⚛️ 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

STDIO mode (for desktop MCP clients):

python -m mcp_atomictoolkit.mcp_server

[!IMPORTANT] STDIO transports must keep stdout clean for JSON-RPC. Avoid print() or logging to stdout when running the server in STDIO mode.

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
• single_point_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 /docs — lightweight documentation (README)
• 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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🧪 Workflow Notes (for MCP clients)

Structure building coverage

build_structure_workflow supports:

• bulk (ASE bulk)
• surface (ASE surface)
• molecule (ASE molecule)
• supercell (multiplication of a base structure)
• amorphous/liquid (random packed structures)
• bicrystal and polycrystal (grain stacking/rotation)

For interfaces, doped structures, adsorbates, or custom slabs, prefer:

1. Generate the structure with ASE/pymatgen (or an external builder), then
2. Use write_structure_workflow to persist the final geometry for downstream steps.

This ensures MCP callers can still handle advanced structures even when a specialized builder is required.

Builder kwargs cheat sheet

Common builder_kwargs for build_structure_workflow:

• surface: indices, layers, vacuum
• supercell: size, base_structure_type, base_crystal_system, base_lattice_constant, base_kwargs
• amorphous/liquid: num_atoms, box_length, relax, relax_steps, relax_fmax
• bicrystal: grain_size, interface_axis, rotation_angle, rotation_axis, interface_gap
• polycrystal: num_grains, grain_size, rotation_angle

Optimization options

optimize_structure_workflow exposes:

• max_steps, fmax (convergence)
• maxstep, alpha (BFGS step/damping controls)
• constraints (fixed_atoms, fixed_bonds, fixed_cell)

Single-point calculations

single_point_workflow computes energy, forces, and stress (if periodic) without modifying the structure, making it suitable for quick evaluations.

MD integrators / ensembles

run_md_workflow supports:

• velocityverlet / nve (NVE)
• langevin / nvt-langevin (NVT)
• nvt / nvt-berendsen (NVT)

Tune temperature_K, friction, and taut to control thermostat behavior.

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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.