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Changeset 14257 for NEMO – NEMO

Changeset 14257 for NEMO


Ignore:
Timestamp:
2021-01-04T16:13:36+01:00 (3 years ago)
Author:
nicolasmartin
Message:

Overall review of LaTeX sources (not tested completely as of now):

  • Reworking global files: main document.tex, add glossary.tex, cosmetic changes...
  • Ignore missing namelists (namsbc_isf, namsbc_iscpl and namptr)
  • Removal of references for unused indices (\hfile, \ifile and \jp)
  • Update of .svnignore and svn:ignore properties accordingly
  • Split of manual abstract into a common NEMO abs for all and a specific one for each engine
  • Shrinking variables names used in the frontmatter
Location:
NEMO/trunk/doc
Files:
5 added
1 deleted
46 edited
3 copied
1 moved

Legend:

Unmodified
Added
Removed

  • NEMO/trunk/doc/latex/.svnignore

    r14113 r14257  
    1111*.toc 
    1212*.xdv 
    13 _minted-* 
     13cache* 

  • NEMO/trunk/doc/latex/NEMO/build

    • Property svn:ignore

      •  

        old new  
        1111*.toc 
        1212*.xdv 
        13 _minted-* 
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  • NEMO/trunk/doc/latex/NEMO/main/abstract.tex

    r11591 r14257  
    1 %% ================================================================ 
    2 %% Abstract 
    3 %% ================================================================ 
     1%% ================================================================================================= 
     2%% Specific abstract 
     3%% ================================================================================================= 
    44 
    5 %% Common part between NEMO-SI3-TOP 
    6 \NEMO\ (``Nucleus for European Modelling of the Ocean'') is a framework of ocean-related engines. 
    7 It is intended to be a flexible tool for studying the ocean dynamics and thermodynamics (``blue ocean''), 
    8 as well as its interactions with the components of the Earth climate system over 
    9 a wide range of space and time scales. 
    10 Within \NEMO, the ocean engine is interfaced with a sea-ice model (\SIcube\ or 
    11 \href{http://github.com/CICE-Consortium/CICE}{CICE}), 
    12 passive tracers and biogeochemical models (\TOP) and, 
    13 via the \href{http://portal.enes.org/oasis}{OASIS} coupler, 
    14 with several atmospheric general circulation models. 
    15 It also supports two-way grid embedding by means of the \href{http://agrif.imag.fr}{AGRIF} software. 
     5%% Common part 
     6\input{../../global/nemo} 
    167 
    178%% Specific part 

  • NEMO/trunk/doc/latex/NEMO/main/appendices.tex

    r14113 r14257  
     1%% ================================================================================================= 
     2%% Appendices 
     3%% ================================================================================================= 
    14 
    25\subfile{../subfiles/apdx_s_coord}      %% A. Generalised vertical coordinate 

  • NEMO/trunk/doc/latex/NEMO/main/authors.tex

    r11591 r14257  
    1 %Romain Bourdall\'{e}-Badie 
    2 %\orcid{0000-0002-8742-3289} \\ 
    3 %Mike Bell                   \\ 
    4 %J\'{e}r\^{o}me Chanut       \\ 
    5 %Emanuela Clementi 
    6 %\orcid{0000-0002-5752-1849} \\ 
    7 %Andrew Coward 
    8 %\orcid{0000-0002-0456-129X} \\ 
    9 %Massimiliano Drudi 
    10 %\orcid{0000-0002-9951-740X} \\ 
    11 %Christian \'{E}th\'{e}      \\ 
    12 %Doroteaciro Iovino 
    13 %\orcid{0000-0001-5132-7255} \\ 
    14 %Dan Lea                     \\ 
    15 %Claire L\'{e}vy 
    16 %\orcid{0000-0003-2518-6692} \\ 
    17 %Gurvan Madec 
    18 %\orcid{0000-0002-6447-4198} \\ 
    19 %Nicolas Martin              \\ 
    20 %S\'{e}bastien Masson 
    21 %\orcid{0000-0002-1694-8117} \\ 
    22 %Pierre Mathiot              \\ 
    23 %Silvia Mocavero 
    24 %\orcid{0000-0002-6309-8282} \\ 
    25 %Simon M\"{u}ller            \\ 
    26 %George Nurser               \\ 
    27 %Guillaume Samson 
    28 %\orcid{0000-0001-7481-6369} \\ 
    29 %Dave Storkey 
     1%% ================================================================================================= 
     2%% Authors 
     3%% ================================================================================================= 
    304 
     5\orcid{0000-0002-6447-4198} Gurvan Madec                \\ 
     6                            Mike Bell                   \\ 
    317\orcid{0000-0002-8742-3289} Romain Bourdall\'{e}-Badie  \\ 
    32                             Mike Bell                   \\ 
    338                            J\'{e}r\^{o}me Chanut       \\ 
    349\orcid{0000-0002-5752-1849} Emanuela Clementi           \\ 
    … …  
    3914                            Dan Lea                     \\ 
    4015\orcid{0000-0003-2518-6692} Claire L\'{e}vy             \\ 
    41 \orcid{0000-0002-6447-4198} Gurvan Madec                \\ 
    4216                            Nicolas Martin              \\ 
    4317\orcid{0000-0002-1694-8117} S\'{e}bastien Masson        \\ 

  • NEMO/trunk/doc/latex/NEMO/main/chapters.tex

    r14113 r14257  
    1 \subfile{../subfiles/chap_model_basics}   %% 1. 
    2 \subfile{../subfiles/chap_time_domain}    %% 2.  Time discretisation (time stepping strategy) 
    3 \subfile{../subfiles/chap_DOM}            %% 3.  Space discretisation 
    4 \subfile{../subfiles/chap_TRA}            %% 4.  Tracer advection/diffusion equation 
    5 \subfile{../subfiles/chap_DYN}            %% 5.  Dynamics : momentum equation 
    6 \subfile{../subfiles/chap_SBC}            %% 6.  Surface Boundary Conditions 
    7 \subfile{../subfiles/chap_LBC}            %% 7.  Lateral Boundary Conditions 
    8 \subfile{../subfiles/chap_LDF}            %% 8.  Lateral diffusion 
    9 \subfile{../subfiles/chap_ZDF}            %% 9.  Vertical diffusion 
    10 \subfile{../subfiles/chap_DIA}            %% 10. Outputs and Diagnostics 
    11 \subfile{../subfiles/chap_OBS}            %% 11. Observation operator 
    12 \subfile{../subfiles/chap_ASM}            %% 12. Assimilation increments 
    13 \subfile{../subfiles/chap_STO}            %% 13. Stochastic param. 
    14 \subfile{../subfiles/chap_misc}           %% 14. Miscellaneous topics 
    15 \subfile{../subfiles/chap_cfgs}           %% 15. Predefined configurations 
     1%% ================================================================================================= 
     2%% Chapters 
     3%% ================================================================================================= 
     4 
     5\subfile{../subfiles/chap_model_basics} %% Continuous equations and assumptions 
     6\subfile{../subfiles/chap_time_domain}  %% Time discretisation (time stepping strategy) 
     7\subfile{../subfiles/chap_DOM}          %% Space discretisation 
     8\subfile{../subfiles/chap_TRA}          %% Tracer advection/diffusion equation 
     9\subfile{../subfiles/chap_DYN}          %% Dynamics : momentum equation 
     10\subfile{../subfiles/chap_SBC}          %% Surface Boundary Conditions 
     11\subfile{../subfiles/chap_LBC}          %% Lateral Boundary Conditions 
     12\subfile{../subfiles/chap_LDF}          %% Lateral diffusion 
     13\subfile{../subfiles/chap_ZDF}          %% Vertical diffusion 
     14\subfile{../subfiles/chap_DIA}          %% Outputs and Diagnostics 
     15\subfile{../subfiles/chap_OBS}          %% Observation operator 
     16\subfile{../subfiles/chap_ASM}          %% Assimilation increments 
     17\subfile{../subfiles/chap_STO}          %% Stochastic param. 
     18\subfile{../subfiles/chap_misc}         %% Miscellaneous topics 
     19\subfile{../subfiles/chap_cfgs}         %% Predefined configurations 
    1620 
    1721%% Not included 

  • NEMO/trunk/doc/latex/NEMO/main/introduction.tex

    r11543 r14257  
    1  
    21\chapter*{Introduction} 
    3  
    4 %\chaptertoc 
    5  
    6 %\paragraph{Changes record} ~\\ 
    7  
    8 %\thispagestyle{plain} 
    9  
    10 %{\footnotesize 
    11 %  \begin{tabularx}{\textwidth}{l||X|X} 
    12 %    Release & Author(s) & Modifications \\ 
    13 %    \hline 
    14 %    {\em x.x} & {\em ...} & {\em ...}   \\ 
    15 %    {\em ...} & {\em ...} & {\em ...}   \\ 
    16 %  \end{tabularx} 
    17 %} 
    18  
    19 %\clearpage 
    202 
    213The \textbf{N}ucleus for \textbf{E}uropean \textbf{M}odelling of the \textbf{O}cean (\NEMO) is 

  • NEMO/trunk/doc/latex/NEMO/main/settings.tex

    r11591 r14257  
    1 %% Engine (subfolder name) 
    2 \def \engine{NEMO} 
     1%% Engine 
     2\def\eng{NEMO} 
    33 
    4 %% Cover page settings 
    5 \def \spacetop{  \vspace*{1.85cm} } 
    6 \def \heading{NEMO ocean engine} 
    7 %\def \subheading{} 
    8 \def \spacedown{ \vspace*{0.75cm } } 
    9 \def \authorswidth{ 0.3\linewidth} 
    10 \def \rulelenght{270pt} 
    11 \def \abstractwidth{0.6\linewidth} 
     4%% Cover page 
     5\def\spcup{\vspace*{2.15cm}} 
     6\def\hdg{NEMO ocean engine} 
     7%\def\shdg{} 
     8\def\spcdn{\vspace*{1cm}} 
     9\def\autwd{0.25\linewidth} 
     10\def\lnlg{270pt} 
     11\def\abswd{0.65\linewidth} 
    1212 
    13 %% Manual color (frontpage banner, links and chapter boxes) 
    14 \def \setmanualcolor{ \definecolor{manualcolor}{cmyk}{1, .60, 0, .4} } 
     13%% Color in cmyk model for manual theme (frontpage banner, links and chapter boxes) 
     14\def\clr{1,.60,0,.4} 
    1515 
    1616%% IPSL publication number 
    17 \def \ipslnum{27} 
     17\def\ipsl{27} 
    1818 
    19 %% Zenodo ID, i.e. doi:10.5281/zenodo.\([0-9]*\) 
    20 \def \zid{1464816} 
     19%% Zenodo ID, i.e. doi:10.5281/zenodo.\zid 
     20\def\zid{1464816} 

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

    r14178 r14257  
    77 
    88%    {\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} 
    119 
    1210\chaptertoc 
    … …  
    9189 \item [{\np{jphgr_mesh}{jphgr\_mesh}=0}]  The most general curvilinear orthogonal grids. 
    9290  The coordinates and their first derivatives with respect to $i$ and $j$ are provided 
    93   in a input file (\ifile{coordinates}), read in \rou{hgr\_read} subroutine of the domhgr module. 
     91  in a input file (\textit{coordinates.nc}), read in \rou{hgr\_read} subroutine of the domhgr module. 
    9492  This is now the only option available within \NEMO\ itself from v4.0 onwards. 
    9593\item [{\np{jphgr_mesh}{jphgr\_mesh}=1 to 5}] A few simple analytical grids are provided (see below). 
    … …  
    156154The reference coordinate transformation $z_0(k)$ defines the arrays $gdept_0$ and 
    157155$gdepw_0$ for $t$- and $w$-points, respectively. See \autoref{sec:DOMCFG_sco} for the 
    158 S-coordinate options.  As indicated on \autoref{fig:DOM_index_vert} \jp{jpk} is the number of 
    159 $w$-levels.  $gdepw_0(1)$ is the ocean surface.  There are at most \jp{jpk}-1 $t$-points 
     156S-coordinate options.  As indicated on \autoref{fig:DOM_index_vert} \texttt{jpk} is the number of 
     157$w$-levels.  $gdepw_0(1)$ is the ocean surface.  There are at most \texttt{jpk}-1 $t$-points 
    160158inside the ocean, the additional $t$-point at $jk = jpk$ is below the sea floor and is not 
    161159used.  The vertical location of $w$- and $t$-levels is defined from the analytic 
    … …  
    167165 
    168166It is possible to define a simple regular vertical grid by giving zero stretching 
    169 (\np[=0]{ppacr}{ppacr}).  In that case, the parameters \jp{jpk} (number of $w$-levels) 
     167(\np[=0]{ppacr}{ppacr}).  In that case, the parameters \texttt{jpk} (number of $w$-levels) 
    170168and \np{pphmax}{pphmax} (total ocean depth in meters) fully define the grid. 
    171169 
    … …  
    179177\end{gather} 
    180178 
    181 where $k = 1$ to \jp{jpk} for $w$-levels and $k = 1$ to $k = 1$ for $t-$levels.  Such an 
     179where $k = 1$ to \texttt{jpk} for $w$-levels and $k = 1$ to $k = 1$ for $t-$levels.  Such an 
    182180expression allows us to define a nearly uniform vertical location of levels at the ocean 
    183181top and bottom with a smooth hyperbolic tangent transition in between (\autoref{fig:DOMCFG_zgr}). 
    … …  
    227225\end{equation} 
    228226 
    229 With the choice of the stretching $h_{cr} = 3$ and the number of levels \jp{jpk}~$= 31$, 
     227With the choice of the stretching $h_{cr} = 3$ and the number of levels \texttt{jpk}~$= 31$, 
    230228the four coefficients $h_{sur}$, $h_0$, $h_1$, and $h_{th}$ in 
    231229\autoref{eq:DOMCFG_zgr_ana_2} have been determined such that \autoref{eq:DOMCFG_zgr_coef} 
    … …  
    245243  Values from $3$ to $10$ are usual. 
    246244\item \np{ppkth}{ppkth}~$= h_{th}$: is approximately the model level at which maximum stretching occurs 
    247   (nondimensional, usually of order 1/2 or 2/3 of \jp{jpk}) 
     245  (nondimensional, usually of order 1/2 or 2/3 of \texttt{jpk}) 
    248246\item \np{ppdzmin}{ppdzmin}: minimum thickness for the top layer (in meters). 
    249247\item \np{pphmax}{pphmax}: total depth of the ocean (meters). 
    … …  
    251249 
    252250As an example, for the $45$ layers used in the DRAKKAR configuration those parameters are: 
    253 \jp{jpk}~$= 46$, \np{ppacr}{ppacr}~$= 9$, \np{ppkth}{ppkth}~$= 23.563$, \np{ppdzmin}{ppdzmin}~$= 6~m$, 
     251\texttt{jpk}~$= 46$, \np{ppacr}{ppacr}~$= 9$, \np{ppkth}{ppkth}~$= 23.563$, \np{ppdzmin}{ppdzmin}~$= 6~m$, 
    254252\np{pphmax}{pphmax}~$= 5750~m$. 
    255253 
    … …  
    346344  This is meant for the "EEL-R5" configuration, a periodic or open boundary channel with a seamount. 
    347345\item [{\np[=1]{nn_bathy}{nn\_bathy}}]: read a bathymetry and ice shelf draft (if needed). 
    348   The \ifile{bathy\_meter} file (Netcdf format) provides the ocean depth (positive, in meters) at 
     346  The \textit{bathy\_meter.nc} file (Netcdf format) provides the ocean depth (positive, in meters) at 
    349347  each grid point of the model grid. 
    350348  The bathymetry is usually built by interpolating a standard bathymetry product (\eg\ ETOPO2) onto 
    … …  
    353351  no wet levels are defined (all levels are masked). 
    354352 
    355   The \ifile{isfdraft\_meter} file (Netcdf format) provides the ice shelf draft (positive, in meters) at 
     353  The \textit{isfdraft\_meter.nc} file (Netcdf format) provides the ice shelf draft (positive, in meters) at 
    356354  each grid point of the model grid. 
    357355  This file is only needed if \np[=.true.]{ln_isfcav}{ln\_isfcav}. 
    … …  
    396394bathymetry varies by less than one level thickness from one grid point to the next).  The 
    397395reference layer thicknesses $e_{3t}^0$ have been defined in the absence of bathymetry. 
    398 With partial steps, layers from 1 to \jp{jpk}-2 can have a thickness smaller than 
     396With partial steps, layers from 1 to \texttt{jpk-2} can have a thickness smaller than 
    399397$e_{3t}(jk)$. 
    400398 
    401 The model deepest layer (\jp{jpk}-1) is allowed to have either a smaller or larger 
     399The model deepest layer (\texttt{jpk-1}) is allowed to have either a smaller or larger 
    402400thickness than $e_{3t}(jpk)$: the maximum thickness allowed is $2*e_{3t}(jpk - 1)$. 
    403401 

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

    r11693 r14257  
    55\chapter{Note on some algorithms} 
    66\label{apdx:ALGOS} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 

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

    r11693 r14257  
    55\chapter{Diffusive Operators} 
    66\label{apdx:DIFFOPERS} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 

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

    r11693 r14257  
    55\chapter{Discrete Invariants of the Equations} 
    66\label{apdx:INVARIANTS} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 

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

    r11693 r14257  
    88%    {\em 4.0} & {\em Mike Bell} & {\em review}  \\ 
    99%    {\em 3.x} & {\em Gurvan Madec} & {\em original}  \\ 
    10  
    11 \thispagestyle{plain} 
    1210 
    1311\chaptertoc 

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

    r14113 r14257  
    1515\chapter{Iso-Neutral Diffusion and Eddy Advection using Triads} 
    1616\label{apdx:TRIADS} 
    17  
    18 \thispagestyle{plain} 
    1917 
    2018\chaptertoc 

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

    r11693 r14257  
    88%    {\em 4.0} & {\em D. J. Lea} & {\em \NEMO\ 4.0 updates}  \\ 
    99%    {\em 3.4} & {\em D. J. Lea, M. Martin, K. Mogensen, A. Weaver} & {\em Initial version}  \\ 
    10  
    11 \thispagestyle{plain} 
    1210 
    1311\chaptertoc 

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

    r13970 r14257  
    1111%    {\em 3.4} & {\em Gurvan Madec, Rachid Benshila, Andrew Coward } & {\em }  \\ 
    1212%    {\em }      & {\em Christian Ethe, Sebastien Masson } & {\em }  \\ 
    13  
    14 \thispagestyle{plain} 
    1513 
    1614\chaptertoc 
    … …  
    666664\end{forlines} 
    667665 
    668 \noindent will give the following file name radical: \ifile{myfile\_ORCA2\_19891231\_freq1d} 
     666\noindent will give the following file name radical: \textit{myfile\_ORCA2\_19891231\_freq1d} 
    669667 
    670668%% ================================================================================================= 
    … …  
    19421940When \np[=.true.]{ln_subbas}{ln\_subbas}, transports and stream function are computed for the Atlantic, Indian, 
    19431941Pacific and Indo-Pacific Oceans (defined north of 30\deg{S}) as well as for the World Ocean. 
    1944 The sub-basin decomposition requires an input file (\ifile{subbasins}) which contains three 2D mask arrays, 
     1942The sub-basin decomposition requires an input file (\textit{subbasins}) which contains three 2D mask arrays, 
    19451943the Indo-Pacific mask been deduced from the sum of the Indian and Pacific mask (\autoref{fig:DIA_mask_subasins}). 
    19461944 
    19471945\begin{listing} 
    1948   \nlst{namptr} 
     1946%  \nlst{namptr} 
    19491947  \caption{\forcode{&namptr}} 
    19501948  \label{lst:namptr} 

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

    r11693 r14257  
    55\chapter{Diurnal SST Models (DIU)} 
    66\label{chap:DIU} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 

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

    r11693 r14257  
    1414% -    domclo: closed sea and lakes.... 
    1515%              management of closea sea area: specific to global cfg, both forced and coupled 
    16  
    17 \thispagestyle{plain} 
    1816 
    1917\chaptertoc 
    … …  
    368366\label{subsec:DOM_size} 
    369367 
    370 The total size of the computational domain is set by the parameters \jp{jpiglo}, \jp{jpjglo} and 
    371 \jp{jpkglo} for the $i$, $j$ and $k$ directions, respectively. 
     368The total size of the computational domain is set by the parameters \texttt{jpiglo}, \texttt{jpjglo} and 
     369\texttt{jpkglo} for the $i$, $j$ and $k$ directions, respectively. 
    372370Note, that the variables \texttt{jpi} and \texttt{jpj} refer to 
    373371the size of each processor subdomain when the code is run in parallel using domain decomposition 
    … …  
    379377in which case \np{cn_cfg}{cn\_cfg} and \np{nn_cfg}{nn\_cfg} are set from these values accordingly). 
    380378 
    381 The global lateral boundary condition type is selected from 8 options using parameter \jp{jperio}. 
     379The global lateral boundary condition type is selected from 8 options using parameter \texttt{jperio}. 
    382380See \autoref{sec:LBC_jperio} for details on the available options and 
    383 the corresponding values for \jp{jperio}. 
     381the corresponding values for \texttt{jperio}. 
    384382 
    385383%% ================================================================================================= 
    … …  
    465463\begin{enumerate} 
    466464\item the bathymetry given in meters; 
    467 \item the number of levels of the model (\jp{jpk}); 
     465\item the number of levels of the model (\texttt{jpk}); 
    468466\item the analytical transformation $z(i,j,k)$ and the vertical scale factors 
    469467  (derivatives of the transformation); and 
    … …  
    575573every gridcell in the model regardless of the choice of vertical coordinate. 
    576574With constant z-levels, e3 metrics will be uniform across each horizontal level. 
    577 In the partial step case each e3 at the \jp{bottom\_level} 
    578 (and, possibly, \jp{top\_level} if ice cavities are present) 
     575In the partial step case each e3 at the \texttt{bottom\_level} 
     576(and, possibly, \texttt{top\_level} if ice cavities are present) 
    579577may vary from its horizontal neighbours. 
    580578And, in s-coordinates, variations can occur throughout the water column. 
    … …  
    585583those arising from a flat sea surface with zero elevation. 
    586584 
    587 The \jp{bottom\_level} and \jp{top\_level} 2D arrays define 
    588 the \jp{bottom\_level} and top wet levels in each grid column. 
    589 Without ice cavities, \jp{top\_level} is essentially a land mask (0 on land; 1 everywhere else). 
    590 With ice cavities, \jp{top\_level} determines the first wet point below the overlying ice shelf. 
     585The \texttt{bottom\_level} and \texttt{top\_level} 2D arrays define 
     586the \texttt{bottom\_level} and top wet levels in each grid column. 
     587Without ice cavities, \texttt{top\_level} is essentially a land mask (0 on land; 1 everywhere else). 
     588With ice cavities, \texttt{top\_level} determines the first wet point below the overlying ice shelf. 
    591589 
    592590%% ================================================================================================= 
    … …  
    594592\label{subsec:DOM_msk} 
    595593 
    596 From \jp{top\_level} and \jp{bottom\_level} fields, the mask fields are defined as follows: 
     594From \texttt{top\_level} and \texttt{bottom\_level} fields, the mask fields are defined as follows: 
    597595\begin{align*} 
    598596  tmask(i,j,k) &= 

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

    r14177 r14257  
    55\chapter{Ocean Dynamics (DYN)} 
    66\label{chap:DYN} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 

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

    r14178 r14257  
    55\chapter{Lateral Boundary Condition (LBC)} 
    66\label{chap:LBC} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 
    … …  
    161159 
    162160%% ================================================================================================= 
    163 \section[Model domain boundary condition (\forcode{jperio})]{Model domain boundary condition (\protect\jp{jperio})} 
     161\section{Model domain boundary condition (\forcode{jperio})} 
    164162\label{sec:LBC_jperio} 
    165163 
    … …  
    170168 
    171169%% ================================================================================================= 
    172 \subsection[Closed, cyclic (\forcode{=0,1,2,7})]{Closed, cyclic (\protect\jp{jperio}\forcode{=0,1,2,7})} 
     170\subsection{Closed, cyclic (\forcode{jperio={0,1,2,7}})} 
    173171\label{subsec:LBC_jperio012} 
    174172 
    175173The choice of closed or cyclic model domain boundary condition is made by 
    176 setting \jp{jperio} to 0, 1, 2 or 7 in namelist \nam{cfg}{cfg}. 
     174setting \forcode{jperio} to 0, 1, 2 or 7 in namelist \nam{cfg}{cfg}. 
    177175Each time such a boundary condition is needed, it is set by a call to routine \mdl{lbclnk}. 
    178176The computation of momentum and tracer trends proceeds from $i=2$ to $i=jpi-1$ and from $j=2$ to $j=jpj-1$, 
    … …  
    183181\begin{description} 
    184182 
    185 \item [For closed boundary (\jp{jperio}\forcode{=0})], solid walls are imposed at all model boundaries: 
     183\item [For closed boundary (\forcode{jperio=0})], solid walls are imposed at all model boundaries: 
    186184  first and last rows and columns are set to zero. 
    187185 
    188 \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 
     186\item [For cyclic east-west boundary (\forcode{jperio=1})], first and last rows are set to zero (closed) whilst the first column is set to 
    189187  the value of the last-but-one column and the last column to the value of the second one 
    190188  (\autoref{fig:LBC_jperio}-a). 
    191189  Whatever flows out of the eastern (western) end of the basin enters the western (eastern) end. 
    192190 
    193 \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 
     191\item [For cyclic north-south boundary (\forcode{jperio=2})], first and last columns are set to zero (closed) whilst the first row is set to 
    194192  the value of the last-but-one row and the last row to the value of the second one 
    195193  (\autoref{fig:LBC_jperio}-a). 
    196194  Whatever flows out of the northern (southern) end of the basin enters the southern (northern) end. 
    197195 
    198 \item [Bi-cyclic east-west and north-south boundary (\jp{jperio}\forcode{=7})] combines cases 1 and 2. 
     196\item [Bi-cyclic east-west and north-south boundary (\forcode{jperio=7})] combines cases 1 and 2. 
    199197 
    200198\end{description} 
    … …  
    209207 
    210208%% ================================================================================================= 
    211 \subsection[North-fold (\forcode{=3,6})]{North-fold (\protect\jp{jperio}\forcode{=3,6})} 
     209\subsection{North-fold (\forcode{jperio={3,6}})} 
    212210\label{subsec:LBC_north_fold} 
    213211 
    … …  
    288286Each processor is independent and without message passing or synchronous process, programs run alone and access just its own local memory. 
    289287For this reason, 
    290 the main model dimensions are now the local dimensions of the subdomain (pencil) that are named \jp{jpi}, \jp{jpj}, \jp{jpk}. 
     288the main model dimensions are now the local dimensions of the subdomain (pencil) that are named \texttt{jpi}, \texttt{jpj}, \texttt{jpk}. 
    291289These dimensions include the internal domain and the overlapping rows. 
    292 The number of rows to exchange (known as the halo) is usually set to one (nn\_hls=1, in \mdl{par\_oce}, 
     290The number of rows to exchange (known as the halo) is usually set to one (\forcode{nn_hls=1}, in \mdl{par\_oce}, 
    293291and must be kept to one until further notice). 
    294 The whole domain dimensions are named \jp{jpiglo}, \jp{jpjglo} and \jp{jpk}. 
     292The whole domain dimensions are named \texttt{jpiglo}, \texttt{jpjglo} and \texttt{jpk}. 
    295293The relationship between the whole domain and a sub-domain is: 
    296294\begin{gather*} 
    … …  
    299297\end{gather*} 
    300298 
    301 One also defines variables nldi and nlei which correspond to the internal domain bounds, and the variables nimpp and njmpp which are the position of the (1,1) grid-point in the global domain (\autoref{fig:LBC_mpp}). Note that since the version 4, there is no more extra-halo area as defined in \autoref{fig:LBC_mpp} so \jp{jpi} is now always equal to nlci and \jp{jpj} equal to nlcj. 
     299One also defines variables nldi and nlei which correspond to the internal domain bounds, and the variables nimpp and njmpp which are the position of the (1,1) grid-point in the global domain (\autoref{fig:LBC_mpp}). Note that since the version 4, there is no more extra-halo area as defined in \autoref{fig:LBC_mpp} so \texttt{jpi} is now always equal to nlci and \texttt{jpj} equal to nlcj. 
    302300 
    303301An element of $T_{l}$, a local array (subdomain) corresponds to an element of $T_{g}$, 
    … …  
    309307with $1 \leq i \leq jpi$, $1  \leq j \leq jpj $ , and  $1  \leq k \leq jpk$. 
    310308 
    311 The 1-d arrays $mig(1:\jp{jpi})$ and $mjg(1:\jp{jpj})$, defined in \rou{dom\_glo} routine (\mdl{domain} module), should be used to get global domain indices from local domain indices. The 1-d arrays, $mi0(1:\jp{jpiglo})$, $mi1(1:\jp{jpiglo})$ and $mj0(1:\jp{jpjglo})$, $mj1(1:\jp{jpjglo})$ have the reverse purpose and should be used to define loop indices expressed in global domain indices (see examples in \mdl{dtastd} module).\\ 
     309The 1-d arrays $mig(1:\texttt{jpi})$ and $mjg(1:\texttt{jpj})$, defined in \rou{dom\_glo} routine (\mdl{domain} module), should be used to get global domain indices from local domain indices. The 1-d arrays, $mi0(1:\texttt{jpiglo})$, $mi1(1:\texttt{jpiglo})$ and $mj0(1:\texttt{jpjglo})$, $mj1(1:\texttt{jpjglo})$ have the reverse purpose and should be used to define loop indices expressed in global domain indices (see examples in \mdl{dtastd} module).\\ 
    312310 
    313311The \NEMO\ model computes equation terms with the help of mask arrays (0 on land points and 1 on sea points). It is therefore possible that an MPI subdomain contains only land points. To save ressources, we try to supress from the computational domain as much land subdomains as possible. For example if $N_{mpi}$ processes are allocated to NEMO, the domain decomposition will be given by the following equation: 
    … …  
    372370The number of boundary sets is defined by \np{nb_bdy}{nb\_bdy}. 
    373371Each boundary set can be either defined as a series of straight line segments directly in the namelist 
    374 (\np[=.false.]{ln_coords_file}{ln\_coords\_file}, and a namelist block \forcode{&nambdy_index} must be included for each set) or read in from a file (\np[=.true.]{ln_coords_file}{ln\_coords\_file}, and a ``\ifile{coordinates.bdy}'' file must be provided). 
    375 The coordinates.bdy file is analagous to the usual \NEMO\ ``\ifile{coordinates}'' file. 
     372(\np[=.false.]{ln_coords_file}{ln\_coords\_file}, and a namelist block \forcode{&nambdy_index} must be included for each set) or read in from a file (\np[=.true.]{ln_coords_file}{ln\_coords\_file}, and a ``\textit{coordinates.bdy.nc}'' file must be provided). 
     373The coordinates.bdy file is analagous to the usual \NEMO\ ``\textit{coordinates.nc}'' file. 
    376374In the example above, there are two boundary sets, the first of which is defined via a file and 
    377375the second is defined in the namelist. 
    … …  
    570568 
    571569The boundary geometry for each set may be defined in a namelist \forcode{&nambdy_index} or 
    572 by reading in a ``\ifile{coordinates.bdy}'' file. 
    573 The \texttt{nambdy\_index} namelist defines a series of straight-line segments for north, east, south and west boundaries. 
    574 One \texttt{nambdy\_index} namelist block is needed for each boundary condition defined by indexes. 
     570by reading in a ``\textit{coordinates.bdy.nc}'' file. 
     571The \forcode{&nambdy_index} namelist defines a series of straight-line segments for north, east, south and west boundaries. 
     572One \forcode{&nambdy_index} namelist block is needed for each boundary condition defined by indexes. 
    575573For the northern boundary, \texttt{nbdysegn} gives the number of segments, 
    576 \jp{jpjnob} gives the $j$ index for each segment and \jp{jpindt} and 
    577 \jp{jpinft} give the start and end $i$ indices for each segment with similar for the other boundaries. 
     574\texttt{jpjnob} gives the $j$ index for each segment and \texttt{jpindt} and 
     575\texttt{jpinft} give the start and end $i$ indices for each segment with similar for the other boundaries. 
    578576These segments define a list of $T$ grid points along the outermost row of the boundary ($nbr\,=\, 1$). 
    579577The code deduces the $U$ and $V$ points and also the points for $nbr\,>\, 1$ if \np[>1]{nn_rimwidth}{nn\_rimwidth}. 
    580578 
    581 The boundary geometry may also be defined from a ``\ifile{coordinates.bdy}'' file. 
     579The boundary geometry may also be defined from a ``\textit{coordinates.bdy.nc}'' file. 
    582580\autoref{fig:LBC_nc_header} gives an example of the header information from such a file, based on the description of geometrical setup given above. 
    583581The file should contain the index arrays for each of the $T$, $U$ and $V$ grids. 
    … …  
    633631  \centering 
    634632  \includegraphics[width=0.66\textwidth]{LBC_nc_header} 
    635   \caption[Header for a \protect\ifile{coordinates.bdy} file]{ 
    636     Example of the header for a \protect\ifile{coordinates.bdy} file} 
     633  \caption[Header for a \textit{coordinates.bdy.nc} file]{ 
     634    Example of the header for a \textit{coordinates.bdy.nc} file} 
    637635  \label{fig:LBC_nc_header} 
    638636\end{figure} 
    … …  
    684682\texttt{<constituent>\_z1} and \texttt{<constituent>\_z2} for the real and imaginary parts of 
    685683SSH, respectively, are expected to be available in file 
    686 \ifile{<input>\_grid\_T}, variables \texttt{<constituent>\_u1} and 
     684\textit{<input>\_grid\_T.nc}, variables \texttt{<constituent>\_u1} and 
    687685\texttt{<constituent>\_u2} for the real and imaginary parts of u, respectively, in file 
    688 \ifile{<input>\_grid\_U}, and \texttt{<constituent>\_v1} and 
     686\textit{<input>\_grid\_U.nc}, and \texttt{<constituent>\_v1} and 
    689687\texttt{<constituent>\_v2} for the real and imaginary parts of v, respectively, in file 
    690 \ifile{<input>\_grid\_V}; when data along open boundary segments is used, 
     688\textit{<input>\_grid\_V.nc}; when data along open boundary segments is used, 
    691689variables \texttt{z1} and \texttt{z2} (real and imaginary part of SSH) are 
    692 expected to be available in file \ifile{<input><constituent>\_grid\_T}, 
     690expected to be available in file \textit{<input><constituent>\_grid\_T.nc}, 
    693691variables \texttt{u1} and \texttt{u2} (real and imaginary part of u) in file 
    694 \ifile{<input><constituent>\_grid\_U}, and variables \texttt{v1} and \texttt{v2} 
     692\textit{<input><constituent>\_grid\_U.nc}, and variables \texttt{v1} and \texttt{v2} 
    695693(real and imaginary part of v) in file 
    696 \ifile{<input><constituent>\_grid\_V}.\par 
     694\textit{<input><constituent>\_grid\_V.nc}.\par 
    697695 
    698696Note that the barotropic velocity components are assumed to be defined 

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

    r14113 r14257  
    55\chapter{Lateral Ocean Physics (LDF)} 
    66\label{chap:LDF} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 

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

    r14177 r14257  
    1414%    {\em --\texttt{"}--} & {\em ... K. Mogensen, A. Vidard, A. Weaver} & {\em ---\texttt{"}---}  \\ 
    1515%\end{tabular} 
    16  
    17 \thispagestyle{plain} 
    1816 
    1917\chaptertoc 
    … …  
    420418 
    421419To use Sea Level Anomaly (SLA) data the mean dynamic topography (MDT) must be provided in a separate file defined on 
    422 the model grid called \ifile{slaReferenceLevel}. 
     420the model grid called \textit{slaReferenceLevel.nc}. 
    423421The MDT is required in order to produce the model equivalent sea level anomaly from the model sea surface height. 
    424422Below is an example header for this file (on the ORCA025 grid). 

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

    r14177 r14257  
    55\chapter{Surface Boundary Condition (SBC, SAS, ISF, ICB, TDE)} 
    66\label{chap:SBC} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 
    … …  
    646644parameters. It is therefore recommended to chose version 3.6 over 3. 
    647645 
    648 \subsection{Cool-skin and warm-layer parametrizations} 
    649 %\subsection[Cool-skin and warm-layer parameterizations (\forcode{ln_skin_cs} \& \forcode{ln_skin_wl})]{Cool-skin and warm-layer parameterizations (\protect\np{ln_skin_cs}{ln\_skin\_cs} \& \np{ln_skin_wl}{ln\_skin\_wl})} 
     646\subsection[Cool-skin and warm-layer parameterizations (   \forcode{ln_skin_cs}               \& \forcode{ln_skin_wl}              )] 
     647           {Cool-skin and warm-layer parameterizations (\protect\np{ln_skin_cs}{ln\_skin\_cs} \&      \np{ln_skin_wl}{ln\_skin\_wl})} 
    650648\label{subsec:SBC_skin} 
    651649 
    … …  
    979977  ocean tide model}: Mf, Mm, Ssa, Mtm, Msf, Msqm, Sa, K1, O1, P1, Q1, J1, S1, 
    980978M2, S2, N2, K2, nu2, mu2, 2N2, L2, T2, eps2, lam2, R2, M3, MKS2, MN4, MS4, M4, 
    981 N4, S4, M6, and M8; see file \hf{tide} and \mdl{tide\_mod} for further 
     979N4, S4, M6, and M8; see file \textit{tide.h90} and \mdl{tide\_mod} for further 
    982980information and references\footnote{As a legacy option \np{ln_tide_var} can be 
    983981  set to \forcode{0}, in which case the 19 tidal constituents (M2, N2, 2N2, S2, 
    984982  K2, K1, O1, Q1, P1, M4, Mf, Mm, Msqm, Mtm, S1, MU2, NU2, L2, and T2; see file 
    985   \hf{tide}) and associated parameters that have been available in NEMO version 
     983  \textit{tide.h90}) and associated parameters that have been available in NEMO version 
    986984  4.0 and earlier are available}. Constituents to be included in the tidal forcing 
    987985(surface and lateral boundaries) are selected by enumerating their respective 
    … …  
    10131011potential). The tidal tilt factor $\gamma = 1 + k - h$ includes the 
    10141012Love numbers $k$ and $h$ \citep{love_PRSL09}; this factor is 
    1015 configurable using \np{rn_tide_gamma} (default value 0.7). Optionally, 
     1013configurable using \np{rn_tide_gamma}{rn\_tide\_gamma} (default value 0.7). Optionally, 
    10161014when \np[=.true.]{ln_tide_ramp}{ln\_tide\_ramp}, the equilibrium tidal 
    10171015forcing can be ramped up linearly from zero during the initial 
    … …  
    11871185 
    11881186\begin{listing} 
    1189   \nlst{namsbc_isf} 
     1187%  \nlst{namsbc_isf} 
    11901188  \caption{\forcode{&namsbc_isf}} 
    11911189  \label{lst:namsbc_isf} 
    … …  
    12921290 
    12931291\begin{listing} 
    1294   \nlst{namsbc_iscpl} 
     1292%  \nlst{namsbc_iscpl} 
    12951293  \caption{\forcode{&namsbc_iscpl}} 
    12961294  \label{lst:namsbc_iscpl} 

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

    r11693 r14257  
    55\chapter{Stochastic Parametrization of EOS (STO)} 
    66\label{chap:STO} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 

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

    r13476 r14257  
    55\chapter{Ocean Tracers (TRA)} 
    66\label{chap:TRA} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 
    … …  
    930928When \np{nn_geoflx}{nn\_geoflx} is set to 2, 
    931929a spatially varying geothermal heat flux is introduced which is provided in 
    932 the \ifile{geothermal\_heating} NetCDF file 
     930the \textit{geothermal\_heating.nc} NetCDF file 
    933931(\autoref{fig:TRA_geothermal}) \citep{emile-geay.madec_OS09}. 
    934932 
    … …  
    11511149\citep{madec.delecluse.ea_JPO96}. 
    11521150 
    1153 For generating \ifile{resto}, 
     1151For generating \textit{resto.nc}, 
    11541152see the documentation for the DMP tools provided with the source code under \path{./tools/DMP_TOOLS}. 
    11551153 
    … …  
    11751173$\gamma$ is initialized as \np{rn_atfp}{rn\_atfp}, its default value is \forcode{10.e-3}. 
    11761174Note that the forcing correction term in the filter is not applied in linear free surface 
    1177 (\jp{ln\_linssh}\forcode{=.true.}) (see \autoref{subsec:TRA_sbc}). 
     1175(\np[=.true.]{ln_linssh}{ln\_linssh}) (see \autoref{subsec:TRA_sbc}). 
    11781176Not also that in constant volume case, the time stepping is performed on $T$, 
    11791177not on its content, $e_{3t}T$. 

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

    r14177 r14257  
    88\chapter{Vertical Ocean Physics (ZDF)} 
    99\label{chap:ZDF} 
    10  
    11 \thispagestyle{plain} 
    1210 
    1311\chaptertoc 
    … …  
    11811179These values are assigned in \mdl{zdfdrg}. 
    11821180Note that there is support for local enhancement of these values via an externally defined 2D mask array 
    1183 (\np[=.true.]{ln_boost}{ln\_boost}) given in the \ifile{bfr\_coef} input NetCDF file. 
     1181(\np[=.true.]{ln_boost}{ln\_boost}) given in the \textit{bfr\_coef.nc} input NetCDF file. 
    11841182The mask values should vary from 0 to 1. 
    11851183Locations with a non-zero mask value will have the friction coefficient increased by 

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

    r14196 r14257  
    55\chapter{Configurations} 
    66\label{chap:CFGS} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 
    … …  
    8583the SI3 model (ORCA-ICE) and possibly with PISCES biogeochemical model (ORCA-ICE-PISCES). 
    8684An appropriate namelist is available in \path{./cfgs/ORCA2_ICE_PISCES/EXPREF/namelist_cfg} for ORCA2. 
    87 The domain of ORCA2 configuration is defined in \ifile{ORCA\_R2\_zps\_domcfg} file, 
     85The domain of ORCA2 configuration is defined in \textit{ORCA\_R2\_zps\_domcfg.nc} file, 
    8886this file is available in tar file on the \NEMO\ community zenodo platform: \\ 
    8987https://doi.org/10.5281/zenodo.2640723 
    … …  
    152150Each of configuration is set through the \textit{domain\_cfg} domain configuration file, 
    153151which sets the grid size and configuration name parameters. 
    154 The \NEMO\ System Team provides only ORCA2 domain input file "\ifile{ORCA\_R2\_zps\_domcfg}" file 
     152The \NEMO\ System Team provides only ORCA2 domain input file "\textit{ORCA\_R2\_zps\_domcfg.nc}" file 
    155153(\autoref{tab:CFGS_ORCA}). 
    156154 
    … …  
    158156  \centering 
    159157  \begin{tabular}{p{4cm} c c c c} 
    160     Horizontal Grid & \jp{ORCA\_index} & \jp{jpiglo} & \jp{jpjglo} \\ 
     158    Horizontal Grid & \texttt{ORCA\_index} & \texttt{jpiglo} & \texttt{jpjglo} \\ 
    161159    \hline \hline 
    162160    % 4   \deg\ &              4   &          92 &          76 \\ 
    … …  
    246244Its horizontal resolution (and thus the size of the domain) is determined by 
    247245setting \np{nn_GYRE}{nn\_GYRE} in \nam{usr_def}{usr\_def}: 
     246 
    248247\begin{align*} 
    249   \jp{jpiglo} = 30 \times \text{\np{nn_GYRE}{nn\_GYRE}} + 2 + 2 \times \text{\np{nn_hls}{nn\_hls}} \\ 
    250   \jp{jpjglo} = 20 \times \text{\np{nn_GYRE}{nn\_GYRE}} + 2 + 2 \times \text{\np{nn_hls}{nn\_hls}} 
     248   jpiglo = 30 \times \text{\np{nn_GYRE}{nn\_GYRE}} + 2 + 2 \times \text{\np{nn_hls}{nn\_hls}} \\ 
     249   jpjglo = 20 \times \text{\np{nn_GYRE}{nn\_GYRE}} + 2 + 2 \times \text{\np{nn_hls}{nn\_hls}} 
    251250\end{align*} 
    252251 
    253252Obviously, the namelist parameters have to be adjusted to the chosen resolution, 
    254253see the Configurations pages on the \NEMO\ web site (\NEMO\ Configurations). 
    255 In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}\forcode{ = 31}) (\autoref{fig:DOM_zgr_e3}). 
     254In the vertical, GYRE uses the default 30 ocean levels (\forcode{jpk = 31}, \autoref{fig:DOM_zgr_e3}). 
    256255 
    257256\begin{listing} 

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

    r11693 r14257  
    55\chapter{Invariants of the Primitive Equations} 
    66\label{chap:CONS} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 

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

    r14113 r14257  
    55\chapter{Miscellaneous Topics} 
    66\label{chap:MISC} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 
    … …  
    205203 
    206204\noindent Consider an ORCA1 
    207 configuration using the extended grid domain configuration file: \ifile{eORCA1\_domcfg.nc} 
     205configuration using the extended grid domain configuration file: \textit{eORCA1\_domcfg.nc} 
    208206This file define a horizontal domain of 362x332.  The first row with 
    209207open ocean wet points in the non-isf bathymetry for this set is row 42 (\fortran\ indexing) 
    … …  
    226224\noindent Note that with this option, the j-size of the global domain is (extended 
    227225j-size minus \np{open_ocean_jstart}{open\_ocean\_jstart} + 1 ) and this must match the \texttt{jpjglo} value 
    228 for the configuration. This means an alternative version of \ifile{eORCA1\_domcfg.nc} must 
     226for the configuration. This means an alternative version of \textit{eORCA1\_domcfg.nc} must 
    229227be created for when \np{ln_use_jattr}{ln\_use\_jattr} is active. The \texttt{ncap2} tool provides a 
    230228convenient way of achieving this: 
    … …  
    234232\end{cmds} 
    235233 
    236 The domain configuration file is unique in this respect since it also contains the value of \jp{jpjglo} 
     234The domain configuration file is unique in this respect since it also contains the value of \texttt{jpjglo} 
    237235that is read and used by the model. 
    238236Any other global, 2D and 3D, netcdf, input field can be prepared for use in a reduced domain by adding the 
    … …  
    374372 
    375373When more information is required for monitoring or debugging purposes, the various 
    376 forms of output can be selected via the \np{sn\_cfctl} structure. As well as simple 
     374forms of output can be selected via the \np{sn_cfctl}{sn\_cfctl} structure. As well as simple 
    377375on-off switches this structure also allows selection of a range of processors for 
    378376individual reporting (where appropriate) and a time-increment option to restrict 
    … …  
    449447systems so bug-hunting efforts using this facility should also utilise the \fortran: 
    450448 
    451 \begin{forlines}  
    452    CALL FLUSH(numout) 
    453 \end{forlines} 
     449\forline|CALL FLUSH(numout)| 
    454450 
    455451statement after any additional write statements to ensure that file contents reflect 
    … …  
    482478 
    483479\begin{forlines} 
    484    sn_cfctl%l_glochk = .FALSE.    ! Range sanity checks are local (F) or global (T). Set T for debugging only 
    485    sn_cfctl%l_allon  = .FALSE.    ! IF T activate all options. If F deactivate all unless l_config is T 
    486      sn_cfctl%l_config = .TRUE.     ! IF .true. then control which reports are written with the following 
    487        sn_cfctl%l_runstat = .FALSE. ! switches and which areas produce reports with the proc integer settings. 
    488        sn_cfctl%l_trcstat = .FALSE. ! The default settings for the proc integers should ensure 
    489        sn_cfctl%l_oceout  = .FALSE. ! that  all areas report. 
    490        sn_cfctl%l_layout  = .FALSE. ! 
    491        sn_cfctl%l_prtctl  = .FALSE. ! 
    492        sn_cfctl%l_prttrc  = .FALSE. ! 
    493        sn_cfctl%l_oasout  = .FALSE. ! 
    494        sn_cfctl%procmin   = 0       ! Minimum area number for reporting [default:0] 
    495        sn_cfctl%procmax   = 1000000 ! Maximum area number for reporting [default:1000000] 
    496        sn_cfctl%procincr  = 1       ! Increment for optional subsetting of areas [default:1] 
    497        sn_cfctl%ptimincr  = 1       ! Timestep increment for writing time step progress info 
     480   sn_cfctl%l_glochk  = .false. ! Range sanity checks are local (F) or global (T). Set T for debugging only 
     481   sn_cfctl%l_allon   = .false. ! IF T activate all options. If F deactivate all unless l_config is T 
     482   sn_cfctl%l_config  = .true.  ! IF .true. then control which reports are written with the following 
     483   sn_cfctl%l_runstat = .false. ! switches and which areas produce reports with the proc integer settings. 
     484   sn_cfctl%l_trcstat = .false. ! The default settings for the proc integers should ensure 
     485   sn_cfctl%l_oceout  = .false. ! that  all areas report. 
     486   sn_cfctl%l_layout  = .false. ! 
     487   sn_cfctl%l_prtctl  = .false. ! 
     488   sn_cfctl%l_prttrc  = .false. ! 
     489   sn_cfctl%l_oasout  = .false. ! 
     490   sn_cfctl%procmin   = 0       ! Minimum area number for reporting [default:0] 
     491   sn_cfctl%procmax   = 1000000 ! Maximum area number for reporting [default:1000000] 
     492   sn_cfctl%procincr  = 1       ! Increment for optional subsetting of areas [default:1] 
     493   sn_cfctl%ptimincr  = 1       ! Timestep increment for writing time step progress info 
    498494\end{forlines} 
    499495 

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

    r14113 r14257  
    55\chapter{Model Basics} 
    66\label{chap:MB} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 

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

    r14178 r14257  
    44 
    55\chapter{ essai \zstar \sstar} 
    6  
    7 \thispagestyle{plain} 
    86 
    97\chaptertoc 

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

    r11693 r14257  
    55\chapter{Time Domain} 
    66\label{chap:TD} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 

  • NEMO/trunk/doc/latex/SI3/build

    • Property svn:ignore

      •  

        old new  
        1111*.toc 
        1212*.xdv 
        13 _minted-* 
         13cache* 

  • NEMO/trunk/doc/latex/TOP/build

    • Property svn:ignore

      •  

        old new  
        1111*.toc 
        1212*.xdv 
        13 _minted-* 
         13cache* 

  • NEMO/trunk/doc/latex/global

    • Property svn:ignore set to
      *.aux
      *.bbl
      *.blg
      *.fdb*
      *.fls
      *.idx
      *.ilg
      *.ind
      *.lo*
      *.out
      *.toc
      *.xdv
      cache*

  • NEMO/trunk/doc/latex/global/document.tex

    r14113 r14257  
    1  
    21%% ================================================================================================= 
    3 %% Template structure for reference manuals 
     2%% Manual structure 
    43%% ================================================================================================= 
    54 
    6 %% NEMO release version 
    7 \def \version{trunk} 
    8  
    9 %% Preamble 
     5%% Preamble: global configuration 
    106%% ================================================================================================= 
    117 
    12 %% Document layout 
    13 \documentclass[fontsize = 10pt, twoside, abstract]{scrreprt} 
     8%% Layout 
     9%\documentclass[fontsize=10pt,twoside,abstract,draft]{scrreprt} 
     10\documentclass[fontsize=10pt,twoside,abstract      ]{scrreprt} 
    1411 
    15 %% Load manual configuration 
    16 \input{../../global/prologue} 
     12%% Overall configuration  
     13\input{../../global/preamble} 
    1714 
    18 %% End of common preamble between main and sub-files 
    19 %% Override custom cmds for full manual compilation 
    20 \newcommand{\subinc}[1]{#1} 
    21 \newcommand{\subexc}[1]{} 
     15%% Special cmds around to {in,ex}clude content only in subfile 
     16  \newcommand{\subinc}[1]{#1} 
     17  \newcommand{\subexc}[1]{  } 
    2218 
    2319\begin{document} 
    2420 
    25 \renewcommand{\subinc}[1]{} 
     21\renewcommand{\subinc}[1]{  } 
    2622\renewcommand{\subexc}[1]{#1} 
    2723 
    28  
    29 %% Frontmatter 
     24%% Frontmatter: covers 
     25%% ({sub}title, DOI, authors, abstract and color theme are specific to each manual) 
    3026%% ================================================================================================= 
    3127 
     28%\frontmatter %% Not recognized in 'scrreprt' document class 
    3229\pagenumbering{gobble}   %% Disable page numbering temporarily 
     30\pagestyle{empty} 
    3331 
    34 %% Title page 
    3532\input{../../global/frontpage} 
    36  
    37 %% Footer for introductory parts (no header by cleaning default) 
    38 \ofoot[]{\engine\ Reference Manual} \ifoot[]{\pagemark} 
    39  
    40 %% Information page (2nd page) 
    4133\input{../../global/info_page} 
    4234 
     35\cleardoublepage 
     36 
     37\pagenumbering{Roman} %% Reactivate page numbering (uppercase roman numbers) 
     38\pagestyle{plain} 
     39%\lastpageref{pagesLTS.0} 
     40 
     41\tableofcontents 
    4342\listoffigures 
    4443\listoflistings 
    4544\listoftables 
     45%\listoftodos 
     46%\lastpageref{pagesLTS.Roman} 
    4647 
    47 \clearpage 
     48\cleardoublepage 
    4849 
    49 \pagenumbering{roman} 
    50 \ofoot[]{\engine\ Reference Manual} \ifoot[]{\pagemark} 
     50%% Mainmatter: toc, lists, introduction and primary chapters 
     51%% ================================================================================================= 
     52 
     53%\mainmatter %% Not recognized in 'scrreprt' document class 
     54\pagenumbering{arabic} %% Standard page numbering 
     55\pagestyle{plain} 
    5156 
    5257\input{introduction} 
    5358 
    54 %% Table of Contents 
    55 \tableofcontents 
     59\cleardoublepage 
    5660 
    57 \clearpage 
     61\pagestyle{scrheadings} 
     62\renewcommand{\chapterpagestyle}{empty} 
    5863 
     64\input{chapters} 
    5965 
    60 %% Mainmatter 
     66%% Appendix: subordinate chapters 
    6167%% ================================================================================================= 
    6268 
    63 %% Headings for document body 
    64 \pagenumbering{arabic} 
    65 \lohead{Chap.\ \thechapter\ \leftmark} \rehead{Sect.\ \thesection\ \rightmark} 
    66 \ifoot[]{Page\ \pagemark\ of \pageref*{LastPage}} 
     69\appendix %% Chapter numbering with letters by now 
     70\lohead{Apdx \thechapter\ \leftmark} 
    6771 
    68 \include{chapters} 
     72\input{appendices} 
    6973 
     74\input{../../global/coding_rules} %% Add coding rules on every manual 
    7075 
    71 %% Appendix 
     76%\lastpageref{pagesLTS.arabic} 
     77\cleardoublepage 
     78 
     79%% Backmatter: bibliography, glossaries and indices 
    7280%% ================================================================================================= 
    7381 
    74 \appendix   %% Chapter numbering with letters by now 
    75 \lohead{Apdx\ \thechapter\ \leftmark} 
    76 \include{appendices} 
     82%\backmatter %% Not recognized in 'scrreprt' document class 
     83\pagenumbering{roman} %% Lowercase roman numbers 
     84\pagestyle{plain} 
    7785 
    78 %% Append coding rules for every manual 
    79 \input{../../global/coding_rules} 
    80  
    81  
    82 %% Backmatter 
    83 %% ================================================================================================= 
    84  
    85 %% Bibliography and indexes 
    8686\input{../../global/epilogue} 
    8787 
     88%\lastpageref{pagesLTS.roman} 
     89 
    8890\end{document} 

  • NEMO/trunk/doc/latex/global/epilogue.tex

    r11907 r14257  
    1  
    2 \clearpage 
     1%% ================================================================================================= 
     2%% Backmatter 
     3%% ================================================================================================= 
    34 
    45%% Bibliography 
     6%% ================================================================================================= 
     7 
    58\phantomsection 
    69\addcontentsline{toc}{chapter}{Bibliography} 
    7 \lohead{Bibliography} \rehead{Bibliography} 
     10\lohead{Bibliography} 
     11\rehead{Bibliography} 
    812\bibliography{../main/bibliography} 
    913 
    1014\clearpage 
    1115 
    12 %% Indexes 
     16%% Indices 
     17%% ================================================================================================= 
     18 
    1319\phantomsection 
    14 \addcontentsline{toc}{chapter}{Indexes} 
    15 \lohead{Indexes} \rehead{Indexes} 
     20\addcontentsline{toc}{chapter}{Indices} 
     21\lohead{Indices} 
     22\rehead{Indices} 
    1623\printindex[blocks] 
    1724\printindex[keys] 
    … …  
    1926\printindex[parameters] 
    2027\printindex[subroutines] 
     28 
     29\clearpage 
     30 
     31%% Glossary 
     32%% ================================================================================================= 
     33 
     34%\phantomsection 
     35%\addcontentsline{toc}{chapter}{Glossary} 
     36%\lohead{Glossary}\rehead{Glossary} 
     37%\printglossaries 

  • NEMO/trunk/doc/latex/global/frontpage.tex

    r14113 r14257  
     1%% ================================================================================================= 
     2%% Front cover 
     3%% ================================================================================================= 
    14 
    25\begin{titlepage} 
    3 %  \newgeometry{hmargin = 1.5cm, vmargin = 3cm} 
    4   \setlength{\parindent}{0pt} 
     6%   \newgeometry{hmargin=1.5cm,vmargin=3cm} 
     7   \setlength{\parindent}{0pt} 
    58 
    6   \begin{center} 
    7     \begin{minipage}{0.3\textwidth} 
    8       \includegraphics[height=1.5cm]{logos/NEMO_grey} 
    9     \end{minipage}\begin{minipage}{0.6\textwidth} 
    10       \begin{center} 
    11       \Large\slshape 
    12       \textbf{N}ucleus for \textbf{E}uropean \textbf{M}odelling of the \textbf{O}cean \\ 
     9   \begin{center} 
     10 
     11      \begin{minipage}{0.3\textwidth} 
     12         \includegraphics[height=1.5cm]{NEMO_grey} 
     13      \end{minipage} %% Don't insert void line between `minipage` envs 
     14      \begin{minipage}{0.6\textwidth} 
     15         \begin{center} 
     16            \Large\slshape 
     17            \textbf{N}ucleus for \textbf{E}uropean \textbf{M}odelling of the \textbf{O}cean \\ 
     18            \medskip 
     19            \hyperref[resources]{ 
     20               \faWordpress \hspace{1cm} \faCodeFork      \hspace{1cm} 
     21               \faGithub    \hspace{1cm} \faCloudDownload \hspace{1cm} \faEnvelope 
     22            } 
     23         \end{center} 
     24      \end{minipage} 
     25 
     26   \end{center} 
     27 
     28   \spcup 
     29   \textcolor{white}{\fontsize{0.8cm}{0.8cm}\selectfont\textbf{\hdg}} 
     30   \ifdef{\shdg}{\medskip\par\textcolor{white}{\Huge\shdg}}{} 
     31   \spcdn 
     32 
     33   \begin{center} 
     34      \LARGE Version {\ver} - {\today} \\ 
    1335      \medskip 
    14       \hyperref[resources]{\textcolor{black}{ 
    15           \faWordpress \hspace{0.75cm} \faCodeFork      \hspace{0.75cm} 
    16           \faGithub    \hspace{0.75cm} \faCloudDownload \hspace{0.75cm} \faEnvelope 
    17         } 
    18       } 
    19       \end{center} 
    20     \end{minipage} 
    21   \end{center} 
     36      \href{http://doi.org/10.5281/zenodo.\zid}{\includegraphics{zenodo.\zid}} 
     37   \end{center} 
    2238 
    23   \spacetop 
    24   \textcolor{white}{\fontsize{0.8cm}{0.8cm}\selectfont\textbf{\heading}} 
    25   \ifdef{\subheading}{ 
    26     \medskip 
    27     \par 
    28     \textcolor{white}{\Huge \subheading} 
    29   }{} 
    30   \spacedown 
     39   \vfill 
    3140 
    32   \begin{center} 
    33     \LARGE Version \version\ -\ \today \\ 
    34     \medskip 
    35     \href{http://doi.org/10.5281/zenodo.\zid}{ \includegraphics{badges/zenodo.\zid} } 
    36   \end{center} 
     41   \begin{minipage}{\autwd} 
     42      \raggedleft\input{authors} 
     43   \end{minipage} 
     44   \hspace{15pt} %% Don't insert void line between `minipage` envs 
     45   \begin{minipage}{0.02\linewidth} 
     46      \rule{1pt}{\lnlg} 
     47   \end{minipage} 
     48   \hspace{ 5pt} %%   "     ""    ""   ""     "        ""      "" 
     49   \begin{minipage}{\abswd} 
     50      \begin{abstract} 
     51         \input{abstract} 
     52      \end{abstract} 
     53   \end{minipage} 
    3754 
    38   \vfill 
     55   \vfill 
    3956 
    40   \begin{minipage}{\authorswidth} 
    41     \raggedleft 
    42     \input{authors} 
    43   \end{minipage}\hspace{15pt}\begin{minipage}{0.02\linewidth} 
    44     \rule{1pt}{\rulelenght} 
    45   \end{minipage}\hspace{ 5pt}\begin{minipage}{\abstractwidth} 
    46     \begin{abstract} 
    47       \input{abstract} 
    48     \end{abstract} 
    49   \end{minipage} 
    50  
    51   \vfill 
    52  
    53   \begin{center} 
    54     \Large 
    55     \href{http://www.cmcc.it          }{ \includegraphics[height=1cm]{logos/CMCC} } \hspace{0.25cm} 
    56     \href{http://www.cnrs.fr          }{ \includegraphics[height=1cm]{logos/CNRS} } \hspace{0.25cm} 
    57     \href{http://www.mercator-ocean.fr}{ \includegraphics[height=1cm]{logos/MOI}  } \hspace{0.25cm} 
    58     \href{http://www.metoffice.gov.uk }{ \includegraphics[height=1cm]{logos/UKMO} } \hspace{0.25cm} 
    59     \href{http://nerc.ukri.org        }{ \includegraphics[height=1cm]{logos/NERC} } \\ 
    60     \medskip 
    61     \slshape 
    62     {C}ommunity \hspace{1.5em} {O}cean \hspace{1.5em} {M}odel \\ 
    63   \end{center} 
     57   \begin{center} 
     58      \Large 
     59      \CMCC{\includegraphics[height=1cm]{CMCC}} \hspace{0.25cm} 
     60      \CNRS{\includegraphics[height=1cm]{CNRS}} \hspace{0.25cm} 
     61       \MOI{\includegraphics[height=1cm]{MOI} } \hspace{0.25cm} 
     62      \UKMO{\includegraphics[height=1cm]{UKMO}} \hspace{0.25cm} 
     63      \NERC{\includegraphics[height=1cm]{NERC}}                 \\ 
     64      \medskip 
     65      \slshape 
     66         {C}ommunity \hspace{1.5em} {O}cean \hspace{1.5em} {M}odel 
     67   \end{center} 
    6468 
    6569\end{titlepage} 
    6670 
    67 \restoregeometry 
     71%\restoregeometry 

  • NEMO/trunk/doc/latex/global/highlighting.tex

    r14113 r14257  
     1%% ================================================================================================= 
    12%% Syntax highlighting configuration 
    2 %% ============================================================================== 
    3  
    4 \usepackage[outputdir=../build, chapter, newfloat]{minted} 
     3%% ================================================================================================= 
    54 
    65%% Global highlighting style 
    7 \definecolor{bg}{HTML}{f8f8f8} 
     6\definecolor{bg}{HTML}{f8f8f8} %% ? 
    87\usemintedstyle{emacs} 
    9 \setminted{bgcolor=bg, fontsize=\scriptsize, breaklines} 
    10 \setminted[xml]{style=borland} %% Specific per language 
     8\setminted{bgcolor=bg,fontsize=\scriptsize,breaklines} 
     9\setminted[xml]{style=borland} %% Specific style for XML 
     10 
     11%% Inline 
     12\newmintinline[forcode]{fortran}{bgcolor=,fontsize=auto} %% \forcode{...} 
     13\newmintinline[xmlcode]{xml}{    bgcolor=,fontsize=auto} %% \xmlcode{...} 
     14\newmintinline[snippet]{console}{bgcolor=,fontsize=auto} %% \snippet{...} 
    1115 
    1216%% Oneliner 
    13 \newmint[forline]{fortran}{}   % \forline|...| 
    14 \newmint[xmlline]{xml}{}       % \xmlline|...| 
    15 \newmint[cmd]{console}{}       % \cmd|...| 
     17\newmint[forline]{fortran}{} %% \forline|...| 
     18\newmint[xmlline]{xml    }{} %% \xmlline|...| 
     19\newmint[cmd]{    console}{} %% \cmd|...| 
    1620 
    1721%% Multi-lines 
    18 \newminted[forlines]{fortran}{}   % \begin{forlines} 
    19 \newminted[xmllines]{xml}{}       % \begin{xmllines} 
    20 \newminted[cmds]{console}{}       % \begin{cmds} 
    21 \newminted[clines]{c}{}           % \begin{clines} 
     22\newminted[forlines]{fortran}{} %% \begin{forlines} 
     23\newminted[xmllines]{xml    }{} %% \begin{xmllines} 
     24\newminted[cmds]{    console}{} %% \begin{cmds} 
     25\newminted[clines]{  c      }{} %% \begin{clines} 
    2226 
    23 %% File 
     27%% File (namelist or module) 
    2428\newmintedfile[forfile]{fortran}{} 
    25  
    26 %% Inline 
    27 \newmintinline[forcode]{fortran}{bgcolor=, fontsize=auto}   % \forcode{...} 
    28 \newmintinline[xmlcode]{xml}{    bgcolor=, fontsize=auto}   % \xmlcode{...} 
    29 \newmintinline[snippet]{console}{bgcolor=, fontsize=auto}   % \snippet{...} 
    3029 
    3130%% Namelists inclusion 
    3231\newcommand{\nlst}[1]{\forfile{../../../namelists/#1}} 
     32%\newcommand{\nlst}[1]{ 
     33%   \begin{listing} 
     34%      \newmintedfile{fortran}{../../../namelists/#1} 
     35%      \caption{\forcode{&#1}} 
     36%      \label{lst:#1} 
     37%   \end{listing} 
     38%} 

  • NEMO/trunk/doc/latex/global/indices.tex

    r14256 r14257  
    1  
    2 \usepackage{imakeidx} 
    3  
    4 %% Naming customization 
    5 \renewcommand{\listingname}{namelist} 
    6 \renewcommand{\listlistingname}{List of Namelists} 
     1%% ================================================================================================= 
     2%% Indices 
     3%% ================================================================================================= 
    74 
    85%% Index entries (italic font for files, preformat for code) 
    9 \newcommand{\hf}[1]{   \index{h90 files!#1}             \textit{#1.h90}          } 
    10 \newcommand{\ifile}[1]{\index{Input NetCDF files!#1.nc} \textit{#1.nc}           } 
    11 \newcommand{\jp}[1]{   \index{Model parameters!#1}      \texttt{#1}              } 
    12 \newcommand{\key}[1]{  \index[keys]{#1@\texttt{\textbf{key\_#1}}} \texttt{\textbf{key\_#1}}} 
    13 \newcommand{\mdl}[1]{  \index[modules]{#1@\textit{#1.F90}}        \textit{#1.F90}          } 
    14 \newcommand{\nam}[2]{  \index[blocks]{#1@\texttt{\&nam#2}}        \forcode{&nam#1} (\autoref{lst:nam#1})} 
    15 \newcommand{\np}[3][]{ \index[parameters]{#3@\texttt{#3}}         \forcode{#2#1}           } 
    16 \newcommand{\rou}[1]{  \index[subroutines]{#1@\texttt{#1}}        \texttt{#1}              } 
     6\newcommand{\key}[1]{ 
     7   \index[keys]{       #1@\texttt{\textbf{key\_#1}}} \texttt{\textbf{key\_#1}} 
     8}              
     9\newcommand{\mdl}[1]{ 
     10   \index[modules]{    #1@\textit{#1.F90}          } \textit{#1.F90} 
     11} 
     12\newcommand{\nam}[2]{ 
     13   \index[blocks]{     #1@\texttt{\&nam#2}         } \forcode{&nam#1} (\autoref{lst:nam#1}) 
     14} 
     15\newcommand{\np}[3][]{ 
     16   \index[parameters]{ #3@\texttt{#3}              } \forcode{#2#1} 
     17} 
     18\newcommand{\rou}[1]{ 
     19   \index[subroutines]{#1@\texttt{#1}              } \texttt{#1} 
     20} 
    1721 
     22\indexsetup{toclevel=section,othercode=\small} 
    1823 
    19 \indexsetup{toclevel=section, othercode=\small} 
    20  
    21 \makeindex[intoc=true, name=blocks     , title=Namelist blocks      , columns=3] 
    22 \makeindex[intoc=true, name=keys       , title=CPP keys                        ] 
    23 \makeindex[intoc=true, name=modules    , title=\fortran\ modules    , columns=3] 
    24 \makeindex[intoc=true, name=parameters , title=Namelist parameters  , columns=3] 
    25 \makeindex[intoc=true, name=subroutines, title=\fortran\ subroutines           ] 
     24\makeindex[intoc=true,name=blocks     ,title=Namelist blocks      ,columns=3] 
     25\makeindex[intoc=true,name=keys       ,title=CPP keys                       ] 
     26\makeindex[intoc=true,name=modules    ,title=\fortran\ modules    ,columns=3] 
     27\makeindex[intoc=true,name=parameters ,title=Namelist parameters  ,columns=3] 
     28\makeindex[intoc=true,name=subroutines,title=\fortran\ subroutines          ] 

  • NEMO/trunk/doc/latex/global/info_page.tex

    r14113 r14257  
     1%% ================================================================================================= 
     2%% Back cover 
     3%% ================================================================================================= 
    14 
    2 \thispagestyle{plain} 
     5%% Disclaimer 
     6%% ================================================================================================= 
    37 
    4 %% ================================================================ 
    5 %% Disclaimer 
    6 %% ================================================================ 
    78\subsubsection*{Disclaimer} 
    89 
    910Like all components of the modelling framework, 
    10 the \engine\ core engine is developed under the \href{http://www.cecill.info}{CECILL license}, 
     11the \eng\ core engine is developed under the \href{http://www.cecill.info}{CECILL license}, 
    1112which is a French adaptation of the GNU GPL (\textbf{G}eneral \textbf{P}ublic \textbf{L}icense). 
    1213Anyone may use it freely for research purposes, and is encouraged to 
    … …  
    2021The authors assume no responsibility for problems, errors, or incorrect usage of \NEMO. 
    2122 
    22 %% ================================================================ 
    2323%% External resources 
    24 %% ================================================================ 
     24%% ================================================================================================= 
     25 
    2526\subsubsection*{Other resources} 
    2627\label{resources} 
    2728 
    2829Additional information can be found on: 
     30 
    2931\begin{itemize} 
    30 \item \faWordpress\ the \href{http://www.nemo-ocean.eu}{website} of the project detailing several 
    31   associated applications and an exhaustive users bibliography 
    32 \item \faCodeFork\ the \href{http://forge.ipsl.jussieu.fr/nemo}{development platform} of 
    33   the model with the code repository for the shared reference and some main resources 
    34   (wiki, ticket system, forums, \ldots) \\ 
    35   \faGithub\ the \href{http://github.com/NEMO-ocean/NEMO-examples} 
    36   {repository of the demonstration cases} for research or training 
    37 \item \faCloudDownload\ the \href{http://zenodo.org/communities/nemo-ocean}{online archive} 
    38   delivering the publications issued by the consortium (manuals, reports, datasets, \ldots) 
    39 \item \faEnvelope\ two mailing lists: 
    40   the \href{http://listes.ipsl.fr/sympa/info/nemo-newsletter}{newsletter} for 
    41   top-down communications from the project 
    42   (announcements, calls, job opportunities, \ldots) 
    43   and the \href{http://listes.ipsl.fr/sympa/info/nemo-forge}{forge updates} 
    44   (commits, tickets and forums) 
     32   \item \faWordpress\ the \href{http://www.nemo-ocean.eu}{website} of the project detailing 
     33      several associated applications and an exhaustive users bibliography 
     34   \item \faCodeFork\ the \href{http://forge.ipsl.jussieu.fr/nemo}{development platform} of 
     35      the model with the code repository for the shared reference and some main resources 
     36      (wiki, ticket system, forums, \ldots) \\ 
     37      \faGithub\ the \href{http://github.com/NEMO-ocean/NEMO-examples} 
     38      {repository of the demonstration cases} for research or training 
     39   \item \faCloudDownload\ the \href{http://zenodo.org/communities/nemo-ocean}{online archive} 
     40      delivering the publications issued by the consortium (manuals, reports, datasets, \ldots) 
     41   \item \faEnvelope\ two mailing lists: 
     42      the \href{http://listes.ipsl.fr/sympa/info/nemo-newsletter}{newsletter} for 
     43      top-down communications from the project (announcements, calls, job opportunities, \ldots) 
     44      and the \href{http://listes.ipsl.fr/sympa/info/nemo-forge}{forge updates} 
     45      (commits, tickets and forums) 
    4546\end{itemize} 
    4647 
    47 %% ================================================================ 
    4848%% Citation 
    49 %% ================================================================ 
     49%% ================================================================================================= 
     50 
    5051\subsubsection*{Citation} 
    5152 
    … …  
    5556 
    5657\begin{sloppypar} 
    57   ``{\bfseries \heading}\ifdef{\subheading}{ -- \subheading}{}'', 
    58   {\em Scientific Notes of Climate Modelling Center}, \textbf{\ipslnum} --- ISSN 1288-1619, 
    59   Institut Pierre-Simon Laplace (IPSL), 
    60   \href{https://doi.org/10.5281/zenodo.\zid}{doi:10.5281/zenodo.\zid} 
     58   ``{\bfseries \hdg}\ifdef{\shdg}{ -- \shdg}{}'', 
     59   {\em Scientific Notes of Climate Modelling Center}, \textbf{\ipsl} --- ISSN 1288-1619, 
     60   Institut Pierre-Simon Laplace (IPSL), 
     61   \href{https://doi.org/10.5281/zenodo.\zid}{doi:10.5281/zenodo.\zid} 
    6162\end{sloppypar} 
    6263 
    6364\begin{figure}[b] 
    64   \begin{minipage}[c]{0.7\textwidth} 
    65     \small 
    66     \ttfamily{ 
    67       Scientific Notes of Climate Modelling Center \\ 
    68       ISSN 1288-1619                               \\ 
    69       Institut Pierre-Simon Laplace (IPSL) 
    70     } 
    71   \end{minipage} 
    72   \hfill 
    73   \begin{minipage}[c]{0.25\textwidth} 
    74     \href{http://www.cmc.ipsl.fr}{\includegraphics[width=\textwidth]{logos/IPSL_master}} 
    75   \end{minipage} 
     65 
     66   \begin{minipage}[c]{0.7\textwidth} 
     67      \small 
     68      \ttfamily{ 
     69         Scientific Notes of Climate Modelling Center \\ 
     70         ISSN 1288-1619                               \\ 
     71         Institut Pierre-Simon Laplace (IPSL) 
     72      } 
     73   \end{minipage} 
     74   \hfill %% Don't insert void line between `minipage` envs 
     75   \begin{minipage}[c]{0.25\textwidth} 
     76      \href{http://www.cmc.ipsl.fr}{\includegraphics[width=\textwidth]{IPSL_master}} 
     77   \end{minipage} 
     78 
    7679\end{figure} 

  • NEMO/trunk/doc/latex/global/latexmk.pl

    r13574 r14257  
    1  
    21## Defaults 
    3 $silent   = 1; 
    4 $pdf_mode = 1; 
     2#$silent   = 1; 
     3$pdf_mode = 5; 
    54 
    65## Using relative paths 
    7 $ENV{'openout_any'}='a'; 
    8 $out_dir = '../build'; 
     6$ENV{'openout_any'} = 'a'       ; 
     7$do_cd              = 1         ; 
     8$out_dir            = '../build'; 
    99 
    1010## Custom cmds 
     11set_tex_cmds('-shell-escape -interaction=batchmode'); 
     12#set_tex_cmds('-shell-escape'); 
    1113$makeindex = 'makeindex -s %R.ist %O -o %D %S'; 
    12 $pdflatex  = 'pdflatex -shell-escape %O %S'; 
    13  
    14 #@BIBINPUTS=('.', '../main'); 
    15 #$bibtex    = 'bibtex %O ../main/bibliography.bib'; 
    16 #$kpsewhich = 'kpsewhich bibliography.bib' 
    17  

  • NEMO/trunk/doc/latex/global/new_cmds.tex

    r14113 r14257  
    1 %% Global custom commands: \newcommand{<name>}[<args>][<first argument value>]{<code>} 
    2 %% ============================================================================== 
     1%% ================================================================================================= 
     2%% Global custom commands 
     3%% ================================================================================================= 
    34 
    4 %% Same slanted font for NEMO and its core engines 
    5 \newcommand{\NEMO  }{\textsl{NEMO}} 
    6 \newcommand{\OPA   }{\textsl{OPA}} 
    7 \newcommand{\SIcube}{\textsl{SI$^3$}} 
    8 \newcommand{\TOP   }{\textsl{TOP}} 
    9 \newcommand{\PISCES}{\textsl{PISCES}} 
     5%% \newcommand{<name>}[<args>][<first argument value>]{<code>} 
     6 
     7%% Same font for NEMO and its core engines 
     8\newcommand{\NEMO   }{\textsl{NEMO}} 
     9\newcommand{\OPA    }{\textsl{OPA}} 
     10\newcommand{\SIcube }{\textsl{SI$^3$}} 
     11\newcommand{\TOP    }{\textsl{TOP}} 
     12\newcommand{\PISCES }{\textsl{PISCES}} 
    1013\newcommand{\NEMOVAR}{\textsl{NEMOVAR}} 
    1114 
    12 %% Links for external components 
    13 \newcommand{\AGRIF}{\href{http://agrif.imag.fr}{AGRIF}} 
     15%% URL links for consortium institutes and external components 
     16\newcommand{\CMCC }{\href{http://www.cmcc.it}          } 
     17\newcommand{\CNRS }{\href{http://www.cnrs.fr}          } 
     18\newcommand{\MOI  }{\href{http://www.mercator-ocean.fr}} 
     19\newcommand{\UKMO }{\href{http://www.metoffice.gov.uk} } 
     20\newcommand{\NERC }{\href{http://nerc.ukri.org}        } 
     21\newcommand{\AGRIF}{\href{http://agrif.imag.fr                  }{AGRIF}} 
     22\newcommand{\BFM  }{\href{http://bfm-community.eu               }{BFM}} 
    1423\newcommand{\CICE }{\href{http://github.com/CICE-Consortium/CICE}{CICE}} 
    15 \newcommand{\OASIS}{\href{http://portal.enes.org/oasis}{OASIS}} 
    16 \newcommand{\XIOS }{\href{http://forge.ipsl.jussieu.fr/ioserver}{XIOS}} 
     24\newcommand{\OASIS}{\href{http://portal.enes.org/oasis          }{OASIS}} 
     25\newcommand{\XIOS }{\href{http://forge.ipsl.jussieu.fr/ioserver }{XIOS}} 
    1726 
    1827%% Fortran in small capitals 
    … …  
    2231%% Common aliases 
    2332\renewcommand{\deg}[1][]{\ensuremath{^{\circ}#1}} 
     33\newcommand{\eg    }{\ensuremath{e.g.}} 
     34\newcommand{\ie    }{\ensuremath{i.e.}} 
    2435\newcommand{\zstar }{\ensuremath{z^\star}} 
    2536\newcommand{\sstar }{\ensuremath{s^\star}} 
    2637\newcommand{\ztilde}{\ensuremath{\tilde z}} 
    2738\newcommand{\stilde}{\ensuremath{\tilde s}} 
    28 \newcommand{\ie}{\ensuremath{i.e.}} 
    29 \newcommand{\eg}{\ensuremath{e.g.}} 
    30  
    31 %% Inline maths 
    32 \newcommand{\fractext}[2]{\textstyle \frac{#1}{#2}} 
    33 \newcommand{\rdt}{\Delta t} 
    3439 
    3540%% Gurvan's comments 
    3641\newcommand{\cmtgm}[1]{} 
    3742 
    38 %% Maths 
     43%% Maths: reduce equation 
     44\newcommand{\fractext}[2]{\textstyle\frac{#1}{#2}} 
    3945\newcommand{\lt}{\left} 
     46\newcommand{\pd}[2][]{\ensuremath{\frac{\partial #1}{\partial #2}}} 
     47\newcommand{\rdt}{\Delta t} 
    4048\newcommand{\rt}{\right} 
    41 \newcommand{\vect}[1]{\ensuremath{ \mathbf{#1} }} 
    42 \newcommand{\pd}[2][]{\ensuremath{\frac{\partial #1}{\partial #2}}} 
    43  
    44 %% Convert chapter/section headings to lowercase 
    45 \renewcommand{\chaptermark}[1]{\markboth{#1}{}} 
    46 \renewcommand{\sectionmark}[1]{\markright{#1}{}} 
     49\newcommand{\vect}[1][]{\ensuremath{\mathbf{#1}}} 
    4750 
    4851%% Retrieve month name 
    4952\renewcommand{\today}{ 
    50   \ifcase \month\or January\or February\or March\or 
    51                     April\or   May\or      June\or 
    52                     July\or    August\or   September\or 
    53                     October\or November\or December 
     53  \ifcase \month\or   January\or February\or    March\or    April\or 
     54                          May\or     June\or     July\or   August\or 
     55                    September\or  October\or November\or December 
    5456  \fi, \number \year 
    5557} 
    5658 
    57 %% Link to orcid profile 
    58 \newcommand{\orcid}[1]{\href{http://orcid.org/#1}{\textcolor{orcidcolor}\aiOrcidSquare}} 
     59%% Workaround for \listoffigures issue 
     60\DeclareRobustCommand{\triad}[6]{ 
     61  \ensuremath{{}_{#2}^{#3}{\mathbb{#4}_{#1}}_{#5}^{\,#6}} 
     62} 
    5963 
    60 %% Workaround for \listoffigures 
    61 \DeclareRobustCommand{\triad}[6][]{\ensuremath{ {}_{#2}^{#3} { \mathbb{#4}_{#1} }_{#5}^{\,#6} }} 
    62  
    63 %% New command for ToC 
    64 \newcommand{\chaptertoc}[1][Table of contents]{% 
    65   \thispagestyle{empty} 
    66   \etocsettocstyle{\addsec*{#1}}{}% 
    67   \localtableofcontents% 
     64%% New command for ToC (?) 
     65\newcommand{\chaptertoc}[1][Table of contents]{ 
     66  \etocsettocstyle{\addsec*{#1}}{} 
     67  \localtableofcontents 
    6868  \vfill 
    6969} 
     70 
     71%% ORCID links 
     72\newcommand{\orcid}[1]{\href{http://orcid.org/#1}{\textcolor{orcidclr}\aiOrcidSquare}} 

  • NEMO/trunk/doc/latex/global/packages.tex

    r14113 r14257  
     1%% ================================================================================================= 
     2%% Packages 
     3%% ================================================================================================= 
    14 
    2 %% LaTeX packages in use 
    3 %% ============================================================================== 
     5%% Document class 
     6\usepackage[footsepline=0.25pt,headsepline=0.25pt]{scrlayer-scrpage} %% KOMA-script 
    47 
    5 %% 'hyperref' pkg is loaded at the end of the preamble for higher compatibility 
    6  
    7 %% KOMA-script 
    8 \usepackage[footsepline=0.25pt, headsepline=0.25pt]{scrlayer-scrpage} 
    9  
    10 %% customization (layout, header/footer styles & contents, background) 
    11 \usepackage{draftwatermark} 
    12 \usepackage[margin = 2cm]{geometry} 
    13 \usepackage[pages = some]{background}   %% 'some' for title page 
    14 \usepackage[Bjornstrup]{fncychap} 
     8%% Customisation (cover page, chapter headings and mark of draft copy) 
     9\usepackage[margin=2cm]{geometry} %% Why 2cm margin? Load geometry before background! 
     10\usepackage[pages=some]{background} %% 'some' for title page 
     11\usepackage[scale=15,color=pink]{draftwatermark} 
     12\usepackage[Bjornstrup]{fncychap} %% Chapter style 
    1513 
    1614%% Fonts 
    1715\usepackage{fontspec} 
    18 %% Issue with fontawesome pkg: path to FontAwesome.otf has to be hard-coded 
    19 \defaultfontfeatures{ 
    20     Path = /home/nicolas/.local/texlive/2020/texmf-dist/fonts/opentype/public/fontawesome/ 
    21 } 
    22 \usepackage{academicons, fontawesome, newtxtext} 
     16%% Issue with path to 'FontAwesome.otf' 
     17\defaultfontfeatures{Path=/usr/local/texlive/2020/texmf-dist/fonts/opentype/public/fontawesome/} 
     18\usepackage{academicons,fontawesome} 
    2319 
    2420%% Formatting 
    2521\usepackage[inline]{enumitem} 
    26 \usepackage{etoc, tabularx, xcolor} 
     22\usepackage{etoc,tabularx,xcolor} 
    2723 
    2824%% Graphics 
    29 \usepackage{caption, graphicx, grffile} 
     25\usepackage{caption} 
     26\graphicspath{{../../../badges/}{../figures/}{../../../logos/}} 
    3027 
    3128%% Labels 
    32 \usepackage{lastpage, natbib} 
     29\usepackage{lastpage,natbib} 
     30%\usepackage{natbib,pageslts} 
    3331 
    34 %% Mathematics 
    35 \usepackage{amsmath, amssymb, mathtools} 
     32%% Mathematics: 'amsmath' is loaded by 'mathtools' 
     33\usepackage{mathtools,amssymb} 
    3634 
    3735%% Versatility 
    3836\usepackage{subfiles} 
    3937 
    40 %% Configuration 
    41 \graphicspath{ {../../../} {../figures/} } 
     38%% Source code listings 
     39\usepackage[cachedir=cache,outputdir=../build,chapter,newfloat]{minted} 
     40%% chapter? newfloat? 
     41 
     42%% Indexing and cross-referencing, loaded at the end for higher compatibility 
     43\usepackage{hyperref,imakeidx} 
    4244 
    4345%% Missing utmr8a font 
    4446\usepackage{times} 
    45  
    46 \usepackage{hyperref}   %% links 

  • NEMO/trunk/doc/latex/global/preamble.tex

    r13574 r14257  
     1%% ================================================================================================= 
     2%% Preamble 
     3%% ================================================================================================= 
    14 
    2 \input{../../global/packages} 
     5\def\ver{trunk} 
     6 
     7%% Specific configuration 
     8\input{../main/settings} 
     9 
     10%% Global configuration 
     11\input{../../global/packages} % First obviously 
     12\input{../../global/styles} % Color definitions 
    313\input{../../global/highlighting} 
     14\input{../../global/indices} 
    415\input{../../global/new_cmds} 
    5 \input{../../global/styles} 
    616%\input{../../global/todonotes} 
    7  
     17%\input{../../global/glossaries} 

  • NEMO/trunk/doc/latex/global/styles.tex

    r14113 r14257  
    1  
     1%% ================================================================================================= 
    22%% Styles 
    3 %% ============================================================================== 
     3%% ================================================================================================= 
    44 
    55%% Colors 
    6 \setmanualcolor 
    7 \colorlet{manualcolorshaded}{manualcolor!60} 
    8 \definecolor{orcidcolor}{HTML}{A6CE39} 
     6\definecolor{orcidclr}{HTML}{A6CE39} 
     7\definecolor{manclr}{cmyk}{\clr} %% \clr defined for each manual from local settings.tex 
     8\colorlet{manclrshd}{manclr!60} %% Derived color for chapter heading, see below 
     9 
     10%% Cover page 
     11\backgroundsetup{ 
     12   firstpage=true,scale  =1, 
     13   angle    =0   ,opacity=1, 
     14   contents ={ 
     15      \begin{tikzpicture}[remember picture,overlay] 
     16         \path[fill=manclr] (-0.5\paperwidth,7) rectangle (0.5\paperwidth,10); 
     17      \end{tikzpicture} 
     18    } 
     19} 
    920 
    1021%% Page layout 
    11 \pagestyle{scrheadings} 
     22%\pagestyle{scrheadings} 
     23%\renewcommand{\chapterpagestyle}{empty} 
     24\renewcommand{\chaptermark}[1]{ \markboth{#1}{}} %% Convert mark to lowercase 
     25\renewcommand{\sectionmark}[1]{\markright{#1}{}} %%    "     ""  ""     "   
     26\ohead{} %% Clear default headings 
     27\lohead{Chap. \thechapter\  \leftmark} 
     28\rehead{Sect. \thesection\ \rightmark} 
     29\ifoot{Page \thepage\ of \pageref*{LastPage}} 
     30%\ifoot[\pagemark]{Page \thepage\ of \lastpageref*{pagesLTS.arabic}} 
     31\ofoot{\eng\ Reference Manual} 
    1232\addtokomafont{pagehead}{  \sffamily              } 
    1333\addtokomafont{pagefoot}{  \sffamily \footnotesize} 
    1434\addtokomafont{pagenumber}{\sffamily \slshape     } 
    15 \addtokomafont{chapter}{\color{white}} 
    16 \ohead{} \ofoot{}   %% Clear defaults 
     35%\addtokomafont{chapter}{\color{white}} 
    1736 
    18 %% Caption 
    19 \captionsetup{font = footnotesize, justification = justified} 
     37%% Cross-referencing 
     38\hypersetup{ 
     39   pdftitle=\hdg                                          , 
     40   pdfauthor=Gurvan Madec and NEMO System Team            , 
     41   pdfsubject=Reference manual of NEMO modelling framework, 
     42   pdfkeywords=ocean circulation modelling                , 
     43   colorlinks                                             , 
     44   allcolors=manclr 
     45} 
     46\renewcommand{\appendixautorefname}{appendix}          %% `\autoref` uncapitalization 
     47\renewcommand{\equationautorefname}{equation}          %%     ""            "" 
     48\renewcommand{\figureautorefname  }{figure}            %%     ""            "" 
     49\renewcommand{\listingname        }{namelist}          %%     ""            "" 
     50\renewcommand{\listlistingname    }{List of Namelists} %%     ""            "" 
     51\renewcommand{\tableautorefname   }{table}             %%     ""            "" 
    2052 
    21 %% Footnote 
     53%% Misc. (caption and footnote) 
     54\captionsetup{font=footnotesize,justification=justified} 
    2255\renewcommand{\thefootnote}{\fnsymbol{footnote}} 
    2356 
    … …  
    2861\renewcommand{\bibpostamble}{  \end{multicols}   } 
    2962 
    30 %% Catcodes 
     63%% Catcodes (between `\makeatletter` and `\makeatother`) 
    3164\makeatletter 
    3265 
    33 %% Prevent error with tikz and namelist inclusion 
    34 \global\let\tikz@ensure@dollar@catcode=\relax 
     66%\global\let\tikz@ensure@dollar@catcode=\relax %% Prevent error with tikz and namelist inclusion 
    3567 
    36 %% First page 
    37 \backgroundsetup{ 
    38   firstpage = true, 
    39   scale = 1, angle = 0, opacity = 1, 
    40   contents = { 
    41     \begin{tikzpicture}[remember picture, overlay] 
    42       \path [fill = manualcolor] (-0.5\paperwidth, 7) rectangle (0.5\paperwidth, 10); 
    43     \end{tikzpicture} 
    44   } 
     68%% Apply manual color for chap. headings (original snippets from fncychap.sty) 
     69%% !!! Let trailing percent sign to avoid space insertion 
     70\renewcommand{\DOCH}{% %% Upper box with chapter number 
     71   \settowidth{\py}{\CNoV\thechapter}% 
     72   \addtolength{\py}{-10pt}% %% Amount of space by which the number is shifted right 
     73   \fboxsep=0pt% 
     74   \colorbox{manclr}{\rule{0pt}{40pt}\parbox[b]{\textwidth}{\hfill}}% 
     75   \kern-\py\raise20pt% 
     76   \hbox{\color{manclrshd}\CNoV\thechapter}\\ 
     77} 
     78\renewcommand{\DOTI}[1]{% %% Lower box with chapter title 
     79   \nointerlineskip\raggedright% 
     80   \fboxsep=\myhi% 
     81   \vskip-1ex% 
     82   \colorbox{manclr}{\parbox[t]{\mylen}{\color{white}\CTV\FmTi{#1}}}\par\nobreak% 
     83   \vskip 40\p@% 
     84} 
     85\renewcommand{\DOTIS}[1]{% %% Box for unumbered chapter 
     86   \fboxsep=0pt% 
     87   \colorbox{manclr}{\rule{0pt}{40pt}\parbox[b]{\textwidth}{\hfill}}\\ 
     88   \nointerlineskip\raggedright% 
     89   \fboxsep=\myhi% 
     90   \vskip-1ex% %% Remove white 1pt line 
     91   \colorbox{manclr}{\parbox[t]{\mylen}{\color{white}\CTV\FmTi{#1}}}\par\nobreak% 
     92   \vskip 40\p@% 
    4593} 
    4694 
    47 %% Apply engine color for chapter headings: tweaking snippets from fncychap.sty 
    48 \renewcommand{\DOCH}{% 
    49   \settowidth{\py}{\CNoV\thechapter} 
    50   \addtolength{\py}{-10pt}      % Amount of space by which the 
    51 %                                  % number is shifted right 
    52   \fboxsep=0pt% 
    53   \colorbox{manualcolor}{\rule{0pt}{40pt}\parbox[b]{\textwidth}{\hfill}}% 
    54   \kern-\py\raise20pt% 
    55   \hbox{\color{manualcolorshaded}\CNoV\thechapter}\\% 
    56 } 
    57 \renewcommand{\DOTI}[1]{% 
    58   \nointerlineskip\raggedright% 
    59   \fboxsep=\myhi% 
    60   \vskip-1ex% 
    61   \colorbox{manualcolor}{\parbox[t]{\mylen}{\color{white}\CTV\FmTi{#1}}}\par\nobreak% 
    62   \vskip 40\p@% 
    63 } 
    64 \renewcommand{\DOTIS}[1]{% 
    65   \fboxsep=0pt 
    66   \colorbox{manualcolor}{\rule{0pt}{40pt}\parbox[b]{\textwidth}{\hfill}}\\% 
    67   \nointerlineskip\raggedright% 
    68   \fboxsep=\myhi% 
    69   \vskip-1ex% Remove white 1pt line 
    70   \colorbox{manualcolor}{\parbox[t]{\mylen}{\color{white}\CTV\FmTi{#1}}}\par\nobreak% 
    71   \vskip 40\p@% 
    72 } 
    73  
    74 %% Temporary fix 
    75 \def\set@curr@file#1{% 
    76   \begingroup 
    77     \escapechar\m@ne 
    78     \xdef\@curr@file{\expandafter\string\csname #1\endcsname}% 
    79   \endgroup 
    80 } 
    81 \def\quote@name#1{"\quote@@name#1\@gobble""} 
    82 \def\quote@@name#1"{#1\quote@@name} 
    83 \def\unquote@name#1{\quote@@name#1\@gobble"} 
     95%% Temporary fix? 
     96%\def\set@curr@file#1{ 
     97%  \begingroup 
     98%    \escapechar\m@ne 
     99%    \xdef\@curr@file{\expandafter\string\csname #1\endcsname} 
     100%  \endgroup 
     101%} 
     102%\def\quote@name#1{"\quote@@name#1\@gobble""} 
     103%\def\quote@@name#1"{#1\quote@@name} 
     104%\def\unquote@name#1{\quote@@name#1\@gobble"} 
    84105 
    85106\makeatother 

  • NEMO/trunk/doc/latex/global/todonotes.tex

    r11187 r14257  
    1 \usepackage[]{todonotes} 
     1%% ================================================================================================= 
     2%% Notes 
     3%% ================================================================================================= 
     4 
     5\usepackage{todonotes} 
    26 
    37\newcounter{ubcomment} 
    4 \newcommand{\ubcomment}[2][]{% 
    5 \refstepcounter{ubcomment}% 
    6 {% 
    7 \todo[linecolor=black,backgroundcolor={green!40!},size=\footnotesize]{% 
    8 \textbf{Fixme: UB [\uppercase{#1}\theubcomment]:}~#2}% 
    9 }} 
    10 \newcommand{\ubcommentinline}[2][]{% 
    11 \refstepcounter{ubcomment}% 
    12 {% 
    13 \todo[linecolor=black,inline,backgroundcolor={green!40!},size=\footnotesize]{% 
    14 \textbf{Fixme: UB [\uppercase{#1}\theubcomment]:}~#2}% 
     8 
     9\newcommand{\ubcomment         }[2][]{ 
     10\refstepcounter{ubcomment} 
     11{ 
     12\todo[linecolor=black,       backgroundcolor={green!40!},size=\footnotesize ]{ 
     13\textbf{Fixme: UB [\uppercase{#1}\theubcomment]:}~#2} 
    1514}} 
    1615 
    17 \newcommand{\ubcommentmultiline}[2]{% 
    18 \refstepcounter{ubcomment}% 
    19 {% 
    20 \todo[linecolor=black,inline,caption={\textbf{{Fixme: UB} 
    21     [\theubcomment] #1}} ,backgroundcolor={green!40!},size=\footnotesize]{% 
    22 \textbf{Fixme: UB [\theubcomment]:}~#2}% 
     16\newcommand{\ubcommentinline   }[2][]{ 
     17\refstepcounter{ubcomment} 
     18{ 
     19\todo[linecolor=black,inline,backgroundcolor={green!40!},size=\footnotesize ]{ 
     20\textbf{Fixme: UB [\uppercase{#1}\theubcomment]:}~#2} 
     21}} 
     22 
     23\newcommand{\ubcommentmultiline}[2]{ 
     24\refstepcounter{ubcomment} 
     25{ 
     26\todo[linecolor=black,inline,backgroundcolor={green!40!},size=\footnotesize, 
     27      caption={\textbf{{Fixme: UB} [\theubcomment] #1}}                     ]{ 
     28\textbf{Fixme: UB [              \theubcomment]:}~#2} 
    2329}} 
    2430 

  • NEMO/trunk/doc/manual_build.sh

    r11594 r14257  
    2121 
    2222## LaTeX installation, find latexmk should be enough 
    23 [ -z $( which latexmk ) ] && { echo 'latexmk not installed => QUIT'; exit 2; } 
     23[ -z "$( which latexmk )" ] && { echo 'latexmk not installed => QUIT'; exit 2; } 
    2424 
    2525## Pygments package for syntax highlighting of source code (namelists & snippets) 
    2626[ -n "$( ./tools/check_pkg.py pygments )" ] && { echo 'Python pygments is missing => QUIT'; exit 2; } 
    27  
    28 ## Retrieve figures if not already there 
    29 #if [ ! -d latex/figures ]; then 
    30 #    printf "Downloading of shared figures and logos\n\n" 
    31 #    svn co http://forge.ipsl.jussieu.fr/nemo/svn/utils/figures latex/figures > /dev/null 
    32 #fi 
    33  
    3427 
    3528## Loop on the models 

  • NEMO/trunk/doc/tools/check_pkg.py

    r11008 r14257  
    1 #!/usr/bin/env python 
     1#!/usr/bin/env python3 
    22 
    33import sys, importlib 
    … …  
    77      importlib.import_module(argv) 
    88   except ImportError: 
    9       print("Package %s is missing in Python" % argv) 
     9      print("Package %s is missing in Python 3" % argv) 
    1010 

  • NEMO/trunk/doc/tools/shr_func.sh

    r14113 r14257  
    88 
    99build() { 
    10     printf "\t¤ Generation of the PDF format\n" 
    11     latexmk -r ./latex/global/latexmk.pl -pdfxe ./latex/$1/main/$1_manual \ 
    12 #  1> /dev/null 
     10    printf "\t¤ Generation of the PDF export of the manual\n" 
     11    latexmk -r ./latex/global/latexmk.pl ./latex/$1/main/$1_manual \ 
     12   1> /dev/null 
    1313    [ -f ./latex/$1/build/$1_manual.pdf ] && mv ./latex/$1/build/$1_manual.pdf . 
    1414    echo 
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