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Add units to comments in MOM_neutral_diffusion
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  Added or corrected the units in comments describing about 200 real variables
in MOM_hor_bnd_diffusion and MOM_neutral_diffusion, and corrected spelling
errors or other issues in about another 20 comments.  Only comments are changed
and all answers are bitwise identical.
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@Hallberg-NOAA @marshallward
Hallberg-NOAA authored and marshallward committed Nov 23, 2023
1 parent 7cc191a commit 34b880f
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Showing 2 changed files with 302 additions and 184 deletions.
94 changes: 52 additions & 42 deletions src/tracer/MOM_hor_bnd_diffusion.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ module MOM_hor_bnd_diffusion
public boundary_k_range, hor_bnd_diffusion_end

! Private parameters to avoid doing string comparisons for bottom or top boundary layer
integer, public, parameter :: SURFACE = -1 !< Set a value that corresponds to the surface bopundary
integer, public, parameter :: SURFACE = -1 !< Set a value that corresponds to the surface boundary
integer, public, parameter :: BOTTOM = 1 !< Set a value that corresponds to the bottom boundary
#include <MOM_memory.h>

Expand All @@ -53,7 +53,7 @@ module MOM_hor_bnd_diffusion
!! Angstrom or larger without changing it at the bit level [H ~> m or kg m-2].
!! If Angstrom is 0 or exceedingly small, this is negligible compared to 1e-17 m.
! HBD dynamic grids
real, allocatable, dimension(:,:,:) :: hbd_grd_u !< HBD thicknesses at t-points adjecent to
real, allocatable, dimension(:,:,:) :: hbd_grd_u !< HBD thicknesses at t-points adjacent to
!! u-points [H ~> m or kg m-2]
real, allocatable, dimension(:,:,:) :: hbd_grd_v !< HBD thicknesses at t-points adjacent to
!! v-points (left and right) [H ~> m or kg m-2]
Expand Down Expand Up @@ -182,11 +182,19 @@ subroutine hor_bnd_diffusion(G, GV, US, h, Coef_x, Coef_y, dt, Reg, CS)
!! [conc H L2 ~> conc m3 or conc kg]
real, dimension(SZI_(G),SZJB_(G)) :: vwork_2d !< Layer summed v-flux transport
!! [conc H L2 ~> conc m3 or conc kg]
real, dimension(SZI_(G),SZJ_(G),SZK_(GV)) :: tendency !< tendency array for diagnostic [conc T-1 ~> conc s-1]
real, dimension(SZI_(G),SZJ_(G)) :: tendency_2d !< depth integrated content tendency for diagn
type(tracer_type), pointer :: tracer => NULL() !< Pointer to the current tracer
real, dimension(SZI_(G),SZJ_(G),SZK_(GV)) :: tendency !< tendency array for diagnostics at first in
!! [H conc T-1 ~> m conc s-1 or kg m-2 conc s-1],
!! then converted to [conc T-1 ~> conc s-1].
! For temperature these units are
! [C H T-1 ~> degC m s-1 or degC kg m-2 s-1] and
! then [C T-1 ~> degC s-1].
real, dimension(SZI_(G),SZJ_(G)) :: tendency_2d !< depth integrated content tendency for diagnostics in
!! [H conc T-1 ~> m conc s-1 or kg m-2 conc s-1].
!! For temperature these units are
!! [C H T-1 ~> degC m s-1 or degC kg m-2 s-1].
type(tracer_type), pointer :: tracer => NULL() !< Pointer to the current tracer [conc]
real, dimension(SZI_(G),SZJ_(G),SZK_(GV)) :: tracer_old !< local copy of the initial tracer concentration,
!! only used to compute tendencies.
!! only used to compute tendencies [conc].
real :: tracer_int_prev !< Globally integrated tracer before HBD is applied, in mks units [conc kg]
real :: tracer_int_end !< Integrated tracer after HBD is applied, in mks units [conc kg]
real :: Idt !< inverse of the time step [T-1 ~> s-1]
Expand Down Expand Up @@ -323,7 +331,7 @@ subroutine hor_bnd_diffusion(G, GV, US, h, Coef_x, Coef_y, dt, Reg, CS)

end subroutine hor_bnd_diffusion

!> Build the HBD grid where tracers will be rammaped to.
!> Build the HBD grid where tracers will be remapped to.
subroutine hbd_grid(boundary, G, GV, hbl, h, CS)
integer, intent(in ) :: boundary !< Which boundary layer SURFACE or BOTTOM [nondim]
type(ocean_grid_type), intent(inout) :: G !< Grid type
Expand Down Expand Up @@ -393,8 +401,8 @@ end subroutine hbd_grid
!> Calculate the harmonic mean of two quantities
!! See \ref section_harmonic_mean.
real function harmonic_mean(h1,h2)
real :: h1 !< Scalar quantity
real :: h2 !< Scalar quantity
real :: h1 !< Scalar quantity [arbitrary]
real :: h2 !< Scalar quantity [arbitrary]
if (h1 + h2 == 0.) then
harmonic_mean = 0.
else
Expand All @@ -407,10 +415,10 @@ end function harmonic_mean
integer function find_minimum(x, s, e)
integer, intent(in) :: s !< start index
integer, intent(in) :: e !< end index
real, dimension(e), intent(in) :: x !< 1D array to be checked
real, dimension(e), intent(in) :: x !< 1D array to be checked [arbitrary]

! local variables
real :: minimum
real :: minimum ! Minimum value in the same units as x [arbitrary]
integer :: location
integer :: i

Expand All @@ -427,11 +435,11 @@ end function find_minimum

!> Swaps the values of its two formal arguments.
subroutine swap(a, b)
real, intent(inout) :: a !< First value to be swaped
real, intent(inout) :: b !< Second value to be swaped
real, intent(inout) :: a !< First value to be swapped [arbitrary]
real, intent(inout) :: b !< Second value to be swapped [arbitrary]

! local variables
real :: tmp
real :: tmp ! A temporary copy of a [arbitrary]

tmp = a
a = b
Expand All @@ -440,8 +448,8 @@ end subroutine swap

!> Receives a 1D array x and sorts it into ascending order.
subroutine sort(x, n)
integer, intent(in ) :: n !< # of pts in the array
real, dimension(n), intent(inout) :: x !< 1D array to be sorted
integer, intent(in ) :: n !< Number of points in the array
real, dimension(n), intent(inout) :: x !< 1D array to be sorted [arbitrary]

! local variables
integer :: i, location
Expand All @@ -454,15 +462,15 @@ end subroutine sort

!> Returns the unique values in a 1D array.
subroutine unique(val, n, val_unique, val_max)
integer, intent(in ) :: n !< # of pts in the array.
real, dimension(n), intent(in ) :: val !< 1D array to be checked.
real, dimension(:), allocatable, intent(inout) :: val_unique !< Returned 1D array with unique values.
integer, intent(in ) :: n !< Number of points in the array.
real, dimension(n), intent(in ) :: val !< 1D array to be checked [arbitrary]
real, dimension(:), allocatable, intent(inout) :: val_unique !< Returned 1D array with unique values [arbitrary]
real, optional, intent(in ) :: val_max !< sets the maximum value in val_unique to
!! this value.
!! this value [arbitrary]
! local variables
real, dimension(n) :: tmp
real, dimension(n) :: tmp ! The list of unique values [arbitrary]
integer :: i, j, ii
real :: min_val, max_val
real :: min_val, max_val ! The minimum and maximum values in the list [arbitrary]
logical :: limit

limit = .false.
Expand Down Expand Up @@ -510,12 +518,14 @@ subroutine merge_interfaces(nk, h_L, h_R, hbl_L, hbl_R, H_subroundoff, h)

! Local variables
integer :: n !< Number of layers in eta_all
real, dimension(nk+1) :: eta_L, eta_R!< Interfaces in the left and right coloumns
real, dimension(:), allocatable :: eta_all !< Combined interfaces in the left/right columns + hbl_L and hbl_R
real, dimension(:), allocatable :: eta_unique !< Combined interfaces (eta_L, eta_R), possibly hbl_L and hbl_R
real :: min_depth !< Minimum depth
real :: max_depth !< Maximum depth
real :: max_bld !< Deepest BLD
real, dimension(nk+1) :: eta_L, eta_R!< Interfaces in the left and right columns [H ~> m or kg m-2]
real, dimension(:), allocatable :: eta_all !< Combined list of interfaces in the left and right columns
!! plus hbl_L and hbl_R [H ~> m or kg m-2]
real, dimension(:), allocatable :: eta_unique !< Combined list of unique interfaces (eta_L, eta_R), possibly
!! hbl_L and hbl_R [H ~> m or kg m-2]
real :: min_depth !< Minimum depth [H ~> m or kg m-2]
real :: max_depth !< Maximum depth [H ~> m or kg m-2]
real :: max_bld !< Deepest BLD [H ~> m or kg m-2]
integer :: k, kk, nk1 !< loop indices (k and kk) and array size (nk1)

n = (2*nk)+3
Expand Down Expand Up @@ -564,7 +574,7 @@ subroutine flux_limiter(F_layer, area_L, area_R, phi_L, phi_R, h_L, h_R)
real, intent(in) :: phi_R !< Tracer concentration in the right cell [conc]

! local variables
real :: F_max !< maximum flux allowed
real :: F_max !< maximum flux allowed [conc H L2 ~> conc m3 or conc kg]
! limit the flux to 0.2 of the tracer *gradient*
! Why 0.2?
! t=0 t=inf
Expand Down Expand Up @@ -723,7 +733,7 @@ subroutine fluxes_layer_method(boundary, ke, hbl_L, hbl_R, h_L, h_R, phi_L, phi_
! thicknesses at velocity points & khtr_u at layer centers
do k = 1,ke
h_vel(k) = harmonic_mean(h_L(k), h_R(k))
! GMM, writting 0.5 * (A(k) + A(k+1)) as A(k) + 0.5 * (A(k+1) - A(k)) to recover
! GMM, writing 0.5 * (A(k) + A(k+1)) as A(k) + 0.5 * (A(k+1) - A(k)) to recover
! answers with depth-independent khtr
khtr_ul(k) = khtr_u(k) + 0.5 * (khtr_u(k+1) - khtr_u(k))
enddo
Expand All @@ -741,7 +751,7 @@ subroutine fluxes_layer_method(boundary, ke, hbl_L, hbl_R, h_L, h_R, phi_L, phi_
k_bot_max = MAX(k_bot_L, k_bot_R)
k_bot_diff = (k_bot_max - k_bot_min)

! tracer flux where the minimum BLD intersets layer
! tracer flux where the minimum BLD intersects layer
if ((CS%linear) .and. (k_bot_diff > 1)) then
! apply linear decay at the base of hbl
do k = k_bot_min,1,-1
Expand Down Expand Up @@ -815,17 +825,17 @@ logical function near_boundary_unit_tests( verbose )
! Local variables
integer, parameter :: nk = 2 ! Number of layers
real, dimension(nk+1) :: eta1 ! Updated interfaces with one extra value [m]
real, dimension(:), allocatable :: h1 ! Upates layer thicknesses [m]
real, dimension(:), allocatable :: h1 ! Updated list of layer thicknesses or other field [m] or [arbitrary]
real, dimension(nk) :: phi_L, phi_R ! Tracer values (left and right column) [conc]
real, dimension(nk) :: h_L, h_R ! Layer thickness (left and right) [m]
real, dimension(nk+1) :: khtr_u ! Horizontal diffusivities at U-point and interfaces[m2 s-1]
real :: hbl_L, hbl_R ! Depth of the boundary layer (left and right) [m]
real, dimension(nk) :: F_layer ! Diffusive flux within each layer at U-point [conc m3 s-1]
character(len=120) :: test_name ! Title of the unit test
integer :: k_top ! Index of cell containing top of boundary
real :: zeta_top ! Nondimension position [nondim]
real :: zeta_top ! Fractional position in the cell of the top [nondim]
integer :: k_bot ! Index of cell containing bottom of boundary
real :: zeta_bot ! Nondimension position [nondim]
real :: zeta_bot ! Fractional position in the cell of the bottom [nondim]
type(hbd_CS), pointer :: CS

allocate(CS)
Expand Down Expand Up @@ -1058,8 +1068,8 @@ logical function test_layer_fluxes(verbose, nk, test_name, F_calc, F_ans)
logical, intent(in) :: verbose !< If true, write results to stdout
character(len=80), intent(in) :: test_name !< Brief description of the unit test
integer, intent(in) :: nk !< Number of layers
real, dimension(nk), intent(in) :: F_calc !< Fluxes of the unitless tracer from the algorithm [s^-1]
real, dimension(nk), intent(in) :: F_ans !< Fluxes of the unitless tracer calculated by hand [s^-1]
real, dimension(nk), intent(in) :: F_calc !< Fluxes or other quantity from the algorithm [arbitrary]
real, dimension(nk), intent(in) :: F_ans !< Expected value calculated by hand [arbitrary]
! Local variables
integer :: k

Expand All @@ -1081,13 +1091,13 @@ end function test_layer_fluxes
logical function test_boundary_k_range(k_top, zeta_top, k_bot, zeta_bot, k_top_ans, zeta_top_ans,&
k_bot_ans, zeta_bot_ans, test_name, verbose)
integer :: k_top !< Index of cell containing top of boundary
real :: zeta_top !< Nondimension position
real :: zeta_top !< Fractional position in the cell of the top boundary [nondim]
integer :: k_bot !< Index of cell containing bottom of boundary
real :: zeta_bot !< Nondimension position
integer :: k_top_ans !< Index of cell containing top of boundary
real :: zeta_top_ans !< Nondimension position
integer :: k_bot_ans !< Index of cell containing bottom of boundary
real :: zeta_bot_ans !< Nondimension position
real :: zeta_bot !< Fractional position in the cell of the bottom boundary [nondim]
integer :: k_top_ans !< Expected index of cell containing top of boundary
real :: zeta_top_ans !< Expected fractional position of the top boundary [nondim]
integer :: k_bot_ans !< Expected index of cell containing bottom of boundary
real :: zeta_bot_ans !< Expected fractional position of the bottom boundary [nondim]
character(len=80) :: test_name !< Name of the unit test
logical :: verbose !< If true always print output

Expand Down
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