Regression test gold standard v3

Regression test gold standard, now containing outflow regression test.

v0.3.0

Date: 10/29/2020

Added (new features/APIs/variables/...)

• [PR 317] Add initial support for particles (no MPI support)
• [PR 311] Bugfix::Restart. Fixed restart parallel bug and also restart bug for simulations with reflecting boundary conditions. Added ability to write restart files with or without ghost cells by setting ghost_zones in the output block similar to other output formats.
• [PR 314] Generalized par_for abstractions to provide for reductions with a consistent interface.
• [PR 308] Added the ability to register and name MeshBlockPacks in the Mesh or in package initialization.
• [PR 285] Parthenon can now be linked in CMake as Parthenon::parthenon when used as a subdirectory, matching install.

Changed (changing behavior/API/variables/...)

• [PR 303] Changed Mesh::BlockList from a std::list<MeshBlock> to a std::vector<std::shared_ptr<MeshBlock>>, making FindMeshBlock run in constant, rather than linear, time. Loops over block_list in application drivers must be cahnged accordingly.
• [PR 300]: Changes to AddTask function signature. Requires re-ordering task dependency argument to front.
• [PR 307] Changed back-pointers in mesh structure to weak pointers. Cleaned up MeshBlock constructor and implemented MeshBlock factory function.

Fixed (not changing behavior/API/variables/...)

• [PR 293] Changed VariablePack and related objects to use ParArray1D objects instead of ParArrayND objects under the hood to reduce the size of the captured objects.
• [PR 313] Add include guards for Kokkos in cmake.
• [PR 321] Make inner loop pattern tags constexpr

Infrastructure (changes irrelevant to downstream codes)

• [PR 336] Automated testing now checks for extraneous HtoD or DtoH copies.
• [PR 325] Fixes regression in convergence tests with multiple MPI ranks.
• [PR 310] Fix Cuda 11 builds.
• [PR 281] Allows one to run regression tests with more than one cuda device, Also improves readability of regression tests output.
• [PR 330] Fixes restart regression test.

v0.2.0

Date: 9/12/2020

Added

• [PR 250] Feature::Restart. If output file format 'rst' is specified restart files are written using independent variables and those marked with Restart metadata flag. Simulations can be restarted with a '-r <restartFile>' argument to the code.
• [PR 263] Added MeshBlockPack, a mechanism for looping over the whole mesh at once within a Kokkos kernel. See documentation
• [PR 267] Introduced TaskRegions and TaskCollections to allow for task launches on multiple blocks.
• [PR 287] Added machine configuration file for compile options, see documentation
• [PR 290] Added per cycle performance output diagnostic.
• [PR 298] Introduced Partition, a tiny utility for partitioning STL containers. Used for MeshBlockPacks, to enable packing over a fraction of the mesh.

Changed

• #68 Moved default par_for wrappers to MeshBlock
• [PR 243] Automatically find/check Python version used in regression tests. Bumps CMake minimum version to 3.12
• [PR 266]: It is no longer necessary to specify Kokkos_ENABLE_OPENMP this is by default enabled, to turn off one can specify PARTHENON_DISABLE_OPENMP.

Fixed

• [PR 271]: Fix setting default CXX standard.
• [PR 262] Fix setting of "coverage" label in testing. Automatically applies coverage tag to all tests not containing "performance" label.
• [PR 276] Decrease required Python version from 3.6 to 3.5.
• [PR 283] Change CI to extended nightly develop tests and short push tests.
• [PR 282] Integrated MeshBlockPack and tasking in pi example
• [PR 294] Fix IndexShape::GetTotal(IndexDomain) - previously was returning opposite of expected domain result.

v0.1.0

Date: 8/4/2020

Initial release of Parthenon AMR infrastructure.

Changed

[PR 214]: The weak linked routines for user-specified parthenon behavior have been removed in favor of a more portable approach. See the documentation.

Regression test gold standard v2

Merge pull request #210 from lanl/jmm/cleanup-params-error-checking

Clean up error checking in params