Atomizer/docs/09_DIAGRAMS/00_INDEX.md

Atomizer Diagrams Index

Last Updated: 2025-11-21 Purpose: Visual documentation of Atomizer's architecture, workflows, and protocols

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Overview

This directory contains comprehensive visual documentation using Mermaid diagrams. These diagrams are designed to be:

• Rendered automatically in GitHub, VS Code, and documentation sites
• Easy to maintain as plain text with version control
• Comprehensive covering architecture, workflows, and protocol details

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Available Diagrams

1. System Architecture

File: architecture_overview.md

Complete system architecture showing:

• Core components and their relationships
• Data flow between optimization engine, NX solver, and dashboard
• Plugin system and extensibility points
• Protocol integration layers

2. Protocol Workflows

File: protocol_workflows.md

Detailed protocol execution flows:

• Protocol 10: Intelligent Multi-Strategy Optimization (IMSO)
• Protocol 11: Multi-Objective Support
• Protocol 13: Real-Time Dashboard Tracking
• LLM-assisted optimization workflow (Hybrid Mode)

3. Optimization Lifecycle

File: optimization_lifecycle.md

Trial-by-trial execution flow:

• Study initialization
• Design variable sampling
• NX model update and solving
• Result extraction and objective calculation
• Optuna feedback loop

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Viewing Diagrams

GitHub

Diagrams render automatically when viewing .md files on GitHub.

VS Code

Install the Markdown Preview Mermaid Support extension:

code --install-extension bierner.markdown-mermaid

Documentation Sites

Mermaid diagrams are supported by:

• MkDocs (with pymdown-extensions)
• Docusaurus
• GitBook
• Most modern documentation generators

Online Viewer

Copy diagram code to: https://mermaid.live/

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Diagram Conventions

Color Coding

• Blue (#4A90E2): Core optimization components
• Green (#7CB342): NX/Solver integration
• Orange (#FF9800): Dashboard/Tracking
• Purple (#9C27B0): Protocol logic
• Red (#E53935): LLM/Hybrid features
• Gray (#757575): Data/Configuration

Node Shapes

• Rectangles: Processes/Components
• Rounded Rectangles: Modules/Systems
• Diamonds: Decision points
• Cylinders: Databases/Storage
• Circles: Entry/Exit points

Arrow Types

• Solid arrow (→): Data flow
• Dashed arrow (-->): Control flow
• Thick arrow (==>): Critical path
• Dotted arrow (-.): Optional/Conditional

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Maintenance

Updating Diagrams

When code changes affect architecture:

1. Update relevant diagram file
2. Test rendering in VS Code or GitHub preview
3. Update "Last Updated" date in diagram header
4. Commit with descriptive message: docs: Update architecture diagram for [feature]

Creating New Diagrams

For new features or protocols:

1. Create new .md file in this directory
2. Use existing diagrams as templates
3. Follow naming convention: feature_name.md
4. Add entry to this index
5. Link from relevant protocol documentation

Testing Diagrams

Before committing:

# Check syntax with Mermaid CLI (if installed)
mmdc -i diagram.md -o test.svg

# Or test in browser
# Copy code to https://mermaid.live/

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Quick Links

Documentation

• Main Index
• Protocols
• Architecture

Implementation

• Optimization Engine
• NX Integration
• Dashboard

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Maintained By: Atomizer Development Team Feedback: Open GitHub issue with "documentation" label