Finalize v5.14.1 and audit VSIM test surface#6
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…try, provenance demo, shell visualization
…Tier 1 Identity: formula, atom count, composition, canonical ordering Tier 2 Topology: Morgan+FNV-1a graph hash, bond signature, coordination Tier 3 Geometry: pairwise distance hash, geometry/symmetry class, pose-normalized Tests: topo invariance under perturbation, geom invariance under rigid transforms (translate/rotate/reflect), atom-order permutation invariance, near-degenerate sensitivity, 500-molecule scale collision detection, full provenance record audit
…clear domain added to Scale 1->2 (Atomistic->CG) transition so displacement energy and Frenkel pair targets propagate from atomistic through grain. NuclearCore registry: Pu-239 active (Ed=35 eV, fissility=37.03, monoclinic-alpha), U-238 and Th-232 as inactive fertile species. Version lineage updated: 4.0-LB now records Z=94 core active.
…xcel XML Time-limited runner (--minutes 10-20) with Pu-239/UO2/Zircaloy-4 nuclear fuel injection (~20% of cases). Output: master_report.tex (compilable LaTeX with booktabs/siunitx/longtable), data.xml (SpreadsheetML with nuclear row highlighting), summary.csv, and individual .md reports. Tested: 59658 reports in 1 min at 994 reports/sec.
…cture (129/129 tests pass) - particle_id.hpp: ParticleID enum (-1..-18) with 7 constexpr predicates (is_reserved, is_decay_particle, is_transportable, is_bookkeeping_only, is_energy_carrier, is_defect_or_virtual, is_ghost) + to_string + helpers - decay_event.hpp: DecayEvent record (parent/daughter IDs, emitted array[8], energy fractions, damage score, overflow-guarded add_emitted) - decay_event_builder.hpp: make_alpha_decay, make_beta_minus_decay, make_gamma_decay with physics-correct default fractions - kinetic_event_kind.hpp: coarse EventKind enum (11 kinds) - kinetic_event_record.hpp: KineticEventRecord with std::variant payload (DecayEvent | GenericTransportEvent) - legacy/c_api: C99 particle_ids.h/c + decay_event.h/c (portable C API) Fix: malformed block comment in particle_ids.h (-9..-14 range was swallowed) - gas2_tui.hpp: pure-ANSI interactive TUI (937 lines, 7 screens) - cmake: vsepr_legacy_c STATIC library + test_particle_id_decay CTest target - tests/CMakeLists.txt: ParticleIDDecayTest (core nuclear physics quick)
Beta-6 instrumentation release (developed alongside v4.1.x, distinct goals). New: src/analysis/diffusion_analysis.hpp -- DiffusionRecord, DiffusionTracker, TransportInference, TransportAnalyzer, ActivationTrend, annotate_defect_ratios, annotate_formation_context New: src/analysis/packing_analysis.hpp -- PackingRecord, PackingTracker, PackingInference, PackingAnalyzer, compute_compressibility New: tests/test_macro_inference.cpp (Group 24) -- 12 diffusion cases + 4 packing cases. D_eff from MSD slope only. All macro properties analysis-only. Formation-context annotation. Formation codebase survey. Architecture rule: no inferred property stored in State or xyzFull.
- src/gen/metal_presets.hpp: static DB for Nitinol(B2), W(BCC), Inconel625(FCC), Ti-6Al-4V(HCP) with occupancy-cycle support for substitutional disorder - src/gen/lattice_builder.hpp: BCC/FCC/B2/HCP supercell builder → XYZFrame; 3-frame thermal trajectory generator (T=0/300/600 K placeholders) - src/gen/step_writer.hpp: minimal STEP AP203 writer (ISO-10303-21), CARTESIAN_POINT per atom — engineering geometry truth artifact - src/gen/metal_gen.cpp: driver emitting .xyz .xyza .xyzc .xyzf .step + geometry_map.json per material; reuses vsepr::io XYZ writer API throughout Generates 21 artifacts (5 per material) + geometry_map.json in gen_out/ Branch: v5.0.0-beta.7-step-attempt
- src/gen/.gitignore: suppress exe, gen_out/ from VCS - src/gen/README.md: full module doc — presets, builder, STEP writer, build/run instructions, artifact contract, extension guide - docs/FILE_FORMATS.md: add STEP AP203 section (structure, role, limitations, writer API); update Overview table to include .xyzf and .step; add src/gen/ cross-reference at bottom
tests/test_metal_gen.cpp — 15 test categories, 399 checks: 1. Preset database integrity 2. Atom count correctness (BCC/FCC/B2/HCP, 1^3–8^3 and asymmetric) 3. Coordinate bounds (cubic orthorhombic; HCP z-only due to hex cell) 4. Species fractions (alloy occupancy cycle verification) 5. XYZFrame invariants (N, has_* flags, PBC, T, E) 6. Per-atom fields (q, v, e present; build-time v==0) 7. Determinism (identical frames from independent calls) 8. Thermal trajectory (frame count, T values, T=0 zero velocity) 9. STEP AP203 output (header/footer tokens, CARTESIAN_POINT count) 10. geometry_map.json required keys 11. Scaling stress — 8x8x8, 2048 atoms, finite coords, valid STEP 12. Energy accumulation (frame total == N * ref_energy_per_atom) 13. Zero-velocity at build time 14. HCP geometry (NN distance using hex convention sqrt(a^2/9+c^2/4)) 15. B2 site ordering (even=Ni corner, odd=Ti body-centre) src/gen/lattice_builder.hpp — fix HCP box: - box.ay is now |a2| = ny*a (lattice vector length), not ny*a*sqrt3 - lattice[] matrix now stores the actual hex 3x3 vectors correctly All 399 checks PASS.
Simulates common new-user loop mistakes against the metal_gen pipeline:
Loop A (for) — off-by-one: i <= frame.N accesses atoms[N] (UB)
Fix: strict i < frame.N
Loop B (while) — missing ++i increment causes infinite loop
Guarded at 100k iters; produces -8.73e6 vs correct -4714.2
Fix: add ++i before closing brace
Loop C (for) — min_e initialised to 0.0 instead of +inf
Masks all all-positive energy blocks (returns 0, not 50.0)
Fix: std::numeric_limits<double>::max() as initial value
All 3 bugs demonstrated to produce wrong output; all 3 fixes verified correct.
8/8 checks pass.
VizMode::BATCH_PASSIVE (src/vis/viz_config.hpp) - New enum variant: zero overhead preset for extended batch runs - Disables outlines, shadows, AA, motion blur, interpolation - Adds batch_display_fps, batch_show_status, batch_run_label fields - apply_mode_preset() case sets target_fps = batch_display_fps BatchWindowBridge (src/vis/batch_window_bridge.hpp) - Lock-free frame slot: std::atomic<shared_ptr<XYZFrame>> (C++20) - Producer API: push_frame(), push_status(), push_progress(), start(), finish() - Consumer API: latest_frame(), status_text(), status_snapshot(), display_tick() - BatchStatus: run_label, frame/artifact counters, elapsed time, current_op - display_tick() throttle: returns true only when 1/target_fps has elapsed - Drop-oldest policy: producer never blocks; stale frame silently replaced ContinuousRunDisplay (src/vis/continuous_run_display.hpp) - Top-level wiring: configure() -> open() -> run_event_loop() pattern - ConsoleProgressBar fallback for headless / no-GL environments - Single-step tick() variant for embedding into existing event loops - GL window init deferred to continuous_run_display.cpp (beta.8 GL layer) - Does NOT modify existing Window::run_with_ui() interactive path Deprioritizes interactive UI layer per architecture directive: - BATCH_PASSIVE preset strips all interactive rendering features - No ImGui panel changes; overlay text injected via existing status path - Producer thread and display thread fully decoupled
- xyz_to_snapshot.hpp: XYZFrame -> FrameSnapshot inline converter - window.hpp/cpp: add run_batch(bridge, fps) -- throttled passive GL loop, BATCH_PASSIVE preset, no ImGui, exits when bridge.is_done() - continuous_run_display.hpp: clean interface (configure/open/close/bridge/ run_event_loop), pimpl-style GL delegation to .cpp - continuous_run_display.cpp: open() constructs Window, run_gl_loop() delegates to Window::run_batch(), run_console_loop() is headless fallback - Removed orphaned auto_pilot stanza that was floating outside any function in window.cpp
- continuous_run_display.hpp: WindowDeleter with #ifdef guards so the non-GL path needs no .cpp linkage; run_gl_loop() is inline no-op when VSEPR_HAS_GL not set - continuous_run_display.cpp: WindowDeleter body + GL loop (GL builds only) - metal_gen.cpp: wired ContinuousRunDisplay; worker thread owns generation; main thread runs display.run_event_loop() (console bar when no GL) - metal_gen builds clean, runs, shows live progress bar during batch
stress test (src/gen/batch_display_stress.cpp):
12 tests -- T1 round-trip, T2 10k-frame flood, T3 monotonicity,
T4 torn-read guard, T5 elapsed monotonic, T6 tick throttle,
T7 lifecycle FSM, T8 multi-cycle, T9 threaded console loop,
T10 empty-label guard, T11 late consumer, T12 zero-atom edge case
result: 12/12 ALL PASS
docs (docs/vis/):
batch_display_api.md -- full API reference for all public types
batch_display_usage.md -- thread model, build variants, integration
walkthrough, cadence guide, file map,
known limitations / future work
…ashboardRecord wiring + T1-T8 377/377
…figures — 46 pages, clean compile
…ocumentation - Add render_interval (step-count) to VisualSection and VisualExternalSection - Parse render_interval in vsim_parser.cpp for both visual scopes - Gate render dispatch in beta10_demo.cpp and kernel_demo.cpp - Create Group 35 acceptance tests (test_render_interval.cpp) - Create VSIM_LANGUAGE.md: canonical language guide - Create VSIM_REFERENCE.md: field reference adjacent to README - Create VSIM_DEVELOPMENT.md: 5-step add/wire/test/document checklist - Update STAGE.md and docs/wo/WO_56C.md to mark Day 57 D complete render_interval is orthogonal to display_fps; it controls simulation-step emission cadence for render and export layers, defaulting to 1 (render every step).
- Bump version date to 2026-05-07 - Add beta-7 Day 57 progress block with commit ref 142fb5e4 - Add Section 4: render_interval doctrine (orthogonal to display_fps) - Add Section 7: developer procedure 5-step checklist - Add Section 8: key reference files table - Renumber Terminology -> 5, System Layers -> 6
Beta-8 closes the runtime foundation stage for VSEPR-SIM. Runtime layer: - PBC wired into FIRE minimiser (wrap_coords after position update) - Ewald summation for ionic crystals (real + k-space + self-energy) - render_interval cadence field (WO-VSIM-57D, Group 35) Export / artifacts: - Export flushing (flush_exports, flush_pipeline_artifacts) - Dashboard SVG + PNG raster export (stb / PPM fallback) - STEP sidecar export foundation (point-cloud; B-Rep deferred) - Pipeline audit JSONL, report MD + JSON, run manifest Language / schema (WO-VSIM-03B): - Intent-based authoring: [material], [run], [environment] - [excite.*], [observe], [[override.particle]], [[raw.object]] - resolve_structure_alias(): 70-entry canonical alias map (ionic, metals, covalent, oxides, geometry, polymers, porous/framework, bead/premacro) - Group 36 acceptance tests (IntentAuthoringTest) - VSIM_LANGUAGE.md and VSIM_REFERENCE.md updated Stage / docs: - STAGE.md: beta-8 CLOSED, beta-9 promoted - WO-VSEPR-SIM-58A gate table (all 8 gates closed) - docs/wo/WO_58A.md work order record - VSIM_REFERENCE.md: beta-9 owned items table Deferred to beta-9: registry resolution engine (WO-VSIM-03C) Deferred to beta-10: installation / consumer packaging
Day 61 | WO-VSIM-61A–61D + WO-VSEPR-SIM-62A Schema ------ * vsim_document.hpp — added VsimSystemSection, VsimStructureAnalysisSection, VsimSamplingSection (RDF/MSD/unwrap_pbc), VsimScaleSamplingSection (field_projection / RVE), VsimAnalysisInferenceSection (packing/mobility regime), VsimVerifySection + verify sub-sections (structure / rdf / msd / mass) for the empirical verification layer (WO-62A) * VsimDocument gains: pipeline_system, pipeline_structure, pipeline_sampling, pipeline_scale_sampling, pipeline_inference, pipeline_output, pipeline_verify Parser / Runtime ----------------- * vsim_parser.cpp / vsim_parser.hpp — parse [analysis.structure], [analysis.sampling], [analysis.scale_sampling], [analysis.inference], [verify], [verify.structure], [verify.rdf], [verify.msd], [verify.mass] * vsim_runtime.hpp — runtime surface updated for analysis/verify pass New headers ----------- * include/vsim/exit.hpp — exit-code constants * include/vsim/reaction_bridge.hpp — ReactionBridge API * include/vsim/vsim_output_layout.hpp — AppDataPaths + run-folder helpers * include/vsim/vsim_registry.hpp — RegistryBundle + RegistryResolver * include/vsim_override/vsim/ — override copies synced Examples / scripts ------------------ * examples/wo61c_pipeline_test.vsim + wo61d_*.vsim — pipeline scenario files * scripts/demo_0[1-7]_*.vsim + val_0[1-8]_*.vsim — beta-11 demo and validation scripts for registry, PBC, laser-MD, variance, batch sweep, CaF2/ZnS/TiO2/SiO2/MFI/graphite/Ar/S22 empirical targets Documentation ------------- * STAGE.md — rebuilt from scratch; eliminated 4448-line corruption blob * VSIM_REFERENCE.md — appended WO-62A verify-layer section (encoding corruption repaired: 10 x U+FFFD and broken surrogate pair removed); WO-62B and WO-62C batch-study schema sections added * VSIM_LANGUAGE_REFERENCE.md — new language quick-reference * docs/VSIM_LANGUAGE.md — language spec updated * VSIM_DEVELOPMENT.md — naming-convention note added * tests/CMakeLists.txt — Day 62 group comment corrected (header vs source file) * CMakeLists.txt / atomistic/CMakeLists.txt / coarse_grain/CMakeLists.txt — build wiring updated Test groups passing: G39 (WO-62A verify, 19/19)
- Rewrote demo_approach1_defect_diffusion.vsim: [material] B1_NaCl + 4 batch jobs (vacancy_na, vacancy_cl, schottky_pair, frenkel_na), research_report export profile, SVG visual output - Rewrote demo_approach2_formation_path.vsim: 5 batch jobs for thermal protocols (slow_cool, rapid_quench, stepped_cool, reheat_cycle, isothermal_anneal), memory overlay for nucleation analysis - Rewrote demo_approach3_powder_sintering.vsim: [material] premacro_powder_bed MgO + 5 batch jobs (loose_drop, compressed, vibrated, bimodal, contaminated) - All three scripts: registry resolves B1_NaCl / premacro_powder_bed, 4-5 batch jobs confirmed, BOM-free, validate OK - Added reports/report_approach1.md (Sections 0-8, 12/12 sigs passed) - Added reports/report_approach2.md (Sections 0-8, 16/16 sigs passed) - Added reports/report_approach3.md (Sections 0-8, 17/17 sigs passed)
Leftover template workflow was firing on every branch push and failing because scripts/labelme_test.sh does not exist in this repo. VSEPR-SIM does not use labelme.
… routing
- Bump version 2.0.0 -> 5.0.0, publisher LMSM3, URL -> LMSM3/VSEPR-SIM
- Add kernel (vsepr.exe, vsepr-cli.exe, vsepr_batch.exe), vsim parser
headers (include/vsim/*), scripts/, VSIM_REFERENCE.md to [Files]
- Remove stale references: CHANGELOG.md, vsepr.bat, installer_banner.bmp
- Add installer/bin/open_xyz.cmd: thin pythonw launcher with multi-path
fallback (PATH -> LOCALAPPDATA -> C:\PythonXXX -> powershell msgbox)
- Wire .xyz and .vsxyz registry associations -> open_xyz.cmd (was vsepr.exe)
- Add .vsim script association -> vsepr-cli.exe
- All associations are optional installer Tasks (opt-in)
- tools/vsepr_xyz_popup.pyw: detect installed layout ({app}/bin/) in
find_project_root, resolve BUILD_DIR for both dev and installed trees,
update docstring to cover .xyz + .vsxyz
…uild paths AUDIT FINDINGS -------------- - Duplicate installer logic: dist/VSEPR-SIM-5.0.0-local/installer/ register-file-associations.ps1 (beta-10, canonical) was not referenced by setup.iss — the Inno Setup [Registry] block re-implemented the same associations independently. Removed the duplication. - build\bin\ does not exist; binaries land in build\ flat. Fixed 5 scripts that referenced the non-existent path. - No filename collisions between archive/legacy/bridge_beta and live source. INSTALLER CHANGES (setup.iss) ------------------------------ - Removed entire [Registry] block (was duplicating register-file-associations.ps1) - Added [UninstallRun] to call PS script -Unregister on removal - File associations now owned exclusively by register-file-associations.ps1 under HKCU — no admin required, clean uninstall guaranteed - [Tasks]: collapsed 3 per-ext tasks into one 'fileassoc' task - [Files]: added vsepr-sim.exe, register-file-associations.ps1; renamed open_xyz.cmd -> open_vsim_file.cmd UNIVERSAL OPENER (open_vsim_file.cmd, replaces open_xyz.cmd) ------------------------------------------------------------- - Single handler for .xyz .xyza .xyzA .xyzc .xyzf .xyzF .xyzfull .vsxyz .vsim - Priority: vsepr-sim.exe open -> vsepr.exe open -> pythonw popup - Python fallback probes PATH then common install locations ASSOCIATION SCRIPT (installer/register-file-associations.ps1) -------------------------------------------------------------- - Copied from dist/ (beta-10 canonical) into installer/ so Inno Setup can package it and it is tracked in version control - Added .vsxyz (full takeover) and .xyzfull lowercase mapping - All XYZ open commands now route through \ = open_vsim_file.cmd instead of hardcoded vsepr-sim.exe; preserves priority order SCRIPT PATH FIXES ----------------- - scripts/automate_review.ps1: build\bin\vsepr.exe -> build\vsepr.exe - scripts/random_discovery.ps1: same - scripts/run_cli_tests.ps1: all build\bin\ -> build\ (bulk replace) - scripts/create_portable_zip.bat: paths + version 2.0.0 -> 5.0.0 - scripts/build_formula_tests.ps1: build\bin\ -> build"
…taller vsepr.exe path; rewrite QUICKBUILD for v5; add deprecation policy - bridge_beta/CMakeLists.txt renamed to .disabled (cmake-invisible) - README stubs added to legacy/, archive/, bridge_beta/, v4/, v5/ - installer/setup.iss [Run]: -BinaryPath now vsepr.exe (was vsepr-sim.exe, missing binary) - installer/register-file-associations.ps1: fix error message to match vsepr.exe - QUICKBUILD.md: full v5 rewrite (was v2.4.0 meso-build era, stale binary/script names) - CONTRIBUTING-DEPRECATION.md: new file documenting deprecation criteria and archive workflow Closes 3.1 3.2 3.3 4.1 4.2
demo_viz_01_xyz_single — Ar gas cloud (64 atoms, 30 Ang, PBC): - emits via vsepr Ar@gas emit --cloud 64 - validates .vsim (visual section with advanced overlays) - opens in vsepr-sim terminal 3D viewer demo_viz_02_xyzf_anim — OsO4 NVT trajectory (5 frames, 450 atoms): - generates .xyzf via gen_xyz_demo - validates .vsim (visual.external export_trajectory) - opens in vsepr-sim trajectory player ([q]=quit [p]=pause) File associations re-registered from dev-tree (register-file-associations.ps1) pointing at build\vsepr.exe. Double-click any .xyzf file to launch the player.
…yback, Qt bridge, docs overhaul - FormationOutput -> KernelEventLog -> DashboardRecord pipeline wired (WO-57D) - Gas-mixing MD demo: four-corner N2/O2/H2O/Ar injection at 1200K, N>1200 - region + velocity_drift schema/parser support in vsim_document/vsim_parser - molecule_atoms_from_formula() helper (no hardcoded gas lists) - xyzf trajectory writer in cmd_run_vsim.cpp - Qt workstation: auto-launch with --xyzf on scripted run completion - EngineAdapter: multi-frame xyzf trajectory import, symbol_to_Z CPK fix - Organic formula parser added (chem/organic/) - Peptide formation updates and new test coverage - node_accessor: VSIM document node traversal helper - vsim_document_new: extended schema draft - Gallery VSIM scripts: helium reactor, NaCl PBC, calibration HTGR, room reactor - Installer: vsepr.cmd launcher, vsepr_xyz_popup.pyw, open_vsim_file.cmd updated - README: v5.0.0 rewrite — What's New section, vsper Quick Start, beta-gate validation status, v5 repo tree, softened closing tone, Python refs removed - TOUR.md: v5 architecture rewrite, Python/pykernel references removed - VSIM_LANGUAGE.md, VSIM_REFERENCE.md: schema updates for render_interval, velocity_drift, region fields - cmake/CoreBuild.cmake: build config template wired - tests: smoke_motd, smoke_tui, test_domain_audit, test_gallery_parse added
- Add pykernel/pillars/empirical_chem.py (Pillar F, v5.1.3)
Sources: PubChem REST API + PeriodicTableJSON warm fallback
+ NIST SRD-128 polarizability + Alvarez/Bondi/Shannon radii tables
- Generate data/elements.empirical.json (118 elements, schema v1)
Fields: atomic_weight, en_pauling, IE1, EA, radii (cov/vdW/ionic),
polarizability, electron_config, melt/boil, density,
molar_heat, phase — all with per-field _sources tags
- Add docs/audit/chem_audit_empirical.md (field coverage audit)
- Add pykernel/pillars/_verify_v5113.py (30-check verification suite)
Passes: pillar imports, JSON integrity, EA/IE unit sanity,
source-tag audit, API smoke test
- Update pykernel/pillars/__init__.py to export empirical_chem
Pre-electron / high-accuracy classical MD baseline checkpoint.
Verification: 30/30 PASS exit=0
…ocument.hpp - step6 analysis: +7 fields (cutoffs, msd, rmsd, variance/n_evolution probes); step7 export: +10 fields matching ExportSection keys, +new export.visual sub-module (8 fields); step8 visual: +18 fields (7 output_type choices, animation_mode fix, all VisualSection flags, GL/web/pacing options). All sourced from vsim_document.hpp. Demo verified, build clean.
…track WO-MF-01 ledger; add PROGRESS_SUMMARY.md
…ty, formal_charge, orphaned tests registered, reaction engine smoke test - types.hpp: add Atom::formal_charge (int8_t, default 0) - chemistry_v2.hpp: replace detect_rings() stub with DFS cycle detection - chemistry_v2.hpp: replace detect_aromaticity() stub with Hückel 4n+2 impl - chemistry_v2.hpp: wire formal_charge into validate_atom() (closes TODO) - chemistry_v2.hpp: switch include to element_data_integrated.hpp (production DB) - chemistry_universal_test.cpp: fix include + load_from_json_file() call (re-enables) - tests/CMakeLists.txt: register ElementDBPhase1Full, ChemistryValidation, ChemistryUniversal - tests/test_reaction_engine.cpp: new 17-check audit (RE-01..RE-17) - tests/CMakeLists.txt: register ReactionEngineAudit Chemistry CTest result: 12/12 PASS (was 4/12 before this commit)
- Implement DFS ring detection + Huckel aromaticity (chemistry_v2.hpp) - Implement simplified CIP tetrahedral R/S chirality (isomer_signature.hpp) - Fix Molecule::add_atom() mass lookup via chemistry_db().get_mass(Z) - Fix ReactionEngine element lookup from State::type (engine.cpp) - Wire evaluate_organic_diagnostics + flush_organic_diagnostics (vsim_runtime.hpp) - Re-enable ChemistryUniversalV2, Phase2ComplexMolecules, IsomerTest targets - Add init_chemistry_db() to 14 pre-existing tests that lacked DB init: energy_tests, optimizer_tests, angle_tests, vsepr_tests, torsion_tests, test_torsion_analysis, torsion_validation_tests, alkane_torsion_tests, butane_scan, vsepr_domain_test, basic_molecule_validation, test_ethane_torsion, test_thermal_animation, test_formation_event_wiring - Promote MF-C03 (chirality detection) -> COMPLETE in WO-MF-01 - Update PROGRESS_SUMMARY.md: 95% critical path, 87% overall velocity
MF-F01 (STAGE.md missing — was 🔴): - Recreated STAGE.md at repo root from git history (d734759) + current state - Updated milestone table: v5.13.4 COMMITTED, v5.13.5 IN PROGRESS - Full test group registry Groups 1-89 + ChemistryUniversalV2/Phase2/IsomerTest - Day 74 section: WO-74A/B/C all COMPLETE (per WO-74 doc) - Day 75 section: WO-75A Part A COMPLETE, B PENDING, C COMPLETE - v5.13.5 release gate table with accurate per-criterion status - Promoted MF-F01 to COMPLETE in WO-MF-01 WO-75A Part C (IKK Python time-series — was 🟡): - Added discover_identity_sidecar(search_dir) to reporting/generate_report.py - Added plot_dist_timeseries(sidecar_path, out_path): reads .identity.json, dual-axis matplotlib figure (D_rec left / entropy proxy right), amber identity-loss band, D=0.5 reference line, ASCII-safe cp1252-compatible caption - Updated generate_consolidated_report() to accept optional captions dict - Added step 2.5 in main(): scan sidecars, generate PNGs, pass captions - Graceful fallback (None, None) when matplotlib unavailable - Promoted MF-E02 to COMPLETE in WO-MF-01 Test count unchanged: 167/167 passing
- Calls vsepr classify on H2O, NH3, CO2 - Verifies vsepr_report, conf values, fallback state, automation branch - Exports dark-mode 3D matplotlib PNG per molecule to out/wo84s/ - 16 PASS / 0 FAIL (Day 84+ PNG export rule satisfied)
…5 demo PASS, PNG confirmed)
…VSIM_LANGUAGE_REFERENCE
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Summary
Validation