Changeset 11179 for NEMO/trunk/doc/latex/NEMO/subfiles/chap_TRA.tex

Timestamp:

2019-06-25T15:46:19+02:00 (5 years ago)

Author:

nicolasmartin

Message:

Add alternate section titles to avoid useless index links in ToC

File:

• NEMO/trunk/doc/latex/NEMO/subfiles/chap_TRA.tex (modified) (48 diffs)

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

@@ -55 +55 @@
 
 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}.
 
 % ================================================================
 % Tracer Advection
 % ================================================================
-\section{Tracer advection (\protect\mdl{traadv})}
+\section[Tracer advection (\textit{traadv.F90})]
+{Tracer advection (\protect\mdl{traadv})}
 \label{sec:TRA_adv}
 %------------------------------------------namtra_adv-----------------------------------------------------
@@ -81 +82 @@
 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
@@ -119 +120 @@
 \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
@@ -127 +128 @@
   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.
@@ -183 +184 @@
 %        2nd and 4th order centred schemes
 % -------------------------------------------------------------------------------------------------------------
-\subsection{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 $4$.
@@ -220 +222 @@
   \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,
@@ -250 +252 @@
 %        FCT scheme  
 % -------------------------------------------------------------------------------------------------------------
-\subsection{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 $4$.
@@ -300 +303 @@
 %        MUSCL scheme  
 % -------------------------------------------------------------------------------------------------------------
-\subsection{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.
 
@@ -331 +335 @@
 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 (\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.
 
@@ -369 +374 @@
 \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\_cen\_v}~\forcode{= 2 or 4}).
+(\np{nn\_cen\_v}\forcode{ = 2 or 4}).
 
 For stability reasons (see \autoref{chap:STP}), the first term  in \autoref{eq:tra_adv_ubs}
@@ -408 +413 @@
 %        QCK scheme  
 % -------------------------------------------------------------------------------------------------------------
-\subsection{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.
 
@@ -431 +437 @@
 % Tracer Lateral Diffusion
 % ================================================================
-\section{Tracer lateral diffusion (\protect\mdl{traldf})}
+\section[Tracer lateral diffusion (\textit{traldf.F90})]
+{Tracer lateral diffusion (\protect\mdl{traldf})}
 \label{sec:TRA_ldf}
 %-----------------------------------------nam_traldf------------------------------------------------------
@@ -453 +460 @@
 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}.
 
@@ -459 +466 @@
 %        Type of operator
 % -------------------------------------------------------------------------------------------------------------
-\subsection[Type of operator (\protect\np{ln\_traldf}\{\_NONE,\_lap,\_blp\}\})]{Type of operator (\protect\np{ln\_traldf\_NONE}, \protect\np{ln\_traldf\_lap}, or \protect\np{ln\_traldf\_blp}) } 
+\subsection[Type of operator (\texttt{ln\_traldf}\{\texttt{\_NONE,\_lap,\_blp}\})]
+{Type of operator (\protect\np{ln\_traldf\_NONE}, \protect\np{ln\_traldf\_lap}, or \protect\np{ln\_traldf\_blp}) } 
 \label{subsec:TRA_ldf_op}
 
@@ -465 +473 @@
 
 \begin{description}
-\item[\np{ln\_traldf\_NONE}~\forcode{= .true.}:]
+\item[\np{ln\_traldf\_NONE}\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:  $\mathpzc{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:
@@ -493 +501 @@
 %        Direction of action
 % -------------------------------------------------------------------------------------------------------------
-\subsection[Action direction (\protect\np{ln\_traldf}\{\_lev,\_hor,\_iso,\_triad\})]{Direction of action (\protect\np{ln\_traldf\_lev}, \protect\np{ln\_traldf\_hor}, \protect\np{ln\_traldf\_iso}, or \protect\np{ln\_traldf\_triad}) } 
+\subsection[Action direction (\texttt{ln\_traldf}\{\texttt{\_lev,\_hor,\_iso,\_triad}\})]
+{Direction of action (\protect\np{ln\_traldf\_lev}, \protect\np{ln\_traldf\_hor}, \protect\np{ln\_traldf\_iso}, or \protect\np{ln\_traldf\_triad}) } 
 \label{subsec:TRA_ldf_dir}
 
 The choice of a direction of action determines the form of operator used.
 The operator is a simple (re-entrant) laplacian acting in the (\textbf{i},\textbf{j}) plane when
-iso-level option is used (\np{ln\_traldf\_lev}~\forcode{= .true.}) or
+iso-level option is used (\np{ln\_traldf\_lev}\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.}).
@@ -519 +528 @@
 %       iso-level operator
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Iso-level (bi -)laplacian operator ( \protect\np{ln\_traldf\_iso}) }
+\subsection[Iso-level (bi-)laplacian operator (\texttt{ln\_traldf\_iso})]
+{Iso-level (bi-)laplacian operator ( \protect\np{ln\_traldf\_iso})}
 \label{subsec:TRA_ldf_lev}
 
@@ -537 +547 @@
 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.
@@ -550 +560 @@
 %         Rotated laplacian operator
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Standard and triad (bi -)laplacian operator}
+\subsection{Standard and triad (bi-)laplacian operator}
 \label{subsec:TRA_ldf_iso_triad}
 
-%&&    Standard rotated (bi -)laplacian operator
+%&&    Standard rotated (bi-)laplacian operator
 %&& ----------------------------------------------
-\subsubsection{Standard rotated (bi -)laplacian operator (\protect\mdl{traldf\_iso})}
+\subsubsection[Standard rotated (bi-)laplacian operator (\textit{traldf\_iso.F90})]
+{Standard rotated (bi-)laplacian operator (\protect\mdl{traldf\_iso})}
 \label{subsec:TRA_ldf_iso}
 The general form of the second order lateral tracer subgrid scale physics (\autoref{eq:PE_zdf})
@@ -574 +585 @@
 $r_1$ 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
@@ -592 +603 @@
 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}.
 
-%&&     Triad rotated (bi -)laplacian operator
+%&&     Triad rotated (bi-)laplacian operator
 %&&  -------------------------------------------
-\subsubsection{Triad rotated (bi -)laplacian operator (\protect\np{ln\_traldf\_triad})}
+\subsubsection[Triad rotated (bi-)laplacian operator (\textit{ln\_traldf\_triad})]
+{Triad rotated (bi-)laplacian operator (\protect\np{ln\_traldf\_triad})}
 \label{subsec:TRA_ldf_triad}
 
-If the Griffies triad scheme is employed (\np{ln\_traldf\_triad}~\forcode{= .true.}; see \autoref{apdx:triad})
+If the Griffies triad scheme is employed (\np{ln\_traldf\_triad}\forcode{ = .true.}; see \autoref{apdx:triad})
 
 An alternative scheme developed by \cite{griffies.gnanadesikan.ea_JPO98} which ensures tracer variance decreases
-is also available in \NEMO (\np{ln\_traldf\_grif}~\forcode{= .true.}).
+is also available in \NEMO (\np{ln\_traldf\_grif}\forcode{ = .true.}).
 A complete description of the algorithm is given in \autoref{apdx:triad}.
 
@@ -632 +644 @@
 % Tracer Vertical Diffusion
 % ================================================================
-\section{Tracer vertical diffusion (\protect\mdl{trazdf})}
+\section[Tracer vertical diffusion (\textit{trazdf.F90})]
+{Tracer vertical diffusion (\protect\mdl{trazdf})}
 \label{sec:TRA_zdf}
 %--------------------------------------------namzdf---------------------------------------------------------
@@ -663 +676 @@
 
 The large eddy coefficient found in the mixed layer together with high vertical resolution implies that
-in the case of explicit time stepping (\np{ln\_zdfexp}~\forcode{= .true.})
+in the case of explicit time stepping (\np{ln\_zdfexp}\forcode{ = .true.})
 there would be too restrictive a constraint on the time step.
 Therefore, the default implicit time stepping is preferred for the vertical diffusion since
 it overcomes the stability constraint.
-A forward time differencing scheme (\np{ln\_zdfexp}~\forcode{= .true.}) using
+A forward time differencing scheme (\np{ln\_zdfexp}\forcode{ = .true.}) using
 a time splitting technique (\np{nn\_zdfexp} $> 1$) is provided as an alternative.
 Namelist variables \np{ln\_zdfexp} and \np{nn\_zdfexp} apply to both tracers and dynamics.
@@ -680 +693 @@
 %        surface boundary condition
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Surface boundary condition (\protect\mdl{trasbc})}
+\subsection[Surface boundary condition (\textit{trasbc.F90})]
+{Surface boundary condition (\protect\mdl{trasbc})}
 \label{subsec:TRA_sbc}
 
@@ -730 +744 @@
 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 $Q_{ns}$.
@@ -753 +767 @@
 %        Solar Radiation Penetration 
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Solar radiation penetration (\protect\mdl{traqsr})}
+\subsection[Solar radiation penetration (\textit{traqsr.F90})]
+{Solar radiation penetration (\protect\mdl{traqsr})}
 \label{subsec:TRA_qsr}
 %--------------------------------------------namqsr--------------------------------------------------------
@@ -761 +776 @@
 
 Options are defined through the \ngn{namtra\_qsr} namelist variables.
-When the penetrative solar radiation option is used (\np{ln\_flxqsr}~\forcode{= .true.}),
+When the penetrative solar radiation option is used (\np{ln\_flxqsr}\forcode{ = .true.}),
 the solar radiation penetrates the top few tens of meters of the ocean.
-If it is not used (\np{ln\_flxqsr}~\forcode{= .false.}) all the heat flux is absorbed in the first ocean level.
+If it is not used (\np{ln\_flxqsr}\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 
@@ -792 +807 @@
 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}:
@@ -820 +835 @@
 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
 61 nonuniform chlorophyll classes ranging from 0.01 to 10 g.Chl/L
@@ -827 +842 @@
 
 \begin{description}
-\item[\np{nn\_chdta}~\forcode{= 0}]
+\item[\np{nn\_chdta}\forcode{ = 0}]
   a constant 0.05 g.Chl/L value everywhere ; 
-\item[\np{nn\_chdta}~\forcode{= 1}]
+\item[\np{nn\_chdta}\forcode{ = 1}]
   an observed time varying chlorophyll deduced from satellite surface ocean color measurement spread uniformly in
   the vertical direction;
-\item[\np{nn\_chdta}~\forcode{= 2}]
+\item[\np{nn\_chdta}\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
@@ -874 +889 @@
 %        Bottom Boundary Condition
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Bottom boundary condition (\protect\mdl{trabbc})}
+\subsection[Bottom boundary condition (\textit{trabbc.F90})]
+{Bottom boundary condition (\protect\mdl{trabbc})}
 \label{subsec:TRA_bbc}
 %--------------------------------------------nambbc--------------------------------------------------------
@@ -912 +928 @@
 % Bottom Boundary Layer
 % ================================================================
-\section{Bottom boundary layer (\protect\mdl{trabbl} - \protect\key{trabbl})}
+\section[Bottom boundary layer (\textit{trabbl.F90} - \texttt{\textbf{key\_trabbl}})]
+{Bottom boundary layer (\protect\mdl{trabbl} - \protect\key{trabbl})}
 \label{sec:TRA_bbl}
 %--------------------------------------------nambbl---------------------------------------------------------
@@ -944 +961 @@
 %        Diffusive BBL
 % -------------------------------------------------------------------------------------------------------------
-\subsection{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}
 
@@ -983 +1001 @@
 %        Advective BBL
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Advective bottom boundary layer  (\protect\np{nn\_bbl\_adv}~\forcode{= 1..2})}
+\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}
 
@@ -1014 +1033 @@
 %%%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}.
@@ -1025 +1044 @@
 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}.
@@ -1074 +1093 @@
 % Tracer damping
 % ================================================================
-\section{Tracer damping (\protect\mdl{tradmp})}
+\section[Tracer damping (\textit{tradmp.F90})]
+{Tracer damping (\protect\mdl{tradmp})}
 \label{sec:TRA_dmp}
 %--------------------------------------------namtra_dmp-------------------------------------------------
@@ -1129 +1149 @@
 % Tracer time evolution
 % ================================================================
-\section{Tracer time evolution (\protect\mdl{tranxt})}
+\section[Tracer time evolution (\textit{tranxt.F90})]
+{Tracer time evolution (\protect\mdl{tranxt})}
 \label{sec:TRA_nxt}
 %--------------------------------------------namdom-----------------------------------------------------
@@ -1151 +1172 @@
 (\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{lk\_vvl}~\forcode{= .false.}) (see \autoref{subsec:TRA_sbc}).
+(\jp{lk\_vvl}\forcode{ = .false.}) (see \autoref{subsec:TRA_sbc}).
 Not also that in constant volume case, the time stepping is performed on $T$, not on its content, $e_{3t}T$.
 
@@ -1166 +1187 @@
 % Equation of State (eosbn2) 
 % ================================================================
-\section{Equation of state (\protect\mdl{eosbn2}) }
+\section[Equation of state (\textit{eosbn2.F90})]
+{Equation of state (\protect\mdl{eosbn2})}
 \label{sec:TRA_eosbn2}
 %--------------------------------------------nameos-----------------------------------------------------
@@ -1176 +1198 @@
 %        Equation of State
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Equation of seawater (\protect\np{nn\_eos}~\forcode{= -1..1})}
+\subsection[Equation of seawater (\forcode{nn_eos = {-1,1}})]
+{Equation of seawater (\protect\np{nn\_eos}\forcode{ = {-1,1}})}
 \label{subsec:TRA_eos}
 
@@ -1210 +1233 @@
 
 \begin{description}
-\item[\np{nn\_eos}~\forcode{= -1}]
+\item[\np{nn\_eos}\forcode{ = -1}]
   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,
@@ -1229 +1252 @@
   either computing the air-sea and ice-sea fluxes (forced mode) or
   sending the SST field to the atmosphere (coupled mode).
-\item[\np{nn\_eos}~\forcode{= 0}]
+\item[\np{nn\_eos}\forcode{ = 0}]
   the polyEOS80-bsq equation of seawater is used.
   It takes the same polynomial form as the polyTEOS10, but the coefficients have been optimized to
@@ -1241 +1264 @@
   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{nn\_eos}~\forcode{= 1}]
+\item[\np{nn\_eos}\forcode{ = 1}]
   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
@@ -1303 +1326 @@
 %        Brunt-V\"{a}is\"{a}l\"{a} Frequency
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Brunt-V\"{a}is\"{a}l\"{a} frequency (\protect\np{nn\_eos}~\forcode{= 0..2})}
+\subsection[Brunt-V\"{a}is\"{a}l\"{a} frequency (\forcode{nn_eos = [0-2]})]
+{Brunt-V\"{a}is\"{a}l\"{a} frequency (\protect\np{nn\_eos}\forcode{ = [0-2]})}
 \label{subsec:TRA_bn2}
 
@@ -1357 +1381 @@
 % Horizontal Derivative in zps-coordinate 
 % ================================================================
-\section{Horizontal derivative in \textit{zps}-coordinate (\protect\mdl{zpshde})}
+\section[Horizontal derivative in \textit{zps}-coordinate (\textit{zpshde.F90})]
+{Horizontal derivative in \textit{zps}-coordinate (\protect\mdl{zpshde})}
 \label{sec:TRA_zpshde}
 
@@ -1363 +1388 @@
 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.
@@ -1383 +1408 @@
       \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.