Atomizer/.claude/skills/01_CHEATSHEET.md

skill_id, version, last_updated, type, code_dependencies, requires_skills

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

{
  "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

# 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!

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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