AbstractCardiacCellFactory.cpp

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#include "AbstractCardiacCellFactory.hpp"
#include "FakeBathCell.hpp"
#include "AbstractCvodeCell.hpp"
#include "HeartConfig.hpp"
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractCardiacCellInterface*  AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::CreateCardiacCellForNode(
    Node<SPACE_DIM>* pNode)
{
    if (HeartRegionCode::IsRegionBath( pNode->GetRegion() ))
    {
        return new FakeBathCell(this->mpSolver, this->mpZeroStimulus);
    }
    else
    {
        AbstractCardiacCellInterface* p_cell = CreateCardiacCellForTissueNode(pNode);
#ifdef CHASTE_CVODE
        if (dynamic_cast<AbstractCvodeCell*>(p_cell))
        {
#if CHASTE_SUNDIALS_VERSION >= 20400
            // Tell the single cell model solver not to re-initialise on subsequent Solve calls.
            // Unfortunately the oldest CVODE we currently support (2.5.0 in Sundials 2.3.0) doesn't
            // work very well this this enabled, so we will go without and take a performance hit.
            static_cast<AbstractCvodeCell*>(p_cell)->SetMinimalReset(true);
#endif // SUNDIALS_VERSION
            // Use the PDE timestep as the [maximum] CVODE timestep.
            static_cast<AbstractCvodeCell*>(p_cell)->SetTimestep(HeartConfig::Instance()->GetPdeTimeStep());
        }
#endif // CHASTE_CVODE
        return p_cell;
    }
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::FinaliseCellCreation(
    std::vector< AbstractCardiacCellInterface* >* pCellsDistributed,
    unsigned lo,
    unsigned hi)
{
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::FillInCellularTransmuralAreas()
{
    EXCEPTION("To get here you have probably asked for Epi/Mid/Endo CellularHeterogeneities in your HeartConfig "
              "options or configuration .xml file, to use this you will need to provide a method"
              " `FillInCellularTransmuralAreas()` in your cell factory to override this one.");
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::GetNumberOfCells()
{
    assert(mpMesh != NULL);
    return mpMesh->GetNumNodes();
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::AbstractCardiacCellFactory(
        boost::shared_ptr<AbstractIvpOdeSolver> pSolver)
    : mpMesh(NULL),
      mpHeartGeometryInformation(NULL),
      mpZeroStimulus(new ZeroStimulus),
      mpSolver(pSolver)
{
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::~AbstractCardiacCellFactory()
{
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::SetMesh(AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh)
{
    mpMesh = pMesh;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::GetMesh()
{
    if (mpMesh == NULL)
    {
        EXCEPTION("The mesh object has not been set in the cell factory");
    }
    return mpMesh;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::SetHeartGeometryInformation(HeartGeometryInformation<SPACE_DIM>* pHeartGeometryInformation)
{
    mpHeartGeometryInformation = pHeartGeometryInformation;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
HeartGeometryInformation<SPACE_DIM>* AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>::GetHeartGeometryInformation()
{
    if (mpHeartGeometryInformation == NULL)
    {
        EXCEPTION("HeartGeometryInformation object has not been set in the cell factory");
    }
    return mpHeartGeometryInformation;
}
 
// Explicit instantiation
template class AbstractCardiacCellFactory<1,1>;
template class AbstractCardiacCellFactory<1,2>;
template class AbstractCardiacCellFactory<1,3>;
template class AbstractCardiacCellFactory<2,2>;
template class AbstractCardiacCellFactory<3,3>;