/*
  Copyright 2013, 2015 SINTEF ICT, Applied Mathematics.
  Copyright 2014, 2015 Dr. Blatt - HPC-Simulation-Software & Services
  Copyright 2014, 2015 Statoil ASA.
  Copyright 2015 NTNU
  Copyright 2015, 2016, 2017 IRIS AS

  This file is part of the Open Porous Media project (OPM).

  OPM is free software: you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
  the Free Software Foundation, either version 3 of the License, or
  (at your option) any later version.

  OPM 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 General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with OPM.  If not, see <http://www.gnu.org/licenses/>.
*/

#ifndef OPM_BLACKOILMODELEBOS_HEADER_INCLUDED
#define OPM_BLACKOILMODELEBOS_HEADER_INCLUDED

#include <ebos/eclproblem.hh>
#include <ewoms/common/start.hh>

#include <opm/autodiff/BlackoilModelParameters.hpp>
#include <opm/autodiff/BlackoilWellModel.hpp>
#include <opm/autodiff/BlackoilAquiferModel.hpp>
#include <opm/autodiff/GridHelpers.hpp>
#include <opm/autodiff/GeoProps.hpp>
#include <opm/autodiff/WellConnectionAuxiliaryModule.hpp>
#include <opm/autodiff/BlackoilDetails.hpp>
#include <opm/autodiff/NewtonIterationBlackoilInterface.hpp>

#include <opm/grid/UnstructuredGrid.h>
#include <opm/core/simulator/SimulatorReport.hpp>
#include <opm/core/linalg/LinearSolverInterface.hpp>
#include <opm/core/linalg/ParallelIstlInformation.hpp>
#include <opm/core/props/phaseUsageFromDeck.hpp>
#include <opm/common/ErrorMacros.hpp>
#include <opm/common/Exceptions.hpp>
#include <opm/common/OpmLog/OpmLog.hpp>
#include <opm/parser/eclipse/Units/Units.hpp>
#include <opm/simulators/timestepping/SimulatorTimer.hpp>
#include <opm/common/utility/parameters/ParameterGroup.hpp>
#include <opm/parser/eclipse/EclipseState/EclipseState.hpp>
#include <opm/parser/eclipse/EclipseState/Tables/TableManager.hpp>

#include <opm/autodiff/ISTLSolver.hpp>
#include <opm/common/data/SimulationDataContainer.hpp>

#include <dune/istl/owneroverlapcopy.hh>
#include <dune/common/parallel/collectivecommunication.hh>
#include <dune/common/timer.hh>
#include <dune/common/unused.hh>

#include <cassert>
#include <cmath>
#include <iostream>
#include <iomanip>
#include <limits>
#include <vector>
#include <algorithm>
//#include <fstream>



namespace Ewoms {
namespace Properties {
NEW_TYPE_TAG(EclFlowProblem, INHERITS_FROM(BlackOilModel, EclBaseProblem));
SET_STRING_PROP(EclFlowProblem, EclOutputDir, "");
SET_BOOL_PROP(EclFlowProblem, DisableWells, true);
SET_BOOL_PROP(EclFlowProblem, EnableDebuggingChecks, false);
SET_BOOL_PROP(EclFlowProblem, ExportGlobalTransmissibility, true);
// default in flow is to formulate the equations in surface volumes
SET_BOOL_PROP(EclFlowProblem, BlackoilConserveSurfaceVolume, true);
SET_BOOL_PROP(EclFlowProblem, UseVolumetricResidual, false);

// disable all extensions supported by black oil model. this should not really be
// necessary but it makes things a bit more explicit
SET_BOOL_PROP(EclFlowProblem, EnablePolymer, false);
SET_BOOL_PROP(EclFlowProblem, EnableSolvent, false);
SET_BOOL_PROP(EclFlowProblem, EnableTemperature, true);
SET_BOOL_PROP(EclFlowProblem, EnableEnergy, false);
}}

namespace Opm {
    /// A model implementation for three-phase black oil.
    ///
    /// The simulator is capable of handling three-phase problems
    /// where gas can be dissolved in oil and vice versa. It
    /// uses an industry-standard TPFA discretization with per-phase
    /// upwind weighting of mobilities.
    template <class TypeTag>
    class BlackoilModelEbos
    {
    public:
        // ---------  Types and enums  ---------
        typedef BlackoilState ReservoirState;
        typedef WellStateFullyImplicitBlackoil WellState;
        typedef BlackoilModelParameters ModelParameters;

        typedef typename GET_PROP_TYPE(TypeTag, Simulator)         Simulator;
        typedef typename GET_PROP_TYPE(TypeTag, Grid)              Grid;
        typedef typename GET_PROP_TYPE(TypeTag, ElementContext)    ElementContext;
        typedef typename GET_PROP_TYPE(TypeTag, SolutionVector)    SolutionVector ;
        typedef typename GET_PROP_TYPE(TypeTag, PrimaryVariables)  PrimaryVariables ;
        typedef typename GET_PROP_TYPE(TypeTag, FluidSystem)       FluidSystem;
        typedef typename GET_PROP_TYPE(TypeTag, Indices)           Indices;
        typedef typename GET_PROP_TYPE(TypeTag, MaterialLaw)       MaterialLaw;
        typedef typename GET_PROP_TYPE(TypeTag, MaterialLawParams) MaterialLawParams;

        typedef double Scalar;
        static const int numEq = Indices::numEq;
        static const int contiSolventEqIdx = Indices::contiSolventEqIdx;
        static const int contiPolymerEqIdx = Indices::contiPolymerEqIdx;
        static const int contiEnergyEqIdx = Indices::contiEnergyEqIdx;
        static const int solventSaturationIdx = Indices::solventSaturationIdx;
        static const int polymerConcentrationIdx = Indices::polymerConcentrationIdx;
        static const int temperatureIdx = Indices::temperatureIdx;

        typedef Dune::FieldVector<Scalar, numEq >        VectorBlockType;
        typedef Dune::FieldMatrix<Scalar, numEq, numEq >        MatrixBlockType;
        typedef Dune::BCRSMatrix <MatrixBlockType>      Mat;
        typedef Dune::BlockVector<VectorBlockType>      BVector;

        typedef ISTLSolver< MatrixBlockType, VectorBlockType, Indices::pressureSwitchIdx >  ISTLSolverType;
        //typedef typename SolutionVector :: value_type            PrimaryVariables ;

        // ---------  Public methods  ---------

        /// Construct the model. It will retain references to the
        /// arguments of this functions, and they are expected to
        /// remain in scope for the lifetime of the solver.
        /// \param[in] param            parameters
        /// \param[in] grid             grid data structure
        /// \param[in] wells            well structure
        /// \param[in] vfp_properties   Vertical flow performance tables
        /// \param[in] linsolver        linear solver
        /// \param[in] eclState         eclipse state
        /// \param[in] terminal_output  request output to cout/cerr
        BlackoilModelEbos(Simulator& ebosSimulator,
                          const ModelParameters& param,
                          BlackoilWellModel<TypeTag>& well_model,
                          BlackoilAquiferModel<TypeTag>& aquifer_model,
                          const NewtonIterationBlackoilInterface& linsolver,
                          const bool terminal_output
                          )
        : ebosSimulator_(ebosSimulator)
        , grid_(ebosSimulator_.vanguard().grid())
        , istlSolver_( dynamic_cast< const ISTLSolverType* > (&linsolver) )
        , phaseUsage_(phaseUsageFromDeck(eclState()))
        , has_disgas_(FluidSystem::enableDissolvedGas())
        , has_vapoil_(FluidSystem::enableVaporizedOil())
        , has_solvent_(GET_PROP_VALUE(TypeTag, EnableSolvent))
        , has_polymer_(GET_PROP_VALUE(TypeTag, EnablePolymer))
        , has_energy_(GET_PROP_VALUE(TypeTag, EnableEnergy))
        , param_( param )
        , well_model_ (well_model)
        , aquifer_model_(aquifer_model)
        , terminal_output_ (terminal_output)
        , current_relaxation_(1.0)
        , dx_old_(UgGridHelpers::numCells(grid_))
        {
            // compute global sum of number of cells
            global_nc_ = detail::countGlobalCells(grid_);
            if (!istlSolver_)
            {
                OPM_THROW(std::logic_error,"solver down cast to ISTLSolver failed");
            }
        }

        bool isParallel() const
        { return  grid_.comm().size() > 1; }

        const EclipseState& eclState() const
        { return ebosSimulator_.vanguard().eclState(); }

        /// Called once before each time step.
        /// \param[in] timer                  simulation timer
        /// \param[in, out] reservoir_state   reservoir state variables
        /// \param[in, out] well_state        well state variables
        void prepareStep(const SimulatorTimerInterface& timer,
                         const ReservoirState& /*reservoir_state*/,
                         const WellState& /* well_state */)
        {

            // update the solution variables in ebos
            if ( timer.lastStepFailed() ) {
                ebosSimulator_.model().updateFailed();
            } else {
                ebosSimulator_.model().advanceTimeLevel();
            }

            // set the timestep size and index in ebos explicitly
            // we use our own time stepper.
            ebosSimulator_.startNextEpisode( timer.currentStepLength() );
            ebosSimulator_.setEpisodeIndex( timer.reportStepNum() );
            ebosSimulator_.setTimeStepSize( timer.currentStepLength() );
            ebosSimulator_.setTimeStepIndex( timer.reportStepNum() );

            ebosSimulator_.problem().beginTimeStep();

            unsigned numDof = ebosSimulator_.model().numGridDof();
            wasSwitched_.resize(numDof);
            std::fill(wasSwitched_.begin(), wasSwitched_.end(), false);

            wellModel().beginTimeStep();

            if (param_.update_equations_scaling_) {
                std::cout << "equation scaling not suported yet" << std::endl;
                //updateEquationsScaling();
            }
        }


        /// Called once per nonlinear iteration.
        /// This model will perform a Newton-Raphson update, changing reservoir_state
        /// and well_state. It will also use the nonlinear_solver to do relaxation of
        /// updates if necessary.
        /// \param[in] iteration              should be 0 for the first call of a new timestep
        /// \param[in] timer                  simulation timer
        /// \param[in] nonlinear_solver       nonlinear solver used (for oscillation/relaxation control)
        /// \param[in, out] reservoir_state   reservoir state variables
        /// \param[in, out] well_state        well state variables
        template <class NonlinearSolverType>
        SimulatorReport nonlinearIteration(const int iteration,
                                           const SimulatorTimerInterface& timer,
                                           NonlinearSolverType& nonlinear_solver,
                                           ReservoirState& /*reservoir_state*/,
                                           WellState& /*well_state*/)
        {
            SimulatorReport report;
            failureReport_ = SimulatorReport();
            Dune::Timer perfTimer;

            perfTimer.start();
            if (iteration == 0) {
                // For each iteration we store in a vector the norms of the residual of
                // the mass balance for each active phase, the well flux and the well equations.
                residual_norms_history_.clear();
                current_relaxation_ = 1.0;
                dx_old_ = 0.0;
            }

            report.total_linearizations = 1;

            try {
                report += assemble(timer, iteration);
                report.assemble_time += perfTimer.stop();
            }
            catch (...) {
                report.assemble_time += perfTimer.stop();
                failureReport_ += report;
                // todo (?): make the report an attribute of the class
                throw; // continue throwing the stick
            }

            std::vector<double> residual_norms;
            perfTimer.reset();
            perfTimer.start();
            // the step is not considered converged until at least minIter iterations is done
            report.converged = getConvergence(timer, iteration,residual_norms) && iteration > nonlinear_solver.minIter();

             // checking whether the group targets are converged
             if (wellModel().wellCollection().groupControlActive()) {
                  report.converged = report.converged && wellModel().wellCollection().groupTargetConverged(wellModel().wellState().wellRates());
             }

            report.update_time += perfTimer.stop();
            residual_norms_history_.push_back(residual_norms);
            if (!report.converged) {
                perfTimer.reset();
                perfTimer.start();
                report.total_newton_iterations = 1;

                // enable single precision for solvers when dt is smaller then 20 days
                //residual_.singlePrecision = (unit::convert::to(dt, unit::day) < 20.) ;

                // Compute the nonlinear update.
                const int nc = UgGridHelpers::numCells(grid_);
                BVector x(nc);

                try {
                    solveJacobianSystem(x);
                    report.linear_solve_time += perfTimer.stop();
                    report.total_linear_iterations += linearIterationsLastSolve();
                }
                catch (...) {
                    report.linear_solve_time += perfTimer.stop();
                    report.total_linear_iterations += linearIterationsLastSolve();

                    failureReport_ += report;
                    throw; // re-throw up
                }

                perfTimer.reset();
                perfTimer.start();

                // handling well state update before oscillation treatment is a decision based
                // on observation to avoid some big performance degeneration under some circumstances.
                // there is no theorectical explanation which way is better for sure.
                wellModel().recoverWellSolutionAndUpdateWellState(x);

                if (param_.use_update_stabilization_) {
                    // Stabilize the nonlinear update.
                    bool isOscillate = false;
                    bool isStagnate = false;
                    nonlinear_solver.detectOscillations(residual_norms_history_, iteration, isOscillate, isStagnate);
                    if (isOscillate) {
                        current_relaxation_ -= nonlinear_solver.relaxIncrement();
                        current_relaxation_ = std::max(current_relaxation_, nonlinear_solver.relaxMax());
                        if (terminalOutputEnabled()) {
                            std::string msg = "    Oscillating behavior detected: Relaxation set to "
                                    + std::to_string(current_relaxation_);
                            OpmLog::info(msg);
                        }
                    }
                    nonlinear_solver.stabilizeNonlinearUpdate(x, dx_old_, current_relaxation_);
                }

                // Apply the update, with considering model-dependent limitations and
                // chopping of the update.
                updateState(x);

                report.update_time += perfTimer.stop();
            }

            return report;
        }

        void printIf(int c, double x, double y, double eps, std::string type) {
            if (std::abs(x-y) > eps) {
                std::cout << type << " " <<c << ": "<<x << " " << y << std::endl;
            }
        }


        /// Called once after each time step.
        /// In this class, this function does nothing.
        /// \param[in] timer                  simulation timer
        /// \param[in, out] reservoir_state   reservoir state variables
        /// \param[in, out] well_state        well state variables
        void afterStep(const SimulatorTimerInterface& timer,
                       const ReservoirState& reservoir_state,
                       WellState& well_state)
        {
            // DUNE_UNUSED_PARAMETER(timer);
            DUNE_UNUSED_PARAMETER(reservoir_state);
            DUNE_UNUSED_PARAMETER(well_state);

            wellModel().timeStepSucceeded();
            aquiferModel().timeStepSucceeded(timer);
            ebosSimulator_.problem().endTimeStep();

        }

        /// Assemble the residual and Jacobian of the nonlinear system.
        /// \param[in]      reservoir_state   reservoir state variables
        /// \param[in, out] well_state        well state variables
        /// \param[in]      initial_assembly  pass true if this is the first call to assemble() in this timestep
        SimulatorReport assemble(const SimulatorTimerInterface& timer,
                                 const int iterationIdx)
        {
            // -------- Mass balance equations --------
            ebosSimulator_.model().newtonMethod().setIterationIndex(iterationIdx);
            ebosSimulator_.problem().beginIteration();
            ebosSimulator_.model().linearizer().linearize();
            ebosSimulator_.problem().endIteration();

            // -------- Well and aquifer common variables ----------
            double dt = timer.currentStepLength();

            // -------- Aquifer models ----------
            try
            {
                // Modify the Jacobian and residuals according to the aquifer models
                aquiferModel().assemble(timer, iterationIdx);
            }
            catch( const Dune::FMatrixError& e )
            {
                OPM_THROW(Opm::NumericalProblem,"Error when assembling aquifer models");
            }

            // -------- Well equations ----------

            try
            {
                // assembles the well equations and applies the wells to
                // the reservoir equations as a source term.
                wellModel().assemble(iterationIdx, dt);
            }
            catch ( const Dune::FMatrixError& )
            {
                OPM_THROW(Opm::NumericalIssue,"Error encounted when solving well equations");
            }

            auto& ebosJac = ebosSimulator_.model().linearizer().matrix();
            if (param_.matrix_add_well_contributions_) {
                wellModel().addWellContributions(ebosJac);
            }
            if ( param_.preconditioner_add_well_contributions_ &&
                 ! param_.matrix_add_well_contributions_ ) {
                matrix_for_preconditioner_ .reset(new Mat(ebosJac));
                wellModel().addWellContributions(*matrix_for_preconditioner_);
            }

            return wellModel().lastReport();
        }

        // compute the "relative" change of the solution between time steps
        template <class Dummy>
        double relativeChange(const Dummy&, const Dummy&) const
        {
            Scalar resultDelta = 0.0;
            Scalar resultDenom = 0.0;

            const auto& elemMapper = ebosSimulator_.model().elementMapper();
            const auto& gridView = ebosSimulator_.gridView();
            auto elemIt = gridView.template begin</*codim=*/0>();
            const auto& elemEndIt = gridView.template end</*codim=*/0>();
            for (; elemIt != elemEndIt; ++elemIt) {
                const auto& elem = *elemIt;
                if (elem.partitionType() != Dune::InteriorEntity)
                    continue;

        unsigned globalElemIdx = elemMapper.index(elem);
                const auto& priVarsNew = ebosSimulator_.model().solution(/*timeIdx=*/0)[globalElemIdx];

                Scalar pressureNew;
        pressureNew = priVarsNew[Indices::pressureSwitchIdx];

        Scalar saturationsNew[FluidSystem::numPhases] = { 0.0 };
                Scalar oilSaturationNew = 1.0;
                if (FluidSystem::phaseIsActive(FluidSystem::waterPhaseIdx)) {
                    saturationsNew[FluidSystem::waterPhaseIdx] = priVarsNew[Indices::waterSaturationIdx];
                    oilSaturationNew -= saturationsNew[FluidSystem::waterPhaseIdx];
                }

                if (FluidSystem::phaseIsActive(FluidSystem::gasPhaseIdx) && priVarsNew.primaryVarsMeaning() == PrimaryVariables::Sw_po_Sg) {
                    saturationsNew[FluidSystem::gasPhaseIdx] = priVarsNew[Indices::compositionSwitchIdx];
                    oilSaturationNew -= saturationsNew[FluidSystem::gasPhaseIdx];
                }

                if (FluidSystem::phaseIsActive(FluidSystem::oilPhaseIdx)) {
                    saturationsNew[FluidSystem::oilPhaseIdx] = oilSaturationNew;
                }

                const auto& priVarsOld = ebosSimulator_.model().solution(/*timeIdx=*/1)[globalElemIdx];

                Scalar pressureOld;
                pressureOld = priVarsOld[Indices::pressureSwitchIdx];

                Scalar saturationsOld[FluidSystem::numPhases] = { 0.0 };
                Scalar oilSaturationOld = 1.0;
                if (FluidSystem::phaseIsActive(FluidSystem::waterPhaseIdx)) {
                    saturationsOld[FluidSystem::waterPhaseIdx] = priVarsOld[Indices::waterSaturationIdx];
                    oilSaturationOld -= saturationsOld[FluidSystem::waterPhaseIdx];
                }

                if (FluidSystem::phaseIsActive(FluidSystem::gasPhaseIdx) && priVarsOld.primaryVarsMeaning() == PrimaryVariables::Sw_po_Sg) {
                    saturationsOld[FluidSystem::gasPhaseIdx] = priVarsOld[Indices::compositionSwitchIdx];
                    oilSaturationOld -= saturationsOld[FluidSystem::gasPhaseIdx];
                }

                if (FluidSystem::phaseIsActive(FluidSystem::oilPhaseIdx)) {
                    saturationsOld[FluidSystem::oilPhaseIdx] = oilSaturationOld;
                }

                Scalar tmp = pressureNew - pressureOld;
                resultDelta += tmp*tmp;
                resultDenom += pressureNew*pressureNew;

                for (unsigned phaseIdx = 0; phaseIdx < FluidSystem::numPhases; ++ phaseIdx) {
                    Scalar tmp = saturationsNew[phaseIdx] - saturationsOld[phaseIdx];
            resultDelta += tmp*tmp;
                    resultDenom += saturationsNew[phaseIdx]*saturationsNew[phaseIdx];
                }
            }

            resultDelta = gridView.comm().sum(resultDelta);
            resultDenom = gridView.comm().sum(resultDenom);

        if (resultDenom > 0.0)
          return resultDelta/resultDenom;
        return 0.0;
        }


        /// Number of linear iterations used in last call to solveJacobianSystem().
        int linearIterationsLastSolve() const
        {
            return istlSolver().iterations();
        }

        /// Solve the Jacobian system Jx = r where J is the Jacobian and
        /// r is the residual.
        void solveJacobianSystem(BVector& x) const
        {
            const auto& ebosJac = ebosSimulator_.model().linearizer().matrix();
            auto& ebosResid = ebosSimulator_.model().linearizer().residual();

            // J = [A, B; C, D], where A is the reservoir equations, B and C the interaction of well
            // with the reservoir and D is the wells itself.
            // The full system is reduced to a number of cells X number of cells system via Schur complement
            // A -= B^T D^-1 C
            // Instead of modifying A, the Ax operator is modified. i.e Ax -= B^T D^-1 C x in the WellModelMatrixAdapter.
            // The residual is modified similarly.
            // r = [r, r_well], where r is the residual and r_well the well residual.
            // r -= B^T * D^-1 r_well

            // apply well residual to the residual.
            wellModel().apply(ebosResid);

            // set initial guess
            x = 0.0;

            const Mat& actual_mat_for_prec = matrix_for_preconditioner_ ? *matrix_for_preconditioner_.get() : ebosJac;
            // Solve system.
            if( isParallel() )
            {
                typedef WellModelMatrixAdapter< Mat, BVector, BVector, BlackoilWellModel<TypeTag>, true > Operator;
                Operator opA(ebosJac, actual_mat_for_prec, wellModel(),
                             istlSolver().parallelInformation() );
                assert( opA.comm() );
                istlSolver().solve( opA, x, ebosResid, *(opA.comm()) );
            }
            else
            {
                typedef WellModelMatrixAdapter< Mat, BVector, BVector, BlackoilWellModel<TypeTag>, false > Operator;
                Operator opA(ebosJac, actual_mat_for_prec, wellModel());
                istlSolver().solve( opA, x, ebosResid );
            }
        }

        //=====================================================================
        // Implementation for ISTL-matrix based operator
        //=====================================================================

        /*!
           \brief Adapter to turn a matrix into a linear operator.

           Adapts a matrix to the assembled linear operator interface
         */
        template<class M, class X, class Y, class WellModel, bool overlapping >
        class WellModelMatrixAdapter : public Dune::AssembledLinearOperator<M,X,Y>
        {
          typedef Dune::AssembledLinearOperator<M,X,Y> BaseType;

        public:
          typedef M matrix_type;
          typedef X domain_type;
          typedef Y range_type;
          typedef typename X::field_type field_type;

#if HAVE_MPI
          typedef Dune::OwnerOverlapCopyCommunication<int,int> communication_type;
#else
          typedef Dune::CollectiveCommunication< Grid > communication_type;
#endif

#if DUNE_VERSION_NEWER(DUNE_ISTL, 2, 6)
          Dune::SolverCategory::Category category() const override
          {
            return overlapping ?
                   Dune::SolverCategory::overlapping : Dune::SolverCategory::sequential;
          }
#else
          enum {
            //! \brief The solver category.
            category = overlapping ?
                Dune::SolverCategory::overlapping :
                Dune::SolverCategory::sequential
          };
#endif

          //! constructor: just store a reference to a matrix
          WellModelMatrixAdapter (const M& A,
                                  const M& A_for_precond,
                                  const WellModel& wellMod,
                                  const boost::any& parallelInformation = boost::any() )
              : A_( A ), A_for_precond_(A_for_precond), wellMod_( wellMod ), comm_()
          {
#if HAVE_MPI
            if( parallelInformation.type() == typeid(ParallelISTLInformation) )
            {
              const ParallelISTLInformation& info =
                  boost::any_cast<const ParallelISTLInformation&>( parallelInformation);
              comm_.reset( new communication_type( info.communicator() ) );
            }
#endif
          }

          virtual void apply( const X& x, Y& y ) const
          {
            A_.mv( x, y );
            // add well model modification to y
            wellMod_.apply(x, y );

#if HAVE_MPI
            if( comm_ )
              comm_->project( y );
#endif
          }

          // y += \alpha * A * x
          virtual void applyscaleadd (field_type alpha, const X& x, Y& y) const
          {
            A_.usmv(alpha,x,y);
            // add scaled well model modification to y
            wellMod_.applyScaleAdd( alpha, x, y );

#if HAVE_MPI
            if( comm_ )
              comm_->project( y );
#endif
          }

          virtual const matrix_type& getmat() const { return A_for_precond_; }

          communication_type* comm()
          {
              return comm_.operator->();
          }

        protected:
          const matrix_type& A_ ;
          const matrix_type& A_for_precond_ ;
          const WellModel& wellMod_;
          std::unique_ptr< communication_type > comm_;
        };

        /// Apply an update to the primary variables, chopped if appropriate.
        /// \param[in]      dx                updates to apply to primary variables
        /// \param[in, out] reservoir_state   reservoir state variables
        /// \param[in, out] well_state        well state variables
        void updateState(const BVector& dx)
        {
            const auto& ebosProblem = ebosSimulator_.problem();

            unsigned numSwitched = 0;
            ElementContext elemCtx( ebosSimulator_ );
            const auto& gridView = ebosSimulator_.gridView();
            const auto& elemEndIt = gridView.template end</*codim=*/0>();
            SolutionVector& solution = ebosSimulator_.model().solution( 0 /* timeIdx */ );

            for (auto elemIt = gridView.template begin</*codim=*/0>();
                 elemIt != elemEndIt;
                 ++elemIt)
            {
                const auto& elem = *elemIt;

                elemCtx.updatePrimaryStencil(elem);
                elemCtx.updatePrimaryIntensiveQuantities(/*timeIdx=*/0);
                const unsigned cell_idx = elemCtx.globalSpaceIndex(/*spaceIdx=*/0, /*timeIdx=*/0);

                PrimaryVariables& priVars = solution[ cell_idx ];

                const double& dp = dx[cell_idx][Indices::pressureSwitchIdx];
                double& p = priVars[Indices::pressureSwitchIdx];
                const double& dp_rel_max = dpMaxRel();
                const int sign_dp = dp > 0 ? 1: -1;
                p -= sign_dp * std::min(std::abs(dp), std::abs(p)*dp_rel_max);
                p = std::max(p, 0.0);

                // Saturation updates.
                const double dsw = FluidSystem::phaseIsActive(FluidSystem::waterPhaseIdx) ? dx[cell_idx][Indices::waterSaturationIdx] : 0.0;
                const double dxvar = FluidSystem::phaseIsActive(FluidSystem::gasPhaseIdx) ? dx[cell_idx][Indices::compositionSwitchIdx] : 0.0;

                double dso = 0.0;
                double dsg = 0.0;
                double drs = 0.0;
                double drv = 0.0;

                // determine the saturation delta values
                if (priVars.primaryVarsMeaning() == PrimaryVariables::Sw_po_Sg) {
                    dsg = dxvar;
                }
                else if (priVars.primaryVarsMeaning() == PrimaryVariables::Sw_po_Rs) {
                    drs = dxvar;
                }
                else {
                    assert(priVars.primaryVarsMeaning() == PrimaryVariables::Sw_pg_Rv);
                    drv = dxvar;
                    dsg = 0.0;
                }

                // solvent
                const double dss = has_solvent_ ? dx[cell_idx][Indices::solventSaturationIdx] : 0.0;

                // polymer
                const double dc = has_polymer_ ? dx[cell_idx][Indices::polymerConcentrationIdx] : 0.0;

                // oil
                dso = - (dsw + dsg + dss);

                // compute a scaling factor for the saturation update so that the maximum
                // allowed change of saturations between iterations is not exceeded
                double maxVal = 0.0;
                maxVal = std::max(std::abs(dsw),maxVal);
                maxVal = std::max(std::abs(dsg),maxVal);
                maxVal = std::max(std::abs(dso),maxVal);
                maxVal = std::max(std::abs(dss),maxVal);

                double satScaleFactor = 1.0;
                if (maxVal > dsMax()) {
                    satScaleFactor = dsMax()/maxVal;
                }

                if (FluidSystem::phaseIsActive(FluidSystem::waterPhaseIdx)) {
                    double& sw = priVars[Indices::waterSaturationIdx];
                    sw -= satScaleFactor * dsw;
                }

                if (FluidSystem::phaseIsActive(FluidSystem::gasPhaseIdx)) {
                     if (priVars.primaryVarsMeaning() == PrimaryVariables::Sw_po_Sg) {
                           double& sg = priVars[Indices::compositionSwitchIdx];
                           sg -= satScaleFactor * dsg;
                     }
                }

                if (has_solvent_) {
                    double& ss = priVars[Indices::solventSaturationIdx];
                    ss -= satScaleFactor * dss;
                    ss = std::min(std::max(ss, 0.0),1.0);
                }
                if (has_polymer_) {
                    double& c = priVars[Indices::polymerConcentrationIdx];
                    c -= satScaleFactor * dc;
                    c = std::max(c, 0.0);
                }

                if (has_energy_) {
                    double& T = priVars[Indices::temperatureIdx];
                    const double dT = dx[cell_idx][Indices::temperatureIdx];
                    T -= dT;
                }

                // Update rs and rv
                if (FluidSystem::phaseIsActive(FluidSystem::gasPhaseIdx) && FluidSystem::phaseIsActive(FluidSystem::oilPhaseIdx) ) {
                    unsigned pvtRegionIdx = ebosSimulator_.problem().pvtRegionIndex(cell_idx);
                    const double drmaxrel = drMaxRel();
                    if (has_disgas_) {
                        if (priVars.primaryVarsMeaning() == PrimaryVariables::Sw_po_Rs) {
                            Scalar RsSat =
                                FluidSystem::oilPvt().saturatedGasDissolutionFactor(pvtRegionIdx, 300.0, p);

                            double& rs = priVars[Indices::compositionSwitchIdx];
                            rs -= ((drs<0)?-1:1)*std::min(std::abs(drs), RsSat*drmaxrel);
                            rs = std::max(rs, 0.0);
                        }

                    }
                    if (has_vapoil_) {
                        if (priVars.primaryVarsMeaning() == PrimaryVariables::Sw_pg_Rv) {
                            Scalar RvSat =
                                FluidSystem::gasPvt().saturatedOilVaporizationFactor(pvtRegionIdx, 300.0, p);

                            double& rv = priVars[Indices::compositionSwitchIdx];
                            rv -= ((drv<0)?-1:1)*std::min(std::abs(drv), RvSat*drmaxrel);
                            rv = std::max(rv, 0.0);
                        }
                    }
                }

               // Add an epsilon to make it harder to switch back immediately after the primary variable was changed.
                if (wasSwitched_[cell_idx])
                    wasSwitched_[cell_idx] = priVars.adaptPrimaryVariables(ebosProblem, cell_idx, 1e-5);
                else
                    wasSwitched_[cell_idx] = priVars.adaptPrimaryVariables(ebosProblem, cell_idx);

                if (wasSwitched_[cell_idx])
                    ++numSwitched;
            }

            // if the solution is updated the intensive Quantities need to be recalculated
            ebosSimulator_.model().invalidateIntensiveQuantitiesCache(/*timeIdx=*/0);

        }

        /// Return true if output to cout is wanted.
        bool terminalOutputEnabled() const
        {
            return terminal_output_;
        }

        template <class CollectiveCommunication>
        double convergenceReduction(const CollectiveCommunication& comm,
                                    const double pvSumLocal,
                                    std::vector< Scalar >& R_sum,
                                    std::vector< Scalar >& maxCoeff,
                                    std::vector< Scalar >& B_avg)
        {
            // Compute total pore volume (use only owned entries)
            double pvSum = pvSumLocal;

            if( comm.size() > 1 )
            {
                // global reduction
                std::vector< Scalar > sumBuffer;
                std::vector< Scalar > maxBuffer;
                const int numComp = B_avg.size();
                sumBuffer.reserve( 2*numComp + 1 ); // +1 for pvSum
                maxBuffer.reserve( numComp );
                for( int compIdx = 0; compIdx < numComp; ++compIdx )
                {
                    sumBuffer.push_back( B_avg[ compIdx ] );
                    sumBuffer.push_back( R_sum[ compIdx ] );
                    maxBuffer.push_back( maxCoeff[ compIdx ] );
                }

                // Compute total pore volume
                sumBuffer.push_back( pvSum );

                // compute global sum
                comm.sum( sumBuffer.data(), sumBuffer.size() );

                // compute global max
                comm.max( maxBuffer.data(), maxBuffer.size() );

                // restore values to local variables
                for( int compIdx = 0, buffIdx = 0; compIdx < numComp; ++compIdx, ++buffIdx )
                {
                    B_avg[ compIdx ]    = sumBuffer[ buffIdx ];
                    ++buffIdx;

                    R_sum[ compIdx ]       = sumBuffer[ buffIdx ];
                }

                for( int compIdx = 0; compIdx < numComp; ++compIdx )
                {
                    maxCoeff[ compIdx ] = maxBuffer[ compIdx ];
                }

                // restore global pore volume
                pvSum = sumBuffer.back();
            }

            // return global pore volume
            return pvSum;
        }

        /// Compute convergence based on total mass balance (tol_mb) and maximum
        /// residual mass balance (tol_cnv).
        /// \param[in]   timer       simulation timer
        /// \param[in]   dt          timestep length
        /// \param[in]   iteration   current iteration number
        bool getConvergence(const SimulatorTimerInterface& timer, const int iteration, std::vector<double>& residual_norms)
        {
            typedef std::vector< Scalar > Vector;

            const double dt = timer.currentStepLength();
            const double tol_mb    = param_.tolerance_mb_;
            const double tol_cnv   = param_.tolerance_cnv_;
            const double tol_cnv_relaxed = param_.tolerance_cnv_relaxed_;

            const int numComp = numEq;

            Vector R_sum(numComp, 0.0 );
            Vector B_avg(numComp, 0.0 );
            Vector maxCoeff(numComp, std::numeric_limits< Scalar >::lowest() );

            const auto& ebosModel = ebosSimulator_.model();
            const auto& ebosProblem = ebosSimulator_.problem();

            const auto& ebosResid = ebosSimulator_.model().linearizer().residual();

            ElementContext elemCtx(ebosSimulator_);
            const auto& gridView = ebosSimulator().gridView();
            const auto& elemEndIt = gridView.template end</*codim=*/0, Dune::Interior_Partition>();

            double pvSumLocal = 0.0;
            for (auto elemIt = gridView.template begin</*codim=*/0, Dune::Interior_Partition>();
                 elemIt != elemEndIt;
                 ++elemIt)
            {
                const auto& elem = *elemIt;
                elemCtx.updatePrimaryStencil(elem);
                elemCtx.updatePrimaryIntensiveQuantities(/*timeIdx=*/0);
                const unsigned cell_idx = elemCtx.globalSpaceIndex(/*spaceIdx=*/0, /*timeIdx=*/0);
                const auto& intQuants = elemCtx.intensiveQuantities(/*spaceIdx=*/0, /*timeIdx=*/0);
                const auto& fs = intQuants.fluidState();

                const double pvValue = ebosProblem.porosity(cell_idx) * ebosModel.dofTotalVolume( cell_idx );
                pvSumLocal += pvValue;

                for (unsigned phaseIdx = 0; phaseIdx < FluidSystem::numPhases; ++phaseIdx)
                {
                    if (!FluidSystem::phaseIsActive(phaseIdx)) {
                        continue;
                    }

                    const unsigned compIdx = Indices::canonicalToActiveComponentIndex(FluidSystem::solventComponentIndex(phaseIdx));

                    B_avg[ compIdx ] += 1.0 / fs.invB(phaseIdx).value();
                    const auto R2 = ebosResid[cell_idx][compIdx];

                    R_sum[ compIdx ] += R2;
                    maxCoeff[ compIdx ] = std::max( maxCoeff[ compIdx ], std::abs( R2 ) / pvValue );
                }

                if ( has_solvent_ ) {
                    B_avg[ contiSolventEqIdx ] += 1.0 / intQuants.solventInverseFormationVolumeFactor().value();
                    const auto R2 = ebosResid[cell_idx][contiSolventEqIdx];
                    R_sum[ contiSolventEqIdx ] += R2;
                    maxCoeff[ contiSolventEqIdx ] = std::max( maxCoeff[ contiSolventEqIdx ], std::abs( R2 ) / pvValue );
                }
                if (has_polymer_ ) {
                    B_avg[ contiPolymerEqIdx ] += 1.0 / fs.invB(FluidSystem::waterPhaseIdx).value();
                    const auto R2 = ebosResid[cell_idx][contiPolymerEqIdx];
                    R_sum[ contiPolymerEqIdx ] += R2;
                    maxCoeff[ contiPolymerEqIdx ] = std::max( maxCoeff[ contiPolymerEqIdx ], std::abs( R2 ) / pvValue );
                }
                if (has_energy_ ) {
                    B_avg[ contiEnergyEqIdx ] += 1.0;
                    const auto R2 = ebosResid[cell_idx][contiEnergyEqIdx];
                    R_sum[ contiEnergyEqIdx ] += R2;
                    maxCoeff[ contiEnergyEqIdx ] = std::max( maxCoeff[ contiEnergyEqIdx ], std::abs( R2 ) / pvValue );
                }

            }

            // compute local average in terms of global number of elements
            const int bSize = B_avg.size();
            for ( int i = 0; i<bSize; ++i )
            {
                B_avg[ i ] /= Scalar( global_nc_ );
            }

            // TODO: we remove the maxNormWell for now because the convergence of wells are on a individual well basis.
            // Anyway, we need to provide some infromation to help debug the well iteration process.


            // compute global sum and max of quantities
            const double pvSum = convergenceReduction(grid_.comm(), pvSumLocal,
                                                      R_sum, maxCoeff, B_avg);

            Vector CNV(numComp);
            Vector mass_balance_residual(numComp);

            bool converged_MB = true;
            bool converged_CNV = true;
            // Finish computation
            for ( int compIdx = 0; compIdx < numComp; ++compIdx )
            {
                CNV[compIdx]                    = B_avg[compIdx] * dt * maxCoeff[compIdx];
                mass_balance_residual[compIdx]  = std::abs(B_avg[compIdx]*R_sum[compIdx]) * dt / pvSum;
                converged_MB                    = converged_MB && (mass_balance_residual[compIdx] < tol_mb);
                if (iteration < param_.max_strict_iter_)
                    converged_CNV = converged_CNV && (CNV[compIdx] < tol_cnv);
                else
                    converged_CNV = converged_CNV && (CNV[compIdx] < tol_cnv_relaxed);

                residual_norms.push_back(CNV[compIdx]);
            }

            const bool converged_Well = wellModel().getWellConvergence(B_avg);

            bool converged = converged_MB && converged_Well;

            converged = converged && converged_CNV;

            if ( terminal_output_ )
            {
                // Only rank 0 does print to std::cout
                if (iteration == 0) {
                    std::string msg = "Iter";

                    std::vector< std::string > key( numComp );
                    for (unsigned phaseIdx = 0; phaseIdx < FluidSystem::numPhases; ++phaseIdx) {
                        if (!FluidSystem::phaseIsActive(phaseIdx)) {
                            continue;
                        }

                        const unsigned canonicalCompIdx = FluidSystem::solventComponentIndex(phaseIdx);
                        const std::string& compName = FluidSystem::componentName(canonicalCompIdx);
                        const unsigned compIdx = Indices::canonicalToActiveComponentIndex(canonicalCompIdx);
                        key[ compIdx ] = std::toupper( compName.front() );
                    }
                    if (has_solvent_) {
                        key[ solventSaturationIdx ] = "S";
                    }

                    if (has_polymer_) {
                        key[ polymerConcentrationIdx ] = "P";
                    }

                    if (has_energy_) {
                        key[ temperatureIdx ] = "E";
                    }

                    for (int compIdx = 0; compIdx < numComp; ++compIdx) {
                        msg += "    MB(" + key[ compIdx ] + ")  ";
                    }
                    for (int compIdx = 0; compIdx < numComp; ++compIdx) {
                        msg += "    CNV(" + key[ compIdx ] + ") ";
                    }
                    OpmLog::debug(msg);
                }
                std::ostringstream ss;
                const std::streamsize oprec = ss.precision(3);
                const std::ios::fmtflags oflags = ss.setf(std::ios::scientific);
                ss << std::setw(4) << iteration;
                for (int compIdx = 0; compIdx < numComp; ++compIdx) {
                    ss << std::setw(11) << mass_balance_residual[compIdx];
                }
                for (int compIdx = 0; compIdx < numComp; ++compIdx) {
                    ss << std::setw(11) << CNV[compIdx];
                }
                ss.precision(oprec);
                ss.flags(oflags);
                OpmLog::debug(ss.str());
            }

            for (unsigned phaseIdx = 0; phaseIdx < FluidSystem::numPhases; ++phaseIdx) {
                if (!FluidSystem::phaseIsActive(phaseIdx))
                    continue;

                const unsigned canonicalCompIdx = FluidSystem::solventComponentIndex(phaseIdx);
                const std::string& compName = FluidSystem::componentName(canonicalCompIdx);
                const unsigned compIdx = Indices::canonicalToActiveComponentIndex(canonicalCompIdx);

                if (std::isnan(mass_balance_residual[compIdx])
                    || std::isnan(CNV[compIdx])) {
                    OPM_THROW(Opm::NumericalIssue, "NaN residual for " << compName << " equation");
                }
                if (mass_balance_residual[compIdx] > maxResidualAllowed()
                    || CNV[compIdx] > maxResidualAllowed()) {
                    OPM_THROW(Opm::NumericalIssue, "Too large residual for " << compName << " equation");
                }
                if (mass_balance_residual[compIdx] < 0
                    || CNV[compIdx] < 0) {
                    OPM_THROW(Opm::NumericalIssue, "Negative residual for " << compName << " equation");
                }
            }

            return converged;
        }


        /// The number of active fluid phases in the model.
        int numPhases() const
        {
            return phaseUsage_.num_phases;
        }

        /// Wrapper required due to not following generic API
        template<class T>
        std::vector<std::vector<double> >
        computeFluidInPlace(const T&, const std::vector<int>& fipnum) const
        {
            return computeFluidInPlace(fipnum);
        }

        /// Should not be called
        std::vector<std::vector<double> >
        computeFluidInPlace(const std::vector<int>& /*fipnum*/) const
        {            
            //assert(true)
            //return an empty vector
            std::vector<std::vector<double> > regionValues(0, std::vector<double>(0,0.0));
            return regionValues;
        }

        const Simulator& ebosSimulator() const
        { return ebosSimulator_; }

        /// return the statistics if the nonlinearIteration() method failed
        const SimulatorReport& failureReport() const
        { return failureReport_; }

    protected:
        const ISTLSolverType& istlSolver() const
        {
            assert( istlSolver_ );
            return *istlSolver_;
        }

        // ---------  Data members  ---------

        Simulator& ebosSimulator_;
        const Grid&            grid_;
        const ISTLSolverType*  istlSolver_;
        const PhaseUsage phaseUsage_;
        const bool has_disgas_;
        const bool has_vapoil_;
        const bool has_solvent_;
        const bool has_polymer_;
        const bool has_energy_;

        ModelParameters                 param_;
        SimulatorReport failureReport_;

        // Well Model
        BlackoilWellModel<TypeTag>& well_model_;

        // Aquifer Model
        BlackoilAquiferModel<TypeTag>& aquifer_model_;

        /// \brief Whether we print something to std::cout
        bool terminal_output_;
        /// \brief The number of cells of the global grid.
        long int global_nc_;

        std::vector<std::vector<double>> residual_norms_history_;
        double current_relaxation_;
        BVector dx_old_;

        std::unique_ptr<Mat> matrix_for_preconditioner_;

    public:
        /// return the StandardWells object
        BlackoilWellModel<TypeTag>&
        wellModel() { return well_model_; }

        const BlackoilWellModel<TypeTag>&
        wellModel() const { return well_model_; }

        BlackoilAquiferModel<TypeTag>&
        aquiferModel() { return aquifer_model_; }

        const BlackoilAquiferModel<TypeTag>&
        aquiferModel() const { return aquifer_model_; }

        void beginReportStep()
        {
            ebosSimulator_.problem().beginEpisode();
        }

        void endReportStep()
        {
            ebosSimulator_.problem().endEpisode();
        }

    private:

        double dpMaxRel() const { return param_.dp_max_rel_; }
        double dsMax() const { return param_.ds_max_; }
        double drMaxRel() const { return param_.dr_max_rel_; }
        double maxResidualAllowed() const { return param_.max_residual_allowed_; }

    public:
        std::vector<bool> wasSwitched_;
    };
} // namespace Opm

#endif // OPM_BLACKOILMODELBASE_IMPL_HEADER_INCLUDED