Running a simple example: propagation in a tissue fibre

Getting the data

Download and save the attached file Propagation1d.tgz. Either use an Archive Manager to extract the content to disk or save it and then unpack it with

tar xvfz  Propagation1d.tgz

Running the simulation

Change directory to Propagation1d

cd 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
• 1dResults.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 1dResults_mesh

and visualise the results by loading the 1dResults_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.