CardiacElectroMechanicsProblem.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 CARDIACELECTROMECHANICSPROBLEM_HPP_
#define CARDIACELECTROMECHANICSPROBLEM_HPP_

#include <vector>
#include <string>
#include "UblasIncludes.hpp"

#include "AbstractCardiacCellFactory.hpp"
#include "MonodomainProblem.hpp"
#include "ImplicitCardiacMechanicsAssembler.hpp"
#include "TetrahedralMesh.hpp"
#include "QuadraticMesh.hpp"

// if including Cinv in monobidomain equations
//#include "NodewiseData.hpp"


/* Todos:
 *  Go through and tidy/refactor, perhaps make elements and weights safer
 *  Think about architecture (of AbstractCardiacProblem) when this is done properly..
 */



template<unsigned DIM>
struct ElementAndWeights
{
    unsigned ElementNum;
    c_vector<double,DIM+1> Weights;
};



template<unsigned DIM>
class CardiacElectroMechanicsProblem
{

friend class TestCardiacElectroMechanicsProblem;

protected :
    MonodomainProblem<DIM>* mpMonodomainProblem;
    ImplicitCardiacMechanicsAssembler<DIM>* mpCardiacMechAssembler;

    double mEndTime;
    double mElectricsTimeStep;
    double mMechanicsTimeStep;
    unsigned mNumElecTimestepsPerMechTimestep;
    double mNhsOdeTimeStep;

    TetrahedralMesh<DIM,DIM>* mpElectricsMesh;
    QuadraticMesh<DIM>* mpMechanicsMesh;

    std::vector<ElementAndWeights<DIM> > mElementAndWeightsForQuadPoints;

    std::string mOutputDirectory;
    std::string mDeformationOutputDirectory;
    bool mWriteOutput;
    bool mNoElectricsOutput;

    const static int WRITE_EVERY_NTH_TIME = 1; //hardcoded for the time being ///\todo, allow user to set this

    bool mIsWatchedLocation;
    c_vector<double,DIM> mWatchedLocation;
    unsigned mWatchedElectricsNodeIndex;
    unsigned mWatchedMechanicsNodeIndex;
    out_stream mpWatchedLocationFile;

    std::vector<unsigned> mFixedNodes;

    void DetermineWatchedNodes();


    void WriteWatchedLocationData(double time, Vec voltage);

public :
    CardiacElectroMechanicsProblem(TetrahedralMesh<DIM,DIM>* pElectricsMesh,
                                   QuadraticMesh<DIM>* pMechanicsMesh,
                                   std::vector<unsigned> fixedMechanicsNodes,
                                   AbstractCardiacCellFactory<DIM>* pCellFactory,
                                   double endTime,
                                   unsigned numElecTimeStepsPerMechTimestep,
                                   double nhsOdeTimeStep,
                                   std::string outputDirectory);

    virtual ~CardiacElectroMechanicsProblem();

    void Initialise();

    void Solve();

    // short helper function - the max of a std::vec. this is in the wrong place
    double Max(std::vector<double>& vec);

    void SetNoElectricsOutput();

    void SetWatchedPosition(c_vector<double,DIM> watchedLocation);
    
    std::vector<c_vector<double,DIM> >& rGetDeformedPosition();
};



#endif /*CARDIACELECTROMECHANICSPROBLEM_HPP_*/

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