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Doxygenize set_diff + read background kinematic viscosity
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@gustavo-marques
gustavo-marques committed May 23, 2018
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Showing 1 changed file with 109 additions and 92 deletions.
201 changes: 109 additions & 92 deletions src/parameterizations/vertical/MOM_set_diffusivity.F90
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Expand Up @@ -45,95 +45,94 @@ module MOM_set_diffusivity
public set_diffusivity_end

type, public :: set_diffusivity_CS ; private
logical :: debug ! If true, write verbose checksums for debugging.

logical :: bulkmixedlayer ! If true, a refined bulk mixed layer is used with
! GV%nk_rho_varies variable density mixed & buffer
! layers.
real :: FluxRi_max ! The flux Richardson number where the stratification is
! large enough that N2 > omega2. The full expression for
! the Flux Richardson number is usually
! FLUX_RI_MAX*N2/(N2+OMEGA2). The default is 0.2.
logical :: bottomdraglaw ! If true, the bottom stress is calculated with a
! drag law c_drag*|u|*u.
logical :: BBL_mixing_as_max ! If true, take the maximum of the diffusivity
! from the BBL mixing and the other diffusivities.
! Otherwise, diffusivities from the BBL_mixing is
! added.
logical :: use_LOTW_BBL_diffusivity ! If true, use simpler/less precise, BBL diffusivity.
logical :: LOTW_BBL_use_omega ! If true, use simpler/less precise, BBL diffusivity.
real :: BBL_effic ! efficiency with which the energy extracted
! by bottom drag drives BBL diffusion (nondim)
real :: cdrag ! quadratic drag coefficient (nondim)
real :: IMax_decay ! inverse of a maximum decay scale for
! bottom-drag driven turbulence, (1/m)

real :: Kd ! interior diapycnal diffusivity (m2/s)
real :: Kd_min ! minimum diapycnal diffusivity (m2/s)
real :: Kd_max ! maximum increment for diapycnal diffusivity (m2/s)
! Set to a negative value to have no limit.
real :: Kd_add ! uniform diffusivity added everywhere without
! filtering or scaling (m2/s)
real :: Kv ! interior vertical viscosity (m2/s)
real :: Kdml ! mixed layer diapycnal diffusivity (m2/s)
! when bulkmixedlayer==.false.
real :: Hmix ! mixed layer thickness (meter) when
! bulkmixedlayer==.false.
logical :: debug !< If true, write verbose checksums for debugging.

logical :: bulkmixedlayer !< If true, a refined bulk mixed layer is used with
!! GV%nk_rho_varies variable density mixed & buffer
!! layers.
real :: FluxRi_max !< The flux Richardson number where the stratification is
!! large enough that N2 > omega2. The full expression for
!! the Flux Richardson number is usually
!! FLUX_RI_MAX*N2/(N2+OMEGA2). The default is 0.2.
logical :: bottomdraglaw !< If true, the bottom stress is calculated with a
!! drag law c_drag*|u|*u.
logical :: BBL_mixing_as_max !< If true, take the maximum of the diffusivity
!! from the BBL mixing and the other diffusivities.
!! Otherwise, diffusivities from the BBL_mixing is
!! added.
logical :: use_LOTW_BBL_diffusivity !< If true, use simpler/less precise, BBL diffusivity.
logical :: LOTW_BBL_use_omega !< If true, use simpler/less precise, BBL diffusivity.
real :: BBL_effic !< efficiency with which the energy extracted
!! by bottom drag drives BBL diffusion (nondim)
real :: cdrag !< quadratic drag coefficient (nondim)
real :: IMax_decay !< inverse of a maximum decay scale for
!! bottom-drag driven turbulence, (1/m)
real :: Kv !< The interior vertical viscosity (m2/s)
real :: Kd !< interior diapycnal diffusivity (m2/s)
real :: Kd_min !< minimum diapycnal diffusivity (m2/s)
real :: Kd_max !< maximum increment for diapycnal diffusivity (m2/s)
!! Set to a negative value to have no limit.
real :: Kd_add !< uniform diffusivity added everywhere without
!! filtering or scaling (m2/s)
real :: Kdml !< mixed layer diapycnal diffusivity (m2/s)
!! when bulkmixedlayer==.false.
real :: Hmix !< mixed layer thickness (meter) when
!! bulkmixedlayer==.false.
type(diag_ctrl), pointer :: diag ! structure to regulate diagn output timing

logical :: limit_dissipation ! If enabled, dissipation is limited to be larger
! than the following:
real :: dissip_min ! Minimum dissipation (W/m3)
real :: dissip_N0 ! Coefficient a in minimum dissipation = a+b*N (W/m3)
real :: dissip_N1 ! Coefficient b in minimum dissipation = a+b*N (J/m3)
real :: dissip_N2 ! Coefficient c in minimum dissipation = c*N2 (W m-3 s2)
real :: dissip_Kd_min ! Minimum Kd (m2/s) with dissipatio Rho0*Kd_min*N^2

real :: TKE_itide_max ! maximum internal tide conversion (W m-2)
! available to mix above the BBL
real :: omega ! Earth's rotation frequency (s-1)
logical :: ML_radiation ! allow a fraction of TKE available from wind work
! to penetrate below mixed layer base with a vertical
! decay scale determined by the minimum of
! (1) The depth of the mixed layer, or
! (2) An Ekman length scale.
! Energy availble to drive mixing below the mixed layer is
! given by E = ML_RAD_COEFF*MSTAR*USTAR**3. Optionally, if
! ML_rad_TKE_decay is true, this is further reduced by a factor
! of exp(-h_ML*Idecay_len_TkE), where Idecay_len_TKE is
! calculated the same way as in the mixed layer code.
! The diapycnal diffusivity is KD(k) = E/(N2(k)+OMEGA2),
! where N2 is the squared buoyancy frequency (s-2) and OMEGA2
! is the rotation rate of the earth squared.
real :: ML_rad_kd_max ! Maximum diapycnal diffusivity due to turbulence
! radiated from the base of the mixed layer (m2/s)
real :: ML_rad_efold_coeff ! non-dim coefficient to scale penetration depth
real :: ML_rad_coeff ! coefficient, which scales MSTAR*USTAR^3 to
! obtain energy available for mixing below
! mixed layer base (nondimensional)
logical :: ML_rad_TKE_decay ! If true, apply same exponential decay
! to ML_rad as applied to the other surface
! sources of TKE in the mixed layer code.
real :: ustar_min ! A minimum value of ustar to avoid numerical
! problems (m/s). If the value is small enough,
! this parameter should not affect the solution.
real :: TKE_decay ! ratio of natural Ekman depth to TKE decay scale (nondim)
real :: mstar ! ratio of friction velocity cubed to
! TKE input to the mixed layer (nondim)
logical :: ML_use_omega ! If true, use absolute rotation rate instead
! of the vertical component of rotation when
! setting the decay scale for mixed layer turbulence.
real :: ML_omega_frac ! When setting the decay scale for turbulence, use
! this fraction of the absolute rotation rate blended
! with the local value of f, as f^2 ~= (1-of)*f^2 + of*4*omega^2.
logical :: user_change_diff ! If true, call user-defined code to change diffusivity.
logical :: useKappaShear ! If true, use the kappa_shear module to find the
! shear-driven diapycnal diffusivity.
logical :: use_CVMix_shear ! If true, use one of the CVMix modules to find
! shear-driven diapycnal diffusivity.
logical :: use_CVMix_ddiff ! If true, enable double-diffusive mixing via CVMix.
logical :: simple_TKE_to_Kd ! If true, uses a simple estimate of Kd/TKE that
! does not rely on a layer-formulation.
logical :: limit_dissipation !< If enabled, dissipation is limited to be larger
!! than the following:
real :: dissip_min !< Minimum dissipation (W/m3)
real :: dissip_N0 !< Coefficient a in minimum dissipation = a+b*N (W/m3)
real :: dissip_N1 !< Coefficient b in minimum dissipation = a+b*N (J/m3)
real :: dissip_N2 !< Coefficient c in minimum dissipation = c*N2 (W m-3 s2)
real :: dissip_Kd_min !< Minimum Kd (m2/s) with dissipatio Rho0*Kd_min*N^2

real :: TKE_itide_max !< maximum internal tide conversion (W m-2)
!! available to mix above the BBL
real :: omega !< Earth's rotation frequency (s-1)
logical :: ML_radiation !< allow a fraction of TKE available from wind work
!! to penetrate below mixed layer base with a vertical
!! decay scale determined by the minimum of
!! (1) The depth of the mixed layer, or
!! (2) An Ekman length scale.
!! Energy availble to drive mixing below the mixed layer is
!! given by E = ML_RAD_COEFF*MSTAR*USTAR**3. Optionally, if
!! ML_rad_TKE_decay is true, this is further reduced by a factor
!! of exp(-h_ML*Idecay_len_TkE), where Idecay_len_TKE is
!! calculated the same way as in the mixed layer code.
!! The diapycnal diffusivity is KD(k) = E/(N2(k)+OMEGA2),
!! where N2 is the squared buoyancy frequency (s-2) and OMEGA2
!! is the rotation rate of the earth squared.
real :: ML_rad_kd_max !< Maximum diapycnal diffusivity due to turbulence
!! radiated from the base of the mixed layer (m2/s)
real :: ML_rad_efold_coeff !< non-dim coefficient to scale penetration depth
real :: ML_rad_coeff !< coefficient, which scales MSTAR*USTAR^3 to
!! obtain energy available for mixing below
!! mixed layer base (nondimensional)
logical :: ML_rad_TKE_decay !< If true, apply same exponential decay
!! to ML_rad as applied to the other surface
!! sources of TKE in the mixed layer code.
real :: ustar_min !< A minimum value of ustar to avoid numerical
!! problems (m/s). If the value is small enough,
!! this parameter should not affect the solution.
real :: TKE_decay !< ratio of natural Ekman depth to TKE decay scale (nondim)
real :: mstar !! ratio of friction velocity cubed to
!! TKE input to the mixed layer (nondim)
logical :: ML_use_omega !< If true, use absolute rotation rate instead
!! of the vertical component of rotation when
!! setting the decay scale for mixed layer turbulence.
real :: ML_omega_frac !< When setting the decay scale for turbulence, use
!! this fraction of the absolute rotation rate blended
!! with the local value of f, as f^2 ~= (1-of)*f^2 + of*4*omega^2.
logical :: user_change_diff !< If true, call user-defined code to change diffusivity.
logical :: useKappaShear !< If true, use the kappa_shear module to find the
!! shear-driven diapycnal diffusivity.
logical :: use_CVMix_shear !< If true, use one of the CVMix modules to find
!! shear-driven diapycnal diffusivity.
logical :: use_CVMix_ddiff !< If true, enable double-diffusive mixing via CVMix.
logical :: simple_TKE_to_Kd !< If true, uses a simple estimate of Kd/TKE that
!! does not rely on a layer-formulation.

character(len=200) :: inputdir
type(user_change_diff_CS), pointer :: user_change_diff_CSp => NULL()
Expand Down Expand Up @@ -177,6 +176,17 @@ module MOM_set_diffusivity

contains

!> Sets the interior vertical diffusion of scalars due to the following processes:
!! 1) Shear-driven mixing: two options, Jackson et at. and KPP interior;
!! 2) Background mixing via CVMix (Bryan-Lewis profile) or the scheme described by
!! Harrison & Hallberg, JPO 2008;
!! 3) Double-diffusion aplpied via CVMix;
!! 4) Tidal mixing: many options available, see MOM_tidal_mixing.F90;
!! In addition, this subroutine has the option to set the interior vertical
!! viscosity associated with processes 2-4 listed above, which is stored in
!! visc%Kv_slow. Vertical viscosity due to shear-driven mixing is passed via
!! visc%Kv_shear
!! GMM, TODO: add contribution from tidal mixing into visc%Kv_slow
subroutine set_diffusivity(u, v, h, u_h, v_h, tv, fluxes, optics, visc, dt, &
G, GV, CS, Kd, Kd_int)
type(ocean_grid_type), intent(in) :: G !< The ocean's grid structure.
Expand All @@ -188,9 +198,9 @@ subroutine set_diffusivity(u, v, h, u_h, v_h, tv, fluxes, optics, visc, dt, &
real, dimension(SZI_(G),SZJ_(G),SZK_(G)), &
intent(in) :: h !< Layer thicknesses, in H (usually m or kg m-2).
real, dimension(SZI_(G),SZJ_(G),SZK_(G)), &
intent(in) :: u_h
intent(in) :: u_h !< zonal thickness transport m^2/s.
real, dimension(SZI_(G),SZJ_(G),SZK_(G)), &
intent(in) :: v_h
intent(in) :: v_h !< meridional thickness transport m^2/s.
type(thermo_var_ptrs), intent(inout) :: tv !< Structure with pointers to thermodynamic
!! fields. Out is for tv%TempxPmE.
type(forcing), intent(in) :: fluxes !< Structure of surface fluxes that may be
Expand Down Expand Up @@ -270,7 +280,7 @@ subroutine set_diffusivity(u, v, h, u_h, v_h, tv, fluxes, optics, visc, dt, &
! If nothing else is specified, this will be the value used.
Kd(:,:,:) = CS%Kd
Kd_int(:,:,:) = CS%Kd
visc%Kv_slow(:,:,:) = CS%Kv
if (associated(visc%Kv_slow)) visc%Kv_slow(:,:,:) = CS%Kv

! Set up arrays for diagnostics.

Expand Down Expand Up @@ -331,6 +341,10 @@ subroutine set_diffusivity(u, v, h, u_h, v_h, tv, fluxes, optics, visc, dt, &
elseif (CS%use_CVMix_shear) then
!NOTE{BGR}: this needs to be cleaned up. It works in 1D case, but has not been tested outside.
call calculate_CVMix_shear(u_h, v_h, h, tv, visc%Kd_shear, visc%Kv_shear,G,GV,CS%CVMix_shear_csp)
if (CS%debug) then
call hchksum(visc%Kd_shear, "after CVMix_shear visc%Kd_shear",G%HI)
call hchksum(visc%Kv_shear, "after CVMix_shear visc%Kv_shear",G%HI)
endif
elseif (associated(visc%Kv_shear)) then
visc%Kv_shear(:,:,:) = 0. ! needed if calculate_kappa_shear is not enabled
endif
Expand All @@ -342,8 +356,6 @@ subroutine set_diffusivity(u, v, h, u_h, v_h, tv, fluxes, optics, visc, dt, &
! set surface diffusivities (CS%bkgnd_mixing_csp%Kd_sfc)
call sfc_bkgnd_mixing(G, CS%bkgnd_mixing_csp)

! GMM, fix OMP calls below

!$OMP parallel do default(none) shared(is,ie,js,je,nz,G,GV,CS,h,tv,T_f,S_f,fluxes,dd, &
!$OMP Kd,visc, &
!$OMP Kd_int,dt,u,v,Omega2) &
Expand Down Expand Up @@ -1826,6 +1838,11 @@ subroutine set_diffusivity_init(Time, G, GV, param_file, diag, CS, diag_to_Z_CSp
! set params releted to the background mixing
call bkgnd_mixing_init(Time, G, GV, param_file, CS%diag, CS%bkgnd_mixing_csp)

call get_param(param_file, mdl, "KV", CS%Kv, &
"The background kinematic viscosity in the interior. \n"//&
"The molecular value, ~1e-6 m2 s-1, may be used.", &
units="m2 s-1", fail_if_missing=.true.)

call get_param(param_file, mdl, "KD", CS%Kd, &
"The background diapycnal diffusivity of density in the \n"//&
"interior. Zero or the molecular value, ~1e-7 m2 s-1, \n"//&
Expand Down

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