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Changeset 6992 for branches/2015/nemo_v3_6_STABLE – NEMO

Ignore:
Timestamp:
2016-10-05T14:07:19+02:00 (8 years ago)
Author:
nicolasmartin
Message:

Global reorganisation of DOC directory to ensure the export of NEMO Reference Manual both in PDF & HTML

  • Move 'Figures' and 'Namelists' from ./TexFiles? to the root, create 'Styles' directory in ./TexFiles? with corresponding files and generate EPS version of all figures
  • Fix LaTex? typos, add the possibility to compile each chapter separately with 'subfiles' package and clean the main LaTeX file by creating 'Preamble.tex' & 'Top_Matter.tex' in ./TexFiles?
  • Provide LaTeX2HTML.sh script for producing HTML output (LaTeX2HTML tool needed with patch)
  • Remove PDF files from versionned files
Location:
branches/2015/nemo_v3_6_STABLE/DOC
Files:
77 added
2 deleted
29 edited
9 moved

Legend:

Unmodified
Added
Removed

  • branches/2015/nemo_v3_6_STABLE/DOC/NEMO_book.tex

    r6275 r6992  
    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  
    136 \usepackage{times}                % use times font for text 
    137 %\usepackage{mathtime}                          % font for illustrator to work (belleek fonts ) 
    138 %\usepackage[latin1]{inputenc}                % allows some unicode removed (agn) 
    139  
    140  
    141 %%% essai commande 
    142 \newcommand{\nl} [1] {\texttt{\small {\textcolor{blue}{#1}} } } 
    143 \newcommand{\nlv} [1] {\texttt{\footnotesize#1}\xspace} 
    144 \newcommand{\smnlv} [1] {\texttt{\scriptsize#1}\xspace} 
    145  
    146 %%%% namelist & code display................................ 
    147 \usepackage{alltt}      %%  alltt for namelist 
    148 \usepackage{verbatim}   %%  alltt for namelist 
    149 % namelists 
    150 \newcommand{\namdisplay} [1] { 
    151 \begin{alltt} 
    152 {\tiny \verbatiminput{./TexFiles/Namelist/#1}} 
    153 \end{alltt} 
    154   \vspace{-10pt} 
    155 } 
    156 % code display 
    157 %\newcommand{\codedisplay} [1] { \begin{alltt} {\tiny  {\begin{verbatim} {#1}} \end{verbatim} }  \end{alltt}   } 
    158  
    159  
    160  
    161 %%%% commands for working with text................................ 
    162 % command to "comment out" portions of text ({} argument) or not ({#1} argument) 
    163 \newcommand{\amtcomment}[1]{}    % command to "commented out" portions of text or not (#1 in argument) 
    164 \newcommand{\sgacomment}[1]{}    % command to "commented out" portions of 
    165 \newcommand{\gmcomment}[1]{}     % command to "commented out" portions of 
    166 %                                               % text that span line breaks 
    167 %Red (NR) or Yellow(WARN) 
    168 %\newcommand{\NR} {\colorbox{red}{#1}} 
    169 %\newcommand{\WARN} {{ \colorbox{yellow}{#1}} } 
    170  
    171  
    172  
    173 %%% index commands...................... 
    174 \usepackage{makeidx} 
    175 %\usepackage{showidx}            % show the index entry 
    176  
    177 \newcommand{\mdl} [1] {\textit{#1.F90}\index{Modules!#1}}         %module (mdl) 
    178 \newcommand{\rou} [1] {\textit{#1}\index{Routines!#1}}            %module (routine) 
    179 \newcommand{\hf} [1] {\textit{#1.h90}\index{h90 file!#1}}            %module (h90 files) 
    180 \newcommand{\ngn} [1] {\textit{#1}\index{Namelist Group Name!#1}}    %namelist name (nampar) 
    181 \newcommand{\np} [1] {\textit{#1}\index{Namelist variables!#1}}             %namelist variable 
    182 \newcommand{\jp} [1] {\textit{#1}\index{Model parameters!#1}}        %model parameter (jp) 
    183 \newcommand{\pp} [1] {\textit{#1}\index{Model parameters!#1}}        %namelist parameter (pp) 
    184 \newcommand{\ifile} [1] {\textit{#1.nc}\index{Input NetCDF files!#1.nc}}   %input NetCDF files (.nc) 
    185 \newcommand{\key} [1] {\textbf{key\_#1}\index{CPP keys!key\_#1}}  %key_cpp (key) 
    186 \newcommand{\NEMO} {\textit{NEMO}\xspace}                %NEMO (nemo) 
    187  
    188 %%%%   Bibliography   ............. 
    189 \usepackage[nottoc, notlof, notlot]{tocbibind} 
    190 \usepackage[square, comma]{natbib} 
    191 \bibpunct{[}{]}{,}{a}{}{;}                           %suppress "," after "et al." 
    192 \providecommand{\bibfont}{\small} 
    193  
     16\include{TexFiles/Top_Matter} 
    19417 
    19518% ================================================================ 
    196 % FRONT PAGE 
    197 % ================================================================ 
    198  
    199 %\usepackage{pstricks} 
    200 \title{ 
    201 %\psset{unit=1.1in,linewidth=4pt}   %parameters of the units for pstricks 
    202 % \rput(0,2){ \includegraphics[width=1.1\textwidth]{./TexFiles/Figures/logo_ALL.pdf}             } \\ 
    203 % \vspace{0.1cm} 
    204 \vspace{-6.0cm} 
    205 \includegraphics[width=1.1\textwidth]{./TexFiles/Figures/logo_ALL.pdf}\\ 
    206 \vspace{5.1cm} 
    207 \includegraphics[width=0.9\textwidth]{./TexFiles/Figures/NEMO_logo_Black.pdf} \\ 
    208 \vspace{1.4cm} 
    209 \rule{345pt}{1.5pt} \\ 
    210 \vspace{0.45cm} 
    211 {\Huge NEMO ocean engine} 
    212 \rule{345pt}{1.5pt} \\ 
    213  } 
    214 %{ -- Draft --}   } 
    215 %\date{\today} 
    216 \date{ 
    217 January 2016  \\ 
    218 {\small  -- version 3.6 stable --} \\ 
    219 ~  \\ 
    220 \textit{\small Note du P\^ole de mod\'{e}lisation de l'Institut Pierre-Simon Laplace No 27 }\\ 
    221 \vspace{0.45cm} 
    222 { ISSN No 1288-1619.} 
    223 } 
    224  
    225  
    226 \author{ 
    227 \Large Gurvan Madec, and the NEMO team  \\ 
    228  \texttt{\small gurvan.madec@locean-ipsl.umpc.fr} \\ 
    229  \texttt{\small nemo\_st@locean-ipsl.umpc.fr} \\ 
    230 %{\small Laboratoire d'Oc\'{e}anographie  et du Climat: Exp\'{e}rimentation et Approches Num\'{e}riques } 
    231 } 
    232  
    233 \dominitoc 
    234 \makeindex        %type this first :     makeindex -s NEMO.ist NEMO_book.idx 
    235  
    236 % ================================================================ 
    237 %      Include ONLY order 
    238 % ================================================================ 
    239  
    240 %\includeonly{./TexFiles/Chapters/Chap_MISC} 
    241 %\includeonly{./TexFiles/Chapters/Chap_ZDF} 
    242 %\includeonly{./TexFiles/Chapters/Chap_STP,./TexFiles/Chapters/Chap_SBC,./TexFiles/Chapters/Chap_TRA} 
    243 %\includeonly{./TexFiles/Chapters/Chap_LBC,./TexFiles/Chapters/Chap_MISC} 
    244 %\includeonly{./TexFiles/Chapters/Chap_Model_Basics} 
    245 %\includeonly{./TexFiles/Chapters/Annex_A,./TexFiles/Chapters/Annex_B,./TexFiles/Chapters/Annex_C,./TexFiles/Chapters/Annex_D} 
    246  
    247 % ================================================================ 
     19% DOCUMENT 
    24820% ================================================================ 
    24921 
    … …  
    26436% ================================================================ 
    26537 
    266 \include{./TexFiles/Chapters/Abstracts_Foreword} 
     38\subfile{TexFiles/Chapters/Abstracts_Foreword} 
    26739 
    26840% ================================================================ 
    … …  
    27042% ================================================================ 
    27143 
    272 \include{./TexFiles/Chapters/Introduction} 
     44\subfile{TexFiles/Chapters/Introduction} 
    27345 
    27446% ================================================================ 
    … …  
    27648% ================================================================ 
    27749 
    278 \include{./TexFiles/Chapters/Chap_Model_Basics} 
     50\subfile{TexFiles/Chapters/Chap_Model_Basics} 
    27951 
    280 \include{./TexFiles/Chapters/Chap_STP}       % Time discretisation (time stepping strategy) 
     52\subfile{TexFiles/Chapters/Chap_STP}         % Time discretisation (time stepping strategy) 
    28153 
    282 \include{./TexFiles/Chapters/Chap_DOM}       % Space discretisation 
     54\subfile{TexFiles/Chapters/Chap_DOM}         % Space discretisation 
    28355 
    284 \include{./TexFiles/Chapters/Chap_TRA}       % Tracer advection/diffusion equation 
     56\subfile{TexFiles/Chapters/Chap_TRA}         % Tracer advection/diffusion equation 
    28557 
    286 \include{./TexFiles/Chapters/Chap_DYN}       % Dynamics : momentum equation 
     58\subfile{TexFiles/Chapters/Chap_DYN}         % Dynamics : momentum equation 
    28759 
    288 \include{./TexFiles/Chapters/Chap_SBC}       % Surface Boundary Conditions 
     60\subfile{TexFiles/Chapters/Chap_SBC}         % Surface Boundary Conditions 
    28961 
    290 \include{./TexFiles/Chapters/Chap_LBC}       % Lateral Boundary Conditions 
     62\subfile{TexFiles/Chapters/Chap_LBC}         % Lateral Boundary Conditions 
    29163 
    292 \include{./TexFiles/Chapters/Chap_LDF}       % Lateral diffusion 
     64\subfile{TexFiles/Chapters/Chap_LDF}         % Lateral diffusion 
    29365 
    294 \include{./TexFiles/Chapters/Chap_ZDF}       % Vertical diffusion 
     66\subfile{TexFiles/Chapters/Chap_ZDF}         % Vertical diffusion 
    29567 
    296 \include{./TexFiles/Chapters/Chap_DIA}       % Outputs and Diagnostics 
     68\subfile{TexFiles/Chapters/Chap_DIA}         % Outputs and Diagnostics 
    29769 
    298 \include{./TexFiles/Chapters/Chap_OBS}          % Observation operator 
     70\subfile{TexFiles/Chapters/Chap_OBS}                    % Observation operator 
    29971 
    300 \include{./TexFiles/Chapters/Chap_ASM}          % Assimilation increments 
     72\subfile{TexFiles/Chapters/Chap_ASM}                    % Assimilation increments 
    30173 
    302 \include{./TexFiles/Chapters/Chap_STO}          % Stochastic param. 
     74\subfile{TexFiles/Chapters/Chap_STO}                    % Stochastic param. 
    30375 
    304 \include{./TexFiles/Chapters/Chap_MISC}         % Miscellaneous topics 
     76\subfile{TexFiles/Chapters/Chap_MISC}        % Miscellaneous topics 
    30577 
    306 \include{./TexFiles/Chapters/Chap_CFG}       % Predefined configurations 
     78\subfile{TexFiles/Chapters/Chap_CFG}         % Predefined configurations 
    30779 
    30880% ================================================================ 
    … …  
    31284\appendix 
    31385 
    314 %\include{./TexFiles/Chapters/Chap_Conservation} 
    315 \include{./TexFiles/Chapters/Annex_A}        % generalised vertical coordinate 
    316 \include{./TexFiles/Chapters/Annex_B}        % diffusive operator 
    317 \include{./TexFiles/Chapters/Annex_C}        % Discrete invariants of the eqs. 
    318 \include{./TexFiles/Chapters/Annex_ISO}                     % Isoneutral diffusion using triads 
    319 \include{./TexFiles/Chapters/Annex_D}        % Coding rules 
    320 %\include{./TexFiles/Chapters/Annex_E}                   % Notes on some on going staff (no included in the DOC) 
    321 %\include{./TexFiles/Chapters/Annex_Fox-Kemper}   % Notes on Fox-Kemper (no included in the DOC) 
    322 %\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) 
    32395 
    32496% ================================================================ 
    … …  
    334106 
    335107%%\bibliographystyle{plainat} 
    336 \bibliographystyle{./TexFiles/ametsoc}    % AMS biblio style (JPO) 
    337 \bibliography{./TexFiles/Biblio/Biblio} 
     108\bibliographystyle{TexFiles/Styles/ametsoc}     % AMS biblio style (JPO) 
     109\bibliography{TexFiles/Bibliography/Biblio} 
    338110 
    339111% ================================================================ 

  • branches/2015/nemo_v3_6_STABLE/DOC/NEMO_coding.conv.tex

    r2738 r6992  
    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/2015/nemo_v3_6_STABLE/DOC/Namelists/nambdy

    r6377 r6992  
    22&nambdy        !  unstructured open boundaries                          ("key_bdy") 
    33!----------------------------------------------------------------------- 
    4     nb_bdy = 2                               !  number of open boundary sets        
    5     ln_coords_file = .true.,.false.          !  =T : read bdy coordinates from file 
    6     cn_coords_file = 'coordinates.bdy.nc','' !  bdy coordinates files 
    7     ln_mask_file = .false.                   !  =T : read mask from file 
    8     cn_mask_file = ''                        !  name of mask file (if ln_mask_file=.TRUE.) 
    9     cn_dyn2d       = 'none','none'           ! 
    10     nn_dyn2d      =  2, 0                    !  boundary conditions for barotropic fields 
    11     nn_dyn2d_dta  =  3, 0                    !  = 0, bdy data are equal to the initial state 
    12                                              !  = 1, bdy data are read in 'bdydata   .nc' files 
    13                                              !  = 2, use tidal harmonic forcing data from files 
    14                                              !  = 3, use external data AND tidal harmonic forcing 
    15     cn_dyn3d      =  'none',' none'          ! 
    16     nn_dyn3d      =  0, 0                    !  boundary conditions for baroclinic velocities 
    17     nn_dyn3d_dta  =  0, 0                    !  = 0, bdy data are equal to the initial state 
    18                                              !  = 1, bdy data are read in 'bdydata   .nc' files 
    19     cn_tra        =  'none', 'none'          ! 
    20     nn_tra_dta    =  1, 1                    !  = 0, bdy data are equal to the initial state 
    21                                              !  = 1, bdy data are read in 'bdydata   .nc' files 
    22     cn_ice_lim      =  'none','none'         ! 
    23     nn_ice_lim_dta  =  0, 0                  !  = 0, bdy data are equal to the initial state 
    24                                              !  = 1, bdy data are read in 'bdydata   .nc' files 
    25     rn_ice_tem      = 270., 270.             !  lim3 only: arbitrary temperature of incoming sea ice 
    26     rn_ice_sal      = 10.,  10.              !  lim3 only:      --   salinity           -- 
    27     rn_ice_age      = 30., 30.               !  lim3 only:      --   age                -- 
    28     ln_tra_dmp    = .false.,.false.          !  open boudaries conditions for tracers 
    29     ln_dyn3d_dmp  = .false.,.false.          !  open boundary condition for baroclinic velocities 
    30     rn_time_dmp   =  1., 1.                  ! Damping time scale in days 
    31     rn_time_dmp_out =  1., 1.                ! Outflow damping time scale 
    32     nn_rimwidth  = 10, 5                     !  width of the relaxation zone 
    33     ln_vol     = .false.                     !  total volume correction (see nn_volctl parameter) 
    34     nn_volctl  = 1                           !  = 0, the total water flux across open boundaries is zero 
     4    nb_bdy         = 0                    !  number of open boundary sets 
     5    ln_coords_file = .true.               !  =T : read bdy coordinates from file 
     6    cn_coords_file = 'coordinates.bdy.nc' !  bdy coordinates files 
     7    ln_mask_file   = .false.              !  =T : read mask from file 
     8    cn_mask_file   = ''                   !  name of mask file (if ln_mask_file=.TRUE.) 
     9    cn_dyn2d       = 'none'               ! 
     10    nn_dyn2d_dta   =  0                   !  = 0, bdy data are equal to the initial state 
     11                                          !  = 1, bdy data are read in 'bdydata   .nc' files 
     12                                          !  = 2, use tidal harmonic forcing data from files 
     13                                          !  = 3, use external data AND tidal harmonic forcing 
     14    cn_dyn3d      =  'none'               ! 
     15    nn_dyn3d_dta  =  0                    !  = 0, bdy data are equal to the initial state 
     16                                          !  = 1, bdy data are read in 'bdydata   .nc' files 
     17    cn_tra        =  'none'               ! 
     18    nn_tra_dta    =  0                    !  = 0, bdy data are equal to the initial state 
     19                                          !  = 1, bdy data are read in 'bdydata   .nc' files 
     20    cn_ice_lim      =  'none'             ! 
     21    nn_ice_lim_dta  =  0                  !  = 0, bdy data are equal to the initial state 
     22                                          !  = 1, bdy data are read in 'bdydata   .nc' files 
     23    rn_ice_tem      = 270.                !  lim3 only: arbitrary temperature of incoming sea ice 
     24    rn_ice_sal      = 10.                 !  lim3 only:      --   salinity           -- 
     25    rn_ice_age      = 30.                 !  lim3 only:      --   age                -- 
     26 
     27    ln_tra_dmp    =.false.                !  open boudaries conditions for tracers 
     28    ln_dyn3d_dmp  =.false.                !  open boundary condition for baroclinic velocities 
     29    rn_time_dmp   =  1.                   ! Damping time scale in days 
     30    rn_time_dmp_out =  1.                 ! Outflow damping time scale 
     31    nn_rimwidth   = 10                    !  width of the relaxation zone 
     32    ln_vol        = .false.               !  total volume correction (see nn_volctl parameter) 
     33    nn_volctl     = 1                     !  = 0, the total water flux across open boundaries is zero 
    3534/ 

  • branches/2015/nemo_v3_6_STABLE/DOC/Namelists/nambdy_dta

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  • branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Abstracts_Foreword.tex

    r6275 r6992  
     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}rature 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} 

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    r3294 r6992  
     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/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Annex_B.tex

    r3294 r6992  
     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/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Annex_C.tex

    r6275 r6992  
     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/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Annex_D.tex

    r6275 r6992  
     1%\documentclass[NEMO_book]{subfiles} 
     2%\begin{document} 
    13% ================================================================ 
    24% Appendix D Ñ Coding Rules 
    … …  
    202204 
    203205To be done.... 
     206%\end{document} 

  • branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Annex_E.tex

    r3294 r6992  
     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/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Annex_ISO.tex

    r4147 r6992  
     1%\documentclass[NEMO_book]{subfiles} 
     2%\begin{document} 
    13% ================================================================ 
    24% Iso-neutral diffusion : 
    … …  
    201203% >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    202204\begin{figure}[h] \begin{center} 
    203     \includegraphics[width=1.05\textwidth]{./TexFiles/Figures/Fig_GRIFF_triad_fluxes} 
     205    \includegraphics[width=1.05\textwidth]{Fig_GRIFF_triad_fluxes} 
    204206    \caption{ \label{fig:triad:ISO_triad} 
    205207      (a) Arrangement of triads $S_i$ and tracer gradients to 
    … …  
    269271% >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    270272\begin{figure}[h] \begin{center} 
    271     \includegraphics[width=0.80\textwidth]{./TexFiles/Figures/Fig_GRIFF_qcells} 
     273    \includegraphics[width=0.80\textwidth]{Fig_GRIFF_qcells} 
    272274    \caption{   \label{fig:triad:qcells} 
    273275    Triad notation for quarter cells. $T$-cells are inside 
    … …  
    676678% >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    677679\begin{figure}[h] \begin{center} 
    678     \includegraphics[width=0.60\textwidth]{./TexFiles/Figures/Fig_GRIFF_bdry_triads} 
     680    \includegraphics[width=0.60\textwidth]{Fig_GRIFF_bdry_triads} 
    679681    \caption{  \label{fig:triad:bdry_triads} 
    680682      (a) Uppermost model layer $k=1$ with $i,1$ and $i+1,1$ tracer 
    … …  
    849851    different $i_p,k_p$, denoted by different colours, (e.g. the green 
    850852    triad $i_p=1/2,k_p=-1/2$) are tapered to the appropriate basal triad.}} 
    851   {\includegraphics[width=0.60\textwidth]{./TexFiles/Figures/Fig_GRIFF_MLB_triads}} 
     853  {\includegraphics[width=0.60\textwidth]{Fig_GRIFF_MLB_triads}} 
    852854\end{figure} 
    853855% >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    … …  
    11931195\end{split} 
    11941196\end{equation} 
     1197%\end{document} 

  • branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_ASM.tex

    r4147 r6992  
     1%\documentclass[NEMO_book]{subfiles} 
     2%\begin{document} 
    13% ================================================================ 
    24% Chapter Assimilation increments (ASM) 
    … …  
    172174\end{verbatim} 
    173175\end{alltt} 
     176%\end{document} 

  • branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_CFG.tex

    r4147 r6992  
     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/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_Conservation.tex

    r3294 r6992  
     1%\documentclass[NEMO_book]{subfiles} 
     2%\begin{document} 
    13 
    24% ================================================================ 
    … …  
    333335not been implemented. 
    334336 
     337%\end{document} 

  • branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_DIA.tex

    r6275 r6992  
     1%\documentclass[NEMO_book]{subfiles} 
     2%\begin{document} 
    13% ================================================================ 
    24% Chapter I/O & Diagnostics 
    … …  
    14781480- the turbocline depth (based on a turbulent mixing coefficient criterion) (\mdl{diahth}) 
    14791481 
    1480 - the depth of the 20\deg C isotherm (\mdl{diahth}) 
     1482- the depth of the 20\degC isotherm (\mdl{diahth}) 
    14811483 
    14821484- the depth of the thermocline (maximum of the vertical temperature gradient) (\mdl{diahth}) 
    … …  
    14861488\np{ln\_diaptr} to true (see the \textit{\ngn{namptr} } namelist below).   
    14871489When \np{ln\_subbas}~=~true, transports and stream function are computed  
    1488 for the Atlantic, Indian, Pacific and Indo-Pacific Oceans (defined north of 30\deg S)  
     1490for the Atlantic, Indian, Pacific and Indo-Pacific Oceans (defined north of 30\degS)  
    14891491as well as for the World Ocean. The sub-basin decomposition requires an input file  
    14901492(\ifile{subbasins}) which contains three 2D mask arrays, the Indo-Pacific mask  
    … …  
    14961498%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    14971499\begin{figure}[!t]     \begin{center} 
    1498 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_mask_subasins.pdf} 
     1500\includegraphics[width=1.0\textwidth]{Fig_mask_subasins} 
    14991501\caption{   \label{Fig_mask_subasins} 
    15001502Decomposition of the World Ocean (here ORCA2) into sub-basin used in to compute 
    … …  
    16821684 
    16831685 
     1686%\end{document} 

  • branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_DOM.tex

    r6396 r6992  
     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,  
    … …  
    210212%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    211213\begin{figure}[!tb]  \begin{center} 
    212 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_index_hor.pdf} 
     214\includegraphics[width=0.90\textwidth]{Fig_index_hor} 
    213215\caption{   \label{Fig_index_hor}     
    214216Horizontal integer indexing used in the \textsc{Fortran} code. The dashed area indicates  
    … …  
    260262%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    261263\begin{figure}[!pt]    \begin{center} 
    262 \includegraphics[width=.90\textwidth]{./TexFiles/Figures/Fig_index_vert.pdf} 
     264\includegraphics[width=.90\textwidth]{Fig_index_vert} 
    263265\caption{ \label{Fig_index_vert}      
    264266Vertical integer indexing used in the \textsc{Fortran } code. Note that  
    … …  
    358360%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    359361\begin{figure}[!t]     \begin{center} 
    360 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_zgr_e3.pdf} 
     362\includegraphics[width=0.90\textwidth]{Fig_zgr_e3} 
    361363\caption{ \label{Fig_zgr_e3}     
    362364Comparison of (a) traditional definitions of grid-point position and grid-size in the vertical,  
    … …  
    467469%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    468470\begin{figure}[!tb]    \begin{center} 
    469 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_z_zps_s_sps.pdf} 
     471\includegraphics[width=1.0\textwidth]{Fig_z_zps_s_sps} 
    470472\caption{  \label{Fig_z_zps_s_sps}    
    471473The ocean bottom as seen by the model:  
    … …  
    578580%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    579581\begin{figure}[!tb]    \begin{center} 
    580 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_zgr.pdf} 
     582\includegraphics[width=0.90\textwidth]{Fig_zgr} 
    581583\caption{ \label{Fig_zgr}     
    582584Default vertical mesh for ORCA2: 30 ocean levels (L30). Vertical level functions for  
    … …  
    802804%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    803805\begin{figure}[!ht]    \begin{center} 
    804 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_sco_function.pdf} 
     806\includegraphics[width=1.0\textwidth]{Fig_sco_function} 
    805807\caption{  \label{Fig_sco_function}    
    806808Examples of the stretching function applied to a seamount; from left to right:  
    … …  
    842844%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    843845\begin{figure}[!ht] 
    844    \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/FIG_DOM_compare_coordinates_surface.pdf} 
     846   \includegraphics[width=1.0\textwidth]{FIG_DOM_compare_coordinates_surface} 
    845847        \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.} 
    846848    \label{fig_compare_coordinates_surface} 
    … …  
    939941(typical of the tropical ocean), see \rou{istate\_t\_s} subroutine called from \mdl{istate} module. 
    940942\end{description} 
     943%\end{document} 

  • branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_DYN.tex

    r6396 r6992  
     1%\documentclass[NEMO_book]{subfiles} 
     2%\begin{document} 
    13% ================================================================ 
    24% Chapter ——— Ocean Dynamics (DYN) 
    … …  
    293295%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    294296\begin{figure}[!ht]    \begin{center} 
    295 \includegraphics[width=0.70\textwidth]{./TexFiles/Figures/Fig_DYN_een_triad.pdf} 
     297\includegraphics[width=0.70\textwidth]{Fig_DYN_een_triad} 
    296298\caption{ \label{Fig_DYN_een_triad}   
    297299Triads used in the energy and enstrophy conserving scheme (een) for  
    … …  
    660662$\bullet$ The main hypothesis to compute the ice shelf load is that the ice shelf is in isostatic equilibrium. 
    661663 The top pressure is computed integrating a reference density profile (prescribed as density of a water at 34.4  
    662 PSU and -1.9$\degres C$) from the sea surface to the ice shelf base, which corresponds to the load of the water 
     664PSU and -1.9$^{\circ}C$) from the sea surface to the ice shelf base, which corresponds to the load of the water 
    663665column in which the ice shelf is floatting. This top pressure is constant over time. A detailed description of  
    664666this method is described in \citet{Losch2008}.\\ 
    … …  
    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  
    … …  
    13321334 
    13331335% ================================================================ 
     1336%\end{document} 

  • branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_LBC.tex

    r6275 r6992  
     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 ($rn\_shlat=2$)  
    … …  
    195197%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    196198\begin{figure}[!t]     \begin{center} 
    197 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_LBC_jperio.pdf} 
     199\includegraphics[width=1.0\textwidth]{Fig_LBC_jperio} 
    198200\caption{    \label{Fig_LBC_jperio} 
    199201setting of (a) east-west cyclic  (b) symmetric across the equator boundary conditions.} 
    … …  
    214216%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    215217\begin{figure}[!t]    \begin{center} 
    216 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_North_Fold_T.pdf} 
     218\includegraphics[width=0.90\textwidth]{Fig_North_Fold_T} 
    217219\caption{    \label{Fig_North_Fold_T}  
    218220North fold boundary with a $T$-point pivot and cyclic east-west boundary condition  
    … …  
    277279%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    278280\begin{figure}[!t]    \begin{center} 
    279 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_mpp.pdf} 
     281\includegraphics[width=0.90\textwidth]{Fig_mpp} 
    280282\caption{   \label{Fig_mpp}  
    281283Positioning of a sub-domain when massively parallel processing is used. } 
    … …  
    351353%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    352354\begin{figure}[!ht]     \begin{center} 
    353 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_mppini2.pdf} 
     355\includegraphics[width=0.90\textwidth]{Fig_mppini2} 
    354356\caption {    \label{Fig_mppini2} 
    355357Example of Atlantic domain defined for the CLIPPER projet. Initial grid is  
    … …  
    582584%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    583585\begin{figure}[!t]      \begin{center} 
    584 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_LBC_bdy_geom.pdf} 
     586\includegraphics[width=1.0\textwidth]{Fig_LBC_bdy_geom} 
    585587\caption {      \label{Fig_LBC_bdy_geom} 
    586588Example of geometry of unstructured open boundary} 
    … …  
    623625%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    624626\begin{figure}[!t]     \begin{center} 
    625 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_LBC_nc_header.pdf} 
     627\includegraphics[width=1.0\textwidth]{Fig_LBC_nc_header} 
    626628\caption {     \label{Fig_LBC_nc_header}  
    627629Example of the header for a coordinates.bdy.nc file} 
    … …  
    660662 
    661663 
     664%\end{document} 

  • branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_LDF.tex

    r6303 r6992  
     1%\documentclass[NEMO_book]{subfiles} 
     2%\begin{document} 
    13 
    24% ================================================================ 
    … …  
    105107Other formulations can be introduced by the user for a given configuration.  
    106108For example, in the ORCA2 global ocean model (see Configurations), the laplacian  
    107 viscosity operator uses \np{rn\_ahm\_0\_lap}~= 4.10$^4$ m$^2$/s poleward of 20$^{\circ}$  
     109viscosity operator uses \np{rn\_ahm\_0\_lap}~= 4.10$^4$ m$^2$/s poleward of 20\deg  
    108110north and south and decreases linearly to \np{rn\_aht\_0}~= 2.10$^3$ m$^2$/s  
    109111at the equator \citep{Madec_al_JPO96, Delecluse_Madec_Bk00}. This modification  
    … …  
    231233values are $0$). However, the technique used to compute the isopycnal  
    232234slopes is intended to get rid of such a background diffusion, since it introduces  
    233 spurious diapycnal diffusion (see {\S\ref{LDF_slp}). 
     235spurious diapycnal diffusion (see \S\ref{LDF_slp}). 
    234236 
    235237(4) when an eddy induced advection term is used (\key{traldf\_eiv}), $A^{eiv}$,  
    … …  
    444446%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    445447\begin{figure}[!ht]      \begin{center} 
    446 \includegraphics[width=0.70\textwidth]{./TexFiles/Figures/Fig_LDF_ZDF1.pdf} 
     448\includegraphics[width=0.70\textwidth]{Fig_LDF_ZDF1} 
    447449\caption {    \label{Fig_LDF_ZDF1} 
    448450averaging procedure for isopycnal slope computation.} 
    … …  
    472474%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    473475\begin{figure}[!ht]     \begin{center} 
    474 \includegraphics[width=0.70\textwidth]{./TexFiles/Figures/Fig_eiv_slp.pdf} 
     476\includegraphics[width=0.70\textwidth]{Fig_eiv_slp} 
    475477\caption {     \label{Fig_eiv_slp} 
    476478Vertical profile of the slope used for lateral mixing in the mixed layer :  
    … …  
    514516diffusion along model level surfaces, i.e. using the shear computed along  
    515517the model levels and with no additional friction at the ocean bottom (see  
    516 {\S\ref{LBC_coast}). 
     518\S\ref{LBC_coast}). 
    517519 
    518520 
    … …  
    555557 
    556558 
     559%\end{document} 

  • branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_MISC.tex

    r6275 r6992  
     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  
    … …  
    194196%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    195197\begin{figure}[!ht]    \begin{center} 
    196 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_LBC_zoom.pdf} 
     198\includegraphics[width=0.90\textwidth]{Fig_LBC_zoom} 
    197199\caption{   \label{Fig_LBC_zoom} 
    198200Position of a model domain compared to the data input domain when the zoom functionality is used.} 
    … …  
    632634 
    633635 
     636%\end{document} 

  • branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_Model_Basics.tex

    r6322 r6992  
     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  
    … …  
    811813%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    812814\begin{figure}[!b]    \begin{center} 
    813 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_z_zstar.pdf} 
     815\includegraphics[width=1.0\textwidth]{Fig_z_zstar} 
    814816\caption{   \label{Fig_z_zstar}  
    815817(a) $z$-coordinate in linear free-surface case ;  
    … …  
    12801282\end{equation} 
    12811283 
     1284%\end{document} 

  • branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_Model_Basics_zstar.tex

    r6275 r6992  
     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/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_OBS.tex

    r4245 r6992  
     1%\documentclass[NEMO_book]{subfiles} 
     2%\begin{document} 
    13% ================================================================ 
    24% Chapter observation operator (OBS) 
    … …  
    732734%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    733735\begin{figure}      \begin{center} 
    734 \includegraphics[width=10cm,height=12cm,angle=-90.]{./TexFiles/Figures/Fig_ASM_obsdist_local} 
     736\includegraphics[width=10cm,height=12cm,angle=-90.]{Fig_ASM_obsdist_local} 
    735737\caption{      \label{fig:obslocal} 
    736738Example of the distribution of observations with the geographical distribution of observational data.}  
    … …  
    759761%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    760762\begin{figure}     \begin{center} 
    761 \includegraphics[width=10cm,height=12cm,angle=-90.]{./TexFiles/Figures/Fig_ASM_obsdist_global} 
     763\includegraphics[width=10cm,height=12cm,angle=-90.]{Fig_ASM_obsdist_global} 
    762764\caption{      \label{fig:obsglobal} 
    763765Example of the distribution of observations with the round-robin distribution of observational data.} 
    … …  
    13761378%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    13771379\begin{figure}     \begin{center} 
    1378 %\includegraphics[width=10cm,height=12cm,angle=-90.]{./TexFiles/Figures/Fig_OBS_dataplot_main} 
    1379 \includegraphics[width=9cm,angle=-90.]{./TexFiles/Figures/Fig_OBS_dataplot_main} 
     1380%\includegraphics[width=10cm,height=12cm,angle=-90.]{Fig_OBS_dataplot_main} 
     1381\includegraphics[width=9cm,angle=-90.]{Fig_OBS_dataplot_main} 
    13801382\caption{      \label{fig:obsdataplotmain} 
    13811383Main window of dataplot.} 
    … …  
    13881390%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    13891391\begin{figure}     \begin{center} 
    1390 %\includegraphics[width=10cm,height=12cm,angle=-90.]{./TexFiles/Figures/Fig_OBS_dataplot_prof} 
    1391 \includegraphics[width=7cm,angle=-90.]{./TexFiles/Figures/Fig_OBS_dataplot_prof} 
     1392%\includegraphics[width=10cm,height=12cm,angle=-90.]{Fig_OBS_dataplot_prof} 
     1393\includegraphics[width=7cm,angle=-90.]{Fig_OBS_dataplot_prof} 
    13921394\caption{      \label{fig:obsdataplotprofile} 
    13931395Profile plot from dataplot produced by right clicking on a point in the main window.} 
    … …  
    13981400 
    13991401 
     1402%\end{document} 

  • branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_SBC.tex

    r6396 r6992  
     1%\documentclass[NEMO_book]{subfiles} 
     2%\begin{document} 
    13% ================================================================ 
    24% Chapter —— Surface Boundary Condition (SBC, ISF, ICB)  
    … …  
    952954%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    953955\begin{figure}[!h]    \begin{center} 
    954 \includegraphics[width=0.8\textwidth]{./TexFiles/Figures/Fig_SBC_isf.pdf} 
     956\includegraphics[width=0.8\textwidth]{Fig_SBC_isf} 
    955957\caption{ \label{Fig_SBC_isf} 
    956958Schematic for all the options available trough \np{nn\_isf}.} 
    … …  
    11291131%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    11301132\begin{figure}[!t]    \begin{center} 
    1131 \includegraphics[width=0.8\textwidth]{./TexFiles/Figures/Fig_SBC_diurnal.pdf} 
     1133\includegraphics[width=0.8\textwidth]{Fig_SBC_diurnal} 
    11321134\caption{ \label{Fig_SBC_diurnal}     
    11331135Example of recontruction of the diurnal cycle variation of short wave flux   
    … …  
    11621164%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    11631165\begin{figure}[!t]  \begin{center} 
    1164 \includegraphics[width=0.7\textwidth]{./TexFiles/Figures/Fig_SBC_dcy.pdf} 
     1166\includegraphics[width=0.7\textwidth]{Fig_SBC_dcy} 
    11651167\caption{ \label{Fig_SBC_dcy}    
    11661168Example of recontruction of the diurnal cycle variation of short wave flux   
    … …  
    13571359 
    13581360 
     1361%\end{document} 

  • branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_STO.tex

    r6307 r6992  
     1%\documentclass[NEMO_book]{subfiles} 
     2%\begin{document} 
    13% ================================================================ 
    24% Chapter stochastic parametrization of EOS (STO) 
    … …  
    157159 
    158160 
     161%\end{document} 

  • branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_STP.tex

    r4147 r6992  
     1%\documentclass[NEMO_book]{subfiles} 
     2%\begin{document} 
    13 
    24% ================================================================ 
    … …  
    196198%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    197199\begin{figure}[!t]     \begin{center} 
    198 \includegraphics[width=0.7\textwidth]{./TexFiles/Figures/Fig_TimeStepping_flowchart.pdf} 
     200\includegraphics[width=0.7\textwidth]{Fig_TimeStepping_flowchart} 
    199201\caption{   \label{Fig_TimeStep_flowchart} 
    200202Sketch of the leapfrog time stepping sequence in \NEMO from \citet{Leclair_Madec_OM09}.  
    … …  
    288290%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    289291\begin{figure}[!t]     \begin{center} 
    290 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_MLF_forcing.pdf} 
     292\includegraphics[width=0.90\textwidth]{Fig_MLF_forcing} 
    291293\caption{   \label{Fig_MLF_forcing} 
    292294Illustration of forcing integration methods.  
    … …  
    424426} 
    425427%% 
     428%\end{document} 

  • branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_TRA.tex

    r6322 r6992  
     1%\documentclass[NEMO_book]{subfiles} 
     2%\begin{document} 
    13% ================================================================ 
    24% Chapter 1 ——— Ocean Tracers (TRA) 
    … …  
    8991%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    9092\begin{figure}[!t]    \begin{center} 
    91 \includegraphics[width=0.9\textwidth]{./TexFiles/Figures/Fig_adv_scheme.pdf} 
     93\includegraphics[width=0.9\textwidth]{Fig_adv_scheme} 
    9294\caption{   \label{Fig_adv_scheme}  
    9395Schematic representation of some ways used to evaluate the tracer value  
    … …  
    778780%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    779781\begin{figure}[!t]     \begin{center} 
    780 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_TRA_Irradiance.pdf} 
     782\includegraphics[width=1.0\textwidth]{Fig_TRA_Irradiance} 
    781783\caption{    \label{Fig_traqsr_irradiance} 
    782784Penetration profile of the downward solar irradiance calculated by four models.  
    … …  
    799801%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    800802\begin{figure}[!t]     \begin{center} 
    801 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_TRA_geoth.pdf} 
     803\includegraphics[width=1.0\textwidth]{Fig_TRA_geoth} 
    802804\caption{   \label{Fig_geothermal} 
    803805Geothermal Heat flux (in $mW.m^{-2}$) used by \cite{Emile-Geay_Madec_OS09}. 
    … …  
    909911%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    910912\begin{figure}[!t]   \begin{center} 
    911 \includegraphics[width=0.7\textwidth]{./TexFiles/Figures/Fig_BBL_adv.pdf} 
     913\includegraphics[width=0.7\textwidth]{Fig_BBL_adv} 
    912914\caption{   \label{Fig_bbl}   
    913915Advective/diffusive Bottom Boundary Layer. The BBL parameterisation is  
    … …  
    10671069The restoration coefficient can be set to zero in equatorial regions by specifying a positive value of \np{nn\_hdmp}.  
    10681070Equatorward of this latitude the restoration coefficient will be zero with a smooth transition to  
    1069 the full values of a 10$^{\circ}$ latitud band.  
     1071the full values of a 10\deg latitud band.  
    10701072This is often used because of the short adjustment time scale in the equatorial region  
    10711073\citep{Reverdin1991, Fujio1991, Marti_PhD92}. The time scale associated with the damping depends on the depth as a  
    … …  
    11671169rational function approximation for hydrographic data analysis  \citep{TEOS10}.  
    11681170A key point is that conservative state variables are used:  
    1169 Absolute Salinity (unit: g/kg, notation: $S_A$) and Conservative Temperature (unit: $\degres C$, notation: $\Theta$). 
     1171Absolute Salinity (unit: g/kg, notation: $S_A$) and Conservative Temperature (unit: \degC, notation: $\Theta$). 
    11701172The pressure in decibars is approximated by the depth in meters.  
    11711173With TEOS10, the specific heat capacity of sea water, $C_p$, is a constant. It is set to  
    1172 $C_p=3991.86795711963~J\,Kg^{-1}\,\degres K^{-1}$, according to \citet{TEOS10}. 
     1174$C_p=3991.86795711963~J\,Kg^{-1}\,^{\circ}K^{-1}$, according to \citet{TEOS10}. 
    11731175 
    11741176Choosing polyTEOS10-bsq implies that the state variables used by the model are  
    … …  
    11831185to accurately fit EOS80 (Roquet, personal comm.). The state variables used in both the EOS80  
    11841186and the ocean model are:  
    1185 the Practical Salinity ((unit: psu, notation: $S_p$)) and Potential Temperature (unit: $\degres C$, notation: $\theta$). 
     1187the Practical Salinity ((unit: psu, notation: $S_p$)) and Potential Temperature (unit: $^{\circ}C$, notation: $\theta$). 
    11861188The pressure in decibars is approximated by the depth in meters.   
    11871189With thsi EOS, the specific heat capacity of sea water, $C_p$, is a function of temperature,  
    … …  
    13051307%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    13061308\begin{figure}[!p]    \begin{center} 
    1307 \includegraphics[width=0.9\textwidth]{./TexFiles/Figures/Partial_step_scheme.pdf} 
     1309\includegraphics[width=0.9\textwidth]{Partial_step_scheme} 
    13081310\caption{   \label{Fig_Partial_step_scheme}  
    13091311Discretisation of the horizontal difference and average of tracers in the $z$-partial  
    … …  
    13841386 with $\widetilde {Z}_{T_k}$ the depth of the point $\widetilde {T}_{k}$ in case of $z^*$ coordinates  
    13851387(this term = 0 in z-coordinates) 
     1388%\end{document} 

  • branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_ZDF.tex

    r6322 r6992  
     1%\documentclass[NEMO_book]{subfiles} 
     2%\begin{document} 
    13% ================================================================ 
    24% Chapter  Vertical Ocean Physics (ZDF) 
    … …  
    233235%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    234236\begin{figure}[!t] \begin{center} 
    235 \includegraphics[width=1.00\textwidth]{./TexFiles/Figures/Fig_mixing_length.pdf} 
     237\includegraphics[width=1.00\textwidth]{Fig_mixing_length} 
    236238\caption{ \label{Fig_mixing_length}  
    237239Illustration of the mixing length computation. } 
    … …  
    407409%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    408410\begin{figure}[!t]   \begin{center} 
    409 \includegraphics[width=1.00\textwidth]{./TexFiles/Figures/Fig_ZDF_TKE_time_scheme.pdf} 
     411\includegraphics[width=1.00\textwidth]{Fig_ZDF_TKE_time_scheme} 
    410412\caption{ \label{Fig_TKE_time_scheme}  
    411413Illustration of the TKE time integration and its links to the momentum and tracer time integration. } 
    … …  
    586588value near physical boundaries (logarithmic boundary layer law). $C_{\mu}$ and $C_{\mu'}$  
    587589are calculated from stability function proposed by \citet{Galperin_al_JAS88}, or by \citet{Kantha_Clayson_1994}  
    588 or one of the two functions suggested by \citet{Canuto_2001}  (\np{nn\_stab\_func} = 0, 1, 2 or 3, resp.}).  
     590or one of the two functions suggested by \citet{Canuto_2001}  (\np{nn\_stab\_func} = 0, 1, 2 or 3, resp.).  
    589591The value of $C_{0\mu}$ depends of the choice of the stability function. 
    590592 
    … …  
    658660%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    659661\begin{figure}[!htb]    \begin{center} 
    660 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_npc.pdf} 
     662\includegraphics[width=0.90\textwidth]{Fig_npc} 
    661663\caption{  \label{Fig_npc}  
    662664Example of an unstable density profile treated by the non penetrative  
    … …  
    814816%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    815817\begin{figure}[!t]   \begin{center} 
    816 \includegraphics[width=0.99\textwidth]{./TexFiles/Figures/Fig_zdfddm.pdf} 
     818\includegraphics[width=0.99\textwidth]{Fig_zdfddm} 
    817819\caption{  \label{Fig_zdfddm} 
    818820From \citet{Merryfield1999} : (a) Diapycnal diffusivities $A_f^{vT}$  
    … …  
    11431145baroclinic and barotropic components which is appropriate when using either the 
    11441146explicit or filtered surface pressure gradient algorithms (\key{dynspg\_exp} or  
    1145 {\key{dynspg\_flt}). Extra attention is required, however, when using  
     1147\key{dynspg\_flt}). Extra attention is required, however, when using  
    11461148split-explicit time stepping (\key{dynspg\_ts}). In this case the free surface  
    11471149equation is solved with a small time step \np{rn\_rdt}/\np{nn\_baro}, while the three  
    … …  
    12581260%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    12591261\begin{figure}[!t]   \begin{center} 
    1260 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_ZDF_M2_K1_tmx.pdf} 
     1262\includegraphics[width=0.90\textwidth]{Fig_ZDF_M2_K1_tmx} 
    12611263\caption{  \label{Fig_ZDF_M2_K1_tmx}  
    12621264(a) M2 and (b) K1 internal wave drag energy from \citet{Carrere_Lyard_GRL03} ($W/m^2$). } 
    … …  
    13691371 
    13701372 
     1373%\end{document} 

  • branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Introduction.tex

    r6322 r6992  
     1%\documentclass[NEMO_book]{subfiles} 
     2%\begin{document} 
    13 
    24% ================================================================ 
    … …  
    290292 
    291293 
     294%\end{document} 

  • branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Styles/math_abbrev.sty

    r6982 r6992  
    1818\newcommand{\curl}{\nabla \times} % for curl 
    1919\newcommand{\pd}[2][]{\frac{\partial #1}{\partial #2}} 
    20 \def\deg{\degres}                            % degrees  (NB: \r{} can % % also be used) 
     20\def\deg{$^{\circ}$}                           % degrees  (NB: \r{} can % % also be used) 
     21\def\degC{$^{\circ}C$} 
     22\def\degK{$^{\circ}K$} 
     23\def\degN{$^{\circ}N$} 
     24\def\degS{$^{\circ}S$} 
    2125\newcommand{\alpbet} {\left(\alpha / \beta \right)}   % alpha/beta  for slp computation 
    2226\newcommand{\triad}[6][]{\ensuremath{{}_{#2}^{#3}{\mathbb{#4}_{#1}}_{#5}^{\,#6}}} 

  • branches/2015/nemo_v3_6_STABLE/DOC/namelist_split.sh

    • Property svn:executable set to *
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