Implement general 2D forest meshes

[lroberts36]

PR Summary

This PR implements the minimum necessary technology for defining meshes based on generally connected forests of octrees. I have left details of coordinates to a future PR, so for now each tree must cover a hyper-rectangular domain defined by $\vec{x}_\text{min}$ and $\Delta \vec{x}$. Some rough notes about my implementation are in ForestOfOctreesNotes.pdf, which is now also included in doc/latex/main.pdf.

The four major things this PR accomplishes:

• Add forest::Node, forest::Edge, and forest::Face for defining the forest mesh topology. forest::Face contains routines for finding neighbors and then calculating the correct logical coordinate transformations to those neighbors. For now, I have stuck to defining 2D forests but the mechanisms used here should generalize to 3D relatively easily in a future PR.
• Add forest::Forest::Make2D that builds a Forest from a forest::ForestDefinition. ForestDefinition contains a set of Faces, boundary conditions defined on forest::Edges, RegionSizes associated with each block, and a set of initial LogicalLocations to refine.
• Add Mesh constructor as well as ParthenonManager::ParthenonInitPackagesAndMesh that takes a forest::ForestDefinition and constructs a mesh based on a general 2D forest.
• Thread logical coordinate transformations through boundary communication routines so that neighbor blocks that are non-simply oriented can communicate boundaries.

Smaller things also included in the PR:

• Rename RelativeOrientation -> LogicalLocationCoordinateTransformation for clarity.
• Move MeshBndryFnctn to Mesh::forest::trees instead of Mesh and add appropriate registration routines.
• Adds an example and associated regression test that communicates gids and other information through boundaries to ensure that neighbor communication is occurring correctly. The gold file has just been verified by hand.
• Adds a unit test that performs refinement on non-simply connected forests.

Things this PR does not do (but maybe a future PR should):

• Deal with physical coordinates on trees beyond the simplest choice.
• Implement periodic boundary conditions for general forests.
• Allow for 3D meshes.
• Allow for 6+ valent points in the macro-mesh.
• Deal with corner communication for 5-valent corners or generally store information about valence of corners and edges in MeshBlock.
• Make a better interface for users to define general forests.

Some examples of properly nested refinement near singular mesh points (this mesh configuration is tested in the newly added unit test):

Boundaries filled with neighbor gids in a 2x2 forest where the lower left tree coordinates are rotated by 90 degrees relative to the other trees (results of the boundary communication regression test):

PR Checklist

• Refactor Mesh Constructors #1055 is merged
• Particle BCs without relocatable device code #1026 is merged
• Code passes cpplint
• New features are documented.
• Adds a test for any bugs fixed. Adds tests for new features.
• Code is formatted
• Changes are summarized in CHANGELOG.md
• CI has been triggered on Darwin for performance regression tests.
• Docs build
• (@lanl.gov employees) Update copyright on changed files

[adamdempsey90]

Our 2 downstream codes run fine without modification.