Fixing the first adding of dt to time

By moving the position_update_kernels to after the first kernel loop

Author: erikvansebille

src/parcels/_core/kernel.py

@@ -233,10 +233,6 @@ def execute(self, pset, endtime, dt):
 
         pset._data["state"][:] = StatusCode.Evaluate
 
-        if not self._positionupdate_kernels_added:
-            self.add_positionupdate_kernels()
-            self._positionupdate_kernels_added = True
-
         while (len(pset) > 0) and np.any(np.isin(pset.state, [StatusCode.Evaluate, StatusCode.Repeat])):
             time_to_endtime = compute_time_direction * (endtime - pset.time)
 
@@ -283,4 +279,8 @@ def execute(self, pset, endtime, dt):
                     else:
                         error_func(pset[inds].z, pset[inds].lat, pset[inds].lon)
 
+            if not self._positionupdate_kernels_added:
+                self.add_positionupdate_kernels()
+                self._positionupdate_kernels_added = True
+
         return pset

src/parcels/_core/particleset.py

@@ -538,10 +538,6 @@ def execute(
 
         next_output = start_time if output_file else None
 
-        # TODO clean up two lines below: -dt is needed because in SetCoords dt gets added again
-        start_time -= dt
-        self._data["time"][:] -= dt
-
         time = start_time
         while sign_dt * (time - end_time) < 0:
             if next_output is not None:

tests/test_particleset_execute.py

@@ -207,7 +207,7 @@ def AddLat(particles, fieldset):  # pragma: no cover
         particles.dlat += 0.1
 
     k_add = pset.Kernel(AddLat)
-    for _ in range(n + 1):
+    for _ in range(n):
         pset.execute(k_add, runtime=np.timedelta64(1, "s"), dt=np.timedelta64(1, "s"))
         if with_delete:
             pset.remove_indices(len(pset) - 1)
@@ -244,7 +244,7 @@ def AddLon(particles, fieldset):  # pragma: no cover
 
     np.testing.assert_array_equal(pset.lon, [9, 7, 0])
     assert pset.time[0:1] == endtime
-    assert pset.time[2] == start_times[2] - dt  # this particle has not been executed  # TODO check why -dt is needed
+    assert pset.time[2] == start_times[2]  # this particle has not been executed
 
     # Test backward in time (note third particle is outside endtime)
     start_times = [fieldset.time_interval.right - np.timedelta64(t, "s") for t in [0, 2, 10]]
@@ -255,7 +255,7 @@ def AddLon(particles, fieldset):  # pragma: no cover
 
     np.testing.assert_array_equal(pset.lon, [9, 7, 0])
     assert pset.time[0:1] == endtime
-    assert pset.time[2] == start_times[2] + dt  # this particle has not been executed
+    assert pset.time[2] == start_times[2]  # this particle has not been executed
 
 
 def test_some_particles_throw_outofbounds(zonal_flow_fieldset):