Fitzhugh-Nagamo

Question

Hello,

I would like to simulate plane waves, slits and some heterogeneties... I'm thinking of the Fitzhugh-Nagamo model to do so, or a simmilar one. Does anyone have an advice on how I can start? Is there a built-in model I can use for these purposes and just change parameters?

Answer 1

I recommend these examples:

• Basic Tissue EP
• Heterogeneities

One of the simplest cellular models provided is the Mitchell Schaeffer model but you can also start with the default model.

Comments

Hi Axel! I'm trying the reentry induction example (code: https://git.opencarp.org/openCARP/experiments/-/blob/master/tutorials/02_EP_tissue/21_reentry_induction/run.py ) but I am getting the following errors when I run the script (with --visualize)

  File "/usr/local/lib/python3.9/dist-packages/bin/tuneCV", line 157, in <module>
    run()
  File "/usr/local/lib/python3.9/dist-packages/carputils/tools.py", line 528, in wrapped
    ret = run(args, job)
  File "/usr/local/lib/python3.9/dist-packages/bin/tuneCV", line 140, in run
    to.iterateCV(job)
  File "/usr/local/lib/python3.9/dist-packages/carputils/tuning.py", line 561, in iterateCV
    self.vel_ = self.measureCV(os.path.join(ItJobID, 'init_acts_lats-thresh.dat'))
  File "/usr/local/lib/python3.9/dist-packages/carputils/tuning.py", line 477, in measureCV
    lats = loadtxt(actsFile)
  File "/usr/local/lib/python3.9/dist-packages/numpy/lib/npyio.py", line 961, in loadtxt
    fh = np.lib._datasource.open(fname, 'rt', encoding=encoding)
  File "/usr/local/lib/python3.9/dist-packages/numpy/lib/_datasource.py", line 195, in open
    return ds.open(path, mode, encoding=encoding, newline=newline)
  File "/usr/local/lib/python3.9/dist-packages/numpy/lib/_datasource.py", line 535, in open
    raise IOError("%s not found." % path)
OSError: imp_Courtemanche_vel_0.3_dx_400.0_It_0/init_acts_lats-thresh.dat not found.
Traceback (most recent call last):
  File "/home/mariaduda/Desktop/reentry.py", line 729, in <module>
    run()
  File "/usr/local/lib/python3.9/dist-packages/carputils/tools.py", line 528, in wrapped
    ret = run(args, job)
  File "/home/mariaduda/Desktop/reentry.py", line 456, in run
    converge_CV(args,job)
  File "/home/mariaduda/Desktop/reentry.py", line 656, in converge_CV
    job.bash(cmd)
  File "/usr/local/lib/python3.9/dist-packages/carputils/job/job.py", line 242, in bash
    self.register(ShellCommand(cmd, message), *args, **kwargs)
  File "/usr/local/lib/python3.9/dist-packages/carputils/job/job.py", line 119, in register
    self._queue.pop(0).execute()
  File "/usr/local/lib/python3.9/dist-packages/carputils/job/command.py", line 163, in execute
    divertoutput.call(self._cmd, stdout=self._stdout, stderr=self._stderr)
  File "/usr/local/lib/python3.9/dist-packages/carputils/divertoutput.py", line 43, in wrapped
    return func(cmd, *args, **kwargs)
  File "/usr/local/lib/python3.9/dist-packages/carputils/divertoutput.py", line 147, in call
    raise subprocess.CalledProcessError(proc.returncode, cmd[0])
subprocess.CalledProcessError: Command '/usr/local/lib/python3.9/dist-packages/bin/tuneCV' returned non-zero exit status 1.


Do I need anything else besides the code or is it another problem? Would you know?
Thanks again :)

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Is this with the Mitchell Schaeffer model?
If yes, I assume the problem is related to this issue: https://opencarp.org/q2a/445/tunecv-and-mms-model-tissue-doesnt-activate