Atomizer/README.md

# Atomizer

> Advanced LLM-native optimization platform for Siemens NX Simcenter

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## Overview

Atomizer is an **LLM-native optimization framework** for Siemens NX Simcenter that transforms how engineers interact with optimization workflows. Instead of manual JSON configuration and scripting, Atomizer uses AI as a collaborative engineering assistant.

### Core Philosophy

Atomizer enables engineers to:
- **Describe optimizations in natural language** instead of writing configuration files
- **Generate custom analysis functions on-the-fly** (RSS metrics, weighted objectives, constraints)
- **Get intelligent recommendations** based on optimization results and surrogate models
- **Generate comprehensive reports** with AI-written insights and visualizations
- **Extend the framework autonomously** through LLM-driven code generation

### Key Features

- **LLM-Driven Workflow**: Natural language study creation, configuration, and analysis
- **Advanced Optimization**: Optuna-powered TPE, Gaussian Process surrogates, multi-objective Pareto fronts
- **Dynamic Code Generation**: AI writes custom Python functions and NX journal scripts during optimization
- **Intelligent Decision Support**: Surrogate quality assessment, sensitivity analysis, engineering recommendations
- **Real-Time Monitoring**: Interactive web dashboard with live progress tracking
- **Extensible Architecture**: Plugin system with hooks for pre/post mesh, solve, and extraction phases
- **Self-Improving**: Feature registry that learns from user workflows and expands capabilities

---

📘 **For Developers**: See [DEVELOPMENT_GUIDANCE.md](DEVELOPMENT_GUIDANCE.md) for comprehensive status report, current priorities, and strategic direction.

📘 **Vision & Roadmap**: See [DEVELOPMENT_ROADMAP.md](DEVELOPMENT_ROADMAP.md) for the long-term vision and phase-by-phase implementation plan.

📘 **Development Status**: See [DEVELOPMENT.md](DEVELOPMENT.md) for detailed task tracking and completed work.

## Architecture

```
┌─────────────────────────────────────────────────────────┐
│                 LLM Interface Layer                     │
│  Claude Skill + Natural Language Parser + Workflow Mgr  │
└─────────────────────────────────────────────────────────┘
                          ↕
┌─────────────────────────────────────────────────────────┐
│              Optimization Engine Core                   │
│  Plugin System + Feature Registry + Code Generator      │
└─────────────────────────────────────────────────────────┘
                          ↕
┌─────────────────────────────────────────────────────────┐
│           Execution Layer                               │
│  NX Solver (via Journals) + Optuna + Result Extractors  │
└─────────────────────────────────────────────────────────┘
                          ↕
┌─────────────────────────────────────────────────────────┐
│              Analysis & Reporting                       │
│  Surrogate Quality + Sensitivity + Report Generator     │
└─────────────────────────────────────────────────────────┘
```

## Quick Start

### Prerequisites

- **Siemens NX 2412** with NX Nastran solver
- **Python 3.10+** (recommend Anaconda)
- **Git** for version control

### Installation

1. **Clone the repository**:
   ```bash
   git clone https://github.com/yourusername/Atomizer.git
   cd Atomizer
   ```

2. **Create Python environment**:
   ```bash
   conda create -n atomizer python=3.10
   conda activate atomizer
   ```

3. **Install dependencies**:
   ```bash
   pip install -r requirements.txt
   ```

4. **Configure NX path** (edit if needed):
   - Default NX path: `C:\Program Files\Siemens\NX2412\NXBIN\run_journal.exe`
   - Update in `optimization_engine/nx_solver.py` if different

### Basic Usage

#### Example 1: Natural Language Optimization (LLM Mode - Available Now!)

**New in Phase 3.2**: Describe your optimization in natural language - no JSON config needed!

```bash
python optimization_engine/run_optimization.py \
  --llm "Minimize displacement and mass while keeping stress below 200 MPa. \
        Design variables: beam_half_core_thickness (15-30 mm), \
        beam_face_thickness (15-30 mm). Run 10 trials using TPE." \
  --prt studies/simple_beam_optimization/1_setup/model/Beam.prt \
  --sim studies/simple_beam_optimization/1_setup/model/Beam_sim1.sim \
  --trials 10
```

**What happens automatically:**
- ✅ LLM parses your natural language request
- ✅ Auto-generates result extractors (displacement, stress, mass)
- ✅ Auto-generates inline calculations (safety factor, RSS objectives)
- ✅ Auto-generates post-processing hooks (plotting, reporting)
- ✅ Runs optimization with Optuna
- ✅ Saves results, plots, and best design

**Example**: See [examples/llm_mode_simple_example.py](examples/llm_mode_simple_example.py) for a complete walkthrough.

**Requirements**: Claude Code integration (no API key needed) or provide `--api-key` for Anthropic API.

#### Example 2: Current JSON Configuration

Create `studies/my_study/config.json`:

```json
{
  "sim_file": "studies/bracket_stress_minimization/model/Bracket_sim1.sim",
  "design_variables": [
    {
      "name": "wall_thickness",
      "expression_name": "wall_thickness",
      "min": 3.0,
      "max": 8.0,
      "units": "mm"
    }
  ],
  "objectives": [
    {
      "name": "max_stress",
      "extractor": "stress_extractor",
      "metric": "max_von_mises",
      "direction": "minimize",
      "weight": 1.0,
      "units": "MPa"
    }
  ],
  "optimization_settings": {
    "n_trials": 50,
    "sampler": "TPE",
    "n_startup_trials": 20
  }
}
```

Run optimization:
```bash
python tests/test_journal_optimization.py
# Or use the quick 5-trial test:
python run_5trial_test.py
```

## Features

- **Intelligent Optimization**: Optuna-powered TPE sampler with multi-objective support
- **NX Integration**: Seamless journal-based control of Siemens NX Simcenter
- **Smart Logging**: Detailed per-trial logs + high-level optimization progress tracking
- **Plugin System**: Extensible hooks at pre-solve, post-solve, and post-extraction points
- **Study Management**: Isolated study folders with automatic result organization
- **Substudy System**: NX-like hierarchical studies with shared models and independent configurations
- **Live History Tracking**: Real-time incremental JSON updates for monitoring progress
- **Resume Capability**: Interrupt and resume optimizations without data loss
- **Web Dashboard**: Real-time monitoring and configuration UI
- **Example Study**: Bracket displacement maximization with full substudy workflow

## Current Status

**Development Phase**: Alpha - 80-90% Complete

- ✅ **Phase 1 (Plugin System)**: 100% Complete & Production Ready
- ✅ **Phases 2.5-3.1 (LLM Intelligence)**: 100% Complete - Components built and tested
- ✅ **Phase 3.2 Week 1 (LLM Mode)**: **COMPLETE** - Natural language optimization now available!
- 🎯 **Phase 3.2 Week 2-4 (Robustness)**: **IN PROGRESS** - Validation, safety, learning system
- 🔬 **Phase 3.4 (NXOpen Docs)**: Research & investigation phase

**What's Working**:
- ✅ Complete optimization engine with Optuna + NX Simcenter
- ✅ Substudy system with live history tracking
- ✅ **LLM Mode**: Natural language → Auto-generated code → Optimization → Results
- ✅ LLM components (workflow analyzer, code generators, research agent) - production integrated
- ✅ 50-trial optimization validated with real results
- ✅ End-to-end workflow: `--llm "your request"` → results

**Current Focus**: Adding robustness, safety checks, and learning capabilities to LLM mode.

See [DEVELOPMENT_GUIDANCE.md](DEVELOPMENT_GUIDANCE.md) for comprehensive status and priorities.

## Project Structure

```
Atomizer/
├── optimization_engine/        # Core optimization logic
│   ├── runner.py              # Main optimization runner
│   ├── nx_solver.py           # NX journal execution
│   ├── nx_updater.py          # NX model parameter updates
│   ├── pynastran_research_agent.py  # Phase 3: Auto OP2 code gen ✅
│   ├── hook_generator.py      # Phase 2.9: Auto hook generation ✅
│   ├── result_extractors/     # OP2/F06 parsers
│   │   └── extractors.py      # Stress, displacement extractors
│   └── plugins/               # Plugin system (Phase 1 ✅)
│       ├── hook_manager.py    # Hook registration & execution
│       ├── hooks.py           # HookPoint enum, Hook dataclass
│       ├── pre_solve/         # Pre-solve lifecycle hooks
│       │   ├── detailed_logger.py
│       │   └── optimization_logger.py
│       ├── post_solve/        # Post-solve lifecycle hooks
│       │   └── log_solve_complete.py
│       ├── post_extraction/   # Post-extraction lifecycle hooks
│       │   ├── log_results.py
│       │   └── optimization_logger_results.py
│       └── post_calculation/  # Post-calculation hooks (Phase 2.9 ✅)
│           ├── weighted_objective_test.py
│           ├── safety_factor_hook.py
│           └── min_to_avg_ratio_hook.py
├── dashboard/                  # Web UI
│   ├── api/                   # Flask backend
│   ├── frontend/              # HTML/CSS/JS
│   └── scripts/               # NX expression extraction
├── studies/                    # Optimization studies
│   ├── README.md              # Comprehensive studies guide
│   └── bracket_displacement_maximizing/  # Example study with substudies
│       ├── README.md          # Study documentation
│       ├── SUBSTUDIES_README.md  # Substudy system guide
│       ├── model/             # Shared FEA model files (.prt, .sim, .fem)
│       ├── config/            # Substudy configuration templates
│       ├── substudies/        # Independent substudy results
│       │   ├── coarse_exploration/   # Fast 20-trial coarse search
│       │   │   ├── config.json
│       │   │   ├── optimization_history_incremental.json  # Live updates
│       │   │   └── best_design.json
│       │   └── fine_tuning/          # Refined 50-trial optimization
│       ├── run_substudy.py    # Substudy runner with continuation support
│       └── run_optimization.py  # Standalone optimization runner
├── tests/                      # Unit and integration tests
│   ├── test_hooks_with_bracket.py
│   ├── run_5trial_test.py
│   └── test_journal_optimization.py
├── docs/                       # Documentation
├── atomizer_paths.py          # Intelligent path resolution
├── DEVELOPMENT_ROADMAP.md      # Future vision and phases
└── README.md                  # This file
```

## Example: Bracket Displacement Maximization with Substudies

A complete working example is in `studies/bracket_displacement_maximizing/`:

```bash
# Run standalone optimization (20 trials)
cd studies/bracket_displacement_maximizing
python run_optimization.py

# Or run a substudy (hierarchical organization)
python run_substudy.py coarse_exploration  # 20-trial coarse search
python run_substudy.py fine_tuning         # 50-trial refinement with continuation

# View live progress
cat substudies/coarse_exploration/optimization_history_incremental.json
```

**What it does**:
1. Loads `Bracket_sim1.sim` with parametric geometry
2. Varies `tip_thickness` (15-25mm) and `support_angle` (20-40°)
3. Runs FEA solve for each trial using NX journal mode
4. Extracts displacement and stress from OP2 files
5. Maximizes displacement while maintaining safety factor >= 4.0

**Substudy System**:
- **Shared Models**: All substudies use the same model files
- **Independent Configs**: Each substudy has its own parameter bounds and settings
- **Continuation Support**: Fine-tuning substudy continues from coarse exploration results
- **Live History**: Real-time JSON updates for monitoring progress

**Results** (typical):
- Best thickness: ~4.2mm
- Stress reduction: 15-20% vs. baseline
- Convergence: ~30 trials to plateau

## Dashboard Usage

Start the dashboard:
```bash
python dashboard/start_dashboard.py
```

Features:
- **Create studies** with folder structure (sim/, results/, config.json)
- **Drop .sim/.prt files** into study folders
- **Explore .sim files** to extract expressions via NX
- **Configure optimization** with 5-step wizard:
  1. Simulation files
  2. Design variables
  3. Objectives
  4. Constraints
  5. Optimization settings
- **Monitor progress** with real-time charts
- **View results** with trial history and best parameters

## Vision: LLM-Native Engineering Assistant

Atomizer is evolving into a comprehensive AI-powered engineering platform. See [DEVELOPMENT_ROADMAP.md](DEVELOPMENT_ROADMAP.md) for details on:

- **Phase 1-7 development plan** with timelines and deliverables
- **Example use cases** demonstrating natural language workflows
- **Architecture diagrams** showing plugin system and LLM integration
- **Success metrics** for each phase

### Future Capabilities

```
User: "Add RSS function combining stress and displacement"
→ LLM: Writes Python function, validates, registers as custom objective

User: "Use surrogate to predict these 10 parameter sets"
→ LLM: Checks surrogate R² > 0.9, runs predictions with confidence intervals

User: "Make an optimization report"
→ LLM: Generates HTML with plots, insights, recommendations (30 seconds)

User: "Why did trial #34 perform best?"
→ LLM: "Trial #34 had optimal stress distribution due to thickness 4.2mm
       creating uniform load paths. Fillet radius 3.1mm reduced stress
       concentration by 18%. This combination is Pareto-optimal."
```

## Development Status

### Completed Phases

- [x] **Phase 1**: Core optimization engine & Plugin system ✅
  - NX journal integration
  - Web dashboard
  - Lifecycle hooks (pre-solve, post-solve, post-extraction)

- [x] **Phase 2.5**: Intelligent Codebase-Aware Gap Detection ✅
  - Scans existing capabilities before requesting examples
  - Matches workflow steps to implemented features
  - 80-90% accuracy on complex optimization requests

- [x] **Phase 2.6**: Intelligent Step Classification ✅
  - Distinguishes engineering features from inline calculations
  - Identifies post-processing hooks vs FEA operations
  - Foundation for smart code generation

- [x] **Phase 2.7**: LLM-Powered Workflow Intelligence ✅
  - Replaces static regex with Claude AI analysis
  - Detects ALL intermediate calculation steps
  - Understands engineering context (PCOMP, CBAR, element forces, etc.)
  - 95%+ expected accuracy with full nuance detection

- [x] **Phase 2.8**: Inline Code Generation ✅
  - LLM-generates Python code for simple math operations
  - Handles avg/min/max, normalization, percentage calculations
  - Direct integration with Phase 2.7 LLM output
  - Optional automated code generation for calculations

- [x] **Phase 2.9**: Post-Processing Hook Generation ✅
  - LLM-generates standalone Python middleware scripts
  - Integrated with Phase 1 lifecycle hook system
  - Handles weighted objectives, custom formulas, constraints, comparisons
  - Complete JSON-based I/O for optimization loops
  - Optional automated scripting for post-processing operations

- [x] **Phase 3**: pyNastran Documentation Integration ✅
  - LLM-enhanced OP2 extraction code generation
  - Documentation research via WebFetch
  - 3 core extraction patterns (displacement, stress, force)
  - Knowledge base for learned patterns
  - Successfully tested on real OP2 files
  - Optional automated code generation for result extraction!

- [x] **Phase 3.1**: LLM-Enhanced Automation Pipeline ✅
  - Extractor orchestrator integrates Phase 2.7 + Phase 3.0
  - Optional automatic extractor generation from LLM output
  - Dynamic loading and execution on real OP2 files
  - End-to-end test passed: Request → Code → Execution → Objective
  - LLM-enhanced workflow with user flexibility achieved!

### Next Priorities

- [ ] **Phase 3.2**: Optimization runner integration with orchestrator
- [ ] **Phase 3.5**: NXOpen introspection & pattern curation
- [ ] **Phase 4**: Code generation for complex FEA features
- [ ] **Phase 5**: Analysis & decision support
- [ ] **Phase 6**: Automated reporting

**For Developers**:
- [DEVELOPMENT.md](DEVELOPMENT.md) - Current status, todos, and active development
- [DEVELOPMENT_ROADMAP.md](DEVELOPMENT_ROADMAP.md) - Strategic vision and long-term plan
- [CHANGELOG.md](CHANGELOG.md) - Version history and changes

## License

Proprietary - Atomaste © 2025

## Support

- **Documentation**: [docs/](docs/)
- **Studies**: [studies/](studies/) - Optimization study templates and examples
- **Development Roadmap**: [DEVELOPMENT_ROADMAP.md](DEVELOPMENT_ROADMAP.md)
- **Email**: antoine@atomaste.com

## Resources

### NXOpen References
- **Official API Docs**: [Siemens NXOpen Documentation](https://docs.sw.siemens.com/en-US/doc/209349590/)
- **NXOpenTSE**: [The Scripting Engineer's Guide](https://nxopentsedocumentation.thescriptingengineer.com/)
- **Our Guide**: [NXOpen Resources](docs/NXOPEN_RESOURCES.md)

### Optimization
- **Optuna Documentation**: [optuna.readthedocs.io](https://optuna.readthedocs.io/)
- **pyNastran**: [github.com/SteveDoyle2/pyNastran](https://github.com/SteveDoyle2/pyNastran)

---

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