AbstractCvodeCell.hpp

/*

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/>.

*/

#ifdef CHASTE_CVODE
#ifndef _ABSTRACTCVODECELL_HPP_
#define _ABSTRACTCVODECELL_HPP_

#include <vector>
#include <string>
#include <boost/shared_ptr.hpp>

// Chaste headers
#include "OdeSolution.hpp"
#include "AbstractOdeSystemInformation.hpp"
#include "AbstractStimulusFunction.hpp"
#include "AbstractIvpOdeSolver.hpp"

// CVODE headers
#include <nvector/nvector_serial.h>

class AbstractCvodeCell
{
protected:
    unsigned mNumberOfStateVariables;
    unsigned mVoltageIndex;
    N_Vector mStateVariables;

    boost::shared_ptr<AbstractOdeSystemInformation> mpSystemInfo;

    boost::shared_ptr<AbstractStimulusFunction> mpIntracellularStimulus;

    double mRelTol;
    double mAbsTol;

    void* mpCvodeMem;
    long int mMaxSteps;

    double mLastInternalStepSize;

    bool mSetVoltageDerivativeToZero;

    std::string DumpState(const std::string& message,
                          N_Vector Y = NULL);

    void Init();

    N_Vector CopyVector(N_Vector originalVec);

public:
    AbstractCvodeCell(boost::shared_ptr<AbstractIvpOdeSolver> /* unused; should be empty */,
                      unsigned numberOfStateVariables,
                      unsigned voltageIndex,
                      boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus);

    virtual ~AbstractCvodeCell();

    unsigned GetVoltageIndex();

    double GetVoltage();

    void SetVoltage(double voltage);

    void SetStimulusFunction(boost::shared_ptr<AbstractStimulusFunction> pStimulus);

    double GetStimulus(double time);

    unsigned GetNumberOfStateVariables();

    const std::vector<std::string>& rGetVariableNames() const;

    const std::vector<std::string>& rGetVariableUnits() const;

    unsigned GetStateVariableNumberByName(const std::string name) const;

    double GetStateVariableValueByNumber(unsigned varNumber) const;

    std::string GetStateVariableUnitsByNumber(unsigned varNumber) const;

    boost::shared_ptr<const AbstractOdeSystemInformation> GetSystemInformation() const;

    N_Vector GetInitialConditions();

    void SetStateVariables(N_Vector stateVars);

    void SetStateVariablesUsingACopyOfThisVector(N_Vector stateVars);

    N_Vector GetStateVariables();

    N_Vector rGetStateVariables();

    virtual void EvaluateRhs(realtype t,
                             N_Vector y,
                             N_Vector ydot)=0;

    virtual void VerifyStateVariables()
    {
    }

    //
    // Solver methods
    //

    void SetVoltageDerivativeToZero(bool clamp=true);

    OdeSolution Solve(realtype tStart,
                      realtype tEnd,
                      realtype maxDt,
                      realtype tSamp);

    void Solve(realtype tStart,
               realtype tEnd,
               realtype maxDt);

    void SetMaxSteps(long int numSteps);

    long int GetMaxSteps();

    void SetTolerances(double relTol=1e-4, double absTol=1e-6);

    double GetRelativeTolerance();

    double GetAbsoluteTolerance();

    double GetLastStepSize();

private:

    void SetupCvode(N_Vector initialConditions,
                    realtype tStart,
                    realtype maxDt);

    void FreeCvodeMemory();

    void CvodeError(int flag, const char * msg);

    std::vector<double> MakeStdVec(N_Vector v);

};


#endif // _ABSTRACTCVODECELL_HPP_
#endif // CHASTE_CVODE