CvodeAdaptor.cpp

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*/
 
#ifdef CHASTE_CVODE
 
#include "CvodeAdaptor.hpp"
 
#include "Exception.hpp"
#include "MathsCustomFunctions.hpp" // For tolerance check.
#include "TimeStepper.hpp"
#include "VectorHelperFunctions.hpp"
 
#include <iostream>
#include <sstream>
 
// CVODE headers
#include <sundials/sundials_nvector.h>
 
#if CHASTE_SUNDIALS_VERSION >= 30000
#if CHASTE_SUNDIALS_VERSION < 70000
#include <cvode/cvode_direct.h> /* access to CVDls interface            */
#endif
#include <sundials/sundials_types.h> /* defs. of realtype, sunindextype      */
#include <sunlinsol/sunlinsol_dense.h> /* access to dense SUNLinearSolver      */
#include <sunmatrix/sunmatrix_dense.h> /* access to dense SUNMatrix            */
#else
#include <cvode/cvode_dense.h>
#endif
 
#if CHASTE_SUNDIALS_VERSION >= 60000
#include "CvodeContextManager.hpp"  // access to shared SUNContext object required by Sundials 6.0+
#endif
 
int CvodeRhsAdaptor(realtype t, N_Vector y, N_Vector ydot, void* pData)
{
    assert(pData != nullptr);
    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 != nullptr);
    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;
// }
 
#if CHASTE_SUNDIALS_VERSION >= 70000
void CvodeErrorHandler(int errorCode, const char* module, const char* function,
                       const char* message, SUNErrCode errCode, void* pData, SUNContext sunContext)
#else
void CvodeErrorHandler(int errorCode, const char* module, const char* function,
                       char* message, void* pData)
#endif
{
    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);
 
#if CHASTE_SUNDIALS_VERSION >= 60000
    N_Vector initial_values = N_VMake_Serial(rInitialY.size(), &(rInitialY[0]), CvodeContextManager::Instance()->GetSundialsContext());
#else
    N_Vector initial_values = N_VMake_Serial(rInitialY.size(), &(rInitialY[0]));
#endif
    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 || mForceReset || !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.
#if CHASTE_SUNDIALS_VERSION >= 60000
        mpCvodeMem = CVodeCreate(CV_BDF, CvodeContextManager::Instance()->GetSundialsContext());
#elif CHASTE_SUNDIALS_VERSION >= 40000
        //  v4.0.0 release notes: instead of specifying the nonlinear iteration type when creating the CVODE(S) memory structure,
        //  CVODE(S) uses the SUNNONLINSOL_NEWTON module implementation of a Newton iteration by default.
        mpCvodeMem = CVodeCreate(CV_BDF);
#else
        mpCvodeMem = CVodeCreate(CV_BDF, CV_NEWTON);
#endif
 
        if (mpCvodeMem == nullptr)
            EXCEPTION("Failed to SetupCvode CVODE"); // LCOV_EXCL_LINE
        // Set error handler
#if CHASTE_SUNDIALS_VERSION >= 70000
        SUNContext_PushErrHandler(CvodeContextManager::Instance()->GetSundialsContext(),  CvodeErrorHandler, nullptr);
#else
        CVodeSetErrHandlerFn(mpCvodeMem, CvodeErrorHandler, nullptr);
#endif
        // 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
        }
 
        /* Create dense SUNMatrix for use in linear solves */
#if CHASTE_SUNDIALS_VERSION >= 60000
        mpSundialsDenseMatrix = SUNDenseMatrix(rInitialY.size(), rInitialY.size(), CvodeContextManager::Instance()->GetSundialsContext());
#elif CHASTE_SUNDIALS_VERSION >= 30000
        mpSundialsDenseMatrix = SUNDenseMatrix(rInitialY.size(), rInitialY.size());
#endif
 
#if CHASTE_SUNDIALS_VERSION >= 60000
        /* Create dense SUNLinearSolver object for use by CVode */
        mpSundialsLinearSolver = SUNLinSol_Dense(initial_values, mpSundialsDenseMatrix, CvodeContextManager::Instance()->GetSundialsContext());
 
        /* Call CVodeSetLinearSolver to attach the matrix and linear solver to CVode */
        CVodeSetLinearSolver(mpCvodeMem, mpSundialsLinearSolver, mpSundialsDenseMatrix);
#elif CHASTE_SUNDIALS_VERSION >= 40000
        /* Create dense SUNLinearSolver object for use by CVode */
        mpSundialsLinearSolver = SUNLinSol_Dense(initial_values, mpSundialsDenseMatrix);
 
        /* Call CVodeSetLinearSolver to attach the matrix and linear solver to CVode */
        CVodeSetLinearSolver(mpCvodeMem, mpSundialsLinearSolver, mpSundialsDenseMatrix);
#elif CHASTE_SUNDIALS_VERSION >= 30000
        /* Create dense SUNLinearSolver object for use by CVode */
        mpSundialsLinearSolver = SUNDenseLinearSolver(initial_values, mpSundialsDenseMatrix);
 
        /* Call CVDlsSetLinearSolver to attach the matrix and linear solver to CVode */
        CVDlsSetLinearSolver(mpCvodeMem, mpSundialsLinearSolver, mpSundialsDenseMatrix);
#else
        // CVODE < v3.0.0
        // Attach a linear solver for Newton iteration
        CVDense(mpCvodeMem, rInitialY.size());
#endif
    }
    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
 
#if CHASTE_SUNDIALS_VERSION >= 30000
        if (mpSundialsLinearSolver)
        {
            /* Free the linear solver memory */
            SUNLinSolFree(mpSundialsLinearSolver);
        }
        if (mpSundialsDenseMatrix)
        {
            /* Free the matrix memory */
            SUNMatDestroy(mpSundialsDenseMatrix);
        }
 
        /* Create dense matrix of type SUNDenseMatrix for use in linear solves */
#if CHASTE_SUNDIALS_VERSION >= 60000
        mpSundialsDenseMatrix = SUNDenseMatrix(rInitialY.size(), rInitialY.size(), CvodeContextManager::Instance()->GetSundialsContext());
#else
        mpSundialsDenseMatrix = SUNDenseMatrix(rInitialY.size(), rInitialY.size());
#endif
 
#if CHASTE_SUNDIALS_VERSION >= 60000
        /* Create dense SUNLinSol_Dense object for use by CVode */
        mpSundialsLinearSolver = SUNLinSol_Dense(initial_values, mpSundialsDenseMatrix, CvodeContextManager::Instance()->GetSundialsContext());
 
        /* Call CVodeSetLinearSolver to attach the matrix and linear solver to CVode */
        CVodeSetLinearSolver(mpCvodeMem, mpSundialsLinearSolver, mpSundialsDenseMatrix);
#elif CHASTE_SUNDIALS_VERSION >= 40000
        /* Create dense SUNLinSol_Dense object for use by CVode */
        mpSundialsLinearSolver = SUNLinSol_Dense(initial_values, mpSundialsDenseMatrix);
 
        /* Call CVodeSetLinearSolver to attach the matrix and linear solver to CVode */
        CVodeSetLinearSolver(mpCvodeMem, mpSundialsLinearSolver, mpSundialsDenseMatrix);
#else
        /* Create dense SUNLinearSolver object for use by CVode */
        mpSundialsLinearSolver = SUNDenseLinearSolver(initial_values, mpSundialsDenseMatrix);
 
        /* Call CVDlsSetLinearSolver to attach the matrix and linear solver to CVode */
        CVDlsSetLinearSolver(mpCvodeMem, mpSundialsLinearSolver, mpSundialsDenseMatrix);
#endif
#else
        // Attach a linear solver for Newton iteration
        CVDense(mpCvodeMem, rInitialY.size());
#endif
    }
 
    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 = nullptr;
 
#if CHASTE_SUNDIALS_VERSION >= 30000
    if (mpSundialsLinearSolver)
    {
        /* Free the linear solver memory */
        SUNLinSolFree(mpSundialsLinearSolver);
    }
    mpSundialsLinearSolver = nullptr;
 
    if (mpSundialsDenseMatrix)
    {
        /* Free the matrix memory */
        SUNMatDestroy(mpSundialsDenseMatrix);
    }
    mpSundialsDenseMatrix = nullptr;
#endif
}
 
void CvodeAdaptor::SetForceReset(bool autoReset)
{
    mForceReset = autoReset;
    if (mForceReset)
    {
        SetMinimalReset(false);
        ResetSolver();
    }
}
 
void CvodeAdaptor::SetMinimalReset(bool minimalReset)
{
    mForceMinimalReset = minimalReset;
    if (mForceMinimalReset)
    {
        SetForceReset(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);
#if CHASTE_SUNDIALS_VERSION >= 60000
    N_Vector yout = N_VMake_Serial(rYValues.size(), &(rYValues[0]), CvodeContextManager::Instance()->GetSundialsContext());
#else
    N_Vector yout = N_VMake_Serial(rYValues.size(), &(rYValues[0]));
#endif
 
    // 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)
    {
        // This should stop CVODE going past the end of where we wanted and interpolating back.
        int ierr = CVodeSetStopTime(mpCvodeMem, stepper.GetNextTime());
        assert(ierr == CV_SUCCESS);
        UNUSED_OPT(ierr); // avoid unused var warning
 
        double tend;
        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;
        }
        mLastSolutionTime = tend;
        stepper.AdvanceOneTimeStep();
    }
 
    // stepper.EstimateTimeSteps may have been an overestimate...
    solutions.SetNumberOfTimeSteps(stepper.GetTotalTimeStepsTaken());
 
    int ierr = CVodeGetLastStep(mpCvodeMem, &mLastInternalStepSize);
    assert(ierr == CV_SUCCESS);
    UNUSED_OPT(ierr); // avoid unused var warning
    RecordStoppingPoint(mLastSolutionTime, 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);
 
#if CHASTE_SUNDIALS_VERSION >= 60000
    N_Vector yout = N_VMake_Serial(rYValues.size(), &(rYValues[0]), CvodeContextManager::Instance()->GetSundialsContext());
#else
    N_Vector yout = N_VMake_Serial(rYValues.size(), &(rYValues[0]));
#endif
 
    // This should stop CVODE going past the end of where we wanted and interpolating back.
    int ierr = CVodeSetStopTime(mpCvodeMem, endTime);
    assert(ierr == CV_SUCCESS);
    UNUSED_OPT(ierr); // avoid unused var warning
 
    double tend;
    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);
    UNUSED_OPT(ierr); // avoid unused var warning
    RecordStoppingPoint(tend, yout);
    DeleteVector(yout);
}
 
CvodeAdaptor::CvodeAdaptor(double relTol, double absTol)
        : AbstractIvpOdeSolver(),
          mpCvodeMem(nullptr),
          mRelTol(relTol),
          mAbsTol(absTol),
          mLastInternalStepSize(-0.0),
          mMaxSteps(0),
          mCheckForRoots(false),
          mLastSolutionState(nullptr),
          mLastSolutionTime(0.0),
#if CHASTE_SUNDIALS_VERSION >= 20400
          mForceReset(false),
#else
          mForceReset(true),
#endif
          mForceMinimalReset(false)
#if CHASTE_SUNDIALS_VERSION >= 30000
          ,
          mpSundialsDenseMatrix(nullptr),
          mpSundialsLinearSolver(nullptr)
#endif
{
}
 
CvodeAdaptor::~CvodeAdaptor()
{
    FreeCvodeMemory();
    DeleteVector(mLastSolutionState);
}
 
void CvodeAdaptor::RecordStoppingPoint(double stopTime, N_Vector yEnd)
{
    if (!mForceReset)
    {
        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