Changeset 9407 for branches/2017/dev_merge_2017/DOC/tex_sub/chap_SBC.tex

Timestamp:

2018-03-15T17:40:35+01:00 (6 years ago)

Author:

nicolasmartin

Message:

Complete refactoring of cross-referencing

• Use of \autoref instead of simple \ref for contextual text depending on target type
• creation of few prefixes for marker to identify the type reference: apdx|chap|eq|fig|sec|subsec|tab

File:

• branches/2017/dev_merge_2017/DOC/tex_sub/chap_SBC.tex (modified) (55 diffs)

branches/2017/dev_merge_2017/DOC/tex_sub/chap_SBC.tex

@@ -5 +5 @@
 % ================================================================
 \chapter{Surface Boundary Condition (SBC, ISF, ICB) }
-\label{SBC}
+\label{chap:SBC}
 \minitoc
 
@@ -40 +40 @@
 need not be supplied on the model grid. Instead a file of coordinates and weights can 
 be supplied which maps the data from the supplied grid to the model points 
-(so called "Interpolation on the Fly", see \S\ref{SBC_iof}).
+(so called "Interpolation on the Fly", see \autoref{subsec:SBC_iof}).
 If the Interpolation on the Fly option is used, input data belonging to land points (in the native grid),
 can be masked to avoid spurious results in proximity of the coasts  as large sea-land gradients characterize
@@ -65 +65 @@
 Next the scheme for interpolation on the fly is described.
 Finally, the different options that further modify the fluxes applied to the ocean are discussed.
-One of these is modification by icebergs (see \S\ref{ICB_icebergs}), which act as drifting sources of fresh water.
-Another example of modification is that due to the ice shelf melting/freezing (see \S\ref{SBC_isf}), 
+One of these is modification by icebergs (see \autoref{sec:ICB_icebergs}), which act as drifting sources of fresh water.
+Another example of modification is that due to the ice shelf melting/freezing (see \autoref{sec:SBC_isf}), 
 which provides additional sources of fresh water.
 
@@ -74 +74 @@
 % ================================================================
 \section{Surface boundary condition for the ocean}
-\label{SBC_general}
+\label{sec:SBC_general}
 
 The surface ocean stress is the stress exerted by the wind and the sea-ice 
 on the ocean. It is applied in \mdl{dynzdf} module as a surface boundary condition of the 
-computation of the momentum vertical mixing trend (see \eqref{Eq_dynzdf_sbc} in \S\ref{DYN_zdf}).
+computation of the momentum vertical mixing trend (see \autoref{eq:dynzdf_sbc} in \autoref{sec:DYN_zdf}).
 As such, it has to be provided as a 2D vector interpolated 
 onto the horizontal velocity ocean mesh, $i.e.$ resolved onto the model 
@@ -88 +88 @@
 plus the heat content of the mass exchange with the atmosphere and sea-ice). 
 It is applied in \mdl{trasbc} module as a surface boundary condition trend of 
-the first level temperature time evolution equation (see \eqref{Eq_tra_sbc} 
-and \eqref{Eq_tra_sbc_lin} in \S\ref{TRA_sbc}). 
+the first level temperature time evolution equation (see \autoref{eq:tra_sbc} 
+and \autoref{eq:tra_sbc_lin} in \autoref{subsec:TRA_sbc}). 
 The latter is the penetrative part of the heat flux. It is applied as a 3D 
 trends of the temperature equation (\mdl{traqsr} module) when \np{ln\_traqsr}\forcode{ = .true.}.
 The way the light penetrates inside the water column is generally a sum of decreasing 
-exponentials (see \S\ref{TRA_qsr}). 
+exponentials (see \autoref{subsec:TRA_qsr}). 
 
 The surface freshwater budget is provided by the \textit{emp} field.
@@ -130 +130 @@
 The ocean model provides, at each time step, to the surface module (\mdl{sbcmod}) 
 the surface currents, temperature and salinity.  
-These variables are averaged over \np{nn\_fsbc} time-step (\ref{Tab_ssm}), 
+These variables are averaged over \np{nn\_fsbc} time-step (\autoref{tab:ssm}), 
 and it is these averaged fields which are used to computes the surface fluxes 
 at a frequency of \np{nn\_fsbc} time-step.
@@ -144 +144 @@
 Sea surface salinty              & sss\_m & $psu$        & T \\   \hline
 \end{tabular}
-\caption{  \protect\label{Tab_ssm}   
+\caption{  \protect\label{tab:ssm}   
 Ocean variables provided by the ocean to the surface module (SBC). 
 The variable are averaged over nn{\_}fsbc time step, 
@@ -158 +158 @@
 % ================================================================
 \section{Input data generic interface}
-\label{SBC_input}
+\label{sec:SBC_input}
 
 A generic interface has been introduced to manage the way input data (2D or 3D fields, 
@@ -181 +181 @@
 
 The only constraints are that the input file is a NetCDF file, the file name follows a nomenclature 
-(see \S\ref{SBC_fldread}), the period it cover is one year, month, week or day, and, if on-the-fly 
-interpolation is used, a file of weights must be supplied (see \S\ref{SBC_iof}).
+(see \autoref{subsec:SBC_fldread}), the period it cover is one year, month, week or day, and, if on-the-fly 
+interpolation is used, a file of weights must be supplied (see \autoref{subsec:SBC_iof}).
 
 Note that when an input data is archived on a disc which is accessible directly 
@@ -193 +193 @@
 % -------------------------------------------------------------------------------------------------------------
 \subsection{Input data specification (\protect\mdl{fldread})}
-\label{SBC_fldread}
+\label{subsec:SBC_fldread}
 
 The structure associated with an input variable contains the following information:
@@ -205 +205 @@
 This stem will be completed automatically by the model, with the addition of a '.nc' at its end 
 and by date information and possibly a prefix (when using AGRIF). 
-Tab.\ref{Tab_fldread} provides the resulting file name in all possible cases according to whether 
+Tab.\autoref{tab:fldread} provides the resulting file name in all possible cases according to whether 
 it is a climatological file or not, and to the open/close frequency (see below for definition). 
 
@@ -218 +218 @@
 \end{tabular}
 \end{center}
-\caption{ \protect\label{Tab_fldread}   naming nomenclature for climatological or interannual input file, 
+\caption{ \protect\label{tab:fldread}   naming nomenclature for climatological or interannual input file, 
 as a function of the Open/close frequency. The stem name is assumed to be 'fn'. 
 For weekly files, the 'LLL' corresponds to the first three letters of the first day of the week ($i.e.$ 'sun','sat','fri','thu','wed','tue','mon'). The 'YYYY', 'MM' and 'DD' should be replaced by the 
@@ -259 +259 @@
 
 \item[Others]: 'weights filename', 'pairing rotation' and 'land/sea mask' are associted with on-the-fly interpolation 
-which is described in \S\ref{SBC_iof}.
+which is described in \autoref{subsec:SBC_iof}.
 
 \end{description}
@@ -301 +301 @@
 % -------------------------------------------------------------------------------------------------------------
 \subsection{Interpolation on-the-fly}
-\label{SBC_iof}
+\label{subsec:SBC_iof}
 
 Interpolation on the Fly allows the user to supply input files required
@@ -325 +325 @@
 
 \subsubsection{Bilinear interpolation}
-\label{SBC_iof_bilinear}
+\label{subsec:SBC_iof_bilinear}
 
 The input weights file in this case has two sets of variables: src01, src02,
@@ -347 +347 @@
 
 \subsubsection{Bicubic interpolation}
-\label{SBC_iof_bicubic}
+\label{subsec:SBC_iof_bicubic}
 
 Again there are two sets of variables: "src" and "wgt".
@@ -363 +363 @@
 
 \subsubsection{Implementation}
-\label{SBC_iof_imp}
+\label{subsec:SBC_iof_imp}
 
 To activate this option, a non-empty string should be supplied in the weights filename column 
@@ -398 +398 @@
 
 \subsubsection{Limitations}
-\label{SBC_iof_lim}
+\label{subsec:SBC_iof_lim}
 
 \begin{enumerate}  
@@ -412 +412 @@
 
 \subsubsection{Utilities}
-\label{SBC_iof_util}
+\label{subsec:SBC_iof_util}
 
 % to be completed
@@ -422 +422 @@
 % -------------------------------------------------------------------------------------------------------------
 \subsection{Standalone surface boundary condition scheme}
-\label{SAS_iof}
+\label{subsec:SAS_iof}
 
 %---------------------------------------namsbc_ana--------------------------------------------------
@@ -482 +482 @@
 % ================================================================
 \section{Analytical formulation (\protect\mdl{sbcana})}
-\label{SBC_ana}
+\label{sec:SBC_ana}
 
 %---------------------------------------namsbc_ana--------------------------------------------------
@@ -506 +506 @@
 % ================================================================
 \section{Flux formulation (\protect\mdl{sbcflx})}
-\label{SBC_flx}
+\label{sec:SBC_flx}
 %------------------------------------------namsbc_flx----------------------------------------------------
 \forfile{../namelists/namsbc_flx} 
@@ -516 +516 @@
 read in the file, the time frequency at which it is given (in hours), and a logical 
 setting whether a time interpolation to the model time step is required 
-for this field. See \S\ref{SBC_fldread} for a more detailed description of the parameters.
+for this field. See \autoref{subsec:SBC_fldread} for a more detailed description of the parameters.
 
 Note that in general, a flux formulation is used in associated with a 
-restoring term to observed SST and/or SSS. See \S\ref{SBC_ssr} for its 
+restoring term to observed SST and/or SSS. See \autoref{subsec:SBC_ssr} for its 
 specification.
 
@@ -528 +528 @@
 \section[Bulk formulation {(\textit{sbcblk\{\_core,\_clio,\_mfs\}.F90})}]
          {Bulk formulation {(\protect\mdl{sbcblk\_core}, \protect\mdl{sbcblk\_clio}, \protect\mdl{sbcblk\_mfs})}}
-\label{SBC_blk}
+\label{sec:SBC_blk}
 
 In the bulk formulation, the surface boundary condition fields are computed 
@@ -545 +545 @@
 % -------------------------------------------------------------------------------------------------------------
 \subsection{CORE formulea (\protect\mdl{sbcblk\_core}, \protect\np{ln\_core}\forcode{ = .true.})}
-\label{SBC_blk_core}
+\label{subsec:SBC_blk_core}
 %------------------------------------------namsbc_core----------------------------------------------------
 %\forfile{../namelists/namsbc_core}
@@ -566 +566 @@
 
 %--------------------------------------------------TABLE--------------------------------------------------
-\begin{table}[htbp]   \label{Tab_CORE}
+\begin{table}[htbp]   \label{tab:CORE}
 \begin{center}
 \begin{tabular}{|l|c|c|c|}
@@ -609 +609 @@
 % -------------------------------------------------------------------------------------------------------------
 \subsection{CLIO formulea (\protect\mdl{sbcblk\_clio}, \protect\np{ln\_clio}\forcode{ = .true.})}
-\label{SBC_blk_clio}
+\label{subsec:SBC_blk_clio}
 %------------------------------------------namsbc_clio----------------------------------------------------
 %\forfile{../namelists/namsbc_clio}
@@ -623 +623 @@
 
 %--------------------------------------------------TABLE--------------------------------------------------
-\begin{table}[htbp]   \label{Tab_CLIO}
+\begin{table}[htbp]   \label{tab:CLIO}
 \begin{center}
 \begin{tabular}{|l|l|l|l|}
@@ -643 +643 @@
 As for the flux formulation, information about the input data required by the 
 model is provided in the namsbc\_blk\_core or namsbc\_blk\_clio 
-namelist (see \S\ref{SBC_fldread}). 
+namelist (see \autoref{subsec:SBC_fldread}). 
 
 % -------------------------------------------------------------------------------------------------------------
@@ -649 +649 @@
 % -------------------------------------------------------------------------------------------------------------
 \subsection{MFS formulea (\protect\mdl{sbcblk\_mfs}, \protect\np{ln\_mfs}\forcode{ = .true.})}
-\label{SBC_blk_mfs}
+\label{subsec:SBC_blk_mfs}
 %------------------------------------------namsbc_mfs----------------------------------------------------
 %\forfile{../namelists/namsbc_mfs}
@@ -687 +687 @@
 % ================================================================
 \section{Coupled formulation (\protect\mdl{sbccpl})}
-\label{SBC_cpl}
+\label{sec:SBC_cpl}
 %------------------------------------------namsbc_cpl----------------------------------------------------
 \forfile{../namelists/namsbc_cpl} 
@@ -725 +725 @@
 % ================================================================
 \section{Atmospheric pressure (\protect\mdl{sbcapr})}
-\label{SBC_apr}
+\label{sec:SBC_apr}
 %------------------------------------------namsbc_apr----------------------------------------------------
 \forfile{../namelists/namsbc_apr} 
@@ -737 +737 @@
 pressure is further transformed into an equivalent inverse barometer sea surface height, 
 $\eta_{ib}$, using:
-\begin{equation} \label{SBC_ssh_ib}
+\begin{equation} \label{eq:SBC_ssh_ib}
    \eta_{ib} = -  \frac{1}{g\,\rho_o}  \left( P_{atm} - P_o \right) 
 \end{equation}
@@ -759 +759 @@
 % ================================================================
 \section{Tidal potential (\protect\mdl{sbctide})}
-\label{SBC_tide}
+\label{sec:SBC_tide}
 
 %------------------------------------------nam_tide---------------------------------------
@@ -814 +814 @@
 % ================================================================
 \section{River runoffs (\protect\mdl{sbcrnf})}
-\label{SBC_rnf}
+\label{sec:SBC_rnf}
 %------------------------------------------namsbc_rnf----------------------------------------------------
 \forfile{../namelists/namsbc_rnf} 
@@ -826 +826 @@
 %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 \S\ref{SBC_dcy}.}.
+%required to properly represent the diurnal cycle \citep{Bernie_al_JC05}. see also \autoref{fig:SBC_dcy}.}.
 
 
@@ -847 +847 @@
 more common in 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 \S\ref{SBC_dcy}.}.
+required to properly represent the diurnal cycle \citep{Bernie_al_JC05}. see also \autoref{fig:SBC_dcy}.}.
 
 As such from V~3.3 onwards it is possible to add river runoff through a non-zero depth, and for the 
@@ -929 +929 @@
 % ================================================================
 \section{Ice shelf melting (\protect\mdl{sbcisf})}
-\label{SBC_isf}
+\label{sec:SBC_isf}
 %------------------------------------------namsbc_isf----------------------------------------------------
 \forfile{../namelists/namsbc_isf}
@@ -1006 +1006 @@
 The fw addition due to the ice shelf melting is, at each relevant depth level, added to the horizontal divergence 
 (\textit{hdivn}) in the subroutine \rou{sbc\_isf\_div}, called from \mdl{divcur}. 
-See the runoff section \ref{SBC_rnf} for all the details about the divergence correction. 
+See the runoff section \autoref{sec:SBC_rnf} for all the details about the divergence correction. 
 
 
 \section{Ice sheet coupling}
-\label{SBC_iscpl}
+\label{sec:SBC_iscpl}
 %------------------------------------------namsbc_iscpl----------------------------------------------------
 \forfile{../namelists/namsbc_iscpl}
@@ -1048 +1048 @@
 % ================================================================
 \section{Handling of icebergs (ICB)}
-\label{ICB_icebergs}
+\label{sec:ICB_icebergs}
 %------------------------------------------namberg----------------------------------------------------
 \forfile{../namelists/namberg}
@@ -1113 +1113 @@
 % ================================================================
 \section{Miscellaneous options}
-\label{SBC_misc}
+\label{sec:SBC_misc}
 
 % -------------------------------------------------------------------------------------------------------------
@@ -1119 +1119 @@
 % -------------------------------------------------------------------------------------------------------------
 \subsection{Diurnal cycle (\protect\mdl{sbcdcy})}
-\label{SBC_dcy}
+\label{subsec:SBC_dcy}
 %------------------------------------------namsbc_rnf----------------------------------------------------
 %\forfile{../namelists/namsbc} 
@@ -1127 +1127 @@
 \begin{figure}[!t]    \begin{center}
 \includegraphics[width=0.8\textwidth]{Fig_SBC_diurnal}
-\caption{ \protect\label{Fig_SBC_diurnal}    
+\caption{ \protect\label{fig:SBC_diurnal}    
 Example of recontruction of the diurnal cycle variation of short wave flux  
 from daily mean values. The reconstructed diurnal cycle (black line) is chosen 
@@ -1149 +1149 @@
 can be found in the appendix~A of \cite{Bernie_al_CD07}. The algorithm preserve the daily 
 mean incomming SWF as the reconstructed SWF at a given time step is the mean value 
-of the analytical cycle over this time step (Fig.\ref{Fig_SBC_diurnal}). 
+of the analytical cycle over this time step (\autoref{fig:SBC_diurnal}). 
 The use of diurnal cycle reconstruction requires the input SWF to be daily 
 ($i.e.$ a frequency of 24 and a time interpolation set to true in \np{sn\_qsr} namelist parameter).
 Furthermore, it is recommended to have a least 8 surface module time step per day,
 that is  $\rdt \ nn\_fsbc < 10,800~s = 3~h$. An example of recontructed SWF 
-is given in Fig.\ref{Fig_SBC_dcy} for a 12 reconstructed diurnal cycle, one every 2~hours 
+is given in \autoref{fig:SBC_dcy} for a 12 reconstructed diurnal cycle, one every 2~hours 
 (from 1am to 11pm).
 
@@ -1160 +1160 @@
 \begin{figure}[!t]  \begin{center}
 \includegraphics[width=0.7\textwidth]{Fig_SBC_dcy}
-\caption{ \protect\label{Fig_SBC_dcy}   
+\caption{ \protect\label{fig:SBC_dcy}   
 Example of recontruction of the diurnal cycle variation of short wave flux  
 from daily mean values on an ORCA2 grid with a time sampling of 2~hours (from 1am to 11pm). 
@@ -1176 +1176 @@
 % -------------------------------------------------------------------------------------------------------------
 \subsection{Rotation of vector pairs onto the model grid directions}
-\label{SBC_rotation}
+\label{subsec:SBC_rotation}
 
 When using a flux (\np{ln\_flx}\forcode{ = .true.}) or bulk (\np{ln\_clio}\forcode{ = .true.} or \np{ln\_core}\forcode{ = .true.}) formulation, 
@@ -1195 +1195 @@
 % -------------------------------------------------------------------------------------------------------------
 \subsection{Surface restoring to observed SST and/or SSS (\protect\mdl{sbcssr})}
-\label{SBC_ssr}
+\label{subsec:SBC_ssr}
 %------------------------------------------namsbc_ssr----------------------------------------------------
 \forfile{../namelists/namsbc_ssr} 
@@ -1203 +1203 @@
 n forced mode using a flux formulation (\np{ln\_flx}\forcode{ = .true.}), a 
 feedback term \emph{must} be added to the surface heat flux $Q_{ns}^o$:
-\begin{equation} \label{Eq_sbc_dmp_q}
+\begin{equation} \label{eq:sbc_dmp_q}
 Q_{ns} = Q_{ns}^o + \frac{dQ}{dT} \left( \left. T \right|_{k=1} - SST_{Obs} \right)
 \end{equation}
@@ -1216 +1216 @@
 equivalent freshwater flux, it takes the following expression :
 
-\begin{equation} \label{Eq_sbc_dmp_emp}
+\begin{equation} \label{eq:sbc_dmp_emp}
 \textit{emp} = \textit{emp}_o + \gamma_s^{-1} e_{3t}  \frac{  \left(\left.S\right|_{k=1}-SSS_{Obs}\right)}
                                              {\left.S\right|_{k=1}}
@@ -1226 +1226 @@
 $\left.S\right|_{k=1}$ 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 \ref{Eq_sbc_dmp_emp} as the atmosphere 
+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 SSS restoring 
 term should be viewed as a flux correction on freshwater fluxes to reduce the 
@@ -1235 +1235 @@
 % -------------------------------------------------------------------------------------------------------------
 \subsection{Handling of ice-covered area  (\textit{sbcice\_...})}
-\label{SBC_ice-cover}
+\label{subsec:SBC_ice-cover}
 
 The presence at the sea surface of an ice covered area modifies all the fluxes 
@@ -1264 +1264 @@
 
 \subsection{Interface to CICE (\protect\mdl{sbcice\_cice})}
-\label{SBC_cice}
+\label{subsec:SBC_cice}
 
 It is now possible to couple a regional or global NEMO configuration (without AGRIF) to the CICE sea-ice
@@ -1291 +1291 @@
 % -------------------------------------------------------------------------------------------------------------
 \subsection{Freshwater budget control (\protect\mdl{sbcfwb})}
-\label{SBC_fwb}
+\label{subsec:SBC_fwb}
 
 For global ocean simulation it can be useful to introduce a control of the mean sea 
@@ -1313 +1313 @@
 \subsection[Neutral drag coeff. from external wave model (\protect\mdl{sbcwave})]
             {Neutral drag coefficient from external wave model (\protect\mdl{sbcwave})}
-\label{SBC_wave}
+\label{subsec:SBC_wave}
 %------------------------------------------namwave----------------------------------------------------
 \forfile{../namelists/namsbc_wave}
@@ -1322 +1322 @@
 The \mdl{sbcwave} module containing the routine \np{sbc\_wave} reads the
 namelist \ngn{namsbc\_wave} (for external data names, locations, frequency, interpolation and all 
-the miscellanous options allowed by Input Data generic Interface see \S\ref{SBC_input}) 
+the miscellanous options allowed by Input Data generic Interface see \autoref{sec:SBC_input}) 
 and a 2D field of neutral drag coefficient. 
 Then using the routine TURB\_CORE\_1Z or TURB\_CORE\_2Z, and starting from the neutral drag coefficent provided,