label in Structure.as_dict() is None in the latest version

[njzjz]

Description

The latest version gives the 'label': None in Structure.as_dict(). I want to confirm if it is expected, as it breaks the tests in our downstream package.

Repro

from pymatgen.core import Structure
import numpy as np
s = Structure(np.eye(3), ["H"], np.zeros((1, 3)), coords_are_cartesian=True)
print(s.as_dict())

{'@module': 'pymatgen.core.structure', '@class': 'Structure', 'charge': 0, 'lattice': {'matrix': [[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]], 'pbc': (True, True, True), 'a': 1.0, 'b': 1.0, 'c': 1.0, 'alpha': 90.0, 'beta': 90.0, 'gamma': 90.0, 'volume': 1.0}, 'sites': [{'species': [{'element': 'H', 'occu': 1}], 'abc': [0.0, 0.0, 0.0], 'xyz': [0.0, 0.0, 0.0], 'label': None, 'properties': {}}]}

Expected behavior

In previous versions, label is H.

Environment

Relevant versions and platform info:

• OS: Linux
• Version 2023.7.17

Additional context

[janosh]

@njzjz Thanks for reporting. This is not intended.

This was caused by #3135. @stefsmeets Could you take a look? label should still be H here.

[stefsmeets]

Thanks for pinging me!

I added Site.label is a new attribute (default None), so it was never 'H' to begin with unless explicitly set by the user or any code that uses it. So this behaviour is as expected (or at least the way intended).

I can submit a PR to set the default to the species name if that is more sensible.

[stefsmeets]

Ah, I found the culprit:

pymatgen/pymatgen/core/sites.py

Lines 586 to 591 in 80aa781

	if verbosity > 0:
	dct["xyz"] = [float(c) for c in self.coords]
	dct["label"] = self.species_string
	dct["properties"] = self.properties
	dct["label"] = self.label

Structure.as_dict() writes with verbosity=1, which adds "label" to the dict. This causes a name collision with the .label property.