Unable to find entity in map, 3D mesh gmsh

[dokken]

Historically, transfinite surfaces and volumes do not play well with FEniCS, ref:

Issue reading the mesh tags imported from gmsh

Inspecting your mesh, i see that there are more points in your mesh than those that are part of the cells: (Pdb++) triangle_mesh.points.shape (64010, 2) (Pdb++) len(np.unique(triangle_mesh.cells_dict["quad"].reshape(-1))) 63593 which is problematic. This is probably due to the definition of Transfinite surfaces after making Physical Surface and Physical Curve.

The key thing to check is that if all the nodes, describing the facets of the mesh is part of the volume mesh, as done in: Fail to read tagged facets from mesh generated with GMSH - #2 by dokken
i.e. do something along the lines of:

line_vertices = np.unique(line_mesh.cells_dict["line"].flatten())
triangle_vertices = np.unique(triangle_mesh.cells_dict["triangle"].flatten())
print(line_vertices)
print(triangle_vertices)
print(np.isin(line_vertices, triangle_vertices))

just with tetrahedra and triangles.