MLatom

MLatom is an open-source package for atomistic simulations with machine learning and quantum chemical methods — DFT, wavefunction-based, and semi-empirical approximations. Use it as a Python library, through input files, or from the command line — run it locally, or online with no installation.

Website · Documentation · Protomia · Aitomistic Hub · Aitomistic Lab@XMU · Releases

Run online — no installation

Run MLatom in your browser on either online platform — both powered by Protomia, with an AI assistant for autonomous atomistic simulations:

• Aitomistic Hub — free registration.
• Aitomistic Lab@XMU — free for academic users (registration with an academic email).

Local installation

The easiest way to run MLatom is online — no installation. To install locally:

python3 -m pip install -U mlatom

That pulls in the required dependencies automatically (including the PyTorch/TorchANI and geometry-optimization backends the AIQM2 quick start uses). A few features need one more package — install only what you use:

AIQM2 additionally needs the DFT-D4 program, installed via conda:

conda install -c conda-forge 'dftd4==3.6.0'   # the version MLatom is tested against
export dftd4bin=$(which dftd4)   # point MLatom at the dftd4 executable

See the installation guide for the full dependency list and other methods.

Quick start

Optimize the geometry of a water molecule with AIQM2 — an AI-enhanced quantum-mechanical method (native to MLatom, CHNO elements) that reaches beyond-DFT accuracy at semi-empirical cost:

import mlatom as ml

mol = ml.data.molecule.from_xyz_string('''3

O    0.00000    0.00000    0.11779
H    0.00000    0.75545   -0.47116
H    0.00000   -0.75545   -0.47116
''')
aiqm2 = ml.methods(method='AIQM2')
opt = ml.optimize_geometry(model=aiqm2, initial_molecule=mol).optimized_molecule
print(opt.energy)          # optimized energy in hartree (≈ -76.3838)

The same calculation as an input file (geomopt.inp, with init.xyz holding the geometry):

AIQM2               # method
geomopt             # task: geometry optimization
xyzfile=init.xyz    # input geometry
optxyz=opt.xyz      # output geometry

mlatom geomopt.inp

Prefer zero setup? Run these online on the Aitomistic Hub or Aitomistic Lab@XMU (both powered by Protomia) — no installation needed.

Features & documentation

Full manuals and tutorials are at mlatom.com/docs — begin with installation and get started.

• Methods — universal ML potentials (ANI, AIMNet2); AI-enhanced QM methods (UAIQM, AIQM1, AIQM2) approaching coupled-cluster accuracy at semi-empirical cost; and DFT, semi-empirical, and wavefunction methods via interfaces (PySCF, Gaussian, ORCA, xtb, MNDO, Turbomole, DFTB+, Sparrow, Columbus).
• ML models — train and use ML potentials (KREG, GAP-SOAP, ANI, MACE, and more) with active learning, Δ-learning, transfer learning, and self-correction.
• Simulations — geometry optimization, transition-state search, IRC, frequencies & thermochemistry, molecular dynamics, nonadiabatic dynamics, IR/Raman/UV–vis spectra, and periodic boundary conditions.
• Workflows — compose methods and tasks into complex pipelines from Python, input files, or the command line.

How to cite

If you use MLatom in scientific work, please cite:

Pavlo O. Dral et al. MLatom 3: A Platform for Machine Learning-Enhanced Computational Chemistry Simulations and Workflows. J. Chem. Theory Comput. 2024, 20, 1193–1213. DOI: 10.1021/acs.jctc.3c01203

Feature-specific references appear in the program output and in CITATION.cff. The full list with BibTeX is on the License and citations page.

Ecosystem

• MLatom Skills — agent skills for MLatom (new and growing rapidly).
• Aitomic add-ons — cutting-edge methods (e.g. AIQM3), free for academic, non-commercial use.
• Aitomia — an AI assistant for autonomous atomistic simulations with MLatom.

Recent releases

Full release notes · CHANGELOG.md

• 3.25 — fine-tuning of the universal models on your own data: ANI, AIQM1, AIQM2, AIQM3, UAIQM, OMNI-P1 and OMNI-P2x all through the same train() call, with dispersion handled on both sides so the fine-tuned model keeps the long-range behaviour.
• 3.23 — AIQM3 public add-on (pip install aitomic-addons); direct Gaussian workflows; version/commit/build-date banner with a daily update check.
• 3.22 — OMNI-P2x model; faster nonadiabatic dynamics.
• 3.21 — refactored ORCA interface supporting many more excited-state methods.
• 3.18 — FSSH; MDtrajNet-1 (directly predicting MD trajectories); KRR in Julia; ECTS diffusion model for transition states.

Contributing

Contributions are welcome — see CONTRIBUTING.md and the Code of Conduct. Report bugs and request features via GitHub issues. You may also create your own private derivatives by following the license requirements.

Stay updated

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About

MLatom was founded by Pavlo O. Dral on 10 September 2013, who continues to lead its development. It is open-source under the Apache License 2.0 and supported by Aitomistic.