Get started

The quickest way to use MLatom is to run it online on the Aitomistic Hub or Aitomistic Lab@XMU — nothing to install. To run locally, just install MLatom — it pulls in the required dependencies automatically (including the PyTorch/TorchANI and geometry-optimization backends the AIQM2 example below uses). AIQM2 additionally needs the DFT-D4 program (via conda):

pip install -U mlatom
conda install -c conda-forge dftd4
export dftd4bin=$(which dftd4)   # point MLatom at the dftd4 executable

From MLatom 3.25.0 on, any dftd4 version gives the same energies for AIQM1, AIQM2, OMNI-P1 and the ANI -D4 models, because MLatom sets the D4 damping parameters itself instead of selecting them by functional name. Pick dftd4 3.5.0 if you need Hessians, i.e. frequencies and thermochemistry.

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.

Python API

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

To check your setup worked, the printed energy should be approximately:

-76.3838

Command line (input file)

The same calculation from the command line. Save the geometry as init.xyz:

3

O    0.00000    0.00000    0.11779
H    0.00000    0.75545   -0.47116
H    0.00000   -0.75545   -0.47116

and the input as geomopt.inp:

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

then run:

mlatom geomopt.inp

The optimized geometry is written to opt.xyz, and the output reports the optimized energy (≈ -76.3838 hartree). You can also download geomopt.inp and init.xyz.

Note

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