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Changeset 7492 – NEMO

Changeset 7492


Ignore:
Timestamp:
2016-12-13T17:45:59+01:00 (8 years ago)
Author:
timgraham
Message:

Final merge of head of v3.6 STABLE branch into this branch

Location:
branches/UKMO/v3_6_extra_CMIP6_diagnostics
Files:
12 deleted
47 edited
11 copied

Legend:

Unmodified
Added
Removed

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/DOC/NEMO_book.tex

    r7491 r7492  
    44% (C) Xavier Perseguers 2002 - xavier.perseguers@epfl.ch 
    55 
    6 \documentclass[a4paper,11pt]{book} 
    7 %\documentclass[a4paper,11pt,makeidx]{book} <== may need this to generate index 
     6% ================================================================ 
     7% PREAMBLE 
     8% ================================================================ 
    89 
    9 %  makeindex NEMO_book     <== to regenerate the index 
    10 %  bibtex         NEMO_book   <== to generate  the bibliography 
     10\include{TexFiles/Preamble} 
    1111 
    1212% ================================================================ 
    13 % HEADERS DEFINITION 
     13% TOP MATTER 
    1414% ================================================================ 
    1515 
    16 \usepackage[french]{babel} 
    17 %\usepackage{color} 
    18 \usepackage{xcolor} 
    19 %\usepackage{graphics}           % allows insertion of pictures 
    20 \usepackage{graphicx}            % allows insertion of pictures 
    21 \usepackage[capbesideposition={top,center}]{floatrow} % allows captions 
    22 \floatsetup[table]{style=plaintop}                                   % beside pictures 
    23 \usepackage[margin=10pt,font={small},labelsep=colon,labelfont={bf}]{caption} % Gives small font for captions 
    24 \usepackage{enumitem}                          % allows non-bold description items 
    25 \usepackage{longtable}                         % allows multipage tables 
    26 %\usepackage{colortbl}                           % gives coloured panels behind table columns 
    27  
    28 %hyperref 
    29 \usepackage[               % 
    30   pdftitle={NEMO ocean engine},  % 
    31   pdfauthor={Gurvan Madec},      % pdfsubject={The preprint document class 
    32                                        % elsart},% pdfkeywords={diapycnal diffusion,numerical mixing,z-level models},% 
    33   pdfstartview=FitH,          % 
    34   bookmarks=true,          % 
    35   bookmarksopen=true,         % 
    36   breaklinks=true,            % 
    37   colorlinks=true,            % 
    38   linkcolor=blue,anchorcolor=blue,  % 
    39   citecolor=blue,filecolor=blue,    % 
    40  menucolor=blue,                    % 
    41   urlcolor=blue]{hyperref} 
    42 %  usage of exteranl hyperlink :  \href{mailto:my_address@wikibooks.org}{my\_address@wikibooks.org} 
    43 %                                                 \url{http://www.wikibooks.org} 
    44 %                                     or         \href{http://www.wikibooks.org}{wikibooks home} 
    45  
    46  
    47  
    48 %%%% page styles etc................ 
    49 \usepackage{fancyhdr} 
    50 \pagestyle{fancy} 
    51 % with this we ensure that the chapter and section 
    52 % headings are in lowercase. 
    53 \renewcommand{\chaptermark}[1]{\markboth{#1}{}} 
    54 \renewcommand{\sectionmark}[1]{\markright{\thesection.\ #1}} 
    55 \fancyhf{}             % delete current setting for header and footer 
    56 \fancyhead[LE,RO]{\bfseries\thepage} 
    57 \fancyhead[LO]{\bfseries\hspace{-0em}\rightmark} 
    58 \fancyhead[RE]{\bfseries\leftmark} 
    59 \renewcommand{\headrulewidth}{0.5pt} 
    60 \renewcommand{\footrulewidth}{0pt} 
    61 \addtolength{\headheight}{2.6pt}   % make space for the rule 
    62 %\addtolength{\headheight}{1.6pt}   % make space for the rule 
    63 \fancypagestyle{plain}{ 
    64   \fancyhead{}         % get rid of headers on plain pages 
    65   \renewcommand{\headrulewidth}{0pt}  % and the line 
    66 } 
    67  
    68  
    69 %%%%  Section number in Margin....... 
    70 % typeset the number of each section in the left margin, with the start of each instance of 
    71 % sectional heading text aligned with the left hand edge of  the body text. 
    72 \makeatletter 
    73 \def\@seccntformat#1{\protect\makebox[0pt][r]{\csname the#1\endcsname\quad}} 
    74 \makeatother 
    75  
    76 % Leave blank pages completely empty, w/o header 
    77 \makeatletter 
    78 \def\cleardoublepage{\clearpage\if@twoside \ifodd\c@page\else 
    79   \hbox{} 
    80   \vspace*{\fill} 
    81   \vspace{\fill} 
    82   \thispagestyle{empty} 
    83   \newpage 
    84   \if@twocolumn\hbox{}\newpage\fi\fi\fi} 
    85 \makeatother 
    86  
    87 %%%% define the chapter  style ................ 
    88 \usepackage{minitoc}          %In French : \usepackage[french]{minitoc} 
    89 %\usepackage{mtcoff}          % invalidate the use of minitocs 
    90 \usepackage{fancybox} 
    91  
    92 \makeatletter 
    93 \def\LigneVerticale{\vrule height 5cm depth 2cm\hspace{0.1cm}\relax} 
    94 \def\LignesVerticales{% 
    95   \let\LV\LigneVerticale\LV\LV\LV\LV\LV\LV\LV\LV\LV\LV} 
    96 \def\GrosCarreAvecUnChiffre#1{% 
    97   \rlap{\vrule height 0.8cm width 1cm depth 0.2cm}% 
    98  \rlap{\hbox to 1cm{\hss\mbox{\color{white} #1}\hss}}% 
    99   \vrule height 0pt width 1cm depth 0pt} 
    100 \def\GrosCarreAvecTroisChiffre#1{% 
    101   \rlap{\vrule height 0.8cm width 1.6cm depth 0.2cm}% 
    102  \rlap{\hbox to 1.5cm{\hss\mbox{\color{white} #1}\hss}}% 
    103   \vrule height 0pt width 1cm depth 0pt} 
    104  
    105 \def\@makechapterhead#1{\hbox{% 
    106    \huge 
    107     \LignesVerticales 
    108     \hspace{-0.5cm}% 
    109     \GrosCarreAvecUnChiffre{\thechapter} 
    110     \hspace{0.2cm}\hbox{#1}% 
    111 %    \GrosCarreAvecTroisChiffre{\thechapter} 
    112 %    \hspace{1cm}\hbox{#1}% 
    113 %}\par\vskip 2cm} 
    114 }\par\vskip 1cm} 
    115 \def\@makeschapterhead#1{\hbox{% 
    116    \huge 
    117     \LignesVerticales 
    118     %\hspace{0.5cm}% 
    119     \hbox{#1}% 
    120 }\par\vskip 2cm} 
    121 \makeatother 
    122  
    123 %\def\thechapter{\Roman{chapter}}      % chapter number to be Roman 
    124  
    125  
    126 %%%%           Mathematics............... 
    127 %\documentclass{amsart} 
    128 \usepackage{xspace}                              % helpd ensure correct spacing after macros 
    129 \usepackage{latexsym} 
    130 \usepackage{amssymb} 
    131 \usepackage{amsmath} 
    132 \allowdisplaybreaks[1]           % allow page breaks in the middle of equations 
    133 \usepackage{./TexFiles/math_abbrev}    % use maths shortcuts 
    134  
    135  
    136 \usepackage{times}                % use times font for text 
    137 %\usepackage{mathtime}                          % font for illustrator to work (belleek fonts ) 
    138 %\usepackage[latin1]{inputenc}                % allows some unicode removed (agn) 
    139  
    140  
    141 %%% essai commande 
    142 \newcommand{\nl} [1] {\texttt{\small {\textcolor{blue}{#1}} } } 
    143 \newcommand{\nlv} [1] {\texttt{\footnotesize#1}\xspace} 
    144 \newcommand{\smnlv} [1] {\texttt{\scriptsize#1}\xspace} 
    145  
    146 %%%% namelist & code display................................ 
    147 \usepackage{alltt}      %%  alltt for namelist 
    148 \usepackage{verbatim}   %%  alltt for namelist 
    149 % namelists 
    150 \newcommand{\namdisplay} [1] { 
    151 \begin{alltt} 
    152 {\tiny \verbatiminput{./TexFiles/Namelist/#1}} 
    153 \end{alltt} 
    154   \vspace{-10pt} 
    155 } 
    156 % code display 
    157 %\newcommand{\codedisplay} [1] { \begin{alltt} {\tiny  {\begin{verbatim} {#1}} \end{verbatim} }  \end{alltt}   } 
    158  
    159  
    160  
    161 %%%% commands for working with text................................ 
    162 % command to "comment out" portions of text ({} argument) or not ({#1} argument) 
    163 \newcommand{\amtcomment}[1]{}    % command to "commented out" portions of text or not (#1 in argument) 
    164 \newcommand{\sgacomment}[1]{}    % command to "commented out" portions of 
    165 \newcommand{\gmcomment}[1]{}     % command to "commented out" portions of 
    166 %                                               % text that span line breaks 
    167 %Red (NR) or Yellow(WARN) 
    168 %\newcommand{\NR} {\colorbox{red}{#1}} 
    169 %\newcommand{\WARN} {{ \colorbox{yellow}{#1}} } 
    170  
    171  
    172  
    173 %%% index commands...................... 
    174 \usepackage{makeidx} 
    175 %\usepackage{showidx}            % show the index entry 
    176  
    177 \newcommand{\mdl} [1] {\textit{#1.F90}\index{Modules!#1}}         %module (mdl) 
    178 \newcommand{\rou} [1] {\textit{#1}\index{Routines!#1}}            %module (routine) 
    179 \newcommand{\hf} [1] {\textit{#1.h90}\index{h90 file!#1}}            %module (h90 files) 
    180 \newcommand{\ngn} [1] {\textit{#1}\index{Namelist Group Name!#1}}    %namelist name (nampar) 
    181 \newcommand{\np} [1] {\textit{#1}\index{Namelist variables!#1}}             %namelist variable 
    182 \newcommand{\jp} [1] {\textit{#1}\index{Model parameters!#1}}        %model parameter (jp) 
    183 \newcommand{\pp} [1] {\textit{#1}\index{Model parameters!#1}}        %namelist parameter (pp) 
    184 \newcommand{\ifile} [1] {\textit{#1.nc}\index{Input NetCDF files!#1.nc}}   %input NetCDF files (.nc) 
    185 \newcommand{\key} [1] {\textbf{key\_#1}\index{CPP keys!key\_#1}}  %key_cpp (key) 
    186 \newcommand{\NEMO} {\textit{NEMO}\xspace}                %NEMO (nemo) 
    187  
    188 %%%%   Bibliography   ............. 
    189 \usepackage[nottoc, notlof, notlot]{tocbibind} 
    190 \usepackage[square, comma]{natbib} 
    191 \bibpunct{[}{]}{,}{a}{}{;}                           %suppress "," after "et al." 
    192 \providecommand{\bibfont}{\small} 
    193  
     16\include{TexFiles/Top_Matter} 
    19417 
    19518% ================================================================ 
    196 % FRONT PAGE 
    197 % ================================================================ 
    198  
    199 %\usepackage{pstricks} 
    200 \title{ 
    201 %\psset{unit=1.1in,linewidth=4pt}   %parameters of the units for pstricks 
    202 % \rput(0,2){ \includegraphics[width=1.1\textwidth]{./TexFiles/Figures/logo_ALL.pdf}             } \\ 
    203 % \vspace{0.1cm} 
    204 \vspace{-6.0cm} 
    205 \includegraphics[width=1.1\textwidth]{./TexFiles/Figures/logo_ALL.pdf}\\ 
    206 \vspace{5.1cm} 
    207 \includegraphics[width=0.9\textwidth]{./TexFiles/Figures/NEMO_logo_Black.pdf} \\ 
    208 \vspace{1.4cm} 
    209 \rule{345pt}{1.5pt} \\ 
    210 \vspace{0.45cm} 
    211 {\Huge NEMO ocean engine} 
    212 \rule{345pt}{1.5pt} \\ 
    213  } 
    214 %{ -- Draft --}   } 
    215 %\date{\today} 
    216 \date{ 
    217 January 2016  \\ 
    218 {\small  -- version 3.6 stable --} \\ 
    219 ~  \\ 
    220 \textit{\small Note du P\^ole de mod\'{e}lisation de l'Institut Pierre-Simon Laplace No 27 }\\ 
    221 \vspace{0.45cm} 
    222 { ISSN No 1288-1619.} 
    223 } 
    224  
    225  
    226 \author{ 
    227 \Large Gurvan Madec, and the NEMO team  \\ 
    228  \texttt{\small gurvan.madec@locean-ipsl.umpc.fr} \\ 
    229  \texttt{\small nemo\_st@locean-ipsl.umpc.fr} \\ 
    230 %{\small Laboratoire d'Oc\'{e}anographie  et du Climat: Exp\'{e}rimentation et Approches Num\'{e}riques } 
    231 } 
    232  
    233 \dominitoc 
    234 \makeindex        %type this first :     makeindex -s NEMO.ist NEMO_book.idx 
    235  
    236 % ================================================================ 
    237 %      Include ONLY order 
    238 % ================================================================ 
    239  
    240 %\includeonly{./TexFiles/Chapters/Chap_MISC} 
    241 %\includeonly{./TexFiles/Chapters/Chap_ZDF} 
    242 %\includeonly{./TexFiles/Chapters/Chap_STP,./TexFiles/Chapters/Chap_SBC,./TexFiles/Chapters/Chap_TRA} 
    243 %\includeonly{./TexFiles/Chapters/Chap_LBC,./TexFiles/Chapters/Chap_MISC} 
    244 %\includeonly{./TexFiles/Chapters/Chap_Model_Basics} 
    245 %\includeonly{./TexFiles/Chapters/Annex_A,./TexFiles/Chapters/Annex_B,./TexFiles/Chapters/Annex_C,./TexFiles/Chapters/Annex_D} 
    246  
    247 % ================================================================ 
     19% DOCUMENT 
    24820% ================================================================ 
    24921 
    … …  
    26436% ================================================================ 
    26537 
    266 \include{./TexFiles/Chapters/Abstracts_Foreword} 
     38\subfile{TexFiles/Chapters/Abstracts_Foreword} 
    26739 
    26840% ================================================================ 
    … …  
    27042% ================================================================ 
    27143 
    272 \include{./TexFiles/Chapters/Introduction} 
     44\subfile{TexFiles/Chapters/Introduction} 
    27345 
    27446% ================================================================ 
    … …  
    27648% ================================================================ 
    27749 
    278 \include{./TexFiles/Chapters/Chap_Model_Basics} 
     50\subfile{TexFiles/Chapters/Chap_Model_Basics} 
    27951 
    280 \include{./TexFiles/Chapters/Chap_STP}       % Time discretisation (time stepping strategy) 
     52\subfile{TexFiles/Chapters/Chap_STP}         % Time discretisation (time stepping strategy) 
    28153 
    282 \include{./TexFiles/Chapters/Chap_DOM}       % Space discretisation 
     54\subfile{TexFiles/Chapters/Chap_DOM}         % Space discretisation 
    28355 
    284 \include{./TexFiles/Chapters/Chap_TRA}       % Tracer advection/diffusion equation 
     56\subfile{TexFiles/Chapters/Chap_TRA}         % Tracer advection/diffusion equation 
    28557 
    286 \include{./TexFiles/Chapters/Chap_DYN}       % Dynamics : momentum equation 
     58\subfile{TexFiles/Chapters/Chap_DYN}         % Dynamics : momentum equation 
    28759 
    288 \include{./TexFiles/Chapters/Chap_SBC}       % Surface Boundary Conditions 
     60\subfile{TexFiles/Chapters/Chap_SBC}         % Surface Boundary Conditions 
    28961 
    290 \include{./TexFiles/Chapters/Chap_LBC}       % Lateral Boundary Conditions 
     62\subfile{TexFiles/Chapters/Chap_LBC}         % Lateral Boundary Conditions 
    29163 
    292 \include{./TexFiles/Chapters/Chap_LDF}       % Lateral diffusion 
     64\subfile{TexFiles/Chapters/Chap_LDF}         % Lateral diffusion 
    29365 
    294 \include{./TexFiles/Chapters/Chap_ZDF}       % Vertical diffusion 
     66\subfile{TexFiles/Chapters/Chap_ZDF}         % Vertical diffusion 
    29567 
    296 \include{./TexFiles/Chapters/Chap_DIA}       % Outputs and Diagnostics 
     68\subfile{TexFiles/Chapters/Chap_DIA}         % Outputs and Diagnostics 
    29769 
    298 \include{./TexFiles/Chapters/Chap_OBS}          % Observation operator 
     70\subfile{TexFiles/Chapters/Chap_OBS}                    % Observation operator 
    29971 
    300 \include{./TexFiles/Chapters/Chap_ASM}          % Assimilation increments 
     72\subfile{TexFiles/Chapters/Chap_ASM}                    % Assimilation increments 
    30173 
    302 \include{./TexFiles/Chapters/Chap_STO}          % Stochastic param. 
     74\subfile{TexFiles/Chapters/Chap_STO}                    % Stochastic param. 
    30375 
    304 \include{./TexFiles/Chapters/Chap_MISC}         % Miscellaneous topics 
     76\subfile{TexFiles/Chapters/Chap_MISC}        % Miscellaneous topics 
    30577 
    306 \include{./TexFiles/Chapters/Chap_CFG}       % Predefined configurations 
     78\subfile{TexFiles/Chapters/Chap_CFG}         % Predefined configurations 
    30779 
    30880% ================================================================ 
    … …  
    31284\appendix 
    31385 
    314 %\include{./TexFiles/Chapters/Chap_Conservation} 
    315 \include{./TexFiles/Chapters/Annex_A}        % generalised vertical coordinate 
    316 \include{./TexFiles/Chapters/Annex_B}        % diffusive operator 
    317 \include{./TexFiles/Chapters/Annex_C}        % Discrete invariants of the eqs. 
    318 \include{./TexFiles/Chapters/Annex_ISO}                     % Isoneutral diffusion using triads 
    319 \include{./TexFiles/Chapters/Annex_D}        % Coding rules 
    320 %\include{./TexFiles/Chapters/Annex_E}                   % Notes on some on going staff (no included in the DOC) 
    321 %\include{./TexFiles/Chapters/Annex_Fox-Kemper}   % Notes on Fox-Kemper (no included in the DOC) 
    322 %\include{./TexFiles/Chapters/Annex_EVP}           % Notes on EVP (no included in the DOC) 
     86%\subfile{TexFiles/Chapters/Chap_Conservation} 
     87\subfile{TexFiles/Chapters/Annex_A}       % generalised vertical coordinate 
     88\subfile{TexFiles/Chapters/Annex_B}       % diffusive operator 
     89\subfile{TexFiles/Chapters/Annex_C}       % Discrete invariants of the eqs. 
     90\subfile{TexFiles/Chapters/Annex_ISO}                    % Isoneutral diffusion using triads 
     91\subfile{TexFiles/Chapters/Annex_D}       % Coding rules 
     92%\subfile{TexFiles/Chapters/Annex_E}                     % Notes on some on going staff (no included in the DOC) 
     93%\subfile{TexFiles/Chapters/Annex_Fox-Kemper}   % Notes on Fox-Kemper (no included in the DOC) 
     94%\subfile{TexFiles/Chapters/Annex_EVP}          % Notes on EVP (no included in the DOC) 
    32395 
    32496% ================================================================ 
    … …  
    334106 
    335107%%\bibliographystyle{plainat} 
    336 \bibliographystyle{./TexFiles/ametsoc}    % AMS biblio style (JPO) 
    337 \bibliography{./TexFiles/Biblio/Biblio} 
     108\bibliographystyle{TexFiles/Styles/ametsoc}     % AMS biblio style (JPO) 
     109\bibliography{TexFiles/Bibliography/Biblio} 
    338110 
    339111% ================================================================ 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/DOC/NEMO_coding.conv.tex

    r7491 r7492  
    77\usepackage{framed}  
    88\usepackage{makeidx}  
    9  
     9\graphicspath{{Figures/}} 
    1010 
    1111%%%%%%% 
    … …  
    3131 
    3232\title{  
    33 \includegraphics[width=0.3\textwidth]{./TexFiles/Figures/NEMO_logo_Black.pdf} \\ 
     33\includegraphics[width=0.3\textwidth]{NEMO_logo_Black} \\ 
    3434\vspace{1.0cm} 
    3535\rule{345pt}{1.5pt} \\ 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/DOC/TexFiles/Chapters/Abstracts_Foreword.tex

    r7491 r7492  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13 
    24% ================================================================ 
    … …  
    2426 
    2527% ================================================================ 
    26  \vspace{0.5cm} 
     28% \vspace{0.5cm} 
    2729 
    28 Le moteur oc\'{e}anique de NEMO (Nucleus for European Modelling of the Ocean) est un  
    29 mod\`{e}le aux \'{e}quations primitives de la circulation oc\'{e}anique r\'{e}gionale et globale.  
    30 Il se veut un outil flexible pour \'{e}tudier sur un vaste spectre spatiotemporel l'oc\'{e}an et ses  
    31 interactions avec les autres composantes du syst\`{e}me climatique terrestre.  
    32 Les variables pronostiques sont le champ tridimensionnel de vitesse, une hauteur de la mer  
    33 lin\'{e}aire, la Temp\'{e}rature Conservative et la Salinit\'{e} Absolue.  
    34 La distribution des variables se fait sur une grille C d'Arakawa tridimensionnelle utilisant une  
    35 coordonn\'{e}e verticale $z$ \`{a} niveaux entiers ou partiels, ou une coordonn\'{e}e s, ou encore  
    36 une combinaison des deux. Diff\'{e}rents choix sont propos\'{e}s pour d\'{e}crire la physique  
    37 oc\'{e}anique, incluant notamment des physiques verticales TKE et GLS. A travers l'infrastructure  
    38 NEMO, l'oc\'{e}an est interfac\'{e} avec des mod\`{e}les de glace de mer (LIM ou CICE),  
    39 de biog\'{e}ochimie marine et de traceurs passifs, et, via le coupleur OASIS, \`{a} plusieurs  
    40 mod\`{e}les de circulation g\'{e}n\'{e}rale atmosph\'{e}rique.  
    41 Il supporte \'{e}galement l'embo\^{i}tement interactif de maillages via le logiciel AGRIF. 
     30%Le moteur oc\'{e}anique de NEMO (Nucleus for European Modelling of the Ocean) est un  
     31%mod\`{e}le aux \'{e}quations primitives de la circulation oc\'{e}anique r\'{e}gionale et globale.  
     32%Il se veut un outil flexible pour \'{e}tudier sur un vaste spectre spatiotemporel l'oc\'{e}an et ses  
     33%interactions avec les autres composantes du syst\`{e}me climatique terrestre.  
     34%Les variables pronostiques sont le champ tridimensionnel de vitesse, une hauteur de la mer  
     35%lin\'{e}aire, la Temp\'{e}rature Conservative et la Salinit\'{e} Absolue.  
     36%La distribution des variables se fait sur une grille C d'Arakawa tridimensionnelle utilisant une  
     37%coordonn\'{e}e verticale $z$ \`{a} niveaux entiers ou partiels, ou une coordonn\'{e}e s, ou encore  
     38%une combinaison des deux. Diff\'{e}rents choix sont propos\'{e}s pour d\'{e}crire la physique  
     39%oc\'{e}anique, incluant notamment des physiques verticales TKE et GLS. A travers l'infrastructure  
     40%NEMO, l'oc\'{e}an est interfac\'{e} avec des mod\`{e}les de glace de mer (LIM ou CICE),  
     41%de biog\'{e}ochimie marine et de traceurs passifs, et, via le coupleur OASIS, \`{a} plusieurs  
     42%mod\`{e}les de circulation g\'{e}n\'{e}rale atmosph\'{e}rique.  
     43%Il supporte \'{e}galement l'embo\^{i}tement interactif de maillages via le logiciel AGRIF. 
    4244}  
    4345 
    … …  
    6971 \vspace{0.5cm} 
    7072 
     73\end{document} 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/DOC/TexFiles/Chapters/Annex_A.tex

    r7491 r7492  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13 
    24% ================================================================ 
    … …  
    532534expression of the 3D divergence in the $s-$coordinates established above.  
    533535 
     536\end{document} 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/DOC/TexFiles/Chapters/Annex_B.tex

    r7491 r7492  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter Ñ Appendix B : Diffusive Operators 
    … …  
    364366\eqref{Apdx_B_Lap_U} is used in both $z$- and $s$-coordinate systems, that is 
    365367a Laplacian diffusion is applied on momentum along the coordinate directions. 
     368\end{document} 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/DOC/TexFiles/Chapters/Annex_C.tex

    r7491 r7492  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter Ñ Appendix C : Discrete Invariants of the Equations 
    … …  
    15311533%%%%  end of appendix in gm comment 
    15321534%} 
     1535\end{document} 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/DOC/TexFiles/Chapters/Annex_D.tex

    r7491 r7492  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Appendix D Ñ Coding Rules 
    … …  
    202204 
    203205To be done.... 
     206\end{document} 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/DOC/TexFiles/Chapters/Annex_E.tex

    r7491 r7492  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Appendix E : Note on some algorithms 
    … …  
    299301\begin{figure}[!ht] \label{Fig_ISO_triad} 
    300302\begin{center} 
    301 \includegraphics[width=0.70\textwidth]{./TexFiles/Figures/Fig_ISO_triad.pdf} 
     303\includegraphics[width=0.70\textwidth]{Fig_ISO_triad} 
    302304\caption{  \label{Fig_ISO_triad}    
    303305Triads used in the Griffies's like iso-neutral diffision scheme for  
    … …  
    806808tracer is preserved by the discretisation of the skew fluxes. 
    807809 
     810\end{document} 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/DOC/TexFiles/Chapters/Annex_ISO.tex

    r7491 r7492  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Iso-neutral diffusion : 
    … …  
    201203% >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    202204\begin{figure}[h] \begin{center} 
    203     \includegraphics[width=1.05\textwidth]{./TexFiles/Figures/Fig_GRIFF_triad_fluxes} 
     205    \includegraphics[width=1.05\textwidth]{Fig_GRIFF_triad_fluxes} 
    204206    \caption{ \label{fig:triad:ISO_triad} 
    205207      (a) Arrangement of triads $S_i$ and tracer gradients to 
    … …  
    269271% >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    270272\begin{figure}[h] \begin{center} 
    271     \includegraphics[width=0.80\textwidth]{./TexFiles/Figures/Fig_GRIFF_qcells} 
     273    \includegraphics[width=0.80\textwidth]{Fig_GRIFF_qcells} 
    272274    \caption{   \label{fig:triad:qcells} 
    273275    Triad notation for quarter cells. $T$-cells are inside 
    … …  
    676678% >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    677679\begin{figure}[h] \begin{center} 
    678     \includegraphics[width=0.60\textwidth]{./TexFiles/Figures/Fig_GRIFF_bdry_triads} 
     680    \includegraphics[width=0.60\textwidth]{Fig_GRIFF_bdry_triads} 
    679681    \caption{  \label{fig:triad:bdry_triads} 
    680682      (a) Uppermost model layer $k=1$ with $i,1$ and $i+1,1$ tracer 
    … …  
    849851    different $i_p,k_p$, denoted by different colours, (e.g. the green 
    850852    triad $i_p=1/2,k_p=-1/2$) are tapered to the appropriate basal triad.}} 
    851   {\includegraphics[width=0.60\textwidth]{./TexFiles/Figures/Fig_GRIFF_MLB_triads}} 
     853  {\includegraphics[width=0.60\textwidth]{Fig_GRIFF_MLB_triads}} 
    852854\end{figure} 
    853855% >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    … …  
    11931195\end{split} 
    11941196\end{equation} 
     1197\end{document} 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/DOC/TexFiles/Chapters/Chap_ASM.tex

    r7491 r7492  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter Assimilation increments (ASM) 
    … …  
    172174\end{verbatim} 
    173175\end{alltt} 
     176\end{document} 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/DOC/TexFiles/Chapters/Chap_CFG.tex

    r7491 r7492  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter � Configurations 
    … …  
    8890%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    8991\begin{figure}[!t]   \begin{center} 
    90 \includegraphics[width=0.98\textwidth]{./TexFiles/Figures/Fig_ORCA_NH_mesh.pdf} 
     92\includegraphics[width=0.98\textwidth]{Fig_ORCA_NH_mesh} 
    9193\caption{  \label{Fig_MISC_ORCA_msh}      
    92 ORCA mesh conception. The departure from an isotropic Mercator grid start poleward of 20\deg N. 
     94ORCA mesh conception. The departure from an isotropic Mercator grid start poleward of 20\degN. 
    9395The two "north pole" are the foci of a series of embedded ellipses (blue curves)  
    9496which are determined analytically and form the i-lines of the ORCA mesh (pseudo latitudes).  
    … …  
    115117%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    116118\begin{figure}[!tbp]  \begin{center} 
    117 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_ORCA_NH_msh05_e1_e2.pdf} 
    118 \includegraphics[width=0.80\textwidth]{./TexFiles/Figures/Fig_ORCA_aniso.pdf} 
     119\includegraphics[width=1.0\textwidth]{Fig_ORCA_NH_msh05_e1_e2} 
     120\includegraphics[width=0.80\textwidth]{Fig_ORCA_aniso} 
    119121\caption {  \label{Fig_MISC_ORCA_e1e2} 
    120122\textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and  
    121123\textit{Bottom}: ratio of anisotropy ($e_1 / e_2$) 
    122 for ORCA 0.5\deg ~mesh. South of 20\deg N a Mercator grid is used ($e_1 = e_2$)  
    123 so that the anisotropy ratio is 1. Poleward of 20\deg N, the two "north pole"  
     124for ORCA 0.5\deg ~mesh. South of 20\degN a Mercator grid is used ($e_1 = e_2$)  
     125so that the anisotropy ratio is 1. Poleward of 20\degN, the two "north pole"  
    124126introduce a weak anisotropy over the ocean areas ($< 1.2$) except in vicinity of Victoria Island  
    125127(Canadian Arctic Archipelago). } 
    … …  
    129131 
    130132The method is applied to Mercator grid ($i.e.$ same zonal and meridional grid spacing) poleward  
    131 of $20\deg$N, so that the Equator is a mesh line, which provides a better numerical solution  
     133of 20\degN, so that the Equator is a mesh line, which provides a better numerical solution  
    132134for equatorial dynamics. The choice of the series of embedded ellipses (position of the foci and  
    133135variation of the ellipses) is a compromise between maintaining  the ratio of mesh anisotropy  
    … …  
    178180The ORCA\_R2 configuration has the following specificity : starting from a 2\deg~ORCA mesh,  
    179181local mesh refinements were applied to the Mediterranean, Red, Black and Caspian Seas,  
    180 so that the resolution is $1\deg \time 1\deg$ there. A local transformation were also applied  
     182so that the resolution is 1\deg \time 1\deg there. A local transformation were also applied  
    181183with in the Tropics in order to refine the meridional resolution up to 0.5\deg at the Equator. 
    182184 
    … …  
    227229 
    228230The domain geometry is a closed rectangular basin on the $\beta$-plane centred  
    229 at $\sim 30\deg$N and rotated by 45\deg, 3180~km long, 2120~km wide  
     231at $\sim$ 30\degN and rotated by 45\deg, 3180~km long, 2120~km wide  
    230232and 4~km deep (Fig.~\ref{Fig_MISC_strait_hand}).  
    231233The domain is bounded by vertical walls and by a flat bottom. The configuration is  
    … …  
    234236The applied forcings vary seasonally in a sinusoidal manner between winter  
    235237and summer extrema \citep{Levy_al_OM10}.  
    236 The wind stress is zonal and its curl changes sign at 22\deg N and 36\deg N.  
     238The wind stress is zonal and its curl changes sign at 22\degN and 36\degN.  
    237239It forces a subpolar gyre in the north, a subtropical gyre in the wider part of the domain  
    238240and a small recirculation gyre in the southern corner.  
    … …  
    261263%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    262264\begin{figure}[!t]   \begin{center} 
    263 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_GYRE.pdf} 
     265\includegraphics[width=1.0\textwidth]{Fig_GYRE} 
    264266\caption{  \label{Fig_GYRE}    
    265267Snapshot of relative vorticity at the surface of the model domain  
    … …  
    311313temperature data. 
    312314 
     315\end{document} 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/DOC/TexFiles/Chapters/Chap_Conservation.tex

    r7491 r7492  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13 
    24% ================================================================ 
    … …  
    333335not been implemented. 
    334336 
     337\end{document} 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/DOC/TexFiles/Chapters/Chap_DIA.tex

    r7491 r7492  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter I/O & Diagnostics 
    … …  
    14781480- the turbocline depth (based on a turbulent mixing coefficient criterion) (\mdl{diahth}) 
    14791481 
    1480 - the depth of the 20\deg C isotherm (\mdl{diahth}) 
     1482- the depth of the 20\degC isotherm (\mdl{diahth}) 
    14811483 
    14821484- the depth of the thermocline (maximum of the vertical temperature gradient) (\mdl{diahth}) 
    … …  
    14861488\np{ln\_diaptr} to true (see the \textit{\ngn{namptr} } namelist below).   
    14871489When \np{ln\_subbas}~=~true, transports and stream function are computed  
    1488 for the Atlantic, Indian, Pacific and Indo-Pacific Oceans (defined north of 30\deg S)  
     1490for the Atlantic, Indian, Pacific and Indo-Pacific Oceans (defined north of 30\degS)  
    14891491as well as for the World Ocean. The sub-basin decomposition requires an input file  
    14901492(\ifile{subbasins}) which contains three 2D mask arrays, the Indo-Pacific mask  
    … …  
    14961498%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    14971499\begin{figure}[!t]     \begin{center} 
    1498 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_mask_subasins.pdf} 
     1500\includegraphics[width=1.0\textwidth]{Fig_mask_subasins} 
    14991501\caption{   \label{Fig_mask_subasins} 
    15001502Decomposition of the World Ocean (here ORCA2) into sub-basin used in to compute 
    … …  
    16821684 
    16831685 
     1686\end{document} 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/DOC/TexFiles/Chapters/Chap_DOM.tex

    r7491 r7492  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter 2 ——— Space and Time Domain (DOM) 
    … …  
    4042%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    4143\begin{figure}[!tb]    \begin{center} 
    42 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_cell.pdf} 
     44\includegraphics[width=0.90\textwidth]{Fig_cell} 
    4345\caption{ \label{Fig_cell}     
    4446Arrangement of variables. $t$ indicates scalar points where temperature,  
    … …  
    210212%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    211213\begin{figure}[!tb]  \begin{center} 
    212 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_index_hor.pdf} 
     214\includegraphics[width=0.90\textwidth]{Fig_index_hor} 
    213215\caption{   \label{Fig_index_hor}     
    214216Horizontal integer indexing used in the \textsc{Fortran} code. The dashed area indicates  
    … …  
    260262%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    261263\begin{figure}[!pt]    \begin{center} 
    262 \includegraphics[width=.90\textwidth]{./TexFiles/Figures/Fig_index_vert.pdf} 
     264\includegraphics[width=.90\textwidth]{Fig_index_vert} 
    263265\caption{ \label{Fig_index_vert}      
    264266Vertical integer indexing used in the \textsc{Fortran } code. Note that  
    … …  
    358360%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    359361\begin{figure}[!t]     \begin{center} 
    360 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_zgr_e3.pdf} 
     362\includegraphics[width=0.90\textwidth]{Fig_zgr_e3} 
    361363\caption{ \label{Fig_zgr_e3}     
    362364Comparison of (a) traditional definitions of grid-point position and grid-size in the vertical,  
    … …  
    467469%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    468470\begin{figure}[!tb]    \begin{center} 
    469 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_z_zps_s_sps.pdf} 
     471\includegraphics[width=1.0\textwidth]{Fig_z_zps_s_sps} 
    470472\caption{  \label{Fig_z_zps_s_sps}    
    471473The ocean bottom as seen by the model:  
    … …  
    578580%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    579581\begin{figure}[!tb]    \begin{center} 
    580 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_zgr.pdf} 
     582\includegraphics[width=0.90\textwidth]{Fig_zgr} 
    581583\caption{ \label{Fig_zgr}     
    582584Default vertical mesh for ORCA2: 30 ocean levels (L30). Vertical level functions for  
    … …  
    802804%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    803805\begin{figure}[!ht]    \begin{center} 
    804 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_sco_function.pdf} 
     806\includegraphics[width=1.0\textwidth]{Fig_sco_function} 
    805807\caption{  \label{Fig_sco_function}    
    806808Examples of the stretching function applied to a seamount; from left to right:  
    … …  
    842844%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    843845\begin{figure}[!ht] 
    844    \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/FIG_DOM_compare_coordinates_surface.pdf} 
     846   \includegraphics[width=1.0\textwidth]{FIG_DOM_compare_coordinates_surface} 
    845847        \caption{A comparison of the \citet{Song_Haidvogel_JCP94} $S$-coordinate (solid lines), a 50 level $Z$-coordinate (contoured surfaces) and the \citet{Siddorn_Furner_OM12} $S$-coordinate (dashed lines) in the surface 100m for a idealised bathymetry that goes from 50m to 5500m depth. For clarity every third coordinate surface is shown.} 
    846848    \label{fig_compare_coordinates_surface} 
    … …  
    939941(typical of the tropical ocean), see \rou{istate\_t\_s} subroutine called from \mdl{istate} module. 
    940942\end{description} 
     943\end{document} 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/DOC/TexFiles/Chapters/Chap_DYN.tex

    r7491 r7492  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter ——— Ocean Dynamics (DYN) 
    … …  
    293295%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    294296\begin{figure}[!ht]    \begin{center} 
    295 \includegraphics[width=0.70\textwidth]{./TexFiles/Figures/Fig_DYN_een_triad.pdf} 
     297\includegraphics[width=0.70\textwidth]{Fig_DYN_een_triad} 
    296298\caption{ \label{Fig_DYN_een_triad}   
    297299Triads used in the energy and enstrophy conserving scheme (een) for  
    … …  
    660662$\bullet$ The main hypothesis to compute the ice shelf load is that the ice shelf is in isostatic equilibrium. 
    661663 The top pressure is computed integrating a reference density profile (prescribed as density of a water at 34.4  
    662 PSU and -1.9$\degres C$) from the sea surface to the ice shelf base, which corresponds to the load of the water 
     664PSU and -1.9$^{\circ}C$) from the sea surface to the ice shelf base, which corresponds to the load of the water 
    663665column in which the ice shelf is floatting. This top pressure is constant over time. A detailed description of  
    664666this method is described in \citet{Losch2008}.\\ 
    … …  
    827829%>   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   > 
    828830\begin{figure}[!t]    \begin{center} 
    829 \includegraphics[width=0.7\textwidth]{./TexFiles/Figures/Fig_DYN_dynspg_ts.pdf} 
     831\includegraphics[width=0.7\textwidth]{Fig_DYN_dynspg_ts} 
    830832\caption{  \label{Fig_DYN_dynspg_ts} 
    831833Schematic of the split-explicit time stepping scheme for the external  
    … …  
    13321334 
    13331335% ================================================================ 
     1336\end{document} 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/DOC/TexFiles/Chapters/Chap_LBC.tex

    r7491 r7492  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter — Lateral Boundary Condition (LBC)  
    … …  
    5355%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    5456\begin{figure}[!t]     \begin{center} 
    55 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_LBC_uv.pdf} 
     57\includegraphics[width=0.90\textwidth]{Fig_LBC_uv} 
    5658\caption{  \label{Fig_LBC_uv} 
    5759Lateral boundary (thick line) at T-level. The velocity normal to the boundary is set to zero.} 
    … …  
    7678%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    7779\begin{figure}[!p] \begin{center} 
    78 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_LBC_shlat.pdf} 
     80\includegraphics[width=0.90\textwidth]{Fig_LBC_shlat} 
    7981\caption{     \label{Fig_LBC_shlat}  
    8082lateral boundary condition (a) free-slip ($rn\_shlat=0$) ; (b) no-slip ($rn\_shlat=2$)  
    … …  
    195197%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    196198\begin{figure}[!t]     \begin{center} 
    197 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_LBC_jperio.pdf} 
     199\includegraphics[width=1.0\textwidth]{Fig_LBC_jperio} 
    198200\caption{    \label{Fig_LBC_jperio} 
    199201setting of (a) east-west cyclic  (b) symmetric across the equator boundary conditions.} 
    … …  
    214216%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    215217\begin{figure}[!t]    \begin{center} 
    216 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_North_Fold_T.pdf} 
     218\includegraphics[width=0.90\textwidth]{Fig_North_Fold_T} 
    217219\caption{    \label{Fig_North_Fold_T}  
    218220North fold boundary with a $T$-point pivot and cyclic east-west boundary condition  
    … …  
    277279%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    278280\begin{figure}[!t]    \begin{center} 
    279 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_mpp.pdf} 
     281\includegraphics[width=0.90\textwidth]{Fig_mpp} 
    280282\caption{   \label{Fig_mpp}  
    281283Positioning of a sub-domain when massively parallel processing is used. } 
    … …  
    351353%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    352354\begin{figure}[!ht]     \begin{center} 
    353 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_mppini2.pdf} 
     355\includegraphics[width=0.90\textwidth]{Fig_mppini2} 
    354356\caption {    \label{Fig_mppini2} 
    355357Example of Atlantic domain defined for the CLIPPER projet. Initial grid is  
    … …  
    582584%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    583585\begin{figure}[!t]      \begin{center} 
    584 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_LBC_bdy_geom.pdf} 
     586\includegraphics[width=1.0\textwidth]{Fig_LBC_bdy_geom} 
    585587\caption {      \label{Fig_LBC_bdy_geom} 
    586588Example of geometry of unstructured open boundary} 
    … …  
    623625%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    624626\begin{figure}[!t]     \begin{center} 
    625 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_LBC_nc_header.pdf} 
     627\includegraphics[width=1.0\textwidth]{Fig_LBC_nc_header} 
    626628\caption {     \label{Fig_LBC_nc_header}  
    627629Example of the header for a coordinates.bdy.nc file} 
    … …  
    660662 
    661663 
     664\end{document} 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/DOC/TexFiles/Chapters/Chap_LDF.tex

    r7491 r7492  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13 
    24% ================================================================ 
    … …  
    105107Other formulations can be introduced by the user for a given configuration.  
    106108For example, in the ORCA2 global ocean model (see Configurations), the laplacian  
    107 viscosity operator uses \np{rn\_ahm\_0\_lap}~= 4.10$^4$ m$^2$/s poleward of 20$^{\circ}$  
     109viscosity operator uses \np{rn\_ahm\_0\_lap}~= 4.10$^4$ m$^2$/s poleward of 20\deg  
    108110north and south and decreases linearly to \np{rn\_aht\_0}~= 2.10$^3$ m$^2$/s  
    109111at the equator \citep{Madec_al_JPO96, Delecluse_Madec_Bk00}. This modification  
    … …  
    231233values are $0$). However, the technique used to compute the isopycnal  
    232234slopes is intended to get rid of such a background diffusion, since it introduces  
    233 spurious diapycnal diffusion (see {\S\ref{LDF_slp}). 
     235spurious diapycnal diffusion (see \S\ref{LDF_slp}). 
    234236 
    235237(4) when an eddy induced advection term is used (\key{traldf\_eiv}), $A^{eiv}$,  
    … …  
    444446%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    445447\begin{figure}[!ht]      \begin{center} 
    446 \includegraphics[width=0.70\textwidth]{./TexFiles/Figures/Fig_LDF_ZDF1.pdf} 
     448\includegraphics[width=0.70\textwidth]{Fig_LDF_ZDF1} 
    447449\caption {    \label{Fig_LDF_ZDF1} 
    448450averaging procedure for isopycnal slope computation.} 
    … …  
    472474%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    473475\begin{figure}[!ht]     \begin{center} 
    474 \includegraphics[width=0.70\textwidth]{./TexFiles/Figures/Fig_eiv_slp.pdf} 
     476\includegraphics[width=0.70\textwidth]{Fig_eiv_slp} 
    475477\caption {     \label{Fig_eiv_slp} 
    476478Vertical profile of the slope used for lateral mixing in the mixed layer :  
    … …  
    514516diffusion along model level surfaces, i.e. using the shear computed along  
    515517the model levels and with no additional friction at the ocean bottom (see  
    516 {\S\ref{LBC_coast}). 
     518\S\ref{LBC_coast}). 
    517519 
    518520 
    … …  
    555557 
    556558 
     559\end{document} 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/DOC/TexFiles/Chapters/Chap_MISC.tex

    r7491 r7492  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter � Miscellaneous Topics 
    … …  
    6062%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    6163\begin{figure}[!tbp]     \begin{center} 
    62 \includegraphics[width=0.80\textwidth]{./TexFiles/Figures/Fig_Gibraltar.pdf} 
    63 \includegraphics[width=0.80\textwidth]{./TexFiles/Figures/Fig_Gibraltar2.pdf} 
     64\includegraphics[width=0.80\textwidth]{Fig_Gibraltar} 
     65\includegraphics[width=0.80\textwidth]{Fig_Gibraltar2} 
    6466\caption{   \label{Fig_MISC_strait_hand}  
    65 Example of the Gibraltar strait defined in a $1\deg \times 1\deg$ mesh.  
     67Example of the Gibraltar strait defined in a $1^{\circ} \times 1^{\circ}$ mesh.  
    6668\textit{Top}: using partially open cells. The meridional scale factor at $v$-point  
    6769is reduced on both sides of the strait to account for the real width of the strait  
    … …  
    194196%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    195197\begin{figure}[!ht]    \begin{center} 
    196 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_LBC_zoom.pdf} 
     198\includegraphics[width=0.90\textwidth]{Fig_LBC_zoom} 
    197199\caption{   \label{Fig_LBC_zoom} 
    198200Position of a model domain compared to the data input domain when the zoom functionality is used.} 
    … …  
    632634 
    633635 
     636\end{document} 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/DOC/TexFiles/Chapters/Chap_Model_Basics.tex

    r7491 r7492  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter 1 Ñ Model Basics 
    … …  
    114116%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    115117\begin{figure}[!ht]   \begin{center} 
    116 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_I_ocean_bc.pdf} 
     118\includegraphics[width=0.90\textwidth]{Fig_I_ocean_bc} 
    117119\caption{    \label{Fig_ocean_bc}  
    118120The ocean is bounded by two surfaces, $z=-H(i,j)$ and $z=\eta(i,j,t)$, where $H$  
    … …  
    312314%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    313315\begin{figure}[!tb]   \begin{center} 
    314 \includegraphics[width=0.60\textwidth]{./TexFiles/Figures/Fig_I_earth_referential.pdf} 
     316\includegraphics[width=0.60\textwidth]{Fig_I_earth_referential} 
    315317\caption{   \label{Fig_referential}  
    316318the geographical coordinate system $(\lambda,\varphi,z)$ and the curvilinear  
    … …  
    811813%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    812814\begin{figure}[!b]    \begin{center} 
    813 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_z_zstar.pdf} 
     815\includegraphics[width=1.0\textwidth]{Fig_z_zstar} 
    814816\caption{   \label{Fig_z_zstar}  
    815817(a) $z$-coordinate in linear free-surface case ;  
    … …  
    12801282\end{equation} 
    12811283 
     1284\end{document} 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/DOC/TexFiles/Chapters/Chap_Model_Basics_zstar.tex

    r7491 r7492  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter 1 ——— Model Basics 
    … …  
    121123%>   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   > 
    122124\begin{figure}[!t]   \begin{center} 
    123 \includegraphics[width=0.90\textwidth]{./Figures/Fig_DYN_dynspg_ts.pdf} 
     125\includegraphics[width=0.90\textwidth]{Fig_DYN_dynspg_ts} 
    124126\caption{    \label{Fig_DYN_dynspg_ts} 
    125127Schematic of the split-explicit time stepping scheme for the barotropic and baroclinic modes,  
    … …  
    256258 
    257259 
     260\end{document} 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/DOC/TexFiles/Chapters/Chap_OBS.tex

    r7491 r7492  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter observation operator (OBS) 
    … …  
    732734%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    733735\begin{figure}      \begin{center} 
    734 \includegraphics[width=10cm,height=12cm,angle=-90.]{./TexFiles/Figures/Fig_ASM_obsdist_local} 
     736\includegraphics[width=10cm,height=12cm,angle=-90.]{Fig_ASM_obsdist_local} 
    735737\caption{      \label{fig:obslocal} 
    736738Example of the distribution of observations with the geographical distribution of observational data.}  
    … …  
    759761%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    760762\begin{figure}     \begin{center} 
    761 \includegraphics[width=10cm,height=12cm,angle=-90.]{./TexFiles/Figures/Fig_ASM_obsdist_global} 
     763\includegraphics[width=10cm,height=12cm,angle=-90.]{Fig_ASM_obsdist_global} 
    762764\caption{      \label{fig:obsglobal} 
    763765Example of the distribution of observations with the round-robin distribution of observational data.} 
    … …  
    13761378%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    13771379\begin{figure}     \begin{center} 
    1378 %\includegraphics[width=10cm,height=12cm,angle=-90.]{./TexFiles/Figures/Fig_OBS_dataplot_main} 
    1379 \includegraphics[width=9cm,angle=-90.]{./TexFiles/Figures/Fig_OBS_dataplot_main} 
     1380%\includegraphics[width=10cm,height=12cm,angle=-90.]{Fig_OBS_dataplot_main} 
     1381\includegraphics[width=9cm,angle=-90.]{Fig_OBS_dataplot_main} 
    13801382\caption{      \label{fig:obsdataplotmain} 
    13811383Main window of dataplot.} 
    … …  
    13881390%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    13891391\begin{figure}     \begin{center} 
    1390 %\includegraphics[width=10cm,height=12cm,angle=-90.]{./TexFiles/Figures/Fig_OBS_dataplot_prof} 
    1391 \includegraphics[width=7cm,angle=-90.]{./TexFiles/Figures/Fig_OBS_dataplot_prof} 
     1392%\includegraphics[width=10cm,height=12cm,angle=-90.]{Fig_OBS_dataplot_prof} 
     1393\includegraphics[width=7cm,angle=-90.]{Fig_OBS_dataplot_prof} 
    13921394\caption{      \label{fig:obsdataplotprofile} 
    13931395Profile plot from dataplot produced by right clicking on a point in the main window.} 
    … …  
    13981400 
    13991401 
     1402\end{document} 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/DOC/TexFiles/Chapters/Chap_SBC.tex

    r7491 r7492  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter —— Surface Boundary Condition (SBC, ISF, ICB)  
    … …  
    952954%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    953955\begin{figure}[!h]    \begin{center} 
    954 \includegraphics[width=0.8\textwidth]{./TexFiles/Figures/Fig_SBC_isf.pdf} 
     956\includegraphics[width=0.8\textwidth]{Fig_SBC_isf} 
    955957\caption{ \label{Fig_SBC_isf} 
    956958Schematic for all the options available trough \np{nn\_isf}.} 
    … …  
    11291131%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    11301132\begin{figure}[!t]    \begin{center} 
    1131 \includegraphics[width=0.8\textwidth]{./TexFiles/Figures/Fig_SBC_diurnal.pdf} 
     1133\includegraphics[width=0.8\textwidth]{Fig_SBC_diurnal} 
    11321134\caption{ \label{Fig_SBC_diurnal}     
    11331135Example of recontruction of the diurnal cycle variation of short wave flux   
    … …  
    11621164%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    11631165\begin{figure}[!t]  \begin{center} 
    1164 \includegraphics[width=0.7\textwidth]{./TexFiles/Figures/Fig_SBC_dcy.pdf} 
     1166\includegraphics[width=0.7\textwidth]{Fig_SBC_dcy} 
    11651167\caption{ \label{Fig_SBC_dcy}    
    11661168Example of recontruction of the diurnal cycle variation of short wave flux   
    … …  
    13571359 
    13581360 
     1361\end{document} 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/DOC/TexFiles/Chapters/Chap_STO.tex

    r7491 r7492  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter stochastic parametrization of EOS (STO) 
    … …  
    157159 
    158160 
     161\end{document} 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/DOC/TexFiles/Chapters/Chap_STP.tex

    r7491 r7492  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13 
    24% ================================================================ 
    … …  
    196198%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    197199\begin{figure}[!t]     \begin{center} 
    198 \includegraphics[width=0.7\textwidth]{./TexFiles/Figures/Fig_TimeStepping_flowchart.pdf} 
     200\includegraphics[width=0.7\textwidth]{Fig_TimeStepping_flowchart} 
    199201\caption{   \label{Fig_TimeStep_flowchart} 
    200202Sketch of the leapfrog time stepping sequence in \NEMO from \citet{Leclair_Madec_OM09}.  
    … …  
    288290%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    289291\begin{figure}[!t]     \begin{center} 
    290 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_MLF_forcing.pdf} 
     292\includegraphics[width=0.90\textwidth]{Fig_MLF_forcing} 
    291293\caption{   \label{Fig_MLF_forcing} 
    292294Illustration of forcing integration methods.  
    … …  
    424426} 
    425427%% 
     428\end{document} 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/DOC/TexFiles/Chapters/Chap_TRA.tex

    r7491 r7492  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter 1 ——— Ocean Tracers (TRA) 
    … …  
    8991%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    9092\begin{figure}[!t]    \begin{center} 
    91 \includegraphics[width=0.9\textwidth]{./TexFiles/Figures/Fig_adv_scheme.pdf} 
     93\includegraphics[width=0.9\textwidth]{Fig_adv_scheme} 
    9294\caption{   \label{Fig_adv_scheme}  
    9395Schematic representation of some ways used to evaluate the tracer value  
    … …  
    778780%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    779781\begin{figure}[!t]     \begin{center} 
    780 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_TRA_Irradiance.pdf} 
     782\includegraphics[width=1.0\textwidth]{Fig_TRA_Irradiance} 
    781783\caption{    \label{Fig_traqsr_irradiance} 
    782784Penetration profile of the downward solar irradiance calculated by four models.  
    … …  
    799801%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    800802\begin{figure}[!t]     \begin{center} 
    801 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_TRA_geoth.pdf} 
     803\includegraphics[width=1.0\textwidth]{Fig_TRA_geoth} 
    802804\caption{   \label{Fig_geothermal} 
    803805Geothermal Heat flux (in $mW.m^{-2}$) used by \cite{Emile-Geay_Madec_OS09}. 
    … …  
    909911%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    910912\begin{figure}[!t]   \begin{center} 
    911 \includegraphics[width=0.7\textwidth]{./TexFiles/Figures/Fig_BBL_adv.pdf} 
     913\includegraphics[width=0.7\textwidth]{Fig_BBL_adv} 
    912914\caption{   \label{Fig_bbl}   
    913915Advective/diffusive Bottom Boundary Layer. The BBL parameterisation is  
    … …  
    10671069The restoration coefficient can be set to zero in equatorial regions by specifying a positive value of \np{nn\_hdmp}.  
    10681070Equatorward of this latitude the restoration coefficient will be zero with a smooth transition to  
    1069 the full values of a 10$^{\circ}$ latitud band.  
     1071the full values of a 10\deg latitud band.  
    10701072This is often used because of the short adjustment time scale in the equatorial region  
    10711073\citep{Reverdin1991, Fujio1991, Marti_PhD92}. The time scale associated with the damping depends on the depth as a  
    … …  
    11671169rational function approximation for hydrographic data analysis  \citep{TEOS10}.  
    11681170A key point is that conservative state variables are used:  
    1169 Absolute Salinity (unit: g/kg, notation: $S_A$) and Conservative Temperature (unit: $\degres C$, notation: $\Theta$). 
     1171Absolute Salinity (unit: g/kg, notation: $S_A$) and Conservative Temperature (unit: \degC, notation: $\Theta$). 
    11701172The pressure in decibars is approximated by the depth in meters.  
    11711173With TEOS10, the specific heat capacity of sea water, $C_p$, is a constant. It is set to  
    1172 $C_p=3991.86795711963~J\,Kg^{-1}\,\degres K^{-1}$, according to \citet{TEOS10}. 
     1174$C_p=3991.86795711963~J\,Kg^{-1}\,^{\circ}K^{-1}$, according to \citet{TEOS10}. 
    11731175 
    11741176Choosing polyTEOS10-bsq implies that the state variables used by the model are  
    … …  
    11831185to accurately fit EOS80 (Roquet, personal comm.). The state variables used in both the EOS80  
    11841186and the ocean model are:  
    1185 the Practical Salinity ((unit: psu, notation: $S_p$)) and Potential Temperature (unit: $\degres C$, notation: $\theta$). 
     1187the Practical Salinity ((unit: psu, notation: $S_p$)) and Potential Temperature (unit: $^{\circ}C$, notation: $\theta$). 
    11861188The pressure in decibars is approximated by the depth in meters.   
    11871189With thsi EOS, the specific heat capacity of sea water, $C_p$, is a function of temperature,  
    … …  
    13051307%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    13061308\begin{figure}[!p]    \begin{center} 
    1307 \includegraphics[width=0.9\textwidth]{./TexFiles/Figures/Partial_step_scheme.pdf} 
     1309\includegraphics[width=0.9\textwidth]{Partial_step_scheme} 
    13081310\caption{   \label{Fig_Partial_step_scheme}  
    13091311Discretisation of the horizontal difference and average of tracers in the $z$-partial  
    … …  
    13841386 with $\widetilde {Z}_{T_k}$ the depth of the point $\widetilde {T}_{k}$ in case of $z^*$ coordinates  
    13851387(this term = 0 in z-coordinates) 
     1388\end{document} 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/DOC/TexFiles/Chapters/Chap_ZDF.tex

    r7491 r7492  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13% ================================================================ 
    24% Chapter  Vertical Ocean Physics (ZDF) 
    … …  
    233235%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    234236\begin{figure}[!t] \begin{center} 
    235 \includegraphics[width=1.00\textwidth]{./TexFiles/Figures/Fig_mixing_length.pdf} 
     237\includegraphics[width=1.00\textwidth]{Fig_mixing_length} 
    236238\caption{ \label{Fig_mixing_length}  
    237239Illustration of the mixing length computation. } 
    … …  
    407409%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    408410\begin{figure}[!t]   \begin{center} 
    409 \includegraphics[width=1.00\textwidth]{./TexFiles/Figures/Fig_ZDF_TKE_time_scheme.pdf} 
     411\includegraphics[width=1.00\textwidth]{Fig_ZDF_TKE_time_scheme} 
    410412\caption{ \label{Fig_TKE_time_scheme}  
    411413Illustration of the TKE time integration and its links to the momentum and tracer time integration. } 
    … …  
    586588value near physical boundaries (logarithmic boundary layer law). $C_{\mu}$ and $C_{\mu'}$  
    587589are calculated from stability function proposed by \citet{Galperin_al_JAS88}, or by \citet{Kantha_Clayson_1994}  
    588 or one of the two functions suggested by \citet{Canuto_2001}  (\np{nn\_stab\_func} = 0, 1, 2 or 3, resp.}).  
     590or one of the two functions suggested by \citet{Canuto_2001}  (\np{nn\_stab\_func} = 0, 1, 2 or 3, resp.).  
    589591The value of $C_{0\mu}$ depends of the choice of the stability function. 
    590592 
    … …  
    658660%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    659661\begin{figure}[!htb]    \begin{center} 
    660 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_npc.pdf} 
     662\includegraphics[width=0.90\textwidth]{Fig_npc} 
    661663\caption{  \label{Fig_npc}  
    662664Example of an unstable density profile treated by the non penetrative  
    … …  
    814816%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    815817\begin{figure}[!t]   \begin{center} 
    816 \includegraphics[width=0.99\textwidth]{./TexFiles/Figures/Fig_zdfddm.pdf} 
     818\includegraphics[width=0.99\textwidth]{Fig_zdfddm} 
    817819\caption{  \label{Fig_zdfddm} 
    818820From \citet{Merryfield1999} : (a) Diapycnal diffusivities $A_f^{vT}$  
    … …  
    11431145baroclinic and barotropic components which is appropriate when using either the 
    11441146explicit or filtered surface pressure gradient algorithms (\key{dynspg\_exp} or  
    1145 {\key{dynspg\_flt}). Extra attention is required, however, when using  
     1147\key{dynspg\_flt}). Extra attention is required, however, when using  
    11461148split-explicit time stepping (\key{dynspg\_ts}). In this case the free surface  
    11471149equation is solved with a small time step \np{rn\_rdt}/\np{nn\_baro}, while the three  
    … …  
    12581260%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    12591261\begin{figure}[!t]   \begin{center} 
    1260 \includegraphics[width=0.90\textwidth]{./TexFiles/Figures/Fig_ZDF_M2_K1_tmx.pdf} 
     1262\includegraphics[width=0.90\textwidth]{Fig_ZDF_M2_K1_tmx} 
    12611263\caption{  \label{Fig_ZDF_M2_K1_tmx}  
    12621264(a) M2 and (b) K1 internal wave drag energy from \citet{Carrere_Lyard_GRL03} ($W/m^2$). } 
    … …  
    13691371 
    13701372 
     1373\end{document} 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/DOC/TexFiles/Chapters/Introduction.tex

    r7491 r7492  
     1\documentclass[NEMO_book]{subfiles} 
     2\begin{document} 
    13 
    24% ================================================================ 
    … …  
    290292 
    291293 
     294\end{document} 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/ARCH/CMCC/arch-ifort_athena_xios.fcm

    r7491 r7492  
    3434 
    3535# required modules 
    36 # module load  INTEL/intel_xe_2013 NETCDF/netcdf-4.3_parallel NETCDF/parallel-netcdf-1.3.1 HDF5/hdf5-1.8.11_parallel 
     36# module load  INTEL/intel_xe_2013 NETCDF/netcdf-4.3_parallel NETCDF/parallel-netcdf-1.7.0 HDF5/hdf5-1.8.11_parallel 
    3737 
    38 # Environment variables set by user. Others should automatically define when loading modules. 
     38# NETCDF and PNETCDF should be set automatically when loading modules. 
     39# The following environment variables must be set by the user. 
    3940#export XIOS=/users/home/models/nemo/xios 
    4041#export HDF5=/users/home/opt/hdf5/hdf5-1.8.11_parallel 
    41 #export NETCDF=/users/home/opt/netcdf/netcdf-4.3_parallel 
    4242 
    43 %NCDF_INC            -I${NETCDF}/include  
    44 %NCDF_LIB            -L${NETCDF}/lib -lnetcdff -lnetcdf 
     43%NCDF_INC            -I${NETCDF}/include -I${PNETCDF}/include 
     44%NCDF_LIB            -L${NETCDF}/lib -lnetcdff -lnetcdf -L${PNETCDF}/lib -lpnetcdf 
    4545%HDF5_INC            -I${HDF5}/include 
    4646%HDF5_LIB            -L${HDF5}/lib -lhdf5_hl -lhdf5 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/CONFIG/SHARED/field_def.xml

    r7491 r7492  
    544544 
    545545          <!-- available with ln_diahsb --> 
    546        <field id="bgtemper"     long_name="drift in global mean temperature wrt timestep 1"                 standard_name="change_over_time_in_sea_water_potential_temperature"   unit="degree_C"     /> 
    547        <field id="bgsaline"     long_name="drift in global mean salinity wrt timestep 1"                    standard_name="change_over_time_in_sea_water_practical_salinity"      unit="0.001"     /> 
     546       <field id="bgtemper"     long_name="drift in global mean temperature wrt timestep 1"                 standard_name="change_over_time_in_sea_water_potential_temperature"   unit="degC"     /> 
     547       <field id="bgsaline"     long_name="drift in global mean salinity wrt timestep 1"                    standard_name="change_over_time_in_sea_water_practical_salinity"      unit="0.001"    /> 
    548548       <field id="bgheatco"     long_name="drift in global mean heat content wrt timestep 1"                                                                                      unit="1.e20J"   /> 
    549549       <field id="bgheatfx"     long_name="drift in global mean heat flux    wrt timestep 1"                                                                                      unit="W/m2"     /> 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/NEMO/OPA_SRC/SBC/sbccpl.F90

    r7491 r7492  
    14951495      IF( iom_use('snow_ai_cea') )   CALL iom_put( 'snow_ai_cea', sprecip(:,:) *           zsnw(:,:)   )  ! Snow over sea-ice         (cell average) 
    14961496#else 
    1497 ! runoffs and calving (put in emp_tot) 
     1497      ! runoffs and calving (put in emp_tot) 
    14981498      IF( srcv(jpr_rnf)%laction )   rnf(:,:) = frcv(jpr_rnf)%z3(:,:,1) 
    14991499      IF( iom_use('hflx_rnf_cea') )   & 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/SETTE/sette.sh

    r7491 r7492  
    123123# Directory to run the tests 
    124124SETTE_DIR=$(cd $(dirname "$0"); pwd) 
    125 MAIN_DIR=${SETTE_DIR%/SETTE} 
     125MAIN_DIR=$(dirname $SETTE_DIR) 
    126126CONFIG_DIR=${MAIN_DIR}/CONFIG 
    127127TOOLS_DIR=${MAIN_DIR}/TOOLS 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/NESTING/agulhas

    r7491 r7492  
    4141    N  = 31 
    4242    ldbletanh   = .FALSE. 
    43     ppa2        = 0.0 
     43    pa2         = 0.0 
    4444    ppkth2      = 0.0 
    4545    ppacr2      = 0.0 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/NESTING/src/agrif_types.f90

    r7491 r7492  
    7676  NAMELIST /nesting/imin,imax,jmin,jmax,rho,rhot,bathy_update,updated_parent_file       
    7777  ! 
    78   NAMELIST /vertical_grid/ppkth,ppacr,ppdzmin,pphmax,psur,pa0,pa1,N,ldbletanh,ppa2,ppkth2,ppacr2 
     78  NAMELIST /vertical_grid/ppkth,ppacr,ppdzmin,pphmax,psur,pa0,pa1,N,ldbletanh,pa2,ppkth2,ppacr2 
    7979  !  
    8080  NAMELIST /partial_cells/partial_steps,parent_bathy_meter,parent_batmet_name,e3zps_min,e3zps_rat       

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/REBUILD_NEMO/icb_combrest.py

    r7491 r7492  
    169169    sys.exit(15) 
    170170  fo = Dataset(pathout, 'w') 
    171   for dim in ['x','y','c']: 
     171  for dim in ['x','y','c','k']: 
    172172    indim = fi.dimensions[dim] 
    173173    fo.createDimension(dim, len(indim)) 
    174   for var in ['calving','calving_hflx','stored_ice','stored_heat']: 
     174  for var in ['kount','calving','calving_hflx','stored_ice','stored_heat']: 
    175175    invar = fi.variables[var] 
    176176    fo.createVariable(var, invar.datatype, invar.dimensions) 
    177177    fo.variables[var][:] = invar[:] 
    178     fo.variables[var].long_name = invar.long_name 
    179     fo.variables[var].units = invar.units 
    180     os.remove(pathout.replace('.nc','_WORK.nc')) 
     178    if "long_name" in invar.ncattrs(): 
     179        fo.variables[var].long_name = invar.long_name 
     180    if "units" in invar.ncattrs(): 
     181        fo.variables[var].units = invar.units 
     182  os.remove(pathout.replace('.nc','_WORK.nc')) 
    181183# 
    182184add_k = 1 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/README

    r7491 r7492  
    1 This is a first release of SIREN. 
    21 
    3 To create SIREN documentation, go to ./src and run doxygen  
     2To create SIREN documentation, run doxygen in TOOLS/SIREN directory 
    43(http://www.stack.nl/~dimitri/doxygen/index.html version 1.8.3.1 or upper) 
    54then 
    6    open ../doc/index.html  
     5   open ./TOOLS/SIREN/doc/html/index.html in your web browser  
    76or  
    8    run ../doc/latex/gmake and open refman.pdf  
    9  
    10  
    11 templates of namelists could be find in templates directory. 
    12 read documentation for more information. 
    13  
    14  1- program to create coordinate file : 
    15  
    16    ./create_coord create_coord.nam 
    17  
    18  
    19  Variables are extracted from the input coordinates coarse grid and 
    20  interpolated to create fine coordinates files. 
    21  
    22  2- program to create bathymetry file: 
    23  
    24  ./create_bathy create_bathy.nam 
    25  
    26  Bathymetry could be extracted from fine grid Bathymetry file, or 
    27  interpolated from coarse grid Bathymetry file. 
    28  
    29  3- program to merge bathymetry file at boundaries : 
    30  
    31  ./merge_bathy merge_bathy.nam 
    32  
    33  Coarse grid Bathymetry is interpolated on fine grid. 
    34  Then fine Bathymetry and refined coarse bathymetry are merged at 
    35  boundaries. 
    36  
    37  4- program to create restart file : 
    38  
    39  ./create_restart create_restart.nam 
    40  
    41  Variables are read from restart file, or standard output. 
    42  Then theses variables are interpolated on fine grid. 
    43  Finally table are split over new decomposition. 
    44  
    45  5- program to create boundary files (OBC) : 
    46  
    47  ./create_boundary create_boundary.nam 
    48  
    49  Variables are read from standard output. 
    50  Then theses variables are interpolated on fine grid boundaries. 
     7   run ./TOOLS/SIREN/doc/latex/gmake and open ./TOOLS/SIREN/doc/latex/refman.pdf  

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/boundary.f90

    r7491 r7492  
    15291529   !> @author J.Paul  
    15301530   !> @date November, 2013 - Initial Version  
    1531    !  
     1531   !> @date June, 2016 
     1532   !> - Bug fix: take into account that boundaries are compute on T point, 
     1533   !>   but expressed on U,V point 
     1534   !> 
    15321535   !> @param[inout] td_bdy boundary structure  
    15331536   !> @param[in] td_var    variable structure  
    … …  
    15521555      il_max(jp_west )=td_var%t_dim(2)%i_len 
    15531556  
    1554       il_maxindex(jp_north)=td_var%t_dim(2)%i_len-ip_ghost 
     1557      ! index expressed on U,V point, move on T point. 
     1558      il_maxindex(jp_north)=td_var%t_dim(2)%i_len-ip_ghost+1 
    15551559      il_maxindex(jp_south)=td_var%t_dim(2)%i_len-ip_ghost 
    1556       il_maxindex(jp_east )=td_var%t_dim(1)%i_len-ip_ghost 
     1560      il_maxindex(jp_east )=td_var%t_dim(1)%i_len-ip_ghost+1 
    15571561      il_maxindex(jp_west )=td_var%t_dim(1)%i_len-ip_ghost 
    15581562 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/docsrc/1_install.md

    r7491 r7492  
    2020  <b> 
    2121  - @ref index 
    22   - @ref md_docsrc_2_quickstart 
    23   - @ref md_docsrc_3_support_bug 
    24   - @ref md_docsrc_4_codingRules 
    25   - @ref md_docsrc_5_changeLog 
     22  - @ref md_src_docsrc_2_quickstart 
     23  - @ref md_src_docsrc_3_support_bug 
     24  - @ref md_src_docsrc_4_codingRules 
     25  - @ref md_src_docsrc_5_changeLog 
    2626  - @ref todo 
    2727  </b> 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/docsrc/2_quickstart.md

    r7491 r7492  
    3535Here after we briefly describe how to use each programs, 
    3636and so how to create your own regional configuration. 
    37 @note A set of GLORYS files (global reanalysis on *ORCA025* 
    38 grid), as well as examples of namelists are available in dods repository.<br/> 
    39 You could create and forced a first release of your own regional configuration, 
    40 with those files.  
     37@note As demonstrator for a first start a set of GLORYS files (global reanalysis on *ORCA025* grid), as well as examples of namelists are available [here](https://cloud.mercator-ocean.fr/public.php?service=files&t=1658ec1aaeda2878f2b3915ed140af37). 
     38 
    4139<!-- ######################################################################  --> 
    4240# Create coordinates file # {#coord} 
    … …  
    121119example: ORCA05</dd> 
    122120</dl> 
    123 @sa For more information see @ref md_docsrc_6_perio 
     121@sa For more information see @ref md_src_docsrc_6_perio 
    124122</dd> 
    125123</dl> 
    … …  
    442440Finally, this **namout** sub-namelist defines the output files.<br/> 
    443441Here we ask for output on 81 processors, with *restart_out.nc* as file "basename".<br/> 
    444 So SIREN computes the optimal layout for 81 porcessors 
     442So SIREN computes the optimal layout for 81 processors 
    445443available,<br/> 
    446 and split restart on output files named *restart_out_num.nc*, where *num* is the porc number. 
     444and split restart on output files named *restart_out_num.nc*, where *num* is the proc number. 
    447445 
    448446@note SIREN could also create the other fields you may need for 
    … …  
    592590   <b> 
    593591   - @ref index 
    594    - @ref md_docsrc_1_install 
    595    - @ref md_docsrc_2_quickstart 
    596    - @ref md_docsrc_3_support_bug 
    597    - @ref md_docsrc_4_codingRules 
    598    - @ref md_docsrc_5_changeLog 
     592   - @ref md_src_docsrc_1_install 
     593   - @ref md_src_docsrc_2_quickstart 
     594   - @ref md_src_docsrc_3_support_bug 
     595   - @ref md_src_docsrc_4_codingRules 
     596   - @ref md_src_docsrc_5_changeLog 
    599597   - @ref todo 
    600598   </b> 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/docsrc/3_support_bug.md

    r7491 r7492  
    2020   <b> 
    2121   - @ref index 
    22    - @ref md_docsrc_1_install 
    23    - @ref md_docsrc_2_quickstart 
    24    - @ref md_docsrc_3_support_bug 
    25    - @ref md_docsrc_4_codingRules 
    26    - @ref md_docsrc_5_changeLog 
     22   - @ref md_src_docsrc_1_install 
     23   - @ref md_src_docsrc_2_quickstart 
     24   - @ref md_src_docsrc_3_support_bug 
     25   - @ref md_src_docsrc_4_codingRules 
     26   - @ref md_src_docsrc_5_changeLog 
    2727   - @ref todo 
    2828   </b> 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/docsrc/4_codingRules.md

    r7491 r7492  
    1515_GET_COMMAND_ARGUMENT_.<br/> 
    1616There exist no equivalent for those Fortran 03 intrinsec functions in Fortran 
    17 95.<br/> At least none convenient for compilers tested (see @ref md_docsrc_1_install).  
     1795.<br/> At least none convenient for compilers tested (see @ref md_src_docsrc_1_install).  
    1818 
    1919#  Free Form Source {#free} 
    … …  
    9393   <b> 
    9494   - @ref index 
    95    - @ref md_docsrc_1_install 
    96    - @ref md_docsrc_2_quickstart 
    97    - @ref md_docsrc_3_support_bug 
    98    - @ref md_docsrc_5_changeLog 
     95   - @ref md_src_docsrc_1_install 
     96   - @ref md_src_docsrc_2_quickstart 
     97   - @ref md_src_docsrc_3_support_bug 
     98   - @ref md_src_docsrc_5_changeLog 
    9999   - @ref todo 
    100100   </b> 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/docsrc/5_changeLog.md

    r7491 r7492  
    33@tableofcontents 
    44 
    5 # Release $Revision$ 
    6 Initial release (2016-03-17) 
     5# Release 2016-11-28 
    76 
    87## Changes 
    98## New Features 
    109## Bug fixes 
     10 - boundary.f90: take into account that boundaries are compute on T point, but expressed on U,V point 
     11 - iom_cdf.f90: define type cdf4 as cdf 
     12 
     13release (2016-07-01) 
     14 
     15## Changes 
     16## New Features 
     17## Bug fixes 
     18 - correct check of boundary indices 
     19 
     20# Release 
     21Initial release (2016-04-11) 
    1122 
    1223 <HR> 
    1324   <b> 
    1425   - @ref index 
    15    - @ref md_docsrc_1_install 
    16    - @ref md_docsrc_2_quickstart 
    17    - @ref md_docsrc_3_support_bug 
    18    - @ref md_docsrc_4_codingRules 
     26   - @ref md_src_docsrc_1_install 
     27   - @ref md_src_docsrc_2_quickstart 
     28   - @ref md_src_docsrc_3_support_bug 
     29   - @ref md_src_docsrc_4_codingRules 
    1930   - @ref todo 
    2031   </b> 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/docsrc/6_perio.md

    r7491 r7492  
    66<dd>ghost cells (solid walls) are imposed at all model boundaries.</dd>  
    77@image html perio0_20.png  
    8 @image latex perio0_20.png 
     8@latexonly 
     9\begin{center} 
     10\includegraphics{perio0_20.png} 
     11\end{center} 
     12@endlatexonly 
    913<dt>cyclic east-west boundary (in_perio=1)</dt> 
    1014<dd>first and last rows are closed, whilst the first column is set to the value of the last-but-one column and the last column to the value of the second one.</dd>   
    1115@image html perio1_20.png  
    12 @image latex perio1_20.png 
     16@latexonly 
     17\begin{center} 
     18\includegraphics{perio1_20.png} 
     19\end{center} 
     20@endlatexonly 
    1321<dt>symmetric boundary condition across the equator. (in_perio=2)</dt> 
    1422<dd>last row, and first and last columns are closed. </dd>  
    1523@image html perio2_20.png  
    16 @image latex perio2_20.png 
     24@latexonly 
     25\begin{center} 
     26\includegraphics{perio2_20.png} 
     27\end{center} 
     28@endlatexonly 
    1729<dt>North fold boundary with a T -point pivot (in_perio=3)</dt> 
    1830<dd>first row, and first and last columns are closed. </dd>  
    1931@image html perio3_20.png  
    20 @image latex perio3_20.png 
     32@latexonly 
     33\begin{center} 
     34\includegraphics{perio3_20.png} 
     35\end{center} 
     36@endlatexonly 
    2137<dt>North fold boundary with a T -point pivot and cyclic east-west boundary (in_perio=4)</dt> 
    2238<dd>first row is closed. The first column is set to the value of the last-but-one column and the last column to the value of the second one. </dd>  
    2339@image html perio4_20.png  
    24 @image latex perio4_20.png 
     40@latexonly 
     41\begin{center} 
     42\includegraphics{perio4_20.png} 
     43\end{center} 
     44@endlatexonly 
    2545<dt>North fold boundary with a F -point pivot (in_perio=5)</dt> 
    2646<dd>first row, and first and last columns are closed. </dd>  
    2747@image html perio5_20.png  
    28 @image latex perio5_20.png 
     48@latexonly 
     49\begin{center} 
     50\includegraphics{perio5_20.png} 
     51\end{center} 
     52@endlatexonly 
    2953<dt>North fold boundary with a F -point pivot and cyclic east-west boundary (in_perio=6)</dt> 
    3054<dd>first row is closed. The first column is set to the value of the last-but-one column and the last column to the value of the second one.</dd>  
    3155@image html perio6_20.png  
    32 @image latex perio6_20.png 
     56@image html perio5_20.png  
     57@latexonly 
     58\begin{center} 
     59\includegraphics{perio6_20.png} 
     60\end{center} 
     61@endlatexonly 
    3362</dl> 
    3463@sa For more information about NEMO periodicity, see _Model Boundary Condition_ chapter in [NEMO documentation](http://www.nemo-ocean.eu/About-NEMO/Reference-manuals)) 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/docsrc/main.dox

    r7491 r7492  
    22 @mainpage About  
    33 
    4  SIREN is a software to create regional configuration with [NEMO](http://www.nemo-ocean.eu).<br/>  
    5  Actually SIREN create input files needed for a basic NEMO configuration.<br/> 
     4 SIREN is a software to set up regional configuration with [NEMO](http://www.nemo-ocean.eu).<br/>  
     5 Actually SIREN creates the input files you need to run a NEMO regional configuration.<br/> 
     6  
     7 SIREN allows you to create your own regional configuration embedded in a wider one.<br/> 
    68 
    7  SIREN allows you to create your own regional configuration embedded in a wider one.<br/> 
    8  In order to help you, a set of GLORYS files (global reanalysis on ORCA025 grid), as well as examples 
    9  of namelists are available in dods repository. 
     9 To know how to install SIREN see @ref md_src_docsrc_1_install. 
    1010 
    11  @note This software was created, and is maintain by the Configuration Manager Working Group, composed 
    12  of NEMO system team members. 
    13   
    14  To know how to install SIREN see @ref md_docsrc_1_install. 
    15  
    16  You could find a tutorial for a quick start with SIREN in @ref md_docsrc_2_quickstart.<br/> 
     11 You could find a tutorial for a quick start with SIREN in @ref md_src_docsrc_2_quickstart.<br/> 
    1712 For more information about how to use each component of SIREN 
    1813 - see create_coord.f90 to create fine grid coordinate file 
    … …  
    2419<HR> 
    2520   <b> 
    26    - @ref md_docsrc_1_install 
    27    - @ref md_docsrc_2_quickstart 
    28    - @ref md_docsrc_3_support_bug 
    29    - @ref md_docsrc_4_codingRules 
    30    - @ref md_docsrc_5_changeLog 
     21   - @ref md_src_docsrc_1_install 
     22   - @ref md_src_docsrc_2_quickstart 
     23   - @ref md_src_docsrc_3_support_bug 
     24   - @ref md_src_docsrc_4_codingRules 
     25   - @ref md_src_docsrc_5_changeLog 
    3126   - @ref todo 
    3227   </b> 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/file.f90

    r7491 r7492  
    495495         END SELECT 
    496496      ELSE 
     497         CALL logger_debug("FILE INIT: look for file type "//TRIM(file_init%c_name)) 
    497498         file_init%c_type=TRIM(file_get_type(cd_file)) 
    498499      ENDIF 
    … …  
    572573         CASE('.nc','.cdf') 
    573574            CALL logger_debug(" FILE GET TYPE: file "//TRIM(cd_file)//" is cdf") 
     575            ! Warning : type could be change to cdf4 when opening file. 
    574576            file_get_type='cdf' 
    575577         CASE('.dimg') 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/grid.f90

    r7491 r7492  
    13411341         il_dim(:)=td_var%t_dim(:)%i_len 
    13421342 
    1343          CALL logger_debug("GRID GET PERIO: use varibale "//TRIM(td_var%c_name)) 
     1343         CALL logger_debug("GRID GET PERIO: use variable "//TRIM(td_var%c_name)) 
    13441344         CALL logger_debug("GRID GET PERIO: fill value "//TRIM(fct_str(td_var%d_fill))) 
    13451345         CALL logger_debug("GRID GET PERIO: first value "//TRIM(fct_str(td_var%d_value(1,1,1,1)))) 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/iom.f90

    r7491 r7492  
    174174         CASE('cdf') 
    175175            CALL iom_cdf_open(td_file) 
     176         !CASE('cdf4') 
    176177         CASE('dimg') 
    177178            CALL iom_rstdimg_open(td_file) 
    … …  
    240241            CALL iom_rstdimg_close(td_file) 
    241242         CASE DEFAULT 
     243            CALL logger_debug( "IOM CLOSE: type "//TRIM(td_file%c_type)) 
    242244            CALL logger_error( "IOM CLOSE: can't close file "//& 
    243245            &               TRIM(td_file%c_name)//": type unknown " ) 

  • branches/UKMO/v3_6_extra_CMIP6_diagnostics/NEMOGCM/TOOLS/SIREN/src/iom_cdf.f90

    r7491 r7492  
    340340            td_file%c_type='cdf' 
    341341         CASE(nf90_format_netcdf4, nf90_format_netcdf4_classic) 
    342             td_file%c_type='cdf4' 
     342            td_file%c_type='cdf' 
     343            !td_file%c_type='cdf4' 
    343344      END SELECT 
     345      CALL logger_debug("IOM CDF GET INFO: type "//TRIM(td_file%c_type))  
    344346 
    345347      ! record header infos 
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