MCP LAMMPS Server

# MCP LAMMPS Documentation Welcome to the documentation for the MCP LAMMPS package - a Model Context Protocol (MCP) server that enables AI assistants to interact with LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) for molecular dynamics simulations. ## Quick Start - **[Installation Guide](installation.md)** - How to install and set up MCP LAMMPS - **[User Guide](user-guide.md)** - Basic usage and common workflows - **[API Reference](api-reference.md)** - Complete API documentation - **[Examples](examples.md)** - Working examples and tutorials - **[Configuration](configuration.md)** - Server configuration options ## What is MCP LAMMPS? MCP LAMMPS is a Model Context Protocol server that provides a standardized interface for controlling LAMMPS molecular dynamics simulations through natural language commands. It enables AI assistants to: - Set up and configure molecular dynamics simulations - Run equilibration and production simulations - Monitor simulation progress in real-time - Analyze simulation results - Manage simulation workflows ## Key Features ### 🚀 **Simulation Management** - Create, configure, and run LAMMPS simulations - Support for multiple force fields and ensembles - Automated workflow management ### 📊 **Real-time Monitoring** - Track simulation progress and system properties - Monitor energy components and structural properties - Real-time data visualization capabilities ### 🔬 **Analysis Tools** - Process trajectories and calculate thermodynamic properties - Generate plots and export data in various formats - Comprehensive analysis workflows ### 🛠️ **Structure Handling** - Load molecular structures from various formats - Create simple test structures - Support for complex molecular systems ## Architecture ``` ┌─────────────────┐ ┌─────────────────┐ ┌─────────────────┐ │ AI Assistant │◄──►│ MCP LAMMPS │◄──►│ LAMMPS │ │ │ │ Server │ │ Simulation │ └─────────────────┘ └─────────────────┘ └─────────────────┘ │ ▼ ┌─────────────────┐ │ Data Handler │ │ & Analysis │ └─────────────────┘ ``` ## Getting Help - **Issues**: Report bugs and request features on [GitHub Issues](https://github.com/mcp-lammps/mcp-lammps/issues) - **Discussions**: Join the community on [GitHub Discussions](https://github.com/mcp-lammps/mcp-lammps/discussions) - **Documentation**: This documentation is hosted on [Read the Docs](https://mcp-lammps.readthedocs.io/) ## Contributing We welcome contributions! Please see our [Contributing Guide](contributing.md) for details on how to get started. ## License This project is licensed under the Apache License - see the [LICENSE](../LICENSE) file for details.