BidomainWithBathMatrixBasedAssembler.hpp

00001 /*
00002 
00003 Copyright (C) University of Oxford, 2005-2010
00004 
00005 University of Oxford means the Chancellor, Masters and Scholars of the
00006 University of Oxford, having an administrative office at Wellington
00007 Square, Oxford OX1 2JD, UK.
00008 
00009 This file is part of Chaste.
00010 
00011 Chaste is free software: you can redistribute it and/or modify it
00012 under the terms of the GNU Lesser General Public License as published
00013 by the Free Software Foundation, either version 2.1 of the License, or
00014 (at your option) any later version.
00015 
00016 Chaste is distributed in the hope that it will be useful, but WITHOUT
00017 ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
00018 FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
00019 License for more details. The offer of Chaste under the terms of the
00020 License is subject to the License being interpreted in accordance with
00021 English Law and subject to any action against the University of Oxford
00022 being under the jurisdiction of the English Courts.
00023 
00024 You should have received a copy of the GNU Lesser General Public License
00025 along with Chaste. If not, see <http://www.gnu.org/licenses/>.
00026 
00027 */
00028 
00029 // This assembler is not doing anything different from its non matrix based counterpart
00030 
00031 #ifndef BIDOMAINWITHBATHMATRIXBASEDASSEMBLER_HPP_
00032 #define BIDOMAINWITHBATHMATRIXBASEDASSEMBLER_HPP_
00033 
00034 #include "BidomainDg0Assembler.hpp"
00035 #include "BidomainMatrixBasedAssembler.hpp"
00036 #include "BidomainWithBathAssembler.hpp"
00037 #include "HeartConfig.hpp"
00038 
00056 template<unsigned DIM>
00057 class BidomainWithBathRhsMatrixAssembler
00058     : public AbstractLinearAssembler<DIM, DIM, 2, false, BidomainWithBathRhsMatrixAssembler<DIM> >
00060     //    : public BidomainRhsMatrixAssembler<DIM>
00061 {
00062 public:
00063     static const unsigned E_DIM = DIM; 
00064     static const unsigned S_DIM = DIM; 
00065     static const unsigned P_DIM = 2u; 
00077     virtual c_matrix<double,2*(DIM+1),2*(DIM+1)> ComputeMatrixTerm(
00078         c_vector<double, DIM+1> &rPhi,
00079         c_matrix<double, DIM, DIM+1> &rGradPhi,
00080         ChastePoint<DIM> &rX,
00081         c_vector<double,2> &rU,
00082         c_matrix<double,2,DIM> &rGradU /* not used */,
00083         Element<DIM,DIM>* pElement);
00084 
00096     virtual c_vector<double,2*(DIM+1)> ComputeVectorTerm(
00097         c_vector<double, DIM+1> &rPhi,
00098         c_matrix<double, DIM, DIM+1> &rGradPhi,
00099         ChastePoint<DIM> &rX,
00100         c_vector<double,2> &rU,
00101         c_matrix<double, 2, DIM> &rGradU /* not used */,
00102         Element<DIM,DIM>* pElement);
00103 
00113     virtual c_vector<double, 2*DIM> ComputeVectorSurfaceTerm(
00114         const BoundaryElement<DIM-1,DIM> &rSurfaceElement,
00115         c_vector<double, DIM> &rPhi,
00116         ChastePoint<DIM> &rX);
00117 
00123     BidomainWithBathRhsMatrixAssembler(AbstractTetrahedralMesh<DIM,DIM>* pMesh);
00124 
00128     ~BidomainWithBathRhsMatrixAssembler();
00129 
00133     Mat* GetMatrix();
00134 };
00135 
00138 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00139 class BidomainWithBathMatrixBasedAssembler
00140     : public BidomainMatrixBasedAssembler<ELEMENT_DIM, SPACE_DIM>,
00141       public BidomainWithBathAssembler<ELEMENT_DIM, SPACE_DIM>
00142 {
00143 protected:
00145     BidomainWithBathRhsMatrixAssembler<SPACE_DIM>* mpBidomainWithBathRhsMatrixAssembler;
00146 
00147 public:
00148 
00157     BidomainWithBathMatrixBasedAssembler(AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh,
00158                                  BidomainPde<SPACE_DIM>* pPde,
00159                                  BoundaryConditionsContainer<ELEMENT_DIM, SPACE_DIM, 2>* pBcc,
00160                                  unsigned numQuadPoints = 2);
00161 
00165     ~BidomainWithBathMatrixBasedAssembler();
00166 
00172     void ConstructVectorForMatrixBasedRhsAssembly(Vec existingSolution);
00173 
00174 };
00175 
00176 #endif /*BIDOMAINWITHBATHMATRIXBASEDASSEMBLER_HPP_*/

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