AbstractCvodeCell.cpp

/*

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*/

#ifdef CHASTE_CVODE

#include <sstream>
#include <iostream>
#include <cmath>

#include "AbstractCvodeCell.hpp"
#include "Exception.hpp"
#include "HeartConfig.hpp"
#include "VectorHelperFunctions.hpp"


AbstractCvodeCell::AbstractCvodeCell(boost::shared_ptr<AbstractIvpOdeSolver> /* unused */,
                                     unsigned numberOfStateVariables,
                                     unsigned voltageIndex,
                                     boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus)
    : AbstractCardiacCellInterface(boost::shared_ptr<AbstractIvpOdeSolver>(), voltageIndex, pIntracellularStimulus),
      AbstractCvodeSystem(numberOfStateVariables),
      mMaxDt(DOUBLE_UNSET)
{
}


AbstractCvodeCell::~AbstractCvodeCell()
{
}

double AbstractCvodeCell::GetVoltage()
{
    assert(mStateVariables);
    return AbstractCvodeSystem::GetAnyVariable(mVoltageIndex);
}

void AbstractCvodeCell::SetVoltage(double voltage)
{
    assert(mStateVariables);
    SetAnyVariable(mVoltageIndex, voltage);
    SetFixedVoltage(voltage);
}


void AbstractCvodeCell::SetMaxTimestep(double maxDt)
{
    SetTimestep(maxDt); // Note: SetTimestep() sets the maximum timestep.
}

void AbstractCvodeCell::SetTimestep(double maxDt)
{
    mMaxDt = maxDt;
}

double AbstractCvodeCell::GetTimestep()
{
    return mMaxDt;
}


void AbstractCvodeCell::SolveAndUpdateState(double tStart, double tEnd)
{
    if (mMaxDt == DOUBLE_UNSET)
    {
        SetTimestep(HeartConfig::Instance()->GetPrintingTimeStep());
    }
    Solve(tStart, tEnd, mMaxDt);
}

OdeSolution AbstractCvodeCell::Compute(double tStart, double tEnd, double tSamp)
{
    if (tSamp == 0.0)
    {
        tSamp = HeartConfig::Instance()->GetPrintingTimeStep();
    }
    if (mMaxDt == DOUBLE_UNSET)
    {
        SetTimestep(tSamp);
    }
    return Solve(tStart, tEnd, mMaxDt, tSamp);
}


void AbstractCvodeCell::ComputeExceptVoltage(double tStart, double tEnd)
{
    double saved_voltage = GetVoltage();

    AbstractCardiacCellInterface::SetVoltageDerivativeToZero(true);
    SolveAndUpdateState(tStart, tEnd);
    AbstractCardiacCellInterface::SetVoltageDerivativeToZero(false);

    SetVoltage(saved_voltage); // In case of naughty models

#ifndef NDEBUG
    // Note that tests which rely on this throwing  (e.g. such-and-such a variable is out of range)
    // ought to be annotated with the NDEBUG macro
    VerifyStateVariables();
#endif // NDEBUG
}


void AbstractCvodeCell::SetVoltageDerivativeToZero(bool clamp)
{
    if (clamp != mSetVoltageDerivativeToZero)
    {
        ResetSolver();
    }
    AbstractCardiacCellInterface::SetVoltageDerivativeToZero(clamp);
}

unsigned AbstractCvodeCell::GetNumberOfStateVariables() const
{
    return AbstractCvodeSystem::GetNumberOfStateVariables();
}

unsigned AbstractCvodeCell::GetNumberOfParameters() const
{
    return AbstractCvodeSystem::GetNumberOfParameters();
}

std::vector<double> AbstractCvodeCell::GetStdVecStateVariables()
{
    std::vector<double> state_variables(GetNumberOfStateVariables());
    CopyToStdVector(AbstractCvodeSystem::rGetStateVariables(), state_variables);
    return state_variables;
}

const std::vector<std::string>& AbstractCvodeCell::rGetStateVariableNames() const
{
    return AbstractCvodeSystem::rGetStateVariableNames();
}

void AbstractCvodeCell::SetStateVariables(const std::vector<double>& rVariables)
{
    N_Vector vars = MakeNVector(rVariables);
    AbstractCvodeSystem::SetStateVariables(vars);
    DeleteVector(vars);
}

void AbstractCvodeCell::SetStateVariables(const N_Vector& rVariables)
{
    AbstractCvodeSystem::SetStateVariables(rVariables);
}

void AbstractCvodeCell::SetStateVariable(unsigned index, double newValue)
{
    AbstractCvodeSystem::SetStateVariable(index, newValue);
}

void AbstractCvodeCell::SetStateVariable(const std::string& rName, double newValue)
{
    AbstractCvodeSystem::SetStateVariable(rName, newValue);
}

double AbstractCvodeCell::GetAnyVariable(const std::string& rName, double time)
{
    return AbstractCvodeSystem::GetAnyVariable(rName,time);
}

double AbstractCvodeCell::GetParameter(const std::string& rParameterName)
{
    return AbstractCvodeSystem::GetParameter(rParameterName);
}

double AbstractCvodeCell::GetParameter(unsigned parameterIndex)
{
    return AbstractCvodeSystem::GetParameter(parameterIndex);
}

void AbstractCvodeCell::SetParameter(const std::string& rParameterName, double value)
{
    AbstractCvodeSystem::SetParameter(rParameterName,value);
}

#endif // CHASTE_CVODE