MOM6 Merge branch 'nicjhan-62-z-ALE-remapping' into dev/master

- NOAA-GFDL/MOM6@d00d001 Merge branch 'nicjhan-62-z-ALE-remapping' into dev/master
- NOAA-GFDL/MOM6@d556620 Improve specification of grid definition file,variable used for diagnostic remapping. The format is now:         DIAG_REMAP_Z_GRID_DEF = "FILE:OM3_zgrid.nc,zw"
- NOAA-GFDL/MOM6@70e5686 Remove unnecessary include. NOAA-GFDL#62
- NOAA-GFDL/MOM6@d4e25ec Change name of ALE remapped Z level diagnostics to have _z_new suffix, avoids conflict with existing Z level diagnostics. NOAA-GFDL#62
- NOAA-GFDL/MOM6@423b0ee Remove unnecessary addition of optional arguments. NOAA-GFDL#62
- NOAA-GFDL/MOM6@9ab9b68 Don't move call to diag_mediator_init, setup pointer to H with setter method. NOAA-GFDL#62
- NOAA-GFDL/MOM6@9ecfe58 Set the minimum layer thickness for remapping only. NOAA-GFDL#62
- NOAA-GFDL/MOM6@d38f434 Reduce the minimum regridding thickness. Necessary for conservation when there are many thin layers. NOAA-GFDL#62
- NOAA-GFDL/MOM6@f320f0a Create diag variation that remaps T+layer diagnostics automatically. NOAA-GFDL#62
- NOAA-GFDL/MOM6@51c9ec6 Disable old Z space diagnostic remapping for tracers. Will eventually be removed. NOAA-GFDL#62
- NOAA-GFDL/MOM6@b10da82 Only initialise diag_mediator after h and G have been set up. NOAA-GFDL#62
- NOAA-GFDL/MOM6@6911097 Fix output from remapping conservation check. NOAA-GFDL#62
- NOAA-GFDL/MOM6@0dda96c Split Zstar grid creation up so can be done column-by-column. NOAA-GFDL#62

coupled_AM2_LM3_SIS/AM2_MOM6i_1deg/MOM_parameter_doc.all

@@ -455,6 +455,14 @@ APPLY_OBC_U = False             !   [Boolean] default = False
 APPLY_OBC_V = False             !   [Boolean] default = False
                                 ! If true, open boundary conditions may be set at some
                                 ! v-points, with the configuration controlled by OBC_CONFIG
+DIAG_REMAP_Z_GRID_DEF = ""      ! default = ""
+                                ! This sets the file and variable names that define the
+                                ! vertical grid used for diagnostic output remapping to
+                                ! Z space. It should look like:
+                                !  FILE:<file>,<variable> - where <file> is a file within
+                                !                           the INPUTDIR, <variable> is
+                                !                           the name of the variable that
+                                !                           contains interface positions.
 
 ! === module MOM_MEKE ===
 USE_MEKE = False                !   [Boolean] default = False

coupled_AM2_LM3_SIS/CM2G63L/MOM_parameter_doc.all

@@ -455,6 +455,14 @@ APPLY_OBC_U = False             !   [Boolean] default = False
 APPLY_OBC_V = False             !   [Boolean] default = False
                                 ! If true, open boundary conditions may be set at some
                                 ! v-points, with the configuration controlled by OBC_CONFIG
+DIAG_REMAP_Z_GRID_DEF = ""      ! default = ""
+                                ! This sets the file and variable names that define the
+                                ! vertical grid used for diagnostic output remapping to
+                                ! Z space. It should look like:
+                                !  FILE:<file>,<variable> - where <file> is a file within
+                                !                           the INPUTDIR, <variable> is
+                                !                           the name of the variable that
+                                !                           contains interface positions.
 
 ! === module MOM_MEKE ===
 USE_MEKE = False                !   [Boolean] default = False

coupled_AM2_LM3_SIS2/AM2_SIS2B_MOM6i_1deg/MOM_parameter_doc.all

@@ -455,6 +455,14 @@ APPLY_OBC_U = False             !   [Boolean] default = False
 APPLY_OBC_V = False             !   [Boolean] default = False
                                 ! If true, open boundary conditions may be set at some
                                 ! v-points, with the configuration controlled by OBC_CONFIG
+DIAG_REMAP_Z_GRID_DEF = ""      ! default = ""
+                                ! This sets the file and variable names that define the
+                                ! vertical grid used for diagnostic output remapping to
+                                ! Z space. It should look like:
+                                !  FILE:<file>,<variable> - where <file> is a file within
+                                !                           the INPUTDIR, <variable> is
+                                !                           the name of the variable that
+                                !                           contains interface positions.
 
 ! === module MOM_MEKE ===
 USE_MEKE = False                !   [Boolean] default = False

coupled_AM2_LM3_SIS2/AM2_SIS2_MOM6i_1deg/MOM_parameter_doc.all

@@ -455,6 +455,14 @@ APPLY_OBC_U = False             !   [Boolean] default = False
 APPLY_OBC_V = False             !   [Boolean] default = False
                                 ! If true, open boundary conditions may be set at some
                                 ! v-points, with the configuration controlled by OBC_CONFIG
+DIAG_REMAP_Z_GRID_DEF = ""      ! default = ""
+                                ! This sets the file and variable names that define the
+                                ! vertical grid used for diagnostic output remapping to
+                                ! Z space. It should look like:
+                                !  FILE:<file>,<variable> - where <file> is a file within
+                                !                           the INPUTDIR, <variable> is
+                                !                           the name of the variable that
+                                !                           contains interface positions.
 
 ! === module MOM_MEKE ===
 USE_MEKE = False                !   [Boolean] default = False

ice_ocean_SIS/GOLD_SIS/MOM_parameter_doc.all

@@ -482,6 +482,14 @@ APPLY_OBC_U = False             !   [Boolean] default = False
 APPLY_OBC_V = False             !   [Boolean] default = False
                                 ! If true, open boundary conditions may be set at some
                                 ! v-points, with the configuration controlled by OBC_CONFIG
+DIAG_REMAP_Z_GRID_DEF = ""      ! default = ""
+                                ! This sets the file and variable names that define the
+                                ! vertical grid used for diagnostic output remapping to
+                                ! Z space. It should look like:
+                                !  FILE:<file>,<variable> - where <file> is a file within
+                                !                           the INPUTDIR, <variable> is
+                                !                           the name of the variable that
+                                !                           contains interface positions.
 
 ! === module MOM_MEKE ===
 USE_MEKE = False                !   [Boolean] default = False

ice_ocean_SIS/GOLD_SIS/available_diags.000000

@@ -71,6 +71,9 @@
     ! long_name: Ocean lateral biharmonic viscosity
     ! units: m4 s-1
     ! standard_name: ocean_momentum_xy_biharmonic_diffusivity
+"ocean_model_z_new", "Ahh"  [Unused]
+    ! long_name: Biharmonic Horizontal Viscosity at h Points
+    ! units: meter4 second-1
 "ocean_model", "Ahq"  [Unused]
     ! long_name: Biharmonic Horizontal Viscosity at q Points
     ! units: meter4 second-1
@@ -81,12 +84,18 @@
     ! long_name: Ocean lateral Laplacian viscosity
     ! units: m2 s-1
     ! standard_name: ocean_momentum_xy_laplacian_diffusivity
+"ocean_model_z_new", "Khh"  [Unused]
+    ! long_name: Laplacian Horizontal Viscosity at h Points
+    ! units: meter2 second-1
 "ocean_model", "Khq"  [Unused]
     ! long_name: Laplacian Horizontal Viscosity at q Points
     ! units: meter2 second-1
 "ocean_model", "FrictWork"  [Unused]
     ! long_name: Integral work done by lateral friction terms
     ! units: Watt meter-2
+"ocean_model_z_new", "FrictWork"  [Unused]
+    ! long_name: Integral work done by lateral friction terms
+    ! units: Watt meter-2
 "ocean_model", "FrictWorkIntz"  [Unused]
     ! long_name: Depth integrated work done by lateral friction
     ! units: Watt meter-2
@@ -368,6 +377,10 @@
     ! long_name: Mass per unit area of liquid ocean grid cell
     ! units: kg m-2
     ! standard_name: sea_water_mass_per_unit_area
+"ocean_model_z_new", "masscello"  [Unused]
+    ! long_name: Mass per unit area of liquid ocean grid cell
+    ! units: kg m-2
+    ! standard_name: sea_water_mass_per_unit_area
 "ocean_model", "masso"  [Unused]
     ! long_name: Mass of liquid ocean
     ! units: kg
@@ -376,6 +389,10 @@
     ! long_name: Cell Thickness
     ! units: m
     ! standard_name: cell_thickness
+"ocean_model_z_new", "thkcello"  [Unused]
+    ! long_name: Cell Thickness
+    ! units: m
+    ! standard_name: cell_thickness
 "ocean_model", "thetaoga"  [Unused]
     ! long_name: Global Mean Ocean Potential Temperature
     ! units: Celsius
@@ -409,9 +426,15 @@
 "ocean_model", "Rml"  [Unused]
     ! long_name: Mixed Layer Coordinate Potential Density
     ! units: kg meter-3
+"ocean_model_z_new", "Rml"  [Unused]
+    ! long_name: Mixed Layer Coordinate Potential Density
+    ! units: kg meter-3
 "ocean_model", "Rho_cv"  [Unused]
     ! long_name: Coordinate Potential Density
     ! units: kg meter-3
+"ocean_model_z_new", "Rho_cv"  [Unused]
+    ! long_name: Coordinate Potential Density
+    ! units: kg meter-3
 "ocean_model", "dudt"  [Unused]
     ! long_name: Zonal Acceleration
     ! units: meter second-2
@@ -421,9 +444,15 @@
 "ocean_model", "dhdt"  [Unused]
     ! long_name: Thickness tendency
     ! units: meter second-1
+"ocean_model_z_new", "dhdt"  [Unused]
+    ! long_name: Thickness tendency
+    ! units: meter second-1
 "ocean_model", "h_rho"  [Unused]
     ! long_name: Layer thicknesses in pure potential density coordinates
     ! units: meter
+"ocean_model_z_new", "h_rho"  [Unused]
+    ! long_name: Layer thicknesses in pure potential density coordinates
+    ! units: meter
 "ocean_model", "uh_rho"  [Unused]
     ! long_name: Zonal volume transport in pure potential density coordinates
     ! units: meter3 second-1
@@ -439,27 +468,51 @@
 "ocean_model", "KE"  [Unused]
     ! long_name: Layer kinetic energy per unit mass
     ! units: meter2 second-2
+"ocean_model_z_new", "KE"  [Unused]
+    ! long_name: Layer kinetic energy per unit mass
+    ! units: meter2 second-2
 "ocean_model", "dKE_dt"  [Unused]
     ! long_name: Kinetic Energy Tendency of Layer
     ! units: meter3 second-3
+"ocean_model_z_new", "dKE_dt"  [Unused]
+    ! long_name: Kinetic Energy Tendency of Layer
+    ! units: meter3 second-3
 "ocean_model", "PE_to_KE"  [Unused]
     ! long_name: Potential to Kinetic Energy Conversion of Layer
     ! units: meter3 second-3
+"ocean_model_z_new", "PE_to_KE"  [Unused]
+    ! long_name: Potential to Kinetic Energy Conversion of Layer
+    ! units: meter3 second-3
 "ocean_model", "KE_Coradv"  [Unused]
     ! long_name: Kinetic Energy Source from Coriolis and Advection
     ! units: meter3 second-3
+"ocean_model_z_new", "KE_Coradv"  [Unused]
+    ! long_name: Kinetic Energy Source from Coriolis and Advection
+    ! units: meter3 second-3
 "ocean_model", "KE_adv"  [Unused]
     ! long_name: Kinetic Energy Source from Advection
     ! units: meter3 second-3
+"ocean_model_z_new", "KE_adv"  [Unused]
+    ! long_name: Kinetic Energy Source from Advection
+    ! units: meter3 second-3
 "ocean_model", "KE_visc"  [Unused]
     ! long_name: Kinetic Energy Source from Vertical Viscosity and Stresses
     ! units: meter3 second-3
+"ocean_model_z_new", "KE_visc"  [Unused]
+    ! long_name: Kinetic Energy Source from Vertical Viscosity and Stresses
+    ! units: meter3 second-3
 "ocean_model", "KE_horvisc"  [Unused]
     ! long_name: Kinetic Energy Source from Horizontal Viscosity
     ! units: meter3 second-3
+"ocean_model_z_new", "KE_horvisc"  [Unused]
+    ! long_name: Kinetic Energy Source from Horizontal Viscosity
+    ! units: meter3 second-3
 "ocean_model", "KE_dia"  [Unused]
     ! long_name: Kinetic Energy Source from Diapycnal Diffusion
     ! units: meter3 second-3
+"ocean_model_z_new", "KE_dia"  [Unused]
+    ! long_name: Kinetic Energy Source from Diapycnal Diffusion
+    ! units: meter3 second-3
 "ocean_model", "cg1"  [Unused]
     ! long_name: First baroclinic gravity wave speed
     ! units: meter second-1
@@ -533,9 +586,15 @@
 "ocean_model", "ea"  [Unused]
     ! long_name: Layer entrainment from above per timestep
     ! units: meter
+"ocean_model_z_new", "ea"  [Unused]
+    ! long_name: Layer entrainment from above per timestep
+    ! units: meter
 "ocean_model", "eb"  [Unused]
     ! long_name: Layer entrainment from below per timestep
     ! units: meter
+"ocean_model_z_new", "eb"  [Unused]
+    ! long_name: Layer entrainment from below per timestep
+    ! units: meter
 "ocean_model", "dudt_dia"  [Unused]
     ! long_name: Zonal Acceleration from Diapycnal Mixing
     ! units: meter second-2
@@ -601,15 +660,24 @@
 "ocean_model", "Kd_layer"  [Unused]
     ! long_name: Diapycnal diffusivity of layers (as set)
     ! units: meter2 second-1
+"ocean_model_z_new", "Kd_layer"  [Unused]
+    ! long_name: Diapycnal diffusivity of layers (as set)
+    ! units: meter2 second-1
 "ocean_model", "TKE_itidal"  [Unused]
     ! long_name: Internal Tide Driven Turbulent Kinetic Energy
     ! units: Watt meter-2
 "ocean_model", "maxTKE"  [Unused]
     ! long_name: Maximum layer TKE
     ! units: meter3 second-3
+"ocean_model_z_new", "maxTKE"  [Unused]
+    ! long_name: Maximum layer TKE
+    ! units: meter3 second-3
 "ocean_model", "TKE_to_Kd"  [Unused]
     ! long_name: Convert TKE to Kd
     ! units: second2 meter
+"ocean_model_z_new", "TKE_to_Kd"  [Unused]
+    ! long_name: Convert TKE to Kd
+    ! units: second2 meter
 "ocean_model", "Nb"  [Unused]
     ! long_name: Bottom Buoyancy Frequency
     ! units: sec-1
@@ -634,12 +702,21 @@
 "ocean_model", "Kd_Work"  [Unused]
     ! long_name: Work done by Diapycnal Mixing
     ! units: Watts m-2
+"ocean_model_z_new", "Kd_Work"  [Unused]
+    ! long_name: Work done by Diapycnal Mixing
+    ! units: Watts m-2
 "ocean_model", "Kd_Itidal_Work"  [Unused]
     ! long_name: Work done by Internal Tide Diapycnal Mixing
     ! units: Watts m-2
+"ocean_model_z_new", "Kd_Itidal_Work"  [Unused]
+    ! long_name: Work done by Internal Tide Diapycnal Mixing
+    ! units: Watts m-2
 "ocean_model", "Kd_Nikurashin_Work"  [Unused]
     ! long_name: Work done by Nikurashin Lee Wave Drag Scheme
     ! units: Watts m-2
+"ocean_model_z_new", "Kd_Nikurashin_Work"  [Unused]
+    ! long_name: Work done by Nikurashin Lee Wave Drag Scheme
+    ! units: Watts m-2
 "ocean_model", "N2"  [Unused]
     ! long_name: Buoyancy frequency squared
     ! units: sec-2
@@ -679,6 +756,9 @@
 "ocean_model", "Kd_effective"  [Unused]
     ! long_name: Diapycnal diffusivity as applied
     ! units: meter2 second-1
+"ocean_model_z_new", "Kd_effective"  [Unused]
+    ! long_name: Diapycnal diffusivity as applied
+    ! units: meter2 second-1
 "ocean_model", "diff_work"  [Unused]
     ! long_name: Work actually done by diapycnal diffusion across each interface
     ! units: W m-2
@@ -739,12 +819,21 @@
 "ocean_model", "opac_1"  [Unused]
     ! long_name: Opacity for shortwave radiation in band 1
     ! units: meter-1
+"ocean_model_z_new", "opac_1"  [Unused]
+    ! long_name: Opacity for shortwave radiation in band 1
+    ! units: meter-1
 "ocean_model", "opac_2"  [Unused]
     ! long_name: Opacity for shortwave radiation in band 2
     ! units: meter-1
+"ocean_model_z_new", "opac_2"  [Unused]
+    ! long_name: Opacity for shortwave radiation in band 2
+    ! units: meter-1
 "ocean_model", "opac_3"  [Unused]
     ! long_name: Opacity for shortwave radiation in band 3
     ! units: meter-1
+"ocean_model_z_new", "opac_3"  [Unused]
+    ! long_name: Opacity for shortwave radiation in band 3
+    ! units: meter-1
 "ocean_model", "Chl_opac"  [Unused]
     ! long_name: Surface chlorophyll A concentration used to find opacity
     ! units: mg meter-3
@@ -771,6 +860,9 @@
 "ocean_model", "h"  [Used]
     ! long_name: Layer Thickness
     ! units: meter
+"ocean_model_z_new", "h"  [Unused]
+    ! long_name: Layer Thickness
+    ! units: meter
 "ocean_model", "volo"  [Unused]
     ! long_name: Total volume of liquid ocean
     ! units: m3
@@ -801,13 +893,19 @@
 "ocean_model", "temp"  [Used]
     ! long_name: Potential Temperature
     ! units: Celsius
+"ocean_model_z_new", "temp"  [Unused]
+    ! long_name: Potential Temperature
+    ! units: Celsius
 "ocean_model", "salt"  [Used]
     ! long_name: Salinity
     ! units: PPT
 "ocean_model", "so"  [Unused]
     ! long_name: Sea Water Salinity
     ! units: ppt
     ! standard_name: sea_water_salinity
+"ocean_model_z_new", "salt"  [Unused]
+    ! long_name: Salinity
+    ! units: PPT
 "ocean_model", "tob"  [Unused]
     ! long_name: Sea Water Potential Temperature at Sea Floor
     ! units: degC
@@ -910,15 +1008,24 @@
 "ocean_model", "h_predia"  [Unused]
     ! long_name: Layer Thickness before diabatic forcing
     ! units: meter
+"ocean_model_z_new", "h_predia"  [Unused]
+    ! long_name: Layer Thickness before diabatic forcing
+    ! units: meter
 "ocean_model", "e_predia"  [Unused]
     ! long_name: Interface Heights before diabatic forcing
     ! units: meter
 "ocean_model", "temp_predia"  [Unused]
     ! long_name: Potential Temperature
     ! units: Celsius
+"ocean_model_z_new", "temp_predia"  [Unused]
+    ! long_name: Potential Temperature
+    ! units: Celsius
 "ocean_model", "salt_predia"  [Unused]
     ! long_name: Salinity
     ! units: PPT
+"ocean_model_z_new", "salt_predia"  [Unused]
+    ! long_name: Salinity
+    ! units: PPT
 "ocean_model_z", "temp"  [Used]
     ! long_name: Potential Temperature
     ! units: degC
@@ -938,6 +1045,9 @@
 "ocean_model", "age"  [Unused]
     ! long_name: Ideal Age Tracer
     ! units: years
+"ocean_model_z_new", "age"  [Unused]
+    ! long_name: Ideal Age Tracer
+    ! units: years
 "ocean_model", "age_adx"  [Unused]
     ! long_name: Ideal Age Tracer advective zonal flux
     ! units: years m3 s-1
@@ -957,13 +1067,19 @@
 "ocean_model", "CFC11"  [Unused]
     ! long_name: CFC-11 Concentration
     ! units: mol m-3
+"ocean_model_z_new", "CFC11"  [Unused]
+    ! long_name: CFC-11 Concentration
+    ! units: mol m-3
 "ocean_model_z", "CFC11"  [Unused]
     ! long_name: CFC-11 Concentration
     ! units: mol m-3
     ! standard_name: not provided
 "ocean_model", "CFC12"  [Unused]
     ! long_name: CFC-12 Concentration
     ! units: mol m-3
+"ocean_model_z_new", "CFC12"  [Unused]
+    ! long_name: CFC-12 Concentration
+    ! units: mol m-3
 "ocean_model_z", "CFC12"  [Unused]
     ! long_name: CFC-12 Concentration
     ! units: mol m-3