Changeset 11598


Ignore:
Timestamp:
2019-09-25T22:00:42+02:00 (12 months ago)
Author:
nicolasmartin
Message:

Add template of versioning record at the beginning of chapters

Location:
NEMO/trunk/doc
Files:
25 edited

Legend:

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

    r11597 r11598  
    22 
    33\begin{document} 
     4 
    45\chapter{A brief guide to the DOMAINcfg tool} 
    56\label{apdx:DOMCFG} 
    67 
     8%    {\em 4.0} & {\em Andrew Coward} & {\em Created at v4.0 from materials removed from chap\_DOM that are still relevant to the \forcode{DOMAINcfg} tool and which illustrate and explain the choices to be made by the user when setting up new domains }  \\ 
     9 
     10\thispagestyle{plain} 
     11 
    712\chaptertoc 
    8 \vfill 
    9 \begin{figure}[b] 
    10 %% ================================================================================================= 
    11 \subsubsection*{Changes record} 
    12 \begin{tabular}{m{0.08\linewidth}||m{0.32\linewidth}|m{0.6\linewidth}} 
    13     Release   & Author(s)     & Modifications \\ 
    14 \hline 
    15     {\em 4.0} & {\em Andrew Coward} & {\em Created at v4.0 from materials removed from chap\_DOM that are still relevant to the \forcode{DOMAINcfg} tool and which illustrate and explain the choices to be made by the user when setting up new domains }  \\ 
    16 \end{tabular} 
    17 \end{figure} 
     13 
     14\paragraph{Changes record} ~\\ 
     15 
     16{\footnotesize 
     17  \begin{tabularx}{\textwidth}{l||X|X} 
     18    Release & Author(s) & Modifications \\ 
     19    \hline 
     20    {\em   4.0} & {\em ...} & {\em ...} \\ 
     21    {\em   3.6} & {\em ...} & {\em ...} \\ 
     22    {\em   3.4} & {\em ...} & {\em ...} \\ 
     23    {\em <=3.4} & {\em ...} & {\em ...} 
     24  \end{tabularx} 
     25} 
     26 
     27\clearpage 
    1828 
    1929This appendix briefly describes some of the options available in the 
     
    3444\section{Choice of horizontal grid} 
    3545\label{sec:DOMCFG_hor} 
    36  
    3746 
    3847\begin{listing} 
     
    298307\np{nn_bathy}{nn\_bathy} (found in \nam{dom}{dom} namelist (\texttt{DOMAINCFG} variant) ): 
    299308\begin{description} 
    300 \item [{\np[=0]{nn_bathy}{nn\_bathy}}]: 
    301   a flat-bottom domain is defined. 
     309\item [{\np[=0]{nn_bathy}{nn\_bathy}}]: a flat-bottom domain is defined. 
    302310  The total depth $z_w (jpk)$ is given by the coordinate transformation. 
    303311  The domain can either be a closed basin or a periodic channel depending on the parameter \np{jperio}{jperio}. 
    304 \item [{\np[=-1]{nn_bathy}{nn\_bathy}}]: 
    305   a domain with a bump of topography one third of the domain width at the central latitude. 
     312\item [{\np[=-1]{nn_bathy}{nn\_bathy}}]: a domain with a bump of topography one third of the domain width at the central latitude. 
    306313  This is meant for the "EEL-R5" configuration, a periodic or open boundary channel with a seamount. 
    307 \item [{\np[=1]{nn_bathy}{nn\_bathy}}]: 
    308   read a bathymetry and ice shelf draft (if needed). 
     314\item [{\np[=1]{nn_bathy}{nn\_bathy}}]: read a bathymetry and ice shelf draft (if needed). 
    309315  The \ifile{bathy\_meter} file (Netcdf format) provides the ocean depth (positive, in meters) at 
    310316  each grid point of the model grid. 
     
    326332After reading the bathymetry, the algorithm for vertical grid definition differs between the different options: 
    327333\begin{description} 
    328 \item [\forcode{ln_zco = .true.}] 
    329   set a reference coordinate transformation $z_0(k)$, and set $z(i,j,k,t) = z_0(k)$ where $z_0(k)$ is the closest match to the depth at $(i,j)$. 
    330 \item [\forcode{ln_zps = .true.}] 
    331   set a reference coordinate transformation $z_0(k)$, and calculate the thickness of the deepest level at 
     334\item [\forcode{ln_zco = .true.}] set a reference coordinate transformation $z_0(k)$, and set $z(i,j,k,t) = z_0(k)$ where $z_0(k)$ is the closest match to the depth at $(i,j)$. 
     335\item [\forcode{ln_zps = .true.}] set a reference coordinate transformation $z_0(k)$, and calculate the thickness of the deepest level at 
    332336  each $(i,j)$ point using the bathymetry, to obtain the final three-dimensional depth and scale factor arrays. 
    333 \item [\forcode{ln_sco = .true.}] 
    334   smooth the bathymetry to fulfill the hydrostatic consistency criteria and 
     337\item [\forcode{ln_sco = .true.}] smooth the bathymetry to fulfill the hydrostatic consistency criteria and 
    335338  set the three-dimensional transformation. 
    336 \item [\forcode{s-z and s-zps}] 
    337   smooth the bathymetry to fulfill the hydrostatic consistency criteria and 
     339\item [\forcode{s-z and s-zps}] smooth the bathymetry to fulfill the hydrostatic consistency criteria and 
    338340  set the three-dimensional transformation $z(i,j,k)$, 
    339341  and possibly introduce masking of extra land points to better fit the original bathymetry file. 
  • NEMO/trunk/doc/latex/NEMO/subfiles/apdx_algos.tex

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    22 
    33\begin{document} 
     4 
    45\chapter{Note on some algorithms} 
    56\label{apdx:ALGOS} 
    67 
     8\thispagestyle{plain} 
     9 
    710\chaptertoc 
     11 
     12\paragraph{Changes record} ~\\ 
     13 
     14{\footnotesize 
     15  \begin{tabularx}{\textwidth}{l||X|X} 
     16    Release & Author(s) & Modifications \\ 
     17    \hline 
     18    {\em   4.0} & {\em ...} & {\em ...} \\ 
     19    {\em   3.6} & {\em ...} & {\em ...} \\ 
     20    {\em   3.4} & {\em ...} & {\em ...} \\ 
     21    {\em <=3.4} & {\em ...} & {\em ...} 
     22  \end{tabularx} 
     23} 
     24 
     25\clearpage 
    826 
    927This appendix some on going consideration on algorithms used or planned to be used in \NEMO. 
     
    356374This expression of the iso-neutral diffusion has been chosen in order to satisfy the following six properties: 
    357375\begin{description} 
    358 \item [$\bullet$ horizontal diffusion] 
    359   The discretization of the diffusion operator recovers the traditional five-point Laplacian in 
    360   the limit of flat iso-neutral direction: 
     376\item [Horizontal diffusion] The discretization of the diffusion operator recovers the traditional five-point Laplacian in the limit of flat iso-neutral direction: 
    361377  \[ 
    362378    % \label{eq:ALGOS_Gf_property1a} 
     
    366382    { _i^k \mathbb{R}_{i_p}^{k_p} }=0 
    367383  \] 
    368  
    369 \item [$\bullet$ implicit treatment in the vertical] 
    370   In the diagonal term associated with the vertical divergence of the iso-neutral fluxes 
     384\item [Implicit treatment in the vertical] In the diagonal term associated with the vertical divergence of the iso-neutral fluxes 
    371385  \ie\ the term associated with a second order vertical derivative) 
    372386  appears only tracer values associated with a single water column. 
     
    380394  \] 
    381395  can be quite large. 
    382  
    383 \item [$\bullet$ pure iso-neutral operator] 
    384   The iso-neutral flux of locally referenced potential density is zero, \ie 
     396\item [Pure iso-neutral operator] The iso-neutral flux of locally referenced potential density is zero, \ie 
    385397  \begin{align*} 
    386398    % \label{eq:ALGOS_Gf_property2} 
     
    396408  This result is trivially obtained using the \autoref{eq:ALGOS_Gf_triads} applied to $T$ and $S$ and 
    397409  the definition of the triads' slopes \autoref{eq:ALGOS_Gf_slopes}. 
    398  
    399 \item [$\bullet$ conservation of tracer] 
    400   The iso-neutral diffusion term conserve the total tracer content, \ie 
     410\item [Conservation of tracer] The iso-neutral diffusion term conserve the total tracer content, \ie 
    401411  \[ 
    402412    % \label{eq:ALGOS_Gf_property1} 
     
    404414  \] 
    405415This property is trivially satisfied since the iso-neutral diffusive operator is written in flux form. 
    406  
    407 \item [$\bullet$ decrease of tracer variance] 
    408   The iso-neutral diffusion term does not increase the total tracer variance, \ie 
     416\item [Decrease of tracer variance] The iso-neutral diffusion term does not increase the total tracer variance, \ie 
    409417  \[ 
    410418    % \label{eq:ALGOS_Gf_property1} 
     
    417425It therfore ensures that, when the diffusivity coefficient is large enough, 
    418426the field on which it is applied become free of grid-point noise. 
    419  
    420 \item [$\bullet$ self-adjoint operator] 
    421   The iso-neutral diffusion operator is self-adjoint, \ie 
     427\item [Self-adjoint operator] The iso-neutral diffusion operator is self-adjoint, \ie 
    422428  \[ 
    423429    % \label{eq:ALGOS_Gf_property1} 
     
    583589\ie\ it does not include a diffusive component but is a "pure" advection term. 
    584590 
    585 $\ $\newpage      %force an empty line 
    586591%% ================================================================================================= 
    587592\subsection{Discrete invariants of the iso-neutral diffrusion} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/apdx_diff_opers.tex

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    22 
    33\begin{document} 
     4 
    45\chapter{Diffusive Operators} 
    56\label{apdx:DIFFOPERS} 
    67 
     8\thispagestyle{plain} 
     9 
    710\chaptertoc 
     11 
     12\paragraph{Changes record} ~\\ 
     13 
     14{\footnotesize 
     15  \begin{tabularx}{\textwidth}{l||X|X} 
     16    Release & Author(s) & Modifications \\ 
     17    \hline 
     18    {\em   4.0} & {\em ...} & {\em ...} \\ 
     19    {\em   3.6} & {\em ...} & {\em ...} \\ 
     20    {\em   3.4} & {\em ...} & {\em ...} \\ 
     21    {\em <=3.4} & {\em ...} & {\em ...} 
     22  \end{tabularx} 
     23} 
     24 
     25\clearpage 
    826 
    927%% ================================================================================================= 
  • NEMO/trunk/doc/latex/NEMO/subfiles/apdx_invariants.tex

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    22 
    33\begin{document} 
     4 
    45\chapter{Discrete Invariants of the Equations} 
    56\label{apdx:INVARIANTS} 
    67 
     8\thispagestyle{plain} 
     9 
    710\chaptertoc 
     11 
     12\paragraph{Changes record} ~\\ 
     13 
     14{\footnotesize 
     15  \begin{tabularx}{\textwidth}{l||X|X} 
     16    Release & Author(s) & Modifications \\ 
     17    \hline 
     18    {\em   4.0} & {\em ...} & {\em ...} \\ 
     19    {\em   3.6} & {\em ...} & {\em ...} \\ 
     20    {\em   3.4} & {\em ...} & {\em ...} \\ 
     21    {\em <=3.4} & {\em ...} & {\em ...} 
     22  \end{tabularx} 
     23} 
     24 
     25\clearpage 
    826 
    927%%%  Appendix put in gmcomment as it has not been updated for \zstar and s coordinate 
  • NEMO/trunk/doc/latex/NEMO/subfiles/apdx_s_coord.tex

    r11597 r11598  
    66\label{apdx:SCOORD} 
    77 
     8%    {\em 4.0} & {\em Mike Bell} & {\em review}  \\ 
     9%    {\em 3.x} & {\em Gurvan Madec} & {\em original}  \\ 
     10 
     11\thispagestyle{plain} 
     12 
    813\chaptertoc 
    914 
    10 \vfill 
    11 \begin{figure}[b] 
    12 %% ================================================================================================= 
    13 \subsubsection*{Changes record} 
    14 \begin{tabular}{l||l|m{0.65\linewidth}} 
    15     Release   & Author        & Modifications \\ 
    16     {\em 4.0} & {\em Mike Bell} & {\em review}  \\ 
    17     {\em 3.x} & {\em Gurvan Madec} & {\em original}  \\ 
    18 \end{tabular} 
    19 \end{figure} 
    20  
    21 %% ================================================================================================= 
     15\paragraph{Changes record} ~\\ 
     16 
     17{\footnotesize 
     18  \begin{tabularx}{\textwidth}{l||X|X} 
     19    Release & Author(s) & Modifications \\ 
     20    \hline 
     21    {\em   4.0} & {\em ...} & {\em ...} \\ 
     22    {\em   3.6} & {\em ...} & {\em ...} \\ 
     23    {\em   3.4} & {\em ...} & {\em ...} \\ 
     24    {\em <=3.4} & {\em ...} & {\em ...} 
     25  \end{tabularx} 
     26} 
     27 
     28\clearpage 
     29 
    2230\section{Chain rule for $s-$coordinates} 
    2331\label{sec:SCOORD_chain} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/apdx_triads.tex

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    1212 
    1313\begin{document} 
     14 
    1415\chapter{Iso-Neutral Diffusion and Eddy Advection using Triads} 
    1516\label{apdx:TRIADS} 
    1617 
     18\thispagestyle{plain} 
     19 
    1720\chaptertoc 
    1821 
     22\paragraph{Changes record} ~\\ 
     23 
     24{\footnotesize 
     25  \begin{tabularx}{\textwidth}{l||X|X} 
     26    Release & Author(s) & Modifications \\ 
     27    \hline 
     28    {\em   4.0} & {\em ...} & {\em ...} \\ 
     29    {\em   3.6} & {\em ...} & {\em ...} \\ 
     30    {\em   3.4} & {\em ...} & {\em ...} \\ 
     31    {\em <=3.4} & {\em ...} & {\em ...} 
     32  \end{tabularx} 
     33} 
     34 
     35\clearpage 
     36 
    1937%% ================================================================================================= 
    2038\section[Choice of \forcode{namtra\_ldf} namelist parameters]{Choice of \protect\nam{tra_ldf}{tra\_ldf} namelist parameters} 
    21  
    2239 
    2340Two scheme are available to perform the iso-neutral diffusion. 
     
    3653The options specific to the Griffies scheme include: 
    3754\begin{description} 
    38 \item [{\np{ln_triad_iso}{ln\_triad\_iso}}] 
    39   See \autoref{sec:TRIADS_taper}. 
     55\item [{\np{ln_triad_iso}{ln\_triad\_iso}}] See \autoref{sec:TRIADS_taper}. 
    4056  If this is set false (the default), 
    4157  then `iso-neutral' mixing is accomplished within the surface mixed-layer along slopes linearly decreasing with 
     
    4763  giving an almost pure horizontal diffusive tracer flux within the mixed layer. 
    4864  This is similar to the tapering suggested by \citet{gerdes.koberle.ea_CD91}. See \autoref{subsec:TRIADS_Gerdes-taper} 
    49 \item [{\np{ln_botmix_triad}{ln\_botmix\_triad}}] 
    50   See \autoref{sec:TRIADS_iso_bdry}. 
     65\item [{\np{ln_botmix_triad}{ln\_botmix\_triad}}] See \autoref{sec:TRIADS_iso_bdry}. 
    5166  If this is set false (the default) then the lateral diffusive fluxes 
    5267  associated with triads partly masked by topography are neglected. 
    5368  If it is set true, however, then these lateral diffusive fluxes are applied, 
    5469  giving smoother bottom tracer fields at the cost of introducing diapycnal mixing. 
    55 \item [{\np{rn_sw_triad}{rn\_sw\_triad}}] 
    56   blah blah to be added.... 
     70\item [{\np{rn_sw_triad}{rn\_sw\_triad}}] blah blah to be added.... 
    5771\end{description} 
    5872The options shared with the Standard scheme include: 
    5973\begin{description} 
    60 \item [{\np{ln_traldf_msc}{ln\_traldf\_msc}}]   blah blah to be added 
    61 \item [{\np{rn_slpmax}{rn\_slpmax}}]  blah blah to be added 
     74\item [{\np{ln_traldf_msc}{ln\_traldf\_msc}}] blah blah to be added 
     75\item [{\np{rn_slpmax}{rn\_slpmax}}]          blah blah to be added 
    6276\end{description} 
    6377 
     
    196210% Instead of multiplying the mean slope calculated at the $u$-point by 
    197211% the mean vertical gradient at the $u$-point, 
    198 % >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    199212\begin{figure}[tb] 
    200213  \centering 
     
    207220  \label{fig:TRIADS_ISO_triad} 
    208221\end{figure} 
    209 % >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    210222They get the skew flux from the products of the vertical gradients at each $w$-point surrounding the $u$-point with 
    211223the corresponding `triad' slope calculated from the lateral density gradient across the $u$-point divided by 
     
    258270while the metrics are calculated at the $u$- and $w$-points on the arms. 
    259271 
    260 % >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    261272\begin{figure}[tb] 
    262273  \centering 
     
    269280  \label{fig:TRIADS_qcells} 
    270281\end{figure} 
    271 % >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    272282 
    273283Each triad $\{_i^{k}\:_{i_p}^{k_p}\}$ is associated (\autoref{fig:TRIADS_qcells}) with the quarter cell that is 
     
    549559where $b_T= e_{1T}\,e_{2T}\,e_{3T}$ is the volume of $T$-cells. 
    550560The diffusion scheme satisfies the following six properties: 
     561 
    551562\begin{description} 
    552 \item [$\bullet$ horizontal diffusion] 
    553   The discretization of the diffusion operator recovers the traditional five-point Laplacian 
     563\item [Horizontal diffusion] The discretization of the diffusion operator recovers the traditional five-point Laplacian 
    554564  \autoref{eq:TRIADS_lat-normal} in the limit of flat iso-neutral direction: 
    555565  \[ 
     
    560570    \text{when} \quad { _i^k \mathbb{R}_{i_p}^{k_p} }=0 
    561571  \] 
    562  
    563 \item [$\bullet$ implicit treatment in the vertical] 
    564   Only tracer values associated with a single water column appear in the expression \autoref{eq:TRIADS_i33} for 
     572\item [Implicit treatment in the vertical] Only tracer values associated with a single water column appear in the expression \autoref{eq:TRIADS_i33} for 
    565573  the $_{33}$ fluxes, vertical fluxes driven by vertical gradients. 
    566574  This is of paramount importance since it means that a time-implicit algorithm can be used to 
     
    576584  \] 
    577585  (where $b_w= e_{1w}\,e_{2w}\,e_{3w}$ is the volume of $w$-cells) can be quite large. 
    578  
    579 \item [$\bullet$ pure iso-neutral operator] 
    580   The iso-neutral flux of locally referenced potential density is zero. 
     586\item [Pure iso-neutral operator] The iso-neutral flux of locally referenced potential density is zero. 
    581587  See \autoref{eq:TRIADS_latflux-rho} and \autoref{eq:TRIADS_vertflux-triad2}. 
    582  
    583 \item [$\bullet$ conservation of tracer] 
    584   The iso-neutral diffusion conserves tracer content, \ie 
     588\item [Conservation of tracer] The iso-neutral diffusion conserves tracer content, \ie 
    585589  \[ 
    586590    % \label{eq:TRIADS_iso_property1} 
     
    588592  \] 
    589593  This property is trivially satisfied since the iso-neutral diffusive operator is written in flux form. 
    590  
    591 \item [$\bullet$ no increase of tracer variance] 
    592   The iso-neutral diffusion does not increase the tracer variance, \ie 
     594\item [No increase of tracer variance] The iso-neutral diffusion does not increase the tracer variance, \ie 
    593595  \[ 
    594596    % \label{eq:TRIADS_iso_property2} 
     
    601603  It therefore ensures that, when the diffusivity coefficient is large enough, 
    602604  the field on which it is applied becomes free of grid-point noise. 
    603  
    604 \item [$\bullet$ self-adjoint operator] 
    605   The iso-neutral diffusion operator is self-adjoint, \ie 
     605\item [Self-adjoint operator] The iso-neutral diffusion operator is self-adjoint, \ie 
    606606  \begin{equation} 
    607607    \label{eq:TRIADS_iso_property3} 
     
    655655(\np[=.true.]{ln_trabbl}{ln\_trabbl}, with \np[=1]{nn_bbl_ldf}{nn\_bbl\_ldf}), or for simple idealized problems. 
    656656For setups with topography without bbl mixing, \np[=.true.]{ln_botmix_triad}{ln\_botmix\_triad} may be necessary. 
    657 % >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    658657\begin{figure}[h] 
    659658  \centering 
     
    679678  \label{fig:TRIADS_bdry_triads} 
    680679\end{figure} 
    681 % >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    682680 
    683681%% ================================================================================================= 
     
    808806\end{enumerate} 
    809807 
    810 % >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    811808\begin{figure}[h] 
    812809  \centering 
     
    831828  \label{fig:TRIADS_MLB_triad} 
    832829\end{figure} 
    833 % >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    834830 
    835831%% ================================================================================================= 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_ASM.tex

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    22 
    33\begin{document} 
     4 
    45\chapter{Apply Assimilation Increments (ASM)} 
    56\label{chap:ASM} 
    67 
     8%    {\em 4.0} & {\em D. J. Lea} & {\em \NEMO\ 4.0 updates}  \\ 
     9%    {\em 3.4} & {\em D. J. Lea, M. Martin, K. Mogensen, A. Weaver} & {\em Initial version}  \\ 
     10 
     11\thispagestyle{plain} 
     12 
    713\chaptertoc 
    814 
    9 \vfill 
    10 \begin{figure}[b] 
    11 %% ================================================================================================= 
    12 \subsubsection*{Changes record} 
    13 \begin{tabular}{l||l|m{0.65\linewidth}} 
    14     Release   & Author        & Modifications \\ 
    15     {\em 4.0} & {\em D. J. Lea} & {\em \NEMO\ 4.0 updates}  \\ 
    16     {\em 3.4} & {\em D. J. Lea, M. Martin, K. Mogensen, A. Weaver} & {\em Initial version}  \\ 
    17 \end{tabular} 
    18 \end{figure} 
     15\paragraph{Changes record} ~\\ 
     16 
     17{\footnotesize 
     18  \begin{tabularx}{\textwidth}{l||X|X} 
     19    Release & Author(s) & Modifications \\ 
     20    \hline 
     21    {\em   4.0} & {\em ...} & {\em ...} \\ 
     22    {\em   3.6} & {\em ...} & {\em ...} \\ 
     23    {\em   3.4} & {\em ...} & {\em ...} \\ 
     24    {\em <=3.4} & {\em ...} & {\em ...} 
     25  \end{tabularx} 
     26} 
     27 
     28\clearpage 
    1929 
    2030The ASM code adds the functionality to apply increments to the model variables: temperature, salinity, 
     
    2535There is a brief description of all the namelist options provided. 
    2636To build the ASM code \key{asminc} must be set. 
    27  
    28 %=============================================================== 
    2937 
    3038%% ================================================================================================= 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex

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    22 
    33\begin{document} 
     4 
    45\chapter{Output and Diagnostics (IOM, DIA, TRD, FLO)} 
    56\label{chap:DIA} 
    67 
     8%    {\em 4.0} & {\em Mirek Andrejczuk, Massimiliano Drudi} & {\em }  \\ 
     9%    {\em }      & {\em Dorotea Iovino, Nicolas Martin} & {\em }  \\ 
     10%    {\em 3.6} & {\em Gurvan Madec, Sebastien Masson } & {\em }  \\ 
     11%    {\em 3.4} & {\em Gurvan Madec, Rachid Benshila, Andrew Coward } & {\em }  \\ 
     12%    {\em }      & {\em Christian Ethe, Sebastien Masson } & {\em }  \\ 
     13 
     14\thispagestyle{plain} 
     15 
    716\chaptertoc 
    817 
    9 \vfill 
    10 \begin{figure}[b] 
    11 %% ================================================================================================= 
    12 \subsubsection*{Changes record} 
    13 \begin{tabular}{l||l|m{0.65\linewidth}} 
    14     Release   & Author        & Modifications \\ 
    15     {\em 4.0} & {\em Mirek Andrejczuk, Massimiliano Drudi} & {\em }  \\ 
    16     {\em }      & {\em Dorotea Iovino, Nicolas Martin} & {\em }  \\ 
    17     {\em 3.6} & {\em Gurvan Madec, Sebastien Masson } & {\em }  \\ 
    18     {\em 3.4} & {\em Gurvan Madec, Rachid Benshila, Andrew Coward } & {\em }  \\ 
    19     {\em }      & {\em Christian Ethe, Sebastien Masson } & {\em }  \\ 
    20 \end{tabular} 
    21 \end{figure} 
     18\paragraph{Changes record} ~\\ 
     19 
     20{\footnotesize 
     21  \begin{tabularx}{\textwidth}{l||X|X} 
     22    Release & Author(s) & Modifications \\ 
     23    \hline 
     24    {\em   4.0} & {\em ...} & {\em ...} \\ 
     25    {\em   3.6} & {\em ...} & {\em ...} \\ 
     26    {\em   3.4} & {\em ...} & {\em ...} \\ 
     27    {\em <=3.4} & {\em ...} & {\em ...} 
     28  \end{tabularx} 
     29} 
     30 
     31\clearpage 
    2232 
    2333%% ================================================================================================= 
     
    134144 
    135145If an additional variable must be written to a restart file, the following steps are needed: 
    136 \begin{description} 
    137    \item [step 1:] add variable name to a list of restart variables (in subroutine \rou{iom\_set\_rst\_vars,} \mdl{iom}) and 
     146\begin{enumerate} 
     147\item Add variable name to a list of restart variables (in subroutine \rou{iom\_set\_rst\_vars,} \mdl{iom}) and 
    138148define correct grid for the variable (\forcode{grid_N_3D} - 3D variable, \forcode{grid_N} - 2D variable, \forcode{grid_vector} - 
    1391491D variable, \forcode{grid_scalar} - scalar), 
    140    \item [step 2:] add variable to the list of fields written by restart.  This can be done either in subroutine 
     150\item Add variable to the list of fields written by restart.  This can be done either in subroutine 
    141151\rou{iom\_set\_rstw\_core} (\mdl{iom}) or by calling  \rou{iom\_set\_rstw\_active} (\mdl{iom}) with the name of a variable 
    142152as an argument. This convention follows approach for writing restart using iom, where variables are 
    143153written either by \rou{rst\_write} or by calling \rou{iom\_rstput} from individual routines. 
    144 \end{description} 
     154\end{enumerate} 
    145155 
    146156An older versions of XIOS do not support reading functionality. It's recommended to use at least XIOS2@1451. 
     
    266276 
    267277\begin{enumerate} 
    268 \item [1.] 
    269   in \NEMO\ code, add a \forcode{CALL iom_put( 'identifier', array )} where you want to output a 2D or 3D array. 
    270 \item [2.] 
    271   If necessary, add \forcode{USE iom ! I/O manager library} to the list of used modules in 
     278\item in \NEMO\ code, add a \forcode{CALL iom_put( 'identifier', array )} where you want to output a 2D or 3D array. 
     279\item If necessary, add \forcode{USE iom ! I/O manager library} to the list of used modules in 
    272280  the upper part of your module. 
    273 \item [3.] 
    274   in the field\_def.xml file, add the definition of your variable using the same identifier you used in the f90 code 
     281\item in the field\_def.xml file, add the definition of your variable using the same identifier you used in the f90 code 
    275282  (see subsequent sections for a details of the XML syntax and rules). 
    276283  For example: 
    277  
    278284\begin{xmllines} 
    279285<field_definition> 
     
    284290</field_definition> 
    285291\end{xmllines} 
    286  
    287292Note your definition must be added to the field\_group whose reference grid is consistent with the size of 
    288293the array passed to iomput. 
     
    291296(iom\_set\_domain\_attr and iom\_set\_axis\_attr in \mdl{iom}) or defined in the domain\_def.xml file. 
    292297\eg: 
    293  
    294298\begin{xmllines} 
    295299<grid id="grid_T_3D" domain_ref="grid_T" axis_ref="deptht"/> 
    296300\end{xmllines} 
    297  
    298301Note, if your array is computed within the surface module each \np{nn_fsbc}{nn\_fsbc} time\_step, 
    299302add the field definition within the field\_group defined with the id "SBC": 
    300303\xmlcode{<field_group id="SBC" ...>} which has been defined with the correct frequency of operations 
    301304(iom\_set\_field\_attr in \mdl{iom}) 
    302 \item [4.] 
    303   add your field in one of the output files defined in iodef.xml 
     305\item add your field in one of the output files defined in iodef.xml 
    304306  (again see subsequent sections for syntax and rules) 
    305  
    306307\begin{xmllines} 
    307308<file id="file1" .../> 
     
    311312</file> 
    312313\end{xmllines} 
    313  
    314314\end{enumerate} 
    315315 
     
    13421342\NEMO\ executables linked with NetCDF4 libraries can be made to produce NetCDF3 files by 
    13431343setting the \np{ln_nc4zip}{ln\_nc4zip} logical to false in the \nam{nc4}{nc4} namelist: 
    1344  
    13451344 
    13461345\begin{listing} 
     
    14421441\label{sec:DIA_trd} 
    14431442 
    1444  
    14451443\begin{listing} 
    14461444  \nlst{namtrd} 
     
    14581456 
    14591457\begin{description} 
    1460 \item [{\np{ln_glo_trd}{ln\_glo\_trd}}]: 
    1461   at each \np{nn_trd}{nn\_trd} time-step a check of the basin averaged properties of 
     1458\item [{\np{ln_glo_trd}{ln\_glo\_trd}}]: at each \np{nn_trd}{nn\_trd} time-step a check of the basin averaged properties of 
    14621459  the momentum and tracer equations is performed. 
    14631460  This also includes a check of $T^2$, $S^2$, $\tfrac{1}{2} (u^2+v2)$, 
    14641461  and potential energy time evolution equations properties; 
    1465 \item [{\np{ln_dyn_trd}{ln\_dyn\_trd}}]: 
    1466   each 3D trend of the evolution of the two momentum components is output; 
    1467 \item [{\np{ln_dyn_mxl}{ln\_dyn\_mxl}}]: 
    1468   each 3D trend of the evolution of the two momentum components averaged over the mixed layer is output; 
    1469 \item [{\np{ln_vor_trd}{ln\_vor\_trd}}]: 
    1470   a vertical summation of the moment tendencies is performed, 
     1462\item [{\np{ln_dyn_trd}{ln\_dyn\_trd}}]: each 3D trend of the evolution of the two momentum components is output; 
     1463\item [{\np{ln_dyn_mxl}{ln\_dyn\_mxl}}]: each 3D trend of the evolution of the two momentum components averaged over the mixed layer is output; 
     1464\item [{\np{ln_vor_trd}{ln\_vor\_trd}}]: a vertical summation of the moment tendencies is performed, 
    14711465  then the curl is computed to obtain the barotropic vorticity tendencies which are output; 
    1472 \item [{\np{ln_KE_trd}{ln\_KE\_trd}}] : 
    1473   each 3D trend of the Kinetic Energy equation is output; 
    1474 \item [{\np{ln_tra_trd}{ln\_tra\_trd}}]: 
    1475   each 3D trend of the evolution of temperature and salinity is output; 
    1476 \item [{\np{ln_tra_mxl}{ln\_tra\_mxl}}]: 
    1477   each 2D trend of the evolution of temperature and salinity averaged over the mixed layer is output; 
     1466\item [{\np{ln_KE_trd}{ln\_KE\_trd}}]  : each 3D trend of the Kinetic Energy equation is output; 
     1467\item [{\np{ln_tra_trd}{ln\_tra\_trd}}]: each 3D trend of the evolution of temperature and salinity is output; 
     1468\item [{\np{ln_tra_mxl}{ln\_tra\_mxl}}]: each 2D trend of the evolution of temperature and salinity averaged over the mixed layer is output; 
    14781469\end{description} 
    14791470 
     
    16381629\section[Transports across sections (\texttt{\textbf{key\_diadct}})]{Transports across sections (\protect\key{diadct})} 
    16391630\label{sec:DIA_diag_dct} 
    1640  
    16411631 
    16421632\begin{listing} 
     
    19931983\end{figure} 
    19941984 
    1995 % ----------------------------------------------------------- 
    1996 %       CMIP specific diagnostics 
    1997 % ----------------------------------------------------------- 
    19981985%% ================================================================================================= 
    19991986\subsection[CMIP specific diagnostics (\textit{diaar5.F90}, \textit{diaptr.F90})]{CMIP specific diagnostics (\protect\mdl{diaar5})} 
     
    20152002the Indo-Pacific mask been deduced from the sum of the Indian and Pacific mask (\autoref{fig:DIA_mask_subasins}). 
    20162003 
    2017  
    20182004\begin{listing} 
    20192005  \nlst{namptr} 
     
    20222008\end{listing} 
    20232009 
    2024 % ----------------------------------------------------------- 
    2025 %       25 hour mean and hourly Surface, Mid and Bed 
    2026 % ----------------------------------------------------------- 
    20272010%% ================================================================================================= 
    20282011\subsection{25 hour mean output for tidal models} 
    2029  
    20302012 
    20312013\begin{listing} 
     
    20402022This diagnostic is actived with the logical $ln\_dia25h$. 
    20412023 
    2042 % ----------------------------------------------------------- 
    2043 %     Top Middle and Bed hourly output 
    2044 % ----------------------------------------------------------- 
    20452024%% ================================================================================================= 
    20462025\subsection{Top middle and bed hourly output} 
    2047  
    20482026 
    20492027\begin{listing} 
     
    20592037This diagnostic is actived with the logical $ln\_diatmb$. 
    20602038 
    2061 % ----------------------------------------------------------- 
    2062 %     Courant numbers 
    2063 % ----------------------------------------------------------- 
    20642039%% ================================================================================================= 
    20652040\subsection{Courant numbers} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIU.tex

    r11597 r11598  
    22 
    33\begin{document} 
     4 
    45\chapter{Diurnal SST Models (DIU)} 
    56\label{chap:DIU} 
    67 
     8\thispagestyle{plain} 
     9 
    710\chaptertoc 
    811 
    9 $\ $\newline % force a new line 
     12\paragraph{Changes record} ~\\ 
     13 
     14{\footnotesize 
     15  \begin{tabularx}{\textwidth}{l||X|X} 
     16    Release & Author(s) & Modifications \\ 
     17    \hline 
     18    {\em   4.0} & {\em ...} & {\em ...} \\ 
     19    {\em   3.6} & {\em ...} & {\em ...} \\ 
     20    {\em   3.4} & {\em ...} & {\em ...} \\ 
     21    {\em <=3.4} & {\em ...} & {\em ...} 
     22  \end{tabularx} 
     23} 
     24 
     25\clearpage 
    1026 
    1127Code to produce an estimate of the diurnal warming and cooling of the sea surface skin 
     
    3753This namelist contains only two variables: 
    3854\begin{description} 
    39 \item [{\np{ln_diurnal}{ln\_diurnal}}] 
    40   A logical switch for turning on/off both the cool skin and warm layer. 
    41 \item [{\np{ln_diurnal_only}{ln\_diurnal\_only}}] 
    42   A logical switch which if \forcode{.true.} will run the diurnal model without the other dynamical parts of \NEMO. 
     55\item [{\np{ln_diurnal}{ln\_diurnal}}] A logical switch for turning on/off both the cool skin and warm layer. 
     56\item [{\np{ln_diurnal_only}{ln\_diurnal\_only}}] A logical switch which if \forcode{.true.} will run the diurnal model without the other dynamical parts of \NEMO. 
    4357  \np{ln_diurnal_only}{ln\_diurnal\_only} must be \forcode{.false.} if \np{ln_diurnal}{ln\_diurnal} is \forcode{.false.}. 
    4458\end{description} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DOM.tex

    r11597 r11598  
    22 
    33\begin{document} 
     4 
    45\chapter{Space Domain (DOM)} 
    56\label{chap:DOM} 
    6  
    7 \chaptertoc 
    87 
    98% Missing things: 
     
    1514%     - domclo:  closed sea and lakes.... management of closea sea area : specific to global configuration, both forced and coupled 
    1615 
    17 \vfill 
    18  
    19 \begin{table}[b] 
    20   \footnotesize 
    21   \caption*{Changes record} 
     16%    {\em 4.0} & {\em Simon M\"{u}ller \& Andrew Coward} & 
     17%    {\em 
     18%      Compatibility changes Major simplification has moved many of the options to external domain configuration tools. 
     19%      (see \autoref{apdx:DOMCFG}) 
     20%    }                                                                                            \\ 
     21%    {\em 3.x} & {\em Rachid Benshila, Gurvan Madec \& S\'{e}bastien Masson} & 
     22%    {\em First version}                                                                          \\ 
     23 
     24\thispagestyle{plain} 
     25 
     26\chaptertoc 
     27 
     28\paragraph{Changes record} ~\\ 
     29 
     30{\footnotesize 
    2231  \begin{tabularx}{\textwidth}{l||X|X} 
    23     Release & Author(s) & Modifications                                                          \\ 
    24     \hline 
    25     {\em 4.0} & {\em Simon M\"{u}ller \& Andrew Coward} & 
    26     {\em 
    27       Compatibility changes Major simplification has moved many of the options to external domain configuration tools. 
    28       (see \autoref{apdx:DOMCFG}) 
    29     }                                                                                            \\ 
    30     {\em 3.x} & {\em Rachid Benshila, Gurvan Madec \& S\'{e}bastien Masson} & 
    31     {\em First version}                                                                          \\ 
     32    Release & Author(s) & Modifications \\ 
     33    \hline 
     34    {\em   4.0} & {\em ...} & {\em ...} \\ 
     35    {\em   3.6} & {\em ...} & {\em ...} \\ 
     36    {\em   3.4} & {\em ...} & {\em ...} \\ 
     37    {\em <=3.4} & {\em ...} & {\em ...} 
    3238  \end{tabularx} 
    33 \end{table} 
     39} 
     40 
     41\clearpage 
    3442 
    3543Having defined the continuous equations in \autoref{chap:MB} and chosen a time discretisation \autoref{chap:TD}, 
     
    259267Furthermore, the direction of the vertical indexing has been reversed and the surface level set at $k = 1$. 
    260268 
    261 % ----------------------------------- 
    262 %        Horizontal Indexing 
    263 % ----------------------------------- 
    264269%% ================================================================================================= 
    265270\subsubsection{Horizontal indexing} 
     
    272277A $t$-point and its nearest north-east $f$-point have the same $i$-and $j$-indices. 
    273278 
    274 % ----------------------------------- 
    275 %        Vertical indexing 
    276 % ----------------------------------- 
    277279%% ================================================================================================= 
    278280\subsubsection{Vertical indexing} 
     
    342344and the vertical grid (\autoref{subsec:DOM_zgr}). 
    343345 
    344 % ----------------------------------- 
    345 %        Domain Size 
    346 % ----------------------------------- 
    347346%% ================================================================================================= 
    348347\subsection{Domain size} 
     
    639638 
    640639\begin{description} 
    641 \item [{\np[=.true.]{ln_tsd_init}{ln\_tsd\_init}}] 
    642   Use T and S input files that can be given on the model grid itself or on their native input data grids. 
     640\item [{\np[=.true.]{ln_tsd_init}{ln\_tsd\_init}}] Use T and S input files that can be given on the model grid itself or on their native input data grids. 
    643641  In the latter case, the data will be interpolated on-the-fly both in the horizontal and the vertical to the model grid 
    644642  (see \autoref{subsec:SBC_iof}). 
    645643  The information relating to the input files are specified in the \np{sn_tem}{sn\_tem} and \np{sn_sal}{sn\_sal} structures. 
    646644  The computation is done in the \mdl{dtatsd} module. 
    647 \item [{\np[=.false.]{ln_tsd_init}{ln\_tsd\_init}}] 
    648   Initial values for T and S are set via a user supplied \rou{usr\_def\_istate} routine contained in \mdl{userdef\_istate}. 
     645\item [{\np[=.false.]{ln_tsd_init}{ln\_tsd\_init}}] Initial values for T and S are set via a user supplied \rou{usr\_def\_istate} routine contained in \mdl{userdef\_istate}. 
    649646  The default version sets horizontally uniform T and profiles as used in the GYRE configuration 
    650647  (see \autoref{sec:CFGS_gyre}). 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DYN.tex

    r11597 r11598  
    22 
    33\begin{document} 
     4 
    45\chapter{Ocean Dynamics (DYN)} 
    56\label{chap:DYN} 
    67 
     8\thispagestyle{plain} 
     9 
    710\chaptertoc 
     11 
     12\paragraph{Changes record} ~\\ 
     13 
     14{\footnotesize 
     15  \begin{tabularx}{\textwidth}{l||X|X} 
     16    Release & Author(s) & Modifications \\ 
     17    \hline 
     18    {\em   4.0} & {\em ...} & {\em ...} \\ 
     19    {\em   3.6} & {\em ...} & {\em ...} \\ 
     20    {\em   3.4} & {\em ...} & {\em ...} \\ 
     21    {\em <=3.4} & {\em ...} & {\em ...} 
     22  \end{tabularx} 
     23} 
     24 
     25\clearpage 
    826 
    927Using the representation described in \autoref{chap:DOM}, 
     
    149167(see \autoref{subsec:DOM_Num_Index_vertical}). 
    150168 
    151  
    152169%% ================================================================================================= 
    153170\section{Coriolis and advection: vector invariant form} 
     
    301318  \label{fig:DYN_een_triad} 
    302319\end{figure} 
    303 % >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    304320 
    305321A key point in \autoref{eq:DYN_een_e3f} is how the averaging in the \textbf{i}- and \textbf{j}- directions is made. 
     
    387403a similar split-explicit time stepping should be used on vertical advection of tracer to ensure a better stability, 
    388404an option which is only available with a TVD scheme (see \np{ln_traadv_tvd_zts}{ln\_traadv\_tvd\_zts} in \autoref{subsec:TRA_adv_tvd}). 
    389  
    390405 
    391406%% ================================================================================================= 
     
    834849(see their figure 12, lower left). 
    835850 
    836 %>   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   > 
    837851\begin{figure}[!t] 
    838852  \centering 
     
    859873  \label{fig:DYN_spg_ts} 
    860874\end{figure} 
    861 %>   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   > 
    862875 
    863876In the default case (\np[=.true.]{ln_bt_fw}{ln\_bt\_fw}), 
     
    909922it is still significant as shown by \citet{levier.treguier.ea_rpt07} in the case of an analytical barotropic Kelvin wave. 
    910923 
    911 %>>>>>=============== 
    912924\gmcomment{               %%% copy from griffies Book 
    913925 
     
    10281040 
    10291041}            %%end gm comment (copy of griffies book) 
    1030  
    1031 %>>>>>=============== 
    10321042 
    10331043%% ================================================================================================= 
     
    12511261the snow-ice mass is taken into account when computing the surface pressure gradient. 
    12521262 
    1253  
    12541263\gmcomment{ missing : the lateral boundary condition !!!   another external forcing 
    12551264 } 
     
    13071316The final sub-section covers some additional considerations that are relevant to both schemes. 
    13081317 
    1309  
    13101318%   Iterative limiters 
    13111319%% ================================================================================================= 
     
    13361344to be its depth times its velocity. This depth is considered to be zero at ``dry'' $u$-points consistent with its 
    13371345treatment in the calculation of the flux of mass across the cell face. 
    1338  
    13391346 
    13401347\cite{warner.defne.ea_CG13} state that in their scheme the velocity masks at the cell faces for the baroclinic 
     
    14621469directional limiter does. 
    14631470 
    1464  
    14651471%      Surface pressure gradients 
    14661472%% ================================================================================================= 
     
    14811487column.  The three possible combinations are illustrated in \autoref{fig:DYN_WAD_dynhpg}. 
    14821488 
    1483 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    14841489\begin{figure}[!ht] 
    14851490  \centering 
     
    14911496  \label{fig:DYN_WAD_dynhpg} 
    14921497\end{figure} 
    1493 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    14941498 
    14951499The first logical, $\mathrm{ll\_tmp1}$, is set to true if and only if the water depth at 
     
    15541558See the WAD tests MY\_DOC documention for details of the WAD test cases. 
    15551559 
    1556  
    1557  
    15581560%% ================================================================================================= 
    15591561\section[Time evolution term (\textit{dynnxt.F90})]{Time evolution term (\protect\mdl{dynnxt})} 
    15601562\label{sec:DYN_nxt} 
    1561  
    15621563 
    15631564Options are defined through the \nam{dom}{dom} namelist variables. 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_LBC.tex

    r11597 r11598  
    22 
    33\begin{document} 
     4 
    45\chapter{Lateral Boundary Condition (LBC)} 
    56\label{chap:LBC} 
    67 
     8\thispagestyle{plain} 
     9 
    710\chaptertoc 
     11 
     12\paragraph{Changes record} ~\\ 
     13 
     14{\footnotesize 
     15  \begin{tabularx}{\textwidth}{l||X|X} 
     16    Release & Author(s) & Modifications \\ 
     17    \hline 
     18    {\em   4.0} & {\em ...} & {\em ...} \\ 
     19    {\em   3.6} & {\em ...} & {\em ...} \\ 
     20    {\em   3.4} & {\em ...} & {\em ...} \\ 
     21    {\em <=3.4} & {\em ...} & {\em ...} 
     22  \end{tabularx} 
     23} 
     24 
     25\clearpage 
    826 
    927%gm% add here introduction to this chapter 
     
    164182\begin{description} 
    165183 
    166 \item [For closed boundary (\jp{jperio}\forcode{=0})], 
    167   solid walls are imposed at all model boundaries: 
     184\item [For closed boundary (\jp{jperio}\forcode{=0})], solid walls are imposed at all model boundaries: 
    168185  first and last rows and columns are set to zero. 
    169186 
    170 \item [For cyclic east-west boundary (\jp{jperio}\forcode{=1})], 
    171   first and last rows are set to zero (closed) whilst the first column is set to 
     187\item [For cyclic east-west boundary (\jp{jperio}\forcode{=1})], first and last rows are set to zero (closed) whilst the first column is set to 
    172188  the value of the last-but-one column and the last column to the value of the second one 
    173189  (\autoref{fig:LBC_jperio}-a). 
    174190  Whatever flows out of the eastern (western) end of the basin enters the western (eastern) end. 
    175191 
    176 \item [For cyclic north-south boundary (\jp{jperio}\forcode{=2})], 
    177   first and last columns are set to zero (closed) whilst the first row is set to 
     192\item [For cyclic north-south boundary (\jp{jperio}\forcode{=2})], first and last columns are set to zero (closed) whilst the first row is set to 
    178193  the value of the last-but-one row and the last row to the value of the second one 
    179194  (\autoref{fig:LBC_jperio}-a). 
     
    215230\section[Exchange with neighbouring processors (\textit{lbclnk.F90}, \textit{lib\_mpp.F90})]{Exchange with neighbouring processors (\protect\mdl{lbclnk}, \protect\mdl{lib\_mpp})} 
    216231\label{sec:LBC_mpp} 
    217  
    218232 
    219233\begin{listing} 
     
    325339\section{Unstructured open boundary conditions (BDY)} 
    326340\label{sec:LBC_bdy} 
    327  
    328341 
    329342\begin{listing} 
     
    645658\label{subsec:LBC_bdy_tides} 
    646659 
    647  
    648660\begin{listing} 
    649661  \nlst{nambdy_tide} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_LDF.tex

    r11597 r11598  
    66\label{chap:LDF} 
    77 
     8\thispagestyle{plain} 
     9 
    810\chaptertoc 
     11 
     12\paragraph{Changes record} ~\\ 
     13 
     14{\footnotesize 
     15  \begin{tabularx}{\textwidth}{l||X|X} 
     16    Release & Author(s) & Modifications \\ 
     17    \hline 
     18    {\em   4.0} & {\em ...} & {\em ...} \\ 
     19    {\em   3.6} & {\em ...} & {\em ...} \\ 
     20    {\em   3.4} & {\em ...} & {\em ...} \\ 
     21    {\em <=3.4} & {\em ...} & {\em ...} 
     22  \end{tabularx} 
     23} 
     24 
     25\clearpage 
    926 
    1027The lateral physics terms in the momentum and tracer equations have been described in \autoref{eq:MB_zdf} and 
     
    2239is described in \autoref{apdx:TRIADS} 
    2340 
    24  
    25  
    2641%% ================================================================================================= 
    2742\section[Lateral mixing operators]{Lateral mixing operators} 
     
    144159 
    145160\begin{description} 
    146  
    147 \item [$z$-coordinate with full step: ] 
    148   in \autoref{eq:LDF_slp_iso} the densities appearing in the $i$ and $j$ derivatives  are taken at the same depth, 
     161\item [$z$-coordinate with full step:] in \autoref{eq:LDF_slp_iso} the densities appearing in the $i$ and $j$ derivatives  are taken at the same depth, 
    149162  thus the $in situ$ density can be used. 
    150163  This is not the case for the vertical derivatives: $\delta_{k+1/2}[\rho]$ is replaced by $-\rho N^2/g$, 
    151164  where $N^2$ is the local Brunt-Vais\"{a}l\"{a} frequency evaluated following \citet{mcdougall_JPO87} 
    152165  (see \autoref{subsec:TRA_bn2}). 
    153  
    154 \item [$z$-coordinate with partial step: ] 
    155   this case is identical to the full step case except that at partial step level, 
     166\item [$z$-coordinate with partial step:] this case is identical to the full step case except that at partial step level, 
    156167  the \emph{horizontal} density gradient is evaluated as described in \autoref{sec:TRA_zpshde}. 
    157  
    158 \item [$s$- or hybrid $s$-$z$- coordinate: ] 
    159   in the current release of \NEMO, iso-neutral mixing is only employed for $s$-coordinates if 
     168\item [$s$- or hybrid $s$-$z$- coordinate:] in the current release of \NEMO, iso-neutral mixing is only employed for $s$-coordinates if 
    160169  the Griffies scheme is used (\np[=.true.]{ln_traldf_triad}{ln\_traldf\_triad}; 
    161170  see \autoref{apdx:TRIADS}). 
     
    207216 
    208217Note that such a formulation could be also used in the $z$-coordinate and $z$-coordinate with partial steps cases. 
    209  
    210218\end{description} 
    211219 
     
    464472\label{sec:LDF_eiv} 
    465473 
    466  
    467474\begin{listing} 
    468475  \nlst{namtra_eiv} 
     
    470477  \label{lst:namtra_eiv} 
    471478\end{listing} 
    472  
    473479 
    474480%%gm  from Triad appendix  : to be incorporated.... 
     
    529535\label{sec:LDF_mle} 
    530536 
    531  
    532537\begin{listing} 
    533538  \nlst{namtra_mle} 
     
    536541\end{listing} 
    537542 
    538  
    539543If  \np[=.true.]{ln_mle}{ln\_mle} in \nam{tra_mle}{tra\_mle} namelist, a parameterization of the mixing due to unresolved mixed layer instabilities is activated (\citet{foxkemper.ferrari_JPO08}). Additional transport is computed in \rou{ldf\_mle\_trp} and added to the eulerian transport in \rou{tra\_adv} as done for eddy induced advection. 
    540544 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_OBS.tex

    r11597 r11598  
    22 
    33\begin{document} 
     4 
    45\chapter{Observation and Model Comparison (OBS)} 
    56\label{chap:OBS} 
    67 
     8%\subsubsection*{Changes record} 
     9%\begin{tabular}{l||l|m{0.65\linewidth}} 
     10%    Release   & Author        & Modifications \\ 
     11%    {\em 4.0} & {\em D. J. Lea} & {\em \NEMO\ 4.0 updates}  \\ 
     12%    {\em 3.6} & {\em M. Martin, A. Ryan} & {\em Add averaging operator, standalone obs oper} \\ 
     13%    {\em 3.4} & {\em D. J. Lea, M. Martin, ...} & {\em Initial version}  \\ 
     14%    {\em --\texttt{"}--} & {\em ... K. Mogensen, A. Vidard, A. Weaver} & {\em ---\texttt{"}---}  \\ 
     15%\end{tabular} 
     16 
     17\thispagestyle{plain} 
     18 
    719\chaptertoc 
    820 
    9 \vfill 
    10 \begin{figure}[b] 
    11 %% ================================================================================================= 
    12 \subsubsection*{Changes record} 
    13 \begin{tabular}{l||l|m{0.65\linewidth}} 
    14     Release   & Author        & Modifications \\ 
    15     {\em 4.0} & {\em D. J. Lea} & {\em \NEMO\ 4.0 updates}  \\ 
    16     {\em 3.6} & {\em M. Martin, A. Ryan} & {\em Add averaging operator, standalone obs oper} \\ 
    17     {\em 3.4} & {\em D. J. Lea, M. Martin, ...} & {\em Initial version}  \\ 
    18     {\em --\texttt{"}--} & {\em ... K. Mogensen, A. Vidard, A. Weaver} & {\em ---\texttt{"}---}  \\ 
    19 \end{tabular} 
    20 \end{figure} 
     21\paragraph{Changes record} ~\\ 
     22 
     23{\footnotesize 
     24  \begin{tabularx}{\textwidth}{l||X|X} 
     25    Release & Author(s) & Modifications \\ 
     26    \hline 
     27    {\em   4.0} & {\em ...} & {\em ...} \\ 
     28    {\em   3.6} & {\em ...} & {\em ...} \\ 
     29    {\em   3.4} & {\em ...} & {\em ...} \\ 
     30    {\em <=3.4} & {\em ...} & {\em ...} 
     31  \end{tabularx} 
     32} 
     33 
     34\clearpage 
    2135 
    2236The observation and model comparison code, the observation operator (OBS), reads in observation files 
     
    111125Here we show a more complete example namelist \nam{obs}{obs} and also show the NetCDF headers of 
    112126the observation files that may be used with the observation operator. 
    113  
    114127 
    115128\begin{listing} 
     
    608621 
    609622\begin{enumerate} 
    610  
    611 \item [1.] {\bfseries Great-Circle distance-weighted interpolation.} 
     623\item {\bfseries Great-Circle distance-weighted interpolation.} 
    612624  The weights are computed as a function of the great-circle distance $s(P, \cdot)$ between $P$ and 
    613625  the model grid points $A$, $B$ etc. 
     
    654666   \end{alignat*} 
    655667 
    656 \item [2.] {\bfseries Great-Circle distance-weighted interpolation with small angle approximation.} 
     668\item {\bfseries Great-Circle distance-weighted interpolation with small angle approximation.} 
    657669  Similar to the previous interpolation but with the distance $s$ computed as 
    658670  \begin{alignat*}{2} 
     
    664676  where $M$ corresponds to $A$, $B$, $C$ or $D$. 
    665677 
    666 \item [3.] {\bfseries Bilinear interpolation for a regular spaced grid.} 
     678\item {\bfseries Bilinear interpolation for a regular spaced grid.} 
    667679  The interpolation is split into two 1D interpolations in the longitude and latitude directions, respectively. 
    668680 
    669 \item [4.] {\bfseries Bilinear remapping interpolation for a general grid.} 
     681\item {\bfseries Bilinear remapping interpolation for a general grid.} 
    670682  An iterative scheme that involves first mapping a quadrilateral cell into 
    671683  a cell with coordinates (0,0), (1,0), (0,1) and (1,1). 
     
    705717  \label{fig:OBS_avgrec} 
    706718\end{figure} 
    707 % >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    708719 
    709720\begin{figure} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_SBC.tex

    r11597 r11598  
    66\label{chap:SBC} 
    77 
     8\thispagestyle{plain} 
     9 
    810\chaptertoc 
    911 
     12\paragraph{Changes record} ~\\ 
     13 
     14{\footnotesize 
     15  \begin{tabularx}{\textwidth}{l||X|X} 
     16    Release & Author(s) & Modifications \\ 
     17    \hline 
     18    {\em   4.0} & {\em ...} & {\em ...} \\ 
     19    {\em   3.6} & {\em ...} & {\em ...} \\ 
     20    {\em   3.4} & {\em ...} & {\em ...} \\ 
     21    {\em <=3.4} & {\em ...} & {\em ...} 
     22  \end{tabularx} 
     23} 
     24 
     25\clearpage 
    1026 
    1127\begin{listing} 
     
    212228where 
    213229\begin{description} 
    214 \item [File name]: 
    215   the stem name of the NetCDF file to be opened. 
     230\item [File name]: the stem name of the NetCDF file to be opened. 
    216231  This stem will be completed automatically by the model, with the addition of a '.nc' at its end and 
    217232  by date information and possibly a prefix (when using AGRIF). 
    218233  \autoref{tab:SBC_fldread} provides the resulting file name in all possible cases according to 
    219234  whether it is a climatological file or not, and to the open/close frequency (see below for definition). 
    220  
    221235  \begin{table}[htbp] 
    222236    \centering 
     
    245259    \label{tab:SBC_fldread} 
    246260  \end{table} 
    247  
    248 \item [Record frequency]: 
    249   the frequency of the records contained in the input file. 
     261\item [Record frequency]: the frequency of the records contained in the input file. 
    250262  Its unit is in hours if it is positive (for example 24 for daily forcing) or in months if negative 
    251263  (for example -1 for monthly forcing or -12 for annual forcing). 
    252264  Note that this frequency must REALLY be an integer and not a real. 
    253265  On some computers, setting it to '24.' can be interpreted as 240! 
    254  
    255 \item [Variable name]: 
    256   the name of the variable to be read in the input NetCDF file. 
    257  
    258 \item [Time interpolation]: 
    259   a logical to activate, or not, the time interpolation. 
     266\item [Variable name]: the name of the variable to be read in the input NetCDF file. 
     267\item [Time interpolation]: a logical to activate, or not, the time interpolation. 
    260268  If set to 'false', the forcing will have a steplike shape remaining constant during each forcing period. 
    261269  For example, when using a daily forcing without time interpolation, the forcing remaining constant from 
     
    265273  For example, when using a daily forcing with time interpolation, 
    266274  linear interpolation will be performed between mid-day of two consecutive days. 
    267  
    268 \item [Climatological forcing]: 
    269   a logical to specify if a input file contains climatological forcing which can be cycle in time, 
     275\item [Climatological forcing]: a logical to specify if a input file contains climatological forcing which can be cycle in time, 
    270276  or an interannual forcing which will requires additional files if 
    271277  the period covered by the simulation exceeds the one of the file. 
    272278  See the above file naming strategy which impacts the expected name of the file to be opened. 
    273  
    274 \item [Open/close frequency]: 
    275   the frequency at which forcing files must be opened/closed. 
     279\item [Open/close frequency]: the frequency at which forcing files must be opened/closed. 
    276280  Four cases are coded: 
    277281  'daily', 'weekLLL' (with 'LLL' the first 3 letters of the first day of the week), 'monthly' and 'yearly' which 
     
    280284  For example, the first record of a yearly file containing daily data is Jan 1st even if 
    281285  the experiment is not starting at the beginning of the year. 
    282  
    283 \item [Others]: 
    284   'weights filename', 'pairing rotation' and 'land/sea mask' are associated with 
     286\item [Others]:  'weights filename', 'pairing rotation' and 'land/sea mask' are associated with 
    285287  on-the-fly interpolation which is described in \autoref{subsec:SBC_iof}. 
    286  
    287288\end{description} 
    288289 
     
    449450\label{subsec:SBC_SAS} 
    450451 
    451  
    452452\begin{listing} 
    453453  \nlst{namsbc_sas} 
     
    477477 
    478478\begin{itemize} 
    479 \item \mdl{nemogcm}: 
    480   This routine initialises the rest of the model and repeatedly calls the stp time stepping routine (\mdl{step}). 
     479\item \mdl{nemogcm}: This routine initialises the rest of the model and repeatedly calls the stp time stepping routine (\mdl{step}). 
    481480  Since the ocean state is not calculated all associated initialisations have been removed. 
    482 \item \mdl{step}: 
    483   The main time stepping routine now only needs to call the sbc routine (and a few utility functions). 
    484 \item \mdl{sbcmod}: 
    485   This has been cut down and now only calculates surface forcing and the ice model required. 
     481\item \mdl{step}: The main time stepping routine now only needs to call the sbc routine (and a few utility functions). 
     482\item \mdl{sbcmod}: This has been cut down and now only calculates surface forcing and the ice model required. 
    486483  New surface modules that can function when only the surface level of the ocean state is defined can also be added 
    487484  (\eg\ icebergs). 
    488 \item \mdl{daymod}: 
    489   No ocean restarts are read or written (though the ice model restarts are retained), 
     485\item \mdl{daymod}: No ocean restarts are read or written (though the ice model restarts are retained), 
    490486  so calls to restart functions have been removed. 
    491487  This also means that the calendar cannot be controlled by time in a restart file, 
    492488  so the user must check that nn\_date0 in the model namelist is correct for his or her purposes. 
    493 \item \mdl{stpctl}: 
    494   Since there is no free surface solver, references to it have been removed from \rou{stp\_ctl} module. 
    495 \item \mdl{diawri}: 
    496   All 3D data have been removed from the output. 
     489\item \mdl{stpctl}: Since there is no free surface solver, references to it have been removed from \rou{stp\_ctl} module. 
     490\item \mdl{diawri}: All 3D data have been removed from the output. 
    497491  The surface temperature, salinity and velocity components (which have been read in) are written along with 
    498492  relevant forcing and ice data. 
     
    502496 
    503497\begin{itemize} 
    504 \item \mdl{sbcsas}: 
    505   This module initialises the input files needed for reading temperature, salinity and 
     498\item \mdl{sbcsas}: This module initialises the input files needed for reading temperature, salinity and 
    506499  velocity arrays at the surface. 
    507500  These filenames are supplied in namelist namsbc\_sas. 
     
    621614their neutral transfer coefficients relationships with neutral wind. 
    622615\begin{itemize} 
    623 \item NCAR (\np[=.true.]{ln_NCAR}{ln\_NCAR}): 
    624   The NCAR bulk formulae have been developed by \citet{large.yeager_rpt04}. 
     616\item NCAR (\np[=.true.]{ln_NCAR}{ln\_NCAR}): The NCAR bulk formulae have been developed by \citet{large.yeager_rpt04}. 
    625617  They have been designed to handle the NCAR forcing, a mixture of NCEP reanalysis and satellite data. 
    626618  They use an inertial dissipative method to compute the turbulent transfer coefficients 
     
    630622  Note that substituting ERA40 to NCEP reanalysis fields does not require changes in the bulk formulea themself. 
    631623  This is the so-called DRAKKAR Forcing Set (DFS) \citep{brodeau.barnier.ea_OM10}. 
    632 \item COARE 3.0 (\np[=.true.]{ln_COARE_3p0}{ln\_COARE\_3p0}): 
    633   See \citet{fairall.bradley.ea_JC03} for more details 
    634 \item COARE 3.5 (\np[=.true.]{ln_COARE_3p5}{ln\_COARE\_3p5}): 
    635   See \citet{edson.jampana.ea_JPO13} for more details 
    636 \item ECMWF (\np[=.true.]{ln_ECMWF}{ln\_ECMWF}): 
    637   Based on \href{https://www.ecmwf.int/node/9221}{IFS (Cy31)} implementation and documentation. 
     624\item COARE 3.0 (\np[=.true.]{ln_COARE_3p0}{ln\_COARE\_3p0}): See \citet{fairall.bradley.ea_JC03} for more details 
     625\item COARE 3.5 (\np[=.true.]{ln_COARE_3p5}{ln\_COARE\_3p5}): See \citet{edson.jampana.ea_JPO13} for more details 
     626\item ECMWF (\np[=.true.]{ln_ECMWF}{ln\_ECMWF}): Based on \href{https://www.ecmwf.int/node/9221}{IFS (Cy31)} implementation and documentation. 
    638627  Surface roughness lengths needed for the Obukhov length are computed following \citet{beljaars_QJRMS95}. 
    639628\end{itemize} 
     
    741730\label{sec:SBC_tide} 
    742731 
    743  
    744732\begin{listing} 
    745733  \nlst{nam_tide} 
     
    924912 
    925913\begin{description} 
    926  
    927   \item [{\np[=1]{nn_isf}{nn\_isf}}]: 
    928   The ice shelf cavity is represented (\np[=.true.]{ln_isfcav}{ln\_isfcav} needed). 
     914  \item [{\np[=1]{nn_isf}{nn\_isf}}]: The ice shelf cavity is represented (\np[=.true.]{ln_isfcav}{ln\_isfcav} needed). 
    929915  The fwf and heat flux are depending of the local water properties. 
    930916 
     
    932918 
    933919   \begin{description} 
    934    \item [{\np[=1]{nn_isfblk}{nn\_isfblk}}]: 
    935      The melt rate is based on a balance between the upward ocean heat flux and 
     920   \item [{\np[=1]{nn_isfblk}{nn\_isfblk}}]: The melt rate is based on a balance between the upward ocean heat flux and 
    936921     the latent heat flux at the ice shelf base. A complete description is available in \citet{hunter_rpt06}. 
    937    \item [{\np[=2]{nn_isfblk}{nn\_isfblk}}]: 
    938      The melt rate and the heat flux are based on a 3 equations formulation 
     922   \item [{\np[=2]{nn_isfblk}{nn\_isfblk}}]: The melt rate and the heat flux are based on a 3 equations formulation 
    939923     (a heat flux budget at the ice base, a salt flux budget at the ice base and a linearised freezing point temperature equation). 
    940924     A complete description is available in \citet{jenkins_JGR91}. 
     
    952936     There are 3 different ways to compute the exchange coeficient: 
    953937   \begin{description} 
    954         \item [{\np[=0]{nn_gammablk}{nn\_gammablk}}]: 
    955      The salt and heat exchange coefficients are constant and defined by \np{rn_gammas0}{rn\_gammas0} and \np{rn_gammat0}{rn\_gammat0}. 
     938        \item [{\np[=0]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are constant and defined by \np{rn_gammas0}{rn\_gammas0} and \np{rn_gammat0}{rn\_gammat0}. 
    956939     \begin{gather*} 
    957940       % \label{eq:SBC_isf_gamma_iso} 
     
    960943     \end{gather*} 
    961944     This is the recommended formulation for ISOMIP. 
    962    \item [{\np[=1]{nn_gammablk}{nn\_gammablk}}]: 
    963      The salt and heat exchange coefficients are velocity dependent and defined as 
     945   \item [{\np[=1]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are velocity dependent and defined as 
    964946     \begin{gather*} 
    965947       \gamma^{T} = rn\_gammat0 \times u_{*} \\ 
     
    968950     where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters). 
    969951     See \citet{jenkins.nicholls.ea_JPO10} for all the details on this formulation. It is the recommended formulation for realistic application. 
    970    \item [{\np[=2]{nn_gammablk}{nn\_gammablk}}]: 
    971      The salt and heat exchange coefficients are velocity and stability dependent and defined as: 
     952   \item [{\np[=2]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are velocity and stability dependent and defined as: 
    972953\[ 
    973954\gamma^{T,S} = \frac{u_{*}}{\Gamma_{Turb} + \Gamma^{T,S}_{Mole}} 
     
    979960     This formulation has not been extensively tested in \NEMO\ (not recommended). 
    980961   \end{description} 
    981   \item [{\np[=2]{nn_isf}{nn\_isf}}]: 
    982    The ice shelf cavity is not represented. 
     962  \item [{\np[=2]{nn_isf}{nn\_isf}}]: The ice shelf cavity is not represented. 
    983963   The fwf and heat flux are computed using the \citet{beckmann.goosse_OM03} parameterisation of isf melting. 
    984964   The fluxes are distributed along the ice shelf edge between the depth of the average grounding line (GL) 
     
    986966   (\np{sn_depmin_isf}{sn\_depmin\_isf}) as in (\np[=3]{nn_isf}{nn\_isf}). 
    987967   The effective melting length (\np{sn_Leff_isf}{sn\_Leff\_isf}) is read from a file. 
    988   \item [{\np[=3]{nn_isf}{nn\_isf}}]: 
    989    The ice shelf cavity is not represented. 
     968  \item [{\np[=3]{nn_isf}{nn\_isf}}]: The ice shelf cavity is not represented. 
    990969   The fwf (\np{sn_rnfisf}{sn\_rnfisf}) is prescribed and distributed along the ice shelf edge between 
    991970   the depth of the average grounding line (GL) (\np{sn_depmax_isf}{sn\_depmax\_isf}) and 
    992971   the base of the ice shelf along the calving front (\np{sn_depmin_isf}{sn\_depmin\_isf}). 
    993972   The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. 
    994   \item [{\np[=4]{nn_isf}{nn\_isf}}]: 
    995    The ice shelf cavity is opened (\np[=.true.]{ln_isfcav}{ln\_isfcav} needed). 
     973  \item [{\np[=4]{nn_isf}{nn\_isf}}]: The ice shelf cavity is opened (\np[=.true.]{ln_isfcav}{ln\_isfcav} needed). 
    996974   However, the fwf is not computed but specified from file \np{sn_fwfisf}{sn\_fwfisf}). 
    997975   The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. 
     
    10371015At each restart step: 
    10381016 
    1039 \begin{description} 
    1040 \item [Step 1]: the ice sheet model send a new bathymetry and ice shelf draft netcdf file. 
    1041 \item [Step 2]: a new domcfg.nc file is built using the DOMAINcfg tools. 
    1042 \item [Step 3]: \NEMO\ run for a specific period and output the average melt rate over the period. 
    1043 \item [Step 4]: the ice sheet model run using the melt rate outputed in step 4. 
    1044 \item [Step 5]: go back to 1. 
    1045 \end{description} 
     1017\begin{enumerate} 
     1018\item the ice sheet model send a new bathymetry and ice shelf draft netcdf file. 
     1019\item a new domcfg.nc file is built using the DOMAINcfg tools. 
     1020\item \NEMO\ run for a specific period and output the average melt rate over the period. 
     1021\item the ice sheet model run using the melt rate outputed in step 4. 
     1022\item go back to 1. 
     1023\end{enumerate} 
    10461024 
    10471025If \np[=.true.]{ln_iscpl}{ln\_iscpl}, the isf draft is assume to be different at each restart step with 
     
    10501028 
    10511029\begin{description} 
    1052 \item [Thin a cell down]: 
    1053   T/S/ssh are unchanged and U/V in the top cell are corrected to keep the barotropic transport (bt) constant 
     1030\item [Thin a cell down]: T/S/ssh are unchanged and U/V in the top cell are corrected to keep the barotropic transport (bt) constant 
    10541031  ($bt_b=bt_n$). 
    1055 \item [Enlarge  a cell]: 
    1056   See case "Thin a cell down" 
    1057 \item [Dry a cell]: 
    1058   mask, T/S, U/V and ssh are set to 0. 
     1032\item [Enlarge  a cell]: See case "Thin a cell down" 
     1033\item [Dry a cell]: mask, T/S, U/V and ssh are set to 0. 
    10591034  Furthermore, U/V into the water column are modified to satisfy ($bt_b=bt_n$). 
    1060 \item [Wet a cell]: 
    1061   mask is set to 1, T/S is extrapolated from neighbours, $ssh_n = ssh_b$ and U/V set to 0. 
     1035\item [Wet a cell]: mask is set to 1, T/S is extrapolated from neighbours, $ssh_n = ssh_b$ and U/V set to 0. 
    10621036  If no neighbours, T/S is extrapolated from old top cell value. 
    10631037  If no neighbours along i,j and k (both previous test failed), T/S/U/V/ssh and mask are set to 0. 
    1064 \item [Dry a column]: 
    1065    mask, T/S, U/V are set to 0 everywhere in the column and ssh set to 0. 
    1066 \item [Wet a column]: 
    1067   set mask to 1, T/S is extrapolated from neighbours, ssh is extrapolated from neighbours and U/V set to 0. 
     1038\item [Dry a column]: mask, T/S, U/V are set to 0 everywhere in the column and ssh set to 0. 
     1039\item [Wet a column]: set mask to 1, T/S is extrapolated from neighbours, ssh is extrapolated from neighbours and U/V set to 0. 
    10681040  If no neighbour, T/S/U/V and mask set to 0. 
    10691041\end{description} 
     
    11091081Two initialisation schemes are possible. 
    11101082\begin{description} 
    1111 \item [{\np{nn_test_icebergs}{nn\_test\_icebergs}~$>$~0}] 
    1112   In this scheme, the value of \np{nn_test_icebergs}{nn\_test\_icebergs} represents the class of iceberg to generate 
     1083\item [{\np{nn_test_icebergs}{nn\_test\_icebergs}~$>$~0}] In this scheme, the value of \np{nn_test_icebergs}{nn\_test\_icebergs} represents the class of iceberg to generate 
    11131084  (so between 1 and 10), and \np{nn_test_icebergs}{nn\_test\_icebergs} provides a lon/lat box in the domain at each grid point of 
    11141085  which an iceberg is generated at the beginning of the run. 
     
    11161087  \np{nn_test_icebergs}{nn\_test\_icebergs} is defined by four numbers in \np{nn_test_box}{nn\_test\_box} representing the corners of 
    11171088  the geographical box: lonmin,lonmax,latmin,latmax 
    1118 \item [{\np[=-1]{nn_test_icebergs}{nn\_test\_icebergs}}] 
    1119   In this scheme, the model reads a calving file supplied in the \np{sn_icb}{sn\_icb} parameter. 
     1089\item [{\np[=-1]{nn_test_icebergs}{nn\_test\_icebergs}}] In this scheme, the model reads a calving file supplied in the \np{sn_icb}{sn\_icb} parameter. 
    11201090  This should be a file with a field on the configuration grid (typically ORCA) 
    11211091  representing ice accumulation rate at each model point. 
     
    11841154\end{description} 
    11851155 
    1186 % ---------------------------------------------------------------- 
    1187 % Neutral drag coefficient from wave model (ln_cdgw) 
    1188  
    1189 % ---------------------------------------------------------------- 
    11901156%% ================================================================================================= 
    11911157\subsection[Neutral drag coefficient from wave model (\forcode{ln_cdgw})]{Neutral drag coefficient from wave model (\protect\np{ln_cdgw}{ln\_cdgw})} 
     
    11981164air-sea interface following \citet{large.yeager_rpt04}. 
    11991165 
    1200 % ---------------------------------------------------------------- 
    1201 % 3D Stokes Drift (ln_sdw, nn_sdrift) 
    1202 % ---------------------------------------------------------------- 
    12031166%% ================================================================================================= 
    12041167\subsection[3D Stokes Drift (\forcode{ln_sdw} \& \forcode{nn_sdrift})]{3D Stokes Drift (\protect\np{ln_sdw}{ln\_sdw} \& \np{nn_sdrift}{nn\_sdrift})} 
     
    12941257\] 
    12951258 
    1296 % ---------------------------------------------------------------- 
    1297 % Stokes-Coriolis term (ln_stcor) 
    1298 % ---------------------------------------------------------------- 
    12991259%% ================================================================================================= 
    13001260\subsection[Stokes-Coriolis term (\forcode{ln_stcor})]{Stokes-Coriolis term (\protect\np{ln_stcor}{ln\_stcor})} 
     
    13081268\np[=.true.]{ln_stcor}{ln\_stcor} has to be set. 
    13091269 
    1310 % ---------------------------------------------------------------- 
    1311 % Waves modified stress (ln_tauwoc, ln_tauw) 
    1312 % ---------------------------------------------------------------- 
    13131270%% ================================================================================================= 
    13141271\subsection[Wave modified stress (\forcode{ln_tauwoc} \& \forcode{ln_tauw})]{Wave modified sress (\protect\np{ln_tauwoc}{ln\_tauwoc} \& \np{ln_tauw}{ln\_tauw})} 
     
    13571314\label{subsec:SBC_dcy} 
    13581315% 
    1359  
    13601316 
    13611317\begin{figure}[!t] 
     
    14751431the value of the \np{nn_ice}{nn\_ice} namelist parameter found in \nam{sbc}{sbc} namelist. 
    14761432\begin{description} 
    1477 \item [nn\_ice = 0] 
    1478   there will never be sea-ice in the computational domain. 
     1433\item [nn\_ice = 0] there will never be sea-ice in the computational domain. 
    14791434  This is a typical namelist value used for tropical ocean domain. 
    14801435  The surface fluxes are simply specified for an ice-free ocean. 
    14811436  No specific things is done for sea-ice. 
    1482 \item [nn\_ice = 1] 
    1483   sea-ice can exist in the computational domain, but no sea-ice model is used. 
     1437\item [nn\_ice = 1] sea-ice can exist in the computational domain, but no sea-ice model is used. 
    14841438  An observed ice covered area is read in a file. 
    14851439  Below this area, the SST is restored to the freezing point and 
     
    14921446  is usually referred as the \textit{ice-if} model. 
    14931447  It can be found in the \mdl{sbcice\_if} module. 
    1494 \item [nn\_ice = 2 or more] 
    1495   A full sea ice model is used. 
     1448\item [nn\_ice = 2 or more] A full sea ice model is used. 
    14961449  This model computes the ice-ocean fluxes, 
    14971450  that are combined with the air-sea fluxes using the ice fraction of each model cell to 
     
    15451498 
    15461499\begin{description} 
    1547 \item [{\np[=0]{nn_fwb}{nn\_fwb}}] 
    1548   no control at all. 
     1500\item [{\np[=0]{nn_fwb}{nn\_fwb}}] no control at all. 
    15491501  The mean sea level is free to drift, and will certainly do so. 
    1550 \item [{\np[=1]{nn_fwb}{nn\_fwb}}] 
    1551   global mean \textit{emp} set to zero at each model time step. 
     1502\item [{\np[=1]{nn_fwb}{nn\_fwb}}] global mean \textit{emp} set to zero at each model time step. 
    15521503  %GS: comment below still relevant ? 
    15531504  %Note that with a sea-ice model, this technique only controls the mean sea level with linear free surface and no mass flux between ocean and ice (as it is implemented in the current ice-ocean coupling). 
    1554 \item [{\np[=2]{nn_fwb}{nn\_fwb}}] 
    1555   freshwater budget is adjusted from the previous year annual mean budget which 
     1505\item [{\np[=2]{nn_fwb}{nn\_fwb}}] freshwater budget is adjusted from the previous year annual mean budget which 
    15561506  is read in the \textit{EMPave\_old.dat} file. 
    15571507  As the model uses the Boussinesq approximation, the annual mean fresh water budget is simply evaluated from 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_STO.tex

    r11597 r11598  
    22 
    33\begin{document} 
     4 
    45\chapter{Stochastic Parametrization of EOS (STO)} 
    56\label{chap:STO} 
    67 
     8\thispagestyle{plain} 
     9 
    710\chaptertoc 
     11 
     12\paragraph{Changes record} ~\\ 
     13 
     14{\footnotesize 
     15  \begin{tabularx}{\textwidth}{l||X|X} 
     16    Release & Author(s) & Modifications \\ 
     17    \hline 
     18    {\em   4.0} & {\em ...} & {\em ...} \\ 
     19    {\em   3.6} & {\em ...} & {\em ...} \\ 
     20    {\em   3.4} & {\em ...} & {\em ...} \\ 
     21    {\em <=3.4} & {\em ...} & {\em ...} 
     22  \end{tabularx} 
     23} 
    824 
    925% \vfill 
     
    1834% \end{figure} 
    1935 
    20 Authors: \\ 
    21 C. Levy release 4.0.1 update \\ 
    22 P.-A. Bouttier release 3.6 inital version 
     36\clearpage 
    2337 
    2438As a result of the nonlinearity of the seawater equation of state, unresolved scales represent a major source of uncertainties in the computation of the large-scale horizontal density gradient from the large-scale temperature and salinity fields. Following  \cite{brankart_OM13}, the impact of these uncertainties can be simulated by random processes representing unresolved T/S fluctuations. The Stochastic Parametrization of EOS (STO) module implements this parametrization. 
     
    178192 
    179193\begin{description} 
    180 \item [{\np{nn_sto_eos}{nn\_sto\_eos}:}]   number of independent random walks 
    181 \item [{\np{rn_eos_stdxy}{rn\_eos\_stdxy}:}] random walk horizontal standard deviation (in grid points) 
    182 \item [{\np{rn_eos_stdz}{rn\_eos\_stdz}:}]  random walk vertical standard deviation (in grid points) 
    183 \item [{\np{rn_eos_tcor}{rn\_eos\_tcor}:}]  random walk time correlation (in timesteps) 
    184 \item [{\np{nn_eos_ord}{nn\_eos\_ord}:}]   order of autoregressive processes 
    185 \item [{\np{nn_eos_flt}{nn\_eos\_flt}:}]   passes of Laplacian filter 
    186 \item [{\np{rn_eos_lim}{rn\_eos\_lim}:}]   limitation factor (default = 3.0) 
     194\item [{\np{nn_sto_eos}{nn\_sto\_eos}:}]     number of independent random walks 
     195\item [{\np{rn_eos_stdxy}{rn\_eos\_stdxy}:}] random walk horizontal standard deviation 
     196  (in grid points) 
     197\item [{\np{rn_eos_stdz}{rn\_eos\_stdz}:}]   random walk vertical standard deviation 
     198  (in grid points) 
     199\item [{\np{rn_eos_tcor}{rn\_eos\_tcor}:}]   random walk time correlation (in timesteps) 
     200\item [{\np{nn_eos_ord}{nn\_eos\_ord}:}]     order of autoregressive processes 
     201\item [{\np{nn_eos_flt}{nn\_eos\_flt}:}]     passes of Laplacian filter 
     202\item [{\np{rn_eos_lim}{rn\_eos\_lim}:}]     limitation factor (default = 3.0) 
    187203\end{description} 
    188204 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_TRA.tex

    r11597 r11598  
    22 
    33\begin{document} 
     4 
    45\chapter{Ocean Tracers (TRA)} 
    56\label{chap:TRA} 
    67 
     8\thispagestyle{plain} 
     9 
    710\chaptertoc 
     11 
     12\paragraph{Changes record} ~\\ 
     13 
     14{\footnotesize 
     15  \begin{tabularx}{\textwidth}{l||X|X} 
     16    Release & Author(s) & Modifications \\ 
     17    \hline 
     18    {\em   4.0} & {\em ...} & {\em ...} \\ 
     19    {\em   3.6} & {\em ...} & {\em ...} \\ 
     20    {\em   3.4} & {\em ...} & {\em ...} \\ 
     21    {\em <=3.4} & {\em ...} & {\em ...} 
     22  \end{tabularx} 
     23} 
     24 
     25\clearpage 
    826 
    927% missing/update 
     
    111129 
    112130\begin{description} 
    113 \item [linear free surface:] 
    114   (\np[=.true.]{ln_linssh}{ln\_linssh}) 
     131\item [linear free surface:] (\np[=.true.]{ln_linssh}{ln\_linssh}) 
    115132  the first level thickness is constant in time: 
    116133  the vertical boundary condition is applied at the fixed surface $z = 0$ rather than on 
     
    119136  $\tau_w|_{k = 1/2} = T_{k = 1}$, \ie\ the product of surface velocity (at $z = 0$) by 
    120137  the first level tracer value. 
    121 \item [non-linear free surface:] 
    122   (\np[=.false.]{ln_linssh}{ln\_linssh}) 
     138\item [non-linear free surface:] (\np[=.false.]{ln_linssh}{ln\_linssh}) 
    123139  convergence/divergence in the first ocean level moves the free surface up/down. 
    124140  There is no tracer advection through it so that the advective fluxes through the surface are also zero. 
     
    435451 
    436452\begin{description} 
    437 \item [{\np[=.true.]{ln_traldf_OFF}{ln\_traldf\_OFF}}] 
    438   no operator selected, the lateral diffusive tendency will not be applied to the tracer equation. 
     453\item [{\np[=.true.]{ln_traldf_OFF}{ln\_traldf\_OFF}}] no operator selected, the lateral diffusive tendency will not be applied to the tracer equation. 
    439454  This option can be used when the selected advection scheme is diffusive enough (MUSCL scheme for example). 
    440 \item [{\np[=.true.]{ln_traldf_lap}{ln\_traldf\_lap}}] 
    441   a laplacian operator is selected. 
     455\item [{\np[=.true.]{ln_traldf_lap}{ln\_traldf\_lap}}] a laplacian operator is selected. 
    442456  This harmonic operator takes the following expression:  $\mathcal{L}(T) = \nabla \cdot A_{ht} \; \nabla T $, 
    443457  where the gradient operates along the selected direction (see \autoref{subsec:TRA_ldf_dir}), 
    444458  and $A_{ht}$ is the eddy diffusivity coefficient expressed in $m^2/s$ (see \autoref{chap:LDF}). 
    445 \item [{\np[=.true.]{ln_traldf_blp}{ln\_traldf\_blp}}]: 
    446   a bilaplacian operator is selected. 
     459\item [{\np[=.true.]{ln_traldf_blp}{ln\_traldf\_blp}}] a bilaplacian operator is selected. 
    447460  This biharmonic operator takes the following expression: 
    448461  $\mathcal{B} = - \mathcal{L}(\mathcal{L}(T)) = - \nabla \cdot b \nabla (\nabla \cdot b \nabla T)$ 
     
    597610\section[Tracer vertical diffusion (\textit{trazdf.F90})]{Tracer vertical diffusion (\protect\mdl{trazdf})} 
    598611\label{sec:TRA_zdf} 
    599  
    600612 
    601613Options are defined through the \nam{zdf}{zdf} namelist variables. 
     
    774786 
    775787\begin{description} 
    776 \item [{\np[=0]{nn_chldta}{nn\_chldta}}] 
    777   a constant 0.05 g.Chl/L value everywhere ; 
    778 \item [{\np[=1]{nn_chldta}{nn\_chldta}}] 
    779   an observed time varying chlorophyll deduced from satellite surface ocean color measurement spread uniformly in 
    780   the vertical direction; 
    781 \item [{\np[=2]{nn_chldta}{nn\_chldta}}] 
    782   same as previous case except that a vertical profile of chlorophyl is used. 
     788\item [{\np[=0]{nn_chldta}{nn\_chldta}}] a constant 0.05 g.Chl/L value everywhere ; 
     789\item [{\np[=1]{nn_chldta}{nn\_chldta}}] an observed time varying chlorophyll deduced from satellite surface ocean color measurement spread uniformly in the vertical direction; 
     790\item [{\np[=2]{nn_chldta}{nn\_chldta}}] same as previous case except that a vertical profile of chlorophyl is used. 
    783791  Following \cite{morel.berthon_LO89}, the profile is computed from the local surface chlorophyll value; 
    784 \item [{\np[=.true.]{ln_qsr_bio}{ln\_qsr\_bio}}] 
    785   simulated time varying chlorophyll by TOP biogeochemical model. 
     792\item [{\np[=.true.]{ln_qsr_bio}{ln\_qsr\_bio}}] simulated time varying chlorophyll by TOP biogeochemical model. 
    786793  In this case, the RGB formulation is used to calculate both the phytoplankton light limitation in 
    787794  PISCES and the oceanic heating rate. 
     
    11341141 
    11351142\begin{description} 
    1136 \item [{\np[=.true.]{ln_teos10}{ln\_teos10}}] 
    1137   the polyTEOS10-bsq equation of seawater \citep{roquet.madec.ea_OM15} is used. 
     1143\item [{\np[=.true.]{ln_teos10}{ln\_teos10}}] the polyTEOS10-bsq equation of seawater \citep{roquet.madec.ea_OM15} is used. 
    11381144  The accuracy of this approximation is comparable to the TEOS-10 rational function approximation, 
    11391145  but it is optimized for a boussinesq fluid and the polynomial expressions have simpler and 
     
    11531159  either computing the air-sea and ice-sea fluxes (forced mode) or 
    11541160  sending the SST field to the atmosphere (coupled mode). 
    1155 \item [{\np[=.true.]{ln_eos80}{ln\_eos80}}] 
    1156   the polyEOS80-bsq equation of seawater is used. 
     1161\item [{\np[=.true.]{ln_eos80}{ln\_eos80}}] the polyEOS80-bsq equation of seawater is used. 
    11571162  It takes the same polynomial form as the polyTEOS10, but the coefficients have been optimized to 
    11581163  accurately fit EOS80 (Roquet, personal comm.). 
     
    11651170  Nevertheless, a severe assumption is made in order to have a heat content ($C_p T_p$) which 
    11661171  is conserved by the model: $C_p$ is set to a constant value, the TEOS10 value. 
    1167 \item [{\np[=.true.]{ln_seos}{ln\_seos}}] 
    1168   a simplified EOS (S-EOS) inspired by \citet{vallis_bk06} is chosen, 
     1172\item [{\np[=.true.]{ln_seos}{ln\_seos}}] a simplified EOS (S-EOS) inspired by \citet{vallis_bk06} is chosen, 
    11691173  the coefficients of which has been optimized to fit the behavior of TEOS10 
    11701174  (Roquet, personal comm.) (see also \citet{roquet.madec.ea_JPO15}). 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_ZDF.tex

    r11597 r11598  
    55 
    66\begin{document} 
     7 
    78\chapter{Vertical Ocean Physics (ZDF)} 
    89\label{chap:ZDF} 
    910 
     11\thispagestyle{plain} 
     12 
    1013\chaptertoc 
     14 
     15\paragraph{Changes record} ~\\ 
     16 
     17{\footnotesize 
     18  \begin{tabularx}{\textwidth}{l||X|X} 
     19    Release & Author(s) & Modifications \\ 
     20    \hline 
     21    {\em   4.0} & {\em ...} & {\em ...} \\ 
     22    {\em   3.6} & {\em ...} & {\em ...} \\ 
     23    {\em   3.4} & {\em ...} & {\em ...} \\ 
     24    {\em <=3.4} & {\em ...} & {\em ...} 
     25  \end{tabularx} 
     26} 
     27 
     28\clearpage 
    1129 
    1230%gm% Add here a small introduction to ZDF and naming of the different physics (similar to what have been written for TRA and DYN. 
     
    3957%and thus of the formulation used (see \autoref{chap:TD}). 
    4058 
    41  
    4259\begin{listing} 
    4360  \nlst{namzdf} 
     
    6986\subsection[Richardson number dependent (\forcode{ln_zdfric})]{Richardson number dependent (\protect\np{ln_zdfric}{ln\_zdfric})} 
    7087\label{subsec:ZDF_ric} 
    71  
    7288 
    7389\begin{listing} 
     
    405421\label{subsec:ZDF_gls} 
    406422 
    407  
    408423\begin{listing} 
    409424  \nlst{namzdf_gls} 
     
    859874  \label{lst:namdrg_bot} 
    860875\end{listing} 
    861  
    862876 
    863877Options to define the top and bottom friction are defined through the \nam{drg}{drg} namelist variables. 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_cfgs.tex

    r11597 r11598  
    22 
    33\begin{document} 
     4 
    45\chapter{Configurations} 
    56\label{chap:CFGS} 
    67 
     8\thispagestyle{plain} 
     9 
    710\chaptertoc 
     11 
     12\paragraph{Changes record} ~\\ 
     13 
     14{\footnotesize 
     15  \begin{tabularx}{\textwidth}{l||X|X} 
     16    Release & Author(s) & Modifications \\ 
     17    \hline 
     18    {\em   4.0} & {\em ...} & {\em ...} \\ 
     19    {\em   3.6} & {\em ...} & {\em ...} \\ 
     20    {\em   3.4} & {\em ...} & {\em ...} \\ 
     21    {\em <=3.4} & {\em ...} & {\em ...} 
     22  \end{tabularx} 
     23} 
     24 
     25\clearpage 
    826 
    927%% ================================================================================================= 
     
    1836though by no means are all options exercised in the reference configurations. 
    1937Configuration is defined manually through the \nam{cfg}{cfg} namelist variables. 
    20  
    2138 
    2239\begin{listing} 
     
    4865and second, the two components of the velocity are moved on a $T$-point. 
    4966Therefore, defining \key{c1d} changes some things in the code behaviour: 
    50 \begin{description} 
    51 \item [(1)] 
    52   a simplified \rou{stp} routine is used (\rou{stp\_c1d}, see \mdl{step\_c1d} module) in which 
     67\begin{enumerate} 
     68\item a simplified \rou{stp} routine is used (\rou{stp\_c1d}, see \mdl{step\_c1d} module) in which 
    5369  both lateral tendancy terms and lateral physics are not called; 
    54 \item [(2)] 
    55   the vertical velocity is zero 
     70\item the vertical velocity is zero 
    5671  (so far, no attempt at introducing a Ekman pumping velocity has been made); 
    57 \item [(3)] 
    58   a simplified treatment of the Coriolis term is performed as $U$- and $V$-points are the same 
     72\item a simplified treatment of the Coriolis term is performed as $U$- and $V$-points are the same 
    5973  (see \mdl{dyncor\_c1d}). 
    60 \end{description} 
     74\end{enumerate} 
    6175All the relevant \textit{\_c1d} modules can be found in the src/OCE/C1D directory of 
    6276the \NEMO\ distribution. 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_conservation.tex

    r11597 r11598  
    66\label{chap:CONS} 
    77 
     8\thispagestyle{plain} 
     9 
    810\chaptertoc 
     11 
     12\paragraph{Changes record} ~\\ 
     13 
     14{\footnotesize 
     15  \begin{tabularx}{\textwidth}{l||X|X} 
     16    Release & Author(s) & Modifications \\ 
     17    \hline 
     18    {\em   4.0} & {\em ...} & {\em ...} \\ 
     19    {\em   3.6} & {\em ...} & {\em ...} \\ 
     20    {\em   3.4} & {\em ...} & {\em ...} \\ 
     21    {\em <=3.4} & {\em ...} & {\em ...} 
     22  \end{tabularx} 
     23} 
     24 
     25\clearpage 
    926 
    1027The continuous equations of motion have many analytic properties. 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_misc.tex

    r11597 r11598  
    22 
    33\begin{document} 
     4 
    45\chapter{Miscellaneous Topics} 
    56\label{chap:MISC} 
    67 
     8\thispagestyle{plain} 
     9 
    710\chaptertoc 
     11 
     12\paragraph{Changes record} ~\\ 
     13 
     14{\footnotesize 
     15  \begin{tabularx}{\textwidth}{l||X|X} 
     16    Release & Author(s) & Modifications \\ 
     17    \hline 
     18    {\em   4.0} & {\em ...} & {\em ...} \\ 
     19    {\em   3.6} & {\em ...} & {\em ...} \\ 
     20    {\em   3.4} & {\em ...} & {\em ...} \\ 
     21    {\em <=3.4} & {\em ...} & {\em ...} 
     22  \end{tabularx} 
     23} 
     24 
     25\clearpage 
    826 
    927%% ================================================================================================= 
     
    397415increment also applies to the time.step file which is otherwise updated every timestep. 
    398416 
     417\onlyinsubfile{\input{../../global/epilogue}} 
     418 
     419\end{document} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics.tex

    r11597 r11598  
    66\label{chap:MB} 
    77 
     8\thispagestyle{plain} 
     9 
    810\chaptertoc 
    911 
    10 %% ================================================================================================= 
     12\paragraph{Changes record} ~\\ 
     13 
     14{\footnotesize 
     15  \begin{tabularx}{\textwidth}{l||X|X} 
     16    Release & Author(s) & Modifications \\ 
     17    \hline 
     18    {\em   4.0} & {\em ...} & {\em ...} \\ 
     19    {\em   3.6} & {\em ...} & {\em ...} \\ 
     20    {\em   3.4} & {\em ...} & {\em ...} \\ 
     21    {\em <=3.4} & {\em ...} & {\em ...} 
     22  \end{tabularx} 
     23} 
     24 
     25\clearpage 
     26 
    1127%% ================================================================================================= 
    1228\section{Primitive equations} 
    1329\label{sec:MB_PE} 
    1430 
    15 %% ================================================================================================= 
    1631%% ================================================================================================= 
    1732\subsection{Vector invariant formulation} 
     
    92107Their nature and formulation are discussed in \autoref{sec:MB_zdf_ldf} and \autoref{subsec:MB_boundary_condition}. 
    93108 
    94 %% ================================================================================================= 
    95109%% ================================================================================================= 
    96110\subsection{Boundary conditions} 
     
    166180 
    167181%% ================================================================================================= 
    168 %% ================================================================================================= 
    169182\section{Horizontal pressure gradient} 
    170183\label{sec:MB_hor_pg} 
    171184 
    172 %% ================================================================================================= 
    173185%% ================================================================================================= 
    174186\subsection{Pressure formulation} 
     
    204216 
    205217%% ================================================================================================= 
    206 %% ================================================================================================= 
    207218\subsection{Free surface formulation} 
    208219\label{subsec:MB_free_surface} 
     
    255266 
    256267%% ================================================================================================= 
    257 %% ================================================================================================= 
    258268\section{Curvilinear \textit{z-}coordinate system} 
    259269\label{sec:MB_zco} 
    260270 
    261 %% ================================================================================================= 
    262271%% ================================================================================================= 
    263272\subsection{Tensorial formalism} 
     
    301310\end{equation} 
    302311 
    303 % >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    304312\begin{figure}[!tb] 
    305313  \centering 
     
    344352where $q$ is a scalar quantity and $\vect A = (a_1,a_2,a_3)$ a vector in the $(i,j,k)$ coordinates system. 
    345353 
    346 %% ================================================================================================= 
    347354%% ================================================================================================= 
    348355\subsection{Continuous model equations} 
     
    530537 
    531538%% ================================================================================================= 
    532 %% ================================================================================================= 
    533539\section{Curvilinear generalised vertical coordinate system} 
    534540\label{sec:MB_gco} 
     
    611617%} 
    612618 
    613 %% ================================================================================================= 
    614619%% ================================================================================================= 
    615620\subsection{\textit{S}-coordinate formulation} 
     
    701706 
    702707%% ================================================================================================= 
    703 %% ================================================================================================= 
    704708\subsection{Curvilinear \zstar-coordinate system} 
    705709\label{subsec:MB_zco_star} 
     
    788792 
    789793%% ================================================================================================= 
    790 %% ================================================================================================= 
    791794\subsection{Curvilinear terrain-following \textit{s}--coordinate} 
    792795\label{subsec:MB_sco} 
    793796 
    794 %% ================================================================================================= 
    795797%% ================================================================================================= 
    796798\subsubsection{Introduction} 
     
    875877 
    876878%% ================================================================================================= 
    877 %% ================================================================================================= 
    878879\subsection{\texorpdfstring{Curvilinear \ztilde-coordinate}{}} 
    879880\label{subsec:MB_zco_tilde} 
     
    884885Its use is therefore not recommended. 
    885886 
    886 %% ================================================================================================= 
    887887%% ================================================================================================= 
    888888\section{Subgrid scale physics} 
     
    909909The formulation of these terms and their underlying physics are briefly discussed in the next two subsections. 
    910910 
    911 %% ================================================================================================= 
    912911%% ================================================================================================= 
    913912\subsection{Vertical subgrid scale physics} 
     
    943942 
    944943%% ================================================================================================= 
    945 %% ================================================================================================= 
    946944\subsection{Formulation of the lateral diffusive and viscous operators} 
    947945\label{subsec:MB_ldf} 
     
    998996 
    999997%% ================================================================================================= 
    1000 %% ================================================================================================= 
    1001998\subsubsection{Lateral laplacian tracer diffusive operator} 
    1002999 
     
    10401037while in $s$-coordinates $\pd[]{k}$ is replaced by $\pd[]{s}$. 
    10411038 
    1042 %% ================================================================================================= 
    10431039%% ================================================================================================= 
    10441040\subsubsection{Eddy induced velocity} 
     
    10791075 
    10801076%% ================================================================================================= 
    1081 %% ================================================================================================= 
    10821077\subsubsection{Lateral bilaplacian tracer diffusive operator} 
    10831078 
     
    10911086the harmonic eddy diffusion coefficient set to the square root of the biharmonic one. 
    10921087 
    1093 %% ================================================================================================= 
    10941088%% ================================================================================================= 
    10951089\subsubsection{Lateral Laplacian momentum diffusive operator} 
     
    11261120 
    11271121%% ================================================================================================= 
    1128 %% ================================================================================================= 
    11291122\subsubsection{Lateral bilaplacian momentum diffusive operator} 
    11301123 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex

    r11597 r11598  
    22 
    33\begin{document} 
     4 
    45\chapter{ essai \zstar \sstar} 
     6 
     7\thispagestyle{plain} 
     8 
     9\chaptertoc 
     10 
     11\paragraph{Changes record} ~\\ 
     12 
     13{\footnotesize 
     14  \begin{tabularx}{\textwidth}{l||X|X} 
     15    Release & Author(s) & Modifications \\ 
     16    \hline 
     17    {\em   4.0} & {\em ...} & {\em ...} \\ 
     18    {\em   3.6} & {\em ...} & {\em ...} \\ 
     19    {\em   3.4} & {\em ...} & {\em ...} \\ 
     20    {\em <=3.4} & {\em ...} & {\em ...} 
     21  \end{tabularx} 
     22} 
     23 
     24\clearpage 
     25 
    526%% ================================================================================================= 
    627\section{Curvilinear \zstar- or \sstar coordinate system} 
     
    126147is a multiple of \np{rdtbt}{rdtbt} in the \nam{dom}{dom} namelist (Figure III.3). 
    127148 
    128 %>   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   > 
    129149\begin{figure}[!t] 
    130150  \centering 
     
    150170  \label{fig:MBZ_dyn_dynspg_ts} 
    151171\end{figure} 
    152 %>   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   > 
    153172 
    154173The split-explicit formulation has a damping effect on external gravity waves, 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_time_domain.tex

    r11597 r11598  
    55\chapter{Time Domain} 
    66\label{chap:TD} 
     7 
     8\thispagestyle{plain} 
     9 
    710\chaptertoc 
     11 
     12\paragraph{Changes record} ~\\ 
     13 
     14{\footnotesize 
     15  \begin{tabularx}{\textwidth}{l||X|X} 
     16    Release & Author(s) & Modifications \\ 
     17    \hline 
     18    {\em   4.0} & {\em ...} & {\em ...} \\ 
     19    {\em   3.6} & {\em ...} & {\em ...} \\ 
     20    {\em   3.4} & {\em ...} & {\em ...} \\ 
     21    {\em <=3.4} & {\em ...} & {\em ...} 
     22  \end{tabularx} 
     23} 
     24 
     25\clearpage 
    826 
    927% Missing things: 
     
    1331  would help  ==> to be added} 
    1432%%%% 
    15  
    1633 
    1734Having defined the continuous equations in \autoref{chap:MB}, we need now to choose a time discretization, 
     
    291308\gmcomment{       % add a subsection here 
    292309 
    293 %        Time Domain 
    294 % ------------------------------------------------------------------------------------------------------------ 
    295310%% ================================================================================================= 
    296311\subsection{Time domain} 
     
    305320 
    306321}        %% end add 
    307  
    308  
    309322 
    310323%% 
  • NEMO/trunk/doc/tools/shr_func.sh

    r11212 r11598  
    22 
    33clean() { 
    4     ## Not sure if this step is needed, guess latexmk should be able to detect a change 
    54    printf "\t¤ Clean previous build" 
    6     find latex/$1/build -mindepth 1 -prune -not -name $1_manual.pyg -exec rm -rf {} \; 
    7  
    8     ## HTML exports 
    9     #printf '   - possible HTML export' 
    10     #find latex/$1 -type d -name 'html*'    -exec rm -r {} \; 
     5    find latex/$1/build -mindepth 1 -delete 
    116 
    127    echo 
     
    1510build() { 
    1611    printf "\t¤ Generation of the PDF format\n" 
    17     latexmk -r  ./latex/global/latexmkrc  \ 
    18        -cd ./latex/$1/main/$1_manual \ 
    19        1> /dev/null 
     12    latexmk -r  ./latex/global/latexmk.pl -pdfxe ./latex/$1/main/$1_manual \ 
     13#  1> /dev/null 
    2014    [ -f ./latex/$1/build/$1_manual.pdf ] && mv ./latex/$1/build/$1_manual.pdf . 
    2115    echo 
    2216} 
    23  
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