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Changeset 9388 – NEMO

Changeset 9388


Ignore:
Timestamp:
2018-03-08T17:57:24+01:00 (7 years ago)
Author:
nicolasmartin
Message:

Global reorganisation of DOC directory: implementation and configuration of syntax highlighting with 'minted' LaTeX package
New macros have been created to insert different source codes (fortran, xml, c and shell-session) in the document.
Pygments Python package is now required to compile the documentation.

Location:
branches/2017/dev_merge_2017/DOC
Files:
3 added
1 deleted
2 edited
29 copied
4 moved

Legend:

Unmodified
Added
Removed

  • branches/2017/dev_merge_2017/DOC/build_NEMO_manual.sh

    r9378 r9388  
    11#!/bin/sh 
    22 
    3 latex     -shell-escape    NEMO_manual 
    4 makeindex                  NEMO_manual 
    5 bibtex                     NEMO_manual 
    6 latex     -shell-escape    NEMO_manual 
     3latex_file='NEMO_manual' 
     4latex_opts='-shell-escape -interaction=nonstopmode' 
    75 
    8 pdflatex  -shell-escape    NEMO_manual 
     6cd tex_main 
     7 
     8latex       ${latex_opts}           ${latex_file} 
     9makeindex   -s ${latex_file}.sty    ${latex_file} 
     10bibtex                              ${latex_file} 
     11 
     12pdflatex    ${latex_opts}           ${latex_file} 
     13 
     14mv ${latex_file}.pdf .. 
     15 
     16cd - 
    917 
    1018exit 0 

  • branches/2017/dev_merge_2017/DOC/clean.sh

    r9378 r9388  
    11#!/bin/bash 
    22 
    3 rm -f $( ls -1 NEMO_manual* | egrep -v "tex" ) 
    4 rm -rf _minted-NEMO_manual html_* 
    5 find texfiles -regextype posix-extended -regex ".*\.(aux|log)" -exec rm -f {} \; 
     3rm -f $( ls -1 tex_main/NEMO_* | egrep -v "\.(bib|sty|tex)$" ) 
     4#rm -rf _minted-* 
     5#rm -rf html* 
     6find tex_* -regextype posix-extended -regex ".*\.(aux|log)$" -exec rm -f {} \; 
    67 
    78exit 0 

  • branches/2017/dev_merge_2017/DOC/tex_main/NEMO_manual.sty

    r9387 r9388  
    11%% ============================================================================== 
    2 %% macros.sty:  
     2%% NEMO_manual.sty: all customizations (packages, ) 
    33%% ============================================================================== 
    44 
     5 
     6%% LaTeX packages 
     7%% ============================================================================== 
     8 
     9\usepackage{natbib}     % bib 
     10\usepackage{caption}    % caption 
     11\usepackage{xcolor}     % color 
     12\usepackage{silence}    % compilation 
     13\usepackage{times}      % font 
     14\usepackage{hyperref}   % hyper 
     15\usepackage{enumitem}   % list 
     16\usepackage{minted}     % listing 
     17\usepackage{amsmath}    % maths 
     18\usepackage{fancyhdr}   % page 
     19\usepackage{minitoc}    % toc 
     20\usepackage{subfiles}   % subdocs 
     21 
     22 
     23%% Extensions in bundle package 
     24 
     25\usepackage{amssymb, graphicx, longtable, makeidx, xspace} 
     26 
     27 
     28%% Configuration 
     29 
     30\captionsetup{margin=10pt, font={small}, labelsep=colon, labelfont={bf}} 
     31\graphicspath{{../figures/}} 
     32\hypersetup{ 
     33   pdftitle={NEMO ocean engine}, pdfauthor={Gurvan Madec, and the NEMO team}, 
     34   colorlinks 
     35} 
     36 
     37 
     38%% Styles 
     39%% ============================================================================== 
     40 
     41%% Additionnal fonts 
     42 
     43\DeclareMathAlphabet{\mathpzc}{OT1}{pzc}{m}{it} 
     44 
     45 
     46%% Page layout 
     47 
     48\fancyhf{} 
     49\fancyhead[LE,RO]{\bfseries\thepage} 
     50\fancyhead[LO]{\bfseries\hspace{-0em}\rightmark} 
     51\renewcommand{\sectionmark}[1]{\markright{\thesection.\ #1}} 
     52\fancyhead[RE]{\bfseries\leftmark} 
     53\renewcommand{\chaptermark}[1]{\markboth{#1}{}} 
     54\renewcommand{\headrulewidth}{0.5pt} 
     55\renewcommand{\footrulewidth}{0pt  } 
     56\addtolength{\headheight}{2.6pt} 
     57 
     58 
     59%% Catcodes 
     60 
     61\makeatletter 
     62\def\LigneVerticale{\vrule height 5cm depth 2cm\hspace{0.1cm}\relax} 
     63\def\LignesVerticales{\let\LV\LigneVerticale\LV\LV\LV\LV\LV\LV\LV\LV\LV\LV} 
     64\def\GrosCarreAvecUnChiffre#1{% 
     65   \rlap{\vrule height 0.8cm width 1cm depth 0.2cm}% 
     66   \rlap{\hbox to 1cm{\hss\mbox{\color{white} #1}\hss}}% 
     67   \vrule height 0pt width 1cm depth 0pt% 
     68} 
     69\def\@makechapterhead#1{ 
     70   \hbox{ 
     71      \huge\LignesVerticales 
     72      \hspace{-0.5cm} 
     73      \GrosCarreAvecUnChiffre{\thechapter} 
     74      \hspace{0.2cm} 
     75      \hbox{#1} 
     76   } 
     77   \par\vskip 
     781cm 
     79} 
     80\def\@makeschapterhead#1{ 
     81   \hbox{ 
     82      \huge\LignesVerticales 
     83      \hbox{#1} 
     84   } 
     85   \par\vskip 
     862cm 
     87} 
     88\def\cleardoublepage{\clearpage\if@twoside \ifodd\c@page\else 
     89  \hbox{} 
     90  \vspace*{\fill} 
     91  \vspace{\fill} 
     92  \thispagestyle{empty} 
     93  \newpage 
     94  \if@twocolumn\hbox{}\newpage\fi\fi\fi} 
     95\def\@seccntformat#1{\protect\makebox[0pt][r]{\csname the#1\endcsname\quad}} 
     96\makeatother 
     97 
     98 
     99%% Macros (to check) 
    5100 
    6101\def\deg{$^{\circ}$} 
    … …  
    22117\def\rdt{\Delta t} 
    23118 
     119 
     120%% New commands 
     121 
    24122\newcommand{ \gmcomment}[1]{} 
    25123\newcommand{ \sfcomment}[1]{} 
    … …  
    29127\newcommand{\NEMO}{\textit{NEMO}\xspace} 
    30128 
    31 \newcommand{    \ifile}[1]{\textit{  #1.nc}\index{Input NetCDF files!#1.nc}} 
    32 \newcommand{       \jp}[1]{\textit{     #1}\index{     Model parameters!#1}} 
    33 \newcommand{       \hf}[1]{\textit{ #1.h90}\index{             h90 file!#1}} 
    34 \newcommand{      \key}[1]{\textbf{key\_#1}\index{        CPP keys!key\_#1}} 
    35 \newcommand{      \mdl}[1]{\textit{ #1.F90}\index{              Modules!#1}} 
    36 \newcommand{      \ngn}[1]{\textit{     #1}\index{  Namelist Group Name!#1}} 
    37 \newcommand{       \np}[1]{\textit{     #1}\index{   Namelist variables!#1}} 
    38 \newcommand{       \pp}[1]{\textit{     #1}\index{     Model parameters!#1}} 
    39 \newcommand{      \rou}[1]{\textit{     #1}\index{             Routines!#1}} 
     129\newcommand{\ifile}[1]{\textit{  #1.nc}\index{Input NetCDF files!#1.nc}} 
     130\newcommand{   \jp}[1]{\textit{     #1}\index{     Model parameters!#1}} 
     131\newcommand{   \hf}[1]{\textit{ #1.h90}\index{             h90 file!#1}} 
     132\newcommand{  \key}[1]{\textbf{key\_#1}\index{        CPP keys!key\_#1}} 
     133\newcommand{  \mdl}[1]{\textit{ #1.F90}\index{              Modules!#1}} 
     134\newcommand{  \ngn}[1]{\textit{     #1}\index{  Namelist Group Name!#1}} 
     135\newcommand{   \np}[1]{\textit{     #1}\index{   Namelist variables!#1}} 
     136\newcommand{   \pp}[1]{\textit{     #1}\index{     Model parameters!#1}} 
     137\newcommand{  \rou}[1]{\textit{     #1}\index{             Routines!#1}} 
    40138 
    41139\newcommand{\grad}{\nabla} 

  • branches/2017/dev_merge_2017/DOC/tex_main/NEMO_manual.tex

    r9387 r9388  
    44 
    55 
    6 %% Run build_NEMO_manual.sh to generate the PDF version (with pdflatex) 
     6%% Run ../build_NEMO_manual.sh to generate the PDF version (with pdflatex) 
     7 
     8%% Document layout 
     9%% ============================================================================== 
     10 
     11\documentclass[a4paper, 11pt]{book} 
    712 
    813 
    … …  
    1015%% ============================================================================== 
    1116 
    12 \include{texfiles/preamble} 
     17\usepackage{../tex_main/NEMO_manual} 
     18\usepackage{../tex_sub/minted} 
     19\pagestyle{fancy} 
     20\bibliographystyle{../tex_sub/ametsoc} 
     21 
     22\makeindex 
     23 
     24 
     25%%  
     26%% ============================================================================== 
    1327 
    1428\begin{document} 
    15  
    16  
    17 %% 'minted' env. & shortcuts for syntax highlighting 
    18  
    19 \setminted[fortran]{fontsize=\tiny, breaklines} 
    20 \newminted{fortran}{}         % \begin{fortrancode} 
    21 \newmintinline{fortran}{}     % \fortraninline 
    22 \newmintedfile{fortran}{}     % \fortranfile 
    23 \newminted{xml}{fontsize=\tiny, breaklines} 
    24 \newminted{sh}{} 
    25 \newminted{c}{} 
    2629 
    2730 
    … …  
    2932%% ============================================================================== 
    3033 
    31 \subfile{texfiles/top_matter} 
     34%% Frontpage 
    3235 
     36\title{ 
     37\vspace{-6.0cm}\includegraphics[width=1.1\textwidth]{logo_ALL}          \\ 
     38\vspace{ 5.1cm}\includegraphics[width=0.9\textwidth]{NEMO_logo_Black}   \\ 
     39\vspace{ 1.4cm}\rule{345pt}{1.5pt}                                      \\ 
     40\vspace{0.45cm}{\Huge NEMO ocean engine}                                \\ 
     41\rule{345pt}{1.5pt} 
     42} 
    3343 
    34 %% Frontpage 
     44\author{ 
     45\Large Gurvan Madec, and the NEMO team                                                          \\ 
     46\texttt{\small\href{mailto:gurvan.madec@locean-ipsl.umpc.fr}{gurvan.madec@locean-ipsl.umpc.fr}} \\ 
     47} 
     48 
     49\date{ 
     50Decembre 2017                                                                                \\ 
     51{\small  -- version 4.0 alpha --}                                                            \\ 
     52~                                                                                            \\ 
     53\textit{\small Note du P\^ole de mod\'{e}lisation de l'Institut Pierre-Simon Laplace No 27 } \\ 
     54\vspace{0.45cm}{ ISSN No 1288-1619.} 
     55} 
     56%\date{\today} 
    3557 
    3658\maketitle 
    … …  
    5274%% Abstract - Foreword 
    5375 
    54 \subfile{texfiles/chapters/abstract_foreword} 
     76\subfile{../tex_sub/abstract_foreword} 
    5577 
    5678 
    5779% Introduction 
    5880 
    59 \subfile{texfiles/chapters/introduction} 
     81\subfile{../tex_sub/introduction} 
    6082 
    6183 
    6284% Chapters 
    6385 
    64 \subfile{texfiles/chapters/chap_model_basics} 
     86\subfile{../tex_sub/chap_model_basics} 
    6587 
    66 \subfile{texfiles/chapters/chap_step}           % Time discretisation (time stepping strategy) 
     88\subfile{../tex_sub/chap_time_domain}           % Time discretisation (time stepping strategy) 
    6789 
    68 \subfile{texfiles/chapters/chap_DOM}            % Space discretisation 
     90\subfile{../tex_sub/chap_DOM}          % Space discretisation 
    6991 
    70 \subfile{texfiles/chapters/chap_TRA}            % Tracer advection/diffusion equation 
     92\subfile{../tex_sub/chap_TRA}          % Tracer advection/diffusion equation 
    7193 
    72 \subfile{texfiles/chapters/chap_DYN}            % Dynamics : momentum equation 
     94\subfile{../tex_sub/chap_DYN}          % Dynamics : momentum equation 
    7395 
    74 \subfile{texfiles/chapters/chap_SBC}            % Surface Boundary Conditions 
     96\subfile{../tex_sub/chap_SBC}          % Surface Boundary Conditions 
    7597 
    76 \subfile{texfiles/chapters/chap_LBC}            % Lateral Boundary Conditions 
     98\subfile{../tex_sub/chap_LBC}          % Lateral Boundary Conditions 
    7799 
    78 \subfile{texfiles/chapters/chap_LDF}            % Lateral diffusion 
     100\subfile{../tex_sub/chap_LDF}          % Lateral diffusion 
    79101 
    80 \subfile{texfiles/chapters/chap_ZDF}            % Vertical diffusion 
     102\subfile{../tex_sub/chap_ZDF}          % Vertical diffusion 
    81103 
    82 \subfile{texfiles/chapters/chap_DIA}            % Outputs and Diagnostics 
     104\subfile{../tex_sub/chap_DIA}          % Outputs and Diagnostics 
    83105 
    84 \subfile{texfiles/chapters/chap_OBS}            % Observation operator 
     106\subfile{../tex_sub/chap_OBS}          % Observation operator 
    85107 
    86 \subfile{texfiles/chapters/chap_ASM}            % Assimilation increments 
     108\subfile{../tex_sub/chap_ASM}          % Assimilation increments 
    87109 
    88 \subfile{texfiles/chapters/chap_STO}            % Stochastic param. 
     110\subfile{../tex_sub/chap_STO}          % Stochastic param. 
    89111 
    90 \subfile{texfiles/chapters/chap_misc}           % Miscellaneous topics 
     112\subfile{../tex_sub/chap_misc}            % Miscellaneous topics 
    91113 
    92 \subfile{texfiles/chapters/chap_CONFIG}         % Predefined configurations 
     114\subfile{../tex_sub/chap_CONFIG}       % Predefined configurations 
    93115 
    94116 
    95 % Appendix 
     117%% Appendix 
    96118 
    97119\appendix 
    98120 
    99 \subfile{texfiles/chapters/annex_A}             % Generalised vertical coordinate 
     121\subfile{../tex_sub/annex_A}              % Generalised vertical coordinate 
    100122 
    101 \subfile{texfiles/chapters/annex_B}             % Diffusive operator 
     123\subfile{../tex_sub/annex_B}              % Diffusive operator 
    102124 
    103 \subfile{texfiles/chapters/annex_C}             % Discrete invariants of the eqs. 
     125\subfile{../tex_sub/annex_C}              % Discrete invariants of the eqs. 
    104126 
    105 \subfile{texfiles/chapters/annex_iso}           % Isoneutral diffusion using triads 
     127\subfile{../tex_sub/annex_iso}            % Isoneutral diffusion using triads 
    106128 
    107 \subfile{texfiles/chapters/annex_D}             % Coding rules 
     129\subfile{../tex_sub/annex_D}              % Coding rules 
    108130 
    109131%% Not included 
    110 %\subfile{texfiles/chapters/chap_conservation}  % 
    111 %\subfile{texfiles/chapters/annex_E}            % Notes on some on going staff 
    112 %\subfile{texfiles/chapters/annex_Fox-Kemper}   % Notes on Fox-Kemper 
    113 %\subfile{texfiles/chapters/annex_EVP}          % Notes on EVP 
     132%\subfile{../tex_sub/chap_conservation}   % 
     133%\subfile{../tex_sub/annex_E}          % Notes on some on going staff 
     134%\subfile{../tex_sub/annex_Fox-Kemper} % Notes on Fox-Kemper 
     135%\subfile{../tex_sub/annex_EVP}           % Notes on EVP 
    114136 
    115137 
    … …  
    128150%% Bibliography 
    129151 
    130 \bibliography{texfiles/bibliography/NEMO_manual} 
     152\bibliography{../tex_main/NEMO_manual} 
    131153 
    132154 

  • branches/2017/dev_merge_2017/DOC/tex_sub/annex_iso.tex

    r9387 r9388  
    1111\section{Choice of \protect\ngn{namtra\_ldf} namelist parameters} 
    1212%-----------------------------------------nam_traldf------------------------------------------------------ 
    13 \fortranfile{namelists/namtra_ldf} 
     13\forfile{../namelists/namtra_ldf} 
    1414%--------------------------------------------------------------------------------------------------------- 
    1515 

  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_ASM.tex

    r9387 r9388  
    131131 
    132132%------------------------------------------namasm----------------------------------------------------- 
    133 %\fortranfile{namelists/namasm} 
     133%\forfile{../namelists/namasm} 
    134134%------------------------------------------------------------------------------------------------------------- 
    135135 
    … …  
    137137\mbox{\textit{ncdump~-h}} is shown below 
    138138 
    139 \begin{ccode} 
     139\begin{clines} 
    140140netcdf assim_background_increments { 
    141141dimensions: 
    … …  
    170170                :DOMAIN_type = "BOX" ; 
    171171} 
    172 \end{ccode} 
     172\end{clines} 
    173173 
    174174\end{document} 

  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_CONFIG.tex

    r9387 r9388  
    2626 
    2727%------------------------------------------namcfg---------------------------------------------------- 
    28 \fortranfile{namelists/namcfg} 
     28\forfile{../namelists/namcfg} 
    2929%------------------------------------------------------------------------------------------------------------- 
    3030 

  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_DIA.tex

    r9387 r9388  
    10521052 
    10531053%------------------------------------------namnc4---------------------------------------------------- 
    1054 \fortranfile{namelists/namnc4} 
     1054\forfile{../namelists/namnc4} 
    10551055%------------------------------------------------------------------------------------------------------------- 
    10561056 
    … …  
    10801080 
    10811081\vspace{-20pt} 
    1082 \begin{fortrancode} 
     1082\begin{forlines} 
    10831083     ichunksz(1) = MIN( idomain_size,MAX( (idomain_size-1)/nn_nchunks_i + 1 ,16 ) ) 
    10841084     ichunksz(2) = MIN( jdomain_size,MAX( (jdomain_size-1)/nn_nchunks_j + 1 ,16 ) ) 
    10851085     ichunksz(3) = MIN( kdomain_size,MAX( (kdomain_size-1)/nn_nchunks_k + 1 , 1 ) ) 
    10861086     ichunksz(4) = 1 
    1087 \end{fortrancode} 
     1087\end{forlines} 
    10881088 
    10891089\noindent As an example, setting: 
    10901090\vspace{-20pt} 
    1091 \begin{fortrancode} 
     1091\begin{forlines} 
    10921092     nn_nchunks_i=4, nn_nchunks_j=4 and nn_nchunks_k=31 
    1093 \end{fortrancode} 
     1093\end{forlines} 
    10941094 
    10951095\noindent for a standard ORCA2\_LIM configuration gives chunksizes of {\small\tt 46x38x1} 
    … …  
    11561156 
    11571157%------------------------------------------namtrd---------------------------------------------------- 
    1158 \fortranfile{namelists/namtrd}  
     1158\forfile{../namelists/namtrd}  
    11591159%------------------------------------------------------------------------------------------------------------- 
    11601160 
    … …  
    11951195\label{FLO} 
    11961196%--------------------------------------------namflo------------------------------------------------------- 
    1197 \fortranfile{namelists/namflo}  
     1197\forfile{../namelists/namflo}  
    11981198%-------------------------------------------------------------------------------------------------------------- 
    11991199 
    … …  
    13051305 
    13061306%------------------------------------------namdia_harm---------------------------------------------------- 
    1307 %\fortranfile{namelists/namdia_harm} 
     1307%\forfile{../namelists/namdia_harm} 
    13081308%---------------------------------------------------------------------------------------------------------- 
    13091309 
    … …  
    13471347 
    13481348%------------------------------------------namdct---------------------------------------------------- 
    1349 \fortranfile{namelists/namdct} 
     1349\forfile{../namelists/namdct} 
    13501350%------------------------------------------------------------------------------------------------------------- 
    13511351 
    … …  
    16761676 
    16771677%------------------------------------------namptr----------------------------------------- 
    1678 \fortranfile{namelists/namptr}  
     1678\forfile{../namelists/namptr}  
    16791679%----------------------------------------------------------------------------------------- 
    16801680 
    … …  
    17191719 
    17201720%------------------------------------------nam_dia25h------------------------------------- 
    1721 \fortranfile{namelists/nam_dia25h} 
     1721\forfile{../namelists/nam_dia25h} 
    17221722%----------------------------------------------------------------------------------------- 
    17231723 
    … …  
    17341734 
    17351735%------------------------------------------nam_diatmb----------------------------------------------------- 
    1736 \fortranfile{namelists/nam_diatmb} 
     1736\forfile{../namelists/nam_diatmb} 
    17371737%---------------------------------------------------------------------------------------------------------- 
    17381738 

  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_DIU.tex

    r9387 r9388  
    3434 
    3535Both the cool skin and warm layer models are controlled through the namelist \ngn{namdiu}: 
    36 \fortranfile{namelists/namdiu} 
     36\forfile{../namelists/namdiu} 
    3737This namelist contains only two variables: 
    3838\begin{description} 

  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_DOM.tex

    r9387 r9388  
    310310  
    311311These fields can be read in an domain input file which name is setted in \np{cn\_domcfg} parameter specified in \ngn{namcfg}. 
    312 \fortranfile{namelists/namcfg} 
     312\forfile{../namelists/namcfg} 
    313313or they can be defined in an analytical way in MY\_SRC directory of the configuration. 
    314314For Reference Configurations of NEMO input domain files are supplied by NEMO System Team. For analytical definition of input fields two routines are supplied: \mdl{userdef\_hgr} and \mdl{userdef\_zgr}. They are an example of GYRE configuration parameters, and they are available in NEMO/OPA\_SRC/USR directory, they provide the horizontal and vertical mesh.  
    … …  
    431431\label{DOM_zgr} 
    432432%-----------------------------------------nam_zgr & namdom------------------------------------------- 
    433 %\fortranfile{namelists/namzgr}  
    434 \fortranfile{namelists/namdom}  
     433%\forfile{../namelists/namzgr}  
     434\forfile{../namelists/namdom}  
    435435%------------------------------------------------------------------------------------------------------------- 
    436436 
    … …  
    692692\label{DOM_zps} 
    693693%--------------------------------------------namdom------------------------------------------------------- 
    694 \fortranfile{namelists/namdom}  
     694\forfile{../namelists/namdom}  
    695695%-------------------------------------------------------------------------------------------------------------- 
    696696 
    … …  
    725725\label{DOM_sco} 
    726726%------------------------------------------nam_zgr_sco--------------------------------------------------- 
    727 %\fortranfile{namelists/namzgr_sco}  
     727%\forfile{../namelists/namzgr_sco}  
    728728%-------------------------------------------------------------------------------------------------------------- 
    729729Options are defined in \ngn{namzgr\_sco}. 
    … …  
    916916\label{DTA_tsd} 
    917917%-----------------------------------------namtsd------------------------------------------- 
    918 \fortranfile{namelists/namtsd}  
     918\forfile{../namelists/namtsd}  
    919919%------------------------------------------------------------------------------------------ 
    920920 

  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_DYN.tex

    r9387 r9388  
    162162\label{DYN_adv_cor_vect} 
    163163%-----------------------------------------nam_dynadv---------------------------------------------------- 
    164 \fortranfile{namelists/namdyn_adv}  
     164\forfile{../namelists/namdyn_adv}  
    165165%------------------------------------------------------------------------------------------------------------- 
    166166 
    … …  
    182182\label{DYN_vor} 
    183183%------------------------------------------nam_dynvor---------------------------------------------------- 
    184 \fortranfile{namelists/namdyn_vor}  
     184\forfile{../namelists/namdyn_vor}  
    185185%------------------------------------------------------------------------------------------------------------- 
    186186 
    … …  
    391391\label{DYN_adv_cor_flux} 
    392392%------------------------------------------nam_dynadv---------------------------------------------------- 
    393 \fortranfile{namelists/namdyn_adv}  
     393\forfile{../namelists/namdyn_adv}  
    394394%------------------------------------------------------------------------------------------------------------- 
    395395 
    … …  
    536536\label{DYN_hpg} 
    537537%------------------------------------------nam_dynhpg--------------------------------------------------- 
    538 \fortranfile{namelists/namdyn_hpg}  
     538\forfile{../namelists/namdyn_hpg}  
    539539%------------------------------------------------------------------------------------------------------------- 
    540540 
    … …  
    736736\label{DYN_spg} 
    737737%-----------------------------------------nam_dynspg---------------------------------------------------- 
    738 \fortranfile{namelists/namdyn_spg}  
     738\forfile{../namelists/namdyn_spg}  
    739739%------------------------------------------------------------------------------------------------------------ 
    740740 
    … …  
    796796\label{DYN_spg_ts} 
    797797%------------------------------------------namsplit----------------------------------------------------------- 
    798 %\fortranfile{namelists/namsplit} 
     798%\forfile{../namelists/namsplit} 
    799799%------------------------------------------------------------------------------------------------------------- 
    800800 
    … …  
    10051005\label{DYN_ldf} 
    10061006%------------------------------------------nam_dynldf---------------------------------------------------- 
    1007 \fortranfile{namelists/namdyn_ldf}  
     1007\forfile{../namelists/namdyn_ldf}  
    10081008%------------------------------------------------------------------------------------------------------------- 
    10091009 
    … …  
    11491149\label{DYN_zdf} 
    11501150%----------------------------------------------namzdf------------------------------------------------------ 
    1151 \fortranfile{namelists/namzdf}  
     1151\forfile{../namelists/namzdf}  
    11521152%------------------------------------------------------------------------------------------------------------- 
    11531153 
    … …  
    12271227 
    12281228%----------------------------------------------namdom---------------------------------------------------- 
    1229 \fortranfile{namelists/namdom}  
     1229\forfile{../namelists/namdom}  
    12301230%------------------------------------------------------------------------------------------------------------- 
    12311231 

  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_LBC.tex

    r9387 r9388  
    2020\label{LBC_coast} 
    2121%--------------------------------------------nam_lbc------------------------------------------------------- 
    22 \fortranfile{namelists/namlbc}  
     22\forfile{../namelists/namlbc}  
    2323%-------------------------------------------------------------------------------------------------------------- 
    2424 
    … …  
    354354 
    355355%-----------------------------------------nambdy-------------------------------------------- 
    356 \fortranfile{namelists/nambdy}  
     356\forfile{../namelists/nambdy}  
    357357%----------------------------------------------------------------------------------------------- 
    358358%-----------------------------------------nambdy_index-------------------------------------------- 
    359 %\fortranfile{namelists/nambdy_index} 
     359%\forfile{../namelists/nambdy_index} 
    360360%----------------------------------------------------------------------------------------------- 
    361361%-----------------------------------------nambdy_dta-------------------------------------------- 
    362 \fortranfile{namelists/nambdy_dta}  
     362\forfile{../namelists/nambdy_dta}  
    363363%----------------------------------------------------------------------------------------------- 
    364364%-----------------------------------------nambdy_dta-------------------------------------------- 
    365 %\fortranfile{namelists/nambdy_dta2}  
     365%\forfile{../namelists/nambdy_dta2}  
    366366%----------------------------------------------------------------------------------------------- 
    367367 
    … …  
    635635 
    636636%-----------------------------------------nambdy_tide-------------------------------------------- 
    637 \fortranfile{namelists/nambdy_tide}  
     637\forfile{../namelists/nambdy_tide}  
    638638%----------------------------------------------------------------------------------------------- 
    639639 

  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_LDF.tex

    r9387 r9388  
    2828 
    2929%-----------------------------------nam_traldf - nam_dynldf-------------------------------------------- 
    30 \fortranfile{namelists/namtra_ldf}  
    31 \fortranfile{namelists/namdyn_ldf}  
     30\forfile{../namelists/namtra_ldf}  
     31\forfile{../namelists/namdyn_ldf}  
    3232%-------------------------------------------------------------------------------------------------------------- 
    3333 

  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_OBS.tex

    r9387 r9388  
    7070 
    7171\item Compile the OBSTOOLS code using:  
    72 \begin{shcode} 
     72\begin{cmds} 
    7373./maketools -n OBSTOOLS -m [ARCH]. 
    74 \end{shcode} 
     74\end{cmds} 
    7575 
    7676\item Convert the EN4 data into feedback format:  
    77 \begin{shcode} 
     77\begin{cmds} 
    7878enact2fb.exe profiles_01.nc EN.4.1.1.f.profiles.g10.YYYYMM.nc 
    79 \end{shcode} 
     79\end{cmds} 
    8080 
    8181\item Include the following in the NEMO namelist to run the observation 
    … …  
    8484 
    8585%------------------------------------------namobs_example----------------------------------------------------- 
    86 %\fortranfile{namelists/namobs_example} 
     86%\forfile{../namelists/namobs_example} 
    8787%------------------------------------------------------------------------------------------------------------- 
    8888 
    … …  
    114114 
    115115%------------------------------------------namobs-------------------------------------------------------- 
    116 \fortranfile{namelists/namobs} 
     116\forfile{../namelists/namobs} 
    117117%------------------------------------------------------------------------------------------------------------- 
    118118 
    … …  
    126126\subsection{Profile feedback} 
    127127 
    128 \begin{ccode} 
     128\begin{clines} 
    129129netcdf profiles_01 { 
    130130dimensions: 
    … …  
    278278          :Convention = "NEMO unified observation operator output" ; 
    279279} 
    280 \end{ccode} 
     280\end{clines} 
    281281 
    282282\subsection{Sea level anomaly feedback} 
    283283 
    284 \begin{ccode} 
     284\begin{clines} 
    285285netcdf sla_01 { 
    286286dimensions: 
    … …  
    402402          :Convention = "NEMO unified observation operator output" ; 
    403403} 
    404 \end{ccode} 
     404\end{clines} 
    405405 
    406406The mean dynamic 
    … …  
    410410surface height. Below is an example header for this file (on the ORCA025 grid). 
    411411 
    412 \begin{ccode} 
     412\begin{clines} 
    413413dimensions: 
    414414        x = 1442 ; 
    … …  
    425425                sossheig:units = "metres" ; 
    426426                sossheig:grid = "orca025T" ; 
    427 \end{ccode} 
     427\end{clines} 
    428428 
    429429\subsection{Sea surface temperature feedback} 
    430430 
    431 \begin{ccode} 
     431\begin{clines} 
    432432netcdf sst_01 { 
    433433dimensions: 
    … …  
    542542          :Convention = "NEMO unified observation operator output" ; 
    543543} 
    544 \end{ccode} 
     544\end{clines} 
    545545 
    546546\section{Theoretical details} 
    … …  
    923923read the second time counter from a single file the namelist would be. 
    924924 
    925 \begin{fortrancode} 
     925\begin{forlines} 
    926926!---------------------------------------------------------------------- 
    927927!       namooo Offline obs_oper namelist 
    … …  
    933933   nn_ooo_idx = 2 
    934934/ 
    935 \end{fortrancode} 
     935\end{forlines} 
    936936 
    937937\subsubsection{Multiple fields per run} 
    … …  
    94194112 hourly fields are to be interpolated in a setup where 288 steps equals 24 hours. 
    942942 
    943 \begin{fortrancode} 
     943\begin{forlines} 
    944944!---------------------------------------------------------------------- 
    945945!       namooo Offline obs_oper namelist 
    … …  
    953953   nn_ooo_freq = 144 
    954954/ 
    955 \end{fortrancode} 
     955\end{forlines} 
    956956 
    957957The above namelist will result in feedback files whose first 12 hours contain 
    … …  
    10611061fields plus an analysis field would be 7 counterparts per observation. 
    10621062 
    1063 \begin{fortrancode} 
     1063\begin{forlines} 
    10641064   cl4_match_len = 7 
    1065 \end{fortrancode} 
     1065\end{forlines} 
    10661066 
    10671067Then to correctly allocate a class 4 file the forecast axis must be defined. This 
    10681068is controlled via \textbf{cl4\_fcst\_len}, which in out above example would be 3. 
    10691069 
    1070 \begin{fortrancode} 
     1070\begin{forlines} 
    10711071   cl4_fcst_len = 3 
    1072 \end{fortrancode} 
     1072\end{forlines} 
    10731073 
    10741074Then for each model field it is necessary to designate what class 4 variable and 
    … …  
    10771077when interpreting the data afterwards.  
    10781078 
    1079 \begin{fortrancode} 
     1079\begin{forlines} 
    10801080   cl4_vars = "forecast" "forecast" "forecast" "persistence" "persistence" 
    10811081              "persistence" "best_estimate" 
    10821082   cl4_fcst_idx = 1 2 3 1 2 3 1 
    10831083   cl4_leadtime = 12 36 60  
    1084 \end{fortrancode} 
     1084\end{forlines} 
    10851085 
    10861086In terms of files and indices of fields inside each file the class 4 approach 
    … …  
    10881088with a single field per file our example inputs will be specified. 
    10891089 
    1090 \begin{fortrancode} 
     1090\begin{forlines} 
    10911091   ooo_files = "F.1.nc" "F.2.nc" "F.3.nc" "P.1.nc" "P.2.nc" "P.3.nc" "A.1.nc" 
    10921092   nn_ooo_idx = 1 1 1 1 1 1 1 
    1093 \end{fortrancode} 
     1093\end{forlines} 
    10941094 
    10951095When we combine all of the naming conventions, global attributes and i/o instructions 
    10961096the class 4 namelist becomes. 
    10971097 
    1098 \begin{fortrancode} 
     1098\begin{forlines} 
    10991099!---------------------------------------------------------------------- 
    11001100!       namooo Offline obs_oper namelist 
    … …  
    11441144   cl4_inst = "UK Met Office" 
    11451145/ 
    1146 \end{fortrancode} 
     1146\end{forlines} 
    11471147 
    11481148\subsubsection{Climatology interpolation} 
    … …  
    11671167operations, 1 per forecast. 
    11681168 
    1169 \begin{fortrancode} 
     1169\begin{forlines} 
    11701170   ooo_files = "F1.nc" "F1.nc" "F2.nc" "F2.nc" 
    11711171... 
    11721172   cl4_fcst_idx = 1 2 
    1173 \end{fortrancode} 
     1173\end{forlines} 
    11741174 
    11751175The above notation reveals the internal split between match up iterators and file 
    … …  
    12051205 
    12061206\footnotesize 
    1207 \begin{shcode} 
     1207\begin{cmds} 
    12081208c4comb.exe outputfile inputfile1 inputfile2 ... 
    1209 \end{shcode} 
     1209\end{cmds} 
    12101210 
    12111211\subsubsection{corio2fb} 
    … …  
    12151215 
    12161216\footnotesize 
    1217 \begin{shcode} 
     1217\begin{cmds} 
    12181218corio2fb.exe outputfile inputfile1 inputfile2 ... 
    1219 \end{shcode} 
     1219\end{cmds} 
    12201220 
    12211221\subsubsection{enact2fb} 
    … …  
    12251225 
    12261226\footnotesize 
    1227 \begin{shcode} 
     1227\begin{cmds} 
    12281228enact2fb.exe outputfile inputfile1 inputfile2 ... 
    1229 \end{shcode} 
     1229\end{cmds} 
    12301230 
    12311231\subsubsection{fbcomb} 
    … …  
    12351235 
    12361236\footnotesize 
    1237 \begin{shcode} 
     1237\begin{cmds} 
    12381238fbcomb.exe outputfile inputfile1 inputfile2 ... 
    1239 \end{shcode} 
     1239\end{cmds} 
    12401240 
    12411241\subsubsection{fbmatchup} 
    … …  
    12451245 
    12461246\footnotesize 
    1247 \begin{shcode} 
     1247\begin{cmds} 
    12481248fbmatchup.exe outputfile inputfile1 varname1 inputfile2 varname2 ... 
    1249 \end{shcode} 
     1249\end{cmds} 
    12501250 
    12511251\subsubsection{fbprint} 
    … …  
    12561256 
    12571257\footnotesize 
    1258 \begin{shcode} 
     1258\begin{cmds} 
    12591259fbprint.exe [options] inputfile 
    12601260 
    … …  
    12761276     -D            print depths 
    12771277     -z            use zipped files 
    1278 \end{shcode} 
     1278\end{cmds} 
    12791279 
    12801280\subsubsection{fbsel} 
    … …  
    12841284 
    12851285\footnotesize 
    1286 \begin{shcode} 
     1286\begin{cmds} 
    12871287fbsel.exe <input filename> <output filename> 
    1288 \end{shcode} 
     1288\end{cmds} 
    12891289 
    12901290\subsubsection{fbstat} 
    … …  
    12941294 
    12951295\footnotesize 
    1296 \begin{shcode} 
     1296\begin{cmds} 
    12971297fbstat.exe [-nmlev] <filenames> 
    1298 \end{shcode} 
     1298\end{cmds} 
    12991299 
    13001300\subsubsection{fbthin} 
    … …  
    13041304 
    13051305\footnotesize 
    1306 \begin{shcode} 
     1306\begin{cmds} 
    13071307fbthin.exe inputfile outputfile 
    1308 \end{shcode} 
     1308\end{cmds} 
    13091309 
    13101310\subsubsection{sla2fb} 
    … …  
    13141314 
    13151315\footnotesize 
    1316 \begin{shcode} 
     1316\begin{cmds} 
    13171317sla2fb.exe [-s type] outputfile inputfile1 inputfile2 ... 
    13181318 
    13191319Option: 
    13201320     -s            Select altimeter data_source 
    1321 \end{shcode} 
     1321\end{cmds} 
    13221322 
    13231323\subsubsection{vel2fb} 
    … …  
    13271327 
    13281328\footnotesize 
    1329 \begin{shcode} 
     1329\begin{cmds} 
    13301330vel2fb.exe outputfile inputfile1 inputfile2 ... 
    1331 \end{shcode} 
     1331\end{cmds} 
    13321332 
    13331333\subsection{building the obstools} 

  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_SBC.tex

    r9387 r9388  
    1111$\ $\newline    % force a new ligne 
    1212%---------------------------------------namsbc-------------------------------------------------- 
    13 \fortranfile{namelists/namsbc} 
     13\forfile{../namelists/namsbc} 
    1414%-------------------------------------------------------------------------------------------------------------- 
    1515$\ $\newline    % force a new ligne 
    … …  
    196196 
    197197The structure associated with an input variable contains the following information: 
    198 \begin{fortrancode} 
     198\begin{forlines} 
    199199!  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !  
    200200!             !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      ! 
    201 \end{fortrancode} 
     201\end{forlines} 
    202202where  
    203203\begin{description}   
    … …  
    425425 
    426426%---------------------------------------namsbc_ana-------------------------------------------------- 
    427 \fortranfile{namelists/namsbc_sas} 
     427\forfile{../namelists/namsbc_sas} 
    428428%-------------------------------------------------------------------------------------------------------------- 
    429429 
    … …  
    486486 
    487487%---------------------------------------namsbc_ana-------------------------------------------------- 
    488 %\fortranfile{namelists/namsbc_ana} 
     488%\forfile{../namelists/namsbc_ana} 
    489489%-------------------------------------------------------------------------------------------------------------- 
    490490 
    … …  
    510510\label{SBC_flx} 
    511511%------------------------------------------namsbc_flx---------------------------------------------------- 
    512 \fortranfile{namelists/namsbc_flx}  
     512\forfile{../namelists/namsbc_flx}  
    513513%------------------------------------------------------------------------------------------------------------- 
    514514 
    … …  
    550550\label{SBC_blk_core} 
    551551%------------------------------------------namsbc_core---------------------------------------------------- 
    552 %\fortranfile{namelists/namsbc_core} 
     552%\forfile{../namelists/namsbc_core} 
    553553%------------------------------------------------------------------------------------------------------------- 
    554554 
    … …  
    615615\label{SBC_blk_clio} 
    616616%------------------------------------------namsbc_clio---------------------------------------------------- 
    617 %\fortranfile{namelists/namsbc_clio} 
     617%\forfile{../namelists/namsbc_clio} 
    618618%------------------------------------------------------------------------------------------------------------- 
    619619 
    … …  
    656656\label{SBC_blk_mfs} 
    657657%------------------------------------------namsbc_mfs---------------------------------------------------- 
    658 %\fortranfile{namelists/namsbc_mfs} 
     658%\forfile{../namelists/namsbc_mfs} 
    659659%---------------------------------------------------------------------------------------------------------- 
    660660 
    … …  
    695695\label{SBC_cpl} 
    696696%------------------------------------------namsbc_cpl---------------------------------------------------- 
    697 \fortranfile{namelists/namsbc_cpl}  
     697\forfile{../namelists/namsbc_cpl}  
    698698%------------------------------------------------------------------------------------------------------------- 
    699699 
    … …  
    734734\label{SBC_apr} 
    735735%------------------------------------------namsbc_apr---------------------------------------------------- 
    736 \fortranfile{namelists/namsbc_apr}  
     736\forfile{../namelists/namsbc_apr}  
    737737%------------------------------------------------------------------------------------------------------------- 
    738738 
    … …  
    770770 
    771771%------------------------------------------nam_tide--------------------------------------- 
    772 \fortranfile{namelists/nam_tide} 
     772\forfile{../namelists/nam_tide} 
    773773%----------------------------------------------------------------------------------------- 
    774774 
    … …  
    825825\label{SBC_rnf} 
    826826%------------------------------------------namsbc_rnf---------------------------------------------------- 
    827 \fortranfile{namelists/namsbc_rnf}  
     827\forfile{../namelists/namsbc_rnf}  
    828828%------------------------------------------------------------------------------------------------------------- 
    829829 
    … …  
    941941\label{SBC_isf} 
    942942%------------------------------------------namsbc_isf---------------------------------------------------- 
    943 \fortranfile{namelists/namsbc_isf} 
     943\forfile{../namelists/namsbc_isf} 
    944944%-------------------------------------------------------------------------------------------------------- 
    945945Namelist variable in \ngn{namsbc}, \np{nn\_isf}, controls the ice shelf representation used.  
    … …  
    10221022\label{SBC_iscpl} 
    10231023%------------------------------------------namsbc_iscpl---------------------------------------------------- 
    1024 \fortranfile{namelists/namsbc_iscpl} 
     1024\forfile{../namelists/namsbc_iscpl} 
    10251025%-------------------------------------------------------------------------------------------------------- 
    10261026Ice sheet/ocean coupling is done through file exchange at the restart step. NEMO, at each restart step,  
    … …  
    10601060\label{ICB_icebergs} 
    10611061%------------------------------------------namberg---------------------------------------------------- 
    1062 \fortranfile{namelists/namberg} 
     1062\forfile{../namelists/namberg} 
    10631063%------------------------------------------------------------------------------------------------------------- 
    10641064 
    … …  
    11321132\label{SBC_dcy} 
    11331133%------------------------------------------namsbc_rnf---------------------------------------------------- 
    1134 %\fortranfile{namelists/namsbc}  
     1134%\forfile{../namelists/namsbc}  
    11351135%------------------------------------------------------------------------------------------------------------- 
    11361136 
    … …  
    12091209\label{SBC_ssr} 
    12101210%------------------------------------------namsbc_ssr---------------------------------------------------- 
    1211 \fortranfile{namelists/namsbc_ssr}  
     1211\forfile{../namelists/namsbc_ssr}  
    12121212%------------------------------------------------------------------------------------------------------------- 
    12131213 
    … …  
    13291329\label{SBC_wave} 
    13301330%------------------------------------------namwave---------------------------------------------------- 
    1331 \fortranfile{namelists/namsbc_wave} 
     1331\forfile{../namelists/namsbc_wave} 
    13321332%------------------------------------------------------------------------------------------------------------- 
    13331333 

  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_STO.tex

    r9387 r9388  
    124124 
    125125%---------------------------------------namsbc-------------------------------------------------- 
    126 \fortranfile{namelists/namsto} 
     126\forfile{../namelists/namsto} 
    127127%-------------------------------------------------------------------------------------------------------------- 
    128128 

  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_TRA.tex

    r9387 r9388  
    6767\label{TRA_adv} 
    6868%------------------------------------------namtra_adv----------------------------------------------------- 
    69 \fortranfile{namelists/namtra_adv} 
     69\forfile{../namelists/namtra_adv} 
    7070%------------------------------------------------------------------------------------------------------------- 
    7171 
    … …  
    432432\label{TRA_ldf} 
    433433%-----------------------------------------nam_traldf------------------------------------------------------ 
    434 \fortranfile{namelists/namtra_ldf} 
     434\forfile{../namelists/namtra_ldf} 
    435435%------------------------------------------------------------------------------------------------------------- 
    436436  
    … …  
    652652\label{TRA_zdf} 
    653653%--------------------------------------------namzdf--------------------------------------------------------- 
    654 \fortranfile{namelists/namzdf} 
     654\forfile{../namelists/namzdf} 
    655655%-------------------------------------------------------------------------------------------------------------- 
    656656 
    … …  
    777777\label{TRA_qsr} 
    778778%--------------------------------------------namqsr-------------------------------------------------------- 
    779 \fortranfile{namelists/namtra_qsr} 
     779\forfile{../namelists/namtra_qsr} 
    780780%-------------------------------------------------------------------------------------------------------------- 
    781781 
    … …  
    888888\label{TRA_bbc} 
    889889%--------------------------------------------nambbc-------------------------------------------------------- 
    890 \fortranfile{namelists/nambbc} 
     890\forfile{../namelists/nambbc} 
    891891%-------------------------------------------------------------------------------------------------------------- 
    892892%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    … …  
    927927\label{TRA_bbl} 
    928928%--------------------------------------------nambbl--------------------------------------------------------- 
    929 \fortranfile{namelists/nambbl} 
     929\forfile{../namelists/nambbl} 
    930930%-------------------------------------------------------------------------------------------------------------- 
    931931 
    … …  
    10871087\label{TRA_dmp} 
    10881088%--------------------------------------------namtra_dmp------------------------------------------------- 
    1089 \fortranfile{namelists/namtra_dmp} 
     1089\forfile{../namelists/namtra_dmp} 
    10901090%-------------------------------------------------------------------------------------------------------------- 
    10911091 
    … …  
    11721172\label{TRA_nxt} 
    11731173%--------------------------------------------namdom----------------------------------------------------- 
    1174 \fortranfile{namelists/namdom} 
     1174\forfile{../namelists/namdom} 
    11751175%-------------------------------------------------------------------------------------------------------------- 
    11761176 
    … …  
    12111211\label{TRA_eosbn2} 
    12121212%--------------------------------------------nameos----------------------------------------------------- 
    1213 \fortranfile{namelists/nameos} 
     1213\forfile{../namelists/nameos} 
    12141214%-------------------------------------------------------------------------------------------------------------- 
    12151215 

  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_ZDF.tex

    r9387 r9388  
    5252\label{ZDF_cst} 
    5353%--------------------------------------------namzdf--------------------------------------------------------- 
    54 \fortranfile{namelists/namzdf} 
     54\forfile{../namelists/namzdf} 
    5555%-------------------------------------------------------------------------------------------------------------- 
    5656 
    … …  
    7878 
    7979%--------------------------------------------namric--------------------------------------------------------- 
    80 \fortranfile{namelists/namzdf_ric} 
     80\forfile{../namelists/namzdf_ric} 
    8181%-------------------------------------------------------------------------------------------------------------- 
    8282 
    … …  
    136136 
    137137%--------------------------------------------namzdf_tke-------------------------------------------------- 
    138 \fortranfile{namelists/namzdf_tke} 
     138\forfile{../namelists/namzdf_tke} 
    139139%-------------------------------------------------------------------------------------------------------------- 
    140140 
    … …  
    512512 
    513513%--------------------------------------------namzdf_gls--------------------------------------------------------- 
    514 \fortranfile{namelists/namzdf_gls} 
     514\forfile{../namelists/namzdf_gls} 
    515515%-------------------------------------------------------------------------------------------------------------- 
    516516 
    … …  
    619619 
    620620%--------------------------------------------namzdf_osm--------------------------------------------------------- 
    621 \fortranfile{namelists/namzdf_osm} 
     621\forfile{../namelists/namzdf_osm} 
    622622%-------------------------------------------------------------------------------------------------------------- 
    623623 
    … …  
    631631 
    632632%--------------------------------------------namzdf-------------------------------------------------------- 
    633 \fortranfile{namelists/namzdf} 
     633\forfile{../namelists/namzdf} 
    634634%-------------------------------------------------------------------------------------------------------------- 
    635635 
    … …  
    651651 
    652652%--------------------------------------------namzdf-------------------------------------------------------- 
    653 \fortranfile{namelists/namzdf} 
     653\forfile{../namelists/namzdf} 
    654654%-------------------------------------------------------------------------------------------------------------- 
    655655 
    … …  
    718718 
    719719%--------------------------------------------namzdf-------------------------------------------------------- 
    720 \fortranfile{namelists/namzdf} 
     720\forfile{../namelists/namzdf} 
    721721%-------------------------------------------------------------------------------------------------------------- 
    722722 
    … …  
    777777 
    778778%-------------------------------------------namzdf_ddm------------------------------------------------- 
    779 %\fortranfile{namelists/namzdf_ddm} 
     779%\forfile{../namelists/namzdf_ddm} 
    780780%-------------------------------------------------------------------------------------------------------------- 
    781781 
    … …  
    859859 
    860860%--------------------------------------------nambfr-------------------------------------------------------- 
    861 %\fortranfile{namelists/nambfr} 
     861%\forfile{../namelists/nambfr} 
    862862%-------------------------------------------------------------------------------------------------------------- 
    863863 
    … …  
    11961196 
    11971197%--------------------------------------------namzdf_tmx-------------------------------------------------- 
    1198 %\fortranfile{namelists/namzdf_tmx} 
     1198%\forfile{../namelists/namzdf_tmx} 
    11991199%-------------------------------------------------------------------------------------------------------------- 
    12001200 
    … …  
    13181318 
    13191319%--------------------------------------------namzdf_tmx_new------------------------------------------ 
    1320 %\fortranfile{namelists/namzdf_tmx_new} 
     1320%\forfile{../namelists/namzdf_tmx_new} 
    13211321%-------------------------------------------------------------------------------------------------------------- 
    13221322 

  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_misc.tex

    r9387 r9388  
    119119\noindent Add the new attribute to any input files requiring a j-row offset, i.e: 
    120120\vspace{-10pt} 
    121 \begin{shcode} 
     121\begin{cmds} 
    122122ncatted  -a open_ocean_jstart,global,a,d,41 eORCA1_coordinates.nc  
    123123ncatted  -a open_ocean_jstart,global,a,d,41 eORCA1_bathymetry_v2.nc 
    124 \end{shcode} 
     124\end{cmds} 
    125125  
    126126\noindent Add the logical switch to \ngn{namcfg} in the configuration namelist and set true: 
    127127%--------------------------------------------namcfg-------------------------------------------------------- 
    128 \fortranfile{namelists/namcfg} 
     128\forfile{../namelists/namcfg} 
    129129%-------------------------------------------------------------------------------------------------------------- 
    130130 
    … …  
    134134and 3D, netcdf, input field by adding the: 
    135135\vspace{-10pt} 
    136 \begin{fortrancode} 
     136\begin{forlines} 
    137137lrowattr=ln_use_jattr 
    138 \end{fortrancode} 
     138\end{forlines} 
    139139optional 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. 
    140140 
    … …  
    235235\label{MISC_opt} 
    236236%--------------------------------------------namctl------------------------------------------------------- 
    237 \fortranfile{namelists/namctl}  
     237\forfile{../namelists/namctl}  
    238238%-------------------------------------------------------------------------------------------------------------- 
    239239 

  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_model_basics_zstar.tex

    r9387 r9388  
    7878\label{DYN_hpg_spg} 
    7979%-----------------------------------------nam_dynspg---------------------------------------------------- 
    80 \fortranfile{namelists/nam_dynspg}  
     80\forfile{../namelists/nam_dynspg}  
    8181%------------------------------------------------------------------------------------------------------------ 
    8282Options are defined through the  \ngn{nam\_dynspg} namelist variables. 
    … …  
    115115\label{DYN_spg_ts} 
    116116%--------------------------------------------namdom---------------------------------------------------- 
    117 \fortranfile{namelists/namdom}  
     117\forfile{../namelists/namdom}  
    118118%-------------------------------------------------------------------------------------------------------------- 
    119119The split-explicit free surface formulation used in OPA follows the one proposed by \citet{Griffies2004}. The general idea is to solve the free surface equation with a small time step, while the three dimensional prognostic variables are solved with a longer time step that is a multiple of \np{rdtbt} 

  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_time_domain.tex

    r9387 r9388  
    286286 
    287287%--------------------------------------------namrun------------------------------------------- 
    288 \fortranfile{namelists/namrun} 
     288\forfile{../namelists/namrun} 
    289289%-------------------------------------------------------------------------------------------------------------- 
    290290 
    … …  
    337337\label{STP_time} 
    338338%--------------------------------------------namrun------------------------------------------- 
    339 \fortranfile{namelists/namdom}          
     339\forfile{../namelists/namdom}          
    340340%-------------------------------------------------------------------------------------------------------------- 
    341341 

  • branches/2017/dev_merge_2017/DOC/tex_sub/introduction.tex

    r9387 r9388  
    9393Usual coding looks like :  
    9494\vspace{-10pt} 
    95 \begin{fortrancode} 
     95\begin{forlines} 
    9696#if defined key_option1 
    9797   ! This part of the FORTRAN code will be active 
    9898   ! only if key_option1 is activated at compiling step 
    9999#endif 
    100 \end{fortrancode} 
     100\end{forlines} 
    101101 
    102102\noindent \index{Namelist} Namelists 
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