AbstractContinuumMechanicsAssembler.hpp

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#ifndef ABSTRACTCONTINUUMMECHANICSASSEMBLER_HPP_
#define ABSTRACTCONTINUUMMECHANICSASSEMBLER_HPP_

#include "AbstractFeAssemblerInterface.hpp"
#include "QuadraticMesh.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"


template<unsigned DIM, bool CAN_ASSEMBLE_VECTOR, bool CAN_ASSEMBLE_MATRIX>
class AbstractContinuumMechanicsAssembler : public AbstractFeAssemblerInterface<CAN_ASSEMBLE_VECTOR,CAN_ASSEMBLE_MATRIX>
{
    static const bool BLOCK_SYMMETRIC_MATRIX = true; //generalise to non-block symmetric matrices later (when needed maybe)

    static const unsigned NUM_VERTICES_PER_ELEMENT = DIM+1;

    static const unsigned NUM_NODES_PER_ELEMENT = (DIM+1)*(DIM+2)/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:
    QuadraticMesh<DIM>* mpMesh;

    GaussianQuadratureRule<DIM>* mpQuadRule;

    void DoAssemble();


    virtual c_matrix<double,SPATIAL_BLOCK_SIZE_ELEMENTAL,SPATIAL_BLOCK_SIZE_ELEMENTAL> ComputeSpatialSpatialMatrixTerm(
        c_vector<double, NUM_NODES_PER_ELEMENT>& rQuadPhi,
        c_matrix<double, DIM, NUM_NODES_PER_ELEMENT>& rGradQuadPhi,
        c_vector<double,DIM>& rX,
        Element<DIM,DIM>* pElement)
    {
        return zero_matrix<double>(SPATIAL_BLOCK_SIZE_ELEMENTAL,SPATIAL_BLOCK_SIZE_ELEMENTAL);
    }

    virtual c_matrix<double,SPATIAL_BLOCK_SIZE_ELEMENTAL,PRESSURE_BLOCK_SIZE_ELEMENTAL> ComputeSpatialPressureMatrixTerm(
        c_vector<double, NUM_NODES_PER_ELEMENT>& rQuadPhi,
        c_matrix<double, DIM, NUM_NODES_PER_ELEMENT>& rGradQuadPhi,
        c_vector<double, NUM_VERTICES_PER_ELEMENT>& rLinearPhi,
        c_matrix<double, DIM, NUM_VERTICES_PER_ELEMENT>& rGradLinearPhi,
        c_vector<double,DIM>& rX,
        Element<DIM,DIM>* pElement)
    {
        return zero_matrix<double>(SPATIAL_BLOCK_SIZE_ELEMENTAL,PRESSURE_BLOCK_SIZE_ELEMENTAL);
    }


    virtual c_matrix<double,PRESSURE_BLOCK_SIZE_ELEMENTAL,PRESSURE_BLOCK_SIZE_ELEMENTAL> ComputePressurePressureMatrixTerm(
        c_vector<double, NUM_VERTICES_PER_ELEMENT>& rLinearPhi,
        c_matrix<double, DIM, NUM_VERTICES_PER_ELEMENT>& rGradLinearPhi,
        c_vector<double,DIM>& rX,
        Element<DIM,DIM>* pElement)
    {
        return zero_matrix<double>(PRESSURE_BLOCK_SIZE_ELEMENTAL,PRESSURE_BLOCK_SIZE_ELEMENTAL);
    }


    virtual c_vector<double,SPATIAL_BLOCK_SIZE_ELEMENTAL> ComputeSpatialVectorTerm(
        c_vector<double, NUM_NODES_PER_ELEMENT>& rQuadPhi,
        c_matrix<double, DIM, NUM_NODES_PER_ELEMENT>& rGradQuadPhi,
        c_vector<double,DIM>& rX,
        Element<DIM,DIM>* pElement)
    {
        return zero_vector<double>(SPATIAL_BLOCK_SIZE_ELEMENTAL);
    }


    virtual c_vector<double,PRESSURE_BLOCK_SIZE_ELEMENTAL> ComputePressureVectorTerm(
            c_vector<double, NUM_VERTICES_PER_ELEMENT>& rLinearPhi,
            c_matrix<double, DIM, NUM_VERTICES_PER_ELEMENT>& rGradLinearPhi,
            c_vector<double,DIM>& rX,
            Element<DIM,DIM>* pElement)
    {
        return zero_vector<double>(PRESSURE_BLOCK_SIZE_ELEMENTAL);
    }



    void AssembleOnElement(Element<DIM, DIM>& rElement,
                           c_matrix<double, STENCIL_SIZE, STENCIL_SIZE >& rAElem,
                           c_vector<double, STENCIL_SIZE>& rBElem);

public:
    AbstractContinuumMechanicsAssembler(QuadraticMesh<DIM>* pMesh, unsigned numQuadPoints = 3)
        : AbstractFeAssemblerInterface<CAN_ASSEMBLE_VECTOR,CAN_ASSEMBLE_MATRIX>(),
          mpMesh(pMesh)
    {
        assert(pMesh);
        mpQuadRule = new GaussianQuadratureRule<DIM>(numQuadPoints);
    }


//    void SetCurrentSolution(Vec currentSolution);


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


//template<unsigned DIM, bool CAN_ASSEMBLE_VECTOR, bool CAN_ASSEMBLE_MATRIX>
//void AbstractContinuumMechanicsAssembler<DIM,CAN_ASSEMBLE_VECTOR,CAN_ASSEMBLE_MATRIX>::SetCurrentSolution(Vec currentSolution)
//{
//    assert(currentSolution != NULL);
//
//    // Replicate the current solution and store so can be used in AssembleOnElement
//    HeartEventHandler::BeginEvent(HeartEventHandler::COMMUNICATION);
//    mCurrentSolutionOrGuessReplicated.ReplicatePetscVector(currentSolution);
//    HeartEventHandler::EndEvent(HeartEventHandler::COMMUNICATION);
//
//    // The AssembleOnElement type methods will determine if a current solution or
//    // current guess exists by looking at the size of the replicated vector, so
//    // check the size is zero if there isn't a current solution.
//    assert(mCurrentSolutionOrGuessReplicated.GetSize() > 0);
//}

template<unsigned DIM, bool CAN_ASSEMBLE_VECTOR, bool CAN_ASSEMBLE_MATRIX>
void AbstractContinuumMechanicsAssembler<DIM,CAN_ASSEMBLE_VECTOR,CAN_ASSEMBLE_MATRIX>::DoAssemble()
{
    assert(this->mAssembleMatrix || this->mAssembleVector);
    if (this->mAssembleMatrix)
    {
        if(this->mMatrixToAssemble==NULL)
        {
            EXCEPTION("Matrix to be assembled has not been set");
        }
        if( PetscMatTools::GetSize(this->mMatrixToAssemble) != (DIM+1)*mpMesh->GetNumNodes() )
        {
            EXCEPTION("Matrix provided to be assembled has size " << PetscMatTools::GetSize(this->mMatrixToAssemble) << ", not expected size of " << (DIM+1)*mpMesh->GetNumNodes() << " ((dim+1)*num_nodes)");
        }
    }

    if (this->mAssembleVector)
    {
        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->mAssembleVector && this->mZeroVectorBeforeAssembly)
    {
        // Note PetscVecTools::Finalise(this->mVectorToAssemble); on an unused matrix
        // would "compress" data and make any pre-allocated entries redundant.
        PetscVecTools::Zero(this->mVectorToAssemble);
    }
    if (this->mAssembleMatrix && this->mZeroMatrixBeforeAssembly)
    {
        // Note PetscMatTools::Finalise(this->mMatrixToAssemble); on an unused matrix
        // would "compress" data and make any pre-allocated entries redundant.
        PetscMatTools::Zero(this->mMatrixToAssemble);
    }

    c_matrix<double, STENCIL_SIZE, STENCIL_SIZE> a_elem = zero_matrix<double>(STENCIL_SIZE,STENCIL_SIZE);
    c_vector<double, STENCIL_SIZE> b_elem = zero_vector<double>(STENCIL_SIZE);


    // Loop over elements
    for (typename AbstractTetrahedralMesh<DIM, DIM>::ElementIterator iter = mpMesh->GetElementIteratorBegin();
         iter != mpMesh->GetElementIteratorEnd();
         ++iter)
    {
        Element<DIM, DIM>& r_element = *iter;

        // Test for ownership first, since it's pointless to test the criterion on something which we might know nothing about.
        if ( r_element.GetOwnership() == true  /*&& ElementAssemblyCriterion(r_element)==true*/ )
        {
            #define COVERAGE_IGNORE
            // note: if assemble matrix only
            if(CommandLineArguments::Instance()->OptionExists("-mech_very_verbose") && this->mAssembleMatrix)
            {
                std::cout << "\r[" << PetscTools::GetMyRank() << "]: Element " << r_element.GetIndex() << " of " << mpMesh->GetNumElements() << std::flush;
            }
            #undef COVERAGE_IGNORE


            AssembleOnElement(r_element, a_elem, b_elem);

            // Note that a different ordering is used for the elemental matrix compared to the global matrix.
            // See comments about ordering above.
            unsigned p_indices[STENCIL_SIZE];
            // Work out the mapping for spatial terms
            for (unsigned i=0; i<NUM_NODES_PER_ELEMENT; i++)
            {
                for (unsigned j=0; j<DIM; j++)
                {
                    // DIM+1 on the right-hand side here is the problem dimension
                    p_indices[DIM*i+j] = (DIM+1)*r_element.GetNodeGlobalIndex(i) + j;
                }
            }
            // Work out the mapping for pressure terms
            for (unsigned i=0; i<NUM_VERTICES_PER_ELEMENT; i++)
            {
                p_indices[DIM*NUM_NODES_PER_ELEMENT + i] = (DIM+1)*r_element.GetNodeGlobalIndex(i)+DIM;
            }


            if (this->mAssembleMatrix)
            {
                PetscMatTools::AddMultipleValues<STENCIL_SIZE>(this->mMatrixToAssemble, p_indices, a_elem);
            }

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

template<unsigned DIM, bool CAN_ASSEMBLE_VECTOR, bool CAN_ASSEMBLE_MATRIX>
void AbstractContinuumMechanicsAssembler<DIM,CAN_ASSEMBLE_VECTOR,CAN_ASSEMBLE_MATRIX>::AssembleOnElement(Element<DIM, DIM>& rElement,
                                                                                                         c_matrix<double, STENCIL_SIZE, STENCIL_SIZE >& rAElem,
                                                                                                         c_vector<double, STENCIL_SIZE>& rBElem)
{
    static c_matrix<double,DIM,DIM> jacobian;
    static c_matrix<double,DIM,DIM> inverse_jacobian;
    double jacobian_determinant;

    mpMesh->GetInverseJacobianForElement(rElement.GetIndex(), jacobian, jacobian_determinant, inverse_jacobian);

    if (this->mAssembleMatrix)
    {
        rAElem.clear();
    }

    if (this->mAssembleVector)
    {
        rBElem.clear();
    }


    // Allocate memory for the basis functions values and derivative values
    static c_vector<double, NUM_VERTICES_PER_ELEMENT> linear_phi;
    static c_vector<double, NUM_NODES_PER_ELEMENT> quad_phi;
    static c_matrix<double, DIM, NUM_NODES_PER_ELEMENT> grad_quad_phi;
    static c_matrix<double, DIM, NUM_VERTICES_PER_ELEMENT> grad_linear_phi;

    c_vector<double,DIM> body_force;

    // Loop over Gauss points
    for (unsigned quadrature_index=0; quadrature_index < mpQuadRule->GetNumQuadPoints(); quadrature_index++)
    {
        double wJ = jacobian_determinant * mpQuadRule->GetWeight(quadrature_index);
        const ChastePoint<DIM>& quadrature_point = mpQuadRule->rGetQuadPoint(quadrature_index);

        // Set up basis function info
        LinearBasisFunction<DIM>::ComputeBasisFunctions(quadrature_point, linear_phi);
        QuadraticBasisFunction<DIM>::ComputeBasisFunctions(quadrature_point, quad_phi);
        QuadraticBasisFunction<DIM>::ComputeTransformedBasisFunctionDerivatives(quadrature_point, inverse_jacobian, grad_quad_phi);
        LinearBasisFunction<DIM>::ComputeTransformedBasisFunctionDerivatives(quadrature_point, inverse_jacobian, grad_linear_phi);

        // interpolate X (ie physical location of this quad point).
        c_vector<double,DIM> X = zero_vector<double>(DIM);
        for (unsigned vertex_index=0; vertex_index<NUM_VERTICES_PER_ELEMENT; vertex_index++)
        {
            for(unsigned j=0; j<DIM; j++)
            {
                X(j) += linear_phi(vertex_index)*rElement.GetNode(vertex_index)->rGetLocation()(j);
            }
        }

        if(this->mAssembleVector)
        {
            c_vector<double,SPATIAL_BLOCK_SIZE_ELEMENTAL> b_spatial
                = ComputeSpatialVectorTerm(quad_phi, grad_quad_phi, X, &rElement);
            c_vector<double,PRESSURE_BLOCK_SIZE_ELEMENTAL> b_pressure = ComputePressureVectorTerm(linear_phi, grad_linear_phi, X, &rElement);

            for (unsigned i=0; i<SPATIAL_BLOCK_SIZE_ELEMENTAL; i++)
            {
                rBElem(i) += b_spatial(i)*wJ;
            }


            for (unsigned i=0; i<PRESSURE_BLOCK_SIZE_ELEMENTAL; i++)
            {
                rBElem(SPATIAL_BLOCK_SIZE_ELEMENTAL + i) += b_pressure(i)*wJ;
            }
        }


        if(this->mAssembleMatrix)
        {
            c_matrix<double,SPATIAL_BLOCK_SIZE_ELEMENTAL,SPATIAL_BLOCK_SIZE_ELEMENTAL> a_spatial_spatial
                = ComputeSpatialSpatialMatrixTerm(quad_phi, grad_quad_phi, X, &rElement);

            c_matrix<double,SPATIAL_BLOCK_SIZE_ELEMENTAL,PRESSURE_BLOCK_SIZE_ELEMENTAL> a_spatial_pressure
                = ComputeSpatialPressureMatrixTerm(quad_phi, grad_quad_phi, linear_phi, grad_linear_phi, X, &rElement);

            c_matrix<double,PRESSURE_BLOCK_SIZE_ELEMENTAL,SPATIAL_BLOCK_SIZE_ELEMENTAL> a_pressure_spatial;
            if(!BLOCK_SYMMETRIC_MATRIX)
            {
                NEVER_REACHED; // to-come: non-mixed problems
                //a_pressure_spatial = ComputeSpatialPressureMatrixTerm(quad_phi, grad_quad_phi, lin_phi, grad_lin_phi, x, &rElement);
            }

            c_matrix<double,PRESSURE_BLOCK_SIZE_ELEMENTAL,PRESSURE_BLOCK_SIZE_ELEMENTAL> a_pressure_pressure
                = ComputePressurePressureMatrixTerm(linear_phi, grad_linear_phi, X, &rElement);

            for (unsigned i=0; i<SPATIAL_BLOCK_SIZE_ELEMENTAL; i++)
            {
                for(unsigned j=0; j<SPATIAL_BLOCK_SIZE_ELEMENTAL; j++)
                {
                    rAElem(i,j) += a_spatial_spatial(i,j)*wJ;
                }

                for(unsigned j=0; j<PRESSURE_BLOCK_SIZE_ELEMENTAL; j++)
                {
                    rAElem(i, SPATIAL_BLOCK_SIZE_ELEMENTAL + j) += a_spatial_pressure(i,j)*wJ;
                }
            }

            for(unsigned i=0; i<PRESSURE_BLOCK_SIZE_ELEMENTAL; i++)
            {
                if(BLOCK_SYMMETRIC_MATRIX)
                {
                    for(unsigned j=0; j<SPATIAL_BLOCK_SIZE_ELEMENTAL; j++)
                    {
                        rAElem(SPATIAL_BLOCK_SIZE_ELEMENTAL + i, j) += a_spatial_pressure(j,i)*wJ;
                    }
                }
                else
                {
                    NEVER_REACHED; // to-come: non-mixed problems
                }

                for(unsigned j=0; j<PRESSURE_BLOCK_SIZE_ELEMENTAL; j++)
                {
                    rAElem(SPATIAL_BLOCK_SIZE_ELEMENTAL + i, SPATIAL_BLOCK_SIZE_ELEMENTAL + j) += a_pressure_pressure(i,j)*wJ;
                }
            }
        }
    }
}


#endif // ABSTRACTCONTINUUMMECHANICSASSEMBLER_HPP_