AseAtomsAdaptor: Support arbitrary selective dynamics constraints

[yantar92]

Summary

Major changes:

• Implement full selective_dynamics support when converting to/from ASE atoms.

Todos

If this is work in progress, what else needs to be done?

• I need directions to add tests.

Checklist

• Google format doc strings added. Check with ruff.
• Type annotations included. Check with mypy.
• Tests added for new features/fixes.
• If applicable, new classes/functions/modules have duecredit @due.dcite decorators to reference relevant papers by DOI (example)

Tip: Install pre-commit hooks to auto-check types and linting before every commit:

pip install -U pre-commit
pre-commit install

[jmmshn]

Hi @yantar92,

I need directions to add tests.

You can use this example here:

pymatgen/tests/io/test_ase.py

Lines 186 to 203 in da607e8

	def test_get_structure_dyn(select_dyn):
	atoms = ase.io.read(f"{VASP_IN_DIR}/POSCAR")
	atoms.set_constraint(ase.constraints.FixAtoms(mask=[True] * len(atoms)))
	structure = AseAtomsAdaptor.get_structure(atoms)
	assert structure.site_properties["selective_dynamics"][-1][0] is False
	structure = Structure(
	lattice=Lattice.cubic(5),
	species=("Fe", "O"),
	coords=((0, 0, 0), (0.5, 0.5, 0.5)),
	site_properties={"selective_dynamics": select_dyn},
	)
	structure.sites[0].selective_dynamics = select_dyn
	# mostly testing that this call doesn't raise
	ase_atoms = AseAtomsAdaptor.get_atoms(structure)
	assert len(ase_atoms) == len(structure)

Also can you detail how this is different than the existing set_constraint method? It looks like some ase classes being used there changed, does this change require an update to the ASE version?

[yantar92]

Also can you detail how this is different than the existing set_constraint method? It looks like some ase classes being used there changed, does this change require an update to the ASE version?

I replaced FixAtoms ASE constraint with FixCartesian. FixCartesian allows fixing individual coordinates while FixAtoms fixes everything.

FixCartesian: https://gitlab.com/ase/ase/-/blob/master/ase/constraints.py?ref_type=heads#L835
FixAtoms: https://gitlab.com/ase/ase/-/blob/master/ase/constraints.py?ref_type=heads#L208

FixCartesian thus provides everything needed to implement "selective dynamics" from VASP. It is a strict superset of FixAtoms.

FixCartesian is available in ASE since forever (introduced in e2e1799d5, 16 years ago). There should be no issues with compatibility.