fix adding field to fieldset

Author: reint-fischer

docs/user_guide/examples/tutorial_diffusion.ipynb

@@ -76,13 +76,17 @@
     "\n",
     "The spatial derivatives in the EM and M1 schemes can be approximated by a central difference. Higher order numerical schemes (see [Gräwe et al., 2012](https://doi.org/10.1007/s10236-012-0523-y)) include higher order derivatives.\n",
     "\n",
+    "```{note}\n",
+    "TODO: explore higher order derivatives and numerical schemes (using cubic spline interpolation) in v4 \n",
+    "```\n",
+    "\n",
     "An overview of numerical approximations for SDEs in a particle tracking setting can be found in [Gräwe (2011)](https://doi.org/10.1016/j.ocemod.2010.10.002).\n",
     "\n",
     "## Using Advection-Diffusion Kernels in Parcels\n",
     "\n",
     "The EM and M1 advection-diffusion approximations are available as `AdvectionDiffusionEM` and `AdvectionDiffusionM1`, respectively. The `AdvectionDiffusionM1` kernel should be the default choice, as the increased accuracy comes at negligible computational cost.\n",
     "\n",
-    "The advection component of these kernels is similar to that of the Explicit Euler advection kernel (`AdvectionEE`). In the special case where diffusivity is constant over the entire domain, the diffusion-only kernel `DiffusionUniformKh` can be used in combination with an advection kernel of choice. Since the diffusivity here is space-independent, gradients are not calculated, increasing efficiency. The diffusion-step can in this case be computed after or before advection, thus allowing you to chain kernels using the `+` operator.\n",
+    "The advection component of these kernels is similar to that of the Explicit Euler advection kernel (`AdvectionEE`). In the special case where diffusivity is constant over the entire domain, the diffusion-only kernel `DiffusionUniformKh` can be used in combination with an advection kernel of choice. Since the diffusivity here is space-independent, gradients are not calculated, increasing efficiency. The diffusion-step can in this case be computed after or before advection, thus allowing you to chain kernels in a list.\n",
     "\n",
     "Just like velocities, diffusivities are passed to Parcels in the form of `Field` objects. When using `DiffusionUniformKh`, they should be added to the `FieldSet` object as constant fields, e.g. `fieldset.add_constant_field(\"Kh_zonal\", 1, mesh=\"flat\")`.\n",
     "\n",
@@ -193,8 +197,6 @@
     "ds = simple_UV_dataset(dims=(1, 1, Ny, 1), mesh=\"flat\").isel(time=0, depth=0)\n",
     "ds[\"lat\"][:] = np.linspace(-0.01, 1.01, Ny)\n",
     "ds[\"lon\"][:] = np.ones(len(ds.XG))\n",
-    "# dx, dy = 1.0 / len(ds.XG), 1.0 / len(ds.YG)\n",
-    "ds[\"Kh_zonal\"] = ds[\"U\"] + K_bar * np.ones((Ny, 1))\n",
     "ds[\"Kh_meridional\"] = ds[\"U\"] + Kh_meridional[:, None]\n",
     "ds"
    ]
@@ -209,16 +211,15 @@
     "U = parcels.Field(\"U\", ds[\"U\"], grid, interp_method=parcels.interpolators.XLinear)\n",
     "V = parcels.Field(\"V\", ds[\"V\"], grid, interp_method=parcels.interpolators.XLinear)\n",
     "UV = parcels.VectorField(\"UV\", U, V)\n",
-    "Kh_zonal_field = parcels.Field(\n",
-    "    \"Kh_zonal\", ds[\"Kh_zonal\"], grid, interp_method=parcels.interpolators.XLinear\n",
-    ")\n",
+    "\n",
     "Kh_meridional_field = parcels.Field(\n",
     "    \"Kh_meridional\",\n",
     "    ds[\"Kh_meridional\"],\n",
     "    grid,\n",
     "    interp_method=parcels.interpolators.XLinear,\n",
     ")\n",
-    "fieldset = parcels.FieldSet([U, V, UV, Kh_zonal_field, Kh_meridional_field])\n",
+    "fieldset = parcels.FieldSet([U, V, UV, Kh_meridional_field])\n",
+    "fieldset.add_constant_field(\"Kh_zonal\", 1, mesh=\"flat\")\n",
     "\n",
     "fieldset.add_constant(\"dres\", 0.00005)"
    ]
@@ -244,7 +245,6 @@
     "        lon=np.zeros(100),\n",
     "        lat=np.ones(100) * 0.75,\n",
     "        time=np.repeat(np.timedelta64(0, \"s\"), 100),\n",
-    "        # lonlatdepth_dtype=np.float64,\n",
     "    )"
    ]
   },
@@ -539,22 +539,21 @@
     "da_cell_areas = xr.DataArray(\n",
     "    data=calc_cell_areas(fieldset.U.grid),\n",
     "    coords=dict(\n",
-    "        latitude=([\"latitude\"], ds_fields.latitude.values),\n",
-    "        longitude=([\"longitude\"], ds_fields.longitude.values),\n",
+    "        latitude=([\"lat\"], ds_fields.latitude.values),\n",
+    "        longitude=([\"lon\"], ds_fields.longitude.values),\n",
     "    ),\n",
-    "    dims=[\"latitude\", \"longitude\"],\n",
+    "    dims=[\"lat\", \"lon\"],\n",
     ")\n",
     "\n",
-    "ds_fields[\"cell_areas\"] = da_cell_areas\n",
-    "ds_fields[\"latitude\"].attrs[\"axis\"] = \"Y\"\n",
-    "ds_fields[\"longitude\"].attrs[\"axis\"] = \"X\"\n",
-    "\n",
-    "# TODO: add parcels.Field instead of creating new fieldset once defining from existing XGrid is implemented\n",
-    "fieldset = parcels.FieldSet.from_copernicusmarine(ds_fields)\n",
-    "\n",
-    "fieldset.add_constant(\"Cs\", 0.1)\n",
+    "cell_areas_field = parcels.Field(\n",
+    "    \"cell_areas\",\n",
+    "    da_cell_areas,\n",
+    "    fieldset.U.grid,\n",
+    "    interp_method=parcels.interpolators.XNearest,\n",
+    ")\n",
+    "fieldset.add_field(cell_areas_field)\n",
     "\n",
-    "ds_fields"
+    "fieldset.add_constant(\"Cs\", 0.1)"
    ]
   },
   {
@@ -645,11 +644,6 @@
     "\n",
     "Smagorinsky, J. (1963). “General circulation experiments with primitive equations. 1. The basic experiment.” _Monthly Weather Review_, 91, 99–164. https://doi.org/10.1175/1520-0493(1963)091%3C0099:GCEWTP%3E2.3.CO;2\n"
    ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": []
   }
  ],
  "metadata": {