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NormalizedLinearAttenuator.cpp

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// NormalizedLinearAttenuator.cpp: implementation of the CNormalizedLinearAttenuator class.
//

#include "NormalizedLinearAttenuator.h"

// Construction/Destruction

CNormalizedLinearAttenuator::CNormalizedLinearAttenuator(Chemical *InputChemical, Chemical *OutputChemical, RateConstant *k_atten, std::string reactionName)
:Reaction(reactionName)
{
        // stoichiometry
        this->InputChemical = chemicals.size();
        chemicals.push_back(InputChemical);
        numberOfEachChemicalChangedByReaction.push_back(0);

        this->OutputChemical = chemicals.size();
        chemicals.push_back(OutputChemical);
        numberOfEachChemicalChangedByReaction.push_back(-1);

        // rates
        this->k_atten = rateConstants.size();
        rateConstants.push_back(k_atten);

        // put enough dummy chemicalJacobian elements on the vector 
        // - they are recomputed every time you ask for the chemicalJacobian
        chemicalJacobian.push_back(new JElement(-1,-1));

        this->SetTeXForm();
}

CNormalizedLinearAttenuator::~CNormalizedLinearAttenuator()
{
        
}

double CNormalizedLinearAttenuator::GetRate() const
{
        return ((rateConstants[k_atten]->GetValue())/(chemicals[InputChemical]->GetInitialAmount()))*chemicals[InputChemical]->GetAmount();
}

void CNormalizedLinearAttenuator::SetTeXForm()
{
        strstream stream;
        // TeX form of the reaction
        stream << rateConstants[k_atten]->GetTeXName().c_str();
        stream << "{ " << chemicals[InputChemical]->GetTeXName().c_str() << " \\over ";
        stream << chemicals[InputChemical]->GetTeXName().c_str() << "_0 }";
        stream << ends;
        // set the TeX string equal to what's in the stream
        m_sTeXForm = stream.str();
        // allow memory to be freed
        stream.rdbuf()->freeze(0);
}

std::vector<Reaction::JElement *> *CNormalizedLinearAttenuator::GetChemicalJacobian()
{
        chemicalJacobian[0]->SetWithRespectTo(chemicals[InputChemical]->GetChemicalNumber());
        chemicalJacobian[0]->SetJValue((rateConstants[k_atten]->GetValue())/(chemicals[InputChemical]->GetInitialAmount()));
        
        return &chemicalJacobian;
}

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