Merge branch 'pr1283' into gabls2_before_merge_c0a1c9f

ewquon · Dec 15, 2023 · 847edb2 · 847edb2
2 parents 663583b + e8b228e
commit 847edb2
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Showing 27 changed files with 625 additions and 659 deletions.
diff --git a/CHANGES b/CHANGES
@@ -1,3 +1,16 @@
+#23.11
+
+  -- AMReX submodule set to 23.11 release hash (ae7b64b)
+
+  -- Bug fix with vertical grid stretching and MOST (#1275)
+
+  -- Bug fix with negative K_turb below surface and MYNN2.5 PBL model (#1271)
+
+  -- Correction to equation of state with moisture (#1263)
+
+  -- Generalized multi-level sponge zones. This allows for nudging of fine solution
+     towards coarse solution with complex box arrays. (#1233)
+
 # 23.10
 
   -- First release since JOSS paper. Too many key ERF PRs to summarize.

diff --git a/Source/BoundaryConditions/MOSTStress.H b/Source/BoundaryConditions/MOSTStress.H
@@ -149,7 +149,7 @@ struct adiabatic_charnock
 private:
     most_data mdata;
     similarity_funs sfuns;
-    amrex::Real tol = 1.0e-5;
+    const amrex::Real tol = 1.0e-5;
 };
 
 
@@ -202,7 +202,7 @@ struct adiabatic_mod_charnock
 private:
     most_data mdata;
     similarity_funs sfuns;
-    amrex::Real tol = 1.0e-5;
+    const amrex::Real tol = 1.0e-5;
 };
 
 
@@ -260,7 +260,7 @@ struct surface_flux
 private:
     most_data mdata;
     similarity_funs sfuns;
-    amrex::Real tol = 1.0e-5;
+    const amrex::Real tol = 1.0e-5;
 };
 
 
@@ -323,7 +323,7 @@ struct surface_flux_charnock
 private:
     most_data mdata;
     similarity_funs sfuns;
-    amrex::Real tol = 1.0e-5;
+    const amrex::Real tol = 1.0e-5;
 };
 
 
@@ -387,7 +387,7 @@ struct surface_flux_mod_charnock
 private:
     most_data mdata;
     similarity_funs sfuns;
-    amrex::Real tol = 1.0e-5;
+    const amrex::Real tol = 1.0e-5;
 };
 
 
@@ -447,7 +447,7 @@ struct surface_temp
 private:
     most_data mdata;
     similarity_funs sfuns;
-    amrex::Real tol = 1.0e-5;
+    const amrex::Real tol = 1.0e-5;
 };
 
 
@@ -512,7 +512,7 @@ struct surface_temp_charnock
 private:
     most_data mdata;
     similarity_funs sfuns;
-    amrex::Real tol = 1.0e-5;
+    const amrex::Real tol = 1.0e-5;
 };
 
 
@@ -578,7 +578,7 @@ struct surface_temp_mod_charnock
 private:
     most_data mdata;
     similarity_funs sfuns;
-    amrex::Real tol = 1.0e-5;
+    const amrex::Real tol = 1.0e-5;
 };
 
 
@@ -639,6 +639,7 @@ struct moeng_flux
         rho   = cons_arr(ic,jc,zlo,Rho_comp);
         theta = cons_arr(ic,jc,zlo,RhoTheta_comp) / rho;
         eta   = eta_arr(ie,je,zlo,EddyDiff::Theta_v); // == rho * alpha [kg/m^3 * m^2/s]
+        eta   = amrex::max(eta,eps);
 
         amrex::Real theta_mean  = tm_arr(ic,jc,zlo);
         amrex::Real wsp_mean    = umm_arr(ic,jc,zlo);
@@ -649,7 +650,7 @@ struct moeng_flux
         amrex::Real wsp     = sqrt(velx*velx+vely*vely);
         amrex::Real num1    = (theta-theta_mean)*wsp_mean;
         amrex::Real num2    = (theta_mean-theta_surf)*wsp;
-        amrex::Real moflux  = (std::abs(tstar) > EPS) ?
+        amrex::Real moflux  = (std::abs(tstar) > eps) ?
                               tstar*ustar*(num1+num2)/((theta_mean-theta_surf)*wsp_mean) : 0.0;
         amrex::Real deltaz  = dz * (zlo - k);
 
@@ -700,6 +701,7 @@ struct moeng_flux
                      + cons_arr(ic  ,jc,zlo,Rho_comp) );
         eta   = 0.5 *(  eta_arr(ie-1,je,zlo,EddyDiff::Mom_v)
                       + eta_arr(ie  ,je,zlo,EddyDiff::Mom_v) );
+        eta   = amrex::max(eta,eps);
 
         amrex::Real umean    = um_arr(i,j,zlo);
         amrex::Real wsp_mean = 0.5 * ( umm_arr(ic-1,jc,zlo) + umm_arr(ic,jc,zlo) );
@@ -763,6 +765,7 @@ struct moeng_flux
                     + cons_arr(ic,jc  ,zlo,Rho_comp) );
         eta   = 0.5*(  eta_arr(ie,je-1,zlo,EddyDiff::Mom_v)
                      + eta_arr(ie,je  ,zlo,EddyDiff::Mom_v) );
+        eta   = amrex::max(eta,eps);
 
         amrex::Real vmean     = vm_arr(i,j,zlo);
         amrex::Real wsp_mean  = 0.5 * ( umm_arr(ic,jc-1,zlo) + umm_arr(ic,jc,zlo) );
@@ -784,7 +787,7 @@ struct moeng_flux
 
 private:
     int zlo;
-    static constexpr amrex::Real EPS = 1e-16;
+    const amrex::Real eps = 1e-16;
 };
 
 
@@ -833,6 +836,7 @@ struct donelan_flux
         rho   = cons_arr(ic,jc,zlo,Rho_comp);
         theta = cons_arr(ic,jc,zlo,RhoTheta_comp) / rho;
         eta   =  eta_arr(ie,je,zlo,EddyDiff::Theta_v); // == rho * alpha [kg/m^3 * m^2/s]
+        eta   = amrex::max(eta,eps);
 
         amrex::Real Cd = 0.0012;
         amrex::Real wsp_mean    = umm_arr(ic,jc,zlo);
@@ -888,6 +892,7 @@ struct donelan_flux
                      + cons_arr(ic  ,jc,zlo,Rho_comp) );
         eta   = 0.5 *(  eta_arr(ie-1,je,zlo,EddyDiff::Mom_v)
                       + eta_arr(ie  ,je,zlo,EddyDiff::Mom_v) );
+        eta   = amrex::max(eta,eps);
 
         amrex::Real Cd       = 0.001;
         const amrex::Real c  = 7e-5;
@@ -955,6 +960,7 @@ struct donelan_flux
                     + cons_arr(ic,jc  ,zlo,Rho_comp) );
         eta   = 0.5*(  eta_arr(ie,je-1,zlo,EddyDiff::Mom_v)
                      + eta_arr(ie,je  ,zlo,EddyDiff::Mom_v) );
+        eta   = amrex::max(eta,eps);
 
         amrex::Real Cd       = 0.001;
         const amrex::Real c  = 7e-5;
@@ -980,5 +986,6 @@ struct donelan_flux
 
 private:
     int zlo;
+    const amrex::Real eps = 1e-16;
 };
 #endif
diff --git a/Source/Derive.H b/Source/Derive.H
@@ -6,13 +6,13 @@
 
 namespace derived {
 
-void erf_derrhodivide(
+void erf_derrhodivide (
   const amrex::Box& bx,
   amrex::FArrayBox& derfab,
   const amrex::FArrayBox& datfab,
   const int scalar_index);
 
-void erf_dernull(
+void erf_dernull (
   const amrex::Box& bx,
   amrex::FArrayBox& derfab,
   int dcomp,
@@ -23,7 +23,7 @@ void erf_dernull(
   const int* bcrec,
   const int level);
 
-void erf_derpres(
+void erf_derpres (
   const amrex::Box& bx,
   amrex::FArrayBox& derfab,
   int dcomp,
@@ -34,7 +34,7 @@ void erf_derpres(
   const int* bcrec,
   const int level);
 
-void erf_dersoundspeed(
+void erf_dersoundspeed (
   const amrex::Box& bx,
   amrex::FArrayBox& derfab,
   int dcomp,
@@ -45,7 +45,7 @@ void erf_dersoundspeed(
   const int* bcrec,
   const int level);
 
-void erf_dertemp(
+void erf_dertemp (
   const amrex::Box& bx,
   amrex::FArrayBox& derfab,
   int dcomp,
@@ -56,7 +56,7 @@ void erf_dertemp(
   const int* bcrec,
   const int level);
 
-void erf_dertheta(
+void erf_dertheta (
   const amrex::Box& bx,
   amrex::FArrayBox& derfab,
   int dcomp,
@@ -67,7 +67,7 @@ void erf_dertheta(
   const int* bcrec,
   const int level);
 
-void erf_derscalar(
+void erf_derscalar (
   const amrex::Box& bx,
   amrex::FArrayBox& derfab,
   int dcomp,
@@ -78,7 +78,7 @@ void erf_derscalar(
   const int* bcrec,
   const int level);
 
-void erf_derKE(
+void erf_derKE (
   const amrex::Box& bx,
   amrex::FArrayBox& derfab,
   int dcomp,
@@ -89,7 +89,7 @@ void erf_derKE(
   const int* bcrec,
   const int level);
 
-void erf_derQKE(
+void erf_derQKE (
   const amrex::Box& bx,
   amrex::FArrayBox& derfab,
   int dcomp,
@@ -101,7 +101,7 @@ void erf_derQKE(
   const int level);
 
 #if defined(ERF_USE_MOISTURE)
-void erf_derQt(
+void erf_derQt (
   const amrex::Box& bx,
   amrex::FArrayBox& derfab,
   int dcomp,
@@ -112,7 +112,7 @@ void erf_derQt(
   const int* bcrec,
   const int level);
 
-void erf_derQp(
+void erf_derQp (
   const amrex::Box& bx,
   amrex::FArrayBox& derfab,
   int dcomp,
@@ -123,7 +123,7 @@ void erf_derQp(
   const int* bcrec,
   const int level);
 #elif defined(ERF_USE_WARM_NO_PRECIP)
-void erf_derQv(
+void erf_derQv (
   const amrex::Box& bx,
   amrex::FArrayBox& derfab,
   int dcomp,
@@ -133,7 +133,7 @@ void erf_derQv(
   amrex::Real time,
   const int* bcrec,
   const int level);
-void erf_derQc(
+void erf_derQc (
   const amrex::Box& bx,
   amrex::FArrayBox& derfab,
   int dcomp,

diff --git a/Source/Derive.cpp b/Source/Derive.cpp
@@ -13,7 +13,7 @@ namespace derived {
  * @params[in] datfab array of data used to construct derived quantity
  * @params[in] scalar_index index of quantity to be divided by density
 */
-void erf_derrhodivide(
+void erf_derrhodivide (
   const amrex::Box& bx,
   amrex::FArrayBox& derfab,
   const amrex::FArrayBox& datfab,
@@ -34,7 +34,7 @@ void erf_derrhodivide(
  * Placeholder function that does nothing
 */
 void
-erf_dernull(
+erf_dernull (
   const amrex::Box& /*bx*/,
   amrex::FArrayBox& /*derfab*/,
   int /*dcomp*/,
@@ -54,7 +54,7 @@ erf_dernull(
  * @params[in] datfab array of data used to construct derived quantity
 */
 void
-erf_derpres(
+erf_derpres (
   const amrex::Box& bx,
   amrex::FArrayBox& derfab,
   int /*dcomp*/,
@@ -92,7 +92,7 @@ erf_derpres(
  * @params[in] datfab array of data used to construct derived quantity
 */
 void
-erf_dersoundspeed(
+erf_dersoundspeed (
   const amrex::Box& bx,
   amrex::FArrayBox& derfab,
   int /*dcomp*/,
@@ -125,7 +125,7 @@ erf_dersoundspeed(
  * @params[in] datfab array of data used to construct derived quantity
 */
 void
-erf_dertemp(
+erf_dertemp (
   const amrex::Box& bx,
   amrex::FArrayBox& derfab,
   int /*dcomp*/,
@@ -155,7 +155,7 @@ erf_dertemp(
  * @params[in] datfab array of data used to construct derived quantity
 */
 void
-erf_dertheta(
+erf_dertheta (
   const amrex::Box& bx,
   amrex::FArrayBox& derfab,
   int /*dcomp*/,
@@ -177,7 +177,7 @@ erf_dertheta(
  * @params[in] datfab array of data used to construct derived quantity
 */
 void
-erf_derscalar(
+erf_derscalar (
   const amrex::Box& bx,
   amrex::FArrayBox& derfab,
   int /*dcomp*/,
@@ -199,7 +199,7 @@ erf_derscalar(
  * @params[in] datfab array of data used to construct derived quantity
 */
 void
-erf_derKE(
+erf_derKE (
   const amrex::Box& bx,
   amrex::FArrayBox& derfab,
   int /*dcomp*/,
@@ -221,7 +221,7 @@ erf_derKE(
  * @params[in] datfab array of data used to construct derived quantity
 */
 void
-erf_derQKE(
+erf_derQKE (
   const amrex::Box& bx,
   amrex::FArrayBox& derfab,
   int /*dcomp*/,
@@ -244,7 +244,7 @@ erf_derQKE(
  * @params[in] datfab array of data used to construct derived quantity
 */
 void
-erf_derQt(
+erf_derQt (
   const amrex::Box& bx,
   amrex::FArrayBox& derfab,
   int /*dcomp*/,
@@ -266,7 +266,7 @@ erf_derQt(
  * @params[in] datfab array of data used to construct derived quantity
 */
 void
-erf_derQp(
+erf_derQp (
   const amrex::Box& bx,
   amrex::FArrayBox& derfab,
   int /*dcomp*/,
@@ -288,7 +288,7 @@ erf_derQp(
  * @params[in] datfab array of data used to construct derived quantity
 */
 void
-erf_derQv(
+erf_derQv (
   const amrex::Box& bx,
   amrex::FArrayBox& derfab,
   int /*dcomp*/,
@@ -309,7 +309,7 @@ erf_derQv(
  * @params[in] datfab array of data used to construct derived quantity
 */
 void
-erf_derQc(
+erf_derQc (
   const amrex::Box& bx,
   amrex::FArrayBox& derfab,
   int /*dcomp*/,