AbstractAssembler.hpp

00001 /*
00002 
00003 Copyright (C) University of Oxford, 2005-2009
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 _ABSTRACTASSEMBLER_HPP_
00029 #define _ABSTRACTASSEMBLER_HPP_
00030 
00031 #include "LinearBasisFunction.hpp"
00032 #include "GaussianQuadratureRule.hpp"
00033 #include "BoundaryConditionsContainer.hpp"
00034 #include "LinearSystem.hpp"
00035 #include "GaussianQuadratureRule.hpp"
00036 #include "ReplicatableVector.hpp"
00037 #include "DistributedVector.hpp"
00038 #include "HeartEventHandler.hpp"
00039 
00076 template <unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
00077 class AbstractAssembler
00078 {
00079 protected:
00080 
00082     BoundaryConditionsContainer<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM> *mpBoundaryConditions;
00083 
00084     #define COVERAGE_IGNORE
00085 
00090     virtual void SetMatrixIsConst(bool matrixIsConstant=true)
00091     {
00092     }
00093     #undef COVERAGE_IGNORE
00094 
00114     virtual c_matrix<double,PROBLEM_DIM*(ELEMENT_DIM+1),PROBLEM_DIM*(ELEMENT_DIM+1)> ComputeMatrixTerm(
00115         c_vector<double, ELEMENT_DIM+1>& rPhi,
00116         c_matrix<double, SPACE_DIM, ELEMENT_DIM+1>& rGradPhi,
00117         ChastePoint<SPACE_DIM>& rX,
00118         c_vector<double,PROBLEM_DIM>& rU,
00119         c_matrix<double, PROBLEM_DIM, SPACE_DIM>& rGradU,
00120         Element<ELEMENT_DIM,SPACE_DIM>* pElement)=0;
00121 
00141     virtual c_vector<double,PROBLEM_DIM*(ELEMENT_DIM+1)> ComputeVectorTerm(
00142         c_vector<double, ELEMENT_DIM+1>& rPhi,
00143         c_matrix<double, SPACE_DIM, ELEMENT_DIM+1>& rGradPhi,
00144         ChastePoint<SPACE_DIM>& rX,
00145         c_vector<double,PROBLEM_DIM>& rU,
00146         c_matrix<double, PROBLEM_DIM, SPACE_DIM>& rGradU,
00147         Element<ELEMENT_DIM,SPACE_DIM>* pElement)=0;
00148 
00162     virtual c_vector<double, PROBLEM_DIM*ELEMENT_DIM> ComputeVectorSurfaceTerm(
00163         const BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>& rSurfaceElement,
00164         c_vector<double, ELEMENT_DIM>& rPhi,
00165         ChastePoint<SPACE_DIM>& rX)=0;
00166 
00187     virtual void AssembleOnElement(Element<ELEMENT_DIM,SPACE_DIM>& rElement,
00188                                    c_matrix<double, PROBLEM_DIM*(ELEMENT_DIM+1), PROBLEM_DIM*(ELEMENT_DIM+1) >& rAElem,
00189                                    c_vector<double, PROBLEM_DIM*(ELEMENT_DIM+1)>& rBElem,
00190                                    bool assembleVector,
00191                                    bool assembleMatrix)=0;
00192 
00204     virtual void AssembleOnSurfaceElement(const BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>& rSurfaceElement,
00205                                           c_vector<double, PROBLEM_DIM*ELEMENT_DIM>& rBSurfElem)=0;
00206 
00229     virtual void AssembleSystem(bool assembleVector, bool assembleMatrix,
00230                                 Vec currentSolutionOrGuess=NULL, double currentTime=0.0)=0;
00231 
00236     virtual void PrepareForSolve()=0;
00237 
00247     virtual void PrepareForAssembleSystem(Vec currentSolutionOrGuess, double currentTime)
00248     {}
00249 
00257     virtual void FinaliseAssembleSystem(Vec currentSolutionOrGuess, double currentTime)
00258     {}
00259 
00269     virtual void FinaliseLinearSystem(Vec currentSolutionOrGuess, double currentTime, bool assembleVector, bool assembleMatrix)
00270     {}
00271 
00278     virtual void ApplyDirichletConditions(Vec currentSolutionOrGuess, bool applyToMatrix)=0;
00279 
00283     virtual bool ProblemIsNonlinear()=0;
00284 
00296     virtual Vec StaticSolve(Vec currentSolutionOrGuess=NULL,
00297                             double currentTime=0.0,
00298                             bool assembleMatrix=true)=0;
00299 
00305     virtual void InitialiseForSolve(Vec initialGuess)=0;
00306 
00307 public:
00311     virtual LinearSystem** GetLinearSystem()=0;
00312     
00313 protected:   
00317     virtual ReplicatableVector& rGetCurrentSolutionOrGuess()=0;
00318 
00331     void ApplyNeummanBoundaryConditions();
00332 
00333 public:
00334 
00338     AbstractAssembler();
00339 
00345     void SetBoundaryConditionsContainer(BoundaryConditionsContainer<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>* pBoundaryConditions);
00346 
00350     virtual ~AbstractAssembler()
00351     {
00352     }
00353 
00354     // The following have to be public in order for compilation to work, but shouldn't be called
00355     // by users
00356 
00362     virtual void ResetInterpolatedQuantities()
00363     {}
00364 
00373     virtual void IncrementInterpolatedQuantities(double phiI, const Node<SPACE_DIM>* pNode)
00374     {}
00375 
00376 };
00377 
00378 
00380 // Implementation
00382 
00383 
00384 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
00385 void AbstractAssembler<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::ApplyNeummanBoundaryConditions()
00386 {
00387     assert(mpBoundaryConditions!=NULL);
00388     HeartEventHandler::BeginEvent(HeartEventHandler::NEUMANN_BCS);
00389     if (mpBoundaryConditions->AnyNonZeroNeumannConditions())
00390     {
00391         typename BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM>::NeumannMapIterator
00392             neumann_iterator = mpBoundaryConditions->BeginNeumann();
00393         c_vector<double, PROBLEM_DIM*ELEMENT_DIM> b_surf_elem;
00394 
00395         // Iterate over defined conditions
00396         while (neumann_iterator != mpBoundaryConditions->EndNeumann())
00397         {
00398             const BoundaryElement<ELEMENT_DIM-1,SPACE_DIM>& surf_element = *(neumann_iterator->first);
00399             AssembleOnSurfaceElement(surf_element, b_surf_elem);
00400 
00401             const size_t STENCIL_SIZE=PROBLEM_DIM*ELEMENT_DIM; // problem_dim*num_nodes_on_surface_element
00402             unsigned p_indices[STENCIL_SIZE];
00403             surf_element.GetStiffnessMatrixGlobalIndices(PROBLEM_DIM, p_indices);
00404             (*(this->GetLinearSystem()))->AddRhsMultipleValues(p_indices, b_surf_elem);
00405             ++neumann_iterator;
00406         }
00407     }
00408     HeartEventHandler::EndEvent(HeartEventHandler::NEUMANN_BCS);
00409 }
00410 
00411 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
00412 AbstractAssembler<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::AbstractAssembler()
00413     : mpBoundaryConditions(NULL)
00414 {
00415 }
00416 
00417 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
00418 void AbstractAssembler<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>::SetBoundaryConditionsContainer(BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM>* pBoundaryConditions)
00419 {
00420     mpBoundaryConditions = pBoundaryConditions;
00421 }
00422 
00423 
00424 #endif //_ABSTRACTASSEMBLER_HPP_

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