Merge branch 'dev/gfdl' into fix_units_wavestr

.github/actions/testing-setup/action.yml

@@ -22,6 +22,7 @@ runs:
       shell: bash
       run: |
         echo "::group::Install linux packages"
+        sudo apt-get update
         sudo apt-get install netcdf-bin libnetcdf-dev libnetcdff-dev mpich libmpich-dev
         echo "::endgroup::"
 

.github/workflows/documentation-and-style.yml

@@ -18,11 +18,11 @@ jobs:
       continue-on-error: true
 
     - name: Install packages used when generating documentation
-      run: >
-        sudo apt-get install
-        python3-sphinx python3-lxml perl
-        texlive-binaries texlive-base bibtool tex-common texlive-bibtex-extra
-        graphviz
+      run: |
+        sudo apt-get update
+        sudo apt-get install python3-sphinx python3-lxml perl
+        sudo apt-get install texlive-binaries texlive-base bibtool tex-common texlive-bibtex-extra
+        sudo apt-get install graphviz
 
     - name: Build doxygen HTML
       run: |

.github/workflows/regression.yml

@@ -23,5 +23,5 @@ jobs:
     - name: Create validation data
       run: make run.symmetric -k -s
 
-    - name: Regression test 
+    - name: Regression test
       run: make test.regressions DO_REGRESSION_TESTS=true -k -s

.gitignore

@@ -4,13 +4,7 @@
 html
 
 
-# Build output
-*.o
-*.mod
-MOM6
-
-
-# Autoconf
+# Autoconf output
 aclocal.m4
 autom4te.cache/
 config.log

.readthedocs.yml

@@ -1,8 +1,9 @@
 version: 2
 
 # Extra formats
-formats:
-  - pdf
+# PDF generation is failing for now; disabled on 2020-12-02
+#formats:
+#  - pdf
 
 # Build documentation
 sphinx:

ac/configure.ac

@@ -82,18 +82,57 @@ AX_FC_CHECK_MODULE([mpi],
 
 
 # netCDF configuration
-AC_PATH_PROG([NC_CONFIG], [nc-config])
-AS_IF([test -n "$NC_CONFIG"],
-  [CPPFLAGS="$CPPFLAGS -I$($NC_CONFIG --includedir)"
-  FCFLAGS="$FCFLAGS -I$($NC_CONFIG --includedir)"
-  LDFLAGS="$LDFLAGS -L$($NC_CONFIG --libdir)"],
-  [AC_MSG_ERROR([Could not find nc-config.])])
-
-AX_FC_CHECK_MODULE([netcdf],
-  [], [AC_MSG_ERROR([Could not find netcdf module.])])
-AX_FC_CHECK_LIB([netcdff], [nf_create], [netcdf],
-  [], [AC_MSG_ERROR([Could not link netcdff library.])]
-)
+
+# Search for the Fortran netCDF module, fallback to nf-config.
+AX_FC_CHECK_MODULE([netcdf], [], [
+  AS_UNSET([ax_fc_cv_mod_netcdf])
+  AC_PATH_PROG([NF_CONFIG], [nf-config])
+  AS_IF([test -n "$NF_CONFIG"], [
+    AC_SUBST([FCFLAGS], ["$FCFLAGS -I$($NF_CONFIG --includedir)"])
+    ], [AC_MSG_ERROR([Could not find nf-config.])]
+  )
+  AX_FC_CHECK_MODULE([netcdf], [], [
+    AC_MSG_ERROR([Could not find netcdf module.])
+  ])
+])
+
+# FMS may invoke netCDF C calls, so we link to libnetcdf.
+AC_LANG_PUSH([C])
+AC_CHECK_LIB([netcdf], [nc_create], [], [
+  AS_UNSET([ac_cv_lib_netcdf_nc_create])
+  AC_PATH_PROG([NC_CONFIG], [nc-config])
+  AS_IF([test -n "$NC_CONFIG"], [
+    AC_SUBST([LDFLAGS],
+      ["$LDFLAGS -L$($NC_CONFIG --libdir)"]
+    )
+    ], [AC_MSG_ERROR([Could not find nc-config.])]
+  )
+  AC_CHECK_LIB([netcdf], [nc_create], [], [
+    AC_MSG_ERROR([Could not find libnetcdf.])
+  ])
+])
+AC_LANG_POP([C])
+
+# NOTE: We test for nf_create, rather than nf90_create, because AX_FC_CHECK_LIB
+#   is currently not yet able to properly probe inside modules.
+#   Testing of the nf90_* functions will require a macro update.
+# NOTE: nf-config does not have a --libdir flag, so we use --prefix and assume
+#   that libraries are in the $prefix/lib directory.
+
+# Link to Fortran netCDF library, netcdff
+AX_FC_CHECK_LIB([netcdff], [nf_create], [], [], [
+  AS_UNSET([ax_fc_cv_lib_netcdff_nf_create])
+  AC_PATH_PROG([NF_CONFIG], [nf-config])
+  AS_IF([test -n "$NF_CONFIG"], [
+    AC_SUBST([LDFLAGS],
+      ["$LDFLAGS -L$($NF_CONFIG --prefix)/lib"]
+    )
+    ], [AC_MSG_ERROR([Could not find nf-config.])]
+  )
+  AX_FC_CHECK_LIB([netcdff], [nf_create], [], [], [
+    AC_MSG_ERROR([Could not find libnetcdff.])
+  ])
+])
 
 
 # Force 8-byte reals

ac/deps/Makefile

@@ -13,7 +13,7 @@ MKMF_COMMIT ?= master
 
 # FMS framework
 FMS_URL ?= https://github.com/NOAA-GFDL/FMS.git
-FMS_COMMIT ?= 2019.01.03
+FMS_COMMIT ?= 2020.04
 
 
 # List of source files to link this Makefile's dependencies to model Makefiles

ac/deps/configure.fms.ac

@@ -15,6 +15,7 @@ AC_PROG_CC
 AX_MPI
 CC=$MPICC
 
+
 # FMS configuration
 
 # Linux and macOS have a gettid system call, but it is not implemented in older
@@ -73,18 +74,39 @@ AC_DEFINE([use_libMPI])
 
 
 # netCDF configuration
-AC_PATH_PROG([NC_CONFIG], [nc-config])
-AS_IF([test -n "$NC_CONFIG"],
-  [CPPFLAGS="$CPPFLAGS -I$($NC_CONFIG --includedir)"
-  FCFLAGS="$FCFLAGS -I$($NC_CONFIG --includedir)"
-  LDFLAGS="$LDFLAGS -L$($NC_CONFIG --libdir)"],
-  [AC_MSG_ERROR([Could not find nc-config.])])
-
-AX_FC_CHECK_MODULE([netcdf],
-  [], [AC_MSG_ERROR([Could not find netcdf module.])])
-AX_FC_CHECK_LIB([netcdff], [nf_create], [netcdf],
-  [], [AC_MSG_ERROR([Could not link netcdff library.])]
-)
+
+# Check for netcdf.h header function declarations.
+# If unavailable, then try to invoke nc-create.
+AC_LANG_PUSH([C])
+AC_CHECK_HEADERS([netcdf.h], [], [
+  AS_UNSET([ac_cv_header_netcdf_h])
+  AC_PATH_PROG([NC_CONFIG], [nc-config])
+  AS_IF([test -n "$NC_CONFIG"], [
+      AC_SUBST([CPPFLAGS], ["$CPPFLAGS -I$($NC_CONFIG --includedir)"])
+    ],
+    [AC_MSG_ERROR([Could not find nc-config.])]
+  )
+  AC_CHECK_HEADERS([netcdf.h], [], [
+    AC_MSG_ERROR([Could not find netcdf.h])
+  ])
+])
+AC_LANG_POP([C])
+
+# Search for the Fortran netCDF module, fallback to nf-config.
+AX_FC_CHECK_MODULE([netcdf], [], [
+  AS_UNSET([ax_fc_cv_mod_netcdf])
+  AC_PATH_PROG([NF_CONFIG], [nf-config])
+  AS_IF([test -n "$NF_CONFIG"], [
+      AC_SUBST([FCFLAGS], ["$FCFLAGS -I$($NF_CONFIG --includedir)"])
+    ],
+    [AC_MSG_ERROR([Could not find nf-config.])]
+  )
+  AX_FC_CHECK_MODULE([netcdf], [], [
+    AC_MSG_ERROR([Could not find netcdf module.])
+  ])
+])
+
+# FMS requires this macro to signal netCDF support.
 AC_DEFINE([use_netCDF])
 
 

ac/m4/ax_fc_check_lib.m4

@@ -18,7 +18,7 @@ dnl    library with different -L flags, or perhaps other ld configurations.
 dnl
 dnl Results are cached in the ax_fc_cv_lib_LIBRARY_FUNCTION variable.
 dnl
-AC_DEFUN([AX_FC_CHECK_LIB],[dnl
+AC_DEFUN([AX_FC_CHECK_LIB],[
   AS_VAR_PUSHDEF([ax_fc_Lib], [ax_fc_cv_lib_$1_$2])
   m4_ifval([$6],
     [ax_fc_lib_msg_LDFLAGS=" with $6"],
@@ -29,14 +29,15 @@ AC_DEFUN([AX_FC_CHECK_LIB],[dnl
     LDFLAGS="$6 $LDFLAGS"
     ax_fc_check_lib_save_LIBS=$LIBS
     LIBS="-l$1 $7 $LIBS"
-    AS_IF([test -n $3],
+    AS_IF([test -n "$3"],
       [ax_fc_use_mod="use $3"],
       [ax_fc_use_mod=""])
-    AC_LINK_IFELSE([
-        AC_LANG_PROGRAM([], [dnl
+    AC_LINK_IFELSE([dnl
+dnl Begin 7-column code block
+AC_LANG_PROGRAM([], [dnl
         $ax_fc_use_mod
-        call $2]dnl
-        )
+        call $2])dnl
+dnl End code block
       ],
       [AS_VAR_SET([ax_fc_Lib], [yes])],
       [AS_VAR_SET([ax_fc_Lib], [no])]

config_src/coupled_driver/MOM_surface_forcing_gfdl.F90

@@ -1664,7 +1664,8 @@ subroutine check_mask_val_consistency(val, mask, i, j, varname, G)
 
   real, intent(in) :: val  !< value of flux/variable passed by IOB
   real, intent(in) :: mask !< value of ocean mask
-  integer, intent(in) :: i, j !< model grid cell indices
+  integer, intent(in) :: i !< model grid cell indices
+  integer, intent(in) :: j !< model grid cell indices
   character(len=*), intent(in) :: varname !< variable name
   type(ocean_grid_type), intent(in) :: G !< The ocean's grid structure
   ! Local variables

config_src/coupled_driver/ocean_model_MOM.F90

@@ -48,6 +48,7 @@ module ocean_model_mod
 use MOM_verticalGrid, only : verticalGrid_type
 use MOM_ice_shelf, only : initialize_ice_shelf, shelf_calc_flux, ice_shelf_CS
 use MOM_ice_shelf, only : add_shelf_forces, ice_shelf_end, ice_shelf_save_restart
+use MOM_IS_diag_mediator, only : diag_IS_ctrl => diag_ctrl, diag_mediator_IS_end=>diag_mediator_end
 use coupler_types_mod, only : coupler_1d_bc_type, coupler_2d_bc_type
 use coupler_types_mod, only : coupler_type_spawn, coupler_type_write_chksums
 use coupler_types_mod, only : coupler_type_initialized, coupler_type_copy_data
@@ -121,6 +122,8 @@ module ocean_model_mod
                         !! i.e. dzt(1) + eta_t + patm/rho0/grav [m]
     frazil =>NULL(), &  !< Accumulated heating [J m-2] from frazil
                         !! formation in the ocean.
+    melt_potential => NULL(), & !< Instantaneous heat used to melt sea ice [J m-2].
+    OBLD => NULL(),   & !< Ocean boundary layer depth [m].
     area => NULL()      !< cell area of the ocean surface [m2].
   type(coupler_2d_bc_type) :: fields    !< A structure that may contain named
                                         !! arrays of tracer-related surface fields.
@@ -179,13 +182,13 @@ module ocean_model_mod
                               !! processes before time stepping the dynamics.
 
   type(directories) :: dirs   !< A structure containing several relevant directory paths.
-  type(mech_forcing) :: forces !< A structure with the driving mechanical surface forces
-  type(forcing)   :: fluxes   !< A structure containing pointers to
-                              !! the thermodynamic ocean forcing fields.
-  type(forcing)   :: flux_tmp !< A secondary structure containing pointers to the
+  type(mech_forcing), pointer :: forces => NULL() !< A structure with the driving mechanical surface forces
+  type(forcing), pointer      :: fluxes => NULL()   !< A structure containing pointers to
+                                                    !! the thermodynamic ocean forcing fields.
+  type(forcing), pointer      :: flux_tmp => NULL() !< A secondary structure containing pointers to the
                               !! ocean forcing fields for when multiple coupled
                               !! timesteps are taken per thermodynamic step.
-  type(surface)   :: sfc_state !< A structure containing pointers to
+  type(surface), pointer      :: sfc_state => NULL() !< A structure containing pointers to
                               !! the ocean surface state fields.
   type(ocean_grid_type), pointer :: &
     grid => NULL()            !< A pointer to a grid structure containing metrics
@@ -214,6 +217,9 @@ module ocean_model_mod
                               !! that will be used for MOM restart files.
   type(diag_ctrl), pointer :: &
     diag => NULL()            !< A pointer to the diagnostic regulatory structure
+  type(diag_IS_ctrl), pointer :: &
+    diag_IS => NULL()         !< A pointer to the diagnostic regulatory structure
+                              !! for the ice shelf module.
 end type ocean_state_type
 
 contains
@@ -267,6 +273,10 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, wind_stagger, gas
   endif
   allocate(OS)
 
+  allocate(OS%fluxes)
+  allocate(OS%forces)
+  allocate(OS%flux_tmp)
+
   OS%is_ocean_pe = Ocean_sfc%is_ocean_pe
   if (.not.OS%is_ocean_pe) return
 
@@ -355,6 +365,7 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, wind_stagger, gas
     use_melt_pot=.false.
   endif
 
+  allocate(OS%sfc_state)
   call allocate_surface_state(OS%sfc_state, OS%grid, use_temperature, do_integrals=.true., &
                               gas_fields_ocn=gas_fields_ocn, use_meltpot=use_melt_pot)
 
@@ -368,7 +379,7 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, wind_stagger, gas
 
   if (OS%use_ice_shelf)  then
     call initialize_ice_shelf(param_file, OS%grid, OS%Time, OS%ice_shelf_CSp, &
-                              OS%diag, OS%forces, OS%fluxes)
+                              OS%diag_IS, OS%forces, OS%fluxes)
   endif
   if (OS%icebergs_alter_ocean)  then
     call marine_ice_init(OS%Time, OS%grid, param_file, OS%diag, OS%marine_ice_CSp)
@@ -717,6 +728,8 @@ subroutine ocean_model_end(Ocean_sfc, Ocean_state, Time)
 
   call ocean_model_save_restart(Ocean_state, Time)
   call diag_mediator_end(Time, Ocean_state%diag)
+  if (Ocean_state%use_ice_shelf) &
+    call diag_mediator_IS_end(Time, Ocean_state%diag_IS)
   call MOM_end(Ocean_state%MOM_CSp)
   if (Ocean_state%use_ice_shelf) call ice_shelf_end(Ocean_state%Ice_shelf_CSp)
 end subroutine ocean_model_end
@@ -794,6 +807,8 @@ subroutine initialize_ocean_public_type(input_domain, Ocean_sfc, diag, maskmap,
              Ocean_sfc%v_surf (isc:iec,jsc:jec), &
              Ocean_sfc%sea_lev(isc:iec,jsc:jec), &
              Ocean_sfc%area   (isc:iec,jsc:jec), &
+             Ocean_sfc%melt_potential(isc:iec,jsc:jec), &
+             Ocean_sfc%OBLD   (isc:iec,jsc:jec), &
              Ocean_sfc%frazil (isc:iec,jsc:jec))
 
   Ocean_sfc%t_surf(:,:)  = 0.0  ! time averaged sst (Kelvin) passed to atmosphere/ice model
@@ -802,6 +817,8 @@ subroutine initialize_ocean_public_type(input_domain, Ocean_sfc, diag, maskmap,
   Ocean_sfc%v_surf(:,:)  = 0.0  ! time averaged v-current (m/sec)  passed to atmosphere/ice models
   Ocean_sfc%sea_lev(:,:) = 0.0  ! time averaged thickness of top model grid cell (m) plus patm/rho0/grav
   Ocean_sfc%frazil(:,:)  = 0.0  ! time accumulated frazil (J/m^2) passed to ice model
+  Ocean_sfc%melt_potential(:,:)  = 0.0  ! time accumulated melt potential (J/m^2) passed to ice model
+  Ocean_sfc%OBLD(:,:)    = 0.0  ! ocean boundary layer depth (m)
   Ocean_sfc%area(:,:)    = 0.0
   Ocean_sfc%axes    = diag%axesT1%handles !diag axes to be used by coupler tracer flux diagnostics
 
@@ -887,6 +904,18 @@ subroutine convert_state_to_ocean_type(sfc_state, Ocean_sfc, G, US, patm, press_
     enddo ; enddo
   endif
 
+  if (allocated(sfc_state%melt_potential)) then
+    do j=jsc_bnd,jec_bnd ; do i=isc_bnd,iec_bnd
+      Ocean_sfc%melt_potential(i,j) = US%Q_to_J_kg*US%RZ_to_kg_m2 * sfc_state%melt_potential(i+i0,j+j0)
+    enddo ; enddo
+  endif
+
+  if (allocated(sfc_state%Hml)) then
+    do j=jsc_bnd,jec_bnd ; do i=isc_bnd,iec_bnd
+      Ocean_sfc%OBLD(i,j) = US%Z_to_m * sfc_state%Hml(i+i0,j+j0)
+    enddo ; enddo
+  endif
+
   if (Ocean_sfc%stagger == AGRID) then
     do j=jsc_bnd,jec_bnd ; do i=isc_bnd,iec_bnd
       Ocean_sfc%u_surf(i,j) = G%mask2dT(i+i0,j+j0) * US%L_T_to_m_s * &
@@ -1064,6 +1093,10 @@ subroutine ocean_model_data2D_get(OS, Ocean, name, array2D, isc, jsc)
      array2D(isc:,jsc:) = Ocean%sea_lev(isc:,jsc:)
   case('frazil')
      array2D(isc:,jsc:) = Ocean%frazil(isc:,jsc:)
+  case('melt_pot')
+     array2D(isc:,jsc:) = Ocean%melt_potential(isc:,jsc:)
+  case('obld')
+     array2D(isc:,jsc:) = Ocean%OBLD(isc:,jsc:)
   case default
      call MOM_error(FATAL,'get_ocean_grid_data2D: unknown argument name='//name)
   end select
@@ -1109,7 +1142,7 @@ subroutine ocean_public_type_chksum(id, timestep, ocn)
   write(outunit,100) 'ocean%v_surf   ',mpp_chksum(ocn%v_surf )
   write(outunit,100) 'ocean%sea_lev  ',mpp_chksum(ocn%sea_lev)
   write(outunit,100) 'ocean%frazil   ',mpp_chksum(ocn%frazil )
-
+  write(outunit,100) 'ocean%melt_potential  ',mpp_chksum(ocn%melt_potential)
   call coupler_type_write_chksums(ocn%fields, outunit, 'ocean%')
 100 FORMAT("   CHECKSUM::",A20," = ",Z20)