Update gmshio: FEniCS/dolfinx#3547 (#139)

* Update gmshio

* Update mesh extaction

* Update last demo

python/demos/create_and_export_mesh.py

@@ -209,9 +209,10 @@ def generate_tet_boxes(
         gmsh.option.setNumber("Mesh.MaxNumThreads3D", MPI.COMM_WORLD.size)
         gmsh.model.mesh.generate(3)
         gmsh.model.mesh.setOrder(1)
-    mesh, _, ft = gmshio.model_to_mesh(gmsh.model, MPI.COMM_WORLD, 0)
+    mesh_data = gmshio.model_to_mesh(gmsh.model, MPI.COMM_WORLD, 0)
     gmsh.finalize()
-    return mesh, ft
+    assert mesh_data.facet_tags is not None
+    return mesh_data.mesh, mesh_data.facet_tags
 
 
 def generate_hex_boxes(
@@ -266,11 +267,12 @@ def generate_hex_boxes(
         gmsh.option.setNumber("Mesh.MaxNumThreads3D", MPI.COMM_WORLD.size)
         gmsh.model.mesh.generate(3)
         gmsh.model.mesh.setOrder(1)
-    mesh, _, ft = gmshio.model_to_mesh(gmsh.model, MPI.COMM_WORLD, 0)
+    MPI.COMM_WORLD.barrier()
+    mesh_data = gmshio.model_to_mesh(gmsh.model, MPI.COMM_WORLD, 0)
     gmsh.clear()
     gmsh.finalize()
-    MPI.COMM_WORLD.barrier()
-    return mesh, ft
+    assert mesh_data.facet_tags is not None
+    return mesh_data.mesh, mesh_data.facet_tags
 
 
 def gmsh_2D_stacked(celltype: str, theta: float, verbose: bool = False) -> Tuple[_mesh.Mesh, _mesh.MeshTags]:
@@ -381,15 +383,18 @@ def gmsh_2D_stacked(celltype: str, theta: float, verbose: bool = False) -> Tuple
         gmsh.option.setNumber("Mesh.MaxNumThreads3D", MPI.COMM_WORLD.size)
         gmsh.model.mesh.generate(2)
         gmsh.model.mesh.setOrder(1)
-    mesh, _, ft = gmshio.model_to_mesh(gmsh.model, MPI.COMM_WORLD, 0, gdim=2)
+    MPI.COMM_WORLD.Barrier()
+    mesh_data = gmshio.model_to_mesh(gmsh.model, MPI.COMM_WORLD, 0, gdim=2)
     r_matrix = _utils.rotation_matrix([0, 0, 1], theta)
 
     # NOTE: Hex mesh must be rotated after generation due to gmsh API
+    mesh = mesh_data.mesh
+    assert mesh_data.facet_tags is not None
     mesh.geometry.x[:] = np.dot(r_matrix, mesh.geometry.x.T).T
     gmsh.clear()
     gmsh.finalize()
     MPI.COMM_WORLD.barrier()
-    return mesh, ft
+    return mesh,  mesh_data.facet_tags
 
 
 def mesh_2D_dolfin(celltype: str, theta: float = 0, outdir: Union[str, Path] = Path("meshes")):

python/demos/demo_elasticity_disconnect.py

@@ -111,12 +111,16 @@
     gmsh.model.mesh.optimize("Netgen")
     gmsh.model.mesh.setOrder(2)
 
-
-mesh, ct, ft = gmshio.model_to_mesh(gmsh.model, MPI.COMM_WORLD, 0, gdim=3)
+MPI.COMM_WORLD.barrier()
+mesh_data = gmshio.model_to_mesh(gmsh.model, MPI.COMM_WORLD, 0, gdim=3)
+mesh = mesh_data.mesh
+assert mesh_data.cell_tags is not None
+ct = mesh_data.cell_tags
+assert mesh_data.facet_tags is not None
+ft = mesh_data.facet_tags
 
 gmsh.clear()
 gmsh.finalize()
-MPI.COMM_WORLD.barrier()
 
 V = functionspace(mesh, ("Lagrange", 1, (mesh.geometry.dim,)))
 

python/demos/demo_elasticity_disconnect_2D.py

@@ -67,13 +67,14 @@
     # gmsh.option.setNumber("General.Terminal", 1)
     gmsh.model.mesh.optimize("Netgen")
 
-mesh, ct, _ = gmshio.model_to_mesh(gmsh.model, MPI.COMM_WORLD, 0, gdim=2)
+MPI.COMM_WORLD.barrier()
+mesh_data = gmshio.model_to_mesh(gmsh.model, MPI.COMM_WORLD, 0, gdim=2)
 gmsh.clear()
 gmsh.finalize()
-MPI.COMM_WORLD.barrier()
+mesh = mesh_data.mesh
+assert mesh_data.cell_tags is not None
+ct = mesh_data.cell_tags
 
-with XDMFFile(mesh.comm, "test.xdmf", "w") as xdmf:
-    xdmf.write_mesh(mesh)
 V = functionspace(mesh, ("Lagrange", 1, (mesh.geometry.dim,)))
 tdim = mesh.topology.dim
 fdim = tdim - 1

python/demos/demo_stokes.py

@@ -130,9 +130,10 @@ def create_mesh_gmsh(
         # Generate mesh
         gmsh.model.mesh.generate(2)
     # Convert gmsh model to DOLFINx Mesh and meshtags
-    mesh, _, ft = gmshio.model_to_mesh(gmsh.model, MPI.COMM_WORLD, 0, gdim=2)
+    mesh_data = gmshio.model_to_mesh(gmsh.model, MPI.COMM_WORLD, 0, gdim=2)
     gmsh.finalize()
-    return mesh, ft
+    assert mesh_data.facet_tags is not None
+    return mesh_data.mesh, mesh_data.facet_tags
 
 
 mesh, mt = create_mesh_gmsh(res=0.1)

python/demos/demo_stokes_nest.py

@@ -108,9 +108,11 @@ def create_mesh_gmsh(
         # Generate mesh
         gmsh.model.mesh.generate(2)
     # Convert gmsh model to DOLFINx Mesh and meshtags
-    mesh, _, ft = gmshio.model_to_mesh(gmsh.model, MPI.COMM_WORLD, 0, gdim=2)
+    mesh_data = gmshio.model_to_mesh(gmsh.model, MPI.COMM_WORLD, 0, gdim=2)
+    assert mesh_data.cell_tags is not None
+    ft = mesh_data.facet_tags
     gmsh.finalize()
-    return mesh, ft
+    return mesh_data.mesh, ft
 
 
 # ------------------- Mesh and function space creation ------------------------

python/tests/test_cube_contact.py

@@ -154,12 +154,14 @@ def generate_hex_boxes():
         gmsh.option.setNumber("Mesh.MaxNumThreads3D", MPI.COMM_WORLD.size)
         gmsh.model.mesh.generate(3)
         gmsh.model.mesh.setOrder(1)
-    mesh, _, ft = gmshio.model_to_mesh(gmsh.model, MPI.COMM_WORLD, 0)
+    MPI.COMM_WORLD.barrier()
+    mesh_data = gmshio.model_to_mesh(gmsh.model, MPI.COMM_WORLD, 0)
     gmsh.clear()
     gmsh.finalize()
     # NOTE: Hex mesh must be rotated after generation due to gmsh API
-    mesh.geometry.x[:] = np.dot(r_matrix, mesh.geometry.x.T).T
-    return (mesh, ft)
+    mesh_data.mesh.geometry.x[:] = np.dot(r_matrix, mesh_data.mesh.geometry.x.T).T
+    assert mesh_data.facet_tags is not None
+    return (mesh_data.mesh, mesh_data.facet_tags)
 
 
 @pytest.mark.parametrize("get_assemblers", ["C++", "numba"], indirect=True)