Changeset 11537

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

-                      r11435
+                      r11537
 Typically the increments are spread evenly over the full window.
 In addition, two different weighting functions have been implemented.
 The first function (namelist option \np{niaufn} = 0) employs constant weights,
+The first function (namelist option \np{niaufn}=0) employs constant weights,
 \begin{align}
   \label{eq:F1_i}
 …
 \end{align}
 where $M = m-n$.
 The second function (namelist option \np{niaufn} = 1) employs peaked hat-like weights in order to give maximum weight in the centre of the sub-window,
+The second function (namelist option \np{niaufn}=1) employs peaked hat-like weights in order to give maximum weight in the centre of the sub-window,
 with the weighting reduced linearly to a small value at the window end-points:
 \begin{align}

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

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+                      r11537
 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}\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.
 …
 Obviously, the namelist parameters have to be adjusted to the chosen resolution,
 see the Configurations pages on the \NEMO\ web site (\NEMO\ Configurations).
 In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}\forcode{ = 31}) (\autoref{fig:zgr}).
+In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}\forcode{=31}) (\autoref{fig:zgr}).
 The GYRE configuration is also used in benchmark test as it is very simple to increase its resolution and
 …
 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}\forcode{=.true.} in \nam{usr\_def} in
 namelist \path{./cfgs/GYRE_PISCES/EXPREF/namelist_cfg}.

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

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+                      r11537
 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}\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
 …
 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}\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
 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.
 …
 \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.}).
+and none of the options have been tested with variable volume (\ie\ \np{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}\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}\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}\forcode{=.true.} ),
 \np{jpnflnewflo} can be added in the initialization file.
 …
 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}\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}\forcode{=.false.}) with
 \key{iomput} and outputs selected in iodef.xml.
 Here it is an example of specification to put in files description section:
 …
 Third, the discretisation of \autoref{eq: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}\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}\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}\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,

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

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       (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}\forcode{=.false.}).
       Note that the non-linear free surface can be used with any of the 5 coordinates (a) to (e).
+    }
 …
 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} 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: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} 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).
 …
 \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}\forcode{=.true.}),
+\item $z$-coordinate with partial step ($zps$) bathymetry (\np{ln\_zps}\forcode{=.true.}),
+\item Generalized, $s$-coordinate (\np{ln\_sco}\forcode{=.true.}).
 \end{itemize}
 …
 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}\forcode{=.true.}),
 \textit{before}, \textit{now} and \textit{after} arrays are initially set to
 their reference counterpart and remain fixed.

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

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+                      r11537
 Options are defined through the \nam{dyn\_vor} namelist variables.
 Four discretisations of the vorticity term (\texttt{ln\_dynvor\_xxx}\forcode{ = .true.}) are available:
+Four discretisations of the vorticity term (\texttt{ln\_dynvor\_xxx}\forcode{=.true.}) are available:
 conserving potential enstrophy of horizontally non-divergent flow (ENS scheme);
 conserving horizontal kinetic energy (ENE scheme);
 …
 (EEN scheme) (see \autoref{subsec:C_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}\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 = .true.})]
 {Enstrophy conserving scheme (\protect\np{ln\_dynvor\_ens}\forcode{ = .true.})}
+\subsubsection[Enstrophy conserving scheme (\forcode{ln_dynvor_ens=.true.})]
+{Enstrophy conserving scheme (\protect\np{ln\_dynvor\_ens}\forcode{=.true.})}
 \label{subsec:DYN_vor_ens}
 …
 %                 energy conserving scheme
 %-------------------------------------------------------------
 \subsubsection[Energy conserving scheme (\forcode{ln_dynvor_ene = .true.})]
 {Energy conserving scheme (\protect\np{ln\_dynvor\_ene}\forcode{ = .true.})}
+\subsubsection[Energy conserving scheme (\forcode{ln_dynvor_ene=.true.})]
+{Energy conserving scheme (\protect\np{ln\_dynvor\_ene}\forcode{=.true.})}
 \label{subsec:DYN_vor_ene}
 …
 %                 mix energy/enstrophy conserving scheme
 %-------------------------------------------------------------
 \subsubsection[Mixed energy/enstrophy conserving scheme (\forcode{ln_dynvor_mix = .true.})]
 {Mixed energy/enstrophy conserving scheme (\protect\np{ln\_dynvor\_mix}\forcode{ = .true.})}
+\subsubsection[Mixed energy/enstrophy conserving scheme (\forcode{ln_dynvor_mix=.true.})]
+{Mixed energy/enstrophy conserving scheme (\protect\np{ln\_dynvor\_mix}\forcode{=.true.})}
 \label{subsec:DYN_vor_mix}
 …
 %                 energy and enstrophy conserving scheme
 %-------------------------------------------------------------
 \subsubsection[Energy and enstrophy conserving scheme (\forcode{ln_dynvor_een = .true.})]
 {Energy and enstrophy conserving scheme (\protect\np{ln\_dynvor\_een}\forcode{ = .true.})}
+\subsubsection[Energy and enstrophy conserving scheme (\forcode{ln_dynvor_een=.true.})]
+{Energy and enstrophy conserving scheme (\protect\np{ln\_dynvor\_een}\forcode{=.true.})}
 \label{subsec:DYN_vor_een}
 …
 A key point in \autoref{eq: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}\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}\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}.
 …
 %                 2nd order centred scheme
 %-------------------------------------------------------------
 \subsubsection[CEN2: $2^{nd}$ order centred scheme (\forcode{ln_dynadv_cen2 = .true.})]
 {CEN2: $2^{nd}$ order centred scheme (\protect\np{ln\_dynadv\_cen2}\forcode{ = .true.})}
+\subsubsection[CEN2: $2^{nd}$ order centred scheme (\forcode{ln_dynadv_cen2=.true.})]
+{CEN2: $2^{nd}$ order centred scheme (\protect\np{ln\_dynadv\_cen2}\forcode{=.true.})}
 \label{subsec:DYN_adv_cen2}
 …
 %                 UBS scheme
 %-------------------------------------------------------------
 \subsubsection[UBS: Upstream Biased Scheme (\forcode{ln_dynadv_ubs = .true.})]
 {UBS: Upstream Biased Scheme (\protect\np{ln\_dynadv\_ubs}\forcode{ = .true.})}
+\subsubsection[UBS: Upstream Biased Scheme (\forcode{ln_dynadv_ubs=.true.})]
+{UBS: Upstream Biased Scheme (\protect\np{ln\_dynadv\_ubs}\forcode{=.true.})}
 \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}\forcode{=}\np{ln\_dynldf\_bilap}\forcode{=.false.}),
 and it is recommended to do so.
 …
 %           z-coordinate with full step
 %--------------------------------------------------------------------------------------------------------------
 \subsection[Full step $Z$-coordinate (\forcode{ln_dynhpg_zco = .true.})]
 {Full step $Z$-coordinate (\protect\np{ln\_dynhpg\_zco}\forcode{ = .true.})}
+\subsection[Full step $Z$-coordinate (\forcode{ln_dynhpg_zco=.true.})]
+{Full step $Z$-coordinate (\protect\np{ln\_dynhpg\_zco}\forcode{=.true.})}
 \label{subsec:DYN_hpg_zco}
 …
 %           z-coordinate with partial step
 %--------------------------------------------------------------------------------------------------------------
 \subsection[Partial step $Z$-coordinate (\forcode{ln_dynhpg_zps = .true.})]
 {Partial step $Z$-coordinate (\protect\np{ln\_dynhpg\_zps}\forcode{ = .true.})}
+\subsection[Partial step $Z$-coordinate (\forcode{ln_dynhpg_zps=.true.})]
+{Partial step $Z$-coordinate (\protect\np{ln\_dynhpg\_zps}\forcode{=.true.})}
 \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}\forcode{=.true.})
 \begin{equation}
   \label{eq:dynhpg_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}\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.})
 $\bullet$ 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}\forcode{=.true.}) (currently disabled; under development)
 Note that expression \autoref{eq:dynhpg_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}\forcode{=.true.}) is available as
+an improved option to \np{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.
 …
 \label{subsec:DYN_hpg_isf}
 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}\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 = .{true,false}.})]
 {Time-scheme (\protect\np{ln\_dynhpg\_imp}\forcode{ = .\{true,false\}}.)}
+\subsection[Time-scheme (\forcode{ln_dynhpg_imp={.true.,.false.}})]
+{Time-scheme (\protect\np{ln\_dynhpg\_imp}\forcode{=.true.,.false.})}
 \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}\forcode{=.true.}):
 \begin{equation}
 …
 \end{equation}
 $\bullet$ semi-implicit scheme (\np{ln\_dynhpg\_imp}\forcode{ = .true.}):
+$\bullet$ semi-implicit scheme (\np{ln\_dynhpg\_imp}\forcode{=.true.}):
 \begin{equation}
   \label{eq:dynhpg_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}\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,
 …
 % Explicit free surface formulation
 %--------------------------------------------------------------------------------------------------------------
 \subsection[Explicit free surface (\texttt{ln\_dynspg\_exp}\forcode{ = .true.})]
 {Explicit free surface (\protect\np{ln\_dynspg\_exp}\forcode{ = .true.})}
+\subsection[Explicit free surface (\texttt{ln\_dynspg\_exp}\forcode{=.true.})]
+{Explicit free surface (\protect\np{ln\_dynspg\_exp}\forcode{=.true.})}
 \label{subsec:DYN_spg_exp}
 …
 % Split-explict free surface formulation
 %--------------------------------------------------------------------------------------------------------------
 \subsection[Split-explicit free surface (\texttt{ln\_dynspg\_ts}\forcode{ = .true.})]
 {Split-explicit free surface (\protect\np{ln\_dynspg\_ts}\forcode{ = .true.})}
+\subsection[Split-explicit free surface (\texttt{ln\_dynspg\_ts}\forcode{=.true.})]
+{Split-explicit free surface (\protect\np{ln\_dynspg\_ts}\forcode{=.true.})}
 \label{subsec:DYN_spg_ts}
 %------------------------------------------namsplit-----------------------------------------------------------
 …
 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
+This parameter can be optionally defined automatically (\np{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.
 …
       The former are used to obtain time filtered quantities at $t+\rdt$ while
       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.}.
       b) Centred time integration: \protect\np{ln\_bt\_fw}\forcode{ = .false.},
       \protect\np{ln\_bt\_av}\forcode{ = .true.}.
+      a) Forward time integration: \protect\np{ln\_bt\_fw}\forcode{=.true.},
+      \protect\np{ln\_bt\_av}\forcode{=.true.}.
+      b) Centred time integration: \protect\np{ln\_bt\_fw}\forcode{=.false.},
+      \protect\np{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}\forcode{=.true.}, \protect\np{ln\_bt\_av}\forcode{=.false.}.
+    }
   \end{center}
 …
 %>   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >
 In the default case (\np{ln\_bt\_fw}\forcode{ = .true.}),
+In the default case (\np{ln\_bt\_fw}\forcode{=.true.}),
 the external mode is integrated between \textit{now} and \textit{after} baroclinic time-steps
 (\autoref{fig:DYN_dynspg_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}\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.}).
+(\np{ln\_bt\_fw}\forcode{=.false.}).
 Although more computationaly expensive ( \np{nn\_baro} additional iterations are indeed necessary),
 the baroclinic to barotropic forcing term given at \textit{now} time step become centred in
 …
 One can eventually choose to feedback instantaneous values by not using any time filter
 (\np{ln\_bt\_av}\forcode{ = .false.}).
+(\np{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.
 …
 % ================================================================
 \subsection[Iso-level laplacian (\forcode{ln_dynldf_lap = .true.})]
 {Iso-level laplacian operator (\protect\np{ln\_dynldf\_lap}\forcode{ = .true.})}
+\subsection[Iso-level laplacian (\forcode{ln_dynldf_lap=.true.})]
+{Iso-level laplacian operator (\protect\np{ln\_dynldf\_lap}\forcode{=.true.})}
 \label{subsec:DYN_ldf_lap}
 …
 %           Rotated laplacian operator
 %--------------------------------------------------------------------------------------------------------------
 \subsection[Rotated laplacian (\forcode{ln_dynldf_iso = .true.})]
 {Rotated laplacian operator (\protect\np{ln\_dynldf\_iso}\forcode{ = .true.})}
+\subsection[Rotated laplacian (\forcode{ln_dynldf_iso=.true.})]
+{Rotated laplacian operator (\protect\np{ln\_dynldf\_iso}\forcode{=.true.})}
 \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}\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.
 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}\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 = .true.})]
 {Iso-level bilaplacian operator (\protect\np{ln\_dynldf\_bilap}\forcode{ = .true.})}
+\subsection[Iso-level bilaplacian (\forcode{ln_dynldf_bilap=.true.})]
+{Iso-level bilaplacian operator (\protect\np{ln\_dynldf\_bilap}\forcode{=.true.})}
 \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}\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.})
 (see \autoref{chap:STP}).
 Note that namelist variables \np{ln\_zdfexp} and \np{nn\_zdfexp} apply to both tracers and dynamics.
 …
 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}\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}\forcode{=.true.} and \np{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}\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 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
+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
+\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.
 …
 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}\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}\forcode{=.true.} ; \texttt{vvl?} not defined):
 \[
   % \label{eq:dynnxt_vec}
 …
 $\bullet$ flux form and nonlinear free surface
 (\np{ln\_dynhpg\_vec}\forcode{ = .false.} ; \texttt{vvl?} defined):
+(\np{ln\_dynhpg\_vec}\forcode{=.false.} ; \texttt{vvl?} defined):
 \[
   % \label{eq:dynnxt_flux}
 …
 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}.
+Its default value is \np{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

-                      r11536
+                      r11537
 %        Closed, cyclic (\jp{jperio}\forcode{ = 0..2})
 % -------------------------------------------------------------------------------------------------------------
 \subsection[Closed, cyclic (\forcode{jperio = [0127]})]
 {Closed, cyclic (\protect\jp{jperio}\forcode{ = [0127]})}
+\subsection[Closed, cyclic (\forcode{jperio=[0127]})]
+{Closed, cyclic (\protect\jp{jperio}\forcode{=[0127]})}
 \label{subsec:LBC_jperio012}
 …
 \begin{description}
 \item[For closed boundary (\jp{jperio}\forcode{ = 0})],
+\item[For closed boundary (\jp{jperio}\forcode{=0})],
   solid walls are imposed at all model boundaries:
   first and last rows and columns are set to zero.
 \item[For cyclic east-west boundary (\jp{jperio}\forcode{ = 1})],
+\item[For cyclic east-west boundary (\jp{jperio}\forcode{=1})],
   first and last rows are set to zero (closed) whilst the first column is set to
   the value of the last-but-one column and the last column to the value of the second one
 …
   Whatever flows out of the eastern (western) end of the basin enters the western (eastern) end.
 \item[For cyclic north-south boundary (\jp{jperio}\forcode{ = 2})],
+\item[For cyclic north-south boundary (\jp{jperio}\forcode{=2})],
   first and last columns are set to zero (closed) whilst the first row is set to
   the value of the last-but-one row and the last row to the value of the second one
 …
   Whatever flows out of the northern (southern) end of the basin enters the southern (northern) end.
 \item[Bi-cyclic east-west and north-south boundary (\jp{jperio}\forcode{ = 7})] combines cases 1 and 2.
+\item[Bi-cyclic east-west and north-south boundary (\jp{jperio}\forcode{=7})] combines cases 1 and 2.
 \end{description}
 …
 %        North fold (\textit{jperio = 3 }to $6)$
 % -------------------------------------------------------------------------------------------------------------
 \subsection[North-fold (\forcode{jperio = [3-6]})]
 {North-fold (\protect\jp{jperio}\forcode{ = [3-6]})}
+\subsection[North-fold (\forcode{jperio=[3-6]})]
+{North-fold (\protect\jp{jperio}\forcode{=[3-6]})}
 \label{subsec:LBC_north_fold}

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

-                      r11435
+                      r11537
 (see the \nam{tra\_ldf} and \nam{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}\forcode{=.true.},
 is described in \autoref{apdx:triad}
 …
 {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.},
+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.},
 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
+Setting \protect\np{ln\_traldf\_lap}\forcode{=.true.} and/or \protect\np{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
+Setting \protect\np{ln\_traldf\_blp}\forcode{=.true.} and/or \protect\np{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.
 …
 %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}\forcode{=.true.},
+and either \np{ln\_traldf\_hor}\forcode{=.true.} or \np{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}\forcode{=.true.};
   see \autoref{apdx:triad}).
   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}\forcode{=.true.}).
   In the case of a "true" equation of state, the evaluation of $i$ and $j$ derivatives in \autoref{eq:ldfslp_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:triad}.
+Griffies's scheme is now available in \NEMO\ if \np{ln\_traldf\_triad}\forcode{=.true.}; see \autoref{apdx:triad}.
 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
 …
 The way the mixing coefficients are set in the reference version can be described as follows:
 \subsection[Mixing coefficients read from file (\forcode{nn_aht_ijk_t = -20, -30}, \forcode{nn_ahm_ijk_t = -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{nn_aht_ijk_t=-20, -30}, \forcode{nn_ahm_ijk_t=-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})}
 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}\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}).
 %-------------------------------------------------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}\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
     \end{tabular}
     \caption{
 …
 %--------------------------------------------------------------------------------------------------------------
 \subsection[Constant mixing coefficients (\forcode{nn_aht_ijk_t = 0}, \forcode{nn_ahm_ijk_t = 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{nn_aht_ijk_t=0}, \forcode{nn_ahm_ijk_t=0})]
+{ Constant mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{=0}, \protect\np{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:
 …
  $U_{scl}$ 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{nn_aht_ijk_t = 10}, \forcode{nn_ahm_ijk_t = 10})]
 {Vertically varying mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{ = 10}, \protect\np{nn\_ahm\_ijk\_t}\forcode{ = 10})}
+\subsection[Vertically varying mixing coefficients (\forcode{nn_aht_ijk_t=10}, \forcode{nn_ahm_ijk_t=10})]
+{Vertically varying mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{=10}, \protect\np{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{nn_aht_ijk_t = 20}, \forcode{nn_ahm_ijk_t = 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{nn_aht_ijk_t=20}, \forcode{nn_ahm_ijk_t=20})]
+{Mesh size dependent mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{=20}, \protect\np{nn\_ahm\_ijk\_t}\forcode{=20})}
 In that case, the horizontal variation of the eddy coefficient depends on the local mesh size and
 …
 \colorbox{yellow}{CASE \np{nn\_aht\_ijk\_t} = 21 to be added}
 \subsection[Mesh size and depth dependent mixing coefficients (\forcode{nn_aht_ijk_t = 30}, \forcode{nn_ahm_ijk_t = 30})]
 {Mesh size and depth dependent mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{ = 30}, \protect\np{nn\_ahm\_ijk\_t}\forcode{ = 30})}
+\subsection[Mesh size and depth dependent mixing coefficients (\forcode{nn_aht_ijk_t=30}, \forcode{nn_ahm_ijk_t=30})]
+{Mesh size and depth dependent mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{=30}, \protect\np{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{nn_aht_ijk_t = 31}, \forcode{nn_ahm_ijk_t = 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{nn_aht_ijk_t=31}, \forcode{nn_ahm_ijk_t=31})]
+{Flow dependent mixing coefficients (\protect\np{nn\_aht\_ijk\_t}\forcode{=31}, \protect\np{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}\forcode{=32})}
 This option refers to the \citep{smagorinsky_MW63} scheme which is here implemented for momentum only. Smagorinsky chose as a
 …
 % Eddy Induced Mixing
 % ================================================================
 \section[Eddy induced velocity (\forcode{ln_ldfeiv = .true.})]
 {Eddy induced velocity (\protect\np{ln\_ldfeiv}\forcode{ = .true.})}
+\section[Eddy induced velocity (\forcode{ln_ldfeiv=.true.})]
+{Eddy induced velocity (\protect\np{ln\_ldfeiv}\forcode{=.true.})}
 \label{sec:LDF_eiv}
 …
+}
 When  \citet{gent.mcwilliams_JPO90} diffusion is used (\np{ln\_ldfeiv}\forcode{ = .true.}),
+When  \citet{gent.mcwilliams_JPO90} diffusion is used (\np{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:ldfslp_geo} + \autoref{eq:ldfslp_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}\forcode{=.false.}, the eddy induced velocity is given by:
 \begin{equation}
   \label{eq:ldfeiv}
 …
 \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:triad}.
+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:triad}.
 % ================================================================
 % Mixed layer eddies
 % ================================================================
 \section[Mixed layer eddies (\forcode{ln_mle = .true.})]
 {Mixed layer eddies (\protect\np{ln\_mle}\forcode{ = .true.})}
+\section[Mixed layer eddies (\forcode{ln_mle=.true.})]
+{Mixed layer eddies (\protect\np{ln\_mle}\forcode{=.true.})}
 \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}\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.
 \colorbox{yellow}{TBC}

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

-                      r11435
+                      r11537
 \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}\forcode{=.true.} with four possible bulk algorithms),
+\item
+  a flux formulation (\np{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} or \np{ln\_mixcpl}\forcode{=.true.}),
+\item
+  a user defined formulation (\np{ln\_usr}\forcode{=.true.}).
 \end{itemize}
 …
   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}\forcode{=.true.}),
+\item
+  the addition of a surface restoring term to observed SST and/or SSS (\np{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}\forcode{=0..3}),
+\item
+  the addition of river runoffs as surface freshwater fluxes or lateral inflow (\np{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}\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}\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}\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.}).
 \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}\forcode{=.true.}.
 The way the light penetrates inside the water column is generally a sum of decreasing exponentials
 (see \autoref{subsec:TRA_qsr}).
 …
         \hline
                                         &  daily or weekLL     &  monthly           &  yearly        \\   \hline
         \np{clim}\forcode{ = .false.}  &  fn\_yYYYYmMMdDD.nc  &  fn\_yYYYYmMM.nc   &  fn\_yYYYY.nc  \\   \hline
         \np{clim}\forcode{ = .true.}   &  not possible        &  fn\_m??.nc        &  fn            \\   \hline
+        \np{clim}\forcode{=.false.} &  fn\_yYYYYmMMdDD.nc  &  fn\_yYYYYmMM.nc   &  fn\_yYYYY.nc  \\   \hline
+        \np{clim}\forcode{=.true.}  &  not possible        &  fn\_m??.nc        &  fn            \\   \hline
       \end{tabular}
     \end{center}
 …
 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.
+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.
 In the previous example, this leads to: 1h30'00", 4h30'00", 7h30'00", etc. \\
 …
   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}\forcode{=.true.})
 \end{itemize}
 …
 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.
+ (\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.
 …
 %-------------------------------------------------------------------------------------------------------------
 In the flux formulation (\np{ln\_flx}\forcode{ = .true.}),
+In the flux formulation (\np{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,
 …
 \begin{itemize}
 \item
   NCAR (\np{ln\_NCAR}\forcode{ = .true.}):
+  NCAR (\np{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}\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}\forcode{=.true.}):
   See \citet{edson.jampana.ea_JPO13} for more details
 \item
   ECMWF (\np{ln\_ECMWF}\forcode{ = .true.}):
+  ECMWF (\np{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}.
 …
   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}\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}\forcode{=.true.}):
   Alternative turbulent transfer coefficients formulation between sea-ice
   and atmosphere with distinct momentum and heat coefficients depending
 …
 The optional atmospheric pressure can be used to force ocean and ice dynamics
 (\np{ln\_apr\_dyn}\forcode{ = .true.}, \nam{sbc} namelist).
+(\np{ln\_apr\_dyn}\forcode{=.true.}, \nam{sbc} namelist).
 The input atmospheric forcing defined via \np{sn\_apr} structure (\nam{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.
 …
   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}
+\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
 \forcode{.true.}, the equilibrium tidal forcing can be ramped up
 …
 \begin{description}
   \item[\np{nn\_isf}\forcode{ = 1}]:
   The ice shelf cavity is represented (\np{ln\_isfcav}\forcode{ = .true.} needed).
+  \item[\np{nn\_isf}\forcode{=1}]:
+  The ice shelf cavity is represented (\np{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}\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}\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).
 …
      There are 3 different ways to compute the exchange coeficient:
    \begin{description}
         \item[\np{nn\_gammablk}\forcode{ = 0}]:
+        \item[\np{nn\_gammablk}\forcode{=0}]:
      The salt and heat exchange coefficients are constant and defined by \np{rn\_gammas0} and \np{rn\_gammat0}.
 \[
 …
 \]
      This is the recommended formulation for ISOMIP.
    \item[\np{nn\_gammablk}\forcode{ = 1}]:
+   \item[\np{nn\_gammablk}\forcode{=1}]:
      The salt and heat exchange coefficients are velocity dependent and defined as
 \[
 …
      where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{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}\forcode{=2}]:
      The salt and heat exchange coefficients are velocity and stability dependent and defined as:
 \[
 …
      This formulation has not been extensively tested in \NEMO\ (not recommended).
    \end{description}
   \item[\np{nn\_isf}\forcode{ = 2}]:
+  \item[\np{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}).
+   (\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}]:
+  \item[\np{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 base of the ice shelf along the calving front (\np{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).
+  \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}).
    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}\forcode{=1}, the fluxes are spread over the top boundary layer thickness (\np{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}\forcode{=1} and \np{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}\forcode{=3} and \np{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
 …
 \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}\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:
 …
 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}\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.
 …
 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}\forcode{=.true.}.
 Two initialisation schemes are possible.
 …
   \np{nn\_test\_icebergs} is defined by four numbers in \np{nn\_test\_box} representing the corners of
   the geographical box: lonmin,lonmax,latmin,latmax
 \item[\np{nn\_test\_icebergs}\forcode{ = -1}]
+\item[\np{nn\_test\_icebergs}\forcode{=-1}]
   In this scheme, the model reads a calving file supplied in the \np{sn\_icb} parameter.
   This should be a file with a field on the configuration grid (typically ORCA)
 …
 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}\forcode{=.true.} in \nam{sbc} namelist. In addition, specific flags accounting for
 different processes should be activated as explained in the following sections.
 …
 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}\forcode{=.true.} has to be set.
 …
 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}\forcode{=.true.}, or through the zonal and
+meridional stress components by setting \np{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}\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.}).
 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}.
 …
 \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}\forcode{=.true.}) or bulk (\np{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.}),
+On forced mode using a flux formulation (\np{ln\_flx}\forcode{=.true.}),
 a feedback term \emph{must} be added to the surface heat flux $Q_{ns}^o$:
 \[
 …
 (seek advice from UKMO if necessary).
 Currently, the code is only designed to work when using the NCAR forcing option for \NEMO\ %GS: still true ?
 (with \textit{calc\_strair}\forcode{ = .true.} and \textit{calc\_Tsfc}\forcode{ = .true.} in the CICE name-list),
+(with \textit{calc\_strair}\forcode{=.true.} and \textit{calc\_Tsfc}\forcode{=.true.} in the CICE name-list),
 or alternatively when \NEMO\ is coupled to the HadGAM3 atmosphere model
 (with \textit{calc\_strair}\forcode{ = .false.} and \textit{calc\_Tsfc}\forcode{ = false}).
+(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
 (although coupling ocean and ice less frequently should work,
 …
 \begin{description}
 \item[\np{nn\_fwb}\forcode{ = 0}]
+\item[\np{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}\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}\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_TRA.tex

-                      r11524
+                      r11537
 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} or \np{ln\_tra\_mxl}\forcode{=.true.}), as described in \autoref{chap:DIA}.
 % ================================================================
 …
 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}\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
 the continuous equations.
 In other words, by setting $\tau = 1$ in (\autoref{eq:tra_adv}) we recover the discrete form of
+In other words, by setting $\tau=1$ in (\autoref{eq:tra_adv}) we recover the discrete form of
 the continuity equation which is used to calculate the vertical velocity.
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 …
 \begin{description}
 \item[linear free surface:]
   (\np{ln\_linssh}\forcode{ = .true.})
+  (\np{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}\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.
 …
 %        2nd and 4th order centred schemes
 % -------------------------------------------------------------------------------------------------------------
 \subsection[CEN: Centred scheme (\forcode{ln_traadv_cen = .true.})]
 {CEN: Centred scheme (\protect\np{ln\_traadv\_cen}\forcode{ = .true.})}
+\subsection[CEN: Centred scheme (\forcode{ln_traadv_cen=.true.})]
+{CEN: Centred scheme (\protect\np{ln\_traadv\_cen}\forcode{=.true.})}
 \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}\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 $4$.
 …
   \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}\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 = .true.})]
 {FCT: Flux Corrected Transport scheme (\protect\np{ln\_traadv\_fct}\forcode{ = .true.})}
+\subsection[FCT: Flux Corrected Transport scheme (\forcode{ln_traadv_fct=.true.})]
+{FCT: Flux Corrected Transport scheme (\protect\np{ln\_traadv\_fct}\forcode{=.true.})}
 \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}\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 $4$.
 …
 %        MUSCL scheme
 % -------------------------------------------------------------------------------------------------------------
 \subsection[MUSCL: Monotone Upstream Scheme for Conservative Laws (\forcode{ln_traadv_mus = .true.})]
 {MUSCL: Monotone Upstream Scheme for Conservative Laws (\protect\np{ln\_traadv\_mus}\forcode{ = .true.})}
+\subsection[MUSCL: Monotone Upstream Scheme for Conservative Laws (\forcode{ln_traadv_mus=.true.})]
+{MUSCL: Monotone Upstream Scheme for Conservative Laws (\protect\np{ln\_traadv\_mus}\forcode{=.true.})}
 \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}\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}\forcode{=.true.}).
 % -------------------------------------------------------------------------------------------------------------
 %        UBS scheme
 % -------------------------------------------------------------------------------------------------------------
 \subsection[UBS a.k.a. UP3: Upstream-Biased Scheme (\forcode{ln_traadv_ubs = .true.})]
 {UBS a.k.a. UP3: Upstream-Biased Scheme (\protect\np{ln\_traadv\_ubs}\forcode{ = .true.})}
+\subsection[UBS a.k.a. UP3: Upstream-Biased Scheme (\forcode{ln_traadv_ubs=.true.})]
+{UBS a.k.a. UP3: Upstream-Biased Scheme (\protect\np{ln\_traadv\_ubs}\forcode{=.true.})}
 \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}\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}\forcode{=2 or 4}).
 For stability reasons (see \autoref{chap:STP}), the first term  in \autoref{eq:tra_adv_ubs}
 …
 %        QCK scheme
 % -------------------------------------------------------------------------------------------------------------
 \subsection[QCK: QuiCKest scheme (\forcode{ln_traadv_qck = .true.})]
 {QCK: QuiCKest scheme (\protect\np{ln\_traadv\_qck}\forcode{ = .true.})}
+\subsection[QCK: QuiCKest scheme (\forcode{ln_traadv_qck=.true.})]
+{QCK: QuiCKest scheme (\protect\np{ln\_traadv\_qck}\forcode{=.true.})}
 \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}\forcode{=.true.}.
 QUICKEST implementation can be found in the \mdl{traadv\_qck} module.
 …
 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:STP}).
 When \np{ln\_traldf\_msc}\forcode{ = .true.}, a Method of Stabilizing Correction is used in which
+When \np{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}.
 …
 \begin{description}
 \item[\np{ln\_traldf\_OFF}\forcode{ = .true.}:]
+\item[\np{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}\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}\forcode{=.true.}]:
   a bilaplacian operator is selected.
   This biharmonic operator takes the following expression:
 …
 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}\forcode{=.true.}) or
 when a horizontal (\ie\ geopotential) operator is demanded in \textit{z}-coordinate
 (\np{ln\_traldf\_hor} and \np{ln\_zco} equal \forcode{.true.}).
+(\np{ln\_traldf\_hor} and \np{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} equals \forcode{.true.},
+(\np{ln\_traldf\_iso} or \np{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} equal \forcode{.true.})
+(\np{ln\_traldf\_hor} and \np{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
 …
 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} 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.}.
 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}\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}\forcode{=.true.},
+we have \np{ln\_traldf\_iso}\forcode{=.true.},
+or both \np{ln\_traldf\_hor}\forcode{=.true.} and \np{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}\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}.
 …
 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}\forcode{=.true.}).
 A complete description of the algorithm is given in \autoref{apdx:triad}.
 …
 respectively.
 Generally, $A_w^{vT} = A_w^{vS}$ except when double diffusive mixing is parameterised
 (\ie\ \np{ln\_zdfddm} equals \forcode{.true.},).
+(\ie\ \np{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:STP}).
 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}\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.}),
+When the penetrative solar radiation option is used (\np{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}\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:PE_tra_T} and
 the surface boundary condition is modified to take into account only the non-penetrative part of the surface
 …
 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}\forcode{=.true.})
 a chlorophyll-independent monochromatic formulation is chosen for the shorter wavelengths,
 leading to the following expression \citep{paulson.simpson_JPO77}:
 …
 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}\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}\forcode{=0}]
   a constant 0.05 g.Chl/L value everywhere ;
 \item[\np{nn\_chldta}\forcode{ = 1}]
+\item[\np{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}\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}\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 = .true.})]
+\subsection[Bottom boundary condition (\textit{trabbc.F90}) - \forcode{ln_trabbc=.true.})]
 {Bottom boundary condition (\protect\mdl{trabbc})}
 \label{subsec:TRA_bbc}
 …
 % Bottom Boundary Layer
 % ================================================================
 \section[Bottom boundary layer (\textit{trabbl.F90} - \forcode{ln_trabbl = .true.})]
 {Bottom boundary layer (\protect\mdl{trabbl} - \protect\np{ln\_trabbl}\forcode{ = .true.})}
+\section[Bottom boundary layer (\textit{trabbl.F90} - \forcode{ln_trabbl=.true.})]
+{Bottom boundary layer (\protect\mdl{trabbl} - \protect\np{ln\_trabbl}\forcode{=.true.})}
 \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}\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}\forcode{=.true.} and \np{nn\_bbl\_ldf} set to 1),
 the diffusive flux between two adjacent cells at the ocean floor is given by
 \[
 …
 %        Advective BBL
 % -------------------------------------------------------------------------------------------------------------
 \subsection[Advective bottom boundary layer (\forcode{nn_bbl_adv = [12]})]
 {Advective bottom boundary layer (\protect\np{nn\_bbl\_adv}\forcode{ = [12]})}
+\subsection[Advective bottom boundary layer (\forcode{nn_bbl_adv=[12]})]
+{Advective bottom boundary layer (\protect\np{nn\_bbl\_adv}\forcode{=[12]})}
 \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}\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}\forcode{=1}:
 the downslope velocity is chosen to be the Eulerian ocean velocity just above the topographic step
 (see black arrow in \autoref{fig: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}\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}.
 …
 (\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}.
+Its default value is \np{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}).
+(\jp{ln\_linssh}\forcode{=.true.}) (see \autoref{subsec:TRA_sbc}).
 Not also that in constant volume case, the time stepping is performed on $T$, not on its content, $e_{3t}T$.
 …
 \begin{description}
 \item[\np{ln\_teos10}\forcode{ = .true.}]
+\item[\np{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}\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}\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
 …
 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}\forcode{=.true.}) at bottom and top (\np{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}\forcode{=.true.}) are computed in the same way as
 for the bottom.
 So, only the bottom interpolation is explained below.
 …
       \protect\label{fig:Partial_step_scheme}
       Discretisation of the horizontal difference and average of tracers in the $z$-partial step coordinate
       (\protect\np{ln\_zps}\forcode{ = .true.}) in the case $(e3w_k^{i + 1} - e3w_k^i) > 0$.
+      (\protect\np{ln\_zps}\forcode{=.true.}) in the case $(e3w_k^{i + 1} - e3w_k^i) > 0$.
       A linear interpolation is used to estimate $\widetilde T_k^{i + 1}$,
       the tracer value at the depth of the shallower tracer point of the two adjacent bottom $T$-points.

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

-                      r11435
+                      r11537
 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}\forcode{=.true.}) or a backward time stepping scheme
+%(\np{ln\_zdfexp}\forcode{=.false.}) depending on the magnitude of the mixing coefficients,
 %and thus of the formulation used (see \autoref{chap:STP}).
 …
 %        Constant
 % -------------------------------------------------------------------------------------------------------------
 \subsection[Constant (\forcode{ln_zdfcst = .true.})]
 {Constant (\protect\np{ln\_zdfcst}\forcode{ = .true.})}
+\subsection[Constant (\forcode{ln_zdfcst=.true.})]
+{Constant (\protect\np{ln\_zdfcst}\forcode{=.true.})}
 \label{subsec:ZDF_cst}
 …
 %        Richardson Number Dependent
 % -------------------------------------------------------------------------------------------------------------
 \subsection[Richardson number dependent (\forcode{ln_zdfric = .true.})]
 {Richardson number dependent (\protect\np{ln\_zdfric}\forcode{ = .true.})}
+\subsection[Richardson number dependent (\forcode{ln_zdfric=.true.})]
+{Richardson number dependent (\protect\np{ln\_zdfric}\forcode{=.true.})}
 \label{subsec:ZDF_ric}
 …
 %--------------------------------------------------------------------------------------------------------------
 When \np{ln\_zdfric}\forcode{ = .true.}, a local Richardson number dependent formulation for the vertical momentum and
+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.
 The vertical mixing coefficients are diagnosed from the large scale variables computed by the model.
 …
 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}\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
 …
 %        TKE Turbulent Closure Scheme
 % -------------------------------------------------------------------------------------------------------------
 \subsection[TKE turbulent closure scheme (\forcode{ln_zdftke = .true.})]
 {TKE turbulent closure scheme (\protect\np{ln\_zdftke}\forcode{ = .true.})}
+\subsection[TKE turbulent closure scheme (\forcode{ln_zdftke=.true.})]
+{TKE turbulent closure scheme (\protect\np{ln\_zdftke}\forcode{=.true.})}
 \label{subsec:ZDF_tke}
 %--------------------------------------------namzdf_tke--------------------------------------------------
 …
 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}\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}\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:tke_mxl0_1} and then bounded such that:
 …
 where $l^{(k)}$ is computed using \autoref{eq: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)$, while in the \np{nn\_mxl}\forcode{ = 3} case,
+In the \np{nn\_mxl}\forcode{=2} case, the dissipation and mixing length scales take the same value:
+$ l_k=  l_\epsilon = \min \left(\ l_{up} \;,\;  l_{dwn}\ \right)$, while in the \np{nn\_mxl}\forcode{=3} case,
 the dissipation and mixing turbulent length scales are give as in \citet{gaspar.gregoris.ea_JGR90}:
 \[
 …
 (\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}\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,
 …
 (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 vertical mixing length scale, $h_\tau$, can be set as a 10~m uniform value (\np{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}\forcode{=1}).
+Note that two other option exist, \np{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.
 …
 %        GLS Generic Length Scale Scheme
 % -------------------------------------------------------------------------------------------------------------
 \subsection[GLS: Generic Length Scale (\forcode{ln_zdfgls = .true.})]
 {GLS: Generic Length Scale (\protect\np{ln\_zdfgls}\forcode{ = .true.})}
+\subsection[GLS: Generic Length Scale (\forcode{ln_zdfgls=.true.})]
+{GLS: Generic Length Scale (\protect\np{ln\_zdfgls}\forcode{=.true.})}
 \label{subsec:ZDF_gls}
 …
       \protect\label{tab:GLS}
       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}\forcode{=.true.} and controlled by the \protect\np{nn\_clos} namelist variable in \protect\nam{zdf\_gls}.
+    }
   \end{center}
 …
 $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}\forcode{=0, 3}, resp.).
 The value of $C_{0\mu}$ depends on the choice of the stability function.
 …
 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.},
+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.
 …
 %        OSM OSMOSIS BL Scheme
 % -------------------------------------------------------------------------------------------------------------
 \subsection[OSM: OSMosis boundary layer scheme (\forcode{ln_zdfosm = .true.})]
 {OSM: OSMosis boundary layer scheme (\protect\np{ln\_zdfosm}\forcode{ = .true.})}
+\subsection[OSM: OSMosis boundary layer scheme (\forcode{ln_zdfosm=.true.})]
+{OSM: OSMosis boundary layer scheme (\protect\np{ln\_zdfosm}\forcode{=.true.})}
 \label{subsec:ZDF_osm}
 %--------------------------------------------namzdf_osm---------------------------------------------------------
 …
 %       Non-Penetrative Convective Adjustment
 % -------------------------------------------------------------------------------------------------------------
 \subsection[Non-penetrative convective adjustment (\forcode{ln_tranpc = .true.})]
 {Non-penetrative convective adjustment (\protect\np{ln\_tranpc}\forcode{ = .true.})}
+\subsection[Non-penetrative convective adjustment (\forcode{ln_tranpc=.true.})]
+{Non-penetrative convective adjustment (\protect\np{ln\_tranpc}\forcode{=.true.})}
 \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.}.
+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 water column, but only until the density structure becomes neutrally stable
 …
 %       Enhanced Vertical Diffusion
 % -------------------------------------------------------------------------------------------------------------
 \subsection[Enhanced vertical diffusion (\forcode{ln_zdfevd = .true.})]
 {Enhanced vertical diffusion (\protect\np{ln\_zdfevd}\forcode{ = .true.})}
+\subsection[Enhanced vertical diffusion (\forcode{ln_zdfevd=.true.})]
+{Enhanced vertical diffusion (\protect\np{ln\_zdfevd}\forcode{=.true.})}
 \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}\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}\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},
 the four neighbouring $A_u^{vm} \;\mbox{and}\;A_v^{vm}$ values also, are set equal to
 the namelist parameter \np{rn\_avevd}.
 …
 %       Turbulent Closure Scheme
 % -------------------------------------------------------------------------------------------------------------
 \subsection{Handling convection with turbulent closure schemes (\forcode{ln_zdf\{tke,gls,osm\} = .true.})}
+\subsection{Handling convection with turbulent closure schemes (\forcode{ln_zdf{tke,gls,osm}=.true.})}
 \label{subsec:ZDF_tcs}
 …
 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}\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 = .true.})]
 {Double diffusion mixing (\protect\np{ln\_zdfddm}\forcode{ = .true.})}
+\section[Double diffusion mixing (\forcode{ln_zdfddm=.true.})]
+{Double diffusion mixing (\protect\np{ln\_zdfddm}\forcode{=.true.})}
 \label{subsec:ZDF_ddm}
 …
 %       Linear Bottom Friction
 % -------------------------------------------------------------------------------------------------------------
  \subsection[Linear top/bottom friction (\forcode{ln_lin = .true.})]
  {Linear top/bottom friction (\protect\np{ln\_lin}\forcode{ = .true.)}}
+ \subsection[Linear top/bottom friction (\forcode{ln_lin=.true.})]
+ {Linear top/bottom friction (\protect\np{ln\_lin}\forcode{=.true.)}}
  \label{subsec:ZDF_drg_linear}
 …
 \]
 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.
+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.
 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}\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
 …
 %       Non-Linear Bottom Friction
 % -------------------------------------------------------------------------------------------------------------
  \subsection[Non-linear top/bottom friction (\forcode{ln_non_lin = .true.})]
  {Non-linear top/bottom friction (\protect\np{ln\_non\_lin}\forcode{ = .true.})}
+ \subsection[Non-linear top/bottom friction (\forcode{ln_non_lin=.true.})]
+ {Non-linear top/bottom friction (\protect\np{ln\_non\_lin}\forcode{=.true.})}
  \label{subsec:ZDF_drg_nonlinear}
 …
 $C_D$= \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.}).
+(\np{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}.
 …
 %       Bottom Friction Log-layer
 % -------------------------------------------------------------------------------------------------------------
  \subsection[Log-layer top/bottom friction (\forcode{ln_loglayer = .true.})]
  {Log-layer top/bottom friction (\protect\np{ln\_loglayer}\forcode{ = .true.})}
+ \subsection[Log-layer top/bottom friction (\forcode{ln_loglayer=.true.})]
+ {Log-layer top/bottom friction (\protect\np{ln\_loglayer}\forcode{=.true.})}
  \label{subsec:ZDF_drg_loglayer}
 …
 \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.}).
+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}.
 …
 %       Explicit bottom Friction
 % -------------------------------------------------------------------------------------------------------------
  \subsection{Explicit top/bottom friction (\forcode{ln_drgimp = .false.})}
+ \subsection{Explicit top/bottom friction (\forcode{ln_drgimp=.false.})}
  \label{subsec:ZDF_drg_stability}
 …
 %       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}\forcode{=.true.})}
  \label{subsec:ZDF_drg_imp}
 …
  \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}\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 = .true.})]
 {Internal wave-driven mixing (\protect\np{ln\_zdfiwm}\forcode{ = .true.})}
+\section[Internal wave-driven mixing (\forcode{ln_zdfiwm=.true.})]
+{Internal wave-driven mixing (\protect\np{ln\_zdfiwm}\forcode{=.true.})}
 \label{subsec:ZDF_tmx_new}
 …
 % surface wave-induced mixing
 % ================================================================
 \section[Surface wave-induced mixing (\forcode{ln_zdfswm = .true.})]
 {Surface wave-induced mixing (\protect\np{ln\_zdfswm}\forcode{ = .true.})}
+\section[Surface wave-induced mixing (\forcode{ln_zdfswm=.true.})]
+{Surface wave-induced mixing (\protect\np{ln\_zdfswm}\forcode{=.true.})}
 \label{subsec:ZDF_swm}
 …
 and diffusivity coefficients.
 In order to account for this contribution set: \forcode{ln_zdfswm = .true.},
 then wave interaction has to be activated through \forcode{ln_wave = .true.},
 the Stokes Drift can be evaluated by setting \forcode{ln_sdw = .true.}
+In order to account for this contribution set: \forcode{ln_zdfswm=.true.},
+then wave interaction has to be activated through \forcode{ln_wave=.true.},
+the Stokes Drift can be evaluated by setting \forcode{ln_sdw=.true.}
 (see \autoref{subsec:SBC_wave_sdw})
 and the needed wave fields can be provided either in forcing or coupled mode
 …
 % Adaptive-implicit vertical advection
 % ================================================================
 \section[Adaptive-implicit vertical advection (\forcode{ln_zad_Aimp = .true.})]
 {Adaptive-implicit vertical advection(\protect\np{ln\_zad\_Aimp}\forcode{ = .true.})}
+\section[Adaptive-implicit vertical advection (\forcode{ln_zad_Aimp=.true.})]
+{Adaptive-implicit vertical advection(\protect\np{ln\_zad\_Aimp}\forcode{=.true.})}
 \label{subsec:ZDF_aimp}
 …
 interest or due to short-lived conditions such that the extra numerical diffusion or
 viscosity does not greatly affect the overall solution. With such applications, setting:
 \forcode{ln_zad_Aimp = .true.} should allow much longer model timesteps to be used whilst
+\forcode{ln_zad_Aimp=.true.} should allow much longer model timesteps to be used whilst
 retaining the accuracy of the high order explicit schemes over most of the domain.
 …
 \noindent which were chosen to provide a slightly more stable and less noisy solution. The
 result when using the default value of \forcode{nn_rdt = 10.} without adaptive-implicit
+result when using the default value of \forcode{nn_rdt=10.} without adaptive-implicit
 vertical velocity is illustrated in \autoref{fig:zad_Aimp_overflow_frames}. The mass of
 cold water, initially sitting on the shelf, moves down the slope and forms a
 bottom-trapped, dense plume. Even with these extra physics choices the model is close to
 stability limits and attempts with \forcode{nn_rdt = 30.} will fail after about 5.5 hours
+stability limits and attempts with \forcode{nn_rdt=30.} will fail after about 5.5 hours
 with excessively high horizontal velocities. This time-scale corresponds with the time the
 plume reaches the steepest part of the topography and, although detected as a horizontal
 …
 significantly altering the solution (although at this extreme the plume is more diffuse
 and has not travelled so far).  Notably, the solution with and without the scheme is
 slightly different even with \forcode{nn_rdt = 10.}; suggesting that the base run was
+slightly different even with \forcode{nn_rdt=10.}; suggesting that the base run was
 close enough to instability to trigger the scheme despite completing successfully.
 To assist in diagnosing how active the scheme is, in both location and time, the 3D

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

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304	304	The default value is 1, as recommended by \citet{Roullet2000?}
305	305
306		\colorbox{red}{\np{rnu}\forcode{ = 1} to be suppressed from namelist !}
	306	\colorbox{red}{\np{rnu}\forcode{=1} to be suppressed from namelist !}
307	307
308	308	%-------------------------------------------------------------

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

-                      r11435
+                      r11537
 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:STP_mLF}),
+Its default value is \np{rn\_atfp}\forcode{=10.e-3} (see \autoref{sec:STP_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}\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}\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:TimeStep_flowchart}).

NEMO/trunk/doc/latex/SI3/main/chapters.tex

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1	1	\subfile{../subfiles/todolist}
2
3		~~\subfile{../subfiles/introduction} % Introduction~~
4	2
5	3	\subfile{../subfiles/chap_model_basics}

NEMO/trunk/doc/latex/SI3/main/definitions.tex

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12	12
13	13	%% Color for document (frontpage banner, links and chapter boxes)
14		\def \setcolor{ \definecolor{manualcolor}{cmyk}{0, 0, 0, 0.4} }
	14	\def \setmanualcolor{ \definecolor{manualcolor}{cmyk}{0, 0, 0, 0.4} }
15	15
16	16	%% IPSL publication number

NEMO/trunk/doc/latex/SI3/subfiles/chap_bdy_agrif.tex

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9	9	\chapter{BDY and AGRIF with SI$^3$}
10	10	\label{chap:REG}
11		\~~mini~~toc
	11	\chaptertoc
12	12
13	13	\newpage

NEMO/trunk/doc/latex/SI3/subfiles/chap_domain.tex

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10	10	\chapter{Time, space and thickness space domain}
11	11	\label{chap:DOM}
12		\~~mini~~toc
	12	\chaptertoc
13	13
14	14	\newpage

NEMO/trunk/doc/latex/SI3/subfiles/chap_dynamics.tex

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10	10	\chapter{Ice dynamics}
11	11	\label{chap:DYN}
12		\~~mini~~toc
	12	\chaptertoc
13	13
14	14	\newpage

NEMO/trunk/doc/latex/SI3/subfiles/chap_interfaces.tex

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9	9	\chapter{Ice-atmosphere and ice-ocean interfaces}
10	10	\label{chap:INT}
11		\~~mini~~toc
	11	\chaptertoc
12	12
13	13	\newpage

NEMO/trunk/doc/latex/SI3/subfiles/chap_miscellaneous.tex

r11015	r11537
9	9	\chapter{Miscellaneous topics}
10	10	\label{chap:MIS}
11		\~~mini~~toc
	11	\chaptertoc
12	12
13	13	\newpage

NEMO/trunk/doc/latex/SI3/subfiles/chap_model_basics.tex

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9	9	\chapter{Model Basics}
10	10	\label{chap:MB}
11		\~~mini~~toc
	11	\chaptertoc
12	12
13	13	\newpage

NEMO/trunk/doc/latex/SI3/subfiles/chap_output_diagnostics.tex

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9	9	\chapter{Output and diagnostics}
10	10	\label{chap:DIA}
11		\~~mini~~toc
	11	\chaptertoc
12	12
13	13	\newpage

NEMO/trunk/doc/latex/SI3/subfiles/chap_radiative_transfer.tex

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13	13	\chapter{Radiative transfer}
14	14	\label{chap:RAD}
15		\~~mini~~toc
	15	\chaptertoc
16	16
17	17	\newpage

NEMO/trunk/doc/latex/SI3/subfiles/chap_ridging_rafting.tex

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10	10	\chapter{Ridging and rafting}
11	11	\label{chap:RDG}
12		\~~mini~~toc
	12	\chaptertoc
13	13
14	14	\newpage

NEMO/trunk/doc/latex/SI3/subfiles/chap_single_category_use.tex

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11	11
12	12	\label{chap:INT}
13		\~~mini~~toc
	13	\chaptertoc
14	14
15	15	\newpage

NEMO/trunk/doc/latex/SI3/subfiles/chap_thermo.tex

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9	9	\chapter{Ice thermodynamics}
10	10	\label{chap:THD}
11		\~~mini~~toc
	11	\chaptertoc
12	12
13	13	\newpage

NEMO/trunk/doc/latex/SI3/subfiles/chap_transport.tex

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10	10	\chapter{Ice transport}
11	11	\label{chap:TRP}
12		\~~mini~~toc
	12	\chaptertoc
13	13
14	14	\newpage

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