Added some comments

festim-dev · Jun 30, 2023 · 2c77e59 · 2c77e59
1 parent 8b23206
commit 2c77e59
Showing 1 changed file with 39 additions and 31 deletions.
diff --git a/tasks/task5.ipynb b/tasks/task5.ipynb
@@ -28,7 +28,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Create a mesh with FEniCS and mark the subdomains."
+    "Create a mesh with FEniCS and mark the subdomains.\n",
+    "\n",
+    "For more information on FEniCS meshes, please visit [the mesh demo](https://fenicsproject.org/olddocs/dolfin/latest/python/demos/built-in-meshes/demo_built-in-meshes.py.html) and the [subdomains demo](https://fenicsproject.org/pub/tutorial/sphinx1/._ftut1005.html)."
    ]
   },
   {
@@ -39,8 +41,8 @@
     {
      "data": {
       "text/plain": [
-       "[<matplotlib.lines.Line2D at 0x7fd430cac4f0>,\n",
-       " <matplotlib.lines.Line2D at 0x7fd430cacdc0>]"
+       "[<matplotlib.lines.Line2D at 0x7f7c9536b910>,\n",
+       " <matplotlib.lines.Line2D at 0x7f7c953ac220>]"
       ]
      },
      "execution_count": 2,
@@ -100,7 +102,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The mesh can now be passed to a `festim.Mesh` object."
+    "The mesh can now be passed to a `festim.Mesh` instance.\n",
+    "\n",
+    "The volume markers and surface markers also need to be passed to the `festim.Mesh` instance."
    ]
   },
   {
@@ -109,7 +113,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# creating mesh with FESTIM\n",
     "my_model.mesh = F.Mesh(\n",
     "    mesh=mesh_fenics,\n",
     "    volume_markers=volume_markers,\n",
@@ -139,7 +142,7 @@
     "my_model.boundary_conditions = [\n",
     "    F.DirichletBC(field=0, surfaces=top_and_bottom_id, value=0),\n",
     "    F.DirichletBC(field=0, surfaces=left_id, value=1)\n",
-    "    ]\n",
+    "]\n",
     "\n",
     "my_model.settings = F.Settings(\n",
     "    absolute_tolerance=1e-10,\n",
@@ -165,26 +168,18 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Calling FFC just-in-time (JIT) compiler, this may take some time.\n",
-      "Calling FFC just-in-time (JIT) compiler, this may take some time.\n",
-      "Calling FFC just-in-time (JIT) compiler, this may take some time.\n",
-      "Calling FFC just-in-time (JIT) compiler, this may take some time.\n",
-      "Calling FFC just-in-time (JIT) compiler, this may take some time.\n",
-      "Calling FFC just-in-time (JIT) compiler, this may take some time.\n",
       "Defining initial values\n",
       "Defining variational problem\n",
       "Defining source terms\n",
       "Defining boundary conditions\n",
       "Solving steady state problem...\n",
-      "Calling FFC just-in-time (JIT) compiler, this may take some time.\n",
-      "Calling FFC just-in-time (JIT) compiler, this may take some time.\n",
-      "Solved problem in 1.00 s\n"
+      "Solved problem in 0.00 s\n"
      ]
     },
     {
      "data": {
       "text/plain": [
-       "<matplotlib.tri._tricontour.TriContourSet at 0x7fd42b7f65c0>"
+       "<matplotlib.tri._tricontour.TriContourSet at 0x7f7c931f0e80>"
       ]
      },
      "execution_count": 5,
@@ -279,9 +274,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Now that we created a FEniCS function representing the velocity, let's add an advection term.\n",
+    "Now that we created a FEniCS function representing the velocity, let's add an advection term to the governing equation.\n",
     "\n",
-    "The governing equation needs to be:\n",
+    "The governing equation for steady state advection-diffusion is:\n",
     "\n",
     "$$\\nabla \\cdot (D \\nabla c) - v \\cdot \\nabla c = 0$$\n",
     "\n",
@@ -297,6 +292,23 @@
    "cell_type": "code",
    "execution_count": 8,
    "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "{ (grad(c)) . (grad(v_0)) } * dx(<Mesh #0>[1], {})\n"
+     ]
+    }
+   ],
+   "source": [
+    "print(my_model.h_transport_problem.F)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
    "outputs": [
     {
      "name": "stdout",
@@ -305,7 +317,9 @@
       "Defining initial values\n",
       "Defining variational problem\n",
       "Defining source terms\n",
-      "Defining boundary conditions\n"
+      "Defining boundary conditions\n",
+      "{ (grad(c)) . (grad(v_0)) } * dx(<Mesh #0>[1], {})\n",
+      "  +  { (conj((v_0))) * ((grad(c)) . (f_90)) } * dx(<Mesh #0>[everywhere], {})\n"
      ]
     }
    ],
@@ -319,7 +333,8 @@
     "\n",
     "advection_term = inner(dot(grad(hydrogen_concentration), velocity), test_function_solute) * my_model.mesh.dx\n",
     "\n",
-    "my_model.h_transport_problem.F += advection_term"
+    "my_model.h_transport_problem.F += advection_term\n",
+    "print(my_model.h_transport_problem.F)"
    ]
   },
   {
@@ -332,23 +347,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
       "Solving steady state problem...\n",
-      "Calling FFC just-in-time (JIT) compiler, this may take some time.\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Calling FFC just-in-time (JIT) compiler, this may take some time.\n",
-      "Solved problem in 1.20 s\n"
+      "Solved problem in 0.00 s\n"
      ]
     },
     {
@@ -374,7 +381,8 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The concentration field is greatly affected as particles are now pushed towards the right hand side of the domain!\n",
+    "The concentration field is greatly affected as particles are now pushed towards the right hand side of the domain.\n",
+    "\n",
     "# Task:\n",
     "\n",
     "Vary the velocity field to investigate its influence on the mobile concentration"