# How to import xdmf mesh generated by gmsh into fenics
**URL:** https://fenicsproject.discourse.group/t/how-to-import-xdmf-mesh-generated-by-gmsh-into-fenics/10045
**Category:** General
**Created:** [December 27, 2022, 2:30am UTC](https://fenicsproject.discourse.group/t/how-to-import-xdmf-mesh-generated-by-gmsh-into-fenics/10045 "2022-12-27T02:30:05Z")
**Posts on this page:** 8
**Page:** 2
### Author:  [@taytay33](https://fenicsproject.discourse.group/u/taytay33)
#### Post date: [January 5, 2023, 9:59am UTC](https://fenicsproject.discourse.group/t/how-to-import-xdmf-mesh-generated-by-gmsh-into-fenics/10045/24 "2023-01-05T09:59:07Z")
I have cell neighbours of each element. How can I differentiate the two and define different material.
---
### Author:  [@dokken](https://fenicsproject.discourse.group/u/dokken)
#### Post date: [January 5, 2023, 10:29am UTC](https://fenicsproject.discourse.group/t/how-to-import-xdmf-mesh-generated-by-gmsh-into-fenics/10045/25 "2023-01-05T10:29:34Z")
As I told you
> [@dokken](#):
>
> 1. Write a recursive script looping through
> a. For each interface of an object find each connected cell.
> b. Check each connected cells loop through neighbours (going through each of their respective facets,
So start at a marked interface, find the two cells connected to that facet.
Give each of the cells a unique number (say cell0 is marked with 5 cell1 is marked with 7).
in sudo-code this is what you need to do for each cell:
```python
def mark_neigbours(cell, tag, interface_markers, volume_markers, visited_cells):
if c in visited_cells:
return
c_facets = facets(cell)
for facet in c_facets:
if facet in (interface markers):
pass
else
connected_cells=cells(facet)
for c in connected_cells:
if c!= cell
volume_markers[c] = tag
visited_cells.append(c)
mark_neigbours(c, tag, interface_markers, visited_cells)
```
As I said, this is a recursive algorithm, which is going to be quite complex (and I might have made mistakes in the pseudo code). You should really let the mesh generator handle the tagging of cells.
---
### Author:  [@taytay33](https://fenicsproject.discourse.group/u/taytay33)
#### Post date: [January 5, 2023, 10:47am UTC](https://fenicsproject.discourse.group/t/how-to-import-xdmf-mesh-generated-by-gmsh-into-fenics/10045/26 "2023-01-05T10:47:08Z")
after marking neighbours how will define the different material for each cell?
---
### Author:  [@dokken](https://fenicsproject.discourse.group/u/dokken)
#### Post date: [January 5, 2023, 10:51am UTC](https://fenicsproject.discourse.group/t/how-to-import-xdmf-mesh-generated-by-gmsh-into-fenics/10045/27 "2023-01-05T10:51:12Z")
That is the whole point of `volume_markers`, which should be a `MeshFunction`, which you can modify the array of, with the appropriate tags, such that you can compute integrals over subdomains.
---
### Author:  [@taytay33](https://fenicsproject.discourse.group/u/taytay33)
#### Post date: [January 5, 2023, 11:03am UTC](https://fenicsproject.discourse.group/t/how-to-import-xdmf-mesh-generated-by-gmsh-into-fenics/10045/28 "2023-01-05T11:03:31Z")
OO I’m such a dumb.
I imported the mesh file
```auto
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)
```
Than I found the cell\_neighbours:
```auto
tdim = mesh.topology().dim()
mesh.init(tdim - 1, tdim)
cell_neighbours = {}
for cell in cells(mesh):
index = cell.index()
cell_neighbours[index] = []
for facet in facets(cell):
facet_cells = facet.entities(tdim)
for facet_cell in facet_cells:
if (index!=facet_cell):
cell_neighbours[index].append(facet_cell)
~~~~~~~
to mark the Interface, have to use this function
~~~~~
def mark_neigbours(cell, tag, interface_markers, volume_markers, visited_cells):
if c in visited_cells:
return
c_facets = facets(cell)
for facet in c_facets:
if facet in (interface_markers):
pass
else:
connected_cells=cells(facet)
for c in connected_cells:
if (c!= cell):
volume_markers[c] = tag
visited_cells.append(c)
mark_neigbours(c, tag, interface_markers, visited_cells)
```
I have not understood a single thing what to give in this function and proceed next.
---
### Author:  [@dokken](https://fenicsproject.discourse.group/u/dokken)
#### Post date: [January 5, 2023, 3:18pm UTC](https://fenicsproject.discourse.group/t/how-to-import-xdmf-mesh-generated-by-gmsh-into-fenics/10045/29 "2023-01-05T15:18:54Z")
> [@taytay33](#):
>
> I have not understood a single thing what to give in this function and proceed next.
As I’ve stated, this is a complicated way of doing it, as the mesh generator should have a way easier time of determining these volumes. I do not have time to write out this algorithm for you.
---
### Author:  [@taytay33](https://fenicsproject.discourse.group/u/taytay33)
#### Post date: [January 20, 2023, 1:07am UTC](https://fenicsproject.discourse.group/t/how-to-import-xdmf-mesh-generated-by-gmsh-into-fenics/10045/30 "2023-01-20T01:07:26Z")
I’m getting this error. Any Idea? Solution???
```auto
UMFPACK V5.7.9 (Oct 20, 2019): ERROR: out of memory
Traceback (most recent call last):
File "/mnt/c/downloads/run.py", line 90, in
solve(A_ass, u.vector(), L_ass)
File "/usr/lib/petsc/lib/python3/dist-packages/dolfin/fem/solving.py", line 240, in solve
return dolfin.la.solver.solve(*args)
File "/usr/lib/petsc/lib/python3/dist-packages/dolfin/la/solver.py", line 72, in solve
return cpp.la.solve(A, x, b, method, preconditioner)
RuntimeError:
*** -------------------------------------------------------------------------
*** DOLFIN encountered an error. If you are not able to resolve this issue
*** using the information listed below, you can ask for help at
***
*** fenics-support@googlegroups.com
***
*** Remember to include the error message listed below and, if possible,
*** include a *minimal* running example to reproduce the error.
***
*** -------------------------------------------------------------------------
*** Error: Unable to successfully call PETSc function 'KSPSolve'.
*** Reason: PETSc error code is: 76 (Error in external library).
*** Where: This error was encountered inside ./dolfin/la/PETScKrylovSolver.cpp.
*** Process: 0
***
*** DOLFIN version: 2019.2.0.dev0
*** Git changeset: unknown
```
---
### Author:  [@dokken](https://fenicsproject.discourse.group/u/dokken)
#### Post date: [January 20, 2023, 5:26am UTC](https://fenicsproject.discourse.group/t/how-to-import-xdmf-mesh-generated-by-gmsh-into-fenics/10045/31 "2023-01-20T05:26:37Z")
See for instance [UMFPACK error: out of memory despite system having free memory - #2 by plugged](https://fenicsproject.discourse.group/t/umfpack-error-out-of-memory-despite-system-having-free-memory/984/2)
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