AbstractCardiacCell.cpp

/*
 
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This file is part of Chaste.
 
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 * Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.
 * Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
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   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.
 
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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*/
#include "AbstractCardiacCell.hpp"
 
#include <cassert>
#include <iostream>
 
#include "HeartConfig.hpp"
#include "Exception.hpp"
 
AbstractCardiacCell::AbstractCardiacCell(boost::shared_ptr<AbstractIvpOdeSolver> pOdeSolver,
                                         unsigned numberOfStateVariables,
                                         unsigned voltageIndex,
                                         boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus)
    : AbstractCardiacCellInterface(pOdeSolver, voltageIndex, pIntracellularStimulus),
      AbstractOdeSystem(numberOfStateVariables),
      mDt(HeartConfig::Instance()->GetOdeTimeStep())
{
    // The second clause is to allow for FakeBathCell.
    assert(voltageIndex < mNumberOfStateVariables || mNumberOfStateVariables == 0);
}
 
AbstractCardiacCell::~AbstractCardiacCell()
{
}
 
void AbstractCardiacCell::Init()
{
    ResetToInitialConditions();
    mParameters.resize(rGetParameterNames().size());
}
 
void AbstractCardiacCell::SetTimestep(double dt)
{
    mDt = dt;
}
 
void AbstractCardiacCell::SolveAndUpdateState(double tStart, double tEnd)
{
    mpOdeSolver->SolveAndUpdateStateVariable(this, tStart, tEnd, mDt);
}
 
OdeSolution AbstractCardiacCell::Compute(double tStart, double tEnd, double tSamp)
{
    if (tSamp < mDt)
    {
        tSamp = mDt;
    }
    OdeSolution solution = mpOdeSolver->Solve(this, rGetStateVariables(), tStart, tEnd, mDt, tSamp);
#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
    return solution;
}
 
void AbstractCardiacCell::ComputeExceptVoltage(double tStart, double tEnd)
{
    double saved_voltage = GetVoltage();
 
    SetVoltageDerivativeToZero(true);
    mpOdeSolver->SolveAndUpdateStateVariable(this, tStart, tEnd, mDt);
    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 AbstractCardiacCell::SetVoltage(double voltage)
{
    SetAnyVariable(mVoltageIndex, voltage);
    SetFixedVoltage(voltage);
}
 
double AbstractCardiacCell::GetVoltage()
{
    return AbstractOdeSystem::GetAnyVariable(mVoltageIndex);
}
 
unsigned AbstractCardiacCell::GetNumberOfStateVariables() const
{
    return AbstractOdeSystem::GetNumberOfStateVariables();
}
 
unsigned AbstractCardiacCell::GetNumberOfParameters() const
{
    return AbstractOdeSystem::GetNumberOfParameters();
}
 
std::vector<double> AbstractCardiacCell::GetStdVecStateVariables()
{
    return AbstractOdeSystem::GetStateVariables();
}
 
const std::vector<std::string>& AbstractCardiacCell::rGetStateVariableNames() const
{
    return AbstractOdeSystem::rGetStateVariableNames();
}
 
void AbstractCardiacCell::SetStateVariables(const std::vector<double>& rVariables)
{
    AbstractOdeSystem::SetStateVariables(rVariables);
}
 
void AbstractCardiacCell::SetStateVariable(unsigned index, double newValue)
{
    AbstractOdeSystem::SetStateVariable(index, newValue);
}
 
void AbstractCardiacCell::SetStateVariable(const std::string& rName, double newValue)
{
    AbstractOdeSystem::SetStateVariable(rName, newValue);
}
 
double AbstractCardiacCell::GetAnyVariable(const std::string& rName, double time)
{
    return AbstractOdeSystem::GetAnyVariable(rName, time);
}
 
double AbstractCardiacCell::GetParameter(const std::string& rParameterName)
{
    return AbstractOdeSystem::GetParameter(rParameterName);
}
 
double AbstractCardiacCell::GetParameter(unsigned parameterIndex)
{
    return AbstractOdeSystem::GetParameter(parameterIndex);
}
 
void AbstractCardiacCell::SetParameter(const std::string& rParameterName, double value)
{
    AbstractOdeSystem::SetParameter(rParameterName,value);
}
 
#include "LuoRudy1991.hpp"
#include "LuoRudy1991BackwardEuler.hpp"
void AbstractCardiacCell::CheckForArchiveFix()
{
    if (dynamic_cast<CellLuoRudy1991FromCellML*>(this) || dynamic_cast<CellLuoRudy1991FromCellMLBackwardEuler*>(this))
    {
        // If you do reach this, then you can try un-commenting the below, but you would be better re-generating your archive with a new version of Chaste.
        NEVER_REACHED;
//        // The LR91 model saved in previous Chaste versions had a different ordering of state variables...
//        // Old is h, j, m, CaI, V, d, f, x
//        // New is V, m, h, j, d, f, X, [Ca]
//        assert(GetNumberOfStateVariables() == 8);
//        unsigned var_index_map[8] = {2, 3, 1, 7, 0, 4, 5, 6};
//        std::vector<double> old_state(this->mStateVariables);
//        for (unsigned i=0; i<8; i++)
//        {
//            this->mStateVariables[var_index_map[i]] = old_state[i];
//        }
//        // It also didn't used to have parameters...
//        this->mParameters.resize(this->rGetParameterNames().size());
//        assert(this->mParameters.size() == 3u);
//        this->mParameters[0] = 0.09;
//        this->mParameters[1] = 23.0;
//        this->mParameters[2] = 0.282;
    }
}
 
 
/*
 *  METHODS NEEDED BY FAST CARDIAC CELLS
 */
void AbstractCardiacCell::SetState(CellModelState state)
{
    EXCEPTION("Non fast-slow cell model being used in a fast-slow problem.");
}
 
void AbstractCardiacCell::SetSlowValues(const std::vector<double> &rSlowValues)
{
    EXCEPTION("Non fast-slow cell model being used in a fast-slow problem.");
}
 
void AbstractCardiacCell::GetSlowValues(std::vector<double>& rSlowValues)
{
    EXCEPTION("Non fast-slow cell model being used in a fast-slow problem.");
}
 
bool AbstractCardiacCell::IsFastOnly()
{
    EXCEPTION("Non fast-slow cell model being used in a fast-slow problem.");
}
 
unsigned AbstractCardiacCell::GetNumSlowValues()
{
    EXCEPTION("Non fast-slow cell model being used in a fast-slow problem.");
}
 
void AbstractCardiacCell::AdjustOutOfRangeSlowValues(std::vector<double>& rSlowValues)
{
    EXCEPTION("Non fast-slow cell model being used in a fast-slow problem.");
}