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Update MOM6 and ocean_BGC tags (#130)
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* update parameter docs

* turn off tide test for now due to bug in MOM_sum_output.F90

* Updated MOM6 and ocean_BGC tags

* reactivate tide case and update parameter files
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@yichengt900
yichengt900 authored Jan 8, 2025
1 parent 787e98a commit d832842
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29 changes: 22 additions & 7 deletions exps/NEP10.COBALT/MOM_parameter_doc.all
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Original file line number Diff line number Diff line change
Expand Up @@ -382,7 +382,7 @@ 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
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
Expand Down Expand Up @@ -1138,7 +1138,7 @@ TIDAL_SAL_FROM_FILE = False ! [Boolean] default = False
USE_PREVIOUS_TIDES = False ! [Boolean] default = False
! If true, use the SAL from the previous iteration of the tides to facilitate
! convergent iteration. This is only used if TIDES is true.
TIDE_REF_DATE = 1993, 1, 1 ! default = 0
TIDE_REF_DATE = 1993, 1, 1 ! default = 0, 0, 0
! Year,month,day to use as reference date for tidal forcing. If not specified,
! defaults to 0.
TIDE_USE_EQ_PHASE = True ! [Boolean] default = False
Expand Down Expand Up @@ -1951,6 +1951,11 @@ MKE_TO_TKE_EFFIC = 0.0 ! [nondim] default = 0.0
TKE_DECAY = 0.001 ! [nondim] default = 2.5
! TKE_DECAY relates the vertical rate of decay of the TKE available for
! mechanical entrainment to the natural Ekman depth.
DIRECT_EPBL_MIXING_CALC = False ! [Boolean] default = False
! If true and there is no conversion from mean kinetic energy to ePBL turbulent
! kinetic energy, use a direct calculation of the diffusivity that is supported
! by a given energy input instead of the more general but slower iterative
! solver.
EPBL_MSTAR_SCHEME = "REICHL_H18" ! default = "CONSTANT"
! EPBL_MSTAR_SCHEME selects the method for setting mstar. Valid values are:
! CONSTANT - Use a fixed mstar given by MSTAR
Expand All @@ -1960,7 +1965,7 @@ MSTAR_CAP = 10.0 ! [nondim] default = -1.0
! If this value is positive, it sets the maximum value of mstar allowed in ePBL.
! (This is not used if EPBL_MSTAR_SCHEME = CONSTANT).
RH18_MSTAR_CN1 = 0.275 ! [nondim] default = 0.275
! MSTAR_N coefficient 1 (outter-most coefficient for fit). The value of 0.275 is
! MSTAR_N coefficient 1 (outer-most coefficient for fit). The value of 0.275 is
! given in RH18. Increasing this coefficient increases MSTAR for all values of
! Hf/ust, but more effectively at low values (weakly developed OSBLs).
RH18_MSTAR_CN2 = 8.0 ! [nondim] default = 8.0
Expand Down Expand Up @@ -2005,10 +2010,13 @@ EPBL_MLD_BISECTION = True ! [Boolean] default = False
! mixed layer depth. Otherwise use the false position after a maximum and
! minimum bound have been evaluated and the returned value or bisection before
! this.
EPBL_MLD_ITER_BUG = True ! [Boolean] default = True
! If true, use buggy logic that gives the wrong bounds for the next iteration
! when successive guesses increase by exactly EPBL_MLD_TOLERANCE.
EPBL_MLD_MAX_ITS = 20 ! default = 20
! The maximum number of iterations that can be used to find a self-consistent
! mixed layer depth. If EPBL_MLD_BISECTION is true, the maximum number
! iteractions needed is set by Depth/2^MAX_ITS < EPBL_MLD_TOLERANCE.
! mixed layer depth. If EPBL_MLD_BISECTION is true, the maximum number of
! iterations needed is set by Depth/2^MAX_ITS < EPBL_MLD_TOLERANCE.
EPBL_MIN_MIX_LEN = 0.0 ! [meter] default = 0.0
! The minimum mixing length scale that will be used by ePBL. The default (0)
! does not set a minimum.
Expand All @@ -2031,6 +2039,9 @@ EPBL_VEL_SCALE_FACTOR = 0.5477 ! [nondim] default = 1.0
! the PBL diffusivity.
VSTAR_SURF_FAC = 1.8258 ! [nondim] default = 1.2
! The proportionality times ustar to set vstar at the surface.
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.
USE_LA_LI2016 = True ! [Boolean] default = False
! A logical to use the Li et al. 2016 (submitted) formula to determine the
! Langmuir number.
Expand All @@ -2040,12 +2051,12 @@ EPBL_LANGMUIR_SCHEME = "ADDITIVE" ! default = "NONE"
! NONE - Do not do any extra mixing due to Langmuir turbulence
! RESCALE - Use a multiplicative rescaling of mstar to account for Langmuir
! turbulence
! ADDITIVE - Add a Langmuir turblence contribution to mstar to other
! ADDITIVE - Add a Langmuir turbulence contribution to mstar to other
! contributions
LT_ENHANCE_COEF = 0.1056 ! [nondim] default = 0.447
! Coefficient for Langmuir enhancement of mstar
LT_ENHANCE_EXP = -1.0 ! [nondim] default = -1.33
! Exponent for Langmuir enhancementt of mstar
! Exponent for Langmuir enhancement of mstar
LT_MOD_LAC1 = 0.0 ! [nondim] default = -0.87
! Coefficient for modification of Langmuir number due to MLD approaching Ekman
! depth.
Expand All @@ -2061,6 +2072,10 @@ LT_MOD_LAC4 = 0.8 ! [nondim] default = 0.95
LT_MOD_LAC5 = 0.8 ! [nondim] default = 0.95
! Coefficient for modification of Langmuir number due to ratio of Ekman to
! unstable Obukhov depth.
EPBL_OPTIONS_DIFF = 0 ! default = 0
! If positive, this is a coded integer indicating a pair of settings whose
! differences are diagnosed in a passive diagnostic mode via extra calls to
! ePBL_column. If this is 0 or negative no extra calls occur.
!EPBL_USTAR_MIN = 1.45842E-18 ! [m s-1]
! The (tiny) minimum friction velocity used within the ePBL code, derived from
! OMEGA and ANGSTROM.
Expand Down
2 changes: 1 addition & 1 deletion exps/NEP10.COBALT/MOM_parameter_doc.layout
View file
Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ NJPROC = 56 !
! in MOM_memory.h at compile time.
LAYOUT = 20, 56 !
! The processor layout that was actually used.
IO_LAYOUT = 1, 1 ! default = 1
IO_LAYOUT = 1, 1 ! default = 1, 1
! The processor layout to be used, or 0,0 to automatically set the io_layout to
! be the same as the layout.

Expand Down
8 changes: 4 additions & 4 deletions exps/NEP10.COBALT/MOM_parameter_doc.short
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Original file line number Diff line number Diff line change
Expand Up @@ -167,7 +167,7 @@ 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
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 ===
Expand Down Expand Up @@ -391,7 +391,7 @@ TIDE_MF = True ! [Boolean] default = False
TIDE_MM = True ! [Boolean] default = False
! If true, apply tidal momentum forcing at the MM frequency. This is only used
! if TIDES is true.
TIDE_REF_DATE = 1993, 1, 1 ! default = 0
TIDE_REF_DATE = 1993, 1, 1 ! default = 0, 0, 0
! Year,month,day to use as reference date for tidal forcing. If not specified,
! defaults to 0.
TIDE_USE_EQ_PHASE = True ! [Boolean] default = False
Expand Down Expand Up @@ -653,12 +653,12 @@ EPBL_LANGMUIR_SCHEME = "ADDITIVE" ! default = "NONE"
! NONE - Do not do any extra mixing due to Langmuir turbulence
! RESCALE - Use a multiplicative rescaling of mstar to account for Langmuir
! turbulence
! ADDITIVE - Add a Langmuir turblence contribution to mstar to other
! ADDITIVE - Add a Langmuir turbulence contribution to mstar to other
! contributions
LT_ENHANCE_COEF = 0.1056 ! [nondim] default = 0.447
! Coefficient for Langmuir enhancement of mstar
LT_ENHANCE_EXP = -1.0 ! [nondim] default = -1.33
! Exponent for Langmuir enhancementt of mstar
! Exponent for Langmuir enhancement of mstar
LT_MOD_LAC1 = 0.0 ! [nondim] default = -0.87
! Coefficient for modification of Langmuir number due to MLD approaching Ekman
! depth.
Expand Down
2 changes: 1 addition & 1 deletion exps/NEP10.COBALT/SIS_parameter_doc.layout
View file
Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@ NJPROC = 56 !
! in SIS2_memory.h at compile time.
LAYOUT = 20, 56 !
! The processor layout that was actually used.
IO_LAYOUT = 1, 1 ! default = 1
IO_LAYOUT = 1, 1 ! default = 1, 1
! The processor layout to be used, or 0,0 to automatically set the io_layout to
! be the same as the layout.
NIBLOCK = 1 ! default = 1
Expand Down
29 changes: 22 additions & 7 deletions exps/NWA12.COBALT/MOM_parameter_doc.all
View file
Original file line number Diff line number Diff line change
Expand Up @@ -376,7 +376,7 @@ 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
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
Expand Down Expand Up @@ -1150,7 +1150,7 @@ TIDAL_SAL_FROM_FILE = False ! [Boolean] default = False
USE_PREVIOUS_TIDES = False ! [Boolean] default = False
! If true, use the SAL from the previous iteration of the tides to facilitate
! convergent iteration. This is only used if TIDES is true.
TIDE_REF_DATE = 1993, 1, 1 ! default = 0
TIDE_REF_DATE = 1993, 1, 1 ! default = 0, 0, 0
! Year,month,day to use as reference date for tidal forcing. If not specified,
! defaults to 0.
TIDE_USE_EQ_PHASE = True ! [Boolean] default = False
Expand Down Expand Up @@ -1983,6 +1983,11 @@ MKE_TO_TKE_EFFIC = 0.0 ! [nondim] default = 0.0
TKE_DECAY = 0.001 ! [nondim] default = 2.5
! TKE_DECAY relates the vertical rate of decay of the TKE available for
! mechanical entrainment to the natural Ekman depth.
DIRECT_EPBL_MIXING_CALC = False ! [Boolean] default = False
! If true and there is no conversion from mean kinetic energy to ePBL turbulent
! kinetic energy, use a direct calculation of the diffusivity that is supported
! by a given energy input instead of the more general but slower iterative
! solver.
EPBL_MSTAR_SCHEME = "REICHL_H18" ! default = "CONSTANT"
! EPBL_MSTAR_SCHEME selects the method for setting mstar. Valid values are:
! CONSTANT - Use a fixed mstar given by MSTAR
Expand All @@ -1992,7 +1997,7 @@ MSTAR_CAP = 10.0 ! [nondim] default = -1.0
! If this value is positive, it sets the maximum value of mstar allowed in ePBL.
! (This is not used if EPBL_MSTAR_SCHEME = CONSTANT).
RH18_MSTAR_CN1 = 0.275 ! [nondim] default = 0.275
! MSTAR_N coefficient 1 (outter-most coefficient for fit). The value of 0.275 is
! MSTAR_N coefficient 1 (outer-most coefficient for fit). The value of 0.275 is
! given in RH18. Increasing this coefficient increases MSTAR for all values of
! Hf/ust, but more effectively at low values (weakly developed OSBLs).
RH18_MSTAR_CN2 = 8.0 ! [nondim] default = 8.0
Expand Down Expand Up @@ -2037,10 +2042,13 @@ EPBL_MLD_BISECTION = True ! [Boolean] default = False
! mixed layer depth. Otherwise use the false position after a maximum and
! minimum bound have been evaluated and the returned value or bisection before
! this.
EPBL_MLD_ITER_BUG = True ! [Boolean] default = True
! If true, use buggy logic that gives the wrong bounds for the next iteration
! when successive guesses increase by exactly EPBL_MLD_TOLERANCE.
EPBL_MLD_MAX_ITS = 40 ! default = 20
! The maximum number of iterations that can be used to find a self-consistent
! mixed layer depth. If EPBL_MLD_BISECTION is true, the maximum number
! iteractions needed is set by Depth/2^MAX_ITS < EPBL_MLD_TOLERANCE.
! mixed layer depth. If EPBL_MLD_BISECTION is true, the maximum number of
! iterations needed is set by Depth/2^MAX_ITS < EPBL_MLD_TOLERANCE.
EPBL_MIN_MIX_LEN = 0.0 ! [meter] default = 0.0
! The minimum mixing length scale that will be used by ePBL. The default (0)
! does not set a minimum.
Expand All @@ -2063,6 +2071,9 @@ EPBL_VEL_SCALE_FACTOR = 0.5477 ! [nondim] default = 1.0
! the PBL diffusivity.
VSTAR_SURF_FAC = 1.8258 ! [nondim] default = 1.2
! The proportionality times ustar to set vstar at the surface.
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.
USE_LA_LI2016 = True ! [Boolean] default = False
! A logical to use the Li et al. 2016 (submitted) formula to determine the
! Langmuir number.
Expand All @@ -2072,12 +2083,12 @@ EPBL_LANGMUIR_SCHEME = "ADDITIVE" ! default = "NONE"
! NONE - Do not do any extra mixing due to Langmuir turbulence
! RESCALE - Use a multiplicative rescaling of mstar to account for Langmuir
! turbulence
! ADDITIVE - Add a Langmuir turblence contribution to mstar to other
! ADDITIVE - Add a Langmuir turbulence contribution to mstar to other
! contributions
LT_ENHANCE_COEF = 0.1056 ! [nondim] default = 0.447
! Coefficient for Langmuir enhancement of mstar
LT_ENHANCE_EXP = -1.0 ! [nondim] default = -1.33
! Exponent for Langmuir enhancementt of mstar
! Exponent for Langmuir enhancement of mstar
LT_MOD_LAC1 = 0.0 ! [nondim] default = -0.87
! Coefficient for modification of Langmuir number due to MLD approaching Ekman
! depth.
Expand All @@ -2093,6 +2104,10 @@ LT_MOD_LAC4 = 0.8 ! [nondim] default = 0.95
LT_MOD_LAC5 = 0.8 ! [nondim] default = 0.95
! Coefficient for modification of Langmuir number due to ratio of Ekman to
! unstable Obukhov depth.
EPBL_OPTIONS_DIFF = 0 ! default = 0
! If positive, this is a coded integer indicating a pair of settings whose
! differences are diagnosed in a passive diagnostic mode via extra calls to
! ePBL_column. If this is 0 or negative no extra calls occur.
!EPBL_USTAR_MIN = 1.45842E-18 ! [m s-1]
! The (tiny) minimum friction velocity used within the ePBL code, derived from
! OMEGA and ANGSTROM.
Expand Down
2 changes: 1 addition & 1 deletion exps/NWA12.COBALT/MOM_parameter_doc.layout
View file
Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ NJPROC = 25 !
! in MOM_memory.h at compile time.
LAYOUT = 25, 25 !
! The processor layout that was actually used.
IO_LAYOUT = 1, 1 ! default = 1
IO_LAYOUT = 1, 1 ! default = 1, 1
! The processor layout to be used, or 0,0 to automatically set the io_layout to
! be the same as the layout.

Expand Down
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