Move timers and @trixi_timeit to TrixiBase.jl
#543
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## main #543 +/- ##
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- Coverage 68.73% 68.61% -0.13%
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Files 69 69
Lines 4053 4037 -16
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- Hits 2786 2770 -16
Misses 1267 1267
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LasNikas
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Jul 3, 2024
* add .md and .bib files * add description of system interaction * revise [skip ci] * The grand reopening Part 2: Add overview page (#432) * implement * Revert "implement" This reverts commit 171505a. * some improvements to the documentation * some more fixes * add install documentation * add more info * update * Update get_started.md * add tutorial * fix * add stubs * update * include the example files * update * update * format * add more info to error message * fix path * add overview page * add diagram * add text * Update overview.md * add development page * refine text * [skip ci] * update * fix * fix * rm get_started * update URL of diagram * fix error * update * update * fix * update * update * rename * rename * update * change to img tags * remove minimal * update images * update * remove old stuff * fix images * fix * make wider * format * format * Update docs/src/development.md Co-authored-by: Erik Faulhaber <[email protected]> * review * rm css * add new picture * update time * move back --------- Co-authored-by: Erik Faulhaber <[email protected]> Co-authored-by: Niklas Neher <[email protected]> * add build workflow * add workflow name [skip ci] * test workflow * test workflow again * change event * fix paper.big bug * Bump crate-ci/typos from 1.18.2 to 1.19.0 (#480) Bumps [crate-ci/typos](https://github.com/crate-ci/typos) from 1.18.2 to 1.19.0. - [Release notes](https://github.com/crate-ci/typos/releases) - [Changelog](https://github.com/crate-ci/typos/blob/master/CHANGELOG.md) - [Commits](crate-ci/typos@v1.18.2...v1.19.0) --- updated-dependencies: - dependency-name: crate-ci/typos dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Fix another closures error on macOS-ARM (#489) * test images storage * add images * add oss to .bib * fix bullet list * fix formatting * literature fix * modify image * add missing references * description: TP vs other OSS * remove table * update * Add wrapper for internal use of interpolation functions (#466) * add wrapper * fix tests * fix tests * implement suggestions * quick dirty fix --------- Co-authored-by: Sven Berger <[email protected]> * add beam validation * modify order * figure side by side * rework images * refs * image size * Reopen #382: Extrude shapes/geometry (#437) * implement `ExtrudeFace` * use `sample_face` in `interpolate_plane_3d` * add docs * add tests * fix bug * fix bug * add `tlsph=true` * fix tuple bug * fix typo * fix again * fix layers * calculate particle spacing differently * change `floor` to `ceil` * change `round` to `isapprox` * adapt docs * implement suggestions * add doctests * try to fix doctest * implement suggestions * implement suggestion * add svens summary suggestion * amend refs and minor stuff * Optimization bnd pressure computation (#475) * optimization * optimization * fix calc for 1 thread * format * update describtion * remove +1 * update reference files * update error bounds * fix * Update src/schemes/boundary/dummy_particles/dummy_particles.jl Co-authored-by: Erik Faulhaber <[email protected]> * Update src/schemes/boundary/dummy_particles/dummy_particles.jl Co-authored-by: Erik Faulhaber <[email protected]> * Update src/schemes/boundary/dummy_particles/dummy_particles.jl Co-authored-by: Erik Faulhaber <[email protected]> * Update src/schemes/boundary/dummy_particles/dummy_particles.jl Co-authored-by: Erik Faulhaber <[email protected]> * review --------- Co-authored-by: Erik Faulhaber <[email protected]> * Add `show` for `SolutionSavingCallback` with `save_times` (#485) * Add hacky `show` for solution saving callback with `save_times` * Unify comments * Add tests for saving callback show * Reformat * handle TODOs and revise text * rework * change image format * change image size * Remove TrixiParticles dependency in docs environment (#501) * Fix doc string of solution_saving.jl (#499) * fix doc string * missing comma * Update solution_saving.jl Fix indent --------- Co-authored-by: Erik Faulhaber <[email protected]> * implement suggestion * fix refs * apply italic * update * remove corrections * Make array types in structs generic (#486) * Make array types in structs generic * Use `Ref{Bool}` instead of `Vector{Bool}` * Make array types of EDAC system generic * Reformat * Fix tests * Make `DensityDiffusionAntuono` generic * Fix tests * Implement suggestions * Bump crate-ci/typos from 1.19.0 to 1.21.0 (#507) * Bump crate-ci/typos from 1.19.0 to 1.21.0 Bumps [crate-ci/typos](https://github.com/crate-ci/typos) from 1.19.0 to 1.21.0. - [Release notes](https://github.com/crate-ci/typos/releases) - [Changelog](https://github.com/crate-ci/typos/blob/master/CHANGELOG.md) - [Commits](crate-ci/typos@v1.19.0...v1.21.0) --- updated-dependencies: - dependency-name: crate-ci/typos dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> * Fix/ignore typos --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Michael Schlottke-Lakemper <[email protected]> * Bump julia-actions/setup-julia from 1 to 2 (#506) Bumps [julia-actions/setup-julia](https://github.com/julia-actions/setup-julia) from 1 to 2. - [Release notes](https://github.com/julia-actions/setup-julia/releases) - [Commits](julia-actions/setup-julia@v1...v2) --- updated-dependencies: - dependency-name: julia-actions/setup-julia dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * The grand reopening Part 3: Add basic DEM (#433) * implement basic dem * fix * fix bnd * get basic simulation working * fix * format * fix spellcheck * add docs * update readme and news * format * add to examples run list * add basic test * ignore author name * remove * most of the review stuff * format * forgot to remove one thing * one more * rework interaction * format * update * typo * fix doctest * fix test * fix doc * fix tests again * fix doc and test * fix test * fix incorrect test * review * format * typo * review * review * format * realign line * fix test * update * Document proper release management (#508) * Mark Release V0.1.1 (#510) * Set to development version (#511) * Recursively convert (adapt) `Semidiscretization` object to GPU types with Adapt.jl (#492) * Adapt `Semidiscretization` before running the simulation * Modify constructors to be compatible with Adapt.jl * Only adapt the semidiscretization when using an explicit data type * Adapt `DensityDiffusionAntuono` * Adapt `BoundaryModelMonaghanKajtar` to GPUs * Add comments * Remove unnecessary types * CompatHelper: add new compat entry for Adapt at version 4, (keep existing compat) (#515) Co-authored-by: CompatHelper Julia <[email protected]> * Change compat of Adapt to 3 (#517) * Reopen #390: Update callback (#440) * add `UpdateCallback` * fix typo * apply formatter * remove update bool * adapt docstring * implement suggestions * remove redundant comment * first update after michaels review * adapt graphics * CompatHelper: bump compat for Adapt to 4, (keep existing compat) (#519) Co-authored-by: CompatHelper Julia <[email protected]> * embed pdf image * undo embed pdf * big rework * update * resize image * change image order * add blank line * fix typos * fix references * try to fix references * fix again * Create output directory for post process callback (#527) * Manually increase CairoMakie Version (#528) * Move neighborhood search to a new standalone package (#516) * Move neighborhood search to a new standalone package * Remove Morton.jl dependency * Remove tests for neighborhood search * Remove ThreadingUtilities.jl dependency * Fix interpolation * Add docs for neighborhood search * Dispatch `update_nhs!` instead of `nhs_coords` * Reformat code * Update NHS with coordinates of both systems * Initialize NHS with coordinates of both systems * Fix broken functions * Rename package to PointNeighbors.jl * Reformat code * Resort Project.toml * Change PointNeighbors compat to 0.2 * Fix `InitialCondition` set operations * Fix interpolation and tests * Fix docs * Fix example tests * Fix doctests * Fix n-body * Add more comments * update * Remove `pinv` in correction matrix inversion step (#526) * Remove `pinv` in correction matrix inversion step * Improve comment * Update validation files for dam break * Revert "Update validation files for dam break" This reverts commit d08c06d. * Update WCSPH validation files * Update WCSPH validation files * Add single-threaded validation files (see #481) * adapt summary * syntax * CFD abbreviation * adapt wording * avoid single-physics * Adapt some code to GPUs (#533) * Statically return zero verlocity and acceleration without `movement` * Make `write_v0!` and `write_u0!` GPU-compatible * Remove hardcoded float type in rectangular tank setup * Replace more hardcoded `Float64` types * Simplify zero SVector even more * Modify error message (#531) * change message * fix tests --------- Co-authored-by: Erik Faulhaber <[email protected]> * The Grand ReReReReReopening the final straw part 9: Intra-Particle-Force Surface Tension model (#434) * merge by hand * fix merge problems * fix merge * fix merge * fix merge * fix merge * fix merge * more merge fixes * format * fix * fix * fix * fix * fix * more fixes * fix * fix * fix * more fixes * fix * fix * format * running * update * update * optimization * update * update * update * update * format * up * update * remove unused code * switch to support radius * update * fix doc * add adhesion coefficient * update_broken * update * format * add to examples * fix tests * fix merge * fix typos * add basic test * format * rename * format * rename container system * reduce example run time * update news and readme * format * fix test * reduce run time * format * fix * correct merge * update doc test * revert * fix tests * fix * fix * review comments * fix * fix * correct some stuff * init with empty initial condition * review update * rename function * remove unnecessary if * docs * fix doc * revert one change * fix typo * update * try to avoid allocs * fix mem allocs * review update * update docs * update * review * fix * format * make examples smaller * reduce resolution * review * rename * use trixi_include * format * use trixi_include * update * update * review update * format * fix test errors * update * fix surface normal calculation * adjust testcases and review comments * update examples * remove saving interval * fix comment * remove dt * Fix n-body benchmark (#525) * Fix n-body benchmark * suppress warning * fix formatting * for real --------- Co-authored-by: Sven Berger <[email protected]> * Push new version number (#536) Co-authored-by: Erik Faulhaber <[email protected]> * Mark 0.1.3-dev (#537) Co-authored-by: Erik Faulhaber <[email protected]> * Add type `GPUSystem` to determine if a system is stored on the CPU or GPU (#532) * Add type `GPUSystem` to determine if a system is stored on the CPU or GPU * Fix systems and tests * Reformat * Fix tests * Fix n-body system * Reformat * Clean up callback conditions (#538) * Bump julia-actions/cache from 1 to 2 (#541) Bumps [julia-actions/cache](https://github.com/julia-actions/cache) from 1 to 2. - [Release notes](https://github.com/julia-actions/cache/releases) - [Changelog](https://github.com/julia-actions/cache/blob/main/devdocs/making_a_new_release.md) - [Commits](julia-actions/cache@v1...v2) --- updated-dependencies: - dependency-name: julia-actions/cache dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * final update * fix bib * test * test * fix bug * modify image * fine tuning * fine tuning * fine tuning * image size * fix typo * Update Michael's affiliation to U of Augsburg (#545) * Precompute git hash to avoid overhead (#542) * Precompute git hash * Store git hash in callbacks * Fix --------- Co-authored-by: Niklas Neher <[email protected]> * Move timers and `@trixi_timeit` to TrixiBase.jl (#543) * Move timers and `@trixi_timeit` to TrixiBase.jl * Require latest version of TrixiBase.jl * Fix tests --------- Co-authored-by: Niklas Neher <[email protected]> * Add `trixi2vtk` wrapper for `InitialCondition` (#546) * add wrapper * modify kwarg * implement suggestions * Example on how to save interpolated planes using postprocessing callback (#462) * add example * replace MSE with MRE * Revert "replace MSE with MRE" This reverts commit 1e00907. * revert * update * format * fix and reduce runtime * Fix comment * implement suggestions * format --------- Co-authored-by: Erik Faulhaber <[email protected]> * Add open boundaries (#442) * implement `ExtrudeFace` * use `sample_face` in `interpolate_plane_3d` * add docs * add tests * fix bug * create `OpenBoundarySPHSystem` * export OpenBoundarySPHSystem * fix bug * add `tlsph=true` * fix tuple bug * fix typo * fix again * fix for tests * fix layers * calculate particle spacing differently * add show-tests * add `within_boundary_zone` * change `floor` to `ceil` * boundary zone tests * add `evaluate_characteristics` * add tests * add reference functions * add `update_quantities!` * add buffer * add `SystemBuffer` tests * cosmetic change in tests * change `round` to `isapprox` * add update callback * add `UpdateCallback` * add `update_open_boundaries` * fix bugs * add timers * write prescribed quantities * improve dispatching * add example `pipe_flow_2d.jl` * add docs `UpdateCallback` * add `UpdateCallback` * fix typo * apply formatter * modify system buffer * add docstring * add docs * fix tests * fix typos * apply formatter * fix tests * add comment * fix tests * remove update bool * adapt docstring * implement suggestions * fix test * add check if callback is used * add comments in example file * generic types * merge main * undo combining compact support with DEM * remove density and pressure setter * implement suggestions * fix tests * Revert "remove density and pressure setter" This reverts commit 0203a3a. * implement suggestions * rework in- and outflow * rename setter functions * rename function * adapt tests * add docs * rename function * apply formatter * fix tests * fix bug in plot recipes * apply formatter * implement suggestions for `boundary_zone.jl` * rename kwarg * implement suggestions * implement suggestions * modify `check_domain!` * add comments and check for fluid system with buffer * modify error message * fix tests * fix `callback_used` * using Measurements * fix tests * sqrt(eps()) * fix tests again * add doc to `boundary.md` * link single fluid system * fix tests * implement suggestions * fix tests * change the order of functions * modify example * fix tests * fix test again * implement doc suggestions * modify dos * fix typos * implement suggestions * implement suggestions * add EDAC to the example * implement suggestions * modify tests * adapt docs * add `initial_callback_flag` * add to `NEWS.md` and `README.md` * implement suggestions * fix typo * New Feature Release (#548) Open Boundaries have been added * Set to development version 0.1.4 (#549) * Set to development version 0.1.4 * Update Project.toml * Rewrite `@threaded` macro to work with GPUs (#534) * Fix wrapping for GPU arrays * Adapt `@threaded` macro to work with GPUs * Use new `@threaded` macro * Fix NHS to run GPU code with CPU arrays * Import `@index` from KernelAbstractions.jl For some reason it doesn't run on the CPU otherwise. * Add proper docs for `@threaded` * Fix `foreach_neighbor` * Reformat * Add test for GPU code on the CPU * Fix unit tests * Add unit tests for GPU interaction * Also add tests for GPU versions of `wrap_v` and `wrap_u` * Add kwarg `neighborhood_search` to dam break example * Fix tests * Reformat * Add function `wrap_array` * Fix merge * Fix open boundary code * Implement suggestions * Fix syntax error from merge * Fix `wrap_u` and `wrap_v` for GPU array types * Fix constructor of `BoundarySPHSystem` * CompatHelper: add new compat entry for KernelAbstractions at version 0.9, (keep existing compat) (#551) Co-authored-by: CompatHelper Julia <[email protected]> * fix name (#554) * Manually set GPU_ARRAY compat (#555) Co-authored-by: Erik Faulhaber <[email protected]> * Add Viscosity Formulation as per Morris et al. (#504) * Add Viscosity Moris * format * fix * implement suggestions * other suggestions * fix equation * format * review comments * fixes * fix * update test * update * fix open boundary * update reference files * update validation criteria * update reference file * new reference files * ups * update ref file * update validation error bounds * update error bound * update error bound * add comment and correct setting of 'v' * final review part 1 * Feature highlights -> Features * Cleanup Viscosity/Boundary Model (#566) * extract changes from #564 * fix * add `custom_quantities...` (#567) Co-authored-by: Erik Faulhaber <[email protected]> * add acknowledgement * add link * change link * change link again --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: Sven Berger <[email protected]> Co-authored-by: Erik Faulhaber <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Michael Schlottke-Lakemper <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: CompatHelper Julia <[email protected]>
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Based on trixi-framework/TrixiBase.jl#25.