Merge branch 'dev/gfdl' into nonBous_brine_plume

.github/workflows/coupled-api.yml

@@ -28,7 +28,3 @@ jobs:
     - name: Compile MOM6 for the NUOPC driver
       shell: bash
       run: make check_mom6_api_nuopc -j
-
-    - name: Compile MOM6 for the MCT driver
-      shell: bash
-      run: make check_mom6_api_mct -j

.readthedocs.yml

@@ -1,5 +1,14 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
 # Extra formats
 # PDF generation is failing for now; disabled on 2020-12-02
 #formats:
@@ -10,7 +19,5 @@ sphinx:
   configuration: docs/conf.py
 
 python:
-  # make sure we're using Python 3
-  version: 3
   install:
     - requirements: docs/requirements.txt

.testing/Makefile

@@ -75,7 +75,7 @@ MAKEFLAGS += -R
 -include config.mk
 
 # Set the infra framework
-FRAMEWORK ?= fms1
+FRAMEWORK ?= fms2
 
 # Set the MPI launcher here
 # TODO: This needs more automated configuration
@@ -245,43 +245,33 @@ COV_LDFLAGS := LDFLAGS="$(LDFLAGS_COVERAGE) $(LDFLAGS_DEPS) $(LDFLAGS_USER)"
 
 
 # Environment variable configuration
-build/symmetric/Makefile: MOM_ENV=$(PATH_FMS) $(SYMMETRIC_FCFLAGS) $(MOM_LDFLAGS)
-build/asymmetric/Makefile: MOM_ENV=$(PATH_FMS) $(ASYMMETRIC_FCFLAGS) $(MOM_LDFLAGS) \
+MOM_ENV := $(PATH_FMS)
+build/symmetric/Makefile: MOM_ENV += $(SYMMETRIC_FCFLAGS) $(MOM_LDFLAGS)
+build/asymmetric/Makefile: MOM_ENV += $(ASYMMETRIC_FCFLAGS) $(MOM_LDFLAGS) \
   MOM_MEMORY=../../../config_src/memory/dynamic_nonsymmetric/MOM_memory.h
-build/repro/Makefile: MOM_ENV=$(PATH_FMS) $(REPRO_FCFLAGS) $(MOM_LDFLAGS)
-build/openmp/Makefile: MOM_ENV=$(PATH_FMS) $(OPENMP_FCFLAGS) $(MOM_LDFLAGS)
-build/target/Makefile: MOM_ENV=$(PATH_FMS) $(TARGET_FCFLAGS) $(MOM_LDFLAGS)
-build/opt/Makefile: MOM_ENV=$(PATH_FMS) $(OPT_FCFLAGS) $(MOM_LDFLAGS)
-build/opt_target/Makefile: MOM_ENV=$(PATH_FMS) $(OPT_FCFLAGS) $(MOM_LDFLAGS)
-build/coupled/Makefile: MOM_ENV=$(PATH_FMS) $(SYMMETRIC_FCFLAGS) $(MOM_LDFLAGS)
-build/nuopc/Makefile: MOM_ENV=$(PATH_FMS) $(SYMMETRIC_FCFLAGS) $(MOM_LDFLAGS)
-build/mct/Makefile: MOM_ENV=$(PATH_FMS) $(SYMMETRIC_FCFLAGS) $(MOM_LDFLAGS)
-build/cov/Makefile: MOM_ENV=$(PATH_FMS) $(COV_FCFLAGS) $(COV_LDFLAGS)
-build/unit/Makefile: MOM_ENV=$(PATH_FMS) $(COV_FCFLAGS) $(COV_LDFLAGS)
+build/repro/Makefile: MOM_ENV += $(REPRO_FCFLAGS) $(MOM_LDFLAGS)
+build/openmp/Makefile: MOM_ENV += $(OPENMP_FCFLAGS) $(MOM_LDFLAGS)
+build/target/Makefile: MOM_ENV += $(TARGET_FCFLAGS) $(MOM_LDFLAGS)
+build/opt/Makefile: MOM_ENV += $(OPT_FCFLAGS) $(MOM_LDFLAGS)
+build/opt_target/Makefile: MOM_ENV += $(OPT_FCFLAGS) $(MOM_LDFLAGS)
+build/coupled/Makefile: MOM_ENV += $(SYMMETRIC_FCFLAGS) $(MOM_LDFLAGS)
+build/nuopc/Makefile: MOM_ENV += $(SYMMETRIC_FCFLAGS) $(MOM_LDFLAGS)
+build/cov/Makefile: MOM_ENV += $(COV_FCFLAGS) $(COV_LDFLAGS)
+build/unit/Makefile: MOM_ENV += $(COV_FCFLAGS) $(COV_LDFLAGS)
 
 # Configure script flags
-build/symmetric/Makefile: MOM_ACFLAGS=
-build/asymmetric/Makefile: MOM_ACFLAGS=
-build/repro/Makefile: MOM_ACFLAGS=
-build/openmp/Makefile: MOM_ACFLAGS=--enable-openmp
-build/target/Makefile: MOM_ACFLAGS=
-build/opt/Makefile: MOM_ACFLAGS=
-build/opt_target/Makefile: MOM_ACFLAGS=
-build/coupled/Makefile: MOM_ACFLAGS=--with-driver=FMS_cap
-build/nuopc/Makefile: MOM_ACFLAGS=--with-driver=nuopc_cap
-build/mct/Makefile: MOM_ACFLAGS=--with-driver=mct_cap
-build/cov/Makefile: MOM_ACFLAGS=
-build/unit/Makefile: MOM_ACFLAGS=--with-driver=unit_tests
+MOM_ACFLAGS := --with-framework=$(FRAMEWORK)
+build/openmp/Makefile: MOM_ACFLAGS += --enable-openmp
+build/coupled/Makefile: MOM_ACFLAGS += --with-driver=FMS_cap
+build/nuopc/Makefile: MOM_ACFLAGS += --with-driver=nuopc_cap
+build/unit/Makefile: MOM_ACFLAGS += --with-driver=unit_tests
 
 # Fetch regression target source code
 build/target/Makefile: | $(TARGET_CODEBASE)
 build/opt_target/Makefile: | $(TARGET_CODEBASE)
 
 
 # Define source code dependencies
-# NOTE: ./configure is too much, but Makefile is not enough!
-#   Ideally we only want to re-run both Makefile and mkmf, but the mkmf call
-#   is inside ./configure, so we must re-run ./configure as well.
 build/target_codebase/configure: $(TARGET_SOURCE)
 
 
@@ -297,8 +287,8 @@ build/%/MOM6: build/%/Makefile $(MOM_SOURCE)
 build/%/Makefile: ../ac/configure ../ac/Makefile.in deps/lib/libFMS.a
 	mkdir -p $(@D)
 	cd $(@D) \
-	  && $(MOM_ENV) ../../../ac/configure $(MOM_ACFLAGS) --with-framework=$(FRAMEWORK) \
-	  || (cat config.log && false)
+	&& $(MOM_ENV) ../../../ac/configure $(MOM_ACFLAGS) \
+	|| (cat config.log && false)
 
 
 ../ac/configure: ../ac/configure.ac ../ac/m4
@@ -310,8 +300,8 @@ build/target/Makefile build/opt_target/Makefile: \
   $(TARGET_CODEBASE)/ac/configure deps/lib/libFMS.a
 	mkdir -p $(@D)
 	cd $(@D) \
-	  && $(MOM_ENV) ../../$(TARGET_CODEBASE)/ac/configure $(MOM_ACFLAGS) \
-	  || (cat config.log && false)
+	&& $(MOM_ENV) ../../$(TARGET_CODEBASE)/ac/configure $(MOM_ACFLAGS) \
+	|| (cat config.log && false)
 
 
 $(TARGET_CODEBASE)/ac/configure: $(TARGET_CODEBASE)
@@ -370,11 +360,6 @@ build/coupled/ocean_model_MOM.o: build/coupled/Makefile
 	cd $(@D) && make $(@F)
 check_mom6_api_coupled: build/coupled/ocean_model_MOM.o
 
-# MCT driver
-build/mct/mom_ocean_model_mct.o: build/mct/Makefile
-	cd $(@D) && make $(@F)
-check_mom6_api_mct: build/mct/mom_ocean_model_mct.o
-
 
 #---
 # Testing

ac/deps/Makefile

@@ -8,7 +8,7 @@ MAKEFLAGS += -R
 
 # FMS framework
 FMS_URL ?= https://github.com/NOAA-GFDL/FMS.git
-FMS_COMMIT ?= 2019.01.03
+FMS_COMMIT ?= 2023.03
 
 
 # List of source files to link this Makefile's dependencies to model Makefiles

ac/deps/Makefile.fms.in

@@ -23,4 +23,4 @@ ARFLAGS = @ARFLAGS@
 .PHONY: depend
 depend: Makefile.dep
 Makefile.dep:
-	$(PYTHON) $(MAKEDEP) -o Makefile.dep -e -x libFMS.a @srcdir@
+	$(PYTHON) $(MAKEDEP) -o Makefile.dep -e -x libFMS.a -s @srcdir@/test_fms @srcdir@

ac/makedep

@@ -25,12 +25,12 @@ re_procedure = re.compile(
 )
 
 
-def create_deps(src_dirs, makefile, debug, exec_target, fc_rule,
+def create_deps(src_dirs, skip_dirs, makefile, debug, exec_target, fc_rule,
                 link_externals, script_path):
     """Create "makefile" after scanning "src_dis"."""
 
     # Scan everything Fortran related
-    all_files = find_files(src_dirs)
+    all_files = find_files(src_dirs, skip_dirs)
 
     # Lists of things
     #  ... all F90 source
@@ -332,10 +332,15 @@ def object_file(src_file):
     return os.path.splitext(os.path.basename(src_file))[0] + '.o'
 
 
-def find_files(src_dirs):
+def find_files(src_dirs, skip_dirs):
     """Return sorted list of all source files starting from each directory in
     the list "src_dirs"."""
 
+    if skip_dirs is not None:
+        skip = [os.path.normpath(s) for s in skip_dirs]
+    else:
+        skip = []
+
     # TODO: Make this a user-defined argument
     extensions = ('.f90', '.f', '.c', '.inc', '.h',  '.fh')
 
@@ -345,6 +350,8 @@ def find_files(src_dirs):
         if not os.path.isdir(path):
             raise ValueError("Directory '{}' was not found".format(path))
         for p, d, f in os.walk(os.path.normpath(path), followlinks=True):
+            d[:] = [s for s in d if os.path.join(p, s) not in skip]
+
             for file in f:
                 if any(file.lower().endswith(ext) for ext in extensions):
                     files.append(p+'/'+file)
@@ -392,8 +399,13 @@ parser.add_argument(
     action='store_true',
     help="Annotate the makefile with extra information."
 )
+parser.add_argument(
+    '-s', '--skip',
+    action='append',
+    help="Skip directory in source code search."
+)
 args = parser.parse_args()
 
 # Do the thing
-create_deps(args.path, args.makefile, args.debug, args.exec_target,
+create_deps(args.path, args.skip, args.makefile, args.debug, args.exec_target,
             args.fc_rule, args.link_externals, sys.argv[0])

config_src/drivers/FMS_cap/ocean_model_MOM.F90

@@ -1197,6 +1197,14 @@ subroutine ocean_model_get_UV_surf(OS, Ocean, name, array2D, isc, jsc)
       array2D(i,j) = G%mask2dBu(I+i0,J+j0) * &
                 0.5*(sfc_state%v(i+i0,J+j0)+sfc_state%v(i+i0+1,J+j0))
     enddo ; enddo
+  case('uc')
+    do j=jsc_bnd,jec_bnd ; do i=isc_bnd,iec_bnd
+      array2D(i,j) = G%mask2dCu(I+i0,J+j0) * sfc_state%u(I+i0,j+j0)
+    enddo ; enddo
+  case('vc')
+    do j=jsc_bnd,jec_bnd ; do i=isc_bnd,iec_bnd
+      array2D(i,j) = G%mask2dCv(I+i0,J+j0) * sfc_state%v(i+i0,J+j0)
+    enddo ; enddo
   case default
     call MOM_error(FATAL,'ocean_model_get_UV_surf: unknown argument name='//name)
   end select

config_src/drivers/mct_cap/mom_ocean_model_mct.F90 → config_src/drivers/STALE_mct_cap/mom_ocean_model_mct.F90

@@ -369,7 +369,7 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, gas_fields_ocn, i
 
   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, Time_init, OS%dirs%output_directory, OS%forces, OS%fluxes)
   endif
 
   if (OS%icebergs_alter_ocean)  then

config_src/drivers/ice_solo_driver/ice_shelf_driver.F90

@@ -24,7 +24,7 @@ program Shelf_main
   use MOM_cpu_clock,       only : cpu_clock_id, cpu_clock_begin, cpu_clock_end
   use MOM_cpu_clock,       only : CLOCK_COMPONENT
   use MOM_debugging,       only : MOM_debugging_init
-  use MOM_diag_mediator,   only : diag_mediator_init, diag_mediator_infrastructure_init
+  use MOM_diag_mediator,   only : diag_mediator_init, diag_mediator_infrastructure_init, set_axes_info
   use MOM_diag_mediator,   only : diag_mediator_end, diag_ctrl, diag_mediator_close_registration
   use MOM_domains,         only : MOM_infra_init, MOM_infra_end
   use MOM_domains,         only : MOM_domains_init, clone_MOM_domain, pass_var
@@ -54,6 +54,8 @@ program Shelf_main
   use MOM_verticalGrid,    only : verticalGrid_type, verticalGridInit, verticalGridEnd
   use MOM_write_cputime,   only : write_cputime, MOM_write_cputime_init
   use MOM_write_cputime,   only : write_cputime_start_clock, write_cputime_CS
+  use MOM_forcing_type,    only : forcing
+  use MOM_ice_shelf_initialize, only : initialize_ice_SMB
 
   use MOM_ice_shelf, only : initialize_ice_shelf, ice_shelf_end, ice_shelf_CS
   use MOM_ice_shelf, only : ice_shelf_save_restart, solo_step_ice_shelf
@@ -75,7 +77,9 @@ program Shelf_main
   ! CPU time limit.  nmax is determined by evaluating the CPU time used between successive calls to
   ! write_cputime.  Initially it is set to be very large.
   integer :: nmax=2000000000
-
+  ! A structure containing pointers to the thermodynamic forcing fields
+  ! at the ocean surface.
+  type(forcing) :: fluxes
   ! A structure containing several relevant directory paths.
   type(directories) :: dirs
 
@@ -104,7 +108,7 @@ program Shelf_main
   real :: time_step               ! The time step [T ~> s]
 
   ! A pointer to a structure containing metrics and related information.
-  type(ocean_grid_type), pointer :: ocn_grid
+  type(ocean_grid_type), pointer :: ocn_grid => NULL()
 
   type(dyn_horgrid_type), pointer :: dG => NULL()   ! A dynamic version of the horizontal grid
   type(hor_index_type),   pointer :: HI => NULL()   ! A hor_index_type for array extents
@@ -114,7 +118,7 @@ program Shelf_main
   type(ocean_OBC_type),          pointer :: OBC => NULL()
 
   ! A pointer to a structure containing dimensional unit scaling factors.
-  type(unit_scale_type), pointer :: US
+  type(unit_scale_type), pointer :: US => NULL()
 
   type(diag_ctrl), pointer :: &
     diag => NULL()              ! A pointer to the diagnostic regulatory structure
@@ -138,8 +142,9 @@ program Shelf_main
   integer :: yr, mon, day, hr, mins, sec   ! Temp variables for writing the date.
   type(param_file_type) :: param_file      ! The structure indicating the file(s)
                                            ! containing all run-time parameters.
+  real :: smb !A constant surface mass balance that can be specified in the param_file
   character(len=9)  :: month
-  character(len=16) :: calendar = 'julian'
+  character(len=16) :: calendar = 'noleap'
   integer :: calendar_type=-1
 
   integer :: unit, io_status, ierr
@@ -184,6 +189,8 @@ program Shelf_main
     endif
   endif
 
+  ! Get the names of the I/O directories and initialization file.
+  ! Also calls the subroutine that opens run-time parameter files.
   call Get_MOM_Input(param_file, dirs)
 
   ! Read ocean_solo restart, which can override settings from the namelist.
@@ -252,8 +259,11 @@ program Shelf_main
   ! Set up the ocean model domain and grid; the ice model grid is set in initialize_ice_shelf,
   ! but the grids have strong commonalities in this configuration, and the ocean grid is required
   ! to set up the diag mediator control structure.
-  call MOM_domains_init(ocn_grid%domain, param_file)
+  allocate(ocn_grid)
+  call MOM_domains_init(ocn_grid%domain, param_file) !, domain_name='MOM')
+  allocate(HI)
   call hor_index_init(ocn_grid%Domain, HI, param_file)
+  allocate(dG)
   call create_dyn_horgrid(dG, HI)
   call clone_MOM_domain(ocn_grid%Domain, dG%Domain)
 
@@ -266,11 +276,17 @@ program Shelf_main
   ! Initialize the diag mediator.  The ocean's vertical grid is not really used here, but at
   ! present the interface to diag_mediator_init assumes the presence of ocean-specific information.
   call verticalGridInit(param_file, GV, US)
+  allocate(diag)
   call diag_mediator_init(ocn_grid, GV, US, GV%ke, param_file, diag, doc_file_dir=dirs%output_directory)
 
   call callTree_waypoint("returned from diag_mediator_init()")
 
-  call initialize_ice_shelf(param_file, ocn_grid, Time, ice_shelf_CSp, diag)
+  call set_axes_info(ocn_grid, GV, US, param_file, diag)
+
+  call initialize_ice_shelf(param_file, ocn_grid, Time, ice_shelf_CSp, diag, &
+                            Start_time, dirs%output_directory, fluxes_in=fluxes, solo_ice_sheet_in=.true.)
+
+  call initialize_ice_SMB(fluxes%shelf_sfc_mass_flux, ocn_grid, US, param_file)
 
   ! This is the end of the code that is the counterpart of MOM_initialization.
   call callTree_waypoint("End of ice shelf initialization.")
@@ -378,7 +394,7 @@ program Shelf_main
 
     ! This call steps the model over a time time_step.
     Time1 = Master_Time ; Time = Master_Time
-    call solo_step_ice_shelf(ice_shelf_CSp, Time_step_shelf, ns_ice, Time)
+    call solo_step_ice_shelf(ice_shelf_CSp, Time_step_shelf, ns_ice, Time, fluxes_in=fluxes)
 
 !   Time = Time + Time_step_shelf
 !   This is here to enable fractional-second time steps.
@@ -412,6 +428,20 @@ program Shelf_main
       if (BTEST(Restart_control,0)) then
         call ice_shelf_save_restart(ice_shelf_CSp, Time, dirs%restart_output_dir)
       endif
+      ! Write ice shelf solo restart file.
+      if (is_root_pe())then
+        call open_ASCII_file(unit, trim(dirs%restart_output_dir)//'shelf.res')
+        write(unit, '(i6,8x,a)') calendar_type, &
+          '(Calendar: no_calendar=0, thirty_day_months=1, julian=2, gregorian=3, noleap=4)'
+
+        call get_date(Start_time, yr, mon, day, hr, mins, sec)
+        write(unit, '(6i6,8x,a)') yr, mon, day, hr, mins, sec, &
+          'Model start time:   year, month, day, hour, minute, second'
+        call get_date(Time, yr, mon, day, hr, mins, sec)
+        write(unit, '(6i6,8x,a)') yr, mon, day, hr, mins, sec, &
+          'Current model time: year, month, day, hour, minute, second'
+        call close_file(unit)
+      endif
       restart_time = restart_time + restint
     endif
 
@@ -456,12 +486,11 @@ program Shelf_main
   endif
 
   call callTree_waypoint("End Shelf_main")
+  call ice_shelf_end(ice_shelf_CSp)
   call diag_mediator_end(Time, diag, end_diag_manager=.true.)
   if (cpu_steps > 0) call write_cputime(Time, ns-1, write_CPU_CSp, call_end=.true.)
   call cpu_clock_end(termClock)
 
   call io_infra_end ; call MOM_infra_end
 
-  call ice_shelf_end(ice_shelf_CSp)
-
 end program Shelf_main