+Replace SZK_(G) with SZK_(GV)

  Use the vertical extent from the verticalGrid_type argument GV instead of the
extent from the ocean_grid_type argument G to specify the vertical extent of
arrays in memory in array declarations.  There 18 subroutines where new
vertical_grid_type arguqments were needed, and some comments were corrected.  All
answers are bitwise identical, but there are new (non-optional) arguments to 18
subroutines.

config_src/unit_drivers/MOM_sum_driver.F90

@@ -18,8 +18,6 @@ program MOM_main
   use MOM_coms, only : EFP_type, operator(+), operator(-), assignment(=), EFP_to_real, real_to_EFP
   use MOM_cpu_clock, only : cpu_clock_id, cpu_clock_begin, cpu_clock_end
   use MOM_cpu_clock, only : CLOCK_COMPONENT
-!  use MOM_diag_mediator, only : diag_mediator_end, diag_mediator_init
-!  use MOM_diag_mediator, only : diag_mediator_close_registration
   use MOM_domains, only : MOM_domains_init, MOM_infra_init, MOM_infra_end
   use MOM_error_handler, only : MOM_error, MOM_mesg, WARNING, FATAL, is_root_pe
   use MOM_error_handler, only : MOM_set_verbosity
@@ -39,11 +37,10 @@ program MOM_main
 
   type(param_file_type) :: param_file ! The structure indicating the file(s)
                                 ! containing all run-time parameters.
-  real    :: max_depth
+  real    :: max_depth          ! The maximum ocean depth [m]
   integer :: verbosity
   integer :: num_sums
-  integer :: n, i, j, is, ie, js, je, nz
-  integer :: isd, ied, jsd, jed, IsdB, IedB, JsdB, JedB
+  integer :: n, i, j, is, ie, js, je, isd, ied, jsd, jed
 
   integer :: unit, io_status, ierr
   logical :: unit_in_use
@@ -55,8 +52,8 @@ program MOM_main
   !-----------------------------------------------------------------------
 
   character(len=4), parameter :: vers_num = 'v2.0'
-! This include declares and sets the variable "version".
-#include "version_variable.h"
+  ! This include declares and sets the variable "version".
+# include "version_variable.h"
   character(len=40)  :: mdl = "MOM_main (MOM_sum_driver)" ! This module's name.
   character(len=200) :: mesg
 
@@ -85,9 +82,8 @@ program MOM_main
 !  call diag_mediator_init(param_file)
   call MOM_grid_init(grid, param_file)
 
-  is = grid%isc ; ie = grid%iec ; js = grid%jsc ; je = grid%jec ; nz = grid%ke
+  is = grid%isc ; ie = grid%iec ; js = grid%jsc ; je = grid%jec
   isd = grid%isd ; ied = grid%ied ; jsd = grid%jsd ; jed = grid%jed
-  IsdB = grid%IsdB ; IedB = grid%IedB ; JsdB = grid%JsdB ; JedB = grid%JedB
 
   ! Read all relevant parameters and write them to the model log.
   call log_version(param_file, "MOM", version, "")
@@ -165,27 +161,25 @@ program MOM_main
 
 contains
 
+!> This subroutine sets up the benchmark test case topography for debugging
 subroutine benchmark_init_topog_local(D, G, param_file, max_depth)
   type(ocean_grid_type),            intent(in)  :: G    !< The ocean's grid structure
   real, dimension(SZI_(G),SZJ_(G)), intent(out) :: D    !< The ocean bottom depth in m
   type(param_file_type),            intent(in)  :: param_file !< A structure to parse for run-time parameters
-  real,                             intent(in)  :: max_depth !< The maximum ocean depth in m
+  real,                             intent(in)  :: max_depth !< The maximum ocean depth [m]
 
-! This subroutine sets up the benchmark test case topography
   real :: min_depth            ! The minimum ocean depth in m.
   real :: PI                   ! 3.1415926... calculated as 4*atan(1)
   real :: D0                   ! A constant to make the maximum     !
                                ! basin depth MAXIMUM_DEPTH.         !
   real :: x, y
-! This include declares and sets the variable "version".
-#include "version_variable.h"
-  character(len=40)  :: mdl = "benchmark_initialize_topography" ! This subroutine's name.
+  ! This include declares and sets the variable "version".
+# include "version_variable.h"
+  character(len=40)  :: mdl = "benchmark_init_topog_local" ! This subroutine's name.
   integer :: i, j, is, ie, js, je, isd, ied, jsd, jed
   is = G%isc ; ie = G%iec ; js = G%jsc ; je = G%jec
   isd = G%isd ; ied = G%ied ; jsd = G%jsd ; jed = G%jed
 
-  call MOM_mesg("  benchmark_initialization.F90, benchmark_initialize_topography: setting topography", 5)
-
   call log_version(param_file, mdl, version)
   call get_param(param_file, mdl, "MINIMUM_DEPTH", min_depth, &
                  "The minimum depth of the ocean.", units="m", default=0.0)

src/core/MOM.F90

@@ -1133,7 +1133,7 @@ subroutine step_MOM_tracer_dyn(CS, G, GV, US, h, Time_local)
   type(ocean_grid_type),    intent(inout) :: G      !< ocean grid structure
   type(verticalGrid_type),  intent(in)    :: GV     !< ocean vertical grid structure
   type(unit_scale_type),    intent(in)    :: US     !< A dimensional unit scaling type
-  real, dimension(SZI_(G),SZJ_(G),SZK_(G)),  &
+  real, dimension(SZI_(G),SZJ_(G),SZK_(GV)), &
                             intent(in)    :: h      !< layer thicknesses after the transports [H ~> m or kg m-2]
   type(time_type),          intent(in)    :: Time_local !< The model time at the end
                                                     !! of the time step.
@@ -1214,11 +1214,11 @@ subroutine step_MOM_thermo(CS, G, GV, US, u, v, h, tv, fluxes, dtdia, &
   type(ocean_grid_type),    intent(inout) :: G      !< ocean grid structure
   type(verticalGrid_type),  intent(inout) :: GV     !< ocean vertical grid structure
   type(unit_scale_type),    intent(in)    :: US     !< A dimensional unit scaling type
-  real, dimension(SZIB_(G),SZJ_(G),SZK_(G)), &
+  real, dimension(SZIB_(G),SZJ_(G),SZK_(GV)), &
                             intent(inout) :: u      !< zonal velocity [L T-1 ~> m s-1]
-  real, dimension(SZI_(G),SZJB_(G),SZK_(G)), &
+  real, dimension(SZI_(G),SZJB_(G),SZK_(GV)), &
                             intent(inout) :: v      !< meridional velocity [L T-1 ~> m s-1]
-  real, dimension(SZI_(G),SZJ_(G),SZK_(G)),  &
+  real, dimension(SZI_(G),SZJ_(G),SZK_(GV)), &
                             intent(inout) :: h      !< layer thickness [H ~> m or kg m-2]
   type(thermo_var_ptrs),    intent(inout) :: tv     !< A structure pointing to various thermodynamic variables
   type(forcing),            intent(inout) :: fluxes !< pointers to forcing fields
@@ -1247,7 +1247,7 @@ subroutine step_MOM_thermo(CS, G, GV, US, u, v, h, tv, fluxes, dtdia, &
   call enable_averages(dtdia, Time_end_thermo, CS%diag)
 
   if (associated(CS%odaCS)) then
-    call apply_oda_tracer_increments(US%T_to_s*dtdia,G,tv,h,CS%odaCS)
+    call apply_oda_tracer_increments(US%T_to_s*dtdia, G, GV, tv, h, CS%odaCS)
   endif
 
   if (associated(fluxes%p_surf) .or. associated(fluxes%p_surf_full)) then
@@ -2800,7 +2800,7 @@ subroutine finish_MOM_initialization(Time, dirs, CS, restart_CSp)
   if (CS%write_IC) then
     allocate(restart_CSp_tmp)
     restart_CSp_tmp = restart_CSp
-    allocate(z_interface(SZI_(G),SZJ_(G),SZK_(G)+1))
+    allocate(z_interface(SZI_(G),SZJ_(G),SZK_(GV)+1))
     call find_eta(CS%h, CS%tv, G, GV, US, z_interface, eta_to_m=1.0)
     call register_restart_field(z_interface, "eta", .true., restart_CSp_tmp, &
                                 "Interface heights", "meter", z_grid='i')

src/core/MOM_CoriolisAdv.F90

@@ -114,23 +114,23 @@ module MOM_CoriolisAdv
 
 !> Calculates the Coriolis and momentum advection contributions to the acceleration.
 subroutine CorAdCalc(u, v, h, uh, vh, CAu, CAv, OBC, AD, G, GV, US, CS)
-  type(ocean_grid_type),                     intent(in)    :: G  !< Ocen grid structure
-  type(verticalGrid_type),                   intent(in)    :: GV !< Vertical grid structure
-  real, dimension(SZIB_(G),SZJ_(G),SZK_(G)), intent(in)    :: u  !< Zonal velocity [L T-1 ~> m s-1]
-  real, dimension(SZI_(G),SZJB_(G),SZK_(G)), intent(in)    :: v  !< Meridional velocity [L T-1 ~> m s-1]
-  real, dimension(SZI_(G),SZJ_(G),SZK_(G)),  intent(in)    :: h  !< Layer thickness [H ~> m or kg m-2]
-  real, dimension(SZIB_(G),SZJ_(G),SZK_(G)), intent(in)    :: uh !< Zonal transport u*h*dy
-                                                                 !! [H L2 T-1 ~> m3 s-1 or kg s-1]
-  real, dimension(SZI_(G),SZJB_(G),SZK_(G)), intent(in)    :: vh !< Meridional transport v*h*dx
-                                                                 !! [H L2 T-1 ~> m3 s-1 or kg s-1]
-  real, dimension(SZIB_(G),SZJ_(G),SZK_(G)), intent(out)   :: CAu !< Zonal acceleration due to Coriolis
+  type(ocean_grid_type),                      intent(in)    :: G  !< Ocen grid structure
+  type(verticalGrid_type),                    intent(in)    :: GV !< Vertical grid structure
+  real, dimension(SZIB_(G),SZJ_(G),SZK_(GV)), intent(in)    :: u  !< Zonal velocity [L T-1 ~> m s-1]
+  real, dimension(SZI_(G),SZJB_(G),SZK_(GV)), intent(in)    :: v  !< Meridional velocity [L T-1 ~> m s-1]
+  real, dimension(SZI_(G),SZJ_(G),SZK_(GV)),  intent(in)    :: h  !< Layer thickness [H ~> m or kg m-2]
+  real, dimension(SZIB_(G),SZJ_(G),SZK_(GV)), intent(in)    :: uh !< Zonal transport u*h*dy
+                                                                  !! [H L2 T-1 ~> m3 s-1 or kg s-1]
+  real, dimension(SZI_(G),SZJB_(G),SZK_(GV)), intent(in)    :: vh !< Meridional transport v*h*dx
+                                                                  !! [H L2 T-1 ~> m3 s-1 or kg s-1]
+  real, dimension(SZIB_(G),SZJ_(G),SZK_(GV)), intent(out)   :: CAu !< Zonal acceleration due to Coriolis
                                                                   !! and momentum advection [L T-2 ~> m s-2].
-  real, dimension(SZI_(G),SZJB_(G),SZK_(G)), intent(out)   :: CAv !< Meridional acceleration due to Coriolis
+  real, dimension(SZI_(G),SZJB_(G),SZK_(GV)), intent(out)   :: CAv !< Meridional acceleration due to Coriolis
                                                                   !! and momentum advection [L T-2 ~> m s-2].
-  type(ocean_OBC_type),                      pointer       :: OBC !< Open boundary control structure
-  type(accel_diag_ptrs),                     intent(inout) :: AD  !< Storage for acceleration diagnostics
-  type(unit_scale_type),                     intent(in)    :: US  !< A dimensional unit scaling type
-  type(CoriolisAdv_CS),                      pointer       :: CS  !< Control structure for MOM_CoriolisAdv
+  type(ocean_OBC_type),                       pointer       :: OBC !< Open boundary control structure
+  type(accel_diag_ptrs),                      intent(inout) :: AD  !< Storage for acceleration diagnostics
+  type(unit_scale_type),                      intent(in)    :: US  !< A dimensional unit scaling type
+  type(CoriolisAdv_CS),                       pointer       :: CS  !< Control structure for MOM_CoriolisAdv
 
   ! Local variables
   real, dimension(SZIB_(G),SZJB_(G)) :: &
@@ -174,7 +174,7 @@ subroutine CorAdCalc(u, v, h, uh, vh, CAu, CAv, OBC, AD, G, GV, US, CS)
     min_fvq, &  ! The minimum of the adjacent values of (-u) times absolute vorticity [L T-2 ~> m s-2].
     max_fuq, &  ! The maximum of the adjacent values of u times absolute vorticity [L T-2 ~> m s-2].
     min_fuq     ! The minimum of the adjacent values of u times absolute vorticity [L T-2 ~> m s-2].
-  real, dimension(SZIB_(G),SZJB_(G),SZK_(G)) :: &
+  real, dimension(SZIB_(G),SZJB_(G),SZK_(GV)) :: &
     PV, &       ! A diagnostic array of the potential vorticities [H-1 T-1 ~> m-1 s-1 or m2 kg-1 s-1].
     RV          ! A diagnostic array of the relative vorticities [T-1 ~> s-1].
   real :: fv1, fv2, fu1, fu2   ! (f+rv)*v or (f+rv)*u [L T-2 ~> m s-2].
@@ -927,9 +927,9 @@ end subroutine CorAdCalc
 subroutine gradKE(u, v, h, KE, KEx, KEy, k, OBC, G, GV, US, CS)
   type(ocean_grid_type),                      intent(in)  :: G !< Ocen grid structure
   type(verticalGrid_type),                    intent(in)  :: GV !< Vertical grid structure
-  real, dimension(SZIB_(G),SZJ_(G),SZK_(G)),  intent(in)  :: u !< Zonal velocity [L T-1 ~> m s-1]
-  real, dimension(SZI_(G),SZJB_(G),SZK_(G)),  intent(in)  :: v !< Meridional velocity [L T-1 ~> m s-1]
-  real, dimension(SZI_(G),SZJ_(G),SZK_(G)),   intent(in)  :: h !< Layer thickness [H ~> m or kg m-2]
+  real, dimension(SZIB_(G),SZJ_(G),SZK_(GV)), intent(in)  :: u !< Zonal velocity [L T-1 ~> m s-1]
+  real, dimension(SZI_(G),SZJB_(G),SZK_(GV)), intent(in)  :: v !< Meridional velocity [L T-1 ~> m s-1]
+  real, dimension(SZI_(G),SZJ_(G),SZK_(GV)),  intent(in)  :: h !< Layer thickness [H ~> m or kg m-2]
   real, dimension(SZI_(G) ,SZJ_(G) ),         intent(out) :: KE !< Kinetic energy per unit mass [L2 T-2 ~> m2 s-2]
   real, dimension(SZIB_(G),SZJ_(G) ),         intent(out) :: KEx !< Zonal acceleration due to kinetic
                                                                  !! energy gradient [L T-2 ~> m s-2]

src/core/MOM_PressureForce.F90

@@ -41,19 +41,19 @@ subroutine PressureForce(h, tv, PFu, PFv, G, GV, US, CS, ALE_CSp, p_atm, pbce, e
   type(ocean_grid_type),   intent(in)  :: G    !< The ocean's grid structure
   type(verticalGrid_type), intent(in)  :: GV   !< The ocean's vertical grid structure
   type(unit_scale_type),   intent(in)  :: US   !< A dimensional unit scaling type
-  real, dimension(SZI_(G),SZJ_(G),SZK_(G)), &
+  real, dimension(SZI_(G),SZJ_(G),SZK_(GV)), &
                            intent(in)  :: h    !< Layer thicknesses [H ~> m or kg m-2]
   type(thermo_var_ptrs),   intent(in)  :: tv   !< A structure pointing to various thermodynamic variables
-  real, dimension(SZIB_(G),SZJ_(G),SZK_(G)), &
+  real, dimension(SZIB_(G),SZJ_(G),SZK_(GV)), &
                            intent(out) :: PFu  !< Zonal pressure force acceleration [L T-2 ~> m s-2]
-  real, dimension(SZI_(G),SZJB_(G),SZK_(G)), &
+  real, dimension(SZI_(G),SZJB_(G),SZK_(GV)), &
                            intent(out) :: PFv  !< Meridional pressure force acceleration [L T-2 ~> m s-2]
   type(PressureForce_CS),  pointer     :: CS   !< Pressure force control structure
   type(ALE_CS),            pointer     :: ALE_CSp !< ALE control structure
   real, dimension(:,:), &
                  optional, pointer     :: p_atm !< The pressure at the ice-ocean or
                                                !! atmosphere-ocean interface [R L2 T-2 ~> Pa].
-  real, dimension(SZI_(G),SZJ_(G),SZK_(G)), &
+  real, dimension(SZI_(G),SZJ_(G),SZK_(GV)), &
                  optional, intent(out) :: pbce !< The baroclinic pressure anomaly in each layer
                                                !! due to eta anomalies [L2 T-2 H-1 ~> m s-2 or m4 s-2 kg-1].
   real, dimension(SZI_(G),SZJ_(G)), &