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Anto01 f13563d7ab feat: Major update - Physics docs, Zernike OPD, insights, NX journals, tools

Documentation:
- Add docs/06_PHYSICS/ with Zernike fundamentals and OPD method docs
- Add docs/guides/CMA-ES_EXPLAINED.md optimization guide
- Update CLAUDE.md and ATOMIZER_CONTEXT.md with current architecture
- Update OP_01_CREATE_STUDY protocol

Planning:
- Add DYNAMIC_RESPONSE plans for random vibration/PSD support
- Add OPTIMIZATION_ENGINE_MIGRATION_PLAN for code reorganization

Insights System:
- Update design_space, modal_analysis, stress_field, thermal_field insights
- Improve error handling and data validation

NX Journals:
- Add analyze_wfe_zernike.py for Zernike WFE analysis
- Add capture_study_images.py for automated screenshots
- Add extract_expressions.py and introspect_part.py utilities
- Add user_generated_journals/journal_top_view_image_taking.py

Tests & Tools:
- Add comprehensive Zernike OPD test suite
- Add audit_v10 tests for WFE validation
- Add tools for Pareto graphs and mirror data extraction
- Add migrate_studies_to_topics.py utility

Knowledge Base:
- Initialize LAC (Learning Atomizer Core) with failure/success patterns

Dashboard:
- Update Setup.tsx and launch_dashboard.py
- Add restart-dev.bat helper script

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

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

2025-12-23 19:47:37 -05:00

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Physics Documentation Index

This folder contains detailed physics and domain-specific documentation for Atomizer's analysis capabilities. These documents explain the engineering and scientific foundations behind the extractors and insights.

Document Catalog

Document	Topic	When to Read
ZERNIKE_FUNDAMENTALS.md	Zernike polynomial basics, RMS calculation, multi-subcase analysis	Setting up mirror optimization, understanding WFE metrics
ZERNIKE_OPD_METHOD.md	Rigorous OPD method for lateral displacement correction	Lateral support optimization, validating WFE accuracy

For Mirror/Optics Optimization

New to Zernike? Start with ZERNIKE_FUNDAMENTALS.md
Lateral support optimization? Read ZERNIKE_OPD_METHOD.md - critical
Mid-spatial frequency analysis? See SYS_16 (msf_zernike insight)

For Structural Optimization

Stress extraction: See SYS_12_EXTRACTOR_LIBRARY.md (E3, E12)
Strain energy: See SYS_12_EXTRACTOR_LIBRARY.md (E13)

For Thermal Analysis

Temperature extraction: See SYS_12_EXTRACTOR_LIBRARY.md (E15-E17)

Location	Content
`.claude/skills/modules/extractors-catalog.md`	Quick extractor lookup
`.claude/skills/modules/insights-catalog.md`	Quick insight lookup
`docs/protocols/system/SYS_12_EXTRACTOR_LIBRARY.md`	Extractor specifications
`docs/protocols/system/SYS_16_STUDY_INSIGHTS.md`	Insight specifications

Contributing Physics Documentation

When adding new physics documentation:

Naming: Use {TOPIC}_{SUBTOPIC}.md format (e.g., THERMAL_GRADIENTS.md)
Structure: Follow the pattern in existing documents:
- Executive Summary
- Mathematical Formulation
- When This Matters
- Implementation Details
- Usage Guide
- Validation
Cross-reference: Update this index and related skill modules
Link to code: Reference the implementing extractors/insights

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