LinearSystem.hpp

/*

Copyright (C) University of Oxford, 2005-2010

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" // meeds to be 'first'

#include "PetscTools.hpp"
#include "OutputFileHandler.hpp"
#include "PCBlockDiagonal.hpp"
#include "PCLDUFactorisation.hpp"
#include "ArchiveLocationInfo.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 TestPCLDUFactorisation;

private:

    Mat mLhsMatrix;  
    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;


#ifdef TRACE_KSP
    unsigned mNumSolves;
    unsigned mTotalNumIterations;
    unsigned mMaxNumIterations;
#endif

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        //MatNullSpace mMatNullSpace; ///\todo archive mMatNullSpace.

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

        //Vec mDirichletBoundaryConditionsVector; ///\todo archive mDirichletBoundaryConditionsVector.
    }

public:

    LinearSystem(PetscInt lhsVectorSize, MatType matType=(MatType) MATMPIAIJ);

    LinearSystem(Vec templateVector);

    LinearSystem(Vec residualVector, Mat jacobianMatrix);

    LinearSystem(PetscInt lhsVectorSize, Mat lhsMatrix, Vec rhsVector, MatType matType=(MatType) MATMPIAIJ);

    ~LinearSystem();

    void SetupVectorAndMatrix(MatType matType);

//    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 AssembleFinalLhsMatrix();

    void AssembleIntermediateLhsMatrix();

    void AssembleRhsVector();

    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);

    void DisplayMatrix();

    void DisplayRhs();

    void SetMatrixRow(PetscInt row, double value);

    Vec GetMatrixRowDistributed(unsigned row_index);

    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;

    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)
    {
        PetscInt matrix_row_indices[MATRIX_SIZE];
        PetscInt num_rows_owned = 0;
        PetscInt global_row;

        for (unsigned row = 0; row<MATRIX_SIZE; row++)
        {
            global_row = matrixRowAndColIndices[row];
            if (global_row >=mOwnershipRangeLo && global_row <mOwnershipRangeHi)
            {
                matrix_row_indices[num_rows_owned++] = global_row;
            }
        }

        if ( num_rows_owned == MATRIX_SIZE)
        {
            MatSetValues(mLhsMatrix,
                         num_rows_owned,
                         matrix_row_indices,
                         MATRIX_SIZE,
                         (PetscInt*) matrixRowAndColIndices,
                         rSmallMatrix.data(),
                         ADD_VALUES);
        }
        else
        {
            // We need continuous data, if some of the rows do not belong to the processor their values
            // are not passed to MatSetValues
            double values[MATRIX_SIZE*MATRIX_SIZE];
            unsigned num_values_owned = 0;
            for (unsigned row = 0; row<MATRIX_SIZE; row++)
            {
                global_row = matrixRowAndColIndices[row];
                if (global_row >=mOwnershipRangeLo && global_row <mOwnershipRangeHi)
                {
                    for (unsigned col=0; col<MATRIX_SIZE; col++)
                    {
                        values[num_values_owned++] = rSmallMatrix(row, col);
                    }
                }
            }

            MatSetValues(mLhsMatrix,
                         num_rows_owned,
                         matrix_row_indices,
                         MATRIX_SIZE,
                         (PetscInt*) matrixRowAndColIndices,
                         values,
                         ADD_VALUES);
        }
    };

    template<size_t VECTOR_SIZE>
    void AddRhsMultipleValues(unsigned* vectorIndices, c_vector<double, VECTOR_SIZE>& smallVector)
    {
        PetscInt indices_owned[VECTOR_SIZE];
        PetscInt num_indices_owned = 0;
        PetscInt global_row;

        for (unsigned row = 0; row<VECTOR_SIZE; row++)
        {
            global_row = vectorIndices[row];
            if (global_row >=mOwnershipRangeLo && global_row <mOwnershipRangeHi)
            {
                indices_owned[num_indices_owned++] = global_row;
            }
        }

        if (num_indices_owned == VECTOR_SIZE)
        {
            VecSetValues(mRhsVector,
                         num_indices_owned,
                         indices_owned,
                         smallVector.data(),
                         ADD_VALUES);
        }
        else
        {
            // We need continuous data, if some of the rows do not belong to the processor their values
            // are not passed to MatSetValues
            double values[VECTOR_SIZE];
            unsigned num_values_owned = 0;

            for (unsigned row = 0; row<VECTOR_SIZE; row++)
            {
                global_row = vectorIndices[row];
                if (global_row >=mOwnershipRangeLo && global_row <mOwnershipRangeHi)
                {
                    values[num_values_owned++] = smallVector(row);
                }
            }

            VecSetValues(mRhsVector,
                         num_indices_owned,
                         indices_owned,
                         values,
                         ADD_VALUES);
        }
    }

};

#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)
     {
#if (PETSC_VERSION_MAJOR == 3) //PETSc 3.x.x
        MatSetOption(new_mat, MAT_SYMMETRIC, PETSC_TRUE);
        MatSetOption(new_mat, MAT_SYMMETRY_ETERNAL, PETSC_TRUE);
#else
        MatSetOption(new_mat, MAT_SYMMETRIC);
        MatSetOption(new_mat, MAT_SYMMETRY_ETERNAL);
#endif
     }

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

#endif //_LINEARSYSTEM_HPP_