Consolidate buffer packing functions with less atomics

[alexrlongne]

PR Summary

• Profiling with NSIGHT systems revealed that the LoadBuffer_ function in swarm_comms.cpp took 20% of the GPU time in the particles example that used much more particles (1e6 per block). NSIGHT compute showed that the expensive kernel in LoadBuffer_ had many stalls, we speculated this was due to waiting on the atomic_fetch_add function in LoadBuffer_. This PR reworks LoadBuffer_ and CountParticlesToSend_ to remove atomics and instead sort the particles by buffer ID and use their sorted order to determine their size and index into that buffer.

• Removing atomics reduces the runtime by about 20% in the million particle example and more in a 10 million particle version. A case where the particles are photons may involves even more cell block crossings as c*delta_t could be large compared to a block size (in the particles example the particle's path length is equal to a block size).

• The reason for the atomic in both cases was that the loops were over particles where the particle buffer was determined and that was then used to atomically update a buffer specific field.

• As a rider, this PR also updates some sampling functions in the particle example to use less transcendentals, which has shown improvement in a Parthenon downstream code. I can separate into another PR if desired.

Changes

• Fold in buffer sizing to the load buffer function
• Use a sort and a discontinuity check instead of an atomic_fetch_add inside of LoadBuffer_ to get particle index into buffer
• Reduce transcendental functions call in particle sourcing in particle example

PR Checklist

• 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
• Change is breaking (API, behavior, ...)
  • Change is additionally added to CHANGELOG.md in the breaking section
  • PR is marked as breaking
  • Short summary API changes at the top of the PR (plus optionally with an automated update/fix script)
• CI has been triggered on Darwin for performance regression tests.
• Docs build
• (@lanl.gov employees) Update copyright on changed files

[brryan]

@alexrlongne This looks great, I think with just formatting, cleanup of the SwarmKey cell_idx_1d name, and removing the dynamic memory allocs, this is ready to go.

[brryan]

Looks great! Just one more query about r^2 vs r^-2