Geometry optimisation error

[ElliottKasoar]

Summary

Seems to be related to a new update to phonopy, and relates to setting the space group for non-periodic systems:

janus_core/calculations/geom_opt.py:326: in run
    s_grp = spacegroup(self.struct, self.symmetry_tolerance, self.angle_tolerance)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
janus_core/processing/symmetry.py:32: in spacegroup
    return get_spacegroup(
.venv/lib/python3.11/site-packages/spglib/spg.py:482: in get_spacegroup
    _set_or_throw_error(exc)
.venv/lib/python3.11/site-packages/spglib/error.py:117: in _set_or_throw_error
    raise exc
.venv/lib/python3.11/site-packages/spglib/spg.py:475: in get_spacegroup
    dataset = get_symmetry_dataset(
.venv/lib/python3.11/site-packages/spglib/spg.py:452: in get_symmetry_dataset
    _set_or_throw_error(exc, _throw)
.venv/lib/python3.11/site-packages/spglib/error.py:117: in _set_or_throw_error
    raise exc



        lattice, positions, numbers, _ = _expand_cell(cell)
    
        try:
>           spg_ds = _spglib.dataset(
                lattice,
                positions,
                numbers,
                int(hall_number),
                float(symprec),
                float(angle_tolerance),
            )
E           spglib._spglib.SpglibCppError: too close distance between atoms

Platform

3.12

Version

0.8.6

Python version

No response

[ElliottKasoar]

#671 was a temporary solution, so we should figure out why this was happening and unpin phonopy

[ElliottKasoar]

This happens as phonopy now sets spglib.error.OLD_ERROR_HANDLING = True somewhere along the way when we import from phonopy.structure.atoms import PhonopyAtoms in janus_core.helpers.struct_io.

We may want PhonopyAtoms to only be imported with if TYPE_CHECKING, but since this option is being flipped and then deprecated by spglib, we need to handle this separately too quite soon.