[10414] | 1 | \documentclass[../main/NEMO_manual]{subfiles} |
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| 2 | |
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[6997] | 3 | \begin{document} |
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[2376] | 4 | % ================================================================ |
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[10414] | 5 | % Chapter Configurations |
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[2376] | 6 | % ================================================================ |
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| 7 | \chapter{Configurations} |
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[9407] | 8 | \label{chap:CFG} |
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[10414] | 9 | |
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[11512] | 10 | \chaptertoc |
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[2376] | 11 | |
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| 12 | \newpage |
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| 13 | |
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| 14 | % ================================================================ |
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| 15 | % Introduction |
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| 16 | % ================================================================ |
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| 17 | \section{Introduction} |
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[9407] | 18 | \label{sec:CFG_intro} |
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[2376] | 19 | |
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[11512] | 20 | The purpose of this part of the manual is to introduce the \NEMO\ reference configurations. |
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[10354] | 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 we are running. |
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| 23 | This form of verification is critical as one adopts the code for his or her particular research purposes. |
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| 24 | The reference configurations also provide a sense for some of the options available in the code, |
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| 25 | though by no means are all options exercised in the reference configurations. |
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[11512] | 26 | Configuration is defined manually through the \nam{cfg} namelist variables. |
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[2376] | 27 | |
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[4147] | 28 | %------------------------------------------namcfg---------------------------------------------------- |
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[10146] | 29 | |
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| 30 | \nlst{namcfg} |
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[4147] | 31 | %------------------------------------------------------------------------------------------------------------- |
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[2376] | 32 | |
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| 33 | % ================================================================ |
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[3764] | 34 | % 1D model configuration |
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[2376] | 35 | % ================================================================ |
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[11263] | 36 | \section[C1D: 1D Water column model (\texttt{\textbf{key\_c1d}})] |
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| 37 | {C1D: 1D Water column model (\protect\key{c1d})} |
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[9407] | 38 | \label{sec:CFG_c1d} |
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[2376] | 39 | |
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[11512] | 40 | The 1D model option simulates a stand alone water column within the 3D \NEMO\ system. |
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[10354] | 41 | It can be applied to the ocean alone or to the ocean-ice system and can include passive tracers or a biogeochemical model. |
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| 42 | It is set up by defining the position of the 1D water column in the grid |
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[11512] | 43 | (see \path{./cfgs/SHARED/namelist\_ref}). |
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[10354] | 44 | The 1D model is a very useful tool |
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| 45 | \textit{(a)} to learn about the physics and numerical treatment of vertical mixing processes; |
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| 46 | \textit{(b)} to investigate suitable parameterisations of unresolved turbulence |
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| 47 | (surface wave breaking, Langmuir circulation, ...); |
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| 48 | \textit{(c)} to compare the behaviour of different vertical mixing schemes; |
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| 49 | \textit{(d)} to perform sensitivity studies on the vertical diffusion at a particular point of an ocean domain; |
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[2376] | 50 | \textit{(d)} to produce extra diagnostics, without the large memory requirement of the full 3D model. |
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| 51 | |
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[11263] | 52 | The methodology is based on the configuration of the smallest possible domain: |
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| 53 | a 3x3 domain with 75 vertical levels. |
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[2376] | 54 | |
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[10354] | 55 | The 1D model has some specifies. First, all the horizontal derivatives are assumed to be zero, |
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[11512] | 56 | and second, the two components of the velocity are moved on a $T$-point. |
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| 57 | Therefore, defining \key{c1d} changes some things in the code behaviour: |
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[3764] | 58 | \begin{description} |
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[10354] | 59 | \item[(1)] |
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| 60 | a simplified \rou{stp} routine is used (\rou{stp\_c1d}, see \mdl{step\_c1d} module) in which |
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| 61 | both lateral tendancy terms and lateral physics are not called; |
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[11263] | 62 | \item[(2)] |
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[10354] | 63 | the vertical velocity is zero |
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| 64 | (so far, no attempt at introducing a Ekman pumping velocity has been made); |
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[11263] | 65 | \item[(3)] |
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[10354] | 66 | 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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[3764] | 68 | \end{description} |
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[11263] | 69 | All the relevant \textit{\_c1d} modules can be found in the src/OCE/C1D directory of |
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[11512] | 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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[9393] | 77 | \section{ORCA family: global ocean with tripolar grid} |
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[9407] | 78 | \label{sec:CFG_orca} |
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[2376] | 79 | |
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[10354] | 80 | The ORCA family is a series of global ocean configurations that are run together with |
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[11263] | 81 | the SI3 model (ORCA-ICE) and possibly with PISCES biogeochemical model (ORCA-ICE-PISCES). |
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[11512] | 82 | An appropriate namelist is available in \path{./cfgs/ORCA2_ICE_PISCES/EXPREF/namelist_cfg} for ORCA2. |
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[10354] | 83 | The domain of ORCA2 configuration is defined in \ifile{ORCA\_R2\_zps\_domcfg} file, |
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[11512] | 84 | this file is available in tar file on the \NEMO\ community zenodo platform: \\ |
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[11263] | 85 | https://doi.org/10.5281/zenodo.2640723 |
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| 86 | |
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[11512] | 87 | In this namelist\_cfg the name of domain input file is set in \nam{cfg} block of namelist. |
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[2376] | 88 | |
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[2381] | 89 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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[10354] | 90 | \begin{figure}[!t] |
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| 91 | \begin{center} |
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[11263] | 92 | \includegraphics[width=\textwidth]{Fig_ORCA_NH_mesh} |
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[10414] | 93 | \caption{ |
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| 94 | \protect\label{fig:MISC_ORCA_msh} |
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[10354] | 95 | ORCA mesh conception. |
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[10442] | 96 | The departure from an isotropic Mercator grid start poleward of 20\deg{N}. |
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[10354] | 97 | The two "north pole" are the foci of a series of embedded ellipses (blue curves) which |
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| 98 | are determined analytically and form the i-lines of the ORCA mesh (pseudo latitudes). |
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[11263] | 99 | Then, following \citet{madec.imbard_CD96}, the normal to the series of ellipses (red curves) is computed which |
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[10414] | 100 | provides the j-lines of the mesh (pseudo longitudes). |
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| 101 | } |
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[10354] | 102 | \end{center} |
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| 103 | \end{figure} |
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[2381] | 104 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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| 105 | |
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[2376] | 106 | % ------------------------------------------------------------------------------------------------------------- |
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| 107 | % ORCA tripolar grid |
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| 108 | % ------------------------------------------------------------------------------------------------------------- |
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| 109 | \subsection{ORCA tripolar grid} |
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[9407] | 110 | \label{subsec:CFG_orca_grid} |
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[2376] | 111 | |
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[11263] | 112 | The ORCA grid is a tripolar grid based on the semi-analytical method of \citet{madec.imbard_CD96}. |
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[10354] | 113 | It allows to construct a global orthogonal curvilinear ocean mesh which has no singularity point inside |
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[2376] | 114 | the computational domain since two north mesh poles are introduced and placed on lands. |
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[10354] | 115 | The method involves defining an analytical set of mesh parallels in the stereographic polar plan, |
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| 116 | computing the associated set of mesh meridians, and projecting the resulting mesh onto the sphere. |
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| 117 | The set of mesh parallels used is a series of embedded ellipses which foci are the two mesh north poles |
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| 118 | (\autoref{fig:MISC_ORCA_msh}). |
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| 119 | The resulting mesh presents no loss of continuity in either the mesh lines or the scale factors, |
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[11512] | 120 | or even the scale factor derivatives over the whole ocean domain, as the mesh is not a composite mesh. |
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[2376] | 121 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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[10354] | 122 | \begin{figure}[!tbp] |
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| 123 | \begin{center} |
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[11263] | 124 | \includegraphics[width=\textwidth]{Fig_ORCA_NH_msh05_e1_e2} |
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| 125 | \includegraphics[width=\textwidth]{Fig_ORCA_aniso} |
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[10414] | 126 | \caption { |
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| 127 | \protect\label{fig:MISC_ORCA_e1e2} |
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[10354] | 128 | \textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and |
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| 129 | \textit{Bottom}: ratio of anisotropy ($e_1 / e_2$) |
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| 130 | for ORCA 0.5\deg ~mesh. |
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[10442] | 131 | South of 20\deg{N} a Mercator grid is used ($e_1 = e_2$) so that the anisotropy ratio is 1. |
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| 132 | Poleward of 20\deg{N}, the two "north pole" introduce a weak anisotropy over the ocean areas ($< 1.2$) except in |
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[10414] | 133 | vicinity of Victoria Island (Canadian Arctic Archipelago). |
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| 134 | } |
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| 135 | \end{center} |
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| 136 | \end{figure} |
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[2376] | 137 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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| 138 | |
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[11512] | 139 | The method is applied to Mercator grid (\ie\ same zonal and meridional grid spacing) poleward of 20\deg{N}, |
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[10354] | 140 | so that the Equator is a mesh line, which provides a better numerical solution for equatorial dynamics. |
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| 141 | The choice of the series of embedded ellipses (position of the foci and variation of the ellipses) |
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| 142 | is a compromise between maintaining the ratio of mesh anisotropy ($e_1 / e_2$) close to one in the ocean |
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| 143 | (especially in area of strong eddy activities such as the Gulf Stream) and keeping the smallest scale factor in |
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| 144 | the northern hemisphere larger than the smallest one in the southern hemisphere. |
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| 145 | The resulting mesh is shown in \autoref{fig:MISC_ORCA_msh} and \autoref{fig:MISC_ORCA_e1e2} for |
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| 146 | a half a degree grid (ORCA\_R05). |
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| 147 | The smallest ocean scale factor is found in along Antarctica, |
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[11512] | 148 | while the ratio of anisotropy remains close to one except near the Victoria Island in the Canadian Archipelago. |
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[2376] | 149 | |
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| 150 | % ------------------------------------------------------------------------------------------------------------- |
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[11263] | 151 | % ORCA-ICE(-PISCES) configurations |
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[2376] | 152 | % ------------------------------------------------------------------------------------------------------------- |
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[2381] | 153 | \subsection{ORCA pre-defined resolution} |
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[9407] | 154 | \label{subsec:CFG_orca_resolution} |
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[2376] | 155 | |
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[11512] | 156 | The \NEMO\ system is provided with five built-in ORCA configurations which differ in the horizontal resolution. |
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[10354] | 157 | The value of the resolution is given by the resolution at the Equator expressed in degrees. |
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| 158 | Each of configuration is set through the \textit{domain\_cfg} domain configuration file, |
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| 159 | which sets the grid size and configuration name parameters. |
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[11512] | 160 | The \NEMO\ System Team provides only ORCA2 domain input file "\ifile{ORCA\_R2\_zps\_domcfg}" file |
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| 161 | (\autoref{tab:ORCA}). |
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[2376] | 162 | |
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[2381] | 163 | %--------------------------------------------------TABLE-------------------------------------------------- |
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[10414] | 164 | \begin{table}[!t] |
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| 165 | \begin{center} |
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| 166 | \begin{tabular}{p{4cm} c c c c} |
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[11512] | 167 | Horizontal Grid & \jp{ORCA\_index} & \jp{jpiglo} & \jp{jpjglo} \\ |
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| 168 | \hline \hline |
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| 169 | % 4 \deg & 4 & 92 & 76 \\ |
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| 170 | 2 \deg & 2 & 182 & 149 \\ |
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| 171 | 1 \deg & 1 & 362 & 292 \\ |
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| 172 | 0.5 \deg & 05 & 722 & 511 \\ |
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| 173 | 0.25\deg & 025 & 1442 & 1021 \\ |
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| 174 | \hline \hline |
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[10414] | 175 | \end{tabular} |
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| 176 | \caption{ |
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| 177 | \protect\label{tab:ORCA} |
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| 178 | Domain size of ORCA family configurations. |
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| 179 | The flag for configurations of ORCA family need to be set in \textit{domain\_cfg} file. |
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| 180 | } |
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| 181 | \end{center} |
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[2381] | 182 | \end{table} |
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| 183 | %-------------------------------------------------------------------------------------------------------------- |
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| 184 | |
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| 185 | |
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[10354] | 186 | The ORCA\_R2 configuration has the following specificity: starting from a 2\deg~ORCA mesh, |
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| 187 | local mesh refinements were applied to the Mediterranean, Red, Black and Caspian Seas, |
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[11263] | 188 | so that the resolution is 1\deg~ there. |
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[10354] | 189 | A local transformation were also applied with in the Tropics in order to refine the meridional resolution up to |
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[11263] | 190 | 0.5\deg~ at the Equator. |
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[2376] | 191 | |
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[10354] | 192 | The ORCA\_R1 configuration has only a local tropical transformation to refine the meridional resolution up to |
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| 193 | 1/3\deg~at the Equator. |
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| 194 | Note that the tropical mesh refinements in ORCA\_R2 and R1 strongly increases the mesh anisotropy there. |
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[2376] | 195 | |
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[11512] | 196 | The ORCA\_R05 and higher global configurations do not incorporate any regional refinements. |
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[2376] | 197 | |
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[10354] | 198 | For ORCA\_R1 and R025, setting the configuration key to 75 allows to use 75 vertical levels, otherwise 46 are used. |
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| 199 | In the other ORCA configurations, 31 levels are used |
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[11263] | 200 | (see \autoref{tab:orca_zgr}). %\sfcomment{HERE I need to put new table for ORCA2 values} and \autoref{fig:zgr}). |
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[2381] | 201 | |
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[11512] | 202 | Only the ORCA\_R2 is provided with all its input files in the \NEMO\ distribution. |
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[11263] | 203 | %It is very similar to that used as part of the climate model developed at IPSL for the 4th IPCC assessment of |
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| 204 | %climate change (Marti et al., 2009). |
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[11512] | 205 | %It is also the basis for the \NEMO\ contribution to the Coordinate Ocean-ice Reference Experiments (COREs) |
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| 206 | %documented in \citet{griffies.biastoch.ea_OM09}. |
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[2376] | 207 | |
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[10354] | 208 | This version of ORCA\_R2 has 31 levels in the vertical, with the highest resolution (10m) in the upper 150m |
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[11512] | 209 | (see \autoref{tab:orca_zgr} and \autoref{fig:zgr}). |
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| 210 | The bottom topography and the coastlines are derived from the global atlas of Smith and Sandwell (1997). |
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| 211 | The default forcing uses the boundary forcing from \citet{large.yeager_rpt04} (see \autoref{subsec:SBC_blk_core}), |
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[10354] | 212 | which was developed for the purpose of running global coupled ocean-ice simulations without |
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| 213 | an interactive atmosphere. |
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[11263] | 214 | This \citet{large.yeager_rpt04} dataset is available through |
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[10354] | 215 | the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}. |
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[11512] | 216 | The "normal year" of \citet{large.yeager_rpt04} has been chosen of the \NEMO\ distribution since release v3.3. |
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[2376] | 217 | |
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[11512] | 218 | ORCA\_R2 pre-defined configuration can also be run with multiply online nested zooms (\ie\ with AGRIF, \key{agrif} defined). |
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| 219 | This is available as the AGRIF\_DEMO configuration that can be found in the \path{./cfgs/AGRIF_DEMO/} directory. |
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[11263] | 220 | |
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[10354] | 221 | A regional Arctic or peri-Antarctic configuration is extracted from an ORCA\_R2 or R05 configurations using |
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[11512] | 222 | sponge layers at open boundaries. |
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[2376] | 223 | |
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| 224 | % ------------------------------------------------------------------------------------------------------------- |
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| 225 | % GYRE family: double gyre basin |
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| 226 | % ------------------------------------------------------------------------------------------------------------- |
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[11263] | 227 | \section{GYRE family: double gyre basin} |
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[9407] | 228 | \label{sec:CFG_gyre} |
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[2376] | 229 | |
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[11263] | 230 | The GYRE configuration \citep{levy.klein.ea_OM10} has been built to |
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[10354] | 231 | simulate the seasonal cycle of a double-gyre box model. |
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[11263] | 232 | It consists in an idealized domain similar to that used in the studies of \citet{drijfhout_JPO94} and |
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| 233 | \citet{hazeleger.drijfhout_JPO98, hazeleger.drijfhout_JPO99, hazeleger.drijfhout_JGR00, hazeleger.drijfhout_JPO00}, |
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[10354] | 234 | over which an analytical seasonal forcing is applied. |
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[11512] | 235 | This allows to investigate the spontaneous generation of a large number of interacting, transient mesoscale eddies |
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| 236 | and their contribution to the large scale circulation. |
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[2376] | 237 | |
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[11263] | 238 | The GYRE configuration run together with the PISCES biogeochemical model (GYRE-PISCES). |
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[10442] | 239 | The domain geometry is a closed rectangular basin on the $\beta$-plane centred at $\sim$ 30\deg{N} and |
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[10354] | 240 | rotated by 45\deg, 3180~km long, 2120~km wide and 4~km deep (\autoref{fig:MISC_strait_hand}). |
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| 241 | The domain is bounded by vertical walls and by a flat bottom. |
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| 242 | The configuration is meant to represent an idealized North Atlantic or North Pacific basin. |
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| 243 | The circulation is forced by analytical profiles of wind and buoyancy fluxes. |
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[11512] | 244 | The applied forcings vary seasonally in a sinusoidal manner between winter and summer extrema \citep{levy.klein.ea_OM10}. |
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[10442] | 245 | The wind stress is zonal and its curl changes sign at 22\deg{N} and 36\deg{N}. |
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[10354] | 246 | It forces a subpolar gyre in the north, a subtropical gyre in the wider part of the domain and |
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| 247 | a small recirculation gyre in the southern corner. |
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| 248 | The net heat flux takes the form of a restoring toward a zonal apparent air temperature profile. |
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| 249 | A portion of the net heat flux which comes from the solar radiation is allowed to penetrate within the water column. |
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| 250 | The fresh water flux is also prescribed and varies zonally. |
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| 251 | It is determined such as, at each time step, the basin-integrated flux is zero. |
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| 252 | The basin is initialised at rest with vertical profiles of temperature and salinity uniformly applied to |
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| 253 | the whole domain. |
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[2376] | 254 | |
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[10354] | 255 | The GYRE configuration is set like an analytical configuration. |
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[11512] | 256 | Through \np{ln\_read\_cfg}\forcode{ = .false.} in \nam{cfg} namelist defined in |
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| 257 | the reference configuration \path{./cfgs/GYRE_PISCES/EXPREF/namelist_cfg} |
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[10354] | 258 | analytical definition of grid in GYRE is done in usrdef\_hrg, usrdef\_zgr routines. |
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| 259 | Its horizontal resolution (and thus the size of the domain) is determined by |
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[11512] | 260 | setting \np{nn\_GYRE} in \nam{usr\_def}: \\ |
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[11263] | 261 | |
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[11512] | 262 | \jp{jpiglo} $= 30 \times$ \np{nn\_GYRE} + 2 \\ |
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[11263] | 263 | |
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[11512] | 264 | \jp{jpjglo} $= 20 \times$ \np{nn\_GYRE} + 2 \\ |
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[11263] | 265 | |
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[10354] | 266 | Obviously, the namelist parameters have to be adjusted to the chosen resolution, |
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[11512] | 267 | see the Configurations pages on the \NEMO\ web site (\NEMO\ Configurations). |
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[9407] | 268 | In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}\forcode{ = 31}) (\autoref{fig:zgr}). |
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[2376] | 269 | |
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[10354] | 270 | The GYRE configuration is also used in benchmark test as it is very simple to increase its resolution and |
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| 271 | as it does not requires any input file. |
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| 272 | For example, keeping a same model size on each processor while increasing the number of processor used is very easy, |
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| 273 | even though the physical integrity of the solution can be compromised. |
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[11512] | 274 | Benchmark is activate via \np{ln\_bench}\forcode{ = .true.} in \nam{usr\_def} in |
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| 275 | namelist \path{./cfgs/GYRE_PISCES/EXPREF/namelist_cfg}. |
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[2376] | 276 | |
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| 277 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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[10354] | 278 | \begin{figure}[!t] |
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| 279 | \begin{center} |
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[11263] | 280 | \includegraphics[width=\textwidth]{Fig_GYRE} |
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[10414] | 281 | \caption{ |
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| 282 | \protect\label{fig:GYRE} |
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[10354] | 283 | Snapshot of relative vorticity at the surface of the model domain in GYRE R9, R27 and R54. |
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[11263] | 284 | From \citet{levy.klein.ea_OM10}. |
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[10414] | 285 | } |
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[10354] | 286 | \end{center} |
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| 287 | \end{figure} |
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[2376] | 288 | %>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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| 289 | |
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| 290 | % ------------------------------------------------------------------------------------------------------------- |
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[3294] | 291 | % AMM configuration |
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[2376] | 292 | % ------------------------------------------------------------------------------------------------------------- |
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[9393] | 293 | \section{AMM: atlantic margin configuration} |
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[9407] | 294 | \label{sec:MISC_config_AMM} |
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[2376] | 295 | |
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[10354] | 296 | The AMM, Atlantic Margins Model, is a regional model covering the Northwest European Shelf domain on |
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| 297 | a regular lat-lon grid at approximately 12km horizontal resolution. |
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[11512] | 298 | The appropriate \textit{\&namcfg} namelist is available in \path{./cfgs/AMM12/EXPREF/namelist\_cfg}. |
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[4147] | 299 | It is used to build the correct dimensions of the AMM domain. |
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[2376] | 300 | |
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[11512] | 301 | This configuration tests several features of \NEMO\ functionality specific to the shelf seas. |
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[11263] | 302 | In particular, the AMM uses $s$-coordinates in the vertical rather than $z$-coordinates and |
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| 303 | is forced with tidal lateral boundary conditions using a Flather boundary condition from the BDY module. |
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| 304 | Also specific to the AMM configuration is the use of the GLS turbulence scheme (\np{ln\_zdfgls} \forcode{= .true.}). |
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[2376] | 305 | |
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[10354] | 306 | In addition to the tidal boundary condition the model may also take open boundary conditions from |
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| 307 | a North Atlantic model. |
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| 308 | Boundaries may be 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 are included to test a realistic model run. |
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| 310 | The Baltic boundary is included within the river input file and is specified as a river source. |
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| 311 | Unlike ordinary river points the Baltic inputs also include salinity and temperature data. |
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[2376] | 312 | |
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[10414] | 313 | \biblio |
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| 314 | |
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[10442] | 315 | \pindex |
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| 316 | |
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[6997] | 317 | \end{document} |
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