.xdmf mixed type - problem with generating mesh

[p1rx]

Hi,
i have a problem with importing mesh generated in gmsh. The .msh file is being read and transformed to .xdmf by meshio 5.3.4. Although my mesh contains only triangular elements when it is being generated based on more than one physical group (surface) the generated .xdmf file is type “mixed”.
Files created based on the mesh generated on just one physical group work just fine

[dokken]

There are plenty of other posts on the forum regarding this, see:

Transitioning from mesh.xml to mesh.xdmf, from dolfin-convert to meshio

I dont really now how to help you further. If you use the docker to install fenics, and then run the following: docker run -ti --rm -v $(pwd):/home/fenics/shared quay.io/fenicsproject/stable:latest sudo pip install meshio lxml h5py I used gmsh 3.0.6 to generate the msh file. Then running the following script: import meshio msh = meshio.read("file.msh") meshio.write("mesh.xdmf", meshio.Mesh(points=msh.points, cells={"tetra": msh.cells["tetra"]})) meshio.write("mf.xdmf", meshio.Mesh(points=…

Extracting mesh regions for gmsh mesh

As I said in the previous post, follow my newest tutorial. I copied your geo output and created an msh file (mesh2.msh), which I then converted with the following script from the tutorial: import meshio mesh_from_file = meshio.read("mesh2.msh") import numpy def create_mesh(mesh, cell_type, prune_z=False): cells = numpy.vstack([cell.data for cell in mesh.cells if cell.type==cell_type]) cell_data = numpy.hstack([mesh.cell_data_dict["gmsh:physical"][key] for key …

Gmsh import error

It seems like you have not read the post I linked you to. You cannot use the meshio-convert script out of the box for XDMF, and you have to use the meshio python interface. See the second section of: Mesh generation and conversion with GMSH and PYGMSH | Jørgen S. Dokken where I read in a mesh: import meshio mesh_from_file = meshio.read("mesh.msh") extract data for a given cell type def create_mesh(mesh, cell_type, prune_z=False): cells = numpy.vstack([cell.data for cell in mesh.cells if …

[p1rx]

@Extracting mesh regions for gmsh mesh

rted with the followin

And indeed it worked. I have previously seen those answers but i thought that after said process the information about the physical groups would be lost and not passed to the new xdmf file, but apparently it does work as i intended.

[p1rx]

ok, the physical group information is stored in the dict mesh.cell_data_dict[“gmsh:physical”] of the cell objects