[2376] | 1 | % ================================================================ |
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| 2 | % Chapter Ñ Configurations |
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| 3 | % ================================================================ |
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| 4 | \chapter{Configurations} |
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[2541] | 5 | \label{CFG} |
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[2376] | 6 | \minitoc |
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| 7 | |
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| 8 | \newpage |
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| 9 | $\ $\newline % force a new ligne |
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| 10 | |
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| 11 | % ================================================================ |
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| 12 | % Introduction |
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| 13 | % ================================================================ |
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| 14 | \section{Introduction} |
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| 15 | \label{CFG_intro} |
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| 16 | |
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| 17 | |
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| 18 | The purpose of this part of the manual is to introduce the \NEMO predefined configuration. |
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| 19 | These configurations are offered as means to explore various numerical and physical options, |
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| 20 | thus allowing the user to verify that the code is performing in a manner consistent with that |
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| 21 | we are running. This form of verification is critical as one adopts the code for his or her particular |
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| 22 | research purposes. The test cases also provide a sense for some of the options available |
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| 23 | in the code, though by no means are all options exercised in the predefined configurations. |
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| 24 | |
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| 25 | |
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| 26 | %There is several predefined ocean configuration which use is controlled by a specific CPP key. |
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| 27 | |
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| 28 | %The key set the domain sizes (\jp{jpiglo}, \jp{jpjglo}, \jp{jpk}), the mesh and the bathymetry, |
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| 29 | %and, in some cases, add to the model physics some specific treatments. |
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| 30 | |
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| 31 | |
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| 32 | % ================================================================ |
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[3720] | 33 | % 1D model configuration |
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[2376] | 34 | % ================================================================ |
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[2414] | 35 | \section{Water column model: 1D model (C1D) (\key{c1d})} |
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[2376] | 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 \key{c1d} CPP key. |
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| 41 | The 1D model is a very useful tool |
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| 42 | \textit{(a)} to learn about the physics and numerical treatment of vertical mixing processes ; |
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[2381] | 43 | \textit{(b)} to investigate suitable parameterisations of unresolved turbulence (surface wave |
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| 44 | breaking, Langmuir circulation, ...) ; |
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[2376] | 45 | \textit{(c)} to compare the behaviour of different vertical mixing schemes ; |
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| 46 | \textit{(d)} to perform sensitivity studies on the vertical diffusion at a particular point of an ocean domain ; |
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| 47 | \textit{(d)} to produce extra diagnostics, without the large memory requirement of the full 3D model. |
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| 48 | |
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| 49 | The methodology is based on the use of the zoom functionality over the smallest possible |
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[3720] | 50 | domain : a 3x3 domain centred on the grid point of interest (see \S\ref{MISC_zoom}), |
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[2376] | 51 | with some extra routines. There is no need to define a new mesh, bathymetry, |
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| 52 | initial state or forcing, since the 1D model will use those of the configuration it is a zoom of. |
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[3720] | 53 | The chosen grid point is set in \mdl{par\_oce} module by setting the \jp{jpizoom} and \jp{jpjzoom} |
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[2376] | 54 | parameters to the indices of the location of the chosen grid point. |
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| 55 | |
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[3720] | 56 | The 1D model has some specifies. First, all the horizontal derivatives are assumed to be zero, and |
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| 57 | second, the two components of the velocity are moved on a $T$-point. |
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| 58 | Therefore, defining \key{c1d} changes five main things in the code behaviour: |
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| 59 | \begin{description} |
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| 60 | \item[(1)] the lateral boundary condition routine (\rou{lbc\_lnk}) set the value of the central column |
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| 61 | of the 3x3 domain is imposed over the whole domain ; |
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| 62 | \item[(3)] a call to \rou{lbc\_lnk} is systematically done when reading input data ($i.e.$ in \mdl{iom}) ; |
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| 63 | \item[(3)] a simplified \rou{stp} routine is used (\rou{stp\_c1d}, see \mdl{step\_c1d} module) in which |
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| 64 | both lateral tendancy terms and lateral physics are not called ; |
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| 65 | \item[(4)] the vertical velocity is zero (so far, no attempt at introducing a Ekman pumping velocity |
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| 66 | has been made) ; |
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| 67 | \item[(5)] a simplified treatment of the Coriolis term is performed as $U$- and $V$-points are the same |
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| 68 | (see \mdl{dyncor\_c1d}). |
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| 69 | \end{description} |
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| 70 | All the relevant \textit{\_c1d} modules can be found in the NEMOGCM/NEMO/OPA\_SRC/C1D directory of |
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[2381] | 71 | the \NEMO distribution. |
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[2376] | 72 | |
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[2381] | 73 | % to be added: a test case on the yearlong Ocean Weather Station (OWS) Papa dataset of Martin (1985) |
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| 74 | |
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[2376] | 75 | % ================================================================ |
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| 76 | % ORCA family configurations |
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| 77 | % ================================================================ |
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[2541] | 78 | \section{ORCA family: global ocean with tripolar grid (\key{orca\_rX})} |
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[2376] | 79 | \label{CFG_orca} |
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| 80 | |
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| 81 | The ORCA family is a series of global ocean configurations that are run together with |
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| 82 | the LIM sea-ice model (ORCA-LIM) and possibly with PISCES biogeochemical model |
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| 83 | (ORCA-LIM-PISCES), using various resolutions. |
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| 84 | |
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[2381] | 85 | |
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| 86 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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| 87 | \begin{figure}[!t] \begin{center} |
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| 88 | \includegraphics[width=0.98\textwidth]{./TexFiles/Figures/Fig_ORCA_NH_mesh.pdf} |
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| 89 | \caption{ \label{Fig_MISC_ORCA_msh} |
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| 90 | ORCA mesh conception. The departure from an isotropic Mercator grid start poleward of 20\deg N. |
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| 91 | The two "north pole" are the foci of a series of embedded ellipses (blue curves) |
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| 92 | which are determined analytically and form the i-lines of the ORCA mesh (pseudo latitudes). |
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| 93 | Then, following \citet{Madec_Imbard_CD96}, the normal to the series of ellipses (red curves) is computed |
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| 94 | which provide the j-lines of the mesh (pseudo longitudes). } |
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| 95 | \end{center} \end{figure} |
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| 96 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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| 97 | |
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[2376] | 98 | % ------------------------------------------------------------------------------------------------------------- |
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| 99 | % ORCA tripolar grid |
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| 100 | % ------------------------------------------------------------------------------------------------------------- |
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| 101 | \subsection{ORCA tripolar grid} |
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| 102 | \label{CFG_orca_grid} |
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| 103 | |
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| 104 | The ORCA grid is a tripolar is based on the semi-analytical method of \citet{Madec_Imbard_CD96}. |
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| 105 | It allows to construct a global orthogonal curvilinear ocean mesh which has no singularity point inside |
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| 106 | the computational domain since two north mesh poles are introduced and placed on lands. |
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| 107 | The method involves defining an analytical set of mesh parallels in the stereographic polar plan, |
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| 108 | computing the associated set of mesh meridians, and projecting the resulting mesh onto the sphere. |
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| 109 | The set of mesh parallels used is a series of embedded ellipses which foci are the two mesh north |
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| 110 | poles (Fig.~\ref{Fig_MISC_ORCA_msh}). The resulting mesh presents no loss of continuity in |
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| 111 | either the mesh lines or the scale factors, or even the scale factor derivatives over the whole |
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| 112 | ocean domain, as the mesh is not a composite mesh. |
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| 113 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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| 114 | \begin{figure}[!tbp] \begin{center} |
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| 115 | \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_ORCA_NH_msh05_e1_e2.pdf} |
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| 116 | \includegraphics[width=0.80\textwidth]{./TexFiles/Figures/Fig_ORCA_aniso.pdf} |
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| 117 | \caption { \label{Fig_MISC_ORCA_e1e2} |
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| 118 | \textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and |
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| 119 | \textit{Bottom}: ratio of anisotropy ($e_1 / e_2$) |
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| 120 | for ORCA 0.5\deg ~mesh. South of 20\deg N a Mercator grid is used ($e_1 = e_2$) |
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| 121 | so that the anisotropy ratio is 1. Poleward of 20\deg N, the two "north pole" |
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| 122 | introduce a weak anisotropy over the ocean areas ($< 1.2$) except in vicinity of Victoria Island |
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| 123 | (Canadian Arctic Archipelago). } |
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| 124 | \end{center} \end{figure} |
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| 125 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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| 126 | |
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| 127 | |
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[2381] | 128 | The method is applied to Mercator grid ($i.e.$ same zonal and meridional grid spacing) poleward |
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| 129 | of $20\deg$N, so that the Equator is a mesh line, which provides a better numerical solution |
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| 130 | for equatorial dynamics. The choice of the series of embedded ellipses (position of the foci and |
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| 131 | variation of the ellipses) is a compromise between maintaining the ratio of mesh anisotropy |
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| 132 | ($e_1 / e_2$) close to one in the ocean (especially in area of strong eddy activities such as |
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| 133 | the Gulf Stream) and keeping the smallest scale factor in the northern hemisphere larger |
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| 134 | than the smallest one in the southern hemisphere. |
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| 135 | The resulting mesh is shown in Fig.~\ref{Fig_MISC_ORCA_msh} and \ref{Fig_MISC_ORCA_e1e2} |
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| 136 | for a half a degree grid (ORCA\_R05). The smallest ocean scale factor is found in along |
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| 137 | Antarctica, while the ratio of anisotropy remains close to one except near the Victoria Island |
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| 138 | in the Canadian Archipelago. |
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[2376] | 139 | |
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| 140 | % ------------------------------------------------------------------------------------------------------------- |
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| 141 | % ORCA-LIM(-PISCES) configurations |
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| 142 | % ------------------------------------------------------------------------------------------------------------- |
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[2381] | 143 | \subsection{ORCA pre-defined resolution} |
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| 144 | \label{CFG_orca_resolution} |
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[2376] | 145 | |
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| 146 | |
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[2381] | 147 | The NEMO system is provided with five built-in ORCA configurations which differ in the |
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| 148 | horizontal resolution. The value of the resolution is given by the resolution at the Equator |
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[2541] | 149 | expressed in degrees. Each of configuration is set through a CPP key, \key{orca\_rX} |
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| 150 | (with X being an indicator of the resolution), which set the grid size and configuration |
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| 151 | name parameters (Tab.~\ref{Tab_ORCA}). |
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[2381] | 152 | . |
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[2376] | 153 | |
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[2381] | 154 | %--------------------------------------------------TABLE-------------------------------------------------- |
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[2414] | 155 | \begin{table}[!t] \begin{center} |
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[2381] | 156 | \begin{tabular}{p{4cm} c c c c} |
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| 157 | CPP key & \jp{jp\_cfg} & \jp{jpiglo} & \jp{jpiglo} & \\ |
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| 158 | \hline \hline |
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| 159 | \key{orca\_r4} & 4 & 92 & 76 & \\ |
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| 160 | \key{orca\_r2} & 2 & 182 & 149 & \\ |
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| 161 | \key{orca\_r1} & 1 & 362 & 292 & \\ |
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| 162 | \key{orca\_r05} & 05 & 722 & 511 & \\ |
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| 163 | \key{orca\_r025} & 025 & 1442 & 1021 & \\ |
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| 164 | %\key{orca\_r8} & 8 & 2882 & 2042 & \\ |
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| 165 | %\key{orca\_r12} & 12 & 4322 & 3062 & \\ |
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| 166 | \hline \hline |
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| 167 | \end{tabular} |
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| 168 | \caption{ \label{Tab_ORCA} |
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| 169 | Set of predefined parameters for ORCA family configurations. |
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| 170 | In all cases, the name of the configuration is set to "orca" ($i.e.$ \jp{cp\_cfg}~=~orca). } |
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| 171 | \end{center} |
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| 172 | \end{table} |
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| 173 | %-------------------------------------------------------------------------------------------------------------- |
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| 174 | |
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| 175 | |
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[2376] | 176 | The ORCA\_R2 configuration has the following specificity : starting from a 2\deg~ORCA mesh, |
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| 177 | local mesh refinements were applied to the Mediterranean, Red, Black and Caspian Seas, |
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| 178 | so that the resolution is $1\deg \time 1\deg$ there. A local transformation were also applied |
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| 179 | with in the Tropics in order to refine the meridional resolution up to 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 |
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| 182 | resolution up to 1/3\deg~at the Equator. Note that the tropical mesh refinements in ORCA\_R2 |
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| 183 | and R1 strongly increases the mesh anisotropy there. |
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| 184 | |
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[2381] | 185 | The ORCA\_R05 and higher global configurations do not incorporate any regional refinements. |
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[2376] | 186 | |
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[2381] | 187 | For ORCA\_R1 and R025, setting the configuration key to 75 allows to use 75 vertical levels, |
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| 188 | otherwise 46 are used. In the other ORCA configurations, 31 levels are used |
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| 189 | (see Tab.~\ref{Tab_orca_zgr} and Fig.~\ref{Fig_zgr}). |
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| 190 | |
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[2376] | 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 |
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| 193 | assessment of climate change (Marti et al., 2009). It is also the basis for the \NEMO contribution |
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| 194 | to the Coordinate Ocean-ice Reference Experiments (COREs) documented in \citet{Griffies_al_OM09}. |
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| 195 | |
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| 196 | This version of ORCA\_R2 has 31 levels in the vertical, with the highest resolution (10m) |
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[2381] | 197 | in the upper 150m (see Tab.~\ref{Tab_orca_zgr} and Fig.~\ref{Fig_zgr}). |
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| 198 | The bottom topography and the coastlines are derived from the global atlas of Smith and Sandwell (1997). |
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| 199 | The default forcing employ the boundary forcing from \citet{Large_Yeager_Rep04} (see \S\ref{SBC_blk_core}), |
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[2376] | 200 | which was developed for the purpose of running global coupled ocean-ice simulations |
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| 201 | without an interactive atmosphere. This \citet{Large_Yeager_Rep04} dataset is available |
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[2414] | 202 | through the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}. |
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[2376] | 203 | The "normal year" of \citet{Large_Yeager_Rep04} has been chosen of the \NEMO distribution |
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| 204 | since release v3.3. |
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| 205 | |
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[2440] | 206 | ORCA\_R2 pre-defined configuration can also be run with an AGRIF zoom over the Agulhas |
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| 207 | current area ( \key{agrif} defined) and, by setting the key \key{arctic} or \key{antarctic}, |
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| 208 | a regional Arctic or peri-Antarctic configuration is extracted from an ORCA\_R2 or R05 configurations |
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| 209 | using sponge layers at open boundaries. |
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[2376] | 210 | |
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| 211 | % ------------------------------------------------------------------------------------------------------------- |
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| 212 | % GYRE family: double gyre basin |
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| 213 | % ------------------------------------------------------------------------------------------------------------- |
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| 214 | \section{GYRE family: double gyre basin (\key{gyre})} |
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[3683] | 215 | \label{CFG_gyre} |
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[2376] | 216 | |
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| 217 | The GYRE configuration \citep{Levy_al_OM10} have been built to simulated |
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| 218 | the seasonal cycle of a double-gyre box model. It consist in an idealized domain |
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| 219 | similar to that used in the studies of \citet{Drijfhout_JPO94} and \citet{Hazeleger_Drijfhout_JPO98, |
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| 220 | Hazeleger_Drijfhout_JPO99, Hazeleger_Drijfhout_JGR00, Hazeleger_Drijfhout_JPO00}, |
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| 221 | over which an analytical seasonal forcing is applied. This allows to investigate the |
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| 222 | 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 domain geometry is a closed rectangular basin on the $\beta$-plane centred |
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| 226 | at $\sim 30\deg$N and rotated by 45\deg, 3180~km long, 2120~km wide |
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| 227 | and 4~km deep (Fig.~\ref{Fig_MISC_strait_hand}). |
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[3294] | 228 | The domain is bounded by vertical walls and by a flat bottom. The configuration is |
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[2376] | 229 | meant to represent an idealized North Atlantic or North Pacific basin. |
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[3294] | 230 | The circulation is forced by analytical profiles of wind and buoyancy fluxes. |
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[2376] | 231 | The applied forcings vary seasonally in a sinusoidal manner between winter |
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| 232 | and summer extrema \citep{Levy_al_OM10}. |
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| 233 | The wind stress is zonal and its curl changes sign at 22\deg N and 36\deg N. |
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| 234 | It forces a subpolar gyre in the north, a subtropical gyre in the wider part of the domain |
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| 235 | and a small recirculation gyre in the southern corner. |
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[3294] | 236 | The net heat flux takes the form of a restoring toward a zonal apparent air |
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| 237 | temperature profile. A portion of the net heat flux which comes from the solar radiation |
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[2376] | 238 | is allowed to penetrate within the water column. |
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[3294] | 239 | The fresh water flux is also prescribed and varies zonally. |
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| 240 | It is determined such as, at each time step, the basin-integrated flux is zero. |
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[2376] | 241 | The basin is initialised at rest with vertical profiles of temperature and salinity |
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| 242 | uniformly applied to the whole domain. |
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| 243 | |
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| 244 | The GYRE configuration is set through the \key{gyre} CPP key. Its horizontal resolution |
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| 245 | (and thus the size of the domain) is determined by setting \jp{jp\_cfg} in \hf{par\_GYRE} file: \\ |
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| 246 | \jp{jpiglo} $= 30 \times$ \jp{jp\_cfg} + 2 \\ |
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| 247 | \jp{jpjglo} $= 20 \times$ \jp{jp\_cfg} + 2 \\ |
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| 248 | Obviously, the namelist parameters have to be adjusted to the chosen resolution. |
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| 249 | In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}=31) (Fig.~\ref{Fig_zgr}). |
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| 250 | |
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| 251 | The GYRE configuration is also used in benchmark test as it is very simple to increase |
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| 252 | its resolution and as it does not requires any input file. For example, keeping a same model size |
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| 253 | on each processor while increasing the number of processor used is very easy, even though the |
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| 254 | physical integrity of the solution can be compromised. |
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| 255 | |
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| 256 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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| 257 | \begin{figure}[!t] \begin{center} |
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| 258 | \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_GYRE.pdf} |
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| 259 | \caption{ \label{Fig_GYRE} |
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| 260 | Snapshot of relative vorticity at the surface of the model domain |
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| 261 | in GYRE R9, R27 and R54. From \citet{Levy_al_OM10}.} |
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| 262 | \end{center} \end{figure} |
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| 263 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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| 264 | |
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| 265 | % ------------------------------------------------------------------------------------------------------------- |
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| 266 | % EEL family configuration |
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| 267 | % ------------------------------------------------------------------------------------------------------------- |
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| 268 | \section{EEL family: periodic channel} |
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| 269 | \label{MISC_config_EEL} |
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| 270 | |
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| 271 | \begin{description} |
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| 272 | \item[\key{eel\_r2}] to be described.... |
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| 273 | \item[\key{eel\_r5}] |
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| 274 | \item[\key{eel\_r6}] |
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| 275 | \end{description} |
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| 276 | |
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| 277 | % ------------------------------------------------------------------------------------------------------------- |
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[3294] | 278 | % AMM configuration |
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[2376] | 279 | % ------------------------------------------------------------------------------------------------------------- |
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[3294] | 280 | \section{AMM: atlantic margin configuration (\key{amm\_12km})} |
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| 281 | \label{MISC_config_AMM} |
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[2376] | 282 | |
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[3294] | 283 | The AMM, Atlantic Margins Model, is a regional model covering the |
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| 284 | Northwest European Shelf domain on a regular lat-lon grid at |
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| 285 | approximately 12km horizontal resolution. The key \key{amm\_12km} |
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| 286 | is used to create the correct dimensions of the AMM domain. |
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[2376] | 287 | |
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[3294] | 288 | This configuration tests several features of NEMO functionality specific |
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| 289 | to the shelf seas. |
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| 290 | In particular, the AMM uses $S$-coordinates in the vertical rather than |
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| 291 | $z$-coordinates and is forced with tidal lateral boundary conditions |
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| 292 | using a flather boundary condition from the BDY module (key\_bdy). |
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| 293 | The AMM configuration uses the GLS (key\_zdfgls) turbulence scheme, the |
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| 294 | VVL non-linear free surface(key\_vvl) and time-splitting |
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| 295 | (key\_dynspg\_ts). |
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[2376] | 296 | |
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[3294] | 297 | In addition to the tidal boundary condition the model may also take |
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| 298 | open boundary conditions from a North Atlantic model. Boundaries may be |
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| 299 | completely ommited by removing the BDY key (key\_bdy). |
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| 300 | Sample surface fluxes, river forcing and a sample initial restart file |
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| 301 | are included to test a realistic model run. The Baltic boundary is |
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| 302 | included within the river input file and is specified as a river source. |
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| 303 | Unlike ordinary river points the Baltic inputs also include salinity and |
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| 304 | temperature data. |
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[2376] | 305 | |
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