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Swarm rework / dev merged #330

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49f267d
Update __init__.py
lmoresi Mar 26, 2025
0a35525
Update NextSteps.qmd
lmoresi Mar 27, 2025
0b3a4b3
Update UW-Background.bib
lmoresi Mar 27, 2025
dc8887d
Update build_deploy_pdoc.yml
lmoresi Mar 28, 2025
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
bf3cdec
Merge branch 'main' into swarm-rework-dev-merged
lmoresi Jun 28, 2025
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113 changes: 70 additions & 43 deletions docs/user/Notebooks/1-Meshes.ipynb
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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 Down Expand Up @@ -109,15 +106,26 @@
},
"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 Down Expand Up @@ -152,9 +160,9 @@
" [-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,
Expand All @@ -166,6 +174,14 @@
"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 @@ -266,7 +282,7 @@
" "
],
"text/plain": [
"<IPython.lib.display.IFrame at 0x155c7fc90>"
"<IPython.lib.display.IFrame at 0x338a8d820>"
]
},
"execution_count": 6,
Expand Down Expand Up @@ -320,10 +336,10 @@
{
"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 @@ -381,34 +397,45 @@
"text": [
"\n",
"\n",
"Mesh # 0: .meshes/uw_cubed_spherical_shell_ro1.0_ri0.547_elts8_plexFalse.msh\n",
"Mesh # 0: .meshes/uw_cubed_spherical_shell_ro1.0_ri0.547_elts8_plexTrue.msh\n",
"\n"
]
},
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "2fe9b56bf1674abc9ec058d5c23de562",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"Widget(value='<iframe src=\"http://localhost:53921/index.html?ui=P_0x33e147c50_1&reconnect=auto\" class=\"pyvista…"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Number of cells: 7615\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 @@ -454,9 +481,9 @@
],
"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 +495,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.10"
"version": "3.12.11"
}
},
"nbformat": 4,
Expand Down
82 changes: 46 additions & 36 deletions docs/user/Notebooks/4-Solvers.ipynb
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Expand Up @@ -48,7 +48,7 @@
},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": 2,
"id": "042970c2-ab87-4483-b68c-3fe6b8e633a2",
"metadata": {
"editable": true,
Expand Down Expand Up @@ -85,36 +85,46 @@
"\n",
"\n",
"Mesh # 0: .meshes/uw_simplexbox_minC(0.0, 0.0)_maxC(1.0, 1.0)_csize0.08333333333333333_regFalse.msh\n",
"\n"
]
},
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "6880c7554aa44bf686d534271771e287",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"Widget(value='<iframe src=\"http://localhost:54175/index.html?ui=P_0x34f4d36b0_0&reconnect=auto\" class=\"pyvista…"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Number of cells: 346\n",
"\n",
"No variables are defined on the mesh\n",
"\n",
"| Boundary Name | ID | Min Size | Max Size |\n",
"| ------------------------------------------------------ |\n",
"| Bottom | 11 | 23 | 23 |\n",
"| Top | 12 | 23 | 23 |\n",
"| Right | 13 | 23 | 23 |\n",
"| Left | 14 | 23 | 23 |\n",
"| All_Boundaries | 1001 | 48 | 48 |\n",
"| UW_Boundaries | -- | 92 | 92 |\n",
"| ------------------------------------------------------ |\n",
"| Boundary Name | ID |\n",
"| -------------------------------- |\n",
"| Bottom | 11 |\n",
"| Top | 12 |\n",
"| Right | 13 |\n",
"| Left | 14 |\n",
"| Null_Boundary | 666 |\n",
"| All_Boundaries | 1001 |\n",
"| All_Boundaries | 1001 |\n",
"| UW_Boundaries | -- |\n",
"| -------------------------------- |\n",
"\n",
"\n",
"DM Object: uw_.meshes/uw_simplexbox_minC(0.0, 0.0)_maxC(1.0, 1.0)_csize0.08333333333333333_regFalse.msh 1 MPI process\n",
" type: plex\n",
"uw_.meshes/uw_simplexbox_minC(0.0, 0.0)_maxC(1.0, 1.0)_csize0.08333333333333333_regFalse.msh in 2 dimensions:\n",
" Number of 0-cells per rank: 198\n",
" Number of 1-cells per rank: 543\n",
" Number of 2-cells per rank: 346\n",
"Labels:\n",
" depth: 3 strata with value/size (0 (198), 1 (543), 2 (346))\n",
" All_Boundaries: 1 strata with value/size (1001 (48))\n",
" Bottom: 1 strata with value/size (11 (23))\n",
" Elements: 1 strata with value/size (99999 (496))\n",
" Left: 1 strata with value/size (14 (23))\n",
" Right: 1 strata with value/size (13 (23))\n",
" Top: 1 strata with value/size (12 (23))\n",
" celltype: 3 strata with value/size (0 (198), 1 (543), 3 (346))\n",
" UW_Boundaries: 4 strata with value/size (11 (23), 12 (23), 13 (23), 14 (23))\n"
"Use view(1) to view detailed mesh information.\n",
"\n"
]
}
],
Expand Down Expand Up @@ -186,7 +196,7 @@
"$$\n",
"\\nabla \\cdot\n",
" \\color{Blue}{\\underbrace{\\Bigl[ \\boldsymbol\\kappa \\nabla u \\Bigr]}_{\\mathbf{F}}} =\n",
" \\color{Maroon}{\\underbrace{\\Bigl[ f \\Bigl] }_{\\mathbf{f}}}\n",
" \\color{Maroon}{\\underbrace{\\Bigl[ f \\Bigl] }_{\\mathbf{h}}}\n",
"$$\n",
"\n",
"The term $\\mathbf{F}$ relates the flux to gradients in the unknown $u$\n",
Expand Down Expand Up @@ -234,9 +244,9 @@
"The projection implemented by creating a solver for this problem\n",
"\n",
"$$\n",
"\\nabla \\cdot\n",
"-\\nabla \\cdot\n",
" \\color{Blue}{\\underbrace{\\Bigl[ \\boldsymbol\\alpha \\nabla u \\Bigr]}_{\\mathbf{F}}} -\n",
" \\color{Maroon}{\\underbrace{\\Bigl[ u - \\tilde{f} \\Bigl] }_{\\mathbf{f}}} = 0\n",
" \\color{Maroon}{\\underbrace{\\Bigl[ u - \\tilde{f} \\Bigl] }_{\\mathbf{h}}} = 0\n",
"$$\n",
"\n",
"Where the term $\\mathbf{F}$ provides a smoothing regularization. $\\alpha$ can be zero.\n"
Expand Down Expand Up @@ -395,12 +405,12 @@
{
"data": {
"text/latex": [
"$\\displaystyle \\left[\\begin{matrix}- 3 {T}_{,0}^{ 2 }(\\mathbf{x}) - {T}_{,1}^{ 2 }(\\mathbf{x}) + 1 & - 2 {T}_{,0}(\\mathbf{x}) {T}_{,1}(\\mathbf{x})\\\\- 2 {T}_{,0}(\\mathbf{x}) {T}_{,1}(\\mathbf{x}) & - {T}_{,0}^{ 2 }(\\mathbf{x}) - 3 {T}_{,1}^{ 2 }(\\mathbf{x}) + 1\\end{matrix}\\right]$"
"$\\displaystyle \\left[\\begin{matrix}- 3 { \\hspace{ 0.02pt } {T} }_{,0}^{ 2 }(\\mathbf{x}) - { \\hspace{ 0.02pt } {T} }_{,1}^{ 2 }(\\mathbf{x}) + 1 & - 2 { \\hspace{ 0.02pt } {T} }_{,0}(\\mathbf{x}) { \\hspace{ 0.02pt } {T} }_{,1}(\\mathbf{x})\\\\- 2 { \\hspace{ 0.02pt } {T} }_{,0}(\\mathbf{x}) { \\hspace{ 0.02pt } {T} }_{,1}(\\mathbf{x}) & - { \\hspace{ 0.02pt } {T} }_{,0}^{ 2 }(\\mathbf{x}) - 3 { \\hspace{ 0.02pt } {T} }_{,1}^{ 2 }(\\mathbf{x}) + 1\\end{matrix}\\right]$"
],
"text/plain": [
"Matrix([\n",
"[-3*{T}_{,0}(N.x, N.y)**2 - {T}_{,1}(N.x, N.y)**2 + 1, -2*{T}_{,0}(N.x, N.y)*{T}_{,1}(N.x, N.y)],\n",
"[ -2*{T}_{,0}(N.x, N.y)*{T}_{,1}(N.x, N.y), -{T}_{,0}(N.x, N.y)**2 - 3*{T}_{,1}(N.x, N.y)**2 + 1]])"
"[-3*{ \\hspace{ 0.02pt } {T} }_{,0}(N.x, N.y)**2 - { \\hspace{ 0.02pt } {T} }_{,1}(N.x, N.y)**2 + 1, -2*{ \\hspace{ 0.02pt } {T} }_{,0}(N.x, N.y)*{ \\hspace{ 0.02pt } {T} }_{,1}(N.x, N.y)],\n",
"[ -2*{ \\hspace{ 0.02pt } {T} }_{,0}(N.x, N.y)*{ \\hspace{ 0.02pt } {T} }_{,1}(N.x, N.y), -{ \\hspace{ 0.02pt } {T} }_{,0}(N.x, N.y)**2 - 3*{ \\hspace{ 0.02pt } {T} }_{,1}(N.x, N.y)**2 + 1]])"
]
},
"metadata": {},
Expand Down Expand Up @@ -494,7 +504,7 @@
" "
],
"text/plain": [
"<IPython.lib.display.IFrame at 0x157b68bd0>"
"<IPython.lib.display.IFrame at 0x372d715e0>"
]
},
"execution_count": 11,
Expand Down Expand Up @@ -528,9 +538,9 @@
],
"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 @@ -542,7 +552,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.10"
"version": "3.12.11"
}
},
"nbformat": 4,
Expand Down
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