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2 | % ================================================================ |
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3 | % INTRODUCTION |
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4 | % ================================================================ |
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5 | |
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6 | \chapter{Introduction} |
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7 | |
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8 | The Nucleus for European Modelling of the Ocean (\NEMO) is a framework of ocean |
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9 | related engines, namely OPA\footnote{OPA = Oc\'{e}an PArall\'{e}lis\'{e}} for the |
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10 | ocean dynamics and thermodynamics, LIM\footnote{LIM= Louvain)la-neuve Ice |
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11 | Model} for the sea-ice dynamics and thermodynamics, TOP\footnote{TOP = Tracer |
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12 | in the Ocean Paradigm} for the biogeochemistry (both transport (TRP) and sources |
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13 | minus sinks (LOBSTER, PISCES)\footnote{Both LOBSTER and PISCES are not |
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14 | acronyms just name}. It is intended to be a flexible tool for studying the ocean and |
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15 | its interactions with the other components of the earth climate system (atmosphere, |
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16 | sea-ice, biogeochemical tracers, ...) over a wide range of space and time scales. |
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17 | This documentation provides information about the physics represented by the ocean |
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18 | component of \NEMO and the rationale for the choice of numerical schemes and |
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19 | the model design. More specific information about running the model on different |
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20 | computers, or how to set up a configuration, are found on the \NEMO web site |
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21 | (www.locean-ipsl.upmc.fr/NEMO). |
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22 | |
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23 | The ocean component of \NEMO has been developed from the OPA model, |
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24 | release 8.2, described in \citet{Madec1998}. This model has been used for a wide |
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25 | range of applications, both regional or global, as a forced ocean model and as a |
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26 | model coupled with the atmosphere. A complete list of references is found on the |
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27 | \NEMO web site. |
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28 | |
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29 | This manual is organised in as follows. Chapter~\ref{PE} presents the model basics, |
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30 | $i.e.$ the equations and their assumptions, the vertical coordinates used, and the |
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31 | subgrid scale physics. This part deals with the continuous equations of the model |
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32 | (primitive equations, with potential temperature, salinity and an equation of state). |
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33 | The equations are written in a curvilinear coordinate system, with a choice of vertical |
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34 | coordinates ($z$ or $s$, with the rescaled height coordinate formulation \textit{z*}, or |
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35 | \textit{s*}). Momentum equations are formulated in the vector invariant form or in the |
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36 | flux form. Dimensional units in the meter, kilogram, second (MKS) international system |
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37 | are used throughout. |
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38 | |
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39 | The following chapters deal with the discrete equations. Chapter~\ref{STP} presents the |
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40 | time domain. The model time stepping environment is a three level scheme in which |
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41 | the tendency terms of the equations are evaluated either centered in time, or forward, |
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42 | or backward depending of the nature of the term. |
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43 | Chapter~\ref{DOM} presents the space domain. The model is discretised on a staggered |
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44 | grid (Arakawa C grid) with masking of land areas. Vertical discretisation used depends |
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45 | on both how the bottom topography is represented and whether the free surface is linear or not. |
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46 | Full step or partial step $z$-coordinate or $s$- (terrain-following) coordinate is used |
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47 | with linear free surface (level position are then fixed in time). In non-linear free surface, |
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48 | the corresponding rescaled height coordinate formulation (\textit{z*} or \textit{s*}) is used |
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49 | (the level position then vary in time as a function of the sea surface heigh). |
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50 | The following two chapters (\ref{TRA} and \ref{DYN}) describe the discretisation of the |
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51 | prognostic equations for the active tracers and the momentum. Explicit, split-explicit |
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52 | and filtered free surface formulations are implemented. |
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53 | A number of numerical schemes are available for momentum advection, for the computation |
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54 | of the pressure gradients, as well as for the advection of tracers (second or higher |
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55 | order advection schemes, including positive ones). |
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56 | |
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57 | Surface boundary conditions (chapter~\ref{SBC}) can be implemented as prescribed |
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58 | fluxes, or bulk formulations for the surface fluxes (wind stress, heat, freshwater). The |
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59 | model allows penetration of solar radiation There is an optional geothermal heating at |
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60 | the ocean bottom. Within the \NEMO system the ocean model is interactively coupled |
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61 | with a sea ice model (LIM) and with biogeochemistry models (PISCES, LOBSTER). |
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62 | Interactive coupling to Atmospheric models is possible via the OASIS coupler |
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63 | \citep{OASIS2006}. Two-way nesting is also available through an interface to the |
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64 | AGRIF package (Adaptative Grid Refinement in \textsc{Fortran}) \citep{Debreu_al_CG2008}. |
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65 | |
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66 | Other model characteristics are the lateral boundary conditions (chapter~\ref{LBC}). |
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67 | Global configurations of the model make use of the ORCA tripolar grid, with special north |
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68 | fold boundary condition. Free-slip or no-slip boundary conditions are allowed at land |
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69 | boundaries. Closed basin geometries as well as periodic domains and open boundary |
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70 | conditions are possible. |
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71 | |
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72 | Physical parameterisations are described in chapters~\ref{LDF} and \ref{ZDF}. The |
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73 | model includes an implicit treatment of vertical viscosity and diffusivity. The lateral |
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74 | Laplacian and biharmonic viscosity and diffusion can be rotated following a geopotential |
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75 | or neutral direction. There is an optional eddy induced velocity \citep{Gent1990} with a |
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76 | space and time variable coefficient \citet{Treguier1997}. The model has vertical harmonic |
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77 | viscosity and diffusion with a space and time variable coefficient, with options to compute |
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78 | the coefficients with \citet{Blanke1993}, \citet{Large_al_RG94}, \citet{Pacanowski_Philander_JPO81}, |
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79 | or \citet{Umlauf_Burchard_JMS03} mixing schemes. |
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80 | |
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81 | Model outputs management and specific online diagnostics are described in chapters~\ref{DIA}. |
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82 | The diagnostics includes the output of all the tendencies of the momentum and tracers equations, |
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83 | the output of tracers tendencies averaged over the time evolving mixed layer, the output of |
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84 | the tendencies of the barotropic vorticity equation, the computation of on-line floats trajectories... |
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85 | Chapter~\ref{OBS} describes a tool which reads in observation files (profile temperature |
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86 | and salinity, sea surface temperature, sea level anomaly and sea ice concentration) |
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87 | and calculates an interpolated model equivalent value at the observation location |
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88 | and nearest model timestep. Originally developed of data assimilation, it is a fantastic |
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89 | tool for model and data comparison. Chapter~\ref{ASM} describes how increments |
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90 | produced by data assimilation may be applied to the model equations. |
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91 | Finally, Chapter~\ref{CFG} provides a brief introduction to the pre-defined model |
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92 | configurations (water column model, ORCA and GYRE families of configurations). |
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93 | |
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94 | The model is implemented in \textsc{Fortran 90}, with preprocessing (C-pre-processor). |
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95 | It runs under UNIX. It is optimized for vector computers and parallelised by domain |
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96 | decomposition with MPI. All input and output is done in NetCDF (Network Common Data |
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97 | Format) with a optional direct access format for output. To ensure the clarity and |
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98 | readability of the code it is necessary to follow coding rules. The coding rules for OPA |
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99 | include conventions for naming variables, with different starting letters for different types |
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100 | of variables (real, integer, parameter\ldots). Those rules are briefly presented in |
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101 | Appendix~\ref{Apdx_D} and a more complete document is available on the \NEMO web site. |
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102 | |
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103 | The model is organized with a high internal modularity based on physics. For example, |
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104 | each trend ($i.e.$, a term in the RHS of the prognostic equation) for momentum and |
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105 | tracers is computed in a dedicated module. To make it easier for the user to find his way |
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106 | around the code, the module names follow a three-letter rule. For example, \mdl{traldf} |
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107 | is a module related to the TRAcers equation, computing the Lateral DiFfussion. |
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108 | %The complete list of module names is presented in Appendix~\ref{Apdx_D}. %====>>>> to be done ! |
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109 | Furthermore, modules are organized in a few directories that correspond to their category, |
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110 | as indicated by the first three letters of their name (Tab.~\ref{Tab_chap}). |
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111 | |
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112 | The manual mirrors the organization of the model. |
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113 | After the presentation of the continuous equations (Chapter \ref{PE}), the following chapters |
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114 | refer to specific terms of the equations each associated with a group of modules (Tab.~\ref{Tab_chap}). |
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115 | |
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116 | |
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117 | %--------------------------------------------------TABLE-------------------------------------------------- |
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118 | \begin{table}[!t] |
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119 | %\begin{center} \begin{tabular}{|p{143pt}|l|l|} \hline |
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120 | \caption{ \label{Tab_chap} Organization of Chapters mimicking the one of the model directories. } |
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121 | \begin{center} \begin{tabular}{|l|l|l|} \hline |
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122 | Chapter \ref{STP} & - & model time STePping environment \\ \hline |
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123 | Chapter \ref{DOM} & DOM & model DOMain \\ \hline |
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124 | Chapter \ref{TRA} & TRA & TRAcer equations (potential temperature and salinity) \\ \hline |
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125 | Chapter \ref{DYN} & DYN & DYNamic equations (momentum) \\ \hline |
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126 | Chapter \ref{SBC} & SBC & Surface Boundary Conditions \\ \hline |
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127 | Chapter \ref{LBC} & LBC & Lateral Boundary Conditions (also OBC and BDY) \\ \hline |
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128 | Chapter \ref{LDF} & LDF & Lateral DiFfusion (parameterisations) \\ \hline |
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129 | Chapter \ref{ZDF} & ZDF & vertical (Z) DiFfusion (parameterisations) \\ \hline |
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130 | Chapter \ref{DIA} & DIA & I/O and DIAgnostics (also IOM, FLO and TRD) \\ \hline |
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131 | Chapter \ref{OBS} & OBS & OBServation and model comparison \\ \hline |
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132 | Chapter \ref{ASM} & ASM & ASsiMilation increment \\ \hline |
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133 | Chapter \ref{MISC} & SOL & Miscellaneous topics (including solvers) \\ \hline |
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134 | Chapter \ref{CFG} & - & predefined configurations (including C1D) \\ \hline |
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135 | \end{tabular} |
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136 | \end{center} \end{table} |
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137 | %-------------------------------------------------------------------------------------------------------------- |
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138 | |
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139 | |
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140 | \subsubsection{Changes between releases} |
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141 | NEMO/OPA, like all research tools, is in perpetual evolution. The present document describes |
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142 | the OPA version include in the release 3.3 of NEMO. This release differs significantly |
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143 | from version 8, documented in \citet{Madec1998}.\\ |
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144 | |
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145 | $\bullet$ The main modifications from OPA v8 and NEMO/OPA v3.2 are :\\ |
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146 | (1) transition to full native \textsc{Fortran} 90, deep code restructuring and drastic |
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147 | reduction of CPP keys; \\ |
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148 | (2) introduction of partial step representation of bottom topography \citep{Barnier_al_OD06, Le_Sommer_al_OM09, Penduff_al_OS07}; \\ |
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149 | (3) partial reactivation of a terrain-following vertical coordinate ($s$- and hybrid $s$-$z$) |
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150 | with the addition of several options for pressure gradient computation \footnote{Partial |
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151 | support of $s$-coordinate: there is presently no support for neutral physics in $s$- |
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152 | coordinate and for the new options for horizontal pressure gradient computation with |
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153 | a non-linear equation of state.}; \\ |
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154 | (4) more choices for the treatment of the free surface: full explicit, split-explicit or filtered schemes. \\ |
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155 | (5) suppression of the rigid-lid option;\\ |
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156 | (6) non linear free surface option (associated with the rescaled height coordinate |
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157 | \textit{z*} or \textit{s}); \\ |
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158 | (6) additional schemes for vector and flux forms of the momentum advection; \\ |
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159 | (7) additional advection schemes for tracers; \\ |
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160 | (8) implementation of the AGRIF package (Adaptative Grid Refinement in \textsc{Fortran}) \citep{Debreu_al_CG2008}; \\ |
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161 | (9) online diagnostics : tracers trend in the mixed layer and vorticity balance; \\ |
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162 | (10) rewriting of the I/O management with the use of an I/O server; \\ |
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163 | (11) generalized ocean-ice-atmosphere-CO2 coupling interface, interfaced with OASIS 3 coupler. \\ |
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164 | (12) surface module (SBC) that simplify the way the ocean is forced and include two |
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165 | bulk formulea (CLIO and CORE) and which includes an on-the-fly interpolation of input forcing fields\\ |
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166 | (13) RGB light penetration and optional use of ocean color |
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167 | (14) major changes in the TKE schemes: it now includes a Langmuir cell parameterization \citep{Axell_JGR02}, |
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168 | the \citet{Mellor_Blumberg_JPO04} surface wave breaking parameterization, and has a time discretization |
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169 | which is energetically consistent with the ocean model equations \citep{Burchard_OM02, Marsaleix_al_OM08}; \\ |
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170 | (15) tidal mixing parametrisation (bottom intensification) + Indonesian specific tidal mixing \citep{Koch-Larrouy_al_GRL07}; \\ |
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171 | (16) introduction of LIM-3, the new Louvain-la-Neuve sea-ice model (C-grid rheology and |
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172 | new thermodynamics including bulk ice salinity) \citep{Vancoppenolle_al_OM09a, Vancoppenolle_al_OM09b} |
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173 | |
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174 | \vspace{1cm} |
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175 | $\bullet$ The main modifications from NEMO/OPA v3.2 and v3.3 are :\\ |
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176 | (1) introduction of a modified leapfrog-Asselin filter time stepping scheme \citep{Leclair_Madec_OM09}; \\ |
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177 | (2) additional scheme for iso-neutral mixing \citep{Griffies_al_JPO98}, although it is still a "work in progress"; \\ |
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178 | (3) a rewriting of the bottom boundary layer scheme, following \citet{Campin_Goosse_Tel99}; \\ |
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179 | (4) addition of a Generic Length Scale vertical mixing scheme, following \citet{Umlauf_Burchard_JMS03}; |
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180 | (5) addition of the atmospheric pressure as an external forcing on both ocean and sea-ice dynamics; \\ |
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181 | (6) addition of a diurnal cycle on solar radiation \citep{Bernie_al_CD07}; \\ |
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182 | (7) river runoffs added through a non-zero depth, and having its own temperature and salinity; \\ |
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183 | (8) CORE II normal year forcing set as the default forcing of ORCA2-LIM configuration ; \\ |
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184 | (9) generalisation of the use of \mdl{fldread} for all input fields (ocean, climatology, sea-ice damping...) |
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185 | (10) addition of an on-line observation and model comparison (thanks to NEMOVAR project); \\ |
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186 | (11) optional application of an assimilation increment (thanks to NEMOVAR project); \\ |
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187 | (12) coupling interface adjusted for WRF atmospheric model |
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188 | (13) C-grid ice rheology now available fro both LIM-2 and LIM-3 \citep{Bouillon_al_OM09}; \\ |
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189 | (14) a deep re-writting and simplification of the off-line tracer component (OFF\_SRC) ; \\ |
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190 | (15) the merge of passive and active advection and diffusion modules \\ |
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191 | (16) Use of the Flexible Configuration Manager (FCM) to build configurations, generate the Makefile and produce the executable ; \\ |
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192 | (17) Linear-tangent and Adjoint component (TAM) added, phased with v3.0 |
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193 | |
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194 | \vspace{1cm} |
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195 | In addition, several minor modifications in the coding have been introduced with the constant |
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196 | concern of improving the model performance. |
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197 | |
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