atomli.atoms

Generated from the public Python surface of Atomli 0.1.4.

`Atoms(symbols=None, positions=None, cell=None, pbc=None, charge=0.0, unpaired=0)`

A collection of atoms. ASE method surface (properties via Python).

`center(self, /, vacuum=None, axis=None)`

Center atoms (in place). Optional vacuum in angstrom along axes.

vacuum: Vacuum padding in angstrom, or None. axis: Which axes to center; True/False or length-3 sequence.

`copy(self, /)`

`get_atomic_numbers(self, /)`

`get_calculator(self, /)`

`get_cell(self, complete=False)`

The cell, as ASE returns it: detached, but geometry-aware.

ASE’s get_cell returns an ase.cell.Cell, not a bare array, and code relies on it — ase.filters.FrechetCellFilter calls get_cell() and then asks for .volume. complete=True fills zero vectors with unit normals, matching ASE.

`get_center_of_mass(self, /)`

Center of mass in angstrom, shape (3,).

`get_chemical_formula(self, /)`

Hill-system chemical formula string (e.g. "H2O").

`get_chemical_symbols(self, /)`

`get_distance(self, /, a0, a1, mic=False)`

Distance between two atoms in angstrom.

a0: First atom index. a1: Second atom index. mic: Use minimum-image convention when True.

`get_forces(self, /, apply_constraint=True, md=False)`

`get_initial_charges(self, /)`

`get_initial_magnetic_moments(self, /)`

`get_kinetic_energy(self, /)`

`get_masses(self, /)`

`get_momenta(self, /)`

Momenta as mass times ASE velocity units, shape (n, 3).

Numerically identical to ASE Atoms.get_momenta().

`get_pbc(self, /)`

`get_positions(self, /)`

`get_potential_energy(self, /, force_consistent=False, apply_constraint=True)`

`get_scaled_positions(self, /, wrap=True)`

Fractional (scaled) positions, shape (n, 3). Needs a cell.

wrap: Wrap into the cell along the periodic directions. ASE defaults to True, so atomli does too: without it a periodic structure silently reports coordinates outside [0, 1).

`get_stress(self, /, voigt=True, apply_constraint=True, include_ideal_gas=False)`

`get_tags(self, /)`

Integer tags per atom, shape (n,).

`get_temperature(self, /)`

`get_total_energy(self, /)`

`get_velocities(self, /)`

`get_volume(self, /)`

Unit-cell volume in angstrom^3.

Matches ASE: with fewer than three lattice vectors the volume is not defined and this raises ValueError. Returning zero instead would turn the error into a silent division by zero downstream.

`repeat(self, /, rep)`

`set_calculator(self, value=None)`

`set_cell(self, /, cell, scale_atoms=False, *, pbc=None)`

`set_constraint(self, constraint=None)`

`set_initial_charges(self, /, charges)`

`set_initial_magnetic_moments(self, /, moments)`

`set_masses(self, /, masses)`

`set_momenta(self, /, momenta)`

Set ASE-compatible momenta; updates velocities.

`set_pbc(self, /, pbc)`

`set_positions(self, /, positions)`

`set_scaled_positions(self, /, scaled)`

Set fractional positions (requires a cell).

`set_tags(self, /, tags)`

Replace integer tags (length n).

`set_velocities(self, /, velocities)`

`wrap(self, /)`

Wrap positions into the unit cell (in place). Needs PBC cell.