Using fibre directions and postprocessing

Fibres#

Fibres directions must currently be read from a file. Hence simulations with fibres can only be done for meshes that are read in, not auto-generated. Altering the XML parameters file to tell the executable to read fibres is trivial: instead of doing

<Mesh unit="cm">
    <LoadMesh name="sheet_800_elements"/>
</Mesh>

do

<Mesh unit="cm">
    <LoadMesh name="sheet_800_elements" conductivity_media="Orthotropic"/>
</Mesh>

The options for the last parameters are “NoFibreOrientation”, “Axisymmetric” or “Orthotropic”. If “Axisymmetric”, the file sheet_800_elements.axi will also be read, if “Orthotropic”, sheet_800_elements.ortho will be read. See the file formats documentation for full descriptions of these formats, but basically .axi files provide the fibre direction for each element in the mesh, and .ortho files provide the fibre, sheet (and normal in 3D) directions for each element in the mesh.

In the example attached to this page, fibres have been defined for each element in the constant (1,1) direction.

Postprocessing#

Various postprocessing options are available. The following for example computes the conduction velocity between node 200 and all the other nodes in the mesh, writing the results to the file <output_directory>/output/ConductionVelocityFromNode200.dat.

<PostProcessing>
    <ConductionVelocityMap origin_node="200"/>
</PostProcessing>

As well as conduction velocity, it is also possible to obtain APD at a prescribed repolarisation percent, activation times and upstroke velocities. See the “full format” example parameters file for usage.