V2.0 #198
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V2.0 #198
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still need to implement proper restart with planets
-PlanetPlanetRKR4D validates restart dumps for multiple planets
Tolerance are expected to be slightly affected in v2.0 because v2.0 does not store the cell centered- fields in its dump, while v1.0 did. As a result, the error is computed on the remaining fields, and hence is slightly larger (because cell-centered fields are an average, so the error due to those is expected to be half).
Clean up viscosity operators in planet tests which were incorrectly coded, and/or behaving incorrectly In particular: planetMigration2D was setting alpha=1e-3, but computation was actually performed with alpha=0. For this reason, the values for this test have been recomputed.
ensure that viscosityStatus is in sync with viscosity object. See merge request discs/idefix!314
field included (and no reconstruction)
emf boundary exchange routines are not needed anymore (because ghost zones are fully exchanged) Add back BX1s... fields in dump files even when we're using vector potential, so that the code can be restarted without vector potentials
(which are not needed anymore in principle)
RFC: deduplicate ouptut.CheckForWrites for initial conditions See merge request discs/idefix!315
…181) * use UGA's gitlab as LFS server to avoid github bandwidth limitations * use a public repo * try disabling lfs fetch * remove all lfs references in github workflow
* move away all reference files to a submodule fix idefix test suite accordingly * add the references as a submodule * no more LFS in CIs * [pre-commit.ci lite] apply automatic fixes * fix linter * remove useless vtk refs since we now use .dmp as reference. Move back the 1D solution for Sedov into the main repo. * don't use the same name to avoid conflict with previous lfs * Update pytools/idfx_test.py Co-authored-by: Clément Robert <cr52@protonmail.com> * Update pytools/idfx_test.py Co-authored-by: Clément Robert <cr52@protonmail.com> * replace thisDir by testDir 2/2 --------- Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com> Co-authored-by: Clément Robert <cr52@protonmail.com>
* DOC: add badges to README.md (#175) * MNT: update pre-commit hooks and fix newly detected linting errors (#178) * MNT: update pre-commit hooks * lint: remove redundant import statement in test file * Update idefix-ci.yml to get action in private repo * add eos files * first working implementation of the EOS module * works with 1D shocks * working isothermal impl. * working version with MHD * reforumation without explicit wave speed formulation when adiabatic * fix thermal diffusion being initialised before the EOS * apply the same logic to viscosity (avoid early initialisation) * use the EOS's get gamma function in setups * add custom EOS from cmake. Check that the template works * add doc * update naming in CMakeLists.txt * make sure GetGamma() can be called even for the isothermal EOS * fix some typo * fix drag with new EOS class * do not get on uninitialized eos unique_ptr --------- Co-authored-by: Clément Robert <cr52@protonmail.com>
* DOC: add badges to README.md (#175) * MNT: update pre-commit hooks and fix newly detected linting errors (#178) * MNT: update pre-commit hooks * lint: remove redundant import statement in test file * Xdmf io in `Idefix` (#13) * [ENH] Added `HighFive` hdf5 io submodule * [ENH] Added `Xdmf` IO feature * [RFC] Removed redundant prints * [DOC] Updated documentation describing `xdmf` dumps * [RFC] Native `HDF5` dump feature * [FIX] Fixed datatype of `vect3D` to match dump datatype * [ENH] Added more info to attributes in hdf5 file * [FIX] Fixed missing hyperslab select in serial io * [FIX] Fixed output for all dimensions * [ADD] Added a 3D test problem with unequal extent * [FIX] Made `hdf5` includes optional * [FIX] Optional `hdf5` include * [FIX] More optional `hdf5` fixes * [FIX] Linter fixes * [FIX] Fixed hdf5 optional include pre-processor flags * [FIX] Fixed hdf5 optional include pre-processor flags * Used `IDEFIX_ERROR` macro for missing hdf5 linking * [RFC] Incorporated changes suggested by @glesur * Broken CI by XDMF (#186) * force HDF5 in tests that requires XDMF outputs * correctly add HDF5 files when HDF5 is enabled through a setup CMakeLists Incidentally allow the user to enable MPI in a setup CMakeLists.txt * restore back the vtk frequency for CIs * remove xdmf from KHI test (not needed) * add xdmf to datablock * make xdmf work with new I/O layout * update the doc * fix xdmf implementation with varying directory * [pre-commit.ci lite] apply automatic fixes * make linter happy --------- Co-authored-by: Clément Robert <cr52@protonmail.com> Co-authored-by: Alankar Dutta <dutta.alankar@gmail.com> Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com>
* add push/popRegion to idefix_for and idefix_reduce when DEBUG is enabled * Force Kokkos::fence at the end of each idefix_for when DEBUG is enabled * implement on the fly profiler * fix documentation with the new profiling tool
* update changelog * remove references to git lfs * remove references to git lfs add some configuration examples for cmake * Doc: add example configuration add copy/paste button some minor typos/clarifications * fix dumpimage documentation
* Braginskii thermal conduction and diffusivity in every dimensions suitable for Idefix v2.0 * braginskii doc * Braginskii doc done * [pre-commit.ci lite] apply automatic fixes --------- Co-authored-by: Geoffroy Lesur <geoffroy.lesur@univ-grenoble-alpes.fr> Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com>
…ing at restart (#192) * ENH: add CLI flag to force calling Setup::InitFlow ahead of dump reading at restart * Update commandline.rst --------- Co-authored-by: Geoffroy Lesur <geoffroy.lesur@univ-grenoble-alpes.fr>
* ENH: define reusable macros for runtime checks * DOC: add documentation for RUNTIME_CHECK macros
* introduce pre-computation of self-gravity Laplacian operator * make the iterative solver deriving from a Laplacian functor * dust mass also contributes to the self-gravitating field
…n grids (#196) * check whether the grid is regular or not * slopelimiter construction now pushed during initialisation to allow the computation of plm coefficients * Add PLM reconstruction coefficient in non-cartesian grids * refactor slope limiters * add Paul Segretain's fix to curvature term in spherical coordinates (no motion in constant pressure setups) * fix axis flux on which we had a small (but measurable) leek of conserved quantities when in perfect equilibrium fix tolerance in planet planet case * update reference for CI/CD
add changelog fix test suite for -noplot
Co-authored-by: Clément Robert <cr52@protonmail.com>
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Introduce Idefix v2.0: self-gravity, dust, passive tracers, planets plus a number of bug fixes. See Changelog for details.