Meshing issue- likely in how I'm constructing my meshes in GMSH

mesh
2

Hi @Sean_Breckling,

I believe the issue is the physical groups and the default behavior of Gmsh when physical groups are defined:

Since you have defined a physical group of surfaces, but not of volumes, your volume elements are not being exported. Hence the error when you try to define a tetrahedron finite element, since your mesh contains only triangles. To fix this, you can add Physical Volume(1) = {1,2}; to the end of your .geo file.

To convert the mesh, you can use the meshio Python package (note: not the meshio-convert script). Copy the following to a .py file (e.g. convert_mesh.py) and run using python convert_mesh.py:

import meshio

mesh_name = "mesh"

msh = meshio.read(mesh_name+".msh")

tet_data = msh.cell_data_dict["gmsh:physical"]["tetra"]
meshio.write(mesh_name+".xdmf",
    meshio.Mesh(points=msh.points,
        cells={"tetra": msh.cells_dict["tetra"]},
        cell_data={"dom_marker": [tet_data]}
    )
)

tri_data = msh.cell_data_dict["gmsh:physical"]["triangle"]
meshio.write(mesh_name+"_surf.xdmf",
    meshio.Mesh(points=msh.points,
        cells={"triangle": msh.cells_dict["triangle"]},
        cell_data={"bnd_marker": [tri_data]}
    )
)

This will give you two files, one containing the domain markers and one containing the surface markers. To read the mesh, use

from fenics import *

mesh = Mesh()
with XDMFFile("mesh.xdmf") as file:
    file.read(mesh)

P.S. There’s a birthday cake emoji appearing beside your username today. Happy birthday!

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