UserTutorials/BidomainWithBathAndFibres

This tutorial is automatically generated from the file trunk/heart/test/tutorials/TestBidomainWithBathAndFibresTutorial.hpp at revision r20767. Note that the code is given in full at the bottom of the page.

Running a bidomain simulation with a bath and fibres

In this tutorial we run a bidomain simulation with both a bath and fibres

We include the same headers as in the previous fibre tutorial 

#include <cxxtest/TestSuite.h>
#include "BidomainProblem.hpp"
#include "LuoRudy1991BackwardEuler.hpp"
#include "PetscSetupAndFinalize.hpp"
#include "PlaneStimulusCellFactory.hpp"

Define the test class as before 

class TestBidomainWithBathAndFibresTutorial : public CxxTest::TestSuite
{
public:
    void TestSimulation() throw(Exception)
    {
        HeartConfig::Instance()->SetSimulationDuration(5.0);  //ms
        HeartConfig::Instance()->SetOutputDirectory("BidomainTutorialWithBathAndFibres");
        HeartConfig::Instance()->SetOutputFilenamePrefix("results");

Bath problems seem to require decreased ODE timesteps. We use the Backward Euler version of the Luo-Rudy model (see below) instead to improve code performance. 

        HeartConfig::Instance()->SetOdeTimeStep(0.01);  //ms

Use the PlaneStimulusCellFactory to define a set of Luo-Rudy cells, in this case with a Backward Euler solver. We pass the stimulus magnitude as 0.0 as we don't want any stimulated cells. 

        PlaneStimulusCellFactory<CellLuoRudy1991FromCellMLBackwardEuler,2> cell_factory(0.0);

Note that in the previous bath example, a mesh was read in and elements where then set to be bath elements in the test. With fibres as well, in a bath simulation, it is better to read in a mesh that has all the information: this mesh has bath elements defined as an extra column in the .ele file, and a .ortho file which defines the fibre direction for each element. Note that the .ortho file should include fibre information for bath elements as well, but they won't be used in the simulation. (The fibres read here are the same 'kinked' fibres as in the previous fibre tutorial). 

        HeartConfig::Instance()->SetMeshFileName("mesh/test/data/2D_0_to_1mm_800_elements_bath_sides", cp::media_type::Orthotropic);

Set anistropic conductivities. 

        HeartConfig::Instance()->SetIntracellularConductivities(Create_c_vector(1.75, 0.175));
        HeartConfig::Instance()->SetExtracellularConductivities(Create_c_vector(7.0, 0.7));

and now we define the electrodes.. 

        double magnitude = -9.0e3; // uA/cm^2
        double start_time = 0.0;
        double duration = 2; //ms
        HeartConfig::Instance()->SetElectrodeParameters(false, 0, magnitude, start_time, duration);

Now create the problem class, using the cell factory and passing in true as the second argument to indicate we are solving a bath problem, and solve. 

        BidomainProblem<2> bidomain_problem( &cell_factory, true );
        bidomain_problem.Initialise();
        bidomain_problem.Solve();
    }
};

Code

The full code is given below

File name TestBidomainWithBathAndFibresTutorial.hpp

#include <cxxtest/TestSuite.h>
#include "BidomainProblem.hpp"
#include "LuoRudy1991BackwardEuler.hpp"
#include "PetscSetupAndFinalize.hpp"
#include "PlaneStimulusCellFactory.hpp"

class TestBidomainWithBathAndFibresTutorial : public CxxTest::TestSuite
{
public:
    void TestSimulation() throw(Exception)
    {
        HeartConfig::Instance()->SetSimulationDuration(5.0);  //ms
        HeartConfig::Instance()->SetOutputDirectory("BidomainTutorialWithBathAndFibres");
        HeartConfig::Instance()->SetOutputFilenamePrefix("results");

        HeartConfig::Instance()->SetOdeTimeStep(0.01);  //ms

        PlaneStimulusCellFactory<CellLuoRudy1991FromCellMLBackwardEuler,2> cell_factory(0.0);

        HeartConfig::Instance()->SetMeshFileName("mesh/test/data/2D_0_to_1mm_800_elements_bath_sides", cp::media_type::Orthotropic);

        HeartConfig::Instance()->SetIntracellularConductivities(Create_c_vector(1.75, 0.175));
        HeartConfig::Instance()->SetExtracellularConductivities(Create_c_vector(7.0, 0.7));

        double magnitude = -9.0e3; // uA/cm^2
        double start_time = 0.0;
        double duration = 2; //ms
        HeartConfig::Instance()->SetElectrodeParameters(false, 0, magnitude, start_time, duration);

        BidomainProblem<2> bidomain_problem( &cell_factory, true );
        bidomain_problem.Initialise();
        bidomain_problem.Solve();
    }
};