Changeset 14079

Timestamp:

2020-12-04T12:06:34+01:00 (3 years ago)

Author:

nicolasmartin

Message:

#2414 Updating bibtex keys for references in LaTeX files in compliance with previous commit

Location:

NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex

Files:

• NEMO/subfiles/chap_DYN.tex (modified) (2 diffs)
• NEMO/subfiles/chap_LBC.tex (modified) (1 diff)
• NEMO/subfiles/chap_LDF.tex (modified) (2 diffs)
• NEMO/subfiles/chap_SBC.tex (modified) (13 diffs)
• NEMO/subfiles/chap_ZDF.tex (modified) (5 diffs)
• NEMO/subfiles/chap_cfgs.tex (modified) (1 diff)
• NEMO/subfiles/chap_model_basics.tex (modified) (2 diffs)
• NEMO/subfiles/chap_model_basics_zstar.tex (modified) (3 diffs)
• global/annex_D.tex (modified) (1 diff)
• global/coding_rules.tex (modified) (1 diff)

NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/NEMO/subfiles/chap_DYN.tex

@@ -657 +657 @@
 Note that expression \autoref{eq:DYN_hpg_sco} is commonly used when the variable volume formulation is activated
 (\texttt{vvl?}) because in that case, even with a flat bottom,
-the coordinate surfaces are not horizontal but follow the free surface \citep{levier.treguier.ea_rpt07}.
+the coordinate surfaces are not horizontal but follow the free surface \citep{levier.treguier.ea_trpt07}.
 The pressure jacobian scheme (\np[=.true.]{ln_dynhpg_prj}{ln\_dynhpg\_prj}) is available as
 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.
 Although the damping is lower than for the filtered free surface,
-it is still significant as shown by \citet{levier.treguier.ea_rpt07} in the case of an analytical barotropic Kelvin wave.
+it is still significant as shown by \citet{levier.treguier.ea_trpt07} in the case of an analytical barotropic Kelvin wave.
 
 \cmtgm{               %%% copy from griffies Book

NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/NEMO/subfiles/chap_LBC.tex

@@ -358 +358 @@
 
 The BDY module was modelled on the OBC module (see \NEMO\ 3.4) and shares many features and
-a similar coding structure \citep{chanut_rpt05}.
+a similar coding structure \citep{chanut_trpt05}.
 The specification of the location of the open boundary is completely flexible and
 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

@@ -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})}
 
-This option refers to the \citep{smagorinsky_MW63} scheme which is here implemented for momentum only. Smagorinsky chose as a
+This option refers to the \citep{smagorinsky_MWR63} scheme which is here implemented for momentum only. Smagorinsky chose as a
 characteristic time scale $T_{smag}$ the deformation rate and for the lengthscale $L_{smag}$ the maximum wavenumber possible on the horizontal grid, e.g.:
 
@@ -540 +540 @@
 \end{listing}
 
-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.
+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.
 
 \colorbox{yellow}{TBC}

NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/NEMO/subfiles/chap_SBC.tex

@@ -550 +550 @@
 initially developed (and are still developed in parallel) in
 the \href{https://brodeau.github.io/aerobulk}{\texttt{AeroBulk}} open-source project
-\citep{brodeau.barnier.ea_JPO17}.
+\citep{brodeau.barnier.ea_JPO16}.
 
 %%% Bulk formulae are this:
@@ -592 +592 @@
 respectively. $\gamma z$ is a temperature correction term which accounts for the
 adiabatic lapse rate and approximates the potential temperature at height
-$z$ \citep{josey.gulev.ea_2013}.
+$z$ \citep{josey.gulev.ea_OCC13}.
 $\mathbf{U}_z$ is the wind speed vector at height $z$ above the sea surface
-(possibly referenced to the surface current $\mathbf{u_0}$,
-\autoref{s_res1}.\autoref{ss_current}).
+(possibly referenced to the surface current $\mathbf{u_0}$).%,
+%\autoref{s_res1}.\autoref{ss_current}). %% Undefined references
 The bulk scalar wind speed, namely $U_B$, is the scalar wind speed,
 $|\mathbf{U}_z|$, with the potential inclusion of a gustiness contribution.
@@ -602 +602 @@
 $T_s$ is the sea surface temperature. $q_s$ is the saturation specific humidity
 of air at temperature $T_s$; it includes a 2\% reduction to account for the
-presence of salt in seawater \citep{sverdrup.johnson.ea_1942,kraus.businger_QJRMS96}.
+presence of salt in seawater \citep{sverdrup.johnson.ea_bk42,kraus.businger_QJRMS96}.
 Depending on the bulk parametrization used, $T_s$ can either be the temperature
 at the air-sea interface (skin temperature, hereafter SSST) or at typically a
@@ -617 +617 @@
 
 For more details on all these aspects the reader is invited to refer
-to \citet{brodeau.barnier.ea_JPO17}.
+to \citet{brodeau.barnier.ea_JPO16}.
 
 \subsection{Bulk parametrizations}
@@ -633 +633 @@
 
 \begin{itemize}
-\item NCAR, formerly known as CORE, \citep{large.yeager_rpt04,large.yeager_CD09}
+\item NCAR, formerly known as CORE, \citep{large.yeager_trpt04,large.yeager_CD09}
 \item COARE 3.0 \citep{fairall.bradley.ea_JC03}
 \item COARE 3.6 \citep{edson.jampana.ea_JPO13}
@@ -642 +642 @@
 bulk parametrization are built around improvements in the representation of the
 effects of waves on
-fluxes \citep{edson.jampana.ea_JPO13,brodeau.barnier.ea_JPO17}. This includes
+fluxes \citep{edson.jampana.ea_JPO13,brodeau.barnier.ea_JPO16}. This includes
 improved relationships of surface roughness, and whitecap fraction on wave
 parameters. It is therefore recommended to chose version 3.6 over 3.
@@ -663 +663 @@
 
 For the cool-skin scheme parametrization COARE and ECMWF algorithms share the same
-basis: \citet{fairall.bradley.ea_JGR96}. With some minor updates based
+basis: \citet{fairall.bradley.ea_JGRO96}. With some minor updates based
 on \citet{zeng.beljaars_GRL05} for ECMWF, and \citet{fairall.ea_19} for COARE
 3.6.
@@ -837 +837 @@
 %their neutral transfer coefficients relationships with neutral wind.
 %\begin{itemize}
-%\item NCAR (\np[=.true.]{ln_NCAR}{ln\_NCAR}): The NCAR bulk formulae have been developed by \citet{large.yeager_rpt04}.
+%\item NCAR (\np[=.true.]{ln_NCAR}{ln\_NCAR}): The NCAR bulk formulae have been developed by \citet{large.yeager_trpt04}.
 %  They have been designed to handle the NCAR forcing, a mixture of NCEP reanalysis and satellite data.
 %  They use an inertial dissipative method to compute the turbulent transfer coefficients
 %  (momentum, sensible heat and evaporation) from the 10m wind speed, air temperature and specific humidity.
-%  This \citet{large.yeager_rpt04} dataset is available through
+%  This \citet{large.yeager_trpt04} dataset is available through
 %  the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/NCAR.html}{GFDL web site}.
 %  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:
 a constant transfer coefficient (1.4e-3; default
-value), \citet{lupkes.gryanik.ea_JGR12} (\np{ln_Cd_L12}{ln\_Cd\_L12}),
+value), \citet{lupkes.gryanik.ea_JGRA12} (\np{ln_Cd_L12}{ln\_Cd\_L12}),
 and \citet{lupkes.gryanik_JGR15} (\np{ln_Cd_L15}{ln\_Cd\_L15}) parameterizations
 \texttt{\#out\_of\_place.}
@@ -868 +868 @@
 \item Constant value (\forcode{Cd_ice=1.4e-3}):
   default constant value used for momentum and heat neutral transfer coefficients
-\item \citet{lupkes.gryanik.ea_JGR12} (\np[=.true.]{ln_Cd_L12}{ln\_Cd\_L12}):
+\item \citet{lupkes.gryanik.ea_JGRA12} (\np[=.true.]{ln_Cd_L12}{ln\_Cd\_L12}):
   This scheme adds a dependency on edges at leads, melt ponds and flows
   of the constant neutral air-ice drag. After some approximations,
@@ -1204 +1204 @@
   \begin{description}
   \item [{\np[=1]{nn_isfblk}{nn\_isfblk}}]: The melt rate is based on a balance between the upward ocean heat flux and
-    the latent heat flux at the ice shelf base. A complete description is available in \citet{hunter_rpt06}.
+    the latent heat flux at the ice shelf base. A complete description is available in \citet{hunter_trpt06}.
   \item [{\np[=2]{nn_isfblk}{nn\_isfblk}}]: The melt rate and the heat flux are based on a 3 equations formulation
     (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,
 the drag coefficient is computed according to the stable/unstable conditions of the
-air-sea interface following \citet{large.yeager_rpt04}.
+air-sea interface following \citet{large.yeager_trpt04}.
 
 %% =================================================================================================
@@ -1558 +1558 @@
 
 The surface stress felt by the ocean is the atmospheric stress minus the net stress going
-into the waves \citep{janssen.breivik.ea_rpt13}. Therefore, when waves are growing, momentum and energy is spent and is not
+into the waves \citep{janssen.breivik.ea_trpt13}. Therefore, when waves are growing, momentum and energy is spent and is not
 available for forcing the mean circulation, while in the opposite case of a decaying sea
 state, more momentum is available for forcing the ocean.

NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/NEMO/subfiles/chap_ZDF.tex

@@ -532 +532 @@
 the TKE case described in \autoref{subsec:ZDF_tke_ene} \citep{burchard_OM02}.
 Evaluation of the 4 GLS turbulent closure schemes can be found in \citet{warner.sherwood.ea_OM05} in ROMS model and
- in \citet{reffray.guillaume.ea_GMD15} for the \NEMO\ model.
+ in \citet{reffray.bourdalle-badie.ea_GMD15} for the \NEMO\ model.
 
 % -------------------------------------------------------------------------------------------------------------
@@ -608 +608 @@
 classical shear turbulence. Instead they are in a regime known as
 `Langmuir turbulence',  dominated by an
-interaction between the currents and the Stokes drift of the surface waves \citep[e.g.][]{mcwilliams.ea_JFM97}.
+interaction between the currents and the Stokes drift of the surface waves \citep[e.g.][]{mcwilliams.sullivan.ea_JFM97}.
 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 $\mathrm{La}_{t}=(u_{\ast}/u_{s0}) > 0.4$.
 
@@ -617 +617 @@
 The OSMOSIS turbulent closure scheme is a similarity-scale scheme in
 the same spirit as the K-profile
-parameterization (KPP) scheme of \citet{large.ea_RG97}.
+parameterization (KPP) scheme of \citet{large.mcwilliams.ea_RG94}.
 A specified shape of diffusivity, scaled by the (OSBL) depth
 $h_{\mathrm{BL}}$ 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
 energy budget considerations reminiscent of the classical mixed layer
-models of \citet{kraus.turner_tellus67}.
+models of \citet{kraus.turner_T67}.
 The model also includes an explicit parametrization of the structure
 of the pycnocline (the stratified region at the bottom of the OSBL).
 
 Presently, mixing below the OSBL is handled by the Richardson
-number-dependent mixing scheme used in \citet{large.ea_RG97}.
+number-dependent mixing scheme used in \citet{large.mcwilliams.ea_RG94}.
 
 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
 \citep{grant+etal18} of a generalization of that used in mixed-layer
-models e.g.\ \citet{kraus.turner_tellus67}, in which the thickness of the pycnocline is taken to be zero.
+models e.g.\ \citet{kraus.turner_T67}, in which the thickness of the pycnocline is taken to be zero.
 
 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

@@ -198 +198 @@
 (see \autoref{tab:CFGS_ORCA} and \autoref{fig:DOM_zgr_e3}).
 The bottom topography and the coastlines are derived from the global atlas of Smith and Sandwell (1997).
-The default forcing uses the boundary forcing from \citet{large.yeager_rpt04} (see \autoref{subsec:SBC_blk_ocean}),
+The default forcing uses the boundary forcing from \citet{large.yeager_trpt04} (see \autoref{subsec:SBC_blk_ocean}),
 which was developed for the purpose of running global coupled ocean-ice simulations without
 an interactive atmosphere.
-This \citet{large.yeager_rpt04} dataset is available through
+This \citet{large.yeager_trpt04} dataset is available through
 the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}.
-The "normal year" of \citet{large.yeager_rpt04} has been chosen of the \NEMO\ distribution since release v3.3.
+The "normal year" of \citet{large.yeager_trpt04} has been chosen of the \NEMO\ distribution since release v3.3.
 
 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

@@ -706 +706 @@
 In this case, the free surface equation is nonlinear,
 and the variations of volume are fully taken into account.
-These coordinates systems is presented in a report \citep{levier.treguier.ea_rpt07} available on
+These coordinates systems is presented in a report \citep{levier.treguier.ea_trpt07} available on
 the \NEMO\ web site.
 
@@ -841 +841 @@
 This problem can be at least partially overcome by mixing $s$-coordinate and
 step-like representation of bottom topography
-\citep{gerdes_JGR93*a,gerdes_JGR93*b,madec.delecluse.ea_JPO96}.
+\citep{gerdes_JGR93,gerdes_JGR93*a,madec.delecluse.ea_JPO96}.
 However, the definition of the model domain vertical coordinate becomes then a non-trivial thing for
 a realistic bottom topography:

NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex

@@ -30 +30 @@
 
 In that case, the free surface equation is nonlinear, and the variations of volume are fully taken into account.
-These coordinates systems is presented in a report \citep{levier.treguier.ea_rpt07} available on the \NEMO\ web site.
+These coordinates systems is presented in a report \citep{levier.treguier.ea_trpt07} available on the \NEMO\ web site.
 
 \colorbox{yellow}{  end of to be updated}
@@ -170 +170 @@
 
 The split-explicit formulation has a damping effect on external gravity waves,
-which is weaker than the filtered free surface but still significant as shown by \citet{levier.treguier.ea_rpt07} in
+which is weaker than the filtered free surface but still significant as shown by \citet{levier.treguier.ea_trpt07} in
 the case of an analytical barotropic Kelvin wave.
 
@@ -306 +306 @@
 
 In the non-linear free surface formulation, the variations of volume are fully taken into account.
-This option is presented in a report \citep{levier.treguier.ea_rpt07} available on the \NEMO\ web site.
+This option is presented in a report \citep{levier.treguier.ea_trpt07} available on the \NEMO\ web site.
 The three time-stepping methods (explicit, split-explicit and filtered) are the same as in
 \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

@@ -32 +32 @@
 
 To satisfy part of these aims, \NEMO\ is written with a coding standard which is close to the ECMWF rules,
-named DOCTOR \citep{gibson_rpt86}. 
+named DOCTOR \citep{gibson_trpt86}. 
 These rules present some advantages like:
 

NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/global/coding_rules.tex

@@ -24 +24 @@
 
 To satisfy part of these aims, \NEMO\ is written with a coding standard which is close to the ECMWF rules,
-named DOCTOR \citep{gibson_rpt86}.
+named DOCTOR \citep{gibson_trpt86}.
 These rules present some advantages like: