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Changeset 7341 for branches/2016/dev_NOC_2016/DOC – NEMO

Ignore:
Timestamp:
2016-11-25T16:49:05+01:00 (7 years ago)
Author:
acc
Message:

Ticket #1802. Merged in trunk changes from 6393:6998 and resolved single conflicit in cfg.txt

Location:
branches/2016/dev_NOC_2016/DOC
Files:
11 deleted
28 edited
9 copied

Legend:

Unmodified
Added
Removed

  • branches/2016/dev_NOC_2016/DOC/NEMO_book.tex

    r6289 r7341  
    44% (C) Xavier Perseguers 2002 - xavier.perseguers@epfl.ch 
    55 
    6 \documentclass[a4paper,11pt]{book} 
    7 %\documentclass[a4paper,11pt,makeidx]{book} <== may need this to generate index 
     6% ================================================================ 
     7% PREAMBLE 
     8% ================================================================ 
    89 
    9 %  makeindex NEMO_book     <== to regenerate the index 
    10 %  bibtex         NEMO_book   <== to generate  the bibliography 
     10\include{TexFiles/Preamble} 
    1111 
    1212% ================================================================ 
    13 % HEADERS DEFINITION 
     13% TOP MATTER 
    1414% ================================================================ 
    1515 
    16 \usepackage[french]{babel} 
    17 %\usepackage{color} 
    18 \usepackage{xcolor} 
    19 %\usepackage{graphics}           % allows insertion of pictures 
    20 \usepackage{graphicx}            % allows insertion of pictures 
    21 \usepackage[capbesideposition={top,center}]{floatrow} % allows captions 
    22 \floatsetup[table]{style=plaintop}                                   % beside pictures 
    23 \usepackage[margin=10pt,font={small},labelsep=colon,labelfont={bf}]{caption} % Gives small font for captions 
    24 \usepackage{enumitem}                          % allows non-bold description items 
    25 \usepackage{longtable}                         % allows multipage tables 
    26 %\usepackage{colortbl}                           % gives coloured panels behind table columns 
    27  
    28 %hyperref 
    29 \usepackage[               % 
    30   pdftitle={NEMO ocean engine},  % 
    31   pdfauthor={Gurvan Madec},      % pdfsubject={The preprint document class 
    32                                        % elsart},% pdfkeywords={diapycnal diffusion,numerical mixing,z-level models},% 
    33   pdfstartview=FitH,          % 
    34   bookmarks=true,          % 
    35   bookmarksopen=true,         % 
    36   breaklinks=true,            % 
    37   colorlinks=true,            % 
    38   linkcolor=blue,anchorcolor=blue,  % 
    39   citecolor=blue,filecolor=blue,    % 
    40  menucolor=blue,                    % 
    41   urlcolor=blue]{hyperref} 
    42 %  usage of exteranl hyperlink :  \href{mailto:my_address@wikibooks.org}{my\_address@wikibooks.org} 
    43 %                                                 \url{http://www.wikibooks.org} 
    44 %                                     or         \href{http://www.wikibooks.org}{wikibooks home} 
    45  
    46  
    47  
    48 %%%% page styles etc................ 
    49 \usepackage{fancyhdr} 
    50 \pagestyle{fancy} 
    51 % with this we ensure that the chapter and section 
    52 % headings are in lowercase. 
    53 \renewcommand{\chaptermark}[1]{\markboth{#1}{}} 
    54 \renewcommand{\sectionmark}[1]{\markright{\thesection.\ #1}} 
    55 \fancyhf{}             % delete current setting for header and footer 
    56 \fancyhead[LE,RO]{\bfseries\thepage} 
    57 \fancyhead[LO]{\bfseries\hspace{-0em}\rightmark} 
    58 \fancyhead[RE]{\bfseries\leftmark} 
    59 \renewcommand{\headrulewidth}{0.5pt} 
    60 \renewcommand{\footrulewidth}{0pt} 
    61 \addtolength{\headheight}{2.6pt}   % make space for the rule 
    62 %\addtolength{\headheight}{1.6pt}   % make space for the rule 
    63 \fancypagestyle{plain}{ 
    64   \fancyhead{}         % get rid of headers on plain pages 
    65   \renewcommand{\headrulewidth}{0pt}  % and the line 
    66 } 
    67  
    68  
    69 %%%%  Section number in Margin....... 
    70 % typeset the number of each section in the left margin, with the start of each instance of 
    71 % sectional heading text aligned with the left hand edge of  the body text. 
    72 \makeatletter 
    73 \def\@seccntformat#1{\protect\makebox[0pt][r]{\csname the#1\endcsname\quad}} 
    74 \makeatother 
    75  
    76 % Leave blank pages completely empty, w/o header 
    77 \makeatletter 
    78 \def\cleardoublepage{\clearpage\if@twoside \ifodd\c@page\else 
    79   \hbox{} 
    80   \vspace*{\fill} 
    81   \vspace{\fill} 
    82   \thispagestyle{empty} 
    83   \newpage 
    84   \if@twocolumn\hbox{}\newpage\fi\fi\fi} 
    85 \makeatother 
    86  
    87 %%%% define the chapter  style ................ 
    88 \usepackage{minitoc}          %In French : \usepackage[french]{minitoc} 
    89 %\usepackage{mtcoff}          % invalidate the use of minitocs 
    90 \usepackage{fancybox} 
    91  
    92 \makeatletter 
    93 \def\LigneVerticale{\vrule height 5cm depth 2cm\hspace{0.1cm}\relax} 
    94 \def\LignesVerticales{% 
    95   \let\LV\LigneVerticale\LV\LV\LV\LV\LV\LV\LV\LV\LV\LV} 
    96 \def\GrosCarreAvecUnChiffre#1{% 
    97   \rlap{\vrule height 0.8cm width 1cm depth 0.2cm}% 
    98  \rlap{\hbox to 1cm{\hss\mbox{\color{white} #1}\hss}}% 
    99   \vrule height 0pt width 1cm depth 0pt} 
    100 \def\GrosCarreAvecTroisChiffre#1{% 
    101   \rlap{\vrule height 0.8cm width 1.6cm depth 0.2cm}% 
    102  \rlap{\hbox to 1.5cm{\hss\mbox{\color{white} #1}\hss}}% 
    103   \vrule height 0pt width 1cm depth 0pt} 
    104  
    105 \def\@makechapterhead#1{\hbox{% 
    106    \huge 
    107     \LignesVerticales 
    108     \hspace{-0.5cm}% 
    109     \GrosCarreAvecUnChiffre{\thechapter} 
    110     \hspace{0.2cm}\hbox{#1}% 
    111 %    \GrosCarreAvecTroisChiffre{\thechapter} 
    112 %    \hspace{1cm}\hbox{#1}% 
    113 %}\par\vskip 2cm} 
    114 }\par\vskip 1cm} 
    115 \def\@makeschapterhead#1{\hbox{% 
    116    \huge 
    117     \LignesVerticales 
    118     %\hspace{0.5cm}% 
    119     \hbox{#1}% 
    120 }\par\vskip 2cm} 
    121 \makeatother 
    122  
    123 %\def\thechapter{\Roman{chapter}}      % chapter number to be Roman 
    124  
    125  
    126 %%%%           Mathematics............... 
    127 %\documentclass{amsart} 
    128 \usepackage{xspace}                              % helpd ensure correct spacing after macros 
    129 \usepackage{latexsym} 
    130 \usepackage{amssymb} 
    131 \usepackage{amsmath} 
    132 \allowdisplaybreaks[1]           % allow page breaks in the middle of equations 
    133 \usepackage{./TexFiles/math_abbrev}    % use maths shortcuts 
    134  
    135 \DeclareMathAlphabet{\mathpzc}{OT1}{pzc}{m}{it} 
    136  
    137 \usepackage{times}                % use times font for text 
    138 %\usepackage{mathtime}                          % font for illustrator to work (belleek fonts ) 
    139 %\usepackage[latin1]{inputenc}                % allows some unicode removed (agn) 
    140  
    141  
    142 %%% essai commande 
    143 \newcommand{\nl} [1] {\texttt{\small {\textcolor{blue}{#1}} } } 
    144 \newcommand{\nlv} [1] {\texttt{\footnotesize#1}\xspace} 
    145 \newcommand{\smnlv} [1] {\texttt{\scriptsize#1}\xspace} 
    146  
    147 %%%% namelist & code display................................ 
    148 \usepackage{alltt}      %%  alltt for namelist 
    149 \usepackage{verbatim}   %%  alltt for namelist 
    150 % namelists 
    151 \newcommand{\namdisplay} [1] { 
    152 \begin{alltt} 
    153 {\tiny \verbatiminput{./TexFiles/Namelist/#1}} 
    154 \end{alltt} 
    155   \vspace{-10pt} 
    156 } 
    157 % namelist_tools 
    158 \newcommand{\namtools} [1] { 
    159 \begin{alltt} 
    160 {\tiny \verbatiminput{./TexFiles/Namelist_tools/#1}} 
    161 \end{alltt} 
    162   \vspace{-10pt} 
    163 } 
    164 % code display 
    165 %\newcommand{\codedisplay} [1] { \begin{alltt} {\tiny  {\begin{verbatim} {#1}} \end{verbatim} }  \end{alltt}   } 
    166  
    167  
    168  
    169 %%%% commands for working with text................................ 
    170 % command to "comment out" portions of text ({} argument) or not ({#1} argument) 
    171 \newcommand{\amtcomment}[1]{}    % command to "commented out" portions of text or not (#1 in argument) 
    172 \newcommand{\sgacomment}[1]{}    % command to "commented out" portions of 
    173 \newcommand{\gmcomment}[1]{}     % command to "commented out" portions of 
    174 %                                               % text that span line breaks 
    175 %Red (NR) or Yellow(WARN) 
    176 %\newcommand{\NR} {\colorbox{red}{#1}} 
    177 %\newcommand{\WARN} {{ \colorbox{yellow}{#1}} } 
    178  
    179  
    180  
    181 %%% index commands...................... 
    182 \usepackage{makeidx} 
    183 %\usepackage{showidx}            % show the index entry 
    184  
    185 \newcommand{\mdl} [1] {\textit{#1.F90}\index{Modules!#1}}         %module (mdl) 
    186 \newcommand{\rou} [1] {\textit{#1}\index{Routines!#1}}            %module (routine) 
    187 \newcommand{\hf} [1] {\textit{#1.h90}\index{h90 file!#1}}            %module (h90 files) 
    188 \newcommand{\ngn} [1] {\textit{#1}\index{Namelist Group Name!#1}}    %namelist name (nampar) 
    189 \newcommand{\np} [1] {\textit{#1}\index{Namelist variables!#1}}             %namelist variable 
    190 \newcommand{\jp} [1] {\textit{#1}\index{Model parameters!#1}}        %model parameter (jp) 
    191 \newcommand{\pp} [1] {\textit{#1}\index{Model parameters!#1}}        %namelist parameter (pp) 
    192 \newcommand{\ifile} [1] {\textit{#1.nc}\index{Input NetCDF files!#1.nc}}   %input NetCDF files (.nc) 
    193 \newcommand{\key} [1] {\textbf{key\_#1}\index{CPP keys!key\_#1}}  %key_cpp (key) 
    194 \newcommand{\NEMO} {\textit{NEMO}\xspace}                %NEMO (nemo) 
    195  
    196 %%%%   Bibliography   ............. 
    197 \usepackage[nottoc, notlof, notlot]{tocbibind} 
    198 \usepackage[square, comma]{natbib} 
    199 \bibpunct{[}{]}{,}{a}{}{;}                           %suppress "," after "et al." 
    200 \providecommand{\bibfont}{\small} 
    201  
     16\include{TexFiles/Top_Matter} 
    20217 
    20318% ================================================================ 
    204 % FRONT PAGE 
    205 % ================================================================ 
    206  
    207 %\usepackage{pstricks} 
    208 \title{ 
    209 %\psset{unit=1.1in,linewidth=4pt}   %parameters of the units for pstricks 
    210 % \rput(0,2){ \includegraphics[width=1.1\textwidth]{./TexFiles/Figures/logo_ALL.pdf}             } \\ 
    211 % \vspace{0.1cm} 
    212 \vspace{-6.0cm} 
    213 \includegraphics[width=1.1\textwidth]{./TexFiles/Figures/logo_ALL.pdf}\\ 
    214 \vspace{5.1cm} 
    215 \includegraphics[width=0.9\textwidth]{./TexFiles/Figures/NEMO_logo_Black.pdf} \\ 
    216 \vspace{1.4cm} 
    217 \rule{345pt}{1.5pt} \\ 
    218 \vspace{0.45cm} 
    219 {\Huge NEMO ocean engine} 
    220 \rule{345pt}{1.5pt} \\ 
    221  } 
    222 %{ -- Draft --}   } 
    223 %\date{\today} 
    224 \date{ 
    225 January 2016  \\ 
    226 {\small  -- draft of version 4.0 --} \\ 
    227 ~  \\ 
    228 \textit{\small Note du P\^ole de mod\'{e}lisation de l'Institut Pierre-Simon Laplace No 27 }\\ 
    229 \vspace{0.45cm} 
    230 { ISSN No 1288-1619.} 
    231 } 
    232  
    233  
    234 \author{ 
    235 \Large Gurvan Madec, and the NEMO team  \\ 
    236  \texttt{\small gurvan.madec@locean-ipsl.umpc.fr} \\ 
    237  \texttt{\small nemo\_st@locean-ipsl.umpc.fr} \\ 
    238 %{\small Laboratoire d'Oc\'{e}anographie  et du Climat: Exp\'{e}rimentation et Approches Num\'{e}riques } 
    239 } 
    240  
    241 \dominitoc 
    242 \makeindex        %type this first :     makeindex -s NEMO.ist NEMO_book.idx 
    243  
    244 % ================================================================ 
    245 %      Include ONLY order 
    246 % ================================================================ 
    247  
    248 %\includeonly{./TexFiles/Chapters/Chap_MISC} 
    249 %\includeonly{./TexFiles/Chapters/Chap_ZDF} 
    250 %\includeonly{./TexFiles/Chapters/Chap_STP,./TexFiles/Chapters/Chap_SBC,./TexFiles/Chapters/Chap_TRA} 
    251 %\includeonly{./TexFiles/Chapters/Chap_LBC,./TexFiles/Chapters/Chap_MISC} 
    252 %\includeonly{./TexFiles/Chapters/Chap_Model_Basics} 
    253 %\includeonly{./TexFiles/Chapters/Annex_A,./TexFiles/Chapters/Annex_B,./TexFiles/Chapters/Annex_C,./TexFiles/Chapters/Annex_D} 
    254  
    255 % ================================================================ 
     19% DOCUMENT 
    25620% ================================================================ 
    25721 
    … …  
    27236% ================================================================ 
    27337 
    274 \include{./TexFiles/Chapters/Abstracts_Foreword} 
     38\subfile{TexFiles/Chapters/Abstracts_Foreword} 
    27539 
    27640% ================================================================ 
    … …  
    27842% ================================================================ 
    27943 
    280 \include{./TexFiles/Chapters/Introduction} 
     44\subfile{TexFiles/Chapters/Introduction} 
    28145 
    28246% ================================================================ 
    … …  
    28448% ================================================================ 
    28549 
    286 \include{./TexFiles/Chapters/Chap_Model_Basics} 
     50\subfile{TexFiles/Chapters/Chap_Model_Basics} 
    28751 
    288 \include{./TexFiles/Chapters/Chap_STP}       % Time discretisation (time stepping strategy) 
     52\subfile{TexFiles/Chapters/Chap_STP}         % Time discretisation (time stepping strategy) 
    28953 
    290 \include{./TexFiles/Chapters/Chap_DOM}       % Space discretisation 
     54\subfile{TexFiles/Chapters/Chap_DOM}         % Space discretisation 
    29155 
    292 \include{./TexFiles/Chapters/Chap_TRA}       % Tracer advection/diffusion equation 
     56\subfile{TexFiles/Chapters/Chap_TRA}         % Tracer advection/diffusion equation 
    29357 
    294 \include{./TexFiles/Chapters/Chap_DYN}       % Dynamics : momentum equation 
     58\subfile{TexFiles/Chapters/Chap_DYN}         % Dynamics : momentum equation 
    29559 
    296 \include{./TexFiles/Chapters/Chap_SBC}       % Surface Boundary Conditions 
     60\subfile{TexFiles/Chapters/Chap_SBC}         % Surface Boundary Conditions 
    29761 
    298 \include{./TexFiles/Chapters/Chap_LBC}       % Lateral Boundary Conditions 
     62\subfile{TexFiles/Chapters/Chap_LBC}         % Lateral Boundary Conditions 
    29963 
    300 \include{./TexFiles/Chapters/Chap_LDF}       % Lateral diffusion 
     64\subfile{TexFiles/Chapters/Chap_LDF}         % Lateral diffusion 
    30165 
    302 \include{./TexFiles/Chapters/Chap_ZDF}       % Vertical diffusion 
     66\subfile{TexFiles/Chapters/Chap_ZDF}         % Vertical diffusion 
    30367 
    304 \include{./TexFiles/Chapters/Chap_DIA}       % Outputs and Diagnostics 
     68\subfile{TexFiles/Chapters/Chap_DIA}         % Outputs and Diagnostics 
    30569 
    306 \include{./TexFiles/Chapters/Chap_OBS}          % Observation operator 
     70\subfile{TexFiles/Chapters/Chap_OBS}                    % Observation operator 
    30771 
    308 \include{./TexFiles/Chapters/Chap_ASM}          % Assimilation increments 
     72\subfile{TexFiles/Chapters/Chap_ASM}                    % Assimilation increments 
    30973 
    310 \include{./TexFiles/Chapters/Chap_STO}          % Stochastic param. 
     74\subfile{TexFiles/Chapters/Chap_STO}                    % Stochastic param. 
    31175 
    312 \include{./TexFiles/Chapters/Chap_DIU}          % Diurnal SST models. 
     76\subfile{TexFiles/Chapters/Chap_MISC}        % Miscellaneous topics 
    31377 
    314 \include{./TexFiles/Chapters/Chap_MISC}         % Miscellaneous topics 
    315  
    316 \include{./TexFiles/Chapters/Chap_CFG}       % Predefined configurations 
     78\subfile{TexFiles/Chapters/Chap_CFG}         % Predefined configurations 
    31779 
    31880% ================================================================ 
    … …  
    32284\appendix 
    32385 
    324 %\include{./TexFiles/Chapters/Chap_Conservation} 
    325 \include{./TexFiles/Chapters/Annex_A}        % generalised vertical coordinate 
    326 \include{./TexFiles/Chapters/Annex_B}        % diffusive operator 
    327 \include{./TexFiles/Chapters/Annex_C}        % Discrete invariants of the eqs. 
    328 \include{./TexFiles/Chapters/Annex_ISO}                     % Isoneutral diffusion using triads 
    329 \include{./TexFiles/Chapters/Annex_D}        % Coding rules 
    330 %\include{./TexFiles/Chapters/Annex_E}                   % Notes on some on going staff (no included in the DOC) 
    331 %\include{./TexFiles/Chapters/Annex_Fox-Kemper}   % Notes on Fox-Kemper (no included in the DOC) 
    332 %\include{./TexFiles/Chapters/Annex_EVP}           % Notes on EVP (no included in the DOC) 
     86%\subfile{TexFiles/Chapters/Chap_Conservation} 
     87\subfile{TexFiles/Chapters/Annex_A}       % generalised vertical coordinate 
     88\subfile{TexFiles/Chapters/Annex_B}       % diffusive operator 
     89\subfile{TexFiles/Chapters/Annex_C}       % Discrete invariants of the eqs. 
     90\subfile{TexFiles/Chapters/Annex_ISO}                    % Isoneutral diffusion using triads 
     91\subfile{TexFiles/Chapters/Annex_D}       % Coding rules 
     92%\subfile{TexFiles/Chapters/Annex_E}                     % Notes on some on going staff (no included in the DOC) 
     93%\subfile{TexFiles/Chapters/Annex_Fox-Kemper}   % Notes on Fox-Kemper (no included in the DOC) 
     94%\subfile{TexFiles/Chapters/Annex_EVP}          % Notes on EVP (no included in the DOC) 
    33395 
    33496% ================================================================ 
    … …  
    344106 
    345107%%\bibliographystyle{plainat} 
    346 \bibliographystyle{./TexFiles/ametsoc}    % AMS biblio style (JPO) 
    347 \bibliography{./TexFiles/Biblio/Biblio} 
     108\bibliographystyle{TexFiles/Styles/ametsoc}     % AMS biblio style (JPO) 
     109\bibliography{TexFiles/Bibliography/Biblio} 
    348110 
    349111% ================================================================ 

  • branches/2016/dev_NOC_2016/DOC/NEMO_coding.conv.tex

    r2738 r7341  
    77\usepackage{framed}  
    88\usepackage{makeidx}  
    9  
     9\graphicspath{{Figures/}} 
    1010 
    1111%%%%%%% 
    … …  
    3131 
    3232\title{  
    33 \includegraphics[width=0.3\textwidth]{./TexFiles/Figures/NEMO_logo_Black.pdf} \\ 
     33\includegraphics[width=0.3\textwidth]{NEMO_logo_Black} \\ 
    3434\vspace{1.0cm} 
    3535\rule{345pt}{1.5pt} \\ 

  • branches/2016/dev_NOC_2016/DOC/TexFiles/Chapters/Abstracts_Foreword.tex

    r6289 r7341  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13 
    24% ================================================================ 
    … …  
    2426 
    2527% ================================================================ 
    26  \vspace{0.5cm} 
     28% \vspace{0.5cm} 
    2729 
    28 Le moteur oc\'{e}anique de NEMO (Nucleus for European Modelling of the Ocean) est un  
    29 mod\`{e}le aux \'{e}quations primitives de la circulation oc\'{e}anique r\'{e}gionale et globale.  
    30 Il se veut un outil flexible pour \'{e}tudier sur un vaste spectre spatiotemporel l'oc\'{e}an et ses  
    31 interactions avec les autres composantes du syst\`{e}me climatique terrestre.  
    32 Les variables pronostiques sont le champ tridimensionnel de vitesse, une hauteur de la mer  
    33 lin\'{e}aire, la Temp\'{e}erature Conservative et la Salinit\'{e} Absolue.  
    34 La distribution des variables se fait sur une grille C d'Arakawa tridimensionnelle utilisant une  
    35 coordonn\'{e}e verticale $z$ \`{a} niveaux entiers ou partiels, ou une coordonn\'{e}e s, ou encore  
    36 une combinaison des deux. Diff\'{e}rents choix sont propos\'{e}s pour d\'{e}crire la physique  
    37 oc\'{e}anique, incluant notamment des physiques verticales TKE et GLS. A travers l'infrastructure  
    38 NEMO, l'oc\'{e}an est interfac\'{e} avec des mod\`{e}les de glace de mer (LIM ou CICE),  
    39 de biog\'{e}ochimie marine et de traceurs passifs, et, via le coupleur OASIS, \`{a} plusieurs  
    40 mod\`{e}les de circulation g\'{e}n\'{e}rale atmosph\'{e}rique.  
    41 Il supporte \'{e}galement l'embo\^{i}tement interactif de maillages via le logiciel AGRIF. 
     30%Le moteur oc\'{e}anique de NEMO (Nucleus for European Modelling of the Ocean) est un  
     31%mod\`{e}le aux \'{e}quations primitives de la circulation oc\'{e}anique r\'{e}gionale et globale.  
     32%Il se veut un outil flexible pour \'{e}tudier sur un vaste spectre spatiotemporel l'oc\'{e}an et ses  
     33%interactions avec les autres composantes du syst\`{e}me climatique terrestre.  
     34%Les variables pronostiques sont le champ tridimensionnel de vitesse, une hauteur de la mer  
     35%lin\'{e}aire, la Temp\'{e}rature Conservative et la Salinit\'{e} Absolue.  
     36%La distribution des variables se fait sur une grille C d'Arakawa tridimensionnelle utilisant une  
     37%coordonn\'{e}e verticale $z$ \`{a} niveaux entiers ou partiels, ou une coordonn\'{e}e s, ou encore  
     38%une combinaison des deux. Diff\'{e}rents choix sont propos\'{e}s pour d\'{e}crire la physique  
     39%oc\'{e}anique, incluant notamment des physiques verticales TKE et GLS. A travers l'infrastructure  
     40%NEMO, l'oc\'{e}an est interfac\'{e} avec des mod\`{e}les de glace de mer (LIM ou CICE),  
     41%de biog\'{e}ochimie marine et de traceurs passifs, et, via le coupleur OASIS, \`{a} plusieurs  
     42%mod\`{e}les de circulation g\'{e}n\'{e}rale atmosph\'{e}rique.  
     43%Il supporte \'{e}galement l'embo\^{i}tement interactif de maillages via le logiciel AGRIF. 
    4244}  
    4345 
    … …  
    6971 \vspace{0.5cm} 
    7072 
     73\end{document} 

  • branches/2016/dev_NOC_2016/DOC/TexFiles/Chapters/Annex_A.tex

    r3294 r7341  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13 
    24% ================================================================ 
    … …  
    532534expression of the 3D divergence in the $s-$coordinates established above.  
    533535 
     536\end{document} 

  • branches/2016/dev_NOC_2016/DOC/TexFiles/Chapters/Annex_B.tex

    r3294 r7341  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter Ñ Appendix B : Diffusive Operators 
    … …  
    364366\eqref{Apdx_B_Lap_U} is used in both $z$- and $s$-coordinate systems, that is 
    365367a Laplacian diffusion is applied on momentum along the coordinate directions. 
     368\end{document} 

  • branches/2016/dev_NOC_2016/DOC/TexFiles/Chapters/Annex_C.tex

    r6289 r7341  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter Ñ Appendix C : Discrete Invariants of the Equations 
    … …  
    15311533%%%%  end of appendix in gm comment 
    15321534%} 
     1535\end{document} 

  • branches/2016/dev_NOC_2016/DOC/TexFiles/Chapters/Annex_D.tex

    r6289 r7341  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Appendix D Ñ Coding Rules 
    … …  
    202204 
    203205To be done.... 
     206\end{document} 

  • branches/2016/dev_NOC_2016/DOC/TexFiles/Chapters/Annex_E.tex

    r3294 r7341  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Appendix E : Note on some algorithms 
    … …  
    299301\begin{figure}[!ht] \label{Fig_ISO_triad} 
    300302\begin{center} 
    301 \includegraphics[width=0.70\textwidth]{./TexFiles/Figures/Fig_ISO_triad.pdf} 
     303\includegraphics[width=0.70\textwidth]{Fig_ISO_triad} 
    302304\caption{  \label{Fig_ISO_triad}    
    303305Triads used in the Griffies's like iso-neutral diffision scheme for  
    … …  
    806808tracer is preserved by the discretisation of the skew fluxes. 
    807809 
     810\end{document} 

  • branches/2016/dev_NOC_2016/DOC/TexFiles/Chapters/Annex_ISO.tex

    r6289 r7341  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Iso-neutral diffusion : 
    … …  
    190192% >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    191193\begin{figure}[tb] \begin{center} 
    192     \includegraphics[width=1.05\textwidth]{./TexFiles/Figures/Fig_GRIFF_triad_fluxes} 
     194    \includegraphics[width=1.05\textwidth]{Fig_GRIFF_triad_fluxes} 
    193195    \caption{ \label{fig:triad:ISO_triad} 
    194196      (a) Arrangement of triads $S_i$ and tracer gradients to 
    … …  
    254256% >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    255257\begin{figure}[tb] \begin{center} 
    256     \includegraphics[width=0.80\textwidth]{./TexFiles/Figures/Fig_GRIFF_qcells} 
     258    \includegraphics[width=0.80\textwidth]{Fig_GRIFF_qcells} 
    257259    \caption{   \label{fig:triad:qcells} 
    258260    Triad notation for quarter cells. $T$-cells are inside 
    … …  
    658660% >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    659661\begin{figure}[h] \begin{center} 
    660     \includegraphics[width=0.60\textwidth]{./TexFiles/Figures/Fig_GRIFF_bdry_triads} 
     662    \includegraphics[width=0.60\textwidth]{Fig_GRIFF_bdry_triads} 
    661663    \caption{  \label{fig:triad:bdry_triads} 
    662664      (a) Uppermost model layer $k=1$ with $i,1$ and $i+1,1$ tracer 
    … …  
    831833    different $i_p,k_p$, denoted by different colours, (e.g. the green 
    832834    triad $i_p=1/2,k_p=-1/2$) are tapered to the appropriate basal triad.}} 
    833   {\includegraphics[width=0.60\textwidth]{./TexFiles/Figures/Fig_GRIFF_MLB_triads}} 
     835  {\includegraphics[width=0.60\textwidth]{Fig_GRIFF_MLB_triads}} 
    834836\end{figure} 
    835837% >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    … …  
    11751177\end{split} 
    11761178\end{equation} 
     1179\end{document} 

  • branches/2016/dev_NOC_2016/DOC/TexFiles/Chapters/Chap_ASM.tex

    r4147 r7341  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter Assimilation increments (ASM) 
    … …  
    172174\end{verbatim} 
    173175\end{alltt} 
     176\end{document} 

  • branches/2016/dev_NOC_2016/DOC/TexFiles/Chapters/Chap_CFG.tex

    r4147 r7341  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter � Configurations 
    … …  
    8890%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    8991\begin{figure}[!t]   \begin{center} 
    90 \includegraphics[width=0.98\textwidth]{./TexFiles/Figures/Fig_ORCA_NH_mesh.pdf} 
     92\includegraphics[width=0.98\textwidth]{Fig_ORCA_NH_mesh} 
    9193\caption{  \label{Fig_MISC_ORCA_msh}      
    92 ORCA mesh conception. The departure from an isotropic Mercator grid start poleward of 20\deg N. 
     94ORCA mesh conception. The departure from an isotropic Mercator grid start poleward of 20\degN. 
    9395The two "north pole" are the foci of a series of embedded ellipses (blue curves)  
    9496which are determined analytically and form the i-lines of the ORCA mesh (pseudo latitudes).  
    … …  
    115117%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    116118\begin{figure}[!tbp]  \begin{center} 
    117 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_ORCA_NH_msh05_e1_e2.pdf} 
    118 \includegraphics[width=0.80\textwidth]{./TexFiles/Figures/Fig_ORCA_aniso.pdf} 
     119\includegraphics[width=1.0\textwidth]{Fig_ORCA_NH_msh05_e1_e2} 
     120\includegraphics[width=0.80\textwidth]{Fig_ORCA_aniso} 
    119121\caption {  \label{Fig_MISC_ORCA_e1e2} 
    120122\textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and  
    121123\textit{Bottom}: ratio of anisotropy ($e_1 / e_2$) 
    122 for ORCA 0.5\deg ~mesh. South of 20\deg N a Mercator grid is used ($e_1 = e_2$)  
    123 so that the anisotropy ratio is 1. Poleward of 20\deg N, the two "north pole"  
     124for ORCA 0.5\deg ~mesh. South of 20\degN a Mercator grid is used ($e_1 = e_2$)  
     125so that the anisotropy ratio is 1. Poleward of 20\degN, the two "north pole"  
    124126introduce a weak anisotropy over the ocean areas ($< 1.2$) except in vicinity of Victoria Island  
    125127(Canadian Arctic Archipelago). } 
    … …  
    129131 
    130132The method is applied to Mercator grid ($i.e.$ same zonal and meridional grid spacing) poleward  
    131 of $20\deg$N, so that the Equator is a mesh line, which provides a better numerical solution  
     133of 20\degN, so that the Equator is a mesh line, which provides a better numerical solution  
    132134for equatorial dynamics. The choice of the series of embedded ellipses (position of the foci and  
    133135variation of the ellipses) is a compromise between maintaining  the ratio of mesh anisotropy  
    … …  
    178180The ORCA\_R2 configuration has the following specificity : starting from a 2\deg~ORCA mesh,  
    179181local mesh refinements were applied to the Mediterranean, Red, Black and Caspian Seas,  
    180 so that the resolution is $1\deg \time 1\deg$ there. A local transformation were also applied  
     182so that the resolution is 1\deg \time 1\deg there. A local transformation were also applied  
    181183with in the Tropics in order to refine the meridional resolution up to 0.5\deg at the Equator. 
    182184 
    … …  
    227229 
    228230The domain geometry is a closed rectangular basin on the $\beta$-plane centred  
    229 at $\sim 30\deg$N and rotated by 45\deg, 3180~km long, 2120~km wide  
     231at $\sim$ 30\degN and rotated by 45\deg, 3180~km long, 2120~km wide  
    230232and 4~km deep (Fig.~\ref{Fig_MISC_strait_hand}).  
    231233The domain is bounded by vertical walls and by a flat bottom. The configuration is  
    … …  
    234236The applied forcings vary seasonally in a sinusoidal manner between winter  
    235237and summer extrema \citep{Levy_al_OM10}.  
    236 The wind stress is zonal and its curl changes sign at 22\deg N and 36\deg N.  
     238The wind stress is zonal and its curl changes sign at 22\degN and 36\degN.  
    237239It forces a subpolar gyre in the north, a subtropical gyre in the wider part of the domain  
    238240and a small recirculation gyre in the southern corner.  
    … …  
    261263%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    262264\begin{figure}[!t]   \begin{center} 
    263 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_GYRE.pdf} 
     265\includegraphics[width=1.0\textwidth]{Fig_GYRE} 
    264266\caption{  \label{Fig_GYRE}    
    265267Snapshot of relative vorticity at the surface of the model domain  
    … …  
    311313temperature data. 
    312314 
     315\end{document} 

  • branches/2016/dev_NOC_2016/DOC/TexFiles/Chapters/Chap_Conservation.tex

    r3294 r7341  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13 
    24% ================================================================ 
    … …  
    333335not been implemented. 
    334336 
     337\end{document} 

  • branches/2016/dev_NOC_2016/DOC/TexFiles/Chapters/Chap_DIA.tex

    r6289 r7341  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter I/O & Diagnostics 
    … …  
    14091411 
    14101412% ------------------------------------------------------------------------------------------------------------- 
    1411 %       25 hour mean and hourly Surface, Mid and Bed  
    1412 % ------------------------------------------------------------------------------------------------------------- 
    1413 \section{25 hour mean output for tidal models } 
    1414  
    1415 A module is available to compute a crudely detided M2 signal by obtaining a 25 hour mean. 
    1416 The 25 hour mean is available for daily runs by summing up the 25 hourly instantananeous hourly values from 
    1417 midnight at the start of the day to midight at the day end. 
    1418 This diagnostic is actived with the logical  $ln\_dia25h$ 
    1419  
    1420 %------------------------------------------nam_dia25h------------------------------------------------------ 
    1421 \namdisplay{nam_dia25h} 
    1422 %---------------------------------------------------------------------------------------------------------- 
    1423  
    1424 \section{Top Middle and Bed hourly output } 
    1425  
    1426 A module is available to output the surface (top), mid water and bed diagnostics of a set of standard variables.  
    1427 This can be a useful diagnostic when hourly or sub-hourly output is required in high resolution tidal outputs. 
    1428 The tidal signal is retained but the overall data usage is cut to just three vertical levels. Also the bottom level  
    1429 is calculated for each cell. 
    1430 This diagnostic is actived with the logical  $ln\_diatmb$ 
    1431  
    1432 %------------------------------------------nam_diatmb----------------------------------------------------- 
    1433 \namdisplay{nam_diatmb} 
    1434 %---------------------------------------------------------------------------------------------------------- 
    1435  
    1436 % ------------------------------------------------------------------------------------------------------------- 
    14371413%       Sections transports 
    14381414% ------------------------------------------------------------------------------------------------------------- 
    … …  
    14401416\label{DIA_diag_dct} 
    14411417 
     1418%------------------------------------------namdct---------------------------------------------------- 
     1419\namdisplay{namdct} 
     1420%------------------------------------------------------------------------------------------------------------- 
     1421 
    14421422A module is available to compute the transport of volume, heat and salt through sections.  
    14431423This diagnostic is actived with \key{diadct}. 
    … …  
    14591439and the time scales over which they are averaged, as well as the level of output for debugging: 
    14601440 
    1461 %------------------------------------------namdct---------------------------------------------------- 
    1462 \namdisplay{namdct} 
    1463 %------------------------------------------------------------------------------------------------------------- 
    1464  
    14651441\np{nn\_dct}: frequency of instantaneous transports computing 
    14661442 
    … …  
    14691445\np{nn\_debug}: debugging of the section 
    14701446 
    1471 \subsubsection{ To create a binary file containing the pathway of each section } 
    1472  
    1473 In \texttt{NEMOGCM/TOOLS/SECTIONS\_DIADCT/run}, the file \texttt{ {list\_sections.ascii\_global}} 
     1447\subsubsection{ Creating a binary file containing the pathway of each section } 
     1448 
     1449In \texttt{NEMOGCM/TOOLS/SECTIONS\_DIADCT/run}, the file \textit{ {list\_sections.ascii\_global}} 
    14741450contains a list of all the sections that are to be computed (this list of sections is based on MERSEA project metrics). 
    14751451 
    … …  
    15831559\texttt{=/0, =/ 1000.}   &  diagonal   & eastward  & westward  & postive: eastward  \\ \hline                 
    15841560\end{tabular} 
    1585  
    1586  
    1587  
    1588 % ------------------------------------------------------------------------------------------------------------- 
    1589 %       Other Diagnostics 
    1590 % ------------------------------------------------------------------------------------------------------------- 
    1591 \section{Other Diagnostics (\key{diahth}, \key{diaar5})} 
    1592 \label{DIA_diag_others} 
    1593  
    1594  
    1595 Aside from the standard model variables, other diagnostics can be computed  
    1596 on-line. The available ready-to-add diagnostics routines can be found in directory DIA.  
    1597 Among the available diagnostics the following ones are obtained when defining  
    1598 the \key{diahth} CPP key:  
    1599  
    1600 - the mixed layer depth (based on a density criterion \citep{de_Boyer_Montegut_al_JGR04}) (\mdl{diahth}) 
    1601  
    1602 - the turbocline depth (based on a turbulent mixing coefficient criterion) (\mdl{diahth}) 
    1603  
    1604 - the depth of the 20\deg C isotherm (\mdl{diahth}) 
    1605  
    1606 - the depth of the thermocline (maximum of the vertical temperature gradient) (\mdl{diahth}) 
    1607  
    1608 The poleward heat and salt transports, their advective and diffusive component, and  
    1609 the meriodional stream function can be computed on-line in \mdl{diaptr}  
    1610 \np{ln\_diaptr} to true (see the \textit{\ngn{namptr} } namelist below).   
    1611 When \np{ln\_subbas}~=~true, transports and stream function are computed  
    1612 for the Atlantic, Indian, Pacific and Indo-Pacific Oceans (defined north of 30\deg S)  
    1613 as well as for the World Ocean. The sub-basin decomposition requires an input file  
    1614 (\ifile{subbasins}) which contains three 2D mask arrays, the Indo-Pacific mask  
    1615 been deduced from the sum of the Indian and Pacific mask (Fig~\ref{Fig_mask_subasins}).  
    1616  
    1617 %------------------------------------------namptr---------------------------------------------------- 
    1618 \namdisplay{namptr}  
    1619 %------------------------------------------------------------------------------------------------------------- 
    1620 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    1621 \begin{figure}[!t]     \begin{center} 
    1622 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_mask_subasins.pdf} 
    1623 \caption{   \label{Fig_mask_subasins} 
    1624 Decomposition of the World Ocean (here ORCA2) into sub-basin used in to compute 
    1625 the heat and salt transports as well as the meridional stream-function: Atlantic basin (red),  
    1626 Pacific basin (green), Indian basin (bleue), Indo-Pacific basin (bleue+green).  
    1627 Note that semi-enclosed seas (Red, Med and Baltic seas) as well as Hudson Bay  
    1628 are removed from the sub-basins. Note also that the Arctic Ocean has been split  
    1629 into Atlantic and Pacific basins along the North fold line.  } 
    1630 \end{center}   \end{figure}   
    1631 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    1632  
    1633 In addition, a series of diagnostics has been added in the \mdl{diaar5}.  
    1634 They corresponds to outputs that are required for AR5 simulations  
    1635 (see Section \ref{DIA_steric} below for one of them).  
    1636 Activating those outputs requires to define the \key{diaar5} CPP key. 
    1637 \\ 
    1638 \\ 
    1639  
    1640 \section{Courant numbers} 
    1641 Courant numbers provide a theoretical indication of the model's numerical stability. The advective Courant numbers can be calculated according to 
    1642 \begin{equation} 
    1643 \label{eq:CFL} 
    1644 C_u = |u|\frac{\rdt}{e_{1u}}, \quad C_v = |v|\frac{\rdt}{e_{2v}}, \quad C_w = |w|\frac{\rdt}{e_{3w}} 
    1645 \end{equation} 
    1646 in the zonal, meridional and vertical directions respectively. The vertical component is included although it is not strictly valid as the vertical velocity is calculated from the continuity equation rather than as a prognostic variable. Physically this represents the rate at which information is propogated across a grid cell. Values greater than 1 indicate that information is propagated across more than one grid cell in a single time step. 
    1647  
    1648 The variables can be activated by setting the \np{nn\_diacfl} namelist parameter to 1 in the \ngn{namctl} namelist. The diagnostics will be written out to an ascii file named cfl\_diagnostics.ascii. In this file the maximum value of $C_u$, $C_v$, and $C_w$ are printed at each timestep along with the coordinates of where the maximum value occurs. At the end of the model run the maximum value of $C_u$, $C_v$, and $C_w$ for the whole model run is printed along with the coordinates of each. The maximum values from the run are also copied to the ocean.output file.  
    16491561 
    16501562 
    … …  
    18021714the \key{diaar5} defined to be called. 
    18031715 
     1716 
     1717 
     1718% ------------------------------------------------------------------------------------------------------------- 
     1719%       Other Diagnostics 
     1720% ------------------------------------------------------------------------------------------------------------- 
     1721\section{Other Diagnostics (\key{diahth}, \key{diaar5})} 
     1722\label{DIA_diag_others} 
     1723 
     1724 
     1725Aside from the standard model variables, other diagnostics can be computed on-line.  
     1726The available ready-to-add diagnostics modules can be found in directory DIA.  
     1727 
     1728\subsection{Depth of various quantities (\mdl{diahth})} 
     1729 
     1730Among the available diagnostics the following ones are obtained when defining  
     1731the \key{diahth} CPP key:  
     1732 
     1733- the mixed layer depth (based on a density criterion \citep{de_Boyer_Montegut_al_JGR04}) (\mdl{diahth}) 
     1734 
     1735- the turbocline depth (based on a turbulent mixing coefficient criterion) (\mdl{diahth}) 
     1736 
     1737- the depth of the 20\deg C isotherm (\mdl{diahth}) 
     1738 
     1739- the depth of the thermocline (maximum of the vertical temperature gradient) (\mdl{diahth}) 
     1740 
     1741% ----------------------------------------------------------- 
     1742%     Poleward heat and salt transports 
     1743% ----------------------------------------------------------- 
     1744 
     1745\subsection{Poleward heat and salt transports (\mdl{diaptr})} 
     1746 
     1747%------------------------------------------namptr----------------------------------------- 
     1748\namdisplay{namptr}  
     1749%----------------------------------------------------------------------------------------- 
     1750 
     1751The poleward heat and salt transports, their advective and diffusive component, and  
     1752the meriodional stream function can be computed on-line in \mdl{diaptr}  
     1753\np{ln\_diaptr} to true (see the \textit{\ngn{namptr} } namelist below).   
     1754When \np{ln\_subbas}~=~true, transports and stream function are computed  
     1755for the Atlantic, Indian, Pacific and Indo-Pacific Oceans (defined north of 30\deg S)  
     1756as well as for the World Ocean. The sub-basin decomposition requires an input file  
     1757(\ifile{subbasins}) which contains three 2D mask arrays, the Indo-Pacific mask  
     1758been deduced from the sum of the Indian and Pacific mask (Fig~\ref{Fig_mask_subasins}).  
     1759 
     1760%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     1761\begin{figure}[!t]     \begin{center} 
     1762\includegraphics[width=1.0\textwidth]{Fig_mask_subasins} 
     1763\caption{   \label{Fig_mask_subasins} 
     1764Decomposition of the World Ocean (here ORCA2) into sub-basin used in to compute 
     1765the heat and salt transports as well as the meridional stream-function: Atlantic basin (red),  
     1766Pacific basin (green), Indian basin (bleue), Indo-Pacific basin (bleue+green).  
     1767Note that semi-enclosed seas (Red, Med and Baltic seas) as well as Hudson Bay  
     1768are removed from the sub-basins. Note also that the Arctic Ocean has been split  
     1769into Atlantic and Pacific basins along the North fold line.  } 
     1770\end{center}   \end{figure}   
     1771%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     1772 
     1773 
     1774% ----------------------------------------------------------- 
     1775%       CMIP specific diagnostics  
     1776% ----------------------------------------------------------- 
     1777\subsection{CMIP specific diagnostics (\mdl{diaar5})} 
     1778 
     1779A series of diagnostics has been added in the \mdl{diaar5}.  
     1780They corresponds to outputs that are required for AR5 simulations (CMIP5) 
     1781(see also Section \ref{DIA_steric} for one of them).  
     1782Activating those outputs requires to define the \key{diaar5} CPP key. 
     1783 
     1784 
     1785% ----------------------------------------------------------- 
     1786%       25 hour mean and hourly Surface, Mid and Bed  
     1787% ----------------------------------------------------------- 
     1788\subsection{25 hour mean output for tidal models } 
     1789 
     1790%------------------------------------------nam_dia25h------------------------------------- 
     1791\namdisplay{nam_dia25h} 
     1792%----------------------------------------------------------------------------------------- 
     1793 
     1794A module is available to compute a crudely detided M2 signal by obtaining a 25 hour mean. 
     1795The 25 hour mean is available for daily runs by summing up the 25 hourly instantananeous hourly values from 
     1796midnight at the start of the day to midight at the day end. 
     1797This diagnostic is actived with the logical  $ln\_dia25h$ 
     1798 
     1799 
     1800% ----------------------------------------------------------- 
     1801%     Top Middle and Bed hourly output 
     1802% ----------------------------------------------------------- 
     1803\subsection{Top Middle and Bed hourly output } 
     1804 
     1805%------------------------------------------nam_diatmb----------------------------------------------------- 
     1806\namdisplay{nam_diatmb} 
     1807%---------------------------------------------------------------------------------------------------------- 
     1808 
     1809A module is available to output the surface (top), mid water and bed diagnostics of a set of standard variables.  
     1810This can be a useful diagnostic when hourly or sub-hourly output is required in high resolution tidal outputs. 
     1811The tidal signal is retained but the overall data usage is cut to just three vertical levels. Also the bottom level  
     1812is calculated for each cell. 
     1813This diagnostic is actived with the logical  $ln\_diatmb$ 
     1814 
     1815 
     1816 
     1817% ----------------------------------------------------------- 
     1818%     Courant numbers 
     1819% ----------------------------------------------------------- 
     1820\subsection{Courant numbers} 
     1821Courant numbers provide a theoretical indication of the model's numerical stability. The advective Courant numbers can be calculated according to 
     1822\begin{equation} 
     1823\label{eq:CFL} 
     1824C_u = |u|\frac{\rdt}{e_{1u}}, \quad C_v = |v|\frac{\rdt}{e_{2v}}, \quad C_w = |w|\frac{\rdt}{e_{3w}} 
     1825\end{equation} 
     1826in the zonal, meridional and vertical directions respectively. The vertical component is included although it is not strictly valid as the vertical velocity is calculated from the continuity equation rather than as a prognostic variable. Physically this represents the rate at which information is propogated across a grid cell. Values greater than 1 indicate that information is propagated across more than one grid cell in a single time step. 
     1827 
     1828The variables can be activated by setting the \np{nn\_diacfl} namelist parameter to 1 in the \ngn{namctl} namelist. The diagnostics will be written out to an ascii file named cfl\_diagnostics.ascii. In this file the maximum value of $C_u$, $C_v$, and $C_w$ are printed at each timestep along with the coordinates of where the maximum value occurs. At the end of the model run the maximum value of $C_u$, $C_v$, and $C_w$ for the whole model run is printed along with the coordinates of each. The maximum values from the run are also copied to the ocean.output file.  
     1829 
     1830 
    18041831% ================================================================ 
    18051832 
    … …  
    18151842 
    18161843 
     1844\end{document} 

  • branches/2016/dev_NOC_2016/DOC/TexFiles/Chapters/Chap_DIU.tex

    r6289 r7341  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Diurnal SST models (DIU) 
    … …  
    162164\end{equation} 
    163165 
    164  
     166\end{document} 

  • branches/2016/dev_NOC_2016/DOC/TexFiles/Chapters/Chap_DOM.tex

    r6320 r7341  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter 2 ——— Space and Time Domain (DOM) 
    … …  
    4042%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    4143\begin{figure}[!tb]    \begin{center} 
    42 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_cell.pdf} 
     44\includegraphics[width=0.90\textwidth]{Fig_cell} 
    4345\caption{ \label{Fig_cell}     
    4446Arrangement of variables. $t$ indicates scalar points where temperature,  
    … …  
    201203%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    202204\begin{figure}[!tb]  \begin{center} 
    203 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_index_hor.pdf} 
     205\includegraphics[width=0.90\textwidth]{Fig_index_hor} 
    204206\caption{   \label{Fig_index_hor}     
    205207Horizontal integer indexing used in the \textsc{Fortran} code. The dashed area indicates  
    … …  
    251253%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    252254\begin{figure}[!pt]    \begin{center} 
    253 \includegraphics[width=.90\textwidth]{./TexFiles/Figures/Fig_index_vert.pdf} 
     255\includegraphics[width=.90\textwidth]{Fig_index_vert} 
    254256\caption{ \label{Fig_index_vert}      
    255257Vertical integer indexing used in the \textsc{Fortran } code. Note that  
    … …  
    349351%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    350352\begin{figure}[!t]     \begin{center} 
    351 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_zgr_e3.pdf} 
     353\includegraphics[width=0.90\textwidth]{Fig_zgr_e3} 
    352354\caption{ \label{Fig_zgr_e3}     
    353355Comparison of (a) traditional definitions of grid-point position and grid-size in the vertical,  
    … …  
    458460%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    459461\begin{figure}[!tb]    \begin{center} 
    460 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_z_zps_s_sps.pdf} 
     462\includegraphics[width=1.0\textwidth]{Fig_z_zps_s_sps} 
    461463\caption{  \label{Fig_z_zps_s_sps}    
    462464The ocean bottom as seen by the model:  
    … …  
    486488The last choice in terms of vertical coordinate concerns the presence (or not) in the model domain  
    487489of ocean cavities beneath ice shelves. Setting \np{ln\_isfcav} to true allows to manage ocean cavities,  
    488 otherwise they are filled in. 
     490otherwise they are filled in. This option is currently only available in $z$- or $zps$-coordinate, 
     491and partial step are also applied at the ocean/ice shelf interface.  
    489492 
    490493Contrary to the horizontal grid, the vertical grid is computed in the code and no  
    … …  
    567570%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    568571\begin{figure}[!tb]    \begin{center} 
    569 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_zgr.pdf} 
     572\includegraphics[width=0.90\textwidth]{Fig_zgr} 
    570573\caption{ \label{Fig_zgr}     
    571574Default vertical mesh for ORCA2: 30 ocean levels (L30). Vertical level functions for  
    … …  
    772775\end{equation} 
    773776 
    774 where $s_{min}$ is the depth at which the s-coordinate stretching starts and  
    775 allows a z-coordinate to placed on top of the stretched coordinate,  
    776 and z is the depth (negative down from the asea surface). 
     777where $s_{min}$ is the depth at which the $s$-coordinate stretching starts and  
     778allows a $z$-coordinate to placed on top of the stretched coordinate,  
     779and $z$ is the depth (negative down from the asea surface). 
    777780 
    778781\begin{equation} 
    … …  
    800803%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    801804\begin{figure}[!ht]    \begin{center} 
    802 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_sco_function.pdf} 
     805\includegraphics[width=1.0\textwidth]{Fig_sco_function} 
    803806\caption{  \label{Fig_sco_function}    
    804807Examples of the stretching function applied to a seamount; from left to right:  
    … …  
    846849%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    847850\begin{figure}[!ht] 
    848    \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/FIG_DOM_compare_coordinates_surface.pdf} 
     851   \includegraphics[width=1.0\textwidth]{FIG_DOM_compare_coordinates_surface} 
    849852        \caption{A comparison of the \citet{Song_Haidvogel_JCP94} $S$-coordinate (solid lines), a 50 level $Z$-coordinate (contoured surfaces) and the \citet{Siddorn_Furner_OM12} $S$-coordinate (dashed lines) in the surface 100m for a idealised bathymetry that goes from 50m to 5500m depth. For clarity every third coordinate surface is shown.} 
    850853    \label{fig_compare_coordinates_surface} 
    … …  
    886889that do not communicate with another ocean point at the same level are eliminated. 
    887890 
    888 In case of ice shelf cavities, as for the representation of bathymetry, a 2D integer array, misfdep, is created.  
    889 misfdep defines the level of the first wet $t$-point (ie below the ice-shelf/ocean interface). All the cells between $k=1$ and $misfdep(i,j)-1$ are masked.  
    890 By default, $misfdep(:,:)=1$ and no cells are masked. 
    891 Modifications of the model bathymetry and ice shelf draft into  
     891As for the representation of bathymetry, a 2D integer array, misfdep, is created.  
     892misfdep defines the level of the first wet $t$-point. All the cells between $k=1$ and $misfdep(i,j)-1$ are masked.  
     893By default, misfdep(:,:)=1 and no cells are masked. 
     894 
     895In case of ice shelf cavities, modifications of the model bathymetry and ice shelf draft into  
    892896the cavities are performed in the \textit{zgr\_isf} routine. The compatibility between ice shelf draft and bathymetry is checked.  
    893897All the locations where the isf cavity is thinnest than \np{rn\_isfhmin} meters are grounded ($i.e.$ masked).  
    … …  
    903907vmask(i,j,k) &=         \; tmask(i,j,k) \ * \ tmask(i,j+1,k)   \\ 
    904908fmask(i,j,k) &=         \; tmask(i,j,k) \ * \ tmask(i+1,j,k)   \\ 
    905                    & \ \ \, * tmask(i,j,k) \ * \ tmask(i+1,j,k) \\ 
     909             &    \ \ \, * tmask(i,j,k) \ * \ tmask(i+1,j,k) \\ 
    906910wmask(i,j,k) &=         \; tmask(i,j,k) \ * \ tmask(i,j,k-1) \text{ with } wmask(i,j,1) = tmask(i,j,1)  
    907911\end{align*} 
    908912 
    909 Note, wmask is now defined. It allows, in case of ice shelves,  
    910 to deal with the top boundary (ice shelf/ocean interface) exactly in the same way as for the bottom boundary.  
     913Note that, without ice shelves cavities, masks at $t-$ and $w-$points are identical with  
     914the numerical indexing used (\S~\ref{DOM_Num_Index}). Nevertheless, $wmask$ are required  
     915with oceean cavities to deal with the top boundary (ice shelf/ocean interface)  
     916exactly in the same way as for the bottom boundary.  
    911917 
    912918The specification of closed lateral boundaries requires that at least the first and last  
    … …  
    916922(and so too the mask arrays) (see \S~\ref{LBC_jperio}). 
    917923 
    918 %%% 
    919 \gmcomment{   \colorbox{yellow}{Add one word on tricky trick !} mbathy in further modified in zdfbfr{\ldots}.  } 
    920 %%% 
    921924 
    922925% ================================================================ 
    … …  
    942945(typical of the tropical ocean), see \rou{istate\_t\_s} subroutine called from \mdl{istate} module. 
    943946\end{description} 
     947\end{document} 

  • branches/2016/dev_NOC_2016/DOC/TexFiles/Chapters/Chap_DYN.tex

    r6320 r7341  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter ——— Ocean Dynamics (DYN) 
    … …  
    294296%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    295297\begin{figure}[!ht]    \begin{center} 
    296 \includegraphics[width=0.70\textwidth]{./TexFiles/Figures/Fig_DYN_een_triad.pdf} 
     298\includegraphics[width=0.70\textwidth]{Fig_DYN_een_triad} 
    297299\caption{ \label{Fig_DYN_een_triad}   
    298300Triads used in the energy and enstrophy conserving scheme (een) for  
    … …  
    663665$\bullet$ The main hypothesis to compute the ice shelf load is that the ice shelf is in an isostatic equilibrium. 
    664666 The top pressure is computed integrating from surface to the base of the ice shelf a reference density profile  
    665 (prescribed as density of a water at 34.4 PSU and -1.9$\degres C$) and corresponds to the water replaced by the ice shelf.  
     667(prescribed as density of a water at 34.4 PSU and -1.9\degC) and corresponds to the water replaced by the ice shelf.  
    666668This top pressure is constant over time. A detailed description of this method is described in \citet{Losch2008}.\\ 
    667669 
    … …  
    827829%>   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   > 
    828830\begin{figure}[!t]    \begin{center} 
    829 \includegraphics[width=0.7\textwidth]{./TexFiles/Figures/Fig_DYN_dynspg_ts.pdf} 
     831\includegraphics[width=0.7\textwidth]{Fig_DYN_dynspg_ts} 
    830832\caption{  \label{Fig_DYN_dynspg_ts} 
    831833Schematic of the split-explicit time stepping scheme for the external  
    … …  
    12631265 
    12641266% ================================================================ 
     1267\end{document} 

  • branches/2016/dev_NOC_2016/DOC/TexFiles/Chapters/Chap_LBC.tex

    r6289 r7341  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter — Lateral Boundary Condition (LBC)  
    … …  
    5355%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    5456\begin{figure}[!t]     \begin{center} 
    55 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_LBC_uv.pdf} 
     57\includegraphics[width=0.90\textwidth]{Fig_LBC_uv} 
    5658\caption{  \label{Fig_LBC_uv} 
    5759Lateral boundary (thick line) at T-level. The velocity normal to the boundary is set to zero.} 
    … …  
    7678%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    7779\begin{figure}[!p] \begin{center} 
    78 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_LBC_shlat.pdf} 
     80\includegraphics[width=0.90\textwidth]{Fig_LBC_shlat} 
    7981\caption{     \label{Fig_LBC_shlat}  
    8082lateral boundary condition (a) free-slip ($rn\_shlat=0$) ; (b) no-slip ($rn\_shlat=2$)  
    … …  
    177179%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    178180\begin{figure}[!t]     \begin{center} 
    179 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_LBC_jperio.pdf} 
     181\includegraphics[width=1.0\textwidth]{Fig_LBC_jperio} 
    180182\caption{    \label{Fig_LBC_jperio} 
    181183setting of (a) east-west cyclic  (b) symmetric across the equator boundary conditions.} 
    … …  
    196198%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    197199\begin{figure}[!t]    \begin{center} 
    198 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_North_Fold_T.pdf} 
     200\includegraphics[width=0.90\textwidth]{Fig_North_Fold_T} 
    199201\caption{    \label{Fig_North_Fold_T}  
    200202North fold boundary with a $T$-point pivot and cyclic east-west boundary condition  
    … …  
    259261%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    260262\begin{figure}[!t]    \begin{center} 
    261 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_mpp.pdf} 
     263\includegraphics[width=0.90\textwidth]{Fig_mpp} 
    262264\caption{   \label{Fig_mpp}  
    263265Positioning of a sub-domain when massively parallel processing is used. } 
    … …  
    333335%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    334336\begin{figure}[!ht]     \begin{center} 
    335 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_mppini2.pdf} 
     337\includegraphics[width=0.90\textwidth]{Fig_mppini2} 
    336338\caption {    \label{Fig_mppini2} 
    337339Example of Atlantic domain defined for the CLIPPER projet. Initial grid is  
    … …  
    564566%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    565567\begin{figure}[!t]      \begin{center} 
    566 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_LBC_bdy_geom.pdf} 
     568\includegraphics[width=1.0\textwidth]{Fig_LBC_bdy_geom} 
    567569\caption {      \label{Fig_LBC_bdy_geom} 
    568570Example of geometry of unstructured open boundary} 
    … …  
    605607%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    606608\begin{figure}[!t]     \begin{center} 
    607 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_LBC_nc_header.pdf} 
     609\includegraphics[width=1.0\textwidth]{Fig_LBC_nc_header} 
    608610\caption {     \label{Fig_LBC_nc_header}  
    609611Example of the header for a coordinates.bdy.nc file} 
    … …  
    642644 
    643645 
     646\end{document} 

  • branches/2016/dev_NOC_2016/DOC/TexFiles/Chapters/Chap_LDF.tex

    r6289 r7341  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13 
    24% ================================================================ 
    … …  
    228230%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    229231\begin{figure}[!ht]      \begin{center} 
    230 \includegraphics[width=0.70\textwidth]{./TexFiles/Figures/Fig_LDF_ZDF1.pdf} 
     232\includegraphics[width=0.70\textwidth]{Fig_LDF_ZDF1} 
    231233\caption {    \label{Fig_LDF_ZDF1} 
    232234averaging procedure for isopycnal slope computation.} 
    … …  
    256258%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    257259\begin{figure}[!ht]     \begin{center} 
    258 \includegraphics[width=0.70\textwidth]{./TexFiles/Figures/Fig_eiv_slp.pdf} 
     260\includegraphics[width=0.70\textwidth]{Fig_eiv_slp} 
    259261\caption {     \label{Fig_eiv_slp} 
    260262Vertical profile of the slope used for lateral mixing in the mixed layer :  
    … …  
    298300diffusion along model level surfaces, i.e. using the shear computed along  
    299301the model levels and with no additional friction at the ocean bottom (see  
    300 {\S\ref{LBC_coast}). 
     302\S\ref{LBC_coast}). 
    301303 
    302304 
    … …  
    425427values are $0$). However, the technique used to compute the isopycnal  
    426428slopes is intended to get rid of such a background diffusion, since it introduces  
    427 spurious diapycnal diffusion (see {\S\ref{LDF_slp}). 
     429spurious diapycnal diffusion (see \S\ref{LDF_slp}). 
    428430 
    429431(4) when an eddy induced advection term is used (\key{traldf\_eiv}), $A^{eiv}$,  
    … …  
    499501 
    500502 
    501  
     503\end{document} 

  • branches/2016/dev_NOC_2016/DOC/TexFiles/Chapters/Chap_MISC.tex

    r6289 r7341  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter ——— Miscellaneous Topics 
    … …  
    6062%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    6163\begin{figure}[!tbp]     \begin{center} 
    62 \includegraphics[width=0.80\textwidth]{./TexFiles/Figures/Fig_Gibraltar.pdf} 
    63 \includegraphics[width=0.80\textwidth]{./TexFiles/Figures/Fig_Gibraltar2.pdf} 
     64\includegraphics[width=0.80\textwidth]{Fig_Gibraltar} 
     65\includegraphics[width=0.80\textwidth]{Fig_Gibraltar2} 
    6466\caption{   \label{Fig_MISC_strait_hand}  
    65 Example of the Gibraltar strait defined in a $1\deg \times 1\deg$ mesh.  
     67Example of the Gibraltar strait defined in a $1^{\circ} \times 1^{\circ}$ mesh.  
    6668\textit{Top}: using partially open cells. The meridional scale factor at $v$-point  
    6769is reduced on both sides of the strait to account for the real width of the strait  
    … …  
    181183%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    182184\begin{figure}[!ht]    \begin{center} 
    183 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_LBC_zoom.pdf} 
     185\includegraphics[width=0.90\textwidth]{Fig_LBC_zoom} 
    184186\caption{   \label{Fig_LBC_zoom} 
    185187Position of a model domain compared to the data input domain when the zoom functionality is used.} 
    … …  
    317319 
    318320% ================================================================ 
    319  
    320  
    321  
    322  
    323  
     321\end{document} 
     322 
     323 
     324 
     325 

  • branches/2016/dev_NOC_2016/DOC/TexFiles/Chapters/Chap_Model_Basics.tex

    r6289 r7341  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter 1 Ñ Model Basics 
    … …  
    114116%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    115117\begin{figure}[!ht]   \begin{center} 
    116 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_I_ocean_bc.pdf} 
     118\includegraphics[width=0.90\textwidth]{Fig_I_ocean_bc} 
    117119\caption{    \label{Fig_ocean_bc}  
    118120The ocean is bounded by two surfaces, $z=-H(i,j)$ and $z=\eta(i,j,t)$, where $H$  
    … …  
    312314%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    313315\begin{figure}[!tb]   \begin{center} 
    314 \includegraphics[width=0.60\textwidth]{./TexFiles/Figures/Fig_I_earth_referential.pdf} 
     316\includegraphics[width=0.60\textwidth]{Fig_I_earth_referential} 
    315317\caption{   \label{Fig_referential}  
    316318the geographical coordinate system $(\lambda,\varphi,z)$ and the curvilinear  
    … …  
    807809%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    808810\begin{figure}[!b]    \begin{center} 
    809 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_z_zstar.pdf} 
     811\includegraphics[width=1.0\textwidth]{Fig_z_zstar} 
    810812\caption{   \label{Fig_z_zstar}  
    811813(a) $z$-coordinate in linear free-surface case ;  
    … …  
    12471249not available in the iso-neutral case. 
    12481250 
     1251\end{document} 
     1252 

  • branches/2016/dev_NOC_2016/DOC/TexFiles/Chapters/Chap_Model_Basics_zstar.tex

    r6140 r7341  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter 1 ——— Model Basics 
    … …  
    121123%>   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   > 
    122124\begin{figure}[!t]   \begin{center} 
    123 \includegraphics[width=0.90\textwidth]{./Figures/Fig_DYN_dynspg_ts.pdf} 
     125\includegraphics[width=0.90\textwidth]{Fig_DYN_dynspg_ts} 
    124126\caption{    \label{Fig_DYN_dynspg_ts} 
    125127Schematic of the split-explicit time stepping scheme for the barotropic and baroclinic modes,  
    … …  
    256258 
    257259 
     260\end{document} 

  • branches/2016/dev_NOC_2016/DOC/TexFiles/Chapters/Chap_OBS.tex

    r6140 r7341  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter observation operator (OBS) 
    … …  
    744746%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    745747\begin{figure}      \begin{center} 
    746 \includegraphics[width=10cm,height=12cm,angle=-90.]{./TexFiles/Figures/Fig_ASM_obsdist_local} 
     748\includegraphics[width=10cm,height=12cm,angle=-90.]{Fig_ASM_obsdist_local} 
    747749\caption{      \label{fig:obslocal} 
    748750Example of the distribution of observations with the geographical distribution of observational data.}  
    … …  
    771773%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    772774\begin{figure}     \begin{center} 
    773 \includegraphics[width=10cm,height=12cm,angle=-90.]{./TexFiles/Figures/Fig_ASM_obsdist_global} 
     775\includegraphics[width=10cm,height=12cm,angle=-90.]{Fig_ASM_obsdist_global} 
    774776\caption{      \label{fig:obsglobal} 
    775777Example of the distribution of observations with the round-robin distribution of observational data.} 
    … …  
    13881390%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    13891391\begin{figure}     \begin{center} 
    1390 %\includegraphics[width=10cm,height=12cm,angle=-90.]{./TexFiles/Figures/Fig_OBS_dataplot_main} 
    1391 \includegraphics[width=9cm,angle=-90.]{./TexFiles/Figures/Fig_OBS_dataplot_main} 
     1392%\includegraphics[width=10cm,height=12cm,angle=-90.]{Fig_OBS_dataplot_main} 
     1393\includegraphics[width=9cm,angle=-90.]{Fig_OBS_dataplot_main} 
    13921394\caption{      \label{fig:obsdataplotmain} 
    13931395Main window of dataplot.} 
    … …  
    14001402%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    14011403\begin{figure}     \begin{center} 
    1402 %\includegraphics[width=10cm,height=12cm,angle=-90.]{./TexFiles/Figures/Fig_OBS_dataplot_prof} 
    1403 \includegraphics[width=7cm,angle=-90.]{./TexFiles/Figures/Fig_OBS_dataplot_prof} 
     1404%\includegraphics[width=10cm,height=12cm,angle=-90.]{Fig_OBS_dataplot_prof} 
     1405\includegraphics[width=7cm,angle=-90.]{Fig_OBS_dataplot_prof} 
    14041406\caption{      \label{fig:obsdataplotprofile} 
    14051407Profile plot from dataplot produced by right clicking on a point in the main window.} 
    … …  
    14101412 
    14111413 
     1414\end{document} 

  • branches/2016/dev_NOC_2016/DOC/TexFiles/Chapters/Chap_SBC.tex

    r6320 r7341  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter —— Surface Boundary Condition (SBC, ISF, ICB)  
    … …  
    128130The ocean model provides, at each time step, to the surface module (\mdl{sbcmod})  
    129131the surface currents, temperature and salinity.   
    130 These variables are averaged over \np{nf\_sbc} time-step (\ref{Tab_ssm}),  
     132These variables are averaged over \np{nn\_fsbc} time-step (\ref{Tab_ssm}),  
    131133and it is these averaged fields which are used to computes the surface fluxes  
    132 at a frequency of \np{nf\_sbc} time-step. 
     134at a frequency of \np{nn\_fsbc} time-step. 
    133135 
    134136 
    … …  
    144146\caption{  \label{Tab_ssm}    
    145147Ocean variables provided by the ocean to the surface module (SBC).  
    146 The variable are averaged over nf{\_}sbc time step, $i.e.$ the frequency of  
    147 computation of surface fluxes.} 
     148The variable are averaged over nn{\_}fsbc time step,  
     149$i.e.$ the frequency of computation of surface fluxes.} 
    148150\end{center}   \end{table} 
    149151%-------------------------------------------------------------------------------------------------------------- 
    … …  
    592594or larger than the one of the input atmospheric fields. 
    593595 
     596The \np{sn\_wndi}, \np{sn\_wndj}, \np{sn\_qsr}, \np{sn\_qlw}, \np{sn\_tair}, \np{sn\_humi}, 
     597\np{sn\_prec}, \np{sn\_snow}, \np{sn\_tdif} parameters describe the fields  
     598and the way they have to be used (spatial and temporal interpolations).  
     599 
     600\np{cn\_dir} is the directory of location of bulk files 
     601\np{ln\_taudif} is the flag to specify if we use Hight Frequency (HF) tau information (.true.) or not (.false.) 
     602\np{rn\_zqt}: is the height of humidity and temperature measurements (m) 
     603\np{rn\_zu}: is the height of wind measurements (m) 
     604 
     605Three multiplicative factors are availables :  
     606\np{rn\_pfac} and \np{rn\_efac} allows to adjust (if necessary) the global freshwater budget  
     607by increasing/reducing the precipitations (total and snow) and or evaporation, respectively. 
     608The third one,\np{rn\_vfac}, control to which extend the ice/ocean velocities are taken into account  
     609in the calculation of surface wind stress. Its range should be between zero and one,  
     610and it is recommended to set it to 0. 
     611 
    594612% ------------------------------------------------------------------------------------------------------------- 
    595613%        CLIO Bulk formulea 
    … …  
    926944\begin{description} 
    927945\item[\np{nn\_isf}~=~1] 
    928 The ice shelf cavity is represented (\np{ln\_isfcav}~=~true needed). The fwf and heat flux are computed. Two different bulk formula are available: 
     946The ice shelf cavity is represented (\np{ln\_isfcav}~=~true needed). The fwf and heat flux are computed.  
     947Two different bulk formula are available: 
    929948   \begin{description} 
    930949   \item[\np{nn\_isfblk}~=~1] 
    … …  
    9881007This parameter is only used if \np{nn\_isf}~=~1 or \np{nn\_isf}~=~4 
    9891008 
    990 If \np{rn\_hisf\_tbl} = 0.0, the fluxes are put in the top level whatever is its tickness.  
    991  
    992 If \np{rn\_hisf\_tbl} $>$ 0.0, the fluxes are spread over the first \np{rn\_hisf\_tbl} m (ie over one or several cells).\\ 
     1009If \np{rn\_hisf\_tbl} = 0., the fluxes are put in the top level whatever is its tickness.  
     1010 
     1011If \np{rn\_hisf\_tbl} $>$ 0., the fluxes are spread over the first \np{rn\_hisf\_tbl} m (ie over one or several cells).\\ 
    9931012 
    9941013The ice shelf melt is implemented as a volume flux with in the same way as for the runoff. 
    … …  
    11161135%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    11171136\begin{figure}[!t]    \begin{center} 
    1118 \includegraphics[width=0.8\textwidth]{./TexFiles/Figures/Fig_SBC_diurnal.pdf} 
     1137\includegraphics[width=0.8\textwidth]{Fig_SBC_diurnal} 
    11191138\caption{ \label{Fig_SBC_diurnal}     
    11201139Example of recontruction of the diurnal cycle variation of short wave flux   
    … …  
    11491168%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    11501169\begin{figure}[!t]  \begin{center} 
    1151 \includegraphics[width=0.7\textwidth]{./TexFiles/Figures/Fig_SBC_dcy.pdf} 
     1170\includegraphics[width=0.7\textwidth]{Fig_SBC_dcy} 
    11521171\caption{ \label{Fig_SBC_dcy}    
    11531172Example of recontruction of the diurnal cycle variation of short wave flux   
    … …  
    13441363 
    13451364 
     1365\end{document} 

  • branches/2016/dev_NOC_2016/DOC/TexFiles/Chapters/Chap_STO.tex

    r6289 r7341  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter stochastic parametrization of EOS (STO) 
    … …  
    57\label{STO} 
    68 
     9Authors: P.-A. Bouttier 
     10 
    711\minitoc 
    812 
     13\newpage 
    914 
    10 \newpage 
    11 $\ $\newline    % force a new line 
     15 
     16The stochastic parametrization module aims to explicitly simulate uncertainties in the model.  
     17More particularly, \cite{Brankart_OM2013} has shown that,  
     18because of the nonlinearity of the seawater equation of state, unresolved scales represent  
     19a major source of uncertainties in the computation of the large scale horizontal density gradient  
     20(from T/S large scale fields), and that the impact of these uncertainties can be simulated  
     21by random processes representing unresolved T/S fluctuations. 
     22 
     23The stochastic formulation of the equation of state can be written as: 
     24\begin{equation} 
     25 \label{eq:eos_sto} 
     26  \rho = \frac{1}{2} \sum_{i=1}^m\{ \rho[T+\Delta T_i,S+\Delta S_i,p_o(z)] + \rho[T-\Delta T_i,S-\Delta S_i,p_o(z)] \} 
     27\end{equation} 
     28where $p_o(z)$ is the reference pressure depending on the depth and,  
     29$\Delta T_i$ and $\Delta S_i$ are a set of T/S perturbations defined as the scalar product  
     30of the respective local T/S gradients with random walks $\mathbf{\xi}$: 
     31\begin{equation} 
     32 \label{eq:sto_pert} 
     33 \Delta T_i = \mathbf{\xi}_i \cdot \nabla T \qquad \hbox{and} \qquad \Delta S_i = \mathbf{\xi}_i \cdot \nabla S 
     34\end{equation} 
     35$\mathbf{\xi}_i$ are produced by a first-order autoregressive processes (AR-1) with  
     36a parametrized decorrelation time scale, and horizontal and vertical standard deviations $\sigma_s$.  
     37$\mathbf{\xi}$ are uncorrelated over the horizontal and fully correlated along the vertical. 
     38 
     39 
     40\section{Stochastic processes} 
     41\label{STO_the_details} 
     42 
     43The starting point of our implementation of stochastic parameterizations 
     44in NEMO is to observe that many existing parameterizations are based 
     45on autoregressive processes, which are used as a basic source of randomness 
     46to transform a deterministic model into a probabilistic model. 
     47A generic approach is thus to add one single new module in NEMO, 
     48generating processes with appropriate statistics 
     49to simulate each kind of uncertainty in the model 
     50(see \cite{Brankart_al_GMD2015} for more details). 
     51 
     52In practice, at every model grid point, independent Gaussian autoregressive 
     53processes~$\xi^{(i)},\,i=1,\ldots,m$ are first generated 
     54using the same basic equation: 
     55 
     56\begin{equation} 
     57\label{eq:autoreg} 
     58\xi^{(i)}_{k+1} = a^{(i)} \xi^{(i)}_k + b^{(i)} w^{(i)} + c^{(i)} 
     59\end{equation} 
     60 
     61\noindent 
     62where $k$ is the index of the model timestep; and 
     63$a^{(i)}$, $b^{(i)}$, $c^{(i)}$ are parameters defining 
     64the mean ($\mu^{(i)}$) standard deviation ($\sigma^{(i)}$) 
     65and correlation timescale ($\tau^{(i)}$) of each process: 
     66 
     67\begin{itemize} 
     68\item for order~1 processes, $w^{(i)}$ is a Gaussian white noise, 
     69with zero mean and standard deviation equal to~1, and the parameters 
     70$a^{(i)}$, $b^{(i)}$, $c^{(i)}$ are given by: 
     71 
     72\begin{equation} 
     73\label{eq:ord1} 
     74\left\{ 
     75\begin{array}{l} 
     76a^{(i)} = \varphi \\ 
     77b^{(i)} = \sigma^{(i)} \sqrt{ 1 - \varphi^2 }  
     78 \qquad\qquad\mbox{with}\qquad\qquad 
     79\varphi = \exp \left( - 1 / \tau^{(i)} \right) \\ 
     80c^{(i)} = \mu^{(i)} \left( 1 - \varphi \right) \\ 
     81\end{array} 
     82\right. 
     83\end{equation} 
     84 
     85\item for order~$n>1$ processes, $w^{(i)}$ is an order~$n-1$ autoregressive process, 
     86with zero mean, standard deviation equal to~$\sigma^{(i)}$; correlation timescale 
     87equal to~$\tau^{(i)}$; and the parameters $a^{(i)}$, $b^{(i)}$, $c^{(i)}$ are given by: 
     88 
     89\begin{equation} 
     90\label{eq:ord2} 
     91\left\{ 
     92\begin{array}{l} 
     93a^{(i)} = \varphi \\ 
     94b^{(i)} = \frac{n-1}{2(4n-3)} \sqrt{ 1 - \varphi^2 }  
     95 \qquad\qquad\mbox{with}\qquad\qquad 
     96\varphi = \exp \left( - 1 / \tau^{(i)} \right) \\ 
     97c^{(i)} = \mu^{(i)} \left( 1 - \varphi \right) \\ 
     98\end{array} 
     99\right. 
     100\end{equation} 
     101 
     102\end{itemize} 
     103 
     104\noindent 
     105In this way, higher order processes can be easily generated recursively using  
     106the same piece of code implementing Eq.~(\ref{eq:autoreg}),  
     107and using succesively processes from order $0$ to~$n-1$ as~$w^{(i)}$. 
     108The parameters in Eq.~(\ref{eq:ord2}) are computed so that this recursive application 
     109of Eq.~(\ref{eq:autoreg}) leads to processes with the required standard deviation 
     110and correlation timescale, with the additional condition that 
     111the $n-1$ first derivatives of the autocorrelation function 
     112are equal to zero at~$t=0$, so that the resulting processes 
     113become smoother and smoother as $n$ is increased. 
     114 
     115Overall, this method provides quite a simple and generic way of generating  
     116a wide class of stochastic processes.  
     117However, this also means that new model parameters are needed to specify each of  
     118these stochastic processes. As in any parameterization of lacking physics,  
     119a very important issues then to tune these new parameters using either first principles,  
     120model simulations, or real-world observations. 
     121 
     122\section{Implementation details} 
     123\label{STO_thech_details} 
     124 
    12125%---------------------------------------namsbc-------------------------------------------------- 
    13126\namdisplay{namsto} 
    14127%-------------------------------------------------------------------------------------------------------------- 
    15 $\ $\newline    % force a new ligne 
     128 
     129The computer code implementing stochastic parametrisations can be found in the STO directory. 
     130It involves three modules :  
     131\begin{description} 
     132\item[\mdl{stopar}] : define the Stochastic parameters and their time evolution. 
     133\item[\mdl{storng}] : a random number generator based on (and includes) the 64-bit KISS  
     134                      (Keep It Simple Stupid) random number generator distributed by George Marsaglia  
     135                      (see \href{https://groups.google.com/forum/#!searchin/comp.lang.fortran/64-bit$20KISS$20RNGs}{here}) 
     136\item[\mdl{stopts}] : stochastic parametrisation associated with the non-linearity of the equation of seawater,  
     137 implementing Eq~\ref{eq:sto_pert} and specific piece of code in the equation of state implementing Eq~\ref{eq:eos_sto}. 
     138\end{description} 
     139 
     140The \mdl{stopar} module has 3 public routines to be called by the model (in our case, NEMO): 
     141 
     142The first routine (\rou{sto\_par}) is a direct implementation of Eq.~(\ref{eq:autoreg}), 
     143applied at each model grid point (in 2D or 3D),  
     144and called at each model time step ($k$) to update 
     145every autoregressive process ($i=1,\ldots,m$). 
     146This routine also includes a filtering operator, applied to $w^{(i)}$, 
     147to introduce a spatial correlation between the stochastic processes. 
     148 
     149The second routine (\rou{sto\_par\_init}) is an initialization routine mainly dedicated 
     150to the computation of parameters $a^{(i)}, b^{(i)}, c^{(i)}$ 
     151for each autoregressive process, as a function of the statistical properties 
     152required by the model user (mean, standard deviation, time correlation, 
     153order of the process,\ldots).  
     154 
     155Parameters for the processes can be specified through the following \ngn{namsto} namelist parameters: 
     156\begin{description} 
     157   \item[\np{nn\_sto\_eos}]   : number of independent random walks  
     158   \item[\np{rn\_eos\_stdxy}] : random walk horz. standard deviation (in grid points) 
     159   \item[\np{rn\_eos\_stdz}]  : random walk vert. standard deviation (in grid points) 
     160   \item[\np{rn\_eos\_tcor}]  : random walk time correlation (in timesteps) 
     161   \item[\np{nn\_eos\_ord}]   : order of autoregressive processes 
     162   \item[\np{nn\_eos\_flt}]   : passes of Laplacian filter 
     163   \item[\np{rn\_eos\_lim}]   : limitation factor (default = 3.0) 
     164\end{description} 
     165This routine also includes the initialization (seeding) of the random number generator. 
     166 
     167The third routine (\rou{sto\_rst\_write}) writes a restart file (which suffix name is  
     168given by \np{cn\_storst\_out} namelist parameter) containing the current value of  
     169all autoregressive processes to allow restarting a simulation from where it has been interrupted. 
     170This file also contains the current state of the random number generator. 
     171When \np{ln\_rststo} is set to \textit{true}), the restart file (which suffix name is  
     172given by \np{cn\_storst\_in} namelist parameter) is read by the initialization routine  
     173(\rou{sto\_par\_init}). The simulation will continue exactly as if it was not interrupted 
     174only  when \np{ln\_rstseed} is set to \textit{true}, $i.e.$ when the state of  
     175the random number generator is read in the restart file. 
    16176 
    17177 
    18 See \cite{Brankart_OM2013} and \cite{Brankart_al_GMD2015} papers for a description of the parameterization. 
     178\end{document} 

  • branches/2016/dev_NOC_2016/DOC/TexFiles/Chapters/Chap_STP.tex

    r6140 r7341  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13 
    24% ================================================================ 
    … …  
    204206%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    205207\begin{figure}[!t]     \begin{center} 
    206 \includegraphics[width=0.7\textwidth]{./TexFiles/Figures/Fig_TimeStepping_flowchart.pdf} 
     208\includegraphics[width=0.7\textwidth]{Fig_TimeStepping_flowchart} 
    207209\caption{   \label{Fig_TimeStep_flowchart} 
    208210Sketch of the leapfrog time stepping sequence in \NEMO from \citet{Leclair_Madec_OM09}.  
    … …  
    266268%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    267269\begin{figure}[!t]     \begin{center} 
    268 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_MLF_forcing.pdf} 
     270\includegraphics[width=0.90\textwidth]{Fig_MLF_forcing} 
    269271\caption{   \label{Fig_MLF_forcing} 
    270272Illustration of forcing integration methods.  
    … …  
    402404} 
    403405%% 
     406\end{document} 

  • branches/2016/dev_NOC_2016/DOC/TexFiles/Chapters/Chap_TRA.tex

    r6320 r7341  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter 1 ——— Ocean Tracers (TRA) 
    … …  
    9092%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    9193\begin{figure}[!t]    \begin{center} 
    92 \includegraphics[width=0.9\textwidth]{./TexFiles/Figures/Fig_adv_scheme.pdf} 
     94\includegraphics[width=0.9\textwidth]{Fig_adv_scheme} 
    9395\caption{   \label{Fig_adv_scheme}  
    9496Schematic representation of some ways used to evaluate the tracer value  
    … …  
    734736(see \S\ref{SBC_rnf} for further detail of how it acts on temperature and salinity tendencies) 
    735737 
    736 $\bullet$ \textit{fwfisf}, the mass flux associated with ice shelf melt, (see \S\ref{SBC_isf} for further details  
    737 on how the ice shelf melt is computed and applied). 
     738$\bullet$ \textit{fwfisf}, the mass flux associated with ice shelf melt,  
     739(see \S\ref{SBC_isf} for further details on how the ice shelf melt is computed and applied). 
    738740 
    739741The surface boundary condition on temperature and salinity is applied as follows: 
    … …  
    840842($i.e.$ the inverses of the extinction length scales) are tabulated over 61 nonuniform  
    841843chlorophyll classes ranging from 0.01 to 10 g.Chl/L (see the routine \rou{trc\_oce\_rgb}  
    842 in \mdl{trc\_oce} module). Three types of chlorophyll can be chosen in the RGB formulation: 
    843 (1) a constant 0.05 g.Chl/L value everywhere (\np{nn\_chdta}=0) ; (2) an observed  
    844 time varying chlorophyll (\np{nn\_chdta}=1) ; (3) simulated time varying chlorophyll 
    845 by TOP biogeochemical model (\np{ln\_qsr\_bio}=true). In the latter case, the RGB  
    846 formulation is used to calculate both the phytoplankton light limitation in PISCES  
    847 or LOBSTER and the oceanic heating rate.  
    848  
     844in \mdl{trc\_oce} module). Four types of chlorophyll can be chosen in the RGB formulation: 
     845\begin{description}  
     846\item[\np{nn\_chdta}=0]  
     847a constant 0.05 g.Chl/L value everywhere ;  
     848\item[\np{nn\_chdta}=1]   
     849an observed time varying chlorophyll deduced from satellite surface ocean color measurement  
     850spread uniformly in the vertical direction ;  
     851\item[\np{nn\_chdta}=2]   
     852same as previous case except that a vertical profile of chlorophyl is used.  
     853Following \cite{Morel_Berthon_LO89}, the profile is computed from the local surface chlorophyll value ; 
     854\item[\np{ln\_qsr\_bio}=true]   
     855simulated time varying chlorophyll by TOP biogeochemical model.  
     856In this case, the RGB formulation is used to calculate both the phytoplankton  
     857light limitation in PISCES or LOBSTER and the oceanic heating rate.  
     858\end{description}  
    849859The trend in \eqref{Eq_tra_qsr} associated with the penetration of the solar radiation  
    850860is added to the temperature trend, and the surface heat flux is modified in routine \mdl{traqsr}.  
    … …  
    861871%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    862872\begin{figure}[!t]     \begin{center} 
    863 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_TRA_Irradiance.pdf} 
     873\includegraphics[width=1.0\textwidth]{Fig_TRA_Irradiance} 
    864874\caption{    \label{Fig_traqsr_irradiance} 
    865875Penetration profile of the downward solar irradiance calculated by four models.  
    … …  
    882892%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    883893\begin{figure}[!t]     \begin{center} 
    884 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_TRA_geoth.pdf} 
     894\includegraphics[width=1.0\textwidth]{Fig_TRA_geoth} 
    885895\caption{   \label{Fig_geothermal} 
    886896Geothermal Heat flux (in $mW.m^{-2}$) used by \cite{Emile-Geay_Madec_OS09}. 
    … …  
    9921002%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    9931003\begin{figure}[!t]   \begin{center} 
    994 \includegraphics[width=0.7\textwidth]{./TexFiles/Figures/Fig_BBL_adv.pdf} 
     1004\includegraphics[width=0.7\textwidth]{Fig_BBL_adv} 
    9951005\caption{   \label{Fig_bbl}   
    9961006Advective/diffusive Bottom Boundary Layer. The BBL parameterisation is  
    … …  
    11501160The restoration coefficient can be set to zero in equatorial regions by specifying a positive value of \np{nn\_hdmp}.  
    11511161Equatorward of this latitude the restoration coefficient will be zero with a smooth transition to  
    1152 the full values of a 10$^{\circ}$ latitud band.  
     1162the full values of a 10\deg latitud band.  
    11531163This is often used because of the short adjustment time scale in the equatorial region  
    11541164\citep{Reverdin1991, Fujio1991, Marti_PhD92}. The time scale associated with the damping depends on the depth as a  
    … …  
    12501260rational function approximation for hydrographic data analysis  \citep{TEOS10}.  
    12511261A key point is that conservative state variables are used:  
    1252 Absolute Salinity (unit: g/kg, notation: $S_A$) and Conservative Temperature (unit: $\degres C$, notation: $\Theta$). 
     1262Absolute Salinity (unit: g/kg, notation: $S_A$) and Conservative Temperature (unit: \degC, notation: $\Theta$). 
    12531263The pressure in decibars is approximated by the depth in meters.  
    12541264With TEOS10, the specific heat capacity of sea water, $C_p$, is a constant. It is set to  
    1255 $C_p=3991.86795711963~J\,Kg^{-1}\,\degres K^{-1}$, according to \citet{TEOS10}. 
     1265$C_p=3991.86795711963~J\,Kg^{-1}\,^{\circ}K^{-1}$, according to \citet{TEOS10}. 
    12561266 
    12571267Choosing polyTEOS10-bsq implies that the state variables used by the model are  
    … …  
    12661276to accurately fit EOS80 (Roquet, personal comm.). The state variables used in both the EOS80  
    12671277and the ocean model are:  
    1268 the Practical Salinity ((unit: psu, notation: $S_p$)) and Potential Temperature (unit: $\degres C$, notation: $\theta$). 
     1278the Practical Salinity ((unit: psu, notation: $S_p$)) and Potential Temperature (unit: $^{\circ}C$, notation: $\theta$). 
    12691279The pressure in decibars is approximated by the depth in meters.   
    12701280With thsi EOS, the specific heat capacity of sea water, $C_p$, is a function of temperature,  
    … …  
    13851395                   I've changed "derivative" to "difference" and "mean" to "average"} 
    13861396 
    1387 With partial cells (\np{ln\_zps}=true) at bottom and top (\np{ln\_isfcav}=true), in general, tracers in horizontally  
    1388 adjacent cells live at different depths. Horizontal gradients of tracers are needed  
    1389 for horizontal diffusion (\mdl{traldf} module) and for the hydrostatic pressure  
    1390 gradient (\mdl{dynhpg} module) to be active. The partial cell properties  
    1391 at the top (\np{ln\_isfcav}=true) are computed in the same way as for the bottom. So, only the bottom interpolation is shown. 
    1392 \gmcomment{STEVEN from gm : question: not sure of  what -to be active- means} 
     1397With partial cells (\np{ln\_zps}=true) at bottom and top (\np{ln\_isfcav}=true), in general,  
     1398tracers in horizontally adjacent cells live at different depths.  
     1399Horizontal gradients of tracers are needed for horizontal diffusion (\mdl{traldf} module)  
     1400and the hydrostatic pressure gradient calculations (\mdl{dynhpg} module).  
     1401The partial cell properties at the top (\np{ln\_isfcav}=true) are computed in the same way as for the bottom.  
     1402So, only the bottom interpolation is explained below. 
    13931403 
    13941404Before taking horizontal gradients between the tracers next to the bottom, a linear  
    … …  
    14001410%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    14011411\begin{figure}[!p]    \begin{center} 
    1402 \includegraphics[width=0.9\textwidth]{./TexFiles/Figures/Partial_step_scheme.pdf} 
     1412\includegraphics[width=0.9\textwidth]{Partial_step_scheme} 
    14031413\caption{   \label{Fig_Partial_step_scheme}  
    14041414Discretisation of the horizontal difference and average of tracers in the $z$-partial  
    … …  
    14671477\gmcomment{gm :   this last remark has to be done} 
    14681478%%% 
     1479\end{document} 

  • branches/2016/dev_NOC_2016/DOC/TexFiles/Chapters/Chap_ZDF.tex

    r6320 r7341  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter  Vertical Ocean Physics (ZDF) 
    … …  
    234236%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    235237\begin{figure}[!t] \begin{center} 
    236 \includegraphics[width=1.00\textwidth]{./TexFiles/Figures/Fig_mixing_length.pdf} 
     238\includegraphics[width=1.00\textwidth]{Fig_mixing_length} 
    237239\caption{ \label{Fig_mixing_length}  
    238240Illustration of the mixing length computation. } 
    … …  
    262264\end{equation} 
    263265 
    264 At the ocean surface, a non zero length scale is set through the  \np{rn\_lmin0} namelist  
     266At the ocean surface, a non zero length scale is set through the  \np{rn\_mxl0} namelist  
    265267parameter. Usually the surface scale is given by $l_o = \kappa \,z_o$  
    266268where $\kappa = 0.4$ is von Karman's constant and $z_o$ the roughness  
    267269parameter of the surface. Assuming $z_o=0.1$~m \citep{Craig_Banner_JPO94}  
    268 leads to a 0.04~m, the default value of \np{rn\_lsurf}. In the ocean interior  
     270leads to a 0.04~m, the default value of \np{rn\_mxl0}. In the ocean interior  
    269271a minimum length scale is set to recover the molecular viscosity when $\bar{e}$  
    270272reach its minimum value ($1.10^{-6}= C_k\, l_{min} \,\sqrt{\bar{e}_{min}}$ ). 
    … …  
    295297As the surface boundary condition on TKE is prescribed through $\bar{e}_o = e_{bb} |\tau| / \rho_o$,  
    296298with $e_{bb}$ the \np{rn\_ebb} namelist parameter, setting \np{rn\_ebb}~=~67.83 corresponds  
    297 to $\alpha_{CB} = 100$. further setting  \np{ln\_lsurf} to true applies \eqref{ZDF_Lsbc}  
    298 as surface boundary condition on length scale, with $\beta$ hard coded to the Stacet's value. 
     299to $\alpha_{CB} = 100$. Further setting  \np{ln\_mxl0} to true applies \eqref{ZDF_Lsbc}  
     300as surface boundary condition on length scale, with $\beta$ hard coded to the Stacey's value. 
    299301Note that a minimal threshold of \np{rn\_emin0}$=10^{-4}~m^2.s^{-2}$ (namelist parameters)  
    300302is applied on surface $\bar{e}$ value. 
    … …  
    408410%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    409411\begin{figure}[!t]   \begin{center} 
    410 \includegraphics[width=1.00\textwidth]{./TexFiles/Figures/Fig_ZDF_TKE_time_scheme.pdf} 
     412\includegraphics[width=1.00\textwidth]{Fig_ZDF_TKE_time_scheme} 
    411413\caption{ \label{Fig_TKE_time_scheme}  
    412414Illustration of the TKE time integration and its links to the momentum and tracer time integration. } 
    … …  
    587589value near physical boundaries (logarithmic boundary layer law). $C_{\mu}$ and $C_{\mu'}$  
    588590are calculated from stability function proposed by \citet{Galperin_al_JAS88}, or by \citet{Kantha_Clayson_1994}  
    589 or one of the two functions suggested by \citet{Canuto_2001}  (\np{nn\_stab\_func} = 0, 1, 2 or 3, resp.}).  
     591or one of the two functions suggested by \citet{Canuto_2001}  (\np{nn\_stab\_func} = 0, 1, 2 or 3, resp.).  
    590592The value of $C_{0\mu}$ depends of the choice of the stability function. 
    591593 
    … …  
    643645%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    644646\begin{figure}[!htb]    \begin{center} 
    645 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_npc.pdf} 
     647\includegraphics[width=0.90\textwidth]{Fig_npc} 
    646648\caption{  \label{Fig_npc}  
    647649Example of an unstable density profile treated by the non penetrative  
    … …  
    799801%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    800802\begin{figure}[!t]   \begin{center} 
    801 \includegraphics[width=0.99\textwidth]{./TexFiles/Figures/Fig_zdfddm.pdf} 
     803\includegraphics[width=0.99\textwidth]{Fig_zdfddm} 
    802804\caption{  \label{Fig_zdfddm} 
    803805From \citet{Merryfield1999} : (a) Diapycnal diffusivities $A_f^{vT}$  
    … …  
    852854The bottom friction represents the friction generated by the bathymetry.  
    853855The top friction represents the friction generated by the ice shelf/ocean interface.  
    854 As the friction processes at the top and bottom are represented similarly, only the bottom friction is described in detail below.\\ 
     856As the friction processes at the top and bottom are treated in similar way,  
     857only the bottom friction is described in detail below. 
    855858 
    856859 
    … …  
    926929$H = 4000$~m, the resulting friction coefficient is $r = 4\;10^{-4}$~m\;s$^{-1}$.  
    927930This is the default value used in \NEMO. It corresponds to a decay time scale  
    928 of 115~days. It can be changed by specifying \np{rn\_bfric1} (namelist parameter). 
     931of 115~days. It can be changed by specifying \np{rn\_bfri1} (namelist parameter). 
    929932 
    930933For the linear friction case the coefficients defined in the general  
    … …  
    936939\end{split} 
    937940\end{equation} 
    938 When \np{nn\_botfr}=1, the value of $r$ used is \np{rn\_bfric1}.  
     941When \np{nn\_botfr}=1, the value of $r$ used is \np{rn\_bfri1}.  
    939942Setting \np{nn\_botfr}=0 is equivalent to setting $r=0$ and leads to a free-slip  
    940943bottom boundary condition. These values are assigned in \mdl{zdfbfr}.  
    … …  
    943946in the \ifile{bfr\_coef} input NetCDF file. The mask values should vary from 0 to 1.  
    944947Locations with a non-zero mask value will have the friction coefficient increased  
    945 by $mask\_value$*\np{rn\_bfrien}*\np{rn\_bfric1}. 
     948by $mask\_value$*\np{rn\_bfrien}*\np{rn\_bfri1}. 
    946949 
    947950% ------------------------------------------------------------------------------------------------------------- 
    … …  
    963966$e_b = 2.5\;10^{-3}$m$^2$\;s$^{-2}$, while the FRAM experiment \citep{Killworth1992}  
    964967uses $C_D = 1.4\;10^{-3}$ and $e_b =2.5\;\;10^{-3}$m$^2$\;s$^{-2}$.  
    965 The CME choices have been set as default values (\np{rn\_bfric2} and \np{rn\_bfeb2}  
     968The CME choices have been set as default values (\np{rn\_bfri2} and \np{rn\_bfeb2}  
    966969namelist parameters). 
    967970 
    … …  
    978981\end{equation} 
    979982 
    980 The coefficients that control the strength of the non-linear bottom friction are  
    981 initialised as namelist parameters: $C_D$= \np{rn\_bfri2}, and $e_b$ =\np{rn\_bfeb2}.  
    982 Note for applications which treat tides explicitly a low or even zero value of  
    983 \np{rn\_bfeb2} is recommended. From v3.2 onwards a local enhancement of $C_D$  
    984 is possible via an externally defined 2D mask array (\np{ln\_bfr2d}=true).  
    985 See previous section for details. 
     983The coefficients that control the strength of the non-linear bottom friction are 
     984initialised as namelist parameters: $C_D$= \np{rn\_bfri2}, and $e_b$ =\np{rn\_bfeb2}. 
     985Note for applications which treat tides explicitly a low or even zero value of 
     986\np{rn\_bfeb2} is recommended. From v3.2 onwards a local enhancement of $C_D$ is possible 
     987via an externally defined 2D mask array (\np{ln\_bfr2d}=true).  This works in the same way 
     988as for the linear bottom friction case with non-zero masked locations increased by 
     989$mask\_value$*\np{rn\_bfrien}*\np{rn\_bfri2}. 
     990 
     991% ------------------------------------------------------------------------------------------------------------- 
     992%       Bottom Friction Log-layer 
     993% ------------------------------------------------------------------------------------------------------------- 
     994\subsection{Log-layer Bottom Friction enhancement (\np{nn\_botfr} = 2, \np{ln\_loglayer} = .true.)} 
     995\label{ZDF_bfr_loglayer} 
     996 
     997In the non-linear bottom friction case, the drag coefficient, $C_D$, can be optionally 
     998enhanced using a "law of the wall" scaling. If  \np{ln\_loglayer} = .true., $C_D$ is no 
     999longer constant but is related to the thickness of the last wet layer in each column by: 
     1000 
     1001\begin{equation} 
     1002C_D = \left ( {\kappa \over {\rm log}\left ( 0.5e_{3t}/rn\_bfrz0 \right ) } \right )^2 
     1003\end{equation} 
     1004 
     1005\noindent where $\kappa$ is the von-Karman constant and \np{rn\_bfrz0} is a roughness 
     1006length provided via the namelist. 
     1007 
     1008For stability, the drag coefficient is bounded such that it is kept greater or equal to 
     1009the base \np{rn\_bfri2} value and it is not allowed to exceed the value of an additional 
     1010namelist parameter: \np{rn\_bfri2\_max}, i.e.: 
     1011 
     1012\begin{equation} 
     1013rn\_bfri2 \leq C_D \leq rn\_bfri2\_max 
     1014\end{equation} 
     1015 
     1016\noindent Note also that a log-layer enhancement can also be applied to the top boundary 
     1017friction if under ice-shelf cavities are in use (\np{ln\_isfcav}=.true.).  In this case, the 
     1018relevant namelist parameters are \np{rn\_tfrz0}, \np{rn\_tfri2} 
     1019and \np{rn\_tfri2\_max}. 
    9861020 
    9871021% ------------------------------------------------------------------------------------------------------------- 
    … …  
    10971131baroclinic and barotropic components which is appropriate when using either the 
    10981132explicit or filtered surface pressure gradient algorithms (\key{dynspg\_exp} or  
    1099 {\key{dynspg\_flt}). Extra attention is required, however, when using  
     1133\key{dynspg\_flt}). Extra attention is required, however, when using  
    11001134split-explicit time stepping (\key{dynspg\_ts}). In this case the free surface  
    11011135equation is solved with a small time step \np{rn\_rdt}/\np{nn\_baro}, while the three  
    … …  
    12121246%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    12131247\begin{figure}[!t]   \begin{center} 
    1214 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_ZDF_M2_K1_tmx.pdf} 
     1248\includegraphics[width=0.90\textwidth]{Fig_ZDF_M2_K1_tmx} 
    12151249\caption{  \label{Fig_ZDF_M2_K1_tmx}  
    12161250(a) M2 and (b) K1 internal wave drag energy from \citet{Carrere_Lyard_GRL03} ($W/m^2$). } 
    … …  
    12671301 
    12681302% ================================================================ 
     1303% Internal wave-driven mixing 
     1304% ================================================================ 
     1305\section{Internal wave-driven mixing (\key{zdftmx\_new})} 
     1306\label{ZDF_tmx_new} 
     1307 
     1308%--------------------------------------------namzdf_tmx_new------------------------------------------ 
     1309\namdisplay{namzdf_tmx_new} 
     1310%-------------------------------------------------------------------------------------------------------------- 
     1311 
     1312The parameterization of mixing induced by breaking internal waves is a generalization  
     1313of the approach originally proposed by \citet{St_Laurent_al_GRL02}.  
     1314A three-dimensional field of internal wave energy dissipation $\epsilon(x,y,z)$ is first constructed,  
     1315and the resulting diffusivity is obtained as  
     1316\begin{equation} \label{Eq_Kwave} 
     1317A^{vT}_{wave} =  R_f \,\frac{ \epsilon }{ \rho \, N^2 } 
     1318\end{equation} 
     1319where $R_f$ is the mixing efficiency and $\epsilon$ is a specified three dimensional distribution  
     1320of the energy available for mixing. If the \np{ln\_mevar} namelist parameter is set to false,  
     1321the mixing efficiency is taken as constant and equal to 1/6 \citep{Osborn_JPO80}.  
     1322In the opposite (recommended) case, $R_f$ is instead a function of the turbulence intensity parameter  
     1323$Re_b = \frac{ \epsilon}{\nu \, N^2}$, with $\nu$ the molecular viscosity of seawater,  
     1324following the model of \cite{Bouffard_Boegman_DAO2013}  
     1325and the implementation of \cite{de_lavergne_JPO2016_efficiency}. 
     1326Note that $A^{vT}_{wave}$ is bounded by $10^{-2}\,m^2/s$, a limit that is often reached when the mixing efficiency is constant. 
     1327 
     1328In addition to the mixing efficiency, the ratio of salt to heat diffusivities can chosen to vary  
     1329as a function of $Re_b$ by setting the \np{ln\_tsdiff} parameter to true, a recommended choice).  
     1330This parameterization of differential mixing, due to \cite{Jackson_Rehmann_JPO2014},  
     1331is implemented as in \cite{de_lavergne_JPO2016_efficiency}. 
     1332 
     1333The three-dimensional distribution of the energy available for mixing, $\epsilon(i,j,k)$, is constructed  
     1334from three static maps of column-integrated internal wave energy dissipation, $E_{cri}(i,j)$,  
     1335$E_{pyc}(i,j)$, and $E_{bot}(i,j)$, combined to three corresponding vertical structures  
     1336(de Lavergne et al., in prep): 
     1337\begin{align*} 
     1338F_{cri}(i,j,k) &\propto e^{-h_{ab} / h_{cri} }\\ 
     1339F_{pyc}(i,j,k) &\propto N^{n\_p}\\ 
     1340F_{bot}(i,j,k) &\propto N^2 \, e^{- h_{wkb} / h_{bot} } 
     1341\end{align*}  
     1342In the above formula, $h_{ab}$ denotes the height above bottom,  
     1343$h_{wkb}$ denotes the WKB-stretched height above bottom, defined by 
     1344\begin{equation*} 
     1345h_{wkb} = H \, \frac{ \int_{-H}^{z} N \, dz' } { \int_{-H}^{\eta} N \, dz'  } \; , 
     1346\end{equation*} 
     1347The $n_p$ parameter (given by \np{nn\_zpyc} in \ngn{namzdf\_tmx\_new} namelist)  controls the stratification-dependence of the pycnocline-intensified dissipation.  
     1348It can take values of 1 (recommended) or 2. 
     1349Finally, the vertical structures $F_{cri}$ and $F_{bot}$ require the specification of  
     1350the decay scales $h_{cri}(i,j)$ and $h_{bot}(i,j)$, which are defined by two additional input maps.  
     1351$h_{cri}$ is related to the large-scale topography of the ocean (etopo2)  
     1352and $h_{bot}$ is a function of the energy flux $E_{bot}$, the characteristic horizontal scale of  
     1353the abyssal hill topography \citep{Goff_JGR2010} and the latitude. 
     1354 
     1355% ================================================================ 
     1356 
     1357 
     1358 
     1359\end{document} 

  • branches/2016/dev_NOC_2016/DOC/TexFiles/Chapters/Introduction.tex

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