Draft: Rework MMFF loop to warp iteration

[scal444]

Do not merge until perf tested

[greptile-apps]

Greptile Overview

Greptile Summary

Refactors MMFF force field loop iteration from thread-strided to warp-based chunked approach using CUDA cooperative groups.

• Converts molEnergy and molGrad functions to use warp-level parallelism via cooperative_groups::tiled_partition<32>
• Distributes work chunks across warps in round-robin fashion instead of per-thread striding
• Accumulates prefix sums of term type counts to determine which term type each chunk belongs to
• The indexing logic for bounds checking (baseIdx + laneId < numTerms) is correct
• Adds <cooperative_groups.h> header for warp-level primitives
• Parameters tid and stride in function signatures are no longer used but remain for API compatibility

Confidence Score: 4/5

• This PR is safe to merge pending performance testing as indicated in the PR description.
• The warp-based iteration logic appears mathematically correct - bounds checking properly guards memory accesses and chunk distribution covers all terms. The refactor is a performance optimization that maintains functional equivalence. However, the PR author explicitly states "Do not merge until perf tested" which suggests additional validation is needed.
• No files require special attention - the single file change has correct bounds checking throughout.

Important Files Changed

File Analysis

Filename	Score	Overview
src/forcefields/mmff_kernels_device.cuh	4/5	Refactored molEnergy and molGrad from thread-strided iteration to warp-based chunked iteration using cooperative groups. The indexing logic appears correct. Parameters tid and stride are now unused.

[greptile-apps]

Additional Comments (2)

1. src/forcefields/mmff_kernels_device.cuh, line 670-671 (link)

   style: The tid and stride parameters are no longer used after the refactor to warp-based iteration. Consider removing them from the function signature.

2. src/forcefields/mmff_kernels_device.cuh, line 836-837 (link)

   style: Same as molEnergy - tid and stride parameters are unused after this refactor.

_{1 file reviewed, 2 comments}

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