Changeset 13825 for NEMO

Timestamp:

2020-11-19T09:46:43+01:00 (3 years ago)

Author:

nicolasmartin

Message:

#2414 Skechty fixes to complete the manual compilation

Location:

NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc

Files:

• latex/NEMO/main/appendices.tex (modified) (1 diff)
• latex/NEMO/main/bibliography.bib (modified) (1 diff)
• latex/NEMO/main/chapters.tex (modified) (1 diff)
• latex/NEMO/subfiles/apdx_triads.tex (modified) (2 diffs)
• latex/NEMO/subfiles/chap_ZDF.tex (modified) (1 diff)
• latex/NEMO/subfiles/chap_misc.tex (modified) (8 diffs)
• latex/global/document.tex (modified) (2 diffs)
• latex/global/indexes.tex (modified) (1 diff)
• latex/global/latexmkrc (modified) (2 diffs)
• latex/global/new_cmds.tex (modified) (3 diffs)
• latex/global/packages.tex (modified) (3 diffs)
• tools/shr_func.sh (modified) (2 diffs)

NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/NEMO/main/appendices.tex

@@ -1 +1 @@
 
-\subfile{../subfiles/annex_A}             %% Generalised vertical coordinate
-\subfile{../subfiles/annex_B}             %% Diffusive operator
-\subfile{../subfiles/annex_C}             %% Discrete invariants of the eqs.
-\subfile{../subfiles/annex_iso}            %% Isoneutral diffusion using triads
-\subfile{../subfiles/annex_D}             %% Coding rules
+\subfile{../subfiles/apdx_s_coord}      %% A. Generalised vertical coordinate
+\subfile{../subfiles/apdx_diff_opers}   %% B. Diffusive operators
+\subfile{../subfiles/apdx_invariants}   %% C. Discrete invariants of the eqs.
+\subfile{../subfiles/apdx_triads}       %% D. Isoneutral diffusion using triads
+\subfile{../subfiles/apdx_DOMAINcfg}    %% E. Brief notes on DOMAINcfg
 
 %% Not included

NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/NEMO/main/bibliography.bib

@@ -3160 +3160 @@
 author = "E. B. Kraus and J. A. Businger",
 title = "Atmosphere-ocean interaction.",
-journal="Quarterly Journal of the Royal Meteorological Society",,
+journal="Quarterly Journal of the Royal Meteorological Society",
 year = "1996",
 volume = "122",

NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/NEMO/main/chapters.tex

@@ -14 +14 @@
 \subfile{../subfiles/chap_STO}            %% Stochastic param.
 \subfile{../subfiles/chap_misc}           %% Miscellaneous topics
-\subfile{../subfiles/chap_CONFIG}         %% Predefined configurations
+\subfile{../subfiles/chap_cfgs}         %% Predefined configurations

NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/NEMO/subfiles/apdx_triads.tex

@@ -1 +1 @@
 \documentclass[../main/NEMO_manual]{subfiles}
+
+\begin{document}
 
 %% Local cmds
@@ -10 +12 @@
 \newcommand{\rtriad}[2][]{\ensuremath{\triad[#1]{i}{k}{#2}{i_p}{k_p}}}
 \newcommand{\rtriadt}[1]{\ensuremath{\triadt{i}{k}{#1}{i_p}{k_p}}}
-
-\begin{document}
 
 \chapter{Iso-Neutral Diffusion and Eddy Advection using Triads}

NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/NEMO/subfiles/chap_ZDF.tex

@@ -1 +1 @@
 \documentclass[../main/NEMO_manual]{subfiles}
+
+\begin{document}
 
 %% Custom aliases
 \newcommand{\cf}{\ensuremath{C\kern-0.14em f}}
-
-\begin{document}
 
 \chapter{Vertical Ocean Physics (ZDF)}

NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/NEMO/subfiles/chap_misc.tex

@@ -382 +382 @@
 with their default settings:
 
-\begin{verbatim}
+\begin{forlines}
    sn_cfctl%l_allon  = .FALSE.    ! IF T activate all options. If F deactivate all unless l_config is T
      sn_cfctl%l_config = .TRUE.     ! IF .true. then control which reports are written with the following
-\end{verbatim}
+\end{forlines}
 
 The first switch is a convenience option which can be used to switch on and off all
 sub-options. However, if it is false then switching off all sub-options is only done
-if \texttt{sn_cfctl%l\_config} is also false. Specifically, the logic is:
-
-\begin{verbatim}
+if \forcode{sn_cfctl%l\_config} is also false. Specifically, the logic is:
+
+\begin{forlines}
   IF ( sn_cfctl%l_allon ) THEN
     set all suboptions .TRUE.
@@ -400 +400 @@
     set all suboptions .FALSE.
   ENDIF
-\end{verbatim}
+\end{forlines}
 
 Details of the suboptions follow but first an explanation of the stand-alone option:
-\texttt{sn_cfctl%l_glochk}.  This option modifies the action of the early warning checks
-carried out in \textt{stpctl.F90}. These checks detect probable numerical instabilites
+\forcode{sn_cfctl%l_glochk}.  This option modifies the action of the early warning checks
+carried out in \texttt{stpctl.F90}. These checks detect probable numerical instabilites
 by searching for excessive sea surface heights or velocities and salinity values
 outside a sensible physical range. If breaches are detected then the default behaviour
 is to locate and report the local indices of the grid-point in breach. These indices
 are included in the error message that precedes the model shutdown. When true,
-\texttt{sn_cfctl%l_glochk} modifies this action by performing a global location of
+\forcode{sn_cfctl%l_glochk} modifies this action by performing a global location of
 the various minimum and maximum values and the global indices are reported. This has
 some value in locating the most severe error in cases where the first detected error
@@ -427 +427 @@
 average tracer value for each passive tracer. Collecting these metrics involves
 global communications and will impact on model efficiency so both these options are
-disabled by default by setting the respective options, \texttt{sn\_cfctl%runstat} and
-\texttt{sn\_cfctl%trcstat} to false. A compromise can be made by activating either or
-both of these options and setting the \texttt{sn\_cfctl%timincr} entry to an integer
+disabled by default by setting the respective options, \forcode{sn\_cfctl%runstat} and
+\forcode{sn\_cfctl%trcstat} to false. A compromise can be made by activating either or
+both of these options and setting the \forcode{sn\_cfctl%timincr} entry to an integer
 value greater than one. This increment determines the time-step frequency at which
 the global metrics are collected and reported.  This increment also applies to the
@@ -440 +440 @@
 any warning or error messages generated during execution. A \texttt{layout.dat}
 file is also produced which details the MPI-decomposition used by the model. The
-suboptions: \texttt{sn\_cfctl%oceout} and \texttt{sn\_cfctl%layout} can be used
+suboptions: \forcode{sn\_cfctl%oceout} and \forcode{sn\_cfctl%layout} can be used
 to activate the creation of these files by all ocean processes.  For example,
-when \texttt{sn\_cfctl%oceout} is true all processors produce their own version of
+when \forcode{sn\_cfctl%oceout} is true all processors produce their own version of
 \texttt{ocean.output}.  All files, beyond the the normal reporting processor (narea == 1), are
 named with a \_XXXX extension to their name, where XXXX is a 4-digit area number (with
@@ -449 +449 @@
 systems so bug-hunting efforts using this facility should also utilise the \fortran:
 
-\begin{verbatim} 
+\begin{forlines} 
    CALL FLUSH(numout)
-\end{verbatim}
+\end{forlines}
 
 statement after any additional write statements to ensure that file contents reflect
-the last model state. Associated with the \texttt{sn\_cfctl%oceout} option is the
-additional \texttt{sn\_cfctl%oasout} suboption. This does not activate its own output
+the last model state. Associated with the \forcode{sn\_cfctl%oceout} option is the
+additional \forcode{sn\_cfctl%oasout} suboption. This does not activate its own output
 file but rather activates the writing of addition information regarding the OASIS
 configuration when coupling via oasis and the sbccpl routine. This information is
@@ -467 +467 @@
 http://forge.ipsl.jussieu.fr/nemo/attachment/wiki/Documentation/prtctl_NEMO_doc_v2.pdf}{The
 control print option in NEMO} The switches to activate production of the control sums
-of trends for either the physics or passive tracers are the \texttt{sn\_cfctl%prtctl}
-and \texttt{sn\_cfctl%prttrc} suboptions, respectively. Although, perhaps, of limited use for its
+of trends for either the physics or passive tracers are the \forcode{sn\_cfctl%prtctl}
+and \forcode{sn\_cfctl%prttrc} suboptions, respectively. Although, perhaps, of limited use for its
 original intention, the ability to produce these control sums of trends in specific
 areas provides another tool for diagnosing model behaviour.  If only the output from a
 select few regions is required then additional options are available to activate options
-for only a simple subset of processing regions. These are: \texttt{sn\_cfctl%procmin},
-\texttt{sn\_cfctl%procmax} and \texttt{sn\_cfctl%procincr} which can be used to specify
+for only a simple subset of processing regions. These are: \forcode{sn\_cfctl%procmin},
+\forcode{sn\_cfctl%procmax} and \forcode{sn\_cfctl%procincr} which can be used to specify
 the minimum and maximum active areas and the increment. The default values are set
 such that all regions will be active. Note this subsetting can also be used to limit
@@ -481 +481 @@
 \end{enumerate}
 
-
+\begin{forlines}
    sn_cfctl%l_glochk = .FALSE.    ! Range sanity checks are local (F) or global (T). Set T for debugging only
    sn_cfctl%l_allon  = .FALSE.    ! IF T activate all options. If F deactivate all unless l_config is T
@@ -496 +496 @@
        sn_cfctl%procincr  = 1       ! Increment for optional subsetting of areas [default:1]
        sn_cfctl%ptimincr  = 1       ! Timestep increment for writing time step progress info
-
-
+\end{forlines}
 
 \subinc{\input{../../global/epilogue}}

NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/global/document.tex

@@ -11 +11 @@
 
 %% Document layout
-\documentclass[draft]{scrreprt}
+\documentclass[]{scrreprt}
 
 %% Load the configuration of the manual
@@ -27 +27 @@
 %% End of common preamble between main and sub-files
 %% Override custom cmds for full manual compilation
-\newcommand{\onlyinsubfile}[1]{#1}
+\newcommand{\subinc}[1]{#1}
 \newcommand{\notinsubfile}[1]{}
 
 \begin{document}
 
-\renewcommand{\onlyinsubfile}[1]{}
+\renewcommand{\subinc}[1]{}
 \renewcommand{\notinsubfile}[1]{#1}
 

NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/global/indexes.tex

@@ -8 +8 @@
 \newcommand{\key}[1]{\index[keys]{#1}        \texttt{\textbf{key\_#1}}}
 \newcommand{\mdl}[1]{\index[modules]{#1}     \textit{#1.F90}          }
-\newcommand{\ngn}[1]{\index[blocks]{#1}      \texttt{#1}              }
-\newcommand{\np}[1]{ \index[parameters]{#1}  \texttt{#1}              }
+\newcommand{\nam}[2]{  \index[blocks]{#1@\texttt{\&nam#2}}        \forcode{&nam#1} (\autoref{lst:nam#1})}
+\newcommand{\np}[3][]{ \index[parameters]{#3@\texttt{#3}}         \forcode{#2#1}           }
 \newcommand{\rou}[1]{\index[subroutines]{#1} \texttt{#1}              }
 

NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/global/latexmkrc

@@ -1 +1 @@
 
 ## Defaults
-$silent   = 1;
+#$silent   = 1;
 $pdf_mode = 1;
 
@@ -7 +7 @@
 $ENV{'openout_any'}='a';
 $out_dir = '../build';
+$do_cd = 1;
 
 ## Custom cmds
+set_tex_cmds( '-shell-escape' );
 $makeindex = 'makeindex -s %R.ist %O -o %D %S';
 $pdflatex  = 'pdflatex -shell-escape %O %S';

NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/global/new_cmds.tex

@@ -9 +9 @@
 %% NEMO and Fortran in small capitals
 \newcommand{\NEMO}{\textsc{nemo}~}
+\newcommand{\TOP   }{\textsl{TOP}}
+\newcommand{\PISCES}{\textsl{PISCES}}
 \newcommand{\fortran}{\textsc{Fortran}~}
 \newcommand{\fninety}{\textsc{Fortran 90}~}
@@ -25 +27 @@
 \newcommand{\rdt}{\Delta t}
 
-%% Text env. for Gurvan
-\newcommand{\gmcomment}[1]{}
+%% Gurvan's comments
+\newcommand{\cmtgm}[1]{}
 
 %% Maths
@@ -36 +38 @@
 %% Workaround for issue with \listoffigures
 \DeclareRobustCommand{\triad}[6][]{\ensuremath{{}_{#2}^{#3}{\mathbb{#4}_{#1}}_{#5}^{\,#6}}}
+
+%% New command for ToC
+\newcommand{\chaptertoc}[1][Table of contents]{
+  \thispagestyle{empty}
+  \etocsettocstyle{\addsec*{#1}}{}
+  \localtableofcontents
+  \vfill
+}

NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/global/packages.tex

@@ -7 +7 @@
 \usepackage{xcolor}                      %% color
 \usepackage{times}                       %% font
-\usepackage{enumitem}                    %% list
+\usepackage[inline]{enumitem}                    %% list
 \usepackage{amsmath}                     %% maths
 %\usepackage{fancyhdr}                    %% page
@@ -14 +14 @@
 \usepackage{draftwatermark}              %% watermark
 \usepackage{titling}                     %% titlepage
+\usepackage{etoc}
+\usepackage{mathtools}
+\usepackage{academicons}
 
 %% Extensions in bundle package
@@ -20 +23 @@
 
 %% Configuration
-\graphicspath{ {../../figures/} {../../figures/\engine/} }
+\graphicspath{ {../../../} {../figures/} }
 %\captionsetup{margin=10pt, font={small}, labelsep=colon, labelfont={bf}}
 \renewcommand{\bibfont}{\small}

NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/tools/shr_func.sh

@@ -4 +4 @@
     printf "\t¤ Clean previous build"
     find latex/$1/build -mindepth 1 -delete
-
     echo
 }
@@ -10 +9 @@
 build() {
     printf "\t¤ Generation of the PDF format\n"
-    latexmk -r  ./latex/global/latexmk.pl -pdfxe ./latex/$1/main/$1_manual \
+    latexmk -r ./latex/global/latexmkrc -pdfxe ./latex/$1/main/$1_manual \
 #  1> /dev/null
     [ -f ./latex/$1/build/$1_manual.pdf ] && mv ./latex/$1/build/$1_manual.pdf .