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update ci build and MOM_parameter_doc for NEP
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@yichengt900
yichengt900 committed Jul 12, 2024
1 parent ebf7cff commit a3bc545
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2 changes: 1 addition & 1 deletion builds/ci_build_driver.sh
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Expand Up @@ -21,7 +21,7 @@ platform="ncrc5.intel23"
target="repro"
flavor="fms1_mom6sis2"

FMSlib_PATH="/gpfs/f5/cefi/scratch/Yi-cheng.Teng/github/FMS/2023.04_FMS1"
FMSlib_PATH="/gpfs/f5/cefi/scratch/Yi-cheng.Teng/github/FMS/2024.02_FMS1"
rootdir=$(pwd)
abs_rootdir=$rootdir

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53 changes: 50 additions & 3 deletions exps/NEP10.COBALT/MOM_parameter_doc.all
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Expand Up @@ -358,6 +358,10 @@ 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 = True ! [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
Expand Down Expand Up @@ -637,6 +641,11 @@ REMAP_BOUNDARY_EXTRAP = False ! [Boolean] default = False
INIT_BOUNDARY_EXTRAP = False ! [Boolean] default = False
! If true, values at the interfaces of boundary cells are extrapolated instead
! of piecewise constant during initialization.Defaults to REMAP_BOUNDARY_EXTRAP.
REMAPPING_USE_OM4_SUBCELLS = True ! [Boolean] default = True
! This selects the remapping algorithm used in OM4 that does not use the full
! reconstruction for the top- and lower-most sub-layers, but instead assumes
! they are always vanished (untrue) and so just uses their edge values. We
! recommend setting this option to false.
PARTIAL_CELL_VELOCITY_REMAP = False ! [Boolean] default = False
! If true, use partial cell thicknesses at velocity points that are masked out
! where they extend below the shallower of the neighboring bathymetry for
Expand Down Expand Up @@ -699,6 +708,10 @@ 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 = True ! [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.
USE_INDEX_DIAGNOSTIC_AXES = False ! [Boolean] default = False
! If true, use a grid index coordinate convention for diagnostic axes.
DIAG_COORDS = "z Z ZSTAR" ! default = "z Z ZSTAR"
Expand Down Expand Up @@ -966,6 +979,17 @@ STORE_CORIOLIS_ACCEL = True ! [Boolean] default = True
! 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
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.

! === module MOM_continuity_PPM ===
MONOTONIC_CONTINUITY = False ! [Boolean] default = False
Expand Down Expand Up @@ -1007,6 +1031,9 @@ 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 @@ -1208,8 +1235,8 @@ HOR_VISC_ANSWER_DATE = 99991231 ! default = 99991231
! 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
! optioncurrently only works with split mode.
! If true, use thickness at velocity points from continuity solver. This option
! currently only works with split mode.
LAPLACIAN = False ! [Boolean] default = False
! If true, use a Laplacian horizontal viscosity.
BIHARMONIC = True ! [Boolean] default = True
Expand Down Expand Up @@ -1255,6 +1282,10 @@ USE_LAND_MASK_FOR_HVISC = True ! [Boolean] default = True
HORVISC_BOUND_COEF = 0.8 ! [nondim] default = 0.8
! The nondimensional coefficient of the ratio of the viscosity bounds to the
! theoretical maximum for stability without considering other terms.
FRICTWORK_BUG = True ! [Boolean] default = True
! If true, retain an answer-changing bug in calculating the FrictWork, which
! cancels the h in thickness flux and the h at velocity point. This isnot
! recommended.

! === module MOM_vert_friction ===
VERT_FRICTION_ANSWER_DATE = 99991231 ! default = 99991231
Expand Down Expand Up @@ -1381,8 +1412,12 @@ BT_CORIOLIS_SCALE = 1.0 ! [nondim] default = 1.0
! A factor by which the barotropic Coriolis anomaly terms are scaled.
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 uuse more
! 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.
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 @@ -1504,6 +1539,10 @@ TAIL_DH = 0.0 ! [nondim] default = 0.0
! smoother stream function at the base of the mixed-layer.
USE_STANLEY_TVAR = False ! [Boolean] default = False
! If true, turn on Stanley SGS T variance parameterization in ML restrat code.
USE_CR_GRID = False ! [Boolean] default = False
! If true, read in a spatially varying Cr field.
USE_MLD_GRID = False ! [Boolean] default = False
! If true, read in a spatially varying MLD_decaying_Tfilt field.
%MLE
MLE_USE_PBL_MLD = True ! [Boolean] default = False
! If true, the MLE parameterization will use the mixed-layer depth provided by
Expand All @@ -1524,6 +1563,10 @@ 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 = True ! [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.
Expand Down Expand Up @@ -1746,6 +1789,10 @@ KAPPA_N_OVER_S_SCALE_COEF2 = 0.0 ! [nondim] default = 0.0
! The square of the ratio of the coefficients of the buoyancy and shear scales
! in the diffusivity equation, Set this to 0 (the default) to eliminate the
! shear scale. This is only used if USE_JACKSON_PARAM is true.
LZ_RESCALE = 1.0 ! [nondim] default = 1.0
! A coefficient to rescale the distance to the nearest solid boundary. This
! adjustment is to account for regions where 3 dimensional turbulence prevents
! the growth of shear instabilies [nondim].
KAPPA_SHEAR_TOL_ERR = 0.1 ! [nondim] default = 0.1
! The fractional error in kappa that is tolerated. Iteration stops when changes
! between subsequent iterations are smaller than this everywhere in a column.
Expand Down
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