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Changeset 10368 for NEMO/branches/2018/dev_r10164_HPC09_ESIWACE_PREP_MERGE/doc/latex/NEMO/subfiles/chap_CONFIG.tex – NEMO

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Timestamp:
2018-12-03T12:45:01+01:00 (5 years ago)
Author:
smasson
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dev_r10164_HPC09_ESIWACE_PREP_MERGE: merge with trunk@10365, see #2133

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  • NEMO/branches/2018/dev_r10164_HPC09_ESIWACE_PREP_MERGE/doc/latex/NEMO/subfiles/chap_CONFIG.tex

    r10146 r10368  
    1818 
    1919 
    20 The purpose of this part of the manual is to introduce the \NEMO reference configurations.  
    21 These configurations are offered as means to explore various numerical and physical options,  
    22 thus allowing the user to verify that the code is performing in a manner consistent with that  
    23 we are running. This form of verification is critical as one adopts the code for his or her particular  
    24 research purposes. The reference configurations also provide a sense for some of the options available  
    25 in the code, though by no means are all options exercised in the reference configurations. 
     20The purpose of this part of the manual is to introduce the \NEMO reference configurations. 
     21These configurations are offered as means to explore various numerical and physical options, 
     22thus allowing the user to verify that the code is performing in a manner consistent with that we are running. 
     23This form of verification is critical as one adopts the code for his or her particular research purposes. 
     24The reference configurations also provide a sense for some of the options available in the code, 
     25though by no means are all options exercised in the reference configurations. 
    2626 
    2727%------------------------------------------namcfg---------------------------------------------------- 
    … …  
    4040$\ $\newline 
    4141 
    42 The 1D model option simulates a stand alone water column within the 3D \NEMO system.  
    43 It can be applied to the ocean alone or to the ocean-ice system and can include passive tracers  
    44 or a biogeochemical model. It is set up by defining the position of the 1D water column in the grid  
     42The 1D model option simulates a stand alone water column within the 3D \NEMO system. 
     43It can be applied to the ocean alone or to the ocean-ice system and can include passive tracers or a biogeochemical model. 
     44It is set up by defining the position of the 1D water column in the grid 
    4545(see \textit{CONFIG/SHARED/namelist\_ref} ).  
    46 The 1D model is a very useful tool   
    47 \textit{(a)} to learn about the physics and numerical treatment of vertical mixing processes ;  
    48 \textit{(b)} to investigate suitable parameterisations of unresolved turbulence (surface wave 
    49 breaking, Langmuir circulation, ...) ;  
    50 \textit{(c)} to compare the behaviour of different vertical mixing schemes  ;  
    51 \textit{(d)} to perform sensitivity studies on the vertical diffusion at a particular point of an ocean domain ;  
     46The 1D model is a very useful tool 
     47\textit{(a)} to learn about the physics and numerical treatment of vertical mixing processes; 
     48\textit{(b)} to investigate suitable parameterisations of unresolved turbulence 
     49(surface wave breaking, Langmuir circulation, ...); 
     50\textit{(c)} to compare the behaviour of different vertical mixing schemes; 
     51\textit{(d)} to perform sensitivity studies on the vertical diffusion at a particular point of an ocean domain; 
    5252\textit{(d)} to produce extra diagnostics, without the large memory requirement of the full 3D model. 
    5353 
    54 The methodology is based on the use of the zoom functionality over the smallest possible  
    55 domain : a 3x3 domain centered on the grid point of interest,  
    56 with some extra routines. There is no need to define a new mesh, bathymetry,  
    57 initial state or forcing, since the 1D model will use those of the configuration it is a zoom of.  
    58 The chosen grid point is set in \textit{\ngn{namcfg}} namelist by setting the \np{jpizoom} and \np{jpjzoom}  
    59 parameters to the indices of the location of the chosen grid point. 
    60  
    61 The 1D model has some specifies. First, all the horizontal derivatives are assumed to be zero, and 
    62 second, the two components of the velocity are moved on a $T$-point.  
     54The methodology is based on the use of the zoom functionality over the smallest possible domain: 
     55a 3x3 domain centered on the grid point of interest, with some extra routines. 
     56There is no need to define a new mesh, bathymetry, initial state or forcing, 
     57since the 1D model will use those of the configuration it is a zoom of. 
     58The chosen grid point is set in \textit{\ngn{namcfg}} namelist by 
     59setting the \np{jpizoom} and \np{jpjzoom} parameters to the indices of the location of the chosen grid point. 
     60 
     61The 1D model has some specifies. First, all the horizontal derivatives are assumed to be zero, 
     62and second, the two components of the velocity are moved on a $T$-point.  
    6363Therefore, defining \key{c1d} changes five main things in the code behaviour:  
    6464\begin{description} 
    65 \item[(1)] the lateral boundary condition routine (\rou{lbc\_lnk}) set the value of the central column  
    66 of the 3x3 domain is imposed over the whole domain ;  
    67 \item[(3)] a call to \rou{lbc\_lnk} is systematically done when reading input data ($i.e.$ in \mdl{iom}) ;  
    68 \item[(3)] a simplified \rou{stp} routine is used (\rou{stp\_c1d}, see \mdl{step\_c1d} module) in which  
    69 both lateral tendancy terms and lateral physics are not called ;  
    70 \item[(4)] the vertical velocity is zero (so far, no attempt at introducing a Ekman pumping velocity  
    71 has been made) ;  
    72 \item[(5)] a simplified treatment of the Coriolis term is performed as $U$- and $V$-points are the same  
    73 (see \mdl{dyncor\_c1d}). 
     65\item[(1)] 
     66  the lateral boundary condition routine (\rou{lbc\_lnk}) set the value of the central column of 
     67  the 3x3 domain is imposed over the whole domain; 
     68\item[(3)] 
     69  a call to \rou{lbc\_lnk} is systematically done when reading input data ($i.e.$ in \mdl{iom}); 
     70\item[(3)] 
     71  a simplified \rou{stp} routine is used (\rou{stp\_c1d}, see \mdl{step\_c1d} module) in which 
     72  both lateral tendancy terms and lateral physics are not called; 
     73\item[(4)] 
     74  the vertical velocity is zero 
     75  (so far, no attempt at introducing a Ekman pumping velocity has been made); 
     76\item[(5)] 
     77  a simplified treatment of the Coriolis term is performed as $U$- and $V$-points are the same 
     78  (see \mdl{dyncor\_c1d}). 
    7479\end{description} 
    75 All the relevant \textit{\_c1d} modules can be found in the NEMOGCM/NEMO/OPA\_SRC/C1D directory of  
     80All the relevant \textit{\_c1d} modules can be found in the NEMOGCM/NEMO/OPA\_SRC/C1D directory of 
    7681the \NEMO distribution. 
    7782 
    … …  
    8489\label{sec:CFG_orca} 
    8590 
    86 The ORCA family is a series of global ocean configurations that are run together with  
    87 the LIM sea-ice model (ORCA-LIM) and possibly with PISCES biogeochemical model  
    88 (ORCA-LIM-PISCES), using various resolutions. 
    89 An appropriate namelist is available in \path{CONFIG/ORCA2_LIM3_PISCES/EXP00/namelist_cfg}  
    90 for ORCA2. 
    91 The domain of ORCA2 configuration is defined in \ifile{ORCA\_R2\_zps\_domcfg} file, this file is available in tar file in the wiki of NEMO : \\ 
     91The ORCA family is a series of global ocean configurations that are run together with 
     92the LIM sea-ice model (ORCA-LIM) and possibly with PISCES biogeochemical model (ORCA-LIM-PISCES), 
     93using various resolutions. 
     94An appropriate namelist is available in \path{CONFIG/ORCA2_LIM3_PISCES/EXP00/namelist_cfg} for ORCA2. 
     95The domain of ORCA2 configuration is defined in \ifile{ORCA\_R2\_zps\_domcfg} file, 
     96this file is available in tar file in the wiki of NEMO: \\ 
    9297https://forge.ipsl.jussieu.fr/nemo/wiki/Users/ReferenceConfigurations/ORCA2\_LIM3\_PISCES \\ 
    9398In this namelist\_cfg the name of domain input file is set in \ngn{namcfg} block of namelist.  
    9499 
    95100%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    96 \begin{figure}[!t]   \begin{center} 
    97 \includegraphics[width=0.98\textwidth]{Fig_ORCA_NH_mesh} 
    98 \caption{  \protect\label{fig:MISC_ORCA_msh}      
    99 ORCA mesh conception. The departure from an isotropic Mercator grid start poleward of 20\degN. 
    100 The two "north pole" are the foci of a series of embedded ellipses (blue curves)  
    101 which are determined analytically and form the i-lines of the ORCA mesh (pseudo latitudes).  
    102 Then, following \citet{Madec_Imbard_CD96}, the normal to the series of ellipses (red curves) is computed  
    103 which provide the j-lines of the mesh (pseudo longitudes).  } 
    104 \end{center}   \end{figure} 
     101\begin{figure}[!t] 
     102  \begin{center} 
     103    \includegraphics[width=0.98\textwidth]{Fig_ORCA_NH_mesh} 
     104    \caption{  \protect\label{fig:MISC_ORCA_msh} 
     105      ORCA mesh conception. 
     106      The departure from an isotropic Mercator grid start poleward of 20\degN. 
     107      The two "north pole" are the foci of a series of embedded ellipses (blue curves) which 
     108      are determined analytically and form the i-lines of the ORCA mesh (pseudo latitudes). 
     109      Then, following \citet{Madec_Imbard_CD96}, the normal to the series of ellipses (red curves) is computed which 
     110      provides the j-lines of the mesh (pseudo longitudes).  } 
     111  \end{center} 
     112\end{figure} 
    105113%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    106114 
    … …  
    111119\label{subsec:CFG_orca_grid} 
    112120 
    113 The ORCA grid is a tripolar is based on the semi-analytical method of \citet{Madec_Imbard_CD96}.  
    114 It allows to construct a global orthogonal curvilinear ocean mesh which has no singularity point inside  
     121The ORCA grid is a tripolar is based on the semi-analytical method of \citet{Madec_Imbard_CD96}. 
     122It allows to construct a global orthogonal curvilinear ocean mesh which has no singularity point inside 
    115123the computational domain since two north mesh poles are introduced and placed on lands. 
    116 The method involves defining an analytical set of mesh parallels in the stereographic polar plan,  
    117 computing the associated set of mesh meridians, and projecting the resulting mesh onto the sphere.  
    118 The set of mesh parallels used is a series of embedded ellipses which foci are the two mesh north  
    119 poles (\autoref{fig:MISC_ORCA_msh}). The resulting mesh presents no loss of continuity in  
    120 either the mesh lines or the scale factors, or even the scale factor derivatives over the whole  
    121 ocean domain, as the mesh is not a composite mesh.  
    122 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    123 \begin{figure}[!tbp]  \begin{center} 
    124 \includegraphics[width=1.0\textwidth]{Fig_ORCA_NH_msh05_e1_e2} 
    125 \includegraphics[width=0.80\textwidth]{Fig_ORCA_aniso} 
    126 \caption {  \protect\label{fig:MISC_ORCA_e1e2} 
    127 \textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and  
    128 \textit{Bottom}: ratio of anisotropy ($e_1 / e_2$) 
    129 for ORCA 0.5\deg ~mesh. South of 20\degN a Mercator grid is used ($e_1 = e_2$)  
    130 so that the anisotropy ratio is 1. Poleward of 20\degN, the two "north pole"  
    131 introduce a weak anisotropy over the ocean areas ($< 1.2$) except in vicinity of Victoria Island  
    132 (Canadian Arctic Archipelago). } 
     124The method involves defining an analytical set of mesh parallels in the stereographic polar plan, 
     125computing the associated set of mesh meridians, and projecting the resulting mesh onto the sphere. 
     126The set of mesh parallels used is a series of embedded ellipses which foci are the two mesh north poles 
     127(\autoref{fig:MISC_ORCA_msh}). 
     128The resulting mesh presents no loss of continuity in either the mesh lines or the scale factors, 
     129or even the scale factor derivatives over the whole ocean domain, as the mesh is not a composite mesh.  
     130%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     131\begin{figure}[!tbp] 
     132  \begin{center} 
     133    \includegraphics[width=1.0\textwidth]{Fig_ORCA_NH_msh05_e1_e2} 
     134    \includegraphics[width=0.80\textwidth]{Fig_ORCA_aniso} 
     135    \caption {  \protect\label{fig:MISC_ORCA_e1e2} 
     136      \textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and 
     137      \textit{Bottom}: ratio of anisotropy ($e_1 / e_2$) 
     138      for ORCA 0.5\deg ~mesh. 
     139      South of 20\degN a Mercator grid is used ($e_1 = e_2$) so that the anisotropy ratio is 1. 
     140      Poleward of 20\degN, the two "north pole" introduce a weak anisotropy over the ocean areas ($< 1.2$) except in 
     141      vicinity of Victoria Island (Canadian Arctic Archipelago). } 
    133142\end{center}   \end{figure} 
    134143%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    135144 
    136145 
    137 The method is applied to Mercator grid ($i.e.$ same zonal and meridional grid spacing) poleward  
    138 of 20\degN, so that the Equator is a mesh line, which provides a better numerical solution  
    139 for equatorial dynamics. The choice of the series of embedded ellipses (position of the foci and  
    140 variation of the ellipses) is a compromise between maintaining  the ratio of mesh anisotropy  
    141 ($e_1 / e_2$) close to one in the ocean (especially in area of strong eddy activities such as  
    142 the Gulf Stream) and keeping the smallest scale factor in the northern hemisphere larger  
    143 than the smallest one in the southern hemisphere. 
    144 The resulting mesh is shown in \autoref{fig:MISC_ORCA_msh} and \autoref{fig:MISC_ORCA_e1e2}  
    145 for a half a degree grid (ORCA\_R05). 
    146 The smallest ocean scale factor is found in along  Antarctica, while the ratio of anisotropy remains close to one except near the Victoria Island  
    147 in the Canadian Archipelago.  
     146The method is applied to Mercator grid ($i.e.$ same zonal and meridional grid spacing) poleward of 20\degN, 
     147so that the Equator is a mesh line, which provides a better numerical solution for equatorial dynamics. 
     148The choice of the series of embedded ellipses (position of the foci and variation of the ellipses) 
     149is a compromise between maintaining the ratio of mesh anisotropy ($e_1 / e_2$) close to one in the ocean 
     150(especially in area of strong eddy activities such as the Gulf Stream) and keeping the smallest scale factor in 
     151the northern hemisphere larger than the smallest one in the southern hemisphere. 
     152The resulting mesh is shown in \autoref{fig:MISC_ORCA_msh} and \autoref{fig:MISC_ORCA_e1e2} for 
     153a half a degree grid (ORCA\_R05). 
     154The smallest ocean scale factor is found in along Antarctica, 
     155while the ratio of anisotropy remains close to one except near the Victoria Island in the Canadian Archipelago.  
    148156 
    149157% ------------------------------------------------------------------------------------------------------------- 
    … …  
    154162 
    155163 
    156 The NEMO system is provided with five built-in ORCA configurations which differ in the  
    157 horizontal resolution. The value of the resolution is given by the resolution at the Equator  
    158 expressed in degrees. Each of configuration is set through the \textit{domain\_cfg} domain configuration file,  
    159 which sets the grid size and configuration name parameters. The NEMO System Team provides only ORCA2 domain input file "\ifile{ORCA\_R2\_zps\_domcfg}" file  (Tab. \autoref{tab:ORCA}). 
     164The NEMO system is provided with five built-in ORCA configurations which differ in the horizontal resolution. 
     165The value of the resolution is given by the resolution at the Equator expressed in degrees. 
     166Each of configuration is set through the \textit{domain\_cfg} domain configuration file, 
     167which sets the grid size and configuration name parameters. 
     168The NEMO System Team provides only ORCA2 domain input file "\ifile{ORCA\_R2\_zps\_domcfg}" file 
     169(Tab. \autoref{tab:ORCA}). 
    160170 
    161171 
    … …  
    176186\hline   \hline 
    177187\end{tabular} 
    178 \caption{ \protect\label{tab:ORCA}    
    179 Domain size of ORCA family configurations. 
    180 The flag for configurations of ORCA family need to be set in \textit{domain\_cfg} file. } 
     188\caption{ \protect\label{tab:ORCA} 
     189  Domain size of ORCA family configurations. 
     190  The flag for configurations of ORCA family need to be set in \textit{domain\_cfg} file. } 
    181191\end{center} 
    182192\end{table} 
    … …  
    184194 
    185195 
    186 The ORCA\_R2 configuration has the following specificity : starting from a 2\deg~ORCA mesh,  
    187 local mesh refinements were applied to the Mediterranean, Red, Black and Caspian Seas,  
    188 so that the resolution is 1\deg \time 1\deg there. A local transformation were also applied  
    189 with in the Tropics in order to refine the meridional resolution up to 0.5\deg at the Equator. 
    190  
    191 The ORCA\_R1 configuration has only a local tropical transformation  to refine the meridional  
    192 resolution up to 1/3\deg~at the Equator. Note that the tropical mesh refinements in ORCA\_R2  
    193 and R1 strongly increases the mesh anisotropy there. 
     196The ORCA\_R2 configuration has the following specificity: starting from a 2\deg~ORCA mesh, 
     197local mesh refinements were applied to the Mediterranean, Red, Black and Caspian Seas, 
     198so that the resolution is 1\deg \time 1\deg there. 
     199A local transformation were also applied with in the Tropics in order to refine the meridional resolution up to 
     2000.5\deg at the Equator. 
     201 
     202The ORCA\_R1 configuration has only a local tropical transformation to refine the meridional resolution up to 
     2031/3\deg~at the Equator. 
     204Note that the tropical mesh refinements in ORCA\_R2 and R1 strongly increases the mesh anisotropy there. 
    194205 
    195206The ORCA\_R05 and higher global configurations do not incorporate any regional refinements.   
    196207 
    197 For ORCA\_R1 and R025, setting the configuration key to 75 allows to use 75 vertical levels,  
    198 otherwise 46 are used. In the other ORCA configurations, 31 levels are used  
     208For ORCA\_R1 and R025, setting the configuration key to 75 allows to use 75 vertical levels, otherwise 46 are used. 
     209In the other ORCA configurations, 31 levels are used 
    199210(see \autoref{tab:orca_zgr} \sfcomment{HERE I need to put new table for ORCA2 values} and \autoref{fig:zgr}). 
    200211 
    201 Only the ORCA\_R2 is provided with all its input files in the \NEMO distribution.  
    202 It is very similar to that used as part of the climate model developed at IPSL for the 4th IPCC  
    203 assessment of climate change (Marti et al., 2009). It is also the basis for the \NEMO contribution  
    204 to the Coordinate Ocean-ice Reference Experiments (COREs) documented in \citet{Griffies_al_OM09}.  
    205  
    206 This version of ORCA\_R2 has 31 levels in the vertical, with the highest resolution (10m)  
    207 in the upper 150m (see \autoref{tab:orca_zgr} and \autoref{fig:zgr}).  
     212Only the ORCA\_R2 is provided with all its input files in the \NEMO distribution. 
     213It is very similar to that used as part of the climate model developed at IPSL for the 4th IPCC assessment of 
     214climate change (Marti et al., 2009). 
     215It is also the basis for the \NEMO contribution to the Coordinate Ocean-ice Reference Experiments (COREs) 
     216documented in \citet{Griffies_al_OM09}.  
     217 
     218This version of ORCA\_R2 has 31 levels in the vertical, with the highest resolution (10m) in the upper 150m 
     219(see \autoref{tab:orca_zgr} and \autoref{fig:zgr}).  
    208220The bottom topography and the coastlines are derived from the global atlas of Smith and Sandwell (1997).  
    209221The default forcing uses the boundary forcing from \citet{Large_Yeager_Rep04} (see \autoref{subsec:SBC_blk_core}),  
    210 which was developed for the purpose of running global coupled ocean-ice simulations  
    211 without an interactive atmosphere. This \citet{Large_Yeager_Rep04} dataset is available  
    212 through the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}.  
    213 The "normal year" of \citet{Large_Yeager_Rep04} has been chosen of the \NEMO distribution  
    214 since release v3.3.  
    215  
    216 ORCA\_R2 pre-defined configuration can also be run with an AGRIF zoom over the Agulhas  
    217 current area ( \key{agrif}  defined) and, by setting the appropriate variables, see \path{CONFIG/SHARED/namelist_ref} 
    218 a regional Arctic or peri-Antarctic configuration is extracted from an ORCA\_R2 or R05 configurations 
    219 using sponge layers at open boundaries.  
     222which was developed for the purpose of running global coupled ocean-ice simulations without 
     223an interactive atmosphere. 
     224This \citet{Large_Yeager_Rep04} dataset is available through 
     225the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}. 
     226The "normal year" of \citet{Large_Yeager_Rep04} has been chosen of the \NEMO distribution since release v3.3.  
     227 
     228ORCA\_R2 pre-defined configuration can also be run with an AGRIF zoom over the Agulhas current area 
     229(\key{agrif} defined) and, by setting the appropriate variables, see \path{CONFIG/SHARED/namelist_ref}. 
     230A regional Arctic or peri-Antarctic configuration is extracted from an ORCA\_R2 or R05 configurations using 
     231sponge layers at open boundaries.  
    220232 
    221233% ------------------------------------------------------------------------------------------------------------- 
    … …  
    225237\label{sec:CFG_gyre} 
    226238 
    227 The GYRE configuration \citep{Levy_al_OM10} has been built to simulate 
    228 the seasonal cycle of a double-gyre box model. It consists in an idealized domain  
    229 similar to that used in the studies of \citet{Drijfhout_JPO94} and \citet{Hazeleger_Drijfhout_JPO98,  
    230 Hazeleger_Drijfhout_JPO99, Hazeleger_Drijfhout_JGR00, Hazeleger_Drijfhout_JPO00},  
    231 over which an analytical seasonal forcing is applied. This allows to investigate the  
    232 spontaneous generation of a large number of interacting, transient mesoscale eddies  
     239The GYRE configuration \citep{Levy_al_OM10} has been built to 
     240simulate the seasonal cycle of a double-gyre box model. 
     241It consists in an idealized domain similar to that used in the studies of \citet{Drijfhout_JPO94} and 
     242\citet{Hazeleger_Drijfhout_JPO98, Hazeleger_Drijfhout_JPO99, Hazeleger_Drijfhout_JGR00, Hazeleger_Drijfhout_JPO00}, 
     243over which an analytical seasonal forcing is applied. 
     244This allows to investigate the spontaneous generation of a large number of interacting, transient mesoscale eddies  
    233245and their contribution to the large scale circulation.  
    234246 
    235 The domain geometry is a closed rectangular basin on the $\beta$-plane centred  
    236 at $\sim$ 30\degN and rotated by 45\deg, 3180~km long, 2120~km wide  
    237 and 4~km deep (\autoref{fig:MISC_strait_hand}).  
    238 The domain is bounded by vertical walls and by a flat bottom. The configuration is  
    239 meant to represent an idealized North Atlantic or North Pacific basin.  
    240 The circulation is forced by analytical profiles of wind and buoyancy fluxes.  
    241 The applied forcings vary seasonally in a sinusoidal manner between winter  
    242 and summer extrema \citep{Levy_al_OM10}.  
    243 The wind stress is zonal and its curl changes sign at 22\degN and 36\degN.  
    244 It forces a subpolar gyre in the north, a subtropical gyre in the wider part of the domain  
    245 and a small recirculation gyre in the southern corner.  
    246 The net heat flux takes the form of a restoring toward a zonal apparent air  
    247 temperature profile. A portion of the net heat flux which comes from the solar radiation 
    248 is allowed to penetrate within the water column.  
    249 The fresh water flux is also prescribed and varies zonally.  
    250 It is determined such as, at each time step, the basin-integrated flux is zero.  
    251 The basin is initialised at rest with vertical profiles of temperature and salinity  
    252 uniformly applied to the whole domain. 
    253  
    254 The GYRE configuration is set like an analytical configuration. Through \np{ln\_read\_cfg}\forcode{ = .false.} in \textit{namcfg} namelist defined in the reference configuration \path{CONFIG/GYRE/EXP00/namelist_cfg} anaylitical definition of grid in GYRE is done in usrdef\_hrg, usrdef\_zgr routines. Its horizontal resolution  
    255 (and thus the size of the domain) is determined by setting \np{nn\_GYRE} in  \ngn{namusr\_def}: \\ 
     247The domain geometry is a closed rectangular basin on the $\beta$-plane centred at $\sim$ 30\degN and 
     248rotated by 45\deg, 3180~km long, 2120~km wide and 4~km deep (\autoref{fig:MISC_strait_hand}). 
     249The domain is bounded by vertical walls and by a flat bottom. 
     250The configuration is meant to represent an idealized North Atlantic or North Pacific basin. 
     251The circulation is forced by analytical profiles of wind and buoyancy fluxes. 
     252The applied forcings vary seasonally in a sinusoidal manner between winter and summer extrema \citep{Levy_al_OM10}.  
     253The wind stress is zonal and its curl changes sign at 22\degN and 36\degN. 
     254It forces a subpolar gyre in the north, a subtropical gyre in the wider part of the domain and 
     255a small recirculation gyre in the southern corner. 
     256The net heat flux takes the form of a restoring toward a zonal apparent air temperature profile. 
     257A portion of the net heat flux which comes from the solar radiation is allowed to penetrate within the water column. 
     258The fresh water flux is also prescribed and varies zonally. 
     259It is determined such as, at each time step, the basin-integrated flux is zero. 
     260The basin is initialised at rest with vertical profiles of temperature and salinity uniformly applied to 
     261the whole domain. 
     262 
     263The GYRE configuration is set like an analytical configuration. 
     264Through \np{ln\_read\_cfg}\forcode{ = .false.} in \textit{namcfg} namelist defined in 
     265the reference configuration \path{CONFIG/GYRE/EXP00/namelist_cfg} 
     266analytical definition of grid in GYRE is done in usrdef\_hrg, usrdef\_zgr routines. 
     267Its horizontal resolution (and thus the size of the domain) is determined by 
     268setting \np{nn\_GYRE} in \ngn{namusr\_def}: \\ 
    256269\np{jpiglo} $= 30 \times$ \np{nn\_GYRE} + 2   \\ 
    257270\np{jpjglo} $= 20 \times$ \np{nn\_GYRE} + 2   \\ 
    258 Obviously, the namelist parameters have to be adjusted to the chosen resolution, see the Configurations  
    259 pages on the NEMO web site (Using NEMO\/Configurations) . 
     271Obviously, the namelist parameters have to be adjusted to the chosen resolution, 
     272see the Configurations pages on the NEMO web site (Using NEMO\/Configurations). 
    260273In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}\forcode{ = 31}) (\autoref{fig:zgr}). 
    261274 
    262 The GYRE configuration is also used in benchmark test as it is very simple to increase  
    263 its resolution and as it does not requires any input file. For example, keeping a same model size  
    264 on each processor while increasing the number of processor used is very easy, even though the  
    265 physical integrity of the solution can be compromised. Benchmark is activate via \np{ln\_bench}\forcode{ = .true.} in \ngn{namusr\_def} in namelist \path{CONFIG/GYRE/EXP00/namelist_cfg}. 
    266  
    267 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    268 \begin{figure}[!t]   \begin{center} 
    269 \includegraphics[width=1.0\textwidth]{Fig_GYRE} 
    270 \caption{  \protect\label{fig:GYRE}    
    271 Snapshot of relative vorticity at the surface of the model domain  
    272 in GYRE R9, R27 and R54. From \citet{Levy_al_OM10}.} 
    273 \end{center}   \end{figure} 
     275The GYRE configuration is also used in benchmark test as it is very simple to increase its resolution and 
     276as it does not requires any input file. 
     277For example, keeping a same model size on each processor while increasing the number of processor used is very easy, 
     278even though the physical integrity of the solution can be compromised. 
     279Benchmark is activate via \np{ln\_bench}\forcode{ = .true.} in \ngn{namusr\_def} in 
     280namelist \path{CONFIG/GYRE/EXP00/namelist_cfg}. 
     281 
     282%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     283\begin{figure}[!t] 
     284  \begin{center} 
     285    \includegraphics[width=1.0\textwidth]{Fig_GYRE} 
     286    \caption{  \protect\label{fig:GYRE} 
     287      Snapshot of relative vorticity at the surface of the model domain in GYRE R9, R27 and R54. 
     288      From \citet{Levy_al_OM10}.} 
     289  \end{center} 
     290\end{figure} 
    274291%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    275292 
    … …  
    280297\label{sec:MISC_config_AMM} 
    281298 
    282 The AMM, Atlantic Margins Model, is a regional model covering the 
    283 Northwest European Shelf domain on a regular lat-lon grid at 
    284 approximately 12km horizontal resolution. The appropriate  
    285 \textit{\&namcfg} namelist  is available in \textit{CONFIG/AMM12/EXP00/namelist\_cfg}. 
     299The AMM, Atlantic Margins Model, is a regional model covering the Northwest European Shelf domain on 
     300a regular lat-lon grid at approximately 12km horizontal resolution. 
     301The appropriate \textit{\&namcfg} namelist  is available in \textit{CONFIG/AMM12/EXP00/namelist\_cfg}. 
    286302It is used to build the correct dimensions of the AMM domain. 
    287303 
    288 This configuration tests several features of NEMO functionality specific 
    289 to the shelf seas. 
    290 In particular, the AMM uses $S$-coordinates in the vertical rather than 
    291 $z$-coordinates and is forced with tidal lateral boundary conditions 
    292 using a flather boundary condition from the BDY module. 
    293 The AMM configuration  uses the GLS (\key{zdfgls}) turbulence scheme, the 
    294 VVL non-linear free surface(\key{vvl}) and time-splitting 
    295 (\key{dynspg\_ts}). 
    296  
    297 In addition to the tidal boundary condition the model may also take 
    298 open boundary conditions from a North Atlantic model. Boundaries may be 
    299 completely omitted by setting \np{ln\_bdy} to false. 
    300 Sample surface fluxes, river forcing and a sample initial restart file 
    301 are included to test a realistic model run. The Baltic boundary is 
    302 included within the river input file and is specified as a river source. 
    303 Unlike ordinary river points the Baltic inputs also include salinity and 
    304 temperature data. 
     304This configuration tests several features of NEMO functionality specific to the shelf seas. 
     305In particular, the AMM uses $S$-coordinates in the vertical rather than $z$-coordinates and 
     306is forced with tidal lateral boundary conditions using a flather boundary condition from the BDY module. 
     307The AMM configuration uses the GLS (\key{zdfgls}) turbulence scheme, 
     308the VVL non-linear free surface(\key{vvl}) and time-splitting (\key{dynspg\_ts}). 
     309 
     310In addition to the tidal boundary condition the model may also take open boundary conditions from 
     311a North Atlantic model. 
     312Boundaries may be completely omitted by setting \np{ln\_bdy} to false. 
     313Sample surface fluxes, river forcing and a sample initial restart file are included to test a realistic model run. 
     314The Baltic boundary is included within the river input file and is specified as a river source. 
     315Unlike ordinary river points the Baltic inputs also include salinity and temperature data. 
    305316 
    306317\end{document} 
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