Version 6 (modified by lovato, 3 years ago) (diff)

TOP interface User Quick Guide (NEMO 4.0+)

TOP interface structure

TOP (Tracers in the Ocean Paradigm) is the NEMO hardwired interface toward biogeochemical models and provide the physical constraints/boundaries for oceanic tracers. It consists of a modular framework to handle multiple ocean tracers, including also a variety of built-in modules. TOP interfaces has the following location in the code repository


and the following modules are available:

TRP Interface to NEMO physical core for computing tracers transport
CFC Inert carbon tracers (CFC11,CFC12, SF6)
C14 Radiocarbon passive tracer
AGE Water age tracking
MY_TRC Template for creation of new modules and external BGC models coupling
PISCES Built in BGC model

The usage of TOP is activated by i) including in the configuration definition the component “TOP_SRC” and ii) adding the macro key_top in the configuration cpp file.

As an example, the user can refer to simplest configurations already available in the code GYRE_BFM or GYRE_PISCES.

Note that, since version 4.0, TOP interface core functionalities are activated by means of logical keys and all sub-module preprocessing macros from previous versions were removed.

Here below the list of preprocessing keys that applies to the TOP interface (beside key_top):

key_iomput : use XIOS I/O

key_zdfddm & key_zdftke & key_zdfgls: vertical schemes (need to be updated after Merge2017 finalization)

key_trabbl : bottom boundary layer parameterization

key_agrif : enable AGRIF coupling

key_trdtrc & key_trdmxl_trc : trend computation for tracers

TOP synthetic Workflow

A synthetic description of the TOP interface workflow is given below to summarize the steps involved in the computation of biogeochemical and physical trends and their time integration and outputs, by reporting also the principal Fortran subroutine herein involved.

Model initialization (nemogcm.F90)

call to trc_init (trcini.F90)

↳ call trc_nam (trcnam.F90) to initialize TOP tracers and run setting

↳ call trc_ini_sms, to initialize all modules

↳ call trc_ini_trp, to initialize transport for tracers

↳ call trc_ice_ini, to initialize tracers in seaice

↳ call trc_ini_state, read passive tracers from a restart or input data

↳ call trc_sub_ini, setup substepping if nn_dttrc /= 1

Time marching procedure (OPA_SRC/stp.F90)

call to trc_stp.F90 (trcstp.F90)

↳ call trc_sub_stp, averaging physical variables for sub-stepping

↳ call trc_wri, call XIOS for output of data

↳ call trc_sms, compute BGC trends for all modules

↳ call trc_sms_my_trc, includes also surface and coastal BCs trends

↳ call trc_trp (TRP/trctrp.F90), compute physical trends

↳ call trc_sbc, get trend due to surface concentration/dilution

↳ call trc_adv, compute tracers advection

↳ call to trc_ldf, compute tracers lateral diffusion

↳ call to trc_zdf, vertical mixing and after tracer fields

↳ call to trc_nxt, tracer fields at next time step    

↳ call to trc_rad, Correct artificial negative concentrations

↳ call trc_rst_wri, output tracers restart files

TOP namelist Walkthrough

Here below are listed the features/options of the TOP interface accessible through the namelist_top_ref and modifiable by means of namelist_top_cfg (as for NEMO physical ones).