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yichengt900 merged 10 commits into from
May 21, 2025
Merged

Updated mom6 tag #182

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56d6014
update mom6 and ocean_BGC tags
yichengt900 May 19, 2025
6beac6a
Added MARBAL interface path when building model
yichengt900 May 19, 2025
f622d02
Update parameter documentation files for 1D case
github-actions[bot] May 19, 2025
38cdfd2
Update parameter documentation files for NWA12 tide case
github-actions[bot] May 19, 2025
192f426
updated nep10k xml
yichengt900 May 20, 2025
d2a6838
revert BGC tag back to main one
yichengt900 May 21, 2025
c0f4be8
Update parameter documentation files for 1D case
github-actions[bot] May 21, 2025
09bd2ca
Updated mom6 tag with Theresa's fix
yichengt900 May 21, 2025
cdbdc1e
Update parameter documentation files for NWA12.COBALT
yichengt900 May 21, 2025
d9f6292
Update parameter documentation files for NEP10.COBALT
yichengt900 May 21, 2025
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16 changes: 8 additions & 8 deletions .gitmodules
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Expand Up @@ -22,14 +22,6 @@
path = src/mkmf
url = https://github.com/NOAA-GFDL/mkmf.git
branch = 2025.01
[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/FMS"]
path = src/FMS
url = https://github.com/NOAA-GFDL/FMS.git
Expand All @@ -46,3 +38,11 @@
path = src/land_null
url = https://github.com/NOAA-GFDL/land_null.git
branch = 2025.02
[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
6 changes: 3 additions & 3 deletions builds/linux-build.bash
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Expand Up @@ -140,7 +140,7 @@ build_mom6_fms2() {
mkdir -p $target_dir
pushd $target_dir
rm -f path_names
$srcdir/mkmf/bin/list_paths $srcdir/MOM6/{config_src/infra/FMS2,config_src/memory/dynamic_symmetric,config_src/drivers/FMS_cap,config_src/external/ODA_hooks,config_src/external/database_comms,config_src/external/drifters,config_src/external/stochastic_physics,pkg/GSW-Fortran/{modules,toolbox}/,src/{*,*/*}/} $srcdir/SIS2/{config_src/dynamic_symmetric,config_src/external/Icepack_interfaces,src} $srcdir/icebergs/src $srcdir/FMS/{coupler,include}/ $srcdir/{ocean_BGC/generic_tracers,ocean_BGC/mocsy/src}/ $srcdir/{atmos_null,ice_param,land_null,coupler/shared/,coupler/full/}/
$srcdir/mkmf/bin/list_paths $srcdir/MOM6/{config_src/infra/FMS2,config_src/memory/dynamic_symmetric,config_src/drivers/FMS_cap,config_src/external/MARBL,config_src/external/ODA_hooks,config_src/external/database_comms,config_src/external/drifters,config_src/external/stochastic_physics,pkg/GSW-Fortran/{modules,toolbox}/,src/{*,*/*}/} $srcdir/SIS2/{config_src/dynamic_symmetric,config_src/external/Icepack_interfaces,src} $srcdir/icebergs/src $srcdir/FMS/{coupler,include}/ $srcdir/{ocean_BGC/generic_tracers,ocean_BGC/mocsy/src}/ $srcdir/{atmos_null,ice_param,land_null,coupler/shared/,coupler/full/}/

# Compiler and linker options
compiler_options='-DINTERNAL_FILE_NML -DUSE_FMS2_IO -Duse_yaml -DMAX_FIELDS_=600 -DNOT_SET_AFFINITY -D_USE_MOM6_DIAG -D_USE_GENERIC_TRACER -DUSE_PRECISION=2 -D_USE_LEGACY_LAND_ -Duse_AM3_physics'
Expand Down Expand Up @@ -168,7 +168,7 @@ build_mom6_fms1() {
mkdir -p $target_dir
pushd $target_dir
rm -f path_names
$srcdir/mkmf/bin/list_paths $srcdir/MOM6/{config_src/infra/FMS1,config_src/memory/dynamic_symmetric,config_src/drivers/FMS_cap,config_src/external/ODA_hooks,config_src/external/database_comms,config_src/external/drifters,config_src/external/stochastic_physics,pkg/GSW-Fortran/{modules,toolbox}/,src/{*,*/*}/} $srcdir/SIS2/{config_src/dynamic_symmetric,config_src/external/Icepack_interfaces,src} $srcdir/icebergs/src $srcdir/FMS/{coupler,include}/ $srcdir/{ocean_BGC/generic_tracers,ocean_BGC/mocsy/src}/ $srcdir/{atmos_null,ice_param,land_null,coupler/shared/,coupler/full/}/
$srcdir/mkmf/bin/list_paths $srcdir/MOM6/{config_src/infra/FMS1,config_src/memory/dynamic_symmetric,config_src/drivers/FMS_cap,config_src/external/MARBL,config_src/external/ODA_hooks,config_src/external/database_comms,config_src/external/drifters,config_src/external/stochastic_physics,pkg/GSW-Fortran/{modules,toolbox}/,src/{*,*/*}/} $srcdir/SIS2/{config_src/dynamic_symmetric,config_src/external/Icepack_interfaces,src} $srcdir/icebergs/src $srcdir/FMS/{coupler,include}/ $srcdir/{ocean_BGC/generic_tracers,ocean_BGC/mocsy/src}/ $srcdir/{atmos_null,ice_param,land_null,coupler/shared/,coupler/full/}/

# Compiler and linker options
compiler_options='-DINTERNAL_FILE_NML -DUSE_FMS1_IO -Duse_yaml -DMAX_FIELDS_=600 -DNOT_SET_AFFINITY -D_USE_MOM6_DIAG -D_USE_GENERIC_TRACER -DUSE_PRECISION=2 -D_USE_LEGACY_LAND_ -Duse_AM3_physics'
Expand Down Expand Up @@ -196,7 +196,7 @@ build_mom6solo() {
mkdir -p $target_dir
pushd $target_dir
rm -f path_names
$srcdir/mkmf/bin/list_paths $srcdir/MOM6/{config_src/infra/FMS2,config_src/memory/dynamic_symmetric,config_src/drivers/solo_driver,config_src/external/GFDL_ocean_BGC,config_src/external/ODA_hooks,config_src/external/database_comms,config_src/external/drifters,config_src/external/stochastic_physics,pkg/GSW-Fortran/{modules,toolbox}/,src/{*,*/*}}/
$srcdir/mkmf/bin/list_paths $srcdir/MOM6/{config_src/infra/FMS2,config_src/memory/dynamic_symmetric,config_src/drivers/solo_driver,config_src/external/GFDL_ocean_BGC,config_src/external/MARBL,config_src/external/ODA_hooks,config_src/external/database_comms,config_src/external/drifters,config_src/external/stochastic_physics,pkg/GSW-Fortran/{modules,toolbox}/,src/{*,*/*}}/

# Compiler and linker options
compiler_options='-DUSE_FMS2_IO -Duse_yaml -DMAX_FIELDS_=600 -Duse_netCDF -DSPMD'
Expand Down
2 changes: 1 addition & 1 deletion ci/NWA/Dockerfile
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Expand Up @@ -85,7 +85,7 @@ RUN bld_dir=/apps/mom6_sis2_generic_4p_compile_symm_yaml/exec \
&& mkmf_template=/apps/mkmf/templates/hpcme-intel24.mk \
&& mkdir -p $bld_dir/mom6 \
&& echo "Making makefile for MOM6" \
&& list_paths -l -o $bld_dir/mom6/pathnames_mom6 $src_dir/mom6/src/MOM6/config_src/memory/dynamic_symmetric $src_dir/mom6/src/MOM6/config_src/drivers/FMS_cap $src_dir/mom6/src/MOM6/src/*/ $src_dir/mom6/src/MOM6/src/*/*/ $src_dir/mom6/src/MOM6/config_src/external/ODA_hooks $src_dir/mom6/src/MOM6/config_src/external/stochastic_physics $src_dir/mom6/src/MOM6/config_src/external/drifters $src_dir/mom6/src/MOM6/config_src/external/database_comms $src_dir/mom6/src/ocean_BGC/generic_tracers $src_dir/mom6/src/ocean_BGC/mocsy/src $src_dir/mom6/src/MOM6/pkg/GSW-Fortran/modules $src_dir/mom6/src/MOM6/pkg/GSW-Fortran/toolbox $src_dir/mom6/src/MOM6/config_src/infra/FMS2 \
&& list_paths -l -o $bld_dir/mom6/pathnames_mom6 $src_dir/mom6/src/MOM6/config_src/memory/dynamic_symmetric $src_dir/mom6/src/MOM6/config_src/drivers/FMS_cap $src_dir/mom6/src/MOM6/src/*/ $src_dir/mom6/src/MOM6/src/*/*/ $src_dir/mom6/src/MOM6/config_src/external/MARBL $src_dir/mom6/src/MOM6/config_src/external/ODA_hooks $src_dir/mom6/src/MOM6/config_src/external/stochastic_physics $src_dir/mom6/src/MOM6/config_src/external/drifters $src_dir/mom6/src/MOM6/config_src/external/database_comms $src_dir/mom6/src/ocean_BGC/generic_tracers $src_dir/mom6/src/ocean_BGC/mocsy/src $src_dir/mom6/src/MOM6/pkg/GSW-Fortran/modules $src_dir/mom6/src/MOM6/pkg/GSW-Fortran/toolbox $src_dir/mom6/src/MOM6/config_src/infra/FMS2 \
&& cd $bld_dir/mom6 \
&& mkmf -m Makefile -a $src_dir -b $bld_dir -p libmom6.a -t $mkmf_template -c "-DINTERNAL_FILE_NML -g -DINTERNAL_FILE_NML -DMAX_FIELDS_=600 -DUSE_FMS2_IO -DNOT_SET_AFFINITY -D_USE_MOM6_DIAG -D_USE_GENERIC_TRACER -DUSE_PRECISION=2 " -o "-I$bld_dir/FMS " -I${src_dir}/mom6/src/FMS/fms2_io/include -I${src_dir}/mom6/src/FMS/include -I${src_dir}/mom6/src/FMS/mpp/include -I${src_dir}/mom6/src/MOM6/pkg/CVMix-src/include $bld_dir/mom6/pathnames_mom6
## Make makefile for SIS2
Expand Down
35 changes: 30 additions & 5 deletions exps/NEP10.COBALT/MOM_parameter_doc.all
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Expand Up @@ -166,6 +166,8 @@ WRITE_GEOM = 0 ! 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.
GEOM_FILE = "ocean_geometry" ! default = "ocean_geometry"
! The file into which to write the ocean geometry.
USE_DBCLIENT = False ! [Boolean] default = False
! If true, initialize a client to a remote database that can be used for online
! analysis and machine-learning inference.
Expand Down Expand Up @@ -203,6 +205,9 @@ NIHALO = 4 ! default = 4
NJHALO = 4 ! default = 4
! The number of halo points on each side in the y-direction. How this is set
! varies with the calling component and static or dynamic memory configuration.
SAVE_UNMASKED_GEOM_FILE = False ! [Boolean] default = False
! If true and a mask table is used, create an unmasked MOM domain that is saved
! in the ocean geometry file.

! === module MOM_hor_index ===
! Sets the horizontal array index types.
Expand Down Expand Up @@ -488,6 +493,13 @@ TFREEZE_FORM = "MILLERO_78" ! default = "LINEAR"
! TFREEZE_FORM determines which expression should be used for the freezing
! point. Currently, the valid choices are "LINEAR", "MILLERO_78", "TEOS_POLY",
! "TEOS10"
TFREEZE_S_IS_PRACS = True ! [Boolean] default = True
! When True, the model will check if the model internal salinity is practical
! salinity. If the model uses absolute salinity, a conversion will be applied.
TFREEZE_T_IS_POTT = True ! [Boolean] default = True
! When True, the model will check if the model internal temperature is potential
! temperature. If the model uses conservative temperature, a conversion will be
! applied.

! === module MOM_restart ===
PARALLEL_RESTARTFILES = False ! [Boolean] default = False
Expand Down Expand Up @@ -525,6 +537,8 @@ USE_RGC_TRACER = False ! [Boolean] default = False
! If true, use the RGC_tracer tracer package.
USE_IDEAL_AGE_TRACER = False ! [Boolean] default = False
! If true, use the ideal_age_example tracer package.
USE_MARBL_TRACERS = False ! [Boolean] default = False
! If true, use the MARBL tracer package.
USE_REGIONAL_DYES = False ! [Boolean] default = False
! If true, use the regional_dyes tracer package.
USE_OIL_TRACER = False ! [Boolean] default = False
Expand Down Expand Up @@ -700,6 +714,10 @@ REMAP_VEL_MASK_BBL_THICK = -0.001 ! [m] default = -0.001
! A thickness of a bottom boundary layer below which velocities in thin layers
! are zeroed out after remapping, following practice with Hybgen remapping, or a
! negative value to avoid such filtering altogether.
REMAP_VEL_CONSERVE_KE = False ! [Boolean] default = False
! If true, a correction is applied to the baroclinic component of velocity after
! remapping so that total KE is conserved. KE may not be conserved when
! (CS%BBL_h_vel_mask > 0.0) .and. (CS%h_vel_mask > 0.0)

! === module MOM_state_initialization ===
FATAL_INCONSISTENT_RESTART_TIME = False ! [Boolean] default = False
Expand Down Expand Up @@ -973,8 +991,6 @@ MEKE_GM_SRC_ALT = False ! [Boolean] default = False
MEKE_GEOMETRIC = False ! [Boolean] default = False
! If true, uses the GM coefficient formulation from the GEOMETRIC framework
! (Marshall et al., 2012).
USE_KH_IN_MEKE = False ! [Boolean] default = False
! If true, uses the thickness diffusivity calculated here to diffuse MEKE.
USE_GME = False ! [Boolean] default = False
! If true, use the GM+E backscatter scheme in association with the Gent and
! McWilliams parameterization.
Expand Down Expand Up @@ -1014,7 +1030,8 @@ STORE_CORIOLIS_ACCEL = True ! [Boolean] default = True
! If true, calculate the Coriolis accelerations at the end of each timestep for
! use in the predictor step of the next split RK2 timestep.
FPMIX = False ! [Boolean] default = False
! If true, apply profiles of momentum flux magnitude and direction
! If true, add non-local momentum flux increments and diffuse down the Eulerian
! gradient.
VISC_REM_BUG = True ! [Boolean] default = True
! If true, visc_rem_[uv] in split mode is incorrectly calculated or accounted
! for in two places. This parameter controls the defaults of two individual
Expand Down Expand Up @@ -1636,7 +1653,11 @@ USE_MLD_GRID = False ! [Boolean] default = False
MLE_USE_PBL_MLD = True ! [Boolean] default = False
! If true, the MLE parameterization will use the mixed-layer depth provided by
! the active PBL parameterization. If false, MLE will estimate a MLD based on a
! density difference with the surface using the parameter MLE_DENSITY_DIFF.
! density difference with the surface using the parameter MLE_DENSITY_DIFF,
! unless BODNER_DETECT_MLD is true.
BODNER_DETECT_MLD = False ! [Boolean] default = False
! If true, the Bodner parameterization will use the mixed-layer depth detected
! via the density difference criterion MLE_DENSITY_DIFF.

! === module MOM_diagnostics ===
DIAG_EBT_MONO_N2_COLUMN_FRACTION = 0.0 ! [nondim] default = 0.0
Expand Down Expand Up @@ -2143,6 +2164,7 @@ OPACITY_SCHEME = "MANIZZA_05" ! default = "MANIZZA_05"
! into opacities. Currently valid options include:
! MANIZZA_05 - Use Manizza et al., GRL, 2005.
! MOREL_88 - Use Morel, JGR, 1988.
! OHLMANN_03 - Use Ohlmann, J Clim, 2003. (only use if dz(1)>2.0m)
BLUE_FRAC_SW = 0.5 ! [nondim] default = 0.5
! The fraction of the penetrating shortwave radiation that is in the blue band.
PEN_SW_NBANDS = 3 ! default = 1
Expand Down Expand Up @@ -2280,9 +2302,12 @@ ENERGYSAVEDAYS_GEOMETRIC = 0.0 ! [days] default = 0.0

! === module ocean_stochastics_init ===
DO_SPPT = False ! [Boolean] default = False
! If true, then stochastically perturb the thermodynamic tendemcies of T,S, amd
! If true, then stochastically perturb the thermodynamic tendencies of T,S, amd
! h. Amplitude and correlations are controlled by the nam_stoch namelist in the
! UFS model only.
DO_SKEB = False ! [Boolean] default = False
! If true, then stochastically perturb the currents using the stochastic kinetic
! energy backscatter scheme.
PERT_EPBL = False ! [Boolean] default = False
! If true, then stochastically perturb the kinetic energy production and
! dissipation terms. Amplitude and correlations are controlled by the nam_stoch
Expand Down
3 changes: 2 additions & 1 deletion exps/NEP10.COBALT/MOM_parameter_doc.short
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Expand Up @@ -506,7 +506,8 @@ MIN_WSTAR2 = 1.0E-09 ! [m2 s-2] default = 1.0E-24
MLE_USE_PBL_MLD = True ! [Boolean] default = False
! If true, the MLE parameterization will use the mixed-layer depth provided by
! the active PBL parameterization. If false, MLE will estimate a MLD based on a
! density difference with the surface using the parameter MLE_DENSITY_DIFF.
! density difference with the surface using the parameter MLE_DENSITY_DIFF,
! unless BODNER_DETECT_MLD is true.

! === module MOM_diagnostics ===

Expand Down
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