[2376] | 1 | % ================================================================ |
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[4147] | 2 | % Chapter � Configurations |
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[2376] | 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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[4147] | 18 | The purpose of this part of the manual is to introduce the \NEMO reference configurations. |
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[2376] | 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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[4147] | 23 | in the code, though by no means are all options exercised in the reference configurations. |
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[2376] | 24 | |
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[4147] | 25 | Configuration is defined mainly through the \ngn{namcfg} namelist variables: |
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| 26 | %------------------------------------------namcfg---------------------------------------------------- |
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| 27 | \namdisplay{namcfg} |
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| 28 | %------------------------------------------------------------------------------------------------------------- |
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[2376] | 29 | |
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| 30 | % ================================================================ |
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[3764] | 31 | % 1D model configuration |
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[2376] | 32 | % ================================================================ |
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[4147] | 33 | \section{Water column model: 1D model (C1D) (\key{c1d}) } |
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[2376] | 34 | \label{CFG_c1d} |
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| 35 | |
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| 36 | The 1D model option simulates a stand alone water column within the 3D \NEMO system. |
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| 37 | It can be applied to the ocean alone or to the ocean-ice system and can include passive tracers |
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[4147] | 38 | or a biogeochemical model. It is set up by defining the position of the 1D water column in the grid |
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| 39 | (see \textit{CONFIG/SHARED/namelist\_ref} ). |
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[2376] | 40 | The 1D model is a very useful tool |
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| 41 | \textit{(a)} to learn about the physics and numerical treatment of vertical mixing processes ; |
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[2381] | 42 | \textit{(b)} to investigate suitable parameterisations of unresolved turbulence (surface wave |
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| 43 | breaking, Langmuir circulation, ...) ; |
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[2376] | 44 | \textit{(c)} to compare the behaviour of different vertical mixing schemes ; |
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| 45 | \textit{(d)} to perform sensitivity studies on the vertical diffusion at a particular point of an ocean domain ; |
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| 46 | \textit{(d)} to produce extra diagnostics, without the large memory requirement of the full 3D model. |
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| 47 | |
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| 48 | The methodology is based on the use of the zoom functionality over the smallest possible |
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[4147] | 49 | domain : a 3x3 domain centered on the grid point of interest, |
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[2376] | 50 | with some extra routines. There is no need to define a new mesh, bathymetry, |
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| 51 | initial state or forcing, since the 1D model will use those of the configuration it is a zoom of. |
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[4147] | 52 | The chosen grid point is set in \textit{\ngn{namcfg}} namelist by setting the \np{jpizoom} and \np{jpjzoom} |
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[2376] | 53 | parameters to the indices of the location of the chosen grid point. |
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| 54 | |
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[3764] | 55 | The 1D model has some specifies. First, all the horizontal derivatives are assumed to be zero, and |
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| 56 | second, the two components of the velocity are moved on a $T$-point. |
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| 57 | Therefore, defining \key{c1d} changes five main things in the code behaviour: |
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| 58 | \begin{description} |
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| 59 | \item[(1)] the lateral boundary condition routine (\rou{lbc\_lnk}) set the value of the central column |
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| 60 | of the 3x3 domain is imposed over the whole domain ; |
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| 61 | \item[(3)] a call to \rou{lbc\_lnk} is systematically done when reading input data ($i.e.$ in \mdl{iom}) ; |
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| 62 | \item[(3)] a simplified \rou{stp} routine is used (\rou{stp\_c1d}, see \mdl{step\_c1d} module) in which |
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| 63 | both lateral tendancy terms and lateral physics are not called ; |
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| 64 | \item[(4)] the vertical velocity is zero (so far, no attempt at introducing a Ekman pumping velocity |
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| 65 | has been made) ; |
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| 66 | \item[(5)] a simplified treatment of the Coriolis term is performed as $U$- and $V$-points are the same |
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| 67 | (see \mdl{dyncor\_c1d}). |
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| 68 | \end{description} |
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| 69 | All the relevant \textit{\_c1d} modules can be found in the NEMOGCM/NEMO/OPA\_SRC/C1D directory of |
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[2381] | 70 | the \NEMO distribution. |
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[2376] | 71 | |
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[2381] | 72 | % to be added: a test case on the yearlong Ocean Weather Station (OWS) Papa dataset of Martin (1985) |
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| 73 | |
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[2376] | 74 | % ================================================================ |
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| 75 | % ORCA family configurations |
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| 76 | % ================================================================ |
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[4147] | 77 | \section{ORCA family: global ocean with tripolar grid } |
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[2376] | 78 | \label{CFG_orca} |
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| 79 | |
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| 80 | The ORCA family is a series of global ocean configurations that are run together with |
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| 81 | the LIM sea-ice model (ORCA-LIM) and possibly with PISCES biogeochemical model |
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| 82 | (ORCA-LIM-PISCES), using various resolutions. |
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[4147] | 83 | The appropriate \textit{\&namcfg} namelist is available in \textit{CONFIG/ORCA2\_LIM/EXP00/namelist\_cfg} |
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| 84 | for ORCA2 and in \textit{CONFIG/SHARED/README\_other\_configurations\_namelist\_namcfg} |
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| 85 | for other resolutions |
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[2376] | 86 | |
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[2381] | 87 | |
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| 88 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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| 89 | \begin{figure}[!t] \begin{center} |
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| 90 | \includegraphics[width=0.98\textwidth]{./TexFiles/Figures/Fig_ORCA_NH_mesh.pdf} |
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| 91 | \caption{ \label{Fig_MISC_ORCA_msh} |
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| 92 | ORCA mesh conception. The departure from an isotropic Mercator grid start poleward of 20\deg N. |
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| 93 | The two "north pole" are the foci of a series of embedded ellipses (blue curves) |
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| 94 | which are determined analytically and form the i-lines of the ORCA mesh (pseudo latitudes). |
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| 95 | Then, following \citet{Madec_Imbard_CD96}, the normal to the series of ellipses (red curves) is computed |
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| 96 | which provide the j-lines of the mesh (pseudo longitudes). } |
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| 97 | \end{center} \end{figure} |
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| 98 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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| 99 | |
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[2376] | 100 | % ------------------------------------------------------------------------------------------------------------- |
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| 101 | % ORCA tripolar grid |
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| 102 | % ------------------------------------------------------------------------------------------------------------- |
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| 103 | \subsection{ORCA tripolar grid} |
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| 104 | \label{CFG_orca_grid} |
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| 105 | |
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| 106 | The ORCA grid is a tripolar is based on the semi-analytical method of \citet{Madec_Imbard_CD96}. |
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| 107 | It allows to construct a global orthogonal curvilinear ocean mesh which has no singularity point inside |
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| 108 | the computational domain since two north mesh poles are introduced and placed on lands. |
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| 109 | The method involves defining an analytical set of mesh parallels in the stereographic polar plan, |
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| 110 | computing the associated set of mesh meridians, and projecting the resulting mesh onto the sphere. |
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| 111 | The set of mesh parallels used is a series of embedded ellipses which foci are the two mesh north |
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| 112 | poles (Fig.~\ref{Fig_MISC_ORCA_msh}). The resulting mesh presents no loss of continuity in |
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| 113 | either the mesh lines or the scale factors, or even the scale factor derivatives over the whole |
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| 114 | ocean domain, as the mesh is not a composite mesh. |
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| 115 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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| 116 | \begin{figure}[!tbp] \begin{center} |
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| 117 | \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_ORCA_NH_msh05_e1_e2.pdf} |
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| 118 | \includegraphics[width=0.80\textwidth]{./TexFiles/Figures/Fig_ORCA_aniso.pdf} |
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| 119 | \caption { \label{Fig_MISC_ORCA_e1e2} |
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| 120 | \textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and |
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| 121 | \textit{Bottom}: ratio of anisotropy ($e_1 / e_2$) |
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| 122 | for ORCA 0.5\deg ~mesh. South of 20\deg N a Mercator grid is used ($e_1 = e_2$) |
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| 123 | so that the anisotropy ratio is 1. Poleward of 20\deg N, the two "north pole" |
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| 124 | introduce a weak anisotropy over the ocean areas ($< 1.2$) except in vicinity of Victoria Island |
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| 125 | (Canadian Arctic Archipelago). } |
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| 126 | \end{center} \end{figure} |
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| 127 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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| 128 | |
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| 129 | |
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[2381] | 130 | The method is applied to Mercator grid ($i.e.$ same zonal and meridional grid spacing) poleward |
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| 131 | of $20\deg$N, so that the Equator is a mesh line, which provides a better numerical solution |
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| 132 | for equatorial dynamics. The choice of the series of embedded ellipses (position of the foci and |
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| 133 | variation of the ellipses) is a compromise between maintaining the ratio of mesh anisotropy |
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| 134 | ($e_1 / e_2$) close to one in the ocean (especially in area of strong eddy activities such as |
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| 135 | the Gulf Stream) and keeping the smallest scale factor in the northern hemisphere larger |
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| 136 | than the smallest one in the southern hemisphere. |
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| 137 | The resulting mesh is shown in Fig.~\ref{Fig_MISC_ORCA_msh} and \ref{Fig_MISC_ORCA_e1e2} |
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| 138 | for a half a degree grid (ORCA\_R05). The smallest ocean scale factor is found in along |
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| 139 | Antarctica, while the ratio of anisotropy remains close to one except near the Victoria Island |
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| 140 | in the Canadian Archipelago. |
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[2376] | 141 | |
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| 142 | % ------------------------------------------------------------------------------------------------------------- |
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| 143 | % ORCA-LIM(-PISCES) configurations |
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| 144 | % ------------------------------------------------------------------------------------------------------------- |
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[2381] | 145 | \subsection{ORCA pre-defined resolution} |
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| 146 | \label{CFG_orca_resolution} |
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[2376] | 147 | |
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| 148 | |
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[2381] | 149 | The NEMO system is provided with five built-in ORCA configurations which differ in the |
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| 150 | horizontal resolution. The value of the resolution is given by the resolution at the Equator |
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[4147] | 151 | expressed in degrees. Each of configuration is set through the \textit{\ngn{namcfg}} namelist, |
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| 152 | which sets the grid size and configuration |
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| 153 | name parameters (Tab. \ref{Tab_ORCA}). |
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[2381] | 154 | . |
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[2376] | 155 | |
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[2381] | 156 | %--------------------------------------------------TABLE-------------------------------------------------- |
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[2414] | 157 | \begin{table}[!t] \begin{center} |
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[2381] | 158 | \begin{tabular}{p{4cm} c c c c} |
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[4147] | 159 | Horizontal Grid & \np{jp\_cfg} & \np{jpiglo} & \np{jpjglo} & \\ |
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[2381] | 160 | \hline \hline |
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[4147] | 161 | \~4\deg & 4 & 92 & 76 & \\ |
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| 162 | \~2\deg & 2 & 182 & 149 & \\ |
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| 163 | \~1\deg & 1 & 362 & 292 & \\ |
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| 164 | \~0.5\deg & 05 & 722 & 511 & \\ |
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| 165 | \~0.25\deg & 025 & 1442 & 1021 & \\ |
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[2381] | 166 | %\key{orca\_r8} & 8 & 2882 & 2042 & \\ |
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| 167 | %\key{orca\_r12} & 12 & 4322 & 3062 & \\ |
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| 168 | \hline \hline |
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| 169 | \end{tabular} |
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| 170 | \caption{ \label{Tab_ORCA} |
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| 171 | Set of predefined parameters for ORCA family configurations. |
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[4147] | 172 | In all cases, the name of the configuration is set to "orca" ($i.e.$ \np{cp\_cfg}~=~orca). } |
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[2381] | 173 | \end{center} |
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| 174 | \end{table} |
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| 175 | %-------------------------------------------------------------------------------------------------------------- |
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| 176 | |
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| 177 | |
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[2376] | 178 | The ORCA\_R2 configuration has the following specificity : starting from a 2\deg~ORCA mesh, |
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| 179 | local mesh refinements were applied to the Mediterranean, Red, Black and Caspian Seas, |
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| 180 | so that the resolution is $1\deg \time 1\deg$ there. A local transformation were also applied |
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| 181 | with in the Tropics in order to refine the meridional resolution up to 0.5\deg at the Equator. |
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| 182 | |
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| 183 | The ORCA\_R1 configuration has only a local tropical transformation to refine the meridional |
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| 184 | resolution up to 1/3\deg~at the Equator. Note that the tropical mesh refinements in ORCA\_R2 |
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| 185 | and R1 strongly increases the mesh anisotropy there. |
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| 186 | |
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[2381] | 187 | The ORCA\_R05 and higher global configurations do not incorporate any regional refinements. |
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[2376] | 188 | |
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[2381] | 189 | For ORCA\_R1 and R025, setting the configuration key to 75 allows to use 75 vertical levels, |
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| 190 | otherwise 46 are used. In the other ORCA configurations, 31 levels are used |
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| 191 | (see Tab.~\ref{Tab_orca_zgr} and Fig.~\ref{Fig_zgr}). |
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| 192 | |
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[2376] | 193 | Only the ORCA\_R2 is provided with all its input files in the \NEMO distribution. |
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| 194 | It is very similar to that used as part of the climate model developed at IPSL for the 4th IPCC |
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| 195 | assessment of climate change (Marti et al., 2009). It is also the basis for the \NEMO contribution |
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| 196 | to the Coordinate Ocean-ice Reference Experiments (COREs) documented in \citet{Griffies_al_OM09}. |
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| 197 | |
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| 198 | This version of ORCA\_R2 has 31 levels in the vertical, with the highest resolution (10m) |
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[2381] | 199 | in the upper 150m (see Tab.~\ref{Tab_orca_zgr} and Fig.~\ref{Fig_zgr}). |
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| 200 | The bottom topography and the coastlines are derived from the global atlas of Smith and Sandwell (1997). |
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[4147] | 201 | The default forcing uses the boundary forcing from \citet{Large_Yeager_Rep04} (see \S\ref{SBC_blk_core}), |
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[2376] | 202 | which was developed for the purpose of running global coupled ocean-ice simulations |
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| 203 | without an interactive atmosphere. This \citet{Large_Yeager_Rep04} dataset is available |
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[2414] | 204 | through the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}. |
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[2376] | 205 | The "normal year" of \citet{Large_Yeager_Rep04} has been chosen of the \NEMO distribution |
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| 206 | since release v3.3. |
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| 207 | |
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[2440] | 208 | ORCA\_R2 pre-defined configuration can also be run with an AGRIF zoom over the Agulhas |
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[4147] | 209 | current area ( \key{agrif} defined) and, by setting the appropriate variables in |
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| 210 | \textit{\&namcfg}, see \textit{CONFIG/SHARED/namelist\_ref} |
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[2440] | 211 | a regional Arctic or peri-Antarctic configuration is extracted from an ORCA\_R2 or R05 configurations |
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| 212 | using sponge layers at open boundaries. |
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[2376] | 213 | |
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| 214 | % ------------------------------------------------------------------------------------------------------------- |
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| 215 | % GYRE family: double gyre basin |
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| 216 | % ------------------------------------------------------------------------------------------------------------- |
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[4147] | 217 | \section{GYRE family: double gyre basin } |
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[3764] | 218 | \label{CFG_gyre} |
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[2376] | 219 | |
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[4147] | 220 | The GYRE configuration \citep{Levy_al_OM10} has been built to simulate |
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| 221 | the seasonal cycle of a double-gyre box model. It consists in an idealized domain |
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[2376] | 222 | similar to that used in the studies of \citet{Drijfhout_JPO94} and \citet{Hazeleger_Drijfhout_JPO98, |
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| 223 | Hazeleger_Drijfhout_JPO99, Hazeleger_Drijfhout_JGR00, Hazeleger_Drijfhout_JPO00}, |
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| 224 | over which an analytical seasonal forcing is applied. This allows to investigate the |
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| 225 | spontaneous generation of a large number of interacting, transient mesoscale eddies |
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| 226 | and their contribution to the large scale circulation. |
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| 227 | |
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| 228 | The domain geometry is a closed rectangular basin on the $\beta$-plane centred |
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| 229 | at $\sim 30\deg$N and rotated by 45\deg, 3180~km long, 2120~km wide |
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| 230 | and 4~km deep (Fig.~\ref{Fig_MISC_strait_hand}). |
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[3294] | 231 | The domain is bounded by vertical walls and by a flat bottom. The configuration is |
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[2376] | 232 | meant to represent an idealized North Atlantic or North Pacific basin. |
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[3294] | 233 | The circulation is forced by analytical profiles of wind and buoyancy fluxes. |
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[2376] | 234 | The applied forcings vary seasonally in a sinusoidal manner between winter |
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| 235 | and summer extrema \citep{Levy_al_OM10}. |
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| 236 | The wind stress is zonal and its curl changes sign at 22\deg N and 36\deg N. |
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| 237 | It forces a subpolar gyre in the north, a subtropical gyre in the wider part of the domain |
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| 238 | and a small recirculation gyre in the southern corner. |
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[3294] | 239 | The net heat flux takes the form of a restoring toward a zonal apparent air |
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| 240 | temperature profile. A portion of the net heat flux which comes from the solar radiation |
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[2376] | 241 | is allowed to penetrate within the water column. |
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[3294] | 242 | The fresh water flux is also prescribed and varies zonally. |
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| 243 | It is determined such as, at each time step, the basin-integrated flux is zero. |
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[2376] | 244 | The basin is initialised at rest with vertical profiles of temperature and salinity |
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| 245 | uniformly applied to the whole domain. |
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| 246 | |
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[4147] | 247 | The GYRE configuration is set through the \textit{\&namcfg} namelist defined in the reference |
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| 248 | configuration \textit{CONFIG/GYRE/EXP00/namelist\_cfg}. Its horizontal resolution |
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| 249 | (and thus the size of the domain) is determined by setting \np{jp\_cfg} : \\ |
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| 250 | \np{jpiglo} $= 30 \times$ \np{jp\_cfg} + 2 \\ |
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| 251 | \np{jpjglo} $= 20 \times$ \np{jp\_cfg} + 2 \\ |
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| 252 | Obviously, the namelist parameters have to be adjusted to the chosen resolution, see the Configurations |
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| 253 | pages on the NEMO web site (Using NEMO\/Configurations) . |
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| 254 | In the vertical, GYRE uses the default 30 ocean levels (\pp{jpk}=31) (Fig.~\ref{Fig_zgr}). |
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[2376] | 255 | |
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| 256 | The GYRE configuration is also used in benchmark test as it is very simple to increase |
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| 257 | its resolution and as it does not requires any input file. For example, keeping a same model size |
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| 258 | on each processor while increasing the number of processor used is very easy, even though the |
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| 259 | physical integrity of the solution can be compromised. |
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| 260 | |
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| 261 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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| 262 | \begin{figure}[!t] \begin{center} |
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| 263 | \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_GYRE.pdf} |
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| 264 | \caption{ \label{Fig_GYRE} |
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| 265 | Snapshot of relative vorticity at the surface of the model domain |
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| 266 | in GYRE R9, R27 and R54. From \citet{Levy_al_OM10}.} |
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| 267 | \end{center} \end{figure} |
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| 268 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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| 269 | |
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| 270 | % ------------------------------------------------------------------------------------------------------------- |
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| 271 | % EEL family configuration |
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| 272 | % ------------------------------------------------------------------------------------------------------------- |
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| 273 | \section{EEL family: periodic channel} |
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| 274 | \label{MISC_config_EEL} |
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| 275 | |
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| 276 | \begin{description} |
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[4147] | 277 | \item[eel\_r2] to be described.... |
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| 278 | \item[eel\_r5] |
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| 279 | \item[eel\_r6] |
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[2376] | 280 | \end{description} |
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[4147] | 281 | The appropriate \textit{\&namcfg} namelists are available in |
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| 282 | \textit{CONFIG/SHARED/README\_other\_configurations\_namelist\_namcfg} |
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[2376] | 283 | % ------------------------------------------------------------------------------------------------------------- |
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[3294] | 284 | % AMM configuration |
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[2376] | 285 | % ------------------------------------------------------------------------------------------------------------- |
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[4147] | 286 | \section{AMM: atlantic margin configuration } |
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[3294] | 287 | \label{MISC_config_AMM} |
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[2376] | 288 | |
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[3294] | 289 | The AMM, Atlantic Margins Model, is a regional model covering the |
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| 290 | Northwest European Shelf domain on a regular lat-lon grid at |
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[4147] | 291 | approximately 12km horizontal resolution. The appropriate |
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| 292 | \textit{\&namcfg} namelist is available in \textit{CONFIG/AMM12/EXP00/namelist\_cfg}. |
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| 293 | It is used to build the correct dimensions of the AMM domain. |
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[2376] | 294 | |
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[3294] | 295 | This configuration tests several features of NEMO functionality specific |
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| 296 | to the shelf seas. |
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| 297 | In particular, the AMM uses $S$-coordinates in the vertical rather than |
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| 298 | $z$-coordinates and is forced with tidal lateral boundary conditions |
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| 299 | using a flather boundary condition from the BDY module (key\_bdy). |
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| 300 | The AMM configuration uses the GLS (key\_zdfgls) turbulence scheme, the |
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| 301 | VVL non-linear free surface(key\_vvl) and time-splitting |
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| 302 | (key\_dynspg\_ts). |
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[2376] | 303 | |
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[3294] | 304 | In addition to the tidal boundary condition the model may also take |
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| 305 | open boundary conditions from a North Atlantic model. Boundaries may be |
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| 306 | completely ommited by removing the BDY key (key\_bdy). |
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| 307 | Sample surface fluxes, river forcing and a sample initial restart file |
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| 308 | are included to test a realistic model run. The Baltic boundary is |
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| 309 | included within the river input file and is specified as a river source. |
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| 310 | Unlike ordinary river points the Baltic inputs also include salinity and |
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| 311 | temperature data. |
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[2376] | 312 | |
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