What is wrong with my mesh?

[dokken]

I cannot reproduce any errors with:

import meshio
import numpy as np


def create_mesh(mesh: meshio.Mesh, cell_type: str, data_name: str = "name_to_read",
                prune_z: bool = False):
    cells = mesh.get_cells_type(cell_type)
    cell_data = mesh.get_cell_data("gmsh:physical", cell_type)
    points = mesh.points[:, :2] if prune_z else mesh.points
    out_mesh = meshio.Mesh(points=points, cells={cell_type: cells}, cell_data={
                           data_name: [cell_data]})
    return out_mesh


# import and convert msh file to xdmf
msh = meshio.read('mesh.msh')

print(msh)
facet_mesh = create_mesh(msh, "triangle")
meshio.write("test_facet.xdmf", facet_mesh)

triangle_mesh = create_mesh(msh, "tetra")
meshio.write("test_mesh.xdmf", triangle_mesh)

which prints

<meshio mesh object>
  Number of points: 199
  Number of cells:
    triangle: 16
    triangle: 16
    tetra: 512
  Cell sets: gmsh:bounding_entities
  Point data: gmsh:dim_tags
  Cell data: gmsh:physical, gmsh:geometrical

Please look at all the other posts regarding gmsh/meshio

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

As far as I can tell you would like to have a 3D mesh (tetrahedrons). Then you also need to mark the volumes: // Gmsh project created on Tue May 18 16:34:55 2021 SetFactory("OpenCASCADE"); //+ Circle(1) = {0, 00, 00, 0.6, 0, 2*Pi}; //+ Circle(2) = {0, 00, 00, 0.4, 0, 2*Pi}; //+ Curve Loop(1) = {1}; //+ Curve Loop(2) = {2}; //+ Plane Surface(1) = {1, 2}; //+ Extrude {0, 0, 10} { Curve{2}; Curve{1}; Layers {1}; Recombine; } //+ Curve Loop(5) = {6}; //+ Curve Loop(6) = {4}; //+ Plane Surface(4) …

Need help converting GMSH to FEniCS

Please note that you have some errors in your geo-file, i.e. Correcting these, and adding Physical Surface("surf", 1) = {2}; at the end, the following file (mesh.geo) // Gmsh project created on Thu Nov 18 16:23:27 2021 SetFactory("OpenCASCADE"); Rectangle(1) = {0, 0, 0, 18, 6, 0}; Point(5) = {3, 2.8, 0, 0.05}; Point(6) = {3, 3.2, 0, 0.05}; Point(7) = {3.3464, 3.4, 0, 0.05}; Point(8) = {3.3464, 2.6, 0, 0.05}; Point(9) = {3.6928, 2.8, 0, 0.05}; Point(10) = {3.6928, 3.2, 0, 0.05}; Point(11) = …

as they contain a lot of tips and tricks.