fix some writing

Author: reint-fischer

docs/user_guide/examples/tutorial_diffusion.ipynb

@@ -253,7 +253,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Now we will simulate the advection and diffusion of the particles using the `AdvectionDiffusionM1` kernel. We run the simulation for 0.3 seconds, with a numerical timestep $\\Delta t = 0.001$s. We also write away particle locations at each timestep for plotting. Note that this will hinder a runtime comparison between kernels, since it will cause most time to be spent on I/O.\n"
+    "Now we will simulate the advection and diffusion of the particles using the `AdvectionDiffusionM1` kernel. We run the simulation for 0.3 seconds, with a numerical timestep $\\Delta t = 0.001$ s. We also write away particle locations at each timestep for plotting. Note that this will hinder a runtime comparison between kernels, since it will cause most time to be spent on I/O.\n"
    ]
   },
   {
@@ -463,7 +463,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Reading velocity fields from netcdf files\n"
+    "Reading velocity fields from a Copernicus Marine Service dataset:\n"
    ]
   },
   {
@@ -562,15 +562,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "In the example, particles are released at one location periodically (every hour) for 12 hours\n"
-   ]
-  },
-  {
-   "attachments": {},
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Simulating the particles moving during 7 days using advection (`AdvectionRK4`) and diffusion (`smagdiff`) kernels.\n"
+    "In the example, particles are released at one location and simulated for 2 days using advection (`AdvectionRK4`) and diffusion (`smagdiff`) kernels."
    ]
   },
   {
@@ -579,11 +571,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "time = np.repeat(\n",
-    "    fieldset.time_interval.left, 13\n",
-    ")  # np.arange(fieldset.time_interval.left, fieldset.time_interval.left+np.timedelta64(13,\"h\"), np.timedelta64(1,'h'))\n",
+    "time = np.repeat(fieldset.time_interval.left, 13)\n",
     "lon = [32] * len(time)\n",
-    "lat = [-30.5] * len(time)\n",
+    "lat = [-30.1] * len(time)\n",
     "z = [ds_fields.depth[0]] * len(time)\n",
     "pset = parcels.ParticleSet(\n",
     "    fieldset=fieldset,\n",
@@ -602,7 +592,7 @@
     "\n",
     "pset.execute(\n",
     "    [parcels.kernels.AdvectionRK4, smagdiff],\n",
-    "    runtime=np.timedelta64(3, \"D\"),\n",
+    "    runtime=np.timedelta64(2, \"D\"),\n",
     "    dt=np.timedelta64(5, \"m\"),\n",
     "    output_file=output_file,\n",
     ")"
@@ -613,7 +603,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Visualize the trajectories using the trajan package\n"
+    "When we visualize the trajectories using the trajan package, we can see that the particles released at the same time and location spread out over time:\n"
    ]
   },
   {
@@ -623,7 +613,13 @@
    "outputs": [],
    "source": [
     "ds_particles = xr.open_zarr(\"smagdiff.zarr\")\n",
-    "ds_particles.traj.plot()\n",
+    "temperature = ds_fields.isel(time=0, depth=0).thetao.plot(cmap=\"magma\")\n",
+    "velocity = ds_fields.isel(time=0, depth=0).plot.quiver(\n",
+    "    x=\"longitude\", y=\"latitude\", u=\"uo\", v=\"vo\"\n",
+    ")\n",
+    "ds_particles.traj.plot(color=\"blue\")\n",
+    "plt.ylim(-31, -30)\n",
+    "plt.xlim(31, 32.1)\n",
     "plt.show()"
    ]
   },
@@ -649,6 +645,11 @@
     "\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": {