docs: Major documentation overhaul - restructure folders, update tagline, add Getting Started guide
- Restructure docs/ folder (remove numeric prefixes): - 04_USER_GUIDES -> guides/ - 05_API_REFERENCE -> api/ - 06_PHYSICS -> physics/ - 07_DEVELOPMENT -> development/ - 08_ARCHIVE -> archive/ - 09_DIAGRAMS -> diagrams/ - Replace tagline 'Talk, don't click' with 'LLM-driven optimization framework' in 9 files - Create comprehensive docs/GETTING_STARTED.md: - Prerequisites and quick setup - Project structure overview - First study tutorial (Claude or manual) - Dashboard usage guide - Neural acceleration introduction - Rewrite docs/00_INDEX.md with correct paths and modern structure - Archive obsolete files: - 01_PROTOCOLS.md -> archive/historical/01_PROTOCOLS_legacy.md - 03_GETTING_STARTED.md -> archive/historical/ - ATOMIZER_PODCAST_BRIEFING.md -> archive/marketing/ - Update timestamps to 2026-01-20 across all key files - Update .gitignore to exclude docs/generated/ - Version bump: ATOMIZER_CONTEXT v1.8 -> v2.0
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# Atomizer System Architecture
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**Last Updated**: 2025-11-21
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**Version**: 1.0
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**Status**: ✅ Complete
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---
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## Overview
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This document provides comprehensive visual documentation of Atomizer's architecture, showing how components interact to provide intelligent, multi-strategy structural optimization powered by NX Nastran.
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---
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## High-Level System Architecture
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```mermaid
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graph TB
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subgraph User["👤 User Interface"]
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CLI[Command Line Interface]
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Dashboard[React Dashboard<br/>Real-time Monitoring]
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Config[JSON Configuration<br/>optimization_config.json]
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end
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subgraph Core["🧠 Atomizer Core (Python)"]
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direction TB
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subgraph Engine["Optimization Engine"]
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IntelOpt[IntelligentOptimizer<br/>Protocol 10: IMSO]
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Optuna[Optuna Study<br/>Multi-objective Support]
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Strategy[Strategy Portfolio<br/>TPE/NSGA-II/CMA-ES/...]
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Landscape[Landscape Analyzer<br/>Adaptive Characterization]
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end
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subgraph Tracking["Real-time Tracking"]
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RTTracker[RealtimeTracker<br/>Protocol 13]
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TrialLog[trial_log.json]
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OptimizerState[optimizer_state.json]
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Intelligence[intelligence_report.json]
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end
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subgraph Extractors["Extractor Library<br/>Protocol 12"]
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FreqExt[Frequency Extractor]
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MassExt[Mass Extractor]
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StressExt[Stress Extractor]
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CustomExt[Custom Extractors]
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end
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end
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subgraph NX["⚙️ NX Nastran Integration"]
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SessionMgr[NX Session Manager<br/>Session Pooling]
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ModelUpdate[Model Updater<br/>Design Variable Injection]
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Solver[NX Solver<br/>FEA Execution]
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Results[Result Extraction<br/>Extractor Execution]
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end
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subgraph Storage["💾 Storage Layer"]
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StudyDB[(Optuna SQLite DB<br/>study.db)]
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ModelFiles[(CAD Models<br/>.prt, .sim, .fem)]
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Reports[(Reports & Logs<br/>Markdown, JSON)]
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end
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%% User interactions
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CLI --> Config
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Config --> IntelOpt
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Dashboard -.->|WebSocket Updates| RTTracker
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%% Core optimization flow
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IntelOpt --> Landscape
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Landscape --> Strategy
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Strategy --> Optuna
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IntelOpt --> RTTracker
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%% Optimization loop
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Optuna -->|Trial Parameters| ModelUpdate
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ModelUpdate --> SessionMgr
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SessionMgr --> Solver
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Solver --> Results
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Results --> Extractors
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Extractors -->|Objectives| Optuna
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%% Tracking
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RTTracker --> TrialLog
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RTTracker --> OptimizerState
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Landscape --> Intelligence
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%% Storage
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Optuna --> StudyDB
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SessionMgr --> ModelFiles
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IntelOpt --> Reports
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%% Dashboard reads
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Dashboard -.->|REST API| StudyDB
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Dashboard -.->|File Polling| TrialLog
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%% Styling
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classDef userClass fill:#E3F2FD,stroke:#1976D2,stroke-width:2px
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classDef coreClass fill:#E8F5E9,stroke:#388E3C,stroke-width:2px
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classDef nxClass fill:#FFF3E0,stroke:#F57C00,stroke-width:2px
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classDef storageClass fill:#F3E5F5,stroke:#7B1FA2,stroke-width:2px
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class CLI,Dashboard,Config userClass
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class IntelOpt,Optuna,Strategy,Landscape,RTTracker,FreqExt,MassExt,StressExt,CustomExt coreClass
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class SessionMgr,ModelUpdate,Solver,Results nxClass
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class StudyDB,ModelFiles,Reports storageClass
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```
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---
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## Component Details
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### 1. Optimization Engine Core
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```mermaid
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graph LR
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subgraph IntelligentOptimizer["IntelligentOptimizer (Protocol 10)"]
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Init[Initialize Study]
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Config[Load Configuration]
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Phase[Determine Phase]
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Execute[Execute Trials]
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Finalize[Generate Report]
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end
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subgraph Protocols["Protocol Support"]
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P10[Protocol 10: IMSO<br/>Adaptive Strategy]
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P11[Protocol 11: Multi-Obj<br/>NSGA-II Support]
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P13[Protocol 13: Tracking<br/>Real-time Updates]
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end
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Init --> Config
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Config --> Phase
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Phase -->|Single-Objective| P10
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Phase -->|Multi-Objective| P11
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P10 --> Execute
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P11 --> Execute
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Execute --> P13
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P13 --> Finalize
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classDef protocolClass fill:#E1BEE7,stroke:#6A1B9A,stroke-width:2px
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class P10,P11,P13 protocolClass
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```
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### 2. NX Integration Architecture
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```mermaid
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graph TB
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subgraph SessionManagement["NX Session Manager"]
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Pool[Session Pool<br/>Reusable Sessions]
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Create[Create Session]
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Reuse[Reuse Session]
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Cleanup[Cleanup on Error]
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end
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subgraph ModelOperation["Model Operations"]
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Load[Load CAD Model<br/>.prt file]
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Update[Update Parameters<br/>Design Variables]
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Solve[Run FEA Solver<br/>.sim file]
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Extract[Extract Results<br/>Custom Extractors]
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end
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subgraph ErrorHandling["Error Handling"]
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Timeout[Timeout Detection]
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Retry[Retry Logic]
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FallbackCreate[Fallback: New Session]
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end
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Pool --> Reuse
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Pool -->|No Available| Create
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Reuse --> Load
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Create --> Load
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Load --> Update
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Update --> Solve
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Solve --> Extract
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Solve -.->|Error| Timeout
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Timeout --> Retry
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Retry -->|Fail| FallbackCreate
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FallbackCreate --> Cleanup
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classDef sessionClass fill:#FFEBEE,stroke:#C62828,stroke-width:2px
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classDef modelClass fill:#E0F2F1,stroke:#00695C,stroke-width:2px
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class Pool,Create,Reuse,Cleanup sessionClass
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class Load,Update,Solve,Extract modelClass
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```
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### 3. Data Flow Architecture
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```mermaid
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sequenceDiagram
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participant User
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participant IntelOpt as IntelligentOptimizer
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participant Optuna
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participant NX as NX Solver
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participant Extractor
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participant Tracker as RealtimeTracker
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participant Dashboard
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User->>IntelOpt: Start Optimization
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IntelOpt->>Optuna: Create Study
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loop For each trial
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Optuna->>Optuna: Sample Design Variables
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Optuna->>NX: Trial Parameters
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NX->>NX: Update CAD Model
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NX->>NX: Run FEA Solver
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NX->>Extractor: Simulation Results
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Extractor->>Extractor: Calculate Objectives
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Extractor->>Optuna: Objective Values
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Optuna->>Tracker: Trial Complete
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Tracker->>Tracker: Write trial_log.json
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Tracker->>Tracker: Write optimizer_state.json
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Tracker-->>Dashboard: File Update Signal
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Dashboard-->>User: Live UI Update
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end
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Optuna->>IntelOpt: Study Complete
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IntelOpt->>IntelOpt: Generate Report
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IntelOpt->>User: Optimization Results
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```
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---
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## Protocol Integration
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### Protocol 10: Intelligent Multi-Strategy Optimization (IMSO)
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```mermaid
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stateDiagram-v2
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[*] --> Initialization
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Initialization --> TypeCheck: Load Config
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TypeCheck --> SingleObj: Single Objective
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TypeCheck --> MultiObj: Multi-Objective
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SingleObj --> Characterization: Protocol 10 Active
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Characterization --> LandscapeAnalysis: Min trials reached
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LandscapeAnalysis --> StrategySelection: Confidence ≥ 0.85
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StrategySelection --> Optimization: Strategy Selected
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MultiObj --> NSGAIISetup: Protocol 11 Active
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NSGAIISetup --> Optimization: NSGA-II Configured
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Optimization --> TrialExecution: Run Trial
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TrialExecution --> RealtimeTracking: Protocol 13
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RealtimeTracking --> TrialExecution: Next Trial
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TrialExecution --> Finalization: All trials complete
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Finalization --> [*]: Report Generated
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note right of Characterization
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Adaptive phase
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10-30 trials
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Random/Sobol sampling
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end note
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note right of LandscapeAnalysis
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Analyzes:
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- Smoothness
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- Multimodality
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- Separability
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- Noise level
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end note
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note right of NSGAIISetup
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Multi-objective:
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- Skips characterization
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- Direct NSGA-II
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- Pareto front optimization
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end note
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```
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### Protocol 11: Multi-Objective Support
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```mermaid
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graph TB
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subgraph Detection["Multi-Objective Detection"]
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CheckObj[Check len objectives]
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Single{objectives == 1?}
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Multi{objectives > 1?}
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end
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subgraph SinglePath["Single-Objective Path"]
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BestValue[study.best_value]
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BestTrial[study.best_trial]
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TrialValue[trial.value]
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end
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subgraph MultiPath["Multi-Objective Path"]
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BestTrials[study.best_trials<br/>Pareto Front]
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TrialValues[trial.values<br/>Multiple objectives]
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NSGAII[NSGA-II Sampler]
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end
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subgraph Validation["Protocol 11 Compliance"]
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CheckAPI{API call type?}
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UseSingle[Use .value]
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UseMulti[Use .values]
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SkipChar[Skip Characterization]
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SkipStag[Skip Stagnation]
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end
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CheckObj --> Single
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CheckObj --> Multi
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Single --> SinglePath
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Multi --> MultiPath
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SinglePath --> CheckAPI
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MultiPath --> CheckAPI
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CheckAPI -->|Single| UseSingle
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CheckAPI -->|Multi| UseMulti
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UseMulti --> SkipChar
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UseMulti --> SkipStag
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classDef errorClass fill:#FFCDD2,stroke:#C62828,stroke-width:3px
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classDef safeClass fill:#C8E6C9,stroke:#2E7D32,stroke-width:3px
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class UseSingle,UseMulti safeClass
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```
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### Protocol 13: Real-Time Dashboard Tracking
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```mermaid
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sequenceDiagram
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participant Trial as Optuna Trial
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participant Callback as Optuna Callback
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participant Tracker as RealtimeTracker
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participant FS as File System
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participant Dashboard
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||||
|
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Trial->>Callback: Trial Complete
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Callback->>Tracker: after_trial()
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activate Tracker
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Tracker->>Tracker: Prepare Trial Data
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Tracker->>FS: Write trial_log.json
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Tracker->>FS: Write optimizer_state.json
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alt Characterization Phase
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Tracker->>Tracker: Update Progress
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Tracker->>FS: Write characterization_progress.json
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end
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alt Landscape Analysis
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Tracker->>Tracker: Analyze Landscape
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Tracker->>FS: Write intelligence_report.json
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end
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alt Strategy Transition
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Tracker->>Tracker: Log Transition
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Tracker->>FS: Write strategy_transitions.json
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||||
end
|
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deactivate Tracker
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FS-->>Dashboard: File Watch Event
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Dashboard->>FS: Read JSON Files
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||||
Dashboard->>Dashboard: Update UI
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Dashboard-->>Dashboard: Render Charts
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||||
```
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||||
---
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## Extractor Library (Protocol 12)
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```mermaid
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||||
graph TB
|
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subgraph ExtractorLibrary["Extractor Library (optimization_engine/extractors/)"]
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Base[base_extractor.py<br/>BaseExtractor ABC]
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||||
|
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subgraph Builtin["Built-in Extractors"]
|
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Freq[frequency_extractor.py<br/>FrequencyExtractor]
|
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Mass[mass_extractor.py<br/>MassExtractor]
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||||
Stress[stress_extractor.py<br/>StressExtractor]
|
||||
Disp[displacement_extractor.py<br/>DisplacementExtractor]
|
||||
end
|
||||
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Custom[Custom User Extractors<br/>Extend BaseExtractor]
|
||||
end
|
||||
|
||||
subgraph Usage["Extractor Usage Flow"]
|
||||
Registry[Extractor Registry<br/>Map name -> class]
|
||||
Load[Load by Name]
|
||||
Execute[Execute Extraction]
|
||||
Return[Return Value]
|
||||
end
|
||||
|
||||
Base --> Freq
|
||||
Base --> Mass
|
||||
Base --> Stress
|
||||
Base --> Disp
|
||||
Base --> Custom
|
||||
|
||||
Freq --> Registry
|
||||
Mass --> Registry
|
||||
Stress --> Registry
|
||||
Disp --> Registry
|
||||
Custom --> Registry
|
||||
|
||||
Registry --> Load
|
||||
Load --> Execute
|
||||
Execute --> Return
|
||||
|
||||
classDef extractorClass fill:#FFF9C4,stroke:#F57F17,stroke-width:2px
|
||||
class Freq,Mass,Stress,Disp,Custom extractorClass
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
## Study Directory Structure
|
||||
|
||||
```mermaid
|
||||
graph TB
|
||||
subgraph StudyRoot["studies/my_optimization/"]
|
||||
Setup["1_setup/"]
|
||||
Results["2_results/"]
|
||||
end
|
||||
|
||||
subgraph SetupContents["1_setup/"]
|
||||
Model["model/<br/>.prt, .sim, .fem files"]
|
||||
OptConfig["optimization_config.json"]
|
||||
RunScript["run_optimization.py"]
|
||||
end
|
||||
|
||||
subgraph ResultsContents["2_results/"]
|
||||
StudyDB["study.db<br/>Optuna SQLite"]
|
||||
Summary["optimization_summary.json"]
|
||||
|
||||
subgraph IntelFolder["intelligent_optimizer/"]
|
||||
TrialLog["trial_log.json"]
|
||||
OptimizerState["optimizer_state.json"]
|
||||
CharProgress["characterization_progress.json"]
|
||||
IntelReport["intelligence_report.json"]
|
||||
StratTrans["strategy_transitions.json"]
|
||||
end
|
||||
|
||||
Report["final_report.md<br/>Markdown summary"]
|
||||
end
|
||||
|
||||
StudyRoot --> Setup
|
||||
StudyRoot --> Results
|
||||
|
||||
Setup --> Model
|
||||
Setup --> OptConfig
|
||||
Setup --> RunScript
|
||||
|
||||
Results --> StudyDB
|
||||
Results --> Summary
|
||||
Results --> IntelFolder
|
||||
Results --> Report
|
||||
|
||||
IntelFolder --> TrialLog
|
||||
IntelFolder --> OptimizerState
|
||||
IntelFolder --> CharProgress
|
||||
IntelFolder --> IntelReport
|
||||
IntelFolder --> StratTrans
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
## Philosophy & Design Principles
|
||||
|
||||
### 1. Separation of Concerns
|
||||
|
||||
```mermaid
|
||||
graph LR
|
||||
subgraph Philosophy["Atomizer Philosophy"]
|
||||
Engine[Optimization Engine<br/>Pure algorithmic logic]
|
||||
NX[NX Integration<br/>CAD/FEA operations]
|
||||
Track[Tracking System<br/>Observability]
|
||||
User[User Interface<br/>Configuration & Monitoring]
|
||||
end
|
||||
|
||||
Engine -.->|Clean API| NX
|
||||
Engine -.->|Events| Track
|
||||
Track -.->|Data| User
|
||||
User -.->|Config| Engine
|
||||
|
||||
note1[No tight coupling<br/>Each layer independent]
|
||||
note2[Swap NX for Ansys?<br/>Just change integration layer]
|
||||
note3[Add new optimizer?<br/>Implement strategy interface]
|
||||
|
||||
Engine -.-> note2
|
||||
NX -.-> note2
|
||||
Track -.-> note3
|
||||
```
|
||||
|
||||
### 2. Protocol-Based Architecture
|
||||
|
||||
```mermaid
|
||||
mindmap
|
||||
root((Protocols))
|
||||
Protocol 10: IMSO
|
||||
Adaptive Characterization
|
||||
Landscape Analysis
|
||||
Strategy Selection
|
||||
Dynamic Switching
|
||||
Protocol 11: Multi-Obj
|
||||
Pareto Front
|
||||
NSGA-II
|
||||
API Consistency
|
||||
Backward Compatible
|
||||
Protocol 13: Tracking
|
||||
Real-time Updates
|
||||
JSON File Writes
|
||||
Dashboard Integration
|
||||
Observability
|
||||
Future Protocols
|
||||
Protocol 14: ?
|
||||
Protocol 15: ?
|
||||
Extensible System
|
||||
```
|
||||
|
||||
### 3. Extensibility Points
|
||||
|
||||
```mermaid
|
||||
graph TB
|
||||
subgraph Core["Atomizer Core<br/>(Unchangeable)"]
|
||||
CoreEngine[Optimization Engine]
|
||||
CoreProtocols[Protocol System]
|
||||
end
|
||||
|
||||
subgraph Extension["Extension Points"]
|
||||
CustomExtractor[Custom Extractors<br/>BaseExtractor ABC]
|
||||
CustomStrategy[Custom Strategies<br/>Optuna Sampler]
|
||||
CustomSolver[Custom Solvers<br/>Solver Interface]
|
||||
CustomCallback[Custom Callbacks<br/>Optuna Callback]
|
||||
end
|
||||
|
||||
subgraph User["User Code"]
|
||||
MyExtractor[MyCustomExtractor]
|
||||
MyStrategy[MyCustomSampler]
|
||||
MySolver[MyFEASolver]
|
||||
end
|
||||
|
||||
CoreEngine --> CustomExtractor
|
||||
CoreEngine --> CustomStrategy
|
||||
CoreEngine --> CustomSolver
|
||||
CoreEngine --> CustomCallback
|
||||
|
||||
CustomExtractor -.->|Implement| MyExtractor
|
||||
CustomStrategy -.->|Implement| MyStrategy
|
||||
CustomSolver -.->|Implement| MySolver
|
||||
|
||||
classDef coreClass fill:#BBDEFB,stroke:#1565C0,stroke-width:3px
|
||||
classDef extClass fill:#C8E6C9,stroke:#2E7D32,stroke-width:2px
|
||||
classDef userClass fill:#FFE082,stroke:#F57F00,stroke-width:2px
|
||||
|
||||
class CoreEngine,CoreProtocols coreClass
|
||||
class CustomExtractor,CustomStrategy,CustomSolver,CustomCallback extClass
|
||||
class MyExtractor,MyStrategy,MySolver userClass
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
## Technology Stack
|
||||
|
||||
```mermaid
|
||||
graph TB
|
||||
subgraph Frontend["Frontend Layer"]
|
||||
React[React 18<br/>TypeScript]
|
||||
Vite[Vite<br/>Build Tool]
|
||||
Recharts[Recharts<br/>Visualization]
|
||||
end
|
||||
|
||||
subgraph Backend["Backend Layer"]
|
||||
FastAPI[FastAPI<br/>REST API]
|
||||
Uvicorn[Uvicorn<br/>ASGI Server]
|
||||
end
|
||||
|
||||
subgraph Core["Core Engine"]
|
||||
Python[Python 3.8+]
|
||||
Optuna[Optuna 3.x<br/>Hyperparameter Optimization]
|
||||
NumPy[NumPy/SciPy<br/>Numerical Computing]
|
||||
end
|
||||
|
||||
subgraph Integration["Integration"]
|
||||
NXOpen[NX Open API<br/>Python Journals]
|
||||
SQLite[SQLite<br/>Study Storage]
|
||||
end
|
||||
|
||||
React --> FastAPI
|
||||
FastAPI --> Optuna
|
||||
Optuna --> SQLite
|
||||
Optuna --> NXOpen
|
||||
|
||||
classDef frontClass fill:#E1F5FE,stroke:#0277BD
|
||||
classDef backClass fill:#F3E5F5,stroke:#6A1B9A
|
||||
classDef coreClass fill:#E8F5E9,stroke:#2E7D32
|
||||
classDef integClass fill:#FFF3E0,stroke:#E65100
|
||||
|
||||
class React,Vite,Recharts frontClass
|
||||
class FastAPI,Uvicorn backClass
|
||||
class Python,Optuna,NumPy coreClass
|
||||
class NXOpen,SQLite integClass
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
## Performance Characteristics
|
||||
|
||||
```mermaid
|
||||
graph LR
|
||||
subgraph Timing["Typical Trial Timing (100 trials)"]
|
||||
T1[Trial Overhead<br/>~0.5s]
|
||||
T2[NX Model Update<br/>~1s]
|
||||
T3[FEA Solve<br/>~5-10s]
|
||||
T4[Result Extraction<br/>~0.5s]
|
||||
T5[Optuna Update<br/>~0.1s]
|
||||
end
|
||||
|
||||
T1 --> T2 --> T3 --> T4 --> T5
|
||||
|
||||
Total[Total: ~7-12s per trial<br/>100 trials = 12-20 minutes]
|
||||
|
||||
T5 -.-> Total
|
||||
|
||||
note1[Parallelization possible<br/>Multiple NX sessions]
|
||||
note2[Session reuse saves<br/>~2s per trial]
|
||||
|
||||
T3 -.-> note1
|
||||
T2 -.-> note2
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
## Next Steps
|
||||
|
||||
For protocol-specific workflows, see:
|
||||
- [Protocol Workflows](protocol_workflows.md) - Detailed protocol execution diagrams
|
||||
- [Optimization Lifecycle](optimization_lifecycle.md) - Trial-by-trial flow
|
||||
|
||||
For implementation details, see:
|
||||
- [Main Documentation Index](../00_INDEX.md)
|
||||
- [Protocol Specifications](../01_PROTOCOLS.md)
|
||||
Reference in New Issue
Block a user