ExtendedBidomainProblem.hpp

/*

Copyright (C) University of Oxford, 2005-2011

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/


#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)
        {
            std::string filename = ArchiveLocationInfo::GetArchiveDirectory() + "AbstractCardiacProblem_mSolution.vec";

            Hdf5DataWriter writer(*this->mpMesh->GetDistributedVectorFactory(), ArchiveLocationInfo::GetArchiveRelativePath(), "AbstractCardiacProblem_mSolution", false);
            writer.DefineFixedDimension(this->mpMesh->GetDistributedVectorFactory()->GetProblemSize());
            writer.DefineUnlimitedDimension("Time", "msec", 1);

            // Make sure the file does not take more disc space than really needed (#1200)
            writer.SetFixedChunkSize(1);

            assert(HeartConfig::Instance()->GetOutputUsingOriginalNodeOrdering() == false );

            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);

            //re-arrange to write out voltages...
            Vec voltages_to_be_written =  this->mpMesh->GetDistributedVectorFactory()->CreateVec(3);
            DistributedVector wrapped_voltages_to_be_written = this->mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(voltages_to_be_written);

            DistributedVector distr_solution = this->mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(this->mSolution);
            DistributedVector::Stripe phi_i_first_cell_stripe(distr_solution,0);
            DistributedVector::Stripe phi_i_second_cell_stripe(distr_solution,1);
            DistributedVector::Stripe phi_e_stripe(distr_solution,2);


            DistributedVector::Stripe wrapped_voltages_to_be_written_first_stripe(wrapped_voltages_to_be_written,0);
            DistributedVector::Stripe wrapped_voltages_to_be_written_second_stripe(wrapped_voltages_to_be_written,1);
            DistributedVector::Stripe wrapped_voltages_to_be_written_third_stripe(wrapped_voltages_to_be_written,2);

            for (DistributedVector::Iterator index = distr_solution.Begin();
                 index != distr_solution.End();
                 ++index)
            {
                wrapped_voltages_to_be_written_first_stripe[index] = phi_i_first_cell_stripe[index] - phi_e_stripe[index];
                wrapped_voltages_to_be_written_second_stripe[index] = phi_i_second_cell_stripe[index] - phi_e_stripe[index];
                wrapped_voltages_to_be_written_third_stripe[index] = phi_e_stripe[index];
            }
            distr_solution.Restore();
            wrapped_voltages_to_be_written.Restore();

            writer.PutStripedVector(variable_ids, voltages_to_be_written);
            VecDestroy(voltages_to_be_written);
        }
    }

    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)
        {
            std::string filename = ArchiveLocationInfo::GetArchiveDirectory() + "AbstractCardiacProblem_mSolution.vec";

            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_phi_1(mSolution_distri,0);
            DistributedVector::Stripe mSolution_phi_2(mSolution_distri,1);
            DistributedVector::Stripe mSolution_phie(mSolution_distri,2);

            for (DistributedVector::Iterator index = mSolution_distri.Begin();
                 index != mSolution_distri.End();
                 ++index)
            {
                mSolution_phi_1[index] = vm_first_cell_distri[index] + phie_distri[index];//phi_i = Vm + phi_e
                mSolution_phi_2[index] = vm_second_cell_distri[index] + phie_distri[index];
                mSolution_phie[index] = phie_distri[index];
            }
            VecDestroy(V);
            VecDestroy(V_2);
            VecDestroy(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();

    ~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_*/