I want to load an external mesh . It throws an error at stim = mesh.block_bc_opencarp(geom, 'stim', 0, 'x', True).

Question

I'm guessing it's because my mesh might not be correctly defined as a Block. It throws an assertion error. I'm just trying to run the example experiments using my own mesh. How can I make this work?

This is the error - Traceback (most recent call last):
  File "/home/diya/Documents/openCARP/external/experiments/tutorials/02_EP_tissue/00_simple/./run.py", line 179, in <module>
    run()
  File "/usr/local/lib/python3.10/dist-packages/carputils/tools.py", line 547, in wrapped
    ret = run(args, job)
  File "/home/diya/Documents/openCARP/external/experiments/tutorials/02_EP_tissue/00_simple/./run.py", line 101, in run
    geom = mesh.generate(meshname)
  File "/usr/local/lib/python3.10/dist-packages/carputils/mesh/generate.py", line 65, in generate
    assert isinstance(geom, Block), 'generate only works with Block for now'
AssertionError: generate only works with Block for now.

Answer 1

Lines 89 to 98 of the basic example are only relevant if you want to generate a simple block mesh on the fly: https://git.opencarp.org/openCARP/experiments/-/blob/master/tutorials/02_EP_tissue/00_simple/run.py#L86

If you want to load an existing mesh instead, remove those lines and load it by just passing the meshname parameter to the simulator as for example done here: https://git.opencarp.org/openCARP/experiments/-/blob/master/tutorials/02_EP_tissue/21_reentry_induction/run.py#L516

Comments

I really appreciate the quick response. This is my code.
def run(args, job):
    # Path to your mesh file
    meshname = "/home/diya/Documents/openCARP/external/experiments/tutorials/02_EP_tissue/00_simple/atrial"
    

    # Load the mesh
    #geom = mesh.load(meshname)

    # Get basic command line, including solver options from external .par file
    cmd = tools.carp_cmd(tools.simfile_path(os.path.join(EXAMPLE_DIR, 'simple.par')))
    
    # Attach electrophysiology physics (monodomain) to mesh region with tag 1
    cmd += tools.gen_physics_opts(IntraTags=[1])

    cmd += ['-simID',    job.ID,
            '-meshname', meshname,
            '-tend',     args.tend]

    # Set monodomain conductivities
    cmd += ['-num_gregions',         1,
            '-gregion[0].name',     "myocardium",
            '-gregion[0].num_IDs',  1,
            '-gregion[0].ID',       "1",
            '-gregion[0].g_el',     0.625,
            '-gregion[0].g_et',     0.236,
            '-gregion[0].g_en',     0.236,
            '-gregion[0].g_il',     0.174,
            '-gregion[0].g_it',     0.019,
            '-gregion[0].g_in',     0.019,
            '-gregion[0].g_mult',   0.5]

    # Define the ionic model to use
    cmd += ['num_imp_regions',      1,
            'imp_region[0].im',     'Courtemanche',
            'imp_region[0].num_IDs',1,
            'imp_region[0].ID[0]',  1]

    # Define the geometry of the stimulus directly in the command line
    # Replace with your specific stimulus location and parameters
    cmd += ['-stimulus', 'x', '0', '100', '0', '1']

    if args.visualize:
        cmd += ['-gridout_i', 3]    # output both surface & volumetric mesh for visualization

    # Run simulation
    job.carp(cmd)

    # Do visualization
    if args.visualize and not settings.platform.BATCH:
        geom = os.path.join(job.ID, os.path.basename(meshname)+'_i')
        data = os.path.join(job.ID, 'vm.igb.gz')
        view = tools.simfile_path(os.path.join(EXAMPLE_DIR, 'simple.mshz'))
        job.meshalyzer(geom, data, view)
I have converted my vtk file into .elem,.pts,.lon files. But it wont open on my meshalyzer. Could you please help me out?
This is the error I'm getting -
*** Unrecognized keyword stim[0].num_IDs

 
*** Error reading parameters

Error: 2024-07-01_simple_100.0_petsc_np1/vm.igb.gz does not exist!
#-------------------------------------------------------------------------------
#                             Launching Meshalyzer
#-------------------------------------------------------------------------------

/usr/local/bin/meshalyzer/meshalyzer \
  2024-07-01_simple_100.0_petsc_np1/atrial_i \
  2024-07-01_simple_100.0_petsc_np1/vm.igb.gz \
  /home/diya/Documents/openCARP/external/experiments/tutorials/02_EP_tissue/00_simple/./simple.mshz

Error: could not open /home/diya/Documents/openCARP/external/experiments/tutorials/02_EP_tissue/00_simple/atrial.elem.pts for reading! Reason:
No such file or directory
Unable to read proper points file
/usr/local/bin/meshalyzer/meshalyzer failed with error code 1

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We can probably have a look if you add a link to your original and converted mesh files

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https://github.com/DiyaKalyanpur/cardiac_simulation

Thank you so so much

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There are unsupported elements in your mesh. How did you create it?

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I had a vtk file that I converted into elem,pts,lion files using the meshtool command.

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My guess is that the VTK file did not only contain triangles and tetrahedra but also other types of elements

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Ah makes sense. How can I go forward with this?

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Also, are there any atrial meshes available that I could use?  
Does opencarp not support other types of elements?

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This depends on your meshing tool etc. While unrelated to openCARP, you can for example have a look at the Tetrahedralize and Triangulate filters in ParaView.

For meshes etc., the collection of community-sourced modeling resources can be a good starting point: https://opencarp.org/community/modeling-resources

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Got the mesh working. Thanks so much!