AveragedSourceParabolicPde.hpp

/*

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*/

#ifndef AVERAGESOURCEPARABOLICPDE_HPP_
#define AVERAGESOURCEPARABOLICPDE_HPP_

#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>

#include "AbstractCellPopulation.hpp"
#include "TetrahedralMesh.hpp"
#include "AbstractLinearParabolicPde.hpp"

template<unsigned DIM>
class AveragedSourceParabolicPde : public AbstractLinearParabolicPde<DIM,DIM>
{
    friend class TestCellBasedParabolicPdes;

private:

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
       archive & boost::serialization::base_object<AbstractLinearParabolicPde<DIM, DIM> >(*this);
       archive & mDuDtCoefficient;
       archive & mDiffusionCoefficient;
       archive & mSourceCoefficient;
       archive & mCellDensityOnCoarseElements;
    }

protected:

    AbstractCellPopulation<DIM, DIM>& mrCellPopulation;

    double mDuDtCoefficient;

    double mDiffusionCoefficient;

    double mSourceCoefficient;

    std::vector<double> mCellDensityOnCoarseElements;

public:

    AveragedSourceParabolicPde(AbstractCellPopulation<DIM, DIM>& rCellPopulation,
                               double duDtCoefficient=1.0,
                               double diffusionCoefficient=1.0,
                               double sourceCoefficient=0.0);

    const AbstractCellPopulation<DIM>& rGetCellPopulation() const;

    void virtual SetupSourceTerms(TetrahedralMesh<DIM,DIM>& rCoarseMesh, std::map<CellPtr, unsigned>* pCellPdeElementMap=nullptr);

    virtual double ComputeDuDtCoefficientFunction(const ChastePoint<DIM>& rX);

    virtual double ComputeSourceTerm(const ChastePoint<DIM>& rX,
                                     double u,
                                     Element<DIM,DIM>* pElement=NULL);

    virtual double ComputeSourceTermAtNode(const Node<DIM>& rNode, double u);

    virtual c_matrix<double,DIM,DIM> ComputeDiffusionTerm(const ChastePoint<DIM>& rX, Element<DIM,DIM>* pElement=NULL);

    double GetUptakeRateForElement(unsigned elementIndex);
};

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(AveragedSourceParabolicPde)

namespace boost
{
namespace serialization
{
template<class Archive, unsigned DIM>
inline void save_construct_data(
    Archive & ar, const AveragedSourceParabolicPde<DIM>* t, const unsigned int file_version)
{
    // Save data required to construct instance
    const AbstractCellPopulation<DIM, DIM>* p_cell_population = &(t->rGetCellPopulation());
    ar & p_cell_population;
}

template<class Archive, unsigned DIM>
inline void load_construct_data(
    Archive & ar, AveragedSourceParabolicPde<DIM>* t, const unsigned int file_version)
{
    // Retrieve data from archive required to construct new instance
    AbstractCellPopulation<DIM, DIM>* p_cell_population;
    ar >> p_cell_population;

    // Invoke inplace constructor to initialise instance
    ::new(t)AveragedSourceParabolicPde<DIM>(*p_cell_population);
}
}
} // namespace ...

#endif /*AVERAGESOURCEPARABOLICPDE_HPP_*/