Changeset 3989

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/NEMO_book.tex

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 \newcommand{\rou} [1] {\textit{#1}\index{Routines!#1}}            %module (routine)
 \newcommand{\hf} [1] {\textit{#1.h90}\index{h90 file!#1}}            %module (h90 files)
+\newcommand{\np} [1] {\textit{#1}\index{Namelist parameters!#1}}     %namelist parameter (nampar)
+\newcommand{\ngn} [1] {\textit{#1}\index{Namelist Group Name!#1}}    %namelist name (nampar)
+\newcommand{\np} [1] {\textit{#1}\index{Namelist variables!#1}}             %namelist variable
 \newcommand{\jp} [1] {\textit{#1}\index{Model parameters!#1}}        %model parameter (jp)
 \newcommand{\pp} [1] {\textit{#1}\index{Model parameters!#1}}        %namelist parameter (pp)
 …
 % ================================================================
 % ================================================================
 \begin{document}
 …
 \include{./TexFiles/Chapters/Chap_ZDF}       % Vertical diffusion
 \include{./TexFiles/Chapters/Chap_DIA}       % Miscellaneous topics
+\include{./TexFiles/Chapters/Chap_DIA}       % Outputs and Diagnostics
 \include{./TexFiles/Chapters/Chap_OBS}                  % Observation operator

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Chapters/Annex_ISO.tex

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 \minitoc
 \pagebreak
 \section{Choice of namelist parameters}
+\section{Choice of \ngn{namtra\_ldf} namelist parameters}
 %-----------------------------------------nam_traldf------------------------------------------------------
 \namdisplay{namtra_ldf}
 …
 \np{rn\_aeiv\_0}. If 2D-varying coefficients are set with
 \key{traldf\_c2d} then $A_l$ is reduced in proportion with horizontal
 scale factor according to \eqref{Eq_title} \footnote{Except in global
   $0.5^{\circ}$ runs (\key{orca\_r05}) with \key{traldf\_eiv}, where
+scale factor according to \eqref{Eq_title} \footnote{Except in global ORCA
+  $0.5^{\circ}$ runs with \key{traldf\_eiv}, where
   $A_l$ is set like $A_e$ but with a minimum vale of
   $100\;\mathrm{m}^2\;\mathrm{s}^{-1}$}. In idealised setups with
 \key{traldf\_c2d}, $A_e$ is reduced similarly, but if \key{traldf\_eiv}
+is set in the global configurations \key{orca\_r2}, \key{orca\_r1} or
+\key{orca\_r05} with \key{traldf\_c2d}, a horizontally varying $A_e$ is
+is set in the global configurations with \key{traldf\_c2d}, a horizontally varying $A_e$ is
 instead set from the Held-Larichev parameterisation\footnote{In this
   case, $A_e$ at low latitudes $|\theta|<20^{\circ}$ is further

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Chapters/Chap_ASM.tex

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 assimilation code.  The code can also output model background fields which are used
 as an input to data assimilation code. This is all controlled by the namelist
 \textit{nam\_asminc}.  There is a brief description of all the namelist options
+\textit{\ngn{nam\_asminc} }.  There is a brief description of all the namelist options
 provided.  To build the ASM code \key{asminc} must be set.
 …
 \label{ASM_details}
 Here we show an example namelist and the header of an example assimilation
+Here we show an example \ngn{namasm} namelist and the header of an example assimilation
 increments file on the ORCA2 grid.

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Chapters/Chap_CFG.tex

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 % ================================================================
 % Chapter Ñ Configurations
+% Chapter � Configurations
 % ================================================================
 \chapter{Configurations}
 …
 The purpose of this part of the manual is to introduce the \NEMO predefined configuration.
+The purpose of this part of the manual is to introduce the \NEMO reference configurations.
 These configurations are offered as means to explore various numerical and physical options,
 thus allowing the user to verify that the code is performing in a manner consistent with that
 we are running. This form of verification is critical as one adopts the code for his or her particular
 research purposes. The test cases also provide a sense for some of the options available
+in the code, though by no means are all options exercised in the predefined configurations.
+%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.
+in the code, though by no means are all options exercised in the reference configurations.
+Configuration is defined mainly through the \ngn{namcfg} namelist variables:
+%------------------------------------------namcfg----------------------------------------------------
+\namdisplay{namcfg}
+%-------------------------------------------------------------------------------------------------------------
 % ================================================================
 % 1D model configuration
 % ================================================================
 \section{Water column model: 1D model (C1D) (\key{c1d})}
+\section{Water column model: 1D model (C1D) (\key{c1d}) }
 \label{CFG_c1d}
 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.
+or a biogeochemical model. It is set up by defining the position of the 1D water column in the grid
+(see \textit{CONFIG/SHARED/namelist\_ref} ).
 The 1D model is a very useful tool
 \textit{(a)} to learn about the physics and numerical treatment of vertical mixing processes ;
 …
 The methodology is based on the use of the zoom functionality over the smallest possible
 domain : a 3x3 domain centred on the grid point of interest (see \S\ref{MISC_zoom}),
+domain : a 3x3 domain centered on the grid point of interest,
 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 \mdl{par\_oce} module by setting the \jp{jpizoom} and \jp{jpjzoom}
+The chosen grid point is set in \textit{\ngn{namcfg}} namelist by setting the \np{jpizoom} and \np{jpjzoom}
 parameters to the indices of the location of the chosen grid point.
 …
 % ORCA family configurations
 % ================================================================
 \section{ORCA family: global ocean with tripolar grid (\key{orca\_rX})}
+\section{ORCA family: global ocean with tripolar grid }
 \label{CFG_orca}
 …
 the LIM sea-ice model (ORCA-LIM) and possibly with PISCES biogeochemical model
 (ORCA-LIM-PISCES), using various resolutions.
+The appropriate \textit{\&namcfg} namelist is available in \textit{CONFIG/ORCA2\_LIM/EXP00/namelist\_cfg}
+for ORCA2 and in \textit{CONFIG/SHARED/README\_other\_configurations\_namelist\_namcfg}
+for other resolutions
 …
 The NEMO system is provided with five built-in ORCA configurations which differ in the
 horizontal resolution. The value of the resolution is given by the resolution at the Equator
 expressed in degrees. Each of configuration is set through a CPP key, \key{orca\_rX}
 (with X being an indicator of the resolution), which set the grid size and configuration
 name parameters  (Tab.~\ref{Tab_ORCA}).
+expressed in degrees. Each of configuration is set through the \textit{\ngn{namcfg}} namelist,
+which sets the grid size and configuration
+name parameters  (Tab. \ref{Tab_ORCA}).
+.
 …
 \begin{table}[!t]     \begin{center}
 \begin{tabular}{p{4cm} c c c c}
 CPP key                        & \jp{jp\_cfg} &  \jp{jpiglo} & \jp{jpiglo} &       \\
+Horizontal Grid                         & \np{jp\_cfg} &  \np{jpiglo} & \np{jpjglo} &       \\
 \hline  \hline
 \key{orca\_r4}        &        4         &         92     &      76      &       \\
 \key{orca\_r2}       &        2         &       182     &    149      &        \\
 \key{orca\_r1}       &        1         &       362     &     292     &        \\
 \key{orca\_r05}     &        05       &       722     &     511     &        \\
 \key{orca\_r025}   &        025     &      1442    &   1021     &        \\
+\~4\deg     &        4         &         92     &      76      &       \\
+\~2\deg        &        2         &       182     &    149      &        \\
+\~1\deg        &        1         &       362     &     292     &        \\
+\~0.5\deg     &        05       &       722     &     511     &        \\
+\~0.25\deg   &        025     &      1442    &   1021     &        \\
 %\key{orca\_r8}       &        8         &      2882    &   2042     &        \\
 %\key{orca\_r12}     &      12         &      4322    &   3062      &       \\
 …
 \caption{ \label{Tab_ORCA}
 Set of predefined parameters for ORCA family configurations.
 In all cases, the name of the configuration is set to "orca" ($i.e.$ \jp{cp\_cfg}~=~orca). }
+In all cases, the name of the configuration is set to "orca" ($i.e.$ \np{cp\_cfg}~=~orca). }
 \end{center}
 \end{table}
 …
 in the upper 150m (see Tab.~\ref{Tab_orca_zgr} and Fig.~\ref{Fig_zgr}).
 The bottom topography and the coastlines are derived from the global atlas of Smith and Sandwell (1997).
 The default forcing employ the boundary forcing from \citet{Large_Yeager_Rep04} (see \S\ref{SBC_blk_core}),
+The default forcing uses 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
 …
 ORCA\_R2 pre-defined configuration can also be run with an AGRIF zoom over the Agulhas
+current area ( \key{agrif}  defined) and,  by setting the key \key{arctic} or \key{antarctic},
+current area ( \key{agrif}  defined) and,  by setting the appropriate variables in
+\textit{\&namcfg}, see \textit{CONFIG/SHARED/namelist\_ref}
 a regional Arctic or peri-Antarctic configuration is extracted from an ORCA\_R2 or R05 configurations
 using sponge layers at open boundaries.
 …
 %       GYRE family: double gyre basin
 % -------------------------------------------------------------------------------------------------------------
 \section{GYRE family: double gyre basin (\key{gyre})}
+\section{GYRE family: double gyre basin }
 \label{CFG_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
+The GYRE configuration \citep{Levy_al_OM10} has been built to simulate
+the seasonal cycle of a double-gyre box model. It consists 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},
 …
 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 set through the \textit{\&namcfg} namelist defined in the reference
+configuration \textit{CONFIG/GYRE/EXP00/namelist\_cfg}. Its horizontal resolution
+(and thus the size of the domain) is determined by setting \np{jp\_cfg} : \\
+\np{jpiglo} $= 30 \times$ \np{jp\_cfg} + 2   \\
+\np{jpjglo} $= 20 \times$ \np{jp\_cfg} + 2   \\
+Obviously, the namelist parameters have to be adjusted to the chosen resolution, see the Configurations
+pages on the NEMO web site (Using NEMO\/Configurations) .
+In the vertical, GYRE uses the default 30 ocean levels (\pp{jpk}=31) (Fig.~\ref{Fig_zgr}).
 The GYRE configuration is also used in benchmark test as it is very simple to increase
 …
 \begin{description}
 \item[\key{eel\_r2}]  to be described....
 \item[\key{eel\_r5}]
 \item[\key{eel\_r6}]
+\item[eel\_r2]  to be described....
+\item[eel\_r5]
+\item[eel\_r6]
 \end{description}
+The appropriate \textit{\&namcfg} namelists are available in
+\textit{CONFIG/SHARED/README\_other\_configurations\_namelist\_namcfg}
 % -------------------------------------------------------------------------------------------------------------
 %       AMM configuration
 % -------------------------------------------------------------------------------------------------------------
 \section{AMM: atlantic margin configuration (\key{amm\_12km})}
+\section{AMM: atlantic margin configuration }
 \label{MISC_config_AMM}
 The AMM, Atlantic Margins Model, is a regional model covering the
 Northwest European Shelf domain on a regular lat-lon grid at
+approximately 12km horizontal resolution. The key \key{amm\_12km}
+is used to create the correct dimensions of the AMM domain.
+approximately 12km horizontal resolution. The appropriate
+\textit{\&namcfg} namelist  is available in \textit{CONFIG/AMM12/EXP00/namelist\_cfg}.
+It is used to build the correct dimensions of the AMM domain.
 This configuration tests several features of NEMO functionality specific

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Chapters/Chap_DIA.tex

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 % ================================================================
 % Chapter Ñ I/O & Diagnostics
+% Chapter � I/O & Diagnostics
 % ================================================================
 \chapter{Ouput and Diagnostics (IOM, DIA, TRD, FLO)}
 …
 set via an equivalent and identically named namelist to \textit{namnc4}
 in \np{xmlio\_server.def}. Typically this namelist serves the mean files
 whilst the \np{ namnc4} in the main namelist file continues to serve the
+whilst the \ngn{ namnc4} in the main namelist file continues to serve the
 restart files. This duplication is unfortunate but appropriate since, if
 using io\_servers, the domain sizes of the individual files produced by the
 …
 trend of the dynamics and/or temperature and salinity time evolution equations
 is stored in three-dimensional arrays just after their computation ($i.e.$ at the end
+of each $dyn\cdots.F90$ and/or $tra\cdots.F90$ routines). These trends are then
+of each $dyn\cdots.F90$ and/or $tra\cdots.F90$ routines). Options are defined by
+\ngn{namtrd} namelist variables. These trends are then
 used in \mdl{trdmod} (see TRD directory) every \textit{nn\_trd } time-steps.
 …
 The on-line computation of floats advected either by the three dimensional velocity
 field or constraint to remain at a given depth ($w = 0$ in the computation) have been
+introduced in the system during the CLIPPER project. The algorithm used is based
+introduced in the system during the CLIPPER project. Options are defined by \ngn{namflo}
+namelis variables. The algorithm used is based
 either on the work of \cite{Blanke_Raynaud_JPO97} (default option), or on a $4^th$
 Runge-Hutta algorithm (\np{ln\_flork4}=true). Note that the \cite{Blanke_Raynaud_JPO97}
 …
 In case of Ariane convention, input filename is \np{"init\_float\_ariane"}. Its format is:
+In case of Ariane convention, input filename is \np{init\_float\_ariane}. Its format is:
 \texttt{ I J K nisobfl itrash itrash }
 …
 In the other case ( longitude and latitude ), input filename is \np{"init\_float"}. Its format is:
+In the other case ( longitude and latitude ), input filename is init\_float. Its format is:
 \texttt{ Long Lat depth nisobfl ngrpfl itrash}
 …
 \np{jpnfl} is the total number of floats during the run.
 When initial positions are read in a restart file ( \np{ln\_rstflo= .TRUE.} ),  \np{jpnflnewflo}
+When initial positions are read in a restart file ( \np{ln\_rstflo}= .TRUE. ),  \np{jpnflnewflo}
 can be added in the initialization file.
 …
 is the frequency of creation of the float restart file.
 Output data can be written in ascii files (\np{ln\_flo\_ascii = .TRUE.} ). In that case,
 output filename is \np{is trajec\_float}.
 Another possiblity of writing format is Netcdf (\np{ln\_flo\_ascii = .FALSE.} ). There are 2 possibilities:
  - if (\key{iomput}) is used, outputs are selected in  \np{iodef.xml}. Here it is an example of specification
+Output data can be written in ascii files (\np{ln\_flo\_ascii} = .TRUE. ). In that case,
+output filename is trajec\_float.
+Another possiblity of writing format is Netcdf (\np{ln\_flo\_ascii} = .FALSE. ). There are 2 possibilities:
+ - if (\key{iomput}) is used, outputs are selected in  iodef.xml. Here it is an example of specification
    to put in files description section:
 …
  -  if (\key{iomput}) is not used, a file called \np{trajec\_float.nc} will be created by IOIPSL library.
+ -  if (\key{iomput}) is not used, a file called trajec\_float.nc will be created by IOIPSL library.
 …
 %----------------------------------------------------------------------------------------------------------
+Concerning the on-line Harmonic analysis, some parameters are available in namelist:
+Concerning the on-line Harmonic analysis, some parameters are available in namelist
+\ngn{namdia\_harm} :
 - \texttt{nit000\_han} is the first time step used for harmonic analysis
 …
 Namelist parameters control how frequently the flows are summed and the time scales over which
  they are averaged, as well as the level of output for debugging:
+Namelist variables in \ngn{namdct} control how frequently the flows are summed
+and the time scales over which they are averaged, as well as the level of output for debugging:
 %------------------------------------------namdct----------------------------------------------------
 …
 The poleward heat and salt transports, their advective and diffusive component, and
 the meriodional stream function can be computed on-line in \mdl{diaptr} by setting
 \np{ln\_diaptr} to true (see the \textit{namptr} namelist below).
+the meriodional stream function can be computed on-line in \mdl{diaptr}
+\np{ln\_diaptr} to true (see the \textit{\ngn{namptr} } namelist below).
 When \np{ln\_subbas}~=~true, transports and stream function are computed
 for the Atlantic, Indian, Pacific and Indo-Pacific Oceans (defined north of 30\deg S)

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Chapters/Chap_DOM.tex

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 % ================================================================
 % Chapter 2 Ñ Space and Time Domain (DOM)
+% Chapter 2 � Space and Time Domain (DOM)
 % ================================================================
 \chapter{Space Domain (DOM) }
 …
 directory routines as well as the DOM (DOMain) directory.
 $\ $\newline    % force a new ligne
+$\ $\newline    % force a new lign
 % ================================================================
 …
 \label{DOM_size}
+The total size of the computational domain is set by the parameters \jp{jpiglo},
+\jp{jpjglo} and \jp{jpk} in the $i$, $j$ and $k$ directions respectively. They are
+given as parameters in the \mdl{par\_oce} module\footnote{When a specific
+configuration is used (ORCA2 global ocean, etc...) the parameter are actually
+defined in additional files introduced by \mdl{par\_oce} module via CPP
+\textit{include} command. For example, ORCA2 parameters are set in
+\textit{par\_ORCA\_R2.h90} file}. The use of parameters rather than variables
+(together with dynamic allocation of arrays) was chosen because it ensured that
+the compiler would optimize the executable code efficiently, especially on vector
+machines (optimization may be less efficient when the problem size is unknown
+at the time of compilation). Nevertheless, it is possible to set up the code with full
+dynamical allocation by using the AGRIF packaged \citep{Debreu_al_CG2008}.
+%
+\gmcomment{  add the following ref
+\colorbox{yellow}{(ref part of the doc)} }
+%
+Note that are other parameters in \mdl{par\_oce} that refer to the domain size.
+The two parameters $jpidta$ and $jpjdta$ may be larger than $jpiglo$, $jpjglo$
+The total size of the computational domain is set by the parameters \np{jpiglo},
+\np{jpjglo} and \np{jpkdta} in the $i$, $j$ and $k$ directions respectively. They are
+given as namelist variables in the \ngn{namcfg} namelist.
+Note that are other namelist variables in the \ngn{namcfg} namelist that refer to
+ the domain size.
+The two variables \np{jpidta} and \np{jpjdta} may be larger than \np{jpiglo}, \np{jpjglo}
 when the user wants to use only a sub-region of a given configuration. This is
 the "zoom" capability described in \S\ref{MISC_zoom}. In most applications of
 …
 $\ $\newline    % force a new ligne
+$\ $\newline    % force a new lign
 % ================================================================
 …
 The user has three options available in defining a horizontal grid, which involve
 the parameter $jphgr\_mesh$ of the \mdl{par\_oce} module.
+the namelist variable \np{jphgr\_mesh} of the \ngn{namcfg} namelist.
 \begin{description}
 \item[\jp{jphgr\_mesh}=0]  The most general curvilinear orthogonal grids.
+\item[\np{jphgr\_mesh}=0]  The most general curvilinear orthogonal grids.
 The coordinates and their first derivatives with respect to $i$ and $j$ are provided
 in a input file (\ifile{coordinates}), read in \rou{hgr\_read} subroutine of the domhgr module.
 \item[\jp{jphgr\_mesh}=1 to 5] A few simple analytical grids are provided (see below).
+\item[\np{jphgr\_mesh}=1 to 5] A few simple analytical grids are provided (see below).
 For other analytical grids, the \mdl{domhgr} module must be modified by the user.
 \end{description}
 There are two simple cases of geographical grids on the sphere. With
 \jp{jphgr\_mesh}=1, the grid (expressed in degrees) is regular in space,
 with grid sizes specified by parameters \pp{ppe1\_deg} and \pp{ppe2\_deg},
+\np{jphgr\_mesh}=1, the grid (expressed in degrees) is regular in space,
+with grid sizes specified by parameters \np{ppe1\_deg} and \np{ppe2\_deg},
 respectively. Such a geographical grid can be very anisotropic at high latitudes
 because of the convergence of meridians (the zonal scale factors $e_1$
 become much smaller than the meridional scale factors $e_2$). The Mercator
 grid (\jp{jphgr\_mesh}=4) avoids this anisotropy by refining the meridional scale
+grid (\np{jphgr\_mesh}=4) avoids this anisotropy by refining the meridional scale
 factors in the same way as the zonal ones. In this case, meridional scale factors
 and latitudes are calculated analytically using the formulae appropriate for
 a Mercator projection, based on \pp{ppe1\_deg} which is a reference grid spacing
+a Mercator projection, based on \np{ppe1\_deg} which is a reference grid spacing
 at the equator (this applies even when the geographical equator is situated outside
 the model domain).
 …
 \gmcomment{ give here the analytical expression of the Mercator mesh}
 %%%
 In these two cases (\jp{jphgr\_mesh}=1 or 4), the grid position is defined by the
 longitude and latitude of the south-westernmost point (\pp{ppglamt0}
 and \pp{ppgphi0}). Note that for the Mercator grid the user need only provide
+In these two cases (\np{jphgr\_mesh}=1 or 4), the grid position is defined by the
+longitude and latitude of the south-westernmost point (\np{ppglamt0}
+and \np{ppgphi0}). Note that for the Mercator grid the user need only provide
 an approximate starting latitude: the real latitude will be recalculated analytically,
 in order to ensure that the equator corresponds to line passing through $t$-
 …
 Rectangular grids ignoring the spherical geometry are defined with
 \jp{jphgr\_mesh} = 2, 3, 5. The domain is either an $f$-plane (\jp{jphgr\_mesh} = 2,
 Coriolis factor is constant) or a beta-plane (\jp{jphgr\_mesh} = 3, the Coriolis factor
+\np{jphgr\_mesh} = 2, 3, 5. The domain is either an $f$-plane (\np{jphgr\_mesh} = 2,
+Coriolis factor is constant) or a beta-plane (\np{jphgr\_mesh} = 3, the Coriolis factor
 is linear in the $j$-direction). The grid size is uniform in meter in each direction,
 and given by the parameters \pp{ppe1\_m} and \pp{ppe2\_m} respectively.
+and given by the parameters \np{ppe1\_m} and \np{ppe2\_m} respectively.
 The zonal grid coordinate (\textit{glam} arrays) is in kilometers, starting at zero
 with the first $t$-point. The meridional coordinate (gphi. arrays) is in kilometers,
 and the second $t$-point corresponds to coordinate $gphit=0$. The input
 parameter \pp{ppglam0} is ignored. \pp{ppgphi0} is used to set the reference
+variable \np{ppglam0} is ignored. \np{ppgphi0} is used to set the reference
 latitude for computation of the Coriolis parameter. In the case of the beta plane,
 \pp{ppgphi0} corresponds to the center of the domain. Finally, the special case
 \jp{jphgr\_mesh}=5 corresponds to a beta plane in a rotated domain for the
+\np{ppgphi0} corresponds to the center of the domain. Finally, the special case
+\np{jphgr\_mesh}=5 corresponds to a beta plane in a rotated domain for the
 GYRE configuration, representing a classical mid-latitude double gyre system.
 The rotation allows us to maximize the jet length relative to the gyre areas
 …
 The choice of the grid must be consistent with the boundary conditions specified
 by the parameter \jp{jperio} (see {\S\ref{LBC}).
+by the parameter \np{jperio} (see {\S\ref{LBC}).
 % -------------------------------------------------------------------------------------------------------------
 …
 All the arrays relating to a particular ocean model configuration (grid-point
 position, scale factors, masks) can be saved in files if $\np{nn\_msh} \not= 0$
 (namelist parameter). This can be particularly useful for plots and off-line
+(namelist variable in \ngn{namdom}). This can be particularly useful for plots and off-line
 diagnostics. In some cases, the user may choose to make a local modification
 of a scale factor in the code. This is the case in global configurations when
 …
 the output grid written when $\np{nn\_msh} \not=0$ is no more equal to the input grid.
 $\ $\newline    % force a new ligne
+$\ $\newline    % force a new lign
 % ================================================================
 …
 %-------------------------------------------------------------------------------------------------------------
+Variables are defined through the \ngn{namzgr} and \ngn{namdom} namelists.
 In the vertical, the model mesh is determined by four things:
 (1) the bathymetry given in meters ;
 …
 \item[\np{nn\_bathy} = 0] a flat-bottom domain is defined. The total depth $z_w (jpk)$
 is given by the coordinate transformation. The domain can either be a closed
 basin or a periodic channel depending on the parameter \jp{jperio}.
+basin or a periodic channel depending on the parameter \np{jperio}.
 \item[\np{nn\_bathy} = -1] a domain with a bump of topography one third of the
 domain width at the central latitude. This is meant for the "EEL-R5" configuration,
 …
 vertical scale factors. The user must provide the analytical expression of both
 $z_0$ and its first derivative with respect to $k$. This is done in routine \mdl{domzgr}
 through statement functions, using parameters provided in the \textit{par\_oce.h90} file.
 It is possible to define a simple regular vertical grid by giving zero stretching (\pp{ppacr=0}).
 In that case, the parameters \jp{jpk} (number of $w$-levels) and \pp{pphmax}
+through statement functions, using parameters provided in the \ngn{namcfg} namelist.
+It is possible to define a simple regular vertical grid by giving zero stretching (\np{ppacr=0}).
+In that case, the parameters \jp{jpk} (number of $w$-levels) and \np{pphmax}
 (total ocean depth in meters) fully define the grid.
 …
 scale factors as a function of the model levels are shown in Fig.~\ref{Fig_zgr} and
 given in Table \ref{Tab_orca_zgr}. Those values correspond to the parameters
 \pp{ppsur}, \pp{ppa0}, \pp{ppa1}, \pp{ppkth} in the parameter file \mdl{par\_oce}.
+\np{ppsur}, \np{ppa0}, \np{ppa1}, \np{ppkth} in \ngn{namcfg} namelist.
 Rather than entering parameters $h_{sur}$, $h_{0}$, and $h_{1}$ directly, it is
 possible to recalculate them. In that case the user sets
 \pp{ppsur}=\pp{ppa0}=\pp{ppa1}=\pp{pp\_to\_be\_computed}, in \mdl{par\_oce},
+\np{ppsur}=\np{ppa0}=\np{ppa1}=999999., in \ngn{namcfg} namelist,
 and specifies instead the four following parameters:
 \begin{itemize}
 \item    \pp{ppacr}=$h_{cr} $: stretching factor (nondimensional). The larger
 \pp{ppacr}, the smaller the stretching. Values from $3$ to $10$ are usual.
 \item    \pp{ppkth}=$h_{th} $: is approximately the model level at which maximum
+\item    \np{ppacr}=$h_{cr} $: stretching factor (nondimensional). The larger
+\np{ppacr}, the smaller the stretching. Values from $3$ to $10$ are usual.
+\item    \np{ppkth}=$h_{th} $: is approximately the model level at which maximum
 stretching occurs (nondimensional, usually of order 1/2 or 2/3 of \jp{jpk})
 \item    \pp{ppdzmin}: minimum thickness for the top layer (in meters)
 \item    \pp{pphmax}: total depth of the ocean (meters).
+\item    \np{ppdzmin}: minimum thickness for the top layer (in meters)
+\item    \np{pphmax}: total depth of the ocean (meters).
 \end{itemize}
 As an example, for the $45$ layers used in the DRAKKAR configuration those
 parameters are: \jp{jpk}=46, \pp{ppacr}=9, \pp{ppkth}=23.563, \pp{ppdzmin}=6m,
 \pp{pphmax}=5750m.
+parameters are: \jp{jpk}=46, \np{ppacr}=9, \np{ppkth}=23.563, \np{ppdzmin}=6m,
+\np{pphmax}=5750m.
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 …
 is allowed to have either a smaller or larger thickness than $e_{3t}(jpk)$: the
 maximum thickness allowed is $2*e_{3t}(jpk-1)$. This has to be kept in mind when
+specifying the maximum depth \pp{pphmax} in partial steps: for example, with
+\pp{pphmax}$=5750~m$ for the DRAKKAR 45 layer grid, the maximum ocean depth
+specifying values in \ngn{namdom} namelist, as the maximum depth \np{pphmax}
+in partial steps: for example, with
+\np{pphmax}$=5750~m$ for the DRAKKAR 45 layer grid, the maximum ocean depth
 allowed is actually $6000~m$ (the default thickness $e_{3t}(jpk-1)$ being $250~m$).
 Two variables in the namdom namelist are used to define the partial step
 …
 \namdisplay{namzgr_sco}
 %--------------------------------------------------------------------------------------------------------------
+Options are defined in \ngn{namzgr\_sco}.
 In $s$-coordinate (\np{ln\_sco}~=~true), the depth and thickness of the model
 levels are defined from the product of a depth field and either a stretching
 …
 %------------------------------------------------------------------------------------------
+Options are defined in \ngn{namtsd}.
 By default, the ocean start from rest (the velocity field is set to zero) and the initialization of
 temperature and salinity fields is controlled through the \np{ln\_tsd\_ini} namelist parameter.

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Chapters/Chap_DYN.tex

-                      r3764
+                      r3989
 % ================================================================
 % Chapter Ñ Ocean Dynamics (DYN)
+% Chapter � Ocean Dynamics (DYN)
 % ================================================================
 \chapter{Ocean Dynamics (DYN)}
 …
 The vector invariant form of the momentum equations is the one most
 often used in applications of the \NEMO ocean model. The flux form option
+(see next section) has been present since version $2$.
+(see next section) has been present since version $2$. Options are defined
+through the \ngn{namdyn\_adv} namelist variables
 Coriolis and momentum advection terms are evaluated using a leapfrog
 scheme, $i.e.$ the velocity appearing in these expressions is centred in
 …
 %-------------------------------------------------------------------------------------------------------------
+Options are defined through the \ngn{namdyn\_vor} namelist variables.
 Four discretisations of the vorticity term (\textit{ln\_dynvor\_xxx}=true) are available:
 conserving potential enstrophy of horizontally non-divergent flow (ENS scheme) ;
 …
 %-------------------------------------------------------------------------------------------------------------
+Options are defined through the \ngn{namdyn\_adv} namelist variables.
 In the flux form (as in the vector invariant form), the Coriolis and momentum
 advection terms are evaluated using a leapfrog scheme, $i.e.$ the velocity
 …
 %-------------------------------------------------------------------------------------------------------------
+Options are defined through the \ngn{namdyn\_hpg} namelist variables.
 The key distinction between the different algorithms used for the hydrostatic
 pressure gradient is the vertical coordinate used, since HPG is a \emph{horizontal}
 …
 %%%
+Options are defined through the \ngn{namdyn\_spg} namelist variables.
 The surface pressure gradient term is related to the representation of the free surface (\S\ref{PE_hor_pg}). The main distinction is between the fixed volume case (linear free surface) and the variable volume case (nonlinear free surface, \key{vvl} is defined). In the linear free surface case (\S\ref{PE_free_surface}) the vertical scale factors $e_{3}$ are fixed in time, while they are time-dependent in the nonlinear case (\S\ref{PE_free_surface}). With both linear and nonlinear free surface, external gravity waves are allowed in the equations, which imposes a very small time step when an explicit time stepping is used. Two methods are proposed to allow a longer time step for the three-dimensional equations: the filtered free surface, which is a modification of the continuous equations (see \eqref{Eq_PE_flt}), and the split-explicit free surface described below. The extra term introduced in the filtered method is calculated implicitly, so that the update of the next velocities is done in module \mdl{dynspg\_flt} and not in \mdl{dynnxt}.
 …
 %-------------------------------------------------------------------------------------------------------------
+Options are defined through the \ngn{namdyn\_ldf} namelist variables.
 The options available for lateral diffusion are to use either laplacian
 (rotated or not) or biharmonic operators. The coefficients may be constant
 …
 %-------------------------------------------------------------------------------------------------------------
+Options are defined through the \ngn{namzdf} namelist variables.
 The large vertical diffusion coefficient found in the surface mixed layer together
 with high vertical resolution implies that in the case of explicit time stepping there
 …
 %-------------------------------------------------------------------------------------------------------------
+Options are defined through the \ngn{namdom} namelist variables.
 The general framework for dynamics time stepping is a leap-frog scheme,
 $i.e.$ a three level centred time scheme associated with an Asselin time filter

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Chapters/Chap_LBC.tex

-                      r3294
+                      r3989
 % ================================================================
 % Chapter Ñ Lateral Boundary Condition (LBC)
+% Chapter � Lateral Boundary Condition (LBC)
 % ================================================================
 \chapter{Lateral Boundary Condition (LBC) }
 …
 %OPA allows land and topography grid points in the computational domain due to the presence of continents or islands, and includes the use of a full or partial step representation of bottom topography. The computation is performed over the whole domain, i.e. we do not try to restrict the computation to ocean-only points. This choice has two motivations. Firstly, working on ocean only grid points overloads the code and harms the code readability. Secondly, and more importantly, it drastically reduces the vector portion of the computation, leading to a dramatic increase of CPU time requirement on vector computers.  The current section describes how the masking affects the computation of the various terms of the equations with respect to the boundary condition at solid walls. The process of defining which areas are to be masked is described in \S\ref{DOM_msk}.
+Options are defined through the \ngn{namlbc} namelist variables.
 The discrete representation of a domain with complex boundaries (coastlines and
 bottom topography) leads to arrays that include large portions where a computation
 …
 % Boundary Condition around the Model Domain
 % ================================================================
 \section{Model Domain Boundary Condition (\jp{jperio})}
+\section{Model Domain Boundary Condition (\np{jperio})}
 \label{LBC_jperio}
 …
 % -------------------------------------------------------------------------------------------------------------
 %        Closed, cyclic, south symmetric (\jp{jperio} = 0, 1 or 2)
+%        Closed, cyclic, south symmetric (\np{jperio} = 0, 1 or 2)
 % -------------------------------------------------------------------------------------------------------------
 \subsection{Closed, cyclic, south symmetric (\jp{jperio} = 0, 1 or 2)}
+\subsection{Closed, cyclic, south symmetric (\np{jperio} = 0, 1 or 2)}
 \label{LBC_jperio012}
 The choice of closed, cyclic or symmetric model domain boundary condition is made
 by setting \jp{jperio} to 0, 1 or 2 in file \mdl{par\_oce}. Each time such a boundary
+by setting \np{jperio} to 0, 1 or 2 in namelist \ngn{namcfg}. Each time such a boundary
 condition is needed, it is set by a call to routine \mdl{lbclnk}. The computation of
 momentum and tracer trends proceeds from $i=2$ to $i=jpi-1$ and from $j=2$ to
 …
  domain and the overlapping rows. The number of rows to exchange (known as
  the halo) is usually set to one (\jp{jpreci}=1, in \mdl{par\_oce}). The whole domain
  dimensions are named \jp{jpiglo}, \jp{jpjglo} and \jp{jpk}. The relationship between
+ dimensions are named \np{jpiglo}, \np{jpjglo} and \jp{jpk}. The relationship between
  the whole domain and a sub-domain is:
 \begin{eqnarray}
 …
 \end{itemize}
+Options are defined through the \ngn{namobc} namelist variables.
 The package resides in the OBC directory. It is described here in four parts: the
 boundary geometry (parameters to be set in \mdl{obc\_par}), the forcing data at
 …
 Logical flag  &                 &                            &                     \\
 \hline
 West          & \jp{jpiwob} $>= 2$         &  \jp{jpjwd}$>= 2$          &  \jp{jpjwf}<= \jp{jpjglo}-1 \\
+West          & \jp{jpiwob} $>= 2$         &  \jp{jpjwd}$>= 2$          &  \jp{jpjwf}<= \np{jpjglo}-1 \\
 lp\_obc\_west & $i$-index of a $u$ point   & $j$ of a $T$ point   &$j$ of a $T$ point \\
 \hline
 East            & \jp{jpieob}$<=$\jp{jpiglo}-2&\jp{jpjed} $>= 2$         & \jp{jpjef}$<=$ \jp{jpjglo}-1 \\
+East            & \jp{jpieob}$<=$\np{jpiglo}-2&\jp{jpjed} $>= 2$         & \jp{jpjef}$<=$ \np{jpjglo}-1 \\
  lp\_obc\_east  & $i$-index of a $u$ point    & $j$ of a $T$ point & $j$ of a $T$ point \\
 \hline
 South           & \jp{jpjsob} $>= 2$         & \jp{jpisd} $>= 2$          & \jp{jpisf}$<=$\jp{jpiglo}-1 \\
+South           & \jp{jpjsob} $>= 2$         & \jp{jpisd} $>= 2$          & \jp{jpisf}$<=$\np{jpiglo}-1 \\
 lp\_obc\_south  & $j$-index of a $v$ point   & $i$ of a $T$ point   & $i$ of a $T$ point \\
 \hline
 North           & \jp{jpjnob} $<=$ \jp{jpjglo}-2& \jp{jpind} $>= 2$        & \jp{jpinf}$<=$\jp{jpiglo}-1 \\
+North           & \jp{jpjnob} $<=$ \np{jpjglo}-2& \jp{jpind} $>= 2$        & \jp{jpinf}$<=$\np{jpiglo}-1 \\
 lp\_obc\_north  & $j$-index of a $v$ point      & $i$  of a $T$ point & $i$ of a $T$ point \\
 \hline
 …
 %-----------------------------------------------------------------------------------------------
+Options are defined through the \ngn{nambdy} \ngn{nambdy\_index}
+\ngn{nambdy\_dta} \ngn{nambdy\_dta2} namelist variables.
 The BDY module is an alternative implementation of open boundary
 conditions for regional configurations. It implements the Flow
 …
 %-----------------------------------------------------------------------------------------------
+To be written....
+Options are defined through the  \ngn{nambdy\_tide} namelist variables.
+ To be written....

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Chapters/Chap_LDF.tex

-                      r3294
+                      r3989
 % ================================================================
 % Chapter Ñ Lateral Ocean Physics (LDF)
+% Chapter � Lateral Ocean Physics (LDF)
 % ================================================================
 \chapter{Lateral Ocean Physics (LDF)}
 …
 and for tracers only, eddy induced advection on tracers). These three aspects
 of the lateral diffusion are set through namelist parameters and CPP keys
 (see the \textit{nam\_traldf} and \textit{nam\_dynldf} below). Note
+(see the \textit{\ngn{nam\_traldf}} and \textit{\ngn{nam\_dynldf}} below). Note
 that this chapter describes the default implementation of iso-neutral
 tracer mixing, and Griffies's implementation, which is used if
 …
 Other formulations can be introduced by the user for a given configuration.
 For example, in the ORCA2 global ocean model (\key{orca\_r2}), the laplacian
+For example, in the ORCA2 global ocean model (see Configurations), the laplacian
 viscosity operator uses \np{rn\_ahm0}~= 4.10$^4$ m$^2$/s poleward of 20$^{\circ}$
 north and south and decreases linearly to \np{rn\_aht0}~= 2.10$^3$ m$^2$/s
 …
 can be found in routine \rou{ldf\_dyn\_c2d\_orca} defined in \mdl{ldfdyn\_c2d}.
 Similar modified horizontal variations can be found with the Antarctic or Arctic
+sub-domain options of ORCA2 and ORCA05 (\key{antarctic} or \key{arctic}
+defined, see \hf{ldfdyn\_antarctic} and \hf{ldfdyn\_arctic}).
+sub-domain options of ORCA2 and ORCA05 (see \&namcfg namelist).
 \subsubsection{Space Varying Mixing Coefficients (\key{traldf\_c3d} and \key{dynldf\_c3d})}
 …
 There is no default specification of space and time varying mixing coefficient.
 The only case available is specific to the ORCA2 and ORCA05 global ocean
 configurations (\key{orca\_r2} or \key{orca\_r05}). It provides only a tracer
+configurations. It provides only a tracer
 mixing coefficient for eddy induced velocity (ORCA2) or both iso-neutral and
 eddy induced velocity (ORCA05) that depends on the local growth rate of

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Chapters/Chap_MISC.tex

-                      r3294
+                      r3989
 % ================================================================
 % Chapter Ñ Miscellaneous Topics
+% Chapter � Miscellaneous Topics
 % ================================================================
 \chapter{Miscellaneous Topics}
 …
 Note that such modifications are so specific to a given configuration that no attempt
 has been made to set them in a generic way. However, examples of how
+they can be set up is given in the ORCA 2\deg and 0.5\deg configurations (search for
+\key{orca\_r2} or \key{orca\_r05} in the code).
+they can be set up is given in the ORCA 2\deg and 0.5\deg configurations. For example,
+for details of implementation in ORCA2, search:
+\vspace{-10pt}
+\begin{alltt}
+\tiny
+\begin{verbatim}
+IF( cp_cfg == "orca" .AND. jp_cfg == 2 )
+\end{verbatim}
+\end{alltt}
 % -------------------------------------------------------------------------------------------------------------
 …
 \colorbox{yellow}{Add a short description of CLA staff here or in lateral boundary condition chapter?}
+Options are defined through the  \ngn{namcla} namelist variables.
 %The problem is resolved here by allowing the mixing of tracers and mass/volume between non-adjacent water columns at nominated regions within the model. Momentum is not mixed. The scheme conserves total tracer content, and total volume (the latter in $z*$- or $s*$-coordinate), and maintains compatibility between the tracer and mass/volume budgets.
 …
 % Sub-Domain Functionality (\textit{nizoom, njzoom}, namelist parameters)
 % ================================================================
 \section{Sub-Domain Functionality (\jp{jpizoom}, \jp{jpjzoom})}
+\section{Sub-Domain Functionality (\np{jpizoom}, \np{jpjzoom})}
 \label{MISC_zoom}
 …
 In order to easily define a sub-domain over which the computation can be
 performed, the dimension of all input arrays (ocean mesh, bathymetry,
 forcing, initial state, ...) are defined as \jp{jpidta}, \jp{jpjdta} and \jp{jpkdta}
 (\mdl{par\_oce} module), while the computational domain is defined through
 \jp{jpiglo}, \jp{jpjglo} and \jp{jpk} (\mdl{par\_oce} module). When running the
 model over the whole domain, the user sets \jp{jpiglo}=\jp{jpidta} \jp{jpjglo}=\jp{jpjdta}
+forcing, initial state, ...) are defined as \np{jpidta}, \np{jpjdta} and \np{jpkdta}
+( in \ngn{namcfg} namelist), while the computational domain is defined through
+\np{jpiglo}, \np{jpjglo} and \jp{jpk} (\ngn{namcfg} namelist). When running the
+model over the whole domain, the user sets \np{jpiglo}=\np{jpidta} \np{jpjglo}=\np{jpjdta}
 and \jp{jpk}=\jp{jpkdta}. When running the model over a sub-domain, the user
 has to provide the size of the sub-domain, (\jp{jpiglo}, \jp{jpjglo}, \jp{jpkglo}),
 and the indices of the south western corner as \jp{jpizoom} and \jp{jpjzoom} in
 the \mdl{par\_oce} module (Fig.~\ref{Fig_LBC_zoom}).
+has to provide the size of the sub-domain, (\np{jpiglo}, \np{jpjglo}, \np{jpkglo}),
+and the indices of the south western corner as \np{jpizoom} and \np{jpjzoom} in
+the  \ngn{namcfg} namelist (Fig.~\ref{Fig_LBC_zoom}).
 Note that a third set of dimensions exist, \jp{jpi}, \jp{jpj} and \jp{jpk} which is
 actually used to perform the computation. It is set by default to \jp{jpi}=\jp{jpjglo}
 and \jp{jpj}=\jp{jpjglo}, except for massively parallel computing where the
+actually used to perform the computation. It is set by default to \jp{jpi}=\np{jpjglo}
+and \jp{jpj}=\np{jpjglo}, except for massively parallel computing where the
 computational domain is laid out on local processor memories following a 2D
 horizontal splitting. % (see {\S}IV.2-c) ref to the section to be updated
 …
 trajectory to reach it.
+Options are defined through the  \ngn{namdom} namelist variables.
 The acceleration of convergence option is used when \np{nn\_acc}=1. In that case,
 $\rdt=rn\_rdt$ is the time step of dynamics while $\widetilde{\rdt}=rdttra$ is the
 …
  \gmcomment{why not make these bullets into subsections?}
+Options are defined through the  \ngn{namctl} namelist variables.
 $\bullet$ Vector optimisation:
 …
 a Successive-Over-Relaxation scheme (SOR) and a preconditioned conjugate gradient
 scheme(PCG) \citep{Madec_al_OM88, Madec_PhD90}. The solver is selected trough the
 the value of \np{nn\_solv} (namelist parameter).
+the value of \np{nn\_solv}   \ngn{namsol} namelist variable.
 The PCG is a very efficient method for solving elliptic equations on vector computers.

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Chapters/Chap_Model_Basics_zstar.tex

-                      r3294
+                      r3989
 % ================================================================
 % Chapter 1 Ñ Model Basics
+% Chapter 1 � Model Basics
 % ================================================================
 % ================================================================
 …
 Because $z^\star$ has a time independent range, all grid cells have static increments
 ds, and the sum of the ver tical increments yields the time independent ocean
 depth %·k ds = H.
+depth %�k ds = H.
 The $z^\star$ coordinate is therefore invisible to undulations of the
 free surface, since it moves along with the free surface. This proper ty means that
 …
 \namdisplay{nam_dynspg}
 %------------------------------------------------------------------------------------------------------------
+Options are defined through the  \ngn{nam\_dynspg} namelist variables.
 The surface pressure gradient term is related to the representation of the free surface (\S\ref{PE_hor_pg}). The main distinction is between the fixed volume case (linear free surface or rigid lid) and the variable volume case (nonlinear free surface, \key{vvl} is active). In the linear free surface case (\S\ref{PE_free_surface}) and rigid lid (\S\ref{PE_rigid_lid}), the vertical scale factors $e_{3}$ are fixed in time, while in the nonlinear case (\S\ref{PE_free_surface}) they are time-dependent. With both linear and nonlinear free surface, external gravity waves are allowed in the equations, which imposes a very small time step when an explicit time stepping is used. Two methods are proposed to allow a longer time step for the three-dimensional equations: the filtered free surface, which is a modification of the continuous equations (see \eqref{Eq_PE_flt}), and the split-explicit free surface described below. The extra term introduced in the filtered method is calculated implicitly, so that the update of the next velocities is done in module \mdl{dynspg\_flt} and not in \mdl{dynnxt}.
 …
 \namdisplay{namdom}
 %--------------------------------------------------------------------------------------------------------------
+The split-explicit free surface formulation used in OPA follows the one proposed by \citet{Griffies2004}. The general idea is to solve the free surface equation with a small time step, while the three dimensional prognostic variables are solved with a longer time step that is a multiple of \np{rdtbt} (Figure III.3).
+The split-explicit free surface formulation used in OPA follows the one proposed by \citet{Griffies2004}. The general idea is to solve the free surface equation with a small time step, while the three dimensional prognostic variables are solved with a longer time step that is a multiple of \np{rdtbt}
+in the  \ngn{namdom} namelist.
+(Figure III.3).
 %>   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Chapters/Chap_OBS.tex

-                      r3294
+                      r3989
 can be used for validation or verification of model or  any other data assimilation system.
 The OBS code is called from \np{opa.F90} for model initialisation and to calculate the model
+The OBS code is called from \mdl{nemogcm.F90} for model initialisation and to calculate the model
 equivalent values for observations on the 0th timestep. The code is then called again after
 each timestep from \np{step.F90}. To build with the OBS code active \key{diaobs} must be
+each timestep from \mdl{step.F90}. To build with the OBS code active \key{diaobs} must be
 set.
 …
 \item Add the following to the NEMO namelist to run the observation
 operator on this data. Set the \np{enactfiles} namelist parameter to the
+operator on this data. Set the \np{enactfiles} namelist variable to the
 observation  file name:
 \end{enumerate}
 …
 %-------------------------------------------------------------------------------------------------------------
+Options are defined through the  \ngn{namobs} namelist variables.
 The options \np{ln\_t3d} and \np{ln\_s3d} switch on the temperature and salinity
 profile observation operator code. The \np{ln\_ena} switch turns on the reading
 …
 \label{OBS_details}
 Here we show a more complete example namelist and also show the NetCDF headers
+Here we show a more complete example namelist  \ngn{namobs} and also show the NetCDF headers
 of the observation
 files that may be used with the observation operator

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Chapters/Chap_SBC.tex

-                      r3795
+                      r3989
 % ================================================================
 % Chapter Ñ Surface Boundary Condition (SBC, ICB)
+% Chapter � Surface Boundary Condition (SBC, ICB)
 % ================================================================
 \chapter{Surface Boundary Condition (SBC, ICB) }
 …
 Five different ways to provide the first six fields to the ocean are available which
 are controlled by namelist variables: an analytical formulation (\np{ln\_ana}~=~true),
+are controlled by namelist \ngn{namsbc} variables: an analytical formulation (\np{ln\_ana}~=~true),
 a flux formulation (\np{ln\_flx}~=~true), a bulk formulae formulation (CORE
 (\np{ln\_core}~=~true), CLIO (\np{ln\_clio}~=~true) or MFS
 …
 %--------------------------------------------------------------------------------------------------------------
+In some circumstances it may be useful to avoid calculating the 3D temperature, salinity and velocity fields and
+simply read them in from  a previous run.  For example:
+In some circumstances it may be useful to avoid calculating the 3D temperature, salinity and velocity fields and simply read them in from  a previous run.
+Options are defined through the  \ngn{namsbc\_sas} namelist variables.
+For example:
 \begin{enumerate}
 …
 In this case, all the six fluxes needed by the ocean are assumed to
 be uniform in space. They take constant values given in the namelist
 namsbc{\_}ana by the variables \np{rn\_utau0}, \np{rn\_vtau0}, \np{rn\_qns0},
+\ngn{namsbc{\_}ana} by the variables \np{rn\_utau0}, \np{rn\_vtau0}, \np{rn\_qns0},
 \np{rn\_qsr0}, and \np{rn\_emp0} ($\textit{emp}=\textit{emp}_S$). The runoff is set to zero.
 In addition, the wind is allowed to reach its nominal value within a given number
 …
 In the flux formulation (\np{ln\_flx}=true), the surface boundary
 condition fields are directly read from input files. The user has to define
 in the namelist namsbc{\_}flx the name of the file, the name of the variable
+in the namelist \ngn{namsbc{\_}flx} the name of the file, the name of the variable
 read in the file, the time frequency at which it is given (in hours), and a logical
 setting whether a time interpolation to the model time step is required
 …
 This is the so-called DRAKKAR Forcing Set (DFS) \citep{Brodeau_al_OM09}.
+Options are defined through the  \ngn{namsbc\_core} namelist variables.
 The required 8 input fields are:
 …
 compute the radiative fluxes from a climatological cloud cover.
+Options are defined through the  \ngn{namsbc\_clio} namelist variables.
 The required 7 input fields are:
 …
 Details on the bulk formulae used can be found in \citet{Maggiore_al_PCE98} and \citet{Castellari_al_JMS1998}.
+Options are defined through the  \ngn{namsbc\_mfs} namelist variables.
 The required 7 input fields must be provided on the model Grid-T and  are:
 \begin{itemize}
 …
 When PISCES biogeochemical model (\key{top} and \key{pisces}) is also used in the coupled system,
 the whole carbon cycle is computed by defining \key{cpl\_carbon\_cycle}. In this case,
+CO$_2$ fluxes will be exchanged between the atmosphere and the ice-ocean system (and need to be activated
+in namsbc{\_}cpl).
+The new namelist above allows control of various aspects of the coupling fields (particularly for
+CO$_2$ fluxes will be exchanged between the atmosphere and the ice-ocean system (and need to be activated in \ngn{namsbc{\_}cpl} ).
+The namelist above allows control of various aspects of the coupling fields (particularly for
 vectors) and now allows for any coupling fields to have multiple sea ice categories (as required by LIM3
 and CICE).  When indicating a multi-category coupling field in namsbc{\_}cpl the number of categories will be
 …
 The optional atmospheric pressure can be used to force ocean and ice dynamics
 (\np{ln\_apr\_dyn}~=~true, \textit{namsbc} namelist ).
+(\np{ln\_apr\_dyn}~=~true, \textit{\ngn{namsbc}} namelist ).
 The input atmospheric forcing defined via \np{sn\_apr} structure (\textit{namsbc\_apr} namelist)
 can be interpolated in time to the model time step, and even in space when the
 …
 %-------------------------------------------------------------------------------------------------------------
 Concerning the tidal potential, some parameters are available in namelist:
 - \texttt{ln\_tide\_pot} activate the tidal potential forcing
 - \texttt{nb\_harmo} is the number of constituent used
 - \texttt{clname} is the name of constituent
+Concerning the tidal potential, some parameters are available in namelist \ngn{nam\_tide}:
+- \np{ln\_tide\_pot} activate the tidal potential forcing
+- \np{nb\_harmo} is the number of constituent used
+- \np{clname} is the name of constituent
 …
 depth (in metres) which the river should be added to.
 Namelist options, \np{ln\_rnf\_depth}, \np{ln\_rnf\_sal} and \np{ln\_rnf\_temp} control whether
+Namelist variables in \ngn{namsbc\_rnf}, \np{ln\_rnf\_depth}, \np{ln\_rnf\_sal} and \np{ln\_rnf\_temp} control whether
 the river attributes (depth, salinity and temperature) are read in and used.  If these are set
 as false the river is added to the surface box only, assumed to be fresh (0~psu), and/or
 …
 Their physical behaviour is controlled by equations as described in  \citet{Martin_Adcroft_OM10} ).
 (Note that the authors kindly provided a copy of their code to act as a basis for implementation in NEMO.)
 Icebergs are initially spawned into one of ten classes which have specific mass and thickness as described by
+Icebergs are initially spawned into one of ten classes which have specific mass and thickness as described in the \ngn{namberg} namelist:
 \np{rn\_initial\_mass} and \np{rn\_initial\_thickness}.
 Each class has an associated scaling (\np{rn\_mass\_scaling}), which is an integer representing how many icebergs
 …
 the diurnal cycle of SWF is a scaling of the top of the atmosphere diurnal cycle
 of incident SWF. The \cite{Bernie_al_CD07} reconstruction algorithm is available
 in \NEMO by setting \np{ln\_dm2dc}~=~true (a \textit{namsbc} namelist parameter) when using
+in \NEMO by setting \np{ln\_dm2dc}~=~true (a \textit{\ngn{namsbc}} namelist variable) when using
 CORE bulk formulea (\np{ln\_blk\_core}~=~true) or the flux formulation (\np{ln\_flx}~=~true).
 The reconstruction is performed in the \mdl{sbcdcy} module. The detail of the algoritm used
 …
 %-------------------------------------------------------------------------------------------------------------
+In forced mode using a flux formulation (\np{ln\_flx}~=~true), a
+IOptions are defined through the  \ngn{namsbc\_ssr} namelist variables.
+n forced mode using a flux formulation (\np{ln\_flx}~=~true), a
 feedback term \emph{must} be added to the surface heat flux $Q_{ns}^o$:
 \begin{equation} \label{Eq_sbc_dmp_q}
 …
  in $namsbc$ namelist must be defined ${.true.}$.
 The \mdl{sbcwave} module containing the routine \np{sbc\_wave} reads the
 namelist ${namsbc\_wave}$ (for external data names, locations, frequency, interpolation and all
+namelist \ngn{namsbc\_wave} (for external data names, locations, frequency, interpolation and all
 the miscellanous options allowed by Input Data generic Interface see \S\ref{SBC_input})
 and a 2D field of neutral drag coefficient. Then using the routine
 …
 % Griffies doc:
 % When running ocean-ice simulations, we are not explicitly representing land processes, such as rivers, catchment areas, snow accumulation, etc. However, to reduce model drift, it is important to balance the hydrological cycle in ocean-ice models. We thus need to prescribe some form of global normalization to the precipitation minus evaporation plus river runoff. The result of the normalization should be a global integrated zero net water input to the ocean-ice system over a chosen time scale.
 %How often the normalization is done is a matter of choice. In mom4p1, we choose to do so at each model time step, so that there is always a zero net input of water to the ocean-ice system. Others choose to normalize over an annual cycle, in which case the net imbalance over an annual cycle is used to alter the subsequent yearÕs water budget in an attempt to damp the annual water imbalance. Note that the annual budget approach may be inappropriate with interannually varying precipitation forcing.
+%How often the normalization is done is a matter of choice. In mom4p1, we choose to do so at each model time step, so that there is always a zero net input of water to the ocean-ice system. Others choose to normalize over an annual cycle, in which case the net imbalance over an annual cycle is used to alter the subsequent year�s water budget in an attempt to damp the annual water imbalance. Note that the annual budget approach may be inappropriate with interannually varying precipitation forcing.
 %When running ocean-ice coupled models, it is incorrect to include the water transport between the ocean and ice models when aiming to balance the hydrological cycle. The reason is that it is the sum of the water in the ocean plus ice that should be balanced when running ocean-ice models, not the water in any one sub-component. As an extreme example to illustrate the issue, consider an ocean-ice model with zero initial sea ice. As the ocean-ice model spins up, there should be a net accumulation of water in the growing sea ice, and thus a net loss of water from the ocean. The total water contained in the ocean plus ice system is constant, but there is an exchange of water between the subcomponents. This exchange should not be part of the normalization used to balance the hydrological cycle in ocean-ice models.

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Chapters/Chap_STP.tex

-                      r3294
+                      r3989
 % ================================================================
 % Chapter 2 Ñ Time Domain (step.F90)
+% Chapter 2 � Time Domain (step.F90)
 % ================================================================
 \chapter{Time Domain (STP) }
 …
 When restarting, if the the time step has been changed, a restart using an Euler time
 stepping scheme is imposed.
+Options are defined through the  \ngn{namrun} namelist variables.
 %%%
 \gmcomment{
 …
 %--------------------------------------------------------------------------------------------------------------
+Options are defined through the  \ngn{namdom} namelist variables.
  \colorbox{yellow}{add here a few word on nit000 and nitend}

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Chapters/Chap_TRA.tex

-                      r3764
+                      r3989
 % ================================================================
 % Chapter 1 Ñ Ocean Tracers (TRA)
+% Chapter 1 � Ocean Tracers (TRA)
 % ================================================================
 \chapter{Ocean Tracers (TRA)}
 …
 \textit{effective} velocity ($i.e.$ the sum of the eulerian and eiv velocities) which is used.
 The choice of an advection scheme is made in the \textit{nam\_traadv} namelist, by
+The choice of an advection scheme is made in the \textit{\ngn{nam\_traadv}} namelist, by
 setting to \textit{true} one and only one of the logicals \textit{ln\_traadv\_xxx}. The
 corresponding code can be found in the \textit{traadv\_xxx.F90} module, where
 …
 %-------------------------------------------------------------------------------------------------------------
+Options are defined through the  \ngn{namtra\_ldf} namelist variables.
 The options available for lateral diffusion are a laplacian (rotated or not)
 or a biharmonic operator, the latter being more scale-selective (more
 …
 %--------------------------------------------------------------------------------------------------------------
+Options are defined through the  \ngn{namzdf} namelist variables.
 The formulation of the vertical subgrid scale tracer physics is the same
 for all the vertical coordinates, and is based on a laplacian operator.
 …
 %--------------------------------------------------------------------------------------------------------------
+Options are defined through the  \ngn{namtra\_qsr} namelist variables.
 When the penetrative solar radiation option is used (\np{ln\_flxqsr}=true),
 the solar radiation penetrates the top few tens of meters of the ocean. If it is not used
 …
 Bottom Water) by a few Sverdrups  \citep{Emile-Geay_Madec_OS09}.
+Options are defined through the  \ngn{namtra\_bbc} namelist variables.
 The presence of geothermal heating is controlled by setting the namelist
 parameter  \np{ln\_trabbc} to true. Then, when \np{nn\_geoflx} is set to 1,
 …
 %--------------------------------------------------------------------------------------------------------------
+Options are defined through the  \ngn{nambbl} namelist variables.
 In a $z$-coordinate configuration, the bottom topography is represented by a
 series of discrete steps. This is not adequate to represent gravity driven
 …
 where $\gamma$ is the inverse of a time scale, and $T_o$ and $S_o$
 are given temperature and salinity fields (usually a climatology).
+Options are defined through the  \ngn{namtra\_dmp} namelist variables.
 The restoring term is added when the namelist parameter \np{ln\_tradmp} is set to true.
 It also requires that both \np{ln\_tsd\_init} and \np{ln\_tsd\_tradmp} are set to true
 …
 %--------------------------------------------------------------------------------------------------------------
+Options are defined through the  \ngn{namdom} namelist variables.
 The general framework for tracer time stepping is a modified leap-frog scheme
 \citep{Leclair_Madec_OM09}, $i.e.$ a three level centred time scheme associated
 …
 \citep{Gill1982}.
+Options are defined through the  \ngn{nameos} namelist variables.
 The default option (namelist parameter \np{nn\_eos}=0) is the \citet{JackMcD1995}
 equation of state. Its use is highly recommended. However, for process studies,
 …
 coefficients, and $\rho_o$, the reference volumic mass, $rau0$.
 ($\alpha$ and $\beta$ can be modified through the \np{rn\_alpha} and
 \np{rn\_beta} namelist parameters). Note that when $d_a$ is a function
+\np{rn\_beta} namelist variables). Note that when $d_a$ is a function
 of $T$ only (\np{nn\_eos}=1), the salinity is a passive tracer and can be
 used as such.

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Chapters/Chap_ZDF.tex

-                      r3764
+                      r3989
 %--------------------------------------------------------------------------------------------------------------
+Options are defined through the  \ngn{namzdf} namelist variables.
 When \key{zdfcst} is defined, the momentum and tracer vertical eddy coefficients
 are set to constant values over the whole ocean. This is the crudest way to define
 …
 When \key{zdfric} is defined, a local Richardson number dependent formulation
+for the vertical momentum and tracer eddy coefficients is set. The vertical mixing
+for the vertical momentum and tracer eddy coefficients is set through the  \ngn{namzdf\_ric}
+namelist variables.The vertical mixing
 coefficients are diagnosed from the large scale variables computed by the model.
 \textit{In situ} measurements have been used to link vertical turbulent activity to
 …
             \end{cases}
 \end{align*}
+The choice of $P_{rt}$ is controlled by the \np{nn\_pdl} namelist parameter.
+Options are defined through the  \ngn{namzdfy\_tke} namelist variables.
+The choice of $P_{rt}$ is controlled by the \np{nn\_pdl} namelist variable.
 At the sea surface, the value of $\bar{e}$ is prescribed from the wind
 …
 \caption{   \label{Tab_GLS}
 Set of predefined GLS parameters, or equivalently predefined turbulence models available
 with \key{zdfgls} and controlled by the \np{nn\_clos} namelist parameter.}
+with \key{zdfgls} and controlled by the \np{nn\_clos} namelist variable in \ngn{namzdf\_gls} .}
 \end{center}   \end{table}
 %--------------------------------------------------------------------------------------------------------------
 …
 The KKP scheme has been implemented by J. Chanut ...
+Options are defined through the  \ngn{namzdf\_kpp} namelist variables.
 \colorbox{yellow}{Add a description of KPP here.}
 …
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+Options are defined through the  \ngn{namzdf} namelist variables.
 The non-penetrative convective adjustment is used when \np{ln\_zdfnpc}=true.
 It is applied at each \np{nn\_npc} time step and mixes downwards instantaneously
 …
 %--------------------------------------------------------------------------------------------------------------
+Options are defined through the  \ngn{namzdf} namelist variables.
 The enhanced vertical diffusion parameterisation is used when \np{ln\_zdfevd}=true.
 In this case, the vertical eddy mixing coefficients are assigned very large values
 …
 %--------------------------------------------------------------------------------------------------------------
+Options are defined through the  \ngn{namzdf\_ddm} namelist variables.
 Double diffusion occurs when relatively warm, salty water overlies cooler, fresher
 water, or vice versa. The former condition leads to salt fingering and the latter
 …
 %--------------------------------------------------------------------------------------------------------------
+Options are defined through the  \ngn{nambfr} namelist variables.
 Both the surface momentum flux (wind stress) and the bottom momentum
 flux (bottom friction) enter the equations as a condition on the vertical
 …
 \label{ZDF_tmx_bottom}
+Options are defined through the  \ngn{namzdf\_tmx} namelist variables.
 The parameterization of tidal mixing follows the general formulation for
 the vertical eddy diffusivity proposed by \citet{St_Laurent_al_GRL02} and

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Chapters/Introduction.tex

-                      r3625
+                      r3989
 the coefficients with \citet{Blanke1993}, \citet{Large_al_RG94}, \citet{Pacanowski_Philander_JPO81},
 or \citet{Umlauf_Burchard_JMS03} mixing schemes.
+ \vspace{1cm}
+\noindent CPP keys and namelists are used for inputs to the code.  \newline
+\noindent \index{CPP keys} CPP keys \newline
+Some CPP keys are implemented in the FORTRAN code to allow code selection at compiling step. This selection of code at compilation time reduces the reliability of the whole platform since it changes the code from one set of CPP keys to the other. It is used only when the addition/suppression of the part of code highly changes the amount of memory at run time.
+Usual coding looks like :
+ \vspace{-10pt}
+\begin{alltt}
+\tiny
+\begin{verbatim}
+#if defined key_option1
+             This part of the FORTRAN code will be active
+             only if key_option1 is activated at compiling step
+#endif
+\end{verbatim}
+\end{alltt}
+\noindent \index{Namelist} Namelists
+The namelist allows to input variables (character, logical, real and integer) into the code. There is one namelist file for each component of NEMO (dynamics, sea-ice, biogeochemistry...) containing all the FOTRAN namelists needed. The implementation in NEMO uses a two step process. For each FORTRAN namelist, two files are read:
+\begin{enumerate}
+\item A reference namelist ( in \textit{CONFIG/SHARED/namelist\_ref} ) is read first. This file contains all the namelist variables which are initialised to default values
+\item A configuration namelist ( in \textit{CONFIG/CFG\_NAME/EXP00/namelist\_cfg} ) is read aferwards. This file contains only the namelist variables which are changed from default values, and overwrites those.
+\end{enumerate}
+A template can be found in \textit{NEMO/OPA\_SRC/module.example}
+The effective namelist, taken in account during the run, is stored at execution time in an output\_namelist\_dyn (or \_ice or \_top) file.
+ \vspace{1cm}
 Model outputs management and specific online diagnostics are described in chapters~\ref{DIA}.

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/nam_tide

-                      r3294
+                      r3989
 !-----------------------------------------------------------------------
 !       nam_tide       tide parameters (#ifdef key_tide)
+&nam_tide      !   tide parameters (#ifdef key_tide)
 !-----------------------------------------------------------------------
+!  ln_tide_pot    = use tidal potential forcing
+!  nb_harmo    = number of constituents used
+!  name(1)     = 'M2', 'K1', etc name of constituent
+&nam_tide
+   ln_tide_pot           = .true.
+   nb_harmo    = 11
+   clname(1)     =   'M2'
+   ln_tide_pot   = .true.   !  use tidal potential forcing
+   clname(1)     =   'M2'   !  name of constituent
    clname(2)     =   'S2'
    clname(3)     =   'N2'

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namasm

-                      r3764
+                      r3989
 &nam_asminc   !   assimilation increments                               ('key_asminc')
 !-----------------------------------------------------------------------
     ln_bkgwri = .false.    !  Logical switch for writing out background state
+    ln_bkgwri = .false.    !  Logical switch for writing out background state
     ln_trainc = .false.    !  Logical switch for applying tracer increments
     ln_dyninc = .false.    !  Logical switch for applying velocity increments
     ln_sshinc = .false.    !  Logical switch for applying SSH increments
+    ln_sshinc = .false.    !  Logical switch for applying SSH increments
     ln_asmdin = .false.    !  Logical switch for Direct Initialization (DI)
     ln_asmiau = .false.    !  Logical switch for Incremental Analysis Updating (IAU)
 …
     ln_salfix = .false.    !  Logical switch for ensuring that the sa > salfixmin
     salfixmin = -9999      !  Minimum salinity after applying the increments
     ndivdmp   = 0          !  Number of iterations of divergence damping operator
+    nn_divdmp = 0          !  Number of iterations of divergence damping operator
+/

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/nambdy

-                      r3294
+                      r3989
 &nambdy        !  unstructured open boundaries                          ("key_bdy")
 !-----------------------------------------------------------------------
     nb_bdy = 2                               !  number of open boundary sets
     ln_coords_file = .true.,.false.          !  =T : read bdy coordinates from file
     cn_coords_file = 'coordinates.bdy.nc','' !  bdy coordinates files
     ln_mask_file = .false.                   !  =T : read mask from file
     cn_mask_file = ''                        !  name of mask file (if ln_mask_file=.TRUE.)
     nn_dyn2d      =  2, 0                    !  boundary conditions for barotropic fields
     nn_dyn2d_dta  =  3, 0                    !  = 0, bdy data are equal to the initial state
                                              !  = 1, bdy data are read in 'bdydata   .nc' files
                                              !  = 2, use tidal harmonic forcing data from files
                                              !  = 3, use external data AND tidal harmonic forcing
     nn_dyn3d      =  0, 0                    !  boundary conditions for baroclinic velocities
     nn_dyn3d_dta  =  0, 0                    !  = 0, bdy data are equal to the initial state
                                              !  = 1, bdy data are read in 'bdydata   .nc' files
     nn_tra        =  1, 1                    !  boundary conditions for T and S
     nn_tra_dta    =  1, 1                    !  = 0, bdy data are equal to the initial state
                                              !  = 1, bdy data are read in 'bdydata   .nc' files
     nn_rimwidth  = 10, 5                     !  width of the relaxation zone
     ln_vol     = .false.                     !  total volume correction (see nn_volctl parameter)
     nn_volctl  = 1                           !  = 0, the total water flux across open boundaries is zero
+    nb_bdy = 1                            !  number of open boundary sets
+    ln_coords_file = .true.               !  =T : read bdy coordinates from file
+    cn_coords_file = 'coordinates.bdy.nc' !  bdy coordinates files
+    ln_mask_file = .false.                !  =T : read mask from file
+    cn_mask_file = ''                     !  name of mask file (if ln_mask_file=.TRUE.)
+    nn_dyn2d      =  2                    !  boundary conditions for barotropic fields
+    nn_dyn2d_dta  =  3                    !  = 0, bdy data are equal to the initial state
+                                          !  = 1, bdy data are read in 'bdydata   .nc' files
+                                          !  = 2, use tidal harmonic forcing data from files
+                                          !  = 3, use external data AND tidal harmonic forcing
+    nn_dyn3d      =  0                    !  boundary conditions for baroclinic velocities
+    nn_dyn3d_dta  =  0                    !  = 0, bdy data are equal to the initial state
+                           !  = 1, bdy data are read in 'bdydata   .nc' files
+    nn_tra        =  1                    !  boundary conditions for T and S
+    nn_tra_dta    =  1                    !  = 0, bdy data are equal to the initial state
+                           !  = 1, bdy data are read in 'bdydata   .nc' files
+    nn_rimwidth  = 10                      !  width of the relaxation zone
+    ln_vol     = .false.                  !  total volume correction (see nn_volctl parameter)
+    nn_volctl  = 1                        !  = 0, the total water flux across open boundaries is zero
+/

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/nambdy_tide

-                      r3294
+                      r3989
 !-----------------------------------------------------------------------
 &nambdy_tide     ! tidal forcing at open boundaries
+&nambdy_tide     ! tidal forcing at open boundaries
 !-----------------------------------------------------------------------
+   filtide      = 'bdydta/amm12_bdytide_'         !  file name root of tidal forcing files
+    tide_cpt(1)   ='Q1'  !  names of tidal components used
+    tide_cpt(2)   ='O1'  !  names of tidal components used
+    tide_cpt(3)   ='P1'  !  names of tidal components used
+    tide_cpt(4)   ='S1'  !  names of tidal components used
+    tide_cpt(5)   ='K1'  !  names of tidal components used
+    tide_cpt(6)   ='2N2' !  names of tidal components used
+    tide_cpt(7)   ='MU2' !  names of tidal components used
+    tide_cpt(8)   ='N2'  !  names of tidal components used
+    tide_cpt(9)   ='NU2' !  names of tidal components used
+    tide_cpt(10)   ='M2'  !  names of tidal components used
+    tide_cpt(11)   ='L2'  !  names of tidal components used
+    tide_cpt(12)   ='T2'  !  names of tidal components used
+    tide_cpt(13)   ='S2'  !  names of tidal components used
+    tide_cpt(14)   ='K2'  !  names of tidal components used
+    tide_cpt(15)   ='M4'  !  names of tidal components used
+    tide_speed(1)   = 13.398661 !  phase speeds of tidal components (deg/hour)
+    tide_speed(2)   = 13.943036 !  phase speeds of tidal components (deg/hour)
+    tide_speed(3)   = 14.958932 !  phase speeds of tidal components (deg/hour)
+    tide_speed(4)   = 15.000001 !  phase speeds of tidal components (deg/hour)
+    tide_speed(5)   = 15.041069 !  phase speeds of tidal components (deg/hour)
+    tide_speed(6)   = 27.895355 !  phase speeds of tidal components (deg/hour)
+    tide_speed(7)   = 27.968210 !  phase speeds of tidal components (deg/hour)
+    tide_speed(8)   = 28.439730 !  phase speeds of tidal components (deg/hour)
+    tide_speed(9)   = 28.512585 !  phase speeds of tidal components (deg/hour)
+    tide_speed(10)   = 28.984106 !  phase speeds of tidal components (deg/hour)
+    tide_speed(11)   = 29.528479 !  phase speeds of tidal components (deg/hour)
+    tide_speed(12)   = 29.958935 !  phase speeds of tidal components (deg/hour)
+    tide_speed(13)   = 30.000002 !  phase speeds of tidal components (deg/hour)
+    tide_speed(14)   = 30.082138 !  phase speeds of tidal components (deg/hour)
+    tide_speed(15)   = 57.968212 !  phase speeds of tidal components (deg/hour)
+    ln_tide_date = .true.               !  adjust tidal harmonics for start date of run
+   filtide          = 'bdydta/amm12_bdytide_'         !  file name root of tidal forcing files
+   ln_bdytide_2ddta = .false.
+   ln_bdytide_conj  = .false.
+/

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namberg

-                      r3609
+                      r3989
 &namberg       !   iceberg parameters
 !-----------------------------------------------------------------------
       ln_icebergs              = .true.
+      ln_icebergs              = .false.
       ln_bergdia               = .true.               ! Calculate budgets
       nn_verbose_level         = 1                    ! Turn on more verbose output if level > 0
       nn_verbose_write         = 15                   ! Timesteps between verbose messages
       nn_sample_rate           = 1                    ! Timesteps between sampling for trajectory storage
+                                                      ! Initial mass required for an iceberg of each class
       rn_initial_mass          = 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
+                                                      ! Proportion of calving mass to apportion to each class
       rn_distribution          = 0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02
                                                       ! Ratio between effective and real iceberg mass (non-dim)
+                                                      ! i.e. number of icebergs represented at a point
       rn_mass_scaling          = 2000, 200, 50, 20, 10, 5, 2, 1, 1, 1
                                                       ! Total thickness of newly calved bergs (m)
+                                                      ! thickness of newly calved bergs (m)
       rn_initial_thickness     = 40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
       rn_rho_bergs             = 850.                 ! Density of icebergs
 …
       rn_bits_erosion_fraction = 0.                   ! Fraction of erosion melt flux to divert to bergy bits
       rn_sicn_shift            = 0.                   ! Shift of sea-ice concn in erosion flux (0<sicn_shift<1)
+      ln_passive_mode          = .false.              ! iceberg - ocean decoupling
+      nn_test_icebergs         =  10                  ! Create icebergs in absence of a calving file (-1 = no)
+      rn_test_box              = -61.0,  -55.0,  59.0,  65.0
+      rn_speed_limit           = 0.                   ! CFL speed limit for a berg
+      ln_passive_mode          = .false.              ! iceberg - ocean decoupling
+      nn_test_icebergs         =  10                  ! Create test icebergs of this class (-1 = no)
+                                                      ! Put a test iceberg at each gridpoint in box (lon1,lon2,lat1,lat2)
+      rn_test_box              = 108.0,  116.0, -66.0, -58.0
+      rn_speed_limit           = 0.                   ! CFL speed limit for a berg
                ! filename ! freq (hours) ! variable ! time interp. ! clim  !'yearly' or ! weights  ! rotation !
                !          ! (<0  months) !   name   !  (logical)   ! (T/F) ! 'monthly'  ! filename ! pairing  !
       sn_icb =  'calving' ,     -1       , 'calvingmask',  .true.      , .true., 'yearly'   , ' '      , ' '
       cn_dir = './'
+      cn_dir = './'
+/

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/nambfr

-                      r3294
+                      r3989
    rn_bfri2    =    1.e-3  !  bottom drag coefficient (non linear case)
    rn_bfeb2    =    2.5e-3 !  bottom turbulent kinetic energy background  (m2/s2)
+   rn_bfrz0    =    3.e-3  ! bottom roughness for loglayer bfr coeff
    ln_bfr2d    = .false.   !  horizontal variation of the bottom friction coef (read a 2D mask file )
    rn_bfrien   =    50.    !  local multiplying factor of bfr (ln_bfr2d=T)
    ln_bfrimp   = .false.   !  implicit bottom friction (requires ln_zdfexp = .false. if true)
+   ln_bfrimp   = .true.    !  implicit bottom friction (requires ln_zdfexp = .false. if true)
+/

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namctl

r3294	r3989
12	12	nn_bench = 0 ! Bench mode (1/0): CAUTION use zero except for bench
13	13	! (no physical validity of the results)
	14	nn_timing = 0 ! timing by routine activated (=1) creates timing.output file, or not (=0)
14	15	/

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namdct

r3294	r3989
4	4	nn_dct = 15 ! time step frequency for transports computing
5	5	nn_dctwri = 15 ! time step frequency for transports writing
6		nn_secdebug = 0 ! 0 : no section to debug
	6	nn_secdebug = 112 ! 0 : no section to debug
7	7	! -1 : debug all section
8	8	! 0 < n : debug section number n

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namdia_harm

-                      r3294
+                      r3989
 &nam_diaharm   !   Harmonic analysis of tidal constituents ('key_diaharm')
 !-----------------------------------------------------------------------
     nit000_han=1           ! First time step used for harmonic analysis
     nitend_han=105         ! Last time step used for harmonic analysis
     nstep_han=1            ! Time step frequency for harmonic analysis
     nb_ana=1               ! Number of harmonics to analyse
     tname(1)='M2'          ! Name of tidal constituents
+    nit000_han = 1         ! First time step used for harmonic analysis
+    nitend_han = 75        ! Last time step used for harmonic analysis
+    nstep_han  = 15        ! Time step frequency for harmonic analysis
+    tname(1)   = 'M2'      ! Name of tidal constituents
+    tname(2)   = 'K1'
+/

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namdyn_hpg

r3294	r3989
2	2	&namdyn_hpg ! Hydrostatic pressure gradient option
3	3	!-----------------------------------------------------------------------
4		ln_hpg_zco = .false. ! z-coordinate - full steps
	4	ln_hpg_zco = .false. ! z-coordinate - full steps
5	5	ln_hpg_zps = .true. ! z-coordinate - partial steps (interpolation)
6	6	ln_hpg_sco = .false. ! s-coordinate (standard jacobian formulation)

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namdyn_ldf

-                      r3294
+                      r3989
 &namdyn_ldf    !   lateral diffusion on momentum
 !-----------------------------------------------------------------------
    !                       !  Type of the operator :
    ln_dynldf_lap    =  .true.   !  laplacian operator
    ln_dynldf_bilap  =  .false.  !  bilaplacian operator
    !                       !  Direction of action  :
    ln_dynldf_level  =  .false.  !  iso-level
+   !                       !  Type of the operator :
+   ln_dynldf_lap    =  .true.   !  laplacian operator
+   ln_dynldf_bilap  =  .false.  !  bilaplacian operator
+   !                       !  Direction of action  :
+   ln_dynldf_level  =  .false.  !  iso-level
    ln_dynldf_hor    =  .true.   !  horizontal (geopotential)            (require "key_ldfslp" in s-coord.)
    ln_dynldf_iso    =  .false.  !  iso-neutral                          (require "key_ldfslp")
 …
    rn_ahm_0_lap     = 40000.    !  horizontal laplacian eddy viscosity   [m2/s]
    rn_ahmb_0        =     0.    !  background eddy viscosity for ldf_iso [m2/s]
+   rn_ahm_0_blp     =     0.    !  horizontal bilaplacian eddy viscosity [m4/s]
+   rn_ahm_0_blp     =     0.    !  horizontal bilaplacian eddy viscosity [m4/s]
+   rn_cmsmag_1      =     3.    !  constant in laplacian Smagorinsky viscosity
+   rn_cmsmag_2      =     3     !  constant in bilaplacian Smagorinsky viscosity
+   rn_cmsh          =     1.    !  1 or 0 , if 0 -use only shear for Smagorinsky viscosity
+   rn_ahm_m_blp     =    -1.e12 !  upper limit for bilap  abs(ahm) < min( dx^4/128rdt, rn_ahm_m_blp)
+   rn_ahm_m_lap     = 40000.    !  upper limit for lap  ahm < min(dx^2/16rdt, rn_ahm_m_lap)
+/

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namdyn_nept

-                      r3294
+                      r3989
 !-----------------------------------------------------------------------
 &nam_dynnept  !   Neptune effect (simplified: lateral and vertical diffusions removed)
+&namdyn_nept  !   Neptune effect (simplified: lateral and vertical diffusions removed)
 !-----------------------------------------------------------------------
    ! Suggested lengthscale values are those of Eby & Holloway (1994) for a coarse model
 …
    ! Specify whether to ramp down the Neptune velocity in shallow
    ! water, and if so the depth range controlling such ramping down
    ln_neptramp       = .false.  ! ramp down Neptune velocity in shallow water
+   ln_neptramp       = .true.   ! ramp down Neptune velocity in shallow water
    rn_htrmin         =  100.0   ! min. depth of transition range
    rn_htrmax         =  200.0   ! max. depth of transition range

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namdyn_vor

-                      r3764
+                      r3989
 &namdyn_vor    !   option of physics/algorithm (not control by CPP keys)
 !-----------------------------------------------------------------------
+   ln_dynvor_ene = .false. !  energy    conserving scheme
+   ln_dynvor_ens = .false. !  enstrophy conserving scheme
+   ln_dynvor_mix = .false. !  mixed scheme
+   ln_dynvor_een = .true.  !  energy & enstrophy scheme
+   ln_dynvor_con = .false. !  consistency of BC with analytical eqs.
+   ln_dynvor_ene = .false. !  enstrophy conserving scheme
+   ln_dynvor_ens = .false. !  energy conserving scheme
+   ln_dynvor_mix = .false. !  mixed scheme
+   ln_dynvor_een = .true.  !  energy & enstrophy scheme
+/

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namflo

-                      r3294
+                      r3989
 &namflo       !   float parameters                                      ("key_float")
 !-----------------------------------------------------------------------
    jpnfl      = 1          !  total number of floats during the run
    jpnnewflo  = 0          !  number of floats for the restart
    ln_rstflo  = .false.    !  float restart (T) or not (F)
    nn_writefl =      75    !  frequency of writing in float output file
    nn_stockfl =    5475    !  frequency of creation of the float restart file
    ln_argo    = .false.    !  Argo type floats (stay at the surface each 10 days)
    ln_flork4  = .false.    !  trajectories computed with a 4th order Runge-Kutta (T)
                            !  or computed with Blanke' scheme (F)
    ln_ariane  = .true.     !  Input with Ariane tool convention(T)
    ln_ascii   = .true.     !  Output with Ariane tool netcdf convention(T) or ascii file (F)
+   jpnfl         = 1          !  total number of floats during the run
+   jpnnewflo     = 0          !  number of floats for the restart
+   ln_rstflo     = .false.    !  float restart (T) or not (F)
+   nn_writefl    =      75    !  frequency of writing in float output file
+   nn_stockfl    =    5475    !  frequency of creation of the float restart file
+   ln_argo       = .false.    !  Argo type floats (stay at the surface each 10 days)
+   ln_flork4     = .false.    !  trajectories computed with a 4th order Runge-Kutta (T)
+                              !  or computed with Blanke' scheme (F)
+   ln_ariane     = .true.     !  Input with Ariane tool convention(T)
+   ln_flo_ascii  = .true.     !  Output with Ariane tool netcdf convention(F) or ascii file (T)
+/

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namlbc

r3294	r3989
4	4	rn_shlat = 2. ! shlat = 0 ! 0 < shlat < 2 ! shlat = 2 ! 2 < shlat
5	5	! free slip ! partial slip ! no slip ! strong slip
	6	ln_vorlat = .false. ! consistency of vorticity boundary condition with analytical eqs.
6	7	/

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/nammpp

-                      r3294
+                      r3989
                            !  buffer blocking send or immediate non-blocking sends, resp.
    nn_buffer   =   0       !  size in bytes of exported buffer ('B' case), 0 no exportation
+   ln_nnogather=  .false.  !  activate code to avoid mpi_allgather use at the northfold
+   jpni        =   0       !  jpni   number of processors following i (set automatically if < 1)
+   jpnj        =   0       !  jpnj   number of processors following j (set automatically if < 1)
+   jpnij       =   0       !  jpnij  number of local domains (set automatically if < 1)
+/

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namobc

r3294	r3989
4	4	ln_obc_clim = .false. ! climatological obc data files (T) or not (F)
5	5	ln_vol_cst = .true. ! impose the total volume conservation (T) or not (F)
6		ln_obc_fla = .false. ! Flather open boundary condition
	6	ln_obc_fla = .false. ! Flather open boundary condition
7	7	nn_obcdta = 1 ! = 0 the obc data are equal to the initial state
8	8	! = 1 the obc data are read in 'obc.dta' files

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namobs

-                      r2540
+                      r3989
 &namobs       !  observation usage switch                               ('key_diaobs')
 !-----------------------------------------------------------------------
    ln_t3d     = .false.    ! Logical switch for T profile observations
    ln_s3d     = .false.    ! Logical switch for S profile observations
    ln_ena     = .false.    ! Logical switch for ENACT insitu data set
    !                       !     ln_cor                  Logical switch for Coriolis insitu data set
    ln_profb   = .false.    ! Logical switch for feedback insitu data set
    ln_sla     = .false.    ! Logical switch for SLA observations
+   ln_t3d     = .false.    ! Logical switch for T profile observations
+   ln_s3d     = .false.    ! Logical switch for S profile observations
+   ln_ena     = .false.    ! Logical switch for ENACT insitu data set
+   !                       !     ln_cor                  Logical switch for Coriolis insitu data set
+   ln_profb   = .false.    ! Logical switch for feedback insitu data set
+   ln_sla     = .false.    ! Logical switch for SLA observations
    ln_sladt   = .false.    ! Logical switch for AVISO SLA data
+   ln_sladt   = .false.    ! Logical switch for AVISO SLA data
    ln_slafb   = .false.    ! Logical switch for feedback SLA data
                            !     ln_ssh                  Logical switch for SSH observations
+   ln_slafb   = .false.    ! Logical switch for feedback SLA data
+                           !     ln_ssh                  Logical switch for SSH observations
    ln_sst     = .false.    ! Logical switch for SST observations
                            !     ln_reysst               Logical switch for Reynolds observations
                            !     ln_ghrsst               Logical switch for GHRSST observations
+   ln_sst     = .true.     ! Logical switch for SST observations
+   ln_reysst  = .true.     !     ln_reysst               Logical switch for Reynolds observations
+   ln_ghrsst  = .false.    !     ln_ghrsst               Logical switch for GHRSST observations
    ln_sstfb   = .false.    ! Logical switch for feedback SST data
                            !     ln_sss                  Logical switch for SSS observations
                            !     ln_seaice               Logical switch for Sea Ice observations
                            !     ln_vel3d                Logical switch for velocity observations
                            !     ln_velavcur             Logical switch for velocity daily av. cur.
                            !     ln_velhrcur             Logical switch for velocity high freq. cur.
                            !     ln_velavadcp            Logical switch for velocity daily av. ADCP
+   ln_sstfb   = .false.    ! Logical switch for feedback SST data
+                           !     ln_sss                  Logical switch for SSS observations
+                           !     ln_seaice               Logical switch for Sea Ice observations
+                           !     ln_vel3d                Logical switch for velocity observations
+                           !     ln_velavcur             Logical switch for velocity daily av. cur.
+                           !     ln_velhrcur             Logical switch for velocity high freq. cur.
+                           !     ln_velavadcp            Logical switch for velocity daily av. ADCP
                            !     ln_velhradcp            Logical switch for velocity high freq. ADCP
                            !     ln_velfb                Logical switch for feedback velocity data
                            !     ln_grid_global          Global distribtion of observations
                            !     ln_grid_search_lookup   Logical switch for obs grid search w/lookup table
                            !     grid_search_file        Grid search lookup file header
                            !     enactfiles              ENACT input observation file names
                            !     coriofiles              Coriolis input observation file name
    !                       ! profbfiles: Profile feedback input observation file name
+                           !     ln_velfb                Logical switch for feedback velocity data
+                           !     ln_grid_global          Global distribtion of observations
+                           !     ln_grid_search_lookup   Logical switch for obs grid search w/lookup table
+                           !     grid_search_file        Grid search lookup file header
+                           !     enactfiles              ENACT input observation file names
+                           !     coriofiles              Coriolis input observation file name
+   !                       ! profbfiles: Profile feedback input observation file name
    profbfiles = 'profiles_01.nc'
                            !     ln_profb_enatim         Enact feedback input time setting switch
+                           !     ln_profb_enatim         Enact feedback input time setting switch
                            !     slafilesact             Active SLA input observation file name
                            !     slafilespas             Passive SLA input observation file name
    !                       ! slafbfiles: Feedback SLA input observation file name
+                           !     slafilespas             Passive SLA input observation file name
+   !                       ! slafbfiles: Feedback SLA input observation file name
    slafbfiles = 'sla_01.nc'
                            !     sstfiles                GHRSST input observation file name
    !                       ! sstfbfiles: Feedback SST input observation file name
+                           !     sstfiles                GHRSST input observation file name
+   !                       ! sstfbfiles: Feedback SST input observation file name
    sstfbfiles = 'sst_01.nc' 'sst_02.nc' 'sst_03.nc' 'sst_04.nc' 'sst_05.nc'
                            !     seaicefiles             Sea Ice input observation file name
                            !     velavcurfiles           Vel. cur. daily av. input file name
                            !     velhvcurfiles           Vel. cur. high freq. input file name
                            !     velavadcpfiles          Vel. ADCP daily av. input file name
                            !     velhvadcpfiles          Vel. ADCP high freq. input file name
                            !     velfbfiles              Vel. feedback input observation file name
                            !     dobsini                 Initial date in window YYYYMMDD.HHMMSS
                            !     dobsend                 Final date in window YYYYMMDD.HHMMSS
                            !     n1dint                  Type of vertical interpolation method
                            !     n2dint                  Type of horizontal interpolation method
                            !     ln_nea                  Rejection of observations near land switch
    nmsshc     = 0          ! MSSH correction scheme
                            !     mdtcorr                 MDT  correction
                            !     mdtcutoff               MDT cutoff for computed correction
    ln_altbias = .false.    ! Logical switch for alt bias
    ln_ignmis  = .true.     ! Logical switch for ignoring missing files
                            !     endailyavtypes   ENACT daily average types
+                           !     seaicefiles             Sea Ice input observation file name
+                           !     velavcurfiles           Vel. cur. daily av. input file name
+                           !     velhvcurfiles           Vel. cur. high freq. input file name
+                           !     velavadcpfiles          Vel. ADCP daily av. input file name
+                           !     velhvadcpfiles          Vel. ADCP high freq. input file name
+                           !     velfbfiles              Vel. feedback input observation file name
+                           !     dobsini                 Initial date in window YYYYMMDD.HHMMSS
+                           !     dobsend                 Final date in window YYYYMMDD.HHMMSS
+                           !     n1dint                  Type of vertical interpolation method
+                           !     n2dint                  Type of horizontal interpolation method
+                           !     ln_nea                  Rejection of observations near land switch
+   nmsshc     = 0          ! MSSH correction scheme
+                           !     mdtcorr                 MDT  correction
+                           !     mdtcutoff               MDT cutoff for computed correction
+   ln_altbias = .false.    ! Logical switch for alt bias
+   ln_ignmis  = .true.     ! Logical switch for ignoring missing files
+                           !     endailyavtypes   ENACT daily average types
    ln_grid_global = .true.
    ln_grid_search_lookup = .false.
+/
+/

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namptr

r3294	r3989
4	4	ln_diaptr = .false. ! Poleward heat and salt transport (T) or not (F)
5	5	ln_diaznl = .true. ! Add zonal means and meridional stream functions
6		ln_subbas = .true. ! Atlantic/Pacific/Indian basins computation (T) or not
	6	ln_subbas = .true. ! Atlantic/Pacific/Indian basins computation (T) or not
7	7	! (orca configuration only, need input basins mask file named "subbasins.nc"
8	8	ln_ptrcomp = .true. ! Add decomposition : overturning

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namrun

-                      r3306
+                      r3989
 !-----------------------------------------------------------------------
    nn_no       =       0   !  job number (no more used...)
    cn_exp      =  "ORCA2"  !  experience name
+   cn_exp      =  "ORCA2"  !  experience name
    nn_it000    =       1   !  first time step
    nn_itend    =    5475   !  last  time step (std 5475)
+   nn_date0    =  010101   !  date at nit_0000 (format yyyymmdd)
+                           !  used if ln_rstart=F or (ln_rstart=T and nn_rstctl=0 or 1)
+   nn_date0    =  010101   !  date at nit_0000 (format yyyymmdd) used if ln_rstart=F or (ln_rstart=T and nn_rstctl=0 or 1)
    nn_leapy    =       0   !  Leap year calendar (1) or not (0)
    ln_rstart   = .false.   !  start from rest (F) or from a restart file (T)
    nn_rstctl   =       0   !  restart control => activated only if ln_rstart = T
        !  = 0 nn_date0 read in namelist ; nn_it000 : read in namelist
        !  = 1 nn_date0 read in namelist ; nn_it000 : check consistancy between namelist and restart
        !  = 2 nn_date0 read in restart  ; nn_it000 : check consistancy between namelist and restart
+                           !    = 0 nn_date0 read in namelist ; nn_it000 : read in namelist
+                           !    = 1 nn_date0 read in namelist ; nn_it000 : check consistancy between namelist and restart
+                           !    = 2 nn_date0 read in restart  ; nn_it000 : check consistancy between namelist and restart
    cn_ocerst_in  = "restart"   !  suffix of ocean restart name (input)
    cn_ocerst_out = "restart"   !  suffix of ocean restart name (output)

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namsbc

-                      r3294
+                      r3989
 &namsbc        !   Surface Boundary Condition (surface module)
 !-----------------------------------------------------------------------
    nn_fsbc     = 5         !  frequency of surface boundary condition computation
+   nn_fsbc     = 5         !  frequency of surface boundary condition computation
                            !     (also = the frequency of sea-ice model call)
    ln_ana      = .false.   !  analytical formulation                    (T => fill namsbc_ana )
+   ln_ana      = .false.   !  analytical formulation                    (T => fill namsbc_ana )
    ln_flx      = .false.   !  flux formulation                          (T => fill namsbc_flx )
    ln_blk_clio = .false.   !  CLIO bulk formulation                     (T => fill namsbc_clio)
    ln_blk_core = .true.    !  CORE bulk formulation                     (T => fill namsbc_core)
+   ln_blk_clio = .false.   !  CLIO bulk formulation                     (T => fill namsbc_clio)
+   ln_blk_core = .true.    !  CORE bulk formulation                     (T => fill namsbc_core)
    ln_blk_mfs  = .false.   !  MFS bulk formulation                      (T => fill namsbc_mfs )
    ln_cpl      = .false.   !  Coupled formulation                       (T => fill namsbc_cpl )
 …
                            !  =1 use observed ice-cover      ,
                            !  =2 ice-model used                         ("key_lim3" or "key_lim2)
+   nn_ice_embd = 0         !  =0 levitating ice (no mass exchange, concentration/dilution effect)
+                           !  =1 levitating ice with mass and salt exchange but no presure effect
+                           !  =2 embedded sea-ice (full salt and mass exchanges and pressure)
    ln_dm2dc    = .false.   !  daily mean to diurnal cycle on short wave
    ln_rnf      = .true.    !  runoffs                                   (T => fill namsbc_rnf)
    ln_ssr      = .true.    !  Sea Surface Restoring on T and/or S       (T => fill namsbc_ssr)
    nn_fwb      = 3         !  FreshWater Budget: =0 unchecked
                            !     =1 global mean of e-p-r set to zero at each time step
+   nn_fwb      = 3         !  FreshWater Budget: =0 unchecked
+                           !     =1 global mean of e-p-r set to zero at each time step
                            !     =2 annual global mean of e-p-r set to zero
                            !     =3 global emp set to zero and spread out over erp area
+   ln_wave = .false.       !  Activate coupling with wave (either Stokes Drift or Drag coefficient, or both)  (T => fill namsbc_wave)
    ln_cdgw = .false.       !  Neutral drag coefficient read from wave model (T => fill namsbc_wave)
+   ln_sdw  = .false.       !  Computation of 3D stokes drift                (T => fill namsbc_wave)
+/

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namsbc_alb

-                      r3294
+                      r3989
 &namsbc_alb    !   albedo parameters
 !-----------------------------------------------------------------------
    rn_cloud    =    0.06   !  cloud correction to snow and ice albedo
+   rn_cloud    =    0.06   !  cloud correction to snow and ice albedo
    rn_albice   =    0.53   !  albedo of melting ice in the arctic and antarctic
    rn_alphd    =    0.80   !  coefficients for linear interpolation used to
    rn_alphc    =    0.65   !  compute albedo between two extremes values
+   rn_alphc    =    0.65   !  compute albedo between two extremes values
    rn_alphdi   =    0.72   !  (Pyane, 1972)
+/

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namsbc_clio

r3294	r3989
1	1	!-----------------------------------------------------------------------
2		&namsbc_clio ! namsbc_clio CLIO bulk formulea
	2	&namsbc_clio ! namsbc_clio CLIO bulk formulae
3	3	!-----------------------------------------------------------------------
4	4	! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation !

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namsbc_core

-                      r3294
+                      r3989
 !-----------------------------------------------------------------------
 &namsbc_core   !   namsbc_core  CORE bulk formulea
+&namsbc_core   !   namsbc_core  CORE bulk formulae
 !-----------------------------------------------------------------------
 !              !  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation !
 !              !             !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  !
    sn_wndi = 'u_10.15JUNE2009_orca2'       ,  6  , 'U_10_MOD',   .false.    , .true. , 'yearly'  , ''       , 'Uwnd'
    sn_wndj = 'v_10.15JUNE2009_orca2'       ,  6  , 'V_10_MOD',   .false.    , .true. , 'yearly'  , ''       , 'Vwnd'
    sn_qsr  = 'ncar_rad.15JUNE2009_orca2'   , 24  , 'SWDN_MOD',   .false.    , .true. , 'yearly'  , ''       , ''
    sn_qlw  = 'ncar_rad.15JUNE2009_orca2'   , 24  , 'LWDN_MOD',   .false.    , .true. , 'yearly'  , ''       , ''
    sn_tair = 't_10.15JUNE2009_orca2'       ,  6  , 'T_10_MOD',   .false.    , .true. , 'yearly'  , ''       , ''
    sn_humi = 'q_10.15JUNE2009_orca2'       ,  6  , 'Q_10_MOD',   .false.    , .true. , 'yearly'  , ''       , ''
    sn_prec = 'ncar_precip.15JUNE2009_orca2', -1  , 'PRC_MOD1',   .false.    , .true. , 'yearly'  , ''       , ''
    sn_snow = 'ncar_precip.15JUNE2009_orca2', -1  , 'SNOW'    ,   .false.    , .true. , 'yearly'  , ''       , ''
    sn_tdif = 'taudif_core'                 , 24  , 'taudif'  ,   .false.    , .true. , 'yearly'  , ''       , ''
+!              !  file name                    ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation !
+!              !                               !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  !
+   sn_wndi     = 'u_10.15JUNE2009_orca2'       ,         6         , 'U_10_MOD',   .false.    , .true. , 'yearly'  , ''       , 'Uwnd'
+   sn_wndj     = 'v_10.15JUNE2009_orca2'       ,         6         , 'V_10_MOD',   .false.    , .true. , 'yearly'  , ''       , 'Vwnd'
+   sn_qsr      = 'ncar_rad.15JUNE2009_orca2'   ,        24         , 'SWDN_MOD',   .false.    , .true. , 'yearly'  , ''       , ''
+   sn_qlw      = 'ncar_rad.15JUNE2009_orca2'   ,        24         , 'LWDN_MOD',   .false.    , .true. , 'yearly'  , ''       , ''
+   sn_tair     = 't_10.15JUNE2009_orca2'       ,         6         , 'T_10_MOD',   .false.    , .true. , 'yearly'  , ''       , ''
+   sn_humi     = 'q_10.15JUNE2009_orca2'       ,         6         , 'Q_10_MOD',   .false.    , .true. , 'yearly'  , ''       , ''
+   sn_prec     = 'ncar_precip.15JUNE2009_orca2',        -1         , 'PRC_MOD1',   .false.    , .true. , 'yearly'  , ''       , ''
+   sn_snow     = 'ncar_precip.15JUNE2009_orca2',        -1         , 'SNOW'    ,   .false.    , .true. , 'yearly'  , ''       , ''
+   sn_tdif     = 'taudif_core'                 ,        24         , 'taudif'  ,   .false.    , .true. , 'yearly'  , ''       , ''
    cn_dir      = './'      !  root directory for the location of the bulk files

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namsbc_cpl

-                      r3294
+                      r3989
 !                    !                       ! categories !  reference  !    orientation       ! grids  !
 ! send
 sn_snd_temp   =       'weighted oce and ice' ,    'no'    ,     ''      ,         ''           ,   ''
 sn_snd_alb    =       'weighted ice'         ,    'no'    ,     ''      ,         ''           ,   ''
 sn_snd_thick  =       'none'                 ,    'no'    ,     ''      ,         ''           ,   ''
 sn_snd_crt    =       'none'                 ,    'no'    , 'spherical' , 'eastward-northward' ,  'T'
 sn_snd_co2    =       'coupled'              ,    'no'    ,     ''      ,         ''           ,   ''
+sn_snd_temp   =       'weighted oce and ice' ,    'no'    ,     ''      ,         ''           ,   ''
+sn_snd_alb    =       'weighted ice'         ,    'no'    ,     ''      ,         ''           ,   ''
+sn_snd_thick  =       'none'                 ,    'no'   ,     ''      ,         ''           ,   ''
+sn_snd_crt    =       'none'                 ,    'no'    , 'spherical' , 'eastward-northward' ,  'T'
+sn_snd_co2    =       'coupled'              ,    'no'    ,     ''      ,         ''           ,   ''
 ! receive
 sn_rcv_w10m   =       'none'                 ,    'no'    ,     ''      ,         ''          ,   ''
 sn_rcv_taumod =       'coupled'              ,    'no'    ,     ''      ,         ''          ,   ''
 sn_rcv_tau    =       'oce only'             ,    'no'    , 'cartesian' , 'eastward-northward',  'U,V'
 sn_rcv_dqnsdt =       'coupled'              ,    'no'    ,     ''      ,         ''          ,   ''
 sn_rcv_qsr    =       'oce and ice'          ,    'no'    ,     ''      ,         ''          ,   ''
 sn_rcv_qns    =       'oce and ice'          ,    'no'    ,     ''      ,         ''          ,   ''
 sn_rcv_emp    =       'conservative'         ,    'no'    ,     ''      ,         ''          ,   ''
 sn_rcv_rnf    =       'coupled'              ,    'no'    ,     ''      ,         ''          ,   ''
 sn_rcv_cal    =       'coupled'              ,    'no'    ,     ''      ,         ''          ,   ''
 sn_rcv_co2    =       'coupled'              ,    'no'    ,     ''      ,         ''          ,   ''
+sn_rcv_w10m   =       'none'                 ,    'no'    ,     ''      ,         ''          ,   ''
+sn_rcv_taumod =       'coupled'              ,    'no'    ,     ''      ,         ''          ,   ''
+sn_rcv_tau    =       'oce only'             ,    'no'    , 'cartesian' , 'eastward-northward',  'U,V'
+sn_rcv_dqnsdt =       'coupled'              ,    'no'    ,     ''      ,         ''          ,   ''
+sn_rcv_qsr    =       'oce and ice'          ,    'no'    ,     ''      ,         ''          ,   ''
+sn_rcv_qns    =       'oce and ice'          ,    'no'    ,     ''      ,         ''          ,   ''
+sn_rcv_emp    =       'conservative'         ,    'no'    ,     ''      ,         ''          ,   ''
+sn_rcv_rnf    =       'coupled'              ,    'no'    ,     ''      ,         ''          ,   ''
+sn_rcv_cal    =       'coupled'              ,    'no'    ,     ''      ,         ''          ,   ''
+sn_rcv_co2    =       'coupled'              ,    'no'    ,     ''      ,         ''          ,   ''
+/

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namsbc_flx

r3294	r3989
11	11
12	12	cn_dir = './' ! root directory for the location of the flux files
13		/
	13	/

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namsbc_mfs

r3294	r3989
10	10	sn_tair = 'ecmwf' , 6 , 't2' , .true. , .false. , 'daily' ,'bicubic.nc' , ''
11	11	sn_rhm = 'ecmwf' , 6 , 'rh' , .true. , .false. , 'daily' ,'bilinear.nc', ''
12		sn_prec = '~~precip' , 6 , 'precip' , .true. , .false. , 'daily' ,'bicubic'~~ , ''
	12	sn_prec = 'ecmwf' , 6 , 'precip' , .true. , .true. , 'daily' ,'bicubic.nc' , ''
13	13
14	14	cn_dir = './ECMWF/' ! root directory for the location of the bulk files

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namsbc_rnf

-                      r3294
+                      r3989
 &namsbc_rnf    !   runoffs namelist surface boundary condition
 !-----------------------------------------------------------------------
 !              !  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation !
 !              !             !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  !
    sn_rnf      = 'runoff_core_monthly',    -1    , 'sorunoff',   .true.     , .true. , 'yearly'  , ''       , ''
    sn_cnf      = 'runoff_core_monthly',     0    , 'socoefr0',   .false.    , .true. , 'yearly'  , ''       , ''
    sn_s_rnf    = 'runoffs'            ,    24    , 'rosaline',   .true.     , .true. , 'yearly'  , ''       , ''
    sn_t_rnf    = 'runoffs'            ,    24    , 'rotemper',   .true.     , .true. , 'yearly'  , ''       , ''
    sn_dep_rnf  = 'runoffs'            ,     0    , 'rodepth' ,   .false.    , .true. , 'yearly'  , ''       , ''
+!              !  file name           ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation !
+!              !                      !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  !
+   sn_rnf      = 'runoff_core_monthly',        -1         , 'sorunoff',   .true.     , .true. , 'yearly'  , ''       , ''
+   sn_cnf      = 'runoff_core_monthly',         0         , 'socoefr0',   .false.    , .true. , 'yearly'  , ''       , ''
+   sn_s_rnf    = 'runoffs'            ,        24         , 'rosaline',   .true.     , .true. , 'yearly'  , ''       , ''
+   sn_t_rnf    = 'runoffs'            ,        24         , 'rotemper',   .true.     , .true. , 'yearly'  , ''       , ''
+   sn_dep_rnf  = 'runoffs'            ,         0         , 'rodepth' ,   .false.    , .true. , 'yearly'  , ''       , ''
    cn_dir       = './'      !  root directory for the location of the runoff files

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namsbc_ssr

-                      r3294
+                      r3989
    cn_dir      = './'      !  root directory for the location of the runoff files
    nn_sstr     =     0     !  add a retroaction term in the surface heat       flux (=1) or not (=0)
    nn_sssr     =     2     !  add a damping     term in the surface freshwater flux (=2)
+   nn_sssr     =     2     !  add a damping     term in the surface freshwater flux (=2)
                            !  or to SSS only (=1) or no damping term (=0)
    rn_dqdt     =   -40.    !  magnitude of the retroaction on temperature   [W/m2/K]
    rn_deds     =   -27.7   !  magnitude of the damping on salinity   [mm/day]
+   rn_deds     =  -166.67  !  magnitude of the damping on salinity   [mm/day]
    ln_sssr_bnd =   .true.  !  flag to bound erp term (associated with nn_sssr=2)
    rn_sssr_bnd =   4.e0    !  ABS(Max/Min) value of the damping erp term [mm/day]
+/
+/

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namsbc_wave

-                      r3294
+                      r3989
 !              !  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation !
 !              !             !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  !
+   sn_cdg      =  'cdg_wave' ,        1          , 'drag_coeff' , .true.    , .false. , 'daily'  , ''       , ''
+   sn_cdg      =  'cdg_wave' ,        1          , 'drag_coeff' , .true.   , .false. , 'daily'  ,''         , ''
+   sn_usd      =  'sdw_wave' ,        1          , 'u_sd2d'     , .true.   , .false. , 'daily'  ,''         , ''
+   sn_vsd      =  'sdw_wave' ,        1          , 'v_sd2d'     , .true.   , .false. , 'daily'  ,''         , ''
+   sn_wn       =  'sdw_wave' ,        1          , 'wave_num'   , .true.   , .false. , 'daily'  ,''         , ''
+!
    cn_dir_cdg  = './'  !  root directory for the location of drag coefficient files

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namsol

r3294	r3989
1	1	!-----------------------------------------------------------------------
2		&namsol ! elliptic solver / island / free surface
	2	&namsol ! elliptic solver / island / free surface
3	3	!-----------------------------------------------------------------------
4	4	nn_solv = 1 ! elliptic solver: =1 preconditioned conjugate gradient (pcg)

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namtra_adv

-                      r3294
+                      r3989
 !-----------------------------------------------------------------------
 &namtra_adv    !   advection scheme for tracer
+&namtra_adv    !   advection scheme for tracer
 !-----------------------------------------------------------------------
+   ln_traadv_cen2   =  .false.  !  2nd order centered scheme
+   ln_traadv_tvd    =  .true.   !  TVD scheme
+   ln_traadv_muscl  =  .false.  !  MUSCL scheme
+   ln_traadv_muscl2 =  .false.  !  MUSCL2 scheme + cen2 at boundaries
+   ln_traadv_ubs    =  .false.  !  UBS scheme
+   ln_traadv_qck    =  .false.  !  QUCIKEST scheme
+   ln_traadv_cen2   =  .false.  !  2nd order centered scheme
+   ln_traadv_tvd    =  .true.   !  TVD scheme
+   ln_traadv_muscl  =  .false.  !  MUSCL scheme
+   ln_traadv_muscl2 =  .false.  !  MUSCL2 scheme + cen2 at boundaries
+   ln_traadv_ubs    =  .false.  !  UBS scheme
+   ln_traadv_qck    =  .false.  !  QUICKEST scheme
+   ln_traadv_msc_ups=  .false.  !  use upstream scheme within muscl
+/

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namtra_bbc

-                      r2540
+                      r3989
 !-----------------------------------------------------------------------
    ln_trabbc   = .true.    !  Apply a geothermal heating at the ocean bottom
    nn_geoflx   =    2      !  geothermal heat flux: = 0 no flux
+   nn_geoflx   =    2      !  geothermal heat flux: = 0 no flux
                            !     = 1 constant flux
                            !     = 2 variable flux (read in geothermal_heating.nc in mW/m2)
+                           !     = 2 variable flux (read in geothermal_heating.nc in mW/m2)
    rn_geoflx_cst = 86.4e-3 !  Constant value of geothermal heat flux [W/m2]
+/

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namtra_ldf

-                      r3296
+                      r3989
    rn_ahtb_0        =     0.    !  background eddy diffusivity for ldf_iso [m2/s]
    !                                           (normally=0; not used with Griffies)
+   rn_slpmax        =     0.01  !  slope limit
+   rn_chsmag        =     1.    !  multiplicative factor in Smagorinsky diffusivity
+   rn_smsh          =     1.    !  Smagorinsky diffusivity: = 0 - use only sheer
+   rn_aht_m         =  2000.    !  upper limit or stability criteria for lateral eddy diffusivity (m2/s)
+/

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namtsd

-                      r3294
+                      r3989
 &namtsd    !   data : Temperature  & Salinity
 !-----------------------------------------------------------------------
 !          ! file name ! frequency (hours)         ! variable     ! time interp. ! clim  !'yearly' or ! weights  ! rotation !
 !          !           !  (if <0  months)          !   name       !  (logical)   ! (T/F) ! 'monthly'  ! filename ! pairing  !
    sn_tem  = 'data_1m_potential_temperature_nomask', -1,'votemper',  .true.      , .true., 'yearly'   , ' '      , ' '
    sn_sal  = 'data_1m_salinity_nomask'             , -1,'vosaline',  .true.      , .true., 'yearly'   , ''       , ' '
+!          ! file name ! frequency (hours)    ! variable ! time interp. ! clim  !'yearly' or ! weights  ! rotation !
+!          !           !  (if <0  months)     !   name   !  (logical)   ! (T/F) ! 'monthly'  ! filename ! pairing  !
+   sn_tem  = 'data_1m_potential_temperature_nomask', -1,'votemper',  .true.  , .true., 'yearly'   , ' '      , ' '
+   sn_sal  = 'data_1m_salinity_nomask'             , -1,'vosaline',  .true.  , .true., 'yearly'   , ''       , ' '
+   !
    cn_dir        = './'     !  root directory for the location of the runoff files

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namzdf_kpp

-                      r3294
+                      r3989
 &namzdf_kpp    !   K-Profile Parameterization dependent vertical mixing  ("key_zdfkpp", and optionally:
 !------------------------------------------------------------------------ "key_kppcustom" or "key_kpplktb")
    ln_kpprimix = .true.    !  shear instability mixing
+   ln_kpprimix = .true.    !  shear instability mixing
    rn_difmiw   =  1.0e-04  !  constant internal wave viscosity [m2/s]
    rn_difsiw   =  0.1e-04  !  constant internal wave diffusivity [m2/s]
    rn_riinfty  =  0.8      !  local Richardson Number limit for shear instability
    rn_difri    =  0.0050   !  maximum shear mixing at Rig = 0    [m2/s]
    rn_bvsqcon  = -0.01e-07 !  Brunt-Vaisala squared for maximum convection [1/s2]
    rn_difcon   =  1.       !  maximum mixing in interior convection [m2/s]
+   rn_bvsqcon  = -0.01e-07 !  Brunt-Vaisala squared for maximum convection [1/s2]
+   rn_difcon   =  1.       !  maximum mixing in interior convection [m2/s]
    nn_avb      =  0        !  horizontal averaged (=1) or not (=0) on avt and amv
    nn_ave      =  1        !  constant (=0) or profile (=1) background on avt

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namzdf_tke

r3294	r3989
7	7	rn_emin = 1.e-6 ! minimum value of tke [m2/s2]
8	8	rn_emin0 = 1.e-4 ! surface minimum value of tke [m2/s2]
	9	rn_bshear = 1.e-20 ! background shear (>0) currently a numerical threshold (do not change it)
9	10	nn_mxl = 2 ! mixing length: = 0 bounded by the distance to surface and bottom
10	11	! = 1 bounded by the local vertical scale factor

branches/2013/dev_r3853_CNRS9_ConfSetting/DOC/TexFiles/Namelist/namzdf_tmx

r2540	r3989
5	5	rn_n2min = 1.e-8 ! threshold of the Brunt-Vaisala frequency (s-1)
6	6	rn_tfe = 0.333 ! tidal dissipation efficiency
7		rn_me = 0.2 ! mixing efficiency
	7	rn_me = 0.2 ! mixing efficiency
8	8	ln_tmx_itf = .true. ! ITF specific parameterisation
9	9	rn_tfe_itf = 1. ! ITF tidal dissipation efficiency

branches/2013/dev_r3853_CNRS9_ConfSetting/NEMOGCM/CONFIG/SHARED/README_other_configurations_namelist_namcfg

-                      r3973
+                      r3989
 !-----------------------------------------------------------------------
    cp_cfg      =  "orca"               !  name of the configuration
+   cp_cfz      =  "antarctic"          !  name of the zoom of configuration
    jp_cfg      =      05               !  resolution of the configuration
    jpidta      =     722               !  1st lateral dimension ( >= jpi )
 …
 !-----------------------------------------------------------------------
    cp_cfg      =  "orca"               !  name of the configuration
+   cp_cfz      =  "arctic"             !  name of the zoom of configuration
    jp_cfg      =      05               !  resolution of the configuration
    jpidta      =     722               !  1st lateral dimension ( >= jpi )
 …
    ppacr2      =  999999.0             !
+/
+ORCA2 - Antarctic zoom
+======================
+!-----------------------------------------------------------------------
+&namcfg        !   parameters of the configuration
+!-----------------------------------------------------------------------
+   cp_cfg      =  "orca"               !  name of the configuration
+   cp_cfz      =  "antarctic"          !  name of the zoom of configuration
+   jp_cfg      =       2               !  resolution of the configuration
+   jpidta      =     182               !  1st lateral dimension ( >= jpi )
+   jpjdta      =     149               !  2nd    "         "    ( >= jpj )
+   jpkdta      =      31               !  number of levels      ( >= jpk )
+   jpiglo      =     182               !  1st dimension of global domain --> i =jpidta
+   jpjglo      =      50               !  2nd    -                  -    --> j  =jpjdta
+   jpizoom     =       1               !  left bottom (i,j) indices of the zoom
+   jpjzoom     =       1               !  in data domain indices
+   jperio      =       1               !  lateral cond. type (between 0 and 6)
+   jphgr_msh   =       0               !  type of horizontal mesh
+   ppglam0     =  999999.0             !  longitude of first raw and column T-point (jphgr_msh = 1)
+   ppgphi0     =  999999.0             ! latitude  of first raw and column T-point (jphgr_msh = 1)
+   ppe1_deg    =  999999.0             !  zonal      grid-spacing (degrees)
+   ppe2_deg    =  999999.0             !  meridional grid-spacing (degrees)
+   ppe1_m      =  999999.0             !  zonal      grid-spacing (degrees)
+   ppe2_m      =  999999.0             !  meridional grid-spacing (degrees)
+   ppsur       =   -4762.96143546300   !  ORCA r4, r2 and r05 coefficients
+   ppa0        =     255.58049070440   ! (default coefficients)
+   ppa1        =     245.58132232490   !
+   ppkth       =      21.43336197938   !
+   ppacr       =       3.0             !
+   ppdzmin     =  999999.              !  Minimum vertical spacing
+   pphmax      =  999999.              !  Maximum depth
+   ldbletanh   =  .FALSE.              !  Use/do not use double tanf function for vertical coordinates
+   ppa2        =  999999.              !  Double tanh function parameters
+   ppkth2      =  999999.              !
+   ppacr2      =  999999.              !
+/
+ORCA2 - Arctic zoom
+===================
+!-----------------------------------------------------------------------
+&namcfg        !   parameters of the configuration
+!-----------------------------------------------------------------------
+   cp_cfg      =  "orca"               !  name of the configuration
+   cp_cfz      =  "arctic"             !  name of the zoom of configuration
+   jp_cfg      =       2               !  resolution of the configuration
+   jpidta      =     182               !  1st lateral dimension ( >= jpi )
+   jpjdta      =     149               !  2nd    "         "    ( >= jpj )
+   jpkdta      =      31               !  number of levels      ( >= jpk )
+   jpiglo      =     142               !  1st dimension of global domain --> i =jpidta
+   jpjglo      =      53               !  2nd    -                  -    --> j  =jpjdta
+   jpizoom     =      21               !  left bottom (i,j) indices of the zoom
+   jpjzoom     =      97               !  in data domain indices
+   jperio      =       3               !  lateral cond. type (between 0 and 6)
+   jphgr_msh   =       0               !  type of horizontal mesh
+   ppglam0     =  999999.0             !  longitude of first raw and column T-point (jphgr_msh = 1)
+   ppgphi0     =  999999.0             ! latitude  of first raw and column T-point (jphgr_msh = 1)
+   ppe1_deg    =  999999.0             !  zonal      grid-spacing (degrees)
+   ppe2_deg    =  999999.0             !  meridional grid-spacing (degrees)
+   ppe1_m      =  999999.0             !  zonal      grid-spacing (degrees)
+   ppe2_m      =  999999.0             !  meridional grid-spacing (degrees)
+   ppsur       =   -4762.96143546300   !  ORCA r4, r2 and r05 coefficients
+   ppa0        =     255.58049070440   ! (default coefficients)
+   ppa1        =     245.58132232490   !
+   ppkth       =      21.43336197938   !
+   ppacr       =       3.0             !
+   ppdzmin     =  999999.              !  Minimum vertical spacing
+   pphmax      =  999999.              !  Maximum depth
+   ldbletanh   =  .FALSE.              !  Use/do not use double tanf function for vertical coordinates
+   ppa2        =  999999.              !  Double tanh function parameters
+   ppkth2      =  999999.              !
+   ppacr2      =  999999.              !
+/
 ORCA025 - 75 vertical levels
 =======
 …
    ppacr2      =  999999.0             !
+/
+C1D - 1D configuration. Add key_c1d in active cpp keys
+!-----------------------------------------------------------------------
+&namcfg        !   parameters of the configuration
+!-----------------------------------------------------------------------
+   cp_cfg      =  "orca"               !  name of the configuration
+   jp_cfg      =       2               !  resolution of the configuration
+   jpidta      =     182               !  1st lateral dimension ( >= jpi )
+   jpjdta      =     149               !  2nd    "         "    ( >= jpj )
+   jpkdta      =      31               !  number of levels      ( >= jpk )
+   jpiglo      =       3               !  1st dimension of global domain --> i =jpidta
+   jpjglo      =       3               !  2nd    -                  -    --> j  =jpjdta
+! Choose postion of the 1D column:
+!            jpizoom =   61, jpjzoom =   133  (160W,75N)
+!            jpizoom =   61, jpjzoom =   110  (160W,50N)
+!            jpizoom =   61, jpjzoom =   97   (160W,30N)
+!            jpizoom =   61, jpjzoom =   86   (160W,10N)
+!            jpizoom =   61, jpjzoom =   49   (160W,30S)
+!            jpizoom =   61, jpjzoom =   27   (160W,60S)
+!            jpizoom =   61, jpjzoom =    7   (160W,75S)
+!            jpizoom =   110,jpjzoom =   97   (64W,31.5N) BATS site
+   jpizoom     =       1               !  left bottom (i,j) indices of the zoom
+   jpjzoom     =       1               !  in data domain indices
+   jperio      =       0               !  lateral cond. type (between 0 and 6)
+   jphgr_msh   =       0               !  type of horizontal mesh
+   ppglam0     =  999999.0             !  longitude of first raw and column T-point (jphgr_msh = 1)
+   ppgphi0     =  999999.0             ! latitude  of first raw and column T-point (jphgr_msh = 1)
+   ppe1_deg    =  999999.0             !  zonal      grid-spacing (degrees)
+   ppe2_deg    =  999999.0             !  meridional grid-spacing (degrees)
+   ppe1_m      =  999999.0             !  zonal      grid-spacing (degrees)
+   ppe2_m      =  999999.0             !  meridional grid-spacing (degrees)
+   ppsur       =   -4762.96143546300   !  ORCA r4, r2 and r05 coefficients
+   ppa0        =     255.58049070440   ! (default coefficients)
+   ppa1        =     245.58132232490   !
+   ppkth       =      21.43336197938   !
+   ppacr       =       3.0             !
+   ppdzmin     =  999999.              !  Minimum vertical spacing
+   pphmax      =  999999.              !  Maximum depth
+   ldbletanh   =  .FALSE.              !  Use/do not use double tanf function for vertical coordinates
+   ppa2        =  999999.              !  Double tanh function parameters
+   ppkth2      =  999999.              !
+   ppacr2      =  999999.              !
+/

branches/2013/dev_r3853_CNRS9_ConfSetting/NEMOGCM/CONFIG/SHARED/namelist_ref

-                      r3973
+                      r3989
+!
 !-----------------------------------------------------------------------
+&namcfg     !   parameters of the configuration (to be changed in your namelist_cfg in CONFIG/"YOUR_CONFIG"/EXP00
+!      For ORCA2 Antartic zoom, use &namcfg from ORCA2_LIM/EXP00/namelist_cfg changing
+!          jpjglo = 50, jperio = 1,
+!      For ORCA2 Arctic zoom, use &namcfg from ORCA2_LIM/EXP00/namelist_cfg changing
+!          jpiglo = 142, jpjglo = jpjdta-97+1, jpizoom =  21, jpjzoom = 97, jperio = 3
+!      For 1D configuration, use &namcfg from ORCA2_LIM/EXP00/namelist_cfg changing
+!          jpiglo = 3, jpjglo = 3, jperio = 0 and choose postion of the 1D column:
+!            jpizoom =   61, jpjzoom =   133  (160W,75N)
+!            jpizoom =   61, jpjzoom =   110  (160W,50N)
+!            jpizoom =   61, jpjzoom =   97   (160W,30N)
+!            jpizoom =   61, jpjzoom =   86   (160W,10N)
+!            jpizoom =   61, jpjzoom =   49   (160W,30S)
+!            jpizoom =   61, jpjzoom =   27   (160W,60S)
+!            jpizoom =   61, jpjzoom =    7   (160W,75S)
+!            jpizoom =   110,jpjzoom =   97   (64W,31.5N) BATS site
+!
+&namcfg     !   default parameters of the configuration
 !-----------------------------------------------------------------------
    cp_cfg      =  "default"            !  name of the configuration
+   cp_cfz      =         ''            !  name of the zoom of configuration
    jp_cfg      =       0               !  resolution of the configuration
    jpidta      =      10               !  1st lateral dimension ( >= jpi )

branches/2013/dev_r3853_CNRS9_ConfSetting/NEMOGCM/NEMO/OPA_SRC/DOM/dom_oce.F90

r3973	r3989
72	72	LOGICAL, PUBLIC :: lzoom_s = .FALSE. !: South zoom type flag
73	73	LOGICAL, PUBLIC :: lzoom_n = .FALSE. !: North zoom type flag
74		~~LOGICAL, PUBLIC :: lzoom_arct = .FALSE. !: ORCA arctic zoom flag~~
75		~~LOGICAL, PUBLIC :: lzoom_anta = .FALSE. !: ORCA antarctic zoom flag~~
76	74
77	75	! !!! domain parameters linked to mpp

branches/2013/dev_r3853_CNRS9_ConfSetting/NEMOGCM/NEMO/OPA_SRC/DOM/domcfg.F90

-                      r3973
+                      r3989
          SELECT CASE ( jp_cfg )
          CASE ( 2 )                               !  ORCA_R2 configuration
+            IF(  jpiglo  == 142    .AND. jpjglo  ==  53 .AND.   &
+               & jpizoom ==  21    .AND. jpjzoom ==  97         )   lzoom_arct = .TRUE.
+            IF(  jpiglo  == jpidta .AND. jpjglo  ==  50 .AND.   &
+               & jpizoom ==   1    .AND. jpjzoom ==   1         )   lzoom_anta = .TRUE.
+            IF(  cp_cfz == "arctic"    .AND. jpiglo  == 142    .AND. jpjglo  ==  53 .AND.   &
+               & jpizoom ==  21    .AND. jpjzoom ==  97         )   THEN
+              IF(lwp) WRITE(numout,*) '          ORCA configuration: arctic zoom '
+            ENDIF
+            IF(  cp_cfz == "antarctic" .AND. jpiglo  == jpidta .AND. jpjglo  ==  50 .AND.   &
+               & jpizoom ==   1    .AND. jpjzoom ==   1         )   THEN
+              IF(lwp) WRITE(numout,*) '          ORCA configuration: antarctic zoom '
+            ENDIF
+            !
          CASE ( 05 )                              !  ORCA_R05 configuration
+            IF(  jpiglo  == 562    .AND. jpjglo  == 202 .AND.   &
+               & jpizoom ==  81    .AND. jpjzoom == 301         )   lzoom_arct = .TRUE.
+            IF(  jpiglo  == jpidta .AND. jpjglo  == 187 .AND.   &
+               & jpizoom ==   1    .AND. jpjzoom ==   1         )   lzoom_anta = .TRUE.
+            IF(    cp_cfz == "arctic"    .AND. jpiglo  == 562    .AND. jpjglo  == 202 .AND.   &
+               & jpizoom ==  81    .AND. jpjzoom == 301         )   THEN
+              IF(lwp) WRITE(numout,*) '          ORCA configuration: arctic zoom '
+            ENDIF
+            IF(    cp_cfz == "antarctic" .AND. jpiglo  == jpidta .AND. jpjglo  == 187 .AND.   &
+               & jpizoom ==   1    .AND. jpjzoom ==   1         )   THEN
+              IF(lwp) WRITE(numout,*) '          ORCA configuration: antarctic zoom '
+            ENDIF
          END SELECT
+         !
-         IF(lwp) WRITE(numout,*) '          ORCA configuration: antarctic/arctic zoom flags : '
-         IF(lwp) WRITE(numout,*) '             lzoom_arct = ', lzoom_arct, ' (T=   arctic zoom, F=global)'
-         IF(lwp) WRITE(numout,*) '             lzoom_anta = ', lzoom_anta, ' (T=antarctic zoom, F=global)'
+         !
       ENDIF

branches/2013/dev_r3853_CNRS9_ConfSetting/NEMOGCM/NEMO/OPA_SRC/DOM/domzgr.F90

r3901	r3989
564	564	! Configuration specific domain modifications
565	565	! (here, ORCA arctic configuration: suppress Med Sea)
566		IF( cp_cfg == "orca" .AND. ~~lzoom_arct~~ ) THEN
	566	IF( cp_cfg == "orca" .AND. cp_cfz == "arctic" ) THEN
567	567	SELECT CASE ( jp_cfg )
568	568	! ! =======================

branches/2013/dev_r3853_CNRS9_ConfSetting/NEMOGCM/NEMO/OPA_SRC/LDF/ldfdyn_c2d.h90

-                      r3294
+                      r3989
       IF(lwp) WRITE(numout,*) '        orca ocean configuration'
+#if defined key_antarctic
+#     include "ldfdyn_antarctic.h90"
+#elif defined key_arctic
+#     include "ldfdyn_arctic.h90"
+#else
+      ! Read 2d integer array to specify western boundary increase in the
+      ! ===================== equatorial strip (20N-20S) defined at t-points
+      CALL ctl_opn( inum, 'ahmcoef', 'OLD', 'FORMATTED', 'SEQUENTIAL', -1, numout, lwp )
+      READ(inum,9101) clexp, iim, ijm
+      READ(inum,'(/)')
+      ifreq = 40
+      il1 = 1
+      DO jn = 1, jpidta/ifreq+1
+      IF( cp_cfg == "orca" .AND. cp_cfz == "antarctic" ) THEN
+!
+! 1.2 Modify ahm
+! --------------
+         IF(lwp)WRITE(numout,*) ' inildf: Antarctic ocean'
+         IF(lwp)WRITE(numout,*) '         no tropics, no reduction of ahm'
+         IF(lwp)WRITE(numout,*) '         north boundary increase'
+         ahm1(:,:) = ahm0
+         ahm2(:,:) = ahm0
+         ijpt0=max(1,min(49 -njmpp+1,jpj))
+         ijpt1=max(0,min(49-njmpp+1,jpj-1))
+         DO jj=ijpt0,ijpt1
+            ahm2(:,jj)=ahm0*2.
+            ahm1(:,jj)=ahm0*2.
+         END DO
+         ijpt0=max(1,min(48 -njmpp+1,jpj))
+         ijpt1=max(0,min(48-njmpp+1,jpj-1))
+         DO jj=ijpt0,ijpt1
+            ahm2(:,jj)=ahm0*1.9
+            ahm1(:,jj)=ahm0*1.75
+         END DO
+         ijpt0=max(1,min(47 -njmpp+1,jpj))
+         ijpt1=max(0,min(47-njmpp+1,jpj-1))
+         DO jj=ijpt0,ijpt1
+            ahm2(:,jj)=ahm0*1.5
+            ahm1(:,jj)=ahm0*1.25
+         END DO
+         ijpt0=max(1,min(46 -njmpp+1,jpj))
+         ijpt1=max(0,min(46-njmpp+1,jpj-1))
+         DO jj=ijpt0,ijpt1
+            ahm2(:,jj)=ahm0*1.1
+         END DO
+      ELSE IF( cp_cfg == "orca" .AND. cp_cfz == "arctic" ) THEN
+! 1.2 Modify ahm
+! --------------
+         IF(lwp)WRITE(numout,*) ' inildf: Arctic ocean'
+         IF(lwp)WRITE(numout,*) '         no tropics, no reduction of ahm'
+         IF(lwp)WRITE(numout,*) '         south and west boundary increase'
+         ahm1(:,:) = ahm0
+         ahm2(:,:) = ahm0
+         ijpt0=max(1,min(98-jpjzoom+1-njmpp+1,jpj))
+         ijpt1=max(0,min(98-jpjzoom+1-njmpp+1,jpj-1))
+         DO jj=ijpt0,ijpt1
+            ahm2(:,jj)=ahm0*2.
+            ahm1(:,jj)=ahm0*2.
+         END DO
+         ijpt0=max(1,min(99-jpjzoom+1-njmpp+1,jpj))
+         ijpt1=max(0,min(99-jpjzoom+1-njmpp+1,jpj-1))
+         DO jj=ijpt0,ijpt1
+            ahm2(:,jj)=ahm0*1.9
+            ahm1(:,jj)=ahm0*1.75
+         END DO
+         ijpt0=max(1,min(100-jpjzoom+1-njmpp+1,jpj))
+         ijpt1=max(0,min(100-jpjzoom+1-njmpp+1,jpj-1))
+         DO jj=ijpt0,ijpt1
+            ahm2(:,jj)=ahm0*1.5
+            ahm1(:,jj)=ahm0*1.25
+         END DO
+         ijpt0=max(1,min(101-jpjzoom+1-njmpp+1,jpj))
+         ijpt1=max(0,min(101-jpjzoom+1-njmpp+1,jpj-1))
+         DO jj=ijpt0,ijpt1
+            ahm2(:,jj)=ahm0*1.1
+         END DO
+      ELSE
+         ! Read 2d integer array to specify western boundary increase in the
+         ! ===================== equatorial strip (20N-20S) defined at t-points
+         CALL ctl_opn( inum, 'ahmcoef', 'OLD', 'FORMATTED', 'SEQUENTIAL', -1, numout, lwp )
+         READ(inum,9101) clexp, iim, ijm
          READ(inum,'(/)')
+         il2 = MIN( jpidta, il1+ifreq-1 )
+         READ(inum,9201) ( ii, ji = il1, il2, 5 )
+         READ(inum,'(/)')
+         DO jj = jpjdta, 1, -1
+            READ(inum,9202) ij, ( idata(ji,jj), ji = il1, il2 )
+         END DO
+         il1 = il1 + ifreq
+      END DO
+      DO jj = 1, nlcj
+         DO ji = 1, nlci
+            icof(ji,jj) = idata( mig(ji), mjg(jj) )
+         END DO
+      END DO
+      DO jj = nlcj+1, jpj
+         DO ji = 1, nlci
+            icof(ji,jj) = icof(ji,nlcj)
+         END DO
+      END DO
+      DO jj = 1, jpj
+         DO ji = nlci+1, jpi
+            icof(ji,jj) = icof(nlci,jj)
+         END DO
+      END DO
+FORMAT(1x,a15,2i8)
+FORMAT(3x,13(i3,12x))
+FORMAT(i3,41i3)
+      ! Set ahm1 and ahm2  ( T- and F- points) (used for laplacian operator)
+      ! =================
+      ! define ahm1 and ahm2 at the right grid point position
+      ! (USER: modify ahm1 and ahm2 following your desiderata)
+      ! Decrease ahm to zahmeq m2/s in the tropics
+      ! (from 90 to 20 degre: ahm = constant
+      ! from 20 to  2.5 degre: ahm = decrease in (1-cos)/2
+      ! from  2.5 to  0 degre: ahm = constant
+      ! symmetric in the south hemisphere)
+      zahmeq = aht0
+      DO jj = 1, jpj
+         DO ji = 1, jpi
+            IF( ABS( gphif(ji,jj) ) >= 20. ) THEN
+               ahm2(ji,jj) =  ahm0
+            ELSEIF( ABS( gphif(ji,jj) ) <= 2.5 ) THEN
+               ahm2(ji,jj) =  zahmeq
+            ELSE
+               ahm2(ji,jj) = zahmeq + (ahm0-zahmeq)/2.   &
+                  * ( 1. - COS( rad * ( ABS(gphif(ji,jj))-2.5 ) * 180. / 17.5 ) )
+            ENDIF
+            IF( ABS( gphit(ji,jj) ) >= 20. ) THEN
+               ahm1(ji,jj) =  ahm0
+            ELSEIF( ABS( gphit(ji,jj) ) <= 2.5 ) THEN
+               ahm1(ji,jj) =  zahmeq
+            ELSE
+               ahm1(ji,jj) = zahmeq + (ahm0-zahmeq)/2.   &
+                  * ( 1. - COS( rad * ( ABS(gphit(ji,jj))-2.5 ) * 180. / 17.5 ) )
+            ENDIF
+         END DO
+      END DO
+      ! increase along western boundaries of equatorial strip
+      ! t-point
+      DO jj = 1, jpjm1
+         DO ji = 1, jpim1
+            zcoft = FLOAT( icof(ji,jj) ) / 100.
+            ahm1(ji,jj) = zcoft * ahm0 + (1.-zcoft) * ahm1(ji,jj)
+         END DO
+      END DO
+      ! f-point
+      icof(:,:) = icof(:,:) * tmask(:,:,1)
+      DO jj = 1, jpjm1
+         DO ji = 1, jpim1   ! NO vector opt.
+            zmsk = tmask(ji,jj+1,1) + tmask(ji+1,jj+1,1) + tmask(ji,jj,1) + tmask(ji,jj+1,1)
+            IF( zmsk == 0. ) THEN
+               zcoff = 1.
+            ELSE
+               zcoff = FLOAT( icof(ji,jj+1) + icof(ji+1,jj+1) + icof(ji,jj) + icof(ji,jj+1) )   &
+         ifreq = 40
+         il1 = 1
+         DO jn = 1, jpidta/ifreq+1
+            READ(inum,'(/)')
+            il2 = MIN( jpidta, il1+ifreq-1 )
+            READ(inum,9201) ( ii, ji = il1, il2, 5 )
+            READ(inum,'(/)')
+            DO jj = jpjdta, 1, -1
+               READ(inum,9202) ij, ( idata(ji,jj), ji = il1, il2 )
+            END DO
+            il1 = il1 + ifreq
+         END DO
+         DO jj = 1, nlcj
+            DO ji = 1, nlci
+               icof(ji,jj) = idata( mig(ji), mjg(jj) )
+            END DO
+         END DO
+         DO jj = nlcj+1, jpj
+            DO ji = 1, nlci
+               icof(ji,jj) = icof(ji,nlcj)
+            END DO
+         END DO
+         DO jj = 1, jpj
+            DO ji = nlci+1, jpi
+               icof(ji,jj) = icof(nlci,jj)
+            END DO
+         END DO
+     FORMAT(1x,a15,2i8)
+     FORMAT(3x,13(i3,12x))
+     FORMAT(i3,41i3)
+         ! Set ahm1 and ahm2  ( T- and F- points) (used for laplacian operator)
+         ! =================
+         ! define ahm1 and ahm2 at the right grid point position
+         ! (USER: modify ahm1 and ahm2 following your desiderata)
+         ! Decrease ahm to zahmeq m2/s in the tropics
+         ! (from 90 to 20 degre: ahm = constant
+         ! from 20 to  2.5 degre: ahm = decrease in (1-cos)/2
+         ! from  2.5 to  0 degre: ahm = constant
+         ! symmetric in the south hemisphere)
+         zahmeq = aht0
+         DO jj = 1, jpj
+            DO ji = 1, jpi
+               IF( ABS( gphif(ji,jj) ) >= 20. ) THEN
+                  ahm2(ji,jj) =  ahm0
+               ELSEIF( ABS( gphif(ji,jj) ) <= 2.5 ) THEN
+                  ahm2(ji,jj) =  zahmeq
+               ELSE
+                  ahm2(ji,jj) = zahmeq + (ahm0-zahmeq)/2.   &
+                     * ( 1. - COS( rad * ( ABS(gphif(ji,jj))-2.5 ) * 180. / 17.5 ) )
+               ENDIF
+               IF( ABS( gphit(ji,jj) ) >= 20. ) THEN
+                  ahm1(ji,jj) =  ahm0
+               ELSEIF( ABS( gphit(ji,jj) ) <= 2.5 ) THEN
+                  ahm1(ji,jj) =  zahmeq
+               ELSE
+                  ahm1(ji,jj) = zahmeq + (ahm0-zahmeq)/2.   &
+                     * ( 1. - COS( rad * ( ABS(gphit(ji,jj))-2.5 ) * 180. / 17.5 ) )
+               ENDIF
+            END DO
+         END DO
+         ! increase along western boundaries of equatorial strip
+         ! t-point
+         DO jj = 1, jpjm1
+            DO ji = 1, jpim1
+               zcoft = FLOAT( icof(ji,jj) ) / 100.
+               ahm1(ji,jj) = zcoft * ahm0 + (1.-zcoft) * ahm1(ji,jj)
+            END DO
+         END DO
+         ! f-point
+         icof(:,:) = icof(:,:) * tmask(:,:,1)
+         DO jj = 1, jpjm1
+            DO ji = 1, jpim1   ! NO vector opt.
+               zmsk = tmask(ji,jj+1,1) + tmask(ji+1,jj+1,1) + tmask(ji,jj,1) + tmask(ji,jj+1,1)
+               IF( zmsk == 0. ) THEN
+                  zcoff = 1.
+               ELSE
+                  zcoff = FLOAT( icof(ji,jj+1) + icof(ji+1,jj+1) + icof(ji,jj) + icof(ji,jj+1) )   &
                      / (zmsk * 100.)
             ENDIF
             ahm2(ji,jj) = zcoff * ahm0 + (1.-zcoff) * ahm2(ji,jj)
          END DO
       END DO
+#endif
+               ENDIF
+               ahm2(ji,jj) = zcoff * ahm0 + (1.-zcoff) * ahm2(ji,jj)
+            END DO
+         END DO
+      ENDIF
       ! Lateral boundary conditions on ( ahm1, ahm2 )
 …
       IF(lwp) WRITE(numout,*) '        orca_r1 configuration'
+#if defined key_antarctic
+#     include "ldfdyn_antarctic.h90"
+#elif defined key_arctic
+#     include "ldfdyn_arctic.h90"
+#else
+      ! Read 2d integer array to specify western boundary increase in the
+      ! ===================== equatorial strip (20N-20S) defined at t-points
+      CALL ctl_opn( inum, 'ahmcoef', 'UNKNOWN', 'FORMATTED', 'SEQUENTIAL',   &
+         &           1, numout, lwp )
+      REWIND inum
+      READ(inum,9101) clexp, iim, ijm
+      READ(inum,'(/)')
+      ifreq = 40
+      il1 = 1
+      DO jn = 1, jpidta/ifreq+1
+      IF( cp_cfg == "orca" .AND. cp_cfz == "antarctic" ) THEN
+!
+! 1.2 Modify ahm
+! --------------
+         IF(lwp)WRITE(numout,*) ' inildf: Antarctic ocean'
+         IF(lwp)WRITE(numout,*) '         no tropics, no reduction of ahm'
+         IF(lwp)WRITE(numout,*) '         north boundary increase'
+         ahm1(:,:) = ahm0
+         ahm2(:,:) = ahm0
+         ijpt0=max(1,min(49 -njmpp+1,jpj))
+         ijpt1=max(0,min(49-njmpp+1,jpj-1))
+         DO jj=ijpt0,ijpt1
+            ahm2(:,jj)=ahm0*2.
+            ahm1(:,jj)=ahm0*2.
+         END DO
+         ijpt0=max(1,min(48 -njmpp+1,jpj))
+         ijpt1=max(0,min(48-njmpp+1,jpj-1))
+         DO jj=ijpt0,ijpt1
+            ahm2(:,jj)=ahm0*1.9
+            ahm1(:,jj)=ahm0*1.75
+         END DO
+         ijpt0=max(1,min(47 -njmpp+1,jpj))
+         ijpt1=max(0,min(47-njmpp+1,jpj-1))
+         DO jj=ijpt0,ijpt1
+            ahm2(:,jj)=ahm0*1.5
+            ahm1(:,jj)=ahm0*1.25
+         END DO
+         ijpt0=max(1,min(46 -njmpp+1,jpj))
+         ijpt1=max(0,min(46-njmpp+1,jpj-1))
+         DO jj=ijpt0,ijpt1
+            ahm2(:,jj)=ahm0*1.1
+         END DO
+      ELSE IF( cp_cfg == "orca" .AND. cp_cfz == "arctic" ) THEN
+! 1.2 Modify ahm
+! --------------
+         IF(lwp)WRITE(numout,*) ' inildf: Arctic ocean'
+         IF(lwp)WRITE(numout,*) '         no tropics, no reduction of ahm'
+         IF(lwp)WRITE(numout,*) '         south and west boundary increase'
+         ahm1(:,:) = ahm0
+         ahm2(:,:) = ahm0
+         ijpt0=max(1,min(98-jpjzoom+1-njmpp+1,jpj))
+         ijpt1=max(0,min(98-jpjzoom+1-njmpp+1,jpj-1))
+         DO jj=ijpt0,ijpt1
+            ahm2(:,jj)=ahm0*2.
+            ahm1(:,jj)=ahm0*2.
+         END DO
+         ijpt0=max(1,min(99-jpjzoom+1-njmpp+1,jpj))
+         ijpt1=max(0,min(99-jpjzoom+1-njmpp+1,jpj-1))
+         DO jj=ijpt0,ijpt1
+            ahm2(:,jj)=ahm0*1.9
+            ahm1(:,jj)=ahm0*1.75
+         END DO
+         ijpt0=max(1,min(100-jpjzoom+1-njmpp+1,jpj))
+         ijpt1=max(0,min(100-jpjzoom+1-njmpp+1,jpj-1))
+         DO jj=ijpt0,ijpt1
+            ahm2(:,jj)=ahm0*1.5
+            ahm1(:,jj)=ahm0*1.25
+         END DO
+         ijpt0=max(1,min(101-jpjzoom+1-njmpp+1,jpj))
+         ijpt1=max(0,min(101-jpjzoom+1-njmpp+1,jpj-1))
+         DO jj=ijpt0,ijpt1
+            ahm2(:,jj)=ahm0*1.1
+         END DO
+      ELSE
+         ! Read 2d integer array to specify western boundary increase in the
+         ! ===================== equatorial strip (20N-20S) defined at t-points
+         CALL ctl_opn( inum, 'ahmcoef', 'UNKNOWN', 'FORMATTED', 'SEQUENTIAL',   &
+            &           1, numout, lwp )
+         REWIND inum
+         READ(inum,9101) clexp, iim, ijm
          READ(inum,'(/)')
+         il2 = MIN( jpidta, il1+ifreq-1 )
+         READ(inum,9201) ( ii, ji = il1, il2, 5 )
+         READ(inum,'(/)')
+         DO jj = jpjdta, 1, -1
+            READ(inum,9202) ij, ( idata(ji,jj), ji = il1, il2 )
+         END DO
+         il1 = il1 + ifreq
+      END DO
+      DO jj = 1, nlcj
+         DO ji = 1, nlci
+            icof(ji,jj) = idata( mig(ji), mjg(jj) )
+         END DO
+      END DO
+      DO jj = nlcj+1, jpj
+         DO ji = 1, nlci
+            icof(ji,jj) = icof(ji,nlcj)
+         END DO
+      END DO
+      DO jj = 1, jpj
+         DO ji = nlci+1, jpi
+            icof(ji,jj) = icof(nlci,jj)
+         END DO
+      END DO
+FORMAT(1x,a15,2i8)
+FORMAT(3x,13(i3,12x))
+FORMAT(i3,41i3)
+      ! Set ahm1 and ahm2  ( T- and F- points) (used for laplacian operator)
+      ! =================
+      ! define ahm1 and ahm2 at the right grid point position
+      ! (USER: modify ahm1 and ahm2 following your desiderata)
+      ! Decrease ahm to zahmeq m2/s in the tropics
+      ! (from 90   to 20   degrees: ahm = scaled by local metrics
+      !  from 20   to  2.5 degrees: ahm = decrease in (1-cos)/2
+      !  from  2.5 to  0   degrees: ahm = constant
+      ! symmetric in the south hemisphere)
+      zahmeq = aht0
+      zam20s = ahm0*COS( rad * 20. )
+      DO jj = 1, jpj
+         DO ji = 1, jpi
+            IF( ABS( gphif(ji,jj) ) >= 20. ) THEN
+!              leave as set in ldf_dyn_c2d
+            ELSEIF( ABS( gphif(ji,jj) ) <= 2.5 ) THEN
+               ahm2(ji,jj) =  zahmeq
+            ELSE
+               ahm2(ji,jj) =  zahmeq + (zam20s-zahmeq)/2.   &
+                  * ( 1. - COS( rad * ( ABS(gphif(ji,jj))-2.5 ) * 180. / 17.5 ) )
+            ENDIF
+            IF( ABS( gphit(ji,jj) ) >= 20. ) THEN
+!             leave as set in ldf_dyn_c2d
+            ELSEIF( ABS( gphit(ji,jj) ) <= 2.5 ) THEN
+               ahm1(ji,jj) =  zahmeq
+            ELSE
+               ahm1(ji,jj) =  zahmeq + (zam20s-zahmeq)/2.   &
+                  * ( 1. - COS( rad * ( ABS(gphit(ji,jj))-2.5 ) * 180. / 17.5 ) )
+            ENDIF
+         END DO
+      END DO
+      ! increase along western boundaries of equatorial strip
+      ! t-point
+      DO jj = 1, jpjm1
+         DO ji = 1, jpim1
+          IF( ABS( gphit(ji,jj) ) < 20. ) THEN
+            zcoft = FLOAT( icof(ji,jj) ) / 100.
+            ahm1(ji,jj) = zcoft * ahm0 + (1.-zcoft) * ahm1(ji,jj)
+          ENDIF
+         END DO
+      END DO
+      ! f-point
+      icof(:,:) = icof(:,:) * tmask(:,:,1)
+      DO jj = 1, jpjm1
+         DO ji = 1, jpim1
+          IF( ABS( gphif(ji,jj) ) < 20. ) THEN
+            zmsk = tmask(ji,jj+1,1) + tmask(ji+1,jj+1,1) + tmask(ji,jj,1) + tmask(ji,jj+1,1)
+            IF( zmsk == 0. ) THEN
+               zcoff = 1.
+            ELSE
+               zcoff = FLOAT( icof(ji,jj+1) + icof(ji+1,jj+1) + icof(ji,jj) + icof(ji,jj+1) )   &
+                     / (zmsk * 100.)
+            ENDIF
+            ahm2(ji,jj) = zcoff * ahm0 + (1.-zcoff) * ahm2(ji,jj)
+          ENDIF
+         END DO
+      END DO
+#endif
+         ifreq = 40
+         il1 = 1
+         DO jn = 1, jpidta/ifreq+1
+            READ(inum,'(/)')
+            il2 = MIN( jpidta, il1+ifreq-1 )
+            READ(inum,9201) ( ii, ji = il1, il2, 5 )
+            READ(inum,'(/)')
+            DO jj = jpjdta, 1, -1
+               READ(inum,9202) ij, ( idata(ji,jj), ji = il1, il2 )
+            END DO
+            il1 = il1 + ifreq
+         END DO
+         DO jj = 1, nlcj
+            DO ji = 1, nlci
+               icof(ji,jj) = idata( mig(ji), mjg(jj) )
+            END DO
+         END DO
+         DO jj = nlcj+1, jpj
+            DO ji = 1, nlci
+               icof(ji,jj) = icof(ji,nlcj)
+            END DO
+         END DO
+         DO jj = 1, jpj
+            DO ji = nlci+1, jpi
+               icof(ji,jj) = icof(nlci,jj)
+            END DO
+         END DO
+     FORMAT(1x,a15,2i8)
+     FORMAT(3x,13(i3,12x))
+     FORMAT(i3,41i3)
+         ! Set ahm1 and ahm2  ( T- and F- points) (used for laplacian operator)
+         ! =================
+         ! define ahm1 and ahm2 at the right grid point position
+         ! (USER: modify ahm1 and ahm2 following your desiderata)
+         ! Decrease ahm to zahmeq m2/s in the tropics
+         ! (from 90   to 20   degrees: ahm = scaled by local metrics
+         !  from 20   to  2.5 degrees: ahm = decrease in (1-cos)/2
+         !  from  2.5 to  0   degrees: ahm = constant
+         ! symmetric in the south hemisphere)
+         zahmeq = aht0
+         zam20s = ahm0*COS( rad * 20. )
+         DO jj = 1, jpj
+            DO ji = 1, jpi
+               IF( ABS( gphif(ji,jj) ) >= 20. ) THEN
+                  !              leave as set in ldf_dyn_c2d
+               ELSEIF( ABS( gphif(ji,jj) ) <= 2.5 ) THEN
+                  ahm2(ji,jj) =  zahmeq
+               ELSE
+                  ahm2(ji,jj) =  zahmeq + (zam20s-zahmeq)/2.   &
+                     * ( 1. - COS( rad * ( ABS(gphif(ji,jj))-2.5 ) * 180. / 17.5 ) )
+               ENDIF
+               IF( ABS( gphit(ji,jj) ) >= 20. ) THEN
+                  !             leave as set in ldf_dyn_c2d
+               ELSEIF( ABS( gphit(ji,jj) ) <= 2.5 ) THEN
+                  ahm1(ji,jj) =  zahmeq
+               ELSE
+                  ahm1(ji,jj) =  zahmeq + (zam20s-zahmeq)/2.   &
+                     * ( 1. - COS( rad * ( ABS(gphit(ji,jj))-2.5 ) * 180. / 17.5 ) )
+               ENDIF
+            END DO
+         END DO
+         ! increase along western boundaries of equatorial strip
+         ! t-point
+         DO jj = 1, jpjm1
+            DO ji = 1, jpim1
+               IF( ABS( gphit(ji,jj) ) < 20. ) THEN
+                  zcoft = FLOAT( icof(ji,jj) ) / 100.
+                  ahm1(ji,jj) = zcoft * ahm0 + (1.-zcoft) * ahm1(ji,jj)
+               ENDIF
+            END DO
+         END DO
+         ! f-point
+         icof(:,:) = icof(:,:) * tmask(:,:,1)
+         DO jj = 1, jpjm1
+            DO ji = 1, jpim1
+               IF( ABS( gphif(ji,jj) ) < 20. ) THEN
+                  zmsk = tmask(ji,jj+1,1) + tmask(ji+1,jj+1,1) + tmask(ji,jj,1) + tmask(ji,jj+1,1)
+                  IF( zmsk == 0. ) THEN
+                     zcoff = 1.
+                  ELSE
+                     zcoff = FLOAT( icof(ji,jj+1) + icof(ji+1,jj+1) + icof(ji,jj) + icof(ji,jj+1) )   &
+                        / (zmsk * 100.)
+                  ENDIF
+                  ahm2(ji,jj) = zcoff * ahm0 + (1.-zcoff) * ahm2(ji,jj)
+               ENDIF
+            END DO
+         END DO
+      ENDIF
       ! Lateral boundary conditions on ( ahm1, ahm2 )

branches/2013/dev_r3853_CNRS9_ConfSetting/NEMOGCM/NEMO/OPA_SRC/TRA/tradmp.F90

-                      r3901
+                      r3989
       !                                           ! ====================================================
       IF( lzoom_arct .AND. lzoom_anta ) THEN      !  ORCA configuration : arctic zoom or antarctic zoom
+      IF( cp_cfz == "arctic" . OR. cp_cfz == "antarctic" ) THEN   !  ORCA configuration : arctic or antarctic zoom
          !                                        ! ====================================================
          IF(lwp) WRITE(numout,*)
          IF(lwp .AND. lzoom_arct ) WRITE(numout,*) '              dtacof_zoom : ORCA    Arctic zoom'
          IF(lwp .AND. lzoom_arct ) WRITE(numout,*) '              dtacof_zoom : ORCA Antarctic zoom'
+         IF(lwp .AND. cp_cfz == "arctic" ) WRITE(numout,*) '              dtacof_zoom : ORCA    Arctic zoom'
+         IF(lwp .AND. cp_cfz == "antarctic" ) WRITE(numout,*) '           dtacof_zoom : ORCA Antarctic zoom'
          IF(lwp) WRITE(numout,*)
+         !

branches/2013/dev_r3853_CNRS9_ConfSetting/NEMOGCM/NEMO/OPA_SRC/nemogcm.F90

-                      r3973
+                      r3989
          &             nn_isplt, nn_jsplt, nn_jctls, nn_jctle,   &
          &             nn_bench, nn_timing
       NAMELIST/namcfg/ cp_cfg, jp_cfg, jpidta, jpjdta, jpkdta, jpiglo, jpjglo, &
+      NAMELIST/namcfg/ cp_cfg, cp_cfz, jp_cfg, jpidta, jpjdta, jpkdta, jpiglo, jpjglo, &
          &             jpizoom, jpjzoom, jperio, jphgr_msh, &
          &             ppglam0, ppgphi0, ppe1_deg, ppe2_deg, ppe1_m, ppe2_m, &
 …
          WRITE(numout,*) '   Namelist namcfg'
          WRITE(numout,*) '      configuration name              cp_cfg      = ', TRIM(cp_cfg)
+         WRITE(numout,*) '      configuration zoom name         cp_cfz      = ', TRIM(cp_cfz)
          WRITE(numout,*) '      configuration resolution        jp_cfg      = ', jp_cfg
          WRITE(numout,*) '      1st lateral dimension ( >= jpi ) jpidta     = ', jpidta

branches/2013/dev_r3853_CNRS9_ConfSetting/NEMOGCM/NEMO/OPA_SRC/par_oce.F90

r3973	r3989
29	29	!!----------------------------------------------------------------------
30	30	CHARACTER(lc) :: cp_cfg !: name of the configuration
	31	CHARACTER(lc) :: cp_cfz !: name of the zoom of configuration
31	32	INTEGER :: jp_cfg !: resolution of the configuration
32	33

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