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Update docs based on files produced in 44cea06 
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‎docs/MOM_parameter_doc.all‎

Lines changed: 43 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -60,6 +60,14 @@ BATHYMETRY_AT_VEL = False ! [Boolean] default = False
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! If true, there are separate values for the basin depths at velocity points.
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! Otherwise the effects of topography are entirely determined from thickness
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! points.
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ENABLE_BUGS_BY_DEFAULT = True ! [Boolean] default = True
64+
! If true, the defaults for certain recently added bug-fix flags are set to
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! recreate the bugs so that the code can be moved forward without changing
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! answers for existing configurations. The defaults for groups of bug-fix flags
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! are periodcially changed to correct the bugs, at which point this parameter
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! will no longer be used to set their default. Setting this to false means that
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! bugs are only used if they are actively selected, but it also means that
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! answers may change when code is updated due to newly found bugs.
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DT = 600.0 ! [s]
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! The (baroclinic) dynamics time step. The time-step that is actually used will
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! be an integer fraction of the forcing time-step (DT_FORCING in ocean-only mode
@@ -85,14 +93,11 @@ TRADV_SPANS_COUPLING = True ! [Boolean] default = True
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! the coupling timestep. The actual tracer advection timestep that is used in
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! this case is the largest integer multiple of the coupling timestep that is
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! less than or equal to DT_TRACER_ADVECT.
88-
THICKNESSDIFFUSE = True ! [Boolean] default = False
96+
THICKNESSDIFFUSE = False ! [Boolean] default = False
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! If true, isopycnal surfaces are diffused with a Laplacian coefficient of KHTH.
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APPLY_INTERFACE_FILTER = False ! [Boolean] default = False
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! If true, model interface heights are subjected to a grid-scale dependent
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! spatial smoothing, often with biharmonic filter.
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THICKNESSDIFFUSE_FIRST = True ! [Boolean] default = False
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! If true, do thickness diffusion or interface height smoothing before dynamics.
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! This is only used if THICKNESSDIFFUSE or APPLY_INTERFACE_FILTER is true.
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HMIX_SFC_PROP = 1.0 ! [m] default = 1.0
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! If BULKMIXEDLAYER is false, HMIX_SFC_PROP is the depth over which to average
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! to find surface properties like SST and SSS or density (but not surface
@@ -329,6 +334,8 @@ OBC_TIDE_N_CONSTITUENTS = 0 ! default = 0
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EXTERIOR_OBC_BUG = True ! [Boolean] default = True
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! If true, recover a bug in barotropic solver and other routines when boundary
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! contitions interior to the domain are used.
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OBC_HOR_INDEXING_BUG = True ! [Boolean] default = True
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! If true, recover set of a horizontal indexing bugs in the OBC code.
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OBC_SEGMENT_001 = "J=N,I=N:0,FLATHER,ORLANSKI,NUDGED" !
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! Documentation needs to be dynamic?????
334341
OBC_SEGMENT_001_VELOCITY_NUDGING_TIMESCALES = 0.3, 360.0 ! [days]
@@ -440,6 +447,13 @@ DTFREEZE_DS = -0.054 ! [degC ppt-1] default = -0.054
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DTFREEZE_DP = -7.75E-08 ! [degC Pa-1] default = 0.0
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! When TFREEZE_FORM=LINEAR, this is the derivative of the freezing potential
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! temperature with pressure.
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TFREEZE_S_IS_PRACS = True ! [Boolean] default = True
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! When True, the model will check if the model internal salinity is practical
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! salinity. If the model uses absolute salinity, a conversion will be applied.
453+
TFREEZE_T_IS_POTT = True ! [Boolean] default = True
454+
! When True, the model will check if the model internal temperature is potential
455+
! temperature. If the model uses conservative temperature, a conversion will be
456+
! applied.
443457

444458
! === module MOM_restart ===
445459
PARALLEL_RESTARTFILES = False ! [Boolean] default = False
@@ -769,6 +783,10 @@ ODA_INCUPD = False ! [Boolean] default = False
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SPONGE = False ! [Boolean] default = False
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! If true, sponges may be applied anywhere in the domain. The exact location and
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! properties of those sponges are specified via SPONGE_CONFIG.
786+
OBC_RESERVOIR_INIT_BUG = True ! [Boolean] default = True
787+
! If true, set the OBC tracer reservoirs at the startup of a new run from the
788+
! interior tracer concentrations regardless of properties that may be explicitly
789+
! specified for the reservoir concentrations.
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OBC_SEGMENT_001_DATA = "U=file:forcing_access_yr2_8km_fill.nc(u),V=file:forcing_access_yr2_8km_fill.nc(v),SSH=file:forcing_access_yr2_8km_fill.nc(eta_t),TEMP=file:forcing_access_yr2_8km_fill.nc(pot_temp),SALT=file:forcing_access_yr2_8km_fill.nc(salt)" !
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! OBC segment docs
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OBC_USER_CONFIG = "none" ! default = "none"
@@ -902,9 +920,6 @@ BACKSCAT_EBT_POWER = 0.0 ! [nondim] default = 0.0
902920
BS_USE_SQG_STRUCT = False ! [Boolean] default = False
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! If true, the SQG vertical structure is used for backscatter on the condition
904922
! that BS_EBT_power=0
905-
SQG_EXPO = 1.0 ! [nondim] default = 1.0
906-
! Nondimensional exponent coeffecient of the SQG mode that is used for the
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! vertical struture of diffusivities.
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KHTH_USE_EBT_STRUCT = False ! [Boolean] default = False
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! If true, uses the equivalent barotropic structure as the vertical structure of
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! thickness diffusivity.
@@ -939,6 +954,10 @@ VERY_SMALL_FREQUENCY = 1.0E-17 ! [s-1] default = 1.0E-17
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USE_STANLEY_ISO = False ! [Boolean] default = False
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! If true, turn on Stanley SGS T variance parameterization in isopycnal slope
941956
! code.
957+
MIXING_COEFS_OBC_BUG = True ! [Boolean] default = True
958+
! If false, use only interior data for thickness weighting in lateral mixing
959+
! coefficient calculations and to calculate stratification and other fields at
960+
! open boundary condition faces.
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KD_SMOOTH = 1.0E-06 ! [m2 s-1] default = 1.0E-06
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! A diapycnal diffusivity that is used to interpolate more sensible values of T
944963
! & S into thin layers.
@@ -1934,6 +1953,11 @@ VERTEX_SHEAR = True ! [Boolean] default = False
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VERTEX_SHEAR_VISCOSITY_BUG = True ! [Boolean] default = True
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! If true, use a bug in vertex shear that zeros out viscosities at vertices on
19361955
! coastlines.
1956+
VERTEX_SHEAR_OBC_BUG = True ! [Boolean] default = True
1957+
! If false, use extra masking when interpolating thicknesses to velocity points
1958+
! for setting up the shear velocities at vertices to avoid using external
1959+
! thicknesses at open boundaries. When OBCs are not in use, this parameter does
1960+
! not change answers, but true is more efficient.
19371961
VERTEX_SHEAR_GEOMETRIC_MEAN = False ! [Boolean] default = False
19381962
! If true, use a geometric mean for moving diffusivity from vertices to tracer
19391963
! points. False uses algebraic mean.
@@ -2201,6 +2225,14 @@ LT_MOD_LAC4 = 0.0 ! [nondim] default = 0.95
22012225
LT_MOD_LAC5 = 0.22 ! [nondim] default = 0.95
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! Coefficient for modification of Langmuir number due to ratio of Ekman to
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! unstable Obukhov depth.
2228+
EPBL_EQD_DIFFUSIVITY_SHAPE = False ! [nondim] default = False
2229+
! Logical flag for activating ML equation for shape function that uses forcing
2230+
! to change its structure.
2231+
EPBL_EQD_DIFFUSIVITY_VELOCITY = False ! [nondim] default = False
2232+
! Logical flag for activating ML equation discovery for velocity scale
2233+
EPBL_EQD_DIFFUSIVITY_VELOCITY_H = False ! [nondim] default = False
2234+
! Logical flag for activating ML equation discovery for velocity scale with h as
2235+
! input
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EPBL_OPTIONS_DIFF = 0 ! default = 0
22052237
! If positive, this is a coded integer indicating a pair of settings whose
22062238
! differences are diagnosed in a passive diagnostic mode via extra calls to
@@ -2260,7 +2292,8 @@ KHTR = 0.0 ! [m2 s-1] default = 0.0
22602292
KHTR_MIN = 0.0 ! [m2 s-1] default = 0.0
22612293
! The minimum along-isopycnal tracer diffusivity.
22622294
KHTR_MAX = 0.0 ! [m2 s-1] default = 0.0
2263-
! The maximum along-isopycnal tracer diffusivity.
2295+
! The maximum along-isopycnal tracer diffusivity. Set to a positive value to
2296+
! activate.
22642297
KHTR_PASSIVITY_COEFF = 0.0 ! [nondim] default = 0.0
22652298
! The coefficient that scales deformation radius over grid-spacing in passivity,
22662299
! where passivity is the ratio between along isopycnal mixing of tracers to
@@ -2317,6 +2350,8 @@ ENERGYFILE = "ocean.stats" ! default = "ocean.stats"
23172350
! The file to use to write the energies and globally summed diagnostics.
23182351
DATE_STAMPED_STDOUT = True ! [Boolean] default = True
23192352
! If true, use dates (not times) in messages to stdout
2353+
ISO_DATE_STAMPED_STDOUT = False ! [Boolean] default = False
2354+
! If true, use ISO formatted dates in messages to stdout
23202355
TIMEUNIT = 8.64E+04 ! [s] default = 8.64E+04
23212356
! The time unit in seconds a number of input fields
23222357
READ_DEPTH_LIST = False ! [Boolean] default = False

‎docs/MOM_parameter_doc.debugging‎

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Original file line numberDiff line numberDiff line change
@@ -36,13 +36,18 @@ DEBUG = False ! [Boolean] default = False
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! If true, write out verbose debugging data.
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DEBUG_TRUNCATIONS = False ! [Boolean] default = False
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! If true, calculate all diagnostics that are useful for debugging truncations.
39+
DEBUG_OBCS = False ! [Boolean] default = False
40+
! If true, write out verbose debugging data about OBCs.
3941
ROTATE_INDEX = False ! [Boolean] default = False
4042
! Enable rotation of the horizontal indices.
4143
DEBUG_CHKSUMS = False ! [Boolean] default = False
4244
! If true, checksums are performed on arrays in the various vec_chksum routines.
4345
DEBUG_REDUNDANT = False ! [Boolean] default = False
4446
! If true, debug redundant data points during calls to the various vec_chksum
4547
! routines.
48+
OBC_DEBUGGING_TESTS = False ! [Boolean] default = False
49+
! If true, do additional calls resetting certain values to help verify the
50+
! correctness of the open boundary condition code.
4651

4752
! === module MOM_verticalGrid ===
4853
! Parameters providing information about the vertical grid.

‎docs/MOM_parameter_doc.layout‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -67,6 +67,10 @@ BT_USE_WIDE_HALOS = True ! [Boolean] default = True
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! efficiency.
6868
BTHALO = 0 ! default = 0
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! The minimum halo size for the barotropic solver.
70+
BT_WIDE_HALO_MIN_STENCIL = 0 ! default = 0
71+
! The minimum stencil width to use with the wide halo iterations. A nonzero
72+
! value may be useful for debugging purposes, but at the cost of reducing the
73+
! efficiency gain from BT_USE_WIDE_HALOS.
7074
!BT x-halo = 4 !
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! The barotropic x-halo size that is actually used.
7276
!BT y-halo = 4 !

‎docs/MOM_parameter_doc.short‎

Lines changed: 0 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -18,11 +18,6 @@ THERMO_SPANS_COUPLING = True ! [Boolean] default = False
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! coupling timestep. The actual thermodynamic timestep that is used in this case
1919
! is the largest integer multiple of the coupling timestep that is less than or
2020
! equal to DT_THERM.
21-
THICKNESSDIFFUSE = True ! [Boolean] default = False
22-
! If true, isopycnal surfaces are diffused with a Laplacian coefficient of KHTH.
23-
THICKNESSDIFFUSE_FIRST = True ! [Boolean] default = False
24-
! If true, do thickness diffusion or interface height smoothing before dynamics.
25-
! This is only used if THICKNESSDIFFUSE or APPLY_INTERFACE_FILTER is true.
2621
HFREEZE = 10.0 ! [m] default = -1.0
2722
! If HFREEZE > 0, melt potential will be computed. The actual depth over which
2823
! melt potential is computed will be min(HFREEZE, OBLD), where OBLD is the

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