text: // ---------------------------------------------------------------------
  //
  // Copyright (c) 2021 - 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.
  //
  // ---------------------------------------------------------------------
  
  #include <ibamr/AdvDiffHierarchyIntegrator.h>
  #include <ibamr/IBExplicitHierarchyIntegrator.h>
  #include <ibamr/IBMethod.h>
  #include <ibamr/IBRedundantInitializer.h>
  #include <ibamr/INSStaggeredHierarchyIntegrator.h>
  
  #include <ibtk/AppInitializer.h>
  #include <ibtk/IBTKInit.h>
  #include <ibtk/IBTK_MPI.h>
  #include <ibtk/muParserCartGridFunction.h>
  
  #include <petscsys.h>
  
  #include <BergerRigoutsos.h>
  #include <CartesianGridGeometry.h>
  #include <LoadBalancer.h>
  #include <LocationIndexRobinBcCoefs.h>
  #include <SAMRAI_config.h>
  #include <StandardTagAndInitialize.h>
  #include <VisItDataWriter.h>
  
  #include <ibamr/app_namespaces.h>
  
  class DummyAdvDiffIntegrator : public AdvDiffHierarchyIntegrator
  {
  public:
      DummyAdvDiffIntegrator(std::string object_name, Pointer<Database> input_db)
          : AdvDiffHierarchyIntegrator(std::move(object_name), input_db, true)
      {
      }
  
      ~DummyAdvDiffIntegrator() = default;
  
      void integrateHierarchy(double current_time, double new_time, int cycle_num = 0) override
      {
          HierarchyIntegrator::integrateHierarchy(current_time, new_time, cycle_num);
          return;
      }
  
  protected:
      void regridHierarchyBeginSpecialized() override
      {
          plog << d_object_name << ": regridHierarchyBeginSpecialized()\n";
      }
      void regridHierarchyEndSpecialized() override
      {
          plog << d_object_name << ": regridHierarchyEndSpecialized()\n";
      }
      double getMinimumTimeStepSizeSpecialized() override
      {
          plog << d_object_name << ": getMinimumTimeStepSizeSpecialized()\n";
          return std::numeric_limits<double>::min();
      }
      double getMaximumTimeStepSizeSpecialized() override
      {
          plog << d_object_name << ": getMaximumTimeStepSizeSpecialized()\n";
          return std::numeric_limits<double>::max();
      }
      void synchronizeHierarchyDataSpecialized(VariableContextType /*ctx_type*/) override
      {
          plog << d_object_name << ": synchronizeHierarchyDataSpecialized()\n";
      }
      void resetTimeDependentHierarchyDataSpecialized(const double /*new_time*/) override
      {
          plog << d_object_name << ": resetTimeDependentHierarchyDataSpecialized()\n";
      }
      void resetIntegratorToPreadvanceStateSpecialized() override
      {
          plog << d_object_name << ": resetIntegratorToPreadvanceStateSpecialized()\n";
      }
      bool atRegridPointSpecialized() const override
      {
          plog << d_object_name << ": atRegridPointSpecialized()\n";
          return false;
      }
      void setupPlotDataSpecialized() override
      {
          plog << d_object_name << ": setupPlotDataSpecialized()\n";
      }
      void initializeCompositeHierarchyDataSpecialized(double /*init_data_time*/, bool /*initial_time*/) override
      {
          plog << d_object_name << ": initializeCompositeHierarchyDataSpecialized()\n";
      }
      void initializeLevelDataSpecialized(Pointer<BasePatchHierarchy<NDIM> > /*hierarchy*/,
                                          int /*level_number*/,
                                          double /*init_data_time*/,
                                          bool /*can_be_refined*/,
                                          bool /*initial_time*/,
                                          Pointer<BasePatchLevel<NDIM> > /*old_level*/,
                                          bool /*allocate_data*/) override
      {
          plog << d_object_name << ": initializeLevelDataSpecialized()\n";
      }
      void resetHierarchyConfigurationSpecialized(Pointer<BasePatchHierarchy<NDIM> > /*hierarchy*/,
                                                  int /*coarsest_level*/,
                                                  int /*finest_level*/) override
      {
          plog << d_object_name << ": resetHierarchyConfigurationSpecialized()\n";
      }
      void putToDatabaseSpecialized(Pointer<Database> /*db*/) override
      {
          plog << d_object_name << ": putToDatabaseSpecialized()\n";
      }
      void addWorkloadEstimate(Pointer<PatchHierarchy<NDIM> > /*hierarchy*/, const int /*workload_data_idx*/) override
      {
          plog << d_object_name << ": addWorkloadEstimate()\n";
      }
      void executePreprocessIntegrateHierarchyCallbackFcns(double /*current_time*/,
                                                           double /*new_time*/,
                                                           int /*num_cycles*/) override
      {
          plog << d_object_name << ": executePreprocessIntegrateHierarchyCallbackFcns()\n";
      }
  };
  
  void
  generate_structure(const unsigned int& /*strct_num*/,
                     const int& /*ln*/,
                     int& num_vertices,
                     std::vector<IBTK::Point>& vertex_posn)
  {
      num_vertices = 1;
      vertex_posn.resize(num_vertices);
      vertex_posn[0] = Point(0.5, 0.5);
  }
  
  /*******************************************************************************
   * 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);
  
  #ifndef IBTK_HAVE_SILO
      // Suppress warnings caused by running without silo
      SAMRAI::tbox::Logger::getInstance()->setWarning(false);
  #endif
  
      { // cleanup dynamically allocated objects prior to shutdown
        // prevent a warning about timer initialization
          TimerManager::createManager(nullptr);
  
          // 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, "adv_diff.log");
          Pointer<Database> input_db = app_initializer->getInputDatabase();
          Pointer<Database> main_db = app_initializer->getComponentDatabase("Main");
  
          // 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_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<AdvDiffHierarchyIntegrator> adv_diff_integrator =
              new DummyAdvDiffIntegrator("DummyAdvDiff", app_initializer->getComponentDatabase("DummyAdvDiff"));
          Pointer<INSStaggeredHierarchyIntegrator> navier_stokes_integrator = new INSStaggeredHierarchyIntegrator(
              "INSStaggeredHierarchyIntegrator",
              app_initializer->getComponentDatabase("INSStaggeredHierarchyIntegrator"));
          navier_stokes_integrator->registerAdvDiffHierarchyIntegrator(adv_diff_integrator);
          Pointer<IBMethod> ib_method_ops = new IBMethod("IBMethod", app_initializer->getComponentDatabase("IBMethod"));
          Pointer<IBHierarchyIntegrator> time_integrator =
              new IBExplicitHierarchyIntegrator("IBHierarchyIntegrator",
                                                app_initializer->getComponentDatabase("IBHierarchyIntegrator"),
                                                ib_method_ops,
                                                navier_stokes_integrator);
          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);
          // Configure the IB solver.
          Pointer<IBRedundantInitializer> ib_initializer = new IBRedundantInitializer(
              "IBRedundantInitializer", app_initializer->getComponentDatabase("IBRedundantInitializer"));
          std::vector<std::string> struct_list_vec = { "dummy" };
          ib_initializer->setStructureNamesOnLevel(input_db->getInteger("MAX_LEVELS") - 1, struct_list_vec);
          ib_initializer->registerInitStructureFunction(generate_structure);
          ib_method_ops->registerLInitStrategy(ib_initializer);
  
          // Set up visualization plot file writer.
          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);
  
          // Close the restart manager.
          RestartManager::getManager()->closeRestartFile();
  
          // 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();
          }
  
          // 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,
              // and print out timer data.
              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();
              }
              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);
              }
          }
  
      } // cleanup dynamically allocated objects prior to shutdown
  
  } // main
  