AbstractCorrectionTermAssembler.cpp

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#include "AbstractCorrectionTermAssembler.hpp"
#include <typeinfo>
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
AbstractCorrectionTermAssembler<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM>::AbstractCorrectionTermAssembler(
        AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh,
        AbstractCardiacTissue<ELEMENT_DIM,SPACE_DIM>* pTissue)
    : AbstractCardiacFeVolumeIntegralAssembler<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM,true,false,CARDIAC>(pMesh,pTissue)
{
    // Work out which elements can do SVI
    mElementsCanDoSvi.resize(pMesh->GetNumElements(), true);
    for (typename AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::ElementIterator iter = pMesh->GetElementIteratorBegin();
         iter != pMesh->GetElementIteratorEnd();
         ++iter)
    {
        Element<ELEMENT_DIM, SPACE_DIM>& r_element = *iter;
        if (r_element.GetOwnership())
        {
            unsigned element_index = r_element.GetIndex();
            // If bath element, don't try to use SVI
            if (HeartRegionCode::IsRegionBath(r_element.GetUnsignedAttribute()))
            {
                mElementsCanDoSvi[element_index] = false;
                continue;
            }
            // See if the nodes in this element all use the same cell model
            unsigned node_zero = r_element.GetNodeGlobalIndex(0);
            AbstractCardiacCellInterface* p_cell_zero = this->mpCardiacTissue->GetCardiacCellOrHaloCell(node_zero);
            const std::type_info& r_zero_info = typeid(*p_cell_zero);
            // Check the other nodes match. If they don't, no SVI
            for (unsigned local_index=1; local_index<r_element.GetNumNodes(); local_index++)
            {
                unsigned global_index = r_element.GetNodeGlobalIndex(local_index);
                AbstractCardiacCellInterface* p_cell = this->mpCardiacTissue->GetCardiacCellOrHaloCell(global_index);
                const std::type_info& r_info = typeid(*p_cell);
                if (r_zero_info != r_info)
                {
                    mElementsCanDoSvi[element_index] = false;
                    break;
                }
            }
        }
    }
    // Note: the mStateVariables std::vector is resized if correction will be applied to a given element
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCorrectionTermAssembler<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM>::ResetInterpolatedQuantities()
{
    // reset ionic current, and state variables
    mIionicInterp = 0;
    for (unsigned i=0; i<mStateVariablesAtQuadPoint.size(); i++)
    {
        mStateVariablesAtQuadPoint[i] = 0;
    }
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractCorrectionTermAssembler<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM>::IncrementInterpolatedQuantities(
            double phiI, const Node<SPACE_DIM>* pNode)
{
    // interpolate ionic current
    unsigned node_global_index = pNode->GetIndex();
    mIionicInterp  += phiI * this->mpCardiacTissue->rGetIionicCacheReplicated()[ node_global_index ];
    // and state variables
    std::vector<double> state_vars = this->mpCardiacTissue->GetCardiacCellOrHaloCell(node_global_index)->GetStdVecStateVariables();
    for (unsigned i=0; i<mStateVariablesAtQuadPoint.size(); i++)
    {
        mStateVariablesAtQuadPoint[i] += phiI * state_vars[i];
    }
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
bool AbstractCorrectionTermAssembler<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM>::ElementAssemblyCriterion(Element<ELEMENT_DIM,SPACE_DIM>& rElement)
{
    // Check that SVI is allowed on this element
    if (!mElementsCanDoSvi[rElement.GetIndex()])
    {
        return false;
    }
    double DELTA_IIONIC = 1; // tolerance
 
    //The criterion and the correction both need the ionic cache, so we better make sure that it's up-to-date
    assert(this->mpCardiacTissue->GetDoCacheReplication());
    ReplicatableVector& r_cache = this->mpCardiacTissue->rGetIionicCacheReplicated();
 
    double diionic = fabs(r_cache[rElement.GetNodeGlobalIndex(0)] - r_cache[rElement.GetNodeGlobalIndex(1)]);
 
    if (ELEMENT_DIM > 1)
    {
        diionic = std::max(diionic, fabs(r_cache[rElement.GetNodeGlobalIndex(0)] - r_cache[rElement.GetNodeGlobalIndex(2)]) );
        diionic = std::max(diionic, fabs(r_cache[rElement.GetNodeGlobalIndex(1)] - r_cache[rElement.GetNodeGlobalIndex(2)]) );
    }
 
    if (ELEMENT_DIM > 2)
    {
        diionic = std::max(diionic, fabs(r_cache[rElement.GetNodeGlobalIndex(0)] - r_cache[rElement.GetNodeGlobalIndex(3)]) );
        diionic = std::max(diionic, fabs(r_cache[rElement.GetNodeGlobalIndex(1)] - r_cache[rElement.GetNodeGlobalIndex(3)]) );
        diionic = std::max(diionic, fabs(r_cache[rElement.GetNodeGlobalIndex(2)] - r_cache[rElement.GetNodeGlobalIndex(3)]) );
    }
 
    bool will_assemble = (diionic > DELTA_IIONIC);
 
    if (will_assemble)
    {
        unsigned any_node = rElement.GetNodeGlobalIndex(0);
        mStateVariablesAtQuadPoint.resize(this->mpCardiacTissue->GetCardiacCellOrHaloCell(any_node)->GetNumberOfStateVariables() );
    }
 
    return will_assemble;
}
bool AbstractCorrectionTermAssembler<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM>::ElementAssemblyCriterion(Element<ELEMENT_DIM,SPACE_DIM>& rElement) {…}
 
// Explicit instantiation
template class AbstractCorrectionTermAssembler<1,1,1>;
template class AbstractCorrectionTermAssembler<1,2,1>;
template class AbstractCorrectionTermAssembler<1,3,1>;
template class AbstractCorrectionTermAssembler<2,2,1>;
template class AbstractCorrectionTermAssembler<3,3,1>;
template class AbstractCorrectionTermAssembler<1,1,2>;
template class AbstractCorrectionTermAssembler<2,2,2>;
template class AbstractCorrectionTermAssembler<3,3,2>;
    // interpolate ionic current {…}
void AbstractCorrectionTermAssembler<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM>::IncrementInterpolatedQuantities( {…}
    for (unsigned i=0; i<mStateVariablesAtQuadPoint.size(); i++) {…}
void AbstractCorrectionTermAssembler<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM>::ResetInterpolatedQuantities() {…}
    } {…}
            unsigned node_zero = r_element.GetNodeGlobalIndex(0); {…}
AbstractCorrectionTermAssembler<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM>::AbstractCorrectionTermAssembler( {…}