2025.01 update part 3

.gitmodules

@@ -26,10 +26,6 @@
 	path = src/ice_param
 	url = https://github.com/NOAA-GFDL/ice_param.git
 	branch = 2024.02
-[submodule "src/MOM6"]
-	path = src/MOM6
-	url = https://github.com/NOAA-CEFI-Regional-Ocean-Modeling/MOM6.git
-	branch = dev/cefi
 [submodule "src/FMS"]
 	path = src/FMS
 	url = https://github.com/NOAA-GFDL/FMS.git
@@ -46,3 +42,7 @@
 	path = src/ocean_BGC
 	url = https://github.com/NOAA-CEFI-Regional-Ocean-Modeling/ocean_BGC.git
 	branch = dev/cefi
+[submodule "src/MOM6"]
+	path = src/MOM6
+	url = https://github.com/NOAA-CEFI-Regional-Ocean-Modeling/MOM6.git
+	branch = dev/cefi

exps/NEP10.COBALT/INPUT/MOM_input

@@ -205,10 +205,10 @@ OBC_TRACER_RESERVOIR_LENGTH_SCALE_IN = 9000.0 !   [m] default = 0.0
 
 OBC_TIDE_N_CONSTITUENTS = 10
 OBC_TIDE_CONSTITUENTS = "M2,S2,N2,K2,K1,O1,P1,Q1,MM,MF"
-OBC_TIDE_REF_DATE = 1993,1,1
-OBC_TIDE_ADD_EQ_PHASE = True
-OBC_TIDE_ADD_NODAL = True
-OBC_TIDE_NODAL_REF_DATE = 1993,7,2
+TIDE_REF_DATE = 1993,1,1
+TIDE_ADD_EQ_PHASE = True
+TIDE_ADD_NODAL = True
+TIDE_NODAL_REF_DATE = 1993,7,2
 TIDAL_SAL_FLATHER = True
 ! === module MOM_boundary_update ===
 
@@ -921,7 +921,6 @@ TIDE_SAL_SCALAR_VALUE = 0.010   !   [m m-1]
                                 ! The constant of proportionality between sea surface height (really it should
                                 ! be bottom pressure) anomalies and bottom geopotential anomalies. This is only
                                 ! used if TIDES and TIDE_USE_SAL_SCALAR are true.
-TIDE_REF_DATE = 1993,1,1
 TIDE_USE_EQ_PHASE = True
 
 ! === module ocean_model_init ===

exps/NEP10.COBALT/INPUT/MOM_override

@@ -4,7 +4,7 @@
 #override DO_GEOTHERMAL = True
 #override DT = 400
 # Update the nodal modulation of the tide every year
-#override OBC_TIDE_NODAL_REF_DATE = 1993,7,2
+#override TIDE_NODAL_REF_DATE = 1993,7,2
 #override MLE%USE_BODNER23 = True
 #override MLE%CR = 0.03
 #override MLE%BLD_DECAYING_TFILTER = 8.64E+04

exps/NEP10.COBALT/MOM_parameter_doc.all

@@ -70,15 +70,26 @@ DT = 400.0                      !   [s]
                                 ! be an integer fraction of the forcing time-step (DT_FORCING in ocean-only mode
                                 ! or the coupling timestep in coupled mode.)
 DT_THERM = 1200.0               !   [s] default = 400.0
-                                ! The thermodynamic and tracer advection time step. Ideally DT_THERM should be
-                                ! an integer multiple of DT and less than the forcing or coupling time-step,
-                                ! unless THERMO_SPANS_COUPLING is true, in which case DT_THERM can be an integer
-                                ! multiple of the coupling timestep.  By default DT_THERM is set to DT.
+                                ! The thermodynamic time step. Ideally DT_THERM should be an integer multiple of
+                                ! DT and of DT_TRACER_ADVECT and less than the forcing or coupling time-step.
+                                ! However, if THERMO_SPANS_COUPLING is true, DT_THERM can be an integer multiple
+                                ! of the coupling timestep. By default DT_THERM is set to DT.
 THERMO_SPANS_COUPLING = False   !   [Boolean] default = False
-                                ! If true, the MOM will take thermodynamic and tracer timesteps that can be
-                                ! longer than the coupling timestep. The actual thermodynamic timestep that is
-                                ! used in this case is the largest integer multiple of the coupling timestep
-                                ! that is less than or equal to DT_THERM.
+                                ! If true, the MOM will take thermodynamic timesteps that can be longer than the
+                                ! coupling timestep. The actual thermodynamic timestep that is used in this case
+                                ! is the largest integer multiple of the coupling timestep that is less than or
+                                ! equal to DT_THERM.
+DT_TRACER_ADVECT = 1200.0       !   [s] default = 1200.0
+                                ! The tracer advection time step. Ideally DT_TRACER_ADVECT should be an integer
+                                ! multiple of DT, less than DT_THERM, and less than the forcing or coupling
+                                ! time-step. However, if TRADV_SPANS_COUPLING is true, DT_TRACER_ADVECT can be
+                                ! longer than the coupling timestep. By default DT_TRACER_ADVECT is set to
+                                ! DT_THERM.
+TRADV_SPANS_COUPLING = False    !   [Boolean] default = False
+                                ! If true, the MOM will take tracer advection timesteps that can be longer than
+                                ! the coupling timestep. The actual tracer advection timestep that is used in
+                                ! this case is the largest integer multiple of the coupling timestep that is
+                                ! less than or equal to DT_TRACER_ADVECT.
 HMIX_SFC_PROP = 1.0             !   [m] default = 1.0
                                 ! If BULKMIXEDLAYER is false, HMIX_SFC_PROP is the depth over which to average
                                 ! to find surface properties like SST and SSS or density (but not surface
@@ -376,14 +387,6 @@ OBC_REMAPPING_USE_OM4_SUBCELLS = False !   [Boolean] default = False
                                 ! option to false.
 OBC_TIDE_CONSTITUENTS = "M2,S2,N2,K2,K1,O1,P1,Q1,MM,MF" !
                                 ! Names of tidal constituents being added to the open boundaries.
-OBC_TIDE_ADD_EQ_PHASE = True    !   [Boolean] default = False
-                                ! If true, add the equilibrium phase argument to the specified tidal phases.
-OBC_TIDE_ADD_NODAL = True       !   [Boolean] default = False
-                                ! If true, include 18.6 year nodal modulation in the boundary tidal forcing.
-OBC_TIDE_REF_DATE = 1993, 1, 1  !
-                                ! Reference date to use for tidal calculations and equilibrium phase.
-OBC_TIDE_NODAL_REF_DATE = 1993, 7, 2 ! default = 0, 0, 0
-                                ! Fixed reference date to use for nodal modulation of boundary tides.
 TIDE_M2_FREQ = 1.405189E-04     !   [rad s-1] default = 1.405189E-04
                                 ! Frequency of the M2 tidal constituent. This is only used if TIDES and TIDE_M2
                                 ! are true, or if OBC_TIDE_N_CONSTITUENTS > 0 and M2 is in
@@ -497,12 +500,9 @@ RESTART_CHECKSUMS_REQUIRED = True !   [Boolean] default = True
                                 ! may want to avoid this comparison if for example the restarts are made from a
                                 ! run with a different mask_table than the current run, in which case the
                                 ! checksums will not match and cause crash.
-STREAMING_FILTER_M2 = False     !   [Boolean] default = False
-                                ! If true, turn on streaming band-pass filter for detecting instantaneous tidal
-                                ! signals.
-STREAMING_FILTER_K1 = False     !   [Boolean] default = False
-                                ! If true, turn on streaming band-pass filter for detecting instantaneous tidal
-                                ! signals.
+USE_FILTER = False              !   [Boolean] default = False
+                                ! If true, use streaming band-pass filters to detect the instantaneous tidal
+                                ! signals in the simulation.
 
 ! === module MOM_tracer_flow_control ===
 USE_USER_TRACER_EXAMPLE = False !   [Boolean] default = False
@@ -1090,6 +1090,10 @@ PV_ADV_SCHEME = "PV_ADV_CENTERED" ! default = "PV_ADV_CENTERED"
                                 !    PV_ADV_UPWIND1  - upwind, first order
 
 ! === module MOM_self_attr_load ===
+SAL_USE_BPA = False             !   [Boolean] default = False
+                                ! If true, use bottom pressure anomaly to calculate self-attraction and loading
+                                ! (SAL). Otherwise sea surface height anomaly is used, which is only correct for
+                                ! homogenous flow.
 SAL_SCALAR_APPROX = True        !   [Boolean] default = True
                                 ! If true, use the scalar approximation to calculate self-attraction and
                                 ! loading.
@@ -1203,6 +1207,11 @@ TIDE_MM_AMP = 0.022191          !   [m] default = 0.022191
 TIDE_MM_PHASE_T0 = -2.542600025447928 !   [radians] default = -2.542600025447928
                                 ! Phase of the MM tidal constituent at time 0. This is only used if TIDES and
                                 ! TIDE_MM are true.
+TIDE_ADD_NODAL = True           !   [Boolean] default = False
+                                ! If true, include 18.6 year nodal modulation in the astronomical tidal forcing.
+TIDE_NODAL_REF_DATE = 1993, 7, 2 ! default = 0, 0, 0
+                                ! Fixed reference date to use for nodal modulation of astronomical tidal
+                                ! forcing.
 HA_START_TIME = 0.0             !   [days] default = 0.0
                                 ! Start time of harmonic analysis, in units of days after the start of the
                                 ! current run segment. Must be smaller than HA_END_TIME, otherwise harmonic
@@ -1235,9 +1244,18 @@ RHO_PGF_REF = 1035.0            !   [kg m-3] default = 1035.0
                                 ! non-Boussinesq mode.  The default is RHO_0.
 TIDES_ANSWER_DATE = 20230630    ! default = 20230630
                                 ! The vintage of self-attraction and loading (SAL) and tidal forcing
-                                ! calculations in Boussinesq mode. Values below 20230701 recover the old answers
-                                ! in which the SAL is part of the tidal forcing calculation.  The change is due
-                                ! to a reordered summation and the difference is only at bit level.
+                                ! calculations.  Setting dates before 20230701 recovers old answers (Boussinesq
+                                ! and non-Boussinesq modes) when SAL is part of the tidal forcing calculation.
+                                ! The answer difference is only at bit level and due to a reordered summation.
+                                ! Setting dates before 20250201 recovers answers (Boussinesq mode) that
+                                ! interface heights are modified before pressure force integrals are calculated.
+BOUSSINESQ_SAL_TIDES = False    !   [Boolean] default = False
+                                ! If true, in Boussinesq mode, use an alternative method to include
+                                ! self-attraction and loading (SAL) and tidal forcings in pressure gradient, in
+                                ! which their gradients are calculated separately, instead of adding
+                                ! geopotential anomalies as corrections to the interface height.  This
+                                ! alternative method elimates a baroclinic component of the SAL and tidal
+                                ! forcings.
 SSH_IN_EOS_PRESSURE_FOR_PGF = False !   [Boolean] default = False
                                 ! If true, include contributions from the sea surface height in the height-based
                                 ! pressure used in the equation of state calculations for the Boussinesq
@@ -1705,6 +1723,8 @@ SET_DIFF_ANSWER_DATE = 99991231 ! default = 99991231
                                 ! The vintage of the order of arithmetic and expressions in the set diffusivity
                                 ! calculations.  Values below 20190101 recover the answers from the end of 2018,
                                 ! while higher values use updated and more robust forms of the same expressions.
+                                ! Values above 20250301 also use less confusing expressions to set the
+                                ! bottom-drag generated diffusivity when USE_LOTW_BBL_DIFFUSIVITY is false.
 
 ! === module MOM_tidal_mixing ===
 ! Vertical Tidal Mixing Parameterization
@@ -2042,6 +2062,9 @@ VSTAR_SURF_FAC = 1.8258         !   [nondim] default = 1.2
 EPBL_BBL_EFFIC = 0.0            !   [nondim] default = 0.0
                                 ! The efficiency of bottom boundary layer mixing via ePBL.  Setting this to a
                                 ! value that is greater than 0 to enable bottom boundary layer mixing from EPBL.
+EPBL_BBL_TIDAL_EFFIC = 0.0      !   [nondim] default = 0.0
+                                ! The efficiency of bottom boundary layer mixing via ePBL driven by the bottom
+                                ! drag dissipation of tides, as provided in fluxes%BBL_tidal_dis.
 USE_LA_LI2016 = True            !   [Boolean] default = False
                                 ! A logical to use the Li et al. 2016 (submitted) formula to determine the
                                 ! Langmuir number.
@@ -2107,6 +2130,18 @@ PEN_SW_FLUX_ABSORB = 2.5E-11    !   [degC m s-1] default = 2.5E-11
 PEN_SW_ABSORB_MINTHICK = 1.0    !   [m] default = 1.0
                                 ! A thickness that is used to absorb the remaining penetrating shortwave heat
                                 ! flux when it drops below PEN_SW_FLUX_ABSORB.
+OPACITY_VALUES_MANIZZA = 0.0232, 0.074, 0.225, 0.037, 2.86, 0.0 !   [m-1] default = 0.0232, 0.074, 0.225, 0.037, 2.86, 0.0
+                                ! Pairs of opacity coefficients for blue, red and near-infrared radiation with
+                                ! parameterizations following the functional form from Manizza et al., GRL 2005,
+                                ! namely in the form opacity = coef_1 + coef_2 * chl**pow for each band.
+                                ! Although coefficients are set for 3 bands, more or less bands may actually be
+                                ! used, with extra bands following the same properties as band 3.
+CHOROPHYLL_POWER_MANIZZA = 0.674, 0.629, 0.0 !   [nondim] default = 0.674, 0.629, 0.0
+                                ! Powers of chlorophyll for blue, red and near-infrared radiation bands in
+                                ! expressions for opacity of the form opacity = coef_1 + coef_2 * chl**pow.
+OPACITY_BAND_WAVELENGTHS = 0.0, 550.0, 700.0, 2800.0 !   [nm] default = 0.0, 550.0, 700.0, 2800.0
+                                ! The bounding wavelengths for the various bands of shortwave radiation, with
+                                ! defaults that depend on the setting for OPACITY_SCHEME.
 OPACITY_LAND_VALUE = 10.0       !   [m-1] default = 10.0
                                 ! The value to use for opacity over land. The default is 10 m-1 - a value for
                                 ! muddy water.

exps/NEP10.COBALT/MOM_parameter_doc.short

@@ -14,10 +14,10 @@ DT = 400.0                      !   [s]
                                 ! be an integer fraction of the forcing time-step (DT_FORCING in ocean-only mode
                                 ! or the coupling timestep in coupled mode.)
 DT_THERM = 1200.0               !   [s] default = 400.0
-                                ! The thermodynamic and tracer advection time step. Ideally DT_THERM should be
-                                ! an integer multiple of DT and less than the forcing or coupling time-step,
-                                ! unless THERMO_SPANS_COUPLING is true, in which case DT_THERM can be an integer
-                                ! multiple of the coupling timestep.  By default DT_THERM is set to DT.
+                                ! The thermodynamic time step. Ideally DT_THERM should be an integer multiple of
+                                ! DT and of DT_TRACER_ADVECT and less than the forcing or coupling time-step.
+                                ! However, if THERMO_SPANS_COUPLING is true, DT_THERM can be an integer multiple
+                                ! of the coupling timestep. By default DT_THERM is set to DT.
 FRAZIL = True                   !   [Boolean] default = False
                                 ! If true, water freezes if it gets too cold, and the accumulated heat deficit
                                 ! is returned in the surface state.  FRAZIL is only used if
@@ -161,14 +161,6 @@ BRUSHCUTTER_MODE = True         !   [Boolean] default = False
                                 ! If true, read external OBC data on the supergrid.
 OBC_TIDE_CONSTITUENTS = "M2,S2,N2,K2,K1,O1,P1,Q1,MM,MF" !
                                 ! Names of tidal constituents being added to the open boundaries.
-OBC_TIDE_ADD_EQ_PHASE = True    !   [Boolean] default = False
-                                ! If true, add the equilibrium phase argument to the specified tidal phases.
-OBC_TIDE_ADD_NODAL = True       !   [Boolean] default = False
-                                ! If true, include 18.6 year nodal modulation in the boundary tidal forcing.
-OBC_TIDE_REF_DATE = 1993, 1, 1  !
-                                ! Reference date to use for tidal calculations and equilibrium phase.
-OBC_TIDE_NODAL_REF_DATE = 1993, 7, 2 ! default = 0, 0, 0
-                                ! Fixed reference date to use for nodal modulation of boundary tides.
 
 ! === module MOM_verticalGrid ===
 ! Parameters providing information about the vertical grid.
@@ -396,6 +388,11 @@ TIDE_REF_DATE = 1993, 1, 1      ! default = 0, 0, 0
                                 ! defaults to 0.
 TIDE_USE_EQ_PHASE = True        !   [Boolean] default = False
                                 ! Correct phases by calculating equilibrium phase arguments for TIDE_REF_DATE.
+TIDE_ADD_NODAL = True           !   [Boolean] default = False
+                                ! If true, include 18.6 year nodal modulation in the astronomical tidal forcing.
+TIDE_NODAL_REF_DATE = 1993, 7, 2 ! default = 0, 0, 0
+                                ! Fixed reference date to use for nodal modulation of astronomical tidal
+                                ! forcing.
 
 ! === module MOM_PressureForce ===
 

exps/NEP10.COBALT/driver.sh

@@ -72,7 +72,7 @@ mv ocean.stats RESTART_24hrs_rst
 # Define the directories containing the files
 module load nccmp
 DIR1="./RESTART_24hrs_rst"
-DIR2="/gpfs/f6/ira-cefi/proj-shared/github/ci_data/reference/main/NEP10.COBALT/20241115" 
+DIR2="/gpfs/f6/ira-cefi/proj-shared/github/ci_data/reference/main/NEP10.COBALT/20250131" 
 
 # Define the files to compare
 FILES=("$DIR2"/MOM.res*.nc)