Changeset 14079 for NEMO/branches
- Timestamp:
- 2020-12-04T12:06:34+01:00 (4 years ago)
- Location:
- NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex
- Files:
-
- 10 edited
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NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/NEMO/subfiles/chap_DYN.tex
r14066 r14079 657 657 Note that expression \autoref{eq:DYN_hpg_sco} is commonly used when the variable volume formulation is activated 658 658 (\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}.659 the coordinate surfaces are not horizontal but follow the free surface \citep{levier.treguier.ea_trpt07}. 660 660 The pressure jacobian scheme (\np[=.true.]{ln_dynhpg_prj}{ln\_dynhpg\_prj}) is available as 661 661 an improved option to \np[=.true.]{ln_dynhpg_sco}{ln\_dynhpg\_sco} when \texttt{vvl?} is active. … … 913 913 external gravity waves in idealized or weakly non-linear cases. 914 914 Although 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.915 it is still significant as shown by \citet{levier.treguier.ea_trpt07} in the case of an analytical barotropic Kelvin wave. 916 916 917 917 \cmtgm{ %%% copy from griffies Book -
NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/NEMO/subfiles/chap_LBC.tex
r14066 r14079 358 358 359 359 The 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}.360 a similar coding structure \citep{chanut_trpt05}. 361 361 The specification of the location of the open boundary is completely flexible and 362 362 allows 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/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/NEMO/subfiles/chap_LDF.tex
r11693 r14079 418 418 \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})} 419 419 420 This option refers to the \citep{smagorinsky_MW 63} scheme which is here implemented for momentum only. Smagorinsky chose as a420 This option refers to the \citep{smagorinsky_MWR63} scheme which is here implemented for momentum only. Smagorinsky chose as a 421 421 characteristic time scale $T_{smag}$ the deformation rate and for the lengthscale $L_{smag}$ the maximum wavenumber possible on the horizontal grid, e.g.: 422 422 … … 540 540 \end{listing} 541 541 542 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{fox kemper.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.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{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. 543 543 544 544 \colorbox{yellow}{TBC} -
NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/NEMO/subfiles/chap_SBC.tex
r14066 r14079 550 550 initially developed (and are still developed in parallel) in 551 551 the \href{https://brodeau.github.io/aerobulk}{\texttt{AeroBulk}} open-source project 552 \citep{brodeau.barnier.ea_JPO1 7}.552 \citep{brodeau.barnier.ea_JPO16}. 553 553 554 554 %%% Bulk formulae are this: … … 592 592 respectively. $\gamma z$ is a temperature correction term which accounts for the 593 593 adiabatic lapse rate and approximates the potential temperature at height 594 $z$ \citep{josey.gulev.ea_ 2013}.594 $z$ \citep{josey.gulev.ea_OCC13}. 595 595 $\mathbf{U}_z$ is the wind speed vector at height $z$ above the sea surface 596 (possibly referenced to the surface current $\mathbf{u_0}$ ,597 \autoref{s_res1}.\autoref{ss_current}). 596 (possibly referenced to the surface current $\mathbf{u_0}$).%, 597 %\autoref{s_res1}.\autoref{ss_current}). %% Undefined references 598 598 The bulk scalar wind speed, namely $U_B$, is the scalar wind speed, 599 599 $|\mathbf{U}_z|$, with the potential inclusion of a gustiness contribution. … … 602 602 $T_s$ is the sea surface temperature. $q_s$ is the saturation specific humidity 603 603 of air at temperature $T_s$; it includes a 2\% reduction to account for the 604 presence of salt in seawater \citep{sverdrup.johnson.ea_ 1942,kraus.businger_QJRMS96}.604 presence of salt in seawater \citep{sverdrup.johnson.ea_bk42,kraus.businger_QJRMS96}. 605 605 Depending on the bulk parametrization used, $T_s$ can either be the temperature 606 606 at the air-sea interface (skin temperature, hereafter SSST) or at typically a … … 617 617 618 618 For more details on all these aspects the reader is invited to refer 619 to \citet{brodeau.barnier.ea_JPO1 7}.619 to \citet{brodeau.barnier.ea_JPO16}. 620 620 621 621 \subsection{Bulk parametrizations} … … 633 633 634 634 \begin{itemize} 635 \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} 636 636 \item COARE 3.0 \citep{fairall.bradley.ea_JC03} 637 637 \item COARE 3.6 \citep{edson.jampana.ea_JPO13} … … 642 642 bulk parametrization are built around improvements in the representation of the 643 643 effects of waves on 644 fluxes \citep{edson.jampana.ea_JPO13,brodeau.barnier.ea_JPO1 7}. This includes644 fluxes \citep{edson.jampana.ea_JPO13,brodeau.barnier.ea_JPO16}. This includes 645 645 improved relationships of surface roughness, and whitecap fraction on wave 646 646 parameters. It is therefore recommended to chose version 3.6 over 3. … … 663 663 664 664 For the cool-skin scheme parametrization COARE and ECMWF algorithms share the same 665 basis: \citet{fairall.bradley.ea_JGR 96}. With some minor updates based665 basis: \citet{fairall.bradley.ea_JGRO96}. With some minor updates based 666 666 on \citet{zeng.beljaars_GRL05} for ECMWF, and \citet{fairall.ea_19} for COARE 667 667 3.6. … … 837 837 %their neutral transfer coefficients relationships with neutral wind. 838 838 %\begin{itemize} 839 %\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}. 840 840 % They have been designed to handle the NCAR forcing, a mixture of NCEP reanalysis and satellite data. 841 841 % They use an inertial dissipative method to compute the turbulent transfer coefficients 842 842 % (momentum, sensible heat and evaporation) from the 10m wind speed, air temperature and specific humidity. 843 % This \citet{large.yeager_ rpt04} dataset is available through843 % This \citet{large.yeager_trpt04} dataset is available through 844 844 % the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/NCAR.html}{GFDL web site}. 845 845 % Note that substituting ERA40 to NCEP reanalysis fields does not require changes in the bulk formulea themself. … … 859 859 For sea-ice, three possibilities can be selected: 860 860 a constant transfer coefficient (1.4e-3; default 861 value), \citet{lupkes.gryanik.ea_JGR 12} (\np{ln_Cd_L12}{ln\_Cd\_L12}),861 value), \citet{lupkes.gryanik.ea_JGRA12} (\np{ln_Cd_L12}{ln\_Cd\_L12}), 862 862 and \citet{lupkes.gryanik_JGR15} (\np{ln_Cd_L15}{ln\_Cd\_L15}) parameterizations 863 863 \texttt{\#out\_of\_place.} … … 868 868 \item Constant value (\forcode{Cd_ice=1.4e-3}): 869 869 default constant value used for momentum and heat neutral transfer coefficients 870 \item \citet{lupkes.gryanik.ea_JGR 12} (\np[=.true.]{ln_Cd_L12}{ln\_Cd\_L12}):870 \item \citet{lupkes.gryanik.ea_JGRA12} (\np[=.true.]{ln_Cd_L12}{ln\_Cd\_L12}): 871 871 This scheme adds a dependency on edges at leads, melt ponds and flows 872 872 of the constant neutral air-ice drag. After some approximations, … … 1204 1204 \begin{description} 1205 1205 \item [{\np[=1]{nn_isfblk}{nn\_isfblk}}]: The melt rate is based on a balance between the upward ocean heat flux and 1206 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}. 1207 1207 \item [{\np[=2]{nn_isfblk}{nn\_isfblk}}]: The melt rate and the heat flux are based on a 3 equations formulation 1208 1208 (a heat flux budget at the ice base, a salt flux budget at the ice base and a linearised freezing point temperature equation). … … 1447 1447 Then using the routine \rou{sbcblk\_algo\_ncar} and starting from the neutral drag coefficent provided, 1448 1448 the drag coefficient is computed according to the stable/unstable conditions of the 1449 air-sea interface following \citet{large.yeager_ rpt04}.1449 air-sea interface following \citet{large.yeager_trpt04}. 1450 1450 1451 1451 %% ================================================================================================= … … 1558 1558 1559 1559 The surface stress felt by the ocean is the atmospheric stress minus the net stress going 1560 into the waves \citep{janssen.breivik.ea_ rpt13}. Therefore, when waves are growing, momentum and energy is spent and is not1560 into the waves \citep{janssen.breivik.ea_trpt13}. Therefore, when waves are growing, momentum and energy is spent and is not 1561 1561 available for forcing the mean circulation, while in the opposite case of a decaying sea 1562 1562 state, more momentum is available for forcing the ocean. -
NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/NEMO/subfiles/chap_ZDF.tex
r14066 r14079 532 532 the TKE case described in \autoref{subsec:ZDF_tke_ene} \citep{burchard_OM02}. 533 533 Evaluation 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. 535 535 536 536 % ------------------------------------------------------------------------------------------------------------- … … 608 608 classical shear turbulence. Instead they are in a regime known as 609 609 `Langmuir turbulence', dominated by an 610 interaction between the currents and the Stokes drift of the surface waves \citep[e.g.][]{mcwilliams. ea_JFM97}.610 interaction between the currents and the Stokes drift of the surface waves \citep[e.g.][]{mcwilliams.sullivan.ea_JFM97}. 611 611 This regime is characterised by strong vertical turbulent motion, and appears when the surface Stokes drift $u_{s0}$ is much greater than the friction velocity $u_{\ast}$. More specifically Langmuir turbulence is thought to be crucial where the turbulent Langmuir number $\mathrm{La}_{t}=(u_{\ast}/u_{s0}) > 0.4$. 612 612 … … 617 617 The OSMOSIS turbulent closure scheme is a similarity-scale scheme in 618 618 the same spirit as the K-profile 619 parameterization (KPP) scheme of \citet{large. ea_RG97}.619 parameterization (KPP) scheme of \citet{large.mcwilliams.ea_RG94}. 620 620 A specified shape of diffusivity, scaled by the (OSBL) depth 621 621 $h_{\mathrm{BL}}$ and a turbulent velocity scale, is imposed throughout the … … 628 628 as in KPP, it is set by a prognostic equation that is informed by 629 629 energy budget considerations reminiscent of the classical mixed layer 630 models of \citet{kraus.turner_ tellus67}.630 models of \citet{kraus.turner_T67}. 631 631 The model also includes an explicit parametrization of the structure 632 632 of the pycnocline (the stratified region at the bottom of the OSBL). 633 633 634 634 Presently, mixing below the OSBL is handled by the Richardson 635 number-dependent mixing scheme used in \citet{large. ea_RG97}.635 number-dependent mixing scheme used in \citet{large.mcwilliams.ea_RG94}. 636 636 637 637 Convective parameterizations such as described in \autoref{sec:ZDF_conv} … … 748 748 based on the potential energy budget of the OSBL, is the leading term 749 749 \citep{grant+etal18} of a generalization of that used in mixed-layer 750 models e.g.\ \citet{kraus.turner_ tellus67}, in which the thickness of the pycnocline is taken to be zero.750 models e.g.\ \citet{kraus.turner_T67}, in which the thickness of the pycnocline is taken to be zero. 751 751 752 752 The entrainment flux for the combination of convective and Langmuir turbulence is given by -
NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/NEMO/subfiles/chap_cfgs.tex
r11693 r14079 198 198 (see \autoref{tab:CFGS_ORCA} and \autoref{fig:DOM_zgr_e3}). 199 199 The 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}),200 The default forcing uses the boundary forcing from \citet{large.yeager_trpt04} (see \autoref{subsec:SBC_blk_ocean}), 201 201 which was developed for the purpose of running global coupled ocean-ice simulations without 202 202 an interactive atmosphere. 203 This \citet{large.yeager_ rpt04} dataset is available through203 This \citet{large.yeager_trpt04} dataset is available through 204 204 the \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 v3.3.205 The "normal year" of \citet{large.yeager_trpt04} has been chosen of the \NEMO\ distribution since release v3.3. 206 206 207 207 ORCA\_R2 pre-defined configuration can also be run with multiply online nested zooms (\ie\ with AGRIF, \key{agrif} defined). -
NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/NEMO/subfiles/chap_model_basics.tex
r11693 r14079 706 706 In this case, the free surface equation is nonlinear, 707 707 and the variations of volume are fully taken into account. 708 These coordinates systems is presented in a report \citep{levier.treguier.ea_ rpt07} available on708 These coordinates systems is presented in a report \citep{levier.treguier.ea_trpt07} available on 709 709 the \NEMO\ web site. 710 710 … … 841 841 This problem can be at least partially overcome by mixing $s$-coordinate and 842 842 step-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}. 844 844 However, the definition of the model domain vertical coordinate becomes then a non-trivial thing for 845 845 a realistic bottom topography: -
NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex
r11693 r14079 30 30 31 31 In 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.32 These coordinates systems is presented in a report \citep{levier.treguier.ea_trpt07} available on the \NEMO\ web site. 33 33 34 34 \colorbox{yellow}{ end of to be updated} … … 170 170 171 171 The 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} in172 which is weaker than the filtered free surface but still significant as shown by \citet{levier.treguier.ea_trpt07} in 173 173 the case of an analytical barotropic Kelvin wave. 174 174 … … 306 306 307 307 In 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.308 This option is presented in a report \citep{levier.treguier.ea_trpt07} available on the \NEMO\ web site. 309 309 The three time-stepping methods (explicit, split-explicit and filtered) are the same as in 310 310 \autoref{?:DYN_spg_linear?} except that the ocean depth is now time-dependent. -
NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/global/annex_D.tex
r13841 r14079 32 32 33 33 To satisfy part of these aims, \NEMO\ is written with a coding standard which is close to the ECMWF rules, 34 named DOCTOR \citep{gibson_ rpt86}.34 named DOCTOR \citep{gibson_trpt86}. 35 35 These rules present some advantages like: 36 36 -
NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/global/coding_rules.tex
r13841 r14079 24 24 25 25 To satisfy part of these aims, \NEMO\ is written with a coding standard which is close to the ECMWF rules, 26 named DOCTOR \citep{gibson_ rpt86}.26 named DOCTOR \citep{gibson_trpt86}. 27 27 These rules present some advantages like: 28 28
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