1 | \documentclass[../main/NEMO_manual]{subfiles} |
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2 | |
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3 | \begin{document} |
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4 | |
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5 | \chapter{Configurations} |
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6 | \label{chap:CFGS} |
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7 | |
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8 | \thispagestyle{plain} |
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9 | |
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10 | \chaptertoc |
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11 | |
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12 | \paragraph{Changes record} ~\\ |
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13 | |
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14 | {\footnotesize |
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15 | \begin{tabularx}{\textwidth}{l||X|X} |
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16 | Release & Author(s) & Modifications \\ |
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17 | \hline |
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18 | {\em 4.0} & {\em ...} & {\em ...} \\ |
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19 | {\em 3.6} & {\em ...} & {\em ...} \\ |
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20 | {\em 3.4} & {\em ...} & {\em ...} \\ |
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21 | {\em <=3.4} & {\em ...} & {\em ...} |
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22 | \end{tabularx} |
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23 | } |
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24 | |
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25 | \clearpage |
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26 | |
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27 | %% ================================================================================================= |
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28 | \section{Introduction} |
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29 | \label{sec:CFGS_intro} |
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30 | |
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31 | The purpose of this part of the manual is to introduce the \NEMO\ reference configurations. |
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32 | These configurations are offered as means to explore various numerical and physical options, |
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33 | thus allowing the user to verify that the code is performing in a manner consistent with that we are running. |
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34 | This form of verification is critical as one adopts the code for his or her particular research purposes. |
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35 | The reference configurations also provide a sense for some of the options available in the code, |
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36 | though by no means are all options exercised in the reference configurations. |
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37 | Configuration is defined manually through the \nam{cfg}{cfg} namelist variables. |
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38 | |
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39 | \begin{listing} |
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40 | \nlst{namcfg} |
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41 | \caption{\forcode{&namcfg}} |
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42 | \label{lst:namcfg} |
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43 | \end{listing} |
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44 | |
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45 | %% ================================================================================================= |
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46 | \section[C1D: 1D Water column model (\texttt{\textbf{key\_c1d}})]{C1D: 1D Water column model (\protect\key{c1d})} |
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47 | \label{sec:CFGS_c1d} |
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48 | |
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49 | The 1D model option simulates a stand alone water column within the 3D \NEMO\ system. |
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50 | It can be applied to the ocean alone or to the ocean-ice system and can include passive tracers or a biogeochemical model. |
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51 | It is set up by defining the position of the 1D water column in the grid |
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52 | (see \path{./cfgs/SHARED/namelist\_ref}). |
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53 | The 1D model is a very useful tool |
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54 | \textit{(a)} to learn about the physics and numerical treatment of vertical mixing processes; |
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55 | \textit{(b)} to investigate suitable parameterisations of unresolved turbulence |
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56 | (surface wave breaking, Langmuir circulation, ...); |
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57 | \textit{(c)} to compare the behaviour of different vertical mixing schemes; |
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58 | \textit{(d)} to perform sensitivity studies on the vertical diffusion at a particular point of an ocean domain; |
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59 | \textit{(d)} to produce extra diagnostics, without the large memory requirement of the full 3D model. |
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60 | |
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61 | The methodology is based on the configuration of the smallest possible domain: |
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62 | a 3x3 domain with 75 vertical levels. |
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63 | |
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64 | The 1D model has some specifies. First, all the horizontal derivatives are assumed to be zero, |
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65 | and second, the two components of the velocity are moved on a $T$-point. |
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66 | Therefore, defining \key{c1d} changes some things in the code behaviour: |
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67 | \begin{enumerate} |
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68 | \item a simplified \rou{stp} routine is used (\rou{stp\_c1d}, see \mdl{step\_c1d} module) in which |
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69 | both lateral tendancy terms and lateral physics are not called; |
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70 | \item the vertical velocity is zero |
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71 | (so far, no attempt at introducing a Ekman pumping velocity has been made); |
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72 | \item a simplified treatment of the Coriolis term is performed as $U$- and $V$-points are the same |
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73 | (see \mdl{dyncor\_c1d}). |
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74 | \end{enumerate} |
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75 | All the relevant \textit{\_c1d} modules can be found in the src/OCE/C1D directory of |
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76 | the \NEMO\ distribution. |
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77 | |
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78 | % to be added: a test case on the yearlong Ocean Weather Station (OWS) Papa dataset of Martin (1985) |
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79 | |
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80 | %% ================================================================================================= |
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81 | \section{ORCA family: global ocean with tripolar grid} |
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82 | \label{sec:CFGS_orca} |
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83 | |
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84 | The ORCA family is a series of global ocean configurations that are run together with |
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85 | the SI3 model (ORCA-ICE) and possibly with PISCES biogeochemical model (ORCA-ICE-PISCES). |
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86 | An appropriate namelist is available in \path{./cfgs/ORCA2_ICE_PISCES/EXPREF/namelist_cfg} for ORCA2. |
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87 | The domain of ORCA2 configuration is defined in \ifile{ORCA\_R2\_zps\_domcfg} file, |
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88 | this file is available in tar file on the \NEMO\ community zenodo platform: \\ |
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89 | https://doi.org/10.5281/zenodo.2640723 |
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90 | |
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91 | In this namelist\_cfg the name of domain input file is set in \nam{cfg}{cfg} block of namelist. |
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92 | |
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93 | \begin{figure}[!t] |
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94 | \centering |
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95 | \includegraphics[width=0.66\textwidth]{CFGS_ORCA_NH_mesh} |
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96 | \caption[ORCA mesh conception]{ |
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97 | ORCA mesh conception. |
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98 | The departure from an isotropic Mercator grid start poleward of 20\deg{N}. |
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99 | The two "north pole" are the foci of a series of embedded ellipses (blue curves) which |
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100 | are determined analytically and form the i-lines of the ORCA mesh (pseudo latitudes). |
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101 | Then, following \citet{madec.imbard_CD96}, |
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102 | the normal to the series of ellipses (red curves) is computed which |
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103 | provides the j-lines of the mesh (pseudo longitudes).} |
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104 | \label{fig:CFGS_ORCA_msh} |
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105 | \end{figure} |
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106 | |
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107 | %% ================================================================================================= |
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108 | \subsection{ORCA tripolar grid} |
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109 | \label{subsec:CFGS_orca_grid} |
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110 | |
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111 | The ORCA grid is a tripolar grid based on the semi-analytical method of \citet{madec.imbard_CD96}. |
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112 | It allows to construct a global orthogonal curvilinear ocean mesh which has no singularity point inside |
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113 | the computational domain since two north mesh poles are introduced and placed on lands. |
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114 | The method involves defining an analytical set of mesh parallels in the stereographic polar plan, |
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115 | computing the associated set of mesh meridians, and projecting the resulting mesh onto the sphere. |
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116 | The set of mesh parallels used is a series of embedded ellipses which foci are the two mesh north poles |
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117 | (\autoref{fig:CFGS_ORCA_msh}). |
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118 | The resulting mesh presents no loss of continuity in either the mesh lines or the scale factors, |
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119 | or even the scale factor derivatives over the whole ocean domain, as the mesh is not a composite mesh. |
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120 | \begin{figure}[!tbp] |
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121 | \centering |
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122 | \includegraphics[width=0.66\textwidth]{CFGS_ORCA_NH_msh05_e1_e2} |
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123 | \includegraphics[width=0.66\textwidth]{CFGS_ORCA_aniso} |
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124 | \caption[Horizontal scale factors and ratio of anisotropy for ORCA 0.5\deg\ mesh]{ |
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125 | \textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and |
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126 | \textit{Bottom}: ratio of anisotropy ($e_1 / e_2$) |
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127 | for ORCA 0.5\deg\ mesh. |
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128 | South of 20\deg{N} a Mercator grid is used ($e_1 = e_2$) so that the anisotropy ratio is 1. |
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129 | Poleward of 20\deg{N}, |
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130 | the two "north pole" introduce a weak anisotropy over the ocean areas ($< 1.2$) except in |
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131 | vicinity of Victoria Island (Canadian Arctic Archipelago).} |
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132 | \label{fig:CFGS_ORCA_e1e2} |
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133 | \end{figure} |
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134 | |
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135 | The method is applied to Mercator grid (\ie\ same zonal and meridional grid spacing) poleward of 20\deg{N}, |
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136 | so that the Equator is a mesh line, which provides a better numerical solution for equatorial dynamics. |
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137 | The choice of the series of embedded ellipses (position of the foci and variation of the ellipses) |
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138 | is a compromise between maintaining the ratio of mesh anisotropy ($e_1 / e_2$) close to one in the ocean |
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139 | (especially in area of strong eddy activities such as the Gulf Stream) and keeping the smallest scale factor in |
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140 | the northern hemisphere larger than the smallest one in the southern hemisphere. |
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141 | The resulting mesh is shown in \autoref{fig:CFGS_ORCA_msh} and \autoref{fig:CFGS_ORCA_e1e2} for |
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142 | a half a degree grid (ORCA\_R05). |
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143 | The smallest ocean scale factor is found in along Antarctica, |
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144 | while the ratio of anisotropy remains close to one except near the Victoria Island in the Canadian Archipelago. |
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145 | |
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146 | %% ================================================================================================= |
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147 | \subsection{ORCA pre-defined resolution} |
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148 | \label{subsec:CFGS_orca_resolution} |
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149 | |
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150 | The \NEMO\ system is provided with five built-in ORCA configurations which differ in the horizontal resolution. |
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151 | The value of the resolution is given by the resolution at the Equator expressed in degrees. |
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152 | Each of configuration is set through the \textit{domain\_cfg} domain configuration file, |
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153 | which sets the grid size and configuration name parameters. |
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154 | The \NEMO\ System Team provides only ORCA2 domain input file "\ifile{ORCA\_R2\_zps\_domcfg}" file |
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155 | (\autoref{tab:CFGS_ORCA}). |
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156 | |
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157 | \begin{table}[!t] |
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158 | \centering |
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159 | \begin{tabular}{p{4cm} c c c c} |
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160 | Horizontal Grid & \jp{ORCA\_index} & \jp{jpiglo} & \jp{jpjglo} \\ |
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161 | \hline \hline |
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162 | % 4 \deg\ & 4 & 92 & 76 \\ |
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163 | 2 \deg\ & 2 & 182 & 149 \\ |
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164 | 1 \deg\ & 1 & 362 & 292 \\ |
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165 | 0.5 \deg\ & 05 & 722 & 511 \\ |
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166 | 0.25\deg\ & 025 & 1442 & 1021 \\ |
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167 | \hline \hline |
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168 | \end{tabular} |
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169 | \caption[Domain size of ORCA family configurations]{ |
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170 | Domain size of ORCA family configurations. |
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171 | The flag for configurations of ORCA family need to be set in \textit{domain\_cfg} file.} |
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172 | \label{tab:CFGS_ORCA} |
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173 | \end{table} |
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174 | |
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175 | The ORCA\_R2 configuration has the following specificity: starting from a 2\deg\ ORCA mesh, |
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176 | local mesh refinements were applied to the Mediterranean, Red, Black and Caspian Seas, |
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177 | so that the resolution is 1\deg\ there. |
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178 | A local transformation were also applied with in the Tropics in order to refine the meridional resolution up to |
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179 | 0.5\deg\ at the Equator. |
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180 | |
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181 | The ORCA\_R1 configuration has only a local tropical transformation to refine the meridional resolution up to |
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182 | 1/3\deg\ at the Equator. |
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183 | Note that the tropical mesh refinements in ORCA\_R2 and R1 strongly increases the mesh anisotropy there. |
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184 | |
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185 | The ORCA\_R05 and higher global configurations do not incorporate any regional refinements. |
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186 | |
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187 | For ORCA\_R1 and R025, setting the configuration key to 75 allows to use 75 vertical levels, otherwise 46 are used. |
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188 | In the other ORCA configurations, 31 levels are used |
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189 | (see \autoref{tab:CFGS_ORCA}). %\sfcomment{HERE I need to put new table for ORCA2 values} and \autoref{fig:DOM_zgr_e3}). |
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190 | |
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191 | Only the ORCA\_R2 is provided with all its input files in the \NEMO\ distribution. |
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192 | %It is very similar to that used as part of the climate model developed at IPSL for the 4th IPCC assessment of |
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193 | %climate change (Marti et al., 2009). |
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194 | %It is also the basis for the \NEMO\ contribution to the Coordinate Ocean-ice Reference Experiments (COREs) |
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195 | %documented in \citet{griffies.biastoch.ea_OM09}. |
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196 | |
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197 | This version of ORCA\_R2 has 31 levels in the vertical, with the highest resolution (10m) in the upper 150m |
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198 | (see \autoref{tab:CFGS_ORCA} and \autoref{fig:DOM_zgr_e3}). |
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199 | The bottom topography and the coastlines are derived from the global atlas of Smith and Sandwell (1997). |
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200 | The default forcing uses the boundary forcing from \citet{large.yeager_rpt04} (see \autoref{subsec:SBC_blk_ocean}), |
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201 | which was developed for the purpose of running global coupled ocean-ice simulations without |
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202 | an interactive atmosphere. |
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203 | This \citet{large.yeager_rpt04} dataset is available through |
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204 | the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}. |
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205 | The "normal year" of \citet{large.yeager_rpt04} has been chosen of the \NEMO\ distribution since release v3.3. |
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206 | |
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207 | ORCA\_R2 pre-defined configuration can also be run with multiply online nested zooms (\ie\ with AGRIF, \key{agrif} defined). |
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208 | This is available as the AGRIF\_DEMO configuration that can be found in the \path{./cfgs/AGRIF_DEMO/} directory. |
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209 | |
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210 | A regional Arctic or peri-Antarctic configuration is extracted from an ORCA\_R2 or R05 configurations using |
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211 | sponge layers at open boundaries. |
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212 | |
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213 | %% ================================================================================================= |
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214 | \section{GYRE family: double gyre basin} |
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215 | \label{sec:CFGS_gyre} |
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216 | |
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217 | The GYRE configuration \citep{levy.klein.ea_OM10} has been built to |
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218 | simulate the seasonal cycle of a double-gyre box model. |
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219 | It consists in an idealized domain similar to that used in the studies of \citet{drijfhout_JPO94} and |
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220 | \citet{hazeleger.drijfhout_JPO98, hazeleger.drijfhout_JPO99, hazeleger.drijfhout_JGR00, hazeleger.drijfhout_JPO00}, |
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221 | over which an analytical seasonal forcing is applied. |
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222 | This allows to investigate the spontaneous generation of a large number of interacting, transient mesoscale eddies |
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223 | and their contribution to the large scale circulation. |
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224 | |
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225 | The GYRE configuration run together with the PISCES biogeochemical model (GYRE-PISCES). |
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226 | The domain geometry is a closed rectangular basin on the $\beta$-plane centred at $\sim$ 30\deg{N} and |
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227 | rotated by 45\deg, 3180~km long, 2120~km wide and 4~km deep (\autoref{fig:MISC_strait_hand}). |
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228 | The domain is bounded by vertical walls and by a flat bottom. |
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229 | The configuration is meant to represent an idealized North Atlantic or North Pacific basin. |
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230 | The circulation is forced by analytical profiles of wind and buoyancy fluxes. |
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231 | The applied forcings vary seasonally in a sinusoidal manner between winter and summer extrema \citep{levy.klein.ea_OM10}. |
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232 | The wind stress is zonal and its curl changes sign at 22\deg{N} and 36\deg{N}. |
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233 | It forces a subpolar gyre in the north, a subtropical gyre in the wider part of the domain and |
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234 | a small recirculation gyre in the southern corner. |
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235 | The net heat flux takes the form of a restoring toward a zonal apparent air temperature profile. |
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236 | A portion of the net heat flux which comes from the solar radiation is allowed to penetrate within the water column. |
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237 | The fresh water flux is also prescribed and varies zonally. |
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238 | It is determined such as, at each time step, the basin-integrated flux is zero. |
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239 | The basin is initialised at rest with vertical profiles of temperature and salinity uniformly applied to |
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240 | the whole domain. |
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241 | |
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242 | The GYRE configuration is set like an analytical configuration. |
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243 | Through \np[=.false.]{ln_read_cfg}{ln\_read\_cfg} in \nam{cfg}{cfg} namelist defined in |
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244 | the reference configuration \path{./cfgs/GYRE_PISCES/EXPREF/namelist_cfg} |
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245 | analytical definition of grid in GYRE is done in usrdef\_hrg, usrdef\_zgr routines. |
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246 | Its horizontal resolution (and thus the size of the domain) is determined by |
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247 | setting \np{nn_GYRE}{nn\_GYRE} in \nam{usr_def}{usr\_def}: \\ |
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248 | |
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249 | \jp{jpiglo} $= 30 \times$ \np{nn_GYRE}{nn\_GYRE} + 2 \\ |
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250 | |
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251 | \jp{jpjglo} $= 20 \times$ \np{nn_GYRE}{nn\_GYRE} + 2 \\ |
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252 | |
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253 | Obviously, the namelist parameters have to be adjusted to the chosen resolution, |
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254 | see the Configurations pages on the \NEMO\ web site (\NEMO\ Configurations). |
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255 | In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}\forcode{ = 31}) (\autoref{fig:DOM_zgr_e3}). |
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256 | |
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257 | The GYRE configuration is also used in benchmark test as it is very simple to increase its resolution and |
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258 | as it does not requires any input file. |
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259 | For example, keeping a same model size on each processor while increasing the number of processor used is very easy, |
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260 | even though the physical integrity of the solution can be compromised. |
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261 | Benchmark is activate via \np[=.true.]{ln_bench}{ln\_bench} in \nam{usr_def}{usr\_def} in |
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262 | namelist \path{./cfgs/GYRE_PISCES/EXPREF/namelist_cfg}. |
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263 | |
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264 | \begin{figure}[!t] |
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265 | \centering |
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266 | \includegraphics[width=0.66\textwidth]{CFGS_GYRE} |
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267 | \caption[Snapshot of relative vorticity at the surface of the model domain in GYRE R9, R27 and R54]{ |
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268 | Snapshot of relative vorticity at the surface of the model domain in GYRE R9, R27 and R54. |
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269 | From \citet{levy.klein.ea_OM10}.} |
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270 | \label{fig:CFGS_GYRE} |
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271 | \end{figure} |
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272 | |
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273 | %% ================================================================================================= |
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274 | \section{AMM: atlantic margin configuration} |
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275 | \label{sec:CFGS_config_AMM} |
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276 | |
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277 | The AMM, Atlantic Margins Model, is a regional model covering the Northwest European Shelf domain on |
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278 | a regular lat-lon grid at approximately 12km horizontal resolution. |
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279 | The appropriate \textit{\&namcfg} namelist is available in \path{./cfgs/AMM12/EXPREF/namelist\_cfg}. |
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280 | It is used to build the correct dimensions of the AMM domain. |
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281 | |
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282 | This configuration tests several features of \NEMO\ functionality specific to the shelf seas. |
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283 | In particular, the AMM uses $s$-coordinates in the vertical rather than $z$-coordinates and |
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284 | is forced with tidal lateral boundary conditions using a Flather boundary condition from the BDY module. |
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285 | Also specific to the AMM configuration is the use of the GLS turbulence scheme (\np[=.true.]{ln_zdfgls}{ln\_zdfgls}). |
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286 | |
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287 | In addition to the tidal boundary condition the model may also take open boundary conditions from |
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288 | a North Atlantic model. |
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289 | Boundaries may be completely omitted by setting \np{ln_bdy}{ln\_bdy} to false. |
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290 | Sample surface fluxes, river forcing and a sample initial restart file are included to test a realistic model run. |
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291 | The Baltic boundary is included within the river input file and is specified as a river source. |
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292 | Unlike ordinary river points the Baltic inputs also include salinity and temperature data. |
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293 | |
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294 | \onlyinsubfile{\input{../../global/epilogue}} |
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295 | |
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296 | \end{document} |
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