Mahesh's changes for extrema threshold

Author: n8xm

Source/Driver/Nyx.H

@@ -996,6 +996,10 @@ protected:
   // Seed mass of SMBH
   //
   static amrex::Real mass_seed;
+
+  static int min_halo_n_cells;
+  static amrex::Real halo_component_threshold;
+  static amrex::Real halo_extrema_threshold;
 #endif
 
   // Previous maximum number of steps for sundials

Source/Driver/Nyx.cpp

@@ -204,6 +204,9 @@ Real Nyx::he_species        = 0.24;
 #ifdef REEBER
 Real Nyx::mass_halo_min     = 1.e10;
 Real Nyx::mass_seed         = 1.e5;
+Real Nyx::halo_component_threshold = 81.66;
+Real Nyx::halo_extrema_threshold = 160.0;
+int Nyx::min_halo_n_cells = 10;
 #endif
 
 #ifdef _OPENMP
@@ -445,6 +448,10 @@ Nyx::read_params ()
 #ifdef REEBER
     pp_nyx.query("mass_halo_min", mass_halo_min);
     pp_nyx.query("mass_seed", mass_seed);
+	ParmParse pp_reeber("reeber");
+    pp_reeber.query("min_halo_n_cells", min_halo_n_cells);
+    pp_reeber.query("halo_component_threshold", halo_component_threshold);
+    pp_reeber.query("halo_extrema_threshold", halo_extrema_threshold);
 #endif
 }
 

Source/IO/Nyx_output.cpp

@@ -1070,7 +1070,7 @@ Nyx::forcing_check_point (const std::string& dir)
 int
 Nyx::updateInSitu ()
 {
-#if defined(BL_USE_SENSEI_INSITU) || defined(AMREX_USE_ASCENT)
+#if defined(BL_USE_SENSEI_INSITU) || defined(AMREX_USE_ASCENT) || defined(REEBER)
     BL_PROFILE("Nyx::UpdateInSitu()");
 
 #if defined(BL_USE_SENSEI_INSITU)

Util/reeber/src/reeber.cpp

@@ -395,7 +395,8 @@ std::vector<Halo> compute_halos(diy::mpi::communicator& world,
                                 diy::DiscreteBounds diy_domain,
                                 Real absolute_rho,
                                 bool negate,
-                                Real min_halo_n_cells)
+                                Real min_halo_n_cells,
+                                Real halo_extrema_threshold)
 {
     bool debug = false; //world.rank() == 0;
     std::string prefix = "./DIY.XXXXXX";
@@ -467,9 +468,9 @@ std::vector<Halo> compute_halos(diy::mpi::communicator& world,
 
     }
 
-    master.foreach([](Block* b, const diy::Master::ProxyWithLink& cp) {
+    master.foreach([halo_extrema_threshold](Block* b, const diy::Master::ProxyWithLink& cp) {
         b->compute_final_connected_components();
-        b->compute_local_integral();
+        b->compute_local_integral(halo_extrema_threshold);
     });
 
     //if (debug) fmt::print(std::cerr, "Local integrals computed");
@@ -598,9 +599,7 @@ void Nyx::runReeberAnalysis(Vector<MultiFab*>& new_state,
 
     diy::DiscreteBounds diy_domain(3);
 
-    // TODO: take rho, min_halo_n_cells as parameters
-    Real min_halo_n_cells = 10;
-    Real rho = 81.66;
+	Real rho = halo_component_threshold;
 
     Real absolute_rho = (Nyx::average_dm_density + Nyx::average_gas_density) * rho;
     bool negate = true;  // sweep superlevel sets, highest density = root
@@ -619,7 +618,7 @@ void Nyx::runReeberAnalysis(Vector<MultiFab*>& new_state,
 
     BL_PROFILE_VAR("Nyx::runReeberAnalysis()::compute_halos",compute_halos_var);
 
-    reeber_halos = compute_halos(world, master_reader, geom_in, threads, diy_domain, absolute_rho, negate, min_halo_n_cells);
+    reeber_halos = compute_halos(world, master_reader, geom_in, threads, diy_domain, absolute_rho, negate, min_halo_n_cells, halo_extrema_threshold);
     if (verbose and world.rank() == 0) fmt::print(std::cerr, "compute_halos finished, result.size = {}\n", reeber_halos.size());
 
     BL_PROFILE_VAR_STOP(compute_halos_var);