AbstractCardiacPde.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 ABSTRACTCARDIACPDE_HPP_
#define ABSTRACTCARDIACPDE_HPP_

#include <vector>
#include <climits> // Work around a boost bug - see #1024.
#include <boost/serialization/access.hpp>
#include <boost/serialization/is_abstract.hpp>
#include <boost/serialization/base_object.hpp>
#include <boost/shared_ptr.hpp>
#include <boost/serialization/shared_ptr.hpp>
#include <boost/serialization/vector.hpp>

#include <boost/numeric/ublas/matrix.hpp>

#include "AbstractCardiacCell.hpp"
#include "AbstractCardiacCellFactory.hpp"
#include "AbstractConductivityTensors.hpp"

#include "ReplicatableVector.hpp"
#include "HeartConfig.hpp"
#include "ArchiveLocationInfo.hpp"

// Needs to be included last
#include "TemplatedExport.hpp"


// IMPORTANT NOTE: the inheritance of AbstractPde has to be 'virtual'
// ie "class AbstractCardiacPde : public virtual AbstractPde"
// because AbstractPde will be the top class in a 'dreaded diamond':
//      A
//     / \     A = AbstractPde, B = AbstractCardiac, C = AbstractLinearParabolic (etc)
//    B   C    D = MonodomainPde
//     \ /
//      D
//
// B and C must use virtual inheritence of A in order for D to only contain 1 instance
// of the member variables in A

template <unsigned ELEM_DIM, unsigned SPACE_DIM = ELEM_DIM>
class AbstractCardiacPde
{
private:

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        //Archive vector factory?  Do we have one available?  (If not - do it in the test to guard against errors)

        //Archive cells using handler.GetProcessUniqueFilePath("") and ArchiveLocationInfo


        archive & mpDistributedVectorFactory;
    }

protected:

    AbstractConductivityTensors<SPACE_DIM> *mpIntracellularConductivityTensors;

    std::vector< AbstractCardiacCell* > mCellsDistributed;

    ReplicatableVector mIionicCacheReplicated;
    
    ReplicatableVector mIntracellularStimulusCacheReplicated;

    const unsigned mStride;

    HeartConfig* mpConfig;

    bool mDoCacheReplication;
    
    bool mDoOneCacheReplication;

    DistributedVectorFactory* mpDistributedVectorFactory;
    
    bool mpFactoryWasUnarchived;
public:
    AbstractCardiacPde(AbstractCardiacCellFactory<ELEM_DIM,SPACE_DIM>* pCellFactory,
                       const unsigned stride=1);

    AbstractCardiacPde(std::vector<AbstractCardiacCell*> & rCellsDistributed,
                       const unsigned stride = 1);

    virtual ~AbstractCardiacPde();

    void SetCacheReplication(bool doCacheReplication);

    const c_matrix<double, SPACE_DIM, SPACE_DIM>& rGetIntracellularConductivityTensor(unsigned elementIndex);

    AbstractCardiacCell* GetCardiacCell( unsigned globalIndex );

    virtual void SolveCellSystems(Vec existingSolution, double time, double nextTime);

    ReplicatableVector& rGetIionicCacheReplicated();

    ReplicatableVector& rGetIntracellularStimulusCacheReplicated();


    void UpdateCaches(unsigned globalIndex, unsigned localIndex, double nextTime);

    void ReplicateCaches();

    const std::vector<AbstractCardiacCell*>& GetCellsDistributed() const;

};

// Declare identifier for the serializer
EXPORT_ABSTRACT_TEMPLATE_CLASS_ALL_DIMS(AbstractCardiacPde);

#endif /*ABSTRACTCARDIACPDE_HPP_*/

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