How to mark boundaries of irregular mesh


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6 months ago by
Ovais  
Hi community ,

I have a 3D (realistic) mesh of heart ventricles that i have obtained from a repo. I want to mark inner ,outer and top boundary of the mesh. Is there any way to do that ? The boundary is close to realistic hence the boundary isnt like an ideal ellipsoid.

I use paraview but i coudnt find this type of feature in paraview.
Can anyone suggest some efficient way to do that ? may be through some software ?. The mesh is in xml format. Info on how to select boundary of a prepared mesh in xml is what i require.


Regards
Community: FEniCS Project

1 Answer


3
6 months ago by
Emek  
Hi,

I find the best way to do this over Salome. You can mark geometric regions and then use them in the mesh (mesh is also generated via Salome, for example by using NetGen algorithms). Then export med, generate gmsh file, export to dolfin. You can find the detailed instruction in the Appendix of this book:

https://link.springer.com/book/10.1007%2F978-981-10-2444-3

Download the Back Matter and go to the pdf-page 5.

Best, Emek

Thanks Emek I am doing that.
written 6 months ago by Ovais  
Hi emak , i have downloaded salome 8.3.0 that works on windows and now trying to import my mesh but salome only supports BREP,STEP ,IGES,STL and XAO formats. My mesh is in .xml format which i have converted to .msh format using meshio but meshio isnt converting my mesh to .stl format because its composed on tetrahedrons where as stl supports triangles.

Can you suggest a way to convert my mesh in .xml or .msh format to a format acceptable to salome.
written 6 months ago by Ovais  
Dear Ovais: Geometry includes the topology saved in brep, step, iges. However, mesh files like msh or xml have only the node coordinates and their connectivity, but no topology. If you want to work with xml converted to msh, then you can open in msh in gmsh and find out the numbers of the faces to be used in FEniCS, if the file includes the surfaces as well (I doubt that). For example a face to be clamped has the number 223, then you can use in FEniCS ds(223) to integrate over this face or in DirichletBC(....facet_list, 223) to apply a Dirichlet bondary condition. Your life would be easier if you can receive a file from a CAD program with the topology (for example a step file).
written 6 months ago by Emek  
Thanks for such good guidance emak! ... i have been able to import the mesh in salome by first converting it .med using gmsh and then importing the mesh. Now working on creating groups and then getting to FEniCS after necessary conversion. But work is in progress but i hope i would be able to do this now.
Grateful!
written 6 months ago by Ovais  
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