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Changeset 12182 for NEMO/branches/2019/dev_r11943_MERGE_2019/doc – NEMO

Ignore:
Timestamp:
2019-12-11T12:38:43+01:00 (4 years ago)
Author:
davestorkey
Message:

2019/dev_r11943_MERGE_2019: Merge in dev_ASINTER-01-05_merge.

Location:
NEMO/branches/2019/dev_r11943_MERGE_2019/doc
Files:
6 deleted
21 edited
20 copied

Legend:

Unmodified
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  • NEMO/branches/2019/dev_r11943_MERGE_2019/doc/README.rst

    r11761 r12182  
    1 ************************** 
    2 Building the documentation 
    3 ************************** 
    41 
    5 .. todo:: 
    6  
    7  
    8  
    9 :file:`latex`    : LaTeX sources and Latexmk configuration to build reference manuals with :file:`manual_build.sh` 
    10  
    11 :file:`namelists`: Namelist blocks included in the documentation 
    12  
    13 :file:`rst`      : |RST man|_ sources and Sphinx configuration to build this guide hereby with :file:`guide_build.sh` 
    14  
    15 .. |RST man| replace:: reStructuredText (rst) 
    162 
    173.. warning:: 

  • NEMO/branches/2019/dev_r11943_MERGE_2019/doc/latex/.svnignore

    r11593 r12182  
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    99*.ind 
    10 *.lo* 
     10*.lof 
     11*.log 
     12*.lot 
    1113*.maf 
    1214*.mtc* 
    … …  
    1416*.pdf 
    1517*.toc 
    16 *.xdv 
    1718_minted-* 

  • NEMO/branches/2019/dev_r11943_MERGE_2019/doc/latex/NEMO/build

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        old new  
        1414*.pdf 
        1515*.toc 
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  • NEMO/branches/2019/dev_r11943_MERGE_2019/doc/latex/NEMO/main/appendices.tex

    r11567 r12182  
    11 
    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 
     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 
    77 
    88%% Not included 
    … …  
    1010%\subfile{../subfiles/chap_DIU} 
    1111%\subfile{../subfiles/chap_conservation} 
    12 %\subfile{../subfiles/apdx_algos}   %% Notes on some on going staff 
     12%\subfile{../subfiles/annex_E}            %% Notes on some on going staff 
     13 

  • NEMO/branches/2019/dev_r11943_MERGE_2019/doc/latex/NEMO/main/bibliography.bib

    r11674 r12182  
    400400} 
    401401 
    402 @article{         brodeau.barnier.ea_JPO16, 
    403   title         = "Climatologically Significant Effects of Some Approximations in the Bulk Parameterizations of Turbulent Air–Sea Fluxes", 
     402@article{         brodeau.barnier.ea_JPO17, 
     403  title         = "Climatologically Significant Effects of Some Approximations in the Bulk Parameterizations of Turbulent Air{\textendash}Sea Fluxes", 
    404404  pages         = "5--28", 
    405405  journal       = "Journal of Physical Oceanography", 
    … …  
    407407  number        = "1", 
    408408  author        = "Brodeau, Laurent and Barnier, Bernard and Gulev, Sergey K. and Woods, Cian", 
    409   year          = "2016", 
     409  year          = "2017", 
    410410  month         = "jan", 
    411411  publisher     = "American Meteorological Society", 
    … …  
    31343134  doi           = "10.1029/92jc00911" 
    31353135} 
     3136 
     3137@article{large.yeager_CD09, 
     3138author="Large, W. G. and Yeager, S. G.", 
     3139title="The Global Climatology of an Interannually Varying Air-Sea Flux Data Set", 
     3140pages = "341--364", 
     3141journal="Climate Dynamics", 
     3142volume = "33", 
     3143number = "2-3", 
     3144year="2009", 
     3145month = "aug", 
     3146publisher = "Springer Science and Business Media LLC", 
     3147doi="10.1007/s00382-008-0441-3" 
     3148} 
     3149 
     3150@book{sverdrup.johnson.ea_1942, 
     3151author = {H. U. Sverdrup and Martin W. Johnson and Richard H. Fleming}, 
     3152title = {The Oceans, Their Physics, Chemistry, and General Biology}, 
     3153publisher = {Prentice-Hall}, 
     3154address = {New York}, 
     3155year = {1942}, 
     3156pages = {1087}, 
     3157} 
     3158 
     3159@article{kraus.businger_QJRMS96, 
     3160author = "E. B. Kraus and J. A. Businger", 
     3161title = "Atmosphere-ocean interaction.", 
     3162journal="Quarterly Journal of the Royal Meteorological Society",, 
     3163year = "1996", 
     3164volume = "122", 
     3165number = "529", 
     3166pages = "324-325", 
     3167publisher = "John Wiley & Sons, Ltd", 
     3168issn = "1477-870X", 
     3169doi = "10.1002/qj.49712252914" 
     3170} 
     3171 
     3172@article{josey.gulev.ea_2013, 
     3173title = "Exchanges through the ocean surface", 
     3174journal = "Ocean Circulation and Climate - A 21st Century Perspective, Int. Geophys. Ser.", 
     3175year = "2013", 
     3176author = "S. A. Josey and S. Gulev and L. Yu", 
     3177pages = "115-140, edited by G. Siedler et al., Academic Press, Oxford", 
     3178volume = "103", 
     3179doi = "10.1016/B978-0-12-391851-2.00005-2" 
     3180} 
     3181 
     3182@article{fairall.bradley.ea_JGR96, 
     3183  year = "1996", 
     3184 journal = "Journal of Geophysical Research: Oceans", 
     3185  month = "jan", 
     3186  publisher = "American Geophysical Union", 
     3187  volume = "101", 
     3188  number = "C1", 
     3189  pages = "1295-1308", 
     3190  author = "C. W. Fairall and E. F. Bradley and J. S. Godfrey and G. A. Wick and J. B. Edson and G. S. Young", 
     3191  title = "Cool-skin and warm-layer effects on sea surface temperature", 
     3192  doi = "10.1029/95jc03190" 
     3193} 
     3194 
     3195@article{zeng.beljaars_GRL05, 
     3196  year = "2005", 
     3197  month = "jul", 
     3198  publisher = "American Geophysical Union", 
     3199  volume = "32", 
     3200  number = "14", 
     3201  author = "Xubin Zeng and Anton Beljaars", 
     3202  title = "A prognostic scheme of sea surface skin temperature for modeling and data assimilation", 
     3203  journal = "Geophysical Research Letters", 
     3204  doi = "10.1029/2005gl023030" 
     3205} 
     3206 

  • NEMO/branches/2019/dev_r11943_MERGE_2019/doc/latex/NEMO/main/chapters.tex

    r11567 r12182  
    1 \subfile{../subfiles/chap_model_basics}   %% 1. 
    2 \subfile{../subfiles/chap_time_domain}    %% 2.  Time discretisation (time stepping strategy) 
    3 \subfile{../subfiles/chap_DOM}            %% 3.  Space discretisation 
    4 \subfile{../subfiles/chap_TRA}            %% 4.  Tracer advection/diffusion equation 
    5 \subfile{../subfiles/chap_DYN}            %% 5.  Dynamics : momentum equation 
    6 \subfile{../subfiles/chap_SBC}            %% 6.  Surface Boundary Conditions 
    7 \subfile{../subfiles/chap_LBC}            %% 7.  Lateral Boundary Conditions 
    8 \subfile{../subfiles/chap_LDF}            %% 8.  Lateral diffusion 
    9 \subfile{../subfiles/chap_ZDF}            %% 9.  Vertical diffusion 
    10 \subfile{../subfiles/chap_DIA}            %% 10. Outputs and Diagnostics 
    11 \subfile{../subfiles/chap_OBS}            %% 11. Observation operator 
    12 \subfile{../subfiles/chap_ASM}            %% 12. Assimilation increments 
    13 \subfile{../subfiles/chap_STO}            %% 13. Stochastic param. 
    14 \subfile{../subfiles/chap_misc}           %% 14. Miscellaneous topics 
    15 \subfile{../subfiles/chap_cfgs}           %% 15. Predefined configurations 
    16  
    17 %% Not included 
    18 %\subfile{../subfiles/chap_model_basics_zstar} 
    19 %\subfile{../subfiles/chap_DIU} 
    20 %\subfile{../subfiles/chap_conservation} 
     1\subfile{../subfiles/introduction}        %% Introduction 
     2\subfile{../subfiles/chap_model_basics} 
     3\subfile{../subfiles/chap_time_domain}    %% Time discretisation (time stepping strategy) 
     4\subfile{../subfiles/chap_DOM}            %% Space discretisation 
     5\subfile{../subfiles/chap_TRA}            %% Tracer advection/diffusion equation 
     6\subfile{../subfiles/chap_DYN}            %% Dynamics : momentum equation 
     7\subfile{../subfiles/chap_SBC}            %% Surface Boundary Conditions 
     8\subfile{../subfiles/chap_LBC}            %% Lateral Boundary Conditions 
     9\subfile{../subfiles/chap_LDF}            %% Lateral diffusion 
     10\subfile{../subfiles/chap_ZDF}            %% Vertical diffusion 
     11\subfile{../subfiles/chap_DIA}            %% Outputs and Diagnostics 
     12\subfile{../subfiles/chap_OBS}            %% Observation operator 
     13\subfile{../subfiles/chap_ASM}            %% Assimilation increments 
     14\subfile{../subfiles/chap_STO}            %% Stochastic param. 
     15\subfile{../subfiles/chap_misc}           %% Miscellaneous topics 
     16\subfile{../subfiles/chap_CONFIG}         %% Predefined configurations 

  • NEMO/branches/2019/dev_r11943_MERGE_2019/doc/latex/NEMO/subfiles/chap_SBC.tex

    r11693 r12182  
    11\documentclass[../main/NEMO_manual]{subfiles} 
     2\usepackage{fontspec} 
     3\usepackage{fontawesome} 
    24 
    35\begin{document} 
    … …  
    4547 
    4648\begin{itemize} 
    47 \item a bulk formulation (\np[=.true.]{ln_blk}{ln\_blk} with four possible bulk algorithms), 
     49\item a bulk formulation (\np[=.true.]{ln_blk}{ln\_blk}), featuring a selection of four bulk parameterization algorithms, 
    4850\item a flux formulation (\np[=.true.]{ln_flx}{ln\_flx}), 
    4951\item a coupled or mixed forced/coupled formulation (exchanges with a atmospheric model via the OASIS coupler), 
    … …  
    504506\label{sec:SBC_flx} 
    505507 
     508% Laurent: DO NOT mix up ``bulk formulae'' (the classic equation) and the ``bulk 
     509% parameterization'' (i.e NCAR, COARE, ECMWF...) 
     510 
    506511\begin{listing} 
    507512  \nlst{namsbc_flx} 
    … …  
    520525See \autoref{subsec:SBC_ssr} for its specification. 
    521526 
    522 %% ================================================================================================= 
     527 
     528 
     529 
     530 
     531 
     532 
     533%% ================================================================================================= 
     534\pagebreak 
     535\newpage 
    523536\section[Bulk formulation (\textit{sbcblk.F90})]{Bulk formulation (\protect\mdl{sbcblk})} 
    524537\label{sec:SBC_blk} 
     538 
     539% L. Brodeau, December 2019... % 
    525540 
    526541\begin{listing} 
    … …  
    530545\end{listing} 
    531546 
    532 In the bulk formulation, the surface boundary condition fields are computed with bulk formulae using atmospheric fields 
    533 and ocean (and sea-ice) variables averaged over \np{nn_fsbc}{nn\_fsbc} time-step. 
    534  
    535 The atmospheric fields used depend on the bulk formulae used. 
    536 In forced mode, when a sea-ice model is used, a specific bulk formulation is used. 
    537 Therefore, different bulk formulae are used for the turbulent fluxes computation 
    538 over the ocean and over sea-ice surface. 
    539 For the ocean, four bulk formulations are available thanks to the \href{https://brodeau.github.io/aerobulk/}{Aerobulk} package (\citet{brodeau.barnier.ea_JPO16}): 
    540 the NCAR (formerly named CORE), COARE 3.0, COARE 3.5 and ECMWF bulk formulae. 
    541 The choice is made by setting to true one of the following namelist variable: 
    542  \np{ln_NCAR}{ln\_NCAR}, \np{ln_COARE_3p0}{ln\_COARE\_3p0},  \np{ln_COARE_3p5}{ln\_COARE\_3p5} and  \np{ln_ECMWF}{ln\_ECMWF}. 
    543 For sea-ice, three possibilities can be selected: 
    544 a constant transfer coefficient (1.4e-3; default value), \citet{lupkes.gryanik.ea_JGR12} (\np{ln_Cd_L12}{ln\_Cd\_L12}), and \citet{lupkes.gryanik_JGR15} (\np{ln_Cd_L15}{ln\_Cd\_L15}) parameterizations 
     547If the bulk formulation is selected (\np[=.true.]{ln_blk}{ln\_blk}), the air-sea 
     548fluxes associated with surface boundary conditions are estimated by means of the 
     549traditional \emph{bulk formulae}. As input, bulk formulae rely on a prescribed 
     550near-surface atmosphere state (typically extracted from a weather reanalysis) 
     551and the prognostic sea (-ice) surface state averaged over \np{nn_fsbc}{nn\_fsbc} 
     552time-step(s). 
     553 
     554% Turbulent air-sea fluxes are computed using the sea surface properties and 
     555% atmospheric SSVs at height $z$ above the sea surface, with the traditional 
     556% aerodynamic bulk formulae: 
     557 
     558Note: all the NEMO Fortran routines involved in the present section have been 
     559 initially developed (and are still developed in parallel) in 
     560 the \href{https://brodeau.github.io/aerobulk/}{\texttt{AeroBulk}} open-source project 
     561\citep{brodeau.barnier.ea_JPO17}. 
     562 
     563%%% Bulk formulae are this: 
     564\subsection{Bulk formulae}\label{subsec:SBC_blkform} 
     565% 
     566In NEMO, the set of equations that relate each component of the surface fluxes 
     567to the near-surface atmosphere and sea surface states writes 
     568% 
     569\begin{subequations}\label{eq_bulk} 
     570  \label{eq:SBC_bulk_form} 
     571  \begin{eqnarray} 
     572    \mathbf{\tau} &=& \rho~ C_D ~ \mathbf{U}_z  ~ U_B \\ 
     573    Q_H           &=& \rho~C_H~C_P~\big[ \theta_z - T_s \big] ~ U_B \\ 
     574    E             &=& \rho~C_E    ~\big[    q_s   - q_z \big] ~ U_B \\ 
     575    Q_L           &=& -L_v \, E \\ 
     576    % 
     577    Q_{sr}        &=& (1 - a) Q_{sw\downarrow} \\ 
     578    Q_{ir}        &=& \delta (Q_{lw\downarrow} -\sigma T_s^4) 
     579  \end{eqnarray} 
     580\end{subequations} 
     581% 
     582with 
     583   \[ \theta_z \simeq T_z+\gamma z \] 
     584   \[  q_s \simeq 0.98\,q_{sat}(T_s,p_a ) \] 
     585% 
     586from which, the the non-solar heat flux is \[ Q_{ns} = Q_L + Q_H + Q_{ir} \] 
     587% 
     588where $\mathbf{\tau}$ is the wind stress vector, $Q_H$ the sensible heat flux, 
     589$E$ the evaporation, $Q_L$ the latent heat flux, and $Q_{ir}$ the net longwave 
     590flux. 
     591% 
     592$Q_{sw\downarrow}$ and $Q_{lw\downarrow}$ are the surface downwelling shortwave 
     593and longwave radiative fluxes, respectively. 
     594% 
     595Note: a positive sign for $\mathbf{\tau}$, $Q_H$, $Q_L$, $Q_{sr}$ or $Q_{ir}$ 
     596implies a gain of the relevant quantity for the ocean, while a positive $E$ 
     597implies a freshwater loss for the ocean. 
     598% 
     599$\rho$ is the density of air. $C_D$, $C_H$ and $C_E$ are the bulk transfer 
     600coefficients for momentum, sensible heat, and moisture, respectively. 
     601% 
     602$C_P$ is the heat capacity of moist air, and $L_v$ is the latent heat of 
     603vaporization of water. 
     604% 
     605$\theta_z$, $T_z$ and $q_z$ are the potential temperature, absolute temperature, 
     606and specific humidity of air at height $z$ above the sea surface, 
     607respectively. $\gamma z$ is a temperature correction term which accounts for the 
     608adiabatic lapse rate and approximates the potential temperature at height 
     609$z$ \citep{josey.gulev.ea_2013}. 
     610% 
     611$\mathbf{U}_z$ is the wind speed vector at height $z$ above the sea surface 
     612(possibly referenced to the surface current $\mathbf{u_0}$, 
     613section \ref{s_res1}.\ref{ss_current}). 
     614% 
     615The bulk scalar wind speed, namely $U_B$, is the scalar wind speed, 
     616$|\mathbf{U}_z|$, with the potential inclusion of a gustiness contribution. 
     617% 
     618$a$ and $\delta$ are the albedo and emissivity of the sea surface, respectively.\\ 
     619% 
     620%$p_a$ is the mean sea-level pressure (SLP). 
     621% 
     622$T_s$ is the sea surface temperature. $q_s$ is the saturation specific humidity 
     623of air at temperature $T_s$; it includes a 2\% reduction to account for the 
     624presence of salt in seawater \citep{sverdrup.johnson.ea_1942,kraus.businger_QJRMS96}. 
     625Depending on the bulk parametrization used, $T_s$ can either be the temperature 
     626at the air-sea interface (skin temperature, hereafter SSST) or at typically a 
     627few tens of centimeters below the surface (bulk sea surface temperature, 
     628hereafter SST). 
     629% 
     630The SSST differs from the SST due to the contributions of two effects of 
     631opposite sign, the \emph{cool skin} and \emph{warm layer} (hereafter CS and WL, 
     632respectively, see section\,\ref{subsec:SBC_skin}). 
     633% 
     634Technically, when the ECMWF or COARE* bulk parametrizations are selected 
     635(\np[=.true.]{ln_ECMWF}{ln\_ECMWF} or \np[=.true.]{ln_COARE*}{ln\_COARE\*}), 
     636$T_s$ is the SSST, as opposed to the NCAR bulk parametrization 
     637(\np[=.true.]{ln_NCAR}{ln\_NCAR}) for which $T_s$ is the bulk SST (\ie~temperature 
     638at first T-point level). 
     639 
     640For more details on all these aspects the reader is invited to refer 
     641to \citet{brodeau.barnier.ea_JPO17}. 
     642 
     643 
     644 
     645\subsection{Bulk parametrizations}\label{subsec:SBC_blk_ocean} 
     646%%%\label{subsec:SBC_param} 
     647 
     648Accuracy of the estimate of surface turbulent fluxes by means of bulk formulae 
     649strongly relies on that of the bulk transfer coefficients: $C_D$, $C_H$ and 
     650$C_E$. They are estimated with what we refer to as a \emph{bulk 
     651parametrization} algorithm. When relevant, these algorithms also perform the 
     652height adjustment of humidity and temperature to the wind reference measurement 
     653height (from \np{rn_zqt}{rn\_zqt} to \np{rn_zu}{rn\_zu}). 
     654 
     655 
     656 
     657For the open ocean, four bulk parametrization algorithms are available in NEMO: 
     658\begin{itemize} 
     659\item NCAR, formerly known as CORE, \citep{large.yeager_rpt04,large.yeager_CD09} 
     660\item COARE 3.0 \citep{fairall.bradley.ea_JC03} 
     661\item COARE 3.6 \citep{edson.jampana.ea_JPO13} 
     662\item ECMWF (IFS documentation, cy45) 
     663\end{itemize} 
     664 
     665 
     666With respect to version 3, the principal advances in version 3.6 of the COARE 
     667bulk parametrization are built around improvements in the representation of the 
     668effects of waves on 
     669fluxes \citep{edson.jampana.ea_JPO13,brodeau.barnier.ea_JPO17}. This includes 
     670improved relationships of surface roughness, and whitecap fraction on wave 
     671parameters. It is therefore recommended to chose version 3.6 over 3. 
     672 
     673 
     674 
     675 
     676\subsection{Cool-skin and warm-layer parametrizations}\label{subsec:SBC_skin} 
     677%\subsection[Cool-skin and warm-layer parameterizations 
     678%(\forcode{ln_skin_cs} \& \forcode{ln_skin_wl})]{Cool-skin and warm-layer parameterizations (\protect\np{ln_skin_cs}{ln\_skin\_cs} \& \np{ln_skin_wl}{ln\_skin\_wl})} 
     679%\label{subsec:SBC_skin} 
     680% 
     681As opposed to the NCAR bulk parametrization, more advanced bulk 
     682parametrizations such as COARE3.x and ECMWF are meant to be used with the skin 
     683temperature $T_s$ rather than the bulk SST (which, in NEMO is the temperature at 
     684the first T-point level, see section\,\ref{subsec:SBC_blkform}). 
     685% 
     686As such, the relevant cool-skin and warm-layer parametrization must be 
     687activated through \np[=T]{ln_skin_cs}{ln\_skin\_cs} 
     688and \np[=T]{ln_skin_wl}{ln\_skin\_wl} to use COARE3.x or ECMWF in a consistent 
     689way. 
     690 
     691\texttt{\#LB: ADD BLBLA ABOUT THE TWO CS/WL PARAMETRIZATIONS (ECMWF and COARE) !!!} 
     692 
     693For the cool-skin scheme parametrization COARE and ECMWF algorithms share the same 
     694basis: \citet{fairall.bradley.ea_JGR96}. With some minor updates based 
     695on \citet{zeng.beljaars_GRL05} for ECMWF, and \citet{fairall.ea_19} for COARE 
     6963.6. 
     697 
     698For the warm-layer scheme, ECMWF is based on \citet{zeng.beljaars_GRL05} with a 
     699recent update from \citet{takaya.bidlot.ea_JGR10} (consideration of the 
     700turbulence input from Langmuir circulation). 
     701 
     702Importantly, COARE warm-layer scheme \citep{fairall.ea_19} includes a prognostic 
     703equation for the thickness of the warm-layer, while it is considered as constant 
     704in the ECWMF algorithm. 
     705 
     706 
     707\subsection{Appropriate use of each bulk parametrization} 
     708 
     709\subsubsection{NCAR} 
     710 
     711NCAR bulk parametrizations (formerly known as CORE) is meant to be used with the 
     712CORE II atmospheric forcing \citep{large.yeager_CD09}. The expected sea surface 
     713temperature is the bulk SST. Hence the following namelist parameters must be 
     714set: 
     715% 
     716\begin{verbatim} 
     717  ... 
     718  ln_NCAR    = .true. 
     719  ... 
     720  rn_zqt     = 10.     ! Air temperature & humidity reference height (m) 
     721  rn_zu      = 10.     ! Wind vector reference height (m) 
     722  ... 
     723  ln_skin_cs = .false. ! use the cool-skin parameterization 
     724  ln_skin_wl = .false. ! use the warm-layer parameterization 
     725  ... 
     726  ln_humi_sph = .true. ! humidity "sn_humi" is specific humidity  [kg/kg] 
     727\end{verbatim} 
     728 
     729 
     730\subsubsection{ECMWF} 
     731% 
     732With an atmospheric forcing based on a reanalysis of the ECMWF, such as the 
     733Drakkar Forcing Set \citep{brodeau.barnier.ea_OM10}, we strongly recommend to 
     734use the ECMWF bulk parametrizations with the cool-skin and warm-layer 
     735parametrizations activated. In ECMWF reanalyzes, since air temperature and 
     736humidity are provided at the 2\,m height, and given that the humidity is 
     737distributed as the dew-point temperature, the namelist must be tuned as follows: 
     738% 
     739\begin{verbatim} 
     740  ... 
     741  ln_ECMWF   = .true. 
     742  ...      
     743  rn_zqt     =  2.     ! Air temperature & humidity reference height (m) 
     744  rn_zu      = 10.     ! Wind vector reference height (m) 
     745  ... 
     746  ln_skin_cs = .true. ! use the cool-skin parameterization 
     747  ln_skin_wl = .true. ! use the warm-layer parameterization 
     748  ... 
     749  ln_humi_dpt = .true. !  humidity "sn_humi" is dew-point temperature [K] 
     750  ... 
     751\end{verbatim} 
     752% 
     753Note: when \np{ln_ECMWF}{ln\_ECMWF} is selected, the selection 
     754of \np{ln_skin_cs}{ln\_skin\_cs} and \np{ln_skin_wl}{ln\_skin\_wl} implicitly 
     755triggers the use of the ECMWF cool-skin and warm-layer parametrizations, 
     756respectively (found in \textit{sbcblk\_skin\_ecmwf.F90}). 
     757 
     758 
     759\subsubsection{COARE 3.x} 
     760% 
     761Since the ECMWF parametrization is largely based on the COARE* parametrization, 
     762the two algorithms are very similar in terms of structure and closure 
     763approach. As such, the namelist tuning for COARE 3.x is identical to that of 
     764ECMWF: 
     765% 
     766\begin{verbatim} 
     767  ... 
     768  ln_COARE3p6 = .true. 
     769  ...      
     770  ln_skin_cs = .true. ! use the cool-skin parameterization 
     771  ln_skin_wl = .true. ! use the warm-layer parameterization 
     772  ... 
     773\end{verbatim} 
     774 
     775Note: when \np[=T]{ln_COARE3p0}{ln\_COARE3p0} is selected, the selection 
     776of \np{ln_skin_cs}{ln\_skin\_cs} and \np{ln_skin_wl}{ln\_skin\_wl} implicitly 
     777triggers the use of the COARE cool-skin and warm-layer parametrizations, 
     778respectively (found in \textit{sbcblk\_skin\_coare.F90}). 
     779 
     780 
     781%lulu 
     782 
     783 
     784 
     785% In a typical bulk algorithm, the BTCs under neutral stability conditions are 
     786% defined using \emph{in-situ} flux measurements while their dependence on the 
     787% stability is accounted through the \emph{Monin-Obukhov Similarity Theory} and 
     788% the \emph{flux-profile} relationships \citep[\eg{}][]{Paulson_1970}. BTCs are 
     789% functions of the wind speed and the near-surface stability of the atmospheric 
     790% surface layer (hereafter ASL), and hence, depend on $U_B$, $T_s$, $T_z$, $q_s$ 
     791% and $q_z$. 
     792 
     793 
     794 
     795\subsection{Prescribed near-surface atmospheric state} 
     796 
     797The atmospheric fields used depend on the bulk formulae used.  In forced mode, 
     798when a sea-ice model is used, a specific bulk formulation is used.  Therefore, 
     799different bulk formulae are used for the turbulent fluxes computation over the 
     800ocean and over sea-ice surface. 
     801% 
     802 
     803%The choice is made by setting to true one of the following namelist 
     804%variable: \np{ln_NCAR}{ln\_NCAR}, \np{ln_COARE_3p0}{ln\_COARE\_3p0}, \np{ln_COARE_3p6}{ln\_COARE\_3p6} 
     805%and \np{ln_ECMWF}{ln\_ECMWF}.  
    545806 
    546807Common options are defined through the \nam{sbc_blk}{sbc\_blk} namelist variables. 
    … …  
    553814    Variable description                 & Model variable & Units              & point \\ 
    554815    \hline 
    555     i-component of the 10m air velocity  & utau           & $m.s^{-1}$         & T     \\ 
     816    i-component of the 10m air velocity  & wndi           & $m.s^{-1}$         & T     \\ 
    556817    \hline 
    557     j-component of the 10m air velocity  & vtau           & $m.s^{-1}$         & T     \\ 
     818    j-component of the 10m air velocity  & wndj           & $m.s^{-1}$         & T     \\ 
    558819    \hline 
    559     10m air temperature                  & tair           & \r{}$K$            & T     \\ 
     820    10m air temperature                  & tair           & $K$               & T     \\ 
    560821    \hline 
    561     Specific humidity                    & humi           & \%                 & T     \\ 
     822    Specific humidity                    & humi           & $-$               & T     \\ 
     823    Relative humidity                    & ~              & $\%$              & T     \\ 
     824    Dew-point temperature                & ~              & $K$               & T     \\     
    562825    \hline 
    563     Incoming long wave radiation         & qlw            & $W.m^{-2}$         & T     \\ 
     826    Downwelling longwave radiation       & qlw            & $W.m^{-2}$         & T     \\ 
    564827    \hline 
    565     Incoming short wave radiation        & qsr            & $W.m^{-2}$         & T     \\ 
     828    Downwelling shortwave radiation      & qsr            & $W.m^{-2}$         & T     \\ 
    566829    \hline 
    567830    Total precipitation (liquid + solid) & precip         & $Kg.m^{-2}.s^{-1}$ & T     \\ 
    … …  
    584847 
    585848\np{cn_dir}{cn\_dir} is the directory of location of bulk files 
    586 \np{ln_taudif}{ln\_taudif} is the flag to specify if we use Hight Frequency (HF) tau information (.true.) or not (.false.) 
     849%\np{ln_taudif}{ln\_taudif} is the flag to specify if we use High Frequency (HF) tau information (.true.) or not (.false.) 
    587850\np{rn_zqt}{rn\_zqt}: is the height of humidity and temperature measurements (m) 
    588851\np{rn_zu}{rn\_zu}: is the height of wind measurements (m) 
    … …  
    595858Its range must be between zero and one, and it is recommended to set it to 0 at low-resolution (ORCA2 configuration). 
    596859 
    597 As for the flux formulation, information about the input data required by the model is provided in 
     860As for the flux parametrization, information about the input data required by the model is provided in 
    598861the namsbc\_blk namelist (see \autoref{subsec:SBC_fldread}). 
    599862 
    600 %% ================================================================================================= 
    601 \subsection[Ocean-Atmosphere Bulk formulae (\textit{sbcblk\_algo\_coare.F90, sbcblk\_algo\_coare3p5.F90, sbcblk\_algo\_ecmwf.F90, sbcblk\_algo\_ncar.F90})]{Ocean-Atmosphere Bulk formulae (\mdl{sbcblk\_algo\_coare}, \mdl{sbcblk\_algo\_coare3p5}, \mdl{sbcblk\_algo\_ecmwf}, \mdl{sbcblk\_algo\_ncar})} 
    602 \label{subsec:SBC_blk_ocean} 
    603  
    604 Four different bulk algorithms are available to compute surface turbulent momentum and heat fluxes over the ocean. 
    605 COARE 3.0, COARE 3.5 and ECMWF schemes mainly differ by their roughness lenghts computation and consequently 
    606 their neutral transfer coefficients relationships with neutral wind. 
    607 \begin{itemize} 
    608 \item NCAR (\np[=.true.]{ln_NCAR}{ln\_NCAR}): The NCAR bulk formulae have been developed by \citet{large.yeager_rpt04}. 
    609   They have been designed to handle the NCAR forcing, a mixture of NCEP reanalysis and satellite data. 
    610   They use an inertial dissipative method to compute the turbulent transfer coefficients 
    611   (momentum, sensible heat and evaporation) from the 10m wind speed, air temperature and specific humidity. 
    612   This \citet{large.yeager_rpt04} dataset is available through 
    613   the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/NCAR.html}{GFDL web site}. 
    614   Note that substituting ERA40 to NCEP reanalysis fields does not require changes in the bulk formulea themself. 
    615   This is the so-called DRAKKAR Forcing Set (DFS) \citep{brodeau.barnier.ea_OM10}. 
    616 \item COARE 3.0 (\np[=.true.]{ln_COARE_3p0}{ln\_COARE\_3p0}): See \citet{fairall.bradley.ea_JC03} for more details 
    617 \item COARE 3.5 (\np[=.true.]{ln_COARE_3p5}{ln\_COARE\_3p5}): See \citet{edson.jampana.ea_JPO13} for more details 
    618 \item ECMWF (\np[=.true.]{ln_ECMWF}{ln\_ECMWF}): Based on \href{https://www.ecmwf.int/node/9221}{IFS (Cy31)} implementation and documentation. 
    619   Surface roughness lengths needed for the Obukhov length are computed following \citet{beljaars_QJRMS95}. 
    620 \end{itemize} 
     863 
     864\subsubsection{Air humidity} 
     865 
     866Air humidity can be provided as three different parameters: specific humidity 
     867[kg/kg], relative humidity [\%], or dew-point temperature [K] (LINK to namelist 
     868parameters)... 
     869 
     870 
     871~\\ 
     872 
     873 
     874 
     875 
     876 
     877 
     878 
     879 
     880 
     881 
     882%% ================================================================================================= 
     883%\subsection[Ocean-Atmosphere Bulk formulae (\textit{sbcblk\_algo\_coare3p0.F90, sbcblk\_algo\_coare3p6.F90, %sbcblk\_algo\_ecmwf.F90, sbcblk\_algo\_ncar.F90})]{Ocean-Atmosphere Bulk formulae (\mdl{sbcblk\_algo\_coare3p0}, %\mdl{sbcblk\_algo\_coare3p6}, \mdl{sbcblk\_algo\_ecmwf}, \mdl{sbcblk\_algo\_ncar})} 
     884%\label{subsec:SBC_blk_ocean} 
     885 
     886%Four different bulk algorithms are available to compute surface turbulent momentum and heat fluxes over the ocean. 
     887%COARE 3.0, COARE 3.6 and ECMWF schemes mainly differ by their roughness lenghts computation and consequently 
     888%their neutral transfer coefficients relationships with neutral wind. 
     889%\begin{itemize} 
     890%\item NCAR (\np[=.true.]{ln_NCAR}{ln\_NCAR}): The NCAR bulk formulae have been developed by \citet{large.yeager_rpt04}. 
     891%  They have been designed to handle the NCAR forcing, a mixture of NCEP reanalysis and satellite data. 
     892%  They use an inertial dissipative method to compute the turbulent transfer coefficients 
     893%  (momentum, sensible heat and evaporation) from the 10m wind speed, air temperature and specific humidity. 
     894%  This \citet{large.yeager_rpt04} dataset is available through 
     895%  the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/NCAR.html}{GFDL web site}. 
     896%  Note that substituting ERA40 to NCEP reanalysis fields does not require changes in the bulk formulea themself. 
     897%  This is the so-called DRAKKAR Forcing Set (DFS) \citep{brodeau.barnier.ea_OM10}. 
     898%\item COARE 3.0 (\np[=.true.]{ln_COARE_3p0}{ln\_COARE\_3p0}): See \citet{fairall.bradley.ea_JC03} for more details 
     899%\item COARE 3.6 (\np[=.true.]{ln_COARE_3p6}{ln\_COARE\_3p6}): See \citet{edson.jampana.ea_JPO13} for more details 
     900%\item ECMWF (\np[=.true.]{ln_ECMWF}{ln\_ECMWF}): Based on \href{https://www.ecmwf.int/node/9204}{IFS (Cy40r1)} %implementation and documentation. 
     901%  Surface roughness lengths needed for the Obukhov length are computed 
     902%  following \citet{beljaars_QJRMS95}. 
     903%\end{itemize} 
    621904 
    622905%% ================================================================================================= 
    623906\subsection{Ice-Atmosphere Bulk formulae} 
    624907\label{subsec:SBC_blk_ice} 
     908 
     909 
     910\texttt{\#out\_of\_place:} 
     911 For sea-ice, three possibilities can be selected: 
     912a constant transfer coefficient (1.4e-3; default 
     913value), \citet{lupkes.gryanik.ea_JGR12} (\np{ln_Cd_L12}{ln\_Cd\_L12}), 
     914and \citet{lupkes.gryanik_JGR15} (\np{ln_Cd_L15}{ln\_Cd\_L15}) parameterizations 
     915\texttt{\#out\_of\_place.} 
     916 
     917 
     918 
    625919 
    626920Surface turbulent fluxes between sea-ice and the atmosphere can be computed in three different ways: 

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     3\subfile{../subfiles/introduction}               % Introduction 
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    12\subfile{../subfiles/model_description} 
    23\subfile{../subfiles/model_setup} 

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    11 
    2 %% ================================================================================================= 
    3 %% Template structure for reference manuals 
    4 %% ================================================================================================= 
     2%% ============================================================================== 
     3%% Template structure for reference manual 
     4%% ============================================================================== 
    55 
    66%% NEMO release version 
    7 \def \version{trunk} 
     7\def \version{4.0rc~} 
    88 
    99%% Preamble 
    10 %% ================================================================================================= 
     10%% ============================================================================== 
    1111 
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    1414 
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     15%% Load the configuration of the manual 
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     17 
     18%% Load global *.tex files 
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    1726 
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     36 
     37\renewcommand{\biblio}{} 
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    2739 
    2840 
    2941%% Frontmatter 
    30 %% ================================================================================================= 
     42%% ============================================================================== 
    3143 
    32 \pagenumbering{gobble}   %% Disable page numbering temporarily 
     44\pagenumbering{gobble} 
    3345 
    3446%% Title page 
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    3648 
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    3951 
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    4254 
    43 \listoffigures 
    44 \listoflistings 
    45 \listoftables 
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    47 \clearpage 
    48  
     55%% Foreword 
     56%\frontmatter   %% Chapter numbering off and Roman numerals for page numbers 
    4957\pagenumbering{roman} 
    50 \ofoot[]{\engine\ Reference Manual} \ifoot[]{\pagemark} 
    51  
    52 \input{introduction} 
     58\input{foreword} 
    5359 
    5460%% Table of Contents 
    5561\tableofcontents 
     62\listoffigures 
     63\listoftables 
     64\listoflistings 
    5665 
    5766\clearpage 
     67%\end{document} 
    5868 
    5969 
    6070%% Mainmatter 
    61 %% ================================================================================================= 
     71%% ============================================================================== 
    6272 
    63 %% Headings for document body 
     73%\mainmatter   %% Chapter numbering on, page numbering is reset with Arabic numerals 
    6474\pagenumbering{arabic} 
    65 \lohead{Chap.\ \thechapter\ \leftmark} \rehead{Sect.\ \thesection\ \rightmark} 
    66 \ifoot[]{Page\ \pagemark\ of \pageref*{LastPage}} 
    6775 
    6876\include{chapters} 
    … …  
    7078 
    7179%% Appendix 
    72 %% ================================================================================================= 
     80%% ============================================================================== 
    7381 
    74 \appendix   %% Chapter numbering with letters by now 
    75 \lohead{Apdx\ \thechapter\ \leftmark} 
     82%% Chapter numbering is reset with letters now 
     83\appendix    
     84 
    7685\include{appendices} 
    77  
    78 %% Append coding rules for every manual 
    79 \input{../../global/coding_rules} 
    8086 
    8187 
    8288%% Backmatter 
    83 %% ================================================================================================= 
     89%% ============================================================================== 
    8490 
    85 %% Bibliography and indexes 
    86 \input{../../global/epilogue} 
     91%\backmatter   %% Chapter numbering off 
     92 
     93%% Bibliography 
     94\phantomsection 
     95\addcontentsline{toc}{chapter}{Bibliography} 
     96\bibliography{../main/bibliography} 
     97 
     98%% Index 
     99\clearpage 
     100\phantomsection 
     101\addcontentsline{toc}{chapter}{Indexes} 
     102\printindex[keys] 
     103\printindex[modules] 
     104\printindex[blocks] 
     105\printindex[parameters] 
     106\printindex[subroutines] 
    87107 
    88108\end{document} 
     109 

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    11       \Large\slshape 
    12       \textbf{N}ucleus for \textbf{E}uropean \textbf{M}odelling of the \textbf{O}cean \\ 
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    56     \href{http://www.cnrs.fr          }{ \includegraphics[height=1cm]{logos/CNRS} } \hspace{0.25cm} 
    57     \href{http://www.mercator-ocean.fr}{ \includegraphics[height=1cm]{logos/MOI}  } \hspace{0.25cm} 
    58     \href{http://www.metoffice.gov.uk }{ \includegraphics[height=1cm]{logos/UKMO} } \hspace{0.25cm} 
    59     \href{http://nerc.ukri.org        }{ \includegraphics[height=1cm]{logos/NERC} } \\ 
    60     \medskip 
    61     \slshape 
    62     {C}ommunity \hspace{1.5em} {O}cean \hspace{1.5em} {M}odel \\ 
    63   \end{center} 
    64  
    65 \end{titlepage} 
    66  
    67 \restoregeometry 

  • NEMO/branches/2019/dev_r11943_MERGE_2019/doc/latex/global/highlighting.tex

    r11572 r12182  
    22%% ============================================================================== 
    33 
    4 \usepackage[outputdir=../build, chapter, newfloat]{minted} 
     4\usepackage[outputdir=../build]{minted} 
    55 
    66%% Global highlighting style 
    77\definecolor{bg}{HTML}{f8f8f8} 
    88\usemintedstyle{emacs} 
    9 \setminted{bgcolor=bg, fontsize=\scriptsize, breaklines} 
     9\setminted{bgcolor=bg, fontsize=\scriptsize, breaklines, frame=leftline} 
    1010\setminted[xml]{style=borland} %% Specific per language 
    1111 
    … …  
    2222 
    2323%% File 
    24 \newmintedfile[forfile]{fortran}{} 
     24\newmintedfile[forfile]{fortran}{}   % \forfile{../namelists/nam...} 
    2525 
    2626%% Inline 
    27 \newmintinline[forcode]{fortran}{bgcolor=, fontsize=auto}   % \forcode{...} 
    28 \newmintinline[xmlcode]{xml}{    bgcolor=, fontsize=auto}   % \xmlcode{...} 
    29 \newmintinline[snippet]{console}{bgcolor=, fontsize=auto}   % \snippet{...} 
     27\newmintinline[forcode]{fortran}{fontsize=auto, frame=lines}   % \forcode{...} 
     28\newmintinline[xmlcode]{xml}{    fontsize=auto, frame=lines}   % \xmlcode{...} 
     29\newmintinline[snippet]{console}{fontsize=auto, frame=lines}   % \snippet{...} 
    3030 
    3131%% Namelists inclusion 
    3232\newcommand{\nlst}[1]{\forfile{../../../namelists/#1}} 
     33 

  • NEMO/branches/2019/dev_r11943_MERGE_2019/doc/latex/global/index.ist

    r11584 r12182  
    11headings_flag 1 
    2 heading_prefix "\\medskip\\hfill\\textnormal{" 
    3 heading_suffix "}\\hfill\\smallskip\n" 
     2heading_prefix "{\\medskip\\hfill\\large\\textsf{\\textbf{" 
     3heading_suffix "}}\\hfill}\\medskip\\nopagebreak\n" 
     4 
    45delim_0 "\\dotfill~" 
     6delim_1 "\\dotfill~" 
     7delim_2 "\\dotfill~" 
     8 

  • NEMO/branches/2019/dev_r11943_MERGE_2019/doc/latex/global/info_page.tex

    r11515 r12182  
    22\thispagestyle{plain} 
    33 
    4 %% ================================================================ 
    5 %% Disclaimer 
    6 %% ================================================================ 
     4% ================================================================ 
     5% Disclaimer 
     6% ================================================================ 
    77\subsubsection*{Disclaimer} 
    88 
    99Like all components of the modelling framework, 
    10 the \engine\ core engine is developed under the \href{http://www.cecill.info}{CECILL license}, 
    11 which is a French adaptation of the GNU GPL (\textbf{G}eneral \textbf{P}ublic \textbf{L}icense). 
     10the \engine~core engine is developed under the \href{http://www.cecill.info}{CECILL license}, 
     11which is a French adaptation of the GNU GPL (General Public License). 
    1212Anyone may use it freely for research purposes, and is encouraged to 
    13 communicate back to the development team its own developments and improvements. 
     13communicate back to the NEMO team its own developments and improvements. 
    1414 
    1515The model and the present document have been made available as a service to the community. 
    … …  
    1818Users are encouraged to bring them to our attention. 
    1919 
    20 The authors assume no responsibility for problems, errors, or incorrect usage of \NEMO. 
     20The authors assume no responsibility for problems, errors, or incorrect usage of NEMO. 
    2121 
    22 %% ================================================================ 
    23 %% External resources 
    24 %% ================================================================ 
     22% ================================================================ 
     23% External resources 
     24% ================================================================ 
    2525\subsubsection*{Other resources} 
    26 \label{resources} 
    2726 
    2827Additional information can be found on: 
    2928\begin{itemize} 
    30 \item \faWordpress\ the \href{http://www.nemo-ocean.eu}{website} of the project detailing several 
     29\item the \href{http://www.nemo-ocean.eu}{website} of the project detailing several 
    3130  associated applications and an exhaustive users bibliography 
    32 \item \faCodeFork\ the \href{http://forge.ipsl.jussieu.fr/nemo}{development platform} of 
    33   the model with the code repository for the shared reference and some main resources 
    34   (wiki, ticket system, forums, \ldots) \\ 
    35   \faGithub\ the \href{http://github.com/NEMO-ocean/NEMO-examples} 
    36   {repository of the demonstration cases} for research or training 
    37 \item \faCloudDownload\ the \href{http://zenodo.org/communities/nemo-ocean}{online archive} 
    38   delivering the publications issued by the consortium (manuals, reports, datasets, \ldots) 
    39 \item \faEnvelope\ two mailing lists: 
     31\item the \href{http://forge.ipsl.jussieu.fr/nemo}{development platform} of the model with 
     32  the code repository and some main resources (wiki, ticket system, forums, \ldots) 
     33\item the \href{http://zenodo.org/communities/nemo-ocean}{online archive} 
     34  delivering the publications issued by the consortium 
     35\item two mailing lists: 
    4036  the \href{http://listes.ipsl.fr/sympa/info/nemo-newsletter}{newsletter} for 
    4137  top-down communications from the project 
    … …  
    4541\end{itemize} 
    4642 
    47 %% ================================================================ 
    48 %% Citation 
    49 %% ================================================================ 
     43% ================================================================ 
     44% Citation 
     45% ================================================================ 
    5046\subsubsection*{Citation} 
    5147 
    5248Reference for papers and other publications is as follows: 
    5349 
    54 \medskip 
     50\vspace{0.5cm} 
    5551 
    56 \begin{sloppypar} 
    57   ``{\bfseries \heading}\ifdef{\subheading}{ -- \subheading}{}'', 
    58   {\em Scientific Notes of Climate Modelling Center}, \textbf{\ipslnum} --- ISSN 1288-1619, 
    59   Institut Pierre-Simon Laplace (IPSL), 
    60   \href{https://doi.org/10.5281/zenodo.\zid}{doi:10.5281/zenodo.\zid} 
    61 \end{sloppypar} 
     52%% \sloppy: workaround for breaking DOI URL 
     53\sloppy 
     54``{\bfseries \heading}'',  
     55\firstauthor and \secondauthor,  
     56{\em Scientific Notes of Climate Modelling Center}, \textbf{\ipslnum} --- ISSN 1288-1619,  
     57Institut Pierre-Simon Laplace (IPSL),  
     58\href{https://doi.org/10.5281/zenodo.\zid}{doi:10.5281/zenodo.\zid} 
    6259 
    6360\begin{figure}[b] 
    64   \begin{minipage}[c]{0.7\textwidth} 
    65     \small 
    66     \ttfamily{ 
    67       Scientific Notes of Climate Modelling Center \\ 
    68       ISSN 1288-1619                               \\ 
     61  \begin{minipage}[c]{0.72\textwidth} 
     62    \small\ttfamily{Scientific Notes of Climate Modelling Center \\ 
     63      ISSN 1288-1619                                             \\ 
    6964      Institut Pierre-Simon Laplace (IPSL) 
    7065    } 
    … …  
    7570  \end{minipage} 
    7671\end{figure} 
     72 

  • NEMO/branches/2019/dev_r11943_MERGE_2019/doc/latex/global/new_cmds.tex

    r11693 r12182  
    22%% ============================================================================== 
    33 
    4 %% Same slanted font for NEMO and its core engines 
    5 \newcommand{\NEMO  }{\textsl{NEMO}} 
    6 \newcommand{\OPA   }{\textsl{OPA}} 
    7 \newcommand{\SIcube}{\textsl{SI$^3$}} 
    8 \newcommand{\TOP   }{\textsl{TOP}} 
    9 \newcommand{\PISCES}{\textsl{PISCES}} 
    10 \newcommand{\NEMOVAR}{\textsl{NEMOVAR}} 
     4%% Include references and index for compilation of single subfile  
     5\newcommand{\mtoc}{\minitoc} 
     6\newcommand{\biblio}{\bibliography{../main/bibliography}} 
     7\newcommand{\pindex}{\printindex} 
    118 
    12 %% Links for external components 
    13 \newcommand{\AGRIF}{\href{http://agrif.imag.fr}{AGRIF}} 
    14 \newcommand{\CICE }{\href{http://github.com/CICE-Consortium/CICE}{CICE}} 
    15 \newcommand{\OASIS}{\href{http://portal.enes.org/oasis}{OASIS}} 
    16 \newcommand{\XIOS }{\href{http://forge.ipsl.jussieu.fr/ioserver}{XIOS}} 
    17  
    18 %% Fortran in small capitals 
    19 \newcommand{\fortran}{\textsc{Fortran}} 
    20 \newcommand{\fninety}{\textsc{Fortran 90}} 
     9%% NEMO and Fortran in small capitals 
     10\newcommand{\NEMO}{\textsc{nemo}~} 
     11\newcommand{\fortran}{\textsc{Fortran}~} 
     12\newcommand{\fninety}{\textsc{Fortran 90}~} 
    2113 
    2214%% Common aliases 
    … …  
    2618\newcommand{\ztilde}{\ensuremath{\tilde z}} 
    2719\newcommand{\stilde}{\ensuremath{\tilde s}} 
    28 \newcommand{\ie}{\ensuremath{i.e.}} 
    29 \newcommand{\eg}{\ensuremath{e.g.}} 
     20\newcommand{\ie}{\ensuremath{i.e.}~} 
     21\newcommand{\eg}{\ensuremath{e.g.}~} 
    3022 
    3123%% Inline maths 
    … …  
    3325\newcommand{\rdt}{\Delta t} 
    3426 
    35 %% Gurvan's comments 
    36 \newcommand{\cmtgm}[1]{} 
     27%% Text env. for Gurvan 
     28\newcommand{\gmcomment}[1]{} 
    3729 
    3830%% Maths 
    3931\newcommand{\lt}{\left} 
    4032\newcommand{\rt}{\right} 
    41 \newcommand{\vect}[1]{\ensuremath{ \mathbf{#1} }} 
     33\newcommand{\vect}[1]{\ensuremath{\mathbf{#1}}} 
    4234\newcommand{\pd}[2][]{\ensuremath{\frac{\partial #1}{\partial #2}}} 
    4335 
    44 %% Convert chapter/section headings to lowercase 
    45 \renewcommand{\chaptermark}[1]{\markboth{#1}{}} 
    46 \renewcommand{\sectionmark}[1]{\markright{#1}{}} 
    47  
    48 %% Retrieve month name 
    49 \renewcommand{\today}{ 
    50   \ifcase \month\or January\or February\or March\or 
    51                     April\or   May\or      June\or 
    52                     July\or    August\or   September\or 
    53                     October\or November\or December 
    54   \fi, \number \year 
    55 } 
    56  
    57 %% Link to orcid profile 
    58 \newcommand{\orcid}[1]{\href{http://orcid.org/#1}{\textcolor{orcidcolor}\aiOrcidSquare}} 
    59  
    60 %% Workaround for \listoffigures 
    61 \DeclareRobustCommand{\triad}[6][]{\ensuremath{ {}_{#2}^{#3} { \mathbb{#4}_{#1} }_{#5}^{\,#6} }} 
    62  
    63 %% New command for ToC 
    64 \newcommand{\chaptertoc}[1][Table of contents]{% 
    65   \thispagestyle{empty} 
    66   \etocsettocstyle{\addsec*{#1}}{}% 
    67   \localtableofcontents% 
    68   \vfill 
    69 } 
     36%% Workaround for issue with \listoffigures 
     37\DeclareRobustCommand{\triad}[6][]{\ensuremath{{}_{#2}^{#3}{\mathbb{#4}_{#1}}_{#5}^{\,#6}}} 

  • NEMO/branches/2019/dev_r11943_MERGE_2019/doc/latex/global/packages.tex

    r11702 r12182  
    33%% ============================================================================== 
    44 
    5 %% 'hyperref' pkg is loaded at the end of the preamble for higher compatibility 
     5\usepackage{natbib}                      %% bib 
     6\usepackage{caption}                     %% caption 
     7\usepackage{xcolor}                      %% color 
     8\usepackage{times}                       %% font 
     9\usepackage{enumitem}                    %% list 
     10\usepackage{amsmath}                     %% maths 
     11%\usepackage{fancyhdr}                    %% page 
     12\usepackage{minitoc}                     %% toc 
     13\usepackage{subfiles}                    %% subdocs 
     14\usepackage{draftwatermark}              %% watermark 
     15\usepackage{titling}                     %% titlepage 
    616 
    7 %% KOMA-script 
    8 \usepackage[footsepline=0.25pt, headsepline=0.25pt]{scrlayer-scrpage} 
    9  
    10 %% customization (layout, header/footer styles & contents, background) 
    11 \usepackage{draftwatermark} 
    12 \usepackage[margin = 2cm]{geometry} 
    13 \usepackage[pages = some]{background}   %% 'some' for title page 
    14 \usepackage[Bjornstrup]{fncychap} 
    15  
    16 %% Fonts 
    17 \usepackage{fontspec} 
    18 %% Issue with fontawesome pkg: path to FontAwesome.otf has to be hard-coded 
    19 \defaultfontfeatures{ 
    20     Path = /usr/local/texlive/2019/texmf-dist/fonts/opentype/public/fontawesome/ 
    21 } 
    22 \usepackage{academicons, fontawesome, newtxtext} 
    23  
    24 %% Formatting 
    25 \usepackage[inline]{enumitem} 
    26 \usepackage{etoc, tabularx, xcolor} 
    27  
    28 %% Graphics 
    29 \usepackage{caption, graphicx, grffile} 
    30  
    31 %% Labels 
    32 \usepackage{lastpage, natbib} 
    33  
    34 %% Mathematics 
    35 \usepackage{amsmath, amssymb, mathtools} 
    36  
    37 %% Versatility 
    38 \usepackage{subfiles} 
     17%% Extensions in bundle package 
     18\usepackage{amssymb, graphicx, tabularx, textcomp} 
     19\usepackage[utf8]{inputenc}              %% input encoding 
    3920 
    4021%% Configuration 
    41 \graphicspath{ {../../../} {../figures/} } 
     22\graphicspath{ {../../figures/} {../../figures/\engine/} } 
     23%\captionsetup{margin=10pt, font={small}, labelsep=colon, labelfont={bf}} 
     24\renewcommand{\bibfont}{\small} 
     25%\renewcommand{\bibsep}{3pt} 
    4226 
    43 %% Missing utmr8a font 
    44 \usepackage{times} 

  • NEMO/branches/2019/dev_r11943_MERGE_2019/doc/latex/global/styles.tex

    r11687 r12182  
    33%% ============================================================================== 
    44 
    5 %% Colors 
    6 \setmanualcolor 
    7 \colorlet{manualcolorshaded}{manualcolor!60} 
    8 \definecolor{orcidcolor}{HTML}{A6CE39} 
     5%\pagestyle{fancy} 
     6\bibliographystyle{../../global/ametsoc} 
     7\renewcommand{\bibpreamble}{\begin{multicols}{2}} 
     8\renewcommand{\bibpostamble}{\end{multicols}} 
     9 
     10%% Additional fonts 
     11\DeclareMathAlphabet{\mathpzc}{OT1}{pzc}{m}{it} 
    912 
    1013%% Page layout 
    11 \pagestyle{scrheadings} 
    12 \addtokomafont{pagehead}{  \sffamily              } 
    13 \addtokomafont{pagefoot}{  \sffamily \footnotesize} 
    14 \addtokomafont{pagenumber}{\sffamily \slshape     } 
    15 \addtokomafont{chapter}{\color{white}} 
    16 \ohead{} \ofoot{}   %% Clear defaults 
     14%\fancyhf{} 
     15%\fancyhead[LE,RO]{\bfseries\thepage} 
     16%\fancyhead[LO]{\bfseries\hspace{-0em}\rightmark} 
     17%\renewcommand{\sectionmark}[1]{\markright{\thesection.\ #1}} 
     18%\fancyhead[RE]{\bfseries\leftmark} 
     19%\renewcommand{\chaptermark}[1]{\markboth{#1}{}} 
     20%\renewcommand{\headrulewidth}{0.5pt} 
     21%\renewcommand{\footrulewidth}{0pt  } 
     22%\addtolength{\headheight}{2.6pt} 
    1723 
    18 %% Caption 
    19 \captionsetup{font = footnotesize, justification = justified} 
    20  
    21 %% Footnote 
    22 \renewcommand{\thefootnote}{\fnsymbol{footnote}} 
    23  
    24 %% Bibliography 
    25 \bibliographystyle{../../global/ametsoc} 
    26 \renewcommand{\bibfont}{\small} 
    27 \renewcommand{\bibpreamble }{\begin{multicols}{2}} 
    28 \renewcommand{\bibpostamble}{  \end{multicols}   } 
    2924 
    3025%% Catcodes 
    31 \makeatletter 
     26%\makeatletter 
     27%\def\LigneVerticale{\vrule height 5cm depth 2cm\hspace{0.1cm}\relax} 
     28%\def\LignesVerticales{\let\LV\LigneVerticale\LV\LV\LV\LV\LV\LV\LV\LV\LV\LV} 
     29%\def\GrosCarreAvecUnChiffre#1{ 
     30%  \rlap{\vrule height 0.8cm width 1cm depth 0.2cm} 
     31%  \rlap{\hbox to 1cm{\hss\mbox{\color{white} #1}\hss}} 
     32%  \vrule height 0pt width 1cm depth 0pt 
     33%} 
     34%\def\@makechapterhead#1{ 
     35%  \hbox{ 
     36%     \huge\LignesVerticales\hspace{-0.5cm} 
     37%     \GrosCarreAvecUnChiffre{\thechapter}\hspace{0.2cm} 
     38%     \hbox{#1} 
     39%  } 
     40%  \par\vskip 
     41%1cm 
     42%} 
     43%\def\@makeschapterhead#1{ 
     44%  \hbox{ 
     45%     \huge\LignesVerticales 
     46%     \hbox{#1} 
     47%  } 
     48%  \par\vskip 
     49%2cm 
     50%} 
     51%\def\cleardoublepage{\clearpage\if@twoside \ifodd\c@page\else 
     52%  \hbox{} 
     53%  \vspace*{\fill} 
     54%  \vspace{\fill} 
     55%  \thispagestyle{empty} 
     56%  \newpage 
     57%  \if@twocolumn\hbox{}\newpage\fi\fi\fi} 
     58%\def\@seccntformat#1{\protect\makebox[0pt][r]{\csname the#1\endcsname\quad}} 
     59%\makeatother 
    3260 
    33 %% Prevent error with tikz and namelist inclusion 
    34 \global\let\tikz@ensure@dollar@catcode=\relax 
    3561 
    36 %% First page 
    37 \backgroundsetup{ 
    38   firstpage = true, 
    39   scale = 1, angle = 0, opacity = 1, 
    40   contents = { 
    41     \begin{tikzpicture}[remember picture, overlay] 
    42       \path [fill = manualcolor] (-0.5\paperwidth, 7) rectangle (0.5\paperwidth, 10); 
    43     \end{tikzpicture} 
    44   } 
    45 } 
    46  
    47 %% Apply engine color for chapter headings: tweaking snippets from fncychap.sty 
    48 \renewcommand{\DOCH}{% 
    49   \settowidth{\py}{\CNoV\thechapter} 
    50   \addtolength{\py}{-10pt}      % Amount of space by which the 
    51 %                                  % number is shifted right 
    52   \fboxsep=0pt% 
    53   \colorbox{manualcolor}{\rule{0pt}{40pt}\parbox[b]{\textwidth}{\hfill}}% 
    54   \kern-\py\raise20pt% 
    55   \hbox{\color{manualcolorshaded}\CNoV\thechapter}\\% 
    56 } 
    57 \renewcommand{\DOTI}[1]{% 
    58   \nointerlineskip\raggedright% 
    59   \fboxsep=\myhi% 
    60   \vskip-1ex% 
    61   \colorbox{manualcolor}{\parbox[t]{\mylen}{\color{white}\CTV\FmTi{#1}}}\par\nobreak% 
    62   \vskip 40\p@% 
    63 } 
    64 \renewcommand{\DOTIS}[1]{% 
    65   \fboxsep=0pt 
    66   \colorbox{manualcolor}{\rule{0pt}{40pt}\parbox[b]{\textwidth}{\hfill}}\\% 
    67   \nointerlineskip\raggedright% 
    68   \fboxsep=\myhi% 
    69   \vskip-1ex% Remove white 1pt line 
    70   \colorbox{manualcolor}{\parbox[t]{\mylen}{\color{white}\CTV\FmTi{#1}}}\par\nobreak% 
    71   \vskip 40\p@% 
    72 } 
    73  
    74 %% Temporary fix 
    75 \def\set@curr@file#1{% 
    76   \begingroup 
    77     \escapechar\m@ne 
    78     \xdef\@curr@file{\expandafter\string\csname #1\endcsname}% 
    79   \endgroup 
    80 } 
    81 \def\quote@name#1{"\quote@@name#1\@gobble""} 
    82 \def\quote@@name#1"{#1\quote@@name} 
    83 \def\unquote@name#1{\quote@@name#1\@gobble"} 
    84  
    85 \makeatother 

  • NEMO/branches/2019/dev_r11943_MERGE_2019/doc/namelists/namsbc_blk

    r11703 r12182  
    11!----------------------------------------------------------------------- 
    2 &namsbc_blk    !   namsbc_blk  generic Bulk formula                     (ln_blk =T) 
     2&namsbc_blk    !   namsbc_blk  generic Bulk formula          (ln_blk =T) 
    33!----------------------------------------------------------------------- 
    44   !                    !  bulk algorithm : 
    5    ln_NCAR     = .false.   ! "NCAR"      algorithm   (Large and Yeager 2008) 
     5   ln_NCAR      = .true.    ! "NCAR"      algorithm   (Large and Yeager 2008) 
    66   ln_COARE_3p0 = .false.   ! "COARE 3.0" algorithm   (Fairall et al. 2003) 
    7    ln_COARE_3p5 = .false.   ! "COARE 3.5" algorithm   (Edson et al. 2013) 
    8    ln_ECMWF    = .false.   ! "ECMWF"     algorithm   (IFS cycle 31) 
     7   ln_COARE_3p6 = .false.   ! "COARE 3.6" algorithm   (Edson et al. 2013) 
     8   ln_ECMWF     = .false.   ! "ECMWF"     algorithm   (IFS cycle 45r1) 
    99      ! 
    10       rn_zqt      = 10.       !  Air temperature & humidity reference height (m) 
    11       rn_zu       = 10.       !  Wind vector reference height (m) 
    12       ln_Cd_L12   = .false.   !  air-ice drags = F(ice concentration) (Lupkes et al. 2012) 
    13       ln_Cd_L15   = .false.   !  air-ice drags = F(ice concentration) (Lupkes et al. 2015) 
    14       ln_taudif   = .false.   !  HF tau contribution: use "mean of stress module - module of the mean stress" data 
    15       rn_pfac     = 1.        !  multiplicative factor for precipitation (total & snow) 
    16       rn_efac     = 1.        !  multiplicative factor for evaporation (0. or 1.) 
    17       rn_vfac     = 0.        !  multiplicative factor for ocean & ice velocity used to 
    18       !                       !  calculate the wind stress (0.=absolute or 1.=relative winds) 
    19  
     10      rn_zqt     = 10.      !  Air temperature & humidity reference height (m) 
     11      rn_zu      = 10.      !  Wind vector reference height (m) 
     12      ln_Cd_L12  = .false.  !  air-ice drags = F(ice conc.) (Lupkes et al. 2012) 
     13      ln_Cd_L15  = .false.  !  air-ice drags = F(ice conc.) (Lupkes et al. 2015) 
     14      !                     !  - module of the mean stress" data 
     15      rn_pfac    = 1.       !  multipl. factor for precipitation (total & snow) 
     16      rn_efac    = 1.       !  multipl. factor for evaporation (0. or 1.) 
     17      rn_vfac    = 0.       !  multipl. factor for ocean & ice velocity  
     18      !                     !  used to calculate the wind stress 
     19      !                     ! (0. => absolute or 1. => relative winds) 
     20      ln_skin_cs = .false.  !  use the cool-skin parameterization 
     21      ln_skin_wl = .false.  !  use the warm-layer parameterization 
     22      !                     !   ==> only available in ECMWF and COARE algorithms 
     23      ln_humi_sph = .true.  !  humidity "sn_humi" is specific humidity  [kg/kg] 
     24      ln_humi_dpt = .false. !  humidity "sn_humi" is dew-point temperature [K] 
     25      ln_humi_rlh = .false. !  humidity "sn_humi" is relative humidity     [%] 
     26   ! 
    2027   cn_dir      = './'      !  root directory for the bulk data location 
    2128   !___________!_________________________!___________________!___________!_____________!________!___________!______________________________________!__________!_______________! 
    … …  
    2835   sn_tair     = 't_10.15JUNE2009_fill'       ,    6.        , 'T_10_MOD',   .false.   , .true. , 'yearly'  , 'weights_core_orca2_bilinear_noc.nc' , ''       , '' 
    2936   sn_humi     = 'q_10.15JUNE2009_fill'       ,    6.        , 'Q_10_MOD',   .false.   , .true. , 'yearly'  , 'weights_core_orca2_bilinear_noc.nc' , ''       , '' 
     37   sn_hpgi     = 'NONE'                       ,   24.        , 'uhpg'    ,   .false.   , .false., 'monthly' , 'weights_ERAI3D_F128_2_ORCA2_bicubic', 'UG'     , '' 
     38   sn_hpgj     = 'NONE'                       ,   24.        , 'vhpg'    ,   .false.   , .false., 'monthly' , 'weights_ERAI3D_F128_2_ORCA2_bicubic', 'VG'     , '' 
    3039   sn_prec     = 'ncar_precip.15JUNE2009_fill',   -1.        , 'PRC_MOD1',   .false.   , .true. , 'yearly'  , 'weights_core_orca2_bilinear_noc.nc' , ''       , '' 
    3140   sn_snow     = 'ncar_precip.15JUNE2009_fill',   -1.        , 'SNOW'    ,   .false.   , .true. , 'yearly'  , 'weights_core_orca2_bilinear_noc.nc' , ''       , '' 
    3241   sn_slp      = 'slp.15JUNE2009_fill'        ,    6.        , 'SLP'     ,   .false.   , .true. , 'yearly'  , 'weights_core_orca2_bilinear_noc.nc' , ''       , '' 
    33    sn_tdif     = 'taudif_core'                ,   24         , 'taudif'  ,   .false.   , .true. , 'yearly'  , 'weights_core_orca2_bilinear_noc.nc' , ''       , '' 
    3442/ 
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