AbstractConvergenceTester.hpp

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#ifndef ABSTRACTCONVERGENCETESTER_HPP_
#define ABSTRACTCONVERGENCETESTER_HPP_

#include "BidomainProblem.hpp"
#include "MonodomainProblem.hpp"

#include <petscvec.h>
#include <vector>
#include <iostream>
#include <fstream>
#include <cmath>
#include <ctime>

#include "AbstractTetrahedralMesh.hpp"
#include "TrianglesMeshReader.hpp"
#include "AbstractCardiacCellFactory.hpp"
#include "OutputFileHandler.hpp"
#include "TrianglesMeshWriter.hpp"
#include "PropagationPropertiesCalculator.hpp"
#include "Hdf5DataReader.hpp"
#include "GeneralPlaneStimulusCellFactory.hpp"
#include "CuboidMeshConstructor.hpp"
#include "ZeroStimulusCellFactory.hpp"
#include "SimpleStimulus.hpp"
#include "ConstBoundaryCondition.hpp"
#include "StimulusBoundaryCondition.hpp"

#include "Warnings.hpp"

typedef enum StimulusType_
{
    PLANE=0,
    QUARTER,
    NEUMANN
} StimulusType;

template <class CELL, unsigned DIM>
class RampedQuarterStimulusCellFactory : public AbstractCardiacCellFactory<DIM>
{
private:
    std::vector< boost::shared_ptr<SimpleStimulus> > mpStimuli;
    double mMeshWidth;
    double mStepSize;
    unsigned mLevels;
public:

    RampedQuarterStimulusCellFactory(double meshWidth, unsigned numElemAcross, double fullStim=-1e7)
        : AbstractCardiacCellFactory<DIM>(),
          mMeshWidth(meshWidth),
          mStepSize(meshWidth/numElemAcross),
          mLevels(numElemAcross/4)
    {
        assert(numElemAcross%4 == 0); //numElemAcross is supposed to be a multiple of 4

        for (unsigned level=0; level<mLevels; level++)
        {
            double this_stim = fullStim - (level*fullStim)/mLevels;
            //this_stim is full_stim at the zero level and would be zero at level=mLevels
            mpStimuli.push_back((boost::shared_ptr<SimpleStimulus>)new SimpleStimulus(this_stim, 0.5));
        }
    }


    AbstractCardiacCellInterface* CreateCardiacCellForTissueNode(Node<DIM>* pNode)
    {
        double x = pNode->GetPoint()[0];
        double d_level = x/mStepSize;
        unsigned level = (unsigned) d_level;
        assert(fabs(level-d_level) < DBL_MAX); //x ought to really be a multiple of the step size

        if (level < mLevels)
        {
            return new CELL(this->mpSolver, this->mpStimuli[level]);
        }
        else
        {
            return new CELL(this->mpSolver, this->mpZeroStimulus);
        }
    }
};


class AbstractUntemplatedConvergenceTester
{
protected:
    double mMeshWidth;
public:
    double OdeTimeStep;
    double PdeTimeStep;
    unsigned MeshNum;
    double RelativeConvergenceCriterion; 
    double LastDifference; 
    double Apd90FirstQn; 
    double Apd90ThirdQn; 
    double ConductionVelocity;  
    bool PopulatedResult;
    bool FixedResult;
    bool UseAbsoluteStimulus;
    double AbsoluteStimulus;
    bool SimulateFullActionPotential; 
    bool Converged; 
    StimulusType Stimulus; 
    double NeumannStimulus; 
    AbstractUntemplatedConvergenceTester();

    virtual void Converge(std::string nameOfTest)=0;

    virtual ~AbstractUntemplatedConvergenceTester();
};

template<class CARDIAC_PROBLEM, unsigned DIM>
void SetConductivities(CARDIAC_PROBLEM& rCardiacProblem);

template<unsigned DIM>
void SetConductivities(BidomainProblem<DIM>& rProblem)
{
    c_vector<double, DIM> conductivities;
    for (unsigned i=0; i<DIM; i++)
    {
        conductivities[i] = 1.75;
    }
    HeartConfig::Instance()->SetIntracellularConductivities(conductivities);

    for (unsigned i=0; i<DIM; i++)
    {
        conductivities[i] = 7.0;
    }
    HeartConfig::Instance()->SetExtracellularConductivities(conductivities);
}

template<unsigned DIM>
void SetConductivities(MonodomainProblem<DIM>& rProblem)
{
    c_vector<double, DIM> conductivities;
    for (unsigned i=0; i<DIM; i++)
    {
        conductivities[i] = 1.75;
    }
    HeartConfig::Instance()->SetIntracellularConductivities(conductivities);
}

template<class CELL, class CARDIAC_PROBLEM, unsigned DIM, unsigned PROBLEM_DIM>
class AbstractConvergenceTester : public AbstractUntemplatedConvergenceTester
{
public:
    void Converge(std::string nameOfTest)
    {
        // Create the meshes on which the test will be based
        const std::string mesh_dir = "ConvergenceMesh";
        OutputFileHandler output_file_handler(mesh_dir);
        ReplicatableVector voltage_replicated;

        unsigned file_num=0;

        // Create a file for storing conduction velocity and AP data and write the header
        OutputFileHandler conv_info_handler("ConvergencePlots"+nameOfTest, false);
        out_stream p_conv_info_file;
        if (PetscTools::AmMaster())
        {
            std::cout << "=========================== Beginning Test...==================================\n";
            p_conv_info_file = conv_info_handler.OpenOutputFile(nameOfTest+"_info.csv");
            (*p_conv_info_file) << "#Abcisa\t"
                                << "l2-norm-full\t"
                                << "l2-norm-onset\t"
                                << "Max absolute err\t"
                                << "APD90_1st_quad\t"
                                << "APD90_3rd_quad\t"
                                << "Conduction velocity (relative diffs)" << std::endl;
        }
        SetInitialConvergenceParameters();

        double prev_apd90_first_qn=0.0;
        double prev_apd90_third_qn=0.0;
        double prev_cond_velocity=0.0;
        std::vector<double> prev_voltage;
        std::vector<double> prev_times;
        PopulateStandardResult(prev_voltage, prev_times);

        do
        {
            CuboidMeshConstructor<DIM> constructor;

            //If the printing time step is too fine, then simulations become I/O bound without much improvement in accuracy
            double printing_step = this->PdeTimeStep;
#define COVERAGE_IGNORE
            while (printing_step < 1.0e-4)
            {
                printing_step *= 2.0;
                std::cout<<"Warning: PrintingTimeStep increased\n";
            }
#undef COVERAGE_IGNORE
            HeartConfig::Instance()->SetOdePdeAndPrintingTimeSteps(this->OdeTimeStep, this->PdeTimeStep, printing_step);
#define COVERAGE_IGNORE
            if (SimulateFullActionPotential)
            {
                HeartConfig::Instance()->SetSimulationDuration(400.0);
            }
            else
            {
                HeartConfig::Instance()->SetSimulationDuration(8.0);
            }
#undef COVERAGE_IGNORE
            HeartConfig::Instance()->SetOutputDirectory("Convergence"+nameOfTest);
            HeartConfig::Instance()->SetOutputFilenamePrefix("Results");

            DistributedTetrahedralMesh<DIM, DIM> mesh;
            constructor.Construct(mesh, this->MeshNum, mMeshWidth);

            unsigned num_ele_across = SmallPow(2u, this->MeshNum+2); // number of elements in each dimension

            AbstractCardiacCellFactory<DIM>* p_cell_factory=NULL;

            switch (this->Stimulus)
            {
                case NEUMANN:
                {
                    p_cell_factory = new ZeroStimulusCellFactory<CELL, DIM>();
                    break;
                }
                case PLANE:
                {
                    if (this->UseAbsoluteStimulus)
                    {
                        #define COVERAGE_IGNORE
                        p_cell_factory = new GeneralPlaneStimulusCellFactory<CELL, DIM>(0, this->AbsoluteStimulus, true);
                        #undef COVERAGE_IGNORE
                    }
                    else
                    {
                        p_cell_factory = new GeneralPlaneStimulusCellFactory<CELL, DIM>(num_ele_across, constructor.GetWidth(), false, this->AbsoluteStimulus);
                    }
                    break;
                }
                case QUARTER:
                {
                    p_cell_factory = new RampedQuarterStimulusCellFactory<CELL, DIM>(constructor.GetWidth(), num_ele_across, this->AbsoluteStimulus/10.0);
                    break;
                }
                default:
                    NEVER_REACHED;
            }


            CARDIAC_PROBLEM cardiac_problem(p_cell_factory);
            cardiac_problem.SetMesh(&mesh);

            // Calculate positions of nodes 1/4 and 3/4 through the mesh
            unsigned third_quadrant_node;
            unsigned first_quadrant_node;
            switch(DIM)
            {
                case 1:
                {
                    first_quadrant_node = (unsigned) (0.25*constructor.GetNumElements());
                    third_quadrant_node = (unsigned) (0.75*constructor.GetNumElements());
                    break;
                }
                case 2:
                {
                    unsigned n= SmallPow (2u, this->MeshNum+2);
                    first_quadrant_node =   (n+1)*(n/2)+  n/4 ;
                    third_quadrant_node =   (n+1)*(n/2)+3*n/4 ;
                    break;
                }
                case 3:
                {
                    const unsigned first_quadrant_nodes_3d[5]={61, 362, 2452, 17960, 137296};
                    const unsigned third_quadrant_nodes_3d[5]={63, 366, 2460, 17976, 137328};
                    assert(this->PdeTimeStep<5);
                    first_quadrant_node = first_quadrant_nodes_3d[this->MeshNum];
                    third_quadrant_node = third_quadrant_nodes_3d[this->MeshNum];
                    break;
                }

                default:
                    NEVER_REACHED;
            }

            double mesh_width=constructor.GetWidth();

            // We only need the output of these two nodes
            std::vector<unsigned> nodes_to_be_output;
            nodes_to_be_output.push_back(first_quadrant_node);
            nodes_to_be_output.push_back(third_quadrant_node);
            cardiac_problem.SetOutputNodes(nodes_to_be_output);

            // The results of the tests were originally obtained with the following conductivity
            // values. After implementing fibre orientation the defaults changed. Here we set
            // the former ones to be used.
            SetConductivities(cardiac_problem);

            cardiac_problem.Initialise();

            boost::shared_ptr<BoundaryConditionsContainer<DIM,DIM,PROBLEM_DIM> > p_bcc(new BoundaryConditionsContainer<DIM,DIM,PROBLEM_DIM>);
            SimpleStimulus stim(NeumannStimulus, 0.5);
            if (Stimulus==NEUMANN)
            {

                StimulusBoundaryCondition<DIM>* p_bc_stim = new StimulusBoundaryCondition<DIM>(&stim);

                // get mesh
                AbstractTetrahedralMesh<DIM, DIM> &r_mesh = cardiac_problem.rGetMesh();
                // loop over boundary elements
                typename AbstractTetrahedralMesh<DIM, DIM>::BoundaryElementIterator iter;
                iter = r_mesh.GetBoundaryElementIteratorBegin();
                while (iter != r_mesh.GetBoundaryElementIteratorEnd())
                {
                    double x = ((*iter)->CalculateCentroid())[0];
                    if (x*x<=1e-10)
                    {
                        p_bcc->AddNeumannBoundaryCondition(*iter, p_bc_stim);
                    }
                    iter++;
                }
                // pass the bcc to the problem
                cardiac_problem.SetBoundaryConditionsContainer(p_bcc);
            }

            DisplayRun();
            double time_before=MPI_Wtime();
            //cardiac_problem.SetWriteInfo();

            try
            {
                cardiac_problem.Solve();
            }
            catch (Exception e)
            {
                WARNING("This run threw an exception.  Check convergence results\n");
                std::cout << e.GetMessage() << std::endl;
            }

            if (PetscTools::AmMaster())
            {
                std::cout << "Time to solve = " << MPI_Wtime()-time_before << " seconds\n";
            }

            OutputFileHandler results_handler("Convergence"+nameOfTest, false);
            Hdf5DataReader results_reader = cardiac_problem.GetDataReader();

            {
                std::vector<double> transmembrane_potential = results_reader.GetVariableOverTime("V", third_quadrant_node);
                std::vector<double> time_series = results_reader.GetUnlimitedDimensionValues();

                OutputFileHandler plot_file_handler("ConvergencePlots"+nameOfTest, false);
                if (PetscTools::AmMaster())
                {
                    // Write out the time series for the node at third quadrant
                    {
                        std::stringstream plot_file_name_stream;
                        plot_file_name_stream<< nameOfTest << "_Third_quadrant_node_run_"<< file_num << ".csv";
                        out_stream p_plot_file = plot_file_handler.OpenOutputFile(plot_file_name_stream.str());
                        for (unsigned data_point = 0; data_point<time_series.size(); data_point++)
                        {
                            (*p_plot_file) << time_series[data_point] << "\t" << transmembrane_potential[data_point] << "\n";
                        }
                        p_plot_file->close();
                    }
                    // Write time series for first quadrant node
                    {
                        std::vector<double> transmembrane_potential_1qd=results_reader.GetVariableOverTime("V", first_quadrant_node);
                        std::vector<double> time_series_1qd = results_reader.GetUnlimitedDimensionValues();
                        std::stringstream plot_file_name_stream;
                        plot_file_name_stream<< nameOfTest << "_First_quadrant_node_run_"<< file_num << ".csv";
                        out_stream p_plot_file = plot_file_handler.OpenOutputFile(plot_file_name_stream.str());
                        for (unsigned data_point = 0; data_point<time_series.size(); data_point++)
                        {
                            (*p_plot_file) << time_series_1qd[data_point] << "\t" << transmembrane_potential_1qd[data_point] << "\n";
                        }
                        p_plot_file->close();
                    }
                }
                // calculate conduction velocity and APD90 error
                PropagationPropertiesCalculator ppc(&results_reader);

                try
                {
                    #define COVERAGE_IGNORE
                    if (SimulateFullActionPotential)
                    {
                        Apd90FirstQn = ppc.CalculateActionPotentialDuration(90.0, first_quadrant_node);
                        Apd90ThirdQn = ppc.CalculateActionPotentialDuration(90.0, third_quadrant_node);
                    }
                    #undef COVERAGE_IGNORE
                    ConductionVelocity  = ppc.CalculateConductionVelocity(first_quadrant_node,third_quadrant_node,0.5*mesh_width);
                }
                catch (Exception e)
                {
                    #define COVERAGE_IGNORE
                    std::cout << "Warning - this run threw an exception in calculating propagation.  Check convergence results\n";
                    std::cout << e.GetMessage() << std::endl;
                    #undef COVERAGE_IGNORE
                }
                double cond_velocity_error = 1e10;
                double apd90_first_qn_error = 1e10;
                double apd90_third_qn_error = 1e10;

                if (this->PopulatedResult)
                {
                    if (prev_cond_velocity != 0.0)
                    {
                        cond_velocity_error = fabs(ConductionVelocity - prev_cond_velocity) / prev_cond_velocity;
                    }
#define COVERAGE_IGNORE
                    if (prev_apd90_first_qn != 0.0)
                    {
                        apd90_first_qn_error = fabs(Apd90FirstQn - prev_apd90_first_qn) / prev_apd90_first_qn;
                    }
                    if (prev_apd90_third_qn != 0.0)
                    {
                        apd90_third_qn_error = fabs(Apd90ThirdQn - prev_apd90_third_qn) / prev_apd90_third_qn;
                    }
                    if (apd90_first_qn_error == 0.0)
                    {
                        apd90_first_qn_error = DBL_EPSILON; //Avoid log zero on plot
                    }
                    if (apd90_third_qn_error == 0.0)
                    {
                        apd90_third_qn_error = DBL_EPSILON; //Avoid log zero on plot
                    }
#undef COVERAGE_IGNORE
                    if (cond_velocity_error == 0.0)
                    {
                        cond_velocity_error = DBL_EPSILON; //Avoid log zero on plot
                    }
                }

                prev_cond_velocity = ConductionVelocity;
                prev_apd90_first_qn = Apd90FirstQn;
                prev_apd90_third_qn = Apd90ThirdQn;

                // calculate l2norm
                double max_abs_error = 0;
                double sum_sq_abs_error =0;
                double sum_sq_prev_voltage = 0;
                double sum_sq_abs_error_full =0;
                double sum_sq_prev_voltage_full = 0;
                if (this->PopulatedResult)
                {
                    //If the PDE step is varying then we'll have twice as much data now as we use to have

                    unsigned time_factor=(time_series.size()-1) / (prev_times.size()-1);
                    assert (time_factor == 1 || time_factor == 2 || time_factor == 8);
                    //Iterate over the shorter time series data
                    for (unsigned data_point = 0; data_point<prev_times.size(); data_point++)
                    {
                        unsigned this_data_point=time_factor*data_point;

                        assert(time_series[this_data_point] == prev_times[data_point]);
                        double abs_error = fabs(transmembrane_potential[this_data_point]-prev_voltage[data_point]);
                        max_abs_error = (abs_error > max_abs_error) ? abs_error : max_abs_error;
                        //Only do resolve the upstroke...
                        sum_sq_abs_error_full += abs_error*abs_error;
                        sum_sq_prev_voltage_full += prev_voltage[data_point] * prev_voltage[data_point];
                        if (time_series[this_data_point] <= 8.0)
                        {
                            //In most regular cases we always do this, since the simulation stops at ms
                            sum_sq_abs_error += abs_error*abs_error;
                            sum_sq_prev_voltage += prev_voltage[data_point] * prev_voltage[data_point];
                        }
                    }

                }
                if (!this->PopulatedResult || !FixedResult)
                {
                    prev_voltage = transmembrane_potential;
                    prev_times = time_series;
                }

                if (this->PopulatedResult)
                {
                    double l2_norm_upstroke = sqrt(sum_sq_abs_error/sum_sq_prev_voltage);
                    double l2_norm_full = sqrt(sum_sq_abs_error_full/sum_sq_prev_voltage_full);

                    if (PetscTools::AmMaster())
                    {
                        (*p_conv_info_file) << std::setprecision(8)
                                            << Abscissa() << "\t"
                                            << l2_norm_full << "\t"
                                            << l2_norm_upstroke << "\t"
                                            << max_abs_error << "\t"
                                            << Apd90FirstQn <<" "<< apd90_first_qn_error <<""<< "\t"
                                            << Apd90ThirdQn <<" "<< apd90_third_qn_error <<""<< "\t"
                                            << ConductionVelocity <<" "<< cond_velocity_error  <<""<< std::endl;
                    }
                    // convergence criterion
                    this->Converged = l2_norm_full < this->RelativeConvergenceCriterion;
                    this->LastDifference = l2_norm_full;
#define COVERAGE_IGNORE
                    assert (time_series.size() != 1u);
                    if (time_series.back() == 0.0)
                    {
                        std::cout << "Failed after successful convergence - give up this convergence test\n";
                        break;
                    }
#undef COVERAGE_IGNORE

                }

                if ( time_series.back() != 0.0)
                {
                    // Simulation ran to completion
                    this->PopulatedResult=true;

                }
            }

            // Get ready for the next test by halving the time step
            if (!this->Converged)
            {
                UpdateConvergenceParameters();
                file_num++;
            }
            delete p_cell_factory;
        }
        while (!GiveUpConvergence() && !this->Converged);


        if (PetscTools::AmMaster())
        {
            p_conv_info_file->close();

            std::cout << "Results: " << std::endl;
            FileFinder info_finder = conv_info_handler.FindFile(nameOfTest + "_info.csv");
            std::ifstream info_file(info_finder.GetAbsolutePath().c_str());
            if (info_file)
            {
                std::cout << info_file.rdbuf();
                info_file.close();
            }
        }

    }

    void DisplayRun()
    {
        if (!PetscTools::AmMaster())
        {
            return; //Only master displays this
        }
        unsigned num_ele_across = SmallPow(2u, this->MeshNum+2);// number of elements in each dimension
        double scaling = mMeshWidth/(double) num_ele_across;

        std::cout<<"================================================================================"<<std::endl;
        std::cout<<"Solving in " << DIM << "D\t";
        std::cout<<"Space step " << scaling << " cm (mesh " << this->MeshNum << ")" << "\n";
        std::cout<<"PDE step " << this->PdeTimeStep << " ms" << "\t";
        std::cout<<"ODE step " << this->OdeTimeStep << " ms" << "\t";
        if (HeartConfig::Instance()->GetUseAbsoluteTolerance())
        {
            std::cout<<"KSP absolute "<<HeartConfig::Instance()->GetAbsoluteTolerance()<<"\t";
        }
        else
        {
            std::cout<<"KSP relative "<<HeartConfig::Instance()->GetRelativeTolerance()<<"\t";
        }
        switch (this->Stimulus)
        {
            case PLANE:
            std::cout<<"Stimulus = Plane\n";
            break;

            case QUARTER:
            std::cout<<"Stimulus = Ramped first quarter\n";
            break;

            case NEUMANN:
            std::cout<<"Stimulus = Neumann\n";
            break;

        }
        // Keep track of what Nightly things are doing
        std::time_t rawtime;
        std::time( &rawtime );
        std::cout << std::ctime(&rawtime);
        if (this->UseAbsoluteStimulus)
        {
            #define COVERAGE_IGNORE
            std::cout<<"Using absolute stimulus of "<<this->AbsoluteStimulus<<std::endl;
            #undef COVERAGE_IGNORE
        }
        std::cout << std::flush;
        //HeartEventHandler::Headings();
        //HeartEventHandler::Report();

    }

public:
    virtual ~AbstractConvergenceTester() {}

    virtual void SetInitialConvergenceParameters()=0;
    virtual void UpdateConvergenceParameters()=0;
    virtual bool GiveUpConvergence()=0;
    virtual double Abscissa()=0;
    virtual void PopulateStandardResult(std::vector<double> &result, std::vector<double> &times)
    {
        assert(this->PopulatedResult==false);
        assert(result.size()==0);
        assert(times.size()==0);
    }

    bool IsConverged()
    {
        return Converged;
    }

    void SetMeshWidth(double meshWidth)
    {
        mMeshWidth=meshWidth;
    }
};

#endif /*ABSTRACTCONVERGENCETESTER_HPP_*/