Using the representation described in Chap. 4, several semi-discrete space forms of the tracer equations are available depending on the vertical coordinate used and on the physics used. In all the equations presented here, the masking has been omitted for simplicity. One must be aware that all the quantities are masked fields and that each time a mean or difference operator is used, the resulting field is multiplied by a mask.
The two active tracers are potential temperature and salinity. Their prognostic equations can be summarized as follows:
NXT stands for next, referring to the time-stepping. From left to right, the terms on the rhs of the tracer equations are the advection (ADV), the lateral diffusion (LDF), the vertical diffusion (ZDF), the contributions from the external forcings (SBC: Surface Boundary Condition, QSR: penetrative Solar Radiation, and BBC: Bottom Boundary Condition), the contribution from the bottom boundary Layer (BBL) parametrisation, and an internal damping (DMP) term. The terms QSR, BBC, BBL and DMP are optional. The external forcings and parameterisations require complex inputs and complex calculations ( bulk formulae, estimation of mixing coefficients) that are carried out in the SBC, LDF and ZDF modules and described in chapters §7, §9 and §10, respectively. Note that tranpc.F90, the non-penetrative convection module, although located in the NEMO/OPA/TRA directory as it directly modifies the tracer fields, is described with the model vertical physics (ZDF) together with other available parameterization of convection.
In the present chapter we also describe the diagnostic equations used to compute the sea-water properties (density, Brunt-Väisälä frequency, specific heat and freezing point with associated modules eosbn2.F90 and phycst.F90).
The different options available to the user are managed by namelist logicals or CPP keys. For each equation term ttt, the namelist logicals are ln_trattt_xxx, where xxx is a 3 or 4 letter acronym corresponding to each optional scheme. The CPP key (when it exists) is key_trattt. The equivalent code can be found in the trattt or trattt_xxx module, in the NEMO/OPA/TRA directory.
The user has the option of extracting each tendency term on the RHS of the tracer equation for output (ln_tra_trd or ln_tra_mxl = true), as described in Chap. 11.
Gurvan Madec and the NEMO Team
NEMO European Consortium2017-02-17