BidomainMatrixBasedAssembler.hpp

/*

Copyright (C) University of Oxford, 2005-2009

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/>.

*/

//
//
//
//
//   NOTE: The main class in this file, BidomainMatrixBasedAssembler, is defined at the 
//   bottom, after BidomainRhsMatrixAssembler
//
//
//
//
//

#ifndef _BIDOMAINMATRIXBASEDASSEMBLER_HPP_
#define _BIDOMAINMATRIXBASEDASSEMBLER_HPP_

#include "BidomainDg0Assembler.hpp"

template<unsigned DIM>
class BidomainRhsMatrixAssembler
    : public AbstractLinearAssembler<DIM, DIM, 2, false, BidomainRhsMatrixAssembler<DIM> >
{
public:
    static const unsigned E_DIM = DIM; 
    static const unsigned S_DIM = DIM; 
    static const unsigned P_DIM = 2u; 
    virtual c_matrix<double,2*(DIM+1),2*(DIM+1)> ComputeMatrixTerm(
        c_vector<double, DIM+1> &rPhi,
        c_matrix<double, DIM, DIM+1> &rGradPhi,
        ChastePoint<DIM> &rX,
        c_vector<double,2> &rU,
        c_matrix<double,2,DIM> &rGradU /* not used */,
        Element<DIM,DIM>* pElement);

    virtual c_vector<double,2*(DIM+1)> ComputeVectorTerm(
        c_vector<double, DIM+1> &rPhi,
        c_matrix<double, DIM, DIM+1> &rGradPhi,
        ChastePoint<DIM> &rX,
        c_vector<double,2> &u,
        c_matrix<double, 2, DIM> &rGradU /* not used */,
        Element<DIM,DIM>* pElement);

    virtual c_vector<double, 2*DIM> ComputeVectorSurfaceTerm(
        const BoundaryElement<DIM-1,DIM> &rSurfaceElement,
        c_vector<double, DIM> &rPhi,
        ChastePoint<DIM> &rX);

    BidomainRhsMatrixAssembler(AbstractTetrahedralMesh<DIM,DIM>* pMesh);

    ~BidomainRhsMatrixAssembler();

    Mat* GetMatrix();
};


template<unsigned DIM>
struct AssemblerTraits<BidomainRhsMatrixAssembler<DIM> >
{
    typedef BidomainRhsMatrixAssembler<DIM> CVT_CLS;
    typedef BidomainRhsMatrixAssembler<DIM> CMT_CLS;
    typedef AbstractAssembler<DIM, DIM, 2> INTERPOLATE_CLS;
};



// IMPORTANT NOTE: the inheritance of BidomainMatrixBasedAssembler has to be 'virtual'
// because BidomainDg0Assembler will be the top class in a 'dreaded diamond':
//      A
//     / \     A = BidomainDg0Assembler, B = BidomainWithBathAssembler,
//    B   C    C = BidomainMatrixBasedAssembler, D = BidomainWithBathMatrixBasedAssembler
//     \ /
//      D
//
// B and C must use virtual inheritence of A in order for D to only contain 1 instance
// of the member variables in A

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class BidomainMatrixBasedAssembler
    : public virtual BidomainDg0Assembler<ELEMENT_DIM, SPACE_DIM>
{
protected:
    BidomainRhsMatrixAssembler<SPACE_DIM>* mpBidomainRhsMatrixAssembler;

public:

    BidomainMatrixBasedAssembler(AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh,
                                 BidomainPde<SPACE_DIM>* pPde,
                                 BoundaryConditionsContainer<ELEMENT_DIM, SPACE_DIM, 2>* pBcc,
                                 unsigned numQuadPoints = 2);

    ~BidomainMatrixBasedAssembler();

    virtual void ConstructVectorForMatrixBasedRhsAssembly(Vec existingSolution);
};

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
struct AssemblerTraits<BidomainMatrixBasedAssembler<ELEMENT_DIM, SPACE_DIM> >
{
    typedef BidomainDg0Assembler<ELEMENT_DIM, SPACE_DIM> CVT_CLS;
    typedef BidomainDg0Assembler<ELEMENT_DIM, SPACE_DIM> CMT_CLS;
    typedef BidomainDg0Assembler<ELEMENT_DIM, SPACE_DIM> INTERPOLATE_CLS;
};

#endif //_BIDOMAINMATRIXBASEDASSEMBLER_HPP_

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