---
skill_id: SKILL_001
version: 2.3
last_updated: 2025-12-29
type: reference
code_dependencies:
  - optimization_engine/extractors/__init__.py
  - optimization_engine/core/method_selector.py
  - optimization_engine/utils/trial_manager.py
  - optimization_engine/utils/dashboard_db.py
requires_skills:
  - SKILL_000
---

# Atomizer Quick Reference Cheatsheet

**Version**: 2.3
**Updated**: 2025-12-29
**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 | Place in `studies/{geometry_type}/`, generate config + runner + **README.md** |
| 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 |
| **Free disk space** | **OP_07** | `archive_study.bat cleanup <study> --execute` |
| Add custom physics extractor | EXT_01 | Create in `optimization_engine/extractors/` |
| Add lifecycle hook | EXT_02 | Create in `optimization_engine/plugins/` |
| Generate physics insight | SYS_16 | `python -m optimization_engine.insights generate <study>` |
| **Manage knowledge/playbook** | **SYS_17** | `from optimization_engine.context import AtomizerPlaybook` |

---

## 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 (standard) | 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 |
| Zernike Analytic | E20 | `extract_zernike_analytic(op2_file, focal_length=5000.0)` |
| **Zernike OPD** | E22 | `extract_zernike_opd(op2_file)` ← **Most rigorous, RECOMMENDED** |

> **Mass extraction tip**: Always use E11 (geometry .prt) over E4 (BDF) for accuracy.
> pyNastran under-reports mass ~7% on hex-dominant meshes with tet/pyramid fills.

**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 |
| **L-BFGS** | **Polish phase (after surrogate)** | **P14** |

### L-BFGS Gradient Optimization (NEW)

Exploits surrogate differentiability for **100-1000x faster** local refinement:

```python
from optimization_engine.core.gradient_optimizer import GradientOptimizer, run_lbfgs_polish

# Quick usage - polish from top FEA candidates
results = run_lbfgs_polish(study_dir, n_starts=20, n_iterations=100)

# Or with more control
optimizer = GradientOptimizer(surrogate, objective_weights=[5.0, 5.0, 1.0])
result = optimizer.optimize(starting_points=top_candidates, method='lbfgs')
```

**CLI usage**:
```bash
python -m optimization_engine.core.gradient_optimizer studies/my_study --n-starts 20

# Or per-study script (if available)
python run_lbfgs_polish.py --n-starts 20 --grid-then-grad
```

**When to use**: After training surrogate, before final FEA validation

---

## 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 --start

# Run with specific trial count
python run_optimization.py --start --trials 50

# Resume interrupted optimization
python run_optimization.py --start --resume

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

# View results in Optuna dashboard
optuna-dashboard sqlite:///3_results/study.db

# Check study status
python -c "import optuna; s=optuna.load_study('my_study', 'sqlite:///3_results/study.db'); print(f'Trials: {len(s.trials)}')"
```

### When to Use --resume

| Scenario | Command |
|----------|---------|
| **First run of NEW study** | `python run_optimization.py --start --trials 50` |
| **First run with SEEDING** (e.g., V15 from V14) | `python run_optimization.py --start --trials 50` |
| **Continue INTERRUPTED run** | `python run_optimization.py --start --resume` |
| **Add MORE trials to completed study** | `python run_optimization.py --start --trials 20 --resume` |

**Key insight**: `--resume` is for continuing an existing `study.db`, NOT for seeding from prior studies. Seeding happens automatically on first run when `source_studies` is configured.

---

## Disk Space Management (OP_07)

FEA studies consume massive disk space. After completion, clean up regenerable files:

### Quick Commands

```bash
# Analyze disk usage
archive_study.bat analyze studies\M1_Mirror

# Cleanup completed study (dry run first!)
archive_study.bat cleanup studies\M1_Mirror\m1_mirror_V12
archive_study.bat cleanup studies\M1_Mirror\m1_mirror_V12 --execute

# Archive to dalidou server
archive_study.bat archive studies\M1_Mirror\m1_mirror_V12 --execute

# List remote archives
archive_study.bat list
```

### What Gets Deleted vs Kept

| KEEP | DELETE |
|------|--------|
| `.op2` (Nastran results) | `.prt, .fem, .sim` (copies of master) |
| `.json` (params/metadata) | `.dat` (solver input) |
| `1_setup/` (master files) | `.f04, .f06, .log` (solver logs) |
| `3_results/` (database) | `.afm, .diag, .bak` (temp files) |

### Typical Savings

| Stage | M1_Mirror Example |
|-------|-------------------|
| Full | 194 GB |
| After cleanup | 114 GB (41% saved) |
| Archived to server | 5 GB local (97% saved) |

**Full details**: `docs/protocols/operations/OP_07_DISK_OPTIMIZATION.md`

---

## LAC (Learning Atomizer Core) Commands

```bash
# View LAC statistics
python knowledge_base/lac.py stats

# Generate full LAC report
python knowledge_base/lac.py report

# View pending protocol updates
python knowledge_base/lac.py pending

# Query insights for a context
python knowledge_base/lac.py insights "bracket mass optimization"
```

### Python API Quick Reference
```python
from knowledge_base.lac import get_lac
lac = get_lac()

# Query prior knowledge
insights = lac.get_relevant_insights("bracket mass")
similar = lac.query_similar_optimizations("bracket", ["mass"])
rec = lac.get_best_method_for("bracket", n_objectives=1)

# Record learning
lac.record_insight("success_pattern", "context", "insight", confidence=0.8)

# Record optimization outcome
lac.record_optimization_outcome(study_name="...", geometry_type="...", ...)
```

---

## 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 | Extractor Library | Physics extraction catalog |
| 13 | Dashboard | Real-time tracking and visualization |
| 14 | Neural | Surrogate model acceleration |
| 15 | Method Selector | Recommends optimization strategy |
| 16 | Study Insights | Physics visualizations (Zernike, stress, modal) |
| 17 | Context Engineering | ACE framework - self-improving knowledge system |

---

## Study Insights Quick Reference (SYS_16)

Generate physics-focused visualizations from FEA results.

### Available Insight Types
| Type | Purpose | Data Required |
|------|---------|---------------|
| `zernike_dashboard` | **RECOMMENDED: Unified WFE dashboard** | OP2 with displacements |
| `zernike_wfe` | WFE with Standard/OPD toggle | OP2 with displacements |
| `zernike_opd_comparison` | Compare Standard vs OPD methods | OP2 with displacements |
| `stress_field` | Von Mises stress contours | OP2 with stresses |
| `modal` | Mode shapes + frequencies | OP2 with eigenvectors |
| `thermal` | Temperature distribution | OP2 with temperatures |
| `design_space` | Parameter-objective landscape | study.db with 5+ trials |

### Zernike Method Comparison
| Method | Use | RMS Difference |
|--------|-----|----------------|
| **Standard (Z-only)** | Quick analysis | Baseline |
| **OPD (X,Y,Z)** ← RECOMMENDED | Any surface with lateral displacement | **+8-11% higher** (more accurate) |

### Commands
```bash
# List available insights for a study
python -m optimization_engine.insights list

# Generate all insights
python -m optimization_engine.insights generate studies/my_study

# Generate specific insight
python -m optimization_engine.insights generate studies/my_study --type zernike_wfe
```

### Python API
```python
from optimization_engine.insights import get_insight, list_available_insights
from pathlib import Path

study_path = Path("studies/my_study")

# Check what's available
available = list_available_insights(study_path)

# Generate Zernike WFE insight
insight = get_insight('zernike_wfe', study_path)
result = insight.generate()
print(result.html_path)  # Path to generated HTML
print(result.summary)    # Key metrics dict
```

**Output**: HTMLs saved to `{study}/3_insights/`

---

## CRITICAL: NXSolver Initialization Pattern

**NEVER pass full config dict to NXSolver. Use named parameters:**

```python
# WRONG - causes TypeError
self.nx_solver = NXSolver(self.config)  # ❌

# CORRECT - use FEARunner pattern from V14/V15
nx_settings = self.config.get('nx_settings', {})
nx_install_dir = nx_settings.get('nx_install_path', 'C:\\Program Files\\Siemens\\NX2506')

# Extract version from path
import re
version_match = re.search(r'NX(\d+)', nx_install_dir)
nastran_version = version_match.group(1) if version_match else "2506"

self.nx_solver = NXSolver(
    master_model_dir=str(self.master_model_dir),  # Path to 1_setup/model
    nx_install_dir=nx_install_dir,
    nastran_version=nastran_version,
    timeout=nx_settings.get('simulation_timeout_s', 600),
    use_iteration_folders=True,
    study_name="my_study_name"
)
```

### FEARunner Class Pattern

Always wrap NXSolver in a `FEARunner` class for:
- Lazy initialization (setup on first use)
- Clean separation of NX setup from optimization logic
- Consistent error handling

```python
class FEARunner:
    def __init__(self, config: Dict):
        self.config = config
        self.nx_solver = None
        self.master_model_dir = SETUP_DIR / "model"

    def setup(self):
        # Initialize NX and solver here
        ...

    def run_fea(self, params: Dict, trial_num: int) -> Optional[Dict]:
        if self.nx_solver is None:
            self.setup()
        # Run simulation...
```

**Reference implementations**:
- `studies/m1_mirror_adaptive_V14/run_optimization.py`
- `studies/m1_mirror_adaptive_V15/run_optimization.py`

---

## Trial Management Utilities

### TrialManager - Unified Trial Folder + DB Management

```python
from optimization_engine.utils.trial_manager import TrialManager

tm = TrialManager(study_dir)

# Start new trial (creates folder, saves params)
trial = tm.new_trial(
    params={'rib_thickness': 10.5, 'mirror_face_thickness': 17.0},
    source="turbo",
    metadata={'turbo_batch': 1, 'predicted_ws': 42.0}
)
# Returns: {'trial_id': 47, 'trial_number': 47, 'folder_path': Path(...)}

# After FEA completes
tm.complete_trial(
    trial_number=trial['trial_number'],
    objectives={'wfe_40_20': 5.63, 'mass_kg': 118.67},
    weighted_sum=42.5,
    is_feasible=True
)

# Mark failed trial
tm.fail_trial(trial_number=47, error="NX solver timeout")
```

### DashboardDB - Optuna-Compatible Database

```python
from optimization_engine.utils.dashboard_db import DashboardDB, convert_custom_to_optuna

# Create new dashboard-compatible database
db = DashboardDB(db_path, study_name="my_study")

# Log a trial
trial_id = db.log_trial(
    params={'rib_thickness': 10.5},
    objectives={'wfe_40_20': 5.63, 'mass_kg': 118.67},
    weighted_sum=42.5,
    is_feasible=True,
    state="COMPLETE"
)

# Mark best trial
db.mark_best(trial_id)

# Get summary
summary = db.get_summary()

# Convert existing custom database to Optuna format
convert_custom_to_optuna(db_path, study_name)
```

### Trial Naming Convention

```
2_iterations/
├── trial_0001/    # Zero-padded, monotonically increasing
├── trial_0002/    # NEVER reset, NEVER overwritten
└── trial_0003/
```

**Key principles**:
- Trial numbers **NEVER reset** across study lifetime
- Surrogate predictions (5K per batch) are NOT logged as trials
- Only FEA-validated results become trials

---

## Context Engineering Quick Reference (SYS_17)

The ACE (Agentic Context Engineering) framework enables self-improving optimization through structured knowledge capture.

### Core Components

| Component | Purpose | Key Function |
|-----------|---------|--------------|
| **AtomizerPlaybook** | Structured knowledge store | `playbook.add_insight()`, `playbook.get_context_for_task()` |
| **AtomizerReflector** | Extracts insights from outcomes | `reflector.analyze_outcome()` |
| **AtomizerSessionState** | Context isolation (exposed/isolated) | `session.get_llm_context()` |
| **FeedbackLoop** | Automated learning | `feedback.process_trial_result()` |
| **CompactionManager** | Long-session handling | `compactor.maybe_compact()` |
| **CacheMonitor** | KV-cache optimization | `optimizer.track_completion()` |

### Python API Quick Reference

```python
from optimization_engine.context import (
    AtomizerPlaybook, AtomizerReflector, get_session,
    InsightCategory, TaskType, FeedbackLoop
)

# Load playbook
playbook = AtomizerPlaybook.load(Path("knowledge_base/playbook.json"))

# Add an insight
playbook.add_insight(
    category=InsightCategory.STRATEGY,  # str, mis, tool, cal, dom, wf
    content="CMA-ES converges faster on smooth mirror surfaces",
    tags=["mirror", "sampler", "convergence"]
)
playbook.save(Path("knowledge_base/playbook.json"))

# Get context for LLM
context = playbook.get_context_for_task(
    task_type="optimization",
    max_items=15,
    min_confidence=0.5
)

# Record feedback
playbook.record_outcome(item_id="str_001", helpful=True)

# Session state
session = get_session()
session.exposed.task_type = TaskType.RUN_OPTIMIZATION
session.add_action("Started optimization run")
llm_context = session.get_llm_context()

# Feedback loop (automated learning)
feedback = FeedbackLoop(playbook_path)
feedback.process_trial_result(
    trial_number=42,
    params={'thickness': 10.5},
    objectives={'mass': 5.2},
    is_feasible=True
)
```

### Insight Categories

| Category | Code | Use For |
|----------|------|---------|
| Strategy | `str` | Optimization approaches that work |
| Mistake | `mis` | Common errors to avoid |
| Tool | `tool` | Tool usage patterns |
| Calculation | `cal` | Formulas and calculations |
| Domain | `dom` | FEA/NX domain knowledge |
| Workflow | `wf` | Process patterns |

### Playbook Item Format

```
[str_001] helpful=5 harmful=0 :: CMA-ES converges faster on smooth surfaces
```

- `net_score = helpful - harmful`
- `confidence = helpful / (helpful + harmful)`
- Items with `net_score < -3` are pruned

### REST API Endpoints

| Endpoint | Method | Purpose |
|----------|--------|---------|
| `/api/context/playbook` | GET | Playbook summary stats |
| `/api/context/playbook/items` | GET | List items with filters |
| `/api/context/playbook/feedback` | POST | Record helpful/harmful |
| `/api/context/playbook/insights` | POST | Add new insight |
| `/api/context/playbook/prune` | POST | Remove harmful items |
| `/api/context/session` | GET | Current session state |
| `/api/context/learning/report` | GET | Comprehensive learning report |

### Dashboard URL

| Service | URL | Purpose |
|---------|-----|---------|
| Context API | `http://localhost:5000/api/context` | Playbook management |

**Full documentation**: `docs/protocols/system/SYS_17_CONTEXT_ENGINEERING.md`