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Atomizer/docs/00_INDEX.md
Anto01 a3f18dc377 chore: Project cleanup and Canvas UX improvements (Phase 7-9) 
## Cleanup (v0.5.0)
- Delete 102+ orphaned MCP session temp files
- Remove build artifacts (htmlcov, dist, __pycache__)
- Archive superseded plan docs (RALPH_LOOP V2/V3, CANVAS V3, etc.)
- Move debug/analysis scripts from tests/ to tools/analysis/
- Archive redundant NX journals to archive/nx_journals/
- Archive monolithic PROTOCOL.md to docs/archive/
- Update .gitignore with missing patterns
- Clean old study files (optimization_log_old.txt, run_optimization_old.py)

## Canvas UX (Phases 7-9)
- Phase 7: Resizable panels with localStorage persistence
  - Left sidebar: 200-400px, Right panel: 280-600px
  - New useResizablePanel hook and ResizeHandle component
- Phase 8: Enable all palette items
  - All 8 node types now draggable
  - Singleton logic for model/solver/algorithm/surrogate
- Phase 9: Solver configuration
  - Add SolverEngine type (nxnastran, mscnastran, python, etc.)
  - Add NastranSolutionType (SOL101-SOL200)
  - Engine/solution dropdowns in config panel
  - Python script path support

## Documentation
- Update CHANGELOG.md with recent versions
- Update docs/00_INDEX.md
- Create examples/README.md
- Add docs/plans/CANVAS_UX_IMPROVEMENTS.md
2026-01-24 15:17:34 -05:00

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# Atomizer Documentation Index
**Last Updated**: 2026-01-24
**Project Version**: 0.5.0 (AtomizerSpec v2.0 - Canvas Builder)
---
## Quick Start
New to Atomizer? Start here:
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
---
## Documentation Structure
### Core Documentation
| Document | Purpose |
|----------|---------|
| **[GETTING_STARTED.md](GETTING_STARTED.md)** | Setup, first study, dashboard basics |
| **[ARCHITECTURE.md](ARCHITECTURE.md)** | System architecture, hooks, data flow |
| **[protocols/README.md](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](guides/CANVAS.md)** | Visual study builder (AtomizerSpec v2.0) |
| **[DASHBOARD.md](guides/DASHBOARD.md)** | Dashboard overview and features |
| **[NEURAL_FEATURES_COMPLETE.md](guides/NEURAL_FEATURES_COMPLETE.md)** | Neural acceleration guide |
| **[NEURAL_WORKFLOW_TUTORIAL.md](guides/NEURAL_WORKFLOW_TUTORIAL.md)** | Data → Training → Optimization |
| **[hybrid_mode.md](guides/hybrid_mode.md)** | Hybrid FEA/NN optimization |
| **[TRAINING_DATA_EXPORT_GUIDE.md](guides/TRAINING_DATA_EXPORT_GUIDE.md)** | Exporting data for neural training |
### API Reference
Located in `api/`:
| 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 |
### Physics Documentation
Located in `physics/`:
| 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 |
### Development
Located in `development/`:
| 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 |
### Diagrams
Located in `diagrams/`:
| Document | Purpose |
|----------|---------|
| **[architecture_overview.md](diagrams/architecture_overview.md)** | System architecture diagrams |
| **[protocol_workflows.md](diagrams/protocol_workflows.md)** | Protocol execution flows |
---
## Documentation by Task
### 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
### 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
### 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
### 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
### 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 |
| **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
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](protocols/system/SYS_12_EXTRACTOR_LIBRARY.md)
---
## Archive
Historical documents are preserved in `archive/`:
- `archive/historical/` - Legacy documents, old protocols
- `archive/marketing/` - Briefings, presentations
- `archive/session_summaries/` - Past development sessions
- `archive/plans/` - Superseded plan documents (RALPH_LOOP V2/V3, CANVAS V3, etc.)
- `archive/PROTOCOL_V1_MONOLITHIC.md` - Original monolithic protocol (Nov 2025)
---
## 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**: 2026-01-24
**Maintained By**: Antoine / Atomaste
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