MonodomainProblem.cpp

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 
00029 #include "MonodomainProblem.hpp"
00030 
00031 #include "Exception.hpp"
00032 #include "ReplicatableVector.hpp"
00033 #include "BasicMonodomainSolver.hpp"
00034 #include "MatrixBasedMonodomainSolver.hpp"
00035 #include "OperatorSplittingMonodomainSolver.hpp"
00036 
00037 
00038 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00039 AbstractCardiacTissue<ELEMENT_DIM,SPACE_DIM>* MonodomainProblem<ELEMENT_DIM, SPACE_DIM>::CreateCardiacTissue()
00040 {
00041     mpMonodomainTissue = new MonodomainTissue<ELEMENT_DIM,SPACE_DIM>(this->mpCellFactory, HeartConfig::Instance()->GetUseStateVariableInterpolation());
00042     return mpMonodomainTissue;
00043 }
00044 
00045 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00046 AbstractDynamicLinearPdeSolver<ELEMENT_DIM, SPACE_DIM, 1>* MonodomainProblem<ELEMENT_DIM, SPACE_DIM>::CreateSolver()
00047 {
00048     assert(mpMonodomainTissue);
00049     /*
00050      * NOTE: The this->mpBoundaryConditionsContainer.get() lines below convert a
00051      * boost::shared_ptr to a normal pointer, as this is what the solvers are
00052      * expecting. We have to be a bit careful though as boost could decide to delete
00053      * them whenever it feels like as it won't count the assembers as using them.
00054      *
00055      * As long as they are kept as member variables here for as long as they are
00056      * required in the solvers it should all work OK.
00057      */
00058      
00059     if(!this->mUseMatrixBasedRhsAssembly)
00060     {
00061         return new BasicMonodomainSolver<ELEMENT_DIM,SPACE_DIM>(this->mpMesh,
00062                                                                 mpMonodomainTissue,
00063                                                                 this->mpBoundaryConditionsContainer.get(),
00064                                                                 2);
00065     }
00066     else if (HeartConfig::Instance()->GetUseReactionDiffusionOperatorSplitting())
00067     {
00068         return new OperatorSplittingMonodomainSolver<ELEMENT_DIM,SPACE_DIM>(this->mpMesh,
00069                                                                             mpMonodomainTissue,
00070                                                                             this->mpBoundaryConditionsContainer.get(),
00071                                                                             2);
00072     }
00073     else
00074     {
00075         return new MatrixBasedMonodomainSolver<ELEMENT_DIM,SPACE_DIM>(this->mpMesh,
00076                                                                       mpMonodomainTissue,
00077                                                                       this->mpBoundaryConditionsContainer.get(),
00078                                                                       2);
00079     }
00080 }
00081 
00082 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00083 MonodomainProblem<ELEMENT_DIM, SPACE_DIM>::MonodomainProblem(AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>* pCellFactory)
00084         : AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, 1>(pCellFactory),
00085           mpMonodomainTissue(NULL)
00086 {
00087 }
00088 
00089 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00090 MonodomainProblem<ELEMENT_DIM, SPACE_DIM>::MonodomainProblem()
00091     : AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, 1>(),
00092       mpMonodomainTissue(NULL)
00093 {
00094 }
00095 
00096 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00097 MonodomainProblem<ELEMENT_DIM, SPACE_DIM>::~MonodomainProblem()
00098 {
00099 }
00100 
00101 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00102 MonodomainTissue<ELEMENT_DIM,SPACE_DIM> * MonodomainProblem<ELEMENT_DIM, SPACE_DIM>::GetMonodomainTissue()
00103 {
00104     assert(mpMonodomainTissue != NULL);
00105     return mpMonodomainTissue;
00106 }
00107 
00108 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00109 void MonodomainProblem<ELEMENT_DIM, SPACE_DIM>::WriteInfo(double time)
00110 {
00111     if (PetscTools::AmMaster())
00112     {
00113         std::cout << "Solved to time " << time << "\n" << std::flush;
00114     }
00115 
00116     double v_max, v_min;
00117 
00118     VecMax( this->mSolution, PETSC_NULL, &v_max );
00119     VecMin( this->mSolution, PETSC_NULL, &v_min );
00120 
00121     if (PetscTools::AmMaster())
00122     {
00123         std::cout << " V = " << "[" <<v_min << ", " << v_max << "]" << "\n" << std::flush;
00124     }
00125 }
00126 
00127 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00128 void MonodomainProblem<ELEMENT_DIM, SPACE_DIM>::DefineWriterColumns(bool extending)
00129 {
00130     AbstractCardiacProblem<ELEMENT_DIM,SPACE_DIM,1>::DefineWriterColumns(extending);
00131     AbstractCardiacProblem<ELEMENT_DIM,SPACE_DIM,1>::DefineExtraVariablesWriterColumns(extending);
00132 }
00133 
00134 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00135 void MonodomainProblem<ELEMENT_DIM, SPACE_DIM>::WriteOneStep(double time, Vec voltageVec)
00136 {
00137     this->mpWriter->PutUnlimitedVariable(time);
00138     this->mpWriter->PutVector(this->mVoltageColumnId, voltageVec);
00139     AbstractCardiacProblem<ELEMENT_DIM,SPACE_DIM,1>::WriteExtraVariablesOneStep();
00140 }
00141 
00142 
00144 // Explicit instantiation
00146 
00147 template class MonodomainProblem<1,1>;
00148 template class MonodomainProblem<1,2>;
00149 template class MonodomainProblem<1,3>;
00150 template class MonodomainProblem<2,2>;
00151 template class MonodomainProblem<3,3>;
00152 
00153 
00154 
00155 // Serialization for Boost >= 1.36
00156 #include "SerializationExportWrapperForCpp.hpp"
00157 EXPORT_TEMPLATE_CLASS2(MonodomainProblem, 1, 1)
00158 EXPORT_TEMPLATE_CLASS2(MonodomainProblem, 1, 2)
00159 EXPORT_TEMPLATE_CLASS2(MonodomainProblem, 1, 3)
00160 EXPORT_TEMPLATE_CLASS2(MonodomainProblem, 2, 2)
00161 EXPORT_TEMPLATE_CLASS2(MonodomainProblem, 3, 3)

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