Running Bidomain Simulations

This tutorial is automatically generated from TestRunningBidomainSimulationsTutorial.hpp at revision 140cb4550f47. Note that the code is given in full at the bottom of the page.

An example showing how to run bidomain simulations

Introduction

In this tutorial we show how Chaste is used to run a standard bidomain simulation. Note that monodomain simulations are run very similarly.

The first thing that needs to be done, when writing any Chaste test, is to include the following header.

#include <cxxtest/TestSuite.h>

The main class to be used for running bidomain simulations is BidomainProblem.

#include "BidomainProblem.hpp"

The type of intracellular stimulus we’ll apply.

#include "SimpleStimulus.hpp"

All tests which run cardiac simulations (which use Petsc) should include PetscSetupAndFinalize.hpp. This class ensures that PetscInitialise() is called with the appropriate arguments before any tests in the suite are run.

#include "PetscSetupAndFinalize.hpp"

The above files are contained in the source release and can be located and studied. Cardiac cell models are different: the C++ code is automatically generated from CellML files. To use a particular CellML file, place it in heart/src/odes/cellml (there are several in here already). If the CellML is called <CELLMODEL>.cellml, a file <CELLMODEL>.hpp will be automatically generated, which will define a class called Cell<CELLMODEL>FromCellML. So to use a particular cell model in a tissue simulation, given the CellML, you just have to do two things: include this .hpp file, and then use the class. For example, we will use the Luo-Rudy 1991 model, so we have to include the following, and later on use CellLuoRudy1991FromCellML as the cell model class. See CodeGenerationFromCellML for more information on this process.

#include "LuoRudy1991.hpp"

Defining a cell factory

All mono/bidomain simulations need a cell factory as input. This is a class which tells the problem class what type of cardiac cells to create. The cell-factory class has to inherit from AbstractCardiacCellFactory<DIM>, which means it must implement the method CreateCardiacCellForTissueNode(Node<DIM>*), which returns a pointer to an AbstractCardiacCell. Note, some concrete cell factories have been defined, such as the PlaneStimulusCellFactory (see later tutorials), which could be used in the simulation, but for completeness we create our own cell factory in this test. For complicated problems with, say, heterogeneous cell types or particular stimuli, a new cell factory will have to be defined by the user for their particular problem.

This cell factory is a simple cell factory where every cell is a Luo-Rudy 91 cell, and only the cell at position (0,0) is given a non-zero stimulus.

class PointStimulus2dCellFactory : public AbstractCardiacCellFactory<2>
{

Declare (smart) pointer to a SimpleStimulus for the cell which is stimulated. Note that AbstractCardiacCellFactory also has as protected members: mpZeroStimulus of type boost::shared_ptr<ZeroStimulus>; mpMesh, a pointer to the mesh used (the problem class will set this before it calls CreateCardiacCellForTissueNode, so it can be used in that method); mTimestep, a double (see below); and boost::shared_ptr<mpSolver> a forward euler ode solver (see below).

private:
    boost::shared_ptr<SimpleStimulus> mpStimulus;

public:

Our contructor takes in nothing. It calls the constructor of AbstractCardiacCellFactory and we also initialise the stimulus to have magnitude -500000 uA/cm^3 and duration 0.5 ms.

    PointStimulus2dCellFactory()
            : AbstractCardiacCellFactory<2>(),
              mpStimulus(new SimpleStimulus(-5e5, 0.5))
    {
    }

Now we implement the pure method which needs to be implemented. We return a LR91 cell for each node, with the nodes in a 0.2mm block given the non-zero stimulus, and all other nodes given the zero stimulus. Note that we use mpMesh, mTimestep, mpZeroStimulus and mpSolver which are all members of the base class. The timestep and solver are defined in the base class just so that the user doesn’t have to create them here.

    AbstractCardiacCell* CreateCardiacCellForTissueNode(Node<2>* pNode)
    {
        double x = pNode->rGetLocation()[0];
        double y = pNode->rGetLocation()[1];
        if (x < 0.02 + 1e-6 && y < 0.02 + 1e-6) // ie if x<=0.02 and y<=0.02 (and we are assuming here x,y>=0).
        {

Create a LR91 cell with the non-zero stimulus. This is a volume stimulus, ie the function on the right-hand side of the first of the two bidomain equations. An equal and opposite extra-cellular stimulus is implicitly enforced by the code, which corresponds to having zero on the right-hand side of the second of the bidomain equations.

            return new CellLuoRudy1991FromCellML(mpSolver, mpStimulus);
        }
        else
        {

The other cells have zero stimuli.

            return new CellLuoRudy1991FromCellML(mpSolver, mpZeroStimulus);
        }
    }

We have no need for a destructor, since the problem class deals with deleting the cells.

};

Running the bidomain simulation

Now we can define the test class, which must inherit from CxxTest::TestSuite as described in the writing basic tests tutorial.

class TestRunningBidomainSimulationsTutorial : public CxxTest::TestSuite
{

Tests should be public…

public:

Define the test.

    void TestSimpleSimulation()
    {

The HeartConfig class is used to set various parameters (see the main ChasteGuides page for information on default parameter values. Parameters in this file can be re-set with HeartConfig if the user wishes, and other parameters such as end time must be set using HeartConfig. Let us begin by setting the end time (in ms), the mesh to use, and the output directory and filename-prefix. Note that the spatial units in cardiac Chaste is CENTIMETRES, so that mesh 2D_0_to_1mm_800_elements is a mesh over [0,0.1]x[0,0.1].

        HeartConfig::Instance()->SetSimulationDuration(5.0); // ms
        HeartConfig::Instance()->SetMeshFileName("mesh/test/data/2D_0_to_1mm_800_elements");
        HeartConfig::Instance()->SetOutputDirectory("BidomainTutorial");
        HeartConfig::Instance()->SetOutputFilenamePrefix("results");

There is an alternate method of loading a mesh that can be seen in Monodomain 3d Example, using DistributedTetrahedralMesh.

It is possible to over-ride the default visualisation output (which is done during simulation post-processing).

        HeartConfig::Instance()->SetVisualizeWithMeshalyzer(true);
        HeartConfig::Instance()->SetVisualizeWithCmgui(true);
        HeartConfig::Instance()->SetVisualizeWithVtk(true);

If the mesh is a DistributedTetrahedralMesh then we can use parallel VTK files (.pvtu)

        // HeartConfig::Instance()->SetVisualizeWithParallelVtk(true);

Next, we have to create a cell factory of the type we defined above.

        PointStimulus2dCellFactory cell_factory;

Now we create a problem class using (a pointer to) the cell factory.

        BidomainProblem<2> bidomain_problem(&cell_factory);

This is enough setup to run a simulation: we could now call Initialise() and Solve() to run…

        // bidomain_problem.Initialise();
        // bidomain_problem.Solve();

..however, instead we show how to set a few more parameters. To set the conductivity values in the principal fibre, sheet and normal directions do the following. Note that Create_c_vector is just a helper method for creating a c_vector<double,DIM> of the correct size (2, in this case). Make sure these methods are called before Initialise().

        HeartConfig::Instance()->SetIntracellularConductivities(Create_c_vector(1.75, 0.19));
        HeartConfig::Instance()->SetExtracellularConductivities(Create_c_vector(6.2, 2.4));

This is how to reset the surface-area-to-volume ratio and the capacitance. (Here, we are actually just resetting them to their default values).

        HeartConfig::Instance()->SetSurfaceAreaToVolumeRatio(1400); // 1/cm
        HeartConfig::Instance()->SetCapacitance(1.0); // uF/cm^2

This is how to set the ode timestep (the timestep used to solve the cell models) the pde timestep (the timestep used in solving the bidomain PDE), and the printing timestep (how often the output is written to file). The defaults are all 0.01, here we increase the printing timestep.

        HeartConfig::Instance()->SetOdePdeAndPrintingTimeSteps(0.01, 0.01, 0.1);

Now we call Initialise()…

        bidomain_problem.Initialise();

Now we call Solve() to run the simulation. The output will be written to /tmp/$USER/testoutput/BidomainTutorial in HDF5 format. The output will also be converted to selected visualiser formats at the end of the simulation. Note that if you want to view the progress of longer simulations go to the the output directory and look at the file progress_status.txt, which will say the percentage of the simulation run.

        bidomain_problem.Solve();

Examining the output

In order to visualise the results, go to one of the sub-folders

/tmp/$USER/testoutput/BidomainTutorial/output for Meshalyzer
/tmp/$USER/testoutput/BidomainTutorial/cmgui_output for Cmgui
/tmp/$USER/testoutput/BidomainTutorial/vtk_output for Paraview (VTK) where you should find the geometric mesh data and simulation output.

Please see ChasteGuides/VisualisationGuides for details of using Meshalyzer/Cmgui/Paraview.

Note: the easiest way to look at the resultant voltage values from the code (for the last timestep - the data for the previous timesteps is written to file but not retained) is to use a ReplicatableVector. bidomain_problem.GetSolution()) returns a PETSc vector of the form (V_0, phi_0, V_1, phi_e_1, … V_n, phi_e_n), and we can create a ReplicatableVector for easy access to this PETSc vector’s data. (This won’t be very efficient with huge problems in parallel - the next tutorial will mention how to do parallel access).

        ReplicatableVector res_repl(bidomain_problem.GetSolution());
        for (unsigned i = 0; i < res_repl.GetSize(); i++)
        {
            //    std::cout << res_repl[i] << "\n";
        }

Behind the scenes there are some logging routines which find out how much time has been spent in the major parts of the code (solving ODEs, assembling matrices etc.) The logging routines are in HeartEventHandler which is enabled by default. If you think this is getting in the way, you can turn it off at the top of your test with HeartEventHandler::Disable(). In this test, we want to get information out of the HeartEventHandler.

Headings() prints a single (very long) line reminding us what catagories of events are being instrumented.

        HeartEventHandler::Headings();

Report() prints a single line with times spent in each catagory. When run in parallel it prints one line of times per process and also lines for average and maximum times. (This can be useful if you need to identify a load imbalance.)

        HeartEventHandler::Report();
    }
};

Full code

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

#include "LuoRudy1991.hpp"

class PointStimulus2dCellFactory : public AbstractCardiacCellFactory<2>
{
private:
    boost::shared_ptr<SimpleStimulus> mpStimulus;

public:
    PointStimulus2dCellFactory()
            : AbstractCardiacCellFactory<2>(),
              mpStimulus(new SimpleStimulus(-5e5, 0.5))
    {
    }

    AbstractCardiacCell* CreateCardiacCellForTissueNode(Node<2>* pNode)
    {
        double x = pNode->rGetLocation()[0];
        double y = pNode->rGetLocation()[1];
        if (x < 0.02 + 1e-6 && y < 0.02 + 1e-6) // ie if x<=0.02 and y<=0.02 (and we are assuming here x,y>=0).
        {
            return new CellLuoRudy1991FromCellML(mpSolver, mpStimulus);
        }
        else
        {
            return new CellLuoRudy1991FromCellML(mpSolver, mpZeroStimulus);
        }
    }

};

class TestRunningBidomainSimulationsTutorial : public CxxTest::TestSuite
{
public:
    void TestSimpleSimulation()
    {
        HeartConfig::Instance()->SetSimulationDuration(5.0); // ms
        HeartConfig::Instance()->SetMeshFileName("mesh/test/data/2D_0_to_1mm_800_elements");
        HeartConfig::Instance()->SetOutputDirectory("BidomainTutorial");
        HeartConfig::Instance()->SetOutputFilenamePrefix("results");

        HeartConfig::Instance()->SetVisualizeWithMeshalyzer(true);
        HeartConfig::Instance()->SetVisualizeWithCmgui(true);
        HeartConfig::Instance()->SetVisualizeWithVtk(true);
        // HeartConfig::Instance()->SetVisualizeWithParallelVtk(true);

        PointStimulus2dCellFactory cell_factory;

        BidomainProblem<2> bidomain_problem(&cell_factory);

        // bidomain_problem.Initialise();
        // bidomain_problem.Solve();

        HeartConfig::Instance()->SetIntracellularConductivities(Create_c_vector(1.75, 0.19));
        HeartConfig::Instance()->SetExtracellularConductivities(Create_c_vector(6.2, 2.4));

        HeartConfig::Instance()->SetSurfaceAreaToVolumeRatio(1400); // 1/cm
        HeartConfig::Instance()->SetCapacitance(1.0); // uF/cm^2

        HeartConfig::Instance()->SetOdePdeAndPrintingTimeSteps(0.01, 0.01, 0.1);

        bidomain_problem.Initialise();

        bidomain_problem.Solve();

        ReplicatableVector res_repl(bidomain_problem.GetSolution());
        for (unsigned i = 0; i < res_repl.GetSize(); i++)
        {
            //    std::cout << res_repl[i] << "\n";
        }

        HeartEventHandler::Headings();
        HeartEventHandler::Report();
    }
};

Running a simulation with multiple-channel drug action

Running Binaries From Command Line

Running Bidomain Simulations

An example showing how to run bidomain simulations#

Introduction#

Defining a cell factory#

Running the bidomain simulation#

Examining the output#

Full code#