New URL for NEMO forge!   http://forge.nemo-ocean.eu

Since March 2022 along with NEMO 4.2 release, the code development moved to a self-hosted GitLab.
This present forge is now archived and remained online for history.
Changeset 9394 – NEMO

Changeset 9394


Ignore:
Timestamp:
2018-03-13T21:21:44+01:00 (6 years ago)
Author:
nicolasmartin
Message:

Fix several typos, reverse (biblio then index) and shrink the manual backmatter (columns, font size, separator height) #1793

Location:
branches/2017/dev_merge_2017/DOC
Files:
13 edited

Legend:

Unmodified
Added
Removed

  • branches/2017/dev_merge_2017/DOC/tex_main/NEMO_manual.bib

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    658647} 
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    678666} 
    679667 
    … …  
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    793780} 
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    824811   title = {On Antarctic Bottom Water consumption in the abyssal ocean}, 
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    828814   abstract = {In studies of ocean mixing, it is generally assumed that small-scale turbulent overturns lose 15-20 \% of their energy in eroding the background stratification. Accumulating evidence that this energy fraction, or mixing efficiency Rf, significantly varies depending on flow properties challenges this assumption, however. Here, we examine the implications of a varying mixing efficiency for ocean energetics and deep water mass transformation. Combining current parameterizations of internal wave-driven mixing with a recent model expressing Rf as a function of a turbulence intensity parameter Reb = εν/νN2, we show that accounting for reduced mixing efficiencies in regions of weak stratification or energetic turbulence (high Reb) strongly limits the ability of breaking internal waves to supply oceanic potential energy and drive abyssal upwelling. Moving from a fixed Rf = 1/6 to a variable efficiency Rf(Reb) causes Antarctic Bottom Water upwelling induced by locally-dissipating internal tides and lee waves to fall from 9 to 4 Sv, and the corresponding potential energy source to plunge from 97 to 44 GW. When adding the contribution of remotely-dissipating internal tides under idealized distributions of energy dissipation, the total rate of Antarctic Bottom Water upwelling is reduced by about a factor of 2, reaching 5-15 Sv compared to 10-33 Sv for a fixed efficiency. Our results suggest that distributed mixing, overflow-related boundary processes and geothermal heating are more effective in consuming abyssal waters than topographically-enhanced mixing by breaking internal waves. Our calculations also point to the importance of accurately constraining Rf(Reb) and including the effect in ocean models.}, 
    829815   journal = {Journal of Physical Oceanography}, 
    … …  
    836822   title = {The impact of a variable mixing efficiency on the abyssal overturning}, 
    837823   issn = {0022-3670}, 
    838    url = {http://dx.doi.org//10.1175/JPO-D-14-0259.1}, 
    839824   doi = {10.1175/JPO-D-14-0259.1}, 
    840825   abstract = {In studies of ocean mixing, it is generally assumed that small-scale turbulent overturns lose 15-20 \% of their energy in eroding the background stratification. Accumulating evidence that this energy fraction, or mixing efficiency Rf, significantly varies depending on flow properties challenges this assumption, however. Here, we examine the implications of a varying mixing efficiency for ocean energetics and deep water mass transformation. Combining current parameterizations of internal wave-driven mixing with a recent model expressing Rf as a function of a turbulence intensity parameter Reb = εν/νN2, we show that accounting for reduced mixing efficiencies in regions of weak stratification or energetic turbulence (high Reb) strongly limits the ability of breaking internal waves to supply oceanic potential energy and drive abyssal upwelling. Moving from a fixed Rf = 1/6 to a variable efficiency Rf(Reb) causes Antarctic Bottom Water upwelling induced by locally-dissipating internal tides and lee waves to fall from 9 to 4 Sv, and the corresponding potential energy source to plunge from 97 to 44 GW. When adding the contribution of remotely-dissipating internal tides under idealized distributions of energy dissipation, the total rate of Antarctic Bottom Water upwelling is reduced by about a factor of 2, reaching 5-15 Sv compared to 10-33 Sv for a fixed efficiency. Our results suggest that distributed mixing, overflow-related boundary processes and geothermal heating are more effective in consuming abyssal waters than topographically-enhanced mixing by breaking internal waves. Our calculations also point to the importance of accurately constraining Rf(Reb) and including the effect in ocean models.}, 
    … …  
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    893877 
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    945928 
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    982965 
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    1005987 
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     1174 
    11921175@ARTICLE{Gerdes1991, 
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    … …  
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    11981181   Title = {The influence of numerical advection schemes on the results of ocean general circulation models}, 
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    12001182   Volume = {5}, 
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    1221    url = {http://dx.doi.org/10.1029/2010JB007867}, 
    12221203   doi = {10.1029/2010JB007867}, 
    12231204   abstract = {Abyssal hills, which are pervasive landforms on the seafloor of the Earth's oceans, represent a potential tectonic record of the history of mid-ocean ridge spreading. However, the most detailed global maps of the seafloor, derived from the satellite altimetry-based gravity field, cannot be used to deterministically characterize such small-scale ({\textless}10 km) morphology. Nevertheless, the small-scale variability of the gravity field can be related to the statistical properties of abyssal hill morphology using the upward continuation formulation. In this paper, I construct a global prediction of abyssal hill root-mean-square (rms) heights from the small-scale variability of the altimetric gravity field. The abyssal hill-related component of the gravity field is derived by first masking distinct features, such as seamounts, mid-ocean ridges, and continental margins, and then applying a newly designed adaptive directional filter algorithm to remove fracture zone/discontinuity fabric. A noise field is derived empirically by correlating the rms variability of the small-scale gravity field to the altimetric noise field in regions of very low relief, and the noise variance is subtracted from the small-scale gravity variance. Suites of synthetically derived, abyssal hill formed gravity fields are generated as a function of water depth, basement rms heights, and sediment thickness and used to predict abyssal hill seafloor rms heights from corrected small-scale gravity rms height. The resulting global prediction of abyssal hill rms heights is validated qualitatively by comparing against expected variations in abyssal hill morphology and quantitatively by comparing against actual measurements of rms heights. Although there is scatter, the prediction appears unbiased.}, 
    … …  
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    33343275  pages = {L08706}, 
    33353276  doi = {10.1029/2007GL029275}, 
    3336   url = {http://dx.doi.org/10.1029/2007GL029275} 
    33373277} 
    33383278 

  • branches/2017/dev_merge_2017/DOC/tex_main/NEMO_manual.sty

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    77%% ============================================================================== 
    88 
    9 \usepackage{natbib}     % bib 
    10 \usepackage{caption}    % caption 
    11 \usepackage{xcolor}     % color 
    12 \usepackage{silence}    % compilation 
    13 \usepackage{times}      % font 
    14 \usepackage{hyperref}   % hyper 
    15 \usepackage{enumitem}   % list 
    16 \usepackage{minted}     % listing 
    17 \usepackage{amsmath}    % maths 
    18 \usepackage{fancyhdr}   % page 
    19 \usepackage{minitoc}    % toc 
    20 \usepackage{subfiles}   % subdocs 
     9\usepackage{natbib}     %% bib 
     10\usepackage{caption}    %% caption 
     11\usepackage{xcolor}     %% color 
     12\usepackage{silence}    %% compilation 
     13\usepackage{times}      %% font 
     14\usepackage{hyperref}   %% hyper 
     15\usepackage{idxlayout}  %% index 
     16\usepackage{enumitem}   %% list 
     17\usepackage{minted}     %% listing 
     18\usepackage{amsmath}    %% maths 
     19\usepackage{fancyhdr}   %% page 
     20\usepackage{minitoc}    %% toc 
     21\usepackage{subfiles}   %% subdocs 
    2122 
    2223 
    … …  
    3435   colorlinks 
    3536} 
     37\idxlayout{font=footnotesize, columns=3} 
     38\renewcommand{\bibfont}{\footnotesize} 
     39\renewcommand{\bibsep}{3pt} 
    3640 
    3741 
    … …  
    4145\pagestyle{fancy} 
    4246\bibliographystyle{../tex_sub/ametsoc} 
     47 
    4348 
    4449%% Additionnal fonts 
    … …  
    121126%% New commands 
    122127 
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    124 \newcommand{ \sfcomment}[1]{} 
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    126131 
    … …  
    161166\newcommand{\mygstrut}[2]{\rule[#1 em]{0pt}{#2 em}} 
    162167\newcommand{\mystrut}{\rule[-.9 em]{0pt}{1.79 em}} 
     168 
     169\newcommand{\doi}[1]{\href{http://dx.doi.org/#1}{full-text}} 

  • branches/2017/dev_merge_2017/DOC/tex_main/NEMO_manual.tex

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    140140 
    141141 
     142%% Bibliography 
     143 
     144\cleardoublepage 
     145\phantomsection 
     146\addcontentsline{toc}{chapter}{Bibliography} 
     147\bibliography{../tex_main/NEMO_manual} 
     148 
     149 
    142150%% Index 
    143151 
     152\cleardoublepage 
     153\phantomsection 
    144154\addcontentsline{toc}{chapter}{Index} 
    145155\printindex 
    146156 
    147157 
    148 %% Bibliography 
    149  
    150 \addcontentsline{toc}{chapter}{Bibliography} 
    151 \bibliography{../tex_main/NEMO_manual} 
    152  
    153  
    154158\end{document} 

  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_CONFIG.tex

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    290290$z$-coordinates and is forced with tidal lateral boundary conditions 
    291291using a flather boundary condition from the BDY module. 
    292 The AMM configuration  uses the GLS (key\_zdfgls) turbulence scheme, the 
    293 VVL non-linear free surface(key\_vvl) and time-splitting 
    294 (key\_dynspg\_ts). 
     292The AMM configuration  uses the GLS (\key{zdfgls}) turbulence scheme, the 
     293VVL non-linear free surface(\key{vvl}) and time-splitting 
     294(\key{dynspg\_ts}). 
    295295 
    296296In addition to the tidal boundary condition the model may also take 

  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_DIA.tex

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    229229with the size of the array passed to iomput.  
    230230The grid\_ref attribute refers to definitions set in iodef.xml which, in turn, reference grids  
    231 and axes either defined in the code (iom\_set\_domain\_attr and iom\_set\_axis\_attr in iom.F90)  
     231and axes either defined in the code (iom\_set\_domain\_attr and iom\_set\_axis\_attr in \mdl{iom})  
    232232or defined in the domain\_def.xml file. $e.g.$: 
    233233\begin{xmllines} 
    … …  
    236236Note, if your array is computed within the surface module each \np{nn\_fsbc} time\_step,  
    237237add the field definition within the field\_group defined with the id ''SBC'': $<$field\_group id=''SBC''...$>$  
    238 which has been defined with the correct frequency of operations (iom\_set\_field\_attr in iom.F90) 
     238which has been defined with the correct frequency of operations (iom\_set\_field\_attr in \mdl{iom}) 
    239239 
    240240\item[4.] add your field in one of the output files defined in iodef.xml (again see subsequent sections for syntax and rules) 
    … …  
    566566\subsubsection{Other controls of the XML attributes from NEMO} 
    567567 
    568 The values of some attributes are defined by subroutine calls within NEMO (calls to iom\_set\_domain\_attr, iom\_set\_axis\_attr and iom\_set\_field\_attr in iom.F90). Any definition given in the xml file will be overwritten. By convention, these attributes are defined to ''auto'' (for string) or ''0000'' (for integer) in the xml file (but this is not necessary).  
     568The values of some attributes are defined by subroutine calls within NEMO (calls to iom\_set\_domain\_attr, iom\_set\_axis\_attr and iom\_set\_field\_attr in \mdl{iom}). Any definition given in the xml file will be overwritten. By convention, these attributes are defined to ''auto'' (for string) or ''0000'' (for integer) in the xml file (but this is not necessary).  
    569569 
    570570Here is the list of these attributes:\\ 

  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_DIU.tex

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    2525\end{itemize} 
    2626 
    27 Models are provided for both the warm layer, diurnal\_bulk.F90, and the cool skin, 
    28 cool\_skin.F90.  Foundation SST is not considered as it can be obtained 
     27Models are provided for both the warm layer, \mdfl{diurnal_bulk}, and the cool skin, 
     28\mdl{cool_skin}.  Foundation SST is not considered as it can be obtained 
    2929either from the main NEMO model ($i.e.$ from the temperature of the top few model levels) 
    3030or from some other source.   

  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_DYN.tex

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    4545For term \textit{ttt} in the momentum equations, the logical namelist variables are \textit{ln\_dynttt\_xxx},  
    4646where \textit{xxx} is a 3 or 4 letter acronym corresponding to each optional scheme.  
    47 If a CPP key is used for this term its name is \textbf{key\_ttt}. The corresponding  
     47If a CPP key is used for this term its name is \key{ttt}. The corresponding  
    4848code can be found in the \textit{dynttt\_xxx} module in the DYN directory, and it is  
    4949usually computed in the \textit{dyn\_ttt\_xxx} subroutine. 

  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_LDF.tex

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    337337The specification of the space variation of the coefficient is made in  
    338338\mdl{ldftra} and \mdl{ldfdyn}, or more precisely in include files  
    339 \textit{traldf\_cNd.h90} and \textit{dynldf\_cNd.h90}, with N=1, 2 or 3.  
     339\hf{traldf\_cNd} and \hf{dynldf\_cNd}, with N=1, 2 or 3.  
    340340The user can modify these include files as he/she wishes. The way the  
    341341mixing coefficient are set in the reference version can be briefly described  
    … …  
    343343 
    344344\subsubsection{Constant mixing coefficients (default option)} 
    345 When none of the \textbf{key\_dynldf\_...} and \textbf{key\_traldf\_...} keys are  
     345When none of the \key{dynldf\_...} and \key{traldf\_...} keys are  
    346346defined, a constant value is used over the whole ocean for momentum and  
    347347tracers, which is specified through the \np{rn\_ahm0} and \np{rn\_aht0} namelist  
    … …  
    430430the eddy induced coefficient has to be defined. Its space variations are controlled  
    431431by the same CPP variable as for the eddy diffusivity coefficient ($i.e.$  
    432 \textbf{key\_traldf\_cNd}).  
     432\key{traldf\_cNd}).  
    433433 
    434434(5) the eddy coefficient associated with a biharmonic operator must be set to a \emph{negative} value. 

  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_OBS.tex

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    882882 
    883883In addition to \emph{OPA\_SRC} the offline obs oper requires the inclusion 
    884 of the \emph{OOO\_SRC} directory. \emph{OOO\_SRC} contains a replacement \textbf{nemo.f90} and 
    885 \textbf{nemogcm.F90} which overwrites the resultant \textbf{nemo.exe}. This is the approach taken 
     884of the \emph{OOO\_SRC} directory. \emph{OOO\_SRC} contains a replacement \mdl{nemo} and 
     885\mdl{nemogcm} which overwrites the resultant \textbf{nemo.exe}. This is the approach taken 
    886886by \emph{SAS\_SRC} and \emph{OFF\_SRC}. 
    887887 

  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_SBC.tex

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    161161 
    162162A generic interface has been introduced to manage the way input data (2D or 3D fields,  
    163 like surface forcing or ocean T and S) are specify in \NEMO. This task is archieved by fldread.F90.  
     163like surface forcing or ocean T and S) are specify in \NEMO. This task is archieved by \mdl{fldread}.  
    164164The module was design with four main objectives in mind:  
    165165\begin{enumerate}   
    … …  
    449449 
    450450\begin{itemize} 
    451 \item \mdl{nemogcm} : This routine initialises the rest of the model and repeatedly calls the stp time stepping routine (step.F90) 
     451\item \mdl{nemogcm} : This routine initialises the rest of the model and repeatedly calls the stp time stepping routine (\mdl{step}) 
    452452       Since the ocean state is not calculated all associated initialisations have been removed. 
    453453\item  \mdl{step} : The main time stepping routine now only needs to call the sbc routine (and a few utility functions). 
    … …  
    12721272and CICE CPP keys \textbf{ORCA\_GRID}, \textbf{CICE\_IN\_NEMO} and \textbf{coupled} should be used (seek advice from UKMO  
    12731273if necessary).  Currently the code is only designed to work when using the CORE forcing option for NEMO (with 
    1274 \textit{calc\_strair~=~true} and \textit{calc\_Tsfc~=~true} in the CICE name-list), or alternatively when NEMO  
    1275 is coupled to the HadGAM3 atmosphere model (with \textit{calc\_strair~=~false} and \textit{calc\_Tsfc~=~false}). 
     1274\textit{calc\_strair}\forcode{ = .true.} and \textit{calc\_Tsfc}\forcode{ = .true.} in the CICE name-list), or alternatively when NEMO  
     1275is coupled to the HadGAM3 atmosphere model (with \textit{calc\_strair}\forcode{ = .false.} and \textit{calc\_Tsfc}\forcode{ = false}). 
    12761276The code is intended to be used with \np{nn\_fsbc} set to 1 (although coupling ocean and ice less frequently  
    12771277should work, it is possible the calculation of some of the ocean-ice fluxes needs to be modified slightly - the 

  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_TRA.tex

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    5353For each equation term  \textit{TTT}, the namelist logicals are \textit{ln\_traTTT\_xxx},  
    5454where \textit{xxx} is a 3 or 4 letter acronym corresponding to each optional scheme.  
    55 The CPP key (when it exists) is \textbf{key\_traTTT}. The equivalent code can be  
     55The CPP key (when it exists) is \key{traTTT}. The equivalent code can be  
    5656found in the \textit{traTTT} or \textit{traTTT\_xxx} module, in the NEMO/OPA/TRA directory. 
    5757 
    … …  
    146146The choice is made in the \textit{\ngn{namtra\_adv}} namelist, by  
    147147setting to \forcode{.true.} one of the logicals \textit{ln\_traadv\_xxx}.  
    148 The corresponding code can be found in the \textit{traadv\_xxx.F90} module,  
     148The corresponding code can be found in the \mdl{traadv\_xxx} module,  
    149149where \textit{xxx} is a 3 or 4 letter acronym corresponding to each scheme.  
    150150By default ($i.e.$ in the reference namelist, \ngn{namelist\_ref}), all the logicals  
    … …  
    11381138\np{ln\_zero\_top\_layer} specifies that the restoration coefficient should be zero in the surface layer.  
    11391139Finally \np{ln\_custom} specifies that the custom module will be called.  
    1140 This module is contained in the file custom.F90 and can be edited by users. For example damping could be applied in a specific region. 
     1140This module is contained in the file \mdl{custom} and can be edited by users. For example damping could be applied in a specific region. 
    11411141 
    11421142The restoration coefficient can be set to zero in equatorial regions by specifying a positive value of \np{nn\_hdmp}.  

  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_misc.tex

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    203203duplicated rows and columns due to cyclic or north fold boundary condition as well as  
    204204overlap MPP areas). The self-compensated summation method should be used in all summation 
    205 in i- and/or j-direction. See closea.F90 module for an example. 
     205in i- and/or j-direction. See \mdl{closea} module for an example. 
    206206Note also that this implementation may be sensitive to the optimization level.  
    207207 

  • branches/2017/dev_merge_2017/DOC/tex_sub/chap_time_domain.tex

    r9393 r9394  
    9292where the subscript $F$ denotes filtered values and $\gamma$ is the Asselin  
    9393coefficient. $\gamma$ is initialized as \np{rn\_atfp} (namelist parameter).  
    94 Its default value is \np{rn_atfp}\forcode{ = 10.e-3} (see \S~\ref{STP_mLF}),  
     94Its default value is \np{rn\_atfp}\forcode{ = 10.e-3} (see \S~\ref{STP_mLF}),  
    9595causing only a weak dissipation of high frequency motions (\citep{Farge1987}).  
    9696The addition of a time filter degrades the accuracy of the  
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