Further reduced use of square brackets in comments

  Repplaced square brackets with parentheses in comments using C-style square
brackets to express the relationships between array arguments in several tracer
column physics routines.  The use of square brackets may be in conflict with the
use of square brackets for links in markup language comments, like dOxyGen. Also
eliminated two trailing blanks.  Only comments are changed and all answers are
bitwise identical.

src/core/MOM_CoriolisAdv.F90

@@ -212,7 +212,7 @@ subroutine CorAdCalc(u, v, h, uh, vh, CAu, CAv, OBC, AD, G, GV, CS)
 ! To work, the following fields must be set outside of the usual
 ! is to ie range before this subroutine is called:
 !   v(is-1:ie+2,js-1:je+1), u(is-1:ie+1,js-1:je+2), h(is-1:ie+2,js-1:je+2),
-!   uh(is-1,ie,js:je+1) and vh(is:ie+1,js-1:je). 
+!   uh(is-1,ie,js:je+1) and vh(is:ie+1,js-1:je).
 
   if (.not.associated(CS)) call MOM_error(FATAL, &
          "MOM_CoriolisAdv: Module must be initialized before it is used.")

src/tracer/DOME_tracer.F90

@@ -284,7 +284,7 @@ end subroutine initialize_DOME_tracer
 !! This is a simple example of a set of advected passive tracers.
 !!
 !! The arguments to this subroutine are redundant in that
-!!     h_new[k] = h_old[k] + ea[k] - eb[k-1] + eb[k] - ea[k+1]
+!!     h_new(k) = h_old(k) + ea(k) - eb(k-1) + eb(k) - ea(k+1)
 subroutine DOME_tracer_column_physics(h_old, h_new,  ea,  eb, fluxes, dt, G, GV, CS, &
               evap_CFL_limit, minimum_forcing_depth)
   type(ocean_grid_type),   intent(in) :: G    !< The ocean's grid structure

src/tracer/ISOMIP_tracer.F90

@@ -277,7 +277,7 @@ subroutine ISOMIP_tracer_column_physics(h_old, h_new,  ea,  eb, fluxes, dt, G, G
                                               !! fluxes can be applied, in m
 
 ! The arguments to this subroutine are redundant in that
-!     h_new[k] = h_old[k] + ea[k] - eb[k-1] + eb[k] - ea[k+1]
+!     h_new(k) = h_old(k) + ea(k) - eb(k-1) + eb(k) - ea(k+1)
 
   ! Local variables
   real :: mmax

src/tracer/MOM_OCMIP2_CFC.F90

@@ -437,7 +437,7 @@ subroutine OCMIP2_CFC_column_physics(h_old, h_new, ea, eb, fluxes, dt, G, GV, CS
 ! flux as a source.
 
 ! The arguments to this subroutine are redundant in that
-!     h_new[k] = h_old[k] + ea[k] - eb[k-1] + eb[k] - ea[k+1]
+!     h_new(k) = h_old(k) + ea(k) - eb(k-1) + eb(k) - ea(k+1)
 
   ! Local variables
   real :: b1(SZI_(G))          ! b1 and c1 are variables used by the

src/tracer/MOM_generic_tracer.F90

@@ -461,7 +461,7 @@ subroutine MOM_generic_tracer_column_physics(h_old, h_new, ea, eb, fluxes, Hml,
     real,          optional, intent(in) :: minimum_forcing_depth !< The smallest depth over which fluxes
                                                 !!  can be applied Stored previously in diabatic CS.
     ! The arguments to this subroutine are redundant in that
-    !     h_new[k] = h_old[k] + ea[k] - eb[k-1] + eb[k] - ea[k+1]
+    !     h_new(k) = h_old(k) + ea(k) - eb(k-1) + eb(k) - ea(k+1)
 
 ! Local variables
     character(len=fm_string_len), parameter :: sub_name = 'MOM_generic_tracer_column_physics'

src/tracer/advection_test_tracer.F90

@@ -290,7 +290,7 @@ subroutine advection_test_tracer_column_physics(h_old, h_new,  ea,  eb, fluxes,
 ! This is a simple example of a set of advected passive tracers.
 
 ! The arguments to this subroutine are redundant in that
-!     h_new[k] = h_old[k] + ea[k] - eb[k-1] + eb[k] - ea[k+1]
+!     h_new(k) = h_old(k) + ea(k) - eb(k-1) + eb(k) - ea(k+1)
   ! Local variables
   real, dimension(SZI_(G),SZJ_(G),SZK_(G)) :: h_work ! Used so that h can be modified
   real :: b1(SZI_(G))          ! b1 and c1 are variables used by the

src/tracer/boundary_impulse_tracer.F90

@@ -240,7 +240,7 @@ subroutine boundary_impulse_tracer_column_physics(h_old, h_new, ea, eb, fluxes,
 ! This is a simple example of a set of advected passive tracers.
 
 ! The arguments to this subroutine are redundant in that
-!     h_new[k] = h_old[k] + ea[k] - eb[k-1] + eb[k] - ea[k+1]
+!     h_new(k) = h_old(k) + ea(k) - eb(k-1) + eb(k) - ea(k+1)
 
   ! Local variables
   real :: Isecs_per_year = 1.0 / (365.0*86400.0)

src/tracer/dye_example.F90

@@ -245,7 +245,7 @@ end subroutine initialize_dye_tracer
 !! tracer physics or chemistry to the tracers from this file.
 !! This is a simple example of a set of advected passive tracers.
 !! The arguments to this subroutine are redundant in that
-!!     h_new[k] = h_old[k] + ea[k] - eb[k-1] + eb[k] - ea[k+1]
+!!     h_new(k) = h_old(k) + ea(k) - eb(k-1) + eb(k) - ea(k+1)
 subroutine dye_tracer_column_physics(h_old, h_new, ea, eb, fluxes, dt, G, GV, CS, &
               evap_CFL_limit, minimum_forcing_depth)
   type(ocean_grid_type),   intent(in) :: G    !< The ocean's grid structure

src/tracer/dyed_obc_tracer.F90

@@ -201,7 +201,7 @@ end subroutine initialize_dyed_obc_tracer
 !! This is a simple example of a set of advected passive tracers.
 !!
 !! The arguments to this subroutine are redundant in that
-!!     h_new[k] = h_old[k] + ea[k] - eb[k-1] + eb[k] - ea[k+1]
+!!     h_new(k) = h_old(k) + ea(k) - eb(k-1) + eb(k) - ea(k+1)
 subroutine dyed_obc_tracer_column_physics(h_old, h_new,  ea,  eb, fluxes, dt, G, GV, CS, &
               evap_CFL_limit, minimum_forcing_depth)
   type(ocean_grid_type),   intent(in) :: G    !< The ocean's grid structure

src/tracer/ideal_age_example.F90

@@ -313,7 +313,7 @@ subroutine ideal_age_tracer_column_physics(h_old, h_new, ea, eb, fluxes, dt, G,
 ! This is a simple example of a set of advected passive tracers.
 
 ! The arguments to this subroutine are redundant in that
-!     h_new[k] = h_old[k] + ea[k] - eb[k-1] + eb[k] - ea[k+1]
+!     h_new(k) = h_old(k) + ea(k) - eb(k-1) + eb(k) - ea(k+1)
   ! Local variables
   real, dimension(SZI_(G),SZJ_(G),SZK_(G)) :: h_work ! Used so that h can be modified
   real :: sfc_val  ! The surface value for the tracers.

src/tracer/oil_tracer.F90

@@ -329,7 +329,7 @@ subroutine oil_tracer_column_physics(h_old, h_new, ea, eb, fluxes, dt, G, GV, CS
 ! This is a simple example of a set of advected passive tracers.
 
 ! The arguments to this subroutine are redundant in that
-!     h_new[k] = h_old[k] + ea[k] - eb[k-1] + eb[k] - ea[k+1]
+!     h_new(k) = h_old(k) + ea(k) - eb(k-1) + eb(k) - ea(k+1)
 
   ! Local variables
   real, dimension(SZI_(G),SZJ_(G),SZK_(G)) :: h_work ! Used so that h can be modified

src/tracer/pseudo_salt_tracer.F90

@@ -205,7 +205,7 @@ subroutine pseudo_salt_tracer_column_physics(h_old, h_new, ea, eb, fluxes, dt, G
 ! tracer physics or chemistry to the tracers from this file.
 
 ! The arguments to this subroutine are redundant in that
-!     h_new[k] = h_old[k] + ea[k] - eb[k-1] + eb[k] - ea[k+1]
+!     h_new(k) = h_old(k) + ea(k) - eb(k-1) + eb(k) - ea(k+1)
 
   ! Local variables
   real :: year, h_total, scale, htot, Ih_limit

src/tracer/tracer_example.F90

@@ -261,7 +261,7 @@ end subroutine USER_initialize_tracer
 !! tracer physics or chemistry to the tracers from this file.
 !! This is a simple example of a set of advected passive tracers.
 !! The arguments to this subroutine are redundant in that
-!!     h_new[k] = h_old[k] + ea[k] - eb[k-1] + eb[k] - ea[k+1]
+!!     h_new(k) = h_old(k) + ea(k) - eb(k-1) + eb(k) - ea(k+1)
 subroutine tracer_column_physics(h_old, h_new,  ea,  eb, fluxes, dt, G, GV, CS)
   type(ocean_grid_type),   intent(in) :: G    !< The ocean's grid structure
   type(verticalGrid_type), intent(in) :: GV   !< The ocean's vertical grid structure

src/user/Phillips_initialization.F90

@@ -98,7 +98,7 @@ subroutine Phillips_initialize_thickness(h, G, GV, US, param_file, just_read_par
     !   This sets the initial thickness (in H ~> m or kg m-2) of the layers.  The
     ! thicknesses are set to insure that: 1. each layer is at least an Angstrom thick, and
     ! 2. the interfaces are where they should be based on the resting depths and interface
-    !    height perturbations, as long at this doesn't interfere with 1.  
+    !    height perturbations, as long at this doesn't interfere with 1.
     eta1D(nz+1) = -G%bathyT(i,j)
     do k=nz,1,-1
       eta1D(K) = eta_im(j,K)