MOM6: Merge branch 'ashao-offline_tracer_updates' into dev/gfdl

- Last commit updates available_diags and MOM_parameter_doc.all (for one expt).

- NOAA-GFDL/MOM6@3486d83 Merge branch 'ashao-offline_tracer_updates' into dev/gfdl
- NOAA-GFDL/MOM6@d96c87b Final changes before PR
- NOAA-GFDL/MOM6@ce44698 Undo some changes made for diagnostic purposes, add comments, and cleanup code before PR
- NOAA-GFDL/MOM6@d8627bc Merge branch 'dev/gfdl' of https://github.com/NOAA-GFDL/MOM6 into offline_tracer_updates
- NOAA-GFDL/MOM6@d20e897 Merge pull request mom-ocean#521 from Hallberg-NOAA/dev/gfdl
- NOAA-GFDL/MOM6@a8565c7 Replaced group_pass of h with pass_var of h
- NOAA-GFDL/MOM6@5daf60f Corrected typos in dOxyGen comments
- NOAA-GFDL/MOM6@e8b7f0e Merge branch 'dev/gfdl' of github.com:NOAA-GFDL/MOM6 into dev/gfdl
- NOAA-GFDL/MOM6@1e8c2b4 Merge pull request mom-ocean#520 from NOAA-GFDL/user/wfcooke/grouphalopass_fix
- NOAA-GFDL/MOM6@db3a5b5 (*)Corrected the barotropic mass source compensation
- NOAA-GFDL/MOM6@833dd84 Bugfix to reintroduce group halo pass check removed in 282a160
- NOAA-GFDL/MOM6@2b8670f Merge pull request mom-ocean#519 from Hallberg-NOAA/dev/gfdl
- NOAA-GFDL/MOM6@b80fc8b Merge branch 'dev/gfdl' of github.com:NOAA-GFDL/MOM6 into dev/gfdl
- NOAA-GFDL/MOM6@144daae Merge branch 'dev/gfdl' of github.com:NOAA-GFDL/MOM6 into dev/gfdl
- NOAA-GFDL/MOM6@e1aed13 +Eliminated calc_bbl from the vertvisc_type
- NOAA-GFDL/MOM6@0576b2b (*)Moved set_viscous_BBL out of the dynamics code
- NOAA-GFDL/MOM6@53d03a7 Fixed conflicts with upstream dev/gfdl
- NOAA-GFDL/MOM6@7ddc722 Added option to intersperse ALE step between horizontal advection iterations.
- NOAA-GFDL/MOM6@af73ea8 Tracer now conserves when remapping input fields onto a different grid. This primarily resulted from an error in the indexing when the fields were being updated. Now to test in OM4_05
- NOAA-GFDL/MOM6@ff690d1 To aid in the debugging of tracer routines, a new subroutine is created in MOM_tracer_registry.F90: MOM_tracer_chkinv. This routine calculates the global inventories of all tracers in the registry. Some of the debugging checksums in the offline tracer routines are updated to use this new function.
- NOAA-GFDL/MOM6@ab0575d Add option to skip convective readjustment when reading offline fields from z inputs
- NOAA-GFDL/MOM6@f4e0063 Changes made so that regridding onto pure isopycnal kind of works. Need to figure out why the redistribution of residual does not fully conserve.
- NOAA-GFDL/MOM6@d2af9df Clean up some changes that were made for development purposes

ocean_only/global_ALE/layer/available_diags.000000

@@ -3039,6 +3039,22 @@
     ! long_name: Vertically Integrated Diffusive Meridional Flux of Salinity
     ! units: PPT meter3 second-1
     ! cell_methods: xh:mean yq:point
+"ocean_model", "h_pre_dyn"  [Unused]
+    ! long_name: Layer Thickness before dynamics step
+    ! units: meter
+    ! cell_methods: xh:mean yh:mean zl:mean
+"ocean_model", "h_pre_dyn_xyave"  [Unused]
+    ! long_name: Layer Thickness before dynamics step
+    ! units: meter
+    ! cell_methods: zl:mean
+"ocean_model_z", "h_pre_dyn"  [Unused]
+    ! long_name: Layer Thickness before dynamics step
+    ! units: meter
+    ! cell_methods: xh:mean yh:mean z_l:mean
+"ocean_model_z", "h_pre_dyn_xyave"  [Unused]
+    ! long_name: Layer Thickness before dynamics step
+    ! units: meter
+    ! cell_methods: z_l:mean
 "ocean_model", "u_predia"  [Unused]
     ! long_name: Zonal velocity before diabatic forcing
     ! units: meter second-1
@@ -3733,7 +3749,7 @@
     ! units: kilogram meter-2
     ! cell_methods: xh:mean yh:mean
 "ocean_model", "massin_flux"  [Unused]
-    ! long_name: Net mass mass flux of freshwater into the ocean (used in boundary flux calculation)
+    ! long_name: Net mass flux of freshwater into the ocean (used in boundary flux calculation)
     ! units: kilogram meter-2
     ! cell_methods: xh:mean yh:mean
 "ocean_model", "total_PRCmE"  [Used]

ocean_only/global_ALE/z/available_diags.000000

@@ -3410,6 +3410,22 @@
     ! long_name: Vertically Integrated Diffusive Meridional Flux of Salinity
     ! units: PPT meter3 second-1
     ! cell_methods: xh:mean yq:point
+"ocean_model", "h_pre_dyn"  [Unused]
+    ! long_name: Layer Thickness before dynamics step
+    ! units: meter
+    ! cell_methods: xh:mean yh:mean zl:mean
+"ocean_model", "h_pre_dyn_xyave"  [Unused]
+    ! long_name: Layer Thickness before dynamics step
+    ! units: meter
+    ! cell_methods: zl:mean
+"ocean_model_z", "h_pre_dyn"  [Unused]
+    ! long_name: Layer Thickness before dynamics step
+    ! units: meter
+    ! cell_methods: xh:mean yh:mean z_l:mean
+"ocean_model_z", "h_pre_dyn_xyave"  [Unused]
+    ! long_name: Layer Thickness before dynamics step
+    ! units: meter
+    ! cell_methods: z_l:mean
 "ocean_model", "u_predia"  [Unused]
     ! long_name: Zonal velocity before diabatic forcing
     ! units: meter second-1
@@ -4422,7 +4438,7 @@
     ! units: kilogram meter-2
     ! cell_methods: xh:mean yh:mean
 "ocean_model", "massin_flux"  [Unused]
-    ! long_name: Net mass mass flux of freshwater into the ocean (used in boundary flux calculation)
+    ! long_name: Net mass flux of freshwater into the ocean (used in boundary flux calculation)
     ! units: kilogram meter-2
     ! cell_methods: xh:mean yh:mean
 "ocean_model", "total_PRCmE"  [Used]

ocean_only/torus_advection_test/MOM_parameter_doc.all

@@ -290,6 +290,11 @@ SPONGE = False                  !   [Boolean] default = False
                                 ! specified from MOM_initialization.F90.
 MASK_TRACERS_IN_MASSLESS_LAYERS = False !   [Boolean] default = False
                                 ! If true, tracers will be masked out in massless layers.
+TRACERS_MAY_REINIT = False      !   [Boolean] default = False
+                                ! If true, tracers may go through the initialization code
+                                ! if they are not found in the restart files.  Otherwise
+                                ! it is a fatal error if the tracers are not found in the
+                                ! restart files of a restarted run.
 
 ! === module MOM_fixed_initialization ===
 INPUTDIR = "INPUT"              ! default = "."