Atoms

Atoms is Atomli’s central data object. It stores chemical identities, Cartesian positions, the simulation cell, periodic boundary flags, arrays, constraints, and an attached calculator.

Construct atoms

from atomli import Atoms

water = Atoms(
    "H2O",
    positions=[
        [0.96, 0.00, 0.00],
        [-0.24, 0.93, 0.00],
        [0.00, 0.00, 0.00],
    ],
)

Chemical formulas use ASE-style grammar. Positions are Cartesian coordinates in angstrom.

Periodic systems

silicon = Atoms(
    "Si2",
    positions=[[0, 0, 0], [1.3575, 1.3575, 1.3575]],
    cell=[5.43, 5.43, 5.43],
    pbc=True,
)

pbc accepts one Boolean or a three-axis mask.

Geometry and arrays

Use familiar methods such as get_positions(), set_positions(), get_cell(), get_atomic_numbers(), get_chemical_symbols(), and get_chemical_formula(). Unsupported ASE behavior raises NotImplementedError instead of returning an approximate or silently wrong value.

Attach a calculator

from atomli.calculators.xtb import XTB

water.calc = XTB(method="gfn2")
print(water.get_potential_energy())

An ASE Python calculator assigned to Atomli Atoms is adapted internally.