ContinuumMechanicsNeumannBcsAssembler.hpp

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#ifndef CONTINUUMMECHANICSNEUMANNBCSASSEMBLER_HPP_
#define CONTINUUMMECHANICSNEUMANNBCSASSEMBLER_HPP_

#include "AbstractFeAssemblerInterface.hpp"
#include "AbstractTetrahedralMesh.hpp"
#include "QuadraticMesh.hpp"
#include "DistributedQuadraticMesh.hpp"
#include "LinearBasisFunction.hpp"
#include "QuadraticBasisFunction.hpp"
#include "ReplicatableVector.hpp"
#include "DistributedVector.hpp"
#include "PetscTools.hpp"
#include "PetscVecTools.hpp"
#include "PetscMatTools.hpp"
#include "GaussianQuadratureRule.hpp"
#include "ContinuumMechanicsProblemDefinition.hpp"


template<unsigned DIM>
class ContinuumMechanicsNeumannBcsAssembler : public AbstractFeAssemblerInterface<true,false>
{
    static const unsigned NUM_VERTICES_PER_ELEMENT = DIM;

    static const unsigned NUM_NODES_PER_ELEMENT = DIM*(DIM+1)/2; // assuming quadratic

    static const unsigned SPATIAL_BLOCK_SIZE_ELEMENTAL = DIM*NUM_NODES_PER_ELEMENT;
    static const unsigned PRESSURE_BLOCK_SIZE_ELEMENTAL = NUM_VERTICES_PER_ELEMENT;

    static const unsigned STENCIL_SIZE = DIM*NUM_NODES_PER_ELEMENT + NUM_VERTICES_PER_ELEMENT;

protected:
    AbstractTetrahedralMesh<DIM,DIM>* mpMesh;

    ContinuumMechanicsProblemDefinition<DIM>* mpProblemDefinition;

    GaussianQuadratureRule<DIM-1>* mpQuadRule;

    void DoAssemble();


    void AssembleOnBoundaryElement(BoundaryElement<DIM-1,DIM>& rElement,
                                   c_vector<double, STENCIL_SIZE>& rBElem,
                                   unsigned boundaryConditionIndex);

public:
    ContinuumMechanicsNeumannBcsAssembler(AbstractTetrahedralMesh<DIM,DIM>* pMesh,
                                          ContinuumMechanicsProblemDefinition<DIM>* pProblemDefinition)
        : AbstractFeAssemblerInterface<true,false>(),
          mpMesh(pMesh),
          mpProblemDefinition(pProblemDefinition)
    {
        assert(pMesh);
        assert(pProblemDefinition);

        //Check that the mesh is Quadratic
        QuadraticMesh<DIM>* p_quad_mesh = dynamic_cast<QuadraticMesh<DIM>* >(pMesh);
        DistributedQuadraticMesh<DIM>* p_distributed_quad_mesh = dynamic_cast<DistributedQuadraticMesh<DIM>* >(pMesh);

        if(p_quad_mesh == NULL && p_distributed_quad_mesh == NULL)
        {
            EXCEPTION("Continuum mechanics solvers require a quadratic mesh");
        }
        // In general a mechanics problem is non-polynomial.
        // We therefore use the highest order integration rule available.
        mpQuadRule = new GaussianQuadratureRule<DIM-1>(3);
    }


    virtual ~ContinuumMechanicsNeumannBcsAssembler()
    {
        delete mpQuadRule;
    }
};


template<unsigned DIM>
void ContinuumMechanicsNeumannBcsAssembler<DIM>::DoAssemble()
{
    if(this->mVectorToAssemble==NULL)
    {
        EXCEPTION("Vector to be assembled has not been set");
    }

    if( PetscVecTools::GetSize(this->mVectorToAssemble) != (DIM+1)*mpMesh->GetNumNodes() )
    {
        EXCEPTION("Vector provided to be assembled has size " << PetscVecTools::GetSize(this->mVectorToAssemble) << ", not expected size of " << (DIM+1)*mpMesh->GetNumNodes() << " ((dim+1)*num_nodes)");
    }

    // Zero the matrix/vector if it is to be assembled
    if (this->mZeroVectorBeforeAssembly)
    {
        PetscVecTools::Zero(this->mVectorToAssemble);
    }


    if (mpProblemDefinition->GetTractionBoundaryConditionType() != NO_TRACTIONS)
    {
        c_vector<double, STENCIL_SIZE> b_elem = zero_vector<double>(STENCIL_SIZE);

        for (unsigned bc_index=0; bc_index<mpProblemDefinition->rGetTractionBoundaryElements().size(); bc_index++)
        {
            BoundaryElement<DIM-1,DIM>& r_boundary_element = *(mpProblemDefinition->rGetTractionBoundaryElements()[bc_index]);
            AssembleOnBoundaryElement(r_boundary_element, b_elem, bc_index);

            unsigned p_indices[STENCIL_SIZE];
            for (unsigned i=0; i<NUM_NODES_PER_ELEMENT; i++)
            {
                for (unsigned j=0; j<DIM; j++)
                {
                    p_indices[DIM*i+j] = (DIM+1)*r_boundary_element.GetNodeGlobalIndex(i) + j;
                }
            }
            // Note: The pressure block of b_elem will be zero, but this bit still needs to be
            // set to avoid memory leaks.
            for (unsigned i=0; i<DIM /*vertices per boundary elem */; i++)
            {
                p_indices[DIM*NUM_NODES_PER_ELEMENT + i] = (DIM+1)*r_boundary_element.GetNodeGlobalIndex(i)+DIM;
            }

            PetscVecTools::AddMultipleValues<STENCIL_SIZE>(this->mVectorToAssemble, p_indices, b_elem);
        }
    }
}



template<unsigned DIM>
void ContinuumMechanicsNeumannBcsAssembler<DIM>::AssembleOnBoundaryElement(BoundaryElement<DIM-1,DIM>& rBoundaryElement,
                                                                           c_vector<double,STENCIL_SIZE>& rBelem,
                                                                           unsigned boundaryConditionIndex)
{
    rBelem.clear();

    c_vector<double, DIM> weighted_direction;
    double jacobian_determinant;
    mpMesh->GetWeightedDirectionForBoundaryElement(rBoundaryElement.GetIndex(), weighted_direction, jacobian_determinant);

    c_vector<double,NUM_NODES_PER_ELEMENT> phi;

    for (unsigned quad_index=0; quad_index<mpQuadRule->GetNumQuadPoints(); quad_index++)
    {
        double wJ = jacobian_determinant * mpQuadRule->GetWeight(quad_index);
        const ChastePoint<DIM-1>& quad_point = mpQuadRule->rGetQuadPoint(quad_index);
        QuadraticBasisFunction<DIM-1>::ComputeBasisFunctions(quad_point, phi);

        c_vector<double,DIM> traction = zero_vector<double>(DIM);
        switch (mpProblemDefinition->GetTractionBoundaryConditionType())
        {
            case ELEMENTWISE_TRACTION:
            {
                traction = mpProblemDefinition->rGetElementwiseTractions()[boundaryConditionIndex];
                break;
            }
            default:
                // Functional traction not implemented yet..
                NEVER_REACHED;
        }

        for (unsigned index=0; index<NUM_NODES_PER_ELEMENT*DIM; index++)
        {
            unsigned spatial_dim = index%DIM;
            unsigned node_index = (index-spatial_dim)/DIM;

            assert(node_index < NUM_NODES_PER_ELEMENT);

            rBelem(index) += traction(spatial_dim) * phi(node_index) * wJ;
        }
    }
}


#endif // CONTINUUMMECHANICSNEUMANNBCSASSEMBLER_HPP_