AbstractCardiacProblem.hpp

/*

Copyright (C) University of Oxford, 2005-2009

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 ABSTRACTCARDIACPROBLEM_HPP_
#define ABSTRACTCARDIACPROBLEM_HPP_

#include <string>
#include <vector>

#include "AbstractCardiacCellFactory.hpp"
#include "AbstractCardiacPde.hpp"
#include "AbstractDynamicAssemblerMixin.hpp"
#include "AbstractMesh.hpp"

#include "BoundaryConditionsContainer.hpp"
#include "Hdf5DataReader.hpp"
#include "Hdf5DataWriter.hpp"

template<unsigned SPACE_DIM, unsigned PROBLEM_DIM>
class AbstractCardiacProblem
{
friend class TestBidomainWithBathAssembler;
    
protected:
    std::string mMeshFilename;

    std::string mNodesPerProcessorFilename;

    std::string  mOutputDirectory, mOutputFilenamePrefix;

    bool mUseMatrixBasedRhsAssembly;
    bool mAllocatedMemoryForMesh;
    bool mWriteInfo;
    bool mPrintOutput;
    bool mCallChaste2Meshalyzer;

    std::vector<unsigned> mNodesToOutput;

    unsigned mVoltageColumnId;
    unsigned mTimeColumnId;
    unsigned mNodeColumnId;

    AbstractCardiacPde<SPACE_DIM>* mpCardiacPde;

    BoundaryConditionsContainer<SPACE_DIM, SPACE_DIM, PROBLEM_DIM>* mpBoundaryConditionsContainer;
    BoundaryConditionsContainer<SPACE_DIM, SPACE_DIM, PROBLEM_DIM>* mpDefaultBoundaryConditionsContainer;
    AbstractDynamicAssemblerMixin<SPACE_DIM, SPACE_DIM, PROBLEM_DIM>* mpAssembler;
    AbstractCardiacCellFactory<SPACE_DIM>* mpCellFactory;
    AbstractMesh<SPACE_DIM,SPACE_DIM>* mpMesh;

    Vec mSolution; 

    virtual AbstractCardiacPde<SPACE_DIM>* CreateCardiacPde() =0;

    virtual AbstractDynamicAssemblerMixin<SPACE_DIM, SPACE_DIM, PROBLEM_DIM>* CreateAssembler() =0;

public:
    // This (and things in MonodomainProblem) being public are hacks for
    // CardiacElectroMechanicsProblem to work.
    // ///\todo CardiacElectroMechanicsProblem should be a friend, but not sure
    // how to get friends to work when both friends are templated and abstract.
    Hdf5DataWriter* mpWriter;

public:
    AbstractCardiacProblem(AbstractCardiacCellFactory<SPACE_DIM>* pCellFactory);

    virtual ~AbstractCardiacProblem();

    /*
     *  Initialise the system. Must be called before Solve()
     */
    void Initialise();

    void SetNodesPerProcessorFilename(const std::string& filename);
    
    void SetBoundaryConditionsContainer(BoundaryConditionsContainer<SPACE_DIM, SPACE_DIM, PROBLEM_DIM> *bcc);
    
    virtual void PreSolveChecks();

    virtual Vec CreateInitialCondition();

    void ConvertOutputToMeshalyzerFormat(bool call = true);

    void SetMesh(AbstractMesh<SPACE_DIM,SPACE_DIM>* pMesh);

    void PrintOutput(bool rPrintOutput);

    void SetWriteInfo(bool writeInfo = true);

    Vec GetSolution();

    AbstractMesh<SPACE_DIM,SPACE_DIM> & rGetMesh();

    AbstractCardiacPde<SPACE_DIM>* GetPde();
    
    void Solve();
    
    void CloseFilesAndPostProcess();


    virtual void WriteInfo(double time)=0;

    virtual void DefineWriterColumns();

    virtual void WriteOneStep(double time, Vec voltageVec);
    
    void InitialiseWriter();
    
    void SetOutputNodes(std::vector<unsigned> &nodesToOutput);
    
    Hdf5DataReader GetDataReader();
    
    void UseMatrixBasedRhsAssembly(bool usematrix=true);
    
    virtual void OnEndOfTimestep(double time)
    {}
    
};
#endif /*ABSTRACTCARDIACPROBLEM_HPP_*/

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