Use shared memory positions in per molecule small kernels

[scal444]

We'd migrated gradients and other shared buffers but were still using global arrays for positions.

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Greptile Overview

Greptile Summary

Refactored per-molecule kernel implementations to use shared memory position buffers instead of global arrays. The device functions (molEnergy, molGrad, etc.) now receive pre-offset molecule-local coordinate pointers rather than performing internal offsetting from global arrays.

Key improvements:

• Eliminated unnecessary global memory copies during BFGS line search iterations
• Consistent shared memory usage across energy and gradient calculations
• Device functions simplified by removing redundant pointer arithmetic
• Added proper bfgs library dependency in CMakeLists.txt

Confidence Score: 5/5

• This PR is safe to merge with minimal risk
• The refactoring is straightforward and maintains correctness by consistently passing molecule-local coordinate buffers. The changes improve memory access patterns without altering computational logic. The CMakeLists.txt change resolves a missing dependency.
• No files require special attention

Important Files Changed

File Analysis

Filename	Score	Overview
src/minimizer/bfgs_minimize_permol_kernels.cu	5/5	Updated to use local position buffers (shared memory) instead of global arrays, removing unnecessary global memory copies during line search
src/forcefields/dist_geom_kernels.cu	5/5	Refactored to pass pre-offset molecule coordinates to device functions for better shared memory utilization
src/forcefields/dist_geom_kernels_device.cuh	5/5	Changed function signatures to accept pre-offset molecule coordinates instead of global arrays with internal offsetting
src/forcefields/mmff_kernels.cu	5/5	Updated kernel calls to pass molecule-local coordinate pointers to device functions
src/forcefields/mmff_kernels_device.cuh	5/5	Modified device function signatures to receive pre-offset coordinate pointers for shared memory optimization
src/CMakeLists.txt	5/5	Added bfgs as PUBLIC dependency to etkdg library for proper linking

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Additional Comments (1)

1. src/minimizer/bfgs_minimize_permol_kernels.cu, line 617-621 (link)

   style: unnecessary copy to global memory during line search - energy functions now read from scratchPos so this write has no effect until position is accepted (line 661)

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[stslxg-nv]

LGTM