Merge branch 'main' into update/archive-more-metadata

NOAA-GFDL · Dec 6, 2024 · 7011f77 · 7011f77
2 parents f6c127c + de21cfe
commit 7011f77
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diff --git a/.github/workflows/get_glorys_test.yaml → .github/workflows/get_glorys_test._yaml b/.github/workflows/get_glorys_test.yaml → .github/workflows/get_glorys_test._yaml
diff --git a/.gitmodules b/.gitmodules
@@ -38,11 +38,11 @@
 	path = src/coupler
 	url = https://github.com/NOAA-GFDL/FMScoupler.git
 	branch = 2024.03
-[submodule "src/ocean_BGC"]
-	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
+[submodule "src/ocean_BGC"]
+	path = src/ocean_BGC
+	url = https://github.com/NOAA-CEFI-Regional-Ocean-Modeling/ocean_BGC.git
+	branch = dev/cefi
diff --git a/exps/NEP10.COBALT/COBALT_parameter_doc.all b/exps/NEP10.COBALT/COBALT_parameter_doc.all
@@ -3,6 +3,16 @@
 ! === module COBALT ===
 init = False                    !   [Boolean] default = False
                                 ! init
+htotal_in = 1.0E-08             ! default = 1.0E-08
+                                ! htotal_in
+wsink = 100.0                   !   [m day-1] default = 100.0
+                                ! wsink
+ice_restart_file = "ice_cobalt.res.nc" ! default = "ice_cobalt.res.nc"
+                                ! ice_restart_file
+ocean_restart_file = "ocean_cobalt.res.nc" ! default = "ocean_cobalt.res.nc"
+                                ! ocean_restart_file
+IC_file = ""                    ! default = ""
+                                ! IC_file
 htotal_scale_lo = 0.01          ! default = 0.01
                                 ! scaling factor for initializing carbon chemistry solver
 htotal_scale_hi = 100.0         ! default = 100.0
@@ -669,3 +679,15 @@ o2_min_nit = 1.0E-08            !   [mol O2 kg-1] default = 1.0E-08
                                 ! o2_min_nit
 tracer_debug = False            !   [Boolean] default = False
                                 ! tracer_debug
+
+! === module MOM_file_parser ===
+SEND_LOG_TO_STDOUT = False      !   [Boolean] default = False
+                                ! If true, all log messages are also sent to stdout.
+DOCUMENT_FILE = "COBALT_parameter_doc" ! default = "MOM_parameter_doc"
+                                ! The basename for files where run-time parameters, their settings, units and
+                                ! defaults are documented. Blank will disable all parameter documentation.
+COMPLETE_DOCUMENTATION = True   !   [Boolean] default = True
+                                ! If true, all run-time parameters are documented in COBALT_parameter_doc.all .
+MINIMAL_DOCUMENTATION = True    !   [Boolean] default = True
+                                ! If true, non-default run-time parameters are documented in
+                                ! COBALT_parameter_doc.short .
diff --git a/exps/NEP10.COBALT/COBALT_parameter_doc.debugging b/exps/NEP10.COBALT/COBALT_parameter_doc.debugging
@@ -1,3 +1,9 @@
 ! This file was written by the model and records the debugging parameters used at run-time.
 
 ! === module COBALT ===
+
+! === module MOM_file_parser ===
+REPORT_UNUSED_PARAMS = True     !   [Boolean] default = True
+                                ! If true, report any parameter lines that are not used in the run.
+FATAL_UNUSED_PARAMS = False     !   [Boolean] default = False
+                                ! If true, kill the run if there are any unused parameters.
diff --git a/exps/NEP10.COBALT/COBALT_parameter_doc.short b/exps/NEP10.COBALT/COBALT_parameter_doc.short
@@ -4,3 +4,8 @@
 do_case2_mod = True             !   [Boolean] default = False
                                 ! When true, modify the opacity of case 2 (coastal) waterswhich are identified
                                 ! based on a salinity and depth threshold
+
+! === module MOM_file_parser ===
+DOCUMENT_FILE = "COBALT_parameter_doc" ! default = "MOM_parameter_doc"
+                                ! The basename for files where run-time parameters, their settings, units and
+                                ! defaults are documented. Blank will disable all parameter documentation.
diff --git a/exps/NEP10.COBALT/MOM_parameter_doc.all b/exps/NEP10.COBALT/MOM_parameter_doc.all
@@ -370,7 +370,7 @@ REMAPPING_ANSWER_DATE = 99991231 ! default = 99991231
                                 ! Values below 20190101 result in the use of older, less accurate expressions
                                 ! that were in use at the end of 2018.  Higher values result in the use of more
                                 ! robust and accurate forms of mathematically equivalent expressions.
-OBC_REMAPPING_USE_OM4_SUBCELLS = False !   [Boolean] default = True
+OBC_REMAPPING_USE_OM4_SUBCELLS = False !   [Boolean] default = False
                                 ! If true, use the OM4 remapping-via-subcells algorithm for neutral diffusion.
                                 ! See REMAPPING_USE_OM4_SUBCELLS for more details. We recommend setting this
                                 ! option to false.
@@ -728,7 +728,7 @@ OBC_USER_CONFIG = "none"        ! default = "none"
 NUM_DIAG_COORDS = 1             ! default = 1
                                 ! The number of diagnostic vertical coordinates to use. For each coordinate, an
                                 ! entry in DIAG_COORDS must be provided.
-DIAG_REMAPPING_USE_OM4_SUBCELLS = False !   [Boolean] default = True
+DIAG_REMAPPING_USE_OM4_SUBCELLS = False !   [Boolean] default = False
                                 ! If true, use the OM4 remapping-via-subcells algorithm for diagnostics. See
                                 ! REMAPPING_USE_OM4_SUBCELLS for details. We recommend setting this option to
                                 ! false.
@@ -1281,11 +1281,6 @@ USE_ZB2020 = False              !   [Boolean] default = False
                                 ! mesoscale eddies.
 
 ! === module MOM_hor_visc ===
-HOR_VISC_ANSWER_DATE = 99991231 ! default = 99991231
-                                ! The vintage of the order of arithmetic and expressions in the horizontal
-                                ! viscosity 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.
 USE_CONT_THICKNESS = False      !   [Boolean] default = False
                                 ! If true, use thickness at velocity points from continuity solver. This option
                                 ! currently only works with split mode.
@@ -1615,7 +1610,7 @@ INTERNAL_WAVE_SPEED_MIN = 0.0   !   [m s-1] default = 0.0
 INTERNAL_WAVE_SPEED_BETTER_EST = True !   [Boolean] default = True
                                 ! If true, use a more robust estimate of the first mode wave speed as the
                                 ! starting point for iterations.
-INTWAVE_REMAPPING_USE_OM4_SUBCELLS = False !   [Boolean] default = True
+INTWAVE_REMAPPING_USE_OM4_SUBCELLS = False !   [Boolean] default = False
                                 ! If true, use the OM4 remapping-via-subcells algorithm for calculating EBT
                                 ! structure. See REMAPPING_USE_OM4_SUBCELLS for details. We recommend setting
                                 ! this option to false.

diff --git a/exps/NEP10.COBALT/MOM_parameter_doc.short b/exps/NEP10.COBALT/MOM_parameter_doc.short
@@ -159,10 +159,6 @@ OBC_TRACER_RESERVOIR_LENGTH_SCALE_IN = 9000.0 !   [m] default = 0.0
                                 ! boundaries to values from the interior when the flow is entering the domain.
 BRUSHCUTTER_MODE = True         !   [Boolean] default = False
                                 ! If true, read external OBC data on the supergrid.
-OBC_REMAPPING_USE_OM4_SUBCELLS = False !   [Boolean] default = True
-                                ! If true, use the OM4 remapping-via-subcells algorithm for neutral diffusion.
-                                ! See REMAPPING_USE_OM4_SUBCELLS for more details. We recommend setting this
-                                ! 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
@@ -290,10 +286,6 @@ OBC_SEGMENT_004_DATA = "U=file:obcs.nc(u),V=file:obcs.nc(v),SSH=file:obcs.nc(zos
                                 ! OBC segment docs
 
 ! === module MOM_diag_mediator ===
-DIAG_REMAPPING_USE_OM4_SUBCELLS = False !   [Boolean] default = True
-                                ! If true, use the OM4 remapping-via-subcells algorithm for diagnostics. See
-                                ! REMAPPING_USE_OM4_SUBCELLS for details. We recommend setting this option to
-                                ! false.
 DIAG_COORD_DEF_Z = "FILE:diag_dz.nc,dz" ! default = "WOA09"
                                 ! Determines how to specify the coordinate resolution. Valid options are:
                                 !  PARAM       - use the vector-parameter DIAG_COORD_RES_Z
@@ -518,10 +510,6 @@ MLE_USE_PBL_MLD = True          !   [Boolean] default = False
                                 ! density difference with the surface using the parameter MLE_DENSITY_DIFF.
 
 ! === module MOM_diagnostics ===
-INTWAVE_REMAPPING_USE_OM4_SUBCELLS = False !   [Boolean] default = True
-                                ! If true, use the OM4 remapping-via-subcells algorithm for calculating EBT
-                                ! structure. See REMAPPING_USE_OM4_SUBCELLS for details. We recommend setting
-                                ! this option to false.
 
 ! === module MOM_diabatic_driver ===
 ! The following parameters are used for diabatic processes.

diff --git a/exps/NWA12.COBALT/COBALT_parameter_doc.all b/exps/NWA12.COBALT/COBALT_parameter_doc.all
@@ -3,6 +3,16 @@
 ! === module COBALT ===
 init = False                    !   [Boolean] default = False
                                 ! init
+htotal_in = 1.0E-08             ! default = 1.0E-08
+                                ! htotal_in
+wsink = 100.0                   !   [m day-1] default = 100.0
+                                ! wsink
+ice_restart_file = "ice_cobalt.res.nc" ! default = "ice_cobalt.res.nc"
+                                ! ice_restart_file
+ocean_restart_file = "ocean_cobalt.res.nc" ! default = "ocean_cobalt.res.nc"
+                                ! ocean_restart_file
+IC_file = ""                    ! default = ""
+                                ! IC_file
 htotal_scale_lo = 0.01          ! default = 0.01
                                 ! scaling factor for initializing carbon chemistry solver
 htotal_scale_hi = 100.0         ! default = 100.0
@@ -669,3 +679,15 @@ o2_min_nit = 1.0E-08            !   [mol O2 kg-1] default = 1.0E-08
                                 ! o2_min_nit
 tracer_debug = False            !   [Boolean] default = False
                                 ! tracer_debug
+
+! === module MOM_file_parser ===
+SEND_LOG_TO_STDOUT = False      !   [Boolean] default = False
+                                ! If true, all log messages are also sent to stdout.
+DOCUMENT_FILE = "COBALT_parameter_doc" ! default = "MOM_parameter_doc"
+                                ! The basename for files where run-time parameters, their settings, units and
+                                ! defaults are documented. Blank will disable all parameter documentation.
+COMPLETE_DOCUMENTATION = True   !   [Boolean] default = True
+                                ! If true, all run-time parameters are documented in COBALT_parameter_doc.all .
+MINIMAL_DOCUMENTATION = True    !   [Boolean] default = True
+                                ! If true, non-default run-time parameters are documented in
+                                ! COBALT_parameter_doc.short .
diff --git a/exps/NWA12.COBALT/COBALT_parameter_doc.debugging b/exps/NWA12.COBALT/COBALT_parameter_doc.debugging
@@ -1,3 +1,9 @@
 ! This file was written by the model and records the debugging parameters used at run-time.
 
 ! === module COBALT ===
+
+! === module MOM_file_parser ===
+REPORT_UNUSED_PARAMS = True     !   [Boolean] default = True
+                                ! If true, report any parameter lines that are not used in the run.
+FATAL_UNUSED_PARAMS = False     !   [Boolean] default = False
+                                ! If true, kill the run if there are any unused parameters.
diff --git a/exps/NWA12.COBALT/COBALT_parameter_doc.short b/exps/NWA12.COBALT/COBALT_parameter_doc.short
@@ -10,3 +10,8 @@ z_denit = 20.0                  !   [m] default = 10.0
                                 ! depth scale for ramping up benthic denitrification
 scale_burial = 1.0              !   [none] default = 0.0
                                 ! scaling factor for particulate organic burial
+
+! === module MOM_file_parser ===
+DOCUMENT_FILE = "COBALT_parameter_doc" ! default = "MOM_parameter_doc"
+                                ! The basename for files where run-time parameters, their settings, units and
+                                ! defaults are documented. Blank will disable all parameter documentation.
diff --git a/exps/NWA12.COBALT/MOM_parameter_doc.all b/exps/NWA12.COBALT/MOM_parameter_doc.all
@@ -1293,11 +1293,6 @@ USE_ZB2020 = False              !   [Boolean] default = False
                                 ! mesoscale eddies.
 
 ! === module MOM_hor_visc ===
-HOR_VISC_ANSWER_DATE = 99991231 ! default = 99991231
-                                ! The vintage of the order of arithmetic and expressions in the horizontal
-                                ! viscosity 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.
 USE_CONT_THICKNESS = False      !   [Boolean] default = False
                                 ! If true, use thickness at velocity points from continuity solver. This option
                                 ! currently only works with split mode.

diff --git a/exps/NWA12.tidesonly/MOM_parameter_doc.all b/exps/NWA12.tidesonly/MOM_parameter_doc.all
@@ -1583,7 +1583,7 @@ USE_WAVES = False               !   [Boolean] default = False
 DT_FORCING = 3600.0             !   [s] default = 600.0
                                 ! The time step for changing forcing, coupling with other components, or
                                 ! potentially writing certain diagnostics. The default value is given by DT.
-DAYMAX = 10.0                   !   [days]
+DAYMAX = 2.0                    !   [days]
                                 ! The final time of the whole simulation, in units of TIMEUNIT seconds.  This
                                 ! also sets the potential end time of the present run segment if the end time is
                                 ! not set via ocean_solo_nml in input.nml.

diff --git a/exps/NWA12.tidesonly/MOM_parameter_doc.short b/exps/NWA12.tidesonly/MOM_parameter_doc.short
@@ -337,7 +337,7 @@ VARIABLE_BUOYFORCE = False      !   [Boolean] default = True
 DT_FORCING = 3600.0             !   [s] default = 600.0
                                 ! The time step for changing forcing, coupling with other components, or
                                 ! potentially writing certain diagnostics. The default value is given by DT.
-DAYMAX = 10.0                   !   [days]
+DAYMAX = 2.0                    !   [days]
                                 ! The final time of the whole simulation, in units of TIMEUNIT seconds.  This
                                 ! also sets the potential end time of the present run segment if the end time is
                                 ! not set via ocean_solo_nml in input.nml.