Re-run notebooks

firedrakeproject · Dec 18, 2024 · 5f92dae · 5f92dae
1 parent f3e5e4a
commit 5f92dae
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Showing 7 changed files with 2,913 additions and 443 deletions.
diff --git a/.gitignore b/.gitignore
@@ -57,3 +57,7 @@ docs/_build/
 target/
 /docs/source/teamgrid.rst
 /docs/source/gusto.rst
+
+# Gusto specific
+jupyter_notebooks/results
+jupyter_notebooks/.ipynb_checkpoints
diff --git a/Makefile b/Makefile
@@ -48,6 +48,7 @@ notebook_test: clean_cache
 
 reset_notebooks:
 	@jupyter-nbconvert --clear-output ./jupyter_notebooks/*.ipynb
+	@rm -rf ./jupyter_notebooks/results
 	@env OMP_NUM_THREADS=1 jupyter-nbconvert \
 		--execute \
 		--ClearMetadataPreprocessor.enabled=True \

diff --git a/jupyter_notebooks/Book_1_Intro_Williamson_2.ipynb b/jupyter_notebooks/Book_1_Intro_Williamson_2.ipynb
diff --git a/jupyter_notebooks/Book_2_Gravity_Wave_Vertical_Slice.ipynb b/jupyter_notebooks/Book_2_Gravity_Wave_Vertical_Slice.ipynb
@@ -31,14 +31,10 @@
    "metadata": {},
    "outputs": [
     {
-     "ename": "ModuleNotFoundError",
-     "evalue": "No module named 'gusto'",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mModuleNotFoundError\u001b[0m                       Traceback (most recent call last)",
-      "Input \u001b[0;32mIn [1]\u001b[0m, in \u001b[0;36m<cell line: 1>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mgusto\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;241m*\u001b[39m\n\u001b[1;32m      2\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mfiredrake\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m (as_vector, SpatialCoordinate, PeriodicIntervalMesh,\n\u001b[1;32m      3\u001b[0m                        ExtrudedMesh, exp, sin, pi, Function)\n",
-      "\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'gusto'"
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO     Running /home/jack/Documents/firedrake/firedrake/lib/python3.12/site-packages/ipykernel_launcher.py -f /tmp/tmpsbm8a_5l.json --HistoryManager.hist_file=:memory:\n"
      ]
     }
    ],
@@ -81,19 +77,7 @@
    "execution_count": 3,
    "id": "844be5eb",
    "metadata": {},
-   "outputs": [
-    {
-     "ename": "NameError",
-     "evalue": "name 'PeriodicIntervalMesh' is not defined",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
-      "Input \u001b[0;32mIn [3]\u001b[0m, in \u001b[0;36m<cell line: 4>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      2\u001b[0m columns \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m150\u001b[39m  \u001b[38;5;66;03m# number of columns\u001b[39;00m\n\u001b[1;32m      3\u001b[0m domain_width \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m3.0e5\u001b[39m\n\u001b[0;32m----> 4\u001b[0m m \u001b[38;5;241m=\u001b[39m \u001b[43mPeriodicIntervalMesh\u001b[49m(columns, domain_width)\n\u001b[1;32m      6\u001b[0m domain_height \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m1.0e4\u001b[39m  \u001b[38;5;66;03m# Height position of the model top\u001b[39;00m\n\u001b[1;32m      7\u001b[0m mesh \u001b[38;5;241m=\u001b[39m ExtrudedMesh(m, layers\u001b[38;5;241m=\u001b[39mnlayers, layer_height\u001b[38;5;241m=\u001b[39mdomain_height\u001b[38;5;241m/\u001b[39mnlayers)\n",
-      "\u001b[0;31mNameError\u001b[0m: name 'PeriodicIntervalMesh' is not defined"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "nlayers = 10  # number of horizontal layers\n",
     "columns = 150  # number of columns\n",
@@ -117,19 +101,7 @@
    "execution_count": 4,
    "id": "8ed9914e",
    "metadata": {},
-   "outputs": [
-    {
-     "ename": "NameError",
-     "evalue": "name 'Domain' is not defined",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
-      "Input \u001b[0;32mIn [4]\u001b[0m, in \u001b[0;36m<cell line: 1>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0m domain \u001b[38;5;241m=\u001b[39m \u001b[43mDomain\u001b[49m(mesh, dt, family\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mCG\u001b[39m\u001b[38;5;124m\"\u001b[39m, degree\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m1\u001b[39m)\n\u001b[1;32m      2\u001b[0m parameters \u001b[38;5;241m=\u001b[39m CompressibleParameters()\n\u001b[1;32m      3\u001b[0m eqns \u001b[38;5;241m=\u001b[39m CompressibleEulerEquations(domain, parameters)\n",
-      "\u001b[0;31mNameError\u001b[0m: name 'Domain' is not defined"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "domain = Domain(mesh, dt, family=\"CG\", degree=1)\n",
     "parameters = CompressibleParameters()\n",
@@ -149,19 +121,7 @@
    "execution_count": 5,
    "id": "754708dd",
    "metadata": {},
-   "outputs": [
-    {
-     "ename": "NameError",
-     "evalue": "name 'OutputParameters' is not defined",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
-      "Input \u001b[0;32mIn [5]\u001b[0m, in \u001b[0;36m<cell line: 2>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      1\u001b[0m dirname \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mgravity_wave\u001b[39m\u001b[38;5;124m'\u001b[39m\n\u001b[0;32m----> 2\u001b[0m output \u001b[38;5;241m=\u001b[39m \u001b[43mOutputParameters\u001b[49m(dirname\u001b[38;5;241m=\u001b[39mdirname,\n\u001b[1;32m      3\u001b[0m                           dumpfreq\u001b[38;5;241m=\u001b[39mdumpfreq)\n\u001b[1;32m      4\u001b[0m Tsurf \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m300.\u001b[39m\n\u001b[1;32m      5\u001b[0m diagnostic_fields \u001b[38;5;241m=\u001b[39m [\n\u001b[1;32m      6\u001b[0m     CourantNumber(), Gradient(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mu\u001b[39m\u001b[38;5;124m'\u001b[39m), Perturbation(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mtheta\u001b[39m\u001b[38;5;124m'\u001b[39m),\n\u001b[1;32m      7\u001b[0m     Gradient(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mtheta_perturbation\u001b[39m\u001b[38;5;124m'\u001b[39m), Perturbation(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mrho\u001b[39m\u001b[38;5;124m'\u001b[39m),\n\u001b[1;32m      8\u001b[0m     RichardsonNumber(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mtheta\u001b[39m\u001b[38;5;124m'\u001b[39m, parameters\u001b[38;5;241m.\u001b[39mg\u001b[38;5;241m/\u001b[39mTsurf), Gradient(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mtheta\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m      9\u001b[0m ]\n",
-      "\u001b[0;31mNameError\u001b[0m: name 'OutputParameters' is not defined"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "dirname = 'gravity_wave'\n",
     "output = OutputParameters(dirname=dirname,\n",
@@ -190,14 +150,17 @@
    "metadata": {},
    "outputs": [
     {
-     "ename": "NameError",
-     "evalue": "name 'SUPGOptions' is not defined",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
-      "Input \u001b[0;32mIn [6]\u001b[0m, in \u001b[0;36m<cell line: 1>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0m theta_opts \u001b[38;5;241m=\u001b[39m \u001b[43mSUPGOptions\u001b[49m()\n\u001b[1;32m      2\u001b[0m subcycling_options \u001b[38;5;241m=\u001b[39m SubcyclingOptions(subcycle_by_courant\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0.25\u001b[39m)\n\u001b[1;32m      4\u001b[0m transported_fields \u001b[38;5;241m=\u001b[39m [\n\u001b[1;32m      5\u001b[0m     SSPRK3(domain, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mu\u001b[39m\u001b[38;5;124m\"\u001b[39m, subcycling_options\u001b[38;5;241m=\u001b[39msubcycling_options),\n\u001b[1;32m      6\u001b[0m     SSPRK3(\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m     13\u001b[0m     )\n\u001b[1;32m     14\u001b[0m ]\n",
-      "\u001b[0;31mNameError\u001b[0m: name 'SUPGOptions' is not defined"
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO     Physical parameters that take non-default values:\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO     \n"
      ]
     }
    ],
@@ -243,19 +206,7 @@
    "execution_count": 7,
    "id": "e61d066d",
    "metadata": {},
-   "outputs": [
-    {
-     "ename": "NameError",
-     "evalue": "name 'stepper' is not defined",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
-      "Input \u001b[0;32mIn [7]\u001b[0m, in \u001b[0;36m<cell line: 2>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[38;5;66;03m# Initial conditions\u001b[39;00m\n\u001b[0;32m----> 2\u001b[0m u0 \u001b[38;5;241m=\u001b[39m \u001b[43mstepper\u001b[49m\u001b[38;5;241m.\u001b[39mfields(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mu\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m      3\u001b[0m rho0 \u001b[38;5;241m=\u001b[39m stepper\u001b[38;5;241m.\u001b[39mfields(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mrho\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m      4\u001b[0m theta0 \u001b[38;5;241m=\u001b[39m stepper\u001b[38;5;241m.\u001b[39mfields(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtheta\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n",
-      "\u001b[0;31mNameError\u001b[0m: name 'stepper' is not defined"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# Initial conditions\n",
     "u0 = stepper.fields(\"u\")\n",
@@ -297,19 +248,7 @@
    "execution_count": 8,
    "id": "b1642c8b",
    "metadata": {},
-   "outputs": [
-    {
-     "ename": "NameError",
-     "evalue": "name 'compressible_hydrostatic_balance' is not defined",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
-      "Input \u001b[0;32mIn [8]\u001b[0m, in \u001b[0;36m<cell line: 1>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43mcompressible_hydrostatic_balance\u001b[49m(eqns, theta_b, rho_b)\n",
-      "\u001b[0;31mNameError\u001b[0m: name 'compressible_hydrostatic_balance' is not defined"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "compressible_hydrostatic_balance(eqns, theta_b, rho_b)"
    ]
@@ -328,19 +267,7 @@
    "execution_count": 9,
    "id": "46852826",
    "metadata": {},
-   "outputs": [
-    {
-     "ename": "NameError",
-     "evalue": "name 'sin' is not defined",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
-      "Input \u001b[0;32mIn [9]\u001b[0m, in \u001b[0;36m<cell line: 3>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      1\u001b[0m a \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m5.0e3\u001b[39m\n\u001b[1;32m      2\u001b[0m deltaTheta \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m1.0e-2\u001b[39m\n\u001b[0;32m----> 3\u001b[0m theta_pert \u001b[38;5;241m=\u001b[39m deltaTheta\u001b[38;5;241m*\u001b[39m\u001b[43msin\u001b[49m(pi\u001b[38;5;241m*\u001b[39mxz[\u001b[38;5;241m1\u001b[39m]\u001b[38;5;241m/\u001b[39mdomain_height)\u001b[38;5;241m/\u001b[39m(\u001b[38;5;241m1\u001b[39m \u001b[38;5;241m+\u001b[39m (xz[\u001b[38;5;241m0\u001b[39m] \u001b[38;5;241m-\u001b[39m domain_width\u001b[38;5;241m/\u001b[39m\u001b[38;5;241m2\u001b[39m)\u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39m\u001b[38;5;241m2\u001b[39m\u001b[38;5;241m/\u001b[39ma\u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39m\u001b[38;5;241m2\u001b[39m)\n\u001b[1;32m      4\u001b[0m theta0\u001b[38;5;241m.\u001b[39minterpolate(theta_b \u001b[38;5;241m+\u001b[39m theta_pert)\n\u001b[1;32m      5\u001b[0m rho0\u001b[38;5;241m.\u001b[39massign(rho_b)\n",
-      "\u001b[0;31mNameError\u001b[0m: name 'sin' is not defined"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "a = 5.0e3\n",
     "deltaTheta = 1.0e-2\n",