Hele-Shaw flow past a circle in dolfinx

[dokken]

Next time it would be useful if you post the whole error message:

Traceback (most recent call last):
  File "/root/shared/mwe123.py", line 49, in <module>
    mesh_obj, a, b = dolfinx.io.gmshio.model_to_mesh(
  File "/usr/local/dolfinx-real/lib/python3.10/dist-packages/dolfinx/io/gmshio.py", line 232, in model_to_mesh
    cell_id = cell_information[perm_sort[-1]]["id"]
IndexError: index -1 is out of bounds for axis 0 with size 0

You can search for the IndexError on the forum to find

Gmshio.model_to_mesh 1D mesh error

You should never call after adding physical groups, as it removes them. I.e. restructuring the code as import dolfinx from mpi4py import MPI import gmsh gmsh.initialize() gmsh.model.add("1d") p1 = gmsh.model.occ.addPoint(1, 1, 0) p2 = gmsh.model.occ.addPoint(2, 1, 0) l1 = gmsh.model.occ.addLine(p1, p2) gmsh.model.occ.synchronize() gmsh.model.addPhysicalGroup(1, [l1], 101) gmsh.model.mesh.generate(1) gdim = 2 gmsh_model_rank = 0 mesh_comm = MPI.COMM_WORLD mesh1, cell_tags1, facet_tags1 = …

Problem with xdmf.read_mesh

So this error message means that you are not using phyiscal entity grouping in Gmsh, Which is adviced to avoid Getting duplicate nodes and cells in your mesh.

Build a torus with gmsh - Error when loading mesh into DOLFINx

You need to add physical groups to your mesh, as the function read_from_msh states Reads a mesh from a msh-file and returns the distributed DOLFINx mesh and cell and facet markers associated with physical groups in the msh file.

which all points you to the fact that you need to add physical groups to your mesh in GMSH to be able to read it with gmshio.model_to_mesh
https://docs.fenicsproject.org/dolfinx/v0.7.3/python/generated/dolfinx.io.gmshio.html?highlight=model_to_mesh#dolfinx.io.gmshio.model_to_mesh