LinearSteadyStateDiffusionReactionPde.cpp

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#include <algorithm>
#include "LinearSteadyStateDiffusionReactionPde.hpp"
#include "BaseUnits.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
LinearSteadyStateDiffusionReactionPde<ELEMENT_DIM, SPACE_DIM>::LinearSteadyStateDiffusionReactionPde() :
            AbstractDiscreteContinuumLinearEllipticPde<ELEMENT_DIM, ELEMENT_DIM>(),
            mLinearInUTerm(0.0 * unit::per_second),
            mDiscreteLinearSourceStrengths()
{

}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
LinearSteadyStateDiffusionReactionPde<ELEMENT_DIM, SPACE_DIM>::~LinearSteadyStateDiffusionReactionPde()
{

}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
boost::shared_ptr<LinearSteadyStateDiffusionReactionPde<ELEMENT_DIM, SPACE_DIM> > LinearSteadyStateDiffusionReactionPde<ELEMENT_DIM, SPACE_DIM>::Create()
{
    MAKE_PTR(LinearSteadyStateDiffusionReactionPde<ELEMENT_DIM>, pSelf);
    return pSelf;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double LinearSteadyStateDiffusionReactionPde<ELEMENT_DIM, SPACE_DIM>::ComputeLinearInUCoeffInSourceTerm(const ChastePoint<SPACE_DIM>& rX,
                                                                                                        Element<ELEMENT_DIM, SPACE_DIM>* pElement)
{
    if(mDiscreteLinearSourceStrengths.size()>0)
    {
        if(pElement->GetIndex() >= mDiscreteLinearSourceStrengths.size())
        {
            EXCEPTION("Requested out of bound grid index in discrete sources. Maybe you forgot to update the source strengths.");
        }
        units::quantity<unit::rate> scaling_factor = (1.0/BaseUnits::Instance()->GetReferenceTimeScale());
        return (mLinearInUTerm + mDiscreteLinearSourceStrengths[pElement->GetIndex()])/scaling_factor;
    }
    else
    {
        units::quantity<unit::rate> scaling_factor = (1.0/BaseUnits::Instance()->GetReferenceTimeScale());
        return mLinearInUTerm/scaling_factor;
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
units::quantity<unit::rate> LinearSteadyStateDiffusionReactionPde<ELEMENT_DIM, SPACE_DIM>::ComputeLinearInUCoeffInSourceTerm(unsigned gridIndex)
{
    if(mDiscreteLinearSourceStrengths.size()>0)
    {
        if(gridIndex >= mDiscreteLinearSourceStrengths.size())
        {
            EXCEPTION("Requested out of bound grid index in discrete sources. Maybe you forgot to update the source strengths.");
        }
        return mLinearInUTerm + mDiscreteLinearSourceStrengths[gridIndex];
    }
    else
    {
        return mLinearInUTerm;
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void LinearSteadyStateDiffusionReactionPde<ELEMENT_DIM, SPACE_DIM>::SetContinuumLinearInUTerm(units::quantity<unit::rate> linearInUTerm)
{
    mLinearInUTerm = linearInUTerm;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void LinearSteadyStateDiffusionReactionPde<ELEMENT_DIM, SPACE_DIM>::UpdateDiscreteSourceStrengths()
{
    AbstractDiscreteContinuumLinearEllipticPde<ELEMENT_DIM, SPACE_DIM>::UpdateDiscreteSourceStrengths();
    if(this->mUseRegularGrid)
    {
        if(!this->mpRegularGrid)
        {
            EXCEPTION("A grid has not been set for the determination of source strengths.");
        }
        mDiscreteLinearSourceStrengths = std::vector<units::quantity<unit::rate> >(this->mpRegularGrid->GetNumberOfPoints(), 0.0*unit::per_second);
        for(unsigned idx=0; idx<this->mDiscreteSources.size(); idx++)
        {
            this->mDiscreteSources[idx]->SetRegularGrid(this->mpRegularGrid);
            std::vector<units::quantity<unit::rate> > result = this->mDiscreteSources[idx]->GetLinearInURegularGridValues();
            std::transform(mDiscreteLinearSourceStrengths.begin( ), mDiscreteLinearSourceStrengths.end( ),
                           result.begin( ), mDiscreteLinearSourceStrengths.begin( ),std::plus<units::quantity<unit::rate> >( ));
        }
    }
    else
    {
        if(!this->mpMesh)
        {
            EXCEPTION("A mesh has not been set for the determination of source strengths.");
        }
        mDiscreteLinearSourceStrengths = std::vector<units::quantity<unit::rate> >(this->mpMesh->GetNumElements(), 0.0*unit::per_second);
        for(unsigned idx=0; idx<this->mDiscreteSources.size(); idx++)
        {
            this->mDiscreteSources[idx]->SetMesh(this->mpMesh);
            std::vector<units::quantity<unit::rate> > result = this->mDiscreteSources[idx]->GetLinearInUMeshValues();
            std::transform(mDiscreteLinearSourceStrengths.begin( ), mDiscreteLinearSourceStrengths.end( ),
                           result.begin( ), mDiscreteLinearSourceStrengths.begin( ),std::plus<units::quantity<unit::rate> >( ));
        }
    }
}

// Explicit instantiation
template class LinearSteadyStateDiffusionReactionPde<2>;
template class LinearSteadyStateDiffusionReactionPde<3>;