\documentclass[../../NEMO/main/NEMO_manual]{subfiles}

\begin{document}

\chapter{ Model Setup}

\section{ Setting up a passive tracer configuration}
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\nlst{namtrc}
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The usage of TOP is activated 

\begin{itemize}
         \item by including in the configuration definition the component TOP\_SRC
         \item by adding the macro \textit{key\_top} in the configuration cpp file
\end{itemize}

As an example, the user can refer to already available configurations in the code, GYRE\_PISCES being the NEMO biogeochemical demonstrator and GYRE\_BFM to see the required configuration elements to couple with an external biogeochemical model (see also section \S\ref{SMS_models}) .

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

There are only three specific keys remaining in TOP

\begin{itemize}
        \item \textit{key\_top} : to enables passive tracer module
        \item \textit{key\_trdtrc} and \textit{key\_trdmxl\_trc} : trend computation for tracers
\end{itemize}

For a remind, the revisited structure of TOP interface now counts for five different modules handled in namelist\_top : 

\begin{itemize}
        \item \textbf{PISCES}, default BGC model
        \item \textbf{MY\_TRC}, template for creation of new modules couplings (maybe run a single passive tracer)
        \item \textbf{CFC}, inert carbon tracers dynamics (CFC11,CFC12,SF6) Updated with OMIP-BGC guidelines (Orr et al, 2016)
        \item \textbf{C14}, radiocarbon passive tracer
        \item \textbf{AGE}, water age tracking revised implementation
\end{itemize}

The modular approach was implemented also in the definition of the total number of passive tracers (jptra). This results from to user setting from the namelist \textit{namtrc}

\section{ TOP Tracer Initialisation}

\section{ TOP Boundaries Conditions}

\end{document}
