Problem when trying to achieve Phase singularity distribution experiment on 3D mesh

Question

Hi,

I have been able to get the correct result of the phase singularity distribution experiment from the reentry induction example on 2D meshes, however, when I was trying to reproduce a similar result on a 3D ellipsoid mesh, I haven't been able to get a correct rotating pattern. But there isn't any error message from the code, so I am wondering which part went wrong. Could you give me some suggestions? Or could you give me some advice on how to simulate arrhythmia?

Thank you.

Answer 1

Please provide a minimum example to reproduce this behavior

Comments

I am using the same code from the example except the model I used is an existing 3D mesh instead of the original 2D mesh. I am not sure what’s causing this problem, is there any parameters I should change?

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Again, please provide a minimum example to reproduce including your mesh and the command you call. If you want us to support, please make it easy.

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Sorry about that. The command I used is
python3 run.py --np 2 --protocol PSD
And the mesh I am using is a simple ellipsoid mesh, it is from https://git.opencarp.org/openCARP/meshalyzer/-/tree/master/example
Thank you

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I am using the code from the reentry example, the only thing I changed is in the setupMesh function, instead of creating a mesh from the code, I loaded an existing mesh using the following code:

meshname = "myMesh/ellipsoid" # basename of the mesh in opencarp format
myMesh = mesh.base.Mesh.from_files("myMesh/ellipsoid")
myMesh.read_points("myMesh/ellipsoid.pts")
myMesh.read_fibres("myMesh/ellipsoid.lon")

Also, I am wondering if it is possible to get the "geom" variable from the existing mesh

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I don't see how this could work given that later in the code of that example, fibrotic tissue is labeled which assumes the slab geometry.
Conceptually the PSD method also works on other meshes (including 3D) but it won't work by just plugging another mesh into this example.

If you provide an actual executable example, I'm happy to have a look again.