MonodomainProblem.cpp

/*

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*/

#include "MonodomainProblem.hpp"

#include "Exception.hpp"
#include "ReplicatableVector.hpp"
#include "MonodomainSolver.hpp"
#include "OperatorSplittingMonodomainSolver.hpp"


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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractDynamicLinearPdeSolver<ELEMENT_DIM, SPACE_DIM, 1>* MonodomainProblem<ELEMENT_DIM, SPACE_DIM>::CreateSolver()
{
    assert(mpMonodomainTissue);
    /*
     * NOTE: The this->mpBoundaryConditionsContainer.get() lines below convert a
     * boost::shared_ptr to a normal pointer, as this is what the solvers are
     * expecting. We have to be a bit careful though as boost could decide to delete
     * them whenever it feels like as it won't count the assembers as using them.
     *
     * As long as they are kept as member variables here for as long as they are
     * required in the solvers it should all work OK.
     */

    if (HeartConfig::Instance()->GetUseReactionDiffusionOperatorSplitting())
    {
        return new OperatorSplittingMonodomainSolver<ELEMENT_DIM,SPACE_DIM>(this->mpMesh,
                                                                            mpMonodomainTissue,
                                                                            this->mpBoundaryConditionsContainer.get());
    }
    else
    {
        return new MonodomainSolver<ELEMENT_DIM,SPACE_DIM>(this->mpMesh,
                                                           mpMonodomainTissue,
                                                           this->mpBoundaryConditionsContainer.get());
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
MonodomainProblem<ELEMENT_DIM, SPACE_DIM>::MonodomainProblem(AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>* pCellFactory)
        : AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, 1>(pCellFactory),
          mpMonodomainTissue(NULL)
{
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
MonodomainProblem<ELEMENT_DIM, SPACE_DIM>::MonodomainProblem()
    : AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, 1>(),
      mpMonodomainTissue(NULL)
{
}

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
MonodomainTissue<ELEMENT_DIM,SPACE_DIM> * MonodomainProblem<ELEMENT_DIM, SPACE_DIM>::GetMonodomainTissue()
{
    assert(mpMonodomainTissue != NULL);
    return mpMonodomainTissue;
}

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

    double v_max, v_min;

    VecMax( this->mSolution, PETSC_NULL, &v_max );
    VecMin( this->mSolution, PETSC_NULL, &v_min );

    if (PetscTools::AmMaster())
    {
        std::cout << " V = " << "[" <<v_min << ", " << v_max << "]" << "\n" << std::flush;
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MonodomainProblem<ELEMENT_DIM, SPACE_DIM>::DefineWriterColumns(bool extending)
{
    AbstractCardiacProblem<ELEMENT_DIM,SPACE_DIM,1>::DefineWriterColumns(extending);
    AbstractCardiacProblem<ELEMENT_DIM,SPACE_DIM,1>::DefineExtraVariablesWriterColumns(extending);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MonodomainProblem<ELEMENT_DIM, SPACE_DIM>::WriteOneStep(double time, Vec voltageVec)
{
    this->mpWriter->PutUnlimitedVariable(time);
    this->mpWriter->PutVector(this->mVoltageColumnId, voltageVec);
    AbstractCardiacProblem<ELEMENT_DIM,SPACE_DIM,1>::WriteExtraVariablesOneStep();
}


// Explicit instantiation

template class MonodomainProblem<1,1>;
template class MonodomainProblem<1,2>;
template class MonodomainProblem<1,3>;
template class MonodomainProblem<2,2>;
template class MonodomainProblem<3,3>;



// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS2(MonodomainProblem, 1, 1)
EXPORT_TEMPLATE_CLASS2(MonodomainProblem, 1, 2)
EXPORT_TEMPLATE_CLASS2(MonodomainProblem, 1, 3)
EXPORT_TEMPLATE_CLASS2(MonodomainProblem, 2, 2)
EXPORT_TEMPLATE_CLASS2(MonodomainProblem, 3, 3)