MOM6: Updated version of MOM6 (PRs 99-111) and MOM_parameter_doc files

  Updated the version of MOM6 that MOM6-examples points to, and updated the
available_diags files to reflect the changes in MOM6.  Also updated other
MOM_parameter_doc files in infrequently run test cases that previous changes had
altered but which were not updated when the corresponding code changes were
introduced.  All answers are bitwise identical.  The MOM6 commits that are
included in this update are:

- NOAA-GFDL/MOM6@684878ee4 Add a deta_dt diagnostic to the split BT/BC mode (#99)
- NOAA-GFDL/MOM6@b4b7368d5 Merge pull request #111 from marshallward/field_size_fixes
- NOAA-GFDL/MOM6@54b8ff50b Merge branch 'dev/gfdl' into field_size_fixes
- NOAA-GFDL/MOM6@f6fc6ce17 FMS2: get_field_sizes with FMS1 emulation
- NOAA-GFDL/MOM6@f54338ad1 Fix non-standard white space (#109)
- NOAA-GFDL/MOM6@d729c679a +Remove append_substring
- NOAA-GFDL/MOM6@d8bc9639e Removal of non-standard extensions
- NOAA-GFDL/MOM6@7a147ad41 +Document or eliminate undocumented interfaces
- NOAA-GFDL/MOM6@e9fdf5de3 Standardized syntax in mask2d logical tests
- NOAA-GFDL/MOM6@7f6dac283 Merge pull request #105 from marshallward/pedantic
- NOAA-GFDL/MOM6@d3d0c8ecc Merge branch 'dev/gfdl' into pedantic
- NOAA-GFDL/MOM6@c150f37a1 Correct --with-driver args for coupled tests (#106)
- NOAA-GFDL/MOM6@6809ee3a4 Fix tides_CS attribute in unsplit mode (#103)
- NOAA-GFDL/MOM6@d2fb2d0ed MOM_random: Set mask with bits rather than integer
- NOAA-GFDL/MOM6@a5350219b Mixed layer restrat statement function refactor
- NOAA-GFDL/MOM6@936b11fb6 Format string fixes; function index reorder

ocean_only/ISOMIP/layer/MOM_parameter_doc.all

@@ -586,7 +586,7 @@ CONVERT_THICKNESS_UNITS = False !   [Boolean] default = False
                                 ! if a restart file is read.
 SURFACE_PRESSURE_FILE = "Ocean1_3D.nc" !
                                 ! The initial condition file for the surface pressure exerted by ice.
-SURFACE_PRESSURE_VAR = "thick"  !   [Pa] default = ""
+SURFACE_PRESSURE_VAR = "thick"  ! default = ""
                                 ! The initial condition variable for the surface pressure exerted by ice.
 SURFACE_PRESSURE_SCALE = 8820.0 !   [file dependent] default = 1.0
                                 ! A scaling factor to convert SURFACE_PRESSURE_VAR from file
@@ -763,6 +763,15 @@ KHTH_MAX_CFL = 0.8              !   [nondimensional] default = 0.8
                                 ! thickness diffusivity. 1.0 is the marginally unstable value in a pure layered
                                 ! model, but much smaller numbers (e.g. 0.1) seem to work better for ALE-based
                                 ! models.
+KH_ETA_CONST = 0.0              !   [m2 s-1] default = 0.0
+                                ! The background horizontal diffusivity of the interface heights (without
+                                ! considering the layer density structure).  If diffusive CFL limits are
+                                ! encountered, the diffusivities of the isopycnals and the interfaces heights
+                                ! are scaled back proportionately.
+KH_ETA_VEL_SCALE = 0.0          !   [m s-1] default = 0.0
+                                ! A velocity scale that is multiplied by the grid spacing to give a contribution
+                                ! to the horizontal diffusivity of the interface heights (without considering
+                                ! the layer density structure).
 DETANGLE_INTERFACES = False     !   [Boolean] default = False
                                 ! If defined add 3-d structured enhanced interface height diffusivities to
                                 ! horizontally smooth jagged layers.

ocean_only/ISOMIP/layer/MOM_parameter_doc.short

@@ -260,7 +260,7 @@ TRIM_IC_FOR_P_SURF = True       !   [Boolean] default = False
                                 ! read from file.
 SURFACE_PRESSURE_FILE = "Ocean1_3D.nc" !
                                 ! The initial condition file for the surface pressure exerted by ice.
-SURFACE_PRESSURE_VAR = "thick"  !   [Pa] default = ""
+SURFACE_PRESSURE_VAR = "thick"  ! default = ""
                                 ! The initial condition variable for the surface pressure exerted by ice.
 SURFACE_PRESSURE_SCALE = 8820.0 !   [file dependent] default = 1.0
                                 ! A scaling factor to convert SURFACE_PRESSURE_VAR from file

ocean_only/ISOMIP/rho/MOM_parameter_doc.all

@@ -399,6 +399,7 @@ REGRIDDING_COORDINATE_MODE = "RHO" ! default = "LAYER"
                                 !  SIGMA - terrain following coordinates
                                 !  RHO   - continuous isopycnal
                                 !  HYCOM1 - HyCOM-like hybrid coordinate
+                                !  HYBGEN - Hybrid coordinate from the Hycom hybgen code
                                 !  SLIGHT - stretched coordinates above continuous isopycnal
                                 !  ADAPTIVE - optimize for smooth neutral density surfaces
 REGRIDDING_COORDINATE_UNITS = "kg m^-3" ! default = "kg m^-3"
@@ -475,8 +476,23 @@ REMAPPING_SCHEME = "PPM_H4"     ! default = "PLM"
                                 ! variables. It can be one of the following schemes: PCM         (1st-order
                                 ! accurate)
                                 ! PLM         (2nd-order accurate)
+                                ! PLM_HYBGEN  (2nd-order accurate)
                                 ! PPM_H4      (3rd-order accurate)
                                 ! PPM_IH4     (3rd-order accurate)
+                                ! PPM_HYBGEN  (3rd-order accurate)
+                                ! WENO_HYBGEN (3rd-order accurate)
+                                ! PQM_IH4IH3  (4th-order accurate)
+                                ! PQM_IH6IH5  (5th-order accurate)
+VELOCITY_REMAPPING_SCHEME = "PPM_H4" ! default = "PPM_H4"
+                                ! This sets the reconstruction scheme used for vertical remapping of velocities.
+                                ! By default it is the same as REMAPPING_SCHEME. It can be one of the following
+                                ! schemes: PCM         (1st-order accurate)
+                                ! PLM         (2nd-order accurate)
+                                ! PLM_HYBGEN  (2nd-order accurate)
+                                ! PPM_H4      (3rd-order accurate)
+                                ! PPM_IH4     (3rd-order accurate)
+                                ! PPM_HYBGEN  (3rd-order accurate)
+                                ! WENO_HYBGEN (3rd-order accurate)
                                 ! PQM_IH4IH3  (4th-order accurate)
                                 ! PQM_IH6IH5  (5th-order accurate)
 FATAL_CHECK_RECONSTRUCTIONS = False !   [Boolean] default = False
@@ -491,6 +507,10 @@ REMAP_BOUND_INTERMEDIATE_VALUES = False !   [Boolean] default = False
 REMAP_BOUNDARY_EXTRAP = False   !   [Boolean] default = False
                                 ! If true, values at the interfaces of boundary cells are extrapolated instead
                                 ! of piecewise constant
+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
+                                ! remapping velocity.
 REMAP_AFTER_INITIALIZATION = False !   [Boolean] default = True
                                 ! If true, applies regridding and remapping immediately after initialization so
                                 ! that the state is ALE consistent. This is a legacy step and should not be
@@ -507,6 +527,10 @@ REGRID_FILTER_DEEP_DEPTH = 0.0  !   [m] default = 0.0
                                 ! The depth below which full time-filtering is applied with time-scale
                                 ! REGRID_TIME_SCALE. Between depths REGRID_FILTER_SHALLOW_DEPTH and
                                 ! REGRID_FILTER_SHALLOW_DEPTH the filter weights adopt a cubic profile.
+REMAP_VEL_MASK_BBL_THICK = -0.001 !   [m] default = -0.001
+                                ! A thickness of a bottom boundary layer below which velocities in thin layers
+                                ! are zeroed out after remapping, following practice with Hybgen remapping, or a
+                                ! negative value to avoid such filtering altogether.
 
 ! === module MOM_domains min_halo ===
 
@@ -702,7 +726,7 @@ CONVERT_THICKNESS_UNITS = False !   [Boolean] default = False
                                 ! if a restart file is read.
 SURFACE_PRESSURE_FILE = "Ocean1_3D.nc" !
                                 ! The initial condition file for the surface pressure exerted by ice.
-SURFACE_PRESSURE_VAR = "thick"  !   [Pa] default = ""
+SURFACE_PRESSURE_VAR = "thick"  ! default = ""
                                 ! The initial condition variable for the surface pressure exerted by ice.
 SURFACE_PRESSURE_SCALE = 8820.0 !   [file dependent] default = 1.0
                                 ! A scaling factor to convert SURFACE_PRESSURE_VAR from file
@@ -879,6 +903,15 @@ KHTH_MAX_CFL = 0.8              !   [nondimensional] default = 0.8
                                 ! thickness diffusivity. 1.0 is the marginally unstable value in a pure layered
                                 ! model, but much smaller numbers (e.g. 0.1) seem to work better for ALE-based
                                 ! models.
+KH_ETA_CONST = 0.0              !   [m2 s-1] default = 0.0
+                                ! The background horizontal diffusivity of the interface heights (without
+                                ! considering the layer density structure).  If diffusive CFL limits are
+                                ! encountered, the diffusivities of the isopycnals and the interfaces heights
+                                ! are scaled back proportionately.
+KH_ETA_VEL_SCALE = 0.0          !   [m s-1] default = 0.0
+                                ! A velocity scale that is multiplied by the grid spacing to give a contribution
+                                ! to the horizontal diffusivity of the interface heights (without considering
+                                ! the layer density structure).
 DETANGLE_INTERFACES = False     !   [Boolean] default = False
                                 ! If defined add 3-d structured enhanced interface height diffusivities to
                                 ! horizontally smooth jagged layers.

ocean_only/ISOMIP/rho/MOM_parameter_doc.short

@@ -165,6 +165,7 @@ REGRIDDING_COORDINATE_MODE = "RHO" ! default = "LAYER"
                                 !  SIGMA - terrain following coordinates
                                 !  RHO   - continuous isopycnal
                                 !  HYCOM1 - HyCOM-like hybrid coordinate
+                                !  HYBGEN - Hybrid coordinate from the Hycom hybgen code
                                 !  SLIGHT - stretched coordinates above continuous isopycnal
                                 !  ADAPTIVE - optimize for smooth neutral density surfaces
 INTERPOLATION_SCHEME = "P1M_H4" ! default = "P1M_H2"
@@ -200,8 +201,11 @@ REMAPPING_SCHEME = "PPM_H4"     ! default = "PLM"
                                 ! variables. It can be one of the following schemes: PCM         (1st-order
                                 ! accurate)
                                 ! PLM         (2nd-order accurate)
+                                ! PLM_HYBGEN  (2nd-order accurate)
                                 ! PPM_H4      (3rd-order accurate)
                                 ! PPM_IH4     (3rd-order accurate)
+                                ! PPM_HYBGEN  (3rd-order accurate)
+                                ! WENO_HYBGEN (3rd-order accurate)
                                 ! PQM_IH4IH3  (4th-order accurate)
                                 ! PQM_IH6IH5  (5th-order accurate)
 REMAP_AFTER_INITIALIZATION = False !   [Boolean] default = True
@@ -304,7 +308,7 @@ TRIM_IC_FOR_P_SURF = True       !   [Boolean] default = False
                                 ! read from file.
 SURFACE_PRESSURE_FILE = "Ocean1_3D.nc" !
                                 ! The initial condition file for the surface pressure exerted by ice.
-SURFACE_PRESSURE_VAR = "thick"  !   [Pa] default = ""
+SURFACE_PRESSURE_VAR = "thick"  ! default = ""
                                 ! The initial condition variable for the surface pressure exerted by ice.
 SURFACE_PRESSURE_SCALE = 8820.0 !   [file dependent] default = 1.0
                                 ! A scaling factor to convert SURFACE_PRESSURE_VAR from file

ocean_only/MESO_025_23L/MOM_parameter_doc.all

@@ -520,12 +520,9 @@ SPONGE_ETA_VAR = "ETA"          ! default = "ETA"
                                 ! The name of the interface height variable in SPONGE_STATE_FILE.
 SPONGE_IDAMP_VAR = "Idamp"      ! default = "Idamp"
                                 ! The name of the inverse damping rate variable in SPONGE_DAMPING_FILE.
-NEW_SPONGES = False             !   [of sponge restoring data.] default = False
-                                ! Set True if using the newer sponging code which performs on-the-fly regridding
-                                ! in lat-lon-time.
-INTERPOLATE_SPONGE_TIME_SPACE = False !   [of sponge restoring data.] default = False
-                                ! Set True if using the newer sponging code which performs on-the-fly regridding
-                                ! in lat-lon-time.
+INTERPOLATE_SPONGE_TIME_SPACE = False !   [Boolean] default = False
+                                ! If True, perform on-the-fly regridding in lat-lon-time of sponge restoring
+                                ! data.
 !Total sponge columns = 19376   !
                                 ! The total number of columns where sponges are applied.
 
@@ -691,6 +688,15 @@ KHTH_MAX_CFL = 0.8              !   [nondimensional] default = 0.8
                                 ! thickness diffusivity. 1.0 is the marginally unstable value in a pure layered
                                 ! model, but much smaller numbers (e.g. 0.1) seem to work better for ALE-based
                                 ! models.
+KH_ETA_CONST = 0.0              !   [m2 s-1] default = 0.0
+                                ! The background horizontal diffusivity of the interface heights (without
+                                ! considering the layer density structure).  If diffusive CFL limits are
+                                ! encountered, the diffusivities of the isopycnals and the interfaces heights
+                                ! are scaled back proportionately.
+KH_ETA_VEL_SCALE = 0.0          !   [m s-1] default = 0.0
+                                ! A velocity scale that is multiplied by the grid spacing to give a contribution
+                                ! to the horizontal diffusivity of the interface heights (without considering
+                                ! the layer density structure).
 DETANGLE_INTERFACES = False     !   [Boolean] default = False
                                 ! If defined add 3-d structured enhanced interface height diffusivities to
                                 ! horizontally smooth jagged layers.
@@ -908,9 +914,6 @@ 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.
-USE_KH_BG_2D = False            !   [Boolean] default = False
-                                ! If true, read a file containing 2-d background harmonic viscosities. The final
-                                ! viscosity is the maximum of the other terms and this background value.
 
 ! === module MOM_vert_friction ===
 VERT_FRICTION_2018_ANSWERS = False !   [Boolean] default = False

ocean_only/MESO_025_63L/MOM_parameter_doc.all

@@ -522,12 +522,9 @@ SPONGE_ETA_VAR = "ETA"          ! default = "ETA"
                                 ! The name of the interface height variable in SPONGE_STATE_FILE.
 SPONGE_IDAMP_VAR = "Idamp"      ! default = "Idamp"
                                 ! The name of the inverse damping rate variable in SPONGE_DAMPING_FILE.
-NEW_SPONGES = False             !   [of sponge restoring data.] default = False
-                                ! Set True if using the newer sponging code which performs on-the-fly regridding
-                                ! in lat-lon-time.
-INTERPOLATE_SPONGE_TIME_SPACE = False !   [of sponge restoring data.] default = False
-                                ! Set True if using the newer sponging code which performs on-the-fly regridding
-                                ! in lat-lon-time.
+INTERPOLATE_SPONGE_TIME_SPACE = False !   [Boolean] default = False
+                                ! If True, perform on-the-fly regridding in lat-lon-time of sponge restoring
+                                ! data.
 !Total sponge columns = 19167   !
                                 ! The total number of columns where sponges are applied.
 
@@ -705,6 +702,15 @@ KHTH_MAX_CFL = 0.8              !   [nondimensional] default = 0.8
                                 ! thickness diffusivity. 1.0 is the marginally unstable value in a pure layered
                                 ! model, but much smaller numbers (e.g. 0.1) seem to work better for ALE-based
                                 ! models.
+KH_ETA_CONST = 0.0              !   [m2 s-1] default = 0.0
+                                ! The background horizontal diffusivity of the interface heights (without
+                                ! considering the layer density structure).  If diffusive CFL limits are
+                                ! encountered, the diffusivities of the isopycnals and the interfaces heights
+                                ! are scaled back proportionately.
+KH_ETA_VEL_SCALE = 0.0          !   [m s-1] default = 0.0
+                                ! A velocity scale that is multiplied by the grid spacing to give a contribution
+                                ! to the horizontal diffusivity of the interface heights (without considering
+                                ! the layer density structure).
 DETANGLE_INTERFACES = False     !   [Boolean] default = False
                                 ! If defined add 3-d structured enhanced interface height diffusivities to
                                 ! horizontally smooth jagged layers.
@@ -922,9 +928,6 @@ 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.
-USE_KH_BG_2D = False            !   [Boolean] default = False
-                                ! If true, read a file containing 2-d background harmonic viscosities. The final
-                                ! viscosity is the maximum of the other terms and this background value.
 
 ! === module MOM_vert_friction ===
 VERT_FRICTION_2018_ANSWERS = False !   [Boolean] default = False

ocean_only/buoy_forced_basin/MOM_parameter_doc.all

@@ -570,6 +570,15 @@ KHTH_MAX_CFL = 0.8              !   [nondimensional] default = 0.8
                                 ! thickness diffusivity. 1.0 is the marginally unstable value in a pure layered
                                 ! model, but much smaller numbers (e.g. 0.1) seem to work better for ALE-based
                                 ! models.
+KH_ETA_CONST = 0.0              !   [m2 s-1] default = 0.0
+                                ! The background horizontal diffusivity of the interface heights (without
+                                ! considering the layer density structure).  If diffusive CFL limits are
+                                ! encountered, the diffusivities of the isopycnals and the interfaces heights
+                                ! are scaled back proportionately.
+KH_ETA_VEL_SCALE = 0.0          !   [m s-1] default = 0.0
+                                ! A velocity scale that is multiplied by the grid spacing to give a contribution
+                                ! to the horizontal diffusivity of the interface heights (without considering
+                                ! the layer density structure).
 DETANGLE_INTERFACES = False     !   [Boolean] default = False
                                 ! If defined add 3-d structured enhanced interface height diffusivities to
                                 ! horizontally smooth jagged layers.

ocean_only/global/MOM_parameter_doc.all

@@ -844,6 +844,15 @@ KHTH_MAX_CFL = 0.8              !   [nondimensional] default = 0.8
                                 ! thickness diffusivity. 1.0 is the marginally unstable value in a pure layered
                                 ! model, but much smaller numbers (e.g. 0.1) seem to work better for ALE-based
                                 ! models.
+KH_ETA_CONST = 0.0              !   [m2 s-1] default = 0.0
+                                ! The background horizontal diffusivity of the interface heights (without
+                                ! considering the layer density structure).  If diffusive CFL limits are
+                                ! encountered, the diffusivities of the isopycnals and the interfaces heights
+                                ! are scaled back proportionately.
+KH_ETA_VEL_SCALE = 0.0          !   [m s-1] default = 0.0
+                                ! A velocity scale that is multiplied by the grid spacing to give a contribution
+                                ! to the horizontal diffusivity of the interface heights (without considering
+                                ! the layer density structure).
 DETANGLE_INTERFACES = False     !   [Boolean] default = False
                                 ! If defined add 3-d structured enhanced interface height diffusivities to
                                 ! horizontally smooth jagged layers.