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TrimerFormation.cpp

Go to the documentation of this file.

// TrimerFormation.cpp: implementation of the CTrimerFormation class.
//

#include "TrimerFormation.h"

// Construction/Destruction

CTrimerFormation::CTrimerFormation(Chemical *A, Chemical *B, Chemical *C, Chemical *Trimer, RateConstant *k_t, std::string reactionName)
:Reaction(reactionName)
{
        // stoichiometry
        this->A = chemicals.size();
        chemicals.push_back(A);
        numberOfEachChemicalChangedByReaction.push_back(-1);

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

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

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

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

        // 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));
        chemicalJacobian.push_back(new JElement(-1,-1));
        chemicalJacobian.push_back(new JElement(-1,-1));

        this->SetTeXForm();

}

CTrimerFormation::~CTrimerFormation()
{

}

double CTrimerFormation::GetRate() const
{
        double amtA = chemicals[A]->GetAmount();
        double amtB = chemicals[B]->GetAmount();
        double amtC = chemicals[C]->GetAmount();
        return rateConstants[k_t]->GetValue()*amtA*amtB*amtC;
}

void CTrimerFormation::SetTeXForm()
{
        strstream stream;
        // TeX form of the reaction
        stream << rateConstants[k_t]->GetTeXName().c_str();
        stream << "\\left [" << chemicals[A]->GetTeXName().c_str();
        stream << "\\right ]";
        stream << " \\left [" << chemicals[B]->GetTeXName().c_str();
        stream << "\\right ]";
        stream << " \\left  [" << chemicals[C]->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 *> *CTrimerFormation::GetChemicalJacobian()
{
        double rate = rateConstants[k_t]->GetValue();
        double amtA = chemicals[A]->GetAmount();
        double amtB = chemicals[B]->GetAmount();
        double amtC = chemicals[C]->GetAmount();
        chemicalJacobian[0]->SetWithRespectTo(chemicals[A]->GetChemicalNumber());
        chemicalJacobian[0]->SetJValue(rate*amtB*amtC);
        chemicalJacobian[1]->SetWithRespectTo(chemicals[B]->GetChemicalNumber());
        chemicalJacobian[1]->SetJValue(rate*amtA*amtC);
        chemicalJacobian[2]->SetWithRespectTo(chemicals[C]->GetChemicalNumber());
        chemicalJacobian[2]->SetJValue(rate*amtA*amtB);
        
        return &chemicalJacobian;
}

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