// ---------------------------------------------------------------------
//
// Copyright (c) 2018 - 2022 by the IBAMR developers
// All rights reserved.
//
// This file is part of IBAMR.
//
// IBAMR is free software and is distributed under the 3-clause BSD
// license. The full text of the license can be found in the file
// COPYRIGHT at the top level directory of IBAMR.
//
// ---------------------------------------------------------------------

// Config files
#include <SAMRAI_config.h>

// Headers for basic PETSc functions
#include <petscsys.h>

// Headers for basic SAMRAI objects
#include <BergerRigoutsos.h>
#include <CartesianGridGeometry.h>
#include <LoadBalancer.h>
#include <StandardTagAndInitialize.h>

// Headers for application-specific algorithm/data structure objects
#include <ibamr/INSVCStaggeredHierarchyIntegrator.h>
#include <ibamr/INSVCStaggeredNonConservativeHierarchyIntegrator.h>

#include <ibtk/AppInitializer.h>
#include <ibtk/IBTKInit.h>
#include <ibtk/IBTK_MPI.h>
#include <ibtk/muParserCartGridFunction.h>
#include <ibtk/muParserRobinBcCoefs.h>

// Set up application namespace declarations
#include <ibamr/app_namespaces.h>

// Applications
#include "SetFluidProperties.h"

// Function prototypes
void output_data(Pointer<PatchHierarchy<NDIM> > patch_hierarchy,
                 Pointer<INSHierarchyIntegrator> ins_integrator,
                 const int iteration_num,
                 const double loop_time,
                 const string& data_dump_dirname);

/*******************************************************************************
 * For each run, the input filename and restart information (if needed) must   *
 * be given on the command line.  For non-restarted case, command line is:     *
 *                                                                             *
 *    executable <input file name>                                             *
 *                                                                             *
 * For restarted run, command line is:                                         *
 *                                                                             *
 *    executable <input file name> <restart directory> <restart number>        *
 *                                                                             *
 *******************************************************************************/
int
main(int argc, char* argv[])
{
    // Initialize IBAMR and libraries. Deinitialization is handled by this object as well.
    IBTKInit ibtk_init(argc, argv, MPI_COMM_WORLD);

    // Increase maximum patch data component indices
    SAMRAIManager::setMaxNumberPatchDataEntries(2500);

    // resize u_err and p_err vectors to hold error data
    std::vector<double> u_err;
    std::vector<double> p_err;
    u_err.resize(3);
    p_err.resize(3);

    { // cleanup dynamically allocated objects prior to shutdown

        // Parse command line options, set some standard options from the input
        // file, initialize the restart database (if this is a restarted run),
        // and enable file logging.
        Pointer<AppInitializer> app_initializer = new AppInitializer(argc, argv, "INS.log");
        Pointer<Database> input_db = app_initializer->getInputDatabase();

        // Get various standard options set in the input file.
        const bool dump_viz_data = app_initializer->dumpVizData();
        const int viz_dump_interval = app_initializer->getVizDumpInterval();
        const bool uses_visit = dump_viz_data && app_initializer->getVisItDataWriter();

        const bool dump_restart_data = app_initializer->dumpRestartData();
        const int restart_dump_interval = app_initializer->getRestartDumpInterval();
        const string restart_dump_dirname = app_initializer->getRestartDumpDirectory();

        const bool dump_postproc_data = app_initializer->dumpPostProcessingData();
        const int postproc_data_dump_interval = app_initializer->getPostProcessingDataDumpInterval();
        const string postproc_data_dump_dirname = app_initializer->getPostProcessingDataDumpDirectory();

        const bool dump_timer_data = app_initializer->dumpTimerData();
        const int timer_dump_interval = app_initializer->getTimerDumpInterval();

        // Create major algorithm and data objects that comprise the
        // application.  These objects are configured from the input database
        // and, if this is a restarted run, from the restart database.
        Pointer<INSVCStaggeredHierarchyIntegrator> time_integrator;
        const string discretization_form = app_initializer->getComponentDatabase("Main")->getStringWithDefault(
            "discretization_form", "NON_CONSERVATIVE");
        if (discretization_form == "NON_CONSERVATIVE")
        {
            time_integrator = new INSVCStaggeredNonConservativeHierarchyIntegrator(
                "INSVCStaggeredNonConservativeHierarchyIntegrator",
                app_initializer->getComponentDatabase("INSVCStaggeredNonConservativeHierarchyIntegrator"));
        }
        else
        {
            TBOX_ERROR("Unknown INSVCStaggeredHierarchyIntegrator type");
        }

        Pointer<CartesianGridGeometry<NDIM> > grid_geometry = new CartesianGridGeometry<NDIM>(
            "CartesianGeometry", app_initializer->getComponentDatabase("CartesianGeometry"));
        Pointer<PatchHierarchy<NDIM> > patch_hierarchy = new PatchHierarchy<NDIM>("PatchHierarchy", grid_geometry);
        Pointer<StandardTagAndInitialize<NDIM> > error_detector =
            new StandardTagAndInitialize<NDIM>("StandardTagAndInitialize",
                                               time_integrator,
                                               app_initializer->getComponentDatabase("StandardTagAndInitialize"));
        Pointer<BergerRigoutsos<NDIM> > box_generator = new BergerRigoutsos<NDIM>();
        Pointer<LoadBalancer<NDIM> > load_balancer =
            new LoadBalancer<NDIM>("LoadBalancer", app_initializer->getComponentDatabase("LoadBalancer"));
        Pointer<GriddingAlgorithm<NDIM> > gridding_algorithm =
            new GriddingAlgorithm<NDIM>("GriddingAlgorithm",
                                        app_initializer->getComponentDatabase("GriddingAlgorithm"),
                                        error_detector,
                                        box_generator,
                                        load_balancer);

        // Create initial condition specification objects.
        Pointer<CartGridFunction> u_init = new muParserCartGridFunction(
            "u_init", app_initializer->getComponentDatabase("VelocityInitialConditions"), grid_geometry);
        time_integrator->registerVelocityInitialConditions(u_init);
        Pointer<CartGridFunction> p_init = new muParserCartGridFunction(
            "p_init", app_initializer->getComponentDatabase("PressureInitialConditions"), grid_geometry);
        time_integrator->registerPressureInitialConditions(p_init);

        // Create boundary condition specification objects (when necessary).
        const IntVector<NDIM>& periodic_shift = grid_geometry->getPeriodicShift();
        vector<RobinBcCoefStrategy<NDIM>*> u_bc_coefs(NDIM);
        if (periodic_shift.min() > 0)
        {
            for (unsigned int d = 0; d < NDIM; ++d)
            {
                u_bc_coefs[d] = NULL;
            }
        }
        else
        {
            for (unsigned int d = 0; d < NDIM; ++d)
            {
                const std::string bc_coefs_name = "u_bc_coefs_" + std::to_string(d);

                const std::string bc_coefs_db_name = "VelocityBcCoefs_" + std::to_string(d);

                u_bc_coefs[d] = new muParserRobinBcCoefs(
                    bc_coefs_name, app_initializer->getComponentDatabase(bc_coefs_db_name), grid_geometry);
            }
            time_integrator->registerPhysicalBoundaryConditions(u_bc_coefs);
        }

        // Create a density and viscosity field for testing purposes
        Pointer<CellVariable<NDIM, double> > rho_var = new CellVariable<NDIM, double>("rho_var");
        Pointer<CellVariable<NDIM, double> > mu_var = new CellVariable<NDIM, double>("mu_var");
        time_integrator->registerMassDensityVariable(rho_var);
        time_integrator->registerViscosityVariable(mu_var);
        Pointer<CartGridFunction> rho_fcn = new muParserCartGridFunction(
            "rho_fcn", app_initializer->getComponentDatabase("DensityFunction"), grid_geometry);
        Pointer<CartGridFunction> mu_fcn = new muParserCartGridFunction(
            "mu_fcn", app_initializer->getComponentDatabase("ViscosityFunction"), grid_geometry);
        SetFluidProperties* ptr_SetFluidProperties = new SetFluidProperties("SetFluidProperties", rho_fcn, mu_fcn);

        // Set the density and viscosity initial condition
        time_integrator->registerViscosityInitialConditions(mu_fcn);
        time_integrator->registerMassDensityInitialConditions(rho_fcn);

        // Reset fluid properties if they are time-dependent.
        time_integrator->registerResetFluidDensityFcn(&callSetFluidDensityCallbackFunction,
                                                      static_cast<void*>(ptr_SetFluidProperties));
        time_integrator->registerResetFluidViscosityFcn(&callSetFluidViscosityCallbackFunction,
                                                        static_cast<void*>(ptr_SetFluidProperties));

        // Register boundary conditions for rho and mu as they are not set by CartGridFunction
        RobinBcCoefStrategy<NDIM>* rho_bc_coef = NULL;
        if (!(periodic_shift.min() > 0) && input_db->keyExists("DensityBoundaryConditions"))
        {
            rho_bc_coef = new muParserRobinBcCoefs(
                "rho_bc_coef", app_initializer->getComponentDatabase("DensityBoundaryConditions"), grid_geometry);
            time_integrator->registerMassDensityBoundaryConditions(rho_bc_coef);
        }

        RobinBcCoefStrategy<NDIM>* mu_bc_coef = NULL;
        if (!(periodic_shift.min() > 0) && input_db->keyExists("ViscosityBoundaryConditions"))
        {
            mu_bc_coef = new muParserRobinBcCoefs(
                "mu_bc_coef", app_initializer->getComponentDatabase("ViscosityBoundaryConditions"), grid_geometry);
            time_integrator->registerViscosityBoundaryConditions(mu_bc_coef);
        }

        // Create body force function specification objects (when necessary).
        if (input_db->keyExists("ForcingFunction"))
        {
            Pointer<CartGridFunction> f_fcn = new muParserCartGridFunction(
                "f_fcn", app_initializer->getComponentDatabase("ForcingFunction"), grid_geometry);
            time_integrator->registerBodyForceFunction(f_fcn);
        }

        // Set up visualization plot file writers.
        Pointer<VisItDataWriter<NDIM> > visit_data_writer = app_initializer->getVisItDataWriter();
        if (uses_visit)
        {
            time_integrator->registerVisItDataWriter(visit_data_writer);
        }

        // Initialize hierarchy configuration and data on all patches.
        time_integrator->initializePatchHierarchy(patch_hierarchy, gridding_algorithm);

        // Deallocate initialization objects.
        app_initializer.setNull();

        // Print the input database contents to the log file.
        plog << "Input database:\n";
        input_db->printClassData(plog);

        // Write out initial visualization data.
        int iteration_num = time_integrator->getIntegratorStep();
        double loop_time = time_integrator->getIntegratorTime();
        if (dump_viz_data && uses_visit)
        {
            pout << "\n\nWriting visualization files...\n\n";
            time_integrator->setupPlotData();
            visit_data_writer->writePlotData(patch_hierarchy, iteration_num, loop_time);
        }

        // Main time step loop.
        double loop_time_end = time_integrator->getEndTime();
        double dt = 0.0;
        while (!IBTK::rel_equal_eps(loop_time, loop_time_end) && time_integrator->stepsRemaining())
        {
            iteration_num = time_integrator->getIntegratorStep();
            loop_time = time_integrator->getIntegratorTime();

            pout << "\n";
            pout << "+++++++++++++++++++++++++++++++++++++++++++++++++++\n";
            pout << "At beginning of timestep # " << iteration_num << "\n";
            pout << "Simulation time is " << loop_time << "\n";

            dt = time_integrator->getMaximumTimeStepSize();
            time_integrator->advanceHierarchy(dt);
            loop_time += dt;

            pout << "\n";
            pout << "At end       of timestep # " << iteration_num << "\n";
            pout << "Simulation time is " << loop_time << "\n";
            pout << "+++++++++++++++++++++++++++++++++++++++++++++++++++\n";
            pout << "\n";

            // At specified intervals, write visualization and restart files,
            // print out timer data, and store hierarchy data for post
            // processing.
            iteration_num += 1;
            const bool last_step = !time_integrator->stepsRemaining();
            if (dump_viz_data && uses_visit && (iteration_num % viz_dump_interval == 0 || last_step))
            {
                pout << "\nWriting visualization files...\n\n";
                time_integrator->setupPlotData();
                visit_data_writer->writePlotData(patch_hierarchy, iteration_num, loop_time);
            }
            if (dump_restart_data && (iteration_num % restart_dump_interval == 0 || last_step))
            {
                pout << "\nWriting restart files...\n\n";
                RestartManager::getManager()->writeRestartFile(restart_dump_dirname, iteration_num);
            }
            if (dump_timer_data && (iteration_num % timer_dump_interval == 0 || last_step))
            {
                pout << "\nWriting timer data...\n\n";
                TimerManager::getManager()->print(plog);
            }
            if (dump_postproc_data && (iteration_num % postproc_data_dump_interval == 0 || last_step))
            {
                output_data(patch_hierarchy, time_integrator, iteration_num, loop_time, postproc_data_dump_dirname);
            }
        }

        // Determine the accuracy of the computed solution.
        pout << "\n"
             << "+++++++++++++++++++++++++++++++++++++++++++++++++++\n"
             << "Computing error norms.\n\n";

        VariableDatabase<NDIM>* var_db = VariableDatabase<NDIM>::getDatabase();

        const Pointer<Variable<NDIM> > u_var = time_integrator->getVelocityVariable();
        const Pointer<VariableContext> u_ctx = time_integrator->getCurrentContext();

        const int u_idx = var_db->mapVariableAndContextToIndex(u_var, u_ctx);
        const int u_cloned_idx = var_db->registerClonedPatchDataIndex(u_var, u_idx);

        const Pointer<Variable<NDIM> > p_var = time_integrator->getPressureVariable();
        const Pointer<VariableContext> p_ctx = time_integrator->getCurrentContext();

        const int p_idx = var_db->mapVariableAndContextToIndex(p_var, p_ctx);
        const int p_cloned_idx = var_db->registerClonedPatchDataIndex(p_var, p_idx);

        const int coarsest_ln = 0;
        const int finest_ln = patch_hierarchy->getFinestLevelNumber();
        for (int ln = coarsest_ln; ln <= finest_ln; ++ln)
        {
            patch_hierarchy->getPatchLevel(ln)->allocatePatchData(u_cloned_idx, loop_time);
            patch_hierarchy->getPatchLevel(ln)->allocatePatchData(p_cloned_idx, loop_time);
        }

        u_init->setDataOnPatchHierarchy(u_cloned_idx, u_var, patch_hierarchy, loop_time);
        p_init->setDataOnPatchHierarchy(p_cloned_idx, p_var, patch_hierarchy, loop_time - 0.5 * dt);

        HierarchyMathOps hier_math_ops("HierarchyMathOps", patch_hierarchy);
        hier_math_ops.setPatchHierarchy(patch_hierarchy);
        hier_math_ops.resetLevels(coarsest_ln, finest_ln);
        const int wgt_cc_idx = hier_math_ops.getCellWeightPatchDescriptorIndex();
        const int wgt_sc_idx = hier_math_ops.getSideWeightPatchDescriptorIndex();

        Pointer<CellVariable<NDIM, double> > u_cc_var = u_var;
        if (u_cc_var)
        {
            HierarchyCellDataOpsReal<NDIM, double> hier_cc_data_ops(patch_hierarchy, coarsest_ln, finest_ln);
            hier_cc_data_ops.subtract(u_idx, u_idx, u_cloned_idx);

            pout << "Error in u_cc at time " << loop_time << ":\n"
                 << "  L1-norm:  " << std::setprecision(10) << hier_cc_data_ops.L1Norm(u_idx, wgt_cc_idx) << "\n"
                 << "  L2-norm:  " << hier_cc_data_ops.L2Norm(u_idx, wgt_cc_idx) << "\n"
                 << "  max-norm: " << hier_cc_data_ops.maxNorm(u_idx, wgt_cc_idx) << "\n";

            u_err[0] = hier_cc_data_ops.L1Norm(u_idx, wgt_sc_idx);
            u_err[1] = hier_cc_data_ops.L2Norm(u_idx, wgt_sc_idx);
            u_err[2] = hier_cc_data_ops.maxNorm(u_idx, wgt_sc_idx);
        }

        Pointer<SideVariable<NDIM, double> > u_sc_var = u_var;
        if (u_sc_var)
        {
            HierarchySideDataOpsReal<NDIM, double> hier_sc_data_ops(patch_hierarchy, coarsest_ln, finest_ln);
            hier_sc_data_ops.subtract(u_idx, u_idx, u_cloned_idx);
            pout << "Error in u_sc at time " << loop_time << ":\n"
                 << "  L1-norm:  " << std::setprecision(10) << hier_sc_data_ops.L1Norm(u_idx, wgt_sc_idx) << "\n"
                 << "  L2-norm:  " << hier_sc_data_ops.L2Norm(u_idx, wgt_sc_idx) << "\n"
                 << "  max-norm: " << hier_sc_data_ops.maxNorm(u_idx, wgt_sc_idx) << "\n";

            u_err[0] = hier_sc_data_ops.L1Norm(u_idx, wgt_sc_idx);
            u_err[1] = hier_sc_data_ops.L2Norm(u_idx, wgt_sc_idx);
            u_err[2] = hier_sc_data_ops.maxNorm(u_idx, wgt_sc_idx);
        }

        HierarchyCellDataOpsReal<NDIM, double> hier_cc_data_ops(patch_hierarchy, coarsest_ln, finest_ln);
        hier_cc_data_ops.subtract(p_idx, p_idx, p_cloned_idx);
        pout << "Error in p at time " << loop_time - 0.5 * dt << ":\n"
             << "  L1-norm:  " << hier_cc_data_ops.L1Norm(p_idx, wgt_cc_idx) << "\n"
             << "  L2-norm:  " << hier_cc_data_ops.L2Norm(p_idx, wgt_cc_idx) << "\n"
             << "  max-norm: " << hier_cc_data_ops.maxNorm(p_idx, wgt_cc_idx) << "\n"
             << "+++++++++++++++++++++++++++++++++++++++++++++++++++\n";

        p_err[0] = hier_cc_data_ops.L1Norm(p_idx, wgt_cc_idx);
        p_err[1] = hier_cc_data_ops.L2Norm(p_idx, wgt_cc_idx);
        p_err[2] = hier_cc_data_ops.maxNorm(p_idx, wgt_cc_idx);

        if (dump_viz_data && uses_visit)
        {
            pout << "Printing velocity and pressure differences as last visit output" << std::endl;
            time_integrator->setupPlotData();
            visit_data_writer->writePlotData(patch_hierarchy, iteration_num + 1, loop_time);
        }

        // Cleanup boundary condition specification objects (when necessary).
        for (unsigned int d = 0; d < NDIM; ++d) delete u_bc_coefs[d];

    } // cleanup dynamically allocated objects prior to shutdown
} // main

void
output_data(Pointer<PatchHierarchy<NDIM> > patch_hierarchy,
            Pointer<INSHierarchyIntegrator> ins_integrator,
            const int iteration_num,
            const double loop_time,
            const string& data_dump_dirname)
{
    plog << "writing hierarchy data at iteration " << iteration_num << " to disk" << endl;
    plog << "simulation time is " << loop_time << endl;
    string file_name = data_dump_dirname + "/" + "hier_data.";
    char temp_buf[128];
    sprintf(temp_buf, "%05d.samrai.%05d", iteration_num, IBTK_MPI::getRank());
    file_name += temp_buf;
    Pointer<HDFDatabase> hier_db = new HDFDatabase("hier_db");
    hier_db->create(file_name);
    VariableDatabase<NDIM>* var_db = VariableDatabase<NDIM>::getDatabase();
    ComponentSelector hier_data;
    hier_data.setFlag(var_db->mapVariableAndContextToIndex(ins_integrator->getVelocityVariable(),
                                                           ins_integrator->getCurrentContext()));
    hier_data.setFlag(var_db->mapVariableAndContextToIndex(ins_integrator->getPressureVariable(),
                                                           ins_integrator->getCurrentContext()));
    patch_hierarchy->putToDatabase(hier_db->putDatabase("PatchHierarchy"), hier_data);
    hier_db->putDouble("loop_time", loop_time);
    hier_db->putInteger("iteration_num", iteration_num);
    hier_db->close();
    return;
} // output_data
