MCP LAMMPS Server

# MCP LAMMPS Server 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. ## Status This is still in experimental status. This package is developed in collaboration with AI coder. ## Overview This MCP is part of our workflow for the autonomous computational materials design with LLM. This MCP server 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 ## Features ### Core Capabilities - **Simulation Management**: Create, configure, and run LAMMPS simulations - **Structure Handling**: Load molecular structures from various formats - **Real-time Monitoring**: Track simulation progress and system properties - **Analysis Tools**: Process trajectories and calculate thermodynamic properties - **Workflow Automation**: Define and execute multi-step simulation workflows ## Installation ### Prerequisites - Python 3.9 or higher - LAMMPS with Python interface ### Quick Start 1. **Clone the repository**: ```bash git clone https://github.com/mcp-lammps/mcp-lammps.git cd mcp-lammps ``` 2. **Create a virtual environment**: ```bash python -m venv venv source venv/bin/activate # On Windows: venv\Scripts\activate ``` 3. **Install dependencies**: ```bash pip install -r requirements.txt ``` 4. **Install in development mode**: ```bash pip install -e . ``` ## Usage ### Basic Usage Start the MCP server: ```bash python -m mcp_lammps.server ``` ### Configuration The server can be configured through environment variables or configuration files: ```bash export MCP_LAMMPS_LOG_LEVEL=INFO export MCP_LAMMPS_WORK_DIR=/path/to/workspace python -m mcp_lammps.server ``` ### Example Prompt ``create a water simulation with 10 water molecules, save the relevant files, run the simulation at 300 K under NVT ensemble in the selected folder (examples)'' ## Development ### Project Structure ``` mcp_lammps/ ├── src/mcp_lammps/ │ ├── server.py # Main MCP server │ ├── lammps_interface.py # LAMMPS wrapper │ ├── simulation_manager.py # Simulation management │ ├── data_handler.py # Data processing │ ├── tools/ # MCP tools │ └── utils/ # Utilities ├── tests/ # Test suite ├── examples/ # Usage examples └── docs/ # Documentation ``` ## Contributing 1. Fork the repository 2. Create a feature branch 3. Make your changes 4. Add tests for new functionality 5. Ensure all tests pass 6. Submit a pull request ## License This project is licensed under the Apache License - see the [LICENSE](LICENSE) file for details. ## Acknowledgments - LAMMPS development team for the molecular dynamics engine - Model Context Protocol community for the MCP framework - Scientific computing community for inspiration and feedback - LLM for writing the code