SpacegroupAnalyzer.get_symmetrized_structure() raises TypeError

[janosh]

Using pymatgen master @ dd884cf and spglib v2.0.2:

import spglib
from pymatgen.core import Structure
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer

print(f"{spglib.__version__=}")

struct = Structure.from_str('{"@module": "pymatgen.core.structure", "@class": "Structure", "charge": 0.0, "lattice": {"matrix": [[3.6062699446, 0.0, -0.8583713603], [-0.20223522530000002, 3.6005949268, -0.8583713603], [0.0, 0.0, 7.98790154]], "pbc": [true, true, true], "a": 3.7070182499562314, "b": 3.7070182499460818, "c": 7.98790154, "alpha": 103.38852319946483, "beta": 103.3885231994275, "gamma": 89.96878548961709, "volume": 103.72064305511611}, "sites": [{"species": [{"element": "Co", "occu": 1.0}], "abc": [0.626832, 0.626832, 0.253544], "xyz": [2.1337578911682575, 2.2569681191558972, 0.9491752350186207], "label": "Co", "properties": {}}, {"species": [{"element": "Co", "occu": 1.0}], "abc": [0.373168, 0.373168, 0.746456], "xyz": [1.2702768281317425, 1.3436268076441025, 5.321983584381379], "label": "Co", "properties": {}}, {"species": [{"element": "Co", "occu": 1.0}], "abc": [0.5, 0.0, 0.0], "xyz": [1.8031349723, 0.0, -0.42918568015], "label": "Co", "properties": {}}, {"species": [{"element": "Co", "occu": 1.0}], "abc": [0.0, 0.5, 0.0], "xyz": [-0.10111761265000001, 1.8002974634, -0.42918568015], "label": "Co", "properties": {}}, {"species": [{"element": "Co", "occu": 1.0}], "abc": [0.749935, 0.250065, 0.5], "xyz": [2.6538960992889566, 0.900382770370242, 3.1355794097], "label": "Co", "properties": {}}, {"species": [{"element": "Co", "occu": 1.0}], "abc": [0.250065, 0.749935, 0.5], "xyz": [0.7501386200110435, 2.700212156429758, 3.1355794097], "label": "Co", "properties": {}}, {"species": [{"element": "Co", "occu": 1.0}], "abc": [0.879784, 0.879784, 0.759311], "xyz": [2.9948152814846316, 3.167745807079811, 4.554938728538589], "label": "Co", "properties": {}}, {"species": [{"element": "Co", "occu": 1.0}], "abc": [0.12021599999999999, 0.12021599999999999, 0.240689], "xyz": [0.4092194378153688, 0.43284911972018875, 1.7162200908614103], "label": "Co", "properties": {}}]}', fmt="json")

spg_analyzer = SpacegroupAnalyzer(struct, symprec=0.1, angle_tolerance=5)
sym_struct = spg_analyzer.get_symmetrized_structure()
>>> TypeError: 'NoneType' object is not subscriptable

stack trace

TypeError                                 Traceback (most recent call last)
/Users/janosh/dev/matbench-discovery/tmp/spglib_None_symmtries.py in line 6
      9 struct = Structure.from_file("2-12269.json")
      12 spg_analyzer = SpacegroupAnalyzer(struct, symprec=0.1, angle_tolerance=5)
----> 13 sym_struct = spg_analyzer.get_symmetrized_structure()

File ~/dev/pmg/pymatgen/symmetry/analyzer.py:285, in SpacegroupAnalyzer.get_symmetrized_structure(self)
    275 """Get a symmetrized structure. A symmetrized structure is one where the sites
    276 have been grouped into symmetrically equivalent groups.
    277 
    278 Returns:
    279     :class:`pymatgen.symmetry.structure.SymmetrizedStructure` object.
    280 """
    281 ds = self.get_symmetry_dataset()
    282 sg = SpacegroupOperations(
    283     self.get_space_group_symbol(),
    284     self.get_space_group_number(),
--> 285     self.get_symmetry_operations(),
    286 )
    287 return SymmetrizedStructure(self._structure, sg, ds["equivalent_atoms"], ds["wyckoffs"])

File ~/dev/pmg/pymatgen/symmetry/analyzer.py:240, in SpacegroupAnalyzer.get_symmetry_operations(self, cartesian)
    233 def get_symmetry_operations(self, cartesian=False):
    234     """Return symmetry operations as a list of SymmOp objects. By default returns
...
--> 225 for t in d["translations"]:
    226     trans.append([float(Fraction.from_float(c).limit_denominator(1000)) for c in t])
    227 trans = np.array(trans)

TypeError: 'NoneType' object is not subscriptable