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.

Related MCP server: MCP Toolkit

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:

Configuration

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

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

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