Merge branch 'dev/gfdl' into FMS2_io

.testing/Makefile

@@ -84,6 +84,9 @@ FCFLAGS_COVERAGE ?=
 # - FMS cannot be built with the same aggressive initialization flags as MOM6,
 #   so FCFLAGS_INIT is used to provide additional MOM6 configuration.
 
+# User-defined LDFLAGS (applied to all builds and FMS)
+LDFLAGS_USER ?=
+
 # Set to `true` to require identical results from DEBUG and REPRO builds
 # NOTE: Many compilers (Intel, GCC on ARM64) do not yet produce identical
 #   results across DEBUG and REPRO builds (as defined below), so we disable on
@@ -217,8 +220,8 @@ REPRO_FCFLAGS := FCFLAGS="$(FCFLAGS_REPRO) $(FCFLAGS_FMS)"
 OPENMP_FCFLAGS := FCFLAGS="$(FCFLAGS_DEBUG) $(FCFLAGS_INIT) $(FCFLAGS_FMS)"
 TARGET_FCFLAGS := FCFLAGS="$(FCFLAGS_DEBUG) $(FCFLAGS_INIT) $(FCFLAGS_FMS)"
 
-MOM_LDFLAGS := LDFLAGS="$(LDFLAGS_FMS)"
-SYMMETRIC_LDFLAGS := LDFLAGS="$(COVERAGE) $(LDFLAGS_FMS)"
+MOM_LDFLAGS := LDFLAGS="$(LDFLAGS_FMS) $(LDFLAGS_USER)"
+SYMMETRIC_LDFLAGS := LDFLAGS="$(COVERAGE) $(LDFLAGS_FMS) $(LDFLAGS_USER)"
 
 
 # Environment variable configuration
@@ -286,7 +289,7 @@ $(TARGET_CODEBASE)/ac/configure: $(TARGET_CODEBASE)
 
 $(TARGET_CODEBASE):
 	git clone --recursive $(MOM_TARGET_URL) $@
-	cd $@ && git checkout $(MOM_TARGET_BRANCH)
+	cd $@ && git checkout --recurse-submodules $(MOM_TARGET_BRANCH)
 
 
 #---

config_src/drivers/mct_cap/mom_surface_forcing_mct.F90

@@ -486,17 +486,18 @@ subroutine convert_IOB_to_fluxes(IOB, fluxes, index_bounds, Time, valid_time, G,
 
     ! latent heat flux (W/m^2)
     fluxes%latent(i,j) = 0.0
-    ! contribution from frozen ppt
+    ! contribution from frozen ppt (notice minus sign since fprec is positive into the ocean)
     if (associated(IOB%fprec)) then
-      fluxes%latent(i,j)              = fluxes%latent(i,j) + &
+      fluxes%latent(i,j)              = fluxes%latent(i,j) - &
           IOB%fprec(i-i0,j-j0)*US%W_m2_to_QRZ_T*CS%latent_heat_fusion
-      fluxes%latent_fprec_diag(i,j)   = G%mask2dT(i,j) * IOB%fprec(i-i0,j-j0)*US%W_m2_to_QRZ_T*CS%latent_heat_fusion
+      fluxes%latent_fprec_diag(i,j)   = - G%mask2dT(i,j) * IOB%fprec(i-i0,j-j0)*US%W_m2_to_QRZ_T*CS%latent_heat_fusion
     endif
-    ! contribution from frozen runoff
+    ! contribution from frozen runoff (notice minus sign since rofi_flux is positive into the ocean)
     if (associated(fluxes%frunoff)) then
-      fluxes%latent(i,j)              = fluxes%latent(i,j) + &
+      fluxes%latent(i,j)              = fluxes%latent(i,j) - &
           IOB%rofi_flux(i-i0,j-j0)*US%W_m2_to_QRZ_T*CS%latent_heat_fusion
-      fluxes%latent_frunoff_diag(i,j) = G%mask2dT(i,j) * IOB%rofi_flux(i-i0,j-j0)*US%W_m2_to_QRZ_T*CS%latent_heat_fusion
+      fluxes%latent_frunoff_diag(i,j) = -G%mask2dT(i,j) &
+          * IOB%rofi_flux(i-i0,j-j0)*US%W_m2_to_QRZ_T*CS%latent_heat_fusion
     endif
     ! contribution from evaporation
     if (associated(IOB%q_flux)) then

config_src/drivers/nuopc_cap/mom_cap.F90

@@ -75,6 +75,7 @@ module MOM_cap_mod
 use ESMF,  only: ESMF_AlarmCreate, ESMF_ClockGetAlarmList, ESMF_AlarmList_Flag
 use ESMF,  only: ESMF_AlarmGet, ESMF_AlarmIsCreated, ESMF_ALARMLIST_ALL, ESMF_AlarmIsEnabled
 use ESMF,  only: ESMF_STATEITEM_NOTFOUND, ESMF_FieldWrite
+use ESMF,  only: ESMF_END_ABORT, ESMF_Finalize
 use ESMF,  only: operator(==), operator(/=), operator(+), operator(-)
 
 ! TODO ESMF_GridCompGetInternalState does not have an explicit Fortran interface.
@@ -135,6 +136,7 @@ module MOM_cap_mod
 logical              :: profile_memory = .true.
 logical              :: grid_attach_area = .false.
 logical              :: use_coldstart = .true.
+logical              :: use_mommesh = .false.
 character(len=128)   :: scalar_field_name = ''
 integer              :: scalar_field_count = 0
 integer              :: scalar_field_idx_grid_nx = 0
@@ -147,7 +149,7 @@ module MOM_cap_mod
 type(ESMF_GeomType_Flag) :: geomtype = ESMF_GEOMTYPE_MESH
 #else
 logical :: cesm_coupled = .false.
-type(ESMF_GeomType_Flag) :: geomtype = ESMF_GEOMTYPE_GRID
+type(ESMF_GeomType_Flag) :: geomtype
 #endif
 character(len=8) :: restart_mode = 'alarms'
 
@@ -347,6 +349,25 @@ subroutine InitializeP0(gcomp, importState, exportState, clock, rc)
   write(logmsg,*) use_coldstart
   call ESMF_LogWrite('MOM_cap:use_coldstart = '//trim(logmsg), ESMF_LOGMSG_INFO)
 
+  use_mommesh = .false.
+  call NUOPC_CompAttributeGet(gcomp, name="use_mommesh", value=value, &
+       isPresent=isPresent, isSet=isSet, rc=rc)
+  if (ChkErr(rc,__LINE__,u_FILE_u)) return
+  if (isPresent .and. isSet) use_mommesh=(trim(value)=="true")
+  write(logmsg,*) use_mommesh
+  call ESMF_LogWrite('MOM_cap:use_mommesh = '//trim(logmsg), ESMF_LOGMSG_INFO)
+
+  if(use_mommesh)then
+    geomtype = ESMF_GEOMTYPE_MESH
+    call NUOPC_CompAttributeGet(gcomp, name='mesh_ocn', isPresent=isPresent, isSet=isSet, rc=rc)
+      if (.not. isPresent .and. .not. isSet) then
+        call ESMF_LogWrite('geomtype set to mesh but mesh_ocn is not specified', ESMF_LOGMSG_INFO)
+        call ESMF_Finalize(endflag=ESMF_END_ABORT)
+     endif
+  else
+    geomtype = ESMF_GEOMTYPE_GRID
+  endif
+
 end subroutine
 
 !> Called by NUOPC to advertise import and export fields.  "Advertise"

config_src/drivers/nuopc_cap/mom_surface_forcing_nuopc.F90

@@ -497,15 +497,17 @@ subroutine convert_IOB_to_fluxes(IOB, fluxes, index_bounds, Time, valid_time, G,
          fluxes%seaice_melt(i,j) = kg_m2_s_conversion * G%mask2dT(i,j) * IOB%seaice_melt(i-i0,j-j0)
 
     fluxes%latent(i,j) = 0.0
+    ! notice minus sign since fprec is positive into the ocean
     if (associated(IOB%fprec)) then
-       fluxes%latent(i,j)            = fluxes%latent(i,j) + &
+       fluxes%latent(i,j)            = fluxes%latent(i,j) - &
            IOB%fprec(i-i0,j-j0)*US%W_m2_to_QRZ_T*CS%latent_heat_fusion
-       fluxes%latent_fprec_diag(i,j) = G%mask2dT(i,j) * IOB%fprec(i-i0,j-j0)*US%W_m2_to_QRZ_T*CS%latent_heat_fusion
+       fluxes%latent_fprec_diag(i,j) = - G%mask2dT(i,j) * IOB%fprec(i-i0,j-j0)*US%W_m2_to_QRZ_T*CS%latent_heat_fusion
     endif
+    ! notice minus sign since frunoff is positive into the ocean
     if (associated(IOB%frunoff)) then
-       fluxes%latent(i,j)              = fluxes%latent(i,j) + &
+       fluxes%latent(i,j)              = fluxes%latent(i,j) - &
            IOB%frunoff(i-i0,j-j0) * US%W_m2_to_QRZ_T * CS%latent_heat_fusion
-       fluxes%latent_frunoff_diag(i,j) = G%mask2dT(i,j) * &
+       fluxes%latent_frunoff_diag(i,j) = - G%mask2dT(i,j) * &
            IOB%frunoff(i-i0,j-j0) * US%W_m2_to_QRZ_T * CS%latent_heat_fusion
     endif
     if (associated(IOB%q_flux)) then
@@ -794,7 +796,7 @@ subroutine convert_IOB_to_forces(IOB, forces, index_bounds, Time, G, US, CS)
       endif
       forces%ustar(i,j) = sqrt(gustiness*Irho0 + Irho0*tau_mag)
     enddo ; enddo
-
+    call pass_vector(forces%taux, forces%tauy, G%Domain, halo=1)
   elseif (wind_stagger == AGRID) then
     call pass_vector(taux_at_h, tauy_at_h, G%Domain, To_All+Omit_Corners, stagger=AGRID, halo=1)
 
@@ -820,7 +822,7 @@ subroutine convert_IOB_to_forces(IOB, forces, index_bounds, Time, G, US, CS)
       forces%ustar(i,j) = sqrt(gustiness*Irho0 + Irho0 * G%mask2dT(i,j) * &
                                sqrt(taux_at_h(i,j)**2 + tauy_at_h(i,j)**2))
     enddo ; enddo
-
+    call pass_vector(forces%taux, forces%tauy, G%Domain, halo=1)
   else ! C-grid wind stresses.
     if (G%symmetric) &
       call fill_symmetric_edges(forces%taux, forces%tauy, G%Domain)

src/initialization/MOM_shared_initialization.F90

@@ -196,6 +196,7 @@ subroutine apply_topography_edits_from_file(D, G, param_file, US)
   character(len=40)  :: mdl = "apply_topography_edits_from_file" ! This subroutine's name.
   integer :: i, j, n, ncid, n_edits, i_file, j_file, ndims, sizes(8)
   logical :: found
+  logical :: topo_edits_change_mask
 
   call callTree_enter(trim(mdl)//"(), MOM_shared_initialization.F90")
 
@@ -206,6 +207,9 @@ subroutine apply_topography_edits_from_file(D, G, param_file, US)
   call get_param(param_file, mdl, "TOPO_EDITS_FILE", topo_edits_file, &
                  "The file from which to read a list of i,j,z topography overrides.", &
                  default="")
+  call get_param(param_file, mdl, "ALLOW_LANDMASK_CHANGES", topo_edits_change_mask, &
+                 "If true, allow topography overrides to change land mask.", &
+                 default=.false.)
 
   if (len_trim(topo_edits_file)==0) return
 
@@ -250,8 +254,14 @@ subroutine apply_topography_edits_from_file(D, G, param_file, US)
           'Ocean topography edit: ', n, ig(n), jg(n), D(i,j)/m_to_Z, '->', abs(new_depth(n)), i, j
         D(i,j) = abs(m_to_Z*new_depth(n)) ! Allows for height-file edits (i.e. converts negatives)
       else
-        call MOM_error(FATAL, trim(mdl)//': A zero depth edit would change the land mask and '//&
-          "is not allowed in"//trim(topo_edits_file))
+        if (topo_edits_change_mask) then
+          write(stdout,'(a,3i5,f8.2,a,f8.2,2i4)') &
+            'Ocean topography edit: ',n,ig(n),jg(n),D(i,j)/m_to_Z,'->',abs(new_depth(n)),i,j
+            D(i,j) = abs(m_to_Z*new_depth(n)) ! Allows for height-file edits (i.e. converts negatives)
+        else
+          call MOM_error(FATAL, ' apply_topography_edits_from_file: '//&
+            "A zero depth edit would change the land mask and is not allowed in"//trim(topo_edits_file))
+        endif
       endif
     endif
   enddo