logical error in isolated atom identification

[sandipde]

At present any configuration with one atom is being ignored unless they are IsolatedAtom. https://github.com/ACEsuit/mace/blob/68f1bd462ef96aa953310fb07e3abceb3b004ff8/mace/data/utils.py#L221C13-L221C13
@davkovacs @ilyes319

I would propose just to use

        for idx, atoms in enumerate(atoms_list):
            isolated_atom_config =False

            if len(atoms) == 1:
                isolated_atom_config = atoms.info.get("config_type") == "IsolatedAtom"
                if isolated_atom_config:
                    if energy_key in atoms.info.keys():
                        atomic_energies_dict[
                            atoms.get_atomic_numbers()[0]
                        ] = atoms.info[energy_key]
                    else:
                        logging.warning(
                            f"Configuration '{idx}' is marked as 'IsolatedAtom' "
                            "but does not contain an energy."
                        )
            else:

        if not isolated_atom_config: atoms_without_iso_atoms.append(atoms)

        if len(atomic_energies_dict) > 0:
            logging.info("Using isolated atom energies from training file")

        atoms_list = atoms_without_iso_atoms

[sandipde]

I believe this is better. tested. works fine

    if extract_atomic_energies:
        atoms_without_iso_atoms = []

        for idx, atoms in enumerate(atoms_list):
            isolated_atom_config = atoms.info.get("config_type") == "IsolatedAtom"
            #if len(atoms) == 1:
            if isolated_atom_config:
                if energy_key in atoms.info.keys():
                    atomic_energies_dict[
                        atoms.get_atomic_numbers()[0]
                    ] = atoms.info[energy_key]
                else:
                    logging.warning(
                        f"Configuration '{idx}' is marked as 'IsolatedAtom' "
                        "but does not contain an energy."
                    )
            else:
                atoms_without_iso_atoms.append(atoms)

        if len(atomic_energies_dict) > 0:
            logging.info("Using isolated atom energies from training file")

        atoms_list = atoms_without_iso_atoms