Antoine/Atomizer
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3 Commits

Author SHA1 Message Date
Anto01
ea437d360e docs: Major documentation overhaul - restructure folders, update tagline, add Getting Started guide 
- Restructure docs/ folder (remove numeric prefixes):
  - 04_USER_GUIDES -> guides/
  - 05_API_REFERENCE -> api/
  - 06_PHYSICS -> physics/
  - 07_DEVELOPMENT -> development/
  - 08_ARCHIVE -> archive/
  - 09_DIAGRAMS -> diagrams/

- Replace tagline 'Talk, don't click' with 'LLM-driven optimization framework' in 9 files

- Create comprehensive docs/GETTING_STARTED.md:
  - Prerequisites and quick setup
  - Project structure overview
  - First study tutorial (Claude or manual)
  - Dashboard usage guide
  - Neural acceleration introduction

- Rewrite docs/00_INDEX.md with correct paths and modern structure

- Archive obsolete files:
  - 01_PROTOCOLS.md -> archive/historical/01_PROTOCOLS_legacy.md
  - 03_GETTING_STARTED.md -> archive/historical/
  - ATOMIZER_PODCAST_BRIEFING.md -> archive/marketing/

- Update timestamps to 2026-01-20 across all key files

- Update .gitignore to exclude docs/generated/

- Version bump: ATOMIZER_CONTEXT v1.8 -> v2.0
 2026-01-20 10:03:45 -05:00
Anto01
b8a04c62b8 docs: Consolidate documentation and fix protocol numbering (partial) 
Phase 2 of restructuring plan:
- Rename SYS_16_STUDY_INSIGHTS -> SYS_17_STUDY_INSIGHTS
- Rename SYS_17_CONTEXT_ENGINEERING -> SYS_18_CONTEXT_ENGINEERING
- Promote Bootstrap V3.0 (Context Engineering) as default
- Archive old Bootstrap V2.0
- Create knowledge_base/playbook.json for ACE framework
- Add OP_08 (Generate Report) to routing tables
- Add SYS_16-18 to protocol tables
- Update docs/protocols/README.md to version 1.1
- Update CLAUDE.md with new protocols
- Create docs/plans/RESTRUCTURING_PLAN.md for continuation

Remaining: Phase 2.8 (Cheatsheet), Phases 3-6

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
 2026-01-07 08:52:07 -05:00
Anto01
d19fc39a2a feat: Add OPD method support to Zernike visualization with Standard/OPD toggle 
Major improvements to Zernike WFE visualization:

- Add ZernikeDashboardInsight: Unified dashboard with all orientations (40°, 60°, 90°)
  on one page with light theme and executive summary
- Add OPD method toggle: Switch between Standard (Z-only) and OPD (X,Y,Z) methods
  in ZernikeWFEInsight with interactive buttons
- Add lateral displacement maps: Visualize X,Y displacement for each orientation
- Add displacement component views: Toggle between WFE, ΔX, ΔY, ΔZ in relative views
- Add metrics comparison table showing both methods side-by-side

New extractors:
- extract_zernike_figure.py: ZernikeOPDExtractor using BDF geometry interpolation
- extract_zernike_opd.py: Parabola-based OPD with focal length

Key finding: OPD method gives 8-11% higher WFE values than Standard method
(more conservative/accurate for surfaces with lateral displacement under gravity)

Documentation updates:
- SYS_12: Added E22 ZernikeOPD as recommended method
- SYS_16: Added ZernikeDashboard, updated ZernikeWFE with OPD features
- Cheatsheet: Added Zernike method comparison table

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
 2025-12-22 21:03:19 -05:00