---
skill_id: SKILL_001
version: 2.0
last_updated: 2025-12-07
type: reference
code_dependencies:
  - optimization_engine/extractors/__init__.py
  - optimization_engine/method_selector.py
requires_skills:
  - SKILL_000
---

# Atomizer Quick Reference Cheatsheet

**Version**: 2.0
**Updated**: 2025-12-07
**Purpose**: Rapid lookup for common operations. "I want X → Use Y"

---

## Task → Protocol Quick Lookup

| I want to... | Use Protocol | Key Command/Action |
|--------------|--------------|-------------------|
| Create a new optimization study | OP_01 | Generate `optimization_config.json` + `run_optimization.py` |
| Run an optimization | OP_02 | `conda activate atomizer && python run_optimization.py` |
| Check optimization progress | OP_03 | Query `study.db` or check dashboard at `localhost:3000` |
| See best results | OP_04 | `optuna-dashboard sqlite:///study.db` or dashboard |
| Export neural training data | OP_05 | `python run_optimization.py --export-training` |
| Fix an error | OP_06 | Read error log → follow diagnostic tree |
| Add custom physics extractor | EXT_01 | Create in `optimization_engine/extractors/` |
| Add lifecycle hook | EXT_02 | Create in `optimization_engine/plugins/` |

---

## Extractor Quick Reference

| Physics | Extractor | Function Call |
|---------|-----------|---------------|
| Max displacement | E1 | `extract_displacement(op2_file, subcase=1)` |
| Natural frequency | E2 | `extract_frequency(op2_file, subcase=1, mode_number=1)` |
| Von Mises stress | E3 | `extract_solid_stress(op2_file, subcase=1, element_type='cquad4')` |
| BDF mass | E4 | `extract_mass_from_bdf(bdf_file)` |
| CAD expression mass | E5 | `extract_mass_from_expression(prt_file, expression_name='p173')` |
| Field data | E6 | `FieldDataExtractor(field_file, result_column, aggregation)` |
| Stiffness (k=F/δ) | E7 | `StiffnessCalculator(...)` |
| Zernike WFE | E8 | `extract_zernike_from_op2(op2_file, bdf_file, subcase)` |
| Zernike relative | E9 | `extract_zernike_relative_rms(op2_file, bdf_file, target, ref)` |
| Zernike builder | E10 | `ZernikeObjectiveBuilder(op2_finder)` |
| Part mass + material | E11 | `extract_part_mass_material(prt_file)` → mass, volume, material |

**Full details**: See `SYS_12_EXTRACTOR_LIBRARY.md` or `modules/extractors-catalog.md`

---

## Protocol Selection Guide

### Single Objective Optimization
```
Question: Do you have ONE goal to minimize/maximize?
├─ Yes, simple problem (smooth, <10 params)
│   └─► Protocol 10 + CMA-ES or GP-BO sampler
│
├─ Yes, complex problem (noisy, many params)
│   └─► Protocol 10 + TPE sampler
│
└─ Not sure about problem characteristics?
    └─► Protocol 10 with adaptive characterization (default)
```

### Multi-Objective Optimization
```
Question: Do you have 2-3 competing goals?
├─ Yes (e.g., minimize mass AND minimize stress)
│   └─► Protocol 11 + NSGA-II sampler
│
└─ Pareto front needed?
    └─► Protocol 11 (returns best_trials, not best_trial)
```

### Neural Network Acceleration
```
Question: Do you need >50 trials OR surrogate model?
├─ Yes
│   └─► Protocol 14 (configure surrogate_settings in config)
│
└─ Training data export needed?
    └─► OP_05_EXPORT_TRAINING_DATA.md
```

---

## Configuration Quick Reference

### optimization_config.json Structure
```json
{
  "study_name": "my_study",
  "design_variables": [
    {"name": "thickness", "min": 1.0, "max": 10.0, "unit": "mm"}
  ],
  "objectives": [
    {"name": "mass", "goal": "minimize", "unit": "kg"}
  ],
  "constraints": [
    {"name": "max_stress", "type": "<=", "threshold": 250, "unit": "MPa"}
  ],
  "optimization_settings": {
    "protocol": "protocol_10_single_objective",
    "sampler": "TPESampler",
    "n_trials": 50
  },
  "simulation": {
    "model_file": "model.prt",
    "sim_file": "model.sim",
    "solver": "nastran"
  }
}
```

### Sampler Quick Selection
| Sampler | Use When | Protocol |
|---------|----------|----------|
| `TPESampler` | Default, robust to noise | P10 |
| `CMAESSampler` | Smooth, unimodal problems | P10 |
| `GPSampler` | Expensive FEA, few trials | P10 |
| `NSGAIISampler` | Multi-objective (2-3 goals) | P11 |
| `RandomSampler` | Characterization phase only | P10 |

---

## Study File Structure

```
studies/{study_name}/
├── 1_setup/
│   ├── model/              # NX files (.prt, .sim, .fem)
│   └── optimization_config.json
├── 2_results/
│   ├── study.db            # Optuna SQLite database
│   ├── optimizer_state.json # Real-time state (P13)
│   └── trial_logs/
├── README.md               # MANDATORY: Engineering blueprint
├── STUDY_REPORT.md         # MANDATORY: Results tracking
└── run_optimization.py     # Entrypoint script
```

---

## Common Commands

```bash
# Activate environment (ALWAYS FIRST)
conda activate atomizer

# Run optimization
python run_optimization.py

# Run with specific trial count
python run_optimization.py --n-trials 100

# Resume interrupted optimization
python run_optimization.py --resume

# Export training data for neural network
python run_optimization.py --export-training

# View results in Optuna dashboard
optuna-dashboard sqlite:///2_results/study.db

# Check study status
python -c "import optuna; s=optuna.load_study('my_study', 'sqlite:///2_results/study.db'); print(f'Trials: {len(s.trials)}')"
```

---

## Error Quick Fixes

| Error | Likely Cause | Quick Fix |
|-------|--------------|-----------|
| "No module named optuna" | Wrong environment | `conda activate atomizer` |
| "NX session timeout" | Model too complex | Increase `timeout` in config |
| "OP2 file not found" | Solve failed | Check NX log for errors |
| "No feasible solutions" | Constraints too tight | Relax constraint thresholds |
| "NSGA-II requires >1 objective" | Wrong protocol | Use P10 for single-objective |
| "Expression not found" | Wrong parameter name | Verify expression names in NX |
| **All trials identical results** | **Missing `*_i.prt`** | **Copy idealized part to study folder!** |

**Full troubleshooting**: See `OP_06_TROUBLESHOOT.md`

---

## CRITICAL: NX FEM Mesh Update

**If all optimization trials produce identical results, the mesh is NOT updating!**

### Required Files for Mesh Updates
```
studies/{study}/1_setup/model/
├── Model.prt           # Geometry
├── Model_fem1_i.prt    # Idealized part ← MUST EXIST!
├── Model_fem1.fem      # FEM
└── Model_sim1.sim      # Simulation
```

### Why It Matters
The `*_i.prt` (idealized part) MUST be:
1. **Present** in the study folder
2. **Loaded** before `UpdateFemodel()` (already implemented in `solve_simulation.py`)

Without it, `UpdateFemodel()` runs but the mesh doesn't change!

---

## Privilege Levels

| Level | Can Create Studies | Can Add Extractors | Can Add Protocols |
|-------|-------------------|-------------------|------------------|
| user | ✓ | ✗ | ✗ |
| power_user | ✓ | ✓ | ✗ |
| admin | ✓ | ✓ | ✓ |

---

## Dashboard URLs

| Service | URL | Purpose |
|---------|-----|---------|
| Atomizer Dashboard | `http://localhost:3000` | Real-time optimization monitoring |
| Optuna Dashboard | `http://localhost:8080` | Trial history, parameter importance |
| API Backend | `http://localhost:5000` | REST API for dashboard |

---

## Protocol Numbers Reference

| # | Name | Purpose |
|---|------|---------|
| 10 | IMSO | Intelligent Multi-Strategy Optimization (adaptive) |
| 11 | Multi-Objective | NSGA-II for Pareto optimization |
| 12 | - | (Reserved) |
| 13 | Dashboard | Real-time tracking and visualization |
| 14 | Neural | Surrogate model acceleration |