Changeset 2376 for branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Chap_MISC.tex

Timestamp:

2010-11-11T18:01:29+01:00 (13 years ago)

Author:

gm

Message:

v3.3beta: better TKE description, CFG a new Chapter, and correction of Fig references

File:

• branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Chap_MISC.tex (modified) (7 diffs)

branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Chap_MISC.tex

@@ -58 +58 @@
 
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-\begin{figure}[!tbp] \label{Fig_MISC_strait_hand}  \begin{center}
+\begin{figure}[!tbp]     \begin{center}
 \includegraphics[width=0.80\textwidth]{./TexFiles/Figures/Fig_Gibraltar.pdf}
 \includegraphics[width=0.80\textwidth]{./TexFiles/Figures/Fig_Gibraltar2.pdf}
-\caption {Example of the Gibraltar strait defined in a $1\deg \times 1\deg$ mesh. 
+\caption{   \label{Fig_MISC_strait_hand} 
+Example of the Gibraltar strait defined in a $1\deg \times 1\deg$ mesh. 
 \textit{Top}: using partially open cells. The meridional scale factor at $v$-point 
 is reduced on both sides of the strait to account for the real width of the strait 
@@ -134 +135 @@
 
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-\begin{figure}[!ht] \label{Fig_LBC_zoom}  \begin{center}
+\begin{figure}[!ht]    \begin{center}
 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_LBC_zoom.pdf}
-\caption {Position of a model domain compared to the data input domain when the zoom functionality is used.}
+\caption{   \label{Fig_LBC_zoom}
+Position of a model domain compared to the data input domain when the zoom functionality is used.}
 \end{center}   \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 
-
-% ================================================================
-% 1D model functionality
-% ================================================================
-\section{Water column model: 1D model (\key{c1d})}
-\label{MISC_1D}
-
-The 1D model option simulates a stand alone water column within the 3D \NEMO system. 
-It can be applied to the ocean alone or to the ocean-ice system and can include passive tracers 
-or a biogeochemical model. It is set up by defining the \key{c1d} CPP key. 
-The 1D model is a very useful tool  
-\textit{(a)} to learn about the physics and numerical treatment of vertical mixing processes ; 
-\textit{(b)} to investigate suitable parameterisations of unresolved turbulence (wind steering, 
-langmuir circulation, skin layers) ; 
-\textit{(c)} to compare the behaviour of different vertical mixing schemes  ; 
-\textit{(d)} to perform sensitivity studies on the vertical diffusion at a particular point of an ocean domain ; 
-\textit{(d)} to produce extra diagnostics, without the large memory requirement of the full 3D model.
-
-The methodology is based on the use of the zoom functionality over the smallest possible 
-domain : a 3 x 3 domain centred on the grid point of interest (see \S\ref{MISC_zoom}), 
-with some extra routines. There is no need to define a new mesh, bathymetry, 
-initial state or forcing, since the 1D model will use those of the configuration it is a zoom of. 
-The chosen grid point is set in par\_oce.F90 module by setting the jpizoom and jpjzoom 
-parameters to the indices of the location of the chosen grid point.
 
 % ================================================================
@@ -260 +238 @@
 The "bit comparison" option has been introduced in order to be able to check that 
 mono-processor and multi-processor runs give exactly the same results. 
+%THIS is to be updated with the mpp_sum_glo  introduced in v3.3
+% nn_bit_cmp  today only check that the nn_cla = 0 (no cross land advection)
 
 $\bullet$  Benchmark (\np{nn\_bench}). This option defines a benchmark run based on 
-a GYRE configuration in which the resolution remains the same whatever the domain 
-size. This allows a very large model domain to be used, just by changing the domain 
-size (\jp{jpiglo}, \jp{jpjglo}) and without adjusting either the time-step or the physical 
-parameterisations. 
+a GYRE configuration (see \S\ref{CFG_gyre}) in which the resolution remains the same 
+whatever the domain size. This allows a very large model domain to be used, just by 
+changing the domain size (\jp{jpiglo}, \jp{jpjglo}) and without adjusting either the time-step 
+or the physical parameterisations. 
 
 
@@ -607 +587 @@
 volume ratio of each processing region.
 
-\begin{table} 
-\begin{tabular}{lrrr}
+%------------------------------------------TABLE----------------------------------------------------
+\begin{table}  \begin{tabular}{lrrr}
 Filename & NetCDF3 & NetCDF4 & Reduction\\
          &filesize & filesize & \% \\
@@ -638 +618 @@
 ORCA2\_2d\_grid\_W\_0007.nc & 4416 & 1368 & 70\%\\
 \end{tabular}
-\caption{\label{Tab_NC4} Filesize comparison between NetCDF3 and NetCDF4 
-with chunking and compression}
+\caption{   \label{Tab_NC4} 
+Filesize comparison between NetCDF3 and NetCDF4 with chunking and compression}
 \end{table}
+%----------------------------------------------------------------------------------------------------
 
 Since version 3.2, an I/O server has been added which provides more
@@ -758 +739 @@
 %-------------------------------------------------------------------------------------------------------------
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-\begin{figure}[!t] \label{Fig_mask_subasins}  \begin{center}
+\begin{figure}[!t]     \begin{center}
 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_mask_subasins.pdf}
-\caption {Decomposition of the World Ocean (here ORCA2) into sub-basin used in to compute
+\caption{   \label{Fig_mask_subasins}
+Decomposition of the World Ocean (here ORCA2) into sub-basin used in to compute
 the heat and salt transports as well as the meridional stream-function: Atlantic basin (red), 
 Pacific basin (green), Indian basin (bleue), Indo-Pacific basin (bleue+green). 
@@ -931 +913 @@
 
 % ================================================================
-% predefined configurations
-% ================================================================
-\section{predefined configurations}
-\label{MISC_config}
-
-There is several predefined ocean configuration which use is controlled by a specific CPP key. 
-
-The key set the domain sizes (\jp{jpiglo}, \jp{jpjglo}, \jp{jpk}), the mesh and the bathymetry, 
-and, in some cases, add to the model physics some specific treatments.
-
-% -------------------------------------------------------------------------------------------------------------
-%       ORCA family configurations
-% -------------------------------------------------------------------------------------------------------------
-\subsection{ORCA family: global ocean with tripolar grid}
-\label{MISC_config_orca}
-
-The NEMO system is provided with four built-in ORCA configurations which differ in the 
-horizontal resolution used:
-\begin{description}
-\item[\key{orca\_r4}]  \jp{cp\_cfg}~=~orca ; \jp{jp\_cfg}~=~4
-\item[\key{orca\_r2}]  \jp{cp\_cfg}~=~orca ; \jp{jp\_cfg}~=~2
-\item[\key{orca\_r1}]  \jp{cp\_cfg}~=~orca ; \jp{jp\_cfg}~=~1
-\item[\key{orca\_r05}]  \jp{cp\_cfg}~=~orca ; \jp{jp\_cfg}~=~05
-\item[\key{orca\_r025}]  \jp{cp\_cfg}~=~orca ; \jp{jp\_cfg}~=~025
-\end{description}
-
-\subsubsection{ORCA mesh}
-
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-\begin{figure}[!t] \label{Fig_MISC_ORCA_msh}  \begin{center}
-\includegraphics[width=0.98\textwidth]{./TexFiles/Figures/Fig_ORCA_NH_mesh.pdf}
-\caption {ORCA mesh conception. The departure from an isotropic Mercator grid start poleward of 20\deg N.
-The two "north pole" are the foci of a series of embedded ellipses (blue curves) 
-which are determined analytically and form the i-lines of the ORCA mesh (pseudo latitudes). 
-Then, following \citet{Madec_Imbard_CD96}, the normal to the series of ellipses (red curves) is computed 
-which provide the j-lines of the mesh (pseudo longitudes).
- }
-\end{center}   \end{figure}
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-
-
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-\begin{figure}[!tbp] \label{Fig_MISC_ORCA_e1e2}  \begin{center}
-\includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_ORCA_NH_msh05_e1_e2.pdf}
-\includegraphics[width=0.80\textwidth]{./TexFiles/Figures/Fig_ORCA_aniso.pdf}
-\caption {\textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and 
-\textit{Bottom}: ratio of anisotropy ($e_1 / e_2$)
-for ORCA 0.5\deg ~mesh. South of 20\deg N a Mercator grid is used ($e_1 = e_2$) 
-so that the anisotropy ratio is 1. Poleward of 20\deg N, the two "north pole" 
-introduce a weak anisotropy over the ocean areas ($< 1.2$) except in vicinity of Victoria Island 
-(Canadian Arctic Archipelago). }
-\end{center}   \end{figure}
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-
-%--------------------------------------------------TABLE--------------------------------------------------
-\begin{table}[htbp]  \label{Tab_ORCA}
-\begin{center}
-\begin{tabular}{ccccc}
-key                         & \jp{jp\_cfg} &  \jp{jpiglo} & \jp{jpiglo} &       \\  
-\hline  \hline
-\key{orca\_r4}        &        4         &         92     &      76      &       \\
-\key{orca\_r2}       &        2         &       182     &    149      &        \\
-%\key{orca\_r1}       &        1         &       362     &     511     &        \\
-\key{orca\_r05}     &        05       &       722     &     261     &        \\
-\key{orca\_r025}   &        025     &      1442    &   1021     &        \\
-%\key{orca\_r8}       &        8         &      2882    &   2042     &        \\
-%\key{orca\_r12}     &      12         &      4322    &   3062      &       \\
-\hline
-\hline
-\end{tabular}
-\caption {Set of predefined ORCA parameters. }
-\end{center}
-\end{table}
-%--------------------------------------------------------------------------------------------------------------
-
-The tripolar grid used in ORCA configuration ....
-
-NB: the two north poles position has been chosen to minimise the anisotropy ratio in 
-the Gulf Stream and kuroshio areas, two highly turbulent regions.
-
-ORCA~2 : a $2\deg$ zonal resolution, and a meridional resolution varying from $0.5\deg$ at the 
-equator to $2\deg cos\phi$ south of $20\deg$S (Fig. 1). The grid features two points of convergence in the 
-Northern Hemisphere, both situated on continents. Minimum resolution in high latitudes is about 
-65~km in the Arctic and 50~km in the Antarctic. Local mesh refinements are applied to the 
-Mediterranean, Red, Black and Caspian Seas. None of them appears to be of particular 
-importance for the study of high latitude climate, but the fine resolution is needed in order to have 
-their local circulation and their role in the World Ocean's circulation considered correctly. 
-
-
- 
-ORCA2-LIM (global ocean sea-ice configuration \citep{Timmermann_al_OM05}. 
-The horizontal mesh is based on a $2\deg \times 2\deg$ Mercator grid ($i.e.$ same zonal and 
-meridional grid spacing) which has been modified poleward  
-of $20\deg$N in order to include two numerical inland poles \citep{Murray_JCP96}. 
-This modification is semi-analytical \citep{Madec_Imbard_CD96} 
-and based on a series of embedded ellipses. It insures that the mesh remains 
-close to isotropy and that the smallest grid cell is along Antarctica. 
-In order to refine the meridional resolution up to $0.5\deg$ at the equator, 
-additional local transformations were applied with in the Tropics. 
-Local mesh refinements are also applied to the Mediterranean, Red, Black 
-and Caspian Seas so that the resolution is $1\deg \time 1\deg$ there. 
-There are 31 levels in the vertical, with the highest resolution (10m) 
-in the upper 150m. The bottom topography and the coastlines are derived 
-from the global atlas of Smith and Sandwell (1997).
-
-\key{orca\_lev10} 10 time more vertical levels
-
-\key{agrif}  : ORCA2-LIM plus an AGRIF zoom over the Agulhas current area
-
-\key{arctic}, \key{antarctic}  (not used in ORCA\_R4)
-
-
-We thus only provide a brief introduction in this chapter. 
-The global coupled ocean-ice configuration is very similar to that used as part of the climate 
-model developed at GFDL for the 4th IPCC assessment of climate change (Griffies et al., 2005; 
-Gnanadesikan et al., 2006). 
-The ORCA2-LIM configuration is also the basis for the \NEMO contribution to the 
-Coordinate Ocean-ice Reference Experiments (COREs) documented in \citet{Griffies_al_OM09}. 
-These experiments employ the boundary forcing from \citet{Large_Yeager_Rep04} (see \S\ref{SBC_blk_core}), 
-which was developed for the purpose of running global coupled ocean-ice simulations without an 
-interactive atmosphere. This \citet{Large_Yeager_Rep04} dataset is available through the GFDL web 
-site \footnote{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}. 
-The "normal year" of \citet{Large_Yeager_Rep04} has been chosen of the \NEMO distribution 
-since release v3.3. 
-
-% -------------------------------------------------------------------------------------------------------------
-%       GYRE family configuration
-% -------------------------------------------------------------------------------------------------------------
-\subsection{GYRE family: double gyre basin (\key{gyre})}
-\label{MISC_config_gyre}
-
-The GYRE configuration \citep{Levy_al_OM10} have been built to simulated 
-the seasonal cycle of a double-gyre box model. It consist in an idealized domain 
-similar to that used in the studies of \citet{Drijfhout_JPO94} and \citet{Hazeleger_Drijfhout_JPO98, 
-Hazeleger_Drijfhout_JPO99, Hazeleger_Drijfhout_JGR00, Hazeleger_Drijfhout_JPO00}, 
-over which an analytical seasonal forcing is applied. This allows to investigate the 
-spontaneous generation of a large number of interacting, transient mesoscale eddies 
-and their contribution to the large scale circulation. 
-
-The domain geometry is a closed rectangular basin on the $\beta$-plane centred 
-at $\sim 30\deg$N and rotated by 45\deg, 3180~km long, 2120~km wide 
-and 4~km deep (Fig.~\ref{Fig_MISC_strait_hand}). 
-The domain is bounded by vertical walls and by a ßat bottom. The configuration is 
-meant to represent an idealized North Atlantic or North Pacific basin. 
-The circulation is forced by analytical profiles of wind and buoyancy ßuxes. 
-The applied forcings vary seasonally in a sinusoidal manner between winter 
-and summer extrema \citep{Levy_al_OM10}. 
-The wind stress is zonal and its curl changes sign at 22\deg N and 36\deg N. 
-It forces a subpolar gyre in the north, a subtropical gyre in the wider part of the domain 
-and a small recirculation gyre in the southern corner. 
-The net heat ßux takes the form of a restoring toward a zonal apparent air 
-temperature profile. A portion of the net heat ßux which comes from the solar radiation
-is allowed to penetrate within the water column. 
-The fresh water ßux is also prescribed and varies zonally. 
-It is determined such as, at each time step, the basin-integrated ßux is zero. 
-The basin is initialised at rest with vertical profiles of temperature and salinity 
-uniformly applied to the whole domain.
-
-The GYRE configuration is set through the \key{gyre} CPP key. Its horizontal resolution 
-(and thus the size of the domain) is determined by setting \jp{jp\_cfg} in \hf{par\_GYRE} file: \\
-\jp{jpiglo} $= 30 \times$ \jp{jp\_cfg} + 2   \\
-\jp{jpjglo} $= 20 \times$ \jp{jp\_cfg} + 2   \\
-Obviously, the namelist parameters have to be adjusted to the chosen resolution.
-In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}=31) (Fig.~\ref{Fig_zgr}).
-
-The GYRE configuration is also used in benchmark test as it is very simple to increase 
-its resolution and as it does not requires any input file. For example, keeping a same model size 
-on each processor while increasing the number of processor used is very easy, even though the 
-physical integrity of the solution can be compromised.
-
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-\begin{figure}[!t] \label{Fig_GYRE}  \begin{center}
-\includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_GYRE.pdf}
-\caption {Snapshot of relative vorticity at the surface of the model domain 
-in GYRE R9, R27 and R54. From \citet{Levy_al_OM10}.}
-\end{center}   \end{figure}
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-
-% -------------------------------------------------------------------------------------------------------------
-%       EEL family configuration
-% -------------------------------------------------------------------------------------------------------------
-\subsection{EEL family: periodic channel}
-\label{MISC_config_EEL}
-
-\begin{description}
-\item[\key{eel\_r2}]  
-\item[\key{eel\_r5}]  
-\item[\key{eel\_r6}]  
-\end{description}
-
-% -------------------------------------------------------------------------------------------------------------
-%       POMME configuration
-% -------------------------------------------------------------------------------------------------------------
-\subsection{POMME: mid-latitude sub-domain}
-\label{MISC_config_POMME}
-
-
-\key{pomme\_r025} 
-
-
-