CaviTracer - refactor for enhanced accuracy and speed of channel identification to be competitive with established SOTA tools - #2249

Merged

karolamik13 merged 35 commits into

briza81:channels-refactor

Jul 20, 2026

Commits on Jul 7, 2026

channels: homogeneous-ball atom substitution to approximate weighted Voronoi by
briza81
committed
f473084
channels: vectorize tessellation filtering and pathfinding by vectorizing ops in delete_simplices3d, delete_section,surface_layer and the neighbour remap (row membership via hashed void-view _rows_…
briza81
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4a3f588
channels: per-stage LOGGER timing in calcChannels with unified reporting of wall-clock timings for homogenization, tessellation, surface filtering, cavity detection and pathfinding, plus an overal…
briza81
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0504b5b
channels: cleaning comments
briza81
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d53d53f
channels: add restrict_channels_to_start_point flag (default False) which is active when a start_point is set. False keeps the existing behavior (seed every cavity, search all channels); True restr…
briza81
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7a86bdb
channels: restrict surface-erosion sphere_fit to the boundary shell in delete_simplices3d. The surface=True pass only ever deletes tetrahedra with a -1 neighbour, but the vectorized code computed n…
briza81
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17c1dcc
channels: record per-channel cost (Dijkstra path weight) and curvature, order channels by ascending cost so channel 0 is the best tunnel. Write a REMARK line with length/bottleneck/curvature/cost b…
briza81
committed
f30fcc7

Commits on Jul 8, 2026

channels: truncate channels at surface mouths to avoid their duplication.
briza81
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4f2e013

Commits on Jul 9, 2026

Commits on Jul 10, 2026

Commits on Jul 13, 2026

Commits on Jul 14, 2026

Commits on Jul 15, 2026

Commits on Jul 16, 2026

Commits on Jul 17, 2026

Update channels.py
karolamik13
authored
4be6430
CaviTracer - calcChannelSurfaceOverlaps() - improved with multiproc calc
karolamik13
committed
5d61cdf
CaviTracer - calcSurfaceCavityOverlaps and channels docs
karolamik13
committed
3e91bdd

Commits on Jul 18, 2026

CaviTracer (#1 in TODO list; input atoms filtering) - _reportAtomsInputComposition
karolamik13
committed
888bfd4

Commits on Jul 20, 2026