# 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:** 9

<div class="post-metadata">

**Author:** ![Rafael\_Ferro](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/rafael_ferro/32/1157_2.png) [@Rafael\_Ferro](https://fenicsproject.discourse.group/u/Rafael_Ferro)\
**Post date:** [April 28, 2021, 12:55pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/165 "2021-04-28T12:55:40Z")

</div>

Dear,

I believe I followed all the procedures written in the posts above, but I am not able to generate the .xdmf file

note: I made the mesh in Gmsh version 4.8.3 on macOS.

Follow the code below and also the file .geo:

```auto
import meshio
msh = meshio.read("two_cantilever.msh")
for key in msh.cell_data_dict["gmsh:physical"].keys():
    if key == "triangle":
        triangle_data = msh.cell_data_dict["gmsh:physical"][key]
    elif key == "tetra":
        tetra_data = msh.cell_data_dict["gmsh:physical"][key]
for cell in msh.cells:
    if cell.type == "tetra":
        tetra_cells = cell.data
    elif cell.type == "triangle":
        triangle_cells = cell.data
tetra_mesh = meshio.Mesh(points=msh.points, cells={"tetra": tetra_cells},
                         cell_data={"Volume":[tetra_data]})
triangle_mesh =meshio.Mesh(points=msh.points,
                           cells=[("triangle", triangle_cells)],
                           cell_data={"Boundary":[triangle_data]})
meshio.write("mesh.xdmf", tetra_mesh)
meshio.write("mf.xdmf", triangle_mesh)

```

See the error:

```auto
 File "/Users/xyz/Desktop/Topopt_final/3dmodel/gmsh_to_xdmf.py", line 66, in <module>
    tetra_mesh = meshio.Mesh(points=msh.points, cells={"tetra": tetra_cells},

  File "/Users/xyz/anaconda3/envs/fenics2/lib/python3.8/site-packages/meshio/_mesh.py", line 77, in __init__
    raise ValueError(

ValueError: Incompatible cell data. Cell block 0 has length 214, but corresponding cell data Volume item has length 66420.

```

two\_cantilever.geo:

```auto
// Gmsh project created on Wed Apr 28 09:20:18 2021
SetFactory("OpenCASCADE");
//+
Box(1) = {0, 0, 0, 3, 0.01, 1};
//+
Box(2) = {-2, -0.03, 0, 3, 0.01, 1};
//+
Cylinder(3) = {0.5, -0.04, 0.25, 0, 0.05, 0, 0.05, 2*Pi};
//+
Cylinder(4) = {0.5, -0.04, 0.75, 0, 0.05, 0, 0.05, 2*Pi};
//+
Physical Surface(1) = {2};
//+
Physical Surface(2) = {7};
//+
Physical Surface(3) = {13};
//+
Physical Surface(4) = {16};
//+
Physical Volume(31) = {1};
//+
Physical Volume(32) = {2};
//+
Physical Volume(33) = {4};
//+
Physical Volume(34) = {3};

```

For my code I need to apply boundary considerations on the extreme faces of the plates and on the outer faces of the cylinders.

Edit .: The .msh file was larger than the size allowed here. Follow the file link:

> **[two\_cantilever.msh](https://drive.google.com/file/d/1eUSgnzqfZFt6i8jl2F3h5Nujs3fM-Ye0/view?usp=sharing)**
>
> Google Drive file.

can anybody help me? @dokken

---

<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:** [April 28, 2021, 7:22pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/166 "2021-04-28T19:22:40Z")

</div>

> [@Rafael\_Ferro](#):
>
> ` tetra_cells = cell.data`

You are not concatenating data stemming from different cell blocks.  
You have not followed the instructions in:

> [@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/412/155):
>
> I disagree with your claim. All the code I have posted above is using msh 4.1. The following illustrates a use case with the latest version of GMSH. Starting from a clean ubuntu 20.04 environment using docker: docker run -ti -v $PWD:/home/shared -w /home/shared --rm ubuntu:20.04 Installation instructions in docker apt-get update -qq apt-get install -y -qq software-properties-common python3-pip libglu1 libxrender1 libcursor1 libxft2 libxinerama1 add-apt-repository -y ppa:fenics-packages/fen…

> [@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/412/158):
>
> I had a play with pygmsh over the weekend, and what seems to be done in the later versions is to save the physical markers to cell sets. I have made the following function for this: def create\_entity\_mesh(mesh, cell\_type, prune\_z=False, remove\_unused\_points=False): """ Given a meshio mesh, extract mesh and physical markers for a given entity. We assume that all unused points are at the end of the mesh.points (this happens when we use physical markers with…

[Need help converting GMSH to FEniCS - #8 by dokken](https://fenicsproject.discourse.group/t/need-help-converting-gmsh-to-fenics/5192/8)

To repost this again:

```auto
import meshio

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("two_cantilever.msh")
facet_mesh = create_mesh(msh, "triangle", prune_z=True)
meshio.write("facet_mesh.xdmf", facet_mesh)

triangle_mesh = create_mesh(msh, "tetra", prune_z=True)
meshio.write("mesh.xdmf", triangle_mesh)

```

Note that you have not used boolean operations on your geometry, resulting in another mesh that what you would like. See: [Using subdomains in diffusion equation - #6 by dokken](https://fenicsproject.discourse.group/t/using-subdomains-in-diffusion-equation/4282/6)

---

<div class="post-metadata">

**Author:** ![Rafael\_Ferro](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/rafael_ferro/32/1157_2.png) [@Rafael\_Ferro](https://fenicsproject.discourse.group/u/Rafael_Ferro)\
**Post date:** [April 29, 2021, 1:53am UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/167 "2021-04-29T01:53:52Z")

</div>

Dear Dokken,

I really appreciate your help.

Well, I made an example with a simpler geometry, a single cantilever without the “holes” (I will study more about gmsh) that follows below. The two\_cantilever here didn’t work! Did you ever run there?

The new code works, however in the result it seems that both the left side BCdirichlet restriction and the right side load insertion are not being considered.

```auto
bc = DirichletBC (V, Constant ((0.0, 0.0, 0.0)), mf, 14)
ds = Measure ("ds", domain = mesh, subdomain_data = mf, subdomain_id = 13)

```

see the code:

```auto
from fenics import *
import meshio

L = 3.0
B = 0.01
H = 1.0

# Load
F = 30
ds_size = 0.1

# Define 3D geometry
mesh = Mesh()
with XDMFFile("untitled.xdmf") as infile:
    infile.read(mesh)

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

mvc2 = MeshValueCollection("size_t", mesh, 3)
with XDMFFile("mesh.xdmf") as infile:
    infile.read(mvc2, "name_to_read")
cf = cpp.mesh.MeshFunctionSizet(mesh, mvc2)

dx = Measure("dx", domain=mesh, subdomain_data=cf, subdomain_id=15)

# Define function space and base functions
V = VectorFunctionSpace(mesh, 'Lagrange', degree=2)

# Boundary Condition
"""
class Left(SubDomain):
    def inside(self, x, on_boundary):
        return on_boundary and near(x[0], -2.0)
left = Left()
bc = DirichletBC(V, Constant((0.0, 0.0, 0.0)), left)
"""
bc = DirichletBC(V, Constant((0.0, 0.0, 0.0)), mf, 14)

# Load
class LoadSurface(SubDomain):
    def inside(self, x, on_boundary):
        return on_boundary and near(x[0], L) and \
               between(x[1], ((B-ds_size)/2.0, (B+ds_size)/2.0)) and \
               between(x[2], ((H-ds_size)/2.0, (H+ds_size)/2.0))
#edited               
loadSurface = LoadSurface()
mf.set_all(0)
loadSurface.mark(mf, 1)
ds = Measure("ds", domain=mesh, subdomain_data=mf, subdomain_id=13)
t = Expression(('q_x', 'q_y', 'q_z'), degree = 3, q_x = 0.0, q_y = 0.0, q_z = -F/ds_size)

## Constitutive relation

def eps(v):
    return sym(grad(v))

E = Constant(1e5)
nu = Constant(0.3)
model = "plane_stress"
mu = E/2/(1+nu)
lmbda = E*nu/(1+nu)/(1-2*nu)
if model == "plane_stress":
    lmbda = 2*mu*lmbda/(lmbda+2*mu)

def sigma(v):
    dim = v.geometric_dimension()
    return lmbda*tr(eps(v))*Identity(dim) + 2.0*mu*eps(v)

## Variational formulation

## Resolution

du = TrialFunction(V)
u_ = TestFunction(V)
a = inner(sigma(du), eps(u_))*dx
L = dot(t, u_)*ds(1)

u = Function(V, name="Displacement")
solve(a == L, u, bc)

file_results = XDMFFile("u_new_3D.xdmf")
file_results.parameters["flush_output"] = True
file_results.parameters["functions_share_mesh"] = True
file_results.write(u, 0.)

```

.geo File:

```auto
//+
SetFactory("OpenCASCADE");
Box(1) = {0, 0, 0, 3, 0.01, 1};
//+
Physical Surface(13) = {2};
//+
Physical Surface(14) = {1};
//+
Physical Volume(15) = {1};

```

.msh File: (Using the code you provided above)

> **[untitled.msh](https://drive.google.com/file/d/1scy5Dx9z_0DroS6krAeDTTzgB_R_rlvp/view?usp=sharing)**
>
> Google Drive file.

---

<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:** [April 29, 2021, 12:11pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/168 "2021-04-29T12:11:06Z")

</div>

There are several things in your code that strikes me as odd.  
First, why are you loading the mesh from another file than the volume tag, i.e.

> [@Rafael\_Ferro](#):
>
> ```auto
> mesh = Mesh()
> with XDMFFile("untitled.xdmf") as infile:
> infile.read(mesh)
> 
> ```

should be

```auto
mesh = Mesh()
mvc2 = MeshValueCollection("size_t", mesh, 3)
with XDMFFile("mesh.xdmf") as infile:
    infile.read(mesh)
    infile.read(mvc2, "name_to_read")
cf = cpp.mesh.MeshFunctionSizet(mesh, mvc2)

```

Secondly, you are overwriting the facet tags you are reading in

> [@Rafael\_Ferro](#):
>
> ```auto
> loadSurface = LoadSurface()
> mf.set_all(0)
> loadSurface.mark(mf, 1)
> 
> ```

Thus you are not setting the load on any subdomain, as you removed the tags `13` by using `set_all`. Before posting more code, please carefully go through your code line for line, and check that you get the expected result for each operation.

---

<div class="post-metadata">

**Author:** ![cweickhmann](https://avatars.discourse-cdn.com/v4/letter/c/bc79bd/32.png) [@cweickhmann](https://fenicsproject.discourse.group/u/cweickhmann)\
**Post date:** [April 29, 2021, 1:08pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/169 "2021-04-29T13:08:12Z")

</div>

One little follow-up question, somewhat unrelated to the main thread…  
I’ve used mesh refinement in gmsh recently and then “Recombine 2D” more by accident and it resulted in a mesh of mixed cell types (triangles and quads).  
Are there any considerations to prefer one over the other or even mix them?

---

<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:** [April 29, 2021, 1:22pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/170 "2021-04-29T13:22:51Z")

</div>

Dolfin does not support Mixed type meshes. (It is in the long term plans of dolfinx).

---

<div class="post-metadata">

**Author:** ![Ryan](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/ryan/32/1668_2.png) [@Ryan](https://fenicsproject.discourse.group/u/Ryan)\
**Post date:** [May 18, 2021, 6:21pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/171 "2021-05-18T18:21:34Z")

</div>

Hello everyone,

I was working with the code given here earlier by @dokken

```auto

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

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

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

```

And am receiving the following error code.

```auto
Traceback (most recent call last):
  File "convert.py", line 25, in <module>
    cells=[("triangle", triangle_cells)],
NameError: name 'triangle_cells' is not defined 

```

File for the cylinder.msh was created on GMSH with version 4.8.4

The “msh” files was to large for this post but you can find it at the following link.

> **[cylinder.msh](https://drive.google.com/file/d/1nmHncnZdggLe7U17glgo42bSYa1t8yLa/view?usp=sharing)**
>
> Google Drive file.

Not sure how the triangles are not defined as the msh is using triangles? What am I missing here?

---

<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 18, 2021, 6:43pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/172 "2021-05-18T18:43:38Z")

</div>

Your msh file does not contain any physical markers (i.e `Physical Line/Volume/Surface`), thus you cannot read in cell\_data.

I would suggest using the following code for reading meshes (from [Accessing and marking imported boundaries - #8 by dokken](https://fenicsproject.discourse.group/t/accessing-and-marking-imported-boundaries/5753/8)). Note that here I have defined a physical surface and physical curve.

```auto
import meshio

msh = meshio.read("cylinder.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

tetra_mesh = create_mesh(msh, "tetra")
triangle_mesh = create_mesh(msh, "triangle")
meshio.write("mesh.xdmf", tetra_mesh)

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

```

---

<div class="post-metadata">

**Author:** ![Ryan](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/ryan/32/1668_2.png) [@Ryan](https://fenicsproject.discourse.group/u/Ryan)\
**Post date:** [May 19, 2021, 12:51am UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/173 "2021-05-19T00:51:50Z")

</div>

@dokken

I appreciate your help and I think that got me one step closer, unfortunately I have hit another issue.

I am using the code you provided from above and have updated my design to have surfaces and volumes and more.

I did take a look at the original post that you directed me to and that one does not cover this error I am now getting.

```auto
Traceback (most recent call last):
  File "convert.py", line 11, in <module>
    msh = meshio.read("cylinderv5.msh")
  File "/usr/local/lib/python3.6/dist-packages/meshio/_helpers.py", line 69, in read
    return reader_map[file_format](filename)
  File "/usr/local/lib/python3.6/dist-packages/meshio/gmsh/main.py", line 19, in read
    mesh = read_buffer(f)
  File "/usr/local/lib/python3.6/dist-packages/meshio/gmsh/main.py", line 48, in read_buffer
    return reader.read_buffer(f, is_ascii, data_size)
  File "/usr/local/lib/python3.6/dist-packages/meshio/gmsh/_gmsh41.py", line 73, in read_buffer
    points, point_tags, point_entities = _read_nodes(f, is_ascii, data_size)
  File "/usr/local/lib/python3.6/dist-packages/meshio/gmsh/_gmsh41.py", line 174, in _read_nodes
    raise ReadError("parametric nodes not implemented")
meshio._exceptions.ReadError: parametric nodes not implemented

```

This error does not seem well documented on the web and the few things I have found refer to using abaqus mesh as the mesher and not GMSH.

Any idea where this error is coming from. I do realize that the mesh is really unrefined but was less worried about resolutions and more worried about converting it.

The new mesh file can be found here

> **[cylinderv5.msh](https://drive.google.com/file/d/19ZSsCZeAAES5l1en8TGWryIs0xY543o6/view?usp=sharing)**
>
> Google Drive file.

Also here is the geo files if that is more helpful

> **[cylinderv5.geo](https://drive.google.com/file/d/1J2JD-jZ0bS6o3B4HLQNS1_5OUSEyftYa/view?usp=sharing)**
>
> Google Drive file.

Thank you much,

---

<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 20, 2021, 8:58am UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/174 "2021-05-20T08:58:02Z")

</div>

As far as I can tell you would like to have a 3D mesh (tetrahedrons). Then you also need to mark the volumes:

```auto
// Gmsh project created on Tue May 18 16:34:55 2021
SetFactory("OpenCASCADE");
//+
Circle(1) = {0, 00, 00, 0.6, 0, 2*Pi};
//+
Circle(2) = {0, 00, 00, 0.4, 0, 2*Pi};
//+
Curve Loop(1) = {1};
//+
Curve Loop(2) = {2};
//+
Plane Surface(1) = {1, 2};
//+
Extrude {0, 0, 10} {
  Curve{2}; Curve{1}; Layers {1}; Recombine;
}
//+
Curve Loop(5) = {6};
//+
Curve Loop(6) = {4};
//+
Plane Surface(4) = {5, 6};
//+
Physical Surface("Brime", 7) = {2};
//+
Physical Surface("AirSide", 8) = {3};
//+
Physical Surface("Top", 9) = {1};
//+
Physical Surface("Bottom", 10) = {4};
//+
Surface Loop(1) = {2, 4, 3, 1};
//+
Volume(1) = {1};
//+
Physical Volume(11) = {1};

```

This file, converted to msh with `gmsh 4.6.0`,  
reads nicely with:

```auto
import meshio

msh = meshio.read("cylinderv5.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

tetra_mesh = create_mesh(msh, "tetra")
triangle_mesh = create_mesh(msh, "triangle")
meshio.write("mesh.xdmf", tetra_mesh)

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

```

---

<div class="post-metadata">

**Author:** ![Jaouane\_Mohammed](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/jaouane_mohammed/32/1133_2.png) [@Jaouane\_Mohammed](https://fenicsproject.discourse.group/u/Jaouane_Mohammed)\
**Post date:** [May 25, 2021, 3:37pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/175 "2021-05-25T15:37:54Z")

</div>

```
Hello everyone, How I can use GMSH file on FEniCS (1D mesh) ? 
my problem was divided into two regions, each region has a different equation, how I can divide the two regions in fenics ?. 

I am using the follows code, but unfortunately I got an error.

 ##########################################################
################### Python code #############################
###########################################################
from fenics import *
import meshio

msh = meshio.read('QW.msh')
meshio.write("mesh.xdmf", meshio.Mesh(points=msh.points, cells={"line": msh.cells["line"]}, cell_data={"line": {"name_to_read":
                        msh.cell_data["line"]["gmsh:physical"]}}))
mesh = Mesh()
with XDMFFile("mesh.xdmf") as infile:
    infile.read(mesh)

mvc = MeshValueCollection("size_t", mesh, 1)
mf = cpp.mesh.MeshFunctionSizet(mesh, mvc)
domains = MeshFunction("size_t", mesh, mesh.topology().dim())
dx = Measure("dx",domain=mesh, subdomain_data=mf)

print(assemble(Constant(1)*dx))
print(assemble(Constant(1)*dx(1)))
print(assemble(Constant(1)*dx(2)))

```

######################################  
################################# Error #############################################  
############################################  
Traceback (most recent call last):  
File “/home/jaouane/Desktop/works/gooog/gmsh.py”, line 17, in   
print(assemble(Constant(1)\*dx))  
File “/home/jaouane/anaconda3/envs/spyder/lib/python3.9/site-packages/dolfin/fem/assembling.py”, line 198, in assemble  
dolfin\_form = \_create\_dolfin\_form(form, form\_compiler\_parameters)  
File “/home/jaouane/anaconda3/envs/spyder/lib/python3.9/site-packages/dolfin/fem/assembling.py”, line 56, in \_create\_dolfin\_form  
return Form(form,  
File “/home/jaouane/anaconda3/envs/spyder/lib/python3.9/site-packages/dolfin/fem/form.py”, line 43, in **init**  
ufc\_form = ffc\_jit(form, form\_compiler\_parameters=form\_compiler\_parameters,  
File “/home/jaouane/anaconda3/envs/spyder/lib/python3.9/site-packages/dolfin/jit/jit.py”, line 47, in mpi\_jit  
return local\_jit(\*args, \*\*kwargs)  
File “/home/jaouane/anaconda3/envs/spyder/lib/python3.9/site-packages/dolfin/jit/jit.py”, line 97, in ffc\_jit  
return ffc.jit(ufl\_form, parameters=p)  
File “/home/jaouane/anaconda3/envs/spyder/lib/python3.9/site-packages/ffc/jitcompiler.py”, line 217, in jit  
module = jit\_build(ufl\_object, module\_name, parameters)  
File “/home/jaouane/anaconda3/envs/spyder/lib/python3.9/site-packages/ffc/jitcompiler.py”, line 130, in jit\_build  
module, signature = dijitso.jit(jitable=ufl\_object,  
File “/home/jaouane/anaconda3/envs/spyder/lib/python3.9/site-packages/dijitso/jit.py”, line 165, in jit  
header, source, dependencies = generate(jitable, name, signature, params[“generator”])  
File “/home/jaouane/anaconda3/envs/spyder/lib/python3.9/site-packages/ffc/jitcompiler.py”, line 76, in jit\_generate  
dep\_module\_name = jit(dep, parameters, indirect=True)  
File “/home/jaouane/anaconda3/envs/spyder/lib/python3.9/site-packages/ffc/jitcompiler.py”, line 217, in jit  
module = jit\_build(ufl\_object, module\_name, parameters)  
File “/home/jaouane/anaconda3/envs/spyder/lib/python3.9/site-packages/ffc/jitcompiler.py”, line 130, in jit\_build  
module, signature = dijitso.jit(jitable=ufl\_object,  
File “/home/jaouane/anaconda3/envs/spyder/lib/python3.9/site-packages/dijitso/jit.py”, line 177, in jit  
build\_shared\_library(signature, header, source, dependencies,  
File “/home/jaouane/anaconda3/envs/spyder/lib/python3.9/site-packages/dijitso/build.py”, line 153, in build\_shared\_library  
status, output = get\_status\_output(cmd)  
File “/home/jaouane/anaconda3/envs/spyder/lib/python3.9/site-packages/dijitso/system.py”, line 40, in \_get\_status\_output\_subprocess  
pipe = subprocess.Popen(cmd, shell=False, cwd=cwd, env=env,  
File “/home/jaouane/anaconda3/envs/spyder/lib/python3.9/subprocess.py”, line 951, in **init**  
self.\_execute\_child(args, executable, preexec\_fn, close\_fds,  
File “/home/jaouane/anaconda3/envs/spyder/lib/python3.9/subprocess.py”, line 1821, in \_execute\_child  
raise child\_exception\_type(errno\_num, err\_msg, err\_filename)  
FileNotFoundError: [Errno 2] No such file or directory: ‘c++’

```
Process finished with exit code 1
```

---

<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 25, 2021, 4:51pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/176 "2021-05-25T16:51:38Z")

</div>

What happens if you try to use a built in mesh (i.e. `IntervalMesh`)? Do you obtain the same error?

Here is a minimal example of reading in a 1D mesh that works with dolfin:  
File `test.geo`

```auto
//+
Point(1) = {0, 0, 0, 1.0};
//+
Point(2) = {1, 0, 0, 1.0};
//+
Line(1) = {1, 2};
//+
Physical Curve(1) = {1};

```

```python
from fenics import *
import meshio

def create_mesh_1D(mesh, cell_type):
    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]})
    return out_mesh

mesh_out = create_mesh_1D(meshio.read("test.msh"), "line")
meshio.write("mesh.xdmf", mesh_out)

mesh = Mesh()
with XDMFFile("mesh.xdmf") as infile:
    infile.read(mesh)

mvc = MeshValueCollection("size_t", mesh, 1)
mf = cpp.mesh.MeshFunctionSizet(mesh, mvc)
domains = MeshFunction("size_t", mesh, mesh.topology().dim())
dx = Measure("dx",domain=mesh, subdomain_data=mf)

print(assemble(Constant(1)*dx))
print(assemble(Constant(1)*dx(1)))

```

---

<div class="post-metadata">

**Author:** ![Jaouane\_Mohammed](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/jaouane_mohammed/32/1133_2.png) [@Jaouane\_Mohammed](https://fenicsproject.discourse.group/u/Jaouane_Mohammed)\
**Post date:** [May 25, 2021, 5:37pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/178 "2021-05-25T17:37:06Z")

</div>

Thank you for your response, I try it with the above code, unfortunately I got same error.  
I am going to try it by using IntervalMesh.

---

<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 25, 2021, 5:46pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/179 "2021-05-25T17:46:16Z")

</div>

Then it Seems like you have an installation issue. I suspected this from the beginning as your error is in the assembly, not reading in the mesh.

---

<div class="post-metadata">

**Author:** ![Jaouane\_Mohammed](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/jaouane_mohammed/32/1133_2.png) [@Jaouane\_Mohammed](https://fenicsproject.discourse.group/u/Jaouane_Mohammed)\
**Post date:** [May 26, 2021, 9:16am UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/180 "2021-05-26T09:16:47Z")

</div>

Thank you very much Dokken, You are right , I have an installation issue, now it’s working fine.

---

<div class="post-metadata">

**Author:** ![rkailash](https://avatars.discourse-cdn.com/v4/letter/r/848f3c/32.png) [@rkailash](https://fenicsproject.discourse.group/u/rkailash)\
**Post date:** [October 21, 2021, 5:47pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/181 "2021-10-21T17:47:56Z")

</div>

Thank you. This works perfectly.  
If anyone is interested in adapting this for a 2D mesh, only minor modifications are necessary, and the code snippet is as follows:

```auto
import gmsh
import pygmsh
import meshio
import numpy
from dolfin import *
msh = meshio.read("mesh2d.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

line_mesh = create_mesh(msh, "line", prune_z=True)
meshio.write("mf.xdmf", line_mesh)

triangle_mesh = create_mesh(msh, "triangle", prune_z=True)
meshio.write("mesh.xdmf", triangle_mesh)

mesh = Mesh()
with XDMFFile("mesh.xdmf") as infile:
    infile.read(mesh)
mvc = MeshValueCollection("size_t", mesh, 1)

with XDMFFile("mf.xdmf") as infile:
    infile.read(mvc, "name_to_read")
mf = cpp.mesh.MeshFunctionSizet(mesh, mvc)
File("dolfinmesh.pvd").write(mesh)
File("dolfincellfunc.pvd").write(mf)

```

---

<div class="post-metadata">

**Author:** ![gangadhara](https://avatars.discourse-cdn.com/v4/letter/g/db5fbb/32.png) [@gangadhara](https://fenicsproject.discourse.group/u/gangadhara)\
**Post date:** [November 16, 2021, 10:51am UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/182 "2021-11-16T10:51:20Z")

</div>

Is the above code will work for 3d domain.?

---

<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 16, 2021, 1:41pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/183 "2021-11-16T13:41:27Z")

</div>

Simply set `prune_z=False` in the `create_mesh` function, as long as replacing `line` with `triangle` and `triangle` with `tetrahedron`. The `MeshValueCollection` should have dimension of `mesh.topology().dim()` if you read in cell markers, and `mesh.topology().dim()-1` if you read in facet markers.

---

<div class="post-metadata">

**Author:** ![gangadhara](https://avatars.discourse-cdn.com/v4/letter/g/db5fbb/32.png) [@gangadhara](https://fenicsproject.discourse.group/u/gangadhara)\
**Post date:** [November 16, 2021, 3:54pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/184 "2021-11-16T15:54:03Z")

</div>

Thank you for your reply,  
Is it I modified correctly as you said.?

```auto
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("bokad2.msh")

triangle_mesh = create_mesh(msh, "triangle", False)
tetra_mesh = create_mesh(msh, "tetra", False)
meshio.write("mesh.xdmf", tetra_mesh)
meshio.write("mf.xdmf", 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 XDMFFile("mesh.xdmf") 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 XDMFFile("mf.xdmf") 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)

```

---

<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 16, 2021, 4:01pm UTC](https://fenicsproject.discourse.group/t/transitioning-from-mesh-xml-to-mesh-xdmf-from-dolfin-convert-to-meshio/412/185 "2021-11-16T16:01:00Z")

</div>

You can easily verify this yourself by looking at the XDMF file in Paraview, or integrate over the subdomains (for instance the volumes or surface areas, using

```python
dx_C = Measure("dx", domain=mesh, subdomain_data=cf)
print(assemble(1*dx_C(value_of_domain))

```

and similarly for `ds`

The code you have supplied is also not properly formatted (missing indentation).

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