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Changeset 10442 for NEMO/trunk/doc/latex/NEMO/subfiles/chap_DOM.tex – NEMO

Ignore:
Timestamp:
2018-12-21T15:18:38+01:00 (5 years ago)
Author:
nicolasmartin
Message:

Front page edition, cleaning in custom LaTeX commands and add index for single subfile compilation

  • Use \thanks storing cmd to refer to the ST members list for 2018 in an footnote on the cover page
  • NEMO and Fortran in small capitals
  • Removing of unused or underused custom cmds, move local cmds to their respective .tex file
  • Addition of new ones (\zstar, \ztilde, \sstar, \stilde, \ie, \eg, \fortran, \fninety)
  • Fonts for indexed items: italic font for files (modules and .nc files), preformat for code (CPP keys, routines names and namelists content)
File:
1 edited

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

    r10414 r10442  
    6464the barotropic stream function $\psi$ is defined at horizontal points overlying the $\zeta$ and $f$-points. 
    6565 
    66 The ocean mesh ($i.e.$ the position of all the scalar and vector points) is defined by 
     66The ocean mesh (\ie the position of all the scalar and vector points) is defined by 
    6767the transformation that gives ($\lambda$ ,$\varphi$ ,$z$) as a function of $(i,j,k)$. 
    6868The grid-points are located at integer or integer and a half value of $(i,j,k)$ as indicated on \autoref{tab:cell}. 
    … …  
    162162 
    163163The vertical average over the whole water column denoted by an overbar becomes for a quantity $q$ which 
    164 is a masked field (i.e. equal to zero inside solid area): 
     164is a masked field (\ie equal to zero inside solid area): 
    165165\begin{equation} 
    166166  \label{eq:DOM_bar} 
    … …  
    191191the differencing operators ($\delta_i$, $\delta_j$ and $\delta_k$) are skew-symmetric linear operators, 
    192192and further that the averaging operators $\overline{\,\cdot\,}^{\,i}$, $\overline{\,\cdot\,}^{\,k}$ and 
    193 $\overline{\,\cdot\,}^{\,k}$) are symmetric linear operators, 
    194 $i.e.$ 
     193$\overline{\,\cdot\,}^{\,k}$) are symmetric linear operators, \ie 
    195194\begin{align} 
    196195  \label{eq:DOM_di_adj} 
    … …  
    219218    \caption{ 
    220219      \protect\label{fig:index_hor} 
    221       Horizontal integer indexing used in the \textsc{Fortran} code. 
     220      Horizontal integer indexing used in the \fortran code. 
    222221      The dashed area indicates the cell in which variables contained in arrays have the same $i$- and $j$-indices 
    223222    } 
    … …  
    226225%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    227226 
    228 The array representation used in the \textsc{Fortran} code requires an integer indexing while 
     227The array representation used in the \fortran code requires an integer indexing while 
    229228the analytical definition of the mesh (see \autoref{subsec:DOM_cell}) is associated with the use of 
    230229integer values for $t$-points and both integer and integer and a half values for all the other points. 
    231230Therefore a specific integer indexing must be defined for points other than $t$-points 
    232 ($i.e.$ velocity and vorticity grid-points). 
     231(\ie velocity and vorticity grid-points). 
    233232Furthermore, the direction of the vertical indexing has been changed so that the surface level is at $k=1$. 
    234233 
    … …  
    252251 
    253252In the vertical, the chosen indexing requires special attention since 
    254 the $k$-axis is re-orientated downward in the \textsc{Fortran} code compared to 
     253the $k$-axis is re-orientated downward in the \fortran code compared to 
    255254the indexing used in the semi-discrete equations and given in \autoref{subsec:DOM_cell}. 
    256255The sea surface corresponds to the $w$-level $k=1$ which is the same index as $t$-level just below 
    … …  
    263262have the same $i$ or $j$ index 
    264263(compare the dashed area in \autoref{fig:index_hor} and \autoref{fig:index_vert}). 
    265 Since the scale factors are chosen to be strictly positive, a \emph{minus sign} appears in the \textsc{Fortran}  
     264Since the scale factors are chosen to be strictly positive, a \emph{minus sign} appears in the \fortran  
    266265code \emph{before all the vertical derivatives} of the discrete equations given in this documentation. 
    267266 
    … …  
    272271    \caption{ 
    273272      \protect\label{fig:index_vert} 
    274       Vertical integer indexing used in the \textsc{Fortran } code. 
     273      Vertical integer indexing used in the \fortran code. 
    275274      Note that the $k$-axis is orientated downward. 
    276275      The dashed area indicates the cell in which variables contained in arrays have the same $k$-index. 
    … …  
    300299\section{Needed fields} 
    301300\label{sec:DOM_fields} 
    302 The ocean mesh ($i.e.$ the position of all the scalar and vector points) is defined by the transformation that gives $(\lambda,\varphi,z)$ as a function of $(i,j,k)$. 
     301The ocean mesh (\ie the position of all the scalar and vector points) is defined by the transformation that gives $(\lambda,\varphi,z)$ as a function of $(i,j,k)$. 
    303302The grid-points are located at integer or integer and a half values of as indicated in \autoref{tab:cell}. 
    304303The associated scale factors are defined using the analytical first derivative of the transformation 
    … …  
    352351\label{subsec:DOM_hgr_coord_e} 
    353352 
    354 The ocean mesh ($i.e.$ the position of all the scalar and vector points) is defined by 
     353The ocean mesh (\ie the position of all the scalar and vector points) is defined by 
    355354the transformation that gives $(\lambda,\varphi,z)$ as a function of $(i,j,k)$. 
    356355The grid-points are located at integer or integer and a half values of as indicated in \autoref{tab:cell}. 
    … …  
    391390 
    392391Note that the definition of the scale factors 
    393 ($i.e.$ as the analytical first derivative of the transformation that 
     392(\ie as the analytical first derivative of the transformation that 
    394393gives $(\lambda,\varphi,z)$ as a function of $(i,j,k)$) 
    395394is specific to the \NEMO model \citep{Marti_al_JGR92}. 
    … …  
    461460(2) the number of levels of the model (\jp{jpk});  
    462461(3) the analytical transformation $z(i,j,k)$ and the vertical scale factors (derivatives of the transformation); and 
    463 (4) the masking system, $i.e.$ the number of wet model levels at each  
     462(4) the masking system, \ie the number of wet model levels at each  
    464463$(i,j)$ column of points. 
    465464 
    … …  
    563562  The \ifile{bathy\_meter} file (Netcdf format) provides the ocean depth (positive, in meters) at 
    564563  each grid point of the model grid. 
    565   The bathymetry is usually built by interpolating a standard bathymetry product ($e.g.$ ETOPO2) onto 
     564  The bathymetry is usually built by interpolating a standard bathymetry product (\eg ETOPO2) onto 
    566565  the horizontal ocean mesh. 
    567566  Defining the bathymetry also defines the coastline: where the bathymetry is zero, 
    … …  
    926925 
    927926% ------------------------------------------------------------------------------------------------------------- 
    928 %        z*- or s*-coordinate 
     927%        \zstar- or \sstar-coordinate 
    929928% ------------------------------------------------------------------------------------------------------------- 
    930929\subsection{$Z^*$- or $S^*$-coordinate (\protect\np{ln\_linssh}\forcode{ = .false.}) } 
    … …  
    945944follow the face of the model cells (step like topography) \citep{Madec_al_JPO96}. 
    946945The distribution of the steps in the horizontal is defined in a 2D integer array, mbathy, 
    947 which gives the number of ocean levels ($i.e.$ those that are not masked) at each $t$-point. 
     946which gives the number of ocean levels (\ie those that are not masked) at each $t$-point. 
    948947mbathy is computed from the meter bathymetry using the definiton of gdept as 
    949948the number of $t$-points which gdept $\leq$ bathy. 
    … …  
    961960the cavities are performed in the \textit{zgr\_isf} routine. 
    962961The compatibility between ice shelf draft and bathymetry is checked.  
    963 All the locations where the isf cavity is thinnest than \np{rn\_isfhmin} meters are grounded ($i.e.$ masked).  
     962All the locations where the isf cavity is thinnest than \np{rn\_isfhmin} meters are grounded (\ie masked).  
    964963If only one cell on the water column is opened at $t$-, $u$- or $v$-points, 
    965964the bathymetry or the ice shelf draft is dug to fit this constrain. 
    … …  
    10171016\biblio 
    10181017 
     1018\pindex 
     1019 
    10191020\end{document} 
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