# Atomizer Examples

This directory contains example configurations and scripts demonstrating Atomizer capabilities.

## Configuration Examples

| File | Description |
|------|-------------|
| `optimization_config_neural.json` | Neural surrogate-accelerated optimization |
| `optimization_config_protocol10.json` | IMSO (Intelligent Multi-Stage Optimization) example |
| `optimization_config_protocol12.json` | Custom extractor with Zernike analysis |
| `optimization_config_zernike_mirror.json` | Telescope mirror WFE optimization |

## Scripts

| File | Description |
|------|-------------|
| `llm_mode_simple_example.py` | Basic LLM-driven optimization setup |
| `interactive_research_session.py` | Interactive research mode with visualization |

## Models

The `Models/` directory contains sample FEA models for testing:
- Bracket geometries
- Beam structures
- Mirror assemblies

## Zernike Reference

The `Zernike_old_reference/` directory contains legacy Zernike extraction code for reference purposes.

## Usage

1. Copy a configuration file to your study directory
2. Modify paths and parameters for your model
3. Run optimization with:

```bash
cd studies/your_study
python run_optimization.py
```

Or use the Canvas Builder in the dashboard (http://localhost:3003).

## See Also

- [Study Creation Guide](../docs/protocols/operations/OP_01_CREATE_STUDY.md)
- [Extractor Library](../docs/protocols/system/SYS_12_EXTRACTOR_LIBRARY.md)
- [Canvas Builder](../docs/guides/CANVAS.md)