1 | \documentclass[NEMO_book]{subfiles} |
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2 | \begin{document} |
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3 | % ================================================================ |
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4 | % Chapter � Configurations |
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5 | % ================================================================ |
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6 | \chapter{Configurations} |
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7 | \label{CFG} |
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8 | \minitoc |
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9 | |
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10 | \newpage |
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11 | $\ $\newline % force a new ligne |
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12 | |
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13 | % ================================================================ |
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14 | % Introduction |
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15 | % ================================================================ |
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16 | \section{Introduction} |
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17 | \label{CFG_intro} |
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18 | |
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19 | |
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20 | The purpose of this part of the manual is to introduce the \NEMO reference configurations. |
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21 | These configurations are offered as means to explore various numerical and physical options, |
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22 | thus allowing the user to verify that the code is performing in a manner consistent with that |
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23 | we are running. This form of verification is critical as one adopts the code for his or her particular |
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24 | research purposes. The test cases also provide a sense for some of the options available |
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25 | in the code, though by no means are all options exercised in the reference configurations. |
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26 | |
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27 | Configuration is defined mainly through the \ngn{namcfg} namelist variables: |
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28 | %------------------------------------------namcfg---------------------------------------------------- |
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29 | \namdisplay{namcfg} |
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30 | %------------------------------------------------------------------------------------------------------------- |
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31 | |
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32 | % ================================================================ |
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33 | % 1D model configuration |
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34 | % ================================================================ |
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35 | \section{Water column model: 1D model (C1D) (\key{c1d}) } |
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36 | \label{CFG_c1d} |
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37 | |
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38 | The 1D model option simulates a stand alone water column within the 3D \NEMO system. |
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39 | It can be applied to the ocean alone or to the ocean-ice system and can include passive tracers |
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40 | or a biogeochemical model. It is set up by defining the position of the 1D water column in the grid |
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41 | (see \textit{CONFIG/SHARED/namelist\_ref} ). |
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42 | The 1D model is a very useful tool |
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43 | \textit{(a)} to learn about the physics and numerical treatment of vertical mixing processes ; |
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44 | \textit{(b)} to investigate suitable parameterisations of unresolved turbulence (surface wave |
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45 | breaking, Langmuir circulation, ...) ; |
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46 | \textit{(c)} to compare the behaviour of different vertical mixing schemes ; |
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47 | \textit{(d)} to perform sensitivity studies on the vertical diffusion at a particular point of an ocean domain ; |
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48 | \textit{(d)} to produce extra diagnostics, without the large memory requirement of the full 3D model. |
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49 | |
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50 | The methodology is based on the use of the zoom functionality over the smallest possible |
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51 | domain : a 3x3 domain centered on the grid point of interest, |
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52 | with some extra routines. There is no need to define a new mesh, bathymetry, |
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53 | initial state or forcing, since the 1D model will use those of the configuration it is a zoom of. |
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54 | The chosen grid point is set in \textit{\ngn{namcfg}} namelist by setting the \np{jpizoom} and \np{jpjzoom} |
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55 | parameters to the indices of the location of the chosen grid point. |
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56 | |
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57 | The 1D model has some specifies. First, all the horizontal derivatives are assumed to be zero, and |
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58 | second, the two components of the velocity are moved on a $T$-point. |
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59 | Therefore, defining \key{c1d} changes five main things in the code behaviour: |
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60 | \begin{description} |
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61 | \item[(1)] the lateral boundary condition routine (\rou{lbc\_lnk}) set the value of the central column |
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62 | of the 3x3 domain is imposed over the whole domain ; |
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63 | \item[(3)] a call to \rou{lbc\_lnk} is systematically done when reading input data ($i.e.$ in \mdl{iom}) ; |
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64 | \item[(3)] a simplified \rou{stp} routine is used (\rou{stp\_c1d}, see \mdl{step\_c1d} module) in which |
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65 | both lateral tendancy terms and lateral physics are not called ; |
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66 | \item[(4)] the vertical velocity is zero (so far, no attempt at introducing a Ekman pumping velocity |
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67 | has been made) ; |
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68 | \item[(5)] a simplified treatment of the Coriolis term is performed as $U$- and $V$-points are the same |
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69 | (see \mdl{dyncor\_c1d}). |
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70 | \end{description} |
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71 | All the relevant \textit{\_c1d} modules can be found in the NEMOGCM/NEMO/OPA\_SRC/C1D directory of |
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72 | the \NEMO distribution. |
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73 | |
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74 | % to be added: a test case on the yearlong Ocean Weather Station (OWS) Papa dataset of Martin (1985) |
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75 | |
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76 | % ================================================================ |
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77 | % ORCA family configurations |
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78 | % ================================================================ |
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79 | \section{ORCA family: global ocean with tripolar grid } |
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80 | \label{CFG_orca} |
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81 | |
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82 | The ORCA family is a series of global ocean configurations that are run together with |
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83 | the LIM sea-ice model (ORCA-LIM) and possibly with PISCES biogeochemical model |
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84 | (ORCA-LIM-PISCES), using various resolutions. |
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85 | The appropriate \textit{\&namcfg} namelist is available in \textit{CONFIG/ORCA2\_LIM/EXP00/namelist\_cfg} |
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86 | for ORCA2 and in \textit{CONFIG/SHARED/README\_other\_configurations\_namelist\_namcfg} |
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87 | for other resolutions |
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88 | |
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89 | |
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90 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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91 | \begin{figure}[!t] \begin{center} |
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92 | \includegraphics[width=0.98\textwidth]{Fig_ORCA_NH_mesh} |
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93 | \caption{ \label{Fig_MISC_ORCA_msh} |
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94 | ORCA mesh conception. The departure from an isotropic Mercator grid start poleward of 20\degN. |
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95 | The two "north pole" are the foci of a series of embedded ellipses (blue curves) |
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96 | which are determined analytically and form the i-lines of the ORCA mesh (pseudo latitudes). |
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97 | Then, following \citet{Madec_Imbard_CD96}, the normal to the series of ellipses (red curves) is computed |
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98 | which provide the j-lines of the mesh (pseudo longitudes). } |
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99 | \end{center} \end{figure} |
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100 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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101 | |
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102 | % ------------------------------------------------------------------------------------------------------------- |
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103 | % ORCA tripolar grid |
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104 | % ------------------------------------------------------------------------------------------------------------- |
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105 | \subsection{ORCA tripolar grid} |
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106 | \label{CFG_orca_grid} |
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107 | |
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108 | The ORCA grid is a tripolar is based on the semi-analytical method of \citet{Madec_Imbard_CD96}. |
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109 | It allows to construct a global orthogonal curvilinear ocean mesh which has no singularity point inside |
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110 | the computational domain since two north mesh poles are introduced and placed on lands. |
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111 | The method involves defining an analytical set of mesh parallels in the stereographic polar plan, |
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112 | computing the associated set of mesh meridians, and projecting the resulting mesh onto the sphere. |
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113 | The set of mesh parallels used is a series of embedded ellipses which foci are the two mesh north |
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114 | poles (Fig.~\ref{Fig_MISC_ORCA_msh}). The resulting mesh presents no loss of continuity in |
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115 | either the mesh lines or the scale factors, or even the scale factor derivatives over the whole |
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116 | ocean domain, as the mesh is not a composite mesh. |
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117 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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118 | \begin{figure}[!tbp] \begin{center} |
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119 | \includegraphics[width=1.0\textwidth]{Fig_ORCA_NH_msh05_e1_e2} |
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120 | \includegraphics[width=0.80\textwidth]{Fig_ORCA_aniso} |
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121 | \caption { \label{Fig_MISC_ORCA_e1e2} |
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122 | \textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and |
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123 | \textit{Bottom}: ratio of anisotropy ($e_1 / e_2$) |
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124 | for ORCA 0.5\deg ~mesh. South of 20\degN a Mercator grid is used ($e_1 = e_2$) |
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125 | so that the anisotropy ratio is 1. Poleward of 20\degN, the two "north pole" |
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126 | introduce a weak anisotropy over the ocean areas ($< 1.2$) except in vicinity of Victoria Island |
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127 | (Canadian Arctic Archipelago). } |
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128 | \end{center} \end{figure} |
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129 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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130 | |
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131 | |
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132 | The method is applied to Mercator grid ($i.e.$ same zonal and meridional grid spacing) poleward |
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133 | of 20\degN, so that the Equator is a mesh line, which provides a better numerical solution |
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134 | for equatorial dynamics. The choice of the series of embedded ellipses (position of the foci and |
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135 | variation of the ellipses) is a compromise between maintaining the ratio of mesh anisotropy |
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136 | ($e_1 / e_2$) close to one in the ocean (especially in area of strong eddy activities such as |
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137 | the Gulf Stream) and keeping the smallest scale factor in the northern hemisphere larger |
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138 | than the smallest one in the southern hemisphere. |
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139 | The resulting mesh is shown in Fig.~\ref{Fig_MISC_ORCA_msh} and \ref{Fig_MISC_ORCA_e1e2} |
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140 | for a half a degree grid (ORCA\_R05). The smallest ocean scale factor is found in along |
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141 | Antarctica, while the ratio of anisotropy remains close to one except near the Victoria Island |
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142 | in the Canadian Archipelago. |
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143 | |
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144 | % ------------------------------------------------------------------------------------------------------------- |
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145 | % ORCA-LIM(-PISCES) configurations |
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146 | % ------------------------------------------------------------------------------------------------------------- |
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147 | \subsection{ORCA pre-defined resolution} |
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148 | \label{CFG_orca_resolution} |
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149 | |
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150 | |
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151 | The NEMO system is provided with five built-in ORCA configurations which differ in the |
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152 | horizontal resolution. The value of the resolution is given by the resolution at the Equator |
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153 | expressed in degrees. Each of configuration is set through the \textit{\ngn{namcfg}} namelist, |
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154 | which sets the grid size and configuration |
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155 | name parameters (Tab. \ref{Tab_ORCA}). |
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156 | . |
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157 | |
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158 | %--------------------------------------------------TABLE-------------------------------------------------- |
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159 | \begin{table}[!t] \begin{center} |
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160 | \begin{tabular}{p{4cm} c c c c} |
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161 | Horizontal Grid & \np{jp\_cfg} & \np{jpiglo} & \np{jpjglo} & \\ |
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162 | \hline \hline |
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163 | \~4\deg & 4 & 92 & 76 & \\ |
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164 | \~2\deg & 2 & 182 & 149 & \\ |
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165 | \~1\deg & 1 & 362 & 292 & \\ |
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166 | \~0.5\deg & 05 & 722 & 511 & \\ |
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167 | \~0.25\deg & 025 & 1442 & 1021 & \\ |
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168 | %\key{orca\_r8} & 8 & 2882 & 2042 & \\ |
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169 | %\key{orca\_r12} & 12 & 4322 & 3062 & \\ |
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170 | \hline \hline |
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171 | \end{tabular} |
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172 | \caption{ \label{Tab_ORCA} |
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173 | Set of predefined parameters for ORCA family configurations. |
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174 | In all cases, the name of the configuration is set to "orca" ($i.e.$ \np{cp\_cfg}~=~orca). } |
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175 | \end{center} |
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176 | \end{table} |
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177 | %-------------------------------------------------------------------------------------------------------------- |
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178 | |
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179 | |
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180 | The ORCA\_R2 configuration has the following specificity : starting from a 2\deg~ORCA mesh, |
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181 | local mesh refinements were applied to the Mediterranean, Red, Black and Caspian Seas, |
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182 | so that the resolution is 1\deg \time 1\deg there. A local transformation were also applied |
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183 | with in the Tropics in order to refine the meridional resolution up to 0.5\deg at the Equator. |
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184 | |
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185 | The ORCA\_R1 configuration has only a local tropical transformation to refine the meridional |
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186 | resolution up to 1/3\deg~at the Equator. Note that the tropical mesh refinements in ORCA\_R2 |
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187 | and R1 strongly increases the mesh anisotropy there. |
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188 | |
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189 | The ORCA\_R05 and higher global configurations do not incorporate any regional refinements. |
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190 | |
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191 | For ORCA\_R1 and R025, setting the configuration key to 75 allows to use 75 vertical levels, |
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192 | otherwise 46 are used. In the other ORCA configurations, 31 levels are used |
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193 | (see Tab.~\ref{Tab_orca_zgr} and Fig.~\ref{Fig_zgr}). |
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194 | |
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195 | Only the ORCA\_R2 is provided with all its input files in the \NEMO distribution. |
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196 | It is very similar to that used as part of the climate model developed at IPSL for the 4th IPCC |
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197 | assessment of climate change (Marti et al., 2009). It is also the basis for the \NEMO contribution |
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198 | to the Coordinate Ocean-ice Reference Experiments (COREs) documented in \citet{Griffies_al_OM09}. |
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199 | |
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200 | This version of ORCA\_R2 has 31 levels in the vertical, with the highest resolution (10m) |
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201 | in the upper 150m (see Tab.~\ref{Tab_orca_zgr} and Fig.~\ref{Fig_zgr}). |
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202 | The bottom topography and the coastlines are derived from the global atlas of Smith and Sandwell (1997). |
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203 | The default forcing uses the boundary forcing from \citet{Large_Yeager_Rep04} (see \S\ref{SBC_blk_core}), |
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204 | which was developed for the purpose of running global coupled ocean-ice simulations |
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205 | without an interactive atmosphere. This \citet{Large_Yeager_Rep04} dataset is available |
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206 | through the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}. |
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207 | The "normal year" of \citet{Large_Yeager_Rep04} has been chosen of the \NEMO distribution |
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208 | since release v3.3. |
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209 | |
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210 | ORCA\_R2 pre-defined configuration can also be run with an AGRIF zoom over the Agulhas |
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211 | current area ( \key{agrif} defined) and, by setting the appropriate variables in |
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212 | \textit{\&namcfg}, see \textit{CONFIG/SHARED/namelist\_ref} |
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213 | a regional Arctic or peri-Antarctic configuration is extracted from an ORCA\_R2 or R05 configurations |
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214 | using sponge layers at open boundaries. |
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215 | |
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216 | % ------------------------------------------------------------------------------------------------------------- |
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217 | % GYRE family: double gyre basin |
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218 | % ------------------------------------------------------------------------------------------------------------- |
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219 | \section{GYRE family: double gyre basin } |
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220 | \label{CFG_gyre} |
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221 | |
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222 | The GYRE configuration \citep{Levy_al_OM10} has been built to simulate |
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223 | the seasonal cycle of a double-gyre box model. It consists in an idealized domain |
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224 | similar to that used in the studies of \citet{Drijfhout_JPO94} and \citet{Hazeleger_Drijfhout_JPO98, |
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225 | Hazeleger_Drijfhout_JPO99, Hazeleger_Drijfhout_JGR00, Hazeleger_Drijfhout_JPO00}, |
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226 | over which an analytical seasonal forcing is applied. This allows to investigate the |
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227 | spontaneous generation of a large number of interacting, transient mesoscale eddies |
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228 | and their contribution to the large scale circulation. |
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229 | |
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230 | The domain geometry is a closed rectangular basin on the $\beta$-plane centred |
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231 | at $\sim$ 30\degN and rotated by 45\deg, 3180~km long, 2120~km wide |
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232 | and 4~km deep (Fig.~\ref{Fig_MISC_strait_hand}). |
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233 | The domain is bounded by vertical walls and by a flat bottom. The configuration is |
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234 | meant to represent an idealized North Atlantic or North Pacific basin. |
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235 | The circulation is forced by analytical profiles of wind and buoyancy fluxes. |
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236 | The applied forcings vary seasonally in a sinusoidal manner between winter |
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237 | and summer extrema \citep{Levy_al_OM10}. |
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238 | The wind stress is zonal and its curl changes sign at 22\degN and 36\degN. |
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239 | It forces a subpolar gyre in the north, a subtropical gyre in the wider part of the domain |
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240 | and a small recirculation gyre in the southern corner. |
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241 | The net heat flux takes the form of a restoring toward a zonal apparent air |
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242 | temperature profile. A portion of the net heat flux which comes from the solar radiation |
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243 | is allowed to penetrate within the water column. |
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244 | The fresh water flux is also prescribed and varies zonally. |
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245 | It is determined such as, at each time step, the basin-integrated flux is zero. |
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246 | The basin is initialised at rest with vertical profiles of temperature and salinity |
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247 | uniformly applied to the whole domain. |
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248 | |
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249 | The GYRE configuration is set through the \textit{\&namcfg} namelist defined in the reference |
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250 | configuration \textit{CONFIG/GYRE/EXP00/namelist\_cfg}. Its horizontal resolution |
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251 | (and thus the size of the domain) is determined by setting \np{jp\_cfg} : \\ |
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252 | \np{jpiglo} $= 30 \times$ \np{jp\_cfg} + 2 \\ |
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253 | \np{jpjglo} $= 20 \times$ \np{jp\_cfg} + 2 \\ |
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254 | Obviously, the namelist parameters have to be adjusted to the chosen resolution, see the Configurations |
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255 | pages on the NEMO web site (Using NEMO\/Configurations) . |
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256 | In the vertical, GYRE uses the default 30 ocean levels (\pp{jpk}=31) (Fig.~\ref{Fig_zgr}). |
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257 | |
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258 | The GYRE configuration is also used in benchmark test as it is very simple to increase |
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259 | its resolution and as it does not requires any input file. For example, keeping a same model size |
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260 | on each processor while increasing the number of processor used is very easy, even though the |
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261 | physical integrity of the solution can be compromised. |
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262 | |
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263 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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264 | \begin{figure}[!t] \begin{center} |
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265 | \includegraphics[width=1.0\textwidth]{Fig_GYRE} |
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266 | \caption{ \label{Fig_GYRE} |
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267 | Snapshot of relative vorticity at the surface of the model domain |
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268 | in GYRE R9, R27 and R54. From \citet{Levy_al_OM10}.} |
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269 | \end{center} \end{figure} |
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270 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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271 | |
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272 | % ------------------------------------------------------------------------------------------------------------- |
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273 | % EEL family configuration |
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274 | % ------------------------------------------------------------------------------------------------------------- |
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275 | \section{EEL family: periodic channel} |
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276 | \label{MISC_config_EEL} |
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277 | |
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278 | \begin{description} |
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279 | \item[eel\_r2] to be described.... |
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280 | \item[eel\_r5] |
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281 | \item[eel\_r6] |
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282 | \end{description} |
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283 | The appropriate \textit{\&namcfg} namelists are available in |
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284 | \textit{CONFIG/SHARED/README\_other\_configurations\_namelist\_namcfg} |
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285 | % ------------------------------------------------------------------------------------------------------------- |
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286 | % AMM configuration |
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287 | % ------------------------------------------------------------------------------------------------------------- |
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288 | \section{AMM: atlantic margin configuration } |
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289 | \label{MISC_config_AMM} |
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290 | |
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291 | The AMM, Atlantic Margins Model, is a regional model covering the |
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292 | Northwest European Shelf domain on a regular lat-lon grid at |
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293 | approximately 12km horizontal resolution. The appropriate |
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294 | \textit{\&namcfg} namelist is available in \textit{CONFIG/AMM12/EXP00/namelist\_cfg}. |
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295 | It is used to build the correct dimensions of the AMM domain. |
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296 | |
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297 | This configuration tests several features of NEMO functionality specific |
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298 | to the shelf seas. |
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299 | In particular, the AMM uses $S$-coordinates in the vertical rather than |
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300 | $z$-coordinates and is forced with tidal lateral boundary conditions |
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301 | using a flather boundary condition from the BDY module. |
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302 | The AMM configuration uses the GLS (key\_zdfgls) turbulence scheme, the |
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303 | VVL non-linear free surface(key\_vvl) and time-splitting |
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304 | (key\_dynspg\_ts). |
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305 | |
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306 | In addition to the tidal boundary condition the model may also take |
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307 | open boundary conditions from a North Atlantic model. Boundaries may be |
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308 | completely omitted by setting \np{ln\_bdy} to false. |
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309 | Sample surface fluxes, river forcing and a sample initial restart file |
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310 | are included to test a realistic model run. The Baltic boundary is |
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311 | included within the river input file and is specified as a river source. |
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312 | Unlike ordinary river points the Baltic inputs also include salinity and |
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313 | temperature data. |
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314 | |
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315 | \end{document} |
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