Changeset 14113


Ignore:
Timestamp:
2020-12-04T20:15:58+01:00 (5 months ago)
Author:
nicolasmartin
Message:

#2414 Reintegration to the trunk, LaTeX manuals are compiling ;-)

Location:
NEMO/trunk
Files:
23 deleted
40 edited
10 copied

Legend:

Unmodified
Added
Removed
  • NEMO/trunk/REFERENCES.bib

    r14086 r14113  
    1 @manual{NEMO_man, 
    2    title="NEMO ocean engine", 
    3    author="NEMO System Team", 
    4    series="Scientific Notes of Climate Modelling Center", 
    5    number="27", 
    6    institution="Institut Pierre-Simon Laplace (IPSL)", 
    7    publisher="Zenodo", 
    8    doi="10.5281/zenodo.1464816", 
     1 
     2@manual{          NEMO_man, 
     3  title         = "NEMO ocean engine", 
     4  series        = "Scientific Notes of Climate Modelling Center", 
     5  number        = "27", 
     6  author        = "Gurvan Madec and NEMO System Team", 
     7  institution   = "Institut Pierre-Simon Laplace (IPSL)", 
     8  publisher     = "Zenodo", 
     9  issn          = "1288-1619", 
     10  doi           = "10.5281/zenodo.1464816" 
    911} 
    1012%   edition="", 
    1113%   year="" 
    1214 
    13 @manual{SI3_man, 
    14    title="Sea Ice modelling Integrated Initiative (SI$^3$) -- The NEMO Sea Ice engine", 
    15    author="NEMO Sea Ice Working Group", 
    16    series="Scientific Notes of Climate Modelling Center", 
    17    number="31", 
    18    institution="Institut Pierre-Simon Laplace (IPSL)", 
    19    publisher="Zenodo", 
    20    doi="10.5281/zenodo.1471689", 
     15@manual{          SI3_man, 
     16  title         = "Sea Ice modelling Integrated Initiative (SI$^3$) -- The 
     17                  NEMO sea ice engine", 
     18  series        = "Scientific Notes of Climate Modelling Center", 
     19  number        = "31", 
     20  author        = "NEMO Sea Ice Working Group", 
     21  institution   = "Institut Pierre-Simon Laplace (IPSL)", 
     22  publisher     = "Zenodo", 
     23  issn          = "1288-1619", 
     24  doi           = "10.5281/zenodo.1471689" 
    2125} 
    2226%   edition="", 
    2327%   year="" 
    2428 
    25 @manual{TOP_man, 
    26    title="Tracers in Ocean Paradigm (TOP) -- The NEMO Tracers engine", 
    27    author="NEMO TOP Working Group", 
    28    series="Scientific Notes of Climate Modelling Center", 
    29    number="28", 
    30    institution="Institut Pierre-Simon Laplace (IPSL)", 
    31    publisher="Zenodo", 
    32    doi="10.5281/zenodo.1471700", 
     29@manual{          TOP_man, 
     30  title         = "Tracers in Ocean Paradigm (TOP) -- The NEMO passive 
     31                  tracers engine", 
     32  series        = "Scientific Notes of Climate Modelling Center", 
     33  number        = "28", 
     34  author        = "NEMO TOP Working Group", 
     35  institution   = "Institut Pierre-Simon Laplace (IPSL)", 
     36  publisher     = "Zenodo", 
     37  issn          = "1288-1619", 
     38  doi           = "10.5281/zenodo.1471700" 
    3339} 
    3440%   edition="", 
    3541%   year="" 
    3642 
    37 @article{TAM_pub, 
    38    author = "Vidard, A. and Bouttier, P.-A. and Vigilant, F.", 
    39    title = "NEMOTAM: Tangent and Adjoint Models for the ocean modelling platform NEMO", 
    40    journal = "Geoscientific Model Development", 
    41    volume = "8", 
    42    year = "2015", 
    43    number = "4", 
    44    pages = "1245--1257", 
    45    doi = "10.5194/gmd-8-1245-2015" 
     43@article{         TAM_pub, 
     44  title         = "NEMOTAM: Tangent and Adjoint Models for the ocean 
     45                  modelling platform NEMO", 
     46  pages         = "1245--1257", 
     47  journal       = "Geoscientific Model Development", 
     48  volume        = "8", 
     49  number        = "4", 
     50  author        = "Vidard, A. and Bouttier, P.-A. and Vigilant, F.", 
     51  year          = "2015", 
     52  doi           = "10.5194/gmd-8-1245-2015" 
    4653} 
  • NEMO/trunk/doc/README.rst

    r12377 r14113  
     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/trunk/doc/latex/.svnignore

    r12377 r14113  
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    87*.ilg 
    98*.ind 
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    11 *.log 
    12 *.lot 
    13 *.maf 
    14 *.mtc* 
     9*.lo* 
    1510*.out 
    16 *.pdf 
    1711*.toc 
     12*.xdv 
    1813_minted-* 
  • NEMO/trunk/doc/latex/NEMO/build

    • Property svn:ignore
      •  

        old new  
        22*.bbl 
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  • NEMO/trunk/doc/latex/NEMO/main/appendices.tex

    r12377 r14113  
    11 
    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 
     2\subfile{../subfiles/apdx_s_coord}      %% A. Generalised vertical coordinate 
     3\subfile{../subfiles/apdx_diff_opers}   %% B. Diffusive operators 
     4\subfile{../subfiles/apdx_invariants}   %% C. Discrete invariants of the eqs. 
     5\subfile{../subfiles/apdx_triads}       %% D. Isoneutral diffusion using triads 
     6\subfile{../subfiles/apdx_DOMAINcfg}    %% E. Brief notes on DOMAINcfg 
    77 
    88%% Not included 
     
    1010%\subfile{../subfiles/chap_DIU} 
    1111%\subfile{../subfiles/chap_conservation} 
    12 %\subfile{../subfiles/annex_E}            %% Notes on some on going staff 
    13  
     12%\subfile{../subfiles/apdx_algos}   %% Notes on some on going staff 
  • NEMO/trunk/doc/latex/NEMO/main/bibliography.bib

    r13916 r14113  
    188188} 
    189189 
    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" 
     190@article{         beljaars_QJRMS95, 
     191  title         = "The parametrization of surface fluxes in large-scale 
     192                  models under free convection", 
     193  pages         = "255--270", 
     194  journal       = "Quarterly Journal of the Royal Meteorological Society", 
     195  volume        = "121", 
     196  number        = "522", 
     197  author        = "Beljaars, Anton C. M.", 
     198  year          = "1995", 
     199  month         = "jan", 
     200  publisher     = "Wiley", 
     201  issn          = "00359009", 
     202  doi           = "10.1002/qj.49712152203" 
    202203} 
    203204 
     
    384385} 
    385386 
     387@article{         brodeau.barnier.ea_JPO16, 
     388  title         = "Climatologically Significant Effects of Some 
     389                  Approximations in the Bulk Parameterizations of Turbulent 
     390                  Air–Sea Fluxes", 
     391  pages         = "5--28", 
     392  journal       = "Journal of Physical Oceanography", 
     393  volume        = "47", 
     394  number        = "1", 
     395  author        = "Brodeau, Laurent and Barnier, Bernard and Gulev, Sergey K. 
     396                  and Woods, Cian", 
     397  year          = "2016", 
     398  month         = "jan", 
     399  publisher     = "American Meteorological Society", 
     400  issn          = "0022-3670", 
     401  doi           = "10.1175/jpo-d-16-0169.1" 
     402} 
     403 
    386404@article{         brodeau.barnier.ea_OM10, 
    387405  title         = "An {ERA40}-based atmospheric forcing for global ocean 
     
    398416  issn          = "1463-5003", 
    399417  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", 
    414418} 
    415419 
     
    519523} 
    520524 
    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, 
     525@techreport{      chanut_trpt05, 
    537526  title         = "Nesting code for {NEMO}", 
    538527  pages         = "25", 
     
    773762} 
    774763 
    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" 
     764@article{         edson.jampana.ea_JPO13, 
     765  title         = "On the Exchange of Momentum over the Open Ocean", 
     766  pages         = "1589--1610", 
     767  journal       = "Journal of Physical Oceanography", 
     768  volume        = "43", 
     769  number        = "8", 
     770  author        = "Edson, James B. and Jampana, Venkata and Weller, Robert A. 
     771                  and Bigorre, Sebastien P. and Plueddemann, Albert J. and 
     772                  Fairall, Christopher W. and Miller, Scott D. and Mahrt, 
     773                  Larry and Vickers, Dean and Hersbach, Hans", 
     774  year          = "2013", 
     775  month         = "aug", 
     776  publisher     = "American Meteorological Society", 
     777  issn          = "0022-3670", 
     778  doi           = "10.1175/JPO-D-12-0173.1" 
    817779} 
    818780 
     
    861823} 
    862824 
    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" 
     825@article{         fairall.bradley.ea_JC03, 
     826  title         = "Bulk parameterization of air-sea fluxes: Updates and 
     827                  verification for the COARE algorithm", 
     828  pages         = "571--591", 
     829  journal       = "Journal of Climate", 
     830  volume        = "16", 
     831  number        = "4", 
     832  author        = "Fairall, C. W. and Bradley, E. F. and Hare, J. E. and 
     833                  Grachev, A. A. and Edson, J. B.", 
     834  year          = "2003", 
     835  publisher     = "American Meteorological Society", 
     836  issn          = "08948755", 
     837  doi           = "10.1175/1520-0442(2003)016<0571:BPOASF>2.0.CO;2" 
     838} 
     839 
     840@article{         fairall.bradley.ea_JGRO96, 
     841  title         = "Cool-skin and warm-layer effects on sea surface 
     842                  temperature", 
     843  pages         = "1295--1308", 
     844  journal       = "Journal of Geophysical Research: Oceans", 
     845  volume        = "101", 
     846  number        = "C1", 
     847  author        = "C. W. Fairall and E. F. Bradley and J. S. Godfrey and G. 
     848                  A. Wick and J. B. Edson and G. S. Young", 
     849  year          = "1996", 
     850  month         = "jan", 
     851  publisher     = "American Geophysical Union", 
     852  doi           = "10.1029/95jc03190" 
    874853} 
    875854 
     
    928907} 
    929908 
    930 @article{         foxkemper.ferrari_JPO08, 
    931   title         = "Parameterization of Mixed Layer Eddies. Part I: Theory and Diagnosis", 
     909@article{         fox-kemper.ferrari.ea_JPO08, 
     910  title         = "Parameterization of Mixed Layer Eddies. Part I: Theory and 
     911                  Diagnosis", 
    932912  pages         = "1145--1165", 
    933913  journal       = "Journal of Physical Oceanography", 
     
    10301010} 
    10311011 
    1032 @article{         gerdes_JGR93*a, 
     1012@article{         gerdes_JGR93, 
    10331013  title         = "A primitive equation ocean circulation model using a 
    10341014                  general vertical coordinate transformation: 1. Description 
     
    10451025} 
    10461026 
    1047 @article{         gerdes_JGR93*b, 
     1027@article{         gerdes_JGR93*a, 
    10481028  title         = "A primitive equation ocean circulation model using a 
    10491029                  general vertical coordinate transformation: 2. Application 
     
    10601040} 
    10611041 
    1062 @techreport{      gibson_rpt86, 
     1042@techreport{      gibson_trpt86, 
    10631043  title         = "Standards for software development and maintenance", 
    10641044  pages         = "21", 
     
    10991079  issn          = "0148-0227", 
    11001080  doi           = "10.1029/2010jb007867" 
    1101 } 
    1102  
    1103 @article{         goosse.deleersnijder.ea_JGR99, 
    1104   title         = "Sensitivity of a global coupled ocean-sea ice model to the 
    1105                   parameterization of vertical mixing", 
    1106   pages         = "13681--13695", 
    1107   journal       = "Journal of Geophysical Research", 
    1108   volume        = "104", 
    1109   number        = "C6", 
    1110   author        = "H. Goosse and E. Deleersnijder and T. Fichefet and M. H. 
    1111                   England", 
    1112   year          = "1999", 
    1113   month         = "jun", 
    1114   publisher     = "American Geophysical Union (AGU)", 
    1115   issn          = "0148-0227", 
    1116   doi           = "10.1029/1999jc900099" 
    11171081} 
    11181082 
     
    13691333} 
    13701334 
    1371 @techreport{      hunter_rpt06, 
     1335@techreport{      hunter_trpt06, 
    13721336  title         = "Specification for Test Models of Ice Shelf Cavities", 
    13731337  pages         = "17", 
     
    14101374} 
    14111375 
    1412 @techreport{      janssen.breivik.ea_rpt13, 
     1376@techreport{      janssen.breivik.ea_trpt13, 
    14131377  title         = "Air-sea interaction and surface waves", 
    14141378  pages         = "36", 
     
    14501414  issn          = "0148-0227", 
    14511415  doi           = "10.1029/91jc01842" 
     1416} 
     1417 
     1418@article{         josey.gulev.ea_OCC13, 
     1419  title         = "Exchanges Through the Ocean Surface", 
     1420  pages         = "115--140", 
     1421  journal       = "Ocean Circulation and Climate", 
     1422  author        = "Josey, Simon A. and Gulev, Serge and Yu, Lisan", 
     1423  year          = "2013", 
     1424  publisher     = "Elsevier", 
     1425  issn          = "0074-6142", 
     1426  isbn          = "9780123918512", 
     1427  doi           = "10.1016/b978-0-12-391851-2.00005-2" 
    14521428} 
    14531429 
     
    15411517} 
    15421518 
    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", 
    1552   year          = "2010", 
    1553   month         = "aug", 
    1554   publisher     = "Springer Nature", 
    1555   issn          = "1432-0894", 
    1556   doi           = "10.1007/s00382-009-0642-4" 
    1557 } 
    1558  
    15591519@article{         koch-larrouy.madec.ea_GRL07, 
    15601520  title         = "On the transformation of Pacific water into Indonesian 
     
    15731533} 
    15741534 
    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, 
    1591   title         = "Physical processes contributing to the water mass 
    1592                   transformation of the Indonesian ThroughFlow", 
    1593   pages         = "275--288", 
    1594   journal       = "Ocean Dynamics", 
    1595   volume        = "58", 
    1596   number        = "3-4", 
    1597   author        = "A. Koch-Larrouy and G. Madec and D. Iudicone and A. 
    1598                   Atmadipoera and R. Molcard", 
    1599   year          = "2008", 
    1600   month         = "oct", 
    1601   publisher     = "Springer Nature", 
    1602   issn          = "1616-7228", 
    1603   doi           = "10.1007/s10236-008-0154-5" 
    1604 } 
    1605  
    16061535@article{         kolmogorov_IANS42, 
    16071536  title         = "Equations of turbulent motion in an incompressible fluid", 
     
    16141543} 
    16151544 
    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, 
     1545@article{         kraus.businger_QJRMS96, 
     1546  title         = "Atmosphere-ocean interaction.", 
     1547  pages         = "324--325", 
     1548  journal       = "Quarterly Journal of the Royal Meteorological Society", 
     1549  volume        = "122", 
     1550  number        = "529", 
     1551  author        = "E. B. Kraus and J. A. Businger", 
     1552  year          = "1996", 
     1553  publisher     = "John Wiley & Sons, Ltd", 
     1554  issn          = "1477-870X", 
     1555  doi           = "10.1002/qj.49712252914" 
     1556} 
     1557 
     1558@article{         kraus.turner_T67, 
     1559  title         = "A one-dimensional model of the seasonal thermocline II. 
     1560                  The general theory and its consequences", 
     1561  pages         = "98--106", 
     1562  journal       = "Tellus", 
     1563  volume        = "19", 
     1564  number        = "1", 
     1565  author        = "Kraus, E. B. and Turner, J. S.", 
     1566  year          = "1967", 
     1567  month         = "Jan", 
     1568  publisher     = "Informa UK Limited", 
     1569  issn          = "2153-3490", 
     1570  doi           = "10.3402/tellusa.v19i1.9753" 
     1571} 
     1572 
     1573@article{         large.mcwilliams.ea_RG94, 
     1574  title         = "Oceanic vertical mixing: {A} review and a model with a 
     1575                  nonlocal boundary layer parameterization", 
     1576  pages         = "363--403", 
     1577  journal       = "Reviews of Geophysics", 
     1578  number        = "4", 
    16261579  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, 
     1580  year          = "1994", 
     1581  publisher     = "AGU", 
     1582  doi           = "10.1029/94RG01872" 
     1583} 
     1584 
     1585@article{         large.yeager_CD09, 
     1586  title         = "The Global Climatology of an Interannually Varying Air-Sea 
     1587                  Flux Data Set", 
     1588  pages         = "341--364", 
     1589  journal       = "Climate Dynamics", 
     1590  volume        = "33", 
     1591  number        = "2-3", 
     1592  author        = "Large, W. G. and Yeager, S. G.", 
     1593  year          = "2009", 
     1594  month         = "aug", 
     1595  publisher     = "Springer Science and Business Media LLC", 
     1596  doi           = "10.1007/s00382-008-0441-3" 
     1597} 
     1598 
     1599@techreport{      large.yeager_trpt04, 
    16371600  title         = "Diurnal to decadal global forcing for ocean and sea-ice 
    16381601                  models: the data sets and flux climatologies", 
     
    18491812} 
    18501813 
    1851 @techreport{      levier.treguier.ea_rpt07, 
     1814@techreport{      levier.treguier.ea_trpt07, 
    18521815  title         = "Free surface and variable volume in the {NEMO} code", 
    18531816  pages         = "47", 
     
    19061869} 
    19071870 
    1908 @Article{        love_PRSLA1909, 
    1909   author       = "A. E. H. Love", 
    1910   title        = "The Yielding of the Earth to Disturbing Forces", 
    1911   journal      = "Proc. R. Soc. Lond. A", 
    1912   year         = "1909", 
    1913   volume       = "82", 
    1914   pages        = "73-88", 
    1915   doi          = "10.1098/rspa.1909.0008" 
    1916 } 
    1917  
    19181871@article{         losch_JGR08, 
    19191872  title         = "Modeling ice shelf cavities in a z coordinate Ocean 
     
    19401893} 
    19411894 
    1942 @article{     lupkes.gryanik.ea_JGR12, 
    1943   author    = "L{\"{u}}pkes, Christof and Gryanik, Vladimir M. and Hartmann, J{\"{o}}rg and Andreas, Edgar L.", 
    1944   doi       = "10.1029/2012JD017630", 
    1945   issn      = "01480227", 
    1946   journal   = "Journal of Geophysical Research Atmospheres", 
    1947   number    = "13", 
    1948   pages  = "1--18", 
    1949   title  = "A parametrization, based on sea ice morphology, of the neutral atmospheric drag coefficients for weather prediction and climate models", 
    1950   volume    = "117", 
    1951   year      = "2012" 
    1952 } 
    1953  
    1954 @article{     lupkes.gryanik_JGR15, 
    1955   author    = "L{\"{u}}pkes, Christof and Gryanik, Vladimir M.", 
    1956   doi       = "10.1002/2014JD022418", 
    1957   issn      = "21562202", 
    1958   journal   = "Journal of Geophysical Research", 
    1959   number    = "2", 
    1960   pages  = "552--581", 
    1961   title  = "A stability-dependent parametrization of transfer coefficients formomentum and heat over polar sea ice to be used in climate models", 
    1962   volume    = "120", 
    1963   year      = "2015" 
     1895@article{         lupkes.gryanik.ea_JGRA12, 
     1896  title         = "A parametrization, based on sea ice morphology, of the 
     1897                  neutral atmospheric drag coefficients for weather 
     1898                  prediction and climate models", 
     1899  pages         = "1--18", 
     1900  journal       = "Journal of Geophysical Research Atmospheres", 
     1901  volume        = "117", 
     1902  number        = "13", 
     1903  author        = "L{\"{u}}pkes, Christof and Gryanik, Vladimir M. and 
     1904                  Hartmann, J{\"{o}}rg and Andreas, Edgar L.", 
     1905  year          = "2012", 
     1906  issn          = "01480227", 
     1907  doi           = "10.1029/2012JD017630" 
     1908} 
     1909 
     1910@article{         lupkes.gryanik_JGR15, 
     1911  title         = "A stability-dependent parametrization of transfer 
     1912                  coefficients formomentum and heat over polar sea ice to be 
     1913                  used in climate models", 
     1914  pages         = "552--581", 
     1915  journal       = "Journal of Geophysical Research", 
     1916  volume        = "120", 
     1917  number        = "2", 
     1918  author        = "L{\"{u}}pkes, Christof and Gryanik, Vladimir M.", 
     1919  year          = "2015", 
     1920  issn          = "21562202", 
     1921  doi           = "10.1002/2014JD022418" 
    19641922} 
    19651923 
     
    22142172} 
    22152173 
    2216 @article{mcwilliams.ea_JFM97, 
    2217    author = {McWilliams, James C. and Sullivan, Peter P. and Moeng, Chin-Hoh}, 
    2218    doi = {10.1017/S0022112096004375}, 
    2219    journal = {Journal of Fluid Mechanics}, 
    2220    pages = {1--30}, 
    2221    title = {Langmuir turbulence in the ocean}, 
    2222    volume = {334}, 
    2223    year = {1997}, 
    2224 } 
     2174@article{         mcwilliams.sullivan.ea_JFM97, 
     2175  title         = "Langmuir turbulence in the ocean", 
     2176  pages         = "1--30", 
     2177  journal       = "Journal of Fluid Mechanics", 
     2178  volume        = "334", 
     2179  author        = "McWilliams, James C. and Sullivan, Peter P. and Moeng, 
     2180                  Chin-Hoh", 
     2181  year          = "1997", 
     2182  doi           = "10.1017/S0022112096004375" 
     2183} 
     2184 
    22252185@article{         mellor.blumberg_JPO04, 
    22262186  title         = "Wave Breaking and Ocean Surface Layer Thermal Response", 
     
    24392399 
    24402400@article{         qiao.yuan.ea_OD10, 
    2441   title         = "A three-dimensional surface wave–ocean circulation coupled  
    2442                   model and its initial testing", 
     2401  title         = "A three-dimensional surface wave–ocean circulation 
     2402                  coupled model and its initial testing", 
    24432403  pages         = "1339--1335", 
    24442404  journal       = "Ocean Dynamics", 
    24452405  volume        = "60", 
    24462406  number        = "5", 
    2447   author        = "F. Qiao and Y. Yuan and T. Ezer and C. Xia and  
    2448                    Y. Yang and X. Lu and Z. Song ", 
     2407  author        = "F. Qiao and Y. Yuan and T. Ezer and C. Xia and Y. Yang and 
     2408                  X. Lu and Z. Song ", 
    24492409  year          = "2010", 
    24502410  month         = "oct", 
     
    24682428} 
    24692429 
    2470 @article{         reffray.guillaume.ea_GMD15, 
    2471   title         = "Modelling turbulent vertical mixing sensitivity using 
    2472                    a 1-D version of NEMO", 
     2430@article{         reffray.bourdalle-badie.ea_GMD15, 
     2431  title         = "Modelling turbulent vertical mixing sensitivity using a 
     2432                  1-D version of NEMO", 
    24732433  pages         = "69--86", 
    24742434  journal       = "Geoscientific Model Development", 
     
    26482608 
    26492609@article{         shchepetkin_OM15, 
    2650   title         = "An Adaptive, Courant-number-dependent implicit 
    2651        scheme for vertical advection in oceanic modeling", 
     2610  title         = "An Adaptive, Courant-number-dependent implicit scheme for 
     2611                  vertical advection in oceanic modeling", 
    26522612  pages         = "38--69", 
    26532613  journal       = "Ocean Modelling", 
     
    26762636} 
    26772637 
    2678 @article{         simmons.jayne.ea_OM04, 
    2679   title         = "Tidally driven mixing in a numerical model of the ocean 
    2680                   general circulation", 
    2681   pages         = "245--263", 
    2682   journal       = "Ocean Modelling", 
    2683   volume        = "6", 
    2684   number        = "3-4", 
    2685   author        = "H. L. Simmons and S. R. Jayne and L. C. {St Laurent} and 
    2686                   A. J. Weaver", 
    2687   year          = "2004", 
    2688   month         = "jan", 
    2689   publisher     = "Elsevier BV", 
    2690   issn          = "1463-5003", 
    2691   doi           = "10.1016/s1463-5003(03)00011-8" 
    2692 } 
    2693  
    2694 @article{         smagorinsky_MW63, 
    2695   title         = "General circulation experiments with the primitive equations: I. The basic experiment ", 
     2638@article{         smagorinsky_MWR63, 
     2639  title         = "General circulation experiments with the primitive 
     2640                  equations: I. The basic experiment ", 
    26962641  pages         = "99--164", 
    26972642  journal       = "Monthly Weather Review", 
     
    27342679  issn          = "1520-0493", 
    27352680  doi           = "10.1175/1520-0493(1998)126<3213:agpgff>2.0.co;2" 
    2736 } 
    2737  
    2738 @article{         st-laurent.nash_DSR04, 
    2739   title         = "An examination of the radiative and dissipative properties 
    2740                   of deep ocean internal tides", 
    2741   pages         = "3029--3042", 
    2742   journal       = "Deep Sea Research", 
    2743   volume        = "51", 
    2744   number        = "25-26", 
    2745   author        = "L. C. {St Laurent} and J. D. Nash", 
    2746   year          = "2004", 
    2747   month         = "dec", 
    2748   publisher     = "Elsevier BV", 
    2749   issn          = "0967-0645", 
    2750   doi           = "10.1016/j.dsr2.2004.09.008" 
    27512681} 
    27522682 
     
    28222752  isbn          = "9780511702242", 
    28232753  doi           = "10.1017/cbo9780511702242.013" 
     2754} 
     2755 
     2756@book{            sverdrup.johnson.ea_bk42, 
     2757  title         = "The Oceans, Their Physics, Chemistry, and General Biology", 
     2758  pages         = "1087", 
     2759  author        = "H. U. Sverdrup and Martin W. Johnson and Richard H. 
     2760                  Fleming", 
     2761  year          = "1942", 
     2762  publisher     = "Prentice-Hall", 
     2763  address       = "New York" 
    28242764} 
    28252765 
     
    29522892} 
    29532893 
    2954 @article{         vancoppenolle.fichefet.ea_OM09*a, 
    2955   title         = "Simulating the mass balance and salinity of Arctic and 
    2956                   Antarctic sea ice. 1. Model description and validation", 
    2957   pages         = "33--53", 
    2958   journal       = "Ocean Modelling", 
    2959   volume        = "27", 
    2960   number        = "1-2", 
    2961   author        = "M. Vancoppenolle and T. Fichefet and H. Goosse and S. 
    2962                   Bouillon and G. Madec and M. A. Morales Maqueda", 
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    2964   month         = "jan", 
    2965   publisher     = "Elsevier BV", 
    2966   issn          = "1463-5003", 
    2967   doi           = "10.1016/j.ocemod.2008.10.005" 
    2968 } 
    2969  
    2970 @article{         vancoppenolle.fichefet.ea_OM09*b, 
    2971   title         = "Simulating the mass balance and salinity of Arctic and 
    2972                   Antarctic sea ice. 2. Importance of sea ice salinity 
    2973                   variations", 
    2974   pages         = "54--69", 
    2975   journal       = "Ocean Modelling", 
    2976   volume        = "27", 
    2977   number        = "1-2", 
    2978   author        = "M. Vancoppenolle and T. Fichefet and H. Goosse", 
    2979   year          = "2009", 
    2980   month         = "jan", 
    2981   publisher     = "Elsevier BV", 
    2982   issn          = "1463-5003", 
    2983   doi           = "10.1016/j.ocemod.2008.11.003" 
    2984 } 
    2985  
    29862894@article{         warner.defne.ea_CG13, 
    29872895  title         = "A wetting and drying scheme for {ROMS}", 
     
    30582966} 
    30592967 
    3060 @article{         white.hoskins.ea_QJRMS05, 
    3061   title         = "Consistent approximate models of the global atmosphere: shallow, deep, 
    3062                   hydrostatic, quasi-hydrostatic and non-hydrostatic", 
    3063   pages         = "2081--2107", 
    3064   journal       = "Quarterly Journal of the Royal Meteorological Society", 
    3065   volume        = "131", 
    3066   author        = "A. A. White and B. J. Hoskins and I. Roulstone and A. Staniforth", 
    3067   year          = "2005", 
    3068   doi           = "10.1256/qj.04.49" 
    3069 } 
    3070  
    30712968@article{         white.adcroft.ea_JCP09, 
    30722969  title         = "High-order regridding-remapping schemes for continuous 
     
    30822979  issn          = "0021-9991", 
    30832980  doi           = "10.1016/j.jcp.2009.08.016" 
     2981} 
     2982 
     2983@article{         white.hoskins.ea_QJRMS05, 
     2984  title         = "Consistent approximate models of the global atmosphere: 
     2985                  shallow, deep, hydrostatic, quasi-hydrostatic and 
     2986                  non-hydrostatic", 
     2987  pages         = "2081--2107", 
     2988  journal       = "Quarterly Journal of the Royal Meteorological Society", 
     2989  volume        = "131", 
     2990  author        = "A. A. White and B. J. Hoskins and I. Roulstone and A. 
     2991                  Staniforth", 
     2992  year          = "2005", 
     2993  doi           = "10.1256/qj.04.49" 
    30842994} 
    30852995 
     
    31313041} 
    31323042 
     3043@article{         zeng.beljaars_GRL05, 
     3044  title         = "A prognostic scheme of sea surface skin temperature for 
     3045                  modeling and data assimilation", 
     3046  journal       = "Geophysical Research Letters", 
     3047  volume        = "32", 
     3048  number        = "14", 
     3049  author        = "Xubin Zeng and Anton Beljaars", 
     3050  year          = "2005", 
     3051  month         = "jul", 
     3052  publisher     = "American Geophysical Union", 
     3053  doi           = "10.1029/2005gl023030" 
     3054} 
     3055 
    31333056@article{         zhang.endoh_JGR92, 
    31343057  title         = "A free surface General Circulation Model for the tropical 
     
    31443067  doi           = "10.1029/92jc00911" 
    31453068} 
    3146  
    3147 @article{large.yeager_CD09, 
    3148 author="Large, W. G. and Yeager, S. G.", 
    3149 title="The Global Climatology of an Interannually Varying Air-Sea Flux Data Set", 
    3150 pages = "341--364", 
    3151 journal="Climate Dynamics", 
    3152 volume = "33", 
    3153 number = "2-3", 
    3154 year="2009", 
    3155 month = "aug", 
    3156 publisher = "Springer Science and Business Media LLC", 
    3157 doi="10.1007/s00382-008-0441-3" 
    3158 } 
    3159  
    3160 @book{sverdrup.johnson.ea_1942, 
    3161 author = {H. U. Sverdrup and Martin W. Johnson and Richard H. Fleming}, 
    3162 title = {The Oceans, Their Physics, Chemistry, and General Biology}, 
    3163 publisher = {Prentice-Hall}, 
    3164 address = {New York}, 
    3165 year = {1942}, 
    3166 pages = {1087}, 
    3167 } 
    3168  
    3169 @article{kraus.businger_QJRMS96, 
    3170 author = "E. B. Kraus and J. A. Businger", 
    3171 title = "Atmosphere-ocean interaction.", 
    3172 journal="Quarterly Journal of the Royal Meteorological Society",, 
    3173 year = "1996", 
    3174 volume = "122", 
    3175 number = "529", 
    3176 pages = "324-325", 
    3177 publisher = "John Wiley & Sons, Ltd", 
    3178 issn = "1477-870X", 
    3179 doi = "10.1002/qj.49712252914" 
    3180 } 
    3181  
    3182 @article{josey.gulev.ea_2013, 
    3183 title = "Exchanges through the ocean surface", 
    3184 journal = "Ocean Circulation and Climate - A 21st Century Perspective, Int. Geophys. Ser.", 
    3185 year = "2013", 
    3186 author = "S. A. Josey and S. Gulev and L. Yu", 
    3187 pages = "115-140, edited by G. Siedler et al., Academic Press, Oxford", 
    3188 volume = "103", 
    3189 doi = "10.1016/B978-0-12-391851-2.00005-2" 
    3190 } 
    3191  
    3192 @article{fairall.bradley.ea_JGR96, 
    3193   year = "1996", 
    3194  journal = "Journal of Geophysical Research: Oceans", 
    3195   month = "jan", 
    3196   publisher = "American Geophysical Union", 
    3197   volume = "101", 
    3198   number = "C1", 
    3199   pages = "1295-1308", 
    3200   author = "C. W. Fairall and E. F. Bradley and J. S. Godfrey and G. A. Wick and J. B. Edson and G. S. Young", 
    3201   title = "Cool-skin and warm-layer effects on sea surface temperature", 
    3202   doi = "10.1029/95jc03190" 
    3203 } 
    3204  
    3205 @article{zeng.beljaars_GRL05, 
    3206   year = "2005", 
    3207   month = "jul", 
    3208   publisher = "American Geophysical Union", 
    3209   volume = "32", 
    3210   number = "14", 
    3211   author = "Xubin Zeng and Anton Beljaars", 
    3212   title = "A prognostic scheme of sea surface skin temperature for modeling and data assimilation", 
    3213   journal = "Geophysical Research Letters", 
    3214   doi = "10.1029/2005gl023030" 
    3215 } 
    3216  
  • NEMO/trunk/doc/latex/NEMO/main/chapters.tex

    r12377 r14113  
    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\subfile{../subfiles/chap_model_basics}   %% 1. 
     2\subfile{../subfiles/chap_time_domain}    %% 2.  Time discretisation (time stepping strategy) 
     3\subfile{../subfiles/chap_DOM}            %% 3.  Space discretisation 
     4\subfile{../subfiles/chap_TRA}            %% 4.  Tracer advection/diffusion equation 
     5\subfile{../subfiles/chap_DYN}            %% 5.  Dynamics : momentum equation 
     6\subfile{../subfiles/chap_SBC}            %% 6.  Surface Boundary Conditions 
     7\subfile{../subfiles/chap_LBC}            %% 7.  Lateral Boundary Conditions 
     8\subfile{../subfiles/chap_LDF}            %% 8.  Lateral diffusion 
     9\subfile{../subfiles/chap_ZDF}            %% 9.  Vertical diffusion 
     10\subfile{../subfiles/chap_DIA}            %% 10. Outputs and Diagnostics 
     11\subfile{../subfiles/chap_OBS}            %% 11. Observation operator 
     12\subfile{../subfiles/chap_ASM}            %% 12. Assimilation increments 
     13\subfile{../subfiles/chap_STO}            %% 13. Stochastic param. 
     14\subfile{../subfiles/chap_misc}           %% 14. Miscellaneous topics 
     15\subfile{../subfiles/chap_cfgs}           %% 15. Predefined configurations 
     16 
     17%% Not included 
     18%\subfile{../subfiles/chap_model_basics_zstar} 
     19%\subfile{../subfiles/chap_DIU} 
     20%\subfile{../subfiles/chap_conservation} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/apdx_triads.tex

    r11693 r14113  
    11\documentclass[../main/NEMO_manual]{subfiles} 
     2 
     3\begin{document} 
    24 
    35%% Local cmds 
     
    1012\newcommand{\rtriad}[2][]{\ensuremath{\triad[#1]{i}{k}{#2}{i_p}{k_p}}} 
    1113\newcommand{\rtriadt}[1]{\ensuremath{\triadt{i}{k}{#1}{i_p}{k_p}}} 
    12  
    13 \begin{document} 
    1414 
    1515\chapter{Iso-Neutral Diffusion and Eddy Advection using Triads} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_DYN.tex

    r13916 r14113  
    657657Note that expression \autoref{eq:DYN_hpg_sco} is commonly used when the variable volume formulation is activated 
    658658(\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}. 
     659the coordinate surfaces are not horizontal but follow the free surface \citep{levier.treguier.ea_trpt07}. 
    660660The pressure jacobian scheme (\np[=.true.]{ln_dynhpg_prj}{ln\_dynhpg\_prj}) is available as 
    661661an improved option to \np[=.true.]{ln_dynhpg_sco}{ln\_dynhpg\_sco} when \texttt{vvl?} is active. 
     
    913913external gravity waves in idealized or weakly non-linear cases. 
    914914Although 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. 
     915it is still significant as shown by \citet{levier.treguier.ea_trpt07} in the case of an analytical barotropic Kelvin wave. 
    916916 
    917917\cmtgm{               %%% copy from griffies Book 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_LBC.tex

    r13916 r14113  
    358358 
    359359The BDY module was modelled on the OBC module (see \NEMO\ 3.4) and shares many features and 
    360 a similar coding structure \citep{chanut_rpt05}. 
     360a similar coding structure \citep{chanut_trpt05}. 
    361361The specification of the location of the open boundary is completely flexible and 
    362362allows any type of setup, from regular boundaries to irregular contour (it includes the possibility to set an open boundary able to follow an isobath). 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_LDF.tex

    r11693 r14113  
    418418\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})} 
    419419 
    420 This option refers to the \citep{smagorinsky_MW63} scheme which is here implemented for momentum only. Smagorinsky chose as a 
     420This option refers to the \citep{smagorinsky_MWR63} scheme which is here implemented for momentum only. Smagorinsky chose as a 
    421421characteristic time scale $T_{smag}$ the deformation rate and for the lengthscale $L_{smag}$ the maximum wavenumber possible on the horizontal grid, e.g.: 
    422422 
     
    540540\end{listing} 
    541541 
    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. 
     542If  \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. 
    543543 
    544544\colorbox{yellow}{TBC} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_SBC.tex

    r13916 r14113  
    11\documentclass[../main/NEMO_manual]{subfiles} 
    2 \usepackage{fontspec} 
    3 \usepackage{fontawesome} 
    42 
    53\begin{document} 
     
    526524See \autoref{subsec:SBC_ssr} for its specification. 
    527525 
    528  
    529  
    530  
    531  
    532  
    533  
    534 %% ================================================================================================= 
    535 \pagebreak 
    536 \newpage 
     526%% ================================================================================================= 
    537527\section[Bulk formulation (\textit{sbcblk.F90})]{Bulk formulation (\protect\mdl{sbcblk})} 
    538528\label{sec:SBC_blk} 
     
    558548 
    559549Note: all the NEMO Fortran routines involved in the present section have been 
    560  initially developed (and are still developed in parallel) in 
    561  the \href{https://brodeau.github.io/aerobulk/}{\texttt{AeroBulk}} open-source project 
    562 \citep{brodeau.barnier.ea_JPO17}. 
     550initially developed (and are still developed in parallel) in 
     551the \href{https://brodeau.github.io/aerobulk}{\texttt{AeroBulk}} open-source project 
     552\citep{brodeau.barnier.ea_JPO16}. 
    563553 
    564554%%% Bulk formulae are this: 
    565 \subsection{Bulk formulae}\label{subsec:SBC_blkform} 
    566 % 
     555\subsection{Bulk formulae} 
     556\label{subsec:SBC_blkform} 
     557 
    567558In NEMO, the set of equations that relate each component of the surface fluxes 
    568559to the near-surface atmosphere and sea surface states writes 
    569 % 
    570 \begin{subequations}\label{eq_bulk} 
     560 
     561\begin{subequations} 
     562  \label{eq:SBC_bulk} 
    571563  \label{eq:SBC_bulk_form} 
    572   \begin{eqnarray} 
    573     \mathbf{\tau} &=& \rho~ C_D ~ \mathbf{U}_z  ~ U_B \\ 
    574     Q_H           &=& \rho~C_H~C_P~\big[ \theta_z - T_s \big] ~ U_B \\ 
    575     E             &=& \rho~C_E    ~\big[    q_s   - q_z \big] ~ U_B \\ 
    576     Q_L           &=& -L_v \, E \\ 
    577     % 
    578     Q_{sr}        &=& (1 - a) Q_{sw\downarrow} \\ 
    579     Q_{ir}        &=& \delta (Q_{lw\downarrow} -\sigma T_s^4) 
    580   \end{eqnarray} 
     564  \begin{align} 
     565    \mathbf{\tau} &= \rho~ C_D ~ \mathbf{U}_z  ~ U_B \\ 
     566    Q_H           &= \rho~C_H~C_P~\big[ \theta_z - T_s \big] ~ U_B \\ 
     567    E             &= \rho~C_E    ~\big[    q_s   - q_z \big] ~ U_B \\ 
     568    Q_L           &= -L_v \, E \\ 
     569    Q_{sr}        &= (1 - a) Q_{sw\downarrow} \\ 
     570    Q_{ir}        &= \delta (Q_{lw\downarrow} -\sigma T_s^4) 
     571  \end{align} 
    581572\end{subequations} 
    582 % 
     573 
    583574with 
    584575   \[ \theta_z \simeq T_z+\gamma z \] 
    585576   \[  q_s \simeq 0.98\,q_{sat}(T_s,p_a ) \] 
    586 % 
    587577from which, the the non-solar heat flux is \[ Q_{ns} = Q_L + Q_H + Q_{ir} \] 
    588 % 
    589578where $\mathbf{\tau}$ is the wind stress vector, $Q_H$ the sensible heat flux, 
    590579$E$ the evaporation, $Q_L$ the latent heat flux, and $Q_{ir}$ the net longwave 
    591580flux. 
    592 % 
    593581$Q_{sw\downarrow}$ and $Q_{lw\downarrow}$ are the surface downwelling shortwave 
    594582and longwave radiative fluxes, respectively. 
    595 % 
    596583Note: a positive sign for $\mathbf{\tau}$, $Q_H$, $Q_L$, $Q_{sr}$ or $Q_{ir}$ 
    597584implies a gain of the relevant quantity for the ocean, while a positive $E$ 
    598585implies a freshwater loss for the ocean. 
    599 % 
    600586$\rho$ is the density of air. $C_D$, $C_H$ and $C_E$ are the bulk transfer 
    601587coefficients for momentum, sensible heat, and moisture, respectively. 
    602 % 
    603588$C_P$ is the heat capacity of moist air, and $L_v$ is the latent heat of 
    604589vaporization of water. 
    605 % 
    606590$\theta_z$, $T_z$ and $q_z$ are the potential temperature, absolute temperature, 
    607591and specific humidity of air at height $z$ above the sea surface, 
    608592respectively. $\gamma z$ is a temperature correction term which accounts for the 
    609593adiabatic lapse rate and approximates the potential temperature at height 
    610 $z$ \citep{josey.gulev.ea_2013}. 
    611 % 
     594$z$ \citep{josey.gulev.ea_OCC13}. 
    612595$\mathbf{U}_z$ is the wind speed vector at height $z$ above the sea surface 
    613 (possibly referenced to the surface current $\mathbf{u_0}$, 
    614 section \ref{s_res1}.\ref{ss_current}). 
    615 % 
     596(possibly referenced to the surface current $\mathbf{u_0}$).%, 
     597%\autoref{s_res1}.\autoref{ss_current}). %% Undefined references 
    616598The bulk scalar wind speed, namely $U_B$, is the scalar wind speed, 
    617599$|\mathbf{U}_z|$, with the potential inclusion of a gustiness contribution. 
    618 % 
    619600$a$ and $\delta$ are the albedo and emissivity of the sea surface, respectively.\\ 
    620 % 
    621601%$p_a$ is the mean sea-level pressure (SLP). 
    622 % 
    623602$T_s$ is the sea surface temperature. $q_s$ is the saturation specific humidity 
    624603of air at temperature $T_s$; it includes a 2\% reduction to account for the 
    625 presence of salt in seawater \citep{sverdrup.johnson.ea_1942,kraus.businger_QJRMS96}. 
     604presence of salt in seawater \citep{sverdrup.johnson.ea_bk42,kraus.businger_QJRMS96}. 
    626605Depending on the bulk parametrization used, $T_s$ can either be the temperature 
    627606at the air-sea interface (skin temperature, hereafter SSST) or at typically a 
    628607few tens of centimeters below the surface (bulk sea surface temperature, 
    629608hereafter SST). 
    630 % 
    631609The SSST differs from the SST due to the contributions of two effects of 
    632610opposite sign, the \emph{cool skin} and \emph{warm layer} (hereafter CS and WL, 
    633 respectively, see section\,\ref{subsec:SBC_skin}). 
    634 % 
     611respectively, see \autoref{subsec:SBC_skin}). 
    635612Technically, when the ECMWF or COARE* bulk parametrizations are selected 
    636613(\np[=.true.]{ln_ECMWF}{ln\_ECMWF} or \np[=.true.]{ln_COARE*}{ln\_COARE\*}), 
     
    640617 
    641618For more details on all these aspects the reader is invited to refer 
    642 to \citet{brodeau.barnier.ea_JPO17}. 
    643  
    644  
    645  
    646 \subsection{Bulk parametrizations}\label{subsec:SBC_blk_ocean} 
     619to \citet{brodeau.barnier.ea_JPO16}. 
     620 
     621\subsection{Bulk parametrizations} 
     622\label{subsec:SBC_blk_ocean} 
    647623%%%\label{subsec:SBC_param} 
    648624 
     
    654630height (from \np{rn_zqt}{rn\_zqt} to \np{rn_zu}{rn\_zu}). 
    655631 
    656  
    657  
    658632For the open ocean, four bulk parametrization algorithms are available in NEMO: 
     633 
    659634\begin{itemize} 
    660 \item NCAR, formerly known as CORE, \citep{large.yeager_rpt04,large.yeager_CD09} 
     635\item NCAR, formerly known as CORE, \citep{large.yeager_trpt04,large.yeager_CD09} 
    661636\item COARE 3.0 \citep{fairall.bradley.ea_JC03} 
    662637\item COARE 3.6 \citep{edson.jampana.ea_JPO13} 
     
    664639\end{itemize} 
    665640 
    666  
    667641With respect to version 3, the principal advances in version 3.6 of the COARE 
    668642bulk parametrization are built around improvements in the representation of the 
    669643effects of waves on 
    670 fluxes \citep{edson.jampana.ea_JPO13,brodeau.barnier.ea_JPO17}. This includes 
     644fluxes \citep{edson.jampana.ea_JPO13,brodeau.barnier.ea_JPO16}. This includes 
    671645improved relationships of surface roughness, and whitecap fraction on wave 
    672646parameters. It is therefore recommended to chose version 3.6 over 3. 
    673647 
    674  
    675  
    676  
    677 \subsection{Cool-skin and warm-layer parametrizations}\label{subsec:SBC_skin} 
    678 %\subsection[Cool-skin and warm-layer parameterizations 
    679 %(\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})} 
    680 %\label{subsec:SBC_skin} 
    681 % 
     648\subsection{Cool-skin and warm-layer parametrizations} 
     649%\subsection[Cool-skin and warm-layer parameterizations (\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})} 
     650\label{subsec:SBC_skin} 
     651 
    682652As opposed to the NCAR bulk parametrization, more advanced bulk 
    683653parametrizations such as COARE3.x and ECMWF are meant to be used with the skin 
    684654temperature $T_s$ rather than the bulk SST (which, in NEMO is the temperature at 
    685 the first T-point level, see section\,\ref{subsec:SBC_blkform}). 
    686 % 
     655the first T-point level, see \autoref{subsec:SBC_blkform}). 
     656 
    687657As such, the relevant cool-skin and warm-layer parametrization must be 
    688658activated through \np[=T]{ln_skin_cs}{ln\_skin\_cs} 
     
    693663 
    694664For the cool-skin scheme parametrization COARE and ECMWF algorithms share the same 
    695 basis: \citet{fairall.bradley.ea_JGR96}. With some minor updates based 
     665basis: \citet{fairall.bradley.ea_JGRO96}. With some minor updates based 
    696666on \citet{zeng.beljaars_GRL05} for ECMWF, and \citet{fairall.ea_19} for COARE 
    6976673.6. 
     
    704674equation for the thickness of the warm-layer, while it is considered as constant 
    705675in the ECWMF algorithm. 
    706  
    707676 
    708677\subsection{Appropriate use of each bulk parametrization} 
     
    714683temperature is the bulk SST. Hence the following namelist parameters must be 
    715684set: 
    716 % 
    717 \begin{verbatim} 
     685 
     686\begin{forlines} 
    718687  ... 
    719688  ln_NCAR    = .true. 
     
    726695  ... 
    727696  ln_humi_sph = .true. ! humidity "sn_humi" is specific humidity  [kg/kg] 
    728 \end{verbatim} 
    729  
     697\end{forlines} 
    730698 
    731699\subsubsection{ECMWF} 
    732 % 
     700 
    733701With an atmospheric forcing based on a reanalysis of the ECMWF, such as the 
    734702Drakkar Forcing Set \citep{brodeau.barnier.ea_OM10}, we strongly recommend to 
     
    737705humidity are provided at the 2\,m height, and given that the humidity is 
    738706distributed as the dew-point temperature, the namelist must be tuned as follows: 
    739 % 
    740 \begin{verbatim} 
     707 
     708\begin{forlines} 
    741709  ... 
    742710  ln_ECMWF   = .true. 
     
    750718  ln_humi_dpt = .true. !  humidity "sn_humi" is dew-point temperature [K] 
    751719  ... 
    752 \end{verbatim} 
    753 % 
     720\end{forlines} 
     721 
    754722Note: when \np{ln_ECMWF}{ln\_ECMWF} is selected, the selection 
    755723of \np{ln_skin_cs}{ln\_skin\_cs} and \np{ln_skin_wl}{ln\_skin\_wl} implicitly 
     
    757725respectively (found in \textit{sbcblk\_skin\_ecmwf.F90}). 
    758726 
    759  
    760727\subsubsection{COARE 3.x} 
    761 % 
     728 
    762729Since the ECMWF parametrization is largely based on the COARE* parametrization, 
    763730the two algorithms are very similar in terms of structure and closure 
    764731approach. As such, the namelist tuning for COARE 3.x is identical to that of 
    765732ECMWF: 
    766 % 
    767 \begin{verbatim} 
     733 
     734\begin{forlines} 
    768735  ... 
    769736  ln_COARE3p6 = .true. 
     
    772739  ln_skin_wl = .true. ! use the warm-layer parameterization 
    773740  ... 
    774 \end{verbatim} 
     741\end{forlines} 
    775742 
    776743Note: when \np[=T]{ln_COARE3p0}{ln\_COARE3p0} is selected, the selection 
     
    779746respectively (found in \textit{sbcblk\_skin\_coare.F90}). 
    780747 
    781  
    782748%lulu 
    783  
    784  
    785749 
    786750% In a typical bulk algorithm, the BTCs under neutral stability conditions are 
     
    792756% and $q_z$. 
    793757 
    794  
    795  
    796758\subsection{Prescribed near-surface atmospheric state} 
    797759 
     
    800762different bulk formulae are used for the turbulent fluxes computation over the 
    801763ocean and over sea-ice surface. 
    802 % 
    803764 
    804765%The choice is made by setting to true one of the following namelist 
     
    862823the namsbc\_blk namelist (see \autoref{subsec:SBC_fldread}). 
    863824 
    864  
    865825\subsubsection{Air humidity} 
    866826 
     
    868828[kg/kg], relative humidity [\%], or dew-point temperature [K] (LINK to namelist 
    869829parameters)... 
    870  
    871  
    872 ~\\ 
    873  
    874  
    875  
    876  
    877  
    878  
    879  
    880  
    881  
    882830 
    883831%% ================================================================================================= 
     
    889837%their neutral transfer coefficients relationships with neutral wind. 
    890838%\begin{itemize} 
    891 %\item NCAR (\np[=.true.]{ln_NCAR}{ln\_NCAR}): The NCAR bulk formulae have been developed by \citet{large.yeager_rpt04}. 
     839%\item NCAR (\np[=.true.]{ln_NCAR}{ln\_NCAR}): The NCAR bulk formulae have been developed by \citet{large.yeager_trpt04}. 
    892840%  They have been designed to handle the NCAR forcing, a mixture of NCEP reanalysis and satellite data. 
    893841%  They use an inertial dissipative method to compute the turbulent transfer coefficients 
    894842%  (momentum, sensible heat and evaporation) from the 10m wind speed, air temperature and specific humidity. 
    895 %  This \citet{large.yeager_rpt04} dataset is available through 
     843%  This \citet{large.yeager_trpt04} dataset is available through 
    896844%  the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/NCAR.html}{GFDL web site}. 
    897845%  Note that substituting ERA40 to NCEP reanalysis fields does not require changes in the bulk formulea themself. 
     
    908856\label{subsec:SBC_blk_ice} 
    909857 
    910  
    911858\texttt{\#out\_of\_place:} 
    912859 For sea-ice, three possibilities can be selected: 
    913860a constant transfer coefficient (1.4e-3; default 
    914 value), \citet{lupkes.gryanik.ea_JGR12} (\np{ln_Cd_L12}{ln\_Cd\_L12}), 
     861value), \citet{lupkes.gryanik.ea_JGRA12} (\np{ln_Cd_L12}{ln\_Cd\_L12}), 
    915862and \citet{lupkes.gryanik_JGR15} (\np{ln_Cd_L15}{ln\_Cd\_L15}) parameterizations 
    916863\texttt{\#out\_of\_place.} 
    917864 
    918  
    919  
    920  
    921865Surface turbulent fluxes between sea-ice and the atmosphere can be computed in three different ways: 
    922866 
    923867\begin{itemize} 
    924 \item Constant value (\np[ Cd_ice=1.4e-3 ]{constant value}{constant\ value}): 
     868\item Constant value (\forcode{Cd_ice=1.4e-3}): 
    925869  default constant value used for momentum and heat neutral transfer coefficients 
    926 \item \citet{lupkes.gryanik.ea_JGR12} (\np[=.true.]{ln_Cd_L12}{ln\_Cd\_L12}): 
     870\item \citet{lupkes.gryanik.ea_JGRA12} (\np[=.true.]{ln_Cd_L12}{ln\_Cd\_L12}): 
    927871  This scheme adds a dependency on edges at leads, melt ponds and flows 
    928872  of the constant neutral air-ice drag. After some approximations, 
     
    12601204  \begin{description} 
    12611205  \item [{\np[=1]{nn_isfblk}{nn\_isfblk}}]: The melt rate is based on a balance between the upward ocean heat flux and 
    1262     the latent heat flux at the ice shelf base. A complete description is available in \citet{hunter_rpt06}. 
     1206    the latent heat flux at the ice shelf base. A complete description is available in \citet{hunter_trpt06}. 
    12631207  \item [{\np[=2]{nn_isfblk}{nn\_isfblk}}]: The melt rate and the heat flux are based on a 3 equations formulation 
    12641208    (a heat flux budget at the ice base, a salt flux budget at the ice base and a linearised freezing point temperature equation). 
     
    13321276The fw addition due to the ice shelf melting is, at each relevant depth level, added to 
    13331277the horizontal divergence (\textit{hdivn}) in the subroutine \rou{sbc\_isf\_div}, called from \mdl{divhor}. 
    1334 See the runoff section \autoref{sec:SBC_rnf} for all the details about the divergence correction.\\ 
     1278See \autoref{sec:SBC_rnf} for all the details about the divergence correction. 
    13351279 
    13361280\begin{figure}[!t] 
     
    15031447Then using the routine \rou{sbcblk\_algo\_ncar} and starting from the neutral drag coefficent provided, 
    15041448the drag coefficient is computed according to the stable/unstable conditions of the 
    1505 air-sea interface following \citet{large.yeager_rpt04}. 
     1449air-sea interface following \citet{large.yeager_trpt04}. 
    15061450 
    15071451%% ================================================================================================= 
     
    16141558 
    16151559The surface stress felt by the ocean is the atmospheric stress minus the net stress going 
    1616 into the waves \citep{janssen.breivik.ea_rpt13}. Therefore, when waves are growing, momentum and energy is spent and is not 
     1560into the waves \citep{janssen.breivik.ea_trpt13}. Therefore, when waves are growing, momentum and energy is spent and is not 
    16171561available for forcing the mean circulation, while in the opposite case of a decaying sea 
    16181562state, more momentum is available for forcing the ocean. 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_ZDF.tex

    r13461 r14113  
    11\documentclass[../main/NEMO_manual]{subfiles} 
     2 
     3\begin{document} 
    24 
    35%% Custom aliases 
    46\newcommand{\cf}{\ensuremath{C\kern-0.14em f}} 
    5  
    6 \begin{document} 
    77 
    88\chapter{Vertical Ocean Physics (ZDF)} 
     
    198198$\bar{e}_o = e_{bb} |\tau| / \rho_o$, with $e_{bb}$ the \np{rn_ebb}{rn\_ebb} namelist parameter. 
    199199The 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}). 
     200taking into account the surface wave breaking (see below \autoref{eq:ZDF_Esbc}). 
    201201The bottom value of TKE is assumed to be equal to the value of the level just above. 
    202202The time integration of the $\bar{e}$ equation may formally lead to negative values because 
     
    532532the TKE case described in \autoref{subsec:ZDF_tke_ene} \citep{burchard_OM02}. 
    533533Evaluation 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. 
     534 in \citet{reffray.bourdalle-badie.ea_GMD15} for the \NEMO\ model. 
    535535 
    536536% ------------------------------------------------------------------------------------------------------------- 
     
    594594Obsolete namelist parameters include: 
    595595\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}. 
     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}. 
    603603\end{description} 
    604604 
     
    608608classical shear turbulence. Instead they are in a regime known as 
    609609`Langmuir turbulence',  dominated by an 
    610 interaction between the currents and the Stokes drift of the surface waves \citep[e.g.][]{mcwilliams.ea_JFM97}. 
     610interaction between the currents and the Stokes drift of the surface waves \citep[e.g.][]{mcwilliams.sullivan.ea_JFM97}. 
    611611This 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 $\mathrm{La}_{t}=(u_{\ast}/u_{s0}) > 0.4$. 
    612612 
     
    617617The OSMOSIS turbulent closure scheme is a similarity-scale scheme in 
    618618the same spirit as the K-profile 
    619 parameterization (KPP) scheme of \citet{large.ea_RG97}. 
     619parameterization (KPP) scheme of \citet{large.mcwilliams.ea_RG94}. 
    620620A specified shape of diffusivity, scaled by the (OSBL) depth 
    621621$h_{\mathrm{BL}}$ and a turbulent velocity scale, is imposed throughout the 
     
    628628as in KPP, it is set by a prognostic equation that is informed by 
    629629energy budget considerations reminiscent of the classical mixed layer 
    630 models of \citet{kraus.turner_tellus67}. 
     630models of \citet{kraus.turner_T67}. 
    631631The model also includes an explicit parametrization of the structure 
    632632of the pycnocline (the stratified region at the bottom of the OSBL). 
    633633 
    634634Presently, 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} 
     635number-dependent mixing scheme used in \citet{large.mcwilliams.ea_RG94}. 
     636 
     637Convective parameterizations such as described in \autoref{sec:ZDF_conv} 
    638638below should not be used with the OSMOSIS-OBL model: instabilities 
    639639within the OSBL are part of the model, while instabilities below the 
     
    641641 
    642642\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). 
     643The model supposes a boundary layer of thickness $h_{\mathrm{bl}}$ enclosing a well-mixed layer of thickness $h_{\mathrm{ml}}$ and a relatively thin pycnocline at the base of thickness $\Delta h$; \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). 
    644644\begin{figure}[!t] 
    645645  \begin{center} 
    646646    %\includegraphics[width=0.7\textwidth]{ZDF_OSM_structure_of_OSBL} 
    647647    \caption{ 
    648       \protect\label{fig: OSBL_structure} 
     648      \protect\label{fig:OSBL_structure} 
    649649     The structure of the entraining  boundary layer. (a) Mean buoyancy profile. (b) Profile of the buoyancy flux. 
    650650    } 
     
    654654 
    655655Consideration 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}; 
     656\begin{equation} 
     657  \label{eq:ZDF_w_La} 
     658  w_{*L}= \left(u_*^2 u_{s\,0}\right)^{1/3}; 
    658659\end{equation} 
    659660but at times the Stokes drift may be weak due to e.g.\ ice cover, short fetch, misalignment with the surface stress, etc.\ so  a composite velocity scale is assumed for the stable (warming) boundary layer: 
    660 \begin{equation}\label{eq:composite-nu} 
     661\begin{equation} 
     662  \label{eq:ZDF_composite-nu} 
    661663  \nu_{\ast}= \left\{ u_*^3 \left[1-\exp(-.5 \mathrm{La}_t^2)\right]+w_{*L}^3\right\}^{1/3}. 
    662664\end{equation} 
    663665For the unstable boundary layer this is merged with the standard convective velocity scale $w_{*C}=\left(\overline{w^\prime b^\prime}_0 \,h_\mathrm{ml}\right)^{1/3}$, where $\overline{w^\prime b^\prime}_0$ is the upwards surface buoyancy flux, to give: 
    664 \begin{equation}\label{eq:vel-scale-unstable} 
    665 \omega_* = \left(\nu_*^3 + 0.5 w_{*C}^3\right)^{1/3}. 
     666\begin{equation} 
     667  \label{eq:ZDF_vel-scale-unstable} 
     668  \omega_* = \left(\nu_*^3 + 0.5 w_{*C}^3\right)^{1/3}. 
    666669\end{equation} 
    667670 
    668671\subsubsection{The flux gradient model} 
    669672The 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 % 
     673 
     674\begin{equation} 
     675  \label{eq:ZDF_flux-grad-gen} 
     676  \overline{w^\prime\chi^\prime}=-K\frac{\partial\overline{\chi}}{\partial z} + N_{\chi,s} +N_{\chi,b} +N_{\chi,t}, 
     677\end{equation} 
     678 
    675679where $\chi$ 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. 
    676680 
    677681In 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 % 
     682 
     683\begin{equation} 
     684  \label{eq:ZDF_sigma} 
     685  \sigma_{\mathrm{ml}}= -z/h_{\mathrm{ml}}; \;\sigma_{\mathrm{bl}}= -z/h_{\mathrm{bl}}, 
     686\end{equation} 
     687 
    683688in 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) 
     689 
     690\begin{align} 
     691  \label{eq:ZDF_diff-unstable} 
     692  K_d=&0.8\, \omega_*\, h_{\mathrm{ml}} \, \sigma_{\mathrm{ml}} \left(1-\beta_d \sigma_{\mathrm{ml}}\right)^{3/2} 
     693  \\ 
     694  \label{eq:ZDF_visc-unstable} 
     695  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) 
    689696\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 % 
     697 
     698where $\beta_d$ 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 
     699 
     700\begin{equation} 
     701  \label{eq:ZDF_diff-wml-base} 
     702  K_{d,\mathrm{ml}}=K_{\nu,\mathrm{ml}}=\,0.16\,\omega_* \Delta h. 
     703\end{equation} 
     704 
    697705For 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). 
     706 
     707\begin{align} 
     708  \label{eq:ZDF_diff-stable} 
     709  K_d= & 0.75\,\, \nu_*\, h_{\mathrm{ml}}\,\,  \exp\left[-2.8 
     710       \left(h_{\mathrm{bl}}/L_L\right)^2\right]\sigma_{\mathrm{ml}} 
     711       \left(1-\sigma_{\mathrm{ml}}\right)^{3/2} \\ 
     712  \label{eq:ZDF_visc-stable} 
     713  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). 
    702714\end{align} 
    703 % 
     715 
    704716The 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} 
     717\begin{equation} 
     718  \label{eq:ZDF_L_L} 
    706719  L_L=-w_{*L}^3/\left<\overline{w^\prime b^\prime}\right>_L, 
    707720\end{equation} 
    708721with 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 % 
     722\begin{equation} 
     723  \label{eq:ZDF_stable-av-buoy-flux} 
     724  \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]. 
     725\end{equation} 
     726 
    713727In unstable conditions the eddy diffusivity and viscosity depend on stability through the velocity scale $\omega_*$, which depends on the two velocity scales $\nu_*$ and $w_{*C}$. 
    714728 
    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). 
     729Details 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). 
    716730 
    717731\subsubsection{Evolution of the boundary layer depth} 
     
    719733The prognostic equation for the depth of the neutral/unstable boundary layer is given by \citep{grant+etal18}, 
    720734 
    721 \begin{equation} \label{eq:dhdt-unstable} 
     735\begin{equation} 
     736  \label{eq:ZDF_dhdt-unstable} 
    722737%\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}} 
     738   \frac{\partial h_\mathrm{bl}}{\partial t} = W_b - \frac{{\overline{w^\prime b^\prime}}_\mathrm{ent}}{\Delta B_\mathrm{bl}} 
    724739\end{equation} 
    725740where $h_\mathrm{bl}$ is the horizontally-varying depth of the OSBL, 
     
    733748based on the potential energy budget of the OSBL, is the leading term 
    734749\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. 
     750models e.g.\ \citet{kraus.turner_T67}, in which the thickness of the pycnocline is taken to be zero. 
    736751 
    737752The entrainment flux for the combination of convective and Langmuir turbulence is given by 
    738 \begin{equation} \label{eq:entrain-flux} 
     753\begin{equation} 
     754  \label{eq:ZDF_entrain-flux} 
    739755  {\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}}} 
    740756  + 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] 
     
    744760For the stable boundary layer, the equation for the depth of the OSBL is: 
    745761 
    746 \begin{equation}\label{eq:dhdt-stable} 
     762\begin{equation} 
     763  \label{eq:ZDF_dhdt-stable} 
    747764\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. 
    748765\end{equation} 
    749766 
    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. 
     767\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. 
    751768 
    752769 
     
    11601177\] 
    11611178When \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. 
     1179Setting \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. 
    11631180 
    11641181These values are assigned in \mdl{zdfdrg}. 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_cfgs.tex

    r11693 r14113  
    198198(see \autoref{tab:CFGS_ORCA} and \autoref{fig:DOM_zgr_e3}). 
    199199The 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}), 
     200The default forcing uses the boundary forcing from \citet{large.yeager_trpt04} (see \autoref{subsec:SBC_blk_ocean}), 
    201201which was developed for the purpose of running global coupled ocean-ice simulations without 
    202202an interactive atmosphere. 
    203 This \citet{large.yeager_rpt04} dataset is available through 
     203This \citet{large.yeager_trpt04} dataset is available through 
    204204the \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. 
     205The "normal year" of \citet{large.yeager_trpt04} has been chosen of the \NEMO\ distribution since release v3.3. 
    206206 
    207207ORCA\_R2 pre-defined configuration can also be run with multiply online nested zooms (\ie\ with AGRIF, \key{agrif} defined). 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_misc.tex

    r12377 r14113  
    382382with their default settings: 
    383383 
    384 \begin{verbatim} 
     384\begin{forlines} 
    385385   sn_cfctl%l_allon  = .FALSE.    ! IF T activate all options. If F deactivate all unless l_config is T 
    386386     sn_cfctl%l_config = .TRUE.     ! IF .true. then control which reports are written with the following 
    387 \end{verbatim} 
     387\end{forlines} 
    388388 
    389389The first switch is a convenience option which can be used to switch on and off all 
    390390sub-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} 
     391if \forcode{sn_cfctl%l\_config} is also false. Specifically, the logic is: 
     392 
     393\begin{forlines} 
    394394  IF ( sn_cfctl%l_allon ) THEN 
    395395    set all suboptions .TRUE. 
     
    400400    set all suboptions .FALSE. 
    401401  ENDIF 
    402 \end{verbatim} 
     402\end{forlines} 
    403403 
    404404Details 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 
     405\forcode{sn_cfctl%l_glochk}.  This option modifies the action of the early warning checks 
     406carried out in \texttt{stpctl.F90}. These checks detect probable numerical instabilites 
    407407by searching for excessive sea surface heights or velocities and salinity values 
    408408outside a sensible physical range. If breaches are detected then the default behaviour 
    409409is to locate and report the local indices of the grid-point in breach. These indices 
    410410are 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 
     411\forcode{sn_cfctl%l_glochk} modifies this action by performing a global location of 
    412412the various minimum and maximum values and the global indices are reported. This has 
    413413some value in locating the most severe error in cases where the first detected error 
     
    427427average tracer value for each passive tracer. Collecting these metrics involves 
    428428global 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 
     429disabled by default by setting the respective options, \forcode{sn\_cfctl%runstat} and 
     430\forcode{sn\_cfctl%trcstat} to false. A compromise can be made by activating either or 
     431both of these options and setting the \forcode{sn\_cfctl%timincr} entry to an integer 
    432432value greater than one. This increment determines the time-step frequency at which 
    433433the global metrics are collected and reported.  This increment also applies to the 
     
    440440any warning or error messages generated during execution. A \texttt{layout.dat} 
    441441file 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 
     442suboptions: \forcode{sn\_cfctl%oceout} and \forcode{sn\_cfctl%layout} can be used 
    443443to 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 
     444when \forcode{sn\_cfctl%oceout} is true all processors produce their own version of 
    445445\texttt{ocean.output}.  All files, beyond the the normal reporting processor (narea == 1), are 
    446446named with a \_XXXX extension to their name, where XXXX is a 4-digit area number (with 
     
    449449systems so bug-hunting efforts using this facility should also utilise the \fortran: 
    450450 
    451 \begin{verbatim}  
     451\begin{forlines}  
    452452   CALL FLUSH(numout) 
    453 \end{verbatim} 
     453\end{forlines} 
    454454 
    455455statement 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 
     456the last model state. Associated with the \forcode{sn\_cfctl%oceout} option is the 
     457additional \forcode{sn\_cfctl%oasout} suboption. This does not activate its own output 
    458458file but rather activates the writing of addition information regarding the OASIS 
    459459configuration when coupling via oasis and the sbccpl routine. This information is 
     
    467467http://forge.ipsl.jussieu.fr/nemo/attachment/wiki/Documentation/prtctl_NEMO_doc_v2.pdf}{The 
    468468control 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 
     469of trends for either the physics or passive tracers are the \forcode{sn\_cfctl%prtctl} 
     470and \forcode{sn\_cfctl%prttrc} suboptions, respectively. Although, perhaps, of limited use for its 
    471471original intention, the ability to produce these control sums of trends in specific 
    472472areas provides another tool for diagnosing model behaviour.  If only the output from a 
    473473select 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 
     474for only a simple subset of processing regions. These are: \forcode{sn\_cfctl%procmin}, 
     475\forcode{sn\_cfctl%procmax} and \forcode{sn\_cfctl%procincr} which can be used to specify 
    476476the minimum and maximum active areas and the increment. The default values are set 
    477477such that all regions will be active. Note this subsetting can also be used to limit 
     
    481481\end{enumerate} 
    482482 
    483  
     483\begin{forlines} 
    484484   sn_cfctl%l_glochk = .FALSE.    ! Range sanity checks are local (F) or global (T). Set T for debugging only 
    485485   sn_cfctl%l_allon  = .FALSE.    ! IF T activate all options. If F deactivate all unless l_config is T 
     
    496496       sn_cfctl%procincr  = 1       ! Increment for optional subsetting of areas [default:1] 
    497497       sn_cfctl%ptimincr  = 1       ! Timestep increment for writing time step progress info 
    498  
    499  
     498\end{forlines} 
    500499 
    501500\subinc{\input{../../global/epilogue}} 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics.tex

    r11693 r14113  
    706706In this case, the free surface equation is nonlinear, 
    707707and 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 
     708These coordinates systems is presented in a report \citep{levier.treguier.ea_trpt07} available on 
    709709the \NEMO\ web site. 
    710710 
     
    841841This problem can be at least partially overcome by mixing $s$-coordinate and 
    842842step-like representation of bottom topography 
    843 \citep{gerdes_JGR93*a,gerdes_JGR93*b,madec.delecluse.ea_JPO96}. 
     843\citep{gerdes_JGR93,gerdes_JGR93*a,madec.delecluse.ea_JPO96}. 
    844844However, the definition of the model domain vertical coordinate becomes then a non-trivial thing for 
    845845a realistic bottom topography: 
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex

    r11693 r14113  
    3030 
    3131In 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. 
     32These coordinates systems is presented in a report \citep{levier.treguier.ea_trpt07} available on the \NEMO\ web site. 
    3333 
    3434\colorbox{yellow}{  end of to be updated} 
     
    170170 
    171171The 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 
     172which is weaker than the filtered free surface but still significant as shown by \citet{levier.treguier.ea_trpt07} in 
    173173the case of an analytical barotropic Kelvin wave. 
    174174 
     
    306306 
    307307In 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. 
     308This option is presented in a report \citep{levier.treguier.ea_trpt07} available on the \NEMO\ web site. 
    309309The three time-stepping methods (explicit, split-explicit and filtered) are the same as in 
    310310\autoref{?:DYN_spg_linear?} except that the ocean depth is now time-dependent. 
  • NEMO/trunk/doc/latex/SI3/build

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        22*.bbl 
        33*.blg 
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        98*.ind 
        109*.lo* 
        11 *.maf 
        12 *.mtc* 
        1310*.out 
        14 *.pdf 
        1511*.toc 
         12*.xdv 
        1613_minted-* 
  • NEMO/trunk/doc/latex/SI3/main/chapters.tex

    r12377 r14113  
    11\subfile{../subfiles/todolist} 
    2  
    3 \subfile{../subfiles/introduction}               % Introduction 
    42 
    53\subfile{../subfiles/chap_model_basics} 
  • NEMO/trunk/doc/latex/TOP/build

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        98*.ind 
        109*.lo* 
        11 *.maf 
        12 *.mtc* 
        1310*.out 
        14 *.pdf 
        1511*.toc 
         12*.xdv 
        1613_minted-* 
  • NEMO/trunk/doc/latex/TOP/main/chapters.tex

    r12377 r14113  
    1 \subfile{../subfiles/introduction} 
    21\subfile{../subfiles/model_description} 
    32\subfile{../subfiles/model_setup} 
  • NEMO/trunk/doc/latex/TOP/subfiles/model_description.tex

    r11694 r14113  
    11\documentclass[../main/TOP_manual]{subfiles} 
     2 
     3\begin{document} 
    24 
    35\newcommand{\cd}{\mathrm{CO_2}} 
     
    911\newcommand{\CODE}[1]{\textsc{#1}} 
    1012%\newcommand{\CODE}[1]{\textcolor{black}{\textsc{#1}}\xspace} 
    11  
    12 \begin{document} 
    1313 
    1414\chapter{Model Description} 
  • NEMO/trunk/doc/latex/global

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  • NEMO/trunk/doc/latex/global/document.tex

    r12377 r14113  
    11 
    2 %% ============================================================================== 
    3 %% Template structure for reference manual 
    4 %% ============================================================================== 
     2%% ================================================================================================= 
     3%% Template structure for reference manuals 
     4%% ================================================================================================= 
    55 
    66%% NEMO release version 
    7 \def \version{4.0rc~} 
     7\def \version{trunk} 
    88 
    99%% Preamble 
    10 %% ============================================================================== 
     10%% ================================================================================================= 
    1111 
    1212%% Document layout 
    13 \documentclass[draft]{scrreprt} 
     13\documentclass[fontsize = 10pt, twoside, abstract]{scrreprt} 
    1414 
    15 %% Load the configuration of the manual 
    16 \input{../main/definitions} 
    17  
    18 %% Load global *.tex files 
    19 \input{../../global/preamble} 
    20  
    21 \dominitoc 
    22  
    23 %% Launch the creation of the indexes 
    24 \input{../../global/indexes} 
    25  
     15%% Load manual configuration 
     16\input{../../global/prologue} 
    2617 
    2718%% End of common preamble between main and sub-files 
    2819%% Override custom cmds for full manual compilation 
    29 \newcommand{\onlyinsubfile}[1]{#1} 
    30 \newcommand{\notinsubfile}[1]{} 
     20\newcommand{\subinc}[1]{#1} 
     21\newcommand{\subexc}[1]{} 
    3122 
    3223\begin{document} 
    3324 
    34 \renewcommand{\onlyinsubfile}[1]{} 
    35 \renewcommand{\notinsubfile}[1]{#1} 
    36  
    37 \renewcommand{\biblio}{} 
    38 \renewcommand{\pindex}{} 
     25\renewcommand{\subinc}[1]{} 
     26\renewcommand{\subexc}[1]{#1} 
    3927 
    4028 
    4129%% Frontmatter 
    42 %% ============================================================================== 
     30%% ================================================================================================= 
    4331 
    44 \pagenumbering{gobble} 
     32\pagenumbering{gobble}   %% Disable page numbering temporarily 
    4533 
    4634%% Title page 
    4735\input{../../global/frontpage} 
    4836 
    49 \maketitle 
    50 \emptythanks 
     37%% Footer for introductory parts (no header by cleaning default) 
     38\ofoot[]{\engine\ Reference Manual} \ifoot[]{\pagemark} 
    5139 
    5240%% Information page (2nd page) 
    5341\input{../../global/info_page} 
    5442 
    55 %% Foreword 
    56 %\frontmatter   %% Chapter numbering off and Roman numerals for page numbers 
     43\listoffigures 
     44\listoflistings 
     45\listoftables 
     46 
     47\clearpage 
     48 
    5749\pagenumbering{roman} 
    58 \input{foreword} 
     50\ofoot[]{\engine\ Reference Manual} \ifoot[]{\pagemark} 
     51 
     52\input{introduction} 
    5953 
    6054%% Table of Contents 
    6155\tableofcontents 
    62 \listoffigures 
    63 \listoftables 
    64 \listoflistings 
    6556 
    6657\clearpage 
    67 %\end{document} 
    6858 
    6959 
    7060%% Mainmatter 
    71 %% ============================================================================== 
     61%% ================================================================================================= 
    7262 
    73 %\mainmatter   %% Chapter numbering on, page numbering is reset with Arabic numerals 
     63%% Headings for document body 
    7464\pagenumbering{arabic} 
     65\lohead{Chap.\ \thechapter\ \leftmark} \rehead{Sect.\ \thesection\ \rightmark} 
     66\ifoot[]{Page\ \pagemark\ of \pageref*{LastPage}} 
    7567 
    7668\include{chapters} 
     
    7870 
    7971%% Appendix 
    80 %% ============================================================================== 
     72%% ================================================================================================= 
    8173 
    82 %% Chapter numbering is reset with letters now 
    83 \appendix    
     74\appendix   %% Chapter numbering with letters by now 
     75\lohead{Apdx\ \thechapter\ \leftmark} 
     76\include{appendices} 
    8477 
    85 \include{appendices} 
     78%% Append coding rules for every manual 
     79\input{../../global/coding_rules} 
    8680 
    8781 
    8882%% Backmatter 
    89 %% ============================================================================== 
     83%% ================================================================================================= 
    9084 
    91 %\backmatter   %% Chapter numbering off 
    92  
    93 %% Bibliography 
    94 \phantomsection 
    95 \addcontentsline{toc}{chapter}{Bibliography} 
    96 \bibliography{../main/bibliography} 
    97  
    98 %% Index 
    99 \clearpage 
    100 \phantomsection 
    101 \addcontentsline{toc}{chapter}{Indexes} 
    102 \printindex[keys] 
    103 \printindex[modules] 
    104 \printindex[blocks] 
    105 \printindex[parameters] 
    106 \printindex[subroutines] 
     85%% Bibliography and indexes 
     86\input{../../global/epilogue} 
    10787 
    10888\end{document} 
    109  
  • NEMO/trunk/doc/latex/global/frontpage.tex

    r12377 r14113  
    11 
    2 \title{\heading} 
    3 \author{\firstauthor \and \secondauthor\thanks{\protect\input{thanks}}} 
    4 \date{\today} 
     2\begin{titlepage} 
     3%  \newgeometry{hmargin = 1.5cm, vmargin = 3cm} 
     4  \setlength{\parindent}{0pt} 
    55 
    6 \pretitle{ 
    76  \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}} 
     7    \begin{minipage}{0.3\textwidth} 
     8      \includegraphics[height=1.5cm]{logos/NEMO_grey} 
     9    \end{minipage}\begin{minipage}{0.6\textwidth} 
     10      \begin{center} 
     11      \Large\slshape 
     12      \textbf{N}ucleus for \textbf{E}uropean \textbf{M}odelling of the \textbf{O}cean \\ 
     13      \medskip 
     14      \hyperref[resources]{\textcolor{black}{ 
     15          \faWordpress \hspace{0.75cm} \faCodeFork      \hspace{0.75cm} 
     16          \faGithub    \hspace{0.75cm} \faCloudDownload \hspace{0.75cm} \faEnvelope 
     17        } 
     18      } 
     19      \end{center} 
     20    \end{minipage} 
     21  \end{center} 
     22 
     23  \spacetop 
     24  \textcolor{white}{\fontsize{0.8cm}{0.8cm}\selectfont\textbf{\heading}} 
     25  \ifdef{\subheading}{ 
     26    \medskip 
     27    \par 
     28    \textcolor{white}{\Huge \subheading} 
     29  }{} 
     30  \spacedown 
     31 
     32  \begin{center} 
     33    \LARGE Version \version\ -\ \today \\ 
     34    \medskip 
     35    \href{http://doi.org/10.5281/zenodo.\zid}{ \includegraphics{badges/zenodo.\zid} } 
     36  \end{center} 
     37 
     38  \vfill 
     39 
     40  \begin{minipage}{\authorswidth} 
     41    \raggedleft 
     42    \input{authors} 
     43  \end{minipage}\hspace{15pt}\begin{minipage}{0.02\linewidth} 
     44    \rule{1pt}{\rulelenght} 
     45  \end{minipage}\hspace{ 5pt}\begin{minipage}{\abstractwidth} 
     46    \begin{abstract} 
     47      \input{abstract} 
     48    \end{abstract} 
    1149  \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{ 
     50 
    2551  \vfill 
     52 
    2653  \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}} 
     54    \Large 
     55    \href{http://www.cmcc.it          }{ \includegraphics[height=1cm]{logos/CMCC} } \hspace{0.25cm} 
     56    \href{http://www.cnrs.fr          }{ \includegraphics[height=1cm]{logos/CNRS} } \hspace{0.25cm} 
     57    \href{http://www.mercator-ocean.fr}{ \includegraphics[height=1cm]{logos/MOI}  } \hspace{0.25cm} 
     58    \href{http://www.metoffice.gov.uk }{ \includegraphics[height=1cm]{logos/UKMO} } \hspace{0.25cm} 
     59    \href{http://nerc.ukri.org        }{ \includegraphics[height=1cm]{logos/NERC} } \\ 
     60    \medskip 
     61    \slshape 
     62    {C}ommunity \hspace{1.5em} {O}cean \hspace{1.5em} {M}odel \\ 
    3263  \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 } 
    4764 
    48 \thanksmarkseries{fnsymbol} 
     65\end{titlepage} 
    4966 
     67\restoregeometry 
  • NEMO/trunk/doc/latex/global/highlighting.tex

    r12377 r14113  
    22%% ============================================================================== 
    33 
    4 \usepackage[outputdir=../build]{minted} 
     4\usepackage[outputdir=../build, chapter, newfloat]{minted} 
    55 
    66%% Global highlighting style 
    77\definecolor{bg}{HTML}{f8f8f8} 
    88\usemintedstyle{emacs} 
    9 \setminted{bgcolor=bg, fontsize=\scriptsize, breaklines, frame=leftline} 
     9\setminted{bgcolor=bg, fontsize=\scriptsize, breaklines} 
    1010\setminted[xml]{style=borland} %% Specific per language 
    1111 
     
    2222 
    2323%% File 
    24 \newmintedfile[forfile]{fortran}{}   % \forfile{../namelists/nam...} 
     24\newmintedfile[forfile]{fortran}{} 
    2525 
    2626%% 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\newmintinline[forcode]{fortran}{bgcolor=, fontsize=auto}   % \forcode{...} 
     28\newmintinline[xmlcode]{xml}{    bgcolor=, fontsize=auto}   % \xmlcode{...} 
     29\newmintinline[snippet]{console}{bgcolor=, fontsize=auto}   % \snippet{...} 
    3030 
    3131%% Namelists inclusion 
    3232\newcommand{\nlst}[1]{\forfile{../../../namelists/#1}} 
    33  
  • NEMO/trunk/doc/latex/global/index.ist

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

    r12377 r14113  
    22\thispagestyle{plain} 
    33 
    4 % ================================================================ 
    5 % Disclaimer 
    6 % ================================================================ 
     4%% ================================================================ 
     5%% Disclaimer 
     6%% ================================================================ 
    77\subsubsection*{Disclaimer} 
    88 
    99Like all components of the modelling framework, 
    10 the \engine~core engine is developed under the \href{http://www.cecill.info}{CECILL license}, 
    11 which is a French adaptation of the GNU GPL (General Public License). 
     10the \engine\ core engine is developed under the \href{http://www.cecill.info}{CECILL license}, 
     11which is a French adaptation of the GNU GPL (\textbf{G}eneral \textbf{P}ublic \textbf{L}icense). 
    1212Anyone may use it freely for research purposes, and is encouraged to 
    13 communicate back to the NEMO team its own developments and improvements. 
     13communicate back to the development team its own developments and improvements. 
    1414 
    1515The model and the present document have been made available as a service to the community. 
     
    1818Users are encouraged to bring them to our attention. 
    1919 
    20 The authors assume no responsibility for problems, errors, or incorrect usage of NEMO. 
     20The authors assume no responsibility for problems, errors, or incorrect usage of \NEMO. 
    2121 
    22 % ================================================================ 
    23 % External resources 
    24 % ================================================================ 
     22%% ================================================================ 
     23%% External resources 
     24%% ================================================================ 
    2525\subsubsection*{Other resources} 
     26\label{resources} 
    2627 
    2728Additional information can be found on: 
    2829\begin{itemize} 
    29 \item the \href{http://www.nemo-ocean.eu}{website} of the project detailing several 
     30\item \faWordpress\ the \href{http://www.nemo-ocean.eu}{website} of the project detailing several 
    3031  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: 
     32\item \faCodeFork\ the \href{http://forge.ipsl.jussieu.fr/nemo}{development platform} of 
     33  the model with the code repository for the shared reference and some main resources 
     34  (wiki, ticket system, forums, \ldots) \\ 
     35  \faGithub\ the \href{http://github.com/NEMO-ocean/NEMO-examples} 
     36  {repository of the demonstration cases} for research or training 
     37\item \faCloudDownload\ the \href{http://zenodo.org/communities/nemo-ocean}{online archive} 
     38  delivering the publications issued by the consortium (manuals, reports, datasets, \ldots) 
     39\item \faEnvelope\ two mailing lists: 
    3640  the \href{http://listes.ipsl.fr/sympa/info/nemo-newsletter}{newsletter} for 
    3741  top-down communications from the project 
     
    4145\end{itemize} 
    4246 
    43 % ================================================================ 
    44 % Citation 
    45 % ================================================================ 
     47%% ================================================================ 
     48%% Citation 
     49%% ================================================================ 
    4650\subsubsection*{Citation} 
    4751 
    4852Reference for papers and other publications is as follows: 
    4953 
    50 \vspace{0.5cm} 
     54\medskip 
    5155 
    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} 
     56\begin{sloppypar} 
     57  ``{\bfseries \heading}\ifdef{\subheading}{ -- \subheading}{}'', 
     58  {\em Scientific Notes of Climate Modelling Center}, \textbf{\ipslnum} --- ISSN 1288-1619, 
     59  Institut Pierre-Simon Laplace (IPSL), 
     60  \href{https://doi.org/10.5281/zenodo.\zid}{doi:10.5281/zenodo.\zid} 
     61\end{sloppypar} 
    5962 
    6063\begin{figure}[b] 
    61   \begin{minipage}[c]{0.72\textwidth} 
    62     \small\ttfamily{Scientific Notes of Climate Modelling Center \\ 
    63       ISSN 1288-1619                                             \\ 
     64  \begin{minipage}[c]{0.7\textwidth} 
     65    \small 
     66    \ttfamily{ 
     67      Scientific Notes of Climate Modelling Center \\ 
     68      ISSN 1288-1619                               \\ 
    6469      Institut Pierre-Simon Laplace (IPSL) 
    6570    } 
     
    6772  \hfill 
    6873  \begin{minipage}[c]{0.25\textwidth} 
    69     \href{http://www.cmc.ipsl.fr}{\includegraphics[width=\textwidth]{logos/IPSL_upright}} 
     74    \href{http://www.cmc.ipsl.fr}{\includegraphics[width=\textwidth]{logos/IPSL_master}} 
    7075  \end{minipage} 
    7176\end{figure} 
    72  
  • NEMO/trunk/doc/latex/global/new_cmds.tex

    r12377 r14113  
    22%% ============================================================================== 
    33 
    4 %% Include references and index for compilation of single subfile  
    5 \newcommand{\mtoc}{\minitoc} 
    6 \newcommand{\biblio}{\bibliography{../main/bibliography}} 
    7 \newcommand{\pindex}{\printindex} 
     4%% Same slanted font for NEMO and its core engines 
     5\newcommand{\NEMO  }{\textsl{NEMO}} 
     6\newcommand{\OPA   }{\textsl{OPA}} 
     7\newcommand{\SIcube}{\textsl{SI$^3$}} 
     8\newcommand{\TOP   }{\textsl{TOP}} 
     9\newcommand{\PISCES}{\textsl{PISCES}} 
     10\newcommand{\NEMOVAR}{\textsl{NEMOVAR}} 
    811 
    9 %% NEMO and Fortran in small capitals 
    10 \newcommand{\NEMO}{\textsc{nemo}~} 
    11 \newcommand{\fortran}{\textsc{Fortran}~} 
    12 \newcommand{\fninety}{\textsc{Fortran 90}~} 
     12%% Links for external components 
     13\newcommand{\AGRIF}{\href{http://agrif.imag.fr}{AGRIF}} 
     14\newcommand{\CICE }{\href{http://github.com/CICE-Consortium/CICE}{CICE}} 
     15\newcommand{\OASIS}{\href{http://portal.enes.org/oasis}{OASIS}} 
     16\newcommand{\XIOS }{\href{http://forge.ipsl.jussieu.fr/ioserver}{XIOS}} 
     17 
     18%% Fortran in small capitals 
     19\newcommand{\fortran}{\textsc{Fortran}} 
     20\newcommand{\fninety}{\textsc{Fortran 90}} 
    1321 
    1422%% Common aliases 
     
    1826\newcommand{\ztilde}{\ensuremath{\tilde z}} 
    1927\newcommand{\stilde}{\ensuremath{\tilde s}} 
    20 \newcommand{\ie}{\ensuremath{i.e.}~} 
    21 \newcommand{\eg}{\ensuremath{e.g.}~} 
     28\newcommand{\ie}{\ensuremath{i.e.}} 
     29\newcommand{\eg}{\ensuremath{e.g.}} 
    2230 
    2331%% Inline maths 
     
    2533\newcommand{\rdt}{\Delta t} 
    2634 
    27 %% Text env. for Gurvan 
    28 \newcommand{\gmcomment}[1]{} 
     35%% Gurvan's comments 
     36\newcommand{\cmtgm}[1]{} 
    2937 
    3038%% Maths 
    3139\newcommand{\lt}{\left} 
    3240\newcommand{\rt}{\right} 
    33 \newcommand{\vect}[1]{\ensuremath{\mathbf{#1}}} 
     41\newcommand{\vect}[1]{\ensuremath{ \mathbf{#1} }} 
    3442\newcommand{\pd}[2][]{\ensuremath{\frac{\partial #1}{\partial #2}}} 
    3543 
    36 %% Workaround for issue with \listoffigures 
    37 \DeclareRobustCommand{\triad}[6][]{\ensuremath{{}_{#2}^{#3}{\mathbb{#4}_{#1}}_{#5}^{\,#6}}} 
     44%% Convert chapter/section headings to lowercase 
     45\renewcommand{\chaptermark}[1]{\markboth{#1}{}} 
     46\renewcommand{\sectionmark}[1]{\markright{#1}{}} 
     47 
     48%% Retrieve month name 
     49\renewcommand{\today}{ 
     50  \ifcase \month\or January\or February\or March\or 
     51                    April\or   May\or      June\or 
     52                    July\or    August\or   September\or 
     53                    October\or November\or December 
     54  \fi, \number \year 
     55} 
     56 
     57%% Link to orcid profile 
     58\newcommand{\orcid}[1]{\href{http://orcid.org/#1}{\textcolor{orcidcolor}\aiOrcidSquare}} 
     59 
     60%% Workaround for \listoffigures 
     61\DeclareRobustCommand{\triad}[6][]{\ensuremath{ {}_{#2}^{#3} { \mathbb{#4}_{#1} }_{#5}^{\,#6} }} 
     62 
     63%% New command for ToC 
     64\newcommand{\chaptertoc}[1][Table of contents]{% 
     65  \thispagestyle{empty} 
     66  \etocsettocstyle{\addsec*{#1}}{}% 
     67  \localtableofcontents% 
     68  \vfill 
     69} 
  • NEMO/trunk/doc/latex/global/packages.tex

    r12377 r14113  
    33%% ============================================================================== 
    44 
    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 
     5%% 'hyperref' pkg is loaded at the end of the preamble for higher compatibility 
    166 
    17 %% Extensions in bundle package 
    18 \usepackage{amssymb, graphicx, tabularx, textcomp} 
    19 \usepackage[utf8]{inputenc}              %% input encoding 
     7%% KOMA-script 
     8\usepackage[footsepline=0.25pt, headsepline=0.25pt]{scrlayer-scrpage} 
     9 
     10%% customization (layout, header/footer styles & contents, background) 
     11\usepackage{draftwatermark} 
     12\usepackage[margin = 2cm]{geometry} 
     13\usepackage[pages = some]{background}   %% 'some' for title page 
     14\usepackage[Bjornstrup]{fncychap} 
     15 
     16%% Fonts 
     17\usepackage{fontspec} 
     18%% Issue with fontawesome pkg: path to FontAwesome.otf has to be hard-coded 
     19\defaultfontfeatures{ 
     20    Path = /home/nicolas/.local/texlive/2020/texmf-dist/fonts/opentype/public/fontawesome/ 
     21} 
     22\usepackage{academicons, fontawesome, newtxtext} 
     23 
     24%% Formatting 
     25\usepackage[inline]{enumitem} 
     26\usepackage{etoc, tabularx, xcolor} 
     27 
     28%% Graphics 
     29\usepackage{caption, graphicx, grffile} 
     30 
     31%% Labels 
     32\usepackage{lastpage, natbib} 
     33 
     34%% Mathematics 
     35\usepackage{amsmath, amssymb, mathtools} 
     36 
     37%% Versatility 
     38\usepackage{subfiles} 
    2039 
    2140%% Configuration 
    22 \graphicspath{ {../../figures/} {../../figures/\engine/} } 
    23 %\captionsetup{margin=10pt, font={small}, labelsep=colon, labelfont={bf}} 
    24 \renewcommand{\bibfont}{\small} 
    25 %\renewcommand{\bibsep}{3pt} 
     41\graphicspath{ {../../../} {../figures/} } 
    2642 
     43%% Missing utmr8a font 
     44\usepackage{times} 
     45 
     46\usepackage{hyperref}   %% links 
  • NEMO/trunk/doc/latex/global/styles.tex

    r12377 r14113  
    33%% ============================================================================== 
    44 
    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} 
     5%% Colors 
     6\setmanualcolor 
     7\colorlet{manualcolorshaded}{manualcolor!60} 
     8\definecolor{orcidcolor}{HTML}{A6CE39} 
    129 
    1310%% 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} 
     11\pagestyle{scrheadings} 
     12\addtokomafont{pagehead}{  \sffamily              } 
     13\addtokomafont{pagefoot}{  \sffamily \footnotesize} 
     14\addtokomafont{pagenumber}{\sffamily \slshape     } 
     15\addtokomafont{chapter}{\color{white}} 
     16\ohead{} \ofoot{}   %% Clear defaults 
    2317 
     18%% Caption 
     19\captionsetup{font = footnotesize, justification = justified} 
     20 
     21%% Footnote 
     22\renewcommand{\thefootnote}{\fnsymbol{footnote}} 
     23 
     24%% Bibliography 
     25\bibliographystyle{../../global/ametsoc} 
     26\renewcommand{\bibfont}{\small} 
     27\renewcommand{\bibpreamble }{\begin{multicols}{2}} 
     28\renewcommand{\bibpostamble}{  \end{multicols}   } 
    2429 
    2530%% 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 
     31\makeatletter 
    6032 
     33%% Prevent error with tikz and namelist inclusion 
     34\global\let\tikz@ensure@dollar@catcode=\relax 
    6135 
     36%% First page 
     37\backgroundsetup{ 
     38  firstpage = true, 
     39  scale = 1, angle = 0, opacity = 1, 
     40  contents = { 
     41    \begin{tikzpicture}[remember picture, overlay] 
     42      \path [fill = manualcolor] (-0.5\paperwidth, 7) rectangle (0.5\paperwidth, 10); 
     43    \end{tikzpicture} 
     44  } 
     45} 
     46 
     47%% Apply engine color for chapter headings: tweaking snippets from fncychap.sty 
     48\renewcommand{\DOCH}{% 
     49  \settowidth{\py}{\CNoV\thechapter} 
     50  \addtolength{\py}{-10pt}      % Amount of space by which the 
     51%                                  % number is shifted right 
     52  \fboxsep=0pt% 
     53  \colorbox{manualcolor}{\rule{0pt}{40pt}\parbox[b]{\textwidth}{\hfill}}% 
     54  \kern-\py\raise20pt% 
     55  \hbox{\color{manualcolorshaded}\CNoV\thechapter}\\% 
     56} 
     57\renewcommand{\DOTI}[1]{% 
     58  \nointerlineskip\raggedright% 
     59  \fboxsep=\myhi% 
     60  \vskip-1ex% 
     61  \colorbox{manualcolor}{\parbox[t]{\mylen}{\color{white}\CTV\FmTi{#1}}}\par\nobreak% 
     62  \vskip 40\p@% 
     63} 
     64\renewcommand{\DOTIS}[1]{% 
     65  \fboxsep=0pt 
     66  \colorbox{manualcolor}{\rule{0pt}{40pt}\parbox[b]{\textwidth}{\hfill}}\\% 
     67  \nointerlineskip\raggedright% 
     68  \fboxsep=\myhi% 
     69  \vskip-1ex% Remove white 1pt line 
     70  \colorbox{manualcolor}{\parbox[t]{\mylen}{\color{white}\CTV\FmTi{#1}}}\par\nobreak% 
     71  \vskip 40\p@% 
     72} 
     73 
     74%% Temporary fix 
     75\def\set@curr@file#1{% 
     76  \begingroup 
     77    \escapechar\m@ne 
     78    \xdef\@curr@file{\expandafter\string\csname #1\endcsname}% 
     79  \endgroup 
     80} 
     81\def\quote@name#1{"\quote@@name#1\@gobble""} 
     82\def\quote@@name#1"{#1\quote@@name} 
     83\def\unquote@name#1{\quote@@name#1\@gobble"} 
     84 
     85\makeatother 
  • NEMO/trunk/doc/rst/source/cfgs.bib

    r11718 r14113  
    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/trunk/doc/rst/source/zooms.bib

    r10201 r14113  
    1 link ../../../cfgs/AGRIF_DEMO/zooms.bib 
     1link ../../../src/NST/zooms.bib 
  • NEMO/trunk/doc/rst/source/zooms.rst

    r10201 r14113  
    1 link ../../../cfgs/AGRIF_DEMO/README.rst 
     1link ../../../src/NST/README.rst 
  • NEMO/trunk/doc/tools/shr_func.sh

    r11598 r14113  
    44    printf "\t¤ Clean previous build" 
    55    find latex/$1/build -mindepth 1 -delete 
    6  
    76    echo 
    87} 
     
    109build() { 
    1110    printf "\t¤ Generation of the PDF format\n" 
    12     latexmk -r  ./latex/global/latexmk.pl -pdfxe ./latex/$1/main/$1_manual \ 
     11    latexmk -r ./latex/global/latexmk.pl -pdfxe ./latex/$1/main/$1_manual \ 
    1312#  1> /dev/null 
    1413    [ -f ./latex/$1/build/$1_manual.pdf ] && mv ./latex/$1/build/$1_manual.pdf . 
  • NEMO/trunk/src/OCE/ASM/README.rst

    r10201 r14113  
    1 link ../../../doc/rst/source/data_assimilation.rst 
     1link ../../../doc/rst/source/da.rst 
  • NEMO/trunk/src/OCE/OBS/README.rst

    r10201 r14113  
    1 link ../../../doc/rst/source/data_assimilation.rst 
     1link ../../../doc/rst/source/da.rst 
  • NEMO/trunk/src/OCE/SBC/README.rst

    r10201 r14113  
    1 link ../../../doc/rst/source/coupling.rst 
     1link ../../../doc/rst/source/cplg.rst 
  • NEMO/trunk/src/SAS/README.rst

    r10201 r14113  
    1 link ../../doc/rst/source/coupling.rst 
     1link ../../doc/rst/source/cplg.rst 
  • NEMO/trunk/tests/test_cases.bib

    r12377 r14113  
    1 @book{HAIDVOGEL1999, 
    2    author = {D. B. Haidvogel and A. Beckmann}, 
    3    publisher = {Imperial College Press, London}, 
    4    year = {1999}, 
    5    title = {Numerical ocean circulation modeling} 
     1 
     2@article{         brodeau.barnier.ea_JPO16, 
     3  title         = "Climatologically Significant Effects of Some 
     4                  Approximations in the Bulk Parameterizations of Turbulent 
     5                  Air–Sea Fluxes", 
     6  pages         = "5--28", 
     7  journal       = "Journal of Physical Oceanography", 
     8  volume        = "47", 
     9  number        = "1", 
     10  author        = "Brodeau, Laurent and Barnier, Bernard and Gulev, Sergey K. 
     11                  and Woods, Cian", 
     12  year          = "2016", 
     13  month         = "Dec", 
     14  publisher     = "American Meteorological Society", 
     15  issn          = "1520-0485", 
     16  doi           = "10.1175/jpo-d-16-0169.1" 
    617} 
    718 
    8 @book{BURCHARD2002, 
    9    title={GETM: A General Estuarine Transport Model; Scientific Documentation}, 
    10    author={Burchard, Hans and Bolding, Karsten}, 
    11    year={2002}, 
    12    publisher={European Commission, Joint Research Centre, Institute for Environment and Sustainability} 
     19@techreport{      burchard.bolding_trpt02, 
     20  title         = "GETM, A General Estuarine Transport Model: Scientific 
     21                  Documentation", 
     22  pages         = "", 
     23  series        = "Tech. Rep. EUR 20253 EN", 
     24  author        = "Burchard, Hans and Bolding, Karsten", 
     25  institution   = "European Commission", 
     26  year          = "2002", 
     27  month         = "01" 
    1328} 
    1429 
    15 @article{ILICAK2012, 
    16    title = "Spurious dianeutral mixing and the role of momentum closure", 
    17    journal = "Ocean Modelling", 
    18    volume = "45-46", 
    19    pages = "37 - 58", 
    20    year = "2012", 
    21    issn = "1463-5003", 
    22    doi = "10.1016/j.ocemod.2011.10.003", 
    23    author = "Mehmet Ilicak and Alistair J. Adcroft and Stephen M. Griffies and Robert W. Hallberg", 
    24    keywords = "Spurious dianeutral transport, Cabbeling, Overflows, Exchange-flow, Ocean models, Momentum transport, Tracer advection, Reference potential energy" 
     30@article{         haidvogel.beckmann_SESM99, 
     31  title         = "Numerical Ocean Circulation Modeling", 
     32  journal       = "Series on Environmental Science and Management", 
     33  author        = "Haidvogel, Dale B and Beckmann, Aike", 
     34  year          = "1999", 
     35  month         = "Apr", 
     36  publisher     = "IMPERIAL COLLEGE PRESS", 
     37  issn          = "0219-9793", 
     38  isbn          = "9781860943935", 
     39  doi           = "10.1142/p097" 
    2540} 
    2641 
    27 @article{DEBREU2012, 
    28    title = "Two-way nesting in split-explicit ocean models: Algorithms, implementation and validation", 
    29    journal = "Ocean Modelling", 
    30    volume = "49-50", 
    31    pages = "1 - 21", 
    32    year = "2012", 
    33    issn = "1463-5003", 
    34    doi = "10.1016/j.ocemod.2012.03.003", 
    35    author = "Laurent Debreu and Patrick Marchesiello and Pierrick Penven and Gildas Cambon", 
    36    keywords = "Two-way nesting, Finite difference method, Modeling, Boundary conditions, Coastal upwelling" 
     42@article{         ilıcak.adcroft.ea_OM12, 
     43  title         = "Spurious dianeutral mixing and the role of momentum 
     44                  closure", 
     45  pages         = "37--58", 
     46  journal       = "Ocean Modelling", 
     47  volume        = "45-46", 
     48  author        = "Ilıcak, Mehmet and Adcroft, Alistair J. and Griffies, 
     49                  Stephen M. and Hallberg, Robert W.", 
     50  year          = "2012", 
     51  month         = "Jan", 
     52  publisher     = "Elsevier BV", 
     53  issn          = "1463-5003", 
     54  doi           = "10.1016/j.ocemod.2011.10.003" 
    3755} 
    3856 
    39 @article{PENVEN2006, 
    40    title = "Evaluation and application of the ROMS 1-way embedding procedure to the central california upwelling system", 
    41    journal = "Ocean Modelling", 
    42    volume = "12", 
    43    number = "1", 
    44    pages = "157 - 187", 
    45    year = "2006", 
    46    issn = "1463-5003", 
    47    doi = "10.1016/j.ocemod.2005.05.002", 
    48    author = "Pierrick Penven and Laurent Debreu and Patrick Marchesiello and James C. McWilliams", 
    49    keywords = "Ocean models, Boundary conditions, Embedding, Coastal upwelling, Mesoscale eddies, Eddy kinetic energy, North America, West Coast, Central upwelling system, Monterey Bay, 35–41°N, 128–121°W" 
     57@article{         lipscomb.hunke_MWR04, 
     58  title         = "Modeling Sea Ice Transport Using Incremental Remapping", 
     59  pages         = "1341--1354", 
     60  journal       = "Monthly Weather Review", 
     61  volume        = "132", 
     62  number        = "6", 
     63  author        = "Lipscomb, William H. and Hunke, Elizabeth C.", 
     64  year          = "2004", 
     65  month         = "Jun", 
     66  publisher     = "American Meteorological Society", 
     67  issn          = "1520-0493", 
     68  doi           = "10.1175/1520-0493(2004)132<1341:msitui>2.0.co;2" 
    5069} 
    5170 
    52 @article{SPALL1991, 
    53    author = {Spall, M. A. and Holland, W. R.}, 
    54    title = {A Nested Primitive Equation Model for Oceanic Applications}, 
    55    journal = {Journal of Physical Oceanography}, 
    56    volume = {21}, 
    57    number = {2}, 
    58    pages = {205-220}, 
    59    year = {1991}, 
    60    doi = {10.1175/1520-0485(1991)021<0205:ANPEMF>2.0.CO;2}, 
     71@article{         losch_JGR08, 
     72  title         = "Modeling ice shelf cavities in a z coordinate ocean 
     73                  general circulation model", 
     74  journal       = "Journal of Geophysical Research", 
     75  volume        = "113", 
     76  number        = "C8", 
     77  author        = "Losch, M.", 
     78  year          = "2008", 
     79  month         = "Aug", 
     80  publisher     = "American Geophysical Union (AGU)", 
     81  issn          = "0148-0227", 
     82  doi           = "10.1029/2007jc004368" 
    6183} 
    6284 
    63 @article{MATHIOT2017, 
    64    author = {Mathiot, P. and Jenkins, A. and Harris, C. and Madec, G.}, 
    65    title = {Explicit representation and parametrised impacts of under ice shelf seas in the ${z}^{\ast}$ coordinate ocean model NEMO 3.6}, 
    66    journal = {Geoscientific Model Development}, 
    67    volume = {10}, 
    68    year = {2017}, 
    69    number = {7}, 
    70    pages = {2849--2874}, 
    71    url = {https://www.geosci-model-dev.net/10/2849/2017/}, 
    72    doi = {10.5194/gmd-10-2849-2017} 
     85@article{         mathiot.jenkins.ea_GMD17, 
     86  title         = "Explicit representation and parametrised impacts of under 
     87                  ice shelf seas in the ${z}^{\ast}$ coordinate ocean model 
     88                  NEMO 3.6", 
     89  pages         = "2849--2874", 
     90  journal       = "Geoscientific Model Development", 
     91  volume        = "10", 
     92  number        = "7", 
     93  author        = "Mathiot, Pierre and Jenkins, Adrian and Harris, 
     94                  Christopher and Madec, Gurvan", 
     95  year          = "2017", 
     96  month         = "Jul", 
     97  publisher     = "Copernicus GmbH", 
     98  issn          = "1991-9603", 
     99  doi           = "10.5194/gmd-10-2849-2017" 
    73100} 
    74101 
    75 @article{LOSCH2008, 
    76    author = {Losch, M.}, 
    77    title = {Modeling ice shelf cavities in a z coordinate ocean general circulation model}, 
    78    journal = {Journal of Geophysical Research: Oceans}, 
    79    volume = {113}, 
    80    year = {2008}, 
    81    number = {C8}, 
    82    pages = {}, 
    83    keywords = {Ice shelf cavities, numerical ocean modeling, z coordinates}, 
    84    doi = {10.1029/2007JC004368}, 
    85    url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2007JC004368}, 
    86    eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2007JC004368}, 
    87    abstract = {Processes at the ice shelf-ocean interface and in particular in ice shelf cavities around Antarctica have an observable effect on the solutions of basin scale to global coupled ice-ocean models. Despite this, these processes are not routinely represented in global ocean and climate models. It is shown that a new ice shelf cavity model for z coordinate models can reproduce results from an intercomparison project of earlier approaches with vertical ?~C or isopycnic coordinates. As a proof of concept, ice shelves are incorporated in a 100-year global integration of a z coordinate model. In this simulation, glacial meltwater can be traced as far as north as 15??S. The observed effects of processes in the ice shelf cavities agree with previous results from a ?~C coordinate model, notably the increase in sea ice thickness. However, melt rates are overestimated probably because the parameterization of basal melting does not suit the low resolution of this configuration.} 
     102@article{         schär.smolarkiewicz_JCP96, 
     103  title         = "A Synchronous and Iterative Flux-Correction Formalism for 
     104                  Coupled Transport Equations", 
     105  pages         = "101--120", 
     106  journal       = "Journal of Computational Physics", 
     107  volume        = "128", 
     108  number        = "1", 
     109  author        = "Schär, Christoph and Smolarkiewicz, Piotr K.", 
     110  year          = "1996", 
     111  month         = "Oct", 
     112  publisher     = "Elsevier BV", 
     113  issn          = "0021-9991", 
     114  doi           = "10.1006/jcph.1996.0198" 
    88115} 
    89  
    90 @article{LIPSCOMB2004, 
    91    author = {Lipscomb, William H. and Hunke, Elizabeth C.}, 
    92    title = {Modeling Sea Ice Transport Using Incremental Remapping}, 
    93    journal = {Monthly Weather Review}, 
    94    volume = {132}, 
    95    number = {6}, 
    96    pages = {1341-1354}, 
    97    year = {2004}, 
    98    doi = {10.1175/1520-0493(2004)132<1341:MSITUI>2.0.CO;2}, 
    99    URL = {https://doi.org/10.1175/1520-0493(2004)132<1341:MSITUI>2.0.CO;2}, 
    100    eprint = {https://doi.org/10.1175/1520-0493(2004)132<1341:MSITUI>2.0.CO;2}, 
    101    abstract = { Abstract Sea ice models contain transport equations for the area, volume, and energy of ice and snow in various thickness categories. These equations typically are solved with first-order-accurate upwind schemes, which are very diffusive; with second-order-accurate centered schemes, which are highly oscillatory; or with more sophisticated second-order schemes that are computationally costly if many quantities must be transported [e.g., multidimensional positive-definite advection transport algorithm (MPDATA)]. Here an incremental remapping scheme, originally designed for horizontal transport in ocean models, is adapted for sea ice transport. This scheme has several desirable features: it preserves the monotonicity of both conserved quantities and tracers; it is second-order accurate except where the accuracy is reduced locally to preserve monotonicity; and it efficiently solves the large number of equations in sea ice models with multiple thickness categories and tracers. Remapping outperforms the first-order upwind scheme and basic MPDATA scheme in several simple test problems. In realistic model runs, remapping is less diffusive than the upwind scheme and about twice as fast as MPDATA. } 
    102 } 
    103  
    104 @article{SCHAR1996, 
    105    author = {Christoph Schär and Piotr K. Smolarkiewicz}, 
    106    title = {A Synchronous and Iterative Flux-Correction Formalism for Coupled Transport Equations}, 
    107    journal = {Journal of Computational Physics}, 
    108    volume = {128}, 
    109    number = {1}, 
    110    pages = {101 - 120}, 
    111    year = {1996}, 
    112    issn = {0021-9991}, 
    113    doi = {https://doi.org/10.1006/jcph.1996.0198}, 
    114    url = {http://www.sciencedirect.com/science/article/pii/S0021999196901989}, 
    115    abstract = {Many problems of fluid dynamics involve the coupled transport of several, density-like, dependent variables (for instance, densities of mass and momenta in elastic flows). In this paper, a conservative and synchronous flux-corrected transport (FCT) formalism is developed which aims at a consistent transport of such variables. The technique differs from traditional FCT algorithms in two respects. First, the limiting of transportive fluxes of the primary variables (e.g., mass and momentum) does not derive from smooth estimates of the variables, but it derives from analytic constraints implied by the Lagrangian form of the governing continuity equations, which are imposed on the specific mixing ratios of the variables (e.g., velocity components). Second, the traditional FCT limiting based on sufficiency conditions is augmented by an iterative procedure which approaches the necessity requirements. This procedure can also be used in the framework of traditional FCT schemes, and a demonstration is provided that it can significantly reduce some of the pathological behaviors of FCT algorithms. Although the approach derived is applicable to the transport of arbitrary conserved quantities, it is particularly useful for the synchronous transport of mass and momenta in elastic flows, where it assures intrinsic stability of the algorithm regardless of the magnitude of the mass-density variable. This latter property becomes especially important in fluids with large density variations, or in models with a material “vertical” coordinate (e.g., geophysical hydrostatic stratified flows in isopycnic/isentropic coordinates), where material surfaces can collapse to zero-mass layers admitting, therefore, arbitrarily large local Courant numbers.} 
    116 } 
    117  
    118 @article{Brodeau_al_2017, 
    119 author={Laurent Brodeau and Bernard Barnier and Sergey Gulev and Cian Woods}, 
    120 title={Climatologically significant effects of some approximations in the bulk parameterizations of turbulent air-sea fluxes}, 
    121 journal={J. Phys. Oceanogr.}, 
    122 doi={10.1175/JPO-D-16-0169.1}, 
    123 year={2017}, 
    124 pages = {5-28}, 
    125 volume={47}, 
    126 number={1} 
    127 } 
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