Backport fix from PR #473

src/sire/mol/_dynamics.py

@@ -415,6 +415,10 @@ def _exit_dynamics_block(
             self._omm_state = self._omm_mols.getState(getEnergy=True)
             self._omm_state_has_cv = (False, False)
 
+        # dynamics has advanced the positions without going through
+        # setPositions(), so the context's energy cache is stale
+        self._omm_mols.clear_energy_cache()
+
         current_time = (
             self._omm_state.getTime().value_in_unit(openmm.unit.nanosecond) * nanosecond
         )
@@ -481,10 +485,6 @@ def _exit_dynamics_block(
                 nrg_sim_lambda_value = nrg
 
                 if lambda_windows is not None:
-                    # Positions have just changed (dynamics completed), so
-                    # invalidate all cached per-group energies before the scan.
-                    self._omm_mols.clear_energy_cache()
-
                     # get the index of the simulation lambda value in the
                     # lambda windows list
                     try:
@@ -544,10 +544,6 @@ def _exit_dynamics_block(
             self._nrgs = nrgs
             self._nrgs_array = nrgs_array
 
-            # Repex synchronisation point: a peer replica may push new
-            # positions into this context, so the cache must be invalidated.
-            self._omm_mols.clear_energy_cache()
-
             # update the interpolation lambda value
             if self._is_interpolate:
                 if delta_lambda:

tests/mol/test_dynamics.py

@@ -196,3 +196,42 @@ def test_crash_report(merged_ethane_methanol, openmm_platform):
     finally:
         # Change back to the old directory.
         os.chdir(old_dir)
+
+
+@pytest.mark.skipif(
+    "openmm" not in sr.convert.supported_formats(),
+    reason="openmm support is not available",
+)
+def test_energy_cache_cleared_after_dynamics(ala_mols):
+    """
+    The context's energy cache must be invalidated after every dynamics block,
+    not just one that saved energies. The integrator advances the positions
+    without going through setPositions(), so nothing else clears it.
+    """
+    import openmm
+
+    mols = ala_mols
+
+    d = mols.dynamics(timestep="1fs", temperature="300K", platform="Reference")
+
+    def direct():
+        return (
+            d.context()
+            .getState(getEnergy=True)
+            .getPotentialEnergy()
+            .value_in_unit(openmm.unit.kilocalorie_per_mole)
+        )
+
+    assert d.current_potential_energy().value() == pytest.approx(direct())
+
+    # A block that doesn't record an energy.
+    d.run("50fs")
+    assert d.current_potential_energy().value() == pytest.approx(direct())
+
+    # A block that does.
+    d.run("50fs", energy_frequency="10fs")
+    assert d.current_potential_energy().value() == pytest.approx(direct())
+
+    # A block that doesn't, again, now that a trajectory exists.
+    d.run("50fs")
+    assert d.current_potential_energy().value() == pytest.approx(direct())