Update fieldset ingestion to use convert modules

benchmarks/fesom2.py

@@ -48,7 +48,7 @@ def pset_execute(self, npart, integrator):
         lat = np.linspace(32.0, 19.0, npart)
 
         pset = ParticleSet(fieldset=fieldset, pclass=Particle, lon=lon, lat=lat)
-        pset.execute(runtime=runtime, dt=dt, pyfunc=integrator)
+        pset.execute(kernels=integrator, runtime=runtime, dt=dt)
 
     def time_pset_execute(self, npart, integrator):
         self.pset_execute(npart, integrator)

benchmarks/moi_curvilinear.py

@@ -3,7 +3,6 @@
 import numpy as np
 import parcels
 import xarray as xr
-import xgcm
 from parcels.interpolators import XLinear
 
 from parcels_benchmarks.benchmark_setup import PARCELS_DATADIR, download_example_dataset
@@ -14,7 +13,6 @@
 
 def _load_ds(datapath, chunk):
     """Helper function to load xarray dataset from datapath with or without chunking"""
-
     fileU = f"{datapath}/psy4v3r1-daily_U_2025-01-0[1-3].nc"
     filenames = {
         "U": glob(fileU),
@@ -32,27 +30,16 @@ def _load_ds(datapath, chunk):
     if chunk:
         fileargs["chunks"] = {"time_counter": 1, "depth": 2, "y": chunk, "x": chunk}
 
-    ds_u = xr.open_mfdataset(filenames["U"], **fileargs)[["vozocrtx"]].drop_vars(
-        ["nav_lon", "nav_lat"]
+    ds_u = xr.open_mfdataset(filenames["U"], **fileargs)[["vozocrtx"]].rename_vars(
+        {"vozocrtx": "U"}
     )
-    ds_v = xr.open_mfdataset(filenames["V"], **fileargs)[["vomecrty"]].drop_vars(
-        ["nav_lon", "nav_lat"]
+    ds_v = xr.open_mfdataset(filenames["V"], **fileargs)[["vomecrty"]].rename_vars(
+        {"vomecrty": "V"}
     )
-    ds_depth = xr.open_mfdataset(filenames["W"], **fileargs)[["depthw"]]
+    da_depth = xr.open_mfdataset(filenames["W"], **fileargs)["depthw"]
     ds_mesh = xr.open_dataset(mesh_mask)[["glamf", "gphif"]].isel(t=0)
-
-    ds = xr.merge([ds_u, ds_v, ds_depth, ds_mesh], compat="identical")
-    ds = ds.rename(
-        {
-            "vozocrtx": "U",
-            "vomecrty": "V",
-            "glamf": "lon",
-            "gphif": "lat",
-            "time_counter": "time",
-            "depthw": "depth",
-        }
-    )
-    ds.deptht.attrs["c_grid_axis_shift"] = -0.5
+    ds_mesh["depthw"] = da_depth
+    ds = parcels.convert.nemo_to_sgrid(fields=dict(U=ds_u, V=ds_v), coords=ds_mesh)
 
     return ds
 
@@ -89,31 +76,13 @@ def time_load_data_3d(self, interpolator, chunk, npart):
 
     def pset_execute_3d(self, interpolator, chunk, npart):
         ds = _load_ds(self.datapath, chunk)
-        coords = {
-            "X": {"left": "x"},
-            "Y": {"left": "y"},
-            "Z": {"center": "deptht", "left": "depth"},
-            "T": {"center": "time"},
-        }
-
-        grid = parcels._core.xgrid.XGrid(
-            xgcm.Grid(ds, coords=coords, autoparse_metadata=False, periodic=False),
-            mesh="spherical",
-        )
-
+        fieldset = parcels.FieldSet.from_sgrid_conventions(ds)
         if interpolator == "XLinear":
-            interp_method = XLinear
+            fieldset.U.interp_method = XLinear
+            fieldset.V.interp_method = XLinear
         else:
             raise ValueError(f"Unknown interpolator: {interpolator}")
 
-        U = parcels.Field("U", ds["U"], grid, interp_method=interp_method)
-        V = parcels.Field("V", ds["V"], grid, interp_method=interp_method)
-        U.units = parcels.GeographicPolar()
-        V.units = parcels.Geographic()
-        UV = parcels.VectorField("UV", U, V)
-
-        fieldset = parcels.FieldSet([U, V, UV])
-
         pclass = parcels.Particle
 
         lon = np.linspace(-10, 10, npart)

results/benchmarks.json

@@ -11,7 +11,7 @@
                 "10000"
             ],
             [
-                "<function AdvectionEE>"
+                "<function AdvectionRK2_3D>"
             ]
         ],
         "type": "peakmemory",
@@ -32,7 +32,7 @@
                 "10000"
             ],
             [
-                "<function AdvectionEE>"
+                "<function AdvectionRK2_3D>"
             ]
         ],
         "repeat": 0,
@@ -57,7 +57,7 @@
                 "10000"
             ],
             [
-                "<function AdvectionEE>"
+                "<function AdvectionRK2_3D>"
             ]
         ],
         "repeat": 0,