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

Since March 2022 along with NEMO 4.2 release, the code development moved to a self-hosted GitLab.
This present forge is now archived and remained online for history.
Changeset 11573 for NEMO/branches/2019/dev_r11233_AGRIF-05_jchanut_vert_coord_interp/doc/latex/NEMO/main – NEMO

Ignore:
Timestamp:
2019-09-19T11:18:03+02:00 (5 years ago)
Author:
jchanut
Message:

#2222, merged with trunk

Location:
NEMO/branches/2019/dev_r11233_AGRIF-05_jchanut_vert_coord_interp/doc/latex/NEMO/main
Files:
1 deleted
6 edited
1 copied

Legend:

Unmodified
Added
Removed

  • NEMO/branches/2019/dev_r11233_AGRIF-05_jchanut_vert_coord_interp/doc/latex/NEMO/main/appendices.tex

    r11187 r11573  
    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/branches/2019/dev_r11233_AGRIF-05_jchanut_vert_coord_interp/doc/latex/NEMO/main/bibliography.bib

    r11213 r11573  
    188188} 
    189189 
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     192pages = "255--270", 
     193journal = "Quarterly Journal of the Royal Meteorological Society", 
     194volume = "121", 
     195number = "522", 
     196author = "Beljaars, Anton C. M.", 
     197year = "1995", 
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     199 publisher     = "Wiley", 
     200issn = "00359009", 
     201doi = "10.1002/qj.49712152203" 
     202} 
     203 
    190204@article{         bernie.guilyardi.ea_CD07, 
    191205  title         = "Impact of resolving the diurnal cycle in an 
    … …  
    386400} 
    387401 
     402@article{         brodeau.barnier.ea_JPO16, 
     403  title         = "Climatologically Significant Effects of Some Approximations in the Bulk Parameterizations of Turbulent Air–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          = "2016", 
     410  month         = "jan", 
     411  publisher     = "American Meteorological Society", 
     412  issn          = "0022-3670", 
     413  doi           = "10.1175/jpo-d-16-0169.1", 
     414} 
     415 
    388416@article{         brown.campana_MWR78, 
    389417  title         = "An economical time-differencing system for numerical 
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    745773} 
    746774 
     775@article{ edson.jampana.ea_JPO13, 
     776title = "On the Exchange of Momentum over the Open Ocean", 
     777pages = "1589--1610", 
     778journal = "Journal of Physical Oceanography", 
     779volume = "43", 
     780number = "8", 
     781author = "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", 
     782year = "2013", 
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     784publisher = "American Meteorological Society", 
     785issn = "0022-3670", 
     786doi = "10.1175/JPO-D-12-0173.1" 
     787} 
     788 
    747789@article{         egbert.ray_JGR01, 
    748790  title         = "Estimates of {M2} tidal energy dissipation from 
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    819861} 
    820862 
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     864title = "Bulk parameterization of air-sea fluxes: Updates and verification for the COARE algorithm", 
     865pages = "571--591", 
     866journal = "Journal of Climate", 
     867volume = "16", 
     868number = "4", 
     869author = "Fairall, C. W. and Bradley, E. F. and Hare, J. E. and Grachev, A. A. and Edson, J. B.", 
     870year = "2003", 
     871publisher = "American Meteorological Society", 
     872issn = "08948755", 
     873doi = "10.1175/1520-0442(2003)016<0571:BPOASF>2.0.CO;2" 
     874} 
     875 
    821876@phdthesis{       farge-coulombier_phd87, 
    822877  title         = "Dynamique non-lin\'{e}aire des ondes et des tourbillons 
    … …  
    871926  publisher     = "UNESCO", 
    872927  url           = "https://unesdoc.unesco.org/ark:/48223/pf0000059832.locale=en" 
     928} 
     929 
     930@article{         foxkemper.ferrari_JPO08, 
     931  title         = "Parameterization of Mixed Layer Eddies. Part I: Theory and Diagnosis", 
     932  pages         = "1145--1165", 
     933  journal       = "Journal of Physical Oceanography", 
     934  volume        = "38", 
     935  number        = "6", 
     936  author        = "B. Fox-Kemper and R. Ferrari and B. Hallberg", 
     937  year          = "2008", 
     938  month         = "jun", 
     939  publisher     = "American Meteorological Society", 
     940  issn          = "1520-0485", 
     941  doi           = "10.1175/2007JPO3792.1" 
    873942} 
    874943 
    … …  
    18391908  author        = "F. Lott and G. Madec and J. Verron", 
    18401909  year          = "1990" 
     1910} 
     1911 
     1912@article{     lupkes.gryanik.ea_JGR12, 
     1913  author    = "L{\"{u}}pkes, Christof and Gryanik, Vladimir M. and Hartmann, J{\"{o}}rg and Andreas, Edgar L.", 
     1914  doi       = "10.1029/2012JD017630", 
     1915  issn      = "01480227", 
     1916  journal   = "Journal of Geophysical Research Atmospheres", 
     1917  number    = "13", 
     1918  pages  = "1--18", 
     1919  title  = "A parametrization, based on sea ice morphology, of the neutral atmospheric drag coefficients for weather prediction and climate models", 
     1920  volume    = "117", 
     1921  year      = "2012" 
     1922} 
     1923 
     1924@article{     lupkes.gryanik_JGR15, 
     1925  author    = "L{\"{u}}pkes, Christof and Gryanik, Vladimir M.", 
     1926  doi       = "10.1002/2014JD022418", 
     1927  issn      = "21562202", 
     1928  journal   = "Journal of Geophysical Research", 
     1929  number    = "2", 
     1930  pages  = "552--581", 
     1931  title  = "A stability-dependent parametrization of transfer coefficients formomentum and heat over polar sea ice to be used in climate models", 
     1932  volume    = "120", 
     1933  year      = "2015" 
    18411934} 
    18421935 
    … …  
    23062399} 
    23072400 
     2401@article{         qiao.yuan.ea_OD10, 
     2402  title         = "A three-dimensional surface wave–ocean circulation coupled  
     2403                  model and its initial testing", 
     2404  pages         = "1339--1335", 
     2405  journal       = "Ocean Dynamics", 
     2406  volume        = "60", 
     2407  number        = "5", 
     2408  author        = "F. Qiao and Y. Yuan and T. Ezer and C. Xia and  
     2409                   Y. Yang and X. Lu and Z. Song ", 
     2410  year          = "2010", 
     2411  month         = "oct", 
     2412  publisher     = "Springer-Verlag", 
     2413  issn          = "1616-7341", 
     2414  doi           = "10.1007/s10236-010-0326-y" 
     2415} 
     2416 
    23082417@article{         redi_JPO82, 
    23092418  title         = "Oceanic isopycnal mixing by coordinate rotation", 
    … …  
    25442653} 
    25452654 
     2655@article{         smagorinsky_MW63, 
     2656  title         = "General circulation experiments with the primitive equations: I. The basic experiment ", 
     2657  pages         = "99--164", 
     2658  journal       = "Monthly Weather Review", 
     2659  volume        = "91", 
     2660  number        = "3", 
     2661  author        = "J. Smagorinsky", 
     2662  year          = "1963", 
     2663  month         = "mar", 
     2664  publisher     = "American Meteorological Society", 
     2665  issn          = "1520-0493", 
     2666  doi           = "10.1175/1520-0493(1963)091<0099:GCEWTP>2.3.CO;2" 
     2667} 
     2668 
    25462669@article{         song.haidvogel_JCP94, 
    25472670  title         = "A semi-implicit ocean circulation model using a 
    … …  
    28963019} 
    28973020 
     3021@article{         white.hoskins.ea_QJRMS05, 
     3022  title         = "Consistent approximate models of the global atmosphere: shallow, deep, 
     3023                  hydrostatic, quasi-hydrostatic and non-hydrostatic", 
     3024  pages         = "2081--2107", 
     3025  journal       = "Quarterly Journal of the Royal Meteorological Society", 
     3026  volume        = "131", 
     3027  author        = "A. A. White and B. J. Hoskins and I. Roulstone and A. Staniforth", 
     3028  year          = "2005", 
     3029  doi           = "10.1256/qj.04.49" 
     3030} 
     3031 
    28983032@article{         white.adcroft.ea_JCP09, 
    28993033  title         = "High-order regridding-remapping schemes for continuous 

  • NEMO/branches/2019/dev_r11233_AGRIF-05_jchanut_vert_coord_interp/doc/latex/NEMO/main/chapters.tex

    r11170 r11573  
    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/branches/2019/dev_r11233_AGRIF-05_jchanut_vert_coord_interp/doc/latex/NEMO/main/definitions.tex

    r11176 r11573  
    1 %% Engine (folder name) 
     1%% Engine (subfolder name) 
    22\def \engine{NEMO} 
    33 
    4 %% Title (variable name already use by 'titling' pkg) 
     4%% Cover page settings 
     5\def \spacetop{  \vspace*{1.85cm} } 
    56\def \heading{NEMO ocean engine} 
     7%\def \subheading{} 
     8\def \spacedown{ \vspace*{0.75cm } } 
     9\def \authorswidth{  0.3\linewidth} 
     10\def \rulelenght{270pt} 
     11\def \abstractwidth{0.6\linewidth} 
    612 
    7 %% Authors (thanks will apply to the second author) 
    8 \def \firstauthor{Gurvan Madec~} 
    9 \def \secondauthor{NEMO System Team} 
     13%% Manual color (frontpage banner, links  and chapter boxes) 
     14\def \setmanualcolor{ \definecolor{manualcolor}{cmyk}{1, .60, 0, .40} } 
    1015 
    1116%% IPSL publication number 

  • NEMO/branches/2019/dev_r11233_AGRIF-05_jchanut_vert_coord_interp/doc/latex/NEMO/main/foreword.tex

    r11176 r11573  
    1 % ================================================================ 
    2 % Foreword 
    3 % ================================================================ 
    4 \chapter*{Foreword} 
     1%% ================================================================ 
     2%% Abstract 
     3%% ================================================================ 
    54 
    6 The ocean engine of NEMO (Nucleus for European Modelling of the Ocean) is a primitive equation model adapted to 
    7 regional and global ocean circulation problems. 
    8 It is intended to be a flexible tool for studying the ocean and its interactions with the others components of 
    9 the earth climate system over a wide range of space and time scales. 
     5%% Common part between NEMO-SI3-TOP 
     6\NEMO\ (``Nucleus for European Modelling of the Ocean'') is a framework of ocean-related engines. 
     7It is intended to be a flexible tool for studying the ocean dynamics and thermodynamics (``blue ocean''), 
     8as well as its interactions with the components of the Earth climate system over 
     9a wide range of space and time scales. 
     10Within \NEMO, the ocean engine is interfaced with a sea-ice model (\SIcube\ or 
     11\href{http://github.com/CICE-Consortium/CICE}{CICE}), 
     12passive tracers and biogeochemical models (\TOP) and, 
     13via the \href{http://portal.enes.org/oasis}{OASIS} coupler, 
     14with several atmospheric general circulation models. 
     15It also supports two-way grid embedding by means of the \href{http://agrif.imag.fr}{AGRIF} software. 
    1016 
     17%% Specific part 
     18The primitive equation model is adapted to regional and global ocean circulation problems down to 
     19kilometric scale. 
    1120Prognostic variables are the three-dimensional velocity field, a non-linear sea surface height, 
    1221the \textit{Conservative} Temperature and the \textit{Absolute} Salinity. 
    13 In the horizontal direction, the model uses a curvilinear orthogonal grid and in the vertical direction, 
    14 a full or partial step $z$-coordinate, or $s$-coordinate, or a mixture of the two. 
     22In the horizontal direction, the model uses a curvilinear orthogonal grid and 
     23in the vertical direction, a full or partial step $z$-coordinate, or $s$-coordinate, or 
     24a mixture of the two. 
    1525The distribution of variables is a three-dimensional Arakawa C-type grid. 
    16 Various physical choices are available to describe ocean physics, including TKE, and GLS vertical physics. 
    17  
    18 Within NEMO, the ocean is interfaced with a sea-ice model (SI$^3$) 
    19  %or \href{https://github.com/CICE-Consortium/CICE}{CICE}), 
    20 passive tracer and biogeochemical models (TOP-PISCES) and, 
    21 via the \href{https://portal.enes.org/oasis}{OASIS} coupler, with several atmospheric general circulation models. 
    22 It also support two-way grid embedding via the \href{http://agrif.imag.fr}{AGRIF} software. 
     26Various physical choices are available to describe ocean physics, 
     27so as various HPC functionalities to improve performances. 

  • NEMO/branches/2019/dev_r11233_AGRIF-05_jchanut_vert_coord_interp/doc/latex/NEMO/main/thanks.tex

    r11212 r11573  
    1 J\'{e}r\^{o}me Chanut, 
    2 Silvia Mocavero 
     1%Romain Bourdall\'{e}-Badie 
     2%\orcid{0000-0002-8742-3289} \\ 
     3%Mike Bell                   \\ 
     4%J\'{e}r\^{o}me Chanut       \\ 
     5%Emanuela Clementi 
     6%\orcid{0000-0002-5752-1849} \\ 
     7%Andrew Coward 
     8%\orcid{0000-0002-0456-129X} \\ 
     9%Massimiliano Drudi 
     10%\orcid{0000-0002-9951-740X} \\ 
     11%Christian \'{E}th\'{e}      \\ 
     12%Doroteaciro Iovino 
     13%\orcid{0000-0001-5132-7255} \\ 
     14%Dan Lea                     \\ 
     15%Claire L\'{e}vy 
     16%\orcid{0000-0003-2518-6692} \\ 
     17%Gurvan Madec 
     18%\orcid{0000-0002-6447-4198} \\ 
     19%Nicolas Martin              \\ 
     20%S\'{e}bastien Masson 
     21%\orcid{0000-0002-1694-8117} \\ 
     22%Pierre Mathiot              \\ 
     23%Silvia Mocavero 
     24%\orcid{0000-0002-6309-8282} \\ 
     25%Simon M\"{u}ller            \\ 
     26%George Nurser               \\ 
     27%Guillaume Samson 
     28%\orcid{0000-0001-7481-6369} \\ 
     29%Dave Storkey 
     30 
     31\orcid{0000-0002-8742-3289} Romain Bourdall\'{e}-Badie  \\ 
     32                            Mike Bell                   \\ 
     33                            J\'{e}r\^{o}me Chanut       \\ 
     34\orcid{0000-0002-5752-1849} Emanuela Clementi           \\ 
     35\orcid{0000-0002-0456-129X} Andrew Coward               \\ 
     36\orcid{0000-0002-9951-740X} Massimiliano Drudi          \\ 
     37                            Christian \'{E}th\'{e}      \\ 
     38\orcid{0000-0001-5132-7255} Doroteaciro Iovino          \\ 
     39                            Dan Lea                     \\ 
     40\orcid{0000-0003-2518-6692} Claire L\'{e}vy             \\ 
     41\orcid{0000-0002-6447-4198} Gurvan Madec                \\ 
     42                            Nicolas Martin              \\ 
     43\orcid{0000-0002-1694-8117} S\'{e}bastien Masson        \\ 
     44                            Pierre Mathiot              \\ 
     45\orcid{0000-0002-6309-8282} Silvia Mocavero             \\ 
     46                            Simon M\"{u}ller            \\ 
     47                            George Nurser               \\ 
     48\orcid{0000-0001-7481-6369} Guillaume Samson            \\ 
     49                            Dave Storkey                \\ 
     50%% Don't forget the last break for the right alignment 
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