AbstractCvodeSystem.cpp

/*

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/>.

*/

#ifdef CHASTE_CVODE

#include <sstream>
#include <cassert>

#include "AbstractCvodeSystem.hpp"
#include "Exception.hpp"
#include "VectorHelperFunctions.hpp"
#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),
      mUseAnalyticJacobian(false),
      mpCvodeMem(NULL),
      mMaxSteps(0)
{
    SetTolerances();
}

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(tEnd);

    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;
}


bool Differs(double v1, double v2)
{
    return fabs(v1 - v2) > DBL_EPSILON;
}


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


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
    bool reinit = !mpCvodeMem || mAutoReset || !mLastSolutionState || Differs(tStart, mLastSolutionTime);
    if (!reinit)
    {
        const unsigned size = GetNumberOfStateVariables();
        for (unsigned i=0; i<size; i++)
        {
            if (Differs(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");
        // 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