UserTutorials/CardiacExecutable/DownloadableSimulations

Example simulations available from the Chaste website

The downloads section of the public Chaste website contains the files required for three simulations in the tarball simulations.tgz. Download and unpack, which will result in the following folders being created:

simulations/propagation1d
simulations/propagation3dparallel
simulations/s1s2protocol

Also, if you haven't done so already, download meshalyzer from the downloads page and unpack.

Running a simple example: propagation in a tissue fibre

Running the simulation

Change directory to simulations/propagation1d

cd simulations/propagation1d

In this folder you will find the following files:

ChasteParameters.xml -- this file describes the simulation, and can be used to override the default parameter values (in releases of the executable up to and including version 2.0, the default parameters were read in from another xml file, ChasteDefaults.xml).
ChasteParameters_2_1.xsd -- XML schema for input validation (in general never has to be altered or touched).

Run the simulation by doing

<path_to_chaste>/Chaste.sh ChasteParameters.xml

Note: in releases up to and including version 2.0, the executable would be called directly (ie: <path_to_chaste>/Chaste ChasteParameters.xml), in release 2.1 the executable should be called via the shell script Chaste.sh; as above.

A folder called testoutput will appear once the simulation has finished.

Visualising the results

Move into the newly created output folder

cd testoutput/ChasteResults

In this folder you will find the following files and folders:

progress_status.txt -- this file can be viewed whilst the simulation is running to gauge how long it will take
SimulationResults.h5 -- the output of the simulation, in HDF5 format
output (folder) -- contains the output converted into meshalyzer format

Move now into the Meshalyzer-compatible output folder

cd output

Launch Meshalyzer with

<path_to_meshalyzer>/meshalyzer SimulationResults_mesh

and visualise the results by loading the SimulationResults_V.dat file.

Understanding the XML parameters file

Open ChasteParameters.xml (it is sensible to do this in a web-browser or XML editor in order to get syntax highlighting). The file should be reasonably readable; it defines:

a 1D simulation that lasts for 500ms
the use of the monodomain model
- to use bidomain, the only thing that needs to be done is to change Mono to Bi
a Luo-Rudy cell model as the default cell model
a 1D autogenerated mesh of length 4cm
a stimulated region in the first 0.2cm (stimulus is applied every 100ms)
- note: in the Cuboid definition, y and z coordinates are ignored in 1D simulations
output directory and filenames
physiological parameters: conductivities, capacitance, surface-area-to-volume ratio
- in monodomain problems, the defined intracellular conductivity is used not a harmonic mean. The extracellular conductivity is therefore ignored, as are the components in the transverse (sheet) and normal directions since this is a 1D simulation.
Numerical parameters including timesteps and KSP (linear solver) options

Running a 2D tissue simulation instead

Now we are going to change our geometry description to create a tissue sheet instead of a fibre.

Go to ChasteParameters.xml and find the following section:

<Mesh unit="cm">
        <Fibre x="4.0" inter_node_space="0.01"/>    
</Mesh>

We can change the geometry to be a tissue sheet:

<Mesh unit="cm">
        <Sheet x="2.0" y="2.0" inter_node_space="0.03"/>    
</Mesh>

In addition, the following parameters need to be modified:

<SpaceDimension>2</SpaceDimension>
<SimulationDuration unit="ms">30.0</SimulationDuration>

Rerun the simulation and follow the previous section to visualise the results.

Further examples

3D on a realistic cardiac geometry

The files in

simulations/propagation3dparallel

define a simulation on a 3D geometry, which can be run identically to above, or in parallel by doing (with 4 processes, say):

<path_to_chaste>/Chaste.sh -np 4 ChasteParameters.xml

Open the parameters XML file. The main difference in this file is that it defines a mesh to be loaded, rather than autogenerated, in this case with prefix heart_chaste2_renum_i_triangles. The executable will look for files heart_chaste2_renum_i_triangles.node, .ele and .face (or .edge in 2D). See the FileFormats.html page supplied with the executable for more information on file formats.

Also note that in this simulation no fibre directions are provided (conductivity_media="NoFibreOrientation"), hence the isotropic conductivities defined later on.

S1-S2 protocol on a sheet

The other simulation

simulations/s1s2protocol

defines a simulation in 2D in which two stimuli are defined, one at t=0ms on one edge to start regular electrical activity, and a second at t=255ms in a rectangular region which causes a re-entrant wave to occur.