# Importing a GMSH mesh into FEniCS

**URL:** <https://fenicsproject.discourse.group/t/importing-a-gmsh-mesh-into-fenics/15561>\
**Category:** General\
**Created:** [August 16, 2024, 12:38pm UTC](https://fenicsproject.discourse.group/t/importing-a-gmsh-mesh-into-fenics/15561 "2024-08-16T12:38:51Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Kieran](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/kieran/32/7432_2.png) [@Kieran](https://fenicsproject.discourse.group/u/Kieran)\
**Post date:** [August 16, 2024, 12:38pm UTC](https://fenicsproject.discourse.group/t/importing-a-gmsh-mesh-into-fenics/15561/1 "2024-08-16T12:38:51Z")

</div>

I am now trying to use FEniCSx/Dolfinx to solve a simple equation but I want to import a gmsh mesh which has boundaries etc. However, whenever I try this I get errors such as:

Traceback (most recent call last):  
File “/home/fenics/HeatConduction/src/heat\_conduction/test4.py”, line 60, in   
msh = xdmf.read\_mesh(name=“Grid”)  
File “/usr/local/dolfinx-real/lib/python3.10/dist-packages/dolfinx/io/utils.py”, line 258, in read\_mesh  
cell\_shape, cell\_degree = super().read\_cell\_type(name, xpath)  
RuntimeError: Cannot recognise cell type. Unknown value: mixed

I am confused to what I am doing wrong!

Note I have tried using Docker Dolfinx and conda but neither works (the later doesn’t even install fenics/dolfinx!). I am on an M3 MBP.

The code I am using is:

```auto
import gmsh
import meshio
from mpi4py import MPI
from dolfinx.io import XDMFFile
import dolfinx.fem as fem

def create_doughnut_mesh(filename, refinement_level):
    gmsh.initialize()
    gmsh.model.add("Doughnut")

    # Define the outer and inner circles
    outer_circle = gmsh.model.occ.addCircle(0, 0, 0, 1)
    inner_circle = gmsh.model.occ.addCircle(0, 0, 0, 0.5)

    # Create the plane surface between the circles
    outer_loop = gmsh.model.occ.addCurveLoop([outer_circle])
    inner_loop = gmsh.model.occ.addCurveLoop([inner_circle])
    surface = gmsh.model.occ.addPlaneSurface([outer_loop, inner_loop])

    # Synchronize the CAD kernel with the Gmsh model
    gmsh.model.occ.synchronize()

    # Ensure no quadrilaterals are created
    gmsh.option.setNumber("Mesh.CharacteristicLengthFactor", 1.0 / refinement_level)

    # Generate the mesh
    gmsh.model.mesh.generate(2)

    # Ensure the mesh contains only triangles
    element_types, element_tags, node_tags = gmsh.model.mesh.getElements()
    if len(element_tags) == 0 or len(element_tags[0]) == 0:
        raise RuntimeError("Mesh generation failed: no elements found.")
    if any(element_type != 2 for element_type in element_types): # 2 corresponds to triangles in Gmsh
        print(element_types)

    # Get the boundary entities
    outer_boundary = gmsh.model.getBoundary([(2, surface)], oriented=False, recursive=False)
    inner_boundary = gmsh.model.getBoundary([(2, surface)], oriented=False, recursive=False)

    # Create physical groups for the boundary edges
    outer_boundary_group = gmsh.model.addPhysicalGroup(1, [edge[1] for edge in outer_boundary], tag=1)
    inner_boundary_group = gmsh.model.addPhysicalGroup(1, [edge[1] for edge in inner_boundary], tag=2)
    gmsh.model.setPhysicalName(1, outer_boundary_group, "OuterBoundary")
    gmsh.model.setPhysicalName(1, inner_boundary_group, "InnerBoundary")

    # Optionally, save the mesh to a file
    gmsh.write(filename)

    gmsh.finalize()

# Example usage
create_doughnut_mesh("doughnut.msh", refinement_level=10)

# Convert the Gmsh mesh to XDMF format
mesh = meshio.read("doughnut.msh")
meshio.write("doughnut_filtered.xdmf", mesh)

# Load the mesh into FEniCSx
with XDMFFile(MPI.COMM_WORLD, "doughnut_filtered.xdmf", "r") as xdmf:
    msh = xdmf.read_mesh(name="Grid")

# Read the filtered mesh from the XDMF file
filtered_mesh = meshio.read("doughnut_filtered.xdmf")

# Extract boundary edges
boundary_edges = []
for cell_block in filtered_mesh.cells:
    if cell_block.type == "triangle":
        for triangle in cell_block.data:
            for i in range(3):
                edge = tuple(sorted([triangle[i], triangle[(i + 1) % 3]]))
                if edge not in boundary_edges:
                    boundary_edges.append(edge)

# Print the boundary edges
print("Boundary edges:")
for edge in boundary_edges:
    print(edge)

V = fem.FunctionSpace(msh, ("CG", 1))

```

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<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:** [August 16, 2024, 3:44pm UTC](https://fenicsproject.discourse.group/t/importing-a-gmsh-mesh-into-fenics/15561/2 "2024-08-16T15:44:05Z")

</div>

See for instance: [Can dolfinx read a GMSH file containing 1D mesh of an ellipse? - #2 by dokken](https://fenicsproject.discourse.group/t/can-dolfinx-read-a-gmsh-file-containing-1d-mesh-of-an-ellipse/9765/2)  
or use the built in GMSH API functionality: [dolfinx.io.gmshio — DOLFINx 0.8.0 documentation](https://docs.fenicsproject.org/dolfinx/v0.8.0/python/generated/dolfinx.io.gmshio.html#dolfinx.io.gmshio.model_to_mesh)  
which work directly on the gmsh model rather than storing it into an intermediate format…

> [@Kieran](#):
>
> Note I have tried using Docker Dolfinx and conda but neither works (the later doesn’t even install fenics/dolfinx!). I am on an M3 MBP.

This seems unrelated to the current post, and you have not provided the steps you followed and your error trace. Steps for installing with conda is outlined at for instance: [https://fenicsproject.org/download/](https://fenicsproject.org/download/)