AMReX-Fluids · asalmgren · Sep 14, 2026 · Sep 14, 2026
diff --git a/Source/CAMR.H b/Source/CAMR.H
@@ -388,7 +388,12 @@ protected:
   static void error_setup ();
 
   void expand_state(amrex::MultiFab& S, const amrex::Real time, const int ng);
-  void clean_state(amrex::MultiFab& S);
+
+  // Floor the density and renormalize the species on the valid region, then
+  // recompute T on the valid region plus ng ghost cells.  ng must not exceed
+  // the number of ghost cells that have actually been filled (0 for state
+  // data, numGrow() for Sborder).
+  void clean_state(amrex::MultiFab& S, int ng);
 #ifdef CAMR_USE_MOVING_EB
   void ZeroingOutForPlotting(amrex::MultiFab& S);
 #endif

diff --git a/Source/CAMR.cpp b/Source/CAMR.cpp
@@ -704,7 +704,7 @@ CAMR::post_timestep(int /*iteration*/)
     // Clean up any aberrant state data generated by the reflux and average-down,
     // and then update quantities like temperature to be consistent.
     amrex::MultiFab& S_new_crse = get_new_data(State_Type);
-    clean_state(S_new_crse);
+    clean_state(S_new_crse, 0);
 
 #ifdef AMREX_USE_EB
     // If we redistribute then the ML redistribution algorithm may change
@@ -715,7 +715,7 @@ CAMR::post_timestep(int /*iteration*/)
     if ( level < finest_level && (redistribution_type != "NoRedist") ) {
         CAMR& fine_level = getLevel(level + 1);
         amrex::MultiFab& S_new_fine = fine_level.get_new_data(State_Type);
-        clean_state(S_new_fine);
+        clean_state(S_new_fine, 0);
     }
 #endif
 
@@ -948,15 +948,14 @@ CAMR::enforce_consistent_e(amrex::MultiFab& S)
 void
 CAMR::enforce_min_density(amrex::MultiFab& S_new)
 {
-  // This routine sets the density in S_new to be larger than the density
-  // floor. Note that it will operate everywhere on S_new, including ghost
-  // zones. S_old is present so that, after the hydro call, we know what the old
-  // density was so that we have a reference for comparison. If you are calling
-  // it elsewhere and there's no meaningful reference state, just pass in the
-  // same amrex::MultiFab twice.
-  //  @return  The return value is the the negative fractional change in the
-  // state that has the largest magnitude. If there is no reference state, this
-  // is meaningless.
+  // This routine resets any zone of S_new whose density is below the density
+  // floor. It operates on the valid region only; the ghost cells of S_new are
+  // left untouched.
+  //
+  // A zone below the floor is overwritten with a copy of whichever of its 27
+  // neighbors within the same tile has the highest (pre-reset) density, or, if
+  // no such neighbor reaches the floor, with a state at (small_dens,
+  // small_temp) and zero velocity.
 
 #ifdef AMREX_USE_EB
     auto const& fact = dynamic_cast<amrex::EBFArrayBoxFactory const&>(S_new.Factory());
@@ -1276,18 +1275,21 @@ CAMR::expand_state(amrex::MultiFab& S, const amrex::Real time, const int ng)
 
     AmrLevel::FillPatch(*this,S,ng,time,State_Type,0,S.nComp());
 
-    clean_state(S);
+    clean_state(S, ng);
 }
 
 void
-CAMR::clean_state(amrex::MultiFab& S)
+CAMR::clean_state(amrex::MultiFab& S, int ng)
 {
+  AMREX_ALWAYS_ASSERT(S.nGrow() >= ng);
+
   // Enforce a minimum density.
   enforce_min_density(S);
 
   normalize_species(S);
 
-  int ng = S.nGrow();
+  // Only touch ghost cells the caller has actually filled: the state data
+  // itself carries state_nghost unfilled ghost cells.
   computeTemp(S,ng);
 }
 

diff --git a/Source/CAMR_advance.cpp b/Source/CAMR_advance.cpp
@@ -80,7 +80,7 @@ CAMR::CAMR_advance (Real time,
     // trusted to respect the consistency between certain state variables
     // (e.g. UEINT and UEDEN) that we demand in every zone.
 
-    clean_state(get_old_data(State_Type));
+    clean_state(get_old_data(State_Type), 0);
 
     MultiFab& S_old = get_old_data(State_Type);
     amrex::ignore_unused(S_old);
@@ -158,14 +158,14 @@ CAMR::CAMR_advance (Real time,
     }
 
     // Sync up state after old sources and hydro source.
-    clean_state(S_new);
+    clean_state(S_new, 0);
 
 
     // "new source" is actually the correction to the old source we've already added
     for (int n = 0; n < src_list.size(); ++n) {
         construct_new_source(src_list[n], time, dt);
         MultiFab::Saxpy(S_new, dt, *new_sources[src_list[n]], 0, 0, NVAR, 0);
-        clean_state(S_new);
+        clean_state(S_new, 0);
     }
 
     Sborder.clear();

diff --git a/Source/CAMR_initial_redist.cpp b/Source/CAMR_initial_redist.cpp
diff --git a/Source/Hydro/CAMR_construct_hydro_source.cpp b/Source/Hydro/CAMR_construct_hydro_source.cpp
@@ -166,7 +166,14 @@ CAMR::construct_hydro_source (const MultiFab& S,
            ngrow_bx = 2;
         }
         const Box& bxg_i  = grow(bx,ngrow_bx);
-        if (flagfab.getType(bxg_i) != FabType::regular) {
+
+        // The non-EB kernels used in the fallback read q up to 4 cells outside
+        // bx (flatten: +-3 around the bxg1 ring) and flatten_eb() returns 1
+        // within 3 cells of a cut cell, so the two paths give the same fluxes
+        // on the faces of bx only if grow(bx,4) is entirely regular.  numGrow()
+        // is at least 5 in EB builds, so the flag fab covers this box.
+        const Box& bx_reg = grow(bx, amrex::max(ngrow_bx,4));
+        if (flagfab.getType(bx_reg) != FabType::regular) {
 
             EBFluxRegister* fr_as_crse = nullptr;
             if (do_reflux && level < parent->finestLevel()) {

diff --git a/Source/Utils/CAMR_io.cpp b/Source/Utils/CAMR_io.cpp
@@ -90,13 +90,18 @@ CAMR::setPlotVariables()
 
   amrex::ParmParse pp("CAMR");
 
+  // Species are dropped from the default ("all state variables") plot list
+  // unless plot_rhoy is set.  If the user gave an explicit amr.plot_vars list
+  // and did not say anything about plot_rhoy, honor that list as written
+  // instead of silently removing the species from it.
   bool plot_rhoy = false;
-  pp.query("plot_rhoy", plot_rhoy);
+  const bool have_plot_rhoy = pp.query("plot_rhoy", plot_rhoy);
+  const bool have_plot_vars = amrex::ParmParse("amr").contains("plot_vars");
   if (plot_rhoy) {
     for (int i = 0; i < NUM_SPECIES; i++) {
       amrex::Amr::addStatePlotVar(desc_lst[State_Type].name(UFS + i));
     }
-  } else {
+  } else if (have_plot_rhoy || !have_plot_vars) {
     for (int i = 0; i < NUM_SPECIES; i++) {
       amrex::Amr::deleteStatePlotVar(desc_lst[State_Type].name(UFS + i));
     }

diff --git a/Source/Utils/Tagging.cpp b/Source/Utils/Tagging.cpp
@@ -6,28 +6,28 @@
 void
 CAMR::read_tagging_params()
 {
+  // Nothing in CAMR reads TaggingParm: CAMR::errorEst tags only through the
+  // amr.refinement_indicators mechanism (CAMR_error.cpp).  Rather than query
+  // these keys -- which hides them from AMReX's unused-inputs report and
+  // silently ignores them -- refuse them with a pointer to what works.
   amrex::ParmParse pp("tagging");
 
-  pp.query("denerr", tagging_parm->denerr);
-  pp.query("max_denerr_lev", tagging_parm->max_denerr_lev);
-  pp.query("dengrad", tagging_parm->dengrad);
-  pp.query("max_dengrad_lev", tagging_parm->max_dengrad_lev);
+  static const char* const unsupported[] = {
+    "denerr",   "max_denerr_lev",   "dengrad",   "max_dengrad_lev",
+    "presserr", "max_presserr_lev", "pressgrad", "max_pressgrad_lev",
+    "velerr",   "max_velerr_lev",   "velgrad",   "max_velgrad_lev",
+    "vorterr",  "max_vorterr_lev",
+    "temperr",  "max_temperr_lev",  "tempgrad",  "max_tempgrad_lev",
+    "ftracerr", "max_ftracerr_lev", "ftracgrad", "max_ftracgrad_lev",
+    "vfracerr", "max_vfracerr_lev"};
 
-  pp.query("presserr", tagging_parm->presserr);
-  pp.query("max_presserr_lev", tagging_parm->max_presserr_lev);
-  pp.query("pressgrad", tagging_parm->pressgrad);
-  pp.query("max_pressgrad_lev", tagging_parm->max_pressgrad_lev);
-
-  pp.query("velerr", tagging_parm->velerr);
-  pp.query("max_velerr_lev", tagging_parm->max_velerr_lev);
-  pp.query("velgrad", tagging_parm->velgrad);
-  pp.query("max_velgrad_lev", tagging_parm->max_velgrad_lev);
-
-  pp.query("temperr", tagging_parm->temperr);
-  pp.query("max_temperr_lev", tagging_parm->max_temperr_lev);
-  pp.query("tempgrad", tagging_parm->tempgrad);
-  pp.query("max_tempgrad_lev", tagging_parm->max_tempgrad_lev);
-
-  pp.query("vfracerr", tagging_parm->vfracerr);
-  pp.query("max_vfracerr_lev", tagging_parm->max_vfracerr_lev);
+  for (const char* name : unsupported) {
+    if (pp.contains(name)) {
+      amrex::Abort(std::string("CAMR: input tagging.") + name +
+                   " is not supported -- CAMR::errorEst ignores all tagging.*"
+                   " keys.  Use amr.refinement_indicators with value_greater /"
+                   " value_less / adjacent_difference_greater / vorticity_greater"
+                   " (see Source/Utils/CAMR_error.cpp).");
+    }
+  }
 }
diff --git a/Source/main.cpp b/Source/main.cpp
@@ -116,6 +116,20 @@ main(int argc, char* argv[])
 
   amrptr->init(strt_time, stop_time);
 
+#ifdef CAMR_USE_MOVING_EB
+  {
+    // The geometry is rebuilt at the start of every coarse step; the level
+    // factories only pick it up when every level (level 0 included) is
+    // regridded at the top of that step.
+    int force_regrid_level_zero = 0;
+    amrex::ParmParse ppa("amr");
+    ppa.query("force_regrid_level_zero", force_regrid_level_zero);
+    if (amrptr->regridInt(0) != 1 || !force_regrid_level_zero) {
+      amrex::Abort("CAMR_USE_MOVING_EB requires amr.regrid_int = 1 and amr.force_regrid_level_zero = 1");
+    }
+  }
+#endif
+
   // If we set the regrid_on_restart flag and if we are *not* going to take
   // a time step then we want to go ahead and regrid here.
   if (
@@ -131,12 +145,23 @@ main(int argc, char* argv[])
          (amrptr->levelSteps(0) < max_step || max_step < 0) &&
          (amrptr->cumTime() < stop_time || stop_time < 0.0)) {
 #ifdef CAMR_USE_MOVING_EB
-    initialize_EB2(amrptr->Geom(amrptr->maxLevel()), amrptr->maxLevel(), amrptr->maxLevel(), amrptr->cumTime());
+    // Build the geometry for this step's start time.  The existing levels
+    // still point into the previous index space until the regrid inside
+    // coarseTimeStep replaces them, so it is erased only after the step.
+    // The initial index space (built above at strt_time) serves the first
+    // step, which does not regrid.
+    amrex::EB2::IndexSpace const* old_is = nullptr;
+    if (amrptr->cumTime() > strt_time) {
+      old_is = amrex::EB2::TopIndexSpaceIfPresent();
+      initialize_EB2(amrptr->Geom(amrptr->maxLevel()), amrptr->maxLevel(), amrptr->maxLevel(), amrptr->cumTime());
+    }
 #endif
     // Do a timestep
     amrptr->coarseTimeStep(stop_time);
 #ifdef CAMR_USE_MOVING_EB
-    finalize_EB2();
+    if (old_is) {
+      amrex::EB2::IndexSpace::erase(const_cast<amrex::EB2::IndexSpace*>(old_is));
+    }
 #endif
   }