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Version 0.4 Merge with Stable (#426)
* Used "signed" version of size_t - ptrdiff_t in io_wrapper.cpp * Remove `KOKKOS_INLINE_FUNCTION` from functions where it's not required/incorrect. * Fix improperly captured `CellVariable` * Reintroduce pack helper function (now with cache support) * Joshua s brown/ci darwin speedup (#347) * Updated ci to use existing spack install on darwin rather than building packages from scratch each time. * Also corrected scheduling to use the develop branch rather than the no longer existing master branch. * Fixing parameter_input * Fix formatting * Added CHANGELOG comment * Darwin should append on to CMAKE_CXX_FLAGS * Add checks for all MPI function calls * Update Changelog * Add more doc * fixed indexing errors in mesh domain for edge cases * finished updating unit domain * finish domain * Fix artifacts * first rewrite of boundaries. More modifications needed. * address some of Josh Browns comments * Pass coarse vs. fine boolean through boundary stack. * jdolence/unify_more * attempt to fix weird boundaries bug * try this fix. Actually flip vector components * fix the weird boundary thing(?) * Seek throw rather than return error * void IOWrapper::Close * template some update functionality * formatting * update advection * trying to limit duplicated code for FluxDivergence * cleanup some * template FillDerived * formatting * add support for FillDerived functionality on both MeshBlockData and MeshData simultaneously * formatting * HDF5 changes: Automatic resource cleanup and error checking * gitignore cmake trash * fix a "C++17" language warning * first pass at boundaries rewrite. Still some debugging to do and the boundaries hack in prolongate/restrict still present. * abstract out par_for_bndry * make Parthenon::AppInput a StateDescriptor that automatically populates a Packages_t * formatting * oops need to return TaskStatus::complete * add test for coarse flag for variable_pack and fix bug it uncovered * added a test for repeated coarse vs fine access to a variable pack and fixed caching bug caught by test * remove dead code. * only prolongate boundaries if multilevel * comment out applyBounds for now * formatting * add support for coexistent calls to EstimateTimestep calls with MeshData and MeshBlockData * remove stray comment * no bool overload for zero lenght pack * formatting and replaced metadata::independent with metadata::fillghost * add documentation * changelog * introduce a Tag function with MeshData and MeshBlockData overloads * formatting * replace special strings with constexpr char arrays * address most of jdolence comments * add advection outflow test * partial gold file update * remove applybounds as it seems unnecessary * update gold standard for regression test * fix warnings * dont need that comment anymore * fix comments in meshblock.hpp * add missing endline * fixed bug where empty variable packs segfault * doc typo * Update src/mesh/domain.hpp * josh browns suggestion of not creating intermediate indexrange object * comment out si and ei which may be needed for face centered fields but are currently unused * variable pack constructor take references to avoid double copy. thanks Josh Brown * add const where suggested * reduce replicated code in bvals_refine and simplify API by using IndexRange * non-member par_for_inner * newline * const * Fix no-mpi build * Brief documentation for H5Handle * Remove unused variable * More thorough error checking PARTHENON_HDF5_CHECK now returns the error value - sometimes it is overloaded as the return value of a function * Revert par_for_outer changes * Update copyright * close restart file prior to MPI finalize * Fail hard on error * Fix missing ; * Remove comment * Add changelog comment * -Werror in parthenon-cuda-unit test * CHANGELOG * Force hard fail with set -e * More elegant solution * Fix submodules by calling update init * Add CHANGELOG comment * Update scripts/darwin/build_fast.sh Co-authored-by: Jonah Miller <[email protected]> * More elegant fix * refactoring back to function pointers instead of params * formatting * some cleanup * some updates to docs * update changelog * making more things const references * generalize Update and Average functions * Update src/parthenon_manager.cpp Co-authored-by: Philipp Grete <[email protected]> * more cleanup * more cleanup * addressing comments * fix linting * oops, undo stupid. * addressing thread safety issue with setting dt * cleanup as suggested by Forrest Glines * update doc * Fix Kokkos ver * Add/remove const and force inline func * addressing review comments * Add more prof regions * cpp-auto-formatter * generalizing update functionality * move to universal references * how about const T * namespace function overloads for task resolution * move from shared_ptr<T> to * * Add Changelog * Add filtered by name for adding MeshBlockDatas to DataCollections * remove extra templating in Add, and include generalized Copy in MeshData * add a little error checking * fix stupid * refactor advection to use new tasks in Update * add profiling for SumData * move FluxDivergence to T * * add some error checking * add some documentation * update changelog * adding a unit test * gpuify test * aghh...formatting * Output on fail * Add Changelog comment * addressing comments * formatting * more review comments * intermediate state descriptor. doesn't compile. * still working on design * fix bug and address comments * working on package conflict resolution * add const that seems required * update changelog * code compiles * making progress on testing * more progress on testing * have everything working, including printed metadata at the start of a run * changelog and documentation * fix stupid cmake * codacy changes * Update CHANGELOG.md Co-authored-by: Andrew Gaspar <[email protected]> * Update changelog to better describe new features. * Update src/interface/state_descriptor.cpp Co-authored-by: Andrew Gaspar <[email protected]> * Update src/interface/metadata.hpp Co-authored-by: Andrew Gaspar <[email protected]> * same bits -> flags * Add GetGlobalSparseID and GetLocalSparseID to VariablePack * For now both these functions dispatch to GetSparse * When sparse variables are actually being used, GetGlobalSparseID should return the global id and GetLocalSparseID should return the variable-pack-local id * Add as contributor * Format fixes * Update CHANGELOG.md and add tests * Change "ID" -> "Id" for consistency * Rename methods * `GetLocalSparseId` -> `GetSparseIndex` * `GetGlobalSparseId` -> `GetSparseId` * Update CHANGELOG.md for changes to method names * Modify c++ linting for when parthenon is submodule * uses the `--repository` argument to cpplint to set the repository to the `${PROJECT_SOURCE_DIR}` * adds `CPPLINT.cfg` as a dependency to the linting command so changes to it will trigger re-linting * update CHANGELOG.md * initial refactoring * fix linting * formatting * address comments by jdolence and agaspar * make Pre/PostExecute virtual * do not explicitly call Driver::PreExecute * Add const correctness to `Params.Get` * update CHANGELOG.md * reimplement with `at(key)` * Update state_descriptor.cpp * Remove old files before running tests (#362) * Remove old files before running tests * Added changelog comment * Fix indentation * Use clean output folder when running tests * Add API to state_descriptor for diagnostic outputs * Extend APIs to support Pre and Post step user work * Fix formatting * update CHANGELOG.md * Time arg const; post-step work after time update * Fix format * Initialize OutputDiagnosticsMesh to nullptr * Implement application level diagnostics output * Raw pointers in `StateDescriptor` -> std::function * Fix init timestep calc for MeshData * Don't overwrite MeshBlockData dt * Update CHANGELOG.md and some comments * expose TaskListStatus to downstream codes * export EvolutionDriver * update CHANGELOG * Cleanup some Codacy warnings (#403) * Cleanup some Codacy warnings * Update Changelog * Update comments * Formatting * Apply suggestions from code review Co-authored-by: Andrew Gaspar <[email protected]> * Update src/parameter_input.cpp Co-authored-by: Andrew Gaspar <[email protected]> Co-authored-by: Andrew Gaspar <[email protected]> * remove unused constructor * Move post-step user work and diagnostics to before time/cycle update * Add documention * Update `StateDescriptor` documentation adding information about `Pre-` and `PostStepDiagnostics` functions * Update `Mesh` documentation to reflect the additions of the `Pre-` and `PostStepUserWorkInLoop` and the `Pre-` and `PostStepDiagnisticsInLoop` * update driver docs * Joshua s brown/version 0.4 (#422) Version 0.4 Co-authored-by: Andrew Gaspar <[email protected]> Co-authored-by: Philipp Grete <[email protected]> Co-authored-by: Josh Dolence <[email protected]> Co-authored-by: Jonah Miller <[email protected]> Co-authored-by: Jonah Miller <[email protected]> Co-authored-by: par-hermes <[email protected]> Co-authored-by: Clell J. (CJ) Solomon <[email protected]> Co-authored-by: clellsolomon <[email protected]> Co-authored-by: Philipp Grete <[email protected]>
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