AbstractBackwardEulerCardiacCell.hpp

/*

Copyright (C) University of Oxford, 2005-2011

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/>.

*/


#ifndef ABSTRACTBACKWARDEULERCARDIACCELL_HPP_
#define ABSTRACTBACKWARDEULERCARDIACCELL_HPP_

#include <cassert>
#include <cmath>

#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>
#include "ClassIsAbstract.hpp"

#include "AbstractCardiacCell.hpp"
#include "Exception.hpp"
#include "PetscTools.hpp"
#include "TimeStepper.hpp"

template<unsigned SIZE>
class AbstractBackwardEulerCardiacCell : public AbstractCardiacCell
{
    private:
    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        // This calls serialize on the base class.
        archive & boost::serialization::base_object<AbstractCardiacCell>(*this);
    }
public:

    AbstractBackwardEulerCardiacCell(
        unsigned numberOfStateVariables,
        unsigned voltageIndex,
        boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus);

    virtual ~AbstractBackwardEulerCardiacCell();

    virtual void ComputeResidual(double time, const double rCurrentGuess[SIZE], double rResidual[SIZE])=0;

    virtual void ComputeJacobian(double time, const double rCurrentGuess[SIZE], double rJacobian[SIZE][SIZE])=0;

    OdeSolution Compute(double tStart, double tEnd, double tSamp=0.0);

    void ComputeExceptVoltage(double tStart, double tEnd);

    void SolveAndUpdateState(double tStart, double tEnd);

private:
#define COVERAGE_IGNORE

    void EvaluateYDerivatives(double time, const std::vector<double> &rY, std::vector<double> &rDY)
    {
        NEVER_REACHED;
    }
#undef COVERAGE_IGNORE

protected:
    virtual void ComputeOneStepExceptVoltage(double tStart)=0;

    virtual void UpdateTransmembranePotential(double time)=0;
};


/*
 * NOTE: Explicit instantiation is not used for this class, because the SIZE
 * template parameter could take arbitrary values.
 */


template <unsigned SIZE>
AbstractBackwardEulerCardiacCell<SIZE>::AbstractBackwardEulerCardiacCell(
    unsigned numberOfStateVariables,
    unsigned voltageIndex,
    boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus)
        : AbstractCardiacCell(boost::shared_ptr<AbstractIvpOdeSolver>(),
                              numberOfStateVariables,
                              voltageIndex,
                              pIntracellularStimulus)
{}

template <unsigned SIZE>
AbstractBackwardEulerCardiacCell<SIZE>::~AbstractBackwardEulerCardiacCell()
{}

template <unsigned SIZE>
OdeSolution AbstractBackwardEulerCardiacCell<SIZE>::Compute(double tStart, double tEnd, double tSamp)
{
    // In this method, we iterate over timesteps, doing the following for each:
    //   - update V using a forward Euler step
    //   - call ComputeExceptVoltage(t) to update the remaining state variables
    //     using backward Euler

    // Check length of time interval
    if (tSamp < mDt)
    {
        tSamp = mDt;
    }
    double _n_steps = (tEnd - tStart) / tSamp;
    const unsigned n_steps = (unsigned) floor(_n_steps+0.5);
    assert(fabs(tStart+n_steps*tSamp - tEnd) < 1e-12);
    const unsigned n_small_steps = (unsigned) floor(tSamp/mDt+0.5);
    assert(fabs(mDt*n_small_steps - tSamp) < 1e-12);

    // Initialise solution store
    OdeSolution solutions;
    solutions.SetNumberOfTimeSteps(n_steps);
    solutions.rGetSolutions().push_back(rGetStateVariables());
    solutions.rGetTimes().push_back(tStart);
    solutions.SetOdeSystemInformation(this->mpSystemInfo);

    // Loop over time
    double curr_time = tStart;
    for (unsigned i=0; i<n_steps; i++)
    {
        for (unsigned j=0; j<n_small_steps; j++)
        {
            curr_time = tStart + i*tSamp + j*mDt;

            // Compute next value of V
            UpdateTransmembranePotential(curr_time);

            // Compute other state variables
            ComputeOneStepExceptVoltage(curr_time);

            // check gating variables are still in range
            VerifyStateVariables();
        }

        // Update solutions
        solutions.rGetSolutions().push_back(rGetStateVariables());
        solutions.rGetTimes().push_back(curr_time+mDt);
    }

    return solutions;
}

template <unsigned SIZE>
void AbstractBackwardEulerCardiacCell<SIZE>::ComputeExceptVoltage(double tStart, double tEnd)
{
    // This method iterates over timesteps, calling ComputeExceptVoltage(t) at
    // each one, to update all state variables except for V, using backward Euler.

    // Check length of time interval
    unsigned n_steps = (unsigned)((tEnd - tStart) / mDt + 0.5);
    assert(fabs(tStart + n_steps*mDt - tEnd) < 1e-12);

    // Loop over time
    double curr_time;
    for (unsigned i=0; i<n_steps; i++)
    {
        curr_time = tStart + i*mDt;

        // Compute other state variables
        ComputeOneStepExceptVoltage(curr_time);

#ifndef NDEBUG
        // Check gating variables are still in range
        VerifyStateVariables();
#endif // NDEBUG
    }
}

template<unsigned SIZE>
void AbstractBackwardEulerCardiacCell<SIZE>::SolveAndUpdateState(double tStart, double tEnd)
{
    TimeStepper stepper(tStart, tEnd, mDt);

    while(!stepper.IsTimeAtEnd())
    {
        double time = stepper.GetTime();

        // Compute next value of V
        UpdateTransmembranePotential(time);

        // Compute other state variables
        ComputeOneStepExceptVoltage(time);

        // check gating variables are still in range
        VerifyStateVariables();

        stepper.AdvanceOneTimeStep();
    }
}


TEMPLATED_CLASS_IS_ABSTRACT_1_UNSIGNED(AbstractBackwardEulerCardiacCell)

#endif /*ABSTRACTBACKWARDEULERCARDIACCELL_HPP_*/