CellBasedSimulationWithPdesAssembler.hpp

00001 /*
00002 
00003 Copyright (C) University of Oxford, 2005-2011
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 #ifndef _CELLBASEDSIMULATIONWITHPDESASSEMBLER_HPP_
00029 #define _CELLBASEDSIMULATIONWITHPDESASSEMBLER_HPP_
00030 
00031 
00032 #include "TetrahedralMesh.hpp"
00033 #include "SimpleLinearEllipticSolver.hpp"
00034 #include "GaussianQuadratureRule.hpp"
00035 
00036 //todo: at some point this class should renamed to CellBasedSimulationWithPdesSolver
00037 
00038 
00046 template<unsigned DIM>
00047 class CellBasedSimulationWithPdesAssembler
00048     : public SimpleLinearEllipticSolver<DIM, DIM>
00049 {
00050 private:
00051 
00056     double mConstantInUSourceTerm;
00057 
00062     double mLinearInUCoeffInSourceTerm;
00063 
00064 protected:
00065 
00077     virtual c_vector<double, 1*(DIM+1)> ComputeVectorTerm(
00078         c_vector<double, DIM+1>& rPhi,
00079         c_matrix<double, DIM, DIM+1>& rGradPhi,
00080         ChastePoint<DIM>& rX,
00081         c_vector<double, 1>& rU,
00082         c_matrix<double, 1, DIM>& rGradU /* not used */,
00083         Element<DIM, DIM>* pElement);
00084 
00096     virtual c_matrix<double, 1*(DIM+1), 1*(DIM+1)> ComputeMatrixTerm(
00097         c_vector<double, DIM+1>& rPhi,
00098         c_matrix<double, DIM, DIM+1>& rGradPhi,
00099         ChastePoint<DIM>& rX,
00100         c_vector<double, 1>& rU,
00101         c_matrix<double, 1, DIM>& rGradU,
00102         Element<DIM, DIM>* pElement);
00103 
00107     void ResetInterpolatedQuantities();
00108 
00115     void IncrementInterpolatedQuantities(double phiI, const Node<DIM>* pNode);
00116 
00123     void InitialiseForSolve(Vec initialSolution);
00124 
00125 public:
00126 
00135     CellBasedSimulationWithPdesAssembler(TetrahedralMesh<DIM,DIM>* pMesh,
00136                                       AbstractLinearEllipticPde<DIM,DIM>* pPde,
00137                                       BoundaryConditionsContainer<DIM,DIM,1>* pBoundaryConditions,
00138                                       unsigned numQuadPoints=2);
00139 
00143     ~CellBasedSimulationWithPdesAssembler();
00144 };
00145 
00146 #endif /*_CELLBASEDSIMULATIONWITHPDESASSEMBLER_HPP_*/

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