How to perform simulations on non-regular meshes?

Question

Hello! I'm new to cardiac electrophysiology simulation using open CARP. I have already performed simulations in cubic regions using the Block and BoxRegion classes, however, now I need to move my simulations to an atrial mesh and I don't know how to do that.

I would like to know a few things:

Are there any carputils classes for this purpose?

What do I need to read?

Is there any example that can help me?
 

Any help is welcome.

Thank you in advance.

Answer 1

carputils is great when you want to generate the meshes on the fly. For more complex meshes, you likely have them already as a file. The workflow then is to 

- if not already in the openCARP format, convert them (e.g. using meshtool: https://bitbucket.org/aneic/meshtool/src/master/)

- directly load the mesh with the raw openCARP command meshname (section 19.2 of the user manual: https://opencarp.org/documentation/user-manual)

I see that this is a frequent use case that's not covered yet by the examples on the openCARP web page. We'd be glad to see community contributions for such an example: https://opencarp.org/community/contribute

I created an issue for it: https://git.opencarp.org/openCARP/experiments/-/issues/41

Comments

Thank you! I also think an example using custom meshes would be very helpful as it would cover specific commands for cases like this that are not present in the currently available examples.

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I believe that would be a very important example as well. I am sharing the same issue with Felipe Fonseca. My overall goal is to get healthy epicardial potentials on a complete heart mesh structure by stimulating heart from the correct nodes. I have already done the first steps you suggested and converted the whole heart mesh structure provided in the following link into openCARP format:

https://zenodo.org/record/3890034

What I got is files with the extension of *.elem, *.Ion, and *.pts. Description for these file formats are given in the openCARP manual. My doubt at this point is, do I have the conductivity and ionic models with the *.Ion file?

Also I am having doubts about whether to follow the tutorial on the Youtube channel ( https://www.youtube.com/watch?v=Idt65RqX_50&t=777s ) or Tissue simulations section in the manual?

About the contribution, I am keeping a good record of the steps I am following. I will make sure to share it when I get a successful simulation model through git or here.

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The .lon file contains the fiber orientation. Details are described in section 4.1.4 of the openCARP manual: https://opencarp.org/documentation/user-manual

Ionic models and tissue conductivities are set per region as for example shown in this tutorial: https://git.opencarp.org/openCARP/experiments/-/blob/master/tutorials/02_EP_tissue/00_simple/run.py#L115

Both the tutorial and the manual are good resources. The manual should always be up to date
while the videos cover parameter names etc. as they were at the time the video was recorded.