Allow increments to be added for ocean and ice cycling. (#1308)

Removed forgotten commented out call to the B-mat j-job in jobs/rocoto/ocnanalbmat.sh ... oops
Provide ocean increments via `mom6_increment.nc`
Link to the JEDI/SOCA increment in ush/forecast_postdet.sh
Fixed a dependency bug in workflow/rocoto/workflow_tasks.py
MOM6 Increment is required in ROTDIR for the first 1/2 cycle, changes reflected in workflow/setup_expt.py
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>

jobs/rocoto/ocnanalbmat.sh

@@ -13,7 +13,7 @@ export jobid="${job}.$$"
 
 ###############################################################
 # Execute the JJOB
-#"${HOMEgfs}"/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_BMAT
+"${HOMEgfs}"/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_BMAT
 echo "BMAT gets run here"
 status=$?
 exit "${status}"

parm/mom6/MOM_input_template_025

@@ -406,7 +406,7 @@ GILL_EQUATORIAL_LD = True       !   [Boolean] default = False
                                 ! radius, otherwise, if false, use Pedlosky's definition. These definitions
                                 ! differ by a factor of 2 in front of the beta term in the denominator. Gill's
                                 ! is the more appropriate definition.
-INTERNAL_WAVE_SPEED_BETTER_EST = False !   [Boolean] default = True 
+INTERNAL_WAVE_SPEED_BETTER_EST = False !   [Boolean] default = True
                                 ! If true, use a more robust estimate of the first mode wave speed as the
                                 ! starting point for iterations.
 
@@ -731,7 +731,7 @@ NSTAR = 0.06                    !   [nondim] default = 0.2
                                 ! The portion of the buoyant potential energy imparted by surface fluxes that is
                                 ! available to drive entrainment at the base of mixed layer when that energy is
                                 ! positive.
-EPBL_MLD_BISECTION = True       !   [Boolean] default = False 
+EPBL_MLD_BISECTION = True       !   [Boolean] default = False
                                 ! If true, use bisection with the iterative determination of the self-consistent
                                 ! mixed layer depth.  Otherwise use the false position after a maximum and
                                 ! minimum bound have been evaluated and the returned value or bisection before
@@ -833,6 +833,30 @@ ENERGYSAVEDAYS = 1.00           !   [days] default = 1.0
 
 ! === module ocean_model_init ===
 
+! === module MOM_oda_incupd ===
+ODA_INCUPD = @[ODA_INCUPD]   ! [Boolean] default = False
+                             ! If true, oda incremental updates will be applied
+                             ! everywhere in the domain.
+ODA_INCUPD_FILE = "mom6_increment.nc"   ! The name of the file with the T,S,h increments.
+
+ODA_TEMPINC_VAR = "Temp"        ! default = "ptemp_inc"
+                                ! The name of the potential temperature inc. variable in
+				      	   ! ODA_INCUPD_FILE.
+ODA_SALTINC_VAR = "Salt"        ! default = "sal_inc"
+                                ! The name of the salinity inc. variable in
+                                ! ODA_INCUPD_FILE.
+ODA_THK_VAR = "h"               ! default = "h"
+                                ! The name of the int. depth inc. variable in
+                                ! ODA_INCUPD_FILE.
+ODA_INCUPD_UV = false           !
+!ODA_UINC_VAR = "u"             ! default = "u_inc"
+                                ! The name of the zonal vel. inc. variable in
+                                ! ODA_INCUPD_UV_FILE.
+!ODA_VINC_VAR = "v"             ! default = "v_inc"
+                                ! The name of the meridional vel. inc. variable in
+                                ! ODA_INCUPD_UV_FILE.
+ODA_INCUPD_NHOURS = @[ODA_INCUPD_NHOURS]            ! default=3.0
+
 ! === module MOM_surface_forcing ===
 OCEAN_SURFACE_STAGGER = "A"     ! default = "C"
                                 ! A case-insensitive character string to indicate the
@@ -868,8 +892,8 @@ LIQUID_RUNOFF_FROM_DATA = @[MOM6_RIVER_RUNOFF]  !   [Boolean] default = False
                                 ! the data_table using the component name 'OCN'.
 ! === module ocean_stochastics ===
 DO_SPPT   = @[DO_OCN_SPPT]      ! [Boolean] default = False
-                                ! If true perturb the diabatic tendencies in MOM_diabadic_driver 
-PERT_EPBL = @[PERT_EPBL]        ! [Boolean] default = False 
+                                ! If true perturb the diabatic tendencies in MOM_diabatic_driver
+PERT_EPBL = @[PERT_EPBL]        ! [Boolean] default = False
                                 ! If true perturb the KE dissipation and destruction in MOM_energetic_PBL
 ! === module MOM_restart ===
 RESTART_CHECKSUMS_REQUIRED = False

parm/mom6/MOM_input_template_050

@@ -419,7 +419,7 @@ GILL_EQUATORIAL_LD = True       !   [Boolean] default = False
                                 ! radius, otherwise, if false, use Pedlosky's definition. These definitions
                                 ! differ by a factor of 2 in front of the beta term in the denominator. Gill's
                                 ! is the more appropriate definition.
-INTERNAL_WAVE_SPEED_BETTER_EST = False !   [Boolean] default = True 
+INTERNAL_WAVE_SPEED_BETTER_EST = False !   [Boolean] default = True
                                 ! If true, use a more robust estimate of the first mode wave speed as the
                                 ! starting point for iterations.
 
@@ -757,7 +757,7 @@ MSTAR2_COEF1 = 0.29             !   [nondim] default = 0.3
 MSTAR2_COEF2 = 0.152            !   [nondim] default = 0.085
                                 ! Coefficient in computing mstar when only rotation limits the total mixing
                                 ! (used if EPBL_MSTAR_SCHEME = OM4)
-EPBL_MLD_BISECTION = True       !   [Boolean] default = False 
+EPBL_MLD_BISECTION = True       !   [Boolean] default = False
                                 ! If true, use bisection with the iterative determination of the self-consistent
                                 ! mixed layer depth.  Otherwise use the false position after a maximum and
                                 ! minimum bound have been evaluated and the returned value or bisection before
@@ -858,8 +858,32 @@ USE_NEUTRAL_DIFFUSION = True    !   [Boolean] default = False
                                 ! If true, enables the neutral diffusion module.
 
 ! === module ocean_model_init ===
-
 RESTART_CHECKSUMS_REQUIRED = False
+
+! === module MOM_oda_incupd ===
+ODA_INCUPD = @[ODA_INCUPD]   ! [Boolean] default = False
+                             ! If true, oda incremental updates will be applied
+                             ! everywhere in the domain.
+ODA_INCUPD_FILE = "mom6_increment.nc"   ! The name of the file with the T,S,h increments.
+
+ODA_TEMPINC_VAR = "Temp"        ! default = "ptemp_inc"
+                                ! The name of the potential temperature inc. variable in
+				      	   ! ODA_INCUPD_FILE.
+ODA_SALTINC_VAR = "Salt"        ! default = "sal_inc"
+                                ! The name of the salinity inc. variable in
+                                ! ODA_INCUPD_FILE.
+ODA_THK_VAR = "h"               ! default = "h"
+                                ! The name of the int. depth inc. variable in
+                                ! ODA_INCUPD_FILE.
+ODA_INCUPD_UV = false           !
+!ODA_UINC_VAR = "u"             ! default = "u_inc"
+                                ! The name of the zonal vel. inc. variable in
+                                ! ODA_INCUPD_UV_FILE.
+!ODA_VINC_VAR = "v"             ! default = "v_inc"
+                                ! The name of the meridional vel. inc. variable in
+                                ! ODA_INCUPD_UV_FILE.
+ODA_INCUPD_NHOURS = @[ODA_INCUPD_NHOURS]            ! default=3.0
+
 ! === module MOM_lateral_boundary_diffusion ===
 ! This module implements lateral diffusion of tracers near boundaries
 
@@ -913,8 +937,8 @@ LIQUID_RUNOFF_FROM_DATA = @[MOM6_RIVER_RUNOFF]  !   [Boolean] default = False
                                 ! the data_table using the component name 'OCN'.
 ! === module ocean_stochastics ===
 DO_SPPT   = @[DO_OCN_SPPT]      ! [Boolean] default = False
-                                ! If true perturb the diabatic tendencies in MOM_diabadic_driver 
-PERT_EPBL = @[PERT_EPBL]        ! [Boolean] default = False 
+                                ! If true perturb the diabatic tendencies in MOM_diabatic_driver
+PERT_EPBL = @[PERT_EPBL]        ! [Boolean] default = False
                                 ! If true perturb the KE dissipation and destruction in MOM_energetic_PBL
 ! === module MOM_restart ===
 

parm/mom6/MOM_input_template_100

@@ -76,7 +76,7 @@ SAVE_INITIAL_CONDS = False      !   [Boolean] default = False
                                 ! If true, write the initial conditions to a file given by IC_OUTPUT_FILE.
 
 ! === module MOM_oda_incupd ===
-ODA_INCUPD = @[MOM_IAU]         ! [Boolean] default = False
+ODA_INCUPD = @[ODA_INCUPD]         ! [Boolean] default = False
                                 ! If true, oda incremental updates will be applied
                                 ! everywhere in the domain.
 ODA_INCUPD_FILE = "mom6_increment.nc" ! The name of the file with the T,S,h increments.
@@ -97,7 +97,7 @@ ODA_UINC_VAR = "u_inc"          ! default = "u_inc"
 ODA_VINC_VAR = "v_inc"          ! default = "v_inc"
                                 ! The name of the meridional vel. inc. variable in
                                 ! ODA_INCUPD_UV_FILE.
-ODA_INCUPD_NHOURS = @[MOM_IAU_HRS] ! default=3.0
+ODA_INCUPD_NHOURS = @[ODA_INCUPD_NHOURS] ! default=3.0
                                 ! Number of hours for full update (0=direct insertion).
 
 ! === module MOM_domains ===
@@ -430,7 +430,7 @@ VISC_RES_FN_POWER = 2           !   [nondim] default = 100
                                 ! used, although even integers are more efficient to calculate.  Setting this
                                 ! greater than 100 results in a step-function being used. This function affects
                                 ! lateral viscosity, Kh, and not KhTh.
-INTERNAL_WAVE_SPEED_BETTER_EST = False !   [Boolean] default = True 
+INTERNAL_WAVE_SPEED_BETTER_EST = False !   [Boolean] default = True
                                 ! If true, use a more robust estimate of the first mode wave speed as the
                                 ! starting point for iterations.
 
@@ -829,6 +829,28 @@ ENERGYSAVEDAYS = 0.25           !   [days] default = 1.0
                                 ! other globally summed diagnostics.
 
 ! === module ocean_model_init ===
+ODA_INCUPD = @[ODA_INCUPD]   ! [Boolean] default = False
+                             ! If true, oda incremental updates will be applied
+                             ! everywhere in the domain.
+ODA_INCUPD_FILE = "mom6_increment.nc"   ! The name of the file with the T,S,h increments.
+
+ODA_TEMPINC_VAR = "Temp"        ! default = "ptemp_inc"
+                                ! The name of the potential temperature inc. variable in
+				      	   ! ODA_INCUPD_FILE.
+ODA_SALTINC_VAR = "Salt"        ! default = "sal_inc"
+                                ! The name of the salinity inc. variable in
+                                ! ODA_INCUPD_FILE.
+ODA_THK_VAR = "h"               ! default = "h"
+                                ! The name of the int. depth inc. variable in
+                                ! ODA_INCUPD_FILE.
+ODA_INCUPD_UV = false           !
+!ODA_UINC_VAR = "u"             ! default = "u_inc"
+                                ! The name of the zonal vel. inc. variable in
+                                ! ODA_INCUPD_UV_FILE.
+!ODA_VINC_VAR = "v"             ! default = "v_inc"
+                                ! The name of the meridional vel. inc. variable in
+                                ! ODA_INCUPD_UV_FILE.
+ODA_INCUPD_NHOURS = @[ODA_INCUPD_NHOURS]            ! default=3.0
 
 ! === module MOM_surface_forcing ===
 OCEAN_SURFACE_STAGGER = "A"     ! default = "C"
@@ -856,7 +878,7 @@ FIX_USTAR_GUSTLESS_BUG = False  !   [Boolean] default = True
                                 ! velocity
 ! === module ocean_stochastics ===
 DO_SPPT   = @[DO_OCN_SPPT]      ! [Boolean] default = False
-                                ! If true perturb the diabatic tendencies in MOM_diabadic_driver
+                                ! If true perturb the diabatic tendencies in MOM_diabatic_driver
 PERT_EPBL = @[PERT_EPBL]        ! [Boolean] default = False
                                 ! If true perturb the KE dissipation and destruction in MOM_energetic_PBL
 

parm/mom6/MOM_input_template_500

@@ -492,10 +492,12 @@ MAXTRUNC = 1000                 !   [truncations save_interval-1] default = 0
                                 ! to stop if there is any truncation of velocities.
 
 ! === module ocean_model_init ===
-ODA_INCUPD = @[MOM_IAU]            ! [Boolean] default = False
+
+! === module MOM_oda_incupd ===
+ODA_INCUPD = @[ODA_INCUPD]   ! [Boolean] default = False
                              ! If true, oda incremental updates will be applied
                              ! everywhere in the domain.
-ODA_INCUPD_FILE = "inc.nc"   ! The name of the file with the T,S,h increments.
+ODA_INCUPD_FILE = "mom6_increment.nc"   ! The name of the file with the T,S,h increments.
 
 ODA_TEMPINC_VAR = "Temp"        ! default = "ptemp_inc"
                                 ! The name of the potential temperature inc. variable in
@@ -513,7 +515,7 @@ ODA_INCUPD_UV = false           !
 !ODA_VINC_VAR = "v"             ! default = "v_inc"
                                 ! The name of the meridional vel. inc. variable in
                                 ! ODA_INCUPD_UV_FILE.
-ODA_INCUPD_NHOURS = @[MOM_IAU_HRS]            ! default=3.0
+ODA_INCUPD_NHOURS = @[ODA_INCUPD_NHOURS]            ! default=3.0
 
 ! === module MOM_surface_forcing ===
 OCEAN_SURFACE_STAGGER = "A"     ! default = "C"

ush/forecast_postdet.sh

@@ -769,6 +769,16 @@ MOM6_postdet() {
     ;;
   esac
 
+  # Link increment
+  if [[ "${DO_JEDIOCNVAR:-NO}" = "YES" ]]; then
+      if [[ ! -f "${ROTDIR}/${CDUMP}.${PDY}/${cyc}/ocean/${CDUMP}.t${cyc}z.ocninc.nc" ]]; then
+          echo "FATAL ERROR: Ocean increment not found, ABORT!"
+          exit 111
+      fi
+      $NLN "${ROTDIR}/${CDUMP}.${PDY}/${cyc}/ocean/${CDUMP}.t${cyc}z.ocninc.nc" "${DATA}/INPUT/mom6_increment.nc"
+      export ODA_INCUPD="true"
+  fi
+
   # Copy MOM6 fixed files
   $NCP -pf $FIXmom/$OCNRES/* $DATA/INPUT/
 

ush/load_ufsda_modules.sh

@@ -1,7 +1,7 @@
 #! /usr/bin/env bash
 
 ###############################################################
-if [[ "${DEBUG_WORKFLOW:-NO}" == "NO" ]]; then
+if [[ "${DEBUG_WORKFLOW}" == "NO" ]]; then
     echo "Loading modules quietly..."
     set +x
 fi

ush/parsing_namelists_MOM6.sh

@@ -15,8 +15,8 @@ MOM6_ALLOW_LANDMASK_CHANGES=${MOM6_ALLOW_LANDMASK_CHANGES:-'False'}
 DO_OCN_SPPT=${DO_OCN_SPPT:-'False'}
 PERT_EPBL=${PERT_EPBL:-'False'}
 
-MOM_IAU=${MOM_IAU:-"false"}
-MOM_IAU_HRS=${MOM_IAU_HRS:-'3.0'}
+ODA_INCUPD=${ODA_INCUPD:-"false"}
+ODA_INCUPD_NHOURS=${ODA_INCUPD_NHOURS:-'3.0'}
 
 if [ $cplwav = ".true." ] ; then
   MOM6_USE_WAVES='True'
@@ -134,8 +134,8 @@ sed -e "s/@\[DT_THERM_MOM6\]/$DT_THERM_MOM6/g" \
     -e "s/@\[CHLCLIM\]/$CHLCLIM/g" \
     -e "s/@\[DO_OCN_SPPT\]/$OCN_SPPT/g" \
     -e "s/@\[PERT_EPBL\]/$PERT_EPBL/g" \
-    -e "s/@\[MOM_IAU_HRS\]/$MOM_IAU_HRS/g" \
-    -e "s/@\[MOM_IAU\]/$MOM_IAU/g" $DATA/INPUT/MOM_input_template_$OCNRES > $DATA/INPUT/MOM_input
+    -e "s/@\[ODA_INCUPD_NHOURS\]/$ODA_INCUPD_NHOURS/g" \
+    -e "s/@\[ODA_INCUPD\]/$ODA_INCUPD/g" $DATA/INPUT/MOM_input_template_$OCNRES > $DATA/INPUT/MOM_input
 rm $DATA/INPUT/MOM_input_template_$OCNRES
 
 #data table for runoff:

workflow/rocoto/workflow_tasks.py

@@ -649,9 +649,8 @@ def _fcst_cycled(self):
         dependencies = rocoto.create_dependency(dep=dep)
 
         if self.app_config.do_jediocnvar:
-            dep_dict = {'type': 'task', 'name': f'{self.cdump}ocnanalrun'}
-            dep = rocoto.add_dependency(dep_dict)
-            dependencies = rocoto.create_dependency(dep=dep)
+            dep_dict = {'type': 'task', 'name': f'{self.cdump}ocnanalpost'}
+            dependencies.append(rocoto.add_dependency(dep_dict))
 
         if self.app_config.do_gldas and self.cdump in ['gdas']:
             dep_dict = {'type': 'task', 'name': f'{self.cdump}gldas'}

workflow/setup_expt.py

@@ -120,6 +120,14 @@ def link_files_from_src_to_dst(src_dir, dst_dir):
         makedirs_if_missing(dst_dir)
         link_files_from_src_to_dst(src_dir, dst_dir)
 
+        # First 1/2 cycle needs a MOM6 increment
+        incdir = f'{inputs.cdump}.{idatestr[:8]}/{idatestr[8:]}'
+        incfile = f'{inputs.cdump}.t{idatestr[8:]}z.ocninc.nc'
+        src_file = os.path.join(inputs.icsdir, incdir, 'ocean', incfile)
+        dst_file = os.path.join(comrot, incdir, 'ocean', incfile)
+        makedirs_if_missing(os.path.join(comrot, incdir, 'ocean'))
+        os.symlink(src_file, dst_file)
+
     # Link ice files
     if do_ice:
         detdir = f'{inputs.cdump}.{rdatestr[:8]}/{rdatestr[8:]}'