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Merged
lmoresi merged 19 commits into from
Jul 24, 2025
Merged

Swarm rework dev merged #2

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49c09b8
Alternative to .vtk for mesh to pyvista
lmoresi Jun 24, 2025
91bec90
"Fix" for pointwise function test
lmoresi Jun 24, 2025
ae32ac5
Geometry tools - add point in simplex etc
lmoresi Jun 24, 2025
bd8bbb3
Formatting changes
lmoresi Jun 24, 2025
4670fe8
Formatting changes
lmoresi Jun 24, 2025
086c0d7
Hiding some functions
lmoresi Jun 24, 2025
4841242
BASIC swarm
lmoresi Jun 24, 2025
a53470b
Hiding some functions
lmoresi Jun 24, 2025
8d6c94b
Advection for BASIC swarm
lmoresi Jun 28, 2025
20c4731
Merge branch 'swarm-rework-lm-2025' into swarm-rework-dev-merged
lmoresi Jun 28, 2025
2722460
kdtree updates propagating into swarm rework code
lmoresi Jun 28, 2025
b1b8dca
Mesh class: clean up code and update KDTree
lmoresi Jul 1, 2025
4cc1209
Add docstrings to swarm classes. NodalPointBasicSwarm
lmoresi Jul 1, 2025
ee394d2
NodalSwarm rework
lmoresi Jul 3, 2025
0778b7d
Fix uw.function.evaluate / eliminate evalf
lmoresi Jul 7, 2025
0c6ed17
Adding back nanoflann code temporarily
lmoresi Jul 7, 2025
f1daed6
Swarm -> evalf rework
lmoresi Jul 7, 2025
5f33fb3
Adding rbf as alternative to evalf in function.evaluate
lmoresi Jul 8, 2025
b8becc6
Minor fixes to quickstart
lmoresi Jul 24, 2025
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146 changes: 87 additions & 59 deletions docs/user/Notebooks/1-Meshes.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -14,15 +14,13 @@
},
"source": [
"<div style=\"float: right; width: 40%\">\n",
"<img src=\"media/SampleSphericalMesh.png\" width=100%>\n",
"<caption>\n",
"<i>\n",
"</i>\n",
"</caption>\n",
" \n",
"![](media/SampleSphericalMesh.png)\n",
"\n",
"</div>\n",
"\n",
"\n",
"# Notebook 1: Meshes\n",
"## Notebook 1: Meshes\n",
"\n",
"Introducing meshes: how to build them, interrogate them and visualise them.\n",
"\n",
Expand All @@ -36,7 +34,6 @@
"\n",
"Mesh adaptivity is a work-in-progress.\n",
"\n",
"\n",
"\n"
]
},
Expand Down Expand Up @@ -64,7 +61,7 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 2,
"id": "5a4437ff-63ae-4ffa-9f2b-8ec1b8b4baeb",
"metadata": {
"editable": true,
Expand All @@ -74,7 +71,15 @@
},
"tags": []
},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"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"
]
}
],
"source": [
"#| output: false # Suppress warnings in html version\n",
"\n",
Expand All @@ -100,7 +105,7 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 22,
"id": "1c928d60-24a9-4415-ab22-41834695c70a",
"metadata": {
"editable": true,
Expand All @@ -109,15 +114,26 @@
},
"tags": []
},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Constructing UW mesh from gmsh .meshes/uw_cubed_spherical_shell_ro1.0_ri0.547_elts8_plexTrue.msh\n",
"Mesh refinement levels: 0\n",
"Mesh coarsening levels: None\n",
"Populating mesh coordinates CoordinateSystemType.SPHERICAL\n"
]
}
],
"source": [
"mesh = uw.meshing.uw.meshing.CubedSphere(\n",
" radiusOuter=1.0,\n",
" radiusInner=0.547,\n",
" numElements=8,\n",
" refinement=0,\n",
" simplex=False,\n",
" verbose=False,\n",
" simplex=True,\n",
" verbose=True,\n",
")"
]
},
Expand All @@ -141,7 +157,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 23,
"id": "b9cfac97-5c19-46b1-aebd-0fb77678b9ed",
"metadata": {},
"outputs": [
Expand All @@ -152,12 +168,12 @@
" [-0.57735027, 0.57735027, -0.57735027],\n",
" [-0.57735027, -0.57735027, -0.57735027],\n",
" ...,\n",
" [ 0.58691901, -0.41511058, -0.41511058],\n",
" [ 0.6269543 , -0.44342636, -0.44342636],\n",
" [ 0.66698958, -0.47174214, -0.47174214]])"
" [ 0.61340251, 0.4866531 , 0.41538064],\n",
" [ 0.56556024, 0.42209717, 0.44274422],\n",
" [ 0.51755571, 0.41031492, 0.44421012]])"
]
},
"execution_count": 4,
"execution_count": 23,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -166,6 +182,14 @@
"mesh.data"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "a7c5dd7e-58d2-45d0-bfc6-eaded6da20f0",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "markdown",
"id": "1ed56724-adc5-49c6-a33b-4552b619cb07",
Expand Down Expand Up @@ -208,7 +232,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 26,
"id": "1cb8378c-cdb8-4e75-bd12-e85f12169ef7",
"metadata": {
"editable": true,
Expand All @@ -226,13 +250,14 @@
"\n",
"pvmesh = vis.mesh_to_pv_mesh(mesh)\n",
"pvmesh.point_data[\"z\"] = vis.scalar_fn_to_pv_points(pvmesh, mesh.CoordinateSystem.X[2])\n",
"pvmesh1 = pvmesh.copy()\n",
"\n",
"if mesh.dim==3:\n",
" pvmesh_c = pvmesh.clip( normal='z', crinkle=True, inplace=False, origin=(0.0,0.0,0.01))\n",
"\n",
"pl = pv.Plotter(window_size=(750, 750))\n",
"pl.add_mesh(pvmesh_c, show_edges=True, show_scalar_bar=False, opacity=1.0)\n",
"pl.add_mesh(pvmesh, show_edges=True, show_scalar_bar=False, opacity=0.3)\n",
"pl.add_mesh(pvmesh1, show_edges=True, show_scalar_bar=False, opacity=0.3)\n",
"\n",
"\n",
"# Save and show the mesh\n",
Expand All @@ -241,7 +266,7 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 27,
"id": "fd6cbed0-3159-4c6c-a482-6a9636158854",
"metadata": {
"editable": true,
Expand All @@ -266,10 +291,10 @@
" "
],
"text/plain": [
"<IPython.lib.display.IFrame at 0x155c7fc90>"
"<IPython.lib.display.IFrame at 0x35f726660>"
]
},
"execution_count": 6,
"execution_count": 27,
"metadata": {},
"output_type": "execute_result"
}
Expand Down Expand Up @@ -320,10 +345,10 @@
{
"data": {
"text/latex": [
"$\\displaystyle \\left[\\begin{matrix}{ r \\hspace{ 0.0pt } } & { \\theta \\hspace{ 0.01pt } } & { \\phi \\hspace{ 0.02pt } }\\end{matrix}\\right]$"
"$\\displaystyle \\left[\\begin{matrix}r & \\theta & \\phi\\end{matrix}\\right]$"
],
"text/plain": [
"Matrix([[{ r \\hspace{ 0.0pt } }, { \\theta \\hspace{ 0.01pt } }, { \\phi \\hspace{ 0.02pt } }]])"
"Matrix([[r, \\theta, \\phi]])"
]
},
"metadata": {},
Expand Down Expand Up @@ -382,33 +407,44 @@
"\n",
"\n",
"Mesh # 0: .meshes/uw_cubed_spherical_shell_ro1.0_ri0.547_elts8_plexFalse.msh\n",
"\n"
]
},
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "f18b77ba1d8d44ae96a3832ea3ffa5a3",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"Widget(value='<iframe src=\"http://localhost:50188/index.html?ui=P_0x307b3b5f0_1&reconnect=auto\" class=\"pyvista…"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Number of cells: 3072\n",
"\n",
"No variables are defined on the mesh\n",
"\n",
"| Boundary Name | ID | Min Size | Max Size |\n",
"| ------------------------------------------------------ |\n",
"| Lower | 1 | 678 | 678 |\n",
"| Upper | 2 | 678 | 678 |\n",
"| All_Boundaries | 1001 | 768 | 768 |\n",
"| UW_Boundaries | -- | 1356 | 1356 |\n",
"| ------------------------------------------------------ |\n",
"| Boundary Name | ID |\n",
"| -------------------------------- |\n",
"| Lower | 1 |\n",
"| Upper | 2 |\n",
"| Null_Boundary | 666 |\n",
"| All_Boundaries | 1001 |\n",
"| All_Boundaries | 1001 |\n",
"| UW_Boundaries | -- |\n",
"| -------------------------------- |\n",
"\n",
"\n",
"DM Object: uw_.meshes/uw_cubed_spherical_shell_ro1.0_ri0.547_elts8_plexFalse.msh 1 MPI process\n",
" type: plex\n",
"uw_.meshes/uw_cubed_spherical_shell_ro1.0_ri0.547_elts8_plexFalse.msh in 3 dimensions:\n",
" Number of 0-cells per rank: 3474\n",
" Number of 1-cells per rank: 10000\n",
" Number of 2-cells per rank: 9600\n",
" Number of 3-cells per rank: 3072\n",
"Labels:\n",
" depth: 4 strata with value/size (0 (3474), 1 (10000), 2 (9600), 3 (3072))\n",
" All_Boundaries: 1 strata with value/size (1001 (768))\n",
" Elements: 1 strata with value/size (99999 (5130))\n",
" Lower: 1 strata with value/size (1 (678))\n",
" Upper: 1 strata with value/size (2 (678))\n",
" celltype: 4 strata with value/size (0 (3474), 1 (10000), 4 (9600), 7 (3072))\n",
" UW_Boundaries: 2 strata with value/size (1 (678), 2 (678))\n"
"Use view(1) to view detailed mesh information.\n",
"\n"
]
}
],
Expand Down Expand Up @@ -438,25 +474,17 @@
{
"cell_type": "code",
"execution_count": null,
"id": "4c23a076-d47a-4d27-80b7-b28b0ad38523",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"id": "85dd4cc4-ae92-4dba-a917-298590533ca0",
"id": "2374ad95-c893-49a8-9915-de68374135ba",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"display_name": "Python (Pixi)",
"language": "python",
"name": "python3"
"name": "pixi-kernel-python3"
},
"language_info": {
"codemirror_mode": {
Expand All @@ -468,7 +496,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.10"
"version": "3.12.11"
}
},
"nbformat": 4,
Expand Down
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