Merge branch 'development' into new_class_for_gmres

erf-model · Nov 23, 2024 · ceb0eef · ceb0eef
2 parents a628645 + 17bb541
commit ceb0eef
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Showing 4 changed files with 36 additions and 5 deletions.
diff --git a/Exec/Make.ERF b/Exec/Make.ERF
@@ -253,8 +253,14 @@ endif
 #turn on NetCDF macro define
 ifeq ($(USE_NETCDF), TRUE)
   DEFINES += -DERF_USE_NETCDF
-  includes += $(shell pkg-config --cflags netcdf)
-  LIBRARIES += $(shell pkg-config --libs netcdf)
+  has_netcdf_mpi := $(shell pkg-config --cflags netcdf-mpi > /dev/null 2>&1; echo $$?)
+  ifeq ($(has_netcdf_mpi),0)
+    includes += $(shell pkg-config --cflags netcdf-mpi)
+    LIBRARIES += $(shell pkg-config --libs netcdf-mpi)
+  else
+    includes += $(shell pkg-config --cflags netcdf)
+    LIBRARIES += $(shell pkg-config --libs netcdf)
+  endif
 endif
 
 ifeq ($(USE_TERRAIN_VELOCITY), TRUE)

diff --git a/Source/BoundaryConditions/ERF_BoundaryConditions_cons.cpp b/Source/BoundaryConditions/ERF_BoundaryConditions_cons.cpp
@@ -70,7 +70,12 @@ void ERFPhysBCFunct_cons::impose_lateral_cons_bcs (const Array4<Real>& dest_arr,
     {
         Box bx_xlo(bx);  bx_xlo.setBig  (0,dom_lo.x-1);
         Box bx_xhi(bx);  bx_xhi.setSmall(0,dom_hi.x+1);
-
+        //
+        // If we are setting Dirichlet values, set them in all ghost cells on an inflow face
+        // "bx" is already grown in the x- and y-directions so here we just grow it in z
+        //
+        bx_xlo.grow(2,ng[2]);
+        bx_xhi.grow(2,ng[2]);
         ParallelFor(
             bx_xlo, ncomp, [=] AMREX_GPU_DEVICE (int i, int j, int k, int n)
             {
@@ -109,6 +114,12 @@ void ERFPhysBCFunct_cons::impose_lateral_cons_bcs (const Array4<Real>& dest_arr,
     {
         Box bx_ylo(bx);  bx_ylo.setBig  (1,dom_lo.y-1);
         Box bx_yhi(bx);  bx_yhi.setSmall(1,dom_hi.y+1);
+        //
+        // If we are setting Dirichlet values, set them in all ghost cells on an inflow face
+        // "bx" is already grown in the x- and y-directions so here we just grow it in z
+        //
+        bx_ylo.grow(2,ng[2]);
+        bx_yhi.grow(2,ng[2]);
 
         ParallelFor(
             bx_ylo, ncomp, [=] AMREX_GPU_DEVICE (int i, int j, int k, int n)

diff --git a/Source/Diffusion/ERF_ComputeTurbulentViscosity.cpp b/Source/Diffusion/ERF_ComputeTurbulentViscosity.cpp
@@ -189,12 +189,12 @@ void ComputeTurbulentViscosityLES (const MultiFab& Tau11, const MultiFab& Tau22,
                                       - cell_data(i,j,k-1,RhoTheta_comp)/cell_data(i,j,k-1,Rho_comp) )*dzInv;
                 }
                 Real E              = amrex::max(cell_data(i,j,k,RhoKE_comp)/cell_data(i,j,k,Rho_comp),Real(0.0));
-                Real stratification = l_abs_g * dtheta_dz * l_inv_theta0; // stratification
+                Real stratification = l_abs_g * dtheta_dz * l_inv_theta0;
                 Real length;
                 if (stratification <= eps) {
                     length = DeltaMsf;
                 } else {
-                    length = 0.76 * std::sqrt(E / stratification);
+                    length = 0.76 * std::sqrt(E / amrex::max(stratification,eps));
                     // mixing length should be _reduced_ for stable stratification
                     length = amrex::min(length, DeltaMsf);
                     // following WRF, make sure the mixing length isn't too small

diff --git a/Source/SourceTerms/ERF_ApplySpongeZoneBCs.cpp b/Source/SourceTerms/ERF_ApplySpongeZoneBCs.cpp
@@ -27,6 +27,13 @@ ApplySpongeZoneBCsForCC (
     const int use_yhi_sponge_damping = spongeChoice.use_yhi_sponge_damping;
     const int use_zlo_sponge_damping = spongeChoice.use_zlo_sponge_damping;
     const int use_zhi_sponge_damping = spongeChoice.use_zhi_sponge_damping;
+    if (!use_xlo_sponge_damping &&
+        !use_xhi_sponge_damping &&
+        !use_ylo_sponge_damping &&
+        !use_yhi_sponge_damping &&
+        !use_zlo_sponge_damping &&
+        !use_zhi_sponge_damping)
+        return;
 
     const Real xlo_sponge_end   = spongeChoice.xlo_sponge_end;
     const Real xhi_sponge_start = spongeChoice.xhi_sponge_start;
@@ -136,6 +143,13 @@ ApplySpongeZoneBCsForMom (
     const int use_yhi_sponge_damping = spongeChoice.use_yhi_sponge_damping;
     const int use_zlo_sponge_damping = spongeChoice.use_zlo_sponge_damping;
     const int use_zhi_sponge_damping = spongeChoice.use_zhi_sponge_damping;
+    if (!use_xlo_sponge_damping &&
+        !use_xhi_sponge_damping &&
+        !use_ylo_sponge_damping &&
+        !use_yhi_sponge_damping &&
+        !use_zlo_sponge_damping &&
+        !use_zhi_sponge_damping)
+        return;
 
     const Real xlo_sponge_end   = spongeChoice.xlo_sponge_end;
     const Real xhi_sponge_start = spongeChoice.xhi_sponge_start;