Wall markers on a GMSH

General
1

Suppose that I have the following function I wrote to generate a rectangle mesh using GMSH:

def generate_mesh_quadrilateral(A,B,C,D,mesh_size):
    

    gmsh.initialize()
    gmsh.option.setNumber("General.Terminal",0) #To hide the mesh output values

    gmesh_point_A   = gmsh.model.geo.add_point(A[0], A[1], 0, mesh_size)
    gmesh_point_B   = gmsh.model.geo.add_point(B[0], B[1], 0, mesh_size)
    gmesh_point_C   = gmsh.model.geo.add_point(C[0], C[1], 0, mesh_size)
    gmesh_point_D   = gmsh.model.geo.add_point(D[0], D[1], 0, mesh_size)

    gmesh_line_AB   = [gmsh.model.geo.add_line(gmesh_point_A, gmesh_point_B)]
    gmesh_line_BC   = [gmsh.model.geo.add_line(gmesh_point_B, gmesh_point_C)]
    gmesh_line_CD   = [gmsh.model.geo.add_line(gmesh_point_C, gmesh_point_D)]
    gmesh_line_DA   = [gmsh.model.geo.add_line(gmesh_point_D, gmesh_point_A)]


    line_list     = gmesh_line_AB+gmesh_line_BC+gmesh_line_CD+gmesh_line_DA
    curve_loop    = gmsh.model.geo.add_curve_loop(line_list)
    plane_surface = gmsh.model.geo.add_plane_surface([curve_loop])

    gmsh.model.geo.synchronize()
    
    
  wall_marker     = int(1e8)
  in_flow_marker  = int(2e8)
  out_flow_marker = int(3e8)
    
    print("gmesh_point_A: ",gmesh_point_A)
    print("wall_marker: ",wall_marker)
    print("plane_surface: ",plane_surface)
    print("gmesh_line_BC: ",gmesh_line_BC)


    gmsh.model.addPhysicalGroup(2, [plane_surface], name = "My surface")
    gmsh.model.addPhysicalGroup(1, gmesh_line_AB+gmesh_line_CD, wall_marker)
    gmsh.model.addPhysicalGroup(1, gmesh_line_BC, out_flow_marker)
    gmsh.model.addPhysicalGroup(1, gmesh_line_DA, in_flow_marker)

    gmsh.model.mesh.generate()  
    domain, cell_tags, facet_tags = model_to_mesh(gmsh.model, MPI.COMM_WORLD, 0,gdim=2)
    gmsh.finalize()

    mesh = domain
    grid = pyvista.UnstructuredGrid(*create_vtk_mesh(mesh, mesh.topology.dim))

    pyvista.start_xvfb()
    plotter = pyvista.Plotter()
    plotter.add_mesh(grid, show_edges=True)
    plotter.view_xy()

    if not pyvista.OFF_SCREEN:
        plotter.show()
    else:
        pyvista.start_xvfb()
        
    output = {"domain":domain, "cell_tags":cell_tags, "facet_tags":facet_tags,
             "wall_marker":wall_marker,"in_flow_marker":in_flow_marker,"out_flow_marker":out_flow_marker }
        
    return output

Let

A = np.array([0,0])
B = np.array([5,0])
C = np.array([5,2])
D = np.array([0,2])

Then

mesh_size = 0.3
mesh_generator_output_without_dimensions= generate_mesh_quadrilateral(A,B,C,D,mesh_size)

will generate the following mesh:

image
image849×178 68.2 KB

My question is, in the code to generate this mesh, I used

wall_marker     = int(1e8)
in_flow_marker  = int(2e8)
out_flow_marker = int(3e8)

Reason for using such a large integer is because, numbers like 1 and 2 will be already allocated for GMSH points. My question is, does it really matter if I mark them as

wall_marker     = int(1)
in_flow_marker  = int(2)
out_flow_marker = int(3)

or should I have to avoid repeating the numbers at all cost? In this case, please note that number 1 is associated with the first GMSH point as well.
And later on, I will be utilizing these markers to implement the Navier stokes sover on FENICSx

Thank you

2

There is a difference between geometrical entities and physical entities in GMSH.

A physically marked entity can have the same integer value as a non-physical entity with no issue. DOLFINx only reads physically marked entities, as this is the default to generate when using Gmsh.

2 Likes
3

Thank you for the quick reply. May I know what you meant by the physical entities and the geometrical entities.

4

I would suggest you read a Gmsh tutorial: Gmsh 4.11.1

1 Like
5

Thanks for the link Dokken. I will go through that