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 and importing structures,
• editing cells (strain, supercell) and defects (vacancy, substitution, interstitial),
• running geometry optimization + NVE/NVT/NPT molecular dynamics,
• estimating bulk modulus,
• 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
• Structure import from xyz/cif/POSCAR text
• Edits and defects: rotate, translate, strain, supercell, wrap, vacancy, substitute, interstitial
• Calculators: auto tries kim → orb → nequix → ASE EMT (Al/Cu/Ag/Au/Ni/Pd/Pt)
• Optimization and single-point energy/forces/stress
• Molecular dynamics: Velocity Verlet, Langevin, NVT Berendsen, NPT Berendsen
• Recipe tool relax_and_md_workflow (relax then MD)
• Isotropic bulk modulus from a 5-point energy-vs-strain fit
• Analysis outputs: RDF + coordination, MSD + thermo trends, VACF + diffusion
• 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

Core install does not require the OpenKIM C++ API:

pip install -r requirements.txt

or:

pip install -e .

OpenKIM (kimpy) is optional. It compiles against the system KIM API, so a default install used to fail on machines without libkim-api.

To enable the KIM calculator:

# Debian/Ubuntu
sudo apt-get install -y libkim-api-dev pkg-config

pip install -e ".[kim]"

macOS (Homebrew): brew install openkim-models kim-api then pip install -e ".[kim]".

Without the extra, use calculator_name='auto', 'emt', 'orb', or 'nequix'. Runtime code already falls back when KIM is missing. EMT covers Al, Cu, Ag, Au, Ni, Pd, and Pt.

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:

• list_workspace_capabilities_workflow
• build_structure_workflow
• import_structure_workflow
• manipulate_structure_workflow
• analyze_structure_workflow
• write_structure_workflow
• optimize_structure_workflow
• single_point_workflow
• estimate_elastic_workflow
• run_md_workflow
• relax_and_md_workflow
• analyze_trajectory_workflow
• autocorrelation_workflow

Legacy aliases are also registered: build_structure, read_structure_file, write_structure_file, optimize_with_mlip.

Call list_workspace_capabilities_workflow first from an agent. It reports which calculators imported, EMT element support, integrators, structure types, and edit operations.

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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

The image installs libkim-api-dev and the optional [kim] extra.

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)

Paste an existing geometry with import_structure_workflow (xyz, cif, or poscar text).

Edits and defects

manipulate_structure_workflow operations:

• rotate, translate, strain, supercell, wrap
• vacancy (operation_kwargs.index)
• substitute (index, symbol)
• interstitial (symbol, optional position)

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 and elasticity

single_point_workflow computes energy, forces, and stress (if periodic).

estimate_elastic_workflow fits E(strain) at five isotropic strains and returns bulk_modulus_GPa plus calculator_used.

MD integrators / ensembles

run_md_workflow supports:

• velocityverlet / nve (NVE)
• langevin / nvt-langevin (NVT)
• nvt / nvt-berendsen (NVT)
• npt / npt-berendsen (NPT; pressure_GPa, taup)

relax_and_md_workflow chains optimization then MD.

Every energy/MD result includes calculator_requested, calculator_used, and calculator_fallbacks so an EMT copper run is not mistaken for an MLIP result.

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📈 GitHub Pulse

Star history

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🤝 Contributing

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

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📄 License

MIT — see LICENSE.