Electrodes.cpp

/*

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#include "Electrodes.hpp"
#include "DistributedTetrahedralMesh.hpp"
#include "IsNan.hpp"
#include "HeartConfig.hpp"

template<unsigned DIM>
Electrodes<DIM>::Electrodes(AbstractTetrahedralMesh<DIM,DIM>& rMesh)
    : mpMesh(&rMesh),
      mLeftElectrodeArea(0.0),
      mRightElectrodeArea(0.0)
{
    unsigned axis_index;
    double magnitude, duration;

    HeartConfig::Instance()->GetElectrodeParameters(mGroundSecondElectrode, axis_index, magnitude, mStartTime, duration);

    assert(axis_index < DIM);
    assert(duration > 0);
    mEndTime = mStartTime + duration;
    mAreActive = false; // consider electrodes initially switched off!

    ChasteCuboid<DIM> bounding_box = mpMesh->CalculateBoundingBox();
    double global_min = bounding_box.rGetLowerCorner()[axis_index];
    double global_max = bounding_box.rGetUpperCorner()[axis_index];

    mpBoundaryConditionsContainer.reset(new BoundaryConditionsContainer<DIM,DIM,2>);


    double input_flux;
    double output_flux;

    try
    {
        ComputeElectrodesAreasAndCheckEquality(axis_index, global_min, global_max);
        input_flux = magnitude;
        output_flux = -input_flux;

    }
    catch (Exception&)
    {
        // magnitude of second electrode scaled so that left_area*magnitude_left = -right_area*magnitude_right
        input_flux = magnitude;
        output_flux = -input_flux*mLeftElectrodeArea/mRightElectrodeArea;

        // Paranoia. In case one of the areas is 0
        assert( ! std::isnan(output_flux));
        assert( output_flux != 0.0);
    }

    ConstBoundaryCondition<DIM>* p_bc_flux_in = new ConstBoundaryCondition<DIM>(input_flux);
    ConstBoundaryCondition<DIM>* p_bc_flux_out = new ConstBoundaryCondition<DIM>(output_flux);

    // loop over boundary elements and add a non-zero phi_e boundary condition (ie extracellular
    // stimulus) if (assuming axis_index=0, etc) x=lowerValue (where x is the x-value of the centroid)
    for (typename AbstractTetrahedralMesh<DIM,DIM>::BoundaryElementIterator iter
            = mpMesh->GetBoundaryElementIteratorBegin();
       iter != mpMesh->GetBoundaryElementIteratorEnd();
       iter++)
    {
        if (fabs((*iter)->CalculateCentroid()[axis_index] - global_min) < 1e-6)
        {
            mpBoundaryConditionsContainer->AddNeumannBoundaryCondition(*iter, p_bc_flux_in,  1);
        }

        if (!mGroundSecondElectrode)
        {
            if (fabs((*iter)->CalculateCentroid()[axis_index] - global_max) < 1e-6)
            {
                mpBoundaryConditionsContainer->AddNeumannBoundaryCondition(*iter, p_bc_flux_out, 1);
            }
        }
    }

    // set up mGroundedNodes using opposite surface ie second electrode is
    // grounded
    if (mGroundSecondElectrode)
    {
        ConstBoundaryCondition<DIM>* p_zero_bc = new ConstBoundaryCondition<DIM>(0.0);
        // We will need to recalculate this when HasDirichletBoundaryConditions() is called.
        this->mpBoundaryConditionsContainer->ResetDirichletCommunication();

        for (typename AbstractTetrahedralMesh<DIM,DIM>::NodeIterator iter=mpMesh->GetNodeIteratorBegin();
             iter != mpMesh->GetNodeIteratorEnd();
             ++iter)
        {
            if (fabs((*iter).rGetLocation()[axis_index]-global_max) < 1e-6)
            {
                mpBoundaryConditionsContainer->AddDirichletBoundaryCondition(&(*iter), p_zero_bc, 1);
            }
        }

        //Unused boundary conditions will not be deleted by the b.c. container
        delete p_bc_flux_out;
    }
}



template<unsigned DIM>
boost::shared_ptr<BoundaryConditionsContainer<DIM,DIM,2> > Electrodes<DIM>::GetBoundaryConditionsContainer()
{
    //assert(mAreActive);
    return mpBoundaryConditionsContainer;
}


template<unsigned DIM>
bool Electrodes<DIM>::SwitchOff(double time)
{
    // This smidge has to be the same as the one below
    double smidge = 1e-10;
    if (mAreActive && time>mEndTime-smidge)
    {
        mAreActive = false;
        return true;
    }

    return false;
}

template<unsigned DIM>
bool Electrodes<DIM>::SwitchOn(double time)
{
    // This smidge has to be the same as the one above.
    double smidge = 1e-10;
    if (!mAreActive && time>=mStartTime && time<=mEndTime - smidge)
    {
        mAreActive = true;
        return true;
    }

    return false;
}

template<unsigned DIM>
void Electrodes<DIM>::ComputeElectrodesAreasAndCheckEquality(unsigned dimensionIndex, double lowerValue, double upperValue)
{
    //
    // loop over boundary elements and determine areas of the electrode faces
    //
    double local_left_area = 0.0;
    double local_right_area = 0.0;

    c_vector<double,DIM> weighted_direction;
    double jacobian_determinant;


    for (typename AbstractTetrahedralMesh<DIM,DIM>::BoundaryElementIterator iter
             = mpMesh->GetBoundaryElementIteratorBegin();
         iter != mpMesh->GetBoundaryElementIteratorEnd();
         iter++)
    {
        if ( mpMesh->CalculateDesignatedOwnershipOfBoundaryElement( (*iter)->GetIndex() ))
        {
            if (fabs((*iter)->CalculateCentroid()[dimensionIndex] - lowerValue) < 1e-6)
            {
                mpMesh->GetWeightedDirectionForBoundaryElement((*iter)->GetIndex(), weighted_direction, jacobian_determinant);
                local_left_area += jacobian_determinant;
            }

            if (fabs((*iter)->CalculateCentroid()[dimensionIndex] - upperValue) < 1e-6)
            {
                mpMesh->GetWeightedDirectionForBoundaryElement((*iter)->GetIndex(), weighted_direction, jacobian_determinant);
                local_right_area += jacobian_determinant;
            }
        }
    }

    if(DIM==3)
    {
        // if the dimension of the face is 1, the mapping is from the face to the canonical element [0,1], so the
        // jacobian_determinants used above will be exactly the areas of the faces
        // if the dimension of the face is 1, the mapping is from the face to the canonical element, the triangle
        // with nodes (0,0), (0,1), (1,0), which has area 0.5, so scale the jacobian_determinants by 0.5 to
        // get the face areas, ie scale the total area by 0.5:
        // (Not technically needed as it is only the ratio of these that is used but since we are calling the variables
        // 'area's we ought to be correct).
        local_left_area /= 2.0;
        local_right_area /= 2.0;
    }

    int mpi_ret = MPI_Allreduce(&local_left_area, &mLeftElectrodeArea, 1, MPI_DOUBLE, MPI_SUM, PETSC_COMM_WORLD);
    UNUSED_OPT(mpi_ret);
    assert(mpi_ret == MPI_SUCCESS);

    mpi_ret = MPI_Allreduce(&local_right_area, &mRightElectrodeArea, 1, MPI_DOUBLE, MPI_SUM, PETSC_COMM_WORLD);
    assert(mpi_ret == MPI_SUCCESS);

    if (mLeftElectrodeArea != mRightElectrodeArea)
    {
        EXCEPTION("Electrodes have different area");
    }
}


// Explicit instantiation

template class Electrodes<1>;
template class Electrodes<2>;
template class Electrodes<3>;


// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(Electrodes)