Changeset 11525


Ignore:
Timestamp:
2019-09-10T16:18:42+02:00 (12 months ago)
Author:
smasson
Message:

dev_r10984_HPC-13 : merge with trunk@,11524 see #2285

Location:
NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex
Files:
2 deleted
14 edited
1 copied

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  • NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/NEMO/main/chapters.tex

    r11263 r11525  
    1 \subfile{../subfiles/introduction}        %% Introduction 
    21\subfile{../subfiles/chap_model_basics} 
    32\subfile{../subfiles/chap_time_domain}    %% Time discretisation (time stepping strategy) 
     
    1514\subfile{../subfiles/chap_misc}           %% Miscellaneous topics 
    1615\subfile{../subfiles/chap_CONFIG}         %% Predefined configurations 
     16 
     17%% Not included 
     18%\subfile{../subfiles/chap_model_basics_zstar} 
     19%\subfile{../subfiles/chap_DIU} 
     20%\subfile{../subfiles/chap_conservation} 
  • NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/NEMO/main/definitions.tex

    r11512 r11525  
    22\def \engine{NEMO} 
    33 
    4 %% Title and cover page settings 
     4%% Cover page settings 
    55\def \spacetop{  \vspace*{1.85cm} } 
    66\def \heading{NEMO ocean engine} 
    7 \def \subheading{} 
     7%\def \subheading{} 
    88\def \spacedown{ \vspace*{0.75cm } } 
    9 \def \authorswidth{ 0.3\linewidth} 
     9\def \authorswidth{  0.3\linewidth} 
    1010\def \rulelenght{270pt} 
    1111\def \abstractwidth{0.6\linewidth} 
    1212 
    13 %% Color for document (frontpage banner, links  and chapter boxes) 
    14 \def \setcolor{ \definecolor{manualcolor}{cmyk}{1, .60, 0, .40} } 
     13%% Manual color (frontpage banner, links  and chapter boxes) 
     14\def \setmanualcolor{ \definecolor{manualcolor}{cmyk}{1, .60, 0, .40} } 
    1515 
    1616%% IPSL publication number 
  • NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/NEMO/main/thanks.tex

    r11512 r11525  
    4747                            George Nurser               \\ 
    4848\orcid{0000-0001-7481-6369} Guillaume Samson            \\ 
    49                             Dave Storkey 
     49                            Dave Storkey                \\ 
     50%% Don't forget the last break for the right alignment 
  • NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/NEMO/subfiles/chap_TRA.tex

    r11512 r11525  
    139139two quantities that are not correlated \citep{roullet.madec_JGR00, griffies.pacanowski.ea_MWR01, campin.adcroft.ea_OM04}. 
    140140 
    141 The velocity field that appears in (\autoref{eq:tra_adv} is  
     141The velocity field that appears in (\autoref{eq:tra_adv} is 
    142142the centred (\textit{now}) \textit{effective} ocean velocity, \ie\ the \textit{eulerian} velocity 
    143143(see \autoref{chap:DYN}) plus the eddy induced velocity (\textit{eiv}) and/or 
     
    471471\item[\np{ln\_traldf\_lap}\forcode{ = .true.}:] 
    472472  a laplacian operator is selected. 
    473   This harmonic operator takes the following expression:  $\mathpzc{L}(T) = \nabla \cdot A_{ht} \; \nabla T $, 
     473  This harmonic operator takes the following expression:  $\mathcal{L}(T) = \nabla \cdot A_{ht} \; \nabla T $, 
    474474  where the gradient operates along the selected direction (see \autoref{subsec:TRA_ldf_dir}), 
    475475  and $A_{ht}$ is the eddy diffusivity coefficient expressed in $m^2/s$ (see \autoref{chap:LDF}). 
     
    477477  a bilaplacian operator is selected. 
    478478  This biharmonic operator takes the following expression: 
    479   $\mathpzc{B} = - \mathpzc{L}(\mathpzc{L}(T)) = - \nabla \cdot b \nabla (\nabla \cdot b \nabla T)$ 
     479  $\mathcal{B} = - \mathcal{L}(\mathcal{L}(T)) = - \nabla \cdot b \nabla (\nabla \cdot b \nabla T)$ 
    480480  where the gradient operats along the selected direction, 
    481481  and $b^2 = B_{ht}$ is the eddy diffusivity coefficient expressed in $m^4/s$ (see \autoref{chap:LDF}). 
     
    534534where zero diffusive fluxes is assumed across solid boundaries, 
    535535first (and third in bilaplacian case) horizontal tracer derivative are masked. 
    536 It is implemented in the \rou{tra\_ldf\_lap} subroutine found in the \mdl{traldf\_lap\_blp}} module. 
     536It is implemented in the \rou{tra\_ldf\_lap} subroutine found in the \mdl{traldf\_lap\_blp} module. 
    537537The module also contains \rou{tra\_ldf\_blp}, the subroutine calling twice \rou{tra\_ldf\_lap} in order to 
    538538compute the iso-level bilaplacian operator. 
     
    12171217density in the World Ocean varies by no more than 2$\%$ from that value \citep{gill_bk82}. 
    12181218 
    1219 Options which control the EOS used are defined through the \ngn{nameos} namelist variables. 
     1219Options which control the EOS used are defined through the \nam{eos} namelist variables. 
    12201220 
    12211221\begin{description} 
  • NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/global/ametsoc.bst

    r11128 r11525  
    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_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/global/coding_rules.tex

    r11512 r11525  
    33\label{apdx:coding} 
    44 
    5 \minitoc 
     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 
    2425To 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}.  
     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 
     
    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 
    4950the expertise of the \NEMO System Team. 
     
    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} 
     
    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 
     
    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\_}                                                                               & 
     
    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_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/global/document.tex

    r11512 r11525  
    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[draft, fontsize = 10pt, 
     14twoside = semi, abstract = on, 
     15open = right]{scrreprt} 
    1416 
    1517%% Load configurations 
    1618\input{../../global/preamble} 
    17  
    18 \dominitoc 
    1919 
    2020%% End of common preamble between main and sub-files 
     
    3333 
    3434%% Frontmatter 
    35 %% ============================================================================== 
     35%% ================================================================================================= 
    3636 
    37 %% Disable page numbering temporarily 
    38 \pagenumbering{gobble} 
     37\pagenumbering{gobble}   %% Disable page numbering temporarily 
    3938 
    4039%% Title page 
    41 %\input{../../global/frontpage} 
    42 \input{../../global/frontpage_new} 
     40\input{../../global/frontpage} 
    4341 
    44 %\maketitle 
    45 %\emptythanks 
     42%% Footer for introductory parts (no header by cleaning default) 
     43\ofoot[]{\engine\ Reference Manual} \ifoot[]{\pagemark} 
    4644 
    4745%% Information page (2nd page) 
    4846\input{../../global/info_page} 
    4947 
    50 %% Headings for introductory parts (no header, simple footer) 
    51 \ofoot{\engine\ Reference Manual}\ifoot{\pagemark} 
     48\clearpage 
     49 
    5250\pagenumbering{roman} 
    53  
    54 %% Foreword 
    55 %\input{foreword} 
     51\input{introduction} 
    5652 
    5753%% Table of Contents 
    5854\tableofcontents 
    59 %\listoffigures 
    60 %\listoftables 
    61 %\listoflistings 
     55\listoffigures \listoftables \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 
    8375\include{appendices} 
    8476 
     
    8880 
    8981%% Backmatter 
    90 %% ============================================================================== 
    91  
    92 %\backmatter   %% Chapter numbering off 
     82%% ================================================================================================= 
    9383 
    9484%% Bibliography 
    9585\phantomsection 
    9686\addcontentsline{toc}{chapter}{Bibliography} 
     87\lohead{Bibliography} \rehead{Bibliography} 
    9788\bibliography{../main/bibliography} 
    9889 
    99 %% Index 
    10090\clearpage 
     91 
     92%% Indexes 
    10193\phantomsection 
    10294\addcontentsline{toc}{chapter}{Indexes} 
     95\lohead{Indexes} \rehead{Indexes} 
    10396\printindex[keys] 
    10497\printindex[modules] 
  • NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/global/frontpage.tex

    r11512 r11525  
    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{thanks} 
     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{foreword} 
     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_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/global/highlighting.tex

    r11353 r11525  
    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 
     
    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_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/global/info_page.tex

    r11512 r11525  
    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_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/global/new_cmds.tex

    r11512 r11525  
    33 
    44%% Include references and index for compilation of single subfile 
    5 \newcommand{\mtoc}{\minitoc} 
     5%\newcommand{\mtoc}{\minitoc} 
    66\newcommand{\biblio}{ \bibliography{../main/bibliography} } 
    77\newcommand{\pindex}{\printindex} 
    88 
    9 %% NEMO and Fortran in small capitals 
    10 \newcommand{\NEMO   }{\textsc{nemo}} 
    11 \newcommand{\SIcube }{\textsc{si$^3$}} 
    12 \newcommand{\TOP    }{\textsc{top}} 
     9%% Same slanted font for NEMO and its core engines 
     10\newcommand{\NEMO  }{\textsl{NEMO}} 
     11\newcommand{\OPA   }{\textsl{OPA}} 
     12\newcommand{\SIcube}{\textsl{SI$^3$}} 
     13\newcommand{\TOP   }{\textsl{TOP}} 
     14\newcommand{\PISCES}{\textsl{PISCES}} 
     15\newcommand{\NEMOVAR}{\textsl{NEMOVAR}} 
     16 
     17%% Links for external components 
     18\newcommand{\AGRIF}{\href{http://agrif.imag.fr}{AGRIF}} 
     19\newcommand{\CICE }{\href{http://github.com/CICE-Consortium/CICE}{CICE}} 
     20\newcommand{\OASIS}{\href{http://portal.enes.org/oasis}{OASIS}} 
     21\newcommand{\XIOS }{\href{http://forge.ipsl.jussieu.fr/ioserver}{XIOS}} 
     22 
     23%% Fortran in small capitals 
    1324\newcommand{\fortran}{\textsc{Fortran}} 
    1425\newcommand{\fninety}{\textsc{Fortran 90}} 
     
    5465%% Workaround for issue with \listoffigures 
    5566\DeclareRobustCommand{\triad}[6][]{\ensuremath{ {}_{#2}^{#3} { \mathbb{#4}_{#1} }_{#5}^{\,#6} }} 
     67 
     68\newcommand{\chaptertoc}[1][Table of contents]{% 
     69  \thispagestyle{empty} 
     70  \etocsettocstyle{\addsec*{#1}}{}% 
     71  \localtableofcontents% 
     72  \vfill 
     73} 
  • NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/global/packages.tex

    r11512 r11525  
    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{scrhack} 
     9\usepackage[footsepline=0.25pt, 
     10headsepline=0.25pt]{scrlayer-scrpage} 
     11 
     12%% customization (layout, header/footer styles & contents, background) 
     13\usepackage{draftwatermark} 
     14\usepackage[pass]{geometry}             %% 'pass' to enable \restoregeometry only 
     15\usepackage[pages = some]{background}   %% 'some' for title page 
     16\usepackage[Bjornstrup]{fncychap} 
     17 
     18%% fonts 
    1619\usepackage{fontspec} 
    17 %\setmainfont[Ligatures=TeX]{Georgia} 
    18 %\setsansfont[Ligatures=TeX]{Arial} 
     20%% Issue with fontawesome pkg: path to FontAwesome.otf has to be hard-coded 
    1921\defaultfontfeatures{ 
    2022    Path = /home/ntmlod/.local/texlive2019/texmf-dist/fonts/opentype/public/fontawesome/ 
    2123} 
    22 \usepackage{academicons}            %% font 
    23 \usepackage{fontawesome}            %% font 
    24 \usepackage{lastpage}               %% label 
    25 \usepackage[pages = some]{background}             %% decoration 
    26 \usepackage{geometry}               %% margin 
     24\usepackage{academicons, fontawesome, newtxtext} 
    2725 
    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 
     26%% formatting 
     27\usepackage{tabularx, etoc, xcolor} 
     28 
     29%% graphics 
     30\usepackage{caption, graphicx} 
     31 
     32%% labels 
     33\usepackage{bookmark, lastpage, natbib} 
     34 
     35%% mathematics 
     36\usepackage{amsmath, amssymb} 
     37 
     38%% versatility 
     39\usepackage{subfiles} 
    3340 
    3441%% Configuration 
    3542\graphicspath{ {../../figures/} {../../figures/\engine/} } 
    36 \geometry{showframe} 
     43 
     44%% Missing utmr8a font 
     45\usepackage{times} 
  • NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/global/preamble.tex

    r11512 r11525  
    88\input{../../global/indexes} 
    99\input{../../global/styles} 
     10\input{../../global/new_cmds} 
     11%\input{../../global/todonotes} 
     12 
     13%% Load hyperref at the end of the preamble to make it work with other pkgs 
     14\usepackage{hyperref}   %% links 
     15\hypersetup{ 
     16  colorlinks, 
     17  citecolor = manualcolor, linkcolor = manualcolor, urlcolor = manualcolor, 
     18  final = true  %% Links even with draft building 
     19} 
     20 
    1021\backgroundsetup{ 
    1122  firstpage = true, 
     
    1728  } 
    1829} 
    19 \input{../../global/new_cmds} 
    20 %\input{../../global/todonotes} 
    21  
    22 %% Load hyperref at the end of the preamble to make it work with other pkgs 
    23 \usepackage{hyperref}   %% links 
    24 \hypersetup{ 
    25   colorlinks, 
    26   citecolor = manualcolor, linkcolor = manualcolor, urlcolor = manualcolor, 
    27   final   %% Links even with draft building 
    28 } 
  • NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/global/styles.tex

    r11512 r11525  
    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 
    1718%% Caption 
    1819\captionsetup{font = footnotesize, justification = justified} 
    19  
    20 %% Additional fonts 
    21 \DeclareMathAlphabet{\mathpzc}{OT1}{pzc}{m}{it} 
    2220 
    2321%% Bibliography 
     
    3331\global\let\tikz@ensure@dollar@catcode=\relax 
    3432 
    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 %} 
     33%% Apply engine color for chapter headings: tweaking snippets from fncychap.sty 
     34\renewcommand{\DOCH}{% 
     35  \settowidth{\py}{\CNoV\thechapter} 
     36  \addtolength{\py}{-10pt}      % Amount of space by which the 
     37%                                  % number is shifted right 
     38  \fboxsep=0pt% 
     39  \colorbox{manualcolor}{\rule{0pt}{40pt}\parbox[b]{\textwidth}{\hfill}}% 
     40  \kern-\py\raise20pt% 
     41  \hbox{\color{manualcolorshaded}\CNoV\thechapter}\\% 
     42} 
     43\renewcommand{\DOTI}[1]{% 
     44  \nointerlineskip\raggedright% 
     45  \fboxsep=\myhi% 
     46  \vskip-1ex% 
     47  \colorbox{manualcolor}{\parbox[t]{\mylen}{\color{white}\CTV\FmTi{#1}}}\par\nobreak% 
     48  \vskip 40\p@% 
     49} 
     50\renewcommand{\DOTIS}[1]{% 
     51  \fboxsep=0pt 
     52  \colorbox{manualcolor}{\rule{0pt}{40pt}\parbox[b]{\textwidth}{\hfill}}\\% 
     53  \nointerlineskip\raggedright% 
     54  \fboxsep=\myhi% 
     55  \vskip-1ex% Remove white 1pt line 
     56  \colorbox{manualcolor}{\parbox[t]{\mylen}{\color{white}\CTV\FmTi{#1}}}\par\nobreak% 
     57  \vskip 40\p@% 
     58} 
    4359 
    4460\makeatother 
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