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marshallward merged 2 commits into from
Nov 25, 2022
Merged

Better document parameter units in 4 user modules #241

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Better document parameter units in 4 user modules
Hallberg-NOAA Nov 15, 2022
b8c044d
Merge branch 'dev/gfdl' into user_module_units
marshallward Nov 25, 2022
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80 changes: 47 additions & 33 deletions src/user/DOME2d_initialization.F90
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Expand Up @@ -45,9 +45,13 @@ subroutine DOME2d_initialize_topography( D, G, param_file, max_depth )
real, intent(in) :: max_depth !< Maximum ocean depth in arbitrary units

! Local variables
real :: bay_depth ! Depth of shelf, as fraction of basin depth [nondim]
real :: l1, l2 ! Fractional horizontal positions where the slope changes [nondim]
real :: x ! Fractional horizontal positions [nondim]
real :: dome2d_width_bay ! Width of shelf, as fraction of domain [nondim]
real :: dome2d_width_bottom ! Width of deep ocean basin, as fraction of domain [nondim]
real :: dome2d_depth_bay ! Depth of shelf, as fraction of basin depth [nondim]
integer :: i, j
real :: x, bay_depth, l1, l2
real :: dome2d_width_bay, dome2d_width_bottom, dome2d_depth_bay
! This include declares and sets the variable "version".
# include "version_variable.h"

Expand Down Expand Up @@ -106,28 +110,30 @@ subroutine DOME2d_initialize_thickness ( h, depth_tot, G, GV, US, param_file, ju
real :: e0(SZK_(GV)) ! The resting interface heights, in depth units [Z ~> m], usually
! negative because it is positive upward.
real :: eta1D(SZK_(GV)+1)! Interface height relative to the sea surface
! positive upward, in depth units [Z ~> m].
integer :: i, j, k, is, ie, js, je, nz
real :: x
real :: min_thickness
real :: dome2d_width_bay, dome2d_width_bottom, dome2d_depth_bay
! positive upward, in depth units [Z ~> m]
real :: x ! Fractional horizontal positions [nondim]
real :: min_thickness ! Minimum layer thicknesses [Z ~> m]
real :: dome2d_width_bay ! Width of shelf, as fraction of domain [nondim]
real :: dome2d_width_bottom ! Width of deep ocean basin, as fraction of domain [nondim]
real :: dome2d_depth_bay ! Depth of shelf, as fraction of basin depth [nondim]
character(len=40) :: verticalCoordinate
integer :: i, j, k, is, ie, js, je, nz

is = G%isc ; ie = G%iec ; js = G%jsc ; je = G%jec ; nz = GV%ke

if (.not.just_read) &
call MOM_mesg("MOM_initialization.F90, DOME2d_initialize_thickness: setting thickness")

call get_param(param_file, mdl,"MIN_THICKNESS",min_thickness, &
call get_param(param_file, mdl,"MIN_THICKNESS", min_thickness, &
default=1.e-3, units="m", do_not_log=.true., scale=US%m_to_Z)
call get_param(param_file, mdl,"REGRIDDING_COORDINATE_MODE", verticalCoordinate, &
default=DEFAULT_COORDINATE_MODE, do_not_log=.true.)
call get_param(param_file, mdl, "DOME2D_SHELF_WIDTH", dome2d_width_bay, &
default=0.1, do_not_log=.true.)
units="nondim", default=0.1, do_not_log=.true.)
call get_param(param_file, mdl, "DOME2D_BASIN_WIDTH", dome2d_width_bottom, &
default=0.3, do_not_log=.true.)
units="nondim", default=0.3, do_not_log=.true.)
call get_param(param_file, mdl, "DOME2D_SHELF_DEPTH", dome2d_depth_bay, &
default=0.2, do_not_log=.true.)
units="nondim", default=0.2, do_not_log=.true.)

if (just_read) return ! All run-time parameters have been read, so return.

Expand Down Expand Up @@ -229,28 +235,30 @@ subroutine DOME2d_initialize_temperature_salinity ( T, S, h, G, GV, US, param_fi
logical, intent(in) :: just_read !< If true, this call will
!! only read parameters without changing T & S.

integer :: i, j, k, is, ie, js, je, nz
real :: x
integer :: index_bay_z
real :: delta_S
real :: S_ref, T_ref ! Reference salinity [S ~> ppt] and temperature [C ~> degC] within surface layer
real :: S_range, T_range ! Range of salinities [S ~> ppt] and temperatures [C ~> degC] over the vertical
real :: xi0, xi1
real :: x ! Fractional horizontal positions [nondim]
real :: delta_S ! Change in salinity between layers [S ~> ppt]
real :: S_ref, T_ref ! Reference salinity [S ~> ppt] and temperature [C ~> degC] within surface layer
real :: S_range, T_range ! Range of salinities [S ~> ppt] and temperatures [C ~> degC] over the vertical
real :: xi0, xi1 ! Fractional vertical positions [nondim]
real :: dome2d_width_bay ! Width of shelf, as fraction of domain [nondim]
real :: dome2d_width_bottom ! Width of deep ocean basin, as fraction of domain [nondim]
real :: dome2d_depth_bay ! Depth of shelf, as fraction of basin depth [nondim]
character(len=40) :: verticalCoordinate
real :: dome2d_width_bay, dome2d_width_bottom, dome2d_depth_bay
integer :: index_bay_z
integer :: i, j, k, is, ie, js, je, nz

is = G%isc ; ie = G%iec ; js = G%jsc ; je = G%jec ; nz = GV%ke

call get_param(param_file, mdl, "REGRIDDING_COORDINATE_MODE", verticalCoordinate, &
default=DEFAULT_COORDINATE_MODE, do_not_log=.true.)
call get_param(param_file, mdl, "DOME2D_SHELF_WIDTH", dome2d_width_bay, &
default=0.1, do_not_log=.true.)
units="nondim", default=0.1, do_not_log=.true.)
call get_param(param_file, mdl, "DOME2D_BASIN_WIDTH", dome2d_width_bottom, &
default=0.3, do_not_log=.true.)
units="nondim", default=0.3, do_not_log=.true.)
call get_param(param_file, mdl, "DOME2D_SHELF_DEPTH", dome2d_depth_bay, &
default=0.2, do_not_log=.true.)
units="nondim", default=0.2, do_not_log=.true.)
call get_param(param_file, mdl, "S_REF", S_ref, 'Reference salinity', &
default=35.0, units='1e-3', scale=US%ppt_to_S, do_not_log=just_read)
units='1e-3', default=35.0, scale=US%ppt_to_S, do_not_log=just_read)
call get_param(param_file, mdl, "T_REF", T_ref, 'Reference temperature', &
units='degC', scale=US%degC_to_C, fail_if_missing=.not.just_read, do_not_log=just_read)
call get_param(param_file, mdl, "S_RANGE", S_range,' Initial salinity range', &
Expand Down Expand Up @@ -370,10 +378,16 @@ subroutine DOME2d_initialize_sponges(G, GV, US, tv, depth_tot, param_file, use_A
real :: eta1D(SZK_(GV)+1) ! Interface height relative to the sea surface
! positive upward [Z ~> m].
real :: d_eta(SZK_(GV)) ! The layer thickness in a column [Z ~> m].
real :: dome2d_width_bay, dome2d_width_bottom, dome2d_depth_bay
real :: dome2d_width_bay ! Width of shelf, as fraction of domain [nondim]
real :: dome2d_width_bottom ! Width of deep ocean basin, as fraction of domain [nondim]
real :: dome2d_depth_bay ! Depth of shelf, as fraction of basin depth [nondim]
real :: dome2d_west_sponge_time_scale, dome2d_east_sponge_time_scale ! Sponge timescales [T ~> s]
real :: dome2d_west_sponge_width, dome2d_east_sponge_width
real :: dummy1, x, z
real :: dome2d_west_sponge_width ! The fraction of the domain in which the western sponge for
! restoring T/S is active [nondim]
real :: dome2d_east_sponge_width ! The fraction of the domain in which the eastern sponge for
! restoring T/S is active [nondim]
real :: dummy1, x ! Nondimensional local variables indicating horizontal positions [nondim]
real :: z ! Vertical positions [Z ~> m]
integer :: i, j, k, is, ie, js, je, isd, ied, jsd, jed, nz

is = G%isc ; ie = G%iec ; js = G%jsc ; je = G%jec ; nz = GV%ke
Expand Down Expand Up @@ -405,15 +419,15 @@ subroutine DOME2d_initialize_sponges(G, GV, US, tv, depth_tot, param_file, use_A
"DOME2d_initialize_sponges called with an associated ALE-sponge control structure.")

call get_param(param_file, mdl, "DOME2D_SHELF_WIDTH", dome2d_width_bay, &
default=0.1, do_not_log=.true.)
units="nondim", default=0.1, do_not_log=.true.)
call get_param(param_file, mdl, "DOME2D_BASIN_WIDTH", dome2d_width_bottom, &
default=0.3, do_not_log=.true.)
units="nondim", default=0.3, do_not_log=.true.)
call get_param(param_file, mdl, "DOME2D_SHELF_DEPTH", dome2d_depth_bay, &
default=0.2, do_not_log=.true.)
call get_param(param_file, mdl, "S_REF", S_ref, default=35.0, scale=US%ppt_to_S)
call get_param(param_file, mdl, "T_REF", T_ref, scale=US%degC_to_C, fail_if_missing=.false.)
call get_param(param_file, mdl, "S_RANGE", S_range, default=2.0, scale=US%ppt_to_S)
call get_param(param_file, mdl, "T_RANGE", T_range, default=0.0, scale=US%degC_to_C)
units="nondim", default=0.2, do_not_log=.true.)
call get_param(param_file, mdl, "S_REF", S_ref, units="ppt", default=35.0, scale=US%ppt_to_S)
call get_param(param_file, mdl, "T_REF", T_ref, units="degC", scale=US%degC_to_C, fail_if_missing=.false.)
call get_param(param_file, mdl, "S_RANGE", S_range, units="ppt", default=2.0, scale=US%ppt_to_S)
call get_param(param_file, mdl, "T_RANGE", T_range, units="degC", default=0.0, scale=US%degC_to_C)


! Set the sponge damping rate as a function of position
Expand Down
16 changes: 8 additions & 8 deletions src/user/ISOMIP_initialization.F90
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Expand Up @@ -478,22 +478,22 @@ subroutine ISOMIP_initialize_sponges(G, GV, US, tv, depth_tot, PF, use_ALE, CSp,
call get_param(PF, mdl, "REGRIDDING_COORDINATE_MODE", verticalCoordinate, &
default=DEFAULT_COORDINATE_MODE)

call get_param(PF, mdl, "ISOMIP_TNUDG", TNUDG, "Nudging time scale for sponge layers (days)", &
default=0.0, scale=86400.0*US%s_to_T)
call get_param(PF, mdl, "ISOMIP_TNUDG", TNUDG, "Nudging time scale for sponge layers", &
units="days", default=0.0, scale=86400.0*US%s_to_T)

call get_param(PF, mdl, "T_REF", t_ref, "Reference temperature", default=10.0, &
do_not_log=.true.)
call get_param(PF, mdl, "T_REF", t_ref, "Reference temperature", &
units="degC", default=10.0, scale=1.0, do_not_log=.true.)

call get_param(PF, mdl, "S_REF", s_ref, "Reference salinity", default=35.0, &
do_not_log=.true.)
call get_param(PF, mdl, "S_REF", s_ref, "Reference salinity", &
units="ppt", default=35.0, scale=1.0, do_not_log=.true.)

call get_param(PF, mdl, "ISOMIP_S_SUR_SPONGE", s_sur, &
"Surface salinity in sponge layer.", &
units="ppt", default=s_ref, scale=US%ppt_to_S) ! units="ppt")
units="ppt", default=s_ref, scale=US%ppt_to_S)

call get_param(PF, mdl, "ISOMIP_S_BOT_SPONGE", s_bot, &
"Bottom salinity in sponge layer.", &
units="ppt", default=s_ref, scale=US%ppt_to_S) ! units="ppt")
units="ppt", default=s_ref, scale=US%ppt_to_S)

call get_param(PF, mdl, "ISOMIP_T_SUR_SPONGE", t_sur, &
"Surface temperature in sponge layer.", &
Expand Down
12 changes: 6 additions & 6 deletions src/user/Kelvin_initialization.F90
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Expand Up @@ -92,11 +92,11 @@ function register_Kelvin_OBC(param_file, CS, US, OBC_Reg)
endif
if (CS%mode /= 0) then
call get_param(param_file, mdl, "DENSITY_RANGE", CS%rho_range, &
default=2.0, do_not_log=.true., scale=US%kg_m3_to_R)
units="kg m-3", default=2.0, scale=US%kg_m3_to_R, do_not_log=.true.)
call get_param(param_file, mdl, "RHO_0", CS%rho_0, &
default=1035.0, do_not_log=.true., scale=US%kg_m3_to_R)
units="kg m-3", default=1035.0, scale=US%kg_m3_to_R, do_not_log=.true.)
call get_param(param_file, mdl, "MAXIMUM_DEPTH", CS%H0, &
default=1000.0, do_not_log=.true., scale=US%m_to_Z)
units="m", default=1000.0, scale=US%m_to_Z, do_not_log=.true.)
endif

! Register the Kelvin open boundary.
Expand Down Expand Up @@ -135,11 +135,11 @@ subroutine Kelvin_initialize_topography(D, G, param_file, max_depth, US)
call get_param(param_file, mdl, "MINIMUM_DEPTH", min_depth, &
"The minimum depth of the ocean.", units="m", default=0.0, scale=US%m_to_Z)
call get_param(param_file, mdl, "ROTATED_COAST_OFFSET_1", coast_offset1, &
default=100.0, do_not_log=.true.)
units="km", default=100.0, do_not_log=.true.)
call get_param(param_file, mdl, "ROTATED_COAST_OFFSET_2", coast_offset2, &
default=10.0, do_not_log=.true.)
units="km", default=10.0, do_not_log=.true.)
call get_param(param_file, mdl, "ROTATED_COAST_ANGLE", coast_angle, &
default=11.3, do_not_log=.true.)
units="degrees", default=11.3, do_not_log=.true.)

coast_angle = coast_angle * (atan(1.0)/45.) ! Convert to radians
right_angle = 2 * atan(1.0)
Expand Down
34 changes: 24 additions & 10 deletions src/user/seamount_initialization.F90
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Expand Up @@ -128,7 +128,8 @@ subroutine seamount_initialize_thickness (h, depth_tot, G, GV, US, param_file, j
units="ppt", default=34., scale=US%ppt_to_S, do_not_log=.true.)
call get_param(param_file, mdl,"INITIAL_S_RANGE", S_range, &
units="ppt", default=2., scale=US%ppt_to_S, do_not_log=.true.)
call get_param(param_file, mdl, "S_REF", S_ref, default=35.0, do_not_log=.true.)
call get_param(param_file, mdl, "S_REF", S_ref, &
units="ppt", default=35.0, scale=1.0, do_not_log=.true.)
call get_param(param_file, mdl, "TS_RANGE_S_LIGHT", S_light, &
units="ppt", default=S_Ref, scale=US%ppt_to_S, do_not_log=.true.)
call get_param(param_file, mdl, "TS_RANGE_S_DENSE", S_dense, &
Expand Down Expand Up @@ -205,9 +206,19 @@ subroutine seamount_initialize_temperature_salinity(T, S, h, G, GV, US, param_fi
!! only read parameters without changing T & S.

! Local variables
real :: xi0, xi1 ! Fractional positions within the depth range [nondim]
real :: r ! A nondimensional sharpness parameter with an exponetial profile [nondim]
real :: S_Ref ! Default salinity range parameters [ppt].
real :: T_Ref ! Default temperature range parameters [degC].
real :: S_Light, S_Dense, S_surf, S_range ! Salinity range parameters [S ~> ppt].
real :: T_Light, T_Dense, T_surf, T_range ! Temperature range parameters [C ~> degC].
real :: res_rat ! The ratio of density space resolution in the denser part
! of the range to that in the lighter part of the range.
! Setting this greater than 1 increases the resolution for
! the denser water [nondim].
real :: a1, frac_dense, k_frac ! Nondimensional temporary variables [nondim]
integer :: i, j, k, is, ie, js, je, nz, k_light
real :: xi0, xi1, r, S_surf, T_surf, S_range, T_range
real :: T_ref, T_Light, T_Dense, S_ref, S_Light, S_Dense, a1, frac_dense, k_frac, res_rat

character(len=20) :: verticalCoordinate, density_profile

is = G%isc ; ie = G%iec ; js = G%jsc ; je = G%jec ; nz = GV%ke
Expand All @@ -233,17 +244,20 @@ subroutine seamount_initialize_temperature_salinity(T, S, h, G, GV, US, param_fi
select case ( coordinateMode(verticalCoordinate) )
case ( REGRIDDING_LAYER ) ! Initial thicknesses for layer isopycnal coordinates
! These parameters are used in MOM_fixed_initialization.F90 when CONFIG_COORD="ts_range"
call get_param(param_file, mdl, "T_REF", T_ref, default=10.0, do_not_log=.true.)
call get_param(param_file, mdl, "T_REF", T_ref, &
units="degC", default=10.0, do_not_log=.true.)
call get_param(param_file, mdl, "TS_RANGE_T_LIGHT", T_light, &
default=T_Ref, scale=US%degC_to_C, do_not_log=.true.)
units="degC", default=T_Ref, scale=US%degC_to_C, do_not_log=.true.)
call get_param(param_file, mdl, "TS_RANGE_T_DENSE", T_dense, &
default=T_Ref, scale=US%degC_to_C, do_not_log=.true.)
call get_param(param_file, mdl, "S_REF", S_ref, default=35.0, do_not_log=.true.)
units="degC", default=T_Ref, scale=US%degC_to_C, do_not_log=.true.)
call get_param(param_file, mdl, "S_REF", S_ref, &
units="1e-3", default=35.0, scale=1.0, do_not_log=.true.)
call get_param(param_file, mdl, "TS_RANGE_S_LIGHT", S_light, &
default = S_Ref, scale=US%ppt_to_S, do_not_log=.true.)
units="1e-3", default=S_Ref, scale=US%ppt_to_S, do_not_log=.true.)
call get_param(param_file, mdl, "TS_RANGE_S_DENSE", S_dense, &
default = S_Ref, scale=US%ppt_to_S, do_not_log=.true.)
call get_param(param_file, mdl, "TS_RANGE_RESOLN_RATIO", res_rat, default=1.0, do_not_log=.true.)
units="1e-3", default=S_Ref, scale=US%ppt_to_S, do_not_log=.true.)
call get_param(param_file, mdl, "TS_RANGE_RESOLN_RATIO", res_rat, &
units="nondim", default=1.0, do_not_log=.true.)
if (just_read) return ! All run-time parameters have been read, so return.

! Emulate the T,S used in the "ts_range" coordinate configuration code
Expand Down