Import tet mesh in dolfinx

dolfinx
1

Error ehile loading 3D tet mesh in dolfinx.

 mesh, subdomains, boundaries = gmshio.read_from_msh("tet_3D.msh", MPI.COMM_WORLD,0, gdim=3) 

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
Cell In[8], line 1
----> 1 mesh, subdomains, boundaries = gmshio.read_from_msh("tet_3D.msh", MPI.COMM_WORLD,0, gdim=3) 

File /usr/lib/petsc/lib/python3/dist-packages/dolfinx/io/gmshio.py:373, in read_from_msh(filename, comm, rank, gdim, partitioner)
    371 gmsh.model.add("Mesh from file")
    372 gmsh.merge(filename)
--> 373 msh = model_to_mesh(gmsh.model, comm, rank, gdim=gdim, partitioner=partitioner)
    374 gmsh.finalize()
    375 return msh

File /usr/lib/petsc/lib/python3/dist-packages/dolfinx/io/gmshio.py:290, in model_to_mesh(model, comm, rank, gdim, partitioner, dtype)
    287         facet_values = np.empty((0,), dtype=np.int32)
    289 # Create distributed mesh
--> 290 ufl_domain = ufl_mesh(cell_id, gdim, dtype=dtype)
    291 gmsh_cell_perm = cell_perm_array(_cpp.mesh.to_type(str(ufl_domain.ufl_cell())), num_nodes)
    292 cells = cells[:, gmsh_cell_perm].copy()

File /usr/lib/petsc/lib/python3/dist-packages/dolfinx/io/gmshio.py:76, in ufl_mesh(gmsh_cell, gdim, dtype)
     74     raise e
     75 cell = ufl.Cell(shape)
---> 76 element = basix.ufl.element(
     77     basix.ElementFamily.P,
     78     cell.cellname(),
     79     degree,
     80     basix.LagrangeVariant.equispaced,
     81     shape=(gdim,),
     82     dtype=dtype,  # type: ignore[arg-type]
     83 )
     84 return ufl.Mesh(element)

File /usr/lib/python3/dist-packages/basix/ufl.py:2006, in element(family, cell, degree, lagrange_variant, dpc_variant, discontinuous, shape, symmetry, dtype)
   2003     elif family == EF.DPC:
   2004         dpc_variant = _basix.DPCVariant.diagonal_gll
-> 2006 e = _basix.create_element(
   2007     family, cell, degree, lagrange_variant, dpc_variant, discontinuous, dtype=dtype
   2008 )
   2009 ufl_e = _BasixElement(e)
   2011 if shape is None or shape == tuple(e.value_shape):

File /usr/lib/python3/dist-packages/basix/finite_element.py:606, in create_element(family, celltype, degree, lagrange_variant, dpc_variant, discontinuous, dof_ordering, dtype)
    577 def create_element(
    578     family: ElementFamily,
    579     celltype: CellType,
   (...)
    585     dtype: npt.DTypeLike = np.float64,
    586 ) -> FiniteElement:
    587     """Create a finite element.
    588 
    589     Args:
   (...)
    603         A finite element.
    604     """
    605     return FiniteElement(
--> 606         _create_element(
    607             family.value,
    608             celltype.value,
    609             degree,
    610             lagrange_variant.value,
    611             dpc_variant.value,
    612             discontinuous,
    613             dof_ordering if dof_ordering is not None else [],
    614             np.dtype(dtype).char,
    615         )
    616     )

RuntimeError: Cannot pass a DPC variant to this element.

The .msh data:

$MeshFormat
2.2 0 8
$EndMeshFormat
$Nodes
9
1    -2.2299981443473595 0.49374912834507845 10.344827586206897
2    -2.056342014934421 0.42234502598529555 10.544827586206896
3    -2.062486500247639 0.4089720553352334 10.544827586206896
4    -2.0568290303717087 0.4199458559101729 10.744827586206895
5    -2.0573160458089967 0.4175466858350502 10.944827586206895
6    -2.0627328421274402 0.40675703452746365 10.744827586206895
7    -2.234752320279737 0.4861608460276258 10.744827586206895
8    -2.232375232313548 0.48995498718635216 10.544827586206896
9    -2.062240158367838 0.4111870761430031 10.344827586206897
$EndNodes
$Elements
4
1    4    2    0    1 1 2 3 9 
2    4    2    0    1 8 4 3 2 
3    4    2    2    1 8 4 6 3 
4    4    2    2    1 7 5 6 4 
$EndElements

The 4th column is for subdomain data and 5th to 8th column is for element connectivity.

2

Looks like your upgrade is incomplete. Which ubuntu are you using?

3

I completed the upgrade and install fenicx again. The ubuntu is 22.04.3. dolfinx is now working, however, I am getting error in loading .msh file using gmshio.

4

@dparsons
I am getting following error after updation.

import dolfinx
from dolfinx.fem import VectorFunctionSpace, form, petsc, Function, FunctionSpace

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
Cell In[2], line 2
      1 import dolfinx
----> 2 from dolfinx.fem import VectorFunctionSpace, form, petsc, Function, FunctionSpace

ImportError: cannot import name 'VectorFunctionSpace' from 'dolfinx.fem' (/usr/lib/petsc/lib/python3/dist-packages/dolfinx/fem/__init__.py)

It was working previously, but, after updating, it has error.

5

That still looks like an incomplete upgrade. Are you sure you ran sudo apt update before installing or upgrading?

6

Or you mean it fails when you import VectorFunctionSpace? The API changed in v0.8.
See further discussion for instance at Automatic update to Fenicsx 0.8 broke ufl.FiniteElement

2 Likes
7

@dparsons . Thanks for identifying the issue. With new syntax, it works.

import basix
V = dolfinx.fem.functionspace(mesh, basix.ufl.element(
    "CG", mesh.topology.cell_name(), 1, shape=(3, )))