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lmoresilmoresi
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Putting this into a dev branch. We'll need to check against changes in v0.99
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‎.DS_Store‎

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‎.gitignore‎

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@@ -13,6 +13,12 @@ Jupyterbook/**/*.png
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Jupyterbook/**/*.vtk
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Jupyterbook/**/*.h5
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**/WIP/**/*.png
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**/BatPumpkin/**/*.png
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**/?????_debug.txt
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**/Untitled*.ipynb
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**/.jupyter/**
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# Byte-compiled / optimized / DLL files

‎Documentation/Ex_Anisotropy.ipynb‎

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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": "3.11.5"
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"version": "3.12.8"
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},
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"title": "Constitutive Models in Underworld 3"
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},

‎Notebooks/Developers/Timing/Timing_NonLinear_ShearBand.py‎

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# extension: .py
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# format_name: light
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# format_version: '1.5'
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# jupytext_version: 1.14.4
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# jupytext_version: 1.16.6
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# kernelspec:
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# display_name: Python 3 (ipykernel)
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# language: python

‎Notebooks/Developers/Timing/Timing_StokesSinker.py‎

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# extension: .py
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# format_name: light
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# format_version: '1.5'
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# jupytext_version: 1.14.1
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# jupytext_version: 1.16.6
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# kernelspec:
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# display_name: Python 3 (ipykernel)
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# language: python
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time += dt
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# + tags=[]
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timing.print_table(display_fraction=0.999)
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# -
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mesh.write_checkpoint("stokesSinkerTiming", meshUpdates=False, meshVars=[p, v])

‎Notebooks/Developers/WIP/ParallelEvaluate-viz.py‎

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# ---
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# jupyter:
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# jupytext:
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# formats: py:percent
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# text_representation:
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# extension: .py
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# format_name: percent
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# format_version: '1.3'
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# jupytext_version: 1.16.6
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# kernelspec:
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# display_name: Python (Pixi)
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# language: python
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# name: pixi-kernel-python3
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# ---
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# %%
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# This is required to fix pyvista
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# (visualisation) crashes in interactive notebooks (including on binder)
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import nest_asyncio
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nest_asyncio.apply()
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# %%
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import numpy as np
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import sympy
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import underworld3 as uw
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# %%
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index = 12
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basename = "output/Parallel_Evaluate"
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# %%
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meshball = uw.discretisation.Mesh(f"{basename}.mesh.{index:05d}.h5")
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# meshball.view()
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x, y = meshball.CoordinateSystem.X
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r, th = meshball.CoordinateSystem.xR
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unit_rvec = meshball.CoordinateSystem.unit_e_0
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# Orientation of surface normals
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Gamma_N = meshball.Gamma
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# %%
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scalar_var = uw.discretisation.MeshVariable(
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varname="Radius", mesh=meshball, vtype=uw.VarType.SCALAR, varsymbol=r"r"
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)
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rank_var = uw.discretisation.MeshVariable(
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varname="Rank",
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mesh=meshball,
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vtype=uw.VarType.SCALAR,
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varsymbol=r"Ra",
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degree=0,
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)
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# %%
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scalar_var.read_timestep(f"{basename}", "Radius", index, verbose=True)
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rank_var.read_timestep(f"{basename}", "Rank", index, verbose=True)
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# %%
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# %%
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swarm = uw.swarm.Swarm(meshball)
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error_var = uw.swarm.SwarmVariable(
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"Error",
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swarm,
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vtype=uw.VarType.SCALAR,
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_proxy=False,
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)
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s_rank_var = uw.swarm.SwarmVariable(
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"FRank",
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swarm,
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vtype=uw.VarType.SCALAR,
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_proxy=False,
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)
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swarm.read_timestep(
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basename,
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"data_swarm",
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index,
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migrate=False,
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)
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error_var.read_timestep(
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basename,
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"data_swarm",
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"Error",
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index,
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)
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s_rank_var.read_timestep(
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basename,
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"data_swarm",
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"FRank",
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index,
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)
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# %%
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in_or_out = meshball.points_in_domain(swarm.particle_coordinates.array[...].reshape(-1,2))
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# %%
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# %%
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import pyvista as pv
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pvmesh = uw.visualisation.mesh_to_pv_mesh(meshball)
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pvmesh.cell_data["rank"] = uw.visualisation.scalar_fn_to_pv_points(
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pvmesh.cell_centers(), rank_var.sym
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)
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error_swarm = uw.visualisation.swarm_to_pv_cloud(swarm)
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error_swarm.point_data["E"] = np.sqrt(error_var.array[:, 0, 0]**2)
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error_swarm.point_data["E2"] = np.sqrt(error_var.array[:, 0, 0]**2) * in_or_out.astype(float)
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error_swarm.point_data["R"] = np.sqrt(s_rank_var.array[:, 0, 0]**2) * in_or_out.astype(float)
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plotter = pv.Plotter()
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plotter.add_mesh(pvmesh, scalars="rank", cmap="rainbow", show_edges=True, opacity=0.2)
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plotter.add_points(error_swarm, cmap="rainbow", scalars="R", point_size=4)
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# plotter.add_points(error_swarm, scalars="E", point_size=3)
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plotter.show()
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# %%
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swarm.dm.getLocalSize()
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# %%

‎Notebooks/Developers/WIP/ParallelEvaluate.py‎

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# ---
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# jupyter:
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# jupytext:
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# formats: py:percent
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# text_representation:
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# extension: .py
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# format_name: percent
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# format_version: '1.3'
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# jupytext_version: 1.16.6
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# kernelspec:
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# display_name: Python (Pixi)
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# language: python
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# name: pixi-kernel-python3
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# ---
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# %%
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import numpy as np
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import sympy
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import underworld3 as uw
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# %%
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res = 0.05
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r_o = 1.0
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r_int = 0.825
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r_i = 0.55
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meshball = uw.meshing.AnnulusInternalBoundary(radiusOuter=r_o,
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radiusInternal=r_int,
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radiusInner=r_i,
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cellSize_Inner=res,
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cellSize_Internal=res*0.5,
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cellSize_Outer=res,
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centre=False,)
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meshbox = uw.meshing.UnstructuredSimplexBox(
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cellSize=res,
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minCoords=(-1.0, -1.0),
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maxCoords=(+1.0, +1.0),
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qdegree=3,
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)
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mesh = meshball
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x, y = mesh.CoordinateSystem.X
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r, th = mesh.CoordinateSystem.xR
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unit_rvec = mesh.CoordinateSystem.unit_e_0
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# Orientation of surface normals
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Gamma_N = mesh.Gamma
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# %%
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rank_var = uw.discretisation.MeshVariable(
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varname="Rank",
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mesh=mesh,
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vtype = uw.VarType.SCALAR,
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varsymbol=r"Ra",
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continuous=False,
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degree=0,
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)
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scalar_var = uw.discretisation.MeshVariable(
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varname="Radius",
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mesh=mesh,
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vtype = uw.VarType.SCALAR,
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varsymbol=r"r"
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)
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scalar_var.array[...] = uw.function.evaluate(r, scalar_var.coords)
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rank_var.array[...] = uw.mpi.rank
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# %%
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## Functions that we can evaluate anywhere
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scalar_fn = scalar_var.sym[0,0] * sympy.sin(x) * sympy.cos(x)
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# %%
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# Random points in the bounding box of the domain (on each processor)
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coords = 1 - 2 * np.random.random(size=(1000,2))
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# %%
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results, is_extrapolated = uw.function.global_evaluate(scalar_fn, coords, rbf=False, check_extrapolated=True)
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# %%
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rank, is_extrapolated = uw.function.global_evaluate(rank_var.sym[0], coords, rbf=False, check_extrapolated=True)
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# %%
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true_results = uw.function.global_evaluate(r * sympy.sin(x) * sympy.cos(x) , coords, rbf=False, check_extrapolated=False)
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# %%
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inside_domain = mesh.points_in_domain(coords)
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print(f"{uw.mpi.rank} Max difference - {(results - true_results).max()}", flush=True)
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print(f"{uw.mpi.rank} Mean difference - {(results - true_results).mean()}", flush=True)
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print(f"{uw.mpi.rank} Max difference [in domain] - {(results - true_results)[inside_domain].max()}", flush=True)
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print(f"{uw.mpi.rank} Mean difference [in domain] - {(results - true_results)[inside_domain].mean()}", flush=True)
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# %%
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swarm = uw.swarm.Swarm(mesh)
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error_var = uw.swarm.SwarmVariable("Error", swarm, vtype=uw.VarType.SCALAR, _proxy=False)
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s_rank_var = uw.swarm.SwarmVariable("FRank", swarm, vtype=uw.VarType.SCALAR, _proxy=False)
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# %%
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swarm.add_particles_with_global_coordinates(coords, migrate=False)
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# %%
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error_var.array[...] = (results - true_results)
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s_rank_var.array[...] = rank[...]
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uw.mpi.barrier()
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# %%
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mesh.write_timestep(
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"Parallel_Evaluate",
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meshUpdates=True,
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meshVars=[scalar_var, rank_var],
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outputPath="output",
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index=uw.mpi.size,
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)
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# %%
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swarm.write_timestep(
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"Parallel_Evaluate",
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"data_swarm",
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swarmVars=[error_var, s_rank_var],
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outputPath="output",
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index=uw.mpi.size,
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force_sequential=True,
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)
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# %%
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if uw.mpi.rank == 0:
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print("Complete", flush=True)
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# %%
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exit(0)
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# %%

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