Changeset 11179


Ignore:
Timestamp:
2019-06-25T15:46:19+02:00 (14 months ago)
Author:
nicolasmartin
Message:

Add alternate section titles to avoid useless index links in ToC

Location:
NEMO/trunk/doc/latex/NEMO
Files:
1 added
1 deleted
12 edited

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

    r11151 r11179  
    3434% 1D model configuration 
    3535% ================================================================ 
    36 \section{C1D: 1D Water column model (\protect\key{c1d}) } 
     36\section[C1D: 1D Water column model (\texttt{\textbf{key\_c1d}})] 
     37{C1D: 1D Water column model (\protect\key{c1d})} 
    3738\label{sec:CFG_c1d} 
    3839 
     
    227228%       GYRE family: double gyre basin 
    228229% ------------------------------------------------------------------------------------------------------------- 
    229 \section{GYRE family: double gyre basin } 
     230\section{GYRE family: double gyre basin} 
    230231\label{sec:CFG_gyre} 
    231232 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex

    r11151 r11179  
    13321332%       NetCDF4 support 
    13331333% ================================================================ 
    1334 \section{NetCDF4 support (\protect\key{netcdf4})} 
     1334\section[NetCDF4 support (\texttt{\textbf{key\_netcdf4}})] 
     1335{NetCDF4 support (\protect\key{netcdf4})} 
    13351336\label{sec:DIA_nc4} 
    13361337 
     
    14501451%       Tracer/Dynamics Trends 
    14511452% ------------------------------------------------------------------------------------------------------------- 
    1452 \section{Tracer/Dynamics trends  (\protect\ngn{namtrd})} 
     1453\section[Tracer/Dynamics trends (\texttt{namtrd})] 
     1454{Tracer/Dynamics trends (\protect\ngn{namtrd})} 
    14531455\label{sec:DIA_trd} 
    14541456 
     
    14971499%       On-line Floats trajectories 
    14981500% ------------------------------------------------------------------------------------------------------------- 
    1499 \section{FLO: On-Line Floats trajectories (\protect\key{floats})} 
     1501\section[FLO: On-Line Floats trajectories (\texttt{\textbf{key\_floats}})] 
     1502{FLO: On-Line Floats trajectories (\protect\key{floats})} 
    15001503\label{sec:FLO} 
    15011504%--------------------------------------------namflo------------------------------------------------------- 
     
    16051608%       Harmonic analysis of tidal constituents 
    16061609% ------------------------------------------------------------------------------------------------------------- 
    1607 \section{Harmonic analysis of tidal constituents (\protect\key{diaharm}) } 
     1610\section[Harmonic analysis of tidal constituents (\texttt{\textbf{key\_diaharm}})] 
     1611{Harmonic analysis of tidal constituents (\protect\key{diaharm})} 
    16081612\label{sec:DIA_diag_harm} 
    16091613 
     
    16521656%       Sections transports 
    16531657% ------------------------------------------------------------------------------------------------------------- 
    1654 \section{Transports across sections (\protect\key{diadct}) } 
     1658\section[Transports across sections (\texttt{\textbf{key\_diadct}})] 
     1659{Transports across sections (\protect\key{diadct})} 
    16551660\label{sec:DIA_diag_dct} 
    16561661 
     
    19761981%       Other Diagnostics 
    19771982% ------------------------------------------------------------------------------------------------------------- 
    1978 \section{Other diagnostics (\protect\key{diahth}, \protect\key{diaar5})} 
     1983\section[Other diagnostics (\texttt{\textbf{key\_diahth}}, \texttt{\textbf{key\_diaar5}})] 
     1984{Other diagnostics (\protect\key{diahth}, \protect\key{diaar5})} 
    19791985\label{sec:DIA_diag_others} 
    19801986 
     
    19821988The available ready-to-add diagnostics modules can be found in directory DIA. 
    19831989 
    1984 \subsection{Depth of various quantities (\protect\mdl{diahth})} 
     1990\subsection[Depth of various quantities (\textit{diahth.F90})] 
     1991{Depth of various quantities (\protect\mdl{diahth})} 
    19851992 
    19861993Among the available diagnostics the following ones are obtained when defining the \key{diahth} CPP key: 
     
    19982005% ----------------------------------------------------------- 
    19992006 
    2000 \subsection{Poleward heat and salt transports (\protect\mdl{diaptr})} 
     2007\subsection[Poleward heat and salt transports (\textit{diaptr.F90})] 
     2008{Poleward heat and salt transports (\protect\mdl{diaptr})} 
    20012009 
    20022010%------------------------------------------namptr----------------------------------------- 
     
    20322040%       CMIP specific diagnostics  
    20332041% ----------------------------------------------------------- 
    2034 \subsection{CMIP specific diagnostics (\protect\mdl{diaar5})} 
     2042\subsection[CMIP specific diagnostics (\textit{diaar5.F90})] 
     2043{CMIP specific diagnostics (\protect\mdl{diaar5})} 
    20352044 
    20362045A series of diagnostics has been added in the \mdl{diaar5}. 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DOM.tex

    r11151 r11179  
    345345% Domain: Horizontal Grid (mesh)  
    346346% ================================================================ 
    347 \section{Horizontal grid mesh (\protect\mdl{domhgr})} 
     347\section[Horizontal grid mesh (\textit{domhgr.F90})] 
     348{Horizontal grid mesh (\protect\mdl{domhgr})} 
    348349\label{sec:DOM_hgr} 
    349350 
     
    451452% Domain: Vertical Grid (domzgr) 
    452453% ================================================================ 
    453 \section{Vertical grid (\protect\mdl{domzgr})} 
     454\section[Vertical grid (\textit{domzgr.F90})] 
     455{Vertical grid (\protect\mdl{domzgr})} 
    454456\label{sec:DOM_zgr} 
    455457%-----------------------------------------nam_zgr & namdom------------------------------------------- 
     
    480482      (d) hybrid $s-z$ coordinate, 
    481483      (e) hybrid $s-z$ coordinate with partial step, and 
    482       (f) same as (e) but in the non-linear free surface (\protect\np{ln\_linssh}~\forcode{= .false.}). 
     484      (f) same as (e) but in the non-linear free surface (\protect\np{ln\_linssh}\forcode{ = .false.}). 
    483485      Note that the non-linear free surface can be used with any of the 5 coordinates (a) to (e). 
    484486    } 
     
    491493It is not intended as an option which can be enabled or disabled in the middle of an experiment. 
    492494Three main choices are offered (\autoref{fig:z_zps_s_sps}): 
    493 $z$-coordinate with full step bathymetry (\np{ln\_zco}~\forcode{= .true.}), 
    494 $z$-coordinate with partial step bathymetry (\np{ln\_zps}~\forcode{= .true.}), 
    495 or generalized, $s$-coordinate (\np{ln\_sco}~\forcode{= .true.}). 
     495$z$-coordinate with full step bathymetry (\np{ln\_zco}\forcode{ = .true.}), 
     496$z$-coordinate with partial step bathymetry (\np{ln\_zps}\forcode{ = .true.}), 
     497or generalized, $s$-coordinate (\np{ln\_sco}\forcode{ = .true.}). 
    496498Hybridation of the three main coordinates are available: 
    497499$s-z$ or $s-zps$ coordinate (\autoref{fig:z_zps_s_sps} and \autoref{fig:z_zps_s_sps}). 
    498500By default a non-linear free surface is used: the coordinate follow the time-variation of the free surface so that 
    499501the transformation is time dependent: $z(i,j,k,t)$ (\autoref{fig:z_zps_s_sps}). 
    500 When a linear free surface is assumed (\np{ln\_linssh}~\forcode{= .true.}), 
     502When a linear free surface is assumed (\np{ln\_linssh}\forcode{ = .true.}), 
    501503the vertical coordinate are fixed in time, but the seawater can move up and down across the $z_0$ surface 
    502504(in other words, the top of the ocean in not a rigid-lid). 
     
    513515  N.B. in full step $z$-coordinate, a \ifile{bathy\_level} file can replace the \ifile{bathy\_meter} file, 
    514516  so that the computation of the number of wet ocean point in each water column is by-passed}. 
    515 If \np{ln\_isfcav}~\forcode{= .true.}, an extra file input file (\ifile{isf\_draft\_meter}) describing 
     517If \np{ln\_isfcav}\forcode{ = .true.}, an extra file input file (\ifile{isf\_draft\_meter}) describing 
    516518the ice shelf draft (in meters) is needed. 
    517519 
     
    535537%%% 
    536538 
    537 Unless a linear free surface is used (\np{ln\_linssh}~\forcode{= .false.}), 
     539Unless a linear free surface is used (\np{ln\_linssh}\forcode{ = .false.}), 
    538540the arrays describing the grid point depths and vertical scale factors are three set of 
    539541three dimensional arrays $(i,j,k)$ defined at \textit{before}, \textit{now} and \textit{after} time step. 
     
    541543They are updated at each model time step using a fixed reference coordinate system which 
    542544computer names have a $\_0$ suffix. 
    543 When the linear free surface option is used (\np{ln\_linssh}~\forcode{= .true.}), \textit{before}, 
     545When the linear free surface option is used (\np{ln\_linssh}\forcode{ = .true.}), \textit{before}, 
    544546\textit{now} and \textit{after} arrays are simply set one for all to their reference counterpart. 
    545547 
     
    553555(found in \ngn{namdom} namelist):  
    554556\begin{description} 
    555 \item[\np{nn\_bathy}~\forcode{= 0}]: 
     557\item[\np{nn\_bathy}\forcode{ = 0}]: 
    556558  a flat-bottom domain is defined. 
    557559  The total depth $z_w (jpk)$ is given by the coordinate transformation. 
    558560  The domain can either be a closed basin or a periodic channel depending on the parameter \np{jperio}. 
    559 \item[\np{nn\_bathy}~\forcode{= -1}]: 
     561\item[\np{nn\_bathy}\forcode{ = -1}]: 
    560562  a domain with a bump of topography one third of the domain width at the central latitude. 
    561563  This is meant for the "EEL-R5" configuration, a periodic or open boundary channel with a seamount. 
    562 \item[\np{nn\_bathy}~\forcode{= 1}]: 
     564\item[\np{nn\_bathy}\forcode{ = 1}]: 
    563565  read a bathymetry and ice shelf draft (if needed). 
    564566  The \ifile{bathy\_meter} file (Netcdf format) provides the ocean depth (positive, in meters) at 
     
    571573  The \ifile{isfdraft\_meter} file (Netcdf format) provides the ice shelf draft (positive, in meters) at 
    572574  each grid point of the model grid. 
    573   This file is only needed if \np{ln\_isfcav}~\forcode{= .true.}. 
     575  This file is only needed if \np{ln\_isfcav}\forcode{ = .true.}. 
    574576  Defining the ice shelf draft will also define the ice shelf edge and the grounding line position. 
    575577\end{description} 
     
    586588%        z-coordinate  and reference coordinate transformation 
    587589% ------------------------------------------------------------------------------------------------------------- 
    588 \subsection[$Z$-coordinate (\protect\np{ln\_zco}~\forcode{= .true.}) and ref. coordinate] 
    589             {$Z$-coordinate (\protect\np{ln\_zco}~\forcode{= .true.}) and reference coordinate} 
     590\subsection[$Z$-coordinate (\forcode{ln_zco = .true.}) and ref. coordinate] 
     591{$Z$-coordinate (\protect\np{ln\_zco}\forcode{ = .true.}) and reference coordinate} 
    590592\label{subsec:DOM_zco} 
    591593 
     
    616618using parameters provided in the \ngn{namcfg} namelist. 
    617619 
    618 It is possible to define a simple regular vertical grid by giving zero stretching (\np{ppacr}~\forcode{= 0}). 
     620It is possible to define a simple regular vertical grid by giving zero stretching (\np{ppacr}\forcode{ = 0}). 
    619621In that case, the parameters \jp{jpk} (number of $w$-levels) and 
    620622\np{pphmax} (total ocean depth in meters) fully define the grid. 
     
    631633a smooth hyperbolic tangent transition in between (\autoref{fig:zgr}). 
    632634 
    633 If the ice shelf cavities are opened (\np{ln\_isfcav}~\forcode{= .true.}), the definition of $z_0$ is the same. 
     635If the ice shelf cavities are opened (\np{ln\_isfcav}\forcode{ = .true.}), the definition of $z_0$ is the same. 
    634636However, definition of $e_3^0$ at $t$- and $w$-points is respectively changed to: 
    635637\begin{equation} 
     
    765767%        z-coordinate with partial step 
    766768% ------------------------------------------------------------------------------------------------------------- 
    767 \subsection{$Z$-coordinate with partial step (\protect\np{ln\_zps}~\forcode{= .true.})} 
     769\subsection[$Z$-coordinate with partial step (\forcode{ln_zps = .true.})] 
     770{$Z$-coordinate with partial step (\protect\np{ln\_zps}\forcode{ = .true.})} 
    768771\label{subsec:DOM_zps} 
    769772%--------------------------------------------namdom------------------------------------------------------- 
     
    796799%        s-coordinate 
    797800% ------------------------------------------------------------------------------------------------------------- 
    798 \subsection{$S$-coordinate (\protect\np{ln\_sco}~\forcode{= .true.})} 
     801\subsection[$S$-coordinate (\forcode{ln_sco = .true.})] 
     802{$S$-coordinate (\protect\np{ln\_sco}\forcode{ = .true.})} 
    799803\label{subsec:DOM_sco} 
    800804%------------------------------------------nam_zgr_sco--------------------------------------------------- 
     
    803807%-------------------------------------------------------------------------------------------------------------- 
    804808Options are defined in \ngn{namzgr\_sco}. 
    805 In $s$-coordinate (\np{ln\_sco}~\forcode{= .true.}), the depth and thickness of the model levels are defined from 
     809In $s$-coordinate (\np{ln\_sco}\forcode{ = .true.}), the depth and thickness of the model levels are defined from 
    806810the product of a depth field and either a stretching function or its derivative, respectively: 
    807811 
     
    826830 
    827831The original default NEMO s-coordinate stretching is available if neither of the other options are specified as true 
    828 (\np{ln\_s\_SH94}~\forcode{= .false.} and \np{ln\_s\_SF12}~\forcode{= .false.}). 
     832(\np{ln\_s\_SH94}\forcode{ = .false.} and \np{ln\_s\_SF12}\forcode{ = .false.}). 
    829833This uses a depth independent $\tanh$ function for the stretching \citep{madec.delecluse.ea_JPO96}: 
    830834 
     
    846850 
    847851A stretching function, 
    848 modified from the commonly used \citet{song.haidvogel_JCP94} stretching (\np{ln\_s\_SH94}~\forcode{= .true.}), 
     852modified from the commonly used \citet{song.haidvogel_JCP94} stretching (\np{ln\_s\_SH94}\forcode{ = .true.}), 
    849853is also available and is more commonly used for shelf seas modelling: 
    850854 
     
    946950%        z*- or s*-coordinate 
    947951% ------------------------------------------------------------------------------------------------------------- 
    948 \subsection{\zstar- or \sstar-coordinate (\protect\np{ln\_linssh}~\forcode{= .false.})} 
     952\subsection[\zstar- or \sstar-coordinate (\forcode{ln_linssh = .false.})] 
     953{\zstar- or \sstar-coordinate (\protect\np{ln\_linssh}\forcode{ = .false.})} 
    949954\label{subsec:DOM_zgr_star} 
    950955 
     
    10141019% Domain: Initial State (dtatsd & istate) 
    10151020% ================================================================ 
    1016 \section{Initial state (\protect\mdl{istate} and \protect\mdl{dtatsd})} 
     1021\section[Initial state (\textit{istate.F90} and \textit{dtatsd.F90})] 
     1022{Initial state (\protect\mdl{istate} and \protect\mdl{dtatsd})} 
    10171023\label{sec:DTA_tsd} 
    10181024%-----------------------------------------namtsd------------------------------------------- 
     
    10251031salinity fields is controlled through the \np{ln\_tsd\_ini} namelist parameter. 
    10261032\begin{description} 
    1027 \item[\np{ln\_tsd\_init}~\forcode{= .true.}] 
     1033\item[\np{ln\_tsd\_init}\forcode{ = .true.}] 
    10281034  use a T and S input files that can be given on the model grid itself or on their native input data grid. 
    10291035  In the latter case, 
     
    10321038  The information relative to the input files are given in the \np{sn\_tem} and \np{sn\_sal} structures. 
    10331039  The computation is done in the \mdl{dtatsd} module. 
    1034 \item[\np{ln\_tsd\_init}~\forcode{= .false.}] 
     1040\item[\np{ln\_tsd\_init}\forcode{ = .false.}] 
    10351041  use constant salinity value of $35.5~psu$ and an analytical profile of temperature 
    10361042  (typical of the tropical ocean), see \rou{istate\_t\_s} subroutine called from \mdl{istate} module. 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DYN.tex

    r11151 r11179  
    6565%           Horizontal divergence and relative vorticity 
    6666%-------------------------------------------------------------------------------------------------------------- 
    67 \subsection{Horizontal divergence and relative vorticity (\protect\mdl{divcur})} 
     67\subsection[Horizontal divergence and relative vorticity (\textit{divcur.F90})] 
     68{Horizontal divergence and relative vorticity (\protect\mdl{divcur})} 
    6869\label{subsec:DYN_divcur} 
    6970 
     
    101102%           Sea Surface Height evolution 
    102103%-------------------------------------------------------------------------------------------------------------- 
    103 \subsection{Horizontal divergence and relative vorticity (\protect\mdl{sshwzv})} 
     104\subsection[Horizontal divergence and relative vorticity (\textit{sshwzv.F90})] 
     105{Horizontal divergence and relative vorticity (\protect\mdl{sshwzv})} 
    104106\label{subsec:DYN_sshwzv} 
    105107 
     
    181183%        Vorticity term  
    182184% ------------------------------------------------------------------------------------------------------------- 
    183 \subsection{Vorticity term (\protect\mdl{dynvor})} 
     185\subsection[Vorticity term (\textit{dynvor.F90})] 
     186{Vorticity term (\protect\mdl{dynvor})} 
    184187\label{subsec:DYN_vor} 
    185188%------------------------------------------nam_dynvor---------------------------------------------------- 
     
    203206%                 enstrophy conserving scheme 
    204207%------------------------------------------------------------- 
    205 \subsubsection{Enstrophy conserving scheme (\protect\np{ln\_dynvor\_ens}\forcode{ = .true.})} 
     208\subsubsection[Enstrophy conserving scheme (\forcode{ln_dynvor_ens = .true.})] 
     209{Enstrophy conserving scheme (\protect\np{ln\_dynvor\_ens}\forcode{ = .true.})} 
    206210\label{subsec:DYN_vor_ens} 
    207211 
     
    226230%                 energy conserving scheme 
    227231%------------------------------------------------------------- 
    228 \subsubsection{Energy conserving scheme (\protect\np{ln\_dynvor\_ene}\forcode{ = .true.})} 
     232\subsubsection[Energy conserving scheme (\forcode{ln_dynvor_ene = .true.})] 
     233{Energy conserving scheme (\protect\np{ln\_dynvor\_ene}\forcode{ = .true.})} 
    229234\label{subsec:DYN_vor_ene} 
    230235 
     
    246251%                 mix energy/enstrophy conserving scheme 
    247252%------------------------------------------------------------- 
    248 \subsubsection{Mixed energy/enstrophy conserving scheme (\protect\np{ln\_dynvor\_mix}\forcode{ = .true.}) } 
     253\subsubsection[Mixed energy/enstrophy conserving scheme (\forcode{ln_dynvor_mix = .true.})] 
     254{Mixed energy/enstrophy conserving scheme (\protect\np{ln\_dynvor\_mix}\forcode{ = .true.})} 
    249255\label{subsec:DYN_vor_mix} 
    250256 
     
    271277%                 energy and enstrophy conserving scheme 
    272278%------------------------------------------------------------- 
    273 \subsubsection{Energy and enstrophy conserving scheme (\protect\np{ln\_dynvor\_een}\forcode{ = .true.}) } 
     279\subsubsection[Energy and enstrophy conserving scheme (\forcode{ln_dynvor_een = .true.})] 
     280{Energy and enstrophy conserving scheme (\protect\np{ln\_dynvor\_een}\forcode{ = .true.})} 
    274281\label{subsec:DYN_vor_een} 
    275282 
     
    364371%           Kinetic Energy Gradient term 
    365372%-------------------------------------------------------------------------------------------------------------- 
    366 \subsection{Kinetic energy gradient term (\protect\mdl{dynkeg})} 
     373\subsection[Kinetic energy gradient term (\textit{dynkeg.F90})] 
     374{Kinetic energy gradient term (\protect\mdl{dynkeg})} 
    367375\label{subsec:DYN_keg} 
    368376 
     
    384392%           Vertical advection term 
    385393%-------------------------------------------------------------------------------------------------------------- 
    386 \subsection{Vertical advection term (\protect\mdl{dynzad}) } 
     394\subsection[Vertical advection term (\textit{dynzad.F90})] 
     395{Vertical advection term (\protect\mdl{dynzad})} 
    387396\label{subsec:DYN_zad} 
    388397 
     
    430439%           Coriolis plus curvature metric terms 
    431440%-------------------------------------------------------------------------------------------------------------- 
    432 \subsection{Coriolis plus curvature metric terms (\protect\mdl{dynvor}) } 
     441\subsection[Coriolis plus curvature metric terms (\textit{dynvor.F90})] 
     442{Coriolis plus curvature metric terms (\protect\mdl{dynvor})} 
    433443\label{subsec:DYN_cor_flux} 
    434444 
     
    451461%           Flux form Advection term 
    452462%-------------------------------------------------------------------------------------------------------------- 
    453 \subsection{Flux form advection term (\protect\mdl{dynadv}) } 
     463\subsection[Flux form advection term (\textit{dynadv.F90})] 
     464{Flux form advection term (\protect\mdl{dynadv})} 
    454465\label{subsec:DYN_adv_flux} 
    455466 
     
    484495%                 2nd order centred scheme 
    485496%------------------------------------------------------------- 
    486 \subsubsection{CEN2: $2^{nd}$ order centred scheme (\protect\np{ln\_dynadv\_cen2}\forcode{ = .true.})} 
     497\subsubsection[CEN2: $2^{nd}$ order centred scheme (\forcode{ln_dynadv_cen2 = .true.})] 
     498{CEN2: $2^{nd}$ order centred scheme (\protect\np{ln\_dynadv\_cen2}\forcode{ = .true.})} 
    487499\label{subsec:DYN_adv_cen2} 
    488500 
     
    507519%                 UBS scheme 
    508520%------------------------------------------------------------- 
    509 \subsubsection{UBS: Upstream Biased Scheme (\protect\np{ln\_dynadv\_ubs}\forcode{ = .true.})} 
     521\subsubsection[UBS: Upstream Biased Scheme (\forcode{ln_dynadv_ubs = .true.})] 
     522{UBS: Upstream Biased Scheme (\protect\np{ln\_dynadv\_ubs}\forcode{ = .true.})} 
    510523\label{subsec:DYN_adv_ubs} 
    511524 
     
    560573%           Hydrostatic pressure gradient term 
    561574% ================================================================ 
    562 \section{Hydrostatic pressure gradient (\protect\mdl{dynhpg})} 
     575\section[Hydrostatic pressure gradient (\textit{dynhpg.F90})] 
     576{Hydrostatic pressure gradient (\protect\mdl{dynhpg})} 
    563577\label{sec:DYN_hpg} 
    564578%------------------------------------------nam_dynhpg--------------------------------------------------- 
     
    582596%           z-coordinate with full step 
    583597%-------------------------------------------------------------------------------------------------------------- 
    584 \subsection{Full step $Z$-coordinate (\protect\np{ln\_dynhpg\_zco}\forcode{ = .true.})} 
     598\subsection[Full step $Z$-coordinate (\forcode{ln_dynhpg_zco = .true.})] 
     599{Full step $Z$-coordinate (\protect\np{ln\_dynhpg\_zco}\forcode{ = .true.})} 
    585600\label{subsec:DYN_hpg_zco} 
    586601 
     
    627642%           z-coordinate with partial step 
    628643%-------------------------------------------------------------------------------------------------------------- 
    629 \subsection{Partial step $Z$-coordinate (\protect\np{ln\_dynhpg\_zps}\forcode{ = .true.})} 
     644\subsection[Partial step $Z$-coordinate (\forcode{ln_dynhpg_zps = .true.})] 
     645{Partial step $Z$-coordinate (\protect\np{ln\_dynhpg\_zps}\forcode{ = .true.})} 
    630646\label{subsec:DYN_hpg_zps} 
    631647 
     
    712728%           Time-scheme 
    713729%-------------------------------------------------------------------------------------------------------------- 
    714 \subsection{Time-scheme (\protect\np{ln\_dynhpg\_imp}\forcode{ = .true./.false.})} 
     730\subsection[Time-scheme (\forcode{ln_dynhpg_imp = .{true,false}.})] 
     731{Time-scheme (\protect\np{ln\_dynhpg\_imp}\forcode{ = .\{true,false\}}.)} 
    715732\label{subsec:DYN_hpg_imp} 
    716733 
     
    773790% Surface Pressure Gradient 
    774791% ================================================================ 
    775 \section{Surface pressure gradient (\protect\mdl{dynspg})} 
     792\section[Surface pressure gradient (\textit{dynspg.F90})] 
     793{Surface pressure gradient (\protect\mdl{dynspg})} 
    776794\label{sec:DYN_spg} 
    777795%-----------------------------------------nam_dynspg---------------------------------------------------- 
     
    811829% Explicit free surface formulation 
    812830%-------------------------------------------------------------------------------------------------------------- 
    813 \subsection{Explicit free surface (\protect\key{dynspg\_exp})} 
     831\subsection[Explicit free surface (texttt{\textbf{key\_dynspg\_exp}})] 
     832{Explicit free surface (\protect\key{dynspg\_exp})} 
    814833\label{subsec:DYN_spg_exp} 
    815834 
     
    837856% Split-explict free surface formulation 
    838857%-------------------------------------------------------------------------------------------------------------- 
    839 \subsection{Split-explicit free surface (\protect\key{dynspg\_ts})} 
     858\subsection[Split-explicit free surface (texttt{\textbf{key\_dynspg\_ts}})] 
     859{Split-explicit free surface (\protect\key{dynspg\_ts})} 
    840860\label{subsec:DYN_spg_ts} 
    841861%------------------------------------------namsplit----------------------------------------------------------- 
     
    10811101% Filtered free surface formulation 
    10821102%-------------------------------------------------------------------------------------------------------------- 
    1083 \subsection{Filtered free surface (\protect\key{dynspg\_flt})} 
     1103\subsection[Filtered free surface (\texttt{\textbf{key\_dynspg\_flt}})] 
     1104{Filtered free surface (\protect\key{dynspg\_flt})} 
    10841105\label{subsec:DYN_spg_fltp} 
    10851106 
     
    11091130% Lateral diffusion term 
    11101131% ================================================================ 
    1111 \section{Lateral diffusion term and operators (\protect\mdl{dynldf})} 
     1132\section[Lateral diffusion term and operators (\textit{dynldf.F90})] 
     1133{Lateral diffusion term and operators (\protect\mdl{dynldf})} 
    11121134\label{sec:DYN_ldf} 
    11131135%------------------------------------------nam_dynldf---------------------------------------------------- 
     
    11431165 
    11441166% ================================================================ 
    1145 \subsection[Iso-level laplacian (\protect\np{ln\_dynldf\_lap}\forcode{ = .true.})] 
    1146             {Iso-level laplacian operator (\protect\np{ln\_dynldf\_lap}\forcode{ = .true.})} 
     1167\subsection[Iso-level laplacian (\forcode{ln_dynldf_lap = .true.})] 
     1168{Iso-level laplacian operator (\protect\np{ln\_dynldf\_lap}\forcode{ = .true.})} 
    11471169\label{subsec:DYN_ldf_lap} 
    11481170 
     
    11691191%           Rotated laplacian operator 
    11701192%-------------------------------------------------------------------------------------------------------------- 
    1171 \subsection[Rotated laplacian (\protect\np{ln\_dynldf\_iso}\forcode{ = .true.})] 
    1172             {Rotated laplacian operator (\protect\np{ln\_dynldf\_iso}\forcode{ = .true.})} 
     1193\subsection[Rotated laplacian (\forcode{ln_dynldf_iso = .true.})] 
     1194{Rotated laplacian operator (\protect\np{ln\_dynldf\_iso}\forcode{ = .true.})} 
    11731195\label{subsec:DYN_ldf_iso} 
    11741196 
     
    12281250%           Iso-level bilaplacian operator 
    12291251%-------------------------------------------------------------------------------------------------------------- 
    1230 \subsection[Iso-level bilaplacian (\protect\np{ln\_dynldf\_bilap}\forcode{ = .true.})] 
    1231             {Iso-level bilaplacian operator (\protect\np{ln\_dynldf\_bilap}\forcode{ = .true.})} 
     1252\subsection[Iso-level bilaplacian (\forcode{ln_dynldf_bilap = .true.})] 
     1253{Iso-level bilaplacian operator (\protect\np{ln\_dynldf\_bilap}\forcode{ = .true.})} 
    12321254\label{subsec:DYN_ldf_bilap} 
    12331255 
     
    12431265%           Vertical diffusion term 
    12441266% ================================================================ 
    1245 \section{Vertical diffusion term (\protect\mdl{dynzdf})} 
     1267\section[Vertical diffusion term (\textit{dynzdf.F90})] 
     1268{Vertical diffusion term (\protect\mdl{dynzdf})} 
    12461269\label{sec:DYN_zdf} 
    12471270%----------------------------------------------namzdf------------------------------------------------------ 
     
    13721395%   Iterative limiters 
    13731396%----------------------------------------------------------------------------------------- 
    1374 \subsection   [Directional limiter (\textit{wet\_dry})] 
    1375          {Directional limiter (\mdl{wet\_dry})} 
     1397\subsection[Directional limiter (\textit{wet\_dry.F90})] 
     1398{Directional limiter (\mdl{wet\_dry})} 
    13761399\label{subsec:DYN_wd_directional_limiter} 
    13771400The principal idea of the directional limiter is that 
     
    14121435%----------------------------------------------------------------------------------------- 
    14131436 
    1414 \subsection   [Iterative limiter (\textit{wet\_dry})] 
    1415          {Iterative limiter (\mdl{wet\_dry})} 
     1437\subsection[Iterative limiter (\textit{wet\_dry.F90})] 
     1438{Iterative limiter (\mdl{wet\_dry})} 
    14161439\label{subsec:DYN_wd_iterative_limiter} 
    14171440 
    1418 \subsubsection [Iterative flux limiter (\textit{wet\_dry})] 
    1419          {Iterative flux limiter (\mdl{wet\_dry})} 
     1441\subsubsection[Iterative flux limiter (\textit{wet\_dry.F90})] 
     1442{Iterative flux limiter (\mdl{wet\_dry})} 
    14201443\label{subsubsec:DYN_wd_il_spg_limiter} 
    14211444 
     
    15221545%      Surface pressure gradients 
    15231546%---------------------------------------------------------------------------------------- 
    1524 \subsubsection   [Modification of surface pressure gradients (\textit{dynhpg})] 
    1525          {Modification of surface pressure gradients (\mdl{dynhpg})} 
     1547\subsubsection[Modification of surface pressure gradients (\textit{dynhpg.F90})] 
     1548{Modification of surface pressure gradients (\mdl{dynhpg})} 
    15261549\label{subsubsec:DYN_wd_il_spg} 
    15271550 
     
    15881611conditions. 
    15891612 
    1590 \subsubsection   [Additional considerations (\textit{usrdef\_zgr})] 
    1591          {Additional considerations (\mdl{usrdef\_zgr})} 
     1613\subsubsection[Additional considerations (\textit{usrdef\_zgr.F90})] 
     1614{Additional considerations (\mdl{usrdef\_zgr})} 
    15921615\label{subsubsec:WAD_additional} 
    15931616 
     
    16031626%      The WAD test cases 
    16041627%---------------------------------------------------------------------------------------- 
    1605 \subsection   [The WAD test cases (\textit{usrdef\_zgr})] 
    1606          {The WAD test cases (\mdl{usrdef\_zgr})} 
     1628\subsection[The WAD test cases (\textit{usrdef\_zgr.F90})] 
     1629{The WAD test cases (\mdl{usrdef\_zgr})} 
    16071630\label{WAD_test_cases} 
    16081631 
     
    16141637% Time evolution term  
    16151638% ================================================================ 
    1616 \section{Time evolution term (\protect\mdl{dynnxt})} 
     1639\section[Time evolution term (\textit{dynnxt.F90})] 
     1640{Time evolution term (\protect\mdl{dynnxt})} 
    16171641\label{sec:DYN_nxt} 
    16181642 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_LBC.tex

    r11151 r11179  
    1717% Boundary Condition at the Coast 
    1818% ================================================================ 
    19 \section{Boundary condition at the coast (\protect\np{rn\_shlat})} 
     19\section[Boundary condition at the coast (\texttt{rn\_shlat})] 
     20{Boundary condition at the coast (\protect\np{rn\_shlat})} 
    2021\label{sec:LBC_coast} 
    2122%--------------------------------------------nam_lbc------------------------------------------------------- 
     
    147148% Boundary Condition around the Model Domain 
    148149% ================================================================ 
    149 \section{Model domain boundary condition (\protect\np{jperio})} 
     150\section[Model domain boundary condition (\texttt{jperio})] 
     151{Model domain boundary condition (\protect\np{jperio})} 
    150152\label{sec:LBC_jperio} 
    151153 
     
    158160%        Closed, cyclic (\np{jperio}\forcode{ = 0..2})  
    159161% ------------------------------------------------------------------------------------------------------------- 
    160 \subsection{Closed, cyclic (\protect\np{jperio}\forcode{= [0127]})} 
     162\subsection[Closed, cyclic (\forcode{jperio = [0127]})] 
     163{Closed, cyclic (\protect\np{jperio}\forcode{ = [0127]})} 
    161164\label{subsec:LBC_jperio012} 
    162165 
     
    206209%        North fold (\textit{jperio = 3 }to $6)$  
    207210% ------------------------------------------------------------------------------------------------------------- 
    208 \subsection{North-fold (\protect\np{jperio}\forcode{ = 3..6})} 
     211\subsection[North-fold (\forcode{jperio = [3-6]})] 
     212{North-fold (\protect\np{jperio}\forcode{ = [3-6]})} 
    209213\label{subsec:LBC_north_fold} 
    210214 
     
    232236% Exchange with neighbouring processors  
    233237% ==================================================================== 
    234 \section{Exchange with neighbouring processors (\protect\mdl{lbclnk}, \protect\mdl{lib\_mpp})} 
     238\section[Exchange with neighbouring processors (\textit{lbclnk.F90}, \textit{lib\_mpp.F90})] 
     239{Exchange with neighbouring processors (\protect\mdl{lbclnk}, \protect\mdl{lib\_mpp})} 
    235240\label{sec:LBC_mpp} 
    236241 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_LDF.tex

    r11151 r11179  
    3838% Direction of lateral Mixing 
    3939% ================================================================ 
    40 \section{Direction of lateral mixing (\protect\mdl{ldfslp})} 
     40\section[Direction of lateral mixing (\textit{ldfslp.F90})] 
     41{Direction of lateral mixing (\protect\mdl{ldfslp})} 
    4142\label{sec:LDF_slp} 
    4243 
     
    301302% Lateral Mixing Operator 
    302303% ================================================================ 
    303 \section{Lateral mixing operators (\protect\mdl{traldf}, \protect\mdl{traldf}) } 
     304\section[Lateral mixing operators (\textit{traldf.F90})] 
     305{Lateral mixing operators (\protect\mdl{traldf}, \protect\mdl{traldf})} 
    304306\label{sec:LDF_op} 
    305307 
     
    309311% Lateral Mixing Coefficients 
    310312% ================================================================ 
    311 \section{Lateral mixing coefficient (\protect\mdl{ldftra}, \protect\mdl{ldfdyn}) } 
     313\section[Lateral mixing coefficient (\textit{ldftra.F90}, \textit{ldfdyn.F90})] 
     314{Lateral mixing coefficient (\protect\mdl{ldftra}, \protect\mdl{ldfdyn})} 
    312315\label{sec:LDF_coef} 
    313316 
     
    339342which is specified through the \np{rn\_ahm0} and \np{rn\_aht0} namelist parameters. 
    340343 
    341 \subsubsection{Vertically varying mixing coefficients (\protect\key{traldf\_c1d} and \key{dynldf\_c1d})}  
     344\subsubsection[Vertically varying mixing coefficients (\texttt{\textbf{key\_traldf\_c1d}} and \texttt{\textbf{key\_dynldf\_c1d}})] 
     345{Vertically varying mixing coefficients (\protect\key{traldf\_c1d} and \key{dynldf\_c1d})} 
    342346The 1D option is only available when using the $z$-coordinate with full step. 
    343347Indeed in all the other types of vertical coordinate, 
     
    350354This profile is hard coded in file \textit{traldf\_c1d.h90}, but can be easily modified by users. 
    351355 
    352 \subsubsection{Horizontally varying mixing coefficients (\protect\key{traldf\_c2d} and \protect\key{dynldf\_c2d})} 
     356\subsubsection[Horizontally varying mixing coefficients (\texttt{\textbf{key\_traldf\_c2d}} and \texttt{\textbf{key\_dynldf\_c2d}})] 
     357{Horizontally varying mixing coefficients (\protect\key{traldf\_c2d} and \protect\key{dynldf\_c2d})} 
    353358By default the horizontal variation of the eddy coefficient depends on the local mesh size and 
    354359the type of operator used: 
     
    381386ORCA2 and ORCA05 (see \&namcfg namelist). 
    382387 
    383 \subsubsection{Space varying mixing coefficients (\protect\key{traldf\_c3d} and \key{dynldf\_c3d})} 
     388\subsubsection[Space varying mixing coefficients (\texttt{\textbf{key\_traldf\_c3d}} and \texttt{\textbf{key\_dynldf\_c3d}})] 
     389{Space varying mixing coefficients (\protect\key{traldf\_c3d} and \key{dynldf\_c3d})} 
    384390 
    385391The 3D space variation of the mixing coefficient is simply the combination of the 1D and 2D cases, 
     
    430436% Eddy Induced Mixing 
    431437% ================================================================ 
    432 \section{Eddy induced velocity (\protect\mdl{traadv\_eiv}, \protect\mdl{ldfeiv})} 
     438\section[Eddy induced velocity (\textit{traadv\_eiv.F90}, \textit{ldfeiv.F90})] 
     439{Eddy induced velocity (\protect\mdl{traadv\_eiv}, \protect\mdl{ldfeiv})} 
    433440\label{sec:LDF_eiv} 
    434441 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_SBC.tex

    r11151 r11179  
    55% Chapter —— Surface Boundary Condition (SBC, ISF, ICB)  
    66% ================================================================ 
    7 \chapter{Surface Boundary Condition (SBC, ISF, ICB) } 
     7\chapter{Surface Boundary Condition (SBC, ISF, ICB)} 
    88\label{chap:SBC} 
    99\minitoc 
     
    226226% Input Data specification (\mdl{fldread}) 
    227227% ------------------------------------------------------------------------------------------------------------- 
    228 \subsection{Input data specification (\protect\mdl{fldread})} 
     228\subsection[Input data specification (\textit{fldread.F90})] 
     229{Input data specification (\protect\mdl{fldread})} 
    229230\label{subsec:SBC_fldread} 
    230231 
     
    559560% Analytical formulation (sbcana module)  
    560561% ================================================================ 
    561 \section{Analytical formulation (\protect\mdl{sbcana})} 
     562\section[Analytical formulation (\textit{sbcana.F90})] 
     563{Analytical formulation (\protect\mdl{sbcana})} 
    562564\label{sec:SBC_ana} 
    563565 
     
    584586% Flux formulation  
    585587% ================================================================ 
    586 \section{Flux formulation (\protect\mdl{sbcflx})} 
     588\section[Flux formulation (\textit{sbcflx.F90})] 
     589{Flux formulation (\protect\mdl{sbcflx})} 
    587590\label{sec:SBC_flx} 
    588591%------------------------------------------namsbc_flx---------------------------------------------------- 
     
    606609% ================================================================ 
    607610\section[Bulk formulation {(\textit{sbcblk\{\_core,\_clio\}.F90})}] 
    608                         {Bulk formulation {(\protect\mdl{sbcblk\_core}, \protect\mdl{sbcblk\_clio})}} 
     611{Bulk formulation {(\protect\mdl{sbcblk\_core}, \protect\mdl{sbcblk\_clio})}} 
    609612\label{sec:SBC_blk} 
    610613 
     
    625628%        CORE Bulk formulea 
    626629% ------------------------------------------------------------------------------------------------------------- 
    627 \subsection{CORE formulea (\protect\mdl{sbcblk\_core}, \protect\np{ln\_core}\forcode{ = .true.})} 
     630\subsection[CORE formulea (\textit{sbcblk\_core.F90}, \forcode{ln_core = .true.})] 
     631{CORE formulea (\protect\mdl{sbcblk\_core}, \protect\np{ln\_core}\forcode{ = .true.})} 
    628632\label{subsec:SBC_blk_core} 
    629633%------------------------------------------namsbc_core---------------------------------------------------- 
     
    688692%        CLIO Bulk formulea 
    689693% ------------------------------------------------------------------------------------------------------------- 
    690 \subsection{CLIO formulea (\protect\mdl{sbcblk\_clio}, \protect\np{ln\_clio}\forcode{ = .true.})} 
     694\subsection[CLIO formulea (\textit{sbcblk\_clio.F90}, \forcode{ln_clio = .true.})] 
     695{CLIO formulea (\protect\mdl{sbcblk\_clio}, \protect\np{ln\_clio}\forcode{ = .true.})} 
    691696\label{subsec:SBC_blk_clio} 
    692697%------------------------------------------namsbc_clio---------------------------------------------------- 
     
    729734% Coupled formulation 
    730735% ================================================================ 
    731 \section{Coupled formulation (\protect\mdl{sbccpl})} 
     736\section[Coupled formulation (\textit{sbccpl.F90})] 
     737{Coupled formulation (\protect\mdl{sbccpl})} 
    732738\label{sec:SBC_cpl} 
    733739%------------------------------------------namsbc_cpl---------------------------------------------------- 
     
    770776%        Atmospheric pressure 
    771777% ================================================================ 
    772 \section{Atmospheric pressure (\protect\mdl{sbcapr})} 
     778\section[Atmospheric pressure (\textit{sbcapr.F90})] 
     779{Atmospheric pressure (\protect\mdl{sbcapr})} 
    773780\label{sec:SBC_apr} 
    774781%------------------------------------------namsbc_apr---------------------------------------------------- 
     
    806813%        Surface Tides Forcing 
    807814% ================================================================ 
    808 \section{Surface tides (\protect\mdl{sbctide})} 
     815\section[Surface tides (\textit{sbctide.F90})] 
     816{Surface tides (\protect\mdl{sbctide})} 
    809817\label{sec:SBC_tide} 
    810818 
     
    857865%        River runoffs 
    858866% ================================================================ 
    859 \section{River runoffs (\protect\mdl{sbcrnf})} 
     867\section[River runoffs (\textit{sbcrnf.F90})] 
     868{River runoffs (\protect\mdl{sbcrnf})} 
    860869\label{sec:SBC_rnf} 
    861870%------------------------------------------namsbc_rnf---------------------------------------------------- 
     
    982991%        Ice shelf melting 
    983992% ================================================================ 
    984 \section{Ice shelf melting (\protect\mdl{sbcisf})} 
     993\section[Ice shelf melting (\textit{sbcisf.F90})] 
     994{Ice shelf melting (\protect\mdl{sbcisf})} 
    985995\label{sec:SBC_isf} 
    986996%------------------------------------------namsbc_isf---------------------------------------------------- 
     
    12271237%        Interactions with waves (sbcwave.F90, ln_wave) 
    12281238% ------------------------------------------------------------------------------------------------------------- 
    1229 \section{Interactions with waves (\protect\mdl{sbcwave}, \protect\np{ln\_wave})} 
     1239\section[Interactions with waves (\textit{sbcwave.F90}, \texttt{ln\_wave})] 
     1240{Interactions with waves (\protect\mdl{sbcwave}, \protect\np{ln\_wave})} 
    12301241\label{sec:SBC_wave} 
    12311242%------------------------------------------namsbc_wave-------------------------------------------------------- 
     
    12581269 
    12591270% ================================================================ 
    1260 \subsection{Neutral drag coefficient from wave model (\protect\np{ln\_cdgw})} 
     1271\subsection[Neutral drag coefficient from wave model (\texttt{ln\_cdgw})] 
     1272{Neutral drag coefficient from wave model (\protect\np{ln\_cdgw})} 
    12611273\label{subsec:SBC_wave_cdgw} 
    12621274 
     
    12711283% 3D Stokes Drift (ln_sdw, nn_sdrift) 
    12721284% ================================================================ 
    1273 \subsection{3D Stokes Drift (\protect\np{ln\_sdw, nn\_sdrift})} 
     1285\subsection[3D Stokes Drift (\texttt{ln\_sdw}, \texttt{nn\_sdrift})] 
     1286{3D Stokes Drift (\protect\np{ln\_sdw, nn\_sdrift})} 
    12741287\label{subsec:SBC_wave_sdw} 
    12751288 
     
    13671380% Stokes-Coriolis term (ln_stcor) 
    13681381% ================================================================ 
    1369 \subsection{Stokes-Coriolis term (\protect\np{ln\_stcor})} 
     1382\subsection[Stokes-Coriolis term (\texttt{ln\_stcor})] 
     1383{Stokes-Coriolis term (\protect\np{ln\_stcor})} 
    13701384\label{subsec:SBC_wave_stcor} 
    13711385 
     
    13811395% Waves modified stress (ln_tauwoc, ln_tauw) 
    13821396% ================================================================ 
    1383 \subsection{Wave modified sress (\protect\np{ln\_tauwoc, ln\_tauw})}  
     1397\subsection[Wave modified sress (\texttt{ln\_tauwoc}, \texttt{ln\_tauw})] 
     1398{Wave modified sress (\protect\np{ln\_tauwoc, ln\_tauw})} 
    13841399\label{subsec:SBC_wave_tauw} 
    13851400 
     
    14281443%        Diurnal cycle 
    14291444% ------------------------------------------------------------------------------------------------------------- 
    1430 \subsection{Diurnal cycle (\protect\mdl{sbcdcy})} 
     1445\subsection[Diurnal cycle (\textit{sbcdcy.F90})] 
     1446{Diurnal cycle (\protect\mdl{sbcdcy})} 
    14311447\label{subsec:SBC_dcy} 
    14321448%------------------------------------------namsbc_rnf---------------------------------------------------- 
     
    15141530%        Surface restoring to observed SST and/or SSS 
    15151531% ------------------------------------------------------------------------------------------------------------- 
    1516 \subsection{Surface restoring to observed SST and/or SSS (\protect\mdl{sbcssr})} 
     1532\subsection[Surface restoring to observed SST and/or SSS (\textit{sbcssr.F90})] 
     1533{Surface restoring to observed SST and/or SSS (\protect\mdl{sbcssr})} 
    15171534\label{subsec:SBC_ssr} 
    15181535%------------------------------------------namsbc_ssr---------------------------------------------------- 
     
    15931610% {Description of Ice-ocean interface to be added here or in LIM 2 and 3 doc ?} 
    15941611 
    1595 \subsection{Interface to CICE (\protect\mdl{sbcice\_cice})} 
     1612\subsection[Interface to CICE (\textit{sbcice\_cice.F90})] 
     1613{Interface to CICE (\protect\mdl{sbcice\_cice})} 
    15961614\label{subsec:SBC_cice} 
    15971615 
     
    16261644%        Freshwater budget control  
    16271645% ------------------------------------------------------------------------------------------------------------- 
    1628 \subsection{Freshwater budget control (\protect\mdl{sbcfwb})} 
     1646\subsection[Freshwater budget control (\textit{sbcfwb.F90})] 
     1647{Freshwater budget control (\protect\mdl{sbcfwb})} 
    16291648\label{subsec:SBC_fwb} 
    16301649 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_TRA.tex

    r11151 r11179  
    5555 
    5656The user has the option of extracting each tendency term on the RHS of the tracer equation for output 
    57 (\np{ln\_tra\_trd} or \np{ln\_tra\_mxl}~\forcode{= .true.}), as described in \autoref{chap:DIA}. 
     57(\np{ln\_tra\_trd} or \np{ln\_tra\_mxl}\forcode{ = .true.}), as described in \autoref{chap:DIA}. 
    5858 
    5959% ================================================================ 
    6060% Tracer Advection 
    6161% ================================================================ 
    62 \section{Tracer advection (\protect\mdl{traadv})} 
     62\section[Tracer advection (\textit{traadv.F90})] 
     63{Tracer advection (\protect\mdl{traadv})} 
    6364\label{sec:TRA_adv} 
    6465%------------------------------------------namtra_adv----------------------------------------------------- 
     
    8182Indeed, it is obtained by using the following equality: $\nabla \cdot (\vect U \, T) = \vect U \cdot \nabla T$ which 
    8283results from the use of the continuity equation, $\partial_t e_3 + e_3 \; \nabla \cdot \vect U = 0$ 
    83 (which reduces to $\nabla \cdot \vect U = 0$ in linear free surface, \ie \np{ln\_linssh}~\forcode{= .true.}). 
     84(which reduces to $\nabla \cdot \vect U = 0$ in linear free surface, \ie \np{ln\_linssh}\forcode{ = .true.}). 
    8485Therefore it is of paramount importance to design the discrete analogue of the advection tendency so that 
    8586it is consistent with the continuity equation in order to enforce the conservation properties of 
     
    119120\begin{description} 
    120121\item[linear free surface:] 
    121   (\np{ln\_linssh}~\forcode{= .true.}) 
     122  (\np{ln\_linssh}\forcode{ = .true.}) 
    122123  the first level thickness is constant in time: 
    123124  the vertical boundary condition is applied at the fixed surface $z = 0$ rather than on 
     
    127128  the first level tracer value. 
    128129\item[non-linear free surface:] 
    129   (\np{ln\_linssh}~\forcode{= .false.}) 
     130  (\np{ln\_linssh}\forcode{ = .false.}) 
    130131  convergence/divergence in the first ocean level moves the free surface up/down. 
    131132  There is no tracer advection through it so that the advective fluxes through the surface are also zero. 
     
    183184%        2nd and 4th order centred schemes 
    184185% ------------------------------------------------------------------------------------------------------------- 
    185 \subsection{CEN: Centred scheme (\protect\np{ln\_traadv\_cen}~\forcode{= .true.})} 
     186\subsection[CEN: Centred scheme (\forcode{ln_traadv_cen = .true.})] 
     187{CEN: Centred scheme (\protect\np{ln\_traadv\_cen}\forcode{ = .true.})} 
    186188\label{subsec:TRA_adv_cen} 
    187189 
    188190%        2nd order centred scheme   
    189191 
    190 The centred advection scheme (CEN) is used when \np{ln\_traadv\_cen}~\forcode{= .true.}. 
     192The centred advection scheme (CEN) is used when \np{ln\_traadv\_cen}\forcode{ = .true.}. 
    191193Its order ($2^{nd}$ or $4^{th}$) can be chosen independently on horizontal (iso-level) and vertical direction by 
    192194setting \np{nn\_cen\_h} and \np{nn\_cen\_v} to $2$ or $4$. 
     
    220222  \tau_u^{cen4} = \overline{T - \frac{1}{6} \, \delta_i \Big[ \delta_{i + 1/2}[T] \, \Big]}^{\,i + 1/2} 
    221223\end{equation} 
    222 In the vertical direction (\np{nn\_cen\_v}~\forcode{= 4}), 
     224In the vertical direction (\np{nn\_cen\_v}\forcode{ = 4}), 
    223225a $4^{th}$ COMPACT interpolation has been prefered \citep{demange_phd14}. 
    224226In the COMPACT scheme, both the field and its derivative are interpolated, which leads, after a matrix inversion, 
     
    250252%        FCT scheme   
    251253% ------------------------------------------------------------------------------------------------------------- 
    252 \subsection{FCT: Flux Corrected Transport scheme (\protect\np{ln\_traadv\_fct}~\forcode{= .true.})} 
     254\subsection[FCT: Flux Corrected Transport scheme (\forcode{ln_traadv_fct = .true.})] 
     255{FCT: Flux Corrected Transport scheme (\protect\np{ln\_traadv\_fct}\forcode{ = .true.})} 
    253256\label{subsec:TRA_adv_tvd} 
    254257 
    255 The Flux Corrected Transport schemes (FCT) is used when \np{ln\_traadv\_fct}~\forcode{= .true.}. 
     258The Flux Corrected Transport schemes (FCT) is used when \np{ln\_traadv\_fct}\forcode{ = .true.}. 
    256259Its order ($2^{nd}$ or $4^{th}$) can be chosen independently on horizontal (iso-level) and vertical direction by 
    257260setting \np{nn\_fct\_h} and \np{nn\_fct\_v} to $2$ or $4$. 
     
    300303%        MUSCL scheme   
    301304% ------------------------------------------------------------------------------------------------------------- 
    302 \subsection{MUSCL: Monotone Upstream Scheme for Conservative Laws (\protect\np{ln\_traadv\_mus}~\forcode{= .true.})} 
     305\subsection[MUSCL: Monotone Upstream Scheme for Conservative Laws (\forcode{ln_traadv_mus = .true.})] 
     306{MUSCL: Monotone Upstream Scheme for Conservative Laws (\protect\np{ln\_traadv\_mus}\forcode{ = .true.})} 
    303307\label{subsec:TRA_adv_mus} 
    304308 
    305 The Monotone Upstream Scheme for Conservative Laws (MUSCL) is used when \np{ln\_traadv\_mus}~\forcode{= .true.}. 
     309The Monotone Upstream Scheme for Conservative Laws (MUSCL) is used when \np{ln\_traadv\_mus}\forcode{ = .true.}. 
    306310MUSCL implementation can be found in the \mdl{traadv\_mus} module. 
    307311 
     
    331335This choice ensure the \textit{positive} character of the scheme. 
    332336In addition, fluxes round a grid-point where a runoff is applied can optionally be computed using upstream fluxes 
    333 (\np{ln\_mus\_ups}~\forcode{= .true.}). 
     337(\np{ln\_mus\_ups}\forcode{ = .true.}). 
    334338 
    335339% ------------------------------------------------------------------------------------------------------------- 
    336340%        UBS scheme   
    337341% ------------------------------------------------------------------------------------------------------------- 
    338 \subsection{UBS a.k.a. UP3: Upstream-Biased Scheme (\protect\np{ln\_traadv\_ubs}~\forcode{= .true.})} 
     342\subsection[UBS a.k.a. UP3: Upstream-Biased Scheme (\forcode{ln_traadv_ubs = .true.})] 
     343{UBS a.k.a. UP3: Upstream-Biased Scheme (\protect\np{ln\_traadv\_ubs}\forcode{ = .true.})} 
    339344\label{subsec:TRA_adv_ubs} 
    340345 
    341 The Upstream-Biased Scheme (UBS) is used when \np{ln\_traadv\_ubs}~\forcode{= .true.}. 
     346The Upstream-Biased Scheme (UBS) is used when \np{ln\_traadv\_ubs}\forcode{ = .true.}. 
    342347UBS implementation can be found in the \mdl{traadv\_mus} module. 
    343348 
     
    369374\citep{shchepetkin.mcwilliams_OM05, demange_phd14}. 
    370375Therefore the vertical flux is evaluated using either a $2^nd$ order FCT scheme or a $4^th$ order COMPACT scheme 
    371 (\np{nn\_cen\_v}~\forcode{= 2 or 4}). 
     376(\np{nn\_cen\_v}\forcode{ = 2 or 4}). 
    372377 
    373378For stability reasons (see \autoref{chap:STP}), the first term  in \autoref{eq:tra_adv_ubs} 
     
    408413%        QCK scheme   
    409414% ------------------------------------------------------------------------------------------------------------- 
    410 \subsection{QCK: QuiCKest scheme (\protect\np{ln\_traadv\_qck}~\forcode{= .true.})} 
     415\subsection[QCK: QuiCKest scheme (\forcode{ln_traadv_qck = .true.})] 
     416{QCK: QuiCKest scheme (\protect\np{ln\_traadv\_qck}\forcode{ = .true.})} 
    411417\label{subsec:TRA_adv_qck} 
    412418 
    413419The Quadratic Upstream Interpolation for Convective Kinematics with Estimated Streaming Terms (QUICKEST) scheme 
    414 proposed by \citet{leonard_CMAME79} is used when \np{ln\_traadv\_qck}~\forcode{= .true.}. 
     420proposed by \citet{leonard_CMAME79} is used when \np{ln\_traadv\_qck}\forcode{ = .true.}. 
    415421QUICKEST implementation can be found in the \mdl{traadv\_qck} module. 
    416422 
     
    431437% Tracer Lateral Diffusion 
    432438% ================================================================ 
    433 \section{Tracer lateral diffusion (\protect\mdl{traldf})} 
     439\section[Tracer lateral diffusion (\textit{traldf.F90})] 
     440{Tracer lateral diffusion (\protect\mdl{traldf})} 
    434441\label{sec:TRA_ldf} 
    435442%-----------------------------------------nam_traldf------------------------------------------------------ 
     
    453460except for the pure vertical component that appears when a rotation tensor is used. 
    454461This latter component is solved implicitly together with the vertical diffusion term (see \autoref{chap:STP}). 
    455 When \np{ln\_traldf\_msc}~\forcode{= .true.}, a Method of Stabilizing Correction is used in which 
     462When \np{ln\_traldf\_msc}\forcode{ = .true.}, a Method of Stabilizing Correction is used in which 
    456463the pure vertical component is split into an explicit and an implicit part \citep{lemarie.debreu.ea_OM12}. 
    457464 
     
    459466%        Type of operator 
    460467% ------------------------------------------------------------------------------------------------------------- 
    461 \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}) }  
     468\subsection[Type of operator (\texttt{ln\_traldf}\{\texttt{\_NONE,\_lap,\_blp}\})] 
     469{Type of operator (\protect\np{ln\_traldf\_NONE}, \protect\np{ln\_traldf\_lap}, or \protect\np{ln\_traldf\_blp}) }  
    462470\label{subsec:TRA_ldf_op} 
    463471 
     
    465473 
    466474\begin{description} 
    467 \item[\np{ln\_traldf\_NONE}~\forcode{= .true.}:] 
     475\item[\np{ln\_traldf\_NONE}\forcode{ = .true.}:] 
    468476  no operator selected, the lateral diffusive tendency will not be applied to the tracer equation. 
    469477  This option can be used when the selected advection scheme is diffusive enough (MUSCL scheme for example). 
    470 \item[\np{ln\_traldf\_lap}~\forcode{= .true.}:] 
     478\item[\np{ln\_traldf\_lap}\forcode{ = .true.}:] 
    471479  a laplacian operator is selected. 
    472480  This harmonic operator takes the following expression:  $\mathpzc{L}(T) = \nabla \cdot A_{ht} \; \nabla T $, 
    473481  where the gradient operates along the selected direction (see \autoref{subsec:TRA_ldf_dir}), 
    474482  and $A_{ht}$ is the eddy diffusivity coefficient expressed in $m^2/s$ (see \autoref{chap:LDF}). 
    475 \item[\np{ln\_traldf\_blp}~\forcode{= .true.}]: 
     483\item[\np{ln\_traldf\_blp}\forcode{ = .true.}]: 
    476484  a bilaplacian operator is selected. 
    477485  This biharmonic operator takes the following expression: 
     
    493501%        Direction of action 
    494502% ------------------------------------------------------------------------------------------------------------- 
    495 \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}) }  
     503\subsection[Action direction (\texttt{ln\_traldf}\{\texttt{\_lev,\_hor,\_iso,\_triad}\})] 
     504{Direction of action (\protect\np{ln\_traldf\_lev}, \protect\np{ln\_traldf\_hor}, \protect\np{ln\_traldf\_iso}, or \protect\np{ln\_traldf\_triad}) }  
    496505\label{subsec:TRA_ldf_dir} 
    497506 
    498507The choice of a direction of action determines the form of operator used. 
    499508The operator is a simple (re-entrant) laplacian acting in the (\textbf{i},\textbf{j}) plane when 
    500 iso-level option is used (\np{ln\_traldf\_lev}~\forcode{= .true.}) or 
     509iso-level option is used (\np{ln\_traldf\_lev}\forcode{ = .true.}) or 
    501510when a horizontal (\ie geopotential) operator is demanded in \textit{z}-coordinate 
    502511(\np{ln\_traldf\_hor} and \np{ln\_zco} equal \forcode{.true.}). 
     
    519528%       iso-level operator 
    520529% ------------------------------------------------------------------------------------------------------------- 
    521 \subsection{Iso-level (bi -)laplacian operator ( \protect\np{ln\_traldf\_iso}) } 
     530\subsection[Iso-level (bi-)laplacian operator (\texttt{ln\_traldf\_iso})] 
     531{Iso-level (bi-)laplacian operator ( \protect\np{ln\_traldf\_iso})} 
    522532\label{subsec:TRA_ldf_lev} 
    523533 
     
    537547It is a \textit{horizontal} operator (\ie acting along geopotential surfaces) in 
    538548the $z$-coordinate with or without partial steps, but is simply an iso-level operator in the $s$-coordinate. 
    539 It is thus used when, in addition to \np{ln\_traldf\_lap} or \np{ln\_traldf\_blp}~\forcode{= .true.}, 
    540 we have \np{ln\_traldf\_lev}~\forcode{= .true.} or \np{ln\_traldf\_hor}~=~\np{ln\_zco}~\forcode{= .true.}. 
     549It is thus used when, in addition to \np{ln\_traldf\_lap} or \np{ln\_traldf\_blp}\forcode{ = .true.}, 
     550we have \np{ln\_traldf\_lev}\forcode{ = .true.} or \np{ln\_traldf\_hor}~=~\np{ln\_zco}\forcode{ = .true.}. 
    541551In both cases, it significantly contributes to diapycnal mixing. 
    542552It is therefore never recommended, even when using it in the bilaplacian case. 
    543553 
    544 Note that in the partial step $z$-coordinate (\np{ln\_zps}~\forcode{= .true.}), 
     554Note that in the partial step $z$-coordinate (\np{ln\_zps}\forcode{ = .true.}), 
    545555tracers in horizontally adjacent cells are located at different depths in the vicinity of the bottom. 
    546556In this case, horizontal derivatives in (\autoref{eq:tra_ldf_lap}) at the bottom level require a specific treatment. 
     
    550560%         Rotated laplacian operator 
    551561% ------------------------------------------------------------------------------------------------------------- 
    552 \subsection{Standard and triad (bi -)laplacian operator} 
     562\subsection{Standard and triad (bi-)laplacian operator} 
    553563\label{subsec:TRA_ldf_iso_triad} 
    554564 
    555 %&&    Standard rotated (bi -)laplacian operator 
     565%&&    Standard rotated (bi-)laplacian operator 
    556566%&& ---------------------------------------------- 
    557 \subsubsection{Standard rotated (bi -)laplacian operator (\protect\mdl{traldf\_iso})} 
     567\subsubsection[Standard rotated (bi-)laplacian operator (\textit{traldf\_iso.F90})] 
     568{Standard rotated (bi-)laplacian operator (\protect\mdl{traldf\_iso})} 
    558569\label{subsec:TRA_ldf_iso} 
    559570The general form of the second order lateral tracer subgrid scale physics (\autoref{eq:PE_zdf}) 
     
    574585$r_1$ and $r_2$ are the slopes between the surface of computation ($z$- or $s$-surfaces) and 
    575586the surface along which the diffusion operator acts (\ie horizontal or iso-neutral surfaces). 
    576 It is thus used when, in addition to \np{ln\_traldf\_lap}~\forcode{= .true.}, 
    577 we have \np{ln\_traldf\_iso}~\forcode{= .true.}, 
    578 or both \np{ln\_traldf\_hor}~\forcode{= .true.} and \np{ln\_zco}~\forcode{= .true.}. 
     587It is thus used when, in addition to \np{ln\_traldf\_lap}\forcode{ = .true.}, 
     588we have \np{ln\_traldf\_iso}\forcode{ = .true.}, 
     589or both \np{ln\_traldf\_hor}\forcode{ = .true.} and \np{ln\_zco}\forcode{ = .true.}. 
    579590The way these slopes are evaluated is given in \autoref{sec:LDF_slp}. 
    580591At the surface, bottom and lateral boundaries, the turbulent fluxes of heat and salt are set to zero using 
     
    592603any additional background horizontal diffusion \citep{guilyardi.madec.ea_CD01}. 
    593604 
    594 Note that in the partial step $z$-coordinate (\np{ln\_zps}~\forcode{= .true.}), 
     605Note that in the partial step $z$-coordinate (\np{ln\_zps}\forcode{ = .true.}), 
    595606the horizontal derivatives at the bottom level in \autoref{eq:tra_ldf_iso} require a specific treatment. 
    596607They are calculated in module zpshde, described in \autoref{sec:TRA_zpshde}. 
    597608 
    598 %&&     Triad rotated (bi -)laplacian operator 
     609%&&     Triad rotated (bi-)laplacian operator 
    599610%&&  ------------------------------------------- 
    600 \subsubsection{Triad rotated (bi -)laplacian operator (\protect\np{ln\_traldf\_triad})} 
     611\subsubsection[Triad rotated (bi-)laplacian operator (\textit{ln\_traldf\_triad})] 
     612{Triad rotated (bi-)laplacian operator (\protect\np{ln\_traldf\_triad})} 
    601613\label{subsec:TRA_ldf_triad} 
    602614 
    603 If the Griffies triad scheme is employed (\np{ln\_traldf\_triad}~\forcode{= .true.}; see \autoref{apdx:triad}) 
     615If the Griffies triad scheme is employed (\np{ln\_traldf\_triad}\forcode{ = .true.}; see \autoref{apdx:triad}) 
    604616 
    605617An alternative scheme developed by \cite{griffies.gnanadesikan.ea_JPO98} which ensures tracer variance decreases 
    606 is also available in \NEMO (\np{ln\_traldf\_grif}~\forcode{= .true.}). 
     618is also available in \NEMO (\np{ln\_traldf\_grif}\forcode{ = .true.}). 
    607619A complete description of the algorithm is given in \autoref{apdx:triad}. 
    608620 
     
    632644% Tracer Vertical Diffusion 
    633645% ================================================================ 
    634 \section{Tracer vertical diffusion (\protect\mdl{trazdf})} 
     646\section[Tracer vertical diffusion (\textit{trazdf.F90})] 
     647{Tracer vertical diffusion (\protect\mdl{trazdf})} 
    635648\label{sec:TRA_zdf} 
    636649%--------------------------------------------namzdf--------------------------------------------------------- 
     
    663676 
    664677The large eddy coefficient found in the mixed layer together with high vertical resolution implies that 
    665 in the case of explicit time stepping (\np{ln\_zdfexp}~\forcode{= .true.}) 
     678in the case of explicit time stepping (\np{ln\_zdfexp}\forcode{ = .true.}) 
    666679there would be too restrictive a constraint on the time step. 
    667680Therefore, the default implicit time stepping is preferred for the vertical diffusion since 
    668681it overcomes the stability constraint. 
    669 A forward time differencing scheme (\np{ln\_zdfexp}~\forcode{= .true.}) using 
     682A forward time differencing scheme (\np{ln\_zdfexp}\forcode{ = .true.}) using 
    670683a time splitting technique (\np{nn\_zdfexp} $> 1$) is provided as an alternative. 
    671684Namelist variables \np{ln\_zdfexp} and \np{nn\_zdfexp} apply to both tracers and dynamics. 
     
    680693%        surface boundary condition 
    681694% ------------------------------------------------------------------------------------------------------------- 
    682 \subsection{Surface boundary condition (\protect\mdl{trasbc})} 
     695\subsection[Surface boundary condition (\textit{trasbc.F90})] 
     696{Surface boundary condition (\protect\mdl{trasbc})} 
    683697\label{subsec:TRA_sbc} 
    684698 
     
    730744Such time averaging prevents the divergence of odd and even time step (see \autoref{chap:STP}). 
    731745 
    732 In the linear free surface case (\np{ln\_linssh}~\forcode{= .true.}), an additional term has to be added on 
     746In the linear free surface case (\np{ln\_linssh}\forcode{ = .true.}), an additional term has to be added on 
    733747both temperature and salinity. 
    734748On temperature, this term remove the heat content associated with mass exchange that has been added to $Q_{ns}$. 
     
    753767%        Solar Radiation Penetration  
    754768% ------------------------------------------------------------------------------------------------------------- 
    755 \subsection{Solar radiation penetration (\protect\mdl{traqsr})} 
     769\subsection[Solar radiation penetration (\textit{traqsr.F90})] 
     770{Solar radiation penetration (\protect\mdl{traqsr})} 
    756771\label{subsec:TRA_qsr} 
    757772%--------------------------------------------namqsr-------------------------------------------------------- 
     
    761776 
    762777Options are defined through the \ngn{namtra\_qsr} namelist variables. 
    763 When the penetrative solar radiation option is used (\np{ln\_flxqsr}~\forcode{= .true.}), 
     778When the penetrative solar radiation option is used (\np{ln\_flxqsr}\forcode{ = .true.}), 
    764779the solar radiation penetrates the top few tens of meters of the ocean. 
    765 If it is not used (\np{ln\_flxqsr}~\forcode{= .false.}) all the heat flux is absorbed in the first ocean level. 
     780If it is not used (\np{ln\_flxqsr}\forcode{ = .false.}) all the heat flux is absorbed in the first ocean level. 
    766781Thus, in the former case a term is added to the time evolution equation of temperature \autoref{eq:PE_tra_T} and 
    767782the surface boundary condition is modified to take into account only the non-penetrative part of the surface  
     
    792807larger depths where it contributes to local heating. 
    793808The way this second part of the solar energy penetrates into the ocean depends on which formulation is chosen. 
    794 In the simple 2-waveband light penetration scheme (\np{ln\_qsr\_2bd}~\forcode{= .true.}) 
     809In the simple 2-waveband light penetration scheme (\np{ln\_qsr\_2bd}\forcode{ = .true.}) 
    795810a chlorophyll-independent monochromatic formulation is chosen for the shorter wavelengths, 
    796811leading to the following expression \citep{paulson.simpson_JPO77}: 
     
    820835The 2-bands formulation does not reproduce the full model very well. 
    821836 
    822 The RGB formulation is used when \np{ln\_qsr\_rgb}~\forcode{= .true.}. 
     837The RGB formulation is used when \np{ln\_qsr\_rgb}\forcode{ = .true.}. 
    823838The RGB attenuation coefficients (\ie the inverses of the extinction length scales) are tabulated over 
    82483961 nonuniform chlorophyll classes ranging from 0.01 to 10 g.Chl/L 
     
    827842 
    828843\begin{description} 
    829 \item[\np{nn\_chdta}~\forcode{= 0}] 
     844\item[\np{nn\_chdta}\forcode{ = 0}] 
    830845  a constant 0.05 g.Chl/L value everywhere ;  
    831 \item[\np{nn\_chdta}~\forcode{= 1}] 
     846\item[\np{nn\_chdta}\forcode{ = 1}] 
    832847  an observed time varying chlorophyll deduced from satellite surface ocean color measurement spread uniformly in 
    833848  the vertical direction; 
    834 \item[\np{nn\_chdta}~\forcode{= 2}] 
     849\item[\np{nn\_chdta}\forcode{ = 2}] 
    835850  same as previous case except that a vertical profile of chlorophyl is used. 
    836851  Following \cite{morel.berthon_LO89}, the profile is computed from the local surface chlorophyll value; 
    837 \item[\np{ln\_qsr\_bio}~\forcode{= .true.}] 
     852\item[\np{ln\_qsr\_bio}\forcode{ = .true.}] 
    838853  simulated time varying chlorophyll by TOP biogeochemical model. 
    839854  In this case, the RGB formulation is used to calculate both the phytoplankton light limitation in 
     
    874889%        Bottom Boundary Condition 
    875890% ------------------------------------------------------------------------------------------------------------- 
    876 \subsection{Bottom boundary condition (\protect\mdl{trabbc})} 
     891\subsection[Bottom boundary condition (\textit{trabbc.F90})] 
     892{Bottom boundary condition (\protect\mdl{trabbc})} 
    877893\label{subsec:TRA_bbc} 
    878894%--------------------------------------------nambbc-------------------------------------------------------- 
     
    912928% Bottom Boundary Layer 
    913929% ================================================================ 
    914 \section{Bottom boundary layer (\protect\mdl{trabbl} - \protect\key{trabbl})} 
     930\section[Bottom boundary layer (\textit{trabbl.F90} - \texttt{\textbf{key\_trabbl}})] 
     931{Bottom boundary layer (\protect\mdl{trabbl} - \protect\key{trabbl})} 
    915932\label{sec:TRA_bbl} 
    916933%--------------------------------------------nambbl--------------------------------------------------------- 
     
    944961%        Diffusive BBL 
    945962% ------------------------------------------------------------------------------------------------------------- 
    946 \subsection{Diffusive bottom boundary layer (\protect\np{nn\_bbl\_ldf}~\forcode{= 1})} 
     963\subsection[Diffusive bottom boundary layer (\forcode{nn_bbl_ldf = 1})] 
     964{Diffusive bottom boundary layer (\protect\np{nn\_bbl\_ldf}\forcode{ = 1})} 
    947965\label{subsec:TRA_bbl_diff} 
    948966 
     
    9831001%        Advective BBL 
    9841002% ------------------------------------------------------------------------------------------------------------- 
    985 \subsection{Advective bottom boundary layer  (\protect\np{nn\_bbl\_adv}~\forcode{= 1..2})} 
     1003\subsection[Advective bottom boundary layer (\forcode{nn_bbl_adv = [12]})] 
     1004{Advective bottom boundary layer (\protect\np{nn\_bbl\_adv}\forcode{ = [12]})} 
    9861005\label{subsec:TRA_bbl_adv} 
    9871006 
     
    10141033%%%gmcomment   :  this section has to be really written 
    10151034 
    1016 When applying an advective BBL (\np{nn\_bbl\_adv}~\forcode{= 1..2}), an overturning circulation is added which 
     1035When applying an advective BBL (\np{nn\_bbl\_adv}\forcode{ = 1..2}), an overturning circulation is added which 
    10171036connects two adjacent bottom grid-points only if dense water overlies less dense water on the slope. 
    10181037The density difference causes dense water to move down the slope. 
    10191038 
    1020 \np{nn\_bbl\_adv}~\forcode{= 1}: 
     1039\np{nn\_bbl\_adv}\forcode{ = 1}: 
    10211040the downslope velocity is chosen to be the Eulerian ocean velocity just above the topographic step 
    10221041(see black arrow in \autoref{fig:bbl}) \citep{beckmann.doscher_JPO97}. 
     
    10251044if the velocity is directed towards greater depth (\ie $\vect U \cdot \nabla H > 0$). 
    10261045 
    1027 \np{nn\_bbl\_adv}~\forcode{= 2}: 
     1046\np{nn\_bbl\_adv}\forcode{ = 2}: 
    10281047the downslope velocity is chosen to be proportional to $\Delta \rho$, 
    10291048the density difference between the higher cell and lower cell densities \citep{campin.goosse_T99}. 
     
    10741093% Tracer damping 
    10751094% ================================================================ 
    1076 \section{Tracer damping (\protect\mdl{tradmp})} 
     1095\section[Tracer damping (\textit{tradmp.F90})] 
     1096{Tracer damping (\protect\mdl{tradmp})} 
    10771097\label{sec:TRA_dmp} 
    10781098%--------------------------------------------namtra_dmp------------------------------------------------- 
     
    11291149% Tracer time evolution 
    11301150% ================================================================ 
    1131 \section{Tracer time evolution (\protect\mdl{tranxt})} 
     1151\section[Tracer time evolution (\textit{tranxt.F90})] 
     1152{Tracer time evolution (\protect\mdl{tranxt})} 
    11321153\label{sec:TRA_nxt} 
    11331154%--------------------------------------------namdom----------------------------------------------------- 
     
    11511172(\ie fluxes plus content in mass exchanges). 
    11521173$\gamma$ is initialized as \np{rn\_atfp} (\textbf{namelist} parameter). 
    1153 Its default value is \np{rn\_atfp}~\forcode{= 10.e-3}. 
     1174Its default value is \np{rn\_atfp}\forcode{ = 10.e-3}. 
    11541175Note that the forcing correction term in the filter is not applied in linear free surface 
    1155 (\jp{lk\_vvl}~\forcode{= .false.}) (see \autoref{subsec:TRA_sbc}). 
     1176(\jp{lk\_vvl}\forcode{ = .false.}) (see \autoref{subsec:TRA_sbc}). 
    11561177Not also that in constant volume case, the time stepping is performed on $T$, not on its content, $e_{3t}T$. 
    11571178 
     
    11661187% Equation of State (eosbn2)  
    11671188% ================================================================ 
    1168 \section{Equation of state (\protect\mdl{eosbn2}) } 
     1189\section[Equation of state (\textit{eosbn2.F90})] 
     1190{Equation of state (\protect\mdl{eosbn2})} 
    11691191\label{sec:TRA_eosbn2} 
    11701192%--------------------------------------------nameos----------------------------------------------------- 
     
    11761198%        Equation of State 
    11771199% ------------------------------------------------------------------------------------------------------------- 
    1178 \subsection{Equation of seawater (\protect\np{nn\_eos}~\forcode{= -1..1})} 
     1200\subsection[Equation of seawater (\forcode{nn_eos = {-1,1}})] 
     1201{Equation of seawater (\protect\np{nn\_eos}\forcode{ = {-1,1}})} 
    11791202\label{subsec:TRA_eos} 
    11801203 
     
    12101233 
    12111234\begin{description} 
    1212 \item[\np{nn\_eos}~\forcode{= -1}] 
     1235\item[\np{nn\_eos}\forcode{ = -1}] 
    12131236  the polyTEOS10-bsq equation of seawater \citep{roquet.madec.ea_OM15} is used. 
    12141237  The accuracy of this approximation is comparable to the TEOS-10 rational function approximation, 
     
    12291252  either computing the air-sea and ice-sea fluxes (forced mode) or 
    12301253  sending the SST field to the atmosphere (coupled mode). 
    1231 \item[\np{nn\_eos}~\forcode{= 0}] 
     1254\item[\np{nn\_eos}\forcode{ = 0}] 
    12321255  the polyEOS80-bsq equation of seawater is used. 
    12331256  It takes the same polynomial form as the polyTEOS10, but the coefficients have been optimized to 
     
    12411264  Nevertheless, a severe assumption is made in order to have a heat content ($C_p T_p$) which 
    12421265  is conserved by the model: $C_p$ is set to a constant value, the TEOS10 value. 
    1243 \item[\np{nn\_eos}~\forcode{= 1}] 
     1266\item[\np{nn\_eos}\forcode{ = 1}] 
    12441267  a simplified EOS (S-EOS) inspired by \citet{vallis_bk06} is chosen, 
    12451268  the coefficients of which has been optimized to fit the behavior of TEOS10 
     
    13031326%        Brunt-V\"{a}is\"{a}l\"{a} Frequency 
    13041327% ------------------------------------------------------------------------------------------------------------- 
    1305 \subsection{Brunt-V\"{a}is\"{a}l\"{a} frequency (\protect\np{nn\_eos}~\forcode{= 0..2})} 
     1328\subsection[Brunt-V\"{a}is\"{a}l\"{a} frequency (\forcode{nn_eos = [0-2]})] 
     1329{Brunt-V\"{a}is\"{a}l\"{a} frequency (\protect\np{nn\_eos}\forcode{ = [0-2]})} 
    13061330\label{subsec:TRA_bn2} 
    13071331 
     
    13571381% Horizontal Derivative in zps-coordinate  
    13581382% ================================================================ 
    1359 \section{Horizontal derivative in \textit{zps}-coordinate (\protect\mdl{zpshde})} 
     1383\section[Horizontal derivative in \textit{zps}-coordinate (\textit{zpshde.F90})] 
     1384{Horizontal derivative in \textit{zps}-coordinate (\protect\mdl{zpshde})} 
    13601385\label{sec:TRA_zpshde} 
    13611386 
     
    13631388I've changed "derivative" to "difference" and "mean" to "average"} 
    13641389 
    1365 With partial cells (\np{ln\_zps}~\forcode{= .true.}) at bottom and top (\np{ln\_isfcav}~\forcode{= .true.}), 
     1390With partial cells (\np{ln\_zps}\forcode{ = .true.}) at bottom and top (\np{ln\_isfcav}\forcode{ = .true.}), 
    13661391in general, tracers in horizontally adjacent cells live at different depths. 
    13671392Horizontal gradients of tracers are needed for horizontal diffusion (\mdl{traldf} module) and 
    13681393the hydrostatic pressure gradient calculations (\mdl{dynhpg} module). 
    1369 The partial cell properties at the top (\np{ln\_isfcav}~\forcode{= .true.}) are computed in the same way as 
     1394The partial cell properties at the top (\np{ln\_isfcav}\forcode{ = .true.}) are computed in the same way as 
    13701395for the bottom. 
    13711396So, only the bottom interpolation is explained below. 
     
    13831408      \protect\label{fig:Partial_step_scheme} 
    13841409      Discretisation of the horizontal difference and average of tracers in the $z$-partial step coordinate 
    1385       (\protect\np{ln\_zps}~\forcode{= .true.}) in the case $(e3w_k^{i + 1} - e3w_k^i) > 0$. 
     1410      (\protect\np{ln\_zps}\forcode{ = .true.}) in the case $(e3w_k^{i + 1} - e3w_k^i) > 0$. 
    13861411      A linear interpolation is used to estimate $\widetilde T_k^{i + 1}$, 
    13871412      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

    r11151 r11179  
    4646%        Constant  
    4747% ------------------------------------------------------------------------------------------------------------- 
    48 \subsection{Constant (\protect\key{zdfcst})} 
     48\subsection[Constant (\texttt{\textbf{key\_zdfcst}})] 
     49{Constant (\protect\key{zdfcst})} 
    4950\label{subsec:ZDF_cst} 
    5051%--------------------------------------------namzdf--------------------------------------------------------- 
     
    7273%        Richardson Number Dependent 
    7374% ------------------------------------------------------------------------------------------------------------- 
    74 \subsection{Richardson number dependent (\protect\key{zdfric})} 
     75\subsection[Richardson number dependent (\texttt{\textbf{key\_zdfric}})] 
     76{Richardson number dependent (\protect\key{zdfric})} 
    7577\label{subsec:ZDF_ric} 
    7678 
     
    129131%        TKE Turbulent Closure Scheme  
    130132% ------------------------------------------------------------------------------------------------------------- 
    131 \subsection{TKE turbulent closure scheme (\protect\key{zdftke})} 
     133\subsection[TKE turbulent closure scheme (\texttt{\textbf{key\_zdftke}})] 
     134{TKE turbulent closure scheme (\protect\key{zdftke})} 
    132135\label{subsec:ZDF_tke} 
    133136 
     
    408411%        TKE discretization considerations 
    409412% ------------------------------------------------------------------------------------------------------------- 
    410 \subsection{TKE discretization considerations (\protect\key{zdftke})} 
     413\subsection[TKE discretization considerations (\texttt{\textbf{key\_zdftke}})] 
     414{TKE discretization considerations (\protect\key{zdftke})} 
    411415\label{subsec:ZDF_tke_ene} 
    412416 
     
    514518%        GLS Generic Length Scale Scheme  
    515519% ------------------------------------------------------------------------------------------------------------- 
    516 \subsection{GLS: Generic Length Scale (\protect\key{zdfgls})} 
     520\subsection[GLS: Generic Length Scale (\texttt{\textbf{key\_zdfgls}})] 
     521{GLS: Generic Length Scale (\protect\key{zdfgls})} 
    517522\label{subsec:ZDF_gls} 
    518523 
     
    633638%        OSM OSMOSIS BL Scheme  
    634639% ------------------------------------------------------------------------------------------------------------- 
    635 \subsection{OSM: OSMOSIS boundary layer scheme (\protect\key{zdfosm})} 
     640\subsection[OSM: OSMosis boundary layer scheme (\texttt{\textbf{key\_zdfosm}})] 
     641{OSM: OSMosis boundary layer scheme (\protect\key{zdfosm})} 
    636642\label{subsec:ZDF_osm} 
    637643 
     
    664670%       Non-Penetrative Convective Adjustment  
    665671% ------------------------------------------------------------------------------------------------------------- 
    666 \subsection[Non-penetrative convective adjmt (\protect\np{ln\_tranpc}\forcode{ = .true.})] 
    667             {Non-penetrative convective adjustment (\protect\np{ln\_tranpc}\forcode{ = .true.})} 
     672\subsection[Non-penetrative convective adjustment (\forcode{ln_tranpc = .true.})] 
     673{Non-penetrative convective adjustment (\protect\np{ln\_tranpc}\forcode{ = .true.})} 
    668674\label{subsec:ZDF_npc} 
    669675 
     
    736742%       Enhanced Vertical Diffusion  
    737743% ------------------------------------------------------------------------------------------------------------- 
    738 \subsection{Enhanced vertical diffusion (\protect\np{ln\_zdfevd}\forcode{ = .true.})} 
     744\subsection[Enhanced vertical diffusion (\forcode{ln_zdfevd = .true.})] 
     745{Enhanced vertical diffusion (\protect\np{ln\_zdfevd}\forcode{ = .true.})} 
    739746\label{subsec:ZDF_evd} 
    740747 
     
    769776%       Turbulent Closure Scheme  
    770777% ------------------------------------------------------------------------------------------------------------- 
    771 \subsection[Turbulent closure scheme (\protect\key{zdf}\{tke,gls,osm\})]{Turbulent Closure Scheme (\protect\key{zdftke}, \protect\key{zdfgls} or \protect\key{zdfosm})} 
     778\subsection[Turbulent closure scheme (\texttt{\textbf{key\_zdf}}\texttt{\textbf{\{tke,gls,osm\}}})] 
     779{Turbulent Closure Scheme (\protect\key{zdftke}, \protect\key{zdfgls} or \protect\key{zdfosm})} 
    772780\label{subsec:ZDF_tcs} 
    773781 
     
    795803% Double Diffusion Mixing 
    796804% ================================================================ 
    797 \section{Double diffusion mixing (\protect\key{zdfddm})} 
     805\section[Double diffusion mixing (\texttt{\textbf{key\_zdfddm}})] 
     806{Double diffusion mixing (\protect\key{zdfddm})} 
    798807\label{sec:ZDF_ddm} 
    799808 
     
    887896% Bottom Friction 
    888897% ================================================================ 
    889 \section{Bottom and top friction (\protect\mdl{zdfbfr})} 
     898\section[Bottom and top friction (\textit{zdfbfr.F90})] 
     899{Bottom and top friction (\protect\mdl{zdfbfr})} 
    890900\label{sec:ZDF_bfr} 
    891901 
     
    951961%       Linear Bottom Friction 
    952962% ------------------------------------------------------------------------------------------------------------- 
    953 \subsection{Linear bottom friction (\protect\np{nn\_botfr}\forcode{ = 0..1})} 
     963\subsection[Linear bottom friction (\forcode{nn_botfr = [01]})] 
     964{Linear bottom friction (\protect\np{nn\_botfr}\forcode{ = [01])}} 
    954965\label{subsec:ZDF_bfr_linear} 
    955966 
     
    9931004%       Non-Linear Bottom Friction 
    9941005% ------------------------------------------------------------------------------------------------------------- 
    995 \subsection{Non-linear bottom friction (\protect\np{nn\_botfr}\forcode{ = 2})} 
     1006\subsection[Non-linear bottom friction (\forcode{nn_botfr = 2})] 
     1007{Non-linear bottom friction (\protect\np{nn\_botfr}\forcode{ = 2})} 
    9961008\label{subsec:ZDF_bfr_nonlinear} 
    9971009 
     
    10321044%       Bottom Friction Log-layer 
    10331045% ------------------------------------------------------------------------------------------------------------- 
    1034 \subsection[Log-layer btm frict enhncmnt (\protect\np{nn\_botfr}\forcode{ = 2}, \protect\np{ln\_loglayer}\forcode{ = .true.})] 
    1035             {Log-layer bottom friction enhancement (\protect\np{nn\_botfr}\forcode{ = 2}, \protect\np{ln\_loglayer}\forcode{ = .true.})} 
     1046\subsection[Log-layer bottom friction enhancement (\forcode{nn_botfr = 2}, \forcode{ln_loglayer = .true.})] 
     1047{Log-layer bottom friction enhancement (\protect\np{nn\_botfr}\forcode{ = 2}, \protect\np{ln\_loglayer}\forcode{ = .true.})} 
    10361048\label{subsec:ZDF_bfr_loglayer} 
    10371049 
     
    11091121%       Implicit Bottom Friction 
    11101122% ------------------------------------------------------------------------------------------------------------- 
    1111 \subsection{Implicit bottom friction (\protect\np{ln\_bfrimp}\forcode{ = .true.})} 
     1123\subsection[Implicit bottom friction (\forcode{ln_bfrimp = .true.})] 
     1124{Implicit bottom friction (\protect\np{ln\_bfrimp}\forcode{ = .true.})} 
    11121125\label{subsec:ZDF_bfr_imp} 
    11131126 
     
    11621175%       Bottom Friction with split-explicit time splitting 
    11631176% ------------------------------------------------------------------------------------------------------------- 
    1164 \subsection[Bottom friction w/ split-explicit time splitting (\protect\np{ln\_bfrimp})] 
    1165             {Bottom friction with split-explicit time splitting (\protect\np{ln\_bfrimp})} 
     1177\subsection[Bottom friction with split-explicit time splitting (\texttt{ln\_bfrimp})] 
     1178{Bottom friction with split-explicit time splitting (\protect\np{ln\_bfrimp})} 
    11661179\label{subsec:ZDF_bfr_ts} 
    11671180 
     
    12181231% Tidal Mixing 
    12191232% ================================================================ 
    1220 \section{Tidal mixing (\protect\key{zdftmx})} 
     1233\section[Tidal mixing (\texttt{\textbf{key\_zdftmx}})] 
     1234{Tidal mixing (\protect\key{zdftmx})} 
    12211235\label{sec:ZDF_tmx} 
    12221236 
     
    12971311%        Indonesian area specific treatment  
    12981312% ------------------------------------------------------------------------------------------------------------- 
    1299 \subsection{Indonesian area specific treatment (\protect\np{ln\_zdftmx\_itf})} 
     1313\subsection[Indonesian area specific treatment (\texttt{ln\_zdftmx\_itf})] 
     1314{Indonesian area specific treatment (\protect\np{ln\_zdftmx\_itf})} 
    13001315\label{subsec:ZDF_tmx_itf} 
    13011316 
     
    13421357% Internal wave-driven mixing 
    13431358% ================================================================ 
    1344 \section{Internal wave-driven mixing (\protect\key{zdftmx\_new})} 
     1359\section[Internal wave-driven mixing (\texttt{\textbf{key\_zdftmx\_new}})] 
     1360{Internal wave-driven mixing (\protect\key{zdftmx\_new})} 
    13451361\label{sec:ZDF_tmx_new} 
    13461362 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_misc.tex

    r11151 r11179  
    102102% Closed seas 
    103103% ================================================================ 
    104 \section{Closed seas (\protect\mdl{closea})} 
     104\section[Closed seas (\textit{closea.F90})] 
     105{Closed seas (\protect\mdl{closea})} 
    105106\label{sec:MISC_closea} 
    106107 
     
    236237% Accuracy and Reproducibility 
    237238% ================================================================ 
    238 \section{Accuracy and reproducibility (\protect\mdl{lib\_fortran})} 
     239\section[Accuracy and reproducibility (\textit{lib\_fortran.F90})] 
     240{Accuracy and reproducibility (\protect\mdl{lib\_fortran})} 
    239241\label{sec:MISC_fortran} 
    240242 
    241 \subsection{Issues with intrinsinc SIGN function (\protect\key{nosignedzero})} 
     243\subsection[Issues with intrinsinc SIGN function (\texttt{\textbf{key\_nosignedzero}})] 
     244{Issues with intrinsinc SIGN function (\protect\key{nosignedzero})} 
    242245\label{subsec:MISC_sign} 
    243246 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex

    r11151 r11179  
    7373% Surface Pressure Gradient and Sea Surface Height 
    7474% ================================================================ 
    75 \section{Surface pressure gradient and sea surface heigth (\protect\mdl{dynspg})} 
     75\section[Surface pressure gradient and sea surface heigth (\textit{dynspg.F90})] 
     76{Surface pressure gradient and sea surface heigth (\protect\mdl{dynspg})} 
    7677\label{sec:DYN_hpg_spg} 
    7778%-----------------------------------------nam_dynspg---------------------------------------------------- 
     
    9798% Explicit 
    9899%------------------------------------------------------------- 
    99 \subsubsection{Explicit (\protect\key{dynspg\_exp})} 
     100\subsubsection[Explicit (\texttt{\textbf{key\_dynspg\_exp}})] 
     101{Explicit (\protect\key{dynspg\_exp})} 
    100102\label{subsec:DYN_spg_exp} 
    101103 
     
    133135% Split-explicit time-stepping 
    134136%------------------------------------------------------------- 
    135 \subsubsection{Split-explicit time-stepping (\protect\key{dynspg\_ts})} 
     137\subsubsection[Split-explicit time-stepping (\texttt{\textbf{key\_dynspg\_ts}})] 
     138{Split-explicit time-stepping (\protect\key{dynspg\_ts})} 
    136139\label{subsec:DYN_spg_ts} 
    137140%--------------------------------------------namdom---------------------------------------------------- 
     
    291294% Filtered formulation  
    292295%------------------------------------------------------------- 
    293 \subsubsection{Filtered formulation (\protect\key{dynspg\_flt})} 
     296\subsubsection[Filtered formulation (\texttt{\textbf{key\_dynspg\_flt}})] 
     297{Filtered formulation (\protect\key{dynspg\_flt})} 
    294298\label{subsec:DYN_spg_flt} 
    295299 
     
    305309% Non-linear free surface formulation  
    306310%------------------------------------------------------------- 
    307 \subsection{Non-linear free surface formulation (\protect\key{vvl})} 
     311\subsection[Non-linear free surface formulation (\texttt{\textbf{key\_vvl}})] 
     312{Non-linear free surface formulation (\protect\key{vvl})} 
    308313\label{subsec:DYN_spg_vvl} 
    309314 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_time_domain.tex

    r11151 r11179  
    8888where the subscript $F$ denotes filtered values and $\gamma$ is the Asselin coefficient. 
    8989$\gamma$ is initialized as \np{rn\_atfp} (namelist parameter). 
    90 Its default value is \np{rn\_atfp}~\forcode{= 10.e-3} (see \autoref{sec:STP_mLF}), 
     90Its default value is \np{rn\_atfp}\forcode{ = 10.e-3} (see \autoref{sec:STP_mLF}), 
    9191causing only a weak dissipation of high frequency motions (\citep{farge-coulombier_phd87}). 
    9292The addition of a time filter degrades the accuracy of the calculation from second to first order. 
     
    132132but usually the numerical stability condition imposes a strong constraint on the time step. 
    133133Two solutions are available in \NEMO to overcome the stability constraint: 
    134 $(a)$ a forward time differencing scheme using a time splitting technique (\np{ln\_zdfexp}~\forcode{= .true.}) or 
    135 $(b)$ a backward (or implicit) time differencing scheme                   (\np{ln\_zdfexp}~\forcode{= .false.}). 
     134$(a)$ a forward time differencing scheme using a time splitting technique (\np{ln\_zdfexp}\forcode{ = .true.}) or 
     135$(b)$ a backward (or implicit) time differencing scheme                   (\np{ln\_zdfexp}\forcode{ = .false.}). 
    136136In $(a)$, the master time step $\Delta$t is cut into $N$ fractional time steps so that 
    137137the stability criterion is reduced by a factor of $N$. 
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