From cba91e4e46a4a0d611620d10680e1dce5b92ecbd Mon Sep 17 00:00:00 2001
From: "Xiaqiong.Zhou" <Xiaqiong.Zhou@noaa.gov>
Date: Tue, 23 Apr 2024 15:01:59 -0500
Subject: [PATCH 1/7] Point dycore to personal branch

---
 .gitmodules        | 4 ++--
 atmos_cubed_sphere | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 22c723ac1..a32a46cd3 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,7 +1,7 @@
 [submodule "atmos_cubed_sphere"]
   path = atmos_cubed_sphere
-  url = https://github.com/NOAA-GFDL/GFDL_atmos_cubed_sphere
-  branch = dev/emc
+  url = https://github.com/XiaqiongZhou-NOAA/GFDL_atmos_cubed_sphere
+  branch = hydro
 [submodule "ccpp/framework"]
   path = ccpp/framework
   url = https://github.com/NCAR/ccpp-framework
diff --git a/atmos_cubed_sphere b/atmos_cubed_sphere
index 97114888f..aabfdccae 160000
--- a/atmos_cubed_sphere
+++ b/atmos_cubed_sphere
@@ -1 +1 @@
-Subproject commit 97114888f529c2df70ed4a350fd2428df74839ff
+Subproject commit aabfdccae440da7389195762601db7fcc09f6f11

From 2bdfa00b6010d37b05ddaecd783950c66ed2724e Mon Sep 17 00:00:00 2001
From: "Xiaqiong.Zhou" <Xiaqiong.Zhou@noaa.gov>
Date: Tue, 23 Apr 2024 15:14:26 -0500
Subject: [PATCH 2/7] Remove -DUSE_COND and -DMOIST_CAPPA compiling flags for
 hydrostatic runs; Fix the issue to write out omga and geopotential height for
 inline post

---
 CMakeLists.txt      |  9 +++++++-
 ccpp/CMakeLists.txt |  4 +++-
 io/post_fv3.F90     | 51 +++++++++++++++++++++++++++++++--------------
 3 files changed, 46 insertions(+), 18 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index c310110ca..a497fd3bb 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -37,6 +37,9 @@ set(USE_GFSL63  ON)
 if(MOVING_NEST)
   set(MOVING_NEST ON)
 endif()
+if(HYDRO)
+  set(HYDRO ON)
+endif()
 add_subdirectory(atmos_cubed_sphere)
 target_compile_definitions(fv3 PRIVATE BYPASS_BREED_SLP_INLINE)
 
@@ -61,7 +64,11 @@ if(NOT PARALLEL_NETCDF)
 endif()
 
 if(MOVING_NEST)
-  list(APPEND _fv3atm_defs_private MOVING_NEST MOIST_CAPPA USE_COND)
+  list(APPEND _fv3atm_defs_private MOVING_NEST)
+  if (NOT HYDRO)
+    list(APPEND _fv3atm_defs_private MOIST_CAPPA USE_COND)
+  endif()
+
   if(DEBUG)
     list(APPEND _fv3atm_defs_private DEBUG)
   endif()
diff --git a/ccpp/CMakeLists.txt b/ccpp/CMakeLists.txt
index ee2b9c8b2..53f9f0023 100644
--- a/ccpp/CMakeLists.txt
+++ b/ccpp/CMakeLists.txt
@@ -84,8 +84,10 @@ endif(CCPP_32BIT)
 
 #------------------------------------------------------------------------------
 # Add model-specific flags for C/C++/Fortran preprocessor
+if (NOT HYDRO)
 add_definitions(-DMOIST_CAPPA -DUSE_COND -DNEMS_GSM)
-add_definitions(-DINTERNAL_FILE_NML)
+endif()
+add_definitions(-DINTERNAL_FILE_NML -DNEMS_GSM)
 
 if(MULTI_GASES)
   add_definitions(-DMULTI_GASES)
diff --git a/io/post_fv3.F90 b/io/post_fv3.F90
index c0ba56dda..cb2149fb9 100644
--- a/io/post_fv3.F90
+++ b/io/post_fv3.F90
@@ -3562,6 +3562,19 @@ subroutine set_postvars_fv3(wrt_int_state,grid_id,mype,mpicomp)
               enddo
             endif
 
+            ! model level omga
+            if(trim(fieldname)=='omga') then
+              !$omp parallel do default(none) private(i,j,l) shared(lm,jsta,jend,ista,iend,omga,arrayr43d,fillvalue,spval)
+              do l=1,lm
+                do j=jsta,jend
+                  do i=ista, iend
+                    omga(i,j,l) = arrayr43d(i,j,l)
+                    if(abs(arrayr43d(i,j,l)-fillvalue)<small) omga(i,j,l) = spval
+                  enddo
+                enddo
+              enddo
+            endif
+
             ! soilt
             if(trim(fieldname)=='soilt') then
               !$omp parallel do default(none) private(i,j,l) shared(nsoil,jsta,jend,ista,iend,stc,arrayr43d,sm,sice,fillvalue,spval)
@@ -4266,22 +4279,6 @@ subroutine set_postvars_fv3(wrt_int_state,grid_id,mype,mpicomp)
         enddo
       enddo
 
-      do l=lm,1,-1
-!$omp parallel do default(none) private(i,j) shared(l,jsta,jend,omga,wh,dpres,zint,spval,ista,iend)
-        do j=jsta,jend
-          do i=ista,iend
-            if(wh(i,j,l) /= spval) then
-              omga(i,j,l) = (-1.) * wh(i,j,l) * dpres(i,j,l)/zint(i,j,l)
-              zint(i,j,l) = zint(i,j,l) + zint(i,j,l+1)
-            else
-              omga(i,j,l) = spval
-              zint(i,j,l) = spval
-            endif
-          enddo
-        enddo
-      enddo
-!      print *,'in post_lam,omga 3d=',maxval(omga(ista:iend,jsta:jend,1)),minval(omga(ista:iend,jsta:jend,1)), &
-!           'lm=',maxval(omga(ista:iend,jsta:jend,lm)),minval(omga(ista:iend,jsta:jend,lm))
 
 ! compute pint from top down
 !$omp parallel do default(none) private(i,j) shared(jsta,jend,ak5,pint,ista,iend)
@@ -4341,6 +4338,27 @@ subroutine set_postvars_fv3(wrt_int_state,grid_id,mype,mpicomp)
         end do
       end do
 
+      do l=lm,1,-1
+!$omp parallel do default(none) private(i,j) shared(l,jsta,jend,omga,wh,dpres,zint,alpint,q,t,spval,ista,iend)
+        do j=jsta,jend
+          do i=ista,iend
+            if(wh(i,j,l) /= spval) then
+              if (omga(i,j,l) == spval) omga(i,j,l) = (-1.) * wh(i,j,l) * dpres(i,j,l)/zint(i,j,l)
+              zint(i,j,l) = zint(i,j,l) + zint(i,j,l+1)
+            else
+              if(zint(i,j,l+1) /=spval .and. t(i,j,l) /= spval .and.  alpint(i,j,l+1) /= spval  &
+                             .and. alpint(i,j,l) /=spval .and. q(i,j,l) /= spval) then
+                 zint(i,j,l) = zint(i,j,l+1)+(rgas/grav)*t(i,j,l)*(1.+fv*q(i,j,l))*(alpint(i,j,l+1)-alpint(i,j,l))
+               else 
+                 zint(i,j,l) = spval
+              endif
+            endif
+          enddo
+        enddo
+      enddo
+!      print *,'in post_lam,omga 3d=',maxval(omga(ista:iend,jsta:jend,1)),minval(omga(ista:iend,jsta:jend,1)), &
+!           'lm=',maxval(omga(ista:iend,jsta:jend,lm)),minval(omga(ista:iend,jsta:jend,lm))
+
 ! compute zmid
       do l=lm,1,-1
 !$omp parallel do default(none) private(i,j) shared(l,jsta,jend,zmid,zint,pmid,alpint,spval,ista,iend)
@@ -4357,6 +4375,7 @@ subroutine set_postvars_fv3(wrt_int_state,grid_id,mype,mpicomp)
         end do
       end do
 
+
 ! surface potential T, and potential T at roughness length
 !$omp parallel do default(none) private(i,j) shared(jsta,jend,ista,iend,spval,lp1,sm,ths,sst,thz0,sice,pint)
       do j=jsta,jend

From 4bbb4e3f1a7bfaa7c041ef9d2415bf3c0bdef0d6 Mon Sep 17 00:00:00 2001
From: "Xiaqiong.Zhou" <Xiaqiong.Zhou@noaa.gov>
Date: Wed, 1 May 2024 08:45:35 -0500
Subject: [PATCH 3/7] Add the conditions to calculate omega in post

---
 io/post_fv3.F90 | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/io/post_fv3.F90 b/io/post_fv3.F90
index cb2149fb9..6a3b64f61 100644
--- a/io/post_fv3.F90
+++ b/io/post_fv3.F90
@@ -4343,7 +4343,8 @@ subroutine set_postvars_fv3(wrt_int_state,grid_id,mype,mpicomp)
         do j=jsta,jend
           do i=ista,iend
             if(wh(i,j,l) /= spval) then
-              if (omga(i,j,l) == spval) omga(i,j,l) = (-1.) * wh(i,j,l) * dpres(i,j,l)/zint(i,j,l)
+              if (omga(i,j,l) == spval .and. dpres(i,j,l) /= spval .and. zint(i,j,l) /=spval)  &
+                  omga(i,j,l) = (-1.) * wh(i,j,l) * dpres(i,j,l)/zint(i,j,l)
               zint(i,j,l) = zint(i,j,l) + zint(i,j,l+1)
             else
               if(zint(i,j,l+1) /=spval .and. t(i,j,l) /= spval .and.  alpint(i,j,l+1) /= spval  &

From f989c5b83b71c8e2fca61f6b60cdd47b894f4824 Mon Sep 17 00:00:00 2001
From: XiaqiongZhou-NOAA <48254930+XiaqiongZhou-NOAA@users.noreply.github.com>
Date: Mon, 13 May 2024 14:06:02 -0400
Subject: [PATCH 4/7] Update CMakeLists.txt

---
 ccpp/CMakeLists.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ccpp/CMakeLists.txt b/ccpp/CMakeLists.txt
index 53f9f0023..e9a5d56c7 100644
--- a/ccpp/CMakeLists.txt
+++ b/ccpp/CMakeLists.txt
@@ -84,8 +84,8 @@ endif(CCPP_32BIT)
 
 #------------------------------------------------------------------------------
 # Add model-specific flags for C/C++/Fortran preprocessor
-if (NOT HYDRO)
-add_definitions(-DMOIST_CAPPA -DUSE_COND -DNEMS_GSM)
+if(NOT HYDRO)
+  add_definitions(-DMOIST_CAPPA -DUSE_COND -DNEMS_GSM)
 endif()
 add_definitions(-DINTERNAL_FILE_NML -DNEMS_GSM)
 

From fc2630c207f2ac116d9c675081220ac010ba8e9f Mon Sep 17 00:00:00 2001
From: XiaqiongZhou-NOAA <48254930+XiaqiongZhou-NOAA@users.noreply.github.com>
Date: Mon, 13 May 2024 14:07:52 -0400
Subject: [PATCH 5/7] Update CMakeLists.txt

---
 CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index a497fd3bb..cd8eef7e5 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -65,7 +65,7 @@ endif()
 
 if(MOVING_NEST)
   list(APPEND _fv3atm_defs_private MOVING_NEST)
-  if (NOT HYDRO)
+  if(NOT HYDRO)
     list(APPEND _fv3atm_defs_private MOIST_CAPPA USE_COND)
   endif()
 

From b329c2ccc4c5c6936cb1f548eef83d2a1ee36ae2 Mon Sep 17 00:00:00 2001
From: "Xiaqiong.Zhou" <Xiaqiong.Zhou@noaa.gov>
Date: Mon, 13 May 2024 14:07:32 -0500
Subject: [PATCH 6/7] revise conditions to calculate zint

---
 io/post_fv3.F90 | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/io/post_fv3.F90 b/io/post_fv3.F90
index 7b1b1be56..1a679f18d 100644
--- a/io/post_fv3.F90
+++ b/io/post_fv3.F90
@@ -4345,9 +4345,10 @@ subroutine set_postvars_fv3(wrt_int_state,grid_id,mype,mpicomp)
         do j=jsta,jend
           do i=ista,iend
             if(wh(i,j,l) /= spval) then
-              if (omga(i,j,l) == spval .and. dpres(i,j,l) /= spval .and. zint(i,j,l) /=spval)  &
+              if(omga(i,j,l) == spval .and. dpres(i,j,l) /= spval .and. zint(i,j,l) /=spval)  &
                   omga(i,j,l) = (-1.) * wh(i,j,l) * dpres(i,j,l)/zint(i,j,l)
-              zint(i,j,l) = zint(i,j,l) + zint(i,j,l+1)
+              if(zint(i,j,l+1) /=spval .and. zint(i,j,l) /=spval) &
+                  zint(i,j,l) = zint(i,j,l) + zint(i,j,l+1)
             else
               if(zint(i,j,l+1) /=spval .and. t(i,j,l) /= spval .and.  alpint(i,j,l+1) /= spval  &
                              .and. alpint(i,j,l) /=spval .and. q(i,j,l) /= spval) then

From ebb1a9dd9a00c54c166b3c88e01a5cbb9f374cab Mon Sep 17 00:00:00 2001
From: "Xiaqiong.Zhou" <Xiaqiong.Zhou@noaa.gov>
Date: Wed, 15 May 2024 15:16:48 -0500
Subject: [PATCH 7/7] Point dycore to GFDL dev/emc

---
 .gitmodules        | 4 ++--
 atmos_cubed_sphere | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index a32a46cd3..22c723ac1 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,7 +1,7 @@
 [submodule "atmos_cubed_sphere"]
   path = atmos_cubed_sphere
-  url = https://github.com/XiaqiongZhou-NOAA/GFDL_atmos_cubed_sphere
-  branch = hydro
+  url = https://github.com/NOAA-GFDL/GFDL_atmos_cubed_sphere
+  branch = dev/emc
 [submodule "ccpp/framework"]
   path = ccpp/framework
   url = https://github.com/NCAR/ccpp-framework
diff --git a/atmos_cubed_sphere b/atmos_cubed_sphere
index aabfdccae..cc8afe64b 160000
--- a/atmos_cubed_sphere
+++ b/atmos_cubed_sphere
@@ -1 +1 @@
-Subproject commit aabfdccae440da7389195762601db7fcc09f6f11
+Subproject commit cc8afe64b9420dd7379e47cee5e3f30f4ac44b58