Changeset 6997


Ignore:
Timestamp:
2016-10-05T16:26:13+02:00 (4 years ago)
Author:
nicolasmartin
Message:

Duplication of changes in DOC directory for the trunk

Location:
trunk/DOC
Files:
77 added
3 deleted
70 edited
3 copied
8 moved

Legend:

Unmodified
Added
Removed
  • trunk/DOC/NEMO_book.tex

    r6289 r6997  
    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% ================================================================ 
  • trunk/DOC/NEMO_coding.conv.tex

    r2738 r6997  
    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} \\ 
  • trunk/DOC/Namelists/nam_asminc

    r6289 r6997  
    11!----------------------------------------------------------------------- 
    2 &nam_asminc   !   assimilation increments                               ('key_asminc') 
     2&nam_asminc    !   assimilation increments                              ('key_asminc') 
    33!----------------------------------------------------------------------- 
    4     ln_bkgwri = .false.    !  Logical switch for writing out background state 
    5     ln_trainc = .false.    !  Logical switch for applying tracer increments 
    6     ln_dyninc = .false.    !  Logical switch for applying velocity increments 
    7     ln_sshinc = .false.    !  Logical switch for applying SSH increments 
    8     ln_asmdin = .false.    !  Logical switch for Direct Initialization (DI) 
    9     ln_asmiau = .false.    !  Logical switch for Incremental Analysis Updating (IAU) 
    10     nitbkg    = 0          !  Timestep of background in [0,nitend-nit000-1] 
    11     nitdin    = 0          !  Timestep of background for DI in [0,nitend-nit000-1] 
    12     nitiaustr = 1          !  Timestep of start of IAU interval in [0,nitend-nit000-1] 
    13     nitiaufin = 15         !  Timestep of end of IAU interval in [0,nitend-nit000-1] 
    14     niaufn    = 0          !  Type of IAU weighting function 
    15     ln_salfix = .false.    !  Logical switch for ensuring that the sa > salfixmin 
    16     salfixmin = -9999      !  Minimum salinity after applying the increments 
    17     nn_divdmp = 0          !  Number of iterations of divergence damping operator 
     4    ln_bkgwri  = .false.   !  Logical switch for writing out background state 
     5    ln_trainc  = .false.   !  Logical switch for applying tracer increments 
     6    ln_dyninc  = .false.   !  Logical switch for applying velocity increments 
     7    ln_sshinc  = .false.   !  Logical switch for applying SSH increments 
     8    ln_asmdin  = .false.   !  Logical switch for Direct Initialization (DI) 
     9    ln_asmiau  = .false.   !  Logical switch for Incremental Analysis Updating (IAU) 
     10    nitbkg     = 0         !  Timestep of background in [0,nitend-nit000-1] 
     11    nitdin     = 0         !  Timestep of background for DI in [0,nitend-nit000-1] 
     12    nitiaustr  = 1         !  Timestep of start of IAU interval in [0,nitend-nit000-1] 
     13    nitiaufin  = 15        !  Timestep of end of IAU interval in [0,nitend-nit000-1] 
     14    niaufn     = 0         !  Type of IAU weighting function 
     15    ln_salfix  = .false.   !  Logical switch for ensuring that the sa > salfixmin 
     16    salfixmin  = -9999     !  Minimum salinity after applying the increments 
     17    nn_divdmp  = 0         !  Number of iterations of divergence damping operator 
    1818/ 
  • trunk/DOC/Namelists/nam_dia25h

    r6289 r6997  
    11!----------------------------------------------------------------------- 
    2 &nam_dia25h  !  25h Mean Output 
     2&nam_dia25h    !  25h Mean Output                                        (default F) 
    33!----------------------------------------------------------------------- 
    4    ln_dia25h  = .false.    ! Choose 25h mean output or not 
     4   ln_dia25h   = .false.   ! Choose 25h mean output or not 
    55/ 
  • trunk/DOC/Namelists/nam_diaharm

    r6289 r6997  
    11!----------------------------------------------------------------------- 
    2 &nam_diaharm   !   Harmonic analysis of tidal constituents              ('key_diaharm') 
     2&nam_diaharm   !   Harmonic analysis of tidal constituents               ("key_diaharm") 
    33!----------------------------------------------------------------------- 
    44    nit000_han = 1         ! First time step used for harmonic analysis 
  • trunk/DOC/Namelists/nam_diatmb

    r6289 r6997  
    11!----------------------------------------------------------------------- 
    2 &nam_diatmb  !  Top Middle Bottom Output 
     2&nam_diatmb    !  Top Middle Bottom Output                               (default F) 
    33!----------------------------------------------------------------------- 
    4    ln_diatmb  = .false.    !  Choose Top Middle and Bottom output or not 
     4   ln_diatmb   = .false.   !  Choose Top Middle and Bottom output or not 
    55/ 
  • trunk/DOC/Namelists/nam_tide

    r6140 r6997  
    22&nam_tide      !   tide parameters                                      ("key_tide") 
    33!----------------------------------------------------------------------- 
    4    ln_tide_pot   = .true.   !  use tidal potential forcing 
    5    ln_tide_ramp  = .false.  ! 
    6    rdttideramp   =    0.    ! 
    7    clname(1)     = 'DUMMY'  !  name of constituent - all tidal components must be set in namelist_cfg 
     4   ln_tide_pot = .true.    !  use tidal potential forcing 
     5   ln_tide_ramp= .false.   ! 
     6   rdttideramp =    0.     ! 
     7   clname(1)   = 'DUMMY'   !  name of constituent - all tidal components must be set in namelist_cfg 
    88/ 
  • trunk/DOC/Namelists/nam_vvl

    r6289 r6997  
    66   ln_vvl_layer  = .false.          !  full layer vertical coordinate 
    77   ln_vvl_ztilde_as_zstar = .false. !  ztilde vertical coordinate emulating zstar 
    8    ln_vvl_zstar_at_eqtor = .false. !  ztilde near the equator 
     8   ln_vvl_zstar_at_eqtor  = .false. !  ztilde near the equator 
    99   rn_ahe3       = 0.0e0            !  thickness diffusion coefficient 
    1010   rn_rst_e3t    = 30.e0            !  ztilde to zstar restoration timescale [days] 
  • trunk/DOC/Namelists/nambbl

    r6140 r6997  
    22&nambbl        !   bottom boundary layer scheme                         ("key_trabbl") 
    33!----------------------------------------------------------------------- 
    4    nn_bbl_ldf  =  1      !  diffusive bbl (=1)   or not (=0) 
    5    nn_bbl_adv  =  0      !  advective bbl (=1/2) or not (=0) 
    6    rn_ahtbbl   =  1000.  !  lateral mixing coefficient in the bbl  [m2/s] 
    7    rn_gambbl   =  10.    !  advective bbl coefficient                 [s] 
     4   nn_bbl_ldf  =  1        !  diffusive bbl (=1)   or not (=0) 
     5   nn_bbl_adv  =  0        !  advective bbl (=1/2) or not (=0) 
     6   rn_ahtbbl   =  1000.    !  lateral mixing coefficient in the bbl  [m2/s] 
     7   rn_gambbl   =  10.      !  advective bbl coefficient                 [s] 
    88/ 
  • trunk/DOC/Namelists/nambdy_dta

    • Property svn:executable deleted
    r6140 r6997  
    22&nambdy_dta    !  open boundaries - external data                       ("key_bdy") 
    33!----------------------------------------------------------------------- 
    4 !              !  file name      ! frequency (hours) ! variable  ! time interp. !  clim   ! 'yearly'/ ! weights  ! rotation ! land/sea mask ! 
    5 !              !                 !  (if <0  months)  !   name    !  (logical)   !  (T/F ) ! 'monthly' ! filename ! pairing  ! filename      ! 
    6    bn_ssh =     'amm12_bdyT_u2d' ,         24        , 'sossheig',     .true.   , .false. ,  'daily'  ,    ''    ,   ''     , '' 
    7    bn_u2d =     'amm12_bdyU_u2d' ,         24        , 'vobtcrtx',     .true.   , .false. ,  'daily'  ,    ''    ,   ''     , '' 
    8    bn_v2d =     'amm12_bdyV_u2d' ,         24        , 'vobtcrty',     .true.   , .false. ,  'daily'  ,    ''    ,   ''     , '' 
    9    bn_u3d  =    'amm12_bdyU_u3d' ,         24        , 'vozocrtx',     .true.   , .false. ,  'daily'  ,    ''    ,   ''     , '' 
    10    bn_v3d  =    'amm12_bdyV_u3d' ,         24        , 'vomecrty',     .true.   , .false. ,  'daily'  ,    ''    ,   ''     , '' 
    11    bn_tem  =    'amm12_bdyT_tra' ,         24        , 'votemper',     .true.   , .false. ,  'daily'  ,    ''    ,   ''     , '' 
    12    bn_sal  =    'amm12_bdyT_tra' ,         24        , 'vosaline',     .true.   , .false. ,  'daily'  ,    ''    ,   ''     , '' 
     4!              !  file name      ! frequency (hours) ! variable  ! time interp.!  clim   ! 'yearly'/ ! weights  ! rotation ! land/sea mask ! 
     5!              !                 !  (if <0  months)  !   name    !  (logical)  !  (T/F ) ! 'monthly' ! filename ! pairing  ! filename      ! 
     6   bn_ssh      = 'amm12_bdyT_u2d',         24        , 'sossheig',    .true.   , .false. ,  'daily'  ,    ''    ,   ''     ,    '' 
     7   bn_u2d      = 'amm12_bdyU_u2d',         24        , 'vobtcrtx',    .true.   , .false. ,  'daily'  ,    ''    ,   ''     ,    '' 
     8   bn_v2d      = 'amm12_bdyV_u2d',         24        , 'vobtcrty',    .true.   , .false. ,  'daily'  ,    ''    ,   ''     ,    '' 
     9   bn_u3d      = 'amm12_bdyU_u3d',         24        , 'vozocrtx',    .true.   , .false. ,  'daily'  ,    ''    ,   ''     ,    '' 
     10   bn_v3d      = 'amm12_bdyV_u3d',         24        , 'vomecrty',    .true.   , .false. ,  'daily'  ,    ''    ,   ''     ,    '' 
     11   bn_tem      = 'amm12_bdyT_tra',         24        , 'votemper',    .true.   , .false. ,  'daily'  ,    ''    ,   ''     ,    '' 
     12   bn_sal      = 'amm12_bdyT_tra',         24        , 'vosaline',    .true.   , .false. ,  'daily'  ,    ''    ,   ''     ,    '' 
    1313! for lim2 
    14 !   bn_frld  =   'amm12_bdyT_ice' ,         24        , 'ileadfra',     .true.   , .false. ,  'daily'  ,    ''    ,   ''     , '' 
    15 !   bn_hicif =   'amm12_bdyT_ice' ,         24        , 'iicethic',     .true.   , .false. ,  'daily'  ,    ''    ,   ''     , '' 
    16 !   bn_hsnif =   'amm12_bdyT_ice' ,         24        , 'isnowthi',     .true.   , .false. ,  'daily'  ,    ''    ,   ''     , '' 
     14!   bn_frld    = 'amm12_bdyT_ice',         24        , 'ileadfra',    .true.   , .false. ,  'daily'  ,    ''    ,   ''     ,    '' 
     15!   bn_hicif   = 'amm12_bdyT_ice',         24        , 'iicethic',    .true.   , .false. ,  'daily'  ,    ''    ,   ''     ,    '' 
     16!   bn_hsnif   = 'amm12_bdyT_ice',         24        , 'isnowthi',    .true.   , .false. ,  'daily'  ,    ''    ,   ''     ,    '' 
    1717! for lim3 
    18 !   bn_a_i  =    'amm12_bdyT_ice' ,         24        , 'ileadfra',     .true.   , .false. ,  'daily'  ,    ''    ,   ''     , '' 
    19 !   bn_ht_i =    'amm12_bdyT_ice' ,         24        , 'iicethic',     .true.   , .false. ,  'daily'  ,    ''    ,   ''     , '' 
    20 !   bn_ht_s =    'amm12_bdyT_ice' ,         24        , 'isnowthi',     .true.   , .false. ,  'daily'  ,    ''    ,   ''     , '' 
     18!   bn_a_i     = 'amm12_bdyT_ice',         24        , 'ileadfra',    .true.   , .false. ,  'daily'  ,    ''    ,   ''     ,    '' 
     19!   bn_ht_i    = 'amm12_bdyT_ice',         24        , 'iicethic',    .true.   , .false. ,  'daily'  ,    ''    ,   ''     ,    '' 
     20!   bn_ht_s    = 'amm12_bdyT_ice',         24        , 'isnowthi',    .true.   , .false. ,  'daily'  ,    ''    ,   ''     ,    '' 
    2121 
    22    cn_dir      =    'bdydta/'  !  root directory for the location of the bulk files 
    23    ln_full_vel = .false.         
     22   cn_dir      = 'bdydta/' !  root directory for the location of the bulk files 
     23   ln_full_vel = .false.    
    2424/ 
  • trunk/DOC/Namelists/nambdy_tide

    r6289 r6997  
    11!----------------------------------------------------------------------- 
    2 &nambdy_tide     ! tidal forcing at open boundaries 
     2&nambdy_tide   ! tidal forcing at open boundaries 
    33!----------------------------------------------------------------------- 
    44   filtide          = 'bdydta/amm12_bdytide_'   !  file name root of tidal forcing files 
  • trunk/DOC/Namelists/namberg

    r6289 r6997  
    2727      rn_speed_limit           = 0.                   ! CFL speed limit for a berg 
    2828 
    29 !            ! file name ! frequency (hours) !   variable   ! time interp. !  clim   ! 'yearly'/ ! weights  ! rotation ! land/sea mask ! 
    30 !            !           !  (if <0  months)  !     name     !   (logical)  !  (T/F ) ! 'monthly' ! filename ! pairing  ! filename      ! 
    31       sn_icb =  'calving',       -1          , 'calvingmask',  .true.      , .true.  , 'yearly'  , ''       , ''       , '' 
     29!            ! file name ! frequency (hours) !   variable   ! time interp.!  clim   ! 'yearly'/ ! weights  ! rotation ! land/sea mask ! 
     30!            !           !  (if <0  months)  !     name     !  (logical)  !  (T/F ) ! 'monthly' ! filename ! pairing  ! filename      ! 
     31      sn_icb =  'calving',       -1          , 'calvingmask',   .true.    , .true.  , 'yearly'  ,    ''    ,    ''    ,    '' 
    3232 
    3333      cn_dir = './' 
  • trunk/DOC/Namelists/nambfr

    r6140 r6997  
    66   rn_bfri1    =    4.e-4  !  bottom drag coefficient (linear case) 
    77   rn_bfri2    =    1.e-3  !  bottom drag coefficient (non linear case). Minimum coeft if ln_loglayer=T 
    8    rn_bfri2_max =   1.e-1  !  max. bottom drag coefficient (non linear case and ln_loglayer=T) 
     8   rn_bfri2_max=    1.e-1  !  max. bottom drag coefficient (non linear case and ln_loglayer=T) 
    99   rn_bfeb2    =    2.5e-3 !  bottom turbulent kinetic energy background  (m2/s2) 
    1010   rn_bfrz0    =    3.e-3  !  bottom roughness [m] if ln_loglayer=T 
     
    1313   rn_tfri1    =    4.e-4  !  top drag coefficient (linear case) 
    1414   rn_tfri2    =    2.5e-3 !  top drag coefficient (non linear case). Minimum coeft if ln_loglayer=T 
    15    rn_tfri2_max =   1.e-1  !  max. top drag coefficient (non linear case and ln_loglayer=T) 
     15   rn_tfri2_max=    1.e-1  !  max. top drag coefficient (non linear case and ln_loglayer=T) 
    1616   rn_tfeb2    =    0.0    !  top turbulent kinetic energy background  (m2/s2) 
    1717   rn_tfrz0    =    3.e-3  !  top roughness [m] if ln_loglayer=T 
    1818   ln_tfr2d    = .false.   !  horizontal variation of the top friction coef (read a 2D mask file ) 
    19    rn_tfrien   =    50.    !  local multiplying factor of tfr (ln_tfr2d=T) 
     19   rn_tfrien   =   50.     !  local multiplying factor of tfr (ln_tfr2d=T) 
    2020 
    2121   ln_bfrimp   = .true.    !  implicit bottom friction (requires ln_zdfexp = .false. if true) 
  • trunk/DOC/Namelists/namdct

    r6140 r6997  
    11!----------------------------------------------------------------------- 
    2 &namdct        ! transports through some sections 
     2&namdct        ! transports through some sections                        ("key_diadct") 
    33!----------------------------------------------------------------------- 
    4     nn_dct      = 15       !  time step frequency for transports computing 
    5     nn_dctwri   = 15       !  time step frequency for transports writing 
    6     nn_secdebug = 112      !      0 : no section to debug 
    7                            !     -1 : debug all section 
    8                            !  0 < n : debug section number n 
     4    nn_dct     = 15        !  time step frequency for transports computing 
     5    nn_dctwri  = 15        !  time step frequency for transports writing 
     6    nn_secdebug= 112       !      0 : no section to debug 
     7    !                      !     -1 : debug all section 
     8    !                      !  0 < n : debug section number n 
    99/ 
  • trunk/DOC/Namelists/namdiu

    r6289 r6997  
    11!----------------------------------------------------------------------- 
    2 &namdiu !   Cool skin and warm layer models 
     2&namdiu        !   Cool skin and warm layer models                       (default F) 
    33!----------------------------------------------------------------------- 
    44   ln_diurnal      = .false.   !  
  • trunk/DOC/Namelists/namdyn_vor

    r6289 r6997  
    11!----------------------------------------------------------------------- 
    2 &namdyn_vor    !   option of physics/algorithm                          (default: NO) 
     2&namdyn_vor    !   Vorticity / Coriolis scheme                          (default: NO) 
    33!----------------------------------------------------------------------- 
    44   ln_dynvor_ene = .false. !  enstrophy conserving scheme 
  • trunk/DOC/Namelists/nameos

    r6140 r6997  
    22&nameos        !   ocean physical parameters 
    33!----------------------------------------------------------------------- 
    4    nn_eos      =  -1     !  type of equation of state and Brunt-Vaisala frequency 
    5                                  !  =-1, TEOS-10 
    6                                  !  = 0, EOS-80 
    7                                  !  = 1, S-EOS   (simplified eos) 
    8    ln_useCT    = .true.  ! use of Conservative Temp. ==> surface CT converted in Pot. Temp. in sbcssm 
     4   ln_teos10   = .false.         !  = Use TEOS-10 equation of state 
     5   ln_eos80    = .false.         !  = Use EOS80 equation of state 
     6   ln_seos     = .false.         !  = Use simplified equation of state (S-EOS) 
    97                                 ! 
    10    !                     ! S-EOS coefficients : 
    11                                  !  rd(T,S,Z)*rau0 = -a0*(1+.5*lambda*dT+mu*Z+nu*dS)*dT+b0*dS 
     8   !                     ! S-EOS coefficients (ln_seos=T): 
     9   !                             !  rd(T,S,Z)*rau0 = -a0*(1+.5*lambda*dT+mu*Z+nu*dS)*dT+b0*dS 
    1210   rn_a0       =  1.6550e-1      !  thermal expension coefficient (nn_eos= 1) 
    1311   rn_b0       =  7.6554e-1      !  saline  expension coefficient (nn_eos= 1) 
  • trunk/DOC/Namelists/namflo

    r4147 r6997  
    11!----------------------------------------------------------------------- 
    2 &namflo       !   float parameters                                      ("key_float") 
     2&namflo        !   float parameters                                      ("key_float") 
    33!----------------------------------------------------------------------- 
    4    jpnfl         = 1          !  total number of floats during the run 
    5    jpnnewflo     = 0          !  number of floats for the restart 
    6    ln_rstflo     = .false.    !  float restart (T) or not (F) 
    7    nn_writefl    =      75    !  frequency of writing in float output file 
    8    nn_stockfl    =    5475    !  frequency of creation of the float restart file 
    9    ln_argo       = .false.    !  Argo type floats (stay at the surface each 10 days) 
    10    ln_flork4     = .false.    !  trajectories computed with a 4th order Runge-Kutta (T) 
    11                               !  or computed with Blanke' scheme (F) 
    12    ln_ariane     = .true.     !  Input with Ariane tool convention(T) 
    13    ln_flo_ascii  = .true.     !  Output with Ariane tool netcdf convention(F) or ascii file (T) 
     4   jpnfl       = 1         !  total number of floats during the run 
     5   jpnnewflo   = 0         !  number of floats for the restart 
     6   ln_rstflo   = .false.   !  float restart (T) or not (F) 
     7   nn_writefl  =      75   !  frequency of writing in float output file 
     8   nn_stockfl  =    5475   !  frequency of creation of the float restart file 
     9   ln_argo     = .false.   !  Argo type floats (stay at the surface each 10 days) 
     10   ln_flork4   = .false.   !  trajectories computed with a 4th order Runge-Kutta (T) 
     11   !                       !  or computed with Blanke' scheme (F) 
     12   ln_ariane   = .true.    !  Input with Ariane tool convention(T) 
     13   ln_flo_ascii= .true.    !  Output with Ariane tool netcdf convention(F) or ascii file (T) 
    1414/ 
  • trunk/DOC/Namelists/namhsb

    r6140 r6997  
    11!----------------------------------------------------------------------- 
    2 &namhsb       !  Heat and salt budgets                                  (default F) 
     2&namhsb        !  Heat and salt budgets                                  (default F) 
    33!----------------------------------------------------------------------- 
    4    ln_diahsb  = .false.    !  check the heat and salt budgets (T) or not (F) 
     4   ln_diahsb   = .false.   !  check the heat and salt budgets (T) or not (F) 
    55/ 
  • trunk/DOC/Namelists/namnc4

    r2540 r6997  
    11!----------------------------------------------------------------------- 
    2 &namnc4        !   netcdf4 chunking and compression settings            ("key_netcdf4") 
     2&namnc4        !   netcdf4 chunking and compression settings             ("key_netcdf4") 
    33!----------------------------------------------------------------------- 
    44   nn_nchunks_i=   4       !  number of chunks in i-dimension 
    55   nn_nchunks_j=   4       !  number of chunks in j-dimension 
    66   nn_nchunks_k=   31      !  number of chunks in k-dimension 
    7                            !  setting nn_nchunks_k = jpk will give a chunk size of 1 in the vertical which 
    8                            !  is optimal for postprocessing which works exclusively with horizontal slabs 
     7   !                       !  setting nn_nchunks_k = jpk will give a chunk size of 1 in the vertical which 
     8   !                       !  is optimal for postprocessing which works exclusively with horizontal slabs 
    99   ln_nc4zip   = .true.    !  (T) use netcdf4 chunking and compression 
    10                            !  (F) ignore chunking information and produce netcdf3-compatible files 
     10   !                       !  (F) ignore chunking information and produce netcdf3-compatible files 
    1111/ 
  • trunk/DOC/Namelists/namobs

    r6289 r6997  
    11!----------------------------------------------------------------------- 
    2 &namobs       !  observation usage switch 
     2&namobs        !  observation usage switch 
    33!----------------------------------------------------------------------- 
    4    ln_diaobs  = .false.             ! Logical switch for the observation operator 
    5    ln_t3d     = .false.             ! Logical switch for T profile observations 
    6    ln_s3d     = .false.             ! Logical switch for S profile observations 
    7    ln_sla     = .false.             ! Logical switch for SLA observations 
    8    ln_sst     = .false.             ! Logical switch for SST observations 
    9    ln_sic     = .false.             ! Logical switch for Sea Ice observations 
    10    ln_vel3d   = .false.             ! Logical switch for velocity observations 
    11    ln_altbias = .false.             ! Logical switch for altimeter bias correction 
    12    ln_nea     = .false.             ! Logical switch for rejection of observations near land 
    13    ln_grid_global = .true.          ! Logical switch for global distribution of observations 
    14    ln_grid_search_lookup = .false.  ! Logical switch for obs grid search w/lookup table 
    15    ln_ignmis  = .true.              ! Logical switch for ignoring missing files 
    16    ln_s_at_t  = .false.             ! Logical switch for computing model S at T obs if not there 
    17    ln_sstnight = .false.            ! Logical switch for calculating night-time average for SST obs 
     4   ln_diaobs   = .false.             ! Logical switch for the observation operator 
     5   ln_t3d      = .false.             ! Logical switch for T profile observations 
     6   ln_s3d      = .false.             ! Logical switch for S profile observations 
     7   ln_sla      = .false.             ! Logical switch for SLA observations 
     8   ln_sst      = .false.             ! Logical switch for SST observations 
     9   ln_sic      = .false.             ! Logical switch for Sea Ice observations 
     10   ln_vel3d    = .false.             ! Logical switch for velocity observations 
     11   ln_altbias  = .false.             ! Logical switch for altimeter bias correction 
     12   ln_nea      = .false.             ! Logical switch for rejection of observations near land 
     13   ln_grid_global = .true.           ! Logical switch for global distribution of observations 
     14   ln_grid_search_lookup = .false.   ! Logical switch for obs grid search w/lookup table 
     15   ln_ignmis   = .true.              ! Logical switch for ignoring missing files 
     16   ln_s_at_t   = .false.             ! Logical switch for computing model S at T obs if not there 
     17   ln_sstnight = .false.             ! Logical switch for calculating night-time average for SST obs 
    1818! All of the *files* variables below are arrays. Use namelist_cfg to add more files 
    19    cn_profbfiles = 'profiles_01.nc'    ! Profile feedback input observation file names 
    20    cn_slafbfiles = 'sla_01.nc'         ! SLA feedback input observation file names 
    21    cn_sstfbfiles = 'sst_01.nc'         ! SST feedback input observation file names 
    22    cn_sicfbfiles = 'sic_01.nc'         ! SIC feedback input observation file names 
    23    cn_velfbfiles = 'vel_01.nc'         ! Velocity feedback input observation file names 
    24    cn_altbiasfile = 'altbias.nc'       ! Altimeter bias input file name 
    25    cn_gridsearchfile = 'gridsearch.nc' ! Grid search file name 
    26    rn_gridsearchres = 0.5              ! Grid search resolution 
    27    rn_dobsini = 00010101.000000        ! Initial date in window YYYYMMDD.HHMMSS 
    28    rn_dobsend = 00010102.000000        ! Final date in window YYYYMMDD.HHMMSS 
    29    nn_1dint = 0                        ! Type of vertical interpolation method 
    30    nn_2dint = 0                        ! Type of horizontal interpolation method 
    31    nn_msshc = 0                        ! MSSH correction scheme 
    32    rn_mdtcorr = 1.61                   ! MDT  correction 
    33    rn_mdtcutoff = 65.0                 ! MDT cutoff for computed correction 
    34    nn_profdavtypes = -1                ! Profile daily average types - array 
    35    ln_sstbias = .false.  
    36    cn_sstbias_files = 'sstbias.nc' 
     19   cn_profbfiles = 'profiles_01.nc'  ! Profile feedback input observation file names 
     20   cn_slafbfiles = 'sla_01.nc'       ! SLA feedback input observation file names 
     21   cn_sstfbfiles = 'sst_01.nc'       ! SST feedback input observation file names 
     22   cn_sicfbfiles = 'sic_01.nc'       ! SIC feedback input observation file names 
     23   cn_velfbfiles = 'vel_01.nc'       ! Velocity feedback input observation file names 
     24   cn_altbiasfile = 'altbias.nc'     ! Altimeter bias input file name 
     25   cn_gridsearchfile='gridsearch.nc' ! Grid search file name 
     26   rn_gridsearchres = 0.5            ! Grid search resolution 
     27   rn_dobsini  = 00010101.000000     ! Initial date in window YYYYMMDD.HHMMSS 
     28   rn_dobsend  = 00010102.000000     ! Final date in window YYYYMMDD.HHMMSS 
     29   nn_1dint    = 0                   ! Type of vertical interpolation method 
     30   nn_2dint    = 0                   ! Type of horizontal interpolation method 
     31   nn_msshc    = 0                   ! MSSH correction scheme 
     32   rn_mdtcorr  = 1.61                ! MDT  correction 
     33   rn_mdtcutoff = 65.0               ! MDT cutoff for computed correction 
     34   nn_profdavtypes = -1              ! Profile daily average types - array 
     35   ln_sstbias  = .false.             ! 
     36   cn_sstbias_files = 'sstbias.nc'   ! 
    3737/ 
  • trunk/DOC/Namelists/namptr

    r6140 r6997  
    11!----------------------------------------------------------------------- 
    2 &namptr       !   Poleward Transport Diagnostic                         (default F) 
     2&namptr        !   Poleward Transport Diagnostic                         (default F) 
    33!----------------------------------------------------------------------- 
    4    ln_diaptr  = .false.    !  Poleward heat and salt transport (T) or not (F) 
    5    ln_subbas  = .false.     !  Atlantic/Pacific/Indian basins computation (T) or not 
     4   ln_diaptr   = .false.   !  Poleward heat and salt transport (T) or not (F) 
     5   ln_subbas   = .false.   !  Atlantic/Pacific/Indian basins computation (T) or not 
    66/ 
  • trunk/DOC/Namelists/namsbc

    r6289 r6997  
    3939   ln_apr_dyn  = .false.   !  Patm gradient added in ocean & ice Eqs.   (T => fill namsbc_apr ) 
    4040   ln_isf      = .false.   !  ice shelf                                 (T   => fill namsbc_isf) 
    41    ln_wave = .false.       !  coupling with surface wave                (T => fill namsbc_wave) 
    42    nn_lsm  = 0             !  =0 land/sea mask for input fields is not applied (keep empty land/sea mask filename field) , 
     41   ln_wave     = .false.   !  coupling with surface wave                (T => fill namsbc_wave) 
     42   nn_lsm      = 0         !  =0 land/sea mask for input fields is not applied (keep empty land/sea mask filename field) , 
    4343                           !  =1:n number of iterations of land/sea mask application for input fields (fill land/sea mask filename field) 
    4444/ 
  • trunk/DOC/Namelists/namsbc_alb

    r4147 r6997  
    22&namsbc_alb    !   albedo parameters 
    33!----------------------------------------------------------------------- 
    4    rn_cloud    =    0.06   !  cloud correction to snow and ice albedo 
    5    rn_albice   =    0.53   !  albedo of melting ice in the arctic and antarctic 
    6    rn_alphd    =    0.80   !  coefficients for linear interpolation used to 
    7    rn_alphc    =    0.65   !  compute albedo between two extremes values 
    8    rn_alphdi   =    0.72   !  (Pyane, 1972) 
     4   nn_ice_alb  =    0      !  parameterization of ice/snow albedo 
     5                           !     0: Shine & Henderson-Sellers (JGR 1985) 
     6                           !     1: "home made" based on Brandt et al. (J. Climate 2005) 
     7                           !                         and Grenfell & Perovich (JGR 2004) 
     8   rn_albice   =  0.53     !  albedo of bare puddled ice (values from 0.49 to 0.58) 
     9                           !     0.53 (default) => if nn_ice_alb=0 
     10                           !     0.50 (default) => if nn_ice_alb=1 
    911/ 
  • trunk/DOC/Namelists/namsbc_apr

    r6140 r6997  
    11!----------------------------------------------------------------------- 
    2 &namsbc_apr    !   Atmospheric pressure forcing (in ocean or bulk)      (ln_apr_dyn=T) 
     2&namsbc_apr    !   Atmospheric pressure used as ocean forcing or in bulk 
    33!----------------------------------------------------------------------- 
    4 !              !  file name ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask ! 
    5 !              !            !  (if <0  months)  !   name    !  (logical)   !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      ! 
    6    sn_apr      = 'patm'     ,         -1        ,'somslpre',    .true.     , .true. , 'yearly'  ,  ''      ,   ''     , '' 
     4!              ! file name ! frequency (hours) ! variable ! time interp.!  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask ! 
     5!              !           !  (if <0  months)  !   name   !  (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      ! 
     6   sn_apr      = 'patm'    ,         -1        ,'somslpre',   .true.    , .true. , 'yearly'  ,    ''    ,    ''    ,      '' 
    77 
    8    cn_dir      = './'       !  root directory for the location of the bulk files 
    9    rn_pref     = 101000.    !  reference atmospheric pressure   [N/m2]/ 
    10    ln_ref_apr  = .false.    !  ref. pressure: global mean Patm (T) or a constant (F) 
    11    ln_apr_obc  = .false.    !  inverse barometer added to OBC ssh data 
     8   cn_dir      = './'      !  root directory for the location of the bulk files 
     9   rn_pref     = 101000.   !  reference atmospheric pressure   [N/m2]/ 
     10   ln_ref_apr  = .false.   !  ref. pressure: global mean Patm (T) or a constant (F) 
     11   ln_apr_obc  = .false.   !  inverse barometer added to OBC ssh data 
    1212/ 
  • trunk/DOC/Namelists/namsbc_cpl

    r6140 r6997  
    2222   sn_rcv_co2    =   'coupled'              ,    'no'    ,     ''      ,         ''          ,   '' 
    2323! 
    24    nn_cplmodel   =     1     !  Maximum number of models to/from which NEMO is potentialy sending/receiving data 
    25    ln_usecplmask = .false.   !  use a coupling mask file to merge data received from several models 
    26                              !   -> file cplmask.nc with the float variable called cplmask (jpi,jpj,nn_cplmodel) 
     24   nn_cplmodel   =     1   !  Maximum number of models to/from which NEMO is potentialy sending/receiving data 
     25   ln_usecplmask = .false. !  use a coupling mask file to merge data received from several models 
     26   !                       !   -> file cplmask.nc with the float variable called cplmask (jpi,jpj,nn_cplmodel) 
    2727/ 
  • trunk/DOC/Namelists/namsbc_iscpl

    r6289 r6997  
    22&namsbc_iscpl  !   land ice / ocean coupling option                      
    33!----------------------------------------------------------------------- 
    4    nn_drown  = 10       ! number of iteration of the extrapolation loop (fill the new wet cells) 
    5    ln_hsb    = .false.  ! activate conservation module (conservation exact after a time of rn_fiscpl) 
    6    nn_fiscpl = 43800    ! (number of time step) conservation period (maybe should be fix to the coupling frequencey of restart frequency) 
     4   nn_drown    = 10        ! number of iteration of the extrapolation loop (fill the new wet cells) 
     5   ln_hsb      = .false.   ! activate conservation module (conservation exact after a time of rn_fiscpl) 
     6   nn_fiscpl   = 43800     ! (number of time step) conservation period (maybe should be fix to the coupling frequencey of restart frequency) 
    77/ 
  • trunk/DOC/Namelists/namsbc_isf

    r6289 r6997  
    22&namsbc_isf    !  Top boundary layer (ISF)                              (nn_isf >0) 
    33!----------------------------------------------------------------------- 
    4 !              ! file name ! frequency (hours) ! variable ! time interp. !  clim   ! 'yearly'/ ! weights  ! rotation ! land/sea mask ! 
    5 !              !           !  (if <0  months)  !   name   !  (logical)   !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      ! 
     4!              ! file name ! frequency (hours) ! variable ! time interp.!  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask ! 
     5!              !           !  (if <0  months)  !   name   !  (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      ! 
    66! nn_isf == 4 
    7    sn_fwfisf   = 'rnfisf'  ,         -12       ,'sowflisf',   .false.    , .true.  , 'yearly'  ,  ''      ,   ''     , '' 
     7   sn_fwfisf   = 'rnfisf'  ,         -12       ,'sowflisf',   .false.   , .true. , 'yearly'  ,    ''    ,   ''     ,    '' 
    88! nn_isf == 3 
    9    sn_rnfisf   = 'rnfisf'  ,         -12       ,'sofwfisf',   .false.    , .true.  , 'yearly'  ,  ''      ,   ''     , '' 
     9   sn_rnfisf   = 'rnfisf'  ,         -12       ,'sofwfisf',   .false.   , .true. , 'yearly'  ,    ''    ,   ''     ,    '' 
    1010! nn_isf == 2 and 3 
    11    sn_depmax_isf='rnfisf'  ,         -12       ,'sozisfmax',  .false.    , .true.  , 'yearly'  ,  ''      ,   ''     , '' 
    12    sn_depmin_isf='rnfisf'  ,         -12       ,'sozisfmin',  .false.    , .true.  , 'yearly'  ,  ''      ,   ''     , '' 
     11   sn_depmax_isf='rnfisf'  ,         -12       ,'sozisfmax',  .false.   , .true. , 'yearly'  ,    ''    ,   ''     ,    '' 
     12   sn_depmin_isf='rnfisf'  ,         -12       ,'sozisfmin',  .false.   , .true. , 'yearly'  ,    ''    ,   ''     ,    '' 
    1313! nn_isf == 2 
    14    sn_Leff_isf = 'rnfisf'  ,         -12       ,'Leff'    ,   .false.    , .true.  , 'yearly'  ,  ''      ,   ''     , '' 
     14   sn_Leff_isf = 'rnfisf'  ,         -12       ,'Leff'    ,   .false.   , .true. , 'yearly'  ,    ''    ,   ''     ,    '' 
    1515! 
    1616! for all case 
     
    2020                           !  option 1 and 4 need ln_isfcav = .true. (domzgr) 
    2121! only for nn_isf = 1 or 2 
    22    rn_gammat0  = 1.e-4    ! gammat coefficient used in blk formula 
    23    rn_gammas0  = 1.e-4    ! gammas coefficient used in blk formula 
     22   rn_gammat0  = 1.e-4     ! gammat coefficient used in blk formula 
     23   rn_gammas0  = 1.e-4     ! gammas coefficient used in blk formula 
    2424! only for nn_isf = 1 or 4 
    2525   rn_hisf_tbl =  30.      ! thickness of the top boundary layer    (Losh et al. 2008) 
    26                           ! 0 => thickness of the tbl = thickness of the first wet cell 
     26   !                       ! 0 => thickness of the tbl = thickness of the first wet cell 
    2727! only for nn_isf = 1 
    28    nn_isfblk   = 1        ! 1 ISOMIP  like: 2 equations formulation (Hunter et al., 2006) 
    29                           ! 2 ISOMIP+ like: 3 equations formulation (Asay-Davis et al., 2015) 
    30    nn_gammablk = 1        ! 0 = cst Gammat (= gammat/s) 
    31                           ! 1 = velocity dependend Gamma (u* * gammat/s)  (Jenkins et al. 2010) 
    32                           ! 2 = velocity and stability dependent Gamma    (Holland et al. 1999) 
     28   nn_isfblk   = 1         ! 1 ISOMIP  like: 2 equations formulation (Hunter et al., 2006) 
     29   !                       ! 2 ISOMIP+ like: 3 equations formulation (Asay-Davis et al., 2015) 
     30   nn_gammablk = 1         ! 0 = cst Gammat (= gammat/s) 
     31   !                       ! 1 = velocity dependend Gamma (u* * gammat/s)  (Jenkins et al. 2010) 
     32   !                       ! 2 = velocity and stability dependent Gamma    (Holland et al. 1999) 
    3333/ 
  • trunk/DOC/Namelists/namsbc_rnf

    r6140 r6997  
    1010   sn_dep_rnf  = 'runoffs'            ,         0         , 'rodepth' ,   .false.    , .true. , 'yearly'  , ''       , ''       , '' 
    1111 
    12    cn_dir       = './'      !  root directory for the location of the runoff files 
    13    ln_rnf_mouth = .true.    !  specific treatment at rivers mouths 
    14    rn_hrnf      =  15.e0    !  depth over which enhanced vertical mixing is used 
    15    rn_avt_rnf   =   1.e-3   !  value of the additional vertical mixing coef. [m2/s] 
    16    rn_rfact     =   1.e0    !  multiplicative factor for runoff 
    17    ln_rnf_depth = .false.   !  read in depth information for runoff 
    18    ln_rnf_tem   = .false.   !  read in temperature information for runoff 
    19    ln_rnf_sal   = .false.   !  read in salinity information for runoff 
    20    ln_rnf_depth_ini = .false.  ! compute depth at initialisation from runoff file 
    21    rn_rnf_max   = 5.735e-4  !  max value of the runoff climatologie over global domain ( ln_rnf_depth_ini = .true ) 
    22    rn_dep_max   = 150.      !  depth over which runoffs is spread ( ln_rnf_depth_ini = .true ) 
    23    nn_rnf_depth_file = 0    !  create (=1) a runoff depth file or not (=0) 
     12   cn_dir      = './'      !  root directory for the location of the runoff files 
     13   ln_rnf_mouth= .true.    !  specific treatment at rivers mouths 
     14      rn_hrnf     =  15.e0    !  depth over which enhanced vertical mixing is used    (ln_rnf_mouth=T) 
     15      rn_avt_rnf  =   1.e-3   !  value of the additional vertical mixing coef. [m2/s] (ln_rnf_mouth=T) 
     16   rn_rfact    =   1.e0    !  multiplicative factor for runoff 
     17   ln_rnf_depth= .false.   !  read in depth information for runoff 
     18   ln_rnf_tem  = .false.   !  read in temperature information for runoff 
     19   ln_rnf_sal  = .false.   !  read in salinity information for runoff 
     20   ln_rnf_depth_ini = .false. ! compute depth at initialisation from runoff file 
     21      rn_rnf_max  = 5.735e-4  !  max value of the runoff climatologie over global domain ( ln_rnf_depth_ini = .true ) 
     22      rn_dep_max  = 150.      !  depth over which runoffs is spread ( ln_rnf_depth_ini = .true ) 
     23      nn_rnf_depth_file = 0   !  create (=1) a runoff depth file or not (=0) 
    2424/ 
  • trunk/DOC/Namelists/namsbc_sas

    r6140 r6997  
    22&namsbc_sas    !   analytical surface boundary condition 
    33!----------------------------------------------------------------------- 
    4 !              !  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask ! 
    5 !              !             !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      ! 
    6    sn_usp      = 'sas_grid_U' ,    120           , 'vozocrtx' ,  .true.    , .true. ,   'yearly'  , ''       , ''             , '' 
    7    sn_vsp      = 'sas_grid_V' ,    120           , 'vomecrty' ,  .true.    , .true. ,   'yearly'  , ''       , ''             , '' 
    8    sn_tem      = 'sas_grid_T' ,    120           , 'sosstsst' ,  .true.    , .true. ,   'yearly'  , ''       , ''             , '' 
    9    sn_sal      = 'sas_grid_T' ,    120           , 'sosaline' ,  .true.    , .true. ,   'yearly'  , ''       , ''             , '' 
    10    sn_ssh      = 'sas_grid_T' ,    120           , 'sossheig' ,  .true.    , .true. ,   'yearly'  , ''       , ''             , '' 
    11    sn_e3t      = 'sas_grid_T' ,    120           , 'e3t_m'    ,  .true.    , .true. ,   'yearly'  , ''       , ''             , '' 
    12    sn_frq      = 'sas_grid_T' ,    120           , 'frq_m'    ,  .true.    , .true. ,   'yearly'  , ''       , ''             , '' 
     4!              !  file name  ! frequency (hours) ! variable  ! time interp.!  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask ! 
     5!              !             !  (if <0  months)  !   name    !  (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      ! 
     6   sn_usp      = 'sas_grid_U',     120           , 'vozocrtx',   .true.    , .true. , 'yearly'  ,    ''    ,    ''    ,    '' 
     7   sn_vsp      = 'sas_grid_V',     120           , 'vomecrty',   .true.    , .true. , 'yearly'  ,    ''    ,    ''    ,    '' 
     8   sn_tem      = 'sas_grid_T',     120           , 'sosstsst',   .true.    , .true. , 'yearly'  ,    ''    ,    ''    ,    '' 
     9   sn_sal      = 'sas_grid_T',     120           , 'sosaline',   .true.    , .true. , 'yearly'  ,    ''    ,    ''    ,    '' 
     10   sn_ssh      = 'sas_grid_T',     120           , 'sossheig',   .true.    , .true. , 'yearly'  ,    ''    ,    ''    ,    '' 
     11   sn_e3t      = 'sas_grid_T',     120           , 'e3t_m'   ,   .true.    , .true. , 'yearly'  ,    ''    ,    ''    ,    '' 
     12   sn_frq      = 'sas_grid_T',     120           , 'frq_m'   ,   .true.    , .true. , 'yearly'  ,    ''    ,    ''    ,    '' 
    1313 
    1414   ln_3d_uve   = .true.    !  specify whether we are supplying a 3D u,v and e3 field 
    15    ln_read_frq = .false.    !  specify whether we must read frq or not 
     15   ln_read_frq = .false.   !  specify whether we must read frq or not 
    1616   cn_dir      = './'      !  root directory for the location of the bulk files are 
    1717/ 
  • trunk/DOC/Namelists/namsbc_ssr

    r6140 r6997  
    22&namsbc_ssr    !   surface boundary condition : sea surface restoring   (ln_ssr=T) 
    33!----------------------------------------------------------------------- 
    4 !              !  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask ! 
    5 !              !             !  (if <0  months)  !   name    !   (logical) !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      ! 
    6    sn_sst      = 'sst_data'  ,        24         ,  'sst'    ,    .false.   , .false., 'yearly'  , ''       , ''       , '' 
    7    sn_sss      = 'sss_data'  ,        -1         ,  'sss'    ,    .true.    , .true. , 'yearly'  , ''       , ''       , '' 
     4!              ! file name ! frequency (hours) ! variable ! time interp.!  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask ! 
     5!              !           !  (if <0  months)  !   name   !   (logical) !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      ! 
     6   sn_sst      = 'sst_data',        24         ,  'sst'   ,    .false.  , .false., 'yearly'  ,    ''    ,    ''    ,    '' 
     7   sn_sss      = 'sss_data',        -1         ,  'sss'   ,    .true.   , .true. , 'yearly'  ,    ''    ,    ''    ,    '' 
    88 
    99   cn_dir      = './'      !  root directory for the location of the runoff files 
     
    1313   rn_dqdt     =   -40.    !  magnitude of the retroaction on temperature   [W/m2/K] 
    1414   rn_deds     =  -166.67  !  magnitude of the damping on salinity   [mm/day] 
    15    ln_sssr_bnd =   .true.  !  flag to bound erp term (associated with nn_sssr=2) 
     15   ln_sssr_bnd =  .true.   !  flag to bound erp term (associated with nn_sssr=2) 
    1616   rn_sssr_bnd =   4.e0    !  ABS(Max/Min) value of the damping erp term [mm/day] 
    1717/ 
  • trunk/DOC/Namelists/namsbc_wave

    r6140 r6997  
    22&namsbc_wave   ! External fields from wave model                        (ln_wave=T) 
    33!----------------------------------------------------------------------- 
    4 !              !  file name  ! frequency (hours) ! variable    ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask ! 
    5 !              !             !  (if <0  months)  !   name      !  (logical)   !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      ! 
    6    sn_cdg      =  'cdg_wave' ,        1          , 'drag_coeff',     .true.   , .false., 'daily'   ,  ''      , ''       , '' 
    7    sn_usd      =  'sdw_wave' ,        1          , 'u_sd2d'    ,     .true.   , .false., 'daily'   ,  ''      , ''       , '' 
    8    sn_vsd      =  'sdw_wave' ,        1          , 'v_sd2d'    ,     .true.   , .false., 'daily'   ,  ''      , ''       , '' 
    9    sn_wn       =  'sdw_wave' ,        1          , 'wave_num'  ,     .true.   , .false., 'daily'   ,  ''      , ''       , '' 
     4!              ! file name ! frequency (hours) ! variable    ! time interp.!  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask ! 
     5!              !           !  (if <0  months)  !   name      !  (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      ! 
     6   sn_cdg      = 'cdg_wave',        1          , 'drag_coeff',   .true.    , .false., 'daily'   ,    ''      , ''       , '' 
     7   sn_usd      = 'sdw_wave',        1          , 'u_sd2d'    ,   .true.    , .false., 'daily'   ,    ''      , ''       , '' 
     8   sn_vsd      = 'sdw_wave',        1          , 'v_sd2d'    ,   .true.    , .false., 'daily'   ,    ''      , ''       , '' 
     9   sn_wn       = 'sdw_wave',        1          , 'wave_num'  ,   .true.    , .false., 'daily'   ,    ''      , ''       , '' 
    1010! 
    1111   cn_dir_cdg  = './'      !  root directory for the location of drag coefficient files 
    12    ln_cdgw = .false.       !  Neutral drag coefficient read from wave model 
    13    ln_sdw  = .false.       !  Computation of 3D stokes drift                
     12   ln_cdgw     = .false.   !  Neutral drag coefficient read from wave model 
     13   ln_sdw      = .false.   !  Computation of 3D stokes drift                
    1414/ 
  • trunk/DOC/Namelists/namsto

    r6289 r6997  
    11!----------------------------------------------------------------------- 
    2 &namsto       ! Stochastic parametrization of EOS                       (default: NO) 
     2&namsto        ! Stochastic parametrization of EOS                      (default: NO) 
    33!----------------------------------------------------------------------- 
    4    ln_sto_eos   = .false.  ! stochastic equation of state 
    5    nn_sto_eos   = 1        ! number of independent random walks 
    6    rn_eos_stdxy = 1.4      ! random walk horz. standard deviation (in grid points) 
    7    rn_eos_stdz  = 0.7      ! random walk vert. standard deviation (in grid points) 
    8    rn_eos_tcor  = 1440.    ! random walk time correlation (in timesteps) 
    9    nn_eos_ord   = 1        ! order of autoregressive processes 
    10    nn_eos_flt   = 0        ! passes of Laplacian filter 
    11    rn_eos_lim   = 2.0      ! limitation factor (default = 3.0) 
    12    ln_rststo    = .false.  ! start from mean parameter (F) or from restart file (T) 
    13    ln_rstseed = .true.           ! read seed of RNG from restart file 
     4   ln_sto_eos  = .false.   ! stochastic equation of state 
     5   nn_sto_eos  = 1         ! number of independent random walks 
     6   rn_eos_stdxy= 1.4       ! random walk horz. standard deviation (in grid points) 
     7   rn_eos_stdz = 0.7       ! random walk vert. standard deviation (in grid points) 
     8   rn_eos_tcor = 1440.     ! random walk time correlation (in timesteps) 
     9   nn_eos_ord  = 1         ! order of autoregressive processes 
     10   nn_eos_flt  = 0         ! passes of Laplacian filter 
     11   rn_eos_lim  = 2.0       ! limitation factor (default = 3.0) 
     12   ln_rststo   = .false.   ! start from mean parameter (F) or from restart file (T) 
     13   ln_rstseed  = .true.    ! read seed of RNG from restart file 
    1414   cn_storst_in  = "restart_sto" !  suffix of stochastic parameter restart file (input) 
    1515   cn_storst_out = "restart_sto" !  suffix of stochastic parameter restart file (output) 
  • trunk/DOC/Namelists/namtra_adv

    r6140 r6997  
    22&namtra_adv    !   advection scheme for tracer                          (default: NO advection) 
    33!----------------------------------------------------------------------- 
    4    ln_traadv_cen =  .false. !  2nd order centered scheme 
    5       nn_cen_h   =  4               !  =2/4, horizontal 2nd order CEN / 4th order CEN 
    6       nn_cen_v   =  4               !  =2/4, vertical   2nd order CEN / 4th order COMPACT 
    7    ln_traadv_fct =  .false. !  FCT scheme 
    8       nn_fct_h   =  2               !  =2/4, horizontal 2nd / 4th order  
    9       nn_fct_v   =  2               !  =2/4, vertical   2nd / COMPACT 4th order  
    10       nn_fct_zts =  0               !  >=1,  2nd order FCT scheme with vertical sub-timestepping 
    11       !                             !        (number of sub-timestep = nn_fct_zts) 
    12    ln_traadv_mus =  .false. !  MUSCL scheme 
    13       ln_mus_ups =  .false.         !  use upstream scheme near river mouths 
    14    ln_traadv_ubs =  .false. !  UBS scheme 
    15       nn_ubs_v   =  2               !  =2  , vertical 2nd order FCT / COMPACT 4th order 
    16    ln_traadv_qck =  .false. !  QUICKEST scheme 
     4   ln_traadv_cen = .false. !  2nd order centered scheme 
     5      nn_cen_h   =  4            !  =2/4, horizontal 2nd order CEN / 4th order CEN 
     6      nn_cen_v   =  4            !  =2/4, vertical   2nd order CEN / 4th order COMPACT 
     7   ln_traadv_fct = .false. !  FCT scheme 
     8      nn_fct_h   =  2            !  =2/4, horizontal 2nd / 4th order  
     9      nn_fct_v   =  2            !  =2/4, vertical   2nd / COMPACT 4th order  
     10      nn_fct_zts =  0            !  >=1,  2nd order FCT scheme with vertical sub-timestepping 
     11      !                          !        (number of sub-timestep = nn_fct_zts) 
     12   ln_traadv_mus = .false. !  MUSCL scheme 
     13      ln_mus_ups = .false.       !  use upstream scheme near river mouths 
     14   ln_traadv_ubs = .false. !  UBS scheme 
     15      nn_ubs_v   =  2            !  =2  , vertical 2nd order FCT / COMPACT 4th order 
     16   ln_traadv_qck = .false. !  QUICKEST scheme 
    1717/ 
  • trunk/DOC/Namelists/namtra_adv_mle

    r6289 r6997  
    22&namtra_adv_mle !   mixed layer eddy parametrisation (Fox-Kemper param) (default: NO) 
    33!----------------------------------------------------------------------- 
    4    ln_mle    = .false.      ! (T) use the Mixed Layer Eddy (MLE) parameterisation 
    5    rn_ce     = 0.06        ! magnitude of the MLE (typical value: 0.06 to 0.08) 
    6    nn_mle    = 1           ! MLE type: =0 standard Fox-Kemper ; =1 new formulation 
    7    rn_lf     = 5.e+3       ! typical scale of mixed layer front (meters)                      (case rn_mle=0) 
    8    rn_time   = 172800.     ! time scale for mixing momentum across the mixed layer (seconds)  (case rn_mle=0) 
    9    rn_lat    = 20.         ! reference latitude (degrees) of MLE coef.                        (case rn_mle=1) 
    10    nn_mld_uv = 0           ! space interpolation of MLD at u- & v-pts (0=min,1=averaged,2=max) 
    11    nn_conv   = 0           ! =1 no MLE in case of convection ; =0 always MLE 
    12    rn_rho_c_mle  = 0.01    ! delta rho criterion used to calculate MLD for FK 
     4   ln_mle      = .false.   ! (T) use the Mixed Layer Eddy (MLE) parameterisation 
     5   rn_ce       = 0.06      ! magnitude of the MLE (typical value: 0.06 to 0.08) 
     6   nn_mle      = 1         ! MLE type: =0 standard Fox-Kemper ; =1 new formulation 
     7   rn_lf       = 5.e+3     ! typical scale of mixed layer front (meters)                      (case rn_mle=0) 
     8   rn_time     = 172800.   ! time scale for mixing momentum across the mixed layer (seconds)  (case rn_mle=0) 
     9   rn_lat      = 20.       ! reference latitude (degrees) of MLE coef.                        (case rn_mle=1) 
     10   nn_mld_uv   = 0         ! space interpolation of MLD at u- & v-pts (0=min,1=averaged,2=max) 
     11   nn_conv     = 0         ! =1 no MLE in case of convection ; =0 always MLE 
     12   rn_rho_c_mle= 0.01      ! delta rho criterion used to calculate MLD for FK 
    1313/ 
  • trunk/DOC/Namelists/namtra_ldf

    r6289 r6997  
    11!----------------------------------------------------------------------- 
    2 &namtra_ldf    !   lateral diffusion scheme for tracers                 (choice required) 
     2&namtra_ldf    !   lateral diffusion scheme for tracers                 (default: NO diffusion) 
    33!----------------------------------------------------------------------- 
    44   !                       !  Operator type: 
    5    ln_traldf_NONE  =  .false.  !  no operator: no lateral diffusion applied  
     5   !                           !  no diffusion: set ln_traldf_lap=..._blp=F  
    66   ln_traldf_lap   =  .false.  !    laplacian operator 
    77   ln_traldf_blp   =  .false.  !  bilaplacian operator 
     8   ! 
    89   !                       !  Direction of action: 
    910   ln_traldf_lev   =  .false.  !  iso-level 
  • trunk/DOC/Namelists/namtrd

    r6140 r6997  
    11!----------------------------------------------------------------------- 
    2 &namtrd        !   diagnostics on dynamics and/or tracer trends         (default F) 
    3 !              !   and/or mixed-layer trends and/or barotropic vorticity 
     2&namtrd        !   trend diagnostics                                    (default F) 
    43!----------------------------------------------------------------------- 
    54   ln_glo_trd  = .false.   ! (T) global domain averaged diag for T, T^2, KE, and PE 
  • trunk/DOC/Namelists/namtsd

    r6140 r6997  
    11!----------------------------------------------------------------------- 
    2 &namtsd    !   data : Temperature  & Salinity 
     2&namtsd        !   data : Temperature  & Salinity 
    33!----------------------------------------------------------------------- 
    4 !          !  file name                            ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask ! 
    5 !          !                                       !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      ! 
    6    sn_tem  = 'data_1m_potential_temperature_nomask',         -1        ,'votemper' ,    .true.    , .true. , 'yearly'   , ''       ,   ''    ,    '' 
    7    sn_sal  = 'data_1m_salinity_nomask'             ,         -1        ,'vosaline' ,    .true.    , .true. , 'yearly'   , ''       ,   ''    ,    '' 
     4!              !  file name                 ! frequency (hours) ! variable ! time interp.!  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask ! 
     5!              !                            !  (if <0  months)  !   name   !  (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      ! 
     6   sn_tem = 'data_1m_potential_temperature_nomask',     -1      ,'votemper',   .true.    , .true. , 'yearly'  ,    ''    ,    ''    ,    '' 
     7   sn_sal = 'data_1m_salinity_nomask'             ,     -1      ,'vosaline',   .true.    , .true. , 'yearly'  ,    ''    ,    ''    ,    '' 
    88   ! 
    9    cn_dir        = './'     !  root directory for the location of the runoff files 
    10    ln_tsd_init   = .true.   !  Initialisation of ocean T & S with T &S input data (T) or not (F) 
    11    ln_tsd_tradmp = .true.   !  damping of ocean T & S toward T &S input data (T) or not (F) 
     9   cn_dir      = './'      !  root directory for the location of the runoff files 
     10   ln_tsd_init = .true.    !  Initialisation of ocean T & S with T & S input data (T) or not (F) 
     11   ln_tsd_tradmp = .true.  !  damping of ocean T & S toward T & S input data (T) or not (F) 
    1212/ 
  • trunk/DOC/Namelists/namwad

    r6289 r6997  
    11!----------------------------------------------------------------------- 
    2 &namwad  !   Wetting and drying 
     2&namwad        !   Wetting and drying                                   (default F) 
    33!----------------------------------------------------------------------- 
    4    ln_wd             = .false.  ! T/F activation of wetting and drying 
    5    rn_wdmin1         =  0.1     ! Minimum wet depth on dried cells 
    6    rn_wdmin2         =  0.01    ! Tolerance of min wet depth on dried cells 
    7    rn_wdld           =  20.0    ! Land elevation below which wetting/drying is allowed 
    8    nn_wdit           =  10      ! Max iterations for W/D limiter 
     4   ln_wd       = .false.   ! T/F activation of wetting and drying 
     5   rn_wdmin1   =  0.1      ! Minimum wet depth on dried cells 
     6   rn_wdmin2   =  0.01     ! Tolerance of min wet depth on dried cells 
     7   rn_wdld     =  20.0     ! Land elevation below which wetting/drying is allowed 
     8   nn_wdit     =  10       ! Max iterations for W/D limiter 
    99/ 
  • trunk/DOC/Namelists/namzdf

    r3294 r6997  
    77   nn_havtb    =    0      !  horizontal shape for avtb (=1) or not (=0) 
    88   ln_zdfevd   = .true.    !  enhanced vertical diffusion (evd) (T) or not (F) 
    9    nn_evdm     =    0      ! evd apply on tracer (=0) or on tracer and momentum (=1) 
    10    rn_avevd    =  100.     !  evd mixing coefficient [m2/s] 
     9      nn_evdm     =    0        ! evd apply on tracer (=0) or on tracer and momentum (=1) 
     10      rn_avevd    =  100.       !  evd mixing coefficient [m2/s] 
    1111   ln_zdfnpc   = .false.   !  Non-Penetrative Convective algorithm (T) or not (F) 
    12    nn_npc      =    1            ! frequency of application of npc 
    13    nn_npcp     =  365            ! npc control print frequency 
     12      nn_npc      =    1        ! frequency of application of npc 
     13      nn_npcp     =  365        ! npc control print frequency 
    1414   ln_zdfexp   = .false.   !  time-stepping: split-explicit (T) or implicit (F) time stepping 
    15    nn_zdfexp   =    3            ! number of sub-timestep for ln_zdfexp=T 
     15      nn_zdfexp   =    3        ! number of sub-timestep for ln_zdfexp=T 
    1616/ 
  • trunk/DOC/Namelists/namzdf_gls

    r6140 r6997  
    11!----------------------------------------------------------------------- 
    2 &namzdf_gls                !   GLS vertical diffusion                   ("key_zdfgls") 
     2&namzdf_gls    !   GLS vertical diffusion                               ("key_zdfgls") 
    33!----------------------------------------------------------------------- 
    44   rn_emin       = 1.e-7   !  minimum value of e   [m2/s2] 
  • trunk/DOC/Namelists/namzdf_ric

    r6289 r6997  
    22&namzdf_ric    !   richardson number dependent vertical diffusion       ("key_zdfric" ) 
    33!----------------------------------------------------------------------- 
    4    rn_avmri    = 100.e-4   !  maximum value of the vertical viscosity 
    5    rn_alp      =   5.      !  coefficient of the parameterization 
    6    nn_ric      =   2       !  coefficient of the parameterization 
    7    rn_ekmfc    =   0.7     !  Factor in the Ekman depth Equation 
    8    rn_mldmin   =   1.0     !  minimum allowable mixed-layer depth estimate (m) 
    9    rn_mldmax   =1000.0     !  maximum allowable mixed-layer depth estimate (m) 
    10    rn_wtmix    =  10.0     !  vertical eddy viscosity coeff [m2/s] in the mixed-layer 
    11    rn_wvmix    =  10.0     !  vertical eddy diffusion coeff [m2/s] in the mixed-layer 
    12    ln_mldw     = .true.    !  Flag to use or not the mixed layer depth param. 
     4   rn_avmri    =  100.e-4  !  maximum value of the vertical viscosity 
     5   rn_alp      =    5.     !  coefficient of the parameterization 
     6   nn_ric      =    2      !  coefficient of the parameterization 
     7   rn_ekmfc    =    0.7    !  Factor in the Ekman depth Equation 
     8   rn_mldmin   =    1.0    !  minimum allowable mixed-layer depth estimate (m) 
     9   rn_mldmax   = 1000.0    !  maximum allowable mixed-layer depth estimate (m) 
     10   rn_wtmix    =   10.0    !  vertical eddy viscosity coeff [m2/s] in the mixed-layer 
     11   rn_wvmix    =   10.0    !  vertical eddy diffusion coeff [m2/s] in the mixed-layer 
     12   ln_mldw     =  .true.   !  Flag to use or not the mixed layer depth param. 
    1313/ 
  • trunk/DOC/Namelists/namzdf_tke

    r6140 r6997  
    1717   ln_lc       = .true.    !  Langmuir cell parameterisation (Axell 2002) 
    1818   rn_lc       =   0.15    !  coef. associated to Langmuir cells 
    19    nn_etau     =   1       !  penetration of tke below the mixed layer (ML) due to internal & intertial waves 
     19   nn_etau     =   1       !  penetration of tke below the mixed layer (ML) due to near intertial waves 
    2020                           !        = 0 no penetration 
    2121                           !        = 1 add a tke source below the ML 
    2222                           !        = 2 add a tke source just at the base of the ML 
    23                            !        = 3 as = 1 applied on HF part of the stress    ("key_oasis3") 
     23                           !        = 3 as = 1 applied on HF part of the stress           (ln_cpl=T) 
    2424   rn_efr      =   0.05    !  fraction of surface tke value which penetrates below the ML (nn_etau=1 or 2) 
    2525   nn_htau     =   1       !  type of exponential decrease of tke penetration below the ML 
  • trunk/DOC/Namelists/namzgr_sco

    r6140 r6997  
    11!----------------------------------------------------------------------- 
    2 &namzgr_sco    !   s-coordinate or hybrid z-s-coordinate 
     2&namzgr_sco    !   s-coordinate or hybrid z-s-coordinate                (default F) 
    33!----------------------------------------------------------------------- 
    44   ln_s_sh94   = .false.    !  Song & Haidvogel 1994 hybrid S-sigma   (T)| 
  • trunk/DOC/TexFiles/Chapters/Abstracts_Foreword.tex

    r6289 r6997  
     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} 
  • trunk/DOC/TexFiles/Chapters/Annex_A.tex

    r3294 r6997  
     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} 
  • trunk/DOC/TexFiles/Chapters/Annex_B.tex

    r3294 r6997  
     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} 
  • trunk/DOC/TexFiles/Chapters/Annex_C.tex

    r6289 r6997  
     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} 
  • trunk/DOC/TexFiles/Chapters/Annex_D.tex

    r6289 r6997  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Appendix D Ñ Coding Rules 
     
    202204 
    203205To be done.... 
     206\end{document} 
  • trunk/DOC/TexFiles/Chapters/Annex_E.tex

    r3294 r6997  
     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} 
  • trunk/DOC/TexFiles/Chapters/Annex_ISO.tex

    r6289 r6997  
     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} 
  • trunk/DOC/TexFiles/Chapters/Chap_ASM.tex

    r4147 r6997  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter Assimilation increments (ASM) 
     
    172174\end{verbatim} 
    173175\end{alltt} 
     176\end{document} 
  • trunk/DOC/TexFiles/Chapters/Chap_CFG.tex

    r4147 r6997  
     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} 
  • trunk/DOC/TexFiles/Chapters/Chap_Conservation.tex

    r3294 r6997  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13 
    24% ================================================================ 
     
    333335not been implemented. 
    334336 
     337\end{document} 
  • trunk/DOC/TexFiles/Chapters/Chap_DIA.tex

    r6497 r6997  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter I/O & Diagnostics 
     
    17581760%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    17591761\begin{figure}[!t]     \begin{center} 
    1760 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_mask_subasins.pdf} 
     1762\includegraphics[width=1.0\textwidth]{Fig_mask_subasins} 
    17611763\caption{   \label{Fig_mask_subasins} 
    17621764Decomposition of the World Ocean (here ORCA2) into sub-basin used in to compute 
     
    18401842 
    18411843 
     1844\end{document} 
  • trunk/DOC/TexFiles/Chapters/Chap_DIU.tex

    r6289 r6997  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Diurnal SST models (DIU) 
     
    162164\end{equation} 
    163165 
    164  
     166\end{document} 
  • trunk/DOC/TexFiles/Chapters/Chap_DOM.tex

    r6497 r6997  
     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:  
     
    568570%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    569571\begin{figure}[!tb]    \begin{center} 
    570 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_zgr.pdf} 
     572\includegraphics[width=0.90\textwidth]{Fig_zgr} 
    571573\caption{ \label{Fig_zgr}     
    572574Default vertical mesh for ORCA2: 30 ocean levels (L30). Vertical level functions for  
     
    801803%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    802804\begin{figure}[!ht]    \begin{center} 
    803 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_sco_function.pdf} 
     805\includegraphics[width=1.0\textwidth]{Fig_sco_function} 
    804806\caption{  \label{Fig_sco_function}    
    805807Examples of the stretching function applied to a seamount; from left to right:  
     
    847849%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    848850\begin{figure}[!ht] 
    849    \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/FIG_DOM_compare_coordinates_surface.pdf} 
     851   \includegraphics[width=1.0\textwidth]{FIG_DOM_compare_coordinates_surface} 
    850852        \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.} 
    851853    \label{fig_compare_coordinates_surface} 
     
    943945(typical of the tropical ocean), see \rou{istate\_t\_s} subroutine called from \mdl{istate} module. 
    944946\end{description} 
     947\end{document} 
  • trunk/DOC/TexFiles/Chapters/Chap_DYN.tex

    r6320 r6997  
     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} 
  • trunk/DOC/TexFiles/Chapters/Chap_LBC.tex

    r6289 r6997  
     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} 
  • trunk/DOC/TexFiles/Chapters/Chap_LDF.tex

    r6289 r6997  
     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} 
  • trunk/DOC/TexFiles/Chapters/Chap_MISC.tex

    r6289 r6997  
     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 
  • trunk/DOC/TexFiles/Chapters/Chap_Model_Basics.tex

    r6289 r6997  
     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 
  • trunk/DOC/TexFiles/Chapters/Chap_Model_Basics_zstar.tex

    r6140 r6997  
     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} 
  • trunk/DOC/TexFiles/Chapters/Chap_OBS.tex

    r6140 r6997  
     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} 
  • trunk/DOC/TexFiles/Chapters/Chap_SBC.tex

    r6497 r6997  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter —— Surface Boundary Condition (SBC, ISF, ICB)  
     
    11331135%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    11341136\begin{figure}[!t]    \begin{center} 
    1135 \includegraphics[width=0.8\textwidth]{./TexFiles/Figures/Fig_SBC_diurnal.pdf} 
     1137\includegraphics[width=0.8\textwidth]{Fig_SBC_diurnal} 
    11361138\caption{ \label{Fig_SBC_diurnal}     
    11371139Example of recontruction of the diurnal cycle variation of short wave flux   
     
    11661168%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    11671169\begin{figure}[!t]  \begin{center} 
    1168 \includegraphics[width=0.7\textwidth]{./TexFiles/Figures/Fig_SBC_dcy.pdf} 
     1170\includegraphics[width=0.7\textwidth]{Fig_SBC_dcy} 
    11691171\caption{ \label{Fig_SBC_dcy}    
    11701172Example of recontruction of the diurnal cycle variation of short wave flux   
     
    13611363 
    13621364 
     1365\end{document} 
  • trunk/DOC/TexFiles/Chapters/Chap_STO.tex

    r6497 r6997  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter stochastic parametrization of EOS (STO) 
     
    172174only  when \np{ln\_rstseed} is set to \textit{true}, $i.e.$ when the state of  
    173175the random number generator is read in the restart file. 
     176 
     177 
     178\end{document} 
  • trunk/DOC/TexFiles/Chapters/Chap_STP.tex

    r6140 r6997  
     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} 
  • trunk/DOC/TexFiles/Chapters/Chap_TRA.tex

    r6497 r6997  
     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  
     
    869871%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    870872\begin{figure}[!t]     \begin{center} 
    871 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_TRA_Irradiance.pdf} 
     873\includegraphics[width=1.0\textwidth]{Fig_TRA_Irradiance} 
    872874\caption{    \label{Fig_traqsr_irradiance} 
    873875Penetration profile of the downward solar irradiance calculated by four models.  
     
    890892%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    891893\begin{figure}[!t]     \begin{center} 
    892 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_TRA_geoth.pdf} 
     894\includegraphics[width=1.0\textwidth]{Fig_TRA_geoth} 
    893895\caption{   \label{Fig_geothermal} 
    894896Geothermal Heat flux (in $mW.m^{-2}$) used by \cite{Emile-Geay_Madec_OS09}. 
     
    10001002%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    10011003\begin{figure}[!t]   \begin{center} 
    1002 \includegraphics[width=0.7\textwidth]{./TexFiles/Figures/Fig_BBL_adv.pdf} 
     1004\includegraphics[width=0.7\textwidth]{Fig_BBL_adv} 
    10031005\caption{   \label{Fig_bbl}   
    10041006Advective/diffusive Bottom Boundary Layer. The BBL parameterisation is  
     
    11581160The restoration coefficient can be set to zero in equatorial regions by specifying a positive value of \np{nn\_hdmp}.  
    11591161Equatorward of this latitude the restoration coefficient will be zero with a smooth transition to  
    1160 the full values of a 10$^{\circ}$ latitud band.  
     1162the full values of a 10\deg latitud band.  
    11611163This is often used because of the short adjustment time scale in the equatorial region  
    11621164\citep{Reverdin1991, Fujio1991, Marti_PhD92}. The time scale associated with the damping depends on the depth as a  
     
    12581260rational function approximation for hydrographic data analysis  \citep{TEOS10}.  
    12591261A key point is that conservative state variables are used:  
    1260 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: $\Theta$). 
    12611263The pressure in decibars is approximated by the depth in meters.  
    12621264With TEOS10, the specific heat capacity of sea water, $C_p$, is a constant. It is set to  
    1263 $C_p=3991.86795711963~J\,Kg^{-1}\,\degres K^{-1}$, according to \citet{TEOS10}. 
     1265$C_p=3991.86795711963~J\,Kg^{-1}\,^{\circ}K^{-1}$, according to \citet{TEOS10}. 
    12641266 
    12651267Choosing polyTEOS10-bsq implies that the state variables used by the model are  
     
    12741276to accurately fit EOS80 (Roquet, personal comm.). The state variables used in both the EOS80  
    12751277and the ocean model are:  
    1276 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: $\theta$). 
    12771279The pressure in decibars is approximated by the depth in meters.   
    12781280With thsi EOS, the specific heat capacity of sea water, $C_p$, is a function of temperature,  
     
    14081410%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    14091411\begin{figure}[!p]    \begin{center} 
    1410 \includegraphics[width=0.9\textwidth]{./TexFiles/Figures/Partial_step_scheme.pdf} 
     1412\includegraphics[width=0.9\textwidth]{Partial_step_scheme} 
    14111413\caption{   \label{Fig_Partial_step_scheme}  
    14121414Discretisation of the horizontal difference and average of tracers in the $z$-partial  
     
    14751477\gmcomment{gm :   this last remark has to be done} 
    14761478%%% 
     1479\end{document} 
  • trunk/DOC/TexFiles/Chapters/Chap_ZDF.tex

    r6497 r6997  
     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. } 
     
    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 $A_f^{vT}$  
     
    11291131baroclinic and barotropic components which is appropriate when using either the 
    11301132explicit or filtered surface pressure gradient algorithms (\key{dynspg\_exp} or  
    1131 {\key{dynspg\_flt}). Extra attention is required, however, when using  
     1133\key{dynspg\_flt}). Extra attention is required, however, when using  
    11321134split-explicit time stepping (\key{dynspg\_ts}). In this case the free surface  
    11331135equation is solved with a small time step \np{rn\_rdt}/\np{nn\_baro}, while the three  
     
    12441246%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    12451247\begin{figure}[!t]   \begin{center} 
    1246 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_ZDF_M2_K1_tmx.pdf} 
     1248\includegraphics[width=0.90\textwidth]{Fig_ZDF_M2_K1_tmx} 
    12471249\caption{  \label{Fig_ZDF_M2_K1_tmx}  
    12481250(a) M2 and (b) K1 internal wave drag energy from \citet{Carrere_Lyard_GRL03} ($W/m^2$). } 
     
    13551357 
    13561358 
     1359\end{document} 
  • trunk/DOC/TexFiles/Chapters/Introduction.tex

    r6289 r6997  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13 
    24% ================================================================ 
     
    261263\begin{enumerate} 
    262264\item ... ;  
    263 \end{enumerate} 
    264  
    265  
     265 
     266 
     267\end{enumerate} 
     268 
     269 
     270\end{document} 
  • trunk/DOC/TexFiles/Styles/math_abbrev.sty

    r6993 r6997  
    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}}} 
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