshak.hpp
src/RadMarshakAsymptotic/CMakeLists.txt
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp
src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.hpp
src/RadMarshakCGS/CMakeLists.txt
src/RadMarshakCGS/test_radiation_marshak_cgs.cpp
src/RadMarshakCGS/test_radiation_marshak_cgs.hpp
src/RadMatterCoupling/CMakeLists.txt
src/RadMatterCoupling/test_radiation_matter_coupling.cpp
src/RadMatterCoupling/test_radiation_matter_coupling.hpp
src/RadMatterCouplingRSLA/CMakeLists.txt
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.cpp
src/RadMatterCouplingRSLA/test_radiation_matter_coupling_rsla.hpp
src/RadPulse/CMakeLists.txt
src/RadPulse/test_radiation_pulse.cpp
src/RadPulse/test_radiation_pulse.hpp
src/RadShadow/CMakeLists.txt
src/RadShadow/test_radiation_shadow.cpp
src/RadShadow/test_radiation_shadow.hpp
src/RadStreaming/CMakeLists.txt
src/RadStreaming/test_radiation_streaming.cpp
src/RadStreaming/test_radiation_streaming.hpp
src/RadSuOlson/CMakeLists.txt
src/RadSuOlson/test_radiation_SuOlson.cpp
src/RadSuOlson/test_radiation_SuOlson.hpp
src/RadTophat/CMakeLists.txt
src/RadTophat/test_radiation_tophat.cpp
src/RadTophat/test_radiation_tophat.hpp
src/RadTube/CMakeLists.txt
src/RadTube/test_radiation_tube.cpp
src/RadTube/test_radiation_tube.hpp
src/RadhydroShell/CMakeLists.txt
src/RadhydroShell/test_radhydro_shell.cpp
src/RadhydroShell/test_radhydro_shell.hpp
src/RadhydroShock/CMakeLists.txt
src/RadhydroShock/test_radhydro_shock.cpp
src/RadhydroShock/test_radhydro_shock.hpp
src/RadhydroShockCGS/CMakeLists.txt
src/RadhydroShockCGS/test_radhydro_shock_cgs.cpp
src/RadhydroShockCGS/test_radhydro_shock_cgs.hpp

commit 16f049fcdfefc9810bd581896277749132da040a
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Sep 13 08:02:09 2021 +1000

    update kelvin-helmholz test

src/test_hydro2d_kh.cpp
tests/KelvinHelmholz.in

commit 5b6891f744c018c104f21f3483c11e90aaed5bc5
Merge: 8e9f2efc 37103946
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Sep 12 16:08:17 2021 +1000

    Merge branch 'master' of github.com:BenWibking/TwoMomentRad

commit 8e9f2efc4eeb25e8e939ea6392d67f0eaedec7b4
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Sep 12 16:07:54 2021 +1000

    switch to Athena++ version of KH test

CMakeLists.txt
src/test_hydro2d_kh.cpp
tests/KelvinHelmholz.in

commit 371039460159d9cf1c7064e7d887b94794ef4b69
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Sep 11 21:26:37 2021 +1000

    add missing dependencies to CUDA CI

.github/workflows/cmake-cuda.yml

commit ec77c02d14c7fa2e50950a7d0255896a6baa8bfa
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Sep 11 19:58:06 2021 +1000

    fix nvcc path in github CI

.github/workflows/cmake-cuda.yml

commit ce78cbc54f803b265ab42207cd8be5ac5b3762ec
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Sep 11 19:45:21 2021 +1000

    Create cmake-cuda.yml

.github/workflows/cmake-cuda.yml

commit 2205c92f54adee5dbbd853a644eb233b0122093a
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Sep 11 10:06:49 2021 +1000

    workaround mellanox hcoll bug

scripts/run-quokka-sedov-64nodes.pbs
scripts/shell-64nodes.pbs

commit 2578b9202c1947f6a92703cecd6579198415f201
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Sep 10 13:40:01 2021 +1000

    update scaling test scripts

scripts/amr-shell-8nodes.pbs
scripts/gpu_wrapper_sedov_1024.sh
scripts/run-quokka-sedov-1gpu.pbs
scripts/run-quokka-sedov-1node.pbs
scripts/run-quokka-sedov-64nodes.pbs
scripts/run-quokka-sedov-8nodes.pbs

commit f69d6f9d1ab79f1552bb6efd5b2e9a006001d888
Merge: 105255d1 1558e8c0
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Sep 10 10:48:10 2021 +1000

    Merge branch 'master' of github.com:BenWibking/TwoMomentRad

commit 105255d1cb3fd0324814b408ec73f4fba5ba3251
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Sep 10 10:47:43 2021 +1000

    use periodic BC for scaling tests

tests/blast_unigrid_1024.in
tests/blast_unigrid_2048.in
tests/blast_unigrid_256.in
tests/blast_unigrid_512.in
tests/radhydro_shell_1024.in
tests/radhydro_shell_2048.in
tests/radhydro_shell_256.in
tests/radhydro_shell_512.in

commit 1558e8c0eaf0559835088035d9430c455ab8c32f
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Sep 9 21:08:45 2021 +1000

    adjust blocking factor for AMR scaling test

tests/radhydro_shell_amr.in

commit f782fa93329f8ad889d3dc50bd57c966bcf24089
Merge: 7472a39d 7d5f9f02
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Sep 9 20:45:50 2021 +1000

    Merge branch 'master' of github.com:BenWibking/quokka-code

commit 7d5f9f028b55ceb245f009d3cadcd6a572e751e3
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Sep 9 20:28:52 2021 +1000

    added cellUpdatesEachLevel_ counter

src/simulation.hpp

commit 7472a39d717453397e2847f633e5273771f265bc
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Sep 9 19:29:02 2021 +1000

    added amr scaling tests scripts

scripts/amr-shell-2nodes.pbs
scripts/amr-shell-4nodes.pbs

commit 83f3767904ce47b344a2377e7b6692a4b98b5fce
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Sep 9 18:26:02 2021 +1000

    updated AMR shell parameters

tests/radhydro_shell_amr.in

commit 870675916f31bb40225223575056788f1c839a01
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Sep 9 16:34:06 2021 +1000

    update AMR shell test parameters

tests/radhydro_shell_amr.in

commit acf99681e91173e55e2184511c771432476987ba
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Sep 9 12:31:19 2021 +1000

    added new AMR scaling tests

CMakeLists.txt
scripts/amr-shell-1node.pbs
scripts/gpu_wrapper_amr_shell.sh
tests/radhydro_shell_amr.in

commit f2318dfb99edb4a7b69309b0d24236b4a92c3b4b
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Sep 9 12:16:44 2021 +1000

    change coarse-to-fine interpolation

src/simulation.hpp

commit 6d4b8e541497f62e6d58b0ee803a6c4ca247629b
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Sep 9 11:41:23 2021 +1000

    update amrex submodule

extern/amrex

commit 0986ee553d475ef9c0a45997fb6e740c6d181895
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Sep 9 11:35:54 2021 +1000

    update shell test for AMR

src/simulation.hpp
src/test_radhydro_shell.cpp
tests/radhydro_shell.in

commit ced5b3577553f665e6ce262599a32e16f52ab3df
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Sep 8 16:27:32 2021 +1000

    fix lambda capture of 'this'

src/RadhydroSimulation.hpp

commit ad2d2c8a290307e843d84189ac8bf6d0f2291339
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Sep 8 15:46:19 2021 +1000

    update parameters for shell test

tests/radhydro_shell.in

commit 961540f2792ba4df62fe5a6e0b0ec16246725b97
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Sep 8 13:35:20 2021 +1000

    fix radhydro timestep calculation

src/RadhydroSimulation.hpp

commit f6c4fba5c8c57ec1b348c976233839c2fa3ab866
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Sep 8 12:22:08 2021 +1000

    adjust timestep to limit number of radiation subcycles

src/RadhydroSimulation.hpp

commit 3ffa951cdd9d773196f229bd36b27fc2153a47d9
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Sep 4 12:08:06 2021 +1000

    add full box option to shell test

src/RadhydroSimulation.hpp
src/radiation_system.hpp
src/test_radhydro_shell.cpp
src/test_radiation_SuOlson.cpp

commit 1be9b94c8d642757a42f8fbaf4bed104f53e49ce
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Sep 4 11:54:28 2021 +1000

    add option to simulate full box

src/test_hydro3d_blast.cpp

commit c5e639649ed4b54dd31bf4d2aee2aa7b1542660f
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Sep 3 17:04:50 2021 +1000

    update to latest amrex

extern/amrex

commit e7f2b46b5650582d16f1e8459a000b963f4df0b9
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Sep 2 18:00:06 2021 +1000

    added optically-thin radiation force test

CMakeLists.txt
src/CMakeLists.txt
src/test_radiation_force.cpp
src/test_radiation_force.hpp
tests/RadForce.in
tests/RadTube.in

commit 8e5b6088a2235b862ba28b82c7a22124cfaa31e3
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Aug 30 13:45:50 2021 +1000

    fix radiation pressure tube test

extern/pressure_tube/solution.py
src/CMakeLists.txt
src/RadhydroSimulation.hpp
src/interpolate.c
src/radiation_system.hpp
src/test_radiation_marshak_asymptotic.cpp
src/test_radiation_pulse.cpp
src/test_radiation_tube.cpp
tests/RadTube.in

commit c900acb8ae5292c5d98d8323a5552e4cf03de896
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun Aug 29 22:38:21 2021 +1000

    added radiation pressure tube

extern/pressure_tube/initial_conditions.txt
extern/pressure_tube/solution.py
src/test_radiation_tube.cpp
src/test_radiation_tube.hpp

commit a15d23c18e258b36e725018d52fc22677cd8c533
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Aug 28 22:07:54 2021 +1000

    added comments

src/test_radiation_marshak_asymptotic.cpp

commit 6b15297fff70f562c92521e3d71aa600b4416bf8
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Aug 28 21:47:26 2021 +1000

    re-add radiation diffusion tests

src/CMakeLists.txt
src/test_radiation_marshak_asymptotic.cpp
src/test_radiation_pulse.cpp
tests/MarshakAsymptotic.in
tests/RadPulse.in

commit cf75089d64f2127f0c042f9090cbf7e7377018f6
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Aug 27 18:54:02 2021 +1000

    re-added tophat problem

src/CMakeLists.txt
src/test_radiation_tophat.cpp
tests/Tophat.in

commit 77219a8d2abeccf1650b6a531b8e50df4db1e692
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Aug 27 18:22:33 2021 +1000

    re-added radiation streaming test

CMakeLists.txt
src/CMakeLists.txt
src/test_radiation_marshak.cpp
src/test_radiation_streaming.cpp
tests/RadStreaming.in

commit d946b7008d86bbaecb706263790e9227762c3460
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Aug 27 16:30:38 2021 +1000

    added AMR parameter file for shell test

tests/radhydro_shell_amr.in

commit b6e1f2ce9491298d2b9509ea665b2a386353f53a
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Aug 27 15:44:01 2021 +1000

    fix typo

src/RadhydroSimulation.hpp

commit d4c960027d597371b13bfa451360bb8e7c007152
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Aug 27 15:43:35 2021 +1000

    add parameter for radiation reconstruction order

src/RadhydroSimulation.hpp
src/test_radhydro_shell.cpp

commit c9b9dd83b4ff1e2bc44b8232e2a2081ed0cedbb9
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Aug 27 14:49:32 2021 +1000

    compile in 1D by default (for testing only)

CMakeLists.txt

commit e74a21cb1ff1040f61c3603381ed0ffa93de39a2
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Aug 27 14:41:13 2021 +1000

    fix radhydro shell on GPU

src/test_radhydro_shell.cpp

commit a5808a411da7ab57a91825b097538701df5f7107
Merge: 207d2b65 8653dd81
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Aug 27 13:47:47 2021 +1000

    Merge branch 'master' of github.com:BenWibking/quokka-code

commit 8653dd812459bcc5bb15f8570357a19c06d74c30
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Aug 27 12:33:40 2021 +1000

    fix shell test; use PLM for radiation

extern/dust_shell/initial_conditions.txt
extern/dust_shell/solution.py
src/RadhydroSimulation.hpp
src/interpolate.c
src/test_radhydro_shell.cpp

commit 207d2b65079b33d4b6c1526f2133835ef42e9395
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Aug 27 08:53:02 2021 +1000

    adjust parameters for scaling tests

scripts/gpu_wrapper_shell_2048.sh
scripts/shell-64nodes.pbs
src/test_radhydro_shell.cpp
tests/radhydro_shell_2048.in

commit 1b8124c0d7fa825c62e4104df769297b9d5184f8
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Aug 26 22:40:38 2021 +1000

    read initial conditions for shell test from file

src/CMakeLists.txt
src/interpolate.c
src/interpolate.h
src/test_radhydro_shell.cpp

commit d597b6e3e812d011b1f2cb8d0ce86eaa1c115aa6
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Aug 26 22:03:54 2021 +1000

    added steady-state M1 radshell solution

extern/dust_shell/initial_conditions.txt
extern/dust_shell/solution.py

commit 551483033674b59ea66308f7cb7a90bd1d6f8d37
Merge: 01000f11 4fb4e958
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Aug 26 14:34:55 2021 +1000

    Merge branch 'master' of github.com:BenWibking/TwoMomentRad

commit 01000f1138fe53eec434a004460bacf7b18bf479
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Aug 26 14:34:22 2021 +1000

    output avg num of radiation substeps

src/RadhydroSimulation.hpp
src/test_radhydro_shell.cpp

commit 4fb4e9586648e77dbc1581bcfeaf2e56c1d2db38
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Aug 26 14:10:48 2021 +1000

    updated scaling tests

scripts/gpu_wrapper.sh
scripts/gpu_wrapper_sedov.sh
scripts/gpu_wrapper_shell_1024.sh
scripts/gpu_wrapper_shell_256.sh
scripts/gpu_wrapper_shell_512.sh
scripts/run-quokka-sedov-16nodes.pbs
scripts/run-quokka-sedov-4nodes.pbs
scripts/shell-1gpu.pbs
scripts/shell-1node.pbs
scripts/shell-8nodes.pbs
tests/radhydro_shell_1024.in
tests/radhydro_shell_256.in
tests/radhydro_shell_512.in

commit 4257a92a8287168d15c9fc2d9edfcba9e51cef3a
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Aug 25 16:18:59 2021 +1000

    updated radhydro shell test

src/test_radhydro_shell.cpp

commit a0be7c357fb9e84855d057eba4669a352bbc1a25
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Aug 25 14:47:49 2021 +1000

    change radhydro shell parameters

CMakeLists.txt
extern/dust_shell/analyze.py
src/test_radhydro_shell.cpp

commit d483b9744c1e95cb34544fd62835230ee2777392
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Aug 24 21:18:25 2021 +1000

    fix radhydro shell test (again)

extern/dust_shell/solution.py
src/radiation_system.hpp
src/test_radhydro_shell.cpp

commit 84ee8fa2ec7191705e4c8a2fd3e11768bfc13db2
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Aug 24 09:15:45 2021 +1000

    added MPI_Barrier to start of coarse ts

src/simulation.hpp

commit 2be86e5c79d821735556cc8a1c2160e6d1e63519
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Aug 23 20:57:36 2021 +1000

    updated radhydro shell test

src/RadhydroSimulation.hpp
src/radiation_system.hpp
src/simulation.hpp
src/test_radhydro_shell.cpp
tests/radhydro_shell.in

commit c60e473bf85ab52d4fbb651e30c51a9a48b1cc83
Merge: 49aa6b26 ac5adb2e
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Aug 23 10:15:49 2021 +1000

    Merge branch 'master' of github.com:BenWibking/quokka-code

commit 49aa6b26acb233e087b5bc37d42713a9f974568b
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Aug 23 10:15:38 2021 +1000

    updated scaling tests

perfdata/unigrid_cpu/bw0729.1629090348.145871.ipm.xml
perfdata/unigrid_cpu/bw0729.1629091661.837884.ipm.xml
perfdata/unigrid_cpu/bw0729.1629092733.31126.ipm.xml
perfdata/unigrid_cpu/sedov_1node.log
perfdata/unigrid_cpu/sedov_64nodes.log
perfdata/unigrid_cpu/sedov_8nodes.log
scripts/gpu_wrapper_sedov_1024.sh

commit ac5adb2eaee3eb3dd3fe1517baa45d0304ad8a7e
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Aug 19 21:32:50 2021 +1000

    fix radshell

src/test_radhydro_shell.cpp

commit 31a35ed8cad8f6528ea5706844d2b683f13aaf6d
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Aug 19 20:47:39 2021 +1000

    add latex outputs to gitignore

.gitignore

commit 246c3312fac0469c80df9998b00d847fdd41c8fb
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Aug 19 20:46:42 2021 +1000

    update radshell parameters

src/test_radhydro_shell.cpp
tests/radhydro_shell.in

commit b53a9be67ac79b614fd4d8ac21d3637c7106ad64
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Aug 19 20:46:26 2021 +1000

    remove disable_transport_terms

src/RadhydroSimulation.hpp
src/simulation.hpp

commit e7bcafb6a7280193efdb935b7d50e4af56b7577d
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Aug 19 17:32:35 2021 +1000

    update scaling tests

scripts/cpu-sedov-64nodes.pbs
scripts/cpu-sedov-8nodes.pbs
scripts/gpu_wrapper_sedov_1024.sh
scripts/gpu_wrapper_sedov_2048.sh
scripts/gpu_wrapper_sedov_512.sh

commit 7c9c9f5bfcc6111ec031886e2b6f71b96c558f51
Merge: cdd9200f 3c94261b
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Aug 18 20:26:15 2021 +1000

    Merge branch 'master' of github.com:BenWibking/quokka-code

commit cdd9200ffd2f31a2ba84628575f794b0731e04c1
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Aug 18 20:25:59 2021 +1000

    updated scaling tests

scripts/cpu-sedov-1node.pbs
scripts/cpu-sedov-64nodes.pbs
scripts/cpu-sedov-8nodes.pbs
scripts/gpu_wrapper_sedov_1024.sh
scripts/gpu_wrapper_sedov_2048.sh
scripts/gpu_wrapper_sedov_256.sh
scripts/gpu_wrapper_sedov_512.sh
scripts/run-quokka-sedov-1gpu.pbs
src/test_hydro3d_blast.cpp

commit 3c94261bc2b88cfdc2b78c873884489ba8fb4c9a
Merge: 596cb00a a2da970c
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Aug 18 15:51:31 2021 +1000

    Merge branch 'master' of github.com:BenWibking/TwoMomentRad

commit 596cb00a69c5443fda0488b0f7623e97e555edfd
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Aug 18 15:51:27 2021 +1000

    updated text

paper/quokka.tex

commit a2da970c603361135057f0cbf285392dc17c3b91
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Aug 14 10:05:36 2021 +1000

    updated amrex

extern/amrex

commit e41162a6fa0527d73a4a828c0b588f18a1cc4ee0
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Aug 11 18:07:55 2021 +1000

    updated text

paper/quokka.bib
paper/quokka.tex

commit 9e82331502069ed88c467fb860275500d9163d93
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Aug 8 09:21:43 2021 +1000

    fix sonarscan in CI

.github/workflows/cmake.yml

commit 18860c33fbe22a5897c9bc369d28f35da323e57a
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Aug 8 09:20:32 2021 +1000

    Added libhdf5-mpi-dev to CI

.github/workflows/cmake.yml

commit 91d6fdb36a9a08a754ca0fd12bba0d285b1c1f0e
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Aug 7 22:08:21 2021 +1000

    re-enable python integration by default

src/CMakeLists.txt

commit 581162fb7077da92886d55ce9f8681e62651a8af
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Aug 7 22:06:44 2021 +1000

    use parallel HDF5 for plotfiles (no async or chk)

CMakeLists.txt
src/simulation.hpp

commit 214576d38ff1f7adddc9cc1b43dd02c8429fad11
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Aug 7 19:08:27 2021 +1000

    don't try to import codecov into sonarcloud

sonar-project.properties

commit f246cfffc5695e19fa52229a44d05ca749696ffc
Merge: 4e534953 decb9d9e
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Aug 7 16:41:19 2021 +1000

    Merge branch 'master' of github.com:BenWibking/quokka-code

commit 4e534953a6b773ad888dbcee34554c01b71ff3c9
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Aug 7 16:41:09 2021 +1000

    update scaling test scripts

scripts/gpu_wrapper_sedov_1024.sh
scripts/gpu_wrapper_sedov_2048.sh
scripts/gpu_wrapper_sedov_512.sh
scripts/run-quokka-sedov-1node.pbs
scripts/run-quokka-sedov-64nodes.pbs
scripts/run-quokka-sedov-8nodes.pbs
src/test_hydro3d_blast.cpp
tests/blast_unigrid_1024.in
tests/blast_unigrid_2048.in
tests/blast_unigrid_256.in
tests/blast_unigrid_512.in

commit decb9d9e1ad6b21a68e00ad6fb5579a83624fe18
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Aug 7 16:37:29 2021 +1000

    disable code coverage in CI (not working)

.github/workflows/cmake.yml

commit 75c190fe71000f52b3e79f55ecb473c98f240c1b
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Aug 7 12:15:03 2021 +1000

    Update cmake.yml

.github/workflows/cmake.yml

commit ae39647d46d88ce0a577dd839d7c30e0ce000f79
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Aug 6 16:33:52 2021 +1000

    added new scaling tests

scripts/gpu_wrapper_sedov_2048.sh
scripts/run-quokka-sedov-1node.pbs
scripts/run-quokka-sedov-64nodes.pbs
scripts/run-quokka-sedov-8nodes.pbs
tests/blast_amr_2048.in

commit 1ac4d69b36502f2544b576ac1f7d6bd71692a7b6
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Aug 6 16:29:06 2021 +1000

    install fastcov in CI

.github/workflows/cmake.yml

commit 1437309ac2bdc03f78f04d4c20e59475f95c3101
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Aug 6 16:12:43 2021 +1000

    add fastcov to CI

.github/workflows/cmake.yml
sonar-project.properties
src/CMakeLists.txt

commit 1388f35e2ce557b214c63a27ca72a52fb5ad6d3f
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Aug 6 15:27:29 2021 +1000

    switch to fastcov for coverage report

src/CMakeLists.txt

commit c076beb1de7676ebaa3f3fc5d8a11023b8a7ebbe
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Aug 5 17:37:26 2021 +1000

    exclude header files from codecov report

src/CMakeLists.txt

commit 2b2cf375cab6e5ff7627fdf55ed361220c62f80c
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Aug 5 17:15:23 2021 +1000

    use -O1 when testing code coverage

src/CMakeLists.txt

commit 322a2138ae6378d0d325c9c6799bec457119ac9a
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Aug 5 16:00:52 2021 +1000

    switch to 1D for code coverage testing

CMakeLists.txt
src/CMakeLists.txt

commit d64d938d1efc1cc1a1d46b287a54838757124a1a
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Aug 5 15:32:00 2021 +1000

    added coverage target that runs gcov+lcov

cmake/CodeCoverage.cmake
src/CMakeLists.txt

commit d96d9f73e758a6dab5aa9f301443c3c4abf8aaa3
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Aug 5 13:46:55 2021 +1000

    moved files to scripts/ and perfdata/

perfdata/gpu_performance.txt
perfdata/gpu_profiling.txt
perfdata/gpu_profiling_unigrid.txt
scripts/codecov.sh
scripts/gpu_wrapper.sh
scripts/gpu_wrapper_sedov.sh
scripts/gpu_wrapper_sedov_1024.sh
scripts/gpu_wrapper_sedov_512.sh
scripts/run-quokka-sedov-16nodes.pbs
scripts/run-quokka-sedov-1node.pbs
scripts/run-quokka-sedov-2nodes.pbs
scripts/run-quokka-sedov-4nodes.pbs
scripts/run-quokka-sedov-8nodes.pbs
scripts/run-quokka.pbs
tests/blast_amr_1024.in
tests/blast_amr_512.in
timing.txt

commit 88b0159cebbc47e9033855be736cba26ffab873d
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Aug 4 18:32:27 2021 +1000

    added options to enable CUDA-aware MPI

run-quokka-sedov.pbs

commit 0eb7cdd9882e44dcb86bf190a4890de39fe98404
Merge: e0f77873 181aacd9
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Aug 4 15:45:16 2021 +1000

    Merge branch 'master' of github.com:BenWibking/TwoMomentRad

commit e0f7787363b6d605620512e4635838d13dd6a5b4
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Aug 4 15:44:50 2021 +1000

    fix CUDA build in 2D

src/CMakeLists.txt

commit 181aacd99c5c8c0c8d4e0b96357ae8e98f0b599a
Merge: 7a6e91ef 0000453b
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Aug 4 14:34:56 2021 +1000

    Merge branch 'master' of github.com:BenWibking/quokka-code

commit 7a6e91efd55389adcc39f8244c31d865ff1bb900
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Aug 4 14:34:42 2021 +1000

    updated wrapper scripts

gpu_wrapper.sh
gpu_wrapper_sedov.sh
run-quokka-sedov.pbs
run-quokka.pbs

commit 0000453b815333dc12a6a36dc8f50256d92d8905
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Aug 4 14:32:36 2021 +1000

    allow build without python libs

src/CMakeLists.txt
src/test_advection.cpp
src/test_advection.hpp
src/test_advection_semiellipse.cpp
src/test_advection_semiellipse.hpp
src/test_hydro2d_blast.hpp
src/test_hydro2d_kh.hpp
src/test_hydro2d_rm.hpp
src/test_hydro_contact.cpp
src/test_hydro_contact.hpp
src/test_hydro_leblanc.cpp
src/test_hydro_leblanc.hpp
src/test_hydro_shocktube.cpp
src/test_hydro_shocktube.hpp
src/test_hydro_shuosher.cpp
src/test_hydro_shuosher.hpp
src/test_hydro_sms.cpp
src/test_hydro_sms.hpp
src/test_hydro_vacuum.cpp
src/test_hydro_vacuum.hpp
src/test_hydro_wave.cpp
src/test_hydro_wave.hpp
src/test_radhydro_shock.cpp
src/test_radhydro_shock.hpp
src/test_radhydro_shock_cgs.cpp
src/test_radhydro_shock_cgs.hpp
src/test_radiation_SuOlson.cpp
src/test_radiation_SuOlson.hpp
src/test_radiation_marshak.cpp
src/test_radiation_marshak.hpp
src/test_radiation_marshak_asymptotic.hpp
src/test_radiation_marshak_cgs.cpp
src/test_radiation_marshak_cgs.hpp
src/test_radiation_matter_coupling.cpp
src/test_radiation_matter_coupling.hpp
src/test_radiation_matter_coupling_rsla.cpp
src/test_radiation_matter_coupling_rsla.hpp
src/test_radiation_pulse.hpp
src/test_radiation_shadow.hpp
src/test_radiation_streaming.hpp
src/test_radiation_tophat.hpp

commit 029a457cf10f1b63a4a552f27a8c65a43501e233
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Aug 4 14:05:16 2021 +1000

    zero-fill radiation components (unused)

src/test_hydro3d_blast.cpp

commit 924d330e6a98b79ab1d25903f457b362faf43a58
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Aug 4 14:04:43 2021 +1000

    drop v/c terms for tests if exact solution drops

CMakeLists.txt
src/radiation_system.hpp
src/test_radhydro_shell.cpp
src/test_radhydro_shock.cpp
src/test_radhydro_shock_cgs.cpp
src/test_radiation_SuOlson.cpp
src/test_radiation_beam.cpp
src/test_radiation_marshak.cpp
src/test_radiation_marshak_cgs.cpp
src/test_radiation_matter_coupling.cpp
src/test_radiation_matter_coupling_rsla.cpp
src/test_radiation_shadow.cpp

commit 8230abcce937157816f41a05b04d4efe53343b57
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Aug 4 14:02:52 2021 +1000

    use amrex::MFInterpolater

src/RadhydroSimulation.hpp
src/simulation.hpp

commit 81183655c5b7ffe9a6dac669e427576e3a11a303
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Aug 3 15:39:51 2021 +1000

    fix pressure floor on GPU; update performance numbers

gpu_performance.txt
src/hydro_system.hpp
tests/radhydro_shell.in

commit cd0316a4be1b9a80714ce5fe9ce258b278373b99
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Aug 3 13:44:28 2021 +1000

    use MFInterpolater

src/simulation.hpp

commit 6fe0dd4a7af81698f65cb6e7716ef86e79a5dcce
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Aug 3 12:58:10 2021 +1000

    update amrex submodule

extern/amrex

commit ef59f3d217ea5edc5a3c3e15cb15e4d5bd296f0d
Merge: 7a311fce 968e6a52
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Aug 3 12:56:53 2021 +1000

    Merge branch 'master' of github.com:BenWibking/TwoMomentRad

commit 7a311fce7dc7228b8fcef674f3d8c5d20c1a576d
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Aug 3 12:56:23 2021 +1000

    various fixes

CMakeLists.txt
src/CMakeLists.txt
src/RadhydroSimulation.hpp
src/hydro_system.hpp
src/test_hydro_shocktube.cpp
src/test_radhydro_shell.cpp
src/test_radiation_box.cpp
src/test_radiation_box.hpp
tests/MatterEnergyExchangeRSLA.in
tests/energyexchange.in

commit 968e6a5293803262bb4cef430ca391b8552d6d90
Merge: 9477d913 20f36db2
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Aug 2 20:34:47 2021 +1000

    Merge branch 'master' of github.com:BenWibking/quokka-code

commit 9477d913b40995cbdfa31352e68d25352cfba83b
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Aug 2 20:34:38 2021 +1000

    added PBS script

.gitignore
gpu_wrapper.sh
run-quokka.pbs

commit 20f36db2eb64b617012acf6992d31479e3e36bde
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Aug 2 19:12:02 2021 +1000

    updated formatting

paper/quokka.tex

commit db5108ea050eb672bf130b24956522c1f75d9cf3
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Aug 2 14:36:17 2021 +1000

    updated amrex

extern/amrex

commit b84bb374b7ea8f2a9c268d810e1f50a0ca9350c5
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun Aug 1 19:10:50 2021 +1000

    added paper latex files

paper/aas_macros.sty
paper/make_tarball.py
paper/mnras.bst
paper/mnras.cls
paper/quokka.bib
paper/quokka.tex

commit c61b1ecbb07f20373f26d6294fac8481d217cc76
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Aug 1 12:14:37 2021 +1000

    radshell test GPU fixes

src/CMakeLists.txt
src/test_hydro_contact.cpp
src/test_radhydro_shell.cpp
tests/radhydro_shell.in

commit dd097bf5eb8e5ee599d12862a1ccf9ce68c8f01f
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Aug 1 09:56:50 2021 +1000

    updated amrex submodule

extern/amrex

commit fb8678d0193406f71cd05ce44d6ce46061a3500e
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Jul 31 20:49:45 2021 +1000

    use PLM reconstruction

src/test_radhydro_shell.cpp

commit f0e5a11b430072ef2b83c540c2a2426ee8104c55
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Jul 30 16:10:36 2021 +1000

    use amrex::pc_interp for shell problem

src/RadhydroSimulation.hpp
src/simulation.hpp
tests/radhydro_shell.in

commit 2fb424bbe49af89a95e282f8924d3cd8b15cab6b
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Jul 28 16:06:44 2021 +1000

    fix bug in shell test problem (AMR-only bug)

src/RadhydroSimulation.hpp
src/simulation.hpp
src/test_radhydro_shell.cpp

commit e40f649754ed65be441df04913801125e90ee0cf
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jul 27 17:09:43 2021 +1000

    update radhydro shell test to use PLM

src/test_radhydro_shell.cpp
tests/radhydro_shell.in

commit f5898e98ea23bacda01186296044c75431e6c57f
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jul 27 15:50:29 2021 +1000

    fix radhydro shell test

src/radiation_system.hpp
src/test_radhydro_shell.cpp
tests/radhydro_shell.in

commit 56a81620c3b90b0d0a345f7b98df24700fe59f3a
Merge: 0ef940ad e38ff721
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jul 27 12:12:40 2021 +1000

    Merge branch 'master' of github.com:BenWibking/TwoMomentRad

commit 0ef940ad14f45573eabc9ebb53847527e696b43d
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jul 27 12:11:14 2021 +1000

    add marshak wave tests

src/CMakeLists.txt
src/RadhydroSimulation.hpp
src/test_radiation_marshak.cpp
src/test_radiation_marshak_cgs.cpp
tests/Marshak.in
tests/MarshakCGS.in

commit e38ff721d6d9520b1113081c0a87b1a7b333d160
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Jul 26 19:37:45 2021 +1000

    Update README.md

README.md

commit 7baefa101c88fe5f9ef60adc6f4019b1684e987c
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jul 26 16:23:05 2021 +1000

    update matter-radiation coupling test

src/test_radiation_matter_coupling.cpp
src/test_radiation_matter_coupling_rsla.cpp

commit fe3c1104d6d5935c163ca0dfeee67e86345e7785
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jul 26 16:09:46 2021 +1000

    change to 2D so that CI does not time out

CMakeLists.txt

commit 30226b0c3e0f961d70235ad74bfbc2dfb9067930
Merge: 6cdd0bd2 70b5def7
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Jul 26 15:18:14 2021 +1000

    Merge pull request #6 from BenWibking/suolson-test
    
    Fix radiation-only tests

commit 70b5def73fa8df33faaaa10b63c0240a5247f16f
Merge: 3c99db37 6cdd0bd2
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Jul 26 14:23:32 2021 +1000

    Merge branch 'master' into suolson-test

commit 3c99db37f6f5407ac552e78c399a47091bbc082c
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jul 26 13:40:57 2021 +1000

    fix radhydro shock tests

src/test_radhydro_shock.cpp
src/test_radhydro_shock_cgs.cpp

commit f08348af7c253fbfa666e18b75bd3e32c45199a3
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jul 26 13:33:27 2021 +1000

    fix radiation-only test problems

CMakeLists.txt
src/CMakeLists.txt
src/RadhydroSimulation.hpp
src/hydro_system.hpp
src/radiation_system.hpp
src/simulation.hpp
src/test_radiation_SuOlson.cpp
tests/SuOlson.in

commit 6cdd0bd2402a2c86314a906179de9b42db6cf0e7
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jul 25 14:41:06 2021 +1000

    minor updates

CMakeLists.txt
src/RadhydroSimulation.hpp
src/test_radhydro_shell.cpp

commit 3ae3b790de333e014352d25f85055c4a32295b77
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jul 25 10:29:33 2021 +1000

    updated gitignore

.gitignore

commit 5673ab1e4fe17b49f85888075017b522255ef3a8
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jul 25 10:29:15 2021 +1000

    update radhydro shell problem

src/test_radhydro_shell.cpp

commit 3c8042c3901267fd5823c8b73f08cb56dd3dba7d
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jul 25 01:46:06 2021 +1000

    added checkpoint interval to shell test

src/test_radhydro_shell.cpp

commit e0c72e8bb8f40f333e9f01d7abd8bc7bd770d7ea
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jul 25 00:18:25 2021 +1000

    revert to first-order for radhydro shell test

src/test_radhydro_shell.cpp

commit bcfc8c1d04db9d697636643a37c0df6fcabe9193
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jul 25 00:07:58 2021 +1000

    use PLM for radhydro shell test

src/RadhydroSimulation.hpp
src/simulation.hpp
src/test_radhydro_shell.cpp

commit 18f32fa1d918b55b720bec340da83c16d262b490
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Jul 24 23:38:10 2021 +1000

    update parameters for radhydro shell test

src/test_radhydro_shell.cpp
tests/radhydro_shell.in

commit d0ee9d8aa8b85de89254174e28b424a46dcfca36
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Jul 24 23:21:45 2021 +1000

    fix radiation work term update

src/RadhydroSimulation.hpp
src/radiation_system.hpp

commit 34768c4e04cc010beac493c1a929b5bc713c145c
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Jul 24 23:10:15 2021 +1000

    update verbose message during subcycle

src/RadhydroSimulation.hpp

commit c719fcae01f5df572bfa2a3ceba5ca87ff6453b5
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Jul 24 22:54:58 2021 +1000

    add radhydro shell test

src/test_radhydro_shell.cpp
src/test_radhydro_shell.hpp
tests/radhydro_shell.in

commit 12bb18c40429ba99e03997bc6a2a3176f0dc7355
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Jul 24 22:52:59 2021 +1000

    fix radiation subcycling bug

src/CMakeLists.txt
src/RadhydroSimulation.hpp
src/hydro_system.hpp
src/radiation_system.hpp
src/test_radhydro_shock.cpp
src/test_radhydro_shock_cgs.cpp

commit 4a2a4282b95da99ffe9bfa45748728cb3864f108
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Jul 24 16:46:36 2021 +1000

    abort on invalid reconstructionOrder_

src/RadhydroSimulation.hpp

commit a1248569fe27a469cfa54b18c79ced05e75ab18f
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Jul 24 16:39:04 2021 +1000

    fix all warnings and asserts on hydro tests

CMakeLists.txt
src/CMakeLists.txt
src/RadhydroSimulation.hpp
src/hydro_system.hpp
src/simulation.hpp
src/test_advection.cpp
src/test_advection_semiellipse.cpp
src/test_hydro_leblanc.cpp
src/test_hydro_shocktube.cpp
src/test_hydro_shuosher.cpp
src/test_hydro_sms.cpp
src/test_hydro_vacuum.cpp
src/test_hydro_wave.cpp

commit 58ff0eb12818f8c99f717e621045aea7ecac08dd
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Jul 22 11:48:52 2021 +1000

    added sawtooth advection test

src/AdvectionSimulation.hpp
src/CMakeLists.txt
src/test_advection.cpp
src/test_advection_semiellipse.cpp
tests/advection_sawtooth.in

commit 6f82987b9bc6ffa10ac9ff6276d605b189416cad
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Jul 22 11:37:25 2021 +1000

    added semiellipse advection test

src/AdvectionSimulation.hpp
src/CMakeLists.txt
src/test_advection_semiellipse.cpp
tests/advection_semiellipse.in

commit 5fdcaf15851dbd40262226dd0b57665c43135872
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Jul 21 17:13:49 2021 +1000

    added dimensionless radshock test

src/CMakeLists.txt
src/test_radhydro_shock.cpp
tests/radshock_dimensionless.in

commit 4d8f0e02c0a7ff5bc754c2006c3f7908c3196e56
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Jul 21 16:05:51 2021 +1000

    added matter-radiation energy RSLA test

src/CMakeLists.txt
src/test_radiation_matter_coupling.cpp
src/test_radiation_matter_coupling_rsla.cpp
tests/MatterEnergyExchangeRSLA.in

commit e55735eaf78d965211b589f76a627ab9b0b774d0
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Jul 21 15:32:54 2021 +1000

    fixed kelvin-helmholtz test

src/CMakeLists.txt
src/test_hydro2d_kh.cpp
tests/KelvinHelmholz.in

commit a75b01fdc1e9e01040e99df0a824175aa17fdb34
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Jul 21 14:29:34 2021 +1000

    changed wording

src/RadhydroSimulation.hpp

commit 8c18ce599080db3cf04e20b13f5842e0e164e11c
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Jul 21 14:28:21 2021 +1000

    added hydro wave test

src/CMakeLists.txt
src/RadhydroSimulation.hpp
src/test_hydro_vacuum.cpp
src/test_hydro_wave.cpp
tests/hydro_wave.in

commit 1d36b0036ad6eb291e62b3662ffb9b2dc54113d6
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Jul 21 12:42:12 2021 +1000

    added hydro vacuum test

src/test_hydro_vacuum.cpp
tests/vacuum.in

commit 45d53a75560082654e121003a41275b7f33828ca
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Jul 21 12:41:52 2021 +1000

    added slow-moving shock

src/CMakeLists.txt
src/test_hydro_sms.cpp
tests/SlowMovingShock.in

commit 95cb833b0486d817f5feb5cd129dea029b09632c
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jul 20 16:58:32 2021 +1000

    re-added Shu-Osher test

src/CMakeLists.txt
src/test_hydro_shuosher.cpp
tests/ShuOsher.in

commit e5913f1869e73ebbea1a07038383abd47461fba5
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jul 20 16:09:02 2021 +1000

    added Leblanc test to CTest tests

src/CMakeLists.txt

commit d9483fd12f59a8b02cbf895c824918622c219eac
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jul 20 16:08:44 2021 +1000

    re-added Leblanc test

src/test_hydro_leblanc.cpp
tests/leblanc.in

commit 080e943d777049d88541deb93baf593551559b71
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jul 20 15:42:16 2021 +1000

    fix hydro shocktube boundary conditions

src/simulation.hpp
src/test_hydro_shocktube.cpp

commit 30ac840c36414867a3f9bdcf97b7a4208cd13ed2
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jul 20 15:25:49 2021 +1000

    re-added hydro shocktube test

src/CMakeLists.txt
src/RadhydroSimulation.hpp
src/test_hydro_shocktube.cpp
tests/shocktube.in

commit a5e132641c4a80bb87b094e5e3f7a36cfd36b20c
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jul 20 11:52:32 2021 +1000

    re-add contact wave test

src/CMakeLists.txt
src/RadhydroSimulation.hpp
src/test_hydro_contact.cpp
tests/contact_wave.in

commit c0960f8e29110fa24da5bd5855f091fe25604b4a
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jul 19 18:36:34 2021 +1000

    temporarily remove SuOlson test from CI build

src/CMakeLists.txt

commit 2f10103e5f6571e978a6a54a17419a85e7c338de
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jul 19 17:33:53 2021 +1000

    re-add MatterEnergyExchange test problem

CMakeLists.txt
src/AdvectionSimulation.hpp
src/CMakeLists.txt
src/RadhydroSimulation.hpp
src/fextract.cpp
src/radiation_system.hpp
src/simulation.hpp
src/test_radiation_matter_coupling.cpp
tests/energyexchange.in

commit 54e91a93280d5be01e3378fb212183ff6c63f1b1
Merge: aa1728b6 a9c0decb
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jul 18 14:34:33 2021 +1000

    Merge branch 'master' of github.com:BenWibking/quokka-code

commit aa1728b6d48925c66b7515fb91c480d733024fa6
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jul 18 14:34:24 2021 +1000

    added max_grid_size to input file

tests/blast_unigrid.in

commit 221c1f2224c391077e1efbce843681433991a454
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jul 18 14:33:58 2021 +1000

    fix performance metric when nranks > 1

src/simulation.hpp

commit a9c0decb54fceef3385f7389ae131c6ef4134dfd
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Jul 17 23:36:25 2021 +1000

    Update README.md

README.md

commit 973860792451458e483e02824be2367d395f9f80
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Jul 16 16:11:33 2021 +1000

    update amrex submodule

extern/amrex

commit 5ff3b228a6e4bd3a0f0fdf1f8a2fed1b0e34fb28
Merge: 2fffaaf5 6736c756
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Jul 16 16:00:38 2021 +1000

    Merge pull request #4 from BenWibking/amrcore
    
    added AMR using amrex::AmrCore

commit 6736c756c5c0f7f835f6f44ed109e1ce009d86ff
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Jul 16 15:43:16 2021 +1000

    added input files for tests

.gitignore
CMakeLists.txt
src/CMakeLists.txt
src/test_radhydro_shock_cgs.cpp
tests/beam.in
tests/blast2d.in
tests/blast_amr.in
tests/blast_amr_maxlev2.in
tests/blast_unigrid.in
tests/implosion.in
tests/radshock.in
tests/shadow.in

commit a5938b6989ff7463d97a03ede86164dd42d45dc1
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Jul 16 14:57:58 2021 +1000

    update sedov parameters

src/test_hydro3d_blast.cpp

commit 16e83c98debc8be3298a4c6562844cb938e21ed4
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Jul 16 14:19:45 2021 +1000

    new performance numbers on GPU

gpu_performance.txt
gpu_profiling.txt
gpu_profiling_unigrid.txt
src/RadhydroSimulation.hpp
src/hyperbolic_system.hpp
src/simulation.hpp
src/test_hydro3d_blast.cpp

commit d61a36df6db43970a51bdeb04a73fbbf12e128b5
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Jul 16 10:48:00 2021 +1000

    code cleanup

src/simulation.hpp
src/test_radiation_beam.cpp

commit a4fa47eb955edf2e0c79a1011a3a6c019572895e
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Jul 15 18:39:49 2021 +1000

    gpu profiling changes

gpu_profiling.txt
src/RadhydroSimulation.hpp
src/hyperbolic_system.hpp
src/simulation.hpp
src/test_hydro3d_blast.cpp

commit 274899e7ad42d4493d116dc14a35a41669d2cb99
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Jul 15 17:40:33 2021 +1000

    updated rad tests to use new opacity functions

src/radiation_system.hpp
src/test_radhydro_shock_cgs.cpp
src/test_radiation_beam.cpp
src/test_radiation_shadow.cpp

commit c277794d4775ca487154a9b120b345fcd9ec2e03
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Jul 15 17:21:56 2021 +1000

    re-ran GPU profiling on CUDA 11.4

gpu_profiling.txt

commit 2388d5510256ce1ab03abaf2370761969d0f7801
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Jul 15 15:08:47 2021 +1000

    AMR sedov test

CMakeLists.txt
gpu_errors.txt
gpu_performance.txt
gpu_profiling.txt
src/CMakeLists.txt
src/RadhydroSimulation.hpp
src/simulation.hpp
src/test_hydro2d_blast.cpp
src/test_hydro2d_rm.cpp
src/test_hydro3d_blast.cpp

commit 4814f128fcb7b8ebe21ea1d37b2e2d7739a780a2
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jul 13 18:14:47 2021 +1000

    added AMR gpu performance metrics

gpu_performance.txt
src/simulation.hpp
src/test_hydro2d_blast.cpp

commit cfd250f83ac68c0f038523dc6915dd75fb09bf66
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jul 13 17:19:57 2021 +1000

    GPU fix for expandFluxArrays

src/RadhydroSimulation.hpp
src/simulation.hpp
src/test_hydro2d_blast.cpp

commit 83bbd4179b7af2fc5ea7f0a28c534ee2b3e8f434
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jul 13 16:44:20 2021 +1000

    added AMR shadow test; re-added unigrid radshock test

src/.clang-format
src/AdvectionSimulation.hpp
src/CMakeLists.txt
src/RadhydroSimulation.hpp
src/fextract.cpp
src/fextract.hpp
src/simulation.hpp
src/test_radhydro_shock_cgs.cpp
src/test_radiation_shadow.cpp

commit 79e664cd1bad0167e5c9ca189ae53ce899909e11
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jul 12 17:57:07 2021 +1000

    added AMR radiation beam test

src/CMakeLists.txt
src/RadhydroSimulation.hpp
src/radiation_system.hpp
src/simulation.hpp
src/test_radiation_beam.cpp

commit 960b160a27f9fd36d7056437d7208e9bc0815b1f
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jul 12 16:11:25 2021 +1000

    blast2d AMR fixes

CMakeLists.txt
src/RadhydroSimulation.hpp
src/hydro_system.hpp
src/simulation.hpp
src/test_hydro2d_blast.cpp

commit 1099d7d00080558dcad148ee1a78abcee840dbaa
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jul 12 14:36:20 2021 +1000

    added changes from AMRAdvect

default.in
src/AdvectionSimulation.hpp
src/simulation.hpp
src/test_advection2d.cpp
src/test_advection2d.hpp

commit b1ccb2c6fb0a718eff863489af3f3e1fb75db87d
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Jul 8 16:19:27 2021 +1000

    fix tNew_, tOld_ when not using subcycling

src/AdvectionSimulation.hpp
src/simulation.hpp

commit cc133d5fd4f3bb561a5a35388df59f71f78f78c1
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Jul 8 16:00:55 2021 +1000

    add global timestep AMR advance

CMakeLists.txt
default.in
src/AdvectionSimulation.hpp
src/RadhydroSimulation.hpp
src/linear_advection.hpp
src/simulation.hpp
src/test_advection2d.cpp
src/test_hydro2d_blast.cpp

commit b8f59bae9cadba4bd3f03fb8a91855a1570178bf
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jul 6 00:01:27 2021 +1000

    various AMR fixes

src/RadhydroSimulation.hpp
src/simulation.hpp
src/test_hydro2d_blast.cpp

commit 16cb4b8513b6defe280a7fde456794878e0a001e
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jul 5 17:39:43 2021 +1000

    add curvature refinement on density

src/RadhydroSimulation.hpp

commit 0adab6d5b93456d4fccc22c6a0274ea6e16aea99
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jul 5 17:05:29 2021 +1000

    infrastructure for AMR hydro

src/CMakeLists.txt
src/RadhydroSimulation.hpp
src/simulation.hpp
src/test_hydro2d_blast.cpp

commit 7f48336b0d15883ad1406fddf086890917cc5ad2
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jul 5 15:40:32 2021 +1000

    add incrementFluxRegisters to AMRSimulation

src/AdvectionSimulation.hpp
src/simulation.hpp

commit 7bb481c4c4bb264dc701b30c398a80394ea5b4ba
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jul 5 11:43:57 2021 +1000

    turn off verbose amr.v

default.in

commit 038a0a5717560863a368eda8fcc6db2d1f101ad5
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jul 5 11:33:15 2021 +1000

    get rid of Sborder, just fill new state directly

src/AdvectionSimulation.hpp

commit a2d62591386bb83b934e621029e28cc91b955dfe
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jul 4 20:47:34 2021 +1000

    fixes for gpu in refluxing

src/AdvectionSimulation.hpp
src/simulation.hpp

commit db1e8adfb02313c81c0ad154df56387179ff4361
Merge: dd0210ae a13bd70d
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jul 4 12:32:54 2021 +1000

    Merge branch 'amrlevel' of github.com:BenWibking/TwoMomentRad into amrlevel

commit dd0210ae4bd2fba24f52182d23fd941937049bd4
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jul 4 12:32:41 2021 +1000

    fix AMR reflux

default.in
src/AdvectionSimulation.hpp
src/simulation.hpp

commit a13bd70dc9699b0c0014aae88d5831ea0804e03c
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Jul 3 22:15:40 2021 +1000

    added comment

src/simulation.hpp

commit effaac6a71e9b157eacabe494e10d67abbb6b9b6
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Jul 3 21:51:41 2021 +1000

    Update README.md (again)

README.md

commit c82de12981f33ef3b55c43f19226e130074c63b0
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Jul 3 21:48:10 2021 +1000

    Update README.md

README.md

commit d10c38310ba7b77a890532faaa6f146ace77c02e
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Jul 3 18:17:57 2021 +1000

    disable reflux (not working)

default.in
src/AdvectionSimulation.hpp
src/hyperbolic_system.hpp
src/simulation.hpp

commit 1f78d3389944d625799d313357a017e0076a7061
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Jul 3 12:30:08 2021 +1000

    use static_assert

src/test_advection2d.cpp

commit 39fd6369fb2bd6fd58dadf80ad221360403edcee
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Jul 3 12:26:11 2021 +1000

    use default max_grid_size

default.in

commit 00c97c22c41e2b9c1791e0939fe69f05fdbe9d69
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Jul 3 12:15:50 2021 +1000

    working advection with AmrCore

default.in
src/AdvectionSimulation.hpp
src/simulation.hpp

commit c5047b3a282206f05a40687752f94dc2e86f5a4b
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Jul 2 20:17:42 2021 +1000

    not-yet-working AMR advection

CMakeLists.txt
default.in
src/AdvectionSimulation.hpp
src/CMakeLists.txt
src/RadhydroSimulation.hpp
src/main.cpp
src/simulation.hpp
src/test_advection.cpp
src/test_advection2d.cpp
src/test_advection_semiellipse.cpp
src/test_hydro_contact.cpp
src/test_radhydro_shock_cgs.cpp
src/test_radiation_SuOlson.cpp
src/test_radiation_marshak_cgs.cpp
src/test_radiation_matter_coupling.cpp

commit c964286a8dec10fa82fe8f454b4f114610c72b8f
Merge: 7e7f112b 2d3f4f68
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Jun 30 15:58:24 2021 +1000

    Merge branch 'amrlevel' of github.com:BenWibking/TwoMomentRad into amrlevel

commit 7e7f112b5f5b56384e3b1eb87c07005e10c6796e
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Jun 30 15:57:58 2021 +1000

    cleanup code; use AMRSimulation base class

src/AdvectionSimulation.hpp
src/CheckNaN.hpp
src/RadhydroSimulation.hpp
src/math_impl.hpp
src/simulation.hpp
src/test_advection.cpp
src/test_advection2d.cpp
src/test_advection_semiellipse.cpp
src/test_hydro2d_blast.cpp
src/test_hydro2d_kh.cpp
src/test_hydro2d_rm.cpp
src/test_hydro3d_blast.cpp
src/test_hydro_contact.cpp
src/test_radhydro_shock_cgs.cpp
src/test_radiation_SuOlson.cpp
src/test_radiation_beam.cpp
src/test_radiation_box.cpp
src/test_radiation_marshak_cgs.cpp
src/test_radiation_shadow.cpp
src/test_radiation_tophat.cpp

commit 2d3f4f68d663649fb03f283591485419a24f2993
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Jun 29 20:56:33 2021 +1000

    Update sonar-project.properties

sonar-project.properties

commit 642f3f0976a78478124f94910c66465dd73b2a9a
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jun 29 17:37:32 2021 +1000

    use problem_main()

src/CMakeLists.txt
src/main.cpp
src/main.hpp
src/test_advection.cpp
src/test_advection2d.cpp
src/test_advection_semiellipse.cpp
src/test_hydro2d_blast.cpp
src/test_hydro2d_kh.cpp
src/test_hydro2d_rm.cpp
src/test_hydro3d_blast.cpp
src/test_hydro_contact.cpp
src/test_radhydro_shock_cgs.cpp
src/test_radhydro_shock_cgs.hpp
src/test_radiation_SuOlson.cpp
src/test_radiation_beam.cpp
src/test_radiation_box.cpp
src/test_radiation_marshak_cgs.cpp
src/test_radiation_matter_coupling.cpp
src/test_radiation_shadow.cpp
src/test_radiation_tophat.cpp

commit 2fffaaf520dcd64b77feb8b01d8c69c383d51240
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jun 29 14:57:55 2021 +1000

    compare radshock to exact solution and add to CI

src/CMakeLists.txt
src/test_radhydro_shock_cgs.cpp
tests/test2d.inputs

commit 9f8dc7cb72b86246d2e875ca631a9caee1ba26a3
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jun 29 13:10:27 2021 +1000

    remove HydroSimulation class (use RadhydroSimulation instead)

src/HydroSimulation.cpp
src/HydroSimulation.hpp
src/Make.package
src/RadhydroSimulation.hpp
src/main.cpp
src/test_hydro2d_blast.cpp
src/test_hydro2d_kh.cpp
src/test_hydro2d_rm.cpp
src/test_hydro3d_blast.cpp
src/test_hydro_contact.cpp

commit fdd15df9a287f143c4d900b82a7a66f12392f0f4
Merge: 30e63222 0c6946dc
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Jun 28 19:54:39 2021 +1000

    Merge pull request #2 from BenWibking/kernels-refactor
    
    Refactor kernels to use AMReX abstractions

commit 0c6946dca79c642e746bb97ccfde3b780e725216
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Jun 28 19:34:33 2021 +1000

    added ccache dep to CI

.github/workflows/cmake.yml

commit 4941acb4f0d33987cac2531cb08f8c4f3c363ca7
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jun 28 18:37:55 2021 +1000

    gpu fixes

src/test_radhydro_shock_cgs.cpp

commit 83f850708f8844acf368d525fe831cceeed43775
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jun 28 18:22:59 2021 +1000

    added radshock test

CMakeLists.txt
src/CMakeLists.txt
src/test_radhydro_shock_cgs.cpp
src/test_radhydro_shock_cgs.hpp
src/test_radiation_marshak_cgs.cpp

commit 3989e43bccbe19bd7dcb17928bb8b986f0c3a732
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jun 28 16:56:24 2021 +1000

    use ccache by default

CMakeLists.txt

commit a3f3473b856b14b33e75f9f2a6289d1c29f9789e
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jun 28 16:41:31 2021 +1000

    combine HydroSimulation and RadiationSimulation into RadhydroSimulation class

src/RadhydroSimulation.cpp
src/RadhydroSimulation.hpp
src/RadiationSimulation.cpp
src/hydro_system.hpp
src/test_hydro_contact.cpp
src/test_radiation_SuOlson.cpp
src/test_radiation_SuOlson.hpp
src/test_radiation_beam.cpp
src/test_radiation_beam.hpp
src/test_radiation_box.cpp
src/test_radiation_box.hpp
src/test_radiation_marshak_cgs.cpp
src/test_radiation_marshak_cgs.hpp
src/test_radiation_matter_coupling.cpp
src/test_radiation_shadow.cpp
src/test_radiation_shadow.hpp
src/test_radiation_tophat.cpp
src/test_radiation_tophat.hpp

commit 7629ebd6332e07d44e50c7b2fec9fd89cc75799d
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jun 28 14:46:15 2021 +1000

    added flux correction to second stage RK2

src/radiation_system.hpp

commit ec522391c2179c2708d44a0f29e2e44e3d6fd2e4
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Jun 25 16:37:33 2021 +1000

    working (possibly) 3D radiation

gpu_performance.txt
src/radiation_system.hpp

commit 4753deb3e96a47d0ac0ca4a0229c3794981db03d
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Jun 25 16:18:04 2021 +1000

    update beam test parameters

CMakeLists.txt
gpu_performance.txt
src/test_radiation_beam.cpp

commit cd2ad31a862bb83eea54ecea4d42633b4efafa75
Merge: 481792cd 87b70031
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Jun 25 15:19:44 2021 +1000

    Merge branch 'bugfix-radiation-plotfile' into kernels-refactor

commit 87b70031a8f311a352baea03dc98e0e5af8fc18f
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Jun 25 15:10:27 2021 +1000

    bugfix for RadiationSimulation plotfile (wrong ordering)

extern/amrex
src/RadiationSimulation.hpp
src/radiation_system.hpp
src/test_radiation_beam.cpp

commit 481792cd07d0321f86b8c8410edd374936084755
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Jun 25 11:14:40 2021 +1000

    use default max_grid_size

CMakeLists.txt
gpu_performance.txt
src/simulation.hpp

commit 4678028699a6de60447e5da88ee860c09d5624e7
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Jun 24 16:33:40 2021 +1000

    updated amrex submodule (fixes clang build failure)

extern/amrex

commit 4f0c9327225a567485bd857952e0285b60ba6b25
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Jun 24 14:12:38 2021 +1000

    fixes for radiation on gpu

src/radiation_system.hpp
src/simulation.hpp
src/test_advection2d.cpp
src/test_hydro2d_rm.cpp
src/test_radiation_beam.cpp
src/test_radiation_shadow.cpp
src/test_radiation_tophat.cpp

commit 7a077935672bbb401f9bd3a87bc2d8f8fc98d9a7
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Jun 24 13:11:24 2021 +1000

    nvcc bug workaround in radiation code

src/radiation_system.hpp

commit bf77d31db4e6e045817478bdc7633f41729f8c50
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Jun 23 17:23:14 2021 +1000

    added function attribute to disable FMA on gcc/x86_64

src/hyperbolic_system.hpp

commit 33276f2444f5c6372ab86e421659842083d8be83
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Jun 23 13:58:02 2021 +1000

    various fixes for radiation code on GPU; cleanup

src/RadiationSimulation.hpp
src/radiation_system.hpp
src/simulation.hpp
src/test_advection_semiellipse.cpp

commit 5e04d4445a063e010e6ee6c48e434f59b59414c6
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Jun 23 13:36:49 2021 +1000

    update amrex submodule

extern/amrex

commit 0116f6987da5504cc14c38a2f19a27b0068acd68
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jun 22 17:06:52 2021 +1000

    delete meaningless const

CMakeLists.txt
src/RadiationSimulation.hpp

commit c0816b117233f8f66392ca0e924cce4134ca13cd
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jun 22 17:03:58 2021 +1000

    switch order of hydro and radiation variables

src/RadiationSimulation.hpp
src/radiation_system.hpp
src/simulation.hpp

commit 5bf252dacc74a5100fd3ffd946a4a118adb2ed69
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jun 22 16:02:44 2021 +1000

    adjust parameters of beam test

src/RadiationSimulation.hpp
src/radiation_system.hpp
src/test_radiation_beam.cpp

commit abee99c2498455b8349f0b62588c7c8f49641804
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jun 22 14:03:16 2021 +1000

    add 2d radiation beam test

src/CMakeLists.txt
src/test_radiation_beam.cpp
src/test_radiation_beam.hpp

commit a7a8704edab29e027173e6ae655d445e19d1b1dd
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jun 22 12:36:33 2021 +1000

    change shadow test to working parameters

src/test_radiation_shadow.cpp

commit ac0f1e4dc128b90a654c444424eb7f99c6be1d67
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jun 22 12:36:03 2021 +1000

    updated sedov test for GPU benchmarking

gpu_performance.txt
src/test_hydro3d_blast.cpp

commit 060c3f748d9fd9b01939679742e4390b8fc663a8
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jun 21 19:27:43 2021 +1000

    fix ifdef bug in 3D

CMakeLists.txt
src/AdvectionSimulation.hpp
src/HydroSimulation.hpp
src/RadiationSimulation.hpp

commit 789c6f81256ad555031560da7464074b4f872ca9
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jun 21 17:50:58 2021 +1000

    attempt to fix radiation shadow with small c_v

CMakeLists.txt
src/radiation_system.hpp
src/test_radiation_shadow.cpp

commit 6619966bf146694d26f9b2be71f889412c958fe7
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jun 21 15:49:13 2021 +1000

    fix bug in stage2 of RK2 in all simulation classes; revert radiation newton solver changes

src/AdvectionSimulation.hpp
src/HydroSimulation.hpp
src/RadiationSimulation.hpp
src/radiation_system.hpp
src/simulation.hpp
src/test_advection2d.cpp

commit 7931752119f688cb755a9e4a8b0c5331895dcc8f
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Jun 19 17:32:41 2021 +1000

    only show stdout/stderr from tests if they fail

.github/workflows/cmake.yml

commit ae3ef8031c8a4cc742528dacca448e2f0626f6b3
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Jun 19 17:13:46 2021 +1000

    fix advection2d test

src/test_advection2d.cpp
src/test_advection_semiellipse.cpp

commit 268c9267920179b0f2b1562eb049ce254a4cbf99
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Jun 19 13:09:51 2021 +1000

    output plotfile for initial conditions

src/simulation.hpp
src/test_hydro3d_blast.cpp

commit 22b8e621482748948636eb33bf7ced354ddd4b31
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Jun 18 22:09:01 2021 +1000

    add GPU performance numbers for 3d hydro

gpu_performance.txt

commit 5934c0833aa11c8c7bc2d780aef4919186b6c07f
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Jun 18 22:03:30 2021 +1000

    into the third dimension!!

CMakeLists.txt
src/AdvectionSimulation.hpp
src/CMakeLists.txt
src/RadiationSimulation.hpp
src/simulation.hpp
src/test_hydro3d_blast.cpp
src/test_hydro3d_blast.hpp

commit 7d589b60d3784372e582ba5f65cfcb2888e7f46d
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Jun 18 18:53:01 2021 +1000

    added 3d hydro support; fix radiation compile error on GPU

CMakeLists.txt
src/HydroSimulation.hpp
src/RadiationSimulation.hpp
src/hyperbolic_system.hpp
src/radiation_system.hpp
src/test_hydro2d_rm.cpp
src/test_radiation_shadow.cpp

commit 58560639b834afdc7e034861d153232b552abbca
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Jun 17 10:42:02 2021 +1000

    updated README

README.md
extern/quokka.jpg
extern/quokka.png

commit 2ca6d77f53c5790f33a8beae602c37d481e84d48
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jun 15 16:59:46 2021 +1000

    added check for numerical precision

src/test_radiation_shadow.cpp

commit 3d39aef77f6659b500f1cdbc34d752e62893e864
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jun 14 16:04:24 2021 +1000

    add comment about machine precision limits

src/radiation_system.hpp
src/test_radiation_shadow.cpp

commit b0e325784216c1931deb706f84d4d6f33deb710c
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jun 14 15:04:10 2021 +1000

    fix typo in HLL solver

src/radiation_system.hpp
src/test_radiation_shadow.cpp

commit dddabcf476c62c71a4d72c3be2155958e8500d4d
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sat Jun 12 15:03:20 2021 +1000

    updated shadow test parameters

src/radiation_system.hpp
src/test_radiation_shadow.cpp

commit d7325c75d64a72732b930b3092c4a8bfee452c18
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Jun 11 17:08:37 2021 +1000

    added radiation shadow test

src/CMakeLists.txt
src/RadiationSimulation.hpp
src/radiation_system.hpp
src/test_radiation_shadow.cpp
src/test_radiation_shadow.hpp

commit cea2dcdbc2bccc1b6c8e2a470ec277c057dfa5fe
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Jun 11 11:25:37 2021 +1000

    remove extraneous comments

build/GNUmakefile
src/radiation_system.hpp
src/test_radiation_tophat.cpp

commit 3a80c7befe9670a5b76e6ee681d8b1774695b5f3
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Jun 10 17:00:48 2021 +1000

    updated tophat parameters

src/test_radiation_tophat.cpp

commit c5088a8fb2263107df3fc1dc0467249cb8a5f833
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Jun 10 16:09:15 2021 +1000

    add diffusive flux correction to radiation solver

src/radiation_system.hpp

commit 1506eeb3b0fc18839f273919ed9da996bcde7205
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Jun 10 14:59:28 2021 +1000

    add infrastructure for diffusive flux correction

src/RadiationSimulation.hpp
src/radiation_system.hpp

commit a1b4da407b023bdae57ed29f1b79efb50a7faacd
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Jun 10 13:50:22 2021 +1000

    modified classes to accomodate fluxDiffusive

src/RadiationSimulation.hpp
src/radiation_system.hpp

commit 3cb4a0cd9fad820fd362d21ca874d23ce1a71098
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Jun 9 18:06:47 2021 +1000

    change default asymptotic correction

src/RadiationSimulation.hpp
src/radiation_system.hpp

commit e2c1bcd26dfab842d8599e634d48d9885b3027de
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Jun 9 17:45:03 2021 +1000

    make radiation HLL solver less confusing

src/radiation_system.hpp

commit a0e99d91ee99e4942369ca3058d1d001509d75a9
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Jun 9 17:22:23 2021 +1000

    reduce resolution of tophat to test asymptotic preservation

CMakeLists.txt
src/radiation_system.hpp
src/test_radiation_tophat.cpp

commit e9211f4190eb7eb0ffec406d32474bd0353ab54f
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Jun 9 15:25:18 2021 +1000

    add GNUmakefile

build/GNUmakefile
src/Make.package

commit 665cfc4d271af706d027edd4e27fbd39acff89ca
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Jun 9 15:12:54 2021 +1000

    fix CUDA compile

src/HydroSimulation.hpp
src/RadiationSimulation.hpp
src/hydro_system.hpp
src/test_hydro2d_kh.cpp
src/test_hydro2d_kh.hpp

commit c5c55ce9561cc36c029d00dd6add4c169e3f0550
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jun 8 16:26:43 2021 +1000

    use Minerbo closure for tophat test

src/test_radiation_tophat.cpp

commit 2a8299cba782f2a9b6d49ce42141ff9b40cd109e
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jun 8 15:53:34 2021 +1000

    do not output as much

src/test_radiation_tophat.cpp

commit 66d7f16c22babed9a91647f8a63f6f7bcb5ed174
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jun 8 14:00:24 2021 +1000

    fix bug introduced in initialization of RadEnergySource in previous commit

gpu_performance.txt
src/RadiationSimulation.hpp
src/radiation_system.hpp
src/test_hydro2d_rm.cpp
src/test_radiation_box.cpp

commit 704189b89b9184c6e865d2a1519d91be0cc2fed9
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jun 8 11:13:28 2021 +1000

    added comment about fused multiply-add on GPU

CMakeLists.txt

commit 153297af1b49e77c5938054337ac1c187bc3e748
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jun 8 11:11:09 2021 +1000

    various fixes for CUDA

CMakeLists.txt
src/test_advection2d.cpp
src/test_hydro2d_rm.cpp
src/test_radiation_SuOlson.cpp

commit 4055c9fb1719f4f16fabd22d9f8dc4e6419bd51c
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jun 7 23:44:17 2021 +1000

    added /very preliminary/ performance comparisons

gpu_performance.txt

commit 0c788663196a6c4bd184c1d0e718a10dfc345d06
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jun 7 22:21:54 2021 +1000

    increased max timestep limit for implosion problem

src/test_hydro2d_rm.cpp

commit 1c8193db6e1d29bdf86aa58a2f881a848b7dce0f
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jun 7 17:40:56 2021 +1000

    cleanup rm test

src/HydroSimulation.hpp
src/simulation.hpp
src/test_hydro2d_rm.cpp

commit 51c7a81f5232e65667d45f0e28529892d6578a56
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jun 7 17:22:11 2021 +1000

    fix asymmetry caused by shock flattening

src/HydroSimulation.hpp
src/hydro_system.hpp
src/test_hydro2d_rm.cpp

commit faab5bdd62ef7f753e5bea65c1052d1b0127faea
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jun 7 15:25:57 2021 +1000

    add symmetry check to hydro2d_rm

src/test_hydro2d_rm.cpp

commit 52499ddedfb62bc60f8c7e01e29b1c1c526eba93
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jun 7 15:25:22 2021 +1000

    remove constexpr from opacity functions

src/radiation_system.hpp
src/test_radiation_SuOlson.cpp
src/test_radiation_box.cpp
src/test_radiation_marshak_cgs.cpp
src/test_radiation_matter_coupling.cpp
src/test_radiation_tophat.cpp

commit 1608a417a383c723401f3d1b952a802e4aaa8ce2
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jun 7 15:24:58 2021 +1000

    fix asymmetry in HyperbolicSystem RK2 integrator

src/AdvectionSimulation.hpp
src/hyperbolic_system.hpp
src/simulation.hpp
src/test_advection2d.cpp

commit fd21257789c78ce13aaa2fcdf078475dbc8d6345
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Jun 7 09:48:45 2021 +1000

    make opacity functions constexpr

src/test_radiation_marshak_cgs.cpp
src/test_radiation_matter_coupling.cpp

commit 2956739dc1216194d21ad63c002654a99d31268c
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun Jun 6 20:43:31 2021 +1000

    change opacity functions to constexpr

src/test_radiation_tophat.cpp

commit c75eac807b0ed972a6573457bf33eabcddcabbdb
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun Jun 6 20:42:31 2021 +1000

    use ParallelForRNG when generating random numbers

src/test_hydro2d_kh.cpp

commit 7fcf15dadd5d38b4c052c29bc704f32d50c0e958
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun Jun 6 18:10:52 2021 +1000

    various changes so radiation solver will compile for GPU

src/CMakeLists.txt
src/RadiationSimulation.hpp
src/radiation_system.hpp
src/test_hydro2d_kh.cpp
src/test_radiation_SuOlson.cpp
src/test_radiation_box.cpp

commit 0e4f0a0aaf4c47f4f027bbce3195a4cfc33e0a56
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun Jun 6 10:12:38 2021 +1000

    always assert when symmetry not preserved in advection2d

src/test_advection2d.cpp

commit b757b0b66b44ffeab263bff49ba4828ec2b6bdf7
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun Jun 6 10:03:27 2021 +1000

    update to latest amrex

extern/amrex

commit f2e0124d6c01441b2e4bcb28be09599f73f55692
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Jun 4 16:30:21 2021 +1000

    tweak advection2d test settings

CMakeLists.txt
src/AdvectionSimulation.hpp
src/test_advection2d.cpp

commit 5f453681bd9255e1e90cf01404b480a9b1faf00a
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri Jun 4 15:43:53 2021 +1000

    switch back to PPM for radiation by default

src/RadiationSimulation.hpp
src/radiation_system.hpp
src/test_radiation_tophat.cpp

commit 7d772d3299289c3462945e9c3fdd161a026bbdc5
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Jun 3 21:29:33 2021 +1000

    test tophat with first-order P1

CMakeLists.txt
src/RadiationSimulation.hpp
src/test_radiation_tophat.cpp

commit 86420557f7edbabc287fe7228d7ec1ec12ad50bb
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Jun 3 17:17:57 2021 +1000

    go back to PPM for tests; reduce timestep for advection test

src/AdvectionSimulation.hpp
src/CMakeLists.txt
src/RadiationSimulation.hpp
src/hyperbolic_system.hpp
src/radiation_system.hpp
src/test_advection.cpp
src/test_radiation_tophat.cpp

commit 93f1b6b04a5daa4d2df42c7127129ac1fb45f2df
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Jun 3 16:23:37 2021 +1000

    updated tophat test

src/test_radiation_tophat.cpp

commit d0972e256f67c4701567a36cbb8af88554dd88e9
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Jun 3 15:27:13 2021 +1000

    fix bug in radiation Riemann solver

src/AdvectionSimulation.hpp
src/HydroSimulation.hpp
src/RadiationSimulation.hpp
src/radiation_system.hpp
src/simulation.hpp
src/test_radiation_box.cpp
src/test_radiation_tophat.cpp

commit 13db41cd0d7c10373518ed22c0ffe2ae54a0fa04
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Jun 2 17:04:46 2021 +1000

    fixed boundary condition in radiation box test

src/test_radiation_box.cpp

commit b8fd5461c4210232c0c4a3742e9ea7f4d84020e9
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Jun 2 16:25:45 2021 +1000

    added radiation box symmetry test

src/CMakeLists.txt
src/radiation_system.hpp
src/test_radiation_box.cpp
src/test_radiation_box.hpp
src/test_radiation_tophat.cpp

commit e1005ce586a59783d4890c7833a019ecfb01a74c
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Jun 2 16:24:49 2021 +1000

    added 2d advection symmetry test

src/AdvectionSimulation.hpp
src/hyperbolic_system.hpp
src/test_advection2d.cpp

commit bcc933bdd024639d9944100cd2260b1d62b16821
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jun 1 17:10:48 2021 +1000

    updated gitignore

.gitignore

commit 0729504c60955b34644406f4a51f3f5d5b5073cb
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jun 1 17:10:09 2021 +1000

    use actual machine epsilon for symmetry test

src/test_advection2d.cpp

commit a84e8d75f93a1d4b6d17eeca30424af21978f492
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jun 1 16:57:43 2021 +1000

    added note to radiation HLL solver

src/radiation_system.hpp

commit b6f5a295f5d5074018fd11c74fade63db4b6a6a0
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue Jun 1 16:57:27 2021 +1000

    added 2d advection symmetry test

src/AdvectionSimulation.hpp
src/CMakeLists.txt
src/test_advection.cpp
src/test_advection2d.cpp
src/test_advection2d.hpp

commit dbff36b74984f103b80c88da712a116f1d85bcb9
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Jun 1 11:51:16 2021 +1000

    switch to first-order integration for debugging

src/RadiationSimulation.hpp
src/radiation_system.hpp

commit fbd5c2a63f3dc1a428be4a11da1a85e36fa9db4d
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon May 31 09:44:14 2021 +1000

    various changes to debug tophat

src/RadiationSimulation.hpp
src/radiation_system.hpp
src/test_radiation_tophat.cpp

commit 0ca05802cc8aef788388917da84dfd114fc72785
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun May 30 22:38:40 2021 +1000

    attempt to diagnose flux-limiting issues

src/radiation_system.hpp
src/test_radiation_tophat.cpp

commit 51572e41e35e797bcf80f55a7df24b17f4f19b56
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun May 30 20:29:06 2021 +1000

    attempt to fix tophat test (again)

src/test_radiation_tophat.cpp

commit 5292e4fe6cfb3b500d38b1bc4a19f1df307b706d
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun May 30 19:45:08 2021 +1000

    attempt to fix tophat test

src/test_radiation_tophat.cpp

commit aa6a0888e415e197b9febb4d9aa55faae855eb8b
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun May 30 17:34:30 2021 +1000

    added TODO

src/test_radiation_tophat.cpp

commit a1c2527ce5695579d9ebc59bcafe3dc39a730c67
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun May 30 17:26:35 2021 +1000

    modify tophat test

src/test_radiation_tophat.cpp

commit b388d4ecdec90accc2661d5a4994ff05b1f349e7
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun May 30 16:54:03 2021 +1000

    attempt to improve boundary condition for tophat test

src/RadiationSimulation.hpp
src/simulation.hpp
src/test_radiation_tophat.cpp

commit d9fd26ac829733053c882767bc4b7c1a67ce734d
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun May 30 15:13:28 2021 +1000

    add symmetry checks for some tests; fix radiation-matter exchange in 3d

src/AdvectionSimulation.hpp
src/HydroSimulation.hpp
src/RadiationSimulation.hpp
src/radiation_system.hpp
src/simulation.hpp
src/test_hydro2d_kh.cpp
src/test_radiation_tophat.cpp

commit 1c36e196a60c7562704b47f7fef08ec564aa3a8a
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat May 29 16:05:45 2021 +1000

    added y-midplane symmetry check for tophat test

src/radiation_system.hpp
src/test_radiation_tophat.cpp

commit 0d3d4eb876d8dcb7158c1807c2068dd8211cedec
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat May 29 12:47:23 2021 +1000

    changed problem parameters for debugging

src/test_radiation_tophat.cpp

commit 62ef4176019933cd9c9afdee03ab19dcc75bbe90
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat May 29 12:42:12 2021 +1000

    partially fix boundary condition in tophat test

src/test_radiation_tophat.cpp

commit 5674669d2ffe20eb55b12fea967f5b9530e57c96
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat May 29 11:56:58 2021 +1000

    fix bugs introduced in previous commit

src/radiation_system.hpp
src/test_radiation_tophat.cpp

commit 9539bba7310362b54fa62315b23aaaa853c0fdf2
Author: Ben Wibking <ben@wibking.com>
Date:   Sat May 29 11:34:26 2021 +1000

    fix bug in radiation riemann solver

src/radiation_system.hpp

commit cfc34b16dabdace3aa90f1853a2d4f80c6fc2cc3
Author: Ben Wibking <ben@wibking.com>
Date:   Sat May 29 11:24:24 2021 +1000

    increased max grid size for perf

src/simulation.hpp

commit c47d4fa4f93992fc3495761265533f4a9aa907d9
Author: Ben Wibking <ben@wibking.com>
Date:   Sat May 29 11:23:49 2021 +1000

    added bug tracking number

src/linear_advection.hpp

commit 7536d1ea472d080597ea5e5aa2f69ffd1451cec7
Author: Ben Wibking <ben@wibking.com>
Date:   Sat May 29 11:23:36 2021 +1000

    modified radiation HLL solver for 3D

src/radiation_system.hpp

commit 7d1f6ef963da2c7cee482dbf99ac434a52422c03
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri May 28 17:52:07 2021 +1000

    added comments about 2d radiation moments

src/radiation_system.hpp

commit 7aba54ce7cac647f77ec4ee8453910843371f6d4
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri May 28 17:42:54 2021 +1000

    added tophat test problem

src/CMakeLists.txt
src/test_radiation_tophat.cpp
src/test_radiation_tophat.hpp

commit 36aba8e756d11853c43dea9f32f3847c063cd693
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri May 28 16:34:57 2021 +1000

    fix MarshakWaveCGS test in 2D

CMakeLists.txt
src/simulation.hpp
src/test_radiation_marshak_cgs.cpp

commit 84968f31a6389494951052e930dbaf1f1582685f
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri May 28 16:21:28 2021 +1000

    fix radiation-matter coupling test

src/test_radiation_marshak_cgs.cpp
src/test_radiation_matter_coupling.cpp

commit dc6c75a4c6716c34201b7316e9bc61a4c5e90721
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri May 28 16:04:35 2021 +1000

    fix SuOlson and MarshakWave tests

src/CMakeLists.txt
src/RadiationSimulation.hpp
src/main.cpp
src/radiation_system.hpp
src/simulation.hpp
src/test_radiation_SuOlson.cpp
src/test_radiation_SuOlson.hpp

commit 992f6500476c5b9d72d359f75ec98611d7ef048c
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri May 28 14:48:09 2021 +1000

    add radiation-matter exchange test

src/AdvectionSimulation.hpp
src/CMakeLists.txt
src/HydroSimulation.hpp
src/RadiationSimulation.hpp
src/radiation_system.hpp
src/simulation.hpp
src/test_radiation_marshak_cgs.cpp
src/test_radiation_matter_coupling.cpp

commit 6d15df7629b00fea67cdf3196cbcbe38c0284df8
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri May 28 12:14:38 2021 +1000

    fix Marshak problem reference comparison

src/.clang-tidy
src/test_radiation_marshak_cgs.cpp

commit 20566888e29efead4a538a477f14740bcae34bdf
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri May 28 09:19:21 2021 +1000

    fix linting issues

src/test_radiation_marshak_cgs.cpp

commit df52afbe5e737ad36f3a0ecea7f845fc60e73715
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri May 28 09:16:54 2021 +1000

    remove Makefile, we are CMake-only now

CMakeLists.txt
src/Makefile

commit d4995b9f9bf6376f8cb5bfaafe969cd547987858
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri May 28 09:14:14 2021 +1000

    add comment about implicit construction of quokka::valarray

src/valarray.hpp

commit 3f264a4bdb0b2ca3cb2a46b78c8492af730c3203
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu May 27 19:23:37 2021 +1000

    fix bugs introduced in previous commit

CMakeLists.txt
src/AdvectionSimulation.hpp
src/HydroSimulation.hpp
src/RadiationSimulation.hpp
src/simulation.hpp
src/test_radiation_marshak_cgs.cpp

commit de74e59bfe67b29daab1c2ebe1e75396f5524c4e
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu May 27 17:01:20 2021 +1000

    updated marshak test problem

src/test_radiation_marshak_cgs.cpp

commit c706c1e23486795fdd289101981792bbd24c4ca2
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu May 27 16:44:15 2021 +1000

    fixed RadSystem and RadiationSimulation so they do not crash

src/AdvectionSimulation.hpp
src/CMakeLists.txt
src/HydroSimulation.hpp
src/RadiationSimulation.hpp
src/radiation_system.hpp
src/simulation.hpp
src/test_hydro2d_kh.cpp
src/test_hydro2d_rm.cpp
src/test_radiation_marshak_cgs.cpp
src/test_radiation_marshak_cgs.hpp

commit 24b02c0bb23c5db99c44d08fc151e3d9ee859da0
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed May 26 17:42:15 2021 +1000

    added 2d hydro implosion test

src/CMakeLists.txt
src/test_hydro2d_blast.cpp
src/test_hydro2d_rm.cpp
src/test_hydro2d_rm.hpp

commit c00507c94e50ab7d1982906ed9e30261c1987e87
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed May 26 17:09:26 2021 +1000

    fixed hydro boundary conditions

src/HydroSimulation.hpp
src/test_hydro2d_blast.cpp

commit 0feee36f1daa1a67cb9adc1b83fa1920644dfe2f
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed May 26 16:14:50 2021 +1000

    updated hydro 2d tests

src/test_hydro2d_blast.cpp
src/test_hydro2d_kh.cpp
src/test_hydro_contact.cpp

commit b127710e945bd83c0e429a785e9a19a6ccc93f75
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed May 26 15:11:26 2021 +1000

    change SingleLevelSimulation constructor

src/AdvectionSimulation.hpp
src/HydroSimulation.hpp
src/simulation.hpp
src/test_advection.cpp
src/test_advection_semiellipse.cpp
src/test_hydro2d_blast.cpp
src/test_hydro2d_kh.cpp
src/test_hydro_contact.cpp

commit 3da15cc7d3eea82c25f58ef4106b7a5d85b4a580
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue May 25 22:19:20 2021 +1000

    modify parameters for 2d hydro tests

src/test_hydro2d_blast.cpp
src/test_hydro2d_kh.cpp

commit 9ca05a31d75dc26a2bc8cd1bb24b2ea60b3805fc
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue May 25 22:19:01 2021 +1000

    add infrastructure for boundary conditions

src/RadiationSimulation.hpp
src/radiation_system.hpp
src/simulation.hpp

commit 7db1d6825052454c51e71d57f335fd8509bd7998
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue May 25 16:58:12 2021 +1000

    fix header error

src/simulation.cpp
src/simulation.hpp

commit cd991993e723b15c44a47cab46f755b6462fb6bc
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue May 25 16:54:07 2021 +1000

    refactored kernels for RadSystem

src/RadiationSimulation.cpp
src/RadiationSimulation.hpp
src/radiation_system.hpp
src/simulation.cpp
src/simulation.hpp
src/valarray.hpp

commit 896f05b36bce84cf0eb570f3156247c1ece32d55
Author: Ben Wibking <ben@wibking.com>
Date:   Mon May 24 21:08:07 2021 +1000

    remove 2d tests from CI

src/CMakeLists.txt

commit 9281a91d0d2a6252644f3bbced07963f959f3a0f
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon May 24 17:08:38 2021 +1000

    into the second dimension!!

CMakeLists.txt
src/CMakeLists.txt
src/diffusion.cpp
src/diffusion.hpp
src/diffusion_kernel.hpp
src/simulation.hpp
src/test_amrex_2d.cpp
src/test_hydro2d_blast.cpp
src/test_hydro2d_blast.hpp
src/test_hydro2d_kh.cpp
src/test_hydro2d_kh.hpp

commit c680c69313f87131ecb2d3c8cd612c0030929a31
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun May 23 22:05:58 2021 +1000

    use square cells

src/simulation.hpp

commit 01fdf944e9914c275945d27523f7d986ac555b6b
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun May 23 17:16:05 2021 +1000

    added TODO

src/hydro_system.hpp

commit 6f85bc5b2e93bd7dcc9b18412c53ba542e535f0e
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun May 23 17:13:10 2021 +1000

    assert -> AMREX_ASSERT

src/hydro_system.hpp

commit d18fba1cd6ccb5f6a9b8d1b3fa1ecd7e438a6400
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun May 23 17:03:57 2021 +1000

    update hydro Riemann solver for 3D

src/hydro_system.hpp
src/simulation.hpp
src/test_hydro_contact.cpp
src/valarray.hpp

commit 374524ef499a73ec73467f1e8c40a49f19280af3
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri May 21 19:44:18 2021 +1000

    max_signal_speed MultiFab only needs ncomp=1

src/simulation.hpp

commit 8900e4cc1b772687dfdcb4feec791dd39f9b0547
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri May 21 19:41:55 2021 +1000

    updated default dimensions

src/simulation.hpp

commit f987fcf5ed4cffde605393a68553632c86ad24ce
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri May 21 19:35:59 2021 +1000

    added template metaprogramming magic to HydroSystem

src/ArrayView.hpp
src/hydro_system.hpp

commit 5eaa5b64c2953518e2f81fc5bb0d3d9377fe601c
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri May 21 18:40:13 2021 +1000

    partially-working 2d hydro

src/HydroSimulation.hpp
src/hydro_system.hpp

commit 49c199052854b55ac1d0996563cffbc00fc03ee5
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri May 21 18:21:54 2021 +1000

    working 2d advection

CMakeLists.txt
src/AdvectionSimulation.hpp
src/hyperbolic_system.hpp
src/simulation.hpp
src/test_advection.cpp
src/test_advection_semiellipse.cpp

commit 920819a6ea864df30ba7b58bc222b99ea299b177
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri May 21 17:44:47 2021 +1000

    added ifdefs for 2d advections

src/AdvectionSimulation.hpp
src/HydroSimulation.hpp
src/hyperbolic_system.hpp
src/simulation.hpp

commit 2512b1c95354a6b04362c773a09333c61b85bd08
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri May 21 14:41:00 2021 +1000

    started adding support for 2D advection

src/AdvectionSimulation.hpp

commit 0c0d992f36c95591b072268366ca65649ad25d31
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri May 21 14:21:13 2021 +1000

    use Array4View in advection flux function

src/AdvectionSimulation.hpp
src/ArrayView.hpp
src/HydroSimulation.hpp
src/hyperbolic_system.hpp
src/linear_advection.hpp

commit 03d7504157a18ec64bad50e865ac3b2733298801
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri May 21 12:31:42 2021 +1000

    use std::abs

src/linear_advection.hpp

commit 89ebc780a352588220766f0a6919cf61b0b16dcd
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Fri May 21 11:29:02 2021 +1000

    fix typo in docs

docs/about.rst

commit 2bee1f2fe0fb41ba4d8c802d8ab05d53cf3e547b
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu May 20 15:01:30 2021 +1000

    added nvprof output

gpu_profiling.txt

commit a237626223d422c77d27491f6b6990c394d6e71d
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu May 20 14:44:58 2021 +1000

    workaround lambda capture compiler bug in CUDA

src/hyperbolic_system.hpp
src/linear_advection.hpp

commit 06d9dd39efccde125d404ef82d3d293457e2d58b
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed May 19 15:48:02 2021 +1000

    fix implicit lambda capture of *this in advection tests

CMakeLists.txt
gpu_errors.txt
src/simulation.hpp
src/test_advection.cpp
src/test_advection_semiellipse.cpp

commit 2534c0ba72d245917679771f6a4f0096f77b18ba
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed May 19 11:21:59 2021 +1000

    updated parameterfile

default.in
gpu_errors.txt

commit 8e13322331c155e32d4cef376bb2047f28312303
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed May 19 11:06:40 2021 +1000

    added default parameterfile for amrex

default.in

commit 1f20f57898202ec0a86d9e7aa23ad5d0ada755b7
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue May 18 17:12:57 2021 +1000

    tweak CMake settings (again)

CMakeLists.txt

commit 5c5cabce42a87b450314d10be17df3feeb8878ec
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue May 18 14:32:33 2021 +1000

    attempt to fix CMake settings (again)

CMakeLists.txt

commit ce8724b98de1c615b010dd8e2bbc820bae05d891
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue May 18 14:09:59 2021 +1000

    updated CMakeLists

CMakeLists.txt
src/CMakeLists.txt

commit 086960b892d36b99a4d5d42c5f3f1cbf10abfde4
Merge: b8650d79 ca7290df
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue May 18 13:13:44 2021 +1000

    Merge branch 'kernels-refactor' of github.com:BenWibking/TwoMomentRad into kernels-refactor

commit b8650d793aaa264a2a30f10f2dd2d53a94c92894
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Tue May 18 13:13:31 2021 +1000

    update amrex submodule

extern/amrex

commit ca7290df337f673abf8137c43acb5cb7efd5883f
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon May 17 19:43:52 2021 +1000

    cleanup valarray, ArrayView headers

src/ArrayView.hpp
src/valarray.hpp

commit 10186960698415d05889b63f0381df3c7cd93b29
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon May 17 17:09:21 2021 +1000

    switch back to cpu build for now

CMakeLists.txt
src/CMakeLists.txt

commit b8c1cd19eb2393d3583a89f886de511ebd7a4bee
Author: Benjamin Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon May 17 15:39:49 2021 +1000

    replace std::valarray with quokka::valarray

CMakeLists.txt
src/hydro_system.hpp
src/simulation.hpp
src/test_hydro_contact.cpp
src/valarray.hpp
timing.txt

commit 64a60da64866e75b8f360fe0cc855a254797be7b
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri May 7 19:34:44 2021 +1000

    fixes to get it working on GPU

src/hydro_system.hpp
src/hyperbolic_system.hpp
src/radiation_system.hpp
src/simulation.hpp
src/test_hydro_contact.cpp

commit 4a00dd73e0c371612220ed221216550754d4364a
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri May 7 11:21:29 2021 +1000

    remove ::ComputeMass function

src/linear_advection.hpp

commit f3cff3fe734420ef69ed44c6b3b2b6e7bf16616b
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu May 6 09:06:36 2021 +1000

    update minimum CMake version

CMakeLists.txt

commit fa7d791f3e9e21b32e43450c5bcee1ba4984f8ba
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed May 5 11:23:50 2021 +1000

    restructure CMakeLists.txt

CMakeLists.txt

commit ae130147ca4726e3df578d2e6f00e68d36968ed4
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue May 4 12:23:38 2021 +1000

    restructure CMakeLists.txt

CMakeLists.txt
src/CMakeLists.txt

commit 318447b29c5aefbccf1f898fca4cb5eda3d56500
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Apr 26 16:17:11 2021 +1000

    attempt to compile with AMRex CUDA support

CMakeLists.txt
extern/amrex
src/CMakeLists.txt

commit 00c74b4312e3852f99af0513ecac826786c9669a
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Apr 19 15:23:56 2021 +1000

    updated amrex submodule

extern/amrex

commit 1943304b0027916ca8ed5eae6b0769733a110412
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Mar 22 11:48:00 2021 +1100

    remove commented code from radshock.py

extern/LowrieEdwards/radshock.py

commit dc3368161321353c40a88acfd625a1329e0cdf91
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Mar 22 11:45:58 2021 +1100

    updated amrex submodule

extern/amrex

commit b446242bdd59e3f0b8eda7f1ddfbd8b2d58b9aba
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Mar 16 21:58:22 2021 +1100

    re-enabled shock flattening

src/HydroSimulation.hpp
src/simulation.hpp

commit fd793c33d78566daf8fed67ebba0f3c2d43cef74
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Mar 16 15:44:51 2021 +1100

    continue refactor

src/test_hydro_contact.cpp
src/test_hydro_wave.cpp

commit bfddaf9d55a20b4b2293b5c0ae9dce66e1f7983c
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Mar 16 12:07:52 2021 +1100

    fix plotting for hydroContact test

src/test_hydro_contact.cpp

commit 674864dadf1819e914951ec6b90f123b21fe8b54
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Mar 16 10:47:52 2021 +1100

    updated amrex submodule

extern/amrex

commit 7d28f50e5c6ff122cff9c3e1ef2f5caa8ba827dd
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Mar 15 18:54:12 2021 +1100

    revert simulation.hpp

src/HydroSimulation.hpp
src/simulation.hpp

commit 3a81af5bfcef635a318da409783942f5591687e3
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Mar 15 18:46:05 2021 +1100

    fix AMREX_SPACEDIM in CMakeLists.txt

CMakeLists.txt

commit ce614bd7b0b6a68fe0717cfe4ee03082f8c2f1a9
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Mar 15 17:21:32 2021 +1100

    attempt to debug initial conditions of HydroContact

src/simulation.hpp
src/test_hydro_contact.cpp

commit c5df806df6e0f2099540d7de3bd4486285653246
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun Mar 14 19:50:10 2021 +1100

    fix test_hydro_contact plotting

src/test_hydro_contact.cpp

commit 8d37db389cd825a2ac075007b51494b018bc290a
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun Mar 14 19:41:43 2021 +1100

    fix HydroSystem::ComputeFluxes argument order bug

src/HydroSimulation.hpp
src/hydro_system.hpp

commit a090ae13bf1270a7d66c4470c50463c882e06659
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun Mar 14 19:19:51 2021 +1100

    debug HydroSimulation

src/CMakeLists.txt
src/HydroSimulation.hpp
src/hydro_system.hpp
src/hyperbolic_system.cpp
src/hyperbolic_system.hpp
src/simulation.hpp
src/test_advection.cpp
src/test_advection_semiellipse.cpp
src/test_hydro_contact.cpp

commit 8295b98d0e313b5a4581c0a2a8008ce6998a89f0
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun Mar 14 16:49:58 2021 +1100

    export compile commands when building

CMakeLists.txt
extern/LowrieEdwards/radshock.py
src/test_advection_semiellipse.cpp

commit ff24eb3f1c86e106ddf6571f1757564db57a6c90
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Mar 12 17:49:02 2021 +1100

    continue refactor of HydroContact

src/test_hydro_contact.cpp

commit 270202c6e542c3cd4c750df7ef2f2300426d1441
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Mar 10 14:57:49 2021 +1100

    start refactor of HydroContact test

src/HydroSimulation.hpp
src/test_advection.cpp
src/test_hydro_contact.cpp
src/test_hydro_contact.hpp

commit e7c1e137ccdf7e0f5a6dd86ef460e8e8a68141ba
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Mar 10 13:53:16 2021 +1100

    compute timestep using max_signal_speed_ multifab

src/AdvectionSimulation.hpp
src/HydroSimulation.hpp
src/hydro_system.hpp
src/linear_advection.hpp
src/simulation.hpp

commit c396be2b681688158f26579ebaa478b114597df1
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Mar 9 17:08:23 2021 +1100

    add HydroSimulation class

src/HydroSimulation.cpp
src/HydroSimulation.hpp
src/hydro_system.hpp

commit 9790003b5c1095699d153d39e798daa5a9b36382
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Mar 9 15:36:59 2021 +1100

    only plot on I/O processor

src/simulation.hpp
src/test_advection.cpp
src/test_advection_semiellipse.cpp

commit 65814a23eb3ae677c16f4b159e6189e7a59d074b
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Mar 9 14:32:17 2021 +1100

    reimplement plotting of test results

src/AdvectionSimulation.hpp
src/simulation.hpp
src/test_advection.cpp
src/test_advection_semiellipse.cpp

commit 5e37d0c9c8f5ff657648968eb1287fa8e9cf264d
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Mar 9 12:28:11 2021 +1100

    move CheckNaN into simulation.hpp

src/AdvectionSimulation.hpp
src/simulation.hpp

commit 33a4de16da3875a1ce34c8008b49c92f2895ff3b
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Mar 9 12:17:18 2021 +1100

    fix PPM ghost zone issue; use 4D amrex loops

src/AdvectionSimulation.hpp
src/hyperbolic_system.hpp
src/linear_advection.hpp
src/simulation.hpp

commit 3e3693897a660418b7caa26b54db644395349f7e
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Mar 8 21:39:57 2021 +1100

    use async arena for temporary FArrayBoxes

src/AdvectionSimulation.hpp

commit 4c8d27af02e901d8f910ae8f88e68e45340f3c95
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Mar 8 21:37:04 2021 +1100

    upgraded amrex version

extern/amrex

commit 7a2f7365dcfe59009d8b4c82ac706387c1413093
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Mar 8 20:48:33 2021 +1100

    refactor test_advection.cpp

src/CMakeLists.txt
src/simulation.hpp
src/test_advection.cpp
src/test_advection_semiellipse.cpp

commit 19c1aa0907fb35071553948cee9021bfbc0d24c6
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Mar 8 19:20:43 2021 +1100

    increase resolution for AdvectionSimulation test

src/AdvectionSimulation.hpp
src/simulation.hpp

commit 6692635f0b2377d36f4f542a9611b6c7b6521d13
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Mar 8 19:11:51 2021 +1100

    fix cell/node-centered issues (for now)

CMakeLists.txt
src/AdvectionSimulation.hpp
src/CMakeLists.txt
src/linear_advection.hpp
src/simulation.hpp
src/test_advection_semiellipse.cpp

commit 811fd3808444420ec6fea1bc4ddb2d9cf6d1b449
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Mar 8 15:23:22 2021 +1100

    remove comment

src/AdvectionSimulation.hpp

commit b5233e0911f1926493d2f85cd6d8684931091ce2
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Mar 8 15:22:14 2021 +1100

    fix out-of-bounds array access

src/AdvectionSimulation.hpp
src/simulation.hpp
src/test_advection_semiellipse.cpp

commit d48ec2084c57af411dd218e504182eee1c0f05e6
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun Mar 7 21:14:12 2021 +1100

    use amrex::ParallelFor

src/AdvectionSimulation.hpp
src/hyperbolic_system.hpp
src/linear_advection.hpp
src/simulation.hpp
src/test_advection_semiellipse.cpp

commit d3427b6b56204a59c0c8f23d1aca21ac91c05dcd
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun Mar 7 00:26:43 2021 +1100

    fix const correctness in AdvectionSimulation

src/AdvectionSimulation.hpp
src/hyperbolic_system.hpp
src/linear_advection.hpp
src/simulation.hpp

commit 2fc2008da1ec0fcab3156e69cef9526c542f76d2
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Mar 6 21:39:22 2021 +1100

    continue refactor (again)

src/AdvectionSimulation.hpp
src/CMakeLists.txt
src/hyperbolic_system.cpp
src/hyperbolic_system.hpp
src/linear_advection.hpp

commit 871f99d64fe6aa73dc59afe2ae79ce29f74ef39f
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Mar 6 15:27:24 2021 +1100

    continue refactor

src/AdvectionSimulation.hpp
src/hyperbolic_system.hpp

commit bf58195a17e0cf1896f813057e20d2cbe6497352
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Mar 6 12:38:40 2021 +1100

    continue refactoring linear advection

src/AdvectionSimulation.hpp
src/hyperbolic_system.hpp
src/linear_advection.hpp
src/test_advection_semiellipse.cpp
src/test_advection_semiellipse.hpp

commit ebc78827fdea36f6615b5a3cc1c5a346aec553cf
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Mar 5 18:31:28 2021 +1100

    add timestepping routine skeleton to AdvectionSimulation

src/AdvectionSimulation.hpp
src/CMakeLists.txt
src/hyperbolic_system.hpp

commit b85e48a837c9a6f613ee16782b19fea4ef1fad62
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Mar 5 17:48:03 2021 +1100

    convert reconstruction methods to static members

src/AdvectionSimulation.hpp
src/hyperbolic_system.hpp
src/linear_advection.hpp
src/simulation.hpp

commit 30e63222ec30b068ac9449ea343c2f7f1f5d82c2
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Feb 13 11:15:52 2021 +1100

    use harmonic mean

src/radiation_system.hpp

commit d2d3f5043ee54afdec27d161b1a2dc70a071e17f
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Feb 12 15:53:08 2021 +1100

    add MarshakWaveAsymptoticDiffusion test

src/CMakeLists.txt
src/test_radiation_marshak_asymptotic.cpp

commit 46f141f829559d4039c66be93de82f8e6600c0b9
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Feb 12 15:22:32 2021 +1100

    fix asymptotic correction in HLL solver

extern/marshak_similarity.csv
src/radiation_system.hpp
src/test_radiation_marshak_asymptotic.cpp

commit b8d5c1708990312eba3e15b09eb8aff262890a9d
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Feb 9 17:11:53 2021 +1100

    actually fixed SDC2 integrator

src/hyperbolic_system.hpp
src/radiation_system.hpp
src/test_radiation_marshak_asymptotic.cpp
src/test_radiation_pulse.cpp

commit 58b590f6843dcbf17f3df1a5f79a7c418f773f95
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Feb 8 20:27:02 2021 +1100

    fixed asymptotic diffusion test problem

src/radiation_system.hpp
src/test_radiation_marshak_asymptotic.cpp

commit 6414eecbaf7104e8df79a25cc495c37ddc7acbde
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Feb 8 17:48:42 2021 +1100

    fixed SDC2 integrator

src/hyperbolic_system.hpp
src/linear_advection.hpp
src/radiation_system.hpp
src/test_radiation_marshak_asymptotic.cpp
src/test_radiation_pulse.cpp

commit 0b33fa58a5aa98325924d1fd523c406cb2179154
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun Feb 7 15:59:41 2021 +1100

    added test of static diffusion limit

src/CMakeLists.txt
src/hyperbolic_system.hpp
src/test_radiation_marshak_asymptotic.cpp
src/test_radiation_marshak_asymptotic.hpp

commit c10bd7144bd41d019ff7c9d2f08e8ea29fe23173
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Feb 1 15:13:04 2021 +1100

    add AdvectionSimulation class

src/AdvectionSimulation.cpp
src/AdvectionSimulation.hpp
src/simulation.cpp
src/simulation.hpp

commit 372c018eaa010cb554c1c2d9034918e792541f50
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Jan 29 14:07:37 2021 +1100

    add Simulation class; fix some sonarcloud warnings

src/ArrayView.hpp
src/CMakeLists.txt
src/diffusion.cpp
src/diffusion_kernel.hpp
src/hyperbolic_system.hpp
src/radiation_system.hpp
src/simulation.cpp
src/simulation.hpp
src/test_amrex_2d.cpp

commit 74aef55d5e474969ee10edbe500957c5d1cd966e
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jan 20 16:52:33 2021 +1100

    fix flux-limiting condition

src/radiation_system.hpp

commit 9fa9c1b7015917a20000ffc48c81bcab3af5fdd2
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jan 20 16:20:44 2021 +1100

    formatting

src/radiation_system.hpp

commit 8a70e23812915045c2b3b1b4abbc1652a086638a
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jan 20 16:19:26 2021 +1100

    call ComputeFirstOrderFluxes within RK2 steps; do not print flux limiting warnings

src/hyperbolic_system.hpp

commit df15fad748e0bd72898443b4fb4745a808bfc816
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jan 20 15:47:48 2021 +1100

    fix wavespeed calculation for radiation; add ComputeFirstOrderFluxes()

src/hydro_system.hpp
src/hyperbolic_system.hpp
src/linear_advection.hpp
src/radiation_system.hpp

commit 23e870f71e5e5aa1f01615048fa1cb32250d0158
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jan 20 10:06:20 2021 +1100

    add performance metrics (microseconds/zone-cycle) to shocktube

src/test_hydro_shocktube.cpp

commit ba33ccadeb4197f66d4aa3eb4c567291dcb7cf03
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jan 20 10:01:32 2021 +1100

    add performance metrics (microseconds/zone-cycle)

src/test_hydro_wave.cpp

commit 594e1909649ddaeb1011af3bd28f284ce949896e
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Jan 19 17:45:21 2021 +1100

    clang-format and clang-tidy fixes

src/hyperbolic_system.hpp
src/radiation_system.hpp
src/test_radiation_pulse.cpp

commit a770b38aea11726804c6dfc4ee5b12390c17bc1e
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Jan 19 16:55:38 2021 +1100

    use SDC integrator for radiation pulse test

src/CMakeLists.txt
src/hyperbolic_system.hpp
src/radiation_system.hpp
src/test_radiation_pulse.cpp

commit 382f3483a3051b258f22573216c578e35b67180c
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Jan 18 19:16:12 2021 +1100

    add compile_commands.json

compile_commands.json
src/test_radiation_streaming.cpp

commit 1416bce54f4ec401f598c7e0f9b04a2407921d14
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Jan 18 17:49:02 2021 +1100

    fix heat diffusion example; use templated flux function

CMakeLists.txt
src/ArrayView.hpp
src/diffusion.cpp
src/diffusion_kernel.hpp

commit b9d7437381c6e003a7eb6281bee7dceb69ae7a92
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Jan 18 16:10:50 2021 +1100

    add heat diffusion example

src/ArrayView.hpp
src/CMakeLists.txt
src/diffusion.cpp
src/diffusion.hpp
src/diffusion_kernel.hpp
src/test_amrex_2d.cpp
tests/test2d.inputs

commit 85a1cda9e82d319f66c3d61ee4ed89ca52993c72
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Jan 15 15:46:15 2021 +1100

    use AMREX_ASSERT_ALWAYS macros when appropriate

src/hyperbolic_system.hpp

commit f2ba57d446e8837e98cb0178d7f71af4cd04ba59
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Jan 15 15:13:44 2021 +1100

    some preparations to add SDC2 integrator

src/hyperbolic_system.hpp

commit 224c34a9d832cda50b463ffd9b459eda10e23fac
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Jan 14 15:17:27 2021 +1100

    add comment to templatedArray

src/hyperbolic_system.hpp

commit e7ca035bd80db9f0d46f98263197a061748863e7
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Jan 14 15:12:29 2021 +1100

    add infrastructure for template-based array index permutations

src/hyperbolic_system.cpp
src/hyperbolic_system.hpp

commit 06817add7d6742133f0333246fbedd24ee37c292
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Jan 14 10:43:29 2021 +1100

    cleanup CMakeLists.txt

CMakeLists.txt

commit e0126aa9fd9d7744fd7a26c47e2b4f90439dca47
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Jan 14 10:13:07 2021 +1100

    adjust codecov settings for CI

.github/workflows/cmake.yml
sonar-project.properties

commit 58145bce9e0b01ff55caf2030323d5d4ff1fe2e7
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jan 13 17:59:59 2021 +1100

    exclude tests from codecov report

.github/workflows/cmake.yml

commit 36053d0708ec282e3f8935c4070fcc990a5757cf
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jan 13 17:49:05 2021 +1100

    updated CI

.github/workflows/cmake.yml

commit 6ab253ac651c5025900a17bf433d44f22c4c46d8
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jan 13 17:30:01 2021 +1100

    upload code coverage to Sonarcloud

.github/workflows/cmake.yml
cmake/CodeCoverage.cmake
sonar-project.properties

commit 052934aff4501efe171b696dd0dea17ca6f644f5
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jan 13 16:25:29 2021 +1100

    use 2 threads for sonarcloud analysis

sonar-project.properties

commit 341dbb760a3a4188e2f9d82e479efd69f21e3b98
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jan 13 16:16:23 2021 +1100

    use amrex::Print() instead of std::cout

.gitignore
src/hydro_system.hpp
src/hyperbolic_system.hpp
src/radiation_system.hpp
src/test_advection.cpp
src/test_advection_semiellipse.cpp
src/test_hydro_contact.cpp
src/test_hydro_leblanc.cpp
src/test_hydro_shocktube.cpp
src/test_hydro_shuosher.cpp
src/test_hydro_sms.cpp
src/test_hydro_vacuum.cpp
src/test_hydro_wave.cpp
src/test_radhydro_shock.cpp
src/test_radhydro_shock_cgs.cpp
src/test_radiation_SuOlson.cpp
src/test_radiation_marshak.cpp
src/test_radiation_marshak_cgs.cpp
src/test_radiation_matter_coupling.cpp
src/test_radiation_matter_coupling_rsla.cpp
src/test_radiation_pulse.cpp
src/test_radiation_streaming.cpp

commit dc7c4a89f1a3d04c707d57b2eed75233a6081e8a
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jan 13 16:13:33 2021 +1100

    fix typo in CI config

.github/workflows/cmake.yml
sonar-project.properties
src/hyperbolic_system.hpp

commit a2449b97eb996d8cc476b23a093f00ad006f0ae9
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Jan 13 16:00:24 2021 +1100

    fix sonarscan CI

.github/workflows/cmake.yml

commit ee322fbca08fa921b6507ca214c843ebe1a53860
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jan 13 15:49:33 2021 +1100

    fix syntax error in CI

.github/workflows/cmake.yml

commit 20d6525cf216be3ee891bdb789e223a211e355b0
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jan 13 15:45:39 2021 +1100

    re-try adding sonarcloud to CI

.github/workflows/cmake.yml
sonar-project.properties

commit 7a5a05e8db6d81447db44d6e9acb1f208f379513
Merge: fc7e8004 ed66be8c
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jan 13 15:36:15 2021 +1100

    Merge branch 'master' of github.com:BenWibking/TwoMomentRad

commit fc7e800458201d462d8742a6407ad35b1b9a5409
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jan 13 15:36:06 2021 +1100

    remove sonarcloud docker image from CI

.github/workflows/cmake.yml

commit ed66be8c275e6d94175237457422702984388d67
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Wed Jan 13 15:14:08 2021 +1100

    add sonarcloud badges to README

README.md

commit 0575b6d05c4f75cbf4af24434f465eb7da214bc2
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jan 13 15:10:06 2021 +1100

    add sonarcloud analysis to CI

.github/workflows/cmake.yml
cmake/CodeCoverage.cmake
sonar-project.properties

commit 14d3342947ec74b21c8bba464b782e56700368e6
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jan 13 13:45:14 2021 +1100

    fix hydro state variable arrays

src/hydro_system.hpp
src/radiation_system.hpp

commit e79885def6b39d02eaa702934d24514660eed4b8
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Jan 12 17:57:58 2021 +1100

    use amrex data structures; eliminate kokkos dependency

.gitmodules
CMakeLists.txt
extern/kokkos
src/CMakeLists.txt
src/athena_arrays.hpp
src/hydro_system.hpp
src/hyperbolic_system.cpp
src/hyperbolic_system.hpp
src/linear_advection.hpp
src/main.cpp
src/radiation_system.hpp
src/test_advection.cpp
src/test_advection.hpp
src/test_advection_semiellipse.cpp
src/test_advection_semiellipse.hpp
src/test_hydro_contact.cpp
src/test_hydro_contact.hpp
src/test_hydro_leblanc.cpp
src/test_hydro_leblanc.hpp
src/test_hydro_shocktube.cpp
src/test_hydro_shocktube.hpp
src/test_hydro_shuosher.cpp
src/test_hydro_shuosher.hpp
src/test_hydro_sms.cpp
src/test_hydro_sms.hpp
src/test_hydro_vacuum.cpp
src/test_hydro_vacuum.hpp
src/test_hydro_wave.cpp
src/test_hydro_wave.hpp
src/test_radhydro_shock.cpp
src/test_radhydro_shock.hpp
src/test_radhydro_shock_cgs.cpp
src/test_radhydro_shock_cgs.hpp
src/test_radiation_SuOlson.cpp
src/test_radiation_SuOlson.hpp
src/test_radiation_marshak.cpp
src/test_radiation_marshak.hpp
src/test_radiation_marshak_cgs.cpp
src/test_radiation_marshak_cgs.hpp
src/test_radiation_matter_coupling.cpp
src/test_radiation_matter_coupling.hpp
src/test_radiation_matter_coupling_rsla.cpp
src/test_radiation_matter_coupling_rsla.hpp
src/test_radiation_pulse.cpp
src/test_radiation_pulse.hpp
src/test_radiation_streaming.cpp
src/test_radiation_streaming.hpp

commit c06a745046d25dd74acb067ce761081871fce59d
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Jan 12 12:13:51 2021 +1100

    add openmpi dependency

.github/workflows/cmake.yml

commit d26acdfdb5b8338de061bc16077fa7c418ef0c59
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Jan 12 10:41:45 2021 +1100

    build and link amrex

src/CMakeLists.txt
src/radiation_system.hpp

commit 5f00692507b46c15d56b474c2e9409b1b20e46fa
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Jan 11 21:56:52 2021 +1100

    use llvm-cov for code coverage

cmake/CodeCoverage.cmake
codecov.sh
src/CMakeLists.txt

commit 60c794c226e8489bb8dbe6ad2297342c7213c143
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Jan 11 20:24:10 2021 +1100

    fix dependencies

.github/workflows/cmake.yml

commit 2b35463c13d504d6fa216b03235a72da620f22b0
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Jan 11 20:20:57 2021 +1100

    fix dependencies for CI

.github/workflows/cmake.yml

commit 321a7e3f54ed983d4f0ce305d37d7d19f1893c07
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Jan 11 18:41:09 2021 +1100

    add code coverage with gcov

CMakeLists.txt
cmake/CodeCoverage.cmake
src/CMakeLists.txt

commit 61ff39be6c0d76e1e93e7f63f0df178981f41ae8
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun Jan 10 12:38:14 2021 +1100

    fix build error from previous commit

src/test_hydro_sms.cpp

commit 0cf06a5a9f0b01cea12b3c43cde0c71eb9d20c42
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun Jan 10 12:24:53 2021 +1100

    added stationary contact wave test

extern/SuOlson/su_olson.f
src/CMakeLists.txt
src/test_hydro_contact.cpp
src/test_hydro_contact.hpp

commit 432cac088cd62a8f3ee5c7f478d183143cec61b0
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Jan 9 13:47:30 2021 +1100

    added reference solution for Shu-Osher test

docs/tests/hydro_shuosher.png
docs/tests/shu_osher.rst
extern/ShuOsher_athena_3c_hllc_vl.txt
src/CMakeLists.txt
src/test_hydro_shuosher.cpp

commit 0721b5ef51e38aaf9b3122a43b924bca647a0495
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Jan 8 16:30:39 2021 +1100

    added exact solution to temperature equilibrium test

docs/tests/energy_exchange.rst

commit 181ab8a59fc8465554289d5486a0ea06d06c9b42
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Jan 8 16:09:38 2021 +1100

    added semi-ellipse advection test problem

src/CMakeLists.txt
src/test_advection_semiellipse.cpp
src/test_advection_semiellipse.hpp

commit 53ab3a2d792be0ab4b5b8a77f02233dcdb528d62
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Jan 7 15:17:03 2021 +1100

    updated and add documentation for matter-energy exchange test

docs/index.rst
docs/tests/energy_exchange.rst
docs/tests/radcoupling.png
docs/tests/radcoupling_rsla.png
docs/tests/sms.rst
src/test_radiation_matter_coupling.cpp
src/test_radiation_matter_coupling_rsla.cpp

commit f4e799b0dc9cc07eae43f16935a6d66286ae98ac
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Jan 7 12:03:04 2021 +1100

    remove shock flattening from radiation equations; add radiation pulse test

src/CMakeLists.txt
src/hydro_system.hpp
src/radiation_system.hpp
src/test_radiation_pulse.cpp
src/test_radiation_streaming.cpp

commit 4ff4d14cb1435e2fb7a5831912435d8dfc94c3c2
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jan 6 17:11:13 2021 +1100

    added matter-energy exchange test when using RSLA

src/CMakeLists.txt
src/test_radiation_matter_coupling_rsla.cpp
src/test_radiation_matter_coupling_rsla.hpp

commit 6dc55529e904d98c7deaca2f73b4a3f07d62fecb
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jan 6 17:01:41 2021 +1100

    modify radiation pulse parameters

src/test_radiation_pulse.cpp

commit 6d49530cd4c70e61cb5a1cc3e31180fe672d934b
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jan 6 16:59:21 2021 +1100

    test RSLA in radiation streaming problem

src/test_radiation_streaming.cpp

commit 63e5341895d86c9b855e3e83e3fa89390c36b3f8
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jan 6 16:47:42 2021 +1100

    added radiation streaming test

src/CMakeLists.txt
src/radiation_system.hpp
src/test_radiation_streaming.cpp
src/test_radiation_streaming.hpp

commit a868384db944cde4132fde70270c73bc190aa907
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Jan 5 21:08:58 2021 +1100

    remove extraneous plot

src/test_radiation_pulse.cpp

commit bdf6546dbc6ec5826c141990b5f1c0433fea2657
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Jan 5 21:08:44 2021 +1100

    rename code

CMakeLists.txt
README.md
extern/quokka.jpg
src/CMakeLists.txt

commit cd6ddf586b45ef4202fc82908f4d6479281bd8c4
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Jan 5 17:58:17 2021 +1100

    updated documentation about HLL solver

docs/about.rst

commit 94141b2f8b43572f7403049d063c58130d06d755
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Jan 5 17:45:53 2021 +1100

    updated radiation pulse test parameters

src/test_radiation_pulse.cpp

commit d3b4ff492408811d8ea01757b63c47374d0e82f1
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Jan 4 23:11:01 2021 +1100

    more trial and error

src/radiation_system.hpp
src/test_radiation_pulse.cpp

commit 1891c0735c79561c1489a7d95f4808453eea12d6
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Jan 4 20:10:48 2021 +1100

    experimental changes to radiation diffusion pulse

src/test_radiation_pulse.cpp

commit c68e2c1bacaecd9a755563052908fcbea660fff5
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Jan 4 19:14:00 2021 +1100

    fix working dir for hydro wave test

src/CMakeLists.txt

commit 4d9b658fc3b204f08adc96d18b462a330d1a5228
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Jan 4 19:10:54 2021 +1100

    added exact Riemann solver from Toro

extern/Toro/E1RPEX.F
extern/Toro/E1RPEX.INI

commit 61c495bc2ddf127ef32af684f6947e25017f203a
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Jan 4 19:04:12 2021 +1100

    added hydro wave test

src/CMakeLists.txt
src/test_hydro_wave.cpp

commit 4e5c749f65d48f3c0908847670a17e01f5977e5d
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Jan 4 17:44:41 2021 +1100

    added near-vacuum 1-2-3 test problem

extern/Toro/e1rpex.ini
extern/Toro/e1rpex.out
extern/ppm1d/README
extern/ppm1d/ppm.dek
extern/ppm1d/ppm.f90
extern/ppm1d/results_check
src/CMakeLists.txt
src/test_hydro_vacuum.cpp
src/test_hydro_vacuum.hpp

commit 8021f60bb8c1f3a087df47a55244a330b3890834
Merge: 7471417f 3d866bc0
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Jan 4 16:23:27 2021 +1100

    Merge branch 'master' of github.com:BenWibking/TwoMomentRad

commit 7471417f27c80a6c9e119d33b71e16c37a0ac874
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Jan 4 16:23:18 2021 +1100

    increase clang-format to 100 characters per line

src/.clang-format

commit a6f4f1bfe742689093fb853c1151cc9fbb87d215
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Jan 4 16:23:03 2021 +1100

    reduced number of cells in Marshak test

src/radiation_system.hpp
src/test_radiation_marshak.cpp

commit 34ba5e4a388759a21c8b205a1b566cb131fe076d
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Jan 4 16:22:40 2021 +1100

    add HLLC solver; add slow-moving shock test + documentation; use PLM when PPM detects extrema

docs/about.rst
docs/index.rst
docs/references.bib
docs/tests/hydro_sms.png
docs/tests/sms.rst
src/CMakeLists.txt
src/hydro_system.hpp
src/hyperbolic_system.hpp
src/test_hydro_sms.cpp
src/test_hydro_sms.hpp

commit 3d866bc040d9b6788684788b5394a52a6e5749ea
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jan 4 00:29:09 2021 +1100

    fix artifact upload in CI

.github/workflows/cmake.yml

commit 1e349cc24e090e23aed79ba6d6ac2b2fb22cc262
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jan 4 00:21:21 2021 +1100

    always upload test results, even if tests fail

.github/workflows/cmake.yml

commit ea2a48311be1a9ca3e917413e2a0d1a8fc896055
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jan 4 00:14:07 2021 +1100

    retry artifacts upload

.github/workflows/cmake.yml

commit 9df9d6b0d98e9d271418a8048d9206c399532465
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Mon Jan 4 00:04:09 2021 +1100

    switch back to cloud CI

.github/workflows/cmake.yml

commit f4d7f37ce2a074a33bcc3f27a0dd1cc3f5535279
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jan 3 23:59:15 2021 +1100

    fix build artifact upload

.github/workflows/cmake.yml

commit c6bb901849a47cc79c3df9954c926be36480c957
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jan 3 23:51:54 2021 +1100

    save test results for manual inspection if needed

.github/workflows/cmake.yml

commit a23adb865ad74a9d815c2ff32e6b5fb60306c884
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jan 3 23:36:32 2021 +1100

    update CI

.github/workflows/cmake.yml

commit e4c9dc4c63e39be449aac8e6fb66d346621c4684
Merge: 5837e1fb 4e78ebb7
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun Jan 3 23:28:53 2021 +1100

    Merge branch 'master' of github.com:BenWibking/TwoMomentRad

commit 5837e1fb7a46043b4f63a3c7a61000e04ad994c3
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sun Jan 3 23:28:44 2021 +1100

    fix relative paths in test problems

src/CMakeLists.txt
src/test_hydro_leblanc.cpp
src/test_hydro_shocktube.cpp
src/test_radhydro_shock.cpp
src/test_radhydro_shock_cgs.cpp
src/test_radiation_marshak.cpp
src/test_radiation_marshak_cgs.cpp

commit 4e78ebb78d71d6b335920075aaf8de766648738b
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jan 3 23:04:56 2021 +1100

    update CI for self-hosted run

.github/workflows/cmake.yml

commit 7983eb8dcb0693cacc434e532c02b31f5c564592
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jan 3 23:02:55 2021 +1100

    fix CI action

.github/workflows/cmake.yml

commit bc9a499b003c8741bae19b510c7dbc49bd66ce31
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jan 3 23:00:04 2021 +1100

    attempt to use self-hosted CI

.github/workflows/cmake.yml

commit 1b3f7edcc0839d3dbb5e7399d680b4a459467f9e
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jan 3 17:32:53 2021 +1100

    get verbose output from ctest

.github/workflows/cmake.yml

commit f5d2ed8932d7ff6780ee2a5e96e9f4b04c6ad8bc
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jan 3 17:13:14 2021 +1100

    add dependencies to CI

.github/workflows/cmake.yml

commit 149ba45458e11f6f6a73dbb619c80e0c451169a6
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jan 3 17:09:12 2021 +1100

    specify compilers to use for CI

.github/workflows/cmake.yml

commit cbadbcd013a6bbabdc904433e6bfbf50b589cfcc
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jan 3 17:05:25 2021 +1100

    Update cmake.yml to checkout submodules

.github/workflows/cmake.yml

commit b5e401c50c9435924ecbf24144c84cdf74409ac7
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Sun Jan 3 16:17:34 2021 +1100

    Create cmake.yml

.github/workflows/cmake.yml

commit b8c9f24fd38eac6621cb61d1e47fc8c8b08cd0f4
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Jan 2 15:10:10 2021 +1100

    make description of momentum update clearer

docs/about.rst

commit c10d8863989adcd16fbb6f497020f697ec0ad33e
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Jan 2 15:07:22 2021 +1100

    added citation to Shu-Osher test

docs/references.bib
docs/tests/shu_osher.rst

commit 23c140d0aa293c238c9e1cacb0fb3823b56a4f93
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Jan 2 12:39:08 2021 +1100

    added documentation for Shu-Osher test

docs/index.rst
docs/tests/hydro_shuosher.png
docs/tests/shu_osher.rst

commit 91b6174567f548299ab35ba58a6463d92c7b4667
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Jan 2 12:11:49 2021 +1100

    edit radshock documentation

docs/tests/radshock.rst

commit 29240801675d6e110b31b9202b0a6ea344e80344
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Jan 2 12:11:30 2021 +1100

    remove extraneous file

extern/ppm1d/results
src/test_hydro_shuosher.cpp

commit e456ddbe03de11acdd305995403d5a43b889473c
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Jan 2 02:41:02 2021 +1100

    added Shu-Osher test

src/CMakeLists.txt
src/hyperbolic_system.hpp
src/test_hydro_shuosher.cpp
src/test_hydro_shuosher.hpp

commit 63858bed6cf4cd15bf3217a38208bde424fa6988
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Jan 1 20:35:25 2021 +1100

    added radiative shock test to documentation

docs/about.rst
docs/equations.rst
docs/index.rst
docs/references.bib
docs/tests/radshock.rst
docs/tests/radshock_cgs_temperature.png

commit 097a62fb1e9396dfb47d16df1c4ea97138dbe418
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Jan 1 19:40:55 2021 +1100

    fix clang-tidy warnings

src/test_advection.cpp
src/test_hydro_shocktube.cpp
src/test_radhydro_shock.cpp
src/test_radhydro_shock_cgs.cpp
src/test_radiation_SuOlson.cpp

commit 525d44212aa73c1af5d9ee0f7d7118aa3f25f40c
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Jan 1 19:15:55 2021 +1100

    implement RSLA

src/radiation_system.hpp
src/test_radhydro_shock.cpp
src/test_radhydro_shock_cgs.cpp

commit 0b1ecb36984513c4946edee4652df124a3dba9a7
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Dec 31 16:38:29 2020 +1100

    add LeBlanc test problem

extern/ppm1d/exact_leblanc.f
extern/ppm1d/leblanc.dat
src/CMakeLists.txt
src/test_hydro_leblanc.cpp
src/test_hydro_leblanc.hpp

commit a4627cbbd0888ca642ae46f4af62fe89318dd2da
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Dec 31 13:14:30 2020 +1100

    add amrex as submodule

.gitmodules
extern/amrex

commit c879d9f3891074c0825ae6776d263313b85fc960
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Dec 30 21:47:22 2020 +1100

    add text to documentation home

docs/conf.py
docs/index.rst

commit 7d1f483c8f8979bf3b50dc65d25b50d7a3eb4671
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Dec 30 21:25:43 2020 +1100

    simplify CMakeLists.txt

CMakeLists.txt
src/CMakeLists.txt

commit 52c1baf813125e3b694ecde205bfe1f6f9ee74a2
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Dec 30 21:25:14 2020 +1100

    added description of code to documentation

docs/about.rst
docs/bibliography.rst
docs/conf.py
docs/equations.rst
docs/index.rst
docs/references.bib

commit f7d45a8167e8bc615f9acf138141a46316f67d2b
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Dec 24 13:28:52 2020 +1100

    added .clang-tidy file

.gitignore
src/.clang-tidy
src/test_hydro_wave.cpp

commit 4cb44b69266829f440966107c51930baf46e229a
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Dec 7 18:06:45 2020 +1100

    fix header include guards

src/test_radiation_SuOlson.hpp
src/test_radiation_marshak_cgs.hpp
src/test_radiation_pulse.hpp

commit a8124276e5d3fe3ef0c7dacce973c3ef75e795c6
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Nov 25 16:12:05 2020 +1100

    adjust error tolerance for radhydro shock

src/radiation_system.hpp
src/test_radhydro_shock.cpp

commit a0cf2b03e720f8f8ab23458de499a099807c8bda
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Oct 31 21:13:36 2020 +1100

    add vscode workspace

vscode-workspace.code-workspace

commit e439bce7efafb1c8873e3c96862fbee802bbed26
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Oct 31 21:12:29 2020 +1100

    update names of tests; names of figures

src/CMakeLists.txt
src/test_radhydro_shock.cpp
src/test_radhydro_shock_cgs.cpp
src/test_radiation_SuOlson.cpp
src/test_radiation_SuOlson.hpp
src/test_radiation_classical_marshak.cpp
src/test_radiation_marshak.cpp
src/test_radiation_marshak.hpp

commit 2da2e1d57c968a3edfd45863b4a367073286941c
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Oct 31 17:24:46 2020 +1100

    added Marshak test in cgs units

src/test_radiation_marshak_cgs.cpp
src/test_radiation_marshak_cgs.hpp

commit 610409ad01d65c2049463919bf7eeaea31393b12
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Oct 31 17:24:21 2020 +1100

    added reference for parameters

src/test_radhydro_shock_cgs.cpp

commit ddc166ef9775d85bdf805ac49fc9827418367655
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Oct 31 16:42:40 2020 +1100

    added radshock (cgs) test problem

extern/LowrieEdwards/radshock.py
extern/LowrieEdwards/shock.txt
src/CMakeLists.txt
src/hydro_system.hpp
src/radiation_system.hpp
src/test_radhydro_shock_cgs.cpp
src/test_radhydro_shock_cgs.hpp

commit 79eb19c94b6fd425d08a9240a00457dedf0f7347
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Oct 30 19:19:23 2020 +1100

    adjust radshock test to match Skinner+ 2019

extern/LowrieEdwards/radshock.py
extern/LowrieEdwards/shock.txt
src/test_radhydro_shock.cpp

commit 792848da072450272fa2d47e26a19b996dbc761d
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Oct 30 18:21:52 2020 +1100

    use more sensible default parameters for radhydro shock test

src/test_radhydro_shock.cpp

commit 6ffb115432ba65399cbdc85544fb3e30a8979833
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Oct 30 18:16:58 2020 +1100

    use PPM stencil for Marshak boundary condition

src/test_radiation_classical_marshak.cpp

commit e12ea5d7e02bf845d3c5fadaa1c96f4113cee233
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Oct 30 15:41:02 2020 +1100

    switch to using L1 error norm

src/test_advection.cpp
src/test_radiation_marshak.cpp
src/test_radiation_matter_coupling.cpp

commit cb1216effbabf7761dcc397ec1efc760d8bb3b56
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Oct 30 15:39:51 2020 +1100

    fix timestep settings for hydro shocktube

src/test_hydro_shocktube.cpp

commit 03fb6be5455c553c865c49ac7179aa8f00680749
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Oct 30 15:39:14 2020 +1100

    added PPM flattening

src/hydro_system.hpp
src/hyperbolic_system.hpp
src/radiation_system.hpp
src/test_radiation_classical_marshak.cpp

commit 2d910069f295dbe1ee8d0627ef12391c8ce470d0
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Oct 30 15:29:34 2020 +1100

    fix classical Marshak test

src/test_radiation_classical_marshak.cpp

commit 9ddeece6e44e90c83813a56d18fca561f6230a62
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Aug 3 17:30:52 2020 +1000

    updated radhydro tests

CMakeLists.txt
extern/Equilibrium.nb
extern/LowrieEdwards/radshock.py
extern/LowrieEdwards/shock.txt
src/CMakeLists.txt
src/test_radhydro_shock.cpp
src/test_radiation_pulse.cpp

commit 1edc6d28743e371bf0c85e24a0ca82414c007630
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Jul 7 17:24:34 2020 +1000

    added radiation pulse test (not yet complete)

src/test_radiation_pulse.cpp
src/test_radiation_pulse.hpp

commit 48fe1499daffd2380fabccf20db59855c2a15442
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jul 1 16:49:19 2020 +1000

    updated radshock test and semi-analytic ODE code

.gitignore
extern/LowrieEdwards/Tmat_fig30.csv
extern/LowrieEdwards/Trad_fig30.csv
extern/LowrieEdwards/radshock.py
extern/LowrieEdwards/shock.txt
src/hydro_system.hpp
src/hyperbolic_system.hpp
src/radiation_system.hpp
src/test_radhydro_shock.cpp

commit 3c6cf54788cf92d286c2666c07af72f4a0233efd
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Jun 29 20:13:17 2020 +1000

    adjust parameters for radshock test

extern/LowrieEdwards/radshock.py
extern/LowrieEdwards/shock.txt
src/hydro_system.hpp
src/test_radhydro_shock.cpp

commit 40537a0576c0b235f2f18bc42e9bafefea3112c0
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Jun 26 14:50:54 2020 +1000

    added csv output from semi-analytic radshock code

extern/LowrieEdwards/radshock.py
extern/LowrieEdwards/shock.txt

commit b4709c76ca1a06127365528f34455768b8c208f2
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jun 24 20:26:49 2020 +1000

    clean-up semianalytic radshock code

extern/LowrieEdwards/radshock.py

commit 1d75880324c231f27bc856ed7f823e57bf718792
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jun 24 20:22:02 2020 +1000

    fixed bugs in semi-analytic radshock code

extern/LowrieEdwards/radshock.py

commit 7e098af59daf750434c84e0d630307c8904c5de2
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jun 24 16:47:43 2020 +1000

    tighten ODE integration tolerances

extern/LowrieEdwards/radshock.py

commit 2ac2b816a516c38b90d646380a7451c8b3ccb532
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jun 24 13:00:55 2020 +1000

    update shock plotting

extern/LowrieEdwards/radshock.py

commit fd0cb3926af22c5e00df9881191a383ed20715da
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jun 24 12:47:25 2020 +1000

    minor enhancements to semi-analytic shock code

extern/LowrieEdwards/radshock.py

commit 3c627930b915152cd37d54169daee6702a5cef95
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jun 24 12:16:39 2020 +1000

    updated semi-analytic radiative shock code to connect left- and right- side of solution

extern/LowrieEdwards/radshock.py

commit 203e22ee210ced016f246652dc28566fde6bb9ac
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Jun 23 18:46:33 2020 +1000

    added semi-analytic solution for radiative shock

extern/LowrieEdwards/radshock.py

commit 6bc4cb9a2f5366ab90f20aa641f4a10242f5d421
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Jun 20 01:31:05 2020 +1000

    removed advection plot

src/advection.png

commit ae3156eab432d7ab66779f663e8e6feaf0db6f83
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Jun 20 01:30:39 2020 +1000

    minor changes to test problem output formats and code comments

src/test_advection.cpp
src/test_hydro_shocktube.cpp
src/test_hydro_wave.cpp
src/test_radhydro_shock.cpp
src/test_radiation_streaming.cpp

commit dba96a66e0f4c96b8400bdaa2b1b449ba86b3933
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Jun 19 15:46:28 2020 +1000

    fix bugs in HLL hydro solver; increase artificial viscosity in shocks; increase resolution for radiative shock test problem

src/hydro_system.hpp
src/test_radhydro_shock.cpp

commit 0ee2aba081bc3ffd5c9e15c5d47505b2542910fc
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Jun 18 18:54:10 2020 +1000

    fixed (some) bugs in radhydro shock problem

src/radiation_system.hpp
src/test_radhydro_shock.cpp

commit f4dc8fc217a6ef64f35b957a411a0a1725b26397
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Jun 16 23:22:46 2020 +1000

    added hydro shock to test suite; progress on radhydro shock

src/CMakeLists.txt
src/hydro_system.hpp
src/linear_advection.cpp
src/linear_advection.hpp
src/radiation_system.hpp
src/test_advection.cpp
src/test_advection.hpp
src/test_hydro_shocktube.cpp
src/test_hydro_shocktube.hpp
src/test_hydro_wave.cpp
src/test_hydro_wave.hpp
src/test_radhydro_shock.cpp
src/test_radiation_classical_marshak.cpp
src/test_radiation_marshak.cpp

commit 5ad8a95ee1a25858d15b506ea1134d6e6a25e215
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Jun 12 17:04:44 2020 +1000

    added radhydro shock test

src/CMakeLists.txt
src/hydro_system.cpp
src/hydro_system.hpp
src/hyperbolic_system.hpp
src/radiation_system.hpp
src/test_radhydro_shock.cpp
src/test_radhydro_shock.hpp
src/test_radiation_classical_marshak.cpp
src/test_radiation_marshak.cpp
src/test_radiation_matter_coupling.cpp

commit da0d87ea82a155d68d0110d010e15844cb78f2db
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Jun 12 12:59:44 2020 +1000

    remove (broken) SDC code

src/hyperbolic_system.hpp
src/radiation_system.hpp

commit d9a4c4b2b8efd132cf730c331c45f70aaa9d116c
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Jun 12 12:47:02 2020 +1000

    added gas-radiation momentum coupling

src/radiation_system.hpp
src/test_radiation_classical_marshak.cpp

commit 9099b32f8df244b163743fde8e30564c12f5e3bc
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Jun 11 19:18:18 2020 +1000

    fully refactored opacity, heat capacity into templated member functions

src/hyperbolic_system.hpp
src/radiation_system.cpp
src/radiation_system.hpp
src/test_advection.hpp
src/test_hydro_shocktube.hpp
src/test_hydro_wave.hpp
src/test_radiation_classical_marshak.cpp
src/test_radiation_classical_marshak.hpp
src/test_radiation_marshak.cpp
src/test_radiation_marshak.hpp
src/test_radiation_matter_coupling.cpp
src/test_radiation_matter_coupling.hpp
src/test_radiation_streaming.hpp

commit af27d344ac7019307455a102ed76972175fcde33
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jun 10 23:05:26 2020 +1000

    fix Makefile for clang-tidy use

src/Makefile

commit 5b428876b49b2d470ef13cfaff830faa2f0ab3bc
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jun 10 23:04:23 2020 +1000

    compute simulation accuracy w/r/t analytic solutions for tests; restructure code to enable compile-time polymorphism for opacities, heat capacity

CMakeLists.txt
src/CMakeLists.txt
src/hyperbolic_system.hpp
src/interpolate.c
src/interpolate.h
src/radiation_system.cpp
src/radiation_system.hpp
src/test_radiation_classical_marshak.cpp
src/test_radiation_classical_marshak.hpp
src/test_radiation_marshak.cpp
src/test_radiation_marshak.hpp
src/test_radiation_matter_coupling.cpp
src/test_radiation_matter_coupling.hpp

commit b7b5380333f6ed15f1c1012f390dafc1938d575a
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Jun 10 17:26:21 2020 +1000

    added dimensionless output for SuOlson quadrature code

extern/SuOlson/100pt_tau10p0.dat
extern/SuOlson/100pt_tau1p0.dat
extern/SuOlson/su_olson2.f

commit 7e0c2a063b61358fecde8dbf1339726fa74cc8af
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Jun 9 18:27:59 2020 +1000

    updated up to use proper CMake build of fmt library

src/CMakeLists.txt
src/hydro_system.hpp
src/radiation_system.hpp
src/test_advection.hpp
src/test_hydro_shocktube.hpp
src/test_hydro_wave.hpp
src/test_radiation_classical_marshak.hpp
src/test_radiation_marshak.hpp
src/test_radiation_matter_coupling.hpp
src/test_radiation_streaming.hpp

commit a9eec4f0477afa72c7b285bf755781d701b9f4b9
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Jun 4 21:26:42 2020 +1000

    updated autodoc

.gitmodules
docs/Doxyfile
docs/about.rst
docs/conf.py
docs/index.rst
docs/installation.rst
extern/fmt

commit dcdb255461232c39e74ba5d0d634b56e5905e594
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Apr 25 18:32:33 2020 +1000

    removed dead stores

src/Makefile
src/test_radiation_classical_marshak.cpp
src/test_radiation_matter_coupling.cpp

commit 85e35bdb96ce9f20b5a3d86ffd3c7cbda60f2e3b
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Apr 25 18:14:53 2020 +1000

    moved dependencies into extern/

.gitmodules
extern/SuOlson/su_olson.f
extern/SuOlson/su_olson2.f
extern/kokkos
extern/ppm1d/README
extern/ppm1d/exact_riemann.f
extern/ppm1d/output
extern/ppm1d/ppm.dek
extern/ppm1d/ppm.f90
extern/ppm1d/results
extern/ppm1d/results_check
src/CMakeLists.txt

commit 22f375c0dee929085bfdc39b0f54423754fd2d19
Author: Ben Wibking <benwibking@gmail.com>
Date:   Sat Apr 25 18:08:31 2020 +1000

    fixed SuOlson test; changed CMake configuration

.gitignore
CMakeLists.txt
src/CMakeLists.txt
src/Makefile
src/main.cpp
src/marshak_wave.pdf
src/marshak_wave_loglog.pdf
src/radcoupling.pdf
src/radiation_system.hpp
src/test_radiation_classical_marshak.cpp
src/test_radiation_classical_marshak.hpp
src/test_radiation_marshak.cpp
src/test_radiation_matter_coupling.cpp

commit f6d8fa7e06deccf357a79b8db7247368eade77e4
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Apr 15 18:02:20 2020 +1000

    reverted to radiation-matter exchange test

src/main.cpp
src/radiation_system.hpp

commit 465c6d90fd278d909584281a0489c458c167433e
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Apr 15 16:31:28 2020 +1000

    switched to using CMake

.gitignore
src/CMakeLists.txt

commit 3b49c3032afe2f8984b690425562fa8bcd66a236
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Apr 9 19:28:27 2020 +1000

    removed NamedTypes; use template classes to allow arbitrary array classes for fields

.gitmodules
src/Makefile
src/NamedType
src/hydro_system.cpp
src/hydro_system.hpp
src/hyperbolic_system.cpp
src/hyperbolic_system.hpp
src/linear_advection.cpp
src/linear_advection.hpp
src/radiation_system.cpp
src/radiation_system.hpp
src/test_advection.cpp
src/test_advection.hpp
src/test_hydro_shocktube.cpp
src/test_hydro_wave.cpp
src/test_radiation_marshak.cpp
src/test_radiation_matter_coupling.cpp
src/test_radiation_streaming.cpp

commit 7f5068287cc0fc40c44b94067ea1a456dd0f6080
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Mar 13 16:11:22 2020 +1100

    fixed bug in reflecting boundary conditions; still a discrepancy at late times remains in Marshak test

src/marshak_wave.pdf
src/marshak_wave_loglog.pdf
src/radiation_system.cpp
src/test_radiation_marshak.cpp

commit 55f0a2556504fdfe83b702fe4996b00b01246980
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Mar 13 13:21:55 2020 +1100

    switch to using Minerbo (1978) closure

src/marshak_wave.pdf
src/marshak_wave_loglog.pdf
src/radiation_system.cpp
src/test_radiation_marshak.cpp

commit eee3595de68dc4013ab2dd22d4fbb389454e0954
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Mar 12 17:08:59 2020 +1100

    fixed several bugs in radiation solver, Marshak test problem

src/marshak_wave.pdf
src/marshak_wave_loglog.pdf
src/radiation_system.cpp
src/radiation_system.hpp
src/test_radiation_marshak.cpp
src/test_radiation_matter_coupling.cpp

commit 8adc1c814899ee7fcbb5153bf2c5370efc1cb664
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Mar 11 18:23:31 2020 +1100

    fixed wave speeds; added SDC integrator (EXPERIMENTAL)

src/hydro_system.cpp
src/hydro_system.hpp
src/hyperbolic_system.cpp
src/hyperbolic_system.hpp
src/linear_advection.cpp
src/linear_advection.hpp
src/marshak_wave.pdf
src/marshak_wave_loglog.pdf
src/radiation_system.cpp
src/radiation_system.hpp
src/test_radiation_marshak.cpp

commit d0a570b4b8b9df838c991d02172158bb58be9904
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Mar 7 16:43:10 2020 +1100

    refactored HyperbolicSystem interface for subclasses

src/hydro_system.cpp
src/hydro_system.hpp
src/linear_advection.cpp
src/linear_advection.hpp

commit 283946b9c5d3d65488423e4a61e762acd789962c
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Mar 6 18:03:17 2020 +1100

    non-working attempt at SISDC method for RadSystem

src/hyperbolic_system.cpp
src/hyperbolic_system.hpp
src/radiation_system.cpp
src/radiation_system.hpp
src/test_radiation_marshak.cpp
src/test_radiation_matter_coupling.cpp
src/test_radiation_streaming.cpp

commit 2d235c984095b19341111297e813320d122fdbb9
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Mar 5 15:27:12 2020 +1100

    clean-up problem definition for Marshak test

src/marshak_wave.pdf
src/radiation_system.cpp
src/radiation_system.hpp
src/test_radiation_marshak.cpp

commit 4e7d40e9348a131882fc6f7b97406545c62819a6
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Mar 4 12:59:43 2020 +1100

    switched to reconstruction in reduced flux F/cErad

src/hyperbolic_system.cpp
src/marshak_wave.pdf
src/radiation_system.cpp
src/radiation_system.hpp
src/test_radiation_marshak.cpp

commit d9d767c63c2a61355134a48be61c5a627735e6a2
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Mar 3 18:45:48 2020 +1100

    added Su & Olson (1997) test problem, similar to Marshak wave

src/hyperbolic_system.cpp
src/hyperbolic_system.hpp
src/main.cpp
src/marshak_wave.pdf
src/radiation_system.cpp
src/radiation_system.hpp
src/test_radiation_marshak.cpp
src/test_radiation_marshak.hpp

commit 61321c92cecc1720234f24f1f6140ca5d72c411c
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Mar 2 14:29:22 2020 +1100

    updated energy exchange convergence criterion

src/hyperbolic_system.hpp
src/radcoupling.pdf
src/radiation_system.cpp
src/test_radiation_matter_coupling.cpp

commit f272bd0823459cc9bbb5099d00b45f48ac4a2f0f
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Mar 2 14:17:06 2020 +1100

    added exact solution for radiation-matter coupling test

src/radiation_system.cpp
src/test_radiation_matter_coupling.cpp

commit 3b4db3b53e8dad7d6d5a16a3c1fa98d77f2a5aed
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Feb 28 17:38:32 2020 +1100

    added Marshak wave diffusion exact solution codes

src/su_olson.f
src/su_olson2.f

commit 4e4eb53ccb243b567246fbfd23aae874a5e0707e
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Feb 28 17:00:21 2020 +1100

    fixed sign error in Jacobian, fixed rho*kappa factors in rhs/Jacobian, adjusted parameters in test problem

src/radiation_system.cpp
src/radiation_system.hpp
src/test_radiation_matter_coupling.cpp

commit 82668e0ea1aa51b28d921a6596a5653586119732
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Feb 28 16:59:37 2020 +1100

    added xscale() and yscale() to matplotlibcpp.h

src/matplotlibcpp.h

commit 1d51f67375d2deca8e23032d15985c57fabf5541
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Feb 28 16:59:18 2020 +1100

    added new timestepping option

src/hydro_system.cpp
src/hydro_system.hpp
src/hyperbolic_system.cpp
src/hyperbolic_system.hpp
src/linear_advection.cpp
src/linear_advection.hpp

commit 163d81cfc43d6cb0abe0f9ad7292bbf57c7f4a18
Merge: ebe45e70 b7aebb46
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Feb 28 12:20:23 2020 +1100

    merged.

commit ebe45e70f8c2fe4c1b60876860e8f25283f093ee
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Feb 28 12:18:50 2020 +1100

    updates to radiation-energy update

src/radiation_system.cpp
src/radiation_system.hpp

commit b7aebb4643d27ca20475f3d97a1aa7cb1afc6689
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Feb 27 22:42:02 2020 +1100

    add convergence diagnostics to energy exchange

src/radiation_system.cpp
src/radiation_system.hpp
src/test_radiation_matter_coupling.cpp

commit 64000a8bbbf7f561dab4c7a9237c081aaafe900b
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Feb 27 22:04:18 2020 +1100

    restored header files (oops)

src/hydro_system.hpp
src/hyperbolic_system.hpp
src/linear_advection.hpp

commit b564b574513cd2e98be2f1a930fd5e757e2e0e16
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Feb 27 19:03:51 2020 +1100

    first attempt at radiation-matter energy exchange

src/hydro_system.hpp
src/hyperbolic_system.hpp
src/linear_advection.hpp
src/main.cpp
src/radiation_system.cpp
src/radiation_system.hpp
src/test_radiation_matter_coupling.cpp
src/test_radiation_matter_coupling.hpp

commit 128f007577965f912d4d8578ee542ba436390d39
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Feb 27 11:41:55 2020 +1100

    added radiation streaming test problem

src/main.cpp
src/radiation_system.cpp
src/radiation_system.hpp
src/test_radiation_streaming.cpp
src/test_radiation_streaming.hpp

commit 43dd7b32475573b5da7a3e84837ccb06abfec354
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Feb 26 16:59:42 2020 +1100

    compute radiation pressure tensor inside HLL solver

src/radiation_system.cpp
src/radiation_system.hpp

commit a47acee2ff2bab89c11d8e7c43c407a79f5c3695
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Feb 25 18:42:27 2020 +1100

    added runtime checks to radiation HLL solver

src/radiation_system.cpp

commit 42b074991b56a30f7b74ec18a5ccbb1ece5f97a3
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Feb 25 18:35:34 2020 +1100

    updated c_light, c_hat to use canonical class member naming convention

src/radiation_system.cpp
src/radiation_system.hpp

commit 4b7c42dc2e5eb5655a30818f73104c6539c91bd7
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Feb 25 18:27:25 2020 +1100

    first attempt at radiation HLL solver

src/radiation_system.cpp
src/radiation_system.hpp

commit 343e03893fd951aec92544b09ccad3572bdca56e
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Feb 25 16:20:55 2020 +1100

    modified wavespeed computation for hydro system; reduced CFL number for shocktube test

src/hydro_system.cpp
src/test_hydro_shocktube.cpp

commit bfcc92f67738657d05b39b750df0e50ea44359ab
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Feb 25 14:43:39 2020 +1100

    fixed sign error in HLL wavespeeds

src/hydro_system.cpp
src/hyperbolic_system.cpp
src/test_hydro_shocktube.cpp

commit 06b32045a762e43ece81f9aa0812a20a0f51e7cf
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Feb 24 18:55:31 2020 +1100

    modify CFL number for shocktube test

src/hyperbolic_system.cpp
src/test_hydro_shocktube.cpp
src/test_hydro_wave.cpp

commit 63e5ec2c1d4fc416f2cfd5c7af04d592f1725eb4
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Feb 24 18:44:25 2020 +1100

    make wave amplitude smaller to ensure linearity

src/hyperbolic_system.cpp
src/main.cpp
src/test_hydro_wave.cpp
src/test_hydro_wave.hpp

commit 5f5179173d69f85f582135c15dd3b13af9273eed
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Feb 24 17:47:30 2020 +1100

    moved test problems into separate files

src/main.cpp
src/test_advection.cpp
src/test_advection.hpp
src/test_hydro_shocktube.cpp
src/test_hydro_shocktube.hpp

commit e3eeefa7941a0f2922d8244c54b696c0fb110be9
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Feb 24 17:28:42 2020 +1100

    various fixes to shock_tube test

src/hyperbolic_system.cpp
src/hyperbolic_system.hpp
src/main.cpp

commit 198e25323a06b4d3a6e6601c6a94d08930e81a2b
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Feb 24 15:51:44 2020 +1100

    updated gitignore

.gitignore

commit 0be6f5b00cca199697e14c65a11507e1e0860e34
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Feb 24 15:50:43 2020 +1100

    added shock tube test; fixed bug in PLM reconstruction

src/Makefile
src/hydro_system.cpp
src/hydro_system.hpp
src/hyperbolic_system.cpp
src/hyperbolic_system.hpp
src/linear_advection.cpp
src/linear_advection.hpp
src/main.cpp

commit f35265b22ced8147369c16b715c914fb1f7d087e
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Feb 22 17:37:45 2020 +1100

    added working(?) HLL solver for hydro_system.cpp

.gitignore
.gitmodules
src/Makefile
src/fmt
src/hydro_system.cpp
src/hydro_system.hpp
src/main.cpp

commit f9315fb8289fbecc7663934742e7810ab20bbc7c
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Feb 21 19:25:52 2020 +1100

    syntax fixes for clang-tidy

src/linear_advection.cpp
src/linear_advection.hpp
src/main.cpp

commit 869e43af34b0e5641833c422c98204cdcfcf6008
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Feb 21 17:49:31 2020 +1100

    simplified HydroSystem::Hydrosystem()

src/hydro_system.cpp

commit 99e6163a30742d91c04edb1334c311cf4f8070e6
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Feb 21 17:41:56 2020 +1100

    moved all generic utility functions into HyperbolicSystem

src/Makefile
src/hydro_system.cpp
src/hydro_system.hpp
src/hyperbolic_system.cpp
src/hyperbolic_system.hpp
src/linear_advection.cpp
src/linear_advection.hpp
src/main.cpp

commit 9833ffa175f7ceab72d83d310ea93a8911cef8ae
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Feb 21 15:12:40 2020 +1100

    updated Makefile, gitignore

.gitignore
src/Makefile

commit f2baa48d2bd05ab216e83028cc3e3ae83a5f01ae
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Feb 21 15:01:34 2020 +1100

    switch to using Kokkos arrays

.gitmodules
src/Makefile
src/advection.png
src/athena_arrays.hpp
src/hydro_system.cpp
src/hydro_system.hpp
src/kokkos
src/main.cpp

commit 1ffc6b9e5fc5842ae51176be8600fe824d1d03fe
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Feb 20 17:09:47 2020 +1100

    added placeholder code for hydro equations

src/hydro_system.cpp
src/hydro_system.hpp
src/hyperbolic_system.cpp
src/hyperbolic_system.hpp
src/linear_advection.cpp
src/linear_advection.hpp

commit f4e01977fb273aa2def33511ba5e097feb14ad54
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Feb 20 16:34:33 2020 +1100

    switched to using Python 3.6 for plotting

src/Makefile

commit ac58624d8a19894fc006eeeb4be80f057449b926
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Feb 20 16:32:12 2020 +1100

    added note to self

src/linear_advection.cpp

commit d2995b7cf572799271732a31f11993a13bbe5ba1
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Feb 20 16:30:19 2020 +1100

    added shock flattening routine

src/advection.png
src/hyperbolic_system.hpp
src/linear_advection.cpp
src/linear_advection.hpp
src/main.cpp

commit fc73d739a17043d00d84c19dc73ad78368f4f302
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Feb 19 18:12:16 2020 +1100

    added TODO comment

src/linear_advection.cpp

commit abbad3d2a92d4c88e917548b122b0bb67e9d2e38
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Feb 19 17:47:06 2020 +1100

    added MC limiter, tweaks to plotting

src/advection.png
src/hyperbolic_system.hpp
src/linear_advection.cpp
src/linear_advection.hpp
src/main.cpp

commit 50dfcf626fc524fd81dfc95fd0ecfd7e54c3f1b4
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Feb 19 17:07:55 2020 +1100

    use simplified PPM formula

src/advection.png
src/linear_advection.cpp
src/main.cpp

commit f42916f177c9b7ca34871d7740a20cb0649d7d6e
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Feb 19 16:00:22 2020 +1100

    PPM now works!

src/advection.png
src/hyperbolic_system.hpp
src/linear_advection.cpp
src/linear_advection.hpp
src/main.cpp

commit 63f580487cdc7f48b49c3002ee53ee764b452bd7
Author: Ben Wibking <ben@wibking.com>
Date:   Tue Feb 18 22:25:14 2020 +1100

    attempt at adding predictor half-step

src/hyperbolic_system.hpp
src/linear_advection.cpp
src/linear_advection.hpp

commit 5b89cb5d911da0d8e907b478bdac8dce2dc149ed
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Feb 18 19:21:20 2020 +1100

    added TODO comment

src/linear_advection.cpp

commit c0d231613b275adb1fe3e3bcc17955bbf122d5bc
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Feb 18 19:10:51 2020 +1100

    rewrite extremum-checking with C++17 STL idioms

src/advection.png
src/linear_advection.cpp
src/main.cpp

commit 7a7533ddfa0a1292ccd0de3d971377020e076fcb
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Feb 18 17:55:02 2020 +1100

    added plot of initial and advected density profile; there appears to be a sign error in the PPM limiter

src/Makefile
src/advection.png
src/main.cpp
src/matplotlibcpp.h

commit d76794d319bb2fcaa23a2f29fabd8d3d8ce4f980
Author: Ben Wibking <benwibking@gmail.com>
Date:   Tue Feb 18 16:59:57 2020 +1100

    fixes for PPM reconstruction; should match Athena++ with Mignone limiter

src/hyperbolic_system.hpp
src/linear_advection.cpp
src/linear_advection.hpp
src/main.cpp

commit f648061972cfc670e37be603a637de43f0b92824
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Feb 17 21:51:33 2020 +1100

    configure clang-tidy to use C++17

src/Makefile

commit 79b83f1c44f867c67e09d71d80942de1d0bc9ad2
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Feb 17 21:51:19 2020 +1100

    bugfixes for PPM

src/linear_advection.cpp
src/main.cpp

commit 8026424304bb226dbf17ded6525c8824f2e6c951
Merge: 428b8971 99a5eff8
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Feb 17 20:59:50 2020 +1100

    merged changes to linear_advection

commit 428b89712675be39ac1fa6dc79f50223ee56fb05
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Feb 17 20:58:46 2020 +1100

    added whitespace

src/linear_advection.cpp

commit 99a5eff8713f946bb3fd5e1dcbe1ec9da29dc851
Author: Ben Wibking <benwibking@gmail.com>
Date:   Mon Feb 17 18:32:12 2020 +1100

    first attempt at PPM reconstruction for advection

src/hyperbolic_system.hpp
src/linear_advection.cpp
src/linear_advection.hpp
src/main.cpp

commit 0824c5121280e188abeefee172b9edbfa454ef98
Author: Ben Wibking <ben@wibking.com>
Date:   Sun Feb 16 15:32:54 2020 +1100

    use camelCase consistently.

src/hyperbolic_system.hpp
src/linear_advection.cpp
src/linear_advection.hpp
src/main.cpp

commit e0e462c88148fab8cc8123bd928f6158a710189e
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Feb 15 15:34:59 2020 +1100

    added placeholder function for PPM reconstruction

src/linear_advection.cpp
src/linear_advection.hpp

commit b80ae073ddb2037c5c74b3b26486d0e53ce8064c
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Feb 14 22:44:21 2020 +1100

    split reconstruction into two functions

src/hyperbolic_system.hpp
src/linear_advection.cpp
src/linear_advection.hpp

commit bf036ed82da88ca9feddcacd032a912ed4bacef5
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Feb 14 19:36:39 2020 +1100

    force-inlined minmod limiter

src/hyperbolic_system.cpp
src/hyperbolic_system.hpp

commit 5a730ec24e95fb01e1d42cdf88fa4ab065a652ce
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Feb 14 19:24:58 2020 +1100

    added template parameter for slope limiter

src/hyperbolic_system.cpp
src/hyperbolic_system.hpp
src/linear_advection.cpp
src/linear_advection.hpp

commit 83fa2d37a0dd3e57e0eb5a6a24bd2e12e4ae20c6
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Feb 14 18:45:54 2020 +1100

    added piecewise-constant reconstruction w/ minmod limiter

src/hyperbolic_system.cpp
src/hyperbolic_system.hpp
src/linear_advection.cpp
src/linear_advection.hpp

commit 881986512d5edf829507cf65a668433d8a788ae8
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Feb 14 16:02:01 2020 +1100

    added support for NamedType arguments to constructor

.gitmodules
src/NamedType
src/hyperbolic_system.hpp
src/linear_advection.cpp
src/linear_advection.hpp
src/main.cpp

commit 2f5dc1f16f1a595c5a2b1f8d044ec245cf2bbafc
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Feb 14 14:45:42 2020 +1100

    conform to canonical C++ style for class members; use initializer lists for constructors

src/hyperbolic_system.hpp
src/linear_advection.cpp
src/linear_advection.hpp
src/main.cpp

commit f2bb29b193b4bee7dd86c66e06ba739c14cda3ae
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Feb 13 17:28:45 2020 +1100

    added CFL number control to linear advection test

src/hyperbolic_system.hpp
src/linear_advection.cpp
src/linear_advection.hpp
src/main.cpp

commit a51eaf5efa1fb86420b38ee75fd4f6ad8a6bf50f
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Feb 13 17:06:38 2020 +1100

    added mass conservation check to linear advection test

src/main.cpp

commit dfa9c9a98adf48d2bdf752a636a411c7efaefdcb
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Feb 13 16:56:20 2020 +1100

    fix bug in linear advection solver

src/linear_advection.cpp
src/linear_advection.hpp

commit 1f67074bda92a54743f56f494c591d07e7af5bfa
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Feb 13 14:13:10 2020 +1100

    filter out terminal color escape sequences when compiling

src/Makefile

commit 9fe1fd4b9878fa1b3ca4f3f7c9c75dffed9a37f1
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Feb 13 14:12:51 2020 +1100

    added mass conservation check

src/linear_advection.cpp

commit 0993a8896988b7fc3ffeb860b762df6a091048a3
Merge: 391f362e b29b36b5
Author: Ben Wibking <benwibking@gmail.com>
Date:   Thu Feb 13 14:12:23 2020 +1100

    merged.

commit 391f362e90ce501343c63f023757b49365252280
Author: Ben Wibking <benjamin.wibking@anu.edu.au>
Date:   Thu Feb 13 11:14:51 2020 +1100

    updated linear advection solver

src/hyperbolic_system.hpp
src/linear_advection.cpp
src/linear_advection.hpp
src/main.cpp

commit b29b36b5b28b61376d37ba91ce655eebc25854e2
Author: Ben Wibking <ben@wibking.com>
Date:   Thu Feb 13 08:17:51 2020 +1100

    added time loop

src/main.cpp

commit a0dde5c4118eded82fe63a42e481947e15dd0f1c
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Feb 12 22:05:48 2020 +1100

    new-style function return types

src/linear_advection.hpp

commit 2f93e94f1b9ce0290d748637957b5dc1d20b86dc
Author: Ben Wibking <ben@wibking.com>
Date:   Wed Feb 12 22:05:33 2020 +1100

    added clang-analyzer to Makefile

src/Makefile

commit 35b8c30b1bc458d4df1f0371cd2adbaa501cc15d
Author: Ben Wibking <benwibking@gmail.com>
Date:   Wed Feb 12 15:48:39 2020 +1100

    added skeleton implementation of linear advection

src/Makefile
src/linear_advection.cpp
src/linear_advection.hpp
src/main.cpp

commit 460bf4fe5abed90ce439bf578af5574d0cbe9757
Author: Ben Wibking <wibking.1@astronomy.ohio-state.edu>
Date:   Mon Feb 10 22:50:11 2020 +1100

    updated readme

README.md

commit a0a55b513b5534b3eb13cf7d4ee29d14622fedac
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Feb 10 22:47:52 2020 +1100

    fix whitespace

src/linear_advection.cpp

commit 77f2d843b1245e5fdc93026f5c2619b8d3c28c82
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Feb 10 22:46:50 2020 +1100

    updated docstring for HyperbolicSystem

src/hyperbolic_system.hpp

commit 4f36377c98fd6afd5a0594e014413c8befb2e577
Author: Ben Wibking <ben@wibking.com>
Date:   Mon Feb 10 22:41:18 2020 +1100

    added new boilerplate classes

src/Makefile
src/hyperbolic_system.hpp
src/linear_advection.cpp
src/linear_advection.hpp
src/main.cpp

commit 7561302910a48489538c1897dd0c502be01351fc
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Feb 8 22:08:35 2020 +1100

    updated Makefile

src/Makefile

commit de0f126e46ce2c6a7ccc6044b2abad1056b2e2db
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Feb 8 20:45:30 2020 +1100

    added CPPLINT support

src/CPPLINT.cfg
src/Makefile

commit cffb2d152df533230fb8fbf33e06dfd5027adc33
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Feb 8 20:37:58 2020 +1100

    add static analysis to Makefile; add test code to main

src/Makefile
src/main.cpp

commit 66ccd812f7ec85c7b4a917cebc0e1a40db982da1
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Feb 8 19:30:24 2020 +1100

    add driver target to Makefile

src/Makefile
src/main.cpp

commit 23a99fcb9cdd17e9fba76477a1f3cfcd063c99b9
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Feb 8 19:23:52 2020 +1100

    more doxygen documentation

src/main.cpp

commit 55c28ca3160ac13d3787cee2b4b40111047c6209
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Feb 8 19:13:51 2020 +1100

    updated gitignore for doxygen

.gitignore

commit 6b40d034e928b6138353d3984297d7a851f93e4c
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Feb 8 19:13:18 2020 +1100

    added placeholder main() function

src/Makefile
src/athena_arrays.hpp
src/main.cpp

commit 02391d4f83ec857939c16c02a5ce5891b4305daf
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Feb 8 19:09:36 2020 +1100

    updated gitignore

.gitignore

commit 7c0cb1b11de62a1c90a5e9e11510a8e2afe5af9c
Author: Ben Wibking <ben@wibking.com>
Date:   Sat Feb 8 18:55:08 2020 +1100

    added automatic doxygen -> Sphinx layer

docs/Doxyfile
docs/Makefile
docs/conf.py
docs/index.rst

commit dc170e5d9e718b91eaead7a0367375eac95de7f1
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Feb 7 22:06:34 2020 +1100

    comment Makefile

src/Makefile

commit bf91dfded14c43f3d25be7256341363af6bf741c
Author: Ben Wibking <ben@wibking.com>
Date:   Fri Feb 7 22:04:50 2020 +1100

    updated clang-format settings

src/.clang-format
src/Makefile
src/athena_arrays.hpp

commit 5ad5219957304ab4134ff01e249d04095487c667
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Feb 7 18:08:51 2020 +1100

    added Makefile

src/Makefile

commit 4e765b91dc6805b815743920de079dbcc668f7fa
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Feb 7 18:08:06 2020 +1100

    added docs/

.gitignore
docs/Makefile
docs/conf.py
docs/index.rst

commit ac2528dd2d271783108a0584e88c49652dcac2fd
Author: Ben Wibking <benwibking@gmail.com>
Date:   Fri Feb 7 14:34:39 2020 +1100

    added AthenaArrays header

src/athena_arrays.hpp

commit 942e78974966ae0ed5fde447066c8962611d3fb2
Author: Ben Wibking <wibking.1@astronomy.ohio-state.edu>
Date:   Fri Feb 7 14:26:55 2020 +1100

    Initial commit

.gitignore
LICENSE
README.md