My simulation won't run. Can you please help me figure out this error?

Question

-------------------------------------------------------------------------------
#              Launching openCARP Simulation 2024-07-04_basic_20.0
#-------------------------------------------------------------------------------

/usr/local/bin/openCARP \
  +F /home/diya/Documents/openCARP/external/experiments/tutorials/02_EP_tissue/01_basic_usage/./basic.par \
  -ellip_use_pt 0 \
  -parab_use_pt 0 \
  -parab_options_file /usr/local/lib/python3.10/dist-packages/carputils/resources/petsc_options/ilu_cg_opts \
  -ellip_options_file /usr/local/lib/python3.10/dist-packages/carputils/resources/petsc_options/gamg_cg_opts \
  -simID 2024-07-04_basic_20.0 \
  -meshname /home/diya/Documents/openCARP/external/experiments/tutorials/02_EP_tissue/01_basic_usage/tetrahedralized \
  -dt 25 \
  -tend 20.0 \
  -num_stim 1 \
  -stimulus[0].name S1 \
  -stimulus[0].stimtype 0 \
  -stimulus[0].strength -20.0 \
  -stimulus[0].duration 15.0 \
  -num_stim 1 \
  -stimulus[0].name S1 \
  -stimulus[0].stimtype 0 \
  -stimulus[0].strength -20.0 \
  -stimulus[0].duration 15.0 \
  -gridout_i 3 \
  -gridout_e 3 \
  -spacedt 0.1

*** GIT tag:            latest
*** GIT hash:           2271a3cccd7137f1e28c043c10adbd80480f1462
*** GIT repo:           https://gitlab-ci-token:glcbt-64_BKSKSqTv-gBsQkLy27QY@git.opencarp.org/openCARP/openCARP.git
*** dependency commits:

L2 : Output directory exists: 2024-07-04_basic_20.0

L4 : Warning: No physics region defined! Please set phys_region parameters to correctly define physics.
L4 : IntraElec and ExtraElec domains will be derived from fibers.

L1 : Warning: Legacy stimuli defined. Please consider switching to stimulus definition "stim[]"!

    *** Processing meshes ***

Reading reference mesh: /home/diya/Documents/openCARP/external/experiments/tutorials/02_EP_tissue/01_basic_usage/tetrahedralized.*
Done in 0.057064 sec.
Done in 0.000161 sec.
Processing submeshes
All done in 0.089264 sec.
Writing "Autogenerated intracellular Electrics" surface: tetrahedralized_i.surf
Writing "Autogenerated intracellular Electrics" mesh: tetrahedralized_i

    *** Initializing physics ***

Initializing Electrics ..

Setting up ionic models and plugins
-----------------------------------

Assigning IMPS to tagged regions:
    Ionic model: Courtemanche to tag region(s) [0] (implicitely)

    *** Launching simulation ***

PROG    -----     ----    -------    -------|
time    %%comp    time     ctime       ETA  |
0.00    0.0    0.0    0:00:00    0:00:00
L5 : parabolic PDE (PETSc) solver diverged. Reason: iterations exceeded.
Warning: Changing 2024-07-04_basic_20.0/vm.igb.gz to 2024-07-04_basic_20.0/vm.igb!
#-------------------------------------------------------------------------------
#                             Launching Meshalyzer
#-------------------------------------------------------------------------------

/usr/local/bin/meshalyzer/meshalyzer \
  2024-07-04_basic_20.0/tetrahedralized_i \
  2024-07-04_basic_20.0/vm.igb \
  /home/diya/Documents/openCARP/external/experiments/tutorials/02_EP_tissue/01_basic_usage/./view_vm.mshz

I'm trying to run the basic example using my own mesh that has been tetrahedralized using the filter.

Additionally, how can I decide / choose simulation points for my mesh?

Answer 1

Sorry, we won't be able to support without a minimum executable example

Comments

Transferred from separate question:

https://github.com/DiyaKalyanpur/basic_example.

The x0,y0,z0,x1,y1,z1 values are such that we're assuming the mesh is on the origin.

hence (- coordinate/2) to (+coordinate/2).

I'm not sure how to simulate only a certain point or the whole tissue.

If I can just understand how to stimulate using any mesh and where I'm going wrong, I'll be able to work on my complex experiments. As of now, my mesh is successfully imported but the experiment just won't run.

Since its the atrium, I want to simulate depolarization in order to calculate the p wave.

Any suggestions/ recommendations on how I could get that working would be extremely helpful.

---

The recommended way is using the Stim parameter group. It's elec structure let's you define a stimulated region for example as a sphere around a given point. This is described in section 23.3.2 of the user manual: https://opencarp.org/documentation/user-manual

Alternatively, you can also mark the elements you want to stimulate in your mesh and assign them a dedicated material class in a thirdparty meshprocessing tool. Then you can simply use Stim.elec.geomID