Merge pull request #2134 from OceanParcels/particle-particledata

Rework of Particle class, and Particle data creation

Author: VeckoTheGecko

docs/examples/example_globcurrent.py

@@ -196,7 +196,7 @@ def test_globcurrent_particle_independence(rundays=5):
     time0 = fieldset.U.grid.time[0]
 
     def DeleteP0(particle, fieldset, time):  # pragma: no cover
-        if particle.id == 0:
+        if particle.trajectory == 0:
             particle.delete()
 
     pset0 = parcels.ParticleSet(
@@ -244,7 +244,7 @@ def test_globcurrent_pset_fromfile(dt, pid_offset, tmpdir):
     pset.execute(parcels.AdvectionRK4, runtime=timedelta(days=1), dt=dt)
     pset_new.execute(parcels.AdvectionRK4, runtime=timedelta(days=1), dt=dt)
 
-    for var in ["lon", "lat", "depth", "time", "id"]:
+    for var in ["lon", "lat", "depth", "time", "trajectory"]:
         assert np.allclose(
             [getattr(p, var) for p in pset], [getattr(p, var) for p in pset_new]
         )

parcels/_compat.py

@@ -17,3 +17,24 @@
     from sklearn.cluster import KMeans  # type: ignore[no-redef]
 except ModuleNotFoundError:
     pass
+
+
+# for compat with v3 of parcels when users provide `initial=attrgetter("lon")` to a Variable
+# so that particle initial state matches another variable
+class _AttrgetterHelper:
+    """
+    Example usage
+
+    >>> _attrgetter_helper = _AttrgetterHelper()
+    >>> _attrgetter_helper.some_attribute
+    'some_attribute'
+    >>> from operator import attrgetter
+    >>> attrgetter('some_attribute')(_attrgetter_helper)
+    'some_attribute'
+    """
+
+    def __getattr__(self, name):
+        return name
+
+
+_attrgetter_helper = _AttrgetterHelper()

parcels/application_kernels/interaction.py

@@ -25,12 +25,12 @@ def NearestNeighborWithinRange(particle, fieldset, time, neighbors, mutator):
         # undesirable results.
         if dist < min_dist or min_dist < 0:
             min_dist = dist
-            neighbor_id = n.id
+            neighbor_id = n.trajectory
 
     def f(p, neighbor):
         p.nearest_neighbor = neighbor
 
-    mutator[particle.id].append((f, [neighbor_id]))
+    mutator[particle.trajectory].append((f, [neighbor_id]))
 
     return StatusCode.Success
 
@@ -54,14 +54,14 @@ def merge_with_neighbor(p, nlat, nlon, ndepth, nmass):
         p.mass = p.mass + nmass
 
     for n in neighbors:
-        if n.id == particle.nearest_neighbor:
-            if n.nearest_neighbor == particle.id and particle.id < n.id:
+        if n.trajectory == particle.nearest_neighbor:
+            if n.nearest_neighbor == particle.trajectory and particle.trajectory < n.trajectory:
                 # Merge particles:
                 # Delete neighbor
-                mutator[n.id].append((delete_particle, ()))
+                mutator[n.trajectory].append((delete_particle, ()))
                 # Take position at the mid point and sum of masses
                 args = np.array([n.lat, n.lon, n.depth, n.mass])
-                mutator[particle.id].append((merge_with_neighbor, args))
+                mutator[particle.trajectory].append((merge_with_neighbor, args))
 
                 return StatusCode.Success
             else:
@@ -101,6 +101,6 @@ def f(n, dlat, dlon, ddepth):
             n.lon_nextloop += dlon
             n.depth_nextloop += ddepth
 
-        mutator[n.id].append((f, d_vec))
+        mutator[n.trajectory].append((f, d_vec))
 
     return StatusCode.Success

parcels/field.py

@@ -16,7 +16,7 @@
     VectorType,
     assert_valid_mesh,
 )
-from parcels.particle import Particle
+from parcels.particle import KernelParticle
 from parcels.tools.converters import (
     UnitConverter,
     unitconverters_map,
@@ -37,9 +37,9 @@
 
 
 def _deal_with_errors(error, key, vector_type: VectorType):
-    if isinstance(key, Particle):
+    if isinstance(key, KernelParticle):
         key.state = AllParcelsErrorCodes[type(error)]
-    elif isinstance(key[-1], Particle):
+    elif isinstance(key[-1], KernelParticle):
         key[-1].state = AllParcelsErrorCodes[type(error)]
     else:
         raise RuntimeError(f"{error}. Error could not be handled because particle was not part of the Field Sampling.")
@@ -278,7 +278,7 @@ def eval(self, time: datetime, z, y, x, particle=None, applyConversion=True):
     def __getitem__(self, key):
         self._check_velocitysampling()
         try:
-            if isinstance(key, Particle):
+            if isinstance(key, KernelParticle):
                 return self.eval(key.time, key.depth, key.lat, key.lon, key)
             else:
                 return self.eval(*key)
@@ -373,7 +373,7 @@ def eval(self, time: datetime, z, y, x, particle=None, applyConversion=True):
 
     def __getitem__(self, key):
         try:
-            if isinstance(key, Particle):
+            if isinstance(key, KernelParticle):
                 return self.eval(key.time, key.depth, key.lat, key.lon, key)
             else:
                 return self.eval(*key)

parcels/interaction/interactionkernel.py

@@ -157,7 +157,7 @@ def execute_python(self, pset, endtime, dt):
             for particle_idx in active_idx:
                 p = pset[particle_idx]
                 try:
-                    for mutator_func, args in mutator[p.id]:
+                    for mutator_func, args in mutator[p.trajectory]:
                         mutator_func(p, *args)
                 except KeyError:
                     pass
@@ -201,7 +201,7 @@ def execute(self, pset, endtime, dt, output_file=None):
                     pass
                 else:
                     warnings.warn(
-                        f"Deleting particle {p.id} because of non-recoverable error",
+                        f"Deleting particle {p.trajectory} because of non-recoverable error",
                         RuntimeWarning,
                         stacklevel=2,
                     )

parcels/kernel.py

@@ -259,7 +259,7 @@ def execute(self, pset, endtime, dt):
                     pass
                 else:
                     warnings.warn(
-                        f"Deleting particle {p.id} because of non-recoverable error",
+                        f"Deleting particle {p.trajectory} because of non-recoverable error",
                         RuntimeWarning,
                         stacklevel=2,
                     )