pure_convection_tools.h

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// KRATOS ___ ___  _  ___   __   ___ ___ ___ ___ 
//       / __/ _ \| \| \ \ / /__|   \_ _| __| __|
//      | (_| (_) | .` |\ V /___| |) | || _|| _| 
//       \___\___/|_|\_| \_/    |___/___|_| |_|  APPLICATION
//
//  License: BSD License
//                   Kratos default license: kratos/license.txt
//
//  Main authors:  Riccardo Rossi
//
 
#if !defined(KRATOS_PURE_CONVECTION_UTILITIES_INCLUDED )
#define  KRATOS_PURE_CONVECTION_UTILITIES_INCLUDED
 
 
 
// System includes
#include <string>
#include <iostream>
#include <algorithm>
 
// External includes
 
 
// Project includes
#include "includes/define.h"
#include "includes/model_part.h"
#include "includes/node.h"
#include "utilities/geometry_utilities.h"
#include "convection_diffusion_application.h"
 
namespace Kratos
{
 
template<int TDim,class TSparseSpace,class TLinearSolver>
class PureConvectionUtilities
{
public:
 
    typedef typename TSparseSpace::MatrixType TSystemMatrixType;
    typedef typename TSparseSpace::VectorType TSystemVectorType;
    typedef PointerVectorSet< Dof<double> , IndexedObject> DofsArrayType;
 
 
    PureConvectionUtilities() {};
    ~PureConvectionUtilities() {};
 
 
 
    //************************************************************************
    //************************************************************************
    void ConstructSystem(ModelPart& model_part, Variable<double>& rScalarVar, Variable< array_1d<double,3> >& rTransportVel, Variable< array_1d<double,3> >& rMeshVel)
    {
        KRATOS_TRY
 
        //loop over nodes with neighbours
        mDofSet.clear(); // = DofsArrayType();
        //mDofSet.resize(0);
        mDofSet.reserve(model_part.Nodes().size() );
 
        int tot_nnz=0;
        //int tot_row=0;
        for (auto it=model_part.NodesBegin(); it!=model_part.NodesEnd(); ++it)
        {
            if( (it->GetValue(NEIGHBOUR_NODES)).size() != 0 )
            {
                mDofSet.push_back( it->pGetDof(rScalarVar) );
                //tot_row += 1;
                tot_nnz +=  (it->GetValue(NEIGHBOUR_NODES)).size()+1;
            }
        }
 
        //fills the DofList and give a unique progressive tag to each node
 
        int free_id = 0;
        int fix_id = mDofSet.size();
 
        for (typename DofsArrayType::iterator dof_iterator = mDofSet.begin(); dof_iterator != mDofSet.end(); ++dof_iterator)
            if (dof_iterator->IsFixed())
                dof_iterator->SetEquationId(--fix_id);
            else
                dof_iterator->SetEquationId(free_id++);
 
        mEquationSystemSize = fix_id;
 
        std::vector< int > work_array;
        work_array.reserve(1000);
 
        //guessing the total size of the matrix
        mA.resize(mEquationSystemSize, mEquationSystemSize, tot_nnz);
 
        //getting the dof position
        //unsigned int dof_position = (model_part.NodesBegin())->GetDofPosition(rScalarVar);
 
        //building up the matrix graph row by row
        //int total_size = 0;
        for (auto it=model_part.NodesBegin(); it!=model_part.NodesEnd(); ++it)
        {
            unsigned int index_i = it->GetDof(rScalarVar).EquationId();
 
            if(index_i < mEquationSystemSize && (it->GetValue(NEIGHBOUR_NODES)).size() != 0)
            {
                GlobalPointersVector< Node >& neighb_nodes = it->GetValue(NEIGHBOUR_NODES);
 
                //filling the first neighbours list
                work_array.push_back(index_i);
                for( GlobalPointersVector< Node >::iterator i = neighb_nodes.begin(); i != neighb_nodes.end(); i++)
                {
                    unsigned int index_j = i->GetDof(rScalarVar).EquationId();
                    if(index_j < mEquationSystemSize)
                        work_array.push_back(index_j);
                }
 
                //sorting the indices and elminating the duplicates
                std::sort(work_array.begin(),work_array.end());
                typename std::vector<int>::iterator new_end = std::unique(work_array.begin(),work_array.end());
                unsigned int number_of_entries = new_end - work_array.begin();
 
                //filling up the matrix
                for(unsigned int j=0; j<number_of_entries; j++)
                {
                    mA.push_back(index_i,work_array[j] , 0.00);
                }
 
                //clearing the array for the next step
                work_array.erase(work_array.begin(),work_array.end());
                //total_size += number_of_entries;
            }
 
 
 
 
        }
 
        mDx.resize(mA.size1(),false);
        mb.resize(mA.size1(),false);
        KRATOS_CATCH("")
    }
 
    //************************************************************************
    //************************************************************************
    void ConvectScalarVar(ModelPart& model_part,
                          typename TLinearSolver::Pointer linear_solver,
                          Variable<double>& rScalarVar,
                          const Variable< array_1d<double,3> >& rTransportVel,
                          const Variable< array_1d<double,3> >& rMeshVel,
                          const Variable< double >& rProjVar,
                          unsigned int time_order )
    {
        KRATOS_TRY
 
        TSparseSpace::SetToZero(mA);
        TSparseSpace::SetToZero(mb);
        TSparseSpace::SetToZero(mDx);
 
        ProcessInfo& CurrentProcessInfo = model_part.GetProcessInfo();
        double dt = CurrentProcessInfo[DELTA_TIME];
 
        Vector BDFcoeffs(time_order+1);
 
        if(time_order == 2)
        {
            if(model_part.GetBufferSize() < 3)
                KRATOS_THROW_ERROR(std::logic_error,"insufficient buffer size for BDF2","")
 
                BDFcoeffs[0] =  1.5 / dt;   //coefficient for step n+1
            BDFcoeffs[1] =  -2.0 / dt;//coefficient for step n
            BDFcoeffs[2] =  0.5 / dt;//coefficient for step n-1
            KRATOS_WATCH("CONVECTION: BDF_2.......................................................................................");
        }
        else
        {
            BDFcoeffs[0] =  1.0 / dt;   //coefficient for step n+1
            BDFcoeffs[1] =  -1.0 / dt;//coefficient for step n
            KRATOS_WATCH("CONVECTION: BDF_1.......................................................................................");
        }
 
        //**********************************
        //BUILD PHASE
        //**********************************
        BoundedMatrix<double,TDim+1,TDim> DN_DX;
        BoundedMatrix<double,TDim+1,TDim+1> lhs_contribution;
        array_1d<double,TDim+1> N;
        array_1d<unsigned int ,TDim+1> local_indices;
        array_1d<double,TDim+1> rhs_contribution;
        array_1d<double,TDim+1> dp_vector;
        array_1d<double,TDim+1> MassFactors;
        array_1d<double,TDim> vel_gauss;
        array_1d<double,TDim> proj;
        array_1d<double,TDim+1> u_DN;
        array_1d<double,TDim+1> temp_vec_np;
 
 
 
        for(unsigned int i=0; i<TDim+1; i++)
            MassFactors[i] = 1.0/double(TDim+1);
 
        //getting the dof position
//      unsigned int dof_position = (model_part.NodesBegin())->GetDofPosition(rScalarVar);
 
        double lumping_factor = 1.0/double(TDim+1.0);
        const unsigned int number_of_points = TDim+1;
 
        array_1d<double,3> vg;
        for(ModelPart::ElementsContainerType::iterator i = model_part.ElementsBegin();
                i!=model_part.ElementsEnd(); i++)
        {
            Geometry< Node >& geom = i->GetGeometry();
 
            //calculating elemental values
            double Volume;
            GeometryUtils::CalculateGeometryData(geom, DN_DX, N, Volume);
 
 
            //finiding local indices
            for(int ii = 0; ii<TDim+1; ii++)
            {
                local_indices[ii] = geom[ii].GetDof(rScalarVar).EquationId();
 
                /*              dp_vector[ii] = geom[ii].FastGetSolutionStepValue(rScalarVar)
                                        - geom[ii].FastGetSolutionStepValue(rScalarVar,1);*/
            }
 
            //calculating convective velocity
            noalias(vel_gauss) = ZeroVector(TDim);
            double proj = 0.0;
            for(unsigned int i = 0; i<number_of_points; i++)
            {
                const array_1d<double,3>& v = geom[i].FastGetSolutionStepValue(rTransportVel);
                const array_1d<double,3>& w = geom[i].FastGetSolutionStepValue(rMeshVel);
                proj += geom[i].FastGetSolutionStepValue(rProjVar);
                for(unsigned int j = 0; j<TDim; j++)
                {
                    vel_gauss[j] += v[j] - w[j];
                }
            }
            vel_gauss *= lumping_factor;
            proj *= lumping_factor;
 
 
            //CONVECTIVE CONTRIBUTION TO THE STIFFNESS MATRIX
            noalias(u_DN) = prod(DN_DX , vel_gauss);
            noalias(lhs_contribution) = outer_prod(N,u_DN);
 
            //CONVECTION STABILIZING CONTRIBUTION (Suu)
            double tau = CalculateTAU(vel_gauss,Volume);
            noalias(lhs_contribution) += (tau) * outer_prod(u_DN,u_DN);
 
            //INERTIA CONTRIBUTION
            for(unsigned int iii = 0; iii<number_of_points; iii++)
                lhs_contribution(iii,iii) += BDFcoeffs[0] * MassFactors[iii];
 
            //adding projection contribution
            //RHS += Suy * proj[component]
            noalias(rhs_contribution) = (tau*proj)*u_DN;
 
 
            //adding the inertia terms
            // RHS += M*vhistory
            //calculating the historical velocity
            for(unsigned int iii = 0; iii<number_of_points; iii++)
            {
                temp_vec_np[iii] =  BDFcoeffs[1]*geom[iii].FastGetSolutionStepValue(rScalarVar,1);
            }
            for(unsigned int step = 2; step<BDFcoeffs.size(); step++)
            {
                for(unsigned int iii = 0; iii<number_of_points; iii++)
                    temp_vec_np[iii] += BDFcoeffs[step]*geom[iii].FastGetSolutionStepValue(rScalarVar,step);
            }
            for(unsigned int iii = 0; iii<number_of_points; iii++)
                rhs_contribution[iii] -= MassFactors[iii]*temp_vec_np[iii];
//              rhs_contribution[iii] = - MassFactors[iii]*temp_vec_np[iii];
 
 
            //subtracting the dirichlet term
            // RHS -= LHS*rScalarVars
            for(unsigned int iii = 0; iii<number_of_points; iii++)
                temp_vec_np[iii] = geom[iii].FastGetSolutionStepValue(rScalarVar);
            noalias(rhs_contribution) -= prod(lhs_contribution,temp_vec_np);
 
            //multiplying by Volume, rho and density
            rhs_contribution *= Volume;
            lhs_contribution *= Volume;
 
            AssembleLHS(mA,lhs_contribution,local_indices);
            AssembleRHS(mb,rhs_contribution,local_indices);
 
 
 
        }
 
        //**********************************
        //SOLVE PHASE
        //**********************************
        //             KRATOS_WATCH(mA);
        //               KRATOS_WATCH(mb);
        //             KRATOS_WATCH(mDx);
//      std::cout << "convection residual norm" << TSparseSpace::TwoNorm(mb) << std::endl;
 
        linear_solver->Solve(mA,mDx,mb);
        std::cout << *(linear_solver) << std::endl;
        //           KRATOS_WATCH(mDx);
 
        //**********************************
        //UPDATE rScalarVarS
        //**********************************
        for(typename DofsArrayType::iterator i_dof = mDofSet.begin() ; i_dof != mDofSet.end() ; ++i_dof)
        {
            if(i_dof->IsFree())
            {
                i_dof->GetSolutionStepValue() += mDx[i_dof->EquationId()];
            }
        }
 
        KRATOS_CATCH("")
    }
 
 
 
 
 
    //************************************************************************
    //************************************************************************
    void CalculateProjection(ModelPart& model_part,
                             const Variable<double>& rScalarVar,
                             const Variable<double>& rNodalArea,
                             const Variable< array_1d<double,3> >& rTransportVel,
                             const Variable< array_1d<double,3> >& rMeshVel,
                             Variable< double >& rProjVar )
    {
        KRATOS_TRY
 
 
        //**********************************
        //BUILD PHASE
        //**********************************
        BoundedMatrix<double,TDim+1,TDim> DN_DX;
        array_1d<double,TDim+1> N;
        array_1d<double,TDim> vel_gauss;
        array_1d<double,TDim+1> temp_vec_np;
        array_1d<double,TDim+1> u_DN;
 
        double lumping_factor = 1.0/double(TDim+1.0);
        const unsigned int number_of_points = TDim+1;
 
        //set to zero nodal areas
        for(ModelPart::NodesContainerType::iterator i = model_part.NodesBegin();
                i!=model_part.NodesEnd(); i++)
        {
            i->FastGetSolutionStepValue(rNodalArea) = 0.0;
            i->FastGetSolutionStepValue(rProjVar) = 0.0;
        }
 
        //build up nodal areas and projections
        array_1d<double,3> vg;
        for(ModelPart::ElementsContainerType::iterator i = model_part.ElementsBegin();
                i!=model_part.ElementsEnd(); i++)
        {
 
            Geometry< Node >& geom = i->GetGeometry();
 
            //calculating elemental values
            double Volume;
            GeometryUtils::CalculateGeometryData(geom, DN_DX, N, Volume);
 
            //calculating convective velocity
            double nodal_area = Volume*lumping_factor;
            noalias(vel_gauss) = ZeroVector(TDim);
            for(unsigned int i = 0; i<number_of_points; i++)
            {
                const array_1d<double,3>& v = geom[i].FastGetSolutionStepValue(rTransportVel);
                const array_1d<double,3>& w = geom[i].FastGetSolutionStepValue(rMeshVel);
 
                //adding up nodal area as needed
                geom[i].FastGetSolutionStepValue(rNodalArea) += nodal_area;
 
                for(unsigned int j = 0; j<TDim; j++)
                {
                    vel_gauss[j] += v[j] - w[j];
                }
            }
            vel_gauss *= lumping_factor;
 
            //filling up a vector with all of the nodal values
            for(unsigned int iii = 0; iii<number_of_points; iii++)
                temp_vec_np[iii] = geom[iii].FastGetSolutionStepValue(rScalarVar);
 
            //
            noalias(u_DN) = prod(DN_DX , vel_gauss);
            double conv_proj = inner_prod( u_DN , temp_vec_np);
            conv_proj *= Volume * lumping_factor;
 
            for(unsigned int iii = 0; iii<number_of_points; iii++)
                geom[iii].FastGetSolutionStepValue(rProjVar) += conv_proj;
        }
 
        //dividing by the overall mass matrix
        for(ModelPart::NodesContainerType::iterator i = model_part.NodesBegin();
                i!=model_part.NodesEnd(); i++)
        {
            i->FastGetSolutionStepValue(rProjVar) /= i->FastGetSolutionStepValue(rNodalArea);
        }
 
        KRATOS_CATCH("")
    }
 
    void ClearSystem()
    {
        KRATOS_TRY
        mDofSet.clear(); // = DofsArrayType();
        //      mDofSet.resize(0);
        mDx.resize(0,false);
        mb.resize(0,false);
        mA.resize(0,0,false);
 
        KRATOS_CATCH("")
    }
 
 
 
 
private:
 
    unsigned int mEquationSystemSize;
    TSystemVectorType mDx;
    TSystemVectorType mb;
    TSystemMatrixType mA;
    DofsArrayType mDofSet;
 
 
 
 
 
    //**************************************************************************
    void AssembleLHS(
        TSystemMatrixType& A,
        const BoundedMatrix<double,TDim+1,TDim+1>& LHS_Contribution,
        const array_1d<unsigned int,TDim+1>& EquationId
    )
    {
        unsigned int local_size = LHS_Contribution.size1();
 
        for (unsigned int i_local=0; i_local<local_size; i_local++)
        {
            unsigned int i_global=EquationId[i_local];
            if ( i_global < mEquationSystemSize )
            {
                for (unsigned int j_local=0; j_local<local_size; j_local++)
                {
                    unsigned int j_global=EquationId[j_local];
                    if ( j_global < mEquationSystemSize )
                        A(i_global,j_global) += LHS_Contribution(i_local,j_local);
                }
            }
        }
    }
 
 
 
    //**************************************************************************
    void AssembleRHS(
        TSystemVectorType& b,
        const array_1d<double,TDim+1>& RHS_Contribution,
        const array_1d<unsigned int,TDim+1>& EquationId
    )
    {
        unsigned int local_size = RHS_Contribution.size();
 
        for (unsigned int i_local=0; i_local<local_size; i_local++)
        {
            unsigned int i_global=EquationId[i_local];
            if ( i_global < mEquationSystemSize ) //on "free" DOFs
            {
                // ASSEMBLING THE SYSTEM VECTOR
                b[i_global] += RHS_Contribution[i_local];
            }
        }
 
    }
 
    double CalculateTAU(const array_1d<double,2>& vel, const double& Volume)
    {
        //calculating parameter tau
//          double c1 = 4.00;
        double c2 = 2.00;
        double h = sqrt(2.00*Volume);
        double norm_u =norm_2(vel);
        if(norm_u > 1e-15)
            return h / (  c2*norm_u );
        return 0.0;
    }
 
    double CalculateTAU(const array_1d<double,3>& vel, const double& Volume)
    {
        //calculating parameter tau
//          double c1 = 4.00;
        double c2 = 2.00;
        double h =  pow(6.00*Volume,0.3333333);
        double norm_u =norm_2(vel);
        if(norm_u > 1e-15)
            return h / ( c2*norm_u );
        return 0.0;
    }
 
};
 
}  // namespace Kratos.
 
#endif // KRATOS_PURE_CONVECTION_UTILITIES_INCLUDED  defined