What kind of mesh files do I need for pseudo-bidomain simulation?

Question

Hello there. I am trying to do a pseudo-bidomain simulation with existing meshes. I am wondering does the '.elem' file need to contain volumetric meshes belonging to both extracellular and intracellular spaces? And if they are mixed in one mesh file, does the "tag" number play the role of distinguishing extra and intra elements? (tag 0 as extra, nonzero as intra)  Is there other settings used for assigning different domains? Thank you!

Answer 1

Hi Yingnan,

openCARP reconizes the intracellular and extracellular domiain using the physics regions based on the element tag of your mesh. Here is a short example on how to use this parameter:

-num_phys_regions 2

-phys_region[0].name "Extracellular domain"

-phys_region[0].ptype 1

-phys_region[0].num_IDs 2

-phys_region[0].ID[0] 0

-phys_region[0].ID[1] 1

-phys_region[1].name "Intracellular domain"

-phys_region[1].ptype 0

-phys_region[1].num_IDs 1

-phys_region[1].ID[0] 1

Using carputils you can define your physics regions like:

cmd += tools.gen_physics_opts(ExtraTags=[0,1], IntraTags=[1])

Best,

Jorge

Comments

Thank you Jorge, these are really helpful! I also have one question. Since I want to attach specific points for stimulus to this simulation, I used stimulus[0].vtx_file to attach. However, there is always an error no matter how I adjust the points "L5 : Matrix doesn't match index set in fl_getVolumeFromNodeSet."
I am a bit confused about interpreting this error means. For my vtx_file, I just randomly define some center nodes in my intracellular space , and put their indices in the vtx_file (first line number, secondline "intra"). Are there other things I could pay attention to solving this error?

Thanks a lot!


Best,
Yingnan

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Hi Yingnan,

The vertex point should belong to your mesh and can not be a floating-point that is not connected to the mesh. I hope this helps you.

Best,

Jorge