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`.

Commits

2e246cc JSON/TOML backend: introduce abbreviated IO modes (#1493)
c639257 TOUCH IOTask: Avoid setting files as dirty in non-write modes (#1704)
b8ce8a0 Unify Random-Access API and Streaming API into Series::snapshots() (#1592)
77a55a3 HDF5: Delete and re-create attribute when overwriting with diff. type (#1697)
1bd63c7 Properly check for empty HDF5_VERSION in CMake (#1702)
bb45720 Upgrade appleclang14 build to MacOS 13 (#1703)
1628567 Conda: Pin HDF5 to 1.14.1 in CI workflow (#1701)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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`.

Commits

73ef006 Avoid including <iostream> in library code
7470c2d emitter: Support std::string_view
8a9a7b7 Update CONTRIBUTING.md
d45c4fb Update README.md
61db897 Exclude ubuntu/C++ 11/googletest system from the test matrix since it doesn't...
7def204 Fix bazel build, and commit module lock file.
1da813f ensuring local tags are retained after loading a node + test
f878043 Don't install embedded copy of GTest
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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`.

Commits

d1e0aef Merge pull request #148 from BenWibking/delete-compressed-plotfiles
6ab39e5 remove delete exe
d76cf24 Merge pull request #150 from BenWibking/patch-1
be6d77b add bokeh to requirements.txt
e9a20b8 delete compressed plotfiles, executable
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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) Bumps [extern/fmt](https://github.com/fmtlib/fmt) from `385c01d` to `e3ddede`.

Commits

e3ddede Update version
e9ec4fd Bump version
feb7212 Readd FMT_NO_UNIQUE_ADDRESS
8d517e5 Update changelog
563fc74 Update changelog
3e04222 Restore ABI compatibility with 11.0.2
853df39 Mention compile-time formatting
11742a0 Clarify that format_string should be used instead of fstring
da24fac Document fstring
5fa4bdd Define CMake components to allow docs to be installed separately (#4276)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/fmt commit fb24ba35f6bcc5ed62b627a8fbd456e0a578409c Author: Ben Wibking 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 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) 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) 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 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 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 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 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 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 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 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 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 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 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 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 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::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 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`.

Commits

c35aad2 FFT::PoissonHybrid: Add solve() needed by ERF (#4250)
4a3a5ff Add CMake option: AMReX_CUDA_OBJDIR_AS_TEMPDIR (#4246)
1c8b545 FFT::PoissonHybrid: Support non-periodic boundaries in x & y directions (#4247)
f7f3ee9 FFT Poisson Solver: Fill ghost cells in solve() function (#4244)
12d6af2 Update GMRES Comments (#4243)
1424c86 Fix dangling-reference warnings for particle functions. (#4241)
c9546cd Parser: Use malloc if Arena is not ready (#4240)
86f31c5 Add portable implementation of random numbers drawn from the Gamma distributi...
b98eaaf Fix warning and undefined behavior (#4236)
4210fe0 Implementation of Bessel functions of second kind (yn) (#4234)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/amrex commit 8cd876f38880c141dc154ef63fe28a4e05452698 Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun Dec 1 10:48:38 2024 -0500 Bump extern/yaml-cpp from `c2bec4c` to `9ce5a25` (#800) Bumps [extern/yaml-cpp](https://github.com/jbeder/yaml-cpp) from `c2bec4c` to `9ce5a25`.

Commits

9ce5a25 fix: spell fix
ebfbf27 patch: added more defensive programming techniques
06ffaf3 remove reduntant license information
0b94541 fix: add missing include
82f3c04 fix: add YAML_CPP_API for windows-shared library builds
d8de965 patch: move dragonbox.h from 'include' folder to 'src' folder
5d9e4b6 patch: split fp_to_string.h into fptostring.h and fptostring.cpp
28c0a1b doc: add a little more information to dragonbox file
72865f7 fix: remove trailing return types
f4bca79 fix: fp_to_string uses now 2 spaces
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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) Bumps [extern/fmt](https://github.com/fmtlib/fmt) from `4b8e283` to `385c01d`.

Commits

385c01d Allow bit_cast to work for 80bit long double (#4246)
df249d8 Remove an old workaround
dfad80d Remove an old workaround
536cabd Export all range join overloads (#4239)
b1a0547 Remove more MSVC 2015 workarounds and fix string_view checks
bfd9539 Remove MSVC 2015 workaround
9ced61b Replace std::forward for clang-tidy (#4236)
75e5be6 Sort specifiers
a169d7f Fix chrono formatting syntax doc (#4235)
a6c45df Fix modular build
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/fmt commit 2f1fda0168063e71baf09ad349e0342012c414dd Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun Dec 1 10:47:42 2024 -0500 Bump extern/openPMD-api from `94a3a8f` to `269c5e2` (#803) Bumps [extern/openPMD-api](https://github.com/openPMD/openPMD-api) from `94a3a8f` to `269c5e2`.

Commits

269c5e2 Remove mpirun_workaround.sh (#1698)
d1015ee Non-spatial meshes (#1534)
4a040bb Explicitly specify ADIOS2 components in openPMDConfig.cmake (#1693)
67c95fc Take TOML out of Python testing (#1694)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/openPMD-api commit 09f158915e6a72e3bcc1c6200d680f5cb1baaa8d Author: Ben Wibking 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 `[ ]` 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 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) 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) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> .pre-commit-config.yaml commit 727f6031e894fe3003957971785046e17e542a12 Author: ChongChong He 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 _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`. src/problems/BinaryOrbitCIC/particle_orbit_plot.py commit 0ee3ebc059abc1e6a9930e53b768f02771b60dab Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon Nov 25 03:46:24 2024 +0000 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.

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v0.20.1

What's Changed

fix(split-review): search by string in names by @Nerixyz in ZedThree/clang-tidy-review#140

Full Changelog: https://github.com/ZedThree/clang-tidy-review/compare/v0.20.0...v0.20.1

Commits

e005a6d Merge pull request #140 from Nerixyz/fix/split-review
94e0056 chore: remove redundant Path(..)
74d6cb5 fix: search by string in names
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[![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=ZedThree/clang-tidy-review&package-manager=github_actions&previous-version=0.20.0&new-version=0.20.1)](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 alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) ---

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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .github/workflows/clang-tidy-comments.yml .github/workflows/clang-tidy.yml commit 83d3bf95b155a4a3cc9c9b5ac970619ffad91420 Author: Ben Wibking 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 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 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.

Release notes

Sourced from ZedThree/clang-tidy-review's releases.

v0.20.0

What's Changed

ensure diff paths are the same on all platforms by @bwrsandman in ZedThree/clang-tidy-review#130

Fix regression to cull_comments by @bwrsandman in ZedThree/clang-tidy-review#128

fix: support empty commits/PRs by @Nerixyz in ZedThree/clang-tidy-review#132

Add a run time profile report by @bwrsandman in ZedThree/clang-tidy-review#127

Use task queue to spawn multiple processes of tidy by @bwrsandman in ZedThree/clang-tidy-review#126

Fix remaining Ruff lints and (most) type errors by @Nerixyz in ZedThree/clang-tidy-review#137

Fix a bunch of ruff issues by @ZedThree in ZedThree/clang-tidy-review#133

Full Changelog: https://github.com/ZedThree/clang-tidy-review/compare/v0.19.0...v0.20.0

Commits

9539823 Merge pull request #133 from ZedThree/linting
3aea09f Use Path in more places
30fd704 Merge branch 'master' into linting
1ad1991 Merge pull request #137 from Nerixyz/chore/more-linting
87a563c fix: correct various types
5e9fb02 fix: use positional args for regex (B034)
71fa158 fix: merge with (SIM117)
afd3a85 fix: resolve PTH* lints
88d4e32 Merge pull request #126 from bwrsandman/multiprocess
02da243 Use task queue to spawn multiple processes of tidy
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[![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=ZedThree/clang-tidy-review&package-manager=github_actions&previous-version=0.19.0&new-version=0.20.0)](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 alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) ---

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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .github/workflows/clang-tidy-comments.yml .github/workflows/clang-tidy.yml commit e470861fa518d8a9d2c86d1109aa210c19449040 Author: Ben Wibking 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`.

Commits

397d3d2 Add cosmic rays to metal chemistry (#1651)
ca10c3e Update README to mention ISM chemistry (#1652)
01cc637 Correctly handle ices in metal chemistry (#1650)
1e1dc14 Remove unused param (#1648)
d98d39b Define Tdust as aux var (#1649)
3961b43 update changes for 24.09
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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) 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) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> .pre-commit-config.yaml commit 4fa830c2efac48aa56fb2083f137cba5cf07cf92 Author: ChongChong He 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 { static constexpr UnitSystem unit_system = UnitSystem::CGS; ... }; template <> struct RadSystem_Traits { 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 { 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 { 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 { // 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 { 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) Bumps [extern/amrex](https://github.com/AMReX-Codes/amrex) from `6d9c25b` to `b9d549b`.

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b9d549b Add option to do stable redistribute with GPUs (#4200)
47108f0 Fix typo in documentation of Tensor Linear Solver (#4206)
92679ba Remove HIP_INDIRECT_FUNCTION (#4199)
dc745bb Use The_Comms_Arena in particle communication. (#4175)
c060294 Refactor grid-stride loop (#4190)
8f4fbaf Fix a typo in CI build option (#4196)
0c7df10 STL optimization: Bounding volume hierarchy (#4140)
c333708 Bounded sampling (#4195)
b00c828 amrex::FFT (#4193)
62c2a81 SmallMatrix: Structured binding support (#4189)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/amrex 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) Bumps [extern/yaml-cpp](https://github.com/jbeder/yaml-cpp) from `da82fd9` to `c2bec4c`.

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c2bec4c chore(test): moved infiniteloop test to load_node_test suite.
29c59c0 new(test): added a test to avoid future issues with LoadAll().
bc67157 fix(src): avoid possible infinite loop in LoadAll().
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/yaml-cpp 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) Bumps [extern/fmt](https://github.com/fmtlib/fmt) from `c95722a` to `4b8e283`.

Commits

4b8e283 More cleanup
7d4662f Remove FMT_BUILTIN_CTZ
27110bc Minor cleanup
68f3153 Fix narrowing conversion warning in struct fstring (#4210)
168df9a Implement fmt::format_to into std::vector<char> (#4211)
4daa3d5 Fix error: cannot use 'try' with exceptions disabled in Win LLVM Clang (#4208)
e9eaa27 Add std::exception to the docs
2b6a786 Use standard context in print
a16ff57 Add support for code units > 0xFFFF in fill
601be1c Add support for code units > 0xFFFF in fill
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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) Bumps [extern/openPMD-api](https://github.com/openPMD/openPMD-api) from `d2d8f40` to `94a3a8f`.

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94a3a8f [pre-commit.ci] pre-commit autoupdate (#1687)
2a36ef8 Pickle API: Cache unpickled Series to avoid repeated file access (#1654)
de67eff Fix Leftover ADIOS1 Mentions (#1683)
757676d Add OPENPMD_PYTHON_TEST_PREFIX environment variable (#1691)
2593317 Add openPMD version 2.0 to supported API versions (#1551)
7620c47 Version 0.17.0-dev (#1689)
7abdd7c Fix ICX build (#1690)
93df9d5 PYBIND11_FINDPYTHON=ON (#1684)
9806b04 Doc: Fix Shipped Internally (#1682)
d0b5370 Fix 0.16.0 versions (#1680)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/openPMD-api commit d3e2ca29c7cc4f538fa821943427e3f357687cdb Author: Ben Wibking 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 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 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) 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) 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 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] 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) 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) 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 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 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`.

Commits

9286964 Merge pull request #11 from brittonsmith/update
737009c Remove rate coefficients testing file after transitioning test to gold standa...
7499abb Merge pull request #10 from brittonsmith/gtest
ddcc68a Remove obsolete testing answer files.
9a63dbe Merge pull request #9 from brittonsmith/issue6
ee5ff1c Add missing redshift dataset to cooling table.
5d73d81 Merge pull request #8 from brittonsmith/PR126
9084536 Update answers for PR #126.
31ec9d7 Merge pull request #5 from brittonsmith/PR97
9b4ab63 Update answers for PR #97.
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Ben Wibking extern/grackle_data_files commit 80d38c034229685931a4a1d2948ebc199f62fea3 Author: ChongChong He 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:_ - [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: 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 commit 4210608ae643dea542a5375e03eb4d657f38428a Author: Ben Wibking 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 ### 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. .ci/azure-pipelines-regression.yml commit 4f4d128e1cfb4c30a07d083d2f4b4ae754b08b42 Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue Oct 1 13:30:18 2024 +0000 Bump extern/fmt from `621e9c1` to `c95722a` (#759) Bumps [extern/fmt](https://github.com/fmtlib/fmt) from `621e9c1` to `c95722a`.

Commits

c95722a Improve naming consistency
db06b0d Use countl_zero in bigint
b9ec48d Cleanup bigint
3faf6f1 Add min_of/max_of
d64b100 Relax constexpr
ff9ee04 Fix handling FMT_BUILTIN_TYPES
1c5883b Test nondeterministic conversion to format string
cacc310 Don't assume repeated evaluation of string literal produce the same pointer
fade652 Require clang >=15 for _BitInt support (#4176)
96dca56 Module linkage fixes for shared build (#4169)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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`.

Commits

d2d8f40 Script: New Version (#1467)
88089bc CMake Superbuild: Tarball (#1668)
ff0c669 Independent writes: Make workaround more flexible (#1660)
016bb8a Allow numpy 2.0 in requirements.txt (#1669)
b40607a Python Series/Iteration: Fix Length (#1659)
dc58cc5 CMake Superbuild: Repo & Local Source (#1667)
87f30e7 Remove ThirdParty Directories (#1666)
570f155 Replace internal dependencies by FetchContent (#1583)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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`.

Commits

da82fd9 chore(test/integration): refactor some test cases to their own test.
1f2b841 fix(src,include,test): fixed multiple cases where a bad yaml was accepted.
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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) 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) --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> .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.

Release notes

Sourced from ossf/scorecard-action's releases.

v2.4.0

What's Changed

This update bumps the Scorecard version to the v5 release. For a complete list of changes, please refer to the v5.0.0 release notes. 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.

:seedling: Bump github.com/ossf/scorecard/v5 from v5.0.0-rc2 to v5.0.0 by @spencerschrock in ossf/scorecard-action#1410

:bug: lower license sarif alert threshold to 9 by @spencerschrock in ossf/scorecard-action#1411

Documentation

docs: dogfooding badge by @jkowalleck in ossf/scorecard-action#1399

New Contributors

@jkowalleck made their first contribution in ossf/scorecard-action#1399

Full Changelog: https://github.com/ossf/scorecard-action/compare/v2.3.3...v2.4.0

v2.3.3

[!NOTE]
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

What's Changed

:seedling: Bump github.com/ossf/scorecard/v4 (v4.13.1) to github.com/ossf/scorecard/v5 (v5.0.0-rc1) by @spencerschrock in ossf/scorecard-action#1366

:seedling: Bump github.com/ossf/scorecard/v5 from v5.0.0-rc1 to v5.0.0-rc2 by @spencerschrock in ossf/scorecard-action#1374

:seedling: Bump github.com/ossf/scorecard/v5 from v5.0.0-rc2 to v5.0.0-rc2.0.20240509182734-7ce860946928 by @spencerschrock in ossf/scorecard-action#1377

For a full changelist of what these include, see the v5.0.0-rc1 and v5.0.0-rc2 release notes.

Documentation

:book: Move token discussion out of main README. by @spencerschrock in ossf/scorecard-action#1279

:book: link to ossf/scorecard workflow instead of maintaining an example by @spencerschrock in ossf/scorecard-action#1352

:book: update api links to new scorecard.dev site by @spencerschrock in ossf/scorecard-action#1376

Full Changelog: https://github.com/ossf/scorecard-action/compare/v2.3.1...v2.3.3

Commits

62b2cac bump docker tag to v2.4.0 for release (#1414)
c09630c lower license score alert threshold to 9 (#1411)
cf8594c :seedling: Bump github.com/sigstore/cosign/v2 from 2.2.4 to 2.3.0 (#1413)
de5fcb9 :seedling: Bump the github-actions group with 2 updates (#1412)
a46b90b bump scorecard to v5.0.0 release (#1410)
9fc518d :seedling: Bump golang in the docker-images group (#1407)
a8eaa1b :seedling: Bump the github-actions group with 2 updates (#1408)
873d5fd :seedling: Bump the github-actions group across 1 directory with 2 updates (#...
54cc1fe :seedling: Bump the docker-images group with 2 updates (#1401)
82bcb91 :seedling: Bump golang.org/x/net from 0.26.0 to 0.27.0 (#1400)
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[![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=ossf/scorecard-action&package-manager=github_actions&previous-version=2.3.1&new-version=2.4.0)](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 alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) ---

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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .github/workflows/scorecard.yml commit bb00fce0e1a4157e39db74f014e32272befe73e9 Author: Ben Wibking 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 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 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 .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 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 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 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 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 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 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 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) Bumps [extern/amrex](https://github.com/AMReX-Codes/amrex) from `6f039ae` to `74127d6`.

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74127d6 Update CHANGES for 24.09 (#4122)
d06504a Simplify cache cleanup actions (#4121)
7c2ef81 CI: WarpX on development (#4110)
df0d594 Curl Curl Solver: Option to use PCG instead of LU (#3812)
12002e7 Support for multiple periods in FillBoundary and ParallelCopy (#4106)
b05f69f ParmParse::prettyPrintTable (#4101)
dea2432 TinyProfiler:: Add more runtime parameters (#4100)
baec46e Fix start_comp offset in tracer particle routines (#4098)
0e97bad ParmParse: queryarrWithParser (#4073)
68e3741 Add Geometry::RoundoffLo and RoundoffHi functions (#4097)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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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4789924 Merge pull request #146 from EZoni/EZoni_rm_testdir
715ea85 Rename option rm_testdir to clean_testdir
5bd6a57 Check test run, analysis, and comparison
2b047a6 Add rm_testdir option
21c052c Merge pull request #147 from EZoni/EZoni_compare_successful
088c34d Fix typo in compare_successful variable assignment
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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`.

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1c7d7ff Fix memory leak (#1662)
ff21bbc Python: Series to DataFrame (#1506)
fafdac2 Opt-in support for unknown ADIOS2 engines (#1652)
e9dd0e3 HDF5 independent flush config (#1634)
6956b01 setup.py: Transitive ZLIB Static (#1522)
443fdef Use a shared pointer to bool to check if destructor ran (#1657)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/openPMD-api commit 5a2375a7a5ba2e6045223fdf3e13b7dcc8dd7bbf Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun Sep 1 09:59:43 2024 -0400 Bump extern/fmt from `d326c72` to `621e9c1` (#727) Bumps [extern/fmt](https://github.com/fmtlib/fmt) from `d326c72` to `621e9c1`.

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621e9c1 Clarify why we have TYPE in native_formatter
bca7040 Simplify compile-time checks
8c4b17f Simplify compile-time checks
516a2e2 Cleanup FMT_STRING
6797f0c Cleanup compile-time checks
db496b4 Remove old gcc hack
8eda3c8 Cleanup compile-time check
5331690 Move string_literal to format.h
8a484ad Minor cleanup
b446cc9 fwrite_fully -> fwrite_all
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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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47cd272 Remove build debug messages
850ec4f Fix reference types in iterators
84459a7 fix: missing token enum name
ee9c4d1 fix: parse files with '\r' symbols as line ending correctly
b38ac5b Use FetchContent_MakeAvailable
7b469b4 emitterutils: Explicitly include <cstdint>
8fbf344 doc, fix: invalid liquid '{{...}}' tags
06c3d1d fix compile warning(Pull requests #1305)(Issues #1306)
04dddd6 Revert "Fix compile warning with -Wshadow"
1f5e971 Fix compile warning with -Wshadow
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/yaml-cpp commit 76eff2f67c70e6804ce86f626d56b24a648e7884 Author: ChongChong He 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:_ - [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)](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/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:_ - [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 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). - [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`. - [] I have requested a reviewer for this PR. --------- Co-authored-by: Piyush Sharda 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 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 `[ ]` 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.hpp commit 21ba4c2bdd8f552abc27f8e23fdfe029d97af57f Author: ChongChong He 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 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 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 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 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 Co-authored-by: Aditi Vijayan Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Ben Wibking Co-authored-by: Ben Wibking 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 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 .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 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 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 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`.

Commits

83ecf62 Catalyst support (#4011)
a8c5255 Fix typos in FaceDivFree interior interpolation. (#4048)
20e6f2e ParmParse: Fix assertion in new queryarr for IntVect & RealVect (#4051)
6975ae0 ParmParse: Read IntVect & RealVect from array (#4050)
80b0c7e IParser: Use long long int (#4046)
fd1633e ParmParse: Math expression support (#4032)
11d31e5 AmrData: remove dependency on Fortran (#4049)
d9dec56 Remove reliance on managed memory in HDF5 mesh IO (#4047)
3cb7f15 New Feature in MLEBNodeFDLaplacian: MultiFab sigma coefficient (#3968)
930e75e Nodal Solver: Use multi-color Gauss-Seidel on GPU (#4043)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/amrex commit 6b438504cb8653a275822004cecdfea83b15eb77 Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu Aug 1 10:49:44 2024 -0400 Bump extern/Microphysics from `a3bc246` to `24fc854` (#695) Bumps [extern/Microphysics](https://github.com/psharda/Microphysics) from `a3bc246` to `24fc854`.

Commits

24fc854 include higher taylor terms for fast_atan (#1611)
a5408ba update self-consistent NSE SDC update with Tabular NSE (#1569)
b413290 remove some more Fortran comments (#1609)
448132f remove test_nse and rename test_ase -> test_nse_net (#1610)
963ff00 remove the old test_screening (#1608)
d791e67 Remove strang nse (#1549)
4142d4f Update rhoX for nse_solver for SDC and discard strang (#1607)
0b1a231 add NSE bailout to RKC (#1544)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Piyush Sharda <34922596+psharda@users.noreply.github.com> extern/Microphysics commit 3a754c548847a4d84c02b21955f0ca0e6d5bf572 Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu Aug 1 04:36:05 2024 +0000 Bump extern/fmt from `686339f` to `d326c72` (#696) Bumps [extern/fmt](https://github.com/fmtlib/fmt) from `686339f` to `d326c72`.

Commits

d326c72 Fix conversion a surrogate pair (#4095)
6e462b8 Get rid of std::copy
aff640c Make fmt::appender implement std::output_iterator concept (#4093)
e23fb6a Apply clang-format
16b3542 Remove float_specs
29d7e58 Remove float_format
919f7c5 Reduce float_specs usage
a80d668 Diagnose invalid precision
707d7d9 Apply coding conventions
de6ed8d Test alignment
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/fmt commit d1b5764ca47f2be4e35c80c51ef22e01efe450b8 Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu Aug 1 04:13:17 2024 +0000 Bump extern/yaml-cpp from `1d8ca1f` to `b95aa14` (#692) Bumps [extern/yaml-cpp](https://github.com/jbeder/yaml-cpp) from `1d8ca1f` to `b95aa14`.

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b95aa14 fix: use C locale by default
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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`.

Commits

4f83a7e ADIOS2: Override access mode (#1638)
74fdc47 Pickle API: Avoid static Series hack, allow multiple Series (#1633)
ff6cf66 CI: macOS 11->12 (#1653)
0358d09 Compatibility with toml11 4.0 (#1645)
0fa1803 Parse lazily in linear access (#1650)
7efa3b7 Fix Conda CI (#1651)
1e3240b Add missing openPMD_HAVE_MPI guard (#1649)
5a24100 Flush target newstep (#1632)
bda3544 Performance: Flush IOHandler only once, not for each Iteration (#1642)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/openPMD-api commit e6e23a9e6fab5d8c4174b882c8feda82a32bada7 Author: Ben Wibking 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 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:_ - [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> Co-authored-by: Ben Wibking docs/citation.rst docs/references.bib commit 8d855a16461fbd926450b274f9010c7f50f05b3c Author: ChongChong He 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 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 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 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 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 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`. - [ ] I have requested a reviewer for this PR. src/radiation_system.hpp commit 4686c6ae13457126e792fde190127905491ee0f5 Author: ChongChong He 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 _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). - [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> 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 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 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:_ - [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: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> scripts/setonix-cpu.profile scripts/setonix-gpu.profile src/ShockCloud/cloud.cpp commit d719a59626ff55d65bdb1aea5cfc770e399a9220 Author: Ben Wibking 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). - [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/intel.yml commit 14469c023b4c254811e01c20a53c5866d7781ee8 Author: Ben Wibking 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 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 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:_ - [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 extern/Microphysics commit d616a63e7a483785f954682ce7ef233ba71d3464 Author: Ben Wibking 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). - [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/RadhydroSimulation.hpp commit 080145d32d3664eb99f460a3b7f919ceb85a0c8f Author: Ben Wibking 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:_ - [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/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) Bumps [extern/amrex](https://github.com/AMReX-Codes/amrex) from `a65f0a5` to `7418556`.

Commits

7418556 HDF5: Correctly handle writing only some components when writing Particle (#4...
73e46e6 HDF5: Correctly choose datatype of plotfile based on RD numBytes (#4006)
2f93525 Fix L2 norms in C_util/Convergence codes (#4009)
463bdf4 Match the dimensions of reqd_work_group_size to submitted nd_range (#4002)
27b399a GNU Make: try nvidia-smi for CUDA arch if deviceQuery fails (#3997)
259db7c Sundials Update (#3984)
adfc227 Derive: Add MultiFab version of DeriveFunc (#3990)
85bef47 GNU Make: Add support for CUDA LTO (#3993)
0e3e39b Bottom Solver: Keep the unconverged result if it's an improvement (#3991)
36f111b Workaround std::exclusive_scan issue with old compilers (#3996)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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) updates: - [github.com/pre-commit/mirrors-clang-format: v18.1.7 → v18.1.8](https://github.com/pre-commit/mirrors-clang-format/compare/v18.1.7...v18.1.8) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> .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.

Release notes

Sourced from SonarSource/sonarcloud-github-c-cpp's releases.

v3.0.0

What's Changed

SC-12362 Improve the SonarCloud Intro in README.md by @claire-villard-sonarsource in SonarSource/sonarcloud-github-c-cpp#50

Update actions/cache to v4 by @N-Coder in SonarSource/sonarcloud-github-c-cpp#48

SCCPPGHA-2 Support macOS ARM runners by @enzo-pellegrini in SonarSource/sonarcloud-github-c-cpp#55

CPP-5241 Migrate github action from build-wrapper-output to compilation-database by @enzo-pellegrini in SonarSource/sonarcloud-github-c-cpp#54

SCCPPGHA-6 Support Running on Linux ARM64 by @enzo-pellegrini in SonarSource/sonarcloud-github-c-cpp#57

Update sonar-scanner-version to 6.0.0.4432 by @github-actions in SonarSource/sonarcloud-github-c-cpp#58

Full Changelog: https://github.com/SonarSource/sonarcloud-github-c-cpp/compare/v2.0.2...v3.0.0

New Contributors

@claire-villard-sonarsource made their first contribution in SonarSource/sonarcloud-github-c-cpp#50

@N-Coder made their first contribution in SonarSource/sonarcloud-github-c-cpp#48

@vil02 made their first contribution in SonarSource/sonarcloud-github-c-cpp#38

@enzo-pellegrini made their first contribution in SonarSource/sonarcloud-github-c-cpp#55

Update README

No release notes provided.

Commits

e25edae SCCPPGHA-6 Support Running on Linux ARM64 (#57)
905f4e3 Update sonar-scanner-version to 6.0.0.4432 (#58)
5c3c391 CPP-5241 Migrate github action from build-wrapper-output to compilation-datab...
8a10879 SCCPPGHA-2 Support macOS ARM runners (#55)
bc8c862 NO-JIRA Remove duplicated space in README
1602208 This repository is owned by the Analysis Experience squad
388d750 Update actions/cache to v4 (#48)
0f2dd7b Update the SonarCloud intro in README.md (#51)
a5e1e96 SC-12362 Improve the SonarCloud intro in README.md (#50)
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[![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=SonarSource/sonarcloud-github-c-cpp&package-manager=github_actions&previous-version=2&new-version=3)](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 alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) ---

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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .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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686339f Minor cleanup
e355c11 Tweak wording in the changelog
707bb5b Fix grammar
6f68c62 Ignore doxygen files
d059fe4 Ignore vagrant files
43c5b34 Fix package build
e89568e Update vagrant config
f5bf6f7 Update build script
bd9af9a Update changelog
1652108 Fix typo
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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`.

Commits

9184c2e Fix wrong logging of TOUCH task (#1643)
7f5c33d Fix: Add back iteration.close() call (#1641)
3daaa14 CI fixes and documentation for Pybind v2.12.0 and Numpy 2.0 (#1637)
51bcde6 Update Pybind to v2.12.0 (#1640)
a207118 Regexes: Sanitize user input (#1624)
534706f Fix particle patches flush api (#1626)
87cdc96 Fix Python container and pickle API (#1627)
5d9fb34 Workaround for independent writes to Iterations in parallel, better detection...
51caab3 Seems we need the MPI workaround for Conda now too..... (#1628)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/openPMD-api commit d6728ef5914a409a9f15d436277f32dc29aae93e Author: Ben Wibking 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 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 [pre-commit.ci] pre-commit autoupdate (#657) updates: - [github.com/pre-commit/mirrors-clang-format: v18.1.6 → v18.1.7](https://github.com/pre-commit/mirrors-clang-format/compare/v18.1.6...v18.1.7) --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> .pre-commit-config.yaml src/DiagPDF.cpp commit 8191640ae0629f0916b85be85ba6826a87a35005 Author: Ben Wibking 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 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 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 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 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 "" 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 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) updates: - [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.5.0...v4.6.0) - [github.com/pre-commit/mirrors-clang-format: v17.0.6 → v18.1.6](https://github.com/pre-commit/mirrors-clang-format/compare/v17.0.6...v18.1.6) --------- 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 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 Co-authored-by: Ben Wibking 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`.

Commits

a65f0a5 add missing AMReX_SUNDIALS in AMReXConfig.cmake (#3962)
14d56ef Linear Solver: Fix semicoarsening issues with multiple AMR levels (#3961)
28b0101 add DEBUG_LIBSTDCXX option to GNU Make gcc for libstdc++ debug (#3945)
f474963 Fix bug introduced in #3959 (#3960)
8e67cc9 InterpBndryData: Make changes for multi-level hypre (#3959)
74ab071 FabArray: Make some functions static (#3958)
345cb88 MultiArray4: add conversion operator to bool (#3957)
523c11e Overloading Array4::operator(), ptr and contains (#3956)
e6c93bf Fix block size in PermutationForDeposition (#3953)
fed4bc1 Tune PermutationForDeposition for MI250X (#3925)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/amrex 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`.

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1d8ca1f Avoid static reference to temporary
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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`.

Commits

fcd3e1e is_convertible_v -> is_convertible::value (#3983)
dc401b1 Move handlers outside of the docs
f7c5588 Cleanup syntax doc
a4e4067 Fix markdown
3479828 Fix markdown
191b0cb Fix markdown
e80f4a9 Cleanup syntax doc
022d8ef Update doc.yml
ca8eeb0 Add glibc ext for day of month and week of year (#3976)
cddb41f Fix markdown
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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`.

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2c1dbc9 [pre-commit.ci] pre-commit autoupdate (#1613)
4d77fad Bump s-weigand/setup-conda from 1.2.1 to 1.2.2 (#1621)
0baf09f Add rank table for locality-aware streaming (#1505)
8c57285 Span API: Set dirty flag (#1615)
95cbcb6 Fix CI issues for ADIOS2 v2.10: Add openPMD_HAVE_ADIOS2_BP5, datatype fixes i...
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/openPMD-api commit 7a597a57579780a8e0e25ee0220296de479ff4ea Author: ChongChong He 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 `[ ]` 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/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 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:_ - [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`. - [x] I have requested a reviewer for this PR. --------- Co-authored-by: Ben Wibking .github/workflows/docs.yml build_docs.sh docs/conf.py docs/requirements.txt commit 4c1a57659490ef59a5034602e5b9d6acaca070db Author: Ben Wibking 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 _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-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.

Release notes

Sourced from ZedThree/clang-tidy-review's releases.

v0.19.0

What's Changed

Add links to check documentation in review by @bwrsandman in ZedThree/clang-tidy-review#123

Add clang-tidy 18 by @daljit46 in ZedThree/clang-tidy-review#121

Add a hint for generating the compile command outside the container by @m-kuhn in ZedThree/clang-tidy-review#120

New Contributors

@daljit46 made their first contribution in ZedThree/clang-tidy-review#121

@m-kuhn made their first contribution in ZedThree/clang-tidy-review#120

Full Changelog: https://github.com/ZedThree/clang-tidy-review/compare/v0.18.0...v0.19.0

Commits

85799d6 Merge pull request #120 from m-kuhn/patch-1
b719737 Merge pull request #121 from daljit46/clang_tidy_18
3ff13b4 Merge pull request #123 from bwrsandman/links-in-comments
dbe658e Add links to check documentation in review
9bde8c5 Add clang-tidy 18
65fbe78 Add a hint for generating the compile command outside
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .github/workflows/clang-tidy-comments.yml .github/workflows/clang-tidy.yml commit 734ce9bbcd933a193f3c9e4d3d4f398bcf59d3c7 Author: Ben Wibking 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`. - [ ] I have requested a reviewer for this PR. .github/workflows/checkpoint-restart.yml .github/workflows/cmake.yml .github/workflows/hip.yml .github/workflows/warnings.yml commit 314debb80aca086b4808a806d6245a6ca9cb7d2d Author: ChongChong He 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 _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/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 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::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 `[ ]` 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/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 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:_ - [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. - [ ] 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`.

Commits

95a92e2 cleanup of latest changes for 3D EB (#3912)
ddf15b9 3d anisotropic eb (#3907)
d857968 Fix compiler warnings in Parser (#3908)
b029e4f Update for ROCm 6.1.0 (#3898)
aba9891 clarify comment about EnforcePeriodicity (#3903)
b752027 fix a HIP/Frontier issue (#3902)
2c9e432 Update HIP CIs for rocm 6.1.0 (#3897)
64d2360 Set AMD wavefront size according to AMReX_AMD_ARCH (#3881)
96f6d66 Fix offset in recv buffer of single precision particle communication (#3896)
2780fa8 Fix Assertion (#3894)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/amrex commit f7d0e904180a403aff46fbdcf5316c354319215c Author: ChongChong He 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:_ - [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/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`.

Commits

48c9084 Fix CodeQL alert (#3945)
cf1f55f Specialize formatter for all std::basic_string types (#3943)
400f6a8 Dedup ADL begin/end lookup
a3e0931 Update signature in the doc
51eeccd const void* is neither a fundamental nor string type
f30f1fd Document formatter specializations provided by base.h
f4b256c Fix warning C26439
f746a59 Cleanup FMT_ASSERT
ee0c335 Fix format_to + FMT_STRING for wide character type (#3931)
9973576 Fix FMT_USE_NONTYPE_TEMPLATE_ARGS define back (#3937)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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) Bumps [extern/openPMD-api](https://github.com/openPMD/openPMD-api) from `3feb5c5` to `805c760`.

Commits

805c760 Print a hint on what might be wrong when retrieveSeries fails (#1610)
9e53e9a [pre-commit.ci] pre-commit autoupdate (#1607)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/openPMD-api commit 2e7c3aa0a8940943bdd270994e6359e6f66294c3 Author: Ben Wibking 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 `[ ]` 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/dependencies/dependencies_dpcpp.sh .github/workflows/intel.yml commit deabc66dc2c040ae3a2ffce4e2577b4a7970d593 Author: Ben Wibking 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 _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/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:_ - [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 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`. - [x] I have requested a reviewer for this PR. 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:_ - [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: Piyush Sharda 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`. - [x] I have requested a reviewer for this PR. tests/PopIII.in commit 9d44f9156beba9a5e4b91ce460b4323f2e1663c0 Author: Ben Wibking 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:_ - [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/TabulatedCooling.cpp commit f4784d23815c1510a71badfc750ab71e48ad5c1f Author: ChongChong He 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:_ - [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. README.md docs/installation.rst commit a49bfe1819b849846c6451003403321b8e3ceae1 Author: Ben Wibking 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). - [ ] 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> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: ChongChong He 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 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`. - [ ] I have requested a reviewer for this PR. src/RadhydroShockMultigroup/test_radhydro_shock_multigroup.cpp src/radiation_system.hpp commit a210782b115b7ab19314c105fb6b1051dd35c800 Author: Ben Wibking 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 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 _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/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 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:_ - [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/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 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 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). - [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. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> src/RadhydroSimulation.hpp commit dd5c2fd31c7f28e4444df4caf9eef33194050d98 Author: Ben Wibking 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 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 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`.

Commits

124b71b use a helper function to get the index into the NSE tables (#1495)
95cb860 remove redundant rhs and ydot for NSE_NET (#1507)
886498d Optimize fill_merge_indices/nse_grouping for NSE_NET (#1506)
3169bfe remove the is_jacobian_term_used logic in the linear algebra (#1502)
d7e5b84 remove fast reaction cycle check for NSE_NET check. (#1503)
9dd9dbb add more unit test for testing NSE_NET (#1504)
ce331bc update test_linear_algebra to output the Jacobian mask (#1501)
02d46a6 updated changelog for 24.03 (#1498)
2359fab fix RKC integration with SDC (#1497)
695b711 update test_linear_algebra to reflect pivot templating (#1496)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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) Bumps [extern/amrex](https://github.com/AMReX-Codes/amrex) from `2ecafcf` to `47347f7`.

Commits

47347f7 Fix: Resize Component on Add (#3861)
fe6f3de Use less device memory when checkpointing particles (#3238)
f264290 AddRealComp/AddIntComp: Resize SoA (#3615)
1be7257 FabArray: Option to use a single contiguous chunk of memory (#3857)
67523bb Disable AMReX_FLATTEN_FOR by default (#3860)
41df2a5 Curl Curl Solver: Variable beta coefficient (#3810)
7437aa1 MultiFab::deepCopy() (#3848)
dffdeac FabArray\<FAB>::copy Argument Name (#3856)
8d57ebc AMReX_FLATTEN_FOR (#3855)
21a7a66 Use Clang-Tidy 17 in GitHub CI (#3845)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/amrex commit 441434afd98208be69daff372538fb1a5d17f41d Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon Apr 1 13:39:23 2024 -0400 Bump extern/openPMD-api from `c2e0e83` to `3feb5c5` (#592) Bumps [extern/openPMD-api](https://github.com/openPMD/openPMD-api) from `c2e0e83` to `3feb5c5`.

Commits

3feb5c5 [pre-commit.ci] pre-commit autoupdate (#1602)
e4ce81f Fix dirtyRecursive() performance for Series with many steps (#1598)
5940f7c Read JSON config in parallel (#1605)
c8c960a Fix hdf5 dataset specific config (#1600)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/openPMD-api commit 9b11bcb61c7355f1044eb5950248e5fd19babc00 Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon Apr 1 04:23:11 2024 +0000 Bump ZedThree/clang-tidy-review from 0.17.2 to 0.18.0 (#593) Bumps [ZedThree/clang-tidy-review](https://github.com/zedthree/clang-tidy-review) from 0.17.2 to 0.18.0.

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Sourced from ZedThree/clang-tidy-review's releases.

v0.18.0

What's Changed

chore: add num_comments_as_exitcode option by @Nerixyz in ZedThree/clang-tidy-review#119

Full Changelog: https://github.com/ZedThree/clang-tidy-review/compare/v0.17.3...v0.18.0

v0.17.3

What's Changed

fix: download artifacts as binary blobs and follow redirects by @Nerixyz in ZedThree/clang-tidy-review#118

Full Changelog: https://github.com/ZedThree/clang-tidy-review/compare/v0.17.2...v0.17.3

Commits

9008958 Merge pull request #119 from Nerixyz/chore/exit-with-comments
ad2c4db chore: add num_comments_as_exitcode option
fddb616 Merge pull request #118 from Nerixyz/fix/more-pr
1d30432 fix: download artifact as blob and follow redirects
3fb42e9 deps: update to actions/upload-action@v4
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[![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=ZedThree/clang-tidy-review&package-manager=github_actions&previous-version=0.17.2&new-version=0.18.0)](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 alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) ---

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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .github/workflows/clang-tidy-comments.yml .github/workflows/clang-tidy.yml commit a56e5727d7df74815e8e2556b55562c3c4657a2a Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon Apr 1 03:51:34 2024 +0000 Bump extern/fmt from `ae1e93d` to `f5ec5ad` (#589) Bumps [extern/fmt](https://github.com/fmtlib/fmt) from `ae1e93d` to `f5ec5ad`.

Commits

f5ec5ad Update syntax.rst
3b5f3de Make CMake version message less confusing (#3907)
ca91939 Replace std::fill_n with fmt::detail::fill_n (#3909)
74a1872 Implemented fmt::day, fmt::month, fmt::year and related unit tests (#3906)
88620e5 Range formatting documentation (#3905)
5d63e87 Add a formatter for float128
aecec01 Initial support for extended FP types
5af8865 Cleanup
45b772f Improve std::complex formatter to be compatible with P2197R0 (#3900)
5334789 Make line buffering test less flaky
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/fmt commit e275647a7d0a5e42b6c6b7404336a15e6a2fda52 Author: Ben Wibking 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). - [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> 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 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:_ - [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/simulation.hpp commit 4f2e993a655cd34dde9098ee2bb39fb44a400547 Author: ChongChong He 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.

Release notes

Sourced from ZedThree/clang-tidy-review's releases.

v0.17.2

What's Changed

fix: artifact download by @Nerixyz in ZedThree/clang-tidy-review#115

Full Changelog: https://github.com/ZedThree/clang-tidy-review/compare/v0.17.1...v0.17.2

Commits

9a32adc Merge pull request #115 from Nerixyz/fix/pr-stuff
0b130f2 fix: artifact download
See full diff in compare view

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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .github/workflows/clang-tidy.yml 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:_ - [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. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Piyush Sharda src/Chemistry.hpp commit aa95d0cde2c3ed186d0071004c4ee63b1031b76d Author: ChongChong He 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:_ - [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 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:_ - [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. 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). - [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/hydro_system.hpp commit 9f9c30054d3fbb156c05625a1727e78dfe481af8 Author: Ben Wibking 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 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 `[ ]` 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/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 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 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`. - [x] I have requested a reviewer for this PR. .github/workflows/clang-tidy-comments.yml commit e22ce71ab858c68f639aa7ebd4da518db4404d2d Author: Ben Wibking 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`.

Commits

2ecafcf assert wavefront size (#3777)
f924a1d Curl of Curl solver: Tweak restriction (#3765)
c3e7060 Adjust debug info argument for HIP compiler (#3761)
d8d4828 fixed bug in MLCurlCurL::xdoty() to prevent doing MPI sum twice. (#3774)
1959b1f Fix bug in AMREX_ASSUME (#3773)
2230caa Pure SoA: NextID as Long (#3772)
3003edb GNU Make: set COMP_VERSION for hipcc and nvcc (#3771)
4ebd5e0 Make MFParallelFor safer from int overflow (#3768)
398b20b Implement portable assumptions with AMREX_ASSUME (#3770)
99b47cb getParticleTileData: HostVector must be initialized during resize (#3769)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Ben Wibking 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`.

Commits

e587300 some more cleaning of the runtime_parameters.py (#1448)
8fc4cfe template pivoting in the linear algebra (#1454)
adb2600 work on addressing some issues with the Jacobian scaling (#1479)
48bf41c remove some unused includes in test_nse_interp (#1494)
f336cab create a linear algebra unit test (#1493)
9a8c260 clean up some unused vars in unit tests (#1492)
348dad9 remove redundant (and conflicting) typedefs in rhs.H (#1491)
86807d6 update the SDC docs (#1469)
3df6ba0 if we are building with HIP, don't force inlining (#1490)
4f2ee5f fix compilation of nse_table_cell (#1486)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Ben Wibking extern/Microphysics commit bbf934a551e490da802257c89c999dfc30ce12f9 Author: ChongChong He 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:_ - [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/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 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. ### 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. .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> Date: Fri Mar 1 03:30:24 2024 +0000 Bump extern/openPMD-api from `d9fce66` to `c2e0e83` (#549) Bumps [extern/openPMD-api](https://github.com/openPMD/openPMD-api) from `d9fce66` to `c2e0e83`.

Commits

c2e0e83 Filename extensions: Allow specifying wildcards (#1584)
d64dbc2 Parallel JSON (#1475)
5fec415 Joined arrays in ADIOS2 (#1382)
045e416 SerialIOTest: Clang-Tidy Fixes (#1599)
30e5bde HDF5: Explicit control over chunking (#1591)
a0eca32 [pre-commit.ci] pre-commit autoupdate (#1595)
d24c5d2 CI: Fix CircleCI "six" (#1596)
283b2fe Derive PatchComponent from RecordComponent (#1594)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/openPMD-api 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) Bumps [extern/fmt](https://github.com/fmtlib/fmt) from `6321a97` to `ae1e93d`.

Commits

ae1e93d Fix warning C4702 emitted from format.h (MSVC) (#3866)
f68f452 Workaround an ld warning on macOS
ebea573 Fix chrono locale format bug for RHEL gcc (#3859)
ddf0b7d Fix warning C4365 emitted from printf.h (#3865)
0166f45 std.h c++23 build fix (#3856)
8e42eef Don't error on min time_point
91b30e5 More API details
7a63e23 Readd core.h to headers
44c3fe1 Fix handling of static separator
ae181cc C++23 compatibility: basic_string_view cannot be constructed from nullptr (#3...
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/fmt commit 401ad01824f74f430567e345b1d1ad1cee91e413 Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu Feb 29 22:22:23 2024 -0500 Bump extern/yaml-cpp from `4afd53b` to `76dc671` (#548) Bumps [extern/yaml-cpp](https://github.com/jbeder/yaml-cpp) from `4afd53b` to `76dc671`.

Commits

76dc671 Add option YAML_ENABLE_PIC=ON
5c1bbbd Skip Position Independent Code for PSP/PS3
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/yaml-cpp commit 6aca86475ce95a8e9cec545e01dfae1edd52639c Author: ChongChong He 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 _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/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 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. ### 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`. - [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_system.hpp src/valarray.hpp commit 2d863d655ec1e1f684f55ea745021b9c97a03c60 Author: Ben Wibking 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 _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> 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 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 _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/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 ### 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. --------- Co-authored-by: Piyush Sharda Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Piyush Sharda Co-authored-by: Piyush Sharda Co-authored-by: Ben Wibking Co-authored-by: Piyush Sharda Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> 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 Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Piyush Sharda Co-authored-by: Piyush Sharda Co-authored-by: Ben Wibking Co-authored-by: Piyush Sharda Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> .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 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:_ - [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/simulation.hpp commit 185770745bc365a1c5953c947ac11ecb3f393fc1 Author: Ben Wibking 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 _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. src/RadShadow/test_radiation_shadow.cpp commit 3455fc8ef2ce93033df9d7be11651e427a1f49a1 Author: ChongChong He 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 ### 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`. - [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> .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`.

Commits

fbeddb3 update pynucastro nets to have bion/mion constexpr (#1437)
3700590 constexpr some helm EOS table parameters (#1440)
6fceeec update tols for Urca test_react so it runs (#1438)
6dc51ad fix NSE+SDC when we are doing drive_initial_convection (#1431)
d99cee0 update github actions to latest versions (#1429)
a0deaae add struct support for runtime_parameters.py (#1422)
9d0655b update for 24.01
3185974 optional quantum correction terms for chabrier1998 (#1428)
a83fe00 [WIP] fix powi script and bug in chugunov2009 screening (#1432)
32fa759 Replace std::pow with integer powers to amrex::Math::powi (#1426)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Piyush Sharda <34922596+psharda@users.noreply.github.com> 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) Bumps [extern/amrex](https://github.com/AMReX-Codes/amrex) from `b96b731` to `689144d`.

Commits

689144d Update AoS Restrict (#3738)
d861bdf Disable m_aos for SoA Particle (#3736)
09fc44a Add helper function for setting id and cpu simultaneously. (#3733)
33dea1f Disable SYCL on Nvidia and AMD CIs (#3726)
dbc0c6f ParticleCopyPlan for SoA Particles (#3732)
47c4f95 Do not use std::forward twice on the same object in AmrParticleLocator (#3734)
4aeeabe Particle Copy Plan: Default Vals (#3729)
ab99ea6 GitHub Actions: 4 vCPUs are available now on Ubuntu and Windows (#3703)
41397e2 Fix circular header file dependency (#3725)
d5cc579 Follow-on to #3701 (#3702)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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`.

Commits

4afd53b Bump the github-actions group with 1 update
96f5c88 assign fallback value
c67d701 Fix indentation of empty sequences and add test
9eb1142 Fix GIT_TAG field in cmake integration example
c28295b Add CMake integration example
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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`.

Commits

6321a97 Simplify color formatting
4b6b32f Deprecate wide stream function
1b54ba4 Fix UB in format_arg_store implementation. (#3833)
71a4a8d Really fix MSVC warning about <bit> only being available in C++20. (#3832)
8e62172 Fix a warning
28afff3 Improve buffering
af44c29 Separate buffer initialization from flush
a1e1eed Minor cleanup
ffce363 Add glibc stream support
b566951 Don't hang on test failure
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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`.

Commits

d9fce66 Don't allow Container insertion in READ_LINEAR (#1590)
8faadde Initial support for HDF5 subfiling (#1580)
17e757f Refactor: Extract ADIOS2 BufferedActions struct to own file, rename to ADIOS2...
3a8a220 Fix: Strings with a single char in Python (#1585)
d5524ec Fix availableChunks for READ_LINEAR in ADIOS2 (#1586)
7bb2948 Fix docstring for MyPath (#1587)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/openPMD-api commit b4222b7e92d41231fc115e0298c75faf7d6300ca Author: Ben Wibking 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 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 _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. --------- 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 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 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. --------- 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.

Release notes

Sourced from ZedThree/clang-tidy-review's releases.

v0.17.1

What's Changed

auth: Allow private key for apps to be base64 by @bwrsandman in ZedThree/clang-tidy-review#112

Use PyGithub to reuse auth headers to do requests by @bwrsandman in ZedThree/clang-tidy-review#113

Full Changelog: https://github.com/ZedThree/clang-tidy-review/compare/v0.17.0...v0.17.1

Commits

4923dc7 Merge pull request #113 from bwrsandman/authenticated-requests
baadf42 Use set difference to cull comments
40e754e Reuse auth headers to do requests
f527341 Merge pull request #112 from bwrsandman/base64-private-key
d51789b auth: Allow private key for apps to be base64
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[![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=ZedThree/clang-tidy-review&package-manager=github_actions&previous-version=0.17.0&new-version=0.17.1)](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 alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) ---

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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .github/workflows/clang-tidy-comments.yml .github/workflows/clang-tidy.yml commit 97cbab3ed80f75fa73750869ff82c7c870d092ec Author: Ben Wibking 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. --------- 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> 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.

Release notes

Sourced from actions/cache's releases.

v4.0.0

What's Changed

Update action to node20 by @takost in actions/cache#1284

feat: save-always flag by @to-s in actions/cache#1242

New Contributors

@takost made their first contribution in actions/cache#1284

@to-s made their first contribution in actions/cache#1242

Full Changelog: https://github.com/actions/cache/compare/v3...v4.0.0

v3.3.3

What's Changed

Cache v3.3.3 by @robherley in actions/cache#1302

New Contributors

@robherley made their first contribution in actions/cache#1302

Full Changelog: https://github.com/actions/cache/compare/v3...v3.3.3

v3.3.2

What's Changed

Fixed readme with new segment timeout values by @kotewar in actions/cache#1133

Readme fixes by @kotewar in actions/cache#1134

Updated description of the lookup-only input for main action by @kotewar in actions/cache#1130

Change two new actions mention as quoted text by @bishal-pdMSFT in actions/cache#1131

Update Cross-OS Caching tips by @pdotl in actions/cache#1122

Bazel example (Take #2️⃣) by @vorburger in actions/cache#1132

Remove actions to add new PRs and issues to a project board by @jorendorff in actions/cache#1187

Consume latest toolkit and fix dangling promise bug by @chkimes in actions/cache#1217

Bump action version to 3.3.2 by @bethanyj28 in actions/cache#1236

New Contributors

@vorburger made their first contribution in actions/cache#1132

@jorendorff made their first contribution in actions/cache#1187

@chkimes made their first contribution in actions/cache#1217

@bethanyj28 made their first contribution in actions/cache#1236

Full Changelog: https://github.com/actions/cache/compare/v3...v3.3.2

v3.3.1

What's Changed

Reduced download segment size to 128 MB and timeout to 10 minutes by @kotewar in actions/cache#1129

Full Changelog: https://github.com/actions/cache/compare/v3...v3.3.1

v3.3.0

What's Changed

Bug: Permission is missing in cache delete example by @kotokaze in actions/cache#1123

... (truncated)

Changelog

Sourced from actions/cache's changelog.

Releases

3.0.0

Updated minimum runner version support from node 12 -> node 16

3.0.1

Added support for caching from GHES 3.5.

Fixed download issue for files > 2GB during restore.

3.0.2

Added support for dynamic cache size cap on GHES.

3.0.3

Fixed avoiding empty cache save when no files are available for caching. (issue)

3.0.4

Fixed tar creation error while trying to create tar with path as ~/ home folder on ubuntu-latest. (issue)

3.0.5

Removed error handling by consuming actions/cache 3.0 toolkit, Now cache server error handling will be done by toolkit. (PR)

3.0.6

Fixed #809 - zstd -d: no such file or directory error

Fixed #833 - cache doesn't work with github workspace directory

3.0.7

Fixed #810 - 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.

3.0.8

Fix zstd not working for windows on gnu tar in issues #888 and #891.

Allowing users to provide a custom timeout as input for aborting download of a cache segment using an environment variable SEGMENT_DOWNLOAD_TIMEOUT_MINS. Default is 60 minutes.

3.0.9

Enhanced the warning message for cache unavailablity in case of GHES.

3.0.10

Fix a bug with sorting inputs.

Update definition for restore-keys in README.md

... (truncated)

Commits

13aacd8 Merge pull request #1242 from to-s/main
53b35c5 Merge branch 'main' into main
65b8989 Merge pull request #1284 from takost/update-to-node-20
d0be34d Fix dist
66cf064 Merge branch 'main' into update-to-node-20
1326563 Merge branch 'main' into main
e718767 Fix format
0122982 Apply workaround for earlyExit
3185ecf Update "only-" actions to node20
25618a0 Bump version
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[![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=actions/cache&package-manager=github_actions&previous-version=3&new-version=4)](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 alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) ---

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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .github/workflows/codespell.yml .github/workflows/hip.yml 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.

Release notes

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v0.17.0

What's Changed

Don't override original env variables by @bwrsandman in ZedThree/clang-tidy-review#111

Fix default REVIEW_FILES in split workflow post by @bwrsandman in ZedThree/clang-tidy-review#110

Add Github App authentication method by @bwrsandman in ZedThree/clang-tidy-review#109

Fix line filter on for clang compiler on windows by @bwrsandman in ZedThree/clang-tidy-review#108

Full Changelog: https://github.com/ZedThree/clang-tidy-review/compare/v0.16.0...v0.17.0

v0.16.0

What's Changed

Bump PyGithub to 2.1 by @bwrsandman in ZedThree/clang-tidy-review#107

Get username from PR to use in google-readability-todo by @bwrsandman in ZedThree/clang-tidy-review#106

Fix split workflow when no comments can be posted by @bwrsandman in ZedThree/clang-tidy-review#105

Full Changelog: https://github.com/ZedThree/clang-tidy-review/compare/v0.15.1...v0.16.0

Commits

5d848bc Merge pull request #108 from bwrsandman/clang-on-windows
27e8178 Merge pull request #109 from bwrsandman/app-auth
3977392 Merge pull request #110 from bwrsandman/default-post
a771054 Merge pull request #111 from bwrsandman/env
d8b8a3c Apply black changes
882160c Don't override original env variables
4a4f630 Fix default REVIEW_FILES in split workflow post
72b3a12 Apply black changes
8f5e16a Add github app authentication arguments
d08403b github wrapper: Use Auth class to encapsulate token
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[![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=ZedThree/clang-tidy-review&package-manager=github_actions&previous-version=0.15.1&new-version=0.17.0)](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 alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) ---

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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .github/workflows/clang-tidy-comments.yml .github/workflows/clang-tidy.yml commit 08219f8863b24521501f3ef2d7e594d7e91e6a86 Author: Ben Wibking 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 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). - [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: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> 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.

Release notes

Sourced from ZedThree/clang-tidy-review's releases.

v0.15.1

What's Changed

Fix Recursive source clang-tidy by @bwrsandman in ZedThree/clang-tidy-review#104

Full Changelog: https://github.com/ZedThree/clang-tidy-review/compare/v0.15.0...v0.15.1

v0.15.0

What's Changed

Python fixes for running on multiple platforms and outside of docker by @bwrsandman in ZedThree/clang-tidy-review#103

Full Changelog: https://github.com/ZedThree/clang-tidy-review/compare/v0.14.0...v0.15.0

Commits

0dd8d19 Merge pull request #104 from bwrsandman/recursive-source-config
7765f56 Fix Recursive source clang-tidy
7e7ae43 Merge pull request #103 from bwrsandman/windows_shell_fix
406fab7 Apply black changes
e2610c9 Use pathlib for clang_tidy_binary and args list for version
e78c0b1 Add an option to merge multiple comments
a09d6ab Split workflow: return the number of comments
df2e121 Fix review command line to run on windows
828c9a4 Bump versions of actions in README
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[![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=ZedThree/clang-tidy-review&package-manager=github_actions&previous-version=0.14.0&new-version=0.15.1)](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 alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) ---

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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .github/workflows/clang-tidy-comments.yml .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 Co-authored-by: Piyush Sharda 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:_ - [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. 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 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 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 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 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 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`.

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7de2124 an EOS interface with NSE (#1405)
4a44497 initialize nse_table_t members (#1418)
925e0ce fix concurrency for castro-development (#1423)
d742816 add another Castro action that tests against AMReX development (#1421)
8a61b96 a simpler fix for constexpr_for in amrex (#1420)
4d7d029 add a script to test network compatibility with NSE_NET (#1416)
5757fb5 make sure const T evolution (#1408)
01577f3 Revert "Start moving towards zero-based indexing with linpack (#536)" (#1412)
43b5138 add a method to compute the T derivative of an NSE table quantity (#1407)
96f4c7e update hip install for ROCm 6.0 (#1413)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Ben Wibking 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) Bumps [extern/amrex](https://github.com/AMReX-Codes/amrex) from `9b733ec` to `75571e2`.

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75571e2 MLMG: Use free functions instead of MF member functions (#3681)
3407e87 Add a few free functions for MLMG (#3680)
85462ce Eliminating Matrix operations in MLMG CG bottom solver if initial vector is z...
ef38229 Add a for loop that is unrolled at compile time (#3674)
d1e55fb Add PTD version of getParticleCell (#3675)
78c4fda Improve ParIter docs (#3676)
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554b1ca PureSoA IdCpu fixes (#3671)
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0a208bb Clang-Tidy in CI: Keep Going after Errors (#3667)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/amrex commit 6bd8b63fe10c2e05b9f896a9db8bde2f1003f732 Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon Jan 1 16:08:03 2024 +0000 Bump extern/openPMD-api from `e8e2aeb` to `a3fe9b7` (#479) Bumps [extern/openPMD-api](https://github.com/openPMD/openPMD-api) from `e8e2aeb` to `a3fe9b7`.

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a3fe9b7 Remove constexpr from RecordComponent::visit() (#1582)
7296948 Add documentation for typical use cases of openpmd-pipe (#1578)
e668e86 Adios2 warn groupbased encoding (#1498)
b131cd2 Add visit-like pattern for RecordComponent (#1544)
2e89f87 Remove necessity for RecordComponent::SCALAR (#1154)
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495b7cc Bump github/codeql-action from 2 to 3 (#1569)
4ba6da3 [pre-commit.ci] pre-commit autoupdate (#1575)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/openPMD-api commit 38d195cd849613834f3afec9cacd2d3430f87ff4 Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon Jan 1 10:51:44 2024 -0500 Bump extern/yaml-cpp from `eaf7205` to `94710bb` (#481) Bumps [extern/yaml-cpp](https://github.com/jbeder/yaml-cpp) from `eaf7205` to `94710bb`.

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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/yaml-cpp commit bd6c18a979f81a62e6579c045ac1fb44c50d6ff1 Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon Jan 1 10:51:24 2024 -0500 Bump extern/fmt from `99b9fbf` to `a5bacf3` (#478) Bumps [extern/fmt](https://github.com/fmtlib/fmt) from `99b9fbf` to `a5bacf3`.

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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/fmt commit aa18236ba8a0138f246627152bd39dbc4a0b5277 Author: ChongChong He 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 .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.

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v4.0.0

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Deploy pages using artifact IDs @konradpabjan (#251)

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v3.0.1

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Bump eslint from 8.54.0 to 8.55.0 @dependabot (#266)

Bump nock from 13.3.8 to 13.4.0 @dependabot (#267)

Bump eslint-config-prettier from 9.0.0 to 9.1.0 @dependabot (#268)

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Bump @actions/github from 5.1.1 to 6.0.0 @dependabot (#261)

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🧰 Maintenance

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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .github/workflows/docs.yml commit d34f253c8e37660d925a55e03c8adcba9f16e0ae Author: Ben Wibking 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 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.

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v4.0.0

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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.

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@vmjoseph made their first contribution in actions/upload-artifact#464

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v3.1.3

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chore(github): remove trailing whitespaces by @ljmf00 in actions/upload-artifact#313

Bump @actions/artifact version to v1.1.2 by @bethanyj28 in actions/upload-artifact#436

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v3.1.2

Update all @actions/* NPM packages to their latest versions- #374

Update all dev dependencies to their most recent versions - #375

v3.1.1

Update actions/core package to latest version to remove set-output deprecation warning #351

v3.1.0

What's Changed

Bump @actions/artifact to v1.1.0 (actions/upload-artifact#327)

Adds checksum headers on artifact upload (actions/toolkit#1095) (actions/toolkit#1063)

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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .github/workflows/cmake-macos.yml .github/workflows/cmake.yml commit ed906519115c0836d293812dfe6749b4e2eb8d8b Author: Ben Wibking 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`. - [x] I have requested a reviewer for this PR. src/FastMath.hpp commit ed51d0d4985895a8a2a793ad7fdbf32bcfc3454c Author: Ben Wibking 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). - [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/NSCBC_outflow.hpp commit f7f34fcb073484da96b1503612227724a0d30dd6 Author: Ben Wibking 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). - [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: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> .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.

Release notes

Sourced from actions/setup-python's releases.

v5.0.0

What's Changed

In scope of this release, we update node version runtime from node16 to node20 (actions/setup-python#772). Besides, we update dependencies to the latest versions.

Full Changelog: https://github.com/actions/setup-python/compare/v4.8.0...v5.0.0

v4.8.0

What's Changed

In scope of this release we added support for GraalPy (actions/setup-python#694). You can use this snippet to set up GraalPy:
steps:
    - uses: actions/checkout@v4
    - uses: actions/setup-python@v4
      with:
        python-version: 'graalpy-22.3'
    - run: python my_script.py
    
Besides, the release contains such changes as:

Trim python version when reading from file by @FerranPares in actions/setup-python#628

Use non-deprecated versions in examples by @jeffwidman in actions/setup-python#724

Change deprecation comment to past tense by @jeffwidman in actions/setup-python#723

Bump @babel/traverse from 7.9.0 to 7.23.2 by @dependabot in actions/setup-python#743

advanced-usage.md: Encourage the use actions/checkout@v4 by @cclauss in actions/setup-python#729

Examples now use checkout@v4 by @simonw in actions/setup-python#738

Update actions/checkout to v4 by @dmitry-shibanov in actions/setup-python#761

New Contributors

@FerranPares made their first contribution in actions/setup-python#628

@timfel made their first contribution in actions/setup-python#694

@jeffwidman made their first contribution in actions/setup-python#724

Full Changelog: https://github.com/actions/setup-python/compare/v4...v4.8.0

v4.7.1

What's Changed

Bump word-wrap from 1.2.3 to 1.2.4 by @dependabot in actions/setup-python#702

Add range validation for toml files by @dmitry-shibanov in actions/setup-python#726

Full Changelog: https://github.com/actions/setup-python/compare/v4...v4.7.1

v4.7.0

In scope of this release, the support for reading python version from pyproject.toml was added (actions/setup-python#669).
      - name: Setup Python
            uses: actions/setup-python@v4
    </tr></table>
    

... (truncated)

Commits

0a5c615 Update action to node20 (#772)
0ae5836 Add example of GraalPy to docs (#773)
b64ffca update actions/checkout to v4 (#761)
8d28961 Examples now use checkout@v4 (#738)
7bc6abb advanced-usage.md: Encourage the use actions/checkout@v4 (#729)
e8111ce Bump @babel/traverse from 7.9.0 to 7.23.2 (#743)
a00ea43 add fix for graalpy ci (#741)
8635b1c Change deprecation comment to past tense (#723)
f6cc428 Use non-deprecated versions in examples (#724)
5f2af21 Add GraalPy support (#694)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .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.

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v3.0.0

Changelog

Update action to node20 @takost (#256)

See details of all code changes since previous release.

:warning: For use with products other than GitHub.com, such as GitHub Enterprise Server, please consult the compatibility table.

v2.0.5

Changelog

Bump prettier from 3.0.0 to 3.1.0 @dependabot (#264)

Bump @octokit/request-error from 5.0.0 to 5.0.1 @dependabot (#263)

Bump @actions/http-client from 2.1.0 to 2.2.0 @dependabot (#262)

Bump @vercel/ncc from 0.36.1 to 0.38.1 @dependabot (#260)

Bump eslint from 8.44.0 to 8.54.0 @dependabot (#257)

Bump nock from 13.3.1 to 13.3.8 @dependabot (#254)

Bump actions/setup-node from 3 to 4 @dependabot (#246)

Bump release-drafter/release-drafter from 5.24.0 to 5.25.0 @dependabot (#245)

Bump eslint-plugin-github from 4.8.0 to 4.10.1 @dependabot (#232)

Bump jest from 29.6.1 to 29.7.0 @dependabot (#224)

Fix cosmetic error by replacing comma with period @JamesMGreene (#210)

Bump actions/checkout from 3 to 4 @dependabot (#220)

Bump eslint-config-prettier from 8.8.0 to 9.0.0 @dependabot (#209)

Remove "beta" disclaimer from README @JamesMGreene (#243)

See details of all code changes since previous release.

:warning: For use with products other than GitHub.com, such as GitHub Enterprise Server, please consult the compatibility table.

v2.0.4

Changelog

Update GHES compatibility table after verifying with 3.9.x @JamesMGreene (#201)

Bump @octokit/request-error from 4.0.1 to 5.0.0 @dependabot (#194)

Bump prettier from 2.8.8 to 3.0.0 @dependabot (#196)

Bump jest from 29.5.0 to 29.6.1 @dependabot (#195)

Bump release-drafter/release-drafter from 5.23.0 to 5.24.0 @dependabot (#192)

Bump eslint from 8.42.0 to 8.44.0 @dependabot (#191)

Remove circular JSON references for error debugging @JamesMGreene (#197)

See details of all code changes since previous release.

... (truncated)

Commits

13b55b3 Merge pull request #272 from kbdharun/main
c284911 chore/docs: update version, fix typos
ae44070 Merge pull request #266 from actions/dependabot/npm_and_yarn/eslint-8.55.0
34a8f60 Bump eslint from 8.54.0 to 8.55.0
b65643c Merge pull request #267 from actions/dependabot/npm_and_yarn/nock-13.4.0
faceed1 Bump nock from 13.3.8 to 13.4.0
230466c Merge pull request #268 from actions/dependabot/npm_and_yarn/eslint-config-pr...
38d34f8 Bump eslint-config-prettier from 9.0.0 to 9.1.0
cd33125 Merge pull request #269 from actions/dependabot/npm_and_yarn/actions/core-1.10.1
dd970ae Update distributables after Dependabot 🤖
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[![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=actions/deploy-pages&package-manager=github_actions&previous-version=2&new-version=3)](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 alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) ---

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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .github/workflows/docs.yml commit 1bbc41f6e22c5c7af6b8e2880f18d58968a65fbb Author: Ben Wibking 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 `[ ]` 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/instability.rst commit add3105a5575c6f55796bdb4b671b50c4fb61e01 Author: Ben Wibking 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. ### 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. 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 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. ### 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. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> src/RadMarshakAsymptotic/CMakeLists.txt src/RadMarshakAsymptotic/test_radiation_marshak_asymptotic.cpp src/RadhydroSimulation.hpp src/radiation_system.hpp commit dab9342403faa82d06f6071a78b9482dfc0f28a8 Author: Ben Wibking 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 _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/running_on_hpc_clusters.rst commit 6f9863af11f1fc40f34b1f3df0e5ab274b064f34 Author: Ben Wibking 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`. - [x] I have requested a reviewer for this PR. 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) 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) 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 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. --------- Co-authored-by: Mark Krumholz .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 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) Bumps [extern/amrex](https://github.com/AMReX-Codes/amrex) from `601cc4e` to `9b733ec`.

Commits

9b733ec solve_cg: avoid use of MF z (#3637)
0cd1385 Fix: nosmt OMP Threads Default (#3647)
44c5c7a When checking for periodic outs on GPU, copy full particle data (#3646)
4b8dd03 Comments on FAB-related classes and methods (#3636)
4b64003 Comments: correct some typos (#3641)
60b45bc MLEBABecLap: Support Robin BC at Domain Boundaries (#3617)
9e35dc1 Ascent: SoA Particle Support (#3350)
c51e0a3 CI: Ascent + Conduit (#3639)
d75c04b solve_bicgstab: use fewer MFs (#3635)
175b99d solve_bicgstab: cut use of s (#3629)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/amrex 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) Bumps [extern/yaml-cpp](https://github.com/jbeder/yaml-cpp) from `db03655` to `eaf7205`.

Commits

eaf7205 README.md: Describe building with debug libstdc++ mode
1c5a38e workflows/build.yml: Use debug std C++ library on Ubuntu
51adc5f Update yaml-cpp-config.cmake.in
30e6933 Fix yaml-cpp-config.cmake.in
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/yaml-cpp commit a59dec9d8d0f35c04ecebe922a8ed62663b6c845 Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri Dec 1 03:14:53 2023 +0000 Bump extern/fmt from `e0d3e34` to `99b9fbf` (#456) Bumps [extern/fmt](https://github.com/fmtlib/fmt) from `e0d3e34` to `99b9fbf`.

Commits

99b9fbf Add formatter for std::source_location (#3730)
8f83ee2 Apply coding conventions
2a8a694 Clarify that mixing code unit types is deprecated
0471800 Minor cleanup
b87ea22 Add native and generic representation for filesystem::path format spec (#3729)
5cfd28d Experiment with FILE in scan
73fae91 Cleanup .gitignore
6988be3 Bump version
2d1e4bb Remove a useless comment
7f8d419 Fix overflow in time_point formatting with large dates (#3727)
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Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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 src/HLLD.hpp src/HydroState.hpp src/MHDState.hpp src/RadhydroSimulation.hpp src/hydro_system.hpp commit 545acfaa0530dd65227daf3a1c16daa79f3b690b Author: ChongChong He 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 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 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 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 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 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 ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/Microphysics commit fda9b7ba885e91dcc91dc0ca3478e2f619c7d5d4 Author: ChongChong He 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 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] 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] 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] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/yaml-cpp commit daf01c124de3bd2c9eb0fa433f338e8b23827c0d Author: Ben Wibking 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 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] 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 .pre-commit-config.yaml commit cf5bcda3b235dbedfc0350d261bf6713c5f097dc Author: Ben Wibking 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 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 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 * redefined ComputePlanckEnergyFractions to return * cleanup tube.cpp * fix minor bugs * minor fix * fixed "radBoundaries not on device" error. Attempting to pass all tests on GPU. * /azp run * /azp run Update valarray.cpp to match main branch * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix 2 tidy warnings * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix git conflicts * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix 1 tidy warning * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * minor tidy fix * removed some commented code * Removed comments with author initials; removed unnecessary TODOs * add numeric check of E_1 and E_2 in SuOlson * add quadratic interp support to planck_integral * Add E_0 and E_1 to L1 norm check in RadTube test. * reset SuOlson to 1gropu; removed commented-out code. * Improved styling. Cleaned up comments. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed variable unused error * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix warning * fixed first-capture issue * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update submodule Microphysics * update submodule amrex * update submodule fmt * update submodule yaml-cpp * update submodule amrex to correct branch * update fmt to correct branch --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Ben Wibking 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 Date: Wed Oct 4 11:27:30 2023 -0400 Update GPU CI timeout (#417) * Update GPU CI timeout Set timeout to 90 minutes (increased from the default value of 60 minutes). * Update azure-pipelines.yml * Update azure-pipelines.yml * Update azure-pipelines.yml .ci/azure-pipelines.yml commit cb0c1151c5baa510c1c45282d8373431b9d1896b Author: Ben Wibking Date: Tue Oct 3 12:52:45 2023 -0400 Fix typos found by codespell (#416) * Fix typos found by codespell * re-use -> reuse src/AdvectionSimulation.hpp src/StarCluster/perturbation.py commit c374406310a277c4e178df4ddc196c2ff58253ac Author: Ben Wibking Date: Mon Oct 2 22:23:23 2023 -0400 Update issue templates (#414) This adds issue templates with a suggested outline when creating issues for 1. bug reports, and 2. feature proposals. .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) Bumps [extern/amrex](https://github.com/AMReX-Codes/amrex) from `1aea95c` to `b95482d`. - [Release notes](https://github.com/AMReX-Codes/amrex/releases) - [Commits](https://github.com/AMReX-Codes/amrex/compare/1aea95c021a8cbf0cab5e9e81f02a1b6e66249b5...b95482d3b2ad6cab8318c867eb3b71b4f9ee11ac) --- updated-dependencies: - dependency-name: extern/amrex dependency-type: direct:production ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/amrex commit 913b6e4204b8de886f5aefa7a7e3b51e72c60386 Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun Oct 1 08:20:49 2023 -0400 Bump extern/Microphysics from `ced7cc4` to `9c08d80` (#411) Bumps [extern/Microphysics](https://github.com/psharda/Microphysics) from `ced7cc4` to `9c08d80`. - [Commits](https://github.com/psharda/Microphysics/compare/ced7cc41dbafae11ed587c1d446d80e442b9b967...9c08d809b6798df9798691174e2fc3a64c41360c) --- updated-dependencies: - dependency-name: extern/Microphysics dependency-type: direct:production ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/Microphysics commit 076fea564d71f65278701db9ae97a81e63678007 Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun Oct 1 08:20:28 2023 -0400 Bump extern/yaml-cpp from `fcbb819` to `37f1b8b` (#410) Bumps [extern/yaml-cpp](https://github.com/jbeder/yaml-cpp) from `fcbb819` to `37f1b8b`. - [Release notes](https://github.com/jbeder/yaml-cpp/releases) - [Commits](https://github.com/jbeder/yaml-cpp/compare/fcbb8193b94921e058be7b563aea053531e5b2d9...37f1b8b8c9e5172ff3a79a3d5fdbb87f2994842b) --- updated-dependencies: - dependency-name: extern/yaml-cpp dependency-type: direct:production ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/yaml-cpp commit 10afd87980675499bb57207748e049919273b651 Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun Oct 1 08:20:18 2023 -0400 Bump extern/fmt from `e8259c5` to `349e1c4` (#412) Bumps [extern/fmt](https://github.com/fmtlib/fmt) from `e8259c5` to `349e1c4`. - [Release notes](https://github.com/fmtlib/fmt/releases) - [Commits](https://github.com/fmtlib/fmt/compare/e8259c5298513e8cdbff05ce01c46c684fe758d8...349e1c48d14524c761cc8a72c75abb0d33c237a3) --- updated-dependencies: - dependency-name: extern/fmt dependency-type: direct:production ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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) * change 1 * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: Piyush Sharda Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> 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) * add sample script for setonix CPUs * separate setonix CPU and GPU scripts * updated * remove srun options * exclusive node access * updated * remove psharda * updated --------- Co-authored-by: Piyush Sharda 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) * updated README * updated * put back some stuff --------- Co-authored-by: Piyush Sharda README.md commit 033e4f3e98b20243922d1e4407a62209f8282cee Author: ChongChong He Date: Thu Sep 21 23:11:15 2023 +1000 Valarray extended (#391) * first commit: fix CMakeLists for macOS * Extend quokka::valarray with more operators. * Revert "first commit: fix CMakeLists for macOS" This reverts commit 422cfe23067a77c57aa7b1837bd904e8e308037e. * mod .gitignore * small fixes and revert .gitignore * set fillin to a member of valarray * rename fillin to valarray_fillin * define .fillin and .hasnan src/valarray.hpp commit 1cebf4bf5dfc5a676e70e004649e627637d40e77 Author: ChongChong He Date: Thu Sep 21 23:11:02 2023 +1000 update the flowchart on the website (#392) * update the flowchart on the website 1. a prettier look 2. add routines of the radiation module * update flowchart.rst docs/flowchart-v2.jpg docs/flowchart-v2.pdf docs/flowchart.rst commit 2eb8d6c980c2c3e12bf7facd012d4f8306685275 Author: Ben Wibking Date: Tue Sep 19 08:05:35 2023 -0400 update amrex (#387) extern/amrex commit ba35f265efa5eb010b252a520fad7a6384806ac7 Author: Ben Wibking Date: Tue Sep 19 08:02:48 2023 -0400 output multifab to disk if hydro update fails (#385) * write multifab to disk if hydro update fails * call MPI_Abort 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) * return invalid state if mass scalars have negative partial densities * enforce limits on mass scalars * use if constexpr * print cell coords * print cell coords * check for dimensions * amrex spelling * new function for printing coords * fix error * declare const * fix bug * remove clangtidy suggestion --------- Co-authored-by: Piyush Sharda Co-authored-by: Ben Wibking src/RadhydroSimulation.hpp commit 5a4276394416a10b994262955c257bc4a6caedcf Author: Ben Wibking Date: Tue Sep 19 07:59:28 2023 -0400 use minmod limiting for PLM (#384) src/hyperbolic_system.hpp commit 294ad07c3cc2f73e14a566c47dddbe21e34236d3 Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon Sep 18 11:20:40 2023 -0400 Bump ZedThree/clang-tidy-review from 0.13.3 to 0.13.4 (#389) Bumps [ZedThree/clang-tidy-review](https://github.com/zedthree/clang-tidy-review) from 0.13.3 to 0.13.4. - [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/v0.13.3...v0.13.4) --- updated-dependencies: - dependency-name: ZedThree/clang-tidy-review dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .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) * return invalid state if mass scalars have negative partial densities * enforce limits on mass scalars * use if constexpr --------- Co-authored-by: Piyush Sharda src/hydro_system.hpp commit 16d57370dd346603f54d5977aa65c823b26eeec5 Author: Ben Wibking Date: Wed Sep 13 19:05:31 2023 -0500 add LLF fallback solver (#380) * add LLF fallback solver * fix typo src/LLF.hpp src/RadhydroSimulation.hpp src/hydro_system.hpp commit ca3f360580ba184058ac696aadeedb600e94ec72 Author: Ben Wibking Date: Tue Sep 12 20:05:26 2023 -0500 ensure first-order flux correction is consistent at box boundaries (#376) * exchange ghost redoFlags * check ghost cell redoFlags src/RadhydroSimulation.hpp commit 6b0e0c8e37888f7cdbc6f207c8c8b385e3def035 Author: Ben Wibking Date: Tue Sep 12 06:37:03 2023 -0500 revert to first-order space+time flux when RK2 flux fails (#221) * use Roe-average wavespeeds * fix bug in roe-averaged sound speed * use LLF solver with first-order flux * revert to first-order space+time flux * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * cherry-pick fix for SphericalCollapse * remove Riemann solver template parameter * fix typo * remove LLF solver (unused) * Update src/RadhydroSimulation.hpp Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Update src/RadhydroSimulation.hpp Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * update HydroHighMach tolerance --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Mark Krumholz Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> 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) Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .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 Date: Sat Sep 9 17:42:41 2023 -0400 update setonix configuration (#362) * update setonix configuration * update config * use un-hidden cmake * Update setonix.cmake --------- Co-authored-by: Piyush Sharda <34922596+psharda@users.noreply.github.com> 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 Date: Sat Sep 9 07:40:19 2023 -0400 add YAML metadata I/O (#364) * add YAML metadata I/O * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Apply suggestions from code review Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add include * Revert "[pre-commit.ci] auto fixes from pre-commit.com hooks" This reverts commit 944c31a5367f38097862c3356aa62b8a47a94fd8. * Revert "Apply suggestions from code review" This reverts commit 5ab6c481a0dedbd3a94c4039ada555d6b3ab1921. * fix const * fix bad merge --------- 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: Piyush Sharda <34922596+psharda@users.noreply.github.com> src/simulation.hpp commit b169a30c59d57e80eb83fcad77d3fb76d4350334 Author: Ben Wibking Date: Sat Sep 9 07:38:50 2023 -0400 add axis-aligned projection outputs (#367) * add axis-aligned projection outputs * Apply suggestions from code review Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * add const * fix warning --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Piyush Sharda <34922596+psharda@users.noreply.github.com> 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) * remove is_chemistry_enabled * remove is_chemistry_enabled 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 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 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 Date: Thu Sep 7 19:59:45 2023 -0400 copy Blueprint mesh to host (#365) src/simulation.hpp commit 50b22e1781bbe8e26548347f5738d5916784463d Author: Ben Wibking Date: Tue Sep 5 19:41:20 2023 -0400 add yaml-cpp as a submodule (#360) * add yaml-cpp as a submodule * [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> .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) Bumps [extern/amrex](https://github.com/AMReX-Codes/amrex) from `cf8d9f8` to `de7c618`. - [Release notes](https://github.com/AMReX-Codes/amrex/releases) - [Commits](https://github.com/AMReX-Codes/amrex/compare/cf8d9f8e233be2ac68aeb65a95e992adfb483939...de7c6189623bc3ba178a380e703e3173f33f78ef) --- updated-dependencies: - dependency-name: extern/amrex dependency-type: direct:production ... Signed-off-by: dependabot[bot] 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) Bumps [extern/fmt](https://github.com/fmtlib/fmt) from `8a4bec5` to `e8259c5`. - [Release notes](https://github.com/fmtlib/fmt/releases) - [Commits](https://github.com/fmtlib/fmt/compare/8a4bec5cf53387356738a06ba0cf4fdf086241ae...e8259c5298513e8cdbff05ce01c46c684fe758d8) --- updated-dependencies: - dependency-name: extern/fmt dependency-type: direct:production ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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) Bumps [extern/Microphysics](https://github.com/psharda/Microphysics) from `9ecfd8d` to `ced7cc4`. - [Commits](https://github.com/psharda/Microphysics/compare/9ecfd8d22f8e6ccbbd2fa1ab923373f17931307b...ced7cc41dbafae11ed587c1d446d80e442b9b967) --- updated-dependencies: - dependency-name: extern/Microphysics dependency-type: direct:production ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/Microphysics commit 13be468b4ccfe13090d5aa515c026cd2cf482fac Author: Ben Wibking Date: Thu Aug 31 19:52:52 2023 -0400 add Navier-Stokes Characteristic Boundary Conditions (#352) * add updated cloud problem * add coolinglength and mmw functions * fix cloud problem * update param file * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add option to read cloudy tables even if disabled * remove old code * removed unnecessary params * silence clang-tidy warnings * Apply suggestions from code review Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix integratorOrder = 1 * add hydro debugging output * update cloud settings * revert shockcloud to development * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * revert CloudyCooling.hpp * add NSCBC test problem * fix ascent includes * fix typo * fix channel problem * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * allow build in 1d * remove table_data * Update src/simulation.hpp Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * move globals to namespace * fix bad clang-tidy suggestion * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * clean-up channel problem * add sympy notebook * add prototype implementation * fix unicode error * fix cxxcode output * re-derive eigensystem * working prototype * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update problem params to match paper * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * use target temperature for inflow * add ChannelFlow to test suite * add passive scalar * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Apply suggestions from code review (add const) Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update error tolerance * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove shock-cloud param file * refactor * add convecting vortex test * add transverse terms * add all transverse terms, eliminate explicit gamma * add permutations * fix dependent type shadow * add option to outflow along y-axis * removed unused vars * only build vortex test in 2D/3D * fix typo * fix loop indices * fix const * stricter tolerance * fix typo * fix CMakeLists --------- 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> 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) Bumps [ZedThree/clang-tidy-review](https://github.com/zedthree/clang-tidy-review) from 0.13.2 to 0.13.3. - [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/v0.13.2...v0.13.3) --- updated-dependencies: - dependency-name: ZedThree/clang-tidy-review dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .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) * adjust multigrid parameters for gravity solve * add prototype star cluster example * reduce reltol for poisson solve * initialize with gaussian random field * add Jeans refinement * update params * change debugging settings * move settings to runtime params * add derived var * gpu fixes * gpu fix * fix OpenBCSolver init * add StarCluster AMR params file * delete old file * refactor code * read perturbations from file * fix TableData indices * increase max_retries * fix build on Crusher * add TinyProfiler regions * rename file content * define problem_main * generate zdrv.hdf5 * update file * update file * update microp * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix spellings * reorder tests * reorder tests * run python script for starcluster test * add filename * add custom command to run python script * revert changes * use python to generate input file * copy input file to binary * reset maxtries to 4 * make Gconst a runtime parameter with a default value * copy zdrv.hdf5 to tests/ * remove StaarCluster AMR test from repo * remove sim.Gconst * updated microp * produce input file at runtime * check for h5py * synced microp; * update microp * clang-tidy comments * clang-tidy * fix bug * increase simulation time time to ~tff * set Gconst to unity --------- Co-authored-by: Ben Wibking Co-authored-by: Ben Wibking Co-authored-by: Piyush Sharda Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Piyush Sharda Co-authored-by: Piyush Sharda .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) Bumps [ZedThree/clang-tidy-review](https://github.com/zedthree/clang-tidy-review) from 0.13.1 to 0.13.2. - [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/v0.13.1...v0.13.2) --- updated-dependencies: - dependency-name: ZedThree/clang-tidy-review dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .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) Bumps [SonarSource/sonarcloud-github-c-cpp](https://github.com/sonarsource/sonarcloud-github-c-cpp) from 1 to 2. - [Release notes](https://github.com/sonarsource/sonarcloud-github-c-cpp/releases) - [Commits](https://github.com/sonarsource/sonarcloud-github-c-cpp/compare/v1...v2) --- updated-dependencies: - dependency-name: SonarSource/sonarcloud-github-c-cpp dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .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) * add nonlinear wavespeed correction * first step: for ideal gas EOS * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * rename to match other variables * store mass scalars in HydroState * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add massScalars * template HLLC with problem_t * find dedr from Microphysics EOS * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add num mass scalars in template * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * use microphysics to find eos quantities * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix bug * added thermodynamic derivatives * added expression for C_tilde_P * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * cosmetic change * club derivative functions into one to increase speed * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * dont need to declare dedr dpdr dedp * remove comments * calculate Gamma for fundamental derivative * use second order wavespeed correction * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * cleanup * updated microp * implement full equation for G * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * simplified expression for G * updated microp: correct expression for d2pdr2_s * define G directly in microp * updated microp: add primordial chem thermo derivatives --------- Co-authored-by: Ben Wibking Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> 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) Bumps [extern/amrex](https://github.com/AMReX-Codes/amrex) from `9c256b1` to `cf8d9f8`. - [Release notes](https://github.com/AMReX-Codes/amrex/releases) - [Commits](https://github.com/AMReX-Codes/amrex/compare/9c256b12b89f86b30fe1a6f03dd79db351d56fb3...cf8d9f8e233be2ac68aeb65a95e992adfb483939) --- updated-dependencies: - dependency-name: extern/amrex dependency-type: direct:production ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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) Bumps [extern/fmt](https://github.com/fmtlib/fmt) from `e4c8cfe` to `8a4bec5`. - [Release notes](https://github.com/fmtlib/fmt/releases) - [Commits](https://github.com/fmtlib/fmt/compare/e4c8cfe38ed3ae595aab58460f543c2f23a7f670...8a4bec5cf53387356738a06ba0cf4fdf086241ae) --- updated-dependencies: - dependency-name: extern/fmt dependency-type: direct:production ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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) * compute pressure from microphysics eos * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * call EOS to compute pressure * add function to compute pressure * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * return pressure times density * updated microp * change mean mol weight from NAN to arbitrary +ve value to get finite pressure from microp gamma_law * use gamma_law to compute pressure * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * define a finite mean molecular weight * more EOS calls * dont need microp headers * removed unused var * remove unused vars * remove unused var; assert P * fixed warnings * use EOS compute pressure directly * updated microp * updated microp * added ComputeSoundSpeed * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated microp * spell check * pass quokka gamma to microphysics eos * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add function ComputeEintFromPres * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * use EOS to find pres and cs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * replace K_S with sound spped calc * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * avoid re-declaaration * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix warning * use microp EOS * remove ASSERT * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove unused var * fix bug in EintFromPres * declaring P_L as const double * remove unused var * remove declaration of P_L * updated microp: ensure exact cancellation * remove unused var * use finite mean_molecular_weight * use finite mol wt and use microphysics for EOS * use finite mean mol wt * use microphysics eos * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove unused var * if rho = 0, pres is 0 * return finite pressure for isothermal gamma * @psharda return finite pressure for isothermal gamma * use finite mol wt * minor style changes --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> .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) * track branch from max * enable two-EOS compilation * use ifdefs for primordial chem * include actual eos data header * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated microp * updated microp * update microp * updated microphysics * use BEFORE keyword to set right priority of include dirs * updated microp: remove gammalaw eos params from primordial chem eos * updated microp * include QuokkaObjSources * updated microp * remove de-linking quokkaobj lib * only build some tests * reattached microp * add QuokkaObjSources * build all tests * use microp EOS for all tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add gamma_law_sources to all tests * initializes Microphysics EOS * initialize extern_params * use the new chem_eos_t struct * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated microp * updated microp * added hydrogen_mass_code_units as an EOS_Trait * removed EOS_traits * defined hydrogen_mass_code_units in EOS traits * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * specify code units in EOS class * add code units * initialize EOS * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * corrected the name for mean_molecular_weight * corrected code units * corrected code units * scale Tgas by k_B * use microphysics k_B * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * corrected code units * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * code unit changed to 1/n_A * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated microp * use microp constant for hydrogen mass * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * changed mass units * use amu and k_B from microphysics instead of m_H and k_B in quokka * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * revert to hydrogen mass * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * revert to hydrogen mass * use amu * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * use amu * revert to hydrogen mass * changed EOS functions to use microphysics * scaled dedT by kB * fixed bug * fixed bugs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove mass_code_units * remove mass_code_units --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> .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 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) Bumps [extern/amrex](https://github.com/AMReX-Codes/amrex) from `2e1106e` to `9c256b1`. - [Release notes](https://github.com/AMReX-Codes/amrex/releases) - [Commits](https://github.com/AMReX-Codes/amrex/compare/2e1106e246c442514d072f76b049d4f0b02216a2...9c256b12b89f86b30fe1a6f03dd79db351d56fb3) --- updated-dependencies: - dependency-name: extern/amrex dependency-type: direct:production ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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) Bumps [extern/fmt](https://github.com/fmtlib/fmt) from `b2106f3` to `e4c8cfe`. - [Release notes](https://github.com/fmtlib/fmt/releases) - [Commits](https://github.com/fmtlib/fmt/compare/b2106f3639dda5b311966047d1a146edc5f4e663...e4c8cfe38ed3ae595aab58460f543c2f23a7f670) --- updated-dependencies: - dependency-name: extern/fmt dependency-type: direct:production ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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) * track branch from max * enable two-EOS compilation * use ifdefs for primordial chem * include actual eos data header * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated microp * updated microp * update microp * updated microphysics * use BEFORE keyword to set right priority of include dirs * updated microp: remove gammalaw eos params from primordial chem eos * updated microp * include QuokkaObjSources * updated microp * remove de-linking quokkaobj lib * only build some tests * reattached microp * add QuokkaObjSources * build all tests --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> .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 src/PassiveScalar/CMakeLists.txt src/PrimordialChem/CMakeLists.txt src/PrimordialChem/test_primordial_chem.cpp 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 761f4b6f92675ab7ce25a79eafbd260624993619 Author: Ben Wibking 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 * Update dependencies_hip.sh * test ROCm 5.2 * test ROCm 5.3.3 * test ROCm 5.4.3 .github/workflows/dependencies/dependencies_hip.sh commit d6828f8b1e1408040ba1b757071ce70c46309fe4 Author: Ben Wibking Date: Wed Jun 21 16:44:20 2023 +1000 update Setonix CMake settings (#321) * update Setonix CMake settings * 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) updates: - [github.com/pre-commit/mirrors-clang-format: v16.0.4 → v16.0.6](https://github.com/pre-commit/mirrors-clang-format/compare/v16.0.4...v16.0.6) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> .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 * use two cores to ctest azure pipeline .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) * add HIP CI build * update permissions for dep scripts * fix triggers * fetch submodules * add python and HDF5 deps * -Wno-unused-parameter * disable some warnings * don't warn on c++98 incompatibility * don't warn on float conversion * ensure compilation on AMD GPUs * Revert "ensure compilation on AMD GPUs" This reverts commit 3ca5c5cdc043ae513abcbee7350a22d1eb78c99d. * ensure compilation on AMD GPUs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * use nmscalars_variable * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove CXXFLAGS * Revert "[pre-commit.ci] auto fixes from pre-commit.com hooks" This reverts commit 12f100d7bcbf90432c719d34500a4386286f3137. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * revert commit on using unused variable --------- Co-authored-by: Ben Wibking Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> .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) Bumps [extern/amrex](https://github.com/AMReX-Codes/amrex) from `cf6b46b` to `2e1106e`. - [Release notes](https://github.com/AMReX-Codes/amrex/releases) - [Commits](https://github.com/AMReX-Codes/amrex/compare/cf6b46bd95a35a9e0d4e5c83ddc8394e6295e123...2e1106e246c442514d072f76b049d4f0b02216a2) --- updated-dependencies: - dependency-name: extern/amrex dependency-type: direct:production ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Ben Wibking 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) Bumps [extern/fmt](https://github.com/fmtlib/fmt) from `02cae7e` to `b2106f3`. - [Release notes](https://github.com/fmtlib/fmt/releases) - [Commits](https://github.com/fmtlib/fmt/compare/02cae7e48ac9b1d90acb0ee07c76fbde2462a99e...b2106f3639dda5b311966047d1a146edc5f4e663) --- updated-dependencies: - dependency-name: extern/fmt dependency-type: direct:production ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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) Bumps [extern/Microphysics](https://github.com/psharda/Microphysics) from `7fd6094` to `bf80346`. - [Commits](https://github.com/psharda/Microphysics/compare/7fd60944d9431d38c97ebd5ffea2fa82b3da82a5...bf80346094d2424703ee008e5f03f5016fb98584) --- updated-dependencies: - dependency-name: extern/Microphysics dependency-type: direct:production ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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) Bumps [ZedThree/clang-tidy-review](https://github.com/ZedThree/clang-tidy-review) from 0.13.0 to 0.13.1. - [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/v0.13.0...v0.13.1) --- updated-dependencies: - dependency-name: ZedThree/clang-tidy-review dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .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) * defined a new function to retrieve mass scalars * use microphysics EOS for primordial chem * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * rename massFractions --> massScalars * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * defined state.xn for all routines * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * removed old comment * replace massFractions --> massScalars * correctly retrieve massScalars as an array * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed Tgas error * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * initialize chemstate.T for EOS mode rt * initialize chemstate.xn to avoid warning * initialize chemstate.xn in a loop * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * using different int variables for initialization loop * replace ifdef with if constexpr * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * declare constexpr primordial chem * include microphysics headers * declared return variables * initialize return variables to avoid warnings * remove duplicate initialization * implement clang-tidy suggestion * use massScalars in EOS functions * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * use mass scalars for EOS functions * use ComputeMassScalars * move ComputeMassScalars to radiation_system.hpp * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * define another template for CompueMassScalars * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added typename * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * trying templating ArrayType * call function normally * added comment on the usage of ComputeMassScalars requiring additional template --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> 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 * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * rename massFractions --> massScalars * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * defined state.xn for all routines * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * removed old comment * replace massFractions --> massScalars * correctly retrieve massScalars as an array * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed Tgas error * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * initialize chemstate.T for EOS mode rt * initialize chemstate.xn to avoid warning * initialize chemstate.xn in a loop * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * using different int variables for initialization loop * replace ifdef with if constexpr * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * declare constexpr primordial chem * include microphysics headers * declared return variables * initialize return variables to avoid warnings * remove duplicate initialization * implement clang-tidy suggestion --------- 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 * added mass scalars * define optional argument for EOS routines * resolved conflict * ignore unused variable * include AMReX.H * use a different branch in microphysics * revert to version without ignore_unused * updated microphysics: namespace update * updated microphysics * use massFractions in EOS * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * use massFractions in dEint / dt * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated microphysics: primordial CI --------- 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) updates: - [github.com/pre-commit/mirrors-clang-format: v16.0.3 → v16.0.4](https://github.com/pre-commit/mirrors-clang-format/compare/v16.0.3...v16.0.4) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> .pre-commit-config.yaml commit 7d6c8b7ccd616347e5443b37aeb17ed8c1032da2 Author: Ben Wibking 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 Date: Sat May 20 00:33:43 2023 +1000 simplify Setonix SLURM scripts (#289) Co-authored-by: Benjamin Wibking 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 Date: Fri May 19 16:33:38 2023 +1000 treat all compiler warnings as errors (#283) * treat warnings as errors * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix warnings * use range-based for loop * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix signed integer comparisons * update microphysics submodule * ensure that self-gravity is only used in 3D * update Microphysics * add option WARNINGS_AS_ERRORS --------- Co-authored-by: Ben Wibking 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) * optimise load * extending tmp read for fc mf * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update simulation.hpp to include fc var instead of cc var --------- Co-authored-by: Ben Wibking Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> src/simulation.hpp commit 5e6c3e0ea770cd3452228139ffa80c1780cad7bb Author: Ben Wibking 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 Date: Mon May 15 16:29:58 2023 +1000 update Setonix SLURM script (#284) * added Setonix scripts * update SLURM script * add wrapper script * working slurm script using wrapper script * added comments * remove broken SLURM script * add 8- and 64-node Setonix scripts * ensure no extraneous modules are loaded --------- Co-authored-by: Benjamin Wibking Co-authored-by: Benjamin Wibking scripts/setonix-1node.submit scripts/setonix-64nodes.pbs scripts/setonix-8nodes.pbs scripts/setonix.profile commit 5564aa534cee2bd613a38a17d4fe851cd7317882 Author: Ben Wibking Date: Tue May 9 23:51:56 2023 +1000 added Setonix scripts (#282) Co-authored-by: Benjamin Wibking 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) updates: - [github.com/pre-commit/mirrors-clang-format: v16.0.2 → v16.0.3](https://github.com/pre-commit/mirrors-clang-format/compare/v16.0.2...v16.0.3) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> .pre-commit-config.yaml 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) * updated src CMakeLists to include Microphysics * added test_primordial_chem.cpp file * added test_primordial_chem.hpp file * unlinked microphysics as library and added source files variable to primordial chem * deleted .cpp file * added .cpp file * updated .cpp file * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated microphysics * updated microphysics with include dirs variable * included primordial chem dirs * finalized .hpp file * updated . cpp file * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated .cpp and .in files * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated .coo and .in files * added .cpp file * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated .cpp file * updated .cpp file * updated .cpp and .in files * added species * updated .cpp file * updated .cpp file * added grackle and cloudy to executable * updated microphysics * changed filename so parmparse can find it * included parmparse.h * renamed file * renamed .in file * updated microphysics * correctly set boundary conditions * removed scalars * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added scalars * further modifications for primordial chem test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated microphysics * added burn_type.H * modified cmakelists * defined scopes to ensure correct dirs are included * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated microphysics * updated microphysics * added burn state * added enable chemistry parameter * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added chemistry files * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added chemistry runtime parameters * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * corrected some bugs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * removed T_floor * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * renamed microphysics burn state * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added call to compute chemistry * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * redefined chem variable * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * correctly used MultiFab variables * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * cosmetic change * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * cannot include RadhydroSimulation.hpp in Chemistry.hpp * included microphysics dirs in src * initialized eos and network * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added remaining runtime params * added primordial_chem_sources to executable * defined object library for primordial_chem_sources * use primordialchem object lib * defined object lib for primordial chem sources * added primordial_chem as preprocessor variable * add preprocessor variable for primordial chem * wrapped chemistry in ifdefs * removed primrodial_chem_sources * renamed primordialchem object lib * added dimension-based BCs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added dimension-based BCs * updated microphysics * return this CMakeList as it is * return this CMakeList as it is * return this CMakeList as it is * return this CMakeList as it is * return this CMakeList as it is * re-added .json bit * Revert "re-added .json bit" This reverts commit e59932e7949d734129ce1f1e8a098b1b046cc491. * added cuda compilation for promordialchemObj * added primordial_chem_sources * updated microphysics: specified working directory for execute process scripts * commented out primordialchem object lib * removed unwanted code * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * deleted extra loop * fixed bugs * added abort if density > 3e-6 g/cm^3 * use double quotes for amrex::Abort message * renamed primordial chem test input file * added static_cast based on github-actions suggestion * removed primordial_chem_sources * removed primordial_chem_sources * removed primordial_chem_sources * removed primordial_chem_sources * removed primordial_chem_sources * added abort for GPUs if integration fails in VODE in Microphysics * removed ifdef around state.success * updated microphysics * defined runtime parameter for max density threshold in primordial chem * removed substeps * updated abort message when max density exceeded * removed outdated comments * moved initi routines to preCalculateInitialConditions * added runtime param for max density * renamed params * added max_density_allowed as input variable in computeChemistry func * using SimulationData to define all species and temperature * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated microphysics * disabled parallel build in azure CI * azure parallel build with 3 procs * increase timeout to 120 mins * increase procs to 2 * removed Lx Ly Lz as per clang-tidy suggestion * added default label for switch * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed bug * removed default case * removed unenecssary stuff * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * implemented clang-tidy suggestion to use std::array * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added comment on generalizing charge consv * added default case * add dEint to Eint and Ener * multiply microphysics eint with rho to match quokka eint * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * compute eint from egas * parmparsed temp * added #define PRIMORDIAL_CHEM for primordial chem test * increase timeout to 180 mins * removed duplicate include_directories * removed set(PRIMORDIAL_CHEM) as we use target_compile_definitions now * moved burn to .cpp * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * increased timeout to 180 mins * implement clang-tidy suggestion: declare dt as Real dt instead of const Real dt Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Revert "implement clang-tidy suggestion: declare dt as Real dt instead of const Real dt" This reverts commit 48e6f67ba86214c0c226a0c9dde6af5fd3868072. * updated microphysics * define chemburner function * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated microphysics: greatly simplified RHS network file * fixed call to chemburner * fixed chemburner declaration * added GPU flag for chemburner * enable parallel build again * created job with timeout 180 mins * fixed typo * enable parallel build * cosmetic changes * defined const variables * deleted azure pipelines * added azure pipelines * added placeholders for specie flux consv * added flux consv loop * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * revert changes * added flux consv * added flux consv for chem species * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * scale specie fluxes by density * updated microphysics * updated microphysics: application code should abort on failure * Revert "updated microphysics: application code should abort on failure" This reverts commit 0eec679c46b40ced9c4b0f2cb113ed2a2a23f8b1. * updated microphysics * defined mass scalars * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added mass scalars * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added CMA reference * added mass scalars * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added Shocktube CMA test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added CMA test in cmake build * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated microphysics * increased err tolerance * added computeAfterEvolve * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added print statement * added computeAfterTimestep * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated microphysics: simplified primordial chem RHS further * fixed bug * run computeAfterTimestep on each cell * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated microphysics * pass partial densities instead of mass fractions, also plot the results * pass partial densities instead of mass fractions, also plot results * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed file conflict * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Quokka uses partial densities, not mass fractions * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed case * implemented clang-tidy comments * define mass scalars * define mass scalars * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed logic for success * implemented clang-tidy suggestion * turn on artificial viscosity --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Piyush Sharda 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 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 .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) Bumps [extern/Microphysics](https://github.com/psharda/Microphysics) from `4300ac4` to `dcbe5d6`. - [Release notes](https://github.com/psharda/Microphysics/releases) - [Commits](https://github.com/psharda/Microphysics/compare/4300ac4f28118797a88aa99075fb1493c1a2f3d2...dcbe5d6dff3c0749adb23a92856fafdd706c3be1) --- updated-dependencies: - dependency-name: extern/Microphysics dependency-type: direct:production ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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) Bumps [extern/fmt](https://github.com/fmtlib/fmt) from `8ec94ac` to `02cae7e`. - [Release notes](https://github.com/fmtlib/fmt/releases) - [Commits](https://github.com/fmtlib/fmt/compare/8ec94ac6a5cb1a7f8ee8a86bebc1100fd7b212ca...02cae7e48ac9b1d90acb0ee07c76fbde2462a99e) --- updated-dependencies: - dependency-name: extern/fmt dependency-type: direct:production ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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) Bumps [extern/amrex](https://github.com/AMReX-Codes/amrex) from `c1e8e73` to `cf6b46b`. - [Release notes](https://github.com/AMReX-Codes/amrex/releases) - [Commits](https://github.com/AMReX-Codes/amrex/compare/c1e8e73b63dc8b6732c6cdfe51914f7ae144575b...cf6b46bd95a35a9e0d4e5c83ddc8394e6295e123) --- updated-dependencies: - dependency-name: extern/amrex dependency-type: direct:production ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 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) * 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 * added directory for primordial chem test * added .in file for primordial chem test * updated src CMakeLists to include Microphysics * added test_primordial_chem.cpp file * added test_primordial_chem.hpp file * unlinked microphysics as library and added source files variable to primordial chem * deleted .cpp file * added .cpp file * updated .cpp file * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated microphysics * updated microphysics with include dirs variable * included primordial chem dirs * finalized .hpp file * updated . cpp file * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated .cpp and .in files * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated .coo and .in files * added .cpp file * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated .cpp file * updated .cpp file * updated .cpp and .in files * added species * updated .cpp file * updated .cpp file * added grackle and cloudy to executable * updated microphysics * changed filename so parmparse can find it * included parmparse.h * renamed file * renamed .in file * updated microphysics * correctly set boundary conditions * removed scalars * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added scalars * further modifications for primordial chem test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated microphysics * added burn_type.H * modified cmakelists * defined scopes to ensure correct dirs are included * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated microphysics * updated microphysics * added burn state * added enable chemistry parameter * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added chemistry files * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added chemistry runtime parameters * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * corrected some bugs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * removed T_floor * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * renamed microphysics burn state * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added call to compute chemistry * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * redefined chem variable * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * correctly used MultiFab variables * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * cosmetic change * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * cannot include RadhydroSimulation.hpp in Chemistry.hpp * included microphysics dirs in src * initialized eos and network * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added remaining runtime params * added primordial_chem_sources to executable * defined object library for primordial_chem_sources * use primordialchem object lib * defined object lib for primordial chem sources * added primordial_chem as preprocessor variable * add preprocessor variable for primordial chem * wrapped chemistry in ifdefs * removed primrodial_chem_sources * renamed primordialchem object lib * added dimension-based BCs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added dimension-based BCs * updated microphysics * return this CMakeList as it is * return this CMakeList as it is * return this CMakeList as it is * return this CMakeList as it is * return this CMakeList as it is * re-added .json bit * Revert "re-added .json bit" This reverts commit e59932e7949d734129ce1f1e8a098b1b046cc491. * added cuda compilation for promordialchemObj * added primordial_chem_sources * updated microphysics: specified working directory for execute process scripts * commented out primordialchem object lib * removed unwanted code * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * deleted extra loop * fixed bugs * added abort if density > 3e-6 g/cm^3 * use double quotes for amrex::Abort message * renamed primordial chem test input file * added static_cast based on github-actions suggestion * removed primordial_chem_sources * removed primordial_chem_sources * removed primordial_chem_sources * removed primordial_chem_sources * removed primordial_chem_sources * added abort for GPUs if integration fails in VODE in Microphysics * removed ifdef around state.success * updated microphysics * defined runtime parameter for max density threshold in primordial chem * removed substeps * updated abort message when max density exceeded * removed outdated comments * moved initi routines to preCalculateInitialConditions * added runtime param for max density * renamed params * added max_density_allowed as input variable in computeChemistry func * using SimulationData to define all species and temperature * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated microphysics * disabled parallel build in azure CI * azure parallel build with 3 procs * increase timeout to 120 mins * increase procs to 2 * removed Lx Ly Lz as per clang-tidy suggestion * added default label for switch * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed bug * removed default case * removed unenecssary stuff * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * implemented clang-tidy suggestion to use std::array * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added comment on generalizing charge consv * added default case * add dEint to Eint and Ener * multiply microphysics eint with rho to match quokka eint * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * compute eint from egas * parmparsed temp * added #define PRIMORDIAL_CHEM for primordial chem test * increase timeout to 180 mins * removed duplicate include_directories * removed set(PRIMORDIAL_CHEM) as we use target_compile_definitions now * moved burn to .cpp * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * increased timeout to 180 mins * implement clang-tidy suggestion: declare dt as Real dt instead of const Real dt Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Revert "implement clang-tidy suggestion: declare dt as Real dt instead of const Real dt" This reverts commit 48e6f67ba86214c0c226a0c9dde6af5fd3868072. * updated microphysics * define chemburner function * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated microphysics: greatly simplified RHS network file * fixed call to chemburner * fixed chemburner declaration * added GPU flag for chemburner * enable parallel build again * created job with timeout 180 mins * fixed typo * enable parallel build * cosmetic changes * defined const variables * deleted azure pipelines * added azure pipelines --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Piyush Sharda Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> .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 tests/primordial_chem.in commit f002cea8e50388637852e978864848383b526da8 Author: Ben Wibking 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. * fix cmake build * checkout submodules * disable running on PRs .github/workflows/sonarcloud.yml commit 4a74efa67340c3bb076475934b2031449a73c65f Author: Ben Wibking 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. * Update cmake-macos.yml .github/workflows/cmake-macos.yml commit c972a51d8ba6383bc984288318a84a54f95655e5 Author: Ben Wibking 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) * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/pre-commit/mirrors-clang-format: v16.0.1 → v16.0.2](https://github.com/pre-commit/mirrors-clang-format/compare/v16.0.1...v16.0.2) * [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> .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) Bumps [ZedThree/clang-tidy-review](https://github.com/ZedThree/clang-tidy-review) from 0.12.3 to 0.13.0. - [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/v0.12.3...v0.13.0) --- updated-dependencies: - dependency-name: ZedThree/clang-tidy-review dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .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) Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 2 to 3. - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v2...v3) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .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) Bumps [actions/deploy-pages](https://github.com/actions/deploy-pages) from 1 to 2. - [Release notes](https://github.com/actions/deploy-pages/releases) - [Commits](https://github.com/actions/deploy-pages/compare/v1...v2) --- updated-dependencies: - dependency-name: actions/deploy-pages dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .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] 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] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> extern/fmt commit b4a86f3b766443c170d6e3d905662a915db5a0dd Author: Ben Wibking 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 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 [pre-commit.ci] pre-commit autoupdate (#253) updates: - [github.com/pre-commit/mirrors-clang-format: v16.0.0 → v16.0.1](https://github.com/pre-commit/mirrors-clang-format/compare/v16.0.0...v16.0.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> .pre-commit-config.yaml commit 6d2691bb5c1d050269d48c53ece9ba427f229630 Author: Ben Wibking 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 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 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 .github/workflows/clang-tidy.yml .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 Date: Thu Apr 6 01:50:58 2023 -0400 update amrex submodule (#246) extern/amrex commit 9c9d2b2b9bc38fab09c1498024a2e8b3b90654da Author: Ben Wibking 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 for more information, see https://pre-commit.ci * relocate optional indexing arguments to the end of the arguments list * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * 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 for more information, see https://pre-commit.ci * update arg-names in func decl to be consistent with func defn * [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> src/hyperbolic_system.hpp src/radiation_system.hpp commit c4958e9e00bec84896a194f099166395d3f64d5b Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon Mar 27 19:03:15 2023 -0400 [pre-commit.ci] pre-commit autoupdate (#243) * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/pre-commit/mirrors-clang-format: v15.0.7 → v16.0.0](https://github.com/pre-commit/mirrors-clang-format/compare/v15.0.7...v16.0.0) * [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> .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 Date: Tue Feb 14 19:53:59 2023 -0500 updated Delta (NCSA) config (#235) Co-authored-by: Benjamin Wibking 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 for more information, see https://pre-commit.ci * add headerfile defining quantities conserved in the Riemann solver * [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> Co-authored-by: Mark Krumholz src/HLLD.hpp src/MHDState.hpp commit 4c34ac8fd1299192ef8934b7959eb73f83b27bea Author: Ben Wibking Date: Mon Feb 13 07:44:07 2023 -0500 update amrex submodule (#234) extern/amrex commit da42a8c1043d1112569bfa6ac1908884beb5e9c3 Author: Ben Wibking 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 Date: Tue Feb 7 00:54:12 2023 -0500 update amrex to fix sincos on macOS (#232) extern/amrex commit 64b087d30576f3b8c84d0eb1bf127924d076f28d Author: Ben Wibking 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 * [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> src/simulation.hpp tests/SphericalCollapse.in commit b167d9b70b5a06216917c8e5842352875b8dcc04 Author: Ben Wibking 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 src/ShockCloud/cloud.cpp src/ShockCloud/test_cloudy.cpp src/SphericalCollapse/CMakeLists.txt tests/Cooling.in tests/Cooling_1024.in tests/Cooling_2048.in tests/ShockCloud_128.in tests/ShockCloud_512.in commit c6b9b88cddaccb58ab4b816402e6bda6c48aa450 Author: Ben Wibking Date: Tue Jan 31 21:59:54 2023 -0500 update SLURM script for crusher (#226) scripts/crusher-1node.submit commit a6bff7fdad536a87ae09a517119758964de67b88 Author: Ben Wibking 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 src/RadhydroSimulation.hpp src/hydro_system.hpp tests/blast_unigrid_128.in commit e2d19c502a43fa7d7113bd125523b897227a5914 Author: Ben Wibking Date: Tue Jan 31 18:25:30 2023 -0500 fix AppleClang build (#229) src/CMakeLists.txt commit af42820a16bdfd9d9532d8a9c0fa10df7345959b Author: Ben Wibking 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 [pre-commit.ci] pre-commit autoupdate (#230) updates: - [github.com/pre-commit/mirrors-clang-format: v15.0.6 → v15.0.7](https://github.com/pre-commit/mirrors-clang-format/compare/v15.0.6...v15.0.7) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Ben Wibking .pre-commit-config.yaml 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 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 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 * [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> src/HLLC.hpp commit 03483a97eb30b5336a65d353f5d502603178e736 Author: Ben Wibking 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 Date: Thu Dec 22 02:28:22 2022 +1100 update amrex submodule (#213) extern/amrex commit e1f306ca519e2b0aa92049a81dda6e8332070524 Author: Ben Wibking 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 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 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 Date: Wed Dec 21 04:07:09 2022 +1100 add flowchart to docs (#203) Co-authored-by: Mark Krumholz 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 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 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 commit 6daebec4090b70f8a25e4ec26a18d9babc968cf0 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: - [github.com/pre-commit/mirrors-clang-format: v15.0.4 → v15.0.6](https://github.com/pre-commit/mirrors-clang-format/compare/v15.0.4...v15.0.6) 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 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 for more information, see https://pre-commit.ci * remove enforce density * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fixing bug in the enforcelimit function * removing bugged line from radhydro * minor changes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Moving EnforceLimit to hydrosystem and modifying to include EOS traits * Fixing radhydro * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * putting mean molecular wght=NAN in test problem files * Separate limits on the two temperatures from Eint and Etot-Ekin * Setting mean molecular weight to NAN in tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update src/hydro_system.hpp Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Formatting and changing ceilings to INFs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update src/hydro_system.hpp Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Update src/hydro_system.hpp Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Update src/hydro_system.hpp Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * tests were failing * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Minor changes to EnforceLimits to ensure tests don't fail * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * minor changes to hydrosys * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * addressing float to bool conversion and removing extra line * [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> Co-authored-by: Ben Wibking