AbstractParameterisedSystem.cpp

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*/

#include <sstream>
#include <cassert>

#include "AbstractParameterisedSystem.hpp"

#include "Exception.hpp"
#include "VectorHelperFunctions.hpp"


template<typename VECTOR>
AbstractParameterisedSystem<VECTOR>::AbstractParameterisedSystem(unsigned numberOfStateVariables)
    : AbstractUntemplatedParameterisedSystem(numberOfStateVariables)
{
    InitialiseEmptyVector(mParameters);
    InitialiseEmptyVector(mStateVariables);
}

template<typename VECTOR>
std::string AbstractParameterisedSystem<VECTOR>::DumpState(const std::string& rMessage)
{
    return GetStateMessage(rMessage, mStateVariables);
}

template<typename VECTOR>
std::string AbstractParameterisedSystem<VECTOR>::DumpState(const std::string& rMessage,
                                                           VECTOR Y)
{
    return GetStateMessage(rMessage, Y);
}

template<typename VECTOR>
std::string AbstractParameterisedSystem<VECTOR>::DumpState(const std::string& rMessage,
                                                           VECTOR Y,
                                                           double time)
{
    std::stringstream extra_message;
    extra_message << std::endl << "At independent variable (usually time) = " << time;
    std::string new_message = rMessage + extra_message.str();
    return GetStateMessage(new_message, Y);
}

template<typename VECTOR>
std::string AbstractParameterisedSystem<VECTOR>::GetStateMessage(const std::string& rMessage, VECTOR Y)
{
    std::stringstream res;
    res << rMessage << std::endl << "State:" << std::endl;
    assert(rGetStateVariableNames().size()==GetVectorSize(Y));
    const std::vector<std::string>& r_units = rGetStateVariableUnits();
    for (unsigned i=0; i<GetVectorSize(Y); i++)
    {
        res << "\t" << rGetStateVariableNames()[i] << ":" << GetVectorComponent(Y, i);
        if (!r_units.empty())
        {
            res << " " << r_units[i];
        }
        res << std::endl;
    }
    return res.str();
}

template<typename VECTOR>
void AbstractParameterisedSystem<VECTOR>::CheckParametersOnLoad(const std::vector<double>& rParameters, const std::vector<std::string>& rParameterNames)
{
    if (GetVectorSize(mParameters) != rGetParameterNames().size())
    {
        // Subclass constructor didn't give default values, so we need the archive to provide them all
        if (rParameterNames.size() != rGetParameterNames().size())
        {
            EXCEPTION("Number of ODE parameters in archive does not match number in class.");
        }
        CreateVectorIfEmpty(mParameters,rGetParameterNames().size());
    }

    // Check whether the archive specifies parameters that don't appear in this class,
    // and create a map from archive index to local index
    std::vector<unsigned> index_map(rParameterNames.size());
    for (unsigned i=0; i<rParameterNames.size(); ++i)
    {
        index_map[i] = find(rGetParameterNames().begin(), rGetParameterNames().end(), rParameterNames[i])
                       - rGetParameterNames().begin();
        if (index_map[i] == rGetParameterNames().size())
        {
            EXCEPTION("Archive specifies a parameter '" + rParameterNames[i] + "' which does not appear in this class.");
        }
    }

    for (unsigned i=0; i<rParameterNames.size(); ++i)
    {
        SetVectorComponent(mParameters,index_map[i],rParameters[i]);
    }

    // Paranoia check
    assert(GetVectorSize(mParameters) == rGetParameterNames().size());
}

//
// State variable methods
//

template<typename VECTOR>
VECTOR& AbstractParameterisedSystem<VECTOR>::rGetStateVariables()
{
    return mStateVariables;
}

template<typename VECTOR>
VECTOR AbstractParameterisedSystem<VECTOR>::GetStateVariables()
{
    return CopyVector(mStateVariables);
}

template<typename VECTOR>
void AbstractParameterisedSystem<VECTOR>::SetStateVariables(const VECTOR& rStateVariables)
{

    if ( mNumberOfStateVariables != GetVectorSize(rStateVariables) )
    {
        EXCEPTION("The size of the passed in vector must be that of the number of state variables.");
    }

    CreateVectorIfEmpty(mStateVariables, mNumberOfStateVariables);
    for (unsigned i=0; i<mNumberOfStateVariables; i++)
    {
        SetVectorComponent(mStateVariables, i, GetVectorComponent(rStateVariables, i));
    }
}

template<typename VECTOR>
double AbstractParameterisedSystem<VECTOR>::GetStateVariable(unsigned index) const
{
    if (index >= mNumberOfStateVariables)
    {
        EXCEPTION("The index passed in must be less than the number of state variables.");
    }
    return GetVectorComponent(mStateVariables, index);
}

template<typename VECTOR>
double AbstractParameterisedSystem<VECTOR>::GetStateVariable(const std::string& rName) const
{
    return GetStateVariable(GetStateVariableIndex(rName));
}

template<typename VECTOR>
void AbstractParameterisedSystem<VECTOR>::SetStateVariable(unsigned index, double newValue)
{
    if ( mNumberOfStateVariables <= index )
    {
        EXCEPTION("The index passed in must be less than the number of state variables.");
    }
    SetVectorComponent(mStateVariables, index, newValue);
}

template<typename VECTOR>
void AbstractParameterisedSystem<VECTOR>::SetStateVariable(const std::string& rName, double newValue)
{
    SetStateVariable(GetStateVariableIndex(rName), newValue);
}


//
// Initial condition methods
//

template<typename VECTOR>
void AbstractParameterisedSystem<VECTOR>::SetDefaultInitialConditions(const VECTOR& rInitialConditions)
{
    if (GetVectorSize(rInitialConditions) != mNumberOfStateVariables)
    {
        EXCEPTION("The number of initial conditions must be that of the number of state variables.");
    }
    assert(mpSystemInfo);
    std::vector<double> inits;
    CopyToStdVector(rInitialConditions, inits);
    mpSystemInfo->SetDefaultInitialConditions(inits);
}

template<typename VECTOR>
void AbstractParameterisedSystem<VECTOR>::SetDefaultInitialCondition(unsigned index, double initialCondition)
{
    if (index >= mNumberOfStateVariables)
    {
        EXCEPTION("Index is greater than the number of state variables.");
    }
    assert(mpSystemInfo);
    mpSystemInfo->SetDefaultInitialCondition(index, initialCondition);
}

template<typename VECTOR>
VECTOR AbstractParameterisedSystem<VECTOR>::GetInitialConditions() const
{
    assert(mpSystemInfo);
    VECTOR v;
    InitialiseEmptyVector(v);
    CreateVectorIfEmpty(v, mNumberOfStateVariables);
    CopyFromStdVector(mpSystemInfo->GetInitialConditions(), v);
    return v;
}

template<typename VECTOR>
void AbstractParameterisedSystem<VECTOR>::ResetToInitialConditions()
{
    VECTOR inits = GetInitialConditions();
    SetStateVariables(inits);
    DeleteVector(inits);
}

//
// Parameter methods
//

template<typename VECTOR>
double AbstractParameterisedSystem<VECTOR>::GetParameter(unsigned index) const
{
    if (index >= GetVectorSize(mParameters))
    {
        EXCEPTION("The index passed in must be less than the number of parameters.");
    }
    return GetVectorComponent(mParameters, index);
}

template<typename VECTOR>
void AbstractParameterisedSystem<VECTOR>::SetParameter(unsigned index, double value)
{
    if (index >= GetVectorSize(mParameters))
    {
        EXCEPTION("The index passed in must be less than the number of parameters.");
    }
    SetVectorComponent(mParameters, index, value);
}

template<typename VECTOR>
void AbstractParameterisedSystem<VECTOR>::SetParameter(const std::string& rName, double value)
{
    SetVectorComponent(mParameters, GetParameterIndex(rName), value);
}

template<typename VECTOR>
double AbstractParameterisedSystem<VECTOR>::GetParameter(const std::string& rName) const
{
    return GetParameter(GetParameterIndex(rName));
}

//
// "Any variable" methods
//

template<typename VECTOR>
double AbstractParameterisedSystem<VECTOR>::GetAnyVariable(unsigned index, double time,
                                                           VECTOR* pDerivedQuantities)
{
    if (index < mNumberOfStateVariables)
    {
        return GetVectorComponent(mStateVariables, index);
    }
    else if (index - mNumberOfStateVariables < GetVectorSize(mParameters))
    {
        return GetVectorComponent(mParameters, index - mNumberOfStateVariables);
    }
    else
    {
        unsigned offset = mNumberOfStateVariables + GetVectorSize(mParameters);
        if (index - offset < GetNumberOfDerivedQuantities())
        {
            VECTOR dqs;
            if (pDerivedQuantities == NULL)
            {
                dqs = ComputeDerivedQuantitiesFromCurrentState(time);
                pDerivedQuantities = &dqs;
            }
            double value = GetVectorComponent(*pDerivedQuantities, index - offset);
            if (pDerivedQuantities == &dqs)
            {
                DeleteVector(dqs);
            }
            return value;
        }
        else
        {
            EXCEPTION("Invalid index passed to GetAnyVariable.");
        }
    }
}

template<typename VECTOR>
double AbstractParameterisedSystem<VECTOR>::GetAnyVariable(const std::string& rName,
                                                           double time,
                                                           VECTOR* pDerivedQuantities)
{
    return GetAnyVariable(GetAnyVariableIndex(rName), time, pDerivedQuantities);
}

template<typename VECTOR>
void AbstractParameterisedSystem<VECTOR>::SetAnyVariable(unsigned index, double value)
{
    if (index < mNumberOfStateVariables)
    {
        SetVectorComponent(mStateVariables, index, value);
    }
    else if (index - mNumberOfStateVariables < GetVectorSize(mParameters))
    {
        SetVectorComponent(mParameters, index - mNumberOfStateVariables, value);
    }
    else
    {
        EXCEPTION("Cannot set the value of a derived quantity, or invalid index.");
    }
}

template<typename VECTOR>
void AbstractParameterisedSystem<VECTOR>::SetAnyVariable(const std::string& rName, double value)
{
    SetAnyVariable(GetAnyVariableIndex(rName), value);
}

//
// "Derived quantities" methods
//

template<typename VECTOR>
VECTOR AbstractParameterisedSystem<VECTOR>::ComputeDerivedQuantities(double time,
                                                                     const VECTOR& rState)
{
    EXCEPTION("This ODE system does not define derived quantities.");
}

template<typename VECTOR>
VECTOR AbstractParameterisedSystem<VECTOR>::ComputeDerivedQuantitiesFromCurrentState(double time)
{
    return this->ComputeDerivedQuantities(time, mStateVariables);
}


// Explicit instantiation

template class AbstractParameterisedSystem<std::vector<double> >;
#ifdef CHASTE_CVODE
template class AbstractParameterisedSystem<N_Vector>;
#endif