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

Clone the repository:
git clone https://github.com/mcp-lammps/mcp-lammps.git cd mcp-lammps
Create a virtual environment:
python -m venv venv source venv/bin/activate # On Windows: venv\Scripts\activate
Install dependencies:
pip install -r requirements.txt
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

Fork the repository
Create a feature branch
Make your changes
Add tests for new functionality
Ensure all tests pass
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

This server cannot be installed

security - not tested

license - permissive license

quality - not tested

How are these scores calculated?

hybrid server

The server is able to function both locally and remotely, depending on the configuration or use case.

A Model Context Protocol server that enables AI assistants to interact with LAMMPS for molecular dynamics simulations through natural language commands.

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