CvodeAdaptor.cpp

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#ifdef CHASTE_CVODE

#include "CvodeAdaptor.hpp"

#include "Exception.hpp"
#include "TimeStepper.hpp"
#include "VectorHelperFunctions.hpp"
#include "MathsCustomFunctions.hpp" // For tolerance check.

#include <iostream>
#include <sstream>

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


int CvodeRhsAdaptor(realtype t, N_Vector y, N_Vector ydot, void* pData)
{
    assert(pData != NULL);
    CvodeData* p_data = (CvodeData*) pData;
    // Get y, ydot into std::vector<>s
    static std::vector<realtype> ydot_vec;
    CopyToStdVector(y, *p_data->pY);
    CopyToStdVector(ydot, ydot_vec);
    // Call our function
    try
    {
        p_data->pSystem->EvaluateYDerivatives(t, *(p_data->pY), ydot_vec);
    }
    catch (const Exception &e)
    {
        std::cerr << "CVODE RHS Exception: " << e.GetMessage() << std::endl << std::flush;
        return -1;
    }
    // Copy derivative back
    CopyFromStdVector(ydot_vec, ydot);
    return 0;
}

int CvodeRootAdaptor(realtype t, N_Vector y, realtype* pGOut, void* pData)
{
    assert(pData != NULL);
    CvodeData* p_data = (CvodeData*) pData;
    // Get y into a std::vector
    CopyToStdVector(y, *p_data->pY);
    // Call our function
    try
    {
        *pGOut = p_data->pSystem->CalculateRootFunction(t, *p_data->pY);
    }
    catch (const Exception &e)
    {
        std::cerr << "CVODE Root Exception: " << e.GetMessage() << std::endl << std::flush;
        return -1;
    }
    return 0;
}

// /**
//  * Jacobian computation adaptor function.
//  *
//  * If solving an AbstractOdeSystemWithAnalyticJacobian, this function
//  * can be used to allow CVODE to compute the Jacobian analytically.
//  *
//  * Note to self: can test using pSystem->GetUseAnalyticJacobian().
//  */
// int CvodeDenseJacobianAdaptor(long int numberOfStateVariables, DenseMat J,
//                               realtype t, N_Vector y, N_Vector fy,
//                               void* pData,
//                               N_Vector tmp1, N_Vector tmp2, N_Vector tmp3)
// {
//     AbstractOdeSystemWithAnalyticJacobian* pSystem
//         = (AbstractOdeSystemWithAnalyticJacobian*) pData;
//     // Get the current time step
//     double dt;
//     CVodeGetCurrentStep(CvodeMem, &dt);
//     // Get std::vector<> for y and double** for J
//     std::vector<realtype>& y_vec = *NV_DATA_STL(y);
//     double** ppJ = J->data; // organised column-wise: J_{i,j} = ppJ[j][i]
//     // Call our function
//     try
//     {
//         pSystem->AnalyticJacobian(y_vec, ppJ, t, dt);
//     }
//     catch (const Exception &e)
//     {
//         std::cerr << "CVODE J Exception: " << e.GetMessage() << std::endl << std::flush;
//         return -1;
//     }
//     // Update J (if needed)
//     return 0;
// }



void CvodeErrorHandler(int errorCode, const char *module, const char *function,
                       char *message, void* pData)
{
    std::stringstream err;
    err << "CVODE Error " << errorCode << " in module " << module
        << " function " << function << ": " << message;
    std::cerr << "*" << err.str() << std::endl << std::flush;
    // Throwing the exception here causes termination on Maverick (g++ 4.4)
    //EXCEPTION(err.str());
}



void CvodeAdaptor::SetupCvode(AbstractOdeSystem* pOdeSystem,
                              std::vector<double>& rInitialY,
                              double startTime,
                              double maxStep)
{
    assert(rInitialY.size() == pOdeSystem->GetNumberOfStateVariables());
    assert(maxStep > 0.0);

    N_Vector initial_values = N_VMake_Serial(rInitialY.size(), &(rInitialY[0]));
    assert(NV_DATA_S(initial_values) == &(rInitialY[0]));
    assert(!NV_OWN_DATA_S(initial_values));
//    std::cout << " Initial values: "; N_VPrint_Serial(initial_values);
//    std::cout << " Rtol: " << mRelTol << ", Atol: " << mAbsTol << std::endl;
//    std::cout << " Start: " << startTime << " max dt=" << maxStep << std::endl << std::flush;

    // Find out if we need to (re-)initialise
    bool reinit = !mpCvodeMem || mAutoReset || !mLastSolutionState || !CompareDoubles::WithinAnyTolerance(startTime, mLastSolutionTime);
    if (!reinit && !mForceMinimalReset)
    {
        const unsigned size = GetVectorSize(rInitialY);
        for (unsigned i=0; i<size; i++)
        {
            if (!CompareDoubles::WithinAnyTolerance(GetVectorComponent(mLastSolutionState, i), GetVectorComponent(rInitialY, i)))
            {
                reinit = true;
                break;
            }
        }
    }

    if (!mpCvodeMem) // First run of this solver, set up CVODE memory
    {
        // Set up CVODE's memory.
        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
        mData.pSystem = pOdeSystem;
        mData.pY = &rInitialY;
        #if CHASTE_SUNDIALS_VERSION >= 20400
            CVodeSetUserData(mpCvodeMem, (void*)(&mData));
        #else
            CVodeSetFdata(mpCvodeMem, (void*)(&mData));
        #endif

        // Setup CVODE
        #if CHASTE_SUNDIALS_VERSION >= 20400
            CVodeInit(mpCvodeMem, CvodeRhsAdaptor, startTime, initial_values);
            CVodeSStolerances(mpCvodeMem, mRelTol, mAbsTol);
        #else
            CVodeMalloc(mpCvodeMem, CvodeRhsAdaptor, startTime, initial_values,
                        CV_SS, mRelTol, &mAbsTol);
        #endif

        // Set the rootfinder function if wanted
        if (mCheckForRoots)
        {
            #if CHASTE_SUNDIALS_VERSION >= 20400
                CVodeRootInit(mpCvodeMem, 1, CvodeRootAdaptor);
            #else
                CVodeRootInit(mpCvodeMem, 1, CvodeRootAdaptor, (void*)(&mData));
            #endif
        }
        // Attach a linear solver for Newton iteration
        CVDense(mpCvodeMem, rInitialY.size());
    }
    else if (reinit) // Could be new ODE system, or new Y values
    {
        // Set the user data
        mData.pSystem = pOdeSystem; // stays the same on a re-initialize
        mData.pY = &rInitialY; // changes on a re-initialize
        #if CHASTE_SUNDIALS_VERSION >= 20400
            CVodeSetUserData(mpCvodeMem, (void*)(&mData));
        #else
            CVodeSetFdata(mpCvodeMem, (void*)(&mData));
        #endif

        #if CHASTE_SUNDIALS_VERSION >= 20400
            CVodeReInit(mpCvodeMem, startTime, initial_values);
            CVodeSStolerances(mpCvodeMem, mRelTol, mAbsTol);
        #else
            CVodeReInit(mpCvodeMem, CvodeRhsAdaptor, startTime, initial_values,
                        CV_SS, mRelTol, &mAbsTol);
        #endif

        // Attach a linear solver for Newton iteration
        CVDense(mpCvodeMem, rInitialY.size());
    }

    CVodeSetMaxStep(mpCvodeMem, maxStep);
    // Change max steps if wanted
    if (mMaxSteps > 0)
    {
        CVodeSetMaxNumSteps(mpCvodeMem, mMaxSteps);
        CVodeSetMaxErrTestFails(mpCvodeMem, 15);
    }
    DeleteVector(initial_values);
}

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


void CvodeAdaptor::SetAutoReset(bool autoReset)
{
    mAutoReset = autoReset;
    if (mAutoReset)
    {
        SetMinimalReset(false);
        ResetSolver();
    }
}

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

void CvodeAdaptor::ResetSolver()
{
    // Doing this makes the SetupCvode think it needs to reset things.
    DeleteVector(mLastSolutionState);
}

void CvodeAdaptor::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());
}


OdeSolution CvodeAdaptor::Solve(AbstractOdeSystem* pOdeSystem,
                                std::vector<double>& rYValues,
                                double startTime,
                                double endTime,
                                double maxStep,
                                double timeSampling)
{
    assert(endTime > startTime);
    assert(timeSampling > 0.0);

    mStoppingEventOccurred = false;
    if (mCheckForRoots && pOdeSystem->CalculateStoppingEvent(startTime, rYValues) == true)
    {
        EXCEPTION("(Solve with sampling) Stopping event is true for initial condition");
    }

    SetupCvode(pOdeSystem, rYValues, startTime, maxStep);

    TimeStepper stepper(startTime, endTime, timeSampling);
    N_Vector yout = N_VMake_Serial(rYValues.size(), &(rYValues[0]));

    // Set up ODE solution
    OdeSolution solutions;
    solutions.SetNumberOfTimeSteps(stepper.EstimateTimeSteps());
    solutions.rGetSolutions().push_back(rYValues);
    solutions.rGetTimes().push_back(startTime);
    solutions.SetOdeSystemInformation(pOdeSystem->GetSystemInformation());

    // Main time sampling loop
    while (!stepper.IsTimeAtEnd() && !mStoppingEventOccurred)
    {
        double tend;
        int ierr = CVode(mpCvodeMem, stepper.GetNextTime(), yout, &tend, CV_NORMAL);
        if (ierr<0)
        {
            FreeCvodeMemory();
            DeleteVector(yout);
            CvodeError(ierr, "CVODE failed to solve system");
        }
        // Store solution
        solutions.rGetSolutions().push_back(rYValues);
        solutions.rGetTimes().push_back(tend);
        if (ierr == CV_ROOT_RETURN)
        {
            // Stopping event occurred
            mStoppingEventOccurred = true;
            mStoppingTime = tend;
        }
        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(endTime, yout);
    DeleteVector(yout);

    return solutions;
}


void CvodeAdaptor::Solve(AbstractOdeSystem* pOdeSystem,
                         std::vector<double>& rYValues,
                         double startTime,
                         double endTime,
                         double maxStep)
{
    assert(endTime > startTime);

    mStoppingEventOccurred = false;
    if (mCheckForRoots && pOdeSystem->CalculateStoppingEvent(startTime, rYValues) == true)
    {
        EXCEPTION("(Solve) Stopping event is true for initial condition");
    }

    SetupCvode(pOdeSystem, rYValues, startTime, maxStep);

    N_Vector yout = N_VMake_Serial(rYValues.size(), &(rYValues[0]));
    double tend;
    int ierr = CVode(mpCvodeMem, endTime, yout, &tend, CV_NORMAL);
    if (ierr<0)
    {
        FreeCvodeMemory();
        DeleteVector(yout);
        CvodeError(ierr, "CVODE failed to solve system");
    }
    if (ierr == CV_ROOT_RETURN)
    {
        // Stopping event occurred
        mStoppingEventOccurred = true;
        mStoppingTime = tend;
    }
    assert(NV_DATA_S(yout) == &(rYValues[0]));
    assert(!NV_OWN_DATA_S(yout));

//    long int steps;
//    CVodeGetNumSteps(mpCvodeMem, &steps);
//    std::cout << " Solved to " << endTime << " in " << steps << " steps.\n";

    ierr = CVodeGetLastStep(mpCvodeMem, &mLastInternalStepSize);
    assert(ierr == CV_SUCCESS); ierr=ierr; // avoid unused var warning
    RecordStoppingPoint(tend, yout);
    DeleteVector(yout);
}

CvodeAdaptor::CvodeAdaptor(double relTol, double absTol)
    : AbstractIvpOdeSolver(),
      mpCvodeMem(NULL),
      mRelTol(relTol),
      mAbsTol(absTol),
      mLastInternalStepSize(-0.0),
      mMaxSteps(0),
      mCheckForRoots(false),
      mLastSolutionState(NULL),
      mLastSolutionTime(0.0),
      mAutoReset(true),
      mForceMinimalReset(false)
{
}

CvodeAdaptor::~CvodeAdaptor()
{
    FreeCvodeMemory();
    DeleteVector(mLastSolutionState);
}

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

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

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

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

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

void CvodeAdaptor::CheckForStoppingEvents()
{
    mCheckForRoots = true;
}

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

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

// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
CHASTE_CLASS_EXPORT(CvodeAdaptor)

#endif // CHASTE_CVODE