# 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.

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## Document Catalog

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

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## Quick Navigation

### For Mirror/Optics Optimization

1. **New to Zernike?** Start with [ZERNIKE_FUNDAMENTALS.md](ZERNIKE_FUNDAMENTALS.md)
2. **Lateral support optimization?** Read [ZERNIKE_OPD_METHOD.md](ZERNIKE_OPD_METHOD.md) - **critical**
3. **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)

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## Related Documentation

| 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 |

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## Contributing Physics Documentation

When adding new physics documentation:

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