io.github.andylbrummer/molecular-mcp

平台与服务

by andylbrummer

提供 GPU 加速的 MCP server,用于 molecular dynamics、N-body simulations 与 particle systems 计算。

什么是 io.github.andylbrummer/molecular-mcp

提供 GPU 加速的 MCP server,用于 molecular dynamics、N-body simulations 与 particle systems 计算。

README

Math-Physics-ML MCP System

PyPI - Math MCP PyPI - Quantum MCP PyPI - Molecular MCP PyPI - Neural MCP Documentation License: MIT

GPU-accelerated Model Context Protocol servers for computational mathematics, physics simulations, and machine learning.

📚 Documentation

View Full Documentation →

GuideDescription
InstallationSetup instructions for pip, uv, and uvx
ConfigurationClaude Desktop & Claude Code setup
Quick StartGet running in 5 minutes
API ReferenceComplete tool documentation
Visual DemosInteractive physics simulations

About

This system enables AI assistants to perform real scientific computing — from solving differential equations to running molecular dynamics simulations.

<table> <tr> <td align="center" width="50%"> <img src="docs/static/img/demos/double_slit.webp" alt="Double-Slit Interference" width="100%"/> <br/><b>Quantum Wave Mechanics</b><br/> <sub>Double-slit interference pattern from solving the time-dependent Schrödinger equation</sub> </td> <td align="center" width="50%"> <img src="docs/static/img/demos/galaxy_collision.webp" alt="Galaxy Collision" width="100%"/> <br/><b>N-Body Dynamics</b><br/> <sub>Galaxy merger simulation using gravitational N-body calculations</sub> </td> </tr> <tr> <td align="center" width="50%"> <img src="docs/static/img/demos/bragg_hexagonal.webp" alt="Bragg Scattering" width="100%"/> <br/><b>Crystal Diffraction</b><br/> <sub>Bragg scattering from a hexagonal (graphene-like) lattice</sub> </td> <td align="center" width="50%"> <img src="docs/static/img/demos/triple_slit.webp" alt="Triple-Slit" width="100%"/> <br/><b>Multi-Slit Interference</b><br/> <sub>Complex interference patterns from three coherent sources</sub> </td> </tr> </table>

Overview

This system provides 4 specialized MCP servers that bring scientific computing capabilities to AI assistants like Claude:

ServerDescriptionTools
Math MCPSymbolic algebra (SymPy) + numerical computing14
Quantum MCPWave mechanics & Schrodinger simulations12
Molecular MCPClassical molecular dynamics15
Neural MCPNeural network training & evaluation16

Key Features:

  • GPU acceleration with automatic CUDA detection (10-100x speedup)
  • Async task support for long-running simulations
  • Cross-MCP workflows via URI-based data sharing
  • Progressive discovery for efficient tool exploration

Quick Start

Installation with uvx (Recommended)

Run any MCP server directly without installation:

bash
# Run individual servers
uvx scicomp-math-mcp
uvx scicomp-quantum-mcp
uvx scicomp-molecular-mcp
uvx scicomp-neural-mcp

Installation with pip/uv

bash
# Install individual servers
pip install scicomp-math-mcp
pip install scicomp-quantum-mcp
pip install scicomp-molecular-mcp
pip install scicomp-neural-mcp

# Or install all at once
pip install scicomp-math-mcp scicomp-quantum-mcp scicomp-molecular-mcp scicomp-neural-mcp

# With GPU support (requires CUDA)
pip install scicomp-math-mcp[gpu] scicomp-quantum-mcp[gpu] scicomp-molecular-mcp[gpu] scicomp-neural-mcp[gpu]

Configuration

Claude Desktop

Add to your Claude Desktop configuration file:

macOS: ~/Library/Application Support/Claude/claude_desktop_config.json Windows: %APPDATA%\Claude\claude_desktop_config.json

json
{
  "mcpServers": {
    "math-mcp": {
      "command": "uvx",
      "args": ["scicomp-math-mcp"]
    },
    "quantum-mcp": {
      "command": "uvx",
      "args": ["scicomp-quantum-mcp"]
    },
    "molecular-mcp": {
      "command": "uvx",
      "args": ["scicomp-molecular-mcp"]
    },
    "neural-mcp": {
      "command": "uvx",
      "args": ["scicomp-neural-mcp"]
    }
  }
}

Claude Code

Add to your project's .mcp.json:

json
{
  "mcpServers": {
    "math-mcp": {
      "command": "uvx",
      "args": ["scicomp-math-mcp"]
    },
    "quantum-mcp": {
      "command": "uvx",
      "args": ["scicomp-quantum-mcp"]
    }
  }
}

Or configure globally in ~/.claude/settings.json.

Usage Examples

Math MCP

python
# Solve equations symbolically
symbolic_solve(equations="x**3 - 6*x**2 + 11*x - 6")
# Result: [1, 2, 3]

# Compute derivatives
symbolic_diff(expression="sin(x)*exp(-x**2)", variable="x")
# Result: cos(x)*exp(-x**2) - 2*x*sin(x)*exp(-x**2)

# GPU-accelerated matrix operations
result = matrix_multiply(a=matrix_a, b=matrix_b, use_gpu=True)

Quantum MCP

python
# Create a Gaussian wave packet
psi = create_gaussian_wavepacket(
    grid_size=[256],
    position=[64],
    momentum=[2.0],
    width=5.0
)

# Solve time-dependent Schrodinger equation
simulation = solve_schrodinger(
    potential=barrier_potential,
    initial_state=psi,
    time_steps=1000,
    dt=0.1,
    use_gpu=True
)

Molecular MCP

python
# Create particle system
system = create_particles(
    n_particles=1000,
    box_size=[20, 20, 20],
    temperature=1.5
)

# Add Lennard-Jones potential
add_potential(system_id=system, potential_type="lennard_jones")

# Run MD simulation
trajectory = run_nvt(system_id=system, n_steps=100000, temperature=1.0)

# Analyze diffusion
msd = compute_msd(trajectory_id=trajectory)

Neural MCP

python
# Define model
model = define_model(architecture="resnet18", num_classes=10, pretrained=True)

# Load dataset
dataset = load_dataset(dataset_name="CIFAR10", split="train")

# Train
experiment = train_model(
    model_id=model,
    dataset_id=dataset,
    epochs=50,
    batch_size=128,
    use_gpu=True
)

# Export for deployment
export_model(model_id=model, format="onnx", output_path="model.onnx")

Development

bash
# Clone the repository
git clone https://github.com/andylbrummer/math-mcp.git
cd math-mcp

# Install dependencies
uv sync --all-extras

# Install MCP servers in editable mode (required for entry points)
uv pip install --python .venv/bin/python \
  -e servers/math-mcp \
  -e servers/quantum-mcp \
  -e servers/molecular-mcp \
  -e servers/neural-mcp

# Run tests
uv run pytest -m "not gpu"  # CPU only
uv run pytest               # All tests (requires CUDA)

# Run with coverage
uv run pytest --cov=shared --cov=servers

Note: The editable install step is required because uv sync doesn't install entry point scripts for workspace packages. After this step, you can run servers directly with uv run scicomp-math-mcp.

See CONTRIBUTING.md for development guidelines.

Performance

GPU acceleration provides significant speedups for compute-intensive operations:

MCPOperationCPUGPUSpeedup
MathMatrix multiply (4096x4096)2.1s35ms60x
Quantum2D Schrodinger (512x512, 1000 steps)2h2min60x
MolecularMD (100k particles, 10k steps)1h30s120x
NeuralResNet18 training (1 epoch)45min30s90x

Architecture

For technical details about the system architecture, see ARCHITECTURE.md.

License

MIT License - see LICENSE for details.

Contributing

Contributions are welcome! Please see CONTRIBUTING.md for guidelines.

常见问题

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