StokesFlowSolver.hpp

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#ifndef STOKESFLOWSOLVER_HPP_
#define STOKESFLOWSOLVER_HPP_

#include "AbstractContinuumMechanicsSolver.hpp"
#include "LinearSystem.hpp"
#include "LinearBasisFunction.hpp"
#include "QuadraticBasisFunction.hpp"
#include "Timer.hpp"
#include "PetscMatTools.hpp"
#include "PetscVecTools.hpp"
#include "StokesFlowProblemDefinition.hpp"
#include "StokesFlowAssembler.hpp"
#include "StokesFlowPreconditionerAssembler.hpp"
#include "ContinuumMechanicsNeumannBcsAssembler.hpp"

template<unsigned DIM>
class StokesFlowSolver : public AbstractContinuumMechanicsSolver<DIM>
{
    friend class TestStokesFlowSolver;

private:
    StokesFlowProblemDefinition<DIM>& mrProblemDefinition;

    StokesFlowAssembler<DIM>* mpStokesFlowAssembler;

    StokesFlowPreconditionerAssembler<DIM>* mpStokesFlowPreconditionerAssembler;

    ContinuumMechanicsNeumannBcsAssembler<DIM>* mpNeumannBcsAssembler;

    double mKspAbsoluteTol;

    void AssembleSystem();

public:

    StokesFlowSolver(AbstractTetrahedralMesh<DIM,DIM>& rQuadMesh,
                     StokesFlowProblemDefinition<DIM>& rProblemDefinition,
                     std::string outputDirectory);

    virtual ~StokesFlowSolver();

    void Solve();

    void SetKspAbsoluteTolerance(double kspAbsoluteTolerance);


    std::vector<c_vector<double,DIM> >& rGetSpatialSolution();

    std::vector<c_vector<double,DIM> >& rGetVelocities();
};

// Implementation


template<unsigned DIM>
StokesFlowSolver<DIM>::StokesFlowSolver(AbstractTetrahedralMesh<DIM,DIM>& rQuadMesh,
                                        StokesFlowProblemDefinition<DIM>& rProblemDefinition,
                                        std::string outputDirectory)
    : AbstractContinuumMechanicsSolver<DIM>(rQuadMesh, rProblemDefinition, outputDirectory, INCOMPRESSIBLE),
      mrProblemDefinition(rProblemDefinition),
      mKspAbsoluteTol(-1)
{
    assert(DIM==2 || DIM==3);
    assert(!mrProblemDefinition.rGetDirichletNodes().empty());

    mpStokesFlowAssembler = new StokesFlowAssembler<DIM>(&this->mrQuadMesh, &mrProblemDefinition);
    mpStokesFlowPreconditionerAssembler = new StokesFlowPreconditionerAssembler<DIM>(&this->mrQuadMesh, &mrProblemDefinition);
    mpNeumannBcsAssembler = new ContinuumMechanicsNeumannBcsAssembler<DIM>(&this->mrQuadMesh, &mrProblemDefinition);
}

template<unsigned DIM>
StokesFlowSolver<DIM>::~StokesFlowSolver()
{
    delete mpStokesFlowAssembler;
    delete mpStokesFlowPreconditionerAssembler;
    delete mpNeumannBcsAssembler;
}

template<unsigned DIM>
void StokesFlowSolver<DIM>::Solve()
{
    mrProblemDefinition.Validate();

    if (this->mVerbose)
    {
        Timer::Reset();
    }

    // Assemble Jacobian (and preconditioner)
    MechanicsEventHandler::BeginEvent(MechanicsEventHandler::ASSEMBLE);
    AssembleSystem();
    MechanicsEventHandler::EndEvent(MechanicsEventHandler::ASSEMBLE);

    if (this->mVerbose)
    {
        Timer::PrintAndReset("AssembleSystem");
    }

    /*
     * Solve the linear system using PETSc GMRES and an LU factorisation
     * of the preconditioner. Note we don't call Solve on the linear_system
     * as we want to set PETSc options.
     */
    MechanicsEventHandler::BeginEvent(MechanicsEventHandler::SOLVE);

    Vec solution;
    VecDuplicate(this->mLinearSystemRhsVector,&solution);
    PetscVecTools::Zero(solution);

    KSP solver;
    KSPCreate(PETSC_COMM_WORLD,&solver);
#if ((PETSC_VERSION_MAJOR==3) && (PETSC_VERSION_MINOR>=5))
    KSPSetOperators(solver, this->mSystemLhsMatrix, this->mPreconditionMatrix);
#else
    KSPSetOperators(solver, this->mSystemLhsMatrix, this->mPreconditionMatrix, DIFFERENT_NONZERO_PATTERN /*in precond between successive solves*/);
#endif
    KSPSetType(solver, KSPGMRES);

    if (mKspAbsoluteTol < 0)
    {
        double ksp_rel_tol = 1e-6;
        KSPSetTolerances(solver, ksp_rel_tol, PETSC_DEFAULT, PETSC_DEFAULT, 10000 /*max iter*/); //hopefully with the preconditioner this max is way too high
    }
    else
    {
        KSPSetTolerances(solver, 1e-16, mKspAbsoluteTol, PETSC_DEFAULT, 10000 /*max iter*/); //hopefully with the preconditioner this max is way too high
    }
    unsigned num_restarts = 100;
    KSPGMRESSetRestart(solver,num_restarts); // gmres num restarts

    PC pc;
    KSPGetPC(solver, &pc);
    PCSetType(pc, PCJACOBI);

    KSPSetUp(solver);

    KSPSetFromOptions(solver);

//    ///// For printing matrix when debugging
//    OutputFileHandler handler("TEMP");
//    out_stream p_file = handler.OpenOutputFile("matrix.txt");
//    for (unsigned i=0; i<this->mNumDofs; i++)
//    {
//        for (unsigned j=0; j<this->mNumDofs; j++)
//        {
//            *p_file << PetscMatTools::GetElement(this->mSystemLhsMatrix, i, j) << " ";
//        }
//        *p_file << "\n";
//    }
//    p_file->close();
//
//    out_stream p_file2 = handler.OpenOutputFile("rhs.txt");
//    for (unsigned i=0; i<this->mNumDofs; i++)
//    {
//        *p_file2 << PetscVecTools::GetElement(this->mLinearSystemRhsVector, i) << "\n";
//    }
//    p_file2->close();

    if (this->mVerbose)
    {
        Timer::PrintAndReset("KSP Setup");
    }

    KSPSolve(solver,this->mLinearSystemRhsVector,solution);

    KSPConvergedReason reason;
    KSPGetConvergedReason(solver,&reason);
    KSPEXCEPT(reason);

    if (this->mVerbose)
    {
        Timer::PrintAndReset("KSP Solve");
        int num_iters;
        KSPGetIterationNumber(solver, &num_iters);
        std::cout << "[" << PetscTools::GetMyRank() << "]: Num iterations = " << num_iters << "\n" << std::flush;
    }

    MechanicsEventHandler::EndEvent(MechanicsEventHandler::SOLVE);

    // Copy solution into the std::vector
    ReplicatableVector solution_repl(solution);
    for (unsigned i=0; i<this->mNumDofs; i++)
    {
        this->mCurrentSolution[i] = solution_repl[i];
    }

    // Remove pressure dummy values (P=0 at internal nodes, which should have been
    // been the result of the solve above), by linear interpolating from vertices of
    // edges to the internal node
    this->RemovePressureDummyValuesThroughLinearInterpolation();

    PetscTools::Destroy(solution);
    KSPDestroy(PETSC_DESTROY_PARAM(solver));

    this->WriteCurrentSpatialSolution("flow_solution", "nodes");
    this->WriteCurrentPressureSolution();
}

template<unsigned DIM>
void StokesFlowSolver<DIM>::AssembleSystem()
{
    // Use assembler to assemble volume integral part....
    mpStokesFlowAssembler->SetMatrixToAssemble(this->mSystemLhsMatrix, true);
    mpStokesFlowAssembler->SetVectorToAssemble(this->mLinearSystemRhsVector, true);
    mpStokesFlowAssembler->Assemble();

    mpStokesFlowPreconditionerAssembler->SetMatrixToAssemble(this->mPreconditionMatrix, true);
    mpStokesFlowPreconditionerAssembler->AssembleMatrix();

    mpNeumannBcsAssembler->SetVectorToAssemble(this->mLinearSystemRhsVector, false /*don't zero!*/);
    mpNeumannBcsAssembler->AssembleVector();

    PetscVecTools::Finalise(this->mLinearSystemRhsVector);
    PetscMatTools::SwitchWriteMode(this->mSystemLhsMatrix);
    PetscMatTools::SwitchWriteMode(this->mPreconditionMatrix);

    // Note: maintaining symmetry for Dirichlet BCs is possible at the moment (the second parameter)
    // but doing so for the identity block is not yet implemented (the second parameter must be false)
    // Not sure if maintaining symmetry is worth it - may allow CG to work, but matrix is indefinite
    // so GC not guaranteed to work..
    //
    // Note: the identity block needs to be added before the BCs - see comments in
    // PetscMatTools::ZeroRowsWithValueOnDiagonal()
    this->AddIdentityBlockForDummyPressureVariables(LINEAR_PROBLEM);
    this->ApplyDirichletBoundaryConditions(LINEAR_PROBLEM, true);

    PetscVecTools::Finalise(this->mLinearSystemRhsVector);
    PetscMatTools::Finalise(this->mSystemLhsMatrix);
    PetscMatTools::Finalise(this->mPreconditionMatrix);
}

template<unsigned DIM>
void StokesFlowSolver<DIM>::SetKspAbsoluteTolerance(double kspAbsoluteTolerance)
{
    assert(kspAbsoluteTolerance > 0);
    mKspAbsoluteTol = kspAbsoluteTolerance;
}

template<unsigned DIM>
std::vector<c_vector<double,DIM> >& StokesFlowSolver<DIM>::rGetSpatialSolution()
{
    this->mSpatialSolution.resize(this->mrQuadMesh.GetNumNodes(), zero_vector<double>(DIM));
    for (unsigned i=0; i<this->mrQuadMesh.GetNumNodes(); i++)
    {
        for (unsigned j=0; j<DIM; j++)
        {
            // DIM+1 is the problem dimension
            this->mSpatialSolution[i](j) = this->mCurrentSolution[(DIM+1)*i+j];
        }
    }
    return this->mSpatialSolution;
}

template<unsigned DIM>
std::vector<c_vector<double,DIM> >& StokesFlowSolver<DIM>::rGetVelocities()
{
    return rGetSpatialSolution();
}

#endif /* STOKESFLOWSOLVER_HPP_ */