GitLab

refining CMake to convert install prefix to absolute path and to add some variables to the config file for FindXdmf

Rework of HeavyDataController and HDF5Controller to remove extra code and move HeavyDataController away from being too dependent on hdf5 style
XdmfFunction now supports negative numbers in addition to the - operator
Reworked the interaction between array references and reading
Cleaned up some warnings that showed up in pedantic
Adjusted mpi tests to test against the MPIEXEC variable as opposed to hard calling mpirun
Still needs to be changed to work better with Cray mpi style execution
Updates to XdmfArrayType to allow for signed and floating point checking
General test and Documentation updates

Previously, for HDF5 datasets, the number of dimensions in the light data
description had to match the number of dimensions in the heavy data file in
order to properly select a hyperslab. To support older files and be more
flexible, we now allow the number of dimensions to be different as long as
we are reading the entire dataset.

Fully support parsing of nested xincludes in Xdmf files. Add a test to ensure
this remains supported - the test contains an xinclude to an element in a
separate file that itself is another xinclude to an XdmfInformation.

Add HDF5 tree writer test.

Fix reader to properly add content for DataStructure deprecated items.
Move whitespace trimming to reader where it is more convenient since
it can replace a check for the content being all whitespace.

AttributeType (Scalar). Also enable parsing of deprecated DataStructure
tag, synonym of DataItem.

Previously, when converting from xdmf to exodus, spatial partitioning (metis)
in xdmf was written as element blocks in exodus. However, exodus uses element
blocks to specify different materials and not as spatial partitioning for
parallel execution. We now write materials to blocks in exodus, indicated by
Block node sets in xdmf. This now makes the conversion of xdmf -> exodus the
exact inverse of the exodus -> xdmf function.

When converting exodus files to xdmf, element block information is written
to xdmf sets. When converting back to exodus, this information was
previously ignored. Now, we check whether we have block information written
as an xdmf set and use it to reproduce element blocks in exodus during
conversion.

Fix XdmfTopologyType vector to be reference rather than copy.