Hi all,
I am dealing with mixed-dimensional PDEs when I ran into an issue with computing facet tags. Trying to reproduce Dokken’s tutorial I do not see all the desired facets marked in the plot.
The MWE is
from mpi4py import MPI
import dolfinx
import numpy as np
mesh = dolfinx.mesh.create_unit_square(MPI.COMM_WORLD, 40, 40)
def Omega1(x, tol=1e-14):
return x[0] <= 0.7 + tol
def Omega0(x, tol=1e-14):
return 0.7-tol <= x[0]
tdim = mesh.topology.dim
cell_map = mesh.topology.index_map(tdim)
num_cells_local = cell_map.size_local + cell_map.num_ghosts
marker = np.empty(num_cells_local, dtype=np.int32)
heat_marker = 1
stokes_marker = 3
marker[dolfinx.mesh.locate_entities(mesh, tdim, Omega0)] = heat_marker
marker[dolfinx.mesh.locate_entities(mesh, tdim, Omega1)] = stokes_marker
cell_tags = dolfinx.mesh.meshtags(mesh, mesh.topology.dim,
np.arange(num_cells_local, dtype=np.int32),
marker)
# -
# + tags=["remove-input"]
assert len(np.unique(marker)) <= 2
# -
# This section will contain alot of figures, to illustrate the different steps.
# Expand to see the code for creating a plotter of meshes and meshtags.
# + tags=["hide-input"]
import sys, os
import pyvista
if sys.platform == "linux" and (os.getenv("CI") or pyvista.OFF_SCREEN):
pyvista.start_xvfb(0.05)
def plot_mesh(mesh: dolfinx.mesh.Mesh, tags: dolfinx.mesh.MeshTags=None):
plotter = pyvista.Plotter()
mesh.topology.create_connectivity(tdim-1, tdim)
if tags is None:
ugrid = pyvista.UnstructuredGrid(*dolfinx.plot.vtk_mesh(mesh))
else:
# Exclude indices marked zero
exclude_entities = tags.find(0)
marker = np.full_like(tags.values, True, dtype=np.bool_)
marker[exclude_entities] = False
ugrid = pyvista.UnstructuredGrid(*dolfinx.plot.vtk_mesh(mesh, tags.dim, tags.indices[marker]))
print(tags.indices[marker], tags.values[marker])
ugrid.cell_data["Marker"] = tags.values[marker]
plotter.add_mesh(ugrid, show_edges=True, line_width=3)
plotter.show_axes()
plotter.show()
plot_mesh(mesh, cell_tags)
# -
# Next we define the boundaries for our sub-domains
# + tags=["hide-input"]
mesh.topology.create_connectivity(tdim-1, tdim)
facet_map = mesh.topology.index_map(tdim-1)
num_facets_local = facet_map.size_local + facet_map.num_ghosts
facet_values = np.zeros(num_facets_local, dtype=np.int32)
outer_marker = 4
facet_values[dolfinx.mesh.exterior_facet_indices(mesh.topology)] = 4
def inlet(x, tol=1e-14):
return np.isclose(x[0], 0.0) & ((x[1] >= 0.4-tol) & (x[1]<=0.6+tol))
inlet_marker = 1
facet_values[dolfinx.mesh.locate_entities_boundary(mesh, tdim-1, inlet)] = inlet_marker
def outlets(x, tol=1e-14):
return ((np.isclose(x[1], 0.0) & ((0.4 - tol <= x[0]) & (x[0]<=0.6 + tol))) |
(np.isclose(x[1], 1.0) & ((0.2 - tol <= x[0]) & (x[0] <= 0.35 + tol))))
outlet_marker = 2
facet_values[dolfinx.mesh.locate_entities_boundary(mesh, tdim-1, outlets)] = outlet_marker
interface_marker = 3
facet_values[dolfinx.mesh.locate_entities(mesh, tdim-1, lambda x: np.isclose(x[0], 0.7))] = interface_marker
facet_tags = dolfinx.mesh.meshtags(mesh, tdim-1, np.arange(num_facets_local, dtype=np.int32), facet_values)
plot_mesh(mesh, facet_tags)
and I see the follwing for the facet tags:
I guess there is a bug somewhere, but I am not sure. My env is
aiohappyeyeballs 2.6.1 pyhd8ed1ab_0 conda-forge
aiohttp 3.11.16 py310hc74094e_0 conda-forge
aiosignal 1.3.2 pyhd8ed1ab_0 conda-forge
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suitesparse 5.10.1 h79486c6_3 conda-forge
superlu 7.0.0 h742a510_1 conda-forge
superlu_dist 8.2.1 h3dacc9e_1 conda-forge
svt-av1 3.0.2 h8ab69cd_0 conda-forge
tapi 1300.6.5 h03f4b80_0 conda-forge
tbb 2022.1.0 h9541205_0 conda-forge
terminado 0.18.1 pyh31c8845_0 conda-forge
tinycss2 1.4.0 pyhd8ed1ab_0 conda-forge
tk 8.6.13 h5083fa2_1 conda-forge
tomli 2.2.1 pyhd8ed1ab_1 conda-forge
tornado 6.4.2 py310h078409c_0 conda-forge
traitlets 5.14.3 pyhd8ed1ab_1 conda-forge
trame 3.8.2 pyhd8ed1ab_0 conda-forge
trame-client 3.7.1 pyhd8ed1ab_0 conda-forge
trame-server 3.4.0 pyhd8ed1ab_0 conda-forge
trame-vtk 2.8.15 pyhb419c8b_0 conda-forge
trame-vuetify 3.0.1 pyhd8ed1ab_0 conda-forge
types-python-dateutil 2.9.0.20241206 pyhd8ed1ab_0 conda-forge
typing-extensions 4.13.2 h0e9735f_0 conda-forge
typing_extensions 4.13.2 pyh29332c3_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_1 conda-forge
tzdata 2025b h78e105d_0 conda-forge
unicodedata2 16.0.0 py310h078409c_0 conda-forge
uri-template 1.3.0 pyhd8ed1ab_1 conda-forge
urllib3 2.4.0 pyhd8ed1ab_0 conda-forge
utfcpp 4.0.6 h54c0426_0 conda-forge
vtk 9.3.1 qt_py310he4b582b_215 conda-forge
vtk-base 9.3.1 qt_py310h9cd0699_215 conda-forge
vtk-io-ffmpeg 9.3.1 qt_py310he4b582b_215 conda-forge
wcwidth 0.2.13 pyhd8ed1ab_1 conda-forge
webcolors 24.11.1 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_3 conda-forge
websocket-client 1.8.0 pyhd8ed1ab_1 conda-forge
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
widgetsnbextension 4.0.14 pyhd8ed1ab_0 conda-forge
wslink 2.3.3 pyhd8ed1ab_0 conda-forge
x264 1!164.3095 h57fd34a_2 conda-forge
x265 3.5 hbc6ce65_3 conda-forge
xorg-libxau 1.0.12 h5505292_0 conda-forge
xorg-libxdmcp 1.1.5 hd74edd7_0 conda-forge
xz 5.8.1 h9a6d368_0 conda-forge
xz-gpl-tools 5.8.1 h9a6d368_0 conda-forge
xz-tools 5.8.1 h39f12f2_0 conda-forge
yaml 0.2.5 h3422bc3_2 conda-forge
yarl 1.18.3 py310hc74094e_1 conda-forge
zeromq 4.3.5 hc1bb282_7 conda-forge
zfp 0.5.5 hcfdfaf5_8 conda-forge
zipp 3.21.0 pyhd8ed1ab_1 conda-forge
zlib 1.3.1 h8359307_2 conda-forge
zstandard 0.23.0 py310h078409c_1 conda-forge
zstd 1.5.7 h6491c7d_2 conda-forge
Any help is highly appreciated!
Thanks,
Tom