From d4a3d19edc9d2b1865370ce8cb3044b1d0541d1e Mon Sep 17 00:00:00 2001
From: Philipp Grete <pgrete@hs.uni-hamburg.de>
Date: Wed, 20 Sep 2023 11:00:46 +0200
Subject: [PATCH] Use prim scalar for AGN extent

---
 src/pgen/cluster.cpp                    |  1 -
 src/pgen/cluster/cluster_reductions.cpp |  2 +-
 src/pgen/cluster/stellar_feedback.cpp   | 16 +++++++++-------
 src/pgen/cluster/stellar_feedback.hpp   |  2 +-
 4 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/src/pgen/cluster.cpp b/src/pgen/cluster.cpp
index 96a781ba..a2b10f7e 100644
--- a/src/pgen/cluster.cpp
+++ b/src/pgen/cluster.cpp
@@ -322,7 +322,6 @@ void ProblemInitPackageData(ParameterInput *pin, parthenon::StateDescriptor *hyd
   const Real agn_tracer_thresh =
       pin->GetOrAddReal("problem/cluster/reductions", "agn_tracer_thresh", -1.0);
   if (agn_tracer_thresh >= 0) {
-    auto mbar_over_kb = hydro_pkg->Param<Real>("mbar_over_kb");
     PARTHENON_REQUIRE(
         pin->GetOrAddBoolean("problem/cluster/agn_feedback", "enable_tracer", false),
         "AGN Tracer must be enabled to reduce AGN tracer extent");
diff --git a/src/pgen/cluster/cluster_reductions.cpp b/src/pgen/cluster/cluster_reductions.cpp
index 0e8c88ed..9e9edb4b 100644
--- a/src/pgen/cluster/cluster_reductions.cpp
+++ b/src/pgen/cluster/cluster_reductions.cpp
@@ -89,7 +89,7 @@ parthenon::Real LocalReduceAGNExtent(parthenon::MeshData<parthenon::Real> *md) {
 
         const auto r2 = SQR(coords.Xc<1>(k, j, i)) + SQR(coords.Xc<2>(k, j, i)) +
                         SQR(coords.Xc<3>(k, j, i));
-        if (cons(nhydro, k, j, i) > tracer_thresh && r2 > max_r2) {
+        if (cons(nhydro, k, j, i) / cons(IDN, k, j, i) > tracer_thresh && r2 > max_r2) {
           max_r2_team = r2;
         }
       },
diff --git a/src/pgen/cluster/stellar_feedback.cpp b/src/pgen/cluster/stellar_feedback.cpp
index db5c6eae..aa130d65 100644
--- a/src/pgen/cluster/stellar_feedback.cpp
+++ b/src/pgen/cluster/stellar_feedback.cpp
@@ -41,22 +41,24 @@ StellarFeedback::StellarFeedback(parthenon::ParameterInput *pin,
                                                   "number_density_threshold", 0.0)),
       temperatue_threshold_(pin->GetOrAddReal("problem/cluster/stellar_feedback",
                                               "temperature_threshold", 0.0)) {
-  if (stellar_radius_ == 0.0 && exclusion_radius_ == 0.0 && efficiency_ == 0.0 && number_density_threshold_ == 0.0 &&
-      temperatue_threshold_ == 0.0) {
+  if (stellar_radius_ == 0.0 && exclusion_radius_ == 0.0 && efficiency_ == 0.0 &&
+      number_density_threshold_ == 0.0 && temperatue_threshold_ == 0.0) {
     disabled_ = true;
   } else {
     disabled_ = false;
   }
 
-  if (!disabled_ && exclusion_radius_ == 0.0){
+  if (!disabled_ && exclusion_radius_ == 0.0) {
     // If exclusion_radius_ is not specified, use AGN triggering accretion radius.
     // If both are zero, the PARTHENON_REQUIRE will fail
-    exclusion_radius_ = pin->GetOrAddReal("problem/cluster/agn_triggering", "accretion_radius", 0);
+    exclusion_radius_ =
+        pin->GetOrAddReal("problem/cluster/agn_triggering", "accretion_radius", 0);
   }
 
-  PARTHENON_REQUIRE(disabled_ || (stellar_radius_ != 0.0 && exclusion_radius_!= 0.0 && efficiency_ != 0.00 &&
-                                  number_density_threshold_ != 0.0 &&
-                                  temperatue_threshold_ != 0.0),
+  PARTHENON_REQUIRE(disabled_ ||
+                        (stellar_radius_ != 0.0 && exclusion_radius_ != 0.0 &&
+                         efficiency_ != 0.00 && number_density_threshold_ != 0.0 &&
+                         temperatue_threshold_ != 0.0),
                     "Enabling stellar feedback requires setting all parameters.");
 
   hydro_pkg->AddParam<StellarFeedback>("stellar_feedback", *this);
diff --git a/src/pgen/cluster/stellar_feedback.hpp b/src/pgen/cluster/stellar_feedback.hpp
index 973716b4..e3d4b20c 100644
--- a/src/pgen/cluster/stellar_feedback.hpp
+++ b/src/pgen/cluster/stellar_feedback.hpp
@@ -26,7 +26,7 @@ class StellarFeedback {
  private:
   // feedback parameters in code units
   const parthenon::Real stellar_radius_;           // length
-  parthenon::Real exclusion_radius_;         // length
+  parthenon::Real exclusion_radius_;               // length
   const parthenon::Real efficiency_;               // dimless
   const parthenon::Real number_density_threshold_; // 1/(length^3)
   const parthenon::Real temperatue_threshold_;     // K