ExtendedBidomainProblem.hpp

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*/
 
 
#ifndef EXTENDEDBIDOMAINPROBLEM_HPP_
#define EXTENDEDBIDOMAINPROBLEM_HPP_
 
#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>
 
#include <vector>
#include <boost/shared_ptr.hpp>
#include <boost/serialization/shared_ptr.hpp>
 
#include "AbstractCardiacProblem.hpp"
#include "AbstractCardiacTissue.hpp"
#include "AbstractExtendedBidomainSolver.hpp"
#include "AbstractCardiacCellFactory.hpp"
#include "Electrodes.hpp"
#include "ExtendedBidomainTissue.hpp"
 
#include "HeartRegionCodes.hpp"
#include "DistributedTetrahedralMesh.hpp"
#include "AbstractStimulusFactory.hpp"
#include "ElectrodesStimulusFactory.hpp"
 
template<unsigned DIM>
class ExtendedBidomainProblem : public AbstractCardiacProblem<DIM,DIM, 3>
{
    friend class boost::serialization::access;
 
    friend class TestArchivingExtendedBidomain;//for testing
 
    template<class Archive>
    void save(Archive & archive, const unsigned int version) const
    {
        archive & boost::serialization::base_object<AbstractCardiacProblem<DIM, DIM, 3> >(*this);
        archive & mpExtendedBidomainTissue;
        archive & mFixedExtracellularPotentialNodes;
        //archive & mIntracellularConductivitiesSecondCell; not allowed in some versions of boost
        archive & mVariablesIDs;
        archive & mUserSpecifiedSecondCellConductivities;
        archive & mUserHasSetBidomainValuesExplicitly;
        archive & mAmFirstCell;
        archive & mAmSecondCell;
        archive & mAmGap;
        archive & mCmFirstCell;
        archive & mCmSecondCell;
        archive & mGGap;
        archive & mGgapHeterogeneityRegions;
        archive & mGgapHeterogenousValues;
        archive & mRowForAverageOfPhiZeroed;
        archive & mApplyAveragePhieZeroConstraintAfterSolving;
        archive & mUserSuppliedExtracellularStimulus;
        archive & mHasBath;
        //archive & mpSolver;
 
        //archive the values for the conductivies of the second cell
        for (unsigned i = 0; i < DIM; i++)
        {
            double conductivity = mIntracellularConductivitiesSecondCell(i);
            archive & conductivity;
        }
 
        bool has_solution = (this->mSolution != NULL);
        archive & has_solution;
        if (has_solution)
        {
            // Please see the todo tag (#1317) in AbstractCardiacProblem
            Hdf5DataWriter writer(*this->mpMesh->GetDistributedVectorFactory(), ArchiveLocationInfo::GetArchiveRelativePath(), "AbstractCardiacProblem_mSolution", false);
            writer.DefineFixedDimension(this->mpMesh->GetDistributedVectorFactory()->GetProblemSize());
            writer.DefineUnlimitedDimension("Time", "msec", 1);
 
            int V = writer.DefineVariable("V","mV");
            int V_2 = writer.DefineVariable("V_2","mV");
            int phie = writer.DefineVariable("Phi_e","mV");
            std::vector<int> variable_ids;
            variable_ids.push_back(V);
            variable_ids.push_back(V_2);
            variable_ids.push_back(phie);
            writer.EndDefineMode();
            writer.PutUnlimitedVariable(0.0);
 
 
            writer.PutStripedVector(variable_ids, this->mSolution);
        }
    }
 
    template<class Archive>
    void load(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractCardiacProblem<DIM, DIM, 3> >(*this);
        archive & mpExtendedBidomainTissue;
        archive & mFixedExtracellularPotentialNodes;
        //archive & mIntracellularConductivitiesSecondCell; not allowed in some versions of boost
        archive & mVariablesIDs;
        archive & mUserSpecifiedSecondCellConductivities;
        archive & mUserHasSetBidomainValuesExplicitly;
        archive & mAmFirstCell;
        archive & mAmSecondCell;
        archive & mAmGap;
        archive & mCmFirstCell;
        archive & mCmSecondCell;
        archive & mGGap;
        archive & mGgapHeterogeneityRegions;
        archive & mGgapHeterogenousValues;
        archive & mRowForAverageOfPhiZeroed;
        archive & mApplyAveragePhieZeroConstraintAfterSolving;
        archive & mUserSuppliedExtracellularStimulus;
        archive & mHasBath;
        //archive & mpSolver;
 
        //load the values for the conductivies of the second cell
        for (unsigned i = 0; i < DIM; i++)
        {
            double conductivity;
            archive & conductivity;
            mIntracellularConductivitiesSecondCell(i) = conductivity;
        }
 
        bool has_solution;
        archive & has_solution;
 
        if (has_solution)
        {
            this->mSolution = this->mpMesh->GetDistributedVectorFactory()->CreateVec(3);
            DistributedVector mSolution_distri = this->mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(this->mSolution);
 
            std::string archive_dir = ArchiveLocationInfo::GetArchiveRelativePath();
            Hdf5DataReader reader(archive_dir, "AbstractCardiacProblem_mSolution", !FileFinder::IsAbsolutePath(archive_dir));
 
            Vec V = this->mpMesh->GetDistributedVectorFactory()->CreateVec();
            Vec V_2 = this->mpMesh->GetDistributedVectorFactory()->CreateVec();
            Vec phie = this->mpMesh->GetDistributedVectorFactory()->CreateVec();
 
            reader.GetVariableOverNodes(V, "V", 0);
            reader.GetVariableOverNodes(V_2, "V_2", 0);
            reader.GetVariableOverNodes(phie, "Phi_e", 0);
 
            //from transmembrane voltages back to phi_i now...
            DistributedVector vm_first_cell_distri = this->mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(V);
            DistributedVector vm_second_cell_distri = this->mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(V_2);
            DistributedVector phie_distri = this->mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(phie);
 
            DistributedVector::Stripe mSolution_V_1(mSolution_distri,0);
            DistributedVector::Stripe mSolution_V_2(mSolution_distri,1);
            DistributedVector::Stripe mSolution_phie(mSolution_distri,2);
 
            for (DistributedVector::Iterator index = mSolution_distri.Begin();
                 index != mSolution_distri.End();
                 ++index)
            {
                mSolution_V_1[index] = vm_first_cell_distri[index];
                mSolution_V_2[index] = vm_second_cell_distri[index];
                mSolution_phie[index] = phie_distri[index];
            }
            PetscTools::Destroy(V);
            PetscTools::Destroy(V_2);
            PetscTools::Destroy(phie);
 
            mSolution_distri.Restore();
        }
    }
    BOOST_SERIALIZATION_SPLIT_MEMBER()
 
 
protected:
 
    AbstractCardiacCellFactory<DIM,DIM>* mpSecondCellFactory;
 
    ExtendedBidomainTissue<DIM>* mpExtendedBidomainTissue;
 
    std::vector<unsigned> mFixedExtracellularPotentialNodes;
 
    c_vector<double, DIM>  mIntracellularConductivitiesSecondCell;
 
    unsigned mVoltageColumnId_Vm1;
    unsigned mVoltageColumnId_Vm2;
    unsigned mVoltageColumnId_Phie;
    std::vector<signed int> mVariablesIDs;
 
    bool mUserSpecifiedSecondCellConductivities;
 
    bool mUserHasSetBidomainValuesExplicitly;
 
    double mAmFirstCell;
    double mAmSecondCell;
    double mAmGap;
    double mCmFirstCell;
    double mCmSecondCell;
    double mGGap;
 
    std::vector<boost::shared_ptr<AbstractChasteRegion<DIM> > > mGgapHeterogeneityRegions;
 
    std::vector<double> mGgapHeterogenousValues;
 
 
    AbstractStimulusFactory<DIM>* mpExtracellularStimulusFactory;
 
    int mRowForAverageOfPhiZeroed;
 
    unsigned mApplyAveragePhieZeroConstraintAfterSolving;
 
    bool mUserSuppliedExtracellularStimulus;
 
    bool mHasBath;
 
    Vec CreateInitialCondition();
 
    void AnalyseMeshForBath();
 
    void ProcessExtracellularStimulus();
 
    AbstractExtendedBidomainSolver<DIM,DIM>* mpSolver;
 
    virtual AbstractCardiacTissue<DIM> *CreateCardiacTissue();
 
    virtual AbstractDynamicLinearPdeSolver<DIM,DIM,3>* CreateSolver();
 
public:
    ExtendedBidomainProblem(AbstractCardiacCellFactory<DIM>* pCellFactory, AbstractCardiacCellFactory<DIM>* pSecondCellFactory, bool hasBath = false);
 
    ExtendedBidomainProblem();
 
    virtual ~ExtendedBidomainProblem();
 
    void SetFixedExtracellularPotentialNodes(std::vector<unsigned> nodes);
 
    void SetIntracellularConductivitiesForSecondCell(c_vector<double, DIM> conductivities);
 
    void SetExtendedBidomainParameters(double Am1, double Am2, double AmGap, double Cm1, double Cm2, double Ggap);
 
    void SetGgapHeterogeneities ( std::vector<boost::shared_ptr<AbstractChasteRegion<DIM> > >& rGgapHeterogeneityRegions, std::vector<double>& rGgapValues);
 
    void SetExtracellularStimulusFactory( AbstractStimulusFactory<DIM>* pFactory);
 
 
    void SetNodeForAverageOfPhiZeroed(unsigned node);
 
    ExtendedBidomainTissue<DIM>* GetExtendedBidomainTissue();
 
    void WriteInfo(double time);
 
    virtual void DefineWriterColumns(bool extending);
 
    virtual void WriteOneStep(double time, Vec voltageVec);
 
    void PreSolveChecks();
 
    bool GetHasBath();
 
    void SetHasBath(bool hasBath);
};
 
#include "SerializationExportWrapper.hpp" // Must be last
EXPORT_TEMPLATE_CLASS_SAME_DIMS(ExtendedBidomainProblem)
 
#endif /*EXTENDEDBIDOMAINPROBLEM_HPP_*/