% ================================================================ % INTRODUCTION % ================================================================ \chapter{Introduction} The Nucleus for European Modelling of the Ocean (\NEMO) is a framework of ocean related engines, namely OPA\footnote{OPA = Oc\'{e}an PArall\'{e}lis\'{e}} for the ocean dynamics and thermodynamics, LIM\footnote{LIM= Louvain)la-neuve Ice Model} for the sea-ice dynamics and thermodynamics, TOP\footnote{TOP = Tracer in the Ocean Paradigm} for the biogeochemistry (both transport (TRP) and sources minus sinks (LOBSTER, PISCES)\footnote{Both LOBSTER and PISCES are not acronyms just name}. It is intended to be a flexible tool for studying the ocean and its interactions with the other components of the earth climate system (atmosphere, sea-ice, biogeochemical tracers, ...) over a wide range of space and time scales. This documentation provides information about the physics represented by the ocean component of \NEMO and the rationale for the choice of numerical schemes and the model design. More specific information about running the model on different computers, or how to set up a configuration, are found on the \NEMO web site (www.locean-ipsl.upmc.fr/NEMO). The ocean component of \NEMO has been developed from the OPA model, release 8.2, described in \citet{Madec1998}. This model has been used for a wide range of applications, both regional or global, as a forced ocean model and as a model coupled with the atmosphere. A complete list of references is found on the \NEMO web site. This manual is organised in as follows. Chapter~\ref{PE} presents the model basics, $i.e.$ the equations and their assumptions, the vertical coordinates used, and the subgrid scale physics. This part deals with the continuous equations of the model (primitive equations, with potential temperature, salinity and an equation of state). The equations are written in a curvilinear coordinate system, with a choice of vertical coordinates ($z$ or $s$, with the rescaled height coordinate formulation \textit{z*}, or \textit{s*}). Momentum equations are formulated in the vector invariant form or in the flux form. Dimensional units in the meter, kilogram, second (MKS) international system are used throughout. The following chapters deal with the discrete equations. Chapter~\ref{STP} presents the time domain. The model time stepping environment is a three level scheme in which the tendency terms of the equations are evaluated either centered in time, or forward, or backward depending of the nature of the term. Chapter~\ref{DOM} presents the space domain. The model is discretised on a staggered grid (Arakawa C grid) with masking of land areas. Vertical discretisation used depends on both how the bottom topography is represented and whether the free surface is linear or not. Full step or partial step $z$-coordinate or $s$- (terrain-following) coordinate is used with linear free surface (level position are then fixed in time). In non-linear free surface, the corresponding rescaled height coordinate formulation (\textit{z*} or \textit{s*}) is used (the level position then vary in time as a function of the sea surface heigh). The following two chapters (\ref{TRA} and \ref{DYN}) describe the discretisation of the prognostic equations for the active tracers and the momentum. Explicit, split-explicit and filtered free surface formulations are implemented. A number of numerical schemes are available for momentum advection, for the computation of the pressure gradients, as well as for the advection of tracers (second or higher order advection schemes, including positive ones). Surface boundary conditions (chapter~\ref{SBC}) can be implemented as prescribed fluxes, or bulk formulations for the surface fluxes (wind stress, heat, freshwater). The model allows penetration of solar radiation There is an optional geothermal heating at the ocean bottom. Within the \NEMO system the ocean model is interactively coupled with a sea ice model (LIM) and with biogeochemistry models (PISCES, LOBSTER). Interactive coupling to Atmospheric models is possible via the OASIS coupler \citep{OASIS2006}. Two-way nesting is also available through an interface to the AGRIF package (Adaptative Grid Refinement in \textsc{Fortran}) \citep{Debreu_al_CG2008}. Other model characteristics are the lateral boundary conditions (chapter~\ref{LBC}). Global configurations of the model make use of the ORCA tripolar grid, with special north fold boundary condition. Free-slip or no-slip boundary conditions are allowed at land boundaries. Closed basin geometries as well as periodic domains and open boundary conditions are possible. Physical parameterisations are described in chapters~\ref{LDF} and \ref{ZDF}. The model includes an implicit treatment of vertical viscosity and diffusivity. The lateral Laplacian and biharmonic viscosity and diffusion can be rotated following a geopotential or neutral direction. There is an optional eddy induced velocity \citep{Gent1990} with a space and time variable coefficient \citet{Treguier1997}. The model has vertical harmonic viscosity and diffusion with a space and time variable coefficient, with options to compute the coefficients with \citet{Blanke1993}, \citet{Large_al_RG94}, \citet{Pacanowski_Philander_JPO81}, or \citet{Umlauf_Burchard_JMS03} mixing schemes. Model outputs management and specific online diagnostics are described in chapters~\ref{DIA}. The diagnostics includes the output of all the tendencies of the momentum and tracers equations, the output of tracers tendencies averaged over the time evolving mixed layer, the output of the tendencies of the barotropic vorticity equation, the computation of on-line floats trajectories... Chapter~\ref{OBS} describes a tool which reads in observation files (profile temperature and salinity, sea surface temperature, sea level anomaly and sea ice concentration) and calculates an interpolated model equivalent value at the observation location and nearest model timestep. Originally developed of data assimilation, it is a fantastic tool for model and data comparison. Chapter~\ref{ASM} describes how increments produced by data assimilation may be applied to the model equations. Finally, Chapter~\ref{CFG} provides a brief introduction to the pre-defined model configurations (water column model, ORCA and GYRE families of configurations). The model is implemented in \textsc{Fortran 90}, with preprocessing (C-pre-processor). It runs under UNIX. It is optimized for vector computers and parallelised by domain decomposition with MPI. All input and output is done in NetCDF (Network Common Data Format) with a optional direct access format for output. To ensure the clarity and readability of the code it is necessary to follow coding rules. The coding rules for OPA include conventions for naming variables, with different starting letters for different types of variables (real, integer, parameter\ldots). Those rules are briefly presented in Appendix~\ref{Apdx_D} and a more complete document is available on the \NEMO web site. The model is organized with a high internal modularity based on physics. For example, each trend ($i.e.$, a term in the RHS of the prognostic equation) for momentum and tracers is computed in a dedicated module. To make it easier for the user to find his way around the code, the module names follow a three-letter rule. For example, \mdl{traldf} is a module related to the TRAcers equation, computing the Lateral DiFfussion. %The complete list of module names is presented in Appendix~\ref{Apdx_D}. %====>>>> to be done ! Furthermore, modules are organized in a few directories that correspond to their category, as indicated by the first three letters of their name (Tab.~\ref{Tab_chap}). The manual mirrors the organization of the model. After the presentation of the continuous equations (Chapter \ref{PE}), the following chapters refer to specific terms of the equations each associated with a group of modules (Tab.~\ref{Tab_chap}). %--------------------------------------------------TABLE-------------------------------------------------- \begin{table}[!t] %\begin{center} \begin{tabular}{|p{143pt}|l|l|} \hline \caption{ \label{Tab_chap} Organization of Chapters mimicking the one of the model directories. } \begin{center} \begin{tabular}{|l|l|l|} \hline Chapter \ref{STP} & - & model time STePping environment \\ \hline Chapter \ref{DOM} & DOM & model DOMain \\ \hline Chapter \ref{TRA} & TRA & TRAcer equations (potential temperature and salinity) \\ \hline Chapter \ref{DYN} & DYN & DYNamic equations (momentum) \\ \hline Chapter \ref{SBC} & SBC & Surface Boundary Conditions \\ \hline Chapter \ref{LBC} & LBC & Lateral Boundary Conditions (also OBC and BDY) \\ \hline Chapter \ref{LDF} & LDF & Lateral DiFfusion (parameterisations) \\ \hline Chapter \ref{ZDF} & ZDF & vertical (Z) DiFfusion (parameterisations) \\ \hline Chapter \ref{DIA} & DIA & I/O and DIAgnostics (also IOM, FLO and TRD) \\ \hline Chapter \ref{OBS} & OBS & OBServation and model comparison \\ \hline Chapter \ref{ASM} & ASM & ASsiMilation increment \\ \hline Chapter \ref{MISC} & SOL & Miscellaneous topics (including solvers) \\ \hline Chapter \ref{CFG} & - & predefined configurations (including C1D) \\ \hline \end{tabular} \end{center} \end{table} %-------------------------------------------------------------------------------------------------------------- \subsubsection{Changes between releases} NEMO/OPA, like all research tools, is in perpetual evolution. The present document describes the OPA version include in the release 3.3 of NEMO. This release differs significantly from version 8, documented in \citet{Madec1998}.\\ $\bullet$ The main modifications from OPA v8 and NEMO/OPA v3.2 are :\\ (1) transition to full native \textsc{Fortran} 90, deep code restructuring and drastic reduction of CPP keys; \\ (2) introduction of partial step representation of bottom topography \citep{Barnier_al_OD06, Le_Sommer_al_OM09, Penduff_al_OS07}; \\ (3) partial reactivation of a terrain-following vertical coordinate ($s$- and hybrid $s$-$z$) with the addition of several options for pressure gradient computation \footnote{Partial support of $s$-coordinate: there is presently no support for neutral physics in $s$- coordinate and for the new options for horizontal pressure gradient computation with a non-linear equation of state.}; \\ (4) more choices for the treatment of the free surface: full explicit, split-explicit or filtered schemes. \\ (5) suppression of the rigid-lid option;\\ (6) non linear free surface option (associated with the rescaled height coordinate \textit{z*} or \textit{s}); \\ (6) additional schemes for vector and flux forms of the momentum advection; \\ (7) additional advection schemes for tracers; \\ (8) implementation of the AGRIF package (Adaptative Grid Refinement in \textsc{Fortran}) \citep{Debreu_al_CG2008}; \\ (9) online diagnostics : tracers trend in the mixed layer and vorticity balance; \\ (10) rewriting of the I/O management with the use of an I/O server; \\ (11) generalized ocean-ice-atmosphere-CO2 coupling interface, interfaced with OASIS 3 coupler. \\ (12) surface module (SBC) that simplify the way the ocean is forced and include two bulk formulea (CLIO and CORE) and which includes an on-the-fly interpolation of input forcing fields\\ (13) RGB light penetration and optional use of ocean color (14) major changes in the TKE schemes: it now includes a Langmuir cell parameterization \citep{Axell_JGR02}, the \citet{Mellor_Blumberg_JPO04} surface wave breaking parameterization, and has a time discretization which is energetically consistent with the ocean model equations \citep{Burchard_OM02, Marsaleix_al_OM08}; \\ (15) tidal mixing parametrisation (bottom intensification) + Indonesian specific tidal mixing \citep{Koch-Larrouy_al_GRL07}; \\ (16) introduction of LIM-3, the new Louvain-la-Neuve sea-ice model (C-grid rheology and new thermodynamics including bulk ice salinity) \citep{Vancoppenolle_al_OM09a, Vancoppenolle_al_OM09b} \vspace{1cm} $\bullet$ The main modifications from NEMO/OPA v3.2 and v3.3 are :\\ (1) introduction of a modified leapfrog-Asselin filter time stepping scheme \citep{Leclair_Madec_OM09}; \\ (2) additional scheme for iso-neutral mixing \citep{Griffies_al_JPO98}, although it is still a "work in progress"; \\ (3) a rewriting of the bottom boundary layer scheme, following \citet{Campin_Goosse_Tel99}; \\ (4) addition of a Generic Length Scale vertical mixing scheme, following \citet{Umlauf_Burchard_JMS03}; (5) addition of the atmospheric pressure as an external forcing on both ocean and sea-ice dynamics; \\ (6) addition of a diurnal cycle on solar radiation \citep{Bernie_al_CD07}; \\ (7) river runoffs added through a non-zero depth, and having its own temperature and salinity; \\ (8) CORE II normal year forcing set as the default forcing of ORCA2-LIM configuration ; \\ (9) generalisation of the use of \mdl{fldread} for all input fields (ocean, climatology, sea-ice damping...) (10) addition of an on-line observation and model comparison (thanks to NEMOVAR project); \\ (11) optional application of an assimilation increment (thanks to NEMOVAR project); \\ (12) coupling interface adjusted for WRF atmospheric model (13) C-grid ice rheology now available fro both LIM-2 and LIM-3 \citep{Bouillon_al_OM09}; \\ (14) a deep re-writting and simplification of the off-line tracer component (OFF\_SRC) ; \\ (15) the merge of passive and active advection and diffusion modules \\ (16) Use of the Flexible Configuration Manager (FCM) to build configurations, generate the Makefile and produce the executable ; \\ (17) Linear-tangent and Adjoint component (TAM) added, phased with v3.0 \vspace{1cm} In addition, several minor modifications in the coding have been introduced with the constant concern of improving the model performance.