{
  "markdown": "# Math-Physics-ML MCP System\n\n[![PyPI - Math MCP](https://img.shields.io/pypi/v/scicomp-math-mcp?label=scicomp-math-mcp)](https://pypi.org/project/scicomp-math-mcp/)\n[![PyPI - Quantum MCP](https://img.shields.io/pypi/v/scicomp-quantum-mcp?label=scicomp-quantum-mcp)](https://pypi.org/project/scicomp-quantum-mcp/)\n[![PyPI - Molecular MCP](https://img.shields.io/pypi/v/scicomp-molecular-mcp?label=scicomp-molecular-mcp)](https://pypi.org/project/scicomp-molecular-mcp/)\n[![PyPI - Neural MCP](https://img.shields.io/pypi/v/scicomp-neural-mcp?label=scicomp-neural-mcp)](https://pypi.org/project/scicomp-neural-mcp/)\n[![Documentation](https://img.shields.io/badge/docs-GitHub%20Pages-blue)](https://andylbrummer.github.io/math-mcp/)\n[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n\nGPU-accelerated [Model Context Protocol](https://modelcontextprotocol.io) servers for computational mathematics, physics simulations, and machine learning.\n\n## 📚 Documentation\n\n**[View Full Documentation →](https://andylbrummer.github.io/math-mcp/)**\n\n| Guide | Description |\n|-------|-------------|\n| [Installation](https://andylbrummer.github.io/math-mcp/getting-started/installation) | Setup instructions for pip, uv, and uvx |\n| [Configuration](https://andylbrummer.github.io/math-mcp/getting-started/configuration) | Claude Desktop & Claude Code setup |\n| [Quick Start](https://andylbrummer.github.io/math-mcp/getting-started/quick-start) | Get running in 5 minutes |\n| [API Reference](https://andylbrummer.github.io/math-mcp/api/overview) | Complete tool documentation |\n| [Visual Demos](https://andylbrummer.github.io/math-mcp/demos/) | Interactive physics simulations |\n\n## About\n\nThis system enables AI assistants to perform real scientific computing — from solving differential equations to running molecular dynamics simulations.\n\n<table>\n<tr>\n<td align=\"center\" width=\"50%\">\n<img src=\"docs/static/img/demos/double_slit.webp\" alt=\"Double-Slit Interference\" width=\"100%\"/>\n<br/><b>Quantum Wave Mechanics</b><br/>\n<sub>Double-slit interference pattern from solving the time-dependent Schrödinger equation</sub>\n</td>\n<td align=\"center\" width=\"50%\">\n<img src=\"docs/static/img/demos/galaxy_collision.webp\" alt=\"Galaxy Collision\" width=\"100%\"/>\n<br/><b>N-Body Dynamics</b><br/>\n<sub>Galaxy merger simulation using gravitational N-body calculations</sub>\n</td>\n</tr>\n<tr>\n<td align=\"center\" width=\"50%\">\n<img src=\"docs/static/img/demos/bragg_hexagonal.webp\" alt=\"Bragg Scattering\" width=\"100%\"/>\n<br/><b>Crystal Diffraction</b><br/>\n<sub>Bragg scattering from a hexagonal (graphene-like) lattice</sub>\n</td>\n<td align=\"center\" width=\"50%\">\n<img src=\"docs/static/img/demos/triple_slit.webp\" alt=\"Triple-Slit\" width=\"100%\"/>\n<br/><b>Multi-Slit Interference</b><br/>\n<sub>Complex interference patterns from three coherent sources</sub>\n</td>\n</tr>\n</table>\n\n## Overview\n\nThis system provides **4 specialized MCP servers** that bring scientific computing capabilities to AI assistants like Claude:\n\n| Server | Description | Tools |\n|--------|-------------|-------|\n| **Math MCP** | Symbolic algebra (SymPy) + numerical computing | 14 |\n| **Quantum MCP** | Wave mechanics & Schrodinger simulations | 12 |\n| **Molecular MCP** | Classical molecular dynamics | 15 |\n| **Neural MCP** | Neural network training & evaluation | 16 |\n\n**Key Features:**\n- GPU acceleration with automatic CUDA detection (10-100x speedup)\n- Async task support for long-running simulations\n- Cross-MCP workflows via URI-based data sharing\n- Progressive discovery for efficient tool exploration\n\n## Quick Start\n\n### Installation with uvx (Recommended)\n\nRun any MCP server directly without installation:\n\n```bash\n# Run individual servers\nuvx scicomp-math-mcp\nuvx scicomp-quantum-mcp\nuvx scicomp-molecular-mcp\nuvx scicomp-neural-mcp\n```\n\n### Installation with pip/uv\n\n```bash\n# Install individual servers\npip install scicomp-math-mcp\npip install scicomp-quantum-mcp\npip install scicomp-molecular-mcp\npip install scicomp-neural-mcp\n\n# Or install all at once\npip install scicomp-math-mcp scicomp-quantum-mcp scicomp-molecular-mcp scicomp-neural-mcp\n\n# With GPU support (requires CUDA)\npip install scicomp-math-mcp[gpu] scicomp-quantum-mcp[gpu] scicomp-molecular-mcp[gpu] scicomp-neural-mcp[gpu]\n```\n\n## Configuration\n\n### Claude Desktop\n\nAdd to your Claude Desktop configuration file:\n\n**macOS**: `~/Library/Application Support/Claude/claude_desktop_config.json`\n**Windows**: `%APPDATA%\\Claude\\claude_desktop_config.json`\n\n```json\n{\n  \"mcpServers\": {\n    \"math-mcp\": {\n      \"command\": \"uvx\",\n      \"args\": [\"scicomp-math-mcp\"]\n    },\n    \"quantum-mcp\": {\n      \"command\": \"uvx\",\n      \"args\": [\"scicomp-quantum-mcp\"]\n    },\n    \"molecular-mcp\": {\n      \"command\": \"uvx\",\n      \"args\": [\"scicomp-molecular-mcp\"]\n    },\n    \"neural-mcp\": {\n      \"command\": \"uvx\",\n      \"args\": [\"scicomp-neural-mcp\"]\n    }\n  }\n}\n```\n\n### Claude Code\n\nAdd to your project's `.mcp.json`:\n\n```json\n{\n  \"mcpServers\": {\n    \"math-mcp\": {\n      \"command\": \"uvx\",\n      \"args\": [\"scicomp-math-mcp\"]\n    },\n    \"quantum-mcp\": {\n      \"command\": \"uvx\",\n      \"args\": [\"scicomp-quantum-mcp\"]\n    }\n  }\n}\n```\n\nOr configure globally in `~/.claude/settings.json`.\n\n## Usage Examples\n\n### Math MCP\n\n```python\n# Solve equations symbolically\nsymbolic_solve(equations=\"x**3 - 6*x**2 + 11*x - 6\")\n# Result: [1, 2, 3]\n\n# Compute derivatives\nsymbolic_diff(expression=\"sin(x)*exp(-x**2)\", variable=\"x\")\n# Result: cos(x)*exp(-x**2) - 2*x*sin(x)*exp(-x**2)\n\n# GPU-accelerated matrix operations\nresult = matrix_multiply(a=matrix_a, b=matrix_b, use_gpu=True)\n```\n\n### Quantum MCP\n\n```python\n# Create a Gaussian wave packet\npsi = create_gaussian_wavepacket(\n    grid_size=[256],\n    position=[64],\n    momentum=[2.0],\n    width=5.0\n)\n\n# Solve time-dependent Schrodinger equation\nsimulation = solve_schrodinger(\n    potential=barrier_potential,\n    initial_state=psi,\n    time_steps=1000,\n    dt=0.1,\n    use_gpu=True\n)\n```\n\n### Molecular MCP\n\n```python\n# Create particle system\nsystem = create_particles(\n    n_particles=1000,\n    box_size=[20, 20, 20],\n    temperature=1.5\n)\n\n# Add Lennard-Jones potential\nadd_potential(system_id=system, potential_type=\"lennard_jones\")\n\n# Run MD simulation\ntrajectory = run_nvt(system_id=system, n_steps=100000, temperature=1.0)\n\n# Analyze diffusion\nmsd = compute_msd(trajectory_id=trajectory)\n```\n\n### Neural MCP\n\n```python\n# Define model\nmodel = define_model(architecture=\"resnet18\", num_classes=10, pretrained=True)\n\n# Load dataset\ndataset = load_dataset(dataset_name=\"CIFAR10\", split=\"train\")\n\n# Train\nexperiment = train_model(\n    model_id=model,\n    dataset_id=dataset,\n    epochs=50,\n    batch_size=128,\n    use_gpu=True\n)\n\n# Export for deployment\nexport_model(model_id=model, format=\"onnx\", output_path=\"model.onnx\")\n```\n\n## Development\n\n```bash\n# Clone the repository\ngit clone https://github.com/andylbrummer/math-mcp.git\ncd math-mcp\n\n# Install dependencies\nuv sync --all-extras\n\n# Install MCP servers in editable mode (required for entry points)\nuv pip install --python .venv/bin/python \\\n  -e servers/math-mcp \\\n  -e servers/quantum-mcp \\\n  -e servers/molecular-mcp \\\n  -e servers/neural-mcp\n\n# Run tests\nuv run pytest -m \"not gpu\"  # CPU only\nuv run pytest               # All tests (requires CUDA)\n\n# Run with coverage\nuv run pytest --cov=shared --cov=servers\n```\n\n> **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`.\n\nSee [CONTRIBUTING.md](CONTRIBUTING.md) for development guidelines.\n\n## Performance\n\nGPU acceleration provides significant speedups for compute-intensive operations:\n\n| MCP | Operation | CPU | GPU | Speedup |\n|-----|-----------|-----|-----|---------|\n| Math | Matrix multiply (4096x4096) | 2.1s | 35ms | 60x |\n| Quantum | 2D Schrodinger (512x512, 1000 steps) | 2h | 2min | 60x |\n| Molecular | MD (100k particles, 10k steps) | 1h | 30s | 120x |\n| Neural | ResNet18 training (1 epoch) | 45min | 30s | 90x |\n\n## Architecture\n\nFor technical details about the system architecture, see [ARCHITECTURE.md](ARCHITECTURE.md).\n\n## License\n\nMIT License - see [LICENSE](LICENSE) for details.\n\n## Contributing\n\nContributions are welcome! Please see [CONTRIBUTING.md](CONTRIBUTING.md) for guidelines.\n",
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