VectorHelperFunctions.hpp

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   this list of conditions and the following disclaimer.
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OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
*/
 
#ifndef VECTORHELPERFUNCTIONS_HPP_
#define VECTORHELPERFUNCTIONS_HPP_
 
#include <cassert>
#include <vector>
 
#ifdef CHASTE_CVODE
// CVODE headers
#include <nvector/nvector_serial.h>
#if CHASTE_SUNDIALS_VERSION >= 70000
#define realtype sunrealtype
#endif
 
#if CHASTE_SUNDIALS_VERSION >= 60000
#include "CvodeContextManager.hpp"  // access to shared SUNContext object required by Sundials 6.0+
#endif
 
#endif
 
template <typename VECTOR>
inline double GetVectorComponent(const VECTOR& rVec, unsigned index);
 
template <typename VECTOR>
inline void SetVectorComponent(VECTOR& rVec, unsigned index, double value);
 
template <typename VECTOR>
inline unsigned GetVectorSize(const VECTOR& rVec);
 
template <typename VECTOR>
inline void InitialiseEmptyVector(VECTOR& rVec);
 
template <typename VECTOR>
inline void CreateVectorIfEmpty(VECTOR& rVec, unsigned size);
 
template <typename VECTOR>
inline VECTOR CreateEmptyVector();
 
template <typename VECTOR>
inline bool IsEmptyVector(VECTOR& rVec);
 
template <typename VECTOR>
inline void DeleteVector(VECTOR& rVec);
 
template <typename VECTOR>
inline VECTOR CopyVector(VECTOR& rVec);
 
template <typename VECTOR>
inline void CopyToStdVector(const VECTOR& rSrc, std::vector<double>& rDest);
 
template <typename VECTOR>
inline void CopyFromStdVector(const std::vector<double>& rSrc, VECTOR& rDest);
 
// Specialisations for std::vector<double>
 
template <>
inline double GetVectorComponent(const std::vector<double>& rVec, unsigned index)
{
    assert(index < rVec.size());
    return rVec[index];
}
 
template <>
inline void SetVectorComponent(std::vector<double>& rVec, unsigned index, double value)
{
    assert(index < rVec.size());
    rVec[index] = value;
}
 
template <>
inline unsigned GetVectorSize(const std::vector<double>& rVec)
{
    return rVec.size();
}
 
template <>
inline void InitialiseEmptyVector(std::vector<double>& rVec)
{
}
 
template <>
inline void CreateVectorIfEmpty(std::vector<double>& rVec, unsigned size)
{
    if (rVec.empty())
    {
        rVec.resize(size);
    }
}
 
template <>
inline std::vector<double> CreateEmptyVector()
{
    return std::vector<double>();
}
 
template <>
inline bool IsEmptyVector(std::vector<double>& rVec)
{
    return rVec.empty();
}
 
template <>
inline void DeleteVector(std::vector<double>& rVec)
{
}
 
template <>
inline std::vector<double> CopyVector(std::vector<double>& rVec)
{
    return rVec;
}
 
template <>
inline void CopyToStdVector(const std::vector<double>& rSrc, std::vector<double>& rDest)
{
    rDest = rSrc;
}
 
template <>
inline void CopyFromStdVector(const std::vector<double>& rSrc, std::vector<double>& rDest)
{
    rDest = rSrc;
}
 
// Specialisations for N_Vector
 
#ifdef CHASTE_CVODE
 
template <>
inline double GetVectorComponent(const N_Vector& rVec, unsigned index)
{
    assert(rVec != nullptr);
    return NV_Ith_S(rVec, index);
}
 
template <>
inline void SetVectorComponent(N_Vector& rVec, unsigned index, double value)
{
    assert(rVec != nullptr);
    NV_Ith_S(rVec, index) = value;
}
 
template <>
inline unsigned GetVectorSize(const N_Vector& rVec)
{
    assert(rVec != nullptr);
    return NV_LENGTH_S(rVec);
}
 
template <>
inline void InitialiseEmptyVector(N_Vector& rVec)
{
    rVec = nullptr;
}
 
template <>
inline void CreateVectorIfEmpty(N_Vector& rVec, unsigned size)
{
    if (rVec == nullptr)
    {
#if CHASTE_SUNDIALS_VERSION >= 60000
        rVec = N_VNew_Serial(size, CvodeContextManager::Instance()->GetSundialsContext());
#else
        rVec = N_VNew_Serial(size);
#endif
    }
}
 
template <>
inline N_Vector CreateEmptyVector()
{
    return nullptr;
}
 
template <>
inline bool IsEmptyVector(N_Vector& rVec)
{
    return rVec == nullptr;
}
 
template <>
inline void DeleteVector(N_Vector& rVec)
{
    if (rVec)
    {
        rVec->ops->nvdestroy(rVec);
        rVec = nullptr;
    }
}
 
template <>
inline N_Vector CopyVector(N_Vector& rVec)
{
    N_Vector copy = nullptr;
    if (rVec)
    {
        copy = N_VClone(rVec);
        unsigned size = NV_LENGTH_S(rVec);
        for (unsigned i = 0; i < size; i++)
        {
            NV_Ith_S(copy, i) = NV_Ith_S(rVec, i);
        }
    }
    return copy;
}
 
template <>
inline void CopyToStdVector(const N_Vector& rSrc, std::vector<double>& rDest)
{
    // Check for no-op
    realtype* p_src = NV_DATA_S(rSrc);
    if (!rDest.empty() && p_src == &(rDest[0]))
        return;
    // Set dest size
    long size = NV_LENGTH_S(rSrc);
    rDest.resize(size);
    // Copy data
    for (long i = 0; i < size; i++)
    {
        rDest[i] = p_src[i];
    }
}
 
template <>
inline void CopyFromStdVector(const std::vector<double>& rSrc, N_Vector& rDest)
{
    // Check for no-op
    realtype* p_dest = NV_DATA_S(rDest);
    if (p_dest == &(rSrc[0])) return;
 
    // Check dest size
    long size = NV_LENGTH_S(rDest);
    assert(size == (long)rSrc.size());
 
    // Copy data
    for (long i = 0; i < size; i++)
    {
        p_dest[i] = rSrc[i];
    }
}
 
inline std::vector<double> MakeStdVec(N_Vector v)
{
    std::vector<double> sv;
    CopyToStdVector(v, sv);
    return sv;
}
 
inline N_Vector MakeNVector(const std::vector<double>& rSrc)
{
    N_Vector nv = nullptr;
    CreateVectorIfEmpty(nv, rSrc.size());
    CopyFromStdVector(rSrc, nv);
    return nv;
}
 
#endif // CHASTE_CVODE
 
// End of helper functions
 
#endif /*VECTORHELPERFUNCTIONS_HPP_*/