MichaelisMentenSteadyStateDiffusionReactionPde.cpp

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#include "GeometryTools.hpp"
#include "MichaelisMentenSteadyStateDiffusionReactionPde.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
MichaelisMentenSteadyStateDiffusionReactionPde<ELEMENT_DIM, SPACE_DIM>::MichaelisMentenSteadyStateDiffusionReactionPde() :
            AbstractDiscreteContinuumNonLinearEllipticPde<SPACE_DIM>(),
            mMichaelisMentenThreshold(1.0*unit::mole_per_metre_cubed)
{

}

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

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

}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double MichaelisMentenSteadyStateDiffusionReactionPde<ELEMENT_DIM, SPACE_DIM>::ComputeConstantInUSourceTerm(const ChastePoint<SPACE_DIM>& rX, Element<ELEMENT_DIM, SPACE_DIM>* pElement)
{
    return this->mConstantInUTerm/(1.0*unit::mole_per_metre_cubed_per_second);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
units::quantity<unit::concentration_flow_rate> MichaelisMentenSteadyStateDiffusionReactionPde<ELEMENT_DIM, SPACE_DIM>::ComputeConstantInUSourceTerm(unsigned gridIndex)
{
    if(gridIndex >= this->mDiscreteLinearSourceStrengths.size())
    {
        EXCEPTION("Requested out of bound grid index in discrete sources. Maybe you forgot to update the source strengths.");
    }
    return this->mConstantInUTerm + this->mDiscreteConstantSourceStrengths[gridIndex];
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
c_matrix<double, SPACE_DIM, SPACE_DIM> MichaelisMentenSteadyStateDiffusionReactionPde<ELEMENT_DIM, SPACE_DIM>::ComputeDiffusionTerm(const ChastePoint<SPACE_DIM>&, double u)
{
    return this->mDiffusionTensor;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
c_matrix<double, SPACE_DIM, SPACE_DIM> MichaelisMentenSteadyStateDiffusionReactionPde<ELEMENT_DIM, SPACE_DIM>::ComputeDiffusionTermPrime(const ChastePoint<SPACE_DIM>& rX, double u)
{
    return zero_matrix<double>(SPACE_DIM);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double MichaelisMentenSteadyStateDiffusionReactionPde<ELEMENT_DIM, SPACE_DIM>::ComputeLinearInUCoeffInSourceTerm(const ChastePoint<SPACE_DIM>& rX, Element<ELEMENT_DIM, SPACE_DIM>* pElement)
{
    return this->mLinearInUTerm/(1.0*unit::per_second);
}

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double MichaelisMentenSteadyStateDiffusionReactionPde<ELEMENT_DIM, SPACE_DIM>::ComputeLinearSourceTerm(const ChastePoint<SPACE_DIM>& rX)
{
    return 0.0;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double MichaelisMentenSteadyStateDiffusionReactionPde<ELEMENT_DIM, SPACE_DIM>::ComputeNonlinearSourceTerm(const ChastePoint<SPACE_DIM>& rX, double u)
{
    if(u<0.0)
    {
        return 0.0;
    }
    else
    {
        return (this->mConstantInUTerm/unit::mole_per_metre_cubed_per_second) * u / (mMichaelisMentenThreshold/(unit::mole_per_metre_cubed) + u);
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double MichaelisMentenSteadyStateDiffusionReactionPde<ELEMENT_DIM, SPACE_DIM>::ComputeNonlinearSourceTermPrime(const ChastePoint<SPACE_DIM>& rX, double u)
{
    if(u<0.0)
    {
        return (this->mConstantInUTerm / mMichaelisMentenThreshold)*(1.0*unit::seconds);
    }
    else
    {
        units::quantity<unit::concentration> u_scaled = u*unit::mole_per_metre_cubed;
        return (this->mConstantInUTerm * mMichaelisMentenThreshold)/((mMichaelisMentenThreshold + u_scaled)*(mMichaelisMentenThreshold + u_scaled))*(1.0*unit::seconds);
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
units::quantity<unit::concentration_flow_rate> MichaelisMentenSteadyStateDiffusionReactionPde<ELEMENT_DIM, SPACE_DIM>::ComputeNonlinearSourceTerm(unsigned gridIndex,
                                                                                                                                                  units::quantity<unit::concentration> u)
{
    if(u<0.0*unit::mole_per_metre_cubed)
    {
        return this->mDiscreteConstantSourceStrengths[gridIndex];
    }
    else
    {
        return this->mConstantInUTerm * u / (mMichaelisMentenThreshold + u) + this->mDiscreteConstantSourceStrengths[gridIndex] + this->mDiscreteLinearSourceStrengths[gridIndex]*u;
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
units::quantity<unit::rate> MichaelisMentenSteadyStateDiffusionReactionPde<ELEMENT_DIM, SPACE_DIM>::ComputeNonlinearSourceTermPrime(unsigned gridIndex,
                                                                                                                                    units::quantity<unit::concentration> u)
{
    if(u<0.0*unit::mole_per_metre_cubed)
    {
        return (this->mConstantInUTerm / mMichaelisMentenThreshold) + this->mDiscreteLinearSourceStrengths[gridIndex];
    }
    else
    {
        return this->mConstantInUTerm * mMichaelisMentenThreshold/((mMichaelisMentenThreshold + u)*(mMichaelisMentenThreshold + u)) + this->mDiscreteLinearSourceStrengths[gridIndex];
    }

}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
units::quantity<unit::concentration> MichaelisMentenSteadyStateDiffusionReactionPde<ELEMENT_DIM, SPACE_DIM>::GetMichaelisMentenThreshold()
{
    return mMichaelisMentenThreshold;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MichaelisMentenSteadyStateDiffusionReactionPde<ELEMENT_DIM, SPACE_DIM>::SetMichaelisMentenThreshold(units::quantity<unit::concentration> threshold)
{
    mMichaelisMentenThreshold = threshold;
}

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