fixing merge conflict errors

Author: erikvansebille

parcels/_datasets/structured/generated.py

@@ -29,8 +29,8 @@ def radial_rotation_dataset(xdim=200, ydim=200):  # Define 2D flat, square field
     x0 = 30.0  # Define the origin to be the centre of the Field.
     y0 = 30.0
 
-    U = np.zeros((1, 1, ydim, xdim), dtype=np.float32)
-    V = np.zeros((1, 1, ydim, xdim), dtype=np.float32)
+    U = np.zeros((2, 1, ydim, xdim), dtype=np.float32)
+    V = np.zeros((2, 1, ydim, xdim), dtype=np.float32)
 
     omega = 2 * np.pi / 86400.0  # Define the rotational period as 1 day.
 

parcels/application_kernels/advection.py

@@ -116,13 +116,15 @@ def AdvectionRK45(particle, fieldset, time):  # pragma: no cover
     and doubled if error is smaller than 1/10th of tolerance.
     """
     dt = particle.next_dt / np.timedelta64(1, "s")  # TODO: improve API for converting dt to seconds
-    if dt > fieldset.RK45_max_dt:
-        dt = fieldset.RK45_max_dt
-        particle.next_dt = fieldset.RK45_max_dt * np.timedelta64(1, "s")
-    if dt < fieldset.RK45_min_dt:
-        particle.next_dt = fieldset.RK45_min_dt * np.timedelta64(1, "s")
-        return StatusCode.Repeat
+    particle.next_dt = np.where(
+        dt > fieldset.RK45_max_dt, fieldset.RK45_max_dt * np.timedelta64(1, "s"), particle.next_dt
+    )
+    particle.next_dt = np.where(
+        dt < fieldset.RK45_min_dt, fieldset.RK45_min_dt * np.timedelta64(1, "s"), particle.next_dt
+    )
     particle.dt = particle.next_dt
+    particle.state = np.where(dt < fieldset.RK45_min_dt, StatusCode.Repeat, particle.state)
+    dt = np.where(dt > fieldset.RK45_max_dt, fieldset.RK45_max_dt, dt)
 
     c = [1.0 / 4.0, 3.0 / 8.0, 12.0 / 13.0, 1.0, 1.0 / 2.0]
     A = [

parcels/kernel.py

@@ -291,8 +291,11 @@ def evaluate_pset(self, pset, endtime):
 
             pre_dt = pset.dt
             try:  # Use next_dt from AdvectionRK45 if it is set
-                if abs(endtime - pset.time_nextloop) < abs(pset.next_dt) - np.timedelta64(1000, "ns"):
-                    pset.next_dt = sign_dt * (endtime - pset.time_nextloop)
+                pset.next_dt = np.where(
+                    sign_dt * (endtime - pset.time_nextloop) <= pset.next_dt,
+                    np.where(sign_dt * (endtime - pset.time_nextloop) < 0, 0, sign_dt * (endtime - pset.time_nextloop)),
+                    pset.next_dt,
+                )
             except KeyError:
                 pset.dt = np.where(
                     sign_dt * (endtime - pset.time_nextloop) <= pset.dt,

parcels/particleset.py

@@ -150,7 +150,7 @@ def __init__(
                 if isinstance(v.initial, attrgetter):
                     initial = v.initial(self)
                 else:
-                    initial = [np.array(v.initial, dtype=v.dtype)] * len(trajectory_ids)
+                    initial = np.repeat(v.initial, len(trajectory_ids)).astype(v.dtype)
                 self._data[v.name] = initial
 
         # update initial values provided on ParticleSet creation

tests/v4/test_advection.py

@@ -79,9 +79,9 @@ def test_advection_zonal_periodic():
     startlon = np.array([0.5, 0.4])
     pset = ParticleSet(fieldset, pclass=PeriodicParticle, lon=startlon, lat=[0.5, 0.5])
     pset.execute([AdvectionEE, periodicBC], runtime=np.timedelta64(40, "s"), dt=np.timedelta64(1, "s"))
-    np.testing.assertallclose(pset.total_dlon, 4, atol=1e-5)
-    np.testing.assertallclose(pset.lon_nextloop, startlon, atol=1e-5)
-    np.testing.assertallclose(pset.lat_nextloop, 0.5, atol=1e-5)
+    np.testing.assert_allclose(pset.total_dlon, 4, atol=1e-5)
+    np.testing.assert_allclose(pset.lon_nextloop, startlon, atol=1e-5)
+    np.testing.assert_allclose(pset.lat_nextloop, 0.5, atol=1e-5)
 
 
 def test_horizontal_advection_in_3D_flow(npart=10):
@@ -268,12 +268,6 @@ def test_moving_eddy(method, rtol):
         # Use RK45Particles to set next_dt
         RK45Particles = Particle.add_variable(Variable("next_dt", initial=dt, dtype=np.timedelta64))
         fieldset.add_constant("RK45_tol", 1e-6)
-    elif method in ["AdvDiffEM", "AdvDiffM1"]:
-        # Add zero diffusivity field for diffusion kernels
-        ds["Kh"] = (["time", "depth", "YG", "XG"], np.full((len(ds["time"]), 2, 2, 2), 0))
-        fieldset.add_field(Field("Kh", ds["Kh"], grid, interp_method=XLinear), "Kh_zonal")
-        fieldset.add_field(Field("Kh", ds["Kh"], grid, interp_method=XLinear), "Kh_meridional")
-        fieldset.add_constant("dres", 0.1)
 
     pclass = RK45Particles if method == "RK45" else Particle
     pset = ParticleSet(