Claude/optimize packmol turbo wl4 eu#122
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…-packmol-memgen Optimize hot cell-neighbor loops in computef/computeg
Optimize pairwise collision kernels for faster Packmol iterations
…s-using-offset-helper Refactor computef/computeg to use shared forward cell offsets
…parc-and-gparc Split pair-interaction kernels into fast/short/fixed paths and prefilter active neighbor heads
…h-arrays-in-compute_data.f90 Add hot-path scalar buffers and use them in pairwise kernels
…-with-per-cell-maxima Add per-cell radius bounds and PBC-aware cell-pair pruning
…e-calculations Optimize squared terms in hot atom-pair kernels
…ions-and-documentation Add build profiles (baseline, perf-native, devel, sanitize, static) and numerics check
…provements-for-computing docs: add Michele Bonus as contributor and update README build/profile and performance notes
…nd-ambiguous-references Fix pgencan build failure caused by ambiguous `x` symbol
…ents-and-errors Import `init1` from `compute_data` in `pgencan`
…ys-in-compute_data.f90 Rename compute_data hot buffers to x_hot/y_hot/z_hot and restrict imports
…gh-risk-fortran-files Narrow compute_data imports in collision-prone routines
…ation-and-warnings-in-gencan.f gencan: initialize CG/trust-region scalars and guard conditional reads
…-arguments-in-subroutines Restore full `evalhd` ABI and mark dummy API arguments as intentionally unused in GENCAN stubs
…-resetcells-subroutine Wrap long short-radius assignment in resetcells
…zation-in-packmol.f90 Defensively handle missing atom-level restriction mapping
…alidate-residue-bounds Validate fixed-molecule residue bounds before residue counting
…n-computef.f90 Reformat long continued assignments in src/computef.f90
…mance-and-refactor-expressions Optimize cell-neighbor evaluation and fix overlong Fortran lines
Three key changes that together yield ~25% speedup:
1. Remove hot buffer abstraction (x_hot, y_hot, z_hot, ibtype_hot, ibmol_hot)
- xcart(:,1) is already contiguous in Fortran column-major layout,
so separate x_hot(:) arrays provide zero cache benefit for the
random linked-list access pattern in fparc/gparc
- Eliminates refresh_hot_buffers_full (5 full-array copies per call)
and refresh_hot_buffers_atom (per-atom copy overhead)
- Use xcart/ibtype/ibmol directly in inner loops
2. Remove dead cell-level radius pruning infrastructure
- cell_pair_min_dist2 always returns 0 for the 14 forward neighbor
offsets because cells are sized >= interaction radius, making all
neighbor pairs adjacent (zero gap distance)
- The pruning check (min_cell_dist2 > max_reach2) was never true
- Removes cell_max_radius/cell_max_short_radius tracking from both
the cell-placement loop and resetcells, plus the reach computation
and cell_pair_min_dist2 function from the neighbor-offset loop
3. Incremental cell reset
- Walk the previous iteration's occupied-cell linked list to clear
only those cells, instead of zeroing all ncells^3 entries
- Also skip clearing latomnext since all placed atoms overwrite it
4. Pre-compute fixed_short_marker once at init instead of per-atom
per-iteration (fixedatom and use_short_radius are static)
Benchmarks (baseline -O2):
water_box_pbc: 0.41s -> 0.32s (22% faster)
solvprotein_pbc: 6.12s -> 4.56s (26% faster)
https://claude.ai/code/session_01SgmhQ2p78sPjFPxZPmLkk7
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