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+++ 	(revision )
@@ -1,317 +1,0 @@
-%\begin{figure}[htbp]
-%\centerline{\includegraphics[width=1.64in,height=11.72in]{OPA9_Chap_0_Introduction1.eps}}
-%\label{fig1}
-%\end{figure}
-
-\textbf{Institut Pierre Simon Laplace}
-
-\textbf{des Sciences de l'Environnement Global}
-
-\textit{Notes du P\^{o}le de Mod\'{e}lisation}
-
-NEMO : the OPA ocean engine
-
-(NEMO version 2.3)
-
-Gurvan Madec, {\ldots} 
-
-Laboratoire d'Oc\'{e}anographie et du Climat: Exp\'{e}rimentation 
-
-et Approches Num\'{e}riques
-
-%\begin{figure}[htbp]
-%\centerline{\includegraphics[width=4.58in,height=4.35in]{OPA9_Chap_0_Introduction2.eps}}
-%\label{fig2}
-%\end{figure}
-
-\newpage 
-\begin{center}
-NEMO : the OPA ocean engine
-\end{center}
-
-Gurvan Madec
-
-Laboratoire d'Oc\'{e}anographie et du Climat: Exp\'{e}rimentation Approches 
-Num\'{e}riques
-
-CNRS/IRD/UPMC, UMR 7617
-
-\subsection{Abstract}
-\label{subsec:abstract}
-OPA is the ocean engine of NEMO, a framework of ocean related components 
-developed for both research and operational purposes. It is a primitive 
-equation model adapted to regional and global ocean circulation. It is 
-intended to be a flexible tool for studying the ocean and its interactions 
-with the others components of the earth climate system (atmosphere, sea-ice, 
-biogeochemical tracers, ...) over a wide range of space and time scales. 
-Prognostic variables are the three-dimensional velocity field, the sea 
-surface height, the temperature and the salinity. In the horizontal 
-direction, the model uses a curvilinear orthogonal grid and in the vertical 
-direction, a $z$ full or partial step coordinate, or $s$-coordinate, or a mixture 
-of the two. The distribution of variables is a three-dimensional Arakawa 
-C-type grid. Various physical choices are available to describe ocean 
-physics, including a 1.5 turbulent closure or a KPP scheme for the vertical 
-mixing. Within NEMO, OPA is interfaced with a sea-ice model (LIM), passive 
-tracer and biogeochemical models (TOP) and, via the OASIS coupler, with 
-several atmospheric general circulation models. In addition, it can be run 
-on many different computers, including shared and distributed memory 
-multiprocessor computers.
-
-\textsc{\textbf{R\'{e}sum\'{e}}}
-
-OPA est le moteur oc\'{e}anique de NEMO, un syst\`{e}me de mod\'{e}lisation 
-de l'oc\'{e}an d\'{e}velopp\'{e} \`{a} des fins de recherche et 
-d'oc\'{e}anographie op\'{e}rationnelle. Ce moteur est un mod\`{e}le aux 
-\'{e}quations primitives de la circulation oc\'{e}anique r\'{e}gionale et 
-globale. Il se veut un outil flexible pour \'{e}tudier sur un vaste spectre 
-spatiotemporel l'oc\'{e}an et ses interactions avec les autres composantes 
-du syst\`{e}me climatique terrestre (atmosph\`{e}re, glace de mer, traceurs 
-biog\'{e}ochimiques...). Les variables pronostiques sont le champ 
-tridimensionnel de vitesse, la hauteur de la mer , la temperature et la 
-salinit\'{e}. La distribution des variables se fait sur une grille $C$ 
-d'Arakawa tridimensionnelle utilisant une coordonn\'{e}e verticale $z$ \`{a} 
-niveaux entiers ou partiels, ou une coordonn\'{e}e$ s$, ou encore une 
-combinaison des deux. Diff\'{e}rents choix sont propos\'{e}s pour 
-d\'{e}crire la physique oc\'{e}anique, incluant notamment une fermeture 
-turbulente d'ordre 1.5 ou un sch\'{e}ma KPP pour le m\'{e}lange vertical. 
-Via l'infrastructure NEMO, OPA est interfac\'{e} avec un mod\`{e}le de glace 
-de mer, des mod\`{e}les biog\'{e}ochimiques et de traceur passif, et, via le 
-coupleur OASIS, \`{a} plusieurs mod\`{e}les de circulation g\'{e}n\'{e}rale 
-atmosph\'{e}rique. En outre, il peut \^{e}tre ex\'{e}cut\'{e} sur de 
-nombreux calculateurs, y compris des calculateurs multiprocesseurs \`{a} 
-m\'{e}moire partag\'{e}e ou distribu\'{e}e.
-
-\newpage 
-\textbf{PLAN :}
-
-Put it here
-
-\textsc{\textbf{Disclaimer 1}}
-
-\textsc{\textbf{Foreword 3}}
-
-\textsc{\textbf{Introduction 4}}
-
-\textsc{\textbf{Disclaimer}}
-
-OPA (an acronym for Ocean PArall\'{e}lis\'{e}) is the ocean component of 
-NEMO (Nucleus for European Modelling of the Ocean (\underline 
-{www.locean-ipsl.upmc.fr/NEMO}). Like all components of NEMO, it is 
-developed under the CECILL license, which is a french adaptation of the GNU 
-\textbf{GPL} (General Public license). Anyone may use OPA freely for 
-research purposes, and is encouraged to communicate back to the NEMO team 
-its own developments and improvements. The model and the present document 
-have been made available as a service to the community. We cannot certify 
-that the code and its manual are free of errors. Bugs are inevitable and 
-some have undoubtedly survived the testing phase. Users are encouraged to 
-bring them to our attention. The author assumes no responsibility for 
-problems, errors, or incorrect usage of OPA.
-
-The OPA OGCM reference in papers and other publications is as follows: 
-
-Madec, G., 2007: NEMO: the OPA ocean engine. Note du P\^{o}le de 
-mod\'{e}lisation, Institut Pierre-Simon Laplace (IPSL), France, N\r{ }XX, 
-YYpp.
-
-Gurvan Madec: gm@locean-ipsl.upmc.fr
-
-{\ldots}.
-
-\textsc{\textbf{Foreword}}
-
-OPA is the ocean engine of the Nucleus of European Model of the Ocean 
-(NEMO). This model, like all research tools, is in perpetual evolution. The 
-present document describes the OPA model include in the release 2.3 of NEMO. 
-This is the release 9 of OPA. This version differs significantly from 
-version 8, documented in Madec \textit{et al.} (1998). The major modifications are 
-
-(1) transition to full native Fortran 90, deep code restructuring and 
-drastic reduction of CPP keys, 
-
-(2) introduction of partial step representation of bottom topography 
-
-(3) reactivation of a terrain-following vertical coordinate 
-($s-$coordinates) with the addition of several options for pressure gradient 
-computation, 
-
-(4) mixed $z-s$ coordinate
-
-(5) more choices for the treatment of the free surface: full explicit, 
-split-explicit , filtered and rigid-lid 
-
-(6) non linear free surface option (variable level thickness distributed on 
-the whole water column) 
-
-(7) additional schemes for vector and flux forms of the momentum advection
-
-(8) addition of several advection schemes on tracers
-
-(9) implementation of the AGRIF package (Adaptative Grid Refinement in 
-Fortran)
-
-(10) online diagnostics : tracers trend in the mixed layer and vorticity 
-balance
-
-(11) rewriting of the I/O management
-
-(12) OASIS 3 and 4 couplers interfacing with atmospheric global circulation 
-models.
-
-In addition, several minor modifications in the coding have been introduced 
-with the constant concern of improving performance on both scalar and vector 
-computers. 
-
-At the time of this writing, the current release is NEMO 2.3. The new 
-surface module described in this document is not yet part of the current 
-distribution.
-
-\newpage 
-
-\textsc{\textbf{Introduction}}
-
-The Nucleus for European Modelling of the Ocean (NEMO) is a framework of 
-ocean related engines, namely OPA for the Ocean dynamics and thermodynamics, 
-LIM for the sea-ice dynamics and thermodynamics, TOP for the biogeochemistry 
-(both transport (TRP) and sources minus sinks (LOBSTER, PISCES). It is 
-intended to be a flexible tool for studying the ocean and its interactions 
-with the others 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 
-OPA ocean model 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 (\underline {www.locean-ipsl.upmc.fr/NEMO}). 
-
-The ocean component of NEMO has been developed from the OPA8.2 model 
-described in Madec \textit{et al.} (1998). This model has been used for a wide range of 
-applications, either regional or global, as a forced ocean model or coupled 
-with the atmosphere. A complete list of references is found on the NEMO web 
-site. 
-
-This manual is organised in four parts. The first part 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 ($z$, $s$, 
-and variable volumes). Momentum equations are formulated in the vector 
-invariant form. The model equations are written in dimensional units in the 
-meter, kilogram, second (MKS) international system 
-
-The following chapters deal with the discrete equations. The second chapter 
-presents the space and time domain. The model is discretised on a staggered 
-grid (Arakawa C grid) with masking of land areas. Vertical discretisation 
-uses $z$ coordinates (including partial step), $s$ (terrain-following) coordinate 
-(fixed volume thickness and linear free surface), or$ s* $coordinate (variable 
-volume thickness and nonlinear free surface). The following chapters 
-describe the discretisation of the prognostic equations (momentum and 
-tracers). Explicit, split-explicit or implicit free surface formulations are 
-implemented as well as arid-lid approximation. 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).
-
-Physical parameterisations are described in chapters 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 (Gent and McWilliams 1992) with a space and time variable 
-coefficient, with options to compute the coefficients with Tr\'{e}guier et 
-al. (199X), or Visbeck et al. XXX) schemes. The model has vertical harmonic 
-viscosity and diffusion with a space and time variable coefficient, with 
-options to compute the coefficients with Blanke and Delecluse (1992), Large 
-et al. (1994), or Pacanowski and Philander (1981) mixing schemes.
-
-Optional tidal mixing parametrisation
-
-Other model characteristics (chapter {\ldots}) are the lateral boundary 
-conditions. 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. 
-
-Surface boundary conditions 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 (ref!!!) coupler. 
-
-Specific online diagnostics are available in the model: output of all the 
-tendencies of the momentum and tracers equations, output of tracers 
-tendencies averaged over the time evolving mixed layer.
-
-The model is implemented in Fortran 90, with preprocessing (C preprocessor). 
-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 \textit{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 presented in a document 
-available on the NEMO web site..
-
-The model is organized with a high internal modularity based on physics. In 
-particular, each trend (e.g., 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 
-the \textit{three-letter rule}. Each module name is made of three-letter sequences. For example, 
-TRADMP.F90 is a module related to the TRAcers equation, computing the 
-DaMPing. The complete list of module names is presented in annex. 
-Furthermore, modules are organized in a few directories that correspond to 
-their category, as indicated by the first three letters of their name. 
-
-The manual follows this organization. After the presentation of the 
-continuous equations (chapter 1), the following chapters refer to specific 
-terms of the equations each associated with a group of modules .
-
-\begin{table}[htbp]
-\begin{center}
-\begin{tabular}{|p{143pt}|l|l|}
-\hline
-Chapter 2& 
-DOM& 
-Model DOMain \\
-\hline
-Chapter 3& 
-DYN& 
-DYNamic equations (momentum) \\
-\hline
-Chapter 4& 
-TRA& 
-TRAcer equations (potential temperature and salinity) \\
-\hline
-Chapter 5 & 
-SBC& 
-Surface Boundary Conditions \\
-\hline
-Chapter 6& 
-LDF& 
-Lateral DiFfusion (parameterisations) \\
-\hline
-Chapter 7& 
-ZDF& 
-Vertical DiFfusion  \\
-\hline
-Chapter 8& 
-OBC, lbclnk module& 
-Lateral boundary conditions  \\
-\hline
-Chapter 9& 
-miscellaneous& 
- \\
-\hline
-\end{tabular}
-\label{tab1}
-\end{center}
-\end{table}
-
-\textbf{Nota Bene :}
-
-Red color : not in the current reference version (v2.3beta) but expected 
-soon
-
-Yellow : missing references, text to be updated{\ldots}
-
-\end{document}
Index: /trunk/DOC/TexFiles/Chapters/Annex_A.tex
===================================================================
--- /trunk/DOC/TexFiles/Chapters/Annex_A.tex	(revision 995)
+++ /trunk/DOC/TexFiles/Chapters/Annex_A.tex	(revision 996)
@@ -6,4 +6,5 @@
 \label{Apdx_A}
 \minitoc
+
 
 In order to establish the set of Primitive Equation in curvilinear $s$-coordinates ($i.e.$ 
Index: /trunk/DOC/TexFiles/Chapters/Annex_E.tex
===================================================================
--- /trunk/DOC/TexFiles/Chapters/Annex_E.tex	(revision 995)
+++ /trunk/DOC/TexFiles/Chapters/Annex_E.tex	(revision 996)
@@ -14,6 +14,6 @@
 
 The UBS advection scheme is an upstream biased third order scheme based on 
-an upstream-biased parabolic interpolation. It is also known as Cell 
-Averaged QUICK scheme (Quadratic Upstream Interpolation for Convective 
+an upstream-biased parabolic interpolation. It is also known as Cell Averaged 
+QUICK scheme (Quadratic Upstream Interpolation for Convective 
 Kinematics). For example, in the $i$-direction :
 \begin{equation} \label{Eq_tra_adv_ubs2}
Index: /trunk/DOC/TexFiles/Chapters/Chap_Conservation.tex
===================================================================
--- /trunk/DOC/TexFiles/Chapters/Chap_Conservation.tex	(revision 995)
+++ /trunk/DOC/TexFiles/Chapters/Chap_Conservation.tex	(revision 996)
@@ -81,5 +81,7 @@
 \end{equation}
 where $dv = e_1\, e_2\, e_3\, di\, dj\, dk$ is the volume element. 
-(II.4.1a) means that $\varsigma $ is conserved. (II.4.1b) is obtained by an integration by part. It means that $\varsigma^2$ is conserved for a horizontally non-divergent flow. 
+(II.4.1a) means that $\varsigma $ is conserved. (II.4.1b) is obtained by an 
+integration by part. It means that $\varsigma^2$ is conserved for a horizontally 
+non-divergent flow. 
 (II.4.1c) is even satisfied locally since the vorticity term is orthogonal 
 to the horizontal velocity. It means that the vorticity term has no 
Index: /trunk/DOC/TexFiles/Chapters/Chap_DOM.tex
===================================================================
--- /trunk/DOC/TexFiles/Chapters/Chap_DOM.tex	(revision 995)
+++ /trunk/DOC/TexFiles/Chapters/Chap_DOM.tex	(revision 996)
@@ -16,5 +16,6 @@
 %  - domclo:  closed sea and lakes.... management of closea sea area : specific to global configuration, both forced and coupled
 
-\gmcomment{STEVEN :maybe a picture of the directory structure in the introduction which could be referred to here, would help  ==> to be added}
+\gmcomment{STEVEN :maybe a picture of the directory structure in the introduction 
+which could be referred to here, would help  ==> to be added}
 %%%%
 
Index: /trunk/DOC/TexFiles/Chapters/Chap_DYN.tex
===================================================================
--- /trunk/DOC/TexFiles/Chapters/Chap_DYN.tex	(revision 995)
+++ /trunk/DOC/TexFiles/Chapters/Chap_DYN.tex	(revision 996)
@@ -56,5 +56,6 @@
 3D terms.
 %%%
-\gmcomment{STEVEN: not quite sure I've got the sense of the last sentence. does MISC correspond to "extracting tendency terms" or "vorticity balance"?}
+\gmcomment{STEVEN: not quite sure I've got the sense of the last sentence. does 
+MISC correspond to "extracting tendency terms" or "vorticity balance"?}
 
 % ================================================================
Index: /trunk/DOC/TexFiles/Chapters/Chap_LBC.tex
===================================================================
--- /trunk/DOC/TexFiles/Chapters/Chap_LBC.tex	(revision 995)
+++ /trunk/DOC/TexFiles/Chapters/Chap_LBC.tex	(revision 996)
@@ -72,5 +72,7 @@
 \begin{figure}[!p] \label{Fig_LBC_shlat}  \begin{center}
 \includegraphics[width=0.90\textwidth]{./Figures/Fig_LBC_shlat.pdf}
-\caption {lateral boundary condition (a) free-slip ($shlat=0$) ; (b) no-slip ($shlat=2$) ; (c) "partial" free-slip ($0<shlat<2$) and (d) "strong" no-slip ($2<shlat$). Implied "ghost" velocity inside land area is display in grey. }
+\caption {lateral boundary condition (a) free-slip ($shlat=0$) ; (b) no-slip ($shlat=2$) 
+; (c) "partial" free-slip ($0<shlat<2$) and (d) "strong" no-slip ($2<shlat$). 
+Implied "ghost" velocity inside land area is display in grey. }
 \end{center}   \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Index: /trunk/DOC/TexFiles/Chapters/Chap_LDF.tex
===================================================================
--- /trunk/DOC/TexFiles/Chapters/Chap_LDF.tex	(revision 995)
+++ /trunk/DOC/TexFiles/Chapters/Chap_LDF.tex	(revision 996)
@@ -9,8 +9,14 @@
 $\ $\newline    % force a new ligne
 
-The lateral physics on momentum and tracer equations have been given in \S\ref{PE_zdf} and their discrete formulation in \S\ref{TRA_ldf} and \S\ref{DYN_ldf}). In this section we 
-further discuss the choices that underlie each lateral physics option. 
-Choosing one lateral physics means for the user defining, (1) the space and time variations of the eddy coefficients ; (2) the direction along which the lateral diffusive fluxes are evaluated (model level, geopotential or isopycnal surfaces); and (3) the type of operator used (harmonic, or biharmonic operators, and for tracers only, eddy induced advection on tracers). These 
-three aspects of the lateral diffusion are set through namelist parameters and CPP keys (see the nam\_traldf and nam\_dynldf below).
+The lateral physics on momentum and tracer equations have been given in 
+\S\ref{PE_zdf} and their discrete formulation in \S\ref{TRA_ldf} and \S\ref{DYN_ldf}). 
+In this section we further discuss the choices that underlie each lateral physics option. 
+Choosing one lateral physics means for the user defining, (1) the space and time 
+variations of the eddy coefficients ; (2) the direction along which the lateral diffusive 
+fluxes are evaluated (model level, geopotential or isopycnal surfaces); and (3) the 
+type of operator used (harmonic, or biharmonic operators, and for tracers only, eddy 
+induced advection on tracers). These three aspects of the lateral diffusion are set 
+through namelist parameters and CPP keys (see the nam\_traldf and nam\_dynldf 
+below).
 %-----------------------------------nam_traldf - nam_dynldf--------------------------------------------
 \namdisplay{nam_traldf} 
Index: /trunk/DOC/TexFiles/Chapters/Chap_MISC.tex
===================================================================
--- /trunk/DOC/TexFiles/Chapters/Chap_MISC.tex	(revision 995)
+++ /trunk/DOC/TexFiles/Chapters/Chap_MISC.tex	(revision 996)
@@ -306,6 +306,6 @@
 -\left(C_{i+1,j}^{NS} + C_{i,j+1}^{EW} + C_{i,j}^{NS} + C_{i,j}^{EW} \right)   {   \left(  \frac{\partial \psi}{\partial t } \right)    }_{i,j}  =  B_{i,j}
 \end{multline}
-\eqref{Eq_solmat} is a linear symmetric system of equations. All the elements of the 
-corresponding matrix \textbf{A} vanish except those of five diagonals. With 
+\eqref{Eq_solmat} is a linear symmetric system of equations. All the elements of 
+the corresponding matrix \textbf{A} vanish except those of five diagonals. With 
 the natural ordering of the grid points (i.e. from west to east and from 
 south to north), the structure of \textbf{A} is block-tridiagonal with 
Index: /trunk/DOC/TexFiles/Chapters/Chap_Model_Basics.tex
===================================================================
--- /trunk/DOC/TexFiles/Chapters/Chap_Model_Basics.tex	(revision 995)
+++ /trunk/DOC/TexFiles/Chapters/Chap_Model_Basics.tex	(revision 996)
@@ -22,5 +22,8 @@
 
 
-The ocean is a fluid that can be described to a good approximation by the primitive equations, $i.e.$ the Navier-Stokes equations along with a nonlinear equation of state which couples the two active tracers (temperature and salinity) to the fluid velocity, plus the following additional assumptions made from scale considerations:
+The ocean is a fluid that can be described to a good approximation by the primitive 
+equations, $i.e.$ the Navier-Stokes equations along with a nonlinear equation of 
+state which couples the two active tracers (temperature and salinity) to the fluid 
+velocity, plus the following additional assumptions made from scale considerations:
 
 \textit{(1) spherical earth approximation: }the geopotential surfaces are assumed to be spheres so that gravity (local vertical) is parallel to the earth's radius
Index: /trunk/DOC/TexFiles/Chapters/Chap_Model_Basics_zstar.tex
===================================================================
--- /trunk/DOC/TexFiles/Chapters/Chap_Model_Basics_zstar.tex	(revision 995)
+++ /trunk/DOC/TexFiles/Chapters/Chap_Model_Basics_zstar.tex	(revision 996)
@@ -15,6 +15,6 @@
 
 In that case, the free surface equation is nonlinear, and the variations of 
-volume are fully taken into account. These coordinates systems is presented in a report 
-\citep{Levier2007} available on the \NEMO web site. 
+volume are fully taken into account. These coordinates systems is presented in 
+a report \citep{Levier2007} available on the \NEMO web site. 
 
 \colorbox{yellow}{  end of to be updated}
Index: /trunk/DOC/TexFiles/Chapters/Chap_SBC.tex
===================================================================
--- /trunk/DOC/TexFiles/Chapters/Chap_SBC.tex	(revision 995)
+++ /trunk/DOC/TexFiles/Chapters/Chap_SBC.tex	(revision 996)
@@ -408,5 +408,6 @@
 
 The presence at the sea surface of an ice covered area modifies all the fluxes 
-transmitted to the ocean. There are several way to handle sea-ice in the system depending on the value of the \np{nn{\_}ice} namelist parameter.  
+transmitted to the ocean. There are several way to handle sea-ice in the system 
+depending on the value of the \np{nn{\_}ice} namelist parameter.  
 \begin{description}
 \item[nn{\_}ice = 0]  there will never be sea-ice in the computational domain. This is a typical namelist value used for tropical ocean domain. The surface fluxes are simply specified for an ice-free ocean. No specific things are done for sea-ice.
Index: /trunk/DOC/TexFiles/Chapters/Chap_TRA.tex
===================================================================
--- /trunk/DOC/TexFiles/Chapters/Chap_TRA.tex	(revision 995)
+++ /trunk/DOC/TexFiles/Chapters/Chap_TRA.tex	(revision 996)
@@ -258,5 +258,6 @@
 where $c_u$ is a flux limiter function taking values between 0 and 1. There 
 exist many ways to define $c_u$, each correcponding to a different total 
-variance decreasing scheme. The one chosen in \NEMO is described in \citet{Zalesak1979}. $c_u$ only departs from $1$ when the advective term 
+variance decreasing scheme. The one chosen in \NEMO is described in 
+\citet{Zalesak1979}. $c_u$ only departs from $1$ when the advective term 
 produces a local extremum in the tracer field. The resulting scheme is quite 
 expensive but \emph{positive}. It can be used on both active and passive tracers. 
Index: /trunk/DOC/TexFiles/Chapters/Chap_ZDF.tex
===================================================================
--- /trunk/DOC/TexFiles/Chapters/Chap_ZDF.tex	(revision 995)
+++ /trunk/DOC/TexFiles/Chapters/Chap_ZDF.tex	(revision 996)
@@ -599,5 +599,6 @@
 
 This update is done in \mdl{zdfbfr}. The coefficients that control the strength of the 
-non-linear bottom friction are initialized as namelist parameters: $C_D$= \np{bfri2}, and $e_b$ =\np{bfeb2}.
-
-% ================================================================
+non-linear bottom friction are initialized as namelist parameters: $C_D$= \np{bfri2}, 
+and $e_b$ =\np{bfeb2}.
+
+% ================================================================
Index: /trunk/DOC/TexFiles/Chapters/Introduction.tex
===================================================================
--- /trunk/DOC/TexFiles/Chapters/Introduction.tex	(revision 995)
+++ /trunk/DOC/TexFiles/Chapters/Introduction.tex	(revision 996)
@@ -20,11 +20,15 @@
 (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. 
+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 
+(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 
@@ -118,11 +122,18 @@
 
 OPA, like all research tools, is in perpetual evolution. The present document describes 
-the OPA version include in the release 2.3 of NEMO. This release differs significantly
+the OPA version include in the release 3.0 of NEMO. This release differs significantly
 from version 8, documented in \citet{Madec1998}. The main modifications are :\\
-(1) transition to full native \textsc{Fortran} 90, deep code restructuring and drastic reduction of CPP keys; \\
+(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}; \\
-(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 , filtered and rigid-lid; \\
-(5) non linear free surface option (associated with the rescaled height coordinate  \textit{z*} or  \textit{s*}); \\
+(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 , filtered 
+and rigid-lid; \\
+(5) 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; \\
@@ -131,12 +142,9 @@
 (10) rewriting of the I/O management; \\
 (11) OASIS 3 and 4 couplers interfacing with atmospheric global circulation models. 
+(12) surface module (SBC) that simplify the way the ocean is forced and include two
+bulk formulea (CLIO and CORE)
+(13) introduction of LIM 3, the new Louvain-la-Neuve sea-ice model (C-grid rheology and
+new thermodynamics including bulk ice salinity)
 
 In addition, several minor modifications in the coding have been introduced with the constant concern of improving performance on both scalar and vector computers. 
 
-At the time of this writing, the current release is NEMO 2.3. The new surface module described in this document is not yet part of the current distribution.
-
-\vspace{1cm}  
-\colorbox{red}{Red color}: not in the current reference version (v2.3) but expected soon.
- 
-\colorbox{yellow}{Yellow color}: missing references, text to be updated.
-
