Problem : how to remove z-values to force 2d mesh (meshio)

Hi,

I have some problem with the definition of normal when the mesh is imported from gmsh.

Indeed, taking a 2d mesh of gmsh (on my .msh file I have a component in z but which is worth 0 everywhere) and defining a normal like n = FacetNormal (mesh), I get len​​(n) = 3.
So I have the n_z component in addition.

For some other software, I have directly a normal of length 2.

Is it normal ? If not, what is the way to automatically obtain a normal of length 2 (without having to extract the first two components of the 3-dimensional one) ?

Thank you

Hi,
meshio has an option for removing the z-coordinate, see:

Hi dokken,

Thank you very much for your answer.

Hi,

Unfortunately, I have the same problem again.

Indeed, using the command meshio-convert TestPruning.msh TestPruning2.xdmf -p -z on a terminal give me

Number of points: 1088
Number of elements:
line: 128
triangle: 2048
Cell data: gmsh:geometrical, gmsh:physical
Pruned cell types: line

This prunes all my lines !

In consequence, it is impossible to write the mf.xdmf file (since there is no line). The error (expected) from FEniCS is :
cells={"line": msh.cells["line"]},
KeyError: 'line'.

I tried the command meshio-convert TestPruning.msh TestPruning2.xdmf -z but here the FEniCS error message is :

File "/home/amoreno3/anaconda3/envs/fenicsproject/lib/python3.6/site-packages/meshio-2.1.0-py3.6.egg/meshio/xdmf_io.py", line 139, in _translate_mixed_cells
r += xdmf_idx_to_num_nodes[data[r]] + 1
KeyError: 2

Do you have this problem too ?

My .geo file is just a square with a hole (with some physical lines and surface).

Thank you in advance for your answer

hello,
I tried to convert my 2D mesh from .msh file to .xdmf file with the command you posted.
meshio-convert trial.msh mesh.xdmf -p -z
but then i encounted with this error.

  File "/home/fenics/.local/bin/meshio-convert", line 8, in <module>
    sys.exit(convert())
  File "/home/fenics/.local/lib/python3.6/site-packages/meshio/_cli/_convert.py", line 18, in convert
    mesh.prune()
AttributeError: 'Mesh' object has no attribute 'prune'

Please submit an issue at: https://github.com/nschloe/meshio
Please provide a minimal msh file that reproduces the issue.

the trial.msh file is shown as below:

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When i tried to convert it into xdmf file in docker command as below:
meshio-convert trial.msh mesh.xdmf -p -z
The error comes as:

Traceback (most recent call last):
  File "/usr/bin/meshio-convert", line 135, in <module>
    _main()
  File "/usr/bin/meshio-convert", line 14, in _main
    args = _parse_options()
  File "/usr/bin/meshio-convert", line 100, in _parse_options
    choices=meshio.input_filetypes,
AttributeError: module 'meshio' has no attribute 'input_filetypes'

Thank you.

As I said in the previous post, post this as an issue at the meshio page. That is where you should provide the minimal example, error message and which version of meshio you are using.

1 Like

Hi,

I used the gmsh.model.mesh.generate(2) command. Is that not enough for generating a 2D mesh?

Also, regarding the prune option I have two questions:

  1. I need an xdmf file with the lines (facets) of the mesh. However, with this method I only export a mesh.xdmf file, while in the case where I import the whole .msh file into dolfin I can create two files with the triangles and facets separately. How can I do that here?
  2. The prune command eshio-convert mesh.msh mesh_2D.xdmf -p -z returns this warning: UserWarning: prune() will soon be deprecated. Use remove_lower_dimensional_cells(), remove_orphaned_nodes() instead.

Hello,

For your first question, the thing to do is to look directly at the tables on the resulting msh files: if it’s in 2d, a pruning by meshio is not necessary.
I personally don’t use this command.

  1. you must first create two xdmf files (which will be in 3d), from the msh file, containing the surface and line information.
    Then, you will have to do a pruning on each of these xdmf files with the option “-z”.
    You will then be able to make FEniCS read them.

  2. I can only recommend you to use the new syntax even if I still use the old one.

Hi @AMM,

Thank you for your reply.

The top of my mesh file looks like:
`
$MeshFormat

4.1 0 8
$EndMeshFormat
$PhysicalNames
3
1 1 "Inlet"
1 2 "Outlet"
1 3 "Walls"
$EndPhysicalNames
$Entities
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2 0 1 0 0 
3 100 1 0 0 
4 100 0 0 0 
1 0 0 0 0 1 0 1 1 2 1 -2 
2 0 1 0 100 1 0 1 3 2 2 -3 
3 100 0 0 100 1 0 1 2 2 3 -4 
4 0 0 0 100 0 0 1 3 2 4 -1 
1 0 0 0 100 1 0 1 1 4 1 2 3 4 
$EndEntities
$Nodes
9 48231 1 48231
0 1 0 1
`

which then changes to 3 numbers per row, then one and then 4… It is very confusing.

  1. I created these files within fenics. Is there any way to prune within fenics?

Many thanks!

I suggest having a look at my updated pygmsh tutorial, specifically: