Changeset 11522


Ignore:
Timestamp:
2019-09-10T12:21:20+02:00 (12 months ago)
Author:
nicolasmartin
Message:

Review the beginning of the manual
Move the changelog to the common part shared between 3 manuals
Add few paragraphs on the development workflow
Improve the introduction of the manual

Location:
NEMO/trunk/doc/latex/NEMO/main
Files:
3 edited
1 moved

Legend:

Unmodified
Added
Removed
  • NEMO/trunk/doc/latex/NEMO/main/chapters.tex

    r11170 r11522  
    1 \subfile{../subfiles/introduction}        %% Introduction 
    21\subfile{../subfiles/chap_model_basics} 
    32\subfile{../subfiles/chap_time_domain}    %% Time discretisation (time stepping strategy) 
     
    1514\subfile{../subfiles/chap_misc}           %% Miscellaneous topics 
    1615\subfile{../subfiles/chap_CONFIG}         %% Predefined configurations 
     16 
     17%% Not included 
     18%\subfile{../subfiles/chap_model_basics_zstar} 
     19%\subfile{../subfiles/chap_DIU} 
     20%\subfile{../subfiles/chap_conservation} 
  • NEMO/trunk/doc/latex/NEMO/main/definitions.tex

    r11433 r11522  
    22\def \engine{NEMO} 
    33 
    4 %% Title and cover page settings 
     4%% Cover page settings 
    55\def \spacetop{  \vspace*{1.85cm} } 
    66\def \heading{NEMO ocean engine} 
    7 \def \subheading{} 
     7%\def \subheading{} 
    88\def \spacedown{ \vspace*{0.75cm } } 
    9 \def \authorswidth{ 0.3\linewidth} 
     9\def \authorswidth{  0.3\linewidth} 
    1010\def \rulelenght{270pt} 
    1111\def \abstractwidth{0.6\linewidth} 
    1212 
    13 %% Color for document (frontpage banner, links  and chapter boxes) 
    14 \def \setcolor{ \definecolor{manualcolor}{cmyk}{1, .60, 0, .40} } 
     13%% Manual color (frontpage banner, links  and chapter boxes) 
     14\def \setmanualcolor{ \definecolor{manualcolor}{cmyk}{1, .60, 0, .40} } 
    1515 
    1616%% IPSL publication number 
  • NEMO/trunk/doc/latex/NEMO/main/introduction.tex

    r11436 r11522  
    1 \documentclass[../main/NEMO_manual]{subfiles} 
    21 
    3 %% Remove section heading (no section here) 
    4 \rehead{} 
     2\chapter*{Introduction} 
    53 
    6 \begin{document} 
     4%\chaptertoc 
    75 
    8 % ================================================================ 
    9 % INTRODUCTION 
    10 % ================================================================ 
     6%\paragraph{Changes record} ~\\ 
    117 
    12 \chapter{Introduction} 
     8%\thispagestyle{plain} 
    139 
    14 The Nucleus for European Modelling of the Ocean (\NEMO) is a framework of ocean related engines, 
    15 namely OPA \footnote{OPA: Oc\'{e}an PArall\'{e}lis\'{e} (french)} for the ocean dynamics and thermodynamics, 
    16 SI$^3$ \footnote{SI$^3$: Sea-Ice modelling Integrated Initiative} for the sea-ice dynamics and thermodynamics, 
    17 TOP \footnote{TOP: Tracer in the Ocean Paradigm} for the biogeochemistry 
    18 (both transport (TRP) and sources minus sinks 
    19 (PISCES \footnote{PISCES: Pelagic Interactions Scheme for Carbon and Ecosystem Studies})). 
    20 It is intended to be a flexible tool for studying the ocean and its interactions with the other components of 
    21 the earth climate system (atmosphere, sea-ice, biogeochemical tracers, ...) over 
    22 a wide range of space and time scales. 
     10%{\footnotesize 
     11%  \begin{tabularx}{\textwidth}{l||X|X} 
     12%    Release & Author(s) & Modifications \\ 
     13%    \hline 
     14%    {\em x.x} & {\em ...} & {\em ...}   \\ 
     15%    {\em ...} & {\em ...} & {\em ...}   \\ 
     16%  \end{tabularx} 
     17%} 
     18 
     19%\clearpage 
     20 
     21The \textbf{N}ucleus for \textbf{E}uropean \textbf{M}odelling of the \textbf{O}cean (\NEMO) is 
     22a framework of ocean related engines, namely the aforementioned for 
     23the ocean dynamics and thermodynamics, 
     24\SIcube \footnote{\textbf{S}ea-\textbf{I}ce modelling \textbf{I}ntegrated \textbf{I}nitiative} 
     25for the sea-ice dynamics and thermodynamics, 
     26\TOP \footnote{\textbf{T}racer in the \textbf{O}cean \textbf{P}aradigm} for 
     27the biogeochemistry (both transport and sources minus sinks 
     28(\PISCES \footnote{ 
     29  \textbf{P}elagic \textbf{I}nteractions \textbf{S}cheme for 
     30  \textbf{C}arbon and \textbf{E}cosystem \textbf{S}tudies 
     31} 
     32)). 
     33The ocean component has been developed from the legacy of 
     34the \OPA \footnote{\textbf{O}c\'{e}an \textbf{PA}rall\'{e}lis\'{e} (French)} 
     35model, described in \citet{madec.delecluse.ea_NPM98}. 
     36This model has been used for a wide range of applications, both regional or global, 
     37as a forced ocean model and as a model coupled with the sea-ice and/or the atmosphere. 
     38 
    2339This manual provides information about the physics represented by the ocean component of \NEMO\ and 
    2440the rationale for the choice of numerical schemes and the model design. 
    2541For the use of framework, 
    2642a guide which gathers the \texttt{README} files spread out in the source code can be build and 
    27 exported in web or printable format (see \path{./doc/rst}). 
    28 An online version of the guide is also available on the 
    29 \href{http://forge.ipsl.jussieu.fr/nemo}{\NEMO\ forge platform}. 
     43exported in a web or printable format (see \path{./doc/rst}). 
     44Also a online copy is available on the \href{http://forge.ipsl.jussieu.fr/nemo}{forge platform}. 
    3045 
    31 The ocean component of \NEMO\ has been developed from the legacy of the OPA model, release 8.2, 
    32 described in \citet{madec.delecluse.ea_NPM98}. 
    33 This model has been used for a wide range of applications, both regional or global, as a forced ocean model and 
    34 as a model coupled with the sea-ice and/or the atmosphere. 
     46%% ================================================================================================= 
     47\section*{Manual outline} 
    3548 
    36 This manual is organised in as follows. 
    37 \autoref{chap:PE} presents the model basics, \ie\ the equations and their assumptions, 
    38 the vertical coordinates used, and the subgrid scale physics. 
    39 This part deals with the continuous equations of the model 
    40 (primitive equations, with temperature, salinity and an equation of seawater). 
     49\subsection*{Chapters} 
     50 
     51The manual mirrors the organization of the model and it is organised in as follows: 
     52after the presentation of the continuous equations 
     53(primitive equations with temperature and salinity, and an equation of seawater) in the next chapter, 
     54the following chapters refer to specific terms of the equations each associated with 
     55a group of modules. 
     56 
     57\begin{description} 
     58\item [\nameref{chap:PE}] presents the equations and their assumptions, the vertical coordinates used, 
     59and the subgrid scale physics. 
    4160The equations are written in a curvilinear coordinate system, with a choice of vertical coordinates 
    4261($z$, $s$, \zstar, \sstar, \ztilde, \stilde, and a mix of them). 
    4362Momentum equations are formulated in vector invariant or flux form. 
    4463Dimensional units in the meter, kilogram, second (MKS) international system are used throughout. 
    45  
    4664The following chapters deal with the discrete equations. 
    47 \autoref{chap:STP} presents the time domain. 
    48 The model time stepping environment is a three level scheme in which 
    49 the tendency terms of the equations are evaluated either centered in time, or forward, or backward depending of 
    50 the nature of the term. 
    51 \autoref{chap:DOM} presents the space domain. 
    52 The model is discretised on a staggered grid (Arakawa C grid) with masking of land areas. 
     65\item [\nameref{chap:STP}] presents the model time stepping environment. 
     66it is a three level scheme in which the tendency terms of the equations are evaluated either 
     67centered in time, or forward, or backward depending of the nature of the term. 
     68\item [\nameref{chap:DOM}] presents the model \textbf{DOM}ain. 
     69It is discretised on a staggered grid (Arakawa C grid) with masking of land areas. 
    5370Vertical discretisation used depends on both how the bottom topography is represented and whether 
    5471the free surface is linear or not. 
    55 Full step or partial step $z$-coordinate or $s$- (terrain-following) coordinate is used with linear free surface 
    56 (level position are then fixed in time). 
    57 In non-linear free surface, the corresponding rescaled height coordinate formulation (\zstar or \sstar) is used 
     72Full step or partial step $z$-coordinate or $s$- (terrain-following) coordinate is used with 
     73linear free surface (level position are then fixed in time). 
     74In non-linear free surface, the corresponding rescaled height coordinate formulation 
     75(\zstar or \sstar) is used 
    5876(the level position then vary in time as a function of the sea surface heigh). 
    59 The following two chapters (\autoref{chap:TRA} and \autoref{chap:DYN}) describe the discretisation of 
    60 the prognostic equations for the active tracers and the momentum. 
     77\item [\nameref{chap:TRA} and \nameref{chap:DYN}] describe the discretisation of 
     78the prognostic equations for the active \textbf{TRA}cers (potential temperature and salinity) and 
     79the momentum (\textbf{DYN}amic). 
    6180Explicit, split-explicit and filtered free surface formulations are implemented. 
    6281A number of numerical schemes are available for momentum advection, 
    6382for the computation of the pressure gradients, as well as for the advection of tracers 
    6483(second or higher order advection schemes, including positive ones). 
    65  
    66 Surface boundary conditions (\autoref{chap:SBC}) can be implemented as prescribed fluxes, or bulk formulations for 
    67 the surface fluxes (wind stress, heat, freshwater). 
     84\item [\nameref{chap:SBC}] can be implemented as prescribed fluxes, 
     85or bulk formulations for the surface fluxes (wind stress, heat, freshwater). 
    6886The model allows penetration of solar radiation. 
    6987There is an optional geothermal heating at the ocean bottom. 
    70 Within the \NEMO\ system the ocean model is interactively coupled with a sea ice model (SI$^3$) and 
    71 a biogeochemistry model (PISCES). 
    72 Interactive coupling to Atmospheric models is possible via the \href{https://portal.enes.org/oasis}{OASIS coupler}. 
    73 Two-way nesting is also available through an interface to the AGRIF package 
    74 (Adaptative Grid Refinement in \fortran) \citep{debreu.vouland.ea_CG08}. 
    75 % Needs to be reviewed 
    76 %The interface code for coupling to an alternative sea ice model (CICE, \citet{Hunke2008}) has now been upgraded so 
    77 %that it works for both global and regional domains, although AGRIF is still not available. 
    78  
    79 Other model characteristics are the lateral boundary conditions (\autoref{chap:LBC}). 
    80 Global configurations of the model make use of the ORCA tripolar grid, with special north fold boundary condition. 
     88Within the \NEMO\ system the ocean model is interactively coupled with 
     89a sea ice model (\SIcube) and a biogeochemistry model (\PISCES). 
     90Interactive coupling to Atmospheric models is possible via the \OASIS\ coupler. 
     91Two-way nesting is also available through an interface to the \AGRIF\ package, 
     92\ie\ \textbf{A}daptative \textbf{G}rid \textbf{R}efinement in \textbf{F}ortran 
     93\citep{debreu.vouland.ea_CG08}. 
     94The interface code for coupling to an alternative sea ice model (\CICE) has now been upgraded so that 
     95it works for both global and regional domains. 
     96\item [\nameref{chap:LBC}] presents the \textbf{L}ateral 
     97\textbf{B}oun\textbf{D}ar\textbf{Y} \textbf{C}onditions. 
     98Global configurations of the model make use of the ORCA tripolar grid, 
     99with special north fold boundary condition. 
    81100Free-slip or no-slip boundary conditions are allowed at land boundaries. 
    82101Closed basin geometries as well as periodic domains and open boundary conditions are possible. 
    83  
    84 Physical parameterisations are described in \autoref{chap:LDF} and \autoref{chap:ZDF}. 
     102\item [\nameref{chap:LDF} and \nameref{chap:ZDF}] describe the physical parameterisations 
     103(\textbf{L}ateral \textbf{D}i\textbf{F}fusion and vertical \textbf{Z} \textbf{D}i\textbf{F}fusion) 
    85104The model includes an implicit treatment of vertical viscosity and diffusivity. 
    86105The lateral Laplacian and biharmonic viscosity and diffusion can be rotated following 
    87106a geopotential or neutral direction. 
    88 There is an optional eddy induced velocity \citep{gent.mcwilliams_JPO90} with a space and time variable coefficient 
    89 \citet{treguier.held.ea_JPO97}. 
     107There is an optional eddy induced velocity \citep{gent.mcwilliams_JPO90} with 
     108a space and time variable coefficient \citet{treguier.held.ea_JPO97}. 
    90109The model has vertical harmonic viscosity and diffusion with a space and time variable coefficient, 
    91 with options to compute the coefficients with \citet{blanke.delecluse_JPO93}, \citet{pacanowski.philander_JPO81}, or 
    92 \citet{umlauf.burchard_JMR03} mixing schemes. 
     110with options to compute the coefficients with \citet{blanke.delecluse_JPO93}, 
     111\citet{pacanowski.philander_JPO81}, or \citet{umlauf.burchard_JMR03} mixing schemes. 
     112\item [\nameref{chap:DIA}] describes model \textbf{I}n-\textbf{O}utputs \textbf{M}anagement and 
     113specific online \textbf{DIA}gnostics. 
     114The diagnostics includes the output of all the tendencies of the momentum and tracers equations, 
     115the output of tracers \textbf{TR}en\textbf{D}s averaged over the time evolving mixed layer, 
     116the output of the tendencies of the barotropic vorticity equation, 
     117the computation of on-line \textbf{FLO}ats trajectories... 
     118\item [\nameref{chap:OBS}] describes a tool which reads in \textbf{OBS}ervation files 
     119(profile temperature and salinity, sea surface temperature, sea level anomaly and 
     120sea ice concentration) and calculates an interpolated model equivalent value at 
     121the observation location and nearest model timestep. 
     122Originally developed of data assimilation, it is a fantastic tool for model and data comparison. 
     123\item [\nameref{chap:ASM}] describes how increments produced by 
     124data \textbf{A}s\textbf{S}i\textbf{M}ilation may be applied to the model equations. 
     125\item [\nameref{chap:MISC}] (including solvers) 
     126\item [\nameref{chap:CFG}] provides finally a brief introduction to 
     127the pre-defined model configurations 
     128(water column model \texttt{C1D}, ORCA and GYRE families of configurations). 
     129\end{description} 
    93130 
    94 %%gm    To be put somewhere else .... 
    95 %%nm    We should consider creating a glossary for all this kind of stuff (terms, acronyms and symbols) 
    96 %%      http://en.wikibooks.org/wiki/LaTeX/Glossary 
    97 \noindent CPP keys and namelists are used as inputs to the code. 
     131%% ================================================================================================= 
     132\subsection*{Appendices} 
    98133 
    99 \noindent \index{CPP keys} CPP keys 
    100  
    101 Some CPP keys are implemented in the \fortran code to allow code selection at compiling step. 
    102 This selection of code at compilation time reduces the reliability of the whole platform since 
    103 it changes the code from one set of CPP keys to the other. 
    104 It is used only when the addition/suppression of the part of code highly changes the amount of memory at run time. 
    105 Usual coding looks like: 
    106  
    107 \begin{forlines} 
    108 #if defined key_option1 
    109    ! This part of the \fortran code will be active 
    110    ! only if key_option1 is activated at compiling step 
    111 #endif 
    112 \end{forlines} 
    113  
    114 \noindent \index{Namelist} Namelists 
    115  
    116 The namelist allows to input variables (character, logical, real and integer) into the code. 
    117 There is one namelist file for each component of \NEMO\ (dynamics, sea-ice, biogeochemistry...) 
    118 containing all the \fortran namelists needed. 
    119 The implementation in \NEMO\ uses a 2-step process. 
    120 For each \fortran namelist, two files are read: 
    121  
    122 \begin{enumerate} 
    123 \item 
    124   A reference namelist (in \path{./cfgs/SHARED/namelist_ref}) is read first. 
    125   This file contains all the namelist variables which are initialised to default values 
    126 \item 
    127   A configuration namelist (in \path{./cfgs/CFG_NAME/EXP00/namelist_cfg}) is read aferwards. 
    128   This file contains only the namelist variables which are changed from default values, and overwrites those. 
    129 \end{enumerate} 
    130 A template can be found in \path{NEMO/OPA_SRC/module.example}. 
    131 The effective namelist, taken in account during the run, is stored at execution time in 
    132 an \texttt{output\_namelist\_dyn} (or \texttt{\_ice} or \texttt{\_top}) file. 
    133 %%gm  end 
    134  
    135 Model outputs management and specific online diagnostics are described in \autoref{chap:DIA}. 
    136 The diagnostics includes the output of all the tendencies of the momentum and tracers equations, 
    137 the output of tracers tendencies averaged over the time evolving mixed layer, 
    138 the output of the tendencies of the barotropic vorticity equation, 
    139 the computation of on-line floats trajectories... 
    140 \autoref{chap:OBS} describes a tool which reads in observation files 
    141 (profile temperature and salinity, sea surface temperature, sea level anomaly and sea ice concentration) 
    142 and calculates an interpolated model equivalent value at the observation location and nearest model timestep. 
    143 Originally developed of data assimilation, it is a fantastic tool for model and data comparison. 
    144 \autoref{chap:ASM} describes how increments produced by data assimilation may be applied to the model equations. 
    145 Finally, \autoref{chap:CFG} provides a brief introduction to the pre-defined model configurations 
    146 (water column model, ORCA and GYRE families of configurations). 
    147  
    148 %%nm: Add some words on the \NEMO\ dependencies 
    149 The model is implemented in \fninety, with preprocessing (C pre-processor). 
    150 It runs under UNIX. 
    151 It is optimized for vector computers and parallelised by domain decomposition with MPI. 
    152 All input and output is done in NetCDF (Network Common Data Format) with a optional direct access format for output. 
    153 To ensure the clarity and readability of the code it is necessary to follow coding rules. 
    154 The coding rules for OPA include conventions for naming variables, 
    155 with different starting letters for different types of variables (real, integer, parameter\ldots). 
    156 Those rules are briefly presented in \autoref{apdx:coding} and a more complete document is available . 
    157  
    158 The model is organized with a high internal modularity based on physics. 
    159 For example, each trend (\ie, a term in the RHS of the prognostic equation) for momentum and tracers 
    160 is computed in a dedicated module. 
    161 To make it easier for the user to find his way around the code, the module names follow a three-letter rule. 
    162 For example, \mdl{traldf} is a module related to the TRAcers equation, computing the Lateral DiFfussion. 
    163 %The complete list of module names is presented in \autoref{apdx:coding}.      %====>>>> to be done ! 
    164 Furthermore, modules are organized in a few directories that correspond to their category, 
    165 as indicated by the first three letters of their name (\autoref{tab:chapters}). 
    166  
    167 The manual mirrors the organization of the model. 
    168 After the presentation of the continuous equations (\autoref{chap:PE}), 
    169 the following chapters refer to specific terms of the equations each associated with a group of modules 
    170 (\autoref{tab:chapters}). 
    171  
    172 %--------------------------------------------------TABLE-------------------------------------------------- 
    173 \begin{table}[!t] 
    174   \caption{ 
    175     \protect\label{tab:chapters} 
    176     Organization of Chapters mimicking the one of the model directories. 
    177   } 
    178   \begin{center} 
    179     \begin{tabular}{|l|l|l|} 
    180       \hline 
    181       \autoref{chap:STP}  & -   & model time STePping environment \\ 
    182       \hline 
    183       \autoref{chap:DOM}  & DOM & model DOMain \\ 
    184       \hline 
    185       \autoref{chap:TRA}  & TRA & TRAcer equations (potential temperature and salinity) \\ 
    186       \hline 
    187       \autoref{chap:DYN}  & DYN & DYNamic equations (momentum) \\ 
    188       \hline 
    189       \autoref{chap:SBC}  & SBC & Surface Boundary Conditions \\ 
    190       \hline 
    191       \autoref{chap:LBC}  & LBC & Lateral Boundary Conditions (also OBC and BDY)  \\ 
    192       \hline 
    193       \autoref{chap:LDF}  & LDF & Lateral DiFfusion (parameterisations) \\ 
    194       \hline 
    195       \autoref{chap:ZDF}  & ZDF & vertical (Z) DiFfusion (parameterisations)  \\ 
    196       \hline 
    197       \autoref{chap:DIA}  & DIA & I/O and DIAgnostics (also IOM, FLO and TRD) \\ 
    198       \hline 
    199       \autoref{chap:OBS}  & OBS & OBServation and model comparison  \\ 
    200       \hline 
    201       \autoref{chap:ASM}  & ASM & ASsiMilation increment  \\ 
    202       \hline 
    203       \autoref{chap:MISC} & SOL & Miscellaneous  topics (including solvers)  \\ 
    204       \hline 
    205       \autoref{chap:CFG}  & -   & predefined configurations (including C1D) \\ 
    206       \hline 
    207     \end{tabular} 
    208   \end{center} 
    209 \end{table} 
    210 %-------------------------------------------------------------------------------------------------------------- 
    211  
    212 %% nm: the following section has to vastly remodeled to focus only on well-identified versions of \NEMO 
    213 %% (3.4, 3.6, 4.0 and further releases). Then its formatting must be improved too. 
    214 \subsubsection{Changes between releases} 
    215  
    216 \NEMO/OPA, like all research tools, is in perpetual evolution. 
    217 The present document describes the OPA version include in the release 3.4 of \NEMO. 
    218 This release differs significantly from version 8, documented in \citet{madec.delecluse.ea_NPM98}. \\ 
    219  
    220 The main modifications from OPA v8 and \NEMO/OPA v3.2 are : 
    221  
    222 \begin{itemize} 
    223 \item 
    224   transition to full native \fninety, deep code restructuring and drastic reduction of CPP keys; 
    225 \item 
    226   introduction of partial step representation of bottom topography 
    227   \citep{barnier.madec.ea_OD06, le-sommer.penduff.ea_OM09, penduff.le-sommer.ea_OS07}; 
    228 \item 
    229   partial reactivation of a terrain-following vertical coordinate ($s$- and hybrid $s$-$z$) with 
    230   the addition of several options for pressure gradient computation 
    231   \footnote{ 
    232     Partial support of $s$-coordinate: there is presently no support for neutral physics in 
    233     $s$-coordinate and for the new options for horizontal pressure gradient computation with 
    234     a non-linear equation of state. 
    235   } 
    236   ; 
    237 \item 
    238   more choices for the treatment of the free surface: full explicit, split-explicit or filtered schemes, 
    239   and suppression of the rigid-lid option; 
    240 \item 
    241   non linear free surface associated with the rescaled height coordinate \zstar or $s$; 
    242 \item 
    243   additional schemes for vector and flux forms of the momentum advection; 
    244 \item 
    245   additional advection schemes for tracers; 
    246 \item 
    247   implementation of the AGRIF package (Adaptative Grid Refinement in \fortran) \citep{debreu.vouland.ea_CG08}; 
    248 \item 
    249   online diagnostics : tracers trend in the mixed layer and vorticity balance; 
    250 \item 
    251   rewriting of the I/O management with the use of an I/O server; 
    252 \item 
    253   generalized ocean-ice-atmosphere-CO2 coupling interface, interfaced with OASIS 3 coupler; 
    254 \item 
    255   surface module (SBC) that simplify the way the ocean is forced and include two bulk formulea (CLIO and CORE) and 
    256   which includes an on-the-fly interpolation of input forcing fields; 
    257 \item 
    258   RGB light penetration and optional use of ocean color 
    259 \item 
    260   major changes in the TKE schemes: it now includes a Langmuir cell parameterization \citep{axell_JGR02}, 
    261   the \citet{mellor.blumberg_JPO04} surface wave breaking parameterization, and has a time discretization which 
    262   is energetically consistent with the ocean model equations \citep{burchard_OM02, marsaleix.auclair.ea_OM08}; 
    263 \item 
    264   tidal mixing parametrisation (bottom intensification) + Indonesian specific tidal mixing 
    265   \citep{koch-larrouy.madec.ea_GRL07}; 
    266 \item 
    267   introduction of LIM-3, the new Louvain-la-Neuve sea-ice model 
    268   (C-grid rheology and new thermodynamics including bulk ice salinity) 
    269   \citep{vancoppenolle.fichefet.ea_OM09*a, vancoppenolle.fichefet.ea_OM09*b} 
    270 \end{itemize} 
    271  
    272 The main modifications from \NEMO/OPA v3.2 and v3.3 are: 
    273  
    274 \begin{itemize} 
    275 \item 
    276   introduction of a modified leapfrog-Asselin filter time stepping scheme 
    277   \citep{leclair.madec_OM09}; 
    278 \item 
    279   additional scheme for iso-neutral mixing \citep{griffies.gnanadesikan.ea_JPO98}, although it is still a "work in progress"; 
    280 \item 
    281   a rewriting of the bottom boundary layer scheme, following \citet{campin.goosse_T99}; 
    282 \item 
    283   addition of a Generic Length Scale vertical mixing scheme, following \citet{umlauf.burchard_JMR03}; 
    284 \item 
    285   addition of the atmospheric pressure as an external forcing on both ocean and sea-ice dynamics; 
    286 \item 
    287   addition of a diurnal cycle on solar radiation \citep{bernie.guilyardi.ea_CD07}; 
    288 \item 
    289   river runoffs added through a non-zero depth, and having its own temperature and salinity; 
    290 \item 
    291   CORE II normal year forcing set as the default forcing of ORCA2-LIM configuration; 
    292 \item 
    293   generalisation of the use of \mdl{fldread} for all input fields (ocean climatology, sea-ice damping...); 
    294 \item 
    295   addition of an on-line observation and model comparison (thanks to NEMOVAR project); 
    296 \item 
    297   optional application of an assimilation increment (thanks to NEMOVAR project); 
    298 \item 
    299   coupling interface adjusted for WRF atmospheric model; 
    300 \item 
    301   C-grid ice rheology now available fro both LIM-2 and LIM-3 \citep{bouillon.maqueda.ea_OM09}; 
    302 \item 
    303   LIM-3 ice-ocean momentum coupling applied to LIM-2; 
    304 \item 
    305   a deep re-writting and simplification of the off-line tracer component (OFF\_SRC); 
    306 \item 
    307   the merge of passive and active advection and diffusion modules; 
    308 \item 
    309   Use of the Flexible Configuration Manager (FCM) to build configurations, 
    310   generate the Makefile and produce the executable; 
    311 \item 
    312   Linear-tangent and Adjoint component (TAM) added, phased with v3.0 
    313 \end{itemize} 
    314  
    315 \vspace{1cm} 
    316  
    317 In addition, several minor modifications in the coding have been introduced with the constant concern of 
    318 improving the model performance. 
    319  
    320 The main modifications from \NEMO/OPA v3.3 and v3.4 are: 
    321  
    322 \begin{itemize} 
    323 \item finalisation of above iso-neutral mixing \citep{griffies.gnanadesikan.ea_JPO98}"; 
    324 \item "Neptune effect" parametrisation; 
    325 \item horizontal pressure gradient suitable for s-coordinate; 
    326 \item semi -implicit bottom friction; 
    327 \item finalisation of the merge of passive and active tracers advection-diffusion modules; 
    328 \item a new bulk formulae (so-called MFS); 
    329 \item use fldread for the off-line tracer component (OFF\_SRC); 
    330 \item use MPI point to point communications for north fold; 
    331 \item diagnostic of transport; 
    332 \end{itemize} 
    333  
    334 The main modifications from \NEMO/OPA v3.4 and v3.6 are: 
    335  
    336 \begin{itemize} 
    337  \item ...; 
    338 \end{itemize} 
    339  
    340 The main modifications from \NEMO/OPA v3.6 and v4.0 are: 
    341  
    342 \begin{itemize} 
    343 \item new definition of configurations; 
    344 \item bulk formulation; 
    345 \item \NEMO-wave large scale interactions; 
    346 \item ...; 
    347 \end{itemize} 
    348  
    349 \biblio 
    350  
    351 \pindex 
    352  
    353 %% Restore section heading 
    354 \rehead{Sect.\ \thesection\ \rightmark} 
    355  
    356 \end{document} 
     134\begin{description} 
     135\item [\nameref{apdx:s_coord}] 
     136\item [\nameref{apdx:diff_oper}] 
     137\item [\nameref{apdx:invariants}] 
     138\item [\nameref{apdx:triads}] 
     139\item [\nameref{apdx:DOMAINcfg}] 
     140\item [\nameref{apdx:coding}] 
     141\end{description} 
  • NEMO/trunk/doc/latex/NEMO/main/thanks.tex

    r11433 r11522  
    4747                            George Nurser               \\ 
    4848\orcid{0000-0001-7481-6369} Guillaume Samson            \\ 
    49                             Dave Storkey 
     49                            Dave Storkey                \\ 
     50%% Don't forget the last break for the right alignment 
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