AbstractFeSurfaceIntegralAssembler.hpp

/*
 
Copyright (c) 2005-2025, University of Oxford.
All rights reserved.
 
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.
 
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
 * Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.
 * Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.
 * Neither the name of the University of Oxford nor the names of its
   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.
 
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
*/
 
#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;
 
    // LCOV_EXCL_START
    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 c_vector<double, PROBLEM_DIM*ELEMENT_DIM> ComputeVectorSurfaceTerm( {…}
    // LCOV_EXCL_STOP
 
    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;
    }
    void ResetBoundaryConditionsContainer(BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM>* 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);
}
AbstractFeSurfaceIntegralAssembler<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::AbstractFeSurfaceIntegralAssembler( {…}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
AbstractFeSurfaceIntegralAssembler<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::~AbstractFeSurfaceIntegralAssembler()
{
    delete mpSurfaceQuadRule;
}
AbstractFeSurfaceIntegralAssembler<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::~AbstractFeSurfaceIntegralAssembler() {…}
    virtual ~AbstractFeSurfaceIntegralAssembler(); {…}
 
 
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);
}
void AbstractFeSurfaceIntegralAssembler<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::DoAssemble() {…}
 
 
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;
    }
}
void AbstractFeSurfaceIntegralAssembler<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::AssembleOnSurfaceElement( {…}
 
#endif // ABSTRACTFESURFACENTEGRALASSEMBLER_HPP_
    AbstractFeSurfaceIntegralAssembler(AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh, {…}
    void DoAssemble(); {…}
    virtual void AssembleOnSurfaceElement(const BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>& rSurfaceElement, {…}
class AbstractFeSurfaceIntegralAssembler : public AbstractFeAssemblerCommon<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM,true,false,NORMAL> {…};