AbstractFeSurfaceIntegralAssembler.hpp

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#ifndef ABSTRACTFESURFACENTEGRALASSEMBLER_HPP_
#define ABSTRACTFESURFACENTEGRALASSEMBLER_HPP_

#include "AbstractFeAssemblerCommon.hpp"
#include "GaussianQuadratureRule.hpp"
#include "BoundaryConditionsContainer.hpp"
#include "PetscVecTools.hpp"
#include "PetscMatTools.hpp"


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
class AbstractFeSurfaceIntegralAssembler : public AbstractFeAssemblerCommon<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM,true,false,NORMAL>
{
protected:
    AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>* mpMesh;

    BoundaryConditionsContainer<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>* mpBoundaryConditions;

    GaussianQuadratureRule<ELEMENT_DIM-1>* mpSurfaceQuadRule;

    typedef LinearBasisFunction<ELEMENT_DIM-1> SurfaceBasisFunction;

    virtual c_vector<double, PROBLEM_DIM*ELEMENT_DIM> ComputeVectorSurfaceTerm(
        const BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>& rSurfaceElement,
        c_vector<double, ELEMENT_DIM>& rPhi,
        ChastePoint<SPACE_DIM>& rX)
    {
        // If this line is reached this means this method probably hasn't been over-ridden correctly in
        // the concrete class
        NEVER_REACHED;
        return zero_vector<double>(ELEMENT_DIM*PROBLEM_DIM);
    }

    virtual void AssembleOnSurfaceElement(const BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>& rSurfaceElement,
                                          c_vector<double, PROBLEM_DIM*ELEMENT_DIM>& rBSurfElem);


    void DoAssemble();


public:
    AbstractFeSurfaceIntegralAssembler(AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh,
                                       BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM>* pBoundaryConditions);

    virtual ~AbstractFeSurfaceIntegralAssembler();

    void ResetBoundaryConditionsContainer(BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM>* pBoundaryConditions)
    {
        assert(pBoundaryConditions);
        this->mpBoundaryConditions = pBoundaryConditions;
    }
};


template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
AbstractFeSurfaceIntegralAssembler<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::AbstractFeSurfaceIntegralAssembler(
            AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh,
            BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM>* pBoundaryConditions)
    : AbstractFeAssemblerCommon<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM,true,false,NORMAL>(),
      mpMesh(pMesh),
      mpBoundaryConditions(pBoundaryConditions)
{
    assert(pMesh);
    assert(pBoundaryConditions);
    // Default to 2nd order quadrature.  Our default basis functions are piecewise linear
    // which means that we are integrating functions which in the worst case (mass matrix)
    // are quadratic.
    mpSurfaceQuadRule = new GaussianQuadratureRule<ELEMENT_DIM-1>(2);
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
AbstractFeSurfaceIntegralAssembler<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::~AbstractFeSurfaceIntegralAssembler()
{
    delete mpSurfaceQuadRule;
}


template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractFeSurfaceIntegralAssembler<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::DoAssemble()
{
    assert(this->mAssembleVector);

    HeartEventHandler::BeginEvent(HeartEventHandler::NEUMANN_BCS);

    // Loop over surface elements with non-zero Neumann boundary conditions
    if (mpBoundaryConditions->AnyNonZeroNeumannConditions())
    {
        typename BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM>::NeumannMapIterator
            neumann_iterator = mpBoundaryConditions->BeginNeumann();

        c_vector<double, PROBLEM_DIM*ELEMENT_DIM> b_surf_elem;

        // Iterate over defined conditions
        while (neumann_iterator != mpBoundaryConditions->EndNeumann())
        {
            const BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>& r_surf_element = *(neumann_iterator->first);
            AssembleOnSurfaceElement(r_surf_element, b_surf_elem);

            const size_t STENCIL_SIZE=PROBLEM_DIM*ELEMENT_DIM; // problem_dim*num_nodes_on_surface_element
            unsigned p_indices[STENCIL_SIZE];
            r_surf_element.GetStiffnessMatrixGlobalIndices(PROBLEM_DIM, p_indices);
            PetscVecTools::AddMultipleValues<STENCIL_SIZE>(this->mVectorToAssemble, p_indices, b_surf_elem);
            ++neumann_iterator;
        }
    }

    HeartEventHandler::EndEvent(HeartEventHandler::NEUMANN_BCS);
}


template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractFeSurfaceIntegralAssembler<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::AssembleOnSurfaceElement(
            const BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>& rSurfaceElement,
            c_vector<double, PROBLEM_DIM*ELEMENT_DIM>& rBSurfElem)
{
    c_vector<double, SPACE_DIM> weighted_direction;
    double jacobian_determinant;
    mpMesh->GetWeightedDirectionForBoundaryElement(rSurfaceElement.GetIndex(), weighted_direction, jacobian_determinant);

    rBSurfElem.clear();

    // Allocate memory for the basis function values
    c_vector<double, ELEMENT_DIM>  phi;

    // Loop over Gauss points
    for (unsigned quad_index=0; quad_index<mpSurfaceQuadRule->GetNumQuadPoints(); quad_index++)
    {
        const ChastePoint<ELEMENT_DIM-1>& quad_point = mpSurfaceQuadRule->rGetQuadPoint(quad_index);

        SurfaceBasisFunction::ComputeBasisFunctions(quad_point, phi);

        // Interpolation: X only

        // The location of the Gauss point in the original element will be stored in x
        ChastePoint<SPACE_DIM> x(0,0,0);

        this->ResetInterpolatedQuantities();
        for (unsigned i=0; i<rSurfaceElement.GetNumNodes(); i++)
        {
            const c_vector<double, SPACE_DIM> node_loc = rSurfaceElement.GetNode(i)->rGetLocation();
            x.rGetLocation() += phi(i)*node_loc;

            // Allow the concrete version of the assembler to interpolate any desired quantities
            this->IncrementInterpolatedQuantities(phi(i), rSurfaceElement.GetNode(i));
        }


        // Create elemental contribution

        double wJ = jacobian_determinant * mpSurfaceQuadRule->GetWeight(quad_index);
        noalias(rBSurfElem) += ComputeVectorSurfaceTerm(rSurfaceElement, phi, x) * wJ;
    }
}

#endif // ABSTRACTFESURFACENTEGRALASSEMBLER_HPP_