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CombinatorialRunDirector.cpp

Go to the documentation of this file.

// CombinatorialRunDirector.cpp: implementation of the CCombinatorialRunDirector class.
//

#include "CombinatorialRunDirector.h"

// Construction/Destruction

CCombinatorialRunDirector::CCombinatorialRunDirector()
{
        double maxSimTime = 720.0;
        int intTime = (int) maxSimTime + 2;
        double stepSize = 0.001;
        double frequency = 0.1;
        double moveTol = 1.0e-06;
        int seed = 298989;

        m_vpRxnNetworks.push_back(new CCombinatorialNetwork());
//      m_vpRxnNetworks[0]->DumpTeXForm("CombinatorialEquations.tex");
        m_vpRxnMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
//      m_vpRxnMovers.push_back(new CQualityControlRK2TMover(frequency,stepSize,moveTol));
//      m_vpRxnMovers.push_back(new CContinuousTimeMonteCarloMover(seed,frequency));
        int nChemicals = m_vpRxnNetworks[0]->GetNumberOfChemicals();
        m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1));
        m_vpRunnables.push_back(new CRunnable());
        m_vpRunnables[0]->SetComponents(m_vpRxnNetworks[0],m_vpRxnMovers[0],m_vpCellObservers[0]);

        // create an observer for the runnable
        m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver());
        m_vpGnuPlotters[0]->AddChemicalNumberToList(0);
        m_vpGnuPlotters[0]->AddChemicalNumberToList(1);
        m_vpGnuPlotters[0]->AddChemicalNumberToList(2);
        m_vpGnuPlotters[0]->AddChemicalNumberToList(3);
        m_vpGnuPlotters[0]->AddChemicalNumberToList(4);
        m_vpGnuPlotters[0]->AddChemicalNumberToList(5);

        m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver());
        m_vpGnuPlotters[1]->AddChemicalNumberToList(6);
        m_vpGnuPlotters[1]->AddChemicalNumberToList(7);
        m_vpGnuPlotters[1]->AddChemicalNumberToList(8);
        m_vpGnuPlotters[1]->AddChemicalNumberToList(9);
        m_vpGnuPlotters[1]->AddChemicalNumberToList(10);

        m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver());
        m_vpGnuPlotters[2]->AddChemicalNumberToList(11);
        m_vpGnuPlotters[2]->AddChemicalNumberToList(12);
        m_vpGnuPlotters[2]->AddChemicalNumberToList(13);
        m_vpGnuPlotters[2]->AddChemicalNumberToList(14);
        m_vpGnuPlotters[2]->AddChemicalNumberToList(15);

        // attach the observer
        m_vpRunnables[0]->Attach(m_vpGnuPlotters[0]);
        m_vpRunnables[0]->Attach(m_vpGnuPlotters[1]);
        m_vpRunnables[0]->Attach(m_vpGnuPlotters[2]);

        // define runs
        DefineRuns();

}

CCombinatorialRunDirector::~CCombinatorialRunDirector()
{

}

void CCombinatorialRunDirector::DefineRuns()
{
        // set parameters in the runnables to those read from a previous
        // optimization pass; assumes all runnables have same number of 
        // rate constants

        ParameterReader *pReader = new ParameterReader("CombinatorialInput.par");
        int nRC = m_vpRunnables[0]->GetReactionNetwork()->GetNumberOfRateConstants();
        for(int j = 0; j < nRC; j++)
        {
                double rate = pReader->ReadParameter();
                for(int i = 0; i < m_vpRunnables.size(); i++)
                {
                        m_vpRunnables[i]->GetReactionNetwork()->GetRateConstant(j)->SetRateConstant(rate);
                }
        }
        delete pReader;


        // specific to this simulation
        // Strain D016
        m_vpRunnables[0]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.0);
        m_vpRunnables[0]->GetReactionNetwork()->GetChemical(1)->SetInitialAmount(1.0);
        m_vpRunnables[0]->GetReactionNetwork()->RemoveReaction(44);
        m_vpRunnables[0]->GetReactionNetwork()->RemoveReaction(43);
        m_vpRunnables[0]->GetReactionNetwork()->RemoveReaction(42);
        m_vpRunnables[0]->GetReactionNetwork()->RemoveReaction(41);
        m_vpRunnables[0]->GetReactionNetwork()->RemoveReaction(40);
        m_vpRunnables[0]->GetReactionNetwork()->RemoveReaction(39);
        m_vpRunnables[0]->GetReactionNetwork()->RemoveReaction(38);
        m_vpRunnables[0]->GetReactionNetwork()->RemoveReaction(37);
        m_vpRunnables[0]->GetReactionNetwork()->RemoveReaction(36);
        m_vpRunnables[0]->GetReactionNetwork()->RemoveReaction(35);
        m_vpRunnables[0]->GetReactionNetwork()->RemoveReaction(34);
        m_vpRunnables[0]->GetReactionNetwork()->RemoveReaction(33);
        m_vpRunnables[0]->GetReactionNetwork()->RemoveReaction(30);
        m_vpRunnables[0]->GetReactionNetwork()->RemoveReaction(29);
        m_vpRunnables[0]->GetReactionNetwork()->RemoveReaction(28);
        m_vpRunnables[0]->GetReactionNetwork()->RemoveReaction(27);
        m_vpRunnables[0]->GetReactionNetwork()->RemoveReaction(26);
        m_vpRunnables[0]->GetReactionNetwork()->RemoveReaction(25);
        m_vpRunnables[0]->GetReactionNetwork()->RemoveReaction(22);
        m_vpRunnables[0]->GetReactionNetwork()->RemoveReaction(21);
        m_vpRunnables[0]->GetReactionNetwork()->RemoveReaction(20);
        m_vpRunnables[0]->GetReactionNetwork()->RemoveReaction(19);
        m_vpRunnables[0]->GetReactionNetwork()->RemoveReaction(18);
        m_vpRunnables[0]->GetReactionNetwork()->RemoveReaction(17);
        m_vpRunnables[0]->GetReactionNetwork()->RemoveReaction(16);
        m_vpRunnables[0]->GetReactionNetwork()->RemoveReaction(14);
        m_vpRunnables[0]->GetReactionNetwork()->RemoveReaction(12);

        m_vpRunnables[0]->GetReactionNetwork()->ChemicalReset();
        m_vpGnuPlotters[0]->SetTitle("CombinatorialNetwork");


}

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