*** Unable to find cells of supported type. when converting from Gmsh format (.msh, .gmsh) to DOLFIN XML format

mesh
1

Hi, I am trying to convert the following msh file to DOLFIN XML:

$MeshFormat
2.2 0 8
$EndMeshFormat
$PhysicalNames
6
2 6 "contorno"
3 1 "medula"
3 2 "hueso"
3 3 "musculo"
3 4 "grasa"
3 5 "piel"
$EndPhysicalNames
$Nodes
45422
1 47 0 0
2 45 0 0
3 42 0 0
4 34 14 0
5 -6 6 0
6 -14 6 0
7 26 14 0
8 -14 6 175
9 26 14 175
10 34 14 175
11 -6 6 175
12 42 0 175 and so on

and I get the following error from the command dolfin-convert my_mesh.msh my_mesh.xml:

Converting from Gmsh format (.msh, .gmsh) to DOLFIN XML format
*** Unable to find cells of supported type.
2

Hi,
Dolfin-convert is no longer maintained. I suggest you use meshio to convert your mesh:

3

Hi,
I get the same error as @siriusf when converting my gmsh mesh to xml files.
I used the code you sent using meshio, but I get the following error for the part msh.cells[“tetra”]:

TypeError Traceback (most recent call last)
Cell In[97], line 6
1 import meshio
3 msh = meshio.read(“beam.msh”)
----> 6 meshio.write(“mesh.xdmf”, meshio.Mesh(points=msh.points, cells={“tetra”: msh.cells[“tetra”]}))
7 meshio.write(“mf.xdmf”, meshio.Mesh(points=msh.points, cells={“triangle”: msh.cells[“triangle”]},
8 cell_data={“triangle”: {“name_to_read”: msh.cell_data[“triangle”][“gmsh:physical”]}}))
9 meshio.write(“cf.xdmf”, meshio.Mesh(
10 points=msh.points, cells={“tetra”: msh.cells[“tetra”]},
11 cell_data={“tetra”: {“name_to_read”:
12 msh.cell_data[“tetra”][“gmsh:physical”]}}))

TypeError: list indices must be integers or slices, not str

Can you help me with this?

4

That post is 4 years old, and has many updated posts for newer versions below in the same thread. You could also follow: Mesh generation and conversion with GMSH and PYGMSH | Jørgen S. Dokken
which has the latest syntax.

5

Thank you for your reply. I used the one you sent as well but I get the error:

ValueError Traceback (most recent call last)
Cell In[111], line 1
----> 1 line_mesh = create_mesh(mesh_from_file, “line”, prune_z=True)
2 meshio.write(“new_facet_mesh.xdmf”, line_mesh)
4 triangle_mesh = create_mesh(mesh_from_file, “triangle”, prune_z=True)

Cell In[110], line 4, in create_mesh(mesh, cell_type, prune_z)
2 def create_mesh(mesh, cell_type, prune_z=False):
3 cells = mesh.get_cells_type(cell_type)
----> 4 cell_data = mesh.get_cell_data(“gmsh:physical”, cell_type)
5 points = mesh.points[:,:2] if prune_z else mesh.points
6 out_mesh = meshio.Mesh(points=points, cells={cell_type: cells}, cell_data={“name_to_read”:[cell_data]})

File /opt/anaconda3/envs/fenicss/lib/python3.11/site-packages/meshio/_mesh.py:249, in Mesh.get_cell_data(self, name, cell_type)
248 def get_cell_data(self, name: str, cell_type: str):
→ 249 return np.concatenate(
250 [d for c, d in zip(self.cells, self.cell_data[name]) if c.type == cell_type]
251 )

File <array_function internals>:200, in concatenate(*args, **kwargs)

ValueError: need at least one array to concatenate

my gmsh mesh file is looks correct which is:

$MeshFormat
2.2 0 8
$EndMeshFormat
$PhysicalNames
3
2 5 “Fixed”
2 6 “Force”
3 7 “beam”
$EndPhysicalNames
$Nodes
4410
1 0 0 5
2 1.000000003627494e-15 1 5
3 4.163336342344337e-16 0.75 5
4 2.775557561562891e-16 0.5 5
5 1.387778780781446e-16 0.25 5
6 1 0 5
7 0.25 0 5
8 0.5 0 5
9 0.75 0 5
10 1 1 5
11 1 0.25 5
12 1 0.5 5
13 1 0.75 5
14 0.75 1 5
15 0.5 1 5
16 0.25 1 5
17 0.6339163780212402 0.4695656597614288 5
18 0.3135612607002258 0.4157798588275909 5
19 0.437676876783371 0.6760674715042114 5
20 0.5522602200508118 0.2255466431379318 5
.
.
.

6

Please read the post with some care. Each of the create_mesh statements takes in a cell_type.
In your case, as it seems like your mesh is 3D (ie tetrahedral cells and triangular facets), you should use the cell_type: triangle and tetra instead of line and triangle.

7

Thank you dear @dokken . I could create the xdmf files for the fenics.
Can you help me with implementing the BCs? I read different things here but I got confused.
In my .msh file I have these physical regions:
2 4010 “RV”
2 4011 “LV”
2 4012 “Fix”
3 4013 “Vol”
I need to add pressure to the first two surfaces and make the third one fixed.
Thank you so much for your help.

8

Without having the xdmf file, and the script you are trying to use, i cannot really help you any further.

9

Hi, dokken,

Thank you for your pygmsh_tutorial. I have a small problem, when I run this tutorial, there is an error: AttributeError: module ‘pygmsh’ has no attribute ‘geo’. Could you help me fix it?

截屏2024-01-01 21.39.24
截屏2024-01-01 21.39.241564×1094 119 KB

10

What version of pygmsh are you using?

11

I use the osx-64 v6.1.1 installed by anacodna.

12

Update your version of pygmsh, as that release is ~3.5 years old.