LinearSystem.hpp

/*

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*/

#ifndef _LINEARSYSTEM_HPP_
#define _LINEARSYSTEM_HPP_

#include "ChasteSerialization.hpp"
#include "UblasCustomFunctions.hpp" // needs to be 'first'

#include "PetscTools.hpp"
#include "PetscVecTools.hpp"
#include "PetscMatTools.hpp"
#include "OutputFileHandler.hpp"
#include "PCBlockDiagonal.hpp"
#include "PCLDUFactorisation.hpp"
#include "PCTwoLevelsBlockDiagonal.hpp"
#include "ArchiveLocationInfo.hpp"
//#include <boost/serialization/shared_ptr.hpp>

#include <petscvec.h>
#include <petscmat.h>
#include <petscksp.h>
#include <petscviewer.h>

#include <string>
#include <cassert>

class LinearSystem
{
    friend class TestLinearSystem;
    friend class TestPCBlockDiagonal;
    friend class TestPCTwoLevelsBlockDiagonal;
    friend class TestPCLDUFactorisation;
    friend class TestChebyshevIteration;

private:

    Mat mLhsMatrix;  
    Mat mPrecondMatrix; 
    Vec mRhsVector;  
    PetscInt mSize;  
    PetscInt mOwnershipRangeLo; 
    PetscInt mOwnershipRangeHi; 
    MatNullSpace mMatNullSpace; 
    bool mDestroyMatAndVec;

    KSP mKspSolver;   
    bool mKspIsSetup; 
    double mNonZerosUsed;  
    bool mMatrixIsConstant; 
    double mTolerance; 
    bool mUseAbsoluteTolerance;
    std::string mKspType;
    std::string mPcType;
    Vec mDirichletBoundaryConditionsVector; 

    PCBlockDiagonal* mpBlockDiagonalPC;
    PCLDUFactorisation* mpLDUFactorisationPC;
    PCTwoLevelsBlockDiagonal* mpTwoLevelsBlockDiagonalPC;

    boost::shared_ptr<std::vector<PetscInt> > mpBathNodes;

    bool mPrecondMatrixIsNotLhs;

    unsigned mRowPreallocation;

    bool mUseFixedNumberIterations;

    unsigned mEvaluateNumItsEveryNSolves;

    void* mpConvergenceTestContext;

    unsigned mNumSolves;

    PetscReal mEigMin;

    PetscReal mEigMax;

    bool mForceSpectrumReevaluation;

#ifdef TRACE_KSP
    unsigned mTotalNumIterations;
    unsigned mMaxNumIterations;
#endif

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        //MatNullSpace mMatNullSpace; // Gets re-created by calling code on load

        archive & mNonZerosUsed;
        archive & mMatrixIsConstant;
        archive & mTolerance;
        archive & mUseAbsoluteTolerance;
        archive & mKspType;
        archive & mPcType;

        //Vec mDirichletBoundaryConditionsVector; // Gets re-created by calling code on load
    }

public:

    LinearSystem(PetscInt lhsVectorSize, unsigned rowPreallocation=UINT_MAX);

    LinearSystem(Vec templateVector, unsigned rowPreallocation, bool newAllocationError=true);

    LinearSystem(Vec residualVector, Mat jacobianMatrix);

    LinearSystem(PetscInt lhsVectorSize, Mat lhsMatrix, Vec rhsVector);

    ~LinearSystem();

//    bool IsMatrixEqualTo(Mat testMatrix);
//    bool IsRhsVectorEqualTo(Vec testVector);

    void SetMatrixElement(PetscInt row, PetscInt col, double value);

    void AddToMatrixElement(PetscInt row, PetscInt col, double value);

    void AssembleFinalLinearSystem();

    void AssembleIntermediateLinearSystem();

    void FinaliseLhsMatrix();

    void FinalisePrecondMatrix();

    void SwitchWriteModeLhsMatrix();

    void FinaliseRhsVector();

    void SetMatrixIsSymmetric(bool isSymmetric=true);

    bool IsMatrixSymmetric();

    void SetMatrixIsConstant(bool matrixIsConstant);

    void SetRelativeTolerance(double relativeTolerance);

    void SetAbsoluteTolerance(double absoluteTolerance);

    void SetKspType(const char* kspType);

    void SetPcType(const char* pcType, boost::shared_ptr<std::vector<PetscInt> > pBathNodes=boost::shared_ptr<std::vector<PetscInt> >() );

    void DisplayMatrix();

    void DisplayRhs();

    void SetMatrixRow(PetscInt row, double value);

    Vec GetMatrixRowDistributed(unsigned rowIndex);

    void ZeroMatrixRowsWithValueOnDiagonal(std::vector<unsigned>& rRows, double diagonalValue);


    void ZeroMatrixRowsAndColumnsWithValueOnDiagonal(std::vector<unsigned>& rRowColIndices, double diagonalValue);


    void ZeroMatrixColumn(PetscInt col);

    void ZeroLhsMatrix();

    void ZeroRhsVector();

    void ZeroLinearSystem();

    Vec Solve(Vec lhsGuess=NULL);

    void SetRhsVectorElement(PetscInt row, double value);

    void AddToRhsVectorElement(PetscInt row, double value);

    unsigned GetSize() const;

    void SetNullBasis(Vec nullbasis[], unsigned numberOfBases);

    void RemoveNullSpace();

    Vec& rGetRhsVector();

    Vec GetRhsVector() const;

    Mat& rGetLhsMatrix();

    Mat GetLhsMatrix() const;

    Mat& rGetPrecondMatrix();

    Vec& rGetDirichletBoundaryConditionsVector();

    // DEBUGGING CODE:
    void GetOwnershipRange(PetscInt& lo, PetscInt& hi);

    double GetMatrixElement(PetscInt row, PetscInt col);

    double GetRhsVectorElement(PetscInt row);

    unsigned GetNumIterations() const;

    template<size_t MATRIX_SIZE>
    void AddLhsMultipleValues(unsigned* matrixRowAndColIndices, c_matrix<double, MATRIX_SIZE, MATRIX_SIZE>& rSmallMatrix)
    {
        PetscMatTools::AddMultipleValues(mLhsMatrix, matrixRowAndColIndices, rSmallMatrix);
    }

    template<size_t VECTOR_SIZE>
    void AddRhsMultipleValues(unsigned* vectorIndices, c_vector<double, VECTOR_SIZE>& smallVector)
    {
        PetscVecTools::AddMultipleValues(mRhsVector, vectorIndices, smallVector);
    }

    void SetPrecondMatrixIsDifferentFromLhs(bool precondIsDifferent = true);

    void SetUseFixedNumberIterations(bool useFixedNumberIterations = true, unsigned evaluateNumItsEveryNSolves = UINT_MAX);

    void ResetKspSolver();
};

#include "SerializationExportWrapper.hpp"
// Declare identifier for the serializer
CHASTE_CLASS_EXPORT(LinearSystem)

namespace boost
{
namespace serialization
{
template<class Archive>
inline void save_construct_data(
    Archive & ar, const LinearSystem * t, const unsigned int file_version)
{

    std::string archive_filename_lhs = ArchiveLocationInfo::GetArchiveDirectory() + "lhs.mat";
    std::string archive_filename_rhs = ArchiveLocationInfo::GetArchiveDirectory() + "rhs.vec";
    const unsigned size = t->GetSize();
    ar << size;

    PetscTools::DumpPetscObject(t->GetRhsVector(), archive_filename_rhs);
    PetscTools::DumpPetscObject(t->GetLhsMatrix(), archive_filename_lhs);

    //Is the matrix structurally symmetric?
    PetscBool symm_set, is_symmetric;
    is_symmetric = PETSC_FALSE;
    //Note that the following call only changes is_symmetric when symm_set is true
    MatIsSymmetricKnown(t->GetLhsMatrix(), &symm_set, &is_symmetric);
    assert(symm_set == is_symmetric);
    ar << symm_set;
}

template<class Archive>
inline void load_construct_data(
    Archive & ar, LinearSystem * t, const unsigned int file_version)
{
     std::string archive_filename_lhs = ArchiveLocationInfo::GetArchiveDirectory() + "lhs.mat";
     std::string archive_filename_rhs = ArchiveLocationInfo::GetArchiveDirectory() + "rhs.vec";

     PetscInt size;
     ar >> size;

     Vec new_vec;
     PetscTools::ReadPetscObject(new_vec, archive_filename_rhs);

     Mat new_mat;
     PetscTools::ReadPetscObject(new_mat, archive_filename_lhs);

     //This has to occur after the call to MatLoad as the matrix does not exist until MatLoad is called.
     //The property will be copied & set correctly in the LinearSystem constructor.
     PetscBool symm_set;

     ar >> symm_set;
     if (symm_set == PETSC_TRUE)
     {
        PetscMatTools::SetOption(new_mat, MAT_SYMMETRIC);
        PetscMatTools::SetOption(new_mat, MAT_SYMMETRY_ETERNAL);
     }

     ::new(t)LinearSystem(size, new_mat, new_vec);
}
}
} // namespace ...

#endif //_LINEARSYSTEM_HPP_