AbstractFeSurfaceIntegralAssembler.hpp

/*

Copyright (C) University of Oxford, 2005-2011

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/

#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,
                                       unsigned numQuadPoints = 2);

    ~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,
            unsigned numQuadPoints)
    : AbstractFeAssemblerCommon<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM,true,false,NORMAL>(),
      mpMesh(pMesh),
      mpBoundaryConditions(pBoundaryConditions)
{
    assert(pMesh);
    assert(pBoundaryConditions);
    assert(numQuadPoints > 0);

    mpSurfaceQuadRule = new GaussianQuadratureRule<ELEMENT_DIM-1>(numQuadPoints);
}

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_