96b196de58
This commit introduces the GNN-based surrogate for Zernike mirror optimization and the M1 mirror study progression from V12 (GNN validation) to V13 (pure NSGA-II). ## GNN Surrogate Module (optimization_engine/gnn/) New module for Graph Neural Network surrogate prediction of mirror deformations: - `polar_graph.py`: PolarMirrorGraph - fixed 3000-node polar grid structure - `zernike_gnn.py`: ZernikeGNN with design-conditioned message passing - `differentiable_zernike.py`: GPU-accelerated Zernike fitting and objectives - `train_zernike_gnn.py`: ZernikeGNNTrainer with multi-task loss - `gnn_optimizer.py`: ZernikeGNNOptimizer for turbo mode (~900k trials/hour) - `extract_displacement_field.py`: OP2 to HDF5 field extraction - `backfill_field_data.py`: Extract fields from existing FEA trials Key innovation: Design-conditioned convolutions that modulate message passing based on structural design parameters, enabling accurate field prediction. ## M1 Mirror Studies ### V12: GNN Field Prediction + FEA Validation - Zernike GNN trained on V10/V11 FEA data (238 samples) - Turbo mode: 5000 GNN predictions → top candidates → FEA validation - Calibration workflow for GNN-to-FEA error correction - Scripts: run_gnn_turbo.py, validate_gnn_best.py, compute_full_calibration.py ### V13: Pure NSGA-II FEA (Ground Truth) - Seeds 217 FEA trials from V11+V12 - Pure multi-objective NSGA-II without any surrogate - Establishes ground-truth Pareto front for GNN accuracy evaluation - Narrowed blank_backface_angle range to [4.0, 5.0] ## Documentation Updates - SYS_14: Added Zernike GNN section with architecture diagrams - CLAUDE.md: Added GNN module reference and quick start - V13 README: Study documentation with seeding strategy 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Atomizer Protocol Operating System (POS)
Version: 1.0 Last Updated: 2025-12-05
Overview
This directory contains the Protocol Operating System (POS) - a 4-layer documentation architecture optimized for LLM consumption.
Directory Structure
protocols/
├── README.md # This file
├── operations/ # Layer 2: How-to guides
│ ├── 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
├── system/ # Layer 3: Core specifications
│ ├── SYS_10_IMSO.md
│ ├── SYS_11_MULTI_OBJECTIVE.md
│ ├── SYS_12_EXTRACTOR_LIBRARY.md
│ ├── SYS_13_DASHBOARD_TRACKING.md
│ └── SYS_14_NEURAL_ACCELERATION.md
└── extensions/ # Layer 4: Extensibility guides
├── EXT_01_CREATE_EXTRACTOR.md
├── EXT_02_CREATE_HOOK.md
├── EXT_03_CREATE_PROTOCOL.md
├── EXT_04_CREATE_SKILL.md
└── templates/
Layer Descriptions
Layer 1: Bootstrap (.claude/skills/)
Entry point for LLM sessions. Contains:
00_BOOTSTRAP.md- Quick orientation and task routing01_CHEATSHEET.md- "I want X → Use Y" lookup02_CONTEXT_LOADER.md- What to load per taskPROTOCOL_EXECUTION.md- Meta-protocol for execution
Layer 2: Operations (operations/)
Day-to-day how-to guides:
- OP_01: Create optimization study
- OP_02: Run optimization
- OP_03: Monitor progress
- OP_04: Analyze results
- OP_05: Export training data
- OP_06: Troubleshoot issues
Layer 3: System (system/)
Core technical specifications:
- SYS_10: Intelligent Multi-Strategy Optimization (IMSO)
- SYS_11: Multi-Objective Support (MANDATORY)
- SYS_12: Extractor Library
- SYS_13: Real-Time Dashboard Tracking
- SYS_14: Neural Network Acceleration
Layer 4: Extensions (extensions/)
Guides for extending Atomizer:
- EXT_01: Create new extractor
- EXT_02: Create lifecycle hook
- EXT_03: Create new protocol
- EXT_04: Create new skill
Protocol Template
All protocols follow this structure:
# {LAYER}_{NUMBER}_{NAME}.md
<!--
PROTOCOL: {Full Name}
LAYER: {Operations|System|Extensions}
VERSION: {Major.Minor}
STATUS: {Active|Draft|Deprecated}
LAST_UPDATED: {YYYY-MM-DD}
PRIVILEGE: {user|power_user|admin}
LOAD_WITH: [{dependencies}]
-->
## Overview
{1-3 sentence description}
## When to Use
| Trigger | Action |
|---------|--------|
## Quick Reference
{Tables, key parameters}
## Detailed Specification
{Full content}
## Examples
{Working examples}
## Troubleshooting
| Symptom | Cause | Solution |
## Cross-References
- Depends On: []
- Used By: []
Quick Navigation
By Task
| I want to... | Protocol |
|---|---|
| Create a study | OP_01 |
| Run optimization | OP_02 |
| Check progress | OP_03 |
| Analyze results | OP_04 |
| Export neural data | OP_05 |
| Fix errors | OP_06 |
| Add extractor | EXT_01 |
By Protocol Number
| # | Name | Layer |
|---|---|---|
| 10 | IMSO | System |
| 11 | Multi-Objective | System |
| 12 | Extractors | System |
| 13 | Dashboard | System |
| 14 | Neural | System |
Privilege Levels
| Level | Operations | System | Extensions |
|---|---|---|---|
| user | All OP_* | Read SYS_* | None |
| power_user | All OP_* | Read SYS_* | EXT_01, EXT_02 |
| admin | All | All | All |
Version History
| Version | Date | Changes |
|---|---|---|
| 1.0 | 2025-12-05 | Initial Protocol Operating System |