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Fixes for prism refinement from XML input

Dave Moxey requested to merge meshing/nektar:ticket/7-mc-bl-xml into master

This MR addresses issue #7 (closed) and fixes boundary layer splitting with XML input. Specifically, it fixes prismatic input, since hexahedra seem to work. There are two changes:

  • MeshConvert by default reorients elements to align collapsed coordinates. InputNekpp uses this, and since the collapsed coordinates are presumed to be aligned by construction, edges are not reprocessed. This therefore breaks element connectivity when virtually any processing is done on the mesh that alters the connectivity.
  • Address a bug in ProcessBL which causes the geometry to subtly change as elements are refined. This is addressed by constructing a map of the existing elemental geometries before any processing occurs.

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