TestBidomainWithBathAndFibresTutorial.hpp

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/*
 *
 *  Chaste tutorial - this page gets automatically changed to a wiki page
 *  DO NOT remove the comments below, and if the code has to be changed in
 *  order to run, please check the comments are still accurate
 *
 *
 */
#ifndef TESTBIDOMAINWITHBATHANDFIBRESTUTORIAL_HPP_
#define TESTBIDOMAINWITHBATHANDFIBRESTUTORIAL_HPP_
/*
 * ## Running a bidomain simulation with a bath and fibres
 *
 * In this tutorial we run a bidomain simulation with both a bath and fibres
 *
 * EMPTYLINE
 *
 * We include the same headers as in the previous fibre tutorial
 */
#include <cxxtest/TestSuite.h>
#include "BidomainProblem.hpp"
#include "LuoRudy1991BackwardEulerOpt.hpp"
#include "PetscSetupAndFinalize.hpp"
#include "PlaneStimulusCellFactory.hpp"

/* Define the test class as before
 */
class TestBidomainWithBathAndFibresTutorial : public CxxTest::TestSuite
{
public:
    void TestSimulation()
    {
        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<CellLuoRudy1991FromCellMLBackwardEulerOpt,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();
    }
};

#endif /*TESTBIDOMAINWITHBATHANDFIBRESTUTORIAL_HPP_*/