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Develop #18

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merged 5 commits into from
Jul 4, 2024
Merged

Develop #18

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165468f
Protecting output
anaegel Jun 14, 2024
a0564e3
Adding test for bromide diffusion
anaegel Jun 14, 2024
4c95ab2
Merge commit '7a076faa23dc929e14d8894f2107dc34782b5443' into develop
anaegel Jun 14, 2024
a2c3762
Update for skin. Working version for binding.
anaegel Jun 27, 2024
a3382cf
Some geometry files
anaegel Jul 4, 2024
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262 changes: 19 additions & 243 deletions content/brom/BromDiffusion.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": null,
"id": "e6150636",
"metadata": {},
"outputs": [],
Expand All @@ -43,22 +43,10 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": null,
"id": "42847742",
"metadata": {},
"outputs": [
{
"ename": "AttributeError",
"evalue": "module 'ug4py.pyugcore' has no attribute 'Domain3d'",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[3], line 9\u001b[0m\n\u001b[1;32m 5\u001b[0m numRefs \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m2\u001b[39m \u001b[38;5;66;03m# Number of Refinement steps on given grid\u001b[39;00m\n\u001b[1;32m 7\u001b[0m \u001b[38;5;66;03m# Choosing a domain object\u001b[39;00m\n\u001b[1;32m 8\u001b[0m \u001b[38;5;66;03m# (either 1d, 2d or 3d suffix)\u001b[39;00m\n\u001b[0;32m----> 9\u001b[0m dom \u001b[38;5;241m=\u001b[39m \u001b[43mug4\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mDomain3d\u001b[49m()\n\u001b[1;32m 11\u001b[0m \u001b[38;5;66;03m# Loading the given grid into the domain\u001b[39;00m\n\u001b[1;32m 12\u001b[0m \u001b[38;5;28mprint\u001b[39m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mLoading Domain \u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;241m+\u001b[39m gridName \u001b[38;5;241m+\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m...\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n",
"\u001b[0;31mAttributeError\u001b[0m: module 'ug4py.pyugcore' has no attribute 'Domain3d'"
]
}
],
"outputs": [],
"source": [
"# Setup:\n",
"# defining needed subsets, grid and number of refinements\n",
Expand Down Expand Up @@ -86,7 +74,7 @@
"\n",
" print(\"Refining done\")\n",
"\n",
"# checking if geometry has the needed subsets of the probelm\n",
"# checking if geometry has the needed subsets of the problem\n",
"sh = dom.subset_handler()\n",
"for e in requiredSubsets:\n",
" if sh.get_subset_index(e) == -1:\n",
Expand All @@ -105,22 +93,10 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": null,
"id": "8f75da00",
"metadata": {},
"outputs": [
{
"ename": "AttributeError",
"evalue": "module 'ug4py.pyugcore' has no attribute 'ApproximationSpace3d'",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[4], line 6\u001b[0m\n\u001b[1;32m 3\u001b[0m \u001b[38;5;28mtype\u001b[39m \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mLagrange\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 4\u001b[0m order \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m1\u001b[39m \u001b[38;5;66;03m# polynom order for lagrange\u001b[39;00m\n\u001b[0;32m----> 6\u001b[0m approxSpace \u001b[38;5;241m=\u001b[39m \u001b[43mug4\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mApproximationSpace3d\u001b[49m(dom)\n\u001b[1;32m 7\u001b[0m approxSpace\u001b[38;5;241m.\u001b[39madd_fct(fct, \u001b[38;5;28mtype\u001b[39m, order)\n\u001b[1;32m 8\u001b[0m approxSpace\u001b[38;5;241m.\u001b[39minit_levels()\n",
"\u001b[0;31mAttributeError\u001b[0m: module 'ug4py.pyugcore' has no attribute 'ApproximationSpace3d'"
]
}
],
"outputs": [],
"source": [
"\n",
"# Create approximation space which describes the unknowns in the equation\n",
Expand Down Expand Up @@ -181,7 +157,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": null,
"id": "f8e0894b",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -213,7 +189,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": null,
"id": "3140f477",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -255,179 +231,10 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": null,
"id": "1b79efbe",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"+++ Integrating: [0, 1]\n",
"+++ Timestep +++1\n",
"+++ Reassemble (t=0, dt=0.00625)\n",
"+++ Timestep +++2\n",
"+++ Timestep +++3\n",
"+++ Timestep +++4\n",
"+++ Timestep +++5\n",
"+++ Timestep +++6\n",
"+++ Timestep +++7\n",
"+++ Timestep +++8\n",
"+++ Timestep +++9\n",
"+++ Timestep +++10\n",
"+++ Timestep +++11\n",
"+++ Timestep +++12\n",
"+++ Timestep +++13\n",
"+++ Timestep +++14\n",
"+++ Timestep +++15\n",
"+++ Timestep +++16\n",
"+++ Timestep +++17\n",
"+++ Timestep +++18\n",
"+++ Timestep +++19\n",
"+++ Timestep +++20\n",
"+++ Timestep +++21\n",
"+++ Timestep +++22\n",
"+++ Timestep +++23\n",
"+++ Timestep +++24\n",
"+++ Timestep +++25\n",
"+++ Timestep +++26\n",
"+++ Timestep +++27\n",
"+++ Timestep +++28\n",
"+++ Timestep +++29\n",
"+++ Timestep +++30\n",
"+++ Timestep +++31\n",
"+++ Timestep +++32\n",
"+++ Timestep +++33\n",
"+++ Timestep +++34\n",
"+++ Timestep +++35\n",
"+++ Timestep +++36\n",
"+++ Timestep +++37\n",
"+++ Timestep +++38\n",
"+++ Timestep +++39\n",
"+++ Timestep +++40\n",
"+++ Timestep +++41\n",
"+++ Timestep +++42\n",
"+++ Timestep +++43\n",
"+++ Timestep +++44\n",
"+++ Timestep +++45\n",
"+++ Timestep +++46\n",
"+++ Timestep +++47\n",
"+++ Timestep +++48\n",
"+++ Timestep +++49\n",
"+++ Timestep +++50\n",
"+++ Timestep +++51\n",
"+++ Timestep +++52\n",
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"+++ Timestep +++60\n",
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"+++ Timestep +++62\n",
"+++ Timestep +++63\n",
"+++ Timestep +++64\n",
"+++ Timestep +++65\n",
"+++ Timestep +++66\n",
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"+++ Timestep +++68\n",
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"+++ Timestep +++102\n",
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"+++ Timestep +++120\n",
"+++ Timestep +++121\n",
"+++ Timestep +++122\n",
"+++ Timestep +++123\n",
"+++ Timestep +++124\n",
"+++ Timestep +++125\n",
"+++ Timestep +++126\n",
"+++ Timestep +++127\n",
"+++ Timestep +++128\n",
"+++ Timestep +++129\n",
"+++ Timestep +++130\n",
"+++ Timestep +++131\n",
"+++ Timestep +++132\n",
"+++ Timestep +++133\n",
"+++ Timestep +++134\n",
"+++ Timestep +++135\n",
"+++ Timestep +++136\n",
"+++ Timestep +++137\n",
"+++ Timestep +++138\n",
"+++ Timestep +++139\n",
"+++ Timestep +++140\n",
"+++ Timestep +++141\n",
"+++ Timestep +++142\n",
"+++ Timestep +++143\n",
"+++ Timestep +++144\n",
"+++ Timestep +++145\n",
"+++ Timestep +++146\n",
"+++ Timestep +++147\n",
"+++ Timestep +++148\n",
"+++ Timestep +++149\n",
"+++ Timestep +++150\n",
"+++ Timestep +++151\n",
"+++ Timestep +++152\n",
"+++ Timestep +++153\n",
"+++ Timestep +++154\n",
"+++ Timestep +++155\n",
"+++ Timestep +++156\n",
"+++ Timestep +++157\n",
"+++ Timestep +++158\n",
"+++ Timestep +++159\n",
"+++ Timestep +++160\n"
]
}
],
"outputs": [],
"source": [
"\n",
"# Define start time, end time and step size\n",
Expand Down Expand Up @@ -468,53 +275,22 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": null,
"id": "c4a48c79",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"Pyvista input: \n",
"UnstructuredGrid (0x1042a86a0)\n",
" N Cells: 5376\n",
" N Points: 3509\n",
" X Bounds: -1.000e+00, 1.000e+00\n",
" Y Bounds: -1.000e+00, 1.000e+00\n",
" Z Bounds: 0.000e+00, 3.500e+00\n",
" N Arrays: 1\n",
"\n"
]
},
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "4830ded197494a0cb69378fe42e07e22",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"Widget(value=\"<iframe src='http://localhost:55551/index.html?ui=P_0x2a0e72a10_1&reconnect=auto' style='width: …"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"outputs": [],
"source": [
"# Exporting the result to a vtu-file\n",
"# can be visualized in paraview or with a python extension\n",
"ug4.WriteGridFunctionToVTK(usol, \"BromFinal\")\n",
"\n",
"# Plotting the result using pyvista\n",
"import pyvista\n",
"result = pyvista.read('BromFinal.vtu')\n",
"print()\n",
"print(\"Pyvista input: \")\n",
"print(result)\n",
"result.plot(scalars=\"u\", show_edges=True, cmap='hot')\n"
"try:\n",
" # Plotting the result using pyvista\n",
" import pyvista\n",
" result = pyvista.read('BromFinal.vtu')\n",
" result.plot(scalars=\"u\", show_edges=True, cmap='hot')\n",
"except:\n",
" print(\"Plotting failed.\")"
]
},
{
Expand Down
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