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Add assign_magmoms=True keyword to StructOptimizer.relax()#124

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janosh merged 4 commits intomainfrom
relax-assign-magmom-kwarg
Feb 18, 2024
Merged

Add assign_magmoms=True keyword to StructOptimizer.relax()#124
janosh merged 4 commits intomainfrom
relax-assign-magmom-kwarg

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@janosh janosh commented Feb 18, 2024

f347536 update pre-commit and site/package.json deps
9c0b453 swap metrics table of full WBM test set for one restricted to unique+novel WBM prototypes
7409cf8 add assign_magmoms=True keyword to StructOptimizer.relax()
1d59310 cover assign_magmoms: True | False in test_relaxation()

Reason

magmoms and phonopy don't go great together. Makes using chgnet with phonopy more difficult.
phonopy just bails when trying to determine symmetry on structures with magmoms (even though afaik spglib, which phonopy uses, handles magmoms just fine). symmetry is needed to generate efficient structure deformations.

2024-02-18 17:32:08,008 INFO generate_phonon_displacements failed with exception:
Traceback (most recent call last):
  File "jobflow/managers/local.py", line 114, in _run_job
    response = job.run(store=store)
               ^^^^^^^^^^^^^^^^^^^^
  File "jobflow/core/job.py", line 583, in run
    response = function(*self.function_args, **self.function_kwargs)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "atomate2/src/atomate2/common/jobs/phonons.py", line 162, in generate_phonon_displacements
    phonon = Phonopy(
             ^^^^^^^^
  File "phonopy/api_phonopy.py", line 171, in __init__
    self._primitive_matrix = self._set_primitive_matrix(primitive_matrix)
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "phonopy/api_phonopy.py", line 3794, in _set_primitive_matrix
    return guess_primitive_matrix(self._unitcell, symprec=self._symprec)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "phonopy/structure/cells.py", line 1693, in guess_primitive_matrix
    raise RuntimeError(msg)
RuntimeError: Can not be used with the unit cell having magnetic moments.

@janosh janosh added api Application programming interface relax Structure optimization magmom Magnetism related labels Feb 18, 2024
janosh
janosh commented Feb 18, 2024
View reviewed changes
chgnet/model/dynamics.py
loginterval: int | None = 1,
crystal_feas_save_path: str | None = None,
verbose: bool = True,
assign_magmoms: bool = True,
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@janosh janosh Feb 18, 2024 •
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@BowenD-UCB let me know if assign_magmoms makes sense or you'd like a different name or API here

@janosh janosh merged commit 6dbd335 into main Feb 18, 2024
@janosh janosh deleted the relax-assign-magmom-kwarg branch February 18, 2024 17:45
@janosh janosh added the enhancement New feature or request label Mar 11, 2024
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