Experimental setup from Niederer et al. 2011

Question

Dear openCARP community,

I am looking for an openCARP experiment mimicking the proposed benchmark problem in [1]. Yesterday I was at the online user's meeting where I asked if there is an experimental setup available for this. The reply was that it would be in the examples on the website. I checked the examples for "electrophysiology tissue" and could not identify which one corresponds to the benchmark from the paper. Am I overlooking something?

Thank you for your reply.

[1] Niederer, S. A., Kerfoot, E., Benson, A. P., Bernabeu, M. O., Bernus, O., Bradley, C., Cherry, E. M., Clayton, R., Fenton, F. H., Garny, A., Heidenreich, E., Land, S., Maleckar, M., Pathmanathan, P., Plank, G., Rodríguez, J. F., Roy, I., Sachse, F. B., Seemann, G., … Smith, N. P. (2011). Verification of cardiac tissue electrophysiology simulators using an N-version benchmark. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 369(1954), 4331–4351. https://doi.org/10.1098/rsta.2011.0139

Answer 1

Hi Marie,

you are indeed right that we actually don't have the exact reconstruction of the Niederer paper as example on our webpage. I had in mind, that the first tissue example was based on that, but it is much simpler. First the sizes of the block are not matching and additionally, we do not have a reference solution to compare with. I will have a look at this example and will adjust it so that it will represent the Niederer paper.

Sorry for the confusion!

Comments

Dear Gunnar,

No problem. Thank you very much for having a look at it.

If you like, we can send you the data from the benchmark solved with our FD solver for comparison, as the data from the original paper is no longer available.

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Hi Marie,
in the meantime, we have a first version of the Niederer Benchmark. It is not yet documented well but this will follow later this year. You can find it under
https://opencarp.org/documentation/examples/02_ep_tissue/03e_study_resolution
This is also now included in the openCARP regression tests and you would find a reference solution in experiments/regression-references/monodomain.niederer_benchmark_run.
If you want to get the same results as in in the original paper, you have to turn on lumped mass matrix with --lump

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Dear Gunnar, thanks a lot!