# MCP LAMMPS Documentation
Welcome to the MCP LAMMPS documentation! This folder contains comprehensive documentation for the MCP LAMMPS package.
## 📚 Documentation Structure
### Getting Started
- **[Installation Guide](installation.md)** - Complete setup instructions
- **[User Guide](user-guide.md)** - Basic usage and workflows
- **[Examples](examples.md)** - Working code examples and tutorials
### Reference
- **[API Reference](api-reference.md)** - Complete function and class documentation
- **[Configuration Guide](configuration.md)** - Advanced configuration options
### Development
- **[Contributing Guide](contributing.md)** - How to contribute to the project
## 🚀 Quick Start
1. **Install MCP LAMMPS** - See [Installation Guide](installation.md)
2. **Learn the basics** - Read [User Guide](user-guide.md)
3. **Try examples** - Explore [Examples](examples.md)
4. **Configure for your needs** - Check [Configuration Guide](configuration.md)
## 📖 Documentation Overview
### Installation Guide
Complete step-by-step instructions for installing MCP LAMMPS on different platforms, including:
- System requirements
- Prerequisites (Python, LAMMPS)
- Installation methods (pip, conda, source)
- Configuration setup
- Troubleshooting common issues
### User Guide
Comprehensive guide covering:
- Basic usage patterns
- Simulation management
- Real-time monitoring
- Analysis and results
- Best practices
- Common workflows
### API Reference
Complete reference documentation for:
- All functions and classes
- Parameter descriptions
- Return values
- Error handling
- Data structures
- Code examples
### Examples
Working examples demonstrating:
- Basic water simulations
- Custom structure handling
- Real-time monitoring
- Protein simulation workflows
- Temperature dependence studies
- Material properties calculations
- Interactive simulation control
- Batch processing
- Error handling
### Configuration Guide
Advanced configuration options including:
- Environment variables
- YAML configuration files
- Performance tuning
- Security settings
- Monitoring and logging
- Environment-specific configurations
### Contributing Guide
Information for contributors:
- Development setup
- Code style and standards
- Testing guidelines
- Documentation standards
- Pull request process
- Community guidelines
## 🔍 Finding What You Need
### By Task
**I want to...**
- **Install MCP LAMMPS** → [Installation Guide](installation.md)
- **Run my first simulation** → [User Guide](user-guide.md)
- **See working examples** → [Examples](examples.md)
- **Configure the server** → [Configuration Guide](configuration.md)
- **Look up a function** → [API Reference](api-reference.md)
- **Contribute code** → [Contributing Guide](contributing.md)
### By Experience Level
**Beginner**
1. [Installation Guide](installation.md)
2. [User Guide](user-guide.md) - Basic Usage section
3. [Examples](examples.md) - Basic Examples section
**Intermediate**
1. [User Guide](user-guide.md) - Advanced Features section
2. [Examples](examples.md) - Advanced Examples section
3. [Configuration Guide](configuration.md)
**Advanced**
1. [API Reference](api-reference.md)
2. [Configuration Guide](configuration.md) - Advanced Configuration
3. [Contributing Guide](contributing.md)
## 📝 Documentation Standards
This documentation follows these standards:
- **Clear and concise** writing
- **Code examples** for all major features
- **Step-by-step** instructions
- **Troubleshooting** sections
- **Cross-references** between related topics
## 🤝 Contributing to Documentation
We welcome contributions to improve the documentation! See the [Contributing Guide](contributing.md) for details on:
- Documentation standards
- How to submit changes
- Review process
## 📞 Getting Help
If you can't find what you're looking for:
1. **Search the documentation** using your browser's search function
2. **Check the examples** for similar use cases
3. **Look at the API reference** for specific function details
4. **Report issues** on GitHub if you find errors or missing information
## 🔗 External Resources
- **[GitHub Repository](https://github.com/mcp-lammps/mcp-lammps)** - Source code and issues
- **[PyPI Package](https://pypi.org/project/mcp-lammps/)** - Installation via pip
- **[LAMMPS Documentation](https://docs.lammps.org/)** - LAMMPS reference
- **[Model Context Protocol](https://modelcontextprotocol.io/)** - MCP specification
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*This documentation is maintained by the MCP LAMMPS development team. For questions or suggestions, please open an issue on GitHub.*
