AbstractCardiacProblem.hpp

/*

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*/


#ifndef ABSTRACTCARDIACPROBLEM_HPP_
#define ABSTRACTCARDIACPROBLEM_HPP_



#include <string>
#include <vector>
#include <cassert>
#include <climits>
#include <boost/shared_ptr.hpp>

#include "ChasteSerialization.hpp"
#include <boost/serialization/vector.hpp>
#include <boost/serialization/string.hpp>
#include <boost/serialization/split_member.hpp>
#include <boost/serialization/shared_ptr.hpp>
#include "ClassIsAbstract.hpp"
#include "ChasteSerializationVersion.hpp"

#include "AbstractTetrahedralMesh.hpp"
#include "AbstractCardiacCell.hpp"
#include "AbstractCardiacCellFactory.hpp"
#include "AbstractCardiacTissue.hpp"
#include "AbstractDynamicLinearPdeSolver.hpp"
#include "BoundaryConditionsContainer.hpp"
#include "DistributedVectorFactory.hpp"
#include "Hdf5DataReader.hpp"
#include "Hdf5DataWriter.hpp"
#include "Warnings.hpp"
#include "AbstractOutputModifier.hpp"
/*
 * Archiving extravaganza:
 *
 * We archive mesh and tissue through a pointer to an abstract class.  All the potential concrete
 * classes need to be included here, so they are registered with boost.  If not, boost won't be
 * able to find the archiving methods of the concrete class and will throw the following
 * exception:
 *
 *       terminate called after throwing an instance of 'boost::archive::archive_exception'
 *       what():  unregistered class
 *
 * No member variable is defined to be of any of these clases, so removing them won't
 * produce any compiler error.  The exception above will occur at runtime.
 *
 * This might not be even necessary in certain cases, if the file is included implicitly by another
 * header file or by the test itself.  It's safer though.
 */
#include "DistributedTetrahedralMesh.hpp"
#include "TetrahedralMesh.hpp" //May be needed for unarchiving a mesh
#include "MonodomainTissue.hpp"
#include "BidomainTissue.hpp"

class AbstractUntemplatedCardiacProblem : private boost::noncopyable
{
public:
    virtual ~AbstractUntemplatedCardiacProblem()
    {}
};

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
class AbstractCardiacProblem : public AbstractUntemplatedCardiacProblem
{
    friend class TestBidomainWithBath;
    friend class TestMonodomainProblem;
    friend class TestCardiacSimulationArchiver;

    typedef typename boost::shared_ptr<BoundaryConditionsContainer<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM> >
        BccType;

private:
    friend class boost::serialization::access;

    template<class Archive>
    void save(Archive & archive, const unsigned int version) const
    {
        if (version >= 1)
        {
            const unsigned element_dim=ELEMENT_DIM;
            archive & element_dim;
            const unsigned space_dim=SPACE_DIM;
            archive & space_dim;
            const unsigned problem_dim=PROBLEM_DIM;
            archive & problem_dim;
        }
        archive & mMeshFilename;
        archive & mpMesh;
        //archive & mAllocatedMemoryForMesh; // Mesh is deleted by AbstractCardiacTissue

        // We shouldn't ever have to save the old version
        assert(version >= 2);
//        {
//            bool use_matrix_based_assembly = true;
//            archive & use_matrix_based_assembly;
//        }

        archive & mWriteInfo;
        archive & mPrintOutput;
        archive & mNodesToOutput;
        //archive & mVoltageColumnId; // Created by InitialiseWriter, called from Solve
        //archive & mExtraVariablesId; // Created by InitialiseWriter, called from Solve
        //archive & mTimeColumnId; // Created by InitialiseWriter, called from Solve
        //archive & mNodeColumnId; // Created by InitialiseWriter, called from Solve
        //archive & mpWriter; // Created by InitialiseWriter, called from Solve
        archive & mpCardiacTissue;
        //archive & mpSolver; // Only exists during calls to the Solve method
        bool has_solution = (mSolution != NULL);
        archive & has_solution;
        if (has_solution)
        {
            Hdf5DataWriter writer(*mpMesh->GetDistributedVectorFactory(), ArchiveLocationInfo::GetArchiveRelativePath(), "AbstractCardiacProblem_mSolution", false);
            writer.DefineFixedDimension(mpMesh->GetDistributedVectorFactory()->GetProblemSize());
            writer.DefineUnlimitedDimension("Time", "msec", 1);

            int vm_col = writer.DefineVariable("Vm","mV");

            if (PROBLEM_DIM==1)
            {
                writer.EndDefineMode();
                writer.PutUnlimitedVariable(0.0);
                writer.PutVector(vm_col, mSolution);
            }

            if (PROBLEM_DIM==2)
            {
                int phie_col = writer.DefineVariable("Phie","mV");
                std::vector<int> variable_ids;
                variable_ids.push_back(vm_col);
                variable_ids.push_back(phie_col);
                writer.EndDefineMode();
                writer.PutUnlimitedVariable(0.0);
                writer.PutStripedVector(variable_ids, mSolution);
            }

            writer.Close();

        }
        archive & mCurrentTime;

        // Save boundary conditions
        SaveBoundaryConditions(archive, mpMesh, mpBoundaryConditionsContainer);
        SaveBoundaryConditions(archive, mpMesh, mpDefaultBoundaryConditionsContainer);

        if (version>= 3)
        {
            archive & mOutputModifiers;
        }
    }

    template<class Archive>
    void load(Archive & archive, const unsigned int version)
    {
        if (version >= 1)
        {
            unsigned element_dim;
            unsigned space_dim;
            unsigned problem_dim;
            archive & element_dim;
            archive & space_dim;
            archive & problem_dim;
            if ( (element_dim != ELEMENT_DIM) ||(space_dim != SPACE_DIM) ||(problem_dim != PROBLEM_DIM) )
            {
                /*If we carry on from this point then the mesh produced by unarchiving from the
                 * archive is templated as AbstractTetrahedralMesh<element_dim, space_dim>
                 * which doesn't match AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>*  mpMesh.
                 * Boost will through away the unarchived one, without deleting it properly and
                 * then set mpMesh=NULL.  We need to avoid this happening by bailing out.
                 */
                EXCEPTION("Failed to load from checkpoint because the dimensions of the archive do not match the object it's being read into.");
            }
        }
        archive & mMeshFilename;
        archive & mpMesh;
        assert(mpMesh != NULL); //If NULL then loading mesh has failed without an exception so Boost has given up on the mesh.  This would happen if a 2-dimensional mesh was successfully unarchived but mpMesh was expecting a 3-d mesh etc.
        //archive & mAllocatedMemoryForMesh; // Will always be true after a load

        if (version < 2)
        {
            bool use_matrix_based_assembly;
            archive & use_matrix_based_assembly;
        }

        archive & mWriteInfo;
        archive & mPrintOutput;
        archive & mNodesToOutput;
        //archive & mVoltageColumnId; // Created by InitialiseWriter, called from Solve
        //archive & mExtraVariablesId; // Created by InitialiseWriter, called from Solve
        //archive & mTimeColumnId; // Created by InitialiseWriter, called from Solve
        //archive & mNodeColumnId; // Created by InitialiseWriter, called from Solve
        //archive & mpWriter; // Created by InitialiseWriter, called from Solve
        archive & mpCardiacTissue;
        //archive & mpSolver; // Only exists during calls to the Solve method
        bool has_solution;
        archive & has_solution;
        if ((has_solution) && PROBLEM_DIM < 3)
        {
            mSolution = mpMesh->GetDistributedVectorFactory()->CreateVec(PROBLEM_DIM);
            DistributedVector mSolution_distri = mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(mSolution);

            Vec vm = mpMesh->GetDistributedVectorFactory()->CreateVec();
            Vec phie = mpMesh->GetDistributedVectorFactory()->CreateVec();

            std::string archive_dir = ArchiveLocationInfo::GetArchiveRelativePath();
            Hdf5DataReader reader(archive_dir, "AbstractCardiacProblem_mSolution", !FileFinder::IsAbsolutePath(archive_dir));
            reader.GetVariableOverNodes(vm, "Vm", 0);

            if (PROBLEM_DIM==1)
            {
                //reader.Close(); // no need to call close explicitly, done in the destructor

                DistributedVector vm_distri = mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(vm);

                DistributedVector::Stripe mSolution_vm(mSolution_distri,0);

                for (DistributedVector::Iterator index = mSolution_distri.Begin();
                     index != mSolution_distri.End();
                     ++index)
                {
                    mSolution_vm[index] = vm_distri[index];
                }
            }

            if (PROBLEM_DIM==2)
            {
                reader.GetVariableOverNodes(phie, "Phie", 0);
                //reader.Close(); // no need to call close explicitly, done in the destructor

                DistributedVector vm_distri = mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(vm);
                DistributedVector phie_distri = mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(phie);

                DistributedVector::Stripe mSolution_vm(mSolution_distri,0);
                DistributedVector::Stripe mSolution_phie(mSolution_distri,1);

                for (DistributedVector::Iterator index = mSolution_distri.Begin();
                     index != mSolution_distri.End();
                     ++index)
                {
                    mSolution_vm[index] = vm_distri[index];
                    mSolution_phie[index] = phie_distri[index];
                }
            }

            mSolution_distri.Restore();

            PetscTools::Destroy(vm);
            PetscTools::Destroy(phie);

        }
        archive & mCurrentTime;

        // Load boundary conditions
        mpBoundaryConditionsContainer = LoadBoundaryConditions(archive, mpMesh);
        mpDefaultBoundaryConditionsContainer = LoadBoundaryConditions(archive, mpMesh);

        if (version>= 3)
        {
            archive & mOutputModifiers;
        }
    }

    BOOST_SERIALIZATION_SPLIT_MEMBER()

    
    template<class Archive>
    void SaveBoundaryConditions(Archive & archive,
                                AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh,
                                BccType pBcc) const
    {
        (*ProcessSpecificArchive<Archive>::Get()) & pBcc;
    }

    template<class Archive>
    BccType LoadBoundaryConditions(
            Archive & archive,
            AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh)
    {
        // Load pointer from archive
        BccType p_bcc;
        (*ProcessSpecificArchive<Archive>::Get()) & p_bcc;

        // Fill in the conditions, if we have a container and it's not already full
        if (p_bcc)
        {
            p_bcc->LoadFromArchive(*ProcessSpecificArchive<Archive>::Get(), pMesh);
        }

        return p_bcc;
    }

protected:
    std::string mMeshFilename;

    bool mAllocatedMemoryForMesh;
    bool mWriteInfo;
    bool mPrintOutput;

    std::vector<unsigned> mNodesToOutput;

    unsigned mVoltageColumnId;
    std::vector<unsigned> mExtraVariablesId;
    unsigned mTimeColumnId;
    unsigned mNodeColumnId;

    AbstractCardiacTissue<ELEMENT_DIM,SPACE_DIM>* mpCardiacTissue;

    BccType mpBoundaryConditionsContainer;
    BccType mpDefaultBoundaryConditionsContainer;
    AbstractDynamicLinearPdeSolver<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>* mpSolver;
    AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>* mpCellFactory;
    AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* mpMesh;

    Vec mSolution;

    double mCurrentTime;

    AbstractTimeAdaptivityController* mpTimeAdaptivityController;



    virtual AbstractCardiacTissue<ELEMENT_DIM,SPACE_DIM>* CreateCardiacTissue() =0;

    virtual AbstractDynamicLinearPdeSolver<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>* CreateSolver() =0;

    virtual void CreateMeshFromHeartConfig();

    template<unsigned DIM, unsigned ELEC_PROB_DIM>
    friend class CardiacElectroMechanicsProblem;

    Hdf5DataWriter* mpWriter;

    std::vector<boost::shared_ptr<AbstractOutputModifier> > mOutputModifiers;

public:
    AbstractCardiacProblem(AbstractCardiacCellFactory<ELEMENT_DIM,SPACE_DIM>* pCellFactory);

    AbstractCardiacProblem();

    virtual ~AbstractCardiacProblem();

    void Initialise();

    void SetNodesPerProcessorFilename(const std::string& rFilename);

    void SetBoundaryConditionsContainer(BccType pBcc);

    virtual void PreSolveChecks();

    virtual Vec CreateInitialCondition();

    void SetMesh(AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh);

    void PrintOutput(bool rPrintOutput);

    void SetWriteInfo(bool writeInfo = true);

    Vec GetSolution();

    DistributedVector GetSolutionDistributedVector();

    double GetCurrentTime();

    AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM> & rGetMesh();

    AbstractCardiacTissue<ELEMENT_DIM,SPACE_DIM>* GetTissue();

    void Solve();

    void CloseFilesAndPostProcess();

    virtual void WriteInfo(double time)=0;

    virtual void DefineWriterColumns(bool extending);

    void DefineExtraVariablesWriterColumns(bool extending);

    virtual void WriteOneStep(double time, Vec voltageVec) = 0;

    void WriteExtraVariablesOneStep();

    bool InitialiseWriter();

    void SetOutputNodes(std::vector<unsigned> & rNodesToOutput);

    Hdf5DataReader GetDataReader();

    virtual void AtBeginningOfTimestep(double time)
    {}

    virtual void OnEndOfTimestep(double time)
    {}

    virtual void SetUpAdditionalStoppingTimes(std::vector<double>& rAdditionalStoppingTimes)
    {}



    // and no controller, in which case the default is used.

    void SetUseTimeAdaptivityController(bool useAdaptivity,
                                        AbstractTimeAdaptivityController* pController = NULL);

    template<class Archive>
    void LoadExtraArchive(Archive & archive, unsigned version);

    virtual bool GetHasBath();

    virtual void SetElectrodes();

    void AddOutputModifier( boost::shared_ptr<AbstractOutputModifier> pOutputModifier)
    {
        mOutputModifiers.push_back(pOutputModifier);
    }
};

TEMPLATED_CLASS_IS_ABSTRACT_3_UNSIGNED(AbstractCardiacProblem)


template<unsigned DIM>
class BidomainProblem;

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
template<class Archive>
void AbstractCardiacProblem<ELEMENT_DIM,SPACE_DIM,PROBLEM_DIM>::LoadExtraArchive(Archive & archive, unsigned version)
{
    // The vector factory must be loaded, but isn't needed for anything.
    DistributedVectorFactory* p_mesh_factory;
    archive >> p_mesh_factory;

    // How many processes were used by the saving simulation?
    DistributedVectorFactory* p_original_factory = p_mesh_factory->GetOriginalFactory();
    unsigned orig_num_procs = 1;
    if (p_original_factory)
    {
        orig_num_procs = p_original_factory->GetNumProcs();
    }

    // The cardiac cells - load only the cells we actually own
    mpCardiacTissue->LoadCardiacCells(archive, version);

    {
        DistributedVectorFactory* p_pde_factory;
        archive >> p_pde_factory;
        assert(p_pde_factory == p_mesh_factory); // Paranoia...
    }
    // We no longer need this vector factory, since we already have our own.
    delete p_mesh_factory;

    // The boundary conditions
    BccType p_bcc;
    archive >> p_bcc;
    if (p_bcc)
    {
        if (!mpBoundaryConditionsContainer)
        {
            mpBoundaryConditionsContainer = p_bcc;
            mpBoundaryConditionsContainer->LoadFromArchive(archive, mpMesh);
        }
        else
        {
            // If the mesh which was archived was a TetrahedralMesh then we have all the boundary conditions
            // in every process-specific archive.  We no longer test for this.
#define COVERAGE_IGNORE
            if(!dynamic_cast<DistributedTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>*>(mpMesh) && orig_num_procs > 1)
            {
                // The correct way to do this should be:
                // p_bcc->LoadFromArchive(archive, mpMesh);
                WARNING("Loading from a parallel archive which used a non-distributed mesh.  This scenario should work but is not fully tested.");
            }
#undef COVERAGE_IGNORE
            mpBoundaryConditionsContainer->MergeFromArchive(archive, mpMesh);
        }
    }
    BccType p_default_bcc;
    archive >> p_default_bcc;
    if (p_default_bcc)
    {
        // This always holds, so we never need to load the default BCs
        assert(p_bcc == p_default_bcc);
    }

    // Are we a bidomain problem?
    BidomainProblem<ELEMENT_DIM>* p_bidomain_problem = dynamic_cast<BidomainProblem<ELEMENT_DIM>*>(this);
    if (p_bidomain_problem)
    {
        assert(ELEMENT_DIM == SPACE_DIM);
        p_bidomain_problem->LoadExtraArchiveForBidomain(archive, version);
    }
}

namespace boost {
namespace serialization {
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM,  unsigned PROBLEM_DIM>
struct version<AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM> >
{
    CHASTE_VERSION_CONTENT(3);
};
} // namespace serialization
} // namespace boost
#endif /*ABSTRACTCARDIACPROBLEM_HPP_*/