Changeset 9376


Ignore:
Timestamp:
2018-03-06T17:12:34+01:00 (3 years ago)
Author:
nicolasmartin
Message:

Global reorganisation of DOC directory: refactoring & cleaning of TeX source code for readability

Location:
branches/2017/dev_merge_2017/DOC
Files:
2 added
25 edited

Legend:

Unmodified
Added
Removed
  • branches/2017/dev_merge_2017/DOC/LaTeX2HTML.sh

    r9360 r9376  
    11#!/bin/bash 
    22 
    3 sed -i -e 's#\\documentclass#%\\documentclass#' -e '/{document}/ s/^/%/' TexFiles/Chapters/*.tex 
    4 sed -i    '30,${s#\\subfile{#\\include{#g}'                              NEMO_book.tex 
    5 latex -shell-escape NEMO_book && makeindex NEMO_book && bibtex NEMO_book 
    6 mkdir -p html 
    7 latex2html -local_icons -no_footnode -split 4 -link 2 -dir html $* 
    8 sed -i -e 's#%\\documentclass#\\documentclass#' -e '/{document}/ s/^%//' TexFiles/Chapters/*.tex 
    9 sed -i    '30,${s#\\include{#\\subfile{#g}'                              NEMO_book.tex 
     3sed -i -e 's#\\documentclass#%\\documentclass#' -e '/{document}/ s/^/%/' texfiles/chapters/*.tex 
     4sed -i    '30,${s#\\subfile{#\\include{#g}'                              NEMO_manual.tex 
     5 
     6makeindex               NEMO_manual 
     7bibtex                  NEMO_manual 
     8latex    -shell-escape  NEMO_manual 
     9 
     10mkdir -p html_LaTeX2HTML 
     11latex2html -local_icons -no_footnode -split 4 -link 2 -dir html_LaTeX2HTML $* NEMO_manual 
     12 
     13sed -i -e 's#%\\documentclass#\\documentclass#' -e '/{document}/ s/^%//' texfiles/chapters/*.tex 
     14sed -i    '30,${s#\\include{#\\subfile{#g}'                              NEMO_manual.tex 
    1015 
    1116exit 0 
  • branches/2017/dev_merge_2017/DOC/NEMO_manual.tex

    r9373 r9376  
    1 %description: Book template 
     1%% ============================================================================== 
     2%% NEMO_book.tex: build the NEMO Reference Manual 
     3%% ============================================================================== 
    24 
    3 % template of document for LaTeX 
    4 % (C) Xavier Perseguers 2002 - xavier.perseguers@epfl.ch 
    55 
    6 % ================================================================ 
    7 % PREAMBLE 
    8 % ================================================================ 
     6%% Run build_NEMO_manual.sh to generate the PDF version (with pdflatex) 
     7 
     8 
     9%% Preamble 
     10%% ============================================================================== 
    911 
    1012\include{texfiles/preamble} 
    1113 
    12 % ================================================================ 
    13 % TOP MATTER 
    14 % ================================================================ 
     14\begin{document} 
     15 
     16 
     17%% 'minted' env. & shortcuts for syntax highlighting 
     18 
     19\setminted[fortran]{fontsize=\tiny, breaklines} 
     20\newminted{fortran}{}         % \begin{fortrancode} 
     21\newmintinline{fortran}{}     % \fortraninline 
     22\newmintedfile{fortran}{}     % \fortranfile 
     23\newminted{xml}{fontsize=\tiny, breaklines} 
     24\newminted{sh}{} 
     25\newminted{c}{} 
     26 
     27 
     28%% Frontmatter 
     29%% ============================================================================== 
    1530 
    1631\include{texfiles/top_matter} 
    1732 
    18 % ================================================================ 
    19 % DOCUMENT 
    20 % ================================================================ 
    2133 
    22 \begin{document} 
     34%% Frontpage 
    2335 
    24 \maketitle                 % generate the title 
    25  
     36\maketitle 
    2637\frontmatter 
    2738 
    28 \tableofcontents              % generate a table of contents 
    29 %\listoffigures               % generate a list  of figures 
    30 %\listoftables                     % generate a list of tables 
     39 
     40%% ToC i.e. Table of Contents 
     41 
     42\dominitoc 
     43\tableofcontents 
     44 
     45 
     46%% Mainmatter 
     47%% ============================================================================== 
    3148 
    3249\mainmatter 
    3350 
    34 % ================================================================ 
    35 % Abstract - Foreword 
    36 % ================================================================ 
     51 
     52%% Abstract - Foreword 
    3753 
    3854\subfile{texfiles/chapters/abstract_foreword} 
    3955 
    40 % ================================================================ 
    41 % INTRODUCTION 
    42 % ================================================================ 
     56 
     57% Introduction 
    4358 
    4459\subfile{texfiles/chapters/introduction} 
    4560 
    46 % ================================================================ 
    47 % CHAPTERS 
    48 % ================================================================ 
     61 
     62% Chapters 
    4963 
    5064\subfile{texfiles/chapters/chap_model_basics} 
     
    7892\subfile{texfiles/chapters/chap_CONFIG}         % Predefined configurations 
    7993 
    80 % ================================================================ 
    81 % APPENDIX 
    82 % ================================================================ 
     94 
     95% Appendix 
    8396 
    8497\appendix 
    8598 
    86 %\subfile{texfiles/chapters/chap_conservation} 
    87 \subfile{texfiles/chapters/annex_A}       % generalised vertical coordinate 
    88 \subfile{texfiles/chapters/annex_B}       % diffusive operator 
    89 \subfile{texfiles/chapters/annex_C}       % Discrete invariants of the eqs. 
    90 \subfile{texfiles/chapters/annex_iso}                    % Isoneutral diffusion using triads 
    91 \subfile{texfiles/chapters/annex_D}       % Coding rules 
    92 %\subfile{texfiles/chapters/annex_E}                     % Notes on some on going staff (no included in the DOC) 
    93 %\subfile{texfiles/chapters/annex_Fox-Kemper}   % Notes on Fox-Kemper (no included in the DOC) 
    94 %\subfile{texfiles/chapters/annex_EVP}          % Notes on EVP (no included in the DOC) 
     99\subfile{texfiles/chapters/annex_A}             % Generalised vertical coordinate 
    95100 
    96 % ================================================================ 
    97 % INDEX 
    98 % ================================================================ 
     101\subfile{texfiles/chapters/annex_B}             % Diffusive operator 
    99102 
    100 \addcontentsline{toc}{chapter}{Index} 
     103\subfile{texfiles/chapters/annex_C}             % Discrete invariants of the eqs. 
     104 
     105\subfile{texfiles/chapters/annex_iso}           % Isoneutral diffusion using triads 
     106 
     107\subfile{texfiles/chapters/annex_D}             % Coding rules 
     108 
     109%% Not included 
     110%\subfile{texfiles/chapters/chap_conservation}  % 
     111%\subfile{texfiles/chapters/annex_E}            % Notes on some on going staff 
     112%\subfile{texfiles/chapters/annex_Fox-Kemper}   % Notes on Fox-Kemper 
     113%\subfile{texfiles/chapters/annex_EVP}          % Notes on EVP 
     114 
     115 
     116%% Backmatter 
     117%% ============================================================================== 
     118 
     119\backmatter 
     120 
     121 
     122%% Index 
     123 
     124%\addcontentsline{toc}{chapter}{Index} 
    101125\printindex 
    102126 
    103 % ================================================================ 
    104 % BIBLIOGRAPHY 
    105 % ================================================================ 
    106127 
    107 %%\bibliographystyle{plainat} 
    108 \bibliographystyle{texfiles/styles/ametsoc}     % AMS biblio style (JPO) 
     128%% Bibliography 
     129 
    109130\bibliography{texfiles/bibliography/NEMO_manual} 
    110131 
    111 % ================================================================ 
     132 
    112133\end{document} 
  • branches/2017/dev_merge_2017/DOC/clean.sh

    r9373 r9376  
    11#!/bin/bash 
    22 
    3 rm -f $( ls -1 NEMO_manual.* | egrep -v "(tex)" ) *mpgraph* 
    4 find TexFiles -regextype posix-extended -regex ".*\.(aux|log)" -exec rm -f {} \; 
     3rm -f $( ls -1 NEMO_manual.* | egrep -v "tex" ) 
     4find texfiles -regextype posix-extended -regex ".*\.(aux|log)" -exec rm -f {} \; 
    55 
    66exit 0 
  • branches/2017/dev_merge_2017/DOC/texfiles/chapters/abstract_foreword.tex

    r9373 r9376  
    33 
    44% ================================================================ 
    5 % Abstract (English / French) 
     5% Abstract 
    66% ================================================================ 
    77 
    8 \chapter*{Abstract / R\'{e}sum\'{e}} 
     8\chapter*{Abstract} 
    99 
    1010\vspace{-40pt} 
     
    2424biogeochemical models (TOP) and, via the OASIS coupler, with several atmospheric general circulation models.  
    2525It also support two-way grid embedding via the AGRIF software. 
    26  
    27 % ================================================================ 
    28 % \vspace{0.5cm} 
    29  
    30 %Le moteur oc\'{e}anique de NEMO (Nucleus for European Modelling of the Ocean) est un  
    31 %mod\`{e}le aux \'{e}quations primitives de la circulation oc\'{e}anique r\'{e}gionale et globale.  
    32 %Il se veut un outil flexible pour \'{e}tudier sur un vaste spectre spatiotemporel l'oc\'{e}an et ses  
    33 %interactions avec les autres composantes du syst\`{e}me climatique terrestre.  
    34 %Les variables pronostiques sont le champ tridimensionnel de vitesse, une hauteur de la mer  
    35 %lin\'{e}aire, la Temp\'{e}rature Conservative et la Salinit\'{e} Absolue.  
    36 %La distribution des variables se fait sur une grille C d'Arakawa tridimensionnelle utilisant une  
    37 %coordonn\'{e}e verticale $z$ \`{a} niveaux entiers ou partiels, ou une coordonn\'{e}e s, ou encore  
    38 %une combinaison des deux. Diff\'{e}rents choix sont propos\'{e}s pour d\'{e}crire la physique  
    39 %oc\'{e}anique, incluant notamment des physiques verticales TKE et GLS. A travers l'infrastructure  
    40 %NEMO, l'oc\'{e}an est interfac\'{e} avec des mod\`{e}les de glace de mer (LIM ou CICE),  
    41 %de biog\'{e}ochimie marine et de traceurs passifs, et, via le coupleur OASIS, \`{a} plusieurs  
    42 %mod\`{e}les de circulation g\'{e}n\'{e}rale atmosph\'{e}rique.  
    43 %Il supporte \'{e}galement l'embo\^{i}tement interactif de maillages via le logiciel AGRIF. 
    4426}  
    4527 
     
    5840for problems, errors, or incorrect usage of NEMO. 
    5941 
    60  \vspace{1cm} 
     42\vspace{1cm} 
    6143NEMO reference in papers and other publications is as follows: 
    62  \vspace{0.5cm} 
     44\vspace{0.5cm} 
    6345 
    6446Madec, G., and the NEMO team, 2008: NEMO ocean engine.  
     
    6749 
    6850 
    69  \vspace{0.5cm} 
    70 Additional information can be found on \href{http://www.nemo-ocean.eu/}{nemo-ocean.eu} website. 
    71  \vspace{0.5cm} 
     51\vspace{0.5cm} 
     52Additional information can be found on \href{http://www.nemo-ocean.eu/}{www.nemo-ocean.eu}. 
     53\vspace{0.5cm} 
    7254 
    7355\end{document} 
  • branches/2017/dev_merge_2017/DOC/texfiles/chapters/annex_iso.tex

    r9373 r9376  
    1111\section{Choice of \protect\ngn{namtra\_ldf} namelist parameters} 
    1212%-----------------------------------------nam_traldf------------------------------------------------------ 
    13 \namdisplay{namtra_ldf} 
     13\fortranfile{namelists/namtra_ldf} 
    1414%--------------------------------------------------------------------------------------------------------- 
    1515 
  • branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_ASM.tex

    r9373 r9376  
    131131 
    132132%------------------------------------------namasm----------------------------------------------------- 
    133 \namdisplay{namasm} 
     133%\fortranfile{namelists/namasm} 
    134134%------------------------------------------------------------------------------------------------------------- 
    135135 
     
    137137\mbox{\textit{ncdump~-h}} is shown below 
    138138 
    139 \begin{alltt} 
    140 \tiny 
    141 \begin{verbatim} 
     139\begin{ccode} 
    142140netcdf assim_background_increments { 
    143141dimensions: 
     
    172170                :DOMAIN_type = "BOX" ; 
    173171} 
    174 \end{verbatim} 
    175 \end{alltt} 
     172\end{ccode} 
     173 
    176174\end{document} 
  • branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_CONFIG.tex

    r9373 r9376  
    2626 
    2727%------------------------------------------namcfg---------------------------------------------------- 
    28 \namdisplay{namcfg} 
     28\fortranfile{namelists/namcfg} 
    2929%------------------------------------------------------------------------------------------------------------- 
    3030 
  • branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_DIA.tex

    r9373 r9376  
    8282in a very easy way. All details of iomput functionalities are listed in the following subsections.  
    8383Examples of the XML files that control the outputs can be found in: 
    84 \begin{alltt} 
    85 \begin{verbatim} 
    86   NEMOGCM/CONFIG/ORCA2_LIM/EXP00/iodef.xml 
    87   NEMOGCM/CONFIG/SHARED/field_def.xml 
    88   and 
    89   NEMOGCM/CONFIG/SHARED/domain_def.xml. 
    90 \end{verbatim} 
    91 \end{alltt} 
     84\path{NEMOGCM/CONFIG/ORCA2_LIM/EXP00/iodef.xml}, \path{NEMOGCM/CONFIG/SHARED/field_def.xml} and 
     85\path{NEMOGCM/CONFIG/SHARED/domain_def.xml}. 
    9286 
    9387The second functionality targets output performance when running in parallel (\key{mpp\_mpi}).  
     
    201195See the installation guide on the \href{http://forge.ipsl.jussieu.fr/ioserver/wiki}{XIOS} wiki for help and guidance.  
    202196NEMO will need to link to the compiled XIOS library.  
    203 The \href{http://www.nemo-ocean.eu/Using-NEMO/User-Guides/Basics/XIOS-IO-server-installation-and-use}{XIOS with NEMO}  
     197The \href{https://forge.ipsl.jussieu.fr/nemo/wiki/Users/ModelInterfacing/InputsOutputs#Inputs-OutputsusingXIOS}{XIOS with NEMO}  
    204198guide provides an example illustration of how this can be achieved. 
    205199 
     
    223217For example: 
    224218\vspace{-20pt} 
    225 \begin{alltt}  {{\scriptsize 
    226 \begin{verbatim} 
     219\begin{xmlcode} 
    227220   <field_definition> 
    228221      <!-- T grid --> 
     
    233226      ... 
    234227   </field_definition>  
    235 \end{verbatim} 
    236 }}\end{alltt}  
     228\end{xmlcode} 
    237229Note your definition must be added to the field\_group whose reference grid is consistent  
    238230with the size of the array passed to iomput.  
     
    241233or defined in the domain\_def.xml file. $e.g.$: 
    242234\vspace{-20pt} 
    243 \begin{alltt}  {{\scriptsize 
    244 \begin{verbatim} 
     235\begin{xmlcode} 
    245236     <grid id="grid_T_3D" domain_ref="grid_T" axis_ref="deptht"/> 
    246 \end{verbatim} 
    247 }}\end{alltt}  
     237\end{xmlcode} 
    248238Note, if your array is computed within the surface module each nn\_fsbc time\_step,  
    249239add the field definition within the field\_group defined with the id ''SBC'': $<$field\_group id=''SBC''...$>$  
     
    252242\item[4.] add your field in one of the output files defined in iodef.xml (again see subsequent sections for syntax and rules)   \\ 
    253243\vspace{-20pt} 
    254 \begin{alltt}  {{\scriptsize 
    255 \begin{verbatim} 
     244\begin{xmlcode} 
    256245   <file id="file1" .../>    
    257246      ... 
     
    259248      ... 
    260249   </file>    
    261 \end{verbatim} 
    262 }}\end{alltt}  
     250\end{xmlcode} 
    263251 
    264252\end{description} 
     
    394382  
    395383\noindent In NEMO, by default, the field and domain definition is done in 2 separate files: 
    396 {\scriptsize \tt 
    397 \begin{verbatim} 
    398 NEMOGCM/CONFIG/SHARED/field_def.xml 
    399 and 
    400 NEMOGCM/CONFIG/SHARED/domain_def.xml  
    401 \end{verbatim} 
    402 } 
     384\path{NEMOGCM/CONFIG/SHARED/field_def.xml} and \path{NEMOGCM/CONFIG/SHARED/domain_def.xml} 
     385 
    403386\noindent that are included in the main iodef.xml file through the following commands: \\ 
    404387{\scriptsize \verb? <field_definition src="./field_def.xml" /> ? \\ 
     
    415398example 1: Direct inheritance. 
    416399\vspace{-20pt} 
    417 \begin{alltt}  {{\scriptsize     
    418 \begin{verbatim} 
     400\begin{xmlcode} 
    419401   <field_definition operation="average" > 
    420402     <field id="sst"                    />   <!-- averaged      sst -->  
    421403     <field id="sss" operation="instant"/>   <!-- instantaneous sss -->  
    422404   </field_definition>  
    423 \end{verbatim} 
    424 }}\end{alltt}  
    425  
     405\end{xmlcode} 
    426406The field ''sst'' which is part (or a child) of the field\_definition will inherit the value ''average''  
    427407of the attribute ''operation'' from its parent. Note that a child can overwrite  
     
    431411example 2: Inheritance by reference. 
    432412\vspace{-20pt} 
    433 \begin{alltt}  {{\scriptsize 
    434 \begin{verbatim} 
     413\begin{xmlcode} 
    435414   <field_definition> 
    436415     <field id="sst" long_name="sea surface temperature" />    
     
    444423     </file>    
    445424   </file_definition>  
    446 \end{verbatim} 
    447 }}\end{alltt}  
     425\end{xmlcode} 
    448426Inherit (and overwrite, if needed) the attributes of a tag you are refering to. 
    449427 
     
    455433Note that for the field ''toce'', we overwrite the grid definition inherited from the group by ''grid\_T\_3D''. 
    456434\vspace{-20pt} 
    457 \begin{alltt}  {{\scriptsize 
    458 \begin{verbatim} 
     435\begin{xmlcode} 
    459436   <field_group id="grid_T" grid_ref="grid_T_2D"> 
    460437    <field id="toce" long_name="temperature"             unit="degC" grid_ref="grid_T_3D"/> 
     
    463440    <field id="ssh"  long_name="sea surface height"      unit="m"                        /> 
    464441         ... 
    465 \end{verbatim} 
    466 }}\end{alltt}  
     442\end{xmlcode} 
    467443 
    468444Secondly, the group can be used to replace a list of elements.  
     
    470446For example, a short list of the usual variables related to the U grid: 
    471447\vspace{-20pt} 
    472 \begin{alltt}  {{\scriptsize 
    473 \begin{verbatim} 
     448\begin{xmlcode} 
    474449   <field_group id="groupU" > 
    475450    <field field_ref="uoce"  /> 
     
    477452    <field field_ref="utau"  /> 
    478453   </field_group> 
    479 \end{verbatim} 
    480 }}\end{alltt}  
     454\end{xmlcode} 
    481455that can be directly included in a file through the following syntax: 
    482456\vspace{-20pt} 
    483 \begin{alltt}  {{\scriptsize 
    484 \begin{verbatim} 
     457\begin{xmlcode} 
    485458   <file id="myfile_U" output_freq="1d" />    
    486459    <field_group group_ref="groupU"/>   
    487460    <field field_ref="uocetr_eff"  />  <!-- add another field --> 
    488461   </file>    
    489 \end{verbatim} 
    490 }}\end{alltt}  
     462\end{xmlcode} 
    491463 
    492464\subsection{Detailed functionalities } 
     
    501473of a 5 by 5 box with the bottom left corner at point (10,10). 
    502474\vspace{-20pt} 
    503 \begin{alltt}  {{\scriptsize 
    504 \begin{verbatim} 
     475\begin{xmlcode} 
    505476   <domain_group id="grid_T"> 
    506477    <domain id="myzoom" zoom_ibegin="10" zoom_jbegin="10" zoom_ni="5" zoom_nj="5" /> 
    507 \end{verbatim} 
    508 }}\end{alltt}  
     478\end{xmlcode} 
    509479The use of this subdomain is done through the redefinition of the attribute domain\_ref of the tag family field. For example: 
    510480\vspace{-20pt} 
    511 \begin{alltt}  {{\scriptsize 
    512 \begin{verbatim} 
     481\begin{xmlcode} 
    513482   <file id="myfile_vzoom" output_freq="1d" > 
    514483      <field field_ref="toce" domain_ref="myzoom"/> 
    515484   </file> 
    516 \end{verbatim} 
    517 }}\end{alltt}  
     485\end{xmlcode} 
    518486Moorings are seen as an extrem case corresponding to a 1 by 1 subdomain.  
    519487The Equatorial section, the TAO, RAMA and PIRATA moorings are alredy registered in the code  
     
    523491by ''T'' (for example: ''8s137eT'', ''1.5s80.5eT'' ...) 
    524492\vspace{-20pt} 
    525 \begin{alltt}  {{\scriptsize 
    526 \begin{verbatim} 
     493\begin{xmlcode} 
    527494   <file id="myfile_vzoom" output_freq="1d" > 
    528495      <field field_ref="toce" domain_ref="0n180wT"/> 
    529496   </file> 
    530 \end{verbatim} 
    531 }}\end{alltt}  
     497\end{xmlcode} 
    532498Note that if the domain decomposition used in XIOS cuts the subdomain in several parts and if you use the ''multiple\_file'' type for your output files, you will endup with several files you will need to rebuild using unprovided tools (like ncpdq and ncrcat, \href{http://nco.sourceforge.net/nco.html#Concatenation}{see nco manual}). We are therefore advising to use the ''one\_file'' type in this case. 
    533499 
     
    535501Vertical zooms are defined through the attributs zoom\_begin and zoom\_end of the tag family axis. It must therefore be done in the axis part of the XML file. For example, in NEMOGCM/CONFIG/ORCA2\_LIM/iodef\_demo.xml, we provide the following example: 
    536502\vspace{-20pt} 
    537 \begin{alltt}  {{\scriptsize 
    538 \begin{verbatim} 
     503\begin{xmlcode} 
    539504   <axis_group id="deptht" long_name="Vertical T levels" unit="m" positive="down" > 
    540505      <axis id="deptht" /> 
    541506      <axis id="deptht_myzoom" zoom_begin="1" zoom_end="10" /> 
    542 \end{verbatim} 
    543 }}\end{alltt}  
     507\end{xmlcode} 
    544508The use of this vertical zoom is done through the redefinition of the attribute axis\_ref of the tag family field. For example: 
    545509\vspace{-20pt} 
    546 \begin{alltt}  {{\scriptsize 
    547 \begin{verbatim} 
     510\begin{xmlcode} 
    548511   <file id="myfile_hzoom" output_freq="1d" > 
    549512      <field field_ref="toce" axis_ref="deptht_myzoom"/> 
    550513   </file> 
    551 \end{verbatim} 
    552 }}\end{alltt}  
     514\end{xmlcode} 
    553515 
    554516\subsubsection{Control of the output file names} 
     
    556518The output file names are defined by the attributs ''name'' and ''name\_suffix'' of the tag family file. for example: 
    557519\vspace{-20pt} 
    558 \begin{alltt}  {{\scriptsize 
    559 \begin{verbatim} 
     520\begin{xmlcode} 
    560521   <file_group id="1d" output_freq="1d" name="myfile_1d" >  
    561522      <file id="myfileA" name_suffix="_AAA" > <!-- will create file "myfile_1d_AAA"  --> 
     
    566527      </file> 
    567528   </file_group> 
    568 \end{verbatim} 
    569 }}\end{alltt}  
     529\end{xmlcode} 
    570530However it is often very convienent to define the file name with the name of the experiment, the output file frequency and the date of the beginning and the end of the simulation (which are informations stored either in the namelist or in the XML file). To do so, we added the following rule: if the id of the tag file is ''fileN''(where N = 1 to 999 on 1 to 3 digits) or one of the predefined sections or moorings (see next subsection), the following part of the name and the name\_suffix (that can be inherited) will be automatically replaced by:\\ 
    571531\\ 
     
    653613 
    654614\vspace{-20pt} 
    655 \begin{alltt}  {{\scriptsize     
    656 \begin{verbatim} 
     615\begin{xmlcode} 
    657616 <field field\_ref="sst"  name="tosK"  unit="degK" > sst + 273.15 </field> 
    658617 <field field\_ref="taum" name="taum2" unit="N2/m4" long\_name="square of wind stress module" > taum * taum </field> 
    659618 <field field\_ref="qt"   name="stupid\_check" > qt - qsr - qns </field> 
    660 \end{verbatim} 
    661 }}\end{alltt}  
     619\end{xmlcode} 
    662620 
    663621(2) Simple computation: define a new variable and use it in the file definition. 
     
    665623in field\_definition: 
    666624\vspace{-20pt} 
    667 \begin{alltt}  {{\scriptsize     
    668 \begin{verbatim} 
     625\begin{xmlcode} 
    669626 <field id="sst2" long\_name="square of sea surface temperature" unit="degC2" >  sst * sst </field > 
    670 \end{verbatim} 
    671 }}\end{alltt}  
     627\end{xmlcode} 
    672628in file\_definition: 
    673629\vspace{-20pt} 
    674 \begin{alltt}  {{\scriptsize     
    675 \begin{verbatim} 
     630\begin{xmlcode} 
    676631 <field field\_ref="sst2" > sst2 </field> 
    677 \end{verbatim} 
    678 }}\end{alltt}  
     632\end{xmlcode} 
    679633Note that in this case, the following syntaxe $<$field field\_ref="sst2" /$>$ is not working as sst2 won't be evaluated. 
    680634 
     
    682636 
    683637\vspace{-20pt} 
    684 \begin{alltt}  {{\scriptsize     
    685 \begin{verbatim} 
     638\begin{xmlcode} 
    686639     <!-- force to keep real 8 --> 
    687640 <field field\_ref="sst" name="tos\_r8" prec="8" /> 
    688641      <!-- integer 2  with add\_offset and scale\_factor attributes --> 
    689642 <field field\_ref="sss" name="sos\_i2" prec="2" add\_offset="20." scale\_factor="1.e-3" /> 
    690 \end{verbatim} 
    691 }}\end{alltt}  
     643\end{xmlcode} 
    692644Note that, then the code is crashing, writting real4 variables forces a numerical convection from real8 to real4 which will create an internal error in NetCDF and will avoid the creation of the output files. Forcing double precision outputs with prec="8" (for example in the field\_definition) will avoid this problem. 
    693645 
     
    695647 
    696648\vspace{-20pt} 
    697 \begin{alltt}  {{\scriptsize     
    698 \begin{verbatim} 
     649\begin{xmlcode} 
    699650      <file\_group id="1d" output\_freq="1d" output\_level="10" enabled=".TRUE."> <!-- 1d files -->  
    700651   <file id="file1" name\_suffix="\_grid\_T" description="ocean T grid variables" > 
     
    707658       </file> 
    708659     </file\_group>  
    709 \end{verbatim} 
    710 }}\end{alltt}  
     660\end{xmlcode} 
    711661 
    712662(5) use of the ``@'' function: example 1, weighted temporal average 
     
    714664 - define a new variable in field\_definition 
    715665\vspace{-20pt} 
    716 \begin{alltt}  {{\scriptsize     
    717 \begin{verbatim} 
     666\begin{xmlcode} 
    718667 <field id="toce\_e3t" long\_name="temperature * e3t" unit="degC*m" grid\_ref="grid\_T\_3D" > toce * e3t </field > 
    719 \end{verbatim} 
    720 }}\end{alltt} 
     668\end{xmlcode} 
    721669 - use it when defining your file.   
    722670\vspace{-20pt} 
    723 \begin{alltt}  {{\scriptsize     
    724 \begin{verbatim} 
     671\begin{xmlcode} 
    725672<file\_group id="5d" output\_freq="5d"  output\_level="10" enabled=".TRUE." >  <!-- 5d files -->   
    726673 <file id="file1" name\_suffix="\_grid\_T" description="ocean T grid variables" > 
     
    728675 </file> 
    729676</file\_group>  
    730 \end{verbatim} 
    731 }}\end{alltt} 
     677\end{xmlcode} 
    732678The freq\_op="5d" attribute is used to define the operation frequency of the ``@'' function: here 5 day. The temporal operation done by the ``@'' is the one defined in the field definition: here we use the default, average. So, in the above case, @toce\_e3t will do the 5-day mean of toce*e3t. Operation="instant" refers to the temporal operation to be performed on the field''@toce\_e3t / @e3t'': here the temporal average is alreday done by the ``@'' function so we just use instant to do the ratio of the 2 mean values. field\_ref="toce" means that attributes not explicitely defined, are inherited from toce field. Note that in this case, freq\_op must be equal to the file output\_freq. 
    733679 
     
    736682 - define a new variable in field\_definition 
    737683\vspace{-20pt} 
    738 \begin{alltt}  {{\scriptsize     
    739 \begin{verbatim} 
     684\begin{xmlcode} 
    740685 <field id="ssh2" long\_name="square of sea surface temperature" unit="degC2" >  ssh * ssh </field > 
    741 \end{verbatim} 
    742 }}\end{alltt}  
     686\end{xmlcode} 
    743687 - use it when defining your file.   
    744688\vspace{-20pt} 
    745 \begin{alltt}  {{\scriptsize     
    746 \begin{verbatim} 
     689\begin{xmlcode} 
    747690<file\_group id="1m" output\_freq="1m"  output\_level="10" enabled=".TRUE." >  <!-- 1m files -->   
    748691 <file id="file1" name\_suffix="\_grid\_T" description="ocean T grid variables" > 
     
    750693 </file> 
    751694</file\_group>  
    752 \end{verbatim} 
    753 }}\end{alltt} 
     695\end{xmlcode} 
    754696The freq\_op="1m" attribute is used to define the operation frequency of the ``@'' function: here 1 month. The temporal operation done by the ``@'' is the one defined in the field definition: here we use the default, average. So, in the above case, @ssh2 will do the monthly mean of ssh*ssh. Operation="instant" refers to the temporal operation to be performed on the field ''sqrt( @ssh2 - @ssh * @ssh )'': here the temporal average is alreday done by the ``@'' function so we just use instant. field\_ref="ssh" means that attributes not explicitely defined, are inherited from ssh field. Note that in this case, freq\_op must be equal to the file output\_freq. 
    755697 
     
    758700 - define 2 new variables in field\_definition 
    759701\vspace{-20pt} 
    760 \begin{alltt}  {{\scriptsize     
    761 \begin{verbatim} 
     702\begin{xmlcode} 
    762703 <field id="sstmax" field\_ref="sst" long\_name="max of sea surface temperature" operation="maximum" /> 
    763704 <field id="sstmin" field\_ref="sst" long\_name="min of sea surface temperature" operation="minimum" /> 
    764 \end{verbatim} 
    765 }}\end{alltt}  
     705\end{xmlcode} 
    766706 - use these 2 new variables when defining your file.   
    767707\vspace{-20pt} 
    768 \begin{alltt}  {{\scriptsize     
    769 \begin{verbatim} 
     708\begin{xmlcode} 
    770709<file\_group id="1m" output\_freq="1m"  output\_level="10" enabled=".TRUE." >  <!-- 1m files -->   
    771710 <file id="file1" name\_suffix="\_grid\_T" description="ocean T grid variables" > 
     
    773712 </file> 
    774713</file\_group>  
    775 \end{verbatim} 
    776 }}\end{alltt} 
     714\end{xmlcode} 
    777715The freq\_op="1d" attribute is used to define the operation frequency of the ``@'' function: here 1 day. The temporal operation done by the ``@'' is the one defined in the field definition: here maximum for sstmax and minimum for sstmin. So, in the above case, @sstmax will do the daily max and @sstmin the daily min. Operation="average" refers to the temporal operation to be performed on the field ``@sstmax - @sstmin'': here monthly mean (of daily max - daily min of the sst). field\_ref="sst" means that attributes not explicitely defined, are inherited from sst field. 
    778716 
     
    11141052 
    11151053%------------------------------------------namnc4---------------------------------------------------- 
    1116 \namdisplay{namnc4} 
     1054\fortranfile{namelists/namnc4} 
    11171055%------------------------------------------------------------------------------------------------------------- 
    11181056 
     
    11421080 
    11431081\vspace{-20pt} 
    1144 \begin{alltt}  {{\scriptsize  
    1145 \begin{verbatim} 
     1082\begin{fortrancode} 
    11461083     ichunksz(1) = MIN( idomain_size,MAX( (idomain_size-1)/nn_nchunks_i + 1 ,16 ) ) 
    11471084     ichunksz(2) = MIN( jdomain_size,MAX( (jdomain_size-1)/nn_nchunks_j + 1 ,16 ) ) 
    11481085     ichunksz(3) = MIN( kdomain_size,MAX( (kdomain_size-1)/nn_nchunks_k + 1 , 1 ) ) 
    11491086     ichunksz(4) = 1 
    1150 \end{verbatim} 
    1151 }}\end{alltt}  
     1087\end{fortrancode} 
    11521088 
    11531089\noindent As an example, setting: 
    11541090\vspace{-20pt} 
    1155 \begin{alltt}  {{\scriptsize 
    1156 \begin{verbatim} 
     1091\begin{fortrancode} 
    11571092     nn_nchunks_i=4, nn_nchunks_j=4 and nn_nchunks_k=31 
    1158 \end{verbatim} 
    1159 }}\end{alltt} \vspace{-10pt} 
     1093\end{fortrancode} 
    11601094 
    11611095\noindent for a standard ORCA2\_LIM configuration gives chunksizes of {\small\tt 46x38x1} 
     
    12221156 
    12231157%------------------------------------------namtrd---------------------------------------------------- 
    1224 \namdisplay{namtrd}  
     1158\fortranfile{namelists/namtrd}  
    12251159%------------------------------------------------------------------------------------------------------------- 
    12261160 
     
    12611195\label{FLO} 
    12621196%--------------------------------------------namflo------------------------------------------------------- 
    1263 \namdisplay{namflo}  
     1197\fortranfile{namelists/namflo}  
    12641198%-------------------------------------------------------------------------------------------------------------- 
    12651199 
     
    13411275 
    13421276\vspace{-30pt} 
    1343 \begin{alltt}  {{\scriptsize 
    1344 \begin{verbatim} 
    1345  
     1277\begin{xmlcode} 
    13461278     <group id="1d\_grid\_T" name="auto" description="ocean T grid variables" >   } 
    13471279       <file id="floats"  description="floats variables"> }\\ 
     
    13551287       </file>} 
    13561288  </group>} 
    1357  
    1358 \end{verbatim} 
    1359 }}\end{alltt} 
     1289\end{xmlcode} 
    13601290 
    13611291 
     
    13751305 
    13761306%------------------------------------------namdia_harm---------------------------------------------------- 
    1377 \namdisplay{namdia_harm} 
     1307%\fortranfile{namelists/namdia_harm} 
    13781308%---------------------------------------------------------------------------------------------------------- 
    13791309 
     
    14171347 
    14181348%------------------------------------------namdct---------------------------------------------------- 
    1419 \namdisplay{namdct} 
     1349\fortranfile{namelists/namdct} 
    14201350%------------------------------------------------------------------------------------------------------------- 
    14211351 
     
    17461676 
    17471677%------------------------------------------namptr----------------------------------------- 
    1748 \namdisplay{namptr}  
     1678\fortranfile{namelists/namptr}  
    17491679%----------------------------------------------------------------------------------------- 
    17501680 
     
    17891719 
    17901720%------------------------------------------nam_dia25h------------------------------------- 
    1791 \namdisplay{nam_dia25h} 
     1721\fortranfile{namelists/nam_dia25h} 
    17921722%----------------------------------------------------------------------------------------- 
    17931723 
     
    18041734 
    18051735%------------------------------------------nam_diatmb----------------------------------------------------- 
    1806 \namdisplay{nam_diatmb} 
     1736\fortranfile{namelists/nam_diatmb} 
    18071737%---------------------------------------------------------------------------------------------------------- 
    18081738 
  • branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_DIU.tex

    r9373 r9376  
    3434 
    3535Both the cool skin and warm layer models are controlled through the namelist \ngn{namdiu}: 
    36 \namdisplay{namdiu} 
     36\fortranfile{namelists/namdiu} 
    3737This namelist contains only two variables: 
    3838\begin{description} 
  • branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_DOM.tex

    r9373 r9376  
    310310  
    311311These fields can be read in an domain input file which name is setted in \np{cn\_domcfg} parameter specified in \ngn{namcfg}. 
    312 \namdisplay{namcfg} 
     312\fortranfile{namelists/namcfg} 
    313313or they can be defined in an analytical way in MY\_SRC directory of the configuration. 
    314314For Reference Configurations of NEMO input domain files are supplied by NEMO System Team. For analytical definition of input fields two routines are supplied: \mdl{userdef\_hgr} and \mdl{userdef\_zgr}. They are an example of GYRE configuration parameters, and they are available in NEMO/OPA\_SRC/USR directory, they provide the horizontal and vertical mesh.  
     
    431431\label{DOM_zgr} 
    432432%-----------------------------------------nam_zgr & namdom------------------------------------------- 
    433 \namdisplay{namzgr}  
    434 \namdisplay{namdom}  
     433%\fortranfile{namelists/namzgr}  
     434\fortranfile{namelists/namdom}  
    435435%------------------------------------------------------------------------------------------------------------- 
    436436 
     
    692692\label{DOM_zps} 
    693693%--------------------------------------------namdom------------------------------------------------------- 
    694 \namdisplay{namdom}  
     694\fortranfile{namelists/namdom}  
    695695%-------------------------------------------------------------------------------------------------------------- 
    696696 
     
    725725\label{DOM_sco} 
    726726%------------------------------------------nam_zgr_sco--------------------------------------------------- 
    727 \namdisplay{namzgr_sco}  
     727%\fortranfile{namelists/namzgr_sco}  
    728728%-------------------------------------------------------------------------------------------------------------- 
    729729Options are defined in \ngn{namzgr\_sco}. 
     
    916916\label{DTA_tsd} 
    917917%-----------------------------------------namtsd------------------------------------------- 
    918 \namdisplay{namtsd}  
     918\fortranfile{namelists/namtsd}  
    919919%------------------------------------------------------------------------------------------ 
    920920 
  • branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_DYN.tex

    r9373 r9376  
    162162\label{DYN_adv_cor_vect} 
    163163%-----------------------------------------nam_dynadv---------------------------------------------------- 
    164 \namdisplay{namdyn_adv}  
     164\fortranfile{namelists/namdyn_adv}  
    165165%------------------------------------------------------------------------------------------------------------- 
    166166 
     
    182182\label{DYN_vor} 
    183183%------------------------------------------nam_dynvor---------------------------------------------------- 
    184 \namdisplay{namdyn_vor}  
     184\fortranfile{namelists/namdyn_vor}  
    185185%------------------------------------------------------------------------------------------------------------- 
    186186 
     
    391391\label{DYN_adv_cor_flux} 
    392392%------------------------------------------nam_dynadv---------------------------------------------------- 
    393 \namdisplay{namdyn_adv}  
     393\fortranfile{namelists/namdyn_adv}  
    394394%------------------------------------------------------------------------------------------------------------- 
    395395 
     
    536536\label{DYN_hpg} 
    537537%------------------------------------------nam_dynhpg--------------------------------------------------- 
    538 \namdisplay{namdyn_hpg}  
     538\fortranfile{namelists/namdyn_hpg}  
    539539%------------------------------------------------------------------------------------------------------------- 
    540540 
     
    736736\label{DYN_spg} 
    737737%-----------------------------------------nam_dynspg---------------------------------------------------- 
    738 \namdisplay{namdyn_spg}  
     738\fortranfile{namelists/namdyn_spg}  
    739739%------------------------------------------------------------------------------------------------------------ 
    740740 
     
    796796\label{DYN_spg_ts} 
    797797%------------------------------------------namsplit----------------------------------------------------------- 
    798 \namdisplay{namsplit}  
     798%\fortranfile{namelists/namsplit} 
    799799%------------------------------------------------------------------------------------------------------------- 
    800800 
     
    10051005\label{DYN_ldf} 
    10061006%------------------------------------------nam_dynldf---------------------------------------------------- 
    1007 \namdisplay{namdyn_ldf}  
     1007\fortranfile{namelists/namdyn_ldf}  
    10081008%------------------------------------------------------------------------------------------------------------- 
    10091009 
     
    11491149\label{DYN_zdf} 
    11501150%----------------------------------------------namzdf------------------------------------------------------ 
    1151 \namdisplay{namzdf}  
     1151\fortranfile{namelists/namzdf}  
    11521152%------------------------------------------------------------------------------------------------------------- 
    11531153 
     
    12271227 
    12281228%----------------------------------------------namdom---------------------------------------------------- 
    1229 \namdisplay{namdom}  
     1229\fortranfile{namelists/namdom}  
    12301230%------------------------------------------------------------------------------------------------------------- 
    12311231 
  • branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_LBC.tex

    r9373 r9376  
    2020\label{LBC_coast} 
    2121%--------------------------------------------nam_lbc------------------------------------------------------- 
    22 \namdisplay{namlbc}  
     22\fortranfile{namelists/namlbc}  
    2323%-------------------------------------------------------------------------------------------------------------- 
    2424 
     
    354354 
    355355%-----------------------------------------nambdy-------------------------------------------- 
    356 \namdisplay{nambdy}  
     356\fortranfile{namelists/nambdy}  
    357357%----------------------------------------------------------------------------------------------- 
    358358%-----------------------------------------nambdy_index-------------------------------------------- 
    359 \namdisplay{nambdy_index}  
     359%\fortranfile{namelists/nambdy_index} 
    360360%----------------------------------------------------------------------------------------------- 
    361361%-----------------------------------------nambdy_dta-------------------------------------------- 
    362 \namdisplay{nambdy_dta}  
     362\fortranfile{namelists/nambdy_dta}  
    363363%----------------------------------------------------------------------------------------------- 
    364364%-----------------------------------------nambdy_dta-------------------------------------------- 
    365 \namdisplay{nambdy_dta2}  
     365%\fortranfile{namelists/nambdy_dta2}  
    366366%----------------------------------------------------------------------------------------------- 
    367367 
     
    635635 
    636636%-----------------------------------------nambdy_tide-------------------------------------------- 
    637 \namdisplay{nambdy_tide}  
     637\fortranfile{namelists/nambdy_tide}  
    638638%----------------------------------------------------------------------------------------------- 
    639639 
  • branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_LDF.tex

    r9373 r9376  
    2828 
    2929%-----------------------------------nam_traldf - nam_dynldf-------------------------------------------- 
    30 \namdisplay{namtra_ldf}  
    31 \namdisplay{namdyn_ldf}  
     30\fortranfile{namelists/namtra_ldf}  
     31\fortranfile{namelists/namdyn_ldf}  
    3232%-------------------------------------------------------------------------------------------------------------- 
    3333 
  • branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_OBS.tex

    r9373 r9376  
    6565 
    6666\item Download some EN4 data from  
    67 \href{http://www.metoffice.gov.uk/hadobs}{http://www.metoffice.gov.uk/hadobs}. Choose observations which are 
     67\href{http://www.metoffice.gov.uk/hadobs}{www.metoffice.gov.uk/hadobs}. Choose observations which are 
    6868valid for the period of your test run because the observation operator compares 
    6969the model and observations for a matching date and time.  
    7070 
    7171\item Compile the OBSTOOLS code using:  
    72 \begin{verbatim} 
     72\begin{shcode} 
    7373./maketools -n OBSTOOLS -m [ARCH]. 
    74 \end{verbatim} 
     74\end{shcode} 
    7575 
    7676\item Convert the EN4 data into feedback format:  
    77 \begin{verbatim} 
     77\begin{shcode} 
    7878enact2fb.exe profiles_01.nc EN.4.1.1.f.profiles.g10.YYYYMM.nc 
    79 \end{verbatim} 
     79\end{shcode} 
    8080 
    8181\item Include the following in the NEMO namelist to run the observation 
     
    8484 
    8585%------------------------------------------namobs_example----------------------------------------------------- 
    86 \namdisplay{namobs_example} 
     86%\fortranfile{namelists/namobs_example} 
    8787%------------------------------------------------------------------------------------------------------------- 
    8888 
     
    114114 
    115115%------------------------------------------namobs-------------------------------------------------------- 
    116 \namdisplay{namobs} 
     116\fortranfile{namelists/namobs} 
    117117%------------------------------------------------------------------------------------------------------------- 
    118118 
     
    126126\subsection{Profile feedback} 
    127127 
    128 \begin{alltt} 
    129 \tiny 
    130 \begin{verbatim} 
     128\begin{ccode} 
    131129netcdf profiles_01 { 
    132130dimensions: 
     
    280278          :Convention = "NEMO unified observation operator output" ; 
    281279} 
    282 \end{verbatim} 
    283 \end{alltt} 
     280\end{ccode} 
    284281 
    285282\subsection{Sea level anomaly feedback} 
    286283 
    287 \begin{alltt} 
    288 \tiny 
    289 \begin{verbatim} 
     284\begin{ccode} 
    290285netcdf sla_01 { 
    291286dimensions: 
     
    407402          :Convention = "NEMO unified observation operator output" ; 
    408403} 
    409 \end{verbatim} 
    410 \end{alltt} 
     404\end{ccode} 
    411405 
    412406The mean dynamic 
     
    416410surface height. Below is an example header for this file (on the ORCA025 grid). 
    417411 
    418 \begin{alltt} 
    419 \tiny 
    420 \begin{verbatim} 
     412\begin{ccode} 
    421413dimensions: 
    422414        x = 1442 ; 
     
    433425                sossheig:units = "metres" ; 
    434426                sossheig:grid = "orca025T" ; 
    435 \end{verbatim} 
    436 \end{alltt} 
     427\end{ccode} 
    437428 
    438429\subsection{Sea surface temperature feedback} 
    439430 
    440 \begin{alltt} 
    441 \tiny 
    442 \begin{verbatim} 
     431\begin{ccode} 
    443432netcdf sst_01 { 
    444433dimensions: 
     
    553542          :Convention = "NEMO unified observation operator output" ; 
    554543} 
    555 \end{verbatim} 
    556 \end{alltt} 
     544\end{ccode} 
    557545 
    558546\section{Theoretical details} 
     
    935923read the second time counter from a single file the namelist would be. 
    936924 
    937 \begin{alltt} 
    938 \tiny 
    939 \begin{verbatim}  
     925\begin{fortrancode} 
    940926!---------------------------------------------------------------------- 
    941927!       namooo Offline obs_oper namelist 
     
    947933   nn_ooo_idx = 2 
    948934/ 
    949 \end{verbatim}  
    950 \end{alltt} 
     935\end{fortrancode} 
    951936 
    952937\subsubsection{Multiple fields per run} 
     
    95694112 hourly fields are to be interpolated in a setup where 288 steps equals 24 hours. 
    957942 
    958 \begin{alltt} 
    959 \tiny 
    960 \begin{verbatim}  
     943\begin{fortrancode} 
    961944!---------------------------------------------------------------------- 
    962945!       namooo Offline obs_oper namelist 
     
    970953   nn_ooo_freq = 144 
    971954/ 
    972 \end{verbatim}  
    973 \end{alltt} 
     955\end{fortrancode} 
    974956 
    975957The above namelist will result in feedback files whose first 12 hours contain 
     
    10791061fields plus an analysis field would be 7 counterparts per observation. 
    10801062 
    1081 \begin{alltt} 
    1082 \tiny 
    1083 \begin{verbatim} 
     1063\begin{fortrancode} 
    10841064   cl4_match_len = 7 
    1085 \end{verbatim} 
    1086 \end{alltt} 
     1065\end{fortrancode} 
    10871066 
    10881067Then to correctly allocate a class 4 file the forecast axis must be defined. This 
    10891068is controlled via \textbf{cl4\_fcst\_len}, which in out above example would be 3. 
    10901069 
    1091 \begin{alltt} 
    1092 \tiny 
    1093 \begin{verbatim} 
     1070\begin{fortrancode} 
    10941071   cl4_fcst_len = 3 
    1095 \end{verbatim} 
    1096 \end{alltt} 
     1072\end{fortrancode} 
    10971073 
    10981074Then for each model field it is necessary to designate what class 4 variable and 
     
    11011077when interpreting the data afterwards.  
    11021078 
    1103 \begin{alltt} 
    1104 \tiny 
    1105 \begin{verbatim} 
     1079\begin{fortrancode} 
    11061080   cl4_vars = "forecast" "forecast" "forecast" "persistence" "persistence" 
    11071081              "persistence" "best_estimate" 
    11081082   cl4_fcst_idx = 1 2 3 1 2 3 1 
    11091083   cl4_leadtime = 12 36 60  
    1110 \end{verbatim} 
    1111 \end{alltt} 
     1084\end{fortrancode} 
    11121085 
    11131086In terms of files and indices of fields inside each file the class 4 approach 
     
    11151088with a single field per file our example inputs will be specified. 
    11161089 
    1117 \begin{alltt} 
    1118 \tiny 
    1119 \begin{verbatim} 
     1090\begin{fortrancode} 
    11201091   ooo_files = "F.1.nc" "F.2.nc" "F.3.nc" "P.1.nc" "P.2.nc" "P.3.nc" "A.1.nc" 
    11211092   nn_ooo_idx = 1 1 1 1 1 1 1 
    1122 \end{verbatim} 
    1123 \end{alltt} 
     1093\end{fortrancode} 
    11241094 
    11251095When we combine all of the naming conventions, global attributes and i/o instructions 
    11261096the class 4 namelist becomes. 
    11271097 
    1128 \begin{alltt} 
    1129 \tiny 
    1130 \begin{verbatim} 
     1098\begin{fortrancode} 
    11311099!---------------------------------------------------------------------- 
    11321100!       namooo Offline obs_oper namelist 
     
    11761144   cl4_inst = "UK Met Office" 
    11771145/ 
    1178 \end{verbatim} 
    1179 \end{alltt} 
     1146\end{fortrancode} 
    11801147 
    11811148\subsubsection{Climatology interpolation} 
     
    12001167operations, 1 per forecast. 
    12011168 
    1202 \begin{alltt} 
    1203 \tiny 
    1204 \begin{verbatim} 
     1169\begin{fortrancode} 
    12051170   ooo_files = "F1.nc" "F1.nc" "F2.nc" "F2.nc" 
    12061171... 
    12071172   cl4_fcst_idx = 1 2 
    1208 \end{verbatim} 
    1209 \end{alltt} 
     1173\end{fortrancode} 
    12101174 
    12111175The above notation reveals the internal split between match up iterators and file 
     
    12391203MPI run of NEMO offline obs\_oper into a single class 4 file. The program is called in the following way: 
    12401204 
    1241 \begin{alltt} 
     1205 
    12421206\footnotesize 
    1243 \begin{verbatim} 
     1207\begin{shcode} 
    12441208c4comb.exe outputfile inputfile1 inputfile2 ... 
    1245 \end{verbatim} 
    1246 \end{alltt} 
     1209\end{shcode} 
    12471210 
    12481211\subsubsection{corio2fb} 
     
    12511214standard feedback format. The program is called in the following way: 
    12521215 
    1253 \begin{alltt} 
    12541216\footnotesize 
    1255 \begin{verbatim} 
     1217\begin{shcode} 
    12561218corio2fb.exe outputfile inputfile1 inputfile2 ... 
    1257 \end{verbatim} 
    1258 \end{alltt} 
     1219\end{shcode} 
    12591220 
    12601221\subsubsection{enact2fb} 
     
    12631224feedback format. The program is called in the following way: 
    12641225 
    1265 \begin{alltt} 
    12661226\footnotesize 
    1267 \begin{verbatim} 
     1227\begin{shcode} 
    12681228enact2fb.exe outputfile inputfile1 inputfile2 ... 
    1269 \end{verbatim} 
    1270 \end{alltt} 
     1229\end{shcode} 
    12711230 
    12721231\subsubsection{fbcomb} 
     
    12751234MPI run of NEMO into a single feedback file. The program is called in the following way: 
    12761235 
    1277 \begin{alltt} 
    12781236\footnotesize 
    1279 \begin{verbatim} 
     1237\begin{shcode} 
    12801238fbcomb.exe outputfile inputfile1 inputfile2 ... 
    1281 \end{verbatim} 
    1282 \end{alltt} 
     1239\end{shcode} 
    12831240 
    12841241\subsubsection{fbmatchup} 
     
    12871244in the following way: 
    12881245 
    1289 \begin{alltt} 
    12901246\footnotesize 
    1291 \begin{verbatim} 
     1247\begin{shcode} 
    12921248fbmatchup.exe outputfile inputfile1 varname1 inputfile2 varname2 ... 
    1293 \end{verbatim} 
    1294 \end{alltt} 
    1295  
     1249\end{shcode} 
    12961250 
    12971251\subsubsection{fbprint} 
     
    13011255following way: 
    13021256 
    1303 \begin{alltt} 
    13041257\footnotesize 
    1305 \begin{verbatim} 
     1258\begin{shcode} 
    13061259fbprint.exe [options] inputfile 
    13071260 
     
    13231276     -D            print depths 
    13241277     -z            use zipped files 
    1325 \end{verbatim} 
    1326 \end{alltt} 
     1278\end{shcode} 
    13271279 
    13281280\subsubsection{fbsel} 
     
    13311283following way: 
    13321284 
    1333 \begin{alltt} 
    13341285\footnotesize 
    1335 \begin{verbatim} 
     1286\begin{shcode} 
    13361287fbsel.exe <input filename> <output filename> 
    1337 \end{verbatim} 
    1338 \end{alltt} 
     1288\end{shcode} 
    13391289 
    13401290\subsubsection{fbstat} 
     
    13431293files. The program is called in the following way: 
    13441294 
    1345 \begin{alltt} 
    13461295\footnotesize 
    1347 \begin{verbatim} 
     1296\begin{shcode} 
    13481297fbstat.exe [-nmlev] <filenames> 
    1349 \end{verbatim} 
    1350 \end{alltt} 
     1298\end{shcode} 
    13511299 
    13521300\subsubsection{fbthin} 
     
    13551303modified to thin to a different resolution. The program is called in the following way: 
    13561304 
    1357 \begin{alltt} 
    13581305\footnotesize 
    1359 \begin{verbatim} 
     1306\begin{shcode} 
    13601307fbthin.exe inputfile outputfile 
    1361 \end{verbatim} 
    1362 \end{alltt} 
     1308\end{shcode} 
    13631309 
    13641310\subsubsection{sla2fb} 
     
    13671313called in the following way: 
    13681314 
    1369 \begin{alltt} 
    13701315\footnotesize 
    1371 \begin{verbatim} 
     1316\begin{shcode} 
    13721317sla2fb.exe [-s type] outputfile inputfile1 inputfile2 ... 
    13731318 
    13741319Option: 
    13751320     -s            Select altimeter data_source 
    1376 \end{verbatim} 
    1377 \end{alltt} 
     1321\end{shcode} 
    13781322 
    13791323\subsubsection{vel2fb} 
     
    13821326is called in the following way: 
    13831327 
    1384 \begin{alltt} 
    13851328\footnotesize 
    1386 \begin{verbatim} 
     1329\begin{shcode} 
    13871330vel2fb.exe outputfile inputfile1 inputfile2 ... 
    1388 \end{verbatim} 
    1389 \end{alltt} 
     1331\end{shcode} 
    13901332 
    13911333\subsection{building the obstools} 
     
    13981340observations and feedback files. It is possible to zoom in, plot individual profiles and 
    13991341calculate some basic statistics. To plot some data run IDL and then: 
    1400 \begin{alltt} 
    14011342\footnotesize 
    1402 \begin{verbatim} 
     1343\begin{minted}{idl} 
    14031344IDL> dataplot, "filename" 
    1404 \end{verbatim} 
    1405 \end{alltt} 
     1345\end{minted} 
    14061346 
    14071347To read multiple files into dataplot, for example multiple feedback files from different 
    14081348processors or from different days, the easiest method is to use the spawn command to generate 
    14091349a list of files which can then be passed to dataplot. 
    1410 \begin{alltt} 
    14111350\footnotesize 
    1412 \begin{verbatim} 
     1351\begin{minted}{idl} 
    14131352IDL> spawn, 'ls profb*.nc', files 
    14141353IDL> dataplot, files 
    1415 \end{verbatim} 
    1416 \end{alltt} 
     1354\end{minted} 
    14171355 
    14181356Fig~\ref{fig:obsdataplotmain} shows the main window which is launched when dataplot starts. 
  • branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_SBC.tex

    r9373 r9376  
    1111$\ $\newline    % force a new ligne 
    1212%---------------------------------------namsbc-------------------------------------------------- 
    13 \namdisplay{namsbc} 
     13\fortranfile{namelists/namsbc} 
    1414%-------------------------------------------------------------------------------------------------------------- 
    1515$\ $\newline    % force a new ligne 
     
    196196 
    197197The structure associated with an input variable contains the following information: 
    198 \begin{alltt}  {{\tiny     
    199 \begin{verbatim} 
     198\begin{fortrancode} 
    200199!  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !  
    201200!             !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      ! 
    202 \end{verbatim} 
    203 }}\end{alltt}  
     201\end{fortrancode} 
    204202where  
    205203\begin{description}   
     
    427425 
    428426%---------------------------------------namsbc_ana-------------------------------------------------- 
    429 \namdisplay{namsbc_sas} 
     427\fortranfile{namelists/namsbc_sas} 
    430428%-------------------------------------------------------------------------------------------------------------- 
    431429 
     
    488486 
    489487%---------------------------------------namsbc_ana-------------------------------------------------- 
    490 \namdisplay{namsbc_ana} 
     488%\fortranfile{namelists/namsbc_ana} 
    491489%-------------------------------------------------------------------------------------------------------------- 
    492490 
     
    512510\label{SBC_flx} 
    513511%------------------------------------------namsbc_flx---------------------------------------------------- 
    514 \namdisplay{namsbc_flx}  
     512\fortranfile{namelists/namsbc_flx}  
    515513%------------------------------------------------------------------------------------------------------------- 
    516514 
     
    552550\label{SBC_blk_core} 
    553551%------------------------------------------namsbc_core---------------------------------------------------- 
    554 \namdisplay{namsbc_core}  
     552%\fortranfile{namelists/namsbc_core} 
    555553%------------------------------------------------------------------------------------------------------------- 
    556554 
     
    617615\label{SBC_blk_clio} 
    618616%------------------------------------------namsbc_clio---------------------------------------------------- 
    619 \namdisplay{namsbc_clio}  
     617%\fortranfile{namelists/namsbc_clio} 
    620618%------------------------------------------------------------------------------------------------------------- 
    621619 
     
    658656\label{SBC_blk_mfs} 
    659657%------------------------------------------namsbc_mfs---------------------------------------------------- 
    660 \namdisplay{namsbc_mfs}  
     658%\fortranfile{namelists/namsbc_mfs} 
    661659%---------------------------------------------------------------------------------------------------------- 
    662660 
     
    697695\label{SBC_cpl} 
    698696%------------------------------------------namsbc_cpl---------------------------------------------------- 
    699 \namdisplay{namsbc_cpl}  
     697\fortranfile{namelists/namsbc_cpl}  
    700698%------------------------------------------------------------------------------------------------------------- 
    701699 
     
    736734\label{SBC_apr} 
    737735%------------------------------------------namsbc_apr---------------------------------------------------- 
    738 \namdisplay{namsbc_apr}  
     736\fortranfile{namelists/namsbc_apr}  
    739737%------------------------------------------------------------------------------------------------------------- 
    740738 
     
    772770 
    773771%------------------------------------------nam_tide--------------------------------------- 
    774 \namdisplay{nam_tide} 
     772\fortranfile{namelists/nam_tide} 
    775773%----------------------------------------------------------------------------------------- 
    776774 
     
    827825\label{SBC_rnf} 
    828826%------------------------------------------namsbc_rnf---------------------------------------------------- 
    829 \namdisplay{namsbc_rnf}  
     827\fortranfile{namelists/namsbc_rnf}  
    830828%------------------------------------------------------------------------------------------------------------- 
    831829 
     
    943941\label{SBC_isf} 
    944942%------------------------------------------namsbc_isf---------------------------------------------------- 
    945 \namdisplay{namsbc_isf} 
     943\fortranfile{namelists/namsbc_isf} 
    946944%-------------------------------------------------------------------------------------------------------- 
    947945Namelist variable in \ngn{namsbc}, \np{nn\_isf}, controls the ice shelf representation used.  
     
    10241022\label{SBC_iscpl} 
    10251023%------------------------------------------namsbc_iscpl---------------------------------------------------- 
    1026 \namdisplay{namsbc_iscpl} 
     1024\fortranfile{namelists/namsbc_iscpl} 
    10271025%-------------------------------------------------------------------------------------------------------- 
    10281026Ice sheet/ocean coupling is done through file exchange at the restart step. NEMO, at each restart step,  
     
    10621060\label{ICB_icebergs} 
    10631061%------------------------------------------namberg---------------------------------------------------- 
    1064 \namdisplay{namberg} 
     1062\fortranfile{namelists/namberg} 
    10651063%------------------------------------------------------------------------------------------------------------- 
    10661064 
     
    11341132\label{SBC_dcy} 
    11351133%------------------------------------------namsbc_rnf---------------------------------------------------- 
    1136 %\namdisplay{namsbc}  
     1134%\fortranfile{namelists/namsbc}  
    11371135%------------------------------------------------------------------------------------------------------------- 
    11381136 
     
    12111209\label{SBC_ssr} 
    12121210%------------------------------------------namsbc_ssr---------------------------------------------------- 
    1213 \namdisplay{namsbc_ssr}  
     1211\fortranfile{namelists/namsbc_ssr}  
    12141212%------------------------------------------------------------------------------------------------------------- 
    12151213 
     
    13311329\label{SBC_wave} 
    13321330%------------------------------------------namwave---------------------------------------------------- 
    1333 \namdisplay{namsbc_wave} 
     1331\fortranfile{namelists/namsbc_wave} 
    13341332%------------------------------------------------------------------------------------------------------------- 
    13351333 
  • branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_STO.tex

    r9373 r9376  
    124124 
    125125%---------------------------------------namsbc-------------------------------------------------- 
    126 \namdisplay{namsto} 
     126\fortranfile{namelists/namsto} 
    127127%-------------------------------------------------------------------------------------------------------------- 
    128128 
  • branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_TRA.tex

    r9373 r9376  
    6767\label{TRA_adv} 
    6868%------------------------------------------namtra_adv----------------------------------------------------- 
    69 \namdisplay{namtra_adv} 
     69\fortranfile{namelists/namtra_adv} 
    7070%------------------------------------------------------------------------------------------------------------- 
    7171 
     
    432432\label{TRA_ldf} 
    433433%-----------------------------------------nam_traldf------------------------------------------------------ 
    434 \namdisplay{namtra_ldf} 
     434\fortranfile{namelists/namtra_ldf} 
    435435%------------------------------------------------------------------------------------------------------------- 
    436436  
     
    652652\label{TRA_zdf} 
    653653%--------------------------------------------namzdf--------------------------------------------------------- 
    654 \namdisplay{namzdf} 
     654\fortranfile{namelists/namzdf} 
    655655%-------------------------------------------------------------------------------------------------------------- 
    656656 
     
    777777\label{TRA_qsr} 
    778778%--------------------------------------------namqsr-------------------------------------------------------- 
    779 \namdisplay{namtra_qsr} 
     779\fortranfile{namelists/namtra_qsr} 
    780780%-------------------------------------------------------------------------------------------------------------- 
    781781 
     
    888888\label{TRA_bbc} 
    889889%--------------------------------------------nambbc-------------------------------------------------------- 
    890 \namdisplay{nambbc} 
     890\fortranfile{namelists/nambbc} 
    891891%-------------------------------------------------------------------------------------------------------------- 
    892892%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    927927\label{TRA_bbl} 
    928928%--------------------------------------------nambbl--------------------------------------------------------- 
    929 \namdisplay{nambbl} 
     929\fortranfile{namelists/nambbl} 
    930930%-------------------------------------------------------------------------------------------------------------- 
    931931 
     
    10871087\label{TRA_dmp} 
    10881088%--------------------------------------------namtra_dmp------------------------------------------------- 
    1089 \namdisplay{namtra_dmp} 
     1089\fortranfile{namelists/namtra_dmp} 
    10901090%-------------------------------------------------------------------------------------------------------------- 
    10911091 
     
    11401140 
    11411141%--------------------------------------------nam_dmp_create------------------------------------------------- 
    1142 \namtools{namelist_dmp} 
     1142%\namtools{namelist_dmp} 
    11431143%------------------------------------------------------------------------------------------------------- 
    11441144 
     
    11721172\label{TRA_nxt} 
    11731173%--------------------------------------------namdom----------------------------------------------------- 
    1174 \namdisplay{namdom} 
     1174\fortranfile{namelists/namdom} 
    11751175%-------------------------------------------------------------------------------------------------------------- 
    11761176 
     
    12111211\label{TRA_eosbn2} 
    12121212%--------------------------------------------nameos----------------------------------------------------- 
    1213 \namdisplay{nameos} 
     1213\fortranfile{namelists/nameos} 
    12141214%-------------------------------------------------------------------------------------------------------------- 
    12151215 
  • branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_ZDF.tex

    r9373 r9376  
    5252\label{ZDF_cst} 
    5353%--------------------------------------------namzdf--------------------------------------------------------- 
    54 \namdisplay{namzdf} 
     54\fortranfile{namelists/namzdf} 
    5555%-------------------------------------------------------------------------------------------------------------- 
    5656 
     
    7878 
    7979%--------------------------------------------namric--------------------------------------------------------- 
    80 \namdisplay{namzdf_ric} 
     80\fortranfile{namelists/namzdf_ric} 
    8181%-------------------------------------------------------------------------------------------------------------- 
    8282 
     
    136136 
    137137%--------------------------------------------namzdf_tke-------------------------------------------------- 
    138 \namdisplay{namzdf_tke} 
     138\fortranfile{namelists/namzdf_tke} 
    139139%-------------------------------------------------------------------------------------------------------------- 
    140140 
     
    512512 
    513513%--------------------------------------------namzdf_gls--------------------------------------------------------- 
    514 \namdisplay{namzdf_gls} 
     514\fortranfile{namelists/namzdf_gls} 
    515515%-------------------------------------------------------------------------------------------------------------- 
    516516 
     
    619619 
    620620%--------------------------------------------namzdf_osm--------------------------------------------------------- 
    621 \namdisplay{namzdf_osm} 
     621\fortranfile{namelists/namzdf_osm} 
    622622%-------------------------------------------------------------------------------------------------------------- 
    623623 
     
    631631 
    632632%--------------------------------------------namzdf-------------------------------------------------------- 
    633 \namdisplay{namzdf} 
     633\fortranfile{namelists/namzdf} 
    634634%-------------------------------------------------------------------------------------------------------------- 
    635635 
     
    651651 
    652652%--------------------------------------------namzdf-------------------------------------------------------- 
    653 \namdisplay{namzdf} 
     653\fortranfile{namelists/namzdf} 
    654654%-------------------------------------------------------------------------------------------------------------- 
    655655 
     
    718718 
    719719%--------------------------------------------namzdf-------------------------------------------------------- 
    720 \namdisplay{namzdf} 
     720\fortranfile{namelists/namzdf} 
    721721%-------------------------------------------------------------------------------------------------------------- 
    722722 
     
    777777 
    778778%-------------------------------------------namzdf_ddm------------------------------------------------- 
    779 \namdisplay{namzdf_ddm} 
     779%\fortranfile{namelists/namzdf_ddm} 
    780780%-------------------------------------------------------------------------------------------------------------- 
    781781 
     
    859859 
    860860%--------------------------------------------nambfr-------------------------------------------------------- 
    861 \namdisplay{nambfr} 
     861%\fortranfile{namelists/nambfr} 
    862862%-------------------------------------------------------------------------------------------------------------- 
    863863 
     
    11961196 
    11971197%--------------------------------------------namzdf_tmx-------------------------------------------------- 
    1198 \namdisplay{namzdf_tmx} 
     1198%\fortranfile{namelists/namzdf_tmx} 
    11991199%-------------------------------------------------------------------------------------------------------------- 
    12001200 
     
    13181318 
    13191319%--------------------------------------------namzdf_tmx_new------------------------------------------ 
    1320 \namdisplay{namzdf_tmx_new} 
     1320%\fortranfile{namelists/namzdf_tmx_new} 
    13211321%-------------------------------------------------------------------------------------------------------------- 
    13221322 
  • branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_misc.tex

    r9373 r9376  
    105105files: 
    106106\vspace{-10pt} 
    107 \begin{alltt} 
    108 \tiny 
    109107\begin{verbatim} 
    110108eORCA1_bathymetry_v2.nc 
    111109eORCA1_coordinates.nc 
    112110\end{verbatim} 
    113 \end{alltt} 
    114111\noindent These files define a horizontal domain of 362x332. Assuming the first row with 
    115112open ocean wet points in the non-isf bathymetry for this set is row 42 (Fortran indexing) 
     
    122119\noindent Add the new attribute to any input files requiring a j-row offset, i.e: 
    123120\vspace{-10pt} 
    124 \begin{alltt} 
    125 \tiny 
    126 \begin{verbatim} 
     121\begin{shcode} 
    127122ncatted  -a open_ocean_jstart,global,a,d,41 eORCA1_coordinates.nc  
    128123ncatted  -a open_ocean_jstart,global,a,d,41 eORCA1_bathymetry_v2.nc 
    129 \end{verbatim} 
    130 \end{alltt} 
     124\end{shcode} 
    131125  
    132126\noindent Add the logical switch to \ngn{namcfg} in the configuration namelist and set true: 
    133127%--------------------------------------------namcfg-------------------------------------------------------- 
    134 \namdisplay{namcfg} 
     128\fortranfile{namelists/namcfg} 
    135129%-------------------------------------------------------------------------------------------------------------- 
    136130 
     
    140134and 3D, netcdf, input field by adding the: 
    141135\vspace{-10pt} 
    142 \begin{alltt} 
    143 \tiny 
    144 \begin{verbatim} 
     136\begin{fortrancode} 
    145137lrowattr=ln_use_jattr 
    146 \end{verbatim} 
    147 \end{alltt} 
     138\end{fortrancode} 
    148139optional argument to the appropriate \np{iom\_get} call and the \np{open\_ocean\_jstart} attribute to the corresponding input files. It remains the users responsibility to set \np{jpjdta} and \np{jpjglo} values in the \np{namelist\_cfg} file according to their needs. 
    149140 
     
    244235\label{MISC_opt} 
    245236%--------------------------------------------namctl------------------------------------------------------- 
    246 \namdisplay{namctl}  
     237\fortranfile{namelists/namctl}  
    247238%-------------------------------------------------------------------------------------------------------------- 
    248239 
  • branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_model_basics_zstar.tex

    r9373 r9376  
    7878\label{DYN_hpg_spg} 
    7979%-----------------------------------------nam_dynspg---------------------------------------------------- 
    80 \namdisplay{nam_dynspg}  
     80\fortranfile{namelists/nam_dynspg}  
    8181%------------------------------------------------------------------------------------------------------------ 
    8282Options are defined through the  \ngn{nam\_dynspg} namelist variables. 
     
    115115\label{DYN_spg_ts} 
    116116%--------------------------------------------namdom---------------------------------------------------- 
    117 \namdisplay{namdom}  
     117\fortranfile{namelists/namdom}  
    118118%-------------------------------------------------------------------------------------------------------------- 
    119119The split-explicit free surface formulation used in OPA follows the one proposed by \citet{Griffies2004}. The general idea is to solve the free surface equation with a small time step, while the three dimensional prognostic variables are solved with a longer time step that is a multiple of \np{rdtbt} 
  • branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_step.tex

    r9373 r9376  
    284284\section{Start/Restart strategy} 
    285285\label{STP_rst} 
     286 
    286287%--------------------------------------------namrun------------------------------------------- 
    287 %\namdisplay{namrun} 
    288 \lstinputlisting{namelists/namrun} 
    289 %\inputminted[fontsize=\tiny, breaklines=true, breakanywhere]{fortran}{namelists/namrun} 
     288\fortranfile{namelists/namrun} 
    290289%-------------------------------------------------------------------------------------------------------------- 
    291290 
     
    338337\label{STP_time} 
    339338%--------------------------------------------namrun------------------------------------------- 
    340 \namdisplay{namdom}          
     339\fortranfile{namelists/namdom}          
    341340%-------------------------------------------------------------------------------------------------------------- 
    342341 
  • branches/2017/dev_merge_2017/DOC/texfiles/chapters/introduction.tex

    r9373 r9376  
    1010The Nucleus for European Modelling of the Ocean (\NEMO) is a framework of ocean  
    1111related engines, namely OPA\footnote{OPA = Oc\'{e}an PArall\'{e}lis\'{e}} for the  
    12 ocean dynamics and thermodynamics, LIM\footnote{LIM= Louvain)la-neuve Ice  
     12ocean dynamics and thermodynamics, LIM\footnote{LIM = Louvain la-neuve Ice  
    1313Model} for the sea-ice dynamics and thermodynamics, TOP\footnote{TOP = Tracer  
    1414in the Ocean Paradigm} for the biogeochemistry (both transport (TRP) and sources  
    15 minus sinks (LOBSTER, PISCES)\footnote{Both LOBSTER and PISCES are not  
    16 acronyms just name}. It is intended to be a flexible tool for studying the ocean and  
    17 its interactions with the other components of the earth climate system (atmosphere,  
    18 sea-ice, biogeochemical tracers, ...) over a wide range of space and time scales.  
     15minus sinks (LOBSTER\footnote{LOBSTER = Lodyc Ocean Biogeochemical SysTem for  
     16Ecosystem and Resources}, PISCES\footnote{PISCES = Pelagic Interactions Scheme for  
     17Carbon and Ecosystem Studies}). It is intended to be a flexible tool for studying  
     18the ocean and its interactions with the other components of the earth climate system  
     19(atmosphere, sea-ice, biogeochemical tracers, ...) over a wide range of space and time scales.  
    1920This documentation provides information about the physics represented by the ocean  
    2021component of \NEMO and the rationale for the choice of numerical schemes and  
     
    9192Some CPP keys are implemented in the FORTRAN code to allow code selection at compiling step. This selection of code at compilation time reduces the reliability of the whole platform since it changes the code from one set of CPP keys to the other. It is used only when the addition/suppression of the part of code highly changes the amount of memory at run time. 
    9293Usual coding looks like :  
    93  \vspace{-10pt} 
    94 \begin{alltt} 
    95 \tiny   
    96 \begin{verbatim} 
    97 #if defined key_option1     
    98              This part of the FORTRAN code will be active    
    99              only if key_option1 is activated at compiling step  
    100 #endif   
    101 \end{verbatim}  
    102 \end{alltt}      
    103  
     94\vspace{-10pt} 
     95\begin{fortrancode} 
     96#if defined key_option1 
     97   ! This part of the FORTRAN code will be active 
     98   ! only if key_option1 is activated at compiling step 
     99#endif 
     100\end{fortrancode} 
    104101 
    105102\noindent \index{Namelist} Namelists 
  • branches/2017/dev_merge_2017/DOC/texfiles/preamble.tex

    r9373 r9376  
    1 \documentclass[a4paper,11pt]{book} 
    2 %\documentclass[a4paper,11pt,makeidx]{book} <== may need this to generate index 
    3  
    4 %  makeindex NEMO_book  <== to regenerate the index 
    5 %  bibtex    NEMO_book  <== to generate  the bibliography 
    6  
    7 %% Silence package: filter output messages and warnings 
    8 \usepackage{silence} 
    9 %%% LaTeX warnings: package and label 
    10 \WarningFilter*{latex}{Package} 
    11 \WarningFilter*{latex}{Label} 
    12 %%% minitoc hints 
    13 \WarningFilter{minitoc(hints)}{W0023} 
    14 \WarningFilter{minitoc(hints)}{W0024} 
    15 \WarningFilter{minitoc(hints)}{W0028} 
    16 \WarningFilter{minitoc(hints)}{W0030} 
    17 %%% natbib citation warning "Citation ... multiply defined" 
    18 \WarningFilter*{natbib}{Citation} 
    19 %%% Filter all warnings 
    20 %\WarningsOff* 
    21  
    22 \usepackage{graphicx}                            % allows insertion of pictures 
    23 \graphicspath{{figures/}}                                  % Set global directory for pictures 
    24 %\usepackage[capbesideposition={top,center}]{floatrow}      % allows captions 
    25 %\floatsetup[table]{style=plaintop}                         % beside pictures 
    26 \usepackage[margin=10pt,font={small},                      % Gives small font for captions 
    27 labelsep=colon,labelfont={bf}]{caption}                    % 
    28 \usepackage{enumitem}                                      % allows non-bold description items 
    29 \usepackage{longtable}                                     % allows multipage tables 
    30  
    31 %hyperref 
    32 \usepackage[obeyspaces]{url} 
    33 \usepackage[pdftitle={NEMO ocean engine},pdfauthor={Gurvan Madec},pdfstartview=FitH, 
    34 bookmarks=true,bookmarksopen=true,breaklinks=true,colorlinks=true, 
    35 linkcolor=blue,anchorcolor=blue,citecolor=blue,filecolor=blue,menucolor=blue,urlcolor=blue]{hyperref} 
    36 % pdfsubject={The preprint document class 
    37 %   elsart},% pdfkeywords={diapycnal diffusion,numerical mixing,z-level models},%%  usage of exteranl hyperlink :  \href{mailto:my_address@wikibooks.org}{my\_address@wikibooks.org} 
    38 %                                                 \url{http://www.wikibooks.org} 
    39 %                                     or         \href{http://www.wikibooks.org}{wikibooks home} 
     1%% ============================================================================== 
     2%% preamble.tex: Document layout,  
     3%% ============================================================================== 
    404 
    415 
    42 %%%% page styles etc................ 
    43 \usepackage{fancyhdr} 
     6%% Document layout 
     7%% ============================================================================== 
     8 
     9\documentclass[a4paper, 11pt]{book} 
     10 
     11 
     12%% LaTeX packages 
     13%% ============================================================================== 
     14 
     15\usepackage{natbib}     %% bib 
     16\usepackage{caption}    %% caption 
     17\usepackage{xcolor}     %% color 
     18\usepackage{silence}    %% compilation 
     19\usepackage{times}      %% font 
     20\usepackage{hyperref}   %% hyper 
     21\usepackage{enumitem}   %% list 
     22\usepackage{minted}     %% listing 
     23\usepackage{amsmath}    %% maths 
     24\usepackage{fancyhdr}   %% page 
     25\usepackage{minitoc}    %% toc 
     26\usepackage{subfiles}   %% subdocs 
     27 
     28 
     29%% Extensions in bundle package 
     30 
     31\usepackage{amssymb, graphicx, longtable, makeidx, xspace} 
     32 
     33 
     34%% Configuration 
     35%% ============================================================================== 
     36 
     37\captionsetup{margin=10pt, font={small}, labelsep=colon, labelfont={bf}} 
     38\graphicspath{{figures/}} 
     39\hypersetup{ 
     40   pdftitle={NEMO ocean engine}, pdfauthor={Gurvan Madec, and the NEMO team}, 
     41   colorlinks 
     42} 
     43 
     44 
     45%% Styles & Customization 
     46%% ============================================================================== 
     47 
    4448\pagestyle{fancy} 
    45 % with this we ensure that the chapter and section 
    46 % headings are in lowercase. 
    47 \renewcommand{\chaptermark}[1]{\markboth{#1}{}} 
    48 \renewcommand{\sectionmark}[1]{\markright{\thesection.\ #1}} 
    49 \fancyhf{}             % delete current setting for header and footer 
     49\usemintedstyle{emacs} 
     50\bibliographystyle{texfiles/styles/ametsoc} 
     51 
     52 
     53%% Additionnal fonts 
     54\DeclareMathAlphabet{\mathpzc}{OT1}{pzc}{m}{it} 
     55 
     56 
     57%% Custom macros 
     58 
     59\usepackage{texfiles/styles/NEMO_manual} 
     60 
     61 
     62%% Page layout 
     63 
     64\fancyhf{} 
    5065\fancyhead[LE,RO]{\bfseries\thepage} 
    5166\fancyhead[LO]{\bfseries\hspace{-0em}\rightmark} 
     67\renewcommand{\sectionmark}[1]{\markright{\thesection.\ #1}} 
    5268\fancyhead[RE]{\bfseries\leftmark} 
     69\renewcommand{\chaptermark}[1]{\markboth{#1}{}} 
    5370\renewcommand{\headrulewidth}{0.5pt} 
    5471\renewcommand{\footrulewidth}{0pt  } 
    55 \addtolength{\headheight}{2.6pt}   % make space for the rule 
    56 %\addtolength{\headheight}{1.6pt}   % make space for the rule 
    57 % get rid of headers on plain pages 
    58 \fancypagestyle{plain}{\fancyhead{}\renewcommand{\headrulewidth}{0pt}} 
     72\addtolength{\headheight}{2.6pt} 
    5973 
    6074 
    61 %%%%  Section number in Margin....... 
    62 % typeset the number of each section in the left margin, with the start of each instance of 
    63 % sectional heading text aligned with the left hand edge of  the body text. 
     75%% Chapters catcodes 
     76 
    6477\makeatletter 
    65 \def\@seccntformat#1{\protect\makebox[0pt][r]{\csname the#1\endcsname\quad}} 
    66 \makeatother 
    67  
    68 % Leave blank pages completely empty, w/o header 
    69 \makeatletter 
     78\def\LigneVerticale{\vrule height 5cm depth 2cm\hspace{0.1cm}\relax} 
     79\def\LignesVerticales{\let\LV\LigneVerticale\LV\LV\LV\LV\LV\LV\LV\LV\LV\LV} 
     80\def\GrosCarreAvecUnChiffre#1{% 
     81   \rlap{\vrule height 0.8cm width 1cm depth 0.2cm}% 
     82   \rlap{\hbox to 1cm{\hss\mbox{\color{white} #1}\hss}}% 
     83   \vrule height 0pt width 1cm depth 0pt% 
     84} 
     85\def\@makechapterhead#1{ 
     86   \hbox{ 
     87      \huge\LignesVerticales 
     88      \hspace{-0.5cm} 
     89      \GrosCarreAvecUnChiffre{\thechapter} 
     90      \hspace{0.2cm} 
     91      \hbox{#1} 
     92   } 
     93   \par\vskip 
     941cm 
     95} 
     96\def\@makeschapterhead#1{ 
     97   \hbox{ 
     98      \huge\LignesVerticales 
     99      \hbox{#1} 
     100   } 
     101   \par\vskip 
     1022cm 
     103} 
    70104\def\cleardoublepage{\clearpage\if@twoside \ifodd\c@page\else 
    71105  \hbox{} 
     
    75109  \newpage 
    76110  \if@twocolumn\hbox{}\newpage\fi\fi\fi} 
     111\def\@seccntformat#1{\protect\makebox[0pt][r]{\csname the#1\endcsname\quad}} 
    77112\makeatother 
    78113 
    79 %%%% define the chapter  style ................ 
    80 \usepackage{minitoc}          %In French : \usepackage[french]{minitoc} 
    81 %\usepackage{mtcoff}          % invalidate the use of minitocs 
    82 \usepackage{fancybox} 
    83114 
    84 \makeatletter 
    85 \def\LigneVerticale{\vrule height 5cm depth 2cm\hspace{0.1cm}\relax} 
    86 \def\LignesVerticales{% 
    87   \let\LV\LigneVerticale\LV\LV\LV\LV\LV\LV\LV\LV\LV\LV} 
    88 \def\GrosCarreAvecUnChiffre#1{% 
    89   \rlap{\vrule height 0.8cm width 1cm depth 0.2cm}% 
    90  \rlap{\hbox to 1cm{\hss\mbox{\color{white} #1}\hss}}% 
    91   \vrule height 0pt width 1cm depth 0pt} 
    92 \def\GrosCarreAvecTroisChiffre#1{% 
    93   \rlap{\vrule height 0.8cm width 1.6cm depth 0.2cm}% 
    94  \rlap{\hbox to 1.5cm{\hss\mbox{\color{white} #1}\hss}}% 
    95   \vrule height 0pt width 1cm depth 0pt} 
     115%% Indexing 
     116%% ============================================================================== 
    96117 
    97 \def\@makechapterhead#1{\hbox{% 
    98    \huge 
    99     \LignesVerticales 
    100     \hspace{-0.5cm}% 
    101     \GrosCarreAvecUnChiffre{\thechapter} 
    102     \hspace{0.2cm}\hbox{#1}% 
    103 %    \GrosCarreAvecTroisChiffre{\thechapter} 
    104 %    \hspace{1cm}\hbox{#1}% 
    105 %}\par\vskip 2cm} 
    106 }\par\vskip 1cm} 
    107 \def\@makeschapterhead#1{\hbox{% 
    108    \huge 
    109     \LignesVerticales 
    110     %\hspace{0.5cm}% 
    111     \hbox{#1}% 
    112 }\par\vskip 2cm} 
    113 \makeatother 
    114  
    115 %\def\thechapter{\Roman{chapter}}      % chapter number to be Roman 
    116  
    117  
    118 %%%%           Mathematics............... 
    119 %\documentclass{amsart} 
    120 \usepackage{xspace}                              % helpd ensure correct spacing after macros 
    121 \usepackage{latexsym,amssymb,amsmath} 
    122 \allowdisplaybreaks[1]           % allow page breaks in the middle of equations 
    123 \usepackage{texfiles/styles/NEMO_manual}    % use maths shortcuts 
    124  
    125 \usepackage{times}             % use times font for text 
    126 %\usepackage{mathtime}                          % font for illustrator to work (belleek fonts ) 
    127 %\usepackage[latin1]{inputenc}                % allows some unicode removed (agn) 
    128  
    129  
    130 %%% essai commande 
    131 \newcommand{\nl}[1]{\texttt{\small{\textcolor{blue}{#1}}}} 
    132 \newcommand{\nlv}[1]{\texttt{\footnotesize#1}\xspace} 
    133 \newcommand{\smnlv}[1]{\texttt{\scriptsize#1}\xspace} 
    134  
    135 %%%% namelist & code display................................ 
    136 \usepackage{alltt,verbatim}   %%  alltt & verbatim for namelist 
    137 % namelists 
    138 \newcommand{\namdisplay}[1]{\begin{alltt}{\tiny\verbatiminput{namelists/#1}}\end{alltt}\vspace{-10pt}} 
    139 \newcommand{\namtools}[1]{\begin{alltt}{\tiny\verbatiminput{namelists/#1}}\end{alltt}\vspace{-10pt}} 
    140 % code display 
    141 \newcommand{\codedisplay} [1] {\begin{alltt}{\tiny {\begin{verbatim} {#1}} \end{verbatim}} \end{alltt}      } 
    142  
    143  
    144  
    145 %%%% commands for working with text................................ 
    146 % command to "comment out" portions of text ({} argument) or not ({#1} argument) 
    147 \newcommand{\amtcomment}[1]{}    % command to "commented out" portions of text or not (#1 in argument) 
    148 \newcommand{\sgacomment}[1]{}    % command to "commented out" portions of 
    149 \newcommand{\gmcomment}[1]{}     % command to "commented out" portions of 
    150 \newcommand{\sfcomment}[1]{}     % command to "commented out" portions of 
    151 %                                               % text that span line breaks 
    152 %Red (NR) or Yellow(WARN) 
    153 %\newcommand{\NR}   {\colorbox{red}   {#1}} 
    154 %\newcommand{\WARN} {\colorbox{yellow}{#1}} 
    155  
    156  
    157  
    158 %%% index commands...................... 
    159 \usepackage{makeidx} 
    160 %\usepackage{showidx}            % show the index entry 
    161  
    162 \newcommand{\mdl}[1]{\textit{#1.F90}\index{Modules!#1}}  %module (mdl) 
    163 \newcommand{\rou}[1]{\textit{#1}\index{Routines!#1}}  %module (routine) 
    164 \newcommand{\hf}[1]{\textit{#1.h90}\index{h90 file!#1}}  %module (h90 files) 
    165 \newcommand{\ngn}[1]{\textit{#1}\index{Namelist Group Name!#1}}   %namelist name (nampar) 
    166 \newcommand{\np}[1]{\textit{#1}\index{Namelist variables!#1}}        %namelist variable 
    167 \newcommand{\jp}[1]{\textit{#1}\index{Model parameters!#1}} %model parameter (jp) 
    168 \newcommand{\pp}[1]{\textit{#1}\index{Model parameters!#1}}    %namelist parameter (pp) 
    169 \newcommand{\ifile}[1]{\textit{#1.nc  }\index{Input NetCDF files!#1.nc}}   %input NetCDF files (.nc) 
    170 \newcommand{\key}[1]{\textbf{key\_#1}\index{CPP keys!key\_#1}} %key_cpp (key) 
    171 \newcommand{\NEMO}{\textit{NEMO}\xspace}  %NEMO (nemo) 
    172  
    173 %%%%   Bibliography   ............. 
    174 \usepackage[nottoc,notlof,notlot]{tocbibind} 
    175 \usepackage[square,comma]{natbib} 
    176 \bibpunct{[}{]}{,}{a}{}{;}                           %suppress "," after "et al." 
    177 \providecommand{\bibfont}{\small} 
    178  
    179 \usepackage{subfiles}                          % Separate compilation of chapters from whole manual 
    180 %\newcommand{\onlyinsubfile}[1]{#1}             % New commands for printing parts according to 
    181 %\newcommand{\notinsubfile}[1]{}                % the file being compiled 
    182 % Commands to use in the documentfile 
    183 %\renewcommand{\onlyinsubfile}[1]{}                      % Appears only if chapter   .tex file is compiled 
    184 %\renewcommand{\notinsubfile}[1]{#1}                     %    "    ""   "" NEMO_book .tex file is compiled 
    185  
    186 \DeclareMathAlphabet{\mathpzc}{OT1}{pzc}{m}{it} 
    187  
    188 \usepackage{hyphenat} 
    189 \hyphenation{AGRIF FORTRAN NEMOVAR bi-laplacian off-line on-line sea-ice well-known} 
    190  
    191 %% Add source code highlighting 
    192 %% From LaTeX Wikibooks https://en.wikibooks.org/wiki/LaTeX/Source_Code_Listings 
    193 \usepackage{listings} 
    194 \usepackage{xcolor} 
    195 %% Colors from Trac default style 
    196 \definecolor{backgroundcode}{HTML}{f8f8f8} 
    197 \definecolor{graycode}{HTML}{666666} 
    198 \definecolor{greencode}{HTML}{008800} 
    199 \definecolor{purplecode}{HTML}{AA22FF} 
    200 \definecolor{redcode}{HTML}{BB4444} 
    201 \definecolor{yellowcode}{HTML}{B8860B} 
    202 \lstset{language=[90]Fortran, 
    203   backgroundcolor=\color{backgroundcode}, 
    204   basicstyle=\tiny, 
    205   breaklines=true, 
    206   commentstyle=\color{greencode}, 
    207   identifierstyle=\color{yellowcode}, 
    208   keywordstyle=\color{purplecode}, 
    209   numberstyle=\color{graycode}, 
    210   stringstyle=\color{redcode}, 
    211   title=\lstname, 
    212 } 
     118\makeindex 
  • branches/2017/dev_merge_2017/DOC/texfiles/styles/NEMO_manual.sty

    r9373 r9376  
     1%% ============================================================================== 
     2%% macros.sty:  
     3%% ============================================================================== 
     4 
     5 
     6\def\deg{$^{\circ}$} 
     7\def\degC{$^{\circ}C$} 
     8\def\degK{$^{\circ}K$} 
     9\def\degN{$^{\circ}N$} 
     10\def\degS{$^{\circ}S$} 
     11 
    112\def\half{\textstyle\frac{1}{2}} 
    213\def\hhalf{\scriptstyle\frac{1}{2}} 
     14 
    315\def\quarter{\textstyle\frac{1}{4}} 
    416\def\qquarter{\scriptstyle\frac{1}{4}} 
     
    618\def\stwelfth{\sfrac{1}{12}} 
    719\def\sthirtysixth{\sfrac{1}{36}} 
    8 % \newcommand{\grad}{\boldsymbol{\nabla}} 
    9 % \newcommand{\gradh}{\boldsymbol{\nabla}_h} 
     20 
     21\def\bgamma\boldsymbol{\gamma} 
     22\def\rdt{\Delta t} 
     23 
     24\newcommand{ \gmcomment}[1]{} 
     25\newcommand{ \sfcomment}[1]{} 
     26\newcommand{\sgacomment}[1]{} 
     27 
     28\newcommand{\nl}[1]{\texttt{\small{\textcolor{blue}{#1}}}} 
     29\newcommand{\NEMO}{\textit{NEMO}\xspace} 
     30 
     31\newcommand{    \ifile}[1]{\textit{  #1.nc}\index{Input NetCDF files!#1.nc}} 
     32\newcommand{       \jp}[1]{\textit{     #1}\index{     Model parameters!#1}} 
     33\newcommand{       \hf}[1]{\textit{ #1.h90}\index{             h90 file!#1}} 
     34\newcommand{      \key}[1]{\textbf{key\_#1}\index{        CPP keys!key\_#1}} 
     35\newcommand{      \mdl}[1]{\textit{ #1.F90}\index{              Modules!#1}} 
     36\newcommand{      \ngn}[1]{\textit{     #1}\index{  Namelist Group Name!#1}} 
     37\newcommand{       \np}[1]{\textit{     #1}\index{   Namelist variables!#1}} 
     38\newcommand{       \pp}[1]{\textit{     #1}\index{     Model parameters!#1}} 
     39\newcommand{      \rou}[1]{\textit{     #1}\index{             Routines!#1}} 
     40 
    1041\newcommand{\grad}{\nabla} 
    1142\newcommand{\gradh}{\nabla_h} 
    12 \def\bgamma\boldsymbol{\gamma} 
    13 \def\rdt{\Delta t} 
     43 
    1444\newcommand{\ew}[3]{{e_{3#1}}_{\,#2}^{\,#3} } 
    15 \newcommand{\vect}[1]{\ensuremath{\mathbf{#1}}} % for vectors                                % non-italic bold 
     45\newcommand{\vect}[1]{\ensuremath{\mathbf{#1}}} 
    1646\newcommand{\Div}{\grad\cdot} 
    17 % \newcommand{\curl}{\boldsymbol{\nabla} \times} % for curl 
    18 \newcommand{\curl}{\nabla \times} % for curl 
     47\newcommand{\curl}{\nabla \times} 
    1948\newcommand{\pd}[2][]{\frac{\partial #1}{\partial #2}} 
    20 \def\deg{$^{\circ}$}                           % degrees  (NB: \r{} can % % also be used) 
    21 \def\degC{$^{\circ}C$} 
    22 \def\degK{$^{\circ}K$} 
    23 \def\degN{$^{\circ}N$} 
    24 \def\degS{$^{\circ}S$} 
    25 \newcommand{\alpbet} {\left(\alpha / \beta \right)}   % alpha/beta  for slp computation 
     49\newcommand{\alpbet} {\left(\alpha / \beta \right)} 
     50 
    2651\newcommand{\triad}[6][]{\ensuremath{{}_{#2}^{#3}{\mathbb{#4}_{#1}}_{#5}^{\,#6}}} 
    2752\newcommand{\triadd}[5]{\ensuremath{{}_{#1}^{#2}{\mathbb{#3}}_{#4}^{\,#5}}} 
     
    2954\newcommand{\rtriad}[2][]{\ensuremath{\triad[#1]{i}{k}{#2}{i_p}{k_p}}} 
    3055\newcommand{\rtriadt}[1]{\ensuremath{\triadt{i}{k}{#1}{i_p}{k_p}}} 
     56 
    3157\newcommand{\Alts}{{A}} 
    3258\newcommand{\Alt}{{A^{lT}}} 
     59 
    3360\newcommand{\rMLt}[1][i]{\tilde{r}_{\mathrm{ML}\,#1}} 
    3461\newcommand{\rML}[1][i]{r_{\mathrm{ML}\,#1}} 
     62 
    3563\newcommand{\mygstrut}[2]{\rule[#1 em]{0pt}{#2 em}} 
    3664\newcommand{\mystrut}{\rule[-.9 em]{0pt}{1.79 em}} 
  • branches/2017/dev_merge_2017/DOC/texfiles/top_matter.tex

    r9373 r9376  
    1 %\usepackage{pstricks} 
     1%% ============================================================================== 
     2%% top_matter.tex: frontpage with title 
     3%% ============================================================================== 
     4 
     5 
    26\title{ 
    3 %\psset{unit=1.1in,linewidth=4pt}   %parameters of the units for pstricks 
    4 % \rput(0,2){ \includegraphics[width=1.1\textwidth]{logo_ALL.pdf}             } \\ 
    5 % \vspace{0.1cm} 
    6 \vspace{-6.0cm} 
    7 \includegraphics[width=1.1\textwidth]{logo_ALL}\\ 
    8 \vspace{5.1cm} 
    9 \includegraphics[width=0.9\textwidth]{NEMO_logo_Black} \\ 
    10 \vspace{1.4cm} 
    11 \rule{345pt}{1.5pt} \\ 
    12 \vspace{0.45cm} 
    13 {\Huge NEMO ocean engine} 
    14 \rule{345pt}{1.5pt} \\ 
    15  } 
    16 %{ -- Draft --}   } 
    17 %\date{\today} 
    18 \date{ 
    19 Decembre 2017  \\ 
    20 {\small  -- version 4.0 alpha --} \\ 
    21 ~  \\ 
    22 \textit{\small Note du P\^ole de mod\'{e}lisation de l'Institut Pierre-Simon Laplace No 27 }\\ 
    23 \vspace{0.45cm} 
    24 { ISSN No 1288-1619.} 
     7\vspace{-6.0cm}\includegraphics[width=1.1\textwidth]{logo_ALL}          \\ 
     8\vspace{ 5.1cm}\includegraphics[width=0.9\textwidth]{NEMO_logo_Black}   \\ 
     9\vspace{ 1.4cm}\rule{345pt}{1.5pt}                                      \\ 
     10\vspace{0.45cm}{\Huge NEMO ocean engine}                                \\ 
     11\rule{345pt}{1.5pt} 
    2512} 
    2613 
    27  
    2814\author{ 
    29 \Large Gurvan Madec, and the NEMO team  \\ 
    30  \texttt{\small gurvan.madec@locean-ipsl.umpc.fr} \\ 
    31 % \texttt{\small nemo\_st@locean-ipsl.umpc.fr} \\ 
    32 %{\small Laboratoire d'Oc\'{e}anographie  et du Climat: Exp\'{e}rimentation et Approches Num\'{e}riques } 
     15\Large Gurvan Madec, and the NEMO team                                                          \\ 
     16\texttt{\small\href{mailto:gurvan.madec@locean-ipsl.umpc.fr}{gurvan.madec@locean-ipsl.umpc.fr}} \\ 
    3317} 
    3418 
    35 \dominitoc 
    36 \makeindex        %type this first :     makeindex -s NEMO.ist NEMO_book.idx 
     19\date{ 
     20Decembre 2017                                                                                \\ 
     21{\small  -- version 4.0 alpha --}                                                            \\ 
     22~                                                                                            \\ 
     23\textit{\small Note du P\^ole de mod\'{e}lisation de l'Institut Pierre-Simon Laplace No 27 } \\ 
     24\vspace{0.45cm}{ ISSN No 1288-1619.} 
     25} 
     26%\date{\today} 
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