DeltaNotchOdeSystem.cpp

/*

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#include "DeltaNotchOdeSystem.hpp"
#include "CellwiseOdeSystemInformation.hpp"

DeltaNotchOdeSystem::DeltaNotchOdeSystem(std::vector<double> stateVariables)
    : AbstractOdeSystem(2)
{
    mpSystemInfo.reset(new CellwiseOdeSystemInformation<DeltaNotchOdeSystem>);

    SetDefaultInitialCondition(0, 1.0); // soon overwritten
    SetDefaultInitialCondition(1, 1.0); // soon overwritten

    this->mParameters.push_back(0.5);

    if (stateVariables != std::vector<double>())
    {
        SetStateVariables(stateVariables);
    }
}

DeltaNotchOdeSystem::~DeltaNotchOdeSystem()
{
}

void DeltaNotchOdeSystem::EvaluateYDerivatives(double time, const std::vector<double>& rY, std::vector<double>& rDY)
{
    double notch = rY[0];
    double delta = rY[1];
    double mean_delta = this->mParameters[0]; // Shorthand for "this->mParameter("Mean Delta");"

    // The next two lines define the ODE system by Collier et al. (1996)
    rDY[0] = mean_delta*mean_delta/(0.01 + mean_delta*mean_delta) - notch;  // d[Notch]/dt
    rDY[1] = 1.0/(1.0 + 100.0*notch*notch) - delta;                   // d[Delta]/dt
}

template<>
void CellwiseOdeSystemInformation<DeltaNotchOdeSystem>::Initialise()
{
    this->mVariableNames.push_back("Notch");
    this->mVariableUnits.push_back("non-dim");
    this->mInitialConditions.push_back(0.0); // will be filled in later

    this->mVariableNames.push_back("Delta");
    this->mVariableUnits.push_back("non-dim");
    this->mInitialConditions.push_back(0.0); // will be filled in later

    // If this is ever not the first parameter change the line
    // double mean_delta = this->mParameters[0]; in EvaluateYDerivatives().
    this->mParameterNames.push_back("Mean Delta");
    this->mParameterUnits.push_back("non-dim");

    this->mInitialised = true;
}

// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
CHASTE_CLASS_EXPORT(DeltaNotchOdeSystem)