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

[dokken]

@Rafael_Ferro

tetra_cells = cell.data

You are not concatenating data stemming from different cell blocks.
You have not followed the instructions in:

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

I disagree with your claim. All the code I have posted above is using msh 4.1. The following illustrates a use case with the latest version of GMSH. Starting from a clean ubuntu 20.04 environment using docker: docker run -ti -v $PWD:/home/shared -w /home/shared --rm ubuntu:20.04 Installation instructions in docker apt-get update -qq apt-get install -y -qq software-properties-common python3-pip libglu1 libxrender1 libcursor1 libxft2 libxinerama1 add-apt-repository -y ppa:fenics-packages/fen…

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

I had a play with pygmsh over the weekend, and what seems to be done in the later versions is to save the physical markers to cell sets. I have made the following function for this: def create_entity_mesh(mesh, cell_type, prune_z=False, remove_unused_points=False): """ Given a meshio mesh, extract mesh and physical markers for a given entity. We assume that all unused points are at the end of the mesh.points (this happens when we use physical markers with…

Need help converting GMSH to FEniCS - #8 by dokken

To repost this again:

import meshio


def create_mesh(mesh, cell_type, prune_z=False):
    cells = mesh.get_cells_type(cell_type)
    cell_data = mesh.get_cell_data("gmsh:physical", cell_type)
    out_mesh = meshio.Mesh(points=mesh.points, cells={
                           cell_type: cells}, cell_data={"name_to_read": [cell_data]})
    if prune_z:
        out_mesh.prune_z_0()
    return out_mesh


msh = meshio.read("two_cantilever.msh")
facet_mesh = create_mesh(msh, "triangle", prune_z=True)
meshio.write("facet_mesh.xdmf", facet_mesh)

triangle_mesh = create_mesh(msh, "tetra", prune_z=True)
meshio.write("mesh.xdmf", triangle_mesh)

Note that you have not used boolean operations on your geometry, resulting in another mesh that what you would like. See: Using subdomains in diffusion equation - #6 by dokken