Files

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

2.1 KiB

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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_17_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

2.1 KiB Raw Blame History