Index: /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/PDF_creation.sh
===================================================================
--- /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/PDF_creation.sh	(revision 10497)
+++ /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/PDF_creation.sh	(revision 10498)
@@ -1,7 +1,18 @@
 #!/bin/sh
-
 
 export opts='-shell-escape -pdf'
 model='NEMO'
+
+check_python_module() {
+    python -c "
+import sys
+try:
+    import $1
+    print('\nModule $1 is installed')
+except ImportError:
+    print('\nModule $1 is NOT installed')
+    print('')
+    sys.exit(42)"
+}
 
 clean() {
@@ -25,5 +36,9 @@
 }
 
+check_python_module pygments
+if [ $? -ne 0 ]; then echo 'Required python module pygments to correctly build the documentation is missing; exit 42'; echo ''; exit 42; fi
+
 clean
+
 build $model
 
Index: /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/latex/NEMO/main/NEMO_coding_conv.tex
===================================================================
--- /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/latex/NEMO/main/NEMO_coding_conv.tex	(revision 10497)
+++ /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/latex/NEMO/main/NEMO_coding_conv.tex	(revision 10498)
@@ -1,283 +1,340 @@
-\documentclass[a4paper]{article}
-\usepackage{type1cm} 
-\usepackage{times} 
-\usepackage{color} 
-\usepackage{rotating} 
-\usepackage{color} 
-\usepackage{framed} 
-\usepackage{makeidx} 
-\graphicspath{{figures/}}
-
-%%%%%%%
-\pagestyle{empty} 
-\setlength{\leftmargin}{1 cm} 
-\setlength{\rightmargin}{1 cm} 
-\setlength{\oddsidemargin}{0 cm} 
-\setlength{\evensidemargin}{0 cm} 
-\setlength{\topmargin}{-1cm} 
-\setlength{\textwidth}{16 cm} 
-\setlength{\textheight}{25cm} 
-
-%%%%%%%%%essai plus jolis from NEMO book
+\documentclass{article}
+
 \usepackage{fancyhdr}
-
+\usepackage{times}
+\usepackage{graphicx}
+\usepackage{hyperref}
+\usepackage{minted}
+%\usepackage[normalem]{ulem}   % striketrough style with \sout{...}
+
+\hypersetup{pdftitle={NEMO coding conventions}, pdfauthor={NEMO System Team}, colorlinks}
+\setminted{style=emacs, breaklines, frame=leftline}
+\newmintinline[forcode]{fortran}{fontsize=auto, frame=lines}   % \forcode{...}
+\newminted[forlines]{fortran}{}                                % \begin{forlines}
+
+\pagestyle{empty}
+\setlength{\leftmargin}{1 cm}
+\setlength{\rightmargin}{1 cm}
+\setlength{\oddsidemargin}{0 cm}
+\setlength{\evensidemargin}{0 cm}
+\setlength{\topmargin}{-1cm}
+\setlength{\textwidth}{16 cm}
+\setlength{\textheight}{25cm}
 \pagestyle{fancy}
-%\usepackage[colorlinks=true]{hyperref} %%create link
- 
-\makeindex %% run first makeindex NEMO_coding.conv.idx NEMO_coding.conv.ist
-		
+
+\title{
+  \includegraphics[width=0.3\textwidth]{../../../figures/NEMO_grey} \\
+  \vspace{1.0cm} \rule{345pt}{1.5pt} \\
+  \vspace{0.45cm} {\Huge NEMO coding conventions} \rule{345pt}{1.5pt} \\
+}
+%\title{NEMO coding conventions}
+\author{\Large NEMO System Team
+  \thanks{
+    To be completed
+  }
+}
+\date{version X.X -- month year}
+
 \begin{document}
 
-
-\title{ 
-\includegraphics[width=0.3\textwidth]{NEMO_logo_Black} \\
-\vspace{1.0cm}
-\rule{345pt}{1.5pt} \\
-\vspace{0.45cm}
- {\Huge NEMO coding conventions} 
-\rule{345pt}{1.5pt} \\ 
-{\small  -- version 3 --}   }
-%\title{NEMO coding conventions}
-\author{NEMO System Team }
-\date{March 2011}
-
-
 \maketitle
 
 \newpage
 
-\tableofcontents   
-         
+\tableofcontents
+
 \newpage
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \section{Introduction}
-This document describes conventions\index{conventions} used in NEMO coding and suggested for its development. The objectives are to offer a guide to all readers of the NEMO code, and to facilitate the work of all the developers, including the validation of their developments, and eventually the implementation of these developments within the NEMO platform. \\
-A first approach of these rules can be found in the code in $NEMO/OPA\_SRC/module\_example$ where all the basics coding conventions are illustrated. More details can be found below.\\
-This work is based on the coding conventions in use for the Community Climate System Model, \footnote { http://www.cesm.ucar.edu/working\_groups/Software/dev\_guide/dev\_guide/node7.html }
- the previous version of this document (``FORTRAN coding standard in the OPA System'') and the expertise of the NEMO System Team which can be contacted for further information ($nemo\_st@locean-ipsl.upmc.fr$)
-After a general overview below, this document will describe :
-\begin{itemize} 
-\item The style rules, i.e. the syntax, appearance and naming conventions chosen to improve readability of the code;
-\item The content rules, i.e. the conventions to improve the reliability of the different parts of the code;
-\item The package rules to go a step further by improving the reliability of the whole and interfaces between routines and modules.
+
+This document describes conventions\index{conventions} used in NEMO coding and suggested for its development.
+The objectives are to offer a guide to all readers of the NEMO code, and to facilitate the work of
+all the developers, including the validation of their developments, and
+eventually the implementation of these developments within the NEMO platform.
+
+A first approach of these rules can be found in the code in \path{./src/OCE/module_example} where
+all the basics coding conventions are illustrated.
+More details can be found below.
+
+This work is based on the coding conventions in use for the Community Climate System Model
+\footnote {\href{http://www.cesm.ucar.edu/working_groups/Software/dev_guide/dev_guide/node7.html}{UCAR conventions}}, 
+the previous version of this document (``FORTRAN coding standard in the OPA System'') and
+the expertise of the NEMO System Team.
+After a general overview below, this document will describe:
+
+\begin{itemize}
+\item
+  The style rules, $i.e.$ the syntax, appearance and naming conventions chosen to improve readability of the code;
+\item
+  The content rules, $i.e.$ the conventions to improve the reliability of the different parts of the code;
+\item
+  The package rules to go a step further by improving the reliability of the whole and
+  interfaces between routines and modules.
 \end{itemize}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \section{Overview and general conventions}
-NEMO has several different components: ocean dynamics ($OPA\_SRC$), sea-ice ($LIM\_SRC$), ocean biogeochemistry\- ($TOP\_SRC$), linear-tangent and adjoint of the dynamics ($TAM$)É each of them corresponding to a directory.
-In each directory, one will find some FORTRAN files and/or subdirectories, one per functionality of the code: $BDY$ (boundaries), $DIA$ (diagnostics), $DOM$ (domain), $DYN$ (dynamics), $LDF$ (lateral diffusion), etc...\\
-All name are chosen to be as self-explanatory as possible, in English, all prefixes are 3 digits.\\
+
+NEMO has 3 major components: ocean dynamics (\path{./src/OCE}), sea-ice (\path{./src/ICE}) and
+marine biogeochemistry (\path{./src/MBG}).
+%, linear-tangent and adjoint of the dynamics ($TAM$) each of them corresponding to a directory.
+In each directory, one will find some FORTRAN files and/or subdirectories, one per functionality of the code:
+\path{./src/OCE/BDY} (boundaries), \path{./src/OCE/DIA} (diagnostics), \path{./src/OCE/DOM} (domain),
+\path{./src/OCE/DYN} (dynamics), \path{./src/OCE/LDF} (lateral diffusion), etc... \\
+All name are chosen to be as self-explanatory as possible, in English, all prefixes are 3 digits. \\
 English is used for all variables names, comments, and documentation. \\
-Physical units are MKS. The only exception to this is the temperature, which is expressed in degrees Celsius, except in bulk formulae and part of LIM sea-ice model where it is in Kelvin. See $DOM/phycst.F90$ files for conversions.
+Physical units are MKS. The only exception to this is the temperature, which is expressed in degrees Celsius,
+except in bulk formulae and part of SI$^3$ sea-ice model where it is in Kelvin.
+See \path{.src/OCE/DOM/phycst.F90} files for conversions.
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \section{Architecture}
-Within each directory, organisation of files is driven by ÒorthogonalityÓ\index{orthogonality}, i.e. one functionality of the code is intended to be in one and only one directory, and one module and all its related routines are in one file.
+
+Within each directory, organisation of files is driven by orthogonality\index{orthogonality},
+$i.e.$ one functionality of the code is intended to be in one and only one directory, and
+one module and all its related routines are in one file.
 The functional modules\index{module} are:
-\begin{itemize} 
-\item SBC		surface module 
-\item IOM		management of the I/O 
-\item NST		interface to AGRIF (nesting model) for dynamics and biogeochemistry 
-\item OBC, BDY	management of structured and unstructured open boundaries 
-\item C1D		1D (vertical) configuration for dynamics, sea-ice and biogeochemistry 
-\item OFF		off-line module: passive tracer or biogeochemistry alone 
-\item CFG 		tutorial and reference configurations 
-\item DOC		documentation 
+
+\begin{itemize}
+\item \path{SBC}             surface module
+\item \path{IOM}             management of the I/O
+\item \path{NST}             interface to AGRIF (nesting model) for dynamics and biogeochemistry
+\item \path{OBC}, \path{BDY} management of structured and unstructured open boundaries 
+\item \path{C1D}             1D (vertical) configuration for dynamics, sea-ice and biogeochemistry
+\item \path{OFF}             off-line module: passive tracer or biogeochemistry alone
+\item \path{...}
 \end{itemize}
 
-For example, the file $domain.F90$ contains the module $domain$ and all the subroutines related to this module ($ dom\_init, dom\_nam, dom\_ctl$).
+For example, the file \textit{domain.F90} contains the module \texttt{domain} and all the subroutines related to
+this module (\texttt{dom\_init, dom\_nam, dom\_ctl}).
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \section{Style rules}
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Argument list format}
-Routine argument lists will contain a maximum 5 variables\index{variable} per line, whilst continuation lines can be used. 
-This applies both to the calling routine and the dummy argument list in the routine being called. The purpose is to simplify matching up the arguments between caller and callee. 
-
-\begin{verbatim}
+
+Routine argument lists will contain a maximum 5 variables\index{variable} per line,
+whilst continuation lines can be used.
+This applies both to the calling routine and the dummy argument list in the routine being called.
+The purpose is to simplify matching up the arguments between caller and callee.
+
+\begin{forlines}
 SUBROUTINE tra_adv_eiv( kt, pun, pvn, pwn )
 
       CALL tra_adv_eiv( kt, zun, zvn, zwn )
-\end{verbatim}
+\end{forlines}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Array syntax}
-Except for long loops (see below), array notation should be used if possible. To improve readability the array shape must be shown in brackets, e.g.: 
-\begin{verbatim}
-onedarraya(:) = onedarrayb(:) + onedarrayc(:) 
-twodarray (:,:) = scalar * anothertwodarray(:,:) 
-\end{verbatim}
-When accessing sections of arrays, for example in finite difference equations, do so by using the triplet notation on the full array, e.g.:
-\begin{verbatim}
-twodarray(:,2:len2) = scalar                      & 
-   &                * ( twodarray2(:,1:len2-1 )   & 
-   &                -   twodarray2(:,2:len2 ) ) 
-\end{verbatim}   
-For long, complicated loops, explicitly indexed loops should be preferred. In general when using this syntax, the order of the loops indices should reflect the following scheme (for best usage of data locality):
-\begin{verbatim}
-DO jk = 1, jpk 
-   DO jj = 1, jpj 
-      DO ji = 1, jpi 
-         array(ji,jj,jk) = ... 
-      END DO 
-   END DO 
-END DO 
-\end{verbatim}
+
+Except for long loops (see below), array notation should be used if possible.
+To improve readability the array shape must be shown in brackets, $e.g.$:
+
+\begin{forlines}
+onedarraya(:)   = onedarrayb(:) + onedarrayc(:)
+twodarray (:,:) = scalar * anothertwodarray(:,:)
+\end{forlines}
+
+When accessing sections of arrays, for example in finite difference equations,
+do so by using the triplet notation on the full array, $e.g.$:
+
+\begin{forlines}
+twodarray(:,2:len2) =   scalar                      &
+   &                  * ( twodarray2(:,1:len2-1 )   &
+   &                  -   twodarray2(:,2:len2 ) )
+\end{forlines}
+
+For long, complicated loops, explicitly indexed loops should be preferred.
+In general when using this syntax, the order of the loops indices should reflect the following scheme
+(for best usage of data locality):
+
+\begin{forlines}
+DO jk = 1, jpk
+   DO jj = 1, jpj
+      DO ji = 1, jpi
+         threedarray(ji,jj,jk) = ...
+      END DO
+   END DO
+END DO
+\end{forlines}
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Case}
-All FORTRAN keywords are in capital : \begin {verbatim} DIMENSION, WRITE, DO, END DO, NAMELIST \end{verbatim} 
-All other parts of the NEMO code will be written in lower case.	
+
+All FORTRAN keywords are in capital: \forcode{DIMENSION}, \forcode{WRITE}, \forcode{DO}, \forcode{END DO},
+\forcode{NAMELIST}, ... All other parts of the NEMO code will be written in lower case.
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Comments}
+
 Comments in the code are useful when reading the code and changing or developing it. \\
-The full documentation and detailed explanations are to be added in the reference manual (TeX files, aside from the code itself). \\
-In the code, the comments should explain variable content and describe each computational step.\\
-Comments in the header start with ``!!''. For more details on the content of the headers, see ÒContent rules/HeadersÓ in this document.\\
-Comments in the code start with ``!''.\\
-All comments are indented (3, 6, or 9 É blank spaces).\\
-Short comments may be included on the same line as executable code, and an additional line can be used with proper alignment. For example: 
-\begin{verbatim}
-      zx = zx *zzy   ! Describe what is going on and if it is 
-      !              ! too long use another Ô!Õ for proper 
-      !              ! alignment with automatic indentation 
-\end{verbatim}      
-More in-depth comments should be written in the form: 
-\begin{verbatim}
-!   Check of some namelist values
-\end{verbatim}         
-or 
-\begin{verbatim}    
+The full documentation and detailed explanations are to be added in the reference manual
+(TeX files, aside from the code itself). \\
+In the code, the comments should explain variable content and describe each computational step. \\
+Comments in the header start with ``!!''.
+For more details on the content of the headers, see Content rules/Headers in this document. \\
+Comments in the code start with ``!''. \\
+All comments are indented (3, 6, or 9 blank spaces). \\
+Short comments may be included on the same line as executable code, and an additional line can be used with
+proper alignment.
+For example:
+
+\begin{forlines}
+zx = zx *zzy   ! Describe what is going on and if it is
+!              ! too long use another ! for proper
+!              ! alignment with automatic indentation
+\end{forlines}
+
+More in-depth comments should be written in the form:
+
+\begin{forlines}
+   !  Check of some namelist values
+\end{forlines}
+
+or
+
+\begin{forlines}
 !
-!         !<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-!         !  Bottom boundary condition on tke
-!         !<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+!     !<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+!     !  Bottom boundary condition on tke
+!     !<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 !
-\end{verbatim}    
-Key features of this style are 1) it starts with a "!" in the column required for proper indentation, 2) the text is offset above and below by a blank line or a content line built for underlying. 
+\end{forlines}
+
+Key features of this style are
+
+\begin{enumerate}
+\item it starts with a "!" in the column required for proper indentation,
+\item the text is offset above and below by a blank line or a content line built for underlying.
+\end{enumerate}
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Continuation lines}
-Continuation lines can be used with precise alignment for readability. For example: 
-\begin{verbatim}   
-avmu(ji,jj,jk) = avmu(ji,jj,jk) * ( un(ji,jj,jk-1) - un(ji,jj,jk) )   &
-   &                            * ( ub(ji,jj,jk-1) - ub(ji,jj,jk) )   &
-   &           / (  fse3uw_n(ji,jj,jk)         &
-   &              * fse3uw_b(ji,jj,jk) )
-\end{verbatim}    
-Code lines, which are continuation lines of assignment statements, must begin to the right of the column of the assignment operator. Due to the possibility of automatic indentation in some editor (emacs for example), use a ``\&'' as first character of the continuing lines to maintain the alignment. 
+
+Continuation lines can be used with precise alignment for readability. For example:
+
+\begin{forlines}
+avmu(ji,jj,jk) =   avmu(ji,jj,jk) * ( un(ji,jj,jk-1) - un(ji,jj,jk) )   &
+   &                              * ( ub(ji,jj,jk-1) - ub(ji,jj,jk) )   &
+   &             / (   fse3uw_n(ji,jj,jk)                               &
+   &                 * fse3uw_b(ji,jj,jk) )
+\end{forlines}
+
+Code lines, which are continuation lines of assignment statements, must begin to the right of the column of
+the assignment operator.
+Due to the possibility of automatic indentation in some editor (emacs for example),
+use a ``\&'' as first character of the continuing lines to maintain the alignment.
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Declaration of arguments and local variables}
 
-In a routine, input arguments and local variables are declared 1 per line, with a comment field on the same line as the declaration. Multiple comment lines describing a single variable are acceptable if needed. For example: 
-\begin{verbatim}  
+In a routine, input arguments and local variables are declared 1 per line,
+with a comment field on the same line as the declaration.
+Multiple comment lines describing a single variable are acceptable if needed.
+For example:
+
+\begin{forlines}
 INTEGER             ::   kstp   ! ocean time-step index
-\end{verbatim}
+\end{forlines}
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{F90 Standard}
-NEMO software adheres to the FORTRAN 95 language standard and does not rely on any specific language or vendor extensions.
+
+NEMO software adheres to the FORTRAN 95 language standard and does not rely on any specific language or
+vendor extensions.
 
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Free-Form Source}
-Free-form source will be used. The F90/95 standard allows lines of up to 132 characters, but a self-imposed limit of 80 should enhance readability, or print source files with two columns per page. Multi-line comments that extend to column 100 are unacceptable.
+
+Free-form source will be used.
+The F90/95 standard allows lines of up to 132 characters, but a self-imposed limit of 80 should enhance readability,
+or print source files with two columns per page.
+Multi-line comments that extend to column 100 are unacceptable.
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Indentation}
-Code as well as comment lines within loops, if-blocks, continuation lines, MODULE or SUBROUTINE statements will be indented 3 characters for readability. (except for CONTAINS that remains at first column) 
-\begin{verbatim}  
-MODULE mod1 
-   REAL(wp) xx 
-CONTAINS 
-   SUBROUTINE sub76( px, py, pz, pw, pa,   & 
-      &              pb, pc, pd, pe      ) 
-      <instruction> 
-   END SUBROUTINE sub76 
-END MODULE mod1 
-\end{verbatim}
+
+Code as well as comment lines within loops, if-blocks, continuation lines, \forcode{MODULE} or
+\forcode{SUBROUTINE} statements will be indented 3 characters for readability
+(except for \forcode{CONTAINS} that remains at first column).
+
+\begin{forlines}
+MODULE mod1
+   REAL(wp) xx
+CONTAINS
+   SUBROUTINE sub76( px, py, pz, pw, pa,   &
+      &              pb, pc, pd, pe          )
+      <instruction>
+   END SUBROUTINE sub76
+END MODULE mod1
+\end{forlines}
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Loops}
-Loops, if explicit, should be structured with the do-end do construct as opposed to numbered loops. Nevertheless non-numeric labels can be used for a big iterative loop of a recursive algorithm. In the case of a long loop, a self-descriptive label can be used (i.e. not just a number).
+
+Loops, if explicit, should be structured with the do-end do construct as opposed to numbered loops.
+Nevertheless non-numeric labels can be used for a big iterative loop of a recursive algorithm.
+In the case of a long loop, a self-descriptive label can be used ($i.e.$ not just a number).
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Naming Conventions: files}
-A file containing a module will have the same name as the module it contains (because dependency rules used by "make" programs are based on file names).
-\footnote{For example, if routine A "USE"s module B, then "make" must be told of the dependency relation which requires B to be compiled before A. If one can assume that module B resides in file B.o, building a tool to generate this dependency rule (e.g. A.o: B.o) is quite simple. Put another way, it is difficult (to say nothing of CPU-intensive) to search an entire source tree to find the file in which module B resides for each routine or module which "USE"s B.}
+
+A file containing a module will have the same name as the module it contains
+(because dependency rules used by "make" programs are based on file names).
+\footnote{
+  For example, if routine A "\forcode{USE}"s module B, then "make" must be told of the dependency relation which
+  requires B to be compiled before A.
+  If one can assume that module B resides in file B.o,
+  building a tool to generate this dependency rule ($e.g.$ A.o: B.o) is quite simple.
+  Put another way, it is difficult (to say nothing of CPU-intensive) to search an entire source tree to
+  find the file in which module B resides for each routine or module which "\forcode{USE}"s B.
+}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Naming Conventions: modules}
-Use a meaningful English name and the ``3 letters'' naming convention: first 3 letters for the code section, and last 3 to describe the module. For example, zdftke, where ``zdf'' stands for vertical diffusion, and ``tke'' for turbulent kinetic energy. 
-\\
-Note that by implication multiple modules are not allowed in a single file. 
-The use of common blocks is deprecated in Fortran 90 and their use in NEMO is strongly discouraged. Modules are a better way to declare static data. Among the advantages of modules is the ability to freely mix data of various types, and to limit access to contained variables through the use of the ONLY and PRIVATE attributes. 
+
+Use a meaningful English name and the ``3 letters'' naming convention:
+first 3 letters for the code section, and last 3 to describe the module.
+For example, zdftke, where ``zdf'' stands for vertical diffusion, and ``tke'' for turbulent kinetic energy. \\
+Note that by implication multiple modules are not allowed in a single file.
+The use of common blocks is deprecated in Fortran 90 and their use in NEMO is strongly discouraged.
+Modules are a better way to declare static data.
+Among the advantages of modules is the ability to freely mix data of various types, and
+to limit access to contained variables through the use of the \forcode{ONLY} and \forcode{PRIVATE} attributes.
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Naming Conventions: variables}
-All variable should be named as explicitly as possible in English. The naming convention concerns prefix letters of these name, in  order to identify the variable type and status.\\
+
+All variable should be named as explicitly as possible in English.
+The naming convention concerns prefix letters of these name, in order to identify the variable type and status. \\
 Never use a FORTRAN keyword as a routine or variable name. \\
 The table below lists the starting letter(s) to be used for variable naming, depending on their type and status:
 %--------------------------------------------------TABLE--------------------------------------------------
 \begin{table}[htbp]
-\begin{center}
-\begin{tabular}{|p{50pt}|p{50pt}|p{50pt}|p{50pt}|p{50pt}|p{50pt}|p{50pt}|}
-\hline  Type \par / Status &   integer&   real&   logical &   character&   double \par precision&   complex \\  
-\hline
-public  \par or  \par module variable& 
-\textbf{m n} \par \textit{but not } \par \textbf{nn\_}& 
-\textbf{a b e f g h o} \textbf{q} \textit{to} \textbf{x} \par but not \par \textbf{fs rn\_}& 
-\textbf{l} \par \textit{but not} \par \textbf{lp ld ll ln\_}& 
-\textbf{c} \par \textit{but not} \par \textbf{cp cd cl cn\_}& 
-\textbf{d} \par \textit{but not} \par \textbf{dp dd dl dn\_}& 
-\textbf{y} \par \textit{but not} \par \textbf{yp yd yl} \\
-\hline
-dummy \par argument& 
-\textbf{k} \par \textit{but not} \par \textbf{kf}& 
-\textbf{p} \par \textit{but not}  \par \textbf{pp pf}& 
-\textbf{ld}& 
-\textbf{cd}& 
-\textbf{dd}& 
-\textbf{yd} \\
-\hline
-local \par variable& 
-\textbf{i}& 
-\textbf{z}& 
-\textbf{ll}& 
-\textbf{cl}& 
-\textbf{cd}& 
-\textbf{yl} \\
-\hline
-loop \par control& 
-\textbf{j} \par \textit{but not } \par \textbf{jp}& 
-& 
-& 
-& 
-& 
- \\
-\hline
-parameter& 
-\textbf{jp}& 
-\textbf{pp}& 
-\textbf{lp}& 
-\textbf{cp}& 
-\textbf{dp}& 
-\textbf{yp} \\
-\hline
-
-namelist&
-\textbf{nn\_}& 
-\textbf{rn\_}& 
-\textbf{ln\_}& 
-\textbf{cn\_}& 
-\textbf{dn\_}& 
-\\
-\hline
-CPP \par macro& 
-\textbf{kf}& 
-\textbf{sf} \par & 
-& 
-& 
-& 
- \\
-\hline
-\end{tabular}
-\label{tab1}
-\end{center}
+  \begin{center}
+    \begin{tabular}{|p{50pt}|p{50pt}|p{50pt}|p{50pt}|p{50pt}|p{50pt}|p{50pt}|}
+      \hline
+      Type \par / Status &   integer&   real&   logical &   character&   double \par precision&   complex \\
+      \hline
+      public  \par or  \par module variable& \textbf{m n} \par \textit{but not } \par \textbf{nn\_}& \textbf{a b e f g h o} \textbf{q} \textit{to} \textbf{x} \par but not \par \textbf{fs rn\_}& \textbf{l} \par \textit{but not} \par \textbf{lp ld ll ln\_}& \textbf{c} \par \textit{but not} \par \textbf{cp cd cl cn\_}& \textbf{d} \par \textit{but not} \par \textbf{dp dd dl dn\_}& \textbf{y} \par \textit{but not} \par \textbf{yp yd yl} \\
+      \hline
+      dummy \par argument& \textbf{k} \par \textit{but not} \par \textbf{kf}& \textbf{p} \par \textit{but not}  \par \textbf{pp pf}& \textbf{ld}& \textbf{cd}& \textbf{dd}& \textbf{yd} \\
+      \hline
+      local \par variable& \textbf{i}& \textbf{z}& \textbf{ll}& \textbf{cl}& \textbf{cd}& \textbf{yl} \\
+      \hline
+      loop \par control& \textbf{j} \par \textit{but not } \par \textbf{jp}& & & & &  \\
+      \hline
+      parameter& \textbf{jp}& \textbf{pp}& \textbf{lp}& \textbf{cp}& \textbf{dp}& \textbf{yp} \\
+      \hline
+      namelist& \textbf{nn\_}& \textbf{rn\_}& \textbf{ln\_}& \textbf{cn\_}& \textbf{dn\_}& \\
+      \hline
+      CPP \par macro& \textbf{kf}& \textbf{sf} \par & & & & \\
+      \hline
+    \end{tabular}
+    \label{tab1}
+  \end{center}
 \end{table}
 %--------------------------------------------------------------------------------------------------------------
@@ -285,27 +342,45 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Operators}
-Use of the operators $<, >, <=, >=, ==, /= $ is strongly recommended instead of their deprecated counterparts, $lt., .gt., .le., .ge., .eq., and .ne. $ The motivation is readability. In general use the notation: \\
+
+Use of the operators \texttt{<, >, <=, >=, ==, /=} is strongly recommended instead of their deprecated counterparts
+(\texttt{.lt., .gt., .le., .ge., .eq., .ne.}).
+The motivation is readability.
+In general use the notation: \\
 $<Blank><Operator><Blank>$
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Pre processor}
-Where the use of a language pre-processor is required, it will be the C pre-processor (cpp).\\
+
+Where the use of a language pre-processor is required, it will be the C pre-processor (cpp). \\
 The cpp key is the main feature used, allowing to ignore some useless parts of the code at compilation step. \\
 The advantage is to reduce the memory use; the drawback is that compilation of this part of the code isn't checked. \\
-The cpp key feature should only be used for a few limited options, if it reduces the memory usage. In all cases, a logical variable and a FORTRAN $IF$ should be preferred.
-When using a cpp key $key\_optionname$, a corresponding logical variable $lk\_optionname$ should be declared to allow FORTRAN $IF$ tests in the code and  a FORTRAN module with the same name (i.e. $optionname.F90$) should
- be defined. This module is the only place where a ``\#if defined'' command appears, selecting either the whole FORTRAN code or a dummy module. For example, the TKE vertical physics, the module name is $zdftke.F90$, the CPP key is $key\_zdftke$ and the associated logical is $lk\_zdftke$. 
+The cpp key feature should only be used for a few limited options, if it reduces the memory usage.
+In all cases, a logical variable and a FORTRAN \forcode{IF} should be preferred.
+When using a cpp key \textit{key\_optionname},
+a corresponding logical variable \textit{lk\_optionname} should be declared to
+allow FORTRAN \forcode{IF} tests in the code and
+a FORTRAN module with the same name ($i.e.$ \textit{optionname.F90}) should be defined.
+This module is the only place where a \``\#if defined'' command appears, selecting either the whole FORTRAN code or
+a dummy module.
+For example, the TKE vertical physics, the module name is \textit{zdftke.F90},
+the CPP key is \textit{key\_zdftke} and the associated logical is \textit{lk\_zdftke}.
 
 The following syntax:
-\begin{verbatim} 
-#if defined key_optionname 
+
+\begin{forlines}
+#if defined key_optionname
 !! Part of code conditionally compiled if cpp key key_optionname is active
 #endif
-\end{verbatim} 
+\end{forlines}
+
 Is to be used rather than the \#ifdef abbreviate form since it may have conflicts with some Unix scripts.
 
 Tests on cpp keys included in NEMO at compilation step:
+
 \begin{itemize}
-\item The CPP keys used are compared to the previous list of cpp keys (the compilation will stop if trying to specify a Ònon-existing keyÓ)
-\item If a change occurs in the CPP keys used for a given experiment, the whole compilation phase is done again.
+\item
+  The CPP keys used are compared to the previous list of cpp keys
+  (the compilation will stop if trying to specify a non-existing key)
+\item
+  If a change occurs in the CPP keys used for a given experiment, the whole compilation phase is done again.
 \end{itemize}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -314,169 +389,266 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Configurations}
-The configuration defines the domain and the grid on which NEMO is running. It may be useful to associate a cpp key and some variables to a given configuration, although the part of the code changed under each of those keys should be minimized. As an example, the "ORCA2" configuration (global ocean, 2 degrees grid size) is associated with the cpp key $key\_orca2$ for which 
-\begin{verbatim} 
+
+The configuration defines the domain and the grid on which NEMO is running.
+It may be useful to associate a cpp key and some variables to a given configuration, although
+the part of the code changed under each of those keys should be minimized.
+As an example, the "ORCA2" configuration (global ocean, 2 degrees grid size) is associated with
+the cpp key \texttt{key\_orca2} for which
+
+\begin{forlines}
 cp_cfg = "orca"
 jp_cfg = 2
-\end{verbatim} 
+\end{forlines}
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Constants}
-Physical constants (e.g. pi, gas constants) must never be hardwired into the executable portion of a code. Instead, a mnemonically named variable or parameter should be set to the appropriate value, in the setup routine for the package\index{package}. We realize than many parameterizations rely on empirically derived constants or fudge factors, which are not easy to name. In these cases it is not forbidden to leave such factors coded as "magic numbers" buried in executable code, but comments should be included referring to the source of the empirical formula. Hard-coded numbers should never be passed through argument lists. 
+
+Physical constants ($e.g.$ $\pi$, gas constants) must never be hardwired into the executable portion of a code.
+Instead, a mnemonically named variable or parameter should be set to the appropriate value,
+in the setup routine for the package\index{package}.
+We realize than many parameterizations rely on empirically derived constants or fudge factors,
+which are not easy to name.
+In these cases it is not forbidden to leave such factors coded as "magic numbers" buried in executable code, but
+comments should be included referring to the source of the empirical formula.
+Hard-coded numbers should never be passed through argument lists.
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Declaration for variables and constants}
 
-\subsubsection{Rules :}
-Variables used as constants should be declared with attribute PARAMETER and used always without copying to local variables, inorder to prevent from using different values for the same constant or changing it accidentally. 
+\subsubsection{Rules}
+
+Variables used as constants should be declared with attribute \forcode{PARAMETER} and
+used always without copying to local variables, in order to
+prevent from using different values for the same constant or changing it accidentally.
+
 \begin{itemize}
-\item Usage of the DIMENSION statement or attribute is required in declaration statements
-\item The ``::'' notation is quite useful to show that this program unit declaration part is  written in standard FORTRAN syntax, even if there are no attributes to clarify the  declaration section. Always use the notation $<$blank$>$::$<$three blanks$>$ to improve readability. 
-\item Declare the length of a character variable using the CHARACTER (len=xxx) syntax
-\footnote { The len specifier is important because it is possible to have several kinds for characters  (e.g. Unicode using two bytes per character, or there might be a different kind for Japanese e.g. NEC). }
-
-\item For all global data (in contrast to module data, that is all data that can be access by other module) must be accompanied with a comment field  on the same line. 
-\footnote {This allows a easy research of where and how a variable is declared using the unix command: ``grep var *90 |grep !:''. }
-\\
+\item
+  Usage of the \forcode{DIMENSION} statement or attribute is required in declaration statements
+\item
+  The ``::'' notation is quite useful to show that this program unit declaration part is written in
+  standard FORTRAN syntax, even if there are no attributes to clarify the declaration section.
+  Always use the notation $<$blank$>$::$<$three blanks$>$ to improve readability.
+\item
+  Declare the length of a character variable using the \forcode{CHARACTER} (len=xxx) syntax
+  \footnote {
+    The len specifier is important because it is possible to have several kinds for characters
+    ($e.g.$ Unicode using two bytes per character, or there might be a different kind for Japanese $e.g.$ NEC).
+  }
+\item
+  For all global data (in contrast to module data, that is all data that can be access by other module)
+  must be accompanied with a comment field on the same line
+  \footnote {
+    This allows a easy research of where and how a variable is declared using the unix command:
+    ``grep var *90 | grep !:''.
+  }.
+  For example:
+  \begin{forlines}
+  REAL(wp), DIMENSION(jpi,jpj,jpk) ::  ua   ! i-horizontal velocity (m/s)
+  \end{forlines}
+\end{itemize}
+
+\subsubsection{Implicit None}
+
+All subroutines and functions will include an \forcode{IMPLICIT NONE} statement.
+Thus all variables must be explicitly typed.
+It also allows the compiler to detect typographical errors in variable names.
+For modules, one \forcode{IMPLICIT NONE} statement in the modules definition section is needed.
+This also removes the need to have \forcode{IMPLICIT NONE} statements in
+any routines that are \forcode{CONTAINS}'ed in the module.
+Improper data initialisation is another common source of errors
+\footnote{
+  A variable could contain an initial value you did not expect.
+  This can happen for several reasons, $e.g.$ the variable has never been assigned a value, its value is outdated,
+  memory has been allocated for a pointer but you have forgotten to initialise the variable pointed to.
+}.
+To avoid problems, initialise variables as close as possible to where they are first used.
+
+\subsubsection{Attributes}
+
+\forcode{PRIVATE} / \forcode{PUBLIC}:
+All resources of a module are \forcode{PUBLIC} by default.
+A reason to store multiple routines and their data in a single module is that
+the scope of the data defined in the module can be limited to the routines which are in the same module.
+This is accomplished with the \forcode{PRIVATE} attribute. \\
+\forcode{INTENT}:
+All dummy arguments of a routine must include the \forcode{INTENT} clause in their declaration in order to
+improve control of variables in routine calls.
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\subsection{Headers}
+
+Prologues are not used in NEMO for now, although it may become an interesting tool in combination with
+ProTeX auto documentation script in the future.
+Rules to code the headers and layout of a module or a routine are illustrated in the example module available with
+the code: \path{./src/OCE/module_example}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\subsection{Interface blocks}
+
+Explicit interface blocks are required between routines if optional or keyword arguments are to be used.
+They also allow the compiler to check that the type, shape and number of arguments specified in the \forcode{CALL}
+are the same as those specified in the subprogram itself.
+FORTRAN 95 compilers can automatically provide explicit interface blocks for routines contained in a module.
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\subsection{I/O Error Conditions}
+
+I/O statements which need to check an error condition will use the \texttt{iostat=<integer variable>} construct
+instead of the outmoded \texttt{end=} and \forcode{err=}. \\
+Note that a 0 value means success, a positive value means an error has occurred, and
+a negative value means the end of record or end of file was encountered.
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\subsection{PRINT - ASCII output files}
+
+Output listing and errors are directed to \texttt{numout} logical unit =6 and
+produces a file called \textit{ocean.output} (use \texttt{ln\_prt} to have one output per process in MPP).
+Logical \texttt{lwp} variable allows for less verbose outputs.
+To output an error from a routine, one can use the following template:
+
+\begin{forlines}
+IF( nstop /= 0 .AND. lwp ) THEN   ! error print
+   WRITE(numout,cform_err)
+   WRITE(numout,*) nstop, ' error have been found'
+ENDIF
+\end{forlines}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\subsection{Precision}
+
+Parameterizations should not rely on vendor-supplied flags to supply a default floating point precision or
+integer size.
+The F95 \forcode{KIND} feature should be used instead.
+In order to improve portability between 32 and 64 bit platforms,
+it is necessary to make use of kinds by using a specific module \path{./src/OCE/par_kind.F90}
+declaring the "kind definitions" to obtain the required numerical precision and range as well as
+the size of \forcode{INTEGER}.
+It should be noted that numerical constants need to have a suffix of \texttt{\_kindvalue} to
+have the according size. \\
+Thus \forcode{wp} being the "working precision" as declared in \path{./src/OCE/par_kind.F90},
+declaring real array \forcode{zpc} will take the form:
+
+\begin{forlines}
+REAL(wp), DIMENSION(jpi,jpj,jpk) ::  zpc      ! power consumption
+\end{forlines}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\subsection{Structures}
+
+The \forcode{TYPE} structure allowing to declare some variables is more often used in NEMO,
+especially in the modules dealing with reading fields, or interfaces.
 For example:
-\begin{verbatim}
-REAL(wp), DIMENSION(jpi,jpj,jpk) ::  ua  &  !: i-horizontal velocity (m/s) 
-\end{verbatim}
-\end{itemize}
-
-\subsubsection{Implicit None:}
- All subroutines and functions will include an IMPLICIT NONE statement. 
-Thus all variables must be explicitly typed. It also allows the compiler to detect typographical errors in variable names. 
-For modules, one IMPLICIT NONE statement in the modules definition section is needed. This also removes the need to have IMPLICIT NONE statements in any routines that are CONTAIN'd in the module.
-Improper data initialisation is another common source of errors. 
-\footnote{A variable could contain an initial value you did not expect. This can happen for several reasons, e.g. the variable has never been assigned a value, its value is outdated, memory has been allocated for a pointer but you have forgotten to initialise the variable pointed to.} 
-To avoid problems, initialise variables as close as possible to where they are first used. 
-
-\subsubsection{Attributes:}
-$PRIVATE / PUBLIC$ : 
-All resources of a module are $PUBLIC$ by default.
-A reason to store multiple routines and their data in a single module is that the scope of the data defined in the module can be limited to the routines which are in the same module. This is accomplished with the $PRIVATE$ attribute.\\
-$INTENT$ :
-All dummy arguments of a routine must include the $INTENT$ clause in their declaration in order to improve control of variables in routine calls. 
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\subsection{Headers}
-Prologues are not used in NEMO for now, although it may become an interesting tool in combination with ProTeX auto documentation script in the future. 
-Rules to code the headers and layout of a module or a routine are illustrated in the example module available with the code : {\it NEMO/OPA\_SRC/module\_example}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\subsection{Interface blocks}
-Explicit interface blocks are required between routines if optional or keyword arguments are to be used. They also allow the compiler to check that the type, shape and number of arguments specified in the CALL are the same as those specified in the subprogram itself. FORTRAN 95 compilers can automatically provide explicit interface blocks  for routines contained in a module. 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\subsection{I/O Error Conditions}
-I/O statements which need to check an error condition will use the $iostat=<integer variable>$ construct instead of the outmoded end= and err=. \\
-Note that a 0 value means success, a positive value means an error has occurred, and a negative value means the end of record or end of file was encountered. 
- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\subsection{PRINT - ASCII output files}
-Output listing and errors are directed to $numout$ logical unit =6 and produces a file called $ocean.output$  (use ln\_prt to have one output per process in  MPP). Logical $lwp$ variable allows for less verbose outputs.
-To output an error from a routine, one can use the following template:
-\begin{verbatim}
-      IF( nstop /= 0 .AND. lwp ) THEN   ! error print
-         WRITE(numout,cform_err)
-         WRITE(numout,*) nstop, ' error have been found'
-      ENDIF
-\end{verbatim}
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\subsection{Precision}
-Parameterizations should not rely on vendor-supplied flags to supply a default floating point precision or integer size. The F95$ KIND$ feature should be used instead. In order to improve portability between 32 and 64 bit platforms, it is necessary to make use of kinds by using a specific module ($OPA\_SRC/par\_kind.F90$)  declaring the "kind definitions" to obtain the required numerical precision and range as well as the size of INTEGER. It should be noted that numerical constants need to have a suffix of \_$kindvalue$ to have the according size. \\
-Thus $wp$ being the "working precision" as declared in $OPA\_SRC/par\_kind.F90$, declaring real array $zpc$ will take the form:
-\begin{verbatim}
-      REAL(wp), DIMENSION(jpi,jpj,jpk) ::  zpc      ! power consumption
-\end{verbatim}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\subsection{Structures}
-The TYPE structure allowing to declare some variables is more often used in NEMO, especially in the modules dealing with reading fields, or interfaces.For example
-\begin{verbatim}
- ! Definition of a tracer as a structure
-      TYPE PTRACER
-         CHARACTER(len = 20)  :: sname  !: short name
-         CHARACTER(len = 80 ) :: lname  !: long name
-         CHARACTER(len = 20 ) :: unit   !: unit
-         LOGICAL              :: lini   !: read in a file or not
-         LOGICAL              :: lsav   !: ouput the tracer or not
-      END TYPE PTRACER
-
-      TYPE(PTRACER) , DIMENSION(jptra) :: tracer
-\end{verbatim}
- 
- Missing rule on structure name??
- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\begin{forlines}
+! Definition of a tracer as a structure
+TYPE PTRACER
+   CHARACTER(len = 20)  :: sname  ! short name
+   CHARACTER(len = 80 ) :: lname  ! long name
+   CHARACTER(len = 20 ) :: unit   ! unit
+   LOGICAL              :: lini   ! read in a file or not
+   LOGICAL              :: lsav   ! ouput the tracer or not
+END TYPE PTRACER
+
+TYPE(PTRACER) , DIMENSION(jptra) :: tracer
+\end{forlines}
+
+Missing rule on structure name??
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \section{Packages coding rules}
- 
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Bounds checking}
-NEMO is able to run when an array bounds checking option is enabled (provided the cpp key $key\_vectopt\_loop$ is not defined). \\
-Thus, constructs of the  following form are disallowed: 
-\begin{verbatim}
-REAL(wp) :: arr(1) 
-\end{verbatim}
-where "arr" is an input argument into which the user wishes to index beyond 1. Use of the (*) construct in array dimensioning  is forbidden also because it effectively disables array bounds checking.
+
+NEMO is able to run when an array bounds checking option is enabled
+(provided the cpp key \texttt{key\_vectopt\_loop} is not defined). \\
+Thus, constructs of the following form are disallowed:
+
+\begin{forlines}
+REAL(wp) :: arr(1)
+\end{forlines}
+
+where "arr" is an input argument into which the user wishes to index beyond 1.
+Use of the (*) construct in array dimensioning is forbidden also because
+it effectively disables array bounds checking.
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Communication}
-A package should refer only to its own modules and subprograms and to those intrinsic functions included in the Fortran standard.\\
+
+A package should refer only to its own modules and subprograms and to those intrinsic functions included in
+the Fortran standard. \\
 All communication with the package will be through the argument list or namelist input.
-\footnote { The point behind this rule is that packages should not have to know details of the surrounding model data structures, or the names of variables outside of the package. A notable exception to this rule is model resolution parameters. The reason for the exception is to allow compile-time array sizing inside the package. This is often important for efficiency.}
+\footnote{
+  The point behind this rule is that packages should not have to know details of
+  the surrounding model data structures, or the names of variables outside of the package.
+  A notable exception to this rule is model resolution parameters.
+  The reason for the exception is to allow compile-time array sizing inside the package.
+  This is often important for efficiency.
+}
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Error conditions}
-When an error condition occurs inside a package, a message describing what went wrong will be printed (see PRINT - ASCII output files). The name of the routine in which the error occurred must be included. It is acceptable to terminate execution within a package, but the developer may instead wish to return an error flag through the argument list, see $stpctl.F90$.
+
+When an error condition occurs inside a package, a message describing what went wrong will be printed
+(see PRINT - ASCII output files).
+The name of the routine in which the error occurred must be included.
+It is acceptable to terminate execution within a package, but
+the developer may instead wish to return an error flag through the argument list,
+see \textit{stpctl.F90}.
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Memory management}
 
-The main action is to identify and declare which arrays are PUBLIC and
-which are PRIVATE.\\ As of version 3.3.1 of NEMO, the use of static
-arrays (size fixed at compile time) has been deprecated.  All module
-arrays are now declared ALLOCATABLE and allocated in either the
-$<$module\_name$>$\_alloc() or $<$module\_name$>$\_init()
-routines. The success or otherwise of each ALLOCATE must be checked
-using the $Stat=<integer\ variable>$ optional argument.\\
-
-In addition to arrays contained within modules, many routines in NEMO
-require local, ``workspace'' arrays to hold the intermediate results
-of calculations. In previous versions of NEMO, these arrays were
-declared in such a way as to be automatically allocated on the stack
-when the routine was called.  An example of an automatic array is:
-\begin{verbatim}
-SUBROUTINE sub(n) 
-   REAL :: a(n) 
-   ... 
-END SUBROUTINE sub 
-\end{verbatim}
-The downside of this approach is that the program will crash if it
-runs out of stack space and the reason for the crash might not be
-obvious to the user.
-
-Therefore, as of version 3.3.1, the use of automatic arrays is
-deprecated. Instead, a new module, ``wrk\_nemo,'' has been introduced
-which contains 1-,2-,3- and 4-dimensional workspace arrays for use in
-subroutines. These workspace arrays should be used in preference to
-declaring new, local (allocatable) arrays whenever possible. The only
-exceptions to this are when workspace arrays with lower bounds other
-than 1 and/or with extent(s) greater than those in the {\it wrk\_nemo}
-module are required.\\
-
-The 2D, 3D and 4D workspace arrays in {\it wrk\_nemo} have extents
-$jpi$, $jpj$, $jpk$ and $jpts$ ($x$, $y$, $z$ and tracers) in the first,
-second, third and fourth dimensions, respectively. The 1D arrays are
-allocated with extent MAX($jpi\times jpj, jpk\times jpj, jpi\times
-jpk$).\\
-
-The REAL (KIND=$wp$) workspace arrays in {\it wrk\_nemo} are named
-e.g. $wrk\_1d\_1$, $wrk\_4d\_2$ etc. and should be accessed by USE'ing
-the {\it wrk\_nemo} module. Since these arrays are available to any
-routine, some care must be taken that a given workspace array is not
-already being used somewhere up the call stack. To help with this,
-{\it wrk\_nemo} also contains some utility routines; {\it
-  wrk\_in\_use()} and {\it wrk\_not\_released()}. The former first
-checks that the requested arrays are not already in use and then sets
-internal flags to show that they are now in use. The {\it
-  wrk\_not\_released()} routine un-sets those internal flags. A
-subroutine using this functionality for two, 3D workspace arrays named
-$zwrk1$ and $zwrk2$ will look something like:
-\begin{verbatim}
+The main action is to identify and declare which arrays are \forcode{PUBLIC} and which are \forcode{PRIVATE}. \\
+As of version 3.3.1 of NEMO, the use of static arrays (size fixed at compile time) has been deprecated.
+All module arrays are now declared \forcode{ALLOCATABLE} and
+allocated in either the \texttt{<module\_name>\_alloc()} or \texttt{<module\_name>\_init()} routines.
+The success or otherwise of each \forcode{ALLOCATE} must be checked using
+the \texttt{stat=<integer\ variable>} optional argument. \\
+
+In addition to arrays contained within modules, many routines in NEMO require local, ``workspace'' arrays to
+hold the intermediate results of calculations.
+In previous versions of NEMO, these arrays were declared in such a way as to be automatically allocated on
+the stack when the routine was called.
+An example of an automatic array is:
+
+\begin{forlines}
+SUBROUTINE sub(n)
+   REAL :: a(n)
+   ...
+END SUBROUTINE sub
+\end{forlines}
+
+The downside of this approach is that the program will crash if it runs out of stack space and
+the reason for the crash might not be obvious to the user.
+
+Therefore, as of version 3.3.1, the use of automatic arrays is deprecated.
+Instead, a new module, \textit{wrk\_nemo.F90}, has been introduced which
+contains 1-,2-,3- and 4-dimensional workspace arrays for use in subroutines.
+These workspace arrays should be used in preference to declaring new, local (allocatable) arrays whenever possible.
+The only exceptions to this are when workspace arrays with lower bounds other than 1 and/or
+with extent(s) greater than those in the \textit{wrk\_nemo.F90} module are required. \\
+
+The 2D, 3D and 4D workspace arrays in \textit{wrk\_nemo.F90} have extents \texttt{jpi}, \texttt{jpj},
+\texttt{jpk} and \texttt{jpts} ($x$, $y$, $z$ and tracers) in the first, second, third and fourth dimensions,
+respectively.
+The 1D arrays are allocated with extent MAX($jpi \times jpj, jpk \times jpj, jpi \times jpk$). \\
+
+The \forcode{REAL (KIND = wp)} workspace arrays in \textit{wrk\_nemo.F90}
+are named $e.g.$ \texttt{wrk\_1d\_1, wrk\_4d\_2} etc. and
+should be accessed by USE'ing the \textit{wrk\_nemo.F90} module.
+Since these arrays are available to any routine,
+some care must be taken that a given workspace array is not already being used somewhere up the call stack.
+To help with this, \textit{wrk\_nemo.F90} also contains some utility routines;
+\texttt{wrk\_in\_use()} and \texttt{wrk\_not\_released()}.
+The former first checks that the requested arrays are not already in use and then sets internal flags to show that
+they are now in use.
+The \texttt{wrk\_not\_released()} routine un-sets those internal flags.
+A subroutine using this functionality for two, 3D workspace arrays named \texttt{zwrk1} and
+\texttt{zwrk2} will look something like:
+
+\begin{forlines}
 SUBROUTINE sub()
-   USE wrk_nemo, ONLY: wrk_in_use, wrk_not_released 
+   USE wrk_nemo, ONLY: wrk_in_use, wrk_not_released
    USE wrk_nemo, ONLY: zwrk1 => wrk_3d_5, zwrk2 => wrk_3d_6
    !
@@ -485,5 +657,5 @@
       RETURN
    END IF
-   ... 
+   ...
    ...
    IF(wrk_not_released(3, 5,6)THEN
@@ -491,24 +663,21 @@
    END IF
    !
-END SUBROUTINE sub 
-\end{verbatim}
-The first argument to each of the utility routines is the
-dimensionality of the required workspace (1--4). Following this there
-must be one or more integers identifying which workspaces are to be
-used/released.
+END SUBROUTINE sub
+\end{forlines}
+
+The first argument to each of the utility routines is the dimensionality of the required workspace (1--4).
+Following this there must be one or more integers identifying which workspaces are to be used/released.
 Note that, in the interests of keeping the code as simple as possible,
-there is no use of POINTERs etc. in the {\it wrk\_nemo}
-module. Therefore it is the responsibility of the developer to ensure
-that the arguments to {\it wrk\_in\_use()} and {\it
-  wrk\_not\_released()} match the workspace arrays actually being used
-by the subroutine.\\
-
-If a workspace array is required that has extent(s) less than those of
-the arrays in the {\it wrk\_nemo} module then the advantages of
-implicit loops and bounds checking may be retained by defining a
-pointer to a sub-array as follows:
-\begin{verbatim}
+there is no use of \forcode{POINTER}s etc. in the \textit{wrk\_nemo.F90} module.
+Therefore it is the responsibility of the developer to ensure that the arguments to \texttt{wrk\_in\_use()} and
+\texttt{wrk\_not\_released()} match the workspace arrays actually being used by the subroutine. \\
+
+If a workspace array is required that has extent(s) less than those of the arrays in
+the \textit{wrk\_nemo.F90} module then the advantages of implicit loops and bounds checking may be retained by
+defining a pointer to a sub-array as follows:
+
+\begin{forlines}
 SUBROUTINE sub()
-   USE wrk_nemo, ONLY: wrk_in_use, wrk_not_released 
+   USE wrk_nemo, ONLY: wrk_in_use, wrk_not_released
    USE wrk_nemo, ONLY: wrk_3d_5
    !
@@ -521,73 +690,112 @@
    !
    zwrk1 => wrk_3d_5(1:10,1:10,1:10)
-   ... 
-END SUBROUTINE sub 
-\end{verbatim}
-Here, instead of ``use associating'' the variable $zwrk1$ with the
-array $wrk\_3d\_5$ (as in the first example), it is explicitly
-declared as a pointer to a 3D array. It is then associated with a
-sub-array of $wrk\_3d\_5$ once the call to {\it wrk\_in\_use()} has
-completed successfully. Note that in F95 (to which NEMO conforms) it
-is not possible for either the upper or lower array bounds of the
-pointer object to differ from those of the target array.\\
-
-In addition to the REAL (KIND=$wp$) workspace arrays, {\it wrk\_nemo}
-also contains 2D integer arrays and 2D REAL arrays with extent ($jpi$,
-$jpk$), {\it i.e.} $xz$. The utility routines for the integer
-workspaces are {\it iwrk\_in\_use()} and {\it iwrk\_not\_released()}
-while those for the $xz$ workspaces are {\it wrk\_in\_use\_xz()}
-and {\it wrk\_not\_released\_xz()}.
-
-Should a call to one of the {\it wrk\_in\_use()} family of utilities
-fail, an error message is printed along with a table showing which of
-the workspace arrays are currently in use. This should enable the
-developer to choose alternatives for use in the subroutine being
-worked on.\\
-
-When compiling NEMO for production runs, the calls to {\it
-  wrk\_in\_use()}/{\it wrk\_not\_released()} can be reduced to stubs
-that just return $.$FALSE$.$ by setting the cpp key
-{\it key\_no\_workspace\_check}. These stubs may then be inlined (and
-thus effectively removed altogether) by setting appropriate compiler
-flags (e.g. ``-finline'' for the Intel compiler or ``-Q'' for the IBM
-compiler).
-
- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+   ...
+END SUBROUTINE sub
+\end{forlines}
+
+Here, instead of ``use associating'' the variable \texttt{zwrk1} with the array \texttt{wrk\_3d\_5}
+(as in the first example), it is explicitly declared as a pointer to a 3D array.
+It is then associated with a sub-array of \texttt{wrk\_3d\_5} once the call to
+\texttt{wrk\_in\_use()} has completed successfully.
+Note that in F95 (to which NEMO conforms) it is not possible for either the upper or lower array bounds of
+the pointer object to differ from those of the target array. \\
+
+In addition to the \forcode{REAL (KIND = wp)} workspace arrays,
+\textit{wrk\_nemo.F90} also contains 2D integer arrays and 2D REAL arrays with extent (\texttt{jpi}, \texttt{jpk}),
+$i.e.$ $xz$.
+The utility routines for the integer workspaces are \texttt{iwrk\_in\_use()} and \texttt{iwrk\_not\_released()} while
+those for the $xz$ workspaces are \texttt{wrk\_in\_use\_xz()} and \texttt{wrk\_not\_released\_xz()}.
+
+Should a call to one of the \texttt{wrk\_in\_use()} family of utilities fail,
+an error message is printed along with a table showing which of the workspace arrays are currently in use.
+This should enable the developer to choose alternatives for use in the subroutine being worked on. \\
+
+When compiling NEMO for production runs,
+the calls to {\texttt{wrk\_in\_use()} / \texttt{wrk\_not\_released()} can be reduced to stubs that just
+return \forcode{.false.} by setting the cpp key \texttt{key\_no\_workspace\_check}.
+These stubs may then be inlined (and thus effectively removed altogether) by setting appropriate compiler flags
+($e.g.$ ``-finline'' for the Intel compiler or ``-Q'' for the IBM compiler).
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Optimisation}
 
 Considering the new computer architecture, optimisation cannot be considered independently from the computer type.
 In NEMO, portability is a priority, before any too specific optimisation.
-Some tools are available to help: \\
-For vector computers: 
-\begin{itemize} 
-\item  using $key\_vectopt\_loop$ allows to unroll a loop
-\end{itemize}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\subsection{Package attribute: $PRIVATE, PUBLIC, USE, ONLY$}
-Module variables and routines should be encapsulated by using the PRIVATE attribute. What shall be used outside the module can be declared PUBLIC instead. Use USE with the ONLY attribute to specify which of the variables, type definitions etc. defined in a module are to be made available to the using routine. 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\subsection {Parallelism: using MPI}
-NEMO is written in order to be able to run on one processor, or on one or more using MPI (i.e. activating the cpp key $key\_mpp\_mpi$. The domain decomposition divides the global domain in cubes (see NEMO reference manual). Whilst coding a new development, the MPI compatibility has to be taken in account (see $LBC/lib\_mpp.F90$) and should be tested. By default, the $x$-$z$ part of the decomposition is chosen to be as square as possible. However, this may be overriden by specifying the number of subdomains in latitude and longitude in the nammpp section of the namelist file.
+
+Some tools are available to help: for vector computers, \texttt{key\_vectopt\_loop} allows to unroll a loop
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\subsection{Package attribute: \forcode{PRIVATE}, \forcode{PUBLIC}, \forcode{USE}, \forcode{ONLY}}
+
+Module variables and routines should be encapsulated by using the \forcode{PRIVATE} attribute.
+What shall be used outside the module can be declared \forcode{PUBLIC} instead.
+Use \forcode{USE} with the \forcode{ONLY} attribute to specify which of the variables, type definitions etc...
+defined in a module are to be made available to the using routine.
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\subsection {Parallelism using MPI}
+
+NEMO is written in order to be able to run on one processor, or on one or more using MPI
+($i.e.$ activating the cpp key $key\_mpp\_mpi$).
+The domain decomposition divides the global domain in cubes (see NEMO reference manual).
+Whilst coding a new development, the MPI compatibility has to be taken in account
+(see \path{./src/LBC/lib_mpp.F90}) and should be tested.
+By default, the $x$-$z$ part of the decomposition is chosen to be as square as possible.
+However, this may be overriden by specifying the number of subdomains in latitude and longitude in
+the \texttt{nammpp} section of the namelist file.
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \section{Features to be avoided}
 
-The code must follow the current standards of FORTRAN and ANSI C.  In particular, the code should not produce any WARNING at compiling phase, so that users can be easily alerted of potential bugs when some appear in their new developments. ). 
+The code must follow the current standards of FORTRAN and ANSI C.
+In particular, the code should not produce any WARNING at compiling phase, so that
+users can be easily alerted of potential bugs when some appear in their new developments.
 Below is a list of features to avoid:
 \begin{itemize}
-\item COMMON blocks (use the declaration part of MODULEs instead)
-\item EQUIVALENCE (use POINTERs or derived data types instead to form data structures)
-\item Assigned and computed GOTOs (use the CASE construct instead)
-\item Arithmetic IF statements ( use the block IF, ELSE, ELSEIF, ENDIF or SELECT CASE construct instead) 
-\item Labeled DO constructs  (use unlabeled END DO instead) 
-\item FORMAT statements (use character parameters or explicit format- specifiers inside the READ or WRITE statement instead)
-\item GOTO and CONTINUE statement (use IF, CASE, DO WHILE, EXIT or CYCLE statements or a contained 
-\item PAUSE 
-\item ENTRY statements: a subprogram must only have one entry point. 
-\item RETURN Ð it is obsolete and so not necessary at the end of program units
-\item STATEMENT FUNCTION 
- \item Avoid functions with side effects.
-\footnote{ First, the code is easier to understand, if you can rely on the rule that functions don't change their arguments, second, some compilers generate more efficient code for PURE (in FORTRAN 95 there are the attributes PURE and ELEMENTAL) functions, because they can store the arguments in different places. This is especially important on massive parallel and as well on vector machines. }
-\item DATA and BLOCK DATA - (use initialisers)
+\item
+  \forcode{COMMON} block
+  (use the declaration part of \forcode{MODULE} instead)
+\item
+  \forcode{EQUIVALENCE}
+  (use \forcode{POINTER} or derived data type instead to form data structure)
+\item
+  Assigned and computed \forcode{GOTO}
+  (use the \forcode{CASE} construct instead)
+\item
+  Arithmetic \forcode{IF} statement
+  (use the block \forcode{IF}, \forcode{ELSE}, \forcode{ELSEIF}, \forcode{ENDIF} or
+  \forcode{SELECT CASE} construct instead)
+\item
+  Labeled \forcode{DO} construct
+  (use unlabeled \forcode{END DO} instead)
+\item
+  \forcode{FORMAT} statement
+  (use character parameters or
+  explicit format- specifiers inside the \forcode{READ} or \forcode{WRITE} statement instead)
+\item
+  \forcode{GOTO} and \forcode{CONTINUE} statements
+  (use \forcode{IF}, \forcode{CASE}, \forcode{DO WHILE}, \forcode{EXIT} or \forcode{CYCLE} statements or
+  a contained ?)
+\item
+  \forcode{PAUSE}
+\item
+  \forcode{ENTRY} statement: a subprogram must only have one entry point.
+\item
+  \forcode{RETURN} is obsolete and so not necessary at the end of program units
+\item
+  \forcode{FUNCTION} statement
+\item
+  Avoid functions with side effects.
+  \footnote{
+    First, the code is easier to understand, if you can rely on
+    the rule that functions don't change their arguments.
+    Second, some compilers generate more efficient code for PURE functions
+    (in FORTRAN 95 there are the attributes PURE and ELEMENTAL), because
+    they can store the arguments in different places.
+    This is especially important on massive parallel and as well on vector machines.
+  }
+\item
+  \forcode{DATA} and \forcode{BLOCK DATA}
+  (use initialisers)
 \end{itemize}
 
Index: /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/latex/NEMO/main/NEMO_manual.bib
===================================================================
--- /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/latex/NEMO/main/NEMO_manual.bib	(revision 10497)
+++ /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/latex/NEMO/main/NEMO_manual.bib	(revision 10498)
@@ -1,5 +1,2 @@
-This file was created with JabRef 2.2.
-Encoding: UTF8
-
 @STRING{AP = {Academic Press}}
 
@@ -106,2026 +103,2349 @@
 
 @ARTICLE{Adcroft_Campin_OM04,
-  author = {A. Adcroft and J.-M. Campin},
-  title = {Re-scaled height coordinates for accurate representation of free-surface flows in ocean circulation models},
-  journal = OM,
-  year = {2004},
-  volume = {7},
-  pages = {269--284},
-  doi = {10.1016/j.ocemod.2003.09.003},
+  author =       {A. Adcroft and J.-M. Campin},
+  title =        {Re-scaled height coordinates for accurate
+                  representation of free-surface flows in ocean
+                  circulation models},
+  journal =      OM,
+  year =         2004,
+  volume =       7,
+  pages =        {269--284},
+  doi =          {10.1016/j.ocemod.2003.09.003},
 }
 
 @ARTICLE{Arakawa1966,
-  author = {A. Arakawa},
-  title = {Computational design for long term numerical integration of the equations 
-    of fluid motion, two-dimensional incompressible flow, Part. I.},
-  journal = JCP,
-  year = {1966},
-  volume = {I},
-  pages = {119--149}
+  author =       {A. Arakawa},
+  title =        {Computational design for long term numerical
+                  integration of the equations of fluid motion,
+                  two-dimensional incompressible flow, Part. I.},
+  journal =      JCP,
+  year =         1966,
+  volume =       {I},
+  pages =        {119--149}
 }
 
 @ARTICLE{Arakawa_Hsu_MWR90,
-  author = {A. Arakawa and Y.-J. G. Hsu},
-  title = {Energy Conserving and Potential-Enstrophy Dissipating Schemes for the Shallow Water Equations},
-  journal = MWR,
-  year = {1990},
-  volume = {118},  number = {10},
-  pages = {1960--1969},
+  author =       {A. Arakawa and Y.-J. G. Hsu},
+  title =        {Energy Conserving and Potential-Enstrophy
+                  Dissipating Schemes for the Shallow Water Equations},
+  journal =      MWR,
+  year =         1990,
+  volume =       118,
+  number =       10,
+  pages =        {1960--1969},
 }
 
 @ARTICLE{Arakawa_Lamb_MWR81,
-  author = {Arakawa, Akio and Lamb, Vivian R.},
-  title = {A Potential Enstrophy and Energy Conserving Scheme for the Shallow
-           Water Equations},
-  journal = MWR,
-  year = {1981},
-  volume = {109},  number = {1},
-  pages = {18--36}
+  author =       {Arakawa, Akio and Lamb, Vivian R.},
+  title =        {A Potential Enstrophy and Energy Conserving Scheme
+                  for the Shallow Water Equations},
+  journal =      MWR,
+  year =         1981,
+  volume =       109,
+  number =       1,
+  pages =        {18--36}
 }
 
 @ARTICLE{Arbic2004,
-  author = {B. Arbic and S. Garner and R. Hallberg and H. Simmons},
-  title = {The accuracy of surface elevations in forward global barotropic and baroclinic tide models},
-  journal = DSR,
-  year = {2004},
-  volume = {51},
-  pages = {3069-3101}
+  author =       {B. Arbic and S. Garner and R. Hallberg and
+                  H. Simmons},
+  title =        {The accuracy of surface elevations in forward global
+                  barotropic and baroclinic tide models},
+  journal =      DSR,
+  year =         2004,
+  volume =       51,
+  pages =        {3069-3101}
 }
 
 @ARTICLE{Arbic2010,
-  author = {Arbic, Wallcraft, Metzger},
-  title = {Concurrent simulation of the eddying general circulation and tides in a global ocean model},
-  journal = OM,
-  year = {2010},
-  volume = {32},  number = {3-4},
-  pages = {175-187}
+  author =       {Arbic, Wallcraft, Metzger},
+  title =        {Concurrent simulation of the eddying general
+                  circulation and tides in a global ocean model},
+  journal =      OM,
+  year =         2010,
+  volume =       32,
+  number =       {3-4},
+  pages =        {175-187}
 }
 
 @ARTICLE{Arhan2006,
-  author = {M. Arhan and A.M. Treguier and B. Bourles and S. Michel},
-  title = {Diagnosing the annual cycle of the Equatorial Undercurrent in the
-	Atlantic Ocean from a general circulation model},
-  journal = JPO,
-  year = {2006},
-  volume = {36},
-  pages = {1502--1522}
+  author =       {M. Arhan and A.M. Treguier and B. Bourles and
+                  S. Michel},
+  title =        {Diagnosing the annual cycle of the Equatorial
+                  Undercurrent in the Atlantic Ocean from a general
+                  circulation model},
+  journal =      JPO,
+  year =         2006,
+  volume =       36,
+  pages =        {1502--1522}
 }
 
 @ARTICLE{Artale_al_JGR02,
-  author={V. Artale and D. Iudicone and R. Santoleri and V. Rupolo and S. Marullo
-          and F. {D'O}rtenzio},
-  title={Role of surface fluxes in ocean general circulation models using satellite
-          sea surface temperature: Validation of and sensitivity to the forcing
-          frequency of the Mediterranean thermohaline circulation},
-  journal=JGR,
-  year={2002},
-  volume={107},
-  pages={1978-2012},
-  doi = {10.1029/2000JC000452},
+  author =       {V. Artale and D. Iudicone and R. Santoleri and
+                  V. Rupolo and S. Marullo and F. {D'O}rtenzio},
+  title =        {Role of surface fluxes in ocean general circulation
+                  models using satellite sea surface temperature:
+                  Validation of and sensitivity to the forcing
+                  frequency of the Mediterranean thermohaline
+                  circulation},
+  journal =      JGR,
+  year =         2002,
+  volume =       107,
+  pages =        {1978-2012},
+  doi =          {10.1029/2000JC000452},
 }
 
 @ARTICLE{ASSELIN_MWR72,
-  author = {R. Asselin},
-  title = {Frequency Filter for Time Integrations},
-  journal = MWR,
-  year = {1972},
-  volume = {100},  number = {6},
-  pages = {487--490}
+  author =       {R. Asselin},
+  title =        {Frequency Filter for Time Integrations},
+  journal =      MWR,
+  year =         1972,
+  volume =       100,
+  number =       6,
+  pages =        {487--490}
 }
 
 @ARTICLE{Atmadipoera_al_DSR09,
-  author = {A. Atmadipoera and R. Molcard and G. Madec and S.Wijffels and J.
-	Sprintall and A. Koch-Larrouy and I. Jaya and A. Supangat},
-  title = {Characteristics and Variability of the Indonesian Throughflow Water
-	at the Outflow Straits},
-  journal = DSR,
-  year = {2009},
-  volume = {56},  number = {11},
-  pages = {1942--1954},
-  doi = {10.1016/j.dsr.2009.06.004},
+  author =       {A. Atmadipoera and R. Molcard and G. Madec and
+                  S.Wijffels and J.  Sprintall and A. Koch-Larrouy and
+                  I. Jaya and A. Supangat},
+  title =        {Characteristics and Variability of the Indonesian
+                  Throughflow Water at the Outflow Straits},
+  journal =      DSR,
+  year =         2009,
+  volume =       56,
+  number =       11,
+  pages =        {1942--1954},
+  doi =          {10.1016/j.dsr.2009.06.004},
 }
 
 @ARTICLE{Aumont_al_GBC99,
-  author = {O. Aumont and P. Monfray and J. C. Orr and G. Madec and E. Maier-Reimer},
-  title = {Nutrient trapping in the equatorial Pacific: The ocean circulation solution},
-  journal = GBC,
-  year = {1999},
-  volume = {13},
-  pages = {351--369}
+  author =       {O. Aumont and P. Monfray and J. C. Orr and G. Madec
+                  and E. Maier-Reimer},
+  title =        {Nutrient trapping in the equatorial Pacific: The
+                  ocean circulation solution},
+  journal =      GBC,
+  year =         1999,
+  volume =       13,
+  pages =        {351--369}
 }
 
 @ARTICLE{Aumont_al_CD98,
-  author = {O. Aumont and J.C. Orr and D. Jamous and P. Monfray and O. Marti and G. Madec},
-  title = {A degradation approach to accelerate simulations to steady state
-	in a 3-D tracer transport model of the global ocean},
-  journal = CD,
-  year = {1998},
-  volume = {14},
-  pages = {101--116}
+  author =       {O. Aumont and J.C. Orr and D. Jamous and P. Monfray
+                  and O. Marti and G. Madec},
+  title =        {A degradation approach to accelerate simulations to
+                  steady state in a 3-D tracer transport model of the
+                  global ocean},
+  journal =      CD,
+  year =         1998,
+  volume =       14,
+  pages =        {101--116}
 }
 
 @ARTICLE{Axell_JGR02,
-  author = {L. B. Axell},
-  title = {Wind-driven internal waves and Langmuir circulations in a numerical ocean model of the southern Baltic Sea},
-  journal = JGR,
-  year = {2002},
-  volume = {107},
-  doi = {10.1029/2001JC000922},
+  author =       {L. B. Axell},
+  title =        {Wind-driven internal waves and Langmuir circulations
+                  in a numerical ocean model of the southern Baltic
+                  Sea},
+  journal =      JGR,
+  year =         2002,
+  volume =       107,
+  doi =          {10.1029/2001JC000922},
 }
 
 @ARTICLE{Axell_Liungman_EFM01,
-  author = {L. B. Axell and O. Liungman},
-  title = {A one-equation turbulence model for geophysical applications: 
-  Comparison with data and the k-$\epsilon$ model},
-  journal = EFM,
-  year = {2001},
-  volume = {1}, pages = {71--106},
-  doi = {10.1029/2001JC000922},
+  author =       {L. B. Axell and O. Liungman},
+  title =        {A one-equation turbulence model for geophysical
+                  applications: Comparison with data and the
+                  k-$\epsilon$ model},
+  journal =      EFM,
+  year =         2001,
+  volume =       1,
+  pages =        {71--106},
+  doi =          {10.1029/2001JC000922},
 }
 
 @ARTICLE{Ayina_al_JC06,
-  author = {L.-H. Ayina and A. Bentamy and A. Munes-Mestaz and G. Madec},
-  title = {The Impact of Satellite Winds and Latent Heat Fluxes in a Numerical
-	Simulation of the Tropical Pacific Ocean},
-  journal = JC,
-  year = {2006},
-  volume = {19},
-  pages = {5889--5902}
+  author =       {L.-H. Ayina and A. Bentamy and A. Munes-Mestaz and
+                  G. Madec},
+  title =        {The Impact of Satellite Winds and Latent Heat Fluxes
+                  in a Numerical Simulation of the Tropical Pacific
+                  Ocean},
+  journal =      JC,
+  year =         2006,
+  volume =       19,
+  pages =        {5889--5902}
 }
 
 @ARTICLE{Barnier_al_OD06,
-  author = {B. Barnier and G. Madec and T. Penduff and J.-M. Molines and A.-M.
-	Treguier and J. Le Sommer and A. Beckmann and A. Biastoch and C. Boning 
-	and J. Dengg and C. Derval and E. Durand and S. Gulev and
-	E. Remy and C. Talandier and S. Theetten and M. Maltrud and J. McClean and B. De Cuevas},
-  title = {Impact of partial steps and momentum advection schemes in a global
-	ocean circulation model at eddy-permitting resolution.},
-  journal = OD,
-  year = {2006},
-  volume = {56},
-  pages = {543--567},
-  doi = {10.1007/s10236-006-0082-1},
+  author =       {B. Barnier and G. Madec and T. Penduff and
+                  J.-M. Molines and A.-M.  Treguier and J. Le Sommer
+                  and A. Beckmann and A. Biastoch and C. Boning and
+                  J. Dengg and C. Derval and E. Durand and S. Gulev
+                  and E. Remy and C. Talandier and S. Theetten and
+                  M. Maltrud and J. McClean and B. De Cuevas},
+  title =        {Impact of partial steps and momentum advection
+                  schemes in a global ocean circulation model at
+                  eddy-permitting resolution.},
+  journal =      OD,
+  year =         2006,
+  volume =       56,
+  pages =        {543--567},
+  doi =          {10.1007/s10236-006-0082-1},
 }
 
 @INCOLLECTION{Barnier1996,
-  author = {B. Barnier and P. Marchesiello and A.P. de Miranda},
-  title = {Modeling the ocean circulation in the South Atlantic: A strategy for dealing with open boundaries},
-  booktitle = {The South Atlantic: Present and Past Circulation},
-  publisher = {Springer-Verlag, Berlin},
-  year = {1996},
-  editor = {G.Wefer and W.H. Berger and G Siedler and D. Webb},
-  pages = {289-304}
+  author =       {B. Barnier and P. Marchesiello and A.P. de Miranda},
+  title =        {Modeling the ocean circulation in the South
+                  Atlantic: A strategy for dealing with open
+                  boundaries},
+  booktitle =    {The South Atlantic: Present and Past Circulation},
+  publisher =    {Springer-Verlag, Berlin},
+  year =         1996,
+  editor =       {G.Wefer and W.H. Berger and G Siedler and D. Webb},
+  pages =        {289-304}
 }
 
 @ARTICLE{Barnier1998,
-  author = {B. Barnier and P. Marchesiello and A. P. de Miranda and J.M. Molines
-	and M. Coulibaly},
-  title = {A sigma-coordinate primitive equation model for studying the circulation
-	in the South Atlantic I, Model configuration with error estimates},
-  journal = DSR,
-  year = {1998},
-  volume = {45},
-  pages = {543--572}
+  author =       {B. Barnier and P. Marchesiello and A. P. de Miranda
+                  and J.M. Molines and M. Coulibaly},
+  title =        {A sigma-coordinate primitive equation model for
+                  studying the circulation in the South Atlantic I,
+                  Model configuration with error estimates},
+  journal =      DSR,
+  year =         1998,
+  volume =       45,
+  pages =        {543--572}
 }
 
 @ARTICLE{Barthelet_al_CRAS98,
-  author = {P. Barthelet and S. Bony and P. Braconnot and A. Braum and D. Cariolle
-	and E. Cohen-Solal and J.-L. Dufresne and P. Delecluse and M. D\'{e}qu\'{e}
-	and L. Fairhead and M.-A. Filiberti and M. Forichon and J.-Y. Grandpeix
-	and E. Guilyardi and M.-N. Houssais and M. Imbard and H. Le Treut
-	and C. Lévy and Z.X. Li and G. Madec and P. Marquet and O. Marti
-	and S. Planton and L. Terray and O. Thual and S. Valcke},
-  title = {Global coupled simulations of climate change due to increased atmospheric CO2 concentration},
-  journal = {C. R. Acad. Sci Paris},
-  year = {1998},
-  volume = {326},
-  pages = {677--684}
+  author =       {P. Barthelet and S. Bony and P. Braconnot and
+                  A. Braum and D. Cariolle and E. Cohen-Solal and
+                  J.-L. Dufresne and P. Delecluse and M. D\'{e}qu\'{e}
+                  and L. Fairhead and M.-A. Filiberti and M. Forichon
+                  and J.-Y. Grandpeix and E. Guilyardi and
+                  M.-N. Houssais and M. Imbard and H. Le Treut and
+                  C. Lévy and Z.X. Li and G. Madec and P. Marquet and
+                  O. Marti and S. Planton and L. Terray and O. Thual
+                  and S. Valcke},
+  title =        {Global coupled simulations of climate change due to
+                  increased atmospheric CO2 concentration},
+  journal =      {C. R. Acad. Sci Paris},
+  year =         1998,
+  volume =       326,
+  pages =        {677--684}
 }
 
 @ARTICLE{Beckmann2003,
-  author = {A. Beckmann and H. Goosse},
-  title = {A parameterization of ice shelf-ocean interaction for climate models},
-  journal = OM,
-  year = {2003},
-  volume = {5},
-  pages = {157--170}
+  author =       {A. Beckmann and H. Goosse},
+  title =        {A parameterization of ice shelf-ocean interaction
+                  for climate models},
+  journal =      OM,
+  year =         2003,
+  volume =       5,
+  pages =        {157--170}
 }
 
 @ARTICLE{Beckmann1998,
-  author = {A. Beckmann},
-  title = {The representation of bottom boundary layer processes in numerical
-	ocean circulation models.},
-  journal = {Ocean modelling and parameterization, E. P. Chassignet and J. Verron
-	(eds.), NATO Science Series, Kluwer Academic Publishers},
-  year = {1998}
+  author =       {A. Beckmann},
+  title =        {The representation of bottom boundary layer
+                  processes in numerical ocean circulation models.},
+  journal =      {Ocean modelling and parameterization,
+                  E. P. Chassignet and J. Verron (eds.), NATO Science
+                  Series, Kluwer Academic Publishers},
+  year =         1998
 }
 
 @ARTICLE{Beckmann_Doscher1997,
-  author = {A. Beckmann and R. D\"{o}scher},
-  title = {A method for improved representation of dense water spreading over
-	topography in geopotential-coordinate models},
-  journal = JPO,
-  year = {1997},
-  volume = {27},
-  pages = {581--591}
+  author =       {A. Beckmann and R. D\"{o}scher},
+  title =        {A method for improved representation of dense water
+                  spreading over topography in geopotential-coordinate
+                  models},
+  journal =      JPO,
+  year =         1997,
+  volume =       27,
+  pages =        {581--591}
 }
 
 @ARTICLE{Beckmann1993,
-  author = {A. Beckmann and D. B. Haidvogel},
-  title = {Numerical Simulation of Flow around a Tall Isolated Seamount. 
-   Part I - Problem Formulation and Model Accuracy},
-  journal = JPO,
-  year = {1993},
-  volume = {23},  number = {8},
-  pages = {1736--1753}
+  author =       {A. Beckmann and D. B. Haidvogel},
+  title =        {Numerical Simulation of Flow around a Tall Isolated
+                  Seamount.  Part I - Problem Formulation and Model
+                  Accuracy},
+  journal =      JPO,
+  year =         1993,
+  volume =       23,
+  number =       8,
+  pages =        {1736--1753}
 }
 
 @ARTICLE{Bernie_al_CD07,
-  author = {D. Bernie and E. Guilyardi and G. Madec and J. M. Slingo and S. J. Woolnough},
-  title = {Impact of resolving the diurnal cycle in an ocean--atmosphere GCM. Part 1: a diurnally forced OGCM},
-  journal = CD,
-  year = {2007},
-  volume = {29},  number = {6},
-  pages = {575--590}
+  author =       {D. Bernie and E. Guilyardi and G. Madec and
+                  J. M. Slingo and S. J. Woolnough},
+  title =        {Impact of resolving the diurnal cycle in an
+                  ocean--atmosphere GCM. Part 1: a diurnally forced
+                  OGCM},
+  journal =      CD,
+  year =         2007,
+  volume =       29,
+  number =       6,
+  pages =        {575--590}
 }
 
 @ARTICLE{Bernie_al_CD08,
-  author = {D. Bernie and E. Guilyardi and G. Madec and J. M. Slingo and S. J. Woolnough},
-  title = {Impact of resolving the diurnal cycle in an ocean--atmosphere GCM. Part 2: A diurnally coupled CGCM},
-  journal = CD,
-  year = {2008},
-  volume = {31},  number = {7},
-  pages = {909--925},
-  doi = {10.1007/s00382-008-0429-z},
+  author =       {D. Bernie and E. Guilyardi and G. Madec and
+                  J. M. Slingo and S. J. Woolnough},
+  title =        {Impact of resolving the diurnal cycle in an
+                  ocean--atmosphere GCM. Part 2: A diurnally coupled
+                  CGCM},
+  journal =      CD,
+  year =         2008,
+  volume =       31,
+  number =       7,
+  pages =        {909--925},
+  doi =          {10.1007/s00382-008-0429-z},
 }
 
 @ARTICLE{Bernie_al_JC05,
-  author = {D. J. Bernie and S. J. Woolnough and J. M. Slingo and E. Guilyardi},
-  title = {Modelling diurnal and intraseasonal variability of the ocean mixed
-	layer},
-  journal = JC,
-  year = {2005},
-  volume = {18},  number = {8},
-  pages = {1190--1200}
+  author =       {D. J. Bernie and S. J. Woolnough and J. M. Slingo
+                  and E. Guilyardi},
+  title =        {Modelling diurnal and intraseasonal variability of
+                  the ocean mixed layer},
+  journal =      JC,
+  year =         2005,
+  volume =       18,
+  number =       8,
+  pages =        {1190--1200}
 }
 
 @ARTICLE{Bessiere_al_GRL08,
-  author = {L. Bessi\'{e}res and G. Madec and F. Lyard},
-  title = {Global Tidal Residual Mean Circulation: Does it Affect a Climate OGCM?},
-  journal = GRL,
-  year = {2008},
-  volume = {35},
-  pages = {L03609},
-  doi = {10.1029/2007GL032644},
+  author =       {L. Bessi\'{e}res and G. Madec and F. Lyard},
+  title =        {Global Tidal Residual Mean Circulation: Does it
+                  Affect a Climate OGCM?},
+  journal =      GRL,
+  year =         2008,
+  volume =       35,
+  pages =        {L03609},
+  doi =          {10.1029/2007GL032644},
 }
 
 @ARTICLE{Biastoch_al_JC08,
-  author = {A. Biastoch and C. W. Böning and J. Getzlaff and J.-M. Molines and G. Madec},
-  title = {Causes of interannual – decadal variability in the meridional overturning
-	circulation of the mid-latitude North Atlantic Ocean},
-  journal = JC,
-  year = {2008},
-  volume = {21},  number = {24},
-  pages = {6599-6615},
-  doi = {10.1175/2008JCLI2404.1},
+  author =       {A. Biastoch and C. W. Böning and J. Getzlaff and
+                  J.-M. Molines and G. Madec},
+  title =        {Causes of interannual – decadal variability in the
+                  meridional overturning circulation of the
+                  mid-latitude North Atlantic Ocean},
+  journal =      JC,
+  year =         2008,
+  volume =       21,
+  number =       24,
+  pages =        {6599-6615},
+  doi =          {10.1175/2008JCLI2404.1},
 }
 
 @ARTICLE{Bignami_al_JGR95,
-  author = {F. Bignami and S. Marullo and R. Santoleri and M. E. Schiano},
-  title = {Longwave radiation budget in the Mediterranean Sea}, 
-  journal = JGR,
-  year = {1995},
-  volume = {100},  number = {C2},
-  pages = {2501--2514},
-  doi = {10.1029/94JC02496},
+  author =       {F. Bignami and S. Marullo and R. Santoleri and
+                  M. E. Schiano},
+  title =        {Longwave radiation budget in the Mediterranean Sea},
+  journal =      JGR,
+  year =         1995,
+  volume =       100,
+  number =       {C2},
+  pages =        {2501--2514},
+  doi =          {10.1029/94JC02496},
 }
 
 @ARTICLE{Blanke_al_JPO99,
-  author = {B. Blanke and M. Arhan and G. Madec and S. Roche},
-  title = {Warm Water Paths in the Equatorial Atlantic as Diagnosed with a General Circulation Model},
-  journal = JPO,
-  year = {1999},
-  volume = {29},  number = {11},
-  pages = {2753-2768}
+  author =       {B. Blanke and M. Arhan and G. Madec and S. Roche},
+  title =        {Warm Water Paths in the Equatorial Atlantic as
+                  Diagnosed with a General Circulation Model},
+  journal =      JPO,
+  year =         1999,
+  volume =       29,
+  number =       11,
+  pages =        {2753-2768}
 }
 
 @ARTICLE{Blanke1993,
-  author = {B. Blanke and P. Delecluse},
-  title = {Low frequency variability of the tropical Atlantic ocean simulated
-	by a general circulation model with mixed layer physics},
-  journal = JPO,
-  year = {1993},
-  volume = {23},
-  pages = {1363--1388}
+  author =       {B. Blanke and P. Delecluse},
+  title =        {Low frequency variability of the tropical Atlantic
+                  ocean simulated by a general circulation model with
+                  mixed layer physics},
+  journal =      JPO,
+  year =         1993,
+  volume =       23,
+  pages =        {1363--1388}
 }
 
 @ARTICLE{blanke_al_JC97,
-  author = {B. Blanke and J. D. Neelin and D. Gutzler},
-  title = {Estimating the effect of stochastic wind forcing on ENSO irregularity},
-  journal = JC,
-  year = {1997},
-  volume = {10},
-  pages = {1473--1486}
+  author =       {B. Blanke and J. D. Neelin and D. Gutzler},
+  title =        {Estimating the effect of stochastic wind forcing on
+                  ENSO irregularity},
+  journal =      JC,
+  year =         1997,
+  volume =       10,
+  pages =        {1473--1486}
 }
 
 @ARTICLE{Blanke_Raynaud_JPO97,
-  author = {B. Blanke and S. Raynaud},
-  title = {Kinematics of the Pacific Equatorial Undercurrent: An Eulerian and
-	Lagrangian Approach from GCM Results},
-  journal = JPO,
-  year = {1997},
-  volume = {27},  number = {6},
-  pages = {1038--1053}
+  author =       {B. Blanke and S. Raynaud},
+  title =        {Kinematics of the Pacific Equatorial Undercurrent:
+                  An Eulerian and Lagrangian Approach from GCM
+                  Results},
+  journal =      JPO,
+  year =         1997,
+  volume =       27,
+  number =       6,
+  pages =        {1038--1053}
 }
 
 @ARTICLE{Blanke_al_JPO01,
-  author = {B. Blanke and S. Speich and G. Madec and K. Döös},
-  title = {A global Diagnostic of interocean mass transfers},
-  journal = JPO,
-  year = {2001},
-  volume = {31},  number = {6},
-  pages = {1623--1632}
+  author =       {B. Blanke and S. Speich and G. Madec and K. Döös},
+  title =        {A global Diagnostic of interocean mass transfers},
+  journal =      JPO,
+  year =         2001,
+  volume =       31,
+  number =       6,
+  pages =        {1623--1632}
 }
 
 @ARTICLE{Blanke_al_GRL02,
-  author = {B. Blanke and S. Speich and G. Madec and R. Maug\'{e}},
-  title = {A global diagnostic of interior ocean ventilation},
-  journal = GRL,
-  year = {2002},
-  volume = {29},  number = {8},
-  pages = {1081--1084}
+  author =       {B. Blanke and S. Speich and G. Madec and
+                  R. Maug\'{e}},
+  title =        {A global diagnostic of interior ocean ventilation},
+  journal =      GRL,
+  year =         2002,
+  volume =       29,
+  number =       8,
+  pages =        {1081--1084}
 }
 
 @ARTICLE{Blayo2005,
-  author = {E. Blayo and L. Debreu},
-  title = {Revisiting open boundary conditions from the point of view of characteristic
-	variables},
-  journal = OM,
-  year = {2005},
-  volume = {9},
-  pages = {231--252}
+  author =       {E. Blayo and L. Debreu},
+  title =        {Revisiting open boundary conditions from the point
+                  of view of characteristic variables},
+  journal =      OM,
+  year =         2005,
+  volume =       9,
+  pages =        {231--252}
 }
 
 @ARTICLE{Bloom_al_MWR96,
-  author = {S. C. Bloom and L. L. Takacs and A. M. Da Silva and D. Ledvina},
-  title = {Data assimilation using incremental analysis updates},
-  journal = MWR,
-  year = {1996},
-  volume = {124},
-  pages = {1256--1271}
+  author =       {S. C. Bloom and L. L. Takacs and A. M. Da Silva and
+                  D. Ledvina},
+  title =        {Data assimilation using incremental analysis
+                  updates},
+  journal =      MWR,
+  year =         1996,
+  volume =       124,
+  pages =        {1256--1271}
 }
 
 @ARTICLE{Bopp_al_GBC01,
-  author = {L. Bopp and P. Monfray and O. Aumont and J.-L. Dufresne and H. Le Treut 
-    and G. Madec and L. Terray and J.C. Orr},
-  title = {Potential impact of climate change on marine export production},
-  journal = GBC,
-  year = {2001},
-  volume = {15},  number = {1},
-  pages = {81--101}
+  author =       {L. Bopp and P. Monfray and O. Aumont and
+                  J.-L. Dufresne and H. Le Treut and G. Madec and
+                  L. Terray and J.C. Orr},
+  title =        {Potential impact of climate change on marine export
+                  production},
+  journal =      GBC,
+  year =         2001,
+  volume =       15,
+  number =       1,
+  pages =        {81--101}
 }
 
 @article{bouffard_Boegman_DAO2013,
-	author = {D. Bouffard and L. Boegman},
-	title = {A diapycnal diffusivity model for stratified environmental flows},
-	volume = {61-62},
-	issn = {03770265},
-	doi = {10.1016/j.dynatmoce.2013.02.002},
-	journal = DAO,
-	year = {2013},
-	pages = {14--34},
+  author =       {D. Bouffard and L. Boegman},
+  title =        {A diapycnal diffusivity model for stratified
+                  environmental flows},
+  volume =       {61-62},
+  issn =         03770265,
+  doi =          {10.1016/j.dynatmoce.2013.02.002},
+  journal =      DAO,
+  year =         2013,
+  pages =        {14--34},
 }
 
 @ARTICLE{Bougeault1989,
-  author = {P. Bougeault and P. Lacarrere},
-  title = {Parameterization of Orography-Induced Turbulence in a Mesobeta--Scale
-	Model},
-  journal = MWR,
-  year = {1989},
-  volume = {117},  number = {8},
-  pages = {1872--1890},
+  author =       {P. Bougeault and P. Lacarrere},
+  title =        {Parameterization of Orography-Induced Turbulence in
+                  a Mesobeta--Scale Model},
+  journal =      MWR,
+  year =         1989,
+  volume =       117,
+  number =       8,
+  pages =        {1872--1890},
 }
 
 @ARTICLE{Bouillon_al_OM09,
-  author = {S. Bouillon and M.A. Morales Maqueda and V. Legat and T. Fichefet},
-  title = {An Elastic-Viscous-Plastic Sea Ice Model formulated on Arakawa B and C Grids},
-  journal = OM,
-  year = {2009},
-  volume = {27},
-  pages = {174--184},
-  doi = {10.1016/j.ocemod.2009.01.004},
+  author =       {S. Bouillon and M.A. Morales Maqueda and V. Legat
+                  and T. Fichefet},
+  title =        {An Elastic-Viscous-Plastic Sea Ice Model formulated
+                  on Arakawa B and C Grids},
+  journal =      OM,
+  year =         2009,
+  volume =       27,
+  pages =        {174--184},
+  doi =          {10.1016/j.ocemod.2009.01.004},
 }
 
 @ARTICLE{Boulanger_al_GRL01,
-  author = {J.-P. Boulanger and E. Durand and J.-P. Duvel and C. Menkes and P.
-	Delecluse and M. Imbard and M. Lengaigne and G. Madec and S. Masson},
-  title = {Role of non-linear oceanic processes in the response to westerly
-	wind events: new implications for the 1997 El Niño onset},
-  journal = GRL,
-  year = {2001},
-  volume = {28},  number = {8},
-  pages = {1603--1606}
+  author =       {J.-P. Boulanger and E. Durand and J.-P. Duvel and
+                  C. Menkes and P.  Delecluse and M. Imbard and
+                  M. Lengaigne and G. Madec and S. Masson},
+  title =        {Role of non-linear oceanic processes in the response
+                  to westerly wind events: new implications for the
+                  1997 El Niño onset},
+  journal =      GRL,
+  year =         2001,
+  volume =       28,
+  number =       8,
+  pages =        {1603--1606}
 }
 
 @article{Brankart_OM2013,
-author = "J.-M. Brankart",
-title = "Impact of uncertainties in the horizontal density gradient upon low resolution global ocean modelling ",
-journal = OM,
-year = "2013",
-volume = "66", pages = "64--76",
-issn = "1463-5003",
-doi = "http://dx.doi.org/10.1016/j.ocemod.2013.02.004",
+  author =       "J.-M. Brankart",
+  title =        "Impact of uncertainties in the horizontal density
+                  gradient upon low resolution global ocean modelling
+                  ",
+  journal =      OM,
+  year =         2013,
+  volume =       66,
+  pages =        "64--76",
+  issn =         "1463-5003",
+  doi =          "http://dx.doi.org/10.1016/j.ocemod.2013.02.004",
 }
 
 @Article{Brankart_al_GMD2015,
-AUTHOR = {Brankart, J.-M. and Candille, G. and Garnier, F. and Calone, C. and Melet, A. and Bouttier, P.-A. and Brasseur, P. and Verron, J.},
-TITLE = {A generic approach to explicit simulation of uncertainty in the NEMO ocean model},
-JOURNAL = {Geoscientific Model Development},
-VOLUME = {8},
-YEAR = {2015},
-NUMBER = {5},
-PAGES = {1285--1297},
-DOI = {10.5194/gmd-8-1285-2015}
+  AUTHOR =       {Brankart, J.-M. and Candille, G. and Garnier, F. and
+                  Calone, C. and Melet, A. and Bouttier, P.-A. and
+                  Brasseur, P. and Verron, J.},
+  TITLE =        {A generic approach to explicit simulation of
+                  uncertainty in the NEMO ocean model},
+  JOURNAL =      {Geoscientific Model Development},
+  VOLUME =       8,
+  YEAR =         2015,
+  NUMBER =       5,
+  PAGES =        {1285--1297},
+  DOI =          {10.5194/gmd-8-1285-2015}
 }
 
 @ARTICLE{Breivik_al_JPO2014,
-   AUTHOR = {{\O}yvind Breivik and Peter A.E.M. Janssen and Jean-Raymond Bidlot},
-   YEAR = {2014},
-   TITLE = "{Approximate Stokes Drift Profiles in Deep Water}",
-   JOURNAL = {JPO},
-   VOLUME = {44},
-   NUMBER = {9},
-   DOI = {10.1175/JPO-D-14-0020.1.},
-   PAGES = {2433--2445, arXiv:1406.5039}
+  AUTHOR =       {{\O}yvind Breivik and Peter A.E.M. Janssen and
+                  Jean-Raymond Bidlot},
+  YEAR =         2014,
+  TITLE =        "{Approximate Stokes Drift Profiles in Deep Water}",
+  JOURNAL =      {JPO},
+  VOLUME =       44,
+  NUMBER =       9,
+  DOI =          {10.1175/JPO-D-14-0020.1.},
+  PAGES =        {2433--2445, arXiv:1406.5039}
 }
 
 @ARTICLE{Breivik_al_OM2016,
-   AUTHOR = {{\O}yvind Breivik and Jean-Raymond Bidlot and Peter A.E.M. Janssen},
-   YEAR = {2016},
-   TITLE = "{A Stokes drift approximation based on the Phillips spectrum}",
-   JOURNAL = {OM},
-   VOLUME = {100},
-   DOI = {10.1016/j.ocemod.2016.01.005},
-   PAGES = {49--56, arXiv:1601.08092}
+  AUTHOR =       {{\O}yvind Breivik and Jean-Raymond Bidlot and Peter
+                  A.E.M. Janssen},
+  YEAR =         2016,
+  TITLE =        "{A Stokes drift approximation based on the Phillips
+                  spectrum}",
+  JOURNAL =      {OM},
+  VOLUME =       100,
+  DOI =          {10.1016/j.ocemod.2016.01.005},
+  PAGES =        {49--56, arXiv:1601.08092}
 }
 
 @ARTICLE{Brodeau_al_OM09,
-  author = {L. Brodeau and B. Barnier and A.-M. Tr\'{e}guier and T. Penduff and S. Gulev},
-  title = {An ERA40-based atmospheric forcing for global ocean circulation models},
-  journal = OM,
-  year = {2009},
-  volume = {31},  number = {3-4},
-  pages = {88--104}
-}
-
+  author =       {L. Brodeau and B. Barnier and A.-M. Tr\'{e}guier and
+                  T. Penduff and S. Gulev},
+  title =        {An ERA40-based atmospheric forcing for global ocean
+                  circulation models},
+  journal =      OM,
+  year =         2009,
+  volume =       31,
+  number =       {3-4},
+  pages =        {88--104}
+}
 
 @ARTICLE{de_Boyer_Montegut_al_JGR04,
-  author = {C. de Boyer Mont\'{e}gut and G. Madec and A.S. Fischer and A. Lazar and D. Iudicone},
-  title = {Mixed layer depth over the global ocean: An examination of profile
-	data and a profile-based climatology},
-  journal = JGR,
-  year = {2004},
-  volume = {109},
-  pages = {C12003},
-  doi = {10.1029/2004JC002378},
+  author =       {C. de Boyer Mont\'{e}gut and G. Madec and
+                  A.S. Fischer and A. Lazar and D. Iudicone},
+  title =        {Mixed layer depth over the global ocean: An
+                  examination of profile data and a profile-based
+                  climatology},
+  journal =      JGR,
+  year =         2004,
+  volume =       109,
+  pages =        {C12003},
+  doi =          {10.1029/2004JC002378},
 }
 
 @ARTICLE{de_Boyer_Montegut_al_JC07,
-  author = {C. de Boyer Mont\'{e}gut and J. Vialard and F. Durand and G. Madec},
-  title = {Simulated seasonal and interannual variability of mixed layer heat
-	budget in the northern Indian Ocean},
-  journal = JC,
-  year = {2007},
-  volume = {20},  number = {13},
-  pages = {3249--3268}
+  author =       {C. de Boyer Mont\'{e}gut and J. Vialard and
+                  F. Durand and G. Madec},
+  title =        {Simulated seasonal and interannual variability of
+                  mixed layer heat budget in the northern Indian
+                  Ocean},
+  journal =      JC,
+  year =         2007,
+  volume =       20,
+  number =       13,
+  pages =        {3249--3268}
 }
 
 @ARTICLE{Brown_Campana_MWR78,
-  author = {J. A. Brown and K. A. Campana},
-  title = {An Economical Time-Differencing System for Numerical Weather Prediction},
-  journal = MWR,
-  year = {1978},
-  volume = {106},  number = {8},
-  pages = {1125--1136},
+  author =       {J. A. Brown and K. A. Campana},
+  title =        {An Economical Time-Differencing System for Numerical
+                  Weather Prediction},
+  journal =      MWR,
+  year =         1978,
+  volume =       106,
+  number =       8,
+  pages =        {1125--1136},
 }
 
 @ARTICLE{Bryan1997,
-  author = {K. Bryan},
-  title = {A Numerical Method for the Study of the Circulation of the World Ocean},
-  journal = JCP,
-  year = {1997},
-  volume = {135},  number = {2}
+  author =       {K. Bryan},
+  title =        {A Numerical Method for the Study of the Circulation
+                  of the World Ocean},
+  journal =      JCP,
+  year =         1997,
+  volume =       135,
+  number =       2
 }
 
 @ARTICLE{Bryan1984,
-  author = {K. Bryan},
-  title = {Accelerating the convergence to equilibrium of ocean-climate models},
-  journal = JPO,
-  year = {1984},
-  volume = {14},
-  pages = {666--673}
+  author =       {K. Bryan},
+  title =        {Accelerating the convergence to equilibrium of
+                  ocean-climate models},
+  journal =      JPO,
+  year =         1984,
+  volume =       14,
+  pages =        {666--673}
 }
 
 @ARTICLE{Bryden1973,
-  author = {H. L. Bryden},
-  title = {New polynomials for thermal expansion, adiabatic temperature gradient
-    and potential temperature of sea water},
-  journal = DSR,
-  year = {1973},
-  volume = {20},
-  pages = {401--408}
+  author =       {H. L. Bryden},
+  title =        {New polynomials for thermal expansion, adiabatic
+                  temperature gradient and potential temperature of
+                  sea water},
+  journal =      DSR,
+  year =         1973,
+  volume =       20,
+  pages =        {401--408}
 }
 
 @ARTICLE{Burchard_OM02,
-  author = {Hans Burchard},
-  title = {Energy-conserving discretisation of turbulent shear and buoyancy
-	production},
-  journal = OM,
-  year = {2002},
-  volume = {4},  number = {3-4},
-  pages = {347--361},
-  doi = {10.1016/S1463-5003(02)00009-4},
+  author =       {Hans Burchard},
+  title =        {Energy-conserving discretisation of turbulent shear
+                  and buoyancy production},
+  journal =      OM,
+  year =         2002,
+  volume =       4,
+  number =       {3-4},
+  pages =        {347--361},
+  doi =          {10.1016/S1463-5003(02)00009-4},
 }
 
 @ARTICLE{Campin2004,
-  author = {J.-M. Campin and A. Adcroft and C. Hill and J. Marshall},
-  title = {Conservation of properties in a free-surface model},
-  journal = OM,
-  year = {2004},
-  volume = {6},  number = {3-4},
-  pages = {221--244}
+  author =       {J.-M. Campin and A. Adcroft and C. Hill and
+                  J. Marshall},
+  title =        {Conservation of properties in a free-surface model},
+  journal =      OM,
+  year =         2004,
+  volume =       6,
+  number =       {3-4},
+  pages =        {221--244}
 }
 
 @ARTICLE{Campin_al_OM08,
-  author = {J.-M. Campin and J. Marshall and D. Ferreira},
-  title = {Sea ice-ocean coupling using a rescaled vertical coordinate z*},
-  journal = OM,
-  year = {2008},
-  volume = {24},  number = {1-2},
-  pages = {1--14},
-  doi = {10.1016/j.ocemod.2008.05.005},
+  author =       {J.-M. Campin and J. Marshall and D. Ferreira},
+  title =        {Sea ice-ocean coupling using a rescaled vertical
+                  coordinate z*},
+  journal =      OM,
+  year =         2008,
+  volume =       24,
+  number =       {1-2},
+  pages =        {1--14},
+  doi =          {10.1016/j.ocemod.2008.05.005},
 }
 
 @ARTICLE{Campin_Goosse_Tel99,
-  author = {J.-M. Campin and H. Goosse},
-  title = {Parameterization of density-driven downsloping flow for a coarse-resolution ocean model in z-coordinate},
-  journal = {Tellus},
-  year = {1999},
-  volume = {51},
-  pages = {412--430}
+  author =       {J.-M. Campin and H. Goosse},
+  title =        {Parameterization of density-driven downsloping flow
+                  for a coarse-resolution ocean model in z-coordinate},
+  journal =      {Tellus},
+  year =         1999,
+  volume =       51,
+  pages =        {412--430}
 }
 
 @ARTICLE{Carrere_Lyard_GRL03,
-  author = {L. Carr\`{e}re and F. Lyard},
-  title = {Modelling the barotropic response of the global ocean to atmospheric
-	wind and pressure forcing - comparisons with observations},
-  journal = GRL,
-  year = {2003},
-  volume = {30},  number = {6},
-  doi = {10.1029/2002GL016473},
+  author =       {L. Carr\`{e}re and F. Lyard},
+  title =        {Modelling the barotropic response of the global
+                  ocean to atmospheric wind and pressure forcing -
+                  comparisons with observations},
+  journal =      GRL,
+  year =         2003,
+  volume =       30,
+  number =       6,
+  doi =          {10.1029/2002GL016473},
 }
 
 @ARTICLE{Castellari_al_JMS1998,
-  author = {S> Castellari and  N. Pinardi and K. Leaman },
-  title = {A model study of air-sea interactions in the Mediterranean Sea.},
-  journal = JMS,
-  year = {1998},
-  volume = {18},
-  pages = {89--114}
+  author =       {S> Castellari and N. Pinardi and K. Leaman },
+  title =        {A model study of air-sea interactions in the
+                  Mediterranean Sea.},
+  journal =      JMS,
+  year =         1998,
+  volume =       18,
+  pages =        {89--114}
 }
 
 @TECHREPORT{Chanut2005,
- author = {J. Chanut},
- title = {Nesting code for NEMO},
- year = {2005},
- institution = {European Union: Marine Environment and Security for the European Area (MERSEA) Integrated Project},
-note = {MERSEA-WP09-MERCA-TASK-9.1.1}
-} 
+  author =       {J. Chanut},
+  title =        {Nesting code for NEMO},
+  year =         2005,
+  institution =  {European Union: Marine Environment and Security for
+                  the European Area (MERSEA) Integrated Project},
+  note =         {MERSEA-WP09-MERCA-TASK-9.1.1}
+}
 
 @ARTICLE{Chassignet_al_JPO03,
-  author = {Eric P. Chassignet and Linda T. Smith and George R. Halliwell},
-  title = {North Atlantic Simulations with the Hybrid Coordinate Ocean Model
-	(HYCOM): Impact of the Vertical Coordinate Choice, Reference Pressure, and Thermobaricity},
-  journal = JPO,
-  year = {2003},
-  volume = {33},
-  pages = {2504-2526}
+  author =       {Eric P. Chassignet and Linda T. Smith and George
+                  R. Halliwell},
+  title =        {North Atlantic Simulations with the Hybrid
+                  Coordinate Ocean Model (HYCOM): Impact of the
+                  Vertical Coordinate Choice, Reference Pressure, and
+                  Thermobaricity},
+  journal =      JPO,
+  year =         2003,
+  volume =       33,
+  pages =        {2504-2526}
 }
 
 @ARTICLE{Covey_al_CD00,
-  author = {C. Covey and A. Abe-Ouchi and G.J. Boer and B.A. Boville and U. Cubasch
-	and L. Fairhead and G.M. Flato and H. Gordon and E. Guilyardi and X. Jiang 
-	and T.C. Johns and H. Le Treut and G. Madec and G.A. Meehl and R. Miller 
-	and A. Noda and S. B. Power and E. Roeckner and G. Russell and E.K. Schneider 
-	and R.J. Stouffer and L. Terray and J.-S. von Storch},
-  title = {The seasonal cycle in coupled ocean-atmosphere general circulation models},
-  journal = CD,
-  year = {2000},
-  volume = {16},
-  pages = {775--787}
+  author =       {C. Covey and A. Abe-Ouchi and G.J. Boer and
+                  B.A. Boville and U. Cubasch and L. Fairhead and
+                  G.M. Flato and H. Gordon and E. Guilyardi and
+                  X. Jiang and T.C. Johns and H. Le Treut and G. Madec
+                  and G.A. Meehl and R. Miller and A. Noda and
+                  S. B. Power and E. Roeckner and G. Russell and
+                  E.K. Schneider and R.J. Stouffer and L. Terray and
+                  J.-S. von Storch},
+  title =        {The seasonal cycle in coupled ocean-atmosphere
+                  general circulation models},
+  journal =      CD,
+  year =         2000,
+  volume =       16,
+  pages =        {775--787}
 }
 
 @ARTICLE{Canuto_2001,
-  author = {V. M. Canuto and A. Howard and Y. Cheng and M. S. Dubovikov},
-  title = {Ocean turbulence. PartI: One-point closure model-momentum and heat vertical diffusivities},
-  journal = JPO,
-  year = {2001},
-  volume = {24},  number = {12},
-  pages = {2546--2559}
+  author =       {V. M. Canuto and A. Howard and Y. Cheng and
+                  M. S. Dubovikov},
+  title =        {Ocean turbulence. PartI: One-point closure
+                  model-momentum and heat vertical diffusivities},
+  journal =      JPO,
+  year =         2001,
+  volume =       24,
+  number =       12,
+  pages =        {2546--2559}
 }
 
 @ARTICLE{Cox1987,
-  author = {M. Cox},
-  title = {Isopycnal diffusion in a z-coordinate ocean model},
-  journal = OM,
-  year = {1987},
-  volume = {74},
-  pages = {1--9}
+  author =       {M. Cox},
+  title =        {Isopycnal diffusion in a z-coordinate ocean model},
+  journal =      OM,
+  year =         1987,
+  volume =       74,
+  pages =        {1--9}
 }
 
 @ARTICLE{Craig_Banner_JPO94,
-  author = {P. D. Craig and M. L. Banner},
-  title = {Modeling wave-enhanced turbulence in the ocean surface layer},
-  journal = JPO,
-  year = {1994},
-  volume = {24},  number = {12},
-  pages = {2546--2559}
+  author =       {P. D. Craig and M. L. Banner},
+  title =        {Modeling wave-enhanced turbulence in the ocean
+                  surface layer},
+  journal =      JPO,
+  year =         1994,
+  volume =       24,
+  number =       12,
+  pages =        {2546--2559}
 }
 
 @ARTICLE{Craik_Leibovich_JFM76,
-  author = {A. D. D. Craik and S. Leibovich},
-  title = {A rational model for Langmuir circulations},
-  journal = JFM,
-  year = {1976},
-  volume = {73}, 
-  pages = {401--426}
+  author =       {A. D. D. Craik and S. Leibovich},
+  title =        {A rational model for Langmuir circulations},
+  journal =      JFM,
+  year =         1976,
+  volume =       73,
+  pages =        {401--426}
 }
 
 @ARTICLE{Cravatte_al_OM07,
-  author = {Cravatte, S. and G. Madec and T. Izumo and C. Menkes and A. Bozec},
-  title = {Progress in the 3-D circulation of the eastern equatorial Pacific
-	in a climate ocean model},
-  journal = OM,
-  year = {2007},
-  volume = {17},  number = {1},
-  pages = {28--48}
+  author =       {Cravatte, S. and G. Madec and T. Izumo and C. Menkes
+                  and A. Bozec},
+  title =        {Progress in the 3-D circulation of the eastern
+                  equatorial Pacific in a climate ocean model},
+  journal =      OM,
+  year =         2007,
+  volume =       17,
+  number =       1,
+  pages =        {28--48}
 }
 
 @BOOK{Daley_Barker_Bk01,
-  author = {R. Daley and E. Barker},
-  title = {NAVDAS Source Book 2001},
-  publisher = {NRL/PU/7530-01-441, Available from the Naval Research Laboratory, Monterey, CA., 93943-5502},
-  year = {2001},
-  pages = {163pp}
+  author =       {R. Daley and E. Barker},
+  title =        {NAVDAS Source Book 2001},
+  publisher =    {NRL/PU/7530-01-441, Available from the Naval
+                  Research Laboratory, Monterey, CA., 93943-5502},
+  year =         2001,
+  pages =        {163pp}
 }
 
 @ARTICLE{D'Alessio_al_JPO98,
-  author = {S. J. D. D'Alessio and K. Abdella and N. A. McFarlane},
-  title = {A new second-order turbulence closure scheme for modeling the oceanic mixed layer},
-  journal = JPO,
-  year = {1998},
-  volume = {28},
-  pages = {1624--1641}
-}
-
+  author =       {S. J. D. D'Alessio and K. Abdella and
+                  N. A. McFarlane},
+  title =        {A new second-order turbulence closure scheme for
+                  modeling the oceanic mixed layer},
+  journal =      JPO,
+  year =         1998,
+  volume =       28,
+  pages =        {1624--1641}
+}
 
 @ARTICLE{Danabasoglu_al_2008,
-	author = {G. Danabasoglu and R. Ferrari and J. C. McWilliams},
-	title = {Sensitivity of an ocean general circulation model to a parameterization of near-surface eddy fluxes},
-	volume = {21},
-	year = {2008},
-	doi = {10.1175/2007JCLI1508.1},
-	journal = {J. Climate},
-	pages = {1192--1208},
-}
+  author =       {G. Danabasoglu and R. Ferrari and J. C. McWilliams},
+  title =        {Sensitivity of an ocean general circulation model to
+                  a parameterization of near-surface eddy fluxes},
+  volume =       21,
+  year =         2008,
+  doi =          {10.1175/2007JCLI1508.1},
+  journal =      {J. Climate},
+  pages =        {1192--1208},
+}
+
 @ARTICLE{Dandonneau_al_S04,
-  author = {Y. Dandonneau and C. Menkes and T. Gorgues and G. Madec},
-  title = {Reply to Peter Killworth, 2004 : '' Comment on the Oceanic Rossby
-	Waves acting as a “Hay Rake” for ecosystem by-products ''},
-  journal = {Science},
-  year = {2004},
-  volume = {304},
-  pages = {390}
+  author =       {Y. Dandonneau and C. Menkes and T. Gorgues and
+                  G. Madec},
+  title =        {Reply to Peter Killworth, 2004 : '' Comment on the
+                  Oceanic Rossby Waves acting as a “Hay Rake” for
+                  ecosystem by-products ''},
+  journal =      {Science},
+  year =         2004,
+  volume =       304,
+  pages =        390
 }
 
 @ARTICLE{Davies_QJRMS76,
- author = {H.C. Davies},
- title = {A lateral boundary formulation for multi-level prediction models},
- year = {1976},
- journal = QJRMS,
- volume = {102},
- pages = {405--418}
+  author =       {H.C. Davies},
+  title =        {A lateral boundary formulation for multi-level
+                  prediction models},
+  year =         1976,
+  journal =      QJRMS,
+  volume =       102,
+  pages =        {405--418}
 }
 
 @ARTICLE{Debreu_al_CG2008,
-  author = {L. Debreu and C. Vouland and E. Blayo},
-  title = {AGRIF: Adaptive Grid Refinement In Fortran},
-  journal = {Computers and Geosciences},
-  year = {2008},
-  volume = {34},
-  pages = {8--13}
+  author =       {L. Debreu and C. Vouland and E. Blayo},
+  title =        {AGRIF: Adaptive Grid Refinement In Fortran},
+  journal =      {Computers and Geosciences},
+  year =         2008,
+  volume =       34,
+  pages =        {8--13}
 }
 
 @article{de_lavergne_JPO2016_mixing,
-	author = {C. de Lavergne and G. Madec and J. Le Sommer and A. J. G. Nurser and A. C. Naveira Garabato },
-	title = {On Antarctic Bottom Water consumption in the abyssal ocean},
-	issn = {0022-3670},
-	doi= {10.1175/JPO-D-14-0201.1},
-	abstract = {In studies of ocean mixing, it is generally assumed that small-scale turbulent overturns lose 15-20 \% of their energy in eroding the background stratification. Accumulating evidence that this energy fraction, or mixing efficiency Rf, significantly varies depending on flow properties challenges this assumption, however. Here, we examine the implications of a varying mixing efficiency for ocean energetics and deep water mass transformation. Combining current parameterizations of internal wave-driven mixing with a recent model expressing Rf as a function of a turbulence intensity parameter Reb = εν/νN2, we show that accounting for reduced mixing efficiencies in regions of weak stratification or energetic turbulence (high Reb) strongly limits the ability of breaking internal waves to supply oceanic potential energy and drive abyssal upwelling. Moving from a fixed Rf = 1/6 to a variable efficiency Rf(Reb) causes Antarctic Bottom Water upwelling induced by locally-dissipating internal tides and lee waves to fall from 9 to 4 Sv, and the corresponding potential energy source to plunge from 97 to 44 GW. When adding the contribution of remotely-dissipating internal tides under idealized distributions of energy dissipation, the total rate of Antarctic Bottom Water upwelling is reduced by about a factor of 2, reaching 5-15 Sv compared to 10-33 Sv for a fixed efficiency. Our results suggest that distributed mixing, overflow-related boundary processes and geothermal heating are more effective in consuming abyssal waters than topographically-enhanced mixing by breaking internal waves. Our calculations also point to the importance of accurately constraining Rf(Reb) and including the effect in ocean models.},
-	journal = {Journal of Physical Oceanography},
-	year = {2016},
-	volume = {46},  pages = {635-–661}
+  author =       {C. de Lavergne and G. Madec and J. Le Sommer and
+                  A. J. G. Nurser and A. C. Naveira Garabato },
+  title =        {On Antarctic Bottom Water consumption in the abyssal
+                  ocean},
+  issn =         {0022-3670},
+  doi =          {10.1175/JPO-D-14-0201.1},
+  journal =      {Journal of Physical Oceanography},
+  year =         2016,
+  volume =       46,
+  pages =        {635-–661}
 }
 
 @article{de_lavergne_JPO2016_efficiency,
-	author = {C. de Lavergne and G. Madec and J. Le Sommer and A. J. G. Nurser and A. C. Naveira Garabato },
-	title = {The impact of a variable mixing efficiency on the abyssal overturning},
-	issn = {0022-3670},
-	doi = {10.1175/JPO-D-14-0259.1},
-	abstract = {In studies of ocean mixing, it is generally assumed that small-scale turbulent overturns lose 15-20 \% of their energy in eroding the background stratification. Accumulating evidence that this energy fraction, or mixing efficiency Rf, significantly varies depending on flow properties challenges this assumption, however. Here, we examine the implications of a varying mixing efficiency for ocean energetics and deep water mass transformation. Combining current parameterizations of internal wave-driven mixing with a recent model expressing Rf as a function of a turbulence intensity parameter Reb = εν/νN2, we show that accounting for reduced mixing efficiencies in regions of weak stratification or energetic turbulence (high Reb) strongly limits the ability of breaking internal waves to supply oceanic potential energy and drive abyssal upwelling. Moving from a fixed Rf = 1/6 to a variable efficiency Rf(Reb) causes Antarctic Bottom Water upwelling induced by locally-dissipating internal tides and lee waves to fall from 9 to 4 Sv, and the corresponding potential energy source to plunge from 97 to 44 GW. When adding the contribution of remotely-dissipating internal tides under idealized distributions of energy dissipation, the total rate of Antarctic Bottom Water upwelling is reduced by about a factor of 2, reaching 5-15 Sv compared to 10-33 Sv for a fixed efficiency. Our results suggest that distributed mixing, overflow-related boundary processes and geothermal heating are more effective in consuming abyssal waters than topographically-enhanced mixing by breaking internal waves. Our calculations also point to the importance of accurately constraining Rf(Reb) and including the effect in ocean models.},
-	journal = {Journal of Physical Oceanography},
-	year = {2016},
-	volume = {46},  pages = {663-–681}
+  author =       {C. de Lavergne and G. Madec and J. Le Sommer and
+                  A. J. G. Nurser and A. C. Naveira Garabato },
+  title =        {The impact of a variable mixing efficiency on the
+                  abyssal overturning},
+  issn =         {0022-3670},
+  doi =          {10.1175/JPO-D-14-0259.1},
+  journal =      {Journal of Physical Oceanography},
+  year =         2016,
+  volume =       46,
+  pages =        {663-–681}
 }
 
 @ARTICLE{Delecluse_Madec_Bk00,
-  author = {P. Delecluse and G. Madec},
-  title = {Ocean modelling and the role of the ocean in the climate system},
-  journal = {In \textit{Modeling the Earth's Climate and its Variability}, Les
-	Houches, Session, LXVII 1997,
-	Eds. W. R. Holland, S. Joussaume and F. David, Elsevier Science},
-  year = {2000},
-  pages = {237--313}
+  author =       {P. Delecluse and G. Madec},
+  title =        {Ocean modelling and the role of the ocean in the
+                  climate system},
+  journal =      {In \textit{Modeling the Earth's Climate and its
+                  Variability}, Les Houches, Session, LXVII 1997,
+                  Eds. W. R. Holland, S. Joussaume and F. David,
+                  Elsevier Science},
+  year =         2000,
+  pages =        {237--313}
 }
 
 @PHDTHESIS{Demange_PhD2014,
-  author = {J. Demange},
-  title = {Sch\'{e}mas num\'{e}riques d'advection et de propagation d’ondes de gravit\'{e} 
-           dans les mod\`{e}les de circulation oc\'{e}anique.},
-  school = {Doctorat es Applied Mathematiques, Grenoble University, France},
-  year = {2014},
-  pages = {138pp}
+  author =       {J. Demange},
+  title =        {Sch\'{e}mas num\'{e}riques d'advection et de
+                  propagation d’ondes de gravit\'{e} dans les
+                  mod\`{e}les de circulation oc\'{e}anique.},
+  school =       {Doctorat es Applied Mathematiques, Grenoble
+                  University, France},
+  year =         2014,
+  pages =        {138pp}
 }
 
 @ARTICLE{Dobricic_al_OS07,
-  author = {S. Dobricic and N. Pinardi and M. Adani and M. Tonani and 
-            C. Fratianni and A. Bonazzi and V. Fernandez},
-  title = {Daily oceanographic analysis by the Mediterranean basin scale 
-           assimilation system},
-  journal = OS,
-  year = {2007},
-  volume = {3},
-  pages = {149-157}
+  author =       {S. Dobricic and N. Pinardi and M. Adani and
+                  M. Tonani and C. Fratianni and A. Bonazzi and
+                  V. Fernandez},
+  title =        {Daily oceanographic analysis by the Mediterranean
+                  basin scale assimilation system},
+  journal =      OS,
+  year =         2007,
+  volume =       3,
+  pages =        {149-157}
 }
 
 @ARTICLE{Doney_al_GBC04,
-  author = {S.C. Doney and K. Lindsay and K. Caldeira and J.−M. Campin and H.
-	Drange and J.−C. Dutay and M. Follows and Y. Gao and A. Gnanadesikan
-	and N. Gruber and A. Ishida and F. Joos and G. Madec and E. Maier−Reimer
-	and J.C. Marshall and R.J. Matear and P. Monfray and A. Mouchet and
-	R. Najjar and J.C. Orr and G.−K. Plattner and J. Sarmiento and R.
-	Schlitzer and R. Slater and I.J. Totterdell and M.−F. Weirig and
-	Y. Yamanaka and A. Yoo},
-  title = {Evaluating global ocean carbon models: the importance of realistic
-	physics},
-  journal = GBC,
-  year = {2004},
-  volume = {18},
-  pages = {GB3017},
-  doi = {10.1029/2003GB002150},
+  author =       {S.C. Doney and K. Lindsay and K. Caldeira and
+                  J.−M. Campin and H.  Drange and J.−C. Dutay and
+                  M. Follows and Y. Gao and A. Gnanadesikan and
+                  N. Gruber and A. Ishida and F. Joos and G. Madec and
+                  E. Maier−Reimer and J.C. Marshall and R.J. Matear
+                  and P. Monfray and A. Mouchet and R. Najjar and
+                  J.C. Orr and G.−K. Plattner and J. Sarmiento and R.
+                  Schlitzer and R. Slater and I.J. Totterdell and
+                  M.−F. Weirig and Y. Yamanaka and A. Yoo},
+  title =        {Evaluating global ocean carbon models: the
+                  importance of realistic physics},
+  journal =      GBC,
+  year =         2004,
+  volume =       18,
+  pages =        {GB3017},
+  doi =          {10.1029/2003GB002150},
 }
 
 @ARTICLE{Dorscher_Beckmann_JAOT00,
-  author = {R. D\"{o}scher and A. Beckmann},
-  title = {Effects of a Bottom Boundary Layer Parameterization in a Coarse-Resolution
-	Model of the North Atlantic Ocean},
-  journal = JAOT,
-  year = {2000},
-  volume = {17},
-  pages = {698--707}
+  author =       {R. D\"{o}scher and A. Beckmann},
+  title =        {Effects of a Bottom Boundary Layer Parameterization
+                  in a Coarse-Resolution Model of the North Atlantic
+                  Ocean},
+  journal =      JAOT,
+  year =         2000,
+  volume =       17,
+  pages =        {698--707}
 }
 
 @ARTICLE{Drijfhout_JPO94,
-  author = {S. S. Drijfhout},
-  title = {Heat transport by Mesoscale Eddies in an Ocean Circulation Model},
-  journal = JPO,
-  year = {1994},
-  volume = {24},
-  pages = {353--369}
+  author =       {S. S. Drijfhout},
+  title =        {Heat transport by Mesoscale Eddies in an Ocean
+                  Circulation Model},
+  journal =      JPO,
+  year =         1994,
+  volume =       24,
+  pages =        {353--369}
 }
 
 @ARTICLE{Dukowicz1994,
-  author = {J. K. Dukowicz and R. D. Smith},
-  title = {Implicit free-surface method for the Bryan-Cox-Semtner ocean model},
-  journal = JGR,
-  year = {1994},
-  volume = {99},
-  pages = {7991--8014}
+  author =       {J. K. Dukowicz and R. D. Smith},
+  title =        {Implicit free-surface method for the
+                  Bryan-Cox-Semtner ocean model},
+  journal =      JGR,
+  year =         1994,
+  volume =       99,
+  pages =        {7991--8014}
 }
 
 @ARTICLE{Durand_al_JC07,
-  author = {F. Durand and D. Shankar and C. de Boyer Mont\'{e}gut and S.S.C.
-	Shenoi and B. Blanke and G. Madec},
-  title = {Modeling the barrier-layer formation in the South-Eastern Arabian
-	Sea},
-  journal = JC,
-  year = {2007},
-  volume = {20},  number = {10},
-  pages = {2109--2120}
+  author =       {F. Durand and D. Shankar and C. de Boyer
+                  Mont\'{e}gut and S.S.C.  Shenoi and B. Blanke and
+                  G. Madec},
+  title =        {Modeling the barrier-layer formation in the
+                  South-Eastern Arabian Sea},
+  journal =      JC,
+  year =         2007,
+  volume =       20,
+  number =       10,
+  pages =        {2109--2120}
 }
 
 @ARTICLE{Durand_al_GRL04,
-  author = {F. Durand and S. R. Shetye and J. Vialard and D. Shankar and S.S.C.
-	Shenoi and C. Eth\'{e} and G. Madec},
-  title = {Impact of temperature inversions on SST evolution in the South−Eastern
-	Arabian Sea during the pre−summer monsoon season},
-  journal = GRL,
-  year = {2004},
-  volume = {31},
-  pages = {L01305},
-  doi = {10.1029/2003GL018906},
+  author =       {F. Durand and S. R. Shetye and J. Vialard and
+                  D. Shankar and S.S.C.  Shenoi and C. Eth\'{e} and
+                  G. Madec},
+  title =        {Impact of temperature inversions on SST evolution in
+                  the South−Eastern Arabian Sea during the pre−summer
+                  monsoon season},
+  journal =      GRL,
+  year =         2004,
+  volume =       31,
+  pages =        {L01305},
+  doi =          {10.1029/2003GL018906},
 }
 
 @INCOLLECTION{Durran2001,
-  author = {D.R. Durran },
-  title = {Open boundary conditions: fact and fiction},
-  booktitle = {Advances in Mathematical Modelling of Atmosphere and Ocean Dynamics},
-  publisher = {Kluwer Academic Publishers},
-  year = {2001},
-  editor = {P.F. Hodnett}
+  author =       {D.R. Durran },
+  title =        {Open boundary conditions: fact and fiction},
+  booktitle =    {Advances in Mathematical Modelling of Atmosphere and
+                  Ocean Dynamics},
+  publisher =    {Kluwer Academic Publishers},
+  year =         2001,
+  editor =       {P.F. Hodnett}
 }
 
 @ARTICLE{Dutay_al_OM02,
-  author = {J.-C. Dutay and J.L. Bullister and S.C. Doney and J.C. Orr and R.
-	Najjar and K. Caldeira and J.-M. Campin and H. Drange and M. Follows
-	and Y. Gao and N. Gruber and M. W. Hecht and A. Ishida and F. Joos
-	and K. Lindsay and G. Madec and E. Maier-Reimer and J.C. Mashall
-	and R. J. Matear and P. Monfray and G.-K. Plattner and J. Sarmiento
-	and R. Schlitzer and R. Slater and I.J. Totterdell and M.-F. Weirig
-	and Y. Yamanaka and A. Tool},
-  title = {Evaluation of ocean model ventilation with CFC-11: comparison of
-	13 global ocean models},
-  journal = OM,
-  year = {2002},
-  volume = {4},
-  pages = {89--120}
+  author =       {J.-C. Dutay and J.L. Bullister and S.C. Doney and
+                  J.C. Orr and R.  Najjar and K. Caldeira and
+                  J.-M. Campin and H. Drange and M. Follows and Y. Gao
+                  and N. Gruber and M. W. Hecht and A. Ishida and
+                  F. Joos and K. Lindsay and G. Madec and
+                  E. Maier-Reimer and J.C. Mashall and R. J. Matear
+                  and P. Monfray and G.-K. Plattner and J. Sarmiento
+                  and R. Schlitzer and R. Slater and I.J. Totterdell
+                  and M.-F. Weirig and Y. Yamanaka and A. Tool},
+  title =        {Evaluation of ocean model ventilation with CFC-11:
+                  comparison of 13 global ocean models},
+  journal =      OM,
+  year =         2002,
+  volume =       4,
+  pages =        {89--120}
 }
 
 @ARTICLE{Dutay_al_EFM09,
-  author = {J.-C. Dutay and J. Emile-Geay and D. Iudicone and P. Jean-Baptiste
-	and G. Madec and C. Carouge},
-  title = {Helium Isotopic Constraints on Simulated Ocean Circulations - Implications
-	for abyssal theories},
-  journal = EFM,
-  year = {2009},
-  volume = {10},  number = {1-2},
-  pages = {257--273},
-  doi = {10.1007/s10652-009-9159-y}
+  author =       {J.-C. Dutay and J. Emile-Geay and D. Iudicone and
+                  P. Jean-Baptiste and G. Madec and C. Carouge},
+  title =        {Helium Isotopic Constraints on Simulated Ocean
+                  Circulations - Implications for abyssal theories},
+  journal =      EFM,
+  year =         2009,
+  volume =       10,
+  number =       {1-2},
+  pages =        {257--273},
+  doi =          {10.1007/s10652-009-9159-y}
 }
 
 @ARTICLE{Dutay.J.C2004,
-  author = {J. -C. Dutay and P. J. -Baptiste and J. -M. Campin and A. Ishida
-	and E. M. -Reimer and R. J. Matear and A. Mouchet and I. J. Totterdell
-	and Y. Yamanaka and K. Rodgers and G. Madec and J.C. Orr},
-  title = {Evaluation of OCMIP-2 ocean models deep circulation with mantle helium-3},
-  journal = JMS,
-  year = {2004},
-  pages = {1--22}
+  author =       {J. -C. Dutay and P. J. -Baptiste and J. -M. Campin
+                  and A. Ishida and E. M. -Reimer and R. J. Matear and
+                  A. Mouchet and I. J. Totterdell and Y. Yamanaka and
+                  K. Rodgers and G. Madec and J.C. Orr},
+  title =        {Evaluation of OCMIP-2 ocean models deep
+                  circulation with mantle helium-3},
+  journal =      JMS,
+  year =         2004,
+  pages =        {1--22}
 }
 
 @ARTICLE{D'Ortenzio_al_GRL05,
-  author = {F. D\'Ortenzio and D. Iudicone and C. de Boyer Mont\'{e}gut and P.
-	Testor and D. Antoine and S. Marullo and R. Santoleri and G. Madec},
-  title = {Seasonal variability of the mixed layer depth in the Mediterranean
-	Sea : a new climatology based on analysis of individual profiles},
-  journal = GRL,
-  year = {2005},
-  volume = {32},
-  pages = {L12605},
-  doi = {10.1029/2005GL022463},
+  author =       {F. D\'Ortenzio and D. Iudicone and C. de Boyer
+                  Mont\'{e}gut and P.  Testor and D. Antoine and
+                  S. Marullo and R. Santoleri and G. Madec},
+  title =        {Seasonal variability of the mixed layer depth in the
+                  Mediterranean Sea : a new climatology based on
+                  analysis of individual profiles},
+  journal =      GRL,
+  year =         2005,
+  volume =       32,
+  pages =        {L12605},
+  doi =          {10.1029/2005GL022463},
 }
 
 @ARTICLE{Egbert_Ray_JGR01,
-  author = {G.B. Egbert and R.D. Ray},
-  title = {Estimates of M2 tidal energy dissipation from TOPEX/POSEIDON altimeter
-	data},
-  journal = JGR,
-  year = {2001},
-  volume = {106},
-  pages = {22475--22502}
+  author =       {G.B. Egbert and R.D. Ray},
+  title =        {Estimates of M2 tidal energy dissipation from
+                  TOPEX/POSEIDON altimeter data},
+  journal =      JGR,
+  year =         2001,
+  volume =       106,
+  pages =        {22475--22502}
 }
 
 @ARTICLE{Egbert_Ray_Nat00,
-  author = {G.B. Egbert and R.D Ray},
-  title = {Significant dissipation of tidal energy in the deep ocean inferred
-	from satellite altimeter data},
-  journal = {Nature},
-  year = {2000},
-  volume = {405},
-  pages = {775--778}
+  author =       {G.B. Egbert and R.D Ray},
+  title =        {Significant dissipation of tidal energy in the deep
+                  ocean inferred from satellite altimeter data},
+  journal =      {Nature},
+  year =         2000,
+  volume =       405,
+  pages =        {775--778}
 }
 
 @ARTICLE{Eiseman1980,
-  author = {P. R. Eiseman and A. P. Stone},
-  title = {Conservation lows of fluid dynamics -- A survey},
-  journal = {SIAM Review},
-  year = {1980},
-  volume = {22},
-  pages = {12--27}
+  author =       {P. R. Eiseman and A. P. Stone},
+  title =        {Conservation lows of fluid dynamics -- A survey},
+  journal =      {SIAM Review},
+  year =         1980,
+  volume =       22,
+  pages =        {12--27}
 }
 
 @ARTICLE{Emile-Geay_Madec_OS09,
-  author = {J. Emile-Geay and G. Madec},
-  title = {Geothermal heating, diapycnal mixing and the abyssal circulation},
-  journal = OS,
-  year = {2009},
-  volume = {5},
-  pages = {281--325}
+  author =       {J. Emile-Geay and G. Madec},
+  title =        {Geothermal heating, diapycnal mixing and the abyssal
+                  circulation},
+  journal =      OS,
+  year =         2009,
+  volume =       5,
+  pages =        {281--325}
 }
 
 @ARTICLE{Engerdahl_Tel95,
- author = {H. Engerdahl},
- year = {1995},
- title = {Use of the flow relaxation scheme in a three-dimensional baroclinic ocean model with realistic topography},
- journal = {Tellus},
- volume = {47A},
- pages = {365--382}
+  author =       {H. Engerdahl},
+  year =         1995,
+  title =        {Use of the flow relaxation scheme in a
+                  three-dimensional baroclinic ocean model with
+                  realistic topography},
+  journal =      {Tellus},
+  volume =       {47A},
+  pages =        {365--382}
 }
 
 @ARTICLE{EUROMODEL_OA95,
-  author = {EUROMODEL Group (P.M. Lehucher, L. Beautier, M. Chartier, F. Martel,
-	L. Mortier, P. Brehmer, C. Millot, C. Alberola, M. Benzhora, I. Taupier-Letage,
-	G. Chabert d'Hieres, H. Didelle, P. Gleizon, D. Obaton, M. Cr\'{e}pon,
-	C. Herbaut, G. Madec, S. Speich, J. Nihoul, J. M. Beckers, P. Brasseur,
-	E. Deleersnijder, S. Djenidi, J. Font, A. Castellon, E. Garcia-Ladona,
-	M. J. Lopez-Garcia, M. Manriquez, M. Maso, J. Salat, J. Tintore,
-	S. Alonso, D. Gomis, A. Viudez, M. Astraldi, D. Bacciola, M. Borghini,
-	F. Dell'amico, C. Galli, E. Lazzoni, G. P. Gasparini, S. Sparnocchia,
-	and A. Harzallah, 1995 : Progress from 1989 to 1992 in understanding
-	the circulation of the Western Mediterranean Sea. Oceanologica Acta,
-	18, 2, 255-271.},
-  title = {EUROMODEL Group (P.M. Lehucher, L. Beautier, M. Chartier, F. Martel,
-	L. Mortier, P. Brehmer, C. Millot, C. Alberola, M. Benzhora, I. Taupier-Letage,
-	G. Chabert d'Hieres, H. Didelle, P. Gleizon, D. Obaton, M. Cr\'{e}pon,
-	C. Herbaut, G. Madec, S. Speich, J. Nihoul, J. M. Beckers, P. Brasseur,
-	E. Deleersnijder, S. Djenidi, J. Font, A. Castellon, E. Garcia-Ladona,
-	M. J. Lopez-Garcia, M. Manriquez, M. Maso, J. Salat, J. Tintore,
-	S. Alonso, D. Gomis, A. Viudez, M. Astraldi, D. Bacciola, M. Borghini,
-	F. Dell'amico, C. Galli, E. Lazzoni, G. P. Gasparini, S. Sparnocchia,
-	and A. Harzallah, 1995 : Progress from 1989 to 1992 in understanding
-	the circulation of the Western Mediterranean Sea.},
-  journal = {Oceanologica Acta},
-  year = {1995},
-  volume = {18},  number = {2},
-  pages = {255--271}
+  author =       {EUROMODEL Group (P.M. Lehucher, L. Beautier,
+                  M. Chartier, F. Martel, L. Mortier, P. Brehmer,
+                  C. Millot, C. Alberola, M. Benzhora,
+                  I. Taupier-Letage, G. Chabert d'Hieres, H. Didelle,
+                  P. Gleizon, D. Obaton, M. Cr\'{e}pon, C. Herbaut,
+                  G. Madec, S. Speich, J. Nihoul, J. M. Beckers,
+                  P. Brasseur, E. Deleersnijder, S. Djenidi, J. Font,
+                  A. Castellon, E. Garcia-Ladona, M. J. Lopez-Garcia,
+                  M. Manriquez, M. Maso, J. Salat, J. Tintore,
+                  S. Alonso, D. Gomis, A. Viudez, M. Astraldi,
+                  D. Bacciola, M. Borghini, F. Dell'amico, C. Galli,
+                  E. Lazzoni, G. P. Gasparini, S. Sparnocchia, and
+                  A. Harzallah)},
+  title =        {Progress from 1989 to 1992 in
+                  understanding the circulation of the Western
+                  Mediterranean Sea.},
+  journal =      {Oceanologica Acta},
+  year =         1995,
+  volume =       18,
+  number =       2,
+  pages =        {255--271}
 }
 
 @PHDTHESIS{Farge1987,
-  author = {M. Farge},
-  title = {Dynamique non lineaire des ondes et des tourbillons dans les equations de Saint Venant},
-  school = {Doctorat es Mathematiques, Paris VI University, France},
-  year = {1987},
-  pages = {401pp}
+  author =       {M. Farge},
+  title =        {Dynamique non lineaire des ondes et des tourbillons
+                  dans les equations de Saint Venant},
+  school =       {Doctorat es Mathematiques, Paris VI University,
+                  France},
+  year =         1987,
+  pages =        {401pp}
 }
 
 @ARTICLE{Farrow1995,
-  author = {D. E. Farrow and D. P. Stevens},
-  title = {A new tracer advection scheme for Bryan--Cox type ocean general circulation
-	models},
-  journal = JPO,
-  year = {1995},
-  volume = {25},
-  pages = {1731--1741.}
+  author =       {D. E. Farrow and D. P. Stevens},
+  title =        {A new tracer advection scheme for Bryan--Cox type
+                  ocean general circulation models},
+  journal =      JPO,
+  year =         1995,
+  volume =       25,
+  pages =        {1731--1741.}
 }
 
 @ARTICLE{Flather1976,
- author = {R.A. Flather},
- year = {1976},
- title = {A tidal model of the north-west European continental shelf},
- journal = {Memoires de la Societ\'{e} Royale des Sciences de Li\`{e}ge},
- volume = {6},
- pages = {141--164}
+  author =       {R.A. Flather},
+  year =         1976,
+  title =        {A tidal model of the north-west European continental
+                  shelf},
+  journal =      {Memoires de la Societ\'{e} Royale des Sciences de
+                  Li\`{e}ge},
+  volume =       6,
+  pages =        {141--164}
 }
 
 @ARTICLE{Flather_JPO94,
- author = {R.A. Flather},
- year = {1994},
- title = {A storm surge prediction model for the northern Bay of Bengal with application to the cyclone disaster in April 1991},
- journal = JPO,
- volume = {24},
- pages = {172--190}
+  author =       {R.A. Flather},
+  year =         1994,
+  title =        {A storm surge prediction model for the northern Bay
+                  of Bengal with application to the cyclone disaster
+                  in April 1991},
+  journal =      JPO,
+  volume =       24,
+  pages =        {172--190}
 }
 
 @ARTICLE{Fujio1991,
-  author = {S. Fujio and N. Imasato},
-  title = {Diagnostic calculation for circulation and water mass movement in
-	the deep Pacific},
-  journal = JGR,
-  year = {1991},
-  volume = {96},
-  pages = {759--774}
+  author =       {S. Fujio and N. Imasato},
+  title =        {Diagnostic calculation for circulation and water
+                  mass movement in the deep Pacific},
+  journal =      JGR,
+  year =         1991,
+  volume =       96,
+  pages =        {759--774}
 }
 
 @ARTICLE{Galperin_al_JAS88,
-  author = {B. Galperin and L. H. Kantha and S. Hassid and A. Rosati},
-  title = {A quasi-equilibrium turbulent energy model for geophysical flows},
-  journal = JAS,
-  year = {1988},
-  volume = {45},
-  pages = {55--62}
+  author =       {B. Galperin and L. H. Kantha and S. Hassid and
+                  A. Rosati},
+  title =        {A quasi-equilibrium turbulent energy model for
+                  geophysical flows},
+  journal =      JAS,
+  year =         1988,
+  volume =       45,
+  pages =        {55--62}
 }
 
 @ARTICLE{Gargett1984,
-  author = {A. E. Gargett},
-  title = {Vertical eddy diffusivity in the ocean interior},
-  journal = JMR,
-  year = {1984},
-  volume = {42}
+  author =       {A. E. Gargett},
+  title =        {Vertical eddy diffusivity in the ocean interior},
+  journal =      JMR,
+  year =         1984,
+  volume =       42
 }
 
 @ARTICLE{Gaspar1990,
-  author = {P. Gaspar and Y. Gr{\'e}goris and J.-M. Lefevre},
-  title = {A simple eddy kinetic energy model for simulations of the oceanic vertical mixing\: 
-    Tests at Station Papa and long-term upper ocean study site},
-  journal = JGR,
-  year = {1990},
-  volume = {95},  number = {C9}
+  author =       {P. Gaspar and Y. Gr{\'e}goris and J.-M. Lefevre},
+  title =        {A simple eddy kinetic energy model for simulations
+                  of the oceanic vertical mixing\: Tests at Station
+                  Papa and long-term upper ocean study site},
+  journal =      JGR,
+  year =         1990,
+  volume =       95,
+  number =       {C9}
 }
 
 @ARTICLE{Gent1990,
-  author = {P. R. Gent and J. C. Mcwilliams},
-  title = {Isopycnal Mixing in Ocean Circulation Models},
-  journal = JPO,
-  year = {1990},
-  volume = {20},  number = {1},
-  pages = {150--155},
+  author =       {P. R. Gent and J. C. Mcwilliams},
+  title =        {Isopycnal Mixing in Ocean Circulation Models},
+  journal =      JPO,
+  year =         1990,
+  volume =       20,
+  number =       1,
+  pages =        {150--155},
 }
 
 @Article{Gentemann_al_JGR09,
-  author = 	 {C. L. Gentemann  and P. J. Minnett and B. Ward},
-  title =        {Profiles of Ocean Surface heating ({POSH}): A new model 
-                  of upper ocean diurnal warming},
-  journal = 	 JGR,
-  year = 	 {2009},
-  Volume = 	 {114},
-  Pages = 	 {C07017},
-  doi = 	 {10.1029/2008JC004825},
-  OPTannote = 	 {}
+  author =       {C. L. Gentemann and P. J. Minnett and B. Ward},
+  title =        {Profiles of Ocean Surface heating ({POSH}): A new
+                  model of upper ocean diurnal warming},
+  journal =      JGR,
+  year =         2009,
+  Volume =       114,
+  Pages =        {C07017},
+  doi =          {10.1029/2008JC004825}
 }
 
 @ARTICLE{Gerdes1993a,
-  author = {R. Gerdes},
-  title = {A primitive equation ocean circulation model using a general vertical
-	coordinate transformation 1. Description and testing of the model},
-  journal = JGR,
-  year = {1993},
-  volume = {98}
+  author =       {R. Gerdes},
+  title =        {A primitive equation ocean circulation model using a
+                  general vertical coordinate transformation
+                  1. Description and testing of the model},
+  journal =      JGR,
+  year =         1993,
+  volume =       98
 }
 
 @ARTICLE{Gerdes1993b,
-  author = {R. Gerdes},
-  title = {A primitive equation ocean circulation model using a general vertical
-	coordinate transformation 2. Application to an overflow problem},
-  journal = JGR,
-  year = {1993},
-  volume = {98},
-  pages = {14703--14726}
+  author =       {R. Gerdes},
+  title =        {A primitive equation ocean circulation model using a
+                  general vertical coordinate transformation
+                  2. Application to an overflow problem},
+  journal =      JGR,
+  year =         1993,
+  volume =       98,
+  pages =        {14703--14726}
 }
 
 @ARTICLE{Gerdes1991,
-	Author = {Gerdes, R{\"u}diger and K{\"o}berle, Cornelia and Willebrand, J{\"u}rgen},
-	Doi = {10.1007/BF00210006},
-	Journal = {Clim. Dynamics},
-	Number = {4},
-	Pages = {211--226},
-	Title = {The influence of numerical advection schemes on the results of ocean general circulation models},
-	Volume = {5},
-	Year = {1991},
-}
+  Author =       {Gerdes, R{\"u}diger and K{\"o}berle, Cornelia and
+                  Willebrand, J{\"u}rgen},
+  Doi =          {10.1007/BF00210006},
+  Journal =      {Clim. Dynamics},
+  Number =       4,
+  Pages =        {211--226},
+  Title =        {The influence of numerical advection schemes on the
+                  results of ocean general circulation models},
+  Volume =       5,
+  Year =         1991,
+}
+
 @TECHREPORT{Gibson_TR86,
-  author = {J. K. Gibson},
-  title = {Standard software development and maintenance},
-  institution = {Operational Dep., ECMWF, Reading, UK.},
-  year = {1986}
+  author =       {J. K. Gibson},
+  title =        {Standard software development and maintenance},
+  institution =  {Operational Dep., ECMWF, Reading, UK.},
+  year =         1986
 }
 
 @BOOK{Gill1982,
-  title = {Atmosphere-Ocean Dynamics},
-  publisher = {International Geophysics Series, Academic Press, New-York},
-  year = {1982},
-  author = {A. E. Gill}
+  title =        {Atmosphere-Ocean Dynamics},
+  publisher =    {International Geophysics Series, Academic Press,
+                  New-York},
+  year =         1982,
+  author =       {A. E. Gill}
 }
 
 @article{goff_JGR2010,
-	author = {J. A. Goff},
-	title = {Global prediction of abyssal hill root-mean-square heights from small-scale altimetric gravity variability},
-	issn = {2156-2202},
-	doi = {10.1029/2010JB007867},
-	abstract = {Abyssal hills, which are pervasive landforms on the seafloor of the Earth's oceans, represent a potential tectonic record of the history of mid-ocean ridge spreading. However, the most detailed global maps of the seafloor, derived from the satellite altimetry-based gravity field, cannot be used to deterministically characterize such small-scale ({\textless}10 km) morphology. Nevertheless, the small-scale variability of the gravity field can be related to the statistical properties of abyssal hill morphology using the upward continuation formulation. In this paper, I construct a global prediction of abyssal hill root-mean-square (rms) heights from the small-scale variability of the altimetric gravity field. The abyssal hill-related component of the gravity field is derived by first masking distinct features, such as seamounts, mid-ocean ridges, and continental margins, and then applying a newly designed adaptive directional filter algorithm to remove fracture zone/discontinuity fabric. A noise field is derived empirically by correlating the rms variability of the small-scale gravity field to the altimetric noise field in regions of very low relief, and the noise variance is subtracted from the small-scale gravity variance. Suites of synthetically derived, abyssal hill formed gravity fields are generated as a function of water depth, basement rms heights, and sediment thickness and used to predict abyssal hill seafloor rms heights from corrected small-scale gravity rms height. The resulting global prediction of abyssal hill rms heights is validated qualitatively by comparing against expected variations in abyssal hill morphology and quantitatively by comparing against actual measurements of rms heights. Although there is scatter, the prediction appears unbiased.},
-	volume = {115},
-	number = {B12},
-	journal = {Journal of Geophysical Research: Solid Earth},
-	year = {2010},
-	pages = {B12104},
+  author =       {J. A. Goff},
+  title =        {Global prediction of abyssal hill root-mean-square
+                  heights from small-scale altimetric gravity
+                  variability},
+  issn =         {2156-2202},
+  doi =          {10.1029/2010JB007867},
+  volume =       115,
+  number =       {B12},
+  journal =      {Journal of Geophysical Research: Solid Earth},
+  year =         2010,
+  pages =        {B12104},
 }
 
 @ARTICLE{Goosse_al_JGR99,
-  author = {H. Goosse and E. Deleersnijder and T. Fichefet and M. England},
-  title = {Sensitivity of a global coupled ocean-sea ice model to the parameterization of vertical mixing},
-  journal = JGR,
-  year = {1999},
-  volume = {104},
-  pages = {13,681--13,695}
+  author =       {H. Goosse and E. Deleersnijder and T. Fichefet and
+                  M. England},
+  title =        {Sensitivity of a global coupled ocean-sea ice model
+                  to the parameterization of vertical mixing},
+  journal =      JGR,
+  year =         1999,
+  volume =       104,
+  pages =        {13,681--13,695}
 }
 
 @ARTICLE{Gorgues_al_GRL07,
-  author = {T. Gorgues and C. Menkes and O. Aumont and K. Rodgers and G. Madec and Y. Dandonneau},
-  title = {Indonesian Throughflow control of the eastern equatorial Pacific biogeochemistry},
-  journal = GRL,
-  year = {2007},
-  volume = {34},
-  pages = {L05609},
-  doi = {10.1029/2006GL028210},
+  author =       {T. Gorgues and C. Menkes and O. Aumont and
+                  K. Rodgers and G. Madec and Y. Dandonneau},
+  title =        {Indonesian Throughflow control of the eastern
+                  equatorial Pacific biogeochemistry},
+  journal =      GRL,
+  year =         2007,
+  volume =       34,
+  pages =        {L05609},
+  doi =          {10.1029/2006GL028210},
 }
 
 @ARTICLE{Graham_McDougall_JPO13,
-  author = {F.S. Graham and T.J. McDougall},
-  title = {Quantifying the nonconservative production of conservative temperature, potential temperature, and entropy},
-  journal = JPO,
-  year = {2013},
-  volume = {43},
-  pages = {838--862},
-  doi = {10.1175/JPO-D-11-0188.1}
+  author =       {F.S. Graham and T.J. McDougall},
+  title =        {Quantifying the nonconservative production of
+                  conservative temperature, potential temperature, and
+                  entropy},
+  journal =      JPO,
+  year =         2013,
+  volume =       43,
+  pages =        {838--862},
+  doi =          {10.1175/JPO-D-11-0188.1}
 }
 
 @ARTICLE{Greatbatch_JGR94,
-  author = {R. J. Greatbatch},
-  title = {A note on the representation of steric sea level in models that conserve
-	volume rather than mass},
-  journal = JGR,
-  year = {1994},
-  volume = {99},  number = {C6},
-  pages = {12,767--12,771}
+  author =       {R. J. Greatbatch},
+  title =        {A note on the representation of steric sea level in
+                  models that conserve volume rather than mass},
+  journal =      JGR,
+  year =         1994,
+  volume =       99,
+  number =       {C6},
+  pages =        {12,767--12,771}
 }
 
 @BOOK{Griffies_Bk04,
-  title = {Fundamentals of ocean climate models},
-  publisher = {Princeton University Press, 434pp},
-  year = {2004},
-  author = {S.M. Griffies}
+  title =        {Fundamentals of ocean climate models},
+  publisher =    {Princeton University Press, 434pp},
+  year =         2004,
+  author =       {S.M. Griffies}
 }
 
 @ARTICLE{Griffies_JPO98,
-  author = {S.M. Griffies},
-  title = {The Gent-McWilliams skew-flux},
-  journal = JPO,
-  year = {1998},
-  volume = {28},
-  pages = {831--841}
+  author =       {S.M. Griffies},
+  title =        {The Gent-McWilliams skew-flux},
+  journal =      JPO,
+  year =         1998,
+  volume =       28,
+  pages =        {831--841}
 }
 
 @ARTICLE{Griffies_al_OM09,
-  author = {S.M. Griffies and A. Biastoch and C. Boning and F. Bryan and G. Danabasoglu
-	and E. P. Chassignet and M. H. England and R. Gerdes and H. Haak
-	and R. W. Hallberg and W. Hazeleger and J. Jungclaus and W. G. Large
-	and G. Madec and A. Pirani and B. L. Samuels and M. Scheinert and
-	A. Sen Gupta and C. A. Severijns and H. L. Simmons and A.-M. Treguier
-	and M. Winton and S. Yeager and J. Yin},
-  title = {Coordinated Ocean-ice Reference Experiments (COREs)},
-  journal = OM,
-  year = {2009},
-  volume = {26},  number = {1-2},
-  pages = {1--46},
-  doi = {10.1016/j.ocemod.2008.08.007},
+  author =       {S.M. Griffies and A. Biastoch and C. Boning and
+                  F. Bryan and G. Danabasoglu and E. P. Chassignet and
+                  M. H. England and R. Gerdes and H. Haak and
+                  R. W. Hallberg and W. Hazeleger and J. Jungclaus and
+                  W. G. Large and G. Madec and A. Pirani and
+                  B. L. Samuels and M. Scheinert and A. Sen Gupta and
+                  C. A. Severijns and H. L. Simmons and A.-M. Treguier
+                  and M. Winton and S. Yeager and J. Yin},
+  title =        {Coordinated Ocean-ice Reference Experiments (COREs)},
+  journal =      OM,
+  year =         2009,
+  volume =       26,
+  number =       {1-2},
+  pages =        {1--46},
+  doi =          {10.1016/j.ocemod.2008.08.007},
 }
 
 @ARTICLE{Griffies_al_OS05,
-  author = {S.M. Griffies and A. Gnanadesikan and K.W. Dixon and J.P. Dunne and
-	R. Gerdes and M.J. Harrison and A. Rosati and J.L. Russell and B.L.
-	Samuels and M.J. Spelman and M. Winton and R. Zhang},
-  title = {Formulation of an ocean model for global climate simulations},
-  journal = OS,
-  year = {2005},
-  volume = {1},
-  pages = {45--79}
-  }
+  author =       {S.M. Griffies and A. Gnanadesikan and K.W. Dixon and
+                  J.P. Dunne and R. Gerdes and M.J. Harrison and
+                  A. Rosati and J.L. Russell and B.L.  Samuels and
+                  M.J. Spelman and M. Winton and R. Zhang},
+  title =        {Formulation of an ocean model for global climate
+                  simulations},
+  journal =      OS,
+  year =         2005,
+  volume =       1,
+  pages =        {45--79}
+}
 
 @ARTICLE{Griffies_al_JPO98,
-  author = {S.M. Griffies and A. Gnanadesikan and R.C. Pacanowski and V.D. Larichev
-	and J.K. Dukowicz and R.D. Smith},
-  title = {Isoneutral Diffusion in a z-Coordinate Ocean Model},
-  journal = JPO,
-  year = {1998},
-  volume = {28},  number = {5},
-  pages = {805--830},
+  author =       {S.M. Griffies and A. Gnanadesikan and
+                  R.C. Pacanowski and V.D. Larichev and J.K. Dukowicz
+                  and R.D. Smith},
+  title =        {Isoneutral Diffusion in a z-Coordinate Ocean Model},
+  journal =      JPO,
+  year =         1998,
+  volume =       28,
+  number =       5,
+  pages =        {805--830},
 }
 
 @ARTICLE{Griffies_al_MWR01,
-  author = {S.M. Griffies and R.C. Pacanowski and M. Schmidt and V. Balaji},
-  title = {Tracer Conservation with an Explicit Free Surface Method for z-Coordinate
-	Ocean Models},
-  journal = MWR,
-  year = {2001},
-  volume = {129},  number = {5},
-  pages = {1081--1098},
+  author =       {S.M. Griffies and R.C. Pacanowski and M. Schmidt and
+                  V. Balaji},
+  title =        {Tracer Conservation with an Explicit Free Surface
+                  Method for z-Coordinate Ocean Models},
+  journal =      MWR,
+  year =         2001,
+  volume =       129,
+  number =       5,
+  pages =        {1081--1098},
 }
 
 @ARTICLE{Griffies_Hallberg_MWR00,
-  author = {S.M. Griffies and R.W. Hallberg},
-  title = {Biharmonic friction with a Smagorinsky-like viscosity for use in large-scale eddy-permitting ocean models},
-  journal = MWR,
-  year = {2000},
-  volume = {128},  
-  pages = {2935–-2946},
-  doi = {10.1175/1520-0493(2000)128}
+  author =       {S.M. Griffies and R.W. Hallberg},
+  title =        {Biharmonic friction with a Smagorinsky-like
+                  viscosity for use in large-scale eddy-permitting
+                  ocean models},
+  journal =      MWR,
+  year =         2000,
+  volume =       128,
+  pages =        {2935–-2946},
+  doi =          {10.1175/1520-0493(2000)128}
 }
 
 @ARTICLE{Guilyardi_al_JC04,
-  author = {E. Guilyardi and S. Gualdi and J. M. Slingo and A. Navarra and P. Delecluse 
-    and J. Cole and G. Madec and M. Roberts and M. Latif and L. Terray},
-  title = {Representing El Ni\~{n}o in coupled ocean-atmosphere GCMs: the dominant role of the atmospheric component},
-  journal = JC,
-  year = {2004},
-  volume = {17},
-  pages = {4623--4629}
+  author =       {E. Guilyardi and S. Gualdi and J. M. Slingo and
+                  A. Navarra and P. Delecluse and J. Cole and G. Madec
+                  and M. Roberts and M. Latif and L. Terray},
+  title =        {Representing El Ni\~{n}o in coupled ocean-atmosphere
+                  GCMs: the dominant role of the atmospheric
+                  component},
+  journal =      JC,
+  year =         2004,
+  volume =       17,
+  pages =        {4623--4629}
 }
 
 @ARTICLE{Guilyardi_Madec_CD98,
-  author = {E. Guilyardi and G. Madec},
-  title = {Performance of the OPA-ARPEGE-T21 global ocean-atmosphere coupled model},
-  journal = CD,
-  year = {1997},
-  volume = {13},
-  pages = {149--165}
+  author =       {E. Guilyardi and G. Madec},
+  title =        {Performance of the OPA-ARPEGE-T21 global
+                  ocean-atmosphere coupled model},
+  journal =      CD,
+  year =         1997,
+  volume =       13,
+  pages =        {149--165}
 }
 
 @ARTICLE{Guilyardi_al_CD01,
-  author = {E. Guilyardi and G. Madec and L. Terray},
-  title = {The role of lateral ocean physics in the upper ocean thermal balance of a coupled ocean-atmosphere GCM},
-  journal = CD,
-  year = {2001},
-  volume = {17},
-  pages = {589--599},
-  number = {8}
+  author =       {E. Guilyardi and G. Madec and L. Terray},
+  title =        {The role of lateral ocean physics in the upper ocean
+                  thermal balance of a coupled ocean-atmosphere GCM},
+  journal =      CD,
+  year =         2001,
+  volume =       17,
+  pages =        {589--599},
+  number =       8
 }
 
 @ARTICLE{Guilyardi_al_CRAS95,
-  author = {E. Guilyardi and G. Madec and L. Terray and M. D\'{e}qu\'{e} and
-	M. Pontaud and M. Imbard and D. Stephenson and M.-A. Filiberti and
-	D. Cariolle and P. Delecluse and O. Thual},
-  title = {Simulation couplée océan-atmosphère de la variabilité du climat},
-  journal = {C. R. Acad. Sci Paris},
-  year = {1995},
-  volume = {320},  number = {s\'{e}rie IIa},
-  pages = {683--690}
+  author =       {E. Guilyardi and G. Madec and L. Terray and
+                  M. D\'{e}qu\'{e} and M. Pontaud and M. Imbard and
+                  D. Stephenson and M.-A. Filiberti and D. Cariolle
+                  and P. Delecluse and O. Thual},
+  title =        {Simulation couplée océan-atmosphère de la
+                  variabilité du climat},
+  journal =      {C. R. Acad. Sci Paris},
+  year =         1995,
+  volume =       320,
+  number =       {s\'{e}rie IIa},
+  pages =        {683--690}
 }
 
 @ARTICLE{Guyon_al_EP99,
-  author = {M. Guyon and G. Madec and F.-X. Roux and M. Imbard},
-  title = {A Parallel ocean model for high resolution studies},
-  journal = {Lecture Notes in Computer Science},
-  year = {1999},
-  volume = {Euro-Par'99},
-  pages = {603--607}
+  author =       {M. Guyon and G. Madec and F.-X. Roux and M. Imbard},
+  title =        {A Parallel ocean model for high resolution studies},
+  journal =      {Lecture Notes in Computer Science},
+  year =         1999,
+  volume =       {Euro-Par'99},
+  pages =        {603--607}
 }
 
 @ARTICLE{Guyon_al_CalPar99,
-  author = {M. Guyon and G. Madec and F.-X. Roux and M. Imbard and C. Herbaut
-	and P. Fronier},
-  title = {Parallelization of the OPA ocean model},
-  journal = {Calculateurs Paralleles},
-  year = {1999},
-  volume = {11},  number = {4},
-  pages = {499--517}
+  author =       {M. Guyon and G. Madec and F.-X. Roux and M. Imbard
+                  and C. Herbaut and P. Fronier},
+  title =        {Parallelization of the OPA ocean model},
+  journal =      {Calculateurs Paralleles},
+  year =         1999,
+  volume =       11,
+  number =       4,
+  pages =        {499--517}
 }
 
 @BOOK{Haltiner1980,
-  title = {Numerical prediction and dynamic meteorology},
-  publisher = {John Wiley {\&} Sons Eds., second edition},
-  year = {1980},
-  author = {G. J. Haltiner and R. T. Williams},
-  pages = {477pp}
+  title =        {Numerical prediction and dynamic meteorology},
+  publisher =    {John Wiley {\&} Sons Eds., second edition},
+  year =         1980,
+  author =       {G. J. Haltiner and R. T. Williams},
+  pages =        {477pp}
 }
 
 @ARTICLE{Haney1991,
-  author = {R. L. Haney},
-  title = {On the Pressure Gradient Force over Steep Topography in Sigma Coordinate Ocean Models},
-  journal = JPO,
-  year = {1991},
-  volume = {21},  number = {4},
-  pages = {610--619},
+  author =       {R. L. Haney},
+  title =        {On the Pressure Gradient Force over Steep Topography
+                  in Sigma Coordinate Ocean Models},
+  journal =      JPO,
+  year =         1991,
+  volume =       21,
+  number =       4,
+  pages =        {610--619},
 }
 
 @ARTICLE{Hazeleger_Drijfhout_JPO98,
-  author = {W. Hazeleger and S. S. Drijfhout},
-  title = {Mode water variability in a model of the subtropical gyre: response to anomalous forcing},
-  journal = JPO,
-  year = {1998},
-  volume = {28},
-  pages = {266--288},
+  author =       {W. Hazeleger and S. S. Drijfhout},
+  title =        {Mode water variability in a model of the subtropical
+                  gyre: response to anomalous forcing},
+  journal =      JPO,
+  year =         1998,
+  volume =       28,
+  pages =        {266--288},
 }
 
 @ARTICLE{Hazeleger_Drijfhout_JPO99,
-  author = {W. Hazeleger and S. S. Drijfhout},
-  title = {Stochastically forced mode water variability},
-  journal = JPO,
-  year = {1999},
-  volume = {29},
-  pages = {1772--1786},
+  author =       {W. Hazeleger and S. S. Drijfhout},
+  title =        {Stochastically forced mode water variability},
+  journal =      JPO,
+  year =         1999,
+  volume =       29,
+  pages =        {1772--1786},
 }
 
 @ARTICLE{Hazeleger_Drijfhout_JGR00,
-  author = {W. Hazeleger and S. S. Drijfhout},
-  title = {A model study on internally generated variability in subtropical mode water formation},
-  journal = JGR,
-  year = {2000},
-  volume = {105},
-  pages = {13,965--13,979},
-}
+  author =       {W. Hazeleger and S. S. Drijfhout},
+  title =        {A model study on internally generated variability in
+                  subtropical mode water formation},
+  journal =      JGR,
+  year =         2000,
+  volume =       105,
+  pages =        {13,965--13,979},
+}
+
 @ARTICLE{Hazeleger_Drijfhout_JPO00,
-  author = {W. Hazeleger and S. S. Drijfhout},
-  title = {Eddy subduction in a model of the subtropical gyre},
-  journal = JPO,
-  year = {2000},
-  volume = {30},
-  pages = {677--695},
+  author =       {W. Hazeleger and S. S. Drijfhout},
+  title =        {Eddy subduction in a model of the subtropical gyre},
+  journal =      JPO,
+  year =         2000,
+  volume =       30,
+  pages =        {677--695},
 }
 
 @ARTICLE{Hellerman_Rosenstein_JPO83,
-  author = {S. Hellerman and  M. Rosenstein },
-  title = {Normal monthly wind stress over the world ocean with error estimates},
-  journal = JPO,
-  year = {1983},
-  volume = {13},
-  pages = {1093--1104},
+  author =       {S. Hellerman and M. Rosenstein },
+  title =        {Normal monthly wind stress over the world ocean with
+                  error estimates},
+  journal =      JPO,
+  year =         1983,
+  volume =       13,
+  pages =        {1093--1104},
 }
 
 @ARTICLE{He_Ding_JSC01,
-  author = {Y. He and C. H. Q. Ding},
-  title = {Using Accurate Arithmetics to Improve Numerical Reproducibility and Stability in Parallel Applications},
-  journal = JSC,
-  year = {2001},
-  volume = {18},
-  pages = {259--277},
+  author =       {Y. He and C. H. Q. Ding},
+  title =        {Using Accurate Arithmetics to Improve Numerical
+                  Reproducibility and Stability in Parallel
+                  Applications},
+  journal =      JSC,
+  year =         2001,
+  volume =       18,
+  pages =        {259--277},
 }
 
 @ARTICLE{Hirt_al_JCP74,
-  author = {C. W. Hirt and A. A. Amsden and J. L. Cook},
-  title = {An Arbitrary Lagrangian--Eulerian Computing Method for All Flow Speeds},
-  journal = JCP,
-  year = {1974},
-  volume = {14},
-  pages = {227--253}
+  author =       {C. W. Hirt and A. A. Amsden and J. L. Cook},
+  title =        {An Arbitrary Lagrangian--Eulerian Computing Method
+                  for All Flow Speeds},
+  journal =      JCP,
+  year =         1974,
+  volume =       14,
+  pages =        {227--253}
 }
 
 @ARTICLE{Hofmeister_al_OM09,
-  author = {R. Hofmeister and H. Burchard and J.-M. Beckers},
-  title = {Non-uniform adaptive vertical grids for 3D numerical ocean models},
-  journal = OM,
-  year = {2009},
-  volume = {33},
-  pages = {70--86},
-  doi = {10.1016/j.ocemod.2009.12.003},
-  issn = {1463-5003},
-}
-
-@ARTICLE{Holland1999, 
-  author = {D. Holland and A. Jenkins},
-  title = {Modeling Thermodynamic Ice-Ocean Interactions at the Base of an Ice Shelf},
-  journal = JPO,
-  year = {1999},
-  volume = {29},  
-  pages = {1787--1800},
+  author =       {R. Hofmeister and H. Burchard and J.-M. Beckers},
+  title =        {Non-uniform adaptive vertical grids for 3D numerical
+                  ocean models},
+  journal =      OM,
+  year =         2009,
+  volume =       33,
+  pages =        {70--86},
+  doi =          {10.1016/j.ocemod.2009.12.003},
+  issn =         {1463-5003},
+}
+
+@ARTICLE{Holland1999,
+  author =       {D. Holland and A. Jenkins},
+  title =        {Modeling Thermodynamic Ice-Ocean Interactions at the
+                  Base of an Ice Shelf},
+  journal =      JPO,
+  year =         1999,
+  volume =       29,
+  pages =        {1787--1800},
 }
 
 @ARTICLE{HollowayOM86,
-  author = {Greg Holloway},
-  title = {A Shelf Wave/Topographic Pump Drives Mean Coastal Circulation (part I)},
-  journal = OM,
-  year = {1986},
-  volume = {68},  
+  author =       {Greg Holloway},
+  title =        {A Shelf Wave/Topographic Pump Drives Mean Coastal
+                  Circulation (part I)},
+  journal =      OM,
+  year =         1986,
+  volume =       68,
 }
 
 @ARTICLE{HollowayJPO92,
-  author = {Greg Holloway},
-  title = {Representing Topographic Stress for Large-Scale Ocean Models},
-  journal = JPO,
-  year = {1992},
-  volume = {22},  
-  pages = {1033--1046},
+  author =       {Greg Holloway},
+  title =        {Representing Topographic Stress for Large-Scale
+                  Ocean Models},
+  journal =      JPO,
+  year =         1992,
+  volume =       22,
+  pages =        {1033--1046},
 }
 
 @ARTICLE{HollowayJPO94,
-  author = {Michael Eby and Greg Holloway},
-  title = {Sensitivity of a Large-Scale Ocean Model to a Parameterization of Topographic Stress},
-  journal = JPO,
-  year = {1994},
-  volume = {24},  
-  pages = {2577--2587},
+  author =       {Michael Eby and Greg Holloway},
+  title =        {Sensitivity of a Large-Scale Ocean Model to a
+                  Parameterization of Topographic Stress},
+  journal =      JPO,
+  year =         1994,
+  volume =       24,
+  pages =        {2577--2587},
 }
 
 @ARTICLE{HollowayJGR09,
-  author = {Greg Holloway and Zeliang Wang},
-  title = {Representing eddy stress in an Arctic Ocean model},
-  journal = JGR,
-  year = {2009},
-  doi = {10.1029/2008JC005169},  
+  author =       {Greg Holloway and Zeliang Wang},
+  title =        {Representing eddy stress in an Arctic Ocean model},
+  journal =      JGR,
+  year =         2009,
+  doi =          {10.1029/2008JC005169},
 }
 
 @ARTICLE{HollowayOM08,
-  author = {Mathew Maltrud and Greg Holloway},
-  title = {Implementing biharmonic neptune in a global eddying ocean model},
-  journal = OM,
-  year = {2008},
-  volume = {21},  
-  pages = {22--34},
+  author =       {Mathew Maltrud and Greg Holloway},
+  title =        {Implementing biharmonic neptune in a global eddying
+                  ocean model},
+  journal =      OM,
+  year =         2008,
+  volume =       21,
+  pages =        {22--34},
 }
 
 @ARTICLE{Hordoir_al_CD08,
-  author = {R. Hordoir and J. Polcher and J.-C. Brun-Cottan and G. Madec},
-  title = {Towards a parametrization of river discharges into ocean general
-	circulation models: a closure through energy conservation},
-  journal = CD,
-  year = {2008},
-  volume = {31},  number = {7-8},
-  pages = {891--908},
-  doi = {10.1007/s00382-008-0416-4},
+  author =       {R. Hordoir and J. Polcher and J.-C. Brun-Cottan and
+                  G. Madec},
+  title =        {Towards a parametrization of river discharges into
+                  ocean general circulation models: a closure through
+                  energy conservation},
+  journal =      CD,
+  year =         2008,
+  volume =       31,
+  number =       {7-8},
+  pages =        {891--908},
+  doi =          {10.1007/s00382-008-0416-4},
 }
 
 @ARTICLE{Hsu1990,
-  author = {Hsu, Yueh-Jiuan G. and Arakawa, Akio},
-  title = {Numerical Modeling of the Atmosphere with an Isentropic Vertical Coordinate},
-  journal = MWR,
-  year = {1990},
-  volume = {118},  number = {10},
-  pages = {1933--1959},
+  author =       {Hsu, Yueh-Jiuan G. and Arakawa, Akio},
+  title =        {Numerical Modeling of the Atmosphere with an
+                  Isentropic Vertical Coordinate},
+  journal =      MWR,
+  year =         1990,
+  volume =       118,
+  number =       10,
+  pages =        {1933--1959},
 }
 
 @ARTICLE{Huang_JPO93,
-  author = {R.X. Huang},
-  title = {Real freshwater flux as a natural boundary condition for the salinity
-	balance and thermohaline circulation forced by evaporation and precipitation},
-  journal = JPO,
-  year = {1993},
-  volume = {23},
-  pages = {2428--2446}
+  author =       {R.X. Huang},
+  title =        {Real freshwater flux as a natural boundary condition
+                  for the salinity balance and thermohaline
+                  circulation forced by evaporation and precipitation},
+  journal =      JPO,
+  year =         1993,
+  volume =       23,
+  pages =        {2428--2446}
 }
 
 @TECHREPORT{Hunke2008,
-  author = {E.C. Hunke and W.H. Lipscomb},
-  title = {CICE: the Los Alamos sea ice model documentation and software user's manual, 
-        Version 4.0},
-  institution = { Los Alamos National Laboratory, N.M.},
-  publisher = {LA-CC-06-012, Los Alamos National Laboratory, N.M.},
-  year = {2008}
+  author =       {E.C. Hunke and W.H. Lipscomb},
+  title =        {CICE: the Los Alamos sea ice model documentation and
+                  software user's manual, Version 4.0},
+  institution =  { Los Alamos National Laboratory, N.M.},
+  publisher =    {LA-CC-06-012, Los Alamos National Laboratory, N.M.},
+  year =         2008
 }
 
 @TechReport{Hunter2006,
-  Title                    = {Specification for Test Models of Ice Shelf Cavities},
-  Author                   = {J. R. Hunter},
-  Institution              = {Antarctic Climate \& Ecosystems Cooperative Research Centre Private Bag 80, Hobart, Tasmania 7001},
-  Year                     = {2006},
+  Title =        {Specification for Test Models of Ice Shelf Cavities},
+  Author =       {J. R. Hunter},
+  Institution =  {Antarctic Climate \& Ecosystems Cooperative Research
+                  Centre Private Bag 80, Hobart, Tasmania 7001},
+  Year =         2006,
 }
 
 @TECHREPORT{TEOS10,
-  author = {IOC and SCOR and IAPSO},
-  title = {The international thermodynamic equation of seawater - 2010: Calculation and use of thermodynamic properties},
-  institution = {Intergovernmental Oceanographic Commission},
-  publisher = {Manuals and Guides No. 56, UNESCO (English)},
-  year = {2010},
-  pages = {196pp},
-  url = {http://www.teos-10.org/pubs/TEOS-10_Manual.pdf}
+  author =       {IOC and SCOR and IAPSO},
+  title =        {The international thermodynamic equation of seawater
+                  - 2010: Calculation and use of thermodynamic
+                  properties},
+  institution =  {Intergovernmental Oceanographic Commission},
+  publisher =    {Manuals and Guides No. 56, UNESCO (English)},
+  year =         2010,
+  pages =        {196pp},
+  url =          {http://www.teos-10.org/pubs/TEOS-10_Manual.pdf}
 }
 
 @ARTICLE{Iudicone_al_JPO08b,
-  author = {D. Iudicone and G. Madec and B. Blanke and S. Speich},
-  title = {The role of Southern Ocean surface forcings and mixing in the global conveyor},
-  journal = JPO,
-  year = {2008},
-  volume = {38},
-  pages = {1377--1400}
+  author =       {D. Iudicone and G. Madec and B. Blanke and
+                  S. Speich},
+  title =        {The role of Southern Ocean surface forcings and
+                  mixing in the global conveyor},
+  journal =      JPO,
+  year =         2008,
+  volume =       38,
+  pages =        {1377--1400}
 }
 
 @ARTICLE{Iudicone_al_JPO08a,
-  author = {D. Iudicone and G. Madec and T. J. McDougall},
-  title = {Diagnosing water transformations and the key role of light penetration},
-  journal = JPO,
-  year = {2008},
-  volume = {38},
-  pages = {1357--1376}
+  author =       {D. Iudicone and G. Madec and T. J. McDougall},
+  title =        {Diagnosing water transformations and the key role of
+                  light penetration},
+  journal =      JPO,
+  year =         2008,
+  volume =       38,
+  pages =        {1357--1376}
 }
 
 @ARTICLE{Iudicone_al_JPO07,
-  author = {D. Iudicone and K. Rodgers and R. Schopp and G. Madec},
-  title = {An Exchange window for the Antarctic Intermediate Water Injection into the South Pacific},
-  journal = JPO,
-  year = {2007},
-  volume = {37},
-  pages = {31--49}
+  author =       {D. Iudicone and K. Rodgers and R. Schopp and
+                  G. Madec},
+  title =        {An Exchange window for the Antarctic Intermediate
+                  Water Injection into the South Pacific},
+  journal =      JPO,
+  year =         2007,
+  volume =       37,
+  pages =        {31--49}
 }
 
 @ARTICLE{Iudicone_al_JPO08c,
-  author = {D. Iudicone and S. Speich and G. Madec and B. Blanke},
-  title = {The global Conveyor Belt in a Southern Ocean perspective},
-  journal = JPO,
-  year = {2008},
-  volume = {38},
-  pages = {1401--1425}
+  author =       {D. Iudicone and S. Speich and G. Madec and
+                  B. Blanke},
+  title =        {The global Conveyor Belt in a Southern Ocean
+                  perspective},
+  journal =      JPO,
+  year =         2008,
+  volume =       38,
+  pages =        {1401--1425}
 }
 
 @ARTICLE{Izumo_al_CD10,
-  author = {T. Izumo and S.Masson and J. Vialard and C. de Boyer Montegut and
-	S. K. Behera and G. Madec and K. Takahashi and T. Yamagata},
-  title = {Interannual variations of low-frequency Madden-Julian Oscillation in autral summer: Observations},
-  journal = CD,
-  year = {2010},
-  volume = {35},  number = {4},
-  pages = {669--683},
-  doi = {10.1007/s00382-009-0655-z}
+  author =       {T. Izumo and S.Masson and J. Vialard and C. de Boyer
+                  Montegut and S. K. Behera and G. Madec and
+                  K. Takahashi and T. Yamagata},
+  title =        {Interannual variations of low-frequency
+                  Madden-Julian Oscillation in autral summer:
+                  Observations},
+  journal =      CD,
+  year =         2010,
+  volume =       35,
+  number =       4,
+  pages =        {669--683},
+  doi =          {10.1007/s00382-009-0655-z}
 }
 
 @ARTICLE{JackMcD1995,
-  author = {D. R. Jackett and T. J. McDougall},
-  title = {Minimal adjustment of hydrographic data to achieve static stability},
-  journal = JAOT,
-  year = {1995},
-  volume = {12},
-  pages = {381--389}
+  author =       {D. R. Jackett and T. J. McDougall},
+  title =        {Minimal adjustment of hydrographic data to achieve
+                  static stability},
+  journal =      JAOT,
+  year =         1995,
+  volume =       12,
+  pages =        {381--389}
 }
 
 @article{Jackson_Rehmann_JPO2014,
-	author = {P. R. Jackson and C. R. Rehmann},
-	title = {Experiments on differential scalar mixing in turbulence in a sheared, stratified flow},
-	journal = JPO,
-	volume = {44},
-	issn = {0022-3670},
-	doi = {10.1175/JPO-D-14-0027.1},
-	number = {10},
-	year = {2014},
-	pages = {2661--2680},
+  author =       {P. R. Jackson and C. R. Rehmann},
+  title =        {Experiments on differential scalar mixing in
+                  turbulence in a sheared, stratified flow},
+  journal =      JPO,
+  volume =       44,
+  issn =         {0022-3670},
+  doi =          {10.1175/JPO-D-14-0027.1},
+  number =       10,
+  year =         2014,
+  pages =        {2661--2680},
 }
 
 @TECHREPORT{Janssen_al_TM13,
- author = {P.A.E.M. Janssen and {\O}. Breivik and K. Mogensen 
-           and F. Vitart and  M. Balmaseda and J.B. Bidlot and 
-           S. Keeley and M. Leut-becher and L. Magnusson and F. Molteni},
- title = {Air-Sea Interaction and Surface Waves},
- year = {2013},
- volume = {712},
- institution = {ECMWF},
+  author =       {P.A.E.M. Janssen and {\O}. Breivik and K. Mogensen
+                  and F. Vitart and M. Balmaseda and J.B. Bidlot and
+                  S. Keeley and M. Leut-becher and L. Magnusson and
+                  F. Molteni},
+  title =        {Air-Sea Interaction and Surface Waves},
+  year =         2013,
+  volume =       712,
+  institution =  {ECMWF},
 }
 
 @ARTICLE{Jayne_St_Laurent_GRL01,
-  author = {S.R. Jayne and L.C. {St. Laurent}},
-  title = {Parameterizing tidal disspiation over rough topography},
-  journal = GRL,
-  pages = {811--814}
+  author =       {S.R. Jayne and L.C. {St. Laurent}},
+  title =        {Parameterizing tidal disspiation over rough
+                  topography},
+  journal =      GRL,
+  pages =        {811--814}
 }
 
 @ARTICLE{Jenkins1991,
-  author = {A. Jenkins},
-  title = {A one-dimensional model of ice shelf-ocean interaction},
-  journal = JGR,
-  year = {1991},
-  volume = {96},  number = {C11},
-  pages = {2298--2312}
+  author =       {A. Jenkins},
+  title =        {A one-dimensional model of ice shelf-ocean
+                  interaction},
+  journal =      JGR,
+  year =         1991,
+  volume =       96,
+  number =       {C11},
+  pages =        {2298--2312}
 }
 
 @ARTICLE{Jenkins2001,
-  author = {A. Jenkins},
-  title = {The Role of Meltwater Advection in the Formulation of Conservative Boundary Conditions at an Ice-Ocean Interface},
-  journal = JPO,
-  year = {2001},
-  volume = {31},
-  pages = {285--296}
+  author =       {A. Jenkins},
+  title =        {The Role of Meltwater Advection in the Formulation
+                  of Conservative Boundary Conditions at an Ice-Ocean
+                  Interface},
+  journal =      JPO,
+  year =         2001,
+  volume =       31,
+  pages =        {285--296}
 }
 
 @ARTICLE{Jenkins2010,
-  author = {A. Jenkins},
-  title = {observation and parameterization of ablation at the base of Ronne Ice Shelf, Antarctica},
-  journal = JPO,
-  year = {2010},
-  volume = {40},  number = {10},
-  pages = {2298--2312}
+  author =       {A. Jenkins},
+  title =        {observation and parameterization of ablation at the
+                  base of Ronne Ice Shelf, Antarctica},
+  journal =      JPO,
+  year =         2010,
+  volume =       40,
+  number =       10,
+  pages =        {2298--2312}
 }
 
 @BOOK{Jerlov_Bk68,
-  title = {Optical Oceanography},
-  publisher = {Elsevier},
-  year = {1968},
-  author = {N. G. Jerlov},
-  pages = {194pp}
+  title =        {Optical Oceanography},
+  publisher =    {Elsevier},
+  year =         1968,
+  author =       {N. G. Jerlov},
+  pages =        {194pp}
 }
 
 @ARTICLE{Jones_MWR99,
-  author = {P. W. Jones},
-  title = {First- and second-order conservative remapping schemes for grids in spherical coordinates},
-  journal = MWR,
-  year = {1999},
-  volume = {127},
-  pages = {2204--2210}
+  author =       {P. W. Jones},
+  title =        {First- and second-order conservative remapping
+                  schemes for grids in spherical coordinates},
+  journal =      MWR,
+  year =         1999,
+  volume =       127,
+  pages =        {2204--2210}
 }
 
 @BOOK{Jones_Bk01,
-  title = {A User's Guide for SCRIP: A Spherical Coordinate Remapping and Interpolation Package. Version 1.4},
-  publisher = {Los Alamos National Laboratory},
-  year = {2001},
-  author = {P. W. Jones},
-  pages = {27pp},
-  url = {http://climate.lanl.gov/Software/SCRIP/SCRIPusers.pdf}
+  title =        {A User's Guide for SCRIP: A Spherical Coordinate
+                  Remapping and Interpolation Package. Version 1.4},
+  publisher =    {Los Alamos National Laboratory},
+  year =         2001,
+  author =       {P. W. Jones},
+  pages =        {27pp},
+  url =
+                  {http://climate.lanl.gov/Software/SCRIP/SCRIPusers.pdf}
 }
 
 @TECHREPORT{Jones_1998,
-  title = {A User's Guide for SCRIP: A Spherical Coordinate Remapping and Interpolation Package. Version 1.4},
-  institution = {Los Alamos National Laboratory},
-  year = {1998},
-  author = {P. W. Jones},
-  url = {http://climate.lanl.gov/Software/SCRIP/SCRIPusers.pdf}
-} 
+  title =        {A User's Guide for SCRIP: A Spherical Coordinate
+                  Remapping and Interpolation Package. Version 1.4},
+  institution =  {Los Alamos National Laboratory},
+  year =         1998,
+  author =       {P. W. Jones},
+  url =
+                  {http://climate.lanl.gov/Software/SCRIP/SCRIPusers.pdf}
+}
 
 @ARTICLE{Kantha_Clayson_1994,
-  author = {L. H. Kantha and C. A. Clayson},
-  title = {An improved mixed layer model for geophysical applications},
-  journal = JGR,
-  year = {1994},
-  volume = {99},
-  pages = {25,235--25,266}
+  author =       {L. H. Kantha and C. A. Clayson},
+  title =        {An improved mixed layer model for geophysical
+                  applications},
+  journal =      JGR,
+  year =         1994,
+  volume =       99,
+  pages =        {25,235--25,266}
 }
 
 @ARTICLE{Kantha_Carniel_CSR05,
-  author = {L. Kantha and S. Carniel},
-  title = {Comment on ''Generic length-scale equation for geophysical turbulence models'' by L. Umlauf and H. Burchard},
-  journal = JMS, 
-  year = {2005},
-  volume = {61},
-  pages = {693--702}
+  author =       {L. Kantha and S. Carniel},
+  title =        {Comment on ''Generic length-scale equation for
+                  geophysical turbulence models'' by L. Umlauf and
+                  H. Burchard},
+  journal =      JMS,
+  year =         2005,
+  volume =       61,
+  pages =        {693--702}
 }
 
 @ARTICLE{Kasahara_MWR74,
-  author = {A. Kasahara},
-  title = {Various vertical coordinate systems used for numerical weather prediction},
-  journal = MWR,
-  year = {1974},
-  volume = {102},
-  pages = {509--522}
+  author =       {A. Kasahara},
+  title =        {Various vertical coordinate systems used for
+                  numerical weather prediction},
+  journal =      MWR,
+  year =         1974,
+  volume =       102,
+  pages =        {509--522}
 }
 
 @ARTICLE{Killworth_al_JPO91,
-  author = {P.D. Killworth and D. Stainforth and D.J. Webb and S.M. Paterson},
-  title = {The Development of a Free-Surface Bryan-Cox-Semtner Ocean Model},
-  journal = JPO,
-  year = {1991},
-  volume = {21},  number = {9},
-  pages = {1333--1348}
+  author =       {P.D. Killworth and D. Stainforth and D.J. Webb and
+                  S.M. Paterson},
+  title =        {The Development of a Free-Surface Bryan-Cox-Semtner
+                  Ocean Model},
+  journal =      JPO,
+  year =         1991,
+  volume =       21,
+  number =       9,
+  pages =        {1333--1348}
 }
 
 @INPROCEEDINGS{Killworth1989,
-  author = {P. D. Killworth},
-  title = {On the parameterization of deep convection in ocean models},
-  booktitle = {Parameterization of small-scale processes},
-  year = {1989},
-  editor = {Hawaiian winter workshop},
-  month = {January 17-20},
+  author =       {P. D. Killworth},
+  title =        {On the parameterization of deep convection in ocean
+                  models},
+  booktitle =    {Parameterization of small-scale processes},
+  year =         1989,
+  editor =       {Hawaiian winter workshop},
+  month =        {January 17-20},
   organization = {University of Hawaii at Manoa}
 }
 
 @ARTICLE{Killworth1992,
-  author = {P. D. Killworth},
-  title = {An equivalent-barotropic mode in the fine resolution Antarctic model},
-  journal = JPO,
-  year = {1992},
-  volume = {22},
-  pages = {1379--1387}
+  author =       {P. D. Killworth},
+  title =        {An equivalent-barotropic mode in the fine resolution
+                  Antarctic model},
+  journal =      JPO,
+  year =         1992,
+  volume =       22,
+  pages =        {1379--1387}
 }
 
 @ARTICLE{Koch-Larrouy_al_CD10,
-  author = {A. Koch-Larrouy and M. Lengaigne and P. Terray and G. Madec and S. Masson},
-  title = {Tidal mixing in the Indonesian Seas and its effect on the tropical climate system},
-  journal = CD,
-  year = {2010},
-  volume = {34},  number = {6},
-  pages = {891--904},
-  doi = {10.1007/s00382-009-0642-4},
+  author =       {A. Koch-Larrouy and M. Lengaigne and P. Terray and
+                  G. Madec and S. Masson},
+  title =        {Tidal mixing in the Indonesian Seas and its effect
+                  on the tropical climate system},
+  journal =      CD,
+  year =         2010,
+  volume =       34,
+  number =       6,
+  pages =        {891--904},
+  doi =          {10.1007/s00382-009-0642-4},
 }
 
 @ARTICLE{Koch-Larrouy_al_OD08b,
-  author = {A. Koch-Larrouy and G. Madec and B. Blanke and R. Molcard},
-  title = {Water mass transformation along the Indonesian throughflow in an OGCM},
-  journal = OD,
-  year = {2008},
-  volume = {58},  number = {3-4},
-  pages = {289--309},
-  doi = {10.1007/s10236-008-0155-4},
+  author =       {A. Koch-Larrouy and G. Madec and B. Blanke and
+                  R. Molcard},
+  title =        {Water mass transformation along the Indonesian
+                  throughflow in an OGCM},
+  journal =      OD,
+  year =         2008,
+  volume =       58,
+  number =       {3-4},
+  pages =        {289--309},
+  doi =          {10.1007/s10236-008-0155-4},
 }
 
 @ARTICLE{Koch-Larrouy_al_GRL07,
-  author = {A. Koch-Larrouy and G. Madec and P. Bouruet-Aubertot and T. Gerkema and L. Bessieres and R. Molcard},
-  title = {Tidal mixing in the Indonesian Seas and its effect on the tropical climate system},
-  journal = GRL,
-  year = {2007},
-  volume = {34},
-  pages = {L04604},
-  doi = {10.1029/2006GL028405},
+  author =       {A. Koch-Larrouy and G. Madec and P. Bouruet-Aubertot
+                  and T. Gerkema and L. Bessieres and R. Molcard},
+  title =        {Tidal mixing in the Indonesian Seas and its effect
+                  on the tropical climate system},
+  journal =      GRL,
+  year =         2007,
+  volume =       34,
+  pages =        {L04604},
+  doi =          {10.1029/2006GL028405},
 }
 
 @ARTICLE{Koch-Larrouy_al_OD08a,
-  author = {A. Koch-Larrouy and G. Madec and D. Iudicone and A. Atmadipoera and R. Molcard},
-  title = {Physical processes contributing to the water mass transformation of the Indonesian Throughflow},
-  journal = OD,
-  year = {2008},
-  volume = {58},  number = {3-4},
-  pages = {275--288},
-  doi = {10.1007/s10236-008-0154-5},
+  author =       {A. Koch-Larrouy and G. Madec and D. Iudicone and
+                  A. Atmadipoera and R. Molcard},
+  title =        {Physical processes contributing to the water mass
+                  transformation of the Indonesian Throughflow},
+  journal =      OD,
+  year =         2008,
+  volume =       58,
+  number =       {3-4},
+  pages =        {275--288},
+  doi =          {10.1007/s10236-008-0154-5},
 }
 
 @ARTICLE{Kolmogorov1942,
-  author = {A. N. Kolmogorov},
-  title = {The equation of turbulent motion in an incompressible fluid},
-  journal = {Izv. Akad. Nauk SSSR, Ser. Fiz.},
-  year = {1942},
-  volume = {6},
-  pages = {56--58}
-}
+  author =       {A. N. Kolmogorov},
+  title =        {The equation of turbulent motion in an
+                  incompressible fluid},
+  journal =      {Izv. Akad. Nauk SSSR, Ser. Fiz.},
+  year =         1942,
+  volume =       6,
+  pages =        {56--58}
+}
+
 @ARTICLE{Kondo1975,
-  author = {J. Kondo},
-  title = {Air-sea bulk transfer coefficients in diabatic conditions},
-  journal = {Boundary-Layer Meteorol},
-  year = {1975},
-  volume = {9},
-  pages = {91--112}
+  author =       {J. Kondo},
+  title =        {Air-sea bulk transfer coefficients in diabatic
+                  conditions},
+  journal =      {Boundary-Layer Meteorol},
+  year =         1975,
+  volume =       9,
+  pages =        {91--112}
 }
 
 @article{Lemarie_OM2012,
-author = "F. Lemari\'{e} and L. Debreu and A.F. Shchepetkin and J.C. McWilliams",
-title = "On the stability and accuracy of the harmonic and biharmonic isoneutral mixing operators in ocean models ",
-journal = OM,
-year = "2012",
-volume = "52–53", pages = "9--35",
-issn = "1463-5003",
-doi = "http://dx.doi.org/10.1016/j.ocemod.2012.04.007",
-}
-
+  author =       "F. Lemari\'{e} and L. Debreu and A.F. Shchepetkin
+                  and J.C. McWilliams",
+  title =        "On the stability and accuracy of the harmonic and
+                  biharmonic isoneutral mixing operators in ocean
+                  models ",
+  journal =      OM,
+  year =         2012,
+  volume =       "52–53",
+  pages =        "9--35",
+  issn =         "1463-5003",
+  doi =          "http://dx.doi.org/10.1016/j.ocemod.2012.04.007",
+}
 
 @ARTICLE{Lemarie_OM2015,
-  author = {F. Lemari\'{e} and L. Debreu and J. Demange and  G. Madec and J.M. Molines and M. Honnorat},
-  title = {Stability Constraints for Oceanic Numerical Models: 
-           Implications for the Formulation of time and space Discretizations},
-  journal = OM,
-  year = {2015},
-  volume = {92}, 
-  pages = {124--148},
-  doi = {10.1016/j.ocemod.2015.06.006},
+  author =       {F. Lemari\'{e} and L. Debreu and J. Demange and
+                  G. Madec and J.M. Molines and M. Honnorat},
+  title =        {Stability Constraints for Oceanic Numerical Models:
+                  Implications for the Formulation of time and space
+                  Discretizations},
+  journal =      OM,
+  year =         2015,
+  volume =       92,
+  pages =        {124--148},
+  doi =          {10.1016/j.ocemod.2015.06.006},
 }
 
 @ARTICLE{Lermusiaux2001,
-  author = {P. F. J. Lermusiaux},
-  title = {Evolving the subspace of three-dimensional miltiscale ocean variability: Massachusetts Bay},
-  journal = JMS,
-  year = {2001},
-  volume = {29},
-  pages = {385--422}
+  author =       {P. F. J. Lermusiaux},
+  title =        {Evolving the subspace of three-dimensional
+                  miltiscale ocean variability: Massachusetts Bay},
+  journal =      JMS,
+  year =         2001,
+  volume =       29,
+  pages =        {385--422}
 }
 
 @PHDTHESIS{Levy_PhD96,
-  author = {M. L\'{e}vy},
-  title = {Mod\'{e}lisation des processus biog\'{e}ochimiques en M\'{e}diterran\'{e}e
-	        nord-occidentale. Cycle saisonnier et variabilit\'{e} m\'{e}so\'{e}chelle},
-  school = {Universit\'{e} Pierre et Marie Curie, Paris, France, 207pp},
-  year = {1996}
+  author =       {M. L\'{e}vy},
+  title =        {Mod\'{e}lisation des processus biog\'{e}ochimiques
+                  en M\'{e}diterran\'{e}e nord-occidentale. Cycle
+                  saisonnier et variabilit\'{e} m\'{e}so\'{e}chelle},
+  school =       {Universit\'{e} Pierre et Marie Curie, Paris, France,
+                  207pp},
+  year =         1996
 }
 
 @ARTICLE{Levy_al_GRL01,
-  author = {M. L\'{e}vy and A. Estubier and G Madec},
-  title = {Choice of an advection scheme for biogeochemical models},
-  journal = GRL,
-  year = {2001},
-  volume = {28}
+  author =       {M. L\'{e}vy and A. Estubier and G Madec},
+  title =        {Choice of an advection scheme for biogeochemical
+                  models},
+  journal =      GRL,
+  year =         2001,
+  volume =       28
 }
 
 @ARTICLE{Levy_al_OM10,
-  author = {M. L\'{e}vy and P. Klein and A.-M. Tr\'{e}guier and D. Iovino and
-	G. Madec and S. Masson and T. Takahashi},
-  title = {Impacts of sub-mesoscale physics on idealized gyres},
-  journal = OM,
-  year = {2010},
-  volume = {34},  number = {1-2},
-  doi = {10.1016/j.ocemod.2010.04.001},
+  author =       {M. L\'{e}vy and P. Klein and A.-M. Tr\'{e}guier and
+                  D. Iovino and G. Madec and S. Masson and
+                  T. Takahashi},
+  title =        {Impacts of sub-mesoscale physics on idealized gyres},
+  journal =      OM,
+  year =         2010,
+  volume =       34,
+  number =       {1-2},
+  doi =          {10.1016/j.ocemod.2010.04.001},
 }
 
 @ARTICLE{Levy_al_JMS99,
-  author = {M. L\'{e}vy and L. M\'{e}mery and G. Madec},
-  title = {The onset of a bloom after deep winter convection in the Northwestern
-	Mediterranean Sea: mesoscale process study with a primitive equation
-	model},
-  journal = JMS,
-  year = {1999},
-  volume = {16},  number = {1-2},
-  pages = {7--21}
+  author =       {M. L\'{e}vy and L. M\'{e}mery and G. Madec},
+  title =        {The onset of a bloom after deep winter convection in
+                  the Northwestern Mediterranean Sea: mesoscale
+                  process study with a primitive equation model},
+  journal =      JMS,
+  year =         1999,
+  volume =       16,
+  number =       {1-2},
+  pages =        {7--21}
 }
 
 @ARTICLE{Levy_al_DSR98,
-  author = {M. L\'{e}vy and L. M\'{e}mery and G. Madec},
-  title = {The onset of the spring bloom in the MEDOC area: mesoscale spatial
-	variability},
-  journal = DSR,
-  year = {1998},
-  volume = {I},  number = {46},
-  pages = {1137--1160}
+  author =       {M. L\'{e}vy and L. M\'{e}mery and G. Madec},
+  title =        {The onset of the spring bloom in the MEDOC area:
+                  mesoscale spatial variability},
+  journal =      DSR,
+  year =         1998,
+  volume =       {I},
+  number =       46,
+  pages =        {1137--1160}
 }
 
 @ARTICLE{Levy_al_DSR00,
-  author = {M. L\'{e}vy and L. M\'{e}mery and G. Madec},
-  title = {Combined effects of mesoscale processes and atmospheric high-frequency
-	variability on the spring bloom in the MEDOC area},
-  journal = DSR,
-  year = {2000},
-  volume = {47},
-  pages = {527--531}
+  author =       {M. L\'{e}vy and L. M\'{e}mery and G. Madec},
+  title =        {Combined effects of mesoscale processes and
+                  atmospheric high-frequency variability on the spring
+                  bloom in the MEDOC area},
+  journal =      DSR,
+  year =         2000,
+  volume =       47,
+  pages =        {527--531}
 }
 
 @BOOK{Large_Yeager_Rep04,
-  title = {Diurnal to decadal global forcing for ocean and sea-ice models: the data sets and flux climatologies},
-  publisher = {NCAR Technical Note, NCAR/TN-460+STR, CGD Division of the National Center for Atmospheric Research},
-  year = {2004},
-  author = {W. G. Large and S. Yeager}}
+  title =        {Diurnal to decadal global forcing for ocean and
+                  sea-ice models: the data sets and flux
+                  climatologies},
+  publisher =    {NCAR Technical Note, NCAR/TN-460+STR, CGD Division
+                  of the National Center for Atmospheric Research},
+  year =         2004,
+  author =       {W. G. Large and S. Yeager}
+}
 
 @ARTICLE{Large_al_RG94,
-  author = {W. G. Large and J. C. McWilliams and S. C. Doney},
-  title = {Oceanic vertical mixing - a review and a model with a nonlocal boundary layer parameterization},
-  journal = {Reviews of Geophysics},
-  year = {1994},
-  volume = {32},
-  pages = {363--404},
-  doi = {10.1029/94RG01872},
+  author =       {W. G. Large and J. C. McWilliams and S. C. Doney},
+  title =        {Oceanic vertical mixing - a review and a model with
+                  a nonlocal boundary layer parameterization},
+  journal =      {Reviews of Geophysics},
+  year =         1994,
+  volume =       32,
+  pages =        {363--404},
+  doi =          {10.1029/94RG01872},
 }
 
 @ARTICLE{Latif_al_JC06,
-  author = {M. Latif and C. Böning and J. Willebrand and A. Biastoch and J. Dengg
-	and N. Keenlyside and U. Schweckendiek and G. Madec},
-  title = {Is the Thermohaline Circulation Changing?},
-  journal = JC,
-  year = {2006},
-  volume = {19},
-  pages = {4631--4637}
+  author =       {M. Latif and C. Böning and J. Willebrand and
+                  A. Biastoch and J. Dengg and N. Keenlyside and
+                  U. Schweckendiek and G. Madec},
+  title =        {Is the Thermohaline Circulation Changing?},
+  journal =      JC,
+  year =         2006,
+  volume =       19,
+  pages =        {4631--4637}
 }
 
 @PHDTHESIS{Lazar_PhD97,
-  author = {A. Lazar},
-  title = {La branche froide de la circulation thermohaline - sensibilit\'{e}
-	\`{a} la diffusion turbulente dans un mod\`{e}le de circulation g\'{e}n\'{e}rale
-	id\'{e}alis\'{e}e},
-  school = {Universit\'{e} Pierre et Marie Curie, Paris, France, 200pp},
-  year = {1997}
+  author =       {A. Lazar},
+  title =        {La branche froide de la circulation thermohaline -
+                  sensibilit\'{e} \`{a} la diffusion turbulente dans
+                  un mod\`{e}le de circulation g\'{e}n\'{e}rale
+                  id\'{e}alis\'{e}e},
+  school =       {Universit\'{e} Pierre et Marie Curie, Paris, France,
+                  200pp},
+  year =         1997
 }
 
 @ARTICLE{Lazar_al_JPO99,
-  author = {A. Lazar and G. Madec and P. Delecluse},
-  title = {The Deep Interior Downwelling, the Veronis Effect, and Mesoscale
-	Tracer Transport Parameterizations in an OGCM},
-  journal = JPO,
-  year = {1999},
-  volume = {29},  number = {11},
-  pages = {2945--2961},
+  author =       {A. Lazar and G. Madec and P. Delecluse},
+  title =        {The Deep Interior Downwelling, the Veronis Effect,
+                  and Mesoscale Tracer Transport Parameterizations in
+                  an OGCM},
+  journal =      JPO,
+  year =         1999,
+  volume =       29,
+  number =       11,
+  pages =        {2945--2961},
 }
 
 @ARTICLE{Le_Sommer_al_OM09,
-  author = {J. {Le Sommer} and T. Penduff and S. Theetten and G. Madec and B.
-	Barnier},
-  title = {How momentum advection schemes influence current-topography interactions
-	at eddy permitting resolution},
-  journal = OM,
-  year = {2009},
-  volume = {29},  number = {1},
-  pages = {1--14},
-  doi = {10.1016/j.ocemod.2008.11.007},
+  author =       {J. {Le Sommer} and T. Penduff and S. Theetten and
+                  G. Madec and B.  Barnier},
+  title =        {How momentum advection schemes influence
+                  current-topography interactions at eddy permitting
+                  resolution},
+  journal =      OM,
+  year =         2009,
+  volume =       29,
+  number =       1,
+  pages =        {1--14},
+  doi =          {10.1016/j.ocemod.2008.11.007},
 }
 
 @PHDTHESIS{Leclair_PhD2010,
-  author = {M. Leclair},
-  title = {introduction d'une coordonn\'{e}e verticale arbitrairement Lagrangienne
-	Eul\'{e}rienne dans le code NEMO, 180pp.},
-  school = {Universit\'{e} Pierre and Marie Curie},
-  year = {2010}
+  author =       {M. Leclair},
+  title =        {introduction d'une coordonn\'{e}e verticale
+                  arbitrairement Lagrangienne Eul\'{e}rienne dans le
+                  code NEMO, 180pp.},
+  school =       {Universit\'{e} Pierre and Marie Curie},
+  year =         2010
 }
 
 @ARTICLE{Leclair_Madec_OM09,
-  author = {M. Leclair and G. Madec},
-  title = {A conservative leap-frog time stepping method},
-  journal = OM,
-  year = {2009},
-  volume = {30},  number = {2-3},
-  pages = {88-94},
-  doi = {10.1016/j.ocemod.2009.06.006},
+  author =       {M. Leclair and G. Madec},
+  title =        {A conservative leap-frog time stepping method},
+  journal =      OM,
+  year =         2009,
+  volume =       30,
+  number =       {2-3},
+  pages =        {88-94},
+  doi =          {10.1016/j.ocemod.2009.06.006},
 }
 
 @ARTICLE{Leclair_Madec_OM11,
-  author = {M. Leclair and G. Madec},
-  title = {$\tilde{z}$-coordinate, an Arbitrary Lagrangian-Eulerian coordinate separating high and low frequency},
-  journal = OM,
-  year = {2011},
-  volume = {37},  pages = {139--152}, 
-  doi = {10.1016/j.ocemod.2011.02.001},
+  author =       {M. Leclair and G. Madec},
+  title =        {$\tilde{z}$-coordinate, an Arbitrary
+                  Lagrangian-Eulerian coordinate separating high and
+                  low frequency},
+  journal =      OM,
+  year =         2011,
+  volume =       37,
+  pages =        {139--152},
+  doi =          {10.1016/j.ocemod.2011.02.001},
 }
 
 @ARTICLE{Lele_JCP1992,
-  author = {S.K. Lele},
-  title = {Compact finite difference schemes with spectral-like resolution},
-  journal = JCP,
-  year = {1992},
-  volume = {103}, pages = {16--42}
+  author =       {S.K. Lele},
+  title =        {Compact finite difference schemes with spectral-like
+                  resolution},
+  journal =      JCP,
+  year =         1992,
+  volume =       103,
+  pages =        {16--42}
 }
 
 @ARTICLE{Lengaigne_al_JC03,
-  author = {M. Lengaigne and J.-P. Boulanger and C. Menkes and G. Madec and P.
-	Delecluse and E. Guilyardi, and J. Slingo},
-  title = {The March 1997 Westerly Wind Event and the onset of the 1997/98 El
-	Niño: Understanding the role of the atmospheric},
-  journal = JC,
-  year = {2003},
-  volume = {16},  number = {20}, pages = {3330--3343}
+  author =       {M. Lengaigne and J.-P. Boulanger and C. Menkes and
+                  G. Madec and P.  Delecluse and E. Guilyardi, and
+                  J. Slingo},
+  title =        {The March 1997 Westerly Wind Event and the onset of
+                  the 1997/98 El Niño: Understanding the role of the
+                  atmospheric},
+  journal =      JC,
+  year =         2003,
+  volume =       16,
+  number =       20,
+  pages =        {3330--3343}
 }
 
 @ARTICLE{Lengaigne_al_JGR02,
-  author = {M. Lengaigne and J.-P. Boulanger and C. Menkes and S. Masson and
-	G. Madec and P. Delecluse},
-  title = {Ocean response to the March 1997 Westerly Wind Event},
-  journal = JGR,
-  year = {2002},
-  doi = {10.1029/2001JC000841},
+  author =       {M. Lengaigne and J.-P. Boulanger and C. Menkes and
+                  S. Masson and G. Madec and P. Delecluse},
+  title =        {Ocean response to the March 1997 Westerly Wind
+                  Event},
+  journal =      JGR,
+  year =         2002,
+  doi =          {10.1029/2001JC000841},
 }
 
 @ARTICLE{Lengaigne_al_JGR03,
-  author = {M. Lengaigne and G. Madec and G. Alory and C. Menkes},
-  title = {Sensitivity of the tropical Pacific Ocean to isopycnal diffusion
-	on tracer and dynamics},
-  journal = JGR,
-  year = {2003},
-  volume = {108},  number = {C11},
-  pages = {3345},
-  doi = {10.1029/2002JC001704},
+  author =       {M. Lengaigne and G. Madec and G. Alory and
+                  C. Menkes},
+  title =        {Sensitivity of the tropical Pacific Ocean to
+                  isopycnal diffusion on tracer and dynamics},
+  journal =      JGR,
+  year =         2003,
+  volume =       108,
+  number =       {C11},
+  pages =        3345,
+  doi =          {10.1029/2002JC001704},
 }
 
 @ARTICLE{Lengaigne_al_GRL09,
-  author = {M. Lengaigne and G. Madec and L. Bopp and C. Menkes and O. Aumont and P. Cadule},
-  title = {Bio-physical feedbacks in the Arctic Ocean using an Earth System model},
-  journal = GRL,
-  year = {2009},
-  volume = {36},  
-  pages = {L21602},
-  doi = {10.1029/2009GL040145},
+  author =       {M. Lengaigne and G. Madec and L. Bopp and C. Menkes
+                  and O. Aumont and P. Cadule},
+  title =        {Bio-physical feedbacks in the Arctic Ocean using an
+                  Earth System model},
+  journal =      GRL,
+  year =         2009,
+  volume =       36,
+  pages =        {L21602},
+  doi =          {10.1029/2009GL040145},
 }
 
 @ARTICLE{Lengaigne_al_CD07,
-  author = {M. Lengaigne and C. Menkes and O. Aumont and T. Gorgues and L. Bopp and J.-M. Andr\'{e} G. Madec},
-  title = {Bio-physical feedbacks on the tropical Pacific climate in a Coupled
-	General Circulation Model},
-  journal = CD,
-  year = {2007},
-  volume = {28},
-  pages = {503--516}
+  author =       {M. Lengaigne and C. Menkes and O. Aumont and
+                  T. Gorgues and L. Bopp and J.-M. Andr\'{e} G. Madec},
+  title =        {Bio-physical feedbacks on the tropical Pacific
+                  climate in a Coupled General Circulation Model},
+  journal =      CD,
+  year =         2007,
+  volume =       28,
+  pages =        {503--516}
 }
 
 @ARTICLE{Leonard1991,
-  author = {B. P. Leonard},
-  title = {The ULTIMATE conservative difference scheme applied to unsteady one--dimensional advection},
-  journal = {Computer Methods in Applied Mechanics and Engineering},
-  year = {1991},
-  pages = {17--74}
+  author =       {B. P. Leonard},
+  title =        {The ULTIMATE conservative difference scheme applied
+                  to unsteady one--dimensional advection},
+  journal =      {Computer Methods in Applied Mechanics and
+                  Engineering},
+  year =         1991,
+  pages =        {17--74}
 }
 
 @TECHREPORT{Leonard_Rep88,
-  author = {B. P. Leonard},
-  title = {Universal limiter for transient interpolation modelling of the advective transport equations},
-  institution = {Technical Memorandum TM-100916 ICOMP-88-11, NASA},
-  year = {1988}
+  author =       {B. P. Leonard},
+  title =        {Universal limiter for transient interpolation
+                  modelling of the advective transport equations},
+  institution =  {Technical Memorandum TM-100916 ICOMP-88-11, NASA},
+  year =         1988
 }
 
 @ARTICLE{Leonard1979,
-  author = {B. P. Leonard},
-  title = {A stable and accurate convective modelling procedure based on quadratic
-	upstream interpolation},
-  journal = {Computer Methods in Applied Mechanics and Engineering},
-  year = {1979},
-  volume = {19},
-  pages = {59--98},
+  author =       {B. P. Leonard},
+  title =        {A stable and accurate convective modelling procedure
+                  based on quadratic upstream interpolation},
+  journal =      {Computer Methods in Applied Mechanics and
+                  Engineering},
+  year =         1979,
+  volume =       19,
+  pages =        {59--98},
 }
 
 @TECHREPORT{Levier2007,
-  author = {B. Levier and A.-M. Tr\'{e}guier and G. Madec and V. Garnier},
-  title = {Free surface and variable volume in the NEMO code},
-  institution = {MERSEA MERSEA IP report WP09-CNRS-STR-03-1A, 47pp, available on the
-	NEMO web site},
-  year = {2007}
+  author =       {B. Levier and A.-M. Tr\'{e}guier and G. Madec and
+                  V. Garnier},
+  title =        {Free surface and variable volume in the NEMO code},
+  institution =  {MERSEA MERSEA IP report WP09-CNRS-STR-03-1A, 47pp,
+                  available on the NEMO web site},
+  year =         2007
 }
 
 @BOOK{levitus82,
-  title = {Climatological Atlas of the world ocean},
-  publisher = {NOAA professional paper No. 13, 174pp},
-  year = {1982},
-  author = {S Levitus },
-  pages = {173 pp}
-}
-
-@ARTICLE{Li_al_OM2017},
+  title =        {Climatological Atlas of the world ocean},
+  publisher =    {NOAA professional paper No. 13, 174pp},
+  year =         1982,
+  author =       {S Levitus },
+  pages =        {173 pp}
+}
+
+@ARTICLE{Li_al_OM2017
+},
    AUTHOR = {Q Li and B Fox-Kemper and {\O} Breivik and A Webb},
    YEAR = {2017},
@@ -2139,1283 +2459,1443 @@
 
 @ARTICLE{Li_Garrett_JMR93,
-  author = {M. Li and C. Garrett},
-  title = {Cell merging and the jet/downwelling ratio in Langmuir circulation},
-  journal = JMR,
-  year = {1993},
-  volume = {51},
-  pages = {737--769}
+  author =       {M. Li and C. Garrett},
+  title =        {Cell merging and the jet/downwelling ratio in
+                  Langmuir circulation},
+  journal =      JMR,
+  year =         1993,
+  volume =       51,
+  pages =        {737--769}
 }
 
 @ARTICLE{Losch2008,
-  author = {M. Losch},
-  title = {Modeling ice shelf cavities in a z coordinate ocean general circulation model},
-  journal = JGR,
-  year = {2008},
-  volume = {113},  number = {C13},
+  author =       {M. Losch},
+  title =        {Modeling ice shelf cavities in a z coordinate ocean
+                  general circulation model},
+  journal =      JGR,
+  year =         2008,
+  volume =       113,
+  number =       {C13},
 }
 
 @TECHREPORT{Lott1989,
-  author = {F. Lott and G. Madec},
-  title = {Implementation of bottom topography in the Ocean General Circulation
-	Model OPA of the LODYC: formalism and experiments.},
-  institution = {LODYC, France, 36pp.},
-  year = {1989},
-  number = {3}
+  author =       {F. Lott and G. Madec},
+  title =        {Implementation of bottom topography in the Ocean
+                  General Circulation Model OPA of the LODYC:
+                  formalism and experiments.},
+  institution =  {LODYC, France, 36pp.},
+  year =         1989,
+  number =       3
 }
 
 @ARTICLE{Lott_al_OM90,
-  author = {F. Lott and G. Madec and J. Verron},
-  title = {Topographic experiments in an Ocean General Circulation Model},
-  journal = OM,
-  year = {1990},
-  volume = {88},
-  pages = {1--4}
+  author =       {F. Lott and G. Madec and J. Verron},
+  title =        {Topographic experiments in an Ocean General
+                  Circulation Model},
+  journal =      OM,
+  year =         1990,
+  volume =       88,
+  pages =        {1--4}
 }
 
 @ARTICLE{Luo_al_JC05,
-  author = {J.-J. Luo and S. Masson and E. Roeckner and G. Madec and T. Yamagata},
-  title = {Reducing climatology bias in an ocean-atmosphere CGCM with improved
-	coupling physics},
-  journal = JC,
-  year = {2005},
-  volume = {18},  number = {13},
-  pages = {2344--2360}
+  author =       {J.-J. Luo and S. Masson and E. Roeckner and G. Madec
+                  and T. Yamagata},
+  title =        {Reducing climatology bias in an ocean-atmosphere
+                  CGCM with improved coupling physics},
+  journal =      JC,
+  year =         2005,
+  volume =       18,
+  number =       13,
+  pages =        {2344--2360}
 }
 
 @BOOK{Madec_Bk08,
-  title = {NEMO ocean engine},
-  publisher = {Note du P\^ole de mod\'{e}lisation, Institut Pierre-Simon Laplace
-	(IPSL), France, No 27, ISSN No 1288-1619},
-  year = {2008},
-  author = {G. Madec}
+  title =        {NEMO ocean engine},
+  publisher =    {Note du P\^ole de mod\'{e}lisation, Institut
+                  Pierre-Simon Laplace (IPSL), France, No 27, ISSN No
+                  1288-1619},
+  year =         2008,
+  author =       {G. Madec}
 }
 
 @BOOK{Madec_HDR01,
-  title = {Le Cycle des Masses d'Eau Oc\'{e}aniqueset sa variabilit\'{e} dans le Syst\'{e}me Climatique},
-  year = {2001},
-  author = {G. Madec},
-  pages = {63pp.},
-  series = {Habilitation \'{a} Diriger des Recherches, Universit\'{e} Pierre et Marie Curie}
+  title =        {Le Cycle des Masses d'Eau Oc\'{e}aniqueset sa
+                  variabilit\'{e} dans le Syst\'{e}me Climatique},
+  year =         2001,
+  author =       {G. Madec},
+  pages =        {63pp.},
+  series =       {Habilitation \'{a} Diriger des Recherches,
+                  Universit\'{e} Pierre et Marie Curie}
 }
 
 @PHDTHESIS{Madec_PhD90,
-  author = {G. Madec},
-  title = {La formation d'eau profonde et son impact sur la circulation r\'{e}gionale
-	en M\'{e}diterran\'{e}e Occidentale - une approche num\'{e}rique},
-  school = {Universit\'{e} Pierre et Marie Curie, Paris, France, 194pp.},
-  year = {1990},
-  month = {2 mai}
+  author =       {G. Madec},
+  title =        {La formation d'eau profonde et son impact sur la
+                  circulation r\'{e}gionale en M\'{e}diterran\'{e}e
+                  Occidentale - une approche num\'{e}rique},
+  school =       {Universit\'{e} Pierre et Marie Curie, Paris, France,
+                  194pp.},
+  year =         1990,
+  month =        {2 mai}
 }
 
 @ARTICLE{Madec_al_DAO91,
-  author = {G. Madec and M. Chartier and M. Cr\'{e}pon},
-  title = {Effect of thermohaline forcing variability on deep water formation
-	in the Northwestern Mediterranean Sea - a high resulution three-dimensional
-	study},
-  journal = DAO,
-  year = {1991},
-  volume = {15},
-  pages = {301--332}
+  author =       {G. Madec and M. Chartier and M. Cr\'{e}pon},
+  title =        {Effect of thermohaline forcing variability on deep
+                  water formation in the Northwestern Mediterranean
+                  Sea - a high resulution three-dimensional study},
+  journal =      DAO,
+  year =         1991,
+  volume =       15,
+  pages =        {301--332}
 }
 
 @ARTICLE{Madec_al_JPO91,
-  author = {G. Madec and M. Chartier and P. Delecluse and M. Cr\'{e}pon},
-  title = {A three-dimensional numerical study of deep water formation in the Northwestern Mediterranean Sea .},
-  journal = JPO,
-  year = {1991},
-  volume = {21},
-  pages = {1349--1371}
+  author =       {G. Madec and M. Chartier and P. Delecluse and
+                  M. Cr\'{e}pon},
+  title =        {A three-dimensional numerical study of deep water
+                  formation in the Northwestern Mediterranean Sea .},
+  journal =      JPO,
+  year =         1991,
+  volume =       21,
+  pages =        {1349--1371}
 }
 
 @INBOOK{Madec_Crepon_Bk91,
-  chapter = {Thermohaline-driven deep water formation in the Northwestern Mediterranean
-	Sea},
-  pages = {241--265},
-  title = {Deep convection and deep water formation in the oceans},
-  publisher = {Elsevier Oceanographic Series, P.C. Chu and J.C. Gascard (Eds.)},
-  year = {1991},
-  author = {G. Madec and M. Cr\'{e}pon}
+  chapter =      {Thermohaline-driven deep water formation in the
+                  Northwestern Mediterranean Sea},
+  pages =        {241--265},
+  title =        {Deep convection and deep water formation in the
+                  oceans},
+  publisher =    {Elsevier Oceanographic Series, P.C. Chu and
+                  J.C. Gascard (Eds.)},
+  year =         1991,
+  author =       {G. Madec and M. Cr\'{e}pon}
 }
 
 @ARTICLE{Madec1997,
-  author = {G. Madec and P. Delecluse},
-  title = {The OPA/ARPEGE and OPA/LMD Global Ocean-Atmosphere Coupled Model},
-  journal = {Int. WOCE Newsletter},
-  year = {1997},
-  volume = {26},
-  pages = {12--15}
+  author =       {G. Madec and P. Delecluse},
+  title =        {The OPA/ARPEGE and OPA/LMD Global Ocean-Atmosphere
+                  Coupled Model},
+  journal =      {Int. WOCE Newsletter},
+  year =         1997,
+  volume =       26,
+  pages =        {12--15}
 }
 
 @TECHREPORT{Madec1998,
-  author = {G. Madec and P. Delecluse and M. Imbard and C. Levy},
-  title = {OPA 8 Ocean General Circulation Model - Reference Manual},
-  institution = {LODYC/IPSL Note 11},
-  year = {1998}
+  author =       {G. Madec and P. Delecluse and M. Imbard and C. Levy},
+  title =        {OPA 8 Ocean General Circulation Model - Reference
+                  Manual},
+  institution =  {LODYC/IPSL Note 11},
+  year =         1998
 }
 
 @ARTICLE{Madec_Imbard_CD96,
-  author = {G Madec and M Imbard},
-  title = {A global ocean mesh to overcome the north pole singularity},
-  journal = CD,
-  year = {1996},
-  volume = {12},
-  pages = {381--388}
+  author =       {G Madec and M Imbard},
+  title =        {A global ocean mesh to overcome the north pole
+                  singularity},
+  journal =      CD,
+  year =         1996,
+  volume =       12,
+  pages =        {381--388}
 }
 
 @ARTICLE{Madec_al_JPO96,
-  author = {G. Madec and F. Lott and P. Delecluse and M. Cr\'{e}pon},
-  title = {Large-Scale Preconditioning of Deep-Water Formation in the Northwestern
-	Mediterranean Sea},
-  journal = JPO,
-  year = {1996},
-  volume = {26},  number = {8},
-  pages = {1393--1408},
+  author =       {G. Madec and F. Lott and P. Delecluse and
+                  M. Cr\'{e}pon},
+  title =        {Large-Scale Preconditioning of Deep-Water Formation
+                  in the Northwestern Mediterranean Sea},
+  journal =      JPO,
+  year =         1996,
+  volume =       26,
+  number =       8,
+  pages =        {1393--1408},
 }
 
 @ARTICLE{Madec_al_OM88,
-  author = {G. Madec and C. Rahier and M. Chartier},
-  title = {A comparison of two-dimensional elliptic solvers for the streamfunction
-	in a multilevel OGCM},
-  journal = OM,
-  year = {1988},
-  volume = {78},
-  pages = {1-6}
+  author =       {G. Madec and C. Rahier and M. Chartier},
+  title =        {A comparison of two-dimensional elliptic solvers for
+                  the streamfunction in a multilevel OGCM},
+  journal =      OM,
+  year =         1988,
+  volume =       78,
+  pages =        {1-6}
 }
 
 @ARTICLE{Maes_al_CD98,
-  author = {C. Maes and P. Delecluse and G. Madec},
-  title = {Impact of westerly wind bursts on the warm pool of the TOGA-COARE
-	domain in an OGCM},
-  journal = CD,
-  year = {1998},
-  volume = {14},
-  pages = {55--70}
+  author =       {C. Maes and P. Delecluse and G. Madec},
+  title =        {Impact of westerly wind bursts on the warm pool of
+                  the TOGA-COARE domain in an OGCM},
+  journal =      CD,
+  year =         1998,
+  volume =       14,
+  pages =        {55--70}
 }
 
 @ARTICLE{Maes_al_MWR97,
-  author = {C. Maes and G. Madec and P. Delecluse},
-  title = {Sensitivity of an Equatorial Pacific OGCM to the lateral diffusion},
-  journal = MWR,
-  year = {1997},
-  volume = {125},  number = {5},
-  pages = {958--971}
+  author =       {C. Maes and G. Madec and P. Delecluse},
+  title =        {Sensitivity of an Equatorial Pacific OGCM to the
+                  lateral diffusion},
+  journal =      MWR,
+  year =         1997,
+  volume =       125,
+  number =       5,
+  pages =        {958--971}
 }
 
 @ARTICLE{Maggiore_al_PCE98,
-  author = {A. Maggiore and  M. Zavatarelli and M. G. Angelucci and N. Pinardi},
-  title = {Surface heat and water fluxes in the Adriatic Sea: seasonal and interannual variability},
-  journal = {Phys Chem Earth},
-  year = {1998},
-  volume = {23},
-  pages = {561--567}
+  author =       {A. Maggiore and M. Zavatarelli and M. G. Angelucci
+                  and N. Pinardi},
+  title =        {Surface heat and water fluxes in the Adriatic Sea:
+                  seasonal and interannual variability},
+  journal =      {Phys Chem Earth},
+  year =         1998,
+  volume =       23,
+  pages =        {561--567}
 }
 
 @ARTICLE{Maltrud1998,
-  author = {M. E. Maltrud and R. D. Smith and A. J. Semtner and R. C. Malone},
-  title = {Global eddy-resolving ocean simulations driven by 1985-1995 atmospheric
-	winds},
-  journal = JGR,
-  year = {1998},
-  volume = {103},  number = {C13},
-  pages = {30,825--30,854}
+  author =       {M. E. Maltrud and R. D. Smith and A. J. Semtner and
+                  R. C. Malone},
+  title =        {Global eddy-resolving ocean simulations driven by
+                  1985-1995 atmospheric winds},
+  journal =      JGR,
+  year =         1998,
+  volume =       103,
+  number =       {C13},
+  pages =        {30,825--30,854}
 }
 
 @ARTICLE{Marchesiello2001,
-  author = { P. Marchesiello and J. Mc Williams and A. Shchepetkin },
-  title = {Open boundary conditions for long-term integrations of Regional Oceanic
-	Models},
-  journal = OM,
-  year = {2001},
-  volume = {3},
-  pages = {1--20}
+  author =       { P. Marchesiello and J. Mc Williams and
+                  A. Shchepetkin },
+  title =        {Open boundary conditions for long-term integrations
+                  of Regional Oceanic Models},
+  journal =      OM,
+  year =         2001,
+  volume =       3,
+  pages =        {1--20}
 }
 
 @ARTICLE{Marsaleix_al_OM08,
-  author = {P. Marsaleix and F. Auclair and J. W. Floor and M. J. Herrmann and
-	C. Estournel and I. Pairaud and C. Ulses},
-  title = {Energy conservation issues in sigma-coordinate free-surface ocean
-	models},
-  journal = OM,
-  year = {2008},
-  volume = {20},  number = {1},
-  pages = {61--89},
-  doi = {10.1016/j.ocemod.2007.07.005},
+  author =       {P. Marsaleix and F. Auclair and J. W. Floor and
+                  M. J. Herrmann and C. Estournel and I. Pairaud and
+                  C. Ulses},
+  title =        {Energy conservation issues in sigma-coordinate
+                  free-surface ocean models},
+  journal =      OM,
+  year =         2008,
+  volume =       20,
+  number =       1,
+  pages =        {61--89},
+  doi =          {10.1016/j.ocemod.2007.07.005},
 }
 
 @Article{Marsh_GMD2015,
-AUTHOR = {R. Marsh and V. O. Ivchenko and N. Skliris and S. Alderson and G. R. Bigg and G. Madec and A. T. Blaker and Y. Aksenov and B. Sinha and A. C. Coward and J. Le Sommer and N. Merino and V. B. Zalesny},
-TITLE = {NEMO-ICB (v1.0): interactive icebergs in the NEMO ocean model globally configured at eddy-permitting resolution},
-JOURNAL = {Geoscientific Model Development},
-VOLUME = {8},
-YEAR = {2015},
-NUMBER = {5},
-PAGES = {1547--1562},
-DOI = {10.5194/gmd-8-1547-2015}
+  AUTHOR =       {R. Marsh and V. O. Ivchenko and N. Skliris and
+                  S. Alderson and G. R. Bigg and G. Madec and
+                  A. T. Blaker and Y. Aksenov and B. Sinha and
+                  A. C. Coward and J. Le Sommer and N. Merino and
+                  V. B. Zalesny},
+  TITLE =        {NEMO-ICB (v1.0): interactive icebergs in the NEMO
+                  ocean model globally configured at eddy-permitting
+                  resolution},
+  JOURNAL =      {Geoscientific Model Development},
+  VOLUME =       8,
+  YEAR =         2015,
+  NUMBER =       5,
+  PAGES =        {1547--1562},
+  DOI =          {10.5194/gmd-8-1547-2015}
 }
 
 @article{Martin_Adcroft_OM10,
-author = {T. Martin and A. Adcroft},
-title = {Parameterizing the fresh-water flux from land ice to ocean with interactive icebergs in a coupled climate model},
-journal = OM,
-year = {2010},
-volume = {34}, number = {3--4},
-pages = {111--124},
-issn = {1463-5003},
-doi = {10.1016/j.ocemod.2010.05.001},
+  author =       {T. Martin and A. Adcroft},
+  title =        {Parameterizing the fresh-water flux from land ice to
+                  ocean with interactive icebergs in a coupled climate
+                  model},
+  journal =      OM,
+  year =         2010,
+  volume =       34,
+  number =       {3--4},
+  pages =        {111--124},
+  issn =         {1463-5003},
+  doi =          {10.1016/j.ocemod.2010.05.001},
 }
 
 @BOOK{MIT-GCM_2004,
-  title = {MIT-gcm User Manual},
-  year = {2004},
-  editor = {MIT Department of EAPS},
-  author = {J. Marshall and A. Adcroft and J.-M. Campin and P. Heimbach and A.
-	Molod and S. Dutkiewicz and H. Hill and M. Losch and B. Fox-Kemper
-	and D. Menemenlis and D. Ferreira and E. Hill and M. Follows and
-	C. Hill and C. Evangelinos and G. Forget}
-	}
+  title =        {MIT-gcm User Manual},
+  year =         2004,
+  editor =       {MIT Department of EAPS},
+  author =       {J. Marshall and A. Adcroft and J.-M. Campin and
+                  P. Heimbach and A.  Molod and S. Dutkiewicz and
+                  H. Hill and M. Losch and B. Fox-Kemper and
+                  D. Menemenlis and D. Ferreira and E. Hill and
+                  M. Follows and C. Hill and C. Evangelinos and
+                  G. Forget}
+}
 
 @PHDTHESIS{Marti_PhD92,
-  author = {O. Marti},
-  title = {Etude de l'oc\'{e}an mondial : mod\'{e}lisation de la circulation
-	et du transport de traceurs anthropog\'{e}niques},
-  school = {Universit\'{e} Pierre et Marie Curie, Paris, France, 201pp},
-  year = {1992}
+  author =       {O. Marti},
+  title =        {Etude de l'oc\'{e}an mondial : mod\'{e}lisation de
+                  la circulation et du transport de traceurs
+                  anthropog\'{e}niques},
+  school =       {Universit\'{e} Pierre et Marie Curie, Paris, France,
+                  201pp},
+  year =         1992
 }
 
 @ARTICLE{Marti_al_CD10,
-  author = {O. Marti and P. Braconnot and J.-L. Dufresne and J. Bellier and R.
-	Benshila and S. Bony and P. Brockmann and P. Cadule and A. Caubel
-	and F Codron and S. Denvil and L. Fairhead and T. Fichefet and M.-A.
-	Filiberti and M.-A. Foujols and P. Friedlingstein and H. Goosse and
-	J.-Y. Grandpeix and E. Guilyardi and F. Hourdin and G. Krinner and
-	C. L\'{e}vy and G. Madec and J. Mignot and I. Musat and D. Swingedouw
-	and C. Talandier},
-  title = {Key features of the IPSL ocean atmosphere model and its sensitivity
-	to atmospheric resolution},
-  journal = CD,
-  year = {2010},
-  volume = {34},  number = {1},
-  pages = {1--26},
-  doi = {10.1007/s00382-009-0640-6},
+  author =       {O. Marti and P. Braconnot and J.-L. Dufresne and
+                  J. Bellier and R.  Benshila and S. Bony and
+                  P. Brockmann and P. Cadule and A. Caubel and F
+                  Codron and S. Denvil and L. Fairhead and T. Fichefet
+                  and M.-A.  Filiberti and M.-A. Foujols and
+                  P. Friedlingstein and H. Goosse and J.-Y. Grandpeix
+                  and E. Guilyardi and F. Hourdin and G. Krinner and
+                  C. L\'{e}vy and G. Madec and J. Mignot and I. Musat
+                  and D. Swingedouw and C. Talandier},
+  title =        {Key features of the IPSL ocean atmosphere model and
+                  its sensitivity to atmospheric resolution},
+  journal =      CD,
+  year =         2010,
+  volume =       34,
+  number =       1,
+  pages =        {1--26},
+  doi =          {10.1007/s00382-009-0640-6},
 }
 
 @ARTICLE{Marti_al_JGR92,
-  author = {O. Marti and G. Madec and P. Delecluse},
-  title = {Comment on "Net diffusivity in ocean general circulation models with
-	nonuniform grids" by F. L. Yin and I. Y. Fung},
-  journal = JGR,
-  year = {1992},
-  volume = {97},
-  pages = {12,763--12,766}
+  author =       {O. Marti and G. Madec and P. Delecluse},
+  title =        {Comment on "Net diffusivity in ocean general
+                  circulation models with nonuniform grids" by
+                  F. L. Yin and I. Y. Fung},
+  journal =      JGR,
+  year =         1992,
+  volume =       97,
+  pages =        {12,763--12,766}
 }
 
 @INBOOK{Masson_al_Bk08,
-  chapter = {OPA9 - French experiments on the Earth Simulator and Teraflop Workbench
-	tunings},
-  pages = {25-34},
-  title = {In High Performance computing on Vector System 2007, Stuttgart, Germany},
-  publisher = {Springer-Verlag},
-  year = {2008},
-  editor = {Resch M, Roller S, Lammers P, Furui T, Galle M, Bez W},
-  author = {S. Masson and M.-A. Foujols and P. Klein and G. Madec and L. Hua and M. Levy 
-  and H. Sasaki and K. Takahashi and F. Svensson},
-  doi = {10.1007/978-3-540-74384-2},
+  chapter =      {OPA9 - French experiments on the Earth Simulator and
+                  Teraflop Workbench tunings},
+  pages =        {25-34},
+  title =        {In High Performance computing on Vector System 2007,
+                  Stuttgart, Germany},
+  publisher =    {Springer-Verlag},
+  year =         2008,
+  editor =       {Resch M, Roller S, Lammers P, Furui T, Galle M, Bez
+                  W},
+  author =       {S. Masson and M.-A. Foujols and P. Klein and
+                  G. Madec and L. Hua and M. Levy and H. Sasaki and
+                  K. Takahashi and F. Svensson},
+  doi =          {10.1007/978-3-540-74384-2},
 }
 
 @ARTICLE{Masson_al_GRL05,
-  author = {S. Masson and J.-J. Luo and G. Madec and J. Vialard and F. Durand
-	and S. Gualdi and E. Guilyardi and S. Behera and P. Delecluse and
-	A. Navarra and T. Yamagata},
-  title = {Impact of barrier layer on winter-spring variability of the South-Eastern
-	Arabian Sea},
-  journal = GRL,
-  year = {2005},
-  volume = {32},
-  pages = {L07703},
-  doi = {10.1029/2004GL021980},
+  author =       {S. Masson and J.-J. Luo and G. Madec and J. Vialard
+                  and F. Durand and S. Gualdi and E. Guilyardi and
+                  S. Behera and P. Delecluse and A. Navarra and
+                  T. Yamagata},
+  title =        {Impact of barrier layer on winter-spring variability
+                  of the South-Eastern Arabian Sea},
+  journal =      GRL,
+  year =         2005,
+  volume =       32,
+  pages =        {L07703},
+  doi =          {10.1029/2004GL021980},
 }
 
 @ARTICLE{McDougall1987,
-  author = {T. J. McDougall},
-  title = {Neutral Surfaces},
-  journal = JPO,
-  year = {1987},
-  volume = {17},  number = {11},
-  pages = {1950--1964},
+  author =       {T. J. McDougall},
+  title =        {Neutral Surfaces},
+  journal =      JPO,
+  year =         1987,
+  volume =       17,
+  number =       11,
+  pages =        {1950--1964},
 }
 
 @ARTICLE{McDougall_Taylor_JMR84,
-  author = {T. J. McDougall and J. R. Taylor},
-  title = {Flux measurements across a finger interface at low values of the stability ratio},
-  journal = JMR,
-  year = {1984},
-  volume = {42},
-  pages = {1--14}
+  author =       {T. J. McDougall and J. R. Taylor},
+  title =        {Flux measurements across a finger interface at low
+                  values of the stability ratio},
+  journal =      JMR,
+  year =         1984,
+  volume =       42,
+  pages =        {1--14}
 }
 
 @ARTICLE{Mellor_Blumberg_JPO04,
-author = {G. Mellor and A. Blumberg},
-title = {Wave Breaking and Ocean Surface Layer Thermal Response},
-journal = JPO,
-volume = {34}, number = {3},
-pages = {693--698},
-year = {2004},
-doi = {10.1175/2517.1},
+  author =       {G. Mellor and A. Blumberg},
+  title =        {Wave Breaking and Ocean Surface Layer Thermal
+                  Response},
+  journal =      JPO,
+  volume =       34,
+  number =       3,
+  pages =        {693--698},
+  year =         2004,
+  doi =          {10.1175/2517.1},
 }
 
 @ARTICLE{Mellor_Yamada_1982,
-  author = {G. L. Mellor and T. Yamada},
-  title = {Development of a turbulence closure model for geophysical fluid problems},
-  journal = RGSP,
-  year = {1982},
-  volume = {20},
-  pages = {851--875}
+  author =       {G. L. Mellor and T. Yamada},
+  title =        {Development of a turbulence closure model for
+                  geophysical fluid problems},
+  journal =      RGSP,
+  year =         1982,
+  volume =       20,
+  pages =        {851--875}
 }
 
 @ARTICLE{Menkes_al_JPO06,
-  author = {C. Menkes and J. Vialard and S C. Kennan and J.-P. Boulanger and G. Madec},
-  title = {A modelling study of the three-dimensional heat budget of Tropical
-	 Instability Waves in the Equatorial Pacific},
-  journal = JPO,
-  year = {2006},
-  volume = {36},  number = {5},
-  pages = {847--865}
+  author =       {C. Menkes and J. Vialard and S C. Kennan and
+                  J.-P. Boulanger and G. Madec},
+  title =        {A modelling study of the three-dimensional heat
+                  budget of Tropical Instability Waves in the
+                  Equatorial Pacific},
+  journal =      JPO,
+  year =         2006,
+  volume =       36,
+  number =       5,
+  pages =        {847--865}
 }
 
 @ARTICLE{Merryfield1999,
-  author = {W. J. Merryfield and G. Holloway and A. E. Gargett},
-  title = {A Global Ocean Model with Double-Diffusive Mixing},
-  journal = JPO,
-  year = {1999},
-  volume = {29},  number = {6},
-  pages = {1124--1142}
+  author =       {W. J. Merryfield and G. Holloway and A. E. Gargett},
+  title =        {A Global Ocean Model with Double-Diffusive Mixing},
+  journal =      JPO,
+  year =         1999,
+  volume =       29,
+  number =       6,
+  pages =        {1124--1142}
 }
 
 @BOOK{Mesinger_Arakawa_Bk76,
-  title = {Numerical methods used in Atmospheric models},
-  publisher = {GARP Publication Series No 17},
-  year = {1976},
-  author = {F. Mesinger and A. Arakawa}
+  title =        {Numerical methods used in Atmospheric models},
+  publisher =    {GARP Publication Series No 17},
+  year =         1976,
+  author =       {F. Mesinger and A. Arakawa}
 }
 
 @ARTICLE{Morel_JGR88,
-  author = {A. Morel},
-  title = {Optical modeling of the upper ocean in relation to its biogenous matter content (Case I waters)},
-  journal = JGR,
-  year = {1988},
-  volume = {93},
-  pages = {10,749--10,768}
+  author =       {A. Morel},
+  title =        {Optical modeling of the upper ocean in relation to
+                  its biogenous matter content (Case I waters)},
+  journal =      JGR,
+  year =         1988,
+  volume =       93,
+  pages =        {10,749--10,768}
 }
 
 @ARTICLE{Morel_Berthon_LO89,
-  author = {A. Morel and J.-F. Berthon},
-  title = {Surface pigments, algal biomass profiles, and potential production of the euphotic layer: 
-           Relationships reinvestigated in view of remote-sensing applications},
-  journal = {Limnol. Oceanogr.},
-  year = {1989},
-  volume = {34(8)},
-  pages = {1545--1562}
+  author =       {A. Morel and J.-F. Berthon},
+  title =        {Surface pigments, algal biomass profiles, and
+                  potential production of the euphotic layer:
+                  Relationships reinvestigated in view of
+                  remote-sensing applications},
+  journal =      {Limnol. Oceanogr.},
+  year =         1989,
+  volume =       {34(8)},
+  pages =        {1545--1562}
 }
 
 @ARTICLE{Morel_Maritorena_JGR01,
-  author = {A. Morel and S. Maritorena},
-  title = {Bio-optical properties of oceanic waters: a reappraisal},
-  journal = JGR,
-  year = {2001},
-  volume = {106}, number = {C4},
-  pages = {7163--7180}
+  author =       {A. Morel and S. Maritorena},
+  title =        {Bio-optical properties of oceanic waters: a
+                  reappraisal},
+  journal =      JGR,
+  year =         2001,
+  volume =       106,
+  number =       {C4},
+  pages =        {7163--7180}
 }
 
 @ARTICLE{Moun_al_JPO02,
-  author = {J.N. Moum and D.R. Caldwell and J.D. Nash and G.D. Gunderson},
-  title = {Observations of boundary mixing over the continental slope},
-  journal = JPO,
-  year = {2002},
-  volume = {32}, number = {7},
-  pages = {2113--2130}
+  author =       {J.N. Moum and D.R. Caldwell and J.D. Nash and
+                  G.D. Gunderson},
+  title =        {Observations of boundary mixing over the continental
+                  slope},
+  journal =      JPO,
+  year =         2002,
+  volume =       32,
+  number =       7,
+  pages =        {2113--2130}
 }
 
 @ARTICLE{Murray_JCP96,
-  author = {R. J. Murray},
-  title = {Explicit Generation of Orthogonal Grids for Ocean Models},
-  journal = JCP,
-  year = {1996},
-  volume = {126},  number = {2},
-  pages = {251--273},
+  author =       {R. J. Murray},
+  title =        {Explicit Generation of Orthogonal Grids for Ocean
+                  Models},
+  journal =      JCP,
+  year =         1996,
+  volume =       126,
+  number =       2,
+  pages =        {251--273},
 }
 
 @ARTICLE{Oddo_al_OS09,
-  author = {P. Oddo and M. Adani and N. Pinardi and C. Fratianni and M. Tonani and D. Pettenuzzo},
-  title = {A nested Atlantic-Mediterranean Sea general circulation model for operational forecasting},
-  journal = OS,
-  year = {2009},
-  volume = {5},
-  pages = {1--13},
+  author =       {P. Oddo and M. Adani and N. Pinardi and C. Fratianni
+                  and M. Tonani and D. Pettenuzzo},
+  title =        {A nested Atlantic-Mediterranean Sea general
+                  circulation model for operational forecasting},
+  journal =      OS,
+  year =         2009,
+  volume =       5,
+  pages =        {1--13},
+}
+
+@ARTICLE{Oey06,
+   author =      {Lie-Yauw Oey},
+   title =       {An OGCM with movable land-sea boundaries},
+   journal =     {Ocean Modelling},
+   volume =      "13",
+   number =      "2",
+   pages =       "176 - 195",
+   year =        "2006",
+   issn =        "1463-5003",
+   doi =         "https://doi.org/10.1016/j.ocemod.2006.01.001",
+   url =         "http://www.sciencedirect.com/science/article/pii/S1463500306000084",
 }
 
 @PHDTHESIS{Olivier_PhD01,
-  author = {F. Olivier},
-  title = {Etude de l'activit\'{e} biologique et de la circulation oc\'{e}anique
-	dans un jet g\'{e}ostrophique: le front Alm\'{e}ria-Oran},
-  school = {Universit\'{e} Pierre et Marie Curie, Paris, France},
-  year = {2001}
+  author =       {F. Olivier},
+  title =        {Etude de l'activit\'{e} biologique et de la
+                  circulation oc\'{e}anique dans un jet
+                  g\'{e}ostrophique: le front Alm\'{e}ria-Oran},
+  school =       {Universit\'{e} Pierre et Marie Curie, Paris, France},
+  year =         2001
 }
 
 @ARTICLE{Osborn_JPO80,
-  author = {T.R. Osborn},
-  title = {Estimates of the local rate of vertical diffusion from dissipation measurements},
-  journal = JPO,
-  year = {1980},
-  volume = {10},
-  pages = {83--89}
+  author =       {T.R. Osborn},
+  title =        {Estimates of the local rate of vertical diffusion
+                  from dissipation measurements},
+  journal =      JPO,
+  year =         1980,
+  volume =       10,
+  pages =        {83--89}
 }
 
 @ARTICLE{Pacanowski_Philander_JPO81,
-  author = {R.C. Pacanowski and S.G.H. Philander},
-  title = {Parameterization of Vertical Mixing in Numerical Models of Tropical Oceans},
-  journal = JPO,
-  year = {1981},
-  volume = {11},  number = {11},
-  pages = {1443--1451}
+  author =       {R.C. Pacanowski and S.G.H. Philander},
+  title =        {Parameterization of Vertical Mixing in Numerical
+                  Models of Tropical Oceans},
+  journal =      JPO,
+  year =         1981,
+  volume =       11,
+  number =       11,
+  pages =        {1443--1451}
 }
 
 @ARTICLE{Pacanowski_Gnanadesikan_MWR98,
-  author = {R. C. Pacanowski and A. Gnanadesikan},
-  title = {Transient response in a z-level ocean model that resolves topography with partial-cells},
-  journal = MWR,
-  year = {1998},
-  volume = {126},
-  pages = {3248--3270}
+  author =       {R. C. Pacanowski and A. Gnanadesikan},
+  title =        {Transient response in a z-level ocean model that
+                  resolves topography with partial-cells},
+  journal =      MWR,
+  year =         1998,
+  volume =       126,
+  pages =        {3248--3270}
 }
 
 @ARTICLE{Park_al_JC09,
-  author = {W. Park and N. Keenlyside and M. Latif and A. Str\¨{o}h and R. Redler and E. Roeckner and G. Madec},
-  title = {Tropical Pacific Climate and its Response to Global Warming in the
-	Kiel Climate Model},
-  journal = JC,
-  year = {2009},
-  volume = {22},  number = {1},
-  pages = {71--92},
-  doi = {10.1175/2008JCLI2261.1},
+  author =       {W. Park and N. Keenlyside and M. Latif and
+                  A. Str\¨{o}h and R. Redler and E. Roeckner and
+                  G. Madec},
+  title =        {Tropical Pacific Climate and its Response to Global
+                  Warming in the Kiel Climate Model},
+  journal =      JC,
+  year =         2009,
+  volume =       22,
+  number =       1,
+  pages =        {71--92},
+  doi =          {10.1175/2008JCLI2261.1},
 }
 
 @ARTICLE{Paulson1977,
-  author = {C. A. Paulson and J. J. Simpson},
-  title = {Irradiance Measurements in the Upper Ocean},
-  journal = JPO,
-  year = {1977},
-  volume = {7},  number = {6},
-  pages = {952--956}
+  author =       {C. A. Paulson and J. J. Simpson},
+  title =        {Irradiance Measurements in the Upper Ocean},
+  journal =      JPO,
+  year =         1977,
+  volume =       7,
+  number =       6,
+  pages =        {952--956}
 }
 
 @ARTICLE{Payne_JAS72,
-  author = {R. E. Payne},
-  title = {Albedo of the Sea Surface},
-  journal = JAS,
-  year = {1972},
-  volume = {29},
-  pages = {959--970}
+  author =       {R. E. Payne},
+  title =        {Albedo of the Sea Surface},
+  journal =      JAS,
+  year =         1972,
+  volume =       29,
+  pages =        {959--970}
 }
 
 @ARTICLE{Penduff_al_OM06,
-  author = {T. Penduff and B. Barnier and J.-M. Molines and G. Madec},
-  title = {On the use of current meter data to assess the realism of ocean model simulations},
-  journal = OM,
-  year = {2006},
-  volume = {11},  number = {3--4},
-  pages = {399--416}
+  author =       {T. Penduff and B. Barnier and J.-M. Molines and
+                  G. Madec},
+  title =        {On the use of current meter data to assess the
+                  realism of ocean model simulations},
+  journal =      OM,
+  year =         2006,
+  volume =       11,
+  number =       {3--4},
+  pages =        {399--416}
 }
 
 @ARTICLE{Penduff_al_JGR00,
-  author = {T. Penduff and B. Barnier and A. Colin de Verdi\`{e}re},
-  title = {Self-adapting open boundaries for a regional model of the eastern North Atlantic},
-  journal = JGR,
-  year = {2000},
-  volume = {105},
-  pages = {11,279--11,297}
+  author =       {T. Penduff and B. Barnier and A. Colin de
+                  Verdi\`{e}re},
+  title =        {Self-adapting open boundaries for a regional model
+                  of the eastern North Atlantic},
+  journal =      JGR,
+  year =         2000,
+  volume =       105,
+  pages =        {11,279--11,297}
 }
 
 @ARTICLE{Penduff_al_OS07,
-  author = {T. Penduff and J. Le Sommer and B. Barnier and A.M. Treguier and J. Molines and G. Madec},
-  title = {Influence of numerical schemes on current-topography interactions
-	in 1/4$^{\circ}$ global ocean simulations},
-  journal = OS,
-  year = {2007},
-  volume = {3},
-  pages = {509--524}
+  author =       {T. Penduff and J. Le Sommer and B. Barnier and
+                  A.M. Treguier and J. Molines and G. Madec},
+  title =        {Influence of numerical schemes on current-topography
+                  interactions in 1/4$^{\circ}$ global ocean
+                  simulations},
+  journal =      OS,
+  year =         2007,
+  volume =       3,
+  pages =        {509--524}
 }
 
 @ARTICLE{Phillips1959,
-  author = {R. S. Phillips},
-  title = {Dissipative Operators and Hyperbolic Systems of Partial Differential Equations},
-  journal = {Transactions of the American Mathematical Society},
-  year = {1959},
-  volume = {90},  number = {2},
-  pages = {193--254},
-  doi = {10.2307/1993202},
+  author =       {R. S. Phillips},
+  title =        {Dissipative Operators and Hyperbolic Systems of
+                  Partial Differential Equations},
+  journal =      {Transactions of the American Mathematical Society},
+  year =         1959,
+  volume =       90,
+  number =       2,
+  pages =        {193--254},
+  doi =          {10.2307/1993202},
 }
 
 @ARTICLE{Le_Quere_al_GBC00,
-  author = {C. Le Qu\'{e}r\'{e} and J. C. Orr and P. Monfray and O. Aumont and G. Madec},
-  title = {Interannual variability of the global and regional sea-air flux of C02 from 1979 to 1993},
-  journal = GBC,
-  year = {2000},
-  volume = {14},
-  pages = {1247--1266}
+  author =       {C. Le Qu\'{e}r\'{e} and J. C. Orr and P. Monfray and
+                  O. Aumont and G. Madec},
+  title =        {Interannual variability of the global and regional
+                  sea-air flux of C02 from 1979 to 1993},
+  journal =      GBC,
+  year =         2000,
+  volume =       14,
+  pages =        {1247--1266}
 }
 
 @ARTICLE{Raynaud_al_GRL00,
-  author = {S. Raynaud and S. Speich and E. Guilyardi and G. Madec},
-  title = {Impact of the ocean lateral diffusion on the ENSO-like variability of a global coupled GCM},
-  journal = GRL,
-  year = {2000},
-  volume = {27},  number = {19},
-  pages = {3041--3044}
+  author =       {S. Raynaud and S. Speich and E. Guilyardi and
+                  G. Madec},
+  title =        {Impact of the ocean lateral diffusion on the
+                  ENSO-like variability of a global coupled GCM},
+  journal =      GRL,
+  year =         2000,
+  volume =       27,
+  number =       19,
+  pages =        {3041--3044}
 }
 
 @ARTICLE{Redi_JPO82,
-  author = {M. H. Redi},
-  title = {Oceanic isopycnal mixing by coordinate rotation},
-  journal = JPO,
-  year = {1982},
-  volume = {13},
-  pages = {1154--1158}
+  author =       {M. H. Redi},
+  title =        {Oceanic isopycnal mixing by coordinate rotation},
+  journal =      JPO,
+  year =         1982,
+  volume =       13,
+  pages =        {1154--1158}
 }
 
 @ARTICLE{Reed_JPO77,
-  author = {R. K. Reed},
-  title = {On estimating insolation over the ocean},
-  journal = JPO,
-  year = {1977},
-  volume = {1},
-  pages = {874--971}
+  author =       {R. K. Reed},
+  title =        {On estimating insolation over the ocean},
+  journal =      JPO,
+  year =         1977,
+  volume =       1,
+  pages =        {874--971}
 }
 
 @ARTICLE{Reverdin1991,
-  author = {G. Reverdin and P. Delecluse and C. L\'{e}vy and P. Andrich and A. Morli\`{e}re and J. M. Verstraete},
-  title = {The near surface tropical Atlantic in 1982-1984 : results from a numerical simulation and a data analysis},
-  journal = PO,
-  year = {1991},
-  volume = {27},
-  pages = {273--340}
+  author =       {G. Reverdin and P. Delecluse and C. L\'{e}vy and
+                  P. Andrich and A. Morli\`{e}re and J. M. Verstraete},
+  title =        {The near surface tropical Atlantic in 1982-1984 :
+                  results from a numerical simulation and a data
+                  analysis},
+  journal =      PO,
+  year =         1991,
+  volume =       27,
+  pages =        {273--340}
 }
 
 @BOOK{Richtmyer1967,
-  title = {Difference methods for initial-value problems},
-  publisher = {Interscience Publisher, Second Edition},
-  year = {1967},
-  author = {R. D. Richtmyer and K. W. Morton},
-  pages = {405pp}
+  title =        {Difference methods for initial-value problems},
+  publisher =    {Interscience Publisher, Second Edition},
+  year =         1967,
+  author =       {R. D. Richtmyer and K. W. Morton},
+  pages =        {405pp}
 }
 
 @ARTICLE{Robert_JMSJ66,
-  author = {A. J. Robert},
-  title = {The integration of a Low order spectral form of the primitive meteorological equations},
-  journal = JMSJ,
-  year = {1966},
-  volume = {44},  number = {2}
+  author =       {A. J. Robert},
+  title =        {The integration of a Low order spectral form of the
+                  primitive meteorological equations},
+  journal =      JMSJ,
+  year =         1966,
+  volume =       44,
+  number =       2
 }
 
 @ARTICLE{Rodgers_al_GRL04,
-  author = {K. Rodgers and O. Aumont and G. Madec and C. Menkes},
-  title = {Radiocarbon as a thermocline proxy for the eastern equatorial Pacific},
-  journal = GRL,
-  year = {2004},
-  volume = {31},
-  pages = {L14314},
-  doi = {10.1029/2004GL019764},
+  author =       {K. Rodgers and O. Aumont and G. Madec and C. Menkes},
+  title =        {Radiocarbon as a thermocline proxy for the eastern
+                  equatorial Pacific},
+  journal =      GRL,
+  year =         2004,
+  volume =       31,
+  pages =        {L14314},
+  doi =          {10.1029/2004GL019764},
 }
 
 @ARTICLE{Rodgers_al_GRL03,
-  author = {K. Rodgers and B. Blanke and G. Madec and O. Aumont and P. Ciais and J.-C. Dutay},
-  title = {Extratropical sources of equatorial pacific upwelling in an OGCM},
-  journal = GRL,
-  year = {2003},
-  volume = {30},  number = {2},
-  doi = {10.1029/2002GL016003},
+  author =       {K. Rodgers and B. Blanke and G. Madec and O. Aumont
+                  and P. Ciais and J.-C. Dutay},
+  title =        {Extratropical sources of equatorial pacific
+                  upwelling in an OGCM},
+  journal =      GRL,
+  year =         2003,
+  volume =       30,
+  number =       2,
+  doi =          {10.1029/2002GL016003},
 }
 
 @Article{Rodgers_2014,
-AUTHOR = {Rodgers, K. B. and Aumont, O. and Mikaloff Fletcher, S. E. and Plancherel, Y. and Bopp, L. and de Boyer Mont\'egut, C. and Iudicone, D. and Keeling, R. F. and Madec, G. and Wanninkhof, R.},
-TITLE = {Strong sensitivity of Southern Ocean carbon uptake and nutrient cycling to wind stirring},
-JOURNAL = {Biogeosciences},
-VOLUME = {11},
-YEAR = {2014},
-NUMBER = {15},
-PAGES = {4077--4098},
-DOI = {10.5194/bg-11-4077-2014}
+  AUTHOR =       {Rodgers, K. B. and Aumont, O. and Mikaloff Fletcher,
+                  S. E. and Plancherel, Y. and Bopp, L. and de Boyer
+                  Mont\'egut, C. and Iudicone, D. and Keeling,
+                  R. F. and Madec, G. and Wanninkhof, R.},
+  TITLE =        {Strong sensitivity of Southern Ocean carbon uptake
+                  and nutrient cycling to wind stirring},
+  JOURNAL =      {Biogeosciences},
+  VOLUME =       11,
+  YEAR =         2014,
+  NUMBER =       15,
+  PAGES =        {4077--4098},
+  DOI =          {10.5194/bg-11-4077-2014}
 }
 
 @ARTICLE{Rodi_1987,
-  author = {W. Rodi},
-  title = {Examples of calculation methods for flow and mixing in stratified fluids},
-  journal = JGR,
-  year = {1987},
-  volume = {92},  number = {C5},
-  pages = {5305--5328}
+  author =       {W. Rodi},
+  title =        {Examples of calculation methods for flow and mixing
+                  in stratified fluids},
+  journal =      JGR,
+  year =         1987,
+  volume =       92,
+  number =       {C5},
+  pages =        {5305--5328}
 }
 
 @INCOLLECTION{Roed1986,
-  author = {L.P. Roed and C.K. Cooper},
-  title = {Open boundary conditions in numerical ocean models},
-  booktitle = {Advanced Physical Oceanography Numerical Modelling},
-  publisher = { NATO ASI Series, vol. 186.},
-  year = {1986},
-  editor = {J.J. O'Brien}
+  author =       {L.P. Roed and C.K. Cooper},
+  title =        {Open boundary conditions in numerical ocean models},
+  booktitle =    {Advanced Physical Oceanography Numerical Modelling},
+  publisher =    { NATO ASI Series, vol. 186.},
+  year =         1986,
+  editor =       {J.J. O'Brien}
 }
 
 @article{Roquet_OM2015,
-author = "F. Roquet and G. Madec and T.J. McDougall and P.M. Barker",
-title = "Accurate polynomial expressions for the density and specific volume of seawater using the TEOS-10 standard ",
-journal = OM,
-volume = "90",
-pages = "29--43",
-year = "2015",
-issn = "1463-5003",
-doi = "10.1016/j.ocemod.2015.04.002",
+  author =       "F. Roquet and G. Madec and T.J. McDougall and
+                  P.M. Barker",
+  title =        "Accurate polynomial expressions for the density and
+                  specific volume of seawater using the TEOS-10
+                  standard ",
+  journal =      OM,
+  volume =       90,
+  pages =        "29--43",
+  year =         2015,
+  issn =         "1463-5003",
+  doi =          "10.1016/j.ocemod.2015.04.002",
 }
 
 @article{Roquet_JPO2015,
-author = "F. Roquet and G. Madec and L. Brodeau and J. Nycander",
-title = "Defining a Simplified Yet Realistic Equation of State for Seawater",
-journal = JPO,
-volume = "45",
-pages = "2564--2579",
-year = "2015",
-doi = "10.1175/JPO-D-15-0080.1",
+  author =       "F. Roquet and G. Madec and L. Brodeau and
+                  J. Nycander",
+  title =        "Defining a Simplified Yet Realistic Equation of
+                  State for Seawater",
+  journal =      JPO,
+  volume =       45,
+  pages =        "2564--2579",
+  year =         2015,
+  doi =          "10.1175/JPO-D-15-0080.1",
 }
 
 @ARTICLE{Roullet_Madec_JGR00,
-  author = {G. Roullet and G. Madec},
-  title = {salt conservation, free surface, and varying levels: a new formulation
-	for ocean general circulation models},
-  journal = JGR,
-  year = {2000},
-  volume = {105},
-  pages = {23,927--23,942}
+  author =       {G. Roullet and G. Madec},
+  title =        {salt conservation, free surface, and varying levels:
+                  a new formulation for ocean general circulation
+                  models},
+  journal =      JGR,
+  year =         2000,
+  volume =       105,
+  pages =        {23,927--23,942}
 }
 
 @ARTICLE{Rousset_GMD2015,
-  author = {C. Rousset and M. Vancoppenolle and G. Madec and T. Fichefet and S. Flavoni 
-            and A. Barth\'{e}lemy and R. Benshila and J. Chanut and C. L\'{e}vy and S. Masson and F. Vivier },
-  title  = {The Louvain-La-Neuve sea-ice model LIM3.6: Global and regional capabilities},
-  journal= {Geoscientific Model Development},
-  year = {2015},
-  volume = {8}, pages={2991--3005},
-  doi = {10.5194/gmd-8-2991-2015},
+  author =       {C. Rousset and M. Vancoppenolle and G. Madec and
+                  T. Fichefet and S. Flavoni and A. Barth\'{e}lemy and
+                  R. Benshila and J. Chanut and C. L\'{e}vy and
+                  S. Masson and F. Vivier },
+  title =        {The Louvain-La-Neuve sea-ice model LIM3.6: Global
+                  and regional capabilities},
+  journal =      {Geoscientific Model Development},
+  year =         2015,
+  volume =       8,
+  pages =        {2991--3005},
+  doi =          {10.5194/gmd-8-2991-2015},
 }
 
 @ARTICLE{Sadourny1975,
-  author = {R. Sadourny},
-  title = {The Dynamics of Finite-Difference Models of the Shallow-Water Equations},
-  journal = JAS,
-  year = {1975},
-  volume = {32},  number = {4},
-  pages = {680--689},
+  author =       {R. Sadourny},
+  title =        {The Dynamics of Finite-Difference Models of the
+                  Shallow-Water Equations},
+  journal =      JAS,
+  year =         1975,
+  volume =       32,
+  number =       4,
+  pages =        {680--689},
 }
 
 @ARTICLE{Sarmiento1982,
-  author = {J. L. Sarmiento and K. Bryan},
-  title = {Ocean transport model for the North Atlantic},
-  journal = JGR,
-  year = {1982},
-  volume = {87},
-  pages = {394--409}
+  author =       {J. L. Sarmiento and K. Bryan},
+  title =        {Ocean transport model for the North Atlantic},
+  journal =      JGR,
+  year =         1982,
+  volume =       87,
+  pages =        {394--409}
 }
 
 @ARTICLE{Saunders_JAS82,
-  author={P. M. Saunders},
-  title={{The Temperature at the Ocean-air Interface}},
-  journal=JAS,
-  year={1967},
-  volume={24},
-  pages={269-273},
-  doi = {10.1175/1520-0469(1967)024<0269:TTATOA>2.0.CO;2},
+  author =       {P. M. Saunders},
+  title =        {{The Temperature at the Ocean-air Interface}},
+  journal =      JAS,
+  year =         1967,
+  volume =       24,
+  pages =        {269-273},
+  doi =          {10.1175/1520-0469(1967)024<0269:TTATOA>2.0.CO;2},
 }
 
 @BOOK{Shchepetkin_McWilliams_Bk08,
-  author = {A. F. Shchepetkin and J. C. McWilliams},
-  title = {Handbook of Numerical Analysis, Vol. XIV: Computational Methods for the Ocean and the Atmosphere, pp 121-183},
-  publisher = {P. G. Ciarlet, editor, R. Temam and J. Tribbia, guest eds., Elsevier Science},
-  year = {2008},
-  pages = {784}
+  author =       {A. F. Shchepetkin and J. C. McWilliams},
+  title =        {Handbook of Numerical Analysis, Vol. XIV:
+                  Computational Methods for the Ocean and the
+                  Atmosphere, pp 121-183},
+  publisher =    {P. G. Ciarlet, editor, R. Temam and J. Tribbia,
+                  guest eds., Elsevier Science},
+  year =         2008,
+  pages =        784
 }
 
 @ARTICLE{Shchepetkin_McWilliams_OM05,
-  author = {A. F. Shchepetkin and J. C. McWilliams},
-  title = {The regional oceanic modeling system (ROMS) - a split-explicit, free-surface,
-	topography-following-coordinate oceanic modelr},
-  journal = OM,
-  year = {2005},
-  volume = {9},  number = {4},
-  pages = {347--404}
+  author =       {A. F. Shchepetkin and J. C. McWilliams},
+  title =        {The regional oceanic modeling system (ROMS) - a
+                  split-explicit, free-surface,
+                  topography-following-coordinate oceanic modelr},
+  journal =      OM,
+  year =         2005,
+  volume =       9,
+  number =       4,
+  pages =        {347--404}
 }
 
 @ARTICLE{Sacha2003,
-  author = {A. F. Shchepetkin and J. C. McWilliams},
-  title = {A method for computing horizontal pressure-gradient force in an oceanic
-	model with a nonaligned vertical coordinate},
-  journal = JGR,
-  year = {2003},
-  volume = {108},  number = {C3},
-  pages = {3090},
-  doi = {10.1029/2001JC001047},
+  author =       {A. F. Shchepetkin and J. C. McWilliams},
+  title =        {A method for computing horizontal pressure-gradient
+                  force in an oceanic model with a nonaligned vertical
+                  coordinate},
+  journal =      JGR,
+  year =         2003,
+  volume =       108,
+  number =       {C3},
+  pages =        3090,
+  doi =          {10.1029/2001JC001047},
 }
 
 @ARTICLE{Shchepetkin1996,
-  author = {A. F. Shchepetkin and J. J. O'Brien},
-  title = {A Physically Consistent Formulation of Lateral Friction in Shallow-Water Equation Ocean Models},
-  journal = MWR,
-  year = {1996},
-  volume = {124},  number = {6},
-  pages = {1285--1300}
+  author =       {A. F. Shchepetkin and J. J. O'Brien},
+  title =        {A Physically Consistent Formulation of Lateral
+                  Friction in Shallow-Water Equation Ocean Models},
+  journal =      MWR,
+  year =         1996,
+  volume =       124,
+  number =       6,
+  pages =        {1285--1300}
 }
 
 @ARTICLE{Siddorn_Furner_OM12,
-  author = {J. Siddorn and R. Furner},
-  title = {An analytical stretching function that combines the best attributes of geopotential and terrain-following vertical coordinates},
-  journal = OM,
-  year = {2012},
-  pages = {submitted},
+  author =       {J. Siddorn and R. Furner},
+  title =        {An analytical stretching function that combines the
+                  best attributes of geopotential and
+                  terrain-following vertical coordinates},
+  journal =      OM,
+  year =         2012,
+  pages =        {submitted},
 }
 
 @ARTICLE{Simmons_al_OM04,
-  author = {H. L. Simmons and S. R. Jayne and L. C. {St. Laurent} and A. J. Weaver},
-  title = {Tidally driven mixing in a numerical model of the ocean general circulation},
-  journal = OM,
-  year = {2004},
-  pages = {245--263},
+  author =       {H. L. Simmons and S. R. Jayne and
+                  L. C. {St. Laurent} and A. J. Weaver},
+  title =        {Tidally driven mixing in a numerical model of the
+                  ocean general circulation},
+  journal =      OM,
+  year =         2004,
+  pages =        {245--263},
 }
 
 @INBOOK{Smagorinsky_93,
-  author = {Smagorinsky, J.},
-  chapter = {Some historical remarks on the use of non-linear viscosities},
-  title = {Large Eddy Simulation of Complex Engineering and Geophysical Flows},
-  pages = {3--36},
-  year = {1993},
-  publisher = {Cambridge University Press, B. Galperin and S. A. Orszag (eds.)},
+  author =       {Smagorinsky, J.},
+  chapter =      {Some historical remarks on the use of non-linear
+                  viscosities},
+  title =        {Large Eddy Simulation of Complex Engineering and
+                  Geophysical Flows},
+  pages =        {3--36},
+  year =         1993,
+  publisher =    {Cambridge University Press, B. Galperin and
+                  S. A. Orszag (eds.)},
 }
 
 @ARTICLE{Song_Haidvogel_JCP94,
-  author = {Y. Song and D. Haidvogel},
-  title = {A semi-implicit ocean circulation model using a generalized topography-following coordinate system},
-  journal = JCP,
-  year = {1994},
-  volume = {115},  number = {1},
-  pages = {228--244}
+  author =       {Y. Song and D. Haidvogel},
+  title =        {A semi-implicit ocean circulation model using a
+                  generalized topography-following coordinate system},
+  journal =      JCP,
+  year =         1994,
+  volume =       115,
+  number =       1,
+  pages =        {228--244}
 }
 
 @ARTICLE{Song1998,
-  author = {Y. T. Song},
-  title = {A General Pressure Gradient Formulation for Ocean Models. Part I: Scheme Design and Diagnostic Analysis},
-  journal = MWR,
-  year = {1998},
-  volume = {126},  number = {12},
-  pages = {3213--3230}
+  author =       {Y. T. Song},
+  title =        {A General Pressure Gradient Formulation for Ocean
+                  Models. Part I: Scheme Design and Diagnostic
+                  Analysis},
+  journal =      MWR,
+  year =         1998,
+  volume =       126,
+  number =       12,
+  pages =        {3213--3230}
 }
 
 @ARTICLE{SongWright1998,
-  author = {Y. T. Song and D. G. Wright},
-  title = {A General Pressure Gradient Formulation for Ocean Models. 
-    Part II: Energy, Momentum, and Bottom Torque Consistency},
-  journal = MWR,
-  year = {1998},
-  volume = {126},  number = {12},
-  pages = {3231--3247}
+  author =       {Y. T. Song and D. G. Wright},
+  title =        {A General Pressure Gradient Formulation for Ocean
+                  Models.  Part II: Energy, Momentum, and Bottom
+                  Torque Consistency},
+  journal =      MWR,
+  year =         1998,
+  volume =       126,
+  number =       12,
+  pages =        {3231--3247}
 }
 
 @ARTICLE{Speer_al_Tel00,
-  author = {K. Speer and E. Guilyardi and G. Madec},
-  title = {Southern Ocean transformation in a coupled model with and without eddy mass fluxes},
-  journal = {Tellus},
-  year = {2000},
-  volume = {52A},  number = {5},
-  pages = {554--565}
+  author =       {K. Speer and E. Guilyardi and G. Madec},
+  title =        {Southern Ocean transformation in a coupled model
+                  with and without eddy mass fluxes},
+  journal =      {Tellus},
+  year =         2000,
+  volume =       {52A},
+  number =       5,
+  pages =        {554--565}
 }
 
 @PHDTHESIS{Speich_PhD92,
-  author = {S. Speich},
-  title = {Etude du for\c{c}age de la circulation g\'{e}n\'{e}rale oc\'{e}anique
-	par les d\'{e}troits - cas de la mer d'Alboran},
-  school = {Universit\'{e} Pierre et Marie Curie, Paris, France},
-  year = {1992}
+  author =       {S. Speich},
+  title =        {Etude du for\c{c}age de la circulation
+                  g\'{e}n\'{e}rale oc\'{e}anique par les d\'{e}troits
+                  - cas de la mer d'Alboran},
+  school =       {Universit\'{e} Pierre et Marie Curie, Paris, France},
+  year =         1992
 }
 
 @ARTICLE{Speich_al_GRL01,
-  author = {S. Speich and B. Blanke and G. Madec},
-  title = {Warm and cold water paths of an OGCM thermohaline conveyor belt},
-  journal = GRL,
-  year = {2001},
-  volume = {28},  number = {2},
-  pages = {311--314}
+  author =       {S. Speich and B. Blanke and G. Madec},
+  title =        {Warm and cold water paths of an OGCM thermohaline
+                  conveyor belt},
+  journal =      GRL,
+  year =         2001,
+  volume =       28,
+  number =       2,
+  pages =        {311--314}
 }
 
 @ARTICLE{Speich_al_JPO96,
-  author = {S. Speich and G. Madec and M. Cr\'{e}pon},
-  title = {The circulation in the Alboran Sea - a sensitivity study},
-  journal = JPO,
-  year = {1996},
-  volume = {26},  number = {3},
-  pages = {320--340}
+  author =       {S. Speich and G. Madec and M. Cr\'{e}pon},
+  title =        {The circulation in the Alboran Sea - a sensitivity
+                  study},
+  journal =      JPO,
+  year =         1996,
+  volume =       26,
+  number =       3,
+  pages =        {320--340}
 }
 
 @ARTICLE{St_Laurent_Garrett_JPO02,
-  author = {L.C. {St. Laurent} and C. Garrett},
-  title = {The role of internal tides in mixing the deep ocean},
-  journal = JPO,
-  pages = {2882--2899}
+  author =       {L.C. {St. Laurent} and C. Garrett},
+  title =        {The role of internal tides in mixing the deep ocean},
+  journal =      JPO,
+  pages =        {2882--2899}
 }
 
 @ARTICLE{St_Laurent_Nash_DSR04,
-  author = {L.C. {St. Laurent} and J. D. Nash},
-  title = {An examination of the radiative and dissipative properties of deep ocean internal tides},
-  journal = DSR,
-  year = {2004},
-  volume = {II},  number = {51},
-  pages = {3029--3042},
-  doi = {10.1016/j.dsr2.2004.09.008},
+  author =       {L.C. {St. Laurent} and J. D. Nash},
+  title =        {An examination of the radiative and dissipative
+                  properties of deep ocean internal tides},
+  journal =      DSR,
+  year =         2004,
+  volume =       {II},
+  number =       51,
+  pages =        {3029--3042},
+  doi =          {10.1016/j.dsr2.2004.09.008},
 }
 
 @ARTICLE{St_Laurent_al_GRL02,
-  author = {L.C. {St. Laurent} and H.L. Simmons and S.R. Jayne},
-  title = {Estimating tidally driven mixing in the deep ocean},
-  journal = GRL,
-  year = {2002},
-  volume = {29},
-  pages = {2106},
-  doi = {10.1029/2002GL015633},
+  author =       {L.C. {St. Laurent} and H.L. Simmons and S.R. Jayne},
+  title =        {Estimating tidally driven mixing in the deep ocean},
+  journal =      GRL,
+  year =         2002,
+  volume =       29,
+  pages =        2106,
+  doi =          {10.1029/2002GL015633},
 }
 
 @ARTICLE{Stacey_JPO99,
-  author = {M. W. Stacey},
-  title = {Simulations of the wind-forced near-surface circulation in Knight Inlet: 
-             A parameterization of the roughness length},
-  journal = JPO,
-  year = {1999},
-  volume = {29},
-  pages = {1363--1367},
+  author =       {M. W. Stacey},
+  title =        {Simulations of the wind-forced near-surface
+                  circulation in Knight Inlet: A parameterization of
+                  the roughness length},
+  journal =      JPO,
+  year =         1999,
+  volume =       29,
+  pages =        {1363--1367},
 }
 
 @ARTICLE{Steele2001,
-  author = {M. Steele and R. Morley and W. Ermold},
-  title = {PHC- A Global Ocean Hydrography with a High-Quality Arctic Ocean},
-  journal = JC,
-  year = {2001},
-  volume = {14},  number = {9},
-  pages = {2079--2087},
+  author =       {M. Steele and R. Morley and W. Ermold},
+  title =        {PHC- A Global Ocean Hydrography with a High-Quality
+                  Arctic Ocean},
+  journal =      JC,
+  year =         2001,
+  volume =       14,
+  number =       9,
+  pages =        {2079--2087},
 }
 
 @ARTICLE{Stein_Stein_Nat92,
-  author = {C. A. Stein and S. Stein},
-  title = {A model for the global variation in oceanic depth and heat flow with lithospheric age},
-  journal = {Nature},
-  year = {1992},
-  volume = {359},
-  pages = {123--129}
+  author =       {C. A. Stein and S. Stein},
+  title =        {A model for the global variation in oceanic depth
+                  and heat flow with lithospheric age},
+  journal =      {Nature},
+  year =         1992,
+  volume =       359,
+  pages =        {123--129}
 }
 
 @INCOLLECTION{Stokes_1847,
-  author    = {G.G. Stokes},
-  title     = {On the theory of oscillatory waves},
-  booktitle = {Transactions of the Cambridge Philosophy Society},
-  year      = {1847},
-  volume    = {8},
-  Pages     = {441--455}
+  author =       {G.G. Stokes},
+  title =        {On the theory of oscillatory waves},
+  booktitle =    {Transactions of the Cambridge Philosophy Society},
+  year =         1847,
+  volume =       8,
+  Pages =        {441--455}
 }
 
 @ARTICLE{Takaya_al_JGR10,
-  author = {Y. Takaya and J-R. Bidlot and A. C. M. Beljaars and 
+  author =       {Y. Takaya and J-R. Bidlot and A. C. M. Beljaars and
                   P. A. E. M. Janssen},
-  title = {Refinements to a prognostic scheme of sea surface skin temperature},
-  journal = JGR,
-  year   = 	 {2010},
-  Volume = 	 {115},
-  Pages  = 	 {C06009},
-  doi    = {10.1029/2009JC005985},
+  title =        {Refinements to a prognostic scheme of sea surface
+                  skin temperature},
+  journal =      JGR,
+  year =         2010,
+  Volume =       115,
+  Pages =        {C06009},
+  doi =          {10.1029/2009JC005985},
 }
 
 @ARTICLE{Talagrand_JAS72,
-  author = {O. Talagrand},
-  title = {On the damping of high-frequency motions in four-dimensional 
-           assimilation of meteorological data},
-  journal = JAS,
-  year = {1972},
-  volume = {29},
-  pages = {1571-1574}
+  author =       {O. Talagrand},
+  title =        {On the damping of high-frequency motions in
+                  four-dimensional assimilation of meteorological
+                  data},
+  journal =      JAS,
+  year =         1972,
+  volume =       29,
+  pages =        {1571-1574}
 }
 
 @ARTICLE{Thiem_Berntsen_OM06,
-  author = {O. Thiem and J. Berntsen},
-  title = {Internal pressure errors in sigma-coordinate ocean models due to anisotropy},
-  journal = OM,
-  year = {2006},
-  volume = {12},  number = {1-2},
+  author =       {O. Thiem and J. Berntsen},
+  title =        {Internal pressure errors in sigma-coordinate ocean
+                  models due to anisotropy},
+  journal =      OM,
+  year =         2006,
+  volume =       12,
+  number =       {1-2},
 }
 
 @ARTICLE{Timmermann_al_OM05,
-  author = {R. Timmermann and H. Goosse and G. Madec and T. Fichefet and C. \'{E}the and V. Duli\`{e}re},
-  title = {On the representation of high latitude processes in the ORCA-LIM global coupled sea ice-ocean model},
-  journal = OM,
-  year = {2005},
-  volume = {8},
-  pages = {175--201}
+  author =       {R. Timmermann and H. Goosse and G. Madec and
+                  T. Fichefet and C. \'{E}the and V. Duli\`{e}re},
+  title =        {On the representation of high latitude processes in
+                  the ORCA-LIM global coupled sea ice-ocean model},
+  journal =      OM,
+  year =         2005,
+  volume =       8,
+  pages =        {175--201}
 }
 
 @ARTICLE{Tonani_al_OS08,
-  author = {M. Tonani and N. Pinardi and S. Dobricic and I. Pujol and C. Fratianni},
-  title = {A high-resolution free-surface model of the Mediterranean Sea},
-  journal = OS,
-  year = {2008},
-  volume = {4},
-  pages = {1--14}
+  author =       {M. Tonani and N. Pinardi and S. Dobricic and
+                  I. Pujol and C. Fratianni},
+  title =        {A high-resolution free-surface model of the
+                  Mediterranean Sea},
+  journal =      OS,
+  year =         2008,
+  volume =       4,
+  pages =        {1--14}
 }
 
 @ARTICLE{Treguier_JGR92,
-  author = {A.M. Tr\'{e}guier},
-  title = {Kinetic energy analysis of an eddy resolving, primitive equation North Atlantic model},
-  journal = JGR,
-  year = {1992},
-  volume = {97},
-  pages = {687--701}
+  author =       {A.M. Tr\'{e}guier},
+  title =        {Kinetic energy analysis of an eddy resolving,
+                  primitive equation North Atlantic model},
+  journal =      JGR,
+  year =         1992,
+  volume =       97,
+  pages =        {687--701}
 }
 
 @ARTICLE{Treguier_al_JGR01,
-  author = {A.M. Tr\'{e}guier and B. Barnier and A.P. de Miranda and J.M. Molines
-    and N. Grima and M. Imbard and G. Madec and C. Messager and T. Reynaud and S. Michel},
-  title = {An Eddy Permitting model of the Atlantic circulation: evaluating open boundary conditions},
-  journal = JGR,
-  year = {2001},
-  volume = {106},
-  pages = {22,115--22,129}
+  author =       {A.M. Tr\'{e}guier and B. Barnier and A.P. de Miranda
+                  and J.M. Molines and N. Grima and M. Imbard and
+                  G. Madec and C. Messager and T. Reynaud and
+                  S. Michel},
+  title =        {An Eddy Permitting model of the Atlantic
+                  circulation: evaluating open boundary conditions},
+  journal =      JGR,
+  year =         2001,
+  volume =       106,
+  pages =        {22,115--22,129}
 }
 
 @ARTICLE{Treguier_al_DSR03,
-  author = {A.-M. Tr\'{e}guier and O. Boedel and B. Barnier and G. Madec},
-  title = {Agulhas eddy fluxes in a 1/6^o Atlantic model},
-  journal = DSR,
-  year = {2003},
-  pages = {251--280}
+  author =       {A.-M. Tr\'{e}guier and O. Boedel and B. Barnier and
+                  G. Madec},
+  title =        {Agulhas eddy fluxes in a 1/6^o Atlantic model},
+  journal =      DSR,
+  year =         2003,
+  pages =        {251--280}
 }
 
 @ARTICLE{Treguier1996,
-  author = {A.-M. Tr\'{e}guier and J. Dukowicz and K. Bryan},
-  title = {Properties of nonuniform grids used in ocean general circulation models},
-  journal = JGR,
-  year = {1996},
-  volume = {101},
-  pages = {20,877--20,881}
+  author =       {A.-M. Tr\'{e}guier and J. Dukowicz and K. Bryan},
+  title =        {Properties of nonuniform grids used in ocean general
+                  circulation models},
+  journal =      JGR,
+  year =         1996,
+  volume =       101,
+  pages =        {20,877--20,881}
 }
 
 @ARTICLE{Treguier_al_OS07,
-  author = {A.-M. Tr\'{e}guier and M. H. England and S. R. Rintoul and G. Madec and J. Le Sommer and J.-M. Molines},
-  title = {Southern Ocean overturning across streamlines in an eddying simulation of the Antarctic Circumpolar Current},
-  journal = OS,
-  year = {2007},
-  volume = {4},
-  pages = {653--698}
+  author =       {A.-M. Tr\'{e}guier and M. H. England and
+                  S. R. Rintoul and G. Madec and J. Le Sommer and
+                  J.-M. Molines},
+  title =        {Southern Ocean overturning across streamlines in an
+                  eddying simulation of the Antarctic Circumpolar
+                  Current},
+  journal =      OS,
+  year =         2007,
+  volume =       4,
+  pages =        {653--698}
 }
 
 @ARTICLE{Treguier_al_OD06,
-  author = {A.-M. Tr\'{e}guier and C. Gourcuff and P. Lherminier and H. Mercier and B. Barnier 
-  and G. Madec and J.-M. Molines and T. Penduff and L. Czeschel and C. Böning},
-  title = {Internal and forced variability along a section between Greenland
-	and Portugal in the CLIPPER Atlantic model},
-  journal = OD,
-  year = {2006},
-  volume = {56},
-  pages = {568--580},
-  doi = {10.1007/s10236-006-0069-y},
+  author =       {A.-M. Tr\'{e}guier and C. Gourcuff and P. Lherminier
+                  and H. Mercier and B. Barnier and G. Madec and
+                  J.-M. Molines and T. Penduff and L. Czeschel and
+                  C. Böning},
+  title =        {Internal and forced variability along a section
+                  between Greenland and Portugal in the CLIPPER
+                  Atlantic model},
+  journal =      OD,
+  year =         2006,
+  volume =       56,
+  pages =        {568--580},
+  doi =          {10.1007/s10236-006-0069-y},
 }
 
 @ARTICLE{Treguier1997,
-  author = {A. M. Tr\'{e}guier and I. M. Held and V. D. Larichev},
-  title = {Parameterization of Quasigeostrophic Eddies in Primitive Equation Ocean Models},
-  journal = JPO,
-  year = {1997},
-  volume = {27},  number = {4},
-  pages = {567--580}
+  author =       {A. M. Tr\'{e}guier and I. M. Held and
+                  V. D. Larichev},
+  title =        {Parameterization of Quasigeostrophic Eddies in
+                  Primitive Equation Ocean Models},
+  journal =      JPO,
+  year =         1997,
+  volume =       27,
+  number =       4,
+  pages =        {567--580}
 }
 
 @ARTICLE{Tu_Tsuang_GRL05,
-  title={{Cool-skin simulation by a one-column ocean model}},
-  author={{C-Y}. Tu  and {B-J}. Tsuang},
-  journal=GRL,
-  year={2005},
-  volume={32},
-  pages={L22602},
-  doi = {10.1029/2005GL024252},
+  title =        {{Cool-skin simulation by a one-column ocean model}},
+  author =       {{C-Y}. Tu and {B-J}. Tsuang},
+  journal =      GRL,
+  year =         2005,
+  volume =       32,
+  pages =        {L22602},
+  doi =          {10.1029/2005GL024252},
 }
 
 @ARTICLE{Umlauf_Burchard_JMS03,
-  author = {L. Umlauf and H. Burchard},
-  title = {A generic length-scale equation for geophysical turbulence models},
-  journal = JMS, 
-  year = {2003},
-  volume = {61},  number = {2},
-  pages = {235--265}
+  author =       {L. Umlauf and H. Burchard},
+  title =        {A generic length-scale equation for geophysical
+                  turbulence models},
+  journal =      JMS,
+  year =         2003,
+  volume =       61,
+  number =       2,
+  pages =        {235--265}
 }
 
 @ARTICLE{Umlauf_Burchard_CSR05,
-  author = {L. Umlauf and H. Burchard},
-  title = {Second-order turbulence closure models for geophysical boundary layers. A review of recent work},
-  journal = JMS, 
-  year = {2005},
-  volume = {25},
-  pages = {795--827}
+  author =       {L. Umlauf and H. Burchard},
+  title =        {Second-order turbulence closure models for
+                  geophysical boundary layers. A review of recent
+                  work},
+  journal =      JMS,
+  year =         2005,
+  volume =       25,
+  pages =        {795--827}
 }
 
 @BOOK{UNESCO1983,
-  title = {Algorithms for computation of fundamental property of sea water},
-  publisher = {Techn. Paper in Mar. Sci, 44, UNESCO},
-  year = {1983},
-  author = {UNESCO}
+  title =        {Algorithms for computation of fundamental property
+                  of sea water},
+  publisher =    {Techn. Paper in Mar. Sci, 44, UNESCO},
+  year =         1983,
+  author =       {UNESCO}
 }
 
 @TECHREPORT{OASIS2006,
-  author = {S. Valcke},
-  title = {OASIS3 User Guide (prism\_2-5)},
-  institution = {PRISM Support Initiative Report No 3, CERFACS, Toulouse, France},
-  year = {2006},
-  pages = {64pp}
+  author =       {S. Valcke},
+  title =        {OASIS3 User Guide (prism\_2-5)},
+  institution =  {PRISM Support Initiative Report No 3, CERFACS,
+                  Toulouse, France},
+  year =         2006,
+  pages =        {64pp}
 }
 
 @TECHREPORT{Valcke_al_Rep00,
-  author = {S. Valcke and L. Terray and A. Piacentini },
-  title = {The OASIS Coupled User Guide Version 2.4},
-  institution = {CERFACS},
-  year = {2000},
-  number = {TR/CMGC/00-10}
+  author =       {S. Valcke and L. Terray and A. Piacentini },
+  title =        {The OASIS Coupled User Guide Version 2.4},
+  institution =  {CERFACS},
+  year =         2000,
+  number =       {TR/CMGC/00-10}
 }
 
 @ARTICLE{Vancoppenolle_al_OM09b,
-  author = {M. Vancoppenolle and T. Fichefet and H. Goosse},
-  title = {Simulating the mass balance and salinity of Arctic and Antarctic sea ice. 2. 
-     Importance of sea ice salinity variations},
-  journal = OM,
-  year = {2009},
-  volume = {27},
-  pages = {54--69}
+  author =       {M. Vancoppenolle and T. Fichefet and H. Goosse},
+  title =        {Simulating the mass balance and salinity of Arctic
+                  and Antarctic sea ice. 2.  Importance of sea ice
+                  salinity variations},
+  journal =      OM,
+  year =         2009,
+  volume =       27,
+  pages =        {54--69}
 }
 
 @book{Vallis06,
-author = {Vallis, G. K.},
-title = {Atmospheric and Oceanic Fluid Dynamics},
-publisher = {Cambridge University Press},
-address = {Cambridge, U.K.},
-year = {2006},
-pages = {745},
+  author =       {Vallis, G. K.},
+  title =        {Atmospheric and Oceanic Fluid Dynamics},
+  publisher =    {Cambridge University Press},
+  address =      {Cambridge, U.K.},
+  year =         2006,
+  pages =        745,
 }
 
 @ARTICLE{Vancoppenolle_al_OM09a,
-  author = {M. Vancoppenolle and T. Fichefet and H. Goosse and S. Bouillon and
-	G. Madec and M. A. Morales Maqueda},
-  title = {Simulating the mass balance and salinity of Arctic and Antarctic
-	sea ice. 1. Model description and validation},
-  journal = OM,
-  year = {2009},
-  volume = {27},
-  pages = {33--53},
-  doi = {10.1016/j.ocemod.2008.10.005},
+  author =       {M. Vancoppenolle and T. Fichefet and H. Goosse and
+                  S. Bouillon and G. Madec and M. A. Morales Maqueda},
+  title =        {Simulating the mass balance and salinity of Arctic
+                  and Antarctic sea ice. 1. Model description and
+                  validation},
+  journal =      OM,
+  year =         2009,
+  volume =       27,
+  pages =        {33--53},
+  doi =          {10.1016/j.ocemod.2008.10.005},
 }
 
 @ARTICLE{Vialard_al_JPO01,
-  author = {J. Vialard and C. Menkes and J.-P. Boulanger and P. Delecluse and
-	E. Guilyardi and M.J. McPhaden and G. Madec},
-  title = {A Model Study of Oceanic Mechanisms Affecting Equatorial Pacific
-	Sea Surface Temperature During the 1997-98 El Niño},
-  journal = JPO,
-  year = {2001},
-  volume = {31},  number = {7},
-  pages = {1649--1675}
+  author =       {J. Vialard and C. Menkes and J.-P. Boulanger and
+                  P. Delecluse and E. Guilyardi and M.J. McPhaden and
+                  G. Madec},
+  title =        {A Model Study of Oceanic Mechanisms Affecting
+                  Equatorial Pacific Sea Surface Temperature During
+                  the 1997-98 El Niño},
+  journal =      JPO,
+  year =         2001,
+  volume =       31,
+  number =       7,
+  pages =        {1649--1675}
 }
 
 @ARTICLE{Warner_al_OM05,
-  author = {J. C. Warner and C. R. Sherwood and H. G. Arango and R. P. Signell},
-  title = {Performance of four turbulence closure models implemented using a generic length scale method},
-  journal = OM,
-  year = {2005},
-  volume = {8},
-  pages = {81--113},
-  doi = {10.1016/j.ocemod.2003.12.003},
+  author =       {J. C. Warner and C. R. Sherwood and H. G. Arango and
+                  R. P. Signell},
+  title =        {Performance of four turbulence closure models
+                  implemented using a generic length scale method},
+  journal =      OM,
+  year =         2005,
+  volume =       8,
+  pages =        {81--113},
+  doi =          {10.1016/j.ocemod.2003.12.003},
+}
+
+@ARTICLE{WarnerEtal13,
+   author =      {John C. Warner and Zafer Defne and Kevin Haas and
+                  Hernan G. Arango},
+   title =       {A wetting and drying scheme for ROMS},
+   journal =     "Computers \& Geosciences",
+   volume =      "58", 
+   pages =       "54 - 61",
+   year =        "2013",
+   issn =        "0098-3004",
+   doi =         "https://doi.org/10.1016/j.cageo.2013.05.004",
+   url =         "http://www.sciencedirect.com/science/article/pii/S0098300413001362",
 }
 
 @ARTICLE{Weatherly_JMR84,
-  author = {G. L. Weatherly},
-  title = {An estimate of bottom frictional dissipation by Gulf Stream fluctuations},
-  journal = JMR,
-  year = {1984},
-  volume = {42},  number = {2},
-  pages = {289--301}
+  author =       {G. L. Weatherly},
+  title =        {An estimate of bottom frictional dissipation by Gulf
+                  Stream fluctuations},
+  journal =      JMR,
+  year =         1984,
+  volume =       42,
+  number =       2,
+  pages =        {289--301}
 }
 
 @ARTICLE{Weaver_Eby_JPO97,
-  author = {A. J. Weaver and M. Eby},
-  title = {On the numerical implementation of advection schemes for use in conjuction
-	with various mixing parameterizations in the GFDL ocean model},
-  journal = JPO,
-  year = {1997},
-  volume = {27}
+  author =       {A. J. Weaver and M. Eby},
+  title =        {On the numerical implementation of advection schemes
+                  for use in conjuction with various mixing
+                  parameterizations in the GFDL ocean model},
+  journal =      JPO,
+  year =         1997,
+  volume =       27
 }
 
 @ARTICLE{Webb_al_JAOT98,
-  author = {D. J. Webb and B. A. de Cuevas and C. S. Richmond},
-  title = {Improved Advection Schemes for Ocean Models},
-  journal = JAOT,
-  year = {1998},
-  volume = {15},  number = {5},
-  pages = {1171--1187},
+  author =       {D. J. Webb and B. A. de Cuevas and C. S. Richmond},
+  title =        {Improved Advection Schemes for Ocean Models},
+  journal =      JAOT,
+  year =         1998,
+  volume =       15,
+  number =       5,
+  pages =        {1171--1187},
 }
 
 @ARTICLE{White_al_JCP09,
-  author = {L. White and A. Adcroft and R. Hallberg},
-  title = {High-order regridding-remapping schemes for continuous isopycnal
-	and generalized coordinates in ocean models},
-  journal = JC,
-  year = {2009},
-  volume = {228},
-  pages = {8665--8692}
+  author =       {L. White and A. Adcroft and R. Hallberg},
+  title =        {High-order regridding-remapping schemes for
+                  continuous isopycnal and generalized coordinates in
+                  ocean models},
+  journal =      JC,
+  year =         2009,
+  volume =       228,
+  pages =        {8665--8692}
 }
 
 @ARTICLE{Wilcox_1988,
-  author = {D. C. Wilcox},
-  title = {Reassessment of the scale-determining equation for advanced turbulence models},
-  journal = {AIAA journal},
-  year = {1988},
-  volume = {26},  number = {11},
-  pages = {1299--1310}
+  author =       {D. C. Wilcox},
+  title =        {Reassessment of the scale-determining equation for
+                  advanced turbulence models},
+  journal =      {AIAA journal},
+  year =         1988,
+  volume =       26,
+  number =       11,
+  pages =        {1299--1310}
 }
 
 @ARTICLE{Willebrand_al_PO01,
-  author = {J. Willebrand and B. Barnier and C. Boning and C. Dieterich and P.
-	D. Killworth and C. Le Provost and Y. Jia and J.-M. Molines and A. L. New},
-  title = {Circulation characteristics in three eddy-permitting models of the North Atlantic},
-  journal = PO,
-  year = {2001},
-  volume = {48},  number = {2},
-  pages = {123--161}
+  author =       {J. Willebrand and B. Barnier and C. Boning and
+                  C. Dieterich and P.  D. Killworth and C. Le Provost
+                  and Y. Jia and J.-M. Molines and A. L. New},
+  title =        {Circulation characteristics in three eddy-permitting
+                  models of the North Atlantic},
+  journal =      PO,
+  year =         2001,
+  volume =       48,
+  number =       2,
+  pages =        {123--161}
 }
 
 @ARTICLE{Williams_al_DAO09,
-  author = {P.D. Williams and E. Guilyardi and G. Madec and S. Gualdi and E. Scoccimarro},
-  title = {The role of mean ocean salinity on climate},
-  journal = DAO,
-  year = {2010},
-  volume = {49},  number = {2-3},
-  pages = {108--123},
-  doi = {10.1016/j.dynatmoce.2009.02.001},
+  author =       {P.D. Williams and E. Guilyardi and G. Madec and
+                  S. Gualdi and E. Scoccimarro},
+  title =        {The role of mean ocean salinity on climate},
+  journal =      DAO,
+  year =         2010,
+  volume =       49,
+  number =       {2-3},
+  pages =        {108--123},
+  doi =          {10.1016/j.dynatmoce.2009.02.001},
 }
 
 @ARTICLE{Williams_al_GRL07,
-  author = {P.D. Williams and E. Guilyardi and R. Sutton and J.M. Gregory and G. Madec},
-  title = {A new feedback on climate change from the hydrological cycle},
-  journal = GRL,
-  year = {2007},
-  volume = {34},
-  pages = {L08706},
-  doi = {10.1029/2007GL029275},
+  author =       {P.D. Williams and E. Guilyardi and R. Sutton and
+                  J.M. Gregory and G. Madec},
+  title =        {A new feedback on climate change from the
+                  hydrological cycle},
+  journal =      GRL,
+  year =         2007,
+  volume =       34,
+  pages =        {L08706},
+  doi =          {10.1029/2007GL029275},
 }
 
 @ARTICLE{Williams_al_CD06,
-  author = {P.D. Williams and E. Guilyardi and R. Sutton and J.M. Gregory and G. Madec},
-  title = {On the climate response of the low-latitude Pacific ocean to changes in the global freshwater cycle},
-  journal = CD,
-  year = {2006},
-  volume = {27},
-  pages = {593--611}
+  author =       {P.D. Williams and E. Guilyardi and R. Sutton and
+                  J.M. Gregory and G. Madec},
+  title =        {On the climate response of the low-latitude Pacific
+                  ocean to changes in the global freshwater cycle},
+  journal =      CD,
+  year =         2006,
+  volume =       27,
+  pages =        {593--611}
 }
 
 @ARTICLE{Zalesak_JCP79,
-  author = {S. T. Zalesak},
-  title = {Fully multidimensional flux corrected transport algorithms for fluids},
-  journal = JCP,
-  year = {1979},
-  volume = {31}
+  author =       {S. T. Zalesak},
+  title =        {Fully multidimensional flux corrected transport
+                  algorithms for fluids},
+  journal =      JCP,
+  year =         1979,
+  volume =       31
 }
 
 @ARTICLE{Zhang_Endoh_JGR92,
-  author = {Zhang, R.-H. and Endoh, M.},
-  title = {A free surface general circulation model for the tropical Pacific Ocean},
-  journal = JGR,
-  year = {1992},
-  volume = {97},
-  pages = {11,237--11,255}
-}
-
-@ARTICLE{Oey06,
-   title = "An OGCM with movable land-sea boundaries",
-   journal = "Ocean Modelling",
-   volume = "13",
-   number = "2",
-   pages = "176 - 195",
-   year = "2006",
-   issn = "1463-5003",
-   doi = "https://doi.org/10.1016/j.ocemod.2006.01.001",
-   url = "http://www.sciencedirect.com/science/article/pii/S1463500306000084",
-   author = "Lie-Yauw Oey",
-   keywords = "Wetting and drying, Inundations, Ocean general circulation model (OGCM)
-, Princeton Ocean Model (POM), Tides, Tsunamis, Estuarine outflows",
-   abstract = "An ocean general circulation model (OGCM) with wetting and drying (WAD) capabilities removes the vertical-wall coastal assumption and allows simultaneous modeling of open-ocean currents and water run-up (and run-down) across movable land-sea boundaries. This paper implements and tests such a WAD scheme for the Princeton Ocean Model (POM) in its most general three-dimensional setting with stratification, bathymetry and forcing. The scheme can be easily exported to other OGCM's."
-}
-
-@ARTICLE{WarnerEtal13,
-   title = "A wetting and drying scheme for ROMS",
-   journal = "Computers \& Geosciences",
-   volume = "58", 
-   pages = "54 - 61",
-   year = "2013",
-   issn = "0098-3004",
-   doi = "https://doi.org/10.1016/j.cageo.2013.05.004",
-   url = "http://www.sciencedirect.com/science/article/pii/S0098300413001362",
-   author = "John C. Warner and Zafer Defne and Kevin Haas and Hernan G. Arango",
-   keywords = "Wetting and drying, ROMS, Cell-face blocking",
-   abstract = "The processes of wetting and drying have many important physical and biological impacts on shallow water systems. Inundation and dewatering effects on coastal mud flats and beaches occur on various time scales ranging from storm surge, periodic rise and fall of the tide, to infragravity wave motions. To correctly simulate these physical processes with a numerical model requires the capability of the computational cells to become inundated and dewatered. In this paper, we describe a method for wetting and drying based on an approach consistent with a cell-face blocking algorithm. The method allows water to always flow into any cell, but prevents outflow from a cell when the total depth in that cell is less than a user defined critical value. We describe the method, the implementation into the three-dimensional Regional Oceanographic Modeling System (ROMS), and exhibit the new capability under three scenarios: an analytical expression for shallow water flows, a dam break test case, and a realistic application to part of a wetland area along the Georgia Coast, USA."
-}
-
-@comment{jabref-meta: groupsversion:3;}
-
-@comment{jabref-meta: groupstree:
-0 AllEntriesGroup:;
-1 ExplicitGroup:El Nino\;2\;blanketal97\;;
-2 ExplicitGroup:97/98 event\;0\;;
-2 ExplicitGroup:Forecast\;0\;;
-2 ExplicitGroup:GHG change\;0\;;
-2 ExplicitGroup:in GCMs\;0\;;
-2 ExplicitGroup:in MIPs\;0\;;
-2 ExplicitGroup:momentum balance\;0\;;
-2 ExplicitGroup:Obs analysis\;0\;;
-2 ExplicitGroup:Paleo\;0\;;
-2 ExplicitGroup:Previous events\;0\;;
-2 ExplicitGroup:Reviews\;0\;;
-2 ExplicitGroup:Simple models\;0\;Zhang_Endoh_JGR92\;;
-2 ExplicitGroup:SPL, SC, mean\;0\;;
-2 ExplicitGroup:Teleconnections\;0\;;
-2 ExplicitGroup:Low freq\;0\;;
-2 ExplicitGroup:Theory\;0\;;
-2 ExplicitGroup:Energetics\;0\;;
-1 ExplicitGroup:Diurnal in tropics\;0\;;
-1 ExplicitGroup:Indian\;0\;;
-1 ExplicitGroup:Atlantic\;0\;;
-1 ExplicitGroup:MJO, IO, TIW\;2\;;
-2 ExplicitGroup:Obs\;0\;;
-2 ExplicitGroup:GCM\;0\;;
-2 ExplicitGroup:Mechanims\;0\;;
-2 ExplicitGroup:TIW\;0\;;
-1 ExplicitGroup:Observations\;2\;;
-2 ExplicitGroup:ERBE\;0\;;
-2 ExplicitGroup:Tropical\;0\;;
-2 ExplicitGroup:Global\;0\;;
-2 ExplicitGroup:Clouds\;0\;;
-2 ExplicitGroup:Scale interactions\;0\;;
-1 ExplicitGroup:Mechanisms\;2\;;
-2 ExplicitGroup:CRF\;0\;;
-2 ExplicitGroup:Water vapor\;0\;;
-2 ExplicitGroup:Atmos mechanisms\;0\;;
-1 ExplicitGroup:GCMs\;2\;;
-2 ExplicitGroup:Uncertainty\;0\;;
-2 ExplicitGroup:Momentum balance\;0\;;
-1 ExplicitGroup:Climate change\;0\;;
-2 ExplicitGroup:IPCC AR4\;0\;;
-1 ExplicitGroup:Analysis tools\;0\;;
-1 KeywordGroup:EG publis\;0\;author\;guilyardi\;0\;0\;;
-}
-
+  author =       {Zhang, R.-H. and Endoh, M.},
+  title =        {A free surface general circulation model for the
+                  tropical Pacific Ocean},
+  journal =      JGR,
+  year =         1992,
+  volume =       97,
+  pages =        {11,237--11,255}
+}
Index: /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/latex/NEMO/main/NEMO_manual.tex
===================================================================
--- /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/latex/NEMO/main/NEMO_manual.tex	(revision 10497)
+++ /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/latex/NEMO/main/NEMO_manual.tex	(revision 10498)
@@ -1,13 +1,8 @@
 %% ==============================================================================
-%% NEMO_book.tex: build the NEMO Reference Manual
+%% NEMO Reference Manual
 %% ==============================================================================
 
 
-%% Run ../build_NEMO_manual.sh to generate the PDF version (with pdflatex)
-
-%% Document layout
-%% ==============================================================================
-
-\documentclass[a4paper, 11pt]{book}
+%% Run ./PDF_creation.sh to generate the manual with latexmk
 
 
@@ -15,12 +10,9 @@
 %% ==============================================================================
 
-%% Custom style
+%% Document layout
+\documentclass{book}
+
+%% Custom style (.sty)
 \usepackage{../main/NEMO_manual}
-
-\makeindex
-
-
-%% 
-%% ==============================================================================
 
 %% Include references and index for single subfile compilation
@@ -28,4 +20,7 @@
 \newcommand{\pindex}{\printindex}
 
+\makeindex
+
+%% End of common preamble between main and sub-files
 \begin{document}
 
@@ -39,13 +34,13 @@
 
 %% Frontpage
-
 \title{
-%\vspace{-6.0cm}\includegraphics[width=1.1\textwidth]{logo_ALL}				\\
-%\vspace{ 5.1cm}\includegraphics[width=0.9\textwidth]{NEMO_logo_Black}	\\
-\vspace{ 1.4cm}\rule{345pt}{1.5pt}													\\
-\vspace{0.45cm}{\Huge NEMO ocean engine}											\\
-\rule{345pt}{1.5pt}
+  \includegraphics[height=0.05\textheight]{CMCC}\hfill
+  \includegraphics[height=0.05\textheight]{CNRS}\hfill
+  \includegraphics[height=0.05\textheight]{MOI} \hfill
+  \includegraphics[height=0.05\textheight]{UKMO}\hfill
+  \includegraphics[height=0.05\textheight]{NERC}       \\
+  \includegraphics[ width=0.8\textwidth  ]{NEMO_grey}  \\
+  {\Huge NEMO ocean engine}                            \\
 }
-
 \author{
   \Large Gurvan Madec and NEMO System Team
@@ -62,5 +57,4 @@
   \textit{ISSN 1288-1619}
 }
-
 \date{Version 4.0 -- January 2019}
 %\date{\today}
@@ -71,5 +65,4 @@
 
 %% ToC i.e. Table of Contents
-
 \dominitoc
 \tableofcontents
@@ -81,60 +74,33 @@
 \mainmatter
 
-
 %% Foreword
-
 \subfile{../subfiles/foreword}
 
-
-% Introduction
-
+%% Introduction
 \subfile{../subfiles/introduction}
 
-
-% Chapters
-
+%% Chapters
 \subfile{../subfiles/chap_model_basics}
-
 \subfile{../subfiles/chap_time_domain}   % Time discretisation (time stepping strategy)
-
 \subfile{../subfiles/chap_DOM}           % Space discretisation
-
 \subfile{../subfiles/chap_TRA}           % Tracer advection/diffusion equation
-
 \subfile{../subfiles/chap_DYN}           % Dynamics : momentum equation
-
 \subfile{../subfiles/chap_SBC}           % Surface Boundary Conditions
-
 \subfile{../subfiles/chap_LBC}           % Lateral Boundary Conditions
-
 \subfile{../subfiles/chap_LDF}           % Lateral diffusion
-
 \subfile{../subfiles/chap_ZDF}           % Vertical diffusion
-
 \subfile{../subfiles/chap_DIA}           % Outputs and Diagnostics
-
 \subfile{../subfiles/chap_OBS}           % Observation operator
-
 \subfile{../subfiles/chap_ASM}           % Assimilation increments
-
 \subfile{../subfiles/chap_STO}           % Stochastic param.
-
 \subfile{../subfiles/chap_misc}          % Miscellaneous topics
-
 \subfile{../subfiles/chap_CONFIG}        % Predefined configurations
 
-
 %% Appendix
-
 \appendix
-
 \subfile{../subfiles/annex_A}					% Generalised vertical coordinate
-
 \subfile{../subfiles/annex_B}					% Diffusive operator
-
 \subfile{../subfiles/annex_C}					% Discrete invariants of the eqs.
-
 \subfile{../subfiles/annex_iso}				% Isoneutral diffusion using triads
-
 \subfile{../subfiles/annex_D}					% Coding rules
 
@@ -142,6 +108,4 @@
 %\subfile{../subfiles/chap_conservation}	%
 %\subfile{../subfiles/annex_E}				% Notes on some on going staff
-%\subfile{../subfiles/annex_Fox-Kemper}	% Notes on Fox-Kemper
-%\subfile{../subfiles/annex_EVP}				% Notes on EVP
 
 
@@ -151,7 +115,5 @@
 \backmatter
 
-
 %% Bibliography
-
 \cleardoublepage
 \phantomsection
@@ -161,5 +123,4 @@
 
 %% Index
-
 \cleardoublepage
 \phantomsection
Index: /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/latex/NEMO/subfiles/chap_DYN.tex
===================================================================
--- /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/latex/NEMO/subfiles/chap_DYN.tex	(revision 10497)
+++ /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/latex/NEMO/subfiles/chap_DYN.tex	(revision 10498)
@@ -697,10 +697,7 @@
 \label{subsec:DYN_hpg_isf}
 Beneath an ice shelf, the total pressure gradient is the sum of the pressure gradient due to the ice shelf load and
-the pressure gradient due to the ocean load.
-If cavity opened (\np{ln\_isfcav}\forcode{ = .true.}) these 2 terms can be calculated by
-setting \np{ln\_dynhpg\_isf}\forcode{ = .true.}.
-No other scheme are working with the ice shelf.\\
-
-$\bullet$ The main hypothesis to compute the ice shelf load is that the ice shelf is in an isostatic equilibrium.
+the pressure gradient due to the ocean load (\np{ln\_dynhpg\_isf}\forcode{ = .true.}).\\
+
+The main hypothesis to compute the ice shelf load is that the ice shelf is in an isostatic equilibrium.
 The top pressure is computed integrating from surface to the base of the ice shelf a reference density profile
 (prescribed as density of a water at 34.4 PSU and -1.9\deg{C}) and
@@ -709,5 +706,5 @@
 A detailed description of this method is described in \citet{Losch2008}.\\
 
-$\bullet$ The ocean load is computed using the expression \autoref{eq:dynhpg_sco} described in
+The pressure gradient due to ocean load is computed using the expression \autoref{eq:dynhpg_sco} described in
 \autoref{subsec:DYN_hpg_sco}. 
 
Index: /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/latex/NEMO/subfiles/chap_LBC.tex
===================================================================
--- /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/latex/NEMO/subfiles/chap_LBC.tex	(revision 10497)
+++ /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/latex/NEMO/subfiles/chap_LBC.tex	(revision 10498)
@@ -613,11 +613,11 @@
 \label{subsec:BDY_vol_corr}
 
-There is an option to force the total volume in the regional model to be constant,
-similar to the option in the OBC module.
-This is controlled  by the \np{nn\_volctl} parameter in the namelist.
-A value of \np{nn\_volctl}\forcode{ = 0} indicates that this option is not used.
-If \np{nn\_volctl}\forcode{ = 1} then a correction is applied to the normal velocities around the boundary at
+There is an option to force the total volume in the regional model to be constant.
+This is controlled  by the \np{ln\_vol} parameter in the namelist.
+A value of \np{ln\_vol}\forcode{ = .false.} indicates that this option is not used.
+Two options to control the volume are available (\np{nn\_volctl}). 
+If \np{nn\_volctl}\forcode{ = 0} then a correction is applied to the normal barotropic velocities around the boundary at
 each timestep to ensure that the integrated volume flow through the boundary is zero.
-If \np{nn\_volctl}\forcode{ = 2} then the calculation of the volume change on
+If \np{nn\_volctl}\forcode{ = 1} then the calculation of the volume change on
 the timestep includes the change due to the freshwater flux across the surface and
 the correction velocity corrects for this as well.
Index: /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/latex/NEMO/subfiles/chap_SBC.tex
===================================================================
--- /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/latex/NEMO/subfiles/chap_SBC.tex	(revision 10497)
+++ /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/latex/NEMO/subfiles/chap_SBC.tex	(revision 10498)
@@ -921,5 +921,5 @@
 
 The mass/volume addition due to the river runoff is, at each relevant depth level, added to
-the horizontal divergence (\textit{hdivn}) in the subroutine \rou{sbc\_rnf\_div} (called from \mdl{divcur}).
+the horizontal divergence (\textit{hdivn}) in the subroutine \rou{sbc\_rnf\_div} (called from \mdl{divhor}).
 This increases the diffusion term in the vicinity of the river, thereby simulating a momentum flux.
 The sea surface height is calculated using the sum of the horizontal divergence terms,
@@ -990,54 +990,84 @@
 \nlst{namsbc_isf}
 %--------------------------------------------------------------------------------------------------------
-Namelist variable in \ngn{namsbc}, \np{nn\_isf}, controls the ice shelf representation used. 
+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}. 
+The different options are illustrated in \autoref{fig:SBC_isf}.
+
 \begin{description}
-\item[\np{nn\_isf}\forcode{ = 1}]
+\item[\np{nn\_isf}\forcode{ = 1}]:
   The ice shelf cavity is represented (\np{ln\_isfcav}\forcode{ = .true.} needed).
-  The fwf and heat flux are computed.
-  Two different bulk formula are available:
+  The fwf and heat flux are depending of the local water properties.
+  Two different bulk formulae are available:
+
 	\begin{description}
-	\item[\np{nn\_isfblk}\forcode{ = 1}]
-     The bulk formula used to compute the melt is based the one described in \citet{Hunter2006}.
-     This formulation is based on a balance between the upward ocean heat flux and
-     the latent heat flux at the ice shelf base.
-	\item[\np{nn\_isfblk}\forcode{ = 2}]
-     The bulk formula used to compute the melt is based the one described in \citet{Jenkins1991}.
-     This formulation is based on a 3 equations formulation
-     (a heat flux budget, a salt flux budget and a linearised freezing point temperature equation).
+	\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}.
+	\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}.
 	\end{description}
-   For this 2 bulk formulations, there are 3 different ways to compute the exchange coeficient:
+
+     Temperature and salinity used to compute the melt are the average temperature in the top boundary layer \citet{Losch2008}. 
+     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.
+     Then, the fluxes are spread over the same thickness (ie over one or several cells).
+     If \np{rn\_hisf\_tbl} larger than top $e_{3}t$, there is no more feedback between the freezing point at the interface and the the top cell temperature.
+     This can lead to super-cool temperature in the top cell under melting condition.
+     If \np{rn\_hisf\_tbl} smaller than top $e_{3}t$, the top boundary layer thickness is set to the top cell thickness.\\
+
+     Each melt bulk formula depends on a exchange coeficient ($\Gamma^{T,S}$) between the ocean and the ice. 
+     There are 3 different ways to compute the exchange coeficient:
 	\begin{description}
-   \item[\np{nn\_gammablk}\forcode{ = 0}]
-     The salt and heat exchange coefficients are constant and defined by \np{rn\_gammas0} and \np{rn\_gammat0}
-	\item[\np{nn\_gammablk}\forcode{ = 1}]
+        \item[\np{nn\_gammablk}\forcode{ = 0}]:
+     The salt and heat exchange coefficients are constant and defined by \np{rn\_gammas0} and \np{rn\_gammat0}. 
+\[
+  % \label{eq:sbc_isf_gamma_iso}
+\gamma^{T} = \np{rn\_gammat0}
+\]
+\[
+\gamma^{S} = \np{rn\_gammas0}
+\]
+     This is the recommended formulation for ISOMIP.
+	\item[\np{nn\_gammablk}\forcode{ = 1}]:
      The salt and heat exchange coefficients are velocity dependent and defined as
-     \np{rn\_gammas0}$ \times u_{*}$ and \np{rn\_gammat0}$ \times u_{*}$ 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.
-	\item[\np{nn\_gammablk}\forcode{ = 2}]
-     The salt and heat exchange coefficients are velocity and stability dependent and defined as
-     $\gamma_{T,S} = \frac{u_{*}}{\Gamma_{Turb} + \Gamma^{T,S}_{Mole}}$ where
-     $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn\_hisf\_tbl} meters),
+\[
+\gamma^{T} = \np{rn\_gammat0} \times u_{*} 
+\]
+\[
+\gamma^{S} = \np{rn\_gammas0} \times u_{*}
+\]
+     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.
+	\item[\np{nn\_gammablk}\forcode{ = 2}]:
+     The salt and heat exchange coefficients are velocity and stability dependent and defined as:
+\[
+\gamma^{T,S} = \frac{u_{*}}{\Gamma_{Turb} + \Gamma^{T,S}_{Mole}} 
+\]
+     where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn\_hisf\_tbl} meters),
      $\Gamma_{Turb}$ 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{Holland1999} 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}]
-   A parameterisation of isf is used. The ice shelf cavity is not represented.
-   The fwf is distributed along the ice shelf edge between the depth of the average grounding line (GL)
+ \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 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
    (\np{sn\_depmin\_isf}) as in (\np{nn\_isf}\forcode{ = 3}).
-   Furthermore the fwf and heat flux are computed using the \citet{Beckmann2003} parameterisation of isf melting.
    The effective melting length (\np{sn\_Leff\_isf}) is read from a file.
- \item[\np{nn\_isf}\forcode{ = 3}]
-   A simple parameterisation of isf is used. The ice shelf cavity is not represented.
+ \item[\np{nn\_isf}\forcode{ = 3}]:
+   The ice shelf cavity is not represented.
    The fwf (\np{sn\_rnfisf}) is prescribed and 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 (\np{sn\_depmin\_isf}).
    The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$.
- \item[\np{nn\_isf}\forcode{ = 4}]
+ \item[\np{nn\_isf}\forcode{ = 4}]:
    The ice shelf cavity is opened (\np{ln\_isfcav}\forcode{ = .true.} needed).
    However, the fwf is not computed but specified from file \np{sn\_fwfisf}).
-   The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$.\\
+   The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$.
+   As in \np{nn\_isf}\forcode{ = 1}, the fluxes are spread over the top boundary layer thickness (\np{rn\_hisf\_tbl})\\
 \end{description}
 
@@ -1053,18 +1083,20 @@
 for studies where you need to control your heat and fw input.\\ 
 
-A namelist parameters control over how many meters the heat and fw fluxes are spread.
-\np{rn\_hisf\_tbl}] is the top boundary layer thickness as defined in \citet{Losch2008}.
-This parameter is only used if \np{nn\_isf}\forcode{ = 1} or \np{nn\_isf}\forcode{ = 4}.
-
-If \np{rn\_hisf\_tbl}\forcode{ = 0}., the fluxes are put in the top level whatever is its tickness. 
-
-If \np{rn\_hisf\_tbl} $>$ 0., the fluxes are spread over the first \np{rn\_hisf\_tbl} m
-(ie over one or several cells).\\
-
-The ice shelf melt is implemented as a volume flux with in the same way as for the runoff.
+The ice shelf melt is implemented as a volume flux as for the runoff.
 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 \autoref{sec:SBC_rnf} for all the details about the divergence correction.
-
+the horizontal divergence (\textit{hdivn}) in the subroutine \rou{sbc\_isf\_div}, called from \mdl{divhor}.
+See the runoff section \autoref{sec:SBC_rnf} for all the details about the divergence correction.\\
+
+%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+\begin{figure}[!t]
+  \begin{center}
+    \includegraphics[width=0.8\textwidth]{Fig_SBC_isf}
+    \caption{
+      \protect\label{fig:SBC_isf}
+      Illustration the location where the fwf is injected and whether or not the fwf is interactif or not depending of \np{nn\_isf}.
+    }
+  \end{center}
+\end{figure}
+%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 
 \section{Ice sheet coupling}
@@ -1075,42 +1107,54 @@
 %--------------------------------------------------------------------------------------------------------
 Ice sheet/ocean coupling is done through file exchange at the restart step.
-NEMO, at each restart step, read the bathymetry and ice shelf draft variable in a netcdf file.
+At each restart step:
+\begin{description}
+\item[Step 1]: the ice sheet model send a new bathymetry and ice shelf draft netcdf file.
+\item[Step 2]: a new domcfg.nc file is built using the DOMAINcfg tools.
+\item[Step 3]: NEMO run for a specific period and output the average melt rate over the period.
+\item[Step 4]: the ice sheet model run using the melt rate outputed in step 4.
+\item[Step 5]: go back to 1.
+\end{description}
+
 If \np{ln\_iscpl}\forcode{ = .true.}, the isf draft is assume to be different at each restart step with
 potentially some new wet/dry cells due to the ice sheet dynamics/thermodynamics.
-The wetting and drying scheme applied on the restart is very simple and described below for the 6 different cases:
+The wetting and drying scheme applied on the restart is very simple and described below for the 6 different possible cases:
 \begin{description}
-\item[Thin a cell down:]
+\item[Thin a cell down]:
   T/S/ssh are unchanged and U/V in the top cell are corrected to keep the barotropic transport (bt) constant
   ($bt_b=bt_n$).
-\item[Enlarge  a cell:]
+\item[Enlarge  a cell]:
   See case "Thin a cell down"
-\item[Dry a cell:]
+\item[Dry a cell]:
   mask, T/S, U/V and ssh are set to 0.
   Furthermore, U/V into the water column are modified to satisfy ($bt_b=bt_n$).
-\item[Wet a cell:] 
+\item[Wet a cell]: 
   mask is set to 1, T/S is extrapolated from neighbours, $ssh_n = ssh_b$ and U/V set to 0.
-  If no neighbours along i,j and k, T/S/U/V and mask are set to 0.
-\item[Dry a column:]
+  If no neighbours, T/S is extrapolated from old top cell value. 
+  If no neighbours along i,j and k (both previous test failed), T/S/U/V/ssh and mask are set to 0.
+\item[Dry a column]:
 	mask, T/S, U/V are set to 0 everywhere in the column and ssh set to 0.
-\item[Wet a column:]
+\item[Wet a column]:
   set mask to 1, T/S is extrapolated from neighbours, ssh is extrapolated from neighbours and U/V set to 0.
   If no neighbour, T/S/U/V and mask set to 0.
 \end{description}
-The extrapolation is call \np{nn\_drown} times.
+
+Furthermore, as the before and now fields are not compatible (modification of the geometry),
+the restart time step is prescribed to be an euler time step instead of a leap frog and $fields_b = fields_n$.\\
+
+The horizontal extrapolation to fill new cell with realistic value is called \np{nn\_drown} times.
 It means that if the grounding line retreat by more than \np{nn\_drown} cells between 2 coupling steps,
 the code will be unable to fill all the new wet cells properly.
-The default number is set up for the MISOMIP idealised experiments.\\
+The default number is set up for the MISOMIP idealised experiments.
 This coupling procedure is able to take into account grounding line and calving front migration.
 However, it is a non-conservative processe. 
-This could lead to a trend in heat/salt content and volume.
+This could lead to a trend in heat/salt content and volume.\\
+
 In order to remove the trend and keep the conservation level as close to 0 as possible,
 a simple conservation scheme is available with \np{ln\_hsb}\forcode{ = .true.}.
-The heat/salt/vol. gain/loss is diagnose, as well as the location.
-Based on what is done on sbcrnf to prescribed a source of heat/salt/vol.,
-the heat/salt/vol. gain/loss is removed/added, over a period of \np{rn\_fiscpl} time step, into the system. 
-So after \np{rn\_fiscpl} time step, all the heat/salt/vol. gain/loss due to extrapolation process is canceled.\\
-
-As the before and now fields are not compatible (modification of the geometry),
-the restart time step is prescribed to be an euler time step instead of a leap frog and $fields_b = fields_n$.
+The heat/salt/vol. gain/loss is diagnosed, as well as the location.
+A correction increment is computed and apply each time step during the next \np{rn\_fiscpl} time steps. 
+For safety, it is advised to set \np{rn\_fiscpl} equal to the coupling period (smallest increment possible).
+The corrective increment is apply into the cell itself (if it is a wet cell), the neigbouring cells or the closest wet cell (if the cell is now dry).
+
 %
 % ================================================================
Index: /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/latex/NEMO/subfiles/foreword.tex
===================================================================
--- /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/latex/NEMO/subfiles/foreword.tex	(revision 10497)
+++ /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/latex/NEMO/subfiles/foreword.tex	(revision 10498)
@@ -4,56 +4,74 @@
 
 % ================================================================
+% Chapter Foreword
+% ================================================================
+\chapter*{Foreword}
+
+% ================================================================
 % Abstract
 % ================================================================
+\section*{Abstract}
 
-\chapter*{Abstract}
+The ocean engine of NEMO (Nucleus for European Modelling of the Ocean) is a primitive equation model adapted to
+regional and global ocean circulation problems.
+It is intended to be a flexible tool for studying the ocean and its interactions with the others components of
+the earth climate system over a wide range of space and time scales.
 
-\vspace{-40pt}
+Prognostic variables are the three-dimensional velocity field, a non-linear sea surface height,
+the \textit{Conservative} Temperature and the \textit{Absolute} Salinity.
+In the horizontal direction, the model uses a curvilinear orthogonal grid and in the vertical direction,
+a full or partial step $z$-coordinate, or $s$-coordinate, or a mixture of the two.
+The distribution of variables is a three-dimensional Arakawa C-type grid.
+Various physical choices are available to describe ocean physics, including TKE, and GLS vertical physics.
 
-{\small
-  The ocean engine of NEMO (Nucleus for European Modelling of the Ocean) is a primitive equation model adapted to
-  regional and global ocean circulation problems.
-  It is intended to be a flexible tool for studying the ocean and its interactions with
-  the others components of the earth climate system over a wide range of space and time scales.
-  Prognostic variables are the three-dimensional velocity field, a non-linear sea surface height,
-  the \textit{Conservative} Temperature and the \textit{Absolute} Salinity.
-  In the horizontal direction, the model uses a curvilinear orthogonal grid and in the vertical direction,
-  a full or partial step $z$-coordinate, or $s$-coordinate, or a mixture of the two.
-  The distribution of variables is a three-dimensional Arakawa C-type grid.
-  Various physical choices are available to describe ocean physics, including TKE, and GLS vertical physics.
-  Within NEMO, the ocean is interfaced with a sea-ice model (LIM or CICE),
-  passive tracer and biogeochemical models (TOP) and,
-  via the OASIS coupler, with several atmospheric general circulation models.
-  It also support two-way grid embedding via the AGRIF software.
-} 
+Within NEMO, the ocean is interfaced with a sea-ice model (SI$^3$)
+ %or \href{https://github.com/CICE-Consortium/CICE}{CICE}),
+passive tracer and biogeochemical models (TOP-PISCES) and,
+via the \href{https://portal.enes.org/oasis}{OASIS} coupler, with several atmospheric general circulation models.
+It also support two-way grid embedding via the \href{http://agrif.imag.fr}{AGRIF} software.
+
 
 % ================================================================
 % Disclaimer
 % ================================================================
-\chapter*{Disclaimer}
+\section*{Disclaimer}
 
-Like all components of NEMO,
-the ocean component is developed under the \href{http://www.cecill.info/}{CECILL license},
-which is a French adaptation of the GNU GPL (General Public License).
-Anyone may use it freely for research purposes,
-and is encouraged to communicate back to the NEMO team its own developments and improvements.
+Like all components of NEMO, the ocean component is developed under
+the \href{http://www.cecill.info}{CECILL license}, which is a French adaptation of the GNU GPL
+(General Public License).
+Anyone may use it freely for research purposes, and is encouraged to communicate back to the NEMO team
+its own developments and improvements.
+
 The model and the present document have been made available as a service to the community.
 We cannot certify that the code and its manual are free of errors.
 Bugs are inevitable and some have undoubtedly survived the testing phase.
 Users are encouraged to bring them to our attention.
+
 The author assumes no responsibility for problems, errors, or incorrect usage of NEMO.
 
-\vspace{1cm}
-NEMO reference in papers and other publications is as follows:
+% ================================================================
+% Citation
+% ================================================================
+\section*{Citation}
+
+Reference for papers and other publications is as follows:
 \vspace{0.5cm}
 
-Madec, G., and the NEMO team, 2008: NEMO ocean engine. 
-\textit{Note du P\^ole de mod\'{e}lisation}, Institut Pierre-Simon Laplace (IPSL), France, 
-No 27, ISSN No 1288-1619.\\
+{\sffamily
+NEMO ocean engine,
+Madec Gurvan and NEMO System Team, NEMO Consortium,
+Issue 27, Notes du Pôle de modélisation de l'Institut Pierre-Simon Laplace (IPSL), ISSN 1288-1619,
+\href{http://doi.org/10.5281/zenodo.1464816}{doi:10.5281/zenodo.1464816}
+}
 
+% ================================================================
+% External resources
+% ================================================================
+\section*{External resources}
 
-\vspace{0.5cm}
-Additional information can be found on \href{http://www.nemo-ocean.eu/}{www.nemo-ocean.eu}.
-\vspace{0.5cm}
+Additional information can be found on the \href{http://www.nemo-ocean.eu}{website} of the project and
+the \href{http://forge.ipsl.jussieu.fr/nemo}{forge platform} of the source code.
+A \href{http://listes.ipsl.fr/sympa/info/nemo-newsletter}{newsletter list} is also open for subscription to
+receive top-down communication from the consortium (announcements, job opportunities, ...).
 
 \biblio
Index: /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/latex/NEMO/subfiles/introduction.tex
===================================================================
--- /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/latex/NEMO/subfiles/introduction.tex	(revision 10497)
+++ /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/latex/NEMO/subfiles/introduction.tex	(revision 10498)
@@ -10,20 +10,24 @@
 
 The Nucleus for European Modelling of the Ocean (\NEMO) is a framework of ocean related engines,
-namely OPA \footnote{OPA = Oc\'{e}an PArall\'{e}lis\'{e}} for the ocean dynamics and thermodynamics,
-LIM \footnote{LIM = Louvain la-neuve Ice Model} for the sea-ice dynamics and thermodynamics,
-TOP \footnote{TOP = Tracer in the Ocean Paradigm} for the biogeochemistry (both transport (TRP) and sources 
-minus sinks (LOBSTER \footnote{LOBSTER = Lodyc Ocean Biogeochemical SysTem for Ecosystem and Resources},
-PISCES \footnote{PISCES = Pelagic Interactions Scheme for Carbon and Ecosystem Studies})).
+namely OPA \footnote{OPA: Oc\'{e}an PArall\'{e}lis\'{e} (french)} for the ocean dynamics and thermodynamics,
+SI$^3$ \footnote{SI$^3$: Sea-Ice modelling Integrated Initiative} for the sea-ice dynamics and thermodynamics,
+TOP \footnote{TOP: Tracer in the Ocean Paradigm} for the biogeochemistry 
+(both transport (TRP) and sources minus sinks 
+(PISCES \footnote{PISCES: Pelagic Interactions Scheme for Carbon and Ecosystem Studies})).
 It is intended to be a flexible tool for studying the ocean and its interactions with the other components of
 the earth climate system (atmosphere, sea-ice, biogeochemical tracers, ...) over
-a wide range of space and time scales. 
-This documentation provides information about the physics represented by the ocean component of \NEMO and
+a wide range of space and time scales.
+This manual provides information about the physics represented by the ocean component of \NEMO and
 the rationale for the choice of numerical schemes and the model design.
-More specific information about running the model on different computers, or how to set up a configuration,
-are found on the \NEMO web site (www.nemo-ocean.eu). 
-
-The ocean component of \NEMO has been developed from the OPA model, release 8.2, described in \citet{Madec1998}.
-This model has been used for a wide range of applications, both regional or global,
-as a forced ocean model and as a model coupled with the sea-ice and/or the atmosphere.  
+For the use of framework, 
+a guide which gathers the \texttt{README} files spread out in the source code can be build and 
+exported in web or printable format (see \path{./doc/rst}).
+An online version of the guide is also available on the 
+\href{http://forge.ipsl.jussieu.fr/nemo}{\NEMO forge platform}.
+
+The ocean component of \NEMO has been developed from the legacy of the OPA model, release 8.2, 
+described in \citet{Madec1998}.
+This model has been used for a wide range of applications, both regional or global, as a forced ocean model and 
+as a model coupled with the sea-ice and/or the atmosphere.
 
 This manual is organised in as follows.
@@ -33,5 +37,5 @@
 (primitive equations, with temperature, salinity and an equation of seawater).
 The equations are written in a curvilinear coordinate system, with a choice of vertical coordinates
-($z$, $s$, \zstar, \sstar, \ztilde, \stilde, and a mixture of them).
+($z$, $s$, \zstar, \sstar, \ztilde, \stilde, and a mix of them).
 Momentum equations are formulated in vector invariant or flux form.
 Dimensional units in the meter, kilogram, second (MKS) international system are used throughout.
@@ -39,37 +43,39 @@
 The following chapters deal with the discrete equations.
 \autoref{chap:STP} presents the time domain.
-The model time stepping environment is a three level scheme in which the tendency terms of
-the equations are evaluated either centered in time, or forward, or backward depending of the nature of the term.
+The model time stepping environment is a three level scheme in which 
+the tendency terms of the equations are evaluated either centered in time, or forward, or backward depending of 
+the nature of the term.
 \autoref{chap:DOM} presents the space domain.
 The model is discretised on a staggered grid (Arakawa C grid) with masking of land areas.
-Vertical discretisation used depends on both how the bottom topography is represented and
-whether the free surface is linear or not.
-Full step or partial step $z$-coordinate or $s$- (terrain-following) coordinate is used with
-linear free surface (level position are then fixed in time).
-In non-linear free surface,
-the corresponding rescaled height coordinate formulation (\zstar or \sstar) is used
+Vertical discretisation used depends on both how the bottom topography is represented and whether 
+the free surface is linear or not.
+Full step or partial step $z$-coordinate or $s$- (terrain-following) coordinate is used with linear free surface 
+(level position are then fixed in time).
+In non-linear free surface, the corresponding rescaled height coordinate formulation (\zstar or \sstar) is used
 (the level position then vary in time as a function of the sea surface heigh).
 The following two chapters (\autoref{chap:TRA} and \autoref{chap:DYN}) describe the discretisation of
 the prognostic equations for the active tracers and the momentum.
 Explicit, split-explicit and filtered free surface formulations are implemented.
-A number of numerical schemes are available for momentum advection, for the computation of the pressure gradients,
-as well as for the advection of tracers (second or higher order advection schemes, including positive ones).
-
-Surface boundary conditions (\autoref{chap:SBC}) can be implemented as prescribed fluxes,
-or bulk formulations for the surface fluxes (wind stress, heat, freshwater).
+A number of numerical schemes are available for momentum advection, 
+for the computation of the pressure gradients, as well as for the advection of tracers 
+(second or higher order advection schemes, including positive ones).
+
+Surface boundary conditions (\autoref{chap:SBC}) can be implemented as prescribed fluxes, or bulk formulations for 
+the surface fluxes (wind stress, heat, freshwater).
 The model allows penetration of solar radiation.
 There is an optional geothermal heating at the ocean bottom.
-Within the \NEMO system the ocean model is interactively coupled with a sea ice model (LIM) and
-with biogeochemistry models (PISCES, LOBSTER).
+Within the \NEMO system the ocean model is interactively coupled with a sea ice model (SI$^3$) and
+a biogeochemistry model (PISCES).
 Interactive coupling to Atmospheric models is possible via the OASIS coupler \citep{OASIS2006}.
 Two-way nesting is also available through an interface to the AGRIF package
 (Adaptative Grid Refinement in \fortran) \citep{Debreu_al_CG2008}.
-The interface code for coupling to an alternative sea ice model (CICE, \citet{Hunke2008}) has now been upgraded so
-that it works for both global and regional domains, although AGRIF is still not available.
+% Needs to be reviewed
+%The interface code for coupling to an alternative sea ice model (CICE, \citet{Hunke2008}) has now been upgraded so
+%that it works for both global and regional domains, although AGRIF is still not available.
 
 Other model characteristics are the lateral boundary conditions (\autoref{chap:LBC}).
 Global configurations of the model make use of the ORCA tripolar grid, with special north fold boundary condition.
 Free-slip or no-slip boundary conditions are allowed at land boundaries.
-Closed basin geometries as well as periodic domains and open boundary conditions are possible. 
+Closed basin geometries as well as periodic domains and open boundary conditions are possible.
 
 Physical parameterisations are described in \autoref{chap:LDF} and \autoref{chap:ZDF}.
@@ -80,18 +86,20 @@
 \citet{Treguier1997}.
 The model has vertical harmonic viscosity and diffusion with a space and time variable coefficient,
-with options to compute the coefficients with \citet{Blanke1993}, \citet{Pacanowski_Philander_JPO81},
-or \citet{Umlauf_Burchard_JMS03} mixing schemes.
- \vspace{1cm}
+with options to compute the coefficients with \citet{Blanke1993}, \citet{Pacanowski_Philander_JPO81}, or 
+\citet{Umlauf_Burchard_JMS03} mixing schemes.
  
 %%gm    To be put somewhere else ....
-
-\noindent CPP keys and namelists are used for inputs to the code.  \newline
-
-\noindent \index{CPP keys} CPP keys \newline
+%%nm    We should consider creating a glossary for all this kind of stuff (terms, acronyms and symbols)
+%%      http://en.wikibooks.org/wiki/LaTeX/Glossary
+\noindent CPP keys and namelists are used as inputs to the code.
+
+\noindent \index{CPP keys} CPP keys
+
 Some CPP keys are implemented in the \fortran code to allow code selection at compiling step.
 This selection of code at compilation time reduces the reliability of the whole platform since
 it changes the code from one set of CPP keys to the other.
 It is used only when the addition/suppression of the part of code highly changes the amount of memory at run time.
-Usual coding looks like : 
+Usual coding looks like: 
+
 \begin{forlines}
 #if defined key_option1
@@ -105,19 +113,19 @@
 The namelist allows to input variables (character, logical, real and integer) into the code.
 There is one namelist file for each component of NEMO (dynamics, sea-ice, biogeochemistry...)
-containing all the FOTRAN namelists needed.
-The implementation in NEMO uses a two step process. For each \fortran namelist, two files are read:
+containing all the \fortran namelists needed.
+The implementation in NEMO uses a 2-step process. 
+For each \fortran namelist, two files are read:
+
 \begin{enumerate}
 \item
-  A reference namelist (in \path{CONFIG/SHARED/namelist_ref}) is read first.
+  A reference namelist (in \path{./cfgs/SHARED/namelist_ref}) is read first.
   This file contains all the namelist variables which are initialised to default values
 \item
-  A configuration namelist (in \path{CONFIG/CFG_NAME/EXP00/namelist_cfg}) is read aferwards.
+  A configuration namelist (in \path{./cfgs/CFG_NAME/EXP00/namelist_cfg}) is read aferwards.
   This file contains only the namelist variables which are changed from default values, and overwrites those.
 \end{enumerate}
 A template can be found in \path{NEMO/OPA_SRC/module.example}.
 The effective namelist, taken in account during the run, is stored at execution time in
-an output\_namelist\_dyn (or \_ice or \_top) file.
-\vspace{1cm}
-
+an \texttt{output\_namelist\_dyn} (or \texttt{\_ice} or \texttt{\_top}) file.
 %%gm  end
 
@@ -135,5 +143,6 @@
 (water column model, ORCA and GYRE families of configurations).
 
-The model is implemented in \fninety, with preprocessing (C-pre-processor).
+%%nm: Add some words on the NEMO dependencies
+The model is implemented in \fninety, with preprocessing (C pre-processor).
 It runs under UNIX.
 It is optimized for vector computers and parallelised by domain decomposition with MPI.
@@ -142,6 +151,5 @@
 The coding rules for OPA include conventions for naming variables,
 with different starting letters for different types of variables (real, integer, parameter\ldots).
-Those rules are briefly presented in \autoref{apdx:D} and a more complete document is available on
-the \NEMO web site.
+Those rules are briefly presented in \autoref{apdx:D} and a more complete document is available .
 
 The model is organized with a high internal modularity based on physics.
@@ -149,34 +157,49 @@
 is computed in a dedicated module.
 To make it easier for the user to find his way around the code, the module names follow a three-letter rule.
-For example, \mdl{traldf} is a module related to the TRAcers equation, computing the Lateral DiFfussion. 
+For example, \mdl{traldf} is a module related to the TRAcers equation, computing the Lateral DiFfussion.
 %The complete list of module names is presented in \autoref{apdx:D}.      %====>>>> to be done !
 Furthermore, modules are organized in a few directories that correspond to their category,
-as indicated by the first three letters of their name (\autoref{tab:chap}).
+as indicated by the first three letters of their name (\autoref{tab:chapters}).
 
 The manual mirrors the organization of the model.
 After the presentation of the continuous equations (\autoref{chap:PE}),
-the following chapters refer to specific terms of the equations each associated with
-a group of modules (\autoref{tab:chap}).
-
+the following chapters refer to specific terms of the equations each associated with a group of modules 
+(\autoref{tab:chap}).
 
 %--------------------------------------------------TABLE--------------------------------------------------
 \begin{table}[!t]	
-  % \begin{center} \begin{tabular}{|p{143pt}|l|l|}	\hline
-  \caption{ \protect\label{tab:chap}   Organization of Chapters mimicking the one of the model directories. }
+  \caption{
+    \protect\label{tab:chapters}
+    Organization of Chapters mimicking the one of the model directories.
+  }
   \begin{center}
-    \begin{tabular}{|l|l|l|}	\hline
-      \autoref{chap:STP}	& -   		        & model time STePping environment \\		\hline
-      \autoref{chap:DOM}	& DOM		& model DOMain \\		\hline
-      \autoref{chap:TRA}	& TRA		& TRAcer equations (potential temperature and salinity) \\   \hline
-      \autoref{chap:DYN}	& DYN		& DYNamic equations (momentum) \\		\hline
-      \autoref{chap:SBC} 	& SBC		& Surface Boundary Conditions \\			\hline
-      \autoref{chap:LBC}	& LBC		& Lateral Boundary Conditions (also OBC and BDY)  \\ 		\hline
-      \autoref{chap:LDF}	& LDF		& Lateral DiFfusion (parameterisations) \\	\hline
-      \autoref{chap:ZDF}	& ZDF		& vertical (Z) DiFfusion (parameterisations)  \\		\hline
-      \autoref{chap:DIA}	& DIA		& I/O and DIAgnostics (also IOM, FLO and TRD) \\		\hline
-      \autoref{chap:OBS}	& OBS		& OBServation and model comparison  \\		\hline
-      \autoref{chap:ASM}	& ASM		& ASsiMilation increment  \\		\hline
-      \autoref{chap:MISC}	& SOL		& Miscellaneous  topics (including solvers)  \\       \hline
-      \autoref{chap:CFG}	&  - 			& predefined configurations (including C1D) \\		\hline
+    \begin{tabular}{|l|l|l|}
+      \hline
+      \autoref{chap:STP}  & -   & model time STePping environment \\
+      \hline
+      \autoref{chap:DOM}  & DOM & model DOMain \\
+      \hline
+      \autoref{chap:TRA}  & TRA & TRAcer equations (potential temperature and salinity) \\
+      \hline
+      \autoref{chap:DYN}  & DYN & DYNamic equations (momentum) \\
+      \hline
+      \autoref{chap:SBC}  & SBC & Surface Boundary Conditions \\
+      \hline
+      \autoref{chap:LBC}  & LBC & Lateral Boundary Conditions (also OBC and BDY)  \\
+      \hline
+      \autoref{chap:LDF}  & LDF & Lateral DiFfusion (parameterisations) \\
+      \hline
+      \autoref{chap:ZDF}  & ZDF & vertical (Z) DiFfusion (parameterisations)  \\
+      \hline
+      \autoref{chap:DIA}  & DIA & I/O and DIAgnostics (also IOM, FLO and TRD) \\
+      \hline
+      \autoref{chap:OBS}  & OBS & OBServation and model comparison  \\
+      \hline
+      \autoref{chap:ASM}  & ASM & ASsiMilation increment  \\
+      \hline
+      \autoref{chap:MISC} & SOL & Miscellaneous  topics (including solvers)  \\
+      \hline
+      \autoref{chap:CFG}  & -   & predefined configurations (including C1D) \\
+      \hline
     \end{tabular}
   \end{center}
@@ -184,12 +207,15 @@
 %--------------------------------------------------------------------------------------------------------------
 
-
+%% nm: the following section has to vastly remodeled to focus only on well-identified versions of NEMO
+%% (3.4, 3.6, 4.0 and further releases). Then its formatting must be improved too.
 \subsubsection{Changes between releases}
+
 NEMO/OPA, like all research tools, is in perpetual evolution.
 The present document describes the OPA version include in the release 3.4 of NEMO.
-This release differs significantly from version 8, documented in \citet{Madec1998}.\\
-
-$\bullet$ The main modifications from OPA v8 and NEMO/OPA v3.2 are :\\
-\begin{enumerate}
+This release differs significantly from version 8, documented in \citet{Madec1998}. \\
+
+The main modifications from OPA v8 and NEMO/OPA v3.2 are :
+
+\begin{itemize}
 \item
   transition to full native \fninety, deep code restructuring and drastic reduction of CPP keys; 
@@ -200,13 +226,15 @@
   partial reactivation of a terrain-following vertical coordinate ($s$- and hybrid $s$-$z$) with
   the addition of several options for pressure gradient computation
-  \footnote{Partial support of $s$-coordinate: there is presently no support for neutral physics in
+  \footnote{
+    Partial support of $s$-coordinate: there is presently no support for neutral physics in
     $s$-coordinate and for the new options for horizontal pressure gradient computation with
     a non-linear equation of state.
-  };
+  }
+  ;
 \item
   more choices for the treatment of the free surface: full explicit, split-explicit or filtered schemes,
   and suppression of the rigid-lid option;
 \item
-  non linear free surface associated with the rescaled height coordinate \zstar or \textit{s};
+  non linear free surface associated with the rescaled height coordinate \zstar or $s$;
 \item
   additional schemes for vector and flux forms of the momentum advection;
@@ -237,9 +265,9 @@
   (C-grid rheology and new thermodynamics including bulk ice salinity)
   \citep{Vancoppenolle_al_OM09a, Vancoppenolle_al_OM09b}
-\end{enumerate}
-
- \vspace{1cm}
-$\bullet$ The main modifications from NEMO/OPA v3.2 and v3.3 are :\\
-\begin{enumerate}
+\end{itemize}
+
+The main modifications from NEMO/OPA v3.2 and v3.3 are:
+
+\begin{itemize}
 \item
   introduction of a modified leapfrog-Asselin filter time stepping scheme
@@ -280,40 +308,39 @@
 \item
   Linear-tangent and Adjoint component (TAM) added, phased with v3.0
-\end{enumerate}
+\end{itemize}
+
 \vspace{1cm}
+
 In addition, several minor modifications in the coding have been introduced with the constant concern of
-improving the model performance. 
-
-\vspace{1cm}
-$\bullet$ The main modifications from NEMO/OPA v3.3 and  v3.4 are :\\
-\begin{enumerate}
+improving the model performance.
+
+The main modifications from NEMO/OPA v3.3 and v3.4 are:
+
+\begin{itemize}
 \item finalisation of above iso-neutral mixing \citep{Griffies_al_JPO98}";
 \item "Neptune effect" parametrisation;
 \item horizontal pressure gradient suitable for s-coordinate;
-\item semi-implicit bottom friction;
+\item semi -implicit bottom friction;
 \item finalisation of the merge of passive and active tracers advection-diffusion modules;
 \item a new bulk formulae (so-called MFS);
 \item use fldread for the off-line tracer component (OFF\_SRC);
-\item use MPI point to point communications  for north fold;
+\item use MPI point to point communications for north fold;
 \item diagnostic of transport;
-\end{enumerate}
-
-
- \vspace{1cm}
-$\bullet$ The main modifications from NEMO/OPA v3.4 and  v3.6 are :\\
-\begin{enumerate}
- \item ... ; 
-\end{enumerate}
-
-
- \vspace{1cm}
-$\bullet$ The main modifications from NEMO/OPA v3.6 and  v4.0 are :\\
-\begin{enumerate}
-\item new definition of configurations ;
-\item bulk formulation ;
-\item NEMO-wave large scale interactions ;
-\item ... ; 
-\end{enumerate}
-
+\end{itemize}
+
+The main modifications from NEMO/OPA v3.4 and v3.6 are:
+
+\begin{itemize}
+ \item ...;
+\end{itemize}
+
+The main modifications from NEMO/OPA v3.6 and v4.0 are:
+
+\begin{itemize}
+\item new definition of configurations;
+\item bulk formulation;
+\item NEMO-wave large scale interactions;
+\item ...;
+\end{itemize}
 
 \biblio
Index: /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/src/ICE/icedyn_adv_umx.F90
===================================================================
--- /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/src/ICE/icedyn_adv_umx.F90	(revision 10497)
+++ /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/src/ICE/icedyn_adv_umx.F90	(revision 10498)
@@ -193,5 +193,5 @@
             zamsk = 0._wp
             !
-            zhvar(:,:,:) = pv_ip(:,:,:) * z1_ai(:,:,:)
+            zhvar(:,:,:) = pv_ip(:,:,:) * z1_aip(:,:,:)
             CALL adv_umx( zamsk, kn_umx, jt, kt, zdt, zudy, zvdx, zua_ho, zva_ho, zcu_box, zcv_box, zhvar, pv_ip )                 ! mp volume
          ENDIF
@@ -271,9 +271,9 @@
       CASE ( 20 )                          !== centered second order ==!
          !
-         CALL cen2( pamsk, jt, kt, pdt, pt, pu, pv, puc, pvc, ptc, zt_ups, zfu_ups, zfv_ups, zfu_ho, zfv_ho )
+         CALL cen2( pamsk, jt, kt, pdt, pt, pu, pv, zt_ups, zfu_ups, zfv_ups, zfu_ho, zfv_ho )
          !
       CASE ( 1:5 )                         !== 1st to 5th order ULTIMATE-MACHO scheme ==!
          !
-         CALL macho( pamsk, kn_umx, jt, kt, pdt, pt, pu, pv, puc, pvc, pubox, pvbox, ptc, zt_ups, zfu_ups, zfv_ups, zfu_ho, zfv_ho )
+         CALL macho( pamsk, kn_umx, jt, kt, pdt, pt, pu, pv, pubox, pvbox, zt_ups, zfu_ups, zfv_ups, zfu_ho, zfv_ho )
          !
       END SELECT
@@ -282,5 +282,5 @@
       ! new fluxes = u*H  *  u*a / u
       ! ----------------------------
-      IF( pamsk == 0. ) THEN
+      IF( pamsk == 0._wp ) THEN
          DO jl = 1, jpl
             DO jj = 1, jpjm1
@@ -440,5 +440,5 @@
                   &       + pv     (ji,jj   ) - pv     (ji  ,jj-1   ) ) * pt(ji,jj,jl) * (1.-pamsk)
                !
-               pt_ups(ji,jj,jl) = ( pt (ji,jj,jl) + ztra * pdt * r1_e1e2t(ji,jj) ) * tmask(ji,jj,1)
+               pt_ups(ji,jj,jl) = ( pt(ji,jj,jl) + ztra * pdt * r1_e1e2t(ji,jj) ) * tmask(ji,jj,1)
             END DO
          END DO
@@ -449,5 +449,5 @@
 
    
-   SUBROUTINE cen2( pamsk, jt, kt, pdt, pt, pu, pv, puc, pvc, ptc, pt_ups, pfu_ups, pfv_ups, pfu_ho, pfv_ho )
+   SUBROUTINE cen2( pamsk, jt, kt, pdt, pt, pu, pv, pt_ups, pfu_ups, pfv_ups, pfu_ho, pfv_ho )
       !!---------------------------------------------------------------------
       !!                    ***  ROUTINE cen2  ***
@@ -462,6 +462,4 @@
       REAL(wp), DIMENSION(:,:,:)      , INTENT(in   ) ::   pt               ! tracer fields
       REAL(wp), DIMENSION(:,:  )      , INTENT(in   ) ::   pu, pv           ! 2 ice velocity components
-      REAL(wp), DIMENSION(:,:,:)      , INTENT(in   ) ::   puc, pvc         ! 2 ice velocity * A components
-      REAL(wp), DIMENSION(:,:,:)      , INTENT(in   ) ::   ptc              ! tracer content at before time step 
       REAL(wp), DIMENSION(:,:,:)      , INTENT(in   ) ::   pt_ups           ! upstream guess of tracer 
       REAL(wp), DIMENSION(:,:,:)      , INTENT(in   ) ::   pfu_ups, pfv_ups ! upstream fluxes 
@@ -478,9 +476,10 @@
             DO jj = 1, jpjm1
                DO ji = 1, fs_jpim1
-                  pfu_ho(ji,jj,jl) = 0.5 * pu(ji,jj) * ( pt(ji,jj,jl) + pt(ji+1,jj,jl) )
-                  pfv_ho(ji,jj,jl) = 0.5 * pv(ji,jj) * ( pt(ji,jj,jl) + pt(ji,jj+1,jl) )
-               END DO
-            END DO
-         END DO
+                  pfu_ho(ji,jj,jl) = 0.5_wp * pu(ji,jj) * ( pt(ji,jj,jl) + pt(ji+1,jj  ,jl) )
+                  pfv_ho(ji,jj,jl) = 0.5_wp * pv(ji,jj) * ( pt(ji,jj,jl) + pt(ji  ,jj+1,jl) )
+               END DO
+            END DO
+         END DO
+         !
          IF    ( kn_limiter == 1 ) THEN
             CALL nonosc( pamsk, pdt, pu, pv, pt, pt_ups, pfu_ups, pfv_ups, pfu_ho, pfv_ho )
@@ -497,5 +496,5 @@
                DO jj = 1, jpjm1
                   DO ji = 1, fs_jpim1
-                     pfu_ho(ji,jj,jl) = 0.5 * pu(ji,jj) * ( pt(ji,jj,jl) + pt(ji+1,jj,jl) )
+                     pfu_ho(ji,jj,jl) = 0.5_wp * pu(ji,jj) * ( pt(ji,jj,jl) + pt(ji+1,jj,jl) )
                   END DO
                END DO
@@ -518,5 +517,5 @@
                DO jj = 1, jpjm1
                   DO ji = 1, fs_jpim1
-                     pfv_ho(ji,jj,jl) = 0.5 * pv(ji,jj) * ( zpt(ji,jj,jl) + zpt(ji,jj+1,jl) )
+                     pfv_ho(ji,jj,jl) = 0.5_wp * pv(ji,jj) * ( zpt(ji,jj,jl) + zpt(ji,jj+1,jl) )
                   END DO
                END DO
@@ -529,5 +528,5 @@
                DO jj = 1, jpjm1
                   DO ji = 1, fs_jpim1
-                     pfv_ho(ji,jj,jl) = 0.5 * pv(ji,jj) * ( pt(ji,jj,jl) + pt(ji,jj+1,jl) )
+                     pfv_ho(ji,jj,jl) = 0.5_wp * pv(ji,jj) * ( pt(ji,jj,jl) + pt(ji,jj+1,jl) )
                   END DO
                END DO
@@ -550,5 +549,5 @@
                DO jj = 1, jpjm1
                   DO ji = 1, fs_jpim1
-                     pfu_ho(ji,jj,jl) = 0.5 * pu(ji,jj) * ( zpt(ji,jj,jl) + zpt(ji+1,jj,jl) )
+                     pfu_ho(ji,jj,jl) = 0.5_wp * pu(ji,jj) * ( zpt(ji,jj,jl) + zpt(ji+1,jj,jl) )
                   END DO
                END DO
@@ -564,5 +563,5 @@
 
    
-   SUBROUTINE macho( pamsk, kn_umx, jt, kt, pdt, pt, pu, pv, puc, pvc, pubox, pvbox, ptc, pt_ups, pfu_ups, pfv_ups, pfu_ho, pfv_ho )
+   SUBROUTINE macho( pamsk, kn_umx, jt, kt, pdt, pt, pu, pv, pubox, pvbox, pt_ups, pfu_ups, pfv_ups, pfu_ho, pfv_ho )
       !!---------------------------------------------------------------------
       !!                    ***  ROUTINE macho  ***
@@ -581,7 +580,5 @@
       REAL(wp), DIMENSION(:,:,:)      , INTENT(in   ) ::   pt               ! tracer fields
       REAL(wp), DIMENSION(:,:  )      , INTENT(in   ) ::   pu, pv           ! 2 ice velocity components
-      REAL(wp), DIMENSION(:,:,:)      , INTENT(in   ) ::   puc, pvc         ! 2 ice velocity * A components
       REAL(wp), DIMENSION(:,:  )      , INTENT(in   ) ::   pubox, pvbox     ! upstream velocity
-      REAL(wp), DIMENSION(:,:,:)      , INTENT(in   ) ::   ptc              ! tracer content at before time step 
       REAL(wp), DIMENSION(:,:,:)      , INTENT(in   ) ::   pt_ups           ! upstream guess of tracer 
       REAL(wp), DIMENSION(:,:,:)      , INTENT(in   ) ::   pfu_ups, pfv_ups ! upstream fluxes 
@@ -714,6 +711,6 @@
             DO jj = 1, jpjm1
                DO ji = 1, fs_jpim1   ! vector opt.
-                  pt_u(ji,jj,jl) = 0.5_wp * umask(ji,jj,1) * (                           pt(ji+1,jj,jl) + pt(ji,jj,jl)   &
-                     &                                    - SIGN( 1._wp, pu(ji,jj) ) * ( pt(ji+1,jj,jl) - pt(ji,jj,jl) ) )
+                  pt_u(ji,jj,jl) = 0.5_wp * umask(ji,jj,1) * (                                pt(ji+1,jj,jl) + pt(ji,jj,jl)   &
+                     &                                         - SIGN( 1._wp, pu(ji,jj) ) * ( pt(ji+1,jj,jl) - pt(ji,jj,jl) ) )
                END DO
             END DO
@@ -727,5 +724,5 @@
                   zcu  = pu(ji,jj) * r1_e2u(ji,jj) * pdt * r1_e1u(ji,jj)
                   pt_u(ji,jj,jl) = 0.5_wp * umask(ji,jj,1) * (                                pt(ji+1,jj,jl) + pt(ji,jj,jl)   &
-                     &                                               -              zcu   * ( pt(ji+1,jj,jl) - pt(ji,jj,jl) ) ) 
+                     &                                                            - zcu   * ( pt(ji+1,jj,jl) - pt(ji,jj,jl) ) ) 
                END DO
             END DO
@@ -741,6 +738,6 @@
 !!rachid          zdx2 = e1u(ji,jj) * e1t(ji,jj)
                   pt_u(ji,jj,jl) = 0.5_wp * umask(ji,jj,1) * (         (                      pt  (ji+1,jj,jl) + pt  (ji,jj,jl)     &
-                     &                                               -              zcu   * ( pt  (ji+1,jj,jl) - pt  (ji,jj,jl) ) ) &
-                     &        + z1_6 * zdx2 * ( zcu*zcu - 1._wp ) * (                         ztu2(ji+1,jj,jl) + ztu2(ji,jj,jl)     &
+                     &                                                            - zcu   * ( pt  (ji+1,jj,jl) - pt  (ji,jj,jl) ) ) &
+                     &        + z1_6 * zdx2 * ( zcu*zcu - 1._wp ) *    (                      ztu2(ji+1,jj,jl) + ztu2(ji,jj,jl)     &
                      &                                               - SIGN( 1._wp, zcu ) * ( ztu2(ji+1,jj,jl) - ztu2(ji,jj,jl) ) ) )
                END DO
@@ -756,8 +753,8 @@
                   zdx2 = e1u(ji,jj) * e1u(ji,jj)
 !!rachid          zdx2 = e1u(ji,jj) * e1t(ji,jj)
-                  pt_u(ji,jj,jl) = 0.5_wp * umask(ji,jj,1) * (         (                pt  (ji+1,jj,jl) + pt  (ji,jj,jl)     &
-                     &                                               -          zcu * ( pt  (ji+1,jj,jl) - pt  (ji,jj,jl) ) ) &
-                     &        + z1_6 * zdx2 * ( zcu*zcu - 1._wp ) * (                   ztu2(ji+1,jj,jl) + ztu2(ji,jj,jl)     &
-                     &                                               - 0.5_wp * zcu * ( ztu2(ji+1,jj,jl) - ztu2(ji,jj,jl) ) ) )
+                  pt_u(ji,jj,jl) = 0.5_wp * umask(ji,jj,1) * (         (                      pt  (ji+1,jj,jl) + pt  (ji,jj,jl)     &
+                     &                                                            - zcu   * ( pt  (ji+1,jj,jl) - pt  (ji,jj,jl) ) ) &
+                     &        + z1_6 * zdx2 * ( zcu*zcu - 1._wp ) *    (                      ztu2(ji+1,jj,jl) + ztu2(ji,jj,jl)     &
+                     &                                                   - 0.5_wp * zcu   * ( ztu2(ji+1,jj,jl) - ztu2(ji,jj,jl) ) ) )
                END DO
             END DO
@@ -773,8 +770,8 @@
 !!rachid          zdx2 = e1u(ji,jj) * e1t(ji,jj)
                   zdx4 = zdx2 * zdx2
-                  pt_u(ji,jj,jl) = 0.5_wp * umask(ji,jj,1) * (            (                   pt  (ji+1,jj,jl) + pt  (ji,jj,jl)     &
-                     &                                                     -          zcu * ( pt  (ji+1,jj,jl) - pt  (ji,jj,jl) ) ) &
-                     &        + z1_6   * zdx2 * ( zcu*zcu - 1._wp ) *     (                   ztu2(ji+1,jj,jl) + ztu2(ji,jj,jl)     &
-                     &                                                     - 0.5_wp * zcu * ( ztu2(ji+1,jj,jl) - ztu2(ji,jj,jl) ) ) &
+                  pt_u(ji,jj,jl) = 0.5_wp * umask(ji,jj,1) * (        (                       pt  (ji+1,jj,jl) + pt  (ji,jj,jl)     &
+                     &                                                            - zcu   * ( pt  (ji+1,jj,jl) - pt  (ji,jj,jl) ) ) &
+                     &        + z1_6   * zdx2 * ( zcu*zcu - 1._wp ) * (                       ztu2(ji+1,jj,jl) + ztu2(ji,jj,jl)     &
+                     &                                                   - 0.5_wp * zcu   * ( ztu2(ji+1,jj,jl) - ztu2(ji,jj,jl) ) ) &
                      &        + z1_120 * zdx4 * ( zcu*zcu - 1._wp ) * ( zcu*zcu - 4._wp ) * ( ztu4(ji+1,jj,jl) + ztu4(ji,jj,jl)     &
                      &                                               - SIGN( 1._wp, zcu ) * ( ztu4(ji+1,jj,jl) - ztu4(ji,jj,jl) ) ) )
@@ -793,6 +790,6 @@
                DO ji = 1, fs_jpim1
                   IF( pt_u(ji,jj,jl) < 0._wp ) THEN
-                     pt_u(ji,jj,jl) = 0.5_wp * umask(ji,jj,1) * (                           pt(ji+1,jj,jl) + pt(ji,jj,jl)   &
-                        &                                    - SIGN( 1._wp, pu(ji,jj) ) * ( pt(ji+1,jj,jl) - pt(ji,jj,jl) ) )
+                     pt_u(ji,jj,jl) = 0.5_wp * umask(ji,jj,1) * (                                pt(ji+1,jj,jl) + pt(ji,jj,jl)   &
+                        &                                         - SIGN( 1._wp, pu(ji,jj) ) * ( pt(ji+1,jj,jl) - pt(ji,jj,jl) ) )
                   ENDIF
                END DO
@@ -871,6 +868,6 @@
             DO jj = 1, jpjm1
                DO ji = 1, fs_jpim1
-                  pt_v(ji,jj,jl) = 0.5_wp * vmask(ji,jj,1) * (                          ( pt(ji,jj+1,jl) + pt(ji,jj,jl) )  &
-                     &                                     - SIGN( 1._wp, pv(ji,jj) ) * ( pt(ji,jj+1,jl) - pt(ji,jj,jl) ) )
+                  pt_v(ji,jj,jl) = 0.5_wp * vmask(ji,jj,1) * (                                pt(ji,jj+1,jl) + pt(ji,jj,jl)   &
+                     &                                         - SIGN( 1._wp, pv(ji,jj) ) * ( pt(ji,jj+1,jl) - pt(ji,jj,jl) ) )
                END DO
             END DO
@@ -882,10 +879,9 @@
                DO ji = 1, fs_jpim1
                   zcv  = pv(ji,jj) * r1_e1v(ji,jj) * pdt * r1_e2v(ji,jj)
-                  pt_v(ji,jj,jl) = 0.5_wp * vmask(ji,jj,1) * (     ( pt(ji,jj+1,jl) + pt(ji,jj,jl) )  &
-                     &                                     - zcv * ( pt(ji,jj+1,jl) - pt(ji,jj,jl) ) )
-               END DO
-            END DO
-         END DO
-         CALL lbc_lnk( 'icedyn_adv_umx', pt_v, 'V',  1. )
+                  pt_v(ji,jj,jl) = 0.5_wp * vmask(ji,jj,1) * (                                pt(ji,jj+1,jl) + pt(ji,jj,jl)   &
+                     &                                                            - zcv *   ( pt(ji,jj+1,jl) - pt(ji,jj,jl) ) )
+               END DO
+            END DO
+         END DO
          !
       CASE( 3 )                                                !==  3rd order central TIM  ==! (Eq. 24)
@@ -896,6 +892,6 @@
                   zdy2 = e2v(ji,jj) * e2v(ji,jj)
 !!rachid          zdy2 = e2v(ji,jj) * e2t(ji,jj)
-                  pt_v(ji,jj,jl) = 0.5_wp * vmask(ji,jj,1) * (                              ( pt  (ji,jj+1,jl) + pt  (ji,jj,jl)     &
-                     &                                     -                        zcv   * ( pt  (ji,jj+1,jl) - pt  (ji,jj,jl) ) ) &
+                  pt_v(ji,jj,jl) = 0.5_wp * vmask(ji,jj,1) * (      (                         pt  (ji,jj+1,jl) + pt  (ji,jj,jl)     &
+                     &                                                            - zcv   * ( pt  (ji,jj+1,jl) - pt  (ji,jj,jl) ) ) &
                      &        + z1_6 * zdy2 * ( zcv*zcv - 1._wp ) * (                         ztv2(ji,jj+1,jl) + ztv2(ji,jj,jl)     &
                      &                                               - SIGN( 1._wp, zcv ) * ( ztv2(ji,jj+1,jl) - ztv2(ji,jj,jl) ) ) )
@@ -911,8 +907,8 @@
                   zdy2 = e2v(ji,jj) * e2v(ji,jj)
 !!rachid          zdy2 = e2v(ji,jj) * e2t(ji,jj)
-                  pt_v(ji,jj,jl) = 0.5_wp * vmask(ji,jj,1) * (                        ( pt  (ji,jj+1,jl) + pt  (ji,jj,jl)     &
-                     &                                               -          zcv * ( pt  (ji,jj+1,jl) - pt  (ji,jj,jl) ) ) &
-                     &        + z1_6 * zdy2 * ( zcv*zcv - 1._wp ) * (                   ztv2(ji,jj+1,jl) + ztv2(ji,jj,jl)     &
-                     &                                               - 0.5_wp * zcv * ( ztv2(ji,jj+1,jl) - ztv2(ji,jj,jl) ) ) )
+                  pt_v(ji,jj,jl) = 0.5_wp * vmask(ji,jj,1) * (      (                         pt  (ji,jj+1,jl) + pt  (ji,jj,jl)     &
+                     &                                                            - zcv   * ( pt  (ji,jj+1,jl) - pt  (ji,jj,jl) ) ) &
+                     &        + z1_6 * zdy2 * ( zcv*zcv - 1._wp ) * (                         ztv2(ji,jj+1,jl) + ztv2(ji,jj,jl)     &
+                     &                                                   - 0.5_wp * zcv   * ( ztv2(ji,jj+1,jl) - ztv2(ji,jj,jl) ) ) )
                END DO
             END DO
@@ -928,7 +924,7 @@
                   zdy4 = zdy2 * zdy2
                   pt_v(ji,jj,jl) = 0.5_wp * vmask(ji,jj,1) * (                              ( pt  (ji,jj+1,jl) + pt  (ji,jj,jl)     &
-                     &                                                     -          zcv * ( pt  (ji,jj+1,jl) - pt  (ji,jj,jl) ) ) &
-                     &        + z1_6   * zdy2 * ( zcv*zcv - 1._wp ) *     (                   ztv2(ji,jj+1,jl) + ztv2(ji,jj,jl)     &
-                     &                                                     - 0.5_wp * zcv * ( ztv2(ji,jj+1,jl) - ztv2(ji,jj,jl) ) ) &
+                     &                                                            - zcv   * ( pt  (ji,jj+1,jl) - pt  (ji,jj,jl) ) ) &
+                     &        + z1_6   * zdy2 * ( zcv*zcv - 1._wp ) * (                       ztv2(ji,jj+1,jl) + ztv2(ji,jj,jl)     &
+                     &                                                   - 0.5_wp * zcv   * ( ztv2(ji,jj+1,jl) - ztv2(ji,jj,jl) ) ) &
                      &        + z1_120 * zdy4 * ( zcv*zcv - 1._wp ) * ( zcv*zcv - 4._wp ) * ( ztv4(ji,jj+1,jl) + ztv4(ji,jj,jl)     &
                      &                                               - SIGN( 1._wp, zcv ) * ( ztv4(ji,jj+1,jl) - ztv4(ji,jj,jl) ) ) )
@@ -947,6 +943,6 @@
                DO ji = 1, fs_jpim1
                   IF( pt_v(ji,jj,jl) < 0._wp ) THEN
-                     pt_v(ji,jj,jl) = 0.5_wp * vmask(ji,jj,1) * (                          ( pt(ji,jj+1,jl) + pt(ji,jj,jl) )  &
-                        &                                     - SIGN( 1._wp, pv(ji,jj) ) * ( pt(ji,jj+1,jl) - pt(ji,jj,jl) ) )
+                     pt_v(ji,jj,jl) = 0.5_wp * vmask(ji,jj,1) * (                              ( pt(ji,jj+1,jl) + pt(ji,jj,jl) )  &
+                        &                                         - SIGN( 1._wp, pv(ji,jj) ) * ( pt(ji,jj+1,jl) - pt(ji,jj,jl) ) )
                   ENDIF
                END DO
@@ -984,11 +980,10 @@
       !
       INTEGER  ::   ji, jj, jl    ! dummy loop indices
-      REAL(wp) ::   zpos, zneg, zbig, zsml, zup, zdo, z1_dt              ! local scalars
-      REAL(wp) ::   zau, zbu, zcu, zav, zbv, zcv, zsign, zcoef, zzt      !   -      -
+      REAL(wp) ::   zpos, zneg, zbig, zup, zdo, z1_dt              ! local scalars
+      REAL(wp) ::   zau, zbu, zcu, zav, zbv, zcv, zcoef, zzt       !   -      -
       REAL(wp), DIMENSION(jpi,jpj    ) :: zbup, zbdo
       REAL(wp), DIMENSION(jpi,jpj,jpl) :: zbetup, zbetdo, zti_ups, ztj_ups
       !!----------------------------------------------------------------------
       zbig = 1.e+40_wp
-      zsml = epsi20
       
       ! antidiffusive flux : high order minus low order
@@ -1026,17 +1021,17 @@
             DO jj = 2, jpjm1
                DO ji = fs_2, fs_jpim1
-                  IF ( pfu_ho(ji,jj,jl) * ( pt_ups(ji+1,jj,jl) - pt_ups(ji,jj,jl) ) <= 0. .AND.  &
-                     & pfv_ho(ji,jj,jl) * ( pt_ups(ji,jj+1,jl) - pt_ups(ji,jj,jl) ) <= 0. ) THEN
+                  IF ( pfu_ho(ji,jj,jl) * ( pt_ups(ji+1,jj  ,jl) - pt_ups(ji,jj,jl) ) <= 0._wp .AND.  &
+                     & pfv_ho(ji,jj,jl) * ( pt_ups(ji  ,jj+1,jl) - pt_ups(ji,jj,jl) ) <= 0._wp ) THEN
                      !
-                     IF(  pfu_ho(ji,jj,jl) * ( zti_ups(ji+1,jj,jl) - zti_ups(ji,jj,jl) ) <= 0. .AND.  &
-                        & pfv_ho(ji,jj,jl) * ( ztj_ups(ji,jj+1,jl) - ztj_ups(ji,jj,jl) ) <= 0. ) THEN
-                        pfu_ho(ji,jj,jl)=0.
-                        pfv_ho(ji,jj,jl)=0.
+                     IF(  pfu_ho(ji,jj,jl) * ( zti_ups(ji+1,jj  ,jl) - zti_ups(ji,jj,jl) ) <= 0._wp .AND.  &
+                        & pfv_ho(ji,jj,jl) * ( ztj_ups(ji  ,jj+1,jl) - ztj_ups(ji,jj,jl) ) <= 0._wp ) THEN
+                        pfu_ho(ji,jj,jl)=0._wp
+                        pfv_ho(ji,jj,jl)=0._wp
                      ENDIF
                      !
-                     IF(  pfu_ho(ji,jj,jl) * ( pt_ups(ji  ,jj,jl) - pt_ups(ji-1,jj,jl) ) <= 0. .AND.  &
-                        & pfv_ho(ji,jj,jl) * ( pt_ups(ji  ,jj,jl) - pt_ups(ji,jj-1,jl) ) <= 0. ) THEN
-                        pfu_ho(ji,jj,jl)=0.
-                        pfv_ho(ji,jj,jl)=0.
+                     IF(  pfu_ho(ji,jj,jl) * ( pt_ups(ji,jj,jl) - pt_ups(ji-1,jj  ,jl) ) <= 0._wp .AND.  &
+                        & pfv_ho(ji,jj,jl) * ( pt_ups(ji,jj,jl) - pt_ups(ji  ,jj-1,jl) ) <= 0._wp ) THEN
+                        pfu_ho(ji,jj,jl)=0._wp
+                        pfv_ho(ji,jj,jl)=0._wp
                      ENDIF
                      !
@@ -1076,29 +1071,29 @@
             DO ji = fs_2, fs_jpim1   ! vector opt.
                !
-               zup  = MAX( zbup(ji,jj), zbup(ji-1,jj  ), zbup(ji+1,jj  ), zbup(ji  ,jj-1), zbup(ji  ,jj+1) )  ! search max/min in neighbourhood
-               zdo  = MIN( zbdo(ji,jj), zbdo(ji-1,jj  ), zbdo(ji+1,jj  ), zbdo(ji  ,jj-1), zbdo(ji  ,jj+1) )
-               !
-               zpos = MAX( 0., pfu_ho(ji-1,jj,jl) ) - MIN( 0., pfu_ho(ji  ,jj,jl) ) &  ! positive/negative part of the flux
-                  & + MAX( 0., pfv_ho(ji,jj-1,jl) ) - MIN( 0., pfv_ho(ji,jj  ,jl) )
-               zneg = MAX( 0., pfu_ho(ji  ,jj,jl) ) - MIN( 0., pfu_ho(ji-1,jj,jl) ) &
-                  & + MAX( 0., pfv_ho(ji,jj  ,jl) ) - MIN( 0., pfv_ho(ji,jj-1,jl) )
-               !
-               zpos = zpos - (pt(ji,jj,jl) * MIN( 0., pu(ji,jj) - pu(ji-1,jj) ) + pt(ji,jj,jl) * MIN( 0., pv(ji,jj) - pv(ji,jj-1)) &
+               zup  = MAX( zbup(ji,jj), zbup(ji-1,jj), zbup(ji+1,jj), zbup(ji,jj-1), zbup(ji,jj+1) )  ! search max/min in neighbourhood
+               zdo  = MIN( zbdo(ji,jj), zbdo(ji-1,jj), zbdo(ji+1,jj), zbdo(ji,jj-1), zbdo(ji,jj+1) )
+               !
+               zpos = MAX( 0._wp, pfu_ho(ji-1,jj  ,jl) ) - MIN( 0._wp, pfu_ho(ji  ,jj  ,jl) ) &  ! positive/negative part of the flux
+                  & + MAX( 0._wp, pfv_ho(ji  ,jj-1,jl) ) - MIN( 0._wp, pfv_ho(ji  ,jj  ,jl) )
+               zneg = MAX( 0._wp, pfu_ho(ji  ,jj  ,jl) ) - MIN( 0._wp, pfu_ho(ji-1,jj  ,jl) ) &
+                  & + MAX( 0._wp, pfv_ho(ji  ,jj  ,jl) ) - MIN( 0._wp, pfv_ho(ji  ,jj-1,jl) )
+               !
+               zpos = zpos - (pt(ji,jj,jl) * MIN( 0., pu(ji,jj) - pu(ji-1,jj) ) + pt(ji,jj,jl) * MIN( 0., pv(ji,jj) - pv(ji,jj-1) ) &
                   &          ) * ( 1. - pamsk )
-               zneg = zneg + (pt(ji,jj,jl) * MAX( 0., pu(ji,jj) - pu(ji-1,jj) ) + pt(ji,jj,jl) * MAX( 0., pv(ji,jj) - pv(ji,jj-1)) &
+               zneg = zneg + (pt(ji,jj,jl) * MAX( 0., pu(ji,jj) - pu(ji-1,jj) ) + pt(ji,jj,jl) * MAX( 0., pv(ji,jj) - pv(ji,jj-1) ) &
                   &          ) * ( 1. - pamsk )
                !
                !                                  ! up & down beta terms
-               IF( zpos > 0. ) THEN ; zbetup(ji,jj,jl) = MAX( 0._wp, zup - pt_ups(ji,jj,jl) ) / zpos * e1e2t(ji,jj) * z1_dt
-               ELSE                 ; zbetup(ji,jj,jl) = 0. ! zbig
+               IF( zpos > 0._wp ) THEN ; zbetup(ji,jj,jl) = MAX( 0._wp, zup - pt_ups(ji,jj,jl) ) / zpos * e1e2t(ji,jj) * z1_dt
+               ELSE                    ; zbetup(ji,jj,jl) = 0._wp ! zbig
                ENDIF
                !
-               IF( zneg > 0. ) THEN ; zbetdo(ji,jj,jl) = MAX( 0._wp, pt_ups(ji,jj,jl) - zdo ) / zneg * e1e2t(ji,jj) * z1_dt
-               ELSE                 ; zbetdo(ji,jj,jl) = 0. ! zbig
+               IF( zneg > 0._wp ) THEN ; zbetdo(ji,jj,jl) = MAX( 0._wp, pt_ups(ji,jj,jl) - zdo ) / zneg * e1e2t(ji,jj) * z1_dt
+               ELSE                    ; zbetdo(ji,jj,jl) = 0._wp ! zbig
                ENDIF
                !
                ! if all the points are outside ice cover
-               IF( zup == -zbig )   zbetup(ji,jj,jl) = 0. ! zbig
-               IF( zdo ==  zbig )   zbetdo(ji,jj,jl) = 0. ! zbig            
+               IF( zup == -zbig )   zbetup(ji,jj,jl) = 0._wp ! zbig
+               IF( zdo ==  zbig )   zbetdo(ji,jj,jl) = 0._wp ! zbig            
                !
             END DO
@@ -1115,5 +1110,5 @@
                zau = MIN( 1._wp , zbetdo(ji,jj,jl) , zbetup(ji+1,jj,jl) )
                zbu = MIN( 1._wp , zbetup(ji,jj,jl) , zbetdo(ji+1,jj,jl) )
-               zcu = 0.5  + SIGN( 0.5 , pfu_ho(ji,jj,jl) )
+               zcu = 0.5_wp + SIGN( 0.5_wp , pfu_ho(ji,jj,jl) )
                !
                zcoef = ( zcu * zau + ( 1._wp - zcu ) * zbu )
@@ -1128,5 +1123,5 @@
                zav = MIN( 1._wp , zbetdo(ji,jj,jl) , zbetup(ji,jj+1,jl) )
                zbv = MIN( 1._wp , zbetup(ji,jj,jl) , zbetdo(ji,jj+1,jl) )
-               zcv = 0.5  + SIGN( 0.5 , pfv_ho(ji,jj,jl) )
+               zcv = 0.5_wp + SIGN( 0.5_wp , pfv_ho(ji,jj,jl) )
                !
                zcoef = ( zcv * zav + ( 1._wp - zcv ) * zbv )
Index: /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/src/OCE/BDY/bdyini.F90
===================================================================
--- /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/src/OCE/BDY/bdyini.F90	(revision 10497)
+++ /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/src/OCE/BDY/bdyini.F90	(revision 10498)
@@ -133,5 +133,4 @@
       INTEGER  ::   i_offset, j_offset                     !   -       -
       INTEGER , POINTER  ::  nbi, nbj, nbr                 ! short cuts
-      REAL(wp), POINTER  ::  flagu, flagv                  !    -   -
       REAL(wp), POINTER, DIMENSION(:,:)       ::   pmask    ! pointer to 2D mask fields
       REAL(wp) ::   zefl, zwfl, znfl, zsfl                 ! local scalars
@@ -385,4 +384,13 @@
           END SELECT
           IF(lwp) WRITE(numout,*)
+          !
+          ! sanity check if used with tides        
+          IF( ln_tide ) THEN 
+             IF(lwp) WRITE(numout,*) ' The total volume correction is not working with tides. '
+             IF(lwp) WRITE(numout,*) ' Set ln_vol to .FALSE. '
+             IF(lwp) WRITE(numout,*) ' or '
+             IF(lwp) WRITE(numout,*) ' equilibriate your bdy input files '
+             CALL ctl_stop( 'The total volume correction is not working with tides.' )
+          END IF
         ELSE
           IF(lwp) WRITE(numout,*) 'No volume correction applied at open boundaries'
@@ -1244,38 +1252,4 @@
          !
       END DO
-
-      ! Compute total lateral surface for volume correction:
-      ! ----------------------------------------------------
-      ! JC: this must be done at each time step with non-linear free surface
-      bdysurftot = 0._wp 
-      IF( ln_vol ) THEN  
-         igrd = 2      ! Lateral surface at U-points
-         DO ib_bdy = 1, nb_bdy
-            DO ib = 1, idx_bdy(ib_bdy)%nblenrim(igrd)
-               nbi => idx_bdy(ib_bdy)%nbi(ib,igrd)
-               nbj => idx_bdy(ib_bdy)%nbj(ib,igrd)
-               flagu => idx_bdy(ib_bdy)%flagu(ib,igrd)
-               bdysurftot = bdysurftot + hu_n   (nbi  , nbj)                           &
-                  &                    * e2u    (nbi  , nbj) * ABS( flagu ) &
-                  &                    * tmask_i(nbi  , nbj)                           &
-                  &                    * tmask_i(nbi+1, nbj)                   
-            END DO
-         END DO
-
-         igrd=3 ! Add lateral surface at V-points
-         DO ib_bdy = 1, nb_bdy
-            DO ib = 1, idx_bdy(ib_bdy)%nblenrim(igrd)
-               nbi => idx_bdy(ib_bdy)%nbi(ib,igrd)
-               nbj => idx_bdy(ib_bdy)%nbj(ib,igrd)
-               flagv => idx_bdy(ib_bdy)%flagv(ib,igrd)
-               bdysurftot = bdysurftot + hv_n   (nbi, nbj  )                           &
-                  &                    * e1v    (nbi, nbj  ) * ABS( flagv ) &
-                  &                    * tmask_i(nbi, nbj  )                           &
-                  &                    * tmask_i(nbi, nbj+1)
-            END DO
-         END DO
-         !
-         CALL mpp_sum( 'bdyini', bdysurftot )      ! sum over the global domain
-      END IF   
       !
       ! Tidy up
@@ -1284,5 +1258,4 @@
       !
    END SUBROUTINE bdy_segs
-
 
    SUBROUTINE bdy_ctl_seg
Index: /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/src/OCE/BDY/bdyvol.F90
===================================================================
--- /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/src/OCE/BDY/bdyvol.F90	(revision 10497)
+++ /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/src/OCE/BDY/bdyvol.F90	(revision 10498)
@@ -9,4 +9,5 @@
    !!            3.0  !  2008-04  (NEMO team)  add in the reference version
    !!            3.4  !  2011     (D. Storkey) rewrite in preparation for OBC-BDY merge
+   !!            4.0  !  2019-01  (P. Mathiot) adapted to time splitting     
    !!----------------------------------------------------------------------
    USE oce            ! ocean dynamics and tracers 
@@ -24,5 +25,5 @@
    PRIVATE
 
-   PUBLIC   bdy_vol    ! called by ???
+   PUBLIC   bdy_vol2d    ! called by dynspg_ts
 
    !!----------------------------------------------------------------------
@@ -33,5 +34,5 @@
 CONTAINS
 
-   SUBROUTINE bdy_vol( kt )
+   SUBROUTINE bdy_vol2d( kt, kc, pua2d, pva2d, phu, phv )
       !!----------------------------------------------------------------------
       !!                      ***  ROUTINE bdyvol  ***
@@ -40,6 +41,4 @@
       !!      A correction velocity is calculated to correct the total transport 
       !!      through the unstructured OBC. 
-      !!      The total depth used is constant (H0) to be consistent with the 
-      !!      linear free surface coded in OPA 8.2    <<<=== !!gm  ???? true ????
       !!
       !! ** Method  :   The correction velocity (zubtpecor here) is defined calculating
@@ -65,28 +64,28 @@
       !!            (set nn_volctl to 1 in tne namelist for this option)
       !!----------------------------------------------------------------------
-      INTEGER, INTENT(in) ::   kt   ! ocean time-step index
+      INTEGER, INTENT(in) ::   kt, kc   ! ocean time-step index, cycle time-step
       !
       INTEGER  ::   ji, jj, jk, jb, jgrd
       INTEGER  ::   ib_bdy, ii, ij
-      REAL(wp) ::   zubtpecor, z_cflxemp, ztranst
+      REAL(wp) ::   zubtpecor, ztranst
+      REAL(wp), SAVE :: z_cflxemp                                  ! cumulated emp flux
+      REAL(wp), DIMENSION(jpi,jpj), INTENT(inout) :: pua2d, pva2d  ! Barotropic velocities
+      REAL(wp), DIMENSION(jpi,jpj), INTENT(in) :: phu, phv         ! Ocean depth at U- and V-points
       TYPE(OBC_INDEX), POINTER :: idx
       !!-----------------------------------------------------------------------------
       !
-      IF( ln_vol ) THEN
-      !
-      IF( kt == nit000 ) THEN 
-         IF(lwp) WRITE(numout,*)
-         IF(lwp) WRITE(numout,*)'bdy_vol : Correction of velocities along unstructured OBC'
-         IF(lwp) WRITE(numout,*)'~~~~~~~'
-      END IF 
-
       ! Calculate the cumulate surface Flux z_cflxemp (m3/s) over all the domain
       ! -----------------------------------------------------------------------
-!!gm replace these lines :
-      z_cflxemp = SUM ( ( emp(:,:) - rnf(:,:) + fwfisf(:,:) ) * bdytmask(:,:) * e1e2t(:,:) ) / rau0
-      CALL mpp_sum( 'bdyvol', z_cflxemp )     ! sum over the global domain
-!!gm   by :
-!!gm      z_cflxemp = glob_sum(  'bdyvol', ( emp(:,:)-rnf(:,:)+fwfisf(:,:) ) * bdytmask(:,:) * e1e2t(:,:)  ) / rau0
-!!gm
+      IF ( kc == 1 ) z_cflxemp = glob_sum( 'bdyvol', ( emp(:,:) - rnf(:,:) + fwfisf(:,:) ) * bdytmask(:,:) * e1e2t(:,:)  ) / rau0
+
+      ! Compute bdy surface each cycle if non linear free surface
+      ! ---------------------------------------------------------
+      IF ( .NOT. ln_linssh ) THEN
+         ! compute area each time step
+         bdysurftot = bdy_segs_surf( phu, phv )
+      ELSE
+         ! compute area only the first time
+         IF ( ( kt == nit000 ) .AND. ( kc == 1 ) ) bdysurftot = bdy_segs_surf( phu, phv )
+      END IF
 
       ! Transport through the unstructured open boundary
@@ -98,59 +97,70 @@
          jgrd = 2                               ! cumulate u component contribution first 
          DO jb = 1, idx%nblenrim(jgrd)
-            DO jk = 1, jpkm1
+            ii = idx%nbi(jb,jgrd)
+            ij = idx%nbj(jb,jgrd)
+            zubtpecor = zubtpecor + idx%flagu(jb,jgrd) * pua2d(ii,ij) * e2u(ii,ij) * phu(ii,ij) * tmask_i(ii,ij) * tmask_i(ii+1,ij)
+         END DO
+         jgrd = 3                               ! then add v component contribution
+         DO jb = 1, idx%nblenrim(jgrd)
+            ii = idx%nbi(jb,jgrd)
+            ij = idx%nbj(jb,jgrd)
+            zubtpecor = zubtpecor + idx%flagv(jb,jgrd) * pva2d(ii,ij) * e1v(ii,ij) * phv(ii,ij) * tmask_i(ii,ij) * tmask_i(ii,ij+1)
+         END DO
+         !
+      END DO
+      IF( lk_mpp )   CALL mpp_sum( 'bdyvol', zubtpecor )   ! sum over the global domain
+
+      ! The normal velocity correction
+      ! ------------------------------
+      IF( nn_volctl==1 ) THEN   ;   zubtpecor = ( zubtpecor - z_cflxemp ) / bdysurftot  ! maybe should be apply only once at the end
+      ELSE                      ;   zubtpecor =   zubtpecor               / bdysurftot
+      END IF
+
+      ! Correction of the total velocity on the unstructured boundary to respect the mass flux conservation
+      ! -------------------------------------------------------------
+      DO ib_bdy = 1, nb_bdy
+         idx => idx_bdy(ib_bdy)
+         !
+         jgrd = 2                               ! correct u component
+         DO jb = 1, idx%nblenrim(jgrd)
                ii = idx%nbi(jb,jgrd)
                ij = idx%nbj(jb,jgrd)
-               zubtpecor = zubtpecor + idx%flagu(jb,jgrd) * ua(ii,ij, jk) * e2u(ii,ij) * e3u_n(ii,ij,jk)
-            END DO
-         END DO
-         jgrd = 3                               ! then add v component contribution
-         DO jb = 1, idx%nblenrim(jgrd)
-            DO jk = 1, jpkm1
+               pua2d(ii,ij) = pua2d(ii,ij) - idx%flagu(jb,jgrd) * zubtpecor * tmask_i(ii,ij) * tmask_i(ii+1,ij)
+         END DO
+         jgrd = 3                              ! correct v component
+         DO jb = 1, idx%nblenrim(jgrd)
                ii = idx%nbi(jb,jgrd)
                ij = idx%nbj(jb,jgrd)
-               zubtpecor = zubtpecor + idx%flagv(jb,jgrd) * va(ii,ij, jk) * e1v(ii,ij) * e3v_n(ii,ij,jk) 
-            END DO
-         END DO
-         !
-      END DO
-      CALL mpp_sum( 'bdyvol', zubtpecor )   ! sum over the global domain
-
-      ! The normal velocity correction
-      ! ------------------------------
-      IF( nn_volctl==1 ) THEN   ;   zubtpecor = ( zubtpecor - z_cflxemp ) / bdysurftot 
-      ELSE                      ;   zubtpecor =   zubtpecor               / bdysurftot
-      END IF
-
-      ! Correction of the total velocity on the unstructured boundary to respect the mass flux conservation
-      ! -------------------------------------------------------------
-      ztranst = 0._wp
-      DO ib_bdy = 1, nb_bdy
-         idx => idx_bdy(ib_bdy)
-         !
-         jgrd = 2                               ! correct u component
-         DO jb = 1, idx%nblenrim(jgrd)
-            DO jk = 1, jpkm1
-               ii = idx%nbi(jb,jgrd)
-               ij = idx%nbj(jb,jgrd)
-               ua(ii,ij,jk) = ua(ii,ij,jk) - idx%flagu(jb,jgrd) * zubtpecor * umask(ii,ij,jk)
-               ztranst = ztranst + idx%flagu(jb,jgrd) * ua(ii,ij,jk) * e2u(ii,ij) * e3u_n(ii,ij,jk)
-            END DO
-         END DO
-         jgrd = 3                              ! correct v component
-         DO jb = 1, idx%nblenrim(jgrd)
-            DO jk = 1, jpkm1
-               ii = idx%nbi(jb,jgrd)
-               ij = idx%nbj(jb,jgrd)
-               va(ii,ij,jk) = va(ii,ij,jk) -idx%flagv(jb,jgrd) * zubtpecor * vmask(ii,ij,jk)
-               ztranst = ztranst + idx%flagv(jb,jgrd) * va(ii,ij,jk) * e1v(ii,ij) * e3v_n(ii,ij,jk)
-            END DO
-         END DO
-         !
-      END DO
-      CALL mpp_sum( 'bdyvol', ztranst )   ! sum over the global domain
- 
+               pva2d(ii,ij) = pva2d(ii,ij) - idx%flagv(jb,jgrd) * zubtpecor * tmask_i(ii,ij) * tmask_i(ii,ij+1)
+         END DO
+         !
+      END DO
+      ! 
       ! Check the cumulated transport through unstructured OBC once barotropic velocities corrected
       ! ------------------------------------------------------
-      IF( lwp .AND. MOD( kt, nwrite ) == 0 ) THEN
+      IF( MOD( kt, nwrite ) == 0 .AND. ( kc == 1 ) ) THEN
+         !
+         ! compute residual transport across boundary
+         ztranst = 0._wp
+         DO ib_bdy = 1, nb_bdy
+            idx => idx_bdy(ib_bdy)
+            !
+            jgrd = 2                               ! correct u component
+            DO jb = 1, idx%nblenrim(jgrd)
+                  ii = idx%nbi(jb,jgrd)
+                  ij = idx%nbj(jb,jgrd)
+                  ztranst = ztranst + idx%flagu(jb,jgrd) * pua2d(ii,ij) * e2u(ii,ij) * phu(ii,ij) * tmask_i(ii,ij) * tmask_i(ii+1,ij)
+            END DO
+            jgrd = 3                              ! correct v component
+            DO jb = 1, idx%nblenrim(jgrd)
+                  ii = idx%nbi(jb,jgrd)
+                  ij = idx%nbj(jb,jgrd)
+                  ztranst = ztranst + idx%flagv(jb,jgrd) * pva2d(ii,ij) * e1v(ii,ij) * phv(ii,ij) * tmask_i(ii,ij) * tmask_i(ii,ij+1)
+            END DO
+            !
+         END DO
+         IF( lk_mpp )   CALL mpp_sum('bdyvol', ztranst )   ! sum over the global domain
+
+
          IF(lwp) WRITE(numout,*)
          IF(lwp) WRITE(numout,*)'bdy_vol : time step :', kt
@@ -162,8 +172,50 @@
       END IF 
       !
-      END IF ! ln_vol
-      !
-   END SUBROUTINE bdy_vol
-
+   END SUBROUTINE bdy_vol2d
+   !
+   REAL(wp) FUNCTION bdy_segs_surf(phu, phv)
+      !!----------------------------------------------------------------------
+      !!                 ***  ROUTINE bdy_ctl_seg  ***
+      !!
+      !! ** Purpose :   Compute total lateral surface for volume correction
+      !!
+      !!----------------------------------------------------------------------
+
+      REAL(wp), DIMENSION(jpi,jpj), INTENT(in) :: phu, phv ! water column thickness at U and V points
+      INTEGER            ::  igrd, ib_bdy, ib                ! loop indexes
+      INTEGER , POINTER  ::  nbi, nbj                        ! short cuts
+      REAL(wp), POINTER  ::  zflagu, zflagv                  !    -   -
+
+      ! Compute total lateral surface for volume correction:
+      ! ----------------------------------------------------
+      bdy_segs_surf = 0._wp
+      igrd = 2      ! Lateral surface at U-points
+      DO ib_bdy = 1, nb_bdy
+         DO ib = 1, idx_bdy(ib_bdy)%nblenrim(igrd)
+            nbi => idx_bdy(ib_bdy)%nbi(ib,igrd)
+            nbj => idx_bdy(ib_bdy)%nbj(ib,igrd)
+            zflagu => idx_bdy(ib_bdy)%flagu(ib,igrd)
+            bdy_segs_surf = bdy_segs_surf + phu(nbi, nbj)                              &
+               &                            * e2u(nbi, nbj) * ABS( zflagu )            &
+               &                            * tmask_i(nbi, nbj) * tmask_i(nbi+1, nbj)
+         END DO
+      END DO
+
+      igrd=3 ! Add lateral surface at V-points
+      DO ib_bdy = 1, nb_bdy
+         DO ib = 1, idx_bdy(ib_bdy)%nblenrim(igrd)
+            nbi => idx_bdy(ib_bdy)%nbi(ib,igrd)
+            nbj => idx_bdy(ib_bdy)%nbj(ib,igrd)
+            zflagv => idx_bdy(ib_bdy)%flagv(ib,igrd)
+            bdy_segs_surf = bdy_segs_surf + phv(nbi, nbj)                              &
+               &                            * e1v(nbi, nbj) * ABS( zflagv )            &
+               &                            * tmask_i(nbi, nbj) * tmask_i(nbi, nbj+1)
+         END DO
+      END DO
+      !
+      ! redirect the time to bdyvol as this variable is only used by bdyvol
+      IF( lk_mpp )   CALL mpp_sum( 'bdyvol', bdy_segs_surf ) ! sum over the global domain
+      !
+   END FUNCTION bdy_segs_surf
    !!======================================================================
 END MODULE bdyvol
Index: /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/src/OCE/DYN/dynhpg.F90
===================================================================
--- /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/src/OCE/DYN/dynhpg.F90	(revision 10497)
+++ /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/src/OCE/DYN/dynhpg.F90	(revision 10498)
@@ -245,5 +245,5 @@
                END DO
                IF (ikt  >=  2) ziceload(ji,jj) = ziceload(ji,jj) + (2._wp * znad + zrhdtop_isf(ji,jj) + zrhd(ji,jj,ikt-1)) &
-                  &                                              * ( risfdep(ji,jj) - gdept_1d(ikt-1) )
+                  &                                              * ( risfdep(ji,jj) - gdept_n(ji,jj,ikt-1) )
             END DO
          END DO
Index: /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/src/OCE/DYN/dynspg_ts.F90
===================================================================
--- /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/src/OCE/DYN/dynspg_ts.F90	(revision 10497)
+++ /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/src/OCE/DYN/dynspg_ts.F90	(revision 10498)
@@ -41,4 +41,5 @@
    USE wet_dry         ! wetting/drying flux limter
    USE bdy_oce         ! open boundary
+   USE bdyvol          ! open boundary volume conservation
    USE bdytides        ! open boundary condition data
    USE bdydyn2d        ! open boundary conditions on barotropic variables
@@ -792,6 +793,7 @@
          !                                                !* after ssh
          !                                                !  -----------
-         ! One should enforce volume conservation at open boundaries here
-         ! considering fluxes below:
+         !
+         ! Enforce volume conservation at open boundaries:
+         IF( ln_bdy .AND. ln_vol ) CALL bdy_vol2d( kt, jn, ua_e, va_e, zhup2_e, zhvp2_e )
          !
          zwx(:,:) = e2u(:,:) * ua_e(:,:) * zhup2_e(:,:)         ! fluxes at jn+0.5
Index: /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/tests/ISOMIP/MY_SRC/usrdef_zgr.F90
===================================================================
--- /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/tests/ISOMIP/MY_SRC/usrdef_zgr.F90	(revision 10497)
+++ /NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/tests/ISOMIP/MY_SRC/usrdef_zgr.F90	(revision 10498)
@@ -150,4 +150,5 @@
                   ! e3t into the ice shelf
                   pe3t (ji,jj,ik-1) = pdepw(ji,jj,ik  ) - pdepw(ji,jj,ik-1)
+                  pe3w (ji,jj,ik-1) = pdept(ji,jj,ik-1) - pdept(ji,jj,ik-2)
                END IF
             END DO
