LinearSystem.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 _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);

    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?
    PetscTruth 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.
     PetscTruth 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_