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Updated MOM6 tag so now we can do bgc sponge (#117)
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* Updated MOM6 tag so now we can do bgc sponge

* Update NEP10 MOM_parameter_doc files

* Update NWA12 parameter doc files
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@yichengt900
yichengt900 authored Nov 18, 2024
1 parent c836eb2 commit 2184c26
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8 changes: 4 additions & 4 deletions .gitmodules
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Expand Up @@ -38,11 +38,11 @@
path = src/coupler
url = https://github.com/NOAA-GFDL/FMScoupler.git
branch = 2024.03
[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
[submodule "src/MOM6"]
path = src/MOM6
url = https://github.com/NOAA-CEFI-Regional-Ocean-Modeling/MOM6.git
branch = dev/cefi
83 changes: 45 additions & 38 deletions exps/NEP10.COBALT/MOM_parameter_doc.all
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Expand Up @@ -58,7 +58,7 @@ THICKNESSDIFFUSE = False ! [Boolean] default = False
APPLY_INTERFACE_FILTER = False ! [Boolean] default = False
! If true, model interface heights are subjected to a grid-scale dependent
! spatial smoothing, often with biharmonic filter.
USE_POROUS_BARRIER = True ! [Boolean] default = True
USE_POROUS_BARRIER = False ! [Boolean] default = False
! If true, use porous barrier to constrain the widths and face areas at the
! edges of the grid cells.
BATHYMETRY_AT_VEL = False ! [Boolean] default = False
Expand Down Expand Up @@ -351,6 +351,18 @@ OBC_TRACER_RESERVOIR_LENGTH_SCALE_OUT = 9000.0 ! [m] default = 0.0
OBC_TRACER_RESERVOIR_LENGTH_SCALE_IN = 9000.0 ! [m] default = 0.0
! An effective length scale for restoring the tracer concentration at the
! boundaries to values from the interior when the flow is entering the domain.
OBC_REMAPPING_SCHEME = "PPM_H4" ! default = "PPM_H4"
! This sets the reconstruction scheme used for OBC vertical remapping for all
! variables. It can be one of the following schemes:
! PCM (1st-order accurate)
! PLM (2nd-order accurate)
! PLM_HYBGEN (2nd-order accurate)
! PPM_H4 (3rd-order accurate)
! PPM_IH4 (3rd-order accurate)
! PPM_HYBGEN (3rd-order accurate)
! WENO_HYBGEN (3rd-order accurate)
! PQM_IH4IH3 (4th-order accurate)
! PQM_IH6IH5 (5th-order accurate)
BRUSHCUTTER_MODE = True ! [Boolean] default = False
! If true, read external OBC data on the supergrid.
REMAPPING_ANSWER_DATE = 99991231 ! default = 99991231
Expand Down Expand Up @@ -785,12 +797,30 @@ RESOLN_USE_EBT = False ! [Boolean] default = False
BACKSCAT_EBT_POWER = 0.0 ! [nondim] default = 0.0
! Power to raise EBT vertical structure to when backscatter has vertical
! structure.
BS_USE_SQG_STRUCT = False ! [Boolean] default = False
! If true, the SQG vertical structure is used for backscatter on the condition
! that BS_EBT_power=0
SQG_EXPO = 1.0 ! [nondim] default = 1.0
! Nondimensional exponent coeffecient of the SQG mode that is used for the
! vertical struture of diffusivities.
KHTH_USE_EBT_STRUCT = False ! [Boolean] default = False
! If true, uses the equivalent barotropic structure as the vertical structure of
! thickness diffusivity.
KHTH_USE_SQG_STRUCT = False ! [Boolean] default = False
! If true, uses the surface quasigeostrophic structure as the vertical structure
! of thickness diffusivity.
KHTR_USE_EBT_STRUCT = False ! [Boolean] default = False
! If true, uses the equivalent barotropic structure as the vertical structure of
! tracer diffusivity.
KHTR_USE_SQG_STRUCT = False ! [Boolean] default = False
! If true, uses the surface quasigeostrophic structure as the vertical structure
! of tracer diffusivity.
KD_GL90_USE_EBT_STRUCT = False ! [Boolean] default = False
! If true, uses the equivalent barotropic structure as the vertical structure of
! diffusivity in the GL90 scheme.
KD_GL90_USE_SQG_STRUCT = False ! [Boolean] default = False
! If true, uses the equivalent barotropic structure as the vertical structure of
! diffusivity in the GL90 scheme.
KHTH_SLOPE_CFF = 0.0 ! [nondim] default = 0.0
! The nondimensional coefficient in the Visbeck formula for the interface depth
! diffusivity
Expand Down Expand Up @@ -948,23 +978,6 @@ STOCH_EOS = False ! [Boolean] default = False
STANLEY_COEFF = -1.0 ! [nondim] default = -1.0
! Coefficient correlating the temperature gradient and SGS T variance.

! === module MOM_porous_barriers ===
PORBAR_ANSWER_DATE = 99991231 ! default = 99991231
! The vintage of the porous barrier weight function calculations. Values below
! 20220806 recover the old answers in which the layer averaged weights are not
! strictly limited by an upper-bound of 1.0 .
PORBAR_MASKING_DEPTH = 0.0 ! [m] default = 0.0
! If the effective average depth at the velocity cell is shallower than this
! number, then porous barrier is not applied at that location.
! PORBAR_MASKING_DEPTH is assumed to be positive below the sea surface.
PORBAR_ETA_INTERP = "MAX" ! default = "MAX"
! A string describing the method that decides how the interface heights at the
! velocity points are calculated. Valid values are:
! MAX (the default) - maximum of the adjacent cells
! MIN - minimum of the adjacent cells
! ARITHMETIC - arithmetic mean of the adjacent cells
! HARMONIC - harmonic mean of the adjacent cells

! === module MOM_dynamics_split_RK2 ===
TIDES = True ! [Boolean] default = False
! If true, apply tidal momentum forcing.
Expand Down Expand Up @@ -994,15 +1007,13 @@ FPMIX = False ! [Boolean] default = False
! If true, apply profiles of momentum flux magnitude and direction
VISC_REM_BUG = True ! [Boolean] default = True
! If true, visc_rem_[uv] in split mode is incorrectly calculated or accounted
! for in three places. This parameter controls the defaults of three individual
! flags, VISC_REM_TIMESTEP_FIX in MOM_dynamics_split_RK2(b),
! VISC_REM_BT_WEIGHT_FIX in MOM_barotropic, and VISC_REM_CONT_HVEL_FIX in
! MOM_continuity_PPM. Eventually, the three individual flags should be removed
! after tests and the default of VISC_REM_BUG should be to False.
VISC_REM_TIMESTEP_FIX = False ! [Boolean] default = False
! If true, use dt rather than dt_pred in vertvisc_remnant() at the end of
! predictor stage for the following continuity() call and btstep() call in the
! corrector step. This flag should be used with VISC_REM_BT_WEIGHT_FIX.
! for in two places. This parameter controls the defaults of two individual
! flags, VISC_REM_TIMESTEP_BUG in MOM_dynamics_split_RK2(b) and
! VISC_REM_BT_WEIGHT_BUG in MOM_barotropic.
VISC_REM_TIMESTEP_BUG = True ! [Boolean] default = True
! If true, recover a bug that uses dt_pred rather than dt in vertvisc_remnant()
! at the end of predictor stage for the following continuity() and btstep()
! calls in the corrector step. Default of this flag is set by VISC_REM_BUG

! === module MOM_continuity_PPM ===
MONOTONIC_CONTINUITY = False ! [Boolean] default = False
Expand Down Expand Up @@ -1044,9 +1055,6 @@ CONT_PPM_USE_VISC_REM_MAX = True ! [Boolean] default = True
CONT_PPM_MARGINAL_FACE_AREAS = True ! [Boolean] default = True
! If true, use the marginal face areas from the continuity solver for use as the
! weights in the barotropic solver. Otherwise use the transport averaged areas.
VISC_REM_CONT_HVEL_FIX = False ! [Boolean] default = False
! If true, velocity cell thickness h_[uv] from the continuity solver is not
! multiplied by visc_rem_[uv]. Default of this flag is set by VISC_REM_BUG.

! === module MOM_CoriolisAdv ===
NOSLIP = False ! [Boolean] default = False
Expand Down Expand Up @@ -1458,10 +1466,10 @@ BAROTROPIC_ANSWER_DATE = 99991231 ! default = 99991231
! The vintage of the expressions in the barotropic solver. Values below 20190101
! recover the answers from the end of 2018, while higher values use more
! efficient or general expressions.
VISC_REM_BT_WEIGHT_FIX = False ! [Boolean] default = False
! If true, use a normalized weight function for vertical averages of baroclinic
! velocity and forcing. Default of this flag is set by VISC_REM_BUG. This flag
! should be used with VISC_REM_TIMESTEP_FIX.
VISC_REM_BT_WEIGHT_BUG = True ! [Boolean] default = True
! If true, recover a bug in barotropic solver that uses an unnormalized weight
! function for vertical averages of baroclinic velocity and forcing. Default of
! this flag is set by VISC_REM_BUG.
BAROTROPIC_TIDAL_SAL_BUG = False ! [Boolean] default = False
! If true, the tidal self-attraction and loading anomaly in the barotropic
! solver has the wrong sign, replicating a long-standing bug with a scalar
Expand Down Expand Up @@ -1782,7 +1790,7 @@ DISSIPATION_KD_MIN = 0.0 ! [m2 s-1] default = 0.0
DOUBLE_DIFFUSION = True ! [Boolean] default = False
! If true, increase diffusivites for temperature or salinity based on the
! double-diffusive parameterization described in Large et al. (1994).
MAX_RRHO_SALT_FINGERS = 2.55 ! [nondim] default = 2.55
MAX_RRHO_SALT_FINGERS = 1.9 ! [nondim] default = 1.9
! Maximum density ratio for salt fingering regime.
MAX_SALT_DIFF_SALT_FINGERS = 1.0E-04 ! [m2 s-1] default = 1.0E-04
! Maximum salt diffusivity for salt fingering regime.
Expand Down Expand Up @@ -2107,9 +2115,6 @@ USE_HUYNH_STENCIL_BUG = False ! [Boolean] default = False
! === module MOM_tracer_hor_diff ===
KHTR = 0.0 ! [m2 s-1] default = 0.0
! The background along-isopycnal tracer diffusivity.
KHTR_USE_EBT_STRUCT = False ! [Boolean] default = False
! If true, uses the equivalent barotropic structure as the vertical structure of
! the tracer diffusivity.
KHTR_MIN = 0.0 ! [m2 s-1] default = 0.0
! The minimum along-isopycnal tracer diffusivity.
KHTR_MAX = 0.0 ! [m2 s-1] default = 0.0
Expand Down Expand Up @@ -2163,6 +2168,8 @@ PHA_MLD_HREF = 10.0 ! [m] default = 0.0
PHA_MLD_DRHO = 0.03 ! [kg/m3] default = 0.03
! The density difference for a density difference based photoacclimation MLD [kg
! m-3].
DO_SPONGE_GENERIC_TRACER = False ! [Boolean] default = False
! If true, then some generic tracers may be nudged.
OBSOLETE_DIAGNOSTIC_IS_FATAL = True ! [Boolean] default = True
! If an obsolete diagnostic variable appears in the diag_table, cause a FATAL
! error rather than issue a WARNING.
Expand Down
2 changes: 0 additions & 2 deletions exps/NEP10.COBALT/MOM_parameter_doc.short
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Expand Up @@ -348,8 +348,6 @@ KHTH_MAX_CFL = 0.1 ! [nondimensional] default = 0.8
! model, but much smaller numbers (e.g. 0.1) seem to work better for ALE-based
! models.

! === module MOM_porous_barriers ===

! === module MOM_dynamics_split_RK2 ===
TIDES = True ! [Boolean] default = False
! If true, apply tidal momentum forcing.
Expand Down
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