BidomainWithBathAssembler.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 #ifndef BIDOMAINWITHBATHASSEMBLER_HPP_
00030 #define BIDOMAINWITHBATHASSEMBLER_HPP_
00031 
00032 #include "BidomainDg0Assembler.hpp"
00033 #include "HeartConfig.hpp"
00034 
00035 // IMPORTANT NOTE: the inheritance of BidomainWithBathAssembler has to be 'virtual'
00036 // because BidomainDg0Assembler will be the top class in a 'dreaded diamond':
00037 //      A
00038 //     / \     A = BidomainDg0Assembler, B = BidomainWithBathAssembler,
00039 //    B   C    C = BidomainMatrixBasedAssembler, D = BidomainWithBathMatrixBasedAssembler
00040 //     \ /
00041 //      D
00042 //
00043 // B and C must use virtual inheritence of A in order for D to only contain 1 instance
00044 // of the member variables in A
00045 
00048 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00049 class BidomainWithBathAssembler
00050     : public virtual BidomainDg0Assembler<ELEMENT_DIM, SPACE_DIM>
00051 {
00052 public:
00053 
00067     virtual c_matrix<double,2*(ELEMENT_DIM+1),2*(ELEMENT_DIM+1)> ComputeMatrixTerm(
00068         c_vector<double, ELEMENT_DIM+1> &rPhi,
00069         c_matrix<double, SPACE_DIM, ELEMENT_DIM+1> &rGradPhi,
00070         ChastePoint<SPACE_DIM> &rX,
00071         c_vector<double,2> &rU,
00072         c_matrix<double, 2, SPACE_DIM> &rGradU /* not used */,
00073         Element<ELEMENT_DIM,SPACE_DIM>* pElement);
00074 
00085     virtual c_vector<double,2*(ELEMENT_DIM+1)> ComputeVectorTerm(
00086         c_vector<double, ELEMENT_DIM+1> &rPhi,
00087         c_matrix<double, SPACE_DIM, ELEMENT_DIM+1> &rGradPhi,
00088         ChastePoint<SPACE_DIM> &rX,
00089         c_vector<double,2> &rU,
00090         c_matrix<double, 2, SPACE_DIM> &rGradU /* not used */,
00091         Element<ELEMENT_DIM,SPACE_DIM>* pElement);
00092 
00104     void FinaliseLinearSystem(Vec existingSolutionOrGuess, double time, bool assembleVector, bool assembleMatrix);
00105 
00114     BidomainWithBathAssembler(AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh,
00115                               BidomainPde<SPACE_DIM>* pPde,
00116                               BoundaryConditionsContainer<ELEMENT_DIM, SPACE_DIM, 2>* pBcc,
00117                               unsigned numQuadPoints = 2);
00118 };
00119 
00120 #endif /*BIDOMAINWITHBATHASSEMBLER_HPP_*/