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GenerationReaction.cpp

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// GenerationReaction.cpp: implementation of the GenerationReaction class.
//

#include "GenerationReaction.h"

// Construction/Destruction

GenerationReaction::GenerationReaction(Chemical *Generator, Chemical *Product, RateConstant *k_g, std::string reactionName)
:Reaction(reactionName)
{
        // stoichiometry
        this->Generator = chemicals.size();
        chemicals.push_back(Generator);
        numberOfEachChemicalChangedByReaction.push_back(0);

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

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

        // 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();
}

GenerationReaction::~GenerationReaction()
{

}

double GenerationReaction::GetRate() const
{
        return rateConstants[k_g]->GetValue() * chemicals[Generator]->GetAmount();
}

void GenerationReaction::SetTeXForm()
{
        std::stringstream stream;
        // TeX form of the reaction
        stream << rateConstants[k_g]->GetTeXName().c_str();
        stream << "\\left [" << chemicals[Generator]->GetTeXName().c_str();
        stream << "\\right ]";
        // add a NULL
        //int namesize = (chemicals[Generator]->GetName()).length();
        //stream << (chemicals[Generator]->GetName())[namesize];
        stream << ends;
        // set the TeX string equal to what's in the stream
        m_sTeXForm = stream.str();
        // free up the string
//      stream.rdbuf()->freeze(0);
}

std::vector<Reaction::JElement *> *GenerationReaction::GetChemicalJacobian()
{
        chemicalJacobian[0]->SetWithRespectTo(chemicals[Generator]->GetChemicalNumber());
        chemicalJacobian[0]->SetJValue(rateConstants[k_g]->GetValue());
        
        return &chemicalJacobian;
}

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