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Changeset 11799 for NEMO/branches/2019/dev_r11470_HPC_12_mpi3/doc/latex/global – NEMO

Ignore:
Timestamp:
2019-10-25T16:27:34+02:00 (4 years ago)
Author:
mocavero
Message:

Update the branch to v4.0.1 of the trunk

Location:
NEMO/branches/2019/dev_r11470_HPC_12_mpi3/doc
Files:
4 deleted
14 edited
4 copied

Legend:

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    r11128 r11799  
    99%% *** Bibliography style file for ALL AMS Journals...version 1.0  *** 
    1010%% *** Brian Papa - American Meteorological Society *** 
    11 %%  
     11%% 
    1212%% Copyright 1994-2004 Patrick W Daly 
    1313 % =============================================================== 
    … …  
    519519  duplicate$ empty$ 'skip$ 
    520520    { 
    521       "\href{http://dx.doi.org/" swap$ * "}{DOI}" * 
     521      "\href{http://dx.doi.org/" swap$ * "}{\aiDoi}" * 
    522522    } 
    523523  if$ 
    … …  
    11921192  crossref missing$ 
    11931193    { format.in.ed.booktitle "booktitle" output.check 
    1194       format.publisher.address output       
     1194      format.publisher.address output 
    11951195      format.bvolume output 
    11961196      format.number.series output 

  • NEMO/branches/2019/dev_r11470_HPC_12_mpi3/doc/latex/global/annex_D.tex

    r11299 r11799  
    3131- flexible. 
    3232 
    33 To satisfy part of these aims, \NEMO is written with a coding standard which is close to the ECMWF rules, 
     33To satisfy part of these aims, \NEMO\ is written with a coding standard which is close to the ECMWF rules, 
    3434named DOCTOR \citep{gibson_rpt86}.  
    3535These rules present some advantages like: 

  • NEMO/branches/2019/dev_r11470_HPC_12_mpi3/doc/latex/global/coding_rules.tex

    r11433 r11799  
    11 
    22\chapter{Coding Rules} 
    3 \label{apdx:coding} 
    4  
    5 \minitoc 
     3\label{apdx:CODING} 
     4 
     5\chaptertoc 
    66 
    77\newpage 
    … …  
    1313produces fewer bugs and is easier to maintain. 
    1414Therefore, it is essential that the model development follows some rules: 
     15 
    1516\begin{itemize} 
    16    \item well planned and designed 
    17    \item well written 
    18    \item well documented (both on- and off-line) 
    19    \item maintainable 
    20    \item easily portable 
    21    \item flexible. 
     17\item well planned and designed 
     18\item well written 
     19\item well documented (both on- and off-line) 
     20\item maintainable 
     21\item easily portable 
     22\item flexible. 
    2223\end{itemize} 
    2324 
    24 To satisfy part of these aims, \NEMO is written with a coding standard which is close to the ECMWF rules, 
    25 named DOCTOR \citep{gibson_rpt86}.  
     25To satisfy part of these aims, \NEMO\ is written with a coding standard which is close to the ECMWF rules, 
     26named DOCTOR \citep{gibson_rpt86}. 
    2627These rules present some advantages like: 
     28 
    2729\begin{itemize} 
    28    \item to provide a well presented program 
    29    \item to use rules for variable names which allow recognition of their type 
    30    (integer, real, parameter, local or shared variables, etc. ).  
     30\item to provide a well presented program 
     31\item to use rules for variable names which allow recognition of their type   (integer, real, parameter, local or shared variables, etc. ). 
    3132\end{itemize} 
    3233 
    … …  
    3536\section{Introduction} 
    3637 
    37 This document describes conventions used in \NEMO coding and suggested for its development. 
    38 The objectives are to offer a guide to all readers of the \NEMO code, and to facilitate the work of 
     38This document describes conventions used in \NEMO\ coding and suggested for its development. 
     39The objectives are to offer a guide to all readers of the \NEMO\ code, and to facilitate the work of 
    3940all the developers, including the validation of their developments, and 
    40 eventually the implementation of these developments within the \NEMO platform. 
     41eventually the implementation of these developments within the \NEMO\ platform. 
    4142 
    4243A first approach of these rules can be found in the code in \path{./src/OCE/module_example} where 
    … …  
    4546 
    4647This work is based on the coding conventions in use for the Community Climate System Model 
    47 \footnote {\href{http://www.cesm.ucar.edu/working_groups/Software/dev_guide/dev_guide/node7.html}{UCAR conventions}},  
     48\footnote {\href{http://www.cesm.ucar.edu/working_groups/Software/dev_guide/dev_guide/node7.html}{UCAR conventions}}, 
    4849the previous version of this document (``FORTRAN coding standard in the OPA System'') and 
    49 the expertise of the \NEMO System Team. 
     50the expertise of the \NEMO\ System Team. 
    5051After a general overview below, this document will describe: 
    5152 
    5253\begin{itemize} 
    53    \item The style rules, $i.e.$ the syntax, appearance and naming conventions chosen to improve readability of the code; 
    54    \item The content rules, $i.e.$ the conventions to improve the reliability of the different parts of the code; 
    55    \item The package rules to go a step further by improving the reliability of the whole and 
     54\item The style rules, $i.e.$ the syntax, appearance and naming conventions chosen to improve readability of the code; 
     55\item The content rules, $i.e.$ the conventions to improve the reliability of the different parts of the code; 
     56\item The package rules to go a step further by improving the reliability of the whole and 
    5657   interfaces between routines and modules. 
    5758\end{itemize} 
    … …  
    5960\section{Overview and general conventions} 
    6061 
    61 \NEMO has 3 major components: ocean dynamics (\path{./src/OCE}), sea-ice (\path{./src/ICE}) and 
     62\NEMO\ has 3 major components: ocean dynamics (\path{./src/OCE}), sea-ice (\path{./src/ICE}) and 
    6263marine biogeochemistry (\path{./src/MBG}). 
    6364%, linear-tangent and adjoint of the dynamics ($TAM$) each of them corresponding to a directory. 
    … …  
    7980 
    8081\begin{itemize} 
    81    \item \path{SBC}             surface module 
    82    \item \path{IOM}             management of the I/O 
    83    \item \path{NST}             interface to AGRIF (nesting model) for dynamics and biogeochemistry 
    84    \item \path{OBC}, \path{BDY} management of structured and unstructured open boundaries  
    85    \item \path{C1D}             1D (vertical) configuration for dynamics, sea-ice and biogeochemistry 
    86    \item \path{OFF}             off-line module: passive tracer or biogeochemistry alone 
    87    \item \path{...} 
     82\item \path{SBC}             surface module 
     83\item \path{IOM}             management of the I/O 
     84\item \path{NST}             interface to AGRIF (nesting model) for dynamics and biogeochemistry 
     85\item \path{OBC}, \path{BDY} management of structured and unstructured open boundaries 
     86\item \path{C1D}             1D (vertical) configuration for dynamics, sea-ice and biogeochemistry 
     87\item \path{OFF}             off-line module: passive tracer or biogeochemistry alone 
     88\item \path{...} 
    8889\end{itemize} 
    8990 
    … …  
    142143 
    143144All FORTRAN keywords are in capital: \forcode{DIMENSION}, \forcode{WRITE}, \forcode{DO}, \forcode{END DO}, 
    144 \forcode{NAMELIST}, ... All other parts of the \NEMO code will be written in lower case. 
     145\forcode{NAMELIST}, ... All other parts of the \NEMO\ code will be written in lower case. 
    145146 
    146147\subsection{Comments} 
    … …  
    216217\subsection{F90 Standard} 
    217218 
    218 \NEMO software adheres to the \fninety language standard and does not rely on any specific language or 
     219\NEMO\ software adheres to the \fninety language standard and does not rely on any specific language or 
    219220vendor extensions. 
    220221 
    … …  
    268269For example, zdftke, where ``zdf'' stands for vertical diffusion, and ``tke'' for turbulent kinetic energy. \\ 
    269270Note that by implication multiple modules are not allowed in a single file. 
    270 The use of common blocks is deprecated in \fortran 90 and their use in \NEMO is strongly discouraged. 
     271The use of common blocks is deprecated in \fortran 90 and their use in \NEMO\ is strongly discouraged. 
    271272Modules are a better way to declare static data. 
    272273Among the advantages of modules is the ability to freely mix data of various types, and 
    … …  
    292293      complex                                                                                     \\ 
    293294      \hline 
    294       public \par or \par module variable                                                         &  
    295       \textbf{m n} \par \textit{but not} \par \textbf{nn\_}                                       &  
     295      public \par or \par module variable                                                         & 
     296      \textbf{m n} \par \textit{but not} \par \textbf{nn\_}                                       & 
    296297      \textbf{a b e f g h o} \textbf{q} \textit{to} \textbf{x} \par but not \par \textbf{fs rn\_} & 
    297298      \textbf{l} \par \textit{but not} \par \textbf{lp ld ll ln\_}                                & 
    … …  
    301302      \hline 
    302303      dummy \par argument                                                                         & 
    303       \textbf{k} \par \textit{but not} \par \textbf{kf}                                           &  
    304       \textbf{p} \par \textit{but not} \par \textbf{pp pf}                                        &  
     304      \textbf{k} \par \textit{but not} \par \textbf{kf}                                           & 
     305      \textbf{p} \par \textit{but not} \par \textbf{pp pf}                                        & 
    305306      \textbf{ld}                                                                                 & 
    306307      \textbf{cd}                                                                                 & 
    … …  
    309310      \hline 
    310311      local \par variable                                                                         & 
    311       \textbf{i}                                                                                  &  
     312      \textbf{i}                                                                                  & 
    312313      \textbf{z}                                                                                  & 
    313314      \textbf{ll}                                                                                 & 
    … …  
    333334      \hline 
    334335      namelist                                                                                    & 
    335       \textbf{nn\_}                                                                               &  
     336      \textbf{nn\_}                                                                               & 
    336337      \textbf{rn\_}                                                                               & 
    337338      \textbf{ln\_}                                                                               & 
    … …  
    388389Is to be used rather than the \#ifdef abbreviate form since it may have conflicts with some Unix scripts. 
    389390 
    390 Tests on cpp keys included in \NEMO at compilation step: 
     391Tests on cpp keys included in \NEMO\ at compilation step: 
    391392 
    392393\begin{itemize} 
    … …  
    402403\subsection{Configurations} 
    403404 
    404 The configuration defines the domain and the grid on which \NEMO is running. 
     405The configuration defines the domain and the grid on which \NEMO\ is running. 
    405406It may be useful to associate a CPP key and some variables to a given configuration, although 
    406407the part of the code changed under each of those keys should be minimized. 
    … …  
    487488\subsection{Headers} 
    488489 
    489 Prologues are not used in \NEMO for now, although it may become an interesting tool in combination with 
     490Prologues are not used in \NEMO\ for now, although it may become an interesting tool in combination with 
    490491ProTeX auto documentation script in the future. 
    491492Rules to code the headers and layout of a module or a routine are illustrated in the example module available with 
    … …  
    563564\subsection{Bounds checking} 
    564565 
    565 \NEMO is able to run when an array bounds checking option is enabled 
     566\NEMO\ is able to run when an array bounds checking option is enabled 
    566567(provided the cpp key \texttt{key\_vectopt\_loop} is not defined). \\ 
    567568Thus, constructs of the following form are disallowed: 
    … …  
    606607the \texttt{stat=<integer\ variable>} optional argument. \\ 
    607608 
    608 In addition to arrays contained within modules, many routines in \NEMO require local, ``workspace'' arrays to 
     609In addition to arrays contained within modules, many routines in \NEMO\ require local, ``workspace'' arrays to 
    609610hold the intermediate results of calculations. 
    610611In previous versions of \NEMO, these arrays were declared in such a way as to be automatically allocated on 
    … …  
    697698It is then associated with a sub-array of \texttt{wrk\_3d\_5} once the call to 
    698699\texttt{wrk\_in\_use()} has completed successfully. 
    699 Note that in F95 (to which \NEMO conforms) it is not possible for either the upper or lower array bounds of 
     700Note that in F95 (to which \NEMO\ conforms) it is not possible for either the upper or lower array bounds of 
    700701the pointer object to differ from those of the target array. \\ 
    701702 
    … …  
    710711This should enable the developer to choose alternatives for use in the subroutine being worked on. \\ 
    711712 
    712 When compiling \NEMO for production runs, 
     713When compiling \NEMO\ for production runs, 
    713714the calls to {\texttt{wrk\_in\_use()} / \texttt{wrk\_not\_released()} can be reduced to stubs that just 
    714715return \forcode{.false.} by setting the cpp key \texttt{key\_no\_workspace\_check}. 
    … …  
    732733\subsection{Parallelism using MPI} 
    733734 
    734 \NEMO is written in order to be able to run on one processor, or on one or more using MPI 
     735\NEMO\ is written in order to be able to run on one processor, or on one or more using MPI 
    735736($i.e.$ activating the cpp key $key\_mpp\_mpi$). 
    736 The domain decomposition divides the global domain in cubes (see \NEMO reference manual). 
     737The domain decomposition divides the global domain in cubes (see \NEMO\ reference manual). 
    737738Whilst coding a new development, the MPI compatibility has to be taken in account 
    738739(see \path{./src/LBC/lib_mpp.F90}) and should be tested. 
    … …  
    748749Below is a list of features to avoid: 
    749750\begin{itemize} 
    750 \item 
    751   \forcode{COMMON} block 
     751\item \forcode{COMMON} block 
    752752  (use the declaration part of \forcode{MODULE} instead) 
    753 \item 
    754   \forcode{EQUIVALENCE} 
     753\item \forcode{EQUIVALENCE} 
    755754  (use \forcode{POINTER} or derived data type instead to form data structure) 
    756 \item 
    757   Assigned and computed \forcode{GOTO} 
     755\item Assigned and computed \forcode{GOTO} 
    758756  (use the \forcode{CASE} construct instead) 
    759 \item 
    760   Arithmetic \forcode{IF} statement 
     757\item Arithmetic \forcode{IF} statement 
    761758  (use the block \forcode{IF}, \forcode{ELSE}, \forcode{ELSEIF}, \forcode{ENDIF} or 
    762759  \forcode{SELECT CASE} construct instead) 
    763 \item 
    764   Labelled \forcode{DO} construct 
     760\item Labelled \forcode{DO} construct 
    765761  (use unlabelled \forcode{END DO} instead) 
    766 \item 
    767   \forcode{FORMAT} statement 
     762\item \forcode{FORMAT} statement 
    768763  (use character parameters or 
    769764  explicit format- specifiers inside the \forcode{READ} or \forcode{WRITE} statement instead) 
    770 \item 
    771   \forcode{GOTO} and \forcode{CONTINUE} statements 
     765\item \forcode{GOTO} and \forcode{CONTINUE} statements 
    772766  (use \forcode{IF}, \forcode{CASE}, \forcode{DO WHILE}, \forcode{EXIT} or \forcode{CYCLE} statements or 
    773767  a contained ?) 
    774 \item 
    775   \forcode{PAUSE} 
    776 \item 
    777   \forcode{ENTRY} statement: a sub-program must only have one entry point. 
    778 \item 
    779   \forcode{RETURN} is obsolete and so not necessary at the end of program units 
    780 \item 
    781   \forcode{FUNCTION} statement 
    782 \item 
    783   Avoid functions with side effects. 
     768\item \forcode{PAUSE} 
     769\item \forcode{ENTRY} statement: a sub-program must only have one entry point. 
     770\item \forcode{RETURN} is obsolete and so not necessary at the end of program units 
     771\item \forcode{FUNCTION} statement 
     772\item Avoid functions with side effects. 
    784773  \footnote{ 
    785774    First, the code is easier to understand, if you can rely on 
    … …  
    790779    This is especially important on massive parallel and as well on vector machines. 
    791780  } 
    792 \item 
    793   \forcode{DATA} and \forcode{BLOCK DATA} 
     781\item \forcode{DATA} and \forcode{BLOCK DATA} 
    794782  (use initialisers) 
    795783\end{itemize} 
    796784 
     785%% Imported from introduction 
     786%%gm    To be put somewhere else .... 
     787%%nm    We should consider creating a glossary for all this kind of stuff (terms, acronyms and symbols) 
     788%%      http://en.wikibooks.org/wiki/LaTeX/Glossary 
     789%\noindent CPP keys and namelists are used as inputs to the code. 
     790 
     791%\noindent \index{CPP keys} CPP keys 
     792 
     793%Some CPP keys are implemented in the \fortran code to allow code selection at compiling step. 
     794%This selection of code at compilation time reduces the reliability of the whole platform since 
     795%it changes the code from one set of CPP keys to the other. 
     796%It is used only when the addition/suppression of the part of code highly changes the amount of memory at run time. 
     797%Usual coding looks like: 
     798 
     799%\begin{forlines} 
     800%#if defined key_option1 
     801%  ! This part of the \fortran code will be active 
     802%  ! only if key_option1 is activated at compiling step 
     803%#endif 
     804%\end{forlines} 
     805 
     806%\noindent \index{Namelist} Namelists 
     807 
     808%The namelist allows to input variables (character, logical, real and integer) into the code. 
     809%There is one namelist file for each component of \NEMO\ (dynamics, sea-ice, biogeochemistry...) 
     810%containing all the \fortran namelists needed. 
     811%The implementation in \NEMO\ uses a 2-step process. 
     812%For each \fortran namelist, two files are read: 
     813 
     814%\begin{enumerate} 
     815%\item 
     816%  A reference namelist (in \path{./cfgs/SHARED/namelist_ref}) is read first. 
     817%  This file contains all the namelist variables which are initialised to default values 
     818%\item 
     819%  A configuration namelist (in \path{./cfgs/CFG_NAME/EXP00/namelist_cfg}) is read aferwards. 
     820%  This file contains only the namelist variables which are changed from default values, and overwrites those. 
     821%\end{enumerate} 
     822%A template can be found in \path{NEMO/OPA_SRC/module.example}. 
     823%The effective namelist, taken in account during the run, is stored at execution time in 
     824%an \texttt{output\_namelist\_dyn} (or \texttt{\_ice} or \texttt{\_top}) file. 
     825%%gm  end 
     826 
     827%%nm: Add some words on the \NEMO\ dependencies 
     828%The model is implemented in \fninety, with preprocessing (C pre-processor). 
     829%It runs under UNIX. 
     830%It is optimized for vector computers and parallelised by domain decomposition with MPI. 
     831%All input and output is done in NetCDF (Network Common Data Format) with a optional direct access format for output. 
     832%To ensure the clarity and readability of the code it is necessary to follow coding rules. 
     833%The coding rules for OPA include conventions for naming variables, 
     834%with different starting letters for different types of variables (real, integer, parameter\ldots). 
     835%Those rules are briefly presented in \autoref{apdx:coding} and a more complete document is available . 
     836 
     837%The model is organized with a high internal modularity based on physics. 
     838%For example, each trend (\ie, a term in the RHS of the prognostic equation) for momentum and tracers 
     839%is computed in a dedicated module. 
     840%To make it easier for the user to find his way around the code, the module names follow a three-letter rule. 
     841%For example, \mdl{traldf} is a module related to the TRAcers equation, computing the Lateral DiFfussion. 
     842%The complete list of module names is presented in \autoref{apdx:coding}.      %====>>>> to be done ! 
     843%Furthermore, modules are organized in a few directories that correspond to their category, 
     844%as indicated by the first three letters of their name (\autoref{tab:chapters}). 

  • NEMO/branches/2019/dev_r11470_HPC_12_mpi3/doc/latex/global/document.tex

    r11433 r11799  
    11 
    2 %% ============================================================================== 
    3 %% Template structure for reference manual 
    4 %% ============================================================================== 
     2%% ================================================================================================= 
     3%% Template structure for reference manuals 
     4%% ================================================================================================= 
    55 
    66%% NEMO release version 
    … …  
    88 
    99%% Preamble 
    10 %% ============================================================================== 
     10%% ================================================================================================= 
    1111 
    1212%% Document layout 
    13 \documentclass[twoside = semi, abstract = on]{scrreprt} 
     13\documentclass[fontsize = 10pt, twoside, abstract]{scrreprt} 
    1414 
    15 %% Load configurations 
    16 \input{../../global/preamble} 
    17  
    18 \dominitoc 
     15%% Load manual configuration 
     16\input{../../global/prologue} 
    1917 
    2018%% End of common preamble between main and sub-files 
    … …  
    2826\renewcommand{\notinsubfile}[1]{#1} 
    2927 
    30 \renewcommand{\biblio}{} 
    31 \renewcommand{\pindex}{} 
    32  
    3328 
    3429%% Frontmatter 
    35 %% ============================================================================== 
     30%% ================================================================================================= 
    3631 
    37 %% Disable page numbering temporarily 
    38 \pagenumbering{gobble} 
     32\pagenumbering{gobble}   %% Disable page numbering temporarily 
    3933 
    4034%% Title page 
    41 %\input{../../global/frontpage} 
    42 \input{../../global/frontpage_new} 
     35\input{../../global/frontpage} 
    4336 
    44 %\maketitle 
    45 %\emptythanks 
     37%% Footer for introductory parts (no header by cleaning default) 
     38\ofoot[]{\engine\ Reference Manual} \ifoot[]{\pagemark} 
    4639 
    4740%% Information page (2nd page) 
    4841\input{../../global/info_page} 
    4942 
    50 %% Headings for introductory parts (no header, simple footer) 
    51 \ofoot{\engine\ Reference Manual}\ifoot{\pagemark} 
     43\listoffigures 
     44\listoflistings 
     45\listoftables 
     46 
     47\clearpage 
     48 
    5249\pagenumbering{roman} 
     50\ofoot[]{\engine\ Reference Manual} \ifoot[]{\pagemark} 
    5351 
    54 %% Foreword 
    55 %\input{foreword} 
     52\input{introduction} 
    5653 
    5754%% Table of Contents 
    5855\tableofcontents 
    59 %\listoffigures 
    60 %\listoftables 
    61 %\listoflistings 
    6256 
    6357\clearpage 
    … …  
    6559 
    6660%% Mainmatter 
    67 %% ============================================================================== 
     61%% ================================================================================================= 
    6862 
    6963%% Headings for document body 
    70 \lohead{Chap.\ \thechapter\ \leftmark}\rehead{Sect.\ \thesection\ \rightmark} 
    71 \ifoot{Page\ \pagemark\ of \pageref*{LastPage}} 
    7264\pagenumbering{arabic} 
     65\lohead{Chap.\ \thechapter\ \leftmark} \rehead{Sect.\ \thesection\ \rightmark} 
     66\ifoot[]{Page\ \pagemark\ of \pageref*{LastPage}} 
    7367 
    7468\include{chapters} 
    … …  
    7670 
    7771%% Appendix 
    78 %% ============================================================================== 
     72%% ================================================================================================= 
    7973 
    80 %% Chapter numbering is reset with letters now 
    81 \appendix 
    82  
     74\appendix   %% Chapter numbering with letters by now 
     75\lohead{Apdx\ \thechapter\ \leftmark} 
    8376\include{appendices} 
    8477 
    … …  
    8881 
    8982%% Backmatter 
    90 %% ============================================================================== 
     83%% ================================================================================================= 
    9184 
    92 %\backmatter   %% Chapter numbering off 
    93  
    94 %% Bibliography 
    95 \phantomsection 
    96 \addcontentsline{toc}{chapter}{Bibliography} 
    97 \bibliography{../main/bibliography} 
    98  
    99 %% Index 
    100 \clearpage 
    101 \phantomsection 
    102 \addcontentsline{toc}{chapter}{Indexes} 
    103 \printindex[keys] 
    104 \printindex[modules] 
    105 \printindex[blocks] 
    106 \printindex[parameters] 
    107 \printindex[subroutines] 
     85%% Bibliography and indexes 
     86\input{../../global/epilogue} 
    10887 
    10988\end{document} 

  • NEMO/branches/2019/dev_r11470_HPC_12_mpi3/doc/latex/global/frontpage.tex

    r11433 r11799  
    11 
    2 \title{\heading} 
    3 \date{\today} 
    4 \author{\protect\input{thanks}} 
     2\begin{titlepage} 
     3%  \newgeometry{hmargin = 1.5cm, vmargin = 3cm} 
     4  \setlength{\parindent}{0pt} 
    55 
    6 \pretitle{ 
    76  \begin{center} 
    8     \begin{figure}[H] 
    9       \begin{minipage}[c]{0.35\textwidth} 
    10         \href{http://www.nemo-ocean.eu}{\includegraphics[width=0.7\textwidth]{logos/NEMO_grey}} 
    11       \end{minipage} 
    12       \hfill 
    13       \begin{minipage}[c]{0.65\textwidth} 
    14         \centering 
    15         \large{\em{{N}ucleus for {E}uropean {M}odelling of the {O}cean}} 
    16       \end{minipage} 
    17     \end{figure} 
    18     \vfill 
    19     \Huge 
    20 } 
    21 \posttitle{ 
    22   \par 
     7    \begin{minipage}{0.3\textwidth} 
     8      \includegraphics[height=1.5cm]{logos/NEMO_grey} 
     9    \end{minipage}\begin{minipage}{0.6\textwidth} 
     10      \begin{center} 
     11      \Large\slshape 
     12      \textbf{N}ucleus for \textbf{E}uropean \textbf{M}odelling of the \textbf{O}cean \\ 
     13      \medskip 
     14      \hyperref[resources]{\textcolor{black}{ 
     15          \faWordpress \hspace{0.75cm} \faCodeFork      \hspace{0.75cm} 
     16          \faGithub    \hspace{0.75cm} \faCloudDownload \hspace{0.75cm} \faEnvelope 
     17        } 
     18      } 
     19      \end{center} 
     20    \end{minipage} 
    2321  \end{center} 
    24   \vskip 0.5em 
    25 } 
    26 \predate{ 
     22 
     23  \spacetop 
     24  \textcolor{white}{\fontsize{0.8cm}{0.8cm}\selectfont\textbf{\heading}} 
     25  \ifdef{\subheading}{ 
     26    \medskip 
     27    \par 
     28    \textcolor{white}{\Huge \subheading} 
     29  }{} 
     30  \spacedown 
     31 
     32  \begin{center} 
     33    \LARGE Version \version\ -\ \today \\ 
     34    \medskip 
     35    \href{http://doi.org/10.5281/zenodo.\zid}{ \includegraphics{{badges/zenodo.\zid}.pdf} } 
     36  \end{center} 
     37 
    2738  \vfill 
    28   \begin{center} 
    29     \large Version \version --- 
    30 } 
    31 \postdate{ 
    32     \par~\\ 
    33     \href{http://doi.org/10.5281/zenodo.\zid}{\includegraphics{{badges/zenodo.\zid}.pdf}} 
    34   \end{center} 
     39 
     40  \begin{minipage}{\authorswidth} 
     41    \raggedleft 
     42    \input{authors} 
     43  \end{minipage}\hspace{15pt}\begin{minipage}{0.02\linewidth} 
     44    \rule{1pt}{\rulelenght} 
     45  \end{minipage}\hspace{ 5pt}\begin{minipage}{\abstractwidth} 
     46    \begin{abstract} 
     47      \input{abstract} 
     48    \end{abstract} 
     49  \end{minipage} 
     50 
    3551  \vfill 
    36   \begin{center} 
    37     \href{http://www.cmcc.it}{          \includegraphics[height=0.055\textheight]{logos/CMCC}} 
    38     \hspace{0.5em} 
    39     \href{http://www.cnrs.fr}{          \includegraphics[height=0.055\textheight]{logos/CNRS}} 
    40     \hspace{0.9em} 
    41     \href{http://www.mercator-ocean.fr}{\includegraphics[height=0.055\textheight]{logos/MOI} } 
    42     \hspace{0.45em} 
    43     \href{http://www.metoffice.gov.uk}{ \includegraphics[height=0.055\textheight]{logos/UKMO}} 
    44     \hspace{0.5em} 
    45     \href{http://nerc.ukri.org}{        \includegraphics[height=0.055\textheight]{logos/NERC}} \\ 
    46     \large{{\em{C}ommunity \hspace{1.5em} {O}cean \hspace{1.5em} {M}odel}} 
    47   \end{center} 
    48 } 
    4952 
    50 \preauthor{ 
    5153  \begin{center} 
    5254    \Large 
    53     \lineskip 0.5em 
    54     \begin{tabular}[t]{c c c} 
    55 } 
    56 \postauthor{ 
    57     \end{tabular} 
    58     \par 
     55    \href{http://www.cmcc.it          }{ \includegraphics[height=1cm]{logos/CMCC} } \hspace{0.25cm} 
     56    \href{http://www.cnrs.fr          }{ \includegraphics[height=1cm]{logos/CNRS} } \hspace{0.25cm} 
     57    \href{http://www.mercator-ocean.fr}{ \includegraphics[height=1cm]{logos/MOI}  } \hspace{0.25cm} 
     58    \href{http://www.metoffice.gov.uk }{ \includegraphics[height=1cm]{logos/UKMO} } \hspace{0.25cm} 
     59    \href{http://nerc.ukri.org        }{ \includegraphics[height=1cm]{logos/NERC} } \\ 
     60    \medskip 
     61    \slshape 
     62    {C}ommunity \hspace{1.5em} {O}cean \hspace{1.5em} {M}odel \\ 
    5963  \end{center} 
    60 } 
    6164 
    62 \thanksmarkseries{fnsymbol} 
     65\end{titlepage} 
     66 
     67\restoregeometry 

  • NEMO/branches/2019/dev_r11470_HPC_12_mpi3/doc/latex/global/highlighting.tex

    r11310 r11799  
    22%% ============================================================================== 
    33 
    4 \usepackage[outputdir=../build]{minted} 
     4\usepackage[outputdir=../build, chapter, newfloat]{minted} 
    55 
    66%% Global highlighting style 
    77\definecolor{bg}{HTML}{f8f8f8} 
    88\usemintedstyle{emacs} 
    9 \setminted{bgcolor=bg, fontsize=\scriptsize, breaklines, frame=leftline} 
     9\setminted{bgcolor=bg, fontsize=\scriptsize, breaklines} 
    1010\setminted[xml]{style=borland} %% Specific per language 
    1111 
    … …  
    2222 
    2323%% File 
    24 \newmintedfile[forfile]{fortran}{}   % \forfile{../namelists/nam...} 
     24\newmintedfile[forfile]{fortran}{} 
    2525 
    2626%% Inline 
    27 \newmintinline[forcode]{fortran}{bgcolor=, fontsize=auto, frame=lines}   % \forcode{...} 
    28 \newmintinline[xmlcode]{xml}{    bgcolor=, fontsize=auto, frame=lines}   % \xmlcode{...} 
    29 \newmintinline[snippet]{console}{bgcolor=, fontsize=auto, frame=lines}   % \snippet{...} 
     27\newmintinline[forcode]{fortran}{bgcolor=, fontsize=auto}   % \forcode{...} 
     28\newmintinline[xmlcode]{xml}{    bgcolor=, fontsize=auto}   % \xmlcode{...} 
     29\newmintinline[snippet]{console}{bgcolor=, fontsize=auto}   % \snippet{...} 
    3030 
    3131%% Namelists inclusion 
    3232\newcommand{\nlst}[1]{\forfile{../../../namelists/#1}} 
    33  

  • NEMO/branches/2019/dev_r11470_HPC_12_mpi3/doc/latex/global/index.ist

    r11176 r11799  
    11headings_flag 1 
    2 heading_prefix "{\\medskip\\hfill\\large\\textsf{\\textbf{" 
    3 heading_suffix "}}\\hfill}\\medskip\\nopagebreak\n" 
    4  
     2heading_prefix "\\medskip\\hfill\\textnormal{" 
     3heading_suffix "}\\hfill\\smallskip\n" 
    54delim_0 "\\dotfill~" 
    6 delim_1 "\\dotfill~" 
    7 delim_2 "\\dotfill~" 
    8  

  • NEMO/branches/2019/dev_r11470_HPC_12_mpi3/doc/latex/global/info_page.tex

    r11433 r11799  
    22\thispagestyle{plain} 
    33 
    4 % ================================================================ 
    5 % Disclaimer 
    6 % ================================================================ 
     4%% ================================================================ 
     5%% Disclaimer 
     6%% ================================================================ 
    77\subsubsection*{Disclaimer} 
    88 
    … …  
    1111which is a French adaptation of the GNU GPL (\textbf{G}eneral \textbf{P}ublic \textbf{L}icense). 
    1212Anyone may use it freely for research purposes, and is encouraged to 
    13 communicate back to the \NEMO\ team its own developments and improvements. 
     13communicate back to the development team its own developments and improvements. 
    1414 
    1515The model and the present document have been made available as a service to the community. 
    … …  
    1818Users are encouraged to bring them to our attention. 
    1919 
    20 The authors assume no responsibility for problems, errors, or incorrect usage of NEMO. 
     20The authors assume no responsibility for problems, errors, or incorrect usage of \NEMO. 
    2121 
    22 % ================================================================ 
    23 % External resources 
    24 % ================================================================ 
     22%% ================================================================ 
     23%% External resources 
     24%% ================================================================ 
    2525\subsubsection*{Other resources} 
     26\label{resources} 
    2627 
    2728Additional information can be found on: 
    … …  
    4445\end{itemize} 
    4546 
    46 % ================================================================ 
    47 % Citation 
    48 % ================================================================ 
     47%% ================================================================ 
     48%% Citation 
     49%% ================================================================ 
    4950\subsubsection*{Citation} 
    5051 
    5152Reference for papers and other publications is as follows: 
    5253 
    53 ``{\bfseries \heading}'', 
    54 %\firstauthor and \secondauthor, 
    55 {\em Scientific Notes of Climate Modelling Center}, \textbf{\ipslnum} --- ISSN 1288-1619, 
    56 Institut Pierre-Simon Laplace (IPSL), 
    57 \href{https://doi.org/10.5281/zenodo.\zid}{doi:10.5281/zenodo.\zid} 
     54\medskip 
     55 
     56\begin{sloppypar} 
     57  ``{\bfseries \heading}\ifdef{\subheading}{ -- \subheading}{}'', 
     58  {\em Scientific Notes of Climate Modelling Center}, \textbf{\ipslnum} --- ISSN 1288-1619, 
     59  Institut Pierre-Simon Laplace (IPSL), 
     60  \href{https://doi.org/10.5281/zenodo.\zid}{doi:10.5281/zenodo.\zid} 
     61\end{sloppypar} 
    5862 
    5963\begin{figure}[b] 
    … …  
    7175  \end{minipage} 
    7276\end{figure} 
    73  
    74 \end{document} 

  • NEMO/branches/2019/dev_r11470_HPC_12_mpi3/doc/latex/global/new_cmds.tex

    r11433 r11799  
    22%% ============================================================================== 
    33 
    4 %% Include references and index for compilation of single subfile 
    5 \newcommand{\mtoc}{\minitoc} 
    6 \newcommand{\biblio}{ \bibliography{../main/bibliography} } 
    7 \newcommand{\pindex}{\printindex} 
     4%% Same slanted font for NEMO and its core engines 
     5\newcommand{\NEMO  }{\textsl{NEMO}} 
     6\newcommand{\OPA   }{\textsl{OPA}} 
     7\newcommand{\SIcube}{\textsl{SI$^3$}} 
     8\newcommand{\TOP   }{\textsl{TOP}} 
     9\newcommand{\PISCES}{\textsl{PISCES}} 
     10\newcommand{\NEMOVAR}{\textsl{NEMOVAR}} 
    811 
    9 %% NEMO and Fortran in small capitals 
    10 \newcommand{\NEMO   }{\textsc{nemo}} 
    11 \newcommand{\SIcube }{\textsc{si$^3$}} 
    12 \newcommand{\TOP    }{\textsc{top}} 
     12%% Links for external components 
     13\newcommand{\AGRIF}{\href{http://agrif.imag.fr}{AGRIF}} 
     14\newcommand{\CICE }{\href{http://github.com/CICE-Consortium/CICE}{CICE}} 
     15\newcommand{\OASIS}{\href{http://portal.enes.org/oasis}{OASIS}} 
     16\newcommand{\XIOS }{\href{http://forge.ipsl.jussieu.fr/ioserver}{XIOS}} 
     17 
     18%% Fortran in small capitals 
    1319\newcommand{\fortran}{\textsc{Fortran}} 
    1420\newcommand{\fninety}{\textsc{Fortran 90}} 
    … …  
    4955} 
    5056 
    51 %% Macro for link to orcid profile 
    52 \newcommand{\orcid}[1]{ \href{http://orcid.org/#1}{\textcolor{orcidcolor} \aiOrcidSquare} } 
     57%% Link to orcid profile 
     58\newcommand{\orcid}[1]{\href{http://orcid.org/#1}{\textcolor{orcidcolor}\aiOrcidSquare}} 
    5359 
    54 %% Workaround for issue with \listoffigures 
     60%% Workaround for \listoffigures 
    5561\DeclareRobustCommand{\triad}[6][]{\ensuremath{ {}_{#2}^{#3} { \mathbb{#4}_{#1} }_{#5}^{\,#6} }} 
     62 
     63%% New command for ToC 
     64\newcommand{\chaptertoc}[1][Table of contents]{% 
     65  \thispagestyle{empty} 
     66  \etocsettocstyle{\addsec*{#1}}{}% 
     67  \localtableofcontents% 
     68  \vfill 
     69} 

  • NEMO/branches/2019/dev_r11470_HPC_12_mpi3/doc/latex/global/packages.tex

    r11433 r11799  
    33%% ============================================================================== 
    44 
    5 %% 'hyperref' pkg is loaded at the end of the preamble 
    6 \usepackage{natbib}                 %% bibtex 
    7 \usepackage{caption}                %% caption 
    8 \usepackage{xcolor}                 %% colour 
    9 \usepackage{times}                  %% font 
    10 \usepackage{enumitem}               %% list 
    11 \usepackage{amsmath}                %% maths 
    12 \usepackage{minitoc}                %% toc 
    13 \usepackage{subfiles}               %% subdocs 
    14 \usepackage{draftwatermark}         %% watermark 
    15 \usepackage[Bjornstrup]{fncychap}   %% headings 
     5%% 'hyperref' pkg is loaded at the end of the preamble for higher compatibility 
     6 
     7%% KOMA-script 
     8\usepackage[footsepline=0.25pt, headsepline=0.25pt]{scrlayer-scrpage} 
     9 
     10%% customization (layout, header/footer styles & contents, background) 
     11\usepackage{draftwatermark} 
     12\usepackage[margin = 2cm]{geometry} 
     13\usepackage[pages = some]{background}   %% 'some' for title page 
     14\usepackage[Bjornstrup]{fncychap} 
     15 
     16%% Fonts 
    1617\usepackage{fontspec} 
    17 %\setmainfont[Ligatures=TeX]{Georgia} 
    18 %\setsansfont[Ligatures=TeX]{Arial} 
     18%% Issue with fontawesome pkg: path to FontAwesome.otf has to be hard-coded 
    1919\defaultfontfeatures{ 
    20     Path = /home/ntmlod/.local/texlive2019/texmf-dist/fonts/opentype/public/fontawesome/ 
     20    Path = /usr/local/texlive/2019/texmf-dist/fonts/opentype/public/fontawesome/ 
    2121} 
    22 \usepackage{academicons}            %% font 
    23 \usepackage{fontawesome}            %% font 
    24 \usepackage{lastpage}               %% label 
    25 \usepackage[pages = some]{background}             %% decoration 
    26 \usepackage{geometry}               %% margin 
     22\usepackage{academicons, fontawesome, newtxtext} 
    2723 
    28 %% Extensions in bundle package 
    29 \usepackage{amssymb, graphicx, tabularx, textcomp} 
    30 %\usepackage[utf8]{inputenc}         %% encoding 
    31 \usepackage[footsepline=0.25pt, 
    32 headsepline=0.25pt]{scrlayer-scrpage}   %% page layout 
     24%% Formatting 
     25\usepackage[inline, shortlabels]{enumitem} 
     26\usepackage{etoc, tabularx, xcolor} 
     27 
     28%% Graphics 
     29\usepackage{caption, graphicx} 
     30 
     31%% Labels 
     32\usepackage{lastpage, natbib} 
     33 
     34%% Mathematics 
     35\usepackage{amsmath, amssymb, mathtools} 
     36 
     37%% Versatility 
     38\usepackage{subfiles} 
    3339 
    3440%% Configuration 
    35 \graphicspath{ {../../figures/} {../../figures/\engine/} } 
    36 \geometry{showframe} 
     41\graphicspath{ {../../../} {../figures/} } 
     42 
     43%% Missing utmr8a font 
     44\usepackage{times} 

  • NEMO/branches/2019/dev_r11470_HPC_12_mpi3/doc/latex/global/styles.tex

    r11433 r11799  
    33%% ============================================================================== 
    44 
    5 \setcolor 
    6 %\definecolor{ghcolor}{HTML}{000333} 
     5%% Colors 
     6\setmanualcolor 
     7\colorlet{manualcolorshaded}{manualcolor!60} 
    78\definecolor{orcidcolor}{HTML}{A6CE39} 
    8 %\definecolor{wpcolor}{HTML}{464646} 
    99 
    1010%% Page layout 
    … …  
    1313\addtokomafont{pagefoot}{  \sffamily \footnotesize} 
    1414\addtokomafont{pagenumber}{\sffamily \slshape     } 
     15\addtokomafont{chapter}{\color{white}} 
    1516\ohead{} \ofoot{}   %% Clear defaults 
    1617 
    … …  
    1819\captionsetup{font = footnotesize, justification = justified} 
    1920 
    20 %% Additional fonts 
    21 \DeclareMathAlphabet{\mathpzc}{OT1}{pzc}{m}{it} 
     21%% Footnote 
     22\renewcommand{\thefootnote}{\fnsymbol{footnote}} 
    2223 
    2324%% Bibliography 
    … …  
    3334\global\let\tikz@ensure@dollar@catcode=\relax 
    3435 
    35 %% Apply engine color for chapter boxes (code from fncychap.sty) 
    36 %\renewcommand{\DOTI}[1]{ 
    37 %  \nointerlineskip\raggedright 
    38 %  \fboxsep=\myhi 
    39 %  \vskip-1ex 
    40 %  \colorbox[manualcolor]{.85}{\parbox[t]{\mylen}{\CTV\FmTi{#1}}}\par\nobreak 
    41 %  \vskip 40\p@ 
    42 %} 
     36%% First page 
     37\backgroundsetup{ 
     38  firstpage = true, 
     39  scale = 1, angle = 0, opacity = 1, 
     40  contents = { 
     41    \begin{tikzpicture}[remember picture, overlay] 
     42      \path [fill = manualcolor] (-0.5\paperwidth, 7) rectangle (0.5\paperwidth, 10); 
     43    \end{tikzpicture} 
     44  } 
     45} 
     46 
     47%% Apply engine color for chapter headings: tweaking snippets from fncychap.sty 
     48\renewcommand{\DOCH}{% 
     49  \settowidth{\py}{\CNoV\thechapter} 
     50  \addtolength{\py}{-10pt}      % Amount of space by which the 
     51%                                  % number is shifted right 
     52  \fboxsep=0pt% 
     53  \colorbox{manualcolor}{\rule{0pt}{40pt}\parbox[b]{\textwidth}{\hfill}}% 
     54  \kern-\py\raise20pt% 
     55  \hbox{\color{manualcolorshaded}\CNoV\thechapter}\\% 
     56} 
     57\renewcommand{\DOTI}[1]{% 
     58  \nointerlineskip\raggedright% 
     59  \fboxsep=\myhi% 
     60  \vskip-1ex% 
     61  \colorbox{manualcolor}{\parbox[t]{\mylen}{\color{white}\CTV\FmTi{#1}}}\par\nobreak% 
     62  \vskip 40\p@% 
     63} 
     64\renewcommand{\DOTIS}[1]{% 
     65  \fboxsep=0pt 
     66  \colorbox{manualcolor}{\rule{0pt}{40pt}\parbox[b]{\textwidth}{\hfill}}\\% 
     67  \nointerlineskip\raggedright% 
     68  \fboxsep=\myhi% 
     69  \vskip-1ex% Remove white 1pt line 
     70  \colorbox{manualcolor}{\parbox[t]{\mylen}{\color{white}\CTV\FmTi{#1}}}\par\nobreak% 
     71  \vskip 40\p@% 
     72} 
     73 
     74%% Temporary fix 
     75\def\set@curr@file#1{% 
     76  \begingroup 
     77    \escapechar\m@ne 
     78    \xdef\@curr@file{\expandafter\string\csname #1\endcsname}% 
     79  \endgroup 
     80} 
     81\def\quote@name#1{"\quote@@name#1\@gobble""} 
     82\def\quote@@name#1"{#1\quote@@name} 
     83\def\unquote@name#1{\quote@@name#1\@gobble"} 
    4384 
    4485\makeatother 
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