/*
  Copyright 2013 SINTEF ICT, Applied Mathematics.
  Copyright 2014 Dr. Blatt - HPC-Simulation-Software & Services
  Copyright 2015 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/>.
*/


#if HAVE_CONFIG_H
#include "config.h"
#endif // HAVE_CONFIG_H


#include <dune/common/version.hh>

#include <opm/common/utility/platform_dependent/disable_warnings.h>

#if DUNE_VERSION_NEWER(DUNE_COMMON, 2, 3)
#include <dune/common/parallel/mpihelper.hh>
#else
#include <dune/common/mpihelper.hh>
#endif

#if HAVE_DUNE_CORNERPOINT && WANT_DUNE_CORNERPOINTGRID
#define USE_DUNE_CORNERPOINTGRID 1
#include <dune/grid/CpGrid.hpp>
#include <dune/grid/common/GridAdapter.hpp>
#else
#undef USE_DUNE_CORNERPOINTGRID
#endif

#include <opm/common/utility/platform_dependent/reenable_warnings.h>

#include <opm/core/pressure/FlowBCManager.hpp>

#include <opm/core/grid.h>
#include <opm/core/grid/cornerpoint_grid.h>
#include <opm/core/grid/GridManager.hpp>
#include <opm/autodiff/GridHelpers.hpp>
#include <opm/autodiff/createGlobalCellArray.hpp>

#include <opm/core/wells.h>
#include <opm/core/wells/WellsManager.hpp>
#include <opm/common/ErrorMacros.hpp>
#include <opm/core/simulator/initState.hpp>
#include <opm/core/simulator/initStateEquil.hpp>
#include <opm/core/simulator/SimulatorReport.hpp>
#include <opm/core/simulator/SimulatorTimer.hpp>
#include <opm/core/utility/miscUtilities.hpp>
#include <opm/core/utility/parameters/ParameterGroup.hpp>
#include <opm/core/utility/thresholdPressures.hpp> // Note: the GridHelpers must be included before this (to make overloads available). \TODO: Fix.

#include <opm/material/fluidmatrixinteractions/EclMaterialLawManager.hpp>
#include <opm/core/props/BlackoilPropertiesBasic.hpp>
#include <opm/core/props/BlackoilPropertiesFromDeck.hpp>
#include <opm/core/props/rock/RockCompressibility.hpp>

#include <opm/core/linalg/LinearSolverFactory.hpp>
#include <opm/autodiff/NewtonIterationBlackoilSimple.hpp>
#include <opm/autodiff/NewtonIterationBlackoilCPR.hpp>
#include <opm/autodiff/NewtonIterationBlackoilInterleaved.hpp>

#include <opm/core/simulator/BlackoilState.hpp>
#include <opm/autodiff/WellStateFullyImplicitBlackoil.hpp>

#include <opm/autodiff/SimulatorFullyImplicitBlackoil.hpp>
#include <opm/autodiff/BlackoilPropsAdFromDeck.hpp>
#include <opm/autodiff/RedistributeDataHandles.hpp>
#include <opm/autodiff/moduleVersion.hpp>

#include <opm/core/utility/share_obj.hpp>

#include <opm/parser/eclipse/OpmLog/OpmLog.hpp>
#include <opm/parser/eclipse/OpmLog/StreamLog.hpp>
#include <opm/parser/eclipse/OpmLog/CounterLog.hpp>
#include <opm/parser/eclipse/Deck/Deck.hpp>
#include <opm/parser/eclipse/Parser/Parser.hpp>
#include <opm/parser/eclipse/Parser/ParseMode.hpp>
#include <opm/parser/eclipse/EclipseState/checkDeck.hpp>
#include <opm/parser/eclipse/EclipseState/EclipseState.hpp>

#include <boost/filesystem.hpp>
#include <boost/algorithm/string.hpp>

#ifdef _OPENMP
#include <omp.h>
#endif

#include <memory>
#include <algorithm>
#include <cstdlib>
#include <iostream>
#include <vector>
#include <numeric>
#include <cstdlib>

namespace
{
    void warnIfUnusedParams(const Opm::parameter::ParameterGroup& param)
    {
        if (param.anyUnused()) {
            std::cout << "--------------------   Unused parameters:   --------------------\n";
            param.displayUsage();
            std::cout << "----------------------------------------------------------------" << std::endl;
        }
    }
} // anon namespace



// ----------------- Main program -----------------
int
main(int argc, char** argv)
try
{
    using namespace Opm;
#if USE_DUNE_CORNERPOINTGRID
    // Must ensure an instance of the helper is created to initialise MPI.
    const Dune::MPIHelper& mpi_helper = Dune::MPIHelper::instance(argc, argv);
    const int mpi_rank = mpi_helper.rank();
    const int mpi_size = mpi_helper.size();
#else
    // default values for serial run
    const int mpi_rank = 0;
    const int mpi_size = 1;
#endif

    // Write parameters used for later reference. (only if rank is zero)
    const bool output_cout = ( mpi_rank == 0 );

    if (output_cout)
    {
        std::string version = moduleVersionName();
        std::cout << "**********************************************************************\n";
        std::cout << "*                                                                    *\n";
        std::cout << "*                   This is Flow (version " << version << ")"
                  << std::string(26 - version.size(), ' ') << "*\n";
        std::cout << "*                                                                    *\n";
        std::cout << "* Flow is a simulator for fully implicit three-phase black-oil flow, *\n";
        std::cout << "*            and is part of OPM. For more information see:           *\n";
        std::cout << "*                       http://opm-project.org                       *\n";
        std::cout << "*                                                                    *\n";
        std::cout << "**********************************************************************\n\n";
    }

#ifdef _OPENMP
    if (!getenv("OMP_NUM_THREADS")) {
        //Default to at most 4 threads, regardless of 
        //number of cores (unless ENV(OMP_NUM_THREADS) is defined)
        int num_cores = omp_get_num_procs();
        int num_threads = std::min(4, num_cores);
        omp_set_num_threads(num_threads);
    }
#pragma omp parallel
    if (omp_get_thread_num() == 0){
        //opm_get_num_threads() only works as expected within a parallel region.
        std::cout << "OpenMP using " << omp_get_num_threads() << " threads." << std::endl;
    }
#endif

    // Read parameters, see if a deck was specified on the command line.
    if ( output_cout )
    {
        std::cout << "---------------    Reading parameters     ---------------" << std::endl;
    }

    parameter::ParameterGroup param(argc, argv, false, output_cout);
    if( !output_cout )
    {
        param.disableOutput();
    }

    if (!param.unhandledArguments().empty()) {
        if (param.unhandledArguments().size() != 1) {
            std::cerr << "You can only specify a single input deck on the command line.\n";
            return EXIT_FAILURE;
        } else {
            param.insertParameter("deck_filename", param.unhandledArguments()[0]);
        }
    }

    // We must have an input deck. Grid and props will be read from that.
    if (!param.has("deck_filename")) {
        std::cerr << "This program must be run with an input deck.\n"
            "Specify the deck filename either\n"
            "    a) as a command line argument by itself\n"
            "    b) as a command line parameter with the syntax deck_filename=<path to your deck>, or\n"
            "    c) as a parameter in a parameter file (.param or .xml) passed to the program.\n";
        return EXIT_FAILURE;
    }

    // bool check_well_controls = false;
    // int max_well_control_iterations = 0;
    double gravity[3] = { 0.0 };
    std::string deck_filename = param.get<std::string>("deck_filename");

    // Write parameters used for later reference. (only if rank is zero)
    bool output = ( mpi_rank == 0 ) && param.getDefault("output", true);
    std::string output_dir;
    if (output) {
        // Create output directory if needed.
        output_dir =
            param.getDefault("output_dir", std::string("output"));
        boost::filesystem::path fpath(output_dir);
        try {
            create_directories(fpath);
        }
        catch (...) {
            std::cerr << "Creating directories failed: " << fpath << std::endl;
            return EXIT_FAILURE;
        }
        // Write simulation parameters.
        param.writeParam(output_dir + "/simulation.param");
    }

    std::string logFile = output_dir + "/LOGFILE.txt";
    Opm::ParserPtr parser(new Opm::Parser());
    {
        std::shared_ptr<Opm::StreamLog> streamLog = std::make_shared<Opm::StreamLog>(logFile , Opm::Log::DefaultMessageTypes);
        std::shared_ptr<Opm::CounterLog> counterLog = std::make_shared<Opm::CounterLog>(Opm::Log::DefaultMessageTypes);

        Opm::OpmLog::addBackend( "STREAM" , streamLog );
        Opm::OpmLog::addBackend( "COUNTER" , counterLog );
    }

    Opm::ParseMode parseMode({{ ParseMode::PARSE_RANDOM_SLASH , InputError::IGNORE }});
    Opm::DeckConstPtr deck;
    std::shared_ptr<EclipseState> eclipseState;
    try {
        deck = parser->parseFile(deck_filename, parseMode);
        Opm::checkDeck(deck);
        eclipseState.reset(new Opm::EclipseState(deck , parseMode));
    }
    catch (const std::invalid_argument& e) {
        std::cerr << "Failed to create valid ECLIPSESTATE object. See logfile: " << logFile << std::endl;
        std::cerr << "Exception caught: " << e.what() << std::endl;
        return EXIT_FAILURE;
    }

    std::vector<double> porv = eclipseState->getDoubleGridProperty("PORV")->getData();
#if USE_DUNE_CORNERPOINTGRID
    // Dune::CpGrid as grid manager
    typedef Dune::CpGrid  Grid;
    // Grid init
    Grid grid;
    grid.processEclipseFormat(deck, false, false, false, porv);
#else
    // UnstructuredGrid as grid manager
    typedef UnstructuredGrid  Grid;
    GridManager gridManager( eclipseState->getEclipseGrid(), porv );
    const Grid& grid = *(gridManager.c_grid());
#endif

    // Possibly override IOConfig setting (from deck) for how often RESTART files should get written to disk (every N report step)
    if (param.has("output_interval")) {
        int output_interval = param.get<int>("output_interval");
        IOConfigPtr ioConfig = eclipseState->getIOConfig();
        ioConfig->overrideRestartWriteInterval((size_t)output_interval);
    }

    const PhaseUsage pu = Opm::phaseUsageFromDeck(deck);

    std::vector<int> compressedToCartesianIdx;
    Opm::createGlobalCellArray(grid, compressedToCartesianIdx);

    typedef BlackoilPropsAdFromDeck::MaterialLawManager MaterialLawManager;
    auto materialLawManager = std::make_shared<MaterialLawManager>();
    materialLawManager->initFromDeck(deck, eclipseState, compressedToCartesianIdx);

    // Rock and fluid init
    BlackoilPropertiesFromDeck props( deck, eclipseState, materialLawManager,
                                      Opm::UgGridHelpers::numCells(grid),
                                      Opm::UgGridHelpers::globalCell(grid),
                                      Opm::UgGridHelpers::cartDims(grid),
                                      param);

    BlackoilPropsAdFromDeck new_props( deck, eclipseState, materialLawManager, grid );
    // check_well_controls = param.getDefault("check_well_controls", false);
    // max_well_control_iterations = param.getDefault("max_well_control_iterations", 10);
    // Rock compressibility.

    RockCompressibility rock_comp(deck, eclipseState);

    // Gravity.
    gravity[2] = deck->hasKeyword("NOGRAV") ? 0.0 : unit::gravity;

    BlackoilState state;
    // Init state variables (saturation and pressure).
    if (param.has("init_saturation")) {
        initStateBasic(Opm::UgGridHelpers::numCells(grid),
                       Opm::UgGridHelpers::globalCell(grid),
                       Opm::UgGridHelpers::cartDims(grid),
                       Opm::UgGridHelpers::numFaces(grid),
                       Opm::UgGridHelpers::faceCells(grid),
                       Opm::UgGridHelpers::beginFaceCentroids(grid),
                       Opm::UgGridHelpers::beginCellCentroids(grid),
                       Opm::UgGridHelpers::dimensions(grid),
                       props, param, gravity[2], state);

        initBlackoilSurfvol(Opm::UgGridHelpers::numCells(grid), props, state);

        enum { Oil = BlackoilPhases::Liquid, Gas = BlackoilPhases::Vapour };
        if (pu.phase_used[Oil] && pu.phase_used[Gas]) {
            const int numPhases = props.numPhases();
            const int numCells  = Opm::UgGridHelpers::numCells(grid);
            for (int c = 0; c < numCells; ++c) {
                state.gasoilratio()[c] = state.surfacevol()[c*numPhases + pu.phase_pos[Gas]]
                    / state.surfacevol()[c*numPhases + pu.phase_pos[Oil]];
            }
        }
    } else if (deck->hasKeyword("EQUIL") && props.numPhases() == 3) {
        state.init(Opm::UgGridHelpers::numCells(grid),
                   Opm::UgGridHelpers::numFaces(grid),
                   props.numPhases());
        const double grav = param.getDefault("gravity", unit::gravity);
        initStateEquil(grid, props, deck, eclipseState, grav, state);
        state.faceflux().resize(Opm::UgGridHelpers::numFaces(grid), 0.0);
    } else {
        initBlackoilStateFromDeck(Opm::UgGridHelpers::numCells(grid),
                                  Opm::UgGridHelpers::globalCell(grid),
                                  Opm::UgGridHelpers::numFaces(grid),
                                  Opm::UgGridHelpers::faceCells(grid),
                                  Opm::UgGridHelpers::beginFaceCentroids(grid),
                                  Opm::UgGridHelpers::beginCellCentroids(grid),
                                  Opm::UgGridHelpers::dimensions(grid),
                                  props, deck, gravity[2], state);
    }


    // The capillary pressure is scaled in new_props to match the scaled capillary pressure in props.
    if (deck->hasKeyword("SWATINIT")) {
        const int numCells = Opm::UgGridHelpers::numCells(grid);
        std::vector<int> cells(numCells);
        for (int c = 0; c < numCells; ++c) { cells[c] = c; }
        std::vector<double> pc = state.saturation();
        props.capPress(numCells, state.saturation().data(), cells.data(), pc.data(),NULL);
        new_props.setSwatInitScaling(state.saturation(),pc);
    }

    bool use_gravity = (gravity[0] != 0.0 || gravity[1] != 0.0 || gravity[2] != 0.0);
    const double *grav = use_gravity ? &gravity[0] : 0;

    const bool use_local_perm = param.getDefault("use_local_perm", true);

    DerivedGeology geoprops(grid, new_props, eclipseState, use_local_perm, grav);
    boost::any parallel_information;

    // At this point all properties and state variables are correctly initialized
    // If there are more than one processors involved, we now repartition the grid
    // and initilialize new properties and states for it.
    if( mpi_size > 1 )
    {
        Opm::distributeGridAndData( grid, eclipseState, state, new_props, geoprops, parallel_information, use_local_perm );
    }

    // create output writer after grid is distributed, otherwise the parallel output
    // won't work correctly since we need to create a mapping from the distributed to
    // the global view
    Opm::BlackoilOutputWriter outputWriter(grid, param, eclipseState, pu, new_props.permeability() );

    // Solver for Newton iterations.
    std::unique_ptr<NewtonIterationBlackoilInterface> fis_solver;
    {
        const std::string cprSolver = "cpr";
        const std::string interleavedSolver = "interleaved";
        const std::string directSolver = "direct";
        const std::string flowDefaultSolver = interleavedSolver;

        std::shared_ptr<const Opm::SimulationConfig> simCfg = eclipseState->getSimulationConfig();
        std::string solver_approach = flowDefaultSolver;

        if (param.has("solver_approach")) {
            solver_approach = param.get<std::string>("solver_approach");
        }  else {
            if (simCfg->useCPR()) {
                solver_approach = cprSolver;
            }
        }

        if (solver_approach == cprSolver) {
            fis_solver.reset(new NewtonIterationBlackoilCPR(param, parallel_information));
        } else if (solver_approach == interleavedSolver) {
            fis_solver.reset(new NewtonIterationBlackoilInterleaved(param, parallel_information));
        } else if (solver_approach == directSolver) {
            fis_solver.reset(new NewtonIterationBlackoilSimple(param, parallel_information));
        } else {
            OPM_THROW( std::runtime_error , "Internal error - solver approach " << solver_approach << " not recognized.");
        }

    }

    Opm::ScheduleConstPtr schedule = eclipseState->getSchedule();
    Opm::TimeMapConstPtr timeMap(schedule->getTimeMap());
    SimulatorTimer simtimer;

    // initialize variables
    simtimer.init(timeMap);

    std::vector<double> threshold_pressures = thresholdPressures(parseMode, eclipseState, grid);

    SimulatorFullyImplicitBlackoil< Grid >  simulator(param,
                                                      grid,
                                                      geoprops,
                                                      new_props,
                                                      rock_comp.isActive() ? &rock_comp : 0,
                                                      *fis_solver,
                                                      grav,
                                                      deck->hasKeyword("DISGAS"),
                                                      deck->hasKeyword("VAPOIL"),
                                                      eclipseState,
                                                      outputWriter,
                                                      threshold_pressures);

    if (!schedule->initOnly()){
        if( output_cout )
        {
            std::cout << "\n\n================ Starting main simulation loop ===============\n"
                      << std::flush;
        }

        SimulatorReport fullReport = simulator.run(simtimer, state);

        if( output_cout )
        {
            std::cout << "\n\n================    End of simulation     ===============\n\n";
            fullReport.reportFullyImplicit(std::cout);
        }

        if (output) {
            std::string filename = output_dir + "/walltime.txt";
            std::fstream tot_os(filename.c_str(),std::fstream::trunc | std::fstream::out);
            fullReport.reportParam(tot_os);
            warnIfUnusedParams(param);
        }
    } else {
        outputWriter.writeInit( simtimer );
        if ( output_cout )
        {
            std::cout << "\n\n================ Simulation turned off ===============\n" << std::flush;
        }
    }
}
catch (const std::exception &e) {
    std::cerr << "Program threw an exception: " << e.what() << "\n";
    return EXIT_FAILURE;
}