# FEniCS shells mesh **URL:** \ **Category:** mesh\ **Created:** [November 27, 2023, 7:59pm UTC](https://fenicsproject.discourse.group/t/fenics-shells-mesh/12881 "2023-11-27T19:59:49Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![bagla0](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/bagla0/32/4677_2.png) [@bagla0](https://fenicsproject.discourse.group/u/bagla0)\ **Post date:** [November 27, 2023, 7:59pm UTC](https://fenicsproject.discourse.group/t/fenics-shells-mesh/12881/1 "2023-11-27T19:59:49Z")
Hi FEniCS family, I have few queries about FEniCS shells. 1. Importing shell mesh to FEniCS. I have nodes and element connectivity. I tried it importing using gmsh (converted .cgns file to .msh ). On converting to .xml using dolfin-convert, I am getting error " Unable to find cells of supported types". ![gmsh mesh_shell](https://global.discourse-cdn.com/free1/uploads/fenicsproject1/original/2X/6/62aca4fe8399183ceb99f033f7967a5aa206dfcc.png) ![element connect](https://global.discourse-cdn.com/free1/uploads/fenicsproject1/original/2X/e/e3ce09ee9a03ec8de257087f2290af4e656d789c.png) Can you provide a convenient way of importing shell mesh? 1. I want to use my own basis functions. How can I add it to UFL library so that installed FEniCS supports it? Can I define a UFL function in the code itself for new basis functions. (My requirement was to use curvilinear coordinates (xi,eta) to interpolate the geometry as used by commercial software? Is there any existing basis function satisfying this requirement? The basis functions are for 8 noded shell element). Any help is greatly appreciated. ---
**Author:** ![dokken](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/dokken/32/1560_2.png) [@dokken](https://fenicsproject.discourse.group/u/dokken)\ **Post date:** [November 27, 2023, 8:11pm UTC](https://fenicsproject.discourse.group/t/fenics-shells-mesh/12881/2 "2023-11-27T20:11:00Z")
`dolfin-convert` is outdated. Use `meshio` for conversion if you have to stick with legacy FEniCS. If you want to use your own basis functions, I would strongly suggest that you use FEniCSx, as you can define your own finite elements there, see for instance @mscroggs brilliant demo: [Creating TNT elements using Basix’s custom element interface — DOLFINx 0.7.2 documentation](https://docs.fenicsproject.org/dolfinx/v0.7.2/python/demos/demo_tnt-elements.html) ---
**Author:** ![bagla0](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/bagla0/32/4677_2.png) [@bagla0](https://fenicsproject.discourse.group/u/bagla0)\ **Post date:** [November 27, 2023, 8:33pm UTC](https://fenicsproject.discourse.group/t/fenics-shells-mesh/12881/3 "2023-11-27T20:33:23Z")
Thanks @dokken for your response. > [@dokken](#): > > Use `meshio` for conversion if you have to stick with legacy FEniCS I would try to switch to meshio. Can you recommend the specific examples for meshio? Does it treat shell element as a quad element or any other specific element? For FEniCSx, is there any reference guide other than available demos to follow changed basic UFL, Dolfin syntax like in legacy FENiCS (there was an entire available book) for getting better clarity. Any suggestion is helpful. ---
**Author:** ![dokken](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/dokken/32/1560_2.png) [@dokken](https://fenicsproject.discourse.group/u/dokken)\ **Post date:** [November 27, 2023, 8:37pm UTC](https://fenicsproject.discourse.group/t/fenics-shells-mesh/12881/4 "2023-11-27T20:37:29Z")
> [@bagla0](#): > > I would try to switch to meshio. Can you recommend the specific examples for meshio? Does it treat shell element as a quad element or any other specific element? Legacy fenics doesn’t have proper support for quad meshes, so I would really advice to stay away from it. I’ve created several guides on FEniCSx: [https://jsdokken.com/dolfinx-tutorial/](https://jsdokken.com/dolfinx-tutorial/) [https://jsdokken.com/FEniCS23-tutorial/README.html](https://jsdokken.com/FEniCS23-tutorial/README.html) and also the actual demos of DOLFINx [https://docs.fenicsproject.org/dolfinx/v0.7.2/python/demos.html](https://docs.fenicsproject.org/dolfinx/v0.7.2/python/demos.html) ---
**Author:** ![bagla0](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/bagla0/32/4677_2.png) [@bagla0](https://fenicsproject.discourse.group/u/bagla0)\ **Post date:** [November 30, 2023, 9:23pm UTC](https://fenicsproject.discourse.group/t/fenics-shells-mesh/12881/5 "2023-11-30T21:23:03Z")
[Mesh generation and conversion with GMSH and PYGMSH | Jørgen S. Dokken (jsdokken.com)](http://jsdokken.com/src/pygmsh_tutorial.html) In your tutorial, you define that for using meshio, we need to remove the z coordinate. But, my mesh is defined in 3D space using quad elements shown in above figure. I am not able to figure out with meshio. ```auto $MeshFormat 2.2 0 8 $EndMeshFormat $Nodes 40 1 -1.76776695 -0.25 -1.76776695 2 0. -0.25 -2.5 3 1.76776695 -0.25 -1.76776695 4 2.5 -0.25 0. 5 1.76776695 -0.25 1.76776695 6 0. -0.25 2.5 7 -1.76776695 -0.25 1.76776695 8 -2.5 -0.25 0. 9 -1.76776695 0.25 -1.76776695 10 0. 0.25 -2.5 11 1.76776695 0.25 -1.76776695 12 2.5 0.25 0. 13 1.76776695 0.25 1.76776695 14 0. 0.25 2.5 15 -1.76776695 0.25 1.76776695 16 -2.5 0.25 0. 17 -2.30969882 -0.25 -0.95670861 18 -1.76776695 0. -1.76776695 19 -2.30969882 0.25 -0.95670861 20 -2.5 0. 0. 21 -0.95670861 -0.25 -2.30969882 22 0. 0. -2.5 23 -0.95670861 0.25 -2.30969882 24 0.95670861 -0.25 -2.30969882 25 1.76776695 0. -1.76776695 26 0.95670861 0.25 -2.30969882 27 2.30969882 -0.25 -0.95670861 28 2.5 0. 0. 29 2.30969882 0.25 -0.95670861 30 2.30969882 -0.25 0.95670861 31 1.76776695 0. 1.76776695 32 2.30969882 0.25 0.95670861 33 0.95670861 -0.25 2.30969882 34 0. 0. 2.5 35 0.95670861 0.25 2.30969882 36 -0.95670861 -0.25 2.30969882 37 -1.76776695 0. 1.76776695 38 -0.95670861 0.25 2.30969882 39 -2.30969882 -0.25 0.95670861 40 -2.30969882 0.25 0.95670861 $EndNodes $Elements 8 1 3 2 0 1 8 1 9 16 2 3 2 0 1 1 2 10 9 3 3 2 0 1 2 3 11 10 4 3 2 0 1 3 4 12 11 5 3 2 0 1 4 5 13 12 6 3 2 0 1 5 6 14 13 7 3 2 0 1 6 7 15 14 8 3 2 0 1 7 8 16 15 $EndElements ``` Using the above .msh file I tried meshio for the above quad shell element in 3D space. It is reading the shell mesh but, I need to ask how to proceed to get subdomains and mesh used by PBC and functionspace respectively. ```auto import meshio import numpy as np # Read in mesh msh = meshio.read("a.msh") # Helper function to extract the cells and physical data def create_mesh(mesh, cell_type, prune_z=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={"name_to_read":[cell_data]}) return out_mesh print(np.unique(msh.cell_data_dict['gmsh:physical']['quad'])) #print(np.unique(msh.cell_data_dict['gmsh:physical']['hexahedron'])) # Convert mesh to XDMF quad_mesh = create_mesh(msh, "quad", prune_z=False) #meshio.write("3Dmesh/3Dblock_facet_mesh.xdmf", quad_mesh) #hexahedron_mesh = create_mesh(msh, "hexahedron", prune_z=False) #meshio.write("3Dmesh/3Dblock_mesh.xdmf", hexahedron_mesh) quad_mesh Number of points: 40 Number of cells: quad: 8 Cell data: name_to_read ``` My query is: what is the meshio alternative to get mesh and physical space. ```auto mesh = Mesh(fname + ".xml") subdomains = MeshFunction("size_t", mesh, fname + "_physical_region.xml") ``` ---
**Author:** ![dokken](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/dokken/32/1560_2.png) [@dokken](https://fenicsproject.discourse.group/u/dokken)\ **Post date:** [November 30, 2023, 10:07pm UTC](https://fenicsproject.discourse.group/t/fenics-shells-mesh/12881/6 "2023-11-30T22:07:47Z")
Legacy dolfin does not support quadrilateral elements read from file. You would have to use DOLFINx for this. I do not understand the last bit of your question. Reading in cell markers or facet markers has to be done by adding cell data to the corresponding meshes, as done in the tutorials. ---
**Author:** ![bagla0](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/bagla0/32/4677_2.png) [@bagla0](https://fenicsproject.discourse.group/u/bagla0)\ **Post date:** [December 1, 2023, 12:59am UTC](https://fenicsproject.discourse.group/t/fenics-shells-mesh/12881/7 "2023-12-01T00:59:55Z")
Sorry, I was unclear in describing. 1. > [@bagla0](#): > > `quad_mesh` after getting quad\_mesh, how can I use this mesh data to create a Function Space. ```auto Q = FunctionSpace(quad_mesh, ("CG", 1)) ``` ```auto AttributeError Traceback (most recent call last) Cell In[26], line 1 ----> 1 Q = FunctionSpace(quad_mesh, ("CG", 1)) File /usr/lib/petsc/lib/python3/dist-packages/dolfinx/fem/function.py:581, in FunctionSpace(mesh, element, form_compiler_options, jit_options) 561 def FunctionSpace(mesh: Mesh, 562 element: typing.Union[ufl.FiniteElementBase, ElementMetaData, 563 typing.Tuple[str, int, typing.Tuple, bool]], 564 form_compiler_options: typing.Optional[dict[str, typing.Any]] = None, 565 jit_options: typing.Optional[dict[str, typing.Any]] = None) -> FunctionSpaceBase: 566 """Create a finite element function space. 567 568 .. deprecated:: 0.7 (...) 579 580 """ --> 581 return functionspace(mesh, element, form_compiler_options, jit_options) File /usr/lib/petsc/lib/python3/dist-packages/dolfinx/fem/function.py:521, in functionspace(mesh, element, form_compiler_options, jit_options) 519 try: 520 e = ElementMetaData(*element) --> 521 ufl_e = basix.ufl.element(e.family, mesh.basix_cell(), e.degree, shape=e.shape, 522 symmetry=e.symmetry, gdim=mesh.ufl_cell().geometric_dimension()) 523 except TypeError: 524 ufl_e = element # type: ignore AttributeError: 'Mesh' object has no attribute 'basix_cell' ``` (there is no example of FEniCSx where you used external imported mesh and solved the variational problem). Can you give MWE for imported mesh to create FE formulation? 2. ```auto # Convert mesh to XDMF quad_mesh = create_mesh(msh, "quad", prune_z=False) meshio.write("a_phy.xdmf", quad_mesh) ``` ```auto WARNING:py.warnings:/home/bagla0/.local/lib/python3.10/site-packages/h5py/ __init__.py:36: UserWarning: h5py is running against HDF5 1.10.7 when it was built against 1.14.2, this may cause problems _warn(("h5py is running against HDF5 {0} when it was built against {1}, " ``` And with this the kernel dies everytime. 1. In legacy-fenics, we use the below code (MeshFunction) to get different subdomain using MeshFunction. What is MeshFunction alternative in fenicsx to define different subdomains? ```auto subdomains = MeshFunction("size_t", quad_mesh, fname + "_physical_region.xml") ``` ```auto --------------------------------------------------------------------------- NameError Traceback (most recent call last) Cell In[27], line 1 ----> 1 subdomains = MeshFunction("size_t", quad_mesh, fname + "_physical_region.xml") NameError: name 'MeshFunction' is not defined ``` I am new to FEniCSx and facing issues to run a simple problem using imported quad mesh. Any example with imported mesh would be helpful. ---
**Author:** ![dokken](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/dokken/32/1560_2.png) [@dokken](https://fenicsproject.discourse.group/u/dokken)\ **Post date:** [December 1, 2023, 4:15am UTC](https://fenicsproject.discourse.group/t/fenics-shells-mesh/12881/8 "2023-12-01T04:15:09Z")
> [@bagla0](#): > > (there is no example of FEniCSx where you used external imported mesh and solved the variational problem). Can you give MWE for imported mesh to create FE formulation? [https://jsdokken.com/dolfinx-tutorial/chapter1/membrane\_code.html?highlight=gmsh#interfacing-with-gmsh-in-dolfinx](https://jsdokken.com/dolfinx-tutorial/chapter1/membrane_code.html?highlight=gmsh#interfacing-with-gmsh-in-dolfinx) and [Defining subdomains for different materials — FEniCSx tutorial](https://jsdokken.com/dolfinx-tutorial/chapter3/subdomains.html?highlight=gmsh#subdomains-defined-from-external-mesh-data) are two of many examples using external meshes. > [@bagla0](#): > > ```auto > # Convert mesh to XDMF > quad_mesh = create_mesh(msh, "quad", prune_z=False) > meshio.write("a_phy.xdmf", quad_mesh) > > ``` This is related to how you have installed h5py. See for instance [Importing mesh gives error - #8 by dokken](https://fenicsproject.discourse.group/t/importing-mesh-gives-error/7282/8) For final question about meshfunctions, see the demos ive linked to earlier in this post