# Gmsh import error
**URL:** https://fenicsproject.discourse.group/t/gmsh-import-error/4995
**Category:** mesh
**Created:** [January 28, 2021, 2:32pm UTC](https://fenicsproject.discourse.group/t/gmsh-import-error/4995 "2021-01-28T14:32:16Z")
**Posts on this page:** 6
**Page:** 1
### Author:  [@mhechthz](https://fenicsproject.discourse.group/u/mhechthz)
#### Post date: [January 28, 2021, 2:32pm UTC](https://fenicsproject.discourse.group/t/gmsh-import-error/4995/1 "2021-01-28T14:32:16Z")
Hi,
with Gmesh I build a 2D-mesh using:
```
SetFactory("OpenCASCADE");
ln1 = 0.2;
ln2 = 3.0;
lc1 = 0.04;
lc3 = 0.005;
lc4 = 0.01;
Point(1) = {0,0,0,lc3};
Point(2) = {ln1,0.0,0,lc1};
Point(3) = {ln1,0.6,0,lc1};
Point(4) = {ln1,ln2,0,lc1};
Point(5) = {0,ln2,0,lc1};
Line(1) = {1,2};
Line(2) = {2,3};
Line(3) = {3,4};
Line(4) = {4,5};
Line(5) = {5,1};
Curve Loop(5) = {1,2,3,4,5};
Plane Surface(6) = {5};
Field[1] = Distance;
Field[1].CurvesList = {1,2};
Field[1].NumPointsPerCurve = ln2/lc3;
Field[2] = Distance;
Field[2].CurvesList = {3};
Field[2].NumPointsPerCurve = ln2/lc4;
Field[3] = Threshold;
Field[3].InField = 1;
Field[3].SizeMin = lc3;
Field[3].SizeMax = lc1;
Field[3].DistMin = 0.01;
Field[3].DistMax = 0.1;
Field[4] = Threshold;
Field[4].InField = 2;
Field[4].SizeMin = lc4;
Field[4].SizeMax = lc1;
Field[4].DistMin = 0.01;
Field[4].DistMax = 0.2;
Field[5] = Min;
Field[5].FieldsList = {3,4};
Background Field = 5;
Mesh.MeshSizeExtendFromBoundary = 0;
Mesh.MeshSizeFromPoints = 0;
Mesh.MeshSizeFromCurvature = 0;
```
and further
`meshio-convert --input-format gmsh --output-format xdmf mymesh.gmsh mymesh.xdmf`
which should result in a mesh like the attached file.
Doing the following:
```
mesh = Mesh()
filename = "mymesh.xdmf"
f = XDMFFile(MPI.comm_world, filename)
f.read(mesh)
plot(mesh)
```
gives the error:
```
*** Error: Unable to recognise cell type.
*** Reason: Unknown value "mixed".
*** Where: This error was encountered inside XDMFFile.cpp.
*** Process: 0
***
*** DOLFIN version: 2019.2.0.dev0
*** Git changeset: unknown
```
What did I do wrong and how can I just replace
`mesh = RectangleMesh(p0,p1,npX,npY,'left')`
by the Gmsh mesh?
Thank’s ins advance.
---
### Author:  [@dokken](https://fenicsproject.discourse.group/u/dokken)
#### Post date: [January 28, 2021, 3:08pm UTC](https://fenicsproject.discourse.group/t/gmsh-import-error/4995/2 "2021-01-28T15:08:24Z")
Please search the on the forum for your error message before posting a new question.
If you search for
Unknown value “mixed”.
The follow thread comes up.
> [@Transitioning from mesh.xml to mesh.xdmf, from dolfin-convert to meshio](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/127):
>
> First, you need to use physical markers on your lines and surfaces See for instance this tutorial: [https://jsdokken.com/converted\_files/tutorial\_pygmsh.html](https://jsdokken.com/converted_files/tutorial_pygmsh.html) In particular have a look at part 3. What you should also do is inspect the objects that you are trying to access. I.e. print msh.cells[“line”] etc.
---
### Author:  [@mhechthz](https://fenicsproject.discourse.group/u/mhechthz)
#### Post date: [January 28, 2021, 3:26pm UTC](https://fenicsproject.discourse.group/t/gmsh-import-error/4995/3 "2021-01-28T15:26:31Z")
Sorry, I saw this thread but was confused by “mesh.xml to mesh.xdmf” which was the opposite direction for me. I check this out. Thank you.
---
### Author:  [@mhechthz](https://fenicsproject.discourse.group/u/mhechthz)
#### Post date: [January 29, 2021, 8:49am UTC](https://fenicsproject.discourse.group/t/gmsh-import-error/4995/4 "2021-01-29T08:49:00Z")
I added now physical line and surface commands (as described in the other post) even if I’m not totally sure what I’m doing (sorry):
…
Physical Line(10) = {1};
Physical Line(11) = {2};
Physical Line(12) = {3};
Physical Line(13) = {4};
Physical Line(14) = {5};
Physical Surface(15) = {6};
…
I still get problems with xdmf. I’m doing:
```
meshio-convert --input-format gmsh --output-format xdmf --prune-z-0 mymesh.gmsh mymesh.xdmf
meshio-convert --input-format gmsh --output-format dolfin-xml --prune-z-0 mymesh.gmsh mymesh.xml
```
Even if there is a warning on dolfin output it works now to do:
`mesh = Mesh("mymesh.xml")`
While reading xml finally is ok, this
```
mesh = Mesh()
filename = "mymesh.xdmf"
f = XDMFFile(MPI.comm_world, filename)
f.read(mesh)
```
results in the described error message `Unknown value "mixed"`. In the xdmf file there is a setting
`
### Author:  [@dokken](https://fenicsproject.discourse.group/u/dokken)
#### Post date: [January 29, 2021, 8:59am UTC](https://fenicsproject.discourse.group/t/gmsh-import-error/4995/5 "2021-01-29T08:59:56Z")
It seems like you have not read the post I linked you to. You cannot use the `meshio-convert` script out of the box for XDMF, and you have to use the meshio python interface. See the second section of: [Mesh generation and conversion with GMSH and PYGMSH | Jørgen S. Dokken](https://jsdokken.com/converted_files/tutorial_pygmsh.html#second)
where I read in a mesh:
```auto
import meshio
mesh_from_file = meshio.read("mesh.msh")
```
extract data for a given cell type
```auto
def create_mesh(mesh, cell_type, prune_z=False):
cells = numpy.vstack([cell.data for cell in mesh.cells if cell.type==cell_type])
cell_data = numpy.hstack([mesh.cell_data_dict["gmsh:physical"][key]
for key in mesh.cell_data_dict["gmsh:physical"].keys() if key==cell_type])
# Remove z-coordinates from mesh if we have a 2D cell and all points have the same third coordinate
points= mesh.points
if prune_z:
points = points[:,:2]
mesh_new = meshio.Mesh(points=points, cells={cell_type: cells}, cell_data={"name_to_read":[cell_data]})
return mesh_new
```
and write a separate mesh file for the cell and facet data
```auto
line_mesh = create_mesh(mesh_from_file, "line", prune_z=True)
meshio.write("facet_mesh.xdmf", line_mesh)
triangle_mesh = create_mesh(mesh_from_file, "triangle", prune_z=True)
meshio.write("mesh.xdmf", triangle_mesh)
```
---
### Author:  [@mhechthz](https://fenicsproject.discourse.group/u/mhechthz)
#### Post date: [January 30, 2021, 9:44am UTC](https://fenicsproject.discourse.group/t/gmsh-import-error/4995/6 "2021-01-30T09:44:51Z")
Ok, thank you. As not native english speaker it is sometimes difficult to get the main point of a post.