Reeber param input doc

Docs/sphinx_documentation/source/AGN.rst

@@ -188,10 +188,8 @@ Parameter                           Definition                          Acceptab
 =================================== =================================== ===================================== =========
 **reeber.halo_int**                 timesteps between halo finder calls Integer                               -1 (none)
 **reeber.negate**                   allow negative values for analysis  0 if false, 1 if true                 1
-**reeber.halo_density_vars**        density variable list               density, particle_mass_density        “density”
-**reeber.halo_extrema_threshold**   extrema threshold for haloes        Real                                  200.
-**reeber.halo_component_threshold** component threshold for haloes      Real                                  82.
-**reeber.absolute_halo_thresholds** are halo thresholds absolute        0 if multiples of mean, 1 if absolute 0
+**reeber.halo_component_threshold** component threshold for haloes      Real                                  81.66
+**reeber.min_halo_n_cells**         min. number of halo cells           Integer                               10
 =================================== =================================== ===================================== =========
 
 [Table:Reeber-inputs]

Docs/sphinx_documentation/source/InSitu.rst

@@ -56,16 +56,16 @@ Note that these codes are in separate repositories and are not included in Nyx d
 If you intend to use in situ halo finding, you should clone Reeber from its
 `GitHub page <https://github.com/mrzv/reeber>`_ and follow the installation instructions provided there.
 
-In the Nyx inputs file, one should specify the time step interval for halo finder, fields which will be
-used (to use the total density, one should specify both (gas) ``density`` and ``particle_mass_density``),
-and thresholds of the boundary and extrema values::
+.. In the Nyx inputs file, one should specify the time step interval for halo finder, fields which will be
+.. used (to use the total density, one should specify both (gas) ``density`` and ``particle_mass_density``),
+.. and thresholds of the boundary and extrema values::
+In the Nyx inputs file, one should specify the time step interval for the halo finder, whether to permit negative values for analysis, the boundary isovalue threshold, and the minimum number of cells required for a region to be considered a halo::
 
   # Halo Finder
   reeber.halo_int = 1
   reeber.negate = 1
-  reeber.halo_density_vars = density particle_mass_density
-  reeber.halo_extrema_threshold = 20
   reeber.halo_component_threshold = 10
+  reeber.min_n_halo_cells = 10
 
   # Call reeber insitu analysis
   insitu.reeber_int = 100

Exec/LyA/inputs

@@ -1,6 +1,9 @@
 # ------------------  INPUTS TO MAIN PROGRAM  -------------------
 max_step = 10000000
 
+# use managed memory
+amrex.the_arena_is_managed=1
+
 nyx.ppm_type         = 1
 nyx.use_colglaz      = 0
 nyx.corner_coupling  = 1
@@ -140,12 +143,11 @@ nyx.plot_z_values   = 7.0 6.0 5.0 4.0 3.0 2.0
 amr.plot_vars        = density xmom ymom zmom rho_e Temp phi_grav
 amr.derive_plot_vars = particle_mass_density particle_count
 
-# Halo Finder
-#nyx.analysis_z_values = 150 10 5 4 3 2
-reeber.halo_int = 1
+# Halo finder
+reeber.min_halo_n_cells = 10
 reeber.negate = 1
-reeber.halo_density_vars = density particle_mass_density
-reeber.halo_extrema_threshold = 20
+#reeber.halo_density_vars = density particle_mass_density
+#reeber.halo_extrema_threshold = 20
 reeber.halo_component_threshold = 10
 #nyx.mass_halo_min = 1.e11
 #nyx.mass_seed = 1.e6

Source/Driver/Nyx.H

@@ -996,6 +996,11 @@ protected:
   // Seed mass of SMBH
   //
   static amrex::Real mass_seed;
+
+  static int min_halo_n_cells;
+  static bool halo_negate;
+  static amrex::Real halo_component_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;
+int Nyx::min_halo_n_cells = 10;
+bool Nyx::halo_negate = true;
 #endif
 
 #ifdef _OPENMP
@@ -445,6 +448,11 @@ 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("negate", halo_negate);
 #endif
 }
 

Util/reeber/src/reeber.cpp

@@ -598,10 +598,7 @@ 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
     int finest_level = parent->finestLevel();