Add SymmetryUndetermined(ValueError) exception type (materialsproje…

…ct#3872) * Add `SymmetryUndetermined(ValueError)` exception * Add test for `SymmetryUndetermined` * Update docstring for `get_space_group_info` --------- Co-authored-by: Matthew Horton <[email protected]>
gmatteo · Jun 9, 2024 · 624e6eb · 624e6eb
1 parent 735db5b
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Showing 3 changed files with 30 additions and 4 deletions.
diff --git a/pymatgen/core/structure.py b/pymatgen/core/structure.py
@@ -1522,6 +1522,11 @@ def get_space_group_info(
 
         Returns:
             spacegroup_symbol, international_number
+
+        Raises:
+            pymatgen.symmetry.analyzer.SymmetryUndetermined if symmetry cannot
+            be determined. This can happen for numerical reasons, for example if
+            atoms are placed unphysically close together.
         """
         # Avoid circular import
         from pymatgen.symmetry.analyzer import SpacegroupAnalyzer

diff --git a/pymatgen/symmetry/analyzer.py b/pymatgen/symmetry/analyzer.py
@@ -51,12 +51,22 @@
 )
 
 
+class SymmetryUndetermined(ValueError):
+    """
+    An Exception for when symmetry cannot be determined. This might happen
+    when, for example, atoms are very close together.
+    """
+
+
 @lru_cache(maxsize=32)
 def _get_symmetry_dataset(cell, symprec, angle_tolerance):
     """Simple wrapper to cache results of spglib.get_symmetry_dataset since this call is
     expensive.
     """
-    return spglib.get_symmetry_dataset(cell, symprec=symprec, angle_tolerance=angle_tolerance)
+    dataset = spglib.get_symmetry_dataset(cell, symprec=symprec, angle_tolerance=angle_tolerance)
+    if dataset is None:
+        raise SymmetryUndetermined
+    return dataset
 
 
 class SpacegroupAnalyzer:

diff --git a/tests/symmetry/test_analyzer.py b/tests/symmetry/test_analyzer.py
@@ -5,11 +5,17 @@
 import numpy as np
 import pytest
 from numpy.testing import assert_allclose
-from pytest import approx
+from pytest import approx, raises
 
-from pymatgen.core import Molecule, PeriodicSite, Site, Species, Structure
+from pymatgen.core import Lattice, Molecule, PeriodicSite, Site, Species, Structure
 from pymatgen.io.vasp.outputs import Vasprun
-from pymatgen.symmetry.analyzer import PointGroupAnalyzer, SpacegroupAnalyzer, cluster_sites, iterative_symmetrize
+from pymatgen.symmetry.analyzer import (
+    PointGroupAnalyzer,
+    SpacegroupAnalyzer,
+    SymmetryUndetermined,
+    cluster_sites,
+    iterative_symmetrize,
+)
 from pymatgen.symmetry.structure import SymmetrizedStructure
 from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR, VASP_OUT_DIR, PymatgenTest
 
@@ -368,6 +374,11 @@ def test_tricky_structure(self):
         assert spg_analyzer.get_crystal_system() == "tetragonal"
         assert spg_analyzer.get_hall() == "-I 4 2"
 
+    def test_bad_structure(self):
+        struct = Structure(Lattice.cubic(5), ["H", "H"], [[0.0, 0.0, 0.0], [0.001, 0.0, 0.0]])
+        with raises(SymmetryUndetermined):
+            SpacegroupAnalyzer(struct, 0.1)
+
 
 class TestSpacegroup(TestCase):
     def setUp(self):