Using the cardiac executable

This page provides examples of how to use the Chaste cardiac executable.

Building the cardiac executable#

Please see Building Executable Apps for instructions on how to compile the cardiac executable, called simply Chaste.

Running the executable#

If you have built the executable yourself from source on the same machine, then your paths will (probably) be set up already, and you can simply run

./apps/src/Chaste <PATH TO CONFIG FILE>/ChasteParameters.xml

Then to run this in parallel you should use mpirun (or perhaps mpiexec) associated with the mpi/PETSc you used to compile Chaste:

mpirun -np N ./apps/src/Chaste <PATH TO CONFIG FILE>/ChasteParameters.xml

where N is the number of processes to run with.

Visualization#

In all of these examples, you can change to use the visualizer that you want by setting one of these options (meshalyzer, vtk or cmgui) in the <Simulation> block:

<OutputVisualizer meshalyzer="yes" vtk="yes" cmgui="yes" precision="8"/>

vtk (visualized using paraview) seems to be the most well supported and likely to still work if you are reading this in a few years, if not the simplest to use!

Basic simulations#

• UserTutorials/CardiacExecutable/Propagation1d – simple simulation on a 1d fibre
• UserTutorials/CardiacExecutable/S1S2Protocol – 2d spiral wave simulation produced by two stimuli
• UserTutorials/CardiacExecutable/Propagation3d– propagation on a anatomically realistic down-sampled ventricular mesh using fibre directions. This tutorial also discusses visualising the results in different tools.

Examples of further functionality#

• How to determine what the hardcoded cell model options are
  • See below for dynamic loading of CellML files
• UserTutorials/CardiacExecutable/HeterogeneousExample
• UserTutorials/CardiacExecutable/UsingFibreDefinitions – also mentions postprocessing options
• UserTutorials/CardiacExecutable/BidomainSimulationsWithPerfusingBath
• UserTutorials/CardiacExecutable/CheckpointingAndRestarting – how to do checkpoint and restart.

Further examples using dynamic loading of CellML files#

See CodeGenerationFromCellML for more details and options for annotations within CellML files.

• UserTutorials/CardiacExecutable/UsingCellmlFiles – this shows how to use cell models defined directly from a cellml file (not one of the hardcoded options), and how to output cell model variables
• UserTutorials/CardiacExecutable/DrugAction Running a simulation with multiple-channel drug action

Utilities#

• UserTutorials/CardiacExecutable/MeshConvert – making the MeshConvert utility and using it to help produce scalable mesh loading