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MOM6: Merged dev/ncar & dev/master into dev/gfdl
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  Merged an extensive set of changes from dev/ncar onto dev/master, and then
from dev/master into dev/gfdl.  The list of commits include:
 - NOAA-GFDL/MOM6@3c70582 Merge branch 'dev/master' into dev/gfdl
 - NOAA-GFDL/MOM6@77a97ba Merge branch 'NCAR-dev/ncar' into dev/master
 - NOAA-GFDL/MOM6@8050958 Merge pull request NOAA-GFDL#55 from gustavo-marques/deallocate_diabatic
 - NOAA-GFDL/MOM6@648f31b Replace cvmix with CVMix
 - NOAA-GFDL/MOM6@4b21263 Merge pull request NOAA-GFDL#54 from gustavo-marques/deallocate_diabatic
 - NOAA-GFDL/MOM6@165a5eb Comment call diabatic_driver_end
 - NOAA-GFDL/MOM6@9f4ce3a Un-comment call diabatic_driver_end
 - NOAA-GFDL/MOM6@4671c07 Comment call diabatic_driver_end to check if Travis still fails
 - NOAA-GFDL/MOM6@e90fbe9 Return if CS is not associated
 - NOAA-GFDL/MOM6@65527d6 Set useKPP = .false. (default) and comment call to diag_grid_storage_end
 - NOAA-GFDL/MOM6@2800524 Uncomment calls to deallocate KPP related arrays
 - NOAA-GFDL/MOM6@dab30b6 Merge pull request NOAA-GFDL#52 from alperaltuntas/initialize_tidal_ctrl_vars
 - NOAA-GFDL/MOM6@334f124 Merge remote-tracking branch 'gmarques/fix_travis_deallocation' into initialize_tidal_ctrl_vars
 - NOAA-GFDL/MOM6@5153869 initialize boolean control vars in tidal mixing mod
 - NOAA-GFDL/MOM6@43b7968 Commenting out call to diabatic_driver_end in MOM.F90
 - NOAA-GFDL/MOM6@dde5a59 Commenting out deallocation of KPP related arrays
 - NOAA-GFDL/MOM6@dc82c48 Return call if CS is not allocated
 - NOAA-GFDL/MOM6@dabe31b Update CVMix
 - NOAA-GFDL/MOM6@5640daf Attempt to fix deallocating unallocated arrays
 - NOAA-GFDL/MOM6@93eee52 Merge pull request NOAA-GFDL#49 from gustavo-marques/update_cvmix
 - NOAA-GFDL/MOM6@d07120c Remove trailing space
 - NOAA-GFDL/MOM6@69bf4fa Updates CVMix
 - NOAA-GFDL/MOM6@5f19507 Merge pull request NOAA-GFDL#48 from gustavo-marques/fix_cvmix_convection
 - NOAA-GFDL/MOM6@caf1d1e Fixes bug and renames variables
 - NOAA-GFDL/MOM6@869d32f Merge pull request NOAA-GFDL#47 from alperaltuntas/introduce_cvmix_tidal
 - NOAA-GFDL/MOM6@01578c5 fix tidal_mixing_init return
 - NOAA-GFDL/MOM6@86e7074 Merge pull request NOAA-GFDL#46 from alperaltuntas/introduce_cvmix_tidal
 - NOAA-GFDL/MOM6@bf322c8 add tidal mixing-specific prandtl number
 - NOAA-GFDL/MOM6@81a5ef8 Merged with latest master
 - NOAA-GFDL/MOM6@696462c MOM_tidal_mixing. cleaanup
 - NOAA-GFDL/MOM6@3e7cab8 debug calculate_cvmix_tidal
 - NOAA-GFDL/MOM6@78bb40c Merge pull request NOAA-GFDL#44 from NCAR/adding_cvmix
 - NOAA-GFDL/MOM6@4dde603 Avoided a possible seg. fault in set_diffusivity_end
 - NOAA-GFDL/MOM6@36f7a06 Changed kv to a pointer since it might not always be associated
 - NOAA-GFDL/MOM6@0ce9980 By pass reading BULKMIXEDLAYER via get_param
 - NOAA-GFDL/MOM6@1218973 Raname variables Kd -> kd_lay; visc%Kv_slow - > kv
 - NOAA-GFDL/MOM6@ea813b8 add tidal diagnostics for cvmix
 - NOAA-GFDL/MOM6@648018e Rename kv_conv -> kv_conv_const; kd_conv -> kd_conv_const
 - NOAA-GFDL/MOM6@c1acec8 Add vertical background viscosity into visc%Kv_slow
 - NOAA-GFDL/MOM6@a2498a1 Changed name in register_diag_field kd_shear -> kd_shear_cvmix; kv_shear -> kv_shear_cvmix
 - NOAA-GFDL/MOM6@37ca38f Renamed kd_bkgnd_3d -> kd_bkgnd; kv_bkgnd_3d -> kv_bkgnd
 - NOAA-GFDL/MOM6@105094f Add viscosities due to convection into visc%Kv_slow
 - NOAA-GFDL/MOM6@e544290 Allocated/deallocate visc%Kv_slow
 - NOAA-GFDL/MOM6@801a86a Added variable Kv_slow in visc type
 - NOAA-GFDL/MOM6@8977888 Move tidal diagnostics to MOM_tidal_mixing module
 - NOAA-GFDL/MOM6@2430f6e correct tidal energy file dir
 - NOAA-GFDL/MOM6@a3155d6 Add tidal parameter consistency checks.
 - NOAA-GFDL/MOM6@80c33a4 Replaced Kv_turb -> Kv_shear
 - NOAA-GFDL/MOM6@644f200 Replaced Kv_turb -> Kv_shear
 - NOAA-GFDL/MOM6@6a2e864 Replaced Kd_turb -> Kd_shear and Kv_turb -> Kv_shear
 - NOAA-GFDL/MOM6@7376f49 update Kd
 - NOAA-GFDL/MOM6@69ab998 Added a unique Prandtl # for convection and background
 - NOAA-GFDL/MOM6@4cac1e1 Renamed variables (KH to kd; KM to kv) and added diagnostics
 - NOAA-GFDL/MOM6@e992292 Added calculate_cvmix_tidal interface
 - NOAA-GFDL/MOM6@2c451c8 Merge pull request NOAA-GFDL#43 from alperaltuntas/dev/ncar
 - NOAA-GFDL/MOM6@d1cee89 Add timestep initializations to calculate_cvmix_tidal
 - NOAA-GFDL/MOM6@7a81871 Re-structured MOM_bkgnd_mixing
 - NOAA-GFDL/MOM6@3fcdb4c Update to new CVMix tag with tidal mixing changes
 - NOAA-GFDL/MOM6@f361002 Read in tidal energy dissipation
 - NOAA-GFDL/MOM6@4e8dd5a Added a if statement to check if Int_tide_dissipation and Bryan_Lewis are used at the same time.
 - NOAA-GFDL/MOM6@8ef5a1b Renamed Bryan&Lewis coeffs and added a 3D array for depth
 - NOAA-GFDL/MOM6@08db85c Deleted code that has been moved to MOM_bkgnd_mixing.F90
 - NOAA-GFDL/MOM6@1be0248 Added first version of MOM_bkgnd_mixing
 - NOAA-GFDL/MOM6@1116f49 Fixed a problem in cvmix_init_bkgnd_BryanLewis_low
 - NOAA-GFDL/MOM6@83089ff Updated CVMix
 - NOAA-GFDL/MOM6@a101e49 Reduced the numbers of characters in a line
 - NOAA-GFDL/MOM6@53004ec Deleted module MOM_diffConvection
 - NOAA-GFDL/MOM6@0bb899a uncomment cvmix_init_tidal
 - NOAA-GFDL/MOM6@22902de Mv add_int_tide_diffusivity to tidal_mixing module
 - NOAA-GFDL/MOM6@c34ab63 Move diags back from MOM_tidal_mixing to MOM_set_diffusivity (for now)
 - NOAA-GFDL/MOM6@76546aa Move tidal mixing initialization to MOM_tidal_mixing
 - NOAA-GFDL/MOM6@95406ff Rename MOM_cvmix_tidal module as MOM_tidal_mixing (for now)
 - NOAA-GFDL/MOM6@c2dea88 update diabatic driver for MOM_cvmix_tidal module
 - NOAA-GFDL/MOM6@bb7917a comment out call ocn_domain_mct to avoid uninitialized vars for now. more comprehensive cleanup is to come.
 - NOAA-GFDL/MOM6@941bfb6 Updated mixing coeff. due to convection
 - NOAA-GFDL/MOM6@ba2a0a4 Added function cvmix_conv_is_used and register restart fields.
 - NOAA-GFDL/MOM6@c78ac9a Add the new module MOM_cvmix_tidal
 - NOAA-GFDL/MOM6@1d850a6 Changed hbl to an optional pointer; do not apply mixing due to convection within the boundary layer
 - NOAA-GFDL/MOM6@afd8f59 Fixed a bug in the deallocate call
 - NOAA-GFDL/MOM6@a77d114 Fixed a bug in the deallocate call
 - NOAA-GFDL/MOM6@f12702c Dealocate memory via cvmix_shear_end and changed some var names to snake_case convention
 - NOAA-GFDL/MOM6@a209b7a Added a call to diabatic_driver_end
 - NOAA-GFDL/MOM6@e84f706 Fix array allocattion/dealocation
 - NOAA-GFDL/MOM6@7f6d8f1 Added call to KPP_get_BLD
 - NOAA-GFDL/MOM6@fc00e77 Added function to copy KPP surface boundary layer depth into BLD
 - NOAA-GFDL/MOM6@c99e94b Updates visc%Kd_turb and visc%Kv_turb after convection is applied
 - NOAA-GFDL/MOM6@97152b1 Adding first version of convection calls via CVMix
 - NOAA-GFDL/MOM6@dca5736 Add comments for adding additonal CVMix components and clean module
 - NOAA-GFDL/MOM6@c6327d6 Copy OBLdepth from KPP into visc%MLD and Hml
 - NOAA-GFDL/MOM6@71ff26b Changed multi-word names from camelCase to snake_case
 - NOAA-GFDL/MOM6@8095e8f Merge pull request NOAA-GFDL#42 from gustavo-marques/merge-dev-master-2018-02-28
 - NOAA-GFDL/MOM6@bd80a20 Merge branch 'dev/master' into merge-dev-master-2018-02-28
 - NOAA-GFDL/MOM6@2f79ffc Merge pull request NOAA-GFDL#41 from gustavo-marques/merge_dev_master_20feb2018
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Hallberg-NOAA committed Apr 25, 2018
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163 changes: 82 additions & 81 deletions coupled_AM2_LM3_SIS/CM2G63L/MOM_parameter_doc.all
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Original file line number Diff line number Diff line change
Expand Up @@ -1219,29 +1219,81 @@ DIAG_MLD_DENSITY_DIFF = 0.1 ! [kg/m3] default = 0.1
! surface density by the specified amount.

! === module MOM_KPP ===
! This is the MOM wrapper to CVmix:KPP
! See http://code.google.com/p/cvmix/
! This is the MOM wrapper to CVMix:KPP
! See http://cvmix.github.io/
USE_KPP = False ! [Boolean] default = False
! If true, turns on the [CVmix] KPP scheme of Large et al., 1994,
! If true, turns on the [CVMix] KPP scheme of Large et al., 1994,
! to calculate diffusivities and non-local transport in the OBL.
SALT_REJECT_BELOW_ML = False ! [Boolean] default = False
! If true, place salt from brine rejection below the mixed layer,
! into the first non-vanished layer for which the column remains stable

! === module MOM_diffConvection ===
! This module implements enhanced diffusivity as a
! function of static stability, N^2.
USE_CONVECTION = False ! [Boolean] default = False
! If true, turns on the diffusive convection scheme that
! increases diapycnal diffusivities at statically unstable
! interfaces. Relevant parameters are contained in the
! CONVECTION% parameter block.
CONVECTION%
PASSIVE = False ! [Boolean] default = False
! If True, puts KPP into a passive-diagnostic mode.
KD_CONV = 1.0 ! [m2/s] default = 1.0
! DIffusivity used in statically unstable regions of column.
%CONVECTION
! === module MOM_tidal_mixing ===
! Vertical Tidal Mixing Parameterization
USE_CVMix_TIDAL = False ! [Boolean] default = False
! If true, turns on tidal mixing via CVMix
INT_TIDE_DISSIPATION = True ! [Boolean] default = False
! If true, use an internal tidal dissipation scheme to
! drive diapycnal mixing, along the lines of St. Laurent
! et al. (2002) and Simmons et al. (2004).
INT_TIDE_PROFILE = "STLAURENT_02" ! default = "STLAURENT_02"
! INT_TIDE_PROFILE selects the vertical profile of energy
! dissipation with INT_TIDE_DISSIPATION. Valid values are:
! STLAURENT_02 - Use the St. Laurent et al exponential
! decay profile.
! POLZIN_09 - Use the Polzin WKB-streched algebraic
! decay profile.
LEE_WAVE_DISSIPATION = False ! [Boolean] default = False
! If true, use an lee wave driven dissipation scheme to
! drive diapycnal mixing, along the lines of Nikurashin
! (2010) and using the St. Laurent et al. (2002)
! and Simmons et al. (2004) vertical profile
INT_TIDE_LOWMODE_DISSIPATION = False ! [Boolean] default = False
! If true, consider mixing due to breaking low modes that
! have been remotely generated; as with itidal drag on the
! barotropic tide, use an internal tidal dissipation scheme to
! drive diapycnal mixing, along the lines of St. Laurent
! et al. (2002) and Simmons et al. (2004).
INT_TIDE_DECAY_SCALE = 300.3003003003003 ! [m] default = 500.0
! The decay scale away from the bottom for tidal TKE with
! the new coding when INT_TIDE_DISSIPATION is used.
MU_ITIDES = 0.2 ! [nondim] default = 0.2
! A dimensionless turbulent mixing efficiency used with
! INT_TIDE_DISSIPATION, often 0.2.
GAMMA_ITIDES = 0.3333 ! [nondim] default = 0.3333
! The fraction of the internal tidal energy that is
! dissipated locally with INT_TIDE_DISSIPATION.
! THIS NAME COULD BE BETTER.
MIN_ZBOT_ITIDES = 0.0 ! [m] default = 0.0
! Turn off internal tidal dissipation when the total
! ocean depth is less than this value.
KAPPA_ITIDES = 6.28319E-04 ! [m-1] default = 6.283185307179586E-04
! A topographic wavenumber used with INT_TIDE_DISSIPATION.
! The default is 2pi/10 km, as in St.Laurent et al. 2002.
UTIDE = 0.0 ! [m s-1] default = 0.0
! The constant tidal amplitude used with INT_TIDE_DISSIPATION.
KAPPA_H2_FACTOR = 0.75 ! [nondim] default = 1.0
! A scaling factor for the roughness amplitude with nINT_TIDE_DISSIPATION.
TKE_ITIDE_MAX = 0.1 ! [W m-2] default = 1000.0
! The maximum internal tide energy source availble to mix
! above the bottom boundary layer with INT_TIDE_DISSIPATION.
READ_TIDEAMP = True ! [Boolean] default = False
! If true, read a file (given by TIDEAMP_FILE) containing
! the tidal amplitude with INT_TIDE_DISSIPATION.
TIDEAMP_FILE = "tideamp.nc" ! default = "tideamp.nc"
! The path to the file containing the spatially varying
! tidal amplitudes with INT_TIDE_DISSIPATION.
H2_FILE = "sgs_h2.nc" !
! The path to the file containing the sub-grid-scale
! topographic roughness amplitude with INT_TIDE_DISSIPATION.

! === module MOM_CVMix_conv ===
! Parameterization of enhanced mixing due to convection via CVMix
USE_CVMix_CONVECTION = False ! [Boolean] default = False
! If true, turns on the enhanced mixing due to convection
! via CVMix. This scheme increases diapycnal diffs./viscs.
! at statically unstable interfaces. Relevant parameters are
! contained in the CVMix_CONVECTION% parameter block.

! === module MOM_entrain_diffusive ===
CORRECT_DENSITY = True ! [Boolean] default = True
Expand Down Expand Up @@ -1326,9 +1378,22 @@ SIMPLE_TKE_TO_KD = False ! [Boolean] default = False
! If true, uses a simple estimate of Kd/TKE that will
! work for arbitrary vertical coordinates. If false,
! calculates Kd/TKE and bounds based on exact energetics/nfor an isopycnal layer-formulation.

! === module MOM_bkgnd_mixing ===
! Adding static vertical background mixing coefficients
KD = 2.0E-05 ! [m2 s-1]
! The background diapycnal diffusivity of density in the
! interior. Zero or the molecular value, ~1e-7 m2 s-1,
! may be used.
KD_MIN = 2.0E-06 ! [m2 s-1] default = 2.0E-07
! The minimum diapycnal diffusivity.
PRANDTL_BKGND = 1.0 ! [nondim] default = 1.0
! Turbulent Prandtl number used to convert vertical
! background diffusivities into viscosities.
BRYAN_LEWIS_DIFFUSIVITY = False ! [Boolean] default = False
! If true, use a Bryan & Lewis (JGR 1979) like tanh
! profile of background diapycnal diffusivity with depth.
! This is done via CVMix.
HENYEY_IGW_BACKGROUND = True ! [Boolean] default = False
! If true, use a latitude-dependent scaling for the near
! surface background diffusivity, as described in
Expand All @@ -1341,50 +1406,18 @@ HENYEY_N0_2OMEGA = 20.0 ! [nondim] default = 20.0
! The ratio of the typical Buoyancy frequency to twice
! the Earth's rotation period, used with the Henyey
! scaling from the mixing.
N2_FLOOR_IOMEGA2 = 0.0 ! [nondim] default = 1.0
! The floor applied to N2(k) scaled by Omega^2:
! If =0., N2(k) is simply positive definite.
! If =1., N2(k) > Omega^2 everywhere.
KD_TANH_LAT_FN = False ! [Boolean] default = False
! If true, use a tanh dependence of Kd_sfc on latitude,
! like CM2.1/CM2M. There is no physical justification
! for this form, and it can not be used with
! HENYEY_IGW_BACKGROUND.
KD = 2.0E-05 ! [m2 s-1]
! The background diapycnal diffusivity of density in the
! interior. Zero or the molecular value, ~1e-7 m2 s-1,
! may be used.
KD_MIN = 2.0E-06 ! [m2 s-1] default = 2.0E-07
! The minimum diapycnal diffusivity.
KD_MAX = -1.0 ! [m2 s-1] default = -1.0
! The maximum permitted increment for the diapycnal
! diffusivity from TKE-based parameterizations, or a
! negative value for no limit.
KD_ADD = 0.0 ! [m2 s-1] default = 0.0
! A uniform diapycnal diffusivity that is added
! everywhere without any filtering or scaling.
INT_TIDE_DISSIPATION = True ! [Boolean] default = False
! If true, use an internal tidal dissipation scheme to
! drive diapycnal mixing, along the lines of St. Laurent
! et al. (2002) and Simmons et al. (2004).
INT_TIDE_PROFILE = "STLAURENT_02" ! default = "STLAURENT_02"
! INT_TIDE_PROFILE selects the vertical profile of energy
! dissipation with INT_TIDE_DISSIPATION. Valid values are:
! STLAURENT_02 - Use the St. Laurent et al exponential
! decay profile.
! POLZIN_09 - Use the Polzin WKB-streched algebraic
! decay profile.
LEE_WAVE_DISSIPATION = False ! [Boolean] default = False
! If true, use an lee wave driven dissipation scheme to
! drive diapycnal mixing, along the lines of Nikurashin
! (2010) and using the St. Laurent et al. (2002)
! and Simmons et al. (2004) vertical profile
INT_TIDE_LOWMODE_DISSIPATION = False ! [Boolean] default = False
! If true, consider mixing due to breaking low modes that
! have been remotely generated; as with itidal drag on the
! barotropic tide, use an internal tidal dissipation scheme to
! drive diapycnal mixing, along the lines of St. Laurent
! et al. (2002) and Simmons et al. (2004).
USER_CHANGE_DIFFUSIVITY = False ! [Boolean] default = False
! If true, call user-defined code to change the diffusivity.
DISSIPATION_MIN = 0.0 ! [W m-3] default = 0.0
Expand All @@ -1400,38 +1433,6 @@ DISSIPATION_N1 = 6.0E-04 ! [J m-3] default = 0.0
! bound of Kd (a floor): B in eps_min = A + B*N
DISSIPATION_KD_MIN = 0.0 ! [m2 s-1] default = 0.0
! The minimum vertical diffusivity applied as a floor.
INT_TIDE_DECAY_SCALE = 300.3003003003003 ! [m] default = 0.0
! The decay scale away from the bottom for tidal TKE with
! the new coding when INT_TIDE_DISSIPATION is used.
MU_ITIDES = 0.2 ! [nondim] default = 0.2
! A dimensionless turbulent mixing efficiency used with
! INT_TIDE_DISSIPATION, often 0.2.
GAMMA_ITIDES = 0.3333 ! [nondim] default = 0.3333
! The fraction of the internal tidal energy that is
! dissipated locally with INT_TIDE_DISSIPATION.
! THIS NAME COULD BE BETTER.
MIN_ZBOT_ITIDES = 0.0 ! [m] default = 0.0
! Turn off internal tidal dissipation when the total
! ocean depth is less than this value.
KAPPA_ITIDES = 6.28319E-04 ! [m-1] default = 6.283185307179586E-04
! A topographic wavenumber used with INT_TIDE_DISSIPATION.
! The default is 2pi/10 km, as in St.Laurent et al. 2002.
UTIDE = 0.0 ! [m s-1] default = 0.0
! The constant tidal amplitude used with INT_TIDE_DISSIPATION.
KAPPA_H2_FACTOR = 0.75 ! [nondim] default = 1.0
! A scaling factor for the roughness amplitude with nINT_TIDE_DISSIPATION.
TKE_ITIDE_MAX = 0.1 ! [W m-2] default = 1000.0
! The maximum internal tide energy source availble to mix
! above the bottom boundary layer with INT_TIDE_DISSIPATION.
READ_TIDEAMP = True ! [Boolean] default = False
! If true, read a file (given by TIDEAMP_FILE) containing
! the tidal amplitude with INT_TIDE_DISSIPATION.
TIDEAMP_FILE = "tideamp.nc" ! default = "tideamp.nc"
! The path to the file containing the spatially varying
! tidal amplitudes with INT_TIDE_DISSIPATION.
H2_FILE = "sgs_h2.nc" !
! The path to the file containing the sub-grid-scale
! topographic roughness amplitude with INT_TIDE_DISSIPATION.

! === module MOM_kappa_shear ===
! Parameterization of shear-driven turbulence following Jackson, Hallberg and Legg, JPO 2008
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