Arbitrary grid updates

[kubagalecki]

Some updates to the arbitrary grid formulation:

• Edges between bulk nodes removed from the connectivity graph. This reduces the communication volume and associated costs.
• The local permutation strategy can now be set via the (optional) "permutation" attribute of the "ArbitraryLattice" xml node. Valid values are:
  • "none" - use default ordering, not recommended, only for debugging/benchmarking purposes
  • "coords" - sort only by coordinates, this was the previous behavior. This is still the default.
  • "type" - sort only by node type, not recommended, only for debugging/benchmarking purposes
  • "both" - sort by node type, subsort by coordinates. Somewhat surprisingly, for the fontaine benchmark (on a single GPU), this resulted in a ~8.5% performance penalty, meaning less coalesced memory access outweighed the gains from more efficient warp utilization. I still think for some cases this might be more efficient than the "coords" strategy (maybe for very low porosity, or when the geometry is more structured?)
• Added some missing handlers

Outstanding items:

• Symmetry conditions
• Some handlers are still missing
  • Mostly related to things like particles, so implementing them is outside the scope of this project
  • RunR is definitely still broken
  • Failcheck semantics make little sense for arbitrary grid, see #476
  • You can check which handlers still need implementing by grepping for getCartLattice
• Adjoint functionality is definitely broken, the main iteration is missing as well as saving/loading components. There are probably also a bunch of other places where I screwed something up, but I don't really have the bandwidth to go hunting for them.

[codecov-commenter]

Codecov Report

Attention: 421 lines in your changes are missing coverage. Please review.

Comparison is base (b38b8dd) 38.09% compared to head (e02f071) 37.72%.

Files	Patch %	Lines
src/ArbLattice.cpp	0.00%	146 Missing :warning:
src/vtkLattice.cpp	13.33%	65 Missing :warning:
src/Handlers/cbFailcheck.cpp	0.00%	54 Missing :warning:
src/toArb.cpp	0.00%	44 Missing :warning:
src/Handlers/cbSaveCheckpoint.cpp	0.00%	40 Missing :warning:
src/Handlers/cbSaveBinary.cpp	0.00%	16 Missing :warning:
src/Handlers/cbSaveMemoryDump.cpp	0.00%	15 Missing :warning:
src/Handlers/cbTXT.cpp	0.00%	13 Missing :warning:
src/Handlers/acLoadMemoryDump.cpp	0.00%	11 Missing :warning:
src/Handlers/cbBIN.cpp	0.00%	9 Missing :warning:
... and 2 more

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Additional details and impacted files

```diff @@ Coverage Diff @@ ## unstable #477 +/- ## ============================================ - Coverage 38.09% 37.72% -0.38% ============================================ Files 185 185 Lines 8355 8461 +106 ============================================ + Hits 3183 3192 +9 - Misses 5172 5269 +97 ``` | [Flag](https://app.codecov.io/gh/CFD-GO/TCLB/pull/477/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=CFD-GO) | Coverage Δ | | |---|---|---| | [d2q9](https://app.codecov.io/gh/CFD-GO/TCLB/pull/477/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=CFD-GO) | `26.38% <2.32%> (-0.26%)` | :arrow_down: | | [d2q9_bc](https://app.codecov.io/gh/CFD-GO/TCLB/pull/477/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=CFD-GO) | `23.20% <2.32%> (-0.22%)` | :arrow_down: | | [d2q9_kuper](https://app.codecov.io/gh/CFD-GO/TCLB/pull/477/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=CFD-GO) | `23.97% <2.32%> (-0.23%)` | :arrow_down: | | [d3q27_PSM_NEBB](https://app.codecov.io/gh/CFD-GO/TCLB/pull/477/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=CFD-GO) | `31.46% <2.32%> (-0.32%)` | :arrow_down: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=CFD-GO#carryforward-flags-in-the-pull-request-comment) to find out more.

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[llaniewski]

Before Christmas I started some refactoring, and these things are in a bit of a conflict, so there will be some weird merge-magic going on soon :-)

@kubagalecki If I see a single commit after Jan 1 in your TCLB fork, I'll start harassing you about things you are supposed to be doing.