Changeset 11151


Ignore:
Timestamp:
2019-06-20T14:59:58+02:00 (16 months ago)
Author:
nicolasmartin
Message:

New version of NEMO_manual.tex
New class scrreport for the document (KOMA-script version of default report)
Foreword is now placed before ToC.
All figures are configured with 1.0\textwidth as default.
For compatibilty, \frontmatter, \mainmatter and \backmatter cmds have been removed and old fonts in LaTeX subfiles have been replaced

  • \bf\mathbf or \bfseries
  • \it\itshape
  • \rm\mathrm or \rmfamily
  • \tt\ttfamily
Location:
NEMO/trunk/doc/latex/NEMO
Files:
22 edited

Legend:

Unmodified
Added
Removed
  • NEMO/trunk/doc/latex/NEMO/main/NEMO_manual.tex

    r11128 r11151  
    88 
    99%% Document layout 
    10 \documentclass{book} 
     10\documentclass[draft]{scrreport} 
    1111 
    1212%% Custom style (.sty) 
    13 \usepackage{../../styles/NEMO} 
     13\usepackage{../../global/packages} 
    1414\hypersetup{ 
    1515  pdftitle={NEMO ocean engine}, 
    16   pdfauthor={Gurvan Madec, and NEMO System Team}, 
     16  pdfauthor={Gurvan Madec and NEMO System Team}, 
    1717  colorlinks 
    1818} 
     
    2626%% End of common preamble between main and sub-files 
    2727\begin{document} 
     28\pagenumbering{gobble} 
    2829 
    2930%% Override custom cmds for full manual compilation 
     
    3536%% ============================================================================== 
    3637 
    37 \graphicspath{{../../figures/logos/}} 
    38  
    39 %% Frontpage 
    40 \title{ 
    41   \includegraphics[height=0.05\textheight]{CMCC}\hfill 
    42   \includegraphics[height=0.05\textheight]{CNRS}\hfill 
    43   \includegraphics[height=0.05\textheight]{MOI} \hfill 
    44   \includegraphics[height=0.05\textheight]{UKMO}\hfill 
    45   \includegraphics[height=0.05\textheight]{NERC}       \\ 
    46   \includegraphics[ width=0.8\textwidth  ]{NEMO_grey}  \\ 
    47   {\Huge NEMO ocean engine}                                     \\ 
    48 } 
    49 \author{ 
    50   \Large Gurvan Madec and NEMO System Team 
    51 %  \thanks{ 
    52 % 
    53 %  }                                                        \\ 
    54   \textit{Issue 27, Notes du P\^{o}le de mod\'{e}lisation} \\ 
    55   \textit{Institut Pierre-Simon Laplace (IPSL)}            \\ 
    56   \textit{ISSN 1288-1619} 
     38\title{NEMO ocean engine} 
     39\author{Gurvan Madec \and NEMO System Team\thanks{ 
     40    TBD 
     41  } 
    5742} 
    5843\date{\today} 
    5944 
    60 \maketitle 
    61 \frontmatter 
     45%% Title and information pages 
     46\input{../../global/frontpages} 
     47 
     48%% Citation embedded 
     49\textsf{ 
     50``{\bfseries NEMO ocean engine}'',  
     51Madec Gurvan and NEMO System Team,  
     52{\em Scientific Notes of Climate Modelling Center (27)}, ISSN 1288-1619,  
     53Institut Pierre-Simon Laplace (IPSL),  
     54} 
     55 
     56\newpage 
     57%\frontmatter   %% Chapter numbering off and Roman numerals for page numbers 
     58\pagenumbering{roman} 
     59 
     60\subfile{../subfiles/foreword}            %% Foreword 
     61 
    6262 
    6363%% ToC i.e. Table of Contents 
     64\newpage 
    6465\dominitoc 
    6566\tableofcontents 
    6667 
     68\clearpage 
     69%\end{document} 
    6770 
    6871%% Mainmatter 
    6972%% ============================================================================== 
    7073 
    71 \mainmatter 
     74%\mainmatter   %% Chapter numbering on, page numbering is reset with Arabic numerals 
     75\pagenumbering{arabic} 
    7276 
    7377\graphicspath{{../../figures/NEMO/}} 
    7478 
    75 %% Foreword 
    76 \subfile{../subfiles/foreword} 
    77  
    78 %% Introduction 
    79 \subfile{../subfiles/introduction} 
     79\subfile{../subfiles/introduction}        %% Introduction 
    8080 
    8181%% Chapters 
    8282\subfile{../subfiles/chap_model_basics} 
    83 \subfile{../subfiles/chap_time_domain}    % Time discretisation (time stepping strategy) 
    84 \subfile{../subfiles/chap_DOM}            % Space discretisation 
    85 \subfile{../subfiles/chap_TRA}            % Tracer advection/diffusion equation 
    86 \subfile{../subfiles/chap_DYN}            % Dynamics : momentum equation 
    87 \subfile{../subfiles/chap_SBC}            % Surface Boundary Conditions 
    88 \subfile{../subfiles/chap_LBC}            % Lateral Boundary Conditions 
    89 \subfile{../subfiles/chap_LDF}            % Lateral diffusion 
    90 \subfile{../subfiles/chap_ZDF}            % Vertical diffusion 
    91 \subfile{../subfiles/chap_DIA}            % Outputs and Diagnostics 
    92 \subfile{../subfiles/chap_OBS}            % Observation operator 
    93 \subfile{../subfiles/chap_ASM}            % Assimilation increments 
    94 \subfile{../subfiles/chap_STO}            % Stochastic param. 
    95 \subfile{../subfiles/chap_misc}           % Miscellaneous topics 
    96 \subfile{../subfiles/chap_CONFIG}         % Predefined configurations 
     83\subfile{../subfiles/chap_time_domain}    %% Time discretisation (time stepping strategy) 
     84\subfile{../subfiles/chap_DOM}            %% Space discretisation 
     85\subfile{../subfiles/chap_TRA}            %% Tracer advection/diffusion equation 
     86\subfile{../subfiles/chap_DYN}            %% Dynamics : momentum equation 
     87\subfile{../subfiles/chap_SBC}            %% Surface Boundary Conditions 
     88\subfile{../subfiles/chap_LBC}            %% Lateral Boundary Conditions 
     89\subfile{../subfiles/chap_LDF}            %% Lateral diffusion 
     90\subfile{../subfiles/chap_ZDF}            %% Vertical diffusion 
     91\subfile{../subfiles/chap_DIA}            %% Outputs and Diagnostics 
     92\subfile{../subfiles/chap_OBS}            %% Observation operator 
     93\subfile{../subfiles/chap_ASM}            %% Assimilation increments 
     94\subfile{../subfiles/chap_STO}            %% Stochastic param. 
     95\subfile{../subfiles/chap_misc}           %% Miscellaneous topics 
     96\subfile{../subfiles/chap_CONFIG}         %% Predefined configurations 
    9797 
    9898%% Appendix 
    99 \appendix 
    100 \subfile{../subfiles/annex_A}             % Generalised vertical coordinate 
    101 \subfile{../subfiles/annex_B}             % Diffusive operator 
    102 \subfile{../subfiles/annex_C}             % Discrete invariants of the eqs. 
    103 \subfile{../subfiles/annex_iso}            % Isoneutral diffusion using triads 
    104 \subfile{../subfiles/annex_D}             % Coding rules 
     99%% ============================================================================== 
     100 
     101\appendix   % Chapter numbering is reset with letters now 
     102 
     103\subfile{../subfiles/annex_A}             %% Generalised vertical coordinate 
     104\subfile{../subfiles/annex_B}             %% Diffusive operator 
     105\subfile{../subfiles/annex_C}             %% Discrete invariants of the eqs. 
     106\subfile{../subfiles/annex_iso}            %% Isoneutral diffusion using triads 
     107\subfile{../subfiles/annex_D}             %% Coding rules 
    105108 
    106109%% Not included 
     
    108111%\subfile{../subfiles/chap_DIU} 
    109112%\subfile{../subfiles/chap_conservation} 
    110 %\subfile{../subfiles/annex_E}            % Notes on some on going staff 
     113%\subfile{../subfiles/annex_E}            %% Notes on some on going staff 
    111114 
    112115%% Backmatter 
    113116%% ============================================================================== 
    114117 
    115 \backmatter 
     118%\backmatter   %% Chapter numbering off 
    116119 
    117120%% Bibliography 
    118 \cleardoublepage 
    119121\phantomsection 
    120122\addcontentsline{toc}{chapter}{Bibliography} 
     
    122124 
    123125%% Index 
    124 \cleardoublepage 
     126\clearpage 
    125127\phantomsection 
    126128\addcontentsline{toc}{chapter}{Index} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/annex_A.tex

    r11123 r11151  
    7979    { 
    8080    \begin{array}{*{20}l} 
    81       \nabla \cdot {\rm {\bf U}} 
     81      \nabla \cdot {\mathrm {\mathbf U}} 
    8282      &= \frac{1}{e_1 \,e_2 }  \left[ \left. {\frac{\partial (e_2 \,u)}{\partial i}} \right|_z 
    8383        +\left. {\frac{\partial(e_1 \,v)}{\partial j}} \right|_z  \right] 
     
    115115      $, it becomes:} 
    116116    % 
    117       \nabla \cdot {\rm {\bf U}} 
     117      \nabla \cdot {\mathrm {\mathbf U}} 
    118118      & = \frac{1}{e_1 \,e_2 \,e_3 }  \left[ 
    119119        \left.  \frac{\partial (e_2 \,e_3 \,u)}{\partial i} \right|_s 
     
    144144    { 
    145145    \begin{array}{*{20}l} 
    146       \nabla \cdot {\rm {\bf U}} 
     146      \nabla \cdot {\mathrm {\mathbf U}} 
    147147      &= \frac{1}{e_1 \,e_2 \,e_3 }    \left[ 
    148148        \left.  \frac{\partial (e_2 \,e_3 \,u)}{\partial i} \right|_s 
     
    346346  % 
    347347    &= \left. {\frac{\partial u }{\partial t}} \right|_s 
    348     &+ \left.  \nabla \cdot \left(   {{\rm {\bf U}}\,u}   \right)    \right|_s 
     348    &+ \left.  \nabla \cdot \left(   {{\mathrm {\mathbf U}}\,u}   \right)    \right|_s 
    349349      + \,u \frac{1}{e_3 } \frac{\partial e_3}{\partial t} 
    350350      - \frac{v}{e_1 e_2 }\left(    v  \;\frac{\partial e_2 }{\partial i} 
     
    359359  \label{apdx:A_sco_Dt_flux} 
    360360  \left. \frac{D u}{D t} \right|_s   = \frac{1}{e_3}  \left. \frac{\partial ( e_3\,u)}{\partial t} \right|_s 
    361   + \left.  \nabla \cdot \left(   {{\rm {\bf U}}\,u}   \right)    \right|_s 
     361  + \left.  \nabla \cdot \left(   {{\mathrm {\mathbf U}}\,u}   \right)    \right|_s 
    362362  - \frac{v}{e_1 e_2 }\left(    v  \;\frac{\partial e_2 }{\partial i} 
    363363    -u  \;\frac{\partial e_1 }{\partial j}            \right) 
     
    483483    \label{apdx:A_PE_dyn_flux_u} 
    484484    \frac{1}{e_3} \frac{\partial \left(  e_3\,u  \right) }{\partial t} = 
    485     \nabla \cdot \left(   {{\rm {\bf U}}\,u}   \right) 
     485    \nabla \cdot \left(   {{\mathrm {\mathbf U}}\,u}   \right) 
    486486    +   \left\{ {f + \frac{1}{e_1 e_2 }\left(    v  \;\frac{\partial e_2 }{\partial i} 
    487487          -u  \;\frac{\partial e_1 }{\partial j}            \right)} \right\} \,v     \\ 
     
    493493    \label{apdx:A_dyn_flux_v} 
    494494    \frac{1}{e_3}\frac{\partial \left(  e_3\,v  \right) }{\partial t}= 
    495     -  \nabla \cdot \left(   {{\rm {\bf U}}\,v}   \right) 
     495    -  \nabla \cdot \left(   {{\mathrm {\mathbf U}}\,v}   \right) 
    496496    +   \left\{ {f + \frac{1}{e_1 e_2 }\left(    v  \;\frac{\partial e_2 }{\partial i} 
    497497          -u  \;\frac{\partial e_1 }{\partial j}            \right)} \right\} \,u     \\ 
  • NEMO/trunk/doc/latex/NEMO/subfiles/annex_B.tex

    r11123 r11151  
    236236  { 
    237237  \begin{array}{*{20}l} 
    238     \nabla T\;.\left( {{\rm {\bf A}}_{\rm {\bf I}} \nabla T} 
     238    \nabla T\;.\left( {{\mathrm {\mathbf A}}_{\mathrm {\mathbf I}} \nabla T} 
    239239    \right)&=A^{lT}\left[ {\left( {\frac{\partial T}{\partial i}} \right)^2-2a_1 
    240240             \frac{\partial T}{\partial i}\frac{\partial T}{\partial k}+\left( 
     
    379379  - \nabla _h \times \left( {A^{lm}\;\zeta \;{\textbf{k}}} \right) 
    380380  + \frac{1}{e_3 }\frac{\partial }{\partial k}\left( {\frac{A^{vm}\;}{e_3 } 
    381       \frac{\partial {\rm {\bf U}}_h }{\partial k}} \right) \\ 
     381      \frac{\partial {\mathrm {\mathbf U}}_h }{\partial k}} \right) \\ 
    382382\end{equation} 
    383383that is, in expanded form: 
  • NEMO/trunk/doc/latex/NEMO/subfiles/annex_E.tex

    r11123 r11151  
    308308\begin{figure}[!ht] 
    309309  \begin{center} 
    310     \includegraphics[width=0.70\textwidth]{Fig_ISO_triad} 
     310    \includegraphics[width=\textwidth]{Fig_ISO_triad} 
    311311    \caption{ 
    312312      \protect\label{fig:ISO_triad} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/annex_iso.tex

    r11123 r11151  
    201201\begin{figure}[tb] 
    202202  \begin{center} 
    203     \includegraphics[width=1.05\textwidth]{Fig_GRIFF_triad_fluxes} 
     203    \includegraphics[width=\textwidth]{Fig_GRIFF_triad_fluxes} 
    204204    \caption{ 
    205205      \protect\label{fig:ISO_triad} 
     
    265265\begin{figure}[tb] 
    266266  \begin{center} 
    267     \includegraphics[width=0.80\textwidth]{Fig_GRIFF_qcells} 
     267    \includegraphics[width=\textwidth]{Fig_GRIFF_qcells} 
    268268    \caption{ 
    269269      \protect\label{fig:qcells} 
     
    658658\begin{figure}[h] 
    659659  \begin{center} 
    660     \includegraphics[width=0.60\textwidth]{Fig_GRIFF_bdry_triads} 
     660    \includegraphics[width=\textwidth]{Fig_GRIFF_bdry_triads} 
    661661    \caption{ 
    662662      \protect\label{fig:bdry_triads} 
     
    732732\[ 
    733733  % \label{eq:iso_tensor_ML} 
    734   D^{lT}=\nabla {\rm {\bf .}}\left( {A^{lT}\;\Re \;\nabla T} \right) \qquad 
     734  D^{lT}=\nabla {\mathrm {\mathbf .}}\left( {A^{lT}\;\Re \;\nabla T} \right) \qquad 
    735735  \mbox{with}\quad \;\;\Re =\left( {{ 
    736736        \begin{array}{*{20}c} 
     
    829829    (\eg the green triad $i_p=1/2,k_p=-1/2$) are tapered to the appropriate basal triad.} 
    830830  % } 
    831   \includegraphics[width=0.60\textwidth]{Fig_GRIFF_MLB_triads} 
     831  \includegraphics[width=\textwidth]{Fig_GRIFF_MLB_triads} 
    832832\end{figure} 
    833833% >>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    847847\[ 
    848848  % \label{eq:iso_tensor_ML2} 
    849   D^{lT}=\nabla {\rm {\bf .}}\left( {A^{lT}\;\Re \;\nabla T} \right) \qquad 
     849  D^{lT}=\nabla {\mathrm {\mathbf .}}\left( {A^{lT}\;\Re \;\nabla T} \right) \qquad 
    850850  \mbox{with}\quad \;\;\Re =\left( {{ 
    851851        \begin{array}{*{20}c} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_ASM.tex

    r11123 r11151  
    4141IAU is used when \np{ln\_asmiau} is set to true. 
    4242 
    43 With IAU, the model state trajectory ${\bf x}$ in the assimilation window ($t_{0} \leq t_{i} \leq t_{N}$) 
     43With IAU, the model state trajectory ${\mathbf x}$ in the assimilation window ($t_{0} \leq t_{i} \leq t_{N}$) 
    4444is corrected by adding the analysis increments for temperature, salinity, horizontal velocity and SSH as 
    4545additional tendency terms to the prognostic equations: 
    4646\begin{align*} 
    4747  % \label{eq:wa_traj_iau} 
    48   {\bf x}^{a}(t_{i}) = M(t_{i}, t_{0})[{\bf x}^{b}(t_{0})] \; + \; F_{i} \delta \tilde{\bf x}^{a} 
     48  {\mathbf x}^{a}(t_{i}) = M(t_{i}, t_{0})[{\mathbf x}^{b}(t_{0})] \; + \; F_{i} \delta \tilde{\mathbf x}^{a} 
    4949\end{align*} 
    50 where $F_{i}$ is a weighting function for applying the increments $\delta\tilde{\bf x}^{a}$ defined such that 
     50where $F_{i}$ is a weighting function for applying the increments $\delta\tilde{\mathbf x}^{a}$ defined such that 
    5151$\sum_{i=1}^{N} F_{i}=1$. 
    52 ${\bf x}^b$ denotes the model initial state and ${\bf x}^a$ is the model state after the increments are applied. 
     52${\mathbf x}^b$ denotes the model initial state and ${\mathbf x}^a$ is the model state after the increments are applied. 
    5353To control the adjustment time of the model to the increment, 
    5454the increment can be applied over an arbitrary sub-window, $t_{m} \leq t_{i} \leq t_{n}$, 
     
    6262  =\left\{ 
    6363  \begin{array}{ll} 
    64     0     &    {\rm if} \; \; \; t_{i} < t_{m}                \\ 
    65     1/M &    {\rm if} \; \; \; t_{m} < t_{i} \leq t_{n} \\ 
    66     0     &    {\rm if} \; \; \; t_{i} > t_{n} 
     64    0     &    {\mathrm if} \; \; \; t_{i} < t_{m}                \\ 
     65    1/M &    {\mathrm if} \; \; \; t_{m} < t_{i} \leq t_{n} \\ 
     66    0     &    {\mathrm if} \; \; \; t_{i} > t_{n} 
    6767  \end{array} 
    6868            \right.  
     
    7676  =\left\{ 
    7777  \begin{array}{ll} 
    78     0                           &    {\rm if} \; \; \; t_{i}       <     t_{m}                        \\ 
    79     \alpha \, i               &    {\rm if} \; \; \; t_{m}    \leq t_{i}    \leq   t_{M/2}   \\ 
    80     \alpha \, (M - i +1) &    {\rm if} \; \; \; t_{M/2}  <    t_{i}    \leq   t_{n}       \\ 
    81     0                            &   {\rm if} \; \; \; t_{i}        >    t_{n} 
     78    0                           &    {\mathrm if} \; \; \; t_{i}       <     t_{m}                        \\ 
     79    \alpha \, i               &    {\mathrm if} \; \; \; t_{m}    \leq t_{i}    \leq   t_{M/2}   \\ 
     80    \alpha \, (M - i +1) &    {\mathrm if} \; \; \; t_{M/2}  <    t_{i}    \leq   t_{n}       \\ 
     81    0                            &   {\mathrm if} \; \; \; t_{i}        >    t_{n} 
    8282  \end{array} 
    8383                                   \right. 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_CONFIG.tex

    r11128 r11151  
    8989\begin{figure}[!t] 
    9090  \begin{center} 
    91     \includegraphics[width=0.98\textwidth]{Fig_ORCA_NH_mesh} 
     91    \includegraphics[width=\textwidth]{Fig_ORCA_NH_mesh} 
    9292    \caption{ 
    9393      \protect\label{fig:MISC_ORCA_msh} 
     
    121121\begin{figure}[!tbp] 
    122122  \begin{center} 
    123     \includegraphics[width=1.0\textwidth]{Fig_ORCA_NH_msh05_e1_e2} 
    124     \includegraphics[width=0.80\textwidth]{Fig_ORCA_aniso} 
     123    \includegraphics[width=\textwidth]{Fig_ORCA_NH_msh05_e1_e2} 
     124    \includegraphics[width=\textwidth]{Fig_ORCA_aniso} 
    125125    \caption { 
    126126      \protect\label{fig:MISC_ORCA_e1e2} 
     
    280280\begin{figure}[!t] 
    281281  \begin{center} 
    282     \includegraphics[width=1.0\textwidth]{Fig_GYRE} 
     282    \includegraphics[width=\textwidth]{Fig_GYRE} 
    283283    \caption{ 
    284284      \protect\label{fig:GYRE} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex

    r11123 r11151  
    168168\xmlline|<variable id="using_server" type="bool"></variable>| 
    169169 
    170 The {\tt using\_server} setting determines whether or not the server will be used in \textit{attached mode} 
    171 (as a library) [{\tt> false <}] or in \textit{detached mode} 
    172 (as an external executable on N additional, dedicated cpus) [{\tt > true <}]. 
     170The {\ttfamily using\_server} setting determines whether or not the server will be used in \textit{attached mode} 
     171(as a library) [{\ttfamily> false <}] or in \textit{detached mode} 
     172(as an external executable on N additional, dedicated cpus) [{\ttfamily > true <}]. 
    173173The \textit{attached mode} is simpler to use but much less efficient for massively parallel applications. 
    174174The type of each file can be either ''multiple\_file'' or ''one\_file''. 
     
    207207\subsubsection{Control of XIOS: the context in iodef.xml} 
    208208 
    209 As well as the {\tt using\_server} flag, other controls on the use of XIOS are set in the XIOS context in iodef.xml. 
     209As well as the {\ttfamily using\_server} flag, other controls on the use of XIOS are set in the XIOS context in iodef.xml. 
    210210See the XML basics section below for more details on XML syntax and rules. 
    211211 
     
    938938    \hline 
    939939  \end{tabularx} 
    940   \caption{Field tags ("\tt{field\_*}")} 
     940  \caption{Field tags ("\ttfamily{field\_*}")} 
    941941\end{table} 
    942942 
     
    974974    \hline 
    975975  \end{tabularx} 
    976   \caption{File tags ("\tt{file\_*}")} 
     976  \caption{File tags ("\ttfamily{file\_*}")} 
    977977\end{table} 
    978978 
     
    10071007    \hline 
    10081008  \end{tabularx} 
    1009   \caption{Axis tags ("\tt{axis\_*}")} 
     1009  \caption{Axis tags ("\ttfamily{axis\_*}")} 
    10101010\end{table} 
    10111011 
     
    10401040    \hline 
    10411041  \end{tabularx} 
    1042   \caption{Domain tags ("\tt{domain\_*)}"} 
     1042  \caption{Domain tags ("\ttfamily{domain\_*)}"} 
    10431043\end{table} 
    10441044 
     
    10731073    \hline 
    10741074  \end{tabularx} 
    1075   \caption{Grid tags ("\tt{grid\_*}")} 
     1075  \caption{Grid tags ("\ttfamily{grid\_*}")} 
    10761076\end{table} 
    10771077 
     
    11141114    \hline 
    11151115  \end{tabularx} 
    1116   \caption{Reference attributes ("\tt{*\_ref}")} 
     1116  \caption{Reference attributes ("\ttfamily{*\_ref}")} 
    11171117\end{table} 
    11181118 
     
    11501150    \hline 
    11511151  \end{tabularx} 
    1152   \caption{Domain attributes ("\tt{zoom\_*}")} 
     1152  \caption{Domain attributes ("\ttfamily{zoom\_*}")} 
    11531153\end{table} 
    11541154 
     
    13891389\end{forlines} 
    13901390 
    1391 \noindent for a standard ORCA2\_LIM configuration gives chunksizes of {\small\tt 46x38x1} respectively in 
    1392 the mono-processor case (\ie global domain of {\small\tt 182x149x31}). 
     1391\noindent for a standard ORCA2\_LIM configuration gives chunksizes of {\small\ttfamily 46x38x1} respectively in 
     1392the mono-processor case (\ie global domain of {\small\ttfamily 182x149x31}). 
    13931393An illustration of the potential space savings that NetCDF4 chunking and compression provides is given in  
    13941394table \autoref{tab:NC4} which compares the results of two short runs of the ORCA2\_LIM reference configuration with 
     
    20162016\begin{figure}[!t] 
    20172017  \begin{center} 
    2018     \includegraphics[width=1.0\textwidth]{Fig_mask_subasins} 
     2018    \includegraphics[width=\textwidth]{Fig_mask_subasins} 
    20192019    \caption{ 
    20202020      \protect\label{fig:mask_subasins} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIU.tex

    r11123 r11151  
    3333(\ie from the temperature of the top few model levels) or from some other source.   
    3434It must be noted that both the cool skin and warm layer models produce estimates of the change in temperature 
    35 ($\Delta T_{\rm{cs}}$ and $\Delta T_{\rm{wl}}$) and 
     35($\Delta T_{\mathrm{cs}}$ and $\Delta T_{\mathrm{wl}}$) and 
    3636both must be added to a foundation SST to obtain the true skin temperature. 
    3737 
     
    6363This is a simple flux based model that is defined by the equations 
    6464\begin{align} 
    65 \frac{\partial{\Delta T_{\rm{wl}}}}{\partial{t}}&=&\frac{Q(\nu+1)}{D_T\rho_w c_p 
     65\frac{\partial{\Delta T_{\mathrm{wl}}}}{\partial{t}}&=&\frac{Q(\nu+1)}{D_T\rho_w c_p 
    6666\nu}-\frac{(\nu+1)ku^*_{w}f(L_a)\Delta T}{D_T\Phi\!\left(\frac{D_T}{L}\right)} \mbox{,} 
    6767\label{eq:ecmwf1} \\ 
    6868L&=&\frac{\rho_w c_p u^{*^3}_{w}}{\kappa g \alpha_w Q }\mbox{,}\label{eq:ecmwf2} 
    6969\end{align} 
    70 where $\Delta T_{\rm{wl}}$ is the temperature difference between the top of the warm layer and the depth $D_T=3$\,m at which there is assumed to be no diurnal signal. 
     70where $\Delta T_{\mathrm{wl}}$ is the temperature difference between the top of the warm layer and the depth $D_T=3$\,m at which there is assumed to be no diurnal signal. 
    7171In equation (\autoref{eq:ecmwf1}) $\alpha_w=2\times10^{-4}$ is the thermal expansion coefficient of water, 
    7272$\kappa=0.4$ is von K\'{a}rm\'{a}n's constant, $c_p$ is the heat capacity at constant pressure of sea water, 
    7373$\rho_w$ is the water density, and $L$ is the Monin-Obukhov length. 
    7474The tunable variable $\nu$ is a shape parameter that defines the expected subskin temperature profile via 
    75 $T(z) = T(0) - \left( \frac{z}{D_T} \right)^\nu \Delta T_{\rm{wl}}$, 
     75$T(z) = T(0) - \left( \frac{z}{D_T} \right)^\nu \Delta T_{\mathrm{wl}}$, 
    7676where $T$ is the absolute temperature and $z\le D_T$ is the depth below the top of the warm layer. 
    7777The influence of wind on TAKAYA10 comes through the magnitude of the friction velocity of the water $u^*_{w}$, 
     
    8282the diurnal layer, \ie 
    8383\[ 
    84   Q = Q_{\rm{sol}} + Q_{\rm{lw}} + Q_{\rm{h}}\mbox{,} 
     84  Q = Q_{\mathrm{sol}} + Q_{\mathrm{lw}} + Q_{\mathrm{h}}\mbox{,} 
    8585  % \label{eq:e_flux_eqn} 
    8686\] 
    87 where $Q_{\rm{h}}$ is the sensible and latent heat flux, $Q_{\rm{lw}}$ is the long wave flux, 
    88 and $Q_{\rm{sol}}$ is the solar flux absorbed within the diurnal warm layer. 
    89 For $Q_{\rm{sol}}$ the 9 term representation of \citet{gentemann.minnett.ea_JGR09} is used. 
     87where $Q_{\mathrm{h}}$ is the sensible and latent heat flux, $Q_{\mathrm{lw}}$ is the long wave flux, 
     88and $Q_{\mathrm{sol}}$ is the solar flux absorbed within the diurnal warm layer. 
     89For $Q_{\mathrm{sol}}$ the 9 term representation of \citet{gentemann.minnett.ea_JGR09} is used. 
    9090In equation \autoref{eq:ecmwf1} the function $f(L_a)=\max(1,L_a^{\frac{2}{3}})$, 
    9191where $L_a=0.3$\footnote{ 
     
    119119 
    120120The cool skin is modelled using the framework of \citet{saunders_JAS67} who used a formulation of the near surface temperature difference based upon the heat flux and the friction velocity $u^*_{w}$. 
    121 As the cool skin is so thin (~1\,mm) we ignore the solar flux component to the heat flux and the Saunders equation for the cool skin temperature difference $\Delta T_{\rm{cs}}$ becomes 
     121As the cool skin is so thin (~1\,mm) we ignore the solar flux component to the heat flux and the Saunders equation for the cool skin temperature difference $\Delta T_{\mathrm{cs}}$ becomes 
    122122\[ 
    123123  % \label{eq:sunders_eqn} 
    124   \Delta T_{\rm{cs}}=\frac{Q_{\rm{ns}}\delta}{k_t} \mbox{,} 
     124  \Delta T_{\mathrm{cs}}=\frac{Q_{\mathrm{ns}}\delta}{k_t} \mbox{,} 
    125125\] 
    126 where $Q_{\rm{ns}}$ is the, usually negative, non-solar heat flux into the ocean and 
     126where $Q_{\mathrm{ns}}$ is the, usually negative, non-solar heat flux into the ocean and 
    127127$k_t$ is the thermal conductivity of sea water. 
    128128$\delta$ is the thickness of the skin layer and is given by 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DOM.tex

    r11123 r11151  
    4040\begin{figure}[!tb] 
    4141  \begin{center} 
    42     \includegraphics[]{Fig_cell} 
     42    \includegraphics[width=\textwidth]{Fig_cell} 
    4343    \caption{ 
    4444      \protect\label{fig:cell} 
     
    218218\begin{figure}[!tb] 
    219219  \begin{center} 
    220     \includegraphics[]{Fig_index_hor} 
     220    \includegraphics[width=\textwidth]{Fig_index_hor} 
    221221    \caption{ 
    222222      \protect\label{fig:index_hor} 
     
    272272\begin{figure}[!pt] 
    273273  \begin{center} 
    274     \includegraphics[]{Fig_index_vert} 
     274    \includegraphics[width=\textwidth]{Fig_index_vert} 
    275275    \caption{ 
    276276      \protect\label{fig:index_vert} 
     
    410410\begin{figure}[!t] 
    411411  \begin{center} 
    412     \includegraphics[]{Fig_zgr_e3} 
     412    \includegraphics[width=\textwidth]{Fig_zgr_e3} 
    413413    \caption{ 
    414414      \protect\label{fig:zgr_e3} 
     
    471471\begin{figure}[!tb] 
    472472  \begin{center} 
    473     \includegraphics[]{Fig_z_zps_s_sps} 
     473    \includegraphics[width=\textwidth]{Fig_z_zps_s_sps} 
    474474    \caption{ 
    475475      \protect\label{fig:z_zps_s_sps} 
     
    593593\begin{figure}[!tb] 
    594594  \begin{center} 
    595     \includegraphics[]{Fig_zgr} 
     595    \includegraphics[width=\textwidth]{Fig_zgr} 
    596596    \caption{ 
    597597      \protect\label{fig:zgr} 
     
    859859\begin{figure}[!ht] 
    860860  \begin{center} 
    861     \includegraphics[]{Fig_sco_function} 
     861    \includegraphics[width=\textwidth]{Fig_sco_function} 
    862862    \caption{ 
    863863      \protect\label{fig:sco_function} 
     
    911911%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    912912\begin{figure}[!ht] 
    913   \includegraphics[]{Fig_DOM_compare_coordinates_surface} 
     913  \includegraphics[width=\textwidth]{Fig_DOM_compare_coordinates_surface} 
    914914  \caption{ 
    915915    A comparison of the \citet{song.haidvogel_JCP94} $S$-coordinate (solid lines), 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DYN.tex

    r11123 r11151  
    309309\begin{figure}[!ht] 
    310310  \begin{center} 
    311     \includegraphics[width=0.70\textwidth]{Fig_DYN_een_triad} 
     311    \includegraphics[width=\textwidth]{Fig_DYN_een_triad} 
    312312    \caption{ 
    313313      \protect\label{fig:DYN_een_triad} 
     
    862862\begin{equation} 
    863863  \label{eq:BT_dyn} 
    864   \frac{\partial {\rm \overline{{\bf U}}_h} }{\partial t}= 
    865   -f\;{\rm {\bf k}}\times {\rm \overline{{\bf U}}_h} 
    866   -g\nabla _h \eta -\frac{c_b^{\textbf U}}{H+\eta} \rm {\overline{{\bf U}}_h} + \rm {\overline{\bf G}} 
     864  \frac{\partial {\mathrm \overline{{\mathbf U}}_h} }{\partial t}= 
     865  -f\;{\mathrm {\mathbf k}}\times {\mathrm \overline{{\mathbf U}}_h} 
     866  -g\nabla _h \eta -\frac{c_b^{\textbf U}}{H+\eta} \mathrm {\overline{{\mathbf U}}_h} + \mathrm {\overline{\mathbf G}} 
    867867\end{equation} 
    868868\[ 
    869869  % \label{eq:BT_ssh} 
    870   \frac{\partial \eta }{\partial t}=-\nabla \cdot \left[ {\left( {H+\eta } \right) \; {\rm{\bf \overline{U}}}_h \,} \right]+P-E 
     870  \frac{\partial \eta }{\partial t}=-\nabla \cdot \left[ {\left( {H+\eta } \right) \; {\mathrm{\mathbf \overline{U}}}_h \,} \right]+P-E 
    871871\] 
    872872% \end{subequations} 
    873 where $\rm {\overline{\bf G}}$ is a forcing term held constant, containing coupling term between modes, 
     873where $\mathrm {\overline{\mathbf G}}$ is a forcing term held constant, containing coupling term between modes, 
    874874surface atmospheric forcing as well as slowly varying barotropic terms not explicitly computed to gain efficiency. 
    875875The third term on the right hand side of \autoref{eq:BT_dyn} represents the bottom stress 
     
    884884\begin{figure}[!t] 
    885885  \begin{center} 
    886     \includegraphics[width=0.7\textwidth]{Fig_DYN_dynspg_ts} 
     886    \includegraphics[width=\textwidth]{Fig_DYN_dynspg_ts} 
    887887    \caption{ 
    888888      \protect\label{fig:DYN_dynspg_ts} 
     
    10921092  \[ 
    10931093    % \label{eq:spg_flt} 
    1094     \frac{\partial {\rm {\bf U}}_h }{\partial t}= {\rm {\bf M}} 
     1094    \frac{\partial {\mathrm {\mathbf U}}_h }{\partial t}= {\mathrm {\mathbf M}} 
    10951095    - g \nabla \left( \tilde{\rho} \ \eta \right) 
    10961096    - g \ T_c \nabla \left( \widetilde{\rho} \ \partial_t \eta \right) 
     
    10981098  where $T_c$, is a parameter with dimensions of time which characterizes the force, 
    10991099  $\widetilde{\rho} = \rho / \rho_o$ is the dimensionless density, 
    1100   and $\rm {\bf M}$ represents the collected contributions of the Coriolis, hydrostatic pressure gradient, 
     1100  and $\mathrm {\mathbf M}$ represents the collected contributions of the Coriolis, hydrostatic pressure gradient, 
    11011101  non-linear and viscous terms in \autoref{eq:PE_dyn}. 
    11021102}   %end gmcomment 
     
    11521152  \left\{ 
    11531153    \begin{aligned} 
    1154       D_u^{l{\rm {\bf U}}} =\frac{1}{e_{1u} }\delta_{i+1/2} \left[ {A_T^{lm} 
     1154      D_u^{l{\mathrm {\mathbf U}}} =\frac{1}{e_{1u} }\delta_{i+1/2} \left[ {A_T^{lm} 
    11551155          \;\chi } \right]-\frac{1}{e_{2u} {\kern 1pt}e_{3u} }\delta_j \left[  
    11561156        {A_f^{lm} \;e_{3f} \zeta } \right] \\ \\ 
    1157       D_v^{l{\rm {\bf U}}} =\frac{1}{e_{2v} }\delta_{j+1/2} \left[ {A_T^{lm} 
     1157      D_v^{l{\mathrm {\mathbf U}}} =\frac{1}{e_{2v} }\delta_{j+1/2} \left[ {A_T^{lm} 
    11581158          \;\chi } \right]+\frac{1}{e_{1v} {\kern 1pt}e_{3v} }\delta_i \left[  
    11591159        {A_f^{lm} \;e_{3f} \zeta } \right] 
     
    14941494\end{equation} 
    14951495 
    1496 Note a small tolerance ($\mathrm{rn\_wdmin2}$) has been introduced here {\it [Q: Why is 
     1496Note a small tolerance ($\mathrm{rn\_wdmin2}$) has been introduced here {\itshape [Q: Why is 
    14971497this necessary/desirable?]}. Substituting from (\ref{dyn_wd_continuity_coef}) gives an 
    14981498expression for the coefficient needed to multiply the outward flux at this cell in order 
     
    15411541%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    15421542\begin{figure}[!ht] \begin{center} 
    1543 \includegraphics[width=0.8\textwidth]{Fig_WAD_dynhpg} 
     1543\includegraphics[width=\textwidth]{Fig_WAD_dynhpg} 
    15441544\caption{ \label{Fig_WAD_dynhpg} 
    15451545Illustrations of the three possible combinations of the logical variables controlling the 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_LBC.tex

    r11123 r11151  
    5656\begin{figure}[!t] 
    5757  \begin{center} 
    58     \includegraphics[width=0.90\textwidth]{Fig_LBC_uv} 
     58    \includegraphics[width=\textwidth]{Fig_LBC_uv} 
    5959    \caption{ 
    6060      \protect\label{fig:LBC_uv} 
     
    8585\begin{figure}[!p] 
    8686  \begin{center} 
    87     \includegraphics[width=0.90\textwidth]{Fig_LBC_shlat} 
     87    \includegraphics[width=\textwidth]{Fig_LBC_shlat} 
    8888    \caption{ 
    8989      \protect\label{fig:LBC_shlat} 
     
    194194\begin{figure}[!t] 
    195195  \begin{center} 
    196     \includegraphics[width=1.0\textwidth]{Fig_LBC_jperio} 
     196    \includegraphics[width=\textwidth]{Fig_LBC_jperio} 
    197197    \caption{ 
    198198      \protect\label{fig:LBC_jperio} 
     
    218218\begin{figure}[!t] 
    219219  \begin{center} 
    220     \includegraphics[width=0.90\textwidth]{Fig_North_Fold_T} 
     220    \includegraphics[width=\textwidth]{Fig_North_Fold_T} 
    221221    \caption{ 
    222222      \protect\label{fig:North_Fold_T} 
     
    280280\begin{figure}[!t] 
    281281  \begin{center} 
    282     \includegraphics[width=0.90\textwidth]{Fig_mpp} 
     282    \includegraphics[width=\textwidth]{Fig_mpp} 
    283283    \caption{ 
    284284      \protect\label{fig:mpp} 
     
    360360\begin{figure}[!ht] 
    361361  \begin{center} 
    362     \includegraphics[width=0.90\textwidth]{Fig_mppini2} 
     362    \includegraphics[width=\textwidth]{Fig_mppini2} 
    363363    \caption { 
    364364      \protect\label{fig:mppini2} 
     
    636636\begin{figure}[!t] 
    637637  \begin{center} 
    638     \includegraphics[width=1.0\textwidth]{Fig_LBC_bdy_geom} 
     638    \includegraphics[width=\textwidth]{Fig_LBC_bdy_geom} 
    639639    \caption { 
    640640      \protect\label{fig:LBC_bdy_geom} 
     
    670670These restrictions mean that data files used with versions of the 
    671671model prior to Version 3.4 may not work with Version 3.4 onwards. 
    672 A \fortran utility {\it bdy\_reorder} exists in the TOOLS directory which 
     672A \fortran utility {\itshape bdy\_reorder} exists in the TOOLS directory which 
    673673will re-order the data in old BDY data files. 
    674674 
     
    676676\begin{figure}[!t] 
    677677  \begin{center} 
    678     \includegraphics[width=1.0\textwidth]{Fig_LBC_nc_header} 
     678    \includegraphics[width=\textwidth]{Fig_LBC_nc_header} 
    679679    \caption { 
    680680      \protect\label{fig:LBC_nc_header} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_LDF.tex

    r11123 r11151  
    217217\begin{figure}[!ht] 
    218218  \begin{center} 
    219     \includegraphics[width=0.70\textwidth]{Fig_LDF_ZDF1} 
     219    \includegraphics[width=\textwidth]{Fig_LDF_ZDF1} 
    220220    \caption { 
    221221      \protect\label{fig:LDF_ZDF1} 
     
    249249\begin{figure}[!ht] 
    250250  \begin{center} 
    251     \includegraphics[width=0.70\textwidth]{Fig_eiv_slp} 
     251    \includegraphics[width=\textwidth]{Fig_eiv_slp} 
    252252    \caption{ 
    253253      \protect\label{fig:eiv_slp} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_OBS.tex

    r11123 r11151  
    573573\subsubsection{Horizontal interpolation} 
    574574 
    575 Consider an observation point ${\rm P}$ with with longitude and latitude $({\lambda_{}}_{\rm P}, \phi_{\rm P})$ and 
    576 the four nearest neighbouring model grid points ${\rm A}$, ${\rm B}$, ${\rm C}$ and ${\rm D}$ with 
    577 longitude and latitude ($\lambda_{\rm A}$, $\phi_{\rm A}$),($\lambda_{\rm B}$, $\phi_{\rm B}$) etc. 
     575Consider an observation point ${\mathrm P}$ with with longitude and latitude $({\lambda_{}}_{\mathrm P}, \phi_{\mathrm P})$ and 
     576the four nearest neighbouring model grid points ${\mathrm A}$, ${\mathrm B}$, ${\mathrm C}$ and ${\mathrm D}$ with 
     577longitude and latitude ($\lambda_{\mathrm A}$, $\phi_{\mathrm A}$),($\lambda_{\mathrm B}$, $\phi_{\mathrm B}$) etc. 
    578578All horizontal interpolation methods implemented in NEMO estimate the value of a model variable $x$ at point $P$ as 
    579 a weighted linear combination of the values of the model variables at the grid points ${\rm A}$, ${\rm B}$ etc.: 
     579a weighted linear combination of the values of the model variables at the grid points ${\mathrm A}$, ${\mathrm B}$ etc.: 
    580580\begin{align*} 
    581   {x_{}}_{\rm P} & \hspace{-2mm} = \hspace{-2mm} & 
    582                                                    \frac{1}{w} \left( {w_{}}_{\rm A} {x_{}}_{\rm A} + 
    583                                                    {w_{}}_{\rm B} {x_{}}_{\rm B} + 
    584                                                    {w_{}}_{\rm C} {x_{}}_{\rm C} + 
    585                                                    {w_{}}_{\rm D} {x_{}}_{\rm D} \right) 
     581  {x_{}}_{\mathrm P} & \hspace{-2mm} = \hspace{-2mm} & 
     582                                                   \frac{1}{w} \left( {w_{}}_{\mathrm A} {x_{}}_{\mathrm A} + 
     583                                                   {w_{}}_{\mathrm B} {x_{}}_{\mathrm B} + 
     584                                                   {w_{}}_{\mathrm C} {x_{}}_{\mathrm C} + 
     585                                                   {w_{}}_{\mathrm D} {x_{}}_{\mathrm D} \right) 
    586586\end{align*} 
    587 where ${w_{}}_{\rm A}$, ${w_{}}_{\rm B}$ etc. are the respective weights for the model field at 
    588 points ${\rm A}$, ${\rm B}$ etc., and $w = {w_{}}_{\rm A} + {w_{}}_{\rm B} + {w_{}}_{\rm C} + {w_{}}_{\rm D}$. 
     587where ${w_{}}_{\mathrm A}$, ${w_{}}_{\mathrm B}$ etc. are the respective weights for the model field at 
     588points ${\mathrm A}$, ${\mathrm B}$ etc., and $w = {w_{}}_{\mathrm A} + {w_{}}_{\mathrm B} + {w_{}}_{\mathrm C} + {w_{}}_{\mathrm D}$. 
    589589 
    590590Four different possibilities are available for computing the weights. 
     
    592592\begin{enumerate} 
    593593 
    594 \item[1.] {\bf Great-Circle distance-weighted interpolation.} 
     594\item[1.] {\bfseries Great-Circle distance-weighted interpolation.} 
    595595  The weights are computed as a function of the great-circle distance $s(P, \cdot)$ between $P$ and 
    596596  the model grid points $A$, $B$ etc. 
    597   For example, the weight given to the field ${x_{}}_{\rm A}$ is specified as the product of the distances 
    598   from ${\rm P}$ to the other points: 
     597  For example, the weight given to the field ${x_{}}_{\mathrm A}$ is specified as the product of the distances 
     598  from ${\mathrm P}$ to the other points: 
    599599  \begin{align*} 
    600     {w_{}}_{\rm A} = s({\rm P}, {\rm B}) \, s({\rm P}, {\rm C}) \, s({\rm P}, {\rm D}) 
     600    {w_{}}_{\mathrm A} = s({\mathrm P}, {\mathrm B}) \, s({\mathrm P}, {\mathrm C}) \, s({\mathrm P}, {\mathrm D}) 
    601601  \end{align*} 
    602602  where  
    603603  \begin{align*} 
    604     s\left ({\rm P}, {\rm M} \right )  
     604    s\left ({\mathrm P}, {\mathrm M} \right )  
    605605     & \hspace{-2mm} = \hspace{-2mm} &  
    606606      \cos^{-1} \! \left\{  
    607                \sin {\phi_{}}_{\rm P} \sin {\phi_{}}_{\rm M} 
    608              + \cos {\phi_{}}_{\rm P} \cos {\phi_{}}_{\rm M}  
    609                \cos ({\lambda_{}}_{\rm M} - {\lambda_{}}_{\rm P})  
     607               \sin {\phi_{}}_{\mathrm P} \sin {\phi_{}}_{\mathrm M} 
     608             + \cos {\phi_{}}_{\mathrm P} \cos {\phi_{}}_{\mathrm M}  
     609               \cos ({\lambda_{}}_{\mathrm M} - {\lambda_{}}_{\mathrm P})  
    610610                   \right\} 
    611611   \end{align*} 
     
    614614   involves the arcsine function (\eg see p.~101 of \citet{daley.barker_bk01}: 
    615615   \begin{align*} 
    616      s\left( {\rm P}, {\rm M} \right) & \hspace{-2mm} = \hspace{-2mm} & \sin^{-1} \! \left\{ \sqrt{ 1 - x^2 } \right\} 
     616     s\left( {\mathrm P}, {\mathrm M} \right) & \hspace{-2mm} = \hspace{-2mm} & \sin^{-1} \! \left\{ \sqrt{ 1 - x^2 } \right\} 
    617617   \end{align*} 
    618618   where 
    619619   \begin{align*} 
    620620     x & \hspace{-2mm} = \hspace{-2mm} & 
    621                                          {a_{}}_{\rm M} {a_{}}_{\rm P} + {b_{}}_{\rm M} {b_{}}_{\rm P} + {c_{}}_{\rm M} {c_{}}_{\rm P} 
     621                                         {a_{}}_{\mathrm M} {a_{}}_{\mathrm P} + {b_{}}_{\mathrm M} {b_{}}_{\mathrm P} + {c_{}}_{\mathrm M} {c_{}}_{\mathrm P} 
    622622   \end{align*} 
    623623   and  
    624624   \begin{align*} 
    625       {a_{}}_{\rm M} & \hspace{-2mm} = \hspace{-2mm} & \sin {\phi_{}}_{\rm M}, \\ 
    626       {a_{}}_{\rm P} & \hspace{-2mm} = \hspace{-2mm} & \sin {\phi_{}}_{\rm P}, \\ 
    627       {b_{}}_{\rm M} & \hspace{-2mm} = \hspace{-2mm} & \cos {\phi_{}}_{\rm M} \cos {\phi_{}}_{\rm M}, \\ 
    628       {b_{}}_{\rm P} & \hspace{-2mm} = \hspace{-2mm} & \cos {\phi_{}}_{\rm P} \cos {\phi_{}}_{\rm P}, \\ 
    629       {c_{}}_{\rm M} & \hspace{-2mm} = \hspace{-2mm} & \cos {\phi_{}}_{\rm M} \sin {\phi_{}}_{\rm M}, \\ 
    630       {c_{}}_{\rm P} & \hspace{-2mm} = \hspace{-2mm} & \cos {\phi_{}}_{\rm P} \sin {\phi_{}}_{\rm P}. 
     625      {a_{}}_{\mathrm M} & \hspace{-2mm} = \hspace{-2mm} & \sin {\phi_{}}_{\mathrm M}, \\ 
     626      {a_{}}_{\mathrm P} & \hspace{-2mm} = \hspace{-2mm} & \sin {\phi_{}}_{\mathrm P}, \\ 
     627      {b_{}}_{\mathrm M} & \hspace{-2mm} = \hspace{-2mm} & \cos {\phi_{}}_{\mathrm M} \cos {\phi_{}}_{\mathrm M}, \\ 
     628      {b_{}}_{\mathrm P} & \hspace{-2mm} = \hspace{-2mm} & \cos {\phi_{}}_{\mathrm P} \cos {\phi_{}}_{\mathrm P}, \\ 
     629      {c_{}}_{\mathrm M} & \hspace{-2mm} = \hspace{-2mm} & \cos {\phi_{}}_{\mathrm M} \sin {\phi_{}}_{\mathrm M}, \\ 
     630      {c_{}}_{\mathrm P} & \hspace{-2mm} = \hspace{-2mm} & \cos {\phi_{}}_{\mathrm P} \sin {\phi_{}}_{\mathrm P}. 
    631631  \end{align*} 
    632632 
    633 \item[2.] {\bf Great-Circle distance-weighted interpolation with small angle approximation.} 
     633\item[2.] {\bfseries Great-Circle distance-weighted interpolation with small angle approximation.} 
    634634  Similar to the previous interpolation but with the distance $s$ computed as 
    635635  \begin{align*} 
    636     s\left( {\rm P}, {\rm M} \right) 
     636    s\left( {\mathrm P}, {\mathrm M} \right) 
    637637    & \hspace{-2mm} = \hspace{-2mm} & 
    638                                       \sqrt{ \left( {\phi_{}}_{\rm M} - {\phi_{}}_{\rm P} \right)^{2} 
    639                                       + \left( {\lambda_{}}_{\rm M} - {\lambda_{}}_{\rm P} \right)^{2} 
    640                                       \cos^{2} {\phi_{}}_{\rm M} } 
     638                                      \sqrt{ \left( {\phi_{}}_{\mathrm M} - {\phi_{}}_{\mathrm P} \right)^{2} 
     639                                      + \left( {\lambda_{}}_{\mathrm M} - {\lambda_{}}_{\mathrm P} \right)^{2} 
     640                                      \cos^{2} {\phi_{}}_{\mathrm M} } 
    641641  \end{align*} 
    642642  where $M$ corresponds to $A$, $B$, $C$ or $D$. 
    643643 
    644 \item[3.] {\bf Bilinear interpolation for a regular spaced grid.} 
     644\item[3.] {\bfseries Bilinear interpolation for a regular spaced grid.} 
    645645  The interpolation is split into two 1D interpolations in the longitude and latitude directions, respectively. 
    646646 
    647 \item[4.] {\bf Bilinear remapping interpolation for a general grid.} 
     647\item[4.] {\bfseries Bilinear remapping interpolation for a general grid.} 
    648648  An iterative scheme that involves first mapping a quadrilateral cell into 
    649649  a cell with coordinates (0,0), (1,0), (0,1) and (1,1). 
     
    678678\begin{figure} 
    679679  \begin{center} 
    680     \includegraphics[width=0.90\textwidth]{Fig_OBS_avg_rec} 
     680    \includegraphics[width=\textwidth]{Fig_OBS_avg_rec} 
    681681    \caption{ 
    682682      \protect\label{fig:obsavgrec} 
     
    691691\begin{figure} 
    692692  \begin{center} 
    693     \includegraphics[width=0.90\textwidth]{Fig_OBS_avg_rad} 
     693    \includegraphics[width=\textwidth]{Fig_OBS_avg_rad} 
    694694    \caption{ 
    695695      \protect\label{fig:obsavgrad} 
     
    710710This is the most difficult and time consuming part of the 2D interpolation procedure.  
    711711A robust test for determining if an observation falls within a given quadrilateral cell is as follows. 
    712 Let ${\rm P}({\lambda_{}}_{\rm P} ,{\phi_{}}_{\rm P} )$ denote the observation point, 
    713 and let ${\rm A}({\lambda_{}}_{\rm A} ,{\phi_{}}_{\rm A} )$, ${\rm B}({\lambda_{}}_{\rm B} ,{\phi_{}}_{\rm B} )$, 
    714 ${\rm C}({\lambda_{}}_{\rm C} ,{\phi_{}}_{\rm C} )$ and ${\rm D}({\lambda_{}}_{\rm D} ,{\phi_{}}_{\rm D} )$ 
     712Let ${\mathrm P}({\lambda_{}}_{\mathrm P} ,{\phi_{}}_{\mathrm P} )$ denote the observation point, 
     713and let ${\mathrm A}({\lambda_{}}_{\mathrm A} ,{\phi_{}}_{\mathrm A} )$, ${\mathrm B}({\lambda_{}}_{\mathrm B} ,{\phi_{}}_{\mathrm B} )$, 
     714${\mathrm C}({\lambda_{}}_{\mathrm C} ,{\phi_{}}_{\mathrm C} )$ and ${\mathrm D}({\lambda_{}}_{\mathrm D} ,{\phi_{}}_{\mathrm D} )$ 
    715715denote the bottom left, bottom right, top left and top right corner points of the cell, respectively.  
    716716To determine if P is inside the cell, we verify that the cross-products  
    717717\begin{align*} 
    718718  \begin{array}{lllll} 
    719     {{\bf r}_{}}_{\rm PA} \times {{\bf r}_{}}_{\rm PC} 
    720     & = & [({\lambda_{}}_{\rm A}\; -\; {\lambda_{}}_{\rm P} ) 
    721           ({\phi_{}}_{\rm C}   \; -\; {\phi_{}}_{\rm P} ) 
    722           - ({\lambda_{}}_{\rm C}\; -\; {\lambda_{}}_{\rm P} ) 
    723           ({\phi_{}}_{\rm A}   \; -\; {\phi_{}}_{\rm P} )] \; \widehat{\bf k} \\ 
    724     {{\bf r}_{}}_{\rm PB} \times {{\bf r}_{}}_{\rm PA} 
    725     & = & [({\lambda_{}}_{\rm B}\; -\; {\lambda_{}}_{\rm P} ) 
    726           ({\phi_{}}_{\rm A}   \; -\; {\phi_{}}_{\rm P} ) 
    727           - ({\lambda_{}}_{\rm A}\; -\; {\lambda_{}}_{\rm P} ) 
    728           ({\phi_{}}_{\rm B}   \; -\; {\phi_{}}_{\rm P} )] \; \widehat{\bf k} \\ 
    729     {{\bf r}_{}}_{\rm PC} \times {{\bf r}_{}}_{\rm PD} 
    730     & = & [({\lambda_{}}_{\rm C}\; -\; {\lambda_{}}_{\rm P} ) 
    731           ({\phi_{}}_{\rm D}   \; -\; {\phi_{}}_{\rm P} ) 
    732           - ({\lambda_{}}_{\rm D}\; -\; {\lambda_{}}_{\rm P} ) 
    733           ({\phi_{}}_{\rm C}   \; -\; {\phi_{}}_{\rm P} )] \; \widehat{\bf k} \\ 
    734     {{\bf r}_{}}_{\rm PD} \times {{\bf r}_{}}_{\rm PB} 
    735     & = & [({\lambda_{}}_{\rm D}\; -\; {\lambda_{}}_{\rm P} ) 
    736           ({\phi_{}}_{\rm B}   \; -\; {\phi_{}}_{\rm P} ) 
    737           - ({\lambda_{}}_{\rm B}\; -\; {\lambda_{}}_{\rm P} ) 
    738           ({\phi_{}}_{\rm D}  \;  - \; {\phi_{}}_{\rm P} )] \; \widehat{\bf k} \\ 
     719    {{\mathbf r}_{}}_{\mathrm PA} \times {{\mathbf r}_{}}_{\mathrm PC} 
     720    & = & [({\lambda_{}}_{\mathrm A}\; -\; {\lambda_{}}_{\mathrm P} ) 
     721          ({\phi_{}}_{\mathrm C}   \; -\; {\phi_{}}_{\mathrm P} ) 
     722          - ({\lambda_{}}_{\mathrm C}\; -\; {\lambda_{}}_{\mathrm P} ) 
     723          ({\phi_{}}_{\mathrm A}   \; -\; {\phi_{}}_{\mathrm P} )] \; \widehat{\mathbf k} \\ 
     724    {{\mathbf r}_{}}_{\mathrm PB} \times {{\mathbf r}_{}}_{\mathrm PA} 
     725    & = & [({\lambda_{}}_{\mathrm B}\; -\; {\lambda_{}}_{\mathrm P} ) 
     726          ({\phi_{}}_{\mathrm A}   \; -\; {\phi_{}}_{\mathrm P} ) 
     727          - ({\lambda_{}}_{\mathrm A}\; -\; {\lambda_{}}_{\mathrm P} ) 
     728          ({\phi_{}}_{\mathrm B}   \; -\; {\phi_{}}_{\mathrm P} )] \; \widehat{\mathbf k} \\ 
     729    {{\mathbf r}_{}}_{\mathrm PC} \times {{\mathbf r}_{}}_{\mathrm PD} 
     730    & = & [({\lambda_{}}_{\mathrm C}\; -\; {\lambda_{}}_{\mathrm P} ) 
     731          ({\phi_{}}_{\mathrm D}   \; -\; {\phi_{}}_{\mathrm P} ) 
     732          - ({\lambda_{}}_{\mathrm D}\; -\; {\lambda_{}}_{\mathrm P} ) 
     733          ({\phi_{}}_{\mathrm C}   \; -\; {\phi_{}}_{\mathrm P} )] \; \widehat{\mathbf k} \\ 
     734    {{\mathbf r}_{}}_{\mathrm PD} \times {{\mathbf r}_{}}_{\mathrm PB} 
     735    & = & [({\lambda_{}}_{\mathrm D}\; -\; {\lambda_{}}_{\mathrm P} ) 
     736          ({\phi_{}}_{\mathrm B}   \; -\; {\phi_{}}_{\mathrm P} ) 
     737          - ({\lambda_{}}_{\mathrm B}\; -\; {\lambda_{}}_{\mathrm P} ) 
     738          ({\phi_{}}_{\mathrm D}  \;  - \; {\phi_{}}_{\mathrm P} )] \; \widehat{\mathbf k} \\ 
    739739  \end{array} 
    740740  % \label{eq:cross} 
    741741\end{align*} 
    742 point in the opposite direction to the unit normal $\widehat{\bf k}$ 
    743 (\ie that the coefficients of $\widehat{\bf k}$ are negative), 
    744 where ${{\bf r}_{}}_{\rm PA}$, ${{\bf r}_{}}_{\rm PB}$, etc. correspond to 
     742point in the opposite direction to the unit normal $\widehat{\mathbf k}$ 
     743(\ie that the coefficients of $\widehat{\mathbf k}$ are negative), 
     744where ${{\mathbf r}_{}}_{\mathrm PA}$, ${{\mathbf r}_{}}_{\mathrm PB}$, etc. correspond to 
    745745the vectors between points P and A, P and B, etc.. 
    746746The method used is similar to the method used in the \href{https://github.com/SCRIP-Project/SCRIP}{SCRIP interpolation package}. 
     
    772772\begin{figure} 
    773773  \begin{center} 
    774     \includegraphics[width=10cm,height=12cm,angle=-90.]{Fig_ASM_obsdist_local} 
     774    \includegraphics[width=\textwidth]{Fig_ASM_obsdist_local} 
    775775    \caption{ 
    776776      \protect\label{fig:obslocal} 
     
    801801\begin{figure} 
    802802  \begin{center} 
    803     \includegraphics[width=10cm,height=12cm,angle=-90.]{Fig_ASM_obsdist_global} 
     803    \includegraphics[width=\textwidth]{Fig_ASM_obsdist_global} 
    804804    \caption{ 
    805805      \protect\label{fig:obsglobal} 
     
    13701370\begin{figure} 
    13711371  \begin{center} 
    1372     % \includegraphics[width=10cm,height=12cm,angle=-90.]{Fig_OBS_dataplot_main} 
    1373     \includegraphics[width=9cm,angle=-90.]{Fig_OBS_dataplot_main} 
     1372    % \includegraphics[width=\textwidth]{Fig_OBS_dataplot_main} 
     1373    \includegraphics[width=\textwidth]{Fig_OBS_dataplot_main} 
    13741374    \caption{ 
    13751375      \protect\label{fig:obsdataplotmain} 
     
    13861386\begin{figure} 
    13871387  \begin{center} 
    1388     % \includegraphics[width=10cm,height=12cm,angle=-90.]{Fig_OBS_dataplot_prof} 
    1389     \includegraphics[width=7cm,angle=-90.]{Fig_OBS_dataplot_prof} 
     1388    % \includegraphics[width=\textwidth]{Fig_OBS_dataplot_prof} 
     1389    \includegraphics[width=\textwidth]{Fig_OBS_dataplot_prof} 
    13901390    \caption{ 
    13911391      \protect\label{fig:obsdataplotprofile} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_SBC.tex

    r11123 r11151  
    819819\[ 
    820820  % \label{eq:PE_dyn_tides} 
    821   \frac{\partial {\rm {\bf U}}_h }{\partial t}= ... 
     821  \frac{\partial {\mathrm {\mathbf U}}_h }{\partial t}= ... 
    822822  +g\nabla (\Pi_{eq} + \Pi_{sal}) 
    823823\] 
     
    10891089\begin{figure}[!t] 
    10901090  \begin{center} 
    1091     \includegraphics[width=0.8\textwidth]{Fig_SBC_isf} 
     1091    \includegraphics[width=\textwidth]{Fig_SBC_isf} 
    10921092    \caption{ 
    10931093      \protect\label{fig:SBC_isf} 
     
    14381438\begin{figure}[!t] 
    14391439  \begin{center} 
    1440     \includegraphics[width=0.8\textwidth]{Fig_SBC_diurnal} 
     1440    \includegraphics[width=\textwidth]{Fig_SBC_diurnal} 
    14411441    \caption{ 
    14421442      \protect\label{fig:SBC_diurnal} 
     
    14761476\begin{figure}[!t] 
    14771477  \begin{center} 
    1478     \includegraphics[width=0.7\textwidth]{Fig_SBC_dcy} 
     1478    \includegraphics[width=\textwidth]{Fig_SBC_dcy} 
    14791479    \caption{ 
    14801480      \protect\label{fig:SBC_dcy} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_TRA.tex

    r11123 r11151  
    9090\begin{figure}[!t] 
    9191  \begin{center} 
    92     \includegraphics[]{Fig_adv_scheme} 
     92    \includegraphics[width=\textwidth]{Fig_adv_scheme} 
    9393    \caption{ 
    9494      \protect\label{fig:adv_scheme} 
     
    856856\begin{figure}[!t] 
    857857  \begin{center} 
    858     \includegraphics[]{Fig_TRA_Irradiance} 
     858    \includegraphics[width=\textwidth]{Fig_TRA_Irradiance} 
    859859    \caption{ 
    860860      \protect\label{fig:traqsr_irradiance} 
     
    883883\begin{figure}[!t] 
    884884  \begin{center} 
    885     \includegraphics[]{Fig_TRA_geoth} 
     885    \includegraphics[width=\textwidth]{Fig_TRA_geoth} 
    886886    \caption{ 
    887887      \protect\label{fig:geothermal} 
     
    994994\begin{figure}[!t] 
    995995  \begin{center} 
    996     \includegraphics[]{Fig_BBL_adv} 
     996    \includegraphics[width=\textwidth]{Fig_BBL_adv} 
    997997    \caption{ 
    998998      \protect\label{fig:bbl} 
     
    13791379\begin{figure}[!p] 
    13801380  \begin{center} 
    1381     \includegraphics[]{Fig_partial_step_scheme} 
     1381    \includegraphics[width=\textwidth]{Fig_partial_step_scheme} 
    13821382    \caption{ 
    13831383      \protect\label{fig:Partial_step_scheme} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_ZDF.tex

    r11123 r11151  
    237237\begin{figure}[!t] 
    238238  \begin{center} 
    239     \includegraphics[width=1.00\textwidth]{Fig_mixing_length} 
     239    \includegraphics[width=\textwidth]{Fig_mixing_length} 
    240240    \caption{ 
    241241      \protect\label{fig:mixing_length} 
     
    414414\begin{figure}[!t] 
    415415  \begin{center} 
    416     \includegraphics[width=1.00\textwidth]{Fig_ZDF_TKE_time_scheme} 
     416    \includegraphics[width=\textwidth]{Fig_ZDF_TKE_time_scheme} 
    417417    \caption{ 
    418418      \protect\label{fig:TKE_time_scheme} 
     
    676676\begin{figure}[!htb] 
    677677  \begin{center} 
    678     \includegraphics[width=0.90\textwidth]{Fig_npc} 
     678    \includegraphics[width=\textwidth]{Fig_npc} 
    679679    \caption{ 
    680680      \protect\label{fig:npc} 
     
    839839\begin{figure}[!t] 
    840840  \begin{center} 
    841     \includegraphics[width=0.99\textwidth]{Fig_zdfddm} 
     841    \includegraphics[width=\textwidth]{Fig_zdfddm} 
    842842    \caption{ 
    843843      \protect\label{fig:zdfddm} 
     
    10411041the last wet layer in each column by: 
    10421042\[ 
    1043   C_D = \left ( {\kappa \over {\rm log}\left ( 0.5e_{3t}/rn\_bfrz0 \right ) } \right )^2 
     1043  C_D = \left ( {\kappa \over {\mathrm log}\left ( 0.5e_{3t}/rn\_bfrz0 \right ) } \right )^2 
    10441044\] 
    10451045 
     
    12851285\begin{figure}[!t] 
    12861286  \begin{center} 
    1287     \includegraphics[width=0.90\textwidth]{Fig_ZDF_M2_K1_tmx} 
     1287    \includegraphics[width=\textwidth]{Fig_ZDF_M2_K1_tmx} 
    12881288    \caption{ 
    12891289      \protect\label{fig:ZDF_M2_K1_tmx} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_conservation.tex

    r11123 r11151  
    6565  % \label{eq:vor_vorticity} 
    6666  \int_D {{\textbf {k}}\cdot \frac{1}{e_3 }\nabla \times \left( {\varsigma 
    67         \;{\rm {\bf k}}\times {\textbf {U}}_h } \right)\;dv} =0 
     67        \;{\mathrm {\mathbf k}}\times {\textbf {U}}_h } \right)\;dv} =0 
    6868\] 
    6969 
     
    189189\[ 
    190190  % \label{eq:dynldf_dyn} 
    191   \int\limits_D {\frac{1}{e_3 }{\rm {\bf k}}\cdot \nabla \times \left[ {\nabla 
     191  \int\limits_D {\frac{1}{e_3 }{\mathrm {\mathbf k}}\cdot \nabla \times \left[ {\nabla 
    192192        _h \left( {A^{lm}\;\chi } \right)-\nabla _h \times \left( {A^{lm}\;\zeta 
    193             \;{\rm {\bf k}}} \right)} \right]\;dv} =0 
     193            \;{\mathrm {\mathbf k}}} \right)} \right]\;dv} =0 
    194194\] 
    195195 
     
    197197  % \label{eq:dynldf_div} 
    198198  \int\limits_D {\nabla _h \cdot \left[ {\nabla _h \left( {A^{lm}\;\chi } 
    199         \right)-\nabla _h \times \left( {A^{lm}\;\zeta \;{\rm {\bf k}}} \right)} 
     199        \right)-\nabla _h \times \left( {A^{lm}\;\zeta \;{\mathrm {\mathbf k}}} \right)} 
    200200    \right]\;dv} =0 
    201201\] 
     
    203203\[ 
    204204  % \label{eq:dynldf_curl} 
    205   \int_D {{\rm {\bf U}}_h \cdot \left[ {\nabla _h \left( {A^{lm}\;\chi } 
    206         \right)-\nabla _h \times \left( {A^{lm}\;\zeta \;{\rm {\bf k}}} \right)} 
     205  \int_D {{\mathrm {\mathbf U}}_h \cdot \left[ {\nabla _h \left( {A^{lm}\;\chi } 
     206        \right)-\nabla _h \times \left( {A^{lm}\;\zeta \;{\mathrm {\mathbf k}}} \right)} 
    207207    \right]\;dv} \leqslant 0 
    208208\] 
     
    210210\[ 
    211211  % \label{eq:dynldf_curl2} 
    212   \mbox{if}\quad A^{lm}=cste\quad \quad \int_D {\zeta \;{\rm {\bf k}}\cdot 
     212  \mbox{if}\quad A^{lm}=cste\quad \quad \int_D {\zeta \;{\mathrm {\mathbf k}}\cdot 
    213213    \nabla \times \left[ {\nabla _h \left( {A^{lm}\;\chi } \right)-\nabla _h 
    214         \times \left( {A^{lm}\;\zeta \;{\rm {\bf k}}} \right)} \right]\;dv} 
     214        \times \left( {A^{lm}\;\zeta \;{\mathrm {\mathbf k}}} \right)} \right]\;dv} 
    215215  \leqslant 0 
    216216\] 
     
    220220  \mbox{if}\quad A^{lm}=cste\quad \quad \int_D {\chi \;\nabla _h \cdot \left[ 
    221221      {\nabla _h \left( {A^{lm}\;\chi } \right)-\nabla _h \times \left( 
    222           {A^{lm}\;\zeta \;{\rm {\bf k}}} \right)} \right]\;dv} \leqslant 0 
     222          {A^{lm}\;\zeta \;{\mathrm {\mathbf k}}} \right)} \right]\;dv} \leqslant 0 
    223223\] 
    224224 
     
    260260  % \label{eq:dynzdf_vor} 
    261261  \begin{aligned} 
    262     & \int_D {\frac{1}{e_3 }{\rm {\bf k}}\cdot \nabla \times \left( {\frac{1}{e_3 
    263           }\frac{\partial }{\partial k}\left( {\frac{A^{vm}}{e_3 }\frac{\partial {\rm 
    264                   {\bf U}}_h }{\partial k}} \right)} \right)\;dv} =0 \\ 
    265     & \int_D {\zeta \,{\rm {\bf k}}\cdot \nabla \times \left( {\frac{1}{e_3 
    266           }\frac{\partial }{\partial k}\left( {\frac{A^{vm}}{e_3 }\frac{\partial {\rm 
    267                   {\bf U}}_h }{\partial k}} \right)} \right)\;dv} \leq 0 \\ 
     262    & \int_D {\frac{1}{e_3 }{\mathrm {\mathbf k}}\cdot \nabla \times \left( {\frac{1}{e_3 
     263          }\frac{\partial }{\partial k}\left( {\frac{A^{vm}}{e_3 }\frac{\partial {\mathrm 
     264                  {\mathbf U}}_h }{\partial k}} \right)} \right)\;dv} =0 \\ 
     265    & \int_D {\zeta \,{\mathrm {\mathbf k}}\cdot \nabla \times \left( {\frac{1}{e_3 
     266          }\frac{\partial }{\partial k}\left( {\frac{A^{vm}}{e_3 }\frac{\partial {\mathrm 
     267                  {\mathbf U}}_h }{\partial k}} \right)} \right)\;dv} \leq 0 \\ 
    268268  \end{aligned} 
    269269\] 
     
    273273  \begin{aligned} 
    274274    &\int_D {\nabla \cdot \left( {\frac{1}{e_3 }\frac{\partial }{\partial 
    275             k}\left( {\frac{A^{vm}}{e_3 }\frac{\partial {\rm {\bf U}}_h }{\partial k}} 
     275            k}\left( {\frac{A^{vm}}{e_3 }\frac{\partial {\mathrm {\mathbf U}}_h }{\partial k}} 
    276276          \right)} \right)\;dv} =0 \\ 
    277277    & \int_D {\chi \;\nabla \cdot \left( {\frac{1}{e_3 }\frac{\partial }{\partial 
    278             k}\left( {\frac{A^{vm}}{e_3 }\frac{\partial {\rm {\bf U}}_h }{\partial k}} 
     278            k}\left( {\frac{A^{vm}}{e_3 }\frac{\partial {\mathrm {\mathbf U}}_h }{\partial k}} 
    279279          \right)} \right)\;dv} \leq 0 \\ 
    280280  \end{aligned} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_misc.tex

    r11123 r11151  
    6363\begin{figure}[!tbp] 
    6464  \begin{center} 
    65     \includegraphics[width=0.80\textwidth]{Fig_Gibraltar} 
    66     \includegraphics[width=0.80\textwidth]{Fig_Gibraltar2} 
     65    \includegraphics[width=\textwidth]{Fig_Gibraltar} 
     66    \includegraphics[width=\textwidth]{Fig_Gibraltar2} 
    6767    \caption{ 
    6868      \protect\label{fig:MISC_strait_hand} 
     
    8484\begin{figure}[!tbp] 
    8585  \begin{center} 
    86     \includegraphics[width=1.0\textwidth]{Fig_closea_mask_example} 
     86    \includegraphics[width=\textwidth]{Fig_closea_mask_example} 
    8787    \caption{ 
    8888      \protect\label{fig:closea_mask_example} 
     
    122122 
    123123\begin{enumerate} 
    124 \item{{\bf No ``closea\_mask'' field is included in domain configuration 
     124\item{{\bfseries No ``closea\_mask'' field is included in domain configuration 
    125125  file.} In this case the closea module does nothing.} 
    126126 
    127 \item{{\bf A field called closea\_mask is included in the domain 
     127\item{{\bfseries A field called closea\_mask is included in the domain 
    128128configuration file and ln\_closea=.false. in namelist namcfg.} In this 
    129129case the inland seas defined by the closea\_mask field are filled in 
     
    131131closea\_mask that is nonzero is set to be a land point.} 
    132132 
    133 \item{{\bf A field called closea\_mask is included in the domain 
     133\item{{\bfseries A field called closea\_mask is included in the domain 
    134134configuration file and ln\_closea=.true. in namelist namcfg.} Each 
    135135inland sea or group of inland seas is set to a positive integer value 
     
    140140closea\_mask is zero).} 
    141141 
    142 \item{{\bf Fields called closea\_mask and closea\_mask\_rnf are 
     142\item{{\bfseries Fields called closea\_mask and closea\_mask\_rnf are 
    143143included in the domain configuration file and ln\_closea=.true. in 
    144144namelist namcfg.} This option works as for option 3, except that if 
     
    154154ocean.} 
    155155 
    156 \item{{\bf Fields called closea\_mask and closea\_mask\_emp are 
     156\item{{\bfseries Fields called closea\_mask and closea\_mask\_emp are 
    157157included in the domain configuration file and ln\_closea=.true. in 
    158158namelist namcfg.} This option works the same as option 4 except that 
     
    223223\begin{figure}[!ht] 
    224224  \begin{center} 
    225     \includegraphics[width=0.90\textwidth]{Fig_LBC_zoom} 
     225    \includegraphics[width=\textwidth]{Fig_LBC_zoom} 
    226226    \caption{ 
    227227      \protect\label{fig:LBC_zoom} 
     
    314314This alternative method should give identical results to the default \textsc{ALLGATHER} method and 
    315315is recommended for large values of \np{jpni}. 
    316 The new method is activated by setting \np{ln\_nnogather} to be true ({\bf nammpp}). 
     316The new method is activated by setting \np{ln\_nnogather} to be true (\ngn{nammpp}). 
    317317The reproducibility of results using the two methods should be confirmed for each new, 
    318318non-reference configuration. 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics.tex

    r11123 r11151  
    120120\begin{figure}[!ht] 
    121121  \begin{center} 
    122     \includegraphics[]{Fig_I_ocean_bc} 
     122    \includegraphics[width=\textwidth]{Fig_I_ocean_bc} 
    123123    \caption{ 
    124124      \protect\label{fig:ocean_bc} 
     
    323323\begin{figure}[!tb] 
    324324  \begin{center} 
    325     \includegraphics[]{Fig_I_earth_referential} 
     325    \includegraphics[width=\textwidth]{Fig_I_earth_referential} 
    326326    \caption{ 
    327327      \protect\label{fig:referential} 
     
    738738\begin{figure}[!b] 
    739739  \begin{center} 
    740     \includegraphics[]{Fig_z_zstar} 
     740    \includegraphics[width=\textwidth]{Fig_z_zstar} 
    741741    \caption{ 
    742742      \protect\label{fig:z_zstar} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex

    r11123 r11151  
    147147\begin{figure}[!t] 
    148148  \begin{center} 
    149     \includegraphics[width=0.90\textwidth]{Fig_DYN_dynspg_ts} 
     149    \includegraphics[width=\textwidth]{Fig_DYN_dynspg_ts} 
    150150    \caption{ 
    151151      \protect\label{fig:DYN_dynspg_ts} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_time_domain.tex

    r11123 r11151  
    197197\begin{figure}[!t] 
    198198  \begin{center} 
    199     \includegraphics[]{Fig_TimeStepping_flowchart} 
     199    \includegraphics[width=\textwidth]{Fig_TimeStepping_flowchart} 
    200200    \caption{ 
    201201      \protect\label{fig:TimeStep_flowchart} 
     
    261261\begin{figure}[!t] 
    262262  \begin{center} 
    263     \includegraphics[]{Fig_MLF_forcing} 
     263    \includegraphics[width=\textwidth]{Fig_MLF_forcing} 
    264264    \caption{ 
    265265      \protect\label{fig:MLF_forcing} 
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