Merge pull request #1237 from OceanParcels/updating_documentation_notebooks

Updating documentation notebooks

Author: erikvansebille

parcels/examples/documentation_MPI.ipynb

@@ -7,6 +7,13 @@
     "## Tutorial on Parallel Parcels with MPI and `dask` field-chunking"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "<center><i> NOTE THAT THIS DOCUMENTATION NOTEBOOK CAN'T BE RUN WITH THE EXAMPLE-OUTPUT THAT SHIPS WITH PARCELS. THESE DOCUMENTATION NOTEBOOKS ARE FOR BACKGROUND INFO ONLY <i></center>"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

parcels/examples/documentation_homepage_animation.ipynb

@@ -1,5 +1,12 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "<center><i> NOTE THAT THIS DOCUMENTATION NOTEBOOK CAN'T BE RUN WITH THE EXAMPLE-OUTPUT THAT SHIPS WITH PARCELS. THESE DOCUMENTATION NOTEBOOKS ARE FOR BACKGROUND INFO ONLY <i></center>"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,

parcels/examples/documentation_indexing.ipynb

@@ -7,6 +7,13 @@
     "## Documentation on dimensions and indexing in Parcels"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "<center><i> NOTE THAT THIS DOCUMENTATION NOTEBOOK CAN'T BE RUN WITH THE EXAMPLE-OUTPUT THAT SHIPS WITH PARCELS. THESE DOCUMENTATION NOTEBOOKS ARE FOR BACKGROUND INFO ONLY <i></center>"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

parcels/examples/documentation_stuck_particles.ipynb

@@ -8,7 +8,28 @@
     }
    },
    "source": [
-    "# Documentation of particles 'stuck' on boundaries\n",
+    "# Documentation of particles 'stuck' on boundaries"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "slideshow": {
+     "slide_type": "slide"
+    }
+   },
+   "source": [
+    "<center><i> NOTE THAT THIS DOCUMENTATION NOTEBOOK CAN'T BE RUN WITH THE EXAMPLE-OUTPUT THAT SHIPS WITH PARCELS. THESE DOCUMENTATION NOTEBOOKS ARE FOR BACKGROUND INFO ONLY <i></center>"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "slideshow": {
+     "slide_type": "slide"
+    }
+   },
+   "source": [
     "In some Parcels simulations, particles end up moving onto parts of the grid where the velocity field is not defined, such as for example onto land. In this tutorial we look at how this depends on the grid structure. \n",
     "\n",
     "**Short conclusion: Particles can get stuck on Arakawa A grids and B grids but should not get stuck on C grids.**\n",

parcels/examples/documentation_unstuck_Agrid.ipynb

@@ -7,6 +7,13 @@
     "# Tutorial on implementing boundary conditions in an A grid"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "<center><i> NOTE THAT THIS DOCUMENTATION NOTEBOOK CAN'T BE RUN WITH THE EXAMPLE-OUTPUT THAT SHIPS WITH PARCELS. THESE DOCUMENTATION NOTEBOOKS ARE FOR BACKGROUND INFO ONLY <i></center>"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

parcels/examples/tutorial_diffusion.ipynb

@@ -17,7 +17,7 @@
     "    \\mathbf{X}(t_0) &= \\mathbf{x}_0,\n",
     "\\end{aligned}\n",
     "$$\n",
-    "where $\\mathbf{X}$ is the particle position vector ($\\mathbf{x}_0$ being the initial position vector), $\\mathbf{u}$ the velocity vector, $\\mathbf{K} = \\frac{1}{2} \\mathbf{V} \\cdot \\mathbf{V}^T$ the diffusivity tensor, and $d\\mathbf{W}(t)$ a Wiener increment (normally distributed with zero mean and variance $dt$). Particle distributions obtained by solving the above equation are therefore consistent with Eulerian concentrations found by solving the advection-diffusion equation. \n",
+    "where $\\mathbf{X}$ is the particle position vector ($\\mathbf{x}_0$ being the initial position vector), and $\\mathbf{u}$ the velocity vector. $\\mathbf{V}$ is calculated from the diffusivity tensor $\\mathbf{K} = \\frac{1}{2} \\mathbf{V} \\cdot \\mathbf{V}^T$ and $d\\mathbf{W}(t)$ a Wiener increment (normally distributed with zero mean and variance $dt$). Particle distributions obtained by solving the above equation are therefore consistent with Eulerian concentrations found by solving the advection-diffusion equation. \n",
     "\n",
     "In three-dimensional ocean models diffusion operates along slopes of neutral buoyancy. To account for these slopes, the 3D diffusivity tensor $\\mathbf{K}$ (and therefore $\\mathbf{V}$) contains off-diagonal components. Three-dimensional advection-diffusion is not yet implemented in _Parcels_, but it is currently under development. Here we instead focus on the simpler case of diffusion in a horizontal plane, where diffusivity is specified only in the zonal and meridional direction, i.e. \n",
     "$$\\mathbf{K}(x,y)=\\begin{bmatrix}\n",