⚛️ MCP Atomic Toolkit

[!NOTE] This project is under active development. Interfaces and behavior may evolve.

A FastMCP server for atomistic modeling workflows powered by ASE, pymatgen, and modern ML interatomic potentials.

It gives MCP clients a practical toolkit for:

• building structures,
• running geometry optimization + molecular dynamics,
• analyzing structures/trajectories,
• and downloading generated artifacts (data + plots).

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✨ Why this repo

If you need atomistic workflows exposed as MCP tools (instead of hand-wiring scripts), this project gives you:

• ready-to-call MCP tools for common simulation tasks,
• file-first outputs that are easy to inspect/reuse,
• artifact download URLs so clients don’t need binary blobs in chat context,
• deployment-ready HTTP app with health and server-card endpoints.

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🚀 Features

• MCP-native workflows via FastMCP tools
• Structure generation: bulk, surface, molecule, supercell, amorphous, liquid, bicrystal, polycrystal
• Optimization workflows with MLIPs (kim default, nequix/orb supported)
• Molecular dynamics workflows (Velocity Verlet, Langevin, NVT Berendsen)
• Analysis outputs:
  • RDF + coordination stats
  • MSD + thermodynamic trends
  • VACF + diffusion (Green-Kubo)
• Downloadable artifacts (xyz, extxyz, cif, traj, png, svg, csv, dat, ...)
• Registry-friendly endpoints (/healthz, server card, Streamable HTTP root)

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⚡ Quick Start

1) Requirements

• Python 3.11+

2) Install

pip install -r requirements.txt

3) Run locally

uvicorn mcp_atomictoolkit.http_app:app --host 0.0.0.0 --port 10000

Alternative:

python main.py

4) Smoke check

curl -s http://localhost:10000/healthz

Expected response:

{"status":"ok"}

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🧰 Tooling Overview

Main MCP tools exposed by the server:

• build_structure_workflow
• analyze_structure_workflow
• write_structure_workflow
• optimize_structure_workflow
• run_md_workflow
• analyze_trajectory_workflow
• autocorrelation_workflow

Legacy aliases are also included for backward compatibility.

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🌐 Endpoints

• POST / — primary MCP Streamable HTTP endpoint
• GET /healthz — health check
• GET /.well-known/mcp/server-card.json — MCP server card metadata
• GET /artifacts/{artifact_id}/{filename} — artifact download route
• /sse/ — compatibility alias path mounted to the MCP app

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📦 Deployment

Render

render.yaml is included and ready to use.

Default start command:

uvicorn mcp_atomictoolkit.http_app:app --host 0.0.0.0 --port $PORT

Docker

docker build -t mcp-atomictoolkit .
docker run --rm -p 7860:7860 mcp-atomictoolkit

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🗂️ Project Structure

src/mcp_atomictoolkit/
  mcp_server.py          # FastMCP tool definitions
  http_app.py            # Starlette app + routing/endpoints
  workflows/core.py      # High-level workflow orchestration
  analysis/              # Structure/trajectory/VACF analysis logic
  structure_operations.py
  optimizers.py
  md_runner.py
  artifact_store.py      # Download artifact registration + URLs

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🤝 Contributing

• Keep outputs file-based and artifact-friendly.
• When adding tools, usually update both:
  • workflows/core.py
  • mcp_server.py
• Preserve http_app.py compatibility behavior unless intentionally changing deployment contracts.

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📄 License

MIT — see LICENSE.