AbstractCardiacProblem.cpp

/*
 
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*/
#include "AbstractCardiacProblem.hpp"
 
#include "DistributedVector.hpp"
#include "Exception.hpp"
#include "GenericMeshReader.hpp"
#include "Hdf5ToCmguiConverter.hpp"
#include "Hdf5ToMeshalyzerConverter.hpp"
#include "Hdf5ToVtkConverter.hpp"
#include "HeartConfig.hpp"
#include "HeartEventHandler.hpp"
#include "LinearSystem.hpp"
#include "PetscTools.hpp"
#include "PostProcessingWriter.hpp"
#include "ProgressReporter.hpp"
#include "TimeStepper.hpp"
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::AbstractCardiacProblem(
    AbstractCardiacCellFactory<ELEMENT_DIM, SPACE_DIM>* pCellFactory)
        : mMeshFilename(""), // i.e. undefined
          mAllocatedMemoryForMesh(false),
          mWriteInfo(false),
          mPrintOutput(true),
          mpCardiacTissue(NULL),
          mpSolver(NULL),
          mpCellFactory(pCellFactory),
          mpMesh(NULL),
          mSolution(NULL),
          mCurrentTime(0.0),
          mpTimeAdaptivityController(NULL),
          mpWriter(NULL),
          mUseHdf5DataWriterCache(false),
          mHdf5DataWriterChunkSizeAndAlignment(0)
{
    assert(mNodesToOutput.empty());
    if (!mpCellFactory)
    {
        EXCEPTION("AbstractCardiacProblem: Please supply a cell factory pointer to your cardiac problem constructor.");
    }
    HeartEventHandler::BeginEvent(HeartEventHandler::EVERYTHING);
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::AbstractCardiacProblem()
        // It doesn't really matter what we initialise these to, as they'll be overwritten by
        // the serialization methods
        : mMeshFilename(""),
          mAllocatedMemoryForMesh(false), // Handled by AbstractCardiacTissue
          mWriteInfo(false),
          mPrintOutput(true),
          mVoltageColumnId(UINT_MAX),
          mTimeColumnId(UINT_MAX),
          mNodeColumnId(UINT_MAX),
          mpCardiacTissue(NULL),
          mpSolver(NULL),
          mpCellFactory(NULL),
          mpMesh(NULL),
          mSolution(NULL),
          mCurrentTime(0.0),
          mpTimeAdaptivityController(NULL),
          mpWriter(NULL),
          mUseHdf5DataWriterCache(false),
          mHdf5DataWriterChunkSizeAndAlignment(0)
{
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::~AbstractCardiacProblem()
{
    delete mpCardiacTissue;
    if (mSolution)
    {
        PetscTools::Destroy(mSolution);
    }
 
    if (mAllocatedMemoryForMesh)
    {
        delete mpMesh;
    }
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::Initialise()
{
    HeartEventHandler::BeginEvent(HeartEventHandler::READ_MESH);
    if (mpMesh)
    {
        if (PetscTools::IsParallel() && !dynamic_cast<DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>*>(mpMesh))
        {
            WARNING("Using a non-distributed mesh in a parallel simulation is not a good idea.");
        }
    }
    else
    {
        // If no mesh has been passed, we get it from the configuration file
        try
        {
            if (HeartConfig::Instance()->GetLoadMesh())
            {
                CreateMeshFromHeartConfig();
                auto p_mesh_reader = GenericMeshReader<ELEMENT_DIM, SPACE_DIM>(HeartConfig::Instance()->GetMeshName());
                mpMesh->ConstructFromMeshReader(*p_mesh_reader);
            }
            else if (HeartConfig::Instance()->GetCreateMesh())
            {
                CreateMeshFromHeartConfig();
                assert(HeartConfig::Instance()->GetSpaceDimension() == SPACE_DIM);
                double inter_node_space = HeartConfig::Instance()->GetInterNodeSpace();
 
                switch (HeartConfig::Instance()->GetSpaceDimension())
                {
                    case 1:
                    {
                        c_vector<double, 1> fibre_length;
                        HeartConfig::Instance()->GetFibreLength(fibre_length);
                        mpMesh->ConstructRegularSlabMesh(inter_node_space, fibre_length[0]);
                        break;
                    }
                    case 2:
                    {
                        c_vector<double, 2> sheet_dimensions; //cm
                        HeartConfig::Instance()->GetSheetDimensions(sheet_dimensions);
                        mpMesh->ConstructRegularSlabMesh(inter_node_space, sheet_dimensions[0], sheet_dimensions[1]);
                        break;
                    }
                    case 3:
                    {
                        c_vector<double, 3> slab_dimensions; //cm
                        HeartConfig::Instance()->GetSlabDimensions(slab_dimensions);
                        mpMesh->ConstructRegularSlabMesh(inter_node_space, slab_dimensions[0], slab_dimensions[1], slab_dimensions[2]);
                        break;
                    }
                    default:
                        NEVER_REACHED;
                }
            }
            else
            {
                NEVER_REACHED;
            }
 
            mAllocatedMemoryForMesh = true;
        }
        catch (Exception& e)
        {
            EXCEPTION(std::string("No mesh given: define it in XML parameters file or call SetMesh()\n") + e.GetShortMessage());
        }
    }
    mpCellFactory->SetMesh(mpMesh);
    HeartEventHandler::EndEvent(HeartEventHandler::READ_MESH);
 
    HeartEventHandler::BeginEvent(HeartEventHandler::INITIALISE);
 
    // If the user requested transmural stuff, we fill in the mCellHeterogeneityAreas here
    if (HeartConfig::Instance()->AreCellularTransmuralHeterogeneitiesRequested())
    {
        mpCellFactory->FillInCellularTransmuralAreas();
    }
 
    delete mpCardiacTissue; // In case we're called twice
    mpCardiacTissue = CreateCardiacTissue();
 
    HeartEventHandler::EndEvent(HeartEventHandler::INITIALISE);
 
    // Delete any previous solution, so we get a fresh initial condition
    if (mSolution)
    {
        HeartEventHandler::BeginEvent(HeartEventHandler::COMMUNICATION);
        PetscTools::Destroy(mSolution);
        mSolution = NULL;
        HeartEventHandler::EndEvent(HeartEventHandler::COMMUNICATION);
    }
 
    // Always start at time zero
    mCurrentTime = 0.0;
 
    // For Bidomain with bath, this is where we set up the electrodes
    SetElectrodes();
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::CreateMeshFromHeartConfig()
{
    mpMesh = new DistributedTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>(HeartConfig::Instance()->GetMeshPartitioning());
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::SetBoundaryConditionsContainer(boost::shared_ptr<BoundaryConditionsContainer<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM> > pBcc)
{
    this->mpBoundaryConditionsContainer = pBcc;
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::PreSolveChecks()
{
    if (mpCardiacTissue == NULL) // if tissue is NULL, Initialise() probably hasn't been called
    {
        EXCEPTION("Cardiac tissue is null, Initialise() probably hasn't been called");
    }
    if (HeartConfig::Instance()->GetSimulationDuration() <= mCurrentTime)
    {
        EXCEPTION("End time should be in the future");
    }
    if (mPrintOutput)
    {
        if ((HeartConfig::Instance()->GetOutputDirectory() == "") || (HeartConfig::Instance()->GetOutputFilenamePrefix() == ""))
        {
            EXCEPTION("Either explicitly specify not to print output (call PrintOutput(false)) or specify the output directory and filename prefix");
        }
    }
 
    double end_time = HeartConfig::Instance()->GetSimulationDuration();
    double pde_time = HeartConfig::Instance()->GetPdeTimeStep();
 
    /*
     * MatrixIsConstant stuff requires CONSTANT dt - do some checks to make sure
     * the TimeStepper won't find non-constant dt.
     * Note: printing_time does not have to divide end_time, but dt must divide
     * printing_time and end_time.
     * HeartConfig checks pde_dt divides printing dt.
     */
    if (fabs(end_time - pde_time * round(end_time / pde_time)) > 1e-10)
    {
        EXCEPTION("PDE timestep does not seem to divide end time - check parameters");
    }
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
Vec AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::CreateInitialCondition()
{
    DistributedVectorFactory* p_factory = mpMesh->GetDistributedVectorFactory();
    Vec initial_condition = p_factory->CreateVec(PROBLEM_DIM);
    DistributedVector ic = p_factory->CreateDistributedVector(initial_condition);
    std::vector<DistributedVector::Stripe> stripe;
    stripe.reserve(PROBLEM_DIM);
 
    for (unsigned i = 0; i < PROBLEM_DIM; i++)
    {
        stripe.push_back(DistributedVector::Stripe(ic, i));
    }
 
    for (DistributedVector::Iterator index = ic.Begin();
         index != ic.End();
         ++index)
    {
        stripe[0][index] = mpCardiacTissue->GetCardiacCell(index.Global)->GetVoltage();
        if (PROBLEM_DIM == 2)
        {
            stripe[1][index] = 0;
        }
    }
 
    ic.Restore();
 
    return initial_condition;
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::SetMesh(AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>* pMesh)
{
    /*
     * If this fails the mesh has already been set. We assert rather throw
     * an exception to avoid a memory leak when checking it throws correctly.
     */
    assert(mpMesh == NULL);
    assert(pMesh != NULL);
    mAllocatedMemoryForMesh = false;
    mpMesh = pMesh;
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::PrintOutput(bool printOutput)
{
    mPrintOutput = printOutput;
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::SetWriteInfo(bool writeInfo)
{
    mWriteInfo = writeInfo;
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
Vec AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::GetSolution()
{
    return mSolution;
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
DistributedVector AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::GetSolutionDistributedVector()
{
    return mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(mSolution);
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
double AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::GetCurrentTime()
{
    return mCurrentTime;
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>& AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::rGetMesh()
{
    assert(mpMesh);
    return *mpMesh;
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
AbstractCardiacTissue<ELEMENT_DIM, SPACE_DIM>* AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::GetTissue()
{
    if (mpCardiacTissue == NULL)
    {
        EXCEPTION("Tissue not yet set up, you may need to call Initialise() before GetTissue().");
    }
    return mpCardiacTissue;
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::SetUseTimeAdaptivityController(
    bool useAdaptivity,
    AbstractTimeAdaptivityController* pController)
{
    if (useAdaptivity)
    {
        assert(pController);
        mpTimeAdaptivityController = pController;
    }
    else
    {
        mpTimeAdaptivityController = NULL;
    }
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::Solve()
{
    PreSolveChecks();
 
    std::vector<double> additional_stopping_times;
    SetUpAdditionalStoppingTimes(additional_stopping_times);
 
    TimeStepper stepper(mCurrentTime,
                        HeartConfig::Instance()->GetSimulationDuration(),
                        HeartConfig::Instance()->GetPrintingTimeStep(),
                        false,
                        additional_stopping_times);
    // Note that SetUpAdditionalStoppingTimes is a method from the BidomainWithBath class it adds
    // electrode events into the regular time-stepping
    //    EXCEPTION("Electrode switch on/off events should coincide with printing time steps.");
 
    if (!mpBoundaryConditionsContainer) // the user didn't supply a bcc
    {
        // Set up the default bcc
        mpDefaultBoundaryConditionsContainer.reset(new BoundaryConditionsContainer<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>);
        for (unsigned problem_index = 0; problem_index < PROBLEM_DIM; problem_index++)
        {
            mpDefaultBoundaryConditionsContainer->DefineZeroNeumannOnMeshBoundary(mpMesh, problem_index);
        }
        mpBoundaryConditionsContainer = mpDefaultBoundaryConditionsContainer;
    }
 
    assert(mpSolver == NULL);
    mpSolver = CreateSolver(); // passes mpBoundaryConditionsContainer to solver
 
    // If we have already run a simulation, use the old solution as initial condition
    Vec initial_condition;
    if (mSolution)
    {
        initial_condition = mSolution;
    }
    else
    {
        initial_condition = CreateInitialCondition();
    }
 
    std::string progress_reporter_dir;
 
    if (mPrintOutput)
    {
        HeartEventHandler::BeginEvent(HeartEventHandler::WRITE_OUTPUT);
        bool extending_file = false;
        try
        {
            extending_file = InitialiseWriter();
        }
        catch (Exception& e)
        {
            delete mpWriter;
            mpWriter = NULL;
            delete mpSolver;
            if (mSolution != initial_condition)
            {
                /*
                 * A PETSc Vec is a pointer, so we *don't* need to free the memory if it is
                 * freed somewhere else (e.g. in the destructor). If this is a resumed solution
                 * we set initial_condition = mSolution earlier. mSolution is going to be
                 * cleaned up in the constructor. So, only PetscTools::Destroy( initial_condition ) when
                 * it is not equal to mSolution.
                 */
                PetscTools::Destroy(initial_condition);
            }
            throw e;
        }
 
        /*
         * If we are resuming a simulation (i.e. mSolution already exists) and
         * we are extending a .h5 file that already exists then there is no need
         * to write the initial condition to file - it is already there as the
         * final solution of the previous run.
         */
        if (!(mSolution && extending_file))
        {
            WriteOneStep(stepper.GetTime(), initial_condition);
            mpWriter->AdvanceAlongUnlimitedDimension();
        }
        HeartEventHandler::EndEvent(HeartEventHandler::WRITE_OUTPUT);
 
        progress_reporter_dir = HeartConfig::Instance()->GetOutputDirectory();
    }
    else
    {
        progress_reporter_dir = ""; // progress printed to CHASTE_TEST_OUTPUT
    }
    for (boost::shared_ptr<AbstractOutputModifier> p_output_modifier : mOutputModifiers)
    {
        p_output_modifier->InitialiseAtStart(this->mpMesh->GetDistributedVectorFactory(), this->mpMesh->rGetNodePermutation());
        p_output_modifier->ProcessSolutionAtTimeStep(stepper.GetTime(), initial_condition, PROBLEM_DIM);
    }
 
    /*
     * Create a progress reporter so users can track how much has gone and
     * estimate how much time is left. Note this has to be done after the
     * InitialiseWriter above (if mPrintOutput==true).
     */
    ProgressReporter progress_reporter(progress_reporter_dir,
                                       mCurrentTime,
                                       HeartConfig::Instance()->GetSimulationDuration());
    progress_reporter.Update(mCurrentTime);
 
    mpSolver->SetTimeStep(HeartConfig::Instance()->GetPdeTimeStep());
    if (mpTimeAdaptivityController)
    {
        mpSolver->SetTimeAdaptivityController(mpTimeAdaptivityController);
    }
 
    while (!stepper.IsTimeAtEnd())
    {
        // Solve from now up to the next printing time
        mpSolver->SetTimes(stepper.GetTime(), stepper.GetNextTime());
        mpSolver->SetInitialCondition(initial_condition);
 
        AtBeginningOfTimestep(stepper.GetTime());
 
        try
        {
            try
            {
                mSolution = mpSolver->Solve();
            }
            catch (const Exception& e)
            {
#ifndef NDEBUG
                PetscTools::ReplicateException(true);
#endif
                throw e;
            }
#ifndef NDEBUG
            PetscTools::ReplicateException(false);
#endif
        }
        catch (const Exception& e)
        {
            // Free memory
            delete mpSolver;
            mpSolver = NULL;
            if (initial_condition != mSolution)
            {
                /*
                 * A PETSc Vec is a pointer, so we *don't* need to free the memory if it is
                 * freed somewhere else (e.g. in the destructor). Later, in this while loop
                 * we will set initial_condition = mSolution (or, if this is a resumed solution
                 * it may also have been done when initial_condition was created). mSolution
                 * is going to be cleaned up in the destructor. So, only PetscTools::Destroy()
                 * initial_condition when it is not equal to mSolution (see #1695).
                 */
                PetscTools::Destroy(initial_condition);
            }
 
            // Re-throw
            HeartEventHandler::Reset();
            CloseFilesAndPostProcess();
 
            throw e;
        }
 
        // Free old initial condition
        HeartEventHandler::BeginEvent(HeartEventHandler::COMMUNICATION);
        PetscTools::Destroy(initial_condition);
        HeartEventHandler::EndEvent(HeartEventHandler::COMMUNICATION);
 
        // Initial condition for next loop is current solution
        initial_condition = mSolution;
 
        // Update the current time
        stepper.AdvanceOneTimeStep();
        mCurrentTime = stepper.GetTime();
 
        // Print out details at current time if asked for
        if (mWriteInfo)
        {
            HeartEventHandler::BeginEvent(HeartEventHandler::WRITE_OUTPUT);
            WriteInfo(stepper.GetTime());
            HeartEventHandler::EndEvent(HeartEventHandler::WRITE_OUTPUT);
        }
 
        for (boost::shared_ptr<AbstractOutputModifier> p_output_modifier : mOutputModifiers)
        {
            p_output_modifier->ProcessSolutionAtTimeStep(stepper.GetTime(), mSolution, PROBLEM_DIM);
        }
        if (mPrintOutput)
        {
            // Writing data out to the file <FilenamePrefix>.dat
            HeartEventHandler::BeginEvent(HeartEventHandler::WRITE_OUTPUT);
            WriteOneStep(stepper.GetTime(), mSolution);
            // Just flags that we've finished a time-step; won't actually 'extend' unless new data is written.
            mpWriter->AdvanceAlongUnlimitedDimension();
 
            HeartEventHandler::EndEvent(HeartEventHandler::WRITE_OUTPUT);
        }
 
        progress_reporter.Update(stepper.GetTime());
 
        OnEndOfTimestep(stepper.GetTime());
    }
 
    // Free solver
    delete mpSolver;
    mpSolver = NULL;
 
    // Close the file that stores voltage values
    progress_reporter.PrintFinalising();
    for (boost::shared_ptr<AbstractOutputModifier> p_output_modifier : mOutputModifiers)
    {
        p_output_modifier->FinaliseAtEnd();
    }
    CloseFilesAndPostProcess();
    HeartEventHandler::EndEvent(HeartEventHandler::EVERYTHING);
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::CloseFilesAndPostProcess()
{
    // Close files
    if (!mPrintOutput)
    {
        // Nothing to do
        return;
    }
    HeartEventHandler::BeginEvent(HeartEventHandler::WRITE_OUTPUT);
    // If write caching is on, the next line might actually take a significant amount of time.
    delete mpWriter;
    mpWriter = NULL;
    HeartEventHandler::EndEvent(HeartEventHandler::WRITE_OUTPUT);
 
    FileFinder test_output(HeartConfig::Instance()->GetOutputDirectory(), RelativeTo::ChasteTestOutput);
 
    /********************************************************************************
     * Run all post processing.
     *
     * The PostProcessingWriter class examines what is requested in HeartConfig and
     * adds the relevant data to the HDF5 file.
     * This is converted to different visualizer formats along with the solution
     * in the DATA_CONVERSION block below.
     *********************************************************************************/
 
    HeartEventHandler::BeginEvent(HeartEventHandler::POST_PROC);
    if (HeartConfig::Instance()->IsPostProcessingRequested())
    {
        PostProcessingWriter<ELEMENT_DIM, SPACE_DIM> post_writer(*mpMesh,
                                                                 test_output,
                                                                 HeartConfig::Instance()->GetOutputFilenamePrefix(),
                                                                 "V",
                                                                 mHdf5DataWriterChunkSizeAndAlignment);
        post_writer.WritePostProcessingFiles();
    }
    HeartEventHandler::EndEvent(HeartEventHandler::POST_PROC);
 
    /********************************************************************************************
     * Convert HDF5 datasets (solution and postprocessing maps) to different visualizer formats
     ********************************************************************************************/
 
    HeartEventHandler::BeginEvent(HeartEventHandler::DATA_CONVERSION);
    // Only if results files were written and we are outputting all nodes
    if (mNodesToOutput.empty())
    {
        if (HeartConfig::Instance()->GetVisualizeWithMeshalyzer())
        {
            // Convert simulation data to Meshalyzer format
            Hdf5ToMeshalyzerConverter<ELEMENT_DIM, SPACE_DIM> converter(test_output,
                                                                        HeartConfig::Instance()->GetOutputFilenamePrefix(),
                                                                        mpMesh,
                                                                        HeartConfig::Instance()->GetOutputUsingOriginalNodeOrdering(),
                                                                        HeartConfig::Instance()->GetVisualizerOutputPrecision());
            std::string subdirectory_name = converter.GetSubdirectory();
            HeartConfig::Instance()->Write(false, subdirectory_name);
        }
 
        if (HeartConfig::Instance()->GetVisualizeWithCmgui())
        {
            // Convert simulation data to Cmgui format
            Hdf5ToCmguiConverter<ELEMENT_DIM, SPACE_DIM> converter(test_output,
                                                                   HeartConfig::Instance()->GetOutputFilenamePrefix(),
                                                                   mpMesh,
                                                                   GetHasBath(),
                                                                   HeartConfig::Instance()->GetVisualizerOutputPrecision());
            std::string subdirectory_name = converter.GetSubdirectory();
            HeartConfig::Instance()->Write(false, subdirectory_name);
        }
 
        if (HeartConfig::Instance()->GetVisualizeWithVtk())
        {
            // Convert simulation data to VTK format
            Hdf5ToVtkConverter<ELEMENT_DIM, SPACE_DIM> converter(test_output,
                                                                 HeartConfig::Instance()->GetOutputFilenamePrefix(),
                                                                 mpMesh,
                                                                 false,
                                                                 HeartConfig::Instance()->GetOutputUsingOriginalNodeOrdering());
            std::string subdirectory_name = converter.GetSubdirectory();
            HeartConfig::Instance()->Write(false, subdirectory_name);
        }
 
        if (HeartConfig::Instance()->GetVisualizeWithParallelVtk())
        {
            // Convert simulation data to parallel VTK (pvtu) format
            Hdf5ToVtkConverter<ELEMENT_DIM, SPACE_DIM> converter(test_output,
                                                                 HeartConfig::Instance()->GetOutputFilenamePrefix(),
                                                                 mpMesh,
                                                                 true,
                                                                 HeartConfig::Instance()->GetOutputUsingOriginalNodeOrdering());
            std::string subdirectory_name = converter.GetSubdirectory();
            HeartConfig::Instance()->Write(false, subdirectory_name);
        }
    }
    HeartEventHandler::EndEvent(HeartEventHandler::DATA_CONVERSION);
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::DefineWriterColumns(bool extending)
{
    if (!extending)
    {
        if (mNodesToOutput.empty())
        {
            //Set writer to output all nodes
            mpWriter->DefineFixedDimension(mpMesh->GetNumNodes());
        }
        else
        {
            // Added for #2980
            if (mpMesh->rGetNodePermutation().size() > 0)
            {
                if (HeartConfig::Instance()->GetOutputUsingOriginalNodeOrdering())
                {
                    EXCEPTION("HeartConfig setting `GetOutputUsingOriginalNodeOrdering` is meaningless when outputting particular nodes in parallel. (Nodes are written with their original indices by default).");
                }
                std::vector<unsigned> nodes_to_output_permuted(mNodesToOutput.size());
                for (unsigned i = 0; i < mNodesToOutput.size(); i++)
                {
                    nodes_to_output_permuted[i] = mpMesh->rGetNodePermutation()[mNodesToOutput[i]];
                }
                mpWriter->DefineFixedDimension(mNodesToOutput, nodes_to_output_permuted, mpMesh->GetNumNodes());
            } else {
                // Output only the nodes indicated
                mpWriter->DefineFixedDimension(mNodesToOutput, mNodesToOutput, mpMesh->GetNumNodes());
            }
        }
        // mNodeColumnId = mpWriter->DefineVariable("Node", "dimensionless");
        mVoltageColumnId = mpWriter->DefineVariable("V", "mV");
 
        // Only used to get an estimate of the # of timesteps below
        TimeStepper stepper(mCurrentTime,
                            HeartConfig::Instance()->GetSimulationDuration(),
                            HeartConfig::Instance()->GetPrintingTimeStep());
 
        mpWriter->DefineUnlimitedDimension("Time", "msecs", stepper.EstimateTimeSteps() + 1); // plus one for start and end points
    }
    else
    {
        mVoltageColumnId = mpWriter->GetVariableByName("V");
    }
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::DefineExtraVariablesWriterColumns(bool extending)
{
    mExtraVariablesId.clear();
    // Check if any extra output variables have been requested
    if (HeartConfig::Instance()->GetOutputVariablesProvided())
    {
        // Get their names in a vector
        std::vector<std::string> output_variables;
        HeartConfig::Instance()->GetOutputVariables(output_variables);
        const unsigned num_vars = output_variables.size();
        mExtraVariablesId.reserve(num_vars);
 
        // Loop over them
        for (unsigned var_index = 0; var_index < num_vars; var_index++)
        {
            // Get variable name
            std::string var_name = output_variables[var_index];
 
            // Register it (or look it up) in the data writer
            unsigned column_id;
            if (extending)
            {
                column_id = this->mpWriter->GetVariableByName(var_name);
            }
            else
            {
                // Difficult to specify the units, as different cell models
                // at different points in the mesh could be using different units.
                column_id = this->mpWriter->DefineVariable(var_name, "unknown_units");
            }
 
            // Store column id
            mExtraVariablesId.push_back(column_id);
        }
    }
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::WriteExtraVariablesOneStep()
{
    // Get the variable names in a vector
    std::vector<std::string> output_variables;
    unsigned num_vars = mExtraVariablesId.size();
    if (num_vars > 0)
    {
        HeartConfig::Instance()->GetOutputVariables(output_variables);
    }
    assert(output_variables.size() == num_vars);
 
    // Loop over the requested variables
    for (unsigned var_index = 0; var_index < num_vars; var_index++)
    {
        // Create vector for storing values over the local nodes
        Vec variable_data = this->mpMesh->GetDistributedVectorFactory()->CreateVec();
        DistributedVector distributed_var_data = this->mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(variable_data);
 
        // Loop over the local nodes and gather the data
        for (DistributedVector::Iterator index = distributed_var_data.Begin();
             index != distributed_var_data.End();
             ++index)
        {
            // If the region is in the bath
            if (HeartRegionCode::IsRegionBath(this->mpMesh->GetNode(index.Global)->GetRegion()))
            {
                // Then we just pad the output with zeros, user currently needs to find a nice
                // way to deal with this in processing and visualization.
                distributed_var_data[index] = 0.0;
            }
            else
            {
                // Find the variable in the cell model and store its value
                distributed_var_data[index] = this->mpCardiacTissue->GetCardiacCell(index.Global)->GetAnyVariable(output_variables[var_index], mCurrentTime);
            }
        }
        distributed_var_data.Restore();
 
        // Write it to disc
        this->mpWriter->PutVector(mExtraVariablesId[var_index], variable_data);
 
        PetscTools::Destroy(variable_data);
    }
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
bool AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::InitialiseWriter()
{
    bool extend_file = (mSolution != NULL);
 
    // I think this is impossible to trip; certainly it's very difficult!
    assert(!mpWriter);
 
    if (extend_file)
    {
        FileFinder h5_file(OutputFileHandler::GetChasteTestOutputDirectory() + HeartConfig::Instance()->GetOutputDirectory()
                               + "/" + HeartConfig::Instance()->GetOutputFilenamePrefix() + ".h5",
                           RelativeTo::Absolute);
        //We are going to test for existence before creating the file.
        //Therefore we should make sure that this existence test is thread-safe.
        //(If another process creates the file too early then we may get the wrong answer to the
        //existence question).
        PetscTools::Barrier("InitialiseWriter::Extension check");
        if (!h5_file.Exists())
        {
            extend_file = false;
        }
        else // if it does exist check that it is sensible to extend it by running from the archive we loaded.
        {
            Hdf5DataReader reader(HeartConfig::Instance()->GetOutputDirectory(),
                                  HeartConfig::Instance()->GetOutputFilenamePrefix(),
                                  true);
            std::vector<double> times = reader.GetUnlimitedDimensionValues();
            if (times.back() > mCurrentTime)
            {
                EXCEPTION("Attempting to extend " << h5_file.GetAbsolutePath() << " with results from time = " << mCurrentTime << ", but it already contains results up to time = " << times.back() << "."
                                                                                                                                                                                                       " Calling HeartConfig::Instance()->SetOutputDirectory() before Solve() will direct results elsewhere.");
            }
        }
        PetscTools::Barrier("InitialiseWriter::Extension check");
    }
    mpWriter = new Hdf5DataWriter(*mpMesh->GetDistributedVectorFactory(),
                                  HeartConfig::Instance()->GetOutputDirectory(),
                                  HeartConfig::Instance()->GetOutputFilenamePrefix(),
                                  !extend_file, // don't clear directory if extension requested
                                  extend_file,
                                  "Data",
                                  mUseHdf5DataWriterCache);
 
    /* If user has specified a chunk size and alignment parameter, pass it
     * through. We set them to the same value as we think this is the most
     * likely use case, specifically on striped filesystems where a chunk
     * should squeeze into a stripe.
     * Only happens if !extend_file, i.e. we're NOT loading a checkpoint, or
     * we are loading a checkpoint but the H5 file doesn't exist yet.
     */
    if (!extend_file && mHdf5DataWriterChunkSizeAndAlignment)
    {
        mpWriter->SetTargetChunkSize(mHdf5DataWriterChunkSizeAndAlignment);
        mpWriter->SetAlignment(mHdf5DataWriterChunkSizeAndAlignment);
    }
 
    // Define columns, or get the variable IDs from the writer
    DefineWriterColumns(extend_file);
 
    // Possibility of applying a permutation
    if (HeartConfig::Instance()->GetOutputUsingOriginalNodeOrdering())
    {
        bool success = mpWriter->ApplyPermutation(mpMesh->rGetNodePermutation(), true /*unsafe mode - extending*/);
        if (success == false)
        {
            //It's not really a permutation, so reset
            HeartConfig::Instance()->SetOutputUsingOriginalNodeOrdering(false);
        }
    }
 
    if (!extend_file)
    {
        mpWriter->EndDefineMode();
    }
 
    return extend_file;
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::SetUseHdf5DataWriterCache(bool useCache)
{
    mUseHdf5DataWriterCache = useCache;
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::SetHdf5DataWriterTargetChunkSizeAndAlignment(hsize_t size)
{
    mHdf5DataWriterChunkSizeAndAlignment = size;
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::SetOutputNodes(std::vector<unsigned>& nodesToOutput)
{
    mNodesToOutput = nodesToOutput;
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
Hdf5DataReader AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::GetDataReader()
{
    if ((HeartConfig::Instance()->GetOutputDirectory() == "") || (HeartConfig::Instance()->GetOutputFilenamePrefix() == ""))
    {
        EXCEPTION("Data reader invalid as data writer cannot be initialised");
    }
    return Hdf5DataReader(HeartConfig::Instance()->GetOutputDirectory(), HeartConfig::Instance()->GetOutputFilenamePrefix());
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
bool AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::GetHasBath()
{
    return false;
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::SetElectrodes()
{
}
 
// Explicit instantiation
 
// Monodomain
template class AbstractCardiacProblem<1, 1, 1>;
template class AbstractCardiacProblem<1, 2, 1>;
template class AbstractCardiacProblem<1, 3, 1>;
template class AbstractCardiacProblem<2, 2, 1>;
template class AbstractCardiacProblem<3, 3, 1>;
 
// Bidomain
template class AbstractCardiacProblem<1, 1, 2>;
template class AbstractCardiacProblem<2, 2, 2>;
template class AbstractCardiacProblem<3, 3, 2>;
 
// Extended Bidomain
template class AbstractCardiacProblem<1, 1, 3>;
template class AbstractCardiacProblem<2, 2, 3>;
template class AbstractCardiacProblem<3, 3, 3>;