Changeset 12377 for NEMO/trunk/doc


Ignore:
Timestamp:
2020-02-12T15:39:06+01:00 (12 months ago)
Author:
acc
Message:

The big one. Merging all 2019 developments from the option 1 branch back onto the trunk.

This changeset reproduces 2019/dev_r11943_MERGE_2019 on the trunk using a 2-URL merge
onto a working copy of the trunk. I.e.:

svn merge —ignore-ancestry \

svn+ssh://acc@forge.ipsl.jussieu.fr/ipsl/forge/projets/nemo/svn/NEMO/trunk \
svn+ssh://acc@forge.ipsl.jussieu.fr/ipsl/forge/projets/nemo/svn/NEMO/branches/2019/dev_r11943_MERGE_2019 ./

The —ignore-ancestry flag avoids problems that may otherwise arise from the fact that
the merge history been trunk and branch may have been applied in a different order but
care has been taken before this step to ensure that all applicable fixes and updates
are present in the merge branch.

The trunk state just before this step has been branched to releases/release-4.0-HEAD
and that branch has been immediately tagged as releases/release-4.0.2. Any fixes
or additions in response to tickets on 4.0, 4.0.1 or 4.0.2 should be done on
releases/release-4.0-HEAD. From now on future 'point' releases (e.g. 4.0.2) will
remain unchanged with periodic releases as needs demand. Note release-4.0-HEAD is a
transitional naming convention. Future full releases, say 4.2, will have a release-4.2
branch which fulfills this role and the first point release (e.g. 4.2.0) will be made
immediately following the release branch creation.

2020 developments can be started from any trunk revision later than this one.

Location:
NEMO/trunk
Files:
7 deleted
25 edited
20 copied

Legend:

Unmodified
Added
Removed
  • NEMO/trunk

    • Property svn:externals
      •  

        old new  
        33^/utils/build/mk@HEAD         mk 
        44^/utils/tools@HEAD            tools 
        5 ^/vendors/AGRIF/dev@HEAD      ext/AGRIF 
         5^/vendors/AGRIF/dev_r11615_ENHANCE-04_namelists_as_internalfiles_agrif@HEAD      ext/AGRIF 
        66^/vendors/FCM@HEAD            ext/FCM 
        77^/vendors/IOIPSL@HEAD         ext/IOIPSL 
  • NEMO/trunk/doc/README.rst

    r11761 r12377  
    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/trunk/doc/latex/.svnignore

    r11593 r12377  
    88*.ilg 
    99*.ind 
    10 *.lo* 
     10*.lof 
     11*.log 
     12*.lot 
    1113*.maf 
    1214*.mtc* 
     
    1416*.pdf 
    1517*.toc 
    16 *.xdv 
    1718_minted-* 
  • NEMO/trunk/doc/latex/NEMO/build

    • Property svn:ignore
      •  

        old new  
        1414*.pdf 
        1515*.toc 
        16 *.xdv 
        1716_minted-* 
  • NEMO/trunk/doc/latex/NEMO/main/appendices.tex

    r11567 r12377  
    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/trunk/doc/latex/NEMO/main/bibliography.bib

    r11674 r12377  
    400400} 
    401401 
    402 @article{         brodeau.barnier.ea_JPO16, 
    403   title         = "Climatologically Significant Effects of Some Approximations in the Bulk Parameterizations of Turbulent AirSea 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/trunk/doc/latex/NEMO/main/chapters.tex

    r11567 r12377  
    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/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex

    r12206 r12377  
    15801580 
    15811581%% ================================================================================================= 
    1582 \section[Harmonic analysis of tidal constituents (\texttt{\textbf{key\_diaharm}})]{Harmonic analysis of tidal constituents (\protect\key{diaharm})} 
    1583 \label{sec:DIA_diag_harm} 
    1584  
    1585 \begin{listing} 
    1586   \nlst{nam_diaharm} 
    1587   \caption{\forcode{&nam_diaharm}} 
    1588   \label{lst:nam_diaharm} 
    1589 \end{listing} 
    1590  
    1591 A module is available to compute the amplitude and phase of tidal waves. 
    1592 This on-line Harmonic analysis is actived with \key{diaharm}. 
    1593  
    1594 Some parameters are available in namelist \nam{_diaharm}{\_diaharm}: 
    1595  
    1596  - \np{nit000_han}{nit000\_han} is the first time step used for harmonic analysis 
    1597  
    1598  - \np{nitend_han}{nitend\_han} is the  last time step used for harmonic analysis 
    1599  
    1600  - \np{nstep_han}{nstep\_han}  is the  time step frequency for harmonic analysis 
    1601  
    1602 % - \np{nb_ana}{nb\_ana}     is the number of harmonics to analyse 
    1603  
    1604  - \np{tname}{tname}       is an array with names of tidal constituents to analyse 
    1605  
    1606  \np{nit000_han}{nit000\_han} and \np{nitend_han}{nitend\_han} must be between \np{nit000}{nit000} and \np{nitend}{nitend} of the simulation. 
    1607  The restart capability is not implemented. 
    1608  
    1609  The Harmonic analysis solve the following equation: 
    1610  
    1611  \[ 
    1612    h_{i} - A_{0} + \sum^{nb\_ana}_{j=1}[A_{j}cos(\nu_{j}t_{j}-\phi_{j})] = e_{i} 
    1613  \] 
    1614  
    1615 With $A_{j}$, $\nu_{j}$, $\phi_{j}$, the amplitude, frequency and phase for each wave and $e_{i}$ the error. 
    1616 $h_{i}$ is the sea level for the time $t_{i}$ and $A_{0}$ is the mean sea level. \\ 
    1617 We can rewrite this equation: 
    1618  
    1619 \[ 
    1620   h_{i} - A_{0} + \sum^{nb\_ana}_{j=1}[C_{j}cos(\nu_{j}t_{j})+S_{j}sin(\nu_{j}t_{j})] = e_{i} 
    1621 \] 
    1622  
    1623 with $A_{j}=\sqrt{C^{2}_{j}+S^{2}_{j}}$ and $\phi_{j}=arctan(S_{j}/C_{j})$. 
    1624  
    1625 We obtain in output $C_{j}$ and $S_{j}$ for each tidal wave. 
    1626  
    1627 %% ================================================================================================= 
    16281582\section[Transports across sections (\texttt{\textbf{key\_diadct}})]{Transports across sections (\protect\key{diadct})} 
    16291583\label{sec:DIA_diag_dct} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_SBC.tex

    r11693 r12377  
    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: 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_misc.tex

    r11693 r12377  
    362362 
    363363%% ================================================================================================= 
    364 \subsection{Control print} 
    365  
    366 The \np{ln_ctl}{ln\_ctl} switch was originally used as a debugging option in two modes: 
    367  
    368 \begin{enumerate} 
    369 \item {\np{ln_ctl}{ln\_ctl}: compute and print the trends averaged over the interior domain in all TRA, DYN, LDF and 
    370 ZDF modules. 
    371 This option is very helpful when diagnosing the origin of an undesired change in model results. } 
    372  
    373 \item {also \np{ln_ctl}{ln\_ctl} but using the nictl and njctl namelist parameters to check the source of differences between 
    374 mono and multi processor runs.} 
     364\subsection{Status and debugging information output} 
     365 
     366 
     367NEMO can produce a range of text information output either: in the main output 
     368file (ocean.output) written by the normal reporting processor (narea == 1) or various 
     369specialist output files (e.g. layout.dat, run.stat, tracer.stat etc.). Some, for example 
     370run.stat and tracer.stat, contain globally collected values for which a single file is 
     371sufficient. Others, however, contain information that could, potentially, be different 
     372for each processing region. For computational efficiency, the default volume of text 
     373information produced is reduced to just a few files from the narea=1 processor. 
     374 
     375When more information is required for monitoring or debugging purposes, the various 
     376forms of output can be selected via the \np{sn\_cfctl} structure. As well as simple 
     377on-off switches this structure also allows selection of a range of processors for 
     378individual reporting (where appropriate) and a time-increment option to restrict 
     379globally collected values to specified time-step increments. 
     380 
     381Most options within the structure are influenced by the top-level switches shown here 
     382with their default settings: 
     383 
     384\begin{verbatim} 
     385   sn_cfctl%l_allon  = .FALSE.    ! IF T activate all options. If F deactivate all unless l_config is T 
     386     sn_cfctl%l_config = .TRUE.     ! IF .true. then control which reports are written with the following 
     387\end{verbatim} 
     388 
     389The first switch is a convenience option which can be used to switch on and off all 
     390sub-options. However, if it is false then switching off all sub-options is only done 
     391if \texttt{sn_cfctl%l\_config} is also false. Specifically, the logic is: 
     392 
     393\begin{verbatim} 
     394  IF ( sn_cfctl%l_allon ) THEN 
     395    set all suboptions .TRUE. 
     396    and set procmin, procmax and procincr so that all regions are selected ([0,10000000,1], respectively) 
     397  ELSEIF ( sn_cfctl%l_config ) THEN 
     398    honour individual settings of the suboptions from the namelist 
     399  ELSE 
     400    set all suboptions .FALSE. 
     401  ENDIF 
     402\end{verbatim} 
     403 
     404Details of the suboptions follow but first an explanation of the stand-alone option: 
     405\texttt{sn_cfctl%l_glochk}.  This option modifies the action of the early warning checks 
     406carried out in \textt{stpctl.F90}. These checks detect probable numerical instabilites 
     407by searching for excessive sea surface heights or velocities and salinity values 
     408outside a sensible physical range. If breaches are detected then the default behaviour 
     409is to locate and report the local indices of the grid-point in breach. These indices 
     410are included in the error message that precedes the model shutdown. When true, 
     411\texttt{sn_cfctl%l_glochk} modifies this action by performing a global location of 
     412the various minimum and maximum values and the global indices are reported. This has 
     413some value in locating the most severe error in cases where the first detected error 
     414may not be the worst culprit. 
     415 
     416\subsubsection{Control print suboptions} 
     417 
     418The options that can be individually selected fall into three categories: 
     419 
     420\begin{enumerate} \item{Time step progress information} This category includes 
     421\texttt{run.stat} and \texttt{tracer.stat} files which record certain physical and 
     422passive tracer metrics (respectively). Typical contents of \texttt{run.stat} include 
     423global maximums of ssh, velocity; and global minimums and maximums of temperature 
     424and salinity.  A netCDF version of \texttt{run.stat} (\texttt{run.stat.nc}) is also 
     425produced with the same time-series data and this can easily be expanded to include 
     426extra monitoring information.  \texttt{tracer.stat} contains the volume-weighted 
     427average tracer value for each passive tracer. Collecting these metrics involves 
     428global communications and will impact on model efficiency so both these options are 
     429disabled by default by setting the respective options, \texttt{sn\_cfctl%runstat} and 
     430\texttt{sn\_cfctl%trcstat} to false. A compromise can be made by activating either or 
     431both of these options and setting the \texttt{sn\_cfctl%timincr} entry to an integer 
     432value greater than one. This increment determines the time-step frequency at which 
     433the global metrics are collected and reported.  This increment also applies to the 
     434time.step file which is otherwise updated every timestep. 
     435\item{One-time configuration information/progress logs} 
     436 
     437Some run-time configuration information and limited progress information is always 
     438produced by the first ocean process. This includes the \texttt{ocean.output} file 
     439which reports on all the namelist options read by the model and remains open to catch 
     440any warning or error messages generated during execution. A \texttt{layout.dat} 
     441file is also produced which details the MPI-decomposition used by the model. The 
     442suboptions: \texttt{sn\_cfctl%oceout} and \texttt{sn\_cfctl%layout} can be used 
     443to activate the creation of these files by all ocean processes.  For example, 
     444when \texttt{sn\_cfctl%oceout} is true all processors produce their own version of 
     445\texttt{ocean.output}.  All files, beyond the the normal reporting processor (narea == 1), are 
     446named with a \_XXXX extension to their name, where XXXX is a 4-digit area number (with 
     447leading zeros, if required). This is useful as a debugging aid since all processes can 
     448report their local conditions. Note though that these files are buffered on most UNIX 
     449systems so bug-hunting efforts using this facility should also utilise the \fortran: 
     450 
     451\begin{verbatim}  
     452   CALL FLUSH(numout) 
     453\end{verbatim} 
     454 
     455statement after any additional write statements to ensure that file contents reflect 
     456the last model state. Associated with the \texttt{sn\_cfctl%oceout} option is the 
     457additional \texttt{sn\_cfctl%oasout} suboption. This does not activate its own output 
     458file but rather activates the writing of addition information regarding the OASIS 
     459configuration when coupling via oasis and the sbccpl routine. This information is 
     460written to any active \texttt{ocean.output} files. 
     461\item{Control sums of trends for debugging} 
     462 
     463NEMO includes an option for debugging reproducibility differences between 
     464a MPP and mono-processor runs.  This is somewhat dated and clearly only 
     465useful for this purpose when dealing with configurations that can be run 
     466on a single processor. The full details can be found in this report: \href{ 
     467http://forge.ipsl.jussieu.fr/nemo/attachment/wiki/Documentation/prtctl_NEMO_doc_v2.pdf}{The 
     468control print option in NEMO} The switches to activate production of the control sums 
     469of trends for either the physics or passive tracers are the \texttt{sn\_cfctl%prtctl} 
     470and \texttt{sn\_cfctl%prttrc} suboptions, respectively. Although, perhaps, of limited use for its 
     471original intention, the ability to produce these control sums of trends in specific 
     472areas provides another tool for diagnosing model behaviour.  If only the output from a 
     473select few regions is required then additional options are available to activate options 
     474for only a simple subset of processing regions. These are: \texttt{sn\_cfctl%procmin}, 
     475\texttt{sn\_cfctl%procmax} and \texttt{sn\_cfctl%procincr} which can be used to specify 
     476the minimum and maximum active areas and the increment. The default values are set 
     477such that all regions will be active. Note this subsetting can also be used to limit 
     478which additional \texttt{ocean.output} and \texttt{layout.dat} files are produced if 
     479those suboptions are active. 
     480 
    375481\end{enumerate} 
    376482 
    377 However, in recent versions it has also been used to force all processors to assume the 
    378 reporting role. Thus when \np{ln_ctl}{ln\_ctl} is true all processors produce their own versions 
    379 of files such as: ocean.output, layout.dat, etc.  All such files, beyond the the normal 
    380 reporting processor (narea == 1), are named with a \_XXXX extension to their name, where 
    381 XXXX is a 4-digit area number (with leading zeros, if required). Other reporting files 
    382 such as run.stat (and its netCDF counterpart: run.stat.nc) and tracer.stat contain global 
    383 information and are only ever produced by the reporting master (narea == 1). For version 
    384 4.0 a start has been made to return \np{ln_ctl}{ln\_ctl} to its original function by introducing 
    385 a new control structure which allows finer control over which files are produced. This 
    386 feature is still evolving but it does already allow the user to: select individually the 
    387 production of run.stat and tracer.stat files and to toggle the production of other files 
    388 on processors other than the reporting master. These other reporters can be a simple 
    389 subset of processors as defined by a minimum, maximum and incremental processor number. 
    390  
    391 Note, that production of the run.stat and tracer.stat files require global communications. 
    392 For run.stat, these are global min and max operations to find metrics such as the gloabl 
    393 maximum velocity. For tracer.stat these are global sums of tracer fields. To improve model 
    394 performance these operations are disabled by default and, where necessary, any use of the 
    395 global values have been replaced with local calculations. For example, checks on the CFL 
    396 criterion are now done on the local domain and only reported if a breach is detected. 
    397  
    398 Experienced users may wish to still monitor this information as a check on model progress. 
    399 If so, the best compromise will be to activate the files with: 
    400  
    401 \begin{verbatim} 
    402      sn_cfctl%l_config = .TRUE. 
    403        sn_cfctl%l_runstat = .TRUE. 
    404        sn_cfctl%l_trcstat = .TRUE. 
    405 \end{verbatim} 
    406  
    407 and to use the new time increment setting to ensure the values are collected and reported 
    408 at a suitably long interval. For example: 
    409  
    410 \begin{verbatim} 
    411        sn_cfctl%ptimincr  = 25 
    412 \end{verbatim} 
    413  
    414 will carry out the global communications and write the information every 25 timesteps. This 
    415 increment also applies to the time.step file which is otherwise updated every timestep. 
     483 
     484   sn_cfctl%l_glochk = .FALSE.    ! Range sanity checks are local (F) or global (T). Set T for debugging only 
     485   sn_cfctl%l_allon  = .FALSE.    ! IF T activate all options. If F deactivate all unless l_config is T 
     486     sn_cfctl%l_config = .TRUE.     ! IF .true. then control which reports are written with the following 
     487       sn_cfctl%l_runstat = .FALSE. ! switches and which areas produce reports with the proc integer settings. 
     488       sn_cfctl%l_trcstat = .FALSE. ! The default settings for the proc integers should ensure 
     489       sn_cfctl%l_oceout  = .FALSE. ! that  all areas report. 
     490       sn_cfctl%l_layout  = .FALSE. ! 
     491       sn_cfctl%l_prtctl  = .FALSE. ! 
     492       sn_cfctl%l_prttrc  = .FALSE. ! 
     493       sn_cfctl%l_oasout  = .FALSE. ! 
     494       sn_cfctl%procmin   = 0       ! Minimum area number for reporting [default:0] 
     495       sn_cfctl%procmax   = 1000000 ! Maximum area number for reporting [default:1000000] 
     496       sn_cfctl%procincr  = 1       ! Increment for optional subsetting of areas [default:1] 
     497       sn_cfctl%ptimincr  = 1       ! Timestep increment for writing time step progress info 
     498 
     499 
    416500 
    417501\subinc{\input{../../global/epilogue}} 
  • NEMO/trunk/doc/latex/SI3/build

    • Property svn:ignore
      •  

        old new  
        1414*.pdf 
        1515*.toc 
        16 *.xdv 
        1716_minted-* 
  • NEMO/trunk/doc/latex/SI3/main/chapters.tex

    r11537 r12377  
    11\subfile{../subfiles/todolist} 
     2 
     3\subfile{../subfiles/introduction}               % Introduction 
    24 
    35\subfile{../subfiles/chap_model_basics} 
  • NEMO/trunk/doc/latex/TOP/build

    • Property svn:ignore
      •  

        old new  
        1414*.pdf 
        1515*.toc 
        16 *.xdv 
        1716_minted-* 
  • NEMO/trunk/doc/latex/TOP/main/chapters.tex

    r11591 r12377  
     1\subfile{../subfiles/introduction} 
    12\subfile{../subfiles/model_description} 
    23\subfile{../subfiles/model_setup} 
  • NEMO/trunk/doc/latex/global

    • Property svn:ignore set to
      *.aux
  • NEMO/trunk/doc/latex/global/document.tex

    r11693 r12377  
    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 
    1212%% Document layout 
    13 \documentclass[fontsize = 10pt, twoside, abstract]{scrreprt} 
     13\documentclass[draft]{scrreprt} 
    1414 
    15 %% Load manual configuration 
    16 \input{../../global/prologue} 
     15%% Load the configuration of the manual 
     16\input{../main/definitions} 
     17 
     18%% Load global *.tex files 
     19\input{../../global/preamble} 
     20 
     21\dominitoc 
     22 
     23%% Launch the creation of the indexes 
     24\input{../../global/indexes} 
     25 
    1726 
    1827%% End of common preamble between main and sub-files 
    1928%% Override custom cmds for full manual compilation 
    20 \newcommand{\subinc}[1]{#1} 
    21 \newcommand{\subexc}[1]{} 
     29\newcommand{\onlyinsubfile}[1]{#1} 
     30\newcommand{\notinsubfile}[1]{} 
    2231 
    2332\begin{document} 
    2433 
    25 \renewcommand{\subinc}[1]{} 
    26 \renewcommand{\subexc}[1]{#1} 
     34\renewcommand{\onlyinsubfile}[1]{} 
     35\renewcommand{\notinsubfile}[1]{#1} 
     36 
     37\renewcommand{\biblio}{} 
     38\renewcommand{\pindex}{} 
    2739 
    2840 
    2941%% Frontmatter 
    30 %% ================================================================================================= 
     42%% ============================================================================== 
    3143 
    32 \pagenumbering{gobble}   %% Disable page numbering temporarily 
     44\pagenumbering{gobble} 
    3345 
    3446%% Title page 
    3547\input{../../global/frontpage} 
    3648 
    37 %% Footer for introductory parts (no header by cleaning default) 
    38 \ofoot[]{\engine\ Reference Manual} \ifoot[]{\pagemark} 
     49\maketitle 
     50\emptythanks 
    3951 
    4052%% Information page (2nd page) 
    4153\input{../../global/info_page} 
    4254 
    43 \listoffigures 
    44 \listoflistings 
    45 \listoftables 
    46  
    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 
  • NEMO/trunk/doc/latex/global/frontpage.tex

    r11688 r12377  
    11 
    2 \begin{titlepage} 
    3 %  \newgeometry{hmargin = 1.5cm, vmargin = 3cm} 
    4   \setlength{\parindent}{0pt} 
     2\title{\heading} 
     3\author{\firstauthor \and \secondauthor\thanks{\protect\input{thanks}}} 
     4\date{\today} 
    55 
     6\pretitle{ 
    67  \begin{center} 
    7     \begin{minipage}{0.3\textwidth} 
    8       \includegraphics[height=1.5cm]{logos/NEMO_grey} 
    9     \end{minipage}\begin{minipage}{0.6\textwidth} 
    10       \begin{center} 
    11       \Large\slshape 
    12       \textbf{N}ucleus for \textbf{E}uropean \textbf{M}odelling of the \textbf{O}cean \\ 
    13       \medskip 
    14       \hyperref[resources]{\textcolor{black}{ 
    15           \faWordpress \hspace{0.75cm} \faCodeFork      \hspace{0.75cm} 
    16           \faGithub    \hspace{0.75cm} \faCloudDownload \hspace{0.75cm} \faEnvelope 
    17         } 
    18       } 
    19       \end{center} 
    20     \end{minipage} 
     8\begin{figure}[H] 
     9  \begin{minipage}[c]{0.35\textwidth} 
     10    \href{http://www.nemo-ocean.eu}{\includegraphics[width=0.7\textwidth]{logos/NEMO_grey}} 
     11  \end{minipage} 
     12  \hfill 
     13  \begin{minipage}[c]{0.65\textwidth} 
     14    \centering 
     15    \large{\em{{N}ucleus for {E}uropean {M}odelling of the {O}cean}} 
     16  \end{minipage} 
     17\end{figure} 
     18\vfill 
     19    \Huge 
     20} 
     21\posttitle{\par\end{center}\vskip 0.5em} 
     22\preauthor{\begin{center}\Large\lineskip0.5em\begin{tabular}[t]{c}} 
     23\postauthor{\end{tabular}\par\end{center}} 
     24\predate{ 
     25  \vfill 
     26  \begin{center} 
     27    \large Version \version --- 
     28} 
     29\postdate{ 
     30    \par~\\ 
     31    \href{http://doi.org/10.5281/zenodo.\zid}{\includegraphics{{badges/zenodo.\zid}.pdf}} 
    2132  \end{center} 
     33  \vfill 
     34  \begin{center} 
     35    \href{http://www.cmcc.it}{          \includegraphics[height=0.055\textheight]{logos/CMCC}} 
     36    \hspace{0.5em} 
     37    \href{http://www.cnrs.fr}{          \includegraphics[height=0.055\textheight]{logos/CNRS}} 
     38    \hspace{0.9em} 
     39    \href{http://www.mercator-ocean.fr}{\includegraphics[height=0.055\textheight]{logos/MOI} } 
     40    \hspace{0.45em} 
     41    \href{http://www.metoffice.gov.uk}{ \includegraphics[height=0.055\textheight]{logos/UKMO}} 
     42    \hspace{0.5em} 
     43    \href{http://nerc.ukri.org}{        \includegraphics[height=0.055\textheight]{logos/NERC}} \\ 
     44    \large{{\em{C}ommunity \hspace{1.5em} {O}cean \hspace{1.5em} {M}odel}} 
     45  \end{center} 
     46} 
    2247 
    23   \spacetop 
    24   \textcolor{white}{\fontsize{0.8cm}{0.8cm}\selectfont\textbf{\heading}} 
    25   \ifdef{\subheading}{ 
    26     \medskip 
    27     \par 
    28     \textcolor{white}{\Huge \subheading} 
    29   }{} 
    30   \spacedown 
     48\thanksmarkseries{fnsymbol} 
    3149 
    32   \begin{center} 
    33     \LARGE Version \version\ -\ \today \\ 
    34     \medskip 
    35     \href{http://doi.org/10.5281/zenodo.\zid}{ \includegraphics{badges/zenodo.\zid} } 
    36   \end{center} 
    37  
    38   \vfill 
    39  
    40   \begin{minipage}{\authorswidth} 
    41     \raggedleft 
    42     \input{authors} 
    43   \end{minipage}\hspace{15pt}\begin{minipage}{0.02\linewidth} 
    44     \rule{1pt}{\rulelenght} 
    45   \end{minipage}\hspace{ 5pt}\begin{minipage}{\abstractwidth} 
    46     \begin{abstract} 
    47       \input{abstract} 
    48     \end{abstract} 
    49   \end{minipage} 
    50  
    51   \vfill 
    52  
    53   \begin{center} 
    54     \Large 
    55     \href{http://www.cmcc.it          }{ \includegraphics[height=1cm]{logos/CMCC} } \hspace{0.25cm} 
    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/trunk/doc/latex/global/highlighting.tex

    r11572 r12377  
    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/trunk/doc/latex/global/index.ist

    r11584 r12377  
    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/trunk/doc/latex/global/info_page.tex

    r11515 r12377  
    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/trunk/doc/latex/global/new_cmds.tex

    r11693 r12377  
    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/trunk/doc/latex/global/packages.tex

    r11702 r12377  
    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/trunk/doc/latex/global/styles.tex

    r11687 r12377  
    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/trunk/doc/namelists/namctl

    r10601 r12377  
    22&namctl        !   Control prints                                       (default: OFF) 
    33!----------------------------------------------------------------------- 
    4    ln_ctl = .FALSE.                 ! Toggle all report printing on/off (T/F); Ignored if sn_cfctl%l_config is T 
     4   sn_cfctl%l_glochk = .FALSE.    ! Range sanity checks are local (F) or global (T). Set T for debugging only 
     5   sn_cfctl%l_allon  = .FALSE.    ! IF T activate all options. If F deactivate all unless l_config is T 
    56     sn_cfctl%l_config = .TRUE.     ! IF .true. then control which reports are written with the following 
    67       sn_cfctl%l_runstat = .FALSE. ! switches and which areas produce reports with the proc integer settings. 
     
    89       sn_cfctl%l_oceout  = .FALSE. ! that  all areas report. 
    910       sn_cfctl%l_layout  = .FALSE. ! 
    10        sn_cfctl%l_mppout  = .FALSE. ! 
    11        sn_cfctl%l_mpptop  = .FALSE. ! 
     11       sn_cfctl%l_prtctl  = .FALSE. ! 
     12       sn_cfctl%l_prttrc  = .FALSE. ! 
     13       sn_cfctl%l_oasout  = .FALSE. ! 
    1214       sn_cfctl%procmin   = 0       ! Minimum area number for reporting [default:0] 
    1315       sn_cfctl%procmax   = 1000000 ! Maximum area number for reporting [default:1000000] 
  • NEMO/trunk/doc/namelists/namsbc_blk

    r11703 r12377  
    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/ 
Note: See TracChangeset for help on using the changeset viewer.