# Transitioning from mesh.xml to mesh.xdmf, from dolfin-convert to meshio

**URL:** <https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412>\
**Category:** mesh\
**Created:** [March 22, 2019, 9:01am UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412 "2019-03-22T09:01:33Z")\
**Posts on this page:** 20\
**Page:** 12

<div class="post-metadata">

**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:** [May 8, 2023, 6:26am UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/229 "2023-05-08T06:26:35Z")

</div>

Something is wrong with your `msh` file, as you have

> [@haileyfromde](#):
>
> ```auto
> $PhysicalNames
> 2
> 2 1 "b1"
> 2 2 "b2"
> $EndPhysicalNames
> 
> ```

but if you open the mesh in gmsh, there are no `Physical Groups` in the mesh (Tools-\>Visibility-\>Physical Groups). Thus meshio cannot read the mesh.  
If you believe your mesh is correct, I would suggest making an issue at: [Sign in to GitHub · GitHub](https://github.com/nschloe/meshio/issues/new/choose)

---

<div class="post-metadata">

**Author:** ![haileyfromde](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/haileyfromde/32/3643_2.png) [@haileyfromde](https://fenicsproject.discourse.group/u/haileyfromde)\
**Post date:** [May 8, 2023, 4:21pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/230 "2023-05-08T16:21:00Z")

</div>

Thank you, you are right it does not read the msh file correctly. I exported the mesh from gmsh and I am using the same method as before but now it is not working now.

---

<div class="post-metadata">

**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:** [May 8, 2023, 7:57pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/231 "2023-05-08T19:57:49Z")

</div>

I would suggest providing your `.geo` file or the Python script you used to generate the mesh

---

<div class="post-metadata">

**Author:** ![meteoguc](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/meteoguc/32/3416_2.png) [@meteoguc](https://fenicsproject.discourse.group/u/meteoguc)\
**Post date:** [May 25, 2023, 9:27pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/232 "2023-05-25T21:27:40Z")

</div>

I can confirm that I am able to generate my 3d mesh using gmsh app but cannot convert it to xdmf on FEniCS somehow. Here is my code:

```auto
x_max = 2
y_max = 3
z_max = 4

# Mesh size
h = 0.1

mesh_script = "Point(1) = {{{0}, {1}, {2}, {3}}};\n".format(0, 0, 0, 1)
mesh_script += "Point(2) = {{{0}, {1}, {2}, {3}}};\n".format(x_max, 0, 0, 1)
mesh_script += "Point(3) = {{{0}, {1}, {2}, {3}}};\n".format(x_max, y_max, 0, 1)
mesh_script += "Point(4) = {{{0}, {1}, {2}, {3}}};\n".format(0, y_max, 0, 1)

mesh_script += "Point(5) = {{{0}, {1}, {2}, {3}}};\n".format(0, 0, z_max, 1)
mesh_script += "Point(6) = {{{0}, {1}, {2}, {3}}};\n".format(x_max, 0, z_max, 1)
mesh_script += "Point(7) = {{{0}, {1}, {2}, {3}}};\n".format(x_max, y_max, z_max, 1)
mesh_script += "Point(8) = {{{0}, {1}, {2}, {3}}};\n".format(0, y_max, z_max, 1)

mesh_script += "Line(1) = {1, 2};\n"
mesh_script += "Line(2) = {2, 3};\n"
mesh_script += "Line(3) = {3, 4};\n"
mesh_script += "Line(4) = {4, 1};\n"

mesh_script += "Line(5) = {1, 5};\n"
mesh_script += "Line(6) = {2, 6};\n"
mesh_script += "Line(7) = {3, 7};\n"
mesh_script += "Line(8) = {4, 8};\n"

mesh_script += "Line(9) = {5, 6};\n"
mesh_script += "Line(10) = {6, 7};\n"
mesh_script += "Line(11) = {7, 8};\n"
mesh_script += "Line(12) = {8, 5};\n"

mesh_script += "Curve Loop(1) = {8, -11, -7, 3};\n"
mesh_script += "Plane Surface(1) = {1};\n"

mesh_script += "Curve Loop(2) = {7, -10, -6, 2};\n"
mesh_script += "Plane Surface(2) = {2};\n"

mesh_script += "Curve Loop(3) = {2, 3, 4, 1};\n"
mesh_script += "Plane Surface(3) = {3};\n"

mesh_script += "Curve Loop(4) = {4, 5, -12, -8};\n"
mesh_script += "Plane Surface(4) = {4};\n"

mesh_script += "Curve Loop(5) = {12, 9, 10, 11};\n"
mesh_script += "Plane Surface(5) = {5};\n"

mesh_script += "Curve Loop(6) = {6, -9, -5, 1};\n"
mesh_script += "Plane Surface(6) = {6};\n"

mesh_script += "Surface Loop(1) = {4, 3, 2, 1, 5, 6};\n"
mesh_script += "Volume(1) = {1};\n"

mesh_script += "MeshSize {1, 2, 3, 4, 5, 6, 7, 8}"
mesh_script += " = {0};\n".format(h)

mesh_script += "Physical Surface(201) = {1, 2, 3, 4, 5, 6};\n"
mesh_script += "Physical Volume(301) = {1};\n"

print("Running Gmsh...")
geo_file=open("mesh.geo",'w')
geo_file.write(mesh_script)
geo_file.close()
gmsh_err=call(["gmsh", "-3", "mesh.geo", "-o", "mesh.msh"])
if gmsh_err:
    print("...mesh cannot be generated!")
else:
    print("...mesh generated successfully!")

def mesh_generation(mesh_script):

    print("Running Gmsh...")
    geo_file=open("mesh.geo",'w')
    geo_file.write(mesh_script)
    geo_file.close()
    gmsh_err=call(["gmsh", "-3", "mesh.geo", "-o", "mesh.msh"])
    if gmsh_err:
        print("...something bad happened \
        when the mesh was being generated...")
    else:
        print("...mesh generated successfully!")

    msh = meshio.read("mesh.msh")

    line_cells = []
    for cell in msh.cells:
        if cell.type == "triangle":
            triangle_cells = cell.data
        elif cell.type == "line":
            if len(line_cells) == 0:
                line_cells = cell.data
            else:
                line_cells = np.vstack([line_cells, cell.data])

    line_data = []
    for key in msh.cell_data_dict["gmsh:physical"].keys():
        if key == "line":
            if len(line_data) == 0:
                line_data = \
                msh.cell_data_dict["gmsh:physical"][key]
            else:
                line_data = \
                np.vstack([line_data, \
                msh.cell_data_dict["gmsh:physical"][key]])
        elif key == "triangle":
            triangle_data = \
            msh.cell_data_dict["gmsh:physical"][key]

    triangle_mesh = \
    meshio.Mesh(points=msh.points, \
    cells={"triangle": triangle_cells})
    line_mesh = \
    meshio.Mesh(points=msh.points,\
    cells=[("line", line_cells)],\
    cell_data={"name_to_read":[line_data]})
    meshio.write("mesh.xdmf", triangle_mesh)

    meshio.xdmf.write("mf.xdmf", line_mesh)

    mesh = Mesh()
    with XDMFFile("mesh.xdmf") as infile:
        infile.read(mesh)
    mvc = MeshValueCollection("size_t", mesh, 2)
    with XDMFFile("mf.xdmf") as infile:
        infile.read(mvc, "name_to_read")
    mf = cpp.mesh.MeshFunctionSizet(mesh, mvc)
    
    mesh_data = [mesh, mvc, mf]

    return mesh_data

from subprocess import call

mesh_data = mesh_generation(mesh_script)

mesh = mesh_data[0]
mvc = mesh_data[1]
mf = mesh_data[2]

```

I am getting an “IndexError: tuple index out of range”.  
I am trying to follow up .msh to xdmf for 3D from here. Can anyone help? Thanks!

---

<div class="post-metadata">

**Author:** ![hussleJ6](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/husslej6/32/4960_2.png) [@hussleJ6](https://fenicsproject.discourse.group/u/hussleJ6)\
**Post date:** [July 20, 2023, 6:39am UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/233 "2023-07-20T06:39:00Z")

</div>

Maybe this is a bit a silly question, but would it work as well to convert a xdmf file back into both a .msh file and a .xml file? Should only the file types be adjusted, or would such a conversion not be that simple?

```auto
import meshio
msh = meshio.read("mesh.xdmf")
for cell in xdmf.cells:
    if cell.type == "triangle":
        triangle_cells = cell.data
    elif cell.type == "tetra":
        tetra_cells = cell.data

for key in 
xdmf.cell_data_dict["gmsh:physical"].keys():
    if key == "triangle":
        triangle_data = 
xdmf.cell_data_dict["gmsh:physical"][key]
    elif key == "tetra":
        tetra_data = msh.cell_data_dict["gmsh:physical"][key]
tetra_mesh = meshio.Mesh(points=xdmf.points, cells={"tetra": tetra_cells})
triangle_mesh =meshio.Mesh(points=xdmf.points,
                           cells=[("triangle", triangle_cells)],
                           cell_data={"name_to_read":[triangle_data]})
meshio.write("mesh.xml", tetra_mesh)

meshio.write("mf.xml", triangle_mesh)
```

---

<div class="post-metadata">

**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:** [July 20, 2023, 11:06am UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/234 "2023-07-20T11:06:56Z")

</div>

Yes, meshio can convert back to xml or msh. However, Im not sure what support there is for markers in the “to msh” conversion.

For xml i guess you would have to merge the two meshes together, as the input mesh was originally in a single file.

---

<div class="post-metadata">

**Author:** ![NataliaKor](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/nataliakor/32/5871_2.png) [@NataliaKor](https://fenicsproject.discourse.group/u/NataliaKor)\
**Post date:** [October 10, 2023, 10:40am UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/235 "2023-10-10T10:40:34Z")

</div>

Hello, dear @dokken I have several questions.  
Firstly, using Gmsh I created .geo file and .msh file as well. For starting my simulation I need to convert .msh file to .xml.gz file. When I try to use _dolfin-convert_ I get error that:

> File “/usr/lib/python2.7/dist-packages/dolfin\_utils/meshconvert/meshconvert.py”, line 279, in gmsh2xml  
> num\_elements = int(line)  
> ValueError: invalid literal for int() with base 10: ‘124 10780 1 10780\n’

Due to reading your discussion I find information that _dolfin-convert_ isn’t maintained anymore, so I install Meshio for making converting.  
Secondly, while instalation I get message that:

> use --no-warn-script-location.

And Meshio installed on /home/magnumfe/.local/bin , so I change my **~/.bashrc** file and add line _export PATH=“/home/magnumfe/.local/bin:$PATH”_  
Unfortunately, command _meshio convert_ doesn’t work I get message:

> meshio: command not found

And when I try to use script,

> **Summary**
>
> import meshio  
> import numpy
> 
> msh = meshio.read(“newcil.msh”)
> 
> 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)  
> out\_mesh = meshio.Mesh(points=mesh.points, cells={cell\_type: cells}, cell\_data={“name\_to\_read”:[cell\_data]})  
> if prune\_z:  
> out\_mesh.prune\_z\_0()  
> return out\_mesh
> 
> msh=meshio.read(“newcil.msh”)
> 
> triangle\_mesh = create\_mesh(msh, “triangle”, False)  
> tetra\_mesh = create\_mesh(msh, “tetra”, False)  
> meshio.write(“newciltetr.xml”, tetra\_mesh)  
> meshio.write(“newciltri.xml”, triangle\_mesh)  
> #print(msh.cell\_data\_dict)  
> from dolfin import \*  
> parameters[“allow\_extrapolation”] = True  
> parameters[“form\_compiler”][“optimize”] = True
> 
> mesh=Mesh()  
> mvc = MeshValueCollection(“size\_t”, mesh, mesh.topology().dim())  
> with XMLFile(“newciltetr.xml”) as infile:  
> infile.read(mesh)  
> infile.read(mvc, “name\_to\_read”)  
> cf = cpp.mesh.MeshFunctionSizet(mesh, mvc)
> 
> mvc = MeshValueCollection(“size\_t”, mesh, mesh.topology().dim()-1)  
> with XMLFile(“newciltri.xml”) as infile:  
> infile.read(mvc, “name\_to\_read”)  
> mf = cpp.mesh.MeshFunctionSizet(mesh, mvc)
> 
> ds = Measure(“ds”, domain=mesh, subdomain\_data=mf)
> 
> dx=Measure(“dx”, domain=mesh, subdomain\_data=cf)

I get this message:

> AttributeError: ‘module’ object has no attribute ‘read’

So, I will be happy to get any advice about this situation and how I can make converting from .msh to .xml.

This is my .geo file:

> **Summary**
>
> // Gmsh project created on Sun Oct 8 06:12:34 2023
> 
> cl = 2.5;
> 
> Point(0) = { 0, 0, 0, cl};  
> Point(1) = { -30, 0, 0, cl};  
> Point(2) = { 30, 0, 0, cl};  
> Point(3) = { 0, -30, 0, cl};  
> Point(4) = { 0, 30, 0, cl};
> 
> Circle(1) = {1, 0, 3};  
> Circle(2) = {3, 0, 2};  
> Circle(3) = {2, 0, 4};  
> Circle(4) = {4, 0, 1};
> 
> Line Loop(1) = {1, 2, 3, 4};
> 
> Plane Surface(1) = {1};
> 
> s0 = Extrude{0, 0, 10.0} {Surface{1}; Layers{3};};  
> s1 = Extrude{0, 0, -7} {Surface{s0[0]}; Layers{2};};
> 
> Point(26) = { 0, 0, 10, cl};  
> Point(21) = { -10, 0, 10, cl};  
> Point(22) = { 10, 0, 10, cl};  
> Point(23) = { 0, -10, 10, cl};  
> Point(24) = { 0, 10, 10, cl};
> 
> Circle(21) = {21, 26, 23};  
> Circle(22) = {23, 26, 22};  
> Circle(23) = {22, 26, 24};  
> Circle(24) = {24, 26, 21};
> 
> Line Loop(21) = {21, 22, 23, 24};
> 
> Plane Surface(2) = {21};
> 
> s2 = Extrude{0, 0, 4.0} {Surface{2}; Layers{1};};
> 
> my\_new\_surf = Translate {0, 0, 14}{Duplicata {Surface{1};}};  
> Printf(“New surface ‘%g’”, my\_new\_surf[0]);
> 
> s3 = Extrude{0, 0, 6.0} {Surface{71}; Layers{3};};  
> s4 = Extrude{0, 0, -4} {Surface{s0[0]}; Layers{2};};
> 
> Physical Volume(1) = {s0[1]};  
> Physical Volume(2) = {s1[1]};  
> Physical Volume(3) = {s2[1]};  
> Physical Volume(4) = {s3[1]};  
> Physical Volume(5) = {s4[1]};
> 
> Physical Surface(1) = {s0[0]};  
> Physical Surface(2) = {s1[0]};

---

<div class="post-metadata">

**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:** [October 10, 2023, 12:02pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/236 "2023-10-10T12:02:53Z")

</div>

Could you start with trying the following command on your commandline:

```bash
python3 -c "import meshio; print(meshio); print(meshio.read)"

```

and also add what instructions you used to install meshio?

---

<div class="post-metadata">

**Author:** ![NataliaKor](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/nataliakor/32/5871_2.png) [@NataliaKor](https://fenicsproject.discourse.group/u/NataliaKor)\
**Post date:** [October 11, 2023, 9:38am UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/237 "2023-10-11T09:38:31Z")

</div>

> [@dokken](#):
>
> `python3 -c "import meshio; print(meshio); print(meshio.read)"`

I try this command, but get this error:

> Traceback (most recent call last):  
> File “”, line 1, in   
> File “/home/natalia/mesh/meshio.py”, line 6, in   
> msh = meshio.read(“newcil.msh”)  
> AttributeError: partially initialized module ‘meshio’ has no attribute ‘read’ (most likely due to a circular import)

For installation I use instructions from [meshio · PyPI](https://pypi.org/project/meshio/)  
Command:

```auto
pip install meshio

```

And also ```  
pip install meshio[all]

```auto
Linux writes that: *Requirement already satisfied.*
```

---

<div class="post-metadata">

**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:** [October 11, 2023, 2:56pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/238 "2023-10-11T14:56:01Z")

</div>

> [@NataliaKor](#):
>
> File “/home/natalia/mesh/meshio.py”, line 6, in

Do you have a file called `meshio.py` in your current directory? If so, please rename it as it comes first on python’s import priority.

---

<div class="post-metadata">

**Author:** ![NataliaKor](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/nataliakor/32/5871_2.png) [@NataliaKor](https://fenicsproject.discourse.group/u/NataliaKor)\
**Post date:** [October 13, 2023, 12:36pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/239 "2023-10-13T12:36:22Z")

</div>

> [@NataliaKor](#):
>
> /home/natalia/mesh/meshio.py

Yes, I have this file. I rename it and try this command _python3 -c “import meshio; print(meshio); print(meshio.read)”_ again, but get this

> Traceback (most recent call last):  
> File “”, line 1, in   
> ImportError: bad magic number in ‘meshio’: b’\x03\xf3\r\n’

But I don’t have file _string._

---

<div class="post-metadata">

**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:** [October 13, 2023, 1:01pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/240 "2023-10-13T13:01:12Z")

</div>

Remove any `.pyc` files and the ` __pycache__ ` from your directory.

---

<div class="post-metadata">

**Author:** ![NataliaKor](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/nataliakor/32/5871_2.png) [@NataliaKor](https://fenicsproject.discourse.group/u/NataliaKor)\
**Post date:** [October 16, 2023, 10:30am UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/241 "2023-10-16T10:30:22Z")

</div>

> [@dokken](#):
>
> `python3 -c "import meshio; print(meshio); print(meshio.read)"`

Thank for advice. I did everything as you said. And after command _~/mesh$ python3 -c “import meshio; print(meshio); print(meshio.read)”_ get this

> \<module ‘meshio’ from ‘/home/natalia/.local/lib/python3.8/site-packages/meshio/ **init**.py’\>  
> \<function read at 0x7f9bdbaeea60\>

And command _meshio convert_ still doesn’t work. Types that

> meshio: command not found

---

<div class="post-metadata">

**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:** [October 16, 2023, 12:59pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/242 "2023-10-16T12:59:31Z")

</div>

> [@NataliaKor](#):
>
> And command _meshio convert_ still doesn’t work. Types that

I would not use the `meshio convert` script from terminal.  
All the posts in this forum uses `meshio` as a python module, as it has alot more features than the command line tool.

---

<div class="post-metadata">

**Author:** ![NataliaKor](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/nataliakor/32/5871_2.png) [@NataliaKor](https://fenicsproject.discourse.group/u/NataliaKor)\
**Post date:** [October 16, 2023, 1:56pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/243 "2023-10-16T13:56:56Z")

</div>

Got it. So, for converting my mesh file .msh to .xml I will create the python file, correct? Actually i only need one operation (converting), but due to your discussions with other users I’ve realized that meshio is powerful instrument. For using meshio can I found tutorial or information exist only in this branch of dialogue?

---

<div class="post-metadata">

**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:** [October 16, 2023, 2:17pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/244 "2023-10-16T14:17:47Z")

</div>

See for instance: [Mesh generation and conversion with GMSH and PYGMSH | Jørgen S. Dokken](https://jsdokken.com/src/pygmsh_tutorial.html#second)

---

<div class="post-metadata">

**Author:** ![NataliaKor](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/nataliakor/32/5871_2.png) [@NataliaKor](https://fenicsproject.discourse.group/u/NataliaKor)\
**Post date:** [October 30, 2023, 4:01pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/245 "2023-10-30T16:01:03Z")

</div>

Dear, @dokken I have a question (again). Due to converting from .msh to .xml file with this code:

```auto
import meshio
mesh_from_file = meshio.read("my_mesh.msh")

#if I had 3D mesh how I have to put z coordinate back?
import numpy
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]})
    if prune_z:
        out_mesh.prune_z_0()
    return out_mesh

#can I save in .xml format not in .xdmf?
#line_mesh = create_mesh(mesh_from_file, "line", prune_z=True)
#meshio.write("facet_my_mesh.xml", line_mesh)
tetra_mesh = create_mesh(mesh_from_file,"tetra", False)
triangle_mesh = create_mesh(mesh_from_file, "triangle", False)
meshio.write("my_mesh.xml", triangle_mesh)

meshio.write("my_mesh.xml", tetra_mesh) 

```

I get this error:

```auto
Traceback (most recent call last):
  File "convertmsh.py", line 2, in <module>
    mesh_from_file = meshio.read("my_mesh.msh")
  File "/home/magnumfe/.local/lib/python2.7/site-packages/meshio/helpers.py", line 176, in read
    return format_to_reader[file_format].read(filename)
  File "/home/magnumfe/.local/lib/python2.7/site-packages/meshio/msh_io/main.py", line 15, in read
    mesh = read_buffer(f)
  File "/home/magnumfe/.local/lib/python2.7/site-packages/meshio/msh_io/main.py", line 46, in read_buffer
    return reader.read_buffer(f, is_ascii, data_size)
  File "/home/magnumfe/.local/lib/python2.7/site-packages/meshio/msh_io/msh4_1.py", line 61, in read_buffer
    points, point_tags = _read_nodes(f, is_ascii, data_size)
  File "/home/magnumfe/.local/lib/python2.7/site-packages/meshio/msh_io/msh4_1.py", line 137, in _read_nodes
    assert parametric == 0, "parametric nodes not implemented"
AssertionError: parametric nodes not implemented

```

My .geo file is

```auto
// Gmsh project created on Sat Oct 7 09:53:39 2023

cl = 2.5;

Point(1) = { 0, 0, 0, cl};
Point(2) = { 10, 0, 0, cl};
Point(3) = {-30, 0, 0, cl};
Point(4) = { 30, 0, 0, cl};
Point(5) = { 0, 30, 0, cl};
Point(6) = { 0,-30, 0, cl};
Point(7) = {-10, 0, 0, cl};
Point(8) = { 0,-10, 0, cl};
Point(9) = { 0, 10, 0, cl};
Point(10) = { 5, 0, 0, cl};

Ellipse(1) = {5,1,2,3};
Ellipse(2) = {4,1,2,5};
Ellipse(3) = {6,1,2,3};
Ellipse(4) = {4,1,2,6};
Ellipse(5) = {9,1,10,7};
Ellipse(6) = {2,1,10,9};
Ellipse(7) = {8,1,10,7};
Ellipse(8) = {2,1,10,8};

Line Loop(9) = {1,-3,-4,2};
Plane Surface(1) = {9};
Line Loop(10) = {5,-7,-8,6};
Plane Surface(2) = {10};

s0[] = Extrude{0, 0, 8.0} {Surface{1}; Layers{3};};
s1[] = Extrude{0, 0, 3} {Surface{s0[0]}; Layers{1};};
s2[] = Extrude{0, 0, -3.0} {Surface{2}; Layers{4};};

my_new_surf[] = Translate {0, 0, -3}{Duplicata {Surface{1};}};
Printf("New surface '%g'", my_new_surf[0]);

s3[] = Extrude{0, 0, -1.5} {Surface{77}; Layers{6};};
s4[] = Extrude{0, 0, -4} {Surface{s3[0]}; Layers{5};};

Physical Volume(1) = {s0[1]};
Physical Volume(2) = {s1[1]};
Physical Volume(3) = {s2[1]};
Physical Volume(4) = {s3[1]};
Physical Volume(5) = {s4[1]};

```

I read this brunch of dialogue and saw that some people get the same error because they don’t mention physical volume/surface. As you can see my code has Physical Volume. Unfortunately, when I check .msh file I didn’t see any mention about it. Could you give me some suggestions?

[MSH file](https://drive.google.com/file/d/117k9KaikWQh8YRa_M-jjXOkJ5vzps2Hi/view?usp=drive_link)

---

<div class="post-metadata">

**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:** [October 30, 2023, 4:19pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/246 "2023-10-30T16:19:28Z")

</div>

This is a pure `meshio` issue, as it is regarding translating a Gmsh `msh` file with `meshio`. I would strongly recommend you post a question at [Issues · nschloe/meshio · GitHub](https://github.com/nschloe/meshio/issues)  
as the mesh can be read with `dolfinx.io.gmshio` with no issue (which uses gmsh to get the raw data structures). You could use a similar approach by following [https://github.com/FEniCS/dolfinx/blob/main/python/dolfinx/io/gmshio.py#L180-L260](https://github.com/FEniCS/dolfinx/blob/main/python/dolfinx/io/gmshio.py#L180-L260)  
to get the mesh geometry and topology, and use meshio to save it.

I note that you are usinga very outdated version of python (2.7), and your issue might be resolved in a newer version of meshio

---

<div class="post-metadata">

**Author:** ![Quentin](https://avatars.discourse-cdn.com/v4/letter/q/e47c2d/32.png) [@Quentin](https://fenicsproject.discourse.group/u/Quentin)\
**Post date:** [November 20, 2023, 4:47pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/247 "2023-11-20T16:47:56Z")

</div>

Hi Everybody,

as i am struggling to do so, Is there some kind enough to indicate which versions of gmsh/meshio permits to write these two files ?

I use  
gmsh 4.11.1  
meshio 4.4.0

and the following code

```auto
gmsh.initialize()
gmsh.model.add("MODEL")
# get the geometry and define the bounding box
v = gmsh.model.occ.importShapes("SLICE.step")
xmin, ymin, zmin, xmax, ymax, zmax = gmsh.model.occ.getBoundingBox(v[0][0], v[0][1])
Delta_x = xmax - xmin
Delta_y = ymax - ymin
Delta_z = zmax - zmin
Delta = np.min([Delta_x,Delta_y,Delta_z])
h = Delta /50
# add tags for surfaces
gmsh.model.occ.synchronize()

surfaces = gmsh.model.getEntities(dim=2)
for surface in surfaces:
    gmsh.model.addPhysicalGroup(2, [surface[1]], tag=surface[1])
    
gmsh.model.occ.synchronize()

# Define meshing options
gmsh.option.setNumber("Mesh.MeshSizeMin", h)
gmsh.option.setNumber("Mesh.MeshSizeMax", h)
gmsh.option.setNumber("Mesh.Algorithm", 6)   
gmsh.model.mesh.generate(3)
gmsh.model.occ.synchronize()
gmsh.write("SLICE.msh")

mesh = meshio.read("SLICE.msh")

line_cells = []
for cell in mesh.cells:
    if cell.type == "triangle":
        triangle_cells = cell.data
    elif cell.type == "line":
        if len(line_cells) == 0:
            line_cells = cell.data
        else:
            line_cells = np.vstack([line_cells, cell.data])

line_data = []
for key in mesh.cell_data_dict["gmsh:physical"].keys():
    if key == "line":
        if len(line_data) == 0:
            line_data = mesh.cell_data_dict["gmsh:physical"][key]
        else:
            line_data = np.vstack([line_data, mesh.cell_data_dict["gmsh:physical"][key]])
    elif key == "triangle":
        triangle_data = mesh.cell_data_dict["gmsh:physical"][key]

triangle_mesh = meshio.Mesh(points=mesh.points, cells={"triangle": triangle_cells})
line_mesh =meshio.Mesh(points=mesh.points,
                           cells=[("line", line_cells)],
                           cell_data={"name_to_read":[line_data]})
meshio.write("mesh.xdmf", triangle_mesh)

meshio.xdmf.write("mf.xdmf", line_mesh)

```

provide the following error message :

```auto
Traceback (most recent call last):
  File "/mnt/c/Users/quent/Documents/Codes/Python/Mesh_GMSH2MeshIO/XDMF_OUTPUT_BOUNDARIES_TAGS/Conversion_GMSH2MeshIO.py", line 287, in <module>
    meshio.xdmf.write("mf.xdmf", line_mesh)
  File "/home/quentin_digimind/anaconda3/lib/python3.11/site-packages/meshio/xdmf/main.py", line 535, in write
    XdmfWriter(*args, **kwargs)
  File "/home/quentin_digimind/anaconda3/lib/python3.11/site-packages/meshio/xdmf/main.py", line 358, in __init__
    self.write_cells(mesh.cells, grid)
  File "/home/quentin_digimind/anaconda3/lib/python3.11/site-packages/meshio/xdmf/main.py", line 424, in write_cells
    NodesPerElement=str(cells[0].data.shape[1]),
                        ~~~~~~~~~~~~~~~~~~~ ^^^
IndexError: tuple index out of range

```

any help would be appreciated.

thanks,

Quentin

---

<div class="post-metadata">

**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 20, 2023, 6:15pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/248 "2023-11-20T18:15:37Z")

</div>

See up to date scripts at [Mesh generation and conversion with GMSH and PYGMSH | Jørgen S. Dokken](https://jsdokken.com/src/pygmsh_tutorial.html#second)

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