Changeset 11577

NEMO/trunk/doc/latex/NEMO/subfiles/apdx_DOMAINcfg.tex

-                      r11571
+                      r11577
 The user has three options available in defining a horizontal grid, which involve the
 namelist variable \np{jphgr\_mesh} of the \nam{dom} (\texttt{DOMAINcfg} variant only)
+namelist variable \np{jphgr_mesh}{jphgr\_mesh} of the \nam{dom} (\texttt{DOMAINcfg} variant only)
 namelist.
 \begin{description}
  \item[\np{jphgr\_mesh}=0]  The most general curvilinear orthogonal grids.
+ \item[\np{jphgr_mesh}{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.
   This is now the only option available within \NEMO\ itself from v4.0 onwards.
 \item[\np{jphgr\_mesh}=1 to 5] A few simple analytical grids are provided (see below).
+\item[\np{jphgr_mesh}{jphgr\_mesh}=1 to 5] A few simple analytical grids are provided (see below).
   For other analytical grids, the \mdl{domhgr} module (\texttt{DOMAINcfg} variant) must be
   modified by the user. In most cases, modifying the \mdl{usrdef\_hgr} module of \NEMO\ is
 …
 There are two simple cases of geographical grids on the sphere. With
 \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},
+\np{jphgr_mesh}{jphgr\_mesh}=1, the grid (expressed in degrees) is regular in space,
+with grid sizes specified by parameters \np{ppe1_deg}{ppe1\_deg} and \np{ppe2_deg}{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 (\np{jphgr\_mesh}=4) avoids this anisotropy by refining the meridional scale
+grid (\np{jphgr_mesh}{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 \np{ppe1\_deg} which is a reference grid spacing
+a Mercator projection, based on \np{ppe1_deg}{ppe1\_deg} which is a reference grid spacing
 at the equator (this applies even when the geographical equator is situated outside
 the model domain).
 In these two cases (\np{jphgr\_mesh}=1 or 4), the grid position is defined by the
+In these two cases (\np{jphgr_mesh}{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
 …
 Rectangular grids ignoring the spherical geometry are defined with
 \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
+\np{jphgr_mesh}{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}{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 \np{ppe1\_m} and \np{ppe2\_m} respectively.
+and given by the parameters \np{ppe1_m}{ppe1\_m} and \np{ppe2_m}{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,
 …
 latitude for computation of the Coriolis parameter. In the case of the beta plane,
 \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
+\np{jphgr_mesh}{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
 …
 \end{gather}
 If the ice shelf cavities are opened (\np{ln\_isfcav}\forcode{ = .true.}), the definition
+If the ice shelf cavities are opened (\np{ln_isfcav}{ln\_isfcav}\forcode{ = .true.}), the definition
 of $z_0$ is the same.  However, definition of $e_3^0$ at $t$- and $w$-points is
 respectively changed to:
 …
 Three options are possible for defining the bathymetry, according to the namelist variable
 \np{nn\_bathy} (found in \nam{dom} namelist (\texttt{DOMAINCFG} variant) ):
+\np{nn_bathy}{nn\_bathy} (found in \nam{dom} namelist (\texttt{DOMAINCFG} variant) ):
 \begin{description}
 \item[\np{nn\_bathy}\forcode{ = 0}]:
+\item[\np{nn_bathy}{nn\_bathy}\forcode{ = 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 \np{jperio}.
 \item[\np{nn\_bathy}\forcode{ = -1}]:
+\item[\np{nn_bathy}{nn\_bathy}\forcode{ = -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, a periodic or open boundary channel with a seamount.
 \item[\np{nn\_bathy}\forcode{ = 1}]:
+\item[\np{nn_bathy}{nn\_bathy}\forcode{ = 1}]:
   read a bathymetry and ice shelf draft (if needed).
   The \ifile{bathy\_meter} file (Netcdf format) provides the ocean depth (positive, in meters) at
 …
   The \ifile{isfdraft\_meter} file (Netcdf format) provides the ice shelf draft (positive, in meters) at
   each grid point of the model grid.
   This file is only needed if \np{ln\_isfcav}\forcode{ = .true.}.
+  This file is only needed if \np{ln_isfcav}{ln\_isfcav}\forcode{ = .true.}.
   Defining the ice shelf draft will also define the ice shelf edge and the grounding line position.
 \end{description}
 …
 %        z-coordinate with constant thickness
 % -------------------------------------------------------------------------------------------------------------
 \subsubsection[$Z$-coordinate with uniform thickness levels (\forcode{ln_zco})]{$Z$-coordinate with uniform thickness levels (\protect\np{ln\_zco})}
+\subsubsection[$Z$-coordinate with uniform thickness levels (\forcode{ln_zco})]{$Z$-coordinate with uniform thickness levels (\protect\np{ln_zco}{ln\_zco})}
 \label{subsec:DOMCFG_zco}
 …
 %        z-coordinate with partial step
 % -------------------------------------------------------------------------------------------------------------
 \subsubsection[$Z$-coordinate with partial step (\forcode{ln_zps})]{$Z$-coordinate with partial step (\protect\np{ln\_zps})}
+\subsubsection[$Z$-coordinate with partial step (\forcode{ln_zps})]{$Z$-coordinate with partial step (\protect\np{ln_zps}{ln\_zps})}
 \label{subsec:DOMCFG_zps}
 …
 $250~m$).  Two variables in the namdom namelist are used to define the partial step
 vertical grid.  The mimimum water thickness (in meters) allowed for a cell partially
 filled with bathymetry at level jk is the minimum of \np{rn\_e3zps\_min} (thickness in
 meters, usually $20~m$) or $e_{3t}(jk)*$\np{rn\_e3zps\_rat} (a fraction, usually 10\%, of
+filled with bathymetry at level jk is the minimum of \np{rn_e3zps_min}{rn\_e3zps\_min} (thickness in
+meters, usually $20~m$) or $e_{3t}(jk)*$\np{rn_e3zps_rat}{rn\_e3zps\_rat} (a fraction, usually 10\%, of
 the default thickness $e_{3t}(jk)$).
 …
 %        s-coordinate
 % -------------------------------------------------------------------------------------------------------------
 \subsubsection[$S$-coordinate (\forcode{ln_sco})]{$S$-coordinate (\protect\np{ln\_sco})}
+\subsubsection[$S$-coordinate (\forcode{ln_sco})]{$S$-coordinate (\protect\np{ln_sco}{ln\_sco})}
 \label{sec:DOMCFG_sco}
 %------------------------------------------nam_zgr_sco---------------------------------------------------
 …
 \end{listing}
 %--------------------------------------------------------------------------------------------------------------
 Options are defined in \nam{zgr\_sco} (\texttt{DOMAINcfg} only).
 In $s$-coordinate (\np{ln\_sco}\forcode{ = .true.}), the depth and thickness of the model levels are defined from
+Options are defined in \nam{zgr_sco}{zgr\_sco} (\texttt{DOMAINcfg} only).
+In $s$-coordinate (\np{ln_sco}{ln\_sco}\forcode{ = .true.}), the depth and thickness of the model levels are defined from
 the product of a depth field and either a stretching function or its derivative, respectively:
 …
 since a mixed step-like and bottom-following representation of the topography can be used
 (\autoref{fig:DOM_z_zps_s_sps}) or an envelop bathymetry can be defined (\autoref{fig:DOM_z_zps_s_sps}).
 The namelist parameter \np{rn\_rmax} determines the slope at which
+The namelist parameter \np{rn_rmax}{rn\_rmax} determines the slope at which
 the terrain-following coordinate intersects the sea bed and becomes a pseudo z-coordinate.
 The coordinate can also be hybridised by specifying \np{rn\_sbot\_min} and \np{rn\_sbot\_max} as
+The coordinate can also be hybridised by specifying \np{rn_sbot_min}{rn\_sbot\_min} and \np{rn_sbot_max}{rn\_sbot\_max} as
 the minimum and maximum depths at which the terrain-following vertical coordinate is calculated.
 …
 The original default \NEMO\ s-coordinate stretching is available if neither of the other options are specified as true
 (\np{ln\_s\_SH94}\forcode{ = .false.} and \np{ln\_s\_SF12}\forcode{ = .false.}).
+(\np{ln_s_SH94}{ln\_s\_SH94}\forcode{ = .false.} and \np{ln_s_SF12}{ln\_s\_SF12}\forcode{ = .false.}).
 This uses a depth independent $\tanh$ function for the stretching \citep{madec.delecluse.ea_JPO96}:
 …
 A stretching function,
 modified from the commonly used \citet{song.haidvogel_JCP94} stretching (\np{ln\_s\_SH94}\forcode{ = .true.}),
+modified from the commonly used \citet{song.haidvogel_JCP94} stretching (\np{ln_s_SH94}{ln\_s\_SH94}\forcode{ = .true.}),
 is also available and is more commonly used for shelf seas modelling:
 …
 %% %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 where $H_c$ is the critical depth (\np{rn\_hc}) at which the coordinate transitions from pure $\sigma$ to
 the stretched coordinate, and $\theta$ (\np{rn\_theta}) and $b$ (\np{rn\_bb}) are the surface and
+where $H_c$ is the critical depth (\np{rn_hc}{rn\_hc}) at which the coordinate transitions from pure $\sigma$ to
+the stretched coordinate, and $\theta$ (\np{rn_theta}{rn\_theta}) and $b$ (\np{rn_bb}{rn\_bb}) are the surface and
 bottom control parameters such that $0 \leqslant \theta \leqslant 20$, and $0 \leqslant b \leqslant 1$.
 $b$ has been designed to allow surface and/or bottom increase of the vertical resolution
 (\autoref{fig:DOMCFG_sco_function}).
 Another example has been provided at version 3.5 (\np{ln\_s\_SF12}) that allows a fixed surface resolution in
+Another example has been provided at version 3.5 (\np{ln_s_SF12}{ln\_s\_SF12}) that allows a fixed surface resolution in
 an analytical terrain-following stretching \citet{siddorn.furner_OM13}.
 In this case the a stretching function $\gamma$ is defined such that:
 …
 This gives an analytical stretching of $\sigma$ that is solvable in $A$ and $B$ as a function of
 the user prescribed stretching parameter $\alpha$ (\np{rn\_alpha}) that stretches towards
+the user prescribed stretching parameter $\alpha$ (\np{rn_alpha}{rn\_alpha}) that stretches towards
 the surface ($\alpha > 1.0$) or the bottom ($\alpha < 1.0$) and
 user prescribed surface (\np{rn\_zs}) and bottom depths.
+user prescribed surface (\np{rn_zs}{rn\_zs}) and bottom depths.
 The bottom cell depth in this example is given as a function of water depth:
 …
 \]
 where the namelist parameters \np{rn\_zb\_a} and \np{rn\_zb\_b} are $a$ and $b$ respectively.
+where the namelist parameters \np{rn_zb_a}{rn\_zb\_a} and \np{rn_zb_b}{rn\_zb\_b} are $a$ and $b$ respectively.
 %% %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 …
 the critical depth $h_c$.
 In this example two options are available in depths shallower than $h_c$,
 with pure sigma being applied if the \np{ln\_sigcrit} is true and pure z-coordinates if it is false
+with pure sigma being applied if the \np{ln_sigcrit}{ln\_sigcrit} is true and pure z-coordinates if it is false
 (the z-coordinate being equal to the depths of the stretched coordinate at $h_c$).
 …
 %        z*- or s*-coordinate
 % -------------------------------------------------------------------------------------------------------------
 \subsubsection[\zstar- or \sstar-coordinate (\forcode{ln_linssh})]{\zstar- or \sstar-coordinate (\protect\np{ln\_linssh})}
+\subsubsection[\zstar- or \sstar-coordinate (\forcode{ln_linssh})]{\zstar- or \sstar-coordinate (\protect\np{ln_linssh}{ln\_linssh})}
 \label{subsec:DOMCFG_zgr_star}

NEMO/trunk/doc/latex/NEMO/subfiles/apdx_algos.tex

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+                      r11577
 %        UBS scheme
 % -------------------------------------------------------------------------------------------------------------
 \section{Upstream Biased Scheme (UBS) (\protect\np{ln\_traadv\_ubs}\forcode{ = .true.})}
+\section{Upstream Biased Scheme (UBS) (\protect\np{ln_traadv_ubs}{ln\_traadv\_ubs}\forcode{ = .true.})}
 \label{sec:ALGOS_tra_adv_ubs}
 …
 the control of artificial diapycnal fluxes is of paramount importance.
 It has therefore been preferred to evaluate the vertical flux using the TVD scheme when
 \np{ln\_traadv\_ubs}\forcode{ = .true.}.
+\np{ln_traadv_ubs}{ln\_traadv\_ubs}\forcode{ = .true.}.
 For stability reasons, in \autoref{eq:TRA_adv_ubs}, the first term which corresponds to

NEMO/trunk/doc/latex/NEMO/subfiles/apdx_invariants.tex

-                      r11558
+                      r11577
 %       Vorticity Term with ENE scheme
 % -------------------------------------------------------------------------------------------------------------
 \subsubsection{Vorticity term with ENE scheme (\protect\np{ln\_dynvor\_ene}\forcode{ = .true.})}
+\subsubsection{Vorticity term with ENE scheme (\protect\np{ln_dynvor_ene}{ln\_dynvor\_ene}\forcode{ = .true.})}
 \label{subsec:INVARIANTS_vorENE}
 …
 %       Vorticity Term with EEN scheme
 % -------------------------------------------------------------------------------------------------------------
 \subsubsection{Vorticity term with EEN scheme (\protect\np{ln\_dynvor\_een}\forcode{ = .true.})}
+\subsubsection{Vorticity term with EEN scheme (\protect\np{ln_dynvor_een}{ln\_dynvor\_een}\forcode{ = .true.})}
 \label{subsec:INVARIANTS_vorEEN_vect}
 …
 %       Vorticity Term with ENS scheme
 % -------------------------------------------------------------------------------------------------------------
 \subsubsection{Vorticity term with ENS scheme  (\protect\np{ln\_dynvor\_ens}\forcode{ = .true.})}
+\subsubsection{Vorticity term with ENS scheme  (\protect\np{ln_dynvor_ens}{ln\_dynvor\_ens}\forcode{ = .true.})}
 \label{subsec:INVARIANTS_vorENS}
 …
 %       Vorticity Term with EEN scheme
 % -------------------------------------------------------------------------------------------------------------
 \subsubsection{Vorticity Term with EEN scheme (\protect\np{ln\_dynvor\_een}\forcode{ = .true.})}
+\subsubsection{Vorticity Term with EEN scheme (\protect\np{ln_dynvor_een}{ln\_dynvor\_een}\forcode{ = .true.})}
 \label{subsec:INVARIANTS_vorEEN}

NEMO/trunk/doc/latex/NEMO/subfiles/apdx_triads.tex

-                      r11571
+                      r11577
 \newpage
 \section[Choice of \forcode{namtra\_ldf} namelist parameters]{Choice of \protect\nam{tra\_ldf} namelist parameters}
+\section[Choice of \forcode{namtra\_ldf} namelist parameters]{Choice of \protect\nam{tra_ldf}{tra\_ldf} namelist parameters}
 %-----------------------------------------nam_traldf------------------------------------------------------
 …
 Two scheme are available to perform the iso-neutral diffusion.
 If the namelist logical \np{ln\_traldf\_triad} is set true,
+If the namelist logical \np{ln_traldf_triad}{ln\_traldf\_triad} is set true,
 \NEMO\ updates both active and passive tracers using the Griffies triad representation of iso-neutral diffusion and
 the eddy-induced advective skew (GM) fluxes.
 If the namelist logical \np{ln\_traldf\_iso} is set true,
+If the namelist logical \np{ln_traldf_iso}{ln\_traldf\_iso} is set true,
 the filtered version of Cox's original scheme (the Standard scheme) is employed (\autoref{sec:LDF_slp}).
 In the present implementation of the Griffies scheme,
 the advective skew fluxes are implemented even if \np{ln\_traldf\_eiv} is false.
+the advective skew fluxes are implemented even if \np{ln_traldf_eiv}{ln\_traldf\_eiv} is false.
 Values of iso-neutral diffusivity and GM coefficient are set as described in \autoref{sec:LDF_coef}.
 …
 The options specific to the Griffies scheme include:
 \begin{description}
 \item[\np{ln\_triad\_iso}]
+\item[\np{ln_triad_iso}{ln\_triad\_iso}]
   See \autoref{sec:TRIADS_taper}.
   If this is set false (the default),
 …
   This is the same treatment as used in the default implementation
   \autoref{subsec:LDF_slp_iso}; \autoref{fig:LDF_eiv_slp}.
   Where \np{ln\_triad\_iso} is set true,
+  Where \np{ln_triad_iso}{ln\_triad\_iso} is set true,
   the vertical skew flux is further reduced to ensure no vertical buoyancy flux,
   giving an almost pure horizontal diffusive tracer flux within the mixed layer.
   This is similar to the tapering suggested by \citet{gerdes.koberle.ea_CD91}. See \autoref{subsec:TRIADS_Gerdes-taper}
 \item[\np{ln\_botmix\_triad}]
+\item[\np{ln_botmix_triad}{ln\_botmix\_triad}]
   See \autoref{sec:TRIADS_iso_bdry}.
   If this is set false (the default) then the lateral diffusive fluxes
 …
   If it is set true, however, then these lateral diffusive fluxes are applied,
   giving smoother bottom tracer fields at the cost of introducing diapycnal mixing.
 \item[\np{rn\_sw\_triad}]
+\item[\np{rn_sw_triad}{rn\_sw\_triad}]
   blah blah to be added....
 \end{description}
 The options shared with the Standard scheme include:
 \begin{description}
 \item[\np{ln\_traldf\_msc}]   blah blah to be added
 \item[\np{rn\_slpmax}]  blah blah to be added
+\item[\np{ln_traldf_msc}{ln\_traldf\_msc}]   blah blah to be added
+\item[\np{rn_slpmax}{rn\_slpmax}]  blah blah to be added
 \end{description}
 …
 Note that both near bottom triad slopes \triad{i}{k}{R}{1/2}{1/2} and \triad{i+1}{k}{R}{-1/2}{1/2} are masked when
 either of the $i,k+1$ or $i+1,k+1$ tracer points is masked, \ie\ the $i,k+1$ $u$-point is masked.
 The associated lateral fluxes (grey-black dashed line) are masked if \np{ln\_botmix\_triad}\forcode{ = .false.},
 but left unmasked, giving bottom mixing, if \np{ln\_botmix\_triad}\forcode{ = .true.}.
 The default option \np{ln\_botmix\_triad}\forcode{ = .false.} is suitable when the bbl mixing option is enabled
 (\np{ln\_trabbl}\forcode{ = .true.}, with \np{nn\_bbl\_ldf}\forcode{ = 1}), or for simple idealized problems.
 For setups with topography without bbl mixing, \np{ln\_botmix\_triad}\forcode{ = .true.} may be necessary.
+The associated lateral fluxes (grey-black dashed line) are masked if \np{ln_botmix_triad}{ln\_botmix\_triad}\forcode{ = .false.},
+but left unmasked, giving bottom mixing, if \np{ln_botmix_triad}{ln\_botmix\_triad}\forcode{ = .true.}.
+The default option \np{ln_botmix_triad}{ln\_botmix\_triad}\forcode{ = .false.} is suitable when the bbl mixing option is enabled
+(\np{ln_trabbl}{ln\_trabbl}\forcode{ = .true.}, with \np{nn_bbl_ldf}{nn\_bbl\_ldf}\forcode{ = 1}), or for simple idealized problems.
+For setups with topography without bbl mixing, \np{ln_botmix_triad}{ln\_botmix\_triad}\forcode{ = .true.} may be necessary.
 % >>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{figure}[h]
 …
     \ie\ the $i,k+1$ $u$-point is masked.
     The associated lateral fluxes (grey-black dashed line) are masked if
     \protect\np{ln\_botmix\_triad}\forcode{ = .false.}, but left unmasked,
     giving bottom mixing, if \protect\np{ln\_botmix\_triad}\forcode{ = .true.}}
+    \protect\np{ln_botmix_triad}{ln\_botmix\_triad}\forcode{ = .false.}, but left unmasked,
+    giving bottom mixing, if \protect\np{ln_botmix_triad}{ln\_botmix\_triad}\forcode{ = .true.}}
   \label{fig:TRIADS_bdry_triads}
 \end{figure}
 …
 \label{sec:TRIADS_lintaper}
 This is the option activated by the default choice \np{ln\_triad\_iso}\forcode{ = .false.}.
+This is the option activated by the default choice \np{ln_triad_iso}{ln\_triad\_iso}\forcode{ = .false.}.
 Slopes $\tilde{r}_i$ relative to geopotentials are tapered linearly from their value immediately below
 the mixed layer to zero at the surface, as described in option (c) of \autoref{fig:LDF_eiv_slp}, to values
 …
 \label{subsec:TRIADS_Gerdes-taper}
 The alternative option is activated by setting \np{ln\_triad\_iso} = true.
+The alternative option is activated by setting \np{ln_triad_iso}{ln\_triad\_iso} = true.
 This retains the same tapered slope $\rML$  described above for the calculation of the $_{33}$ term of
 the iso-neutral diffusion tensor (the vertical tracer flux driven by vertical tracer gradients),
 …
 computing the tracer advection.
 This is implemented if \texttt{traldf\_eiv?} is set in the default implementation,
 where \np{ln\_traldf\_triad} is set false.
+where \np{ln_traldf_triad}{ln\_traldf\_triad} is set false.
 This allows us to take advantage of all the advection schemes offered for the tracers
 (see \autoref{sec:TRA_adv}) and not just a $2^{nd}$ order advection scheme.
 …
 \emph{positivity} of the advection scheme is of paramount importance.
 However, when \np{ln\_traldf\_triad} is set true,
+However, when \np{ln_traldf_triad}{ln\_traldf\_triad} is set true,
 \NEMO\ instead implements eddy induced advection according to the so-called skew form \citep{griffies_JPO98}.
 It is based on a transformation of the advective fluxes using the non-divergent nature of the eddy induced velocity.
 …
 and both near bottom triad slopes $\triadt{i}{k}{R}{1/2}{1/2}$ and $\triadt{i+1}{k}{R}{-1/2}{1/2}$ are masked when
 either of the $i,k+1$ or $i+1,k+1$ tracer points is masked, \ie\ the $i,k+1$ $u$-point is masked.
 The namelist parameter \np{ln\_botmix\_triad} has no effect on the eddy-induced skew-fluxes.
+The namelist parameter \np{ln_botmix_triad}{ln\_botmix\_triad} has no effect on the eddy-induced skew-fluxes.
 \subsection{Limiting of the slopes within the interior}
 …
 This is option (c) of \autoref{fig:LDF_eiv_slp}.
 This linear tapering for the slopes used to calculate the eddy-induced fluxes is unaffected by
 the value of \np{ln\_triad\_iso}.
+the value of \np{ln_triad_iso}{ln\_triad\_iso}.
 The justification for this linear slope tapering is that, for $A_e$ that is constant or varies only in
 …
 \label{sec:TRIADS_sfdiag}
 Where the namelist parameter \np{ln\_traldf\_gdia}\forcode{ = .true.},
+Where the namelist parameter \np{ln_traldf_gdia}{ln\_traldf\_gdia}\forcode{ = .true.},
 diagnosed mean eddy-induced velocities are output.
 Each time step, streamfunctions are calculated in the $i$-$k$ and $j$-$k$ planes at

NEMO/trunk/doc/latex/NEMO/subfiles/chap_ASM.tex

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+                      r11577
 These are read into the model from a NetCDF file which may be produced by separate data 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 \nam{\_asminc}.
+This is all controlled by the namelist \nam{_asminc}{\_asminc}.
 There is a brief description of all the namelist options provided.
 To build the ASM code \key{asminc} must be set.
 …
 Direct initialization (DI) refers to the instantaneous correction of the model background state using
 the analysis increment.
 DI is used when \np{ln\_asmdin} is set to true.
+DI is used when \np{ln_asmdin}{ln\_asmdin} is set to true.
 \section{Incremental analysis updates}
 …
 This technique is referred to as Incremental Analysis Updates (IAU) \citep{bloom.takacs.ea_MWR96}.
 IAU is a common technique used with 3D assimilation methods such as 3D-Var or OI.
 IAU is used when \np{ln\_asmiau} is set to true.
+IAU is used when \np{ln_asmiau}{ln\_asmiau} is set to true.
 With IAU, the model state trajectory ${\mathbf x}$ in the assimilation window ($t_{0} \leq t_{i} \leq t_{N}$)
 …
 \citep{talagrand_JAS72, dobricic.pinardi.ea_OS07}.
 Diffusion coefficients are defined as $A_D = \alpha e_{1t} e_{2t}$, where $\alpha = 0.2$.
 The divergence damping is activated by assigning to \np{nn\_divdmp} in the \nam{\_asminc} namelist
+The divergence damping is activated by assigning to \np{nn_divdmp}{nn\_divdmp} in the \nam{_asminc}{\_asminc} namelist
 a value greater than zero.
 This specifies the number of iterations of the divergence damping. Setting a value of the order of 100 will result in a significant reduction in the vertical velocity induced by the increments.
 …
 \label{sec:ASM_details}
 Here we show an example \nam{\_asminc} namelist and the header of an example assimilation increments file on
+Here we show an example \nam{_asminc}{\_asminc} namelist and the header of an example assimilation increments file on
 the ORCA2 grid.

NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex

-                      r11571
+                      r11577
 XIOS may be used to read single file restart produced by \NEMO. Currently only the variables written to
 file \forcode{numror} can be handled by XIOS. To activate restart reading using XIOS, set \np{ln\_xios\_read}\forcode{=.true. }
+file \forcode{numror} can be handled by XIOS. To activate restart reading using XIOS, set \np{ln_xios_read}{ln\_xios\_read}\forcode{=.true. }
 in \textit{namelist\_cfg}. This setting will be ignored when multiple restart files are present, and default \NEMO
 functionality will be used for reading. There is no need to change iodef.xml file to use XIOS to read
 …
 dimension \forcode{z} defined in restart file must be renamed to \forcode{nav_lev}.\\
 XIOS can also be used to write \NEMO\ restart. A namelist parameter \np{nn\_wxios} is used to determine the
+XIOS can also be used to write \NEMO\ restart. A namelist parameter \np{nn_wxios}{nn\_wxios} is used to determine the
 type of restart \NEMO\ will write. If it is set to 0, default \NEMO\ functionality will be used - each
 processor writes its own restart file; if it is set to 1 XIOS will write restart into a single file;
 for \np{nn\_wxios}\forcode{=2} the restart will be written by XIOS into multiple files, one for each XIOS server.
 Note, however, that \textbf{\NEMO\ will not read restart generated by XIOS when \np{nn\_wxios}\forcode{=2}}. The restart will
+for \np{nn_wxios}{nn\_wxios}\forcode{=2} the restart will be written by XIOS into multiple files, one for each XIOS server.
+Note, however, that \textbf{\NEMO\ will not read restart generated by XIOS when \np{nn_wxios}{nn\_wxios}\forcode{=2}}. The restart will
 have to be rebuild before continuing the run. This option aims to reduce number of restart files generated by \NEMO\ only,
 and may be useful when there is a need to change number of processors used to run simulation.
 …
 \end{xmllines}
 Note, if your array is computed within the surface module each \np{nn\_fsbc} time\_step,
+Note, if your array is computed within the surface module each \np{nn_fsbc}{nn\_fsbc} time\_step,
 add the field definition within the field\_group defined with the id "SBC":
 \xmlcode{<field_group id="SBC" ...>} which has been defined with the correct frequency of operations
 …
     field\_definition                                                    &
     freq\_op                                                             &
     \np{rn\_rdt}                                                         \\
+    \np{rn_rdt}{rn\_rdt}                                                         \\
     \hline
     SBC                                                                  &
     freq\_op                                                             &
     \np{rn\_rdt} $\times$ \np{nn\_fsbc}                                  \\
+    \np{rn_rdt}{rn\_rdt} $\times$ \np{nn_fsbc}{nn\_fsbc}                                  \\
     \hline
     ptrc\_T                                                              &
     freq\_op                                                             &
     \np{rn\_rdt} $\times$ \np{nn\_dttrc}                                 \\
+    \np{rn_rdt}{rn\_rdt} $\times$ \np{nn_dttrc}{nn\_dttrc}                                 \\
     \hline
     diad\_T                                                              &
     freq\_op                                                             &
     \np{rn\_rdt} $\times$ \np{nn\_dttrc}                                 \\
+    \np{rn_rdt}{rn\_rdt} $\times$ \np{nn_dttrc}{nn\_dttrc}                                 \\
     \hline
     EqT, EqU, EqW                                                        &
 …
 Some metadata that may significantly increase the file size (horizontal cell areas and vertices) are controlled by
 the namelist parameter \np{ln\_cfmeta} in the \nam{run} namelist.
+the namelist parameter \np{ln_cfmeta}{ln\_cfmeta} in the \nam{run} namelist.
 This must be set to true if these metadata are to be included in the output files.
 …
 most analysis codes can be relinked simply with the new libraries and will then read both NetCDF3 and NetCDF4 files.
 \NEMO\ executables linked with NetCDF4 libraries can be made to produce NetCDF3 files by
 setting the \np{ln\_nc4zip} logical to false in the \nam{nc4} namelist:
+setting the \np{ln_nc4zip}{ln\_nc4zip} logical to false in the \nam{nc4} namelist:
 %------------------------------------------namnc4----------------------------------------------------
 …
 If \key{netcdf4} has not been defined, these namelist parameters are not read.
 In this case, \np{ln\_nc4zip} is set false and dummy routines for a few NetCDF4-specific functions are defined.
+In this case, \np{ln_nc4zip}{ln\_nc4zip} is set false and dummy routines for a few NetCDF4-specific functions are defined.
 These functions will not be used but need to be included so that compilation is possible with NetCDF3 libraries.
 …
 \begin{description}
 \item[\np{ln\_glo\_trd}]:
   at each \np{nn\_trd} time-step a check of the basin averaged properties of
+\item[\np{ln_glo_trd}{ln\_glo\_trd}]:
+  at each \np{nn_trd}{nn\_trd} time-step a check of the basin averaged properties of
   the momentum and tracer equations is performed.
   This also includes a check of $T^2$, $S^2$, $\tfrac{1}{2} (u^2+v2)$,
   and potential energy time evolution equations properties;
 \item[\np{ln\_dyn\_trd}]:
+\item[\np{ln_dyn_trd}{ln\_dyn\_trd}]:
   each 3D trend of the evolution of the two momentum components is output;
 \item[\np{ln\_dyn\_mxl}]:
+\item[\np{ln_dyn_mxl}{ln\_dyn\_mxl}]:
   each 3D trend of the evolution of the two momentum components averaged over the mixed layer is output;
 \item[\np{ln\_vor\_trd}]:
+\item[\np{ln_vor_trd}{ln\_vor\_trd}]:
   a vertical summation of the moment tendencies is performed,
   then the curl is computed to obtain the barotropic vorticity tendencies which are output;
 \item[\np{ln\_KE\_trd}] :
+\item[\np{ln_KE_trd}{ln\_KE\_trd}] :
   each 3D trend of the Kinetic Energy equation is output;
 \item[\np{ln\_tra\_trd}]:
+\item[\np{ln_tra_trd}{ln\_tra\_trd}]:
   each 3D trend of the evolution of temperature and salinity is output;
 \item[\np{ln\_tra\_mxl}]:
+\item[\np{ln_tra_mxl}{ln\_tra\_mxl}]:
   each 2D trend of the evolution of temperature and salinity averaged over the mixed layer is output;
 \end{description}
 …
 \textbf{Note that} in the current version (v3.6), many changes has been introduced but not fully tested.
 In particular, options associated with \np{ln\_dyn\_mxl}, \np{ln\_vor\_trd}, and \np{ln\_tra\_mxl} are not working,
 and none of the options have been tested with variable volume (\ie\ \np{ln\_linssh}\forcode{=.true.}).
+In particular, options associated with \np{ln_dyn_mxl}{ln\_dyn\_mxl}, \np{ln_vor_trd}{ln\_vor\_trd}, and \np{ln_tra_mxl}{ln\_tra\_mxl} are not working,
+and none of the options have been tested with variable volume (\ie\ \np{ln_linssh}{ln\_linssh}\forcode{=.true.}).
 % -------------------------------------------------------------------------------------------------------------
 …
 Options are defined by \nam{flo} namelist 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}\forcode{=.true.}).
+or on a $4^th$ Runge-Hutta algorithm (\np{ln_flork4}{ln\_flork4}\forcode{=.true.}).
 Note that the \cite{blanke.raynaud_JPO97} algorithm have the advantage of providing trajectories which
 are consistent with the numeric of the code, so that the trajectories never intercept the bathymetry.
 …
 Initial coordinates can be given with Ariane Tools convention
 (IJK coordinates, (\np{ln\_ariane}\forcode{=.true.}) ) or with longitude and latitude.
+(IJK coordinates, (\np{ln_ariane}{ln\_ariane}\forcode{=.true.}) ) or with longitude and latitude.
 In case of Ariane convention, input filename is \textit{init\_float\_ariane}.
 …
 \np{jpnfl} is the total number of floats during the run.
 When initial positions are read in a restart file (\np{ln\_rstflo}\forcode{=.true.} ),
+When initial positions are read in a restart file (\np{ln_rstflo}{ln\_rstflo}\forcode{=.true.} ),
 \np{jpnflnewflo} can be added in the initialization file.
 \subsubsection{Output data}
 \np{nn\_writefl} is the frequency of writing in float output file and \np{nn\_stockfl} is the frequency of
+\np{nn_writefl}{nn\_writefl} is the frequency of writing in float output file and \np{nn_stockfl}{nn\_stockfl} is the frequency of
 creation of the float restart file.
 Output data can be written in ascii files (\np{ln\_flo\_ascii}\forcode{=.true.}).
+Output data can be written in ascii files (\np{ln_flo_ascii}{ln\_flo\_ascii}\forcode{=.true.}).
 In that case, output filename is trajec\_float.
 Another possiblity of writing format is Netcdf (\np{ln\_flo\_ascii}\forcode{=.false.}) with
+Another possiblity of writing format is Netcdf (\np{ln_flo_ascii}{ln\_flo\_ascii}\forcode{=.false.}) with
 \key{iomput} and outputs selected in iodef.xml.
 Here it is an example of specification to put in files description section:
 …
 This on-line Harmonic analysis is actived with \key{diaharm}.
 Some parameters are available in namelist \nam{\_diaharm}:
  - \np{nit000\_han} is the first time step used for harmonic analysis
  - \np{nitend\_han} is the  last time step used for harmonic analysis
  - \np{nstep\_han}  is the  time step frequency for harmonic analysis
 % - \np{nb\_ana}     is the number of harmonics to analyse
+Some parameters are available in namelist \nam{_diaharm}{\_diaharm}:
+ - \np{nit000_han}{nit000\_han} is the first time step used for harmonic analysis
+ - \np{nitend_han}{nitend\_han} is the  last time step used for harmonic analysis
+ - \np{nstep_han}{nstep\_han}  is the  time step frequency for harmonic analysis
+% - \np{nb_ana}{nb\_ana}     is the number of harmonics to analyse
  - \np{tname}       is an array with names of tidal constituents to analyse
  \np{nit000\_han} and \np{nitend\_han} must be between \np{nit000} and \np{nitend} of the simulation.
+ \np{nit000_han}{nit000\_han} and \np{nitend_han}{nitend\_han} must be between \np{nit000} and \np{nitend} of the simulation.
  The restart capability is not implemented.
 …
 - \texttt{salt\_transport}   for   salt transports (unit: $10^{9}Kg s^{-1}$) \\
 Namelist variables in \nam{\_diadct} control how frequently the flows are summed and the time scales over which
+Namelist variables in \nam{_diadct}{\_diadct} 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:
 \np{nn\_dct}   : frequency of instantaneous transports computing
 \np{nn\_dctwri}: frequency of writing ( mean of instantaneous transports )
 \np{nn\_debug} : debugging of the section
+\np{nn_dct}{nn\_dct}   : frequency of instantaneous transports computing
+\np{nn_dctwri}{nn\_dctwri}: frequency of writing ( mean of instantaneous transports )
+\np{nn_debug}{nn\_debug} : debugging of the section
 \subsubsection{Creating a binary file containing the pathway of each section}
 …
 Third, the discretisation of \autoref{eq:DIA_steric_Bq} depends on the type of free surface which is considered.
 In the non linear free surface case, \ie\ \np{ln\_linssh}\forcode{=.true.}, it is given by
+In the non linear free surface case, \ie\ \np{ln_linssh}{ln\_linssh}\forcode{=.true.}, it is given by
 \[
 …
 sea water pressure at sea floor (botpres), dynamic sea surface height (sshdyn).
 In \mdl{diaptr} when \np{ln\_diaptr}\forcode{=.true.}
+In \mdl{diaptr} when \np{ln_diaptr}{ln\_diaptr}\forcode{=.true.}
 (see the \nam{ptr} namelist below) can be computed on-line the poleward heat and salt transports,
 their advective and diffusive component, and the meriodional stream function .
 When \np{ln\_subbas}\forcode{=.true.}, transports and stream function are computed for the Atlantic, Indian,
+When \np{ln_subbas}{ln\_subbas}\forcode{=.true.}, transports and stream function are computed for the Atlantic, Indian,
 Pacific and Indo-Pacific Oceans (defined north of 30\deg{S}) as well as for the World Ocean.
 The sub-basin decomposition requires an input file (\ifile{subbasins}) which contains three 2D mask arrays,
 …
 Values greater than 1 indicate that information is propagated across more than one grid cell in a single time step.
 The variables can be activated by setting the \np{nn\_diacfl} namelist parameter to 1 in the \nam{ctl} namelist.
+The variables can be activated by setting the \np{nn_diacfl}{nn\_diacfl} namelist parameter to 1 in the \nam{ctl} namelist.
 The diagnostics will be written out to an ascii file named cfl\_diagnostics.ascii.
 In this file the maximum value of $C_u$, $C_v$, and $C_w$ are printed at each timestep along with the coordinates of

NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIU.tex

-                      r11567
+                      r11577
 This namelist contains only two variables:
 \begin{description}
 \item[\np{ln\_diurnal}]
+\item[\np{ln_diurnal}{ln\_diurnal}]
   A logical switch for turning on/off both the cool skin and warm layer.
 \item[\np{ln\_diurnal\_only}]
+\item[\np{ln_diurnal_only}{ln\_diurnal\_only}]
   A logical switch which if \forcode{.true.} will run the diurnal model without the other dynamical parts of \NEMO.
   \np{ln\_diurnal\_only} must be \forcode{.false.} if \np{ln\_diurnal} is \forcode{.false.}.
+  \np{ln_diurnal_only}{ln\_diurnal\_only} must be \forcode{.false.} if \np{ln_diurnal}{ln\_diurnal} is \forcode{.false.}.
 \end{description}

NEMO/trunk/doc/latex/NEMO/subfiles/chap_DOM.tex

-                      r11571
+                      r11577
 Two typical methods are available to specify the spatial domain configuration;
 they can be selected using parameter \np{ln\_read\_cfg} parameter in namelist \nam{cfg}.
 If \np{ln\_read\_cfg} is set to \forcode{.true.},
+they can be selected using parameter \np{ln_read_cfg}{ln\_read\_cfg} parameter in namelist \nam{cfg}.
+If \np{ln_read_cfg}{ln\_read\_cfg} is set to \forcode{.true.},
 the domain-specific parameters and fields are read from a netCDF input file,
 whose name (without its .nc suffix) can be specified as the value of the \np{cn\_domcfg} parameter in namelist \nam{cfg}.
 If \np{ln\_read\_cfg} is set to \forcode{.false.},
+whose name (without its .nc suffix) can be specified as the value of the \np{cn_domcfg}{cn\_domcfg} parameter in namelist \nam{cfg}.
+If \np{ln_read_cfg}{ln\_read\_cfg} is set to \forcode{.false.},
 the domain-specific parameters and fields can be provided (\eg\ analytically computed) by
 subroutines \mdl{usrdef\_hgr} and \mdl{usrdef\_zgr}.
 …
 The next subsections summarise the parameter and fields related to the configuration of the whole model domain.
 These represent the minimum information that must be provided either via the \np{cn\_domcfg} file or set by code
+These represent the minimum information that must be provided either via the \np{cn_domcfg}{cn\_domcfg} file or set by code
 inserted into user-supplied versions of the \texttt{usrdef\_*} subroutines.
 The requirements are presented in three sections:
 …
 see \autoref{sec:LBC_mpp}).
 The name of the configuration is set through parameter \np{cn\_cfg},
 and the nominal resolution through parameter \np{nn\_cfg}
+The name of the configuration is set through parameter \np{cn_cfg}{cn\_cfg},
+and the nominal resolution through parameter \np{nn_cfg}{nn\_cfg}
 (unless in the input file both of variables \texttt{ORCA} and \texttt{ORCA\_index} are present,
 in which case \np{cn\_cfg} and \np{nn\_cfg} are set from these values accordingly).
+in which case \np{cn_cfg}{cn\_cfg} and \np{nn_cfg}{nn\_cfg} are set from these values accordingly).
 The global lateral boundary condition type is selected from 8 options using parameter \jp{jperio}.
 …
 the unaltered surface areas at $u$ and $v$ grid points (\texttt{e1e2u} and \texttt{e1e2v}, respectively) must be read or
 pre-computed in \mdl{usrdef\_hgr}.
 If these arrays are present in the \np{cn\_domcfg} file they are read and the internal computation is suppressed.
+If these arrays are present in the \np{cn_domcfg}{cn\_domcfg} file they are read and the internal computation is suppressed.
 Versions of \mdl{usrdef\_hgr} which set their own values of \texttt{e1e2u} and \texttt{e1e2v} should set
 the surface-area computation flag:
 …
     (d) hybrid $s-z$ coordinate,
     (e) hybrid $s-z$ coordinate with partial step, and
     (f) same as (e) but in the non-linear free surface (\protect\np{ln\_linssh}\forcode{=.false.}).
+    (f) same as (e) but in the non-linear free surface (\protect\np{ln_linssh}{ln\_linssh}\forcode{=.false.}).
     Note that the non-linear free surface can be used with any of the 5 coordinates (a) to (e).}
   \label{fig:DOM_z_zps_s_sps}
 …
 a single configuration file can support both options.
 By default a non-linear free surface is used (\np{ln\_linssh} set to \forcode{=.false.} in \nam{dom}):
+By default a non-linear free surface is used (\np{ln_linssh}{ln\_linssh} set to \forcode{=.false.} in \nam{dom}):
 the coordinate follow the time-variation of the free surface so that the transformation is time dependent:
 $z(i,j,k,t)$ (\eg\ \autoref{fig:DOM_z_zps_s_sps}f).
 When a linear free surface is assumed (\np{ln\_linssh} set to \forcode{=.true.} in \nam{dom}),
+When a linear free surface is assumed (\np{ln_linssh}{ln\_linssh} set to \forcode{=.true.} in \nam{dom}),
 the vertical coordinates are fixed in time, but the seawater can move up and down across the $z_0$ surface
 (in other words, the top of the ocean in not a rigid lid).
 Note that settings:
 \np{ln\_zco}, \np{ln\_zps}, \np{ln\_sco} and \np{ln\_isfcav} mentioned in the following sections
+\np{ln_zco}{ln\_zco}, \np{ln_zps}{ln\_zps}, \np{ln_sco}{ln\_sco} and \np{ln_isfcav}{ln\_isfcav} mentioned in the following sections
 appear to be namelist options but they are no longer truly namelist options for \NEMO.
 Their value is written to and read from the domain configuration file and
 …
 serve both to provide a record of the choices made whilst building the configuration and
 to trigger appropriate code blocks within \NEMO.
 These values should not be altered in the \np{cn\_domcfg} file.
+These values should not be altered in the \np{cn_domcfg}{cn\_domcfg} file.
 \medskip
 The decision on these choices must be made when the \np{cn\_domcfg} file is constructed.
+The decision on these choices must be made when the \np{cn_domcfg}{cn\_domcfg} file is constructed.
 Three main choices are offered (\autoref{fig:DOM_z_zps_s_sps}a-c):
 \begin{itemize}
 \item $z$-coordinate with full step bathymetry (\np{ln\_zco}\forcode{=.true.}),
 \item $z$-coordinate with partial step ($zps$) bathymetry (\np{ln\_zps}\forcode{=.true.}),
 \item Generalized, $s$-coordinate (\np{ln\_sco}\forcode{=.true.}).
+\item $z$-coordinate with full step bathymetry (\np{ln_zco}{ln\_zco}\forcode{=.true.}),
+\item $z$-coordinate with partial step ($zps$) bathymetry (\np{ln_zps}{ln\_zps}\forcode{=.true.}),
+\item Generalized, $s$-coordinate (\np{ln_sco}{ln\_sco}\forcode{=.true.}).
 \end{itemize}
 …
 A further choice related to vertical coordinate concerns
 the presence (or not) of ocean cavities beneath ice shelves within the model domain.
 A setting of \np{ln\_isfcav} as \forcode{.true.} indicates that the domain contains ocean cavities,
+A setting of \np{ln_isfcav}{ln\_isfcav} as \forcode{.true.} indicates that the domain contains ocean cavities,
 otherwise the top, wet layer of the ocean will always be at the ocean surface.
 This option is currently only available for $z$- or $zps$-coordinates.
 …
 They are updated at each model time step.
 The initial fixed reference coordinate system is held in variable names with a $\_0$ suffix.
 When the linear free surface option is used (\np{ln\_linssh}\forcode{=.true.}),
+When the linear free surface option is used (\np{ln_linssh}{ln\_linssh}\forcode{=.true.}),
 \textit{before}, \textit{now} and \textit{after} arrays are initially set to
 their reference counterpart and remain fixed.
 …
 (grid-point position, scale factors)
 can be saved in a file if
 namelist parameter \np{ln\_write\_cfg} (namelist \nam{cfg}) is set to \forcode{.true.};
 the output filename is set through parameter \np{cn\_domcfg\_out}.
+namelist parameter \np{ln_write_cfg}{ln\_write\_cfg} (namelist \nam{cfg}) is set to \forcode{.true.};
+the output filename is set through parameter \np{cn_domcfg_out}{cn\_domcfg\_out}.
 This is only really useful if
 the fields are computed in subroutines \mdl{usrdef\_hgr} or \mdl{usrdef\_zgr} and
 …
 (grid-point position, scale factors, depths and masks)
 can be saved in a file called \texttt{mesh\_mask} if
 namelist parameter \np{ln\_meshmask} (namelist \nam{dom}) is set to \forcode{.true.}.
+namelist parameter \np{ln_meshmask}{ln\_meshmask} (namelist \nam{dom}) is set to \forcode{.true.}.
 This file contains additional fields that can be useful for post-processing applications.
 …
 Basic initial state options are defined in \nam{tsd}.
 By default, the ocean starts from rest (the velocity field is set to zero) and
 the initialization of temperature and salinity fields is controlled through the \np{ln\_tsd\_init} namelist parameter.
+the initialization of temperature and salinity fields is controlled through the \np{ln_tsd_init}{ln\_tsd\_init} namelist parameter.
 \begin{description}
 \item[\np{ln\_tsd\_init}\forcode{= .true.}]
+\item[\np{ln_tsd_init}{ln\_tsd\_init}\forcode{= .true.}]
   Use T and S input files that can be given on the model grid itself or on their native input data grids.
   In the latter case, the data will be interpolated on-the-fly both in the horizontal and the vertical to the model grid
   (see \autoref{subsec:SBC_iof}).
   The information relating to the input files are specified in the \np{sn\_tem} and \np{sn\_sal} structures.
+  The information relating to the input files are specified in the \np{sn_tem}{sn\_tem} and \np{sn_sal}{sn\_sal} structures.
   The computation is done in the \mdl{dtatsd} module.
 \item[\np{ln\_tsd\_init}\forcode{= .false.}]
+\item[\np{ln_tsd_init}{ln\_tsd\_init}\forcode{= .false.}]
   Initial values for T and S are set via a user supplied \rou{usr\_def\_istate} routine contained in \mdl{userdef\_istate}.
   The default version sets horizontally uniform T and profiles as used in the GYRE configuration

NEMO/trunk/doc/latex/NEMO/subfiles/chap_DYN.tex

-                      r11571
+                      r11577
 applications of the \NEMO\ ocean model.
 The flux form option (see next section) has been present since version $2$.
 Options are defined through the \nam{dyn\_adv} namelist variables Coriolis and
+Options are defined through the \nam{dyn_adv}{dyn\_adv} namelist variables Coriolis and
 momentum advection terms are evaluated using a leapfrog scheme,
 \ie\ the velocity appearing in these expressions is centred in time (\textit{now} velocity).
 …
 %-------------------------------------------------------------------------------------------------------------
 Options are defined through the \nam{dyn\_vor} namelist variables.
+Options are defined through the \nam{dyn_vor}{dyn\_vor} namelist variables.
 Four discretisations of the vorticity term (\texttt{ln\_dynvor\_xxx}\forcode{=.true.}) are available:
 conserving potential enstrophy of horizontally non-divergent flow (ENS scheme);
 …
 (EEN scheme) (see \autoref{subsec:INVARIANTS_vorEEN}).
 In the case of ENS, ENE or MIX schemes the land sea mask may be slightly modified to ensure the consistency of
 vorticity term with analytical equations (\np{ln\_dynvor\_con}\forcode{=.true.}).
+vorticity term with analytical equations (\np{ln_dynvor_con}{ln\_dynvor\_con}\forcode{=.true.}).
 The vorticity terms are all computed in dedicated routines that can be found in the \mdl{dynvor} module.
 …
 %                 enstrophy conserving scheme
 %-------------------------------------------------------------
 \subsubsection[Enstrophy conserving scheme (\forcode{ln_dynvor_ens})]{Enstrophy conserving scheme (\protect\np{ln\_dynvor\_ens})}
+\subsubsection[Enstrophy conserving scheme (\forcode{ln_dynvor_ens})]{Enstrophy conserving scheme (\protect\np{ln_dynvor_ens}{ln\_dynvor\_ens})}
 \label{subsec:DYN_vor_ens}
 …
 %                 energy conserving scheme
 %-------------------------------------------------------------
 \subsubsection[Energy conserving scheme (\forcode{ln_dynvor_ene})]{Energy conserving scheme (\protect\np{ln\_dynvor\_ene})}
+\subsubsection[Energy conserving scheme (\forcode{ln_dynvor_ene})]{Energy conserving scheme (\protect\np{ln_dynvor_ene}{ln\_dynvor\_ene})}
 \label{subsec:DYN_vor_ene}
 …
 %                 mix energy/enstrophy conserving scheme
 %-------------------------------------------------------------
 \subsubsection[Mixed energy/enstrophy conserving scheme (\forcode{ln_dynvor_mix})]{Mixed energy/enstrophy conserving scheme (\protect\np{ln\_dynvor\_mix})}
+\subsubsection[Mixed energy/enstrophy conserving scheme (\forcode{ln_dynvor_mix})]{Mixed energy/enstrophy conserving scheme (\protect\np{ln_dynvor_mix}{ln\_dynvor\_mix})}
 \label{subsec:DYN_vor_mix}
 …
 %                 energy and enstrophy conserving scheme
 %-------------------------------------------------------------
 \subsubsection[Energy and enstrophy conserving scheme (\forcode{ln_dynvor_een})]{Energy and enstrophy conserving scheme (\protect\np{ln\_dynvor\_een})}
+\subsubsection[Energy and enstrophy conserving scheme (\forcode{ln_dynvor_een})]{Energy and enstrophy conserving scheme (\protect\np{ln_dynvor_een}{ln\_dynvor\_een})}
 \label{subsec:DYN_vor_een}
 …
 A key point in \autoref{eq:DYN_een_e3f} is how the averaging in the \textbf{i}- and \textbf{j}- directions is made.
 It uses the sum of masked t-point vertical scale factor divided either by the sum of the four t-point masks
 (\np{nn\_een\_e3f}\forcode{=1}), or just by $4$ (\np{nn\_een\_e3f}\forcode{=.true.}).
+(\np{nn_een_e3f}{nn\_een\_e3f}\forcode{=1}), or just by $4$ (\np{nn\_een\_e3f}\forcode{=.true.}).
 The latter case preserves the continuity of $e_{3f}$ when one or more of the neighbouring $e_{3t}$ tends to zero and
 extends by continuity the value of $e_{3f}$ into the land areas.
 …
   \right.
 \]
 When \np{ln\_dynzad\_zts}\forcode{=.true.},
+When \np{ln_dynzad_zts}{ln\_dynzad\_zts}\forcode{=.true.},
 a split-explicit time stepping with 5 sub-timesteps is used on the vertical advection term.
 This option can be useful when the value of the timestep is limited by vertical advection \citep{lemarie.debreu.ea_OM15}.
 Note that in this case,
 a similar split-explicit time stepping should be used on vertical advection of tracer to ensure a better stability,
 an option which is only available with a TVD scheme (see \np{ln\_traadv\_tvd\_zts} in \autoref{subsec:TRA_adv_tvd}).
+an option which is only available with a TVD scheme (see \np{ln_traadv_tvd_zts}{ln\_traadv\_tvd\_zts} in \autoref{subsec:TRA_adv_tvd}).
 …
 %-------------------------------------------------------------------------------------------------------------
 Options are defined through the \nam{dyn\_adv} namelist variables.
+Options are defined through the \nam{dyn_adv}{dyn\_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,
 …
 or a $3^{rd}$ order upstream biased scheme, UBS.
 The latter is described in \citet{shchepetkin.mcwilliams_OM05}.
 The schemes are selected using the namelist logicals \np{ln\_dynadv\_cen2} and \np{ln\_dynadv\_ubs}.
+The schemes are selected using the namelist logicals \np{ln_dynadv_cen2}{ln\_dynadv\_cen2} and \np{ln_dynadv_ubs}{ln\_dynadv\_ubs}.
 In flux form, the schemes differ by the choice of a space and time interpolation to define the value of
 $u$ and $v$ at the centre of each face of $u$- and $v$-cells, \ie\ at the $T$-, $f$-,
 …
 %                 2nd order centred scheme
 %-------------------------------------------------------------
 \subsubsection[CEN2: $2^{nd}$ order centred scheme (\forcode{ln_dynadv_cen2})]{CEN2: $2^{nd}$ order centred scheme (\protect\np{ln\_dynadv\_cen2})}
+\subsubsection[CEN2: $2^{nd}$ order centred scheme (\forcode{ln_dynadv_cen2})]{CEN2: $2^{nd}$ order centred scheme (\protect\np{ln_dynadv_cen2}{ln\_dynadv\_cen2})}
 \label{subsec:DYN_adv_cen2}
 …
 %                 UBS scheme
 %-------------------------------------------------------------
 \subsubsection[UBS: Upstream Biased Scheme (\forcode{ln_dynadv_ubs})]{UBS: Upstream Biased Scheme (\protect\np{ln\_dynadv\_ubs})}
+\subsubsection[UBS: Upstream Biased Scheme (\forcode{ln_dynadv_ubs})]{UBS: Upstream Biased Scheme (\protect\np{ln_dynadv_ubs}{ln\_dynadv\_ubs})}
 \label{subsec:DYN_adv_ubs}
 …
 But the amplitudes of the false extrema are significantly reduced over those in the centred second order method.
 As the scheme already includes a diffusion component, it can be used without explicit lateral diffusion on momentum
 (\ie\ \np{ln\_dynldf\_lap}\forcode{=}\np{ln\_dynldf\_bilap}\forcode{=.false.}),
+(\ie\ \np{ln_dynldf_lap}{ln\_dynldf\_lap}\forcode{=}\np{ln_dynldf_bilap}{ln\_dynldf\_bilap}\forcode{=.false.}),
 and it is recommended to do so.
 …
 %-------------------------------------------------------------------------------------------------------------
 Options are defined through the \nam{dyn\_hpg} namelist variables.
+Options are defined through the \nam{dyn_hpg}{dyn\_hpg} namelist variables.
 The key distinction between the different algorithms used for
 the hydrostatic pressure gradient is the vertical coordinate used,
 …
 %           z-coordinate with full step
 %--------------------------------------------------------------------------------------------------------------
 \subsection[Full step $Z$-coordinate (\forcode{ln_dynhpg_zco})]{Full step $Z$-coordinate (\protect\np{ln\_dynhpg\_zco})}
+\subsection[Full step $Z$-coordinate (\forcode{ln_dynhpg_zco})]{Full step $Z$-coordinate (\protect\np{ln_dynhpg_zco}{ln\_dynhpg\_zco})}
 \label{subsec:DYN_hpg_zco}
 …
 %           z-coordinate with partial step
 %--------------------------------------------------------------------------------------------------------------
 \subsection[Partial step $Z$-coordinate (\forcode{ln_dynhpg_zps})]{Partial step $Z$-coordinate (\protect\np{ln\_dynhpg\_zps})}
+\subsection[Partial step $Z$-coordinate (\forcode{ln_dynhpg_zps})]{Partial step $Z$-coordinate (\protect\np{ln_dynhpg_zps}{ln\_dynhpg\_zps})}
 \label{subsec:DYN_hpg_zps}
 …
 density Jacobian with cubic polynomial method is currently disabled whilst known bugs are under investigation.
 $\bullet$ Traditional coding (see for example \citet{madec.delecluse.ea_JPO96}: (\np{ln\_dynhpg\_sco}\forcode{=.true.})
+$\bullet$ Traditional coding (see for example \citet{madec.delecluse.ea_JPO96}: (\np{ln_dynhpg_sco}{ln\_dynhpg\_sco}\forcode{=.true.})
 \begin{equation}
   \label{eq:DYN_hpg_sco}
 …
 ($e_{3w}$).
 $\bullet$ Traditional coding with adaptation for ice shelf cavities (\np{ln\_dynhpg\_isf}\forcode{=.true.}).
 This scheme need the activation of ice shelf cavities (\np{ln\_isfcav}\forcode{=.true.}).
 $\bullet$ Pressure Jacobian scheme (prj) (a research paper in preparation) (\np{ln\_dynhpg\_prj}\forcode{=.true.})
+$\bullet$ Traditional coding with adaptation for ice shelf cavities (\np{ln_dynhpg_isf}{ln\_dynhpg\_isf}\forcode{=.true.}).
+This scheme need the activation of ice shelf cavities (\np{ln_isfcav}{ln\_isfcav}\forcode{=.true.}).
+$\bullet$ Pressure Jacobian scheme (prj) (a research paper in preparation) (\np{ln_dynhpg_prj}{ln\_dynhpg\_prj}\forcode{=.true.})
 $\bullet$ Density Jacobian with cubic polynomial scheme (DJC) \citep{shchepetkin.mcwilliams_OM05}
 (\np{ln\_dynhpg\_djc}\forcode{=.true.}) (currently disabled; under development)
+(\np{ln_dynhpg_djc}{ln\_dynhpg\_djc}\forcode{=.true.}) (currently disabled; under development)
 Note that expression \autoref{eq:DYN_hpg_sco} is commonly used when the variable volume formulation is activated
 (\texttt{vvl?}) because in that case, even with a flat bottom,
 the coordinate surfaces are not horizontal but follow the free surface \citep{levier.treguier.ea_rpt07}.
 The pressure jacobian scheme (\np{ln\_dynhpg\_prj}\forcode{=.true.}) is available as
 an improved option to \np{ln\_dynhpg\_sco}\forcode{=.true.} when \texttt{vvl?} is active.
+The pressure jacobian scheme (\np{ln_dynhpg_prj}{ln\_dynhpg\_prj}\forcode{=.true.}) is available as
+an improved option to \np{ln_dynhpg_sco}{ln\_dynhpg\_sco}\forcode{=.true.} when \texttt{vvl?} is active.
 The pressure Jacobian scheme uses a constrained cubic spline to
 reconstruct the density profile across the water column.
 …
 Beneath an ice shelf, the total pressure gradient is the sum of the pressure gradient due to the ice shelf load and
 the pressure gradient due to the ocean load (\np{ln\_dynhpg\_isf}\forcode{=.true.}).\\
+the pressure gradient due to the ocean load (\np{ln_dynhpg_isf}{ln\_dynhpg\_isf}\forcode{=.true.}).\\
 The main hypothesis to compute the ice shelf load is that the ice shelf is in an isostatic equilibrium.
 …
 %           Time-scheme
 %--------------------------------------------------------------------------------------------------------------
 \subsection[Time-scheme (\forcode{ln_dynhpg_imp})]{Time-scheme (\protect\np{ln\_dynhpg\_imp})}
+\subsection[Time-scheme (\forcode{ln_dynhpg_imp})]{Time-scheme (\protect\np{ln_dynhpg_imp}{ln\_dynhpg\_imp})}
 \label{subsec:DYN_hpg_imp}
 …
 rather than at the central time level $t$ only, as in the standard leapfrog scheme.
 $\bullet$ leapfrog scheme (\np{ln\_dynhpg\_imp}\forcode{=.true.}):
+$\bullet$ leapfrog scheme (\np{ln_dynhpg_imp}{ln\_dynhpg\_imp}\forcode{=.true.}):
 \begin{equation}
 …
 \end{equation}
 $\bullet$ semi-implicit scheme (\np{ln\_dynhpg\_imp}\forcode{=.true.}):
+$\bullet$ semi-implicit scheme (\np{ln_dynhpg_imp}{ln\_dynhpg\_imp}\forcode{=.true.}):
 \begin{equation}
   \label{eq:DYN_hpg_imp}
 …
 such as the stability limits associated with advection or diffusion.
 In practice, the semi-implicit scheme is used when \np{ln\_dynhpg\_imp}\forcode{=.true.}.
+In practice, the semi-implicit scheme is used when \np{ln_dynhpg_imp}{ln\_dynhpg\_imp}\forcode{=.true.}.
 In this case, we choose to apply the time filter to temperature and salinity used in the equation of state,
 instead of applying it to the hydrostatic pressure or to the density,
 …
 Note that in the semi-implicit case, it is necessary to save the filtered density,
 an extra three-dimensional field, in the restart file to restart the model with exact reproducibility.
 This option is controlled by  \np{nn\_dynhpg\_rst}, a namelist parameter.
+This option is controlled by  \np{nn_dynhpg_rst}{nn\_dynhpg\_rst}, a namelist parameter.
 % ================================================================
 …
 %------------------------------------------------------------------------------------------------------------
 Options are defined through the \nam{dyn\_spg} namelist variables.
+Options are defined through the \nam{dyn_spg}{dyn\_spg} namelist variables.
 The surface pressure gradient term is related to the representation of the free surface (\autoref{sec:MB_hor_pg}).
 The main distinction is between the fixed volume case (linear free surface) and
 …
 % Explicit free surface formulation
 %--------------------------------------------------------------------------------------------------------------
 \subsection[Explicit free surface (\forcode{ln_dynspg_exp})]{Explicit free surface (\protect\np{ln\_dynspg\_exp})}
+\subsection[Explicit free surface (\forcode{ln_dynspg_exp})]{Explicit free surface (\protect\np{ln_dynspg_exp}{ln\_dynspg\_exp})}
 \label{subsec:DYN_spg_exp}
 In the explicit free surface formulation (\np{ln\_dynspg\_exp} set to true),
+In the explicit free surface formulation (\np{ln_dynspg_exp}{ln\_dynspg\_exp} set to true),
 the model time step is chosen to be small enough to resolve the external gravity waves
 (typically a few tens of seconds).
 …
 % Split-explict free surface formulation
 %--------------------------------------------------------------------------------------------------------------
 \subsection[Split-explicit free surface (\forcode{ln_dynspg_ts})]{Split-explicit free surface (\protect\np{ln\_dynspg\_ts})}
+\subsection[Split-explicit free surface (\forcode{ln_dynspg_ts})]{Split-explicit free surface (\protect\np{ln_dynspg_ts}{ln\_dynspg\_ts})}
 \label{subsec:DYN_spg_ts}
 %------------------------------------------namsplit-----------------------------------------------------------
 …
 %-------------------------------------------------------------------------------------------------------------
 The split-explicit free surface formulation used in \NEMO\ (\np{ln\_dynspg\_ts} set to true),
+The split-explicit free surface formulation used in \NEMO\ (\np{ln_dynspg_ts}{ln\_dynspg\_ts} set to true),
 also called the time-splitting formulation, follows the one proposed by \citet{shchepetkin.mcwilliams_OM05}.
 The general idea is to solve the free surface equation and the associated barotropic velocity equations with
 …
 (\autoref{fig:DYN_spg_ts}).
 The size of the small time step, $\rdt_e$ (the external mode or barotropic time step) is provided through
 the \np{nn\_baro} namelist parameter as: $\rdt_e = \rdt / nn\_baro$.
 This parameter can be optionally defined automatically (\np{ln\_bt\_nn\_auto}\forcode{=.true.}) considering that
+the \np{nn_baro}{nn\_baro} namelist parameter as: $\rdt_e = \rdt / nn\_baro$.
+This parameter can be optionally defined automatically (\np{ln_bt_nn_auto}{ln\_bt\_nn\_auto}\forcode{=.true.}) considering that
 the stability of the barotropic system is essentially controled by external waves propagation.
 Maximum Courant number is in that case time independent, and easily computed online from the input bathymetry.
 Therefore, $\rdt_e$ is adjusted so that the Maximum allowed Courant number is smaller than \np{rn\_bt\_cmax}.
+Therefore, $\rdt_e$ is adjusted so that the Maximum allowed Courant number is smaller than \np{rn_bt_cmax}{rn\_bt\_cmax}.
 %%%
 …
     Time increases to the right.
     In this particular exemple,
     a boxcar averaging window over \np{nn\_baro} barotropic time steps is used
     (\np{nn\_bt\_flt}\forcode{=1}) and \np{nn\_baro}\forcode{=5}.
+    a boxcar averaging window over \np{nn_baro}{nn\_baro} barotropic time steps is used
+    (\np{nn\_bt\_flt}\forcode{=1}) and \np{nn_baro}{nn\_baro}\forcode{=5}.
     Internal mode time steps (which are also the model time steps) are denoted by
     $t-\rdt$, $t$ and $t+\rdt$.
 …
     the latter are used to obtain time averaged transports to advect tracers.
     a) Forward time integration:
     \protect\np{ln\_bt\_fw}\forcode{=.true.},  \protect\np{ln\_bt\_av}\forcode{=.true.}.
+    \protect\np{ln_bt_fw}{ln\_bt\_fw}\forcode{=.true.},  \protect\np{ln_bt_av}{ln\_bt\_av}\forcode{=.true.}.
     b) Centred time integration:
     \protect\np{ln\_bt\_fw}\forcode{=.false.}, \protect\np{ln\_bt\_av}\forcode{=.true.}.
+    \protect\np{ln_bt_fw}{ln\_bt\_fw}\forcode{=.false.}, \protect\np{ln_bt_av}{ln\_bt\_av}\forcode{=.true.}.
     c) Forward time integration with no time filtering (POM-like scheme):
     \protect\np{ln\_bt\_fw}\forcode{=.true.},  \protect\np{ln\_bt\_av}\forcode{=.false.}.}
+    \protect\np{ln_bt_fw}{ln\_bt\_fw}\forcode{=.true.},  \protect\np{ln_bt_av}{ln\_bt\_av}\forcode{=.false.}.}
   \label{fig:DYN_spg_ts}
 \end{figure}
 %>   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >
 In the default case (\np{ln\_bt\_fw}\forcode{=.true.}),
+In the default case (\np{ln_bt_fw}{ln\_bt\_fw}\forcode{=.true.}),
 the external mode is integrated between \textit{now} and \textit{after} baroclinic time-steps
 (\autoref{fig:DYN_spg_ts}a).
 To avoid aliasing of fast barotropic motions into three dimensional equations,
 time filtering is eventually applied on barotropic quantities (\np{ln\_bt\_av}\forcode{=.true.}).
+time filtering is eventually applied on barotropic quantities (\np{ln_bt_av}{ln\_bt\_av}\forcode{=.true.}).
 In that case, the integration is extended slightly beyond \textit{after} time step to
 provide time filtered quantities.
 …
 asselin filtering is not applied to barotropic quantities.\\
 Alternatively, one can choose to integrate barotropic equations starting from \textit{before} time step
 (\np{ln\_bt\_fw}\forcode{=.false.}).
 Although more computationaly expensive ( \np{nn\_baro} additional iterations are indeed necessary),
+(\np{ln_bt_fw}{ln\_bt\_fw}\forcode{=.false.}).
+Although more computationaly expensive ( \np{nn_baro}{nn\_baro} additional iterations are indeed necessary),
 the baroclinic to barotropic forcing term given at \textit{now} time step become centred in
 the middle of the integration window.
 …
 One can eventually choose to feedback instantaneous values by not using any time filter
 (\np{ln\_bt\_av}\forcode{=.false.}).
+(\np{ln_bt_av}{ln\_bt\_av}\forcode{=.false.}).
 In that case, external mode equations are continuous in time,
 \ie\ they are not re-initialized when starting a new sub-stepping sequence.
 …
 %-------------------------------------------------------------------------------------------------------------
 Options are defined through the \nam{dyn\_ldf} namelist variables.
+Options are defined through the \nam{dyn_ldf}{dyn\_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 or spatially variable;
 …
 % ================================================================
 \subsection[Iso-level laplacian (\forcode{ln_dynldf_lap})]{Iso-level laplacian operator (\protect\np{ln\_dynldf\_lap})}
+\subsection[Iso-level laplacian (\forcode{ln_dynldf_lap})]{Iso-level laplacian operator (\protect\np{ln_dynldf_lap}{ln\_dynldf\_lap})}
 \label{subsec:DYN_ldf_lap}
 …
 %           Rotated laplacian operator
 %--------------------------------------------------------------------------------------------------------------
 \subsection[Rotated laplacian (\forcode{ln_dynldf_iso})]{Rotated laplacian operator (\protect\np{ln\_dynldf\_iso})}
+\subsection[Rotated laplacian (\forcode{ln_dynldf_iso})]{Rotated laplacian operator (\protect\np{ln_dynldf_iso}{ln\_dynldf\_iso})}
 \label{subsec:DYN_ldf_iso}
 A rotation of the lateral momentum diffusion operator is needed in several cases:
 for iso-neutral diffusion in the $z$-coordinate (\np{ln\_dynldf\_iso}\forcode{=.true.}) and
 for either iso-neutral (\np{ln\_dynldf\_iso}\forcode{=.true.}) or
 geopotential (\np{ln\_dynldf\_hor}\forcode{=.true.}) diffusion in the $s$-coordinate.
+for iso-neutral diffusion in the $z$-coordinate (\np{ln_dynldf_iso}{ln\_dynldf\_iso}\forcode{=.true.}) and
+for either iso-neutral (\np{ln_dynldf_iso}{ln\_dynldf\_iso}\forcode{=.true.}) or
+geopotential (\np{ln_dynldf_hor}{ln\_dynldf\_hor}\forcode{=.true.}) diffusion in the $s$-coordinate.
 In the partial step case, coordinates are horizontal except at the deepest level and
 no rotation is performed when \np{ln\_dynldf\_hor}\forcode{=.true.}.
+no rotation is performed when \np{ln_dynldf_hor}{ln\_dynldf\_hor}\forcode{=.true.}.
 The diffusion operator is defined simply as the divergence of down gradient momentum fluxes on
 each momentum component.
 …
 %           Iso-level bilaplacian operator
 %--------------------------------------------------------------------------------------------------------------
 \subsection[Iso-level bilaplacian (\forcode{ln_dynldf_bilap})]{Iso-level bilaplacian operator (\protect\np{ln\_dynldf\_bilap})}
+\subsection[Iso-level bilaplacian (\forcode{ln_dynldf_bilap})]{Iso-level bilaplacian operator (\protect\np{ln_dynldf_bilap}{ln\_dynldf\_bilap})}
 \label{subsec:DYN_ldf_bilap}
 …
 Two time stepping schemes can be used for the vertical diffusion term:
 $(a)$ a forward time differencing scheme
 (\np{ln\_zdfexp}\forcode{=.true.}) using a time splitting technique (\np{nn\_zdfexp} $>$ 1) or
 $(b)$ a backward (or implicit) time differencing scheme (\np{ln\_zdfexp}\forcode{=.false.})
+(\np{ln_zdfexp}{ln\_zdfexp}\forcode{=.true.}) using a time splitting technique (\np{nn_zdfexp}{nn\_zdfexp} $>$ 1) or
+$(b)$ a backward (or implicit) time differencing scheme (\np{ln_zdfexp}{ln\_zdfexp}\forcode{=.false.})
 (see \autoref{chap:TD}).
 Note that namelist variables \np{ln\_zdfexp} and \np{nn\_zdfexp} apply to both tracers and dynamics.
+Note that namelist variables \np{ln_zdfexp}{ln\_zdfexp} and \np{nn_zdfexp}{nn\_zdfexp} apply to both tracers and dynamics.
 The formulation of the vertical subgrid scale physics is the same whatever the vertical coordinate is.
 …
 three other forcings may enter the dynamical equations by affecting the surface pressure gradient.
 (1) When \np{ln\_apr\_dyn}\forcode{=.true.} (see \autoref{sec:SBC_apr}),
+(1) When \np{ln_apr_dyn}{ln\_apr\_dyn}\forcode{=.true.} (see \autoref{sec:SBC_apr}),
 the atmospheric pressure is taken into account when computing the surface pressure gradient.
 (2) When \np{ln\_tide\_pot}\forcode{=.true.} and \np{ln\_tide}\forcode{=.true.} (see \autoref{sec:SBC_tide}),
+(2) When \np{ln_tide_pot}{ln\_tide\_pot}\forcode{=.true.} and \np{ln_tide}{ln\_tide}\forcode{=.true.} (see \autoref{sec:SBC_tide}),
 the tidal potential is taken into account when computing the surface pressure gradient.
 (3) When \np{nn\_ice\_embd}\forcode{=2} and LIM or CICE is used
+(3) When \np{nn_ice_embd}{nn\_ice\_embd}\forcode{=2} and LIM or CICE is used
 (\ie\ when the sea-ice is embedded in the ocean),
 the snow-ice mass is taken into account when computing the surface pressure gradient.
 …
 The principal idea of the directional limiter is that
 water should not be allowed to flow out of a dry tracer cell (i.e. one whose water depth is less than \np{rn\_wdmin1}).
+water should not be allowed to flow out of a dry tracer cell (i.e. one whose water depth is less than \np{rn_wdmin1}{rn\_wdmin1}).
 All the changes associated with this option are made to the barotropic solver for the non-linear
 …
 The flux across each $u$-face of a tracer cell is multiplied by a factor zuwdmask (an array which depends on ji and jj).
 If the user sets \np{ln\_wd\_dl\_ramp}\forcode{=.false.} then zuwdmask is 1 when the
 flux is from a cell with water depth greater than \np{rn\_wdmin1} and 0 otherwise. If the user sets
 \np{ln\_wd\_dl\_ramp}\forcode{=.true.} the flux across the face is ramped down as the water depth decreases
 from 2 * \np{rn\_wdmin1} to \np{rn\_wdmin1}. The use of this ramp reduced grid-scale noise in idealised test cases.
+If the user sets \np{ln_wd_dl_ramp}{ln\_wd\_dl\_ramp}\forcode{=.false.} then zuwdmask is 1 when the
+flux is from a cell with water depth greater than \np{rn_wdmin1}{rn\_wdmin1} and 0 otherwise. If the user sets
+\np{ln_wd_dl_ramp}{ln\_wd\_dl\_ramp}\forcode{=.true.} the flux across the face is ramped down as the water depth decreases
+from 2 * \np{rn_wdmin1}{rn\_wdmin1} to \np{rn\_wdmin1}. The use of this ramp reduced grid-scale noise in idealised test cases.
 At the point where the flux across a $u$-face is multiplied by zuwdmask , we have chosen
 …
 fields (tracers independent of $x$, $y$ and $z$). Our scheme conserves constant tracers because
 the velocities used at the tracer cell faces on the baroclinic timesteps are carefully calculated by dynspg\_ts
 to equal their mean value during the barotropic steps. If the user sets \np{ln\_wd\_dl\_bc}\forcode{=.true.}, the
+to equal their mean value during the barotropic steps. If the user sets \np{ln_wd_dl_bc}{ln\_wd\_dl\_bc}\forcode{=.true.}, the
 baroclinic velocities are also multiplied by a suitably weighted average of zuwdmask.
 …
 $\bullet$ vector invariant form or linear free surface
 (\np{ln\_dynhpg\_vec}\forcode{=.true.} ; \texttt{vvl?} not defined):
+(\np{ln_dynhpg_vec}{ln\_dynhpg\_vec}\forcode{=.true.} ; \texttt{vvl?} not defined):
 \[
   % \label{eq:DYN_nxt_vec}
 …
 $\bullet$ flux form and nonlinear free surface
 (\np{ln\_dynhpg\_vec}\forcode{=.false.} ; \texttt{vvl?} defined):
+(\np{ln_dynhpg_vec}{ln\_dynhpg\_vec}\forcode{=.false.} ; \texttt{vvl?} defined):
 \[
   % \label{eq:DYN_nxt_flux}
 …
 where RHS is the right hand side of the momentum equation,
 the subscript $f$ denotes filtered values and $\gamma$ is the Asselin coefficient.
 $\gamma$ is initialized as \np{nn\_atfp} (namelist parameter).
 Its default value is \np{nn\_atfp}\forcode{=10.e-3}.
+$\gamma$ is initialized as \np{nn_atfp}{nn\_atfp} (namelist parameter).
+Its default value is \np{nn_atfp}{nn\_atfp}\forcode{=10.e-3}.
 In both cases, the modified Asselin filter is not applied since perfect conservation is not an issue for
 the momentum equations.

NEMO/trunk/doc/latex/NEMO/subfiles/chap_LBC.tex

-                      r11571
+                      r11577
 % Boundary Condition at the Coast
 % ================================================================
 \section[Boundary condition at the coast (\forcode{rn_shlat})]{Boundary condition at the coast (\protect\np{rn\_shlat})}
+\section[Boundary condition at the coast (\forcode{rn_shlat})]{Boundary condition at the coast (\protect\np{rn_shlat}{rn\_shlat})}
 \label{sec:LBC_coast}
 %--------------------------------------------namlbc-------------------------------------------------------
 …
 and is required in order to compute the vorticity at the coast.
 Four different types of lateral boundary condition are available,
 controlled by the value of the \np{rn\_shlat} namelist parameter
+controlled by the value of the \np{rn_shlat}{rn\_shlat} namelist parameter
 (The value of the mask$_{f}$ array along the coastline is set equal to this parameter).
 These are:
 …
   \caption[Lateral boundary conditions]{
     Lateral boundary conditions
     (a) free-slip                       (\protect\np{rn\_shlat}\forcode{=0});
     (b) no-slip                         (\protect\np{rn\_shlat}\forcode{=2});
     (c) "partial" free-slip (\forcode{0<}\protect\np{rn\_shlat}\forcode{<2}) and
     (d) "strong" no-slip    (\forcode{2<}\protect\np{rn\_shlat}).
+    (a) free-slip                       (\protect\np{rn_shlat}{rn\_shlat}\forcode{=0});
+    (b) no-slip                         (\protect\np{rn_shlat}{rn\_shlat}\forcode{=2});
+    (c) "partial" free-slip (\forcode{0<}\protect\np{rn_shlat}{rn\_shlat}\forcode{<2}) and
+    (d) "strong" no-slip    (\forcode{2<}\protect\np{rn_shlat}{rn\_shlat}).
     Implied "ghost" velocity inside land area is display in grey.}
   \label{fig:LBC_shlat}
 …
 \begin{description}
 \item[free-slip boundary condition (\np{rn\_shlat}\forcode{=0}):] the tangential velocity at
+\item[free-slip boundary condition (\np{rn_shlat}{rn\_shlat}\forcode{=0}):] the tangential velocity at
   the coastline is equal to the offshore velocity,
   \ie\ the normal derivative of the tangential velocity is zero at the coast,
 …
   (\autoref{fig:LBC_shlat}-a).
 \item[no-slip boundary condition (\np{rn\_shlat}\forcode{=2}):] the tangential velocity vanishes at the coastline.
+\item[no-slip boundary condition (\np{rn_shlat}{rn\_shlat}\forcode{=2}):] the tangential velocity vanishes at the coastline.
   Assuming that the tangential velocity decreases linearly from
   the closest ocean velocity grid point to the coastline,
 …
   \]
 \item["partial" free-slip boundary condition (0$<$\np{rn\_shlat}$<$2):] the tangential velocity at
+\item["partial" free-slip boundary condition (0$<$\np{rn_shlat}{rn\_shlat}$<$2):] the tangential velocity at
   the coastline is smaller than the offshore velocity, \ie\ there is a lateral friction but
   not strong enough to make the tangential velocity at the coast vanish (\autoref{fig:LBC_shlat}-c).
   This can be selected by providing a value of mask$_{f}$ strictly inbetween $0$ and $2$.
 \item["strong" no-slip boundary condition (2$<$\np{rn\_shlat}):] the viscous boundary layer is assumed to
+\item["strong" no-slip boundary condition (2$<$\np{rn_shlat}{rn\_shlat}):] the viscous boundary layer is assumed to
   be smaller than half the grid size (\autoref{fig:LBC_shlat}-d).
   The friction is thus larger than in the no-slip case.
 …
 If the domain decomposition is automatically defined (when \np{jpni} and \np{jpnj} are < 1), the decomposition chosen by the model will minimise the sub-domain size (defined as $max_{all domains}(jpi \times jpj)$) and maximize the number of eliminated land subdomains. This means that no other domain decomposition (a set of \np{jpni} and \np{jpnj} values) will use less processes than $(jpni  \times  jpnj - N_{land})$ and get a smaller subdomain size.
 In order to specify $N_{mpi}$ properly (minimize $N_{useless}$), you must run the model once with \np{ln\_list} activated. In this case, the model will start the initialisation phase, print the list of optimum decompositions ($N_{mpi}$, \np{jpni} and \np{jpnj}) in \texttt{ocean.output} and directly abort. The maximum value of $N_{mpi}$ tested in this list is given by $max(N_{MPI\_tasks}, jpni \times jpnj)$. For example, run the model on 40 nodes with ln\_list activated and $jpni = 10000$ and $jpnj = 1$, will print the list of optimum domains decomposition from 1 to about 10000.
+In order to specify $N_{mpi}$ properly (minimize $N_{useless}$), you must run the model once with \np{ln_list}{ln\_list} activated. In this case, the model will start the initialisation phase, print the list of optimum decompositions ($N_{mpi}$, \np{jpni} and \np{jpnj}) in \texttt{ocean.output} and directly abort. The maximum value of $N_{mpi}$ tested in this list is given by $max(N_{MPI\_tasks}, jpni \times jpnj)$. For example, run the model on 40 nodes with ln\_list activated and $jpni = 10000$ and $jpnj = 1$, will print the list of optimum domains decomposition from 1 to about 10000.
 Processors are numbered from 0 to $N_{mpi} - 1$. Subdomains containning some ocean points are numbered first from 0 to $jpni * jpnj - N_{land} -1$. The remaining $N_{useless}$ land subdomains are numbered next, which means that, for a given (\np{jpni}, \np{jpnj}), the numbers attributed to he ocean subdomains do not vary with $N_{useless}$.
 When land processors are eliminated, the value corresponding to these locations in the model output files is undefined. \np{ln\_mskland} must be activated in order avoid Not a Number values in output files. Note that it is better to not eliminate land processors when creating a meshmask file (\ie\ when setting a non-zero value to \np{nn\_msh}).
+When land processors are eliminated, the value corresponding to these locations in the model output files is undefined. \np{ln_mskland}{ln\_mskland} must be activated in order avoid Not a Number values in output files. Note that it is better to not eliminate land processors when creating a meshmask file (\ie\ when setting a non-zero value to \np{nn_msh}{nn\_msh}).
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 …
 %-----------------------------------------------------------------------------------------------
 Options are defined through the \nam{bdy} and \nam{bdy\_dta} namelist variables.
+Options are defined through the \nam{bdy} and \nam{bdy_dta}{bdy\_dta} namelist variables.
 The BDY module is the core implementation of open boundary conditions for regional configurations on
 ocean temperature, salinity, barotropic-baroclinic velocities, ice-snow concentration, thicknesses, temperatures, salinity and melt ponds concentration and thickness.
 …
 \label{subsec:LBC_bdy_namelist}
 The BDY module is activated by setting \np{ln\_bdy}\forcode{=.true.} .
+The BDY module is activated by setting \np{ln_bdy}{ln\_bdy}\forcode{=.true.} .
 It is possible to define more than one boundary ``set'' and apply different boundary conditions to each set.
 The number of boundary sets is defined by \np{nb\_bdy}.
+The number of boundary sets is defined by \np{nb_bdy}{nb\_bdy}.
 Each boundary set can be either defined as a series of straight line segments directly in the namelist
 (\np{ln\_coords\_file}\forcode{=.false.}, and a namelist block \nam{bdy\_index} must be included for each set) or read in from a file (\np{ln\_coords\_file}\forcode{=.true.}, and a ``\ifile{coordinates.bdy}'' file must be provided).
+(\np{ln_coords_file}{ln\_coords\_file}\forcode{=.false.}, and a namelist block \nam{bdy_index}{bdy\_index} must be included for each set) or read in from a file (\np{ln\_coords\_file}\forcode{=.true.}, and a ``\ifile{coordinates.bdy}'' file must be provided).
 The coordinates.bdy file is analagous to the usual \NEMO\ ``\ifile{coordinates}'' file.
 In the example above, there are two boundary sets, the first of which is defined via a file and
 …
 (``u2d'':sea-surface height and barotropic velocities), for the baroclinic velocities (``u3d''),
 for the active tracers \footnote{The BDY module does not deal with passive tracers at this version} (``tra''), and for sea-ice (``ice'').
 For each set of variables one has to choose an algorithm and the boundary data (set resp. by \np{cn\_tra} and \np{nn\_tra\_dta} for tracers).\\
+For each set of variables one has to choose an algorithm and the boundary data (set resp. by \np{cn_tra}{cn\_tra} and \np{nn_tra_dta}{nn\_tra\_dta} for tracers).\\
 The choice of algorithm is currently as follows:
 …
 The boundary data is either set to initial conditions
 (\np{nn\_tra\_dta}\forcode{=0}) or forced with external data from a file (\np{nn\_tra\_dta}\forcode{=1}).
+(\np{nn_tra_dta}{nn\_tra\_dta}\forcode{=0}) or forced with external data from a file (\np{nn\_tra\_dta}\forcode{=1}).
 In case the 3d velocity data contain the total velocity (ie, baroclinic and barotropic velocity),
 the bdy code can derived baroclinic and barotropic velocities by setting \np{ln\_full\_vel}\forcode{=.true.}
+the bdy code can derived baroclinic and barotropic velocities by setting \np{ln_full_vel}{ln\_full\_vel}\forcode{=.true.}
 For the barotropic solution there is also the option to use tidal harmonic forcing either by
 itself (\np{nn\_dyn2d\_dta}\forcode{=2}) or in addition to other external data (\np{nn\_dyn2d\_dta}\forcode{=3}).\\
 If not set to initial conditions, sea-ice salinity, temperatures and melt ponds data at the boundary can either be read in a file or defined as constant (by \np{rn\_ice\_sal}, \np{rn\_ice\_tem}, \np{rn\_ice\_apnd}, \np{rn\_ice\_hpnd}). Ice age is constant and defined by \np{rn\_ice\_age}.
 If external boundary data is required then the \nam{bdy\_dta} namelist must be defined.
 One \nam{bdy\_dta} namelist is required for each boundary set, adopting the same order of indexes in which the boundary sets are defined in nambdy.
 In the example given, two boundary sets have been defined. The first one is reading data file in the \nam{bdy\_dta} namelist shown above
+itself (\np{nn_dyn2d_dta}{nn\_dyn2d\_dta}\forcode{=2}) or in addition to other external data (\np{nn\_dyn2d\_dta}\forcode{=3}).\\
+If not set to initial conditions, sea-ice salinity, temperatures and melt ponds data at the boundary can either be read in a file or defined as constant (by \np{rn_ice_sal}{rn\_ice\_sal}, \np{rn_ice_tem}{rn\_ice\_tem}, \np{rn_ice_apnd}{rn\_ice\_apnd}, \np{rn_ice_hpnd}{rn\_ice\_hpnd}). Ice age is constant and defined by \np{rn_ice_age}{rn\_ice\_age}.
+If external boundary data is required then the \nam{bdy_dta}{bdy\_dta} namelist must be defined.
+One \nam{bdy_dta}{bdy\_dta} namelist is required for each boundary set, adopting the same order of indexes in which the boundary sets are defined in nambdy.
+In the example given, two boundary sets have been defined. The first one is reading data file in the \nam{bdy_dta}{bdy\_dta} namelist shown above
 and the second one is using data from intial condition (no namelist block needed).
 The boundary data is read in using the fldread module,
 so the \nam{bdy\_dta} namelist is in the format required for fldread.
+so the \nam{bdy_dta}{bdy\_dta} namelist is in the format required for fldread.
 For each required variable, the filename, the frequency of the files and
 the frequency of the data in the files are given.
 …
 There is currently an option to vertically interpolate the open boundary data onto the native grid at run-time.
 If \np{nn\_bdy\_jpk}$<-1$, it is assumed that the lateral boundary data are already on the native grid.
 However, if \np{nn\_bdy\_jpk} is set to the number of vertical levels present in the boundary data,
+If \np{nn_bdy_jpk}{nn\_bdy\_jpk}$<-1$, it is assumed that the lateral boundary data are already on the native grid.
+However, if \np{nn_bdy_jpk}{nn\_bdy\_jpk} is set to the number of vertical levels present in the boundary data,
 a bilinear interpolation onto the native grid will be triggered at runtime.
 For this to be successful the additional variables: $gdept$, $gdepu$, $gdepv$, $e3t$, $e3u$ and $e3v$, are required to be present in the lateral boundary files.
 …
   \alpha(d) = 1 - \tanh\left(\frac{d-1}{2}\right),       \quad d=1,N
 \]
 The width of the FRS zone is specified in the namelist as \np{nn\_rimwidth}.
+The width of the FRS zone is specified in the namelist as \np{nn_rimwidth}{nn\_rimwidth}.
 This is typically set to a value between 8 and 10.
 …
 \end{equation}
 Generally the relaxation time scale at inward propagation points (\np{rn\_time\_dmp}) is set much shorter than the time scale at outward propagation
 points (\np{rn\_time\_dmp\_out}) so that the solution is constrained more strongly by the external data at inward propagation points.
+Generally the relaxation time scale at inward propagation points (\np{rn_time_dmp}{rn\_time\_dmp}) is set much shorter than the time scale at outward propagation
+points (\np{rn_time_dmp_out}{rn\_time\_dmp\_out}) so that the solution is constrained more strongly by the external data at inward propagation points.
 See \autoref{subsec:LBC_bdy_relaxation} for detailed on the spatial shape of the scaling.\\
 The ``normal propagation of oblique radiation'' or NPO approximation (called \forcode{'orlanski_npo'}) involves assuming
 …
 \label{subsec:LBC_bdy_relaxation}
 In addition to a specific boundary condition specified as \np{cn\_tra} and \np{cn\_dyn3d}, relaxation on baroclinic velocities and tracers variables are available.
 It is control by the namelist parameter \np{ln\_tra\_dmp} and \np{ln\_dyn3d\_dmp} for each boundary set.
 The relaxation time scale value (\np{rn\_time\_dmp} and \np{rn\_time\_dmp\_out}, $\tau$) are defined at the boundaries itself.
 This time scale ($\alpha$) is weighted by the distance ($d$) from the boundary over \np{nn\_rimwidth} cells ($N$):
+In addition to a specific boundary condition specified as \np{cn_tra}{cn\_tra} and \np{cn_dyn3d}{cn\_dyn3d}, relaxation on baroclinic velocities and tracers variables are available.
+It is control by the namelist parameter \np{ln_tra_dmp}{ln\_tra\_dmp} and \np{ln_dyn3d_dmp}{ln\_dyn3d\_dmp} for each boundary set.
+The relaxation time scale value (\np{rn_time_dmp}{rn\_time\_dmp} and \np{rn_time_dmp_out}{rn\_time\_dmp\_out}, $\tau$) are defined at the boundaries itself.
+This time scale ($\alpha$) is weighted by the distance ($d$) from the boundary over \np{nn_rimwidth}{nn\_rimwidth} cells ($N$):
 \[
 …
 \jp{jpinft} give the start and end $i$ indices for each segment with similar for the other boundaries.
 These segments define a list of $T$ grid points along the outermost row of the boundary ($nbr\,=\, 1$).
 The code deduces the $U$ and $V$ points and also the points for $nbr\,>\, 1$ if \np{nn\_rimwidth}\forcode{>1}.
+The code deduces the $U$ and $V$ points and also the points for $nbr\,>\, 1$ if \np{nn_rimwidth}{nn\_rimwidth}\forcode{>1}.
 The boundary geometry may also be defined from a ``\ifile{coordinates.bdy}'' file.
 …
 For example, if an open boundary is defined along an isobath, say at the shelf break,
 then the areas of ocean outside of this boundary will need to be masked out.
 This can be done by reading a mask file defined as \np{cn\_mask\_file} in the nam\_bdy namelist.
+This can be done by reading a mask file defined as \np{cn_mask_file}{cn\_mask\_file} in the nam\_bdy namelist.
 Only one mask file is used even if multiple boundary sets are defined.
 …
 There is an option to force the total volume in the regional model to be constant.
 This is controlled  by the \np{ln\_vol} parameter in the namelist.
 A value of \np{ln\_vol}\forcode{=.false.} indicates that this option is not used.
 Two options to control the volume are available (\np{nn\_volctl}).
 If \np{nn\_volctl}\forcode{=0} then a correction is applied to the normal barotropic velocities around the boundary at
+This is controlled  by the \np{ln_vol}{ln\_vol} parameter in the namelist.
+A value of \np{ln_vol}{ln\_vol}\forcode{=.false.} indicates that this option is not used.
+Two options to control the volume are available (\np{nn_volctl}{nn\_volctl}).
+If \np{nn_volctl}{nn\_volctl}\forcode{=0} then a correction is applied to the normal barotropic velocities around the boundary at
 each timestep to ensure that the integrated volume flow through the boundary is zero.
 If \np{nn\_volctl}\forcode{=1} then the calculation of the volume change on
+If \np{nn_volctl}{nn\_volctl}\forcode{=1} then the calculation of the volume change on
 the timestep includes the change due to the freshwater flux across the surface and
 the correction velocity corrects for this as well.
 …
 Tidal forcing at open boundaries requires the activation of surface
 tides (i.e., in \nam{\_tide}, \np{ln\_tide} needs to be set to
+tides (i.e., in \nam{_tide}{\_tide}, \np{ln_tide}{ln\_tide} needs to be set to
 \forcode{.true.} and the required constituents need to be activated by
 including their names in the \np{clname} array; see
 …
 the complex harmonic amplitudes of elevation (SSH) and barotropic
 velocity (u,v) at open boundaries are defined through the
 \nam{bdy\_tide} namelist parameters.\\
+\nam{bdy_tide}{bdy\_tide} namelist parameters.\\
 The tidal harmonic data at open boundaries can be specified in two
 different ways, either on a two-dimensional grid covering the entire
 model domain or along open boundary segments; these two variants can
 be selected by setting \np{ln\_bdytide\_2ddta } to \forcode{.true.} or
+be selected by setting \np{ln_bdytide_2ddta }{ln\_bdytide\_2ddta } to \forcode{.true.} or
 \forcode{.false.}, respectively. In either case, the real and
 imaginary parts of SSH and the two barotropic velocity components for
 …
 \textit{v1} and \textit{v2} (real and imaginary part of v) are
 expected to be available from file \np{filtide} with suffix
 \ifile{tcname\_grid\_V}. If \np{ln\_bdytide\_conj} is set to
+\ifile{tcname\_grid\_V}. If \np{ln_bdytide_conj}{ln\_bdytide\_conj} is set to
 \forcode{.true.}, the data is expected to be in complex conjugate
 form.

NEMO/trunk/doc/latex/NEMO/subfiles/chap_LDF.tex

-                      r11567
+                      r11577
 (3) the space and time variations of the eddy coefficients.
 These three aspects of the lateral diffusion are set through namelist parameters
 (see the \nam{tra\_ldf} and \nam{dyn\_ldf} below).
+(see the \nam{tra_ldf}{tra\_ldf} and \nam{dyn_ldf}{dyn\_ldf} below).
 Note that this chapter describes the standard implementation of iso-neutral tracer mixing.
 Griffies's implementation, which is used if \np{ln\_traldf\_triad}\forcode{=.true.},
+Griffies's implementation, which is used if \np{ln_traldf_triad}{ln\_traldf\_triad}\forcode{=.true.},
 is described in \autoref{apdx:TRIADS}
 …
 We remind here the different lateral mixing operators that can be used. Further details can be found in \autoref{subsec:TRA_ldf_op} and  \autoref{sec:DYN_ldf}.
 \subsection[No lateral mixing (\forcode{ln_traldf_OFF} \& \forcode{ln_dynldf_OFF})]{No lateral mixing (\protect\np{ln\_traldf\_OFF} \& \protect\np{ln\_dynldf\_OFF})}
 It is possible to run without explicit lateral diffusion on tracers (\protect\np{ln\_traldf\_OFF}\forcode{=.true.}) and/or
 momentum (\protect\np{ln\_dynldf\_OFF}\forcode{=.true.}). The latter option is even recommended if using the
 UBS advection scheme on momentum (\np{ln\_dynadv\_ubs}\forcode{=.true.},
+\subsection[No lateral mixing (\forcode{ln_traldf_OFF} \& \forcode{ln_dynldf_OFF})]{No lateral mixing (\protect\np{ln_traldf_OFF}{ln\_traldf\_OFF} \& \protect\np{ln_dynldf_OFF}{ln\_dynldf\_OFF})}
+It is possible to run without explicit lateral diffusion on tracers (\protect\np{ln_traldf_OFF}{ln\_traldf\_OFF}\forcode{=.true.}) and/or
+momentum (\protect\np{ln_dynldf_OFF}{ln\_dynldf\_OFF}\forcode{=.true.}). The latter option is even recommended if using the
+UBS advection scheme on momentum (\np{ln_dynadv_ubs}{ln\_dynadv\_ubs}\forcode{=.true.},
 see \autoref{subsec:DYN_adv_ubs}) and can be useful for testing purposes.
 \subsection[Laplacian mixing (\forcode{ln_traldf_lap} \& \forcode{ln_dynldf_lap})]{Laplacian mixing (\protect\np{ln\_traldf\_lap} \& \protect\np{ln\_dynldf\_lap})}
 Setting \protect\np{ln\_traldf\_lap}\forcode{=.true.} and/or \protect\np{ln\_dynldf\_lap}\forcode{=.true.} enables
+\subsection[Laplacian mixing (\forcode{ln_traldf_lap} \& \forcode{ln_dynldf_lap})]{Laplacian mixing (\protect\np{ln_traldf_lap}{ln\_traldf\_lap} \& \protect\np{ln_dynldf_lap}{ln\_dynldf\_lap})}
+Setting \protect\np{ln_traldf_lap}{ln\_traldf\_lap}\forcode{=.true.} and/or \protect\np{ln_dynldf_lap}{ln\_dynldf\_lap}\forcode{=.true.} enables
 a second order diffusion on tracers and momentum respectively. Note that in \NEMO\ 4, one can not combine
 Laplacian and Bilaplacian operators for the same variable.
 \subsection[Bilaplacian mixing (\forcode{ln_traldf_blp} \& \forcode{ln_dynldf_blp})]{Bilaplacian mixing (\protect\np{ln\_traldf\_blp} \& \protect\np{ln\_dynldf\_blp})}
 Setting \protect\np{ln\_traldf\_blp}\forcode{=.true.} and/or \protect\np{ln\_dynldf\_blp}\forcode{=.true.} enables
+\subsection[Bilaplacian mixing (\forcode{ln_traldf_blp} \& \forcode{ln_dynldf_blp})]{Bilaplacian mixing (\protect\np{ln_traldf_blp}{ln\_traldf\_blp} \& \protect\np{ln_dynldf_blp}{ln\_dynldf\_blp})}
+Setting \protect\np{ln_traldf_blp}{ln\_traldf\_blp}\forcode{=.true.} and/or \protect\np{ln_dynldf_blp}{ln\_dynldf\_blp}\forcode{=.true.} enables
 a fourth order diffusion on tracers and momentum respectively. It is implemented by calling the above Laplacian operator twice.
 We stress again that from \NEMO\ 4, the simultaneous use Laplacian and Bilaplacian operators is not allowed.
 …
 A direction for lateral mixing has to be defined when the desired operator does not act along the model levels.
 This occurs when $(a)$ horizontal mixing is required on tracer or momentum
 (\np{ln\_traldf\_hor} or \np{ln\_dynldf\_hor}) in $s$- or mixed $s$-$z$- coordinates,
+(\np{ln_traldf_hor}{ln\_traldf\_hor} or \np{ln_dynldf_hor}{ln\_dynldf\_hor}) in $s$- or mixed $s$-$z$- coordinates,
 and $(b)$ isoneutral mixing is required whatever the vertical coordinate is.
 This direction of mixing is defined by its slopes in the \textbf{i}- and \textbf{j}-directions at the face of
 …
 %gm%  caution I'm not sure the simplification was a good idea!
 These slopes are computed once in \rou{ldf\_slp\_init} when \np{ln\_sco}\forcode{=.true.},
 and either \np{ln\_traldf\_hor}\forcode{=.true.} or \np{ln\_dynldf\_hor}\forcode{=.true.}.
+These slopes are computed once in \rou{ldf\_slp\_init} when \np{ln_sco}{ln\_sco}\forcode{=.true.},
+and either \np{ln_traldf_hor}{ln\_traldf\_hor}\forcode{=.true.} or \np{ln_dynldf_hor}{ln\_dynldf\_hor}\forcode{=.true.}.
 \subsection{Slopes for tracer iso-neutral mixing}
 …
 \item[$s$- or hybrid $s$-$z$- coordinate: ]
   in the current release of \NEMO, iso-neutral mixing is only employed for $s$-coordinates if
   the Griffies scheme is used (\np{ln\_traldf\_triad}\forcode{=.true.};
+  the Griffies scheme is used (\np{ln_traldf_triad}{ln\_traldf\_triad}\forcode{=.true.};
   see \autoref{apdx:TRIADS}).
   In other words, iso-neutral mixing will only be accurately represented with a linear equation of state
   (\np{ln\_seos}\forcode{=.true.}).
+  (\np{ln_seos}{ln\_seos}\forcode{=.true.}).
   In the case of a "true" equation of state, the evaluation of $i$ and $j$ derivatives in \autoref{eq:LDF_slp_iso}
   will include a pressure dependent part, leading to the wrong evaluation of the neutral slopes.
 …
 To overcome this problem, several techniques have been proposed in which the numerical schemes of
 the ocean model are modified \citep{weaver.eby_JPO97, griffies.gnanadesikan.ea_JPO98}.
 Griffies's scheme is now available in \NEMO\ if \np{ln\_traldf\_triad}\forcode{ = .true.}; see \autoref{apdx:TRIADS}.
+Griffies's scheme is now available in \NEMO\ if \np{ln_traldf_triad}{ln\_traldf\_triad}\forcode{ = .true.}; see \autoref{apdx:TRIADS}.
 Here, another strategy is presented \citep{lazar_phd97}:
 a local filtering of the iso-neutral slopes (made on 9 grid-points) prevents the development of
 …
 For numerical stability reasons \citep{cox_OM87, griffies_bk04}, the slopes must also be bounded by
 the namelist scalar \np{rn\_slpmax} (usually $1/100$) everywhere.
+the namelist scalar \np{rn_slpmax}{rn\_slpmax} (usually $1/100$) everywhere.
 This constraint is applied in a piecewise linear fashion, increasing from zero at the surface to
 $1/100$ at $70$ metres and thereafter decreasing to zero at the bottom of the ocean
 …
 % Lateral Mixing Coefficients
 % ================================================================
 \section[Lateral mixing coefficient (\forcode{nn_aht_ijk_t} \& \forcode{nn_ahm_ijk_t})]{Lateral mixing coefficient (\protect\np{nn\_aht\_ijk\_t} \& \protect\np{nn\_ahm\_ijk\_t})}
+\section[Lateral mixing coefficient (\forcode{nn_aht_ijk_t} \& \forcode{nn_ahm_ijk_t})]{Lateral mixing coefficient (\protect\np{nn_aht_ijk_t}{nn\_aht\_ijk\_t} \& \protect\np{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t})}
 \label{sec:LDF_coef}
 …
 The way the mixing coefficients are set in the reference version can be described as follows:
 \subsection[Mixing coefficients read from file (\forcode{=-20, -30})]{ Mixing coefficients read from file (\protect\np{nn\_aht\_ijk\_t}\forcode{=-20, -30} \& \protect\np{nn\_ahm\_ijk\_t}\forcode{=-20, -30})}
+\subsection[Mixing coefficients read from file (\forcode{=-20, -30})]{ Mixing coefficients read from file (\protect\np{nn_aht_ijk_t}{nn\_aht\_ijk\_t}\forcode{=-20, -30} \& \protect\np{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}\forcode{=-20, -30})}
 Mixing coefficients can be read from file if a particular geographical variation is needed. For example, in the ORCA2 global ocean model,
 …
 decreases linearly to $A^l$~= 2.10$^3$ m$^2$/s at the equator \citep{madec.delecluse.ea_JPO96, delecluse.madec_icol99}.
 Similar modified horizontal variations can be found with the Antarctic or Arctic sub-domain options of ORCA2 and ORCA05.
 The provided fields can either be 2d (\np{nn\_aht\_ijk\_t}\forcode{=-20}, \np{nn\_ahm\_ijk\_t}\forcode{=-20}) or 3d (\np{nn\_aht\_ijk\_t}\forcode{=-30},  \np{nn\_ahm\_ijk\_t}\forcode{=-30}). They must be given at U, V points for tracers and T, F points for momentum (see \autoref{tab:LDF_files}).
+The provided fields can either be 2d (\np{nn_aht_ijk_t}{nn\_aht\_ijk\_t}\forcode{=-20}, \np{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}\forcode{=-20}) or 3d (\np{nn\_aht\_ijk\_t}\forcode{=-30},  \np{nn\_ahm\_ijk\_t}\forcode{=-30}). They must be given at U, V points for tracers and T, F points for momentum (see \autoref{tab:LDF_files}).
 %-------------------------------------------------TABLE---------------------------------------------------
 …
     \hline
     Namelist parameter                       & Input filename                               & dimensions & variable names                      \\  \hline
     \np{nn\_ahm\_ijk\_t}\forcode{=-20}     & \forcode{eddy_viscosity_2D.nc }            &     $(i,j)$         & \forcode{ahmt_2d, ahmf_2d}  \\  \hline
     \np{nn\_aht\_ijk\_t}\forcode{=-20}           & \forcode{eddy_diffusivity_2D.nc }           &     $(i,j)$           & \forcode{ahtu_2d, ahtv_2d}    \\   \hline
     \np{nn\_ahm\_ijk\_t}\forcode{=-30}        & \forcode{eddy_viscosity_3D.nc }            &     $(i,j,k)$          & \forcode{ahmt_3d, ahmf_3d}  \\  \hline
     \np{nn\_aht\_ijk\_t}\forcode{=-30}     & \forcode{eddy_diffusivity_3D.nc }           &     $(i,j,k)$         & \forcode{ahtu_3d, ahtv_3d}    \\   \hline
+    \np{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}\forcode{=-20}      & \forcode{eddy_viscosity_2D.nc }            &     $(i,j)$         & \forcode{ahmt_2d, ahmf_2d}  \\  \hline
+    \np{nn_aht_ijk_t}{nn\_aht\_ijk\_t}\forcode{=-20}           & \forcode{eddy_diffusivity_2D.nc }           &     $(i,j)$         & \forcode{ahtu_2d, ahtv_2d}    \\   \hline
+    \np{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}\forcode{=-30}      & \forcode{eddy_viscosity_3D.nc }            &     $(i,j,k)$          & \forcode{ahmt_3d, ahmf_3d}  \\  \hline
+    \np{nn_aht_ijk_t}{nn\_aht\_ijk\_t}\forcode{=-30}      & \forcode{eddy_diffusivity_3D.nc }           &     $(i,j,k)$         & \forcode{ahtu_3d, ahtv_3d}    \\   \hline
   \end{tabular}
   \caption{Description of expected input files if mixing coefficients are read from NetCDF files}
 …
 %--------------------------------------------------------------------------------------------------------------
 \subsection[Constant mixing coefficients (\forcode{=0})]{ Constant mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{=0} \& \protect\np{nn\_ahm\_ijk\_t}\forcode{=0})}
+\subsection[Constant mixing coefficients (\forcode{=0})]{ Constant mixing coefficients (\protect\np{nn_aht_ijk_t}{nn\_aht\_ijk\_t}\forcode{=0} \& \protect\np{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}\forcode{=0})}
 If constant, mixing coefficients are set thanks to a velocity and a length scales ($U_{scl}$, $L_{scl}$) such that:
 …
 \end{equation}
  $U_{scl}$ and $L_{scl}$ are given by the namelist parameters \np{rn\_Ud}, \np{rn\_Uv}, \np{rn\_Ld} and \np{rn\_Lv}.
 \subsection[Vertically varying mixing coefficients (\forcode{=10})]{Vertically varying mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{=10} \& \protect\np{nn\_ahm\_ijk\_t}\forcode{=10})}
+ $U_{scl}$ and $L_{scl}$ are given by the namelist parameters \np{rn_Ud}{rn\_Ud}, \np{rn_Uv}{rn\_Uv}, \np{rn_Ld}{rn\_Ld} and \np{rn_Lv}{rn\_Lv}.
+\subsection[Vertically varying mixing coefficients (\forcode{=10})]{Vertically varying mixing coefficients (\protect\np{nn_aht_ijk_t}{nn\_aht\_ijk\_t}\forcode{=10} \& \protect\np{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}\forcode{=10})}
 In the vertically varying case, a hyperbolic variation of the lateral mixing coefficient is introduced in which
 …
 This profile is hard coded in module \mdl{ldfc1d\_c2d}, but can be easily modified by users.
 \subsection[Mesh size dependent mixing coefficients (\forcode{=20})]{Mesh size dependent mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{=20} \& \protect\np{nn\_ahm\_ijk\_t}\forcode{=20})}
+\subsection[Mesh size dependent mixing coefficients (\forcode{=20})]{Mesh size dependent mixing coefficients (\protect\np{nn_aht_ijk_t}{nn\_aht\_ijk\_t}\forcode{=20} \& \protect\np{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}\forcode{=20})}
 In that case, the horizontal variation of the eddy coefficient depends on the local mesh size and
 …
   \right.
 \end{equation}
 where $U_{scl}$ is a user defined velocity scale (\np{rn\_Ud}, \np{rn\_Uv}).
+where $U_{scl}$ is a user defined velocity scale (\np{rn_Ud}{rn\_Ud}, \np{rn_Uv}{rn\_Uv}).
 This variation is intended to reflect the lesser need for subgrid scale eddy mixing where
 the grid size is smaller in the domain.
 …
 especially when using a bilaplacian operator.
 \colorbox{yellow}{CASE \np{nn\_aht\_ijk\_t} = 21 to be added}
 \subsection[Mesh size and depth dependent mixing coefficients (\forcode{=30})]{Mesh size and depth dependent mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{=30} \& \protect\np{nn\_ahm\_ijk\_t}\forcode{=30})}
+\colorbox{yellow}{CASE \np{nn_aht_ijk_t}{nn\_aht\_ijk\_t} = 21 to be added}
+\subsection[Mesh size and depth dependent mixing coefficients (\forcode{=30})]{Mesh size and depth dependent mixing coefficients (\protect\np{nn_aht_ijk_t}{nn\_aht\_ijk\_t}\forcode{=30} \& \protect\np{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}\forcode{=30})}
 The 3D space variation of the mixing coefficient is simply the combination of the 1D and 2D cases above,
 …
 the magnitude of the coefficient.
 \subsection[Velocity dependent mixing coefficients (\forcode{=31})]{Flow dependent mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{=31} \& \protect\np{nn\_ahm\_ijk\_t}\forcode{=31})}
+\subsection[Velocity dependent mixing coefficients (\forcode{=31})]{Flow dependent mixing coefficients (\protect\np{nn_aht_ijk_t}{nn\_aht\_ijk\_t}\forcode{=31} \& \protect\np{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}\forcode{=31})}
 In that case, the eddy coefficient is proportional to the local velocity magnitude so that the Reynolds number $Re =  \lvert U \rvert  e / A_l$ is constant (and here hardcoded to $12$):
 \colorbox{yellow}{JC comment: The Reynolds is effectively set to 12 in the code for both operators but shouldn't it be 2 for Laplacian ?}
 …
 \end{equation}
 \subsection[Deformation rate dependent viscosities (\forcode{nn_ahm_ijk_t=32})]{Deformation rate dependent viscosities (\protect\np{nn\_ahm\_ijk\_t}\forcode{=32})}
+\subsection[Deformation rate dependent viscosities (\forcode{nn_ahm_ijk_t=32})]{Deformation rate dependent viscosities (\protect\np{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t}\forcode{=32})}
 This option refers to the \citep{smagorinsky_MW63} scheme which is here implemented for momentum only. Smagorinsky chose as a
 …
 \end{equation}
 Introducing a user defined constant $C$ (given in the namelist as \np{rn\_csmc}), one can deduce the mixing coefficients as follows:
+Introducing a user defined constant $C$ (given in the namelist as \np{rn_csmc}{rn\_csmc}), one can deduce the mixing coefficients as follows:
 \begin{equation}
 …
 \end{equation}
 where $C_{min}$ and $C_{max}$ are adimensional namelist parameters given by \np{rn\_minfac} and \np{rn\_maxfac} respectively.
+where $C_{min}$ and $C_{max}$ are adimensional namelist parameters given by \np{rn_minfac}{rn\_minfac} and \np{rn_maxfac}{rn\_maxfac} respectively.
 \subsection{About space and time varying mixing coefficients}
 …
 % Eddy Induced Mixing
 % ================================================================
 \section[Eddy induced velocity (\forcode{ln_ldfeiv})]{Eddy induced velocity (\protect\np{ln\_ldfeiv})}
+\section[Eddy induced velocity (\forcode{ln_ldfeiv})]{Eddy induced velocity (\protect\np{ln_ldfeiv}{ln\_ldfeiv})}
 \label{sec:LDF_eiv}
 …
   Values of iso-neutral diffusivity and GM coefficient are set as described in \autoref{sec:LDF_coef}.
   If none of the keys \key{traldf\_cNd}, N=1,2,3 is set (the default), spatially constant iso-neutral $A_l$ and
   GM diffusivity $A_e$ are directly set by \np{rn\_aeih\_0} and \np{rn\_aeiv\_0}.
+  GM diffusivity $A_e$ are directly set by \np{rn_aeih_0}{rn\_aeih\_0} and \np{rn_aeiv_0}{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 \autoref{eq:title}
 …
     In this case, $A_e$ at low latitudes $|\theta|<20^{\circ}$ is further reduced by a factor $|f/f_{20}|$,
     where $f_{20}$ is the value of $f$ at $20^{\circ}$~N
   } (\mdl{ldfeiv}) and \np{rn\_aeiv\_0} is ignored unless it is zero.
+  } (\mdl{ldfeiv}) and \np{rn_aeiv_0}{rn\_aeiv\_0} is ignored unless it is zero.
+}
 When  \citet{gent.mcwilliams_JPO90} diffusion is used (\np{ln\_ldfeiv}\forcode{=.true.}),
+When  \citet{gent.mcwilliams_JPO90} diffusion is used (\np{ln_ldfeiv}{ln\_ldfeiv}\forcode{=.true.}),
 an eddy induced tracer advection term is added,
 the formulation of which depends on the slopes of iso-neutral surfaces.
 …
 and the sum \autoref{eq:LDF_slp_geo} + \autoref{eq:LDF_slp_iso} in $s$-coordinates.
 If isopycnal mixing is used in the standard way, \ie\ \np{ln\_traldf\_triad}\forcode{=.false.}, the eddy induced velocity is given by:
+If isopycnal mixing is used in the standard way, \ie\ \np{ln_traldf_triad}{ln\_traldf\_triad}\forcode{=.false.}, the eddy induced velocity is given by:
 \begin{equation}
   \label{eq:LDF_eiv}
 …
   \end{split}
 \end{equation}
 where $A^{eiv}$ is the eddy induced velocity coefficient whose value is set through \np{nn\_aei\_ijk\_t} \nam{tra\_eiv} namelist parameter.
+where $A^{eiv}$ is the eddy induced velocity coefficient whose value is set through \np{nn_aei_ijk_t}{nn\_aei\_ijk\_t} \nam{tra_eiv}{tra\_eiv} namelist parameter.
 The three components of the eddy induced velocity are computed in \rou{ldf\_eiv\_trp} and
 added to the eulerian velocity in \rou{tra\_adv} where tracer advection is performed.
 …
 At the surface, lateral and bottom boundaries, the eddy induced velocity,
 and thus the advective eddy fluxes of heat and salt, are set to zero.
 The value of the eddy induced mixing coefficient and its space variation is controlled in a similar way as for lateral mixing coefficient described in the preceding subsection (\np{nn\_aei\_ijk\_t}, \np{rn\_Ue}, \np{rn\_Le} namelist parameters).
 \colorbox{yellow}{CASE \np{nn\_aei\_ijk\_t} = 21 to be added}
 In case of setting \np{ln\_traldf\_triad}\forcode{ = .true.}, a skew form of the eddy induced advective fluxes is used, which is described in \autoref{apdx:TRIADS}.
+The value of the eddy induced mixing coefficient and its space variation is controlled in a similar way as for lateral mixing coefficient described in the preceding subsection (\np{nn_aei_ijk_t}{nn\_aei\_ijk\_t}, \np{rn_Ue}{rn\_Ue}, \np{rn_Le}{rn\_Le} namelist parameters).
+\colorbox{yellow}{CASE \np{nn_aei_ijk_t}{nn\_aei\_ijk\_t} = 21 to be added}
+In case of setting \np{ln_traldf_triad}{ln\_traldf\_triad}\forcode{ = .true.}, a skew form of the eddy induced advective fluxes is used, which is described in \autoref{apdx:TRIADS}.
 % ================================================================
 % Mixed layer eddies
 % ================================================================
 \section[Mixed layer eddies (\forcode{ln_mle})]{Mixed layer eddies (\protect\np{ln\_mle})}
+\section[Mixed layer eddies (\forcode{ln_mle})]{Mixed layer eddies (\protect\np{ln_mle}{ln\_mle})}
 \label{sec:LDF_mle}
 …
 %--------------------------------------------------------------------------------------------------------------
 If  \np{ln\_mle}\forcode{=.true.} in \nam{tra\_mle} namelist, a parameterization of the mixing due to unresolved mixed layer instabilities is activated (\citet{foxkemper.ferrari_JPO08}). Additional transport is computed in \rou{ldf\_mle\_trp} and added to the eulerian transport in \rou{tra\_adv} as done for eddy induced advection.
+If  \np{ln_mle}{ln\_mle}\forcode{=.true.} in \nam{tra_mle}{tra\_mle} namelist, a parameterization of the mixing due to unresolved mixed layer instabilities is activated (\citet{foxkemper.ferrari_JPO08}). Additional transport is computed in \rou{ldf\_mle\_trp} and added to the eulerian transport in \rou{tra\_adv} as done for eddy induced advection.
 \colorbox{yellow}{TBC}

NEMO/trunk/doc/latex/NEMO/subfiles/chap_OBS.tex

-                      r11567
+                      r11577
 The OBS code is called from \mdl{nemogcm} for model initialisation and to calculate the model equivalent values for observations on the 0th time step.
 The code is then called again after each time step from \mdl{step}.
 The code is only activated if the \nam{obs} namelist logical \np{ln\_diaobs} is set to true.
+The code is only activated if the \nam{obs} namelist logical \np{ln_diaobs}{ln\_diaobs} is set to true.
 For all data types a 2D horizontal interpolator or averager is needed to
 …
 Some profile observation types (\eg\ tropical moored buoys) are made available as daily averaged quantities.
 The observation operator code can be set-up to calculate the equivalent daily average model temperature fields using
 the \np{nn\_profdavtypes} namelist array.
+the \np{nn_profdavtypes}{nn\_profdavtypes} namelist array.
 Some SST observations are equivalent to a night-time average value and
 the observation operator code can calculate equivalent night-time average model SST fields by
 setting the namelist value \np{ln\_sstnight} to true.
+setting the namelist value \np{ln_sstnight}{ln\_sstnight} to true.
 Otherwise (by default) the model value from the nearest time step to the observation time is used.
 …
 Options are defined through the \nam{obs} namelist variables.
 The options \np{ln\_t3d} and \np{ln\_s3d} switch on the temperature and salinity profile observation operator code.
 The filename or array of filenames are specified using the \np{cn\_profbfiles} variable.
+The options \np{ln_t3d}{ln\_t3d} and \np{ln_s3d}{ln\_s3d} switch on the temperature and salinity profile observation operator code.
+The filename or array of filenames are specified using the \np{cn_profbfiles}{cn\_profbfiles} variable.
 The model grid points for a particular observation latitude and longitude are found using
 the grid searching part of the code.
 This can be expensive, particularly for large numbers of observations,
 setting \np{ln\_grid\_search\_lookup} allows the use of a lookup table which
 is saved into an \np{cn\_gridsearch} file (or files).
+setting \np{ln_grid_search_lookup}{ln\_grid\_search\_lookup} allows the use of a lookup table which
+is saved into an \np{cn_gridsearch}{cn\_gridsearch} file (or files).
 This will need to be generated the first time if it does not exist in the run directory.
 However, once produced it will significantly speed up future grid searches.
 Setting \np{ln\_grid\_global} means that the code distributes the observations evenly between processors.
+Setting \np{ln_grid_global}{ln\_grid\_global} means that the code distributes the observations evenly between processors.
 Alternatively each processor will work with observations located within the model subdomain
 (see \autoref{subsec:OBS_parallel}).
 …
 (for surface observation types only).
 The main namelist option associated with the interpolation/averaging is \np{nn\_2dint}.
+The main namelist option associated with the interpolation/averaging is \np{nn_2dint}{nn\_2dint}.
 This default option can be set to values from 0 to 6.
 Values between 0 to 4 are associated with interpolation while values 5 or 6 are associated with averaging.
 \begin{itemize}
 \item \np{nn\_2dint}\forcode{ = 0}: Distance-weighted interpolation
 \item \np{nn\_2dint}\forcode{ = 1}: Distance-weighted interpolation (small angle)
 \item \np{nn\_2dint}\forcode{ = 2}: Bilinear interpolation (geographical grid)
 \item \np{nn\_2dint}\forcode{ = 3}: Bilinear remapping interpolation (general grid)
 \item \np{nn\_2dint}\forcode{ = 4}: Polynomial interpolation
 \item \np{nn\_2dint}\forcode{ = 5}: Radial footprint averaging with diameter specified in the namelist as
+\item \np{nn_2dint}{nn\_2dint}\forcode{ = 0}: Distance-weighted interpolation
+\item \np{nn_2dint}{nn\_2dint}\forcode{ = 1}: Distance-weighted interpolation (small angle)
+\item \np{nn_2dint}{nn\_2dint}\forcode{ = 2}: Bilinear interpolation (geographical grid)
+\item \np{nn_2dint}{nn\_2dint}\forcode{ = 3}: Bilinear remapping interpolation (general grid)
+\item \np{nn_2dint}{nn\_2dint}\forcode{ = 4}: Polynomial interpolation
+\item \np{nn_2dint}{nn\_2dint}\forcode{ = 5}: Radial footprint averaging with diameter specified in the namelist as
   \texttt{rn\_[var]\_avglamscl} in degrees or metres (set using \texttt{ln\_[var]\_fp\_indegs})
 \item \np{nn\_2dint}\forcode{ = 6}: Rectangular footprint averaging with E/W and N/S size specified in
+\item \np{nn_2dint}{nn\_2dint}\forcode{ = 6}: Rectangular footprint averaging with E/W and N/S size specified in
   the namelist as \texttt{rn\_[var]\_avglamscl} and \texttt{rn\_[var]\_avgphiscl} in degrees or metres
   (set using \texttt{ln\_[var]\_fp\_indegs})
 …
 Replace \texttt{[var]} in the last two options with the observation type (sla, sst, sss or sic) for
 which the averaging is to be performed (see namelist example above).
 The \np{nn\_2dint} default option can be overridden for surface observation types using
+The \np{nn_2dint}{nn\_2dint} default option can be overridden for surface observation types using
 namelist values \texttt{nn\_2dint\_[var]} where \texttt{[var]} is the observation type.

NEMO/trunk/doc/latex/NEMO/subfiles/chap_SBC.tex

-                      r11571
+                      r11577
 \begin{itemize}
 \item
   a bulk formulation (\np{ln\_blk}\forcode{=.true.} with four possible bulk algorithms),
 \item
   a flux formulation (\np{ln\_flx}\forcode{=.true.}),
+  a bulk formulation (\np{ln_blk}{ln\_blk}\forcode{=.true.} with four possible bulk algorithms),
+\item
+  a flux formulation (\np{ln_flx}{ln\_flx}\forcode{=.true.}),
 \item
   a coupled or mixed forced/coupled formulation (exchanges with a atmospheric model via the OASIS coupler),
 (\np{ln\_cpl} or \np{ln\_mixcpl}\forcode{=.true.}),
 \item
   a user defined formulation (\np{ln\_usr}\forcode{=.true.}).
+(\np{ln_cpl}{ln\_cpl} or \np{ln_mixcpl}{ln\_mixcpl}\forcode{=.true.}),
+\item
+  a user defined formulation (\np{ln_usr}{ln\_usr}\forcode{=.true.}).
 \end{itemize}
 The frequency at which the forcing fields have to be updated is given by the \np{nn\_fsbc} namelist parameter.
+The frequency at which the forcing fields have to be updated is given by the \np{nn_fsbc}{nn\_fsbc} namelist parameter.
 When the fields are supplied from data files (bulk, flux and mixed formulations),
 …
   the local grid directions in the model,
 \item
   the use of a land/sea mask for input fields (\np{nn\_lsm}\forcode{=.true.}),
 \item
   the addition of a surface restoring term to observed SST and/or SSS (\np{ln\_ssr}\forcode{=.true.}),
+  the use of a land/sea mask for input fields (\np{nn_lsm}{nn\_lsm}\forcode{=.true.}),
+\item
+  the addition of a surface restoring term to observed SST and/or SSS (\np{ln_ssr}{ln\_ssr}\forcode{=.true.}),
 \item
   the modification of fluxes below ice-covered areas (using climatological ice-cover or a sea-ice model)
   (\np{nn\_ice}\forcode{=0..3}),
 \item
   the addition of river runoffs as surface freshwater fluxes or lateral inflow (\np{ln\_rnf}\forcode{=.true.}),
+  (\np{nn_ice}{nn\_ice}\forcode{=0..3}),
+\item
+  the addition of river runoffs as surface freshwater fluxes or lateral inflow (\np{ln_rnf}{ln\_rnf}\forcode{=.true.}),
 \item
   the addition of ice-shelf melting as lateral inflow (parameterisation) or
   as fluxes applied at the land-ice ocean interface (\np{ln\_isf}\forcode{=.true.}),
+  as fluxes applied at the land-ice ocean interface (\np{ln_isf}{ln\_isf}\forcode{=.true.}),
 \item
   the addition of a freshwater flux adjustment in order to avoid a mean sea-level drift
   (\np{nn\_fwb}\forcode{=0..2}),
+  (\np{nn_fwb}{nn\_fwb}\forcode{=0..2}),
 \item
   the transformation of the solar radiation (if provided as daily mean) into an analytical diurnal cycle
   (\np{ln\_dm2dc}\forcode{=.true.}),
 \item
   the activation of wave effects from an external wave model  (\np{ln\_wave}\forcode{=.true.}),
 \item
   a neutral drag coefficient is read from an external wave model (\np{ln\_cdgw}\forcode{=.true.}),
 \item
   the Stokes drift from an external wave model is accounted for (\np{ln\_sdw}\forcode{=.true.}),
 \item
   the choice of the Stokes drift profile parameterization (\np{nn\_sdrift}\forcode{=0..2}),
 \item
   the surface stress given to the ocean is modified by surface waves (\np{ln\_tauwoc}\forcode{=.true.}),
 \item
   the surface stress given to the ocean is read from an external wave model (\np{ln\_tauw}\forcode{=.true.}),
 \item
   the Stokes-Coriolis term is included (\np{ln\_stcor}\forcode{=.true.}),
 \item
   the light penetration in the ocean (\np{ln\_traqsr}\forcode{=.true.} with namelist \nam{tra\_qsr}),
 \item
   the atmospheric surface pressure gradient effect on ocean and ice dynamics (\np{ln\_apr\_dyn}\forcode{=.true.} with namelist \nam{sbc\_apr}),
 \item
   the effect of sea-ice pressure on the ocean (\np{ln\_ice\_embd}\forcode{=.true.}).
+  (\np{ln_dm2dc}{ln\_dm2dc}\forcode{=.true.}),
+\item
+  the activation of wave effects from an external wave model  (\np{ln_wave}{ln\_wave}\forcode{=.true.}),
+\item
+  a neutral drag coefficient is read from an external wave model (\np{ln_cdgw}{ln\_cdgw}\forcode{=.true.}),
+\item
+  the Stokes drift from an external wave model is accounted for (\np{ln_sdw}{ln\_sdw}\forcode{=.true.}),
+\item
+  the choice of the Stokes drift profile parameterization (\np{nn_sdrift}{nn\_sdrift}\forcode{=0..2}),
+\item
+  the surface stress given to the ocean is modified by surface waves (\np{ln_tauwoc}{ln\_tauwoc}\forcode{=.true.}),
+\item
+  the surface stress given to the ocean is read from an external wave model (\np{ln_tauw}{ln\_tauw}\forcode{=.true.}),
+\item
+  the Stokes-Coriolis term is included (\np{ln_stcor}{ln\_stcor}\forcode{=.true.}),
+\item
+  the light penetration in the ocean (\np{ln_traqsr}{ln\_traqsr}\forcode{=.true.} with namelist \nam{tra_qsr}{tra\_qsr}),
+\item
+  the atmospheric surface pressure gradient effect on ocean and ice dynamics (\np{ln_apr_dyn}{ln\_apr\_dyn}\forcode{=.true.} with namelist \nam{sbc_apr}{sbc\_apr}),
+\item
+  the effect of sea-ice pressure on the ocean (\np{ln_ice_embd}{ln\_ice\_embd}\forcode{=.true.}).
 \end{itemize}
 …
 The latter is the penetrative part of the heat flux.
 It is applied as a 3D trend of the temperature equation (\mdl{traqsr} module) when
 \np{ln\_traqsr}\forcode{=.true.}.
+\np{ln_traqsr}{ln\_traqsr}\forcode{=.true.}.
 The way the light penetrates inside the water column is generally a sum of decreasing exponentials
 (see \autoref{subsec:TRA_qsr}).
 …
 %created!)
+%
 %Especially the \np{nn\_fsbc}, the \mdl{sbc\_oce} module (fluxes + mean sst sss ssu
+%Especially the \np{nn_fsbc}{nn\_fsbc}, the \mdl{sbc\_oce} module (fluxes + mean sst sss ssu
 %ssv) \ie\ information required by flux computation or sea-ice
+%
 …
 The ocean model provides, at each time step, to the surface module (\mdl{sbcmod})
 the surface currents, temperature and salinity.
 These variables are averaged over \np{nn\_fsbc} time-step (\autoref{tab:SBC_ssm}), and
 these averaged fields are used to compute the surface fluxes at the frequency of \np{nn\_fsbc} time-steps.
+These variables are averaged over \np{nn_fsbc}{nn\_fsbc} time-step (\autoref{tab:SBC_ssm}), and
+these averaged fields are used to compute the surface fluxes at the frequency of \np{nn_fsbc}{nn\_fsbc} time-steps.
 …
   \caption[Ocean variables provided to the surface module)]{
     Ocean variables provided to the surface module (\texttt{SBC}).
     The variable are averaged over \protect\np{nn\_fsbc} time-step,
+    The variable are averaged over \protect\np{nn_fsbc}{nn\_fsbc} time-step,
     \ie\ the frequency of computation of surface fluxes.}
   \label{tab:SBC_ssm}
 …
 Note that when an input data is archived on a disc which is accessible directly from the workspace where
 the code is executed, then the user can set the \np{cn\_dir} to the pathway leading to the data.
+the code is executed, then the user can set the \np{cn_dir}{cn\_dir} to the pathway leading to the data.
 By default, the data are assumed to be in the same directory as the executable, so that cn\_dir='./'.
 …
                                   &  daily or weekLL     &  monthly           &  yearly        \\
       \hline
       \np{clim}\forcode{=.false.} &  fn\_yYYYYmMMdDD.nc  &  fn\_yYYYYmMM.nc   &  fn\_yYYYY.nc  \\
+      \np{clim}{clim}\forcode{=.false.} &  fn\_yYYYYmMMdDD.nc  &  fn\_yYYYYmMM.nc   &  fn\_yYYYY.nc  \\
       \hline
       \np{clim}\forcode{=.true.}  &  not possible        &  fn\_m??.nc        &  fn            \\
+      \np{clim}{clim}\forcode{=.true.}  &  not possible        &  fn\_m??.nc        &  fn            \\
       \hline
     \end{tabular}
 …
 a time interpolation will be performed at the following time: 0h30'00", 1h30'00", 2h30'00", etc.
 However, for forcing data related to the surface module,
 values are not needed at every time-step but at every \np{nn\_fsbc} time-step.
 For example with \np{nn\_fsbc}\forcode{=3}, the surface module will be called at time-steps 1, 4, 7, etc.
 The date used for the time interpolation is thus redefined to the middle of \np{nn\_fsbc} time-step period.
+values are not needed at every time-step but at every \np{nn_fsbc}{nn\_fsbc} time-step.
+For example with \np{nn_fsbc}{nn\_fsbc}\forcode{=3}, the surface module will be called at time-steps 1, 4, 7, etc.
+The date used for the time interpolation is thus redefined to the middle of \np{nn_fsbc}{nn\_fsbc} time-step period.
 In the previous example, this leads to: 1h30'00", 4h30'00", 7h30'00", etc. \\
 (2) For code readablility and maintenance issues, we don't take into account the NetCDF input file calendar.
 …
   Spinup of the iceberg floats
 \item
   Ocean/sea-ice simulation with both models running in parallel (\np{ln\_mixcpl}\forcode{=.true.})
+  Ocean/sea-ice simulation with both models running in parallel (\np{ln_mixcpl}{ln\_mixcpl}\forcode{=.true.})
 \end{itemize}
 The Standalone Surface scheme provides this capacity.
 Its options are defined through the \nam{sbc\_sas} namelist variables.
+Its options are defined through the \nam{sbc_sas}{sbc\_sas} namelist variables.
 A new copy of the model has to be compiled with a configuration based on ORCA2\_SAS\_LIM.
 However, no namelist parameters need be changed from the settings of the previous run (except perhaps nn\_date0).
 …
 The user can also choose in the \nam{sbc\_sas} namelist to read the mean (nn\_fsbc time-step) fraction of solar net radiation absorbed in the 1st T level using
  (\np{ln\_flx}\forcode{=.true.}) and to provide 3D oceanic velocities instead of 2D ones (\np{ln\_flx}\forcode{=.true.}). In that last case, only the 1st level will be read in.
+The user can also choose in the \nam{sbc_sas}{sbc\_sas} namelist to read the mean (nn\_fsbc time-step) fraction of solar net radiation absorbed in the 1st T level using
+ (\np{ln_flx}{ln\_flx}\forcode{=.true.}) and to provide 3D oceanic velocities instead of 2D ones (\np{ln_flx}{ln\_flx}\forcode{=.true.}). In that last case, only the 1st level will be read in.
 …
 %-------------------------------------------------------------------------------------------------------------
 In the flux formulation (\np{ln\_flx}\forcode{=.true.}),
+In the flux formulation (\np{ln_flx}{ln\_flx}\forcode{=.true.}),
 the surface boundary condition fields are directly read from input files.
 The user has to define in the namelist \nam{sbc\_flx} the name of the file,
+The user has to define in the namelist \nam{sbc_flx}{sbc\_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 for this field.
 …
 In the bulk formulation, the surface boundary condition fields are computed with bulk formulae using atmospheric fields
 and ocean (and sea-ice) variables averaged over \np{nn\_fsbc} time-step.
+and ocean (and sea-ice) variables averaged over \np{nn_fsbc}{nn\_fsbc} time-step.
 The atmospheric fields used depend on the bulk formulae used.
 …
 the NCAR (formerly named CORE), COARE 3.0, COARE 3.5 and ECMWF bulk formulae.
 The choice is made by setting to true one of the following namelist variable:
  \np{ln\_NCAR}, \np{ln\_COARE\_3p0},  \np{ln\_COARE\_3p5} and  \np{ln\_ECMWF}.
+ \np{ln_NCAR}{ln\_NCAR}, \np{ln_COARE_3p0}{ln\_COARE\_3p0},  \np{ln_COARE_3p5}{ln\_COARE\_3p5} and  \np{ln_ECMWF}{ln\_ECMWF}.
 For sea-ice, three possibilities can be selected:
 a constant transfer coefficient (1.4e-3; default value), \citet{lupkes.gryanik.ea_JGR12} (\np{ln\_Cd\_L12}), and \citet{lupkes.gryanik_JGR15} (\np{ln\_Cd\_L15}) parameterizations
 Common options are defined through the \nam{sbc\_blk} namelist variables.
+a constant transfer coefficient (1.4e-3; default value), \citet{lupkes.gryanik.ea_JGR12} (\np{ln_Cd_L12}{ln\_Cd\_L12}), and \citet{lupkes.gryanik_JGR15} (\np{ln_Cd_L15}{ln\_Cd\_L15}) parameterizations
+Common options are defined through the \nam{sbc_blk}{sbc\_blk} namelist variables.
 The required 9 input fields are:
 …
 the ocean grid size is the same or larger than the one of the input atmospheric fields.
 The \np{sn\_wndi}, \np{sn\_wndj}, \np{sn\_qsr}, \np{sn\_qlw}, \np{sn\_tair}, \np{sn\_humi}, \np{sn\_prec},
 \np{sn\_snow}, \np{sn\_tdif} parameters describe the fields and the way they have to be used
+The \np{sn_wndi}{sn\_wndi}, \np{sn_wndj}{sn\_wndj}, \np{sn_qsr}{sn\_qsr}, \np{sn_qlw}{sn\_qlw}, \np{sn_tair}{sn\_tair}, \np{sn_humi}{sn\_humi}, \np{sn_prec}{sn\_prec},
+\np{sn_snow}{sn\_snow}, \np{sn_tdif}{sn\_tdif} parameters describe the fields and the way they have to be used
 (spatial and temporal interpolations).
 \np{cn\_dir} is the directory of location of bulk files
 \np{ln\_taudif} is the flag to specify if we use Hight Frequency (HF) tau information (.true.) or not (.false.)
 \np{rn\_zqt}: is the height of humidity and temperature measurements (m)
 \np{rn\_zu}: is the height of wind measurements (m)
+\np{cn_dir}{cn\_dir} is the directory of location of bulk files
+\np{ln_taudif}{ln\_taudif} is the flag to specify if we use Hight Frequency (HF) tau information (.true.) or not (.false.)
+\np{rn_zqt}{rn\_zqt}: is the height of humidity and temperature measurements (m)
+\np{rn_zu}{rn\_zu}: is the height of wind measurements (m)
 Three multiplicative factors are available:
 \np{rn\_pfac} and \np{rn\_efac} allow to adjust (if necessary) the global freshwater budget by
+\np{rn_pfac}{rn\_pfac} and \np{rn_efac}{rn\_efac} allow to adjust (if necessary) the global freshwater budget by
 increasing/reducing the precipitations (total and snow) and or evaporation, respectively.
 The third one,\np{rn\_vfac}, control to which extend the ice/ocean velocities are taken into account in
+The third one,\np{rn_vfac}{rn\_vfac}, control to which extend the ice/ocean velocities are taken into account in
 the calculation of surface wind stress.
 Its range must be between zero and one, and it is recommended to set it to 0 at low-resolution (ORCA2 configuration).
 …
 \begin{itemize}
 \item
   NCAR (\np{ln\_NCAR}\forcode{=.true.}):
+  NCAR (\np{ln_NCAR}{ln\_NCAR}\forcode{=.true.}):
   The NCAR bulk formulae have been developed by \citet{large.yeager_rpt04}.
   They have been designed to handle the NCAR forcing, a mixture of NCEP reanalysis and satellite data.
 …
   This is the so-called DRAKKAR Forcing Set (DFS) \citep{brodeau.barnier.ea_OM10}.
 \item
   COARE 3.0 (\np{ln\_COARE\_3p0}\forcode{=.true.}):
+  COARE 3.0 (\np{ln_COARE_3p0}{ln\_COARE\_3p0}\forcode{=.true.}):
   See \citet{fairall.bradley.ea_JC03} for more details
 \item
   COARE 3.5 (\np{ln\_COARE\_3p5}\forcode{=.true.}):
+  COARE 3.5 (\np{ln_COARE_3p5}{ln\_COARE\_3p5}\forcode{=.true.}):
   See \citet{edson.jampana.ea_JPO13} for more details
 \item
   ECMWF (\np{ln\_ECMWF}\forcode{=.true.}):
+  ECMWF (\np{ln_ECMWF}{ln\_ECMWF}\forcode{=.true.}):
   Based on \href{https://www.ecmwf.int/node/9221}{IFS (Cy31)} implementation and documentation.
   Surface roughness lengths needed for the Obukhov length are computed following \citet{beljaars_QJRMS95}.
 …
 \begin{itemize}
 \item
   Constant value (\np{constant\ value}\forcode{ Cd_ice = 1.4e-3 }):
+  Constant value (\np{constant value}{constant\ value}\forcode{ Cd_ice = 1.4e-3 }):
   default constant value used for momentum and heat neutral transfer coefficients
 \item
   \citet{lupkes.gryanik.ea_JGR12} (\np{ln\_Cd\_L12}\forcode{=.true.}):
+  \citet{lupkes.gryanik.ea_JGR12} (\np{ln_Cd_L12}{ln\_Cd\_L12}\forcode{=.true.}):
   This scheme adds a dependency on edges at leads, melt ponds and flows
   of the constant neutral air-ice drag. After some approximations,
 …
   It is theoretically applicable to all ice conditions (not only MIZ).
 \item
   \citet{lupkes.gryanik_JGR15} (\np{ln\_Cd\_L15}\forcode{=.true.}):
+  \citet{lupkes.gryanik_JGR15} (\np{ln_Cd_L15}{ln\_Cd\_L15}\forcode{=.true.}):
   Alternative turbulent transfer coefficients formulation between sea-ice
   and atmosphere with distinct momentum and heat coefficients depending
 …
 the whole carbon cycle is computed.
 In this case, CO$_2$ fluxes will be exchanged between the atmosphere and the ice-ocean system
 (and need to be activated in \nam{sbc\_cpl} ).
+(and need to be activated in \nam{sbc_cpl}{sbc\_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 \nam{sbc\_cpl}, the number of categories will be determined by
+When indicating a multi-category coupling field in \nam{sbc_cpl}{sbc\_cpl}, the number of categories will be determined by
 the number used in the sea ice model.
 In some limited cases, it may be possible to specify single category coupling fields even when
 …
 The optional atmospheric pressure can be used to force ocean and ice dynamics
 (\np{ln\_apr\_dyn}\forcode{=.true.}, \nam{sbc} namelist).
 The input atmospheric forcing defined via \np{sn\_apr} structure (\nam{sbc\_apr} namelist)
+(\np{ln_apr_dyn}{ln\_apr\_dyn}\forcode{=.true.}, \nam{sbc} namelist).
+The input atmospheric forcing defined via \np{sn_apr}{sn\_apr} structure (\nam{sbc_apr}{sbc\_apr} namelist)
 can be interpolated in time to the model time step, and even in space when the interpolation on-the-fly is used.
 When used to force the dynamics, the atmospheric pressure is further transformed into
 …
 \]
 where $P_{atm}$ is the atmospheric pressure and $P_o$ a reference atmospheric pressure.
 A value of $101,000~N/m^2$ is used unless \np{ln\_ref\_apr} is set to true.
+A value of $101,000~N/m^2$ is used unless \np{ln_ref_apr}{ln\_ref\_apr} is set to true.
 In this case, $P_o$ is set to the value of $P_{atm}$ averaged over the ocean domain,
 \ie\ the mean value of $\eta_{ib}$ is kept to zero at all time steps.
 …
 When using time-splitting and BDY package for open boundaries conditions,
 the equivalent inverse barometer sea surface height $\eta_{ib}$ can be added to BDY ssh data:
 \np{ln\_apr\_obc}  might be set to true.
+\np{ln_apr_obc}{ln\_apr\_obc}  might be set to true.
 …
 The tidal forcing, generated by the gravity forces of the Earth-Moon and Earth-Sun sytems,
 is activated if \np{ln\_tide} and \np{ln\_tide\_pot} are both set to \forcode{.true.} in \nam{\_tide}.
+is activated if \np{ln_tide}{ln\_tide} and \np{ln_tide_pot}{ln\_tide\_pot} are both set to \forcode{.true.} in \nam{_tide}{\_tide}.
 This translates as an additional barotropic force in the momentum \autoref{eq:MB_PE_dyn} such that:
 \[
 …
   Msqm, Mtm, S1, MU2, NU2, L2}, and \textit{T2}). Individual
 constituents are selected by including their names in the array
 \np{clname} in \nam{\_tide} (e.g., \np{clname}\forcode{(1)='M2', }
 \np{clname}\forcode{(2)='S2'} to select solely the tidal consituents \textit{M2}
 and \textit{S2}). Optionally, when \np{ln\_tide\_ramp} is set to
+\np{clname}{clname} in \nam{_tide}{\_tide} (e.g., \np{clname}{clname}\forcode{(1)='M2', }
+\np{clname}{clname}\forcode{(2)='S2'} to select solely the tidal consituents \textit{M2}
+and \textit{S2}). Optionally, when \np{ln_tide_ramp}{ln\_tide\_ramp} is set to
 \forcode{.true.}, the equilibrium tidal forcing can be ramped up
 linearly from zero during the initial \np{rdttideramp} days of the
+linearly from zero during the initial \np{rdttideramp}{rdttideramp} days of the
 model run.
 …
 computationally too expensive. Here, two options are available:
 $\Pi_{sal}$ generated by an external model can be read in
 (\np{ln\_read\_load}\forcode{ =.true.}), or a ``scalar approximation'' can be
 used (\np{ln\_scal\_load}\forcode{ =.true.}). In the latter case
+(\np{ln_read_load}{ln\_read\_load}\forcode{ =.true.}), or a ``scalar approximation'' can be
+used (\np{ln_scal_load}{ln\_scal\_load}\forcode{ =.true.}). In the latter case
 \[
   \Pi_{sal} = \beta \eta,
 \]
 where $\beta$ (\np{rn\_scal\_load} with a default value of 0.094) is a
+where $\beta$ (\np{rn_scal_load}{rn\_scal\_load} with a default value of 0.094) is a
 spatially constant scalar, often chosen to minimize tidal prediction
 errors. Setting both \np{ln\_read\_load} and \np{ln\_scal\_load} to
+errors. Setting both \np{ln_read_load}{ln\_read\_load} and \np{ln_scal_load}{ln\_scal\_load} to
 \forcode{.false.} removes the SAL contribution.
 …
 along with the depth (in metres) which the river should be added to.
 Namelist variables in \nam{sbc\_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.
+Namelist variables in \nam{sbc_rnf}{sbc\_rnf}, \np{ln_rnf_depth}{ln\_rnf\_depth}, \np{ln_rnf_sal}{ln\_rnf\_sal} and
+\np{ln_rnf_temp}{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 taken as surface temperature respectively.
 …
 (converted into m/s) to give the heat and salt content of the river runoff.
 After the user specified depth is read ini,
 the number of grid boxes this corresponds to is calculated and stored in the variable \np{nz\_rnf}.
+the number of grid boxes this corresponds to is calculated and stored in the variable \np{nz_rnf}{nz\_rnf}.
 The variable \textit{h\_dep} is then calculated to be the depth (in metres) of
 the bottom of the lowest box the river water is being added to
 …
 %--------------------------------------------------------------------------------------------------------
 The namelist variable in \nam{sbc}, \np{nn\_isf}, controls the ice shelf representation.
 Description and result of sensitivity test to \np{nn\_isf} are presented in \citet{mathiot.jenkins.ea_GMD17}.
+The namelist variable in \nam{sbc}, \np{nn_isf}{nn\_isf}, controls the ice shelf representation.
+Description and result of sensitivity test to \np{nn_isf}{nn\_isf} are presented in \citet{mathiot.jenkins.ea_GMD17}.
 The different options are illustrated in \autoref{fig:SBC_isf}.
 \begin{description}
   \item[\np{nn\_isf}\forcode{=1}]:
   The ice shelf cavity is represented (\np{ln\_isfcav}\forcode{=.true.} needed).
+  \item[\np{nn_isf}{nn\_isf}\forcode{=1}]:
+  The ice shelf cavity is represented (\np{ln_isfcav}{ln\_isfcav}\forcode{=.true.} needed).
   The fwf and heat flux are depending of the local water properties.
 …
    \begin{description}
    \item[\np{nn\_isfblk}\forcode{=1}]:
+   \item[\np{nn_isfblk}{nn\_isfblk}\forcode{=1}]:
      The melt rate is based on a balance between the upward ocean heat flux and
      the latent heat flux at the ice shelf base. A complete description is available in \citet{hunter_rpt06}.
    \item[\np{nn\_isfblk}\forcode{=2}]:
+   \item[\np{nn_isfblk}{nn\_isfblk}\forcode{=2}]:
      The melt rate and the heat flux are based on a 3 equations formulation
      (a heat flux budget at the ice base, a salt flux budget at the ice base and a linearised freezing point temperature equation).
 …
      Temperature and salinity used to compute the melt are the average temperature in the top boundary layer \citet{losch_JGR08}.
      Its thickness is defined by \np{rn\_hisf\_tbl}.
      The fluxes and friction velocity are computed using the mean temperature, salinity and velocity in the the first \np{rn\_hisf\_tbl} m.
+     Its thickness is defined by \np{rn_hisf_tbl}{rn\_hisf\_tbl}.
+     The fluxes and friction velocity are computed using the mean temperature, salinity and velocity in the the first \np{rn_hisf_tbl}{rn\_hisf\_tbl} m.
      Then, the fluxes are spread over the same thickness (ie over one or several cells).
      If \np{rn\_hisf\_tbl} larger than top $e_{3}t$, there is no more feedback between the freezing point at the interface and the the top cell temperature.
+     If \np{rn_hisf_tbl}{rn\_hisf\_tbl} larger than top $e_{3}t$, there is no more feedback between the freezing point at the interface and the the top cell temperature.
      This can lead to super-cool temperature in the top cell under melting condition.
      If \np{rn\_hisf\_tbl} smaller than top $e_{3}t$, the top boundary layer thickness is set to the top cell thickness.\\
+     If \np{rn_hisf_tbl}{rn\_hisf\_tbl} smaller than top $e_{3}t$, the top boundary layer thickness is set to the top cell thickness.\\
      Each melt bulk formula depends on a exchange coeficient ($\Gamma^{T,S}$) between the ocean and the ice.
      There are 3 different ways to compute the exchange coeficient:
    \begin{description}
         \item[\np{nn\_gammablk}\forcode{=0}]:
      The salt and heat exchange coefficients are constant and defined by \np{rn\_gammas0} and \np{rn\_gammat0}.
+        \item[\np{nn_gammablk}{nn\_gammablk}\forcode{=0}]:
+     The salt and heat exchange coefficients are constant and defined by \np{rn_gammas0}{rn\_gammas0} and \np{rn_gammat0}{rn\_gammat0}.
      \begin{gather*}
        % \label{eq:SBC_isf_gamma_iso}
 …
      \end{gather*}
      This is the recommended formulation for ISOMIP.
    \item[\np{nn\_gammablk}\forcode{=1}]:
+   \item[\np{nn_gammablk}{nn\_gammablk}\forcode{=1}]:
      The salt and heat exchange coefficients are velocity dependent and defined as
      \begin{gather*}
 …
        \gamma^{S} = rn\_gammas0 \times u_{*}
      \end{gather*}
      where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn\_hisf\_tbl} meters).
+     where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters).
      See \citet{jenkins.nicholls.ea_JPO10} for all the details on this formulation. It is the recommended formulation for realistic application.
    \item[\np{nn\_gammablk}\forcode{=2}]:
+   \item[\np{nn_gammablk}{nn\_gammablk}\forcode{=2}]:
      The salt and heat exchange coefficients are velocity and stability dependent and defined as:
 \[
 \gamma^{T,S} = \frac{u_{*}}{\Gamma_{Turb} + \Gamma^{T,S}_{Mole}}
 \]
      where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn\_hisf\_tbl} meters),
+     where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters),
      $\Gamma_{Turb}$ the contribution of the ocean stability and
      $\Gamma^{T,S}_{Mole}$ the contribution of the molecular diffusion.
 …
      This formulation has not been extensively tested in \NEMO\ (not recommended).
    \end{description}
   \item[\np{nn\_isf}\forcode{=2}]:
+  \item[\np{nn_isf}{nn\_isf}\forcode{=2}]:
    The ice shelf cavity is not represented.
    The fwf and heat flux are computed using the \citet{beckmann.goosse_OM03} parameterisation of isf melting.
    The fluxes are distributed along the ice shelf edge between the depth of the average grounding line (GL)
    (\np{sn\_depmax\_isf}) and the base of the ice shelf along the calving front
    (\np{sn\_depmin\_isf}) as in (\np{nn\_isf}\forcode{=3}).
    The effective melting length (\np{sn\_Leff\_isf}) is read from a file.
   \item[\np{nn\_isf}\forcode{=3}]:
+   (\np{sn_depmax_isf}{sn\_depmax\_isf}) and the base of the ice shelf along the calving front
+   (\np{sn_depmin_isf}{sn\_depmin\_isf}) as in (\np{nn_isf}{nn\_isf}\forcode{=3}).
+   The effective melting length (\np{sn_Leff_isf}{sn\_Leff\_isf}) is read from a file.
+  \item[\np{nn_isf}{nn\_isf}\forcode{=3}]:
    The ice shelf cavity is not represented.
    The fwf (\np{sn\_rnfisf}) is prescribed and distributed along the ice shelf edge between
    the depth of the average grounding line (GL) (\np{sn\_depmax\_isf}) and
    the base of the ice shelf along the calving front (\np{sn\_depmin\_isf}).
+   The fwf (\np{sn_rnfisf}{sn\_rnfisf}) is prescribed and distributed along the ice shelf edge between
+   the depth of the average grounding line (GL) (\np{sn_depmax_isf}{sn\_depmax\_isf}) and
+   the base of the ice shelf along the calving front (\np{sn_depmin_isf}{sn\_depmin\_isf}).
    The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$.
   \item[\np{nn\_isf}\forcode{=4}]:
    The ice shelf cavity is opened (\np{ln\_isfcav}\forcode{=.true.} needed).
    However, the fwf is not computed but specified from file \np{sn\_fwfisf}).
+  \item[\np{nn_isf}{nn\_isf}\forcode{=4}]:
+   The ice shelf cavity is opened (\np{ln_isfcav}{ln\_isfcav}\forcode{=.true.} needed).
+   However, the fwf is not computed but specified from file \np{sn_fwfisf}{sn\_fwfisf}).
    The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$.
    As in \np{nn\_isf}\forcode{=1}, the fluxes are spread over the top boundary layer thickness (\np{rn\_hisf\_tbl})\\
+   As in \np{nn_isf}{nn\_isf}\forcode{=1}, the fluxes are spread over the top boundary layer thickness (\np{rn_hisf_tbl}{rn\_hisf\_tbl})\\
 \end{description}
 $\bullet$ \np{nn\_isf}\forcode{=1} and \np{nn\_isf}\forcode{=2} compute a melt rate based on
+$\bullet$ \np{nn_isf}{nn\_isf}\forcode{=1} and \np{nn_isf}{nn\_isf}\forcode{=2} compute a melt rate based on
 the water mass properties, ocean velocities and depth.
 This flux is thus highly dependent of the model resolution (horizontal and vertical),
 realism of the water masses onto the shelf ...\\
 $\bullet$ \np{nn\_isf}\forcode{=3} and \np{nn\_isf}\forcode{=4} read the melt rate from a file.
+$\bullet$ \np{nn_isf}{nn\_isf}\forcode{=3} and \np{nn_isf}{nn\_isf}\forcode{=4} read the melt rate from a file.
 You have total control of the fwf forcing.
 This can be useful if the water masses on the shelf are not realistic or
 …
   \caption[Ice shelf location and fresh water flux definition]{
     Illustration of the location where the fwf is injected and
     whether or not the fwf is interactif or not depending of \protect\np{nn\_isf}.}
+    whether or not the fwf is interactif or not depending of \protect\np{nn_isf}{nn\_isf}.}
   \label{fig:SBC_isf}
 \end{figure}
 …
 \end{description}
 If \np{ln\_iscpl}\forcode{=.true.}, the isf draft is assume to be different at each restart step with
+If \np{ln_iscpl}{ln\_iscpl}\forcode{=.true.}, the isf draft is assume to be different at each restart step with
 potentially some new wet/dry cells due to the ice sheet dynamics/thermodynamics.
 The wetting and drying scheme applied on the restart is very simple and described below for the 6 different possible cases:
 …
 the restart time step is prescribed to be an euler time step instead of a leap frog and $fields_b = fields_n$.\\
 The horizontal extrapolation to fill new cell with realistic value is called \np{nn\_drown} times.
 It means that if the grounding line retreat by more than \np{nn\_drown} cells between 2 coupling steps,
+The horizontal extrapolation to fill new cell with realistic value is called \np{nn_drown}{nn\_drown} times.
+It means that if the grounding line retreat by more than \np{nn_drown}{nn\_drown} cells between 2 coupling steps,
 the code will be unable to fill all the new wet cells properly.
 The default number is set up for the MISOMIP idealised experiments.
 …
 In order to remove the trend and keep the conservation level as close to 0 as possible,
 a simple conservation scheme is available with \np{ln\_hsb}\forcode{=.true.}.
+a simple conservation scheme is available with \np{ln_hsb}{ln\_hsb}\forcode{=.true.}.
 The heat/salt/vol. gain/loss is diagnosed, as well as the location.
 A correction increment is computed and apply each time step during the next \np{rn\_fiscpl} time steps.
 For safety, it is advised to set \np{rn\_fiscpl} equal to the coupling period (smallest increment possible).
+A correction increment is computed and apply each time step during the next \np{rn_fiscpl}{rn\_fiscpl} time steps.
+For safety, it is advised to set \np{rn_fiscpl}{rn\_fiscpl} equal to the coupling period (smallest increment possible).
 The corrective increment is apply into the cell itself (if it is a wet cell), the neigbouring cells or the closest wet cell (if the cell is now dry).
 …
 (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 in the \nam{berg} namelist: \np{rn\_initial\_mass} and \np{rn\_initial\_thickness}.
 Each class has an associated scaling (\np{rn\_mass\_scaling}),
+described in the \nam{berg} namelist: \np{rn_initial_mass}{rn\_initial\_mass} and \np{rn_initial_thickness}{rn\_initial\_thickness}.
+Each class has an associated scaling (\np{rn_mass_scaling}{rn\_mass\_scaling}),
 which is an integer representing how many icebergs of this class are being described as one lagrangian point
 (this reduces the numerical problem of tracking every single iceberg).
 They are enabled by setting \np{ln\_icebergs}\forcode{=.true.}.
+They are enabled by setting \np{ln_icebergs}{ln\_icebergs}\forcode{=.true.}.
 Two initialisation schemes are possible.
 \begin{description}
 \item[\np{nn\_test\_icebergs}~$>$~0]
   In this scheme, the value of \np{nn\_test\_icebergs} represents the class of iceberg to generate
   (so between 1 and 10), and \np{nn\_test\_icebergs} provides a lon/lat box in the domain at each grid point of
+\item[\np{nn_test_icebergs}{nn\_test\_icebergs}~$>$~0]
+  In this scheme, the value of \np{nn_test_icebergs}{nn\_test\_icebergs} represents the class of iceberg to generate
+  (so between 1 and 10), and \np{nn_test_icebergs}{nn\_test\_icebergs} provides a lon/lat box in the domain at each grid point of
   which an iceberg is generated at the beginning of the run.
   (Note that this happens each time the timestep equals \np{nn\_nit000}.)
   \np{nn\_test\_icebergs} is defined by four numbers in \np{nn\_test\_box} representing the corners of
+  (Note that this happens each time the timestep equals \np{nn_nit000}{nn\_nit000}.)
+  \np{nn_test_icebergs}{nn\_test\_icebergs} is defined by four numbers in \np{nn_test_box}{nn\_test\_box} representing the corners of
   the geographical box: lonmin,lonmax,latmin,latmax
 \item[\np{nn\_test\_icebergs}\forcode{=-1}]
   In this scheme, the model reads a calving file supplied in the \np{sn\_icb} parameter.
+\item[\np{nn_test_icebergs}{nn\_test\_icebergs}\forcode{=-1}]
+  In this scheme, the model reads a calving file supplied in the \np{sn_icb}{sn\_icb} parameter.
   This should be a file with a field on the configuration grid (typically ORCA)
   representing ice accumulation rate at each model point.
 …
 The latter act to disintegrate the iceberg.
 This is either all melted freshwater,
 or (if \np{rn\_bits\_erosion\_fraction}~$>$~0) into melt and additionally small ice bits
+or (if \np{rn_bits_erosion_fraction}{rn\_bits\_erosion\_fraction}~$>$~0) into melt and additionally small ice bits
 which are assumed to propagate with their larger parent and thus delay fluxing into the ocean.
 Melt water (and other variables on the configuration grid) are written into the main \NEMO\ model output files.
 …
 Extensive diagnostics can be produced.
 Separate output files are maintained for human-readable iceberg information.
 A separate file is produced for each processor (independent of \np{ln\_ctl}).
+A separate file is produced for each processor (independent of \np{ln_ctl}{ln\_ctl}).
 The amount of information is controlled by two integer parameters:
 \begin{description}
 \item[\np{nn\_verbose\_level}] takes a value between one and four and
+\item[\np{nn_verbose_level}{nn\_verbose\_level}] takes a value between one and four and
   represents an increasing number of points in the code at which variables are written,
   and an increasing level of obscurity.
 \item[\np{nn\_verbose\_write}] is the number of timesteps between writes
+\item[\np{nn_verbose_write}{nn\_verbose\_write}] is the number of timesteps between writes
 \end{description}
 Iceberg trajectories can also be written out and this is enabled by setting \np{nn\_sample\_rate}~$>$~0.
+Iceberg trajectories can also be written out and this is enabled by setting \np{nn_sample_rate}{nn\_sample\_rate}~$>$~0.
 A non-zero value represents how many timesteps between writes of information into the output file.
 These output files are in NETCDF format.
 …
 %        Interactions with waves (sbcwave.F90, ln_wave)
 % =============================================================================================================
 \section[Interactions with waves (\textit{sbcwave.F90}, \forcode{ln_wave})]{Interactions with waves (\protect\mdl{sbcwave}, \protect\np{ln\_wave})}
+\section[Interactions with waves (\textit{sbcwave.F90}, \forcode{ln_wave})]{Interactions with waves (\protect\mdl{sbcwave}, \protect\np{ln_wave}{ln\_wave})}
 \label{sec:SBC_wave}
 %------------------------------------------namsbc_wave--------------------------------------------------------
 …
 Physical processes related to ocean surface waves can be accounted by setting the logical variable
 \np{ln\_wave}\forcode{=.true.} in \nam{sbc} namelist. In addition, specific flags accounting for
+\np{ln_wave}{ln\_wave}\forcode{=.true.} in \nam{sbc} namelist. In addition, specific flags accounting for
 different processes should be activated as explained in the following sections.
 Wave fields can be provided either in forced or coupled mode:
 \begin{description}
 \item[forced mode]: wave fields should be defined through the \nam{sbc\_wave} namelist
+\item[forced mode]: wave fields should be defined through the \nam{sbc_wave}{sbc\_wave} namelist
 for external data names, locations, frequency, interpolation and all the miscellanous options allowed by
 Input Data generic Interface (see \autoref{sec:SBC_input}).
 \item[coupled mode]: \NEMO\ and an external wave model can be coupled by setting \np{ln\_cpl} \forcode{= .true.}
 in \nam{sbc} namelist and filling the \nam{sbc\_cpl} namelist.
+\item[coupled mode]: \NEMO\ and an external wave model can be coupled by setting \np{ln_cpl}{ln\_cpl} \forcode{= .true.}
+in \nam{sbc} namelist and filling the \nam{sbc_cpl}{sbc\_cpl} namelist.
 \end{description}
 …
 % ----------------------------------------------------------------
 \subsection[Neutral drag coefficient from wave model (\forcode{ln_cdgw})]{Neutral drag coefficient from wave model (\protect\np{ln\_cdgw})}
+\subsection[Neutral drag coefficient from wave model (\forcode{ln_cdgw})]{Neutral drag coefficient from wave model (\protect\np{ln_cdgw}{ln\_cdgw})}
 \label{subsec:SBC_wave_cdgw}
 The neutral surface drag coefficient provided from an external data source (\ie\ a wave model),
 can be used by setting the logical variable \np{ln\_cdgw} \forcode{= .true.} in \nam{sbc} namelist.
+can be used by setting the logical variable \np{ln_cdgw}{ln\_cdgw} \forcode{= .true.} in \nam{sbc} namelist.
 Then using the routine \rou{sbcblk\_algo\_ncar} and starting from the neutral drag coefficent provided,
 the drag coefficient is computed according to the stable/unstable conditions of the
 …
 % 3D Stokes Drift (ln_sdw, nn_sdrift)
 % ----------------------------------------------------------------
 \subsection[3D Stokes Drift (\forcode{ln_sdw}, \forcode{nn_sdrift})]{3D Stokes Drift (\protect\np{ln\_sdw, nn\_sdrift})}
+\subsection[3D Stokes Drift (\forcode{ln_sdw} \& \forcode{nn_sdrift})]{3D Stokes Drift (\protect\np{ln_sdw}{ln\_sdw} \& \np{nn_sdrift}{nn\_sdrift})}
 \label{subsec:SBC_wave_sdw}
 …
 To simplify, it is customary to use approximations to the full Stokes profile.
 Three possible parameterizations for the calculation for the approximate Stokes drift velocity profile
 are included in the code through the \np{nn\_sdrift} parameter once provided the surface Stokes drift
+are included in the code through the \np{nn_sdrift}{nn\_sdrift} parameter once provided the surface Stokes drift
 $\mathbf{U}_{st |_{z=0}}$ which is evaluated by an external wave model that accurately reproduces the wave spectra
 and makes possible the estimation of the surface Stokes drift for random directional waves in
 …
 \begin{description}
 \item[\np{nn\_sdrift} = 0]: exponential integral profile parameterization proposed by
+\item[\np{nn_sdrift}{nn\_sdrift} = 0]: exponential integral profile parameterization proposed by
 \citet{breivik.janssen.ea_JPO14}:
 …
 where $H_s$ is the significant wave height and $\omega$ is the wave frequency.
 \item[\np{nn\_sdrift} = 1]: velocity profile based on the Phillips spectrum which is considered to be a
+\item[\np{nn_sdrift}{nn\_sdrift} = 1]: velocity profile based on the Phillips spectrum which is considered to be a
 reasonable estimate of the part of the spectrum mostly contributing to the Stokes drift velocity near the surface
 \citep{breivik.bidlot.ea_OM16}:
 …
 where $erf$ is the complementary error function and $k_p$ is the peak wavenumber.
 \item[\np{nn\_sdrift} = 2]: velocity profile based on the Phillips spectrum as for \np{nn\_sdrift} = 1
+\item[\np{nn_sdrift}{nn\_sdrift} = 2]: velocity profile based on the Phillips spectrum as for \np{nn_sdrift}{nn\_sdrift} = 1
 but using the wave frequency from a wave model.
 …
 % Stokes-Coriolis term (ln_stcor)
 % ----------------------------------------------------------------
 \subsection[Stokes-Coriolis term (\forcode{ln_stcor})]{Stokes-Coriolis term (\protect\np{ln\_stcor})}
+\subsection[Stokes-Coriolis term (\forcode{ln_stcor})]{Stokes-Coriolis term (\protect\np{ln_stcor}{ln\_stcor})}
 \label{subsec:SBC_wave_stcor}
 …
 In order to include this term, once evaluated the Stokes drift (using one of the 3 possible
 approximations described in \autoref{subsec:SBC_wave_sdw}),
 \np{ln\_stcor}\forcode{=.true.} has to be set.
+\np{ln_stcor}{ln\_stcor}\forcode{=.true.} has to be set.
 …
 % Waves modified stress (ln_tauwoc, ln_tauw)
 % ----------------------------------------------------------------
 \subsection[Wave modified stress (\forcode{ln_tauwoc} \& \forcode{ln_tauw})]{Wave modified sress (\protect\np{ln\_tauwoc, ln\_tauw})}
+\subsection[Wave modified stress (\forcode{ln_tauwoc} \& \forcode{ln_tauw})]{Wave modified sress (\protect\np{ln_tauwoc}{ln\_tauwoc} \& \np{ln_tauw}{ln\_tauw})}
 \label{subsec:SBC_wave_tauw}
 …
 The wave stress derived from an external wave model can be provided either through the normalized
 wave stress into the ocean by setting \np{ln\_tauwoc}\forcode{=.true.}, or through the zonal and
 meridional stress components by setting \np{ln\_tauw}\forcode{=.true.}.
+wave stress into the ocean by setting \np{ln_tauwoc}{ln\_tauwoc}\forcode{=.true.}, or through the zonal and
+meridional stress components by setting \np{ln_tauw}{ln\_tauw}\forcode{=.true.}.
 …
 assuming that the diurnal cycle of SWF is a scaling of the top of the atmosphere diurnal cycle of incident SWF.
 The \cite{bernie.guilyardi.ea_CD07} reconstruction algorithm is available in \NEMO\ by
 setting \np{ln\_dm2dc}\forcode{=.true.} (a \textit{\nam{sbc}} namelist variable) when
 using a bulk formulation (\np{ln\_blk}\forcode{=.true.}) or
 the flux formulation (\np{ln\_flx}\forcode{=.true.}).
+setting \np{ln_dm2dc}{ln\_dm2dc}\forcode{=.true.} (a \textit{\nam{sbc}} namelist variable) when
+using a bulk formulation (\np{ln_blk}{ln\_blk}\forcode{=.true.}) or
+the flux formulation (\np{ln_flx}{ln\_flx}\forcode{=.true.}).
 The reconstruction is performed in the \mdl{sbcdcy} module.
 The detail of the algoritm used can be found in the appendix~A of \cite{bernie.guilyardi.ea_CD07}.
 …
 a given time step is the mean value of the analytical cycle over this time step (\autoref{fig:SBC_diurnal}).
 The use of diurnal cycle reconstruction requires the input SWF to be daily
 (\ie\ a frequency of 24 hours and a time interpolation set to true in \np{sn\_qsr} namelist parameter).
+(\ie\ a frequency of 24 hours and a time interpolation set to true in \np{sn_qsr}{sn\_qsr} namelist parameter).
 Furthermore, it is recommended to have a least 8 surface module time steps per day,
 that is  $\rdt \ nn\_fsbc < 10,800~s = 3~h$.
 …
 \label{subsec:SBC_rotation}
 When using a flux (\np{ln\_flx}\forcode{=.true.}) or bulk (\np{ln\_blk}\forcode{=.true.}) formulation,
+When using a flux (\np{ln_flx}{ln\_flx}\forcode{=.true.}) or bulk (\np{ln_blk}{ln\_blk}\forcode{=.true.}) formulation,
 pairs of vector components can be rotated from east-north directions onto the local grid directions.
 This is particularly useful when interpolation on the fly is used since here any vectors are likely to
 …
 %-------------------------------------------------------------------------------------------------------------
 Options are defined through the \nam{sbc\_ssr} namelist variables.
 On forced mode using a flux formulation (\np{ln\_flx}\forcode{=.true.}),
+Options are defined through the \nam{sbc_ssr}{sbc\_ssr} namelist variables.
+On forced mode using a flux formulation (\np{ln_flx}{ln\_flx}\forcode{=.true.}),
 a feedback term \emph{must} be added to the surface heat flux $Q_{ns}^o$:
 \[
 …
 The presence at the sea surface of an ice covered area modifies all the fluxes transmitted to the ocean.
 There are several way to handle sea-ice in the system depending on
 the value of the \np{nn\_ice} namelist parameter found in \nam{sbc} namelist.
+the value of the \np{nn_ice}{nn\_ice} namelist parameter found in \nam{sbc} namelist.
 \begin{description}
 \item[nn\_ice = 0]
 …
 or alternatively when \NEMO\ is coupled to the HadGAM3 atmosphere model
 (with \textit{calc\_strair}\forcode{=.false.} and \textit{calc\_Tsfc}\forcode{=false}).
 The code is intended to be used with \np{nn\_fsbc} set to 1
+The code is intended to be used with \np{nn_fsbc}{nn\_fsbc} set to 1
 (although coupling ocean and ice less frequently should work,
 it is possible the calculation of some of the ocean-ice fluxes needs to be modified slightly -
 …
 \begin{description}
 \item[\np{nn\_fwb}\forcode{=0}]
+\item[\np{nn_fwb}{nn\_fwb}\forcode{=0}]
   no control at all.
   The mean sea level is free to drift, and will certainly do so.
 \item[\np{nn\_fwb}\forcode{=1}]
+\item[\np{nn_fwb}{nn\_fwb}\forcode{=1}]
   global mean \textit{emp} set to zero at each model time step.
   %GS: comment below still relevant ?
   %Note that with a sea-ice model, this technique only controls the mean sea level with linear free surface and no mass flux between ocean and ice (as it is implemented in the current ice-ocean coupling).
 \item[\np{nn\_fwb}\forcode{=2}]
+\item[\np{nn_fwb}{nn\_fwb}\forcode{=2}]
   freshwater budget is adjusted from the previous year annual mean budget which
   is read in the \textit{EMPave\_old.dat} file.

NEMO/trunk/doc/latex/NEMO/subfiles/chap_STO.tex

-                      r11567
+                      r11577
 (\rou{sto\_rst\_write}) writes a restart file
 (which suffix name is given by \np{cn\_storst\_out} namelist parameter) containing the current value of
+(which suffix name is given by \np{cn_storst_out}{cn\_storst\_out} namelist parameter) containing the current value of
 all autoregressive processes to allow creating the file needed for a restart.
 This restart file also contains the current state of the random number generator.
 When \np{ln\_rststo} is set to \forcode{.true.}),
 the restart file (which suffix name is given by \np{cn\_storst\_in} namelist parameter) is read by
+When \np{ln_rststo}{ln\_rststo} is set to \forcode{.true.}),
+the restart file (which suffix name is given by \np{cn_storst_in}{cn\_storst\_in} namelist parameter) is read by
 the initialization routine (\rou{sto\_par\_init}).
 The simulation will continue exactly as if it was not interrupted only
 when \np{ln\_rstseed} is set to \forcode{.true.},
+when \np{ln_rstseed}{ln\_rstseed} is set to \forcode{.true.},
 \ie\ when the state of the random number generator is read in the restart file.\\
 …
 Options and parameters \\
 The \np{ln\_sto\_eos} namelist variable activates stochastic parametrisation of equation of state.
+The \np{ln_sto_eos}{ln\_sto\_eos} namelist variable activates stochastic parametrisation of equation of state.
 By default it set to \forcode{.false.}) and not active.
 The set of parameters is available in \nam{sto} namelist
 …
 \begin{description}
 \item[\np{nn\_sto\_eos}:]   number of independent random walks
 \item[\np{rn\_eos\_stdxy}:] random walk horizontal standard deviation (in grid points)
 \item[\np{rn\_eos\_stdz}:]  random walk vertical standard deviation (in grid points)
 \item[\np{rn\_eos\_tcor}:]  random walk time correlation (in timesteps)
 \item[\np{nn\_eos\_ord}:]   order of autoregressive processes
 \item[\np{nn\_eos\_flt}:]   passes of Laplacian filter
 \item[\np{rn\_eos\_lim}:]   limitation factor (default = 3.0)
+\item[\np{nn_sto_eos}{nn\_sto\_eos}:]   number of independent random walks
+\item[\np{rn_eos_stdxy}{rn\_eos\_stdxy}:] random walk horizontal standard deviation (in grid points)
+\item[\np{rn_eos_stdz}{rn\_eos\_stdz}:]  random walk vertical standard deviation (in grid points)
+\item[\np{rn_eos_tcor}{rn\_eos\_tcor}:]  random walk time correlation (in timesteps)
+\item[\np{nn_eos_ord}{nn\_eos\_ord}:]   order of autoregressive processes
+\item[\np{nn_eos_flt}{nn\_eos\_flt}:]   passes of Laplacian filter
+\item[\np{rn_eos_lim}{rn\_eos\_lim}:]   limitation factor (default = 3.0)
 \end{description}

NEMO/trunk/doc/latex/NEMO/subfiles/chap_TRA.tex

-                      r11571
+                      r11577
 The user has the option of extracting each tendency term on the RHS of the tracer equation for output
 (\np{ln\_tra\_trd} or \np{ln\_tra\_mxl}\forcode{=.true.}), as described in \autoref{chap:DIA}.
+(\np{ln_tra_trd}{ln\_tra\_trd} or \np{ln_tra_mxl}{ln\_tra\_mxl}\forcode{=.true.}), as described in \autoref{chap:DIA}.
 % ================================================================
 …
 %-------------------------------------------------------------------------------------------------------------
 When considered (\ie\ when \np{ln\_traadv\_OFF} is not set to \forcode{.true.}),
+When considered (\ie\ when \np{ln_traadv_OFF}{ln\_traadv\_OFF} is not set to \forcode{.true.}),
 the advection tendency of a tracer is expressed in flux form,
 \ie\ as the divergence of the advective fluxes.
 …
 Indeed, it is obtained by using the following equality: $\nabla \cdot (\vect U \, T) = \vect U \cdot \nabla T$ which
 results from the use of the continuity equation, $\partial_t e_3 + e_3 \; \nabla \cdot \vect U = 0$
 (which reduces to $\nabla \cdot \vect U = 0$ in linear free surface, \ie\ \np{ln\_linssh}\forcode{=.true.}).
+(which reduces to $\nabla \cdot \vect U = 0$ in linear free surface, \ie\ \np{ln_linssh}{ln\_linssh}\forcode{=.true.}).
 Therefore it is of paramount importance to design the discrete analogue of the advection tendency so that
 it is consistent with the continuity equation in order to enforce the conservation properties of
 …
 \begin{description}
 \item[linear free surface:]
   (\np{ln\_linssh}\forcode{=.true.})
+  (\np{ln_linssh}{ln\_linssh}\forcode{=.true.})
   the first level thickness is constant in time:
   the vertical boundary condition is applied at the fixed surface $z = 0$ rather than on
 …
   the first level tracer value.
 \item[non-linear free surface:]
   (\np{ln\_linssh}\forcode{=.false.})
+  (\np{ln_linssh}{ln\_linssh}\forcode{=.false.})
   convergence/divergence in the first ocean level moves the free surface up/down.
   There is no tracer advection through it so that the advective fluxes through the surface are also zero.
 …
 Conservative Laws scheme (MUSCL), a $3^{rd}$ Upstream Biased Scheme (UBS, also often called UP3),
 and a Quadratic Upstream Interpolation for Convective Kinematics with Estimated Streaming Terms scheme (QUICKEST).
 The choice is made in the \nam{tra\_adv} namelist, by setting to \forcode{.true.} one of
+The choice is made in the \nam{tra_adv}{tra\_adv} namelist, by setting to \forcode{.true.} one of
 the logicals \textit{ln\_traadv\_xxx}.
 The corresponding code can be found in the \textit{traadv\_xxx.F90} module, where
 …
 %        2nd and 4th order centred schemes
 % -------------------------------------------------------------------------------------------------------------
 \subsection[CEN: Centred scheme (\forcode{ln_traadv_cen})]{CEN: Centred scheme (\protect\np{ln\_traadv\_cen})}
+\subsection[CEN: Centred scheme (\forcode{ln_traadv_cen})]{CEN: Centred scheme (\protect\np{ln_traadv_cen}{ln\_traadv\_cen})}
 \label{subsec:TRA_adv_cen}
 %        2nd order centred scheme
 The centred advection scheme (CEN) is used when \np{ln\_traadv\_cen}\forcode{=.true.}.
+The centred advection scheme (CEN) is used when \np{ln_traadv_cen}{ln\_traadv\_cen}\forcode{=.true.}.
 Its order ($2^{nd}$ or $4^{th}$) can be chosen independently on horizontal (iso-level) and vertical direction by
 setting \np{nn\_cen\_h} and \np{nn\_cen\_v} to $2$ or $4$.
+setting \np{nn_cen_h}{nn\_cen\_h} and \np{nn_cen_v}{nn\_cen\_v} to $2$ or $4$.
 CEN implementation can be found in the \mdl{traadv\_cen} module.
 …
   \tau_u^{cen4} = \overline{T - \frac{1}{6} \, \delta_i \Big[ \delta_{i + 1/2}[T] \, \Big]}^{\,i + 1/2}
 \end{equation}
 In the vertical direction (\np{nn\_cen\_v}\forcode{=4}),
+In the vertical direction (\np{nn_cen_v}{nn\_cen\_v}\forcode{=4}),
 a $4^{th}$ COMPACT interpolation has been prefered \citep{demange_phd14}.
 In the COMPACT scheme, both the field and its derivative are interpolated, which leads, after a matrix inversion,
 …
 %        FCT scheme
 % -------------------------------------------------------------------------------------------------------------
 \subsection[FCT: Flux Corrected Transport scheme (\forcode{ln_traadv_fct})]{FCT: Flux Corrected Transport scheme (\protect\np{ln\_traadv\_fct})}
+\subsection[FCT: Flux Corrected Transport scheme (\forcode{ln_traadv_fct})]{FCT: Flux Corrected Transport scheme (\protect\np{ln_traadv_fct}{ln\_traadv\_fct})}
 \label{subsec:TRA_adv_tvd}
 The Flux Corrected Transport schemes (FCT) is used when \np{ln\_traadv\_fct}\forcode{=.true.}.
+The Flux Corrected Transport schemes (FCT) is used when \np{ln_traadv_fct}{ln\_traadv\_fct}\forcode{=.true.}.
 Its order ($2^{nd}$ or $4^{th}$) can be chosen independently on horizontal (iso-level) and vertical direction by
 setting \np{nn\_fct\_h} and \np{nn\_fct\_v} to $2$ or $4$.
+setting \np{nn_fct_h}{nn\_fct\_h} and \np{nn_fct_v}{nn\_fct\_v} to $2$ or $4$.
 FCT implementation can be found in the \mdl{traadv\_fct} module.
 …
 where $c_u$ is a flux limiter function taking values between 0 and 1.
 The FCT order is the one of the centred scheme used
 (\ie\ it depends on the setting of \np{nn\_fct\_h} and \np{nn\_fct\_v}).
+(\ie\ it depends on the setting of \np{nn_fct_h}{nn\_fct\_h} and \np{nn_fct_v}{nn\_fct\_v}).
 There exist many ways to define $c_u$, each corresponding to a different FCT scheme.
 The one chosen in \NEMO\ is described in \citet{zalesak_JCP79}.
 …
 %        MUSCL scheme
 % -------------------------------------------------------------------------------------------------------------
 \subsection[MUSCL: Monotone Upstream Scheme for Conservative Laws (\forcode{ln_traadv_mus})]{MUSCL: Monotone Upstream Scheme for Conservative Laws (\protect\np{ln\_traadv\_mus})}
+\subsection[MUSCL: Monotone Upstream Scheme for Conservative Laws (\forcode{ln_traadv_mus})]{MUSCL: Monotone Upstream Scheme for Conservative Laws (\protect\np{ln_traadv_mus}{ln\_traadv\_mus})}
 \label{subsec:TRA_adv_mus}
 The Monotone Upstream Scheme for Conservative Laws (MUSCL) is used when \np{ln\_traadv\_mus}\forcode{=.true.}.
+The Monotone Upstream Scheme for Conservative Laws (MUSCL) is used when \np{ln_traadv_mus}{ln\_traadv\_mus}\forcode{=.true.}.
 MUSCL implementation can be found in the \mdl{traadv\_mus} module.
 …
 This choice ensure the \textit{positive} character of the scheme.
 In addition, fluxes round a grid-point where a runoff is applied can optionally be computed using upstream fluxes
 (\np{ln\_mus\_ups}\forcode{=.true.}).
+(\np{ln_mus_ups}{ln\_mus\_ups}\forcode{=.true.}).
 % -------------------------------------------------------------------------------------------------------------
 %        UBS scheme
 % -------------------------------------------------------------------------------------------------------------
 \subsection[UBS a.k.a. UP3: Upstream-Biased Scheme (\forcode{ln_traadv_ubs})]{UBS a.k.a. UP3: Upstream-Biased Scheme (\protect\np{ln\_traadv\_ubs})}
+\subsection[UBS a.k.a. UP3: Upstream-Biased Scheme (\forcode{ln_traadv_ubs})]{UBS a.k.a. UP3: Upstream-Biased Scheme (\protect\np{ln_traadv_ubs}{ln\_traadv\_ubs})}
 \label{subsec:TRA_adv_ubs}
 The Upstream-Biased Scheme (UBS) is used when \np{ln\_traadv\_ubs}\forcode{=.true.}.
+The Upstream-Biased Scheme (UBS) is used when \np{ln_traadv_ubs}{ln\_traadv\_ubs}\forcode{=.true.}.
 UBS implementation can be found in the \mdl{traadv\_mus} module.
 …
 \citep{shchepetkin.mcwilliams_OM05, demange_phd14}.
 Therefore the vertical flux is evaluated using either a $2^nd$ order FCT scheme or a $4^th$ order COMPACT scheme
 (\np{nn\_ubs\_v}\forcode{=2 or 4}).
+(\np{nn_ubs_v}{nn\_ubs\_v}\forcode{=2 or 4}).
 For stability reasons (see \autoref{chap:TD}), the first term  in \autoref{eq:TRA_adv_ubs}
 …
 %        QCK scheme
 % -------------------------------------------------------------------------------------------------------------
 \subsection[QCK: QuiCKest scheme (\forcode{ln_traadv_qck})]{QCK: QuiCKest scheme (\protect\np{ln\_traadv\_qck})}
+\subsection[QCK: QuiCKest scheme (\forcode{ln_traadv_qck})]{QCK: QuiCKest scheme (\protect\np{ln_traadv_qck}{ln\_traadv\_qck})}
 \label{subsec:TRA_adv_qck}
 The Quadratic Upstream Interpolation for Convective Kinematics with Estimated Streaming Terms (QUICKEST) scheme
 proposed by \citet{leonard_CMAME79} is used when \np{ln\_traadv\_qck}\forcode{=.true.}.
+proposed by \citet{leonard_CMAME79} is used when \np{ln_traadv_qck}{ln\_traadv\_qck}\forcode{=.true.}.
 QUICKEST implementation can be found in the \mdl{traadv\_qck} module.
 …
 %-------------------------------------------------------------------------------------------------------------
 Options are defined through the \nam{tra\_ldf} namelist variables.
+Options are defined through the \nam{tra_ldf}{tra\_ldf} namelist variables.
 They are regrouped in four items, allowing to specify
 $(i)$   the type of operator used (none, laplacian, bilaplacian),
 …
 except for the pure vertical component that appears when a rotation tensor is used.
 This latter component is solved implicitly together with the vertical diffusion term (see \autoref{chap:TD}).
 When \np{ln\_traldf\_msc}\forcode{=.true.}, a Method of Stabilizing Correction is used in which
+When \np{ln_traldf_msc}{ln\_traldf\_msc}\forcode{=.true.}, a Method of Stabilizing Correction is used in which
 the pure vertical component is split into an explicit and an implicit part \citep{lemarie.debreu.ea_OM12}.
 …
 %        Type of operator
 % -------------------------------------------------------------------------------------------------------------
 \subsection[Type of operator (\forcode{ln_traldf_}\{\forcode{OFF,lap,blp}\})]{Type of operator (\protect\np{ln\_traldf\_OFF}, \protect\np{ln\_traldf\_lap}, or \protect\np{ln\_traldf\_blp})}
+\subsection[Type of operator (\forcode{ln_traldf_}\{\forcode{OFF,lap,blp}\})]{Type of operator (\protect\np{ln_traldf_OFF}{ln\_traldf\_OFF}, \protect\np{ln_traldf_lap}{ln\_traldf\_lap}, or \protect\np{ln_traldf_blp}{ln\_traldf\_blp})}
 \label{subsec:TRA_ldf_op}
 …
 \begin{description}
 \item[\np{ln\_traldf\_OFF}\forcode{=.true.}:]
+\item[\np{ln_traldf_OFF}{ln\_traldf\_OFF}\forcode{=.true.}:]
   no operator selected, the lateral diffusive tendency will not be applied to the tracer equation.
   This option can be used when the selected advection scheme is diffusive enough (MUSCL scheme for example).
 \item[\np{ln\_traldf\_lap}\forcode{=.true.}:]
+\item[\np{ln_traldf_lap}{ln\_traldf\_lap}\forcode{=.true.}:]
   a laplacian operator is selected.
   This harmonic operator takes the following expression:  $\mathcal{L}(T) = \nabla \cdot A_{ht} \; \nabla T $,
   where the gradient operates along the selected direction (see \autoref{subsec:TRA_ldf_dir}),
   and $A_{ht}$ is the eddy diffusivity coefficient expressed in $m^2/s$ (see \autoref{chap:LDF}).
 \item[\np{ln\_traldf\_blp}\forcode{=.true.}]:
+\item[\np{ln_traldf_blp}{ln\_traldf\_blp}\forcode{=.true.}]:
   a bilaplacian operator is selected.
   This biharmonic operator takes the following expression:
 …
 %        Direction of action
 % -------------------------------------------------------------------------------------------------------------
 \subsection[Action direction (\forcode{ln_traldf_}\{\forcode{lev,hor,iso,triad}\})]{Direction of action (\protect\np{ln\_traldf\_lev}, \protect\np{ln\_traldf\_hor}, \protect\np{ln\_traldf\_iso}, or \protect\np{ln\_traldf\_triad})}
+\subsection[Action direction (\forcode{ln_traldf_}\{\forcode{lev,hor,iso,triad}\})]{Direction of action (\protect\np{ln_traldf_lev}{ln\_traldf\_lev}, \protect\np{ln_traldf_hor}{ln\_traldf\_hor}, \protect\np{ln_traldf_iso}{ln\_traldf\_iso}, or \protect\np{ln_traldf_triad}{ln\_traldf\_triad})}
 \label{subsec:TRA_ldf_dir}
 The choice of a direction of action determines the form of operator used.
 The operator is a simple (re-entrant) laplacian acting in the (\textbf{i},\textbf{j}) plane when
 iso-level option is used (\np{ln\_traldf\_lev}\forcode{=.true.}) or
+iso-level option is used (\np{ln_traldf_lev}{ln\_traldf\_lev}\forcode{=.true.}) or
 when a horizontal (\ie\ geopotential) operator is demanded in \textit{z}-coordinate
 (\np{ln\_traldf\_hor} and \np{ln\_zco}\forcode{=.true.}).
+(\np{ln_traldf_hor}{ln\_traldf\_hor} and \np{ln_zco}{ln\_zco}\forcode{=.true.}).
 The associated code can be found in the \mdl{traldf\_lap\_blp} module.
 The operator is a rotated (re-entrant) laplacian when
 the direction along which it acts does not coincide with the iso-level surfaces,
 that is when standard or triad iso-neutral option is used
 (\np{ln\_traldf\_iso} or \np{ln\_traldf\_triad} = \forcode{.true.},
+(\np{ln_traldf_iso}{ln\_traldf\_iso} or \np{ln_traldf_triad}{ln\_traldf\_triad} = \forcode{.true.},
 see \mdl{traldf\_iso} or \mdl{traldf\_triad} module, resp.), or
 when a horizontal (\ie\ geopotential) operator is demanded in \textit{s}-coordinate
 (\np{ln\_traldf\_hor} and \np{ln\_sco} = \forcode{.true.})
+(\np{ln_traldf_hor}{ln\_traldf\_hor} and \np{ln_sco}{ln\_sco} = \forcode{.true.})
 \footnote{In this case, the standard iso-neutral operator will be automatically selected}.
 In that case, a rotation is applied to the gradient(s) that appears in the operator so that
 …
 %       iso-level operator
 % -------------------------------------------------------------------------------------------------------------
 \subsection[Iso-level (bi-)laplacian operator (\forcode{ln_traldf_iso})]{Iso-level (bi-)laplacian operator ( \protect\np{ln\_traldf\_iso})}
+\subsection[Iso-level (bi-)laplacian operator (\forcode{ln_traldf_iso})]{Iso-level (bi-)laplacian operator ( \protect\np{ln_traldf_iso}{ln\_traldf\_iso})}
 \label{subsec:TRA_ldf_lev}
 …
 It is a \textit{horizontal} operator (\ie acting along geopotential surfaces) in
 the $z$-coordinate with or without partial steps, but is simply an iso-level operator in the $s$-coordinate.
 It is thus used when, in addition to \np{ln\_traldf\_lap} or \np{ln\_traldf\_blp}\forcode{=.true.},
 we have \np{ln\_traldf\_lev}\forcode{=.true.} or \np{ln\_traldf\_hor}~=~\np{ln\_zco}\forcode{=.true.}.
+It is thus used when, in addition to \np{ln_traldf_lap}{ln\_traldf\_lap} or \np{ln_traldf_blp}{ln\_traldf\_blp}\forcode{=.true.},
+we have \np{ln_traldf_lev}{ln\_traldf\_lev}\forcode{=.true.} or \np{ln_traldf_hor}{ln\_traldf\_hor}~=~\np{ln_zco}{ln\_zco}\forcode{=.true.}.
 In both cases, it significantly contributes to diapycnal mixing.
 It is therefore never recommended, even when using it in the bilaplacian case.
 Note that in the partial step $z$-coordinate (\np{ln\_zps}\forcode{=.true.}),
+Note that in the partial step $z$-coordinate (\np{ln_zps}{ln\_zps}\forcode{=.true.}),
 tracers in horizontally adjacent cells are located at different depths in the vicinity of the bottom.
 In this case, horizontal derivatives in (\autoref{eq:TRA_ldf_lap}) at the bottom level require a specific treatment.
 …
 $r_1$ and $r_2$ are the slopes between the surface of computation ($z$- or $s$-surfaces) and
 the surface along which the diffusion operator acts (\ie\ horizontal or iso-neutral surfaces).
 It is thus used when, in addition to \np{ln\_traldf\_lap}\forcode{=.true.},
 we have \np{ln\_traldf\_iso}\forcode{=.true.},
 or both \np{ln\_traldf\_hor}\forcode{=.true.} and \np{ln\_zco}\forcode{=.true.}.
+It is thus used when, in addition to \np{ln_traldf_lap}{ln\_traldf\_lap}\forcode{=.true.},
+we have \np{ln_traldf_iso}{ln\_traldf\_iso}\forcode{=.true.},
+or both \np{ln_traldf_hor}{ln\_traldf\_hor}\forcode{=.true.} and \np{ln_zco}{ln\_zco}\forcode{=.true.}.
 The way these slopes are evaluated is given in \autoref{sec:LDF_slp}.
 At the surface, bottom and lateral boundaries, the turbulent fluxes of heat and salt are set to zero using
 …
 any additional background horizontal diffusion \citep{guilyardi.madec.ea_CD01}.
 Note that in the partial step $z$-coordinate (\np{ln\_zps}\forcode{=.true.}),
+Note that in the partial step $z$-coordinate (\np{ln_zps}{ln\_zps}\forcode{=.true.}),
 the horizontal derivatives at the bottom level in \autoref{eq:TRA_ldf_iso} require a specific treatment.
 They are calculated in module zpshde, described in \autoref{sec:TRA_zpshde}.
 …
 %&&     Triad rotated (bi-)laplacian operator
 %&&  -------------------------------------------
 \subsubsection[Triad rotated (bi-)laplacian operator (\forcode{ln_traldf_triad})]{Triad rotated (bi-)laplacian operator (\protect\np{ln\_traldf\_triad})}
+\subsubsection[Triad rotated (bi-)laplacian operator (\forcode{ln_traldf_triad})]{Triad rotated (bi-)laplacian operator (\protect\np{ln_traldf_triad}{ln\_traldf\_triad})}
 \label{subsec:TRA_ldf_triad}
 An alternative scheme developed by \cite{griffies.gnanadesikan.ea_JPO98} which ensures tracer variance decreases
 is also available in \NEMO\ (\np{ln\_traldf\_triad}\forcode{=.true.}).
+is also available in \NEMO\ (\np{ln_traldf_triad}{ln\_traldf\_triad}\forcode{=.true.}).
 A complete description of the algorithm is given in \autoref{apdx:TRIADS}.
 …
 \begin{itemize}
 \item \np{ln\_traldf\_msc} = Method of Stabilizing Correction (both operators)
 \item \np{rn\_slpmax} = slope limit (both operators)
 \item \np{ln\_triad\_iso} = pure horizontal mixing in ML (triad only)
 \item \np{rn\_sw\_triad} $= 1$ switching triad; $= 0$ all 4 triads used (triad only)
 \item \np{ln\_botmix\_triad} = lateral mixing on bottom (triad only)
+\item \np{ln_traldf_msc}{ln\_traldf\_msc} = Method of Stabilizing Correction (both operators)
+\item \np{rn_slpmax}{rn\_slpmax} = slope limit (both operators)
+\item \np{ln_triad_iso}{ln\_triad\_iso} = pure horizontal mixing in ML (triad only)
+\item \np{rn_sw_triad}{rn\_sw\_triad} $= 1$ switching triad; $= 0$ all 4 triads used (triad only)
+\item \np{ln_botmix_triad}{ln\_botmix\_triad} = lateral mixing on bottom (triad only)
 \end{itemize}
 …
 respectively.
 Generally, $A_w^{vT} = A_w^{vS}$ except when double diffusive mixing is parameterised
 (\ie\ \np{ln\_zdfddm}\forcode{=.true.},).
+(\ie\ \np{ln_zdfddm}{ln\_zdfddm}\forcode{=.true.},).
 The way these coefficients are evaluated is given in \autoref{chap:ZDF} (ZDF).
 Furthermore, when iso-neutral mixing is used, both mixing coefficients are increased by
 …
 Such time averaging prevents the divergence of odd and even time step (see \autoref{chap:TD}).
 In the linear free surface case (\np{ln\_linssh}\forcode{=.true.}), an additional term has to be added on
+In the linear free surface case (\np{ln_linssh}{ln\_linssh}\forcode{=.true.}), an additional term has to be added on
 both temperature and salinity.
 On temperature, this term remove the heat content associated with mass exchange that has been added to $Q_{ns}$.
 …
 %--------------------------------------------------------------------------------------------------------------
 Options are defined through the \nam{tra\_qsr} namelist variables.
 When the penetrative solar radiation option is used (\np{ln\_traqsr}\forcode{=.true.}),
+Options are defined through the \nam{tra_qsr}{tra\_qsr} namelist variables.
+When the penetrative solar radiation option is used (\np{ln_traqsr}{ln\_traqsr}\forcode{=.true.}),
 the solar radiation penetrates the top few tens of meters of the ocean.
 If it is not used (\np{ln\_traqsr}\forcode{=.false.}) all the heat flux is absorbed in the first ocean level.
+If it is not used (\np{ln_traqsr}{ln\_traqsr}\forcode{=.false.}) all the heat flux is absorbed in the first ocean level.
 Thus, in the former case a term is added to the time evolution equation of temperature \autoref{eq:MB_PE_tra_T} and
 the surface boundary condition is modified to take into account only the non-penetrative part of the surface
 …
 heating the upper few tens of centimetres.
 The fraction of $Q_{sr}$ that resides in these almost non-penetrative wavebands, $R$, is $\sim 58\%$
 (specified through namelist parameter \np{rn\_abs}).
+(specified through namelist parameter \np{rn_abs}{rn\_abs}).
 It is assumed to penetrate the ocean with a decreasing exponential profile, with an e-folding depth scale, $\xi_0$,
 of a few tens of centimetres (typically $\xi_0 = 0.35~m$ set as \np{rn\_si0} in the \nam{tra\_qsr} namelist).
+of a few tens of centimetres (typically $\xi_0 = 0.35~m$ set as \np{rn_si0}{rn\_si0} in the \nam{tra_qsr}{tra\_qsr} namelist).
 For shorter wavelengths (400-700~nm), the ocean is more transparent, and solar energy propagates to
 larger depths where it contributes to local heating.
 The way this second part of the solar energy penetrates into the ocean depends on which formulation is chosen.
 In the simple 2-waveband light penetration scheme (\np{ln\_qsr\_2bd}\forcode{=.true.})
+In the simple 2-waveband light penetration scheme (\np{ln_qsr_2bd}{ln\_qsr\_2bd}\forcode{=.true.})
 a chlorophyll-independent monochromatic formulation is chosen for the shorter wavelengths,
 leading to the following expression \citep{paulson.simpson_JPO77}:
 …
 \]
 where $\xi_1$ is the second extinction length scale associated with the shorter wavelengths.
 It is usually chosen to be 23~m by setting the \np{rn\_si0} namelist parameter.
+It is usually chosen to be 23~m by setting the \np{rn_si0}{rn\_si0} namelist parameter.
 The set of default values ($\xi_0, \xi_1, R$) corresponds to a Type I water in Jerlov's (1968) classification
 (oligotrophic waters).
 …
 The 2-bands formulation does not reproduce the full model very well.
 The RGB formulation is used when \np{ln\_qsr\_rgb}\forcode{=.true.}.
+The RGB formulation is used when \np{ln_qsr_rgb}{ln\_qsr\_rgb}\forcode{=.true.}.
 The RGB attenuation coefficients (\ie\ the inverses of the extinction length scales) are tabulated over
 nonuniform chlorophyll classes ranging from 0.01 to 10 g.Chl/L
 …
 \begin{description}
 \item[\np{nn\_chldta}\forcode{=0}]
+\item[\np{nn_chldta}{nn\_chldta}\forcode{=0}]
   a constant 0.05 g.Chl/L value everywhere ;
 \item[\np{nn\_chldta}\forcode{=1}]
+\item[\np{nn_chldta}{nn\_chldta}\forcode{=1}]
   an observed time varying chlorophyll deduced from satellite surface ocean color measurement spread uniformly in
   the vertical direction;
 \item[\np{nn\_chldta}\forcode{=2}]
+\item[\np{nn_chldta}{nn\_chldta}\forcode{=2}]
   same as previous case except that a vertical profile of chlorophyl is used.
   Following \cite{morel.berthon_LO89}, the profile is computed from the local surface chlorophyll value;
 \item[\np{ln\_qsr\_bio}\forcode{=.true.}]
+\item[\np{ln_qsr_bio}{ln\_qsr\_bio}\forcode{=.true.}]
   simulated time varying chlorophyll by TOP biogeochemical model.
   In this case, the RGB formulation is used to calculate both the phytoplankton light limitation in
 …
 %        Bottom Boundary Condition
 % -------------------------------------------------------------------------------------------------------------
 \subsection[Bottom boundary condition (\textit{trabbc.F90}) - \forcode{ln_trabbc})]{Bottom boundary condition (\protect\mdl{trabbc} - \protect\np{ln\_trabbc})}
+\subsection[Bottom boundary condition (\textit{trabbc.F90}) - \forcode{ln_trabbc})]{Bottom boundary condition (\protect\mdl{trabbc} - \protect\np{ln_trabbc}{ln\_trabbc})}
 \label{subsec:TRA_bbc}
 %--------------------------------------------nambbc--------------------------------------------------------
 …
 Options are defined through the \nam{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, a constant geothermal heating is introduced whose value is given by
 the \np{rn\_geoflx\_cst}, which is also a namelist parameter.
 When \np{nn\_geoflx} is set to 2, a spatially varying geothermal heat flux is introduced which is provided in
+The presence of geothermal heating is controlled by setting the namelist parameter \np{ln_trabbc}{ln\_trabbc} to true.
+Then, when \np{nn_geoflx}{nn\_geoflx} is set to 1, a constant geothermal heating is introduced whose value is given by
+the \np{rn_geoflx_cst}{rn\_geoflx\_cst}, which is also a namelist parameter.
+When \np{nn_geoflx}{nn\_geoflx} is set to 2, a spatially varying geothermal heat flux is introduced which is provided in
 the \ifile{geothermal\_heating} NetCDF file (\autoref{fig:TRA_geothermal}) \citep{emile-geay.madec_OS09}.
 …
 % Bottom Boundary Layer
 % ================================================================
 \section[Bottom boundary layer (\textit{trabbl.F90} - \forcode{ln_trabbl})]{Bottom boundary layer (\protect\mdl{trabbl} - \protect\np{ln\_trabbl})}
+\section[Bottom boundary layer (\textit{trabbl.F90} - \forcode{ln_trabbl})]{Bottom boundary layer (\protect\mdl{trabbl} - \protect\np{ln_trabbl}{ln\_trabbl})}
 \label{sec:TRA_bbl}
 %--------------------------------------------nambbl---------------------------------------------------------
 …
 %        Diffusive BBL
 % -------------------------------------------------------------------------------------------------------------
 \subsection[Diffusive bottom boundary layer (\forcode{nn_bbl_ldf=1})]{Diffusive bottom boundary layer (\protect\np{nn\_bbl\_ldf}\forcode{=1})}
+\subsection[Diffusive bottom boundary layer (\forcode{nn_bbl_ldf=1})]{Diffusive bottom boundary layer (\protect\np{nn_bbl_ldf}{nn\_bbl\_ldf}\forcode{=1})}
 \label{subsec:TRA_bbl_diff}
 When applying sigma-diffusion (\np{ln\_trabbl}\forcode{=.true.} and \np{nn\_bbl\_ldf} set to 1),
+When applying sigma-diffusion (\np{ln_trabbl}{ln\_trabbl}\forcode{=.true.} and \np{nn_bbl_ldf}{nn\_bbl\_ldf} set to 1),
 the diffusive flux between two adjacent cells at the ocean floor is given by
 \[
 …
       \end{cases}
 \end{equation}
 where $A_{bbl}$ is the BBL diffusivity coefficient, given by the namelist parameter \np{rn\_ahtbbl} and
+where $A_{bbl}$ is the BBL diffusivity coefficient, given by the namelist parameter \np{rn_ahtbbl}{rn\_ahtbbl} and
 usually set to a value much larger than the one used for lateral mixing in the open ocean.
 The constraint in \autoref{eq:TRA_bbl_coef} implies that sigma-like diffusion only occurs when
 …
 %        Advective BBL
 % -------------------------------------------------------------------------------------------------------------
 \subsection[Advective bottom boundary layer (\forcode{nn_bbl_adv=1,2})]{Advective bottom boundary layer (\protect\np{nn\_bbl\_adv}\forcode{=1,2})}
+\subsection[Advective bottom boundary layer (\forcode{nn_bbl_adv=1,2})]{Advective bottom boundary layer (\protect\np{nn_bbl_adv}{nn\_bbl\_adv}\forcode{=1,2})}
 \label{subsec:TRA_bbl_adv}
 …
 %%%gmcomment   :  this section has to be really written
 When applying an advective BBL (\np{nn\_bbl\_adv}\forcode{=1..2}), an overturning circulation is added which
+When applying an advective BBL (\np{nn_bbl_adv}{nn\_bbl\_adv}\forcode{=1..2}), an overturning circulation is added which
 connects two adjacent bottom grid-points only if dense water overlies less dense water on the slope.
 The density difference causes dense water to move down the slope.
 \np{nn\_bbl\_adv}\forcode{=1}:
+\np{nn_bbl_adv}{nn\_bbl\_adv}\forcode{=1}:
 the downslope velocity is chosen to be the Eulerian ocean velocity just above the topographic step
 (see black arrow in \autoref{fig:TRA_bbl}) \citep{beckmann.doscher_JPO97}.
 …
 if the velocity is directed towards greater depth (\ie\ $\vect U \cdot \nabla H > 0$).
 \np{nn\_bbl\_adv}\forcode{=2}:
+\np{nn_bbl_adv}{nn\_bbl\_adv}\forcode{=2}:
 the downslope velocity is chosen to be proportional to $\Delta \rho$,
 the density difference between the higher cell and lower cell densities \citep{campin.goosse_T99}.
 …
   u^{tr}_{bbl} = \gamma g \frac{\Delta \rho}{\rho_o} e_{1u} \, min ({e_{3u}}_{kup},{e_{3u}}_{kdwn})
 \]
 where $\gamma$, expressed in seconds, is the coefficient of proportionality provided as \np{rn\_gambbl},
+where $\gamma$, expressed in seconds, is the coefficient of proportionality provided as \np{rn_gambbl}{rn\_gambbl},
 a namelist parameter, and \textit{kup} and \textit{kdwn} are the vertical index of the higher and lower cells,
 respectively.
 …
 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  \nam{tra\_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\_dmp} are set to true in
 \nam{tsd} namelist as well as \np{sn\_tem} and \np{sn\_sal} structures are correctly set
+Options are defined through the  \nam{tra_dmp}{tra\_dmp} namelist variables.
+The restoring term is added when the namelist parameter \np{ln_tradmp}{ln\_tradmp} is set to true.
+It also requires that both \np{ln_tsd_init}{ln\_tsd\_init} and \np{ln_tsd_dmp}{ln\_tsd\_dmp} are set to true in
+\nam{tsd} namelist as well as \np{sn_tem}{sn\_tem} and \np{sn_sal}{sn\_sal} structures are correctly set
 (\ie\ that $T_o$ and $S_o$ are provided in input files and read using \mdl{fldread},
 see \autoref{subsec:SBC_fldread}).
 The restoring coefficient $\gamma$ is a three-dimensional array read in during the \rou{tra\_dmp\_init} routine.
 The file name is specified by the namelist variable \np{cn\_resto}.
+The file name is specified by the namelist variable \np{cn_resto}{cn\_resto}.
 The DMP\_TOOLS tool is provided to allow users to generate the netcdf file.
 …
 It tends to prevent deep convection and subsequent deep-water formation, by stabilising the water column too much.
 The namelist parameter \np{nn\_zdmp} sets whether the damping should be applied in the whole water column or
+The namelist parameter \np{nn_zdmp}{nn\_zdmp} sets whether the damping should be applied in the whole water column or
 only below the mixed layer (defined either on a density or $S_o$ criterion).
 It is common to set the damping to zero in the mixed layer as the adjustment time scale is short here
 …
 $\gamma$ is the Asselin coefficient, and $S$ is the total forcing applied on $T$
 (\ie\ fluxes plus content in mass exchanges).
 $\gamma$ is initialized as \np{rn\_atfp} (\textbf{namelist} parameter).
 Its default value is \np{rn\_atfp}\forcode{=10.e-3}.
+$\gamma$ is initialized as \np{rn_atfp}{rn\_atfp} (\textbf{namelist} parameter).
+Its default value is \np{rn_atfp}{rn\_atfp}\forcode{=10.e-3}.
 Note that the forcing correction term in the filter is not applied in linear free surface
 (\jp{ln\_linssh}\forcode{=.true.}) (see \autoref{subsec:TRA_sbc}).
 …
 %        Equation of State
 % -------------------------------------------------------------------------------------------------------------
 \subsection[Equation of seawater (\forcode{ln_}\{\forcode{teos10,eos80,seos}\})]{Equation of seawater (\protect\np{ln\_teos10}, \protect\np{ln\_teos80}, or \protect\np{ln\_seos})}
+\subsection[Equation of seawater (\forcode{ln_}\{\forcode{teos10,eos80,seos}\})]{Equation of seawater (\protect\np{ln_teos10}{ln\_teos10}, \protect\np{ln_teos80}{ln\_teos80}, or \protect\np{ln_seos}{ln\_seos})}
 \label{subsec:TRA_eos}
 …
 \begin{description}
 \item[\np{ln\_teos10}\forcode{=.true.}]
+\item[\np{ln_teos10}{ln\_teos10}\forcode{=.true.}]
   the polyTEOS10-bsq equation of seawater \citep{roquet.madec.ea_OM15} is used.
   The accuracy of this approximation is comparable to the TEOS-10 rational function approximation,
 …
   either computing the air-sea and ice-sea fluxes (forced mode) or
   sending the SST field to the atmosphere (coupled mode).
 \item[\np{ln\_eos80}\forcode{=.true.}]
+\item[\np{ln_eos80}{ln\_eos80}\forcode{=.true.}]
   the polyEOS80-bsq equation of seawater is used.
   It takes the same polynomial form as the polyTEOS10, but the coefficients have been optimized to
 …
   Nevertheless, a severe assumption is made in order to have a heat content ($C_p T_p$) which
   is conserved by the model: $C_p$ is set to a constant value, the TEOS10 value.
 \item[\np{ln\_seos}\forcode{=.true.}]
+\item[\np{ln_seos}{ln\_seos}\forcode{=.true.}]
   a simplified EOS (S-EOS) inspired by \citet{vallis_bk06} is chosen,
   the coefficients of which has been optimized to fit the behavior of TEOS10
 …
     coeff.     & computer name   & S-EOS           & description                      \\
     \hline
     $a_0$       & \np{rn\_a0}     & $1.6550~10^{-1}$ & linear thermal expansion coeff. \\
+    $a_0$       & \np{rn_a0}{rn\_a0}     & $1.6550~10^{-1}$ & linear thermal expansion coeff. \\
     \hline
     $b_0$         & \np{rn\_b0}     & $7.6554~10^{-1}$ & linear haline  expansion coeff. \\
+    $b_0$         & \np{rn_b0}{rn\_b0}       & $7.6554~10^{-1}$ & linear haline  expansion coeff. \\
     \hline
     $\lambda_1$   & \np{rn\_lambda1}& $5.9520~10^{-2}$ & cabbeling coeff. in $T^2$       \\
+    $\lambda_1$   & \np{rn_lambda1}{rn\_lambda1}& $5.9520~10^{-2}$ & cabbeling coeff. in $T^2$       \\
     \hline
     $\lambda_2$   & \np{rn\_lambda2}& $5.4914~10^{-4}$ & cabbeling coeff. in $S^2$       \\
+    $\lambda_2$   & \np{rn_lambda2}{rn\_lambda2}& $5.4914~10^{-4}$ & cabbeling coeff. in $S^2$       \\
     \hline
     $\nu$       & \np{rn\_nu}     & $2.4341~10^{-3}$ & cabbeling coeff. in $T \, S$      \\
+    $\nu$       & \np{rn_nu}{rn\_nu}     & $2.4341~10^{-3}$ & cabbeling coeff. in $T \, S$     \\
     \hline
     $\mu_1$     & \np{rn\_mu1}   & $1.4970~10^{-4}$ & thermobaric coeff. in T         \\
+    $\mu_1$     & \np{rn_mu1}{rn\_mu1}    & $1.4970~10^{-4}$ & thermobaric coeff. in T         \\
     \hline
     $\mu_2$     & \np{rn\_mu2}   & $1.1090~10^{-5}$ & thermobaric coeff. in S         \\
+    $\mu_2$     & \np{rn_mu2}{rn\_mu2}    & $1.1090~10^{-5}$ & thermobaric coeff. in S         \\
     \hline
   \end{tabular}
 …
 I've changed "derivative" to "difference" and "mean" to "average"}
 With partial cells (\np{ln\_zps}\forcode{=.true.}) at bottom and top (\np{ln\_isfcav}\forcode{=.true.}),
+With partial cells (\np{ln_zps}{ln\_zps}\forcode{=.true.}) at bottom and top (\np{ln_isfcav}{ln\_isfcav}\forcode{=.true.}),
 in general, tracers in horizontally adjacent cells live at different depths.
 Horizontal gradients of tracers are needed for horizontal diffusion (\mdl{traldf} module) and
 the hydrostatic pressure gradient calculations (\mdl{dynhpg} module).
 The partial cell properties at the top (\np{ln\_isfcav}\forcode{=.true.}) are computed in the same way as
+The partial cell properties at the top (\np{ln_isfcav}{ln\_isfcav}\forcode{=.true.}) are computed in the same way as
 for the bottom.
 So, only the bottom interpolation is explained below.
 …
   the $z$-partial step coordinate]{
     Discretisation of the horizontal difference and average of tracers in
     the $z$-partial step coordinate (\protect\np{ln\_zps}\forcode{=.true.}) in
+    the $z$-partial step coordinate (\protect\np{ln_zps}{ln\_zps}\forcode{=.true.}) in
     the case $(e3w_k^{i + 1} - e3w_k^i) > 0$.
     A linear interpolation is used to estimate $\widetilde T_k^{i + 1}$,

NEMO/trunk/doc/latex/NEMO/subfiles/chap_ZDF.tex

-                      r11571
+                      r11577
 At the surface they are prescribed from the surface forcing (see \autoref{chap:SBC}),
 while at the bottom they are set to zero for heat and salt,
 unless a geothermal flux forcing is prescribed as a bottom boundary condition (\ie\ \np{ln\_trabbc} defined,
+unless a geothermal flux forcing is prescribed as a bottom boundary condition (\ie\ \np{ln_trabbc}{ln\_trabbc} defined,
 see \autoref{subsec:TRA_bbc}), and specified through a bottom friction parameterisation for momentum
 (see \autoref{sec:ZDF_drg}).
 …
 are computed and added to the general trend in the \mdl{dynzdf} and \mdl{trazdf} modules, respectively.
 %These trends can be computed using either a forward time stepping scheme
 %(namelist parameter \np{ln\_zdfexp}\forcode{=.true.}) or a backward time stepping scheme
 %(\np{ln\_zdfexp}\forcode{=.false.}) depending on the magnitude of the mixing coefficients,
+%(namelist parameter \np{ln_zdfexp}{ln\_zdfexp}\forcode{=.true.}) or a backward time stepping scheme
+%(\np{ln_zdfexp}{ln\_zdfexp}\forcode{=.false.}) depending on the magnitude of the mixing coefficients,
 %and thus of the formulation used (see \autoref{chap:TD}).
 …
 %        Constant
 % -------------------------------------------------------------------------------------------------------------
 \subsection[Constant (\forcode{ln_zdfcst})]{Constant (\protect\np{ln\_zdfcst})}
+\subsection[Constant (\forcode{ln_zdfcst})]{Constant (\protect\np{ln_zdfcst}{ln\_zdfcst})}
 \label{subsec:ZDF_cst}
 Options are defined through the \nam{zdf} namelist variables.
 When \np{ln\_zdfcst} is defined, the momentum and tracer vertical eddy coefficients are set to
+When \np{ln_zdfcst}{ln\_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 the vertical ocean physics.
 …
 \end{align*}
 These values are set through the \np{rn\_avm0} and \np{rn\_avt0} namelist parameters.
+These values are set through the \np{rn_avm0}{rn\_avm0} and \np{rn_avt0}{rn\_avt0} namelist parameters.
 In all cases, do not use values smaller that those associated with the molecular viscosity and diffusivity,
 that is $\sim10^{-6}~m^2.s^{-1}$ for momentum, $\sim10^{-7}~m^2.s^{-1}$ for temperature and
 …
 %        Richardson Number Dependent
 % -------------------------------------------------------------------------------------------------------------
 \subsection[Richardson number dependent (\forcode{ln_zdfric})]{Richardson number dependent (\protect\np{ln\_zdfric})}
+\subsection[Richardson number dependent (\forcode{ln_zdfric})]{Richardson number dependent (\protect\np{ln_zdfric}{ln\_zdfric})}
 \label{subsec:ZDF_ric}
 …
 %--------------------------------------------------------------------------------------------------------------
 When \np{ln\_zdfric}\forcode{=.true.}, a local Richardson number dependent formulation for the vertical momentum and
 tracer eddy coefficients is set through the \nam{zdf\_ric} namelist variables.
+When \np{ln_zdfric}{ln\_zdfric}\forcode{=.true.}, a local Richardson number dependent formulation for the vertical momentum and
+tracer eddy coefficients is set through the \nam{zdf_ric}{zdf\_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 large scale ocean structures.
 …
 (see \autoref{subsec:ZDF_cst}), and $A_{ric}^{vT} = 10^{-4}~m^2.s^{-1}$ is the maximum value that
 can be reached by the coefficient when $Ri\leq 0$, $a=5$ and $n=2$.
 The last three values can be modified by setting the \np{rn\_avmri}, \np{rn\_alp} and
 \np{nn\_ric} namelist parameters, respectively.
+The last three values can be modified by setting the \np{rn_avmri}{rn\_avmri}, \np{rn_alp}{rn\_alp} and
+\np{nn_ric}{nn\_ric} namelist parameters, respectively.
 A simple mixing-layer model to transfer and dissipate the atmospheric forcings
 (wind-stress and buoyancy fluxes) can be activated setting the \np{ln\_mldw}\forcode{=.true.} in the namelist.
+(wind-stress and buoyancy fluxes) can be activated setting the \np{ln_mldw}{ln\_mldw}\forcode{=.true.} in the namelist.
 In this case, the local depth of turbulent wind-mixing or "Ekman depth" $h_{e}(x,y,t)$ is evaluated and
 …
 \]
 is computed from the wind stress vector $|\tau|$ and the reference density $ \rho_o$.
 The final $h_{e}$ is further constrained by the adjustable bounds \np{rn\_mldmin} and \np{rn\_mldmax}.
+The final $h_{e}$ is further constrained by the adjustable bounds \np{rn_mldmin}{rn\_mldmin} and \np{rn_mldmax}{rn\_mldmax}.
 Once $h_{e}$ is computed, the vertical eddy coefficients within $h_{e}$ are set to
 the empirical values \np{rn\_wtmix} and \np{rn\_wvmix} \citep{lermusiaux_JMS01}.
+the empirical values \np{rn_wtmix}{rn\_wtmix} and \np{rn_wvmix}{rn\_wvmix} \citep{lermusiaux_JMS01}.
 % -------------------------------------------------------------------------------------------------------------
 %        TKE Turbulent Closure Scheme
 % -------------------------------------------------------------------------------------------------------------
 \subsection[TKE turbulent closure scheme (\forcode{ln_zdftke})]{TKE turbulent closure scheme (\protect\np{ln\_zdftke})}
+\subsection[TKE turbulent closure scheme (\forcode{ln_zdftke})]{TKE turbulent closure scheme (\protect\np{ln_zdftke}{ln\_zdftke})}
 \label{subsec:ZDF_tke}
 %--------------------------------------------namzdf_tke--------------------------------------------------
 …
 The constants $C_k =  0.1$ and $C_\epsilon = \sqrt {2} /2$ $\approx 0.7$ are designed to deal with
 vertical mixing at any depth \citep{gaspar.gregoris.ea_JGR90}.
 They are set through namelist parameters \np{nn\_ediff} and \np{nn\_ediss}.
+They are set through namelist parameters \np{nn_ediff}{nn\_ediff} and \np{nn_ediss}{nn\_ediss}.
 $P_{rt}$ can be set to unity or, following \citet{blanke.delecluse_JPO93}, be a function of the local Richardson number, $R_i$:
 \begin{align*}
 …
   \end{cases}
 \end{align*}
 The choice of $P_{rt}$ is controlled by the \np{nn\_pdl} namelist variable.
+The choice of $P_{rt}$ is controlled by the \np{nn_pdl}{nn\_pdl} namelist variable.
 At the sea surface, the value of $\bar{e}$ is prescribed from the wind stress field as
 $\bar{e}_o = e_{bb} |\tau| / \rho_o$, with $e_{bb}$ the \np{rn\_ebb} namelist parameter.
+$\bar{e}_o = e_{bb} |\tau| / \rho_o$, with $e_{bb}$ the \np{rn_ebb}{rn\_ebb} namelist parameter.
 The default value of $e_{bb}$ is 3.75. \citep{gaspar.gregoris.ea_JGR90}), however a much larger value can be used when
 taking into account the surface wave breaking (see below Eq. \autoref{eq:ZDF_Esbc}).
 …
 The time integration of the $\bar{e}$ equation may formally lead to negative values because
 the numerical scheme does not ensure its positivity.
 To overcome this problem, a cut-off in the minimum value of $\bar{e}$ is used (\np{rn\_emin} namelist parameter).
+To overcome this problem, a cut-off in the minimum value of $\bar{e}$ is used (\np{rn_emin}{rn\_emin} namelist parameter).
 Following \citet{gaspar.gregoris.ea_JGR90}, the cut-off value is set to $\sqrt{2}/2~10^{-6}~m^2.s^{-2}$.
 This allows the subsequent formulations to match that of \citet{gargett_JMR84} for the diffusion in
 …
 In addition, a cut-off is applied on $K_m$ and $K_\rho$ to avoid numerical instabilities associated with
 too weak vertical diffusion.
 They must be specified at least larger than the molecular values, and are set through \np{rn\_avm0} and
 \np{rn\_avt0} (\nam{zdf} namelist, see \autoref{subsec:ZDF_cst}).
+They must be specified at least larger than the molecular values, and are set through \np{rn_avm0}{rn\_avm0} and
+\np{rn_avt0}{rn\_avt0} (\nam{zdf} namelist, see \autoref{subsec:ZDF_cst}).
 \subsubsection{Turbulent length scale}
 …
 For computational efficiency, the original formulation of the turbulent length scales proposed by
 \citet{gaspar.gregoris.ea_JGR90} has been simplified.
 Four formulations are proposed, the choice of which is controlled by the \np{nn\_mxl} namelist parameter.
+Four formulations are proposed, the choice of which is controlled by the \np{nn_mxl}{nn\_mxl} namelist parameter.
 The first two are based on the following first order approximation \citep{blanke.delecluse_JPO93}:
 \begin{equation}
 …
 which is valid in a stable stratified region with constant values of the Brunt-Vais\"{a}l\"{a} frequency.
 The resulting length scale is bounded by the distance to the surface or to the bottom
 (\np{nn\_mxl}\forcode{=0}) or by the local vertical scale factor (\np{nn\_mxl}\forcode{=1}).
+(\np{nn_mxl}{nn\_mxl}\forcode{=0}) or by the local vertical scale factor (\np{nn\_mxl}\forcode{=1}).
 \citet{blanke.delecluse_JPO93} notice that this simplification has two major drawbacks:
 it makes no sense for locally unstable stratification and the computation no longer uses all
 the information contained in the vertical density profile.
 To overcome these drawbacks, \citet{madec.delecluse.ea_NPM98} introduces the \np{nn\_mxl}\forcode{=2, 3} cases,
+To overcome these drawbacks, \citet{madec.delecluse.ea_NPM98} introduces the \np{nn_mxl}{nn\_mxl}\forcode{=2, 3} cases,
 which add an extra assumption concerning the vertical gradient of the computed length scale.
 So, the length scales are first evaluated as in \autoref{eq:ZDF_tke_mxl0_1} and then bounded such that:
 …
 where $l^{(k)}$ is computed using \autoref{eq:ZDF_tke_mxl0_1}, \ie\ $l^{(k)} = \sqrt {2 {\bar e}^{(k)} / {N^2}^{(k)} }$.
 In the \np{nn\_mxl}\forcode{=2} case, the dissipation and mixing length scales take the same value:
 $ l_k=  l_\epsilon = \min \left(\ l_{up} \;,\;  l_{dwn}\ \right)$, while in the \np{nn\_mxl}\forcode{=3} case,
+In the \np{nn_mxl}{nn\_mxl}\forcode{=2} case, the dissipation and mixing length scales take the same value:
+$ l_k=  l_\epsilon = \min \left(\ l_{up} \;,\;  l_{dwn}\ \right)$, while in the \np{nn_mxl}{nn\_mxl}\forcode{=3} case,
 the dissipation and mixing turbulent length scales are give as in \citet{gaspar.gregoris.ea_JGR90}:
 \[
 …
 \]
 At the ocean surface, a non zero length scale is set through the  \np{rn\_mxl0} namelist parameter.
+At the ocean surface, a non zero length scale is set through the  \np{rn_mxl0}{rn\_mxl0} namelist parameter.
 Usually the surface scale is given by $l_o = \kappa \,z_o$ where $\kappa = 0.4$ is von Karman's constant and
 $z_o$ the roughness parameter of the surface.
 Assuming $z_o=0.1$~m \citep{craig.banner_JPO94} leads to a 0.04~m, the default value of \np{rn\_mxl0}.
+Assuming $z_o=0.1$~m \citep{craig.banner_JPO94} leads to a 0.04~m, the default value of \np{rn_mxl0}{rn\_mxl0}.
 In the ocean interior a minimum length scale is set to recover the molecular viscosity when
 $\bar{e}$ reach its minimum value ($1.10^{-6}= C_k\, l_{min} \,\sqrt{\bar{e}_{min}}$ ).
 …
 $\alpha_{CB} = 100$ the Craig and Banner's value.
 As the surface boundary condition on TKE is prescribed through $\bar{e}_o = e_{bb} |\tau| / \rho_o$,
 with $e_{bb}$ the \np{rn\_ebb} namelist parameter, setting \np{rn\_ebb}\forcode{ = 67.83} corresponds
+with $e_{bb}$ the \np{rn_ebb}{rn\_ebb} namelist parameter, setting \np{rn\_ebb}\forcode{ = 67.83} corresponds
 to $\alpha_{CB} = 100$.
 Further setting  \np{ln\_mxl0}\forcode{ =.true.},  applies \autoref{eq:ZDF_Lsbc} as the surface boundary condition on the length scale,
+Further setting  \np{ln_mxl0}{ln\_mxl0}\forcode{ =.true.},  applies \autoref{eq:ZDF_Lsbc} as the surface boundary condition on the length scale,
 with $\beta$ hard coded to the Stacey's value.
 Note that a minimal threshold of \np{rn\_emin0}$=10^{-4}~m^2.s^{-2}$ (namelist parameters) is applied on the
+Note that a minimal threshold of \np{rn_emin0}{rn\_emin0}$=10^{-4}~m^2.s^{-2}$ (namelist parameters) is applied on the
 surface $\bar{e}$ value.
 …
 The parameterization, tuned against large-eddy simulation, includes the whole effect of LC in
 an extra source term of TKE, $P_{LC}$.
 The presence of $P_{LC}$ in \autoref{eq:ZDF_tke_e}, the TKE equation, is controlled by setting \np{ln\_lc} to
 \forcode{.true.} in the \nam{zdf\_tke} namelist.
+The presence of $P_{LC}$ in \autoref{eq:ZDF_tke_e}, the TKE equation, is controlled by setting \np{ln_lc}{ln\_lc} to
+\forcode{.true.} in the \nam{zdf_tke}{zdf\_tke} namelist.
 By making an analogy with the characteristic convective velocity scale (\eg, \citet{dalessio.abdella.ea_JPO98}),
 …
 where $c_{LC} = 0.15$ has been chosen by \citep{axell_JGR02} as a good compromise to fit LES data.
 The chosen value yields maximum vertical velocities $w_{LC}$ of the order of a few centimeters per second.
 The value of $c_{LC}$ is set through the \np{rn\_lc} namelist parameter,
+The value of $c_{LC}$ is set through the \np{rn_lc}{rn\_lc} namelist parameter,
 having in mind that it should stay between 0.15 and 0.54 \citep{axell_JGR02}.
 …
 (\ie\ near-inertial oscillations and ocean swells and waves).
 When using this parameterization (\ie\ when \np{nn\_etau}\forcode{=1}),
+When using this parameterization (\ie\ when \np{nn_etau}{nn\_etau}\forcode{=1}),
 the TKE input to the ocean ($S$) imposed by the winds in the form of near-inertial oscillations,
 swell and waves is parameterized by \autoref{eq:ZDF_Esbc} the standard TKE surface boundary condition,
 …
 the penetration, and $f_i$ is the ice concentration
 (no penetration if $f_i=1$, \ie\ if the ocean is entirely covered by sea-ice).
 The value of $f_r$, usually a few percents, is specified through \np{rn\_efr} namelist parameter.
 The vertical mixing length scale, $h_\tau$, can be set as a 10~m uniform value (\np{nn\_etau}\forcode{=0}) or
+The value of $f_r$, usually a few percents, is specified through \np{rn_efr}{rn\_efr} namelist parameter.
+The vertical mixing length scale, $h_\tau$, can be set as a 10~m uniform value (\np{nn_etau}{nn\_etau}\forcode{=0}) or
 a latitude dependent value (varying from 0.5~m at the Equator to a maximum value of 30~m at high latitudes
 (\np{nn\_etau}\forcode{=1}).
 Note that two other option exist, \np{nn\_etau}\forcode{=2, 3}.
+(\np{nn_etau}{nn\_etau}\forcode{=1}).
+Note that two other option exist, \np{nn_etau}{nn\_etau}\forcode{=2, 3}.
 They correspond to applying \autoref{eq:ZDF_Ehtau} only at the base of the mixed layer,
 or to using the high frequency part of the stress to evaluate the fraction of TKE that penetrates the ocean.
 …
 % This should be explain better below what this rn_eice parameter is meant for:
 In presence of Sea Ice, the value of this mixing can be modulated by the \np{rn\_eice} namelist parameter.
+In presence of Sea Ice, the value of this mixing can be modulated by the \np{rn_eice}{rn\_eice} namelist parameter.
 This parameter varies from \forcode{0} for no effect to \forcode{4} to suppress the TKE input into the ocean when Sea Ice concentration
 is greater than 25\%.
 …
 %        GLS Generic Length Scale Scheme
 % -------------------------------------------------------------------------------------------------------------
 \subsection[GLS: Generic Length Scale (\forcode{ln_zdfgls})]{GLS: Generic Length Scale (\protect\np{ln\_zdfgls})}
+\subsection[GLS: Generic Length Scale (\forcode{ln_zdfgls})]{GLS: Generic Length Scale (\protect\np{ln_zdfgls}{ln\_zdfgls})}
 \label{subsec:ZDF_gls}
 …
 the choice of the turbulence model.
 Four different turbulent models are pre-defined (\autoref{tab:ZDF_GLS}).
 They are made available through the \np{nn\_clo} namelist parameter.
+They are made available through the \np{nn_clo}{nn\_clo} namelist parameter.
 %--------------------------------------------------TABLE--------------------------------------------------
 …
     \hline
     \hline
     \np{nn\_clo}     & \textbf{0} &   \textbf{1}  &   \textbf{2}   &    \textbf{3}   \\
+    \np{nn_clo}{nn\_clo}     & \textbf{0} &   \textbf{1}  &   \textbf{2}   &    \textbf{3}   \\
     \hline
     $( p , n , m )$         &   ( 0 , 1 , 1 )   & ( 3 , 1.5 , -1 )   & ( -1 , 0.5 , -1 )    &  ( 2 , 1 , -0.67 )  \\
 …
   \caption[Set of predefined GLS parameters or equivalently predefined turbulence models available]{
     Set of predefined GLS parameters, or equivalently predefined turbulence models available with
     \protect\np{ln\_zdfgls}\forcode{=.true.} and controlled by
     the \protect\np{nn\_clos} namelist variable in \protect\nam{zdf\_gls}.}
+    \protect\np{ln_zdfgls}{ln\_zdfgls}\forcode{=.true.} and controlled by
+    the \protect\np{nn_clos}{nn\_clos} namelist variable in \protect\nam{zdf_gls}{zdf\_gls}.}
   \label{tab:ZDF_GLS}
 \end{table}
 …
 $C_{\mu}$ and $C_{\mu'}$ are calculated from stability function proposed by \citet{galperin.kantha.ea_JAS88},
 or by \citet{kantha.clayson_JGR94} or one of the two functions suggested by \citet{canuto.howard.ea_JPO01}
 (\np{nn\_stab\_func}\forcode{=0, 3}, resp.).
+(\np{nn_stab_func}{nn\_stab\_func}\forcode{=0, 3}, resp.).
 The value of $C_{0\mu}$ depends on the choice of the stability function.
 The surface and bottom boundary condition on both $\bar{e}$ and $\psi$ can be calculated thanks to Dirichlet or
 Neumann condition through \np{nn\_bc\_surf} and \np{nn\_bc\_bot}, resp.
+Neumann condition through \np{nn_bc_surf}{nn\_bc\_surf} and \np{nn_bc_bot}{nn\_bc\_bot}, resp.
 As for TKE closure, the wave effect on the mixing is considered when
 \np{rn\_crban}\forcode{ > 0.} \citep{craig.banner_JPO94, mellor.blumberg_JPO04}.
 The \np{rn\_crban} namelist parameter is $\alpha_{CB}$ in \autoref{eq:ZDF_Esbc} and
 \np{rn\_charn} provides the value of $\beta$ in \autoref{eq:ZDF_Lsbc}.
+\np{rn_crban}{rn\_crban}\forcode{ > 0.} \citep{craig.banner_JPO94, mellor.blumberg_JPO04}.
+The \np{rn_crban}{rn\_crban} namelist parameter is $\alpha_{CB}$ in \autoref{eq:ZDF_Esbc} and
+\np{rn_charn}{rn\_charn} provides the value of $\beta$ in \autoref{eq:ZDF_Lsbc}.
 The $\psi$ equation is known to fail in stably stratified flows, and for this reason
 …
 the entrainment depth predicted in stably stratified situations,
 and that its value has to be chosen in accordance with the algebraic model for the turbulent fluxes.
 The clipping is only activated if \np{ln\_length\_lim}\forcode{=.true.},
 and the $c_{lim}$ is set to the \np{rn\_clim\_galp} value.
+The clipping is only activated if \np{ln_length_lim}{ln\_length\_lim}\forcode{=.true.},
+and the $c_{lim}$ is set to the \np{rn_clim_galp}{rn\_clim\_galp} value.
 The time and space discretization of the GLS equations follows the same energetic consideration as for
 …
 %        OSM OSMOSIS BL Scheme
 % -------------------------------------------------------------------------------------------------------------
 \subsection[OSM: OSMosis boundary layer scheme (\forcode{ln_zdfosm})]{OSM: OSMosis boundary layer scheme (\protect\np{ln\_zdfosm})}
+\subsection[OSM: OSMosis boundary layer scheme (\forcode{ln_zdfosm})]{OSM: OSMosis boundary layer scheme (\protect\np{ln_zdfosm}{ln\_zdfosm})}
 \label{subsec:ZDF_osm}
 %--------------------------------------------namzdf_osm---------------------------------------------------------
 …
 %       Non-Penetrative Convective Adjustment
 % -------------------------------------------------------------------------------------------------------------
 \subsection[Non-penetrative convective adjustment (\forcode{ln_tranpc})]{Non-penetrative convective adjustment (\protect\np{ln\_tranpc})}
+\subsection[Non-penetrative convective adjustment (\forcode{ln_tranpc})]{Non-penetrative convective adjustment (\protect\np{ln_tranpc}{ln\_tranpc})}
 \label{subsec:ZDF_npc}
 …
 Options are defined through the \nam{zdf} namelist variables.
 The non-penetrative convective adjustment is used when \np{ln\_zdfnpc}\forcode{=.true.}.
 It is applied at each \np{nn\_npc} time step and mixes downwards instantaneously the statically unstable portion of
+The non-penetrative convective adjustment is used when \np{ln_zdfnpc}{ln\_zdfnpc}\forcode{=.true.}.
+It is applied at each \np{nn_npc}{nn\_npc} time step and mixes downwards instantaneously the statically unstable portion of
 the water column, but only until the density structure becomes neutrally stable
 (\ie\ until the mixed portion of the water column has \textit{exactly} the density of the water just below)
 …
 %       Enhanced Vertical Diffusion
 % -------------------------------------------------------------------------------------------------------------
 \subsection[Enhanced vertical diffusion (\forcode{ln_zdfevd})]{Enhanced vertical diffusion (\protect\np{ln\_zdfevd})}
+\subsection[Enhanced vertical diffusion (\forcode{ln_zdfevd})]{Enhanced vertical diffusion (\protect\np{ln_zdfevd}{ln\_zdfevd})}
 \label{subsec:ZDF_evd}
 Options are defined through the  \nam{zdf} namelist variables.
 The enhanced vertical diffusion parameterisation is used when \np{ln\_zdfevd}\forcode{=.true.}.
+The enhanced vertical diffusion parameterisation is used when \np{ln_zdfevd}{ln\_zdfevd}\forcode{=.true.}.
 In this case, the vertical eddy mixing coefficients are assigned very large values
 in regions where the stratification is unstable
 (\ie\ when $N^2$ the Brunt-Vais\"{a}l\"{a} frequency is negative) \citep{lazar_phd97, lazar.madec.ea_JPO99}.
 This is done either on tracers only (\np{nn\_evdm}\forcode{=0}) or
 on both momentum and tracers (\np{nn\_evdm}\forcode{=1}).
 In practice, where $N^2\leq 10^{-12}$, $A_T^{vT}$ and $A_T^{vS}$, and if \np{nn\_evdm}\forcode{=1},
+This is done either on tracers only (\np{nn_evdm}{nn\_evdm}\forcode{=0}) or
+on both momentum and tracers (\np{nn_evdm}{nn\_evdm}\forcode{=1}).
+In practice, where $N^2\leq 10^{-12}$, $A_T^{vT}$ and $A_T^{vS}$, and if \np{nn_evdm}{nn\_evdm}\forcode{=1},
 the four neighbouring $A_u^{vm} \;\mbox{and}\;A_v^{vm}$ values also, are set equal to
 the namelist parameter \np{rn\_avevd}.
+the namelist parameter \np{rn_avevd}{rn\_avevd}.
 A typical value for $rn\_avevd$ is between 1 and $100~m^2.s^{-1}$.
 This parameterisation of convective processes is less time consuming than
 …
 The turbulent closure schemes presented in \autoref{subsec:ZDF_tke}, \autoref{subsec:ZDF_gls} and
 \autoref{subsec:ZDF_osm} (\ie\ \np{ln\_zdftke} or \np{ln\_zdfgls} or \np{ln\_zdfosm} defined) deal, in theory,
+\autoref{subsec:ZDF_osm} (\ie\ \np{ln_zdftke}{ln\_zdftke} or \np{ln_zdfgls}{ln\_zdfgls} or \np{ln_zdfosm}{ln\_zdfosm} defined) deal, in theory,
 with statically unstable density profiles.
 In such a case, the term corresponding to the destruction of turbulent kinetic energy through stratification in
 …
 because the mixing length scale is bounded by the distance to the sea surface.
 It can thus be useful to combine the enhanced vertical diffusion with the turbulent closure scheme,
 \ie\ setting the \np{ln\_zdfnpc} namelist parameter to true and
 defining the turbulent closure (\np{ln\_zdftke} or \np{ln\_zdfgls} = \forcode{.true.}) all together.
+\ie\ setting the \np{ln_zdfnpc}{ln\_zdfnpc} namelist parameter to true and
+defining the turbulent closure (\np{ln_zdftke}{ln\_zdftke} or \np{ln_zdfgls}{ln\_zdfgls} = \forcode{.true.}) all together.
 The OSMOSIS turbulent closure scheme already includes enhanced vertical diffusion in the case of convection,
 %as governed by the variables $bvsqcon$ and $difcon$ found in \mdl{zdfkpp},
 therefore \np{ln\_zdfevd}\forcode{=.false.} should be used with the OSMOSIS scheme.
+therefore \np{ln_zdfevd}{ln\_zdfevd}\forcode{=.false.} should be used with the OSMOSIS scheme.
 % gm%  + one word on non local flux with KPP scheme trakpp.F90 module...
 …
 % Double Diffusion Mixing
 % ================================================================
 \section[Double diffusion mixing (\forcode{ln_zdfddm})]{Double diffusion mixing (\protect\np{ln\_zdfddm})}
+\section[Double diffusion mixing (\forcode{ln_zdfddm})]{Double diffusion mixing (\protect\np{ln_zdfddm}{ln\_zdfddm})}
 \label{subsec:ZDF_ddm}
 …
 This parameterisation has been introduced in \mdl{zdfddm} module and is controlled by the namelist parameter
 \np{ln\_zdfddm} in \nam{zdf}.
+\np{ln_zdfddm}{ln\_zdfddm} in \nam{zdf}.
 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 to diffusive convection.
 …
 %       Linear Bottom Friction
 % -------------------------------------------------------------------------------------------------------------
 \subsection[Linear top/bottom friction (\forcode{ln_lin})]{Linear top/bottom friction (\protect\np{ln\_lin})}
+\subsection[Linear top/bottom friction (\forcode{ln_lin})]{Linear top/bottom friction (\protect\np{ln_lin}{ln\_lin})}
 \label{subsec:ZDF_drg_linear}
 …
 and assuming an ocean depth $H = 4000$~m, the resulting friction coefficient is $r = 4\;10^{-4}$~m\;s$^{-1}$.
 This is the default value used in \NEMO. It corresponds to a decay time scale of 115~days.
 It can be changed by specifying \np{rn\_Uc0} (namelist parameter).
+It can be changed by specifying \np{rn_Uc0}{rn\_Uc0} (namelist parameter).
  For the linear friction case the drag coefficient used in the general expression \autoref{eq:ZDF_bfr_bdef} is:
 …
     c_b^T = - r
 \]
 When \np{ln\_lin} \forcode{= .true.}, the value of $r$ used is \np{rn\_Uc0}*\np{rn\_Cd0}.
 Setting \np{ln\_OFF} \forcode{= .true.} (and \forcode{ln_lin=.true.}) is equivalent to setting $r=0$ and leads to a free-slip boundary condition.
+When \np{ln_lin}{ln\_lin} \forcode{= .true.}, the value of $r$ used is \np{rn_Uc0}{rn\_Uc0}*\np{rn_Cd0}{rn\_Cd0}.
+Setting \np{ln_OFF}{ln\_OFF} \forcode{= .true.} (and \forcode{ln_lin=.true.}) is equivalent to setting $r=0$ and leads to a free-slip boundary condition.
 These values are assigned in \mdl{zdfdrg}.
 Note that there is support for local enhancement of these values via an externally defined 2D mask array
 (\np{ln\_boost}\forcode{=.true.}) given in the \ifile{bfr\_coef} input NetCDF file.
+(\np{ln_boost}{ln\_boost}\forcode{=.true.}) given in the \ifile{bfr\_coef} input NetCDF file.
 The mask values should vary from 0 to 1.
 Locations with a non-zero mask value will have the friction coefficient increased by
 $mask\_value$ * \np{rn\_boost} * \np{rn\_Cd0}.
+$mask\_value$ * \np{rn_boost}{rn\_boost} * \np{rn_Cd0}{rn\_Cd0}.
 % -------------------------------------------------------------------------------------------------------------
 %       Non-Linear Bottom Friction
 % -------------------------------------------------------------------------------------------------------------
 \subsection[Non-linear top/bottom friction (\forcode{ln_non_lin})]{Non-linear top/bottom friction (\protect\np{ln\_non\_lin})}
+\subsection[Non-linear top/bottom friction (\forcode{ln_non_lin})]{Non-linear top/bottom friction (\protect\np{ln_non_lin}{ln\_non\_lin})}
 \label{subsec:ZDF_drg_nonlinear}
 …
 $e_b = 2.5\;10^{-3}$m$^2$\;s$^{-2}$, while the FRAM experiment \citep{killworth_JPO92} uses $C_D = 1.4\;10^{-3}$ and
 $e_b =2.5\;\;10^{-3}$m$^2$\;s$^{-2}$.
 The CME choices have been set as default values (\np{rn\_Cd0} and \np{rn\_ke0} namelist parameters).
+The CME choices have been set as default values (\np{rn_Cd0}{rn\_Cd0} and \np{rn_ke0}{rn\_ke0} namelist parameters).
 As for the linear case, the friction is imposed in the code by adding the trend due to
 …
 The coefficients that control the strength of the non-linear friction are initialised as namelist parameters:
 $C_D$= \np{rn\_Cd0}, and $e_b$ =\np{rn\_bfeb2}.
 Note that for applications which consider tides explicitly, a low or even zero value of \np{rn\_bfeb2} is recommended. A local enhancement of $C_D$ is again possible via an externally defined 2D mask array
 (\np{ln\_boost}\forcode{=.true.}).
+$C_D$= \np{rn_Cd0}{rn\_Cd0}, and $e_b$ =\np{rn_bfeb2}{rn\_bfeb2}.
+Note that for applications which consider tides explicitly, a low or even zero value of \np{rn_bfeb2}{rn\_bfeb2} is recommended. A local enhancement of $C_D$ is again possible via an externally defined 2D mask array
+(\np{ln_boost}{ln\_boost}\forcode{=.true.}).
 This works in the same way as for the linear friction case with non-zero masked locations increased by
 $mask\_value$ * \np{rn\_boost} * \np{rn\_Cd0}.
+$mask\_value$ * \np{rn_boost}{rn\_boost} * \np{rn_Cd0}{rn\_Cd0}.
 % -------------------------------------------------------------------------------------------------------------
 %       Bottom Friction Log-layer
 % -------------------------------------------------------------------------------------------------------------
 \subsection[Log-layer top/bottom friction (\forcode{ln_loglayer})]{Log-layer top/bottom friction (\protect\np{ln\_loglayer})}
+\subsection[Log-layer top/bottom friction (\forcode{ln_loglayer})]{Log-layer top/bottom friction (\protect\np{ln_loglayer}{ln\_loglayer})}
 \label{subsec:ZDF_drg_loglayer}
 In the non-linear friction case, the drag coefficient, $C_D$, can be optionally enhanced using
 a "law of the wall" scaling. This assumes that the model vertical resolution can capture the logarithmic layer which typically occur for layers thinner than 1 m or so.
 If  \np{ln\_loglayer} \forcode{= .true.}, $C_D$ is no longer constant but is related to the distance to the wall (or equivalently to the half of the top/bottom layer thickness):
+If  \np{ln_loglayer}{ln\_loglayer} \forcode{= .true.}, $C_D$ is no longer constant but is related to the distance to the wall (or equivalently to the half of the top/bottom layer thickness):
 \[
   C_D = \left ( {\kappa \over {\mathrm log}\left ( 0.5 \; e_{3b} / rn\_{z0} \right ) } \right )^2
 \]
 \noindent where $\kappa$ is the von-Karman constant and \np{rn\_z0} is a roughness length provided via the namelist.
+\noindent where $\kappa$ is the von-Karman constant and \np{rn_z0}{rn\_z0} is a roughness length provided via the namelist.
 The drag coefficient is bounded such that it is kept greater or equal to
 the base \np{rn\_Cd0} value which occurs where layer thicknesses become large and presumably logarithmic layers are not resolved at all. For stability reason, it is also not allowed to exceed the value of an additional namelist parameter:
 \np{rn\_Cdmax}, \ie
+the base \np{rn_Cd0}{rn\_Cd0} value which occurs where layer thicknesses become large and presumably logarithmic layers are not resolved at all. For stability reason, it is also not allowed to exceed the value of an additional namelist parameter:
+\np{rn_Cdmax}{rn\_Cdmax}, \ie
 \[
   rn\_Cd0 \leq C_D \leq rn\_Cdmax
 …
 \noindent The log-layer enhancement can also be applied to the top boundary friction if
 under ice-shelf cavities are activated (\np{ln\_isfcav}\forcode{=.true.}).
 %In this case, the relevant namelist parameters are \np{rn\_tfrz0}, \np{rn\_tfri2} and \np{rn\_tfri2\_max}.
+under ice-shelf cavities are activated (\np{ln_isfcav}{ln\_isfcav}\forcode{=.true.}).
+%In this case, the relevant namelist parameters are \np{rn_tfrz0}{rn\_tfrz0}, \np{rn_tfri2}{rn\_tfri2} and \np{rn_tfri2_max}{rn\_tfri2\_max}.
 % -------------------------------------------------------------------------------------------------------------
 %       Explicit bottom Friction
 % -------------------------------------------------------------------------------------------------------------
 \subsection[Explicit top/bottom friction (\forcode{ln_drgimp=.false.})]{Explicit top/bottom friction (\protect\np{ln\_drgimp}\forcode{=.false.})}
+\subsection[Explicit top/bottom friction (\forcode{ln_drgimp=.false.})]{Explicit top/bottom friction (\protect\np{ln_drgimp}{ln\_drgimp}\forcode{=.false.})}
 \label{subsec:ZDF_drg_stability}
 Setting \np{ln\_drgimp} \forcode{= .false.} means that bottom friction is treated explicitly in time, which has the advantage of simplifying the interaction with the split-explicit free surface (see \autoref{subsec:ZDF_drg_ts}). The latter does indeed require the knowledge of bottom stresses in the course of the barotropic sub-iteration, which becomes less straightforward in the implicit case. In the explicit case, top/bottom stresses can be computed using \textit{before} velocities and inserted in the overall momentum tendency budget. This reads:
+Setting \np{ln_drgimp}{ln\_drgimp} \forcode{= .false.} means that bottom friction is treated explicitly in time, which has the advantage of simplifying the interaction with the split-explicit free surface (see \autoref{subsec:ZDF_drg_ts}). The latter does indeed require the knowledge of bottom stresses in the course of the barotropic sub-iteration, which becomes less straightforward in the implicit case. In the explicit case, top/bottom stresses can be computed using \textit{before} velocities and inserted in the overall momentum tendency budget. This reads:
 At the top (below an ice shelf cavity):
 …
 %       Implicit Bottom Friction
 % -------------------------------------------------------------------------------------------------------------
 \subsection[Implicit top/bottom friction (\forcode{ln_drgimp=.true.})]{Implicit top/bottom friction (\protect\np{ln\_drgimp}\forcode{=.true.})}
+\subsection[Implicit top/bottom friction (\forcode{ln_drgimp=.true.})]{Implicit top/bottom friction (\protect\np{ln_drgimp}{ln\_drgimp}\forcode{=.true.})}
 \label{subsec:ZDF_drg_imp}
 An optional implicit form of bottom friction has been implemented to improve model stability.
 We recommend this option for shelf sea and coastal ocean applications. %, especially for split-explicit time splitting.
 This option can be invoked by setting \np{ln\_drgimp} to \forcode{.true.} in the \nam{drg} namelist.
 %This option requires \np{ln\_zdfexp} to be \forcode{.false.} in the \nam{zdf} namelist.
+This option can be invoked by setting \np{ln_drgimp}{ln\_drgimp} to \forcode{.true.} in the \nam{drg} namelist.
+%This option requires \np{ln_zdfexp}{ln\_zdfexp} to be \forcode{.false.} in the \nam{zdf} namelist.
 This implementation is performed in \mdl{dynzdf} where the following boundary conditions are set while solving the fully implicit diffusion step:
 …
 \label{subsec:ZDF_drg_ts}
 With split-explicit free surface, the sub-stepping of barotropic equations needs the knowledge of top/bottom stresses. An obvious way to satisfy this is to take them as constant over the course of the barotropic integration and equal to the value used to update the baroclinic momentum trend. Provided \np{ln\_drgimp}\forcode{= .false.} and a centred or \textit{leap-frog} like integration of barotropic equations is used (\ie\ \forcode{ln_bt_fw=.false.}, cf \autoref{subsec:DYN_spg_ts}), this does ensure that barotropic and baroclinic dynamics feel the same stresses during one leapfrog time step. However, if \np{ln\_drgimp}\forcode{= .true.},  stresses depend on the \textit{after} value of the velocities which themselves depend on the barotropic iteration result. This cyclic dependency makes difficult obtaining consistent stresses in 2d and 3d dynamics. Part of this mismatch is then removed when setting the final barotropic component of 3d velocities to the time splitting estimate. This last step can be seen as a necessary evil but should be minimized since it interferes with the adjustment to the boundary conditions.
+With split-explicit free surface, the sub-stepping of barotropic equations needs the knowledge of top/bottom stresses. An obvious way to satisfy this is to take them as constant over the course of the barotropic integration and equal to the value used to update the baroclinic momentum trend. Provided \np{ln_drgimp}{ln\_drgimp}\forcode{= .false.} and a centred or \textit{leap-frog} like integration of barotropic equations is used (\ie\ \forcode{ln_bt_fw=.false.}, cf \autoref{subsec:DYN_spg_ts}), this does ensure that barotropic and baroclinic dynamics feel the same stresses during one leapfrog time step. However, if \np{ln\_drgimp}\forcode{= .true.},  stresses depend on the \textit{after} value of the velocities which themselves depend on the barotropic iteration result. This cyclic dependency makes difficult obtaining consistent stresses in 2d and 3d dynamics. Part of this mismatch is then removed when setting the final barotropic component of 3d velocities to the time splitting estimate. This last step can be seen as a necessary evil but should be minimized since it interferes with the adjustment to the boundary conditions.
 The strategy to handle top/bottom stresses with split-explicit free surface in \NEMO\ is as follows:
 …
 % Internal wave-driven mixing
 % ================================================================
 \section[Internal wave-driven mixing (\forcode{ln_zdfiwm})]{Internal wave-driven mixing (\protect\np{ln\_zdfiwm})}
+\section[Internal wave-driven mixing (\forcode{ln_zdfiwm})]{Internal wave-driven mixing (\protect\np{ln_zdfiwm}{ln\_zdfiwm})}
 \label{subsec:ZDF_tmx_new}
 …
 where $R_f$ is the mixing efficiency and $\epsilon$ is a specified three dimensional distribution of
 the energy available for mixing.
 If the \np{ln\_mevar} namelist parameter is set to \forcode{.false.}, the mixing efficiency is taken as constant and
+If the \np{ln_mevar}{ln\_mevar} namelist parameter is set to \forcode{.false.}, the mixing efficiency is taken as constant and
 equal to 1/6 \citep{osborn_JPO80}.
 In the opposite (recommended) case, $R_f$ is instead a function of
 …
 In addition to the mixing efficiency, the ratio of salt to heat diffusivities can chosen to vary
 as a function of $Re_b$ by setting the \np{ln\_tsdiff} parameter to \forcode{.true.}, a recommended choice.
+as a function of $Re_b$ by setting the \np{ln_tsdiff}{ln\_tsdiff} parameter to \forcode{.true.}, a recommended choice.
 This parameterization of differential mixing, due to \cite{jackson.rehmann_JPO14},
 is implemented as in \cite{de-lavergne.madec.ea_JPO16}.
 …
   h_{wkb} = H \, \frac{ \int_{-H}^{z} N \, dz' } { \int_{-H}^{\eta} N \, dz'  } \; ,
 \]
 The $n_p$ parameter (given by \np{nn\_zpyc} in \nam{zdf\_iwm} namelist)
+The $n_p$ parameter (given by \np{nn_zpyc}{nn\_zpyc} in \nam{zdf_iwm}{zdf\_iwm} namelist)
 controls the stratification-dependence of the pycnocline-intensified dissipation.
 It can take values of $1$ (recommended) or $2$.
 …
 % surface wave-induced mixing
 % ================================================================
 \section[Surface wave-induced mixing (\forcode{ln_zdfswm})]{Surface wave-induced mixing (\protect\np{ln\_zdfswm})}
+\section[Surface wave-induced mixing (\forcode{ln_zdfswm})]{Surface wave-induced mixing (\protect\np{ln_zdfswm}{ln\_zdfswm})}
 \label{subsec:ZDF_swm}
 …
 % Adaptive-implicit vertical advection
 % ================================================================
 \section[Adaptive-implicit vertical advection (\forcode{ln_zad_Aimp})]{Adaptive-implicit vertical advection(\protect\np{ln\_zad\_Aimp})}
+\section[Adaptive-implicit vertical advection (\forcode{ln_zad_Aimp})]{Adaptive-implicit vertical advection(\protect\np{ln_zad_Aimp}{ln\_zad\_Aimp})}
 \label{subsec:ZDF_aimp}

NEMO/trunk/doc/latex/NEMO/subfiles/chap_cfgs.tex

-                      r11571
+                      r11577
 The GYRE configuration is set like an analytical configuration.
 Through \np{ln\_read\_cfg}\forcode{ = .false.} in \nam{cfg} namelist defined in
+Through \np{ln_read_cfg}{ln\_read\_cfg}\forcode{ = .false.} in \nam{cfg} namelist defined in
 the reference configuration \path{./cfgs/GYRE_PISCES/EXPREF/namelist_cfg}
 analytical definition of grid in GYRE is done in usrdef\_hrg, usrdef\_zgr routines.
 Its horizontal resolution (and thus the size of the domain) is determined by
 setting \np{nn\_GYRE} in \nam{usr\_def}: \\
 \jp{jpiglo} $= 30 \times$ \np{nn\_GYRE} + 2   \\
 \jp{jpjglo} $= 20 \times$ \np{nn\_GYRE} + 2   \\
+setting \np{nn_GYRE}{nn\_GYRE} in \nam{usr_def}{usr\_def}: \\
+\jp{jpiglo} $= 30 \times$ \np{nn_GYRE}{nn\_GYRE} + 2   \\
+\jp{jpjglo} $= 20 \times$ \np{nn_GYRE}{nn\_GYRE} + 2   \\
 Obviously, the namelist parameters have to be adjusted to the chosen resolution,
 …
 For example, keeping a same model size on each processor while increasing the number of processor used is very easy,
 even though the physical integrity of the solution can be compromised.
 Benchmark is activate via \np{ln\_bench}\forcode{ = .true.} in \nam{usr\_def} in
+Benchmark is activate via \np{ln_bench}{ln\_bench}\forcode{ = .true.} in \nam{usr_def}{usr\_def} in
 namelist \path{./cfgs/GYRE_PISCES/EXPREF/namelist_cfg}.
 …
 In particular, the AMM uses $s$-coordinates in the vertical rather than $z$-coordinates and
 is forced with tidal lateral boundary conditions using a Flather boundary condition from the BDY module.
 Also specific to the AMM configuration is the use of the GLS turbulence scheme (\np{ln\_zdfgls} \forcode{= .true.}).
+Also specific to the AMM configuration is the use of the GLS turbulence scheme (\np{ln_zdfgls}{ln\_zdfgls} \forcode{= .true.}).
 In addition to the tidal boundary condition the model may also take open boundary conditions from
 a North Atlantic model.
 Boundaries may be completely omitted by setting \np{ln\_bdy} to false.
+Boundaries may be completely omitted by setting \np{ln_bdy}{ln\_bdy} to false.
 Sample surface fluxes, river forcing and a sample initial restart file are included to test a realistic model run.
 The Baltic boundary is included within the river input file and is specified as a river source.

NEMO/trunk/doc/latex/NEMO/subfiles/chap_misc.tex

-                      r11571
+                      r11577
 \begin{itemize}
 \item Add \texttt{e1e2u} and \texttt{e1e2v} arrays to the \np{cn\_domcfg} file. These 2D
+\item Add \texttt{e1e2u} and \texttt{e1e2v} arrays to the \np{cn_domcfg}{cn\_domcfg} file. These 2D
 arrays should contain the products of the unaltered values of: $\texttt{e1u}*\texttt{e2u}$
 and $\texttt{e1u}*\texttt{e2v}$ respectively. That is the original surface areas of $u$-
 and $v$- cells respectively.  These areas are usually defined by the corresponding product
 within the \NEMO\ code but the presence of \texttt{e1e2u} and \texttt{e1e2v} in the
 \np{cn\_domcfg} file will suppress this calculation and use the supplied fields instead.
+\np{cn_domcfg}{cn\_domcfg} file will suppress this calculation and use the supplied fields instead.
 If the model domain is provided by user-supplied code in \mdl{usrdef\_hgr}, then this
 routine should also return \texttt{e1e2u} and \texttt{e1e2v} and set the integer return
 …
 will suppress the calculation of the areas.
 \item Change values of \texttt{e2u} or \texttt{e1v} (either in the \np{cn\_domcfg} file or
+\item Change values of \texttt{e2u} or \texttt{e1v} (either in the \np{cn_domcfg}{cn\_domcfg} file or
 via code in  \mdl{usrdef\_hgr}), whereever a Strait reduction is required. The choice of
 whether to alter \texttt{e2u} or \texttt{e1v} depends. respectively,  on whether the
 …
 maintain different sets of input fields for use with or without active ice cavities.  This
 subsetting operates for the j-direction only and works by optionally looking for and using
 a global file attribute (named: \np{open\_ocean\_jstart}) to determine the starting j-row
+a global file attribute (named: \np{open_ocean_jstart}{open\_ocean\_jstart}) to determine the starting j-row
 for input.  The use of this option is best explained with an example:
 \medskip
 …
 This file define a horizontal domain of 362x332.  The first row with
 open ocean wet points in the non-isf bathymetry for this set is row 42 (\fortran\ indexing)
 then the formally correct setting for \np{open\_ocean\_jstart} is 41.  Using this value as
+then the formally correct setting for \np{open_ocean_jstart}{open\_ocean\_jstart} is 41.  Using this value as
 the first row to be read will result in a 362x292 domain which is the same size as the
 original ORCA1 domain.  Thus the extended domain configuration file can be used with all
 …
 \end{cmds}
 \item Add the logical switch \np{ln\_use\_jattr} to \nam{cfg} in the configuration
 namelist (if it is not already there) and set \np{.true.}
+\item Add the logical switch \np{ln_use_jattr}{ln\_use\_jattr} to \nam{cfg} in the configuration
+namelist (if it is not already there) and set \forcode{.true.}
 \end{itemize}
 \noindent Note that with this option, the j-size of the global domain is (extended
 j-size minus \np{open\_ocean\_jstart} + 1 ) and this must match the \texttt{jpjglo} value
+j-size minus \np{open_ocean_jstart}{open\_ocean\_jstart} + 1 ) and this must match the \texttt{jpjglo} value
 for the configuration. This means an alternative version of \ifile{eORCA1\_domcfg.nc} must
 be created for when \np{ln\_use\_jattr} is active. The \texttt{ncap2} tool provides a
+be created for when \np{ln_use_jattr}{ln\_use\_jattr} is active. The \texttt{ncap2} tool provides a
 convenient way of achieving this:
 …
 \texttt{open\_ocean\_jstart} attribute to the file's global attributes.
 In particular this is true for any field that is read by \NEMO\ using the following optional argument to
 the appropriate call to \np{iom\_get}.
+the appropriate call to \np{iom_get}{iom\_get}.
 \begin{forlines}
 …
 This alternative method should give identical results to the default \textsc{ALLGATHER} method and
 is recommended for large values of \np{jpni}.
 The new method is activated by setting \np{ln\_nnogather} to be true (\nam{mpp}).
+The new method is activated by setting \np{ln_nnogather}{ln\_nnogather} to be true (\nam{mpp}).
 The reproducibility of results using the two methods should be confirmed for each new,
 non-reference configuration.
 …
 \subsection{Control print}
 The \np{ln\_ctl} switch was originally used as a debugging option in two modes:
+The \np{ln_ctl}{ln\_ctl} switch was originally used as a debugging option in two modes:
 \begin{enumerate}
 \item{\np{ln\_ctl}: compute and print the trends averaged over the interior domain in all TRA, DYN, LDF and
+\item{\np{ln_ctl}{ln\_ctl}: compute and print the trends averaged over the interior domain in all TRA, DYN, LDF and
 ZDF modules.
 This option is very helpful when diagnosing the origin of an undesired change in model results. }
 \item{also \np{ln\_ctl} but using the nictl and njctl namelist parameters to check the source of differences between
+\item{also \np{ln_ctl}{ln\_ctl} but using the nictl and njctl namelist parameters to check the source of differences between
 mono and multi processor runs.}
 \end{enumerate}
 However, in recent versions it has also been used to force all processors to assume the
 reporting role. Thus when \np{ln\_ctl} is true all processors produce their own versions
+reporting role. Thus when \np{ln_ctl}{ln\_ctl} is true all processors produce their own versions
 of files such as: ocean.output, layout.dat, etc.  All such files, beyond the the normal
 reporting processor (narea == 1), are named with a \_XXXX extension to their name, where
 …
 such as run.stat (and its netCDF counterpart: run.stat.nc) and tracer.stat contain global
 information and are only ever produced by the reporting master (narea == 1). For version
 .0 a start has been made to return \np{ln\_ctl} to its original function by introducing
+.0 a start has been made to return \np{ln_ctl}{ln\_ctl} to its original function by introducing
 a new control structure which allows finer control over which files are produced. This
 feature is still evolving but it does already allow the user to: select individually the

NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex

r11571	r11577
79	79	%\nlst{nam_dynspg}
80	80	%------------------------------------------------------------------------------------------------------------
81		Options are defined through the \nam{\_dynspg} namelist variables.
	81	Options are defined through the \nam{_dynspg}{\_dynspg} namelist variables.
82	82	The surface pressure gradient term is related to the representation of the free surface (\autoref{sec:MB_hor_pg}).
83	83	The main distinction is between the fixed volume case (linear free surface or rigid lid) and

NEMO/trunk/doc/latex/NEMO/subfiles/chap_time_domain.tex

-                      r11567
+                      r11577
 \end{equation}
 where the subscript $F$ denotes filtered values and $\gamma$ is the Asselin coefficient.
 $\gamma$ is initialized as \np{rn\_atfp} (namelist parameter).
 Its default value is \np{rn\_atfp}\forcode{ = 10.e-3} (see \autoref{sec:TD_mLF}),
+$\gamma$ is initialized as \np{rn_atfp}{rn\_atfp} (namelist parameter).
+Its default value is \np{rn_atfp}{rn\_atfp}\forcode{ = 10.e-3} (see \autoref{sec:TD_mLF}),
 causing only a weak dissipation of high frequency motions (\citep{farge-coulombier_phd87}).
 The addition of a time filter degrades the accuracy of the calculation from second to first order.
 …
 The leapfrog environment supports a centred in time computation of the surface pressure, \ie\ evaluated
 at \textit{now} time step. This refers to as the explicit free surface case in the code (\np{ln\_dynspg\_exp}\forcode{=.true.}).
+at \textit{now} time step. This refers to as the explicit free surface case in the code (\np{ln_dynspg_exp}{ln\_dynspg\_exp}\forcode{=.true.}).
 This choice however imposes a strong constraint on the time step which should be small enough to resolve the propagation
 of external gravity waves. As a matter of fact, one rather use in a realistic setup, a split-explicit free surface
 (\np{ln\_dynspg\_ts}\forcode{=.true.}) in which barotropic and baroclinic dynamical equations are solved separately with ad-hoc
+(\np{ln_dynspg_ts}{ln\_dynspg\_ts}\forcode{=.true.}) in which barotropic and baroclinic dynamical equations are solved separately with ad-hoc
 time steps. The use of the time-splitting (in combination with non-linear free surface) imposes some constraints on the design of
 the overall flowchart, in particular to ensure exact tracer conservation (see \autoref{fig:TD_TimeStep_flowchart}).
 …
 When restarting, if the time step has been changed, or one of the prognostic variables at \textit{before} time step
 is missing, an Euler time stepping scheme is imposed. A forward initial step can still be enforced by the user by setting
 the namelist variable \np{nn\_euler}\forcode{=0}. Other options to control the time integration of the model
+the namelist variable \np{nn_euler}{nn\_euler}\forcode{=0}. Other options to control the time integration of the model
 are defined through the  \nam{run} namelist variables.
 %%%

NEMO/trunk/doc/latex/global/document.tex

r11572	r11577
11	11
12	12	%% Document layout
13		\documentclass[fontsize = 10pt, twoside, abstract~~, draft~~]{scrreprt}
	13	\documentclass[fontsize = 10pt, twoside, abstract]{scrreprt}
14	14
15	15	%% Load configurations

NEMO/trunk/doc/latex/global/index.ist

-                      r11572
+                      r11577
 headings_flag 1
 heading_prefix "{\\medskip\\hfill\\large{"
 heading_suffix "}}\\hfill}\\smallskip\n"
+heading_prefix "\\medskip\\hfill\\textnormal{"
+heading_suffix "}\\hfill\\smallskip\n"
 delim_0 "\\dotfill~"

NEMO/trunk/doc/latex/global/indexes.tex

-                      r11572
+                      r11577
 \usepackage{imakeidx}
+%% Naming customization
+\renewcommand{\listingname}{namelist}
+\renewcommand{\listlistingname}{List of Namelists}
 %% Index entries (italic font for files, preformat for code)
 …
 \newcommand{\key}[1]{  \index[keys]{#1@\texttt{\textbf{key\_#1}}} \texttt{\textbf{key\_#1}}}
 \newcommand{\mdl}[1]{  \index[modules]{#1@\textit{#1.F90}}        \textit{#1.F90}          }
+\newcommand{\nam}[1]{  \index[blocks]{#1@\texttt{\&nam#1}}        \forcode{&nam#1}         }
+\newcommand{\np}[1]{   \index[parameters]{#1@\texttt{#1}}         \texttt{#1}              }
+\newcommand{\npnew}[2][]{\index[parameters]{#2@\texttt{#2}}       \forcode{#2#1}           }
+\newcommand{\nam}[2]{  \index[blocks]{\texttt{\&nam#2}}   \forcode{&nam#1} (\autoref{lst:nam#1})         }
+\newcommand{\np}[3][]{\index[parameters]{\texttt{#3}}       \forcode{#2#1}           }
+%\newcommand{\nam}[1]{  \index[blocks]{\texttt{\&nam#1}}           \forcode{&nam#1}         }
+%\newcommand{\np}[1]{   \index[parameters]{\texttt{#1}}            \forcode{#1}              }
 \newcommand{\rou}[1]{  \index[subroutines]{#1@\texttt{#1}}        \texttt{#1}              }
 \indexsetup{toclevel=section, othercode=\small}

NEMO/trunk/doc/latex/global/preamble.tex

r11572	r11577
23	23	\renewcommand{\equationautorefname}{equation}
24	24	\renewcommand{\figureautorefname}{figure}
25		~~%\renewcommand{\listingautorefname}{namelist}~~
26	25	\renewcommand{\tableautorefname}{table}

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