CaviTracer - Optimization - #2241

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MatthewLicht wants to merge 16 commits into

MatthewLicht:ct_dev

Commits on Jun 26, 2026

changes sum to the builtin sum to prevent issue with numpy depreciation of np.sum(generator)
MatthewLicht
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d6c025b
changed calcChannels to match new calculator functions
MatthewLicht
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f02cb20
added calcChannelsMultipleAtomGroups which runs calcChannels for multiple unrelated atomgroups
MatthewLicht
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0a88ea1
updated calcChannelsMultipleFrames to use multiprocessing POOL
MatthewLicht
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2665d4a
updated Channel class to be compatible with functions using multiprocressing Poolsuch as _ag_worker and _frame_worker
MatthewLicht
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b64bfcc
vectorized sphere_fit and delete_simplices3d so that spherefit is calculated for all relevant tetrahedra in the vector, rather than a for loop
MatthewLicht
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ec6abb8
updated delete_section for faster mask creation and filtering
MatthewLicht
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3928489
updated surface_layer to take advantage of contiguousarrays and views
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236b013
updated dijkstra to use scipy algorithms and to build paths as nodes and branches
MatthewLicht
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eb72e3b
added centers and radii to process_channel outputs to match changes to Channel class
MatthewLicht
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4b82727
added calc_circumcenters function to ChannelCalculator class
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e52a47e
added normalModeCavityAnalysis
MatthewLicht
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8893430
removed normalModeCavityAnalysis, needed updating
MatthewLicht
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0ba87b1
added additional error handling for multiprocessing
MatthewLicht
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6632c29

Commits on Jul 5, 2026

removed unnecessary import and altered formatting for legibility
MatthewLicht
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e3618d5

Commits on Jul 6, 2026

resolved formatting issues
MatthewLicht
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d9b95d0