AbstractCvodeSystem.cpp

/*

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*/

#ifdef CHASTE_CVODE

#include <sstream>
#include <cassert>

#include "AbstractCvodeSystem.hpp"
#include "Exception.hpp"
#include "VectorHelperFunctions.hpp"
#include "MathsCustomFunctions.hpp" // For tolerance comparison
#include "TimeStepper.hpp"
#include "CvodeAdaptor.hpp" // For CvodeErrorHandler

// CVODE headers
#include <cvode/cvode.h>
#include <sundials/sundials_nvector.h>
#include <cvode/cvode_dense.h>


int AbstractCvodeSystemRhsAdaptor(realtype t, N_Vector y, N_Vector ydot, void *pData)
{
    assert(pData != NULL);
    AbstractCvodeSystem* p_ode_system = (AbstractCvodeSystem*) pData;
    try
    {
        p_ode_system->EvaluateYDerivatives(t, y, ydot);
    }
    catch (const Exception &e)
    {
        std::cerr << "CVODE RHS Exception: " << e.GetMessage()
                  << std::endl << std::flush;
        return -1;
    }
    return 0;
}

AbstractCvodeSystem::AbstractCvodeSystem(unsigned numberOfStateVariables)
    : AbstractParameterisedSystem<N_Vector>(numberOfStateVariables),
      mLastSolutionState(NULL),
      mLastSolutionTime(0.0),
      mAutoReset(true),
      mForceMinimalReset(false),
      mUseAnalyticJacobian(false),
      mpCvodeMem(NULL),
      mMaxSteps(0),
      mLastInternalStepSize(0)
{
    SetTolerances(); // Set the tolerances to the defaults.
}

void AbstractCvodeSystem::Init()
{
    DeleteVector(mStateVariables);
    mStateVariables = GetInitialConditions();
    DeleteVector(mParameters);
    mParameters = N_VNew_Serial(rGetParameterNames().size());
    for (int i=0; i<NV_LENGTH_S(mParameters); i++)
    {
        NV_Ith_S(mParameters, i) = 0.0;
    }
}

AbstractCvodeSystem::~AbstractCvodeSystem()
{
    FreeCvodeMemory();
    DeleteVector(mStateVariables);
    DeleteVector(mParameters);
    DeleteVector(mLastSolutionState);
}

//
//double AbstractCvodeSystem::CalculateRootFunction(double time, const std::vector<double>& rY)
//{
//    bool stop = CalculateStoppingEvent(time, rY);
//    return stop ? 0.0 : 1.0;
//}
//
//bool AbstractCvodeSystem::GetUseAnalyticJacobian()
//{
//    return mUseAnalyticJacobian;
//}



OdeSolution AbstractCvodeSystem::Solve(realtype tStart,
                                       realtype tEnd,
                                       realtype maxDt,
                                       realtype tSamp)
{
    assert(tEnd >= tStart);
    assert(tSamp > 0.0);

    SetupCvode(mStateVariables, tStart, maxDt);

    TimeStepper stepper(tStart, tEnd, tSamp);

    // Set up ODE solution
    OdeSolution solutions;
    solutions.SetNumberOfTimeSteps(stepper.EstimateTimeSteps());
    solutions.rGetSolutions().push_back(MakeStdVec(mStateVariables));
    solutions.rGetTimes().push_back(tStart);
    solutions.SetOdeSystemInformation(mpSystemInfo);

    // Main time sampling loop
    while (!stepper.IsTimeAtEnd())
    {
        double cvode_stopped_at;
        int ierr = CVode(mpCvodeMem, stepper.GetNextTime(), mStateVariables,
                         &cvode_stopped_at, CV_NORMAL);
        if (ierr<0)
        {
            FreeCvodeMemory();
            CvodeError(ierr, "CVODE failed to solve system");
        }
        // Not root finding, so should have reached requested time
        assert(fabs(cvode_stopped_at - stepper.GetNextTime()) < DBL_EPSILON);

        VerifyStateVariables();

        // Store solution
        solutions.rGetSolutions().push_back(MakeStdVec(mStateVariables));
        solutions.rGetTimes().push_back(cvode_stopped_at);
        stepper.AdvanceOneTimeStep();
    }

    // stepper.EstimateTimeSteps may have been an overestimate...
    solutions.SetNumberOfTimeSteps(stepper.GetTotalTimeStepsTaken());

    int ierr = CVodeGetLastStep(mpCvodeMem, &mLastInternalStepSize);
    assert(ierr == CV_SUCCESS); ierr=ierr; // avoid unused var warning

    RecordStoppingPoint(tEnd);

    return solutions;
}

void AbstractCvodeSystem::Solve(realtype tStart,
                                realtype tEnd,
                                realtype maxDt)
{
    assert(tEnd >= tStart);

    SetupCvode(mStateVariables, tStart, maxDt);

    double cvode_stopped_at;
    int ierr = CVode(mpCvodeMem, tEnd, mStateVariables, &cvode_stopped_at, CV_NORMAL);
    if (ierr<0)
    {
        FreeCvodeMemory();
        CvodeError(ierr, "CVODE failed to solve system");
    }
    // Not root finding, so should have reached requested time
    assert(fabs(cvode_stopped_at - tEnd) < DBL_EPSILON);

    ierr = CVodeGetLastStep(mpCvodeMem, &mLastInternalStepSize);
    assert(ierr == CV_SUCCESS); ierr=ierr; // avoid unused var warning

    RecordStoppingPoint(cvode_stopped_at);

    VerifyStateVariables();
}


void AbstractCvodeSystem::SetMaxSteps(long int numSteps)
{
    mMaxSteps = numSteps;
}

long int AbstractCvodeSystem::GetMaxSteps()
{
    return mMaxSteps;
}

void AbstractCvodeSystem::SetTolerances(double relTol, double absTol)
{
    mRelTol = relTol;
    mAbsTol = absTol;
    ResetSolver();
}

double AbstractCvodeSystem::GetRelativeTolerance()
{
    return mRelTol;
}

double AbstractCvodeSystem::GetAbsoluteTolerance()
{
    return mAbsTol;
}

double AbstractCvodeSystem::GetLastStepSize()
{
    return mLastInternalStepSize;
}

void AbstractCvodeSystem::SetAutoReset(bool autoReset)
{
    mAutoReset = autoReset;
    if (mAutoReset)
    {
        ResetSolver();
    }
}

void AbstractCvodeSystem::SetMinimalReset(bool minimalReset)
{
    mForceMinimalReset = minimalReset;
    if (mForceMinimalReset)
    {
        SetAutoReset(false);
    }
}


void AbstractCvodeSystem::ResetSolver()
{
    DeleteVector(mLastSolutionState);
}


void AbstractCvodeSystem::SetupCvode(N_Vector initialConditions,
                                     realtype tStart,
                                     realtype maxDt)
{
    assert((unsigned)NV_LENGTH_S(initialConditions) == GetNumberOfStateVariables());
    assert(maxDt >= 0.0);

    // Find out if we need to (re-)initialise
    //std::cout << "!mpCvodeMem = " << !mpCvodeMem << ", mAutoReset = " << mAutoReset << ", !mLastSolutionState = " << !mLastSolutionState << ", comp doubles = " << !CompareDoubles::WithinAnyTolerance(tStart, mLastSolutionTime) << "\n";
    bool reinit = !mpCvodeMem || mAutoReset || !mLastSolutionState || !CompareDoubles::WithinAnyTolerance(tStart, mLastSolutionTime);
    if (!reinit && !mForceMinimalReset)
    {
        const unsigned size = GetNumberOfStateVariables();
        for (unsigned i=0; i<size; i++)
        {
            if (!CompareDoubles::WithinAnyTolerance(GetVectorComponent(mLastSolutionState, i), GetVectorComponent(mStateVariables, i)))
            {
                reinit = true;
                break;
            }
        }
    }

    if (!mpCvodeMem)
    {
        mpCvodeMem = CVodeCreate(CV_BDF, CV_NEWTON);
        if (mpCvodeMem == NULL) EXCEPTION("Failed to SetupCvode CVODE"); // in one line to avoid coverage problem!

        // Set error handler
        CVodeSetErrHandlerFn(mpCvodeMem, CvodeErrorHandler, NULL);
        // Set the user data
#if CHASTE_SUNDIALS_VERSION >= 20400
        CVodeSetUserData(mpCvodeMem, (void*)(this));
#else
        CVodeSetFdata(mpCvodeMem, (void*)(this));
#endif
        // Setup CVODE
#if CHASTE_SUNDIALS_VERSION >= 20400
        CVodeInit(mpCvodeMem, AbstractCvodeSystemRhsAdaptor, tStart, initialConditions);
        CVodeSStolerances(mpCvodeMem, mRelTol, mAbsTol);
#else
        CVodeMalloc(mpCvodeMem, AbstractCvodeSystemRhsAdaptor, tStart, initialConditions,
                    CV_SS, mRelTol, &mAbsTol);
#endif
        // Attach a linear solver for Newton iteration
        CVDense(mpCvodeMem, NV_LENGTH_S(initialConditions));
    }
    else if (reinit)
    {
#if CHASTE_SUNDIALS_VERSION >= 20400
        CVodeReInit(mpCvodeMem, tStart, initialConditions);
        CVodeSStolerances(mpCvodeMem, mRelTol, mAbsTol);
#else
        CVodeReInit(mpCvodeMem, AbstractCvodeSystemRhsAdaptor, tStart, initialConditions,
                    CV_SS, mRelTol, &mAbsTol);
#endif
    }

    // Set max dt and change max steps if wanted
    CVodeSetMaxStep(mpCvodeMem, maxDt);
    if (mMaxSteps > 0)
    {
        CVodeSetMaxNumSteps(mpCvodeMem, mMaxSteps);
        CVodeSetMaxErrTestFails(mpCvodeMem, 15);
    }
}


void AbstractCvodeSystem::RecordStoppingPoint(double stopTime)
{
    if (!mAutoReset)
    {
        const unsigned size = GetNumberOfStateVariables();
        CreateVectorIfEmpty(mLastSolutionState, size);
        for (unsigned i=0; i<size; i++)
        {
            SetVectorComponent(mLastSolutionState, i, GetVectorComponent(mStateVariables, i));
        }
        mLastSolutionTime = stopTime;
    }
}


void AbstractCvodeSystem::FreeCvodeMemory()
{
    if (mpCvodeMem)
    {
        CVodeFree(&mpCvodeMem);
    }
    mpCvodeMem = NULL;
}


void AbstractCvodeSystem::CvodeError(int flag, const char * msg)
{

    std::stringstream err;
    char* p_flag_name = CVodeGetReturnFlagName(flag);
    err << msg << ": " << p_flag_name;
    free(p_flag_name);
    std::cerr << err.str() << std::endl << std::flush;
    EXCEPTION(err.str());
}


#endif // CHASTE_CVODE