Atomistic Toolkit MCP Server

@XirtamEsrevni

Repository

Basic information

About Atomistic Toolkit MCP Server

An MCP-compatible server providing atomistic simulation capabilities through ASE, pymatgen, etc.

#atomistic#simulation #mcp#ase#pymatgen

Atomistic Toolkit MCP Server config

Add this server to your MCP-compatible client using the configuration below.

{
  "mcpServers": {
    "mcp-atomictoolkit": {
      "command": "python",
      "args": [
        "main.py"
      ]
    }
  }
}

Atomistic Toolkit MCP Server tools

Tool list not available yet

This listing does not currently have a tool list to display. This does not mean the server has no tools; check its documentation for supported capabilities.

We auto-extract tools from the README. The maintainer can list them under a ## Tools heading to populate this section.

Overview

What is Atomistic Toolkit MCP Server?

An MCP (Model Context Protocol) server for atomistic modeling workflows, powered by ASE, pymatgen, and modern machine‑learning interatomic potentials. It exposes ready‑to‑call tools for building structures, running geometry optimization and molecular dynamics, analyzing structures and trajectories, and providing downloadable file artifacts.

How to use Atomistic Toolkit MCP Server?

Requires Python 3.11+. Install dependencies with pip install -r requirements.txt, then start the HTTP server with uvicorn mcp_atomictoolkit.http_app:app --host 0.0.0.0 --port 10000 (or python main.py). For desktop MCP clients, use STDIO mode: python -m mcp_atomictoolkit.mcp_server. Verify with curl -s http://localhost:10000/healthz.

Key features of Atomistic Toolkit MCP Server

MCP‑native workflows via FastMCP tools
Structure generation: bulk, surface, molecule, supercell, amorphous, liquid, bicrystal, polycrystal
Optimization with MLIPs (kim default, nequip, orb)
Molecular dynamics (Velocity Verlet, Langevin, NVT Berendsen)
Analysis: RDF, MSD, VACF (Green‑Kubo), thermodynamic trends
Downloadable artifacts (xyz, extxyz, cif, traj, png, svg, csv, dat)

Use cases of Atomistic Toolkit MCP Server

Automate atomistic simulation workflows without hand‑writing scripts
Run structure building, optimization, and MD from LLM‑based agents or desktop clients
Analyze trajectories for diffusion coefficients and correlation functions
Generate and share simulation artifacts (files + plots) via download URLs

Frequently asked questions

What modes does the server support?

It supports both Streamable HTTP (via uvicorn) and STDIO (for desktop MCP clients). STDIO mode must keep stdout clean of print/logging.

What file formats are available for download?

Artifacts can be downloaded in `.xyz`, `.extxyz`, `.cif`, `.traj`, `.png`, `.svg`, `.csv`, `.dat`, and more.

What endpoints does the server expose?

Primary MCP endpoint is `POST /`. Also includes `GET /healthz`, `GET /docs`, `GET /.well-known/mcp/server-card.json`, `GET /artifacts/{artifact_id}/{filename}`, and `/sse/`.

Can I deploy the server in a container or on Render?

Yes. A `render.yaml` and a `Dockerfile` are provided. Default Docker command runs on port 7860.

What optimization and MD parameters can be tuned?

Optimization supports `max_steps`, `fmax`, `maxstep`, `alpha`, and constraints (fixed atoms, bonds, cell). MD supports `temperature_K`, `friction`, `taut`, and multiple integrators (NVE, NVT‑Langevin, NVT‑Berendsen).

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