Atomizer

Advanced LLM-native optimization platform for Siemens NX Simcenter

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

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Documentation

📚 Complete Documentation Index - Start here for all documentation

Quick Links

• Visual Architecture Diagrams - 🆕 Comprehensive Mermaid diagrams showing system architecture and workflows
• Protocol Specifications - All active protocols (10, 11, 13) consolidated
• Development Guide - Development workflow, testing, contributing
• Dashboard Guide - 🆕 Comprehensive React dashboard with multi-objective visualization
• NX Multi-Solution Protocol - 🆕 Critical fix for multi-solution workflows
• Getting Started - Create your first optimization study

By Topic

• Protocols: PROTOCOLS.md - Protocol 10 (Intelligent Optimization), 11 (Multi-Objective), 13 (Dashboard)
• Architecture: HOOK_ARCHITECTURE.md, NX_SESSION_MANAGEMENT.md
• Dashboard: DASHBOARD_MASTER_PLAN.md, DASHBOARD_REACT_IMPLEMENTATION.md
• Advanced: HYBRID_MODE_GUIDE.md - LLM-assisted workflows

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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:

   git clone https://github.com/yourusername/Atomizer.git
   cd Atomizer
   

2. Create Python environment:

   conda create -n atomizer python=3.10
   conda activate atomizer
   

3. Install dependencies:

   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!

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 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:

{
  "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:

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

Features

• Intelligent Multi-Objective Optimization: NSGA-II algorithm for Pareto-optimal solutions
• Advanced Dashboard: React-based real-time monitoring with parallel coordinates visualization
• NX Integration: Seamless journal-based control of Siemens NX Simcenter
• Multi-Solution Support: Automatic handling of combined analysis types (static + modal, thermal + structural)
• 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
• Pareto Front Analysis: Automatic extraction and visualization of non-dominated solutions
• Parallel Coordinates Plot: Research-grade multi-dimensional visualization with interactive selection

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 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/:

# 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:

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 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

• Phase 1: Core optimization engine & Plugin system ✅

  • NX journal integration
  • Web dashboard
  • Lifecycle hooks (pre-solve, post-solve, post-extraction)

• 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

• Phase 2.6: Intelligent Step Classification ✅

  • Distinguishes engineering features from inline calculations
  • Identifies post-processing hooks vs FEA operations
  • Foundation for smart code generation

• 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

• 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

• 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

• 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!

• 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 - Current status, todos, and active development
• DEVELOPMENT_ROADMAP.md - Strategic vision and long-term plan
• CHANGELOG.md - Version history and changes

License

Proprietary - Atomaste © 2025

Support

• Documentation: docs/
• Studies: studies/ - Optimization study templates and examples
• Development Roadmap: DEVELOPMENT_ROADMAP.md
• Email: antoine@atomaste.com

Resources

NXOpen References

• Official API Docs: Siemens NXOpen Documentation
• NXOpenTSE: The Scripting Engineer's Guide
• Our Guide: NXOpen Resources

Optimization

• Optuna Documentation: optuna.readthedocs.io
• pyNastran: github.com/SteveDoyle2/pyNastran

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