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Merged
merged 4 commits into from
Jan 9, 2025
Merged

AseAtomsAdaptor: Support arbitrary selective dynamics constraints #4229

merged 4 commits into from
Jan 9, 2025

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yantar92
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@yantar92 yantar92 commented Dec 17, 2024 •
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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

@yantar92
AseAtomsAdaptor: Support arbitrary selective dynamics constraints
61c3055 
* src/pymatgen/io/ase.py (AseAtomsAdaptor.get_atoms): Use FixCartesian
constraint instead of FixAtoms.  FixCartesian can constrain individual
coordinates and directly map selective dynamics settings.
(AseAtomsAdaptor.get_structure): Add mapping from FixCartesian
constraint to selective dynamics.
@jmmshn
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jmmshn commented Dec 26, 2024

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
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yantar92 commented Dec 27, 2024 •
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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.

@yantar92
AseAtomsAdaptor.get_atoms: Fix failing tests
881a89c 
* src/pymatgen/io/ase.py (AseAtomsAdaptor.get_atoms): Make sure that
old tests are not failing.  Never create empty constraints.  Prefer
using FixAtoms when possible (as in the past).
@yantar92
Add new tests for converting selective dynamics in Ase/Structure
9294dfa 
* tests/io/test_ase.py (test_get_atoms_from_structure_dyn)
(test_get_structure_dyn): Test mixed coordinate constraint.
@yantar92
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yantar92 commented Jan 7, 2025

I added new tests now.

@shyuep shyuep merged commit 4be17da into materialsproject:master Jan 9, 2025
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shyuep commented Jan 9, 2025

Thanks.

@yantar92 yantar92 mentioned this pull request Apr 10, 2025
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@shyuep shyuep Awaiting requested review from shyuep shyuep is a code owner

@mkhorton mkhorton Awaiting requested review from mkhorton mkhorton is a code owner

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@yantar92 @jmmshn @shyuep