Changeset 10496


Ignore:
Timestamp:
2019-01-10T12:22:27+01:00 (15 months ago)
Author:
nicolasmartin
Message:

Global review of the foreword and introduction chapters of the manual

Location:
NEMO/trunk/doc/latex/NEMO/subfiles
Files:
2 edited

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  • NEMO/trunk/doc/latex/NEMO/subfiles/foreword.tex

    r10442 r10496  
    44 
    55% ================================================================ 
     6% Chapter Foreword 
     7% ================================================================ 
     8\chapter*{Foreword} 
     9 
     10% ================================================================ 
    611% Abstract 
    712% ================================================================ 
     13\section*{Abstract} 
    814 
    9 \chapter*{Abstract} 
     15The ocean engine of NEMO (Nucleus for European Modelling of the Ocean) is a primitive equation model adapted to 
     16regional and global ocean circulation problems. 
     17It is intended to be a flexible tool for studying the ocean and its interactions with the others components of 
     18the earth climate system over a wide range of space and time scales. 
    1019 
    11 \vspace{-40pt} 
     20Prognostic variables are the three-dimensional velocity field, a non-linear sea surface height, 
     21the \textit{Conservative} Temperature and the \textit{Absolute} Salinity. 
     22In the horizontal direction, the model uses a curvilinear orthogonal grid and in the vertical direction, 
     23a full or partial step $z$-coordinate, or $s$-coordinate, or a mixture of the two. 
     24The distribution of variables is a three-dimensional Arakawa C-type grid. 
     25Various physical choices are available to describe ocean physics, including TKE, and GLS vertical physics. 
    1226 
    13 {\small 
    14   The ocean engine of NEMO (Nucleus for European Modelling of the Ocean) is a primitive equation model adapted to 
    15   regional and global ocean circulation problems. 
    16   It is intended to be a flexible tool for studying the ocean and its interactions with 
    17   the others components of the earth climate system over a wide range of space and time scales. 
    18   Prognostic variables are the three-dimensional velocity field, a non-linear sea surface height, 
    19   the \textit{Conservative} Temperature and the \textit{Absolute} Salinity. 
    20   In the horizontal direction, the model uses a curvilinear orthogonal grid and in the vertical direction, 
    21   a full or partial step $z$-coordinate, or $s$-coordinate, or a mixture of the two. 
    22   The distribution of variables is a three-dimensional Arakawa C-type grid. 
    23   Various physical choices are available to describe ocean physics, including TKE, and GLS vertical physics. 
    24   Within NEMO, the ocean is interfaced with a sea-ice model (LIM or CICE), 
    25   passive tracer and biogeochemical models (TOP) and, 
    26   via the OASIS coupler, with several atmospheric general circulation models. 
    27   It also support two-way grid embedding via the AGRIF software. 
    28 }  
     27Within NEMO, the ocean is interfaced with a sea-ice model (SI$^3$) 
     28 %or \href{https://github.com/CICE-Consortium/CICE}{CICE}), 
     29passive tracer and biogeochemical models (TOP-PISCES) and, 
     30via the \href{https://portal.enes.org/oasis}{OASIS} coupler, with several atmospheric general circulation models. 
     31It also support two-way grid embedding via the \href{http://agrif.imag.fr}{AGRIF} software. 
     32 
    2933 
    3034% ================================================================ 
    3135% Disclaimer 
    3236% ================================================================ 
    33 \chapter*{Disclaimer} 
     37\section*{Disclaimer} 
    3438 
    35 Like all components of NEMO, 
    36 the ocean component is developed under the \href{http://www.cecill.info/}{CECILL license}, 
    37 which is a French adaptation of the GNU GPL (General Public License). 
    38 Anyone may use it freely for research purposes, 
    39 and is encouraged to communicate back to the NEMO team its own developments and improvements. 
     39Like all components of NEMO, the ocean component is developed under 
     40the \href{http://www.cecill.info}{CECILL license}, which is a French adaptation of the GNU GPL 
     41(General Public License). 
     42Anyone may use it freely for research purposes, and is encouraged to communicate back to the NEMO team 
     43its own developments and improvements. 
     44 
    4045The model and the present document have been made available as a service to the community. 
    4146We cannot certify that the code and its manual are free of errors. 
    4247Bugs are inevitable and some have undoubtedly survived the testing phase. 
    4348Users are encouraged to bring them to our attention. 
     49 
    4450The author assumes no responsibility for problems, errors, or incorrect usage of NEMO. 
    4551 
    46 \vspace{1cm} 
    47 NEMO reference in papers and other publications is as follows: 
     52% ================================================================ 
     53% Citation 
     54% ================================================================ 
     55\section*{Citation} 
     56 
     57Reference for papers and other publications is as follows: 
    4858\vspace{0.5cm} 
    4959 
    50 Madec, G., and the NEMO team, 2008: NEMO ocean engine.  
    51 \textit{Note du P\^ole de mod\'{e}lisation}, Institut Pierre-Simon Laplace (IPSL), France,  
    52 No 27, ISSN No 1288-1619.\\ 
     60{\sffamily 
     61NEMO ocean engine, 
     62Madec Gurvan and NEMO System Team, NEMO Consortium, 
     63Issue 27, Notes du Pôle de modélisation de l'Institut Pierre-Simon Laplace (IPSL), ISSN 1288-1619, 
     64\href{http://doi.org/10.5281/zenodo.1464816}{doi:10.5281/zenodo.1464816} 
     65} 
    5366 
     67% ================================================================ 
     68% External resources 
     69% ================================================================ 
     70\section*{External resources} 
    5471 
    55 \vspace{0.5cm} 
    56 Additional information can be found on \href{http://www.nemo-ocean.eu/}{www.nemo-ocean.eu}. 
    57 \vspace{0.5cm} 
     72Additional information can be found on the \href{http://www.nemo-ocean.eu}{website} of the project and 
     73the \href{http://forge.ipsl.jussieu.fr/nemo}{forge platform} of the source code. 
     74A \href{http://listes.ipsl.fr/sympa/info/nemo-newsletter}{newsletter list} is also open for subscription to 
     75receive top-down communication from the consortium (announcements, job opportunities, ...). 
    5876 
    5977\biblio 
  • NEMO/trunk/doc/latex/NEMO/subfiles/introduction.tex

    r10442 r10496  
    1010 
    1111The Nucleus for European Modelling of the Ocean (\NEMO) is a framework of ocean related engines, 
    12 namely OPA \footnote{OPA = Oc\'{e}an PArall\'{e}lis\'{e}} for the ocean dynamics and thermodynamics, 
    13 LIM \footnote{LIM = Louvain la-neuve Ice Model} for the sea-ice dynamics and thermodynamics, 
    14 TOP \footnote{TOP = Tracer in the Ocean Paradigm} for the biogeochemistry (both transport (TRP) and sources  
    15 minus sinks (LOBSTER \footnote{LOBSTER = Lodyc Ocean Biogeochemical SysTem for Ecosystem and Resources}, 
    16 PISCES \footnote{PISCES = Pelagic Interactions Scheme for Carbon and Ecosystem Studies})). 
     12namely OPA \footnote{OPA: Oc\'{e}an PArall\'{e}lis\'{e} (french)} for the ocean dynamics and thermodynamics, 
     13SI$^3$ \footnote{SI$^3$: Sea-Ice modelling Integrated Initiative} for the sea-ice dynamics and thermodynamics, 
     14TOP \footnote{TOP: Tracer in the Ocean Paradigm} for the biogeochemistry  
     15(both transport (TRP) and sources minus sinks  
     16(PISCES \footnote{PISCES: Pelagic Interactions Scheme for Carbon and Ecosystem Studies})). 
    1717It is intended to be a flexible tool for studying the ocean and its interactions with the other components of 
    1818the earth climate system (atmosphere, sea-ice, biogeochemical tracers, ...) over 
    19 a wide range of space and time scales.  
    20 This documentation provides information about the physics represented by the ocean component of \NEMO and 
     19a wide range of space and time scales. 
     20This manual provides information about the physics represented by the ocean component of \NEMO and 
    2121the rationale for the choice of numerical schemes and the model design. 
    22 More specific information about running the model on different computers, or how to set up a configuration, 
    23 are found on the \NEMO web site (www.nemo-ocean.eu).  
    24  
    25 The ocean component of \NEMO has been developed from the OPA model, release 8.2, described in \citet{Madec1998}. 
    26 This model has been used for a wide range of applications, both regional or global, 
    27 as a forced ocean model and as a model coupled with the sea-ice and/or the atmosphere.   
     22For the use of framework,  
     23a guide which gathers the \texttt{README} files spread out in the source code can be build and  
     24exported in web or printable format (see \path{./doc/rst}). 
     25An online version of the guide is also available on the  
     26\href{http://forge.ipsl.jussieu.fr/nemo}{\NEMO forge platform}. 
     27 
     28The ocean component of \NEMO has been developed from the legacy of the OPA model, release 8.2,  
     29described in \citet{Madec1998}. 
     30This model has been used for a wide range of applications, both regional or global, as a forced ocean model and  
     31as a model coupled with the sea-ice and/or the atmosphere. 
    2832 
    2933This manual is organised in as follows. 
     
    3337(primitive equations, with temperature, salinity and an equation of seawater). 
    3438The equations are written in a curvilinear coordinate system, with a choice of vertical coordinates 
    35 ($z$, $s$, \zstar, \sstar, \ztilde, \stilde, and a mixture of them). 
     39($z$, $s$, \zstar, \sstar, \ztilde, \stilde, and a mix of them). 
    3640Momentum equations are formulated in vector invariant or flux form. 
    3741Dimensional units in the meter, kilogram, second (MKS) international system are used throughout. 
     
    3943The following chapters deal with the discrete equations. 
    4044\autoref{chap:STP} presents the time domain. 
    41 The model time stepping environment is a three level scheme in which the tendency terms of 
    42 the equations are evaluated either centered in time, or forward, or backward depending of the nature of the term. 
     45The model time stepping environment is a three level scheme in which  
     46the tendency terms of the equations are evaluated either centered in time, or forward, or backward depending of  
     47the nature of the term. 
    4348\autoref{chap:DOM} presents the space domain. 
    4449The model is discretised on a staggered grid (Arakawa C grid) with masking of land areas. 
    45 Vertical discretisation used depends on both how the bottom topography is represented and 
    46 whether the free surface is linear or not. 
    47 Full step or partial step $z$-coordinate or $s$- (terrain-following) coordinate is used with 
    48 linear free surface (level position are then fixed in time). 
    49 In non-linear free surface, 
    50 the corresponding rescaled height coordinate formulation (\zstar or \sstar) is used 
     50Vertical discretisation used depends on both how the bottom topography is represented and whether  
     51the free surface is linear or not. 
     52Full step or partial step $z$-coordinate or $s$- (terrain-following) coordinate is used with linear free surface  
     53(level position are then fixed in time). 
     54In non-linear free surface, the corresponding rescaled height coordinate formulation (\zstar or \sstar) is used 
    5155(the level position then vary in time as a function of the sea surface heigh). 
    5256The following two chapters (\autoref{chap:TRA} and \autoref{chap:DYN}) describe the discretisation of 
    5357the prognostic equations for the active tracers and the momentum. 
    5458Explicit, split-explicit and filtered free surface formulations are implemented. 
    55 A number of numerical schemes are available for momentum advection, for the computation of the pressure gradients, 
    56 as well as for the advection of tracers (second or higher order advection schemes, including positive ones). 
    57  
    58 Surface boundary conditions (\autoref{chap:SBC}) can be implemented as prescribed fluxes, 
    59 or bulk formulations for the surface fluxes (wind stress, heat, freshwater). 
     59A number of numerical schemes are available for momentum advection,  
     60for the computation of the pressure gradients, as well as for the advection of tracers  
     61(second or higher order advection schemes, including positive ones). 
     62 
     63Surface boundary conditions (\autoref{chap:SBC}) can be implemented as prescribed fluxes, or bulk formulations for  
     64the surface fluxes (wind stress, heat, freshwater). 
    6065The model allows penetration of solar radiation. 
    6166There is an optional geothermal heating at the ocean bottom. 
    62 Within the \NEMO system the ocean model is interactively coupled with a sea ice model (LIM) and 
    63 with biogeochemistry models (PISCES, LOBSTER). 
     67Within the \NEMO system the ocean model is interactively coupled with a sea ice model (SI$^3$) and 
     68a biogeochemistry model (PISCES). 
    6469Interactive coupling to Atmospheric models is possible via the OASIS coupler \citep{OASIS2006}. 
    6570Two-way nesting is also available through an interface to the AGRIF package 
    6671(Adaptative Grid Refinement in \fortran) \citep{Debreu_al_CG2008}. 
    67 The interface code for coupling to an alternative sea ice model (CICE, \citet{Hunke2008}) has now been upgraded so 
    68 that it works for both global and regional domains, although AGRIF is still not available. 
     72% Needs to be reviewed 
     73%The interface code for coupling to an alternative sea ice model (CICE, \citet{Hunke2008}) has now been upgraded so 
     74%that it works for both global and regional domains, although AGRIF is still not available. 
    6975 
    7076Other model characteristics are the lateral boundary conditions (\autoref{chap:LBC}). 
    7177Global configurations of the model make use of the ORCA tripolar grid, with special north fold boundary condition. 
    7278Free-slip or no-slip boundary conditions are allowed at land boundaries. 
    73 Closed basin geometries as well as periodic domains and open boundary conditions are possible.  
     79Closed basin geometries as well as periodic domains and open boundary conditions are possible. 
    7480 
    7581Physical parameterisations are described in \autoref{chap:LDF} and \autoref{chap:ZDF}. 
     
    8086\citet{Treguier1997}. 
    8187The model has vertical harmonic viscosity and diffusion with a space and time variable coefficient, 
    82 with options to compute the coefficients with \citet{Blanke1993}, \citet{Pacanowski_Philander_JPO81}, 
    83 or \citet{Umlauf_Burchard_JMS03} mixing schemes. 
    84  \vspace{1cm} 
     88with options to compute the coefficients with \citet{Blanke1993}, \citet{Pacanowski_Philander_JPO81}, or  
     89\citet{Umlauf_Burchard_JMS03} mixing schemes. 
    8590  
    8691%%gm    To be put somewhere else .... 
    87  
    88 \noindent CPP keys and namelists are used for inputs to the code.  \newline 
    89  
    90 \noindent \index{CPP keys} CPP keys \newline 
     92%%nm    We should consider creating a glossary for all this kind of stuff (terms, acronyms and symbols) 
     93%%      http://en.wikibooks.org/wiki/LaTeX/Glossary 
     94\noindent CPP keys and namelists are used as inputs to the code. 
     95 
     96\noindent \index{CPP keys} CPP keys 
     97 
    9198Some CPP keys are implemented in the \fortran code to allow code selection at compiling step. 
    9299This selection of code at compilation time reduces the reliability of the whole platform since 
    93100it changes the code from one set of CPP keys to the other. 
    94101It is used only when the addition/suppression of the part of code highly changes the amount of memory at run time. 
    95 Usual coding looks like :  
     102Usual coding looks like:  
     103 
    96104\begin{forlines} 
    97105#if defined key_option1 
     
    105113The namelist allows to input variables (character, logical, real and integer) into the code. 
    106114There is one namelist file for each component of NEMO (dynamics, sea-ice, biogeochemistry...) 
    107 containing all the FOTRAN namelists needed. 
    108 The implementation in NEMO uses a two step process. For each \fortran namelist, two files are read: 
     115containing all the \fortran namelists needed. 
     116The implementation in NEMO uses a 2-step process.  
     117For each \fortran namelist, two files are read: 
     118 
    109119\begin{enumerate} 
    110120\item 
    111   A reference namelist (in \path{CONFIG/SHARED/namelist_ref}) is read first. 
     121  A reference namelist (in \path{./cfgs/SHARED/namelist_ref}) is read first. 
    112122  This file contains all the namelist variables which are initialised to default values 
    113123\item 
    114   A configuration namelist (in \path{CONFIG/CFG_NAME/EXP00/namelist_cfg}) is read aferwards. 
     124  A configuration namelist (in \path{./cfgs/CFG_NAME/EXP00/namelist_cfg}) is read aferwards. 
    115125  This file contains only the namelist variables which are changed from default values, and overwrites those. 
    116126\end{enumerate} 
    117127A template can be found in \path{NEMO/OPA_SRC/module.example}. 
    118128The effective namelist, taken in account during the run, is stored at execution time in 
    119 an output\_namelist\_dyn (or \_ice or \_top) file. 
    120 \vspace{1cm} 
    121  
     129an \texttt{output\_namelist\_dyn} (or \texttt{\_ice} or \texttt{\_top}) file. 
    122130%%gm  end 
    123131 
     
    135143(water column model, ORCA and GYRE families of configurations). 
    136144 
    137 The model is implemented in \fninety, with preprocessing (C-pre-processor). 
     145%%nm: Add some words on the NEMO dependencies 
     146The model is implemented in \fninety, with preprocessing (C pre-processor). 
    138147It runs under UNIX. 
    139148It is optimized for vector computers and parallelised by domain decomposition with MPI. 
     
    142151The coding rules for OPA include conventions for naming variables, 
    143152with different starting letters for different types of variables (real, integer, parameter\ldots). 
    144 Those rules are briefly presented in \autoref{apdx:D} and a more complete document is available on 
    145 the \NEMO web site. 
     153Those rules are briefly presented in \autoref{apdx:D} and a more complete document is available . 
    146154 
    147155The model is organized with a high internal modularity based on physics. 
     
    149157is computed in a dedicated module. 
    150158To make it easier for the user to find his way around the code, the module names follow a three-letter rule. 
    151 For example, \mdl{traldf} is a module related to the TRAcers equation, computing the Lateral DiFfussion.  
     159For example, \mdl{traldf} is a module related to the TRAcers equation, computing the Lateral DiFfussion. 
    152160%The complete list of module names is presented in \autoref{apdx:D}.      %====>>>> to be done ! 
    153161Furthermore, modules are organized in a few directories that correspond to their category, 
    154 as indicated by the first three letters of their name (\autoref{tab:chap}). 
     162as indicated by the first three letters of their name (\autoref{tab:chapters}). 
    155163 
    156164The manual mirrors the organization of the model. 
    157165After the presentation of the continuous equations (\autoref{chap:PE}), 
    158 the following chapters refer to specific terms of the equations each associated with 
    159 a group of modules (\autoref{tab:chap}). 
    160  
     166the following chapters refer to specific terms of the equations each associated with a group of modules  
     167(\autoref{tab:chap}). 
    161168 
    162169%--------------------------------------------------TABLE-------------------------------------------------- 
    163170\begin{table}[!t]  
    164   % \begin{center} \begin{tabular}{|p{143pt}|l|l|} \hline 
    165   \caption{ \protect\label{tab:chap}   Organization of Chapters mimicking the one of the model directories. } 
     171  \caption{ 
     172    \protect\label{tab:chapters} 
     173    Organization of Chapters mimicking the one of the model directories. 
     174  } 
    166175  \begin{center} 
    167     \begin{tabular}{|l|l|l|}  \hline 
    168       \autoref{chap:STP}   & -                 & model time STePping environment \\    \hline 
    169       \autoref{chap:DOM}   & DOM    & model DOMain \\    \hline 
    170       \autoref{chap:TRA}   & TRA    & TRAcer equations (potential temperature and salinity) \\   \hline 
    171       \autoref{chap:DYN}   & DYN    & DYNamic equations (momentum) \\      \hline 
    172       \autoref{chap:SBC}   & SBC    & Surface Boundary Conditions \\       \hline 
    173       \autoref{chap:LBC}   & LBC    & Lateral Boundary Conditions (also OBC and BDY)  \\     \hline 
    174       \autoref{chap:LDF}   & LDF    & Lateral DiFfusion (parameterisations) \\   \hline 
    175       \autoref{chap:ZDF}   & ZDF    & vertical (Z) DiFfusion (parameterisations)  \\      \hline 
    176       \autoref{chap:DIA}   & DIA    & I/O and DIAgnostics (also IOM, FLO and TRD) \\      \hline 
    177       \autoref{chap:OBS}   & OBS    & OBServation and model comparison  \\    \hline 
    178       \autoref{chap:ASM}   & ASM    & ASsiMilation increment  \\     \hline 
    179       \autoref{chap:MISC}  & SOL    & Miscellaneous  topics (including solvers)  \\       \hline 
    180       \autoref{chap:CFG}   &  -        & predefined configurations (including C1D) \\     \hline 
     176    \begin{tabular}{|l|l|l|} 
     177      \hline 
     178      \autoref{chap:STP}  & -   & model time STePping environment \\ 
     179      \hline 
     180      \autoref{chap:DOM}  & DOM & model DOMain \\ 
     181      \hline 
     182      \autoref{chap:TRA}  & TRA & TRAcer equations (potential temperature and salinity) \\ 
     183      \hline 
     184      \autoref{chap:DYN}  & DYN & DYNamic equations (momentum) \\ 
     185      \hline 
     186      \autoref{chap:SBC}  & SBC & Surface Boundary Conditions \\ 
     187      \hline 
     188      \autoref{chap:LBC}  & LBC & Lateral Boundary Conditions (also OBC and BDY)  \\ 
     189      \hline 
     190      \autoref{chap:LDF}  & LDF & Lateral DiFfusion (parameterisations) \\ 
     191      \hline 
     192      \autoref{chap:ZDF}  & ZDF & vertical (Z) DiFfusion (parameterisations)  \\ 
     193      \hline 
     194      \autoref{chap:DIA}  & DIA & I/O and DIAgnostics (also IOM, FLO and TRD) \\ 
     195      \hline 
     196      \autoref{chap:OBS}  & OBS & OBServation and model comparison  \\ 
     197      \hline 
     198      \autoref{chap:ASM}  & ASM & ASsiMilation increment  \\ 
     199      \hline 
     200      \autoref{chap:MISC} & SOL & Miscellaneous  topics (including solvers)  \\ 
     201      \hline 
     202      \autoref{chap:CFG}  & -   & predefined configurations (including C1D) \\ 
     203      \hline 
    181204    \end{tabular} 
    182205  \end{center} 
     
    184207%-------------------------------------------------------------------------------------------------------------- 
    185208 
    186  
     209%% nm: the following section has to vastly remodeled to focus only on well-identified versions of NEMO 
     210%% (3.4, 3.6, 4.0 and further releases). Then its formatting must be improved too. 
    187211\subsubsection{Changes between releases} 
     212 
    188213NEMO/OPA, like all research tools, is in perpetual evolution. 
    189214The present document describes the OPA version include in the release 3.4 of NEMO. 
    190 This release differs significantly from version 8, documented in \citet{Madec1998}.\\ 
    191  
    192 $\bullet$ The main modifications from OPA v8 and NEMO/OPA v3.2 are :\\ 
    193 \begin{enumerate} 
     215This release differs significantly from version 8, documented in \citet{Madec1998}. \\ 
     216 
     217The main modifications from OPA v8 and NEMO/OPA v3.2 are : 
     218 
     219\begin{itemize} 
    194220\item 
    195221  transition to full native \fninety, deep code restructuring and drastic reduction of CPP keys;  
     
    200226  partial reactivation of a terrain-following vertical coordinate ($s$- and hybrid $s$-$z$) with 
    201227  the addition of several options for pressure gradient computation 
    202   \footnote{Partial support of $s$-coordinate: there is presently no support for neutral physics in 
     228  \footnote{ 
     229    Partial support of $s$-coordinate: there is presently no support for neutral physics in 
    203230    $s$-coordinate and for the new options for horizontal pressure gradient computation with 
    204231    a non-linear equation of state. 
    205   }; 
     232  } 
     233  ; 
    206234\item 
    207235  more choices for the treatment of the free surface: full explicit, split-explicit or filtered schemes, 
    208236  and suppression of the rigid-lid option; 
    209237\item 
    210   non linear free surface associated with the rescaled height coordinate \zstar or \textit{s}; 
     238  non linear free surface associated with the rescaled height coordinate \zstar or $s$; 
    211239\item 
    212240  additional schemes for vector and flux forms of the momentum advection; 
     
    237265  (C-grid rheology and new thermodynamics including bulk ice salinity) 
    238266  \citep{Vancoppenolle_al_OM09a, Vancoppenolle_al_OM09b} 
    239 \end{enumerate} 
    240  
    241  \vspace{1cm} 
    242 $\bullet$ The main modifications from NEMO/OPA v3.2 and v3.3 are :\\ 
    243 \begin{enumerate} 
     267\end{itemize} 
     268 
     269The main modifications from NEMO/OPA v3.2 and v3.3 are: 
     270 
     271\begin{itemize} 
    244272\item 
    245273  introduction of a modified leapfrog-Asselin filter time stepping scheme 
     
    280308\item 
    281309  Linear-tangent and Adjoint component (TAM) added, phased with v3.0 
    282 \end{enumerate} 
     310\end{itemize} 
     311 
    283312\vspace{1cm} 
     313 
    284314In addition, several minor modifications in the coding have been introduced with the constant concern of 
    285 improving the model performance.  
    286  
    287 \vspace{1cm} 
    288 $\bullet$ The main modifications from NEMO/OPA v3.3 and  v3.4 are :\\ 
    289 \begin{enumerate} 
     315improving the model performance. 
     316 
     317The main modifications from NEMO/OPA v3.3 and v3.4 are: 
     318 
     319\begin{itemize} 
    290320\item finalisation of above iso-neutral mixing \citep{Griffies_al_JPO98}"; 
    291321\item "Neptune effect" parametrisation; 
    292322\item horizontal pressure gradient suitable for s-coordinate; 
    293 \item semi-implicit bottom friction; 
     323\item semi -implicit bottom friction; 
    294324\item finalisation of the merge of passive and active tracers advection-diffusion modules; 
    295325\item a new bulk formulae (so-called MFS); 
    296326\item use fldread for the off-line tracer component (OFF\_SRC); 
    297 \item use MPI point to point communications  for north fold; 
     327\item use MPI point to point communications for north fold; 
    298328\item diagnostic of transport; 
    299 \end{enumerate} 
    300  
    301  
    302  \vspace{1cm} 
    303 $\bullet$ The main modifications from NEMO/OPA v3.4 and  v3.6 are :\\ 
    304 \begin{enumerate} 
    305  \item ... ;  
    306 \end{enumerate} 
    307  
    308  
    309  \vspace{1cm} 
    310 $\bullet$ The main modifications from NEMO/OPA v3.6 and  v4.0 are :\\ 
    311 \begin{enumerate} 
    312 \item new definition of configurations ; 
    313 \item bulk formulation ; 
    314 \item NEMO-wave large scale interactions ; 
    315 \item ... ;  
    316 \end{enumerate} 
    317  
     329\end{itemize} 
     330 
     331The main modifications from NEMO/OPA v3.4 and v3.6 are: 
     332 
     333\begin{itemize} 
     334 \item ...; 
     335\end{itemize} 
     336 
     337The main modifications from NEMO/OPA v3.6 and v4.0 are: 
     338 
     339\begin{itemize} 
     340\item new definition of configurations; 
     341\item bulk formulation; 
     342\item NEMO-wave large scale interactions; 
     343\item ...; 
     344\end{itemize} 
    318345 
    319346\biblio 
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