Fixed a conflict in .DoxygenLayout.xml

.DoxygenLayout.xml

@@ -1,31 +1,26 @@
 <doxygenlayout version="1.0">
-	<!-- Generated by doxygen 1.8.6 -->
-	<!-- Navigation index tabs for HTML output -->
-	<navindex>
-		<tab type="mainpage" visible="yes" title="Main page" />
-		<tab type="pages" visible="yes" title="Pages" intro="" />
-		<tab type="modules" visible="yes" title="Modules" intro="" />
-		<tab type="namespaces" visible="no" title="Name Spaces">
-			<tab type="namespacelist" visible="yes" title="Name space list"
-				intro="" />
-			<tab type="namespacemembers" visible="yes" title="Name space members"
-				intro="" />
-		</tab>
-		<tab type="classes" visible="yes" title="F90 modules">
-			<tab type="classlist" visible="yes" title="F90 module list"
-				intro="This is the list of all F90 modules. Some are expandable which shows the defined types that are provided by that module." />
-			<!--tab type="classindex" visible="$ALPHABETICAL_INDEX" title=""/ -->
-			<tab type="hierarchy" visible="yes" title="Hierarchy" intro="" />
-			<tab type="classmembers" visible="yes" title="Module functions and variables"
-				intro="" />
-		</tab>
-		<tab type="files" visible="yes" title="Source files">
-			<tab type="filelist" visible="yes" title="File list" intro="" />
-			<tab type="globals" visible="yes" title="Globals" intro="" />
-		</tab>
-		<tab type="examples" visible="yes" title="Examples" intro="" />
-	</navindex>
-
+  <!-- Generated by doxygen 1.8.13 -->
+  <!-- Navigation index tabs for HTML output -->
+  <navindex>
+    <tab type="mainpage" visible="yes" title="Main page"/>
+    <tab type="pages" visible="yes" title="Pages" intro="Pages"/>
+    <tab type="modules" visible="yes" title="Modules" intro=""/>
+    <tab type="namespaces" visible="no" title="Name Spaces">
+      <tab type="namespacelist" visible="no" title="Name space list" intro=""/>
+      <tab type="namespacemembers" visible="no" title="Name space members" intro=""/>
+    </tab>
+    <tab type="classes" visible="yes" title="F90 modules">
+      <tab type="classlist" visible="yes" title="F90 module list" intro="This is the list of all F90 modules. Some are expandable which shows the defined types that are provided by that module."/>
+      <tab type="classindex" visible="no" title=""/>
+      <tab type="hierarchy" visible="yes" title="Hierarchy" intro=""/>
+      <tab type="classmembers" visible="yes" title="Module functions and variables" intro=""/>
+    </tab>
+    <tab type="files" visible="yes" title="Source files">
+      <tab type="filelist" visible="yes" title="File list" intro=""/>
+      <tab type="globals" visible="yes" title="Globals" intro=""/>
+    </tab>
+    <tab type="examples" visible="yes" title="Examples" intro=""/> 
+  </navindex>
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 		<briefdescription visible="yes" />

.doxygen

@@ -872,7 +872,7 @@ EXCLUDE_SYMBOLS        =
 # that contain example code fragments that are included (see the \include
 # command).
 
-EXAMPLE_PATH           =
+EXAMPLE_PATH           = config_src src
 
 # If the value of the EXAMPLE_PATH tag contains directories, you can use the
 # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
@@ -892,7 +892,7 @@ EXAMPLE_RECURSIVE      = NO
 # that contain images that are to be included in the documentation (see the
 # \image command).
 
-IMAGE_PATH             =
+IMAGE_PATH             = .images config_src src
 
 # The INPUT_FILTER tag can be used to specify a program that doxygen should
 # invoke to filter for each input file. Doxygen will invoke the filter program
@@ -2028,7 +2028,7 @@ SEARCH_INCLUDES        = YES
 # preprocessor.
 # This tag requires that the tag SEARCH_INCLUDES is set to YES.
 
-INCLUDE_PATH           =
+INCLUDE_PATH           = src/framework
 
 # You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
 # patterns (like *.h and *.hpp) to filter out the header-files in the

config_src/coupled_driver/MOM_surface_forcing.F90

@@ -194,6 +194,9 @@ module MOM_surface_forcing
   real, pointer, dimension(:,:) :: fprec                =>NULL() ! mass flux of frozen precip (kg/m2/s)
   real, pointer, dimension(:,:) :: runoff               =>NULL() ! mass flux of liquid runoff (kg/m2/s)
   real, pointer, dimension(:,:) :: calving              =>NULL() ! mass flux of frozen runoff (kg/m2/s)
+  real, pointer, dimension(:,:) :: ustar_berg           =>NULL() ! frictional velocity beneath icebergs (m/s)
+  real, pointer, dimension(:,:) :: area_berg            =>NULL() ! area covered by icebergs(m2/m2)
+  real, pointer, dimension(:,:) :: mass_berg            =>NULL() ! mass of icebergs(kg/m2)
   real, pointer, dimension(:,:) :: runoff_hflx          =>NULL() ! heat content of liquid runoff (W/m2)
   real, pointer, dimension(:,:) :: calving_hflx         =>NULL() ! heat content of frozen runoff (W/m2)
   real, pointer, dimension(:,:) :: p                    =>NULL() ! pressure of overlying ice and atmosphere
@@ -469,6 +472,20 @@ subroutine convert_IOB_to_fluxes(IOB, fluxes, index_bounds, Time, G, CS, state,
     if (ASSOCIATED(IOB%calving)) &
       fluxes%frunoff(i,j) = IOB%calving(i-i0,j-j0) * G%mask2dT(i,j)
 
+    if (((ASSOCIATED(IOB%ustar_berg) .and. (.not. ASSOCIATED(fluxes%ustar_berg)))   &
+      .or. (ASSOCIATED(IOB%area_berg) .and. (.not. ASSOCIATED(fluxes%area_berg)))) &
+      .or. (ASSOCIATED(IOB%mass_berg) .and. (.not. ASSOCIATED(fluxes%mass_berg)))) &
+      call allocate_forcing_type(G, fluxes, iceberg=.true.)
+
+    if (ASSOCIATED(IOB%ustar_berg)) &
+      fluxes%ustar_berg(i,j) = IOB%ustar_berg(i-i0,j-j0) * G%mask2dT(i,j)
+
+    if (ASSOCIATED(IOB%area_berg)) &
+      fluxes%area_berg(i,j) = IOB%area_berg(i-i0,j-j0) * G%mask2dT(i,j)
+
+    if (ASSOCIATED(IOB%mass_berg)) &
+      fluxes%mass_berg(i,j) = IOB%mass_berg(i-i0,j-j0) * G%mask2dT(i,j)
+
     if (ASSOCIATED(IOB%runoff_hflx)) &
       fluxes%heat_content_lrunoff(i,j) = IOB%runoff_hflx(i-i0,j-j0) * G%mask2dT(i,j)
 
@@ -1197,6 +1214,12 @@ subroutine ice_ocn_bnd_type_chksum(id, timestep, iobt)
     write(outunit,100) 'iobt%runoff         ', mpp_chksum( iobt%runoff         )
     write(outunit,100) 'iobt%calving        ', mpp_chksum( iobt%calving        )
     write(outunit,100) 'iobt%p              ', mpp_chksum( iobt%p              )
+    if (ASSOCIATED(iobt%ustar_berg)) &
+      write(outunit,100) 'iobt%ustar_berg     ', mpp_chksum( iobt%ustar_berg     )
+    if (ASSOCIATED(iobt%area_berg)) &
+      write(outunit,100) 'iobt%area_berg      ', mpp_chksum( iobt%area_berg      )
+    if (ASSOCIATED(iobt%mass_berg)) &
+      write(outunit,100) 'iobt%mass_berg      ', mpp_chksum( iobt%mass_berg      )
 
 100 FORMAT("   CHECKSUM::",A20," = ",Z20)
     do n = 1, iobt%fluxes%num_bcs  !{

config_src/coupled_driver/ocean_model_MOM.F90

@@ -67,8 +67,10 @@ module ocean_model_mod
 use mpp_domains_mod, only : domain2d, mpp_get_layout, mpp_get_global_domain
 use mpp_domains_mod, only : mpp_define_domains, mpp_get_compute_domain, mpp_get_data_domain
 use atmos_ocean_fluxes_mod, only : aof_set_coupler_flux
+use MOM_forcing_type, only : allocate_forcing_type
 use fms_mod, only : stdout
 use mpp_mod, only : mpp_chksum
+use MOM_domains, only : pass_var, pass_vector, TO_ALL, CGRID_NE, BGRID_NE
 
 #include <MOM_memory.h>
 
@@ -153,14 +155,17 @@ module ocean_model_mod
 
   integer :: nstep = 0        ! The number of calls to update_ocean.
   logical :: use_ice_shelf    ! If true, the ice shelf model is enabled.
+  logical :: icebergs_apply_rigid_boundary  ! If true, the icebergs can change ocean bd condition.
+  real :: kv_iceberg          ! The viscosity of the icebergs in m2/s (for ice rigidity)
+  real :: density_iceberg     ! A typical density of icebergs in kg/m3 (for ice rigidity) 
   type(ice_shelf_CS), pointer :: Ice_shelf_CSp => NULL()
   logical :: restore_salinity ! If true, the coupled MOM driver adds a term to
                               ! restore salinity to a specified value.
   logical :: restore_temp     ! If true, the coupled MOM driver adds a term to
                               ! restore sst to a specified value.
   real :: press_to_z          ! A conversion factor between pressure and ocean
                               ! depth in m, usually 1/(rho_0*g), in m Pa-1.
-  real :: C_p                 !   The heat capacity of seawater, in J K-1 kg-1.
+  real :: C_p                 ! The heat capacity of seawater, in J K-1 kg-1.
 
   type(directories) :: dirs   ! A structure containing several relevant directory paths.
   type(forcing)   :: fluxes   ! A structure containing pointers to
@@ -280,6 +285,16 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in)
   call get_param(param_file, mod, "ICE_SHELF",  OS%use_ice_shelf, &
                  "If true, enables the ice shelf model.", default=.false.)
 
+  call get_param(param_file, mod, "ICEBERGS_APPLY_RIGID_BOUNDARY",  OS%icebergs_apply_rigid_boundary, &
+                 "If true, allows icebergs to change boundary condition felt by ocean", default=.false.)
+
+  if (OS%icebergs_apply_rigid_boundary) then
+    call get_param(param_file, mod, "KV_ICEBERG",  OS%kv_iceberg, &
+                 "The viscosity of the icebergs",  units="m2 s-1",default=1.0e10)
+    call get_param(param_file, mod, "DENSITY_ICEBERGS",  OS%density_iceberg, &
+                  "A typical density of icebergs.", units="kg m-3", default=917.0)
+  endif
+
   OS%press_to_z = 1.0/(Rho0*G_Earth)
 
   call surface_forcing_init(Time_in, OS%grid, param_file, OS%MOM_CSp%diag, &
@@ -289,6 +304,11 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in)
      call initialize_ice_shelf(param_file, OS%grid, OS%Time, OS%ice_shelf_CSp, &
                                OS%MOM_CSp%diag, OS%fluxes)
   endif
+  if (OS%icebergs_apply_rigid_boundary)  then      
+    !call allocate_forcing_type(OS%grid, OS%fluxes, iceberg=.true.)
+    !This assumes that the iceshelf and ocean are on the same grid. I hope this is true
+    if (.not. OS%use_ice_shelf) call allocate_forcing_type(OS%grid, OS%fluxes, ustar=.true., shelf=.true.)
+  endif
 
   call MOM_sum_output_init(OS%grid, param_file, OS%dirs%output_directory, &
                             OS%MOM_CSp%ntrunc, Time_init, OS%sum_output_CSp)
@@ -394,23 +414,28 @@ subroutine update_ocean_model(Ice_ocean_boundary, OS, Ocean_sfc, &
     call MOM_generic_tracer_fluxes_accumulate(OS%fluxes, weight) !here weight=1, just saving the current fluxes
 #endif
 
-  ! Add ice shelf fluxes
-
+    ! Add ice shelf fluxes
     if (OS%use_ice_shelf) then
       call shelf_calc_flux(OS%State, OS%fluxes, OS%Time, time_step, OS%Ice_shelf_CSp)
     endif
-
+    if (OS%icebergs_apply_rigid_boundary)  then
+      !This assumes that the iceshelf and ocean are on the same grid. I hope this is true
+      call add_berg_flux_to_shelf(OS%grid, OS%fluxes,OS%use_ice_shelf,OS%density_iceberg,OS%kv_iceberg)
+    endif
     ! Indicate that there are new unused fluxes.
     OS%fluxes%fluxes_used = .false.
     OS%fluxes%dt_buoy_accum = time_step
   else
     OS%flux_tmp%C_p = OS%fluxes%C_p
     call convert_IOB_to_fluxes(Ice_ocean_boundary, OS%flux_tmp, index_bnds, OS%Time, &
                                OS%grid, OS%forcing_CSp, OS%state, OS%restore_salinity,OS%restore_temp)
-
     if (OS%use_ice_shelf) then
       call shelf_calc_flux(OS%State, OS%flux_tmp, OS%Time, time_step, OS%Ice_shelf_CSp)
     endif
+    if (OS%icebergs_apply_rigid_boundary)  then
+     !This assumes that the iceshelf and ocean are on the same grid. I hope this is true
+     call add_berg_flux_to_shelf(OS%grid, OS%flux_tmp, OS%use_ice_shelf,OS%density_iceberg,OS%kv_iceberg)
+    endif
 
     call forcing_accumulate(OS%flux_tmp, OS%fluxes, time_step, OS%grid, weight)
 #ifdef _USE_GENERIC_TRACER
@@ -477,6 +502,66 @@ end subroutine update_ocean_model
 !                                      the any restart file name as a prefix. 
 ! </DESCRIPTION>
 !
+
+subroutine add_berg_flux_to_shelf(G, fluxes, use_ice_shelf, density_ice, kv_ice)
+  type(ocean_grid_type),              intent(inout)    :: G
+  type(forcing),                      intent(inout) :: fluxes
+  logical,                            intent(in) :: use_ice_shelf
+  real, intent(in) :: kv_ice       ! The viscosity of ice, in m2 s-1.
+  real, intent(in) :: density_ice  ! A typical density of ice, in kg m-3.
+! Arguments:
+!  (in)      fluxes - A structure of surface fluxes that may be used.
+!  (in)      G - The ocean's grid structure.
+  integer :: i, j, is, ie, js, je, isd, ied, jsd, jed
+  is = G%isc ; ie = G%iec ; js = G%jsc ; je = G%jec
+  isd = G%isd ; jsd = G%jsd ; ied = G%ied ; jed = G%jed
+  !This routine adds iceberg data to the ice shelf data (if ice shelf is used)
+  !which can then be used to change the top of ocean boundary condition used in
+  !the ocean model. This routine is taken from the add_shelf_flux subroutine
+  !within the ice shelf model.
+
+  if (.not. (((associated(fluxes%frac_shelf_h) .and. associated(fluxes%frac_shelf_u)) &
+    .and.(associated(fluxes%frac_shelf_v) .and. associated(fluxes%ustar_shelf)))&
+    .and.(associated(fluxes%rigidity_ice_u) .and. associated(fluxes%rigidity_ice_v)))) return
+
+  if (.not. ((associated(fluxes%area_berg) .and.  associated(fluxes%ustar_berg)) .and. associated(fluxes%mass_berg)  ) )  return
+
+  if (.not. use_ice_shelf) then
+    fluxes%frac_shelf_h(:,:)=0.
+    fluxes%frac_shelf_u(:,:)=0.
+    fluxes%frac_shelf_v(:,:)=0.
+    fluxes%ustar_shelf(:,:)=0.
+    fluxes%rigidity_ice_u(:,:)=0.
+    fluxes%rigidity_ice_v(:,:)=0.
+  endif
+
+    do j=jsd,jed ; do i=isd,ied
+      if (G%areaT(i,j) > 0.0) &
+        fluxes%frac_shelf_h(i,j) = fluxes%frac_shelf_h(i,j) +  fluxes%area_berg(i,j) 
+        fluxes%ustar_shelf(i,j)  = fluxes%ustar_shelf(i,j)  +  fluxes%ustar_berg(i,j)
+    enddo ; enddo
+    !do I=isd,ied-1 ; do j=isd,jed
+    do j=jsd,jed ; do i=isd,ied-1 ! ### changed stride order; i->ied-1?
+      fluxes%frac_shelf_u(I,j) = 0.0
+      if ((G%areaT(i,j) + G%areaT(i+1,j) > 0.0)) & ! .and. (G%dxdy_u(I,j) > 0.0)) &
+        fluxes%frac_shelf_u(I,j) = fluxes%frac_shelf_u(I,j) + (((fluxes%area_berg(i,j)*G%areaT(i,j)) + (fluxes%area_berg(i+1,j)*G%areaT(i+1,j))) / &
+                                    (G%areaT(i,j) + G%areaT(i+1,j)))
+        fluxes%rigidity_ice_u(I,j) = fluxes%rigidity_ice_u(I,j) +((kv_ice / density_ice) * &
+                                    min(fluxes%mass_berg(i,j), fluxes%mass_berg(i+1,j)))
+    enddo ; enddo
+    do j=jsd,jed-1 ; do i=isd,ied ! ### change stride order; j->jed-1?
+    !do i=isd,ied ; do J=isd,jed-1 
+      fluxes%frac_shelf_v(i,J) = 0.0
+      if ((G%areaT(i,j) + G%areaT(i,j+1) > 0.0)) & ! .and. (G%dxdy_v(i,J) > 0.0)) &
+        fluxes%frac_shelf_v(i,J) = fluxes%frac_shelf_v(i,J) + (((fluxes%area_berg(i,j)*G%areaT(i,j)) + (fluxes%area_berg(i,j+1)*G%areaT(i,j+1))) / &
+                                    (G%areaT(i,j) + G%areaT(i,j+1) ))
+      fluxes%rigidity_ice_v(i,J) = fluxes%rigidity_ice_v(i,J) +((kv_ice / density_ice) * &
+                                   max(fluxes%mass_berg(i,j), fluxes%mass_berg(i,j+1)))
+    enddo ; enddo
+    call pass_vector(fluxes%frac_shelf_u, fluxes%frac_shelf_v, G%domain, TO_ALL, CGRID_NE)
+
+end subroutine add_berg_flux_to_shelf
+
 subroutine ocean_model_restart(OS, timestamp)
    type(ocean_state_type),        pointer :: OS
    character(len=*), intent(in), optional :: timestamp

src/ALE/MOM_regridding.F90

@@ -2870,7 +2870,7 @@ end subroutine regridding_memory_deallocation
 !! Most calculations in this module start with the coordinate at the bottom
 !! of the column set to -depth, and use a increasing value of coordinate with
 !! decreasing k. This is consistent with the rest of MOM6 that uses position,
-!!  f$z\f$ which is a negative quantity for most of the ocean.
+!! \f$z\f$ which is a negative quantity for most of the ocean.
 !!
 !! A change in grid is define through a change in position of the interfaces:
 !! \f[

src/core/MOM.F90

@@ -544,8 +544,9 @@ subroutine step_MOM(fluxes, state, Time_start, time_interval, CS)
     call create_group_pass(CS%pass_tau_ustar_psurf, fluxes%ustar(:,:), G%Domain)
   if (ASSOCIATED(fluxes%p_surf)) &
     call create_group_pass(CS%pass_tau_ustar_psurf, fluxes%p_surf(:,:), G%Domain)
-  if (CS%thickness_diffuse .OR. CS%mixedlayer_restrat) &
+  if ((CS%thickness_diffuse  .and. (.not.CS%thickness_diffuse_first .or. CS%dt_trans == 0) )  .OR. CS%mixedlayer_restrat) &
     call create_group_pass(CS%pass_h, h, G%Domain)
+
   if (CS%diabatic_first) then
     if (associated(CS%visc%Ray_u) .and. associated(CS%visc%Ray_v)) &
       call create_group_pass(CS%pass_ray, CS%visc%Ray_u, CS%visc%Ray_v, G%Domain, &
@@ -4079,9 +4080,9 @@ end subroutine MOM_end
 !! * FRAZIL_HEAT_TENDENCY generally has 3d structure, since MOM6 frazil calculation checks the
 !!   full ocean column.
 !!
-!! * FRAZIL_HEAT_TENDENCY[k=@sum] = HFSIFRAZIL = column integrated frazil heating.
+!! * FRAZIL_HEAT_TENDENCY[k=\@sum] = HFSIFRAZIL = column integrated frazil heating.
 !!
-!! * HFDS = FRAZIL_HEAT_TENDENCY[k=@sum] + BOUNDARY_FORCING_HEAT_TENDENCY[k=@sum]
+!! * HFDS = FRAZIL_HEAT_TENDENCY[k=\@sum] + BOUNDARY_FORCING_HEAT_TENDENCY[k=\@sum]
 !!
 !!  Here is an example 2d heat budget (depth summed) diagnostic for MOM.
 !!
@@ -4107,7 +4108,7 @@ end subroutine MOM_end
 !! * BOUNDARY_FORCING_SALT_TENDENCY generally has 3d structure, with k > 1 contributions from
 !!   the case when layers are tiny, in which case MOM6 partitions tendencies into k > 1 layers.
 !!
-!! * SFDSI = BOUNDARY_FORCING_SALT_TENDENCY[k=@sum] 
+!! * SFDSI = BOUNDARY_FORCING_SALT_TENDENCY[k=\@sum] 
 !!
 !!  Here is an example 2d salt budget (depth summed) diagnostic for MOM.
 !!