Future Compatibility - drop pyiron_atomistics atoms in favor of ASE atoms #5
Description
It would be great if these new developments no longer require pyiron_atomistics Atoms objects but rather work with ASE atoms objects. Many of the commonly used conversion functions are available in https://github.com/pyiron/structuretoolkit/blob/main/structuretoolkit/common/helper.py . Some additional ones are included in https://github.com/pyiron/pyiron_vasp and https://github.com/pyiron/pyiron_lammps . For LAMMPS calculation we already have a Python function representation pyiron/pyiron_atomistics#1472 . This functionality is already actively used in projects like https://github.com/glasagent . While the LAMMPS function is currently only available in pyiron_atomistics the goal is to transition this to pyiron_lammps in the future. At that stage there would no longer be a dependency on pyiron_base and the same workflow could also be represented with pyiron_core or pyiron_workflow. The change that was introduced with the LAMMPS function is that it works with ASE atoms rather than pyiron_atomistics atoms. So it would be great if also in this package the pyiron_atomistics atoms could be dropped in favor of ASE atoms.
The same transition is also planned for VASP calculation. A basic Python function interface was proposed in pyiron/pyiron_atomistics#1473 and it is going to be transferred to pyiron_vasp to remove the dependence on pyiron_base.