1 | |
---|
2 | % ================================================================ |
---|
3 | % INTRODUCTION |
---|
4 | % ================================================================ |
---|
5 | |
---|
6 | \chapter{Introduction} |
---|
7 | |
---|
8 | The Nucleus for European Modelling of the Ocean (\NEMO) is a framework of ocean |
---|
9 | related engines, namely OPA\footnote{OPA = Oc\'{e}an PArall\'{e}lis\'{e}} for the |
---|
10 | ocean dynamics and thermodynamics, LIM\footnote{LIM= Louvain)la-neuve Ice |
---|
11 | Model} for the sea-ice dynamics and thermodynamics, TOP\footnote{TOP = Tracer |
---|
12 | in the Ocean Paradigm} for the biogeochemistry (both transport (TRP) and sources |
---|
13 | minus sinks (LOBSTER, PISCES)\footnote{Both LOBSTER and PISCES are not |
---|
14 | acronyms just name}. It is intended to be a flexible tool for studying the ocean and |
---|
15 | its interactions with the other components of the earth climate system (atmosphere, |
---|
16 | sea-ice, biogeochemical tracers, ...) over a wide range of space and time scales. |
---|
17 | This documentation provides information about the physics represented by the ocean |
---|
18 | component of \NEMO and the rationale for the choice of numerical schemes and |
---|
19 | the model design. More specific information about running the model on different |
---|
20 | computers, or how to set up a configuration, are found on the \NEMO web site |
---|
21 | (www.locean-ipsl.upmc.fr/NEMO). |
---|
22 | |
---|
23 | The ocean component of \NEMO has been developed from the OPA model, |
---|
24 | release 8.2, described in \citet{Madec1998}. This model has been used for a wide |
---|
25 | range of applications, both regional or global, as a forced ocean model and as a |
---|
26 | model coupled with the atmosphere. A complete list of references is found on the |
---|
27 | \NEMO web site. |
---|
28 | |
---|
29 | This manual is organised in as follows. Chapter~\ref{PE} presents the model basics, |
---|
30 | $i.e.$ the equations and their assumptions, the vertical coordinates used, and the |
---|
31 | subgrid scale physics. This part deals with the continuous equations of the model |
---|
32 | (primitive equations, with potential temperature, salinity and an equation of state). |
---|
33 | The equations are written in a curvilinear coordinate system, with a choice of vertical |
---|
34 | coordinates ($z$ or $s$, with the rescaled height coordinate formulation \textit{z*}, or |
---|
35 | \textit{s*}). Momentum equations are formulated in the vector invariant form or in the |
---|
36 | flux form. Dimensional units in the meter, kilogram, second (MKS) international system |
---|
37 | are used throughout. |
---|
38 | |
---|
39 | The following chapters deal with the discrete equations. Chapter~\ref{STP} presents the |
---|
40 | time domain. The model time stepping environment is a three level scheme in which |
---|
41 | the tendency terms of the equations are evaluated either centered in time, or forward, |
---|
42 | or backward depending of the nature of the term. |
---|
43 | Chapter~\ref{DOM} presents the space domain. The model is discretised on a staggered |
---|
44 | grid (Arakawa C grid) with masking of land areas. Vertical discretisation used depends |
---|
45 | on both how the bottom topography is represented and whether the free surface is linear or not. |
---|
46 | Full step or partial step $z$-coordinate or $s$- (terrain-following) coordinate is used |
---|
47 | with linear free surface (level position are then fixed in time). In non-linear free surface, |
---|
48 | the corresponding rescaled height coordinate formulation (\textit{z*} or \textit{s*}) is used |
---|
49 | (the level position then vary in time as a function of the sea surface heigh). |
---|
50 | The following two chapters (\ref{TRA} and \ref{DYN}) describe the discretisation of the |
---|
51 | prognostic equations for the active tracers and the momentum. Explicit, split-explicit |
---|
52 | and filtered free surface formulations are implemented. |
---|
53 | A number of numerical schemes are available for momentum advection, for the computation |
---|
54 | of the pressure gradients, as well as for the advection of tracers (second or higher |
---|
55 | order advection schemes, including positive ones). |
---|
56 | |
---|
57 | Surface boundary conditions (chapter~\ref{SBC}) can be implemented as prescribed |
---|
58 | fluxes, or bulk formulations for the surface fluxes (wind stress, heat, freshwater). The |
---|
59 | model allows penetration of solar radiation There is an optional geothermal heating at |
---|
60 | the ocean bottom. Within the \NEMO system the ocean model is interactively coupled |
---|
61 | with a sea ice model (LIM) and with biogeochemistry models (PISCES, LOBSTER). |
---|
62 | Interactive coupling to Atmospheric models is possible via the OASIS coupler |
---|
63 | \citep{OASIS2006}. Two-way nesting is also available through an interface to the |
---|
64 | AGRIF package (Adaptative Grid Refinement in \textsc{Fortran}) \citep{Debreu_al_CG2008}. |
---|
65 | The interface code for coupling to an alternative sea ice model (CICE, \citet{Hunke2008}) is now |
---|
66 | available although this is currently only designed for global domains, without the use of AGRIF. |
---|
67 | |
---|
68 | Other model characteristics are the lateral boundary conditions (chapter~\ref{LBC}). |
---|
69 | Global configurations of the model make use of the ORCA tripolar grid, with special north |
---|
70 | fold boundary condition. Free-slip or no-slip boundary conditions are allowed at land |
---|
71 | boundaries. Closed basin geometries as well as periodic domains and open boundary |
---|
72 | conditions are possible. |
---|
73 | |
---|
74 | Physical parameterisations are described in chapters~\ref{LDF} and \ref{ZDF}. The |
---|
75 | model includes an implicit treatment of vertical viscosity and diffusivity. The lateral |
---|
76 | Laplacian and biharmonic viscosity and diffusion can be rotated following a geopotential |
---|
77 | or neutral direction. There is an optional eddy induced velocity \citep{Gent1990} with a |
---|
78 | space and time variable coefficient \citet{Treguier1997}. The model has vertical harmonic |
---|
79 | viscosity and diffusion with a space and time variable coefficient, with options to compute |
---|
80 | the coefficients with \citet{Blanke1993}, \citet{Large_al_RG94}, \citet{Pacanowski_Philander_JPO81}, |
---|
81 | or \citet{Umlauf_Burchard_JMS03} mixing schemes. |
---|
82 | |
---|
83 | Model outputs management and specific online diagnostics are described in chapters~\ref{DIA}. |
---|
84 | The diagnostics includes the output of all the tendencies of the momentum and tracers equations, |
---|
85 | the output of tracers tendencies averaged over the time evolving mixed layer, the output of |
---|
86 | the tendencies of the barotropic vorticity equation, the computation of on-line floats trajectories... |
---|
87 | Chapter~\ref{OBS} describes a tool which reads in observation files (profile temperature |
---|
88 | and salinity, sea surface temperature, sea level anomaly and sea ice concentration) |
---|
89 | and calculates an interpolated model equivalent value at the observation location |
---|
90 | and nearest model timestep. Originally developed of data assimilation, it is a fantastic |
---|
91 | tool for model and data comparison. Chapter~\ref{ASM} describes how increments |
---|
92 | produced by data assimilation may be applied to the model equations. |
---|
93 | Finally, Chapter~\ref{CFG} provides a brief introduction to the pre-defined model |
---|
94 | configurations (water column model, ORCA and GYRE families of configurations). |
---|
95 | |
---|
96 | The model is implemented in \textsc{Fortran 90}, with preprocessing (C-pre-processor). |
---|
97 | It runs under UNIX. It is optimized for vector computers and parallelised by domain |
---|
98 | decomposition with MPI. All input and output is done in NetCDF (Network Common Data |
---|
99 | Format) with a optional direct access format for output. To ensure the clarity and |
---|
100 | readability of the code it is necessary to follow coding rules. The coding rules for OPA |
---|
101 | include conventions for naming variables, with different starting letters for different types |
---|
102 | of variables (real, integer, parameter\ldots). Those rules are briefly presented in |
---|
103 | Appendix~\ref{Apdx_D} and a more complete document is available on the \NEMO web site. |
---|
104 | |
---|
105 | The model is organized with a high internal modularity based on physics. For example, |
---|
106 | each trend ($i.e.$, a term in the RHS of the prognostic equation) for momentum and |
---|
107 | tracers is computed in a dedicated module. To make it easier for the user to find his way |
---|
108 | around the code, the module names follow a three-letter rule. For example, \mdl{traldf} |
---|
109 | is a module related to the TRAcers equation, computing the Lateral DiFfussion. |
---|
110 | %The complete list of module names is presented in Appendix~\ref{Apdx_D}. %====>>>> to be done ! |
---|
111 | Furthermore, modules are organized in a few directories that correspond to their category, |
---|
112 | as indicated by the first three letters of their name (Tab.~\ref{Tab_chap}). |
---|
113 | |
---|
114 | The manual mirrors the organization of the model. |
---|
115 | After the presentation of the continuous equations (Chapter \ref{PE}), the following chapters |
---|
116 | refer to specific terms of the equations each associated with a group of modules (Tab.~\ref{Tab_chap}). |
---|
117 | |
---|
118 | |
---|
119 | %--------------------------------------------------TABLE-------------------------------------------------- |
---|
120 | \begin{table}[!t] |
---|
121 | %\begin{center} \begin{tabular}{|p{143pt}|l|l|} \hline |
---|
122 | \caption{ \label{Tab_chap} Organization of Chapters mimicking the one of the model directories. } |
---|
123 | \begin{center} \begin{tabular}{|l|l|l|} \hline |
---|
124 | Chapter \ref{STP} & - & model time STePping environment \\ \hline |
---|
125 | Chapter \ref{DOM} & DOM & model DOMain \\ \hline |
---|
126 | Chapter \ref{TRA} & TRA & TRAcer equations (potential temperature and salinity) \\ \hline |
---|
127 | Chapter \ref{DYN} & DYN & DYNamic equations (momentum) \\ \hline |
---|
128 | Chapter \ref{SBC} & SBC & Surface Boundary Conditions \\ \hline |
---|
129 | Chapter \ref{LBC} & LBC & Lateral Boundary Conditions (also OBC and BDY) \\ \hline |
---|
130 | Chapter \ref{LDF} & LDF & Lateral DiFfusion (parameterisations) \\ \hline |
---|
131 | Chapter \ref{ZDF} & ZDF & vertical (Z) DiFfusion (parameterisations) \\ \hline |
---|
132 | Chapter \ref{DIA} & DIA & I/O and DIAgnostics (also IOM, FLO and TRD) \\ \hline |
---|
133 | Chapter \ref{OBS} & OBS & OBServation and model comparison \\ \hline |
---|
134 | Chapter \ref{ASM} & ASM & ASsiMilation increment \\ \hline |
---|
135 | Chapter \ref{MISC} & SOL & Miscellaneous topics (including solvers) \\ \hline |
---|
136 | Chapter \ref{CFG} & - & predefined configurations (including C1D) \\ \hline |
---|
137 | \end{tabular} |
---|
138 | \end{center} \end{table} |
---|
139 | %-------------------------------------------------------------------------------------------------------------- |
---|
140 | |
---|
141 | |
---|
142 | \subsubsection{Changes between releases} |
---|
143 | NEMO/OPA, like all research tools, is in perpetual evolution. The present document describes |
---|
144 | the OPA version include in the release 3.3 of NEMO. This release differs significantly |
---|
145 | from version 8, documented in \citet{Madec1998}.\\ |
---|
146 | |
---|
147 | $\bullet$ The main modifications from OPA v8 and NEMO/OPA v3.2 are :\\ |
---|
148 | \begin{enumerate} |
---|
149 | \item transition to full native \textsc{Fortran} 90, deep code restructuring and drastic |
---|
150 | reduction of CPP keys; |
---|
151 | \item introduction of partial step representation of bottom topography \citep{Barnier_al_OD06, Le_Sommer_al_OM09, Penduff_al_OS07}; |
---|
152 | \item partial reactivation of a terrain-following vertical coordinate ($s$- and hybrid $s$-$z$) |
---|
153 | with the addition of several options for pressure gradient computation \footnote{Partial |
---|
154 | support of $s$-coordinate: there is presently no support for neutral physics in $s$- |
---|
155 | coordinate and for the new options for horizontal pressure gradient computation with |
---|
156 | a non-linear equation of state.}; |
---|
157 | \item more choices for the treatment of the free surface: full explicit, split-explicit or filtered |
---|
158 | schemes, and suppression of the rigid-lid option; |
---|
159 | \item non linear free surface associated with the rescaled height coordinate |
---|
160 | \textit{z*} or \textit{s}; |
---|
161 | \item additional schemes for vector and flux forms of the momentum advection; |
---|
162 | \item additional advection schemes for tracers; |
---|
163 | \item implementation of the AGRIF package (Adaptative Grid Refinement in \textsc{Fortran}) \citep{Debreu_al_CG2008}; |
---|
164 | \item online diagnostics : tracers trend in the mixed layer and vorticity balance; |
---|
165 | \item rewriting of the I/O management with the use of an I/O server; |
---|
166 | \item generalized ocean-ice-atmosphere-CO2 coupling interface, interfaced with OASIS 3 coupler ; |
---|
167 | \item surface module (SBC) that simplify the way the ocean is forced and include two |
---|
168 | bulk formulea (CLIO and CORE) and which includes an on-the-fly interpolation of input forcing fields ; |
---|
169 | \item RGB light penetration and optional use of ocean color |
---|
170 | \item major changes in the TKE schemes: it now includes a Langmuir cell parameterization \citep{Axell_JGR02}, |
---|
171 | the \citet{Mellor_Blumberg_JPO04} surface wave breaking parameterization, and has a time discretization |
---|
172 | which is energetically consistent with the ocean model equations \citep{Burchard_OM02, Marsaleix_al_OM08}; |
---|
173 | \item tidal mixing parametrisation (bottom intensification) + Indonesian specific tidal mixing \citep{Koch-Larrouy_al_GRL07}; |
---|
174 | \item introduction of LIM-3, the new Louvain-la-Neuve sea-ice model (C-grid rheology and |
---|
175 | new thermodynamics including bulk ice salinity) \citep{Vancoppenolle_al_OM09a, Vancoppenolle_al_OM09b} |
---|
176 | \end{enumerate} |
---|
177 | |
---|
178 | \vspace{1cm} |
---|
179 | $\bullet$ The main modifications from NEMO/OPA v3.2 and v3.3 are :\\ |
---|
180 | \begin{enumerate} |
---|
181 | \item introduction of a modified leapfrog-Asselin filter time stepping scheme \citep{Leclair_Madec_OM09}; |
---|
182 | \item additional scheme for iso-neutral mixing \citep{Griffies_al_JPO98}, although it is still a "work in progress"; |
---|
183 | \item a rewriting of the bottom boundary layer scheme, following \citet{Campin_Goosse_Tel99}; |
---|
184 | \item addition of a Generic Length Scale vertical mixing scheme, following \citet{Umlauf_Burchard_JMS03}; |
---|
185 | \item addition of the atmospheric pressure as an external forcing on both ocean and sea-ice dynamics; |
---|
186 | \item addition of a diurnal cycle on solar radiation \citep{Bernie_al_CD07}; |
---|
187 | \item river runoffs added through a non-zero depth, and having its own temperature and salinity; |
---|
188 | \item CORE II normal year forcing set as the default forcing of ORCA2-LIM configuration ; |
---|
189 | \item generalisation of the use of \mdl{fldread} for all input fields (ocean climatology, sea-ice damping...) ; |
---|
190 | \item addition of an on-line observation and model comparison (thanks to NEMOVAR project); |
---|
191 | \item optional application of an assimilation increment (thanks to NEMOVAR project); |
---|
192 | \item coupling interface adjusted for WRF atmospheric model; |
---|
193 | \item C-grid ice rheology now available fro both LIM-2 and LIM-3 \citep{Bouillon_al_OM09}; |
---|
194 | \item LIM-3 ice-ocean momentum coupling applied to LIM-2 ; |
---|
195 | \item a deep re-writting and simplification of the off-line tracer component (OFF\_SRC) ; |
---|
196 | \item the merge of passive and active advection and diffusion modules ; |
---|
197 | \item Use of the Flexible Configuration Manager (FCM) to build configurations, generate the Makefile and produce the executable ; |
---|
198 | \item Linear-tangent and Adjoint component (TAM) added, phased with v3.0 |
---|
199 | \end{enumerate} |
---|
200 | \vspace{1cm} |
---|
201 | In addition, several minor modifications in the coding have been introduced with the constant |
---|
202 | concern of improving the model performance. |
---|
203 | |
---|
204 | \vspace{1cm} |
---|
205 | $\bullet$ The main modifications from NEMO/OPA v3.3 and v3.4 are :\\ |
---|
206 | \begin{enumerate} |
---|
207 | \item finalisation of above iso-neutral mixing \citep{Griffies_al_JPO98}"; |
---|
208 | \item "Neptune effect" parametrisation; |
---|
209 | \item horizontal pressure gradient suitable for s-coordinate; |
---|
210 | \item semi-implicit bottom friction; |
---|
211 | \item finalisation of the merge of passive and active tracers advection-diffusion modules; |
---|
212 | \item a new bulk formulae (so-called MFS); |
---|
213 | \item use fldread for the off-line tracer component (OFF\_SRC) ; |
---|
214 | \item use MPI point to point communications for north fold; |
---|
215 | \item diagnostic of transport ; |
---|
216 | \end{enumerate} |
---|
217 | |
---|
218 | |
---|