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Atomizer/docs/00_INDEX.md
Antoine 8d9d55356c docs: Archive stale docs and create Atomizer-HQ agent documentation 
Archive Management:
- Moved RALPH_LOOP, CANVAS, and dashboard implementation plans to archive/review/ for CEO review
- Moved completed restructuring plan and protocol v1 to archive/historical/
- Moved old session summaries to archive/review/

New HQ Documentation (docs/hq/):
- README.md: Overview of Atomizer-HQ multi-agent optimization team
- PROJECT_STRUCTURE.md: Standard KB-integrated project layout with Hydrotech reference
- KB_CONVENTIONS.md: Knowledge Base accumulation principles with generation tracking
- AGENT_WORKFLOWS.md: Project lifecycle phases and agent handoffs (OP_09 integration)
- STUDY_CONVENTIONS.md: Technical study execution standards and atomizer_spec.json format

Index Update:
- Reorganized docs/00_INDEX.md with HQ docs prominent
- Updated structure to reflect new agent-focused organization
- Maintained core documentation access for engineers

No files deleted, only moved to appropriate archive locations.
2026-02-09 02:48:35 +00:00

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# Atomizer Documentation Index
**Last Updated**: February 9, 2026
**Project Version**: 0.5.0 (AtomizerSpec v2.0 + Atomizer-HQ Multi-Agent Team)
---
## Quick Start
### For AI Agents (Atomizer-HQ Team)
**Start here** if you're an AI agent working on client projects:
1. **[HQ Overview](hq/README.md)** — What Atomizer-HQ is and how agents work together
2. **[Project Structure](hq/PROJECT_STRUCTURE.md)** — Standard project organization
3. **[Agent Workflows](hq/AGENT_WORKFLOWS.md)** — Who does what in the project lifecycle
4. **[Knowledge Base Conventions](hq/KB_CONVENTIONS.md)** — How to accumulate and share knowledge
### For Engineers (Core Optimization)
**Start here** if you're using Atomizer for FEA optimization:
1. **[README.md](../README.md)** - Project overview and philosophy
2. **[Getting Started](GETTING_STARTED.md)** - Installation, first study, dashboard
3. **[Protocol System](protocols/README.md)** - How Atomizer is organized
4. **[Example Studies](../studies/)** - Working examples
---
## Atomizer-HQ Agent Documentation
The multi-agent optimization team that runs client FEA projects.
### Essential HQ Docs
| Document | Purpose | Target Agents |
|----------|---------|---------------|
| **[HQ Overview](hq/README.md)** | What Atomizer-HQ is, how to use these docs | All agents |
| **[Project Structure](hq/PROJECT_STRUCTURE.md)** | Standard KB-integrated project layout | Manager, Technical Lead |
| **[KB Conventions](hq/KB_CONVENTIONS.md)** | Knowledge Base accumulation principles | All agents |
| **[Agent Workflows](hq/AGENT_WORKFLOWS.md)** | Project lifecycle and agent handoffs | All agents |
| **[Study Conventions](hq/STUDY_CONVENTIONS.md)** | Technical study execution standards | Technical Lead, Optimizer |
### Agent Roles Quick Reference
| Agent | Role | Primary Phase | Key Responsibilities |
|-------|------|---------------|---------------------|
| 📋 **Secretary** | CEO interface | Intake | Client requirements, project initiation |
| 🏗️ **Manager** | Coordination | Breakdown | Project structure, team coordination |
| 🔧 **Technical Lead** | FEA expert | Introspection | Model setup, optimization planning |
| ⚡ **Optimizer** | Study execution | Study | FEA optimization execution |
| 📊 **Post-Processor** | Results analysis | Results | Performance analysis, insights |
| 📝 **Reporter** | Documentation | Deliverables | Client reports, final packages |
### Living Examples
- **Reference Project**: [projects/hydrotech-beam/](../projects/hydrotech-beam/) — Complete project structure
- **Project Structure**: Demonstrates KB-integrated organization and study flow
- **Knowledge Accumulation**: Shows generation-tracked knowledge evolution
---
## Core Documentation
Essential reference for understanding Atomizer's optimization framework.
### Foundation Documents
| Document | Purpose |
|----------|---------|
| **[GETTING_STARTED.md](GETTING_STARTED.md)** | Setup, first study, dashboard basics |
| **[ARCHITECTURE.md](ARCHITECTURE.md)** | System architecture, hooks, data flow |
| **[QUICK_REF.md](../QUICK_REF.md)** | Active reference guide |
### Protocol System
The Protocol Operating System (POS) provides structured workflows for optimization:
```
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
│ └── OP_09_AGENT_COMMUNICATION.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
Practical guides for using Atomizer features (engineers + Claude Code era).
### Current User Guides
| Guide | Purpose | Status |
|-------|---------|--------|
| **[CANVAS.md](guides/CANVAS.md)** | Visual study builder (AtomizerSpec v2.0) | Active |
| **[DASHBOARD.md](guides/DASHBOARD.md)** | Dashboard overview and features | Active |
| **[NEURAL_FEATURES_COMPLETE.md](guides/NEURAL_FEATURES_COMPLETE.md)** | Neural acceleration guide | Active |
| **[NEURAL_WORKFLOW_TUTORIAL.md](guides/NEURAL_WORKFLOW_TUTORIAL.md)** | Data → Training → Optimization | Active |
| **[hybrid_mode.md](guides/hybrid_mode.md)** | Hybrid FEA/NN optimization | Active |
| **[TRAINING_DATA_EXPORT_GUIDE.md](guides/TRAINING_DATA_EXPORT_GUIDE.md)** | Exporting data for neural training | Active |
---
## API Reference
Technical integration documentation for developers and advanced users.
| Document | Purpose |
|----------|---------|
| **[system_configuration.md](api/system_configuration.md)** | Configuration format reference |
| **[nx_integration.md](api/nx_integration.md)** | NX Open API integration |
| **[GNN_ARCHITECTURE.md](api/GNN_ARCHITECTURE.md)** | Graph Neural Network details |
| **[NXOPEN_RESOURCES.md](api/NXOPEN_RESOURCES.md)** | NX Open documentation resources |
---
## Domain Knowledge
Physics and engineering domain documentation.
### Physics Documentation
| Document | Purpose |
|----------|---------|
| **[ZERNIKE_FUNDAMENTALS.md](physics/ZERNIKE_FUNDAMENTALS.md)** | Zernike polynomial basics |
| **[ZERNIKE_OPD_METHOD.md](physics/ZERNIKE_OPD_METHOD.md)** | OPD method for mirror optimization |
---
## Workflows and Operations
Operational workflows for common tasks.
### Standard Workflows
| Document | Purpose |
|----------|---------|
| **[CREATE.md](WORKFLOWS/CREATE.md)** | Study creation workflow |
| **[RUN.md](WORKFLOWS/RUN.md)** | Optimization execution workflow |
| **[ANALYZE.md](WORKFLOWS/ANALYZE.md)** | Results analysis workflow |
| **[DELIVER.md](WORKFLOWS/DELIVER.md)** | Deliverable creation workflow |
| **[VALIDATE.md](WORKFLOWS/VALIDATE.md)** | Validation and verification workflow |
| **[REPORT.md](WORKFLOWS/REPORT.md)** | Report generation workflow |
---
## Development and Architecture
Technical development documentation.
### Development Guides
| Document | Purpose |
|----------|---------|
| **[DEVELOPMENT_GUIDANCE.md](development/DEVELOPMENT_GUIDANCE.md)** | Development guidelines |
| **[DEVELOPMENT_ROADMAP.md](development/DEVELOPMENT_ROADMAP.md)** | Future plans |
| **[Philosophy.md](development/Philosophy.md)** | Design philosophy |
### Architecture Documentation
| Document | Purpose |
|----------|---------|
| **[architecture_overview.md](diagrams/architecture_overview.md)** | System architecture diagrams |
| **[protocol_workflows.md](diagrams/protocol_workflows.md)** | Protocol execution flows |
---
## Archive
Historical and review documents preserved for context and CEO review.
### Archive Structure
- **[archive/review/](archive/review/)** — Documents flagged for CEO review
- RALPH_LOOP implementation plans
- Dashboard implementation iterations
- Superseded development plans
- Session summaries and old development notes
- **[archive/historical/](archive/historical/)** — Historical but valuable documents
- Original protocol v1 monolithic document
- Foundational design documents
- Completed restructuring plans
### Key Historical Documents
- **[PROTOCOL_V1_MONOLITHIC.md](archive/historical/PROTOCOL_V1_MONOLITHIC.md)** — Original monolithic protocol (Nov 2025)
- Various implementation plans and session summaries in review directories
---
## Documentation by Task
### For Agents: Project Execution
1. **[Agent Workflows](hq/AGENT_WORKFLOWS.md)** — Project lifecycle and handoffs
2. **[Project Structure](hq/PROJECT_STRUCTURE.md)** — How to organize projects
3. **[Study Conventions](hq/STUDY_CONVENTIONS.md)** — Technical execution standards
4. **[KB Conventions](hq/KB_CONVENTIONS.md)** — Knowledge accumulation
### For Engineers: Creating Studies
1. **[GETTING_STARTED.md](GETTING_STARTED.md)** — First study tutorial
2. **[OP_01_CREATE_STUDY.md](protocols/operations/OP_01_CREATE_STUDY.md)** — Detailed creation protocol
3. **[guides/CANVAS.md](guides/CANVAS.md)** — Visual study builder
### For Engineers: Running Optimizations
1. **[OP_02_RUN_OPTIMIZATION.md](protocols/operations/OP_02_RUN_OPTIMIZATION.md)** — Run protocol
2. **[SYS_10_IMSO.md](protocols/system/SYS_10_IMSO.md)** — Intelligent optimization
3. **[SYS_15_METHOD_SELECTOR.md](protocols/system/SYS_15_METHOD_SELECTOR.md)** — Method selection
### For Engineers: Neural Acceleration
1. **[guides/NEURAL_FEATURES_COMPLETE.md](guides/NEURAL_FEATURES_COMPLETE.md)** — Overview
2. **[SYS_14_NEURAL_ACCELERATION.md](protocols/system/SYS_14_NEURAL_ACCELERATION.md)** — Technical spec
3. **[guides/NEURAL_WORKFLOW_TUTORIAL.md](guides/NEURAL_WORKFLOW_TUTORIAL.md)** — Step-by-step
### For Engineers: Analyzing Results
1. **[OP_04_ANALYZE_RESULTS.md](protocols/operations/OP_04_ANALYZE_RESULTS.md)** — Analysis protocol
2. **[SYS_17_STUDY_INSIGHTS.md](protocols/system/SYS_17_STUDY_INSIGHTS.md)** — Physics visualizations
### For Everyone: Troubleshooting
1. **[OP_06_TROUBLESHOOT.md](protocols/operations/OP_06_TROUBLESHOOT.md)** — Troubleshooting guide
2. **[GETTING_STARTED.md#troubleshooting](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 |
| **OP_09** | Agent Communication | HQ communication standards |
| **SYS_10** | IMSO | Intelligent optimization |
| **SYS_12** | Extractors | Physics extraction library |
| **SYS_14** | Neural | Neural network acceleration |
### Essential Commands
```bash
# Activate environment
conda activate atomizer
# Run optimization (engineers)
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
# KB status check (agents)
cad_kb.py status projects/[project]/kb
```
### 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](protocols/system/SYS_12_EXTRACTOR_LIBRARY.md)
---
## LLM Resources
For Claude/AI integration:
| Resource | Purpose |
|----------|---------|
| **[../CLAUDE.md](../CLAUDE.md)** | System instructions |
| **[../.claude/ATOMIZER_CONTEXT.md](../.claude/ATOMIZER_CONTEXT.md)** | Session context |
| **[../.claude/skills/](../.claude/skills/)** | Skill modules |
---
**Last Updated**: February 9, 2026
**Maintained By**: Atomizer-HQ Team (Manager, Technical Lead, Secretary) + Antoine
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