From ae07d35632a7e42fd0fd9da5faf7f118f80bf770 Mon Sep 17 00:00:00 2001
From: Eliot Quon <eliot.quon@nrel.gov>
Date: Wed, 3 Jan 2024 22:53:48 -0700
Subject: [PATCH] Fix GABLS1 case, do some minor code cleanup (#1359)

* Update inputs doc for clarity

* Update prob info

* Make header and source var names consistent

* Fix misleading comment

* GABLS1 should be dry
---
 Docs/sphinx_doc/Inputs.rst      | 6 +++---
 Exec/RegTests/GABLS1/prob.H     | 6 +++++-
 Exec/RegTests/GABLS1/prob.cpp   | 9 +++++++--
 Source/Advection/Advection.H    | 4 ++--
 Source/DataStructs/DataStruct.H | 2 +-
 5 files changed, 18 insertions(+), 9 deletions(-)

diff --git a/Docs/sphinx_doc/Inputs.rst b/Docs/sphinx_doc/Inputs.rst
index fed1b0655..5fdaf7cc1 100644
--- a/Docs/sphinx_doc/Inputs.rst
+++ b/Docs/sphinx_doc/Inputs.rst
@@ -670,11 +670,11 @@ If we set ``erf.molec_diff_type`` to ``ConstantAlpha``, then
 - the dynamic viscosity in the momentum equation is assumed to have the form :math:`\mu = \rho \alpha_M`
   where :math:`\alpha_M` is a momentum diffusivity constant with units of kinematic viscosity, calculated as
   ``erf.dynamicViscosity`` divided by ``erf.rho0_trans``;
-  this diffusivity is multiplied by the current density :math:`\rho` to form the coefficient in the momentum equation; and
+  this diffusivity is multiplied by the instantaneous local density :math:`\rho` to form the coefficient in the momentum equation; and
 
-- ``erf.alpha_T`` is multiplied by the current density :math:`\rho` to form the coefficient for potential temperature, and
+- ``erf.alpha_T`` is multiplied by the instantaneous local density :math:`\rho` to form the coefficient for potential temperature, and
 
-- ``erf.alpha_C`` is multiplied by the current density :math:`\rho` to form the coefficient for an advected scalar.
+- ``erf.alpha_C`` is multiplied by the instantaneous local density :math:`\rho` to form the coefficient for an advected scalar.
 
 
 PBL Scheme
diff --git a/Exec/RegTests/GABLS1/prob.H b/Exec/RegTests/GABLS1/prob.H
index ebb4d529f..cf5db4fc1 100644
--- a/Exec/RegTests/GABLS1/prob.H
+++ b/Exec/RegTests/GABLS1/prob.H
@@ -1,6 +1,10 @@
 #ifndef _PROB_H_
 #define _PROB_H_
 
+/* Based on ABL problem
+ * - initial QKE based on specified initial TKE profile
+ */
+
 #include <string>
 
 #include "AMReX_REAL.H"
@@ -69,7 +73,7 @@ public:
         const SolverChoice& sc) override;
 
 protected:
-    std::string name() override { return "ABL"; }
+    std::string name() override { return "ABL-GABLS1"; }
 
 private:
     ProbParm parms;
diff --git a/Exec/RegTests/GABLS1/prob.cpp b/Exec/RegTests/GABLS1/prob.cpp
index 748b65691..5aed34a33 100644
--- a/Exec/RegTests/GABLS1/prob.cpp
+++ b/Exec/RegTests/GABLS1/prob.cpp
@@ -63,6 +63,9 @@ Problem::init_custom_pert(
     const SolverChoice& sc)
 {
     const bool use_moisture = (sc.moisture_type != MoistureType::None);
+    if (use_moisture) {
+        amrex::Print() << "Note: GABLS1 is a dry case" << std::endl;
+    }
 
   if (state.nComp() > RhoQKE_comp) {
     amrex::Print() << "Initializing QKE" << std::endl;
@@ -121,8 +124,10 @@ Problem::init_custom_pert(
         }
     }
 
-    state(i, j, k, RhoQ1_comp) = 0.0;
-    state(i, j, k, RhoQ2_comp) = 0.0;
+    if (use_moisture) {
+        state(i, j, k, RhoQ1_comp) = 0.0;
+        state(i, j, k, RhoQ2_comp) = 0.0;
+    }
   });
 
   // Set the x-velocity
diff --git a/Source/Advection/Advection.H b/Source/Advection/Advection.H
index d09dd1537..b859bea48 100644
--- a/Source/Advection/Advection.H
+++ b/Source/Advection/Advection.H
@@ -21,7 +21,7 @@ void AdvectionSrcForRho (const amrex::Box& bx,
                          const amrex::Array4<      amrex::Real>& avg_zmom,
                          const amrex::Array4<const amrex::Real>& z_nd,
                          const amrex::Array4<const amrex::Real>& detJ,
-                         const amrex::GpuArray<amrex::Real, AMREX_SPACEDIM>& cellSize,
+                         const amrex::GpuArray<amrex::Real, AMREX_SPACEDIM>& cellSizeInv,
                          const amrex::Array4<const amrex::Real>& mf_m,
                          const amrex::Array4<const amrex::Real>& mf_u,
                          const amrex::Array4<const amrex::Real>& mf_v,
@@ -37,7 +37,7 @@ void AdvectionSrcForScalars (const amrex::Box& bx,
                              const amrex::Array4<const amrex::Real>& cell_prim,
                              const amrex::Array4<amrex::Real>& src,
                              const amrex::Array4<const amrex::Real>& detJ,
-                             const amrex::GpuArray<amrex::Real, AMREX_SPACEDIM>& cellSize,
+                             const amrex::GpuArray<amrex::Real, AMREX_SPACEDIM>& cellSizeInv,
                              const amrex::Array4<const amrex::Real>& mf_m,
                              const AdvType horiz_adv_type, const AdvType vert_adv_type,
                              const bool use_terrain,
diff --git a/Source/DataStructs/DataStruct.H b/Source/DataStructs/DataStruct.H
index 2192f266a..08df800fb 100644
--- a/Source/DataStructs/DataStruct.H
+++ b/Source/DataStructs/DataStruct.H
@@ -206,7 +206,7 @@ struct SolverChoice {
             turbChoice[lev].init_params(lev,max_level);
         }
 
-        // If running LES/PBL then must use "ConstantAlpha"
+        // If running LES/PBL then molecular diffusion must be "Constant" or "None"
         for (int lev = 0; lev <= max_level; lev++) {
             if (turbChoice[lev].les_type != LESType::None) {
                 if ( diffChoice.molec_diff_type == MolecDiffType::ConstantAlpha ) {