BUG: Clear charge cache before (re-?)building

openff/interchange/_tests/unit_tests/smirnoff/test_create.py

@@ -281,13 +281,11 @@ def test_virtual_site_charge_increments_applied_after_preset_charges_water(
         )
 
         with pytest.warns(PresetChargesAndVirtualSitesWarning):
-            out = tip4p.create_interchange(
+            # This dict is probably ordered O H H VS
+            charges = tip4p.create_interchange(
                 water.to_topology(),
                 charge_from_molecules=[water],
-            )
-
-        # This dict is probably ordered O H H VS
-        charges = out["Electrostatics"].charges
+            )["Electrostatics"].charges
 
         # tip4p_fb.offxml is meant to result in charges of -1.0517362213526 (VS) 0 (O) and 0.5258681106763 (H)
         # the force field has 0.0 for all library charges (skipping AM1-BCC), so preset charges screw this up.
@@ -300,9 +298,6 @@ def test_virtual_site_charge_increments_applied_after_preset_charges_water(
             [-2.0, 1.5258681106763001, 1.5258681106763001, -1.0517362213526],
         )
 
-        # The cache seems to leak charges between tests
-        out["Electrostatics"]._charges.clear()
-
     def test_virtual_site_charge_increments_applied_after_preset_charges_ligand(
         self,
         sage_with_sigma_hole,
@@ -314,13 +309,12 @@ def test_virtual_site_charge_increments_applied_after_preset_charges_ligand(
             "elementary_charge",
         )
 
-        out = sage_with_sigma_hole.create_interchange(
-            ligand.to_topology(),
-            charge_from_molecules=[ligand],
-        )
-
-        # This dict is probably ordered C Cl Cl Cl Cl VS VS VS VS
-        charges = out["Electrostatics"].charges
+        with pytest.warns(PresetChargesAndVirtualSitesWarning):
+            # This dict is probably ordered C Cl Cl Cl Cl VS VS VS VS
+            charges = sage_with_sigma_hole.create_interchange(
+                ligand.to_topology(),
+                charge_from_molecules=[ligand],
+            )["Electrostatics"].charges
 
         # this fake sigma hole parameter shifts 0.1 e from the carbon and 0.2 e from the chlorine, so the
         # resulting charges should be like
@@ -332,9 +326,6 @@ def test_virtual_site_charge_increments_applied_after_preset_charges_ligand(
             [1.6, -0.1, -0.1, -0.1, -0.1, -0.3, -0.3, -0.3, -0.3],
         )
 
-        # The cache seems to leak charges between tests
-        out["Electrostatics"]._charges.clear()
-
 
 @skip_if_missing("openmm")
 class TestPartialBondOrdersFromMolecules:

openff/interchange/smirnoff/_nonbonded.py

@@ -304,6 +304,19 @@ def charges(
     ) -> dict[TopologyKey | LibraryChargeTopologyKey | VirtualSiteKey, _ElementaryChargeQuantity]:
         """Get the total partial charge on each atom, including virtual sites."""
         if len(self._charges) == 0 or self._charges_cached is False:
+            # TODO: Clearing this dict **should not be necessary** but in some cases in appears
+            #       that this class attribute persists in some cases, possibly only on a single
+            #       thread. Ideas to try include
+            #           * Drop @computed_field ?
+            #           * Don't handle caching ourselves and let Pydantic do it (i.e. have this
+            #               function simply retrun ._get_charges(...)
+            #
+            #       Hopefully this isn't a major issue - caches for large systems should still
+            #       only be build once
+            #
+            #       Some more context: https://github.com/openforcefield/openff-interchange/issues/842#issuecomment-2394211357
+            self._charges.clear()
+
             self._charges.update(self._get_charges(include_virtual_sites=True))
             self._charges_cached = True