Avoid symmetry complex-cast warnings

ThermoScreening/thermo/system.py

@@ -1,7 +1,9 @@
 import logging
+import warnings
 import numpy as np
 
 from beartype.typing import List
+from numpy.exceptions import ComplexWarning
 
 from pymatgen.core import Molecule, Structure
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
@@ -15,6 +17,48 @@
 from .cell import Cell
 
 
+def _real_position(position: np.ndarray) -> np.ndarray:
+    """
+    Return a real floating-point atom position for symmetry analysis.
+    """
+
+    real_position = np.real_if_close(np.asarray(position))
+    if np.iscomplexobj(real_position):
+        if not np.allclose(np.imag(real_position), 0.0):
+            raise TSValueError("Atom positions must be real-valued.")
+        real_position = np.real(real_position)
+
+    return np.asarray(real_position, dtype=float)
+
+
+def _molecule_from_atoms(atoms: List[Atom]) -> Molecule:
+    """
+    Build a pymatgen molecule with real-valued coordinates.
+    """
+
+    names = []
+    coordinates = []
+    for atom in atoms:
+        names.append(atom.symbol)
+        coordinates.append(_real_position(atom.position))
+
+    return Molecule(names, coordinates)
+
+
+def _point_group_analyzer(molecule):
+    """
+    Build a pymatgen point-group analyzer without surfacing benign cast warnings.
+    """
+
+    with warnings.catch_warnings():
+        warnings.filterwarnings(
+            "ignore",
+            category=ComplexWarning,
+            module=r"pymatgen\.core\.operations",
+        )
+        return PointGroupAnalyzer(molecule)
+
+
 def linearity(atoms: List[Atom]) -> bool:
     """
     Checks if the system is linear or non-linear.
@@ -197,14 +241,8 @@ def rotational_symmetry_number(atoms: List[Atom]) -> int:
     int
         The symmetry number of the system.
     """
-    name = []
-    coord = []
-    for atom in atoms:
-        name.append(atom.symbol)
-        coord.append(atom.position)
-
-    mol = Molecule(name, coord)
-    symmetry_number = PointGroupAnalyzer(mol).get_rotational_symmetry_number
+    mol = _molecule_from_atoms(atoms)
+    symmetry_number = _point_group_analyzer(mol).get_rotational_symmetry_number
     if callable(symmetry_number):
         return symmetry_number()
     return symmetry_number
@@ -285,14 +323,8 @@ def rotational_group_calc(atoms: List[Atom]) -> str:
     str
         The rotational group of the system.
     """
-    name = []
-    coord = []
-    for atom in atoms:
-        name.append(atom.symbol)
-        coord.append(atom.position)
-
-    mol = Molecule(name, coord)
-    symb = PointGroupAnalyzer(mol).sch_symbol
+    mol = _molecule_from_atoms(atoms)
+    symb = _point_group_analyzer(mol).sch_symbol
     return symb
 
 

tests/thermo/test_system.py

@@ -1,4 +1,5 @@
 import unittest
+import warnings
 import numpy as np
 from ase.atoms import Atoms
 import ThermoScreening.thermo.system as system_module
@@ -44,6 +45,69 @@ def __init__(self, molecule):
     assert rotational_symmetry_number(atoms) == 7
 
 
+def test_symmetry_analysis_converts_zero_imaginary_positions(monkeypatch):
+    captured_coordinates = []
+
+    class FakePointGroupAnalyzer:
+        sch_symbol = "D*h"
+
+        def __init__(self, molecule):
+            self.molecule = molecule
+            self.get_rotational_symmetry_number = 2
+            captured_coordinates.append(np.array(molecule.cart_coords))
+
+    atoms = [
+        Atom(symbol="H", position=np.array([0.0 + 0.0j, 0.0, 0.0])),
+        Atom(symbol="H", position=np.array([1.0 + 0.0j, 0.0, 0.0])),
+    ]
+    monkeypatch.setattr(system_module, "PointGroupAnalyzer", FakePointGroupAnalyzer)
+
+    assert rotational_symmetry_number(atoms) == 2
+    assert system_module.rotational_group_calc(atoms) == "D*h"
+    assert not np.iscomplexobj(captured_coordinates[0])
+    assert not np.iscomplexobj(captured_coordinates[1])
+
+
+def test_real_position_converts_near_zero_imaginary_noise():
+    position = system_module._real_position(np.array([1.0 + 1e-12j, 0.0, 0.0]))
+
+    np.testing.assert_array_equal(position, np.array([1.0, 0.0, 0.0]))
+    assert not np.iscomplexobj(position)
+
+
+def test_point_group_analyzer_suppresses_pymatgen_complex_warning(monkeypatch):
+    class FakePointGroupAnalyzer:
+        sch_symbol = "C1"
+
+        def __init__(self, molecule):
+            self.molecule = molecule
+            warnings.warn_explicit(
+                "Casting complex values to real discards the imaginary part",
+                system_module.ComplexWarning,
+                filename="operations.py",
+                lineno=1,
+                module="pymatgen.core.operations",
+            )
+
+    monkeypatch.setattr(system_module, "PointGroupAnalyzer", FakePointGroupAnalyzer)
+
+    with warnings.catch_warnings():
+        warnings.simplefilter("error", system_module.ComplexWarning)
+        analyzer = system_module._point_group_analyzer(object())
+
+    assert analyzer.sch_symbol == "C1"
+
+
+def test_symmetry_analysis_rejects_imaginary_positions():
+    atoms = [
+        Atom(symbol="H", position=np.array([0.0 + 1.0j, 0.0, 0.0])),
+        Atom(symbol="H", position=np.array([1.0, 0.0, 0.0])),
+    ]
+
+    with pytest.raises(TSValueError, match="Atom positions must be real-valued"):
+        rotational_symmetry_number(atoms)
+
+
 class TestSystem(unittest.TestCase):
     atoms = [
                 Atom(symbol='H', position=np.array([0, 0, 0])),