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dev_r10164_HPC09_ESIWACE_PREP_MERGE: merge with trunk@10365, see #2133

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  • NEMO/branches/2018/dev_r10164_HPC09_ESIWACE_PREP_MERGE/doc/latex/NEMO/subfiles/introduction.tex

    r9407 r10368  
    88\chapter{Introduction} 
    99 
    10 The Nucleus for European Modelling of the Ocean (\NEMO) is a framework of ocean  
    11 related engines, namely OPA\footnote{OPA = Oc\'{e}an PArall\'{e}lis\'{e}} for the  
    12 ocean dynamics and thermodynamics, LIM\footnote{LIM = Louvain la-neuve Ice  
    13 Model} for the sea-ice dynamics and thermodynamics, TOP\footnote{TOP = Tracer  
    14 in the Ocean Paradigm} for the biogeochemistry (both transport (TRP) and sources  
    15 minus sinks (LOBSTER\footnote{LOBSTER = Lodyc Ocean Biogeochemical SysTem for  
    16 Ecosystem and Resources}, PISCES\footnote{PISCES = Pelagic Interactions Scheme for  
    17 Carbon and Ecosystem Studies}). It is intended to be a flexible tool for studying  
    18 the ocean and its interactions with the other components of the earth climate system  
    19 (atmosphere, sea-ice, biogeochemical tracers, ...) over a wide range of space and time scales.  
    20 This documentation provides information about the physics represented by the ocean  
    21 component of \NEMO and the rationale for the choice of numerical schemes and  
    22 the model design. More specific information about running the model on different  
    23 computers, or how to set up a configuration, are found on the \NEMO web site  
    24 (www.nemo-ocean.eu).  
    25  
    26 The ocean component of \NEMO has been developed from the OPA model,  
    27 release 8.2, described in \citet{Madec1998}. This model has been used for a wide  
    28 range of applications, both regional or global, as a forced ocean model and as a  
    29 model coupled with the sea-ice and/or the atmosphere.   
    30  
    31 This manual is organised in as follows. \autoref{chap:PE} presents the model basics,  
    32 $i.e.$ the equations and their assumptions, the vertical coordinates used, and the  
    33 subgrid scale physics. This part deals with the continuous equations of the model  
    34 (primitive equations, with temperature, salinity and an equation of seawater).  
    35 The equations are written in a curvilinear coordinate system, with a choice of vertical  
    36 coordinates ($z$, $s$, \textit{z*}, \textit{s*}, $\tilde{z}$, $\tilde{s}$, and a mixture of them).  
    37 Momentum equations are formulated in vector invariant or flux form.  
    38 Dimensional units in the meter, kilogram, second (MKS) international system  
    39 are used throughout. 
    40  
    41 The following chapters deal with the discrete equations. \autoref{chap:STP} presents the  
    42 time domain. The model time stepping environment is a three level scheme in which  
    43 the tendency terms of the equations are evaluated either centered  in time, or forward,  
    44 or backward depending of the nature of the term. 
    45 \autoref{chap:DOM} presents the space domain. The model is discretised on a staggered  
    46 grid (Arakawa C grid) with masking of land areas. Vertical discretisation used depends  
    47 on both how the bottom topography is represented and whether the free surface is linear or not.  
    48 Full step or partial step $z$-coordinate or $s$- (terrain-following) coordinate is used  
    49 with linear free surface (level position are then fixed in time). In non-linear free surface,  
    50 the corresponding rescaled height coordinate formulation (\textit{z*} or \textit{s*}) is used  
    51 (the level position then vary in time as a function of the sea surface heigh).  
    52 The following two chapters (\autoref{chap:TRA} and \autoref{chap:DYN}) describe the discretisation of the  
    53 prognostic equations for the active tracers and the momentum. Explicit, split-explicit  
    54 and filtered free surface formulations are implemented.  
    55 A number of numerical schemes are available for momentum advection, for the computation  
    56 of the pressure gradients, as well as for the advection of tracers (second or higher  
    57 order advection schemes, including positive ones). 
    58  
    59 Surface boundary conditions (\autoref{chap:SBC}) can be implemented as prescribed 
    60 fluxes, or bulk formulations for the surface fluxes (wind stress, heat, freshwater). The  
    61 model allows penetration of solar radiation  There is an optional geothermal heating at  
    62 the ocean bottom. Within the \NEMO system the ocean model is interactively coupled  
    63 with a sea ice model (LIM) and with biogeochemistry models (PISCES, LOBSTER).  
    64 Interactive coupling to Atmospheric models is possible via the OASIS coupler  
    65 \citep{OASIS2006}. Two-way nesting is also available through an interface to the 
    66 AGRIF package (Adaptative Grid Refinement in \textsc{Fortran}) \citep{Debreu_al_CG2008}. 
    67 The interface code for coupling to an alternative sea ice model (CICE, \citet{Hunke2008}) 
    68 has now been upgraded so that it works for both global and regional domains, although AGRIF  
    69 is still not available. 
    70  
    71 Other model characteristics are the lateral boundary conditions (\autoref{chap:LBC}).   
    72 Global configurations of the model make use of the ORCA tripolar grid, with special north  
    73 fold boundary condition. Free-slip or no-slip boundary conditions are allowed at land  
    74 boundaries. Closed basin geometries as well as periodic domains and open boundary  
    75 conditions are possible.  
    76  
    77 Physical parameterisations are described in \autoref{chap:LDF} and \autoref{chap:ZDF}. The  
    78 model includes an implicit treatment of vertical viscosity and diffusivity. The lateral  
    79 Laplacian and biharmonic viscosity and diffusion can be rotated following a geopotential  
    80 or neutral direction. There is an optional eddy induced velocity \citep{Gent1990} with a  
    81 space and time variable coefficient \citet{Treguier1997}. The model has vertical harmonic  
    82 viscosity and diffusion with a space and time variable coefficient, with options to compute  
    83 the coefficients with \citet{Blanke1993}, \citet{Pacanowski_Philander_JPO81},  
     10The Nucleus for European Modelling of the Ocean (\NEMO) is a framework of ocean related engines, 
     11namely OPA\footnote{OPA = Oc\'{e}an PArall\'{e}lis\'{e}} for the ocean dynamics and thermodynamics, 
     12LIM\footnote{LIM = Louvain la-neuve Ice Model} for the sea-ice dynamics and thermodynamics, 
     13TOP\footnote{TOP = Tracer in the Ocean Paradigm} for the biogeochemistry (both transport (TRP) and sources  
     14minus sinks (LOBSTER\footnote{LOBSTER = Lodyc Ocean Biogeochemical SysTem for Ecosystem and Resources}, 
     15PISCES\footnote{PISCES = Pelagic Interactions Scheme for Carbon and Ecosystem Studies})). 
     16It is intended to be a flexible tool for studying the ocean and its interactions with the other components of 
     17the earth climate system (atmosphere, sea-ice, biogeochemical tracers, ...) over 
     18a wide range of space and time scales.  
     19This documentation provides information about the physics represented by the ocean component of \NEMO and 
     20the rationale for the choice of numerical schemes and the model design. 
     21More specific information about running the model on different computers, or how to set up a configuration, 
     22are found on the \NEMO web site (www.nemo-ocean.eu).  
     23 
     24The ocean component of \NEMO has been developed from the OPA model, release 8.2, described in \citet{Madec1998}. 
     25This model has been used for a wide range of applications, both regional or global, 
     26as a forced ocean model and as a model coupled with the sea-ice and/or the atmosphere.   
     27 
     28This manual is organised in as follows. 
     29\autoref{chap:PE} presents the model basics, $i.e.$ the equations and their assumptions, 
     30the vertical coordinates used, and the subgrid scale physics. 
     31This part deals with the continuous equations of the model 
     32(primitive equations, with temperature, salinity and an equation of seawater). 
     33The equations are written in a curvilinear coordinate system, with a choice of vertical coordinates 
     34($z$, $s$, \textit{z*}, \textit{s*}, $\tilde{z}$, $\tilde{s}$, and a mixture of them). 
     35Momentum equations are formulated in vector invariant or flux form. 
     36Dimensional units in the meter, kilogram, second (MKS) international system are used throughout. 
     37 
     38The following chapters deal with the discrete equations. 
     39\autoref{chap:STP} presents the time domain. 
     40The model time stepping environment is a three level scheme in which the tendency terms of 
     41the equations are evaluated either centered in time, or forward, or backward depending of the nature of the term. 
     42\autoref{chap:DOM} presents the space domain. 
     43The model is discretised on a staggered grid (Arakawa C grid) with masking of land areas. 
     44Vertical discretisation used depends on both how the bottom topography is represented and 
     45whether the free surface is linear or not. 
     46Full step or partial step $z$-coordinate or $s$- (terrain-following) coordinate is used with 
     47linear free surface (level position are then fixed in time). 
     48In non-linear free surface, 
     49the corresponding rescaled height coordinate formulation (\textit{z*} or \textit{s*}) is used 
     50(the level position then vary in time as a function of the sea surface heigh). 
     51The following two chapters (\autoref{chap:TRA} and \autoref{chap:DYN}) describe the discretisation of 
     52the prognostic equations for the active tracers and the momentum. 
     53Explicit, split-explicit and filtered free surface formulations are implemented. 
     54A number of numerical schemes are available for momentum advection, for the computation of the pressure gradients, 
     55as well as for the advection of tracers (second or higher order advection schemes, including positive ones). 
     56 
     57Surface boundary conditions (\autoref{chap:SBC}) can be implemented as prescribed fluxes, 
     58or bulk formulations for the surface fluxes (wind stress, heat, freshwater). 
     59The model allows penetration of solar radiation. 
     60There is an optional geothermal heating at the ocean bottom. 
     61Within the \NEMO system the ocean model is interactively coupled with a sea ice model (LIM) and 
     62with biogeochemistry models (PISCES, LOBSTER). 
     63Interactive coupling to Atmospheric models is possible via the OASIS coupler \citep{OASIS2006}. 
     64Two-way nesting is also available through an interface to the AGRIF package 
     65(Adaptative Grid Refinement in \textsc{Fortran}) \citep{Debreu_al_CG2008}. 
     66The interface code for coupling to an alternative sea ice model (CICE, \citet{Hunke2008}) has now been upgraded so 
     67that it works for both global and regional domains, although AGRIF is still not available. 
     68 
     69Other model characteristics are the lateral boundary conditions (\autoref{chap:LBC}). 
     70Global configurations of the model make use of the ORCA tripolar grid, with special north fold boundary condition. 
     71Free-slip or no-slip boundary conditions are allowed at land boundaries. 
     72Closed basin geometries as well as periodic domains and open boundary conditions are possible.  
     73 
     74Physical parameterisations are described in \autoref{chap:LDF} and \autoref{chap:ZDF}. 
     75The model includes an implicit treatment of vertical viscosity and diffusivity. 
     76The lateral Laplacian and biharmonic viscosity and diffusion can be rotated following 
     77a geopotential or neutral direction. 
     78There is an optional eddy induced velocity \citep{Gent1990} with a space and time variable coefficient 
     79\citet{Treguier1997}. 
     80The model has vertical harmonic viscosity and diffusion with a space and time variable coefficient, 
     81with options to compute the coefficients with \citet{Blanke1993}, \citet{Pacanowski_Philander_JPO81}, 
    8482or \citet{Umlauf_Burchard_JMS03} mixing schemes. 
    8583 \vspace{1cm} 
     
    9088 
    9189\noindent \index{CPP keys} CPP keys \newline 
    92 Some CPP keys are implemented in the FORTRAN code to allow code selection at compiling step. This selection of code at compilation time reduces the reliability of the whole platform since it changes the code from one set of CPP keys to the other. It is used only when the addition/suppression of the part of code highly changes the amount of memory at run time. 
     90Some CPP keys are implemented in the FORTRAN code to allow code selection at compiling step. 
     91This selection of code at compilation time reduces the reliability of the whole platform since 
     92it changes the code from one set of CPP keys to the other. 
     93It is used only when the addition/suppression of the part of code highly changes the amount of memory at run time. 
    9394Usual coding looks like :  
    9495\begin{forlines} 
     
    101102\noindent \index{Namelist} Namelists 
    102103 
    103 The namelist allows to input variables (character, logical, real and integer) into the code. There is one namelist file for each component of NEMO (dynamics, sea-ice, biogeochemistry...) containing all the FOTRAN namelists needed. The implementation in NEMO uses a two step process. For each FORTRAN namelist, two files are read: 
    104 \begin{enumerate} 
    105 \item A reference namelist (in \path{CONFIG/SHARED/namelist_ref}) is read first. This file contains all the namelist variables which are initialised to default values   
    106 \item A configuration namelist (in \path{CONFIG/CFG_NAME/EXP00/namelist_cfg}) is read aferwards. This file contains only the namelist variables which are changed from default values, and overwrites those. 
     104The namelist allows to input variables (character, logical, real and integer) into the code. 
     105There is one namelist file for each component of NEMO (dynamics, sea-ice, biogeochemistry...) 
     106containing all the FOTRAN namelists needed. 
     107The implementation in NEMO uses a two step process. For each FORTRAN namelist, two files are read: 
     108\begin{enumerate} 
     109\item 
     110  A reference namelist (in \path{CONFIG/SHARED/namelist_ref}) is read first. 
     111  This file contains all the namelist variables which are initialised to default values 
     112\item 
     113  A configuration namelist (in \path{CONFIG/CFG_NAME/EXP00/namelist_cfg}) is read aferwards. 
     114  This file contains only the namelist variables which are changed from default values, and overwrites those. 
    107115\end{enumerate} 
    108116A template can be found in \path{NEMO/OPA_SRC/module.example}. 
    109 The effective namelist, taken in account during the run, is stored at execution time in an output\_namelist\_dyn (or \_ice or \_top) file. 
    110  \vspace{1cm} 
     117The effective namelist, taken in account during the run, is stored at execution time in 
     118an output\_namelist\_dyn (or \_ice or \_top) file. 
     119\vspace{1cm} 
    111120 
    112121%%gm  end 
    113122 
    114123Model outputs management and specific online diagnostics are described in \autoref{chap:DIA}. 
    115 The diagnostics includes the output of all the tendencies of the momentum and tracers equations,  
    116 the output of tracers tendencies averaged over the time evolving mixed layer, the output of  
    117 the tendencies of the barotropic vorticity equation, the computation of on-line floats trajectories...  
    118 \autoref{chap:OBS} describes a tool which reads in observation files (profile temperature  
    119 and salinity, sea surface temperature, sea level anomaly and sea ice concentration)  
    120 and calculates an interpolated model equivalent value at the observation location  
    121 and nearest model timestep. Originally developed of data assimilation, it is a fantastic  
    122 tool for model and data comparison. \autoref{chap:ASM} describes how increments  
    123 produced by data assimilation may be applied to the model equations. 
    124 Finally, \autoref{chap:CFG} provides a brief introduction to the pre-defined model  
    125 configurations (water column model, ORCA and GYRE families of configurations). 
    126  
    127 The model is implemented in \textsc{Fortran 90}, with preprocessing (C-pre-processor).  
    128 It runs under UNIX. It is optimized for vector computers and parallelised by domain   
    129 decomposition with MPI. All input and output is done in NetCDF (Network Common Data  
    130 Format) with a optional direct access format for output. To ensure the clarity and  
    131 readability of the code it is necessary to follow coding rules. The coding rules for OPA  
    132 include conventions for naming variables, with different starting letters for different types  
    133 of variables (real, integer, parameter\ldots). Those rules are briefly presented in  
    134 \autoref{apdx:D} and a more complete document is available on the \NEMO web site. 
    135  
    136 The model is organized with a high internal modularity based on physics. For example,  
    137 each trend ($i.e.$, a term in the RHS of the prognostic equation) for momentum and  
    138 tracers is computed in a dedicated module.  To make it easier for the user to find his way  
    139 around the code, the module names follow a three-letter rule. For example, \mdl{traldf}  
    140 is a module related to the TRAcers equation, computing the Lateral DiFfussion.  
     124The diagnostics includes the output of all the tendencies of the momentum and tracers equations, 
     125the output of tracers tendencies averaged over the time evolving mixed layer, 
     126the output of the tendencies of the barotropic vorticity equation, 
     127the computation of on-line floats trajectories... 
     128\autoref{chap:OBS} describes a tool which reads in observation files 
     129(profile temperature and salinity, sea surface temperature, sea level anomaly and sea ice concentration)  
     130and calculates an interpolated model equivalent value at the observation location and nearest model timestep. 
     131Originally developed of data assimilation, it is a fantastic tool for model and data comparison. 
     132\autoref{chap:ASM} describes how increments produced by data assimilation may be applied to the model equations. 
     133Finally, \autoref{chap:CFG} provides a brief introduction to the pre-defined model configurations 
     134(water column model, ORCA and GYRE families of configurations). 
     135 
     136The model is implemented in \textsc{Fortran 90}, with preprocessing (C-pre-processor). 
     137It runs under UNIX. 
     138It is optimized for vector computers and parallelised by domain decomposition with MPI. 
     139All input and output is done in NetCDF (Network Common Data Format) with a optional direct access format for output. 
     140To ensure the clarity and readability of the code it is necessary to follow coding rules. 
     141The coding rules for OPA include conventions for naming variables, 
     142with different starting letters for different types of variables (real, integer, parameter\ldots). 
     143Those rules are briefly presented in \autoref{apdx:D} and a more complete document is available on 
     144the \NEMO web site. 
     145 
     146The model is organized with a high internal modularity based on physics. 
     147For example, each trend ($i.e.$, a term in the RHS of the prognostic equation) for momentum and tracers 
     148is computed in a dedicated module. 
     149To make it easier for the user to find his way around the code, the module names follow a three-letter rule. 
     150For example, \mdl{traldf} is a module related to the TRAcers equation, computing the Lateral DiFfussion.  
    141151%The complete list of module names is presented in \autoref{apdx:D}.      %====>>>> to be done ! 
    142 Furthermore, modules are organized in a few directories that correspond to their category,  
     152Furthermore, modules are organized in a few directories that correspond to their category, 
    143153as indicated by the first three letters of their name (\autoref{tab:chap}). 
    144154 
    145 The manual mirrors the organization of the model.  
    146 After the presentation of the continuous equations (\autoref{chap:PE}), the following chapters  
    147 refer to specific terms of the equations each associated with a group of modules (\autoref{tab:chap}). 
     155The manual mirrors the organization of the model. 
     156After the presentation of the continuous equations (\autoref{chap:PE}), 
     157the following chapters refer to specific terms of the equations each associated with 
     158a group of modules (\autoref{tab:chap}). 
    148159 
    149160 
    150161%--------------------------------------------------TABLE-------------------------------------------------- 
    151162\begin{table}[!t]  
    152 %\begin{center} \begin{tabular}{|p{143pt}|l|l|} \hline 
    153 \caption{ \protect\label{tab:chap}   Organization of Chapters mimicking the one of the model directories. } 
    154 \begin{center}    \begin{tabular}{|l|l|l|}   \hline 
    155 \autoref{chap:STP}   & -                 & model time STePping environment \\    \hline 
    156 \autoref{chap:DOM}   & DOM    & model DOMain \\    \hline 
    157 \autoref{chap:TRA}   & TRA    & TRAcer equations (potential temperature and salinity) \\   \hline 
    158 \autoref{chap:DYN}   & DYN    & DYNamic equations (momentum) \\      \hline 
    159 \autoref{chap:SBC}   & SBC    & Surface Boundary Conditions \\       \hline 
    160 \autoref{chap:LBC}   & LBC    & Lateral Boundary Conditions (also OBC and BDY)  \\     \hline 
    161 \autoref{chap:LDF}   & LDF    & Lateral DiFfusion (parameterisations) \\   \hline 
    162 \autoref{chap:ZDF}   & ZDF    & vertical (Z) DiFfusion (parameterisations)  \\      \hline 
    163 \autoref{chap:DIA}   & DIA    & I/O and DIAgnostics (also IOM, FLO and TRD) \\      \hline 
    164 \autoref{chap:OBS}   & OBS    & OBServation and model comparison  \\    \hline 
    165 \autoref{chap:ASM}   & ASM    & ASsiMilation increment  \\     \hline 
    166 \autoref{chap:MISC}  & SOL    & Miscellaneous  topics (including solvers)  \\       \hline 
    167 \autoref{chap:CFG}   &  -        & predefined configurations (including C1D) \\     \hline 
    168 \end{tabular}   
    169 \end{center}   \end{table} 
     163  % \begin{center} \begin{tabular}{|p{143pt}|l|l|} \hline 
     164  \caption{ \protect\label{tab:chap}   Organization of Chapters mimicking the one of the model directories. } 
     165  \begin{center} 
     166    \begin{tabular}{|l|l|l|}  \hline 
     167      \autoref{chap:STP}   & -                 & model time STePping environment \\    \hline 
     168      \autoref{chap:DOM}   & DOM    & model DOMain \\    \hline 
     169      \autoref{chap:TRA}   & TRA    & TRAcer equations (potential temperature and salinity) \\   \hline 
     170      \autoref{chap:DYN}   & DYN    & DYNamic equations (momentum) \\      \hline 
     171      \autoref{chap:SBC}   & SBC    & Surface Boundary Conditions \\       \hline 
     172      \autoref{chap:LBC}   & LBC    & Lateral Boundary Conditions (also OBC and BDY)  \\     \hline 
     173      \autoref{chap:LDF}   & LDF    & Lateral DiFfusion (parameterisations) \\   \hline 
     174      \autoref{chap:ZDF}   & ZDF    & vertical (Z) DiFfusion (parameterisations)  \\      \hline 
     175      \autoref{chap:DIA}   & DIA    & I/O and DIAgnostics (also IOM, FLO and TRD) \\      \hline 
     176      \autoref{chap:OBS}   & OBS    & OBServation and model comparison  \\    \hline 
     177      \autoref{chap:ASM}   & ASM    & ASsiMilation increment  \\     \hline 
     178      \autoref{chap:MISC}  & SOL    & Miscellaneous  topics (including solvers)  \\       \hline 
     179      \autoref{chap:CFG}   &  -        & predefined configurations (including C1D) \\     \hline 
     180    \end{tabular} 
     181  \end{center} 
     182\end{table} 
    170183%-------------------------------------------------------------------------------------------------------------- 
    171184 
    172185 
    173186\subsubsection{Changes between releases} 
    174 NEMO/OPA, like all research tools, is in perpetual evolution. The present document describes  
    175 the OPA version include in the release 3.4 of NEMO.  This release differs significantly 
    176 from version 8, documented in \citet{Madec1998}.\\ 
     187NEMO/OPA, like all research tools, is in perpetual evolution. 
     188The present document describes the OPA version include in the release 3.4 of NEMO. 
     189This release differs significantly from version 8, documented in \citet{Madec1998}.\\ 
    177190 
    178191$\bullet$ The main modifications from OPA v8 and NEMO/OPA v3.2 are :\\ 
    179192\begin{enumerate} 
    180 \item transition to full native \textsc{Fortran} 90, deep code restructuring and drastic  
    181 reduction of CPP keys;  
    182 \item introduction of partial step representation of bottom topography \citep{Barnier_al_OD06, Le_Sommer_al_OM09, Penduff_al_OS07};  
    183 \item partial reactivation of a terrain-following vertical coordinate ($s$- and hybrid $s$-$z$)  
    184 with the addition of several options for pressure gradient computation \footnote{Partial  
    185 support of $s$-coordinate: there is presently no support for neutral physics in $s$- 
    186 coordinate and for the new options for horizontal pressure gradient computation with  
    187 a non-linear equation of state.};  
    188 \item more choices for the treatment of the free surface: full explicit, split-explicit or filtered  
    189 schemes, and suppression of the rigid-lid option; 
    190 \item non linear free surface associated with the rescaled height coordinate   
    191 \textit{z*} or  \textit{s};  
    192 \item additional schemes for vector and flux forms of the momentum  advection;  
    193 \item additional advection schemes for tracers;  
    194 \item implementation of the AGRIF package (Adaptative Grid Refinement in \textsc{Fortran}) \citep{Debreu_al_CG2008};  
    195 \item online diagnostics : tracers trend in the mixed layer and vorticity balance; 
    196 \item rewriting of the I/O management with the use of an I/O server;  
    197 \item generalized ocean-ice-atmosphere-CO2 coupling interface, interfaced with OASIS 3 coupler ; 
    198 \item surface module (SBC) that simplify the way the ocean is forced and include two 
    199 bulk formulea (CLIO and CORE) and which includes an on-the-fly interpolation of input forcing fields ; 
    200 \item RGB light penetration and optional use of ocean color  
    201 \item major changes in the TKE schemes: it now includes a Langmuir cell parameterization  \citep{Axell_JGR02},  
    202 the \citet{Mellor_Blumberg_JPO04} surface wave breaking parameterization, and has a time discretization  
    203 which is energetically consistent with the ocean model equations \citep{Burchard_OM02, Marsaleix_al_OM08};  
    204 \item tidal mixing parametrisation (bottom intensification) + Indonesian specific tidal mixing \citep{Koch-Larrouy_al_GRL07};  
    205 \item introduction of LIM-3, the new Louvain-la-Neuve sea-ice model (C-grid rheology and 
    206 new thermodynamics including bulk ice salinity) \citep{Vancoppenolle_al_OM09a, Vancoppenolle_al_OM09b} 
     193\item 
     194  transition to full native \textsc{Fortran} 90, deep code restructuring and drastic reduction of CPP keys;  
     195\item 
     196  introduction of partial step representation of bottom topography 
     197  \citep{Barnier_al_OD06, Le_Sommer_al_OM09, Penduff_al_OS07}; 
     198\item 
     199  partial reactivation of a terrain-following vertical coordinate ($s$- and hybrid $s$-$z$) with 
     200  the addition of several options for pressure gradient computation 
     201  \footnote{Partial support of $s$-coordinate: there is presently no support for neutral physics in 
     202    $s$-coordinate and for the new options for horizontal pressure gradient computation with 
     203    a non-linear equation of state. 
     204  }; 
     205\item 
     206  more choices for the treatment of the free surface: full explicit, split-explicit or filtered schemes, 
     207  and suppression of the rigid-lid option; 
     208\item 
     209  non linear free surface associated with the rescaled height coordinate \textit{z*} or \textit{s}; 
     210\item 
     211  additional schemes for vector and flux forms of the momentum advection; 
     212\item 
     213  additional advection schemes for tracers; 
     214\item 
     215  implementation of the AGRIF package (Adaptative Grid Refinement in \textsc{Fortran}) \citep{Debreu_al_CG2008}; 
     216\item 
     217  online diagnostics : tracers trend in the mixed layer and vorticity balance; 
     218\item 
     219  rewriting of the I/O management with the use of an I/O server; 
     220\item 
     221  generalized ocean-ice-atmosphere-CO2 coupling interface, interfaced with OASIS 3 coupler; 
     222\item 
     223  surface module (SBC) that simplify the way the ocean is forced and include two bulk formulea (CLIO and CORE) and 
     224  which includes an on-the-fly interpolation of input forcing fields; 
     225\item 
     226  RGB light penetration and optional use of ocean color  
     227\item 
     228  major changes in the TKE schemes: it now includes a Langmuir cell parameterization \citep{Axell_JGR02}, 
     229  the \citet{Mellor_Blumberg_JPO04} surface wave breaking parameterization, and has a time discretization which 
     230  is energetically consistent with the ocean model equations \citep{Burchard_OM02, Marsaleix_al_OM08}; 
     231\item 
     232  tidal mixing parametrisation (bottom intensification) + Indonesian specific tidal mixing 
     233  \citep{Koch-Larrouy_al_GRL07}; 
     234\item 
     235  introduction of LIM-3, the new Louvain-la-Neuve sea-ice model 
     236  (C-grid rheology and new thermodynamics including bulk ice salinity) 
     237  \citep{Vancoppenolle_al_OM09a, Vancoppenolle_al_OM09b} 
    207238\end{enumerate} 
    208239 
    209240 \vspace{1cm} 
    210 $\bullet$ The main modifications from NEMO/OPA v3.2 and  v3.3 are :\\ 
    211 \begin{enumerate} 
    212 \item introduction of a modified leapfrog-Asselin filter time stepping scheme \citep{Leclair_Madec_OM09};  
    213 \item additional scheme for iso-neutral mixing \citep{Griffies_al_JPO98}, although it is still a "work in progress";  
    214 \item a rewriting of the bottom boundary layer scheme, following \citet{Campin_Goosse_Tel99};  
    215 \item addition of a Generic Length Scale vertical mixing scheme, following \citet{Umlauf_Burchard_JMS03};  
    216 \item addition of the atmospheric pressure as an external forcing on both ocean and sea-ice dynamics;  
    217 \item addition of a diurnal cycle on solar radiation \citep{Bernie_al_CD07};  
    218 \item river runoffs added through a non-zero depth, and having its own temperature and salinity;  
    219 \item CORE II normal year forcing set as the default forcing of ORCA2-LIM configuration ;  
    220 \item generalisation of the use of \mdl{fldread} for all input fields (ocean climatology, sea-ice damping...) ;  
    221 \item addition of an on-line observation and model comparison (thanks to NEMOVAR project);  
    222 \item optional application of an assimilation increment (thanks to NEMOVAR project);  
    223 \item coupling interface adjusted for WRF atmospheric model;  
    224 \item C-grid ice rheology now available fro both LIM-2 and LIM-3 \citep{Bouillon_al_OM09};  
    225 \item LIM-3 ice-ocean momentum coupling applied to LIM-2 ;  
    226 \item a deep re-writting and simplification of the off-line tracer component (OFF\_SRC) ;  
    227 \item the merge of passive and active advection and diffusion modules ; 
    228 \item  Use of the Flexible Configuration Manager (FCM) to build configurations, generate the Makefile and produce the executable ; 
    229 \item Linear-tangent and Adjoint component (TAM) added, phased with v3.0 
    230 \end{enumerate} 
    231  \vspace{1cm} 
    232 In addition, several minor modifications in the coding have been introduced with the constant  
    233 concern of improving the model performance.  
    234  
    235  \vspace{1cm} 
     241$\bullet$ The main modifications from NEMO/OPA v3.2 and v3.3 are :\\ 
     242\begin{enumerate} 
     243\item 
     244  introduction of a modified leapfrog-Asselin filter time stepping scheme 
     245  \citep{Leclair_Madec_OM09};  
     246\item 
     247  additional scheme for iso-neutral mixing \citep{Griffies_al_JPO98}, although it is still a "work in progress"; 
     248\item 
     249  a rewriting of the bottom boundary layer scheme, following \citet{Campin_Goosse_Tel99}; 
     250\item 
     251  addition of a Generic Length Scale vertical mixing scheme, following \citet{Umlauf_Burchard_JMS03}; 
     252\item 
     253  addition of the atmospheric pressure as an external forcing on both ocean and sea-ice dynamics; 
     254\item 
     255  addition of a diurnal cycle on solar radiation \citep{Bernie_al_CD07}; 
     256\item 
     257  river runoffs added through a non-zero depth, and having its own temperature and salinity; 
     258\item 
     259  CORE II normal year forcing set as the default forcing of ORCA2-LIM configuration; 
     260\item 
     261  generalisation of the use of \mdl{fldread} for all input fields (ocean climatology, sea-ice damping...); 
     262\item 
     263  addition of an on-line observation and model comparison (thanks to NEMOVAR project); 
     264\item 
     265  optional application of an assimilation increment (thanks to NEMOVAR project); 
     266\item 
     267  coupling interface adjusted for WRF atmospheric model; 
     268\item 
     269  C-grid ice rheology now available fro both LIM-2 and LIM-3 \citep{Bouillon_al_OM09}; 
     270\item 
     271  LIM-3 ice-ocean momentum coupling applied to LIM-2; 
     272\item 
     273  a deep re-writting and simplification of the off-line tracer component (OFF\_SRC); 
     274\item 
     275  the merge of passive and active advection and diffusion modules; 
     276\item 
     277  Use of the Flexible Configuration Manager (FCM) to build configurations, 
     278  generate the Makefile and produce the executable; 
     279\item 
     280  Linear-tangent and Adjoint component (TAM) added, phased with v3.0 
     281\end{enumerate} 
     282\vspace{1cm} 
     283In addition, several minor modifications in the coding have been introduced with the constant concern of 
     284improving the model performance.  
     285 
     286\vspace{1cm} 
    236287$\bullet$ The main modifications from NEMO/OPA v3.3 and  v3.4 are :\\ 
    237288\begin{enumerate} 
    238 \item finalisation of above iso-neutral mixing \citep{Griffies_al_JPO98}";  
     289\item finalisation of above iso-neutral mixing \citep{Griffies_al_JPO98}"; 
    239290\item "Neptune effect" parametrisation; 
    240 \item horizontal pressure gradient suitable for s-coordinate;  
     291\item horizontal pressure gradient suitable for s-coordinate; 
    241292\item semi-implicit bottom friction; 
    242 \item finalisation of the merge of passive and active tracers advection-diffusion modules;  
     293\item finalisation of the merge of passive and active tracers advection-diffusion modules; 
    243294\item a new bulk formulae (so-called MFS); 
    244 \item use fldread for the off-line tracer component (OFF\_SRC) ;  
     295\item use fldread for the off-line tracer component (OFF\_SRC); 
    245296\item use MPI point to point communications  for north fold; 
    246 \item diagnostic of transport ;  
     297\item diagnostic of transport; 
    247298\end{enumerate} 
    248299 
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