Vertical Mixing Parameterizations
ROMS contains a variety of methods for setting the vertical viscous and diffusive coefficients. The choices range from simply choosing fixed values to the KPP, generic lengthscale (GLS) and MellorYamada turbulence closure schemes. See Large (1998) for a review of surface ocean mixing schemes. Many schemes have a background molecular value which is used when the turbulent processes are assumed to be small (such as in the interior).
KProfile Parameterization
The vertical mixing parameterization introduced by Large, McWilliams and Doney (1994) is a versatile first order scheme which has been shown to perform well in open ocean settings. Its design facilitates experimentation with additional or modified representations of specific turbulent processes.
Surface boundary layer
The Large, McWilliams and Doney scheme (LMD) matches separate parameterizations for vertical mixing of the surface boundary layer and the ocean interior. A formulation based on boundary layer similarity theory is applied in the water column above a calculated boundary layer depth . This parameterization is then matched at the interior with schemes to account for local shear, internal wave and double diffusive mixing effects.
Viscosity and diffusivities at model levels above a calculated surface boundary layer depth ( ) are expressed as the product of the length scale , a turbulent velocity scale and a nondimensional shape function.
(1) 
where is a nondimensional coordinate ranging from 0 to 1 indicating depth within the surface boundary layer. The subscript stands for one of momentum, temperature and salinity.
Surface Boundary layer depth
The boundary layer depth is calculated as the minimum of the Ekman depth, estimated as,
(2) 
(where is the friction velocity ), the MoninObukhov depth:
(3) 
(where is von Karman's contant and is the surface buoyancy flux), and the shallowest depth at which a critical bulk Richardson number is reached. The critical bulk Richardson number () is typically in the range 0.250.5. The bulk Richardson number () is calculated as:
(4) 
where is distance down from the surface, is the buoyancy, is the buoyancy at a near surface reference depth, is the mean horizontal velocity, the velocity at the near surface reference depth and is an estimate of the turbulent velocity contribution to velocity shear.
The turbulent velocity shear term in this equation is given by LMD as,
(5) 
where is the ratio of interior to at the entrainment depth, is ratio of entrainment flux to surface buoyancy flux, and are constants, and is the turbulent velocity scale for scalars. LMD derive (5) based on the expected behavior in the pure convective limit. The empirical rule of convection states that the ratio of the surface buoyancy flux to that at the entrainment depth be a constant. Thus the entrainment flux at the bottom of the boundary layer under such conditions should be independent of the stratification at that depth. Without a turbulent shear term in the denominator of the bulk Richardson number calculation, the estimated boundary layer depth is too shallow and the diffusivity at the entrainment depth is too low to obtain the necessary entrainment flux. Thus by adding a turbulent shear term proportional to the stratification in the denominator, the calculated boundary layer depth will be deeper and will lead to a high enough diffusivity to satisfy the empirical rule of convection.
Turbulent velocity scale
To estimate (where is  momentum or  any scalar) throughout the boundary layer, surface layer similarity theory is utilized. Following an argument by Troen and Mahrt (1986), Large et al. estimate the velocity scale as
(6) 
where is the surface layer stability parameter defined as . is a nondimensional flux profile which varies based on the stability of the boundary layer forcing. The stability parameter used in this equation is assumed to vary over the entire depth of the boundary layer in stable and neutral conditions. In unstable conditions it is assumed only to vary through the surface layer which is defined as (where is set at 0.10) . Beyond this depth is set equal to its value at .
The flux profiles are expressed as analytical fits to atmospheric surface boundary layer data. In stable conditions they vary linearly with the stability parameter as
(7) 
In nearneutral unstable conditions common BusingerDyer forms are used which match with the formulation for stable conditions at . Near neutral conditions are defined as
for momentum and,
for scalars. The non dimensional flux profiles in this regime are,
(8) 
In more unstable conditions is chosen to match the BusingerDyer forms and with the free convective limit. Here the flux profiles are
(9) 
The shape function
The nondimensional shape function is a third order polynomial with coefficients chosen to match the interior viscosity at the bottom of the boundary layer and MoninObukhov similarity theory approaching the surface. This function is defined as a 3rd order polynomial.
(10) 
with the coefficients specified to match surface boundary conditions and to smoothly blend with the interior,
(11) 
where is the viscosity calculated by the interior parameterization at the boundary layer depth.
Countergradient flux term
The second term of the LMD scheme's surface boundary layer formulation is the nonlocal transport term which can play a significant role in mixing during surface cooling events. This is a redistribution term included in the tracer equation separate from the diffusion term and is written as
(12) 
LMD base their formulation for nonlocal scalar transport on a parameterization for pure free convection from Mailhôt and Benoit (1982). They extend this parameterization to cover any unstable surface forcing conditions to give
(13) 
for temperature and
(14) 
for salinity (other scalar quantities with surface fluxes can be treated similarly). LMD argue that although there is evidence of nonlocal transport of momentum as well, the form the term would take is unclear so they simply specify .
The interior scheme
The interior scheme of Large, McWilliams and Doney estimates the viscosity coefficient by adding the effects of several generating mechanisms: shear mixing, doublediffusive mixing and internal wave generated mixing.
(15) 
Shear generated mixing
The shear mixing term is calculated using a gradient Richardson number formulation, with viscosity estimated as:
(16) 
where is , .
Double diffusive processes
The second component of the interior mixing parameterization represents double diffusive mixing. From limited sources of laboratory and field data LMD parameterize the salt fingering case ()
(17) 
For diffusive convection () LMD suggest several formulations from the literature and choose the one with the most significant impact on mixing (Fedorov 1988).
(18) 
for temperature. For other scalars,
!\eqno{(19)}>

(19) 
Internal wave generated mixing
Internal wave generated mixing serves as the background mixing in the LMD scheme. It is specified as a constant for both scalars and momentum. Eddy diffusivity is estimated based on the data of Ledwell et al. (1993), while Peters et al. (1988) suggest eddy viscosity should be 7 to 10 times larger than diffusivity for gradient Richardson numbers below approximately 0.7. Therefore LMD use
(20) 
MellorYamada 2.5
One of the more popular closure schemes is that of Mellor and Yamada (1982). They actually present a hierarchy of closures of increasing complexity. ROMS provides only the "Level 2.5" closure with the Galperin et al. (1988) modifications as described in Allen et al. (1995). This closure scheme adds two prognostic equations, one for the turbulent kinetic energy () and one for the turbulent kinetic energy times a length scale ().
The turbulent kinetic energy equation is:
(21) 
where is the shear production, is the buoyant production and is the dissipation of turbulent kinetic energy. These terms are given by
(22) 
where is a constant. One can also add a traditional horizontal Laplacian or biharmonic diffusion () to the turbulent kinetic energy equation. The form of this equation in the model coordinates becomes
(23) 
The vertical boundary conditions are:
 top (:
 and bottom ():
There is also an equation for the turbulent length scale :
(24) 
where is the wall proximity function:
(25) 
The form of this equation in the model coordinates becomes
(26) 
where is the horizontal diffusion of the quantity . Equations (23) and (26) are timestepped much like the model tracer equations, including an implicit solve for the vertical operations and options for centered second or fourthorder advection. They are timestepped with a predictorcorrector scheme in which the predictor step is only computing the advection.
Given these solutions for and , the vertical viscosity and diffusivity coefficients are:
(27) 
and the stability coefficients , and are found by solving
(28) 
(29) 
(30) 
(31) 
The constants are set to . The quantities and are both constrained to be no smaller than while is set to be no larger than .
Generic Length Scale
Umlauf and Burchard (2003) have come up with a generic twoequation turbulence closure scheme which can be tuned to behave like several of the traditional schemes, including that of Mellor and Yamada 2.5 (above). This is known as the Generic Length Scale, or GLS vertical mixing scheme and was introduced to ROMS in Warner et al. (2005). Its parameters are set in the ROMS input file.
The first of Warner et al.'s equations is the same as equation (21) with . Their dissipation is given by
(32) 
where is a generic parameter that is used to establish the turbulence length scale. The equation for is:
Coefficients and are chosen to be consistent with observations of decaying homogeneous, isotropic turbulence. The parameter has differing values for stable () and unstable () stratification. Also
Depending on the choice of the various parameters, these two equations can be made to solve a variety of traditional twoequation turbulence closure models. The list of parameters is shown in the following table and is also given inside the comments section of the ROMS input file.
