ExtendedBidomainTissue.hpp

/*

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#ifndef EXTENDEDBIDOMAINTISSUE_HPP_
#define EXTENDEDBIDOMAINTISSUE_HPP_

#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>

#include <vector>
#include "UblasMatrixInclude.hpp"

#include "AbstractStimulusFunction.hpp"
#include "AbstractStimulusFactory.hpp"
#include "AbstractConductivityTensors.hpp"

#include "AbstractCardiacTissue.hpp"

template <unsigned SPACE_DIM>
class ExtendedBidomainTissue : public virtual AbstractCardiacTissue<SPACE_DIM>
{
private:
    friend class TestExtendedBidomainTissue; // for testing.

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractCardiacTissue<SPACE_DIM> >(*this);
        // Conductivity tensors are dealt with by HeartConfig, and the caches get regenerated.

        archive & mAmFirstCell;
        archive & mAmSecondCell;
        archive & mAmGap;
        archive & mCmFirstCell;
        archive & mCmSecondCell;
        archive & mGGap;
        archive & mUserSuppliedExtracellularStimulus;
    }

    AbstractConductivityTensors<SPACE_DIM, SPACE_DIM> *mpIntracellularConductivityTensorsSecondCell;

    c_vector<double, SPACE_DIM>  mIntracellularConductivitiesSecondCell;


    AbstractConductivityTensors<SPACE_DIM, SPACE_DIM> *mpExtracellularConductivityTensors;

    ReplicatableVector mExtracellularStimulusCacheReplicated;

    ReplicatableVector mGgapCacheReplicated;

    ReplicatableVector mIionicCacheReplicatedSecondCell;

    ReplicatableVector mIntracellularStimulusCacheReplicatedSecondCell;

    std::vector< AbstractCardiacCellInterface* > mCellsDistributedSecondCell;

    std::vector<boost::shared_ptr<AbstractStimulusFunction> > mExtracellularStimuliDistributed;

    std::vector<double> mGgapDistributed;

    double mAmFirstCell;
    double mAmSecondCell;
    double mAmGap;
    double mCmFirstCell;
    double mCmSecondCell;
    double mGGap;

    bool mUserSuppliedExtracellularStimulus;

    void CreateExtracellularConductivityTensors();

    void UpdateAdditionalCaches(unsigned globalIndex, unsigned localIndex, double nextTime);

    void ReplicateAdditionalCaches();

    std::vector<boost::shared_ptr<AbstractChasteRegion<SPACE_DIM> > > mGgapHeterogeneityRegions;
    std::vector<double> mGgapValues;

public:

    ExtendedBidomainTissue(AbstractCardiacCellFactory<SPACE_DIM>* pCellFactory, AbstractCardiacCellFactory<SPACE_DIM>* pCellFactorySecondCell, AbstractStimulusFactory<SPACE_DIM>* pExtracellularStimulusFactory);

    ExtendedBidomainTissue(std::vector<AbstractCardiacCellInterface*> & rCellsDistributed,
                           std::vector<AbstractCardiacCellInterface*> & rSecondCellsDistributed,
                           std::vector<boost::shared_ptr<AbstractStimulusFunction> > & rExtraStimuliDistributed,
                           std::vector<double>& rGgapsDistributed,
                           AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>* pMesh,
                           c_vector<double, SPACE_DIM>  intracellularConductivitiesSecondCell);

    virtual ~ExtendedBidomainTissue();

    void SetIntracellularConductivitiesSecondCell(c_vector<double, SPACE_DIM> conductivities);

    AbstractCardiacCellInterface* GetCardiacSecondCell( unsigned globalIndex );


    boost::shared_ptr<AbstractStimulusFunction> GetExtracellularStimulus( unsigned globalIndex );

    const std::vector<AbstractCardiacCellInterface*>& rGetSecondCellsDistributed() const;

    const std::vector<double>& rGetGapsDistributed() const;


    const std::vector<boost::shared_ptr<AbstractStimulusFunction> >& rGetExtracellularStimulusDistributed() const;


    c_vector<double, SPACE_DIM> GetIntracellularConductivitiesSecondCell() const;

    virtual void SolveCellSystems(Vec existingSolution, double time, double nextTime, bool updateVoltage = false);

    void CreateIntracellularConductivityTensorSecondCell();

    void SetGgapHeterogeneities ( std::vector<boost::shared_ptr<AbstractChasteRegion<SPACE_DIM> > > & rGgapHeterogeneityRegions, std::vector<double> rGgapValues);

    void CreateGGapConductivities();

     const c_matrix<double, SPACE_DIM, SPACE_DIM>& rGetExtracellularConductivityTensor(unsigned elementIndex);

      const c_matrix<double, SPACE_DIM, SPACE_DIM>& rGetIntracellularConductivityTensorSecondCell(unsigned elementIndex);


     ReplicatableVector& rGetIionicCacheReplicatedSecondCell();

     ReplicatableVector& rGetIntracellularStimulusCacheReplicatedSecondCell();

     ReplicatableVector& rGetExtracellularStimulusCacheReplicated();

     ReplicatableVector& rGetGgapCacheReplicated();

     double GetAmFirstCell();

     double GetAmSecondCell();

     double GetAmGap();

     double GetCmFirstCell();

     double GetCmSecondCell();

     double GetGGap();

     void SetAmFirstCell(double value);

     void SetAmSecondCell(double value);

     void SetAmGap(double value);

     void SetCmFirstCell(double value);

     void SetCmSecondCell(double value);

     void SetGGap(double value);

     bool HasTheUserSuppliedExtracellularStimulus();

     void SetUserSuppliedExtracellularStimulus(bool flag);


     template<class Archive>
     void SaveExtendedBidomainCells(Archive & archive, const unsigned int version) const
     {
         Archive& r_archive = *ProcessSpecificArchive<Archive>::Get();
         const std::vector<AbstractCardiacCellInterface*> & r_cells_distributed = this->rGetCellsDistributed();
         const std::vector<AbstractCardiacCellInterface*> & r_cells_distributed_second_cell = rGetSecondCellsDistributed();
         const std::vector<double> & r_ggaps_distributed = rGetGapsDistributed();

         r_archive & this->mpDistributedVectorFactory; // Needed when loading
         const unsigned num_cells = r_cells_distributed.size();
         r_archive & num_cells;
         for (unsigned i=0; i<num_cells; i++)
         {
             AbstractDynamicallyLoadableEntity* p_entity = dynamic_cast<AbstractDynamicallyLoadableEntity*>(r_cells_distributed[i]);
             bool is_dynamic = (p_entity != NULL);
             r_archive & is_dynamic;
             if (is_dynamic)
             {
 #ifdef CHASTE_CAN_CHECKPOINT_DLLS
                 NEVER_REACHED;
                 //r_archive & p_entity->GetLoader()->GetLoadableModulePath();
 #else
                 // We should have thrown an exception before this point
                 NEVER_REACHED;
 #endif // CHASTE_CAN_CHECKPOINT_DLLS
             }
             r_archive & r_cells_distributed[i];
             r_archive & r_cells_distributed_second_cell[i];
             r_archive & r_ggaps_distributed[i];
         }
     }

     template<class Archive>
     static void LoadExtendedBidomainCells(Archive & archive, const unsigned int version,
                                  std::vector<AbstractCardiacCellInterface*>& rCells,
                                  std::vector<AbstractCardiacCellInterface*>& rSecondCells,
                                  std::vector<double>& rGgaps,
                                  AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>* pMesh)
     {
         assert(pMesh!=NULL);
         DistributedVectorFactory* p_factory;
         archive & p_factory;
         unsigned num_cells;
         archive & num_cells;
         rCells.resize(p_factory->GetLocalOwnership());
         rSecondCells.resize(p_factory->GetLocalOwnership());
         rGgaps.resize(p_factory->GetLocalOwnership());
 #ifndef NDEBUG
         // Paranoia
         assert(rCells.size() == rSecondCells.size());
         for (unsigned i=0; i<rCells.size(); i++)
         {
             assert(rCells[i] == NULL);
             assert(rSecondCells[i] == NULL);
         }
 #endif

         // We don't store a cell index in the archive, so need to work out what global
         // index this tissue starts up.  If we're migrating (so have an
         // original factory) we use the original low index; otherwise we use the current
         // low index.
         unsigned index_low = p_factory->GetOriginalFactory() ? p_factory->GetOriginalFactory()->GetLow() : p_factory->GetLow();

         for (unsigned local_index=0; local_index<num_cells; local_index++)
         {
             unsigned global_index = index_low + local_index;
             unsigned new_local_index = global_index - p_factory->GetLow();
             bool local = p_factory->IsGlobalIndexLocal(global_index);

             bool is_dynamic;
             archive & is_dynamic;

             if (is_dynamic)
             {
 #ifdef CHASTE_CAN_CHECKPOINT_DLLS
                 NEVER_REACHED;
                 // Ensure the shared object file for this cell model is loaded.
                 // We need to do this here, rather than in the class' serialization code,
                 // because that code won't be available until this is done...
//                 std::string shared_object_path;
//                 archive & shared_object_path;
//                 DynamicModelLoaderRegistry::Instance()->GetLoader(shared_object_path);
 #else
                 // Since checkpoints with dynamically loadable cells can only be
                 // created on Boost>=1.37, trying to load such a checkpoint on an
                 // earlier Boost would give an error when first opening the archive.
                 NEVER_REACHED;
 #endif // CHASTE_CAN_CHECKPOINT_DLLS
             }

             AbstractCardiacCellInterface* p_cell;
             AbstractCardiacCellInterface* p_second_cell;
             double g_gap;
             archive & p_cell;
             archive & p_second_cell;
             archive & g_gap;
             if (local)
             {
                 rCells[new_local_index] = p_cell; // Add to local cells
                 rSecondCells[new_local_index] = p_second_cell;
                 rGgaps[new_local_index] = g_gap;
             }
             else
             {
                 //not sure how to cover this, we are already looping over local cells...
                 NEVER_REACHED;
                // Non-local real cell, so free the memory.
                // delete p_cell;
                // delete p_second_cell;
             }
         }
     }

     template<class Archive>
     void SaveExtracellularStimulus(Archive & archive, const unsigned int version) const
     {
         Archive& r_archive = *ProcessSpecificArchive<Archive>::Get();
         const std::vector<boost::shared_ptr<AbstractStimulusFunction> > & r_stimulus_distributed = rGetExtracellularStimulusDistributed();
         r_archive & this->mpDistributedVectorFactory; // Needed when loading
         const unsigned num_cells = r_stimulus_distributed.size();
         r_archive & num_cells;
         for (unsigned i=0; i<num_cells; i++)
         {
             r_archive & r_stimulus_distributed[i];
         }
     }

     template<class Archive>
     void LoadExtracellularStimulus(Archive & archive, const unsigned int version,
                                               std::vector<boost::shared_ptr<AbstractStimulusFunction> >& rStimuli,
                                               AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>* pMesh)
     {

        DistributedVectorFactory* p_factory;
        archive & p_factory;
        unsigned num_cells;
        archive & num_cells;
        rStimuli.resize(p_factory->GetLocalOwnership());
#ifndef NDEBUG
          // Paranoia
          for (unsigned i=0; i<rStimuli.size(); i++)
          {
              assert(rStimuli[i] == NULL);
          }
#endif

        // We don't store a cell index in the archive, so need to work out what global
        // index this tissue starts up.  If we're migrating (so have an
        // original factory) we use the original low index; otherwise we use the current
        // low index.
        unsigned index_low = p_factory->GetOriginalFactory() ? p_factory->GetOriginalFactory()->GetLow() : p_factory->GetLow();

        assert(pMesh!=NULL);
        //unsigned num_cells = pMesh->GetNumNodes();
        for (unsigned local_index=0; local_index<num_cells; local_index++)
        {
          unsigned global_index = index_low + local_index;

          unsigned new_local_index = global_index - p_factory->GetLow();
          bool local = p_factory->IsGlobalIndexLocal(global_index);

          boost::shared_ptr<AbstractStimulusFunction> p_stim;
          archive & p_stim;//get from archive

          if (local)
          {
              rStimuli[new_local_index] = p_stim; // Add stimulus to local cells
          }
          //otherwise we should delete, but I think shared pointers delete themselves?
        }
    }
};

 // Declare identifier for the serializer
 #include "SerializationExportWrapper.hpp"
 EXPORT_TEMPLATE_CLASS_SAME_DIMS(ExtendedBidomainTissue)

 namespace boost
 {
 namespace serialization
 {

 template<class Archive, unsigned SPACE_DIM>
 inline void save_construct_data(
     Archive & ar, const ExtendedBidomainTissue<SPACE_DIM> * t, const unsigned int file_version)
 {
     //archive the conductivity tensor of the second cell (which may not be dealt with by heartconfig)
     c_vector<double, SPACE_DIM>  intracellular_conductivities_second_cell = t->GetIntracellularConductivitiesSecondCell();
     //note that simple: ar & intracellular_conductivities_second_cell may not be liked by some boost versions
     for (unsigned i = 0; i < SPACE_DIM; i++)
     {
         ar & intracellular_conductivities_second_cell(i);
     }

     const AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>* p_mesh = t->pGetMesh();
     ar & p_mesh;

     // Don't use the std::vector serialization for cardiac cells, so that we can load them
     // more cleverly when migrating checkpoints.
     t->SaveExtendedBidomainCells(ar, file_version);
     t->SaveExtracellularStimulus(ar, file_version);

     // Creation of conductivity tensors are called by constructor and uses HeartConfig. So make sure that it is
     // archived too (needs doing before construction so appears here instead of usual archive location).
     HeartConfig* p_config = HeartConfig::Instance();
     ar & *p_config;
     ar & p_config;
 }

 template<class Archive, unsigned SPACE_DIM>
 inline void load_construct_data(
     Archive & ar, ExtendedBidomainTissue<SPACE_DIM> * t, const unsigned int file_version)
 {
     //Load conductivities of the conductivity of the second cell.
     c_vector<double, SPACE_DIM>  intra_cond_second_cell;
     //note that simple: ar & intra_cond_second_cell may not be liked by some boost versions
     for (unsigned i = 0; i < SPACE_DIM; i++)
     {
         double cond;
         ar & cond;
         intra_cond_second_cell(i) = cond;
     }


     std::vector<AbstractCardiacCellInterface*> cells_distributed;
     std::vector<AbstractCardiacCellInterface*> cells_distributed_second_cell;
     std::vector<boost::shared_ptr<AbstractStimulusFunction> > extra_stim;
     std::vector<double> g_gaps;
     AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>* p_mesh;
     ar & p_mesh;

     // Load only the cells we actually own
     t->LoadExtendedBidomainCells(
             *ProcessSpecificArchive<Archive>::Get(), file_version, cells_distributed, cells_distributed_second_cell, g_gaps, p_mesh);

     t->LoadExtracellularStimulus(
             *ProcessSpecificArchive<Archive>::Get(), file_version, extra_stim, p_mesh);

     // CreateIntracellularConductivityTensor() is called by AbstractCardiacTissue constructor and uses HeartConfig.
     // (as does CreateExtracellularConductivityTensor). So make sure that it is
     // archived too (needs doing before construction so appears here instead of usual archive location).
     HeartConfig* p_config = HeartConfig::Instance();
     ar & *p_config;
     ar & p_config;

     ::new(t)ExtendedBidomainTissue<SPACE_DIM>(cells_distributed, cells_distributed_second_cell, extra_stim, g_gaps, p_mesh, intra_cond_second_cell);
 }
 }
 } // namespace ...



#endif /*EXTENDEDBIDOMAINTISSUE_HPP_*/