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NetGen updates #281

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2da3310
Update ngs installation in docker and minor fix for plotting in amr
jorgensd Oct 10, 2025
8765c7f
Docker update
jorgensd Oct 10, 2025
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25 changes: 17 additions & 8 deletions chapter2/amr.ipynb
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -191,6 +191,7 @@
},
"outputs": [],
"source": [
"plotter = pyvista.Plotter()\n",
"curved_grid = pyvista.UnstructuredGrid(*dolfinx.plot.vtk_mesh(curved_mesh))\n",
"curved_grid.cell_data[\"ct\"] = ct.values\n",
"plotter.add_mesh(\n",
Expand Down Expand Up @@ -275,7 +276,8 @@
" else:\n",
" diag_kwargs = {\"diag\": 0.0}\n",
"\n",
" M = dolfinx.fem.petsc.assemble_matrix(dolfinx.fem.form(m), bcs=[bc], **diag_kwargs)\n",
" M = dolfinx.fem.petsc.assemble_matrix(\n",
" dolfinx.fem.form(m), bcs=[bc], **diag_kwargs)\n",
" M.assemble()\n",
"\n",
" # Next, we define the SLEPc Eigenvalue Problem Solver (EPS), and set up to use a shift\n",
Expand Down Expand Up @@ -340,15 +342,19 @@
" eta_squared = dolfinx.fem.Function(W)\n",
" f = dolfinx.fem.Constant(mesh, 1.0)\n",
" h = dolfinx.fem.Function(W)\n",
" h.x.array[:] = mesh.h(mesh.topology.dim, np.arange(len(h.x.array), dtype=np.int32))\n",
" h.x.array[:] = mesh.h(mesh.topology.dim, np.arange(\n",
" len(h.x.array), dtype=np.int32))\n",
" n = ufl.FacetNormal(mesh)\n",
"\n",
" G = ( # compute cellwise error estimator\n",
" ufl.inner(h**2 * (f + ufl.div(ufl.grad(uh_r))) ** 2, w) * ufl.dx\n",
" + ufl.inner(h(\"+\") / 2 * ufl.jump(ufl.grad(uh_r), n) ** 2, w(\"+\")) * ufl.dS\n",
" + ufl.inner(h(\"-\") / 2 * ufl.jump(ufl.grad(uh_r), n) ** 2, w(\"-\")) * ufl.dS\n",
" + ufl.inner(h(\"+\") / 2 * ufl.jump(ufl.grad(uh_r), n)\n",
" ** 2, w(\"+\")) * ufl.dS\n",
" + ufl.inner(h(\"-\") / 2 * ufl.jump(ufl.grad(uh_r), n)\n",
" ** 2, w(\"-\")) * ufl.dS\n",
" )\n",
" dolfinx.fem.petsc.assemble_vector(eta_squared.x.petsc_vec, dolfinx.fem.form(G))\n",
" dolfinx.fem.petsc.assemble_vector(\n",
" eta_squared.x.petsc_vec, dolfinx.fem.form(G))\n",
" eta = dolfinx.fem.Function(W)\n",
" eta.x.array[:] = np.sqrt(eta_squared.x.array[:])\n",
"\n",
Expand Down Expand Up @@ -421,12 +427,14 @@
" uh_sign = np.sign(uh_r_min)\n",
" if np.isclose(uh_sign, 0):\n",
" uh_sign = np.sign(uh_r_max)\n",
" assert not np.isclose(uh_sign, 0), \"uh_r has zero values, cannot determine sign.\"\n",
" assert not np.isclose(\n",
" uh_sign, 0), \"uh_r has zero values, cannot determine sign.\"\n",
" uh_r.x.array[:] *= uh_sign\n",
"\n",
" # Update plot with refined mesh\n",
" grid = pyvista.UnstructuredGrid(*dolfinx.plot.vtk_mesh(mesh))\n",
" curved_grid = pyvista.UnstructuredGrid(*dolfinx.plot.vtk_mesh(uh_r.function_space))\n",
" curved_grid = pyvista.UnstructuredGrid(\n",
" *dolfinx.plot.vtk_mesh(uh_r.function_space))\n",
" curved_grid.point_data[\"u\"] = uh_r.x.array\n",
" curved_grid = curved_grid.tessellate()\n",
" curved_actor = plotter.add_mesh(\n",
Expand Down Expand Up @@ -479,7 +487,8 @@
" )\n",
"\n",
" cells_to_mark = mark_cells(uh_r, lam)\n",
" mesh, (_, ft) = geoModel.refineMarkedElements(mesh.topology.dim, cells_to_mark)\n",
" mesh, (_, ft) = geoModel.refineMarkedElements(\n",
" mesh.topology.dim, cells_to_mark)\n",
" curved_mesh = geoModel.curveField(order)\n",
" write_frame(plotter, uh_r)\n",
"\n",
Expand Down
25 changes: 17 additions & 8 deletions chapter2/amr.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -95,6 +95,7 @@
# Again, we visualize the curved mesh with pyvista.

# + tags=["hide-input"]
plotter = pyvista.Plotter()
curved_grid = pyvista.UnstructuredGrid(*dolfinx.plot.vtk_mesh(curved_mesh))
curved_grid.cell_data["ct"] = ct.values
plotter.add_mesh(
Expand Down Expand Up @@ -157,7 +158,8 @@ def solve(
else:
diag_kwargs = {"diag": 0.0}

M = dolfinx.fem.petsc.assemble_matrix(dolfinx.fem.form(m), bcs=[bc], **diag_kwargs)
M = dolfinx.fem.petsc.assemble_matrix(
dolfinx.fem.form(m), bcs=[bc], **diag_kwargs)
M.assemble()

# Next, we define the SLEPc Eigenvalue Problem Solver (EPS), and set up to use a shift
Expand Down Expand Up @@ -208,15 +210,19 @@ def mark_cells(uh_r: dolfinx.fem.Function, lam: float):
eta_squared = dolfinx.fem.Function(W)
f = dolfinx.fem.Constant(mesh, 1.0)
h = dolfinx.fem.Function(W)
h.x.array[:] = mesh.h(mesh.topology.dim, np.arange(len(h.x.array), dtype=np.int32))
h.x.array[:] = mesh.h(mesh.topology.dim, np.arange(
len(h.x.array), dtype=np.int32))
n = ufl.FacetNormal(mesh)

G = ( # compute cellwise error estimator
ufl.inner(h**2 * (f + ufl.div(ufl.grad(uh_r))) ** 2, w) * ufl.dx
+ ufl.inner(h("+") / 2 * ufl.jump(ufl.grad(uh_r), n) ** 2, w("+")) * ufl.dS
+ ufl.inner(h("-") / 2 * ufl.jump(ufl.grad(uh_r), n) ** 2, w("-")) * ufl.dS
+ ufl.inner(h("+") / 2 * ufl.jump(ufl.grad(uh_r), n)
** 2, w("+")) * ufl.dS
+ ufl.inner(h("-") / 2 * ufl.jump(ufl.grad(uh_r), n)
** 2, w("-")) * ufl.dS
)
dolfinx.fem.petsc.assemble_vector(eta_squared.x.petsc_vec, dolfinx.fem.form(G))
dolfinx.fem.petsc.assemble_vector(
eta_squared.x.petsc_vec, dolfinx.fem.form(G))
eta = dolfinx.fem.Function(W)
eta.x.array[:] = np.sqrt(eta_squared.x.array[:])

Expand Down Expand Up @@ -252,12 +258,14 @@ def write_frame(plotter: pyvista.Plotter, uh_r: dolfinx.fem.Function):
uh_sign = np.sign(uh_r_min)
if np.isclose(uh_sign, 0):
uh_sign = np.sign(uh_r_max)
assert not np.isclose(uh_sign, 0), "uh_r has zero values, cannot determine sign."
assert not np.isclose(
uh_sign, 0), "uh_r has zero values, cannot determine sign."
uh_r.x.array[:] *= uh_sign

# Update plot with refined mesh
grid = pyvista.UnstructuredGrid(*dolfinx.plot.vtk_mesh(mesh))
curved_grid = pyvista.UnstructuredGrid(*dolfinx.plot.vtk_mesh(uh_r.function_space))
curved_grid = pyvista.UnstructuredGrid(
*dolfinx.plot.vtk_mesh(uh_r.function_space))
curved_grid.point_data["u"] = uh_r.x.array
curved_grid = curved_grid.tessellate()
curved_actor = plotter.add_mesh(
Expand Down Expand Up @@ -296,7 +304,8 @@ def write_frame(plotter: pyvista.Plotter, uh_r: dolfinx.fem.Function):
)

cells_to_mark = mark_cells(uh_r, lam)
mesh, (_, ft) = geoModel.refineMarkedElements(mesh.topology.dim, cells_to_mark)
mesh, (_, ft) = geoModel.refineMarkedElements(
mesh.topology.dim, cells_to_mark)
curved_mesh = geoModel.curveField(order)
write_frame(plotter, uh_r)

Expand Down
6 changes: 3 additions & 3 deletions docker/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ RUN curl -sL https://deb.nodesource.com/setup_18.x -o nodesource_setup.sh && \

# Install netgen from source
RUN apt-get update && \
apt-get -y install python3 python3-tk libpython3-dev libxmu-dev tk-dev tcl-dev cmake git g++ libglu1-mesa-dev liblapacke-dev libocct-data-exchange-dev libocct-draw-dev occt-misc libtbb-dev libxi-dev
apt-get -y install python3 python3-tk libpython3-dev libxmu-dev tk-dev tcl-dev cmake git g++ libglu1-mesa-dev liblapacke-dev libocct-data-exchange-dev libocct-draw-dev occt-misc libtbb-dev libxi-dev
WORKDIR /ngsuite
RUN git clone --branch=v6.2.2505 --single-branch https://github.com/NGSolve/netgen.git netgen-src
WORKDIR /ngsuite/netgen-src
Expand All @@ -39,9 +39,9 @@ RUN python3 -m pip install vtk
ADD pyproject.toml /tmp/pyproject.toml
WORKDIR /tmp
# As we install netgen from source we don't need the netgen deps here
RUN python3 -m pip install --no-cache-dir --no-binary=h5py -v .
RUN python3 -m pip install --no-cache-dir --no-binary=h5py --no-build-isolation -v .
RUN python3 -m pip cache purge

RUN python3 -m pip install ngspetsc --no-deps --no-build-isolation
ENV PYVISTA_OFF_SCREEN="false"
ENV PYVISTA_JUPYTER_BACKEND="trame"
ENV LIBGL_ALWAYS_SOFTWARE=1
Expand Down