Changeset 11019


Ignore:
Timestamp:
2019-05-20T22:21:43+02:00 (17 months ago)
Author:
nicolasmartin
Message:

Apply more or less same modifications on TOP as for SI3 for compliance
Despite remaining issues with references, TOP manual can be build like NEMO & SI3 with ./build_manual.sh TOP
For the record, the building of the 3 manuals can be launched with ./manual_build.sh all

Location:
NEMO/trunk/doc/latex/TOP
Files:
3 deleted
4 edited
2 moved

Legend:

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

    r10896 r11019  
    11%% ============================================================================== 
    2 %% NEMO_book.tex: build the NEMO Reference Manual 
     2%% TOP Reference Manual 
    33%% ============================================================================== 
    4  
    5  
    6 %% Run ../build_NEMO_manual.sh to generate the PDF version (with pdflatex) 
    7  
    8 %% Document layout 
    9 %% ============================================================================== 
    10  
    11 \documentclass{book} 
    124 
    135 
     
    157%% ============================================================================== 
    168 
     9%% Document layout 
     10\documentclass{book} 
     11 
     12%% Custom style (.sty) 
    1713\usepackage{../../NEMO/main/NEMO_manual} 
    18 %\usepackage{../../tex_sub/NEMO_minted} 
    1914 
    20 \usepackage{bm} 
     15%% Include references and index for single subfile compilation 
     16\newcommand{\biblio}{\bibliography{../main/TOP_manual}} 
     17\newcommand{\pindex}{\printindex} 
    2118 
    2219\makeindex 
    2320 
     21%% End of common preamble between main and sub-files 
     22\begin{document} 
    2423 
    25 %%  
    26 %% ============================================================================== 
    27  
    28 \begin{document} 
     24%% Override custom cmds for full manual compilation 
     25\renewcommand{\biblio}{} 
     26\renewcommand{\pindex}{} 
    2927 
    3028 
     
    3230%% ============================================================================== 
    3331 
     32\graphicspath{{../../figures/logos/}} 
     33 
    3434%% Frontpage 
     35\title{ 
     36  \includegraphics[height=0.05\textheight]{CMCC}\hfill 
     37  \includegraphics[height=0.05\textheight]{CNRS}\hfill 
     38  \includegraphics[height=0.05\textheight]{MOI} \hfill 
     39  \includegraphics[height=0.05\textheight]{UKMO}\hfill 
     40  \includegraphics[height=0.05\textheight]{NERC}       \\ 
     41  {\Huge TOP \\} 
     42  {\Large Tracer in Ocean Paradigm -- The NEMO Passive Tracer engine}\\ 
     43  \small \textcolor{red}{First draft documentation. Needs completion and rewriting}. \\ 
     44} 
     45\author{The NEMO-TOP Group 
     46  \thanks{ 
     47    Eth\'{e} Christian, Lovato Thomas, Aumont Olivier, Palmi\'{e}ri Julien, 
     48    Mouchet Anne, Nurser Georges, Yool Andrew 
     49  }\\ 
     50  \textit{Issue 27, Notes du P\^{o}le de mod\'{e}lisation} \\ 
     51  \textit{Institut Pierre-Simon Laplace (IPSL)}            \\ 
     52  \textit{ISSN 1288-1619} 
     53} 
     54\date{\today} 
    3555 
    36 \title{ 
    37 \vspace{1.5cm} 
    38 \rule{400pt}{1.5pt} \\ 
    39 \vspace{0.45cm} 
    40  {\Huge TOP \\} 
    41  {\Large -- Tracer in Ocean Paradigm --}\\ 
    42  {\Large The NEMO Passive Tracer engine}\\  
    43 \date{\today} 
    44 \author{The NEMO-TOP Group \\ 
    45 Eth\'e Christian, Lovato Thomas, Aumont Olivier  \\ 
    46 Palmi\'eri Julien, Mouchet Anne, Nurser Georges, Yool Andrew  \\ 
    47 \\ 
    48 \small \textit{Note du P\^ole de mod\'elisation de l'Institut Pierre-Simon Laplace No 31} \\ 
    49 \small \textcolor{red}{First draft documentation. Needs completion and rewriting}. \\ 
    50 \\ 
    51 ISSN No 1288-1619\\ 
    52 } 
    53 \rule{400pt}{1.5pt} 
    54 } 
    55  
    56 \maketitle                 % generate the title 
     56\maketitle 
    5757\frontmatter 
    5858 
     
    6868\mainmatter 
    6969 
     70\graphicspath{{../../figures/TOP/}} 
    7071 
    71 \subfile{../tex_sub/introduction} 
    72 \subfile{../tex_sub/model_description} 
    73 \subfile{../tex_sub/model_setup} 
    74 \subfile{../tex_sub/miscellaneous} 
     72\subfile{../subfiles/introduction} 
     73\subfile{../subfiles/model_description} 
     74\subfile{../subfiles/model_setup} 
     75\subfile{../subfiles/miscellaneous} 
    7576 
    7677%% Appendix 
     
    8384 
    8485%% Bibliography 
    85  
    8686\cleardoublepage 
    8787\phantomsection 
    8888\addcontentsline{toc}{chapter}{Bibliography} 
    89  
    90 \bibliography{../tex_main/TOP_manual.bbl} 
     89\bibliography{../main/TOP_manual} 
    9190 
    9291%% Index 
    93  
    9492\cleardoublepage 
    9593\phantomsection 
  • NEMO/trunk/doc/latex/TOP/subfiles/introduction.tex

    r10896 r11019  
    3737\begin{center} 
    3838\vspace{0cm} 
    39 \includegraphics[width=0.80\textwidth]{../Figures/Fig_TOP_design.png} 
    40 %\includegraphics[height=6cm,angle=-00]{../Figures/Fig_TOP_design.png} 
     39\includegraphics[width=0.80\textwidth]{Fig_TOP_design} 
     40%\includegraphics[height=6cm,angle=-00]{Fig_TOP_design} 
    4141\caption{A schematic view of NEMO-TOP component} 
    4242\label{topdesign} 
  • NEMO/trunk/doc/latex/TOP/subfiles/model_description.tex

    r10896 r11019  
    7171 \subsection{ Advection} 
    7272%------------------------------------------namtrc_adv---------------------------------------------------- 
    73 \forfile{../namelists/namtrc_adv} 
     73\nlst{namtrc_adv} 
    7474%------------------------------------------------------------------------------------------------------------- 
    7575The advection schemes used for the passive tracers are the same than the ones for $T$ and $S$ and described in section 5.1 of \citep{Madec_Bk2008}. The choice of an advection scheme  can be selected independently and  can differ from the ones used for active tracers. This choice is made in the \textit{namtrc\_adv} namelist, by  setting to \textit{true} one and only one of the logicals \textit{ln\_trcadv\_xxx}, the same way of what is done for dynamics. 
     
    7878 \subsection{ Lateral diffusion} 
    7979%------------------------------------------namtrc_ldf---------------------------------------------------- 
    80 \forfile{../namelists/namtrc_ldf} 
     80\nlst{namtrc_ldf} 
    8181%------------------------------------------------------------------------------------------------------------- 
    8282In NEMO v4.0, the passive tracer diffusion has necessarily the same form as the active tracer diffusion, meaning that the numerical scheme must be the same. However the passive tracer mixing coefficient can be chosen as a multiple of the active ones by changing the value of \textit{rn\_ldf\_multi} in namelist \textit{namtrc\_ldf}. The choice of numerical scheme is then set  in the \ngn{namtra\_ldf} namelist for the dynamic described in section 5.2 of \citep{Madec_Bk2008}.  
     
    9191  
    9292%------------------------------------------namtrc_dmp---------------------------------------------------- 
    93 \forfile{../namelists/namtrc_dmp} 
     93\nlst{namtrc_dmp} 
    9494%------------------------------------------------------------------------------------------------------------- 
    9595 
     
    100100  
    101101%------------------------------------------namtrc_rad---------------------------------------------------- 
    102 \forfile{../namelists/namtrc_rad} 
     102\nlst{namtrc_rad} 
    103103%------------------------------------------------------------------------------------------------------------- 
    104104 
     
    110110\label{SMS_models} 
    111111%------------------------------------------namtrc_sms---------------------------------------------------- 
    112 %\forfile{../namelists/namtrc} 
     112%\nlst{namtrc} 
    113113%------------------------------------------------------------------------------------------------------------- 
    114114 
     
    116116%------------------------------------------namage---------------------------------------------------- 
    117117% 
    118 \forfile{../namelists/namage} 
     118\nlst{namage} 
    119119%---------------------------------------------------------------------------------------------------------- 
    120120 
     
    151151%------------------------------------------namage---------------------------------------------------- 
    152152% 
    153 \forfile{../namelists/namcfc} 
     153\nlst{namcfc} 
    154154%---------------------------------------------------------------------------------------------------------- 
    155155 
     
    324324\begin{figure}[!h] 
    325325\centering 
    326 \includegraphics[width=0.80\textwidth]{../Figures/CFC-atm-evol.png} 
     326\includegraphics[width=0.80\textwidth]{CFC-atm-evol} 
    327327  \caption{Atmospheric CFC11, CFC12 and SF6 partial pressure evolution in both hemispheres.} 
    328328\label{img_cfcatm} 
     
    331331\begin{figure}[!h] 
    332332\centering 
    333 \includegraphics[width=0.80\textwidth]{../Figures/CFC_solub.png} 
     333\includegraphics[width=0.80\textwidth]{CFC_solub} 
    334334  \caption{CFC11 solubility in mol m$^{-3}$ pptv$^{-1}$, calculated from the World Ocean Atlas 2013 temperature and salinity annual climatology.} 
    335335\label{img_cfcsol} 
     
    338338\begin{figure}[!h] 
    339339\centering 
    340 \includegraphics[width=0.80\textwidth]{../Figures/CFC_inventory.png} 
     340\includegraphics[width=0.80\textwidth]{CFC_inventory} 
    341341  \caption{CFC11 vertical inventory in $\mu$mol m$^{-2}$, from one of the UK Earth System Model 1 model (UKESM1 - which uses NEMO as ocean component, with TOP for the passive tracers) historical run at year 2000.} 
    342342\label{img_cfcinv} 
     
    348348%------------------------------------------namage---------------------------------------------------- 
    349349% 
    350 \forfile{../namelists/namc14} 
     350\nlst{namc14_fcg} 
     351\nlst{namc14_typ} 
     352\nlst{namc14_sbc} 
    351353%---------------------------------------------------------------------------------------------------------- 
    352354 
     
    444446\begin{figure}[!h] 
    445447\begin{center} 
    446 \includegraphics[width=0.9\hsize]{../Figures/drift-EXP06.png} 
     448\includegraphics[width=0.9\hsize]{drift-EXP06} 
    447449\end{center} 
    448450\vspace{-4ex} 
     
    456458\begin{figure}[!h] 
    457459\begin{center} 
    458 \includegraphics[width=0.9\hsize]{../Figures/C14bombCO2-NB.png} 
     460\includegraphics[width=0.9\hsize]{C14bombCO2-NB} 
    459461\end{center} 
    460462\vspace{-4ex} 
     
    485487\begin{figure}[!h] 
    486488\begin{center} 
    487 \includegraphics[width=0.9\hsize]{../Figures/PaleoCO2C14-NB.png} 
     489\includegraphics[width=0.9\hsize]{PaleoCO2C14-NB} 
    488490\end{center} 
    489491\vspace{-4ex} 
     
    591593 
    592594%------------------------------------------namtrc_sms---------------------------------------------------- 
    593 \forfile{../namelists/namdta_dyn} 
     595\nlst{namdta_dyn} 
    594596%------------------------------------------------------------------------------------------------------------- 
    595597 
  • NEMO/trunk/doc/latex/TOP/subfiles/model_setup.tex

    r10896 r11019  
    77\section{ Setting up a passive tracer configuration} 
    88%------------------------------------------namtrc_int---------------------------------------------------- 
    9 \forfile{../namelists/namtrc} 
     9\nlst{namtrc} 
    1010%------------------------------------------------------------------------------------------------------------- 
    1111 
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