MonodomainPurkinjeProblem.cpp

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#include "MonodomainPurkinjeProblem.hpp"
#include "MonodomainPurkinjeSolver.hpp"
#include "Exception.hpp"
#include "ReplicatableVector.hpp"


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractCardiacTissue<ELEMENT_DIM,SPACE_DIM>* MonodomainPurkinjeProblem<ELEMENT_DIM, SPACE_DIM>::CreateCardiacTissue()
{
    return new MonodomainTissue<ELEMENT_DIM,SPACE_DIM>(this->mpCellFactory, HeartConfig::Instance()->GetUseStateVariableInterpolation());
}


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractDynamicLinearPdeSolver<ELEMENT_DIM, SPACE_DIM, 2>* MonodomainPurkinjeProblem<ELEMENT_DIM, SPACE_DIM>::CreateSolver()
{
    assert(!HeartConfig::Instance()->GetUseReactionDiffusionOperatorSplitting());
    MixedDimensionMesh<ELEMENT_DIM,SPACE_DIM>* p_mesh = dynamic_cast<MixedDimensionMesh<ELEMENT_DIM,SPACE_DIM>*>(this->mpMesh);
    EXCEPT_IF_NOT(p_mesh); 
    MonodomainTissue<ELEMENT_DIM,SPACE_DIM>* p_tissue = dynamic_cast<MonodomainTissue<ELEMENT_DIM,SPACE_DIM>*>(this->GetTissue());
    assert(p_tissue);
    return new MonodomainPurkinjeSolver<ELEMENT_DIM,SPACE_DIM>(p_mesh,
                                                               p_tissue,
                                                               this->mpBoundaryConditionsContainer.get());
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MonodomainPurkinjeProblem<ELEMENT_DIM,SPACE_DIM>::CreateMeshFromHeartConfig()
{
    this->mpMesh = new MixedDimensionMesh<ELEMENT_DIM, SPACE_DIM>(HeartConfig::Instance()->GetMeshPartitioning());
}


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
Vec MonodomainPurkinjeProblem<ELEMENT_DIM, SPACE_DIM>::CreateInitialCondition()
{
    Vec init_cond = AbstractCardiacProblem<ELEMENT_DIM,SPACE_DIM,2>::CreateInitialCondition();

    // Get the Purkinje voltage stripe
    DistributedVector ic = this->mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(init_cond);
    DistributedVector::Stripe purkinje_voltage_stripe = DistributedVector::Stripe(ic, 1);

    for (DistributedVector::Iterator index = ic.Begin();
         index != ic.End();
         ++index)
    {
        purkinje_voltage_stripe[index] = this->GetTissue()->GetPurkinjeCell(index.Global)->GetVoltage();
        // Note that it doesn't matter if the cell is fake, as this will give a zero voltage for nodes not in the
        // Purkinje network.
    }
    ic.Restore();

    return init_cond;
}


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
MonodomainPurkinjeProblem<ELEMENT_DIM, SPACE_DIM>::MonodomainPurkinjeProblem(AbstractPurkinjeCellFactory<ELEMENT_DIM,SPACE_DIM>* pCellFactory)
        : AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, 2>(pCellFactory),
          mPurkinjeVoltageColumnId(UNSIGNED_UNSET)
{
}


// LCOV_EXCL_START
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
MonodomainPurkinjeProblem<ELEMENT_DIM, SPACE_DIM>::MonodomainPurkinjeProblem()
    : AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, 2>(),
      mPurkinjeVoltageColumnId(UNSIGNED_UNSET)
{
}
// LCOV_EXCL_STOP

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
MonodomainPurkinjeProblem<ELEMENT_DIM, SPACE_DIM>::~MonodomainPurkinjeProblem()
{
}


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MonodomainPurkinjeProblem<ELEMENT_DIM, SPACE_DIM>::WriteInfo(double time)
{
    if (PetscTools::AmMaster())
    {
        std::cout << "Solved to time " << time << "\n" << std::flush;
    }

    double v_max, v_min, v_purk_max, v_purk_min;

    VecStrideMax( this->mSolution, 0, PETSC_NULL, &v_max );
    VecStrideMin( this->mSolution, 0, PETSC_NULL, &v_min );

    VecStrideMax( this->mSolution, 1, PETSC_NULL, &v_purk_max );
    VecStrideMin( this->mSolution, 1, PETSC_NULL, &v_purk_min );

    // avoid printing 1e-320 etc
    if(fabs(v_purk_min)<1e-20)
    {
        // It's very hard to hit this, as you'd need the whole Purkinje system to be activated
        v_purk_min = 0.0; // LCOV_EXCL_LINE
    }

    if(fabs(v_purk_max)<1e-20)
    {
        v_purk_max = 0.0;
    }

    if (PetscTools::AmMaster())
    {
        std::cout << " V_myo; V_purk = " << "[" <<v_min << ", " << v_max << "]" << ";\t"
                  << "[" << v_purk_min << ", " << v_purk_max << "]" << "\n"
                  << std::flush;
    }
}


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MonodomainPurkinjeProblem<ELEMENT_DIM, SPACE_DIM>::DefineWriterColumns(bool extending)
{
    AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM,2>::DefineWriterColumns(extending);
    if (extending)
    {
        mPurkinjeVoltageColumnId = this->mpWriter->GetVariableByName("V_purk");
    }
    else
    {
        mPurkinjeVoltageColumnId = this->mpWriter->DefineVariable("V_purk","mV");
    }
    AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM,2>::DefineExtraVariablesWriterColumns(extending);
}


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MonodomainPurkinjeProblem<ELEMENT_DIM, SPACE_DIM>::WriteOneStep(double time, Vec voltageVec)
{
    this->mpWriter->PutUnlimitedVariable(time);
    std::vector<int> variable_ids;
    variable_ids.push_back(this->mVoltageColumnId);
    variable_ids.push_back(mPurkinjeVoltageColumnId);
    this->mpWriter->PutStripedVector(variable_ids, voltageVec);
    AbstractCardiacProblem<ELEMENT_DIM,SPACE_DIM,2>::WriteExtraVariablesOneStep();
}


// Explicit instantiation

template class MonodomainPurkinjeProblem<2,2>;
template class MonodomainPurkinjeProblem<3,3>;



// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS2(MonodomainPurkinjeProblem, 2, 2)
EXPORT_TEMPLATE_CLASS2(MonodomainPurkinjeProblem, 3, 3)