feat: Add MLP surrogate with Turbo Mode for 100x faster optimization

Neural Acceleration (MLP Surrogate): - Add run_nn_optimization.py with hybrid FEA/NN workflow - MLP architecture: 4-layer (64->128->128->64) with BatchNorm/Dropout - Three workflow modes: - --all: Sequential export->train->optimize->validate - --hybrid-loop: Iterative Train->NN->Validate->Retrain cycle - --turbo: Aggressive single-best validation (RECOMMENDED) - Turbo mode: 5000 NN trials + 50 FEA validations in ~12 minutes - Separate nn_study.db to avoid overloading dashboard Performance Results (bracket_pareto_3obj study): - NN prediction errors: mass 1-5%, stress 1-4%, stiffness 5-15% - Found minimum mass designs at boundary (angle~30deg, thick~30mm) - 100x speedup vs pure FEA exploration Protocol Operating System: - Add .claude/skills/ with Bootstrap, Cheatsheet, Context Loader - Add docs/protocols/ with operations (OP_01-06) and system (SYS_10-14) - Update SYS_14_NEURAL_ACCELERATION.md with MLP Turbo Mode docs NX Automation: - Add optimization_engine/hooks/ for NX CAD/CAE automation - Add study_wizard.py for guided study creation - Fix FEM mesh update: load idealized part before UpdateFemodel() New Study: - bracket_pareto_3obj: 3-objective Pareto (mass, stress, stiffness) - 167 FEA trials + 5000 NN trials completed - Demonstrates full hybrid workflow 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-06 20:01:59 -05:00
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+# 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 routing
+- `01_CHEATSHEET.md` - "I want X → Use Y" lookup
+- `02_CONTEXT_LOADER.md` - What to load per task
+- `PROTOCOL_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:
+
+```markdown
+# {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](operations/OP_01_CREATE_STUDY.md) |
+| Run optimization | [OP_02](operations/OP_02_RUN_OPTIMIZATION.md) |
+| Check progress | [OP_03](operations/OP_03_MONITOR_PROGRESS.md) |
+| Analyze results | [OP_04](operations/OP_04_ANALYZE_RESULTS.md) |
+| Export neural data | [OP_05](operations/OP_05_EXPORT_TRAINING_DATA.md) |
+| Fix errors | [OP_06](operations/OP_06_TROUBLESHOOT.md) |
+| Add extractor | [EXT_01](extensions/EXT_01_CREATE_EXTRACTOR.md) |
+
+### By Protocol Number
+
+| # | Name | Layer |
+|---|------|-------|
+| 10 | IMSO | [System](system/SYS_10_IMSO.md) |
+| 11 | Multi-Objective | [System](system/SYS_11_MULTI_OBJECTIVE.md) |
+| 12 | Extractors | [System](system/SYS_12_EXTRACTOR_LIBRARY.md) |
+| 13 | Dashboard | [System](system/SYS_13_DASHBOARD_TRACKING.md) |
+| 14 | Neural | [System](system/SYS_14_NEURAL_ACCELERATION.md) |
+
+---
+
+## 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 |