Changeset 11263 for NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/NEMO/subfiles/chap_SBC.tex

Timestamp:

2019-07-12T12:47:53+02:00 (5 years ago)

Author:

smasson

Message:

dev_r10984_HPC-13 : merge with trunk@11242, see #2285

Location:

NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc

Files:

• . (modified) (1 prop)
• latex (modified) (1 prop)
• latex/NEMO (modified) (1 prop)
• latex/NEMO/subfiles/chap_SBC.tex (modified) (42 diffs)

NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex

@@ -1 @@
-*.aux
-*.bbl
-*.blg
-*.dvi
-*.fdb*
-*.fls
-*.idx
-*.ilg
-*.ind
-*.log
-*.maf
-*.mtc*
-*.out
-*.pdf
-*.toc
-_minted-*
+figures

@@ -1 @@
-*.aux
-*.bbl
-*.blg
-*.dvi
-*.fdb*
-*.fls
-*.idx
-*.ilg
-*.ind
-*.log
-*.maf
-*.mtc*
-*.out
-*.pdf
-*.toc
-_minted-*
+figures

NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/NEMO/subfiles/chap_SBC.tex

@@ -5 +5 @@
 % Chapter —— Surface Boundary Condition (SBC, ISF, ICB) 
 % ================================================================
-\chapter{Surface Boundary Condition (SBC, ISF, ICB) }
+\chapter{Surface Boundary Condition (SBC, ISF, ICB)}
 \label{chap:SBC}
 \minitoc
@@ -226 +226 @@
 % Input Data specification (\mdl{fldread})
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Input data specification (\protect\mdl{fldread})}
+\subsection[Input data specification (\textit{fldread.F90})]
+{Input data specification (\protect\mdl{fldread})}
 \label{subsec:SBC_fldread}
 
@@ -313 +314 @@
 The only tricky point is therefore to specify the date at which we need to do the interpolation and
 the date of the records read in the input files.
-Following \citet{Leclair_Madec_OM09}, the date of a time step is set at the middle of the time step.
+Following \citet{leclair.madec_OM09}, the date of a time step is set at the middle of the time step.
 For example, for an experiment starting at 0h00'00" with a one hour time-step,
 a time interpolation will be performed at the following time: 0h30'00", 1h30'00", 2h30'00", etc.
@@ -559 +560 @@
 % Analytical formulation (sbcana module) 
 % ================================================================
-\section{Analytical formulation (\protect\mdl{sbcana})}
+\section[Analytical formulation (\textit{sbcana.F90})]
+{Analytical formulation (\protect\mdl{sbcana})}
 \label{sec:SBC_ana}
 
@@ -584 +586 @@
 % Flux formulation 
 % ================================================================
-\section{Flux formulation (\protect\mdl{sbcflx})}
+\section[Flux formulation (\textit{sbcflx.F90})]
+{Flux formulation (\protect\mdl{sbcflx})}
 \label{sec:SBC_flx}
 %------------------------------------------namsbc_flx----------------------------------------------------
@@ -606 +609 @@
 % ================================================================
 \section[Bulk formulation {(\textit{sbcblk\{\_core,\_clio\}.F90})}]
-                        {Bulk formulation {(\protect\mdl{sbcblk\_core}, \protect\mdl{sbcblk\_clio})}}
+{Bulk formulation {(\protect\mdl{sbcblk\_core}, \protect\mdl{sbcblk\_clio})}}
 \label{sec:SBC_blk}
 
@@ -625 +628 @@
 %        CORE Bulk formulea
 % -------------------------------------------------------------------------------------------------------------
-\subsection{CORE formulea (\protect\mdl{sbcblk\_core}, \protect\np{ln\_core}\forcode{ = .true.})}
+\subsection[CORE formulea (\textit{sbcblk\_core.F90}, \forcode{ln_core = .true.})]
+{CORE formulea (\protect\mdl{sbcblk\_core}, \protect\np{ln\_core}\forcode{ = .true.})}
 \label{subsec:SBC_blk_core}
 %------------------------------------------namsbc_core----------------------------------------------------
@@ -632 +636 @@
 %-------------------------------------------------------------------------------------------------------------
 
-The CORE bulk formulae have been developed by \citet{Large_Yeager_Rep04}.
+The CORE bulk formulae have been developed by \citet{large.yeager_rpt04}.
 They have been designed to handle the CORE 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 10 metre wind speed, air temperature and specific humidity.
-This \citet{Large_Yeager_Rep04} dataset is available through
+This \citet{large.yeager_rpt04} dataset is available through
 the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}.
 
 Note that substituting ERA40 to NCEP reanalysis fields does not require changes in the bulk formulea themself.
-This is the so-called DRAKKAR Forcing Set (DFS) \citep{Brodeau_al_OM09}.
+This is the so-called DRAKKAR Forcing Set (DFS) \citep{brodeau.barnier.ea_OM10}.
 
 Options are defined through the  \ngn{namsbc\_core} namelist variables.
@@ -688 +692 @@
 %        CLIO Bulk formulea
 % -------------------------------------------------------------------------------------------------------------
-\subsection{CLIO formulea (\protect\mdl{sbcblk\_clio}, \protect\np{ln\_clio}\forcode{ = .true.})}
+\subsection[CLIO formulea (\textit{sbcblk\_clio.F90}, \forcode{ln_clio = .true.})]
+{CLIO formulea (\protect\mdl{sbcblk\_clio}, \protect\np{ln\_clio}\forcode{ = .true.})}
 \label{subsec:SBC_blk_clio}
 %------------------------------------------namsbc_clio----------------------------------------------------
@@ -696 +701 @@
 
 The CLIO bulk formulae were developed several years ago for the Louvain-la-neuve coupled ice-ocean model
-(CLIO, \cite{Goosse_al_JGR99}). 
+(CLIO, \cite{goosse.deleersnijder.ea_JGR99}). 
 They are simpler bulk formulae.
 They assume the stress to be known and compute the radiative fluxes from a climatological cloud cover. 
@@ -729 +734 @@
 % Coupled formulation
 % ================================================================
-\section{Coupled formulation (\protect\mdl{sbccpl})}
+\section[Coupled formulation (\textit{sbccpl.F90})]
+{Coupled formulation (\protect\mdl{sbccpl})}
 \label{sec:SBC_cpl}
 %------------------------------------------namsbc_cpl----------------------------------------------------
@@ -770 +776 @@
 %        Atmospheric pressure
 % ================================================================
-\section{Atmospheric pressure (\protect\mdl{sbcapr})}
+\section[Atmospheric pressure (\textit{sbcapr.F90})]
+{Atmospheric pressure (\protect\mdl{sbcapr})}
 \label{sec:SBC_apr}
 %------------------------------------------namsbc_apr----------------------------------------------------
@@ -806 +813 @@
 %        Surface Tides Forcing
 % ================================================================
-\section{Surface tides (\protect\mdl{sbctide})}
+\section[Surface tides (\textit{sbctide.F90})]
+{Surface tides (\protect\mdl{sbctide})}
 \label{sec:SBC_tide}
 
@@ -819 +827 @@
 \[
   % \label{eq:PE_dyn_tides}
-  \frac{\partial {\rm {\bf U}}_h }{\partial t}= ...
+  \frac{\partial {\mathrm {\mathbf U}}_h }{\partial t}= ...
   +g\nabla (\Pi_{eq} + \Pi_{sal})
 \]
@@ -839 +847 @@
 
 The SAL term should in principle be computed online as it depends on
-the model tidal prediction itself (see \citet{Arbic2004} for a
+the model tidal prediction itself (see \citet{arbic.garner.ea_DSR04} for a
 discussion about the practical implementation of this term).
 Nevertheless, the complex calculations involved would make this
@@ -857 +865 @@
 %        River runoffs
 % ================================================================
-\section{River runoffs (\protect\mdl{sbcrnf})}
+\section[River runoffs (\textit{sbcrnf.F90})]
+{River runoffs (\protect\mdl{sbcrnf})}
 \label{sec:SBC_rnf}
 %------------------------------------------namsbc_rnf----------------------------------------------------
@@ -871 +880 @@
 %coastal modelling and becomes more and more often open ocean and climate modelling 
 %\footnote{At least a top cells thickness of 1~meter and a 3 hours forcing frequency are
-%required to properly represent the diurnal cycle \citep{Bernie_al_JC05}. see also \autoref{fig:SBC_dcy}.}.
+%required to properly represent the diurnal cycle \citep{bernie.woolnough.ea_JC05}. see also \autoref{fig:SBC_dcy}.}.
 
 
@@ -892 +901 @@
 \footnote{
   At least a top cells thickness of 1~meter and a 3 hours forcing frequency are required to
-  properly represent the diurnal cycle \citep{Bernie_al_JC05}.
+  properly represent the diurnal cycle \citep{bernie.woolnough.ea_JC05}.
   see also \autoref{fig:SBC_dcy}.}.
 
@@ -982 +991 @@
 %        Ice shelf melting
 % ================================================================
-\section{Ice shelf melting (\protect\mdl{sbcisf})}
+\section[Ice shelf melting (\textit{sbcisf.F90})]
+{Ice shelf melting (\protect\mdl{sbcisf})}
 \label{sec:SBC_isf}
 %------------------------------------------namsbc_isf----------------------------------------------------
@@ -989 +999 @@
 %--------------------------------------------------------------------------------------------------------
 The namelist variable in \ngn{namsbc}, \np{nn\_isf}, controls the ice shelf representation.
-Description and result of sensitivity test to \np{nn\_isf} are presented in \citet{Mathiot2017}. 
+Description and result of sensitivity test to \np{nn\_isf} are presented in \citet{mathiot.jenkins.ea_GMD17}. 
 The different options are illustrated in \autoref{fig:SBC_isf}.
 
@@ -1001 +1011 @@
    \item[\np{nn\_isfblk}\forcode{ = 1}]:
      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{Hunter2006}.
+     the latent heat flux at the ice shelf base. A complete description is available in \citet{hunter_rpt06}.
    \item[\np{nn\_isfblk}\forcode{ = 2}]:
      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). 
-     A complete description is available in \citet{Jenkins1991}.
+     A complete description is available in \citet{jenkins_JGR91}.
    \end{description}
 
-     Temperature and salinity used to compute the melt are the average temperature in the top boundary layer \citet{Losch2008}. 
+     Temperature and salinity used to compute the melt are the average temperature in the top boundary layer \citet{losch_JGR08}. 
      Its thickness is defined by \np{rn\_hisf\_tbl}.
      The fluxes and friction velocity are computed using the mean temperature, salinity and velocity in the the first \np{rn\_hisf\_tbl} m.
@@ -1038 +1048 @@
 \]
      where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn\_hisf\_tbl} meters).
-     See \citet{Jenkins2010} for all the details on this formulation. It is the recommended formulation for realistic application.
+     See \citet{jenkins.nicholls.ea_JPO10} for all the details on this formulation. It is the recommended formulation for realistic application.
    \item[\np{nn\_gammablk}\forcode{ = 2}]:
      The salt and heat exchange coefficients are velocity and stability dependent and defined as:
@@ -1047 +1057 @@
      $\Gamma_{Turb}$ the contribution of the ocean stability and
      $\Gamma^{T,S}_{Mole}$ the contribution of the molecular diffusion.
-     See \citet{Holland1999} for all the details on this formulation. 
+     See \citet{holland.jenkins_JPO99} for all the details on this formulation. 
      This formulation has not been extensively tested in NEMO (not recommended).
    \end{description}
  \item[\np{nn\_isf}\forcode{ = 2}]:
    The ice shelf cavity is not represented.
-   The fwf and heat flux are computed using the \citet{Beckmann2003} parameterisation of isf melting.
+   The fwf and heat flux are computed using the \citet{beckmann.goosse_OM03} parameterisation of isf melting.
    The fluxes are distributed along the ice shelf edge between the depth of the average grounding line (GL)
    (\np{sn\_depmax\_isf}) and the base of the ice shelf along the calving front
@@ -1089 +1099 @@
 \begin{figure}[!t]
   \begin{center}
-    \includegraphics[width=0.8\textwidth]{Fig_SBC_isf}
+    \includegraphics[width=\textwidth]{Fig_SBC_isf}
     \caption{
       \protect\label{fig:SBC_isf}
@@ -1166 +1176 @@
 %-------------------------------------------------------------------------------------------------------------
 
-Icebergs are modelled as lagrangian particles in NEMO \citep{Marsh_GMD2015}.
-Their physical behaviour is controlled by equations as described in \citet{Martin_Adcroft_OM10} ).
+Icebergs are modelled as lagrangian particles in NEMO \citep{marsh.ivchenko.ea_GMD15}.
+Their physical behaviour is controlled by equations as described in \citet{martin.adcroft_OM10} ).
 (Note that the authors kindly provided a copy of their code to act as a basis for implementation in NEMO).
 Icebergs are initially spawned into one of ten classes which have specific mass and thickness as
@@ -1227 +1237 @@
 %        Interactions with waves (sbcwave.F90, ln_wave)
 % -------------------------------------------------------------------------------------------------------------
-\section{Interactions with waves (\protect\mdl{sbcwave}, \protect\np{ln\_wave})}
+\section[Interactions with waves (\textit{sbcwave.F90}, \texttt{ln\_wave})]
+{Interactions with waves (\protect\mdl{sbcwave}, \protect\np{ln\_wave})}
 \label{sec:SBC_wave}
 %------------------------------------------namsbc_wave--------------------------------------------------------
@@ -1258 +1269 @@
 
 % ================================================================
-\subsection{Neutral drag coefficient from wave model (\protect\np{ln\_cdgw})}
+\subsection[Neutral drag coefficient from wave model (\texttt{ln\_cdgw})]
+{Neutral drag coefficient from wave model (\protect\np{ln\_cdgw})}
 \label{subsec:SBC_wave_cdgw}
 
@@ -1265 +1277 @@
 Then using the routine \rou{turb\_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_Rep04}. 
+air-sea interface following \citet{large.yeager_rpt04}. 
 
 
@@ -1271 +1283 @@
 % 3D Stokes Drift (ln_sdw, nn_sdrift)
 % ================================================================
-\subsection{3D Stokes Drift (\protect\np{ln\_sdw, nn\_sdrift})}
+\subsection[3D Stokes Drift (\texttt{ln\_sdw}, \texttt{nn\_sdrift})]
+{3D Stokes Drift (\protect\np{ln\_sdw, nn\_sdrift})}
 \label{subsec:SBC_wave_sdw}
 
-The Stokes drift is a wave driven mechanism of mass and momentum transport \citep{Stokes_1847}. 
+The Stokes drift is a wave driven mechanism of mass and momentum transport \citep{stokes_ibk09}. 
 It is defined as the difference between the average velocity of a fluid parcel (Lagrangian velocity) 
 and the current measured at a fixed point (Eulerian velocity). 
@@ -1307 +1320 @@
 \begin{description}
 \item[\np{nn\_sdrift} = 0]: exponential integral profile parameterization proposed by 
-\citet{Breivik_al_JPO2014}:
+\citet{breivik.janssen.ea_JPO14}:
 
 \[
@@ -1327 +1340 @@
 \item[\np{nn\_sdrift} = 1]: velocity profile based on the Phillips spectrum which is considered to be a 
 reasonable estimate of the part of the spectrum most contributing to the Stokes drift velocity near the surface
-\citep{Breivik_al_OM2016}:
+\citep{breivik.bidlot.ea_OM16}:
 
 \[
@@ -1367 +1380 @@
 % Stokes-Coriolis term (ln_stcor)
 % ================================================================
-\subsection{Stokes-Coriolis term (\protect\np{ln\_stcor})}
+\subsection[Stokes-Coriolis term (\texttt{ln\_stcor})]
+{Stokes-Coriolis term (\protect\np{ln\_stcor})}
 \label{subsec:SBC_wave_stcor}
 
@@ -1381 +1395 @@
 % Waves modified stress (ln_tauwoc, ln_tauw)
 % ================================================================
-\subsection{Wave modified sress (\protect\np{ln\_tauwoc, ln\_tauw})} 
+\subsection[Wave modified sress (\texttt{ln\_tauwoc}, \texttt{ln\_tauw})]
+{Wave modified sress (\protect\np{ln\_tauwoc, ln\_tauw})}
 \label{subsec:SBC_wave_tauw}
 
 The surface stress felt by the ocean is the atmospheric stress minus the net stress going 
-into the waves \citep{Janssen_al_TM13}. Therefore, when waves are growing, momentum and energy is spent and is not 
+into the waves \citep{janssen.breivik.ea_rpt13}. 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. 
@@ -1428 +1443 @@
 %        Diurnal cycle
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Diurnal cycle (\protect\mdl{sbcdcy})}
+\subsection[Diurnal cycle (\textit{sbcdcy.F90})]
+{Diurnal cycle (\protect\mdl{sbcdcy})}
 \label{subsec:SBC_dcy}
 %------------------------------------------namsbc_rnf----------------------------------------------------
@@ -1438 +1454 @@
 \begin{figure}[!t]
   \begin{center}
-    \includegraphics[width=0.8\textwidth]{Fig_SBC_diurnal}
+    \includegraphics[width=\textwidth]{Fig_SBC_diurnal}
     \caption{
       \protect\label{fig:SBC_diurnal}
@@ -1445 +1461 @@
       the mean value of the analytical cycle (blue line) over a time step,
       not as the mid time step value of the analytically cycle (red square).
-      From \citet{Bernie_al_CD07}.
+      From \citet{bernie.guilyardi.ea_CD07}.
     }
   \end{center}
@@ -1451 +1467 @@
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 
-\cite{Bernie_al_JC05} have shown that to capture 90$\%$ of the diurnal variability of SST requires a vertical resolution in upper ocean of 1~m or better and a temporal resolution of the surface fluxes of 3~h or less.
+\cite{bernie.woolnough.ea_JC05} have shown that to capture 90$\%$ of the diurnal variability of SST requires a vertical resolution in upper ocean of 1~m or better and a temporal resolution of the surface fluxes of 3~h or less.
 Unfortunately high frequency forcing fields are rare, not to say inexistent.
 Nevertheless, it is possible to obtain a reasonable diurnal cycle of the SST knowning only short wave flux (SWF) at
-high frequency \citep{Bernie_al_CD07}.
+high frequency \citep{bernie.guilyardi.ea_CD07}.
 Furthermore, only the knowledge of daily mean value of SWF is needed,
 as higher frequency variations can be reconstructed from them,
 assuming that the diurnal cycle of SWF is a scaling of the top of the atmosphere diurnal cycle of incident SWF.
-The \cite{Bernie_al_CD07} reconstruction algorithm is available in \NEMO by
+The \cite{bernie.guilyardi.ea_CD07} reconstruction algorithm is available in \NEMO by
 setting \np{ln\_dm2dc}\forcode{ = .true.} (a \textit{\ngn{namsbc}} namelist variable) when
 using CORE bulk formulea (\np{ln\_blk\_core}\forcode{ = .true.}) or
 the flux formulation (\np{ln\_flx}\forcode{ = .true.}).
 The reconstruction is performed in the \mdl{sbcdcy} module.
-The detail of the algoritm used can be found in the appendix~A of \cite{Bernie_al_CD07}.
+The detail of the algoritm used can be found in the appendix~A of \cite{bernie.guilyardi.ea_CD07}.
 The algorithm preserve the daily mean incoming SWF as the reconstructed SWF at
 a given time step is the mean value of the analytical cycle over this time step (\autoref{fig:SBC_diurnal}).
@@ -1476 +1492 @@
 \begin{figure}[!t]
   \begin{center}
-    \includegraphics[width=0.7\textwidth]{Fig_SBC_dcy}
+    \includegraphics[width=\textwidth]{Fig_SBC_dcy}
     \caption{
       \protect\label{fig:SBC_dcy}
@@ -1514 +1530 @@
 %        Surface restoring to observed SST and/or SSS
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Surface restoring to observed SST and/or SSS (\protect\mdl{sbcssr})}
+\subsection[Surface restoring to observed SST and/or SSS (\textit{sbcssr.F90})]
+{Surface restoring to observed SST and/or SSS (\protect\mdl{sbcssr})}
 \label{subsec:SBC_ssr}
 %------------------------------------------namsbc_ssr----------------------------------------------------
@@ -1546 +1563 @@
 (observed, climatological or an atmospheric model product),
 \textit{SSS}$_{Obs}$ is a sea surface salinity
-(usually a time interpolation of the monthly mean Polar Hydrographic Climatology \citep{Steele2001}),
+(usually a time interpolation of the monthly mean Polar Hydrographic Climatology \citep{steele.morley.ea_JC01}),
 $\left.S\right|_{k=1}$ is the model surface layer salinity and
 $\gamma_s$ is a negative feedback coefficient which is provided as a namelist parameter.
 Unlike heat flux, there is no physical justification for the feedback term in \autoref{eq:sbc_dmp_emp} as
-the atmosphere does not care about ocean surface salinity \citep{Madec1997}.
+the atmosphere does not care about ocean surface salinity \citep{madec.delecluse_IWN97}.
 The SSS restoring term should be viewed as a flux correction on freshwater fluxes to
 reduce the uncertainties we have on the observed freshwater budget.
@@ -1593 +1610 @@
 % {Description of Ice-ocean interface to be added here or in LIM 2 and 3 doc ?}
 
-\subsection{Interface to CICE (\protect\mdl{sbcice\_cice})}
+\subsection[Interface to CICE (\textit{sbcice\_cice.F90})]
+{Interface to CICE (\protect\mdl{sbcice\_cice})}
 \label{subsec:SBC_cice}
 
@@ -1626 +1644 @@
 %        Freshwater budget control 
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Freshwater budget control (\protect\mdl{sbcfwb})}
+\subsection[Freshwater budget control (\textit{sbcfwb.F90})]
+{Freshwater budget control (\protect\mdl{sbcfwb})}
 \label{subsec:SBC_fwb}
 

@@ -1 @@
-*.aux
-*.bbl
-*.blg
-*.dvi
-*.fdb*
-*.fls
-*.idx
-*.ilg
-*.ind
-*.log
-*.maf
-*.mtc*
-*.out
-*.pdf
-*.toc
-_minted-*
+figures