Add neighboring node indices to dual layouts in Draco_Mesh

[RyanWollaeger]

Background

• There are instances where a dual mesh layout is useful, for instance reconstruction on stencils.
• Both neighboring node and cell data is generally needed for each node.
• The current Dual_Layout in Draco_Mesh can only access cell indices from each node.

Purpose of Pull Request

• Add a node-node connectivity node-centered Dual_Layout type in the Draco_Mesh class.
• For Draco_Mesh, with the changes here, the data access pattern of Dual_Layout is:
  • node index n -> cell index c -> vector of node indices adjacent to n and c.
• Concerns Redmine Issue #2457

Description of changes

• Include pairing of a set of nodes to cells in dual layout types.
• Put neighbor nodes into layouts, in compute_node_to_cell_linkage.
• Update serial unit test tstDraco_Mesh to reflect new dual layout.
• Test new data on simple decomposed meshes in tstDraco_Mesh_DD.
• Fix or update some comments.

Notes:

• This forms a complete but rudimentary dual mesh layout.
• 3D topology will require a different routine (possibly 3
  neighboring nodes per cell for cells neighboring the node).
• MPI for ghost layouts only sends node data for nodes on
  processor bounds, but this is still an allgatherv operation.

Status

• Reference:
  • Pre-Merge Code Review
  • CDash Status
• Checks
  • Travis/Appveyor CI checks pass
  • Code coverage does not decrease
  • Valgrind test passes
  • Toss3 checks pass
  • Trinitite checks pass
  • Code reviewed/approved, sufficient DbC checks, testing, documentation

[RyanWollaeger]

This requires one more modification to get the coordinate values for off-rank nodes neighboring rank-boundary nodes, which should follow the logic of the neighbor node index addition.

[KineticTheory]

@RyanWollaeger You need #include <array> at the top of Draco_Mesh.hh to make LLVM and MSVC happy.

[RyanWollaeger]

@KineticTheory Thank you for catching this - it has gotten me before!

[codecov]

Codecov Report

Merging #1078 (b14875d) into develop (05cffd6) will increase coverage by 0.0%.
The diff coverage is 100.0%.

@@           Coverage Diff           @@
##           develop   #1078   +/-   ##
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  Coverage     88.6%   88.6%           
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  Files          374     374           
  Lines        18577   18579    +2     
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+ Hits         16477   16479    +2     
  Misses        2100    2100           

[KineticTheory]

LGTM

[RyanWollaeger]

Thank you @KineticTheory!