feature/coupled-crow updating to use latest ups-weather

parm/mom6/MOM_input_template_100

@@ -72,15 +72,17 @@ WRITE_GEOM = 2                  ! default = 1
                                 ! If =0, never write the geometry and vertical grid files. If =1, write the
                                 ! geometry and vertical grid files only for a new simulation. If =2, always
                                 ! write the geometry and vertical grid files. Other values are invalid.
+SAVE_INITIAL_CONDS = True       !   [Boolean] default = False
+                                ! If true, write the initial conditions to a file given by IC_OUTPUT_FILE.
 
 ! === module MOM_domains ===
 TRIPOLAR_N = True               !   [Boolean] default = False
                                 ! Use tripolar connectivity at the northern edge of the domain.  With
                                 ! TRIPOLAR_N, NIGLOBAL must be even.
-NIGLOBAL = NX_GLB                  !
+NIGLOBAL = NX_GLB               !
                                 ! The total number of thickness grid points in the x-direction in the physical
                                 ! domain. With STATIC_MEMORY_ this is set in MOM_memory.h at compile time.
-NJGLOBAL = NY_GLB                  !
+NJGLOBAL = NY_GLB               !
                                 ! The total number of thickness grid points in the y-direction in the physical
                                 ! domain. With STATIC_MEMORY_ this is set in MOM_memory.h at compile time.
 
@@ -106,7 +108,7 @@ GRID_ROTATION_ANGLE_BUGS = False  ! [Boolean] default = True
                                 ! If true, use an older algorithm to calculate the sine and
                                 ! cosines needed rotate between grid-oriented directions and
                                 ! true north and east.  Differences arise at the tripolar fold
-USE_TRIPOLAR_GEOLONB_BUG = False !   [Boolean] default = False
+USE_TRIPOLAR_GEOLONB_BUG = False !   [Boolean] default = True
                                 ! If true, use older code that incorrectly sets the longitude in some points
                                 ! along the tripolar fold to be off by 360 degrees.
 TOPO_CONFIG = "file"            !
@@ -165,6 +167,13 @@ CHANNEL_CONFIG = "list"         ! default = "none"
                                 !       NetCDF file on the model grid.
 CHANNEL_LIST_FILE = "MOM_channels_SPEAR" ! default = "MOM_channel_list"
                                 ! The file from which the list of narrowed channels is read.
+GRID_ROTATION_ANGLE_BUGS = False !   [Boolean] default = False
+                                ! If true, use an older algorithm to calculate the sine and cosines needed
+                                ! rotate between grid-oriented directions and true north and east.  Differences
+                                ! arise at the tripolar fold.
+USE_TRIPOLAR_GEOLONB_BUG = False !   [Boolean] default = False
+                                ! If true, use older code that incorrectly sets the longitude in some points
+                                ! along the tripolar fold to be off by 360 degrees.
 
 ! === module MOM_verticalGrid ===
 ! Parameters providing information about the vertical grid.
@@ -291,19 +300,22 @@ INIT_LAYERS_FROM_Z_FILE = True  !   [Boolean] default = False
                                 ! Z-space file on a latitude-longitude grid.
 
 ! === module MOM_initialize_layers_from_Z ===
-TEMP_SALT_Z_INIT_FILE = "MOM6_IC_TS.nc"
+TEMP_SALT_Z_INIT_FILE = "MOM6_IC_TS.nc"  ! default = "temp_salt_z.nc"
                                 ! The name of the z-space input file used to initialize
                                 ! temperatures (T) and salinities (S). If T and S are not
                                 ! in the same file, TEMP_Z_INIT_FILE and SALT_Z_INIT_FILE
                                 ! must be set.
-Z_INIT_FILE_PTEMP_VAR = "temp" ! default = "ptemp"
+Z_INIT_FILE_PTEMP_VAR = "temp"  ! default = "ptemp"
                                 ! The name of the potential temperature variable in
                                 ! TEMP_Z_INIT_FILE.
 Z_INIT_FILE_SALT_VAR = "salt"   ! default = "salt"
                                 ! The name of the salinity variable in
                                 ! SALT_Z_INIT_FILE.
 Z_INIT_ALE_REMAPPING = True     !   [Boolean] default = False
                                 ! If True, then remap straight to model coordinate from file.
+Z_INIT_REMAP_OLD_ALG = True     !   [Boolean] default = False
+                                ! If false, uses the preferred remapping algorithm for initialization. If true,
+                                ! use an older, less robust algorithm for remapping.
 
 ! === module MOM_diag_mediator ===
 !Jiande NUM_DIAG_COORDS = 2             ! default = 1
@@ -317,9 +329,25 @@ DIAG_COORDS = "z Z ZSTAR"
                                 ! is of the form "MODULE_SUFFIX,PARAMETER_SUFFIX,COORDINATE_NAME".
 DIAG_COORD_DEF_Z="FILE:interpolate_zgrid_40L.nc,interfaces=zw"
 DIAG_MISVAL = -1e34
-!Jiande DIAG_COORD_DEF_RHO2 = "RFNC1:35,999.5,1028,1028.5,8.,1038.,0.0078125" ! default = "WOA09"
-                                ! Determines how to specify the coordinate
-                                ! resolution. Valid options are:
+!AVAILABLE_DIAGS_FILE = "available_diags.002160" ! default = "available_diags.000000"
+                                ! A file into which to write a list of all available ocean diagnostics that can
+                                ! be included in a diag_table.
+!DIAG_COORD_DEF_Z = "FILE:vgrid_75_2m.nc,dz" ! default = "WOA09"
+                                ! Determines how to specify the coordinate resolution. Valid options are:
+                                !  PARAM       - use the vector-parameter DIAG_COORD_RES_Z
+                                !  UNIFORM[:N] - uniformly distributed
+                                !  FILE:string - read from a file. The string specifies
+                                !                the filename and variable name, separated
+                                !                by a comma or space, e.g. FILE:lev.nc,dz
+                                !                or FILE:lev.nc,interfaces=zw
+                                !  WOA09[:N]   - the WOA09 vertical grid (approximately)
+                                !  FNC1:string - FNC1:dz_min,H_total,power,precision
+                                !  HYBRID:string - read from a file. The string specifies
+                                !                the filename and two variable names, separated
+                                !                by a comma or space, for sigma-2 and dz. e.g.
+                                !                HYBRID:vgrid.nc,sigma2,dz
+!DIAG_COORD_DEF_RHO2 = "RFNC1:35,999.5,1028,1028.5,8.,1038.,0.0078125" ! default = "WOA09"
+                                ! Determines how to specify the coordinate resolution. Valid options are:
                                 !  PARAM       - use the vector-parameter DIAG_COORD_RES_RHO2
                                 !  UNIFORM[:N] - uniformly distributed
                                 !  FILE:string - read from a file. The string specifies
@@ -377,7 +405,7 @@ KH_RES_FN_POWER = 100           !   [nondim] default = 2
                                 ! The power of dx/Ld in the Kh resolution function.  Any positive integer may be
                                 ! used, although even integers are more efficient to calculate.  Setting this
                                 ! greater than 100 results in a step-function being used.
-!JW VISC_RES_FN_POWER = 2           !   [nondim] default = 100
+VISC_RES_FN_POWER = 2           !   [nondim] default = 100
                                 ! The power of dx/Ld in the Kh resolution function.  Any positive integer may be
                                 ! used, although even integers are more efficient to calculate.  Setting this
                                 ! greater than 100 results in a step-function being used. This function affects
@@ -616,7 +644,7 @@ USE_JACKSON_PARAM = True        !   [Boolean] default = False
 MAX_RINO_IT = 25                !   [nondim] default = 50
                                 ! The maximum number of iterations that may be used to estimate the Richardson
                                 ! number driven mixing.
-VERTEX_SHEAR = True             !   [Boolean] default = False
+VERTEX_SHEAR = False             !   [Boolean] default = False
                                 ! If true, do the calculations of the shear-driven mixing
                                 ! at the cell vertices (i.e., the vorticity points).
 KD_TRUNC_KAPPA_SHEAR = 2.0E-07  !   [m2 s-1] default = 2.0E-07
@@ -639,14 +667,14 @@ KAPPA_SHEAR_ALL_LAYER_TKE_BUG = True !   [Boolean] default = False
 
 ! === module MOM_diabatic_aux ===
 ! The following parameters are used for auxiliary diabatic processes.
-PRESSURE_DEPENDENT_FRAZIL = false !   [Boolean] default = False
+PRESSURE_DEPENDENT_FRAZIL = False !   [Boolean] default = False
                                 ! If true, use a pressure dependent freezing temperature when making frazil. The
                                 ! default is false, which will be faster but is inappropriate with ice-shelf
                                 ! cavities.
 VAR_PEN_SW = True               !   [Boolean] default = False
                                 ! If true, use one of the CHL_A schemes specified by OPACITY_SCHEME to determine
                                 ! the e-folding depth of incoming short wave radiation.
-CHL_FILE = CHLCLIM
+CHL_FILE = CHLCLIM              !
                                 ! CHL_FILE is the file containing chl_a concentrations in the variable CHL_A. It
                                 ! is used when VAR_PEN_SW and CHL_FROM_FILE are true.
 
@@ -692,14 +720,6 @@ MIX_LEN_EXPONENT = 1.0          !   [nondim] default = 2.0
 USE_LA_LI2016 = MOM6_REPRO_LA   !   [nondim] default = False
                                 ! A logical to use the Li et al. 2016 (submitted) formula to determine the
                                 ! Langmuir number.
-EPBL_LANGMUIR_SCHEME = "ADDITIVE" ! default = "NONE"
-                                ! EPBL_LANGMUIR_SCHEME selects the method for including Langmuir turbulence.
-                                ! Valid values are:
-                                !    NONE     - Do not do any extra mixing due to Langmuir turbulence
-                                !    RESCALE  - Use a multiplicative rescaling of mstar to account for Langmuir
-                                !      turbulence
-                                !    ADDITIVE - Add a Langmuir turblence contribution to mstar to other
-                                !      contributions
 USE_WAVES = MOM6_USE_WAVES      !   [Boolean] default = False
                                 ! If true, enables surface wave modules.
 WAVE_METHOD = "SURFACE_BANDS"   ! default = "EMPTY"
@@ -723,6 +743,14 @@ STK_BAND_COUPLER = 3            ! default = 1
                                 ! will fail.
 SURFBAND_WAVENUMBERS = 0.04, 0.11, 0.3305 !   [rad/m] default = 0.12566
                                 ! Central wavenumbers for surface Stokes drift bands.
+EPBL_LANGMUIR_SCHEME = "ADDITIVE" ! default = "NONE"
+                                ! EPBL_LANGMUIR_SCHEME selects the method for including Langmuir turbulence.
+                                ! Valid values are:
+                                !    NONE     - Do not do any extra mixing due to Langmuir turbulence
+                                !    RESCALE  - Use a multiplicative rescaling of mstar to account for Langmuir
+                                !      turbulence
+                                !    ADDITIVE - Add a Langmuir turblence contribution to mstar to other
+                                !      contributions
 LT_ENHANCE_COEF = 0.044         !   [nondim] default = 0.447
                                 ! Coefficient for Langmuir enhancement of mstar
 LT_ENHANCE_EXP = -1.5           !   [nondim] default = -1.33
@@ -778,13 +806,14 @@ ENERGYSAVEDAYS = 0.25           !   [days] default = 1.0
                                 ! other globally summed diagnostics.
 
 ! === module ocean_model_init ===
+
+! === module MOM_surface_forcing ===
 OCEAN_SURFACE_STAGGER = "A"     ! default = "C"
                                 ! A case-insensitive character string to indicate the
                                 ! staggering of the surface velocity field that is
                                 ! returned to the coupler.  Valid values include
                                 ! 'A', 'B', or 'C'.
 
-! === module MOM_surface_forcing ===
 MAX_P_SURF = 0.0                !   [Pa] default = -1.0
                                 ! The maximum surface pressure that can be exerted by the atmosphere and
                                 ! floating sea-ice or ice shelves. This is needed because the FMS coupling

sorc/checkout.sh

@@ -17,8 +17,8 @@ if [[ ! -d ufs_coupled.fd ]] ; then
     git clone https://github.com/ufs-community/ufs-weather-model ufs_coupled.fd >> ${topdir}/checkout-ufs_coupled.log 2>&1
     cd ufs_coupled.fd
     #git checkout develop  
-    #checkout develop branch hash from 11/9/2020: 
-    git checkout 4e8ef6a879ceefb719cc9cebd8ac9c2208a58b16 
+    #checkout develop branch hash from 12/7/2020: 
+    git checkout 0cf031edc217707f3b5c912e0844e2c2b885ff82 
     git submodule update --init --recursive
     cd ${topdir}
 else

ush/cplvalidate.sh

@@ -14,22 +14,24 @@ case $confignamevarfornems in
 	'atm') combination=.false..false..false..false..false.;;
         'datm') combination=.true..true..false..false..false.;;
 	'med_atm_ocn_ice') combination=.true..true..true..false..false.;;
+        'cpld') combination=.true..true..true..false..false.;;
 	'blocked_atm_wav') combination=.true..false..false..true..false.;;
 	'leapfrog_atm_wav')combination=.true..false..false..true..false.;;
 	'med_atm_ocn_ice_wav') combination=.true..true..true..true..false.;;
+        'cpld_wave') combination=.true..true..true..true..false.;;
         'medcold_atm_ocn_ice_wav') combination=.true..true..true..true..false.;;
 	'med_atm_ocn_ice_wav1way') combination=.true..true..true..true..false.;;
 	'med_atm_ocn_ice_wav1waywcurr') combination=.true..true..true..true..false.;;
         'medcold_atm_ocn_ice_wav') combination=.true..true..true..true..false.;;
 	'medcold_atm_ocn_ice') combination=.true..true..true..false..false.;;
 	*) echo "SUB cplvalidate: Combination not supported" 
-		exit ;;
+		exit 1 ;;
 esac
 control=$cpl$cplflx$cplice$cplwav$cplchem
 #echo $control
 if [ $control != $combination ]; then
 	echo "SUB cplvalidate: inconsistent cpl setting!"
-	exit 1
+	exit 2
 else
 	echo "SUB cplvalidate: cpl settings validated!"
 fi

ush/forecast_postdet.sh

@@ -591,7 +591,7 @@ MOM6_postdet()
 
         # Copy mediator restart files to RUNDIR
         if [ $inistep = 'restart' ]; then
-           $NCP $ROTDIR/$CDUMP.$PDY/$cyc/ufs.s2s*.nc $DATA/
+           $NCP $ROTDIR/$CDUMP.$PDY/$cyc/ufs.cpld*.nc $DATA/
            $NCP $ROTDIR/$CDUMP.$PDY/$cyc/rpointer.cpl $DATA/
         fi
 
@@ -623,7 +623,7 @@ MOM6_out()
 	[[ ! -d $COMOUT ]] && mkdir -m 775 -p $COMOUT
 
         if [ $inistep = 'cold' ]; then
-               cp $DATA/ufs.s2s.cold.cpl.r.*.nc $COMOUT/
+               cp $DATA/ufs.cpld.cold.cpl.r.*.nc $COMOUT/
                cp $DATA/rpointer.cpl $COMOUT/
                status=$?
                exit $status

ush/nems.configure.med_atm_ocn_ice.IN → ush/nems.configure.cpld.IN

@@ -31,7 +31,6 @@ OCN_attributes::
   DumpFields = @[DumpFields]
   ProfileMemory = false
   OverwriteSlice = true
-  dbug_flag = 0 
 ::
 
 # ICE #
@@ -43,18 +42,18 @@ ICE_attributes::
   ProfileMemory = false
   OverwriteSlice = true
   mesh_ice = @[MESHICE]
-  stop_n = @[FHMAX]
+  stop_n = @[RESTART_N]
   stop_option = nhours
   stop_ymd = -999
 ::
 
 # CMEPS warm run sequence
 runSeq::
-@@[CPL_SLOW]
+@@[coupling_interval_slow_sec]
    MED med_phases_prep_ocn_accum_avg
    MED -> OCN :remapMethod=redist
    OCN
-   @@[CPL_FAST]
+   @@[coupling_interval_fast_sec]
      MED med_phases_prep_atm
      MED med_phases_prep_ice
      MED -> ATM :remapMethod=redist
@@ -77,7 +76,7 @@ runSeq::
 # CMEPS variables
 
 DRIVER_attributes::
-      mediator_read_restart = @[read_mediator]
+      mediator_read_restart = @[use_coldstart]
 ::
 MED_attributes::
       ATM_model = @[atm_model]
@@ -86,18 +85,18 @@ MED_attributes::
       history_n = 0
       history_option = nhours
       history_ymd = -999
-      coupling_mode = nems_orig
+      coupling_mode = @[CPLMODE]
 ::
 ALLCOMP_attributes::
       ScalarFieldCount = 2
       ScalarFieldIdxGridNX = 1
       ScalarFieldIdxGridNY = 2
       ScalarFieldName = cpl_scalars
-      start_type = startup
-      case_name = ufs.s2s
-      restart_n = @[restart_interval_hours]
+      start_type = @[RUNTYPE]
+      case_name = ./RESTART/ufs.cpld
+      restart_n = @[RESTART_N]
       restart_option = nhours
       restart_ymd = -999
-      dbug_flag = 0
-      use_coldstart = @[read_mediator]
+      dbug_flag = @[cap_dbug_flag]
+      use_coldstart = @[use_coldstart]
 ::

ush/nems.configure.med_atm_ocn_ice_wav.IN → ush/nems.configure.cpld_wave.IN

@@ -42,9 +42,9 @@ ICE_attributes::
   ProfileMemory = false
   OverwriteSlice = true
   mesh_ice = @[MESHICE]
-  stop_n = @[FHMAX]
+  stop_n = @[RESTART_N]
   stop_option = nhours
-  stop_ymd = -999
+  stop_ymd = -999  
 ::
 
 # WAV #
@@ -57,13 +57,13 @@ WAV_attributes::
 
 # CMEPS warm run sequence
 runSeq::
-@@[CPL_SLOW]
+@@[coupling_interval_slow_sec]
    MED med_phases_prep_ocn_accum_avg
    MED -> OCN :remapMethod=redist
    OCN -> WAV
    WAV -> OCN :srcMaskValues=1
    OCN
-   @@[CPL_FAST]
+   @@[coupling_interval_fast_sec]
      MED med_phases_prep_atm
      MED med_phases_prep_ice
      MED -> ATM :remapMethod=redist
@@ -90,7 +90,7 @@ runSeq::
 # CMEPS variables
 
 DRIVER_attributes::
-      mediator_read_restart = @[read_mediator]
+      mediator_read_restart = @[use_coldstart]
 ::
 MED_attributes::
       ATM_model = @[atm_model]
@@ -99,18 +99,18 @@ MED_attributes::
       history_n = 0
       history_option = nhours
       history_ymd = -999
-      coupling_mode = nems_orig
+      coupling_mode = @[CPLMODE]
 ::
 ALLCOMP_attributes::
       ScalarFieldCount = 2
       ScalarFieldIdxGridNX = 1
       ScalarFieldIdxGridNY = 2
       ScalarFieldName = cpl_scalars
-      start_type = startup
-      case_name = ufs.s2s
-      restart_n = @[restart_interval_hours]
+      start_type = @[RUNTYPE]
+      case_name = ./RESTART/ufs.cpld
+      restart_n = @[RESTART_N]
       restart_option = nhours
       restart_ymd = -999
-      dbug_flag = 0
-      use_coldstart = @[read_mediator]
+      dbug_flag = @[cap_dbug_flag]
+      use_coldstart = @[use_coldstart]
 ::

ush/nems.configure.medcold_atm_ocn_ice.IN

@@ -51,8 +51,8 @@ ICE_attributes::
 # CMEPS cold run sequence
 
 runSeq::
-  @@[CPL_SLOW]
-    @@[CPL_FAST]
+  @@[coupling_interval_slow_sec]
+    @@[coupling_interval_fast_sec]
       MED med_phases_prep_atm
       MED -> ATM :remapMethod=redist
       ATM
@@ -94,7 +94,7 @@ ALLCOMP_attributes::
       ScalarFieldIdxGridNY = 2
       ScalarFieldName = cpl_scalars
       start_type = startup
-      case_name = ufs.s2s.cold
+      case_name = ufs.cpld.cold
       restart_n = 1
       restart_option = nhours
       restart_ymd = -999