def _get_fragments_atom_ids(self):
        fragments_atom_ids = []
        for fragment_name, fragment in self.fragments():
            fragment_atomgroup = fragment.get_AtomGroup()
            fragment_atomgroup *= pdf.ANG2AU  # angstrom -> a.u.
            fragment_atom_list = fragment_atomgroup.get_atom_list()
            atom_id_list = []
            for atom in fragment_atom_list:
                atom_id = int(self.pdfparam.find_atom_index(atom))
                if atom_id == -1:
                    logger.critical("not found atom index: {}".format(str(atom)))
                atom_id_list.append(atom_id)
            fragments_atom_ids.append(atom_id_list)
        return fragments_atom_ids