AdaptiveBidomainProblem.hpp

/*

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

*/

/*

Copyright (C) University of Oxford, 2005-2011

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/



#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 "MatrixBasedBidomainSolver.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:

    MatrixBasedBidomainSolver<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_*/

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