Changeset 9389


Ignore:
Timestamp:
2018-03-08T21:56:32+01:00 (2 years ago)
Author:
nicolasmartin
Message:

Starting to use minted macros to highlight namelists parameters: \textit → \forcode
Work in progress as all escape characters (\) have to be removed in namelist parameter ids
Then several \np macros along with their paramater values with will be replaced by \forcode{np = value} apart from section headings for indexing
Fixes: style issue by reordering preamble section, removing \np macros inside equations and editing path to NEMO_manual.tex for subfiles.

Location:
branches/2017/dev_merge_2017/DOC
Files:
28 edited
1 moved

Legend:

Unmodified
Added
Removed
  • branches/2017/dev_merge_2017/DOC/tex_main/NEMO_manual.sty

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    3939%% ============================================================================== 
    4040 
     41\pagestyle{fancy} 
     42\bibliographystyle{../tex_sub/ametsoc} 
     43 
    4144%% Additionnal fonts 
    4245 
     
    6265\def\LigneVerticale{\vrule height 5cm depth 2cm\hspace{0.1cm}\relax} 
    6366\def\LignesVerticales{\let\LV\LigneVerticale\LV\LV\LV\LV\LV\LV\LV\LV\LV\LV} 
    64 \def\GrosCarreAvecUnChiffre#1{% 
    65    \rlap{\vrule height 0.8cm width 1cm depth 0.2cm}% 
    66    \rlap{\hbox to 1cm{\hss\mbox{\color{white} #1}\hss}}% 
    67    \vrule height 0pt width 1cm depth 0pt% 
     67\def\GrosCarreAvecUnChiffre#1{ 
     68   \rlap{\vrule height 0.8cm width 1cm depth 0.2cm} 
     69   \rlap{\hbox to 1cm{\hss\mbox{\color{white} #1}\hss}} 
     70   \vrule height 0pt width 1cm depth 0pt 
    6871} 
    6972\def\@makechapterhead#1{ 
    7073   \hbox{ 
    71       \huge\LignesVerticales 
    72       \hspace{-0.5cm} 
    73       \GrosCarreAvecUnChiffre{\thechapter} 
    74       \hspace{0.2cm} 
     74      \huge\LignesVerticales\hspace{-0.5cm} 
     75      \GrosCarreAvecUnChiffre{\thechapter}\hspace{0.2cm} 
    7576      \hbox{#1} 
    7677   } 
     
    127128\newcommand{\NEMO}{\textit{NEMO}\xspace} 
    128129 
    129 \newcommand{\ifile}[1]{\textit{  #1.nc}\index{Input NetCDF files!#1.nc}} 
    130 \newcommand{   \jp}[1]{\textit{     #1}\index{     Model parameters!#1}} 
    131 \newcommand{   \hf}[1]{\textit{ #1.h90}\index{             h90 file!#1}} 
    132 \newcommand{  \key}[1]{\textbf{key\_#1}\index{        CPP keys!key\_#1}} 
    133 \newcommand{  \mdl}[1]{\textit{ #1.F90}\index{              Modules!#1}} 
    134 \newcommand{  \ngn}[1]{\textit{     #1}\index{  Namelist Group Name!#1}} 
    135 \newcommand{   \np}[1]{\textit{     #1}\index{   Namelist variables!#1}} 
    136 \newcommand{   \pp}[1]{\textit{     #1}\index{     Model parameters!#1}} 
    137 \newcommand{  \rou}[1]{\textit{     #1}\index{             Routines!#1}} 
     130\newcommand{\ifile}[1]{\textit{   #1.nc}\index{Input NetCDF files!#1.nc}} 
     131\newcommand{   \hf}[1]{\textit{  #1.h90}\index{             h90 file!#1}} 
     132\newcommand{  \key}[1]{\textbf{ key\_#1}\index{        CPP keys!key\_#1}} 
     133\newcommand{  \mdl}[1]{\textit{  #1.F90}\index{              Modules!#1}} 
     134\newcommand{  \ngn}[1]{\textit{      #1}\index{  Namelist Group Name!#1}} 
     135\newcommand{  \rou}[1]{\textit{      #1}\index{             Routines!#1}} 
     136 
     137\newcommand{\jp}[1]{\forcode{#1}\index{  Model parameters!#1}} 
     138\newcommand{\np}[1]{\forcode{#1}\index{Namelist variables!#1}} 
    138139 
    139140\newcommand{\grad}{\nabla} 
  • branches/2017/dev_merge_2017/DOC/tex_main/NEMO_manual.tex

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    1616 
    1717\usepackage{../tex_main/NEMO_manual} 
    18 \usepackage{../tex_sub/minted} 
    19 \pagestyle{fancy} 
    20 \bibliographystyle{../tex_sub/ametsoc} 
     18\usepackage{../tex_sub/NEMO_minted} 
    2119 
    2220\makeindex 
  • branches/2017/dev_merge_2017/DOC/tex_sub/NEMO_minted.sty

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    1818%% ============================================================================== 
    1919 
    20 \newmint[forline]{fortran}{}                          % \forline|...| 
    21 \newmint[xmlline]{xml}{    }                          % \xmlline|...| 
    22 \newmint[cmd]{console}{}                              % \cmd|...| 
     20\newmint[forline]{fortran}{}        % \forline|...| 
     21\newmint[xmlline]{xml}{}         % \xmlline|...| 
     22\newmint[cmd]{console}{}         % \cmd|...| 
    2323 
    2424 
     
    2626%% ============================================================================== 
    2727 
    28 \newminted[forlines]{fortran}{}                       % \begin{forlines} 
    29 \newminted[xmllines]{xml}{}                           % \begin{xmllines} 
    30 \newminted[cmds]{console}{}                           % \begin{cmds} 
    31 \newminted[clines]{c}{fontsize=\tiny}                    % \begin{clines} 
     28\newminted[forlines]{fortran}{}        % \begin{forlines} 
     29\newminted[xmllines]{xml}{}         % \begin{xmllines} 
     30\newminted[cmds]{console}{}         % \begin{cmds} 
     31\newminted[clines]{c}{fontsize=\tiny}        % \begin{clines} 
    3232 
    3333 
     
    4040%% ============================================================================== 
    4141 
    42 \newmintinline[forcode]{fortran}{frame=lines}         % \forcode{...} 
    43 \newmintinline[xmlcode]{xml}{    frame=lines}         % \xmlcode{...} 
    44 \newmintinline[snippet]{console}{frame=lines}         % \snippet{...} 
     42\newmintinline[forcode]{fortran}{fontsize=auto, frame=lines}         % \forcode{...} 
     43\newmintinline[xmlcode]{xml}{    fontsize=auto, frame=lines}         % \xmlcode{...} 
     44\newmintinline[snippet]{console}{fontsize=auto, frame=lines}         % \snippet{...} 
  • branches/2017/dev_merge_2017/DOC/tex_sub/abstract_foreword.tex

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    1 \documentclass[NEMO_book]{subfiles} 
     1\documentclass[../tex_main/NEMO_manual]{subfiles} 
    22\begin{document} 
    33 
  • branches/2017/dev_merge_2017/DOC/tex_sub/annex_A.tex

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    1 \documentclass[NEMO_book]{subfiles} 
     1\documentclass[../tex_main/NEMO_manual]{subfiles} 
    22\begin{document} 
    33 
  • branches/2017/dev_merge_2017/DOC/tex_sub/annex_B.tex

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    1 \documentclass[NEMO_book]{subfiles} 
     1\documentclass[../tex_main/NEMO_manual]{subfiles} 
    22\begin{document} 
    33% ================================================================ 
  • branches/2017/dev_merge_2017/DOC/tex_sub/annex_C.tex

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    1 \documentclass[NEMO_book]{subfiles} 
     1\documentclass[../tex_main/NEMO_manual]{subfiles} 
    22\begin{document} 
    33% ================================================================ 
  • branches/2017/dev_merge_2017/DOC/tex_sub/annex_D.tex

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    1 \documentclass[NEMO_book]{subfiles} 
     1\documentclass[../tex_main/NEMO_manual]{subfiles} 
    22\begin{document} 
    33% ================================================================ 
  • branches/2017/dev_merge_2017/DOC/tex_sub/annex_E.tex

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    1 \documentclass[NEMO_book]{subfiles} 
     1\documentclass[../tex_main/NEMO_manual]{subfiles} 
    22\begin{document} 
    33% ================================================================ 
  • branches/2017/dev_merge_2017/DOC/tex_sub/annex_iso.tex

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    1 \documentclass[NEMO_book]{subfiles} 
     1\documentclass[../tex_main/NEMO_manual]{subfiles} 
    22\begin{document} 
    33% ================================================================ 
  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_ASM.tex

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    1 \documentclass[NEMO_book]{subfiles} 
     1\documentclass[../tex_main/NEMO_manual]{subfiles} 
    22\begin{document} 
    33% ================================================================ 
  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_CONFIG.tex

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    1 \documentclass[NEMO_book]{subfiles} 
     1\documentclass[../tex_main/NEMO_manual]{subfiles} 
    22\begin{document} 
    33% ================================================================ 
     
    257257Obviously, the namelist parameters have to be adjusted to the chosen resolution, see the Configurations  
    258258pages on the NEMO web site (Using NEMO\/Configurations) . 
    259 In the vertical, GYRE uses the default 30 ocean levels (\pp{jpk}=31) (Fig.~\ref{Fig_zgr}). 
     259In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}=31) (Fig.~\ref{Fig_zgr}). 
    260260 
    261261The GYRE configuration is also used in benchmark test as it is very simple to increase  
  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_DIA.tex

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    1 \documentclass[NEMO_book]{subfiles} 
     1\documentclass[../tex_main/NEMO_manual]{subfiles} 
    22\begin{document} 
    33% ================================================================ 
  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_DIU.tex

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    1 \documentclass[NEMO_book]{subfiles} 
     1\documentclass[../tex_main/NEMO_manual]{subfiles} 
    22\begin{document} 
    33% ================================================================ 
  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_DOM.tex

    r9388 r9389  
    1 \documentclass[NEMO_book]{subfiles} 
     1\documentclass[../tex_main/NEMO_manual]{subfiles} 
    22\begin{document} 
    33% ================================================================ 
     
    309309ie1e2u\_v is a flag to flag set u and  v surfaces are neither read nor computed.\\ 
    310310  
    311 These fields can be read in an domain input file which name is setted in \np{cn\_domcfg} parameter specified in \ngn{namcfg}. 
     311These fields can be read in an domain input file which name is setted in \np{cn_domcfg} parameter specified in \ngn{namcfg}. 
    312312\forfile{../namelists/namcfg} 
    313313or they can be defined in an analytical way in MY\_SRC directory of the configuration. 
     
    413413 
    414414All the arrays relating to a particular ocean model configuration (grid-point  
    415 position, scale factors, masks) can be saved in files if $\np{nn\_msh} \not= 0$  
     415position, scale factors, masks) can be saved in files if $nn\_msh \not= 0$  
    416416(namelist variable in \ngn{namdom}). This can be particularly useful for plots and off-line  
    417417diagnostics. In some cases, the user may choose to make a local modification  
     
    420420happens to be too wide due to insufficient model resolution). An example  
    421421is Gibraltar Strait in the ORCA2 configuration. When such modifications are done,  
    422 the output grid written when $\np{nn\_msh} \not=0$ is no more equal to the input grid. 
     422the output grid written when $nn\_msh \not= 0$ is no more equal to the input grid. 
    423423 
    424424$\ $\newline    % force a new line 
     
    454454(d) hybrid $s-z$ coordinate,  
    455455(e) hybrid $s-z$ coordinate with partial step, and  
    456 (f) same as (e) but in the non-linear free surface (\protect\np{ln\_linssh}=false).  
     456(f) same as (e) but in the non-linear free surface (\protect\np{ln_linssh}=false).  
    457457Note that the non-linear free surface can be used with any of the  
    4584585 coordinates (a) to (e).} 
     
    464464option which can be enabled or disabled in the middle of an experiment. Three main  
    465465choices are offered (Fig.~\ref{Fig_z_zps_s_sps}a to c): $z$-coordinate with full step  
    466 bathymetry (\np{ln\_zco}~=~true), $z$-coordinate with partial step bathymetry  
    467 (\np{ln\_zps}~=~true), or generalized, $s$-coordinate (\np{ln\_sco}~=~true).  
     466bathymetry (\np{ln_zco}~=~true), $z$-coordinate with partial step bathymetry  
     467(\np{ln_zps}~=~true), or generalized, $s$-coordinate (\np{ln_sco}~=~true).  
    468468Hybridation of the three main coordinates are available: $s-z$ or $s-zps$ coordinate  
    469469(Fig.~\ref{Fig_z_zps_s_sps}d and \ref{Fig_z_zps_s_sps}e). By default a non-linear free surface is used: 
    470470the coordinate follow the time-variation of the free surface so that the transformation is time dependent:  
    471 $z(i,j,k,t)$ (Fig.~\ref{Fig_z_zps_s_sps}f). When a linear free surface is assumed (\np{ln\_linssh}=true),  
     471$z(i,j,k,t)$ (Fig.~\ref{Fig_z_zps_s_sps}f). When a linear free surface is assumed (\np{ln_linssh}=true),  
    472472the vertical coordinate are fixed in time, but the seawater can move up and down across the z=0 surface  
    473473(in other words, the top of the ocean in not a rigid-lid).  
    474474The last choice in terms of vertical coordinate concerns the presence (or not) in the model domain  
    475 of ocean cavities beneath ice shelves. Setting \np{ln\_isfcav} to true allows to manage ocean cavities,  
     475of ocean cavities beneath ice shelves. Setting \np{ln_isfcav} to true allows to manage ocean cavities,  
    476476otherwise they are filled in. This option is currently only available in $z$- or $zps$-coordinate, 
    477477and partial step are also applied at the ocean/ice shelf interface.  
     
    483483\ifile{bathy\_meter} file, so that the computation of the number of wet ocean point  
    484484in each water column is by-passed}.  
    485 If \np{ln\_isfcav}~=~true, an extra file input file describing the ice shelf draft  
     485If \np{ln_isfcav}~=~true, an extra file input file describing the ice shelf draft  
    486486(in meters) (\ifile{isf\_draft\_meter}) is needed. 
    487487 
     
    503503%%% 
    504504 
    505 Unless a linear free surface is used (\np{ln\_linssh}=false), the arrays describing  
     505Unless a linear free surface is used (\np{ln_linssh}=false), the arrays describing  
    506506the grid point depths and vertical scale factors are three set of three dimensional arrays $(i,j,k)$  
    507507defined at \textit{before}, \textit{now} and \textit{after} time step. The time at which they are 
    508508defined is indicated by a suffix:$\_b$, $\_n$, or $\_a$, respectively. They are updated at each model time step 
    509509using a fixed reference coordinate system which computer names have a $\_0$ suffix.  
    510 When the linear free surface option is used (\np{ln\_linssh}=true), \textit{before}, \textit{now}  
     510When the linear free surface option is used (\np{ln_linssh}=true), \textit{before}, \textit{now}  
    511511and \textit{after} arrays are simply set one for all to their reference counterpart.  
    512512 
     
    519519 
    520520Three options are possible for defining the bathymetry, according to the  
    521 namelist variable \np{nn\_bathy} (found in \ngn{namdom} namelist):  
     521namelist variable \np{nn_bathy} (found in \ngn{namdom} namelist):  
    522522\begin{description} 
    523 \item[\np{nn\_bathy} = 0] a flat-bottom domain is defined. The total depth $z_w (jpk)$  
     523\item[\np{nn_bathy} = 0] a flat-bottom domain is defined. The total depth $z_w (jpk)$  
    524524is given by the coordinate transformation. The domain can either be a closed  
    525525basin or a periodic channel depending on the parameter \np{jperio}.  
    526 \item[\np{nn\_bathy} = -1] a domain with a bump of topography one third of the  
     526\item[\np{nn_bathy} = -1] a domain with a bump of topography one third of the  
    527527domain width at the central latitude. This is meant for the "EEL-R5" configuration,  
    528528a periodic or open boundary channel with a seamount.  
    529 \item[\np{nn\_bathy} = 1] read a bathymetry and ice shelf draft (if needed). 
     529\item[\np{nn_bathy} = 1] read a bathymetry and ice shelf draft (if needed). 
    530530 The \ifile{bathy\_meter} file (Netcdf format) provides the ocean depth (positive, in meters) 
    531531 at each grid point of the model grid. The bathymetry is usually built by interpolating a standard bathymetry product  
     
    535535 
    536536The \ifile{isfdraft\_meter} file (Netcdf format) provides the ice shelf draft (positive, in meters) 
    537  at each grid point of the model grid. This file is only needed if \np{ln\_isfcav}~=~true.  
     537 at each grid point of the model grid. This file is only needed if \np{ln_isfcav}~=~true.  
    538538Defining the ice shelf draft will also define the ice shelf edge and the grounding line position. 
    539539\end{description} 
     
    550550%        z-coordinate  and reference coordinate transformation 
    551551% ------------------------------------------------------------------------------------------------------------- 
    552 \subsection[$z$-coordinate (\protect\np{ln\_zco}] 
    553         {$z$-coordinate (\protect\np{ln\_zco}=true) and reference coordinate} 
     552\subsection[$z$-coordinate (\protect\np{ln_zco}] 
     553        {$z$-coordinate (\protect\np{ln_zco}=true) and reference coordinate} 
    554554\label{DOM_zco} 
    555555 
     
    593593(Fig.~\ref{Fig_zgr}). 
    594594 
    595 If the ice shelf cavities are opened (\np{ln\_isfcav}=~true~), the definition of $z_0$ is the same.  
     595If the ice shelf cavities are opened (\np{ln_isfcav}=~true~), the definition of $z_0$ is the same.  
    596596However, definition of $e_3^0$ at $t$- and $w$-points is respectively changed to: 
    597597\begin{equation} \label{DOM_zgr_ana} 
     
    688688%        z-coordinate with partial step 
    689689% ------------------------------------------------------------------------------------------------------------- 
    690 \subsection   [$z$-coordinate with partial step (\protect\np{ln\_zps})] 
    691          {$z$-coordinate with partial step (\protect\np{ln\_zps}=.true.)} 
     690\subsection   [$z$-coordinate with partial step (\protect\np{ln_zps})] 
     691         {$z$-coordinate with partial step (\protect\np{ln_zps}=.true.)} 
    692692\label{DOM_zps} 
    693693%--------------------------------------------namdom------------------------------------------------------- 
     
    712712Two variables in the namdom namelist are used to define the partial step  
    713713vertical grid. The mimimum water thickness (in meters) allowed for a cell  
    714 partially filled with bathymetry at level jk is the minimum of \np{rn\_e3zps\_min}  
    715 (thickness in meters, usually $20~m$) or $e_{3t}(jk)*\np{rn\_e3zps\_rat}$ (a fraction,  
     714partially filled with bathymetry at level jk is the minimum of \np{rn_e3zps_min}  
     715(thickness in meters, usually $20~m$) or $e_{3t}(jk)*rn\_e3zps\_rat$ (a fraction,  
    716716usually 10\%, of the default thickness $e_{3t}(jk)$). 
    717717 
     
    721721%        s-coordinate 
    722722% ------------------------------------------------------------------------------------------------------------- 
    723 \subsection   [$s$-coordinate (\protect\np{ln\_sco})] 
    724            {$s$-coordinate (\protect\np{ln\_sco}=true)} 
     723\subsection   [$s$-coordinate (\protect\np{ln_sco})] 
     724           {$s$-coordinate (\protect\np{ln_sco}=true)} 
    725725\label{DOM_sco} 
    726726%------------------------------------------nam_zgr_sco--------------------------------------------------- 
     
    728728%-------------------------------------------------------------------------------------------------------------- 
    729729Options are defined in \ngn{namzgr\_sco}. 
    730 In $s$-coordinate (\np{ln\_sco}~=~true), the depth and thickness of the model  
     730In $s$-coordinate (\np{ln_sco}~=~true), the depth and thickness of the model  
    731731levels are defined from the product of a depth field and either a stretching  
    732732function or its derivative, respectively: 
     
    744744depth, since a mixed step-like and bottom-following representation of the  
    745745topography can be used (Fig.~\ref{Fig_z_zps_s_sps}d-e) or an envelop bathymetry can be defined (Fig.~\ref{Fig_z_zps_s_sps}f). 
    746 The namelist parameter \np{rn\_rmax} determines the slope at which the terrain-following coordinate intersects  
     746The namelist parameter \np{rn_rmax} determines the slope at which the terrain-following coordinate intersects  
    747747the sea bed and becomes a pseudo z-coordinate.  
    748 The coordinate can also be hybridised by specifying \np{rn\_sbot\_min} and \np{rn\_sbot\_max}  
     748The coordinate can also be hybridised by specifying \np{rn_sbot_min} and \np{rn_sbot_max}  
    749749as the minimum and maximum depths at which the terrain-following vertical coordinate is calculated. 
    750750 
     
    753753 
    754754The original default NEMO s-coordinate stretching is available if neither of the other options  
    755 are specified as true (\np{ln\_s\_SH94}~=~false and \np{ln\_s\_SF12}~=~false).  
     755are specified as true (\np{ln_s_SH94}~=~false and \np{ln_s_SF12}~=~false).  
    756756This uses a depth independent $\tanh$ function for the stretching \citep{Madec_al_JPO96}: 
    757757 
     
    779779 
    780780A stretching function, modified from the commonly used \citet{Song_Haidvogel_JCP94}  
    781 stretching (\np{ln\_s\_SH94}~=~true), is also available and is more commonly used for shelf seas modelling: 
     781stretching (\np{ln_s_SH94}~=~true), is also available and is more commonly used for shelf seas modelling: 
    782782 
    783783\begin{equation} 
     
    796796%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    797797 
    798 where $H_c$ is the critical depth (\np{rn\_hc}) at which the coordinate transitions from  
    799 pure $\sigma$ to the stretched coordinate,  and $\theta$ (\np{rn\_theta}) and $b$ (\np{rn\_bb})  
     798where $H_c$ is the critical depth (\np{rn_hc}) at which the coordinate transitions from  
     799pure $\sigma$ to the stretched coordinate,  and $\theta$ (\np{rn_theta}) and $b$ (\np{rn_bb})  
    800800are the surface and bottom control parameters such that $0\leqslant \theta \leqslant 20$, and  
    801801$0\leqslant b\leqslant 1$. $b$ has been designed to allow surface and/or bottom  
    802802increase of the vertical resolution (Fig.~\ref{Fig_sco_function}). 
    803803 
    804 Another example has been provided at version 3.5 (\np{ln\_s\_SF12}) that allows  
     804Another example has been provided at version 3.5 (\np{ln_s_SF12}) that allows  
    805805a fixed surface resolution in an analytical terrain-following stretching \citet{Siddorn_Furner_OM12}.  
    806806In this case the a stretching function $\gamma$ is defined such that: 
     
    823823 
    824824This gives an analytical stretching of $\sigma$ that is solvable in $A$ and $B$ as a function of  
    825 the user prescribed stretching parameter $\alpha$ (\np{rn\_alpha}) that stretches towards  
    826 the surface ($\alpha > 1.0$) or the bottom ($\alpha < 1.0$) and user prescribed surface (\np{rn\_zs})  
     825the user prescribed stretching parameter $\alpha$ (\np{rn_alpha}) that stretches towards  
     826the surface ($\alpha > 1.0$) or the bottom ($\alpha < 1.0$) and user prescribed surface (\np{rn_zs})  
    827827and bottom depths. The bottom cell depth in this example is given as a function of water depth: 
    828828 
     
    831831\end{equation} 
    832832 
    833 where the namelist parameters \np{rn\_zb\_a} and \np{rn\_zb\_b} are $a$ and $b$ respectively. 
     833where the namelist parameters \np{rn_zb_a} and \np{rn_zb_b} are $a$ and $b$ respectively. 
    834834 
    835835%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    843843This gives a smooth analytical stretching in computational space that is constrained to given specified surface and bottom grid cell thicknesses in real space. This is not to be confused with the hybrid schemes that superimpose geopotential coordinates on terrain following coordinates thus creating a non-analytical vertical coordinate that therefore may suffer from large gradients in the vertical resolutions. This stretching is less straightforward to implement than the \citet{Song_Haidvogel_JCP94} stretching, but has the advantage of resolving diurnal processes in deep water and has generally flatter slopes. 
    844844 
    845 As with the \citet{Song_Haidvogel_JCP94} stretching the stretch is only applied at depths greater than the critical depth $h_c$. In this example two options are available in depths shallower than $h_c$, with pure sigma being applied if the \np{ln\_sigcrit} is true and pure z-coordinates if it is false (the z-coordinate being equal to the depths of the stretched coordinate at $h_c$. 
     845As with the \citet{Song_Haidvogel_JCP94} stretching the stretch is only applied at depths greater than the critical depth $h_c$. In this example two options are available in depths shallower than $h_c$, with pure sigma being applied if the \np{ln_sigcrit} is true and pure z-coordinates if it is false (the z-coordinate being equal to the depths of the stretched coordinate at $h_c$. 
    846846 
    847847Minimising the horizontal slope of the vertical coordinate is important in terrain-following systems as large slopes lead to hydrostatic consistency. A hydrostatic consistency parameter diagnostic following \citet{Haney1991} has been implemented, and is output as part of the model mesh file at the start of the run. 
     
    850850%        z*- or s*-coordinate 
    851851% ------------------------------------------------------------------------------------------------------------- 
    852 \subsection{$z^*$- or $s^*$-coordinate (\protect\np{ln\_linssh}=false) } 
     852\subsection{$z^*$- or $s^*$-coordinate (\protect\np{ln_linssh}=false) } 
    853853\label{DOM_zgr_star} 
    854854 
     
    881881In case of ice shelf cavities, modifications of the model bathymetry and ice shelf draft into  
    882882the cavities are performed in the \textit{zgr\_isf} routine. The compatibility between ice shelf draft and bathymetry is checked.  
    883 All the locations where the isf cavity is thinnest than \np{rn\_isfhmin} meters are grounded ($i.e.$ masked).  
     883All the locations where the isf cavity is thinnest than \np{rn_isfhmin} meters are grounded ($i.e.$ masked).  
    884884If only one cell on the water column is opened at $t$-, $u$- or $v$-points, the bathymetry or the ice shelf draft is dug to fit this constrain. 
    885885If the incompatibility is too strong (need to dig more than 1 cell), the cell is masked.\\  
     
    921921Options are defined in \ngn{namtsd}. 
    922922By default, the ocean start from rest (the velocity field is set to zero) and the initialization of  
    923 temperature and salinity fields is controlled through the \np{ln\_tsd\_ini} namelist parameter. 
     923temperature and salinity fields is controlled through the \np{ln_tsd_ini} namelist parameter. 
    924924\begin{description} 
    925925\item[ln\_tsd\_init = .true.]  use a T and S input files that can be given on the model grid itself or  
    926926on their native input data grid. In the latter case, the data will be interpolated on-the-fly both in the  
    927927horizontal and the vertical to the model grid (see \S~\ref{SBC_iof}). The information relative to the  
    928 input files are given in the \np{sn\_tem} and \np{sn\_sal} structures.  
     928input files are given in the \np{sn_tem} and \np{sn_sal} structures.  
    929929The computation is done in the \mdl{dtatsd} module. 
    930930\item[ln\_tsd\_init = .false.] use constant salinity value of 35.5 psu and an analytical profile of temperature 
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    965965 
    966966   \item[\np{nn\_gammablk~=~1~}] 
    967    The salt and heat exchange coefficients are velocity dependent and defined as $\np{rn\_gammas0} \times u_{*}$ and $\np{rn\_gammat0} \times u_{*}$ 
     967   The salt and heat exchange coefficients are velocity dependent and defined as $rn\_gammas0 \times u_{*}$ and $rn\_gammat0 \times u_{*}$ 
    968968        where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn\_hisf\_tbl} meters). 
    969969        See \citet{Jenkins2010} for all the details on this formulation. 
     
    11641164($i.e.$ a frequency of 24 and a time interpolation set to true in \np{sn\_qsr} namelist parameter). 
    11651165Furthermore, it is recommended to have a least 8 surface module time step per day, 
    1166 that is  $\rdt \ \np{nn\_fsbc} < 10,800~s = 3~h$. An example of recontructed SWF  
     1166that is  $\rdt \ nn\_fsbc < 10,800~s = 3~h$. An example of recontructed SWF  
    11671167is given in Fig.\ref{Fig_SBC_dcy} for a 12 reconstructed diurnal cycle, one every 2~hours  
    11681168(from 1am to 11pm). 
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