Chaste Parameters Writer CLP

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Two pacemaker leads positioned in the left ventricle

General Information

  • Type: CLP
  • Category: Simulation->Chaste
  • Author: Martin Steghöfer
  • Contributor: Xavi Planes
  • Contact: xavier.planes at upf.edu
  • Description: Writes Chaste parameters for simulation

Usage

Parameters

Label Type Flag / Index Default value / Channel Description
Leads
Leads point (coordinateSystem="lps" multiple="true") leads Lead point(s)
Delta double-vector delta 5.0 Delta
Strength double-vector strength -1200000.0 Strength
Duration double-vector duration 30.0 Duration
Delay double-vector delay 0.5 Delay
Parameters
Simulation Duration integer simulationDuration 500 Simulation Duration
Simulation Domain string simulationDomain Mono Simulation Domain
Simulation Ionic Models string simulationIonicModels Fox2002BackwardEuler Simulation Ionic Models
Simulation Mesh File string simulationMeshFile ChasteFile Simulation Mesh File
Intra Conduct Longi float intraConductLongi 3.4 Intra Conduct Longi
Intra Conduct Trans float intraConductTrans 0.6 Intra Conduct Trans
Intra Conduct Normal float intraConductNormal 0.6 Intra Conduct Normal
Extra Conduct Longi float extraConductLongi 6.25 Extra Conduct Longi
Extra Conduct Trans float extraConductTrans 2.36 Extra Conduct Trans
Extra Conduct Normal float extraConductNormal 2.36 Extra Conduct Normal
Num TimeStep Ode float numTimeStepOde 0.01 Num TimeStep Ode
Num TimeStep Pde float numTimeStepPde 0.1 Num TimeStep Pde
Num TimeStep Printing float numTimeStepPrinting 1.0 Num TimeStep Printing
IO
Leads file pointset (fileExtensions=".vtk") leadsFile input Leads file in VTK format
Parameters Reference File file index 0 input Input Parameters Reference File
Output Parameters File file index 1 output Output Parameters File


Examples

Two pacemaker leads have been selected on a left ventricle volumetric mesh. The output parameters have been written into a file.

Two pacemaker leads positioned in the left ventricle

Output file:

<?xml version="1.0" encoding="UTF-8" ?>
<ChasteParameters xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="ChasteParameters.xsd">
   <Simulation>
       <SimulationDuration unit="ms">500</SimulationDuration>
       <Domain>Mono</Domain>
       <IonicModels>
           <Default>Fox2002BackwardEuler</Default>
       </IonicModels>
       <Mesh unit="cm">
           <LoadMesh name="ChasteFile" conductivity_media="Axisymmetric" />
       </Mesh>
       <Stimuli>
           <Stimulus>
               <Strength unit="uA/cm^3">-1200000.000000</Strength>
               <Duration unit="ms">30.000000</Duration>
               <Delay unit="ms">0.500000</Delay>
               <Location unit="cm">
                   <Cuboid>
                       <LowerCoordinates x="15.392400" y="8.581270" z="12.013800" />
                       <UpperCoordinates x="16.392400" y="9.581270" z="13.013800" />
                   </Cuboid>
               </Location>
           </Stimulus>
           <Stimulus>
               <Strength unit="uA/cm^3">-1200000.000000</Strength>
               <Duration unit="ms">30.000000</Duration>
               <Delay unit="ms">0.500000</Delay>
               <Location unit="cm">
                   <Cuboid>
                       <LowerCoordinates x="12.426801" y="6.591050" z="10.964700" />
                       <UpperCoordinates x="13.426801" y="7.591050" z="11.964700" />
                   </Cuboid>
               </Location>
           </Stimulus>
       </Stimuli>
       <OutputDirectory>ChasteResults</OutputDirectory>
       <OutputFilenamePrefix>SimulationResults</OutputFilenamePrefix>
   </Simulation>
   <Physiological>
       <IntracellularConductivities longi="3.4" trans="0.6" normal="0.6" unit="mS/cm" />
       <ExtracellularConductivities longi="6.25" trans="2.36" normal="2.36" unit="mS/cm" />
       <SurfaceAreaToVolumeRatio unit="1/cm">1400</SurfaceAreaToVolumeRatio>
       <Capacitance unit="uF/cm^2">1.0</Capacitance>
   </Physiological>
   <Numerical>
       <TimeSteps ode="0.01" pde="0.1" printing="1" unit="ms" />
       <KSPTolerances>
           <KSPAbsolute>2e-4</KSPAbsolute>
       </KSPTolerances>
       <KSPSolver>gmres</KSPSolver>
       <KSPPreconditioner>jacobi</KSPPreconditioner>
   </Numerical>
</ChasteParameters>


Development

Source code: C++ Source code and XML description

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