CryptSimulation2d.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 CRYPTSIMULATION2D_HPP_
00029 #define CRYPTSIMULATION2D_HPP_
00030 
00031 #include "ChasteSerialization.hpp"
00032 #include <boost/serialization/base_object.hpp>
00033 
00034 #include "CellBasedSimulation.hpp"
00035 #include "SimpleDataWriter.hpp"
00036 #include "MeshBasedCellPopulationWithGhostNodes.hpp"
00037 
00042 class CryptSimulation2d : public CellBasedSimulation<2>
00043 {
00044     // Allow tests to access private members, in order to test computation of
00045     // private functions eg. DoCellBirth
00046     friend class TestCryptSimulation2d;
00047 
00048 protected:
00049 
00051     friend class boost::serialization::access;
00058     template<class Archive>
00059     void serialize(Archive & archive, const unsigned int version)
00060     {
00061         // If Archive is an output archive, then & resolves to <<
00062         // If Archive is an input archive, then & resolves to >>
00063         archive & boost::serialization::base_object<CellBasedSimulation<2> >(*this);
00064         archive & mUseJiggledBottomCells;
00065         archive & mWriteBetaCatenin;
00066     }
00067 
00069     bool mUseJiggledBottomCells;
00070 
00077     bool mWriteBetaCatenin;
00078 
00080     out_stream mVizBetaCateninResultsFile;
00081 
00083     MeshBasedCellPopulationWithGhostNodes<2>* mpStaticCastCellPopulation;
00084 
00095     c_vector<double, 2> CalculateCellDivisionVector(CellPtr pParentCell);
00096 
00102     void WriteVisualizerSetupFile();
00103 
00107     void SetupWriteBetaCatenin();
00108 
00114     virtual void WriteBetaCatenin(double time);
00115 
00121     void SetupSolve();
00122 
00128     void PostSolve();
00129 
00136     void AfterSolve();
00137 
00138 public:
00139 
00147     CryptSimulation2d(AbstractCellPopulation<2>& rCellPopulation,
00148                       bool deleteCellPopulationAndForceCollection=false,
00149                       bool initialiseCells=true);
00150 
00152     void UseJiggledBottomCells();
00153 
00163     void ApplyCellPopulationBoundaryConditions(const std::vector<c_vector<double,2> >& rOldLocations);
00164 
00169     void SetBottomCellAncestors();
00170 
00179     void OutputSimulationParameters(out_stream& rParamsFile);
00180 };
00181 
00182 
00183 #include "SerializationExportWrapper.hpp"
00184 // Declare identifier for the serializer
00185 CHASTE_CLASS_EXPORT(CryptSimulation2d)
00186 
00187 namespace boost
00188 {
00189 namespace serialization
00190 {
00194 template<class Archive>
00195 inline void save_construct_data(
00196     Archive & ar, const CryptSimulation2d * t, const BOOST_PFTO unsigned int file_version)
00197 {
00198     // Save data required to construct instance
00199     const AbstractCellPopulation<2>* p_cell_population = &(t->rGetCellPopulation());
00200     ar & p_cell_population;
00201 }
00202 
00206 template<class Archive>
00207 inline void load_construct_data(
00208     Archive & ar, CryptSimulation2d * t, const unsigned int file_version)
00209 {
00210     // Retrieve data from archive required to construct new instance
00211     AbstractCellPopulation<2>* p_cell_population;
00212     ar & p_cell_population;
00213 
00214     // Invoke inplace constructor to initialise instance
00215     ::new(t)CryptSimulation2d(*p_cell_population, true, false);
00216 }
00217 }
00218 } // namespace
00219 
00220 #endif /*CRYPTSIMULATION2D_HPP_*/
00221 

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