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

Since March 2022 along with NEMO 4.2 release, the code development moved to a self-hosted GitLab.
This present forge is now archived and remained online for history.
Changeset 12928 for NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc – NEMO

Ignore:
Timestamp:
2020-05-14T21:46:00+02:00 (4 years ago)
Author:
smueller
Message:

Synchronizing with /NEMO/trunk@12925 (ticket #2170)

Location:
NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser
Files:
21 deleted
80 edited
38 copied

Legend:

Unmodified
Added
Removed

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser

    • Property svn:externals

      •  

        old new  
        66^/vendors/FCM@HEAD            ext/FCM 
        77^/vendors/IOIPSL@HEAD         ext/IOIPSL 
         8 
         9# SETTE 
         10^/utils/CI/sette@HEAD         sette 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/.svnignore

    r12178 r12928  
    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/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/build

    • Property svn:ignore

      •  

        old new  
        1414*.pdf 
        1515*.toc 
        16 *.xdv 
        1716_minted-* 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/main

    • Property svn:externals deleted

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/main/appendices.tex

    r12178 r12928  
    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_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/main/bibliography.bib

    r12178 r12928  
    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", 
    … …  
    16121612  author        = "A. N. Kolmogorov", 
    16131613  year          = "1942" 
     1614} 
     1615 
     1616@article{         kraus.turner_tellus67, 
     1617  author = {Kraus, E.B. and Turner, J.}, 
     1618  journal = {Tellus}, 
     1619  pages = {98--106}, 
     1620  title = {A one dimensional model of the seasonal thermocline {II}. {T}he general theory and its consequences}, 
     1621  volume = {19}, 
     1622  year = {1967} 
     1623} 
     1624 
     1625@article{        large.ea_RG97, 
     1626  author        = "Large, W. G. and McWilliams, J. C. and Doney, S. C.", 
     1627  doi           = "10.1029/94RG01872", 
     1628  journal       = "Reviews of Geophysics", 
     1629  number        = {4}, 
     1630  pages         = {363--403}, 
     1631  publisher     = {AGU}, 
     1632  title         = "Oceanic vertical mixing: {A} review and a model with a nonlocal boundary layer parameterization", 
     1633  year          = "1994" 
    16141634} 
    16151635 
    … …  
    21842204} 
    21852205 
     2206@article{mcwilliams.ea_JFM97, 
     2207   author = {McWilliams, James C. and Sullivan, Peter P. and Moeng, Chin-Hoh}, 
     2208   doi = {10.1017/S0022112096004375}, 
     2209   journal = {Journal of Fluid Mechanics}, 
     2210   pages = {1--30}, 
     2211   title = {Langmuir turbulence in the ocean}, 
     2212   volume = {334}, 
     2213   year = {1997}, 
     2214} 
    21862215@article{         mellor.blumberg_JPO04, 
    21872216  title         = "Wave Breaking and Ocean Surface Layer Thermal Response", 
    … …  
    31053134  doi           = "10.1029/92jc00911" 
    31063135} 
     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_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/main/chapters.tex

    r12178 r12928  
    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_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/apdx_DOMAINcfg.tex

    r12178 r12928  
    113113\begin{figure}[!tb] 
    114114  \centering 
    115   \includegraphics[width=0.66\textwidth]{Fig_zgr} 
     115  \includegraphics[width=0.66\textwidth]{DOMCFG_zgr} 
    116116  \caption[DOMAINcfg: default vertical mesh for ORCA2]{ 
    117117    Default vertical mesh for ORCA2: 30 ocean levels (L30). 
    … …  
    444444\begin{figure}[!ht] 
    445445  \centering 
    446   \includegraphics[width=0.66\textwidth]{Fig_sco_function} 
     446  \includegraphics[width=0.66\textwidth]{DOMCFG_sco_function} 
    447447  \caption[DOMAINcfg: examples of the stretching function applied to a seamount]{ 
    448448    Examples of the stretching function applied to a seamount; 
    … …  
    493493\begin{figure}[!ht] 
    494494  \centering 
    495   \includegraphics[width=0.66\textwidth]{Fig_DOM_compare_coordinates_surface} 
     495  \includegraphics[width=0.66\textwidth]{DOMCFG_compare_coordinates_surface} 
    496496  \caption[DOMAINcfg: comparison of $s$- and $z$-coordinate]{ 
    497497    A comparison of the \citet{song.haidvogel_JCP94} $S$-coordinate (solid lines), 
    … …  
    530530This option is described in the Report by Levier \textit{et al.} (2007), available on the \NEMO\ web site. 
    531531 
    532 \onlyinsubfile{\input{../../global/epilogue}} 
     532\subinc{\input{../../global/epilogue}} 
    533533 
    534534\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/apdx_algos.tex

    r12178 r12928  
    311311\begin{figure}[!ht] 
    312312  \centering 
    313   \includegraphics[width=0.66\textwidth]{Fig_ISO_triad} 
     313  %\includegraphics[width=0.66\textwidth]{ALGOS_ISO_triad} 
    314314  \caption[Triads used in the Griffies's like iso-neutral diffision scheme for 
    315315    $u$- and $w$-components)]{ 
    … …  
    461461where $A_{e}$ is the eddy induced velocity coefficient, 
    462462and $r_i$ and $r_j$ the slopes between the iso-neutral and the geopotential surfaces. 
    463 %%gm wrong: to be modified with 2 2D streamfunctions 
     463\cmtgm{Wrong: to be modified with 2 2D streamfunctions} 
    464464In other words, the eddy induced velocity can be derived from a vector streamfuntion, $\phi$, 
    465465which is given by $\phi = A_e\,\textbf{r}$ as $\textbf{U}^*  = \textbf{k} \times \nabla \phi$. 
    466 %%end gm 
    467466 
    468467A traditional way to implement this additional advection is to add it to the eulerian velocity prior to 
    … …  
    822821\ie\ the variance of the tracer is preserved by the discretisation of the skew fluxes. 
    823822 
    824 \onlyinsubfile{\input{../../global/epilogue}} 
     823\subinc{\input{../../global/epilogue}} 
    825824 
    826825\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/apdx_diff_opers.tex

    r12178 r12928  
    421421that is a Laplacian diffusion is applied on momentum along the coordinate directions. 
    422422 
    423 \onlyinsubfile{\input{../../global/epilogue}} 
     423\subinc{\input{../../global/epilogue}} 
    424424 
    425425\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/apdx_invariants.tex

    r12178 r12928  
    2525\clearpage 
    2626 
    27 %%%  Appendix put in gmcomment as it has not been updated for \zstar and s coordinate 
     27%%%  Appendix put in cmtgm as it has not been updated for \zstar and s coordinate 
    2828%I'm writting this appendix. It will be available in a forthcoming release of the documentation 
    2929 
    30 %\gmcomment{ 
     30%\cmtgm{ 
    3131 
    3232%% ================================================================================================= 
    … …  
    270270 
    271271%gm comment 
    272 \gmcomment{ 
     272\cmtgm{ 
    273273The last equality comes from the following equation, 
    274274\begin{flalign*} 
    … …  
    583583\label{subsec:INVARIANTS_2.6} 
    584584 
    585 \gmcomment{ 
     585\cmtgm{ 
    586586  A pressure gradient has no contribution to the evolution of the vorticity as the curl of a gradient is zero. 
    587587  In the $z$-coordinate, this property is satisfied locally on a C-grid with 2nd order finite differences 
    … …  
    694694 
    695695%gm comment 
    696 \gmcomment{ 
     696\cmtgm{ 
    697697  \begin{flalign*} 
    698698    \sum\limits_{i,j,k} \biggl\{   p_t\;\partial_t b_t   \biggr\}                                &&&\\ 
    … …  
    14791479%} 
    14801480 
    1481 \onlyinsubfile{\input{../../global/epilogue}} 
     1481\subinc{\input{../../global/epilogue}} 
    14821482 
    14831483\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/apdx_s_coord.tex

    r12178 r12928  
    584584the expression of the 3D divergence in the $s-$coordinates established above. 
    585585 
    586 \onlyinsubfile{\input{../../global/epilogue}} 
     586\subinc{\input{../../global/epilogue}} 
    587587 
    588588\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/apdx_triads.tex

    r12178 r12928  
    212212\begin{figure}[tb] 
    213213  \centering 
    214   \includegraphics[width=0.66\textwidth]{Fig_GRIFF_triad_fluxes} 
     214  \includegraphics[width=0.66\textwidth]{TRIADS_GRIFF_triad_fluxes} 
    215215  \caption[Triads arrangement and tracer gradients to give lateral and vertical tracer fluxes]{ 
    216216    (a) Arrangement of triads $S_i$ and tracer gradients to 
    … …  
    272272\begin{figure}[tb] 
    273273  \centering 
    274   \includegraphics[width=0.66\textwidth]{Fig_GRIFF_qcells} 
     274  \includegraphics[width=0.66\textwidth]{TRIADS_GRIFF_qcells} 
    275275  \caption[Triad notation for quarter cells]{ 
    276276    Triad notation for quarter cells. 
    … …  
    657657\begin{figure}[h] 
    658658  \centering 
    659   \includegraphics[width=0.66\textwidth]{Fig_GRIFF_bdry_triads} 
     659  \includegraphics[width=0.66\textwidth]{TRIADS_GRIFF_bdry_triads} 
    660660  \caption[Boundary triads]{ 
    661661    (a) Uppermost model layer $k=1$ with $i,1$ and $i+1,1$ tracer points (black dots), 
    … …  
    808808\begin{figure}[h] 
    809809  \centering 
    810   \includegraphics[width=0.66\textwidth]{Fig_GRIFF_MLB_triads} 
     810  \includegraphics[width=0.66\textwidth]{TRIADS_GRIFF_MLB_triads} 
    811811  \caption[Definition of mixed-layer depth and calculation of linearly tapered triads]{ 
    812812    Definition of mixed-layer depth and calculation of linearly tapered triads. 
    … …  
    11771177\] 
    11781178 
    1179 \onlyinsubfile{\input{../../global/epilogue}} 
     1179\subinc{\input{../../global/epilogue}} 
    11801180 
    11811181\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_ASM.tex

    r12178 r12928  
    194194\end{clines} 
    195195 
    196 \onlyinsubfile{\input{../../global/epilogue}} 
     196\subinc{\input{../../global/epilogue}} 
    197197 
    198198\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_DIA.tex

    r12178 r12928  
    5555A complete description of the use of this I/O server is presented in the next section. 
    5656 
    57 %\gmcomment{                    % start of gmcomment 
     57%\cmtgm{                    % start of gmcomment 
    5858 
    5959%% ================================================================================================= 
    … …  
    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} 
    … …  
    19671921\begin{figure}[!t] 
    19681922  \centering 
    1969   \includegraphics[width=0.66\textwidth]{Fig_mask_subasins} 
     1923  \includegraphics[width=0.66\textwidth]{DIA_mask_subasins} 
    19701924  \caption[Decomposition of the World Ocean to compute transports as well as 
    19711925  the meridional stream-function]{ 
    … …  
    20221976 
    20231977%% ================================================================================================= 
    2024 \subsection{Top middle and bed hourly output} 
    2025  
    2026 \begin{listing} 
    2027   \nlst{nam_diatmb} 
    2028   \caption{\forcode{&nam_diatmb}} 
    2029   \label{lst:nam_diatmb} 
    2030 \end{listing} 
    2031  
    2032 A module is available to output the surface (top), mid water and bed diagnostics of a set of standard variables. 
    2033 This can be a useful diagnostic when hourly or sub-hourly output is required in high resolution tidal outputs. 
    2034 The tidal signal is retained but the overall data usage is cut to just three vertical levels. 
    2035 Also the bottom level is calculated for each cell. 
    2036 This diagnostic is actived with the logical $ln\_diatmb$. 
    2037  
    2038 %% ================================================================================================= 
    20391978\subsection{Courant numbers} 
    20401979 
    … …  
    20612000The maximum values from the run are also copied to the ocean.output file. 
    20622001 
    2063 \onlyinsubfile{\input{../../global/epilogue}} 
     2002\subinc{\input{../../global/epilogue}} 
    20642003 
    20652004\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_DIU.tex

    r12178 r12928  
    160160\] 
    161161 
    162 \onlyinsubfile{\input{../../global/epilogue}} 
     162\subinc{\input{../../global/epilogue}} 
    163163 
    164164\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_DOM.tex

    r12178 r12928  
    6060\begin{figure} 
    6161  \centering 
    62   \includegraphics[width=0.33\textwidth]{Fig_cell} 
     62  \includegraphics[width=0.33\textwidth]{DOM_cell} 
    6363  \caption[Arrangement of variables in the unit cell of space domain]{ 
    6464    Arrangement of variables in the unit cell of space domain. 
    … …  
    151151\begin{figure} 
    152152  \centering 
    153   \includegraphics[width=0.5\textwidth]{Fig_zgr_e3} 
     153  \includegraphics[width=0.5\textwidth]{DOM_zgr_e3} 
    154154  \caption[Comparison of grid-point position, vertical grid-size and scale factors]{ 
    155155    Comparison of (a) traditional definitions of grid-point position and grid-size in the vertical, 
    … …  
    265265\begin{figure} 
    266266  \centering 
    267   \includegraphics[width=0.33\textwidth]{Fig_index_hor} 
     267  \includegraphics[width=0.33\textwidth]{DOM_index_hor} 
    268268  \caption[Horizontal integer indexing]{ 
    269269    Horizontal integer indexing used in the \fortran\ code. 
    … …  
    316316\begin{figure} 
    317317  \centering 
    318   \includegraphics[width=0.33\textwidth]{Fig_index_vert} 
     318  \includegraphics[width=0.33\textwidth]{DOM_index_vert} 
    319319  \caption[Vertical integer indexing]{ 
    320320    Vertical integer indexing used in the \fortran\ code. 
    … …  
    474474\begin{figure} 
    475475  \centering 
    476   \includegraphics[width=0.5\textwidth]{Fig_z_zps_s_sps} 
     476  \includegraphics[width=0.5\textwidth]{DOM_z_zps_s_sps} 
    477477  \caption[Ocean bottom regarding coordinate systems ($z$, $s$ and hybrid $s-z$)]{ 
    478478    The ocean bottom as seen by the model: 
    … …  
    695695\end{description} 
    696696 
    697 \onlyinsubfile{\input{../../global/epilogue}} 
     697\subinc{\input{../../global/epilogue}} 
    698698 
    699699\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_DYN.tex

    r12178 r12928  
    6767Furthermore, the tendency terms associated with the 2D barotropic vorticity balance (when \texttt{trdvor?} is defined) 
    6868can be derived from the 3D terms. 
    69 \gmcomment{STEVEN: not quite sure I've got the sense of the last sentence. does 
    70 MISC correspond to "extracting tendency terms" or "vorticity balance"?} 
     69\cmtgm{STEVEN: not quite sure I've got the sense of the last sentence. 
     70  Does MISC correspond to "extracting tendency terms" or "vorticity balance"?} 
    7171 
    7272%% ================================================================================================= 
    … …  
    153153as changes in the divergence of the barotropic transport are absorbed into the change of the level thicknesses, 
    154154re-orientated downward. 
    155 \gmcomment{not sure of this...  to be modified with the change in emp setting} 
     155\cmtgm{not sure of this...  to be modified with the change in emp setting} 
    156156In the case of a linear free surface, the time derivative in \autoref{eq:DYN_wzv} disappears. 
    157157The upper boundary condition applies at a fixed level $z=0$. 
    … …  
    287287$u$ and $v$ are located at different grid points, 
    288288a price worth paying to avoid a double averaging in the pressure gradient term as in the $B$-grid. 
    289 \gmcomment{ To circumvent this, Adcroft (ADD REF HERE) 
     289\cmtgm{ To circumvent this, Adcroft (ADD REF HERE) 
    290290Nevertheless, this technique strongly distort the phase and group velocity of Rossby waves....} 
    291291 
    … …  
    311311\begin{figure}[!ht] 
    312312  \centering 
    313   \includegraphics[width=0.66\textwidth]{Fig_DYN_een_triad} 
     313  \includegraphics[width=0.66\textwidth]{DYN_een_triad} 
    314314  \caption[Triads used in the energy and enstrophy conserving scheme (EEN)]{ 
    315315    Triads used in the energy and enstrophy conserving scheme (EEN) for 
    … …  
    516516In the vertical, the centred $2^{nd}$ order evaluation of the advection is preferred, \ie\ $u_{uw}^{ubs}$ and 
    517517$u_{vw}^{ubs}$ in \autoref{eq:DYN_adv_cen2} are used. 
    518 UBS is diffusive and is associated with vertical mixing of momentum. \gmcomment{ gm  pursue the 
     518UBS is diffusive and is associated with vertical mixing of momentum. \cmtgm{ gm  pursue the 
    519519sentence:Since vertical mixing of momentum is a source term of the TKE equation...  } 
    520520 
    … …  
    534534there is also the possibility of using a $4^{th}$ order evaluation of the advective velocity as in ROMS. 
    535535This is an error and should be suppressed soon. 
    536 \gmcomment{action :  this have to be done} 
     536\cmtgm{action :  this have to be done} 
    537537 
    538538%% ================================================================================================= 
    … …  
    846846\begin{figure}[!t] 
    847847  \centering 
    848   \includegraphics[width=0.66\textwidth]{Fig_DYN_dynspg_ts} 
     848  \includegraphics[width=0.66\textwidth]{DYN_dynspg_ts} 
    849849  \caption[Split-explicit time stepping scheme for the external and internal modes]{ 
    850850    Schematic of the split-explicit time stepping scheme for the external and internal modes. 
    … …  
    915915it is still significant as shown by \citet{levier.treguier.ea_rpt07} in the case of an analytical barotropic Kelvin wave. 
    916916 
    917 \gmcomment{               %%% copy from griffies Book 
     917\cmtgm{               %%% copy from griffies Book 
    918918 
    919919\textbf{title: Time stepping the barotropic system } 
    … …  
    10431043 
    10441044%% gm %%======>>>>   given here the discrete eqs provided to the solver 
    1045 \gmcomment{               %%% copy from chap-model basics 
     1045\cmtgm{               %%% copy from chap-model basics 
    10461046  \[ 
    10471047    % \label{eq:DYN_spg_flt} 
    … …  
    10541054  and $\mathrm {\mathbf M}$ represents the collected contributions of the Coriolis, hydrostatic pressure gradient, 
    10551055  non-linear and viscous terms in \autoref{eq:MB_dyn}. 
    1056 }   %end gmcomment 
     1056}   %end cmtgm 
    10571057 
    10581058Note that in the linear free surface formulation (\texttt{vvl?} not defined), 
    … …  
    10821082no slip or partial slip boundary conditions are applied according to the user's choice (see \autoref{chap:LBC}). 
    10831083 
    1084 \gmcomment{ 
     1084\cmtgm{ 
    10851085  Hyperviscous operators are frequently used in the simulation of turbulent flows to 
    10861086  control the dissipation of unresolved small scale features. 
    … …  
    11831183the first derivative term normal to the coast depends on the free or no-slip lateral boundary conditions chosen, 
    11841184while the third derivative terms normal to the coast are set to zero (see \autoref{chap:LBC}). 
    1185 \gmcomment{add a remark on the the change in the position of the coefficient} 
     1185\cmtgm{add a remark on the the change in the position of the coefficient} 
    11861186 
    11871187%% ================================================================================================= 
    … …  
    12521252the snow-ice mass is taken into account when computing the surface pressure gradient. 
    12531253 
    1254 \gmcomment{ missing : the lateral boundary condition !!!   another external forcing 
     1254\cmtgm{ missing : the lateral boundary condition !!!   another external forcing 
    12551255 } 
    12561256 
    … …  
    14801480\begin{figure}[!ht] 
    14811481  \centering 
    1482   \includegraphics[width=0.66\textwidth]{Fig_WAD_dynhpg} 
     1482  \includegraphics[width=0.66\textwidth]{DYN_WAD_dynhpg} 
    14831483  \caption[Combinations controlling the limiting of the horizontal pressure gradient in 
    14841484  wetting and drying regimes]{ 
    … …  
    15961596and only array swapping and Asselin filtering is done in \mdl{dynnxt}. 
    15971597 
    1598 \onlyinsubfile{\input{../../global/epilogue}} 
     1598\subinc{\input{../../global/epilogue}} 
    15991599 
    16001600\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_LBC.tex

    r12178 r12928  
    2525\clearpage 
    2626 
    27 %gm% add here introduction to this chapter 
     27\cmtgm{Add here introduction to this chapter} 
    2828 
    2929%% ================================================================================================= 
    … …  
    7979\begin{figure}[!t] 
    8080  \centering 
    81   \includegraphics[width=0.66\textwidth]{Fig_LBC_uv} 
     81  \includegraphics[width=0.66\textwidth]{LBC_uv} 
    8282  \caption[Lateral boundary at $T$-level]{ 
    8383    Lateral boundary (thick line) at T-level. 
    … …  
    104104\begin{figure}[!p] 
    105105  \centering 
    106   \includegraphics[width=0.66\textwidth]{Fig_LBC_shlat} 
     106  \includegraphics[width=0.66\textwidth]{LBC_shlat} 
    107107  \caption[Lateral boundary conditions]{ 
    108108    Lateral boundary conditions 
    … …  
    201201\begin{figure}[!t] 
    202202  \centering 
    203   \includegraphics[width=0.66\textwidth]{Fig_LBC_jperio} 
     203  \includegraphics[width=0.66\textwidth]{LBC_jperio} 
    204204  \caption[Setting of east-west cyclic and symmetric across the Equator boundary conditions]{ 
    205205    Setting of (a) east-west cyclic (b) symmetric across the Equator boundary conditions} 
    … …  
    219219\begin{figure}[!t] 
    220220  \centering 
    221   \includegraphics[width=0.66\textwidth]{Fig_North_Fold_T} 
     221  \includegraphics[width=0.66\textwidth]{LBC_North_Fold_T} 
    222222  \caption[North fold boundary in ORCA 2\deg, 1/4\deg and 1/12\deg]{ 
    223223    North fold boundary with a $T$-point pivot and cyclic east-west boundary condition ($jperio=4$), 
    … …  
    272272\begin{figure}[!t] 
    273273  \centering 
    274   \includegraphics[width=0.66\textwidth]{Fig_mpp} 
     274  \includegraphics[width=0.66\textwidth]{LBC_mpp} 
    275275  \caption{Positioning of a sub-domain when massively parallel processing is used} 
    276276  \label{fig:LBC_mpp} 
    … …  
    325325\begin{figure}[!ht] 
    326326  \centering 
    327   \includegraphics[width=0.66\textwidth]{Fig_mppini2} 
     327  \includegraphics[width=0.66\textwidth]{LBC_mppini2} 
    328328  \caption[Atlantic domain defined for the CLIPPER projet]{ 
    329329    Example of Atlantic domain defined for the CLIPPER projet. 
    … …  
    596596\begin{figure}[!t] 
    597597  \centering 
    598   \includegraphics[width=0.66\textwidth]{Fig_LBC_bdy_geom} 
     598  \includegraphics[width=0.66\textwidth]{LBC_bdy_geom} 
    599599  \caption[Geometry of unstructured open boundary]{Example of geometry of unstructured open boundary} 
    600600  \label{fig:LBC_bdy_geom} 
    … …  
    631631\begin{figure}[!t] 
    632632  \centering 
    633   \includegraphics[width=0.66\textwidth]{Fig_LBC_nc_header} 
     633  \includegraphics[width=0.66\textwidth]{LBC_nc_header} 
    634634  \caption[Header for a \protect\ifile{coordinates.bdy} file]{ 
    635635    Example of the header for a \protect\ifile{coordinates.bdy} file} 
    … …  
    708708direction of rotation). %, e.g. anticlockwise or clockwise. 
    709709 
    710 \onlyinsubfile{\input{../../global/epilogue}} 
     710\subinc{\input{../../global/epilogue}} 
    711711 
    712712\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_LDF.tex

    r12178 r12928  
    6868\label{sec:LDF_slp} 
    6969 
    70 \gmcomment{ 
     70\cmtgm{ 
    7171  we should emphasize here that the implementation is a rather old one. 
    7272  Better work can be achieved by using \citet{griffies.gnanadesikan.ea_JPO98, griffies_bk04} iso-neutral scheme. 
    … …  
    8484$r_{1f}$, $r_{1vw}$, $r_{2t}$, $r_{2vw}$ for $v$. 
    8585 
    86 %gm% add here afigure of the slope in i-direction 
     86\cmtgm{Add here afigure of the slope in i-direction} 
    8787 
    8888%% ================================================================================================= 
    … …  
    9494the diffusive fluxes in the three directions are set to zero and $T$ is assumed to be horizontally uniform, 
    9595\ie\ a linear function of $z_T$, the depth of a $T$-point. 
    96 %gm { Steven : My version is obviously wrong since I'm left with an arbitrary constant which is the local vertical temperature gradient} 
     96\cmtgm{Steven : My version is obviously wrong since 
     97  I'm left with an arbitrary constant which is the local vertical temperature gradient} 
    9798 
    9899\begin{equation} 
    … …  
    112113\end{equation} 
    113114 
    114 %gm%  caution I'm not sure the simplification was a good idea! 
     115\cmtgm{Caution I'm not sure the simplification was a good idea!} 
    115116 
    116117These slopes are computed once in \rou{ldf\_slp\_init} when \np[=.true.]{ln_sco}{ln\_sco}, 
    … …  
    144145\end{equation} 
    145146 
    146 %gm% rewrite this as the explanation is not very clear !!! 
     147\cmtgm{rewrite this as the explanation is not very clear !!!} 
    147148%In practice, \autoref{eq:LDF_slp_iso} is of little help in evaluating the neutral surface slopes. Indeed, for an unsimplified equation of state, the density has a strong dependancy on pressure (here approximated as the depth), therefore applying \autoref{eq:LDF_slp_iso} using the $in situ$ density, $\rho$, computed at T-points leads to a flattening of slopes as the depth increases. This is due to the strong increase of the $in situ$ density with depth. 
    148149 
    … …  
    173174  will include a pressure dependent part, leading to the wrong evaluation of the neutral slopes. 
    174175 
    175 %gm% 
    176176  Note: The solution for $s$-coordinate passes trough the use of different (and better) expression for 
    177177  the constraint on iso-neutral fluxes. 
    … …  
    182182    \alpha \ \textbf{F}(T) = \beta \ \textbf{F}(S) 
    183183  \] 
    184   % gm{  where vector F is ....} 
     184  \cmtgm{where vector F is ....} 
    185185 
    186186This constraint leads to the following definition for the slopes: 
    … …  
    229229This allows an iso-neutral diffusion scheme without additional background horizontal mixing. 
    230230This technique can be viewed as a diffusion operator that acts along large-scale 
    231 (2~$\Delta$x) \gmcomment{2deltax doesnt seem very large scale} iso-neutral surfaces. 
     231(2~$\Delta$x) \cmtgm{2deltax doesnt seem very large scale} iso-neutral surfaces. 
    232232The diapycnal diffusion required for numerical stability is thus minimized and its net effect on the flow is quite small when compared to the effect of an horizontal background mixing. 
    233233 
    … …  
    237237\begin{figure}[!ht] 
    238238  \centering 
    239   \includegraphics[width=0.66\textwidth]{Fig_LDF_ZDF1} 
     239  \includegraphics[width=0.66\textwidth]{LDF_ZDF1} 
    240240  \caption{Averaging procedure for isopycnal slope computation} 
    241241  \label{fig:LDF_ZDF1} 
    … …  
    263263\begin{figure}[!ht] 
    264264  \centering 
    265   \includegraphics[width=0.66\textwidth]{Fig_eiv_slp} 
     265  \includegraphics[width=0.66\textwidth]{LDF_eiv_slp} 
    266266  \caption[Vertical profile of the slope used for lateral mixing in the mixed layer]{ 
    267267    Vertical profile of the slope used for lateral mixing in the mixed layer: 
    … …  
    478478 
    479479%%gm  from Triad appendix  : to be incorporated.... 
    480 \gmcomment{ 
     480\cmtgm{ 
    481481  Values of iso-neutral diffusivity and GM coefficient are set as described in \autoref{sec:LDF_coef}. 
    482482  If none of the keys \key{traldf\_cNd}, N=1,2,3 is set (the default), spatially constant iso-neutral $A_l$ and 
    … …  
    544544\colorbox{yellow}{TBC} 
    545545 
    546 \onlyinsubfile{\input{../../global/epilogue}} 
     546\subinc{\input{../../global/epilogue}} 
    547547 
    548548\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_OBS.tex

    r12178 r12928  
    711711\begin{figure} 
    712712  \centering 
    713   \includegraphics[width=0.66\textwidth]{Fig_OBS_avg_rec} 
     713  \includegraphics[width=0.66\textwidth]{OBS_avg_rec} 
    714714  \caption[Observational weights with a rectangular footprint]{ 
    715715    Weights associated with each model grid box (blue lines and numbers) 
    … …  
    720720\begin{figure} 
    721721  \centering 
    722   \includegraphics[width=0.66\textwidth]{Fig_OBS_avg_rad} 
     722  \includegraphics[width=0.66\textwidth]{OBS_avg_rad} 
    723723  \caption[Observational weights with a radial footprint]{ 
    724724    Weights associated with each model grid box (blue lines and numbers) 
    … …  
    798798\begin{figure} 
    799799  \centering 
    800   \includegraphics[width=0.66\textwidth]{Fig_ASM_obsdist_local} 
     800  \includegraphics[width=0.66\textwidth]{OBS_obsdist_local} 
    801801  \caption[Observations with the geographical distribution]{ 
    802802    Example of the distribution of observations with 
    … …  
    825825\begin{figure} 
    826826  \centering 
    827   \includegraphics[width=0.66\textwidth]{Fig_ASM_obsdist_global} 
     827  \includegraphics[width=0.66\textwidth]{OBS_obsdist_global} 
    828828  \caption[Observations with the round-robin distribution]{ 
    829829    Example of the distribution of observations with 
    … …  
    855855 
    856856%% ================================================================================================= 
    857 \section{Standalone observation operator} 
     857\section{Standalone observation operator (\texttt{SAO})} 
    858858\label{sec:OBS_sao} 
    859859 
    … …  
    11641164\begin{figure} 
    11651165  \centering 
    1166   \includegraphics[width=0.66\textwidth]{Fig_OBS_dataplot_main} 
     1166  \includegraphics[width=0.66\textwidth]{OBS_dataplot_main} 
    11671167  \caption{Main window of dataplot} 
    11681168  \label{fig:OBS_dataplotmain} 
    … …  
    11741174\begin{figure} 
    11751175  \centering 
    1176   \includegraphics[width=0.66\textwidth]{Fig_OBS_dataplot_prof} 
     1176  \includegraphics[width=0.66\textwidth]{OBS_dataplot_prof} 
    11771177  \caption[Profile plot from dataplot]{ 
    11781178    Profile plot from dataplot produced by right clicking on a point in the main window} 
    … …  
    11801180\end{figure} 
    11811181 
    1182 \onlyinsubfile{\input{../../global/epilogue}} 
     1182\subinc{\input{../../global/epilogue}} 
    11831183 
    11841184\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_SBC.tex

    r12178 r12928  
    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: 
    … …  
    8801174%ENDIF 
    8811175 
    882 %\gmcomment{  word doc of runoffs: 
    883 %In the current \NEMO\ setup river runoff is added to emp fluxes, these are then applied at just the sea surface as a volume change (in the variable volume case this is a literal volume change, and in the linear free surface case the free surface is moved) and a salt flux due to the concentration/dilution effect.  There is also an option to increase vertical mixing near river mouths; this gives the effect of having a 3d river.  All river runoff and emp fluxes are assumed to be fresh water (zero salinity) and at the same temperature as the sea surface. 
    884 %Our aim was to code the option to specify the temperature and salinity of river runoff, (as well as the amount), along with the depth that the river water will affect.  This would make it possible to model low salinity outflow, such as the Baltic, and would allow the ocean temperature to be affected by river runoff. 
    885  
    886 %The depth option makes it possible to have the river water affecting just the surface layer, throughout depth, or some specified point in between. 
    887  
    888 %To do this we need to treat evaporation/precipitation fluxes and river runoff differently in the tra_sbc module.  We decided to separate them throughout the code, so that the variable emp represented solely evaporation minus precipitation fluxes, and a new 2d variable rnf was added which represents the volume flux of river runoff (in kg/m2s to remain consistent with emp).  This meant many uses of emp and emps needed to be changed, a list of all modules which use emp or emps and the changes made are below: 
     1176\cmtgm{  word doc of runoffs: 
     1177In the current \NEMO\ setup river runoff is added to emp fluxes, 
     1178these are then applied at just the sea surface as a volume change (in the variable volume case 
     1179this is a literal volume change, and in the linear free surface case the free surface is moved) 
     1180and a salt flux due to the concentration/dilution effect. 
     1181There is also an option to increase vertical mixing near river mouths; 
     1182this gives the effect of having a 3d river. 
     1183All river runoff and emp fluxes are assumed to be fresh water (zero salinity) and 
     1184at the same temperature as the sea surface. 
     1185Our aim was to code the option to specify the temperature and salinity of river runoff, 
     1186(as well as the amount), along with the depth that the river water will affect. 
     1187This would make it possible to model low salinity outflow, such as the Baltic, 
     1188and would allow the ocean temperature to be affected by river runoff. 
     1189 
     1190The depth option makes it possible to have the river water affecting just the surface layer, 
     1191throughout depth, or some specified point in between. 
     1192 
     1193To do this we need to treat evaporation/precipitation fluxes and river runoff differently in 
     1194the \mdl{tra_sbc} module. 
     1195We decided to separate them throughout the code, 
     1196so that the variable emp represented solely evaporation minus precipitation fluxes, 
     1197and a new 2d variable rnf was added which represents the volume flux of river runoff 
     1198(in $kg/m^2s$ to remain consistent with $emp$). 
     1199This meant many uses of emp and emps needed to be changed, 
     1200a list of all modules which use $emp$ or $emps$ and the changes made are below:} 
    8891201 
    8901202%% ================================================================================================= 
    … …  
    9081220  Two different bulk formulae are available: 
    9091221 
    910    \begin{description} 
    911    \item [{\np[=1]{nn_isfblk}{nn\_isfblk}}]: The melt rate is based on a balance between the upward ocean heat flux and 
    912      the latent heat flux at the ice shelf base. A complete description is available in \citet{hunter_rpt06}. 
    913    \item [{\np[=2]{nn_isfblk}{nn\_isfblk}}]: The melt rate and the heat flux are based on a 3 equations formulation 
    914      (a heat flux budget at the ice base, a salt flux budget at the ice base and a linearised freezing point temperature equation). 
    915      A complete description is available in \citet{jenkins_JGR91}. 
    916    \end{description} 
    917  
    918      Temperature and salinity used to compute the melt are the average temperature in the top boundary layer \citet{losch_JGR08}. 
    919      Its thickness is defined by \np{rn_hisf_tbl}{rn\_hisf\_tbl}. 
    920      The fluxes and friction velocity are computed using the mean temperature, salinity and velocity in the the first \np{rn_hisf_tbl}{rn\_hisf\_tbl} m. 
    921      Then, the fluxes are spread over the same thickness (ie over one or several cells). 
    922      If \np{rn_hisf_tbl}{rn\_hisf\_tbl} larger than top $e_{3}t$, there is no more feedback between the freezing point at the interface and the the top cell temperature. 
    923      This can lead to super-cool temperature in the top cell under melting condition. 
    924      If \np{rn_hisf_tbl}{rn\_hisf\_tbl} smaller than top $e_{3}t$, the top boundary layer thickness is set to the top cell thickness.\\ 
    925  
    926      Each melt bulk formula depends on a exchange coeficient ($\Gamma^{T,S}$) between the ocean and the ice. 
    927      There are 3 different ways to compute the exchange coeficient: 
    928    \begin{description} 
    929         \item [{\np[=0]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are constant and defined by \np{rn_gammas0}{rn\_gammas0} and \np{rn_gammat0}{rn\_gammat0}. 
    930      \begin{gather*} 
     1222  \begin{description} 
     1223  \item [{\np[=1]{nn_isfblk}{nn\_isfblk}}]: The melt rate is based on a balance between the upward ocean heat flux and 
     1224    the latent heat flux at the ice shelf base. A complete description is available in \citet{hunter_rpt06}. 
     1225  \item [{\np[=2]{nn_isfblk}{nn\_isfblk}}]: The melt rate and the heat flux are based on a 3 equations formulation 
     1226    (a heat flux budget at the ice base, a salt flux budget at the ice base and a linearised freezing point temperature equation). 
     1227    A complete description is available in \citet{jenkins_JGR91}. 
     1228  \end{description} 
     1229 
     1230  Temperature and salinity used to compute the melt are the average temperature in the top boundary layer \citet{losch_JGR08}. 
     1231  Its thickness is defined by \np{rn_hisf_tbl}{rn\_hisf\_tbl}. 
     1232  The fluxes and friction velocity are computed using the mean temperature, salinity and velocity in the the first \np{rn_hisf_tbl}{rn\_hisf\_tbl} m. 
     1233  Then, the fluxes are spread over the same thickness (ie over one or several cells). 
     1234  If \np{rn_hisf_tbl}{rn\_hisf\_tbl} larger than top $e_{3}t$, there is no more feedback between the freezing point at the interface and the the top cell temperature. 
     1235  This can lead to super-cool temperature in the top cell under melting condition. 
     1236  If \np{rn_hisf_tbl}{rn\_hisf\_tbl} smaller than top $e_{3}t$, the top boundary layer thickness is set to the top cell thickness.\\ 
     1237 
     1238  Each melt bulk formula depends on a exchange coeficient ($\Gamma^{T,S}$) between the ocean and the ice. 
     1239  There are 3 different ways to compute the exchange coeficient: 
     1240  \begin{description} 
     1241  \item [{\np[=0]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are constant and defined by \np{rn_gammas0}{rn\_gammas0} and \np{rn_gammat0}{rn\_gammat0}. 
     1242    \begin{gather*} 
    9311243       % \label{eq:SBC_isf_gamma_iso} 
    932        \gamma^{T} = rn\_gammat0 \\ 
    933        \gamma^{S} = rn\_gammas0 
    934      \end{gather*} 
    935      This is the recommended formulation for ISOMIP. 
    936    \item [{\np[=1]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are velocity dependent and defined as 
    937      \begin{gather*} 
    938        \gamma^{T} = rn\_gammat0 \times u_{*} \\ 
    939        \gamma^{S} = rn\_gammas0 \times u_{*} 
    940      \end{gather*} 
    941      where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters). 
    942      See \citet{jenkins.nicholls.ea_JPO10} for all the details on this formulation. It is the recommended formulation for realistic application. 
    943    \item [{\np[=2]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are velocity and stability dependent and defined as: 
    944 \[ 
    945 \gamma^{T,S} = \frac{u_{*}}{\Gamma_{Turb} + \Gamma^{T,S}_{Mole}} 
    946 \] 
    947      where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters), 
    948      $\Gamma_{Turb}$ the contribution of the ocean stability and 
    949      $\Gamma^{T,S}_{Mole}$ the contribution of the molecular diffusion. 
    950      See \citet{holland.jenkins_JPO99} for all the details on this formulation. 
    951      This formulation has not been extensively tested in \NEMO\ (not recommended). 
    952    \end{description} 
    953   \item [{\np[=2]{nn_isf}{nn\_isf}}]: The ice shelf cavity is not represented. 
    954    The fwf and heat flux are computed using the \citet{beckmann.goosse_OM03} parameterisation of isf melting. 
    955    The fluxes are distributed along the ice shelf edge between the depth of the average grounding line (GL) 
    956    (\np{sn_depmax_isf}{sn\_depmax\_isf}) and the base of the ice shelf along the calving front 
    957    (\np{sn_depmin_isf}{sn\_depmin\_isf}) as in (\np[=3]{nn_isf}{nn\_isf}). 
    958    The effective melting length (\np{sn_Leff_isf}{sn\_Leff\_isf}) is read from a file. 
    959   \item [{\np[=3]{nn_isf}{nn\_isf}}]: The ice shelf cavity is not represented. 
    960    The fwf (\np{sn_rnfisf}{sn\_rnfisf}) is prescribed and distributed along the ice shelf edge between 
    961    the depth of the average grounding line (GL) (\np{sn_depmax_isf}{sn\_depmax\_isf}) and 
    962    the base of the ice shelf along the calving front (\np{sn_depmin_isf}{sn\_depmin\_isf}). 
    963    The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. 
    964   \item [{\np[=4]{nn_isf}{nn\_isf}}]: The ice shelf cavity is opened (\np[=.true.]{ln_isfcav}{ln\_isfcav} needed). 
    965    However, the fwf is not computed but specified from file \np{sn_fwfisf}{sn\_fwfisf}). 
    966    The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. 
    967    As in \np[=1]{nn_isf}{nn\_isf}, the fluxes are spread over the top boundary layer thickness (\np{rn_hisf_tbl}{rn\_hisf\_tbl})\\ 
     1244      \gamma^{T} = rn\_gammat0 \\ 
     1245      \gamma^{S} = rn\_gammas0 
     1246    \end{gather*} 
     1247    This is the recommended formulation for ISOMIP. 
     1248  \item [{\np[=1]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are velocity dependent and defined as 
     1249    \begin{gather*} 
     1250      \gamma^{T} = rn\_gammat0 \times u_{*} \\ 
     1251      \gamma^{S} = rn\_gammas0 \times u_{*} 
     1252    \end{gather*} 
     1253    where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters). 
     1254    See \citet{jenkins.nicholls.ea_JPO10} for all the details on this formulation. It is the recommended formulation for realistic application. 
     1255  \item [{\np[=2]{nn_gammablk}{nn\_gammablk}}]: The salt and heat exchange coefficients are velocity and stability dependent and defined as: 
     1256    \[ 
     1257      \gamma^{T,S} = \frac{u_{*}}{\Gamma_{Turb} + \Gamma^{T,S}_{Mole}} 
     1258    \] 
     1259    where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters), 
     1260    $\Gamma_{Turb}$ the contribution of the ocean stability and 
     1261    $\Gamma^{T,S}_{Mole}$ the contribution of the molecular diffusion. 
     1262    See \citet{holland.jenkins_JPO99} for all the details on this formulation. 
     1263    This formulation has not been extensively tested in \NEMO\ (not recommended). 
     1264  \end{description} 
     1265\item [{\np[=2]{nn_isf}{nn\_isf}}]: The ice shelf cavity is not represented. 
     1266  The fwf and heat flux are computed using the \citet{beckmann.goosse_OM03} parameterisation of isf melting. 
     1267  The fluxes are distributed along the ice shelf edge between the depth of the average grounding line (GL) 
     1268  (\np{sn_depmax_isf}{sn\_depmax\_isf}) and the base of the ice shelf along the calving front 
     1269  (\np{sn_depmin_isf}{sn\_depmin\_isf}) as in (\np[=3]{nn_isf}{nn\_isf}). 
     1270  The effective melting length (\np{sn_Leff_isf}{sn\_Leff\_isf}) is read from a file. 
     1271\item [{\np[=3]{nn_isf}{nn\_isf}}]: The ice shelf cavity is not represented. 
     1272  The fwf (\np{sn_rnfisf}{sn\_rnfisf}) is prescribed and distributed along the ice shelf edge between 
     1273  the depth of the average grounding line (GL) (\np{sn_depmax_isf}{sn\_depmax\_isf}) and 
     1274  the base of the ice shelf along the calving front (\np{sn_depmin_isf}{sn\_depmin\_isf}). 
     1275  The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. 
     1276\item [{\np[=4]{nn_isf}{nn\_isf}}]: The ice shelf cavity is opened (\np[=.true.]{ln_isfcav}{ln\_isfcav} needed). 
     1277  However, the fwf is not computed but specified from file \np{sn_fwfisf}{sn\_fwfisf}). 
     1278  The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. 
     1279  As in \np[=1]{nn_isf}{nn\_isf}, the fluxes are spread over the top boundary layer thickness (\np{rn_hisf_tbl}{rn\_hisf\_tbl}) 
    9681280\end{description} 
    9691281 
    … …  
    9861298\begin{figure}[!t] 
    9871299  \centering 
    988   \includegraphics[width=0.66\textwidth]{Fig_SBC_isf} 
     1300  \includegraphics[width=0.66\textwidth]{SBC_isf} 
    9891301  \caption[Ice shelf location and fresh water flux definition]{ 
    9901302    Illustration of the location where the fwf is injected and 
    … …  
    13071619\begin{figure}[!t] 
    13081620  \centering 
    1309   \includegraphics[width=0.66\textwidth]{Fig_SBC_diurnal} 
     1621  \includegraphics[width=0.66\textwidth]{SBC_diurnal} 
    13101622  \caption[Reconstruction of the diurnal cycle variation of short wave flux]{ 
    13111623    Example of reconstruction of the diurnal cycle variation of short wave flux from 
    … …  
    13411653\begin{figure}[!t] 
    13421654  \centering 
    1343   \includegraphics[width=0.66\textwidth]{Fig_SBC_dcy} 
     1655  \includegraphics[width=0.66\textwidth]{SBC_dcy} 
    13441656  \caption[Reconstruction of the diurnal cycle variation of short wave flux on an ORCA2 grid]{ 
    13451657    Example of reconstruction of the diurnal cycle variation of short wave flux from 
    … …  
    15211833% in ocean-ice models. 
    15221834 
    1523 \onlyinsubfile{\input{../../global/epilogue}} 
     1835\subinc{\input{../../global/epilogue}} 
    15241836 
    15251837\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_STO.tex

    r12178 r12928  
    205205The first four parameters define the stochastic part of equation of state. 
    206206 
    207 \onlyinsubfile{\input{../../global/epilogue}} 
     207\subinc{\input{../../global/epilogue}} 
    208208 
    209209\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_TRA.tex

    r12178 r12928  
    110110\begin{figure} 
    111111  \centering 
    112   \includegraphics[width=0.66\textwidth]{Fig_adv_scheme} 
     112  \includegraphics[width=0.66\textwidth]{TRA_adv_scheme} 
    113113  \caption[Ways to evaluate the tracer value and the amount of tracer exchanged]{ 
    114114    Schematic representation of some ways used to evaluate the tracer value at $u$-point and 
    … …  
    452452restore this property. 
    453453 
    454 %%%gmcomment   :  Cross term are missing in the current implementation.... 
     454\cmtgm{Cross term are missing in the current implementation....} 
    455455 
    456456%% ================================================================================================= 
    … …  
    880880\begin{figure} 
    881881  \centering 
    882   \includegraphics[width=0.66\textwidth]{Fig_TRA_Irradiance} 
     882  \includegraphics[width=0.66\textwidth]{TRA_Irradiance} 
    883883  \caption[Penetration profile of the downward solar irradiance calculated by four models]{ 
    884884    Penetration profile of the downward solar irradiance calculated by four models. 
    … …  
    904904\begin{figure} 
    905905  \centering 
    906   \includegraphics[width=0.66\textwidth]{Fig_TRA_geoth} 
     906  \includegraphics[width=0.66\textwidth]{TRA_geoth} 
    907907  \caption[Geothermal heat flux]{ 
    908908    Geothermal Heat flux (in $mW.m^{-2}$) used by \cite{emile-geay.madec_OS09}. 
    … …  
    10201020\begin{figure} 
    10211021  \centering 
    1022   \includegraphics[width=0.33\textwidth]{Fig_BBL_adv} 
     1022  \includegraphics[width=0.33\textwidth]{TRA_BBL_adv} 
    10231023  \caption[Advective/diffusive bottom boundary layer]{ 
    10241024    Advective/diffusive Bottom Boundary Layer. 
    … …  
    10371037%!!        i.e. transport proportional to the along-slope density gradient 
    10381038 
    1039 %%%gmcomment   :  this section has to be really written 
     1039\cmtgm{This section has to be really written} 
    10401040 
    10411041When applying an advective BBL (\np[=1..2]{nn_bbl_adv}{nn\_bbl\_adv}), 
    … …  
    13741374\label{sec:TRA_zpshde} 
    13751375 
    1376 \gmcomment{STEVEN: to be consistent with earlier discussion of differencing and averaging operators, 
     1376\cmtgm{STEVEN: to be consistent with earlier discussion of differencing and averaging operators, 
    13771377I've changed "derivative" to "difference" and "mean" to "average"} 
    13781378 
    … …  
    13941394\begin{figure} 
    13951395  \centering 
    1396   \includegraphics[width=0.33\textwidth]{Fig_partial_step_scheme} 
     1396  \includegraphics[width=0.33\textwidth]{TRA_partial_step_scheme} 
    13971397  \caption[Discretisation of the horizontal difference and average of tracers in 
    13981398  the $z$-partial step coordinate]{ 
    … …  
    14641464Sensitivity of the advection schemes to the way horizontal averages are performed in 
    14651465the vicinity of partial cells should be further investigated in the near future. 
    1466 \gmcomment{gm :   this last remark has to be done} 
    1467  
    1468 \onlyinsubfile{\input{../../global/epilogue}} 
     1466\cmtgm{gm :   this last remark has to be done} 
     1467 
     1468\subinc{\input{../../global/epilogue}} 
    14691469 
    14701470\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_ZDF.tex

    r12178 r12928  
    2828\clearpage 
    2929 
    30 %gm% Add here a small introduction to ZDF and naming of the different physics (similar to what have been written for TRA and DYN. 
     30\cmtgm{ Add here a small introduction to ZDF and naming of the different physics 
     31(similar to what have been written for TRA and DYN).} 
    3132 
    3233%% ================================================================================================= 
    … …  
    248249\begin{figure}[!t] 
    249250  \centering 
    250   \includegraphics[width=0.66\textwidth]{Fig_mixing_length} 
     251  \includegraphics[width=0.66\textwidth]{ZDF_mixing_length} 
    251252  \caption[Mixing length computation]{Illustration of the mixing length computation} 
    252253  \label{fig:ZDF_mixing_length} 
    … …  
    533534 in \citet{reffray.guillaume.ea_GMD15} for the \NEMO\ model. 
    534535 
    535 %% ================================================================================================= 
    536 \subsection[OSM: OSMosis boundary layer scheme (\forcode{ln_zdfosm})]{OSM: OSMosis boundary layer scheme (\protect\np{ln_zdfosm}{ln\_zdfosm})} 
     536% ------------------------------------------------------------------------------------------------------------- 
     537%        OSM OSMOSIS BL Scheme 
     538% ------------------------------------------------------------------------------------------------------------- 
     539\subsection[OSM: OSMOSIS boundary layer scheme (\forcode{ln_zdfosm = .true.})] 
     540{OSM: OSMOSIS boundary layer scheme (\protect\np{ln_zdfosm}{ln\_zdfosm})} 
    537541\label{subsec:ZDF_osm} 
    538542 
    … …  
    543547\end{listing} 
    544548 
    545 The OSMOSIS turbulent closure scheme is based on......   TBC 
     549%-------------------------------------------------------------------------------------------------------------- 
     550\paragraph{Namelist choices} 
     551Most of the namelist options refer to how to specify the Stokes 
     552surface drift and penetration depth. There are three options: 
     553\begin{description} 
     554  \item \protect\np[=0]{nn_osm_wave}{nn\_osm\_wave} Default value in \texttt{namelist\_ref}. In this case the Stokes drift is 
     555      assumed to be parallel to the surface wind stress, with 
     556      magnitude consistent with a constant turbulent Langmuir number 
     557    $\mathrm{La}_t=$ \protect\np{rn_m_la} {rn\_m\_la} i.e.\ 
     558    $u_{s0}=\tau/(\mathrm{La}_t^2\rho_0)$.  Default value of 
     559    \protect\np{rn_m_la}{rn\_m\_la} is 0.3. The Stokes penetration 
     560      depth $\delta = $ \protect\np{rn_osm_dstokes}{rn\_osm\_dstokes}; this has default value 
     561      of 5~m. 
     562 
     563  \item \protect\np[=1]{nn_osm_wave}{nn\_osm\_wave} In this case the Stokes drift is 
     564      assumed to be parallel to the surface wind stress, with 
     565      magnitude as in the classical Pierson-Moskowitz wind-sea 
     566      spectrum.  Significant wave height and 
     567      wave-mean period taken from this spectrum are used to calculate the Stokes penetration 
     568      depth, following the approach set out in  \citet{breivik.janssen.ea_JPO14}. 
     569 
     570    \item \protect\np[=2]{nn_osm_wave}{nn\_osm\_wave} In this case the Stokes drift is 
     571      taken from  ECMWF wave model output, though only the component parallel 
     572      to the wind stress is retained. Significant wave height and 
     573      wave-mean period from ECMWF wave model output are used to calculate the Stokes penetration 
     574      depth, again following \citet{breivik.janssen.ea_JPO14}. 
     575 
     576    \end{description} 
     577 
     578    Others refer to the treatment of diffusion and viscosity beneath 
     579    the surface boundary layer: 
     580\begin{description} 
     581   \item \protect\np{ln_kpprimix} {ln\_kpprimix}  Default is \np{.true.}. Switches on KPP-style Ri \#-dependent 
     582     mixing below the surface boundary layer. If this is set 
     583     \texttt{.true.}  the following variable settings are honoured: 
     584    \item \protect\np{rn_riinfty}{rn\_riinfty} Critical value of local Ri \# below which 
     585      shear instability increases vertical mixing from background value. 
     586    \item \protect\np{rn_difri} {rn\_difri} Maximum value of Ri \#-dependent mixing at $\mathrm{Ri}=0$. 
     587    \item \protect\np{ln_convmix}{ln\_convmix} If \texttt{.true.} then, where water column is unstable, specify 
     588       diffusivity equal to \protect\np{rn_dif_conv}{rn\_dif\_conv} (default value is 1 m~s$^{-2}$). 
     589 \end{description} 
     590 Diagnostic output is controlled by: 
     591  \begin{description} 
     592    \item \protect\np{ln_dia_osm}{ln\_dia\_osm} Default is \np{.false.}; allows XIOS output of OSMOSIS internal fields. 
     593  \end{description} 
     594Obsolete namelist parameters include: 
     595\begin{description} 
     596   \item \protect\np{ln_use_osm_la}\np{ln\_use\_osm\_la} With \protect\np[=0]{nn_osm_wave}{nn\_osm\_wave}, 
     597      \protect\np{rn_osm_dstokes} {rn\_osm\_dstokes} is always used to specify the Stokes 
     598      penetration depth. 
     599   \item \protect\np{nn_ave} {nn\_ave} Choice of averaging method for KPP-style Ri \# 
     600      mixing. Not taken account of. 
     601   \item \protect\np{rn_osm_hbl0} {rn\_osm\_hbl0} Depth of initial boundary layer is now set 
     602     by a density criterion similar to that used in calculating \emph{hmlp} (output as \texttt{mldr10\_1}) in \mdl{zdfmxl}. 
     603\end{description} 
     604 
     605\subsubsection{Summary} 
     606Much of the time the turbulent motions in the ocean surface boundary 
     607layer (OSBL) are not given by 
     608classical shear turbulence. Instead they are in a regime known as 
     609`Langmuir turbulence',  dominated by an 
     610interaction between the currents and the Stokes drift of the surface waves \citep[e.g.][]{mcwilliams.ea_JFM97}. 
     611This regime is characterised by strong vertical turbulent motion, and appears when the surface Stokes drift $u_{s0}$ is much greater than the friction velocity $u_{\ast}$. More specifically Langmuir turbulence is thought to be crucial where the turbulent Langmuir number $\mathrm{La}_{t}=(u_{\ast}/u_{s0}) > 0.4$. 
     612 
     613The OSMOSIS model is fundamentally based on results of Large Eddy 
     614Simulations (LES) of Langmuir turbulence and aims to fully describe 
     615this Langmuir regime. The description in this section is of necessity incomplete and further details are available in Grant. A (2019); in prep. 
     616 
     617The OSMOSIS turbulent closure scheme is a similarity-scale scheme in 
     618the same spirit as the K-profile 
     619parameterization (KPP) scheme of \citet{large.ea_RG97}. 
     620A specified shape of diffusivity, scaled by the (OSBL) depth 
     621$h_{\mathrm{BL}}$ and a turbulent velocity scale, is imposed throughout the 
     622boundary layer 
     623$-h_{\mathrm{BL}}<z<\eta$. The turbulent closure model 
     624also includes fluxes of tracers and momentum that are``non-local'' (independent of the local property gradient). 
     625 
     626Rather than the OSBL 
     627depth being diagnosed in terms of a bulk Richardson number criterion, 
     628as in KPP, it is set by a prognostic equation that is informed by 
     629energy budget considerations reminiscent of the classical mixed layer 
     630models of \citet{kraus.turner_tellus67}. 
     631The model also includes an explicit parametrization of the structure 
     632of the pycnocline (the stratified region at the bottom of the OSBL). 
     633 
     634Presently, mixing below the OSBL is handled by the Richardson 
     635number-dependent mixing scheme used in \citet{large.ea_RG97}. 
     636 
     637Convective parameterizations such as described in \ref{sec:ZDF_conv} 
     638below should not be used with the OSMOSIS-OBL model: instabilities 
     639within the OSBL are part of the model, while instabilities below the 
     640ML are handled by the Ri \# dependent scheme. 
     641 
     642\subsubsection{Depth and velocity scales} 
     643The model supposes a boundary layer of thickness $h_{\mathrm{bl}}$ enclosing a well-mixed layer of thickness $h_{\mathrm{ml}}$ and a relatively thin pycnocline at the base of thickness $\Delta h$; Fig.~\ref{fig: OSBL_structure} shows typical (a) buoyancy structure and (b) turbulent buoyancy flux profile for the unstable boundary layer (losing buoyancy at the surface; e.g.\ cooling). 
     644\begin{figure}[!t] 
     645  \begin{center} 
     646    %\includegraphics[width=0.7\textwidth]{ZDF_OSM_structure_of_OSBL} 
     647    \caption{ 
     648      \protect\label{fig: OSBL_structure} 
     649     The structure of the entraining  boundary layer. (a) Mean buoyancy profile. (b) Profile of the buoyancy flux. 
     650    } 
     651  \end{center} 
     652\end{figure} 
     653The pycnocline in the OSMOSIS scheme is assumed to have a finite thickness, and may include a number of model levels. This means that the OSMOSIS scheme must parametrize both the thickness of the pycnocline, and the turbulent fluxes within the pycnocline. 
     654 
     655Consideration of the power input by wind acting on the Stokes drift suggests that the Langmuir turbulence has velocity scale: 
     656\begin{equation}\label{eq:w_La} 
     657w_{*L}= \left(u_*^2 u_{s\,0}\right)^{1/3}; 
     658\end{equation} 
     659but at times the Stokes drift may be weak due to e.g.\ ice cover, short fetch, misalignment with the surface stress, etc.\ so  a composite velocity scale is assumed for the stable (warming) boundary layer: 
     660\begin{equation}\label{eq:composite-nu} 
     661  \nu_{\ast}= \left\{ u_*^3 \left[1-\exp(-.5 \mathrm{La}_t^2)\right]+w_{*L}^3\right\}^{1/3}. 
     662\end{equation} 
     663For the unstable boundary layer this is merged with the standard convective velocity scale $w_{*C}=\left(\overline{w^\prime b^\prime}_0 \,h_\mathrm{ml}\right)^{1/3}$, where $\overline{w^\prime b^\prime}_0$ is the upwards surface buoyancy flux, to give: 
     664\begin{equation}\label{eq:vel-scale-unstable} 
     665\omega_* = \left(\nu_*^3 + 0.5 w_{*C}^3\right)^{1/3}. 
     666\end{equation} 
     667 
     668\subsubsection{The flux gradient model} 
     669The flux-gradient relationships used in the OSMOSIS scheme take the form: 
     670% 
     671\begin{equation}\label{eq:flux-grad-gen} 
     672\overline{w^\prime\chi^\prime}=-K\frac{\partial\overline{\chi}}{\partial z} + N_{\chi,s} +N_{\chi,b} +N_{\chi,t}, 
     673\end{equation} 
     674% 
     675where $\chi$ is a general variable and $N_{\chi,s}, N_{\chi,b} \mathrm{and} N_{\chi,t}$  are the non-gradient terms, and represent the effects of the different terms in the turbulent flux-budget on the transport of $\chi$. $N_{\chi,s}$ represents the effects that the Stokes shear has on the transport of $\chi$, $N_{\chi,b}$  the effect of buoyancy, and $N_{\chi,t}$ the effect of the turbulent transport.  The same general form for the flux-gradient relationship is used to parametrize the transports of momentum, heat and salinity. 
     676 
     677In terms of the non-dimensionalized depth variables 
     678% 
     679\begin{equation}\label{eq:sigma} 
     680\sigma_{\mathrm{ml}}= -z/h_{\mathrm{ml}}; \;\sigma_{\mathrm{bl}}= -z/h_{\mathrm{bl}}, 
     681\end{equation} 
     682% 
     683in unstable conditions the eddy diffusivity ($K_d$) and eddy viscosity ($K_\nu$) profiles are parametrized as: 
     684% 
     685\begin{align}\label{eq:diff-unstable} 
     686K_d=&0.8\, \omega_*\, h_{\mathrm{ml}} \, \sigma_{\mathrm{ml}} \left(1-\beta_d \sigma_{\mathrm{ml}}\right)^{3/2} 
     687\\\label{eq:visc-unstable} 
     688K_\nu =& 0.3\, \omega_* \,h_{\mathrm{ml}}\, \sigma_{\mathrm{ml}} \left(1-\beta_\nu \sigma_{\mathrm{ml}}\right)\left(1-\tfrac{1}{2}\sigma_{\mathrm{ml}}^2\right) 
     689\end{align} 
     690% 
     691where $\beta_d$ and $\beta_\nu$ are parameters that are determined by matching Eqs \ref{eq:diff-unstable} and \ref{eq:visc-unstable} to the eddy diffusivity and viscosity at the base of the well-mixed layer, given by 
     692% 
     693\begin{equation}\label{eq:diff-wml-base} 
     694K_{d,\mathrm{ml}}=K_{\nu,\mathrm{ml}}=\,0.16\,\omega_* \Delta h. 
     695\end{equation} 
     696% 
     697For stable conditions the eddy diffusivity/viscosity profiles are given by: 
     698% 
     699\begin{align}\label{diff-stable} 
     700K_d= & 0.75\,\, \nu_*\, h_{\mathrm{ml}}\,\,  \exp\left[-2.8 \left(h_{\mathrm{bl}}/L_L\right)^2\right]\sigma_{\mathrm{ml}} \left(1-\sigma_{\mathrm{ml}}\right)^{3/2} \\\label{eq:visc-stable} 
     701K_\nu = & 0.375\,\,  \nu_*\, h_{\mathrm{ml}} \,\, \exp\left[-2.8 \left(h_{\mathrm{bl}}/L_L\right)^2\right] \sigma_{\mathrm{ml}} \left(1-\sigma_{\mathrm{ml}}\right)\left(1-\tfrac{1}{2}\sigma_{\mathrm{ml}}^2\right). 
     702\end{align} 
     703% 
     704The shape of the eddy viscosity and diffusivity profiles is the same as the shape in the unstable OSBL. The eddy diffusivity/viscosity depends on the stability parameter $h_{\mathrm{bl}}/{L_L}$ where $ L_L$ is analogous to the Obukhov length, but for Langmuir turbulence: 
     705\begin{equation}\label{eq:L_L} 
     706  L_L=-w_{*L}^3/\left<\overline{w^\prime b^\prime}\right>_L, 
     707\end{equation} 
     708with the mean turbulent buoyancy flux averaged over the boundary layer given in terms of its surface value $\overline{w^\prime b^\prime}_0$ and (downwards) )solar irradiance $I(z)$ by 
     709\begin{equation} \label{eq:stable-av-buoy-flux} 
     710\left<\overline{w^\prime b^\prime}\right>_L = \tfrac{1}{2} {\overline{w^\prime b^\prime}}_0-g\alpha_E\left[\tfrac{1}{2}(I(0)+I(-h))-\left<I\right>\right]. 
     711\end{equation} 
     712% 
     713In unstable conditions the eddy diffusivity and viscosity depend on stability through the velocity scale $\omega_*$, which depends on the two velocity scales $\nu_*$ and $w_{*C}$. 
     714 
     715Details of the non-gradient terms in \eqref{eq:flux-grad-gen} and of the fluxes within the pycnocline $-h_{\mathrm{bl}}<z<h_{\mathrm{ml}}$ can be found in Grant (2019). 
     716 
     717\subsubsection{Evolution of the boundary layer depth} 
     718 
     719The prognostic equation for the depth of the neutral/unstable boundary layer is given by \citep{grant+etal18}, 
     720 
     721\begin{equation} \label{eq:dhdt-unstable} 
     722%\frac{\partial h_\mathrm{bl}}{\partial t} + \mathbf{U}_b\cdot\nabla h_\mathrm{bl}= W_b - \frac{{\overline{w^\prime b^\prime}}_\mathrm{ent}}{\Delta B_\mathrm{bl}} 
     723\frac{\partial h_\mathrm{bl}}{\partial t} = W_b - \frac{{\overline{w^\prime b^\prime}}_\mathrm{ent}}{\Delta B_\mathrm{bl}} 
     724\end{equation} 
     725where $h_\mathrm{bl}$ is the horizontally-varying depth of the OSBL, 
     726$\mathbf{U}_b$ and $W_b$ are the mean horizontal and vertical 
     727velocities at the base of the OSBL, ${\overline{w^\prime 
     728    b^\prime}}_\mathrm{ent}$ is the buoyancy flux due to entrainment 
     729and $\Delta B_\mathrm{bl}$ is the difference between the buoyancy 
     730averaged over the depth of the OSBL (i.e.\ including the ML and 
     731pycnocline) and the buoyancy just below the base of the OSBL. This 
     732equation for the case when the pycnocline has a finite thickness, 
     733based on the potential energy budget of the OSBL, is the leading term 
     734\citep{grant+etal18} of a generalization of that used in mixed-layer 
     735models e.g.\ \citet{kraus.turner_tellus67}, in which the thickness of the pycnocline is taken to be zero. 
     736 
     737The entrainment flux for the combination of convective and Langmuir turbulence is given by 
     738\begin{equation} \label{eq:entrain-flux} 
     739  {\overline{w^\prime b^\prime}}_\mathrm{ent} = -\alpha_{\mathrm{B}} {\overline{w^\prime b^\prime}}_0 - \alpha_{\mathrm{S}} \frac{u_*^3}{h_{\mathrm{ml}}} 
     740  + G\left(\delta/h_{\mathrm{ml}} \right)\left[\alpha_{\mathrm{S}}e^{-1.5\, \mathrm{La}_t}-\alpha_{\mathrm{L}} \frac{w_{\mathrm{*L}}^3}{h_{\mathrm{ml}}}\right] 
     741\end{equation} 
     742where the factor $G\equiv 1 - \mathrm{e}^ {-25\delta/h_{\mathrm{bl}}}(1-4\delta/h_{\mathrm{bl}})$ models the lesser efficiency of Langmuir mixing when the boundary-layer depth is much greater than the Stokes depth, and $\alpha_{\mathrm{B}}$, $\alpha_{S}$  and $\alpha_{\mathrm{L}}$ depend on the ratio of the appropriate eddy turnover time to the inertial timescale $f^{-1}$. Results from the LES suggest $\alpha_{\mathrm{B}}=0.18 F(fh_{\mathrm{bl}}/w_{*C})$, $\alpha_{S}=0.15 F(fh_{\mathrm{bl}}/u_*$  and $\alpha_{\mathrm{L}}=0.035 F(fh_{\mathrm{bl}}/u_{*L})$, where $F(x)\equiv\tanh(x^{-1})^{0.69}$. 
     743 
     744For the stable boundary layer, the equation for the depth of the OSBL is: 
     745 
     746\begin{equation}\label{eq:dhdt-stable} 
     747\max\left(\Delta B_{bl},\frac{w_{*L}^2}{h_\mathrm{bl}}\right)\frac{\partial h_\mathrm{bl}}{\partial t} = \left(0.06 + 0.52\,\frac{ h_\mathrm{bl}}{L_L}\right) \frac{w_{*L}^3}{h_\mathrm{bl}} +\left<\overline{w^\prime b^\prime}\right>_L. 
     748\end{equation} 
     749 
     750Equation. \ref{eq:dhdt-unstable} always leads to the depth of the entraining OSBL increasing (ignoring the effect of the mean vertical motion), but the change in the thickness of the stable OSBL given by Eq. \ref{eq:dhdt-stable} can be positive or negative, depending on the magnitudes of $\left<\overline{w^\prime b^\prime}\right>_L$ and $h_\mathrm{bl}/L_L$. The rate at which the depth of the OSBL can decrease is limited by choosing an effective buoyancy $w_{*L}^2/h_\mathrm{bl}$, in place of $\Delta B_{bl}$ which will be $\approx 0$ for the collapsing OSBL. 
     751 
    546752 
    547753%% ================================================================================================= 
    … …  
    551757\begin{figure}[!t] 
    552758  \centering 
    553   \includegraphics[width=0.66\textwidth]{Fig_ZDF_TKE_time_scheme} 
     759  \includegraphics[width=0.66\textwidth]{ZDF_TKE_time_scheme} 
    554760  \caption[Subgrid kinetic energy integration in GLS and TKE schemes]{ 
    555761    Illustration of the subgrid kinetic energy integration in GLS and TKE schemes and 
    … …  
    663869\begin{figure}[!htb] 
    664870  \centering 
    665   \includegraphics[width=0.66\textwidth]{Fig_npc} 
     871  \includegraphics[width=0.66\textwidth]{ZDF_npc} 
    666872  \caption[Unstable density profile treated by the non penetrative convective adjustment algorithm]{ 
    667873    Example of an unstable density profile treated by 
    … …  
    8081014\begin{figure}[!t] 
    8091015  \centering 
    810   \includegraphics[width=0.66\textwidth]{Fig_zdfddm} 
     1016  \includegraphics[width=0.66\textwidth]{ZDF_ddm} 
    8111017  \caption[Diapycnal diffusivities for temperature and salt in regions of salt fingering and 
    8121018  diffusive convection]{ 
    … …  
    12861492\begin{figure}[!t] 
    12871493  \centering 
    1288   \includegraphics[width=0.66\textwidth]{Fig_ZDF_zad_Aimp_coeff} 
     1494  \includegraphics[width=0.66\textwidth]{ZDF_zad_Aimp_coeff} 
    12891495  \caption[Partitioning coefficient used to partition vertical velocities into parts]{ 
    12901496    The value of the partitioning coefficient (\cf) used to partition vertical velocities into 
    … …  
    13261532\begin{figure}[!t] 
    13271533  \centering 
    1328   \includegraphics[width=0.66\textwidth]{Fig_ZDF_zad_Aimp_overflow_frames} 
     1534  \includegraphics[width=0.66\textwidth]{ZDF_zad_Aimp_overflow_frames} 
    13291535  \caption[OVERFLOW: time-series of temperature vertical cross-sections]{ 
    13301536    A time-series of temperature vertical cross-sections for the OVERFLOW test case. 
    … …  
    14061612\begin{figure}[!t] 
    14071613  \centering 
    1408   \includegraphics[width=0.66\textwidth]{Fig_ZDF_zad_Aimp_overflow_all_rdt} 
     1614  \includegraphics[width=0.66\textwidth]{ZDF_zad_Aimp_overflow_all_rdt} 
    14091615  \caption[OVERFLOW: sample temperature vertical cross-sections from mid- and end-run]{ 
    14101616    Sample temperature vertical cross-sections from mid- and end-run using 
    … …  
    14191625\begin{figure}[!t] 
    14201626  \centering 
    1421   \includegraphics[width=0.66\textwidth]{Fig_ZDF_zad_Aimp_maxCf} 
     1627  \includegraphics[width=0.66\textwidth]{ZDF_zad_Aimp_maxCf} 
    14221628  \caption[OVERFLOW: maximum partitioning coefficient during a series of test runs]{ 
    14231629    The maximum partitioning coefficient during a series of test runs with 
    … …  
    14301636\begin{figure}[!t] 
    14311637  \centering 
    1432   \includegraphics[width=0.66\textwidth]{Fig_ZDF_zad_Aimp_maxCf_loc} 
     1638  \includegraphics[width=0.66\textwidth]{ZDF_zad_Aimp_maxCf_loc} 
    14331639  \caption[OVERFLOW: maximum partitioning coefficient for the case overlaid]{ 
    14341640    The maximum partitioning coefficient for the \forcode{nn_rdt=10.0} case overlaid with 
    … …  
    14371643\end{figure} 
    14381644 
    1439 \onlyinsubfile{\input{../../global/epilogue}} 
     1645\subinc{\input{../../global/epilogue}} 
    14401646 
    14411647\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_cfgs.tex

    r12178 r12928  
    9393\begin{figure}[!t] 
    9494  \centering 
    95   \includegraphics[width=0.66\textwidth]{Fig_ORCA_NH_mesh} 
     95  \includegraphics[width=0.66\textwidth]{CFGS_ORCA_NH_mesh} 
    9696  \caption[ORCA mesh conception]{ 
    9797    ORCA mesh conception. 
    … …  
    120120\begin{figure}[!tbp] 
    121121  \centering 
    122   \includegraphics[width=0.66\textwidth]{Fig_ORCA_NH_msh05_e1_e2} 
    123   \includegraphics[width=0.66\textwidth]{Fig_ORCA_aniso} 
     122  \includegraphics[width=0.66\textwidth]{CFGS_ORCA_NH_msh05_e1_e2} 
     123  \includegraphics[width=0.66\textwidth]{CFGS_ORCA_aniso} 
    124124  \caption[Horizontal scale factors and ratio of anisotropy for ORCA 0.5\deg\ mesh]{ 
    125125    \textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and 
    … …  
    264264\begin{figure}[!t] 
    265265  \centering 
    266   \includegraphics[width=0.66\textwidth]{Fig_GYRE} 
     266  \includegraphics[width=0.66\textwidth]{CFGS_GYRE} 
    267267  \caption[Snapshot of relative vorticity at the surface of the model domain in GYRE R9, R27 and R54]{ 
    268268    Snapshot of relative vorticity at the surface of the model domain in GYRE R9, R27 and R54. 
    … …  
    292292Unlike ordinary river points the Baltic inputs also include salinity and temperature data. 
    293293 
    294 \onlyinsubfile{\input{../../global/epilogue}} 
     294\subinc{\input{../../global/epilogue}} 
    295295 
    296296\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_conservation.tex

    r12178 r12928  
    334334It has not been implemented. 
    335335 
    336 \onlyinsubfile{\input{../../global/epilogue}} 
     336\subinc{\input{../../global/epilogue}} 
    337337 
    338338\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_misc.tex

    r12178 r12928  
    9494\begin{figure}[!tbp] 
    9595  \centering 
    96   \includegraphics[width=0.66\textwidth]{Fig_Gibraltar} 
    97   \includegraphics[width=0.66\textwidth]{Fig_Gibraltar2} 
     96  \includegraphics[width=0.66\textwidth]{MISC_Gibraltar} 
     97  \includegraphics[width=0.66\textwidth]{MISC_Gibraltar2} 
    9898  \caption[Two methods to defined the Gibraltar strait]{ 
    9999    Example of the Gibraltar strait defined in a 1\deg\ $\times$ 1\deg\ mesh. 
    … …  
    111111\begin{figure}[!tbp] 
    112112  \centering 
    113   \includegraphics[width=0.66\textwidth]{Fig_closea_mask_example} 
     113  \includegraphics[width=0.66\textwidth]{MISC_closea_mask_example} 
    114114  \caption[Mask fields for the \protect\mdl{closea} module]{ 
    115115    Example of mask fields for the \protect\mdl{closea} module. 
    … …  
    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. 
    416  
    417 \onlyinsubfile{\input{../../global/epilogue}} 
     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 
     500 
     501\subinc{\input{../../global/epilogue}} 
    418502 
    419503\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_model_basics.tex

    r12178 r12928  
    130130\begin{figure} 
    131131  \centering 
    132   \includegraphics[width=0.66\textwidth]{Fig_I_ocean_bc} 
     132  \includegraphics[width=0.66\textwidth]{MB_ocean_bc} 
    133133  \caption[Ocean boundary conditions]{ 
    134134    The ocean is bounded by two surfaces, $z = - H(i,j)$ and $z = \eta(i,j,t)$, 
    … …  
    327327\begin{figure} 
    328328  \centering 
    329   \includegraphics[width=0.33\textwidth]{Fig_I_earth_referential} 
     329  \includegraphics[width=0.33\textwidth]{MB_earth_referential} 
    330330  \caption[Geographical and curvilinear coordinate systems]{ 
    331331    the geographical coordinate system $(\lambda,\varphi,z)$ and the curvilinear 
    … …  
    579579an explicit computation of vertical advection relative to the moving s-surfaces. 
    580580 
    581 %\gmcomment{ 
    582 %A key point here is that the $s$-coordinate depends on $(i,j)$ ==> horizontal pressure gradient... 
     581\cmtgm{A key point here is that the $s$-coordinate depends on $(i,j)$ 
     582  ==> horizontal pressure gradient...} 
    583583The generalized vertical coordinates used in ocean modelling are not orthogonal, 
    584584which contrasts with many other applications in mathematical physics. 
    … …  
    680680and similar expressions are used for mixing and forcing terms. 
    681681 
    682 \gmcomment{ 
     682\cmtgm{ 
    683683  \colorbox{yellow}{ to be updated $= = >$} 
    684684  Add a few works on z and zps and s and underlies the differences between all of them 
    … …  
    692692\begin{figure} 
    693693  \centering 
    694   \includegraphics[width=0.66\textwidth]{Fig_z_zstar} 
     694  \includegraphics[width=0.66\textwidth]{MB_z_zstar} 
    695695  \caption[Curvilinear z-coordinate systems (\{non-\}linear free-surface cases and re-scaled \zstar)]{ 
    696696    \begin{enumerate*}[label=(\textit{\alph*})] 
    … …  
    11501150Nevertheless it is currently not available in the iso-neutral case. 
    11511151 
    1152 \onlyinsubfile{\input{../../global/epilogue}} 
     1152\subinc{\input{../../global/epilogue}} 
    11531153 
    11541154\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex

    r12178 r12928  
    147147\begin{figure}[!t] 
    148148  \centering 
    149   \includegraphics[width=0.66\textwidth]{Fig_DYN_dynspg_ts} 
     149  %\includegraphics[width=0.66\textwidth]{MBZ_DYN_dynspg_ts} 
    150150  \caption[Schematic of the split-explicit time stepping scheme for 
    151151  the barotropic and baroclinic modes, after \citet{Griffies2004?}]{ 
    … …  
    311311In particular, this means that in filtered case, the matrix to be inverted has to be recomputed at each time-step. 
    312312 
    313 \onlyinsubfile{\input{../../global/epilogue}} 
     313\subinc{\input{../../global/epilogue}} 
    314314 
    315315\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/NEMO/subfiles/chap_time_domain.tex

    r12178 r12928  
    3131% - daymod: definition of the time domain (nit000, nitend and the calendar) 
    3232 
    33 \gmcomment{STEVEN :maybe a picture of the directory structure in the introduction which 
     33\cmtgm{STEVEN :maybe a picture of the directory structure in the introduction which 
    3434could be referred to here, would help  ==> to be added} 
    3535 
    … …  
    158158\end{equation} 
    159159 
    160 %%gm 
    161 %%gm   UPDATE the next paragraphs with time varying thickness ... 
    162 %%gm 
     160\cmtgm{UPDATE the next paragraphs with time varying thickness ...} 
    163161 
    164162This scheme is rather time consuming since it requires a matrix inversion. 
    … …  
    213211Fast barotropic motions (such as tides) are also simulated with a better accuracy. 
    214212 
    215 %\gmcomment{ 
     213%\cmtgm{ 
    216214\begin{figure} 
    217215  \centering 
    218   \includegraphics[width=0.66\textwidth]{Fig_TimeStepping_flowchart_v4} 
     216  \includegraphics[width=0.66\textwidth]{TD_TimeStepping_flowchart_v4} 
    219217  \caption[Leapfrog time stepping sequence with split-explicit free surface]{ 
    220218    Sketch of the leapfrog time stepping sequence in \NEMO\ with split-explicit free surface. 
    … …  
    276274\begin{figure} 
    277275  \centering 
    278   \includegraphics[width=0.66\textwidth]{Fig_MLF_forcing} 
     276  \includegraphics[width=0.66\textwidth]{TD_MLF_forcing} 
    279277  \caption[Forcing integration methods for modified leapfrog (top and bottom)]{ 
    280278    Illustration of forcing integration methods. 
    … …  
    328326the \nam{run}{run} namelist variables. 
    329327 
    330 \gmcomment{ 
     328\cmtgm{ 
    331329add here how to force the restart to contain only one time step for operational purposes 
    332330 
    … …  
    338336} 
    339337 
    340 \gmcomment{       % add a subsection here 
     338\cmtgm{       % add a subsection here 
    341339 
    342340%% ================================================================================================= 
    … …  
    353351}     %% end add 
    354352 
    355 \gmcomment{       % add implicit in vvl case  and Crant-Nicholson scheme 
     353\cmtgm{       % add implicit in vvl case  and Crant-Nicholson scheme 
    356354 
    357355Implicit time stepping in case of variable volume thickness. 
    … …  
    404402} 
    405403 
    406 \onlyinsubfile{\input{../../global/epilogue}} 
     404\subinc{\input{../../global/epilogue}} 
    407405 
    408406\end{document} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/SI3/build

    • Property svn:ignore

      •  

        old new  
        1414*.pdf 
        1515*.toc 
        16 *.xdv 
        1716_minted-* 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/SI3/main

    • Property svn:externals deleted

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/SI3/main/chapters.tex

    r12178 r12928  
    11\subfile{../subfiles/todolist} 
     2 
     3\subfile{../subfiles/introduction}               % Introduction 
    24 
    35\subfile{../subfiles/chap_model_basics} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/SI3/namelists/namdyn_adv

    r11026 r12928  
    22&namdyn_adv     !   Ice advection 
    33!------------------------------------------------------------------------------ 
    4    ln_adv_Pra       = .false.         !  Advection scheme (Prather) 
    5    ln_adv_UMx       = .true.          !  Advection scheme (Ultimate-Macho) 
     4   ln_adv_Pra       = .true.         !  Advection scheme (Prather) 
     5   ln_adv_UMx       = .false.          !  Advection scheme (Ultimate-Macho) 
    66      nn_UMx        =   5             !     order of the scheme for UMx (1-5 ; 20=centered 2nd order) 
    77/ 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/TOP/build

    • Property svn:ignore

      •  

        old new  
        1414*.pdf 
        1515*.toc 
        16 *.xdv 
        1716_minted-* 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/TOP/main

    • Property svn:externals deleted

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/TOP/main/chapters.tex

    r12178 r12928  
     1\subfile{../subfiles/introduction} 
    12\subfile{../subfiles/model_description} 
    23\subfile{../subfiles/model_setup} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/TOP/subfiles/model_description.tex

    r12178 r12928  
    1414\chapter{Model Description} 
    1515\label{chap:ModDes} 
    16 \minitoc 
     16\chaptertoc 
    1717 
    1818\section{Basics} 
    … …  
    8080\nlst{namtrc_ldf} 
    8181%------------------------------------------------------------------------------------------------------------- 
    82 In NEMO v4.0, the passive tracer diffusion has necessarily the same form as the active tracer diffusion, meaning that the numerical scheme must be the same. However the passive tracer mixing coefficient can be chosen as a multiple of the active ones by changing the value of \textit{rn\_ldf\_multi} in namelist \textit{namtrc\_ldf}. The choice of numerical scheme is then set  in the \ngn{namtra\_ldf} namelist for the dynamic described in section 5.2 of \citep{nemo_manual}. 
     82In NEMO v4.0, the passive tracer diffusion has necessarily the same form as the active tracer diffusion, meaning that the numerical scheme must be the same. However the passive tracer mixing coefficient can be chosen as a multiple of the active ones by changing the value of \textit{rn\_ldf\_multi} in namelist \textit{namtrc\_ldf}. The choice of numerical scheme is then set  in the \nam{namtra_ldf}{namtra\_ldf} namelist for the dynamic described in section 5.2 of \citep{nemo_manual}. 
    8383 
    8484 
    … …  
    9595 
    9696The use of newtonian damping  to climatological fields or observations is also coded, sharing the same routine dans active tracers. Boolean variables are defined in the namelist\_top\_ref to select the tracers on which restoring is applied 
    97 Options are defined through the  \ngn{namtrc\_dmp} namelist variables. The restoring term is added when the namelist parameter \np{ln\_trcdmp} is set to true. The restoring coefficient is a three-dimensional array read in a file, which name is specified by the namelist variable \np{cn\_resto\_tr}. This netcdf file can be generated using the DMP\_TOOLS tool. 
     97Options are defined through the \nam{namtrc_dmp}{namtrc\_dmp} namelist variables. The restoring term is added when the namelist parameter \np{ln\_trcdmp} is set to true. The restoring coefficient is a three-dimensional array read in a file, which name is specified by the namelist variable \np{cn\_resto\_tr}. This netcdf file can be generated using the DMP\_TOOLS tool. 
    9898 
    9999 \subsection{ Tracer positivity} 
    … …  
    104104 
    105105Sometimes, numerical scheme can generates negative values of passive tracers concentration that must be positive. For exemple,  isopycnal diffusion can created extrema. The trcrad routine artificially corrects negative concentrations with a very crude solution that either sets negative concentration to zero without adjusting the tracer budget, or by removing negative concentration and keeping mass conservation. 
    106 The treatment of negative concentrations is an option and can be selected in the namelist \ngn{namtrc\_rad} by setting the parameter \np{ln\_trcrad}  to true. 
     106The treatment of negative concentrations is an option and can be selected in the namelist \nam{namtrc_rad}{namtrc\_rad} by setting the parameter \np{ln\_trcrad}  to true. 
    107107 
    108108\section{The SMS modules} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/global

    • Property svn:ignore set to
      *.aux

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/global/document.tex

    r11591 r12928  
    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 
    … …  
    2635\renewcommand{\notinsubfile}[1]{#1} 
    2736 
     37\renewcommand{\biblio}{} 
     38\renewcommand{\pindex}{} 
     39 
    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/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/global/frontpage.tex

    r11591 r12928  
    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}.pdf} } 
    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/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/global/highlighting.tex

    r11572 r12928  
    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_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/global/index.ist

    r11584 r12928  
    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_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/global/info_page.tex

    r11515 r12928  
    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_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/global/new_cmds.tex

    r11584 r12928  
    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 
     27%% Text env. for Gurvan 
    3628\newcommand{\gmcomment}[1]{} 
    3729 
    … …  
    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_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/global/packages.tex

    r11595 r12928  
    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 = /home/ntmlod/.local/texlive2019/texmf-dist/fonts/opentype/public/fontawesome/ 
    21 } 
    22 \usepackage{academicons, fontawesome, newtxtext} 
    23  
    24 %% Formatting 
    25 \usepackage{etoc, tabularx, xcolor} 
    26  
    27 %% Graphics 
    28 \usepackage{caption, graphicx} 
    29  
    30 %% Labels 
    31 \usepackage{lastpage, natbib} 
    32  
    33 %% Mathematics 
    34 \usepackage{amsmath, amssymb} 
    35  
    36 %% Versatility 
    37 \usepackage{subfiles} 
     17%% Extensions in bundle package 
     18\usepackage{amssymb, graphicx, tabularx, textcomp} 
     19\usepackage[utf8]{inputenc}              %% input encoding 
    3820 
    3921%% Configuration 
    40 \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} 
    4126 
    42 %% Missing utmr8a font 
    43 \usepackage{times} 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/latex/global/styles.tex

    r11572 r12928  
    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 \makeatother 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/namelists/nam_diadct

    r12178 r12928  
    11!----------------------------------------------------------------------- 
    2 &nam_diadct     !   transports through some sections                    (default: OFF) 
     2&nam_diadct    !   transports through some sections                     (default: OFF) 
    33!----------------------------------------------------------------------- 
    44    ln_diadct  = .false.   ! Calculate transport thru sections or not 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/namelists/nambdy

    r12178 r12928  
    2626   ln_dyn3d_dmp  =.false.     !  open boundary condition for baroclinic velocities 
    2727   rn_time_dmp   =  1.        !  Damping time scale in days 
    28    rn_time_dmp_out = 1.        !  Outflow damping time scale 
     28   rn_time_dmp_out = 1.       !  Outflow damping time scale 
    2929   nn_rimwidth   = 10         !  width of the relaxation zone 
    3030   ln_vol        = .false.    !  total volume correction (see nn_volctl parameter) 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/namelists/nambdy_dta

    r12178 r12928  
    1111   !           !  file name              ! frequency (hours) ! variable  ! time interp.!  clim  ! 'yearly'/ ! weights filename ! rotation ! land/sea mask ! 
    1212   !           !                         !  (if <0  months)  !   name    !   (logical) !  (T/F) ! 'monthly' !                  ! pairing  !    filename   ! 
    13    bn_ssh      = 'amm12_bdyT_u2d'        ,         24        , 'sossheig',    .true.   , .false.,  'daily'  ,    ''            ,   ''     ,     '' 
    14    bn_u2d      = 'amm12_bdyU_u2d'        ,         24        , 'vobtcrtx',    .true.   , .false.,  'daily'  ,    ''            ,   ''     ,     '' 
    15    bn_v2d      = 'amm12_bdyV_u2d'        ,         24        , 'vobtcrty',    .true.   , .false.,  'daily'  ,    ''            ,   ''     ,     '' 
    16    bn_u3d      = 'amm12_bdyU_u3d'        ,         24        , 'vozocrtx',    .true.   , .false.,  'daily'  ,    ''            ,   ''     ,     '' 
    17    bn_v3d      = 'amm12_bdyV_u3d'        ,         24        , 'vomecrty',    .true.   , .false.,  'daily'  ,    ''            ,   ''     ,     '' 
    18    bn_tem      = 'amm12_bdyT_tra'        ,         24        , 'votemper',    .true.   , .false.,  'daily'  ,    ''            ,   ''     ,     '' 
    19    bn_sal      = 'amm12_bdyT_tra'        ,         24        , 'vosaline',    .true.   , .false.,  'daily'  ,    ''            ,   ''     ,     '' 
     13   bn_ssh      = 'amm12_bdyT_u2d'        ,         24.       , 'sossheig',    .true.   , .false.,  'daily'  ,    ''            ,   ''     ,     '' 
     14   bn_u2d      = 'amm12_bdyU_u2d'        ,         24.       , 'vobtcrtx',    .true.   , .false.,  'daily'  ,    ''            ,   ''     ,     '' 
     15   bn_v2d      = 'amm12_bdyV_u2d'        ,         24.       , 'vobtcrty',    .true.   , .false.,  'daily'  ,    ''            ,   ''     ,     '' 
     16   bn_u3d      = 'amm12_bdyU_u3d'        ,         24.       , 'vozocrtx',    .true.   , .false.,  'daily'  ,    ''            ,   ''     ,     '' 
     17   bn_v3d      = 'amm12_bdyV_u3d'        ,         24.       , 'vomecrty',    .true.   , .false.,  'daily'  ,    ''            ,   ''     ,     '' 
     18   bn_tem      = 'amm12_bdyT_tra'        ,         24.       , 'votemper',    .true.   , .false.,  'daily'  ,    ''            ,   ''     ,     '' 
     19   bn_sal      = 'amm12_bdyT_tra'        ,         24.       , 'vosaline',    .true.   , .false.,  'daily'  ,    ''            ,   ''     ,     '' 
    2020!* for si3 
    2121   bn_a_i      = 'amm12_bdyT_ice'        ,         24.       , 'siconc'  ,    .true.   , .false.,  'daily'  ,    ''            ,   ''     ,     '' 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/namelists/namberg

    r11005 r12928  
    3737   !           !  file name              ! frequency (hours) ! variable  ! time interp.!  clim  ! 'yearly'/ ! weights filename ! rotation ! land/sea mask ! 
    3838   !           !                         !  (if <0  months)  !   name    !   (logical) !  (T/F) ! 'monthly' !                  ! pairing  !    filename   ! 
    39    sn_icb     =  'calving'              ,         -1         ,'calvingmask',  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
     39   sn_icb     =  'calving'              ,         -1.        ,'calvingmask',  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    4040/ 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/namelists/namc1d_uvd

    r10075 r12928  
    1010   !           !  file name              ! frequency (hours) ! variable  ! time interp.!  clim  ! 'yearly'/ ! weights filename ! rotation ! land/sea mask ! 
    1111   !           !                         !  (if <0  months)  !   name    !   (logical) !  (T/F) ! 'monthly' !                  ! pairing  !    filename   ! 
    12    sn_ucur     = 'ucurrent'              ,         -1        ,'u_current',   .false.   , .true. , 'monthly' ,  ''              ,  'Ume'   , '' 
    13    sn_vcur     = 'vcurrent'              ,         -1        ,'v_current',   .false.   , .true. , 'monthly' ,  ''              ,  'Vme'   , '' 
     12   sn_ucur     = 'ucurrent'              ,         -1.       ,'u_current',   .false.   , .true. , 'monthly' ,  ''              ,  'Ume'   , '' 
     13   sn_vcur     = 'vcurrent'              ,         -1.       ,'v_current',   .false.   , .true. , 'monthly' ,  ''              ,  'Vme'   , '' 
    1414/ 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/namelists/namctl

    r10601 r12928  
    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/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/namelists/namdia

    r12178 r12928  
    22&namdia         !   Diagnostics 
    33!------------------------------------------------------------------------------ 
    4    ln_icediachk     = .false.         !  check online the heat, mass & salt budgets at each time step 
    5       !                               !     rate of ice spuriously gained/lost. For ex., rn_icechk=1. <=> 1mm/year, rn_icechk=0.1 <=> 1mm/10years 
    6       rn_icechk_cel =  1.             !     check at any gridcell           => stops the code if violated (and writes a file) 
    7       rn_icechk_glo =  0.1            !     check over the entire ice cover => only prints warnings 
     4   ln_icediachk     = .false.         !  check online heat, mass & salt budgets 
     5      !                               !   rate of ice spuriously gained/lost at each time step => rn_icechk=1 <=> 1.e-6 m/hour 
     6      rn_icechk_cel =  100.           !     check at each gridcell          (1.e-4m/h)=> stops the code if violated (and writes a file) 
     7      rn_icechk_glo =  1.             !     check over the entire ice cover (1.e-6m/h)=> only prints warnings 
    88   ln_icediahsb     = .false.         !  output the heat, mass & salt budgets (T) or not (F) 
    99   ln_icectl        = .false.         !  ice points output for debug (T or F) 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/namelists/namdta_dyn

    r11025 r12928  
    1010   !           !  file name              ! frequency (hours) ! variable  ! time interp.!  clim  ! 'yearly'/ ! weights filename ! rotation ! land/sea mask ! 
    1111   !           !                         !  (if <0  months)  !   name    !   (logical) !  (T/F) ! 'monthly' !                  ! pairing  !    filename   ! 
    12    sn_tem      = 'dyna_grid_T'           ,       120         , 'votemper'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    13    sn_sal      = 'dyna_grid_T'           ,       120         , 'vosaline'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    14    sn_mld      = 'dyna_grid_T'           ,       120         , 'somixhgt'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    15    sn_emp      = 'dyna_grid_T'           ,       120         , 'sowaflup'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    16    sn_fmf      = 'dyna_grid_T'           ,       120         , 'iowaflup'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    17    sn_ice      = 'dyna_grid_T'           ,       120         , 'soicecov'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    18    sn_qsr      = 'dyna_grid_T'           ,       120         , 'soshfldo'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    19    sn_wnd      = 'dyna_grid_T'           ,       120         , 'sowindsp'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    20    sn_uwd      = 'dyna_grid_U'           ,       120         , 'uocetr_eff',  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    21    sn_vwd      = 'dyna_grid_V'           ,       120         , 'vocetr_eff',  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    22    sn_wwd      = 'dyna_grid_W'           ,       120         , 'wocetr_eff',  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    23    sn_avt      = 'dyna_grid_W'           ,       120         , 'voddmavs'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    24    sn_ubl      = 'dyna_grid_U'           ,       120         , 'sobblcox'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    25    sn_vbl      = 'dyna_grid_V'           ,       120         , 'sobblcoy'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
     12   sn_tem      = 'dyna_grid_T'           ,       120.        , 'votemper'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
     13   sn_sal      = 'dyna_grid_T'           ,       120.        , 'vosaline'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
     14   sn_mld      = 'dyna_grid_T'           ,       120.        , 'somixhgt'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
     15   sn_emp      = 'dyna_grid_T'           ,       120.        , 'sowaflup'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
     16   sn_fmf      = 'dyna_grid_T'           ,       120.        , 'iowaflup'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
     17   sn_ice      = 'dyna_grid_T'           ,       120.        , 'soicecov'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
     18   sn_qsr      = 'dyna_grid_T'           ,       120.        , 'soshfldo'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
     19   sn_wnd      = 'dyna_grid_T'           ,       120.        , 'sowindsp'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
     20   sn_uwd      = 'dyna_grid_U'           ,       120.        , 'uocetr_eff',  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
     21   sn_vwd      = 'dyna_grid_V'           ,       120.        , 'vocetr_eff',  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
     22   sn_wwd      = 'dyna_grid_W'           ,       120.        , 'wocetr_eff',  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
     23   sn_avt      = 'dyna_grid_W'           ,       120.        , 'voddmavs'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
     24   sn_ubl      = 'dyna_grid_U'           ,       120.        , 'sobblcox'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
     25   sn_vbl      = 'dyna_grid_V'           ,       120.        , 'sobblcoy'  ,  .true.   , .true. , 'yearly'  , ''               , ''       , '' 
    2626/ 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/namelists/namdyn

    r11025 r12928  
    1010   rn_ishlat        =   2.            !  lbc : free slip (0) ; partial slip (0-2) ; no slip (2) ; strong slip (>2) 
    1111   ln_landfast_L16  = .false.         !  landfast: parameterization from Lemieux 2016 
    12    ln_landfast_home = .false.         !  landfast: parameterization from "home made" 
    1312      rn_depfra     =   0.125         !        fraction of ocean depth that ice must reach to initiate landfast 
    14                                       !          recommended range: [0.1 ; 0.25] - L16=0.125 - home=0.15 
    15       rn_icebfr     =  15.            !        ln_landfast_L16:  maximum bottom stress per unit volume [N/m3] 
    16                                       !        ln_landfast_home: maximum bottom stress per unit area of contact [N/m2] 
    17                                       !          recommended range: ?? L16=15 - home=10 
     13                                      !          recommended range: [0.1 ; 0.25] 
     14      rn_icebfr     =  15.            !        maximum bottom stress per unit volume [N/m3] 
    1815      rn_lfrelax    =   1.e-5         !        relaxation time scale to reach static friction [s-1] 
    19       rn_tensile    =   0.2           !        ln_landfast_L16: isotropic tensile strength 
     16      rn_tensile    =   0.05          !        isotropic tensile strength [0-0.5??] 
    2017/ 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/namelists/namini

    r12178 r12928  
    2323   rn_hpd_ini_n     =   0.05          !  initial pond depth          (m), North 
    2424   rn_hpd_ini_s     =   0.05          !        "            "             South 
    25    !        ! if ln_iceini_file=T 
     25   ! -- for ln_iceini_file = T 
    2626   sn_hti = 'Ice_initialization'    , -12 ,'hti'   ,  .false.  , .true., 'yearly'  , '' , '', '' 
    2727   sn_hts = 'Ice_initialization'    , -12 ,'hts'   ,  .false.  , .true., 'yearly'  , '' , '', '' 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/namelists/nammpp

    r12178 r12928  
    22&nammpp        !   Massively Parallel Processing                        ("key_mpp_mpi") 
    33!----------------------------------------------------------------------- 
     4   ln_listonly =  .false.  !  do nothing else than listing the best domain decompositions (with land domains suppression) 
     5   !                       !  if T: the largest number of cores tested is defined by max(mppsize, jpni*jpnj) 
    46   ln_nnogather =  .true.  !  activate code to avoid mpi_allgather use at the northfold 
    5    jpni        =   0       !  jpni   number of processors following i (set automatically if < 1) 
    6    jpnj        =   0       !  jpnj   number of processors following j (set automatically if < 1) 
     7   jpni        =   0       !  number of processors following i (set automatically if < 1), see also ln_listonly = T 
     8   jpnj        =   0       !  number of processors following j (set automatically if < 1), see also ln_listonly = T 
    79/ 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/namelists/namobs

    r12178 r12928  
    88   ln_sla      = .false.             ! Logical switch for SLA observations 
    99   ln_sst      = .false.             ! Logical switch for SST observations 
    10    ln_sss      = .false.             ! Logical switch for SSS observations 
     10   ln_sss      = .false.             ! Logical swithc for SSS observations 
    1111   ln_sic      = .false.             ! Logical switch for Sea Ice observations 
    1212   ln_vel3d    = .false.             ! Logical switch for velocity observations 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/namelists/nampisatm

    r11025 r12928  
    44!              !  file name   ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask ! 
    55!              !              !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      ! 
    6    sn_patm     = 'presatm'    ,     -1            , 'patm'    ,  .true.      , .true. , 'yearly'  , ''       , ''       , '' 
    7    sn_atmco2   = 'presatmco2' ,     -1            , 'xco2'    ,  .true.      , .true. , 'yearly'  , ''       , ''       , '' 
     6   sn_patm     = 'presatm'    ,     -1.           , 'patm'    ,  .true.      , .true. , 'yearly'  , ''       , ''       , '' 
     7   sn_atmco2   = 'presatmco2' ,     -1.           , 'xco2'    ,  .true.      , .true. , 'yearly'  , ''       , ''       , '' 
    88   cn_dir      = './'     !  root directory for the location of the dynamical files 
    99! 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/namelists/nampisopt

    r11025 r12928  
    44!              !  file name       ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask ! 
    55!              !                  !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      ! 
    6    sn_par      = 'par.orca'       ,     24            , 'fr_par'  ,  .true.      , .true. , 'yearly'  , ''       , ''       , '' 
     6   sn_par      = 'par.orca'       ,     24.           , 'fr_par'  ,  .true.      , .true. , 'yearly'  , ''       , ''       , '' 
    77   cn_dir      = './'      !  root directory for the location of the dynamical files 
    88   ln_varpar   =  .true.   ! boolean for PAR variable 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/namelists/nampissbc

    r11025 r12928  
    44!              !  file name        ! frequency (hours) ! variable      ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask ! 
    55!              !                   !  (if <0  months)  !   name        !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      ! 
    6    sn_dust     = 'dust.orca'       ,     -1            , 'dust'        ,  .true.      , .true. , 'yearly'  , ''       , ''    , '' 
    7    sn_solub    = 'solubility.orca' ,    -12            , 'solubility1' ,  .false.     , .true. , 'yearly'  , ''       , ''    , '' 
    8    sn_riverdic = 'river.orca'      ,    120            , 'riverdic'    ,  .true.      , .true. , 'yearly'  , ''       , ''    , '' 
    9    sn_riverdoc = 'river.orca'      ,    120            , 'riverdoc'    ,  .true.      , .true. , 'yearly'  , ''       , ''    , '' 
    10    sn_riverdin = 'river.orca'      ,    120            , 'riverdin'    ,  .true.      , .true. , 'yearly'  , ''       , ''    , '' 
    11    sn_riverdon = 'river.orca'      ,    120            , 'riverdon'    ,  .true.      , .true. , 'yearly'  , ''       , ''    , '' 
    12    sn_riverdip = 'river.orca'      ,    120            , 'riverdip'    ,  .true.      , .true. , 'yearly'  , ''       , ''    , '' 
    13    sn_riverdop = 'river.orca'      ,    120            , 'riverdop'    ,  .true.      , .true. , 'yearly'  , ''       , ''    , '' 
    14    sn_riverdsi = 'river.orca'      ,    120            , 'riverdsi'    ,  .true.      , .true. , 'yearly'  , ''       , ''    , '' 
    15    sn_ndepo    = 'ndeposition.orca',    -12            , 'ndep'        ,  .false.     , .true. , 'yearly'  , ''       , ''    , '' 
    16    sn_ironsed  = 'bathy.orca'      ,    -12            , 'bathy'       ,  .false.     , .true. , 'yearly'  , ''       , ''    , '' 
    17    sn_hydrofe  = 'hydrofe.orca'    ,    -12            , 'epsdb'       ,  .false.     , .true. , 'yearly'  , ''       , ''    , '' 
     6   sn_dust     = 'dust.orca'       ,     -1.           , 'dust'        ,  .true.      , .true. , 'yearly'  , ''       , ''    , '' 
     7   sn_solub    = 'solubility.orca' ,    -12.           , 'solubility1' ,  .false.     , .true. , 'yearly'  , ''       , ''    , '' 
     8   sn_riverdic = 'river.orca'      ,    120.           , 'riverdic'    ,  .true.      , .true. , 'yearly'  , ''       , ''    , '' 
     9   sn_riverdoc = 'river.orca'      ,    120.           , 'riverdoc'    ,  .true.      , .true. , 'yearly'  , ''       , ''    , '' 
     10   sn_riverdin = 'river.orca'      ,    120.           , 'riverdin'    ,  .true.      , .true. , 'yearly'  , ''       , ''    , '' 
     11   sn_riverdon = 'river.orca'      ,    120.           , 'riverdon'    ,  .true.      , .true. , 'yearly'  , ''       , ''    , '' 
     12   sn_riverdip = 'river.orca'      ,    120.           , 'riverdip'    ,  .true.      , .true. , 'yearly'  , ''       , ''    , '' 
     13   sn_riverdop = 'river.orca'      ,    120.           , 'riverdop'    ,  .true.      , .true. , 'yearly'  , ''       , ''    , '' 
     14   sn_riverdsi = 'river.orca'      ,    120.           , 'riverdsi'    ,  .true.      , .true. , 'yearly'  , ''       , ''    , '' 
     15   sn_ndepo    = 'ndeposition.orca',    -12.           , 'ndep'        ,  .false.     , .true. , 'yearly'  , ''       , ''    , '' 
     16   sn_ironsed  = 'bathy.orca'      ,    -12.           , 'bathy'       ,  .false.     , .true. , 'yearly'  , ''       , ''    , '' 
     17   sn_hydrofe  = 'hydrofe.orca'    ,    -12.           , 'epsdb'       ,  .false.     , .true. , 'yearly'  , ''       , ''    , '' 
    1818! 
    1919   cn_dir      = './'      !  root directory for the location of the dynamical files 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/namelists/namrun

    r11005 r12928  
    1818      cn_ocerst_indir = "."         !  directory from which to read input ocean restarts 
    1919      cn_ocerst_out   = "restart"   !  suffix of ocean restart name (output) 
    20       cn_ocerst_outdir = "."         !  directory in which to write output ocean restarts 
     20      cn_ocerst_outdir = "."        !  directory in which to write output ocean restarts 
    2121   ln_iscpl    = .false.   !  cavity evolution forcing or coupling to ice sheet model 
    2222   nn_istate   =       0   !  output the initial state (1) or not (0) 
    2323   ln_rst_list = .false.   !  output restarts at list of times using nn_stocklist (T) or at set frequency with nn_stock (F) 
    24    nn_stock    =    5840   !  frequency of creation of a restart file (modulo referenced to 1) 
     24   nn_stock    =       0   !  used only if ln_rst_list = F: output restart freqeuncy (modulo referenced to 1) 
     25      !                          !    =  0 force to write restart files only at the end of the run 
     26      !                          !    = -1 do not do any restart 
    2527   nn_stocklist = 0,0,0,0,0,0,0,0,0,0 ! List of timesteps when a restart file is to be written 
    26    nn_write    =    5840   !  frequency of write in the output file   (modulo referenced to nn_it000) 
    27    ln_mskland  = .false.   !  mask land points in NetCDF outputs (costly: + ~15%) 
     28   nn_write    =       0   !  used only if key_iomput is not defined: output frequency (modulo referenced to nn_it000) 
     29      !                          !    =  0 force to write output files only at the end of the run 
     30      !                          !    = -1 do not do any output file 
     31   ln_mskland  = .false.   !  mask land points in NetCDF outputs 
    2832   ln_cfmeta   = .false.   !  output additional data to netCDF files required for compliance with the CF metadata standard 
    2933   ln_clobber  = .true.    !  clobber (overwrite) an existing file 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/namelists/namsbc_apr

    r10075 r12928  
    1010   !           !  file name              ! frequency (hours) ! variable  ! time interp.!  clim  ! 'yearly'/ ! weights filename ! rotation ! land/sea mask ! 
    1111   !           !                         !  (if <0  months)  !   name    !   (logical) !  (T/F) ! 'monthly' !                  ! pairing  !    filename   ! 
    12    sn_apr      = 'patm'                  ,         -1        ,'somslpre' ,   .true.    , .true. , 'yearly'  ,    ''            ,    ''    ,      '' 
     12   sn_apr      = 'patm'                  ,         -1.       ,'somslpre' ,   .true.    , .true. , 'yearly'  ,    ''            ,    ''    ,      '' 
    1313/ 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/namelists/namsbc_blk

    r10445 r12928  
    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   !___________!_________________________!___________________!___________!_____________!________!___________!______________________________________!__________!_______________! 
    2229   !           !  file name              ! frequency (hours) ! variable  ! time interp.!  clim  ! 'yearly'/ !       weights filename               ! rotation ! land/sea mask ! 
    2330   !           !                         !  (if <0  months)  !   name    !   (logical) !  (T/F) ! 'monthly' !                                      ! pairing  !    filename   ! 
    24    sn_wndi     = 'u_10.15JUNE2009_fill'       ,    6         , 'U_10_MOD',   .false.   , .true. , 'yearly'  , 'weights_core_orca2_bicubic_noc.nc'  , 'Uwnd'   , '' 
    25    sn_wndj     = 'v_10.15JUNE2009_fill'       ,    6         , 'V_10_MOD',   .false.   , .true. , 'yearly'  , 'weights_core_orca2_bicubic_noc.nc'  , 'Vwnd'   , '' 
    26    sn_qsr      = 'ncar_rad.15JUNE2009_fill'   ,   24         , 'SWDN_MOD',   .false.   , .true. , 'yearly'  , 'weights_core_orca2_bilinear_noc.nc' , ''       , '' 
    27    sn_qlw      = 'ncar_rad.15JUNE2009_fill'   ,   24         , 'LWDN_MOD',   .false.   , .true. , 'yearly'  , 'weights_core_orca2_bilinear_noc.nc' , ''       , '' 
    28    sn_tair     = 't_10.15JUNE2009_fill'       ,    6         , 'T_10_MOD',   .false.   , .true. , 'yearly'  , 'weights_core_orca2_bilinear_noc.nc' , ''       , '' 
    29    sn_humi     = 'q_10.15JUNE2009_fill'       ,    6         , 'Q_10_MOD',   .false.   , .true. , 'yearly'  , 'weights_core_orca2_bilinear_noc.nc' , ''       , '' 
    30    sn_prec     = 'ncar_precip.15JUNE2009_fill',   -1         , 'PRC_MOD1',   .false.   , .true. , 'yearly'  , 'weights_core_orca2_bilinear_noc.nc' , ''       , '' 
    31    sn_snow     = 'ncar_precip.15JUNE2009_fill',   -1         , 'SNOW'    ,   .false.   , .true. , 'yearly'  , 'weights_core_orca2_bilinear_noc.nc' , ''       , '' 
    32    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' , ''       , '' 
     31   sn_wndi     = 'u_10.15JUNE2009_fill'       ,    6.        , 'U_10_MOD',   .false.   , .true. , 'yearly'  , 'weights_core_orca2_bicubic_noc.nc'  , 'Uwnd'   , '' 
     32   sn_wndj     = 'v_10.15JUNE2009_fill'       ,    6.        , 'V_10_MOD',   .false.   , .true. , 'yearly'  , 'weights_core_orca2_bicubic_noc.nc'  , 'Vwnd'   , '' 
     33   sn_qsr      = 'ncar_rad.15JUNE2009_fill'   ,   24.        , 'SWDN_MOD',   .false.   , .true. , 'yearly'  , 'weights_core_orca2_bilinear_noc.nc' , ''       , '' 
     34   sn_qlw      = 'ncar_rad.15JUNE2009_fill'   ,   24.        , 'LWDN_MOD',   .false.   , .true. , 'yearly'  , 'weights_core_orca2_bilinear_noc.nc' , ''       , '' 
     35   sn_tair     = 't_10.15JUNE2009_fill'       ,    6.        , 'T_10_MOD',   .false.   , .true. , 'yearly'  , 'weights_core_orca2_bilinear_noc.nc' , ''       , '' 
     36   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'     , '' 
     39   sn_prec     = 'ncar_precip.15JUNE2009_fill',   -1.        , 'PRC_MOD1',   .false.   , .true. , 'yearly'  , 'weights_core_orca2_bilinear_noc.nc' , ''       , '' 
     40   sn_snow     = 'ncar_precip.15JUNE2009_fill',   -1.        , 'SNOW'    ,   .false.   , .true. , 'yearly'  , 'weights_core_orca2_bilinear_noc.nc' , ''       , '' 
     41   sn_slp      = 'slp.15JUNE2009_fill'        ,    6.        , 'SLP'     ,   .false.   , .true. , 'yearly'  , 'weights_core_orca2_bilinear_noc.nc' , ''       , '' 
    3442/ 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/namelists/namsbc_flx

    r10075 r12928  
    66   !           !  file name              ! frequency (hours) ! variable  ! time interp.!  clim  ! 'yearly'/ ! weights filename ! rotation ! land/sea mask ! 
    77   !           !                         !  (if <0  months)  !   name    !   (logical) !  (T/F) ! 'monthly' !                  ! pairing  !    filename   ! 
    8    sn_utau     = 'utau'                  ,        24         , 'utau'    , .false.     , .false., 'yearly'  , ''               , ''       , '' 
    9    sn_vtau     = 'vtau'                  ,        24         , 'vtau'    , .false.     , .false., 'yearly'  , ''               , ''       , '' 
    10    sn_qtot     = 'qtot'                  ,        24         , 'qtot'    , .false.     , .false., 'yearly'  , ''               , ''       , '' 
    11    sn_qsr      = 'qsr'                   ,        24         , 'qsr'     , .false.     , .false., 'yearly'  , ''               , ''       , '' 
    12    sn_emp      = 'emp'                   ,        24         , 'emp'     , .false.     , .false., 'yearly'  , ''               , ''       , '' 
     8   sn_utau     = 'utau'                  ,        24.        , 'utau'    , .false.     , .false., 'yearly'  , ''               , ''       , '' 
     9   sn_vtau     = 'vtau'                  ,        24.        , 'vtau'    , .false.     , .false., 'yearly'  , ''               , ''       , '' 
     10   sn_qtot     = 'qtot'                  ,        24.        , 'qtot'    , .false.     , .false., 'yearly'  , ''               , ''       , '' 
     11   sn_qsr      = 'qsr'                   ,        24.        , 'qsr'     , .false.     , .false., 'yearly'  , ''               , ''       , '' 
     12   sn_emp      = 'emp'                   ,        24.        , 'emp'     , .false.     , .false., 'yearly'  , ''               , ''       , '' 
    1313/ 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/namelists/namsbc_isf

    r10445 r12928  
    2424   !           !             !  (if <0  months)  !   name    !  (logical)  !  (T/F)  ! 'monthly' ! filename ! pairing  ! filename      ! 
    2525!* nn_isf = 4 case 
    26    sn_fwfisf   = 'rnfisf'    ,         -12       ,'sowflisf' ,  .false.    , .true.  , 'yearly'  ,    ''    ,   ''     ,    '' 
     26   sn_fwfisf   = 'rnfisf'    ,         -12.      ,'sowflisf' ,  .false.    , .true.  , 'yearly'  ,    ''    ,   ''     ,    '' 
    2727!* nn_isf = 3 case 
    28    sn_rnfisf   = 'rnfisf'    ,         -12       ,'sofwfisf' ,  .false.    , .true.  , 'yearly'  ,    ''    ,   ''     ,    '' 
     28   sn_rnfisf   = 'rnfisf'    ,         -12.      ,'sofwfisf' ,  .false.    , .true.  , 'yearly'  ,    ''    ,   ''     ,    '' 
    2929!* nn_isf = 2 and 3 cases  
    30    sn_depmax_isf ='rnfisf'    ,         -12       ,'sozisfmax',  .false.    , .true.  , 'yearly'  ,    ''    ,   ''     ,    '' 
    31    sn_depmin_isf ='rnfisf'    ,         -12       ,'sozisfmin',  .false.    , .true.  , 'yearly'  ,    ''    ,   ''     ,    '' 
     30   sn_depmax_isf ='rnfisf'   ,         -12.      ,'sozisfmax',  .false.    , .true.  , 'yearly'  ,    ''    ,   ''     ,    '' 
     31   sn_depmin_isf ='rnfisf'   ,         -12.      ,'sozisfmin',  .false.    , .true.  , 'yearly'  ,    ''    ,   ''     ,    '' 
    3232!* nn_isf = 2 case 
    33    sn_Leff_isf = 'rnfisf'    ,         -12       ,'Leff'     ,  .false.    , .true.  , 'yearly'  ,    ''    ,   ''     ,    '' 
     33   sn_Leff_isf = 'rnfisf'    ,         -12.      ,'Leff'     ,  .false.    , .true.  , 'yearly'  ,    ''    ,   ''     ,    '' 
    3434/ 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/namelists/namsbc_rnf

    r10445 r12928  
    1818   !           !  file name              ! frequency (hours) ! variable  ! time interp.!  clim  ! 'yearly'/ ! weights filename ! rotation ! land/sea mask ! 
    1919   !           !                         !  (if <0  months)  !   name    !   (logical) !  (T/F) ! 'monthly' !                  ! pairing  !    filename   ! 
    20    sn_rnf      = 'runoff_core_monthly'   ,        -1         , 'sorunoff',   .true.    , .true. , 'yearly'  , ''               , ''       , '' 
    21    sn_cnf      = 'runoff_core_monthly'   ,         0         , 'socoefr0',   .false.   , .true. , 'yearly'  , ''               , ''       , '' 
    22    sn_s_rnf    = 'runoffs'               ,        24         , 'rosaline',   .true.    , .true. , 'yearly'  , ''               , ''       , '' 
    23    sn_t_rnf    = 'runoffs'               ,        24         , 'rotemper',   .true.    , .true. , 'yearly'  , ''               , ''       , '' 
    24    sn_dep_rnf  = 'runoffs'               ,         0         , 'rodepth' ,   .false.   , .true. , 'yearly'  , ''               , ''       , '' 
     20   sn_rnf      = 'runoff_core_monthly'   ,        -1.        , 'sorunoff',   .true.    , .true. , 'yearly'  , ''               , ''       , '' 
     21   sn_cnf      = 'runoff_core_monthly'   ,         0.        , 'socoefr0',   .false.   , .true. , 'yearly'  , ''               , ''       , '' 
     22   sn_s_rnf    = 'runoffs'               ,        24.        , 'rosaline',   .true.    , .true. , 'yearly'  , ''               , ''       , '' 
     23   sn_t_rnf    = 'runoffs'               ,        24.        , 'rotemper',   .true.    , .true. , 'yearly'  , ''               , ''       , '' 
     24   sn_dep_rnf  = 'runoffs'               ,         0.        , 'rodepth' ,   .false.   , .true. , 'yearly'  , ''               , ''       , '' 
    2525/ 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/namelists/namsbc_sas

    r10075 r12928  
    1010   !           !  file name              ! frequency (hours) ! variable  ! time interp.!  clim  ! 'yearly'/ ! weights filename ! rotation ! land/sea mask ! 
    1111   !           !                         !  (if <0  months)  !   name    !   (logical) !  (T/F) ! 'monthly' !                  ! pairing  !    filename   ! 
    12    sn_usp      = 'sas_grid_U'            ,       120         , 'uos'     ,   .true.    , .true. , 'yearly'  ,    ''            ,    ''    ,    '' 
    13    sn_vsp      = 'sas_grid_V'            ,       120         , 'vos'     ,   .true.    , .true. , 'yearly'  ,    ''            ,    ''    ,    '' 
    14    sn_tem      = 'sas_grid_T'            ,       120         , 'sosstsst',   .true.    , .true. , 'yearly'  ,    ''            ,    ''    ,    '' 
    15    sn_sal      = 'sas_grid_T'            ,       120         , 'sosaline',   .true.    , .true. , 'yearly'  ,    ''            ,    ''    ,    '' 
    16    sn_ssh      = 'sas_grid_T'            ,       120         , 'sossheig',   .true.    , .true. , 'yearly'  ,    ''            ,    ''    ,    '' 
    17    sn_e3t      = 'sas_grid_T'            ,       120         , 'e3t_m'   ,   .true.    , .true. , 'yearly'  ,    ''            ,    ''    ,    '' 
    18    sn_frq      = 'sas_grid_T'            ,       120         , 'frq_m'   ,   .true.    , .true. , 'yearly'  ,    ''            ,    ''    ,    '' 
     12   sn_usp      = 'sas_grid_U'            ,       120.        , 'uos'     ,   .true.    , .true. , 'yearly'  ,    ''            ,    ''    ,    '' 
     13   sn_vsp      = 'sas_grid_V'            ,       120.        , 'vos'     ,   .true.    , .true. , 'yearly'  ,    ''            ,    ''    ,    '' 
     14   sn_tem      = 'sas_grid_T'            ,       120.        , 'sosstsst',   .true.    , .true. , 'yearly'  ,    ''            ,    ''    ,    '' 
     15   sn_sal      = 'sas_grid_T'            ,       120.        , 'sosaline',   .true.    , .true. , 'yearly'  ,    ''            ,    ''    ,    '' 
     16   sn_ssh      = 'sas_grid_T'            ,       120.        , 'sossheig',   .true.    , .true. , 'yearly'  ,    ''            ,    ''    ,    '' 
     17   sn_e3t      = 'sas_grid_T'            ,       120.        , 'e3t_m'   ,   .true.    , .true. , 'yearly'  ,    ''            ,    ''    ,    '' 
     18   sn_frq      = 'sas_grid_T'            ,       120.        , 'frq_m'   ,   .true.    , .true. , 'yearly'  ,    ''            ,    ''    ,    '' 
    1919/ 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/namelists/namsbc_ssr

    r10075 r12928  
    1414   !           !  file name              ! frequency (hours) ! variable  ! time interp.!  clim  ! 'yearly'/ ! weights filename ! rotation ! land/sea mask ! 
    1515   !           !                         !  (if <0  months)  !   name    !   (logical) !  (T/F) ! 'monthly' !                  ! pairing  !    filename   ! 
    16    sn_sst      = 'sst_data'              ,        24         ,  'sst'    ,    .false.  , .false., 'yearly'  ,    ''            ,    ''    ,     '' 
    17    sn_sss      = 'sss_data'              ,        -1         ,  'sss'    ,    .true.   , .true. , 'yearly'  ,    ''            ,    ''    ,     '' 
     16   sn_sst      = 'sst_data'              ,        24.        ,  'sst'    ,    .false.  , .false., 'yearly'  ,    ''            ,    ''    ,     '' 
     17   sn_sss      = 'sss_data'              ,        -1.        ,  'sss'    ,    .true.   , .true. , 'yearly'  ,    ''            ,    ''    ,     '' 
    1818/ 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/namelists/namsbc_wave

    r10445 r12928  
    66   !           !  file name              ! frequency (hours) ! variable  ! time interp.!  clim  ! 'yearly'/ ! weights filename ! rotation ! land/sea mask ! 
    77   !           !                         !  (if <0  months)  !   name    !   (logical) !  (T/F) ! 'monthly' !                  ! pairing  !    filename   ! 
    8    sn_cdg      =  'sdw_ecwaves_orca2'    ,        6          , 'drag_coeff' ,  .true.  , .true. , 'yearly'  ,  ''              , ''       , '' 
    9    sn_usd      =  'sdw_ecwaves_orca2'    ,        6          , 'u_sd2d'     ,  .true.  , .true. , 'yearly'  ,  ''              , ''       , '' 
    10    sn_vsd      =  'sdw_ecwaves_orca2'    ,        6          , 'v_sd2d'     ,  .true.  , .true. , 'yearly'  ,  ''              , ''       , '' 
    11    sn_hsw      =  'sdw_ecwaves_orca2'    ,        6          , 'hs'         ,  .true.  , .true. , 'yearly'  ,  ''              , ''       , '' 
    12    sn_wmp      =  'sdw_ecwaves_orca2'    ,        6          , 'wmp'        ,  .true.  , .true. , 'yearly'  ,  ''              , ''       , '' 
    13    sn_wfr      =  'sdw_ecwaves_orca2'    ,        6          , 'wfr'        ,  .true.  , .true. , 'yearly'  ,  ''              , ''       , '' 
    14    sn_wnum     =  'sdw_ecwaves_orca2'    ,        6          , 'wave_num'   ,  .true.  , .true. , 'yearly'  ,  ''              , ''       , '' 
    15    sn_tauwoc   =  'sdw_ecwaves_orca2'    ,        6          , 'wave_stress',  .true.  , .true. , 'yearly'  ,  ''              , ''       , '' 
    16    sn_tauwx    =  'sdw_ecwaves_orca2'    ,        6          , 'wave_stress',  .true.  , .true. , 'yearly'  ,  ''              , ''       , '' 
    17    sn_tauwy    =  'sdw_ecwaves_orca2'    ,        6          , 'wave_stress',  .true.  , .true. , 'yearly'  ,  ''              , ''       , '' 
     8   sn_cdg      =  'sdw_ecwaves_orca2'    ,        6.         , 'drag_coeff' ,  .true.  , .true. , 'yearly'  ,  ''              , ''       , '' 
     9   sn_usd      =  'sdw_ecwaves_orca2'    ,        6.         , 'u_sd2d'     ,  .true.  , .true. , 'yearly'  ,  ''              , ''       , '' 
     10   sn_vsd      =  'sdw_ecwaves_orca2'    ,        6.         , 'v_sd2d'     ,  .true.  , .true. , 'yearly'  ,  ''              , ''       , '' 
     11   sn_hsw      =  'sdw_ecwaves_orca2'    ,        6.         , 'hs'         ,  .true.  , .true. , 'yearly'  ,  ''              , ''       , '' 
     12   sn_wmp      =  'sdw_ecwaves_orca2'    ,        6.         , 'wmp'        ,  .true.  , .true. , 'yearly'  ,  ''              , ''       , '' 
     13   sn_wfr      =  'sdw_ecwaves_orca2'    ,        6.         , 'wfr'        ,  .true.  , .true. , 'yearly'  ,  ''              , ''       , '' 
     14   sn_wnum     =  'sdw_ecwaves_orca2'    ,        6.         , 'wave_num'   ,  .true.  , .true. , 'yearly'  ,  ''              , ''       , '' 
     15   sn_tauwoc   =  'sdw_ecwaves_orca2'    ,        6.         , 'wave_stress',  .true.  , .true. , 'yearly'  ,  ''              , ''       , '' 
     16   sn_tauwx    =  'sdw_ecwaves_orca2'    ,        6.         , 'wave_stress',  .true.  , .true. , 'yearly'  ,  ''              , ''       , '' 
     17   sn_tauwy    =  'sdw_ecwaves_orca2'    ,        6.         , 'wave_stress',  .true.  , .true. , 'yearly'  ,  ''              , ''       , '' 
    1818/ 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/namelists/namtra_qsr

    r10075 r12928  
    1616   !           !  file name              ! frequency (hours) ! variable  ! time interp.!  clim  ! 'yearly'/ ! weights filename ! rotation ! land/sea mask ! 
    1717   !           !                         !  (if <0  months)  !   name    !   (logical) !  (T/F) ! 'monthly' !                  ! pairing  !    filename   ! 
    18    sn_chl      ='chlorophyll'            ,        -1         , 'CHLA'    ,   .true.    , .true. , 'yearly'  , ''               , ''       , '' 
     18   sn_chl      ='chlorophyll'            ,        -1.        , 'CHLA'    ,   .true.    , .true. , 'yearly'  , ''               , ''       , '' 
    1919/ 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/namelists/namtrc_dta

    r11025 r12928  
    44!                !  file name        ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask ! 
    55!                !                   !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      ! 
    6    sn_trcdta(1)  = 'data_TRC_nomask' ,        -12        ,  'TRC'    ,    .false.   , .true. , 'yearly'  , ''       , ''       , '' 
     6   sn_trcdta(1)  = 'data_TRC_nomask' ,        -12.       ,  'TRC'    ,    .false.   , .true. , 'yearly'  , ''       , ''       , '' 
    77   ! 
    88   cn_dir        =  './'     !  root directory for the location of the data files 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/namelists/namtsd

    r10075 r12928  
    1010   !           !  file name              ! frequency (hours) ! variable  ! time interp.!  clim  ! 'yearly'/ ! weights filename ! rotation ! land/sea mask ! 
    1111   !           !                         !  (if <0  months)  !   name    !   (logical) !  (T/F) ! 'monthly' !                  ! pairing  !    filename   ! 
    12    sn_tem = 'data_1m_potential_temperature_nomask',  -1      , 'votemper',   .true.    , .true. , 'yearly'  ,    ''            ,    ''    ,    '' 
    13    sn_sal = 'data_1m_salinity_nomask'             ,  -1      , 'vosaline',   .true.    , .true. , 'yearly'  ,    ''            ,    ''    ,    '' 
     12   sn_tem = 'data_1m_potential_temperature_nomask',  -1.     , 'votemper',   .true.    , .true. , 'yearly'  ,    ''            ,    ''    ,    '' 
     13   sn_sal = 'data_1m_salinity_nomask'             ,  -1.     , 'vosaline',   .true.    , .true. , 'yearly'  ,    ''            ,    ''    ,    '' 
    1414/ 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/rst/Makefile

    r10990 r12928  
    1 # Minimal makefile for Sphinx documentation 
     1# Makefile for Sphinx documentation 
    22# 
    33 
    … …  
    55SPHINXOPTS    = 
    66SPHINXBUILD   = sphinx-build 
    7 SPHINXPROJ    = NEMO 
    8 SOURCEDIR     = source 
     7PAPER         = 
    98BUILDDIR      = build 
    109 
    11 # Put it first so that "make" without argument is like "make help". 
     10# Internal variables. 
     11PAPEROPT_a4     = -D latex_paper_size=a4 
     12PAPEROPT_letter = -D latex_paper_size=letter 
     13ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source 
     14# the i18n builder cannot share the environment and doctrees with the others 
     15I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source 
     16 
     17.PHONY: help clean html dirhtml drafthtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext 
     18 
    1219help: 
    13    @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 
     20   @echo "Please use \`make <target>' where <target> is one of" 
     21   @echo "  html       to make standalone HTML files" 
     22   @echo "  dirhtml    to make HTML files named index.html in directories" 
     23   @echo "  drafthtml  to make an autoupdate HTML export while editing (todo list included)" 
     24   @echo "  singlehtml to make a single large HTML file" 
     25   @echo "  pickle     to make pickle files" 
     26   @echo "  json       to make JSON files" 
     27   @echo "  htmlhelp   to make HTML files and a HTML help project" 
     28   @echo "  qthelp     to make HTML files and a qthelp project" 
     29   @echo "  devhelp    to make HTML files and a Devhelp project" 
     30   @echo "  epub       to make an epub" 
     31   @echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter" 
     32   @echo "  latexpdf   to make LaTeX files and run them through pdflatex" 
     33   @echo "  text       to make text files" 
     34   @echo "  man        to make manual pages" 
     35   @echo "  texinfo    to make Texinfo files" 
     36   @echo "  info       to make Texinfo files and run them through makeinfo" 
     37   @echo "  gettext    to make PO message catalogs" 
     38   @echo "  changes    to make an overview of all changed/added/deprecated items" 
     39   @echo "  linkcheck  to check all external links for integrity" 
     40   @echo "  doctest    to run all doctests embedded in the documentation (if enabled)" 
    1441 
    15 .PHONY: help Makefile 
     42clean: 
     43   -rm -rf $(BUILDDIR)/* 
    1644 
    17 # Catch-all target: route all unknown targets to Sphinx using the new 
    18 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS). 
    19 %: Makefile 
    20    @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 
     45html: 
     46   $(SPHINXBUILD)   -b html          $(ALLSPHINXOPTS) $(BUILDDIR)/html 
     47   @echo 
     48   @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." 
    2149 
    22 # Watch source directory and rebuild the documentation when a change is detected 
    23 # Browse to 127.0.0.1:8000/NEMO_guide.html 
    24 htmllive: 
    25    sphinx-autobuild $(SPHINXOPTS) $(SOURCEDIR) $(BUILDDIR)/htmllive 
     50dirhtml: 
     51   $(SPHINXBUILD)   -b dirhtml       $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml 
     52   @echo 
     53   @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." 
     54 
     55drafthtml: 
     56   sphinx-autobuild -b html -t draft $(ALLSPHINXOPTS) $(BUILDDIR)/drafthtml 
     57   @echo 
     58   @echo "Build finished. The HTML pages are in $(BUILDDIR)/drafthtml." 
     59 
     60singlehtml: 
     61   $(SPHINXBUILD)   -b singlehtml    $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml 
     62   @echo 
     63   @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." 
     64 
     65pickle: 
     66   $(SPHINXBUILD)   -b pickle        $(ALLSPHINXOPTS) $(BUILDDIR)/pickle 
     67   @echo 
     68   @echo "Build finished; now you can process the pickle files." 
     69 
     70json: 
     71   $(SPHINXBUILD)   -b json          $(ALLSPHINXOPTS) $(BUILDDIR)/json 
     72   @echo 
     73   @echo "Build finished; now you can process the JSON files." 
     74 
     75htmlhelp: 
     76   $(SPHINXBUILD)   -b htmlhelp      $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp 
     77   @echo 
     78   @echo "Build finished; now you can run HTML Help Workshop with the" \ 
     79         ".hhp project file in $(BUILDDIR)/htmlhelp." 
     80 
     81qthelp: 
     82   $(SPHINXBUILD)   -b qthelp        $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp 
     83   @echo 
     84   @echo "Build finished; now you can run "qcollectiongenerator" with the" \ 
     85         ".qhcp project file in $(BUILDDIR)/qthelp, like this:" 
     86   @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/NEMO.qhcp" 
     87   @echo "To view the help file:" 
     88   @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/NEMO.qhc" 
     89 
     90devhelp: 
     91   $(SPHINXBUILD)   -b devhelp       $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp 
     92   @echo 
     93   @echo "Build finished." 
     94   @echo "To view the help file:" 
     95   @echo "# mkdir -p $$HOME/.local/share/devhelp/NEMO" 
     96   @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/NEMO" 
     97   @echo "# devhelp" 
     98 
     99epub: 
     100   $(SPHINXBUILD)   -b epub          $(ALLSPHINXOPTS) $(BUILDDIR)/epub 
     101   @echo 
     102   @echo "Build finished. The epub file is in $(BUILDDIR)/epub." 
     103 
     104latex: 
     105   $(SPHINXBUILD)   -b latex         $(ALLSPHINXOPTS) $(BUILDDIR)/latex 
     106   @echo 
     107   @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." 
     108   @echo "Run \`make' in that directory to run these through (pdf)latex" \ 
     109         "(use \`make latexpdf' here to do that automatically)." 
     110 
     111latexpdf: 
     112   $(SPHINXBUILD)   -b latex         $(ALLSPHINXOPTS) $(BUILDDIR)/latex 
     113   @echo "Running LaTeX files through pdflatex..." 
     114   $(MAKE) -C $(BUILDDIR)/latex all-pdf 
     115   @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." 
     116 
     117text: 
     118   $(SPHINXBUILD)   -b text          $(ALLSPHINXOPTS) $(BUILDDIR)/text 
     119   @echo 
     120   @echo "Build finished. The text files are in $(BUILDDIR)/text." 
     121 
     122man: 
     123   $(SPHINXBUILD)   -b man           $(ALLSPHINXOPTS) $(BUILDDIR)/man 
     124   @echo 
     125   @echo "Build finished. The manual pages are in $(BUILDDIR)/man." 
     126 
     127texinfo: 
     128   $(SPHINXBUILD)   -b texinfo       $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo 
     129   @echo 
     130   @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." 
     131   @echo "Run \`make' in that directory to run these through makeinfo" \ 
     132         "(use \`make info' here to do that automatically)." 
     133 
     134info: 
     135   $(SPHINXBUILD)   -b texinfo       $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo 
     136   @echo "Running Texinfo files through makeinfo..." 
     137   make -C $(BUILDDIR)/texinfo info 
     138   @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." 
     139 
     140gettext: 
     141   $(SPHINXBUILD)   -b gettext      $(I18NSPHINXOPTS) $(BUILDDIR)/locale 
     142   @echo 
     143   @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." 
     144 
     145changes: 
     146   $(SPHINXBUILD)   -b changes       $(ALLSPHINXOPTS) $(BUILDDIR)/changes 
     147   @echo 
     148   @echo "The overview file is in $(BUILDDIR)/changes." 
     149 
     150linkcheck: 
     151   $(SPHINXBUILD)   -b linkcheck     $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck 
     152   @echo 
     153   @echo "Link check complete; look for any errors in the above output " \ 
     154         "or in $(BUILDDIR)/linkcheck/output.txt." 
     155 
     156doctest: 
     157   $(SPHINXBUILD)   -b doctest       $(ALLSPHINXOPTS) $(BUILDDIR)/doctest 
     158   @echo "Testing of doctests in the sources finished, look at the " \ 
     159         "results in $(BUILDDIR)/doctest/output.txt." 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/rst/README.rst

    r10991 r12928  
    33********************** 
    44 
    5 | The NEMO guide is made up of several files written in `ReStructuredText <http://docutils.sourceforge.net/rst.html>`_ (`.rst` extension), a WYSIWYG markup language used in the Python community, and scattered all over the NEMO sources. 
     5| The NEMO guide is made up of several files written in 
     6  `ReStructuredText <http://docutils.sourceforge.net/rst.html>`_ (`.rst` extension), 
     7  a WYSIWYG markup language used in the Python community, and scattered all over the NEMO sources. 
    68| You can view them one by one in plain text from `./source` folder, or export all to a user-friendly guide under `./build` (only HTML format at the moment, PDF expected later). 
    79 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/rst/source/_static/style.css

    r10279 r12928  
    1 .rstblue               { color: blue    ; } 
    2 .rstgrey , .rstgreysup { color: grey    ; } 
    3 .rstgreen              { color: seagreen; } 
     1.blue            { color: blue    ; } 
     2.grey , .greysup { color: grey    ; } 
     3.green           { color: seagreen; } 
    44 
    55.logo { filter: invert(1) !important; } 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/rst/source/conf.py

    r10991 r12928  
    11# -*- coding: utf-8 -*- 
    22# 
    3 # Configuration file for the Sphinx documentation builder. 
    4 # 
    5 # This file does only contain a selection of the most common options. For a 
    6 # full list see the documentation: 
    7 # http://www.sphinx-doc.org/en/master/config 
    8  
    9 # -- Project information ----------------------------------------------------- 
    10  
    11 project = 'NEMO' 
    12 author = 'NEMO System Team' 
    13  
    14 # The short X.Y version 
    15 version = 'trk' 
    16 # The full version, including alpha/beta/rc tags 
    17 release = 'trunk' 
    18  
    19  
    20 # -- General configuration --------------------------------------------------- 
    21  
    22 # Add any Sphinx extension module names here, as strings. They can be 
    23 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom 
    24 # ones. 
    25 extensions = ['sphinx.ext.extlinks', 'sphinxcontrib.bibtex'] 
     3# NEMO documentation build configuration file, created by 
     4# sphinx-quickstart on Tue Oct 15 20:13:55 2019. 
     5# 
     6# This file is execfile()d with the current directory set to its containing dir. 
     7# 
     8# Note that not all possible configuration values are present in this 
     9# autogenerated file. 
     10# 
     11# All configuration values have a default; values that are commented out 
     12# serve to show the default. 
     13 
     14import sys, os 
     15 
     16# If extensions (or modules to document with autodoc) are in another directory, 
     17# add these directories to sys.path here. If the directory is relative to the 
     18# documentation root, use os.path.abspath to make it absolute, like shown here. 
     19#sys.path.insert(0, os.path.abspath('.')) 
     20 
     21# -- General configuration ----------------------------------------------------- 
     22 
     23# If your documentation needs a minimal Sphinx version, state it here. 
     24#needs_sphinx = '1.0' 
     25 
     26# Add any Sphinx extension module names here, as strings. They can be extensions 
     27# coming with Sphinx (named 'sphinx.ext.*') or your custom ones. 
     28extensions = ['sphinx.ext.extlinks', 'sphinxcontrib.bibtex', 
     29              'sphinx.ext.todo'    , 'sphinx.ext.autosectionlabel'] 
    2630 
    2731# Add any paths that contain templates here, relative to this directory. 
    2832templates_path = ['_templates'] 
    2933 
     34# The suffix of source filenames. 
     35source_suffix = '.rst' 
     36 
     37# The encoding of source files. 
     38#source_encoding = 'utf-8-sig' 
     39 
    3040# The master toctree document. 
    31 master_doc = 'NEMO_guide' 
     41master_doc = 'guide' 
     42 
     43# General information about the project. 
     44project = u'NEMO' 
     45copyright = u'2019, NEMO Consortium' 
     46 
     47# The version info for the project you're documenting, acts as replacement for 
     48# |version| and |release|, also used in various other places throughout the 
     49# built documents. 
     50# 
     51# The short X.Y version. 
     52version = 'trk' 
     53# The full version, including alpha/beta/rc tags. 
     54release = 'trunk' 
     55 
     56# The language for content autogenerated by Sphinx. Refer to documentation 
     57# for a list of supported languages. 
     58#language = None 
     59 
     60# There are two options for replacing |today|: either, you set today to some 
     61# non-false value, then it is used: 
     62#today = '' 
     63# Else, today_fmt is used as the format for a strftime call. 
     64#today_fmt = '%B %d, %Y' 
    3265 
    3366# List of patterns, relative to source directory, that match files and 
    3467# directories to ignore when looking for source files. 
    35 # This pattern also affects html_static_path and html_extra_path . 
    36 exclude_patterns = ['global.rst', 'coarsening.rst'] 
     68exclude_patterns = ['global.rst', 'readme.rst'] 
     69 
     70# The reST default role (used for this markup: `text`) to use for all documents. 
     71#default_role = None 
     72 
     73# If true, '()' will be appended to :func: etc. cross-reference text. 
     74#add_function_parentheses = True 
     75 
     76# If true, the current module name will be prepended to all description 
     77# unit titles (such as .. function::). 
     78#add_module_names = True 
     79 
     80# If true, sectionauthor and moduleauthor directives will be shown in the 
     81# output. They are ignored by default. 
     82#show_authors = False 
    3783 
    3884# The name of the Pygments (syntax highlighting) style to use. 
    39 pygments_style = 'sphinx' 
    40  
    41  
    42 # -- Options for HTML output ------------------------------------------------- 
     85pygments_style = 'emacs' 
     86 
     87# A list of ignored prefixes for module index sorting. 
     88#modindex_common_prefix = [] 
     89 
     90 
     91# -- Options for HTML output --------------------------------------------------- 
    4392 
    4493# The theme to use for HTML and HTML Help pages.  See the documentation for 
    4594# a list of builtin themes. 
    46 # 
    4795html_theme = 'sphinx_rtd_theme' 
    4896 
    … …  
    5098# further.  For a list of options available for each theme, see the 
    5199# documentation. 
    52 # 
    53 html_theme_options = {} 
     100#html_theme_options = {} 
     101 
     102# Add any paths that contain custom themes here, relative to this directory. 
     103#html_theme_path = [] 
     104 
     105# The name for this set of Sphinx documents.  If None, it defaults to 
     106# "<project> v<release> documentation". 
     107#html_title = None 
     108 
     109# A shorter title for the navigation bar.  Default is the same as html_title. 
     110#html_short_title = None 
     111 
     112# The name of an image file (relative to this directory) to place at the top 
     113# of the sidebar. 
     114#html_logo = None 
     115 
     116# The name of an image file (within the static path) to use as favicon of the 
     117# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32 
     118# pixels large. 
     119html_favicon = '_static/ORCA.ico' 
    54120 
    55121# Add any paths that contain custom static files (such as style sheets) here, 
    … …  
    58124html_static_path = ['_static'] 
    59125 
    60 html_favicon = '_static/ORCA.ico' 
    61  
    62  
    63 # -- Options for LaTeX output ------------------------------------------------ 
     126# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, 
     127# using the given strftime format. 
     128#html_last_updated_fmt = '%b %d, %Y' 
     129 
     130# If true, SmartyPants will be used to convert quotes and dashes to 
     131# typographically correct entities. 
     132#html_use_smartypants = True 
     133 
     134# Custom sidebar templates, maps document names to template names. 
     135#html_sidebars = {} 
     136 
     137# Additional templates that should be rendered to pages, maps page names to 
     138# template names. 
     139#html_additional_pages = {} 
     140 
     141# If false, no module index is generated. 
     142#html_domain_indices = True 
     143 
     144# If false, no index is generated. 
     145#html_use_index = True 
     146 
     147# If true, the index is split into individual pages for each letter. 
     148#html_split_index = False 
     149 
     150# If true, links to the reST sources are added to the pages. 
     151#html_show_sourcelink = True 
     152 
     153# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. 
     154#html_show_sphinx = True 
     155 
     156# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. 
     157#html_show_copyright = True 
     158 
     159# If true, an OpenSearch description file will be output, and all pages will 
     160# contain a <link> tag referring to it.  The value of this option must be the 
     161# base URL from which the finished HTML is served. 
     162#html_use_opensearch = '' 
     163 
     164# This is the file name suffix for HTML files (e.g. ".xhtml"). 
     165#html_file_suffix = None 
     166 
     167# Output file base name for HTML help builder. 
     168htmlhelp_basename = 'NEMOdoc' 
     169 
     170 
     171# -- Options for LaTeX output -------------------------------------------------- 
    64172 
    65173latex_elements = { 
    66     # The paper size ('letterpaper' or 'a4paper'). 
    67     # 
    68     # 'papersize': 'letterpaper', 
    69  
    70     # The font size ('10pt', '11pt' or '12pt'). 
    71     # 
    72     # 'pointsize': '10pt', 
    73  
    74     # Additional stuff for the LaTeX preamble. 
    75     # 
    76     # 'preamble': '', 
    77  
    78     # Latex figure (float) alignment 
    79     # 
    80     # 'figure_align': 'htbp', 
     174# The paper size ('letterpaper' or 'a4paper'). 
     175#'papersize': 'letterpaper', 
     176 
     177# The font size ('10pt', '11pt' or '12pt'). 
     178#'pointsize': '10pt', 
     179 
     180# Additional stuff for the LaTeX preamble. 
     181#'preamble': '', 
    81182} 
    82183 
    83184# Grouping the document tree into LaTeX files. List of tuples 
    84 # (source start file, target name, title, 
    85 #  author, documentclass [howto, manual, or own class]). 
     185# (source start file, target name, title, author, documentclass [howto/manual]). 
    86186latex_documents = [ 
    87     (master_doc, 'NEMO_guide.tex', 'NEMO Quick Start Guide', 
    88      'NEMO System Team', 'howto'), 
     187  ('guide', 'guide.tex', u'NEMO Quick Start Guide', 
     188   u'NEMO Consortium', 'howto'), 
    89189] 
    90190 
    91  
    92 # -- Customisation ----------------------------------------------------------- 
     191# The name of an image file (relative to this directory) to place at the top of 
     192# the title page. 
     193#latex_logo = None 
     194 
     195# For "manual" documents, if this is true, then toplevel headings are parts, 
     196# not chapters. 
     197#latex_use_parts = False 
     198 
     199# If true, show page references after internal links. 
     200#latex_show_pagerefs = False 
     201 
     202# If true, show URL addresses after external links. 
     203#latex_show_urls = False 
     204 
     205# Documents to append as an appendix to all manuals. 
     206#latex_appendices = [] 
     207 
     208# If false, no module index is generated. 
     209#latex_domain_indices = True 
     210 
     211 
     212# -- Options for manual page output -------------------------------------------- 
     213 
     214# One entry per manual page. List of tuples 
     215# (source start file, name, description, authors, manual section). 
     216man_pages = [ 
     217    ('guide', 'nemo', u'NEMO Documentation', 
     218     [u'NEMO System Team'], 1) 
     219] 
     220 
     221# If true, show URL addresses after external links. 
     222#man_show_urls = False 
     223 
     224 
     225# -- Options for Texinfo output ------------------------------------------------ 
     226 
     227# Grouping the document tree into Texinfo files. List of tuples 
     228# (source start file, target name, title, author, 
     229#  dir menu entry, description, category) 
     230texinfo_documents = [ 
     231  ('guide', 'NEMO', u'NEMO Documentation', 
     232   u'NEMO System Team', 'NEMO', 'Community Ocean Model', 
     233   'Miscellaneous'), 
     234] 
     235 
     236# Documents to append as an appendix to all manuals. 
     237#texinfo_appendices = [] 
     238 
     239# If false, no module index is generated. 
     240#texinfo_domain_indices = True 
     241 
     242# How to display URL addresses: 'footnote', 'no', or 'inline'. 
     243#texinfo_show_urls = 'footnote' 
     244 
     245# -- Customisation ------------------------------------------------------------- 
    93246 
    94247# Timestamping 
    … …  
    99252# Link aliases 
    100253extlinks = { 
    101    'doi'    : ('https://doi.org/%s'                       , None), 
    102    'forge'  : ('https://forge.ipsl.jussieu.fr/nemo/%s'    , None), 
    103    'github' : ('https://github.com/%s'                    , None), 
    104    'xios'   : ('https://forge.ipsl.jussieu.fr/ioserver/%s', None), 
    105    'website': ('https://www.nemo-ocean.eu/%s'             , None), 
    106    'zenodo' : ('https://zenodo.org/publication/%s'        , None) 
     254   'doi'    : ('https://doi.org/%s'                                                    , 'doi:'), 
     255   'manhtml': ('https://forge.ipsl.jussieu.fr/nemo/chrome/site/doc/NEMO/manual/html/%s', None  ), 
     256   'forge'  : ('https://forge.ipsl.jussieu.fr/nemo/%s'                                 , None  ), 
     257   'gmd'    : ('https://www.geosci-model-dev.net/%s'                                   , None  ), 
     258   'github' : ('https://github.com/NEMO-ocean/%s'                                      , None  ), 
     259   'xios'   : ('https://forge.ipsl.jussieu.fr/ioserver/%s'                             , None  ), 
     260   'website': ('https://www.nemo-ocean.eu/%s'                                          , None  ), 
     261   'zenodo' : ('https://zenodo.org/publication/%s'                                     , None  ) 
    107262} 
    108263 
    … …  
    112267# SVN revision 
    113268import subprocess 
    114 revision = subprocess.check_output("svnversion").decode("utf-8") 
    115 rst_prolog = '.. |revision| replace:: %s' % revision 
     269rev = subprocess.check_output("svnversion").decode("utf-8") 
     270rst_prolog = '.. |revision| replace:: %s' % rev 
     271 
     272# 'draft' build tag: DRAFT watermark and TODO list 
     273if tags.has('draft'): 
     274   todo_include_todos = True 
     275   todo_emit_warnings = True 
     276else: 
     277   exclude_patterns = ['global.rst', 'readme.rst', 'todos.rst', 'unpub*'] 
     278 
     279# Default language to highlight set to fortran 
     280highlight_language = 'fortran' 

  • NEMO/branches/2019/dev_r11078_OSMOSIS_IMMERSE_Nurser/doc/rst/source/global.rst

    r10605 r12928  
    1 .. Roles (custom styles related to CSS classes in 'source/_static/style.css') 
     1.. Roles 
    22 
    3 .. role:: rstblue 
    4 .. role:: rstgreen 
    5 .. role:: rstgrey 
    6 .. role:: rstgreysup(sup) 
    7 .. role:: underline  
    8    :class: underline 
     3.. custom styles related to CSS classes in './_static/style.css' 
     4 
     5.. role:: blue 
     6.. role:: green 
     7.. role:: grey 
     8.. role:: greysup(sup) 
     9 
     10.. inline code snippets 
     11 
     12.. role:: python(code) 
     13   :language: python 
     14   :class: highlight 
     15 
     16.. role:: fortran(code) 
     17   :language: fortran 
     18   :class: highlight 
     19 
     20.. role:: console(code) 
     21   :language: console 
     22   :class: highlight 
    923 
    1024.. Substitutions 
    1125 
    12 .. |OPA| replace:: :rstblue:`NEMO-OPA` 
    13 .. |SI3| replace:: :rstgrey:`NEMO-SI`\ :rstgreysup:`3` 
    14 .. |TOP| replace:: :rstgreen:`NEMO-TOP/PISCES` 
     26.. |NEMO-OCE| replace::  :blue:`NEMO-OCE (Ocean dynamics)` 
     27.. |OCE|      replace::  :blue:`NEMO-OCE` 
     28.. |NEMO-ICE| replace::  :grey:`NEMO-SI`\ :greysup:`3`  :grey:`(Sea Ice)` 
     29.. |ICE|      replace::  :grey:`NEMO-SI`\ :greysup:`3` 
     30.. |NEMO-MBG| replace:: :green:`NEMO-TOP/PISCES (Tracers)` 
     31.. |MBG|      replace:: :green:`NEMO-TOP/PISCES` 
    1532 
    16 .. Institutes 
     33.. External links 
    1734 
    18 .. _CMCC:           https://www.cmcc.it  
    19 .. _CNRS:           https://www.cnrs.fr 
    20 .. _Mercator Ocean: https://www.mercator-ocean.fr 
    21 .. _Met Office:     https://www.metoffice.gov.uk 
    22 .. _MOI:            https://www.mercator-ocean.fr 
    23 .. _NERC:           https://nerc.ukri.org 
     35   .. Consortium institutes 
    2436 
    25 .. Models / Softwares 
     37.. _CMCC:       https://www.cmcc.it 
     38.. _CNRS:       https://www.cnrs.fr 
     39.. _Met Office: https://www.metoffice.gov.uk 
     40.. _MOI:        https://www.mercator-ocean.fr 
     41.. _NERC:       https://nerc.ukri.org 
     42 
     43   .. Models / Libraries / Dependencies 
    2644 
    2745.. _AGRIF:  http://agrif.imag.fr 
    28 .. _FCM:    https://metomi.github.io/fcm/doc/ 
     46.. _BFM:    http://www.bfm-community.eu 
     47.. _FCM:    https://metomi.github.io/fcm 
    2948.. _IOIPSL: https://forge.ipsl.jussieu.fr/igcmg/browser/IOIPSL 
     49.. _NEMO:   https://www.nemo-ocean.eu 
    3050.. _OASIS:  https://portal.enes.org/oasis 
     51.. _XIOS:   https://forge.ipsl.jussieu.fr/ioserver 
    3152 
    32 .. NEMO 
     53   .. Misc. 
    3354 
    34 .. _NEMO:          https://www.nemo-ocean.eu 
    35 .. _NEMO strategy: https://doi.org/10.5281/zenodo.1471663 
    36 .. _NEMO guide:    :samp: https://doi.org/10.5281/zenodo.1475325 
    37 .. _NEMO manual:   https://doi.org/10.5281/zenodo.1464816 
    38 .. _SI3 manual:    :samp: https://doi.org/10.5281/zenodo.1471689 
    39 .. _TOP manual:    :samp: https://doi.org/10.5281/zenodo.1471700 
     55.. _EGU: http://www.egu.eu 
     56.. _Special Issue: https://www.geosci-model-dev.net/special_issue40.html 
     57.. _BFM man: https://cmcc-foundation.github.io/www.bfm-community.eu/files/bfm-nemo-manual_r1.0_201508.pdf 
     58.. _RST man: https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html 
     59.. _PAPA station: http://www.pmel.noaa.gov/OCS/Papa/index-Papa.shtml 
     60.. _ISOMIP: http://staff.acecrc.org.au/~bkgalton/ISOMIP/test_cavities.pdf 
     61 
     62.. DOI 
     63 
     64   .. Publications (`:samp:` to deactivate link for unpublished documents) 
     65 
     66.. _DOI man OCE:          https://doi.org/10.5281/zenodo.1464816 
     67.. _DOI man ICE:   :samp: https://doi.org/10.5281/zenodo.1471689 
     68.. _DOI man MBG:   :samp: https://doi.org/10.5281/zenodo.1471700 
     69.. _DOI qsg:       :samp: https://doi.org/10.5281/zenodo.1475325 
     70.. _DOI dev  stgy:        https://doi.org/10.5281/zenodo.1471663 
     71.. _DOI data:             https://doi.org/10.5281/zenodo.1472245 
     72 
     73   .. Badges (same labels as previously, substitution to link images) 
     74 
     75.. |DOI man OCE| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1464816.svg 
     76.. |DOI man ICE| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1471689.svg 
     77.. |DOI man MBG| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1471700.svg 
     78.. |DOI qsg|     image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1475325.svg 
     79.. |DOI data|    image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1472245.svg 
Note: See TracChangeset for help on using the changeset viewer.