Axom-v0.3.1

[Version 0.3.1] - Release date 2019-07-22

Please download the Axom-v0.3.1.tar.gz tarball below, which includes all of the Axom submodules as well.

Added

• Added a new implementation of the Bounding Volume Hierarchy(BVH) spatial
  acceleration data-structure to spin. The new BVH implementation relies on RAJA
  and allows for constructing and using the BVH sequentially or in parallel on
  the CPU or in parallel on the GPU. The new implementation is available only
  when Axom is compiled with RAJA and Umpire support.
• Added Umpire and RAJA to the spack build.
• Centralized Axom's memory management functions in a separate header and extended them
  to use Umpire when enabled.
• Added the ability to point Axom to an UMPIRE build by specifying UMPIRE_DIR either in
  a host-config or at the command line. Axom components can link to Umpire, by specifying
  "umpire" as a dependency. A simple umpire smoke test is also added for regression testing.
• Added for_all_faces to the mint execution model.
• Added support for face connectivity in the mint UnstructuredMesh class.
• Added support for face data and face connectivity in the mint StructuredMesh classes.
• Added Python module for Quest signed distance interface.
  See the file src/axom/quest/interface/python/README.md for more information.
• Added capability in sidre IOManager to read files while running on a number
  of MPI ranks greater than the number of ranks that were used to create
  the files.
• Users can now set the vertex welding threshold parameter in Quest's In/Out query.
  This was previously not exposed to the user. The default value is 1E-9.
• Unify all Axom component libraries into one library named axom.
• The routine that checks if a surface mesh is watertight now marks boundary
  cells. A cell-centered field, named "boundary", is used to mark boundary cells
  with a value of "1" and "0" otherwise. This facilitates in visually inspecting the
  surface mesh and identify the problematic regions for the In/Out and SignedDistance
  queries.

Removed

• Moved mint::Array to axom::Array with sidre storage in sidre::Array;
  also moved mint::IndexType to axom::IndexType.
• Replaced sidre::SidreLength with sidre::IndexType.
• Replaced usage of std::size_t in sidre with sidre::IndexType.
• Added AXOM_ENABLE_EXPORTS which enables CMAKE_ENABLE_EXPORTS to allow demangled
  axom function names in stack traces. This option is ON by default in debug builds.

Changed

• Updated conduit TPL to v0.4.0
• Updated mfem TPL to v4.0
• Slam's Set and Relation classes are now parameterized by a PositionType and ElementType.
  Its Map classes are now parametrized by a SetType.
• Updated the fmt tpl.
• Replaced old quest C-style interface with a new quest inout API.
  Functions related to the inout point containment query are prefixed with "inout_".
  The new API has an option to set the verbosity of the inout initialization and query.
• Changed sidre::IndexType to be a 64bit signed integer.
• Changed slic::stack_trace to slic::internal::stack_trace which now attempts to
  output a demangled stack trace.

Fixed

• Axom can once again be configured with AXOM_ENABLE_EXAMPLES=ON and AXOM_ENABLE_TESTS=OFF.
• Quest's vertex welding now works with small welding threshold values (e.g. 1E-20).
  Welding was previously broken when this value was smaller than 1E-8.
  This fix also resolved an issue with small grid spacing values in primal's RectangularLattice.