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Changeset 13825 – NEMO

Changeset 13825


Ignore:
Timestamp:
2020-11-19T09:46:43+01:00 (4 years ago)
Author:
nicolasmartin
Message:

#2414 Skechty fixes to complete the manual compilation

Location:
NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc
Files:
12 edited

Legend:

Unmodified
Added
Removed
  • NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/NEMO/main/appendices.tex

    r12377 r13825  
    11 
    2 \subfile{../subfiles/annex_A}             %% Generalised vertical coordinate 
    3 \subfile{../subfiles/annex_B}             %% Diffusive operator 
    4 \subfile{../subfiles/annex_C}             %% Discrete invariants of the eqs. 
    5 \subfile{../subfiles/annex_iso}            %% Isoneutral diffusion using triads 
    6 \subfile{../subfiles/annex_D}             %% Coding rules 
     2\subfile{../subfiles/apdx_s_coord}      %% A. Generalised vertical coordinate 
     3\subfile{../subfiles/apdx_diff_opers}   %% B. Diffusive operators 
     4\subfile{../subfiles/apdx_invariants}   %% C. Discrete invariants of the eqs. 
     5\subfile{../subfiles/apdx_triads}       %% D. Isoneutral diffusion using triads 
     6\subfile{../subfiles/apdx_DOMAINcfg}    %% E. Brief notes on DOMAINcfg 
    77 
    88%% Not included 
  • NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/NEMO/main/bibliography.bib

    r12377 r13825  
    31603160author = "E. B. Kraus and J. A. Businger", 
    31613161title = "Atmosphere-ocean interaction.", 
    3162 journal="Quarterly Journal of the Royal Meteorological Society",, 
     3162journal="Quarterly Journal of the Royal Meteorological Society", 
    31633163year = "1996", 
    31643164volume = "122", 
  • NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/NEMO/main/chapters.tex

    r12377 r13825  
    1414\subfile{../subfiles/chap_STO}            %% Stochastic param. 
    1515\subfile{../subfiles/chap_misc}           %% Miscellaneous topics 
    16 \subfile{../subfiles/chap_CONFIG}         %% Predefined configurations 
     16\subfile{../subfiles/chap_cfgs}         %% Predefined configurations 
  • NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/NEMO/subfiles/apdx_triads.tex

    r11693 r13825  
    11\documentclass[../main/NEMO_manual]{subfiles} 
     2 
     3\begin{document} 
    24 
    35%% Local cmds 
     
    1012\newcommand{\rtriad}[2][]{\ensuremath{\triad[#1]{i}{k}{#2}{i_p}{k_p}}} 
    1113\newcommand{\rtriadt}[1]{\ensuremath{\triadt{i}{k}{#1}{i_p}{k_p}}} 
    12  
    13 \begin{document} 
    1414 
    1515\chapter{Iso-Neutral Diffusion and Eddy Advection using Triads} 
  • NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/NEMO/subfiles/chap_ZDF.tex

    r13461 r13825  
    11\documentclass[../main/NEMO_manual]{subfiles} 
     2 
     3\begin{document} 
    24 
    35%% Custom aliases 
    46\newcommand{\cf}{\ensuremath{C\kern-0.14em f}} 
    5  
    6 \begin{document} 
    77 
    88\chapter{Vertical Ocean Physics (ZDF)} 
  • NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/NEMO/subfiles/chap_misc.tex

    r12377 r13825  
    382382with their default settings: 
    383383 
    384 \begin{verbatim} 
     384\begin{forlines} 
    385385   sn_cfctl%l_allon  = .FALSE.    ! IF T activate all options. If F deactivate all unless l_config is T 
    386386     sn_cfctl%l_config = .TRUE.     ! IF .true. then control which reports are written with the following 
    387 \end{verbatim} 
     387\end{forlines} 
    388388 
    389389The first switch is a convenience option which can be used to switch on and off all 
    390390sub-options. However, if it is false then switching off all sub-options is only done 
    391 if \texttt{sn_cfctl%l\_config} is also false. Specifically, the logic is: 
    392  
    393 \begin{verbatim} 
     391if \forcode{sn_cfctl%l\_config} is also false. Specifically, the logic is: 
     392 
     393\begin{forlines} 
    394394  IF ( sn_cfctl%l_allon ) THEN 
    395395    set all suboptions .TRUE. 
     
    400400    set all suboptions .FALSE. 
    401401  ENDIF 
    402 \end{verbatim} 
     402\end{forlines} 
    403403 
    404404Details of the suboptions follow but first an explanation of the stand-alone option: 
    405 \texttt{sn_cfctl%l_glochk}.  This option modifies the action of the early warning checks 
    406 carried out in \textt{stpctl.F90}. These checks detect probable numerical instabilites 
     405\forcode{sn_cfctl%l_glochk}.  This option modifies the action of the early warning checks 
     406carried out in \texttt{stpctl.F90}. These checks detect probable numerical instabilites 
    407407by searching for excessive sea surface heights or velocities and salinity values 
    408408outside a sensible physical range. If breaches are detected then the default behaviour 
    409409is to locate and report the local indices of the grid-point in breach. These indices 
    410410are included in the error message that precedes the model shutdown. When true, 
    411 \texttt{sn_cfctl%l_glochk} modifies this action by performing a global location of 
     411\forcode{sn_cfctl%l_glochk} modifies this action by performing a global location of 
    412412the various minimum and maximum values and the global indices are reported. This has 
    413413some value in locating the most severe error in cases where the first detected error 
     
    427427average tracer value for each passive tracer. Collecting these metrics involves 
    428428global communications and will impact on model efficiency so both these options are 
    429 disabled by default by setting the respective options, \texttt{sn\_cfctl%runstat} and 
    430 \texttt{sn\_cfctl%trcstat} to false. A compromise can be made by activating either or 
    431 both of these options and setting the \texttt{sn\_cfctl%timincr} entry to an integer 
     429disabled by default by setting the respective options, \forcode{sn\_cfctl%runstat} and 
     430\forcode{sn\_cfctl%trcstat} to false. A compromise can be made by activating either or 
     431both of these options and setting the \forcode{sn\_cfctl%timincr} entry to an integer 
    432432value greater than one. This increment determines the time-step frequency at which 
    433433the global metrics are collected and reported.  This increment also applies to the 
     
    440440any warning or error messages generated during execution. A \texttt{layout.dat} 
    441441file is also produced which details the MPI-decomposition used by the model. The 
    442 suboptions: \texttt{sn\_cfctl%oceout} and \texttt{sn\_cfctl%layout} can be used 
     442suboptions: \forcode{sn\_cfctl%oceout} and \forcode{sn\_cfctl%layout} can be used 
    443443to activate the creation of these files by all ocean processes.  For example, 
    444 when \texttt{sn\_cfctl%oceout} is true all processors produce their own version of 
     444when \forcode{sn\_cfctl%oceout} is true all processors produce their own version of 
    445445\texttt{ocean.output}.  All files, beyond the the normal reporting processor (narea == 1), are 
    446446named with a \_XXXX extension to their name, where XXXX is a 4-digit area number (with 
     
    449449systems so bug-hunting efforts using this facility should also utilise the \fortran: 
    450450 
    451 \begin{verbatim}  
     451\begin{forlines}  
    452452   CALL FLUSH(numout) 
    453 \end{verbatim} 
     453\end{forlines} 
    454454 
    455455statement after any additional write statements to ensure that file contents reflect 
    456 the last model state. Associated with the \texttt{sn\_cfctl%oceout} option is the 
    457 additional \texttt{sn\_cfctl%oasout} suboption. This does not activate its own output 
     456the last model state. Associated with the \forcode{sn\_cfctl%oceout} option is the 
     457additional \forcode{sn\_cfctl%oasout} suboption. This does not activate its own output 
    458458file but rather activates the writing of addition information regarding the OASIS 
    459459configuration when coupling via oasis and the sbccpl routine. This information is 
     
    467467http://forge.ipsl.jussieu.fr/nemo/attachment/wiki/Documentation/prtctl_NEMO_doc_v2.pdf}{The 
    468468control print option in NEMO} The switches to activate production of the control sums 
    469 of trends for either the physics or passive tracers are the \texttt{sn\_cfctl%prtctl} 
    470 and \texttt{sn\_cfctl%prttrc} suboptions, respectively. Although, perhaps, of limited use for its 
     469of trends for either the physics or passive tracers are the \forcode{sn\_cfctl%prtctl} 
     470and \forcode{sn\_cfctl%prttrc} suboptions, respectively. Although, perhaps, of limited use for its 
    471471original intention, the ability to produce these control sums of trends in specific 
    472472areas provides another tool for diagnosing model behaviour.  If only the output from a 
    473473select few regions is required then additional options are available to activate options 
    474 for only a simple subset of processing regions. These are: \texttt{sn\_cfctl%procmin}, 
    475 \texttt{sn\_cfctl%procmax} and \texttt{sn\_cfctl%procincr} which can be used to specify 
     474for only a simple subset of processing regions. These are: \forcode{sn\_cfctl%procmin}, 
     475\forcode{sn\_cfctl%procmax} and \forcode{sn\_cfctl%procincr} which can be used to specify 
    476476the minimum and maximum active areas and the increment. The default values are set 
    477477such that all regions will be active. Note this subsetting can also be used to limit 
     
    481481\end{enumerate} 
    482482 
    483  
     483\begin{forlines} 
    484484   sn_cfctl%l_glochk = .FALSE.    ! Range sanity checks are local (F) or global (T). Set T for debugging only 
    485485   sn_cfctl%l_allon  = .FALSE.    ! IF T activate all options. If F deactivate all unless l_config is T 
     
    496496       sn_cfctl%procincr  = 1       ! Increment for optional subsetting of areas [default:1] 
    497497       sn_cfctl%ptimincr  = 1       ! Timestep increment for writing time step progress info 
    498  
    499  
     498\end{forlines} 
    500499 
    501500\subinc{\input{../../global/epilogue}} 
  • NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/global/document.tex

    r12377 r13825  
    1111 
    1212%% Document layout 
    13 \documentclass[draft]{scrreprt} 
     13\documentclass[]{scrreprt} 
    1414 
    1515%% Load the configuration of the manual 
     
    2727%% End of common preamble between main and sub-files 
    2828%% Override custom cmds for full manual compilation 
    29 \newcommand{\onlyinsubfile}[1]{#1} 
     29\newcommand{\subinc}[1]{#1} 
    3030\newcommand{\notinsubfile}[1]{} 
    3131 
    3232\begin{document} 
    3333 
    34 \renewcommand{\onlyinsubfile}[1]{} 
     34\renewcommand{\subinc}[1]{} 
    3535\renewcommand{\notinsubfile}[1]{#1} 
    3636 
  • NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/global/indexes.tex

    r12377 r13825  
    88\newcommand{\key}[1]{\index[keys]{#1}        \texttt{\textbf{key\_#1}}} 
    99\newcommand{\mdl}[1]{\index[modules]{#1}     \textit{#1.F90}          } 
    10 \newcommand{\ngn}[1]{\index[blocks]{#1}      \texttt{#1}              } 
    11 \newcommand{\np}[1]{ \index[parameters]{#1}  \texttt{#1}              } 
     10\newcommand{\nam}[2]{  \index[blocks]{#1@\texttt{\&nam#2}}        \forcode{&nam#1} (\autoref{lst:nam#1})} 
     11\newcommand{\np}[3][]{ \index[parameters]{#3@\texttt{#3}}         \forcode{#2#1}           } 
    1212\newcommand{\rou}[1]{\index[subroutines]{#1} \texttt{#1}              } 
    1313 
  • NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/global/latexmkrc

    r12377 r13825  
    11 
    22## Defaults 
    3 $silent   = 1; 
     3#$silent   = 1; 
    44$pdf_mode = 1; 
    55 
     
    77$ENV{'openout_any'}='a'; 
    88$out_dir = '../build'; 
     9$do_cd = 1; 
    910 
    1011## Custom cmds 
     12set_tex_cmds( '-shell-escape' ); 
    1113$makeindex = 'makeindex -s %R.ist %O -o %D %S'; 
    1214$pdflatex  = 'pdflatex -shell-escape %O %S'; 
  • NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/global/new_cmds.tex

    r12377 r13825  
    99%% NEMO and Fortran in small capitals 
    1010\newcommand{\NEMO}{\textsc{nemo}~} 
     11\newcommand{\TOP   }{\textsl{TOP}} 
     12\newcommand{\PISCES}{\textsl{PISCES}} 
    1113\newcommand{\fortran}{\textsc{Fortran}~} 
    1214\newcommand{\fninety}{\textsc{Fortran 90}~} 
     
    2527\newcommand{\rdt}{\Delta t} 
    2628 
    27 %% Text env. for Gurvan 
    28 \newcommand{\gmcomment}[1]{} 
     29%% Gurvan's comments 
     30\newcommand{\cmtgm}[1]{} 
    2931 
    3032%% Maths 
     
    3638%% Workaround for issue with \listoffigures 
    3739\DeclareRobustCommand{\triad}[6][]{\ensuremath{{}_{#2}^{#3}{\mathbb{#4}_{#1}}_{#5}^{\,#6}}} 
     40 
     41%% New command for ToC 
     42\newcommand{\chaptertoc}[1][Table of contents]{ 
     43  \thispagestyle{empty} 
     44  \etocsettocstyle{\addsec*{#1}}{} 
     45  \localtableofcontents 
     46  \vfill 
     47} 
  • NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/global/packages.tex

    r12377 r13825  
    77\usepackage{xcolor}                      %% color 
    88\usepackage{times}                       %% font 
    9 \usepackage{enumitem}                    %% list 
     9\usepackage[inline]{enumitem}                    %% list 
    1010\usepackage{amsmath}                     %% maths 
    1111%\usepackage{fancyhdr}                    %% page 
     
    1414\usepackage{draftwatermark}              %% watermark 
    1515\usepackage{titling}                     %% titlepage 
     16\usepackage{etoc} 
     17\usepackage{mathtools} 
     18\usepackage{academicons} 
    1619 
    1720%% Extensions in bundle package 
     
    2023 
    2124%% Configuration 
    22 \graphicspath{ {../../figures/} {../../figures/\engine/} } 
     25\graphicspath{ {../../../} {../figures/} } 
    2326%\captionsetup{margin=10pt, font={small}, labelsep=colon, labelfont={bf}} 
    2427\renewcommand{\bibfont}{\small} 
  • NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/tools/shr_func.sh

    r11598 r13825  
    44    printf "\t¤ Clean previous build" 
    55    find latex/$1/build -mindepth 1 -delete 
    6  
    76    echo 
    87} 
     
    109build() { 
    1110    printf "\t¤ Generation of the PDF format\n" 
    12     latexmk -r  ./latex/global/latexmk.pl -pdfxe ./latex/$1/main/$1_manual \ 
     11    latexmk -r ./latex/global/latexmkrc -pdfxe ./latex/$1/main/$1_manual \ 
    1312#  1> /dev/null 
    1413    [ -f ./latex/$1/build/$1_manual.pdf ] && mv ./latex/$1/build/$1_manual.pdf . 
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