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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

7.2 KiB

Raw Blame History

Atomizer Documentation Index

Last Updated: 2026-01-20 Project Version: 1.0.0 (AtomizerSpec v2.0 - Full LLM Integration)

Quick Start

New to Atomizer? Start here:

README.md - Project overview and philosophy
Getting Started - Installation, first study, dashboard
Protocol System - How Atomizer is organized
Example Studies - Working examples

Documentation Structure

Core Documentation

Document	Purpose
GETTING_STARTED.md	Setup, first study, dashboard basics
ARCHITECTURE.md	System architecture, hooks, data flow
protocols/README.md	Protocol Operating System overview

Protocol System

The Protocol Operating System (POS) provides structured workflows:

protocols/
├── README.md              # Protocol system overview
├── operations/            # How-to guides (OP_01-08)
│   ├── OP_01_CREATE_STUDY.md
│   ├── OP_02_RUN_OPTIMIZATION.md
│   ├── OP_03_MONITOR_PROGRESS.md
│   ├── OP_04_ANALYZE_RESULTS.md
│   ├── OP_05_EXPORT_TRAINING_DATA.md
│   ├── OP_06_TROUBLESHOOT.md
│   ├── OP_07_DISK_OPTIMIZATION.md
│   └── OP_08_GENERATE_REPORT.md
├── system/               # Technical specifications (SYS_10-18)
│   ├── SYS_10_IMSO.md           # Intelligent optimization
│   ├── SYS_11_MULTI_OBJECTIVE.md
│   ├── SYS_12_EXTRACTOR_LIBRARY.md
│   ├── SYS_13_DASHBOARD_TRACKING.md
│   ├── SYS_14_NEURAL_ACCELERATION.md
│   ├── SYS_15_METHOD_SELECTOR.md
│   ├── SYS_16_SELF_AWARE_TURBO.md
│   ├── SYS_17_STUDY_INSIGHTS.md
│   └── SYS_18_CONTEXT_ENGINEERING.md
└── extensions/           # Extensibility (EXT_01-04)
    ├── EXT_01_CREATE_EXTRACTOR.md
    ├── EXT_02_CREATE_HOOK.md
    ├── EXT_03_CREATE_PROTOCOL.md
    └── EXT_04_CREATE_SKILL.md

User Guides

Located in guides/:

Guide	Purpose
CANVAS.md	Visual study builder (AtomizerSpec v2.0)
DASHBOARD.md	Dashboard overview and features
NEURAL_FEATURES_COMPLETE.md	Neural acceleration guide
NEURAL_WORKFLOW_TUTORIAL.md	Data → Training → Optimization
hybrid_mode.md	Hybrid FEA/NN optimization
TRAINING_DATA_EXPORT_GUIDE.md	Exporting data for neural training

API Reference

Located in api/:

Document	Purpose
system_configuration.md	Configuration format reference
nx_integration.md	NX Open API integration
GNN_ARCHITECTURE.md	Graph Neural Network details
NXOPEN_RESOURCES.md	NX Open documentation resources

Physics Documentation

Located in physics/:

Document	Purpose
ZERNIKE_FUNDAMENTALS.md	Zernike polynomial basics
ZERNIKE_OPD_METHOD.md	OPD method for mirror optimization

Development

Located in development/:

Document	Purpose
DEVELOPMENT_GUIDANCE.md	Development guidelines
DEVELOPMENT_ROADMAP.md	Future plans
Philosophy.md	Design philosophy

Diagrams

Located in diagrams/:

Document	Purpose
architecture_overview.md	System architecture diagrams
protocol_workflows.md	Protocol execution flows

Documentation by Task

Creating Studies

GETTING_STARTED.md - First study tutorial
OP_01_CREATE_STUDY.md - Detailed creation protocol
guides/CANVAS.md - Visual study builder

Running Optimizations

OP_02_RUN_OPTIMIZATION.md - Run protocol
SYS_10_IMSO.md - Intelligent optimization
SYS_15_METHOD_SELECTOR.md - Method selection

Neural Acceleration

guides/NEURAL_FEATURES_COMPLETE.md - Overview
SYS_14_NEURAL_ACCELERATION.md - Technical spec
guides/NEURAL_WORKFLOW_TUTORIAL.md - Step-by-step

Analyzing Results

OP_04_ANALYZE_RESULTS.md - Analysis protocol
SYS_17_STUDY_INSIGHTS.md - Physics visualizations

Troubleshooting

OP_06_TROUBLESHOOT.md - Troubleshooting guide
GETTING_STARTED.md#troubleshooting - Common issues

Quick Reference

Protocol Summary

Protocol	Name	Purpose
OP_01	Create Study	Study creation workflow
OP_02	Run Optimization	Execution workflow
OP_03	Monitor Progress	Real-time monitoring
OP_04	Analyze Results	Results analysis
OP_06	Troubleshoot	Debugging issues
SYS_10	IMSO	Intelligent optimization
SYS_12	Extractors	Physics extraction library
SYS_14	Neural	Neural network acceleration

Essential Commands

# Activate environment
conda activate atomizer

# Run optimization
python run_optimization.py --start --trials 50

# Resume interrupted run
python run_optimization.py --start --resume

# Start dashboard
python launch_dashboard.py

# Neural turbo mode
python run_nn_optimization.py --turbo --nn-trials 5000

Key Extractors

ID	Physics	Function
E1	Displacement	`extract_displacement()`
E2	Frequency	`extract_frequency()`
E3	Stress	`extract_solid_stress()`
E4	Mass (BDF)	`extract_mass_from_bdf()`
E5	Mass (CAD)	`extract_mass_from_expression()`
E22	Zernike OPD	`extract_zernike_opd()`

Full catalog: SYS_12_EXTRACTOR_LIBRARY.md

LLM Resources

For Claude/AI integration:

Resource	Purpose
../CLAUDE.md	System instructions
../.claude/ATOMIZER_CONTEXT.md	Session context
../.claude/skills/	Skill modules

Last Updated: 2026-01-20 Maintained By: Antoine / Atomaste

7.2 KiB Raw Blame History