docs: edge-linker twist investigation report - #63
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Research report on the edge/linker twist degeneracy: precise diagnosis of the current code (2-point Kabsch under-determination, n_slices=1 collapse), prior-art analysis (geonho42 fork and external MOF builders), an adversarial comparison of three candidate algorithms, and a recommended per-edge numerical approach (relaxation-surviving node-frame seed + 1-D axial optimization extending Locator.locate). Link it from ROADMAP item 1. Produced by a multi-agent investigation; key facts verified against the repo.
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Draft for review (mobile-friendly). A research report investigating the edge/linker twist degeneracy (ROADMAP item 1), plus a link to it from
ROADMAP.md.TL;DR
rss=0; the RMSD objective is flat in the twist. Nothing in the pipeline sets it (locator.py:148-150,:87;builder.py:537-543).Xatoms lie on the connection axis (Xoffaxis=0), so rotating about it leaves bond fusion unchanged — a fix is localized and low-risk.atan2/align_vectors(weights=[inf,w]), verified) + 1-D grid +minimize_scalar(satisfies constraint 2; a 1-D extension ofLocator.locate). Newedge_twist.py+ a newLocatormethod + a one-line swap inbuilder.py:537-543, behind aresolve_edge_twistflag. PR-1 is ~180 lines, numpy-only.E(phi)is non-flat with a coplanar minimum on a built HKUST-1/MOF-5 before wiring the optimizer.Full report:
docs/research/edge-linker-twist-investigation.md(diagnosis, prior art, comparison table with adversarial verdicts, implementation sketch, validation plan, risks).Not for merge — review/comments only. Implementation (PR-1) intentionally not started yet.