BidomainTissue.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 
00030 #ifndef BIDOMAINTISSUE_HPP_
00031 #define BIDOMAINTISSUE_HPP_
00032 
00033 #include "ChasteSerialization.hpp"
00034 #include <boost/serialization/base_object.hpp>
00035 
00036 #include <vector>
00037 #include <boost/numeric/ublas/matrix.hpp>
00038 
00039 #include "AbstractCardiacTissue.hpp"
00040 #include "AbstractConductivityTensors.hpp"
00041 
00042 
00043 
00044 
00052 template <unsigned SPACE_DIM>
00053 class BidomainTissue : public virtual AbstractCardiacTissue<SPACE_DIM>
00054 {
00055 private:
00056     friend class TestBidomainTissue; // for testing.
00057 
00059     friend class boost::serialization::access;
00066     template<class Archive>
00067     void serialize(Archive & archive, const unsigned int version)
00068     {
00069         archive & boost::serialization::base_object<AbstractCardiacTissue<SPACE_DIM> >(*this);
00070         // Conductivity tensors are dealt with by HeartConfig, and the caches get regenerated.
00071     }
00072 
00074     AbstractConductivityTensors<SPACE_DIM,SPACE_DIM> *mpExtracellularConductivityTensors;
00075 
00079     void CreateExtracellularConductivityTensors();
00080 
00081 public:
00087     BidomainTissue(AbstractCardiacCellFactory<SPACE_DIM>* pCellFactory, bool exchangeHalos=false);
00088 
00094     BidomainTissue(AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>* pMesh);
00095 
00099     ~BidomainTissue();
00100 
00105      const c_matrix<double, SPACE_DIM, SPACE_DIM>& rGetExtracellularConductivityTensor(unsigned elementIndex);
00106 };
00107 
00108 // Declare identifier for the serializer
00109 #include "SerializationExportWrapper.hpp"
00110 EXPORT_TEMPLATE_CLASS_SAME_DIMS(BidomainTissue)
00111 
00112 namespace boost
00113 {
00114 namespace serialization
00115 {
00116 
00117 template<class Archive, unsigned SPACE_DIM>
00118 inline void save_construct_data(
00119     Archive & ar, const BidomainTissue<SPACE_DIM> * t, const unsigned int file_version)
00120 {
00121     const AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>* p_mesh = t->pGetMesh();
00122     ar & p_mesh;
00123 
00124     // CreateIntracellularConductivityTensor() is called by constructor and uses HeartConfig. So make sure that it is
00125     // archived too (needs doing before construction so appears here instead of usual archive location).
00126     HeartConfig* p_config = HeartConfig::Instance();
00127     ar & *p_config;
00128     ar & p_config;
00129 }
00130 
00135 template<class Archive, unsigned SPACE_DIM>
00136 inline void load_construct_data(
00137     Archive & ar, BidomainTissue<SPACE_DIM> * t, const unsigned int file_version)
00138 {
00139     AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>* p_mesh;
00140     ar & p_mesh;
00141     
00142     // CreateIntracellularConductivityTensor() is called by AbstractCardiacTissue constructor and uses HeartConfig.
00143     // (as does CreateExtracellularConductivityTensor). So make sure that it is
00144     // archived too (needs doing before construction so appears here instead of usual archive location).
00145     HeartConfig* p_config = HeartConfig::Instance();
00146     ar & *p_config;
00147     ar & p_config;
00148 
00149     ::new(t)BidomainTissue<SPACE_DIM>(p_mesh);
00150 }
00151 }
00152 } // namespace ...
00153 
00154 
00155 #endif /*BIDOMAINTISSUE_HPP_*/

Generated on Tue May 31 14:31:42 2011 for Chaste by  doxygen 1.5.5