AbstractCellCycleModelOdeSolver.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 
00029 #ifndef ABSTRACTCELLCYCLEMODELODESOLVER_HPP_
00030 #define ABSTRACTCELLCYCLEMODELODESOLVER_HPP_
00031 
00032 #include "ChasteSerialization.hpp"
00033 #include "ClassIsAbstract.hpp"
00034 #include <boost/serialization/base_object.hpp>
00035 
00036 #include <boost/shared_ptr.hpp>
00037 
00038 #include "AbstractIvpOdeSolver.hpp"
00039 
00049 class AbstractCellCycleModelOdeSolver
00050 {
00051 private:
00052 
00054     friend class boost::serialization::access;
00066     template<class Archive>
00067     void serialize(Archive & archive, const unsigned int version)
00068     {
00069         archive & mpOdeSolver;
00070         archive & mSizeOfOdeSystem;
00071     }
00072 
00073 protected:
00074 
00076     boost::shared_ptr<AbstractIvpOdeSolver> mpOdeSolver;
00077 
00079     unsigned mSizeOfOdeSystem;
00080 
00081 public:
00082 
00086     AbstractCellCycleModelOdeSolver();
00087 
00091     virtual ~AbstractCellCycleModelOdeSolver();
00092 
00096     virtual bool IsSetUp()=0;
00097 
00101     virtual void Reset();
00102 
00112     void SolveAndUpdateStateVariable(AbstractOdeSystem* pAbstractOdeSystem,
00113                                      double startTime,
00114                                      double endTime,
00115                                      double timeStep);
00116 
00120     virtual void Initialise()=0;
00121 
00126     bool StoppingEventOccurred();
00127 
00133     double GetStoppingTime();
00134 
00140     void SetSizeOfOdeSystem(unsigned sizeOfOdeSystem);
00141 
00145     unsigned GetSizeOfOdeSystem();
00146 
00151     void CheckForStoppingEvents();
00152 
00159     void SetMaxSteps(long int numSteps);
00160 
00168     void SetTolerances(double relTol=1e-4, double absTol=1e-6);
00169     
00177     virtual bool IsAdaptive();
00178 };
00179 
00180 #endif /*ABSTRACTCELLCYCLEMODELODESOLVER_HPP_*/

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