AbstractCardiacCell.cpp

/*

Copyright (C) University of Oxford, 2005-2010

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/
#include "AbstractCardiacCell.hpp"

#include <cassert>
#include <iostream>

AbstractCardiacCell::AbstractCardiacCell(boost::shared_ptr<AbstractIvpOdeSolver> pOdeSolver,
                                         unsigned numberOfStateVariables,
                                         unsigned voltageIndex,
                                         boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus)
    : AbstractOdeSystem(numberOfStateVariables),
      mVoltageIndex(voltageIndex),
      mpOdeSolver(pOdeSolver),
      mDt(HeartConfig::Instance()->GetOdeTimeStep()),
      mpIntracellularStimulus(pIntracellularStimulus),
      mSetVoltageDerivativeToZero(false)
{
    // The second clause is to allow for FakeBathCell.
    assert(voltageIndex < mNumberOfStateVariables || mNumberOfStateVariables == 0);
}

AbstractCardiacCell::~AbstractCardiacCell()
{
}

void AbstractCardiacCell::Init()
{
    SetStateVariables(GetInitialConditions());
}


OdeSolution AbstractCardiacCell::Compute(double tStart, double tEnd)
{
    return mpOdeSolver->Solve(this, rGetStateVariables(), tStart, tEnd, mDt, mDt);
}


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

    mSetVoltageDerivativeToZero = true;
    mpOdeSolver->SolveAndUpdateStateVariable(this, tStart, tEnd, mDt);
    mSetVoltageDerivativeToZero = false;

    SetVoltage(saved_voltage);

    VerifyStateVariables();
}

void AbstractCardiacCell::SetVoltage(double voltage)
{
    rGetStateVariables()[mVoltageIndex] = voltage;
}

double AbstractCardiacCell::GetVoltage()
{
    return rGetStateVariables()[mVoltageIndex];
}

unsigned AbstractCardiacCell::GetVoltageIndex()
{
    return mVoltageIndex;
}

void AbstractCardiacCell::SetStimulusFunction(boost::shared_ptr<AbstractStimulusFunction> pStimulus)
{
    SetIntracellularStimulusFunction(pStimulus);
}

double AbstractCardiacCell::GetStimulus(double time)
{
    return GetIntracellularStimulus(time);
}

void AbstractCardiacCell::SetIntracellularStimulusFunction(boost::shared_ptr<AbstractStimulusFunction> pStimulus)
{
    mpIntracellularStimulus = pStimulus;
}

double AbstractCardiacCell::GetIntracellularStimulus(double time)
{
    return mpIntracellularStimulus->GetStimulus(time);
}


double AbstractCardiacCell::GetIntracellularCalciumConcentration()
{
    EXCEPTION("AbstractCardiacCell::GetIntracellularCalciumConcentration() called. Either model has no [Ca_i] or method has not been implemented yet");
}


/*
 *  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.");
}

// Methods needed by boost serialization.

const boost::shared_ptr<AbstractStimulusFunction> AbstractCardiacCell::GetStimulusFunction() const
{
    return mpIntracellularStimulus;
}

const boost::shared_ptr<AbstractIvpOdeSolver> AbstractCardiacCell::GetSolver() const
{
    return mpOdeSolver;
}