Chaste  Release::2018.1
BidomainTissue.hpp
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36 
37 #ifndef BIDOMAINTISSUE_HPP_
38 #define BIDOMAINTISSUE_HPP_
39 
40 #include "ChasteSerialization.hpp"
41 #include <boost/serialization/base_object.hpp>
42 
43 #include <vector>
44 #include "UblasMatrixInclude.hpp"
45 
46 #include "AbstractCardiacTissue.hpp"
47 #include "AbstractConductivityTensors.hpp"
48 
56 template <unsigned SPACE_DIM>
57 class BidomainTissue : public virtual AbstractCardiacTissue<SPACE_DIM>
58 {
59 private:
60  friend class TestBidomainTissue; // for testing.
61 
63  friend class boost::serialization::access;
70  template<class Archive>
71  void serialize(Archive & archive, const unsigned int version)
72  {
73  archive & boost::serialization::base_object<AbstractCardiacTissue<SPACE_DIM> >(*this);
74  // Conductivity tensors are dealt with by HeartConfig, and the caches get regenerated.
75  }
76 
79 
84 
85 public:
91  BidomainTissue(AbstractCardiacCellFactory<SPACE_DIM>* pCellFactory, bool exchangeHalos=false);
92 
99 
103  ~BidomainTissue();
104 
109  const c_matrix<double, SPACE_DIM, SPACE_DIM>& rGetExtracellularConductivityTensor(unsigned elementIndex);
110 };
111 
112 // Declare identifier for the serializer
115 
116 namespace boost
117 {
118 namespace serialization
119 {
120 
121 template<class Archive, unsigned SPACE_DIM>
122 inline void save_construct_data(
123  Archive & ar, const BidomainTissue<SPACE_DIM> * t, const unsigned int file_version)
124 {
126  ar & p_mesh;
127 
128  // CreateIntracellularConductivityTensor() is called by constructor and uses HeartConfig. So make sure that it is
129  // archived too (needs doing before construction so appears here instead of usual archive location).
130  HeartConfig* p_config = HeartConfig::Instance();
131  ar & *p_config;
132  ar & p_config;
133 }
134 
139 template<class Archive, unsigned SPACE_DIM>
140 inline void load_construct_data(
141  Archive & ar, BidomainTissue<SPACE_DIM> * t, const unsigned int file_version)
142 {
144  ar & p_mesh;
145 
146  // CreateIntracellularConductivityTensor() is called by AbstractCardiacTissue constructor and uses HeartConfig.
147  // (as does CreateExtracellularConductivityTensor). So make sure that it is
148  // archived too (needs doing before construction so appears here instead of usual archive location).
149  HeartConfig* p_config = HeartConfig::Instance();
150  ar & *p_config;
151  ar & p_config;
152 
153  ::new(t)BidomainTissue<SPACE_DIM>(p_mesh);
154 }
155 }
156 } // namespace ...
157 
158 
159 #endif /*BIDOMAINTISSUE_HPP_*/
BidomainTissue(AbstractCardiacCellFactory< SPACE_DIM > *pCellFactory, bool exchangeHalos=false)
void CreateExtracellularConductivityTensors()
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
AbstractConductivityTensors< SPACE_DIM, SPACE_DIM > * mpExtracellularConductivityTensors
void serialize(Archive &archive, const unsigned int version)
gcov doesn't like this file...
static HeartConfig * Instance()
const AbstractTetrahedralMesh< ELEMENT_DIM, ELEMENT_DIM > * pGetMesh() const
const c_matrix< double, SPACE_DIM, SPACE_DIM > & rGetExtracellularConductivityTensor(unsigned elementIndex)