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:

   git clone https://github.com/mcp-lammps/mcp-lammps.git
   cd mcp-lammps
   

2. Create a virtual environment:

   python -m venv venv
   source venv/bin/activate  # On Windows: venv\Scripts\activate
   

3. Install dependencies:

   pip install -r requirements.txt
   

4. Install in development mode:

   pip install -e .
   

Usage

Basic Usage

Start the MCP server:

python -m mcp_lammps.server

Configuration

The server can be configured through environment variables or configuration files:

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 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