Getting salome mesh to FEniCSx python

[dokken]

@otaolafr

import meshio
mesh = meshio.read(
    '/home/franco/Downloads/dummyFiles/test/hexa.med'
)
mesh.write(
    '/home/franco/Downloads/dummyFiles/test/hexa.xdmf' )

Then run it by using python3 test.py, this proven to ‘write’ the mesh in the desired xdmf format, nevertheless, i am having some trouble still:
The groups I have created in salome disappeared, there is only a cell_tags i can see in paraview, that are negative from -12 to 0, where each negative int value looks like it corresponds to one of the groups that i had in salome, from the -12 until the -6 but the -5 to -1 are empty and furthermore the 0 I dont finish of recognizing what corresponds to as it does not completely correspond to anything I have a tag on salome nor the submeshes.

I usually do more than what you have done here when working with meshio.
An example of this (using gmsh) can be found in many posts in the forum, such as):

Import mesh from Salome (med) to dolfinx

Have you had a look at: Defining subdomains for different materials — FEniCSx tutorial

which points to my tutorial and is similar to:

Fail to read tagged facets from mesh generated with GMSH

You are here trying to integrate over the vertices of your mesh? Then you are not integrating over a facet (“ds”) but a vertex (“dp”). However, lets take 10 steps backwards, and consider: import meshio import gmsh gmsh.initialize() gmsh.model.add("my model") c_r = [0, 0, 0] c_R = [0, 0, 0] r = 1 R = 2 resolution = 0.1 print(f"Mesh resolution = {resolution}") disk_r = gmsh.model.occ.addDisk(c_r[0], c_r[1], c_r[2], r, r) disk_R = gmsh.model.occ.addDisk(c_R[0], c_R[1], c_R[2], R, R) ring = gm…

Note that I’ve been rewriting adios4dolfinx to support all kinds of IO backends, including:

• pyvista (meshio)
• VTKHDF
• XDMF

in: General backend support by jorgensd · Pull Request #193 · jorgensd/adios4dolfinx · GitHub

I could help you read the .med file if you provide an example.
For instance I made a bespoke writer for the exodus file format at: GitHub - jorgensd/mesh_converter: A mesh converter from EXODUS 2 to XDMF

@otaolafr

once I get the mesh in the correct format with all the information (point 1.) how can I import it to fenicxs to run a simple simulation over it? I did not find any tutorial with mesh importation + definition of a simple boundary conditions.

There are many demos that does this, for instance at:

Meshes from external sources — FEniCS Workshop

Electromagnetics example — FEniCSx tutorial

Test problem 2: Flow past a cylinder (DFG 2D-3 benchmark) — FEniCSx tutorial

Adaptive mesh refinement with NetGen and DOLFINx — FEniCSx tutorial

Coupling PDEs of multiple dimensions — FEniCS Workshop