AbstractAssembler.hpp

/*

Copyright (C) University of Oxford, 2005-2010

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 _ABSTRACTASSEMBLER_HPP_
#define _ABSTRACTASSEMBLER_HPP_

#include "LinearBasisFunction.hpp"
#include "GaussianQuadratureRule.hpp"
#include "BoundaryConditionsContainer.hpp"
#include "LinearSystem.hpp"
#include "GaussianQuadratureRule.hpp"
#include "ReplicatableVector.hpp"
#include "DistributedVector.hpp"
#include "HeartEventHandler.hpp"

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
class AbstractAssembler
{
protected:

    BoundaryConditionsContainer<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>* mpBoundaryConditions;

    #define COVERAGE_IGNORE

    virtual void SetMatrixIsConst(bool matrixIsConstant=true)
    {
    }
    #undef COVERAGE_IGNORE

    virtual c_matrix<double,PROBLEM_DIM*(ELEMENT_DIM+1),PROBLEM_DIM*(ELEMENT_DIM+1)> ComputeMatrixTerm(
        c_vector<double, ELEMENT_DIM+1>& rPhi,
        c_matrix<double, SPACE_DIM, ELEMENT_DIM+1>& rGradPhi,
        ChastePoint<SPACE_DIM>& rX,
        c_vector<double,PROBLEM_DIM>& rU,
        c_matrix<double, PROBLEM_DIM, SPACE_DIM>& rGradU,
        Element<ELEMENT_DIM,SPACE_DIM>* pElement)=0;

    virtual c_vector<double,PROBLEM_DIM*(ELEMENT_DIM+1)> ComputeVectorTerm(
        c_vector<double, ELEMENT_DIM+1>& rPhi,
        c_matrix<double, SPACE_DIM, ELEMENT_DIM+1>& rGradPhi,
        ChastePoint<SPACE_DIM>& rX,
        c_vector<double,PROBLEM_DIM>& rU,
        c_matrix<double, PROBLEM_DIM, SPACE_DIM>& rGradU,
        Element<ELEMENT_DIM,SPACE_DIM>* pElement)=0;

    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)=0;

    virtual void AssembleOnElement(Element<ELEMENT_DIM,SPACE_DIM>& rElement,
                                   c_matrix<double, PROBLEM_DIM*(ELEMENT_DIM+1), PROBLEM_DIM*(ELEMENT_DIM+1) >& rAElem,
                                   c_vector<double, PROBLEM_DIM*(ELEMENT_DIM+1)>& rBElem,
                                   bool assembleVector,
                                   bool assembleMatrix)=0;

    virtual void AssembleOnSurfaceElement(const BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>& rSurfaceElement,
                                          c_vector<double, PROBLEM_DIM*ELEMENT_DIM>& rBSurfElem)=0;

    virtual void AssembleSystem(bool assembleVector, bool assembleMatrix,
                                Vec currentSolutionOrGuess=NULL, double currentTime=0.0)=0;

    virtual void PrepareForSolve()=0;

    virtual void PrepareForAssembleSystem(Vec currentSolutionOrGuess, double currentTime)
    {}

    virtual void FinaliseAssembleSystem(Vec currentSolutionOrGuess, double currentTime)
    {}

    virtual void FinaliseLinearSystem(Vec currentSolutionOrGuess, double currentTime, bool assembleVector, bool assembleMatrix)
    {}

    virtual void ApplyDirichletConditions(Vec currentSolutionOrGuess, bool applyToMatrix)=0;

    virtual bool ProblemIsNonlinear()=0;

    virtual Vec StaticSolve(Vec currentSolutionOrGuess=NULL,
                            double currentTime=0.0,
                            bool assembleMatrix=true)=0;

    virtual void InitialiseForSolve(Vec initialGuess)=0;

public:
    virtual LinearSystem** GetLinearSystem()=0;

protected:
    virtual ReplicatableVector& rGetCurrentSolutionOrGuess()=0;

    void ApplyNeummanBoundaryConditions();

public:

    AbstractAssembler();

    void SetBoundaryConditionsContainer(BoundaryConditionsContainer<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>* pBoundaryConditions);

    virtual ~AbstractAssembler()
    {
    }

    // The following have to be public in order for compilation to work, but shouldn't be called
    // by users

    virtual void ResetInterpolatedQuantities()
    {}

    virtual void IncrementInterpolatedQuantities(double phiI, const Node<SPACE_DIM>* pNode)
    {}

};


// Implementation


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractAssembler<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::ApplyNeummanBoundaryConditions()
{
    assert(mpBoundaryConditions!=NULL);
    HeartEventHandler::BeginEvent(HeartEventHandler::NEUMANN_BCS);
    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>& surf_element = *(neumann_iterator->first);
            AssembleOnSurfaceElement(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];
            surf_element.GetStiffnessMatrixGlobalIndices(PROBLEM_DIM, p_indices);
            (*(this->GetLinearSystem()))->AddRhsMultipleValues(p_indices, b_surf_elem);
            ++neumann_iterator;
        }
    }
    HeartEventHandler::EndEvent(HeartEventHandler::NEUMANN_BCS);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
AbstractAssembler<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::AbstractAssembler()
    : mpBoundaryConditions(NULL)
{
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
void AbstractAssembler<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::SetBoundaryConditionsContainer(BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM>* pBoundaryConditions)
{
    mpBoundaryConditions = pBoundaryConditions;
}


#endif //_ABSTRACTASSEMBLER_HPP_