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());
}
N_Vector ParameterisedCvode::ComputeDerivedQuantities(double time,
const N_Vector& rState)
{
N_Vector derived_quantities = NULL;
CreateVectorIfEmpty(derived_quantities,1);
SetVectorComponent(derived_quantities, 0,
2*GetVectorComponent(mParameters,0) + GetVectorComponent(rState,0));
return derived_quantities;
}
VECTOR AbstractParameterisedSystem<VECTOR>::GetInitialConditions() const
{
assert(mpSystemInfo);
VECTOR v;
InitialiseEmptyVector(v);
CreateVectorIfEmpty(v, mNumberOfStateVariables);
CopyFromStdVector(mpSystemInfo->GetInitialConditions(), v);
return v;
}
ParameterisedCvode::ParameterisedCvode() : AbstractCvodeSystem(1) // 1 here is the number of variables
{
this->mpSystemInfo = OdeSystemInformation<ParameterisedCvode>::Instance();
Init();
if (!noParameterDefaults)
{
CreateVectorIfEmpty(mParameters,1);
SetVectorComponent(mParameters, 0, 0.0);
if (fakeSecondParameter)
{
SetVectorComponent(mParameters, 1, -1.0);
}
}
}
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));
}
}