CryptSimulation1d.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 CRYPTSIMULATION1D_HPP_
00029 #define CRYPTSIMULATION1D_HPP_
00030 
00031 #include "ChasteSerialization.hpp"
00032 #include <boost/serialization/base_object.hpp>
00033 
00034 #include <cmath>
00035 #include <ctime>
00036 #include <iostream>
00037 
00038 #include "CellBasedSimulation.hpp"
00039 #include "MeshBasedCellPopulation.hpp"
00040 
00045 class CryptSimulation1d : public CellBasedSimulation<1>
00046 {
00047     // Allow tests to access private members to test private functions
00048     friend class TestCryptSimulation1d;
00049 
00050 private:
00051 
00053     friend class boost::serialization::access;
00060     template<class Archive>
00061     void serialize(Archive & archive, const unsigned int version)
00062     {
00063         // If Archive is an output archive, then & resolves to <<
00064         // If Archive is an input archive, then & resolves to >>
00065         archive & boost::serialization::base_object<CellBasedSimulation<1> >(*this);
00066     }
00067 
00069     MeshBasedCellPopulation<1>* mpStaticCastCellPopulation;
00070 
00081     c_vector<double, 1> CalculateCellDivisionVector(CellPtr pParentCell);
00082 
00083 public:
00084 
00092     CryptSimulation1d(AbstractCellPopulation<1>& rCellPopulation,
00093                       bool deleteCellPopulationAndForceCollection=false,
00094                       bool initialiseCells=true);
00095 
00105     void ApplyCellPopulationBoundaryConditions(const std::vector<c_vector<double,1> >& rOldLocations);
00106 
00115     void OutputSimulationParameters(out_stream& rParamsFile);
00116 };
00117 
00118 
00119 // Declare identifier for the serializer
00120 #include "SerializationExportWrapper.hpp"
00121 CHASTE_CLASS_EXPORT(CryptSimulation1d)
00122 
00123 namespace boost
00124 {
00125 namespace serialization
00126 {
00130 template<class Archive>
00131 inline void save_construct_data(
00132     Archive & ar, const CryptSimulation1d * t, const BOOST_PFTO unsigned int file_version)
00133 {
00134     // Save data required to construct instance
00135     const AbstractCellPopulation<1>* p_cell_population = &(t->rGetCellPopulation());
00136     ar & p_cell_population;
00137 }
00138 
00142 template<class Archive>
00143 inline void load_construct_data(
00144     Archive & ar, CryptSimulation1d * t, const unsigned int file_version)
00145 {
00146     // Retrieve data from archive required to construct new instance
00147     AbstractCellPopulation<1>* p_cell_population;
00148     ar & p_cell_population;
00149 
00150     // Invoke inplace constructor to initialise instance
00151     ::new(t)CryptSimulation1d(*p_cell_population, true, false);
00152 }
00153 }
00154 } // namespace
00155 
00156 #endif /*CRYPTSIMULATION1D_HPP_*/

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