Simple Bidomain Example

Module: devtests.bidomain.simple.run

Section author: Andrew Crozier <andrew.crozier@medunigraz.at>

This is a simple bidomain example that is primarily a demonstration of the carputils example and testing framework. In that vein, this documentation illustrates some of the features available when writing test documentation.

Please see the examples and tests sections of the carputils documentation for more information, in particular the subsection on Documenting Examples.

Problem Setup

This example defines a small cuboid on the domain:

-0.5  \leq x \leq 0.5

-0.25 \leq y \leq 0.25

-0.25 \leq z \leq 0.25

And applies an electrical stimulus on the x = -0.5 face. This is illustrated below:

../../_images/bidomain_simple_setup.png

Usage

This example specifies just one optional argument, --tend. Use it to specify how long to simulate for after stimulus, in milliseconds:

./run.py --tend 100

As with other examples, add the --visualize option to automatically load the results in meshalyzer:

./run.py --tend 100 --visualize

Tests

default

Generate short activation sequence on small cuboid and compare V_m against reference.

Tags: FAST SERIAL

Checks:

  • Compare against stored reference: max_error(vm.igb.gz)

Last run: 2021-09-27 00:30:13.910257, revision {‘base’: ‘778659c7’}, dependency revisions {PT_C: 31642c1e,eikonal: b58be0de,elasticity: e4d37cfa}

Runtime: 0:00:00.424660
ALL PASSED
  PASS max_error(vm.igb.gz): 7.62939453125e-06

long

Run longer activation sequence on small cuboid and compare V_m against reference.

Tags: SHORT SERIAL

Checks:

  • Compare against stored reference: max_error(vm.igb.gz)

Last run: 2021-09-27 00:30:14.367896, revision {‘base’: ‘778659c7’}, dependency revisions {PT_C: 31642c1e,eikonal: b58be0de,elasticity: e4d37cfa}

Runtime: 0:00:03.456554
ALL PASSED
  PASS max_error(vm.igb.gz): 3.0517578125e-05