[10414] | 1 | \documentclass[../main/NEMO_manual]{subfiles} |
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[6997] | 3 | \begin{document} |
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[707] | 4 | |
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| 5 | % ================================================================ |
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| 6 | % INTRODUCTION |
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| 7 | % ================================================================ |
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| 8 | |
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| 9 | \chapter{Introduction} |
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| 10 | |
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[10354] | 11 | The Nucleus for European Modelling of the Ocean (\NEMO) is a framework of ocean related engines, |
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[10414] | 12 | namely OPA \footnote{OPA = Oc\'{e}an PArall\'{e}lis\'{e}} for the ocean dynamics and thermodynamics, |
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| 13 | LIM \footnote{LIM = Louvain la-neuve Ice Model} for the sea-ice dynamics and thermodynamics, |
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| 14 | TOP \footnote{TOP = Tracer in the Ocean Paradigm} for the biogeochemistry (both transport (TRP) and sources |
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| 15 | minus sinks (LOBSTER \footnote{LOBSTER = Lodyc Ocean Biogeochemical SysTem for Ecosystem and Resources}, |
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| 16 | PISCES \footnote{PISCES = Pelagic Interactions Scheme for Carbon and Ecosystem Studies})). |
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[10354] | 17 | It is intended to be a flexible tool for studying the ocean and its interactions with the other components of |
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| 18 | the earth climate system (atmosphere, sea-ice, biogeochemical tracers, ...) over |
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| 19 | a wide range of space and time scales. |
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| 20 | This documentation provides information about the physics represented by the ocean component of \NEMO and |
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| 21 | the rationale for the choice of numerical schemes and the model design. |
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| 22 | More specific information about running the model on different computers, or how to set up a configuration, |
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| 23 | are found on the \NEMO web site (www.nemo-ocean.eu). |
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[707] | 24 | |
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[10354] | 25 | The ocean component of \NEMO has been developed from the OPA model, release 8.2, described in \citet{Madec1998}. |
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| 26 | This model has been used for a wide range of applications, both regional or global, |
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| 27 | as a forced ocean model and as a model coupled with the sea-ice and/or the atmosphere. |
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[707] | 28 | |
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[10354] | 29 | This manual is organised in as follows. |
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[10442] | 30 | \autoref{chap:PE} presents the model basics, \ie the equations and their assumptions, |
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[10354] | 31 | the vertical coordinates used, and the subgrid scale physics. |
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| 32 | This part deals with the continuous equations of the model |
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| 33 | (primitive equations, with temperature, salinity and an equation of seawater). |
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| 34 | The equations are written in a curvilinear coordinate system, with a choice of vertical coordinates |
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[10442] | 35 | ($z$, $s$, \zstar, \sstar, \ztilde, \stilde, and a mixture of them). |
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[10354] | 36 | Momentum equations are formulated in vector invariant or flux form. |
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| 37 | Dimensional units in the meter, kilogram, second (MKS) international system are used throughout. |
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[707] | 38 | |
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[10354] | 39 | The following chapters deal with the discrete equations. |
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| 40 | \autoref{chap:STP} presents the time domain. |
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| 41 | The model time stepping environment is a three level scheme in which the tendency terms of |
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| 42 | the equations are evaluated either centered in time, or forward, or backward depending of the nature of the term. |
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| 43 | \autoref{chap:DOM} presents the space domain. |
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| 44 | The model is discretised on a staggered grid (Arakawa C grid) with masking of land areas. |
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| 45 | Vertical discretisation used depends on both how the bottom topography is represented and |
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| 46 | whether the free surface is linear or not. |
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| 47 | Full step or partial step $z$-coordinate or $s$- (terrain-following) coordinate is used with |
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| 48 | linear free surface (level position are then fixed in time). |
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| 49 | In non-linear free surface, |
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[10442] | 50 | the corresponding rescaled height coordinate formulation (\zstar or \sstar) is used |
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[10354] | 51 | (the level position then vary in time as a function of the sea surface heigh). |
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| 52 | The following two chapters (\autoref{chap:TRA} and \autoref{chap:DYN}) describe the discretisation of |
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| 53 | the prognostic equations for the active tracers and the momentum. |
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| 54 | Explicit, split-explicit and filtered free surface formulations are implemented. |
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| 55 | A number of numerical schemes are available for momentum advection, for the computation of the pressure gradients, |
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| 56 | as well as for the advection of tracers (second or higher order advection schemes, including positive ones). |
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[707] | 57 | |
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[10354] | 58 | Surface boundary conditions (\autoref{chap:SBC}) can be implemented as prescribed fluxes, |
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| 59 | or bulk formulations for the surface fluxes (wind stress, heat, freshwater). |
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| 60 | The model allows penetration of solar radiation. |
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| 61 | There is an optional geothermal heating at the ocean bottom. |
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| 62 | Within the \NEMO system the ocean model is interactively coupled with a sea ice model (LIM) and |
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| 63 | with biogeochemistry models (PISCES, LOBSTER). |
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| 64 | Interactive coupling to Atmospheric models is possible via the OASIS coupler \citep{OASIS2006}. |
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| 65 | Two-way nesting is also available through an interface to the AGRIF package |
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[10442] | 66 | (Adaptative Grid Refinement in \fortran) \citep{Debreu_al_CG2008}. |
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[10354] | 67 | The interface code for coupling to an alternative sea ice model (CICE, \citet{Hunke2008}) has now been upgraded so |
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| 68 | that it works for both global and regional domains, although AGRIF is still not available. |
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[707] | 69 | |
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[10354] | 70 | Other model characteristics are the lateral boundary conditions (\autoref{chap:LBC}). |
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| 71 | Global configurations of the model make use of the ORCA tripolar grid, with special north fold boundary condition. |
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| 72 | Free-slip or no-slip boundary conditions are allowed at land boundaries. |
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| 73 | Closed basin geometries as well as periodic domains and open boundary conditions are possible. |
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[707] | 74 | |
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[10354] | 75 | Physical parameterisations are described in \autoref{chap:LDF} and \autoref{chap:ZDF}. |
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| 76 | The model includes an implicit treatment of vertical viscosity and diffusivity. |
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| 77 | The lateral Laplacian and biharmonic viscosity and diffusion can be rotated following |
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| 78 | a geopotential or neutral direction. |
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| 79 | There is an optional eddy induced velocity \citep{Gent1990} with a space and time variable coefficient |
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| 80 | \citet{Treguier1997}. |
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| 81 | The model has vertical harmonic viscosity and diffusion with a space and time variable coefficient, |
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| 82 | with options to compute the coefficients with \citet{Blanke1993}, \citet{Pacanowski_Philander_JPO81}, |
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[2349] | 83 | or \citet{Umlauf_Burchard_JMS03} mixing schemes. |
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[4147] | 84 | \vspace{1cm} |
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| 85 | |
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[6140] | 86 | %%gm To be put somewhere else .... |
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| 87 | |
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[4147] | 88 | \noindent CPP keys and namelists are used for inputs to the code. \newline |
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[707] | 89 | |
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[4147] | 90 | \noindent \index{CPP keys} CPP keys \newline |
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[10442] | 91 | Some CPP keys are implemented in the \fortran code to allow code selection at compiling step. |
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[10354] | 92 | This selection of code at compilation time reduces the reliability of the whole platform since |
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| 93 | it changes the code from one set of CPP keys to the other. |
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| 94 | It is used only when the addition/suppression of the part of code highly changes the amount of memory at run time. |
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[4147] | 95 | Usual coding looks like : |
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[9388] | 96 | \begin{forlines} |
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[9376] | 97 | #if defined key_option1 |
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[10442] | 98 | ! This part of the \fortran code will be active |
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[9376] | 99 | ! only if key_option1 is activated at compiling step |
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| 100 | #endif |
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[9388] | 101 | \end{forlines} |
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[4147] | 102 | |
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| 103 | \noindent \index{Namelist} Namelists |
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| 104 | |
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[10354] | 105 | The namelist allows to input variables (character, logical, real and integer) into the code. |
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| 106 | There is one namelist file for each component of NEMO (dynamics, sea-ice, biogeochemistry...) |
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| 107 | containing all the FOTRAN namelists needed. |
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[10442] | 108 | The implementation in NEMO uses a two step process. For each \fortran namelist, two files are read: |
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[4147] | 109 | \begin{enumerate} |
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[10354] | 110 | \item |
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| 111 | A reference namelist (in \path{CONFIG/SHARED/namelist_ref}) is read first. |
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| 112 | This file contains all the namelist variables which are initialised to default values |
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| 113 | \item |
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| 114 | A configuration namelist (in \path{CONFIG/CFG_NAME/EXP00/namelist_cfg}) is read aferwards. |
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| 115 | This file contains only the namelist variables which are changed from default values, and overwrites those. |
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[4147] | 116 | \end{enumerate} |
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[9360] | 117 | A template can be found in \path{NEMO/OPA_SRC/module.example}. |
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[10354] | 118 | The effective namelist, taken in account during the run, is stored at execution time in |
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| 119 | an output\_namelist\_dyn (or \_ice or \_top) file. |
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| 120 | \vspace{1cm} |
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[4147] | 121 | |
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[6140] | 122 | %%gm end |
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[4147] | 123 | |
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[9407] | 124 | Model outputs management and specific online diagnostics are described in \autoref{chap:DIA}. |
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[10354] | 125 | The diagnostics includes the output of all the tendencies of the momentum and tracers equations, |
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| 126 | the output of tracers tendencies averaged over the time evolving mixed layer, |
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| 127 | the output of the tendencies of the barotropic vorticity equation, |
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| 128 | the computation of on-line floats trajectories... |
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| 129 | \autoref{chap:OBS} describes a tool which reads in observation files |
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| 130 | (profile temperature and salinity, sea surface temperature, sea level anomaly and sea ice concentration) |
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| 131 | and calculates an interpolated model equivalent value at the observation location and nearest model timestep. |
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| 132 | Originally developed of data assimilation, it is a fantastic tool for model and data comparison. |
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| 133 | \autoref{chap:ASM} describes how increments produced by data assimilation may be applied to the model equations. |
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| 134 | Finally, \autoref{chap:CFG} provides a brief introduction to the pre-defined model configurations |
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| 135 | (water column model, ORCA and GYRE families of configurations). |
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[707] | 136 | |
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[10442] | 137 | The model is implemented in \fninety, with preprocessing (C-pre-processor). |
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[10354] | 138 | It runs under UNIX. |
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| 139 | It is optimized for vector computers and parallelised by domain decomposition with MPI. |
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| 140 | All input and output is done in NetCDF (Network Common Data Format) with a optional direct access format for output. |
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| 141 | To ensure the clarity and readability of the code it is necessary to follow coding rules. |
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| 142 | The coding rules for OPA include conventions for naming variables, |
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| 143 | with different starting letters for different types of variables (real, integer, parameter\ldots). |
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| 144 | Those rules are briefly presented in \autoref{apdx:D} and a more complete document is available on |
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| 145 | the \NEMO web site. |
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[707] | 146 | |
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[10354] | 147 | The model is organized with a high internal modularity based on physics. |
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[10442] | 148 | For example, each trend (\ie, a term in the RHS of the prognostic equation) for momentum and tracers |
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[10354] | 149 | is computed in a dedicated module. |
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| 150 | To make it easier for the user to find his way around the code, the module names follow a three-letter rule. |
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| 151 | For example, \mdl{traldf} is a module related to the TRAcers equation, computing the Lateral DiFfussion. |
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[9407] | 152 | %The complete list of module names is presented in \autoref{apdx:D}. %====>>>> to be done ! |
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[10354] | 153 | Furthermore, modules are organized in a few directories that correspond to their category, |
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[9407] | 154 | as indicated by the first three letters of their name (\autoref{tab:chap}). |
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[707] | 155 | |
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[10354] | 156 | The manual mirrors the organization of the model. |
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| 157 | After the presentation of the continuous equations (\autoref{chap:PE}), |
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| 158 | the following chapters refer to specific terms of the equations each associated with |
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| 159 | a group of modules (\autoref{tab:chap}). |
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[707] | 160 | |
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[817] | 161 | |
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[2376] | 162 | %--------------------------------------------------TABLE-------------------------------------------------- |
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| 163 | \begin{table}[!t] |
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[10354] | 164 | % \begin{center} \begin{tabular}{|p{143pt}|l|l|} \hline |
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| 165 | \caption{ \protect\label{tab:chap} Organization of Chapters mimicking the one of the model directories. } |
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| 166 | \begin{center} |
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| 167 | \begin{tabular}{|l|l|l|} \hline |
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| 168 | \autoref{chap:STP} & - & model time STePping environment \\ \hline |
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| 169 | \autoref{chap:DOM} & DOM & model DOMain \\ \hline |
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| 170 | \autoref{chap:TRA} & TRA & TRAcer equations (potential temperature and salinity) \\ \hline |
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| 171 | \autoref{chap:DYN} & DYN & DYNamic equations (momentum) \\ \hline |
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| 172 | \autoref{chap:SBC} & SBC & Surface Boundary Conditions \\ \hline |
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| 173 | \autoref{chap:LBC} & LBC & Lateral Boundary Conditions (also OBC and BDY) \\ \hline |
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| 174 | \autoref{chap:LDF} & LDF & Lateral DiFfusion (parameterisations) \\ \hline |
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| 175 | \autoref{chap:ZDF} & ZDF & vertical (Z) DiFfusion (parameterisations) \\ \hline |
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| 176 | \autoref{chap:DIA} & DIA & I/O and DIAgnostics (also IOM, FLO and TRD) \\ \hline |
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| 177 | \autoref{chap:OBS} & OBS & OBServation and model comparison \\ \hline |
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| 178 | \autoref{chap:ASM} & ASM & ASsiMilation increment \\ \hline |
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| 179 | \autoref{chap:MISC} & SOL & Miscellaneous topics (including solvers) \\ \hline |
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| 180 | \autoref{chap:CFG} & - & predefined configurations (including C1D) \\ \hline |
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| 181 | \end{tabular} |
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| 182 | \end{center} |
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| 183 | \end{table} |
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[2376] | 184 | %-------------------------------------------------------------------------------------------------------------- |
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[707] | 185 | |
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| 186 | |
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[2349] | 187 | \subsubsection{Changes between releases} |
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[10354] | 188 | NEMO/OPA, like all research tools, is in perpetual evolution. |
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| 189 | The present document describes the OPA version include in the release 3.4 of NEMO. |
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| 190 | This release differs significantly from version 8, documented in \citet{Madec1998}.\\ |
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[2349] | 191 | |
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| 192 | $\bullet$ The main modifications from OPA v8 and NEMO/OPA v3.2 are :\\ |
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[2570] | 193 | \begin{enumerate} |
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[10354] | 194 | \item |
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[10442] | 195 | transition to full native \fninety, deep code restructuring and drastic reduction of CPP keys; |
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[10354] | 196 | \item |
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| 197 | introduction of partial step representation of bottom topography |
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| 198 | \citep{Barnier_al_OD06, Le_Sommer_al_OM09, Penduff_al_OS07}; |
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| 199 | \item |
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| 200 | partial reactivation of a terrain-following vertical coordinate ($s$- and hybrid $s$-$z$) with |
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| 201 | the addition of several options for pressure gradient computation |
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| 202 | \footnote{Partial support of $s$-coordinate: there is presently no support for neutral physics in |
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| 203 | $s$-coordinate and for the new options for horizontal pressure gradient computation with |
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| 204 | a non-linear equation of state. |
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| 205 | }; |
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| 206 | \item |
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| 207 | more choices for the treatment of the free surface: full explicit, split-explicit or filtered schemes, |
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| 208 | and suppression of the rigid-lid option; |
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| 209 | \item |
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[10442] | 210 | non linear free surface associated with the rescaled height coordinate \zstar or \textit{s}; |
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[10354] | 211 | \item |
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| 212 | additional schemes for vector and flux forms of the momentum advection; |
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| 213 | \item |
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| 214 | additional advection schemes for tracers; |
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| 215 | \item |
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[10442] | 216 | implementation of the AGRIF package (Adaptative Grid Refinement in \fortran) \citep{Debreu_al_CG2008}; |
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[10354] | 217 | \item |
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| 218 | online diagnostics : tracers trend in the mixed layer and vorticity balance; |
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| 219 | \item |
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| 220 | rewriting of the I/O management with the use of an I/O server; |
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| 221 | \item |
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| 222 | generalized ocean-ice-atmosphere-CO2 coupling interface, interfaced with OASIS 3 coupler; |
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| 223 | \item |
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| 224 | surface module (SBC) that simplify the way the ocean is forced and include two bulk formulea (CLIO and CORE) and |
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| 225 | which includes an on-the-fly interpolation of input forcing fields; |
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| 226 | \item |
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| 227 | RGB light penetration and optional use of ocean color |
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| 228 | \item |
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| 229 | major changes in the TKE schemes: it now includes a Langmuir cell parameterization \citep{Axell_JGR02}, |
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| 230 | the \citet{Mellor_Blumberg_JPO04} surface wave breaking parameterization, and has a time discretization which |
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| 231 | is energetically consistent with the ocean model equations \citep{Burchard_OM02, Marsaleix_al_OM08}; |
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| 232 | \item |
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| 233 | tidal mixing parametrisation (bottom intensification) + Indonesian specific tidal mixing |
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| 234 | \citep{Koch-Larrouy_al_GRL07}; |
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| 235 | \item |
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| 236 | introduction of LIM-3, the new Louvain-la-Neuve sea-ice model |
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| 237 | (C-grid rheology and new thermodynamics including bulk ice salinity) |
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| 238 | \citep{Vancoppenolle_al_OM09a, Vancoppenolle_al_OM09b} |
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[2570] | 239 | \end{enumerate} |
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[707] | 240 | |
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[2349] | 241 | \vspace{1cm} |
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[10354] | 242 | $\bullet$ The main modifications from NEMO/OPA v3.2 and v3.3 are :\\ |
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[2570] | 243 | \begin{enumerate} |
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[10354] | 244 | \item |
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| 245 | introduction of a modified leapfrog-Asselin filter time stepping scheme |
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| 246 | \citep{Leclair_Madec_OM09}; |
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| 247 | \item |
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| 248 | additional scheme for iso-neutral mixing \citep{Griffies_al_JPO98}, although it is still a "work in progress"; |
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| 249 | \item |
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| 250 | a rewriting of the bottom boundary layer scheme, following \citet{Campin_Goosse_Tel99}; |
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| 251 | \item |
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| 252 | addition of a Generic Length Scale vertical mixing scheme, following \citet{Umlauf_Burchard_JMS03}; |
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| 253 | \item |
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| 254 | addition of the atmospheric pressure as an external forcing on both ocean and sea-ice dynamics; |
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| 255 | \item |
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| 256 | addition of a diurnal cycle on solar radiation \citep{Bernie_al_CD07}; |
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| 257 | \item |
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| 258 | river runoffs added through a non-zero depth, and having its own temperature and salinity; |
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| 259 | \item |
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| 260 | CORE II normal year forcing set as the default forcing of ORCA2-LIM configuration; |
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| 261 | \item |
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| 262 | generalisation of the use of \mdl{fldread} for all input fields (ocean climatology, sea-ice damping...); |
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| 263 | \item |
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| 264 | addition of an on-line observation and model comparison (thanks to NEMOVAR project); |
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| 265 | \item |
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| 266 | optional application of an assimilation increment (thanks to NEMOVAR project); |
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| 267 | \item |
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| 268 | coupling interface adjusted for WRF atmospheric model; |
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| 269 | \item |
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| 270 | C-grid ice rheology now available fro both LIM-2 and LIM-3 \citep{Bouillon_al_OM09}; |
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| 271 | \item |
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| 272 | LIM-3 ice-ocean momentum coupling applied to LIM-2; |
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| 273 | \item |
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| 274 | a deep re-writting and simplification of the off-line tracer component (OFF\_SRC); |
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| 275 | \item |
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| 276 | the merge of passive and active advection and diffusion modules; |
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| 277 | \item |
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| 278 | Use of the Flexible Configuration Manager (FCM) to build configurations, |
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| 279 | generate the Makefile and produce the executable; |
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| 280 | \item |
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| 281 | Linear-tangent and Adjoint component (TAM) added, phased with v3.0 |
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[2570] | 282 | \end{enumerate} |
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[10354] | 283 | \vspace{1cm} |
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| 284 | In addition, several minor modifications in the coding have been introduced with the constant concern of |
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| 285 | improving the model performance. |
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[2349] | 286 | |
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[10354] | 287 | \vspace{1cm} |
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[3294] | 288 | $\bullet$ The main modifications from NEMO/OPA v3.3 and v3.4 are :\\ |
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| 289 | \begin{enumerate} |
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[10354] | 290 | \item finalisation of above iso-neutral mixing \citep{Griffies_al_JPO98}"; |
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[3294] | 291 | \item "Neptune effect" parametrisation; |
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[10354] | 292 | \item horizontal pressure gradient suitable for s-coordinate; |
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[3294] | 293 | \item semi-implicit bottom friction; |
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[10354] | 294 | \item finalisation of the merge of passive and active tracers advection-diffusion modules; |
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[3294] | 295 | \item a new bulk formulae (so-called MFS); |
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[10354] | 296 | \item use fldread for the off-line tracer component (OFF\_SRC); |
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[3294] | 297 | \item use MPI point to point communications for north fold; |
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[10354] | 298 | \item diagnostic of transport; |
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[3294] | 299 | \end{enumerate} |
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| 300 | |
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| 301 | |
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[6140] | 302 | \vspace{1cm} |
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| 303 | $\bullet$ The main modifications from NEMO/OPA v3.4 and v3.6 are :\\ |
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| 304 | \begin{enumerate} |
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[9019] | 305 | \item ... ; |
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[6140] | 306 | \end{enumerate} |
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| 307 | |
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| 308 | |
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| 309 | \vspace{1cm} |
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| 310 | $\bullet$ The main modifications from NEMO/OPA v3.6 and v4.0 are :\\ |
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| 311 | \begin{enumerate} |
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[9019] | 312 | \item new definition of configurations ; |
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| 313 | \item bulk formulation ; |
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[10373] | 314 | \item NEMO-wave large scale interactions ; |
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[6140] | 315 | \item ... ; |
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| 316 | \end{enumerate} |
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| 317 | |
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| 318 | |
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[10414] | 319 | \biblio |
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| 320 | |
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[10442] | 321 | \pindex |
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| 322 | |
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[6997] | 323 | \end{document} |
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