Merge branch 'dev/master' into user/ksh/open_bc

src/core/MOM.F90

@@ -1444,8 +1444,15 @@ subroutine initialize_MOM(Time, param_file, dirs, CS, Time_in)
   call diag_mediator_infrastructure_init()
   call MOM_io_init(param_file)
   call MOM_grid_init(G, param_file)
+
+  call create_dyn_horgrid(dG, G%HI)
+  dG%first_direction = G%first_direction
+  dG%bathymetry_at_vel = G%bathymetry_at_vel
+  call clone_MOM_domain(G%Domain, dG%Domain)
+
   call verticalGridInit( param_file, CS%GV )
   GV => CS%GV
+  dG%g_Earth = GV%g_Earth
 
   ! Read relevant parameters and write them to the model log.
   call log_version(param_file, "MOM", version, "")
@@ -1657,20 +1664,20 @@ subroutine initialize_MOM(Time, param_file, dirs, CS, Time_in)
     "MOM: ADIABATIC and BULKMIXEDLAYER can not both be defined.")
 
   ! Allocate the auxiliary non-symmetric domain for debugging or I/O purposes.
-  if (CS%debug .or. G%symmetric) &
-    call clone_MOM_domain(G%Domain, G%Domain_aux, symmetric=.false.)
+  if (CS%debug .or. dG%symmetric) &
+    call clone_MOM_domain(dG%Domain, dG%Domain_aux, symmetric=.false.)
 
   call MOM_timing_init(CS)
 
   call tracer_registry_init(param_file, CS%tracer_Reg)
 
   ! Copy a common variable from the vertical grid to the horizontal grid.
   ! Consider removing this later?
-  G%ke = GV%ke
+!  G%ke = GV%ke
 
-  is   = G%isc   ; ie   = G%iec  ; js   = G%jsc  ; je   = G%jec ; nz = GV%ke
-  isd  = G%isd   ; ied  = G%ied  ; jsd  = G%jsd  ; jed  = G%jed
-  IsdB = G%IsdB  ; IedB = G%IedB ; JsdB = G%JsdB ; JedB = G%JedB
+  is   = dG%isc   ; ie   = dG%iec  ; js   = dG%jsc  ; je   = dG%jec ; nz = GV%ke
+  isd  = dG%isd   ; ied  = dG%ied  ; jsd  = dG%jsd  ; jed  = dG%jed
+  IsdB = dG%IsdB  ; IedB = dG%IedB ; JsdB = dG%JsdB ; JedB = dG%JedB
 
   ! Allocate and initialize space for primary MOM variables.
   ALLOC_(CS%u(IsdB:IedB,jsd:jed,nz))   ; CS%u(:,:,:) = 0.0
@@ -1785,17 +1792,28 @@ subroutine initialize_MOM(Time, param_file, dirs, CS, Time_in)
   call callTree_waypoint("restart registration complete (initialize_MOM)")
 
   call cpu_clock_begin(id_clock_MOM_init)
-  call MOM_initialize_fixed(G, CS%OBC, param_file, write_geom_files, dirs%output_directory)
+  call MOM_initialize_fixed(dG, CS%OBC, param_file, write_geom_files, dirs%output_directory)
   call callTree_waypoint("returned from MOM_initialize_fixed() (initialize_MOM)")
   call MOM_initialize_coord(GV, param_file, write_geom_files, &
-                            dirs%output_directory, CS%tv, G%max_depth)
+                            dirs%output_directory, CS%tv, dG%max_depth)
   call callTree_waypoint("returned from MOM_initialize_coord() (initialize_MOM)")
 
   if (CS%use_ALE_algorithm) then
-    call ALE_init(param_file, GV, G%max_depth, CS%ALE_CSp)
+    call ALE_init(param_file, GV, dG%max_depth, CS%ALE_CSp)
     call callTree_waypoint("returned from ALE_init() (initialize_MOM)")
   endif
 
+  !   Shift from using the temporary dynamic grid type to using the final (potentially
+  ! static) ocean grid type.
+  ! call clone_MOM_domain(dG%Domain, CS%G%Domain)
+  ! call MOM_grid_init(CS%G, param_file)
+
+  call copy_dyngrid_to_MOM_grid(dg, G)
+  ! Allocate the auxiliary non-symmetric domain for debugging or I/O purposes.
+  if (CS%debug .or. G%symmetric) &
+    call clone_MOM_domain(G%Domain, G%Domain_aux, symmetric=.false.)
+  G%ke = GV%ke
+
   call MOM_initialize_state(CS%u, CS%v, CS%h, CS%tv, Time, G, GV, param_file, &
                             dirs, CS%restart_CSp, CS%ALE_CSp, CS%tracer_Reg, &
                             CS%sponge_CSp, CS%ALE_sponge_CSp, CS%OBC, Time_in)
@@ -1805,20 +1823,6 @@ subroutine initialize_MOM(Time, param_file, dirs, CS, Time_in)
   ! From this point, there may be pointers being set, so the final grid type
   ! that will persist through the run has to be used.
 
-  !   Shift from using the temporary dynamic grid type to using the final (potentially
-  ! static) ocean grid type.
-  ! call clone_MOM_domain(dG%Domain, CS%G%Domain)
-  ! call MOM_grid_init(CS%G, param_file)
-  ! call copy_dyngrid_to_MOM_grid(dg, CS%G)
-  ! Allocate the auxiliary non-symmetric domain for debugging or I/O purposes.
-  ! if (CS%debug .or. CS%G%symmetric) &
-  !  call clone_MOM_domain(CS%G%Domain, CS%G%Domain_aux, symmetric=.false.)
-
-  ! ! Copy a common variable from the vertical grid to the horizontal grid.
-  ! ! Consider removing this later?
-  ! CS%G%ke = GV%ke
-  ! G => CS%G
-
   if (test_grid_copy) then
     !  Copy the data from the temporary grid to the dyn_hor_grid to CS%G.
     call create_dyn_horgrid(dG, G%HI)
@@ -1885,12 +1889,12 @@ subroutine initialize_MOM(Time, param_file, dirs, CS, Time_in)
 
    diag    => CS%diag
   ! Initialize the diag mediator.
-  call diag_mediator_init(G, param_file, diag, doc_file_dir=dirs%output_directory)
+  call diag_mediator_init(G, GV%ke, param_file, diag, doc_file_dir=dirs%output_directory)
 
   ! Initialize the diagnostics mask arrays.
   ! This step has to be done after call to MOM_initialize_state
   ! and before MOM_diagnostics_init
-  call diag_masks_set(G, CS%missing, diag)
+  call diag_masks_set(G, GV%ke, CS%missing, diag)
 
   ! Set up a pointers h within diag mediator control structure,
   ! this needs to occur _after_ CS%h has been allocated.

src/core/MOM_transcribe_grid.F90

@@ -139,6 +139,7 @@ subroutine copy_dyngrid_to_MOM_grid(dG, oG)
   oG%south_lat = dG%south_lat ; oG%west_lon  = dG%west_lon
   oG%len_lat = dG%len_lat ; oG%len_lon = dG%len_lon
   oG%Rad_Earth = dG%Rad_Earth ; oG%max_depth = dG%max_depth 
+  oG%g_Earth = dG%g_Earth
 
 ! Update the halos in case the dynamic grid has smaller halos than the ocean grid.
   call pass_var(oG%areaT, oG%Domain)
@@ -288,7 +289,8 @@ subroutine copy_MOM_grid_to_dyngrid(oG, dG)
   dG%areaT_global = oG%areaT_global ; dG%IareaT_global = oG%IareaT_global
   dG%south_lat = oG%south_lat ; dG%west_lon  = oG%west_lon
   dG%len_lat = oG%len_lat ; dG%len_lon = oG%len_lon
-  dG%Rad_Earth = oG%Rad_Earth ; dG%max_depth = oG%max_depth 
+  dG%Rad_Earth = oG%Rad_Earth ; dG%max_depth = oG%max_depth
+  dG%g_Earth = oG%g_Earth
 
 ! Update the halos in case the dynamic grid has smaller halos than the ocean grid.
   call pass_var(dG%areaT, dG%Domain)

src/diagnostics/MOM_diagnostics.F90

@@ -326,7 +326,7 @@ subroutine calculate_diagnostic_fields(u, v, h, uh, vh, tv, ADp, CDp, fluxes, &
 
   ! volume mean potential temperature 
   if (CS%id_thetaoga>0) then
-    thetaoga = global_volume_mean(tv%T, h, G)
+    thetaoga = global_volume_mean(tv%T, h, G, GV)
     call post_data(CS%id_thetaoga, thetaoga, CS%diag)
   endif
 
@@ -341,7 +341,7 @@ subroutine calculate_diagnostic_fields(u, v, h, uh, vh, tv, ADp, CDp, fluxes, &
 
   ! volume mean salinity 
   if (CS%id_soga>0) then
-    soga = global_volume_mean(tv%S, h, G)
+    soga = global_volume_mean(tv%S, h, G, GV)
     call post_data(CS%id_soga, soga, CS%diag)
   endif
 
@@ -356,13 +356,13 @@ subroutine calculate_diagnostic_fields(u, v, h, uh, vh, tv, ADp, CDp, fluxes, &
 
   ! layer mean potential temperature 
   if (CS%id_temp_layer_ave>0) then
-    temp_layer_ave = global_layer_mean(tv%T, h, G)
+    temp_layer_ave = global_layer_mean(tv%T, h, G, GV)
     call post_data_1d_k(CS%id_temp_layer_ave, temp_layer_ave, CS%diag)
   endif
 
   ! layer mean salinity 
   if (CS%id_salt_layer_ave>0) then
-    salt_layer_ave = global_layer_mean(tv%S, h, G)
+    salt_layer_ave = global_layer_mean(tv%S, h, G, GV)
     call post_data_1d_k(CS%id_salt_layer_ave, salt_layer_ave, CS%diag)
   endif
 

src/diagnostics/MOM_sum_output.F90

@@ -592,7 +592,8 @@ subroutine write_energy(u, v, h, tv, day, n, G, GV, CS, tracer_CSp)
     energypath_nc = trim(CS%energyfile) // ".nc"
     if (day > CS%Start_time) then
       call reopen_file(CS%fileenergy_nc, trim(energypath_nc), vars, &
-                       num_nc_fields, G, CS%fields, SINGLE_FILE, CS%timeunit, GV=GV)
+                       num_nc_fields, CS%fields, SINGLE_FILE, CS%timeunit, &
+                       G=G, GV=GV)
     else
       call create_file(CS%fileenergy_nc, trim(energypath_nc), vars, &
                        num_nc_fields, CS%fields, SINGLE_FILE, CS%timeunit, &