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lmoresilmoresi
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Merge pull request #2 from underworldcode/swarm-rework-dev-merged
Swarm rework dev merged - pull all development branch changes back into the swarm rework for synchronisation and testing.
2 parents 9a71dc6 + b8becc6 commit 0de2376

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‎docs/user/Notebooks/1-Meshes.ipynb‎

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},
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"source": [
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"<div style=\"float: right; width: 40%\">\n",
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"<img src=\"media/SampleSphericalMesh.png\" width=100%>\n",
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"<caption>\n",
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"<i>\n",
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"</i>\n",
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"</caption>\n",
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" \n",
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"![](media/SampleSphericalMesh.png)\n",
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"\n",
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"</div>\n",
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"\n",
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"\n",
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"# Notebook 1: Meshes\n",
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"## Notebook 1: Meshes\n",
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"\n",
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"Introducing meshes: how to build them, interrogate them and visualise them.\n",
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"\n",
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"\n",
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"Mesh adaptivity is a work-in-progress.\n",
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"\n",
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"\n",
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"\n"
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]
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},
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},
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{
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"cell_type": "code",
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"execution_count": 9,
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"execution_count": 2,
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"id": "5a4437ff-63ae-4ffa-9f2b-8ec1b8b4baeb",
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"metadata": {
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"editable": true,
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},
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"tags": []
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},
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"outputs": [],
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"PostHog telemetry failed: HTTPSConnectionPool(host='eu.i.posthog.com', port=443): Max retries exceeded with url: /capture/ (Caused by NameResolutionError(\"<urllib3.connection.HTTPSConnection object at 0x3049912b0>: Failed to resolve 'eu.i.posthog.com' ([Errno 8] nodename nor servname provided, or not known)\"))\n"
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]
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}
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],
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"source": [
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"#| output: false # Suppress warnings in html version\n",
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"\n",
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"execution_count": 22,
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"id": "1c928d60-24a9-4415-ab22-41834695c70a",
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"metadata": {
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"editable": true,
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},
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"tags": []
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},
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"outputs": [],
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Constructing UW mesh from gmsh .meshes/uw_cubed_spherical_shell_ro1.0_ri0.547_elts8_plexTrue.msh\n",
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"Mesh refinement levels: 0\n",
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"Mesh coarsening levels: None\n",
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"Populating mesh coordinates CoordinateSystemType.SPHERICAL\n"
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]
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}
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],
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"source": [
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"mesh = uw.meshing.uw.meshing.CubedSphere(\n",
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" radiusOuter=1.0,\n",
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" radiusInner=0.547,\n",
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" numElements=8,\n",
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" refinement=0,\n",
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" simplex=False,\n",
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" verbose=False,\n",
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" simplex=True,\n",
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" verbose=True,\n",
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")"
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]
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},
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"execution_count": 23,
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"id": "b9cfac97-5c19-46b1-aebd-0fb77678b9ed",
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"metadata": {},
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"outputs": [
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" [-0.57735027, 0.57735027, -0.57735027],\n",
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" [-0.57735027, -0.57735027, -0.57735027],\n",
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" ...,\n",
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" [ 0.58691901, -0.41511058, -0.41511058],\n",
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" [ 0.6269543 , -0.44342636, -0.44342636],\n",
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" [ 0.66698958, -0.47174214, -0.47174214]])"
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" [ 0.61340251, 0.4866531 , 0.41538064],\n",
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" [ 0.56556024, 0.42209717, 0.44274422],\n",
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" [ 0.51755571, 0.41031492, 0.44421012]])"
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]
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},
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"execution_count": 4,
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"execution_count": 23,
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"metadata": {},
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"output_type": "execute_result"
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}
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"mesh.data"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "a7c5dd7e-58d2-45d0-bfc6-eaded6da20f0",
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"metadata": {},
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"outputs": [],
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"source": []
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},
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{
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"cell_type": "markdown",
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"id": "1ed56724-adc5-49c6-a33b-4552b619cb07",
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"execution_count": 26,
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"id": "1cb8378c-cdb8-4e75-bd12-e85f12169ef7",
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"metadata": {
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"editable": true,
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"\n",
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"pvmesh = vis.mesh_to_pv_mesh(mesh)\n",
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"pvmesh.point_data[\"z\"] = vis.scalar_fn_to_pv_points(pvmesh, mesh.CoordinateSystem.X[2])\n",
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"pvmesh1 = pvmesh.copy()\n",
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"\n",
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"if mesh.dim==3:\n",
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" pvmesh_c = pvmesh.clip( normal='z', crinkle=True, inplace=False, origin=(0.0,0.0,0.01))\n",
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"\n",
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"pl = pv.Plotter(window_size=(750, 750))\n",
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"pl.add_mesh(pvmesh_c, show_edges=True, show_scalar_bar=False, opacity=1.0)\n",
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"pl.add_mesh(pvmesh, show_edges=True, show_scalar_bar=False, opacity=0.3)\n",
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"pl.add_mesh(pvmesh1, show_edges=True, show_scalar_bar=False, opacity=0.3)\n",
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"\n",
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"\n",
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"# Save and show the mesh\n",
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"execution_count": 27,
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"id": "fd6cbed0-3159-4c6c-a482-6a9636158854",
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"metadata": {
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"editable": true,
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" "
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],
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"text/plain": [
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"<IPython.lib.display.IFrame at 0x155c7fc90>"
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"<IPython.lib.display.IFrame at 0x35f726660>"
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]
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},
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"execution_count": 6,
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"execution_count": 27,
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"metadata": {},
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"output_type": "execute_result"
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}
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{
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"data": {
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"text/latex": [
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"$\\displaystyle \\left[\\begin{matrix}{ r \\hspace{ 0.0pt } } & { \\theta \\hspace{ 0.01pt } } & { \\phi \\hspace{ 0.02pt } }\\end{matrix}\\right]$"
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"$\\displaystyle \\left[\\begin{matrix}r & \\theta & \\phi\\end{matrix}\\right]$"
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],
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"text/plain": [
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"Matrix([[{ r \\hspace{ 0.0pt } }, { \\theta \\hspace{ 0.01pt } }, { \\phi \\hspace{ 0.02pt } }]])"
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"Matrix([[r, \\theta, \\phi]])"
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]
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},
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"metadata": {},
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"\n",
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"\n",
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"Mesh # 0: .meshes/uw_cubed_spherical_shell_ro1.0_ri0.547_elts8_plexFalse.msh\n",
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"\n"
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]
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},
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "f18b77ba1d8d44ae96a3832ea3ffa5a3",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"Widget(value='<iframe src=\"http://localhost:50188/index.html?ui=P_0x307b3b5f0_1&reconnect=auto\" class=\"pyvista…"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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},
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Number of cells: 3072\n",
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"\n",
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"No variables are defined on the mesh\n",
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"\n",
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"| Boundary Name | ID | Min Size | Max Size |\n",
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"| ------------------------------------------------------ |\n",
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"| Lower | 1 | 678 | 678 |\n",
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"| Upper | 2 | 678 | 678 |\n",
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"| All_Boundaries | 1001 | 768 | 768 |\n",
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"| UW_Boundaries | -- | 1356 | 1356 |\n",
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"| ------------------------------------------------------ |\n",
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"| Boundary Name | ID |\n",
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"| -------------------------------- |\n",
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"| Lower | 1 |\n",
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"| Upper | 2 |\n",
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"| Null_Boundary | 666 |\n",
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"| All_Boundaries | 1001 |\n",
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"| All_Boundaries | 1001 |\n",
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"| UW_Boundaries | -- |\n",
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"| -------------------------------- |\n",
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"\n",
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"\n",
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"DM Object: uw_.meshes/uw_cubed_spherical_shell_ro1.0_ri0.547_elts8_plexFalse.msh 1 MPI process\n",
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" type: plex\n",
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"uw_.meshes/uw_cubed_spherical_shell_ro1.0_ri0.547_elts8_plexFalse.msh in 3 dimensions:\n",
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" Number of 0-cells per rank: 3474\n",
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" Number of 1-cells per rank: 10000\n",
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" Number of 2-cells per rank: 9600\n",
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" Number of 3-cells per rank: 3072\n",
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"Labels:\n",
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" depth: 4 strata with value/size (0 (3474), 1 (10000), 2 (9600), 3 (3072))\n",
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" All_Boundaries: 1 strata with value/size (1001 (768))\n",
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" Elements: 1 strata with value/size (99999 (5130))\n",
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" Lower: 1 strata with value/size (1 (678))\n",
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" Upper: 1 strata with value/size (2 (678))\n",
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" celltype: 4 strata with value/size (0 (3474), 1 (10000), 4 (9600), 7 (3072))\n",
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" UW_Boundaries: 2 strata with value/size (1 (678), 2 (678))\n"
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"Use view(1) to view detailed mesh information.\n",
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"\n"
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]
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}
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],
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "4c23a076-d47a-4d27-80b7-b28b0ad38523",
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"metadata": {},
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"outputs": [],
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"source": []
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "85dd4cc4-ae92-4dba-a917-298590533ca0",
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"id": "2374ad95-c893-49a8-9915-de68374135ba",
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"display_name": "Python (Pixi)",
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"language": "python",
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"name": "python3"
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"name": "pixi-kernel-python3"
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"language_info": {
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"codemirror_mode": {
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.11.10"
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"version": "3.12.11"
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}
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},
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"nbformat": 4,

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