Use square-bracket syntax in unit documentation

  Changed comments indicating the units of variables in some of the user
directory modules to use square brackets, following the newly proposed MOM6
syntax convetion.  This has been verified to give correct output via dOxygen.
Only comments have been changed and all answers are bitwise identical.

src/user/Idealized_Hurricane.F90

@@ -45,15 +45,15 @@ module Idealized_hurricane
 type, public :: idealized_hurricane_CS ; private
 
   ! Parameters used to compute Holland radial wind profile
-  real    :: rho_a                !< Mean air density [kg/m3]
+  real    :: rho_a                !< Mean air density [kg m-3]
   real    :: pressure_ambient     !< Pressure at surface of ambient air [Pa]
   real    :: pressure_central     !< Pressure at surface at hurricane center [Pa]
   real    :: rad_max_wind         !< Radius of maximum winds [m]
-  real    :: max_windspeed        !< Maximum wind speeds [m/s]
-  real    :: hurr_translation_spd !< Hurricane translation speed [m/s]
-  real    :: hurr_translation_dir !< Hurricane translation speed [m/s]
-  real    :: gustiness            !< Gustiness (optional, used in u*) [m/s]
-  real    :: Rho0                 !< A reference ocean density [kg/m3]
+  real    :: max_windspeed        !< Maximum wind speeds [m s-1]
+  real    :: hurr_translation_spd !< Hurricane translation speed [m s-1]
+  real    :: hurr_translation_dir !< Hurricane translation speed [m s-1]
+  real    :: gustiness            !< Gustiness (optional, used in u*) [m s-1]
+  real    :: Rho0                 !< A reference ocean density [kg m-3]
   real    :: Hurr_cen_Y0          !< The initial y position of the hurricane
                                   !!  This experiment is conducted in a Cartesian
                                   !!  grid and this is assumed to be in meters [m]
@@ -69,7 +69,7 @@ module Idealized_hurricane
 
 
   ! Parameters used if in SCM (single column model) mode
-  logical :: SCM_mode        !< Single Column Model Mode [nd]
+  logical :: SCM_mode        !< If true this being used in Single Column Model mode
   logical :: BR_BENCH        !< A "benchmark" configuration (which is meant to
                              !!  provide identical wind to reproduce a previous
                              !!  experiment, where that wind formula contained
@@ -198,10 +198,10 @@ end subroutine idealized_hurricane_wind_init
 
 !> Computes the surface wind for the idealized hurricane test cases
 subroutine idealized_hurricane_wind_forcing(state, forces, day, G, US, CS)
-  type(surface),          intent(in)    :: state  !< Surface state structure
-  type(mech_forcing),     intent(inout) :: forces !< A structure with the driving mechanical forces
-  type(time_type),        intent(in)    :: day    !< Time in days
-  type(ocean_grid_type),  intent(inout) :: G      !< Grid structure
+  type(surface),                intent(in)    :: state  !< Surface state structure
+  type(mech_forcing),           intent(inout) :: forces !< A structure with the driving mechanical forces
+  type(time_type),              intent(in)    :: day    !< Time in days
+  type(ocean_grid_type),        intent(inout) :: G      !< Grid structure
   type(unit_scale_type),        intent(in)    :: US     !< A dimensional unit scaling type
   type(idealized_hurricane_CS), pointer       :: CS     !< Container for idealized hurricane parameters
 

src/user/MOM_wave_interface.F90

@@ -1189,7 +1189,7 @@ subroutine StokesMixing(G, GV, DT, h, u, v, Waves )
        intent(in)    :: GV    !< Ocean vertical grid
   real, intent(in)   :: Dt    !< Time step of MOM6 [s] for explicit solver
   real, dimension(SZI_(G),SZJ_(G),SZK_(G)),&
-       intent(in)    :: h     !< Layer/level thicknesses (H ~> m or kg m-2)
+       intent(in)    :: h     !< Layer thicknesses [H ~> m or kg m-2]
   real, dimension(SZIB_(G),SZJ_(G),SZK_(G)), &
        intent(inout) :: u     !< Velocity i-component (m/s)
   real, dimension(SZI_(G),SZJB_(G),SZK_(G)), &
@@ -1257,11 +1257,11 @@ subroutine CoriolisStokes(G, GV, DT, h, u, v, WAVES)
        intent(in)   :: GV     !< Ocean vertical grid
   real, intent(in)  :: Dt     !< Time step of MOM6 [s] CHECK IF PASSING RIGHT TIMESTEP
   real, dimension(SZI_(G),SZJ_(G),SZK_(G)),  &
-       intent(in)    :: h     !< Layer/level thicknesses (H ~> m or kg m-2)
+       intent(in)    :: h     !< Layer thicknesses [H ~> m or kg m-2]
   real, dimension(SZIB_(G),SZJ_(G),SZK_(G)), &
-       intent(inout) :: u     !< Velocity i-component (m/s)
+       intent(inout) :: u     !< Velocity i-component [m s-1]
   real, dimension(SZI_(G),SZJB_(G),SZK_(G)), &
-       intent(inout) :: v     !< Velocity j-component (m/s)
+       intent(inout) :: v     !< Velocity j-component [m s-1]
   type(Wave_parameters_CS), &
        pointer       :: Waves !< Surface wave related control structure.
   ! Local variables

src/user/Phillips_initialization.F90

@@ -39,18 +39,20 @@ subroutine Phillips_initialize_thickness(h, G, GV, US, param_file, just_read_par
   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_(GV)), &
-                           intent(out) :: h          !< The thickness that is being initialized, in H ~> m or kg m-2.
+                           intent(out) :: h          !< The thickness that is being initialized [H ~> m or kg m-2]
   type(param_file_type),   intent(in)  :: param_file !< A structure indicating the open file
                                                      !! to parse for model parameter values.
   logical,       optional, intent(in)  :: just_read_params !< If present and true, this call will
                                                      !! only read parameters without changing h.
 
-  real :: eta0(SZK_(G)+1)   ! The 1-d nominal positions of the interfaces, in Z ~> m.
-  real :: eta_im(SZJ_(G),SZK_(G)+1) ! A temporary array for zonal-mean eta, in Z ~> m.
-  real :: eta1D(SZK_(G)+1)  ! Interface height relative to the sea surface
-                            ! positive upward, in Z ~> m.
-  real :: damp_rate, jet_width, jet_height, y_2
-  real :: half_strat, half_depth
+  real :: eta0(SZK_(G)+1)   ! The 1-d nominal positions of the interfaces [Z ~> m]
+  real :: eta_im(SZJ_(G),SZK_(G)+1) ! A temporary array for zonal-mean eta [Z ~> m]
+  real :: eta1D(SZK_(G)+1)  ! Interface height relative to the sea surface, positive upward [Z ~> m]
+  real :: jet_width         ! The width of the zonal-mean jet [km]
+  real :: jet_height        ! The interface height scale associated with the zonal-mean jet [Z ~> m]
+  real :: y_2
+  real :: half_strat      ! The fractional depth where the stratification is centered [nondim]
+  real :: half_depth      ! The depth where the stratification is centered [Z ~> m]
   logical :: just_read    ! If true, just read parameters but set nothing.
   character(len=40)  :: mdl = "Phillips_initialize_thickness" ! This subroutine's name.
   integer :: i, j, k, is, ie, js, je, isd, ied, jsd, jed, nz
@@ -64,8 +66,9 @@ subroutine Phillips_initialize_thickness(h, G, GV, US, param_file, just_read_par
 
   if (.not.just_read) call log_version(param_file, mdl, version)
   call get_param(param_file, mdl, "HALF_STRAT_DEPTH", half_strat, &
-                 "The maximum depth of the ocean.", units="nondim", &
-                 default = 0.5, do_not_log=just_read)
+!### UNCOMMENT TO FIX THIS "The fractional depth where the stratification is centered.", &
+                 "The maximum depth of the ocean.", &
+                 units="nondim", default = 0.5, do_not_log=just_read)
   call get_param(param_file, mdl, "JET_WIDTH", jet_width, &
                  "The width of the zonal-mean jet.", units="km", &
                  fail_if_missing=.not.just_read, do_not_log=just_read)
@@ -119,15 +122,15 @@ subroutine Phillips_initialize_velocity(u, v, G, GV, US, param_file, just_read_p
   type(verticalGrid_type), intent(in)  :: GV !< Vertical grid structure
   type(unit_scale_type),   intent(in)  :: US !< A dimensional unit scaling type
   real, dimension(SZIB_(G),SZJ_(G),SZK_(G)), &
-                           intent(out) :: u  !< i-component of velocity [m/s]
+                           intent(out) :: u  !< i-component of velocity [m s-1]
   real, dimension(SZI_(G),SZJB_(G),SZK_(G)), &
-                           intent(out) :: v  !< j-component of velocity [m/s]
+                           intent(out) :: v  !< j-component of velocity [m s-1]
   type(param_file_type),   intent(in)  :: param_file !< A structure indicating the open file to
                                                      !! parse for modelparameter values.
   logical,       optional, intent(in)  :: just_read_params !< If present and true, this call will
                                                      !! only read parameters without changing h.
 
-  real :: damp_rate, jet_width, jet_height, x_2, y_2
+  real :: jet_width, jet_height, x_2, y_2
   real :: velocity_amplitude, pi
   integer :: i, j, k, is, ie, js, je, nz, m
   logical :: just_read    ! If true, just read parameters but set nothing.

src/user/Rossby_front_2d_initialization.F90

@@ -28,9 +28,9 @@ module Rossby_front_2d_initialization
 public Rossby_front_initialize_velocity
 
 ! Parameters defining the initial conditions of this test case
-real, parameter :: frontFractionalWidth = 0.5 !< Width of front as fraction of domain
-real, parameter :: HMLmin = 0.25 !< Shallowest ML as fractional depth of ocean
-real, parameter :: HMLmax = 0.75 !< Deepest ML as fractional depth of ocean
+real, parameter :: frontFractionalWidth = 0.5 !< Width of front as fraction of domain [nondim]
+real, parameter :: HMLmin = 0.25 !< Shallowest ML as fractional depth of ocean [nondim]
+real, parameter :: HMLmax = 0.75 !< Deepest ML as fractional depth of ocean [nondim]
 
 contains
 
@@ -39,7 +39,7 @@ subroutine Rossby_front_initialize_thickness(h, G, GV, param_file, just_read_par
   type(ocean_grid_type),   intent(in) :: G            !< Grid structure
   type(verticalGrid_type), intent(in) :: GV           !< Vertical grid structure
   real, dimension(SZI_(G),SZJ_(G),SZK_(GV)), &
-                           intent(out) :: h           !< The thickness that is being initialized, in H ~> m or kg m-2.
+                           intent(out) :: h           !< The thickness that is being initialized [H ~> m or kg m-2]
   type(param_file_type),   intent(in)  :: param_file  !< A structure indicating the open file
                                                       !! to parse for model parameter values.
   logical,       optional, intent(in)  :: just_read_params !< If present and true, this call will
@@ -110,9 +110,9 @@ subroutine Rossby_front_initialize_temperature_salinity(T, S, h, G, GV, &
                    param_file, eqn_of_state, just_read_params)
   type(ocean_grid_type),                     intent(in)  :: G  !< Grid structure
   type(verticalGrid_type),                   intent(in)  :: GV !< The ocean's vertical grid structure.
-  real, dimension(SZI_(G),SZJ_(G), SZK_(G)), intent(out) :: T  !< Potential temperature [deg C]
+  real, dimension(SZI_(G),SZJ_(G), SZK_(G)), intent(out) :: T  !< Potential temperature [degC]
   real, dimension(SZI_(G),SZJ_(G), SZK_(G)), intent(out) :: S  !< Salinity [ppt]
-  real, dimension(SZI_(G),SZJ_(G), SZK_(G)), intent(in)  :: h  !< Thickness in H ~> m or kg m-2
+  real, dimension(SZI_(G),SZJ_(G), SZK_(G)), intent(in)  :: h  !< Thickness [H ~> m or kg m-2]
   type(param_file_type),                     intent(in)  :: param_file   !< Parameter file handle
   type(EOS_type),                            pointer     :: eqn_of_state !< Equation of state structure
   logical,       optional, intent(in)  :: just_read_params !< If present and true, this call will
@@ -163,11 +163,11 @@ subroutine Rossby_front_initialize_velocity(u, v, h, G, GV, param_file, just_rea
   type(ocean_grid_type),      intent(in)  :: G  !< Grid structure
   type(verticalGrid_type),    intent(in)  :: GV !< Vertical grid structure
   real, dimension(SZIB_(G),SZJ_(G),SZK_(G)), &
-                              intent(out) :: u  !< i-component of velocity [m/s]
+                              intent(out) :: u  !< i-component of velocity [m s-1]
   real, dimension(SZI_(G),SZJB_(G),SZK_(G)), &
-                              intent(out) :: v  !< j-component of velocity [m/s]
+                              intent(out) :: v  !< j-component of velocity [m s-1]
   real, dimension(SZI_(G),SZJ_(G), SZK_(G)), &
-                              intent(in)  :: h  !< Thickness [H]
+                              intent(in)  :: h  !< Thickness [H ~> m or kg m-2]
   type(param_file_type),      intent(in)  :: param_file !< A structure indicating the open file
                                                 !! to parse for model parameter values.
   logical,          optional, intent(in)  :: just_read_params !< If present and true, this call

src/user/SCM_CVMix_tests.F90

@@ -30,10 +30,9 @@ module SCM_CVMix_tests
 ! their mks counterparts with notation like "a velocity, in Z T-1 ~> m s-1."
 
 !> Container for surface forcing parameters
-type SCM_CVMix_tests_CS
-private
+type SCM_CVMix_tests_CS ; private
   logical :: UseWindStress  !< True to use wind stress
-  logical :: UseHeatFlux  !< True to use heat flux
+  logical :: UseHeatFlux    !< True to use heat flux
   logical :: UseEvaporation !< True to use evaporation
   logical :: UseDiurnalSW   !< True to use diurnal sw radiation
   real :: tau_x !< (Constant) Wind stress, X (Pa)
@@ -112,8 +111,8 @@ subroutine SCM_CVMix_tests_TS_init(T, S, h, G, GV, US, param_file, just_read_par
     top = 0. ! Reference to surface
     bottom = 0.
     do k=1,nz
-      bottom = bottom - h(i,j,k)*GV%H_to_Z ! Interface below layer (in m)
-      zC = 0.5*( top + bottom )        ! Z of middle of layer (in m)
+      bottom = bottom - h(i,j,k)*GV%H_to_Z ! Interface below layer [Z ~> m]
+      zC = 0.5*( top + bottom )        ! Z of middle of layer [Z ~> m]
       DZ = min(0., zC + UpperLayerTempMLD)
       T(i,j,k) = max(LowerLayerMinTemp,LowerLayerTemp + LowerLayerdTdZ * DZ)
       DZ = min(0., zC + UpperLayerSaltMLD)
@@ -255,7 +254,7 @@ subroutine SCM_CVMix_tests_buoyancy_forcing(state, fluxes, day, G, CS)
 
   if (CS%UseEvaporation) then
     do J=Jsq,Jeq ; do i=is,ie
-    ! Note CVMix test inputs give evaporation in m/s
+    ! Note CVMix test inputs give evaporation in [m s-1]
     ! This therefore must be converted to mass flux
     ! by multiplying by density
       fluxes%evap(i,J) = CS%surf_evap * CS%Rho0

src/user/baroclinic_zone_initialization.F90

@@ -79,9 +79,9 @@ subroutine baroclinic_zone_init_temperature_salinity(T, S, h, G, GV, US, param_f
   type(ocean_grid_type),                     intent(in)  :: G  !< 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)), intent(out) :: T  !< Potential temperature [deg C]
+  real, dimension(SZI_(G),SZJ_(G), SZK_(G)), intent(out) :: T  !< Potential temperature [degC]
   real, dimension(SZI_(G),SZJ_(G), SZK_(G)), intent(out) :: S  !< Salinity [ppt]
-  real, dimension(SZI_(G),SZJ_(G), SZK_(G)), intent(in)  :: h  !< The model thicknesses in H ~> m or kg m-2
+  real, dimension(SZI_(G),SZJ_(G), SZK_(G)), intent(in)  :: h  !< The model thicknesses [H ~> m or kg m-2]
   type(param_file_type),                     intent(in)  :: param_file  !< Parameter file handle
   logical,       optional, intent(in)  :: just_read_params !< If present and true, this call will
                                                       !! only read parameters without changing T & S.
@@ -90,7 +90,7 @@ subroutine baroclinic_zone_init_temperature_salinity(T, S, h, G, GV, US, param_f
   real      :: T_ref, dTdz, dTdx, delta_T ! Parameters describing temperature distribution
   real      :: S_ref, dSdz, dSdx, delta_S ! Parameters describing salinity distribution
   real      :: L_zone ! Width of baroclinic zone
-  real      :: zc, zi ! Depths in depth units (Z ~> m).
+  real      :: zc, zi ! Depths in depth units [Z ~> m]
   real      :: x, xd, xs, y, yd, fn
   real      :: PI                   ! 3.1415926... calculated as 4*atan(1)
   logical :: just_read    ! If true, just read parameters but set nothing.

src/user/dense_water_initialization.F90

@@ -25,8 +25,8 @@ module dense_water_initialization
 
 character(len=40) :: mdl = "dense_water_initialization" !< Module name
 
-real, parameter :: default_sill  = 0.2 !< Default depth of the sill [nondim]
-real, parameter :: default_shelf = 0.4 !< Default depth of the shelf [nondim]
+real, parameter :: default_sill  = 0.2  !< Default depth of the sill [nondim]
+real, parameter :: default_shelf = 0.4  !< Default depth of the shelf [nondim]
 real, parameter :: default_mld   = 0.25 !< Default depth of the mixed layer [nondim]
 
 contains
@@ -100,9 +100,9 @@ subroutine dense_water_initialize_TS(G, GV, param_file, eqn_of_state, T, S, h, j
   type(verticalGrid_type),                   intent(in)  :: GV !< Vertical grid control structure
   type(param_file_type),                     intent(in)  :: param_file !< Parameter file structure
   type(EOS_type),                            pointer     :: eqn_of_state !< EOS structure
-  real, dimension(SZI_(G),SZJ_(G),SZK_(GV)), intent(out) :: T !< Output temperature (degC)
-  real, dimension(SZI_(G),SZJ_(G),SZK_(GV)), intent(out) :: S !< Output salinity (ppt)
-  real, dimension(SZI_(G),SZJ_(G),SZK_(GV)), intent(in)  :: h !< Layer thicknesses
+  real, dimension(SZI_(G),SZJ_(G),SZK_(GV)), intent(out) :: T !< Output temperature [degC]
+  real, dimension(SZI_(G),SZJ_(G),SZK_(GV)), intent(out) :: S !< Output salinity [ppt]
+  real, dimension(SZI_(G),SZJ_(G),SZK_(GV)), intent(in)  :: h !< Layer thicknesses [H ~> m or kg m-2]
   logical,       optional, intent(in)  :: just_read_params !< If present and true, this call will
                                                       !! only read parameters without changing h.
   ! Local variables

src/user/soliton_initialization.F90

@@ -65,9 +65,9 @@ end subroutine soliton_initialize_thickness
 !> Initialization of u and v in the equatorial Rossby soliton test
 subroutine soliton_initialize_velocity(u, v, h, G)
   type(ocean_grid_type),                  intent(in)     :: G  !< Grid structure
-  real, dimension(SZIB_(G),SZJ_(G),SZK_(G)), intent(out) :: u  !< i-component of velocity [m/s]
-  real, dimension(SZI_(G),SZJB_(G),SZK_(G)), intent(out) :: v  !< j-component of velocity [m/s]
-  real, dimension(SZI_(G),SZJ_(G), SZK_(G)), intent(in)  :: h  !< Thickness [H]
+  real, dimension(SZIB_(G),SZJ_(G),SZK_(G)), intent(out) :: u  !< i-component of velocity [m s-1]
+  real, dimension(SZI_(G),SZJB_(G),SZK_(G)), intent(out) :: v  !< j-component of velocity [m s-1]
+  real, dimension(SZI_(G),SZJ_(G), SZK_(G)), intent(in)  :: h  !< Thickness [H ~> m or kg m-2]
 
   real    :: x, y, x0, y0
   real    :: val1, val2, val3, val4

src/user/user_initialization.F90

@@ -107,7 +107,7 @@ end subroutine USER_initialize_thickness
 !> initialize velocities.
 subroutine USER_initialize_velocity(u, v, G, param_file, just_read_params)
   type(ocean_grid_type),                       intent(in)  :: G !< Ocean grid structure.
-  real, dimension(SZIB_(G), SZJ_(G), SZK_(G)), intent(out) :: u !< i-component of velocity [m/s]
+  real, dimension(SZIB_(G), SZJ_(G), SZK_(G)), intent(out) :: u !< i-component of velocity [m s-1]
   real, dimension(SZI_(G), SZJB_(G), SZK_(G)), intent(out) :: v !< j-component of velocity [m/s]
   type(param_file_type),                       intent(in)  :: param_file !< A structure indicating the
                                                             !! open file to parse for model