AdaptiveBidomainProblem.hpp

/*

Copyright (C) Fujitsu Laboratories of Europe, 2009-2010

*/

/*

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*/



#ifndef ADAPTIVEBIDOMAINPROBLEM_HPP_
#define ADAPTIVEBIDOMAINPROBLEM_HPP_

#define CXXBLAS_H    // This stops multiple definition of blas headers (one via Chaste, one via libadaptivity/include/cxxblas.h)
                    // Might break things, no idea, will keep it here until problems appear....

#ifdef CHASTE_ADAPTIVITY

#include <vector>
#include <string>
#include <fstream>
#include <sstream>
#include <cassert>
#include <cmath>

// Include libadaptivity header files.
// Need to add $LIBADAPTIVITY_DIR/include/ to the include path.
#define HAVE_VTK
#define _BACKWARD_BACKWARD_WARNING_H 1 //Cut out the strstream deprecated warning for now (gcc4.3)
#include "vtk.h"
#include "../metric_field/include/DiscreteGeometryConstraints.h"
#include "../metric_field/include/ErrorMeasure.h"
#include "../adapt3d/include/Adaptivity.h"

#include "AbstractCardiacProblem.hpp"
#include "BidomainProblem.hpp"
#include "BidomainSolver.hpp"
#include "BidomainTissue.hpp"
#include "AdaptiveTetrahedralMesh.hpp"
#include "AbstractStimulusFunction.hpp"
#include "StimulusBoundaryCondition.hpp"
#include "VtkMeshReader.hpp"

#include <vtkDoubleArray.h>
#include <vtkCellData.h>
#include <vtkTetra.h>
#include <vtkUnstructuredGrid.h>
#include <vtkUnstructuredGridWriter.h>
#include <vtkXMLUnstructuredGridWriter.h>

class AdaptiveBidomainProblem : public BidomainProblem<3>
{
    friend class TestAdaptiveBidomainProblem;
    friend class TestAdaptiveBidomainProblemNightly;

private:

    BidomainSolver<3,3>* mpSolver;

    AdaptiveTetrahedralMesh *mpAdaptiveMesh;

    bool mIsMeshAdapting;     
    bool mInitializeFromVtu;    
    bool mUseNeumannBoundaryConditions;
    double mNeumannStimulusIndex;
    double mNeumannStimulusLowerValue;
    double mNeumannStimulusUpperValue;
    double mNeumannStimulusMagnitude;
    double mNeumannStimulusDuration;
    double mNeumannStimulusPeriod;
    AbstractStimulusFunction* mpNeumannStimulus;
    StimulusBoundaryCondition<3>* mpNeumannStimulusBoundaryCondition;

//    /**
//     * Determine whether or not an edge of the mesh is of sufficient quality. Edge is "good" if the error metric
//     * associated  with it is in the range [ 1 - mGoodEdgeRange , 1 + mGoodEdgeRange ]
//     */
//    double mGoodEdgeRange;
//
//    /** Proportion of edges that must be deemed "bad" (i.e. not good) before an adapt takes place */
//    double mBadEdgeCriterion;

    std::string mOutputDirectory;

    std::string mOutputFilenamePrefix;

public:
    AdaptiveBidomainProblem(AbstractCardiacCellFactory<3>* pCellFactory, bool hasBath=false);

    ~AdaptiveBidomainProblem();

    void DoNotAdaptMesh();

//
//     * Set the values of mGoodEdgeRange and mBadEdgeCriterion to be used by the AdaptiveTetrahedralMesh
//     * in determining whether an adapt is necessary or if the current mesh is of sufficient quality.
//     *
//     * @param range Value of mGoodEdgeRange to be used
//     * @param criterion Value of mBadEdgeCriterion to be used
//
//    void SetAdaptCriterion(double range, double criterion);

    void AddCurrentSolutionToAdaptiveMesh( Vec solution );

    void InitializeSolutionOnAdaptedMesh( VtkMeshReader<3,3>* reader );

    void AdaptMesh();

    double GetTargetError();

    double GetSigma();

    double GetMaxEdgeLength();

    double GetMinEdgeLength();

    double GetGradation();

    unsigned GetMaxMeshNodes();

    unsigned GetNumAdaptSweeps();

    void UseNeumannBoundaryCondition( unsigned index = 0 );

    void SetNeumannStimulusMagnitudeAndDuration(double magnitude, double duration, double period = DBL_MAX);

    void SetupNeumannBoundaryConditionOnMesh();

    void LoadSimulationFromVtuFile();

    void Solve();
};

#endif // CHASTE_ADAPTIVITY

#endif /*ADAPTIVEBIDOMAINPROBLEM_HPP_*/