Merge branch 'develop' into feature/mean2inst2

ufs-community · Nov 1, 2023 · 3747dcd · 3747dcd
2 parents 57c6987 + fccce42
commit 3747dcd
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Showing 109 changed files with 8,102 additions and 7,878 deletions.
diff --git a/CMEPS-interface/CMEPS b/CMEPS-interface/CMEPS
diff --git a/CMEPS-interface/CMakeLists.txt b/CMEPS-interface/CMakeLists.txt
@@ -29,7 +29,7 @@ endif()
 ### Source files
 ###############################################################################
 
-list(APPEND _nems_util_files
+list(APPEND _ufs_util_files
   CMEPS/ufs/flux_atmocn_mod.F90
   CMEPS/ufs/glc_elevclass_mod.F90
   CMEPS/ufs/ufs_kind_mod.F90
@@ -60,7 +60,7 @@ list(APPEND _mediator_files
   CMEPS/mediator/med_merge_mod.F90
   CMEPS/mediator/med_constants_mod.F90
   CMEPS/mediator/med_kind_mod.F90
-  CMEPS/mediator/esmFldsExchange_nems_mod.F90
+  CMEPS/mediator/esmFldsExchange_ufs_mod.F90
   CMEPS/mediator/med_phases_prep_lnd_mod.F90
   CMEPS/mediator/med_phases_prep_atm_mod.F90
   CMEPS/mediator/med_phases_prep_ocn_mod.F90
@@ -134,7 +134,7 @@ if(CMEPS_AOFLUX)
     endif(return_code EQUAL 0)
 
     ### Add extra driver file to the source
-    list(APPEND _nems_util_files
+    list(APPEND _ufs_util_files
       CMEPS/ufs/ccpp/driver/med_ccpp_driver.F90
       CMEPS/ufs/flux_atmocn_ccpp_mod.F90
       CMEPS/ufs/ufs_io_mod.F90)
@@ -172,7 +172,7 @@ endif()
 ###############################################################################
 
 ### Create target library
-add_library(cmeps STATIC ${_nems_util_files} ${_mediator_files} ${SCHEMES} ${CAPS} ${API})
+add_library(cmeps STATIC ${_ufs_util_files} ${_mediator_files} ${SCHEMES} ${CAPS} ${API})
 
 ### Set PUBLIC interfaces on the library
 set_target_properties(cmeps PROPERTIES Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)

diff --git a/FV3 b/FV3
diff --git a/driver/UFS.F90 b/driver/UFS.F90
@@ -91,7 +91,7 @@ PROGRAM UFS
 !***  Initialize the ESMF framework.
 !-----------------------------------------------------------------------
 !
-      CALL ESMF_Initialize(configFileName="nems.configure"              & !<-- top level configuration
+      CALL ESMF_Initialize(configFileName="ufs.configure"               & !<-- top level configuration
                           ,defaultCalKind =ESMF_CALKIND_GREGORIAN       & !<-- Set up the default calendar.
                           ,VM             =VM                           & !<-- The ESMF Virtual Machine
                           ,rc             =RC)

diff --git a/driver/UFSDriver.F90 b/driver/UFSDriver.F90
@@ -199,13 +199,13 @@ SUBROUTINE UFSDriver_SS(driver,RC)
       ! create, open, and set the config
       config = ESMF_ConfigCreate(rc=RC)
       if (ChkErr(rc,__LINE__,u_FILE_u)) return
-      call ESMF_ConfigLoadFile(config, "nems.configure", rc=RC)
+      call ESMF_ConfigLoadFile(config, "ufs.configure", rc=RC)
       if (ChkErr(rc,__LINE__,u_FILE_u)) return
       call ESMF_GridCompSet(driver, config=config, rc=RC)
       if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
-      ! Load the required entries from the fd_nems.yaml file
-      call NUOPC_FieldDictionarySetup("fd_nems.yaml", rc=rc)
+      ! Load the required entries from the fd_ufs.yaml file
+      call NUOPC_FieldDictionarySetup("fd_ufs.yaml", rc=rc)
       if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
 !-----------------------------------------------------------------------

diff --git a/modulefiles/ufs_gaea.intel.lua b/modulefiles/ufs_gaea.intel.lua
@@ -1,5 +1,5 @@
 help([[
-  This module loads libraries required for building and running UFS Weather Model 
+  This module loads libraries required for building and running UFS Weather Model
   on the NOAA RDHPC machine Gaea using Intel-2022.0.2
 ]])
 
@@ -26,6 +26,9 @@ load("alps")
 
 load("ufs_common")
 
+nccmp_ver=os.getenv("nccmp_ver") or "1.9.0.1"
+load(pathJoin("nccmp", nccmp_ver))
+
 setenv("CC","cc")
 setenv("CXX","CC")
 setenv("FC","ftn")

diff --git a/modulefiles/ufs_hera.gnu.lua b/modulefiles/ufs_hera.gnu.lua
@@ -17,6 +17,9 @@ load(pathJoin("cmake", cmake_ver))
 
 load("ufs_common")
 
+nccmp_ver=os.getenv("nccmp_ver") or "1.9.0.1"
+load(pathJoin("nccmp", nccmp_ver))
+
 setenv("CC", "mpicc")
 setenv("CXX", "mpic++")
 setenv("FC", "mpif90")

diff --git a/modulefiles/ufs_hera.intel.lua b/modulefiles/ufs_hera.intel.lua
@@ -15,6 +15,9 @@ load(pathJoin("cmake", cmake_ver))
 
 load("ufs_common")
 
+nccmp_ver=os.getenv("nccmp_ver") or "1.9.0.1"
+load(pathJoin("nccmp", nccmp_ver))
+
 setenv("CC", "mpiicc")
 setenv("CXX", "mpiicpc")
 setenv("FC", "mpiifort")

diff --git a/modulefiles/ufs_hercules.gnu.lua b/modulefiles/ufs_hercules.gnu.lua
@@ -17,6 +17,9 @@ load(pathJoin("cmake", cmake_ver))
 
 load("ufs_common")
 
+nccmp_ver=os.getenv("nccmp_ver") or "1.9.0.1"
+load(pathJoin("nccmp", nccmp_ver))
+
 setenv("CC", "mpicc")
 setenv("CXX", "mpic++")
 setenv("FC", "mpif90")

diff --git a/modulefiles/ufs_hercules.intel.lua b/modulefiles/ufs_hercules.intel.lua
@@ -15,6 +15,9 @@ load(pathJoin("cmake", cmake_ver))
 
 load("ufs_common")
 
+nccmp_ver=os.getenv("nccmp_ver") or "1.9.0.1"
+load(pathJoin("nccmp", nccmp_ver))
+
 setenv("CC", "mpiicc")
 setenv("CXX", "mpiicpc")
 setenv("FC", "mpiifort")

diff --git a/modulefiles/ufs_jet.intel.lua b/modulefiles/ufs_jet.intel.lua
@@ -15,6 +15,9 @@ load(pathJoin("cmake", cmake_ver))
 
 load("ufs_common")
 
+nccmp_ver=os.getenv("nccmp_ver") or "1.9.0.1"
+load(pathJoin("nccmp", nccmp_ver))
+
 setenv("CC", "mpiicc")
 setenv("CXX", "mpiicpc")
 setenv("FC", "mpiifort")

diff --git a/modulefiles/ufs_orion.intel.lua b/modulefiles/ufs_orion.intel.lua
@@ -15,6 +15,9 @@ load(pathJoin("cmake", cmake_ver))
 
 load("ufs_common")
 
+nccmp_ver=os.getenv("nccmp_ver") or "1.9.0.1"
+load(pathJoin("nccmp", nccmp_ver))
+
 setenv("CC", "mpiicc")
 setenv("CXX", "mpiicpc")
 setenv("FC", "mpiifort")

diff --git a/tests/default_vars.sh b/tests/default_vars.sh
@@ -338,8 +338,8 @@ export CMP_DATAONLY=false
 
 export_fv3 ()
 {
-# nems.configure defaults
-export NEMS_CONFIGURE=nems.configure.atm.IN
+# ufs.configure defaults
+export UFS_CONFIGURE=ufs.configure.atm.IN
 export MODEL_CONFIGURE=model_configure.IN
 export atm_model=fv3
 
@@ -368,6 +368,7 @@ export NUM_FILES=2
 export FILENAME_BASE="'atm' 'sfc'"
 export OUTPUT_GRID="'cubed_sphere_grid'"
 export OUTPUT_FILE="'netcdf'"
+export ZSTANDARD_LEVEL=0
 export IDEFLATE=0
 export NBITS=0
 export ICHUNK2D=0
@@ -708,8 +709,8 @@ export DT_CICE=${DT_ATMOS}
 export DT_DYNAM_MOM6=1800
 export DT_THERM_MOM6=3600
 
-# nems.configure defaults
-export NEMS_CONFIGURE=nems.configure.cpld.IN
+# ufs.configure defaults
+export UFS_CONFIGURE=ufs.configure.cpld.IN
 export med_model=cmeps
 export atm_model=fv3
 export chm_model=gocart
@@ -724,7 +725,7 @@ export coupling_interval_slow_sec=${DT_THERM_MOM6}
 export coupling_interval_fast_sec=${DT_ATMOS}
 
 export RESTART_N=${FHMAX}
-export CPLMODE=nems_frac
+export CPLMODE=ufs.frac
 export cap_dbug_flag=0
 export use_coldstart=false
 export use_mommesh=true
@@ -906,7 +907,7 @@ export MESH_WAV=mesh.${WAVDOMAIN}.nc
 export CICEGRID=grid_cice_NEMS_mx${OCNRES}.nc
 export CICEMASK=kmtu_cice_NEMS_mx${OCNRES}.nc
 export RUNID=unknown
-# set large; restart frequency now controlled by restart_n in nems.configure
+# set large; restart frequency now controlled by restart_n in ufs.configure
 export DUMPFREQ=d
 export DUMPFREQ_N=1000
 export DIAG_FREQ=`expr $FHMAX \* 3600 / $DT_CICE`
@@ -973,8 +974,8 @@ export ICERES=1.00
 export NX_GLB=360
 export NY_GLB=320
 
-# nems.configure
-export NEMS_CONFIGURE=nems.configure.datm_cdeps.IN
+# ufs.configure
+export UFS_CONFIGURE=ufs.configure.datm_cdeps.IN
 export med_model=cmeps
 export atm_model=datm
 export ocn_model=mom6
@@ -1010,7 +1011,7 @@ export coupling_interval_slow_sec=${DT_THERM_MOM6}
 export coupling_interval_fast_sec=${DT_ATMOS}
 
 export RESTART_N=${FHMAX}
-export CPLMODE=nems_orig_data
+export CPLMODE=ufs.nfrac.aoflux
 export cap_dbug_flag=0
 export use_coldstart=false
 export use_mommesh=true
@@ -1065,7 +1066,7 @@ export MESHOCN_ICE=mesh.mx${OCNRES}.nc
 export CICEGRID=grid_cice_NEMS_mx${OCNRES}.nc
 export CICEMASK=kmtu_cice_NEMS_mx${OCNRES}.nc
 export RUNID=unknown
-# set large; restart frequency now controlled by restart_n in nems.configure
+# set large; restart frequency now controlled by restart_n in ufs.configure
 export DUMPFREQ=d
 export DUMPFREQ_N=1000
 export DIAG_FREQ=`expr $FHMAX \* 3600 / $DT_CICE`
@@ -1183,7 +1184,7 @@ export DTPNT="$(printf "%02d" $(( ${WW3OUTDTHR}*3600 )))"
 export OUTPARS_WAV="WND HS T01 T02 DIR FP DP PHS PTP PDIR UST CHA USP"
 export WAV_CUR='C'
 
-# nems.configure
+# ufs.configure
 export med_model=cmeps
 export pio_rearranger=box
 export CAP_DBUG_FLAG=0

diff --git a/tests/fv3_conf/compile_slurm.IN_hercules b/tests/fv3_conf/compile_slurm.IN_hercules
diff --git a/tests/fv3_conf/cpld_control_run.IN b/tests/fv3_conf/cpld_control_run.IN
@@ -119,7 +119,7 @@ else
      ls -1 ${RFILE}>rpointer.cpl
 
      # CMEPS/CCPP restart file
-     if [[ $CPLMODE =~ 'nems_frac_aoflux' ]]; then
+     if [[ $CPLMODE =~ 'ufs.frac.aoflux' ]]; then
        RFILE_CCPP=ufs.cpld.cpl.ccpp.${RESTART_FILE_SUFFIX_SECS}.nc
        cp ../${DEP_RUN}${SUFFIX}/${RFILE_CCPP} .
      fi

diff --git a/tests/fv3_conf/fv3_slurm.IN_hercules b/tests/fv3_conf/fv3_slurm.IN_hercules
+4 −4		doc/source/addendum/req_attributes.rst
+19 −19		doc/source/esmflds.rst
+1 −1		doc/source/generic.rst
+66 −66		doc/source/introduction.rst
+9 −10		doc/source/prep.rst
+1 −1		mediator/CMakeLists.txt
+1 −1		mediator/ESMFConvenienceMacros.h
+1 −2		mediator/ESMFVersionDefine.h
+2 −2		mediator/Makefile
+9 −9		mediator/esmFldsExchange_ufs_mod.F90
+5 −5		mediator/med.F90
+3 −3		mediator/med_fraction_mod.F90
+2 −2		mediator/med_internalstate_mod.F90
+2 −2		mediator/med_map_mod.F90
+6 −6		mediator/med_phases_aofluxes_mod.F90
+1 −2		mediator/med_phases_prep_atm_mod.F90
+1 −1		io/module_fv3_io_def.F90
+57 −80		io/module_write_netcdf.F90
+13 −1		io/module_write_restart_netcdf.F90
+17 −1		io/module_wrt_grid_comp.F90