Changeset 9376 for branches/2017

branches/2017/dev_merge_2017/DOC/LaTeX2HTML.sh

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+                      r9376
 #!/bin/bash
+sed -i -e 's#\\documentclass#%\\documentclass#' -e '/{document}/ s/^/%/' TexFiles/Chapters/*.tex
+sed -i    '30,${s#\\subfile{#\\include{#g}'                              NEMO_book.tex
+latex -shell-escape NEMO_book && makeindex NEMO_book && bibtex NEMO_book
+mkdir -p html
+latex2html -local_icons -no_footnode -split 4 -link 2 -dir html $*
+sed -i -e 's#%\\documentclass#\\documentclass#' -e '/{document}/ s/^%//' TexFiles/Chapters/*.tex
+sed -i    '30,${s#\\include{#\\subfile{#g}'                              NEMO_book.tex
+sed -i -e 's#\\documentclass#%\\documentclass#' -e '/{document}/ s/^/%/' texfiles/chapters/*.tex
+sed -i    '30,${s#\\subfile{#\\include{#g}'                              NEMO_manual.tex
+makeindex               NEMO_manual
+bibtex                  NEMO_manual
+latex    -shell-escape  NEMO_manual
+mkdir -p html_LaTeX2HTML
+latex2html -local_icons -no_footnode -split 4 -link 2 -dir html_LaTeX2HTML $* NEMO_manual
+sed -i -e 's#%\\documentclass#\\documentclass#' -e '/{document}/ s/^%//' texfiles/chapters/*.tex
+sed -i    '30,${s#\\include{#\\subfile{#g}'                              NEMO_manual.tex
 exit 0

branches/2017/dev_merge_2017/DOC/NEMO_manual.tex

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+%description: Book template
+%% ==============================================================================
+%% NEMO_book.tex: build the NEMO Reference Manual
+%% ==============================================================================
-% template of document for LaTeX
-% (C) Xavier Perseguers 2002 - xavier.perseguers@epfl.ch
+% ================================================================
+% PREAMBLE
+% ================================================================
+%% Run build_NEMO_manual.sh to generate the PDF version (with pdflatex)
+%% Preamble
+%% ==============================================================================
 \include{texfiles/preamble}
+% ================================================================
+% TOP MATTER
+% ================================================================
+\begin{document}
+%% 'minted' env. & shortcuts for syntax highlighting
+\setminted[fortran]{fontsize=\tiny, breaklines}
+\newminted{fortran}{}         % \begin{fortrancode}
+\newmintinline{fortran}{}     % \fortraninline
+\newmintedfile{fortran}{}     % \fortranfile
+\newminted{xml}{fontsize=\tiny, breaklines}
+\newminted{sh}{}
+\newminted{c}{}
+%% Frontmatter
+%% ==============================================================================
 \include{texfiles/top_matter}
-% ================================================================
-% DOCUMENT
-% ================================================================
+\begin{document}
+%% Frontpage
+\maketitle                 % generate the title
+\maketitle
 \frontmatter
+\tableofcontents              % generate a table of contents
+%\listoffigures               % generate a list  of figures
+%\listoftables                     % generate a list of tables
+%% ToC i.e. Table of Contents
+\dominitoc
+\tableofcontents
+%% Mainmatter
+%% ==============================================================================
 \mainmatter
+% ================================================================
+% Abstract - Foreword
+% ================================================================
+%% Abstract - Foreword
 \subfile{texfiles/chapters/abstract_foreword}
+% ================================================================
+% INTRODUCTION
+% ================================================================
+% Introduction
 \subfile{texfiles/chapters/introduction}
+% ================================================================
+% CHAPTERS
+% ================================================================
+% Chapters
 \subfile{texfiles/chapters/chap_model_basics}
 …
 \subfile{texfiles/chapters/chap_CONFIG}         % Predefined configurations
+% ================================================================
+% APPENDIX
+% ================================================================
+% Appendix
 \appendix
+%\subfile{texfiles/chapters/chap_conservation}
+\subfile{texfiles/chapters/annex_A}       % generalised vertical coordinate
+\subfile{texfiles/chapters/annex_B}       % diffusive operator
+\subfile{texfiles/chapters/annex_C}       % Discrete invariants of the eqs.
+\subfile{texfiles/chapters/annex_iso}                    % Isoneutral diffusion using triads
+\subfile{texfiles/chapters/annex_D}       % Coding rules
+%\subfile{texfiles/chapters/annex_E}                     % Notes on some on going staff (no included in the DOC)
+%\subfile{texfiles/chapters/annex_Fox-Kemper}   % Notes on Fox-Kemper (no included in the DOC)
+%\subfile{texfiles/chapters/annex_EVP}          % Notes on EVP (no included in the DOC)
+\subfile{texfiles/chapters/annex_A}             % Generalised vertical coordinate
+% ================================================================
+% INDEX
+% ================================================================
+\subfile{texfiles/chapters/annex_B}             % Diffusive operator
+\addcontentsline{toc}{chapter}{Index}
+\subfile{texfiles/chapters/annex_C}             % Discrete invariants of the eqs.
+\subfile{texfiles/chapters/annex_iso}           % Isoneutral diffusion using triads
+\subfile{texfiles/chapters/annex_D}             % Coding rules
+%% Not included
+%\subfile{texfiles/chapters/chap_conservation}  %
+%\subfile{texfiles/chapters/annex_E}            % Notes on some on going staff
+%\subfile{texfiles/chapters/annex_Fox-Kemper}   % Notes on Fox-Kemper
+%\subfile{texfiles/chapters/annex_EVP}          % Notes on EVP
+%% Backmatter
+%% ==============================================================================
+\backmatter
+%% Index
+%\addcontentsline{toc}{chapter}{Index}
 \printindex
-% ================================================================
-% BIBLIOGRAPHY
-% ================================================================
 %%\bibliographystyle{plainat}
+\bibliographystyle{texfiles/styles/ametsoc}     % AMS biblio style (JPO)
+%% Bibliography
 \bibliography{texfiles/bibliography/NEMO_manual}
+% ================================================================
 \end{document}

branches/2017/dev_merge_2017/DOC/clean.sh

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 #!/bin/bash
 rm -f $( ls -1 NEMO_manual.* | egrep -v "(tex)" ) *mpgraph*
 find TexFiles -regextype posix-extended -regex ".*\.(aux|log)" -exec rm -f {} \;
+rm -f $( ls -1 NEMO_manual.* | egrep -v "tex" )
+find texfiles -regextype posix-extended -regex ".*\.(aux|log)" -exec rm -f {} \;
 exit 0

branches/2017/dev_merge_2017/DOC/texfiles/chapters/abstract_foreword.tex

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 % ================================================================
 % Abstract (English / French)
+% Abstract
 % ================================================================
 \chapter*{Abstract / R\'{e}sum\'{e}}
+\chapter*{Abstract}
 \vspace{-40pt}
 …
 biogeochemical models (TOP) and, via the OASIS coupler, with several atmospheric general circulation models.
 It also support two-way grid embedding via the AGRIF software.
-% ================================================================
-% \vspace{0.5cm}
-%Le moteur oc\'{e}anique de NEMO (Nucleus for European Modelling of the Ocean) est un
-%mod\`{e}le aux \'{e}quations primitives de la circulation oc\'{e}anique r\'{e}gionale et globale.
-%Il se veut un outil flexible pour \'{e}tudier sur un vaste spectre spatiotemporel l'oc\'{e}an et ses
-%interactions avec les autres composantes du syst\`{e}me climatique terrestre.
-%Les variables pronostiques sont le champ tridimensionnel de vitesse, une hauteur de la mer
-%lin\'{e}aire, la Temp\'{e}rature Conservative et la Salinit\'{e} Absolue.
-%La distribution des variables se fait sur une grille C d'Arakawa tridimensionnelle utilisant une
-%coordonn\'{e}e verticale $z$ \`{a} niveaux entiers ou partiels, ou une coordonn\'{e}e s, ou encore
-%une combinaison des deux. Diff\'{e}rents choix sont propos\'{e}s pour d\'{e}crire la physique
-%oc\'{e}anique, incluant notamment des physiques verticales TKE et GLS. A travers l'infrastructure
-%NEMO, l'oc\'{e}an est interfac\'{e} avec des mod\`{e}les de glace de mer (LIM ou CICE),
-%de biog\'{e}ochimie marine et de traceurs passifs, et, via le coupleur OASIS, \`{a} plusieurs
-%mod\`{e}les de circulation g\'{e}n\'{e}rale atmosph\'{e}rique.
-%Il supporte \'{e}galement l'embo\^{i}tement interactif de maillages via le logiciel AGRIF.
+}
 …
 for problems, errors, or incorrect usage of NEMO.
  \vspace{1cm}
+\vspace{1cm}
 NEMO reference in papers and other publications is as follows:
  \vspace{0.5cm}
+\vspace{0.5cm}
 Madec, G., and the NEMO team, 2008: NEMO ocean engine.
 …
  \vspace{0.5cm}
 Additional information can be found on \href{http://www.nemo-ocean.eu/}{nemo-ocean.eu} website.
  \vspace{0.5cm}
+\vspace{0.5cm}
+Additional information can be found on \href{http://www.nemo-ocean.eu/}{www.nemo-ocean.eu}.
+\vspace{0.5cm}
 \end{document}

branches/2017/dev_merge_2017/DOC/texfiles/chapters/annex_iso.tex

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11	11	\section{Choice of \protect\ngn{namtra\_ldf} namelist parameters}
12	12	%-----------------------------------------nam_traldf------------------------------------------------------
13		\~~namdisplay{~~namtra_ldf}
	13	\fortranfile{namelists/namtra_ldf}
14	14	%---------------------------------------------------------------------------------------------------------
15	15

branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_ASM.tex

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 %------------------------------------------namasm-----------------------------------------------------
 \namdisplay{namasm}
+%\fortranfile{namelists/namasm}
 %-------------------------------------------------------------------------------------------------------------
 …
 \mbox{\textit{ncdump~-h}} is shown below
+\begin{alltt}
+\tiny
+\begin{verbatim}
+\begin{ccode}
 netcdf assim_background_increments {
 dimensions:
 …
                 :DOMAIN_type = "BOX" ;
+}
 \end{verbatim}
+\end{alltt}
+\end{ccode}
 \end{document}

branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_CONFIG.tex

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26	26
27	27	%------------------------------------------namcfg----------------------------------------------------
28		\~~namdisplay{~~namcfg}
	28	\fortranfile{namelists/namcfg}
29	29	%-------------------------------------------------------------------------------------------------------------
30	30

branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_DIA.tex

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 in a very easy way. All details of iomput functionalities are listed in the following subsections.
 Examples of the XML files that control the outputs can be found in:
+\begin{alltt}
+\begin{verbatim}
+  NEMOGCM/CONFIG/ORCA2_LIM/EXP00/iodef.xml
+  NEMOGCM/CONFIG/SHARED/field_def.xml
+  and
+  NEMOGCM/CONFIG/SHARED/domain_def.xml.
+\end{verbatim}
+\end{alltt}
+\path{NEMOGCM/CONFIG/ORCA2_LIM/EXP00/iodef.xml}, \path{NEMOGCM/CONFIG/SHARED/field_def.xml} and
+\path{NEMOGCM/CONFIG/SHARED/domain_def.xml}.
 The second functionality targets output performance when running in parallel (\key{mpp\_mpi}).
 …
 See the installation guide on the \href{http://forge.ipsl.jussieu.fr/ioserver/wiki}{XIOS} wiki for help and guidance.
 NEMO will need to link to the compiled XIOS library.
 The \href{http://www.nemo-ocean.eu/Using-NEMO/User-Guides/Basics/XIOS-IO-server-installation-and-use}{XIOS with NEMO}
+The \href{https://forge.ipsl.jussieu.fr/nemo/wiki/Users/ModelInterfacing/InputsOutputs#Inputs-OutputsusingXIOS}{XIOS with NEMO}
 guide provides an example illustration of how this can be achieved.
 …
 For example:
 \vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+\begin{xmlcode}
    <field_definition>
       <!-- T grid -->
 …
       ...
    </field_definition>
+\end{verbatim}
+}}\end{alltt}
+\end{xmlcode}
 Note your definition must be added to the field\_group whose reference grid is consistent
 with the size of the array passed to iomput.
 …
 or defined in the domain\_def.xml file. $e.g.$:
 \vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+\begin{xmlcode}
      <grid id="grid_T_3D" domain_ref="grid_T" axis_ref="deptht"/>
+\end{verbatim}
+}}\end{alltt}
+\end{xmlcode}
 Note, if your array is computed within the surface module each nn\_fsbc time\_step,
 add the field definition within the field\_group defined with the id ''SBC'': $<$field\_group id=''SBC''...$>$
 …
 \item[4.] add your field in one of the output files defined in iodef.xml (again see subsequent sections for syntax and rules)   \\
 \vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+\begin{xmlcode}
    <file id="file1" .../>
       ...
 …
       ...
    </file>
+\end{verbatim}
+}}\end{alltt}
+\end{xmlcode}
 \end{description}
 …
 \noindent In NEMO, by default, the field and domain definition is done in 2 separate files:
+{\scriptsize \tt
+\begin{verbatim}
+NEMOGCM/CONFIG/SHARED/field_def.xml
+and
+NEMOGCM/CONFIG/SHARED/domain_def.xml
+\end{verbatim}
+}
+\path{NEMOGCM/CONFIG/SHARED/field_def.xml} and \path{NEMOGCM/CONFIG/SHARED/domain_def.xml}
 \noindent that are included in the main iodef.xml file through the following commands: \\
 {\scriptsize \verb? <field_definition src="./field_def.xml" /> ? \\
 …
 example 1: Direct inheritance.
 \vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+\begin{xmlcode}
    <field_definition operation="average" >
      <field id="sst"                    />   <!-- averaged      sst -->
      <field id="sss" operation="instant"/>   <!-- instantaneous sss -->
    </field_definition>
+\end{verbatim}
+}}\end{alltt}
+\end{xmlcode}
 The field ''sst'' which is part (or a child) of the field\_definition will inherit the value ''average''
 of the attribute ''operation'' from its parent. Note that a child can overwrite
 …
 example 2: Inheritance by reference.
 \vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+\begin{xmlcode}
    <field_definition>
      <field id="sst" long_name="sea surface temperature" />
 …
      </file>
    </file_definition>
+\end{verbatim}
+}}\end{alltt}
+\end{xmlcode}
 Inherit (and overwrite, if needed) the attributes of a tag you are refering to.
 …
 Note that for the field ''toce'', we overwrite the grid definition inherited from the group by ''grid\_T\_3D''.
 \vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+\begin{xmlcode}
    <field_group id="grid_T" grid_ref="grid_T_2D">
     <field id="toce" long_name="temperature"             unit="degC" grid_ref="grid_T_3D"/>
 …
     <field id="ssh"  long_name="sea surface height"      unit="m"                        />
          ...
+\end{verbatim}
+}}\end{alltt}
+\end{xmlcode}
 Secondly, the group can be used to replace a list of elements.
 …
 For example, a short list of the usual variables related to the U grid:
 \vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+\begin{xmlcode}
    <field_group id="groupU" >
     <field field_ref="uoce"  />
 …
     <field field_ref="utau"  />
    </field_group>
+\end{verbatim}
+}}\end{alltt}
+\end{xmlcode}
 that can be directly included in a file through the following syntax:
 \vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+\begin{xmlcode}
    <file id="myfile_U" output_freq="1d" />
     <field_group group_ref="groupU"/>
     <field field_ref="uocetr_eff"  />  <!-- add another field -->
    </file>
+\end{verbatim}
+}}\end{alltt}
+\end{xmlcode}
 \subsection{Detailed functionalities }
 …
 of a 5 by 5 box with the bottom left corner at point (10,10).
 \vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+\begin{xmlcode}
    <domain_group id="grid_T">
     <domain id="myzoom" zoom_ibegin="10" zoom_jbegin="10" zoom_ni="5" zoom_nj="5" />
+\end{verbatim}
+}}\end{alltt}
+\end{xmlcode}
 The use of this subdomain is done through the redefinition of the attribute domain\_ref of the tag family field. For example:
 \vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+\begin{xmlcode}
    <file id="myfile_vzoom" output_freq="1d" >
       <field field_ref="toce" domain_ref="myzoom"/>
    </file>
+\end{verbatim}
+}}\end{alltt}
+\end{xmlcode}
 Moorings are seen as an extrem case corresponding to a 1 by 1 subdomain.
 The Equatorial section, the TAO, RAMA and PIRATA moorings are alredy registered in the code
 …
 by ''T'' (for example: ''8s137eT'', ''1.5s80.5eT'' ...)
 \vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+\begin{xmlcode}
    <file id="myfile_vzoom" output_freq="1d" >
       <field field_ref="toce" domain_ref="0n180wT"/>
    </file>
+\end{verbatim}
+}}\end{alltt}
+\end{xmlcode}
 Note 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.
 …
 Vertical 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:
 \vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+\begin{xmlcode}
    <axis_group id="deptht" long_name="Vertical T levels" unit="m" positive="down" >
       <axis id="deptht" />
       <axis id="deptht_myzoom" zoom_begin="1" zoom_end="10" />
+\end{verbatim}
+}}\end{alltt}
+\end{xmlcode}
 The use of this vertical zoom is done through the redefinition of the attribute axis\_ref of the tag family field. For example:
 \vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+\begin{xmlcode}
    <file id="myfile_hzoom" output_freq="1d" >
       <field field_ref="toce" axis_ref="deptht_myzoom"/>
    </file>
+\end{verbatim}
+}}\end{alltt}
+\end{xmlcode}
 \subsubsection{Control of the output file names}
 …
 The output file names are defined by the attributs ''name'' and ''name\_suffix'' of the tag family file. for example:
 \vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+\begin{xmlcode}
    <file_group id="1d" output_freq="1d" name="myfile_1d" >
       <file id="myfileA" name_suffix="_AAA" > <!-- will create file "myfile_1d_AAA"  -->
 …
       </file>
    </file_group>
+\end{verbatim}
+}}\end{alltt}
+\end{xmlcode}
 However 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:\\
 \\
 …
 \vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+\begin{xmlcode}
  <field field\_ref="sst"  name="tosK"  unit="degK" > sst + 273.15 </field>
  <field field\_ref="taum" name="taum2" unit="N2/m4" long\_name="square of wind stress module" > taum * taum </field>
  <field field\_ref="qt"   name="stupid\_check" > qt - qsr - qns </field>
+\end{verbatim}
+}}\end{alltt}
+\end{xmlcode}
 (2) Simple computation: define a new variable and use it in the file definition.
 …
 in field\_definition:
 \vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+\begin{xmlcode}
  <field id="sst2" long\_name="square of sea surface temperature" unit="degC2" >  sst * sst </field >
+\end{verbatim}
+}}\end{alltt}
+\end{xmlcode}
 in file\_definition:
 \vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+\begin{xmlcode}
  <field field\_ref="sst2" > sst2 </field>
+\end{verbatim}
+}}\end{alltt}
+\end{xmlcode}
 Note that in this case, the following syntaxe $<$field field\_ref="sst2" /$>$ is not working as sst2 won't be evaluated.
 …
 \vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+\begin{xmlcode}
      <!-- force to keep real 8 -->
  <field field\_ref="sst" name="tos\_r8" prec="8" />
       <!-- integer 2  with add\_offset and scale\_factor attributes -->
  <field field\_ref="sss" name="sos\_i2" prec="2" add\_offset="20." scale\_factor="1.e-3" />
+\end{verbatim}
+}}\end{alltt}
+\end{xmlcode}
 Note 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.
 …
 \vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+\begin{xmlcode}
       <file\_group id="1d" output\_freq="1d" output\_level="10" enabled=".TRUE."> <!-- 1d files -->
    <file id="file1" name\_suffix="\_grid\_T" description="ocean T grid variables" >
 …
        </file>
      </file\_group>
+\end{verbatim}
+}}\end{alltt}
+\end{xmlcode}
 (5) use of the ``@'' function: example 1, weighted temporal average
 …
  - define a new variable in field\_definition
 \vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+\begin{xmlcode}
  <field id="toce\_e3t" long\_name="temperature * e3t" unit="degC*m" grid\_ref="grid\_T\_3D" > toce * e3t </field >
+\end{verbatim}
+}}\end{alltt}
+\end{xmlcode}
  - use it when defining your file.
 \vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+\begin{xmlcode}
 <file\_group id="5d" output\_freq="5d"  output\_level="10" enabled=".TRUE." >  <!-- 5d files -->
  <file id="file1" name\_suffix="\_grid\_T" description="ocean T grid variables" >
 …
  </file>
 </file\_group>
+\end{verbatim}
+}}\end{alltt}
+\end{xmlcode}
 The 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.
 …
  - define a new variable in field\_definition
 \vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+\begin{xmlcode}
  <field id="ssh2" long\_name="square of sea surface temperature" unit="degC2" >  ssh * ssh </field >
+\end{verbatim}
+}}\end{alltt}
+\end{xmlcode}
  - use it when defining your file.
 \vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+\begin{xmlcode}
 <file\_group id="1m" output\_freq="1m"  output\_level="10" enabled=".TRUE." >  <!-- 1m files -->
  <file id="file1" name\_suffix="\_grid\_T" description="ocean T grid variables" >
 …
  </file>
 </file\_group>
+\end{verbatim}
+}}\end{alltt}
+\end{xmlcode}
 The 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.
 …
  - define 2 new variables in field\_definition
 \vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+\begin{xmlcode}
  <field id="sstmax" field\_ref="sst" long\_name="max of sea surface temperature" operation="maximum" />
  <field id="sstmin" field\_ref="sst" long\_name="min of sea surface temperature" operation="minimum" />
+\end{verbatim}
+}}\end{alltt}
+\end{xmlcode}
  - use these 2 new variables when defining your file.
 \vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+\begin{xmlcode}
 <file\_group id="1m" output\_freq="1m"  output\_level="10" enabled=".TRUE." >  <!-- 1m files -->
  <file id="file1" name\_suffix="\_grid\_T" description="ocean T grid variables" >
 …
  </file>
 </file\_group>
+\end{verbatim}
+}}\end{alltt}
+\end{xmlcode}
 The 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.
 …
 %------------------------------------------namnc4----------------------------------------------------
 \namdisplay{namnc4}
+\fortranfile{namelists/namnc4}
 %-------------------------------------------------------------------------------------------------------------
 …
 \vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+\begin{fortrancode}
      ichunksz(1) = MIN( idomain_size,MAX( (idomain_size-1)/nn_nchunks_i + 1 ,16 ) )
      ichunksz(2) = MIN( jdomain_size,MAX( (jdomain_size-1)/nn_nchunks_j + 1 ,16 ) )
      ichunksz(3) = MIN( kdomain_size,MAX( (kdomain_size-1)/nn_nchunks_k + 1 , 1 ) )
      ichunksz(4) = 1
+\end{verbatim}
+}}\end{alltt}
+\end{fortrancode}
 \noindent As an example, setting:
 \vspace{-20pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+\begin{fortrancode}
      nn_nchunks_i=4, nn_nchunks_j=4 and nn_nchunks_k=31
+\end{verbatim}
+}}\end{alltt} \vspace{-10pt}
+\end{fortrancode}
 \noindent for a standard ORCA2\_LIM configuration gives chunksizes of {\small\tt 46x38x1}
 …
 %------------------------------------------namtrd----------------------------------------------------
 \namdisplay{namtrd}
+\fortranfile{namelists/namtrd}
 %-------------------------------------------------------------------------------------------------------------
 …
 \label{FLO}
 %--------------------------------------------namflo-------------------------------------------------------
 \namdisplay{namflo}
+\fortranfile{namelists/namflo}
 %--------------------------------------------------------------------------------------------------------------
 …
 \vspace{-30pt}
+\begin{alltt}  {{\scriptsize
+\begin{verbatim}
+\begin{xmlcode}
      <group id="1d\_grid\_T" name="auto" description="ocean T grid variables" >   }
        <file id="floats"  description="floats variables"> }\\
 …
        </file>}
   </group>}
+\end{verbatim}
+}}\end{alltt}
+\end{xmlcode}
 …
 %------------------------------------------namdia_harm----------------------------------------------------
 \namdisplay{namdia_harm}
+%\fortranfile{namelists/namdia_harm}
 %----------------------------------------------------------------------------------------------------------
 …
 %------------------------------------------namdct----------------------------------------------------
 \namdisplay{namdct}
+\fortranfile{namelists/namdct}
 %-------------------------------------------------------------------------------------------------------------
 …
 %------------------------------------------namptr-----------------------------------------
 \namdisplay{namptr}
+\fortranfile{namelists/namptr}
 %-----------------------------------------------------------------------------------------
 …
 %------------------------------------------nam_dia25h-------------------------------------
 \namdisplay{nam_dia25h}
+\fortranfile{namelists/nam_dia25h}
 %-----------------------------------------------------------------------------------------
 …
 %------------------------------------------nam_diatmb-----------------------------------------------------
 \namdisplay{nam_diatmb}
+\fortranfile{namelists/nam_diatmb}
 %----------------------------------------------------------------------------------------------------------

branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_DIU.tex

r9373	r9376
34	34
35	35	Both the cool skin and warm layer models are controlled through the namelist \ngn{namdiu}:
36		\~~namdisplay{~~namdiu}
	36	\fortranfile{namelists/namdiu}
37	37	This namelist contains only two variables:
38	38	\begin{description}

branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_DOM.tex

-                      r9373
+                      r9376
 These fields can be read in an domain input file which name is setted in \np{cn\_domcfg} parameter specified in \ngn{namcfg}.
 \namdisplay{namcfg}
+\fortranfile{namelists/namcfg}
 or they can be defined in an analytical way in MY\_SRC directory of the configuration.
 For 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.
 …
 \label{DOM_zgr}
 %-----------------------------------------nam_zgr & namdom-------------------------------------------
 \namdisplay{namzgr}
 \namdisplay{namdom}
+%\fortranfile{namelists/namzgr}
+\fortranfile{namelists/namdom}
 %-------------------------------------------------------------------------------------------------------------
 …
 \label{DOM_zps}
 %--------------------------------------------namdom-------------------------------------------------------
 \namdisplay{namdom}
+\fortranfile{namelists/namdom}
 %--------------------------------------------------------------------------------------------------------------
 …
 \label{DOM_sco}
 %------------------------------------------nam_zgr_sco---------------------------------------------------
 \namdisplay{namzgr_sco}
+%\fortranfile{namelists/namzgr_sco}
 %--------------------------------------------------------------------------------------------------------------
 Options are defined in \ngn{namzgr\_sco}.
 …
 \label{DTA_tsd}
 %-----------------------------------------namtsd-------------------------------------------
 \namdisplay{namtsd}
+\fortranfile{namelists/namtsd}
 %------------------------------------------------------------------------------------------

branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_DYN.tex

-                      r9373
+                      r9376
 \label{DYN_adv_cor_vect}
 %-----------------------------------------nam_dynadv----------------------------------------------------
 \namdisplay{namdyn_adv}
+\fortranfile{namelists/namdyn_adv}
 %-------------------------------------------------------------------------------------------------------------
 …
 \label{DYN_vor}
 %------------------------------------------nam_dynvor----------------------------------------------------
 \namdisplay{namdyn_vor}
+\fortranfile{namelists/namdyn_vor}
 %-------------------------------------------------------------------------------------------------------------
 …
 \label{DYN_adv_cor_flux}
 %------------------------------------------nam_dynadv----------------------------------------------------
 \namdisplay{namdyn_adv}
+\fortranfile{namelists/namdyn_adv}
 %-------------------------------------------------------------------------------------------------------------
 …
 \label{DYN_hpg}
 %------------------------------------------nam_dynhpg---------------------------------------------------
 \namdisplay{namdyn_hpg}
+\fortranfile{namelists/namdyn_hpg}
 %-------------------------------------------------------------------------------------------------------------
 …
 \label{DYN_spg}
 %-----------------------------------------nam_dynspg----------------------------------------------------
 \namdisplay{namdyn_spg}
+\fortranfile{namelists/namdyn_spg}
 %------------------------------------------------------------------------------------------------------------
 …
 \label{DYN_spg_ts}
 %------------------------------------------namsplit-----------------------------------------------------------
+\namdisplay{namsplit}
+%\fortranfile{namelists/namsplit}
 %-------------------------------------------------------------------------------------------------------------
 …
 \label{DYN_ldf}
 %------------------------------------------nam_dynldf----------------------------------------------------
 \namdisplay{namdyn_ldf}
+\fortranfile{namelists/namdyn_ldf}
 %-------------------------------------------------------------------------------------------------------------
 …
 \label{DYN_zdf}
 %----------------------------------------------namzdf------------------------------------------------------
 \namdisplay{namzdf}
+\fortranfile{namelists/namzdf}
 %-------------------------------------------------------------------------------------------------------------
 …
 %----------------------------------------------namdom----------------------------------------------------
 \namdisplay{namdom}
+\fortranfile{namelists/namdom}
 %-------------------------------------------------------------------------------------------------------------

branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_LBC.tex

-                      r9373
+                      r9376
 \label{LBC_coast}
 %--------------------------------------------nam_lbc-------------------------------------------------------
 \namdisplay{namlbc}
+\fortranfile{namelists/namlbc}
 %--------------------------------------------------------------------------------------------------------------
 …
 %-----------------------------------------nambdy--------------------------------------------
 \namdisplay{nambdy}
+\fortranfile{namelists/nambdy}
 %-----------------------------------------------------------------------------------------------
 %-----------------------------------------nambdy_index--------------------------------------------
+\namdisplay{nambdy_index}
+%\fortranfile{namelists/nambdy_index}
 %-----------------------------------------------------------------------------------------------
 %-----------------------------------------nambdy_dta--------------------------------------------
 \namdisplay{nambdy_dta}
+\fortranfile{namelists/nambdy_dta}
 %-----------------------------------------------------------------------------------------------
 %-----------------------------------------nambdy_dta--------------------------------------------
 \namdisplay{nambdy_dta2}
+%\fortranfile{namelists/nambdy_dta2}
 %-----------------------------------------------------------------------------------------------
 …
 %-----------------------------------------nambdy_tide--------------------------------------------
 \namdisplay{nambdy_tide}
+\fortranfile{namelists/nambdy_tide}
 %-----------------------------------------------------------------------------------------------

branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_LDF.tex

-                      r9373
+                      r9376
 %-----------------------------------nam_traldf - nam_dynldf--------------------------------------------
 \namdisplay{namtra_ldf}
 \namdisplay{namdyn_ldf}
+\fortranfile{namelists/namtra_ldf}
+\fortranfile{namelists/namdyn_ldf}
 %--------------------------------------------------------------------------------------------------------------

branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_OBS.tex

-                      r9373
+                      r9376
 \item Download some EN4 data from
 \href{http://www.metoffice.gov.uk/hadobs}{http://www.metoffice.gov.uk/hadobs}. Choose observations which are
+\href{http://www.metoffice.gov.uk/hadobs}{www.metoffice.gov.uk/hadobs}. Choose observations which are
 valid for the period of your test run because the observation operator compares
 the model and observations for a matching date and time.
 \item Compile the OBSTOOLS code using:
 \begin{verbatim}
+\begin{shcode}
 ./maketools -n OBSTOOLS -m [ARCH].
 \end{verbatim}
+\end{shcode}
 \item Convert the EN4 data into feedback format:
 \begin{verbatim}
+\begin{shcode}
 enact2fb.exe profiles_01.nc EN.4.1.1.f.profiles.g10.YYYYMM.nc
 \end{verbatim}
+\end{shcode}
 \item Include the following in the NEMO namelist to run the observation
 …
 %------------------------------------------namobs_example-----------------------------------------------------
 \namdisplay{namobs_example}
+%\fortranfile{namelists/namobs_example}
 %-------------------------------------------------------------------------------------------------------------
 …
 %------------------------------------------namobs--------------------------------------------------------
 \namdisplay{namobs}
+\fortranfile{namelists/namobs}
 %-------------------------------------------------------------------------------------------------------------
 …
 \subsection{Profile feedback}
+\begin{alltt}
+\tiny
+\begin{verbatim}
+\begin{ccode}
 netcdf profiles_01 {
 dimensions:
 …
           :Convention = "NEMO unified observation operator output" ;
+}
+\end{verbatim}
+\end{alltt}
+\end{ccode}
 \subsection{Sea level anomaly feedback}
+\begin{alltt}
+\tiny
+\begin{verbatim}
+\begin{ccode}
 netcdf sla_01 {
 dimensions:
 …
           :Convention = "NEMO unified observation operator output" ;
+}
+\end{verbatim}
+\end{alltt}
+\end{ccode}
 The mean dynamic
 …
 surface height. Below is an example header for this file (on the ORCA025 grid).
+\begin{alltt}
+\tiny
+\begin{verbatim}
+\begin{ccode}
 dimensions:
         x = 1442 ;
 …
                 sossheig:units = "metres" ;
                 sossheig:grid = "orca025T" ;
+\end{verbatim}
+\end{alltt}
+\end{ccode}
 \subsection{Sea surface temperature feedback}
+\begin{alltt}
+\tiny
+\begin{verbatim}
+\begin{ccode}
 netcdf sst_01 {
 dimensions:
 …
           :Convention = "NEMO unified observation operator output" ;
+}
+\end{verbatim}
+\end{alltt}
+\end{ccode}
 \section{Theoretical details}
 …
 read the second time counter from a single file the namelist would be.
+\begin{alltt}
+\tiny
+\begin{verbatim}
+\begin{fortrancode}
 !----------------------------------------------------------------------
 !       namooo Offline obs_oper namelist
 …
    nn_ooo_idx = 2
+/
+\end{verbatim}
+\end{alltt}
+\end{fortrancode}
 \subsubsection{Multiple fields per run}
 …
 hourly fields are to be interpolated in a setup where 288 steps equals 24 hours.
+\begin{alltt}
+\tiny
+\begin{verbatim}
+\begin{fortrancode}
 !----------------------------------------------------------------------
 !       namooo Offline obs_oper namelist
 …
    nn_ooo_freq = 144
+/
+\end{verbatim}
+\end{alltt}
+\end{fortrancode}
 The above namelist will result in feedback files whose first 12 hours contain
 …
 fields plus an analysis field would be 7 counterparts per observation.
+\begin{alltt}
+\tiny
+\begin{verbatim}
+\begin{fortrancode}
    cl4_match_len = 7
+\end{verbatim}
+\end{alltt}
+\end{fortrancode}
 Then to correctly allocate a class 4 file the forecast axis must be defined. This
 is controlled via \textbf{cl4\_fcst\_len}, which in out above example would be 3.
+\begin{alltt}
+\tiny
+\begin{verbatim}
+\begin{fortrancode}
    cl4_fcst_len = 3
+\end{verbatim}
+\end{alltt}
+\end{fortrancode}
 Then for each model field it is necessary to designate what class 4 variable and
 …
 when interpreting the data afterwards.
+\begin{alltt}
+\tiny
+\begin{verbatim}
+\begin{fortrancode}
    cl4_vars = "forecast" "forecast" "forecast" "persistence" "persistence"
               "persistence" "best_estimate"
    cl4_fcst_idx = 1 2 3 1 2 3 1
    cl4_leadtime = 12 36 60
+\end{verbatim}
+\end{alltt}
+\end{fortrancode}
 In terms of files and indices of fields inside each file the class 4 approach
 …
 with a single field per file our example inputs will be specified.
+\begin{alltt}
+\tiny
+\begin{verbatim}
+\begin{fortrancode}
    ooo_files = "F.1.nc" "F.2.nc" "F.3.nc" "P.1.nc" "P.2.nc" "P.3.nc" "A.1.nc"
    nn_ooo_idx = 1 1 1 1 1 1 1
+\end{verbatim}
+\end{alltt}
+\end{fortrancode}
 When we combine all of the naming conventions, global attributes and i/o instructions
 the class 4 namelist becomes.
+\begin{alltt}
+\tiny
+\begin{verbatim}
+\begin{fortrancode}
 !----------------------------------------------------------------------
 !       namooo Offline obs_oper namelist
 …
    cl4_inst = "UK Met Office"
+/
+\end{verbatim}
+\end{alltt}
+\end{fortrancode}
 \subsubsection{Climatology interpolation}
 …
 operations, 1 per forecast.
+\begin{alltt}
+\tiny
+\begin{verbatim}
+\begin{fortrancode}
    ooo_files = "F1.nc" "F1.nc" "F2.nc" "F2.nc"
 ...
    cl4_fcst_idx = 1 2
+\end{verbatim}
+\end{alltt}
+\end{fortrancode}
 The above notation reveals the internal split between match up iterators and file
 …
 MPI run of NEMO offline obs\_oper into a single class 4 file. The program is called in the following way:
+\begin{alltt}
 \footnotesize
 \begin{verbatim}
+\begin{shcode}
 c4comb.exe outputfile inputfile1 inputfile2 ...
+\end{verbatim}
+\end{alltt}
+\end{shcode}
 \subsubsection{corio2fb}
 …
 standard feedback format. The program is called in the following way:
-\begin{alltt}
 \footnotesize
 \begin{verbatim}
+\begin{shcode}
 corio2fb.exe outputfile inputfile1 inputfile2 ...
+\end{verbatim}
+\end{alltt}
+\end{shcode}
 \subsubsection{enact2fb}
 …
 feedback format. The program is called in the following way:
-\begin{alltt}
 \footnotesize
 \begin{verbatim}
+\begin{shcode}
 enact2fb.exe outputfile inputfile1 inputfile2 ...
+\end{verbatim}
+\end{alltt}
+\end{shcode}
 \subsubsection{fbcomb}
 …
 MPI run of NEMO into a single feedback file. The program is called in the following way:
-\begin{alltt}
 \footnotesize
 \begin{verbatim}
+\begin{shcode}
 fbcomb.exe outputfile inputfile1 inputfile2 ...
+\end{verbatim}
+\end{alltt}
+\end{shcode}
 \subsubsection{fbmatchup}
 …
 in the following way:
-\begin{alltt}
 \footnotesize
 \begin{verbatim}
+\begin{shcode}
 fbmatchup.exe outputfile inputfile1 varname1 inputfile2 varname2 ...
+\end{verbatim}
+\end{alltt}
+\end{shcode}
 \subsubsection{fbprint}
 …
 following way:
-\begin{alltt}
 \footnotesize
 \begin{verbatim}
+\begin{shcode}
 fbprint.exe [options] inputfile
 …
      -D            print depths
      -z            use zipped files
+\end{verbatim}
+\end{alltt}
+\end{shcode}
 \subsubsection{fbsel}
 …
 following way:
-\begin{alltt}
 \footnotesize
 \begin{verbatim}
+\begin{shcode}
 fbsel.exe <input filename> <output filename>
+\end{verbatim}
+\end{alltt}
+\end{shcode}
 \subsubsection{fbstat}
 …
 files. The program is called in the following way:
-\begin{alltt}
 \footnotesize
 \begin{verbatim}
+\begin{shcode}
 fbstat.exe [-nmlev] <filenames>
+\end{verbatim}
+\end{alltt}
+\end{shcode}
 \subsubsection{fbthin}
 …
 modified to thin to a different resolution. The program is called in the following way:
-\begin{alltt}
 \footnotesize
 \begin{verbatim}
+\begin{shcode}
 fbthin.exe inputfile outputfile
+\end{verbatim}
+\end{alltt}
+\end{shcode}
 \subsubsection{sla2fb}
 …
 called in the following way:
-\begin{alltt}
 \footnotesize
 \begin{verbatim}
+\begin{shcode}
 sla2fb.exe [-s type] outputfile inputfile1 inputfile2 ...
 Option:
      -s            Select altimeter data_source
+\end{verbatim}
+\end{alltt}
+\end{shcode}
 \subsubsection{vel2fb}
 …
 is called in the following way:
-\begin{alltt}
 \footnotesize
 \begin{verbatim}
+\begin{shcode}
 vel2fb.exe outputfile inputfile1 inputfile2 ...
+\end{verbatim}
+\end{alltt}
+\end{shcode}
 \subsection{building the obstools}
 …
 observations and feedback files. It is possible to zoom in, plot individual profiles and
 calculate some basic statistics. To plot some data run IDL and then:
-\begin{alltt}
 \footnotesize
 \begin{verbatim}
+\begin{minted}{idl}
 IDL> dataplot, "filename"
+\end{verbatim}
+\end{alltt}
+\end{minted}
 To read multiple files into dataplot, for example multiple feedback files from different
 processors or from different days, the easiest method is to use the spawn command to generate
 a list of files which can then be passed to dataplot.
-\begin{alltt}
 \footnotesize
 \begin{verbatim}
+\begin{minted}{idl}
 IDL> spawn, 'ls profb*.nc', files
 IDL> dataplot, files
+\end{verbatim}
+\end{alltt}
+\end{minted}
 Fig~\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
 $\ $\newline    % force a new ligne
 %---------------------------------------namsbc--------------------------------------------------
 \namdisplay{namsbc}
+\fortranfile{namelists/namsbc}
 %--------------------------------------------------------------------------------------------------------------
 $\ $\newline    % force a new ligne
 …
 The structure associated with an input variable contains the following information:
+\begin{alltt}  {{\tiny
+\begin{verbatim}
+\begin{fortrancode}
 !  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
 !             !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
+\end{verbatim}
+}}\end{alltt}
+\end{fortrancode}
 where
 \begin{description}
 …
 %---------------------------------------namsbc_ana--------------------------------------------------
 \namdisplay{namsbc_sas}
+\fortranfile{namelists/namsbc_sas}
 %--------------------------------------------------------------------------------------------------------------
 …
 %---------------------------------------namsbc_ana--------------------------------------------------
 \namdisplay{namsbc_ana}
+%\fortranfile{namelists/namsbc_ana}
 %--------------------------------------------------------------------------------------------------------------
 …
 \label{SBC_flx}
 %------------------------------------------namsbc_flx----------------------------------------------------
 \namdisplay{namsbc_flx}
+\fortranfile{namelists/namsbc_flx}
 %-------------------------------------------------------------------------------------------------------------
 …
 \label{SBC_blk_core}
 %------------------------------------------namsbc_core----------------------------------------------------
+\namdisplay{namsbc_core}
+%\fortranfile{namelists/namsbc_core}
 %-------------------------------------------------------------------------------------------------------------
 …
 \label{SBC_blk_clio}
 %------------------------------------------namsbc_clio----------------------------------------------------
+\namdisplay{namsbc_clio}
+%\fortranfile{namelists/namsbc_clio}
 %-------------------------------------------------------------------------------------------------------------
 …
 \label{SBC_blk_mfs}
 %------------------------------------------namsbc_mfs----------------------------------------------------
+\namdisplay{namsbc_mfs}
+%\fortranfile{namelists/namsbc_mfs}
 %----------------------------------------------------------------------------------------------------------
 …
 \label{SBC_cpl}
 %------------------------------------------namsbc_cpl----------------------------------------------------
 \namdisplay{namsbc_cpl}
+\fortranfile{namelists/namsbc_cpl}
 %-------------------------------------------------------------------------------------------------------------
 …
 \label{SBC_apr}
 %------------------------------------------namsbc_apr----------------------------------------------------
 \namdisplay{namsbc_apr}
+\fortranfile{namelists/namsbc_apr}
 %-------------------------------------------------------------------------------------------------------------
 …
 %------------------------------------------nam_tide---------------------------------------
 \namdisplay{nam_tide}
+\fortranfile{namelists/nam_tide}
 %-----------------------------------------------------------------------------------------
 …
 \label{SBC_rnf}
 %------------------------------------------namsbc_rnf----------------------------------------------------
 \namdisplay{namsbc_rnf}
+\fortranfile{namelists/namsbc_rnf}
 %-------------------------------------------------------------------------------------------------------------
 …
 \label{SBC_isf}
 %------------------------------------------namsbc_isf----------------------------------------------------
 \namdisplay{namsbc_isf}
+\fortranfile{namelists/namsbc_isf}
 %--------------------------------------------------------------------------------------------------------
 Namelist variable in \ngn{namsbc}, \np{nn\_isf}, controls the ice shelf representation used.
 …
 \label{SBC_iscpl}
 %------------------------------------------namsbc_iscpl----------------------------------------------------
 \namdisplay{namsbc_iscpl}
+\fortranfile{namelists/namsbc_iscpl}
 %--------------------------------------------------------------------------------------------------------
 Ice sheet/ocean coupling is done through file exchange at the restart step. NEMO, at each restart step,
 …
 \label{ICB_icebergs}
 %------------------------------------------namberg----------------------------------------------------
 \namdisplay{namberg}
+\fortranfile{namelists/namberg}
 %-------------------------------------------------------------------------------------------------------------
 …
 \label{SBC_dcy}
 %------------------------------------------namsbc_rnf----------------------------------------------------
 %\namdisplay{namsbc}
+%\fortranfile{namelists/namsbc}
 %-------------------------------------------------------------------------------------------------------------
 …
 \label{SBC_ssr}
 %------------------------------------------namsbc_ssr----------------------------------------------------
 \namdisplay{namsbc_ssr}
+\fortranfile{namelists/namsbc_ssr}
 %-------------------------------------------------------------------------------------------------------------
 …
 \label{SBC_wave}
 %------------------------------------------namwave----------------------------------------------------
 \namdisplay{namsbc_wave}
+\fortranfile{namelists/namsbc_wave}
 %-------------------------------------------------------------------------------------------------------------

branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_STO.tex

r9373	r9376
124	124
125	125	%---------------------------------------namsbc--------------------------------------------------
126		\~~namdisplay{~~namsto}
	126	\fortranfile{namelists/namsto}
127	127	%--------------------------------------------------------------------------------------------------------------
128	128

branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_TRA.tex

-                      r9373
+                      r9376
 \label{TRA_adv}
 %------------------------------------------namtra_adv-----------------------------------------------------
 \namdisplay{namtra_adv}
+\fortranfile{namelists/namtra_adv}
 %-------------------------------------------------------------------------------------------------------------
 …
 \label{TRA_ldf}
 %-----------------------------------------nam_traldf------------------------------------------------------
 \namdisplay{namtra_ldf}
+\fortranfile{namelists/namtra_ldf}
 %-------------------------------------------------------------------------------------------------------------
 …
 \label{TRA_zdf}
 %--------------------------------------------namzdf---------------------------------------------------------
 \namdisplay{namzdf}
+\fortranfile{namelists/namzdf}
 %--------------------------------------------------------------------------------------------------------------
 …
 \label{TRA_qsr}
 %--------------------------------------------namqsr--------------------------------------------------------
 \namdisplay{namtra_qsr}
+\fortranfile{namelists/namtra_qsr}
 %--------------------------------------------------------------------------------------------------------------
 …
 \label{TRA_bbc}
 %--------------------------------------------nambbc--------------------------------------------------------
 \namdisplay{nambbc}
+\fortranfile{namelists/nambbc}
 %--------------------------------------------------------------------------------------------------------------
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 …
 \label{TRA_bbl}
 %--------------------------------------------nambbl---------------------------------------------------------
 \namdisplay{nambbl}
+\fortranfile{namelists/nambbl}
 %--------------------------------------------------------------------------------------------------------------
 …
 \label{TRA_dmp}
 %--------------------------------------------namtra_dmp-------------------------------------------------
 \namdisplay{namtra_dmp}
+\fortranfile{namelists/namtra_dmp}
 %--------------------------------------------------------------------------------------------------------------
 …
 %--------------------------------------------nam_dmp_create-------------------------------------------------
 \namtools{namelist_dmp}
+%\namtools{namelist_dmp}
 %-------------------------------------------------------------------------------------------------------
 …
 \label{TRA_nxt}
 %--------------------------------------------namdom-----------------------------------------------------
 \namdisplay{namdom}
+\fortranfile{namelists/namdom}
 %--------------------------------------------------------------------------------------------------------------
 …
 \label{TRA_eosbn2}
 %--------------------------------------------nameos-----------------------------------------------------
 \namdisplay{nameos}
+\fortranfile{namelists/nameos}
 %--------------------------------------------------------------------------------------------------------------

branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_ZDF.tex

-                      r9373
+                      r9376
 \label{ZDF_cst}
 %--------------------------------------------namzdf---------------------------------------------------------
 \namdisplay{namzdf}
+\fortranfile{namelists/namzdf}
 %--------------------------------------------------------------------------------------------------------------
 …
 %--------------------------------------------namric---------------------------------------------------------
 \namdisplay{namzdf_ric}
+\fortranfile{namelists/namzdf_ric}
 %--------------------------------------------------------------------------------------------------------------
 …
 %--------------------------------------------namzdf_tke--------------------------------------------------
 \namdisplay{namzdf_tke}
+\fortranfile{namelists/namzdf_tke}
 %--------------------------------------------------------------------------------------------------------------
 …
 %--------------------------------------------namzdf_gls---------------------------------------------------------
 \namdisplay{namzdf_gls}
+\fortranfile{namelists/namzdf_gls}
 %--------------------------------------------------------------------------------------------------------------
 …
 %--------------------------------------------namzdf_osm---------------------------------------------------------
 \namdisplay{namzdf_osm}
+\fortranfile{namelists/namzdf_osm}
 %--------------------------------------------------------------------------------------------------------------
 …
 %--------------------------------------------namzdf--------------------------------------------------------
 \namdisplay{namzdf}
+\fortranfile{namelists/namzdf}
 %--------------------------------------------------------------------------------------------------------------
 …
 %--------------------------------------------namzdf--------------------------------------------------------
 \namdisplay{namzdf}
+\fortranfile{namelists/namzdf}
 %--------------------------------------------------------------------------------------------------------------
 …
 %--------------------------------------------namzdf--------------------------------------------------------
 \namdisplay{namzdf}
+\fortranfile{namelists/namzdf}
 %--------------------------------------------------------------------------------------------------------------
 …
 %-------------------------------------------namzdf_ddm-------------------------------------------------
 \namdisplay{namzdf_ddm}
+%\fortranfile{namelists/namzdf_ddm}
 %--------------------------------------------------------------------------------------------------------------
 …
 %--------------------------------------------nambfr--------------------------------------------------------
 \namdisplay{nambfr}
+%\fortranfile{namelists/nambfr}
 %--------------------------------------------------------------------------------------------------------------
 …
 %--------------------------------------------namzdf_tmx--------------------------------------------------
 \namdisplay{namzdf_tmx}
+%\fortranfile{namelists/namzdf_tmx}
 %--------------------------------------------------------------------------------------------------------------
 …
 %--------------------------------------------namzdf_tmx_new------------------------------------------
 \namdisplay{namzdf_tmx_new}
+%\fortranfile{namelists/namzdf_tmx_new}
 %--------------------------------------------------------------------------------------------------------------

branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_misc.tex

-                      r9373
+                      r9376
 files:
 \vspace{-10pt}
-\begin{alltt}
-\tiny
 \begin{verbatim}
 eORCA1_bathymetry_v2.nc
 eORCA1_coordinates.nc
 \end{verbatim}
-\end{alltt}
 \noindent These files define a horizontal domain of 362x332. Assuming the first row with
 open ocean wet points in the non-isf bathymetry for this set is row 42 (Fortran indexing)
 …
 \noindent Add the new attribute to any input files requiring a j-row offset, i.e:
 \vspace{-10pt}
+\begin{alltt}
+\tiny
+\begin{verbatim}
+\begin{shcode}
 ncatted  -a open_ocean_jstart,global,a,d,41 eORCA1_coordinates.nc
 ncatted  -a open_ocean_jstart,global,a,d,41 eORCA1_bathymetry_v2.nc
+\end{verbatim}
+\end{alltt}
+\end{shcode}
 \noindent Add the logical switch to \ngn{namcfg} in the configuration namelist and set true:
 %--------------------------------------------namcfg--------------------------------------------------------
 \namdisplay{namcfg}
+\fortranfile{namelists/namcfg}
 %--------------------------------------------------------------------------------------------------------------
 …
 and 3D, netcdf, input field by adding the:
 \vspace{-10pt}
+\begin{alltt}
+\tiny
+\begin{verbatim}
+\begin{fortrancode}
 lrowattr=ln_use_jattr
+\end{verbatim}
+\end{alltt}
+\end{fortrancode}
 optional 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.
 …
 \label{MISC_opt}
 %--------------------------------------------namctl-------------------------------------------------------
 \namdisplay{namctl}
+\fortranfile{namelists/namctl}
 %--------------------------------------------------------------------------------------------------------------

branches/2017/dev_merge_2017/DOC/texfiles/chapters/chap_model_basics_zstar.tex

-                      r9373
+                      r9376
 \label{DYN_hpg_spg}
 %-----------------------------------------nam_dynspg----------------------------------------------------
 \namdisplay{nam_dynspg}
+\fortranfile{namelists/nam_dynspg}
 %------------------------------------------------------------------------------------------------------------
 Options are defined through the  \ngn{nam\_dynspg} namelist variables.
 …
 \label{DYN_spg_ts}
 %--------------------------------------------namdom----------------------------------------------------
 \namdisplay{namdom}
+\fortranfile{namelists/namdom}
 %--------------------------------------------------------------------------------------------------------------
 The 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
 \section{Start/Restart strategy}
 \label{STP_rst}
 %--------------------------------------------namrun-------------------------------------------
+%\namdisplay{namrun}
+\lstinputlisting{namelists/namrun}
+%\inputminted[fontsize=\tiny, breaklines=true, breakanywhere]{fortran}{namelists/namrun}
+\fortranfile{namelists/namrun}
 %--------------------------------------------------------------------------------------------------------------
 …
 \label{STP_time}
 %--------------------------------------------namrun-------------------------------------------
 \namdisplay{namdom}
+\fortranfile{namelists/namdom}
 %--------------------------------------------------------------------------------------------------------------

branches/2017/dev_merge_2017/DOC/texfiles/chapters/introduction.tex

-                      r9373
+                      r9376
 The Nucleus for European Modelling of the Ocean (\NEMO) is a framework of ocean
 related engines, namely OPA\footnote{OPA = Oc\'{e}an PArall\'{e}lis\'{e}} for the
 ocean dynamics and thermodynamics, LIM\footnote{LIM= Louvain)la-neuve Ice
+ocean dynamics and thermodynamics, LIM\footnote{LIM = Louvain la-neuve Ice
 Model} for the sea-ice dynamics and thermodynamics, TOP\footnote{TOP = Tracer
 in the Ocean Paradigm} for the biogeochemistry (both transport (TRP) and sources
+minus sinks (LOBSTER, PISCES)\footnote{Both LOBSTER and PISCES are not
+acronyms just name}. It is intended to be a flexible tool for studying the ocean and
+its interactions with the other components of the earth climate system (atmosphere,
+sea-ice, biogeochemical tracers, ...) over a wide range of space and time scales.
+minus sinks (LOBSTER\footnote{LOBSTER = Lodyc Ocean Biogeochemical SysTem for
+Ecosystem and Resources}, PISCES\footnote{PISCES = Pelagic Interactions Scheme for
+Carbon and Ecosystem Studies}). It is intended to be a flexible tool for studying
+the ocean and its interactions with the other components of the earth climate system
+(atmosphere, sea-ice, biogeochemical tracers, ...) over a wide range of space and time scales.
 This documentation provides information about the physics represented by the ocean
 component of \NEMO and the rationale for the choice of numerical schemes and
 …
 Some 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.
 Usual coding looks like :
+ \vspace{-10pt}
+\begin{alltt}
+\tiny
+\begin{verbatim}
+#if defined key_option1
+             This part of the FORTRAN code will be active
+             only if key_option1 is activated at compiling step
+#endif
+\end{verbatim}
+\end{alltt}
+\vspace{-10pt}
+\begin{fortrancode}
+#if defined key_option1
+   ! This part of the FORTRAN code will be active
+   ! only if key_option1 is activated at compiling step
+#endif
+\end{fortrancode}
 \noindent \index{Namelist} Namelists

branches/2017/dev_merge_2017/DOC/texfiles/preamble.tex

-                      r9373
+                      r9376
+\documentclass[a4paper,11pt]{book}
+%\documentclass[a4paper,11pt,makeidx]{book} <== may need this to generate index
+%  makeindex NEMO_book  <== to regenerate the index
+%  bibtex    NEMO_book  <== to generate  the bibliography
+%% Silence package: filter output messages and warnings
+\usepackage{silence}
+%%% LaTeX warnings: package and label
+\WarningFilter*{latex}{Package}
+\WarningFilter*{latex}{Label}
+%%% minitoc hints
+\WarningFilter{minitoc(hints)}{W0023}
+\WarningFilter{minitoc(hints)}{W0024}
+\WarningFilter{minitoc(hints)}{W0028}
+\WarningFilter{minitoc(hints)}{W0030}
+%%% natbib citation warning "Citation ... multiply defined"
+\WarningFilter*{natbib}{Citation}
+%%% Filter all warnings
+%\WarningsOff*
+\usepackage{graphicx}                            % allows insertion of pictures
+\graphicspath{{figures/}}                                  % Set global directory for pictures
+%\usepackage[capbesideposition={top,center}]{floatrow}      % allows captions
+%\floatsetup[table]{style=plaintop}                         % beside pictures
+\usepackage[margin=10pt,font={small},                      % Gives small font for captions
+labelsep=colon,labelfont={bf}]{caption}                    %
+\usepackage{enumitem}                                      % allows non-bold description items
+\usepackage{longtable}                                     % allows multipage tables
+%hyperref
+\usepackage[obeyspaces]{url}
+\usepackage[pdftitle={NEMO ocean engine},pdfauthor={Gurvan Madec},pdfstartview=FitH,
+bookmarks=true,bookmarksopen=true,breaklinks=true,colorlinks=true,
+linkcolor=blue,anchorcolor=blue,citecolor=blue,filecolor=blue,menucolor=blue,urlcolor=blue]{hyperref}
+% pdfsubject={The preprint document class
+%   elsart},% pdfkeywords={diapycnal diffusion,numerical mixing,z-level models},%%  usage of exteranl hyperlink :  \href{mailto:my_address@wikibooks.org}{my\_address@wikibooks.org}
+%                                                 \url{http://www.wikibooks.org}
+%                                     or         \href{http://www.wikibooks.org}{wikibooks home}
+%% ==============================================================================
+%% preamble.tex: Document layout,
+%% ==============================================================================
+%%%% page styles etc................
+\usepackage{fancyhdr}
+%% Document layout
+%% ==============================================================================
+\documentclass[a4paper, 11pt]{book}
+%% LaTeX packages
+%% ==============================================================================
+\usepackage{natbib}     %% bib
+\usepackage{caption}    %% caption
+\usepackage{xcolor}     %% color
+\usepackage{silence}    %% compilation
+\usepackage{times}      %% font
+\usepackage{hyperref}   %% hyper
+\usepackage{enumitem}   %% list
+\usepackage{minted}     %% listing
+\usepackage{amsmath}    %% maths
+\usepackage{fancyhdr}   %% page
+\usepackage{minitoc}    %% toc
+\usepackage{subfiles}   %% subdocs
+%% Extensions in bundle package
+\usepackage{amssymb, graphicx, longtable, makeidx, xspace}
+%% Configuration
+%% ==============================================================================
+\captionsetup{margin=10pt, font={small}, labelsep=colon, labelfont={bf}}
+\graphicspath{{figures/}}
+\hypersetup{
+   pdftitle={NEMO ocean engine}, pdfauthor={Gurvan Madec, and the NEMO team},
+   colorlinks
+}
+%% Styles & Customization
+%% ==============================================================================
 \pagestyle{fancy}
+% with this we ensure that the chapter and section
+% headings are in lowercase.
+\renewcommand{\chaptermark}[1]{\markboth{#1}{}}
+\renewcommand{\sectionmark}[1]{\markright{\thesection.\ #1}}
+\fancyhf{}             % delete current setting for header and footer
+\usemintedstyle{emacs}
+\bibliographystyle{texfiles/styles/ametsoc}
+%% Additionnal fonts
+\DeclareMathAlphabet{\mathpzc}{OT1}{pzc}{m}{it}
+%% Custom macros
+\usepackage{texfiles/styles/NEMO_manual}
+%% Page layout
+\fancyhf{}
 \fancyhead[LE,RO]{\bfseries\thepage}
 \fancyhead[LO]{\bfseries\hspace{-0em}\rightmark}
+\renewcommand{\sectionmark}[1]{\markright{\thesection.\ #1}}
 \fancyhead[RE]{\bfseries\leftmark}
+\renewcommand{\chaptermark}[1]{\markboth{#1}{}}
 \renewcommand{\headrulewidth}{0.5pt}
 \renewcommand{\footrulewidth}{0pt  }
+\addtolength{\headheight}{2.6pt}   % make space for the rule
+%\addtolength{\headheight}{1.6pt}   % make space for the rule
+% get rid of headers on plain pages
+\fancypagestyle{plain}{\fancyhead{}\renewcommand{\headrulewidth}{0pt}}
+\addtolength{\headheight}{2.6pt}
+%%%%  Section number in Margin.......
+% typeset the number of each section in the left margin, with the start of each instance of
+% sectional heading text aligned with the left hand edge of  the body text.
+%% Chapters catcodes
 \makeatletter
+\def\@seccntformat#1{\protect\makebox[0pt][r]{\csname the#1\endcsname\quad}}
+\makeatother
+% Leave blank pages completely empty, w/o header
+\makeatletter
+\def\LigneVerticale{\vrule height 5cm depth 2cm\hspace{0.1cm}\relax}
+\def\LignesVerticales{\let\LV\LigneVerticale\LV\LV\LV\LV\LV\LV\LV\LV\LV\LV}
+\def\GrosCarreAvecUnChiffre#1{%
+   \rlap{\vrule height 0.8cm width 1cm depth 0.2cm}%
+   \rlap{\hbox to 1cm{\hss\mbox{\color{white} #1}\hss}}%
+   \vrule height 0pt width 1cm depth 0pt%
+}
+\def\@makechapterhead#1{
+   \hbox{
+      \huge\LignesVerticales
+      \hspace{-0.5cm}
+      \GrosCarreAvecUnChiffre{\thechapter}
+      \hspace{0.2cm}
+      \hbox{#1}
+   }
+   \par\vskip
+cm
+}
+\def\@makeschapterhead#1{
+   \hbox{
+      \huge\LignesVerticales
+      \hbox{#1}
+   }
+   \par\vskip
+cm
+}
 \def\cleardoublepage{\clearpage\if@twoside \ifodd\c@page\else
   \hbox{}
 …
   \newpage
   \if@twocolumn\hbox{}\newpage\fi\fi\fi}
+\def\@seccntformat#1{\protect\makebox[0pt][r]{\csname the#1\endcsname\quad}}
 \makeatother
-%%%% define the chapter  style ................
-\usepackage{minitoc}          %In French : \usepackage[french]{minitoc}
-%\usepackage{mtcoff}          % invalidate the use of minitocs
-\usepackage{fancybox}
+\makeatletter
+\def\LigneVerticale{\vrule height 5cm depth 2cm\hspace{0.1cm}\relax}
+\def\LignesVerticales{%
+  \let\LV\LigneVerticale\LV\LV\LV\LV\LV\LV\LV\LV\LV\LV}
+\def\GrosCarreAvecUnChiffre#1{%
+  \rlap{\vrule height 0.8cm width 1cm depth 0.2cm}%
+ \rlap{\hbox to 1cm{\hss\mbox{\color{white} #1}\hss}}%
+  \vrule height 0pt width 1cm depth 0pt}
+\def\GrosCarreAvecTroisChiffre#1{%
+  \rlap{\vrule height 0.8cm width 1.6cm depth 0.2cm}%
+ \rlap{\hbox to 1.5cm{\hss\mbox{\color{white} #1}\hss}}%
+  \vrule height 0pt width 1cm depth 0pt}
+%% Indexing
+%% ==============================================================================
+\def\@makechapterhead#1{\hbox{%
+   \huge
+    \LignesVerticales
+    \hspace{-0.5cm}%
+    \GrosCarreAvecUnChiffre{\thechapter}
+    \hspace{0.2cm}\hbox{#1}%
+%    \GrosCarreAvecTroisChiffre{\thechapter}
+%    \hspace{1cm}\hbox{#1}%
+%}\par\vskip 2cm}
+}\par\vskip 1cm}
+\def\@makeschapterhead#1{\hbox{%
+   \huge
+    \LignesVerticales
+    %\hspace{0.5cm}%
+    \hbox{#1}%
+}\par\vskip 2cm}
+\makeatother
+%\def\thechapter{\Roman{chapter}}      % chapter number to be Roman
+%%%%           Mathematics...............
+%\documentclass{amsart}
+\usepackage{xspace}                              % helpd ensure correct spacing after macros
+\usepackage{latexsym,amssymb,amsmath}
+\allowdisplaybreaks[1]           % allow page breaks in the middle of equations
+\usepackage{texfiles/styles/NEMO_manual}    % use maths shortcuts
+\usepackage{times}             % use times font for text
+%\usepackage{mathtime}                          % font for illustrator to work (belleek fonts )
+%\usepackage[latin1]{inputenc}                % allows some unicode removed (agn)
+%%% essai commande
+\newcommand{\nl}[1]{\texttt{\small{\textcolor{blue}{#1}}}}
+\newcommand{\nlv}[1]{\texttt{\footnotesize#1}\xspace}
+\newcommand{\smnlv}[1]{\texttt{\scriptsize#1}\xspace}
+%%%% namelist & code display................................
+\usepackage{alltt,verbatim}   %%  alltt & verbatim for namelist
+% namelists
+\newcommand{\namdisplay}[1]{\begin{alltt}{\tiny\verbatiminput{namelists/#1}}\end{alltt}\vspace{-10pt}}
+\newcommand{\namtools}[1]{\begin{alltt}{\tiny\verbatiminput{namelists/#1}}\end{alltt}\vspace{-10pt}}
+% code display
+\newcommand{\codedisplay} [1] {\begin{alltt}{\tiny {\begin{verbatim} {#1}} \end{verbatim}} \end{alltt}      }
+%%%% commands for working with text................................
+% command to "comment out" portions of text ({} argument) or not ({#1} argument)
+\newcommand{\amtcomment}[1]{}    % command to "commented out" portions of text or not (#1 in argument)
+\newcommand{\sgacomment}[1]{}    % command to "commented out" portions of
+\newcommand{\gmcomment}[1]{}     % command to "commented out" portions of
+\newcommand{\sfcomment}[1]{}     % command to "commented out" portions of
+%                                               % text that span line breaks
+%Red (NR) or Yellow(WARN)
+%\newcommand{\NR}   {\colorbox{red}   {#1}}
+%\newcommand{\WARN} {\colorbox{yellow}{#1}}
+%%% index commands......................
+\usepackage{makeidx}
+%\usepackage{showidx}            % show the index entry
+\newcommand{\mdl}[1]{\textit{#1.F90}\index{Modules!#1}}  %module (mdl)
+\newcommand{\rou}[1]{\textit{#1}\index{Routines!#1}}  %module (routine)
+\newcommand{\hf}[1]{\textit{#1.h90}\index{h90 file!#1}}  %module (h90 files)
+\newcommand{\ngn}[1]{\textit{#1}\index{Namelist Group Name!#1}}   %namelist name (nampar)
+\newcommand{\np}[1]{\textit{#1}\index{Namelist variables!#1}}        %namelist variable
+\newcommand{\jp}[1]{\textit{#1}\index{Model parameters!#1}} %model parameter (jp)
+\newcommand{\pp}[1]{\textit{#1}\index{Model parameters!#1}}    %namelist parameter (pp)
+\newcommand{\ifile}[1]{\textit{#1.nc  }\index{Input NetCDF files!#1.nc}}   %input NetCDF files (.nc)
+\newcommand{\key}[1]{\textbf{key\_#1}\index{CPP keys!key\_#1}} %key_cpp (key)
+\newcommand{\NEMO}{\textit{NEMO}\xspace}  %NEMO (nemo)
+%%%%   Bibliography   .............
+\usepackage[nottoc,notlof,notlot]{tocbibind}
+\usepackage[square,comma]{natbib}
+\bibpunct{[}{]}{,}{a}{}{;}                           %suppress "," after "et al."
+\providecommand{\bibfont}{\small}
+\usepackage{subfiles}                          % Separate compilation of chapters from whole manual
+%\newcommand{\onlyinsubfile}[1]{#1}             % New commands for printing parts according to
+%\newcommand{\notinsubfile}[1]{}                % the file being compiled
+% Commands to use in the documentfile
+%\renewcommand{\onlyinsubfile}[1]{}                      % Appears only if chapter   .tex file is compiled
+%\renewcommand{\notinsubfile}[1]{#1}                     %    "    ""   "" NEMO_book .tex file is compiled
+\DeclareMathAlphabet{\mathpzc}{OT1}{pzc}{m}{it}
+\usepackage{hyphenat}
+\hyphenation{AGRIF FORTRAN NEMOVAR bi-laplacian off-line on-line sea-ice well-known}
+%% Add source code highlighting
+%% From LaTeX Wikibooks https://en.wikibooks.org/wiki/LaTeX/Source_Code_Listings
+\usepackage{listings}
+\usepackage{xcolor}
+%% Colors from Trac default style
+\definecolor{backgroundcode}{HTML}{f8f8f8}
+\definecolor{graycode}{HTML}{666666}
+\definecolor{greencode}{HTML}{008800}
+\definecolor{purplecode}{HTML}{AA22FF}
+\definecolor{redcode}{HTML}{BB4444}
+\definecolor{yellowcode}{HTML}{B8860B}
+\lstset{language=[90]Fortran,
+  backgroundcolor=\color{backgroundcode},
+  basicstyle=\tiny,
+  breaklines=true,
+  commentstyle=\color{greencode},
+  identifierstyle=\color{yellowcode},
+  keywordstyle=\color{purplecode},
+  numberstyle=\color{graycode},
+  stringstyle=\color{redcode},
+  title=\lstname,
+}
+\makeindex

branches/2017/dev_merge_2017/DOC/texfiles/styles/NEMO_manual.sty

-                      r9373
+                      r9376
+%% ==============================================================================
+%% macros.sty:
+%% ==============================================================================
+\def\deg{$^{\circ}$}
+\def\degC{$^{\circ}C$}
+\def\degK{$^{\circ}K$}
+\def\degN{$^{\circ}N$}
+\def\degS{$^{\circ}S$}
 \def\half{\textstyle\frac{1}{2}}
 \def\hhalf{\scriptstyle\frac{1}{2}}
 \def\quarter{\textstyle\frac{1}{4}}
 \def\qquarter{\scriptstyle\frac{1}{4}}
 …
 \def\stwelfth{\sfrac{1}{12}}
 \def\sthirtysixth{\sfrac{1}{36}}
+% \newcommand{\grad}{\boldsymbol{\nabla}}
+% \newcommand{\gradh}{\boldsymbol{\nabla}_h}
+\def\bgamma\boldsymbol{\gamma}
+\def\rdt{\Delta t}
+\newcommand{ \gmcomment}[1]{}
+\newcommand{ \sfcomment}[1]{}
+\newcommand{\sgacomment}[1]{}
+\newcommand{\nl}[1]{\texttt{\small{\textcolor{blue}{#1}}}}
+\newcommand{\NEMO}{\textit{NEMO}\xspace}
+\newcommand{    \ifile}[1]{\textit{  #1.nc}\index{Input NetCDF files!#1.nc}}
+\newcommand{       \jp}[1]{\textit{     #1}\index{     Model parameters!#1}}
+\newcommand{       \hf}[1]{\textit{ #1.h90}\index{             h90 file!#1}}
+\newcommand{      \key}[1]{\textbf{key\_#1}\index{        CPP keys!key\_#1}}
+\newcommand{      \mdl}[1]{\textit{ #1.F90}\index{              Modules!#1}}
+\newcommand{      \ngn}[1]{\textit{     #1}\index{  Namelist Group Name!#1}}
+\newcommand{       \np}[1]{\textit{     #1}\index{   Namelist variables!#1}}
+\newcommand{       \pp}[1]{\textit{     #1}\index{     Model parameters!#1}}
+\newcommand{      \rou}[1]{\textit{     #1}\index{             Routines!#1}}
 \newcommand{\grad}{\nabla}
 \newcommand{\gradh}{\nabla_h}
+\def\bgamma\boldsymbol{\gamma}
+\def\rdt{\Delta t}
 \newcommand{\ew}[3]{{e_{3#1}}_{\,#2}^{\,#3} }
 \newcommand{\vect}[1]{\ensuremath{\mathbf{#1}}} % for vectors                                % non-italic bold
+\newcommand{\vect}[1]{\ensuremath{\mathbf{#1}}}
 \newcommand{\Div}{\grad\cdot}
+% \newcommand{\curl}{\boldsymbol{\nabla} \times} % for curl
+\newcommand{\curl}{\nabla \times} % for curl
+\newcommand{\curl}{\nabla \times}
 \newcommand{\pd}[2][]{\frac{\partial #1}{\partial #2}}
+\def\deg{$^{\circ}$}                           % degrees  (NB: \r{} can % % also be used)
+\def\degC{$^{\circ}C$}
+\def\degK{$^{\circ}K$}
+\def\degN{$^{\circ}N$}
+\def\degS{$^{\circ}S$}
+\newcommand{\alpbet} {\left(\alpha / \beta \right)}   % alpha/beta  for slp computation
+\newcommand{\alpbet} {\left(\alpha / \beta \right)}
 \newcommand{\triad}[6][]{\ensuremath{{}_{#2}^{#3}{\mathbb{#4}_{#1}}_{#5}^{\,#6}}}
 \newcommand{\triadd}[5]{\ensuremath{{}_{#1}^{#2}{\mathbb{#3}}_{#4}^{\,#5}}}
 …
 \newcommand{\rtriad}[2][]{\ensuremath{\triad[#1]{i}{k}{#2}{i_p}{k_p}}}
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branches/2017/dev_merge_2017/DOC/texfiles/top_matter.tex

-                      r9373
+                      r9376
+%\usepackage{pstricks}
+%% ==============================================================================
+%% top_matter.tex: frontpage with title
+%% ==============================================================================
 \title{
+%\psset{unit=1.1in,linewidth=4pt}   %parameters of the units for pstricks
+% \rput(0,2){ \includegraphics[width=1.1\textwidth]{logo_ALL.pdf}             } \\
+% \vspace{0.1cm}
+\vspace{-6.0cm}
+\includegraphics[width=1.1\textwidth]{logo_ALL}\\
+\vspace{5.1cm}
+\includegraphics[width=0.9\textwidth]{NEMO_logo_Black} \\
+\vspace{1.4cm}
+\rule{345pt}{1.5pt} \\
+\vspace{0.45cm}
+{\Huge NEMO ocean engine}
+\rule{345pt}{1.5pt} \\
+ }
+%{ -- Draft --}   }
+%\date{\today}
+\date{
+Decembre 2017  \\
+{\small  -- version 4.0 alpha --} \\
+~  \\
+\textit{\small Note du P\^ole de mod\'{e}lisation de l'Institut Pierre-Simon Laplace No 27 }\\
+\vspace{0.45cm}
+{ ISSN No 1288-1619.}
+\vspace{-6.0cm}\includegraphics[width=1.1\textwidth]{logo_ALL}          \\
+\vspace{ 5.1cm}\includegraphics[width=0.9\textwidth]{NEMO_logo_Black}   \\
+\vspace{ 1.4cm}\rule{345pt}{1.5pt}                                      \\
+\vspace{0.45cm}{\Huge NEMO ocean engine}                                \\
+\rule{345pt}{1.5pt}
+}
 \author{
+\Large Gurvan Madec, and the NEMO team  \\
+ \texttt{\small gurvan.madec@locean-ipsl.umpc.fr} \\
+% \texttt{\small nemo\_st@locean-ipsl.umpc.fr} \\
+%{\small Laboratoire d'Oc\'{e}anographie  et du Climat: Exp\'{e}rimentation et Approches Num\'{e}riques }
+\Large Gurvan Madec, and the NEMO team                                                          \\
+\texttt{\small\href{mailto:gurvan.madec@locean-ipsl.umpc.fr}{gurvan.madec@locean-ipsl.umpc.fr}} \\
+}
+\dominitoc
+\makeindex        %type this first :     makeindex -s NEMO.ist NEMO_book.idx
+\date{
+Decembre 2017                                                                                \\
+{\small  -- version 4.0 alpha --}                                                            \\
+~                                                                                            \\
+\textit{\small Note du P\^ole de mod\'{e}lisation de l'Institut Pierre-Simon Laplace No 27 } \\
+\vspace{0.45cm}{ ISSN No 1288-1619.}
+}
+%\date{\today}

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