MOM6: Merge branch 'gustavo-marques-add_old_double_diffusion' into de…

…v/master

- Update to dev/master with commits from dev/ncar
- Introduces new parameters and diagnostics recorded in MOM_parameter_doc files and available_diags

- NOAA-GFDL/MOM6@542be91 Merge branch 'gustavo-marques-add_old_double_diffusion' into dev/master
- NOAA-GFDL/MOM6@714b5ff Merge branch 'add_old_double_diffusion' of https://github.com/gustavo-marques/MOM6 into gustavo-marques-add_old_double_diffusion
- NOAA-GFDL/MOM6@9e36556 Fix a bug
- NOAA-GFDL/MOM6@309b4d4 Fix if statement for fatal error when using double diffusion (old and CVMix)
- NOAA-GFDL/MOM6@c527d5a Add missing code relate to old double-diffusion method
- NOAA-GFDL/MOM6@474d664 Set clock for double-diffusion via CVMix
- NOAA-GFDL/MOM6@65a48f4 Merge branch 'restructure_diabatic_driver' into add_old_double_diffusion
- NOAA-GFDL/MOM6@71e4bea Add fatal error if multiple double-diffusion options are enabled
- NOAA-GFDL/MOM6@56c461c Adds back old double-diffusion code
- NOAA-GFDL/MOM6@42c4f93 Add some comments
- NOAA-GFDL/MOM6@6782ecb Deleted calls related to layer mode
- NOAA-GFDL/MOM6@ec95be9 Merge pull request NOAA-GFDL#60 from gustavo-marques/double_diffusion_cvmix
- NOAA-GFDL/MOM6@720dbc0 Doxygenize set_diff + read background kinematic viscosity
- NOAA-GFDL/MOM6@198d755 Delete visc%kv_slow=0 since this is done in set_diffusivity
- NOAA-GFDL/MOM6@884dd3a Merge remote-tracking branch 'gustavo/double_diffusion_cvmix2' into double_diffusion_cvmix
- NOAA-GFDL/MOM6@1e6cb67 Merge branch 'dev/ncar' into double_diffusion_cvmix
- NOAA-GFDL/MOM6@bf6c003 Clean the ddiff code and improve comments
- NOAA-GFDL/MOM6@8877c17 Rename MOM_cvmix_ddiff.F90 -> MOM_CVMix_ddiff.F90
- NOAA-GFDL/MOM6@70d88e4 Add a flag to control if visc%Kv_slow is used
- NOAA-GFDL/MOM6@148a944 Merge branch 'dev/ncar' into double_diffusion_cvmix
- NOAA-GFDL/MOM6@cc27362 Clean up spaces and comments
- NOAA-GFDL/MOM6@152a707 Change cvmix to CVMix
- NOAA-GFDL/MOM6@abd620c Move description to the end of the module
- NOAA-GFDL/MOM6@d5ce7a4 Avoid NaNs when computing stratification parameter
- NOAA-GFDL/MOM6@05daede Fix indentation
- NOAA-GFDL/MOM6@81265e6 Doxygenize MOM_diabatic_aux
- NOAA-GFDL/MOM6@507d34e First version of Double-diffusion via CVMix
- NOAA-GFDL/MOM6@02acd12 Doxygenize subroutine differential_diffuse_T_S
- NOAA-GFDL/MOM6@191b5be Add a factor of 2 when adding Kv_slow into Kv_add
- NOAA-GFDL/MOM6@3385857 Initialize Kd, Kd_int and Kv_slow using interior values specified by user
- NOAA-GFDL/MOM6@78656bb Add missing halo update for visc%Kv_slow
- NOAA-GFDL/MOM6@9d6cb46 Rename variable in register_diag_field
- NOAA-GFDL/MOM6@a0358fbb Fix bug in MOM_cvmix_conv
- NOAA-GFDL/MOM6@f6a21e7 Merge branch 'dev/ncar' into adding_cvmix_part2
- NOAA-GFDL/MOM6@901c301 Add option to post diags for bkgnd_mixing
- NOAA-GFDL/MOM6@d09e809 Add option to diagnose Kv at u and v points
- NOAA-GFDL/MOM6@dcfb722 Bug fix in MOM_bkgnd_mixing
- NOAA-GFDL/MOM6@d5be1f8 Attempt to add diag. for total vertical visc.
- NOAA-GFDL/MOM6@69c2c96 Remove trailing space
- NOAA-GFDL/MOM6@1488b78 Add option to save Kv_slow and Kv
- NOAA-GFDL/MOM6@fd23f91 Set visc%Kv_slow to zero in diabatic
- NOAA-GFDL/MOM6@d774e5f Add "slow" vertical viscosity in vertvisc_coef
- NOAA-GFDL/MOM6@60f7d66 Initialize visc%Kv_slow and update halos
- NOAA-GFDL/MOM6@0c363ae Always allocate CS%OBLdepth since other modules may need to know OBLdepth
- NOAA-GFDL/MOM6@c4f1f55 Update CVMix
- NOAA-GFDL/MOM6@b14213a Fill Ri_grad in vanished layers with adjacent value, just when Ri smooth is enabled
- NOAA-GFDL/MOM6@99ca9a7 Adding option to smooth Ri using a 1-2-1 filter

coupled_AM2_LM3_SIS/CM2G63L/MOM_parameter_doc.all

@@ -710,6 +710,12 @@ HTBL_SHELF = 10.0 ! [m] default = 10.0
 KV = 1.0E-04 ! [m2 s-1]
  ! The background kinematic viscosity in the interior.
  ! The molecular value, ~1e-6 m2 s-1, may be used.
+ADD_KV_SLOW = False ! [Boolean] default = False
+ ! If true, the background vertical viscosity in the interior
+ ! (i.e., tidal + background + shear + convenction) is addded
+ ! when computing the coupling coefficient. The purpose of this
+ ! flag is to be able to recover previous answers and it will likely
+ ! be removed in the future since this option should always be true.
 KV_BBL_MIN = 0.0 ! [m2 s-1] default = 1.0E-04
  ! The minimum viscosities in the bottom boundary layer.
 KV_TBL_MIN = 0.0 ! [m2 s-1] default = 1.0E-04
@@ -1509,6 +1515,13 @@ USE_PP81 = False ! [Boolean] default = False
  ! If true, use the Pacanowski and Philander (JPO 1981)
  ! shear mixing parameterization.
 
+! === module MOM_CVMix_ddiff ===
+! Parameterization of mixing due to double diffusion processes via CVMix
+USE_CVMIX_DDIFF = False ! [Boolean] default = False
+ ! If true, turns on double diffusive processes via CVMix.
+ ! Note that double diffusive processes on viscosity are ignored
+ ! in CVMix, see https://cvmix.github.io/ for justification.
+
 ! === module MOM_diabatic_aux ===
 ! The following parameters are used for auxiliary diabatic processes.
 RECLAIM_FRAZIL = True ! [Boolean] default = True

coupled_AM2_LM3_SIS/CM2G63L/MOM_parameter_doc.short

@@ -494,6 +494,9 @@ MAX_RINO_IT = 25 ! [nondim] default = 50
 ! === module MOM_CVMix_shear ===
 ! Parameterization of shear-driven turbulence via CVMix (various options)
 
+! === module MOM_CVMix_ddiff ===
+! Parameterization of mixing due to double diffusion processes via CVMix
+
 ! === module MOM_diabatic_aux ===
 ! The following parameters are used for auxiliary diabatic processes.
 

coupled_AM2_LM3_SIS2/AM2_SIS2_MOM6i_1deg/MOM_parameter_doc.all

@@ -710,6 +710,12 @@ HTBL_SHELF = 10.0 ! [m] default = 10.0
 KV = 1.0E-04 ! [m2 s-1]
  ! The background kinematic viscosity in the interior.
  ! The molecular value, ~1e-6 m2 s-1, may be used.
+ADD_KV_SLOW = False ! [Boolean] default = False
+ ! If true, the background vertical viscosity in the interior
+ ! (i.e., tidal + background + shear + convenction) is addded
+ ! when computing the coupling coefficient. The purpose of this
+ ! flag is to be able to recover previous answers and it will likely
+ ! be removed in the future since this option should always be true.
 KV_BBL_MIN = 1.0E-04 ! [m2 s-1] default = 1.0E-04
  ! The minimum viscosities in the bottom boundary layer.
 KV_TBL_MIN = 1.0E-04 ! [m2 s-1] default = 1.0E-04
@@ -1505,6 +1511,13 @@ USE_PP81 = False ! [Boolean] default = False
  ! If true, use the Pacanowski and Philander (JPO 1981)
  ! shear mixing parameterization.
 
+! === module MOM_CVMix_ddiff ===
+! Parameterization of mixing due to double diffusion processes via CVMix
+USE_CVMIX_DDIFF = False ! [Boolean] default = False
+ ! If true, turns on double diffusive processes via CVMix.
+ ! Note that double diffusive processes on viscosity are ignored
+ ! in CVMix, see https://cvmix.github.io/ for justification.
+
 ! === module MOM_diabatic_aux ===
 ! The following parameters are used for auxiliary diabatic processes.
 RECLAIM_FRAZIL = True ! [Boolean] default = True

coupled_AM2_LM3_SIS2/AM2_SIS2_MOM6i_1deg/MOM_parameter_doc.short

@@ -490,6 +490,9 @@ MAX_RINO_IT = 25 ! [nondim] default = 50
 ! === module MOM_CVMix_shear ===
 ! Parameterization of shear-driven turbulence via CVMix (various options)
 
+! === module MOM_CVMix_ddiff ===
+! Parameterization of mixing due to double diffusion processes via CVMix
+
 ! === module MOM_diabatic_aux ===
 ! The following parameters are used for auxiliary diabatic processes.
 

coupled_AM2_LM3_SIS2/Concurrent_ice_1deg/MOM_parameter_doc.all

@@ -710,6 +710,12 @@ HTBL_SHELF = 10.0 ! [m] default = 10.0
 KV = 1.0E-04 ! [m2 s-1]
  ! The background kinematic viscosity in the interior.
  ! The molecular value, ~1e-6 m2 s-1, may be used.
+ADD_KV_SLOW = False ! [Boolean] default = False
+ ! If true, the background vertical viscosity in the interior
+ ! (i.e., tidal + background + shear + convenction) is addded
+ ! when computing the coupling coefficient. The purpose of this
+ ! flag is to be able to recover previous answers and it will likely
+ ! be removed in the future since this option should always be true.
 KV_BBL_MIN = 1.0E-04 ! [m2 s-1] default = 1.0E-04
  ! The minimum viscosities in the bottom boundary layer.
 KV_TBL_MIN = 1.0E-04 ! [m2 s-1] default = 1.0E-04
@@ -1505,6 +1511,13 @@ USE_PP81 = False ! [Boolean] default = False
  ! If true, use the Pacanowski and Philander (JPO 1981)
  ! shear mixing parameterization.
 
+! === module MOM_CVMix_ddiff ===
+! Parameterization of mixing due to double diffusion processes via CVMix
+USE_CVMIX_DDIFF = False ! [Boolean] default = False
+ ! If true, turns on double diffusive processes via CVMix.
+ ! Note that double diffusive processes on viscosity are ignored
+ ! in CVMix, see https://cvmix.github.io/ for justification.
+
 ! === module MOM_diabatic_aux ===
 ! The following parameters are used for auxiliary diabatic processes.
 RECLAIM_FRAZIL = True ! [Boolean] default = True

coupled_AM2_LM3_SIS2/Concurrent_ice_1deg/MOM_parameter_doc.short

@@ -490,6 +490,9 @@ MAX_RINO_IT = 25 ! [nondim] default = 50
 ! === module MOM_CVMix_shear ===
 ! Parameterization of shear-driven turbulence via CVMix (various options)
 
+! === module MOM_CVMix_ddiff ===
+! Parameterization of mixing due to double diffusion processes via CVMix
+
 ! === module MOM_diabatic_aux ===
 ! The following parameters are used for auxiliary diabatic processes.
 

ice_ocean_SIS2/Baltic/MOM_parameter_doc.all

@@ -710,6 +710,12 @@ HTBL_SHELF = 10.0 ! [m] default = 10.0
 KV = 1.0E-04 ! [m2 s-1]
  ! The background kinematic viscosity in the interior.
  ! The molecular value, ~1e-6 m2 s-1, may be used.
+ADD_KV_SLOW = False ! [Boolean] default = False
+ ! If true, the background vertical viscosity in the interior
+ ! (i.e., tidal + background + shear + convenction) is addded
+ ! when computing the coupling coefficient. The purpose of this
+ ! flag is to be able to recover previous answers and it will likely
+ ! be removed in the future since this option should always be true.
 KV_BBL_MIN = 1.0E-04 ! [m2 s-1] default = 1.0E-04
  ! The minimum viscosities in the bottom boundary layer.
 KV_TBL_MIN = 1.0E-04 ! [m2 s-1] default = 1.0E-04
@@ -1505,6 +1511,13 @@ USE_PP81 = False ! [Boolean] default = False
  ! If true, use the Pacanowski and Philander (JPO 1981)
  ! shear mixing parameterization.
 
+! === module MOM_CVMix_ddiff ===
+! Parameterization of mixing due to double diffusion processes via CVMix
+USE_CVMIX_DDIFF = False ! [Boolean] default = False
+ ! If true, turns on double diffusive processes via CVMix.
+ ! Note that double diffusive processes on viscosity are ignored
+ ! in CVMix, see https://cvmix.github.io/ for justification.
+
 ! === module MOM_diabatic_aux ===
 ! The following parameters are used for auxiliary diabatic processes.
 RECLAIM_FRAZIL = True ! [Boolean] default = True

ice_ocean_SIS2/Baltic/MOM_parameter_doc.short

@@ -502,6 +502,9 @@ MAX_RINO_IT = 25 ! [nondim] default = 50
 ! === module MOM_CVMix_shear ===
 ! Parameterization of shear-driven turbulence via CVMix (various options)
 
+! === module MOM_CVMix_ddiff ===
+! Parameterization of mixing due to double diffusion processes via CVMix
+
 ! === module MOM_diabatic_aux ===
 ! The following parameters are used for auxiliary diabatic processes.
 

ice_ocean_SIS2/Baltic_ALE_z_offline_tracers/MOM_parameter_doc.all

@@ -843,6 +843,12 @@ HTBL_SHELF = 10.0 ! [m] default = 10.0
 KV = 1.0E-04 ! [m2 s-1]
  ! The background kinematic viscosity in the interior.
  ! The molecular value, ~1e-6 m2 s-1, may be used.
+ADD_KV_SLOW = False ! [Boolean] default = False
+ ! If true, the background vertical viscosity in the interior
+ ! (i.e., tidal + background + shear + convenction) is addded
+ ! when computing the coupling coefficient. The purpose of this
+ ! flag is to be able to recover previous answers and it will likely
+ ! be removed in the future since this option should always be true.
 KV_BBL_MIN = 1.0E-04 ! [m2 s-1] default = 1.0E-04
  ! The minimum viscosities in the bottom boundary layer.
 KV_TBL_MIN = 1.0E-04 ! [m2 s-1] default = 1.0E-04
@@ -1716,6 +1722,13 @@ USE_PP81 = False ! [Boolean] default = False
  ! If true, use the Pacanowski and Philander (JPO 1981)
  ! shear mixing parameterization.
 
+! === module MOM_CVMix_ddiff ===
+! Parameterization of mixing due to double diffusion processes via CVMix
+USE_CVMIX_DDIFF = False ! [Boolean] default = False
+ ! If true, turns on double diffusive processes via CVMix.
+ ! Note that double diffusive processes on viscosity are ignored
+ ! in CVMix, see https://cvmix.github.io/ for justification.
+
 ! === module MOM_diabatic_aux ===
 ! The following parameters are used for auxiliary diabatic processes.
 RECLAIM_FRAZIL = True ! [Boolean] default = True

ice_ocean_SIS2/Baltic_ALE_z_offline_tracers/MOM_parameter_doc.short

@@ -557,6 +557,9 @@ MAX_RINO_IT = 25 ! [nondim] default = 50
 ! === module MOM_CVMix_shear ===
 ! Parameterization of shear-driven turbulence via CVMix (various options)
 
+! === module MOM_CVMix_ddiff ===
+! Parameterization of mixing due to double diffusion processes via CVMix
+
 ! === module MOM_diabatic_aux ===
 ! The following parameters are used for auxiliary diabatic processes.
 

ice_ocean_SIS2/Baltic_OM4_025/MOM_parameter_doc.all

@@ -905,6 +905,12 @@ HTBL_SHELF = 10.0 ! [m] default = 10.0
 KV = 1.0E-04 ! [m2 s-1]
  ! The background kinematic viscosity in the interior.
  ! The molecular value, ~1e-6 m2 s-1, may be used.
+ADD_KV_SLOW = False ! [Boolean] default = False
+ ! If true, the background vertical viscosity in the interior
+ ! (i.e., tidal + background + shear + convenction) is addded
+ ! when computing the coupling coefficient. The purpose of this
+ ! flag is to be able to recover previous answers and it will likely
+ ! be removed in the future since this option should always be true.
 KV_BBL_MIN = 0.0 ! [m2 s-1] default = 1.0E-04
  ! The minimum viscosities in the bottom boundary layer.
 KV_TBL_MIN = 0.0 ! [m2 s-1] default = 1.0E-04
@@ -1751,6 +1757,13 @@ USE_PP81 = False ! [Boolean] default = False
  ! If true, use the Pacanowski and Philander (JPO 1981)
  ! shear mixing parameterization.
 
+! === module MOM_CVMix_ddiff ===
+! Parameterization of mixing due to double diffusion processes via CVMix
+USE_CVMIX_DDIFF = False ! [Boolean] default = False
+ ! If true, turns on double diffusive processes via CVMix.
+ ! Note that double diffusive processes on viscosity are ignored
+ ! in CVMix, see https://cvmix.github.io/ for justification.
+
 ! === module MOM_diabatic_aux ===
 ! The following parameters are used for auxiliary diabatic processes.
 RECLAIM_FRAZIL = True ! [Boolean] default = True

ice_ocean_SIS2/Baltic_OM4_025/MOM_parameter_doc.short

@@ -676,6 +676,9 @@ MAX_RINO_IT = 25 ! [nondim] default = 50
 ! === module MOM_CVMix_shear ===
 ! Parameterization of shear-driven turbulence via CVMix (various options)
 
+! === module MOM_CVMix_ddiff ===
+! Parameterization of mixing due to double diffusion processes via CVMix
+
 ! === module MOM_diabatic_aux ===
 ! The following parameters are used for auxiliary diabatic processes.
 PRESSURE_DEPENDENT_FRAZIL = True ! [Boolean] default = False

ice_ocean_SIS2/Baltic_OM4_05/MOM_parameter_doc.all

@@ -908,6 +908,12 @@ HTBL_SHELF = 10.0 ! [m] default = 10.0
 KV = 1.0E-04 ! [m2 s-1]
  ! The background kinematic viscosity in the interior.
  ! The molecular value, ~1e-6 m2 s-1, may be used.
+ADD_KV_SLOW = False ! [Boolean] default = False
+ ! If true, the background vertical viscosity in the interior
+ ! (i.e., tidal + background + shear + convenction) is addded
+ ! when computing the coupling coefficient. The purpose of this
+ ! flag is to be able to recover previous answers and it will likely
+ ! be removed in the future since this option should always be true.
 KV_BBL_MIN = 0.0 ! [m2 s-1] default = 1.0E-04
  ! The minimum viscosities in the bottom boundary layer.
 KV_TBL_MIN = 0.0 ! [m2 s-1] default = 1.0E-04
@@ -1764,6 +1770,13 @@ USE_PP81 = False ! [Boolean] default = False
  ! If true, use the Pacanowski and Philander (JPO 1981)
  ! shear mixing parameterization.
 
+! === module MOM_CVMix_ddiff ===
+! Parameterization of mixing due to double diffusion processes via CVMix
+USE_CVMIX_DDIFF = False ! [Boolean] default = False
+ ! If true, turns on double diffusive processes via CVMix.
+ ! Note that double diffusive processes on viscosity are ignored
+ ! in CVMix, see https://cvmix.github.io/ for justification.
+
 ! === module MOM_diabatic_aux ===
 ! The following parameters are used for auxiliary diabatic processes.
 RECLAIM_FRAZIL = True ! [Boolean] default = True

ice_ocean_SIS2/Baltic_OM4_05/MOM_parameter_doc.short

@@ -701,6 +701,9 @@ MAX_RINO_IT = 25 ! [nondim] default = 50
 ! === module MOM_CVMix_shear ===
 ! Parameterization of shear-driven turbulence via CVMix (various options)
 
+! === module MOM_CVMix_ddiff ===
+! Parameterization of mixing due to double diffusion processes via CVMix
+
 ! === module MOM_diabatic_aux ===
 ! The following parameters are used for auxiliary diabatic processes.
 PRESSURE_DEPENDENT_FRAZIL = True ! [Boolean] default = False

ice_ocean_SIS2/OM4_025/MOM_parameter_doc.all

@@ -905,6 +905,12 @@ HTBL_SHELF = 10.0 ! [m] default = 10.0
 KV = 1.0E-04 ! [m2 s-1]
  ! The background kinematic viscosity in the interior.
  ! The molecular value, ~1e-6 m2 s-1, may be used.
+ADD_KV_SLOW = False ! [Boolean] default = False
+ ! If true, the background vertical viscosity in the interior
+ ! (i.e., tidal + background + shear + convenction) is addded
+ ! when computing the coupling coefficient. The purpose of this
+ ! flag is to be able to recover previous answers and it will likely
+ ! be removed in the future since this option should always be true.
 KV_BBL_MIN = 0.0 ! [m2 s-1] default = 1.0E-04
  ! The minimum viscosities in the bottom boundary layer.
 KV_TBL_MIN = 0.0 ! [m2 s-1] default = 1.0E-04
@@ -1751,6 +1757,13 @@ USE_PP81 = False ! [Boolean] default = False
  ! If true, use the Pacanowski and Philander (JPO 1981)
  ! shear mixing parameterization.
 
+! === module MOM_CVMix_ddiff ===
+! Parameterization of mixing due to double diffusion processes via CVMix
+USE_CVMIX_DDIFF = False ! [Boolean] default = False
+ ! If true, turns on double diffusive processes via CVMix.
+ ! Note that double diffusive processes on viscosity are ignored
+ ! in CVMix, see https://cvmix.github.io/ for justification.
+
 ! === module MOM_diabatic_aux ===
 ! The following parameters are used for auxiliary diabatic processes.
 RECLAIM_FRAZIL = True ! [Boolean] default = True

ice_ocean_SIS2/OM4_025/MOM_parameter_doc.short

@@ -685,6 +685,9 @@ MAX_RINO_IT = 25 ! [nondim] default = 50
 ! === module MOM_CVMix_shear ===
 ! Parameterization of shear-driven turbulence via CVMix (various options)
 
+! === module MOM_CVMix_ddiff ===
+! Parameterization of mixing due to double diffusion processes via CVMix
+
 ! === module MOM_diabatic_aux ===
 ! The following parameters are used for auxiliary diabatic processes.
 PRESSURE_DEPENDENT_FRAZIL = True ! [Boolean] default = False