Merge gsl/develop to RRFS_dev

.github/pull_request_template.md

@@ -1,6 +1,6 @@
 # PR Checklist
 
-- [ ] Ths PR is up-to-date with the top of all sub-component repositories except for those sub-components which are the subject of this PR. Please consult the ufs-weather-model [wiki](https://github.com/ufs-community/ufs-weather-model/wiki/Making-code-changes-in-the-UFS-weather-model-and-its-subcomponents) if you are unsure how to do this.
+- [ ] This PR is up-to-date with the top of all sub-component repositories except for those sub-components which are the subject of this PR. Please consult the ufs-weather-model [wiki](https://github.com/ufs-community/ufs-weather-model/wiki/Making-code-changes-in-the-UFS-weather-model-and-its-subcomponents) if you are unsure how to do this.
 
 - [ ] This PR has been tested using a branch which is up-to-date with the top of all sub-component repositories except for those sub-components which are the subject of this PR
 

.gitmodules

@@ -2,10 +2,6 @@
   path = FV3
   url = https://github.com/NOAA-GSL/fv3atm
   branch = RRFS_dev
-[submodule "NEMS"]
-  path = NEMS
-  url = https://github.com/NOAA-EMC/NEMS
-  branch = develop
 [submodule "WW3"]
   path = WW3
   url = https://github.com/NOAA-EMC/WW3

CDEPS-interface/cdeps_files.cmake

@@ -44,6 +44,7 @@ list(APPEND cdeps_datm_files
   CDEPS/datm/datm_datamode_cplhist_mod.F90
   CDEPS/datm/datm_datamode_era5_mod.F90
   CDEPS/datm/datm_datamode_gefs_mod.F90
+  CDEPS/datm/datm_datamode_gfs_mod.F90
   CDEPS/datm/datm_datamode_jra_mod.F90
 )
 

CMEPS-interface/CMakeLists.txt

@@ -19,16 +19,11 @@ else()
 endif()
 
 list(APPEND _nems_util_files
-  CMEPS/util/shr_abort_mod.F90
-  CMEPS/util/shr_log_mod.F90
-  CMEPS/util/shr_sys_mod.F90
-  CMEPS/util/shr_flux_mod.F90
-  CMEPS/util/shr_mpi_mod.F90
-  CMEPS/util/glc_elevclass_mod.F90
-  CMEPS/util/shr_mem_mod.F90
-  CMEPS/util/shr_kind_mod.F90
-  CMEPS/util/perf_mod.F90
-  CMEPS/util/shr_const_mod.F90)
+  CMEPS/ufs/flux_atmocn_mod.F90
+  CMEPS/ufs/glc_elevclass_mod.F90
+  CMEPS/ufs/ufs_kind_mod.F90
+  CMEPS/ufs/perf_mod.F90
+  CMEPS/ufs/ufs_const_mod.F90)
 
 list(APPEND _mediator_files
   CMEPS/mediator/med_phases_restart_mod.F90

CMakeLists.txt

@@ -16,7 +16,7 @@ list(APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/CMakeModules/Modules)
 ###############################################################################
 
 # Valid applications and choices
-list(APPEND VALID_APPS ATM ATMAERO ATMW S2S S2SW HAFS HAFSW HAFS-ALL NG-GODAS NG-GODAS-NEMSDATM)
+list(APPEND VALID_APPS ATM ATMAERO ATMW S2S S2SW HAFS HAFSW HAFS-ALL NG-GODAS)
 set(APP NONE CACHE BOOL "Application Name")
 if(NOT (APP IN_LIST VALID_APPS))
   message(FATAL_ERROR "${APP} is not a valid application.\nValid Applications are: ${VALID_APPS}")
@@ -30,7 +30,6 @@ set(HYCOM           OFF CACHE BOOL "Enable HYCOM")
 set(CICE6           OFF CACHE BOOL "Enable CICE6")
 set(WW3             OFF CACHE BOOL "Enable WW3")
 set(STOCH_PHYS      OFF CACHE BOOL "Enable Stochastic Physics")
-set(NEMSdatm        OFF CACHE BOOL "Enable NEMSdatm")
 set(CMEPS           OFF CACHE BOOL "Enable CMEPS")
 set(CDEPS           OFF CACHE BOOL "Enable CDEPS")
 
@@ -47,7 +46,6 @@ message("HYCOM ............ ${HYCOM}")
 message("CICE6 ............ ${CICE6}")
 message("WW3 .............. ${WW3}")
 message("STOCH_PHYS ....... ${STOCH_PHYS}")
-message("NEMSdatm ......... ${NEMSdatm}")
 message("CDEPS ............ ${CDEPS}")
 message("CMEPS ............ ${CMEPS}")
 
@@ -81,7 +79,7 @@ endif()
 message("")
 message("32BIT ............ ${32BIT}")
 message("AVX2 ............. ${AVX2}")
-message("SIMDMULTIARCH ...  ${SIMDMULTIARCH}")
+message("SIMDMULTIARCH .... ${SIMDMULTIARCH}")
 message("DEBUG ............ ${DEBUG}")
 message("DEBUG_LINKMPI .... ${DEBUG_LINKMPI}")
 message("INLINE_POST ...... ${INLINE_POST}")
@@ -203,24 +201,16 @@ if(CMEPS)
 endif()
 
 ###############################################################################
-### Data Components [NEMSdatm, CDEPS]
+### Data Components [CDEPS]
 ###############################################################################
-if(NEMSdatm)
-  add_subdirectory(DATM/DATM)
-endif()
-
 if(CDEPS)
   add_subdirectory(CDEPS-interface)
 endif()
 
 ###############################################################################
-### UFS Library [NEMS]
+### UFS Library
 ###############################################################################
-list(APPEND _nems_srcs NEMS/src/module_EARTH_GRID_COMP.F90
-                       NEMS/src/module_NEMS_Rusage.F90
-                       NEMS/src/nems_c_rusage.c)
-
-add_library(ufs ${_nems_srcs})
+add_library(ufs driver/EARTH_GRID_COMP.F90)
 set_target_properties(ufs PROPERTIES Fortran_MODULE_DIRECTORY
                                      ${CMAKE_CURRENT_BINARY_DIR}/mod)
 target_include_directories(ufs INTERFACE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/mod>
@@ -249,12 +239,6 @@ if(STOCH_PHYS)
   list(APPEND _ufs_libs_public stochastic_physics)
 endif()
 
-if(NEMSdatm)
-  add_dependencies(ufs datatm)
-  list(APPEND _ufs_defs_private FRONT_NEMS_DATM=datm)
-  list(APPEND _ufs_libs_public datatm)
-endif()
-
 if(FV3)
   add_dependencies(ufs fv3atm)
   list(APPEND _ufs_defs_private FRONT_FV3=fv3gfs_cap_mod)
@@ -298,7 +282,7 @@ target_link_libraries(ufs PUBLIC "${_ufs_libs_public}")
 ###############################################################################
 ### UFS executable
 ###############################################################################
-add_executable(ufs_model NEMS/src/MAIN_NEMS.F90)
+add_executable(ufs_model driver/UFS.F90)
 add_dependencies(ufs_model ufs)
 target_link_libraries(ufs_model ufs esmf w3nco::w3nco_d)
 

MOM6-interface/CMakeLists.txt

@@ -46,6 +46,7 @@ target_include_directories(mom6_nuopc_obj PRIVATE $<BUILD_INTERFACE:${CMAKE_CURR
                                                   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/MOM6/src/framework>)
 target_link_libraries(mom6_nuopc_obj PRIVATE mom6_obj
                                              fms
+                                             stochastic_physics
                                              esmf)
 # OpenMP is disabled in MOM6
 #if(OpenMP_Fortran_FOUND)

MOM6-interface/mom6_files.cmake

@@ -39,6 +39,7 @@ list(APPEND mom6_src_files
   MOM6/src/core/MOM_interface_heights.F90
   MOM6/src/core/MOM_isopycnal_slopes.F90
   MOM6/src/core/MOM_open_boundary.F90
+  MOM6/src/core/MOM_porous_barriers.F90
   MOM6/src/core/MOM_transcribe_grid.F90
   MOM6/src/core/MOM_unit_tests.F90
   MOM6/src/core/MOM_variables.F90
@@ -181,6 +182,8 @@ list(APPEND mom6_src_files
   MOM6/src/parameterizations/CVmix/cvmix_tidal.F90
   MOM6/src/parameterizations/CVmix/cvmix_utils.F90
 
+  MOM6/src/parameterizations/stochastic/MOM_stochastics.F90
+
   MOM6/src/tracer/DOME_tracer.F90
 
   MOM6/src/tracer/ISOMIP_tracer.F90
@@ -255,7 +258,8 @@ list(APPEND mom6_src_files
   MOM6/config_src/external/ODA_hooks/ocean_da_core.F90
   MOM6/config_src/external/ODA_hooks/ocean_da_types.F90
   MOM6/config_src/external/ODA_hooks/write_ocean_obs.F90
-  MOM6/config_src/external/OCEAN_stochastic_phyiscs/MOM_stochastics.F90
+  MOM6/config_src/external/drifters/MOM_particles.F90
+  MOM6/config_src/external/drifters/MOM_particles_types.F90
 
   MOM6/config_src/infra/FMS1/MOM_coms_infra.F90
   MOM6/config_src/infra/FMS1/MOM_constants.F90

build.sh

@@ -11,13 +11,9 @@ export CC=${CC:-mpicc}
 export CXX=${CXX:-mpicxx}
 export FC=${FC:-mpif90}
 
-export ESMFMKFILE=${ESMFMKFILE:?"Please set ESMFMKFILE environment variable"}
-
 BUILD_DIR=${BUILD_DIR:-${UFS_MODEL_DIR}/build}
 mkdir -p ${BUILD_DIR}
 
-[[ -n "${MAPL_ROOT:-""}" ]] && CMAKE_FLAGS+=" -DCMAKE_MODULE_PATH=${MAPL_ROOT}/share/MAPL/cmake"
-
 cd ${BUILD_DIR}
 cmake ${UFS_MODEL_DIR} ${CMAKE_FLAGS}
 # Turn off OpenMP threading for parallel builds

cmake/configure_apps.cmake

@@ -25,19 +25,14 @@ if(APP MATCHES "^(ATM|ATMW)$")
   endif()
 endif()
 
-if(APP MATCHES "^(NG-GODAS|NG-GODAS-NEMSDATM)$")
+if(APP MATCHES "^(NG-GODAS)$")
   set(CMEPS      ON  CACHE BOOL "Enable CMEPS"               FORCE)
   set(STOCH_PHYS ON  CACHE BOOL "Enable Stochastic Physics"  FORCE)
   set(FMS        ON  CACHE BOOL "Enable FMS"                 FORCE)
   set(MOM6       ON  CACHE BOOL "Enable MOM6"                FORCE)
   set(CICE6      ON  CACHE BOOL "Enable CICE6"               FORCE)
-  if(APP MATCHES "NG-GODAS-NEMSDATM")
-    set(NEMSdatm ON  CACHE BOOL "Enable NEMS DataAtm"        FORCE)
-    message("Configuring UFS app in (NEMS) Data Atmosphere mode")
-  elseif(APP MATCHES "NG-GODAS")
-    set(CDEPS    ON  CACHE BOOL "Enable CDEPS"               FORCE)
-    message("Configuring UFS app in (CDEPS) Data Atmosphere mode")
-  endif()
+  set(CDEPS      ON  CACHE BOOL "Enable CDEPS"               FORCE)
+  message("Configuring UFS app in (CDEPS) Data Atmosphere mode")
 endif()
 
 if(APP MATCHES "^(S2S|S2SW)$")

doc/UsersGuide/source/InputsOutputs.rst

@@ -1146,10 +1146,6 @@ shows the following parameters that can be set in *model_configure* at run-time.
      - frequency to output restart file or forecast hours to write out restart file
      - integer
      - 0 (0: write restart file at the end of integration; 12, -1: write out restart every 12 hours; 12 24 write out restart files at fh=12 and 24)
-   * - atm_coupling_interval_sec
-     - fast coupling interval in seconds for atmosphere
-     - real(8)
-     - 900
    * - quilting
      - flag to turn on quilt
      - logical