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

mesh
144

Please look at one thing at the time.
The first step is simply to extract your mesh data (the set of entities, either lines, triangles or tetrahedrons)

def create_mesh(mesh, cell_type, prune_z=False):
    cells = numpy.vstack([cell.data for cell in mesh.cells if cell.type==cell_type])
    # Remove z-coordinates from mesh if we have a 2D cell and all points have the same third coordinate
    points= mesh.points
    if prune_z:
        points = points[:,:2]
    mesh_new = meshio.Mesh(points=points, cells={cell_type: cells})
    return mesh_new
line_mesh = create_mesh(mesh_from_file, "line", prune_z=True)
meshio.write("facet_mesh.xdmf", line_mesh)

triangle_mesh = create_mesh(mesh_from_file, "triangle", prune_z=True)
meshio.write("mesh.xdmf", triangle_mesh)

If this works, it means that you have converted your mesh successfully.
If you have physical markers for your mesh, you should be able to inspect it by printing

print(mesh_from_file.cell_data_dict)

You then need to add the corresponding cell data to the mesh, as shown in the previous post.

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