Update grid generation process for coupled grids (#830)

- Update the grid generation process to create grids for running the
coupled atm/ocn model.
- New program "ocean_merge" that determines the water mask by merging
the lake mask with the mapped ocean mask from MOM6.
- The orog program was modified to optionally read in an external land mask.
Also, when setting the orography at land/water points, use land fraction 
to determine land/water points instead of land mask.
- Updated link_fixdirs.sh to point to the 202310127 version of the 'orog' directory.

Fixes #825

CMakeLists.txt

@@ -30,6 +30,7 @@ option(FVCOMTOOLS "Enable building fvcom_tools.fd" ON)
 option(GBLEVENTS "Enable building gblevents.fd" ON)
 option(CPLD_GRIDGEN "Enable building cpld_gridgen.fd" ON)
 option(WEIGHT_GEN "Enable building weight_gen.fd" ON)
+option(OCEAN_MERGE "Enable building ocean_merge.fd" ON)
 
 # Option to build application specific utilities
 option(GFS "Enable building GFS-only utilities" OFF)
@@ -46,6 +47,7 @@ if(GFS)
   set(GBLEVENTS OFF CACHE BOOL "Disable building gblevents.fd" FORCE)
   set(CPLD_GRIDGEN OFF CACHE BOOL "Disable building cpld_gridgen.fd" FORCE)
   set(WEIGHT_GEN OFF CACHE BOOL "Disable building weight_gen.fd" FORCE)
+  set(OCEAN_MERGE OFF CACHE BOOL "Disable building ocean_merge.fd" FORCE)
 endif()
 
 SET(TEST_FILE_DIR "." CACHE STRING "Check this directory for test files before using FTP.")

cmake/mpiexec.hera

@@ -6,7 +6,7 @@
 #   $2+ - Executable and its arguments
 #
 
-ACCOUNT=gsd-fv3
+ACCOUNT=fv3-cpu
 QOS=debug
 
 NP=$1

docs/main.md

@@ -24,6 +24,9 @@ https://github.com/ufs-community/UFS_UTILS.
 - <a href="chgres_cube/index.html">chgres_cube</a> - Creates cold
   start initial conditions for FV3 model runs.
 
+- <a href="cpld_gridgen/index.html">cpld_gridgen</a> - Utility to 
+  create the Fix and IC files for the S2SW and S2S applications 
+
 - <a href="emcsfc_ice_blend/index.html">emcsfc_ice_blend</a> - Blends
   National Ice Center sea ice cover and EMC sea ice concentration data
   to create a global sea ice analysis used to update the GFS once per
@@ -57,6 +60,15 @@ https://github.com/ufs-community/UFS_UTILS.
   gnomonic grids, and to compute the equivalent global resolution of a
   regional grid.
 
+- <a href="lsm_routines/index.html">lsm_routines</a> - Land surface 
+  model-specific routines that are utilised elsewhere within UFS_UTILS.
+  Currently, contains the routines required by global_cycle to 
+  perform data assimilation updates to land model states
+
+- <a href="ocean_merge/index.html">ocean_merge</a> - Utility to 
+  determine the water mask by merging a lake mask with a mapped
+  ocean mask from MOM6.
+
 - <a href="orog_mask_tools/index.html">orog_mask_tools</a> - Utilities
   to create land mask, terrain and gravity wave drag fields; set lake
   fraction and depth; creates an inland land mask.
@@ -70,14 +82,6 @@ https://github.com/ufs-community/UFS_UTILS.
   top and the number of vertical levels. Outputs the 'ak' and 'bk'
   parameters used by the forecast model to define the hybrid levels.
 
-- <a href="lsm_routines/index.html">lsm_routines</a> - Land surface 
-  model-specific routines that are utilised elsewhere within UFS_UTILS.
-  Currently, contains the routines required by global_cycle to 
-  perform data assimilation updates to land model states
-
-- <a href="cpld_gridgen/index.html">cpld_gridgen</a> - Utility to 
-  create the Fix and IC files for the S2SW and S2S applications 
-
 - <a href="weight_gen/index.html">weight_gen</a> - Utility to 
   create gaussian grid ESMF 'scrip' files for use in creating
   ESMF interpolation weight files.

driver_scripts/driver_grid.hera.sh

@@ -5,10 +5,10 @@
 #SBATCH --open-mode=truncate
 #SBATCH -o log.fv3_grid_driver
 #SBATCH -e log.fv3_grid_driver
-#SBATCH --nodes=1 --ntasks-per-node=24
+#SBATCH --nodes=6 --ntasks-per-node=12
 #SBATCH --partition=bigmem
 #SBATCH -q debug
-#SBATCH -t 00:20:00
+#SBATCH -t 00:30:00
 
 #-----------------------------------------------------------------------
 # Driver script to create a cubic-sphere based model grid on Hera.
@@ -103,7 +103,7 @@ export soil_type_src="bnu.v3.30s" #  Soil type data.
                                 # 3) "statsgo.conus.30s" for CONUS 30s data
                                 # 4) "statsgo.nh.30s" for NH 30s data
                                 # 5) "statsgo.30s" for global 30s data
-                                # For Beijing Norm. Univ. data
+                                 # For Beijing Norm. Univ. data
                                 # 1) "bnu.v3.30s" for global 30s data.
 
 # choose dataset sources for lakefrac & lakedepth so that lake_data_srce=LakeFrac_LakeDepth; 
@@ -115,6 +115,7 @@ if [ $gtype = uniform ]; then
   export add_lake=true         # Add lake frac and depth to orography data.
   export lake_cutoff=0.50      # return 0 if lake_frac <  lake_cutoff & add_lake=T
   export binary_lake=1         # return 1 if lake_frac >= lake_cutoff & add_lake=T
+  export ocn=${ocn:-"025"}     # use one of  "025", "050", "100", "500". Cannot be empty
 elif [ $gtype = stretch ]; then
   export res=96
   export stretch_fac=1.5       # Stretching factor for the grid
@@ -150,14 +151,15 @@ fi
 
 #-----------------------------------------------------------------------
 # Check paths.
+#
 #   home_dir - location of repository.
 #   TEMP_DIR - working directory.
 #   out_dir  - where files will be placed upon completion.
 #-----------------------------------------------------------------------
 
 export home_dir=$SLURM_SUBMIT_DIR/..
 export TEMP_DIR=/scratch2/NCEPDEV/stmp1/$LOGNAME/fv3_grid.$gtype
-export out_dir=/scratch2/NCEPDEV/stmp1/$LOGNAME/my_grids
+export out_dir=/scratch2/NCEPDEV/stmp1/$LOGNAME/my_grids_ocean_fixed/
 
 #-----------------------------------------------------------------------
 # Should not need to change anything below here.

driver_scripts/driver_grid.jet.sh

@@ -113,6 +113,7 @@ if [ $gtype = uniform ]; then
   export add_lake=true         # Add lake frac and depth to orography data.
   export lake_cutoff=0.50      # return 0 if lake_frac <  lake_cutoff & add_lake=T
   export binary_lake=1         # return 1 if lake_frac >= lake_cutoff & add_lake=T
+  export ocn=${ocn:-"025"}     # use one of  "025", "050", "100", "500". Cannot be empty
 elif [ $gtype = stretch ]; then
   export res=96
   export stretch_fac=1.5       # Stretching factor for the grid
@@ -156,7 +157,6 @@ fi
 export home_dir=$SLURM_SUBMIT_DIR/..
 export TEMP_DIR=/lfs4/HFIP/emcda/$LOGNAME/stmp/fv3_grid.$gtype
 export out_dir=/lfs4/HFIP/emcda/$LOGNAME/stmp/my_grids
-
 #-----------------------------------------------------------------------
 # Should not need to change anything below here.
 #-----------------------------------------------------------------------

driver_scripts/driver_grid.orion.sh

@@ -112,6 +112,7 @@ if [ $gtype = uniform ]; then
   export add_lake=true         # Add lake frac and depth to orography data.
   export lake_cutoff=0.50      # return 0 if lake_frac <  lake_cutoff & add_lake=T
   export binary_lake=1         # return 1 if lake_frac >= lake_cutoff & add_lake=T
+  export ocn=${ocn:-"025"}     # use one of  "025", "050", "100", "500". Cannot be empty	
 elif [ $gtype = stretch ]; then
   export res=96
   export stretch_fac=1.5       # Stretching factor for the grid

driver_scripts/driver_grid.wcoss2.sh

@@ -111,6 +111,7 @@ if [ $gtype = uniform ]; then
   export add_lake=true         # Add lake frac and depth to orography data.
   export lake_cutoff=0.50      # return 0 if lake_frac <  lake_cutoff & add_lake=T
   export binary_lake=1         # return 1 if lake_frac >= lake_cutoff & add_lake=T
+  export ocn=${ocn:-"025"}     # use one of  "025", "050", "100", "500". Cannot be empty
 elif [ $gtype = stretch ]; then
   export res=96
   export stretch_fac=1.5       # Stretching factor for the grid
@@ -154,7 +155,6 @@ fi
 export home_dir=$PBS_O_WORKDIR/..
 export TEMP_DIR=/lfs/h2/emc/stmp/$LOGNAME/fv3_grid.$gtype
 export out_dir=/lfs/h2/emc/stmp/$LOGNAME/my_grids
-
 #-----------------------------------------------------------------------
 # Should not need to change anything below here unless you want to
 # to change the job card for the number of tasks to use. Then,

fix/link_fixdirs.sh

@@ -57,7 +57,7 @@ elif [ $machine = "s4" ]; then
 fi
 
 am_ver=${am_ver:-20220805}
-orog_ver=${orog_ver:-20220805}
+orog_ver=${orog_ver:-20231027}
 sfc_climo_ver=${sfc_climo_ver:-20230925}
 
 for dir in am orog orog_raw sfc_climo; do

reg_tests/grid_gen/c96.uniform.sh

@@ -44,7 +44,7 @@ echo "Ending at: " `date`
 cd $out_dir/C96
 
 test_failed=0
-for files in *tile*.nc ./fix_sfc/*tile*.nc
+for files in *tile*.nc ./sfc/*tile*.nc
 do
   if [ -f $files ]; then
     echo CHECK $files

reg_tests/grid_gen/c96.viirs.bnu.sh

@@ -43,7 +43,7 @@ echo "Ending at: " `date`
 cd $out_dir/C96
 
 test_failed=0
-for files in *tile*.nc ./fix_sfc/*tile*.nc
+for files in *tile*.nc ./sfc/*tile*.nc
 do
   if [ -f $files ]; then
     echo CHECK $files

reg_tests/grid_gen/esg.regional.pct.cat.sh

@@ -50,7 +50,7 @@ echo "Ending at: " `date`
 cd $out_dir/C3113
 
 test_failed=0
-for files in *tile*.nc ./fix_sfc/*tile*.nc
+for files in *tile*.nc ./sfc/*tile*.nc
 do
   if [ -f $files ]; then
     echo CHECK $files

reg_tests/grid_gen/esg.regional.sh

@@ -46,7 +46,7 @@ echo "Ending at: " `date`
 cd $out_dir/C3113
 
 test_failed=0
-for files in *tile*.nc ./fix_sfc/*tile*.nc
+for files in *tile*.nc ./sfc/*tile*.nc
 do
   if [ -f $files ]; then
     echo CHECK $files

reg_tests/grid_gen/gfdl.regional.sh

@@ -49,7 +49,7 @@ echo "Ending at: " `date`
 cd $out_dir/C424
 
 test_failed=0
-for files in *tile*.nc ./fix_sfc/*tile*.nc
+for files in *tile*.nc ./sfc/*tile*.nc
 do
   if [ -f $files ]; then
     echo CHECK $files

reg_tests/grid_gen/regional.gsl.gwd.sh

@@ -47,7 +47,7 @@ echo "Ending at: " `date`
 cd $out_dir/C772
 
 test_failed=0
-for files in *tile*.nc ./fix_sfc/*tile*.nc
+for files in *tile*.nc ./sfc/*tile*.nc
 do
   if [ -f $files ]; then
     echo CHECK $files

sorc/CMakeLists.txt

@@ -46,3 +46,7 @@ endif()
 if(WEIGHT_GEN)
   add_subdirectory(weight_gen.fd)
 endif()
+if(OCEAN_MERGE)
+  add_subdirectory(ocean_merge.fd)
+endif()
+

sorc/ocean_merge.fd/CMakeLists.txt

@@ -0,0 +1,26 @@
+list(APPEND fortran_src
+  merge_lake_ocnmsk.f90
+)
+
+if(CMAKE_Fortran_COMPILER_ID MATCHES "^(Intel)$")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -r8 -i4 -convert big_endian")
+elseif(CMAKE_Fortran_COMPILER_ID MATCHES "^(GNU)$")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fdefault-real-8")
+  if(CMAKE_Fortran_COMPILER_VERSION VERSION_GREATER_EQUAL 10)
+    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fallow-argument-mismatch")
+  endif()
+endif()
+
+set(exe_name ocean_merge)
+add_executable(${exe_name} ${fortran_src})
+target_link_libraries(
+  ${exe_name}
+
+  NetCDF::NetCDF_Fortran)
+
+install(TARGETS ${exe_name})
+
+# If doxygen documentation we enabled, build it.
+if(ENABLE_DOCS)
+  add_subdirectory(docs)
+endif()

sorc/ocean_merge.fd/docs/CMakeLists.txt

@@ -0,0 +1,15 @@
+# This is the CMake file for building this docs directory.
+#
+# Ed Hartnett 3/9/21
+
+# Create doxyfile.
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY)
+
+# Build documentation with target all.
+add_custom_target(ocean_merge_doc ALL
+  ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile
+  WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+  COMMENT "Generating API Documentation with Doxygen" VERBATIM)
+
+# Ensure top-level docs have been generated.
+add_dependencies(ocean_merge_doc doc)