Metadata-Version: 2.4
Name: mcp-lammps
Version: 0.1.0
Summary: Model Context Protocol server for LAMMPS molecular dynamics simulations
Author-email: MCP LAMMPS Development Team <dev@mcp-lammps.org>
License: MIT
Project-URL: Homepage, https://github.com/mcp-lammps/mcp-lammps
Project-URL: Repository, https://github.com/mcp-lammps/mcp-lammps.git
Project-URL: Documentation, https://mcp-lammps.readthedocs.io/
Project-URL: Bug Tracker, https://github.com/mcp-lammps/mcp-lammps/issues
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Physics
Requires-Python: >=3.9
Description-Content-Type: text/markdown
Requires-Dist: mcp>=1.0.0
Requires-Dist: lammps>=2023.0.0
Requires-Dist: numpy>=1.21.0
Requires-Dist: scipy>=1.7.0
Requires-Dist: pandas>=1.3.0
Requires-Dist: matplotlib>=3.5.0
Requires-Dist: pydantic>=2.0.0
Requires-Dist: pyyaml>=6.0
Requires-Dist: pathlib2>=2.3.0
Requires-Dist: asyncio-mqtt>=0.11.0
Provides-Extra: dev
Requires-Dist: pytest>=7.0.0; extra == "dev"
Requires-Dist: pytest-asyncio>=0.21.0; extra == "dev"
Requires-Dist: black>=22.0.0; extra == "dev"
Requires-Dist: flake8>=5.0.0; extra == "dev"
Requires-Dist: mypy>=1.0.0; extra == "dev"
Provides-Extra: gpu
Requires-Dist: cupy>=11.0.0; extra == "gpu"
# 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.
## Overview
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
### Supported Operations
- Energy minimization
- NVT and NPT ensemble simulations
- Equilibration and production runs
- Trajectory analysis
- Property calculations
- Data export and visualization
## Installation
### Prerequisites
- Python 3.9 or higher
- LAMMPS with Python interface
- Sufficient RAM for molecular dynamics simulations
### 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 Workflow
1. **Create a simulation**:
```python
# Create a new simulation
result = await server.create_simulation(
name="water_simulation",
structure_file="water.xyz",
force_field="TIP3P"
)
```
2. **Run equilibration**:
```python
# Run equilibration
result = await server.run_equilibration(
simulation_id="water_simulation",
temperature=300,
duration=1000
)
```
3. **Monitor progress**:
```python
# Check simulation status
status = await server.get_simulation_status("water_simulation")
```
## 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
```
### Running Tests
```bash
pytest tests/
```
### Code Formatting
```bash
black src/ tests/
flake8 src/ tests/
mypy src/
```
## 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 MIT 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
## Support
For questions, issues, or contributions, please:
- Open an issue on GitHub
- Check the documentation in the `docs/` directory
- Review the development plan in `dev.md`
## Roadmap
See `dev.md` for the detailed development plan and roadmap.
