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Changeset 14789 for NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc – NEMO

Ignore:
Timestamp:
2021-05-05T13:18:04+02:00 (3 years ago)
Author:
mcastril
Message:

[2021/HPC-11_mcastril_HPDAonline_DiagGPU] Update externals

Location:
NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU
Files:
23 deleted
77 edited
22 copied

Legend:

Unmodified
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  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU

    • Property svn:externals

      •  

        old new  
        33^/utils/build/mk@HEAD         mk 
        44^/utils/tools@HEAD            tools 
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         5^/vendors/AGRIF/dev@HEAD      ext/AGRIF 
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        77^/vendors/IOIPSL@HEAD         ext/IOIPSL 
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        910# SETTE 
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         11^/utils/CI/sette@14244        sette 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/NEMO_manual_state.txt

    r13461 r14789  
    1515chap_misc.tex: key{mpp\_mpi} key{nosignedzero} key{vectopt\_loop} np{iom\_get} np{jpjdta} np{jpjglo} np{nn\_bench} np{nn\_bit\_cmp} np{open\_ocean\_jstart}  
    1616chap_LDF.tex: hf{dynldf\_cNd} hf{ldfdyn\_substitute} hf{ldftra\_substitute} hf{traldf\_c1d} hf{traldf\_cNd} key{dynldf\_c1d} key{dynldf\_c2d} key{dynldf\_c3d} key{traldf\_c1d} key{traldf\_c2d} key{traldf\_c3d} key{traldf\_cNd} key{traldf\_eiv} mdl{ldfdyn\_c2d} mdl{ldfeiv} mdl{traadv\_eiv} np{ln\_dynldf\_bilap} np{ln\_sco} np{nn\_eos} np{rn\_aeih\_0} np{rn\_aeiv} np{rn\_aeiv\_0} np{rn\_ahm0} np{rn\_ahmb0} np{rn\_aht0} np{rn\_ahtb0} np{traldf\_grif} np{traldf\_grif\_iso} rou{ldf\_dyn\_c2d\_orca} rou{ldfslp\_init}  
    17 chap_LBC.tex: jp{jpreci} key{mpp\_mpi} np{jperio} np{jpiglo} np{jpindt} np{jpinft} np{jpjglo} np{jpjnob} np{nbdysegn} np{nn\_bdy\_jpk} np{nn\_msh} np{nn\_tra} rou{inimpp2}  
    18 chap_DOM.tex: key{mpp\_mpi} ngn{namzgr} ngn{namzgr\_sco} nlst{namzgr} nlst{namzgr_sco} np{jperio} np{jpiglo} np{jpjglo} np{jpkglo} np{ln\_sco} np{ln\_sigcrit} np{ln\_s\_SF12} np{ln\_s\_SH94} np{ln\_tsd\_ini} np{ln\_zco} np{ln\_zps} np{nn\_bathy} np{nn\_msh} np{ppa0} np{ppa1} np{ppacr} np{ppdzmin} np{pphmax} np{ppkth} np{ppsur} np{rn\_alpha} np{rn\_bb} np{rn\_e3zps\_min} np{rn\_e3zps\_rat} np{rn\_hc} np{rn\_rmax} np{rn\_sbot\_max} np{rn\_sbot\_min} np{rn\_theta} np{rn\_zb\_a} np{rn\_zb\_b} np{rn\_zs} rou{istate\_t\_s}  
     17chap_LBC.tex: jp{jpreci} key{mpp\_mpi} np{jpiglo} np{jpindt} np{jpinft} np{jpjglo} np{jpjnob} np{nbdysegn} np{nn\_bdy\_jpk} np{nn\_msh} np{nn\_tra} rou{inimpp2}  
     18chap_DOM.tex: key{mpp\_mpi} ngn{namzgr} ngn{namzgr\_sco} nlst{namzgr} nlst{namzgr_sco} np{jpiglo} np{jpjglo} np{jpkglo} np{ln\_sco} np{ln\_sigcrit} np{ln\_s\_SF12} np{ln\_s\_SH94} np{ln\_tsd\_ini} np{ln\_zco} np{ln\_zps} np{nn\_bathy} np{nn\_msh} np{ppa0} np{ppa1} np{ppacr} np{ppdzmin} np{pphmax} np{ppkth} np{ppsur} np{rn\_alpha} np{rn\_bb} np{rn\_e3zps\_min} np{rn\_e3zps\_rat} np{rn\_hc} np{rn\_rmax} np{rn\_sbot\_max} np{rn\_sbot\_min} np{rn\_theta} np{rn\_zb\_a} np{rn\_zb\_b} np{rn\_zs} rou{istate\_t\_s}  
    1919chap_conservation.tex: key{\_}  
    2020annex_iso.tex: key{trabbl} key{traldf\_eiv} np{ln\_traldf\_eiv} np{ln\_traldf\_gdia}  

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/README.rst

    r12377 r14789  
     1************************** 
     2Building the documentation 
     3************************** 
    14 
     5.. todo:: 
     6 
     7 
     8 
     9:file:`latex`    : LaTeX sources and Latexmk configuration to build reference manuals with :file:`manual_build.sh` 
     10 
     11:file:`namelists`: Namelist blocks included in the documentation 
     12 
     13:file:`rst`      : |RST man|_ sources and Sphinx configuration to build this guide hereby with :file:`guide_build.sh` 
     14 
     15.. |RST man| replace:: reStructuredText (rst) 
    216 
    317.. warning:: 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/.svnignore

    r12377 r14789  
    22*.bbl 
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     12*.pyg 
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    1714*.toc 
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  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/build

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  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/main/abstract.tex

    r11591 r14789  
    1 %% ================================================================ 
    2 %% Abstract 
    3 %% ================================================================ 
     1%% ================================================================================================= 
     2%% Specific abstract 
     3%% ================================================================================================= 
    44 
    5 %% Common part between NEMO-SI3-TOP 
    6 \NEMO\ (``Nucleus for European Modelling of the Ocean'') is a framework of ocean-related engines. 
    7 It is intended to be a flexible tool for studying the ocean dynamics and thermodynamics (``blue ocean''), 
    8 as well as its interactions with the components of the Earth climate system over 
    9 a wide range of space and time scales. 
    10 Within \NEMO, the ocean engine is interfaced with a sea-ice model (\SIcube\ or 
    11 \href{http://github.com/CICE-Consortium/CICE}{CICE}), 
    12 passive tracers and biogeochemical models (\TOP) and, 
    13 via the \href{http://portal.enes.org/oasis}{OASIS} coupler, 
    14 with several atmospheric general circulation models. 
    15 It also supports two-way grid embedding by means of the \href{http://agrif.imag.fr}{AGRIF} software. 
     5%% Common part 
     6\input{../../global/nemo} 
    167 
    178%% Specific part 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/main/appendices.tex

    r12377 r14789  
     1%% ================================================================================================= 
     2%% Appendices 
     3%% ================================================================================================= 
    14 
    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 
     5\subfile{../subfiles/apdx_s_coord}      %% A. Generalised vertical coordinate 
     6\subfile{../subfiles/apdx_diff_opers}   %% B. Diffusive operators 
     7\subfile{../subfiles/apdx_invariants}   %% C. Discrete invariants of the eqs. 
     8\subfile{../subfiles/apdx_triads}       %% D. Isoneutral diffusion using triads 
     9\subfile{../subfiles/apdx_DOMAINcfg}    %% E. Brief notes on DOMAINcfg 
    710 
    811%% Not included 
    … …  
    1013%\subfile{../subfiles/chap_DIU} 
    1114%\subfile{../subfiles/chap_conservation} 
    12 %\subfile{../subfiles/annex_E}            %% Notes on some on going staff 
    13  
     15%\subfile{../subfiles/apdx_algos}   %% Notes on some on going staff 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/main/authors.tex

    r11591 r14789  
    1 %Romain Bourdall\'{e}-Badie 
    2 %\orcid{0000-0002-8742-3289} \\ 
    3 %Mike Bell                   \\ 
    4 %J\'{e}r\^{o}me Chanut       \\ 
    5 %Emanuela Clementi 
    6 %\orcid{0000-0002-5752-1849} \\ 
    7 %Andrew Coward 
    8 %\orcid{0000-0002-0456-129X} \\ 
    9 %Massimiliano Drudi 
    10 %\orcid{0000-0002-9951-740X} \\ 
    11 %Christian \'{E}th\'{e}      \\ 
    12 %Doroteaciro Iovino 
    13 %\orcid{0000-0001-5132-7255} \\ 
    14 %Dan Lea                     \\ 
    15 %Claire L\'{e}vy 
    16 %\orcid{0000-0003-2518-6692} \\ 
    17 %Gurvan Madec 
    18 %\orcid{0000-0002-6447-4198} \\ 
    19 %Nicolas Martin              \\ 
    20 %S\'{e}bastien Masson 
    21 %\orcid{0000-0002-1694-8117} \\ 
    22 %Pierre Mathiot              \\ 
    23 %Silvia Mocavero 
    24 %\orcid{0000-0002-6309-8282} \\ 
    25 %Simon M\"{u}ller            \\ 
    26 %George Nurser               \\ 
    27 %Guillaume Samson 
    28 %\orcid{0000-0001-7481-6369} \\ 
    29 %Dave Storkey 
     1%% ================================================================================================= 
     2%% Authors 
     3%% ================================================================================================= 
    304 
     5\orcid{0000-0002-6447-4198} Gurvan Madec                \\ 
     6                            Mike Bell                   \\ 
    317\orcid{0000-0002-8742-3289} Romain Bourdall\'{e}-Badie  \\ 
    32                             Mike Bell                   \\ 
    338                            J\'{e}r\^{o}me Chanut       \\ 
    349\orcid{0000-0002-5752-1849} Emanuela Clementi           \\ 
    … …  
    3914                            Dan Lea                     \\ 
    4015\orcid{0000-0003-2518-6692} Claire L\'{e}vy             \\ 
    41 \orcid{0000-0002-6447-4198} Gurvan Madec                \\ 
    4216                            Nicolas Martin              \\ 
    4317\orcid{0000-0002-1694-8117} S\'{e}bastien Masson        \\ 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/main/bibliography.bib

    • Property svn:eol-style set to native
    r12377 r14789  
    119119  issn          = "0148-0227", 
    120120  doi           = "10.1029/2001jc000922" 
     121} 
     122 
     123@Article{         Asaydavis2016, 
     124  author        = {Asay-Davis, X. S. and Cornford, S. L. and Durand, G. and Galton-Fenzi, B. K. and Gladstone, R. M. and Gudmundsson, G. H. and Hattermann, T. and Holland, D. M. and Holland, D. and Holland, P. R. and Martin, D. F. and Mathiot, P. and Pattyn, F. and Seroussi, H.}, 
     125  title         = {Experimental design for three interrelated marine ice sheet and ocean model intercomparison projects: MISMIP v. 3 (MISMIP$+$), ISOMIP v. 2 (ISOMIP$+$) and MISOMIP v. 1 (MISOMIP1)}, 
     126  journal       = {Geoscientific Model Development}, 
     127  volume        = {9}, 
     128  year          = {2016}, 
     129  number        = {7}, 
     130  pages         = {2471--2497}, 
     131  url           = {https://www.geosci-model-dev.net/9/2471/2016/}, 
     132  doi           = {10.5194/gmd-9-2471-2016} 
    121133} 
    122134 
    … …  
    188200} 
    189201 
    190 @article{ beljaars_QJRMS95, 
    191 title = "The parametrization of surface fluxes in large-scale models under free convection", 
    192 pages = "255--270", 
    193 journal = "Quarterly Journal of the Royal Meteorological Society", 
    194 volume = "121", 
    195 number = "522", 
    196 author = "Beljaars, Anton C. M.", 
    197 year = "1995", 
    198 month = "jan", 
    199  publisher     = "Wiley", 
    200 issn = "00359009", 
    201 doi = "10.1002/qj.49712152203" 
     202@article{         beljaars_QJRMS95, 
     203  title         = "The parametrization of surface fluxes in large-scale 
     204                  models under free convection", 
     205  pages         = "255--270", 
     206  journal       = "Quarterly Journal of the Royal Meteorological Society", 
     207  volume        = "121", 
     208  number        = "522", 
     209  author        = "Beljaars, Anton C. M.", 
     210  year          = "1995", 
     211  month         = "jan", 
     212  publisher     = "Wiley", 
     213  issn          = "00359009", 
     214  doi           = "10.1002/qj.49712152203" 
    202215} 
    203216 
    … …  
    384397} 
    385398 
     399@article{         brodeau.barnier.ea_JPO16, 
     400  title         = "Climatologically Significant Effects of Some 
     401                  Approximations in the Bulk Parameterizations of Turbulent 
     402                  Air–Sea Fluxes", 
     403  pages         = "5--28", 
     404  journal       = "Journal of Physical Oceanography", 
     405  volume        = "47", 
     406  number        = "1", 
     407  author        = "Brodeau, Laurent and Barnier, Bernard and Gulev, Sergey K. 
     408                  and Woods, Cian", 
     409  year          = "2016", 
     410  month         = "jan", 
     411  publisher     = "American Meteorological Society", 
     412  issn          = "0022-3670", 
     413  doi           = "10.1175/jpo-d-16-0169.1" 
     414} 
     415 
    386416@article{         brodeau.barnier.ea_OM10, 
    387417  title         = "An {ERA40}-based atmospheric forcing for global ocean 
    … …  
    398428  issn          = "1463-5003", 
    399429  doi           = "10.1016/j.ocemod.2009.10.005" 
    400 } 
    401  
    402 @article{         brodeau.barnier.ea_JPO17, 
    403   title         = "Climatologically Significant Effects of Some Approximations in the Bulk Parameterizations of Turbulent Air{\textendash}Sea Fluxes", 
    404   pages         = "5--28", 
    405   journal       = "Journal of Physical Oceanography", 
    406   volume        = "47", 
    407   number        = "1", 
    408   author        = "Brodeau, Laurent and Barnier, Bernard and Gulev, Sergey K. and Woods, Cian", 
    409   year          = "2017", 
    410   month         = "jan", 
    411   publisher     = "American Meteorological Society", 
    412   issn          = "0022-3670", 
    413   doi           = "10.1175/jpo-d-16-0169.1", 
    414430} 
    415431 
    … …  
    519535} 
    520536 
    521 @article{         carrere.lyard_GRL03, 
    522   title         = "Modeling the barotropic response of the global ocean to 
    523                   atmospheric wind and pressure forcing - comparisons with 
    524                   observations", 
    525   journal       = "Geophysical Research Letters", 
    526   volume        = "30", 
    527   number        = "6", 
    528   author        = "L. Carr\`{e}re and F. Lyard", 
    529   year          = "2003", 
    530   month         = "mar", 
    531   publisher     = "American Geophysical Union (AGU)", 
    532   issn          = "0094-8276", 
    533   doi           = "10.1029/2002gl016473" 
    534 } 
    535  
    536 @techreport{      chanut_rpt05, 
     537@techreport{      chanut_trpt05, 
    537538  title         = "Nesting code for {NEMO}", 
    538539  pages         = "25", 
    … …  
    773774} 
    774775 
    775 @article{ edson.jampana.ea_JPO13, 
    776 title = "On the Exchange of Momentum over the Open Ocean", 
    777 pages = "1589--1610", 
    778 journal = "Journal of Physical Oceanography", 
    779 volume = "43", 
    780 number = "8", 
    781 author = "Edson, James B. and Jampana, Venkata and Weller, Robert A. and Bigorre, Sebastien P. and Plueddemann, Albert J. and Fairall, Christopher W. and Miller, Scott D. and Mahrt, Larry and Vickers, Dean and Hersbach, Hans", 
    782 year = "2013", 
    783 month = "aug", 
    784 publisher = "American Meteorological Society", 
    785 issn = "0022-3670", 
    786 doi = "10.1175/JPO-D-12-0173.1" 
    787 } 
    788  
    789 @article{         egbert.ray_JGR01, 
    790   title         = "Estimates of {M2} tidal energy dissipation from 
    791                   {TOPEX}/Poseidon altimeter data", 
    792   pages         = "22475--22502", 
    793   journal       = "Journal of Geophysical Research", 
    794   volume        = "106", 
    795   number        = "C10", 
    796   author        = "G. D. Egbert and R. D. Ray", 
    797   year          = "2001", 
    798   month         = "oct", 
    799   publisher     = "American Geophysical Union (AGU)", 
    800   issn          = "0148-0227", 
    801   doi           = "10.1029/2000jc000699" 
    802 } 
    803  
    804 @article{         egbert.ray_N00, 
    805   title         = "Significant dissipation of tidal energy in the deep ocean 
    806                   inferred from satellite altimeter data", 
    807   pages         = "775--778", 
    808   journal       = "Nature", 
    809   volume        = "405", 
    810   number        = "6788", 
    811   author        = "G. D. Egbert and R. D. Ray", 
    812   year          = "2000", 
    813   month         = "jun", 
    814   publisher     = "Springer Nature", 
    815   issn          = "1476-4687", 
    816   doi           = "10.1038/35015531" 
     776@article{         edson.jampana.ea_JPO13, 
     777  title         = "On the Exchange of Momentum over the Open Ocean", 
     778  pages         = "1589--1610", 
     779  journal       = "Journal of Physical Oceanography", 
     780  volume        = "43", 
     781  number        = "8", 
     782  author        = "Edson, James B. and Jampana, Venkata and Weller, Robert A. 
     783                  and Bigorre, Sebastien P. and Plueddemann, Albert J. and 
     784                  Fairall, Christopher W. and Miller, Scott D. and Mahrt, 
     785                  Larry and Vickers, Dean and Hersbach, Hans", 
     786  year          = "2013", 
     787  month         = "aug", 
     788  publisher     = "American Meteorological Society", 
     789  issn          = "0022-3670", 
     790  doi           = "10.1175/JPO-D-12-0173.1" 
    817791} 
    818792 
    … …  
    861835} 
    862836 
    863 @article{ fairall.bradley.ea_JC03, 
    864 title = "Bulk parameterization of air-sea fluxes: Updates and verification for the COARE algorithm", 
    865 pages = "571--591", 
    866 journal = "Journal of Climate", 
    867 volume = "16", 
    868 number = "4", 
    869 author = "Fairall, C. W. and Bradley, E. F. and Hare, J. E. and Grachev, A. A. and Edson, J. B.", 
    870 year = "2003", 
    871 publisher = "American Meteorological Society", 
    872 issn = "08948755", 
    873 doi = "10.1175/1520-0442(2003)016<0571:BPOASF>2.0.CO;2" 
     837@article{         fairall.bradley.ea_JC03, 
     838  title         = "Bulk parameterization of air-sea fluxes: Updates and 
     839                  verification for the COARE algorithm", 
     840  pages         = "571--591", 
     841  journal       = "Journal of Climate", 
     842  volume        = "16", 
     843  number        = "4", 
     844  author        = "Fairall, C. W. and Bradley, E. F. and Hare, J. E. and 
     845                  Grachev, A. A. and Edson, J. B.", 
     846  year          = "2003", 
     847  publisher     = "American Meteorological Society", 
     848  issn          = "08948755", 
     849  doi           = "10.1175/1520-0442(2003)016<0571:BPOASF>2.0.CO;2" 
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     851 
     852@article{         fairall.bradley.ea_JGRO96, 
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     856  journal       = "Journal of Geophysical Research: Oceans", 
     857  volume        = "101", 
     858  number        = "C1", 
     859  author        = "C. W. Fairall and E. F. Bradley and J. S. Godfrey and G. 
     860                  A. Wick and J. B. Edson and G. S. Young", 
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     862  month         = "jan", 
     863  publisher     = "American Geophysical Union", 
     864  doi           = "10.1029/95jc03190" 
    874865} 
    875866 
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    898889  doi           = "10.1175/1520-0485(1995)025<1731:antasf>2.0.co;2" 
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     892@Article{         favier2019, 
     893  author        = {Favier, L. and Jourdain, N. C. and Jenkins, A. and Merino, N. and Durand, G. and Gagliardini, O. and Gillet-Chaulet, F. and Mathiot, P.}, 
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    900903 
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     934  title         = "Parameterization of Mixed Layer Eddies. Part I: Theory and 
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    933937  journal       = "Journal of Physical Oceanography", 
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    1047 @article{         gerdes_JGR93*b, 
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    10611065 
    1062 @techreport{      gibson_rpt86, 
     1066@techreport{      gibson_trpt86, 
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    1107   journal       = "Journal of Geophysical Research", 
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    1110   author        = "H. Goosse and E. Deleersnijder and T. Fichefet and M. H. 
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    1114   publisher     = "American Geophysical Union (AGU)", 
    1115   issn          = "0148-0227", 
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    … …  
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     1215journal         = {Journal of Geophysical Research: Oceans}, 
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    … …  
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     1372@techreport{      hunter_trpt06, 
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    14111412 
    1412 @techreport{      janssen.breivik.ea_rpt13, 
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    14511452  doi           = "10.1029/91jc01842" 
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     1455@article{         jenkins2001, 
     1456  author        = {Jenkins, Adrian and Hellmer, Hartmut H. and Holland, David M.}, 
     1457  title         = {The Role of Meltwater Advection in the Formulation of Conservative Boundary Conditions at an Ice–Ocean Interface}, 
     1458  journal       = {Journal of Physical Oceanography}, 
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     1463  doi           = {10.1175/1520-0485(2001)031<0285:TROMAI>2.0.CO;2}, 
     1464  url           = {https://doi.org/10.1175/1520-0485(2001)031<0285:TROMAI>2.0.CO;2} 
     1465} 
     1466 
     1467@article{         jourdain2017, 
     1468  author        = {Jourdain, Nicolas C. and Mathiot, Pierre and Merino, Nacho and Durand, Gaël and Le Sommer, Julien and Spence, Paul and Dutrieux, Pierre and Madec, Gurvan}, 
     1469  title         = {Ocean circulation and sea-ice thinning induced by melting ice shelves in the Amundsen Sea}, 
     1470  journal       = {Journal of Geophysical Research: Oceans}, 
     1471  volume        = {122}, 
     1472  number        = {3}, 
     1473  pages         = {2550-2573}, 
     1474  keywords      = {Amundsen Sea, ice shelf, efficiency, circumpolar deep water, ocean circulation, sea ice}, 
     1475  doi           = {10.1002/2016JC012509}, 
     1476  url           = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2016JC012509}, 
     1477  year          = {2017} 
     1478} 
     1479 
     1480@article{         josey.gulev.ea_OCC13, 
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     1483  journal       = "Ocean Circulation and Climate", 
     1484  author        = "Josey, Simon A. and Gulev, Serge and Yu, Lisan", 
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     1486  publisher     = "Elsevier", 
     1487  issn          = "0074-6142", 
     1488  isbn          = "9780123918512", 
     1489  doi           = "10.1016/b978-0-12-391851-2.00005-2" 
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    … …  
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    1543 @article{         koch-larrouy.lengaigne.ea_CD10, 
    1544   title         = "Tidal mixing in the Indonesian Seas and its effect on the 
    1545                   tropical climate system", 
    1546   pages         = "891--904", 
    1547   journal       = "Climate Dynamics", 
    1548   volume        = "34", 
    1549   number        = "6", 
    1550   author        = "A. Koch-Larrouy and M. Lengaigne and P. Terray and G. 
    1551                   Madec and S. Masson", 
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    1553   month         = "aug", 
    1554   publisher     = "Springer Nature", 
    1555   issn          = "1432-0894", 
    1556   doi           = "10.1007/s00382-009-0642-4" 
    1557 } 
    1558  
    15591581@article{         koch-larrouy.madec.ea_GRL07, 
    15601582  title         = "On the transformation of Pacific water into Indonesian 
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    15741596 
    1575 @article{         koch-larrouy.madec.ea_OD08*a, 
    1576   title         = "Water mass transformation along the Indonesian ThroughFlow 
    1577                   in an {OGCM}", 
    1578   pages         = "289--309", 
    1579   journal       = "Ocean Dynamics", 
    1580   volume        = "58", 
    1581   number        = "3-4", 
    1582   author        = "A. Koch-Larrouy and G. Madec and B. Blanke and R. Molcard", 
    1583   year          = "2008", 
    1584   month         = "oct", 
    1585   publisher     = "Springer Nature", 
    1586   issn          = "1616-7228", 
    1587   doi           = "10.1007/s10236-008-0155-4" 
    1588 } 
    1589  
    1590 @article{         koch-larrouy.madec.ea_OD08*b, 
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    1594   journal       = "Ocean Dynamics", 
    1595   volume        = "58", 
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    1597   author        = "A. Koch-Larrouy and G. Madec and D. Iudicone and A. 
    1598                   Atmadipoera and R. Molcard", 
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    1600   month         = "oct", 
    1601   publisher     = "Springer Nature", 
    1602   issn          = "1616-7228", 
    1603   doi           = "10.1007/s10236-008-0154-5" 
    1604 } 
    1605  
    16061597@article{         kolmogorov_IANS42, 
    16071598  title         = "Equations of turbulent motion in an incompressible fluid", 
    … …  
    16141605} 
    16151606 
    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, 
     1607@article{         kraus.businger_QJRMS96, 
     1608  title         = "Atmosphere-ocean interaction.", 
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     1610  journal       = "Quarterly Journal of the Royal Meteorological Society", 
     1611  volume        = "122", 
     1612  number        = "529", 
     1613  author        = "E. B. Kraus and J. A. Businger", 
     1614  year          = "1996", 
     1615  publisher     = "John Wiley & Sons, Ltd", 
     1616  issn          = "1477-870X", 
     1617  doi           = "10.1002/qj.49712252914" 
     1618} 
     1619 
     1620@article{         kraus.turner_T67, 
     1621  title         = "A one-dimensional model of the seasonal thermocline II. 
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     1623  pages         = "98--106", 
     1624  journal       = "Tellus", 
     1625  volume        = "19", 
     1626  number        = "1", 
     1627  author        = "Kraus, E. B. and Turner, J. S.", 
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     1629  month         = "Jan", 
     1630  publisher     = "Informa UK Limited", 
     1631  issn          = "2153-3490", 
     1632  doi           = "10.3402/tellusa.v19i1.9753" 
     1633} 
     1634 
     1635@article{         large.mcwilliams.ea_RG94, 
     1636  title         = "Oceanic vertical mixing: {A} review and a model with a 
     1637                  nonlocal boundary layer parameterization", 
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     1639  journal       = "Reviews of Geophysics", 
     1640  number        = "4", 
    16261641  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" 
    1634 } 
    1635  
    1636 @techreport{      large.yeager_rpt04, 
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     1643  publisher     = "AGU", 
     1644  doi           = "10.1029/94RG01872" 
     1645} 
     1646 
     1647@article{         large.yeager_CD09, 
     1648  title         = "The Global Climatology of an Interannually Varying Air-Sea 
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     1650  pages         = "341--364", 
     1651  journal       = "Climate Dynamics", 
     1652  volume        = "33", 
     1653  number        = "2-3", 
     1654  author        = "Large, W. G. and Yeager, S. G.", 
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     1656  month         = "aug", 
     1657  publisher     = "Springer Science and Business Media LLC", 
     1658  doi           = "10.1007/s00382-008-0441-3" 
     1659} 
     1660 
     1661@techreport{      large.yeager_trpt04, 
    16371662  title         = "Diurnal to decadal global forcing for ocean and sea-ice 
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    18501875 
    1851 @techreport{      levier.treguier.ea_rpt07, 
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    … …  
    19301955} 
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    1932 @article{     lupkes.gryanik.ea_JGR12, 
    1933   author    = "L{\"{u}}pkes, Christof and Gryanik, Vladimir M. and Hartmann, J{\"{o}}rg and Andreas, Edgar L.", 
    1934   doi       = "10.1029/2012JD017630", 
    1935   issn      = "01480227", 
    1936   journal   = "Journal of Geophysical Research Atmospheres", 
    1937   number    = "13", 
    1938   pages  = "1--18", 
    1939   title  = "A parametrization, based on sea ice morphology, of the neutral atmospheric drag coefficients for weather prediction and climate models", 
    1940   volume    = "117", 
    1941   year      = "2012" 
    1942 } 
    1943  
    1944 @article{     lupkes.gryanik_JGR15, 
    1945   author    = "L{\"{u}}pkes, Christof and Gryanik, Vladimir M.", 
    1946   doi       = "10.1002/2014JD022418", 
    1947   issn      = "21562202", 
    1948   journal   = "Journal of Geophysical Research", 
    1949   number    = "2", 
    1950   pages  = "552--581", 
    1951   title  = "A stability-dependent parametrization of transfer coefficients formomentum and heat over polar sea ice to be used in climate models", 
    1952   volume    = "120", 
    1953   year      = "2015" 
     1957@article{         love_PRSL09, 
     1958  title         = "The yielding of the earth to disturbing forces", 
     1959  pages         = "73--88", 
     1960  journal       = "Proceedings of the Royal Society of London", 
     1961  series        = "Series A", 
     1962  volume        = "82", 
     1963  number        = "551", 
     1964  author        = "Love, Augustus Edward Hough ", 
     1965  year          = "1909", 
     1966  month         = "Feb", 
     1967  publisher     = "The Royal Society", 
     1968  issn          = "2053-9150", 
     1969  doi           = "10.1098/rspa.1909.0008" 
     1970} 
     1971 
     1972@article{         lupkes.gryanik.ea_JGRA12, 
     1973  title         = "A parametrization, based on sea ice morphology, of the 
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     1975                  prediction and climate models", 
     1976  pages         = "1--18", 
     1977  journal       = "Journal of Geophysical Research Atmospheres", 
     1978  volume        = "117", 
     1979  number        = "13", 
     1980  author        = "L{\"{u}}pkes, Christof and Gryanik, Vladimir M. and 
     1981                  Hartmann, J{\"{o}}rg and Andreas, Edgar L.", 
     1982  year          = "2012", 
     1983  issn          = "01480227", 
     1984  doi           = "10.1029/2012JD017630" 
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     1986 
     1987@article{         lupkes.gryanik_JGR15, 
     1988  title         = "A stability-dependent parametrization of transfer 
     1989                  coefficients formomentum and heat over polar sea ice to be 
     1990                  used in climate models", 
     1991  pages         = "552--581", 
     1992  journal       = "Journal of Geophysical Research", 
     1993  volume        = "120", 
     1994  number        = "2", 
     1995  author        = "L{\"{u}}pkes, Christof and Gryanik, Vladimir M.", 
     1996  year          = "2015", 
     1997  issn          = "21562202", 
     1998  doi           = "10.1002/2014JD022418" 
    19541999} 
    19552000 
    … …  
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    22052250 
    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 } 
     2251@article{         mcwilliams.sullivan.ea_JFM97, 
     2252  title         = "Langmuir turbulence in the ocean", 
     2253  pages         = "1--30", 
     2254  journal       = "Journal of Fluid Mechanics", 
     2255  volume        = "334", 
     2256  author        = "McWilliams, James C. and Sullivan, Peter P. and Moeng, 
     2257                  Chin-Hoh", 
     2258  year          = "1997", 
     2259  doi           = "10.1017/S0022112096004375" 
     2260} 
     2261 
    22152262@article{         mellor.blumberg_JPO04, 
    22162263  title         = "Wave Breaking and Ocean Surface Layer Thermal Response", 
    … …  
    22392286  issn          = "8755-1209", 
    22402287  doi           = "10.1029/rg020i004p00851" 
     2288} 
     2289 
     2290@article{Merino_OM2016, 
     2291title = "Antarctic icebergs melt over the Southern Ocean: Climatology and impact on sea ice", 
     2292journal = "Ocean Modelling", 
     2293volume = "104", 
     2294pages = "99 - 110", 
     2295year = "2016", 
     2296issn = "1463-5003", 
     2297doi = "https://doi.org/10.1016/j.ocemod.2016.05.001", 
     2298url = "http://www.sciencedirect.com/science/article/pii/S1463500316300300", 
     2299author = "Nacho Merino and Julien {Le Sommer} and Gael Durand and Nicolas C. Jourdain and Gurvan Madec and Pierre Mathiot and Jean Tournadre", 
     2300keywords = "Icebergs, Southern Ocean, Sea ice, Freshwater fluxes", 
     2301abstract = "Recent increase in Antarctic freshwater release to the Southern Ocean is suggested to contribute to change in water masses and sea ice. However, climate models differ in their representation of the freshwater sources. Recent improvements in altimetry-based detection of small icebergs and in estimates of the mass loss of Antarctica may help better constrain the values of Antarctic freshwater releases. We propose a model-based seasonal climatology of iceberg melt over the Southern Ocean using state-of-the-art observed glaciological estimates of the Antarctic mass loss. An improved version of a Lagrangian iceberg model is coupled with a global, eddy-permitting ocean/sea ice model and compared to small icebergs observations. Iceberg melt increases sea ice cover, about 10% in annual mean sea ice volume, and decreases sea surface temperature over most of the Southern Ocean, but with distinctive regional patterns. Our results underline the importance of improving the representation of Antarctic freshwater sources. This can be achieved by forcing ocean/sea ice models with a climatological iceberg fresh-water flux." 
    22412302} 
    22422303 
    … …  
    24292490 
    24302491@article{         qiao.yuan.ea_OD10, 
    2431   title         = "A three-dimensional surface wave–ocean circulation coupled  
    2432                   model and its initial testing", 
     2492  title         = "A three-dimensional surface wave–ocean circulation 
     2493                  coupled model and its initial testing", 
    24332494  pages         = "1339--1335", 
    24342495  journal       = "Ocean Dynamics", 
    24352496  volume        = "60", 
    24362497  number        = "5", 
    2437   author        = "F. Qiao and Y. Yuan and T. Ezer and C. Xia and  
    2438                    Y. Yang and X. Lu and Z. Song ", 
     2498  author        = "F. Qiao and Y. Yuan and T. Ezer and C. Xia and Y. Yang and 
     2499                  X. Lu and Z. Song ", 
    24392500  year          = "2010", 
    24402501  month         = "oct", 
    … …  
    24582519} 
    24592520 
    2460 @article{         reffray.guillaume.ea_GMD15, 
    2461   title         = "Modelling turbulent vertical mixing sensitivity using 
    2462                    a 1-D version of NEMO", 
     2521@article{         reffray.bourdalle-badie.ea_GMD15, 
     2522  title         = "Modelling turbulent vertical mixing sensitivity using a 
     2523                  1-D version of NEMO", 
    24632524  pages         = "69--86", 
    24642525  journal       = "Geoscientific Model Development", 
    … …  
    26382699 
    26392700@article{         shchepetkin_OM15, 
    2640   title         = "An Adaptive, Courant-number-dependent implicit 
    2641        scheme for vertical advection in oceanic modeling", 
     2701  title         = "An Adaptive, Courant-number-dependent implicit scheme for 
     2702                  vertical advection in oceanic modeling", 
    26422703  pages         = "38--69", 
    26432704  journal       = "Ocean Modelling", 
    … …  
    26662727} 
    26672728 
    2668 @article{         simmons.jayne.ea_OM04, 
    2669   title         = "Tidally driven mixing in a numerical model of the ocean 
    2670                   general circulation", 
    2671   pages         = "245--263", 
    2672   journal       = "Ocean Modelling", 
    2673   volume        = "6", 
    2674   number        = "3-4", 
    2675   author        = "H. L. Simmons and S. R. Jayne and L. C. {St Laurent} and 
    2676                   A. J. Weaver", 
    2677   year          = "2004", 
    2678   month         = "jan", 
    2679   publisher     = "Elsevier BV", 
    2680   issn          = "1463-5003", 
    2681   doi           = "10.1016/s1463-5003(03)00011-8" 
    2682 } 
    2683  
    2684 @article{         smagorinsky_MW63, 
    2685   title         = "General circulation experiments with the primitive equations: I. The basic experiment ", 
     2729@article{         smagorinsky_MWR63, 
     2730  title         = "General circulation experiments with the primitive 
     2731                  equations: I. The basic experiment ", 
    26862732  pages         = "99--164", 
    26872733  journal       = "Monthly Weather Review", 
    … …  
    27242770  issn          = "1520-0493", 
    27252771  doi           = "10.1175/1520-0493(1998)126<3213:agpgff>2.0.co;2" 
    2726 } 
    2727  
    2728 @article{         st-laurent.nash_DSR04, 
    2729   title         = "An examination of the radiative and dissipative properties 
    2730                   of deep ocean internal tides", 
    2731   pages         = "3029--3042", 
    2732   journal       = "Deep Sea Research", 
    2733   volume        = "51", 
    2734   number        = "25-26", 
    2735   author        = "L. C. {St Laurent} and J. D. Nash", 
    2736   year          = "2004", 
    2737   month         = "dec", 
    2738   publisher     = "Elsevier BV", 
    2739   issn          = "0967-0645", 
    2740   doi           = "10.1016/j.dsr2.2004.09.008" 
    27412772} 
    27422773 
    … …  
    28122843  isbn          = "9780511702242", 
    28132844  doi           = "10.1017/cbo9780511702242.013" 
     2845} 
     2846 
     2847@book{            sverdrup.johnson.ea_bk42, 
     2848  title         = "The Oceans, Their Physics, Chemistry, and General Biology", 
     2849  pages         = "1087", 
     2850  author        = "H. U. Sverdrup and Martin W. Johnson and Richard H. 
     2851                  Fleming", 
     2852  year          = "1942", 
     2853  publisher     = "Prentice-Hall", 
     2854  address       = "New York" 
    28142855} 
    28152856 
    … …  
    29422983} 
    29432984 
    2944 @article{         vancoppenolle.fichefet.ea_OM09*a, 
    2945   title         = "Simulating the mass balance and salinity of Arctic and 
    2946                   Antarctic sea ice. 1. Model description and validation", 
    2947   pages         = "33--53", 
    2948   journal       = "Ocean Modelling", 
    2949   volume        = "27", 
    2950   number        = "1-2", 
    2951   author        = "M. Vancoppenolle and T. Fichefet and H. Goosse and S. 
    2952                   Bouillon and G. Madec and M. A. Morales Maqueda", 
    2953   year          = "2009", 
    2954   month         = "jan", 
    2955   publisher     = "Elsevier BV", 
    2956   issn          = "1463-5003", 
    2957   doi           = "10.1016/j.ocemod.2008.10.005" 
    2958 } 
    2959  
    2960 @article{         vancoppenolle.fichefet.ea_OM09*b, 
    2961   title         = "Simulating the mass balance and salinity of Arctic and 
    2962                   Antarctic sea ice. 2. Importance of sea ice salinity 
    2963                   variations", 
    2964   pages         = "54--69", 
    2965   journal       = "Ocean Modelling", 
    2966   volume        = "27", 
    2967   number        = "1-2", 
    2968   author        = "M. Vancoppenolle and T. Fichefet and H. Goosse", 
    2969   year          = "2009", 
    2970   month         = "jan", 
    2971   publisher     = "Elsevier BV", 
    2972   issn          = "1463-5003", 
    2973   doi           = "10.1016/j.ocemod.2008.11.003" 
    2974 } 
    2975  
    29762985@article{         warner.defne.ea_CG13, 
    29772986  title         = "A wetting and drying scheme for {ROMS}", 
    … …  
    30483057} 
    30493058 
    3050 @article{         white.hoskins.ea_QJRMS05, 
    3051   title         = "Consistent approximate models of the global atmosphere: shallow, deep, 
    3052                   hydrostatic, quasi-hydrostatic and non-hydrostatic", 
    3053   pages         = "2081--2107", 
    3054   journal       = "Quarterly Journal of the Royal Meteorological Society", 
    3055   volume        = "131", 
    3056   author        = "A. A. White and B. J. Hoskins and I. Roulstone and A. Staniforth", 
    3057   year          = "2005", 
    3058   doi           = "10.1256/qj.04.49" 
    3059 } 
    3060  
    30613059@article{         white.adcroft.ea_JCP09, 
    30623060  title         = "High-order regridding-remapping schemes for continuous 
    … …  
    30723070  issn          = "0021-9991", 
    30733071  doi           = "10.1016/j.jcp.2009.08.016" 
     3072} 
     3073 
     3074@article{         white.hoskins.ea_QJRMS05, 
     3075  title         = "Consistent approximate models of the global atmosphere: 
     3076                  shallow, deep, hydrostatic, quasi-hydrostatic and 
     3077                  non-hydrostatic", 
     3078  pages         = "2081--2107", 
     3079  journal       = "Quarterly Journal of the Royal Meteorological Society", 
     3080  volume        = "131", 
     3081  author        = "A. A. White and B. J. Hoskins and I. Roulstone and A. 
     3082                  Staniforth", 
     3083  year          = "2005", 
     3084  doi           = "10.1256/qj.04.49" 
    30743085} 
    30753086 
    … …  
    31213132} 
    31223133 
     3134@article{         zeng.beljaars_GRL05, 
     3135  title         = "A prognostic scheme of sea surface skin temperature for 
     3136                  modeling and data assimilation", 
     3137  journal       = "Geophysical Research Letters", 
     3138  volume        = "32", 
     3139  number        = "14", 
     3140  author        = "Xubin Zeng and Anton Beljaars", 
     3141  year          = "2005", 
     3142  month         = "jul", 
     3143  publisher     = "American Geophysical Union", 
     3144  doi           = "10.1029/2005gl023030" 
     3145} 
     3146 
    31233147@article{         zhang.endoh_JGR92, 
    31243148  title         = "A free surface General Circulation Model for the tropical 
    … …  
    31343158  doi           = "10.1029/92jc00911" 
    31353159} 
    3136  
    3137 @article{large.yeager_CD09, 
    3138 author="Large, W. G. and Yeager, S. G.", 
    3139 title="The Global Climatology of an Interannually Varying Air-Sea Flux Data Set", 
    3140 pages = "341--364", 
    3141 journal="Climate Dynamics", 
    3142 volume = "33", 
    3143 number = "2-3", 
    3144 year="2009", 
    3145 month = "aug", 
    3146 publisher = "Springer Science and Business Media LLC", 
    3147 doi="10.1007/s00382-008-0441-3" 
    3148 } 
    3149  
    3150 @book{sverdrup.johnson.ea_1942, 
    3151 author = {H. U. Sverdrup and Martin W. Johnson and Richard H. Fleming}, 
    3152 title = {The Oceans, Their Physics, Chemistry, and General Biology}, 
    3153 publisher = {Prentice-Hall}, 
    3154 address = {New York}, 
    3155 year = {1942}, 
    3156 pages = {1087}, 
    3157 } 
    3158  
    3159 @article{kraus.businger_QJRMS96, 
    3160 author = "E. B. Kraus and J. A. Businger", 
    3161 title = "Atmosphere-ocean interaction.", 
    3162 journal="Quarterly Journal of the Royal Meteorological Society",, 
    3163 year = "1996", 
    3164 volume = "122", 
    3165 number = "529", 
    3166 pages = "324-325", 
    3167 publisher = "John Wiley & Sons, Ltd", 
    3168 issn = "1477-870X", 
    3169 doi = "10.1002/qj.49712252914" 
    3170 } 
    3171  
    3172 @article{josey.gulev.ea_2013, 
    3173 title = "Exchanges through the ocean surface", 
    3174 journal = "Ocean Circulation and Climate - A 21st Century Perspective, Int. Geophys. Ser.", 
    3175 year = "2013", 
    3176 author = "S. A. Josey and S. Gulev and L. Yu", 
    3177 pages = "115-140, edited by G. Siedler et al., Academic Press, Oxford", 
    3178 volume = "103", 
    3179 doi = "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/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/main/chapters.tex

    r12377 r14789  
    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 
     1%% ================================================================================================= 
     2%% Chapters 
     3%% ================================================================================================= 
     4 
     5\subfile{../subfiles/chap_model_basics} %% Continuous equations and assumptions 
     6\subfile{../subfiles/chap_time_domain}  %% Time discretisation (time stepping strategy) 
     7\subfile{../subfiles/chap_DOM}          %% Space discretisation 
     8\subfile{../subfiles/chap_TRA}          %% Tracer advection/diffusion equation 
     9\subfile{../subfiles/chap_DYN}          %% Dynamics : momentum equation 
     10\subfile{../subfiles/chap_SBC}          %% Surface Boundary Conditions 
     11\subfile{../subfiles/chap_LBC}          %% Lateral Boundary Conditions 
     12\subfile{../subfiles/chap_LDF}          %% Lateral diffusion 
     13\subfile{../subfiles/chap_ZDF}          %% Vertical diffusion 
     14\subfile{../subfiles/chap_DIA}          %% Outputs and Diagnostics 
     15\subfile{../subfiles/chap_OBS}          %% Observation operator 
     16\subfile{../subfiles/chap_ASM}          %% Assimilation increments 
     17\subfile{../subfiles/chap_STO}          %% Stochastic param. 
     18\subfile{../subfiles/chap_misc}         %% Miscellaneous topics 
     19\subfile{../subfiles/chap_cfgs}         %% Predefined configurations 
     20 
     21%% Not included 
     22%\subfile{../subfiles/chap_model_basics_zstar} 
     23%\subfile{../subfiles/chap_DIU} 
     24%\subfile{../subfiles/chap_conservation} 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/main/introduction.tex

    r11543 r14789  
    1  
    21\chapter*{Introduction} 
    3  
    4 %\chaptertoc 
    5  
    6 %\paragraph{Changes record} ~\\ 
    7  
    8 %\thispagestyle{plain} 
    9  
    10 %{\footnotesize 
    11 %  \begin{tabularx}{\textwidth}{l||X|X} 
    12 %    Release & Author(s) & Modifications \\ 
    13 %    \hline 
    14 %    {\em x.x} & {\em ...} & {\em ...}   \\ 
    15 %    {\em ...} & {\em ...} & {\em ...}   \\ 
    16 %  \end{tabularx} 
    17 %} 
    18  
    19 %\clearpage 
    202 
    213The \textbf{N}ucleus for \textbf{E}uropean \textbf{M}odelling of the \textbf{O}cean (\NEMO) is 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/main/settings.tex

    r11591 r14789  
    1 %% Engine (subfolder name) 
    2 \def \engine{NEMO} 
     1%% Engine 
     2\def\eng{NEMO} 
    33 
    4 %% Cover page settings 
    5 \def \spacetop{  \vspace*{1.85cm} } 
    6 \def \heading{NEMO ocean engine} 
    7 %\def \subheading{} 
    8 \def \spacedown{ \vspace*{0.75cm } } 
    9 \def \authorswidth{ 0.3\linewidth} 
    10 \def \rulelenght{270pt} 
    11 \def \abstractwidth{0.6\linewidth} 
     4%% Cover page 
     5\def\spcup{\vspace*{2.15cm}} 
     6\def\hdg{NEMO ocean engine} 
     7%\def\shdg{} %% No subheading 
     8\def\spcdn{\vspace*{1.00cm}} 
     9\def\autwd{0.25\linewidth}\def\lnlg{270pt}\def\abswd{0.65\linewidth} 
    1210 
    13 %% Manual color (frontpage banner, links and chapter boxes) 
    14 \def \setmanualcolor{ \definecolor{manualcolor}{cmyk}{1, .60, 0, .4} } 
     11%% Color in cmyk model for manual theme (frontpage banner, links and chapter boxes) 
     12\def\clr{1.0,0.6,0.0,0.4} 
    1513 
    1614%% IPSL publication number 
    17 \def \ipslnum{27} 
     15\def\ipsl{27} 
    1816 
    19 %% Zenodo ID, i.e. doi:10.5281/zenodo.\([0-9]*\) 
    20 \def \zid{1464816} 
     17%% Zenodo ID, i.e. doi:10.5281/zenodo.\zid 
     18\def\zid{1464816} 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles

    • Property svn:ignore

      •  

        old new  
         1*.aux 
         2*.bbl 
         3*.blg 
         4*.fdb* 
         5*.fls 
         6*.idx 
         7*.ilg 
        18*.ind 
        2 *.ilg 
         9*.lo* 
         10*.out 
         11*.pdf 
         12*.pyg 
         13*.tdo 
         14*.toc 
         15*.xdv 
         16cache* 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/apdx_DOMAINcfg.tex

    r11693 r14789  
    66\label{apdx:DOMCFG} 
    77 
    8 %    {\em 4.0} & {\em Andrew Coward} & {\em Created at v4.0 from materials removed from chap\_DOM that are still relevant to the \forcode{DOMAINcfg} tool and which illustrate and explain the choices to be made by the user when setting up new domains }  \\ 
    9  
    10 \thispagestyle{plain} 
    11  
    128\chaptertoc 
    139 
    … …  
    1612{\footnotesize 
    1713  \begin{tabularx}{\textwidth}{l||X|X} 
    18     Release & Author(s) & Modifications \\ 
    19     \hline 
    20     {\em   4.0} & {\em ...} & {\em ...} \\ 
    21     {\em   3.6} & {\em ...} & {\em ...} \\ 
    22     {\em   3.4} & {\em ...} & {\em ...} \\ 
    23     {\em <=3.4} & {\em ...} & {\em ...} 
     14    Release     & Author(s)            & Modifications                                                \\ 
     15    \hline 
     16    {\em  next} & {\em Pierre Mathiot} & {\em Add ice shelf and closed sea option description        } \\ 
     17    {\em   4.0} & {\em  Andrew Coward} & {\em Creation from materials removed from \autoref{chap:DOM} 
     18                                              that are still relevant to the DOMAINcfg tool 
     19                                              when setting up new domains                            } 
    2420  \end{tabularx} 
    2521} 
    … …  
    4642 
    4743\begin{listing} 
    48   \nlst{namdom_domcfg} 
     44  \begin{forlines} 
     45!----------------------------------------------------------------------- 
     46&namdom        !   space and time domain (bathymetry, mesh, timestep) 
     47!----------------------------------------------------------------------- 
     48   nn_bathy    =    1      !  compute analyticaly (=0) or read (=1) the bathymetry file 
     49                           !  or compute (2) from external bathymetry 
     50   nn_interp   =    1                          ! type of interpolation (nn_bathy =2)                        
     51   cn_topo     =  'bathymetry_ORCA12_V3.3.nc'  ! external topo file (nn_bathy =2) 
     52   cn_bath     =  'Bathymetry'                 ! topo name in file  (nn_bathy =2) 
     53   cn_lon      =  'nav_lon'                    ! lon  name in file  (nn_bathy =2) 
     54   cn_lat      =  'nav_lat'                    ! lat  name in file  (nn_bathy =2) 
     55   rn_scale    = 1 
     56   rn_bathy    =    0.     !  value of the bathymetry. if (=0) bottom flat at jpkm1 
     57   jphgr_msh   =       0               !  type of horizontal mesh 
     58   ppglam0     =  999999.0             !  longitude of first raw and column T-point (jphgr_msh = 1) 
     59   ppgphi0     =  999999.0             ! latitude  of first raw and column T-point (jphgr_msh = 1) 
     60   ppe1_deg    =  999999.0             !  zonal      grid-spacing (degrees) 
     61   ppe2_deg    =  999999.0             !  meridional grid-spacing (degrees) 
     62   ppe1_m      =  999999.0             !  zonal      grid-spacing (degrees) 
     63   ppe2_m      =  999999.0             !  meridional grid-spacing (degrees) 
     64   ppsur       =   -4762.96143546300   !  ORCA r4, r2 and r05 coefficients 
     65   ppa0        =     255.58049070440   ! (default coefficients) 
     66   ppa1        =     245.58132232490   ! 
     67   ppkth       =      21.43336197938   ! 
     68   ppacr       =       3.0             ! 
     69   ppdzmin     =  999999.              !  Minimum vertical spacing 
     70   pphmax      =  999999.              !  Maximum depth 
     71   ldbletanh   =  .FALSE.              !  Use/do not use double tanf function for vertical coordinates 
     72   ppa2        =  999999.              !  Double tanh function parameters 
     73   ppkth2      =  999999.              ! 
     74   ppacr2      =  999999.              ! 
     75/ 
     76  \end{forlines} 
    4977  \caption{\forcode{&namdom_domcfg}} 
    5078  \label{lst:namdom_domcfg} 
    … …  
    5886 \item [{\np{jphgr_mesh}{jphgr\_mesh}=0}]  The most general curvilinear orthogonal grids. 
    5987  The coordinates and their first derivatives with respect to $i$ and $j$ are provided 
    60   in a input file (\ifile{coordinates}), read in \rou{hgr\_read} subroutine of the domhgr module. 
     88  in a input file (\textit{coordinates.nc}), read in \rou{hgr\_read} subroutine of the domhgr module. 
    6189  This is now the only option available within \NEMO\ itself from v4.0 onwards. 
    6290\item [{\np{jphgr_mesh}{jphgr\_mesh}=1 to 5}] A few simple analytical grids are provided (see below). 
    … …  
    123151The reference coordinate transformation $z_0(k)$ defines the arrays $gdept_0$ and 
    124152$gdepw_0$ for $t$- and $w$-points, respectively. See \autoref{sec:DOMCFG_sco} for the 
    125 S-coordinate options.  As indicated on \autoref{fig:DOM_index_vert} \jp{jpk} is the number of 
    126 $w$-levels.  $gdepw_0(1)$ is the ocean surface.  There are at most \jp{jpk}-1 $t$-points 
     153S-coordinate options.  As indicated on \autoref{fig:DOM_index_vert} \texttt{jpk} is the number of 
     154$w$-levels.  $gdepw_0(1)$ is the ocean surface.  There are at most \texttt{jpk}-1 $t$-points 
    127155inside the ocean, the additional $t$-point at $jk = jpk$ is below the sea floor and is not 
    128156used.  The vertical location of $w$- and $t$-levels is defined from the analytic 
    … …  
    134162 
    135163It is possible to define a simple regular vertical grid by giving zero stretching 
    136 (\np[=0]{ppacr}{ppacr}).  In that case, the parameters \jp{jpk} (number of $w$-levels) 
     164(\np[=0]{ppacr}{ppacr}).  In that case, the parameters \texttt{jpk} (number of $w$-levels) 
    137165and \np{pphmax}{pphmax} (total ocean depth in meters) fully define the grid. 
    138166 
    … …  
    146174\end{gather} 
    147175 
    148 where $k = 1$ to \jp{jpk} for $w$-levels and $k = 1$ to $k = 1$ for $t-$levels.  Such an 
     176where $k = 1$ to \texttt{jpk} for $w$-levels and $k = 1$ to $k = 1$ for $t-$levels.  Such an 
    149177expression allows us to define a nearly uniform vertical location of levels at the ocean 
    150178top and bottom with a smooth hyperbolic tangent transition in between (\autoref{fig:DOMCFG_zgr}). 
    … …  
    194222\end{equation} 
    195223 
    196 With the choice of the stretching $h_{cr} = 3$ and the number of levels \jp{jpk}~$= 31$, 
     224With the choice of the stretching $h_{cr} = 3$ and the number of levels \texttt{jpk}~$= 31$, 
    197225the four coefficients $h_{sur}$, $h_0$, $h_1$, and $h_{th}$ in 
    198226\autoref{eq:DOMCFG_zgr_ana_2} have been determined such that \autoref{eq:DOMCFG_zgr_coef} 
    … …  
    212240  Values from $3$ to $10$ are usual. 
    213241\item \np{ppkth}{ppkth}~$= h_{th}$: is approximately the model level at which maximum stretching occurs 
    214   (nondimensional, usually of order 1/2 or 2/3 of \jp{jpk}) 
     242  (nondimensional, usually of order 1/2 or 2/3 of \texttt{jpk}) 
    215243\item \np{ppdzmin}{ppdzmin}: minimum thickness for the top layer (in meters). 
    216244\item \np{pphmax}{pphmax}: total depth of the ocean (meters). 
    … …  
    218246 
    219247As an example, for the $45$ layers used in the DRAKKAR configuration those parameters are: 
    220 \jp{jpk}~$= 46$, \np{ppacr}{ppacr}~$= 9$, \np{ppkth}{ppkth}~$= 23.563$, \np{ppdzmin}{ppdzmin}~$= 6~m$, 
     248\texttt{jpk}~$= 46$, \np{ppacr}{ppacr}~$= 9$, \np{ppkth}{ppkth}~$= 23.563$, \np{ppdzmin}{ppdzmin}~$= 6~m$, 
    221249\np{pphmax}{pphmax}~$= 5750~m$. 
    222250 
    … …  
    313341  This is meant for the "EEL-R5" configuration, a periodic or open boundary channel with a seamount. 
    314342\item [{\np[=1]{nn_bathy}{nn\_bathy}}]: read a bathymetry and ice shelf draft (if needed). 
    315   The \ifile{bathy\_meter} file (Netcdf format) provides the ocean depth (positive, in meters) at 
     343  The \textit{bathy\_meter.nc} file (Netcdf format) provides the ocean depth (positive, in meters) at 
    316344  each grid point of the model grid. 
    317345  The bathymetry is usually built by interpolating a standard bathymetry product (\eg\ ETOPO2) onto 
    … …  
    319347  Defining the bathymetry also defines the coastline: where the bathymetry is zero, 
    320348  no wet levels are defined (all levels are masked). 
    321  
    322   The \ifile{isfdraft\_meter} file (Netcdf format) provides the ice shelf draft (positive, in meters) at 
    323   each grid point of the model grid. 
    324   This file is only needed if \np[=.true.]{ln_isfcav}{ln\_isfcav}. 
    325   Defining the ice shelf draft will also define the ice shelf edge and the grounding line position. 
    326349\end{description} 
    327350 
    … …  
    363386bathymetry varies by less than one level thickness from one grid point to the next).  The 
    364387reference layer thicknesses $e_{3t}^0$ have been defined in the absence of bathymetry. 
    365 With partial steps, layers from 1 to \jp{jpk}-2 can have a thickness smaller than 
     388With partial steps, layers from 1 to \texttt{jpk-2} can have a thickness smaller than 
    366389$e_{3t}(jk)$. 
    367390 
    368 The model deepest layer (\jp{jpk}-1) is allowed to have either a smaller or larger 
     391The model deepest layer (\texttt{jpk-1}) is allowed to have either a smaller or larger 
    369392thickness than $e_{3t}(jpk)$: the maximum thickness allowed is $2*e_{3t}(jpk - 1)$. 
    370393 
    … …  
    383406\subsubsection[$S$-coordinate (\forcode{ln_sco})]{$S$-coordinate (\protect\np{ln_sco}{ln\_sco})} 
    384407\label{sec:DOMCFG_sco} 
     408 
    385409\begin{listing} 
    386   \nlst{namzgr_sco_domcfg} 
    387410  \caption{\forcode{&namzgr_sco_domcfg}} 
    388411  \label{lst:namzgr_sco_domcfg} 
     412  \begin{forlines} 
     413!----------------------------------------------------------------------- 
     414&namzgr_sco    !   s-coordinate or hybrid z-s-coordinate                (default: OFF) 
     415!----------------------------------------------------------------------- 
     416   ln_s_sh94   = .false.    !  Song & Haidvogel 1994 hybrid S-sigma   (T)| 
     417   ln_s_sf12   = .false.   !  Siddorn & Furner 2012 hybrid S-z-sigma (T)| if both are false the NEMO tanh stretching is applied 
     418   ln_sigcrit  = .false.   !  use sigma coordinates below critical depth (T) or Z coordinates (F) for Siddorn & Furner stretch 
     419                           !  stretching coefficients for all functions 
     420   rn_sbot_min =   10.0    !  minimum depth of s-bottom surface (>0) (m) 
     421   rn_sbot_max = 7000.0    !  maximum depth of s-bottom surface (= ocean depth) (>0) (m) 
     422   rn_hc       =  150.0    !  critical depth for transition to stretched coordinates 
     423                        !!!!!!!  Envelop bathymetry 
     424   rn_rmax     =    0.3    !  maximum cut-off r-value allowed (0<r_max<1) 
     425                        !!!!!!!  SH94 stretching coefficients  (ln_s_sh94 = .true.) 
     426   rn_theta    =    6.0    !  surface control parameter (0<=theta<=20) 
     427   rn_bb       =    0.8    !  stretching with SH94 s-sigma 
     428                        !!!!!!!  SF12 stretching coefficient  (ln_s_sf12 = .true.) 
     429   rn_alpha    =    4.4    !  stretching with SF12 s-sigma 
     430   rn_efold    =    0.0    !  efold length scale for transition to stretched coord 
     431   rn_zs       =    1.0    !  depth of surface grid box 
     432                           !  bottom cell depth (Zb) is a linear function of water depth Zb = H*a + b 
     433   rn_zb_a     =    0.024  !  bathymetry scaling factor for calculating Zb 
     434   rn_zb_b     =   -0.2    !  offset for calculating Zb 
     435                        !!!!!!!! Other stretching (not SH94 or SF12) [also uses rn_theta above] 
     436   rn_thetb    =    1.0    !  bottom control parameter  (0<=thetb<= 1) 
     437/ 
     438  \end{forlines} 
    389439\end{listing} 
    390 Options are defined in \nam{zgr_sco}{zgr\_sco} (\texttt{DOMAINcfg} only). 
     440 
     441Options are defined in \forcode{&zgr_sco} (\texttt{DOMAINcfg} only). 
    391442In $s$-coordinate (\np[=.true.]{ln_sco}{ln\_sco}), the depth and thickness of the model levels are defined from 
    392443the product of a depth field and either a stretching function or its derivative, respectively: 
    … …  
    530581This option is described in the Report by Levier \textit{et al.} (2007), available on the \NEMO\ web site. 
    531582 
     583\section{Ice shelf cavity definition} 
     584\label{subsec:zgrisf} 
     585 
     586  If the under ice shelf seas are opened (\np{ln_isfcav}{ln\_isfcav}), the depth of the ice shelf/ocean interface has to be include in  
     587  the \textit{isfdraft\_meter} file (Netcdf format). This file need to include the \textit{isf\_draft} variable.  
     588  A positive value will mean ice shelf/ocean or ice shelf bedrock interface below the reference 0m ssh.  
     589  The exact shape of the ice shelf cavity (grounding line position and minimum thickness of the water column under an ice shelf, ...) can be specify in \nam{zgr_isf}{zgr\_isf}. 
     590 
     591\begin{listing} 
     592  \caption{\forcode{&namzgr_isf}} 
     593  \label{lst:namzgr_isf} 
     594  \begin{forlines} 
     595!----------------------------------------------------------------------- 
     596&namzgr_isf    !   isf cavity geometry definition                       (default: OFF) 
     597!----------------------------------------------------------------------- 
     598   rn_isfdep_min    = 10.         ! minimum isf draft tickness (if lower, isf draft set to this value) 
     599   rn_glhw_min      = 1.e-3       ! minimum water column thickness to define the grounding line 
     600   rn_isfhw_min     = 10          ! minimum water column thickness in the cavity once the grounding line defined. 
     601   ln_isfchannel    = .false.     ! remove channel (based on 2d mask build from isfdraft-bathy) 
     602   ln_isfconnect    = .false.     ! force connection under the ice shelf (based on 2d mask build from isfdraft-bathy) 
     603      nn_kisfmax       = 999         ! limiter in level on the previous condition. (if change larger than this number, get back to value before we enforce the connection) 
     604      rn_zisfmax       = 7000.       ! limiter in m     on the previous condition. (if change larger than this number, get back to value before we enforce the connection) 
     605   ln_isfcheminey   = .false.     ! close cheminey 
     606   ln_isfsubgl      = .false.     ! remove subglacial lake created by the remapping process 
     607      rn_isfsubgllon   =    0.0      !  longitude of the seed to determine the open ocean 
     608      rn_isfsubgllat   =    0.0      !  latitude  of the seed to determine the open ocean 
     609/ 
     610  \end{forlines} 
     611\end{listing} 
     612 
     613   The options available to define the shape of the under ice shelf cavities are listed in \nam{zgr_isf}{zgr\_isf} (\texttt{DOMAINcfg} only, \autoref{lst:namzgr_isf}). 
     614 
     615\subsection{Model ice shelf draft definition} 
     616\label{subsec:zgrisf_isfd} 
     617 
     618First of all, the tool make sure, the ice shelf draft ($h_{isf}$) is sensible and compatible with the bathymetry. 
     619There are 3 compulsory steps to achieve this: 
     620 
     621\begin{description} 
     622\item{\np{rn_isfdep_min}{rn\_isfdep\_min}:} this is the minimum ice shelf draft. This is to make sure there is no ridiculous thin ice shelf. If \np{rn_isfdep_min}{rn\_isfdep\_min} is smaller than the surface level, \np{rn_isfdep_min}{rn\_isfdep\_min} is set to $e3t\_1d(1)$.  
     623  Where $h_{isf} < MAX(e3t\_1d(1),rn\_isfdep\_min)$, $h_{isf}$ is set to \np{rn_isfdep_min}{rn\_isfdep\_min}. 
     624 
     625\item{\np{rn_glhw_min}{rn\_glhw\_min}:} This parameter is used to define the grounding line position. 
     626  Where the difference between the bathymetry and the ice shelf draft is smaller than \np{rn_glhw_min}{rn\_glhw\_min}, the cell are grounded (ie masked).  
     627  This step is needed to take into account possible small mismatch between ice shelf draft value and bathymetry value (sources are coming from different grid, different data processes, rounding error, ...). 
     628 
     629\item{\np{rn_isfhw_min}{rn\_isfhw\_min}:} This parameter is the minimum water column thickness in the cavity.  
     630  Where the water column thickness is lower than \np{rn_isfhw_min}{rn\_isfhw\_min}, the ice shelf draft is adjusted to match this criterion.  
     631  If for any reason, this adjustement break the minimum ice shelf draft allowed (\np{rn_isfdep_min}{rn\_isfdep\_min}), the cell is masked. 
     632\end{description} 
     633 
     634Once all these adjustements are made, if the water column thickness contains one cell wide channels, these channels can be closed using \np{ln_isfchannel}{ln\_isfchannel}.   
     635  
     636\subsection{Model top level definition} 
     637After the definition of the ice shelf draft, the tool defines the top level.  
     638The compulsory criterion is that the water column needs at least 2 wet cells in the water column at U- and V-points. 
     639To do so, if there one cell wide water column, the tools adjust the ice shelf draft to fillful the requierement.\\ 
     640 
     641The process is the following: 
     642\begin{description} 
     643\item{step 1:} The top level is defined in the same way as the bottom level is defined. 
     644\item{step 2:} The isolated grid point in the bathymetry are filled (as it is done in a domain without ice shelf) 
     645\item{step 3:} The tools make sure, the top level is above or equal to the bottom level 
     646\item{step 4:} If the water column at a U- or V- point is one wet cell wide, the ice shelf draft is adjusted. So the actual top cell become fully open and the new 
     647  top cell thickness is set to the minimum cell thickness allowed (following the same logic as for the bottom partial cell). This step is iterated 4 times to ensure the condition is fullfill along the 4 sides of the cell. 
     648\end{description} 
     649 
     650In case of steep slope and shallow water column, it likely that 2 cells are disconnected (bathymetry above its neigbourging ice shelf draft).  
     651The option \np{ln_isfconnect}{ln\_isfconnect} allow the tool to force the connection between these 2 cells. 
     652Some limiters in meter or levels on the digging allowed by the tool are available (respectively, \np{rn_zisfmax}{rn\_zisfmax} or \np{rn_kisfmax}{rn\_kisfmax}). 
     653This will prevent the formation of subglacial lakes at the expense of long vertical pipe to connect cells at very different levels. 
     654 
     655\subsection{Subglacial lakes} 
     656Despite careful setting of your ice shelf draft and bathymetry input file as well as setting described in \autoref{subsec:zgrisf_isfd}, some situation are unavoidable. 
     657For exemple if you setup your ice shelf draft and bathymetry to do ocean/ice sheet coupling,  
     658you may decide to fill the whole antarctic with a bathymetry and an ice shelf draft value (ice/bedrock interface depth when grounded).  
     659If you do so, the subglacial lakes will show up (Vostock for example). An other possibility is with coarse vertical resolution, some ice shelves could be cut in 2 parts:  
     660one connected to the main ocean and an other one closed which can be considered as a subglacial sea be the model.\\ 
     661 
     662The namelist option \np{ln_isfsubgl}{ln\_isfsubgl} allow you to remove theses subglacial lakes. 
     663This may be useful for esthetical reason or for stability reasons: 
     664 
     665\begin{description} 
     666\item $\bullet$ In a subglacial lakes, in case of very weak circulation (often the case), the only heat flux is the conductive heat flux through the ice sheet.  
     667  This will lead to constant freezing until water reaches -20C.  
     668  This is one of the defitiency of the 3 equation melt formulation (for details on this formulation, see: \autoref{sec:isf}). 
     669\item $\bullet$ In case of coupling with an ice sheet model,  
     670  the ssh in the subglacial lakes and the main ocean could be very different (ssh initial adjustement for example),  
     671  and so if for any reason both a connected at some point, the model is likely to fall over.\\ 
     672\end{description} 
     673 
     674\section{Closed sea definition} 
     675\label{sec:clocfg} 
     676 
     677\begin{listing} 
     678  \caption{\forcode{&namclo}} 
     679  \label{lst:namdom_clo} 
     680  \begin{forlines} 
     681!----------------------------------------------------------------------- 
     682&namclo ! (closed sea : need ln_domclo = .true. in namcfg) 
     683!----------------------------------------------------------------------- 
     684   rn_lon_opnsea = -2.0     ! longitude seed of open ocean 
     685   rn_lat_opnsea = -2.0     ! latitude  seed of open ocean 
     686   nn_closea = 8           ! number of closed seas ( = 0; only the open_sea mask will be computed) 
     687   !                name   ! lon_src ! lat_src ! lon_trg ! lat_trg ! river mouth area   ! net evap/precip correction scheme ! radius tgt   ! id trg 
     688   !                       ! (degree)! (degree)! (degree)! (degree)! local/coast/global ! (glo/rnf/emp)                     !     (m)      ! 
     689   ! North American lakes 
     690   sn_lake(1) = 'superior' ,  -86.57 ,  47.30  , -66.49  , 50.45   , 'local'            , 'rnf'                             ,   550000.0 , 2     
     691   sn_lake(2) = 'michigan' ,  -87.06 ,  42.74  , -66.49  , 50.45   , 'local'            , 'rnf'                             ,   550000.0 , 2     
     692   sn_lake(3) = 'huron'    ,  -82.51 ,  44.74  , -66.49  , 50.45   , 'local'            , 'rnf'                             ,   550000.0 , 2     
     693   sn_lake(4) = 'erie'     ,  -81.13 ,  42.25  , -66.49  , 50.45   , 'local'            , 'rnf'                             ,   550000.0 , 2     
     694   sn_lake(5) = 'ontario'  ,  -77.72 ,  43.62  , -66.49  , 50.45   , 'local'            , 'rnf'                             ,   550000.0 , 2     
     695   ! African Lake 
     696   sn_lake(6) = 'victoria' ,   32.93 ,  -1.08  ,  30.44  , 31.37   , 'coast'            , 'emp'                             ,   100000.0 , 3     
     697   ! Asian Lakes 
     698   sn_lake(7) = 'caspian'  ,   50.0  ,  44.0   ,   0.0   ,  0.0    , 'global'           , 'glo'                             ,        0.0 , 1      
     699   sn_lake(8) = 'aral'     ,   60.0  ,  45.0   ,   0.0   ,  0.0    , 'global'           , 'glo'                             ,        0.0 , 1     
     700/ 
     701   \end{forlines} 
     702\end{listing} 
     703 
     704The options available to define the closed seas and how closed sea net fresh water input will be redistributed by NEMO are listed in \nam{dom_clo}{dom\_clo} (\texttt{DOMAINcfg} only). 
     705The individual definition of each closed sea is managed by \np{sn_lake}{sn\_lake}. In this fields the user needs to define:\\ 
     706   \begin{description} 
     707   \item $\bullet$    the name of the closed sea (print output purposes). 
     708   \item $\bullet$    the seed location to define the area of the closed sea (if seed on land because not present in this configuration, this closed sea will be ignored).\\ 
     709   \item $\bullet$    the seed location for the target area. 
     710   \item $\bullet$    the type of target area ('local','coast' or 'global'). See point 6 for definition of these cases. 
     711   \item $\bullet$    the type of redistribution scheme for the net fresh water flux over the closed sea (as a runoff in a target area, as emp in a target area, as emp globally). For the runoff case, if the net fwf is negative, it will be redistribut globally. 
     712   \item $\bullet$    the radius of the target area (not used for the 'global' case). So the target defined by a 'local' target area of a radius of 100km, for example, correspond to all the wet points within this radius. The coastal case will return only the coastal point within the specifid radius. 
     713   \item $\bullet$    the target id. This target id is used to group multiple lakes into the same river ouflow (Great Lakes for example). 
     714   \end{description} 
     715 
     716The closed sea module defines a number of masks in the \textit{domain\_cfg} output: 
     717   \begin{description} 
     718   \item[\textit{mask\_opensea}:] a mask of the main ocean without all the closed seas closed. This mask is defined by a flood filling algorithm with an initial seed (localisation defined by \np{rn_lon_opnsea}{rn\_lon\_opnsea} and \np{rn_lat_opnsea}{rn\_lat\_opnsea}). 
     719   \item[\textit{mask\_csglo}, \textit{mask\_csrnf}, \textit{mask\_csemp}:] a mask of all the closed seas defined in the namelist by \np{sn_lake}{sn\_lake} for each redistribution scheme. The total number of defined closed seas has to be defined in \np{nn_closea}{nn\_closea}. 
     720   \item[\textit{mask\_csgrpglo}, \textit{mask\_csgrprnf}, \textit{mask\_csgrpemp}:] a mask of all the closed seas and targets grouped by target id for each type of redistribution scheme. 
     721   \item[\textit{mask\_csundef}:] a mask of all the closed sea not defined in \np{sn_lake}{sn\_lake}. This will allows NEMO to mask them if needed or to inform the user of potential minor issues in its bathymetry. 
     722   \end{description} 
     723    
    532724\subinc{\input{../../global/epilogue}} 
    533725 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/apdx_algos.tex

    r11693 r14789  
    55\chapter{Note on some algorithms} 
    66\label{apdx:ALGOS} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/apdx_diff_opers.tex

    r11693 r14789  
    55\chapter{Diffusive Operators} 
    66\label{apdx:DIFFOPERS} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/apdx_invariants.tex

    r11693 r14789  
    55\chapter{Discrete Invariants of the Equations} 
    66\label{apdx:INVARIANTS} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/apdx_s_coord.tex

    r11693 r14789  
    88%    {\em 4.0} & {\em Mike Bell} & {\em review}  \\ 
    99%    {\em 3.x} & {\em Gurvan Madec} & {\em original}  \\ 
    10  
    11 \thispagestyle{plain} 
    1210 
    1311\chaptertoc 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/apdx_triads.tex

    r11693 r14789  
    11\documentclass[../main/NEMO_manual]{subfiles} 
    2  
    3 %% Local cmds 
    4 \newcommand{\rML}[1][i]{\ensuremath{_{\mathrm{ML}\,#1}}} 
    5 \newcommand{\rMLt}[1][i]{\tilde{r}_{\mathrm{ML}\,#1}} 
    6 %% Move to ../../global/new_cmds.tex to avoid error with \listoffigures 
    7 %\newcommand{\triad}[6][]{\ensuremath{{}_{#2}^{#3}{\mathbb{#4}_{#1}}_{#5}^{\,#6}} 
    8 \newcommand{\triadd}[5]{\ensuremath{{}_{#1}^{#2}{\mathbb{#3}}_{#4}^{\,#5}}} 
    9 \newcommand{\triadt}[5]{\ensuremath{{}_{#1}^{#2}{\tilde{\mathbb{#3}}}_{#4}^{\,#5}}} 
    10 \newcommand{\rtriad}[2][]{\ensuremath{\triad[#1]{i}{k}{#2}{i_p}{k_p}}} 
    11 \newcommand{\rtriadt}[1]{\ensuremath{\triadt{i}{k}{#1}{i_p}{k_p}}} 
    122 
    133\begin{document} 
    … …  
    155\chapter{Iso-Neutral Diffusion and Eddy Advection using Triads} 
    166\label{apdx:TRIADS} 
    17  
    18 \thispagestyle{plain} 
    197 
    208\chaptertoc 
    … …  
    3624 
    3725%% ================================================================================================= 
    38 \section[Choice of \forcode{namtra\_ldf} namelist parameters]{Choice of \protect\nam{tra_ldf}{tra\_ldf} namelist parameters} 
     26\section[Choice of \forcode{namtra_ldf} namelist parameters]{Choice of \protect\nam{tra_ldf}{tra\_ldf} namelist parameters} 
    3927 
    4028Two scheme are available to perform the iso-neutral diffusion. 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_ASM.tex

    r11693 r14789  
    88%    {\em 4.0} & {\em D. J. Lea} & {\em \NEMO\ 4.0 updates}  \\ 
    99%    {\em 3.4} & {\em D. J. Lea, M. Martin, K. Mogensen, A. Weaver} & {\em Initial version}  \\ 
    10  
    11 \thispagestyle{plain} 
    1210 
    1311\chaptertoc 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_DIA.tex

    r12377 r14789  
    1111%    {\em 3.4} & {\em Gurvan Madec, Rachid Benshila, Andrew Coward } & {\em }  \\ 
    1212%    {\em }      & {\em Christian Ethe, Sebastien Masson } & {\em }  \\ 
    13  
    14 \thispagestyle{plain} 
    1513 
    1614\chaptertoc 
    … …  
    119117\subsection{XIOS: Reading and writing restart file} 
    120118 
    121 XIOS may be used to read single file restart produced by \NEMO. Currently only the variables written to 
    122 file \forcode{numror} can be handled by XIOS. To activate restart reading using XIOS, set \np[=.true. ]{ln_xios_read}{ln\_xios\_read} 
     119XIOS may be used to read single file restart produced by \NEMO. The variables written to 
     120file \forcode{numror} (OCE), \forcode{numrir} (SI3), \forcode{numrtr} (TOP), \forcode{numrsr} (SED) can be handled by XIOS.  
     121To activate restart reading using XIOS, set \np[=.true. ]{ln_xios_read}{ln\_xios\_read} 
    123122in \textit{namelist\_cfg}. This setting will be ignored when multiple restart files are present, and default \NEMO 
    124123functionality will be used for reading. There is no need to change iodef.xml file to use XIOS to read 
    … …  
    142141have to be rebuild before continuing the run. This option aims to reduce number of restart files generated by \NEMO\ only, 
    143142and may be useful when there is a need to change number of processors used to run simulation. 
    144  
    145 If an additional variable must be written to a restart file, the following steps are needed: 
    146 \begin{enumerate} 
    147 \item Add variable name to a list of restart variables (in subroutine \rou{iom\_set\_rst\_vars,} \mdl{iom}) and 
    148 define correct grid for the variable (\forcode{grid_N_3D} - 3D variable, \forcode{grid_N} - 2D variable, \forcode{grid_vector} - 
    149 1D variable, \forcode{grid_scalar} - scalar), 
    150 \item Add variable to the list of fields written by restart.  This can be done either in subroutine 
    151 \rou{iom\_set\_rstw\_core} (\mdl{iom}) or by calling  \rou{iom\_set\_rstw\_active} (\mdl{iom}) with the name of a variable 
    152 as an argument. This convention follows approach for writing restart using iom, where variables are 
    153 written either by \rou{rst\_write} or by calling \rou{iom\_rstput} from individual routines. 
    154 \end{enumerate} 
    155143 
    156144An older versions of XIOS do not support reading functionality. It's recommended to use at least XIOS2@1451. 
    … …  
    676664\end{forlines} 
    677665 
    678 \noindent will give the following file name radical: \ifile{myfile\_ORCA2\_19891231\_freq1d} 
     666\noindent will give the following file name radical: \textit{myfile\_ORCA2\_19891231\_freq1d} 
    679667 
    680668%% ================================================================================================= 
    … …  
    19521940When \np[=.true.]{ln_subbas}{ln\_subbas}, transports and stream function are computed for the Atlantic, Indian, 
    19531941Pacific and Indo-Pacific Oceans (defined north of 30\deg{S}) as well as for the World Ocean. 
    1954 The sub-basin decomposition requires an input file (\ifile{subbasins}) which contains three 2D mask arrays, 
     1942The sub-basin decomposition requires an input file (\textit{subbasins}) which contains three 2D mask arrays, 
    19551943the Indo-Pacific mask been deduced from the sum of the Indian and Pacific mask (\autoref{fig:DIA_mask_subasins}). 
    19561944 
    19571945\begin{listing} 
    1958   \nlst{namptr} 
     1946%  \nlst{namptr} 
    19591947  \caption{\forcode{&namptr}} 
    19601948  \label{lst:namptr} 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_DIU.tex

    r11693 r14789  
    55\chapter{Diurnal SST Models (DIU)} 
    66\label{chap:DIU} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 
    … …  
    5250 
    5351This namelist contains only two variables: 
     52 
    5453\begin{description} 
    5554\item [{\np{ln_diurnal}{ln\_diurnal}}] A logical switch for turning on/off both the cool skin and warm layer. 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_DOM.tex

    r11693 r14789  
    1414% -    domclo: closed sea and lakes.... 
    1515%              management of closea sea area: specific to global cfg, both forced and coupled 
    16  
    17 \thispagestyle{plain} 
    1816 
    1917\chaptertoc 
    … …  
    368366\label{subsec:DOM_size} 
    369367 
    370 The total size of the computational domain is set by the parameters \jp{jpiglo}, \jp{jpjglo} and 
    371 \jp{jpkglo} for the $i$, $j$ and $k$ directions, respectively. 
     368The total size of the computational domain is set by the parameters \texttt{jpiglo}, \texttt{jpjglo} and 
     369\texttt{jpkglo} for the $i$, $j$ and $k$ directions, respectively. 
    372370Note, that the variables \texttt{jpi} and \texttt{jpj} refer to 
    373371the size of each processor subdomain when the code is run in parallel using domain decomposition 
    … …  
    379377in which case \np{cn_cfg}{cn\_cfg} and \np{nn_cfg}{nn\_cfg} are set from these values accordingly). 
    380378 
    381 The global lateral boundary condition type is selected from 8 options using parameter \jp{jperio}. 
     379The global lateral boundary condition type is selected from 8 options using parameters \texttt{l\_Iperio}, \texttt{l\_Jperio}, \texttt{l\_NFold} and \texttt{c\_NFtype}. 
    382380See \autoref{sec:LBC_jperio} for details on the available options and 
    383 the corresponding values for \jp{jperio}. 
     381the corresponding values for \texttt{l\_Iperio}, \texttt{l\_Jperio}, \texttt{l\_NFold} and \texttt{c\_NFtype}. 
    384382 
    385383%% ================================================================================================= 
    … …  
    396394 
    397395\begin{clines} 
    398 int    jpiglo, jpjglo, jpkglo     /* global domain sizes                                    */ 
    399 int    jperio                     /* lateral global domain b.c.                             */ 
    400 double glamt, glamu, glamv, glamf /* geographic longitude (t,u,v and f points respectively) */ 
    401 double gphit, gphiu, gphiv, gphif /* geographic latitude                                    */ 
    402 double e1t, e1u, e1v, e1f         /* horizontal scale factors                               */ 
    403 double e2t, e2u, e2v, e2f         /* horizontal scale factors                               */ 
     396integer   Ni0glo, NjOglo, jpkglo       /* global domain sizes (without MPI halos)                */ 
     397logical   l\_Iperio, l\_Jperio         /* lateral global domain b.c.: i- j-periodicity           */ 
     398logical   l\_NFold                     /* lateral global domain b.c.: North Pole folding         */ 
     399char(1)   c\_NFtype                    /*    type of North pole Folding: T or F point            */ 
     400real      glamt, glamu, glamv, glamf   /* geographic longitude (t,u,v and f points respectively) */ 
     401real      gphit, gphiu, gphiv, gphif   /* geographic latitude                                    */ 
     402real      e1t, e1u, e1v, e1f           /* horizontal scale factors                               */ 
     403real      e2t, e2u, e2v, e2f           /* horizontal scale factors                               */ 
    404404\end{clines} 
    405405 
    … …  
    465465\begin{enumerate} 
    466466\item the bathymetry given in meters; 
    467 \item the number of levels of the model (\jp{jpk}); 
     467\item the number of levels of the model (\texttt{jpk}); 
    468468\item the analytical transformation $z(i,j,k)$ and the vertical scale factors 
    469469  (derivatives of the transformation); and 
    … …  
    575575every gridcell in the model regardless of the choice of vertical coordinate. 
    576576With constant z-levels, e3 metrics will be uniform across each horizontal level. 
    577 In the partial step case each e3 at the \jp{bottom\_level} 
    578 (and, possibly, \jp{top\_level} if ice cavities are present) 
     577In the partial step case each e3 at the \texttt{bottom\_level} 
     578(and, possibly, \texttt{top\_level} if ice cavities are present) 
    579579may vary from its horizontal neighbours. 
    580580And, in s-coordinates, variations can occur throughout the water column. 
    … …  
    585585those arising from a flat sea surface with zero elevation. 
    586586 
    587 The \jp{bottom\_level} and \jp{top\_level} 2D arrays define 
    588 the \jp{bottom\_level} and top wet levels in each grid column. 
    589 Without ice cavities, \jp{top\_level} is essentially a land mask (0 on land; 1 everywhere else). 
    590 With ice cavities, \jp{top\_level} determines the first wet point below the overlying ice shelf. 
     587The \texttt{bottom\_level} and \texttt{top\_level} 2D arrays define 
     588the \texttt{bottom\_level} and top wet levels in each grid column. 
     589Without ice cavities, \texttt{top\_level} is essentially a land mask (0 on land; 1 everywhere else). 
     590With ice cavities, \texttt{top\_level} determines the first wet point below the overlying ice shelf. 
    591591 
    592592%% ================================================================================================= 
    … …  
    594594\label{subsec:DOM_msk} 
    595595 
    596 From \jp{top\_level} and \jp{bottom\_level} fields, the mask fields are defined as follows: 
     596From \texttt{top\_level} and \texttt{bottom\_level} fields, the mask fields are defined as follows: 
    597597\begin{align*} 
    598598  tmask(i,j,k) &= 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_DYN.tex

    r11693 r14789  
    55\chapter{Ocean Dynamics (DYN)} 
    66\label{chap:DYN} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 
    … …  
    657655Note that expression \autoref{eq:DYN_hpg_sco} is commonly used when the variable volume formulation is activated 
    658656(\texttt{vvl?}) because in that case, even with a flat bottom, 
    659 the coordinate surfaces are not horizontal but follow the free surface \citep{levier.treguier.ea_rpt07}. 
     657the coordinate surfaces are not horizontal but follow the free surface \citep{levier.treguier.ea_trpt07}. 
    660658The pressure jacobian scheme (\np[=.true.]{ln_dynhpg_prj}{ln\_dynhpg\_prj}) is available as 
    661659an improved option to \np[=.true.]{ln_dynhpg_sco}{ln\_dynhpg\_sco} when \texttt{vvl?} is active. 
    … …  
    763761which imposes a very small time step when an explicit time stepping is used. 
    764762Two methods are proposed to allow a longer time step for the three-dimensional equations: 
    765 the filtered free surface, which is a modification of the continuous equations (see \autoref{eq:MB_flt?}), 
     763the filtered free surface, which is a modification of the continuous equations \iffalse (see \autoref{eq:MB_flt?}) \fi 
    766764and the split-explicit free surface described below. 
    767765The extra term introduced in the filtered method is calculated implicitly, 
    … …  
    913911external gravity waves in idealized or weakly non-linear cases. 
    914912Although the damping is lower than for the filtered free surface, 
    915 it is still significant as shown by \citet{levier.treguier.ea_rpt07} in the case of an analytical barotropic Kelvin wave. 
     913it is still significant as shown by \citet{levier.treguier.ea_trpt07} in the case of an analytical barotropic Kelvin wave. 
    916914 
    917915\cmtgm{               %%% copy from griffies Book 
    … …  
    12451243the atmospheric pressure is taken into account when computing the surface pressure gradient. 
    12461244 
    1247 (2) When \np[=.true.]{ln_tide_pot}{ln\_tide\_pot} and \np[=.true.]{ln_tide}{ln\_tide} (see \autoref{sec:SBC_tide}), 
     1245(2) When \np[=.true.]{ln_tide_pot}{ln\_tide\_pot} and \np[=.true.]{ln_tide}{ln\_tide} (see \autoref{sec:SBC_TDE}), 
    12481246the tidal potential is taken into account when computing the surface pressure gradient. 
    12491247 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_LBC.tex

    r11693 r14789  
    55\chapter{Lateral Boundary Condition (LBC)} 
    66\label{chap:LBC} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 
    … …  
    1614    Release & Author(s) & Modifications \\ 
    1715    \hline 
     16    {\em  next} & {\em Simon M{\" u}ller} & {\em Minor update of \autoref{subsec:LBC_bdy_tides}} \\[2mm] 
    1817    {\em   4.0} & {\em ...} & {\em ...} \\ 
    1918    {\em   3.6} & {\em ...} & {\em ...} \\ 
    … …  
    160159 
    161160%% ================================================================================================= 
    162 \section[Model domain boundary condition (\forcode{jperio})]{Model domain boundary condition (\protect\jp{jperio})} 
     161\section{Model domain boundary condition} 
    163162\label{sec:LBC_jperio} 
    164163 
    … …  
    169168 
    170169%% ================================================================================================= 
    171 \subsection[Closed, cyclic (\forcode{=0,1,2,7})]{Closed, cyclic (\protect\jp{jperio}\forcode{=0,1,2,7})} 
     170\subsection{Closed, cyclic (\forcode{l_Iperio,l_jperio})} 
    172171\label{subsec:LBC_jperio012} 
    173172 
    174173The choice of closed or cyclic model domain boundary condition is made by 
    175 setting \jp{jperio} to 0, 1, 2 or 7 in namelist \nam{cfg}{cfg}. 
     174setting \forcode{l_Iperio,l_jperio} to true or false in namelist \nam{cfg}{cfg}. 
    176175Each time such a boundary condition is needed, it is set by a call to routine \mdl{lbclnk}. 
    177176The computation of momentum and tracer trends proceeds from $i=2$ to $i=jpi-1$ and from $j=2$ to $j=jpj-1$, 
    … …  
    182181\begin{description} 
    183182 
    184 \item [For closed boundary (\jp{jperio}\forcode{=0})], solid walls are imposed at all model boundaries: 
     183\item [For closed boundary (\forcode{l_Iperio = .false.,l_jperio = .false.})], solid walls are imposed at all model boundaries: 
    185184  first and last rows and columns are set to zero. 
    186185 
    187 \item [For cyclic east-west boundary (\jp{jperio}\forcode{=1})], first and last rows are set to zero (closed) whilst the first column is set to 
     186\item [For cyclic east-west boundary (\forcode{l_Iperio = .true.,l_jperio = .false.})], first and last rows are set to zero (closed) whilst the first column is set to 
    188187  the value of the last-but-one column and the last column to the value of the second one 
    189188  (\autoref{fig:LBC_jperio}-a). 
    190189  Whatever flows out of the eastern (western) end of the basin enters the western (eastern) end. 
    191190 
    192 \item [For cyclic north-south boundary (\jp{jperio}\forcode{=2})], first and last columns are set to zero (closed) whilst the first row is set to 
     191\item [For cyclic north-south boundary (\forcode{l_Iperio = .false.,l_jperio = .true.})], first and last columns are set to zero (closed) whilst the first row is set to 
    193192  the value of the last-but-one row and the last row to the value of the second one 
    194193  (\autoref{fig:LBC_jperio}-a). 
    195194  Whatever flows out of the northern (southern) end of the basin enters the southern (northern) end. 
    196195 
    197 \item [Bi-cyclic east-west and north-south boundary (\jp{jperio}\forcode{=7})] combines cases 1 and 2. 
     196\item [Bi-cyclic east-west and north-south boundary (\forcode{l_Iperio = .true.,l_jperio = .true.})] combines cases 1 and 2. 
    198197 
    199198\end{description} 
    … …  
    208207 
    209208%% ================================================================================================= 
    210 \subsection[North-fold (\forcode{=3,6})]{North-fold (\protect\jp{jperio}\forcode{=3,6})} 
     209\subsection{North-fold (\forcode{l_NFold = .true.})} 
    211210\label{subsec:LBC_north_fold} 
    212211 
    … …  
    221220  \includegraphics[width=0.66\textwidth]{LBC_North_Fold_T} 
    222221  \caption[North fold boundary in ORCA 2\deg, 1/4\deg and 1/12\deg]{ 
    223     North fold boundary with a $T$-point pivot and cyclic east-west boundary condition ($jperio=4$), 
     222    North fold boundary with a $T$-point pivot and cyclic east-west boundary condition ($c\_NFtype='T'$), 
    224223    as used in ORCA 2\deg, 1/4\deg and 1/12\deg. 
    225224    Pink shaded area corresponds to the inner domain mask (see text).} 
    … …  
    287286Each processor is independent and without message passing or synchronous process, programs run alone and access just its own local memory. 
    288287For this reason, 
    289 the main model dimensions are now the local dimensions of the subdomain (pencil) that are named \jp{jpi}, \jp{jpj}, \jp{jpk}. 
     288the main model dimensions are now the local dimensions of the subdomain (pencil) that are named \texttt{jpi}, \texttt{jpj}, \texttt{jpk}. 
    290289These dimensions include the internal domain and the overlapping rows. 
    291 The number of rows to exchange (known as the halo) is usually set to one (nn\_hls=1, in \mdl{par\_oce}, 
     290The number of rows to exchange (known as the halo) is usually set to one (\forcode{nn_hls=1}, in \mdl{par\_oce}, 
    292291and must be kept to one until further notice). 
    293 The whole domain dimensions are named \jp{jpiglo}, \jp{jpjglo} and \jp{jpk}. 
     292The whole domain dimensions are named \texttt{jpiglo}, \texttt{jpjglo} and \texttt{jpk}. 
    294293The relationship between the whole domain and a sub-domain is: 
    295294\begin{gather*} 
    … …  
    298297\end{gather*} 
    299298 
    300 One also defines variables nldi and nlei which correspond to the internal domain bounds, and the variables nimpp and njmpp which are the position of the (1,1) grid-point in the global domain (\autoref{fig:LBC_mpp}). Note that since the version 4, there is no more extra-halo area as defined in \autoref{fig:LBC_mpp} so \jp{jpi} is now always equal to nlci and \jp{jpj} equal to nlcj. 
     299One also defines variables nldi and nlei which correspond to the internal domain bounds, and the variables nimpp and njmpp which are the position of the (1,1) grid-point in the global domain (\autoref{fig:LBC_mpp}). Note that since the version 4, there is no more extra-halo area as defined in \autoref{fig:LBC_mpp} so \texttt{jpi} is now always equal to nlci and \texttt{jpj} equal to nlcj. 
    301300 
    302301An element of $T_{l}$, a local array (subdomain) corresponds to an element of $T_{g}$, 
    … …  
    308307with $1 \leq i \leq jpi$, $1  \leq j \leq jpj $ , and  $1  \leq k \leq jpk$. 
    309308 
    310 The 1-d arrays $mig(1:\jp{jpi})$ and $mjg(1:\jp{jpj})$, defined in \rou{dom\_glo} routine (\mdl{domain} module), should be used to get global domain indices from local domain indices. The 1-d arrays, $mi0(1:\jp{jpiglo})$, $mi1(1:\jp{jpiglo})$ and $mj0(1:\jp{jpjglo})$, $mj1(1:\jp{jpjglo})$ have the reverse purpose and should be used to define loop indices expressed in global domain indices (see examples in \mdl{dtastd} module).\\ 
     309The 1-d arrays $mig(1:\texttt{jpi})$ and $mjg(1:\texttt{jpj})$, defined in \rou{dom\_glo} routine (\mdl{domain} module), should be used to get global domain indices from local domain indices. The 1-d arrays, $mi0(1:\texttt{jpiglo})$, $mi1(1:\texttt{jpiglo})$ and $mj0(1:\texttt{jpjglo})$, $mj1(1:\texttt{jpjglo})$ have the reverse purpose and should be used to define loop indices expressed in global domain indices (see examples in \mdl{dtastd} module).\\ 
    311310 
    312311The \NEMO\ model computes equation terms with the help of mask arrays (0 on land points and 1 on sea points). It is therefore possible that an MPI subdomain contains only land points. To save ressources, we try to supress from the computational domain as much land subdomains as possible. For example if $N_{mpi}$ processes are allocated to NEMO, the domain decomposition will be given by the following equation: 
    … …  
    357356 
    358357The BDY module was modelled on the OBC module (see \NEMO\ 3.4) and shares many features and 
    359 a similar coding structure \citep{chanut_rpt05}. 
     358a similar coding structure \citep{chanut_trpt05}. 
    360359The specification of the location of the open boundary is completely flexible and 
    361360allows any type of setup, from regular boundaries to irregular contour (it includes the possibility to set an open boundary able to follow an isobath). 
    … …  
    371370The number of boundary sets is defined by \np{nb_bdy}{nb\_bdy}. 
    372371Each boundary set can be either defined as a series of straight line segments directly in the namelist 
    373 (\np[=.false.]{ln_coords_file}{ln\_coords\_file}, and a namelist block \nam{bdy_index}{bdy\_index} must be included for each set) or read in from a file (\np[=.true.]{ln_coords_file}{ln\_coords\_file}, and a ``\ifile{coordinates.bdy}'' file must be provided). 
    374 The coordinates.bdy file is analagous to the usual \NEMO\ ``\ifile{coordinates}'' file. 
     372(\np[=.false.]{ln_coords_file}{ln\_coords\_file}, and a namelist block \forcode{&nambdy_index} must be included for each set) or read in from a file (\np[=.true.]{ln_coords_file}{ln\_coords\_file}, and a ``\textit{coordinates.bdy.nc}'' file must be provided). 
     373The coordinates.bdy file is analagous to the usual \NEMO\ ``\textit{coordinates.nc}'' file. 
    375374In the example above, there are two boundary sets, the first of which is defined via a file and 
    376375the second is defined in the namelist. 
    … …  
    568567\autoref{fig:LBC_bdy_geom} shows an example of an irregular boundary. 
    569568 
    570 The boundary geometry for each set may be defined in a namelist nambdy\_index or 
    571 by reading in a ``\ifile{coordinates.bdy}'' file. 
    572 The nambdy\_index namelist defines a series of straight-line segments for north, east, south and west boundaries. 
    573 One nambdy\_index namelist block is needed for each boundary condition defined by indexes. 
     569The boundary geometry for each set may be defined in a namelist \forcode{&nambdy_index} or 
     570by reading in a ``\textit{coordinates.bdy.nc}'' file. 
     571The \forcode{&nambdy_index} namelist defines a series of straight-line segments for north, east, south and west boundaries. 
     572One \forcode{&nambdy_index} namelist block is needed for each boundary condition defined by indexes. 
    574573For the northern boundary, \texttt{nbdysegn} gives the number of segments, 
    575 \jp{jpjnob} gives the $j$ index for each segment and \jp{jpindt} and 
    576 \jp{jpinft} give the start and end $i$ indices for each segment with similar for the other boundaries. 
     574\texttt{jpjnob} gives the $j$ index for each segment and \texttt{jpindt} and 
     575\texttt{jpinft} give the start and end $i$ indices for each segment with similar for the other boundaries. 
    577576These segments define a list of $T$ grid points along the outermost row of the boundary ($nbr\,=\, 1$). 
    578577The code deduces the $U$ and $V$ points and also the points for $nbr\,>\, 1$ if \np[>1]{nn_rimwidth}{nn\_rimwidth}. 
    579578 
    580 The boundary geometry may also be defined from a ``\ifile{coordinates.bdy}'' file. 
     579The boundary geometry may also be defined from a ``\textit{coordinates.bdy.nc}'' file. 
    581580\autoref{fig:LBC_nc_header} gives an example of the header information from such a file, based on the description of geometrical setup given above. 
    582581The file should contain the index arrays for each of the $T$, $U$ and $V$ grids. 
    … …  
    632631  \centering 
    633632  \includegraphics[width=0.66\textwidth]{LBC_nc_header} 
    634   \caption[Header for a \protect\ifile{coordinates.bdy} file]{ 
    635     Example of the header for a \protect\ifile{coordinates.bdy} file} 
     633  \caption[Header for a \textit{coordinates.bdy.nc} file]{ 
     634    Example of the header for a \textit{coordinates.bdy.nc} file} 
    636635  \label{fig:LBC_nc_header} 
    637636\end{figure} 
    … …  
    665664 
    666665Tidal forcing at open boundaries requires the activation of surface 
    667 tides (i.e., in \nam{_tide}{\_tide}, \np{ln_tide}{ln\_tide} needs to be set to 
    668 \forcode{.true.} and the required constituents need to be activated by 
    669 including their names in the \np{clname}{clname} array; see 
    670 \autoref{sec:SBC_tide}). Specific options related to the reading in of 
     666tides (i.e., in \nam{_tide}{\_tide}, \np[=.true.]{ln_tide}{ln\_tide} with the active tidal 
     667constituents listed in the \np{sn_tide_cnames}{sn\_tide\_cnames} array; see 
     668\autoref{sec:SBC_TDE}). The specific options related to the reading in of 
    671669the complex harmonic amplitudes of elevation (SSH) and barotropic 
    672 velocity (u,v) at open boundaries are defined through the 
    673 \nam{bdy_tide}{bdy\_tide} namelist parameters.\\ 
     670velocity components (u,v) at the open boundaries are defined through the 
     671\nam{bdy_tide}{bdy\_tide} namelist parameters.\par 
    674672 
    675673The tidal harmonic data at open boundaries can be specified in two 
    676674different ways, either on a two-dimensional grid covering the entire 
    677675model domain or along open boundary segments; these two variants can 
    678 be selected by setting \np{ln_bdytide_2ddta }{ln\_bdytide\_2ddta } to \forcode{.true.} or 
    679 \forcode{.false.}, respectively. In either case, the real and 
    680 imaginary parts of SSH and the two barotropic velocity components for 
    681 each activated tidal constituent \textit{tcname} have to be provided 
    682 separately: when two-dimensional data is used, variables 
    683 \textit{tcname\_z1} and \textit{tcname\_z2} for real and imaginary SSH, 
    684 respectively, are expected in input file \np{filtide}{filtide} with suffix 
    685 \ifile{\_grid\_T}, variables \textit{tcname\_u1} and 
    686 \textit{tcname\_u2} for real and imaginary u, respectively, are 
    687 expected in input file \np{filtide}{filtide} with suffix \ifile{\_grid\_U}, and 
    688 \textit{tcname\_v1} and \textit{tcname\_v2} for real and imaginary v, 
    689 respectively, are expected in input file \np{filtide}{filtide} with suffix 
    690 \ifile{\_grid\_V}; when data along open boundary segments is used, 
    691 variables \textit{z1} and \textit{z2} (real and imaginary part of SSH) 
    692 are expected to be available from file \np{filtide}{filtide} with suffix 
    693 \ifile{tcname\_grid\_T}, variables \textit{u1} and \textit{u2} (real 
    694 and imaginary part of u) are expected to be available from file 
    695 \np{filtide}{filtide} with suffix \ifile{tcname\_grid\_U}, and variables 
    696 \textit{v1} and \textit{v2} (real and imaginary part of v) are 
    697 expected to be available from file \np{filtide}{filtide} with suffix 
    698 \ifile{tcname\_grid\_V}. If \np{ln_bdytide_conj}{ln\_bdytide\_conj} is set to 
    699 \forcode{.true.}, the data is expected to be in complex conjugate 
    700 form. 
     676be selected by setting \np[=.true.]{ln_bdytide_2ddta}{ln\_bdytide\_2ddta} or 
     677\np[=.false.]{ln_bdytide_2ddta}{ln\_bdytide\_2ddta}, respectively. In either 
     678case, the real and imaginary parts of SSH, u, and v amplitudes associated with 
     679each activated tidal constituent \texttt{<constituent>} have to be provided 
     680separately as fields in input files with names based on 
     681\np[=<input>]{filtide}{filtide}: when two-dimensional data is used, variables 
     682\texttt{<constituent>\_z1} and \texttt{<constituent>\_z2} for the real and imaginary parts of 
     683SSH, respectively, are expected to be available in file 
     684\textit{<input>\_grid\_T.nc}, variables \texttt{<constituent>\_u1} and 
     685\texttt{<constituent>\_u2} for the real and imaginary parts of u, respectively, in file 
     686\textit{<input>\_grid\_U.nc}, and \texttt{<constituent>\_v1} and 
     687\texttt{<constituent>\_v2} for the real and imaginary parts of v, respectively, in file 
     688\textit{<input>\_grid\_V.nc}; when data along open boundary segments is used, 
     689variables \texttt{z1} and \texttt{z2} (real and imaginary part of SSH) are 
     690expected to be available in file \textit{<input><constituent>\_grid\_T.nc}, 
     691variables \texttt{u1} and \texttt{u2} (real and imaginary part of u) in file 
     692\textit{<input><constituent>\_grid\_U.nc}, and variables \texttt{v1} and \texttt{v2} 
     693(real and imaginary part of v) in file 
     694\textit{<input><constituent>\_grid\_V.nc}.\par 
    701695 
    702696Note that the barotropic velocity components are assumed to be defined 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_LDF.tex

    r11693 r14789  
    55\chapter{Lateral Ocean Physics (LDF)} 
    66\label{chap:LDF} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 
    … …  
    418416\subsection[Deformation rate dependent viscosities (\forcode{nn_ahm_ijk_t=32})]{Deformation rate dependent viscosities (\protect\np[=32]{nn_ahm_ijk_t}{nn\_ahm\_ijk\_t})} 
    419417 
    420 This option refers to the \citep{smagorinsky_MW63} scheme which is here implemented for momentum only. Smagorinsky chose as a 
     418This option refers to the \citep{smagorinsky_MWR63} scheme which is here implemented for momentum only. Smagorinsky chose as a 
    421419characteristic time scale $T_{smag}$ the deformation rate and for the lengthscale $L_{smag}$ the maximum wavenumber possible on the horizontal grid, e.g.: 
    422420 
    … …  
    540538\end{listing} 
    541539 
    542 If  \np[=.true.]{ln_mle}{ln\_mle} in \nam{tra_mle}{tra\_mle} namelist, a parameterization of the mixing due to unresolved mixed layer instabilities is activated (\citet{foxkemper.ferrari_JPO08}). Additional transport is computed in \rou{ldf\_mle\_trp} and added to the eulerian transport in \rou{tra\_adv} as done for eddy induced advection. 
     540If  \np[=.true.]{ln_mle}{ln\_mle} in \nam{tra_mle}{tra\_mle} namelist, a parameterization of the mixing due to unresolved mixed layer instabilities is activated (\citet{fox-kemper.ferrari.ea_JPO08}). Additional transport is computed in \rou{ldf\_mle\_trp} and added to the eulerian transport in \rou{tra\_adv} as done for eddy induced advection. 
    543541 
    544542\colorbox{yellow}{TBC} 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_OBS.tex

    r11708 r14789  
    1414%    {\em --\texttt{"}--} & {\em ... K. Mogensen, A. Vidard, A. Weaver} & {\em ---\texttt{"}---}  \\ 
    1515%\end{tabular} 
    16  
    17 \thispagestyle{plain} 
    1816 
    1917\chaptertoc 
    … …  
    420418 
    421419To use Sea Level Anomaly (SLA) data the mean dynamic topography (MDT) must be provided in a separate file defined on 
    422 the model grid called \ifile{slaReferenceLevel}. 
     420the model grid called \textit{slaReferenceLevel.nc}. 
    423421The MDT is required in order to produce the model equivalent sea level anomaly from the model sea surface height. 
    424422Below is an example header for this file (on the ORCA025 grid). 
    … …  
    892890\subsubsection{Running} 
    893891 
    894 The simplest way to use the executable is to edit and append the \textbf{sao.nml} namelist to 
     892The simplest way to use the executable is to edit and append the \nam{sao}{sao} namelist to 
    895893a full \NEMO\ namelist and then to run the executable as if it were nemo.exe. 
    896894 
    … …  
    914912For example, to read the second time counter from a single file the namelist would be. 
    915913 
    916 \begin{forlines} 
     914\begin{listing} 
     915  \begin{forlines} 
    917916!---------------------------------------------------------------------- 
    918917!       namsao Standalone obs_oper namelist 
    … …  
    924923   nn_sao_idx = 2 
    925924/ 
    926 \end{forlines} 
     925  \end{forlines} 
     926  \caption{\forcode{&namsao}} 
     927  \label{lst:namsao} 
     928\end{listing} 
    927929 
    928930%% ================================================================================================= 
    … …  
    11191121To plot some data run IDL and then: 
    11201122 
    1121 \begin{minted}{idl} 
     1123\begin{verbatim} 
    11221124IDL> dataplot, "filename" 
    1123 \end{minted} 
     1125\end{verbatim} 
    11241126 
    11251127To read multiple files into dataplot, 
    … …  
    11271129the easiest method is to use the spawn command to generate a list of files which can then be passed to dataplot. 
    11281130 
    1129 \begin{minted}{idl} 
     1131\begin{verbatim} 
    11301132IDL> spawn, 'ls profb*.nc', files 
    11311133IDL> dataplot, files 
    1132 \end{minted} 
     1134\end{verbatim} 
    11331135 
    11341136\autoref{fig:OBS_dataplotmain} shows the main window which is launched when dataplot starts. 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_SBC.tex

    r13165 r14789  
    11\documentclass[../main/NEMO_manual]{subfiles} 
    2 \usepackage{fontspec} 
    3 \usepackage{fontawesome} 
    42 
    53\begin{document} 
    64 
    7 \chapter{Surface Boundary Condition (SBC, SAS, ISF, ICB)} 
     5\chapter{Surface Boundary Condition (SBC, SAS, ISF, ICB, TDE)} 
    86\label{chap:SBC} 
    9  
    10 \thispagestyle{plain} 
    117 
    128\chaptertoc 
    … …  
    1814    Release & Author(s) & Modifications \\ 
    1915    \hline 
     16    {\em  next} & {\em Simon M{\" u}ller} & {\em Update of \autoref{sec:SBC_TDE}; revision of \autoref{subsec:SBC_fwb}}\\[2mm] 
     17    {\em  next} & {\em Pierre Mathiot} & {\em update of the ice shelf section (2019 developments)}\\[2mm]   
    2018    {\em   4.0} & {\em ...} & {\em ...} \\ 
    2119    {\em   3.6} & {\em ...} & {\em ...} \\ 
    … …  
    7573  (\np[=0..3]{nn_ice}{nn\_ice}), 
    7674\item the addition of river runoffs as surface freshwater fluxes or lateral inflow (\np[=.true.]{ln_rnf}{ln\_rnf}), 
    77 \item the addition of ice-shelf melting as lateral inflow (parameterisation) or 
    78   as fluxes applied at the land-ice ocean interface (\np[=.true.]{ln_isf}{ln\_isf}), 
    7975\item the addition of a freshwater flux adjustment in order to avoid a mean sea-level drift 
    8076  (\np[=0..2]{nn_fwb}{nn\_fwb}), 
    … …  
    10096One of these is modification by icebergs (see \autoref{sec:SBC_ICB_icebergs}), 
    10197which act as drifting sources of fresh water. 
    102 Another example of modification is that due to the ice shelf melting/freezing (see \autoref{sec:SBC_isf}), 
    103 which provides additional sources of fresh water. 
    10498 
    10599%% ================================================================================================= 
    … …  
    525519See \autoref{subsec:SBC_ssr} for its specification. 
    526520 
    527  
    528  
    529  
    530  
    531  
    532  
    533 %% ================================================================================================= 
    534 \pagebreak 
    535 \newpage 
     521%% ================================================================================================= 
    536522\section[Bulk formulation (\textit{sbcblk.F90})]{Bulk formulation (\protect\mdl{sbcblk})} 
    537523\label{sec:SBC_blk} 
    … …  
    557543 
    558544Note: 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}. 
     545initially developed (and are still developed in parallel) in 
     546the \href{https://brodeau.github.io/aerobulk}{\texttt{AeroBulk}} open-source project 
     547\citep{brodeau.barnier.ea_JPO16}. 
    562548 
    563549%%% Bulk formulae are this: 
    564 \subsection{Bulk formulae}\label{subsec:SBC_blkform} 
    565 % 
     550\subsection{Bulk formulae} 
     551\label{subsec:SBC_blkform} 
     552 
    566553In NEMO, the set of equations that relate each component of the surface fluxes 
    567554to the near-surface atmosphere and sea surface states writes 
    568 % 
    569 \begin{subequations}\label{eq_bulk} 
     555 
     556\begin{subequations} 
     557  \label{eq:SBC_bulk} 
    570558  \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} 
     559  \begin{align} 
     560    \mathbf{\tau} &= \rho~ C_D ~ \mathbf{U}_z  ~ U_B \\ 
     561    Q_H           &= \rho~C_H~C_P~\big[ \theta_z - T_s \big] ~ U_B \\ 
     562    E             &= \rho~C_E    ~\big[    q_s   - q_z \big] ~ U_B \\ 
     563    Q_L           &= -L_v \, E \\ 
     564    Q_{sr}        &= (1 - a) Q_{sw\downarrow} \\ 
     565    Q_{ir}        &= \delta (Q_{lw\downarrow} -\sigma T_s^4) 
     566  \end{align} 
    580567\end{subequations} 
    581 % 
     568 
    582569with 
    583570   \[ \theta_z \simeq T_z+\gamma z \] 
    584571   \[  q_s \simeq 0.98\,q_{sat}(T_s,p_a ) \] 
    585 % 
    586572from which, the the non-solar heat flux is \[ Q_{ns} = Q_L + Q_H + Q_{ir} \] 
    587 % 
    588573where $\mathbf{\tau}$ is the wind stress vector, $Q_H$ the sensible heat flux, 
    589574$E$ the evaporation, $Q_L$ the latent heat flux, and $Q_{ir}$ the net longwave 
    590575flux. 
    591 % 
    592576$Q_{sw\downarrow}$ and $Q_{lw\downarrow}$ are the surface downwelling shortwave 
    593577and longwave radiative fluxes, respectively. 
    594 % 
    595578Note: a positive sign for $\mathbf{\tau}$, $Q_H$, $Q_L$, $Q_{sr}$ or $Q_{ir}$ 
    596579implies a gain of the relevant quantity for the ocean, while a positive $E$ 
    597580implies a freshwater loss for the ocean. 
    598 % 
    599581$\rho$ is the density of air. $C_D$, $C_H$ and $C_E$ are the bulk transfer 
    600582coefficients for momentum, sensible heat, and moisture, respectively. 
    601 % 
    602583$C_P$ is the heat capacity of moist air, and $L_v$ is the latent heat of 
    603584vaporization of water. 
    604 % 
    605585$\theta_z$, $T_z$ and $q_z$ are the potential temperature, absolute temperature, 
    606586and specific humidity of air at height $z$ above the sea surface, 
    607587respectively. $\gamma z$ is a temperature correction term which accounts for the 
    608588adiabatic lapse rate and approximates the potential temperature at height 
    609 $z$ \citep{josey.gulev.ea_2013}. 
    610 % 
     589$z$ \citep{josey.gulev.ea_OCC13}. 
    611590$\mathbf{U}_z$ is the wind speed vector at height $z$ above the sea surface 
    612 (possibly referenced to the surface current $\mathbf{u_0}$, 
    613 section \ref{s_res1}.\ref{ss_current}). 
    614 % 
     591(possibly referenced to the surface current $\mathbf{u_0}$).%, 
     592%\autoref{s_res1}.\autoref{ss_current}). %% Undefined references 
    615593The bulk scalar wind speed, namely $U_B$, is the scalar wind speed, 
    616594$|\mathbf{U}_z|$, with the potential inclusion of a gustiness contribution. 
    617 % 
    618595$a$ and $\delta$ are the albedo and emissivity of the sea surface, respectively.\\ 
    619 % 
    620596%$p_a$ is the mean sea-level pressure (SLP). 
    621 % 
    622597$T_s$ is the sea surface temperature. $q_s$ is the saturation specific humidity 
    623598of air at temperature $T_s$; it includes a 2\% reduction to account for the 
    624 presence of salt in seawater \citep{sverdrup.johnson.ea_1942,kraus.businger_QJRMS96}. 
     599presence of salt in seawater \citep{sverdrup.johnson.ea_bk42,kraus.businger_QJRMS96}. 
    625600Depending on the bulk parametrization used, $T_s$ can either be the temperature 
    626601at the air-sea interface (skin temperature, hereafter SSST) or at typically a 
    627602few tens of centimeters below the surface (bulk sea surface temperature, 
    628603hereafter SST). 
    629 % 
    630604The SSST differs from the SST due to the contributions of two effects of 
    631605opposite sign, the \emph{cool skin} and \emph{warm layer} (hereafter CS and WL, 
    632 respectively, see section\,\ref{subsec:SBC_skin}). 
    633 % 
     606respectively, see \autoref{subsec:SBC_skin}). 
    634607Technically, when the ECMWF or COARE* bulk parametrizations are selected 
    635608(\np[=.true.]{ln_ECMWF}{ln\_ECMWF} or \np[=.true.]{ln_COARE*}{ln\_COARE\*}), 
    … …  
    639612 
    640613For more details on all these aspects the reader is invited to refer 
    641 to \citet{brodeau.barnier.ea_JPO17}. 
    642  
    643  
    644  
    645 \subsection{Bulk parametrizations}\label{subsec:SBC_blk_ocean} 
     614to \citet{brodeau.barnier.ea_JPO16}. 
     615 
     616\subsection{Bulk parametrizations} 
     617\label{subsec:SBC_blk_ocean} 
    646618%%%\label{subsec:SBC_param} 
    647619 
    … …  
    653625height (from \np{rn_zqt}{rn\_zqt} to \np{rn_zu}{rn\_zu}). 
    654626 
    655  
    656  
    657627For the open ocean, four bulk parametrization algorithms are available in NEMO: 
     628 
    658629\begin{itemize} 
    659 \item NCAR, formerly known as CORE, \citep{large.yeager_rpt04,large.yeager_CD09} 
     630\item NCAR, formerly known as CORE, \citep{large.yeager_trpt04,large.yeager_CD09} 
    660631\item COARE 3.0 \citep{fairall.bradley.ea_JC03} 
    661632\item COARE 3.6 \citep{edson.jampana.ea_JPO13} 
    … …  
    663634\end{itemize} 
    664635 
    665  
    666636With respect to version 3, the principal advances in version 3.6 of the COARE 
    667637bulk parametrization are built around improvements in the representation of the 
    668638effects of waves on 
    669 fluxes \citep{edson.jampana.ea_JPO13,brodeau.barnier.ea_JPO17}. This includes 
     639fluxes \citep{edson.jampana.ea_JPO13,brodeau.barnier.ea_JPO16}. This includes 
    670640improved relationships of surface roughness, and whitecap fraction on wave 
    671641parameters. It is therefore recommended to chose version 3.6 over 3. 
    672642 
    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 % 
     643\subsection[Cool-skin and warm-layer parameterizations (   \forcode{ln_skin_cs}               \& \forcode{ln_skin_wl}              )] 
     644           {Cool-skin and warm-layer parameterizations (\protect\np{ln_skin_cs}{ln\_skin\_cs} \&      \np{ln_skin_wl}{ln\_skin\_wl})} 
     645\label{subsec:SBC_skin} 
     646 
    681647As opposed to the NCAR bulk parametrization, more advanced bulk 
    682648parametrizations such as COARE3.x and ECMWF are meant to be used with the skin 
    683649temperature $T_s$ rather than the bulk SST (which, in NEMO is the temperature at 
    684 the first T-point level, see section\,\ref{subsec:SBC_blkform}). 
    685 % 
     650the first T-point level, see \autoref{subsec:SBC_blkform}). 
     651 
    686652As such, the relevant cool-skin and warm-layer parametrization must be 
    687653activated through \np[=T]{ln_skin_cs}{ln\_skin\_cs} 
    … …  
    692658 
    693659For the cool-skin scheme parametrization COARE and ECMWF algorithms share the same 
    694 basis: \citet{fairall.bradley.ea_JGR96}. With some minor updates based 
    695 on \citet{zeng.beljaars_GRL05} for ECMWF, and \citet{fairall.ea_19} for COARE 
     660basis: \citet{fairall.bradley.ea_JGRO96}. With some minor updates based 
     661on \citet{zeng.beljaars_GRL05} for ECMWF \iffalse, and \citet{fairall.ea_19?} for COARE \fi 
    6966623.6. 
    697663 
    … …  
    700666turbulence input from Langmuir circulation). 
    701667 
    702 Importantly, COARE warm-layer scheme \citep{fairall.ea_19} includes a prognostic 
     668Importantly, COARE warm-layer scheme \iffalse \citep{fairall.ea_19?} \fi includes a prognostic 
    703669equation for the thickness of the warm-layer, while it is considered as constant 
    704670in the ECWMF algorithm. 
    705  
    706671 
    707672\subsection{Appropriate use of each bulk parametrization} 
    … …  
    713678temperature is the bulk SST. Hence the following namelist parameters must be 
    714679set: 
    715 % 
    716 \begin{verbatim} 
     680 
     681\begin{forlines} 
    717682  ... 
    718683  ln_NCAR    = .true. 
    … …  
    725690  ... 
    726691  ln_humi_sph = .true. ! humidity "sn_humi" is specific humidity  [kg/kg] 
    727 \end{verbatim} 
    728  
     692\end{forlines} 
    729693 
    730694\subsubsection{ECMWF} 
    731 % 
     695 
    732696With an atmospheric forcing based on a reanalysis of the ECMWF, such as the 
    733697Drakkar Forcing Set \citep{brodeau.barnier.ea_OM10}, we strongly recommend to 
    … …  
    736700humidity are provided at the 2\,m height, and given that the humidity is 
    737701distributed as the dew-point temperature, the namelist must be tuned as follows: 
    738 % 
    739 \begin{verbatim} 
     702 
     703\begin{forlines} 
    740704  ... 
    741705  ln_ECMWF   = .true. 
    … …  
    749713  ln_humi_dpt = .true. !  humidity "sn_humi" is dew-point temperature [K] 
    750714  ... 
    751 \end{verbatim} 
    752 % 
     715\end{forlines} 
     716 
    753717Note: when \np{ln_ECMWF}{ln\_ECMWF} is selected, the selection 
    754718of \np{ln_skin_cs}{ln\_skin\_cs} and \np{ln_skin_wl}{ln\_skin\_wl} implicitly 
    … …  
    756720respectively (found in \textit{sbcblk\_skin\_ecmwf.F90}). 
    757721 
    758  
    759722\subsubsection{COARE 3.x} 
    760 % 
     723 
    761724Since the ECMWF parametrization is largely based on the COARE* parametrization, 
    762725the two algorithms are very similar in terms of structure and closure 
    763726approach. As such, the namelist tuning for COARE 3.x is identical to that of 
    764727ECMWF: 
    765 % 
    766 \begin{verbatim} 
     728 
     729\begin{forlines} 
    767730  ... 
    768731  ln_COARE3p6 = .true. 
    … …  
    771734  ln_skin_wl = .true. ! use the warm-layer parameterization 
    772735  ... 
    773 \end{verbatim} 
     736\end{forlines} 
    774737 
    775738Note: when \np[=T]{ln_COARE3p0}{ln\_COARE3p0} is selected, the selection 
    … …  
    778741respectively (found in \textit{sbcblk\_skin\_coare.F90}). 
    779742 
    780  
    781743%lulu 
    782  
    783  
    784744 
    785745% In a typical bulk algorithm, the BTCs under neutral stability conditions are 
    … …  
    791751% and $q_z$. 
    792752 
    793  
    794  
    795753\subsection{Prescribed near-surface atmospheric state} 
    796754 
    … …  
    799757different bulk formulae are used for the turbulent fluxes computation over the 
    800758ocean and over sea-ice surface. 
    801 % 
    802759 
    803760%The choice is made by setting to true one of the following namelist 
    … …  
    861818the namsbc\_blk namelist (see \autoref{subsec:SBC_fldread}). 
    862819 
    863  
    864820\subsubsection{Air humidity} 
    865821 
    … …  
    867823[kg/kg], relative humidity [\%], or dew-point temperature [K] (LINK to namelist 
    868824parameters)... 
    869  
    870  
    871 ~\\ 
    872  
    873  
    874  
    875  
    876  
    877  
    878  
    879  
    880  
    881825 
    882826%% ================================================================================================= 
    … …  
    888832%their neutral transfer coefficients relationships with neutral wind. 
    889833%\begin{itemize} 
    890 %\item NCAR (\np[=.true.]{ln_NCAR}{ln\_NCAR}): The NCAR bulk formulae have been developed by \citet{large.yeager_rpt04}. 
     834%\item NCAR (\np[=.true.]{ln_NCAR}{ln\_NCAR}): The NCAR bulk formulae have been developed by \citet{large.yeager_trpt04}. 
    891835%  They have been designed to handle the NCAR forcing, a mixture of NCEP reanalysis and satellite data. 
    892836%  They use an inertial dissipative method to compute the turbulent transfer coefficients 
    893837%  (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 
     838%  This \citet{large.yeager_trpt04} dataset is available through 
    895839%  the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/NCAR.html}{GFDL web site}. 
    896840%  Note that substituting ERA40 to NCEP reanalysis fields does not require changes in the bulk formulea themself. 
    … …  
    907851\label{subsec:SBC_blk_ice} 
    908852 
    909  
    910853\texttt{\#out\_of\_place:} 
    911854 For sea-ice, three possibilities can be selected: 
    912855a constant transfer coefficient (1.4e-3; default 
    913 value), \citet{lupkes.gryanik.ea_JGR12} (\np{ln_Cd_L12}{ln\_Cd\_L12}), 
     856value), \citet{lupkes.gryanik.ea_JGRA12} (\np{ln_Cd_L12}{ln\_Cd\_L12}), 
    914857and \citet{lupkes.gryanik_JGR15} (\np{ln_Cd_L15}{ln\_Cd\_L15}) parameterizations 
    915858\texttt{\#out\_of\_place.} 
    916859 
    917  
    918  
    919  
    920860Surface turbulent fluxes between sea-ice and the atmosphere can be computed in three different ways: 
    921861 
    922862\begin{itemize} 
    923 \item Constant value (\np[ Cd_ice=1.4e-3 ]{constant value}{constant\ value}): 
     863\item Constant value (\forcode{Cd_ice=1.4e-3}): 
    924864  default constant value used for momentum and heat neutral transfer coefficients 
    925 \item \citet{lupkes.gryanik.ea_JGR12} (\np[=.true.]{ln_Cd_L12}{ln\_Cd\_L12}): 
     865\item \citet{lupkes.gryanik.ea_JGRA12} (\np[=.true.]{ln_Cd_L12}{ln\_Cd\_L12}): 
    926866  This scheme adds a dependency on edges at leads, melt ponds and flows 
    927867  of the constant neutral air-ice drag. After some approximations, 
    … …  
    1013953 
    1014954%% ================================================================================================= 
    1015 \section[Surface tides (\textit{sbctide.F90})]{Surface tides (\protect\mdl{sbctide})} 
    1016 \label{sec:SBC_tide} 
     955\section{Surface tides (TDE)} 
     956\label{sec:SBC_TDE} 
    1017957 
    1018958\begin{listing} 
    … …  
    1022962\end{listing} 
    1023963 
    1024 The tidal forcing, generated by the gravity forces of the Earth-Moon and Earth-Sun sytems, 
    1025 is activated if \np{ln_tide}{ln\_tide} and \np{ln_tide_pot}{ln\_tide\_pot} are both set to \forcode{.true.} in \nam{_tide}{\_tide}. 
    1026 This translates as an additional barotropic force in the momentum \autoref{eq:MB_PE_dyn} such that: 
     964\subsection{Tidal constituents} 
     965Ocean model component TDE provides the common functionality for tidal forcing 
     966and tidal analysis in the model framework. This includes the computation of the gravitational 
     967surface forcing, as well as support for lateral forcing at open boundaries (see 
     968\autoref{subsec:LBC_bdy_tides}) and tidal harmonic analysis \iffalse (see 
     969\autoref{subsec:DIA_diamlr?} and \autoref{subsec:DIA_diadetide?}) \fi . The module is 
     970activated with \np[=.true.]{ln_tide}{ln\_tide} in namelist 
     971\nam{_tide}{\_tide}. It provides the same 34 tidal constituents that are 
     972included in the 
     973\href{https://www.aviso.altimetry.fr/en/data/products/auxiliary-products/global-tide-fes.html}{FES2014 
     974  ocean tide model}: Mf, Mm, Ssa, Mtm, Msf, Msqm, Sa, K1, O1, P1, Q1, J1, S1, 
     975M2, S2, N2, K2, nu2, mu2, 2N2, L2, T2, eps2, lam2, R2, M3, MKS2, MN4, MS4, M4, 
     976N4, S4, M6, and M8; see file \textit{tide.h90} and \mdl{tide\_mod} for further 
     977information and references\footnote{As a legacy option \np{ln_tide_var}{ln\_tide\_var} can be 
     978  set to \forcode{0}, in which case the 19 tidal constituents (M2, N2, 2N2, S2, 
     979  K2, K1, O1, Q1, P1, M4, Mf, Mm, Msqm, Mtm, S1, MU2, NU2, L2, and T2; see file 
     980  \textit{tide.h90}) and associated parameters that have been available in NEMO version 
     981  4.0 and earlier are available}. Constituents to be included in the tidal forcing 
     982(surface and lateral boundaries) are selected by enumerating their respective 
     983names in namelist array \np{sn_tide_cnames}{sn\_tide\_cnames}.\par 
     984 
     985\subsection{Surface tidal forcing} 
     986Surface tidal forcing can be represented in the model through an additional 
     987barotropic force in the momentum equation (\autoref{eq:MB_PE_dyn}) such that: 
    1027988\[ 
    1028   % \label{eq:SBC_PE_dyn_tides} 
    1029   \frac{\partial {\mathrm {\mathbf U}}_h }{\partial t}= ... 
    1030   +g\nabla (\Pi_{eq} + \Pi_{sal}) 
     989  \frac{\partial {\mathrm {\mathbf U}}_h }{\partial t} = \ldots +g\nabla (\gamma 
     990  \Pi_{eq} + \Pi_{sal}) 
    1031991\] 
    1032 where $\Pi_{eq}$ stands for the equilibrium tidal forcing and 
    1033 $\Pi_{sal}$ is a self-attraction and loading term (SAL). 
    1034  
    1035 The equilibrium tidal forcing is expressed as a sum over a subset of 
    1036 constituents chosen from the set of available tidal constituents 
    1037 defined in file \hf{SBC/tide} (this comprises the tidal 
    1038 constituents \textit{M2, N2, 2N2, S2, K2, K1, O1, Q1, P1, M4, Mf, Mm, 
    1039   Msqm, Mtm, S1, MU2, NU2, L2}, and \textit{T2}). Individual 
    1040 constituents are selected by including their names in the array 
    1041 \np{clname}{clname} in \nam{_tide}{\_tide} (e.g., \np{clname}{clname}\forcode{(1)='M2', } 
    1042 \np{clname}{clname}\forcode{(2)='S2'} to select solely the tidal consituents \textit{M2} 
    1043 and \textit{S2}). Optionally, when \np{ln_tide_ramp}{ln\_tide\_ramp} is set to 
    1044 \forcode{.true.}, the equilibrium tidal forcing can be ramped up 
    1045 linearly from zero during the initial \np{rdttideramp}{rdttideramp} days of the 
    1046 model run. 
     992where $\gamma \Pi_{eq}$ stands for the equilibrium tidal forcing scaled by a spatially 
     993uniform tilt factor $\gamma$, and $\Pi_{sal}$ is an optional 
     994self-attraction and loading term (SAL). These additional terms are enabled when, 
     995in addition to \np[=.true.]{ln_tide}{ln\_tide}), 
     996\np[=.true.]{ln_tide_pot}{ln\_tide\_pot}.\par 
     997 
     998The equilibrium tidal forcing is expressed as a sum over the subset of 
     999constituents listed in \np{sn_tide_cnames}{sn\_tide\_cnames} of 
     1000\nam{_tide} (e.g., 
     1001\begin{forlines} 
     1002      sn_tide_cnames(1) = 'M2' 
     1003      sn_tide_cnames(2) = 'K1' 
     1004      sn_tide_cnames(3) = 'S2' 
     1005      sn_tide_cnames(4) = 'O1' 
     1006\end{forlines} 
     1007to select the four tidal constituents of strongest equilibrium tidal 
     1008potential). The tidal tilt factor $\gamma = 1 + k - h$ includes the 
     1009Love numbers $k$ and $h$ \citep{love_PRSL09}; this factor is 
     1010configurable using \np{rn_tide_gamma}{rn\_tide\_gamma} (default value 0.7). Optionally, 
     1011when \np[=.true.]{ln_tide_ramp}{ln\_tide\_ramp}, the equilibrium tidal 
     1012forcing can be ramped up linearly from zero during the initial 
     1013\np{rn_tide_ramp_dt}{rn\_tide\_ramp\_dt} days of the model run.\par 
    10471014 
    10481015The SAL term should in principle be computed online as it depends on 
    10491016the model tidal prediction itself (see \citet{arbic.garner.ea_DSR04} for a 
    1050 discussion about the practical implementation of this term). 
    1051 Nevertheless, the complex calculations involved would make this 
    1052 computationally too expensive. Here, two options are available: 
    1053 $\Pi_{sal}$ generated by an external model can be read in 
    1054 (\np[=.true.]{ln_read_load}{ln\_read\_load}), or a ``scalar approximation'' can be 
    1055 used (\np[=.true.]{ln_scal_load}{ln\_scal\_load}). In the latter case 
     1017discussion about the practical implementation of this term). The complex 
     1018calculations involved in such computations, however, are computationally very 
     1019expensive. Here, two mutually exclusive simpler variants are available: 
     1020amplitudes generated by an external model for oscillatory $\Pi_{sal}$ 
     1021contributions from each of the selected tidal constituents can be read in 
     1022(\np[=.true.]{ln_read_load}{ln\_read\_load}) from the file specified in 
     1023\np{cn_tide_load}{cn\_tide\_load} (the variable names are comprised of the 
     1024tidal-constituent name and suffixes \forcode{_z1} and \forcode{_z2} for the two 
     1025orthogonal components, respectively); alternatively, a ``scalar approximation'' 
     1026can be used (\np[=.true.]{ln_scal_load}{ln\_scal\_load}), where 
    10561027\[ 
    10571028  \Pi_{sal} = \beta \eta, 
    10581029\] 
    1059 where $\beta$ (\np{rn_scal_load}{rn\_scal\_load} with a default value of 0.094) is a 
    1060 spatially constant scalar, often chosen to minimize tidal prediction 
    1061 errors. Setting both \np{ln_read_load}{ln\_read\_load} and \np{ln_scal_load}{ln\_scal\_load} to 
    1062 \forcode{.false.} removes the SAL contribution. 
     1030with a spatially uniform coefficient $\beta$, which can be configured 
     1031via \np{rn_scal_load}{rn\_scal\_load} (default value 0.094) and is 
     1032often tuned to minimize tidal prediction errors.\par 
     1033 
     1034For diagnostic purposes, the forcing potential of the individual tidal 
     1035constituents (incl. load ptential, if activated) and the total forcing 
     1036potential (incl. load potential, if activated) can be made available 
     1037as diagnostic output by setting 
     1038\np[=.true.]{ln_tide_dia}{ln\_tide\_dia} (fields 
     1039\forcode{tide_pot_<constituent>} and \forcode{tide_pot}).\par 
    10631040 
    10641041%% ================================================================================================= 
    … …  
    12011178 
    12021179%% ================================================================================================= 
    1203 \section[Ice shelf melting (\textit{sbcisf.F90})]{Ice shelf melting (\protect\mdl{sbcisf})} 
     1180\section[Ice Shelf (ISF)]{Interaction with ice shelves (ISF)} 
    12041181\label{sec:SBC_isf} 
    12051182 
    12061183\begin{listing} 
    1207   \nlst{namsbc_isf} 
    1208   \caption{\forcode{&namsbc_isf}} 
    1209   \label{lst:namsbc_isf} 
     1184  \nlst{namisf} 
     1185  \caption{\forcode{&namisf}} 
     1186  \label{lst:namisf} 
    12101187\end{listing} 
    12111188 
    1212 The namelist variable in \nam{sbc}{sbc}, \np{nn_isf}{nn\_isf}, controls the ice shelf representation. 
    1213 Description and result of sensitivity test to \np{nn_isf}{nn\_isf} are presented in \citet{mathiot.jenkins.ea_GMD17}. 
    1214 The different options are illustrated in \autoref{fig:SBC_isf}. 
    1215  
     1189The namelist variable in \nam{isf}{isf}, \np{ln_isf}{ln\_isf}, controls the ice shelf interactions: 
    12161190\begin{description} 
    1217   \item [{\np[=1]{nn_isf}{nn\_isf}}]: The ice shelf cavity is represented (\np[=.true.]{ln_isfcav}{ln\_isfcav} needed). 
    1218   The fwf and heat flux are depending of the local water properties. 
    1219  
    1220   Two different bulk formulae are available: 
     1191   \item $\bullet$ representation of the ice shelf/ocean melting/freezing for opened cavity (cav, \np{ln_isfcav_mlt}{ln\_isfcav\_mlt}). 
     1192   \item $\bullet$ parametrisation of the ice shelf/ocean melting/freezing for closed cavities (par, \np{ln_isfpar_mlt}{ln\_isfpar\_mlt}). 
     1193   \item $\bullet$ coupling with an ice sheet model (\np{ln_isfcpl}{ln\_isfcpl}). 
     1194\end{description} 
     1195 
     1196  \subsection{Ocean/Ice shelf fluxes in opened cavities} 
     1197 
     1198     \np{ln_isfcav_mlt}{ln\_isfcav\_mlt}\forcode{ = .true.} activates the ocean/ice shelf thermodynamics interactions at the ice shelf/ocean interface.  
     1199     If \np{ln_isfcav_mlt}{ln\_isfcav\_mlt}\forcode{ = .false.}, thermodynamics interactions are desctivated but the ocean dynamics inside the cavity is still active. 
     1200     The logical flag \np{ln_isfcav}{ln\_isfcav} control whether or not the ice shelf cavities are closed. \np{ln_isfcav}{ln\_isfcav} is not defined in the namelist but in the domcfg.nc input file.\\ 
     1201 
     1202     3 options are available to represent to ice-shelf/ocean fluxes at the interface: 
     1203     \begin{description} 
     1204        \item[\np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = 'spe'}]: 
     1205        The fresh water flux is specified by a forcing fields \np{sn_isfcav_fwf}{sn\_isfcav\_fwf}. Convention of the input file is: positive toward the ocean (i.e. positive for melting and negative for freezing). 
     1206        The latent heat fluxes is derived from the fresh water flux.  
     1207        The heat content flux is derived from the fwf flux assuming a temperature set to the freezing point in the top boundary layer (\np{rn_htbl}{rn\_htbl}) 
     1208 
     1209        \item[\np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = 'oasis'}]: 
     1210        The \forcode{'oasis'} is a prototype of what could be a method to spread precipitation on Antarctic ice sheet as ice shelf melt inside the cavity when a coupled model Atmosphere/Ocean is used.  
     1211        It has not been tested and therefore the model will stop if you try to use it.  
     1212        Actions will be undertake in 2020 to build a comprehensive interface to do so for Greenland, Antarctic and ice shelf (cav), ice shelf (par), icebergs, subglacial runoff and runoff. 
     1213 
     1214        \item[\np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = '2eq'}]: 
     1215        The heat flux and the fresh water flux (negative for melting) resulting from ice shelf melting/freezing are parameterized following \citet{Grosfeld1997}.  
     1216        This formulation is based on a balance between the vertical diffusive heat flux across the ocean top boundary layer (\autoref{eq:ISOMIP1})  
     1217        and the latent heat due to melting/freezing (\autoref{eq:ISOMIP2}): 
     1218 
     1219        \begin{equation} 
     1220        \label{eq:ISOMIP1} 
     1221        \mathcal{Q}_h = \rho c_p \gamma (T_w - T_f) 
     1222        \end{equation} 
     1223        \begin{equation} 
     1224        \label{eq:ISOMIP2} 
     1225        q = \frac{-\mathcal{Q}_h}{L_f} 
     1226        \end{equation} 
     1227         
     1228        where $\mathcal{Q}_h$($W.m^{-2}$) is the heat flux,q($kg.s^{-1}m^{-2}$) the fresh-water flux,  
     1229        $L_f$ the specific latent heat, $T_w$ the temperature averaged over a boundary layer below the ice shelf (explained below),  
     1230        $T_f$ the freezing point using  the  pressure  at  the  ice  shelf  base  and  the  salinity  of the water in the boundary layer,  
     1231        and $\gamma$ the thermal exchange coefficient. 
     1232 
     1233        \item[\np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = '3eq'}]: 
     1234        For realistic studies, the heat and freshwater fluxes are parameterized following \citep{Jenkins2001}. This formulation is based on three equations:  
     1235        a balance between the vertical diffusive heat flux across the boundary layer  
     1236        , the latent heat due to melting/freezing of ice and the vertical diffusive heat flux into the ice shelf (\autoref{eq:3eq1});  
     1237        a balance between the vertical diffusive salt flux across the boundary layer and the salt source or sink represented by the melting/freezing (\autoref{eq:3eq2});  
     1238        and a linear equation for the freezing temperature of sea water (\autoref{eq:3eq3}, detailed of the linearisation coefficient in \citet{AsayDavis2016}): 
     1239 
     1240        \begin{equation} 
     1241        \label{eq:3eq1} 
     1242        c_p \rho \gamma_T (T_w-T_b) = -L_f q - \rho_i c_{p,i} \kappa \frac{T_s - T_b}{h_{isf}} 
     1243        \end{equation} 
     1244        \begin{equation} 
     1245        \label{eq:3eq2} 
     1246        \rho \gamma_S (S_w - S_b) = (S_i - S_b)q 
     1247        \end{equation} 
     1248        \begin{equation} 
     1249        \label{eq:3eq3} 
     1250        T_b = \lambda_1 S_b + \lambda_2 +\lambda_3 z_{isf} 
     1251        \end{equation} 
     1252 
     1253        where $T_b$ is the temperature at the interface, $S_b$ the salinity at the interface, $\gamma_T$ and $\gamma_S$ the exchange coefficients for temperature and salt, respectively,  
     1254        $S_i$ the salinity of the ice (assumed to be 0), $h_{isf}$ the ice shelf thickness, $z_{isf}$ the ice shelf draft, $\rho_i$ the density of the iceshelf,  
     1255        $c_{p,i}$ the specific heat capacity of the ice, $\kappa$ the thermal diffusivity of the ice  
     1256        and $T_s$ the atmospheric surface temperature (at the ice/air interface, assumed to be -20C).  
     1257        The Liquidus slope ($\lambda_1$), the liquidus intercept ($\lambda_2$) and the Liquidus pressure coefficient ($\lambda_3$)  
     1258        for TEOS80 and TEOS10 are described in \citep{AsayDavis2016} and in \citep{Jourdain2017}. 
     1259        The linear system formed by \autoref{eq:3eq1}, \autoref{eq:3eq2} and the linearised equation for the freezing temperature of sea water (\autoref{eq:3eq3}) can be solved for $S_b$ or $T_b$.  
     1260        Afterward, the freshwater flux ($q$) and the heat flux ($\mathcal{Q}_h$) can be computed. 
     1261 
     1262     \end{description} 
     1263 
     1264     \begin{table}[h] 
     1265        \centering 
     1266        \caption{Description of the parameters hard coded into the ISF module} 
     1267        \label{tab:isf} 
     1268        \begin{tabular}{|l|l|l|l|} 
     1269        \hline 
     1270        Symbol    & Description               & Value              & Unit               \\ 
     1271        \hline 
     1272        $C_p$     & Ocean specific heat       & 3992               & $J.kg^{-1}.K^{-1}$ \\ 
     1273        $L_f$     & Ice latent heat of fusion & $3.34 \times 10^5$ & $J.kg^{-1}$        \\ 
     1274        $C_{p,i}$ & Ice specific heat         & 2000               & $J.kg^{-1}.K^{-1}$ \\ 
     1275        $\kappa$  & Heat diffusivity          & $1.54 \times 10^{-6}$& $m^2.s^{-1}$     \\ 
     1276        $\rho_i$  & Ice density               & 920                & $kg.m^3$           \\ 
     1277        \hline 
     1278        \end{tabular} 
     1279     \end{table} 
     1280 
     1281     Temperature and salinity used to compute the fluxes in \autoref{eq:ISOMIP1}, \autoref{eq:3eq1} and \autoref{eq:3eq2} are the average temperature in the top boundary layer \citep{losch_JGR08}.  
     1282     Its thickness is defined by \np{rn_htbl}{rn\_htbl}. 
     1283     The fluxes and friction velocity are computed using the mean temperature, salinity and velocity in the first \np{rn_htbl}{rn\_htbl} m. 
     1284     Then, the fluxes are spread over the same thickness (ie over one or several cells). 
     1285     If \np{rn_htbl}{rn\_htbl} is larger than top $e_{3}t$, there is no more direct feedback between the freezing point at the interface and the top cell temperature. 
     1286     This can lead to super-cool temperature in the top cell under melting condition. 
     1287     If \np{rn_htbl}{rn\_htbl} smaller than top $e_{3}t$, the top boundary layer thickness is set to the top cell thickness.\\ 
     1288 
     1289     Each melt formula (\np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = '3eq'} or \np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = '2eq'}) depends on an exchange coeficient ($\Gamma^{T,S}$) between the ocean and the ice. 
     1290     Below, the exchange coeficient $\Gamma^{T}$ and $\Gamma^{S}$ are respectively defined by \np{rn_gammat0}{rn\_gammat0} and \np{rn_gammas0}{rn\_gammas0}.  
     1291     There are 3 different ways to compute the exchange velocity: 
     1292 
     1293     \begin{description} 
     1294        \item[\np{cn_gammablk}{cn\_gammablk}\forcode{='spe'}]: 
     1295        The salt and heat exchange coefficients are constant and defined by: 
     1296\[ 
     1297\gamma^{T} = \Gamma^{T} 
     1298\] 
     1299\[ 
     1300\gamma^{S} = \Gamma^{S} 
     1301\]  
     1302        This is the recommended formulation for ISOMIP. 
     1303 
     1304   \item[\np{cn_gammablk}{cn\_gammablk}\forcode{='vel'}]: 
     1305        The salt and heat exchange coefficients are velocity dependent and defined as 
     1306\[ 
     1307\gamma^{T} = \Gamma^{T} \times u_{*}  
     1308\] 
     1309\[ 
     1310\gamma^{S} = \Gamma^{S} \times u_{*} 
     1311\] 
     1312        where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_htbl}{rn\_htbl} meters). 
     1313        See \citet{jenkins.nicholls.ea_JPO10} for all the details on this formulation. It is the recommended formulation for realistic application and ISOMIP+/MISOMIP configuration. 
     1314 
     1315   \item[\np{cn_gammablk}{cn\_gammablk}\forcode{'vel\_stab'}]: 
     1316        The salt and heat exchange coefficients are velocity and stability dependent and defined as: 
     1317\[ 
     1318\gamma^{T,S} = \frac{u_{*}}{\Gamma_{Turb} + \Gamma^{T,S}_{Mole}}  
     1319\] 
     1320        where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_tbl}{rn\_htbl} meters), 
     1321        $\Gamma_{Turb}$ the contribution of the ocean stability and 
     1322        $\Gamma^{T,S}_{Mole}$ the contribution of the molecular diffusion. 
     1323        See \citet{holland.jenkins_JPO99} for all the details on this formulation.  
     1324        This formulation has not been extensively tested in NEMO (not recommended). 
     1325     \end{description} 
     1326 
     1327\subsection{Ocean/Ice shelf fluxes in parametrised cavities} 
    12211328 
    12221329  \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}. 
     1330 
     1331     \item[\np{cn_isfpar_mlt}{cn\_isfpar\_mlt}\forcode{ = 'bg03'}]: 
     1332     The ice shelf cavities are not represented. 
     1333     The fwf and heat flux are computed using the \citet{beckmann.goosse_OM03} parameterisation of isf melting. 
     1334     The fluxes are distributed along the ice shelf edge between the depth of the average grounding line (GL) 
     1335     (\np{sn_isfpar_zmax}{sn\_isfpar\_zmax}) and the base of the ice shelf along the calving front 
     1336     (\np{sn_isfpar_zmin}{sn\_isfpar\_zmin}) as in (\np{cn_isfpar_mlt}{cn\_isfpar\_mlt}\forcode{ = 'spe'}). 
     1337     The effective melting length (\np{sn_isfpar_Leff}{sn\_isfpar\_Leff}) is read from a file. 
     1338     This parametrisation has not been tested since a while and based on \citet{Favier2019},  
     1339     this parametrisation should probably not be used. 
     1340 
     1341     \item[\np{cn_isfpar_mlt}{cn\_isfpar\_mlt}\forcode{ = 'spe'}]: 
     1342     The ice shelf cavity is not represented. 
     1343     The fwf (\np{sn_isfpar_fwf}{sn\_isfpar\_fwf}) is prescribed and distributed along the ice shelf edge between 
     1344     the depth of the average grounding line (GL) (\np{sn_isfpar_zmax}{sn\_isfpar\_zmax}) and 
     1345     the base of the ice shelf along the calving front (\np{sn_isfpar_zmin}{sn\_isfpar\_min}). Convention of the input file is positive toward the ocean (i.e. positive for melting and negative for freezing). 
     1346     The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$. 
     1347 
     1348     \item[\np{cn_isfpar_mlt}{cn\_isfpar\_mlt}\forcode{ = 'oasis'}]: 
     1349     The \forcode{'oasis'} is a prototype of what could be a method to spread precipitation on Antarctic ice sheet as ice shelf melt inside the cavity when a coupled model Atmosphere/Ocean is used.  
     1350     It has not been tested and therefore the model will stop if you try to use it.  
     1351     Action will be undertake in 2020 to build a comprehensive interface to do so for Greenland, Antarctic and ice shelf (cav), ice shelf (par), icebergs, subglacial runoff and runoff. 
     1352 
    12281353  \end{description} 
    12291354 
    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*} 
    1243        % \label{eq:SBC_isf_gamma_iso} 
    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}) 
    1280 \end{description} 
    1281  
    1282 $\bullet$ \np[=1]{nn_isf}{nn\_isf} and \np[=2]{nn_isf}{nn\_isf} compute a melt rate based on 
     1355\np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = '2eq'}, \np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = '3eq'} and \np{cn_isfpar_mlt}{cn\_isfpar\_mlt}\forcode{ = 'bg03'} compute a melt rate based on 
    12831356the water mass properties, ocean velocities and depth. 
    1284 This flux is thus highly dependent of the model resolution (horizontal and vertical), 
    1285 realism of the water masses onto the shelf ...\\ 
    1286  
    1287 $\bullet$ \np[=3]{nn_isf}{nn\_isf} and \np[=4]{nn_isf}{nn\_isf} read the melt rate from a file. 
     1357The resulting fluxes are thus highly dependent of the model resolution (horizontal and vertical) and  
     1358realism of the water masses onto the shelf.\\ 
     1359 
     1360\np{cn_isfcav_mlt}{cn\_isfcav\_mlt}\forcode{ = 'spe'} and \np{cn_isfpar_mlt}{cn\_isfpar\_mlt}\forcode{ = 'spe'} read the melt rate from a file. 
    12881361You have total control of the fwf forcing. 
    12891362This can be useful if the water masses on the shelf are not realistic or 
    12901363the resolution (horizontal/vertical) are too coarse to have realistic melting or 
    1291 for studies where you need to control your heat and fw input.\\ 
    1292  
    1293 The ice shelf melt is implemented as a volume flux as for the runoff. 
    1294 The fw addition due to the ice shelf melting is, at each relevant depth level, added to 
    1295 the horizontal divergence (\textit{hdivn}) in the subroutine \rou{sbc\_isf\_div}, called from \mdl{divhor}. 
     1364for studies where you need to control your heat and fw input.  
     1365However, if your forcing is not consistent with the dynamics below you can reach unrealistic low water temperature.\\ 
     1366 
     1367The ice shelf fwf is implemented as a volume flux as for the runoff. 
     1368The fwf addition due to the ice shelf melting is, at each relevant depth level, added to 
     1369the horizontal divergence (\textit{hdivn}) in the subroutine \rou{isf\_hdiv}, called from \mdl{divhor}. 
    12961370See the runoff section \autoref{sec:SBC_rnf} for all the details about the divergence correction.\\ 
     1371 
     1372Description and result of sensitivity tests to \np{ln_isfcav_mlt}{ln\_isfcav\_mlt} and \np{ln_isfpar_mlt}{ln\_isfpar\_mlt} are presented in \citet{mathiot.jenkins.ea_GMD17}.  
     1373The different options are illustrated in \autoref{fig:ISF}. 
    12971374 
    12981375\begin{figure}[!t] 
    12991376  \centering 
    1300   \includegraphics[width=0.66\textwidth]{SBC_isf} 
     1377  \includegraphics[width=0.66\textwidth]{SBC_isf_v4.2} 
    13011378  \caption[Ice shelf location and fresh water flux definition]{ 
    13021379    Illustration of the location where the fwf is injected and 
    1303     whether or not the fwf is interactif or not depending of \protect\np{nn_isf}{nn\_isf}.} 
    1304   \label{fig:SBC_isf} 
     1380    whether or not the fwf is interactive or not.} 
     1381  \label{fig:ISF} 
    13051382\end{figure} 
    13061383 
    1307 %% ================================================================================================= 
    1308 \section{Ice sheet coupling} 
    1309 \label{sec:SBC_iscpl} 
    1310  
    1311 \begin{listing} 
    1312   \nlst{namsbc_iscpl} 
    1313   \caption{\forcode{&namsbc_iscpl}} 
    1314   \label{lst:namsbc_iscpl} 
    1315 \end{listing} 
     1384\subsection{Available outputs} 
     1385The following outputs are availables via XIOS: 
     1386\begin{description} 
     1387   \item[for parametrised cavities]: 
     1388      \begin{xmllines} 
     1389 <field id="isftfrz_par"     long_name="freezing point temperature in the parametrization boundary layer" unit="degC"     /> 
     1390 <field id="fwfisf_par"      long_name="Ice shelf melt rate"                           unit="kg/m2/s"  /> 
     1391 <field id="qoceisf_par"     long_name="Ice shelf ocean  heat flux"                    unit="W/m2"     /> 
     1392 <field id="qlatisf_par"     long_name="Ice shelf latent heat flux"                    unit="W/m2"     /> 
     1393 <field id="qhcisf_par"      long_name="Ice shelf heat content flux of injected water" unit="W/m2"     /> 
     1394 <field id="fwfisf3d_par"    long_name="Ice shelf melt rate"                           unit="kg/m2/s"  grid_ref="grid_T_3D" /> 
     1395 <field id="qoceisf3d_par"   long_name="Ice shelf ocean  heat flux"                    unit="W/m2"     grid_ref="grid_T_3D" /> 
     1396 <field id="qlatisf3d_par"   long_name="Ice shelf latent heat flux"                    unit="W/m2"     grid_ref="grid_T_3D" /> 
     1397 <field id="qhcisf3d_par"    long_name="Ice shelf heat content flux of injected water" unit="W/m2"     grid_ref="grid_T_3D" /> 
     1398 <field id="ttbl_par"        long_name="temperature in the parametrisation boundary layer" unit="degC" /> 
     1399 <field id="isfthermald_par" long_name="thermal driving of ice shelf melting"          unit="degC"     /> 
     1400      \end{xmllines} 
     1401   \item[for open cavities]: 
     1402      \begin{xmllines} 
     1403 <field id="isftfrz_cav"     long_name="freezing point temperature at ocean/isf interface"                unit="degC"     /> 
     1404 <field id="fwfisf_cav"      long_name="Ice shelf melt rate"                           unit="kg/m2/s"  /> 
     1405 <field id="qoceisf_cav"     long_name="Ice shelf ocean  heat flux"                    unit="W/m2"     /> 
     1406 <field id="qlatisf_cav"     long_name="Ice shelf latent heat flux"                    unit="W/m2"     /> 
     1407 <field id="qhcisf_cav"      long_name="Ice shelf heat content flux of injected water" unit="W/m2"     /> 
     1408 <field id="fwfisf3d_cav"    long_name="Ice shelf melt rate"                           unit="kg/m2/s"  grid_ref="grid_T_3D" /> 
     1409 <field id="qoceisf3d_cav"   long_name="Ice shelf ocean  heat flux"                    unit="W/m2"     grid_ref="grid_T_3D" /> 
     1410 <field id="qlatisf3d_cav"   long_name="Ice shelf latent heat flux"                    unit="W/m2"     grid_ref="grid_T_3D" /> 
     1411 <field id="qhcisf3d_cav"    long_name="Ice shelf heat content flux of injected water" unit="W/m2"     grid_ref="grid_T_3D" /> 
     1412 <field id="ttbl_cav"        long_name="temperature in Losch tbl"                      unit="degC"     /> 
     1413 <field id="isfthermald_cav" long_name="thermal driving of ice shelf melting"          unit="degC"     /> 
     1414 <field id="isfgammat"       long_name="Ice shelf heat-transfert velocity"             unit="m/s"      /> 
     1415 <field id="isfgammas"       long_name="Ice shelf salt-transfert velocity"             unit="m/s"      /> 
     1416 <field id="stbl"            long_name="salinity in the Losh tbl"                      unit="1e-3"     /> 
     1417 <field id="utbl"            long_name="zonal current in the Losh tbl at T point"      unit="m/s"      /> 
     1418 <field id="vtbl"            long_name="merid current in the Losh tbl at T point"      unit="m/s"      /> 
     1419 <field id="isfustar"        long_name="ustar at T point used in ice shelf melting"    unit="m/s"      /> 
     1420 <field id="qconisf"         long_name="Conductive heat flux through the ice shelf"    unit="W/m2"     /> 
     1421      \end{xmllines} 
     1422\end{description} 
     1423 
     1424%% ================================================================================================= 
     1425\subsection{Ice sheet coupling} 
     1426\label{subsec:ISF_iscpl} 
    13161427 
    13171428Ice sheet/ocean coupling is done through file exchange at the restart step. 
    1318 At each restart step: 
    1319  
    1320 \begin{enumerate} 
    1321 \item the ice sheet model send a new bathymetry and ice shelf draft netcdf file. 
    1322 \item a new domcfg.nc file is built using the DOMAINcfg tools. 
    1323 \item \NEMO\ run for a specific period and output the average melt rate over the period. 
    1324 \item the ice sheet model run using the melt rate outputed in step 4. 
    1325 \item go back to 1. 
    1326 \end{enumerate} 
    1327  
    1328 If \np[=.true.]{ln_iscpl}{ln\_iscpl}, the isf draft is assume to be different at each restart step with 
     1429At each restart step, the procedure is this one: 
     1430 
     1431\begin{description} 
     1432\item[Step 1]: the ice sheet model send a new bathymetry and ice shelf draft netcdf file. 
     1433\item[Step 2]: a new domcfg.nc file is built using the DOMAINcfg tools. 
     1434\item[Step 3]: NEMO run for a specific period and output the average melt rate over the period. 
     1435\item[Step 4]: the ice sheet model run using the melt rate outputed in step 3. 
     1436\item[Step 5]: go back to 1. 
     1437\end{description} 
     1438 
     1439If \np{ln_iscpl}{ln\_iscpl}\forcode{ = .true.}, the isf draft is assume to be different at each restart step with 
    13291440potentially some new wet/dry cells due to the ice sheet dynamics/thermodynamics. 
    1330 The wetting and drying scheme applied on the restart is very simple and described below for the 6 different possible cases: 
     1441The wetting and drying scheme, applied on the restart, is very simple. The 6 different possible cases for the tracer and ssh are: 
    13311442 
    13321443\begin{description} 
    1333 \item [Thin a cell down]: T/S/ssh are unchanged and U/V in the top cell are corrected to keep the barotropic transport (bt) constant 
    1334   ($bt_b=bt_n$). 
    1335 \item [Enlarge  a cell]: See case "Thin a cell down" 
    1336 \item [Dry a cell]: mask, T/S, U/V and ssh are set to 0. 
    1337   Furthermore, U/V into the water column are modified to satisfy ($bt_b=bt_n$). 
    1338 \item [Wet a cell]: mask is set to 1, T/S is extrapolated from neighbours, $ssh_n = ssh_b$ and U/V set to 0. 
    1339   If no neighbours, T/S is extrapolated from old top cell value. 
    1340   If no neighbours along i,j and k (both previous test failed), T/S/U/V/ssh and mask are set to 0. 
    1341 \item [Dry a column]: mask, T/S, U/V are set to 0 everywhere in the column and ssh set to 0. 
    1342 \item [Wet a column]: set mask to 1, T/S is extrapolated from neighbours, ssh is extrapolated from neighbours and U/V set to 0. 
    1343   If no neighbour, T/S/U/V and mask set to 0. 
     1444   \item[Thin a cell]: 
     1445   T/S/ssh are unchanged. 
     1446 
     1447   \item[Enlarge  a cell]: 
     1448   See case "Thin a cell down" 
     1449 
     1450   \item[Dry a cell]: 
     1451   Mask, T/S, U/V and ssh are set to 0. 
     1452 
     1453   \item[Wet a cell]:  
     1454   Mask is set to 1, T/S is extrapolated from neighbours, $ssh_n = ssh_b$. 
     1455   If no neighbours, T/S is extrapolated from old top cell value.  
     1456   If no neighbours along i,j and k (both previous tests failed), T/S/ssh and mask are set to 0. 
     1457 
     1458   \item[Dry a column]: 
     1459   mask, T/S and ssh are set to 0. 
     1460 
     1461   \item[Wet a column]: 
     1462   set mask to 1, T/S/ssh are extrapolated from neighbours. 
     1463   If no neighbour, T/S/ssh and mask set to 0. 
    13441464\end{description} 
     1465 
     1466The method described above will strongly affect the barotropic transport under an ice shelf when the geometry change. 
     1467In order to keep the model stable, an adjustment of the dynamics at the initialisation after the coupling step is needed.  
     1468The idea behind this is to keep $\pd[\eta]{t}$ as it should be without change in geometry at the initialisation.  
     1469This will prevent any strong velocity due to large pressure gradient.  
     1470To do so, we correct the horizontal divergence before $\pd[\eta]{t}$ is computed in the first time step.\\ 
    13451471 
    13461472Furthermore, as the before and now fields are not compatible (modification of the geometry), 
    … …  
    13491475The horizontal extrapolation to fill new cell with realistic value is called \np{nn_drown}{nn\_drown} times. 
    13501476It means that if the grounding line retreat by more than \np{nn_drown}{nn\_drown} cells between 2 coupling steps, 
    1351 the code will be unable to fill all the new wet cells properly. 
     1477the code will be unable to fill all the new wet cells properly and the model is likely to blow up at the initialisation. 
    13521478The default number is set up for the MISOMIP idealised experiments. 
    13531479This coupling procedure is able to take into account grounding line and calving front migration. 
    1354 However, it is a non-conservative processe. 
     1480However, it is a non-conservative proccess.  
    13551481This could lead to a trend in heat/salt content and volume.\\ 
    13561482 
    13571483In order to remove the trend and keep the conservation level as close to 0 as possible, 
    1358 a simple conservation scheme is available with \np[=.true.]{ln_hsb}{ln\_hsb}. 
    1359 The heat/salt/vol. gain/loss is diagnosed, as well as the location. 
    1360 A correction increment is computed and apply each time step during the next \np{rn_fiscpl}{rn\_fiscpl} time steps. 
    1361 For safety, it is advised to set \np{rn_fiscpl}{rn\_fiscpl} equal to the coupling period (smallest increment possible). 
    1362 The corrective increment is apply into the cell itself (if it is a wet cell), the neigbouring cells or the closest wet cell (if the cell is now dry). 
     1484a simple conservation scheme is available with \np{ln_isfcpl_cons}{ln\_isfcpl\_cons}\forcode{ = .true.}. 
     1485The heat/salt/vol. gain/loss are diagnosed, as well as the location. 
     1486A correction increment is computed and applied each time step during the model run. 
     1487The corrective increment are applied into the cells itself (if it is a wet cell), the neigbouring cells or the closest wet cell (if the cell is now dry). 
    13631488 
    13641489%% ================================================================================================= 
    … …  
    14091534Melt water (and other variables on the configuration grid) are written into the main \NEMO\ model output files. 
    14101535 
     1536By default, iceberg thermodynamic and dynamic are computed using ocean surface variable (sst, ssu, ssv) and the icebergs are not sensible to the bathymetry (only to land) whatever the iceberg draft.  
     1537\citet{Merino_OM2016} developed an option to use vertical profiles of ocean currents and temperature instead (\np{ln_M2016}{ln\_M2016}). 
     1538Full details on the sensitivity to this parameter in done in \citet{Merino_OM2016}.  
     1539If \np{ln_M2016}{ln\_M2016} activated, \np{ln_icb_grd}{ln\_icb\_grd} activate (or not) an option to prevent thick icebergs to move across shallow bank (ie shallower than the iceberg draft). 
     1540This option need to be used with care as it could required to either change the distribution to prevent generation of icebergs with draft larger than the bathymetry  
     1541or to build a variable \forcode{maxclass} to prevent NEMO filling the icebergs classes too thick for the local bathymetry. 
     1542 
    14111543Extensive diagnostics can be produced. 
    14121544Separate output files are maintained for human-readable iceberg information. 
    … …  
    14651597Then using the routine \rou{sbcblk\_algo\_ncar} and starting from the neutral drag coefficent provided, 
    14661598the drag coefficient is computed according to the stable/unstable conditions of the 
    1467 air-sea interface following \citet{large.yeager_rpt04}. 
     1599air-sea interface following \citet{large.yeager_trpt04}. 
    14681600 
    14691601%% ================================================================================================= 
    … …  
    15761708 
    15771709The surface stress felt by the ocean is the atmospheric stress minus the net stress going 
    1578 into the waves \citep{janssen.breivik.ea_rpt13}. Therefore, when waves are growing, momentum and energy is spent and is not 
     1710into the waves \citep{janssen.breivik.ea_trpt13}. Therefore, when waves are growing, momentum and energy is spent and is not 
    15791711available for forcing the mean circulation, while in the opposite case of a decaying sea 
    15801712state, more momentum is available for forcing the ocean. 
    … …  
    17951927\label{subsec:SBC_fwb} 
    17961928 
    1797 For global ocean simulation, it can be useful to introduce a control of the mean sea level in order to 
    1798 prevent unrealistic drift of the sea surface height due to inaccuracy in the freshwater fluxes. 
    1799 In \NEMO, two way of controlling the freshwater budget are proposed: 
     1929\begin{listing} 
     1930  \nlst{namsbc_fwb} 
     1931  \caption{\forcode{&namsbc_fwb}} 
     1932  \label{lst:namsbc_fwb} 
     1933\end{listing} 
     1934 
     1935For global ocean simulations, it can be useful to introduce a control of the 
     1936mean sea level in order to prevent unrealistic drifting of the sea surface 
     1937height due to unbalanced freshwater fluxes. In \NEMO, two options for 
     1938controlling the freshwater budget are proposed. 
    18001939 
    18011940\begin{description} 
    1802 \item [{\np[=0]{nn_fwb}{nn\_fwb}}] no control at all. 
    1803   The mean sea level is free to drift, and will certainly do so. 
    1804 \item [{\np[=1]{nn_fwb}{nn\_fwb}}] global mean \textit{emp} set to zero at each model time step. 
     1941\item [{\np[=0]{nn_fwb}{nn\_fwb}}:] No control at all; the mean sea level is 
     1942  free to drift, and will certainly do so. 
     1943\item [{\np[=1]{nn_fwb}{nn\_fwb}}:] The global mean \textit{emp} is set to zero at each model time step. 
    18051944  %GS: comment below still relevant ? 
    18061945  %Note that with a sea-ice model, this technique only controls the mean sea level with linear free surface and no mass flux between ocean and ice (as it is implemented in the current ice-ocean coupling). 
    1807 \item [{\np[=2]{nn_fwb}{nn\_fwb}}] freshwater budget is adjusted from the previous year annual mean budget which 
    1808   is read in the \textit{EMPave\_old.dat} file. 
    1809   As the model uses the Boussinesq approximation, the annual mean fresh water budget is simply evaluated from 
    1810   the change in the mean sea level at January the first and saved in the \textit{EMPav.dat} file. 
     1946\item [{\np[=2]{nn_fwb}{nn\_fwb}}:] \textit{emp} is adjusted by adding a 
     1947  spatially uniform, annual-mean freshwater flux that balances the freshwater 
     1948  budget at the end of the previous year; as the model uses the Boussinesq 
     1949  approximation, the freshwater budget can be evaluated from the change in the 
     1950  mean sea level and in the ice and snow mass after the end of each simulation 
     1951  year; at the start of the model run, an initial adjustment flux can be set 
     1952  using parameter \np{rn_rwb0}{rn\_fwb0} in namelist \nam{sbc_fwb}{sbc\_fwb}. 
    18111953\end{description} 
    18121954 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_STO.tex

    r11693 r14789  
    55\chapter{Stochastic Parametrization of EOS (STO)} 
    66\label{chap:STO} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_TRA.tex

    r13476 r14789  
    55\chapter{Ocean Tracers (TRA)} 
    66\label{chap:TRA} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 
    … …  
    930928When \np{nn_geoflx}{nn\_geoflx} is set to 2, 
    931929a spatially varying geothermal heat flux is introduced which is provided in 
    932 the \ifile{geothermal\_heating} NetCDF file 
     930the \textit{geothermal\_heating.nc} NetCDF file 
    933931(\autoref{fig:TRA_geothermal}) \citep{emile-geay.madec_OS09}. 
    934932 
    … …  
    11511149\citep{madec.delecluse.ea_JPO96}. 
    11521150 
    1153 For generating \ifile{resto}, 
     1151For generating \textit{resto.nc}, 
    11541152see the documentation for the DMP tools provided with the source code under \path{./tools/DMP_TOOLS}. 
    11551153 
    … …  
    11751173$\gamma$ is initialized as \np{rn_atfp}{rn\_atfp}, its default value is \forcode{10.e-3}. 
    11761174Note that the forcing correction term in the filter is not applied in linear free surface 
    1177 (\jp{ln\_linssh}\forcode{=.true.}) (see \autoref{subsec:TRA_sbc}). 
     1175(\np[=.true.]{ln_linssh}{ln\_linssh}) (see \autoref{subsec:TRA_sbc}). 
    11781176Not also that in constant volume case, the time stepping is performed on $T$, 
    11791177not on its content, $e_{3t}T$. 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_ZDF.tex

    r13461 r14789  
    11\documentclass[../main/NEMO_manual]{subfiles} 
    2  
    3 %% Custom aliases 
    4 \newcommand{\cf}{\ensuremath{C\kern-0.14em f}} 
    52 
    63\begin{document} 
    … …  
    85\chapter{Vertical Ocean Physics (ZDF)} 
    96\label{chap:ZDF} 
    10  
    11 \thispagestyle{plain} 
    127 
    138\chaptertoc 
    … …  
    198193$\bar{e}_o = e_{bb} |\tau| / \rho_o$, with $e_{bb}$ the \np{rn_ebb}{rn\_ebb} namelist parameter. 
    199194The default value of $e_{bb}$ is 3.75. \citep{gaspar.gregoris.ea_JGR90}), however a much larger value can be used when 
    200 taking into account the surface wave breaking (see below Eq. \autoref{eq:ZDF_Esbc}). 
     195taking into account the surface wave breaking (see below \autoref{eq:ZDF_Esbc}). 
    201196The bottom value of TKE is assumed to be equal to the value of the level just above. 
    202197The time integration of the $\bar{e}$ equation may formally lead to negative values because 
    … …  
    532527the TKE case described in \autoref{subsec:ZDF_tke_ene} \citep{burchard_OM02}. 
    533528Evaluation of the 4 GLS turbulent closure schemes can be found in \citet{warner.sherwood.ea_OM05} in ROMS model and 
    534  in \citet{reffray.guillaume.ea_GMD15} for the \NEMO\ model. 
     529 in \citet{reffray.bourdalle-badie.ea_GMD15} for the \NEMO\ model. 
    535530 
    536531% ------------------------------------------------------------------------------------------------------------- 
    … …  
    594589Obsolete namelist parameters include: 
    595590\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}. 
     591\item \protect\np{ln_use_osm_la}\np{ln\_use\_osm\_la} With \protect\np[=0]{nn_osm_wave}{nn\_osm\_wave}, 
     592  \protect\np{rn_osm_dstokes} {rn\_osm\_dstokes} is always used to specify the Stokes 
     593  penetration depth. 
     594\item \protect\np{nn_ave} {nn\_ave} Choice of averaging method for KPP-style Ri \# 
     595  mixing. Not taken account of. 
     596\item \protect\np{rn_osm_hbl0} {rn\_osm\_hbl0} Depth of initial boundary layer is now set 
     597  by a density criterion similar to that used in calculating \emph{hmlp} (output as \texttt{mldr10\_1}) in \mdl{zdfmxl}. 
    603598\end{description} 
    604599 
    … …  
    608603classical shear turbulence. Instead they are in a regime known as 
    609604`Langmuir turbulence',  dominated by an 
    610 interaction between the currents and the Stokes drift of the surface waves \citep[e.g.][]{mcwilliams.ea_JFM97}. 
     605interaction between the currents and the Stokes drift of the surface waves \citep[e.g.][]{mcwilliams.sullivan.ea_JFM97}. 
    611606This 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 $\mathrm{La}_{t}=(u_{\ast}/u_{s0}) > 0.4$. 
    612607 
    … …  
    617612The OSMOSIS turbulent closure scheme is a similarity-scale scheme in 
    618613the same spirit as the K-profile 
    619 parameterization (KPP) scheme of \citet{large.ea_RG97}. 
     614parameterization (KPP) scheme of \citet{large.mcwilliams.ea_RG94}. 
    620615A specified shape of diffusivity, scaled by the (OSBL) depth 
    621616$h_{\mathrm{BL}}$ and a turbulent velocity scale, is imposed throughout the 
    … …  
    628623as in KPP, it is set by a prognostic equation that is informed by 
    629624energy budget considerations reminiscent of the classical mixed layer 
    630 models of \citet{kraus.turner_tellus67}. 
     625models of \citet{kraus.turner_T67}. 
    631626The model also includes an explicit parametrization of the structure 
    632627of the pycnocline (the stratified region at the bottom of the OSBL). 
    633628 
    634629Presently, mixing below the OSBL is handled by the Richardson 
    635 number-dependent mixing scheme used in \citet{large.ea_RG97}. 
    636  
    637 Convective parameterizations such as described in \ref{sec:ZDF_conv} 
     630number-dependent mixing scheme used in \citet{large.mcwilliams.ea_RG94}. 
     631 
     632Convective parameterizations such as described in \autoref{sec:ZDF_conv} 
    638633below should not be used with the OSMOSIS-OBL model: instabilities 
    639634within the OSBL are part of the model, while instabilities below the 
    … …  
    641636 
    642637\subsubsection{Depth and velocity scales} 
    643 The 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). 
     638The 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 $\Delta h$; \autoref{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). 
    644639\begin{figure}[!t] 
    645640  \begin{center} 
    646641    %\includegraphics[width=0.7\textwidth]{ZDF_OSM_structure_of_OSBL} 
    647642    \caption{ 
    648       \protect\label{fig: OSBL_structure} 
     643      \protect\label{fig:OSBL_structure} 
    649644     The structure of the entraining  boundary layer. (a) Mean buoyancy profile. (b) Profile of the buoyancy flux. 
    650645    } 
    … …  
    654649 
    655650Consideration 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} 
    657 w_{*L}= \left(u_*^2 u_{s\,0}\right)^{1/3}; 
     651\begin{equation} 
     652  \label{eq:ZDF_w_La} 
     653  w_{*L}= \left(u_*^2 u_{s\,0}\right)^{1/3}; 
    658654\end{equation} 
    659655but 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} 
     656\begin{equation} 
     657  \label{eq:ZDF_composite-nu} 
    661658  \nu_{\ast}= \left\{ u_*^3 \left[1-\exp(-.5 \mathrm{La}_t^2)\right]+w_{*L}^3\right\}^{1/3}. 
    662659\end{equation} 
    663660For 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}. 
     661\begin{equation} 
     662  \label{eq:ZDF_vel-scale-unstable} 
     663  \omega_* = \left(\nu_*^3 + 0.5 w_{*C}^3\right)^{1/3}. 
    666664\end{equation} 
    667665 
    668666\subsubsection{The flux gradient model} 
    669667The 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 % 
     668 
     669\begin{equation} 
     670  \label{eq:ZDF_flux-grad-gen} 
     671  \overline{w^\prime\chi^\prime}=-K\frac{\partial\overline{\chi}}{\partial z} + N_{\chi,s} +N_{\chi,b} +N_{\chi,t}, 
     672\end{equation} 
     673 
    675674where $\chi$ 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. 
    676675 
    677676In 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 % 
     677 
     678\begin{equation} 
     679  \label{eq:ZDF_sigma} 
     680  \sigma_{\mathrm{ml}}= -z/h_{\mathrm{ml}}; \;\sigma_{\mathrm{bl}}= -z/h_{\mathrm{bl}}, 
     681\end{equation} 
     682 
    683683in unstable conditions the eddy diffusivity ($K_d$) and eddy viscosity ($K_\nu$) profiles are parametrized as: 
    684 % 
    685 \begin{align}\label{eq:diff-unstable} 
    686 K_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} 
    688 K_\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) 
     684 
     685\begin{align} 
     686  \label{eq:ZDF_diff-unstable} 
     687  K_d=&0.8\, \omega_*\, h_{\mathrm{ml}} \, \sigma_{\mathrm{ml}} \left(1-\beta_d \sigma_{\mathrm{ml}}\right)^{3/2} 
     688  \\ 
     689  \label{eq:ZDF_visc-unstable} 
     690  K_\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) 
    689691\end{align} 
    690 % 
    691 where $\beta_d$ 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} 
    694 K_{d,\mathrm{ml}}=K_{\nu,\mathrm{ml}}=\,0.16\,\omega_* \Delta h. 
    695 \end{equation} 
    696 % 
     692 
     693where $\beta_d$ and $\beta_\nu$ are parameters that are determined by matching \autoref{eq:ZDF_diff-unstable} and \autoref{eq:ZDF_visc-unstable} to the eddy diffusivity and viscosity at the base of the well-mixed layer, given by 
     694 
     695\begin{equation} 
     696  \label{eq:ZDF_diff-wml-base} 
     697  K_{d,\mathrm{ml}}=K_{\nu,\mathrm{ml}}=\,0.16\,\omega_* \Delta h. 
     698\end{equation} 
     699 
    697700For stable conditions the eddy diffusivity/viscosity profiles are given by: 
    698 % 
    699 \begin{align}\label{diff-stable} 
    700 K_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} 
    701 K_\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). 
     701 
     702\begin{align} 
     703  \label{eq:ZDF_diff-stable} 
     704  K_d= & 0.75\,\, \nu_*\, h_{\mathrm{ml}}\,\,  \exp\left[-2.8 
     705       \left(h_{\mathrm{bl}}/L_L\right)^2\right]\sigma_{\mathrm{ml}} 
     706       \left(1-\sigma_{\mathrm{ml}}\right)^{3/2} \\ 
     707  \label{eq:ZDF_visc-stable} 
     708  K_\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). 
    702709\end{align} 
    703 % 
     710 
    704711The 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} 
     712\begin{equation} 
     713  \label{eq:ZDF_L_L} 
    706714  L_L=-w_{*L}^3/\left<\overline{w^\prime b^\prime}\right>_L, 
    707715\end{equation} 
    708716with 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 % 
     717\begin{equation} 
     718  \label{eq:ZDF_stable-av-buoy-flux} 
     719  \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]. 
     720\end{equation} 
     721 
    713722In unstable conditions the eddy diffusivity and viscosity depend on stability through the velocity scale $\omega_*$, which depends on the two velocity scales $\nu_*$ and $w_{*C}$. 
    714723 
    715 Details 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). 
     724Details of the non-gradient terms in \autoref{eq:ZDF_flux-grad-gen} and of the fluxes within the pycnocline $-h_{\mathrm{bl}}<z<h_{\mathrm{ml}}$ can be found in Grant (2019). 
    716725 
    717726\subsubsection{Evolution of the boundary layer depth} 
    718727 
    719 The 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} 
     728The prognostic equation for the depth of the neutral/unstable boundary layer is given by \iffalse \citep{grant+etal18?}, \fi 
     729 
     730\begin{equation} 
     731  \label{eq:ZDF_dhdt-unstable} 
    722732%\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}} 
     733   \frac{\partial h_\mathrm{bl}}{\partial t} = W_b - \frac{{\overline{w^\prime b^\prime}}_\mathrm{ent}}{\Delta B_\mathrm{bl}} 
    724734\end{equation} 
    725735where $h_\mathrm{bl}$ is the horizontally-varying depth of the OSBL, 
    … …  
    732742equation for the case when the pycnocline has a finite thickness, 
    733743based 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 
    735 models e.g.\ \citet{kraus.turner_tellus67}, in which the thickness of the pycnocline is taken to be zero. 
     744\iffalse \citep{grant+etal18?} \fi of a generalization of that used in mixed-layer 
     745models e.g.\ \citet{kraus.turner_T67}, in which the thickness of the pycnocline is taken to be zero. 
    736746 
    737747The entrainment flux for the combination of convective and Langmuir turbulence is given by 
    738 \begin{equation} \label{eq:entrain-flux} 
     748\begin{equation} 
     749  \label{eq:ZDF_entrain-flux} 
    739750  {\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}}} 
    740751  + 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] 
    … …  
    744755For the stable boundary layer, the equation for the depth of the OSBL is: 
    745756 
    746 \begin{equation}\label{eq:dhdt-stable} 
     757\begin{equation} 
     758  \label{eq:ZDF_dhdt-stable} 
    747759\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. 
    748760\end{equation} 
    749761 
    750 Equation. \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. 
     762\autoref{eq:ZDF_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 \autoref{eq:ZDF_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. 
    751763 
    752764 
    … …  
    10681080  \label{lst:namdrg} 
    10691081\end{listing} 
     1082 
    10701083\begin{listing} 
    10711084  \nlst{namdrg_top} 
    … …  
    10731086  \label{lst:namdrg_top} 
    10741087\end{listing} 
     1088 
    10751089\begin{listing} 
    10761090  \nlst{namdrg_bot} 
    … …  
    11601174\] 
    11611175When \np[=.true.]{ln_lin}{ln\_lin}, the value of $r$ used is \np{rn_Uc0}{rn\_Uc0}*\np{rn_Cd0}{rn\_Cd0}. 
    1162 Setting \np[=.true.]{ln_drg_OFF}{ln\_OFF} (and \forcode{ln_lin=.true.}) is equivalent to setting $r=0$ and leads to a free-slip boundary condition. 
     1176Setting \np[=.true.]{ln_drg_OFF}{ln\_drg\_OFF} (and \forcode{ln_lin=.true.}) is equivalent to setting $r=0$ and leads to a free-slip boundary condition. 
    11631177 
    11641178These values are assigned in \mdl{zdfdrg}. 
    11651179Note that there is support for local enhancement of these values via an externally defined 2D mask array 
    1166 (\np[=.true.]{ln_boost}{ln\_boost}) given in the \ifile{bfr\_coef} input NetCDF file. 
     1180(\np[=.true.]{ln_boost}{ln\_boost}) given in the \textit{bfr\_coef.nc} input NetCDF file. 
    11671181The mask values should vary from 0 to 1. 
    11681182Locations with a non-zero mask value will have the friction coefficient increased by 
    … …  
    15471561by only a few extra physics choices namely: 
    15481562 
    1549 \begin{verbatim} 
     1563\begin{forlines} 
    15501564     ln_dynldf_OFF = .false. 
    15511565     ln_dynldf_lap = .true. 
    … …  
    15551569        nn_fct_h   =  2 
    15561570        nn_fct_v   =  2 
    1557 \end{verbatim} 
     1571\end{forlines} 
    15581572 
    15591573\noindent which were chosen to provide a slightly more stable and less noisy solution. The 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_cfgs.tex

    r11693 r14789  
    55\chapter{Configurations} 
    66\label{chap:CFGS} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 
    … …  
    8583the SI3 model (ORCA-ICE) and possibly with PISCES biogeochemical model (ORCA-ICE-PISCES). 
    8684An appropriate namelist is available in \path{./cfgs/ORCA2_ICE_PISCES/EXPREF/namelist_cfg} for ORCA2. 
    87 The domain of ORCA2 configuration is defined in \ifile{ORCA\_R2\_zps\_domcfg} file, 
     85The domain of ORCA2 configuration is defined in \textit{ORCA\_R2\_zps\_domcfg.nc} file, 
    8886this file is available in tar file on the \NEMO\ community zenodo platform: \\ 
    8987https://doi.org/10.5281/zenodo.2640723 
    … …  
    152150Each of configuration is set through the \textit{domain\_cfg} domain configuration file, 
    153151which sets the grid size and configuration name parameters. 
    154 The \NEMO\ System Team provides only ORCA2 domain input file "\ifile{ORCA\_R2\_zps\_domcfg}" file 
     152The \NEMO\ System Team provides only ORCA2 domain input file "\textit{ORCA\_R2\_zps\_domcfg.nc}" file 
    155153(\autoref{tab:CFGS_ORCA}). 
    156154 
    … …  
    158156  \centering 
    159157  \begin{tabular}{p{4cm} c c c c} 
    160     Horizontal Grid & \jp{ORCA\_index} & \jp{jpiglo} & \jp{jpjglo} \\ 
     158    Horizontal Grid & \texttt{ORCA\_index} & \texttt{jpiglo} & \texttt{jpjglo} \\ 
    161159    \hline \hline 
    162160    % 4   \deg\ &              4   &          92 &          76 \\ 
    … …  
    198196(see \autoref{tab:CFGS_ORCA} and \autoref{fig:DOM_zgr_e3}). 
    199197The bottom topography and the coastlines are derived from the global atlas of Smith and Sandwell (1997). 
    200 The default forcing uses the boundary forcing from \citet{large.yeager_rpt04} (see \autoref{subsec:SBC_blk_ocean}), 
     198The default forcing uses the boundary forcing from \citet{large.yeager_trpt04} (see \autoref{subsec:SBC_blk_ocean}), 
    201199which was developed for the purpose of running global coupled ocean-ice simulations without 
    202200an interactive atmosphere. 
    203 This \citet{large.yeager_rpt04} dataset is available through 
     201This \citet{large.yeager_trpt04} dataset is available through 
    204202the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}. 
    205 The "normal year" of \citet{large.yeager_rpt04} has been chosen of the \NEMO\ distribution since release v3.3. 
     203The "normal year" of \citet{large.yeager_trpt04} has been chosen of the \NEMO\ distribution since release v3.3. 
    206204 
    207205ORCA\_R2 pre-defined configuration can also be run with multiply online nested zooms (\ie\ with AGRIF, \key{agrif} defined). 
    … …  
    243241Through \np[=.false.]{ln_read_cfg}{ln\_read\_cfg} in \nam{cfg}{cfg} namelist defined in 
    244242the reference configuration \path{./cfgs/GYRE_PISCES/EXPREF/namelist_cfg} 
    245 analytical definition of grid in GYRE is done in usrdef\_hrg, usrdef\_zgr routines. 
     243analytical definition of grid in GYRE is done in mdl{usrdef\_hrg}, \mdl{usrdef\_zgr} routines. 
    246244Its horizontal resolution (and thus the size of the domain) is determined by 
    247 setting \np{nn_GYRE}{nn\_GYRE} in \nam{usr_def}{usr\_def}: \\ 
    248  
    249 \jp{jpiglo} $= 30 \times$ \np{nn_GYRE}{nn\_GYRE} + 2   \\ 
    250  
    251 \jp{jpjglo} $= 20 \times$ \np{nn_GYRE}{nn\_GYRE} + 2   \\ 
     245setting \np{nn_GYRE}{nn\_GYRE} in \nam{usr_def}{usr\_def}: 
     246 
     247\begin{align*} 
     248   jpiglo = 30 \times \text{\np{nn_GYRE}{nn\_GYRE}} + 2 + 2 \times \text{\np{nn_hls}{nn\_hls}} \\ 
     249   jpjglo = 20 \times \text{\np{nn_GYRE}{nn\_GYRE}} + 2 + 2 \times \text{\np{nn_hls}{nn\_hls}} 
     250\end{align*} 
    252251 
    253252Obviously, the namelist parameters have to be adjusted to the chosen resolution, 
    254253see the Configurations pages on the \NEMO\ web site (\NEMO\ Configurations). 
    255 In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}\forcode{ = 31}) (\autoref{fig:DOM_zgr_e3}). 
     254In the vertical, GYRE uses the default 30 ocean levels (\forcode{jpk = 31}, \autoref{fig:DOM_zgr_e3}). 
     255 
     256\begin{listing} 
     257  \begin{forlines} 
     258!----------------------------------------------------------------------- 
     259&namusr_def    !   GYRE user defined namelist   
     260!----------------------------------------------------------------------- 
     261   nn_GYRE     =     1     !  GYRE resolution [1/degrees] 
     262   ln_bench    = .false.   !  ! =T benchmark with gyre: the gridsize is kept constant 
     263   jpkglo      =    31     !  number of model levels 
     264/ 
     265  \end{forlines} 
     266  \caption{\forcode{&namusr_def}} 
     267  \label{lst:namusr_def} 
     268\end{listing} 
    256269 
    257270The GYRE configuration is also used in benchmark test as it is very simple to increase its resolution and 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_conservation.tex

    r11693 r14789  
    55\chapter{Invariants of the Primitive Equations} 
    66\label{chap:CONS} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_misc.tex

    r12377 r14789  
    66\label{chap:MISC} 
    77 
    8 \thispagestyle{plain} 
    9  
    108\chaptertoc 
    119 
    … …  
    1412{\footnotesize 
    1513  \begin{tabularx}{\textwidth}{l||X|X} 
    16     Release & Author(s) & Modifications \\ 
     14    Release     & Author(s)            & Modifications                      \\ 
    1715    \hline 
    18     {\em   4.0} & {\em ...} & {\em ...} \\ 
    19     {\em   3.6} & {\em ...} & {\em ...} \\ 
    20     {\em   3.4} & {\em ...} & {\em ...} \\ 
    21     {\em <=3.4} & {\em ...} & {\em ...} 
     16    {\em   X.X} & {\em Pierre Mathiot} & {Update of the closed sea section} \\ 
     17    {\em   4.0} & {\em ...           } & {\em ...                         } \\ 
     18    {\em   3.6} & {\em ...           } & {\em ...                         } \\ 
     19    {\em   3.4} & {\em ...           } & {\em ...                         } \\ 
     20    {\em <=3.4} & {\em ...           } & {\em ...                         } 
    2221  \end{tabularx} 
    2322} 
    … …  
    109108\end{figure} 
    110109 
    111 \begin{figure}[!tbp] 
    112   \centering 
    113   \includegraphics[width=0.66\textwidth]{MISC_closea_mask_example} 
    114   \caption[Mask fields for the \protect\mdl{closea} module]{ 
    115     Example of mask fields for the \protect\mdl{closea} module. 
    116     \textit{Left}: a closea\_mask field; 
    117     \textit{Right}: a closea\_mask\_rnf field. 
    118     In this example, if \protect\np{ln_closea}{ln\_closea} is set to \forcode{.true.}, 
    119     the mean freshwater flux over each of the American Great Lakes will be set to zero, 
    120     and the total residual for all the lakes, if negative, will be put into 
    121     the St Laurence Seaway in the area shown.} 
    122   \label{fig:MISC_closea_mask_example} 
    123 \end{figure} 
    124  
    125110%% ================================================================================================= 
    126111\section[Closed seas (\textit{closea.F90})]{Closed seas (\protect\mdl{closea})} 
    127112\label{sec:MISC_closea} 
     113 
     114\begin{listing} 
     115  \nlst{namclo} 
     116  \caption{\forcode{&namclo}} 
     117  \label{lst:namclo} 
     118\end{listing} 
    128119 
    129120Some configurations include inland seas and lakes as ocean 
    … …  
    138129to zero and put the residual flux into the ocean. 
    139130 
    140 Prior to \NEMO\ 4 the locations of inland seas and lakes was set via 
    141 hardcoded indices for various ORCA configurations. From \NEMO\ 4 onwards 
    142 the inland seas and lakes are defined using mask fields in the 
    143 domain configuration file. The options are as follows. 
    144  
    145 \begin{enumerate} 
    146 \item {{\bfseries No ``closea\_mask'' field is included in domain configuration 
    147   file.} In this case the closea module does nothing.} 
    148  
    149 \item {{\bfseries A field called closea\_mask is included in the domain 
    150 configuration file and ln\_closea=.false. in namelist namcfg.} In this 
    151 case the inland seas defined by the closea\_mask field are filled in 
    152 (turned to land points) at run time. That is every point in 
    153 closea\_mask that is nonzero is set to be a land point.} 
    154  
    155 \item {{\bfseries A field called closea\_mask is included in the domain 
    156 configuration file and ln\_closea=.true. in namelist namcfg.} Each 
    157 inland sea or group of inland seas is set to a positive integer value 
    158 in the closea\_mask field (see \autoref{fig:MISC_closea_mask_example} 
    159 for an example). The net surface flux over each inland sea or group of 
     131The inland seas and lakes are defined using mask fields in the 
     132domain configuration file. Special treatment of the closed sea (redistribution of net freshwater or mask those), are defined in \autoref{lst:namclo} and 
     133can be trigger by \np{ln_closea}{ln\_closea}\forcode{=.true.} in namelist namcfg. 
     134 
     135The options available are the following: 
     136\begin{description} 
     137\item[\np{ln_maskcs}{ln\_maskcs}\forcode{ = .true.}] All the closed seas are masked using \textit{mask\_opensea} variable. 
     138\item[\np{ln_maskcs}{ln\_maskcs}\forcode{ = .false.}] The net surface flux over each inland sea or group of 
    160139inland seas is set to zero each timestep and the residual flux is 
    161 distributed over the global ocean (ie. all ocean points where 
    162 closea\_mask is zero).} 
    163  
    164 \item {{\bfseries Fields called closea\_mask and closea\_mask\_rnf are 
    165 included in the domain configuration file and ln\_closea=.true. in 
    166 namelist namcfg.} This option works as for option 3, except that if 
    167 the net surface flux over an inland sea is negative (net 
    168 precipitation) it is put into the ocean at specified runoff points. A 
    169 net positive surface flux (net evaporation) is still spread over the 
    170 global ocean. The mapping from inland seas to runoff points is defined 
    171 by the closea\_mask\_rnf field. Each mapping is defined by a positive 
    172 integer value for the inland sea(s) and the corresponding runoff 
    173 points. An example is given in 
    174 \autoref{fig:MISC_closea_mask_example}. If no mapping is provided for a 
    175 particular inland sea then the residual is spread over the global 
    176 ocean.} 
    177  
    178 \item {{\bfseries Fields called closea\_mask and closea\_mask\_emp are 
    179 included in the domain configuration file and ln\_closea=.true. in 
    180 namelist namcfg.} This option works the same as option 4 except that 
    181 the nonzero net surface flux is sent to the ocean at the specified 
    182 runoff points regardless of whether it is positive or negative. The 
    183 mapping from inland seas to runoff points in this case is defined by 
    184 the closea\_mask\_emp field.} 
    185 \end{enumerate} 
    186  
    187 There is a python routine to create the closea\_mask fields and append 
    188 them to the domain configuration file in the utils/tools/DOMAINcfg directory. 
     140distributed over a target area. 
     141\end{description} 
     142 
     143When \np{ln_maskcs}{ln\_maskcs}\forcode{ = .false.},  
     1443 options are available for the redistribution (set up of these options is done in the tool DOMAINcfg): 
     145\begin{description}[font=$\bullet$ ] 
     146\item[ glo]: The residual flux is redistributed globally. 
     147\item[ emp]: The residual flux is redistributed as emp in a river outflow. 
     148\item[ rnf]: The residual flux is redistributed as rnf in a river outflow if negative. If there is a net evaporation, the residual flux is redistributed globally. 
     149\end{description} 
     150 
     151For each case, 2 masks are needed (\autoref{fig:MISC_closea_mask_example}):  
     152\begin{description} 
     153\item $\bullet$ one describing the 'sources' (ie the closed seas concerned by each options) called \textit{mask\_csglo}, \textit{mask\_csrnf}, \textit{mask\_csemp}.  
     154\item $\bullet$ one describing each group of inland seas (the Great Lakes for example) and the target area (river outflow or world ocean) for each group of inland seas (St Laurence for the Great Lakes for example) called 
     155\textit{mask\_csgrpglo}, \textit{mask\_csgrprnf}, \textit{mask\_csgrpemp}. 
     156\end{description} 
     157 
     158\begin{figure}[!tbp] 
     159  \centering 
     160  \includegraphics[width=0.66\textwidth]{MISC_closea_mask_example} 
     161  \caption[Mask fields for the \protect\mdl{closea} module]{ 
     162    Example of mask fields for the \protect\mdl{closea} module. 
     163    \textit{Left}: a \textit{mask\_csrnf} field; 
     164    \textit{Right}: a \textit{mask\_csgrprnf} field. 
     165    In this example, if \protect\np{ln_closea}{ln\_closea} is set to \forcode{.true.}, 
     166    the mean freshwater flux over each of the American Great Lakes will be set to zero, 
     167    and the total residual for all the lakes, if negative, will be put into 
     168    the St Laurence Seaway in the area shown.} 
     169  \label{fig:MISC_closea_mask_example} 
     170\end{figure} 
     171 
     172Closed sea not defined (because too small, issue in the bathymetry definition ...) are defined in \textit{mask\_csundef}. 
     173These points can be masked using the namelist option \np{ln_mask_csundef}{ln\_mask\_csundef}\forcode{= .true.} or used to correct the bathymetry input file.\\ 
     174 
     175The masks needed for the closed sea can be created using the DOMAINcfg tool in the utils/tools/DOMAINcfg directory. 
     176See \autoref{sec:clocfg} for details on the usage of definition of the closed sea masks. 
    189177 
    190178%% ================================================================================================= 
    … …  
    205193 
    206194\noindent Consider an ORCA1 
    207 configuration using the extended grid domain configuration file: \ifile{eORCA1\_domcfg.nc} 
     195configuration using the extended grid domain configuration file: \textit{eORCA1\_domcfg.nc} 
    208196This file define a horizontal domain of 362x332.  The first row with 
    209197open ocean wet points in the non-isf bathymetry for this set is row 42 (\fortran\ indexing) 
    … …  
    226214\noindent Note that with this option, the j-size of the global domain is (extended 
    227215j-size minus \np{open_ocean_jstart}{open\_ocean\_jstart} + 1 ) and this must match the \texttt{jpjglo} value 
    228 for the configuration. This means an alternative version of \ifile{eORCA1\_domcfg.nc} must 
     216for the configuration. This means an alternative version of \textit{eORCA1\_domcfg.nc} must 
    229217be created for when \np{ln_use_jattr}{ln\_use\_jattr} is active. The \texttt{ncap2} tool provides a 
    230218convenient way of achieving this: 
    … …  
    234222\end{cmds} 
    235223 
    236 The domain configuration file is unique in this respect since it also contains the value of \jp{jpjglo} 
     224The domain configuration file is unique in this respect since it also contains the value of \texttt{jpjglo} 
    237225that is read and used by the model. 
    238226Any other global, 2D and 3D, netcdf, input field can be prepared for use in a reduced domain by adding the 
    … …  
    374362 
    375363When more information is required for monitoring or debugging purposes, the various 
    376 forms of output can be selected via the \np{sn\_cfctl} structure. As well as simple 
     364forms of output can be selected via the \np{sn_cfctl}{sn\_cfctl} structure. As well as simple 
    377365on-off switches this structure also allows selection of a range of processors for 
    378366individual reporting (where appropriate) and a time-increment option to restrict 
    … …  
    382370with their default settings: 
    383371 
    384 \begin{verbatim} 
     372\begin{forlines} 
    385373   sn_cfctl%l_allon  = .FALSE.    ! IF T activate all options. If F deactivate all unless l_config is T 
    386374     sn_cfctl%l_config = .TRUE.     ! IF .true. then control which reports are written with the following 
    387 \end{verbatim} 
     375\end{forlines} 
    388376 
    389377The first switch is a convenience option which can be used to switch on and off all 
    390378sub-options. However, if it is false then switching off all sub-options is only done 
    391 if \texttt{sn_cfctl%l\_config} is also false. Specifically, the logic is: 
    392  
    393 \begin{verbatim} 
     379if \forcode{sn_cfctl%l\_config} is also false. Specifically, the logic is: 
     380 
     381\begin{forlines} 
    394382  IF ( sn_cfctl%l_allon ) THEN 
    395383    set all suboptions .TRUE. 
    … …  
    400388    set all suboptions .FALSE. 
    401389  ENDIF 
    402 \end{verbatim} 
     390\end{forlines} 
    403391 
    404392Details 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 
    406 carried out in \textt{stpctl.F90}. These checks detect probable numerical instabilites 
     393\forcode{sn_cfctl%l_glochk}.  This option modifies the action of the early warning checks 
     394carried out in \texttt{stpctl.F90}. These checks detect probable numerical instabilites 
    407395by searching for excessive sea surface heights or velocities and salinity values 
    408396outside a sensible physical range. If breaches are detected then the default behaviour 
    409397is to locate and report the local indices of the grid-point in breach. These indices 
    410398are 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 
     399\forcode{sn_cfctl%l_glochk} modifies this action by performing a global location of 
    412400the various minimum and maximum values and the global indices are reported. This has 
    413401some value in locating the most severe error in cases where the first detected error 
    … …  
    427415average tracer value for each passive tracer. Collecting these metrics involves 
    428416global communications and will impact on model efficiency so both these options are 
    429 disabled 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 
    431 both of these options and setting the \texttt{sn\_cfctl%timincr} entry to an integer 
     417disabled by default by setting the respective options, \forcode{sn\_cfctl%runstat} and 
     418\forcode{sn\_cfctl%trcstat} to false. A compromise can be made by activating either or 
     419both of these options and setting the \forcode{sn\_cfctl%timincr} entry to an integer 
    432420value greater than one. This increment determines the time-step frequency at which 
    433421the global metrics are collected and reported.  This increment also applies to the 
    … …  
    440428any warning or error messages generated during execution. A \texttt{layout.dat} 
    441429file is also produced which details the MPI-decomposition used by the model. The 
    442 suboptions: \texttt{sn\_cfctl%oceout} and \texttt{sn\_cfctl%layout} can be used 
     430suboptions: \forcode{sn\_cfctl%oceout} and \forcode{sn\_cfctl%layout} can be used 
    443431to activate the creation of these files by all ocean processes.  For example, 
    444 when \texttt{sn\_cfctl%oceout} is true all processors produce their own version of 
     432when \forcode{sn\_cfctl%oceout} is true all processors produce their own version of 
    445433\texttt{ocean.output}.  All files, beyond the the normal reporting processor (narea == 1), are 
    446434named with a \_XXXX extension to their name, where XXXX is a 4-digit area number (with 
    … …  
    449437systems so bug-hunting efforts using this facility should also utilise the \fortran: 
    450438 
    451 \begin{verbatim}  
    452    CALL FLUSH(numout) 
    453 \end{verbatim} 
     439\forline|CALL FLUSH(numout)| 
    454440 
    455441statement after any additional write statements to ensure that file contents reflect 
    456 the last model state. Associated with the \texttt{sn\_cfctl%oceout} option is the 
    457 additional \texttt{sn\_cfctl%oasout} suboption. This does not activate its own output 
     442the last model state. Associated with the \forcode{sn\_cfctl%oceout} option is the 
     443additional \forcode{sn\_cfctl%oasout} suboption. This does not activate its own output 
    458444file but rather activates the writing of addition information regarding the OASIS 
    459445configuration when coupling via oasis and the sbccpl routine. This information is 
    … …  
    467453http://forge.ipsl.jussieu.fr/nemo/attachment/wiki/Documentation/prtctl_NEMO_doc_v2.pdf}{The 
    468454control print option in NEMO} The switches to activate production of the control sums 
    469 of trends for either the physics or passive tracers are the \texttt{sn\_cfctl%prtctl} 
    470 and \texttt{sn\_cfctl%prttrc} suboptions, respectively. Although, perhaps, of limited use for its 
     455of trends for either the physics or passive tracers are the \forcode{sn\_cfctl%prtctl} 
     456and \forcode{sn\_cfctl%prttrc} suboptions, respectively. Although, perhaps, of limited use for its 
    471457original intention, the ability to produce these control sums of trends in specific 
    472458areas provides another tool for diagnosing model behaviour.  If only the output from a 
    473459select few regions is required then additional options are available to activate options 
    474 for 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 
     460for only a simple subset of processing regions. These are: \forcode{sn\_cfctl%procmin}, 
     461\forcode{sn\_cfctl%procmax} and \forcode{sn\_cfctl%procincr} which can be used to specify 
    476462the minimum and maximum active areas and the increment. The default values are set 
    477463such that all regions will be active. Note this subsetting can also be used to limit 
    … …  
    481467\end{enumerate} 
    482468 
    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  
     469\begin{forlines} 
     470   sn_cfctl%l_glochk  = .false. ! Range sanity checks are local (F) or global (T). Set T for debugging only 
     471   sn_cfctl%l_allon   = .false. ! IF T activate all options. If F deactivate all unless l_config is T 
     472   sn_cfctl%l_config  = .true.  ! IF .true. then control which reports are written with the following 
     473   sn_cfctl%l_runstat = .false. ! switches and which areas produce reports with the proc integer settings. 
     474   sn_cfctl%l_trcstat = .false. ! The default settings for the proc integers should ensure 
     475   sn_cfctl%l_oceout  = .false. ! that  all areas report. 
     476   sn_cfctl%l_layout  = .false. ! 
     477   sn_cfctl%l_prtctl  = .false. ! 
     478   sn_cfctl%l_prttrc  = .false. ! 
     479   sn_cfctl%l_oasout  = .false. ! 
     480   sn_cfctl%procmin   = 0       ! Minimum area number for reporting [default:0] 
     481   sn_cfctl%procmax   = 1000000 ! Maximum area number for reporting [default:1000000] 
     482   sn_cfctl%procincr  = 1       ! Increment for optional subsetting of areas [default:1] 
     483   sn_cfctl%ptimincr  = 1       ! Timestep increment for writing time step progress info 
     484\end{forlines} 
    500485 
    501486\subinc{\input{../../global/epilogue}} 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_model_basics.tex

    r11693 r14789  
    55\chapter{Model Basics} 
    66\label{chap:MB} 
    7  
    8 \thispagestyle{plain} 
    97 
    108\chaptertoc 
    … …  
    706704In this case, the free surface equation is nonlinear, 
    707705and the variations of volume are fully taken into account. 
    708 These coordinates systems is presented in a report \citep{levier.treguier.ea_rpt07} available on 
     706These coordinates systems is presented in a report \citep{levier.treguier.ea_trpt07} available on 
    709707the \NEMO\ web site. 
    710708 
    … …  
    841839This problem can be at least partially overcome by mixing $s$-coordinate and 
    842840step-like representation of bottom topography 
    843 \citep{gerdes_JGR93*a,gerdes_JGR93*b,madec.delecluse.ea_JPO96}. 
     841\citep{gerdes_JGR93,gerdes_JGR93*a,madec.delecluse.ea_JPO96}. 
    844842However, the definition of the model domain vertical coordinate becomes then a non-trivial thing for 
    845843a realistic bottom topography: 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex

    r11693 r14789  
    44 
    55\chapter{ essai \zstar \sstar} 
    6  
    7 \thispagestyle{plain} 
    86 
    97\chaptertoc 
    … …  
    3028 
    3129In that case, the free surface equation is nonlinear, and the variations of volume are fully taken into account. 
    32 These coordinates systems is presented in a report \citep{levier.treguier.ea_rpt07} available on the \NEMO\ web site. 
     30These coordinates systems is presented in a report \citep{levier.treguier.ea_trpt07} available on the \NEMO\ web site. 
    3331 
    3432\colorbox{yellow}{  end of to be updated} 
    … …  
    8583 
    8684%\nlst{nam_dynspg} 
     85 
    8786Options are defined through the \nam{_dynspg}{\_dynspg} namelist variables. 
    8887The surface pressure gradient term is related to the representation of the free surface (\autoref{sec:MB_hor_pg}). 
    … …  
    9594which imposes a very small time step when an explicit time stepping is used. 
    9695Two methods are proposed to allow a longer time step for the three-dimensional equations: 
    97 the filtered free surface, which is a modification of the continuous equations %(see \autoref{eq:MB_flt?}), 
     96the filtered free surface, which is a modification of the continuous equations \iffalse (see \autoref{eq:MB_flt?}) \fi , 
    9897and the split-explicit free surface described below. 
    9998The extra term introduced in the filtered method is calculated implicitly, 
    … …  
    170169 
    171170The split-explicit formulation has a damping effect on external gravity waves, 
    172 which is weaker than the filtered free surface but still significant as shown by \citet{levier.treguier.ea_rpt07} in 
     171which is weaker than the filtered free surface but still significant as shown by \citet{levier.treguier.ea_trpt07} in 
    173172the case of an analytical barotropic Kelvin wave. 
    174173 
    … …  
    306305 
    307306In the non-linear free surface formulation, the variations of volume are fully taken into account. 
    308 This option is presented in a report \citep{levier.treguier.ea_rpt07} available on the \NEMO\ web site. 
     307This option is presented in a report \citep{levier.treguier.ea_trpt07} available on the \NEMO\ web site. 
    309308The three time-stepping methods (explicit, split-explicit and filtered) are the same as in 
    310309\autoref{?:DYN_spg_linear?} except that the ocean depth is now time-dependent. 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/NEMO/subfiles/chap_time_domain.tex

    r11693 r14789  
    66\label{chap:TD} 
    77 
    8 \thispagestyle{plain} 
    9  
    108\chaptertoc 
    119 
    … …  
    1412{\footnotesize 
    1513  \begin{tabularx}{0.5\textwidth}{l||X|X} 
    16     Release          & Author(s)                                       & 
     14    Release          & Author(s)                                       &  
    1715    Modifications                                                      \\ 
    1816    \hline 
    19     {\em        4.0} & {\em J\'{e}r\^{o}me Chanut \newline Tim Graham} & 
     17    {\em        4.0} & {\em J\'{e}r\^{o}me Chanut \newline Tim Graham} &  
    2018    {\em Review \newline Update                                      } \\ 
    21     {\em        3.6} & {\em Christian \'{E}th\'{e}                   } & 
     19    {\em        3.6} & {\em Christian \'{E}th\'{e}                   } &  
    2220    {\em Update                                                      } \\ 
    23     {\em $\leq$ 3.4} & {\em Gurvan Madec                             } & 
     21    {\em $\leq$ 3.4} & {\em Gurvan Madec                             } &  
    2422    {\em First version                                               } \\ 
    2523  \end{tabularx} 
    … …  
    4644 
    4745The time stepping used in \NEMO\ is a three level scheme that can be represented as follows: 
     46 
    4847\begin{equation} 
    4948  \label{eq:TD} 
    5049  x^{t + \rdt} = x^{t - \rdt} + 2 \, \rdt \ \text{RHS}_x^{t - \rdt, \, t, \, t + \rdt} 
    5150\end{equation} 
     51 
    5252where $x$ stands for $u$, $v$, $T$ or $S$; 
    5353RHS is the \textbf{R}ight-\textbf{H}and-\textbf{S}ide of the corresponding time evolution equation; 
    … …  
    9999first designed by \citet{robert_JMSJ66} and more comprehensively studied by \citet{asselin_MWR72}, 
    100100is a kind of laplacian diffusion in time that mixes odd and even time steps: 
     101 
    101102\begin{equation} 
    102103  \label{eq:TD_asselin} 
    103104  x_F^t = x^t + \gamma \, \lt[ x_F^{t - \rdt} - 2 x^t + x^{t + \rdt} \rt] 
    104105\end{equation} 
     106 
    105107where the subscript $F$ denotes filtered values and $\gamma$ is the Asselin coefficient. 
    106108$\gamma$ is initialized as \np{rn_atfp}{rn\_atfp} (namelist parameter). 
    … …  
    134136The conditions for stability of second and fourth order horizontal diffusion schemes are 
    135137\citep{griffies_bk04}: 
     138 
    136139\begin{equation} 
    137140  \label{eq:TD_euler_stability} 
    … …  
    142145  \end{cases} 
    143146\end{equation} 
     147 
    144148where $e$ is the smallest grid size in the two horizontal directions and 
    145149$A^h$ is the mixing coefficient. 
    … …  
    153157To overcome the stability constraint, a backward (or implicit) time differencing scheme is used. 
    154158This scheme is unconditionally stable but diffusive and can be written as follows: 
     159 
    155160\begin{equation} 
    156161  \label{eq:TD_imp} 
    … …  
    170175where RHS is the right hand side of the equation except for the vertical diffusion term. 
    171176We rewrite \autoref{eq:TD_imp} as: 
     177 
    172178\begin{equation} 
    173179  \label{eq:TD_imp_mat} 
    174180  -c(k + 1) \; T^{t + 1}(k + 1) + d(k) \; T^{t + 1}(k) - \; c(k) \; T^{t + 1}(k - 1) \equiv b(k) 
    175181\end{equation} 
     182 
    176183where 
     184 
    177185\[ 
    178186  c(k) = A_w^{vT} (k) \, / \, e_{3w} (k) \text{,} \quad 
    … …  
    241249$Q$ is redistributed over several time step. 
    242250In the modified LF-RA environment, these two formulations have been replaced by: 
     251 
    243252\begin{gather} 
    244253  \label{eq:TD_forcing} 
    … …  
    248257                    - \gamma \, \rdt \, \lt( Q^{t + \rdt / 2} - Q^{t - \rdt / 2} \rt) 
    249258\end{gather} 
     259 
    250260The change in the forcing formulation given by \autoref{eq:TD_forcing} 
    251261(see \autoref{fig:TD_MLF_forcing}) has a significant effect: 
    … …  
    377387  % 
    378388\end{flalign*} 
     389 
    379390\begin{flalign*} 
    380391  \allowdisplaybreaks 
    … …  
    389400  % 
    390401\end{flalign*} 
     402 
    391403\begin{flalign*} 
    392404  \allowdisplaybreaks 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/SI3/build

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  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/SI3/main/chapters.tex

    r12377 r14789  
    11\subfile{../subfiles/todolist} 
    2  
    3 \subfile{../subfiles/introduction}               % Introduction 
    42 
    53\subfile{../subfiles/chap_model_basics} 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/SI3/main/settings.tex

    r11591 r14789  
    1 %% Engine (folder name) 
    2 \def \engine{SI3} 
     1%% Engine 
     2\def\eng{SI3} 
    33 
    4 %% Title and cover page settings 
    5 \def \spacetop{  \vspace*{1.2cm} } 
    6 \def \heading{Sea Ice modelling Integrated Initiative (SI$^3$)} 
    7 \def \subheading{The NEMO sea ice engine} 
    8 \def \spacedown{ \vspace*{  1cm} } 
    9 \def \authorswidth{0.2\linewidth} 
    10 \def \rulelenght{230pt} 
    11 \def \abstractwidth{0.65\linewidth} 
     4%% Cover page 
     5\def\spcup{\vspace*{1.20cm}} 
     6\def \hdg{Sea Ice modelling Integrated Initiative (SI$^3$)} 
     7\def\shdg{The NEMO sea ice engine                         } 
     8\def\spcdn{\vspace*{1.00cm}} 
     9\def\autwd{0.20\linewidth}\def\lnlg{230pt}\def\abswd{0.65\linewidth} 
    1210 
    13 %% Color for document (frontpage banner, links and chapter boxes) 
    14 \def \setmanualcolor{ \definecolor{manualcolor}{cmyk}{0, 0, 0, 0.4} } 
     11%% Color in cmyk model for manual theme (frontpage banner, links and chapter boxes) 
     12\def\clr{0.0,0.0,0.0,0.4} 
    1513 
    1614%% IPSL publication number 
    17 \def \ipslnum{31} 
     15\def\ipsl{31} 
    1816 
    19 %% Zenodo ID, i.e. doi:10.5281/zenodo.\([0-9]*\) 
    20 \def \zid{1471689} 
     17%% Zenodo ID, i.e. doi:10.5281/zenodo.\zid 
     18\def\zid{1471689} 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/SI3/namelists/namdyn_adv

    r11703 r14789  
    22&namdyn_adv     !   Ice advection 
    33!------------------------------------------------------------------------------ 
    4    ln_adv_Pra       = .true.         !  Advection scheme (Prather) 
    5    ln_adv_UMx       = .false.          !  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/ 

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    r11026 r14789  
    33!------------------------------------------------------------------------------ 
    44   rn_cio           =   5.0e-03       !  ice-ocean drag coefficient (-) 
    5    rn_blow_s        =   0.66          !  mesure of snow blowing into the leads 
     5   nn_snwfra        =   2             !  calculate the fraction of ice covered by snow (for zdf and albedo) 
     6                                      !     = 0  fraction = 1 (if snow) or 0 (if no snow) 
     7                                      !     = 1  fraction = 1-exp(-0.2*rhos*hsnw) [MetO formulation] 
     8                                      !     = 2  fraction = hsnw / (hsnw+0.02)    [CICE formulation] 
     9   rn_snwblow       =   0.66          !  mesure of snow blowing into the leads 
    610                                      !     = 1 => no snow blowing, < 1 => some snow blowing 
    711   nn_flxdist       =  -1             !  Redistribute heat flux over ice categories 
    … …  
    1216   ln_cndflx        = .false.         !  Use conduction flux as surface boundary conditions (i.e. for Jules coupling) 
    1317      ln_cndemulate = .false.         !     emulate conduction flux (if not provided in the inputs) 
     18   nn_qtrice        =   1             !  Solar flux transmitted thru the surface scattering layer: 
     19                                      !     = 0  Grenfell and Maykut 1977 (depends on cloudiness and is 0 when there is snow)  
     20                                      !     = 1  Lebrun 2019 (equals 0.3 anytime with different melting/dry snw conductivities) 
    1421/ 

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        1310*.out 
        1411*.pdf 
         12*.pyg 
         13*.tdo 
        1514*.toc 
        16 _minted-* 
         15*.xdv 
         16cache* 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/TOP/main/bibliography.bib

    • Property svn:eol-style set to native
    r11171 r14789  
    185185  journal   = {Global Biogeochemical Cycles}, 
    186186  publisher = {American Geophysical Union (AGU)} 
     187} 
     188 
     189@techreport{      gibson_trpt86, 
     190  title         = "Standards for software development and maintenance", 
     191  pages         = "21", 
     192  series        = "ECMWF Technical Memoranda", 
     193  number        = "120", 
     194  author        = "J. K. Gibson", 
     195  institution   = "ECMWF Operations Department; Reading, United Kingdom", 
     196  year          = "1986", 
     197  month         = "aug", 
     198  doi           = "10.21957/gi113q4gn" 
    187199} 
    188200 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/TOP/main/chapters.tex

    r12377 r14789  
    1 \subfile{../subfiles/introduction} 
    21\subfile{../subfiles/model_description} 
    32\subfile{../subfiles/model_setup} 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/TOP/main/settings.tex

    r11591 r14789  
    1 %% Engine (folder name) 
    2 \def \engine{TOP} 
     1%% Engine 
     2\def\eng{TOP} 
    33 
    4 %% Title and cover page settings 
    5 \def \spacetop{  \vspace*{1.3cm} } 
    6 \def \heading{Tracers in Ocean Paradigm (TOP)} 
    7 \def \subheading{The NEMO passive tracers engine} 
    8 \def \spacedown{ \vspace*{  1cm} } 
    9 \def \authorswidth{0.15\linewidth} 
    10 \def \rulelenght{110pt} 
    11 \def \abstractwidth{0.7\linewidth} 
     4%% Cover page 
     5\def\spcup{\vspace*{1.30cm}} 
     6\def \hdg{Tracers in Ocean Paradigm (TOP)} 
     7\def\shdg{The NEMO passive tracers engine} 
     8\def\spcdn{\vspace*{1.00cm}} 
     9\def\autwd{0.15\linewidth}\def\lnlg{110pt}\def\abswd{0.70\linewidth} 
    1210 
    13 %% Color for document (frontpage banner, links and chapter boxes) 
    14 \def \setmanualcolor{ \definecolor{manualcolor}{cmyk}{1, 0, 1, .4} } 
     11%% Color in cmyk model for manual theme (frontpage banner, links and chapter boxes) 
     12\def\clr{1.0,0.0,1.0,0.4} 
    1513 
    1614%% IPSL publication number 
    17 \def \ipslnum{28} 
     15\def\ipsl{28} 
    1816 
    19 %% Zenodo ID, i.e. doi:10.5281/zenodo.\([0-9]*\) 
    20 \def \zid{1471700} 
     17%% Zenodo ID, i.e. doi:10.5281/zenodo.\zid 
     18\def\zid{1471700} 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/TOP/subfiles

    • Property svn:ignore

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        old new  
         1*.aux 
         2*.bbl 
         3*.blg 
         4*.fdb* 
         5*.fls 
         6*.idx 
        17*.ilg 
        28*.ind 
         9*.lo* 
         10*.out 
         11*.pdf 
         12*.pyg 
         13*.tdo 
         14*.toc 
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  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/TOP/subfiles/miscellaneous.tex

    r11591 r14789  
    2424% 
    2525\begin{minted}{bash} 
    26     bld::tool::fppkeys   key_iomput key_mpp_mpi key_top 
     26    bld::tool::fppkeys   key_xios key_top 
    2727\end{minted} 
    2828 
    … …  
    4242% 
    4343\begin{minted}{bash} 
    44    bld::tool::fppkeys   key_iomput key_mpp_mpi key_top 
     44   bld::tool::fppkeys   key_xios key_top 
    4545 
    4646   src::MYBGC::initialization         <MYBGCPATH>/initialization 
    … …  
    6060%Note that, the additional lines specific for the BGC model source and build paths, can be written into a separate file, e.g. named MYBGC.fcm, and then simply included in the cpp_NEMO_MYBGC.fcm as follow 
    6161% 
    62 %bld::tool::fppkeys  key_zdftke key_dynspg_ts key_iomput key_mpp_mpi key_top 
     62%bld::tool::fppkeys  key_zdftke key_dynspg_ts key_xios key_top 
    6363%inc <MYBGCPATH>/MYBGC.fcm 
    6464%This will enable a more portable compilation structure for all MYBGC related configurations. 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/TOP/subfiles/model_description.tex

    r11694 r14789  
    11\documentclass[../main/TOP_manual]{subfiles} 
     2 
     3\begin{document} 
    24 
    35\newcommand{\cd}{\mathrm{CO_2}} 
    … …  
    79\newcommand{\Dcq}{\Delta ^{14}\mathrm{C}} 
    810\newcommand{\Rq}{\mathrm{^{14}{R}}} 
    9 \newcommand{\CODE}[1]{\textsc{#1}} 
    10 %\newcommand{\CODE}[1]{\textcolor{black}{\textsc{#1}}\xspace} 
    11  
    12 \begin{document} 
    1311 
    1412\chapter{Model Description} 
    … …  
    2826where expressions of $D^{lC}$ and $D^{vC}$ depend on the choice for the lateral and vertical subgrid scale parameterizations, see equations 5.10 and 5.11 in \citep{nemo_manual} 
    2927 
    30 {S(C)} , the first term on the right hand side of \ref{Eq_tracer}; is the SMS - Source Minus Sink - inherent to the tracer.  In the case of biological tracer such as phytoplankton, {S(C)} is the balance between phytoplankton growth and its decay through mortality and grazing. In the case of a tracer comprising carbon,  {S(C)} accounts for gas exchange, river discharge, flux to the sediments, gravitational sinking and other biological processes. In the case of a radioactive tracer, {S(C)} is simply loss due to radioactive decay. 
    31  
    32 The second term (within brackets) represents the advection of the tracer in the three directions. It can be interpreted as the budget between the incoming and outgoing tracer fluxes in a volume $T$-cells $b_t= e_{1t}\,e_{2t}\,e_{3t}$ 
     28{S(C)} , the first term on the right hand side of \autoref{Eq_tracer}; is the SMS - Source Minus Sink - inherent to the tracer. 
     29In the case of biological tracer such as phytoplankton, {S(C)} is the balance between phytoplankton growth and its decay through mortality and grazing. 
     30In the case of a tracer comprising carbon,  {S(C)} accounts for gas exchange, river discharge, flux to the sediments, gravitational sinking and other biological processes. 
     31In the case of a radioactive tracer, {S(C)} is simply loss due to radioactive decay. 
     32 
     33The second term (within brackets) represents the advection of the tracer in the three directions. 
     34It can be interpreted as the budget between the incoming and outgoing tracer fluxes in a volume $T$-cells $b_t= e_{1t}\,e_{2t}\,e_{3t}$ 
    3335 
    3436The third term  represents the change due to lateral diffusion. 
    … …  
    4648\label{sec:TopInt} 
    4749 
    48 TOP is the NEMO hardwired interface toward biogeochemical models and provide the physical constraints/boundaries for oceanic tracers. It consists of a modular framework to handle multiple ocean tracers, including also a variety of built-in modules. 
     50TOP is the NEMO hardwired interface toward biogeochemical models and provide the physical constraints/boundaries for oceanic tracers. 
     51It consists of a modular framework to handle multiple ocean tracers, including also a variety of built-in modules. 
    4952 
    5053This component of the NEMO framework allows one to exploit available modules  and further develop a range of applications, spanning from the implementation of a dye passive tracer to evaluate dispersion processes (by means of MY\_TRC), track water masses age (AGE module), assess the ocean interior penetration of persistent chemical compounds (e.g., gases like CFC or even PCBs), up to the full set of equations involving marine biogeochemical cycles. 
    … …  
    6164        \item \textbf{AGE}     :    Water age tracking 
    6265        \item \textbf{MY\_TRC}  :   Template for creation of new modules and external BGC models coupling 
    63         \item \textbf{PISCES}    :   Built in BGC model. See \citep{aumont_2015} for a throughout description. 
     66        \item \textbf{PISCES}    :   Built in BGC model. 
     67See \citep{aumont_2015} for a throughout description. 
    6468\end{itemize} 
    6569%  ---------------------------------------------------------- 
    … …  
    6973The passive tracer transport component  shares the same advection/diffusion routines with the dynamics, with specific treatment of some features like the surface boundary conditions, or the positivity of passive tracers concentrations. 
    7074 
    71  \subsection{ Advection} 
     75\subsection{Advection} 
    7276%------------------------------------------namtrc_adv---------------------------------------------------- 
    7377\nlst{namtrc_adv} 
    7478%------------------------------------------------------------------------------------------------------------- 
    75 The advection schemes used for the passive tracers are the same than the ones for $T$ and $S$ and described in section 5.1 of \citep{nemo_manual}. The choice of an advection scheme  can be selected independently and  can differ from the ones used for active tracers. This choice is made in the \textit{namtrc\_adv} namelist, by  setting to \textit{true} one and only one of the logicals \textit{ln\_trcadv\_xxx}, the same way of what is done for dynamics. 
    76 cen2, MUSCL2, and UBS are not \textit{positive} schemes meaning that negative values can appear in an initially strictly positive tracer field which is advected, implying that false extrema are permitted. Their use is not recommended on passive tracers 
    77  
    78  \subsection{ Lateral diffusion} 
     79The advection schemes used for the passive tracers are the same than the ones for $T$ and $S$ and described in section 5.1 of \citep{nemo_manual}. 
     80The choice of an advection scheme  can be selected independently and  can differ from the ones used for active tracers. 
     81This choice is made in the \textit{namtrc\_adv} namelist, by  setting to \textit{true} one and only one of the logicals \textit{ln\_trcadv\_xxx}, the same way of what is done for dynamics. 
     82cen2, MUSCL2, and UBS are not \textit{positive} schemes meaning that negative values can appear in an initially strictly positive tracer field which is advected, implying that false extrema are permitted. 
     83Their use is not recommended on passive tracers 
     84 
     85\subsection{Lateral diffusion} 
    7986%------------------------------------------namtrc_ldf---------------------------------------------------- 
    8087\nlst{namtrc_ldf} 
    8188%------------------------------------------------------------------------------------------------------------- 
    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 \nam{namtra_ldf}{namtra\_ldf} namelist for the dynamic described in section 5.2 of \citep{nemo_manual}. 
    83  
     89In 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. 
     90However 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}. 
     91The choice of numerical scheme is then set in the \forcode{&namtra_ldf} namelist for the dynamic described in section 5.2 of \citep{nemo_manual}. 
    8492 
    8593%-----------------We also offers the possibility to increase zonal equatorial diffusion for passive tracers by introducing an enhanced zonal diffusivity coefficent in the equatorial domain which can be defined by the equation below : 
    … …  
    8896%-----------------\end{equation} 
    8997 
    90  \subsection{ Tracer damping} 
     98\subsection{Tracer damping} 
    9199 
    92100%------------------------------------------namtrc_dmp---------------------------------------------------- 
    … …  
    94102%------------------------------------------------------------------------------------------------------------- 
    95103 
    96 The 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 \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. 
    98  
    99  \subsection{ Tracer positivity} 
     104The use of newtonian damping  to climatological fields or observations is also coded, sharing the same routine dans active tracers. 
     105Boolean variables are defined in the namelist\_top\_ref to select the tracers on which restoring is applied 
     106Options are defined through the \nam{trc_dmp}{trc\_dmp} namelist variables. 
     107The restoring term is added when the namelist parameter \np{ln\_trcdmp} is set to true. 
     108The restoring coefficient is a three-dimensional array read in a file, which name is specified by the namelist variable \np{cn\_resto\_tr}. 
     109This netcdf file can be generated using the DMP\_TOOLS tool. 
     110 
     111\subsection{Tracer positivity} 
    100112 
    101113%------------------------------------------namtrc_rad---------------------------------------------------- 
    … …  
    103115%------------------------------------------------------------------------------------------------------------- 
    104116 
    105 Sometimes, 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 \nam{namtrc_rad}{namtrc\_rad} by setting the parameter \np{ln\_trcrad}  to true. 
     117Sometimes, numerical scheme can generates negative values of passive tracers concentration that must be positive. 
     118For exemple,  isopycnal diffusion can created extrema. 
     119The 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. 
     120The treatment of negative concentrations is an option and can be selected in the namelist \nam{trc_rad}{trc\_rad} by setting the parameter \np{ln\_trcrad}  to true. 
    107121 
    108122\section{The SMS modules} 
    … …  
    119133%---------------------------------------------------------------------------------------------------------- 
    120134 
    121  
    122  An `ideal age' tracer is integrated online in TOP when \textit{ln\_age} = \texttt{.true.} in namelist \textit{namtrc}. This tracer marks the length of time in units of years that fluid has spent in the interior of the ocean, insulated from exposure to the atmosphere. Thus, away from the surface for $z<-H_{\mathrm{Age}}$ where $H_{\mathrm{Age}}$ is specified by the \textit{namage} namelist variable \textit{rn\_age\_depth}, whose default value is 10~m, there is a source $\mathrm{SMS_{\mathrm{Age}}}$ of the age tracer $A$: 
     135An `ideal age' tracer is integrated online in TOP when \textit{ln\_age} = \texttt{.true.} in namelist \textit{namtrc}. 
     136This tracer marks the length of time in units of years that fluid has spent in the interior of the ocean, insulated from exposure to the atmosphere. 
     137Thus, away from the surface for $z<-H_{\mathrm{Age}}$ where $H_{\mathrm{Age}}$ is specified by the \textit{namage} namelist variable \textit{rn\_age\_depth}, whose default value is 10~m, there is a source $\mathrm{SMS_{\mathrm{Age}}}$ of the age tracer $A$: 
     138 
    123139\begin{equation} 
    124140  \label{eq:TOP-age-interior} 
    125141  \mathrm{SMS_{\mathrm{Age}}} = 1 \mathrm{yr}\;^{-1} = 1/T_{\mathrm{year}}, 
    126  \end{equation} 
    127  where the length of the current year $T_{\mathrm{year}} = 86400*N_{\mathrm{days\;in\;current\; year}}\;\mathrm{s}$, where $N_{\mathrm{days\;in\;current\; year}}$ may be 366 or 365 depending on whether the current year is a leap year or not. 
    128  Near the surface, for $z>-H_{\mathrm{Age}}$, ideal age is relaxed back to zero: 
     142\end{equation} 
     143 
     144where the length of the current year $T_{\mathrm{year}} = 86400*N_{\mathrm{days\;in\;current\; year}}\;\mathrm{s}$, where $N_{\mathrm{days\;in\;current\; year}}$ may be 366 or 365 depending on whether the current year is a leap year or not. 
     145Near the surface, for $z>-H_{\mathrm{Age}}$, ideal age is relaxed back to zero: 
     146 
    129147\begin{equation} 
    130148  \label{eq:TOP-age-surface} 
    131149   \mathrm{SMS_{\mathrm{Age}}} = -\lambda_{\mathrm{Age}}A, 
    132  \end{equation} 
    133  where the relaxation rate $\lambda_{\mathrm{Age}}$  (units $\mathrm{s}\;^{-1}$) is specified by the \textit{namage} namelist variable \textit{rn\_age\_kill\_rate} and has a default value of 1/7200~s. Since this relaxation is applied explicitly, this relaxation rate in principle should not exceed $1/\Delta t$, where $\Delta t$ is the time step used to step forward passive tracers (2 * \textit{nn\_dttrc * rn\_rdt} when the default  leapfrog time-stepping scheme is employed). 
    134  
    135  Currently the 1-dimensional reference depth of the grid boxes is used rather than the dynamically evolving depth to determine whether the age tracer is incremented or relaxed to zero. This means that the tracer only works correctly in z-coordinates. To ensure that the forcing is independent of the level thicknesses, where the tracer cell at level $k$ has its upper face $z=-depw(k)$ above the depth $-H_{\mathrm{Age}}$, but its lower face $z=-depw(k+1)$ below that depth, then the age source 
    136  \begin{equation} 
     150\end{equation} 
     151 
     152where the relaxation rate $\lambda_{\mathrm{Age}}$  (units $\mathrm{s}\;^{-1}$) is specified by the \textit{namage} namelist variable \textit{rn\_age\_kill\_rate} and has a default value of 1/7200~s. 
     153Since this relaxation is applied explicitly, this relaxation rate in principle should not exceed $1/\Delta t$, where $\Delta t$ is the time step used to step forward passive tracers (2 * \textit{nn\_dttrc * rn\_rdt} when the default  leapfrog time-stepping scheme is employed). 
     154 
     155Currently the 1-dimensional reference depth of the grid boxes is used rather than the dynamically evolving depth to determine whether the age tracer is incremented or relaxed to zero. 
     156This means that the tracer only works correctly in z-coordinates. 
     157To ensure that the forcing is independent of the level thicknesses, where the tracer cell at level $k$ has its upper face $z=-depw(k)$ above the depth $-H_{\mathrm{Age}}$, but its lower face $z=-depw(k+1)$ below that depth, then the age source 
     158 
     159\begin{equation} 
    137160  \label{eq:TOP-age-mixed} 
    138161   \mathrm{SMS_{\mathrm{Age}}} = -f_{\mathrm{kill}}\lambda_{\mathrm{Age}}A +f_{\mathrm{add}}/T_{\mathrm{year}} , 
    139  \end{equation} 
    140  where 
    141  \begin{align} 
     162\end{equation} 
     163 
     164where 
     165 
     166\begin{align} 
    142167    f_{\mathrm{kill}} &= e3t_k^{-1}(H_{\mathrm{Age}} - depw(k)) , \\ 
    143168    f_{\mathrm{add}} &= 1 - f_{\mathrm{kill}}. 
    144  \end{align} 
    145  
    146  
    147  This implementation was first used in the CORE-II intercomparison runs described e.g.\ in \citet{danabasoglu_2014}. 
     169\end{align} 
     170 
     171 
     172This implementation was first used in the CORE-II intercomparison runs described e.g.\ in \citet{danabasoglu_2014}. 
    148173 
    149174\subsection{Inert carbons tracer} 
    … …  
    155180 
    156181Chlorofluorocarbons 11 and 12 (CFC-11 and CFC-12), and sulfur hexafluoride (SF6), are synthetic chemicals manufactured for industrial and domestic applications from the early 20th century onwards. 
    157 CFC-11 (CCl$_{3}$F) is a volatile liquid at room temperature, and was widely used in refrigeration. CFC-12 (CCl$_{2}$F$_{2}$) is a gas at room temperature, and, like CFC-11, was widely used as a refrigerant, 
    158 and additionally as an aerosol propellant. SF6 (SF$_{6}$) is also a gas at room temperature, with a range of applications based around its property as an excellent electrical insulator (often replacing more toxic alternatives). 
    159 All three are relatively inert chemicals that are both non-toxic and non-flammable, and their wide use has led to their accumulation within the Earth's atmosphere. Large-scale production of CFC-11 and CFC-12 began in the 1930s, while production of SF6 began in the 1950s, and their atmospheric concentration time-histories are shown in Figure \ref{img_cfcatm}. 
     182CFC-11 (CCl$_{3}$F) is a volatile liquid at room temperature, and was widely used in refrigeration. 
     183CFC-12 (CCl$_{2}$F$_{2}$) is a gas at room temperature, and, like CFC-11, was widely used as a refrigerant, 
     184and additionally as an aerosol propellant. 
     185SF6 (SF$_{6}$) is also a gas at room temperature, with a range of applications based around its property as an excellent electrical insulator (often replacing more toxic alternatives). 
     186All three are relatively inert chemicals that are both non-toxic and non-flammable, and their wide use has led to their accumulation within the Earth's atmosphere. 
     187Large-scale production of CFC-11 and CFC-12 began in the 1930s, while production of SF6 began in the 1950s, and their atmospheric concentration time-histories are shown in Figure \autoref{img_cfcatm}. 
    160188As can be seen in the figure, while the concentration of SF6 continues to rise to the present  day, the concentrations of both CFC-11 and CFC-12 have levelled off and declined since around the 1990s. 
    161189These declines have been driven by the Montreal Protocol (effective since August 1989), which has banned the production of CFC-11 and CFC-12 (as well as other CFCs) because of their role in the depletion of 
    162 stratospheric ozone (O$_{3}$), critical in decreasing the flux of ultraviolet radiation to the Earth's surface. Separate to this role in ozone-depletion, all three chemicals are significantly more potent greenhouse gases 
     190stratospheric ozone (O$_{3}$), critical in decreasing the flux of ultraviolet radiation to the Earth's surface. 
     191Separate to this role in ozone-depletion, all three chemicals are significantly more potent greenhouse gases 
    163192than CO$_{2}$ (especially SF6), although their relatively low atmospheric concentrations limit their role in climate change. \\ 
    164193 
    … …  
    171200% This release began in the 1930s for CFC-11 and CFC-12, and the 1950s for SF6, and 
    172201% regularly increasing their atmospheric concentration until the 1090s, 2000s for respectively CFC11, CFC12, 
    173 % and is still increasing, and SF6 (see Figure \ref{img_cfcatm}).  \\ 
     202% and is still increasing, and SF6 (see Figure \autoref{img_cfcatm}).  \\ 
    174203 
    175204The ocean is a notable sink for all three gases, and their relatively recent occurrence in the atmosphere, coupled to the ease of making high precision measurements of their dissolved concentrations, has made them 
    … …  
    177206Because they only enter the ocean via surface air-sea exchange, and are almost completely chemically and biologically inert, their distribution within the ocean interior reveals its ventilation via transport and mixing. 
    178207Measuring the dissolved concentrations of the gases -- as well as the mixing ratios between them -- shows circulation pathways within the ocean as well as water mass ages (i.e. the time since last contact with the 
    179 atmosphere). This feature of the gases has made them valuable across a wide range of oceanographic problems. One use lies in ocean modelling, where they can be used to evaluate the realism of the circulation and 
     208atmosphere). 
     209This feature of the gases has made them valuable across a wide range of oceanographic problems. 
     210One use lies in ocean modelling, where they can be used to evaluate the realism of the circulation and 
    180211ventilation of models, key for understanding the behaviour of wider modelled marine biogeochemistry (e.g. \citep{dutay_2002,palmieri_2015}). \\ 
    181212 
    182 Modelling these gases (henceforth CFCs) in NEMO is done within the passive tracer transport module, TOP, using the conservation state equation \ref{Eq_tracer} 
     213Modelling these gases (henceforth CFCs) in NEMO is done within the passive tracer transport module, TOP, using the conservation state equation \autoref{Eq_tracer} 
    183214 
    184215Advection and diffusion of the CFCs in NEMO are calculated by the physical module, OPA, 
    … …  
    198229\end{eqnarray} 
    199230 
    200 Where $K_{w}$ is the piston velocity (in m~s$^{-1}$), as defined in Equation \ref{equ_Kw}; 
    201 $C_{sat}$ is the saturation concentration of the CFC tracer, as defined in Equation \ref{equ_C_sat}; 
     231Where $K_{w}$ is the piston velocity (in m~s$^{-1}$), as defined in Equation \autoref{equ_Kw}; 
     232$C_{sat}$ is the saturation concentration of the CFC tracer, as defined in Equation \autoref{equ_C_sat}; 
    202233$C_{surf}$ is the local surface concentration of the CFC tracer within the model (in mol~m$^{-3}$); 
    203234and $f_{i}$ is the fractional sea-ice cover of the local ocean (ranging between 0.0 for ice-free ocean, 
    … …  
    211242\end{eqnarray} 
    212243 
    213 Where $Sol$ is the gas solubility in mol~m$^{-3}$~pptv$^{-1}$, as defined in Equation \ref{equ_Sol_CFC}; 
     244Where $Sol$ is the gas solubility in mol~m$^{-3}$~pptv$^{-1}$, as defined in Equation \autoref{equ_Sol_CFC}; 
    214245and $P_{cfc}$ is the atmosphere concentration of the CFC (in parts per trillion by volume, pptv). 
    215246This latter concentration is provided to the model by the historical time-series of \citet{bullister_2017}. 
    … …  
    231262$a$ is a constant re-estimated by \citet{wanninkhof_2014} to 0.251 (in $\frac{cm~h^{-1}}{(m~s^{-1})^{2}}$); 
    232263and $u$ is the 10~m wind speed in m~s$^{-1}$ from either an atmosphere model or reanalysis atmospheric forcing. 
    233 $Sc$ is the Schmidt number, and is calculated as follow, using coefficients from \citet{wanninkhof_2014} (see Table \ref{tab_Sc}). 
     264$Sc$ is the Schmidt number, and is calculated as follow, using coefficients from \citet{wanninkhof_2014} (see Table \autoref{tab_Sc}). 
    234265 
    235266\begin{eqnarray} 
    … …  
    238269\end{eqnarray} 
    239270 
    240 The solubility, $Sol$, used in Equation \ref{equ_C_sat} is calculated in mol~l$^{-1}$~atm$^{-1}$, 
     271The solubility, $Sol$, used in Equation \autoref{equ_C_sat} is calculated in mol~l$^{-1}$~atm$^{-1}$, 
    241272and is specific for each gas. 
    242273It has been experimentally estimated by \citet{warner_1985} as a function of temperature 
    … …  
    260291 
    261292Where $T_{X}$ is $\frac{T + 273.16}{100}$, a function of temperature; 
    262 and the $a_{x}$ and $b_{x}$ coefficients are specific for each gas (see Table \ref{tab_ref_CFC}). 
     293and the $a_{x}$ and $b_{x}$ coefficients are specific for each gas (see Table \autoref{tab_ref_CFC}). 
    263294This is then converted to mol~m$^{-3}$~pptv$^{-1}$ assuming a constant atmospheric surface pressure of 1~atm. 
    264295The solubility of CFCs thus decreases with rising $T$ while being relatively insensitive to salinity changes. 
    265 Consequently, this translates to a pattern of solubility where it is greatest in cold, polar regions (see Figure \ref{img_cfcsol}). 
     296Consequently, this translates to a pattern of solubility where it is greatest in cold, polar regions (see Figure \autoref{img_cfcsol}). 
    266297 
    267298% AXY: not 100% sure about the units below; they might be in nanomol, or in seconds or years 
    268299 
    269300The standard outputs of the CFC module are seawater CFC concentrations (in mol~m$^{-3}$), the net air-sea flux (in mol~m$^{-2}$~d$^{-1}$) and the cumulative net air-sea flux (in mol~m$^{-2}$). 
    270 Using XIOS, it is possible to obtain outputs such as the vertical integral of CFC concentrations (in mol~m$^{-2}$; see Figure \ref{img_cfcinv}). 
     301Using XIOS, it is possible to obtain outputs such as the vertical integral of CFC concentrations (in mol~m$^{-2}$; see Figure \autoref{img_cfcinv}). 
    271302This property, when divided by the surface CFC concentration, estimates the local penetration depth (in m) of the CFC. 
    272303 
    … …  
    285316 
    286317\begin{table}[!t] 
    287 \caption{Coefficients for fit of the CFCs solubility (Eq. \ref{equ_Sol_CFC}).} 
     318\caption{Coefficients for fit of the CFCs solubility (Eq. \autoref{equ_Sol_CFC}).} 
    288319\vskip4mm 
    289320\centering 
    … …  
    302333 
    303334\begin{table}[!t] 
    304 \caption{Coefficients for fit of the CFCs Schmidt number (Eq. \ref{equ_Sc}). } 
     335\caption{Coefficients for fit of the CFCs Schmidt number (Eq. \autoref{equ_Sc}). } 
    305336\vskip4mm 
    306337\centering 
    … …  
    353384%---------------------------------------------------------------------------------------------------------- 
    354385 
    355 The C14 package implemented in NEMO by Anne Mouchet models ocean $\Dcq$. It offers several possibilities: $\Dcq$ as a physical tracer of the ocean ventilation (natural $\cq$), assessment of bomb radiocarbon uptake, as well as transient studies of paleo-historical ocean radiocarbon distributions. 
     386The C14 package implemented in NEMO by Anne Mouchet models ocean $\Dcq$. 
     387It offers several possibilities: $\Dcq$ as a physical tracer of the ocean ventilation (natural $\cq$), assessment of bomb radiocarbon uptake, as well as transient studies of paleo-historical ocean radiocarbon distributions. 
    356388 
    357389\subsubsection{Method} 
    358390 
    359  Let  $\Rq$ represent the ratio of $\cq$ atoms to the total number of carbon atoms in the sample, i.e. $\cq/\mathrm{C}$. Then, radiocarbon anomalies are reported as 
     391Let  $\Rq$ represent the ratio of $\cq$ atoms to the total number of carbon atoms in the sample, i.e. $\cq/\mathrm{C}$. 
     392Then, radiocarbon anomalies are reported as 
     393 
    360394\begin{equation} 
    361395\Dcq = \left( \frac{\Rq}{\Rq_\mathrm{ref}} - 1 \right) 10^3, \label{eq:c14dcq} 
    362396\end{equation} 
    363 where $\Rq_{\textrm{ref}}$ is a reference ratio. For the purpose of ocean ventilation studies $\Rq_{\textrm{ref}}$ is set to one. 
     397 
     398where $\Rq_{\textrm{ref}}$ is a reference ratio. 
     399For the purpose of ocean ventilation studies $\Rq_{\textrm{ref}}$ is set to one. 
    364400 
    365401Here we adopt the approach of \cite{fiadeiro_1982} and \cite{toggweiler_1989a,toggweiler_1989b} in which  the ratio $\Rq$ is transported rather than the individual concentrations C and $\cq$. 
    366 This approach calls for a strong assumption, i.e., that of a homogeneous and constant dissolved inorganic carbon (DIC) field \citep{toggweiler_1989a,mouchet_2013}. While in terms of 
    367 oceanic $\Dcq$, it yields similar results to approaches involving carbonate chemistry, it underestimates the bomb radiocarbon inventory because it assumes a constant air-sea $\cd$ disequilibrium (Mouchet, 2013). Yet, field reconstructions of the ocean bomb $\cq$ inventory are also biased low \citep{naegler_2009} since they assume that the anthropogenic perturbation did not affect ocean DIC since the pre-bomb epoch. For these reasons, bomb $\cq$ inventories obtained with the present method are directly comparable to reconstructions based on field measurements. 
    368  
    369 This simplified approach also neglects the effects of fractionation (e.g.,  air-sea exchange) and of biological processes. Previous studies by \cite{bacastow_1990} and \cite{joos_1997} resulted in nearly identical $\Dcq$ distributions among experiments considering biology or not. 
     402This approach calls for a strong assumption, i.e., that of a homogeneous and constant dissolved inorganic carbon (DIC) field \citep{toggweiler_1989a,mouchet_2013}. 
     403While in terms of 
     404oceanic $\Dcq$, it yields similar results to approaches involving carbonate chemistry, it underestimates the bomb radiocarbon inventory because it assumes a constant air-sea $\cd$ disequilibrium (Mouchet, 2013). 
     405Yet, field reconstructions of the ocean bomb $\cq$ inventory are also biased low \citep{naegler_2009} since they assume that the anthropogenic perturbation did not affect ocean DIC since the pre-bomb epoch. 
     406For these reasons, bomb $\cq$ inventories obtained with the present method are directly comparable to reconstructions based on field measurements. 
     407 
     408This simplified approach also neglects the effects of fractionation (e.g.,  air-sea exchange) and of biological processes. 
     409Previous studies by \cite{bacastow_1990} and \cite{joos_1997} resulted in nearly identical $\Dcq$ distributions among experiments considering biology or not. 
    370410Since observed $\Rq$ ratios are corrected for the isotopic fractionation when converted to the standard $\Dcq$ notation \citep{stuiver_1977} the model results are directly comparable to observations. 
    371411 
    … …  
    373413 
    374414The equation governing the transport of $\Rq$  in the ocean is 
     415 
    375416\begin{equation} 
    376417\frac{\partial}{\partial t} {\Rq} =  - \bigtriangledown \cdot ( \mathbf{u} \Rq - \mathbf{K} \cdot \bigtriangledown \Rq )  - \lambda \Rq, \label{eq:quick} 
    377418\end{equation} 
     419 
    378420where $\lambda$ is the radiocarbon decay rate, ${\mathbf{u}}$ the 3-D velocity field, and $\mathbf{K}$ the diffusivity tensor. 
    379421 
    380 At the air-sea interface a Robin boundary condition \citep{haine_2006} is applied to \eqref{eq:quick}, i.e., the flux 
     422At the air-sea interface a Robin boundary condition \citep{haine_2006} is applied to \autoref{eq:quick}, i.e., the flux 
    381423through the interface is proportional to the difference in the ratios between 
    382424the ocean and the atmosphere 
     425 
    383426\begin{equation} 
    384427\mathcal{\!F} =  \kappa_{R}  (\Rq  - \Rq_{a} ), \label{eq:BCR} 
    385428\end{equation} 
    386 where $\mathcal{\!F}$ is the flux out of the ocean, and $\Rq_{a}$ is the atmospheric $\cq/\mathrm{C}$ ratio. The transfer velocity $ \kappa_{R} $ for the radiocarbon ratio in \eqref{eq:BCR} is computed as 
     429 
     430where $\mathcal{\!F}$ is the flux out of the ocean, and $\Rq_{a}$ is the atmospheric $\cq/\mathrm{C}$ ratio. 
     431The transfer velocity $ \kappa_{R} $ for the radiocarbon ratio in \autoref{eq:BCR} is computed as 
     432 
    387433\begin{equation} 
    388434 \kappa_{R} =  \frac{\kappa_{\cd} K_0}{\overline{\Ct}} \, \pacd   \label{eq:Rspeed} 
    389435\end{equation} 
     436 
    390437with $\kappa_{\cd}$ the carbon dioxide transfer or piston velocity, $K_0$ the $\cd$ solubility in seawater, $\pacd$ the atmospheric $\cd$ pressure at sea level, and $\overline{\Ct}$ the average sea-surface dissolved inorganic carbon concentration. 
    391438 
    392  
    393 The $\cd$ transfer velocity is based on the empirical formulation of \cite{wanninkhof_1992} with chemical enhancement \citep{wanninkhof_1996,wanninkhof_2014}. The original formulation is modified to account for the reduction of the  air-sea exchange rate in the presence of sea ice. Hence 
     439The $\cd$ transfer velocity is based on the empirical formulation of \cite{wanninkhof_1992} with chemical enhancement \citep{wanninkhof_1996,wanninkhof_2014}. 
     440The original formulation is modified to account for the reduction of the  air-sea exchange rate in the presence of sea ice. 
     441Hence 
     442 
    394443\begin{equation} 
    395444\kappa_\cd=\left( K_W\,\mathrm{w}^2 + b  \right)\, (1-f_\mathrm{ice})\,\sqrt{660/Sc}, \label{eq:wanc14} 
    396445\end{equation} 
    397446with $\mathrm{w}$ the wind magnitude, $f_\mathrm{ice}$ the fractional ice cover, and $Sc$ the Schmidt number. 
    398 $K_W$ in \eqref{eq:wanc14} is an empirical coefficient with dimension of an inverse velocity. 
     447$K_W$ in \autoref{eq:wanc14} is an empirical coefficient with dimension of an inverse velocity. 
    399448The chemical enhancement term $b$ is represented as a function of temperature $T$ \citep{wanninkhof_1992} 
    400449\begin{equation} 
    … …  
    402451\end{equation} 
    403452 
    404 %We compare the results of equilibrium and transient experiments obtained with both methods in section \ref{sec:UNDEU}. 
     453%We compare the results of equilibrium and transient experiments obtained with both methods in section \autoref{sec:UNDEU}. 
    405454 
    406455% 
    … …  
    413462\label{sec:param} 
    414463 % 
    415 The radiocarbon decay rate (\CODE{rlam14}; in \texttt{trcnam\_c14} module) is set to $\lambda=(1/8267)$ yr$^{-1}$ \citep{stuiver_1977}, which corresponds to a half-life of 5730 yr.\\[1pt] 
    416 % 
    417 The Schmidt number $Sc$, Eq. \eqref{eq:wanc14}, is calculated with the help of the formulation of \cite{wanninkhof_2014}. The $\cd$ solubility $K_0$ in \eqref{eq:Rspeed} is taken from \cite{weiss_1974}. $K_0$ and $Sc$ are computed with the OGCM temperature and salinity fields (\texttt{trcsms\_c14} module).\\[1pt] 
     464The radiocarbon decay rate (\forcode{rlam14}; in \texttt{trcnam\_c14} module) is set to $\lambda=(1/8267)$ yr$^{-1}$ \citep{stuiver_1977}, which corresponds to a half-life of 5730 yr.\\[1pt] 
     465% 
     466The Schmidt number $Sc$, Eq. \autoref{eq:wanc14}, is calculated with the help of the formulation of \cite{wanninkhof_2014}. 
     467The $\cd$ solubility $K_0$ in \autoref{eq:Rspeed} is taken from \cite{weiss_1974}. $K_0$ and $Sc$ are computed with the OGCM temperature and salinity fields (\texttt{trcsms\_c14} module).\\[1pt] 
    418468% 
    419469The following parameters intervening in the air-sea exchange rate are set in \texttt{namelist\_c14}: 
     470 
    420471\begin{itemize} 
    421 \item The reference DIC concentration $\overline{\Ct}$ (\CODE{xdicsur}) intervening in \eqref{eq:Rspeed} is classically set to 2 mol m$^{-3}$ \citep{toggweiler_1989a,orr_2001,butzin_2005}. 
    422 % 
    423 \item The value of the empirical coefficient $K_W$ (\CODE{xkwind}) in \eqref{eq:wanc14} depends on the wind field and on the model upper ocean mixing rate \citep{toggweiler_1989a,wanninkhof_1992,naegler_2009,wanninkhof_2014}. 
     472\item The reference DIC concentration $\overline{\Ct}$ (\forcode{xdicsur}) intervening in \autoref{eq:Rspeed} is classically set to 2 mol m$^{-3}$ \citep{toggweiler_1989a,orr_2001,butzin_2005}. 
     473% 
     474\item The value of the empirical coefficient $K_W$ (\forcode{xkwind}) in \autoref{eq:wanc14} depends on the wind field and on the model upper ocean mixing rate \citep{toggweiler_1989a,wanninkhof_1992,naegler_2009,wanninkhof_2014}. 
    424475It should be adjusted so that the globally averaged $\cd$ piston velocity is $\kappa_\cd = 16.5\pm 3.2$ cm/h \citep{naegler_2009}. 
    425 %The sensitivity to this parametrization is discussed in section \ref{sec:result}. 
    426 % 
    427 \item Chemical enhancement (term $b$  in Eq. \ref{eq:wanchem}) may be set on/off by means of the logical variable \CODE{ln\_chemh}. 
     476%The sensitivity to this parametrization is discussed in section \autoref{sec:result}. 
     477% 
     478\item Chemical enhancement (term $b$  in Eq. \autoref{eq:wanchem}) may be set on/off by means of the logical variable \forcode{ln\_chemh}. 
    428479\end{itemize} 
    429480 
    430481% 
    431482\paragraph{Experiment type} 
    432 The type of experiment is determined by the value given to \CODE{kc14typ} in \texttt{namelist\_c14}. There are three possibilities: 
     483The type of experiment is determined by the value given to \forcode{kc14typ} in \texttt{namelist\_c14}. 
     484There are three possibilities: 
     485 
    433486\begin{enumerate} 
    434 \item natural $\Dcq$: \CODE{kc14typ}=0 
    435 \item bomb $\Dcq$: \CODE{kc14typ}=1 
    436 \item transient paleo-historical $\Dcq$: \CODE{kc14typ}=2 
     487\item natural                    $\Dcq$: \forcode{kc14typ}=0 
     488\item bomb                       $\Dcq$: \forcode{kc14typ}=1 
     489\item transient paleo-historical $\Dcq$: \forcode{kc14typ}=2 
    437490\end{enumerate} 
    438 % 
     491 
     492%  
    439493\textbf{Natural or Equilibrium radiocarbon} 
    440 \CODE{kc14typ}=0 
    441  
    442 Unless otherwise specified in \texttt{namelist\_c14}, the atmospheric $\Rq_a$ (\CODE{rc14at}) is set to one, the atmospheric $\cd$ (\CODE{pco2at}) to 280 ppm, and the ocean $\Rq$ is initialized with \CODE{rc14init=0.85}, i.e., $\Dcq=$-150\textperthousand  \cite[typical for deep-ocean, Fig 6 in][]{key_2004}. 
    443  
    444 Equilibrium experiment should last until 98\% of the ocean volume exhibit a drift of less than 0.001\textperthousand/year \citep{orr_2000}; this is usually achieved after few kyr (Fig. \ref{fig:drift}). 
    445 % 
     494\forcode{kc14typ}=0 
     495 
     496Unless otherwise specified in \texttt{namelist\_c14}, the atmospheric $\Rq_a$ (\forcode{rc14at}) is set to one, the atmospheric $\cd$ (\forcode{pco2at}) to 280 ppm, and the ocean $\Rq$ is initialized with \forcode{rc14init=0.85}, i.e., $\Dcq=$-150\textperthousand \cite[typical for deep-ocean, Fig 6 in][]{key_2004}. 
     497 
     498Equilibrium experiment should last until 98\% of the ocean volume exhibit a drift of less than 0.001\textperthousand/year \citep{orr_2000}; this is usually achieved after few kyr (Fig. \autoref{fig:drift}). 
     499% 
     500 
    446501\begin{figure}[!h] 
    447502\begin{center} 
    … …  
    449504\end{center} 
    450505\vspace{-4ex} 
    451 \caption{ Time evolution of $\Rq$ inventory anomaly for equilibrium run with homogeneous ocean initial state. The anomaly (or drift) is given in \%  change in total ocean inventory per 50 years. Time on x-axis is in simulation year.\label{fig:drift} } 
     506\caption{ Time evolution of $\Rq$ inventory anomaly for equilibrium run with homogeneous ocean initial state. 
     507The anomaly (or drift) is given in \%  change in total ocean inventory per 50 years. 
     508Time on x-axis is in simulation year.\label{fig:drift} } 
    452509\end{figure} 
    453510 
    454511\textbf{Transient: Bomb} 
    455512\label{sec:bomb} 
    456 \CODE{kc14typ}=1 
     513\forcode{kc14typ}=1 
    457514 
    458515\begin{figure}[!h] 
    … …  
    461518\end{center} 
    462519\vspace{-4ex} 
    463 \caption{Atmospheric $\Dcq$ (solid; left axis) and $\cd$ (dashed; right axis)  forcing for the $\cq$-bomb experiments. The $\Dcq$ is illustrated for the three zonal bands (upper, middle, and lower curves correspond to latitudes $> 20$N, $\in [20\mathrm{S},20\mathrm{N}]$, and $< 20$S, respectively.} \label{fig:bomb} 
     520\caption{Atmospheric $\Dcq$ (solid; left axis) and $\cd$ (dashed; right axis)  forcing for the $\cq$-bomb experiments. 
     521The $\Dcq$ is illustrated for the three zonal bands (upper, middle, and lower curves correspond to latitudes $> 20$N, $\in [20\mathrm{S},20\mathrm{N}]$, and $< 20$S, respectively.} \label{fig:bomb} 
    464522\end{figure} 
    465523 
    466 Performing this type of experiment requires that a pre-industrial equilibrium run be performed beforehand (\CODE{ln\_rsttr} should be set to \texttt{.TRUE.}). 
    467  
    468 An exception to this rule is when wishing to perform a perturbation bomb experiment as was possible with the package \texttt{C14b}. It is still possible to easily set-up that type of transient experiment for which no previous run is needed.  In addition to the instructions as given in this section it is however necessary to adapt the \texttt{atmc14.dat} file so that it does no longer contain any negative $\Dcq$ values (Suess effect in the pre-bomb period). 
    469  
    470 The model  is integrated from a given initial date following the observed records provided from 1765 AD on ( Fig. \ref{fig:bomb}). 
    471 The file \texttt{atmc14.dat}  \cite[][\& I. Levin, personal comm.]{enting_1994} provides atmospheric $\Dcq$ for three latitudinal bands: 90S-20S,    20S-20N \&    20N-90N. 
    472 Atmospheric $\cd$ in the file \texttt{splco2.dat} is obtained from a spline fit through ice core data and direct atmospheric measurements \cite[][\& J. Orr, personal comm.]{orr_2000}. 
     524Performing this type of experiment requires that a pre-industrial equilibrium run be performed beforehand (\forcode{ln\_rsttr} should be set to \texttt{.TRUE.}). 
     525 
     526An exception to this rule is when wishing to perform a perturbation bomb experiment as was possible with the package \texttt{C14b}. 
     527It is still possible to easily set-up that type of transient experiment for which no previous run is needed. 
     528In addition to the instructions as given in this section it is however necessary to adapt the \texttt{atmc14.dat} file so that it does no longer contain any negative $\Dcq$ values (Suess effect in the pre-bomb period). 
     529 
     530The model  is integrated from a given initial date following the observed records provided from 1765 AD on ( Fig. \autoref{fig:bomb}). 
     531The file \texttt{atmc14.dat}  \cite[][\& I. 
     532Levin, personal comm.]{enting_1994} provides atmospheric $\Dcq$ for three latitudinal bands: 90S-20S,    20S-20N \&    20N-90N. 
     533Atmospheric $\cd$ in the file \texttt{splco2.dat} is obtained from a spline fit through ice core data and direct atmospheric measurements \cite[][\& J. 
     534Orr, personal comm.]{orr_2000}. 
    473535Dates in these forcing files are expressed as yr AD. 
    474536 
    475537To ensure that the atmospheric forcing is applied properly as well as that output files contain consistent dates and inventories the experiment should be set up carefully: 
     538 
    476539\begin{itemize} 
    477 \item Specify the starting date of the experiment: \CODE{nn\_date0} in \texttt{namelist}.  \CODE{nn\_date0} is written as Year0101 where Year may take any positive value (AD). 
    478 \item Then the parameters \CODE{nn\_rstctl} in  \texttt{namelist} (on-line) and \CODE{nn\_rsttr} in \texttt{namelist\_top} (off-line)  must be \textbf{set to 0} at the start of the experiment (force the date to \CODE{nn\_date0} for the \textbf{first} experiment year). 
    479 \item These two parameters (\CODE{nn\_rstctl} and \CODE{nn\_rsttr}) have then to be \textbf{set to 2} for the following years (the date must be read in the restart file). 
     540\item Specify the starting date of the experiment: \forcode{nn\_date0} in \texttt{namelist}.  \forcode{nn\_date0} is written as Year0101 where Year may take any positive value (AD). 
     541\item Then the parameters \forcode{nn\_rstctl} in  \texttt{namelist} (on-line) and \forcode{nn\_rsttr} in \texttt{namelist\_top} (off-line)  must be \textbf{set to 0} at the start of the experiment (force the date to \forcode{nn\_date0} for the \textbf{first} experiment year). 
     542\item These two parameters (\forcode{nn\_rstctl} and \forcode{nn\_rsttr}) have then to be \textbf{set to 2} for the following years (the date must be read in the restart file). 
    480543\end{itemize} 
    481  If the experiment date is outside the data time span then the first or last atmospheric concentrations are prescribed depending on whether the date is earlier or later. Note that \CODE{tyrc14\_beg} (\texttt{namelist\_c14}) is not used in this context. 
     544 
     545If the experiment date is outside the data time span then the first or last atmospheric concentrations are prescribed depending on whether the date is earlier or later. 
     546Note that \forcode{tyrc14\_beg} (\texttt{namelist\_c14}) is not used in this context. 
    482547 
    483548% 
    484549\textbf{Transient: Past} 
    485 \CODE{kc14typ}=2 
     550\forcode{kc14typ}=2 
    486551% 
    487552\begin{figure}[!h] 
    … …  
    490555\end{center} 
    491556\vspace{-4ex} 
    492 \caption{Atmospheric $\Dcq$ (solid) and $\cd$ (dashed)  forcing for the Paleo experiments. The $\cd$ scale is given on the right axis.} \label{fig:paleo} 
     557\caption{Atmospheric $\Dcq$ (solid) and $\cd$ (dashed)  forcing for the Paleo experiments. 
     558The $\cd$ scale is given on the right axis.} \label{fig:paleo} 
    493559\end{figure} 
    494560 
    495 This experiment type does not need a previous equilibrium run. It should start 5--6 kyr earlier than the period to be analyzed. 
    496 Atmospheric $\Rq_a$ and $\cd$ are prescribed from forcing files. The ocean $\Rq$ is initialized with the value attributed to \CODE{rc14init} in \texttt{namelist\_c14}. 
     561This experiment type does not need a previous equilibrium run. 
     562It should start 5--6 kyr earlier than the period to be analyzed. 
     563Atmospheric $\Rq_a$ and $\cd$ are prescribed from forcing files. 
     564The ocean $\Rq$ is initialized with the value attributed to \forcode{rc14init} in \texttt{namelist\_c14}. 
    497565 
    498566The file \texttt{intcal13.14c} \citep{reimer_2013} contains atmospheric $\Dcq$ from 0 to 50 kyr cal BP\footnote{cal BP: number of years before 1950 AD}. 
    499 The $\cd$ forcing is provided in file \texttt{ByrdEdcCO2.txt}. The content of this file is based on  the high resolution record from EPICA Dome C \citep{monnin_2004} for the Holocene and the Transition, and on Byrd Ice Core CO2 Data for 20--90 kyr BP  \citep{ahn_2008}. These atmospheric values are reproduced in Fig. \ref{fig:paleo}. Dates in these files are expressed as yr BP. 
     567The $\cd$ forcing is provided in file \texttt{ByrdEdcCO2.txt}. 
     568The content of this file is based on  the high resolution record from EPICA Dome C \citep{monnin_2004} for the Holocene and the Transition, and on Byrd Ice Core CO2 Data for 20--90 kyr BP  \citep{ahn_2008}. 
     569These atmospheric values are reproduced in Fig. \autoref{fig:paleo}. 
     570Dates in these files are expressed as yr BP. 
    500571 
    501572To ensure that the atmospheric forcing is applied properly as well as that output files contain consistent dates and inventories the experiment should be set up carefully. 
    502 The true experiment starting date is given by \CODE{tyrc14\_beg} (in yr BP) in \texttt{namelist\_c14}. In consequence, \CODE{nn\_date0} in \texttt{namelist} MUST be set to 00010101.\\ 
    503 Then the parameters \CODE{nn\_rstctl} in  \texttt{namelist} (on-line) and \CODE{nn\_rsttr} in \texttt{namelist\_top} (off-line)  must be set to 0 at the start of the experiment (force the date to \CODE{nn\_date0} for the first experiment year). These two parameters have then to be set to 2 for the following years (read the date in the restart file). \\ 
    504  If the experiment date is outside the data time span then the first or last atmospheric concentrations are prescribed depending on whether the date is earlier or later. 
     573The true experiment starting date is given by \forcode{tyrc14\_beg} (in yr BP) in \texttt{namelist\_c14}. 
     574In consequence, \forcode{nn\_date0} in \texttt{namelist} MUST be set to 00010101.\\ 
     575Then the parameters \forcode{nn\_rstctl} in  \texttt{namelist} (on-line) and \forcode{nn\_rsttr} in \texttt{namelist\_top} (off-line)  must be set to 0 at the start of the experiment (force the date to \forcode{nn\_date0} for the first experiment year). 
     576These two parameters have then to be set to 2 for the following years (read the date in the restart file). \\ 
     577If the experiment date is outside the data time span then the first or last atmospheric concentrations are prescribed depending on whether the date is earlier or later. 
    505578 
    506579% 
    507580\paragraph{Model output} 
    508581\label{sec:output} 
    509 All output fields in Table \ref{tab:out} are routinely computed. It depends on the actual settings in \texttt{iodef.xml} whether they are stored or not. 
     582 
     583All output fields in Table \autoref{tab:out} are routinely computed. 
     584It depends on the actual settings in \texttt{iodef.xml} whether they are stored or not. 
    510585% 
    511586\begin{table}[!h] 
    512587\begin{center} 
    513 \caption{Standard output fields for the C14 package \label{tab:out}. 
    514 } 
     588\caption{Standard output fields for the C14 package \label{tab:out}.} 
    515589%\begin{small} 
    516590\renewcommand{\arraystretch}{1.3}% 
    517591\begin{tabular}[h]{|l*{3}{|c}|l|} 
    518592\hline 
    519 Field & Type & Dim & Units & Description \\ \hline 
    520 RC14 & ptrc & 3-D & -        & Radiocarbon ratio \\ 
    521 DeltaC14 & diad & 3-D & \textperthousand & $\Dcq$\\ 
    522 C14Age & diad & 3-D & yr &   Radiocarbon age \\ 
    523 RAge & diad & 2-D & yr & Reservoir age\\ 
    524 qtr\_c14 &  diad & 2-D & m$^{-2}$ yr$^{-1}$ & Air-to-sea net $\Rq$ flux\\ 
    525 qint\_c14 & diad & 2-D &   m$^{-2}$ &  Cumulative air-to-sea $\Rq$ flux \\ 
    526 AtmCO2 & scalar & 0-D & ppm & Global atmospheric $\cd$ \\ 
    527 AtmC14 & scalar & 0-D & \textperthousand  & Global atmospheric $\Dcq$\\ 
    528 K\_CO2 & scalar & 0-D & cm h$^{-1}$  & Global $\cd$ piston velocity ($ \overline{\kappa_{\cd}}$) \\ 
    529 K\_C14 & scalar & 0-D &m yr$^{-1}$ & Global $\Rq$ transfer velocity  ($ \overline{\kappa_R}$)\\ 
    530 C14Inv & scalar & 0-D & $10^{26}$ atoms & Ocean radiocarbon inventory \\ \hline 
     593Field     & Type   & Dim & Units              & Description                                              \\ \hline 
     594RC14      & ptrc   & 3-D & -                  & Radiocarbon ratio                                        \\ 
     595DeltaC14  & diad   & 3-D & \textperthousand   & $\Dcq$                                                    \\ 
     596C14Age    & diad   & 3-D & yr                 & Radiocarbon age                                          \\ 
     597RAge      & diad   & 2-D & yr                 & Reservoir age                                             \\ 
     598qtr\_c14  & diad   & 2-D & m$^{-2}$ yr$^{-1}$ & Air-to-sea net $\Rq$ flux                                 \\ 
     599qint\_c14 & diad   & 2-D & m$^{-2}$           & Cumulative air-to-sea $\Rq$ flux                          \\ 
     600AtmCO2    & scalar & 0-D & ppm                & Global atmospheric $\cd$                                  \\ 
     601AtmC14    & scalar & 0-D & \textperthousand   & Global atmospheric $\Dcq$                                 \\ 
     602K\_CO2    & scalar & 0-D & cm h$^{-1}$        & Global $\cd$ piston velocity ($ \overline{\kappa_{\cd}}$) \\ 
     603K\_C14    & scalar & 0-D & m yr$^{-1}$        & Global $\Rq$ transfer velocity  ($ \overline{\kappa_R}$)  \\ 
     604C14Inv    & scalar & 0-D & $10^{26}$ atoms    & Ocean radiocarbon inventory                              \\ \hline 
    531605\end{tabular} 
    532606%\end{small} 
    … …  
    539613The radiocarbon age is computed as  $(-1/\lambda) \ln{ \left( \Rq \right)}$, with zero age corresponding to $\Rq=1$. 
    540614 
    541 The reservoir age is the age difference between the ocean uppermost layer and the atmosphere. It is usually reported as conventional radiocarbon age; i.e., computed by means of the Libby radiocarbon mean life \cite[8033 yr;][]{stuiver_1977} 
     615The reservoir age is the age difference between the ocean uppermost layer and the atmosphere. 
     616It is usually reported as conventional radiocarbon age; i.e., computed by means of the Libby radiocarbon mean life \cite[8033 yr;][]{stuiver_1977} 
     617 
    542618\begin{align} 
    543619{^{14}\tau_\mathrm{c}}= -8033 \; \ln \left(1 + \frac{\Dcq}{10^3}\right), \label{eq:convage} 
    544620\end{align} 
    545 where ${^{14}\tau_\mathrm{c}}$ is expressed in years B.P. Here we do not use that convention and compute reservoir ages with the mean lifetime $1/\lambda$. Conversion from one scale to the other is readily performed. The conventional radiocarbon age is lower than the radiocarbon age by $\simeq3\%$. 
     621 
     622where ${^{14}\tau_\mathrm{c}}$ is expressed in years B.P. 
     623Here we do not use that convention and compute reservoir ages with the mean lifetime $1/\lambda$. 
     624Conversion from one scale to the other is readily performed. 
     625The conventional radiocarbon age is lower than the radiocarbon age by $\simeq3\%$. 
    546626 
    547627The ocean radiocarbon  inventory is computed as 
     628 
    548629\begin{equation} 
    549630N_A \Rq_\mathrm{oxa} \overline{\Ct} \left( \int_\Omega \Rq d\Omega \right) /10^{26}, \label{eq:inv} 
    550631\end{equation} 
    551 where $N_A$ is the Avogadro's number ($N_A=6.022\times10^{23}$ at/mol), $\Rq_\mathrm{oxa}$ is the oxalic acid radiocarbon standard \cite[$\Rq_\mathrm{oxa}=1.176\times10^{-12}$;][]{stuiver_1977}, and $\Omega$ is the ocean volume.  Bomb $\cq$ inventories are traditionally reported in units of $10^{26}$ atoms, hence the denominator in \eqref{eq:inv}. 
    552  
    553 All transformations from second to year, and inversely, are performed with the help of the physical constant \CODE{rsiyea} the sideral year length expressed in seconds\footnote{The variable (\CODE{nyear\_len}) which reports the length in days of the previous/current/future year (see \textrm{oce\_trc.F90}) is not a constant. }. 
     632 
     633where $N_A$ is the Avogadro's number ($N_A=6.022\times10^{23}$ at/mol), $\Rq_\mathrm{oxa}$ is the oxalic acid radiocarbon standard \cite[$\Rq_\mathrm{oxa}=1.176\times10^{-12}$;][]{stuiver_1977}, and $\Omega$ is the ocean volume. 
     634Bomb $\cq$ inventories are traditionally reported in units of $10^{26}$ atoms, hence the denominator in \autoref{eq:inv}. 
     635 
     636All transformations from second to year, and inversely, are performed with the help of the physical constant \forcode{rsiyea} the sideral year length expressed in seconds\footnote{The variable (\forcode{nyear\_len}) which reports the length in days of the previous/current/future year (see \textrm{oce\_trc.F90}) is not a constant. }. 
    554637 
    555638The global transfer velocities represent time-averaged\footnote{the actual duration is set in \texttt{iodef.xml}} global integrals of the transfer rates: 
    556  \begin{equation} 
     639 
     640\begin{equation} 
    557641 \overline{\kappa_{\cd}}= \int_\mathcal{S} \kappa_{\cd} d\mathcal{S}  \text{ and } \overline{\kappa_R}= \int_\mathcal{S} \kappa_R d\mathcal{S} 
    558642\end{equation} 
    … …  
    561645\subsection{PISCES biogeochemical model} 
    562646 
    563 PISCES is a biogeochemical model which simulates the lower trophic levels of marine ecosystem (phytoplankton, microzooplankton and mesozooplankton) and the biogeochemical cycles of carbonand of the main nutrients (P, N, Fe, and Si). The  model is intended to be used for both regional and global configurations at high or low spatial resolutions as well as for  short-term (seasonal, interannual) and long-term (climate change, paleoceanography) analyses. 
     647PISCES is a biogeochemical model which simulates the lower trophic levels of marine ecosystem (phytoplankton, microzooplankton and mesozooplankton) and the biogeochemical cycles of carbonand of the main nutrients (P, N, Fe, and Si). 
     648The  model is intended to be used for both regional and global configurations at high or low spatial resolutions as well as for  short-term (seasonal, interannual) and long-term (climate change, paleoceanography) analyses. 
    564649Two versions of PISCES are available in NEMO v4.0 : 
    565650 
    566 PISCES-v2, by setting in namelist\_pisces\_ref  \np{ln\_p4z} to true,  can be seen as one of the many Monod models \citep{monod_1958}. It assumes a constant Redfield ratio and phytoplankton growth depends on the external concentration in nutrients. There are twenty-four prognostic variables (tracers) including two phytoplankton compartments  (diatoms and nanophytoplankton), two zooplankton size-classes (microzooplankton and  mesozooplankton) and a description of the carbonate chemistry. Formulations in PISCES-v2 are based on a mixed Monod/Quota formalism: On one hand, stoichiometry of C/N/P is fixed and growth rate of phytoplankton is limited by the external availability in N, P and Si. On the other hand, the iron and silicium quotas are variable and growth rate of phytoplankton is limited by the internal availability in Fe. Various parameterizations can be activated in PISCES-v2, setting for instance the complexity of iron chemistry or the description of particulate organic materials. 
    567  
    568 PISCES-QUOTA has been built on the PISCES-v2 model described in \citet{aumont_2015}. PISCES-QUOTA has thirty-nine prognostic compartments. Phytoplankton growth can be controlled by five modeled limiting nutrients: Nitrate and Ammonium, Phosphate, Silicate and Iron. Five living compartments are represented: Three phytoplankton size classes/groups corresponding to picophytoplankton, nanophytoplankton and diatoms, and two zooplankton size classes which are microzooplankton and mesozooplankton. For phytoplankton, the prognostic variables are the carbon, nitrogen, phosphorus,  iron, chlorophyll and silicon biomasses (the latter only for diatoms). This means that the N/C, P/C, Fe/C and Chl/C ratios of both phytoplankton groups as well as the Si/C ratio of diatoms are prognostically predicted  by the model. Zooplankton are assumed to be strictly homeostatic \citep[e.g.,][]{sterner_2003,woods_2013,meunier_2014}. As a consequence, the C/N/P/Fe ratios of these groups are maintained constant and are not allowed to vary. In PISCES, the Redfield ratios C/N/P are set to 122/16/1 \citep{takahashi_1985} and the -O/C ratio is set to 1.34 \citep{kortzinger_2001}. No silicified zooplankton is assumed. The bacterial pool is not yet explicitly modeled. 
    569  
    570 There are three non-living compartments: Semi-labile dissolved organic matter, small sinking particles, and large sinking particles. As a consequence of the variable stoichiometric ratios of phytoplankton and of the stoichiometric regulation of zooplankton, elemental ratios in organic matter cannot be supposed constant anymore as that was the case in PISCES-v2. Indeed, the nitrogen, phosphorus, iron, silicon and calcite pools of the particles are now all explicitly modeled. The sinking speed of the particles is not altered by their content in calcite and biogenic silicate (''The ballast effect'', \citep{honjo_1996,armstrong_2001}). The latter particles are assumed to sink at the same speed as the large organic matter particles. All the non-living compartments experience aggregation due to turbulence and differential settling as well as Brownian coagulation for DOM. 
    571  
     651PISCES-v2, by setting in namelist\_pisces\_ref  \np{ln\_p4z} to true,  can be seen as one of the many Monod models \citep{monod_1958}. 
     652It assumes a constant Redfield ratio and phytoplankton growth depends on the external concentration in nutrients. 
     653There are twenty-four prognostic variables (tracers) including two phytoplankton compartments  (diatoms and nanophytoplankton), two zooplankton size-classes (microzooplankton and  mesozooplankton) and a description of the carbonate chemistry. 
     654Formulations in PISCES-v2 are based on a mixed Monod/Quota formalism: On one hand, stoichiometry of C/N/P is fixed and growth rate of phytoplankton is limited by the external availability in N, P and Si. 
     655On the other hand, the iron and silicium quotas are variable and growth rate of phytoplankton is limited by the internal availability in Fe. 
     656Various parameterizations can be activated in PISCES-v2, setting for instance the complexity of iron chemistry or the description of particulate organic materials. 
     657 
     658PISCES-QUOTA has been built on the PISCES-v2 model described in \citet{aumont_2015}. 
     659PISCES-QUOTA has thirty-nine prognostic compartments. 
     660Phytoplankton growth can be controlled by five modeled limiting nutrients: Nitrate and Ammonium, Phosphate, Silicate and Iron. 
     661Five living compartments are represented: Three phytoplankton size classes/groups corresponding to picophytoplankton, nanophytoplankton and diatoms, and two zooplankton size classes which are microzooplankton and mesozooplankton. 
     662For phytoplankton, the prognostic variables are the carbon, nitrogen, phosphorus,  iron, chlorophyll and silicon biomasses (the latter only for diatoms). 
     663This means that the N/C, P/C, Fe/C and Chl/C ratios of both phytoplankton groups as well as the Si/C ratio of diatoms are prognostically predicted  by the model. 
     664Zooplankton are assumed to be strictly homeostatic \citep[e.g.,][]{sterner_2003,woods_2013,meunier_2014}. 
     665As a consequence, the C/N/P/Fe ratios of these groups are maintained constant and are not allowed to vary. 
     666In PISCES, the Redfield ratios C/N/P are set to 122/16/1 \citep{takahashi_1985} and the -O/C ratio is set to 1.34 \citep{kortzinger_2001}. 
     667No silicified zooplankton is assumed. 
     668The bacterial pool is not yet explicitly modeled. 
     669 
     670There are three non-living compartments: Semi-labile dissolved organic matter, small sinking particles, and large sinking particles. 
     671As a consequence of the variable stoichiometric ratios of phytoplankton and of the stoichiometric regulation of zooplankton, elemental ratios in organic matter cannot be supposed constant anymore as that was the case in PISCES-v2. 
     672Indeed, the nitrogen, phosphorus, iron, silicon and calcite pools of the particles are now all explicitly modeled. 
     673The sinking speed of the particles is not altered by their content in calcite and biogenic silicate (''The ballast effect'', \citep{honjo_1996,armstrong_2001}). 
     674The latter particles are assumed to sink at the same speed as the large organic matter particles. 
     675All the non-living compartments experience aggregation due to turbulence and differential settling as well as Brownian coagulation for DOM. 
    572676 
    573677\subsection{MY\_TRC interface for coupling external BGC models} 
    574678\label{Mytrc} 
    575679 
    576 The NEMO-TOP has only one built-in biogeochemical model - PISCES - but there are several BGC models - MEDUSA, ERSEM, BFM or ECO3M - which are meant to be coupled with the NEMO dynamics. Therefore it was necessary to provide to the users a framework for easily add their own BGCM model, that can be a single passive tracer. 
    577 The generalized interface is pivoted on MY\_TRC module that contains template files to build the coupling between NEMO and any external BGC model. The call to MY\_TRC is activated by setting  \textit{ln\_my\_trc} = \texttt{.true.} in namelist \textit{namtrc} 
     680The NEMO-TOP has only one built-in biogeochemical model - PISCES - but there are several BGC models - MEDUSA, ERSEM, BFM or ECO3M - which are meant to be coupled with the NEMO dynamics. 
     681Therefore it was necessary to provide to the users a framework for easily add their own BGCM model, that can be a single passive tracer. 
     682The generalized interface is pivoted on MY\_TRC module that contains template files to build the coupling between NEMO and any external BGC model. 
     683The call to MY\_TRC is activated by setting  \textit{ln\_my\_trc} = \texttt{.true.} in namelist \textit{namtrc} 
    578684 
    579685The following 6 fortran files are available in MY\_TRC with the specific purposes here described. 
    … …  
    581687\begin{itemize} 
    582688   \item \textit{par\_my\_trc.F90} :  This module allows to define additional arrays and public variables to be used within the MY\_TRC interface 
    583    \item \textit{trcini\_my\_trc.F90} :  Here are initialized user defined namelists and the call to the external BGC model initialization procedures to populate general tracer array (trn and trb). Here are also likely to be defined suport arrays related to system metrics that could be needed by the BGC model. 
     689   \item \textit{trcini\_my\_trc.F90} :  Here are initialized user defined namelists and the call to the external BGC model initialization procedures to populate general tracer array (trn and trb). 
     690Here are also likely to be defined suport arrays related to system metrics that could be needed by the BGC model. 
    584691  \item \textit{trcnam\_my\_trc.F90} :  This routine is called at the beginning of trcini\_my\_trc and should contain the initialization of additional namelists for the BGC model or user-defined code. 
    585   \item \textit{trcsms\_my\_trc.F90} :  The routine performs the call to Boundary Conditions and its main purpose is to contain the Source-Minus-Sinks terms due to the biogeochemical processes of the external model. Be aware that lateral boundary conditions are applied in trcnxt routine. IMPORTANT: the routines to compute the light penetration along the water column and the tracer vertical sinking should be defined/called in here, as generalized modules are still missing in the code. 
    586  \item \textit{trcice\_my\_trc.F90} : Here it is possible to prescribe the tracers concentrations in the seaice that will be used as boundary conditions when ice melting occurs (nn\_ice\_tr =1 in namtrc\_ice). See e.g. the correspondent PISCES subroutine. 
    587  \item \textit{trcwri\_my\_trc.F90} : This routine performs the output of the model tracers using IOM module (see Manual Chapter Output and Diagnostics). It is possible to place here the output of additional variables produced by the model, if not done elsewhere in the code, using the call to \textit{iom\_put}. 
     692  \item \textit{trcsms\_my\_trc.F90} :  The routine performs the call to Boundary Conditions and its main purpose is to contain the Source-Minus-Sinks terms due to the biogeochemical processes of the external model. 
     693Be aware that lateral boundary conditions are applied in trcnxt routine. 
     694IMPORTANT: the routines to compute the light penetration along the water column and the tracer vertical sinking should be defined/called in here, as generalized modules are still missing in the code. 
     695 \item \textit{trcice\_my\_trc.F90} : Here it is possible to prescribe the tracers concentrations in the seaice that will be used as boundary conditions when ice melting occurs (nn\_ice\_tr =1 in namtrc\_ice). 
     696See e.g. the correspondent PISCES subroutine. 
     697 \item \textit{trcwri\_my\_trc.F90} : This routine performs the output of the model tracers using IOM module (see Manual Chapter Output and Diagnostics). 
     698It is possible to place here the output of additional variables produced by the model, if not done elsewhere in the code, using the call to \textit{iom\_put}. 
    588699\end{itemize} 
    589  
    590700 
    591701\section{The Offline Option} 
    … …  
    596706%------------------------------------------------------------------------------------------------------------- 
    597707 
    598 Coupling passive tracers offline with NEMO requires precomputed  physical fields from OGCM. Those fields are read from files and interpolated on-the-fly at each model time step 
     708Coupling passive tracers offline with NEMO requires precomputed  physical fields from OGCM. 
     709Those fields are read from files and interpolated on-the-fly at each model time step 
    599710At least the following dynamical parameters should be absolutely passed to the transport : ocean velocities, temperature, salinity, mixed layer depth and for ecosystem models like PISCES, sea ice concentration, short wave radiation at the ocean surface, wind speed (or at least, wind stress). 
    600711The so-called offline mode is useful since it has lower computational costs for example to perform very longer simulations - about 3000 years - to reach equilibrium of CO2 sinks for climate-carbon studies. 
    601712 
    602 The offline interface is located in the code repository : \path{<repository>/src/OFF/}. It is activated by adding the CPP key  \textit{key\_offline} to the CPP keys list. There are two specifics routines for the Offline code : 
     713The offline interface is located in the code repository : \path{<repository>/src/OFF/}. 
     714It is activated by adding the CPP key  \textit{key\_offline} to the CPP keys list. 
     715There are two specifics routines for the Offline code : 
    603716 
    604717\begin{itemize} 
    … …  
    606719   \item \textit{nemogcm.F90} :  a degraded version of the main nemogcm.F90 code of NEMO to manage the time-stepping 
    607720\end{itemize} 
    608  
    609721 
    610722%- 

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    r12377 r14789  
     1%% ================================================================================================= 
     2%% Manual structure 
     3%% ================================================================================================= 
    14 
    2 %% ============================================================================== 
    3 %% Template structure for reference manual 
    4 %% ============================================================================== 
     5%% Preamble: global configuration 
     6%% ================================================================================================= 
    57 
    6 %% NEMO release version 
    7 \def \version{4.0rc~} 
     8%% Layout 
     9\documentclass[fontsize=10pt,twoside,abstract,draft]{scrreprt} 
     10%\documentclass[fontsize=10pt,twoside,abstract      ]{scrreprt} 
    811 
    9 %% Preamble 
    10 %% ============================================================================== 
    11  
    12 %% Document layout 
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    14  
    15 %% Load the configuration of the manual 
    16 \input{../main/definitions} 
    17  
    18 %% Load global *.tex files 
     12%% Overall configuration  
    1913\input{../../global/preamble} 
    2014 
    21 \dominitoc 
    22  
    23 %% Launch the creation of the indexes 
    24 \input{../../global/indexes} 
    25  
    26  
    27 %% End of common preamble between main and sub-files 
    28 %% Override custom cmds for full manual compilation 
    29 \newcommand{\onlyinsubfile}[1]{#1} 
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    3320 
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    3623 
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    38 \renewcommand{\pindex}{} 
     24%% Frontmatter: covers 
     25%% ({sub}title, DOI, authors, abstract and color theme are specific to each manual) 
     26%% ================================================================================================= 
    3927 
     28%\frontmatter %% Not recognized in 'scrreprt' document class 
     29\pagenumbering{gobble}   %% Disable page numbering temporarily 
     30\pagestyle{empty} 
    4031 
    41 %% Frontmatter 
    42 %% ============================================================================== 
    43  
    44 \pagenumbering{gobble} 
    45  
    46 %% Title page 
    4732\input{../../global/frontpage} 
    48  
    49 \maketitle 
    50 \emptythanks 
    51  
    52 %% Information page (2nd page) 
    5333\input{../../global/info_page} 
    5434 
    55 %% Foreword 
    56 %\frontmatter   %% Chapter numbering off and Roman numerals for page numbers 
    57 \pagenumbering{roman} 
    58 \input{foreword} 
     35\cleardoublepage 
    5936 
    60 %% Table of Contents 
     37\pagenumbering{Roman} %% Reactivate page numbering (uppercase roman numbers) 
     38\pagestyle{plain} 
     39%\lastpageref{pagesLTS.0} 
     40 
    6141\tableofcontents 
    6242\listoffigures 
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    6344\listoftables 
    64 \listoflistings 
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     46%\lastpageref{pagesLTS.Roman} 
    6547 
    66 \clearpage 
    67 %\end{document} 
     48\cleardoublepage 
    6849 
     50%% Mainmatter: toc, lists, introduction and primary chapters 
     51%% ================================================================================================= 
    6952 
    70 %% Mainmatter 
    71 %% ============================================================================== 
     53%\mainmatter %% Not recognized in 'scrreprt' document class 
     54\pagenumbering{arabic} %% Standard page numbering 
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    7256 
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    74 \pagenumbering{arabic} 
     57\input{introduction} 
    7558 
    76 \include{chapters} 
     59\cleardoublepage 
    7760 
     61\pagestyle{scrheadings} 
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    7863 
    79 %% Appendix 
    80 %% ============================================================================== 
     64\input{chapters} 
    8165 
    82 %% Chapter numbering is reset with letters now 
    83 \appendix    
     66%% Appendix: subordinate chapters 
     67%% ================================================================================================= 
    8468 
    85 \include{appendices} 
     69\appendix %% Chapter numbering with letters by now 
     70\lohead{Apdx \thechapter\ \leftmark} 
    8671 
     72\input{appendices} 
    8773 
    88 %% Backmatter 
    89 %% ============================================================================== 
     74\input{../../global/coding_rules} %% Add coding rules on every manual 
    9075 
    91 %\backmatter   %% Chapter numbering off 
     76%\lastpageref{pagesLTS.arabic} 
     77\cleardoublepage 
    9278 
    93 %% Bibliography 
    94 \phantomsection 
    95 \addcontentsline{toc}{chapter}{Bibliography} 
    96 \bibliography{../main/bibliography} 
     79%% Backmatter: bibliography, glossaries and indices 
     80%% ================================================================================================= 
    9781 
    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] 
     82%\backmatter %% Not recognized in 'scrreprt' document class 
     83\pagenumbering{roman} %% Lowercase roman numbers 
     84\pagestyle{plain} 
     85 
     86\input{../../global/epilogue} 
     87 
     88%\lastpageref{pagesLTS.roman} 
    10789 
    10890\end{document} 
    109  

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    6 \pretitle{ 
    7   \begin{center} 
    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}} 
    32   \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 } 
     9   \begin{center} 
    4710 
    48 \thanksmarkseries{fnsymbol} 
     11      \begin{minipage}{0.3\textwidth} 
     12         \includegraphics[height=1.5cm]{NEMO_grey} 
     13      \end{minipage} %% Don't insert void line between `minipage` envs 
     14      \begin{minipage}{0.6\textwidth} 
     15         \begin{center} 
     16            \Large\slshape 
     17            \textbf{N}ucleus for \textbf{E}uropean \textbf{M}odelling of the \textbf{O}cean \\ 
     18            \medskip 
     19            \hyperref[resources]{ 
     20               \faWordpress \hspace{1cm} \faCodeFork      \hspace{1cm} 
     21               \faGithub    \hspace{1cm} \faCloudDownload \hspace{1cm} \faEnvelope 
     22            } 
     23         \end{center} 
     24      \end{minipage} 
    4925 
     26   \end{center} 
     27 
     28   \spcup 
     29   \textcolor{white}{\fontsize{0.8cm}{0.8cm}\selectfont\textbf{\hdg}} 
     30   \ifdef{\shdg}{\medskip\par\textcolor{white}{\Huge\shdg}}{} 
     31   \spcdn 
     32 
     33   \begin{center} 
     34      \LARGE Version {\ver} - {\today} \\ 
     35      \medskip 
     36      \href{http://doi.org/10.5281/zenodo.\zid}{\includegraphics{zenodo.\zid}} 
     37   \end{center} 
     38 
     39   \vfill 
     40 
     41   \begin{minipage}{\autwd} 
     42      \raggedleft\input{authors} 
     43   \end{minipage} 
     44   \hspace{15pt} %% Don't insert void line between `minipage` envs 
     45   \begin{minipage}{0.02\linewidth} 
     46      \rule{1pt}{\lnlg} 
     47   \end{minipage} 
     48   \hspace{ 5pt} %%   "     ""    ""   ""     "        ""      "" 
     49   \begin{minipage}{\abswd} 
     50      \begin{abstract} 
     51         \input{abstract} 
     52      \end{abstract} 
     53   \end{minipage} 
     54 
     55   \vfill 
     56 
     57   \begin{center} 
     58      \Large 
     59      \CMCC{\includegraphics[height=1cm]{CMCC}} \hspace{0.25cm} 
     60      \CNRS{\includegraphics[height=1cm]{CNRS}} \hspace{0.25cm} 
     61       \MOI{\includegraphics[height=1cm]{MOI} } \hspace{0.25cm} 
     62      \UKMO{\includegraphics[height=1cm]{UKMO}} \hspace{0.25cm} 
     63      \NERC{\includegraphics[height=1cm]{NERC}}                 \\ 
     64      \medskip 
     65      \slshape 
     66         {C}ommunity \hspace{1.5em} {O}cean \hspace{1.5em} {M}odel 
     67   \end{center} 
     68 
     69\end{titlepage} 
     70 
     71%\restoregeometry 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/global/highlighting.tex

    r12377 r14789  
     1%% ================================================================================================= 
    12%% Syntax highlighting configuration 
    2 %% ============================================================================== 
    3  
    4 \usepackage[outputdir=../build]{minted} 
     3%% ================================================================================================= 
    54 
    65%% Global highlighting style 
    7 \definecolor{bg}{HTML}{f8f8f8} 
     6\definecolor{bg}{HTML}{f8f8f8} %% ? 
    87\usemintedstyle{emacs} 
    9 \setminted{bgcolor=bg, fontsize=\scriptsize, breaklines, frame=leftline} 
    10 \setminted[xml]{style=borland} %% Specific per language 
     8\setminted{bgcolor=bg,fontsize=\scriptsize,breaklines} 
     9\setminted[xml]{style=borland} %% Specific style for XML 
     10 
     11%% Inline 
     12\newmintinline[forcode]{fortran}{bgcolor=,fontsize=auto} %% \forcode{...} 
     13\newmintinline[xmlcode]{xml}{    bgcolor=,fontsize=auto} %% \xmlcode{...} 
     14\newmintinline[snippet]{console}{bgcolor=,fontsize=auto} %% \snippet{...} 
    1115 
    1216%% Oneliner 
    13 \newmint[forline]{fortran}{}   % \forline|...| 
    14 \newmint[xmlline]{xml}{}       % \xmlline|...| 
    15 \newmint[cmd]{console}{}       % \cmd|...| 
     17\newmint[forline]{fortran}{} %% \forline|...| 
     18\newmint[xmlline]{xml    }{} %% \xmlline|...| 
     19\newmint[cmd]{    console}{} %% \cmd|...| 
    1620 
    1721%% Multi-lines 
    18 \newminted[forlines]{fortran}{}   % \begin{forlines} 
    19 \newminted[xmllines]{xml}{}       % \begin{xmllines} 
    20 \newminted[cmds]{console}{}       % \begin{cmds} 
    21 \newminted[clines]{c}{}           % \begin{clines} 
     22\newminted[forlines]{fortran}{} %% \begin{forlines} 
     23\newminted[xmllines]{xml    }{} %% \begin{xmllines} 
     24\newminted[cmds]{    console}{} %% \begin{cmds} 
     25\newminted[clines]{  c      }{} %% \begin{clines} 
    2226 
    23 %% File 
    24 \newmintedfile[forfile]{fortran}{}   % \forfile{../namelists/nam...} 
    25  
    26 %% Inline 
    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{...} 
     27%% File (namelist or module) 
     28\newmintedfile[forfile]{fortran}{} 
    3029 
    3130%% Namelists inclusion 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/global/index.ist

    r12377 r14789  
    11headings_flag 1 
    2 heading_prefix "{\\medskip\\hfill\\large\\textsf{\\textbf{" 
    3 heading_suffix "}}\\hfill}\\medskip\\nopagebreak\n" 
    4  
     2heading_prefix "\\medskip\\hfill\\textnormal{" 
     3heading_suffix "}\\hfill\\smallskip\n" 
    54delim_0 "\\dotfill~" 
    6 delim_1 "\\dotfill~" 
    7 delim_2 "\\dotfill~" 
    8  

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/global/info_page.tex

    r12377 r14789  
     1%% ================================================================================================= 
     2%% Back cover 
     3%% ================================================================================================= 
    14 
    2 \thispagestyle{plain} 
     5%% Disclaimer 
     6%% ================================================================================================= 
    37 
    4 % ================================================================ 
    5 % Disclaimer 
    6 % ================================================================ 
    78\subsubsection*{Disclaimer} 
    89 
    910Like 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 (General Public License). 
     11the \eng\ core engine is developed under the \href{http://www.cecill.info}{CECILL license}, 
     12which is a French adaptation of the GNU GPL (\textbf{G}eneral \textbf{P}ublic \textbf{L}icense). 
    1213Anyone may use it freely for research purposes, and is encouraged to 
    13 communicate back to the NEMO team its own developments and improvements. 
     14communicate back to the development team its own developments and improvements. 
    1415 
    1516The model and the present document have been made available as a service to the community. 
    … …  
    1819Users are encouraged to bring them to our attention. 
    1920 
    20 The authors assume no responsibility for problems, errors, or incorrect usage of NEMO. 
     21The authors assume no responsibility for problems, errors, or incorrect usage of \NEMO. 
    2122 
    22 % ================================================================ 
    23 % External resources 
    24 % ================================================================ 
     23%% External resources 
     24%% ================================================================================================= 
     25 
    2526\subsubsection*{Other resources} 
     27\label{resources} 
    2628 
    2729Additional information can be found on: 
     30 
    2831\begin{itemize} 
    29 \item the \href{http://www.nemo-ocean.eu}{website} of the project detailing several 
    30   associated applications and an exhaustive users bibliography 
    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: 
    36   the \href{http://listes.ipsl.fr/sympa/info/nemo-newsletter}{newsletter} for 
    37   top-down communications from the project 
    38   (announcements, calls, job opportunities, \ldots) 
    39   and the \href{http://listes.ipsl.fr/sympa/info/nemo-forge}{forge updates} 
    40   (commits, tickets and forums) 
     32   \item \faWordpress\ the \href{http://www.nemo-ocean.eu}{website} of the project detailing 
     33      several associated applications and an exhaustive users bibliography 
     34   \item \faCodeFork\ the \href{http://forge.ipsl.jussieu.fr/nemo}{development platform} of 
     35      the model with the code repository for the shared reference and some main resources 
     36      (wiki, ticket system, forums, \ldots) \\ 
     37      \faGithub\ the \href{http://github.com/NEMO-ocean/NEMO-examples} 
     38      {repository of the demonstration cases} for research or training 
     39   \item \faCloudDownload\ the \href{http://zenodo.org/communities/nemo-ocean}{online archive} 
     40      delivering the publications issued by the consortium (manuals, reports, datasets, \ldots) 
     41   \item \faEnvelope\ two mailing lists: 
     42      the \href{http://listes.ipsl.fr/sympa/info/nemo-newsletter}{newsletter} for 
     43      top-down communications from the project (announcements, calls, job opportunities, \ldots) 
     44      and the \href{http://listes.ipsl.fr/sympa/info/nemo-forge}{forge updates} 
     45      (commits, tickets and forums) 
    4146\end{itemize} 
    4247 
    43 % ================================================================ 
    44 % Citation 
    45 % ================================================================ 
     48%% Citation 
     49%% ================================================================================================= 
     50 
    4651\subsubsection*{Citation} 
    4752 
    4853Reference for papers and other publications is as follows: 
    4954 
    50 \vspace{0.5cm} 
     55\medskip 
    5156 
    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,  
    57 Institut Pierre-Simon Laplace (IPSL),  
    58 \href{https://doi.org/10.5281/zenodo.\zid}{doi:10.5281/zenodo.\zid} 
     57\begin{sloppypar} 
     58   ``{\bfseries \hdg}\ifdef{\shdg}{ -- \shdg}{}'', 
     59   {\em Scientific Notes of Climate Modelling Center}, \textbf{\ipsl} --- ISSN 1288-1619, 
     60   Institut Pierre-Simon Laplace (IPSL), 
     61   \href{https://doi.org/10.5281/zenodo.\zid}{doi:10.5281/zenodo.\zid} 
     62\end{sloppypar} 
    5963 
    6064\begin{figure}[b] 
    61   \begin{minipage}[c]{0.72\textwidth} 
    62     \small\ttfamily{Scientific Notes of Climate Modelling Center \\ 
    63       ISSN 1288-1619                                             \\ 
    64       Institut Pierre-Simon Laplace (IPSL) 
    65     } 
    66   \end{minipage} 
    67   \hfill 
    68   \begin{minipage}[c]{0.25\textwidth} 
    69     \href{http://www.cmc.ipsl.fr}{\includegraphics[width=\textwidth]{logos/IPSL_upright}} 
    70   \end{minipage} 
     65 
     66   \begin{minipage}[c]{0.7\textwidth} 
     67      \small 
     68      \ttfamily{ 
     69         Scientific Notes of Climate Modelling Center \\ 
     70         ISSN 1288-1619                               \\ 
     71         Institut Pierre-Simon Laplace (IPSL) 
     72      } 
     73   \end{minipage} 
     74   \hfill %% Don't insert void line between `minipage` envs 
     75   \begin{minipage}[c]{0.25\textwidth} 
     76      \href{http://www.cmc.ipsl.fr}{\includegraphics[width=\textwidth]{IPSL_master}} 
     77   \end{minipage} 
     78 
    7179\end{figure} 
    72  

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/global/new_cmds.tex

    r12377 r14789  
    1 %% Global custom commands: \newcommand{<name>}[<args>][<first argument value>]{<code>} 
    2 %% ============================================================================== 
     1%% ================================================================================================= 
     2%% Global custom commands 
     3%% ================================================================================================= 
    34 
    4 %% Include references and index for compilation of single subfile  
    5 \newcommand{\mtoc}{\minitoc} 
    6 \newcommand{\biblio}{\bibliography{../main/bibliography}} 
    7 \newcommand{\pindex}{\printindex} 
     5%% \newcommand{<name>}[<args>][<first argument value>]{<code>} 
    86 
    9 %% NEMO and Fortran in small capitals 
    10 \newcommand{\NEMO}{\textsc{nemo}~} 
    11 \newcommand{\fortran}{\textsc{Fortran}~} 
    12 \newcommand{\fninety}{\textsc{Fortran 90}~} 
     7%% Same font for NEMO and its core engines 
     8\newcommand{\NEMO   }{\textsl{NEMO}} 
     9\newcommand{\OPA    }{\textsl{OPA}} 
     10\newcommand{\SIcube }{\textsl{SI$^3$}} 
     11\newcommand{\TOP    }{\textsl{TOP}} 
     12\newcommand{\PISCES }{\textsl{PISCES}} 
     13\newcommand{\NEMOVAR}{\textsl{NEMOVAR}} 
     14 
     15%% URL links for consortium institutes and external components 
     16\newcommand{\CMCC }{\href{http://www.cmcc.it}          } 
     17\newcommand{\CNRS }{\href{http://www.cnrs.fr}          } 
     18\newcommand{\MOI  }{\href{http://www.mercator-ocean.fr}} 
     19\newcommand{\UKMO }{\href{http://www.metoffice.gov.uk} } 
     20\newcommand{\NERC }{\href{http://nerc.ukri.org}        } 
     21\newcommand{\AGRIF}{\href{http://agrif.imag.fr                  }{AGRIF}} 
     22\newcommand{\BFM  }{\href{http://bfm-community.eu               }{BFM}} 
     23\newcommand{\CICE }{\href{http://github.com/CICE-Consortium/CICE}{CICE}} 
     24\newcommand{\OASIS}{\href{http://portal.enes.org/oasis          }{OASIS}} 
     25\newcommand{\XIOS }{\href{http://forge.ipsl.jussieu.fr/ioserver }{XIOS}} 
     26 
     27%% Fortran in small capitals 
     28\newcommand{\fortran}{\textsc{Fortran}} 
     29\newcommand{\fninety}{\textsc{Fortran 90}} 
    1330 
    1431%% Common aliases 
    1532\renewcommand{\deg}[1][]{\ensuremath{^{\circ}#1}} 
     33\newcommand{\eg    }{\ensuremath{e.g.}} 
     34\newcommand{\ie    }{\ensuremath{i.e.}} 
    1635\newcommand{\zstar }{\ensuremath{z^\star}} 
    1736\newcommand{\sstar }{\ensuremath{s^\star}} 
    1837\newcommand{\ztilde}{\ensuremath{\tilde z}} 
    1938\newcommand{\stilde}{\ensuremath{\tilde s}} 
    20 \newcommand{\ie}{\ensuremath{i.e.}~} 
    21 \newcommand{\eg}{\ensuremath{e.g.}~} 
    2239 
    23 %% Inline maths 
    24 \newcommand{\fractext}[2]{\textstyle \frac{#1}{#2}} 
     40%% Gurvan's comments 
     41\newcommand{\cmtgm}[1]{} 
     42 
     43%% Maths: reduce equation 
     44\newcommand{\fractext}[2]{\textstyle\frac{#1}{#2}} 
     45\newcommand{\lt}{\left} 
     46\newcommand{\pd}[2][]{\ensuremath{\frac{\partial #1}{\partial #2}}} 
    2547\newcommand{\rdt}{\Delta t} 
     48\newcommand{\rt}{\right} 
     49\newcommand{\vect}[1][]{\ensuremath{\mathbf{#1}}} 
    2650 
    27 %% Text env. for Gurvan 
    28 \newcommand{\gmcomment}[1]{} 
     51%% Retrieve month name 
     52\renewcommand{\today}{ 
     53  \ifcase \month\or   January\or February\or    March\or    April\or 
     54                          May\or     June\or     July\or   August\or 
     55                    September\or  October\or November\or December 
     56  \fi, \number \year 
     57} 
    2958 
    30 %% Maths 
    31 \newcommand{\lt}{\left} 
    32 \newcommand{\rt}{\right} 
    33 \newcommand{\vect}[1]{\ensuremath{\mathbf{#1}}} 
    34 \newcommand{\pd}[2][]{\ensuremath{\frac{\partial #1}{\partial #2}}} 
     59%% Custom aliases 
     60\newcommand{\cf}{\ensuremath{C\kern-0.14em f}} 
     61\newcommand{\rML}[1][i]{\ensuremath{_{\mathrm{ML}\,#1}}} 
     62\newcommand{\rMLt}[1][i]{\tilde{r}_{\mathrm{ML}\,#1}} 
     63\newcommand{\triad}[6][]{\ensuremath{{}_{#2}^{#3}{\mathbb{#4}_{#1}}_{#5}^{\,#6}}} 
     64\newcommand{\triadd}[5]{\ensuremath{{}_{#1}^{#2}{\mathbb{#3}}_{#4}^{\,#5}}} 
     65\newcommand{\triadt}[5]{\ensuremath{{}_{#1}^{#2}{\tilde{\mathbb{#3}}}_{#4}^{\,#5}}} 
     66\newcommand{\rtriad}[2][]{\ensuremath{\triad[#1]{i}{k}{#2}{i_p}{k_p}}} 
     67\newcommand{\rtriadt}[1]{\ensuremath{\triadt{i}{k}{#1}{i_p}{k_p}}} 
    3568 
    36 %% Workaround for issue with \listoffigures 
    37 \DeclareRobustCommand{\triad}[6][]{\ensuremath{{}_{#2}^{#3}{\mathbb{#4}_{#1}}_{#5}^{\,#6}}} 
     69%% New command for ToC (?) 
     70\newcommand{\chaptertoc}[1][Table of contents]{ 
     71  \etocsettocstyle{\addsec*{#1}}{} 
     72  \localtableofcontents 
     73  \vfill 
     74} 
     75 
     76%% ORCID links 
     77\newcommand{\orcid}[1]{\href{http://orcid.org/#1}{\textcolor{orcidclr}\aiOrcidSquare}} 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/global/packages.tex

    r12377 r14789  
     1%% ================================================================================================= 
     2%% Packages 
     3%% ================================================================================================= 
    14 
    2 %% LaTeX packages in use 
    3 %% ============================================================================== 
     5%% Document class 
     6\usepackage[footsepline=0.25pt,headsepline=0.25pt]{scrlayer-scrpage} %% KOMA-script 
    47 
    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 
     8%% Customisation (cover page, chapter headings and mark of draft copy) 
     9\usepackage[margin=2cm]{geometry} %% Why 2cm margin? Load geometry before background! 
     10\usepackage[pages=some]{background} %% 'some' for title page 
     11\usepackage[scale=15,color=pink]{draftwatermark} 
     12\usepackage[Bjornstrup]{fncychap} %% Chapter style 
    1613 
    17 %% Extensions in bundle package 
    18 \usepackage{amssymb, graphicx, tabularx, textcomp} 
    19 \usepackage[utf8]{inputenc}              %% input encoding 
     14%% Fonts 
     15\usepackage{fontspec} 
     16%% Issue with path to 'FontAwesome.otf' 
     17\defaultfontfeatures{Path=/usr/local/texlive/2020/texmf-dist/fonts/opentype/public/fontawesome/} 
     18\usepackage{academicons,fontawesome} 
    2019 
    21 %% Configuration 
    22 \graphicspath{ {../../figures/} {../../figures/\engine/} } 
    23 %\captionsetup{margin=10pt, font={small}, labelsep=colon, labelfont={bf}} 
    24 \renewcommand{\bibfont}{\small} 
    25 %\renewcommand{\bibsep}{3pt} 
     20%% Formatting 
     21\usepackage[inline]{enumitem} 
     22\usepackage{etoc,tabularx,xcolor} 
    2623 
     24%% Graphics 
     25\usepackage{caption} 
     26\graphicspath{{../../../badges/}{../figures/}{../../../logos/}} 
     27 
     28%% Labels 
     29\usepackage{lastpage,natbib} 
     30%\usepackage{natbib,pageslts} 
     31 
     32%% Mathematics: 'amsmath' is loaded by 'mathtools' 
     33\usepackage{mathtools,amssymb} 
     34 
     35%% Versatility 
     36\usepackage{subfiles} 
     37 
     38%% Source code listings 
     39\usepackage[cachedir=cache,outputdir=../build,chapter,newfloat]{minted} 
     40%% chapter? newfloat? 
     41 
     42%% Indexing and cross-referencing, loaded at the end for higher compatibility 
     43\usepackage{hyperref,imakeidx} 
     44 
     45%% Missing utmr8a font 
     46\usepackage{times} 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/global/preamble.tex

    r12377 r14789  
     1%% ================================================================================================= 
     2%% Preamble 
     3%% ================================================================================================= 
    14 
    2 \input{../../global/packages} 
     5\def\ver{trunk} 
     6 
     7%% Specific configuration 
     8\input{../main/settings} 
     9 
     10%% Global configuration 
     11\input{../../global/packages} % First obviously 
     12\input{../../global/styles} % Color definitions 
    313\input{../../global/highlighting} 
     14\input{../../global/indices} 
    415\input{../../global/new_cmds} 
    5 \input{../../global/styles} 
    616%\input{../../global/todonotes} 
    7  
     17%\input{../../global/glossaries} 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/global/styles.tex

    r12377 r14789  
     1%% ================================================================================================= 
     2%% Styles 
     3%% ================================================================================================= 
    14 
    2 %% Styles 
    3 %% ============================================================================== 
     5%% Colors 
     6\definecolor{orcidclr}{HTML}{A6CE39} 
     7\definecolor{manclr}{cmyk}{\clr} %% \clr defined for each manual from local settings.tex 
     8\colorlet{manclrshd}{manclr!60} %% Derived color for chapter heading, see below 
    49 
    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} 
     10%% Cover page 
     11\backgroundsetup{ 
     12   firstpage=true,scale=1,angle=0,opacity=1, 
     13   contents ={ 
     14      \begin{tikzpicture}[remember picture,overlay] 
     15         \path[fill=manclr] (-0.5\paperwidth,7) rectangle (0.5\paperwidth,10); 
     16      \end{tikzpicture} 
     17    } 
     18} 
    1219 
    1320%% Page layout 
    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} 
     21%\pagestyle{scrheadings} 
     22%\renewcommand{\chapterpagestyle}{empty} 
     23\renewcommand{\chaptermark}[1]{\markboth{ #1}{}} %% Convert mark to lowercase 
     24\renewcommand{\sectionmark}[1]{\markright{#1}{}} %%    "     ""  ""     "   
     25\ohead{} %% Clear default headings 
     26\lohead{Chap. \thechapter\  \leftmark} 
     27\rehead{Sect. \thesection\ \rightmark} 
     28\ifoot{Page \thepage\ of \pageref*{LastPage}} 
     29%\ifoot[\pagemark]{Page \thepage\ of \lastpageref*{pagesLTS.arabic}} 
     30\ofoot{\eng\ Reference Manual} 
     31\addtokomafont{pagehead}{  \sffamily              } 
     32\addtokomafont{pagefoot}{  \sffamily \footnotesize} 
     33\addtokomafont{pagenumber}{\sffamily \slshape     } 
     34%\addtokomafont{chapter}{\color{white}} 
    2335 
     36%% Cross-referencing 
     37\hypersetup{ 
     38   pdftitle=\hdg,pdfauthor=Gurvan Madec and NEMO System Team, 
     39   pdfsubject=Reference manual of NEMO modelling framework,pdfkeywords=ocean circulation modelling, 
     40   colorlinks,allcolors=manclr 
     41} 
     42\renewcommand{\appendixautorefname}{appendix}          %% `\autoref` uncapitalization 
     43\renewcommand{\equationautorefname}{equation}          %%     ""            "" 
     44\renewcommand{\figureautorefname  }{figure}            %%     ""            "" 
     45\renewcommand{\listingname        }{namelist}          %%     ""            "" 
     46\renewcommand{\listlistingname    }{List of Namelists} %%     ""            "" 
     47\renewcommand{\tableautorefname   }{table}             %%     ""            "" 
    2448 
    25 %% Catcodes 
    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 
     49%% Misc. (caption and footnote) 
     50\captionsetup{font=footnotesize,justification=justified} 
     51\renewcommand{\thefootnote}{\fnsymbol{footnote}} 
    6052 
     53%% Bibliography 
     54\bibliographystyle{../../global/ametsoc} 
     55\renewcommand{\bibfont}{\small} 
     56\renewcommand{\bibpreamble }{\begin{multicols}{2}} 
     57\renewcommand{\bibpostamble}{  \end{multicols}   } 
    6158 
     59%% Catcodes (between `\makeatletter` and `\makeatother`) 
     60\makeatletter 
     61 
     62%% Apply manual color for chap. headings (original snippets from fncychap.sty) 
     63%% !!! Let trailing percent sign to avoid space insertion 
     64\renewcommand{\DOCH}{% %% Upper box with chapter number 
     65   \settowidth{\py}{\CNoV\thechapter}% 
     66   \addtolength{\py}{-10pt}% %% Amount of space by which the number is shifted right 
     67   \fboxsep=0pt% 
     68   \colorbox{manclr}{\rule{0pt}{40pt}\parbox[b]{\textwidth}{\hfill}}% 
     69   \kern-\py\raise20pt% 
     70   \hbox{\color{manclrshd}\CNoV\thechapter}\\ 
     71} 
     72\renewcommand{\DOTI}[1]{% %% Lower box with chapter title 
     73   \nointerlineskip\raggedright% 
     74   \fboxsep=\myhi% 
     75   \vskip-1ex% 
     76   \colorbox{manclr}{\parbox[t]{\mylen}{\color{white}\CTV\FmTi{#1}}}\par\nobreak% 
     77   \vskip 40\p@% 
     78} 
     79\renewcommand{\DOTIS}[1]{% %% Box for unumbered chapter 
     80   \fboxsep=0pt% 
     81   \colorbox{manclr}{\rule{0pt}{40pt}\parbox[b]{\textwidth}{\hfill}}\\ 
     82   \nointerlineskip\raggedright% 
     83   \fboxsep=\myhi% 
     84   \vskip-1ex% %% Remove white 1pt line 
     85   \colorbox{manclr}{\parbox[t]{\mylen}{\color{white}\CTV\FmTi{#1}}}\par\nobreak% 
     86   \vskip 40\p@% 
     87} 
     88 
     89\makeatother 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/latex/global/todonotes.tex

    r11187 r14789  
    1 \usepackage[]{todonotes} 
     1%% ================================================================================================= 
     2%% Notes 
     3%% ================================================================================================= 
     4 
     5\usepackage{todonotes} 
    26 
    37\newcounter{ubcomment} 
    4 \newcommand{\ubcomment}[2][]{% 
    5 \refstepcounter{ubcomment}% 
    6 {% 
    7 \todo[linecolor=black,backgroundcolor={green!40!},size=\footnotesize]{% 
    8 \textbf{Fixme: UB [\uppercase{#1}\theubcomment]:}~#2}% 
    9 }} 
    10 \newcommand{\ubcommentinline}[2][]{% 
    11 \refstepcounter{ubcomment}% 
    12 {% 
    13 \todo[linecolor=black,inline,backgroundcolor={green!40!},size=\footnotesize]{% 
    14 \textbf{Fixme: UB [\uppercase{#1}\theubcomment]:}~#2}% 
     8 
     9\newcommand{\ubcomment         }[2][]{ 
     10\refstepcounter{ubcomment} 
     11{ 
     12\todo[linecolor=black,       backgroundcolor={green!40!},size=\footnotesize ]{ 
     13\textbf{Fixme: UB [\uppercase{#1}\theubcomment]:}~#2} 
    1514}} 
    1615 
    17 \newcommand{\ubcommentmultiline}[2]{% 
    18 \refstepcounter{ubcomment}% 
    19 {% 
    20 \todo[linecolor=black,inline,caption={\textbf{{Fixme: UB} 
    21     [\theubcomment] #1}} ,backgroundcolor={green!40!},size=\footnotesize]{% 
    22 \textbf{Fixme: UB [\theubcomment]:}~#2}% 
     16\newcommand{\ubcommentinline   }[2][]{ 
     17\refstepcounter{ubcomment} 
     18{ 
     19\todo[linecolor=black,inline,backgroundcolor={green!40!},size=\footnotesize ]{ 
     20\textbf{Fixme: UB [\uppercase{#1}\theubcomment]:}~#2} 
     21}} 
     22 
     23\newcommand{\ubcommentmultiline}[2]{ 
     24\refstepcounter{ubcomment} 
     25{ 
     26\todo[linecolor=black,inline,backgroundcolor={green!40!},size=\footnotesize, 
     27      caption={\textbf{{Fixme: UB} [\theubcomment] #1}}                     ]{ 
     28\textbf{Fixme: UB [              \theubcomment]:}~#2} 
    2329}} 
    2430 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/manual_build.sh

    r11594 r14789  
    2121 
    2222## LaTeX installation, find latexmk should be enough 
    23 [ -z $( which latexmk ) ] && { echo 'latexmk not installed => QUIT'; exit 2; } 
     23[ -z "$( which latexmk )" ] && { echo 'latexmk not installed => QUIT'; exit 2; } 
    2424 
    2525## Pygments package for syntax highlighting of source code (namelists & snippets) 
    2626[ -n "$( ./tools/check_pkg.py pygments )" ] && { echo 'Python pygments is missing => QUIT'; exit 2; } 
    27  
    28 ## Retrieve figures if not already there 
    29 #if [ ! -d latex/figures ]; then 
    30 #    printf "Downloading of shared figures and logos\n\n" 
    31 #    svn co http://forge.ipsl.jussieu.fr/nemo/svn/utils/figures latex/figures > /dev/null 
    32 #fi 
    33  
    3427 
    3528## Loop on the models 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/namelists/nam_tide

    r10075 r14789  
    33!----------------------------------------------------------------------- 
    44   ln_tide     = .false.      ! Activate tides 
    5       ln_tide_pot   = .true.                !  use tidal potential forcing 
     5      nn_tide_var   = 1          !  Variant of tidal parameter set and tide-potential computation 
     6      !                          !     (1: default; 0: compatibility with previous versions) 
     7      ln_tide_dia   = .false.    !  Enable tidal diagnostic output 
     8      ln_tide_pot   = .false.               !  use tidal potential forcing 
     9         rn_tide_gamma = 0.7                   ! Tidal tilt factor 
    610         ln_scal_load  = .false.               ! Use scalar approximation for 
    711            rn_scal_load = 0.094               !     load potential 
    812         ln_read_load  = .false.               ! Or read load potential from file 
    913            cn_tide_load = 'tide_LOAD_grid_T.nc'  ! filename for load potential 
    10             !       
     14            ! 
    1115      ln_tide_ramp  = .false.               !  Use linear ramp for tides at startup 
    12          rdttideramp   =    0.                 !  ramp duration in days 
    13       clname(1)    = 'DUMMY'               !  name of constituent - all tidal components must be set in namelist_cfg 
     16         rn_tide_ramp_dt = 0.               !  ramp duration in days 
     17      sn_tide_cnames(1) = 'DUMMY'               !  name of constituent - all tidal components must be set in namelist_cfg 
    1418/ 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/namelists/nambdy_tide

    r10075 r14789  
    44   filtide          = 'bdydta/amm12_bdytide_'   !  file name root of tidal forcing files 
    55   ln_bdytide_2ddta = .false.                   ! 
    6    ln_bdytide_conj  = .false.                   !  
    76/ 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/namelists/namberg

    r11703 r14789  
    3333   rn_speed_limit          = 0.      ! CFL speed limit for a berg 
    3434 
     35   ln_M2016                = .false. ! use Merino et al. (2016) modification (use of 3d ocean data instead of only sea surface data) 
     36      ln_icb_grd           = .false. ! ground icb when icb bottom level hit oce bottom level (need ln_M2016 to be activated) 
     37 
    3538   cn_dir      = './'      !  root directory for the calving data location 
    3639   !___________!_________________________!___________________!___________!_____________!________!___________!__________________!__________!_______________! 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/namelists/namdyn_rhg

    r13472 r14789  
    33!------------------------------------------------------------------------------ 
    44   ln_rhg_EVP       = .true.          !  EVP rheology 
     5   ln_rhg_EAP       = .false.          !  EAP rheology 
    56      ln_aEVP       = .false.         !     adaptive rheology (Kimmritz et al. 2016 & 2017) 
    67      rn_creepl     =   2.0e-9        !     creep limit [1/s] 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/namelists/nammpp

    r11703 r14789  
    11!----------------------------------------------------------------------- 
    2 &nammpp        !   Massively Parallel Processing                        ("key_mpp_mpi") 
     2&nammpp        !   Massively Parallel Processing 
    33!----------------------------------------------------------------------- 
    44   ln_listonly =  .false.  !  do nothing else than listing the best domain decompositions (with land domains suppression) 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/namelists/namobs

    r11703 r14789  
    2020   ln_sstnight = .false.             ! Logical switch for calculating night-time average for SST obs 
    2121   ln_bound_reject  = .false.        ! Logical to remove obs near boundaries in LAMs. 
     22   ln_default_fp_indegs = .true.     ! Logical: T=> averaging footprint is in degrees, F=> in metres 
    2223   ln_sla_fp_indegs = .true.         ! Logical for SLA: T=> averaging footprint is in degrees, F=> in metres 
    2324   ln_sst_fp_indegs = .true.         ! Logical for SST: T=> averaging footprint is in degrees, F=> in metres 
    … …  
    3940   rn_dobsini  = 00010101.000000     ! Initial date in window YYYYMMDD.HHMMSS 
    4041   rn_dobsend  = 00010102.000000     ! Final date in window YYYYMMDD.HHMMSS 
     42   rn_default_avglamscl = 0.         ! Default E/W diameter of observation footprint (metres/degrees) 
     43   rn_default_avgphiscl = 0.         ! Default N/S diameter of observation footprint (metres/degrees) 
    4144   rn_sla_avglamscl = 0.             ! E/W diameter of SLA observation footprint (metres/degrees) 
    4245   rn_sla_avgphiscl = 0.             ! N/S diameter of SLA observation footprint (metres/degrees) 
    … …  
    4851   rn_sic_avgphiscl = 0.             ! N/S diameter of SIC observation footprint (metres/degrees) 
    4952   nn_1dint = 0                      ! Type of vertical interpolation method 
    50    nn_2dint = 0                      ! Default horizontal interpolation method 
     53   nn_2dint_default = 0              ! Default horizontal interpolation method 
    5154   nn_2dint_sla = 0                  ! Horizontal interpolation method for SLA 
    5255   nn_2dint_sst = 0                  ! Horizontal interpolation method for SST 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/namelists/namrun

    r11703 r14789  
    2626      !                          !    = -1 do not do any restart 
    2727   nn_stocklist = 0,0,0,0,0,0,0,0,0,0 ! List of timesteps when a restart file is to be written 
    28    nn_write    =       0   !  used only if key_iomput is not defined: output frequency (modulo referenced to nn_it000) 
     28   nn_write    =       0   !  used only if key_xios is not defined: output frequency (modulo referenced to nn_it000) 
    2929      !                          !    =  0 force to write output files only at the end of the run 
    3030      !                          !    = -1 do not do any output file 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/rst/source/cfgs.bib

    r11718 r14789  
    1 @article{ODEA2012, 
    2 author = {E J O’Dea and A K Arnold and K P Edwards and R Furner and P Hyder and M J Martin and J R Siddorn and D Storkey and J While and J T Holt and H Liu}, 
    3 title = {An operational ocean forecast system incorporating NEMO and SST data assimilation for the tidally driven European North-West shelf}, 
    4 journal = {Journal of Operational Oceanography}, 
    5 volume = {5}, 
    6 number = {1}, 
    7 pages = {3-17}, 
    8 year  = {2012}, 
    9 publisher = {Taylor & Francis}, 
    10 doi = {10.1080/1755876X.2012.11020128}, 
    11 URL = {https://doi.org/10.1080/1755876X.2012.11020128}, 
    12 eprint = {https://doi.org/10.1080/1755876X.2012.11020128} 
     1 
     2@article{         aumont.ethé.ea_GMD15, 
     3  title         = "PISCES-v2: an ocean biogeochemical model for carbon and 
     4                  ecosystem studies", 
     5  pages         = "2465--2513", 
     6  journal       = "Geoscientific Model Development", 
     7  volume        = "8", 
     8  number        = "8", 
     9  author        = "Aumont, O. and Ethé, C. and Tagliabue, A. and Bopp, L. 
     10                  and Gehlen, M.", 
     11  year          = "2015", 
     12  month         = "Aug", 
     13  publisher     = "Copernicus GmbH", 
     14  issn          = "1991-9603", 
     15  doi           = "10.5194/gmd-8-2465-2015" 
    1316} 
    1417 
    15 @Article{gmd-8-2465-2015, 
    16 AUTHOR = {Aumont, O. and Eth\'e, C. and Tagliabue, A. and Bopp, L. and Gehlen, M.}, 
    17 TITLE = {PISCES-v2: an ocean biogeochemical model for carbon and ecosystem studies}, 
    18 JOURNAL = {Geoscientific Model Development}, 
    19 VOLUME = {8}, 
    20 YEAR = {2015}, 
    21 NUMBER = {8}, 
    22 PAGES = {2465--2513}, 
    23 URL = {https://www.geosci-model-dev.net/8/2465/2015/}, 
    24 DOI = {10.5194/gmd-8-2465-2015} 
     18@article{         o’dea.arnold.ea_JOO12, 
     19  title         = "An operational ocean forecast system incorporating NEMO 
     20                  and SST data assimilation for the tidally driven European 
     21                  North-West shelf", 
     22  pages         = "3--17", 
     23  journal       = "Journal of Operational Oceanography", 
     24  volume        = "5", 
     25  number        = "1", 
     26  author        = "O’Dea, E J and Arnold, A K and Edwards, K P and Furner, 
     27                  R and Hyder, P and Martin, M J and Siddorn, J R and 
     28                  Storkey, D and While, J and Holt, J T and et al.", 
     29  year          = "2012", 
     30  month         = "Feb", 
     31  publisher     = "Informa UK Limited", 
     32  issn          = "1755-8778", 
     33  doi           = "10.1080/1755876x.2012.11020128" 
    2534} 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/rst/source/conf.py

    r11907 r14789  
    4343# General information about the project. 
    4444project = u'NEMO' 
    45 copyright = u'2019, NEMO Consortium' 
     45copyright = u'2020, NEMO Consortium' 
    4646 
    4747# The version info for the project you're documenting, acts as replacement for 
    … …  
    5050# 
    5151# The short X.Y version. 
    52 version = 'trk' 
     52version = 'trunk' 
    5353# The full version, including alpha/beta/rc tags. 
    5454release = 'trunk' 
    … …  
    279279# Default language to highlight set to fortran 
    280280highlight_language = 'fortran' 
     281 
     282# Extra setting for sphinxcontrib.bibtex upgrade to 2.X.X branche 
     283bibtex_bibfiles = ['cfgs.bib', 'ref.bib', 'tests.bib', 'zooms.bib'] 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/rst/source/guide.rst

    r13244 r14789  
    1616.. toctree:: 
    1717   :hidden: 
    18 .. todos:: 
     18 
     19   todos 
    1920 
    2021.. Only displayed with 'make drafthtml' 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/rst/source/zooms.bib

    r10201 r14789  
    1 link ../../../cfgs/AGRIF_DEMO/zooms.bib 
     1link ../../../src/NST/zooms.bib 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/rst/source/zooms.rst

    r10201 r14789  
    1 link ../../../cfgs/AGRIF_DEMO/README.rst 
     1link ../../../src/NST/README.rst 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/tools/check_pkg.py

    r11008 r14789  
    1 #!/usr/bin/env python 
     1#!/usr/bin/env python3 
    22 
    33import sys, importlib 
    … …  
    77      importlib.import_module(argv) 
    88   except ImportError: 
    9       print("Package %s is missing in Python" % argv) 
     9      print("Package %s is missing in Python 3" % argv) 
    1010 

  • NEMO/branches/2021/dev_r13747_HPC-11_mcastril_HPDAonline_DiagGPU/doc/tools/shr_func.sh

    r11598 r14789  
    44    printf "\t¤ Clean previous build" 
    55    find latex/$1/build -mindepth 1 -delete 
    6  
    76    echo 
    87} 
    98 
    109build() { 
    11     printf "\t¤ Generation of the PDF format\n" 
    12     latexmk -r  ./latex/global/latexmk.pl -pdfxe ./latex/$1/main/$1_manual \ 
    13 #  1> /dev/null 
     10    printf "\t¤ Generation of the PDF export of the manual\n" 
     11    latexmk -r ./latex/global/latexmk.pl ./latex/$1/main/$1_manual \ 
     12   1> /dev/null 
    1413    [ -f ./latex/$1/build/$1_manual.pdf ] && mv ./latex/$1/build/$1_manual.pdf . 
    1514    echo 
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