Claude/optimize packmol turbo wl4 eu#122

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MicheleBonus wants to merge 41 commits intom3g:masterfrom

MicheleBonus:claude/optimize-packmol-turbo-Wl4EU

Commits on Mar 11, 2026

Optimize cell neighbor lookup in pairwise loops
MicheleBonus
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Merge pull request #1 from MicheleBonus/codex/optimize-performance-of-packmol-memgen
MicheleBonus
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Optimize pairwise kernels in fparc/gparc
MicheleBonus
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Merge pull request #2 from MicheleBonus/codex/optimize-packmol-for-speed
MicheleBonus
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Refactor forward cell-neighbor traversal with shared offsets
MicheleBonus
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Merge pull request #3 from MicheleBonus/codex/refactor-neighbor-access-using-offset-helper
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Split pair kernels into fast/short/fixed paths and prefilter active atoms
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Merge pull request #4 from MicheleBonus/codex/refactor-hot-logic-in-fparc-and-gparc
MicheleBonus
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Add hot-path scalar streams for pairwise kernels
MicheleBonus
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Merge pull request #5 from MicheleBonus/codex/define-explicit-hot-path-arrays-in-compute_data.f90
MicheleBonus
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Add per-cell radius bounds and pair-distance pruning
MicheleBonus
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Merge pull request #6 from MicheleBonus/codex/extend-cell-bookkeeping-with-per-cell-maxima
MicheleBonus
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Optimize hot-loop square operations in pair kernels
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Merge pull request #7 from MicheleBonus/codex/refactor-hot-loop-square-calculations
MicheleBonus
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Add explicit build profiles and numerics profile check
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Merge pull request #8 from MicheleBonus/codex/update-build-configurations-and-documentation
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docs: update build/profile docs and add Michele Bonus credentials
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Merge pull request #9 from MicheleBonus/codex/plan-adjustments-and-improvements-for-computing
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Fix pgencan module import ambiguity for x
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Merge pull request #10 from MicheleBonus/codex/fix-unused-arguments-and-ambiguous-references
MicheleBonus
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Fix missing init1 import in pgencan
MicheleBonus
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Merge pull request #11 from MicheleBonus/codex/fix-unused-dummy-arguments-and-errors
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Rename hot coordinate buffers and tighten compute_data imports
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Merge pull request #12 from MicheleBonus/codex/rename-hot-buffer-arrays-in-compute_data.f90
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Narrow compute_data imports in collision-prone routines
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Merge pull request #13 from MicheleBonus/codex/refactor-imports-in-high-risk-fortran-files
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Initialize gencan scalars before conditional use
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Merge pull request #14 from MicheleBonus/codex/fix-variable-initialization-and-warnings-in-gencan.f
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Fix GENCAN evalhd interface and mark API dummy args used
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Merge pull request #15 from MicheleBonus/codex/verify-and-clean-dummy-arguments-in-subroutines
MicheleBonus
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Wrap long short-radius assignment in resetcells
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Merge pull request #16 from MicheleBonus/codex/refactor-assignment-in-resetcells-subroutine
MicheleBonus
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Handle missing restriction mapping defensively
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Merge pull request #17 from MicheleBonus/codex/add-defensive-initialization-in-packmol.f90
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Validate fixed-molecule residue bounds before nres
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Merge pull request #18 from MicheleBonus/codex/initialize-ilres-and-validate-residue-bounds
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Reformat long free-form expressions in computef
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Merge pull request #19 from MicheleBonus/codex/reformat-assignments-in-computef.f90
MicheleBonus
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Optimize neighbor reach checks and split long Fortran lines
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Merge pull request #20 from MicheleBonus/codex/improve-program-performance-and-refactor-expressions
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Commits on Mar 12, 2026

Eliminate overhead that cancelled out pairwise kernel optimizations
claude
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