xnn.common.data.ase_io.atoms_to_structure#

xnn.common.data.ase_io.atoms_to_structure(atoms, energy_key='energy', forces_key='forces', stress_key='stress')[source]#

Convert one ASE Atoms object to an xnn structure dict.

Geometry (positions, atomic numbers, cell, pbc) is always extracted; positions are taken as-is (the neighbor-list builder handles unwrapped coordinates). Targets are added when available: with the default key names, first from the attached calculator (get_potential_energy / get_forces / get_stress), then from atoms.info["energy"] / atoms.arrays["forces"] / atoms.info["stress"]. A non-default key selects that entry of info / arrays instead (e.g. MACE-convention REF_energy / REF_forces / REF_stress). Stress is converted to a full (3, 3) matrix.

Parameters:

atoms (ase.Atoms) – The structure to convert.
energy_key (str, optional) – Name of the reference energy in atoms.info.
forces_key (str, optional) – Name of the reference forces in atoms.arrays.
stress_key (str, optional) – Name of the reference stress in atoms.info.

Returns:

Structure dict with keys "pos", "atomic_numbers", "cell" (None for non-periodic frames), "pbc", and optionally "energy", "forces", "stress", "dipole" (from atoms.info["dipole"] or atoms.info["dipole_moment"]), "polarizability" (from atoms.info["polarizability"]), "total_charge" (from atoms.info["total_charge"] or atoms.info["charge"]), "charges" (from atoms.arrays["charges"], reference partial charges), "fragment_charges" (from atoms.arrays["fragment_charges"], the net charge of each atom’s fragment), "spin_multiplicity" (from atoms.info["spin_multiplicity"] or atoms.info["multiplicity"]), the loss weights "weight", "energy_weight", "force_weight" and "stress_weight" (from the same keys of atoms.info) and "atom_force_weight" (from atoms.arrays["atom_force_weight"]).

Return type:

dict