Index: /NEMO/trunk/doc/latex/NEMO/main/definitions.tex
===================================================================
--- /NEMO/trunk/doc/latex/NEMO/main/definitions.tex	(revision 11432)
+++ /NEMO/trunk/doc/latex/NEMO/main/definitions.tex	(revision 11433)
@@ -1,11 +1,16 @@
-%% Engine (folder name)
+%% Engine (subfolder name)
 \def \engine{NEMO}
 
-%% Title (variable name already use by 'titling' pkg)
+%% Title and cover page settings
+\def \spacetop{  \vspace*{1.85cm} }
 \def \heading{NEMO ocean engine}
+\def \subheading{}
+\def \spacedown{ \vspace*{0.75cm } }
+\def \authorswidth{ 0.3\linewidth}
+\def \rulelenght{270pt}
+\def \abstractwidth{0.6\linewidth}
 
-%% Authors (thanks will apply to the second author)
-\def \firstauthor{Gurvan Madec~}
-\def \secondauthor{NEMO System Team}
+%% Color for document (frontpage banner, links  and chapter boxes)
+\def \setcolor{ \definecolor{manualcolor}{cmyk}{1, .60, 0, .40} }
 
 %% IPSL publication number
Index: /NEMO/trunk/doc/latex/NEMO/main/foreword.tex
===================================================================
--- /NEMO/trunk/doc/latex/NEMO/main/foreword.tex	(revision 11432)
+++ /NEMO/trunk/doc/latex/NEMO/main/foreword.tex	(revision 11433)
@@ -1,22 +1,27 @@
-% ================================================================
-% Foreword
-% ================================================================
-\chapter*{Foreword}
+%% ================================================================
+%% 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.
+%% Common part between NEMO-SI3-TOP
+\NEMO\ (``Nucleus for European Modelling of the Ocean'') is a framework of ocean-related engines.
+It is intended to be a flexible tool for studying the ocean dynamics and thermodynamics (``blue ocean''),
+as well as its interactions with the components of the Earth climate system over
+a wide range of space and time scales.
+Within \NEMO, the ocean engine is interfaced with a sea-ice model (\SIcube\ or
+\href{http://github.com/CICE-Consortium/CICE}{CICE}),
+passive tracers and biogeochemical models (\TOP) and,
+via the \href{http://portal.enes.org/oasis}{OASIS} coupler,
+with several atmospheric general circulation models.
+It also supports two-way grid embedding by means of the \href{http://agrif.imag.fr}{AGRIF} software.
 
+%% Specific part
+The primitive equation model is adapted to regional and global ocean circulation problems down to
+kilometric scale.
 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.
+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 (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.
+Various physical choices are available to describe ocean physics,
+so as various HPC functionalities to improve performances.
Index: /NEMO/trunk/doc/latex/NEMO/main/thanks.tex
===================================================================
--- /NEMO/trunk/doc/latex/NEMO/main/thanks.tex	(revision 11432)
+++ /NEMO/trunk/doc/latex/NEMO/main/thanks.tex	(revision 11433)
@@ -1,2 +1,49 @@
-J\'{e}r\^{o}me Chanut,
-Silvia Mocavero
+%Romain Bourdall\'{e}-Badie
+%\orcid{0000-0002-8742-3289} \\
+%Mike Bell                   \\
+%J\'{e}r\^{o}me Chanut       \\
+%Emanuela Clementi
+%\orcid{0000-0002-5752-1849} \\
+%Andrew Coward
+%\orcid{0000-0002-0456-129X} \\
+%Massimiliano Drudi
+%\orcid{0000-0002-9951-740X} \\
+%Christian \'{E}th\'{e}      \\
+%Doroteaciro Iovino
+%\orcid{0000-0001-5132-7255} \\
+%Dan Lea                     \\
+%Claire L\'{e}vy
+%\orcid{0000-0003-2518-6692} \\
+%Gurvan Madec
+%\orcid{0000-0002-6447-4198} \\
+%Nicolas Martin              \\
+%S\'{e}bastien Masson
+%\orcid{0000-0002-1694-8117} \\
+%Pierre Mathiot              \\
+%Silvia Mocavero
+%\orcid{0000-0002-6309-8282} \\
+%Simon M\"{u}ller            \\
+%George Nurser               \\
+%Guillaume Samson
+%\orcid{0000-0001-7481-6369} \\
+%Dave Storkey
+
+\orcid{0000-0002-8742-3289} Romain Bourdall\'{e}-Badie  \\
+                            Mike Bell                   \\
+                            J\'{e}r\^{o}me Chanut       \\
+\orcid{0000-0002-5752-1849} Emanuela Clementi           \\
+\orcid{0000-0002-0456-129X} Andrew Coward               \\
+\orcid{0000-0002-9951-740X} Massimiliano Drudi          \\
+                            Christian \'{E}th\'{e}      \\
+\orcid{0000-0001-5132-7255} Doroteaciro Iovino          \\
+                            Dan Lea                     \\
+\orcid{0000-0003-2518-6692} Claire L\'{e}vy             \\
+\orcid{0000-0002-6447-4198} Gurvan Madec                \\
+                            Nicolas Martin              \\
+\orcid{0000-0002-1694-8117} S\'{e}bastien Masson        \\
+                            Pierre Mathiot              \\
+\orcid{0000-0002-6309-8282} Silvia Mocavero             \\
+                            Simon M\"{u}ller            \\
+                            George Nurser               \\
+\orcid{0000-0001-7481-6369} Guillaume Samson            \\
+                            Dave Storkey
Index: /NEMO/trunk/doc/latex/SI3/main/definitions.tex
===================================================================
--- /NEMO/trunk/doc/latex/SI3/main/definitions.tex	(revision 11432)
+++ /NEMO/trunk/doc/latex/SI3/main/definitions.tex	(revision 11433)
@@ -2,10 +2,15 @@
 \def \engine{SI3}
 
-%% Title (variable name already use by 'titling' pkg)
-\def \heading{Sea Ice modelling Integrated Initiative (SI$^3$) \\ The NEMO sea ice engine}
+%% Title and cover page settings
+\def \spacetop{  \vspace*{1.2cm} }
+\def \heading{Sea Ice modelling Integrated Initiative (SI$^3$)}
+\def \subheading{The NEMO sea ice engine}
+\def \spacedown{ \vspace*{1cm  } }
+\def \authorswidth{0.2\linewidth}
+\def \rulelenght{230pt}
+\def \abstractwidth{0.65\linewidth}
 
-%% Authors (thanks will apply to the second author)
-\def \firstauthor{}
-\def \secondauthor{NEMO Sea Ice Working Group}
+%% Color for document (frontpage banner, links and chapter boxes)
+\def \setcolor{ \definecolor{manualcolor}{cmyk}{0, 0, 0, 0.4} }
 
 %% IPSL publication number
Index: /NEMO/trunk/doc/latex/SI3/main/foreword.tex
===================================================================
--- /NEMO/trunk/doc/latex/SI3/main/foreword.tex	(revision 11432)
+++ /NEMO/trunk/doc/latex/SI3/main/foreword.tex	(revision 11433)
@@ -0,0 +1,25 @@
+%% ================================================================
+%% Abstract
+%% ================================================================
+
+%% Common part between NEMO-SI3-TOP
+``Sea Ice Modelling Integrated Initiative'' (\SIcube) is the sea ice engine of
+the \NEMO\ ocean model (``Nucleus for European Modelling of the Ocean'').
+It is intended to be a flexible tool for studying the sea ice dynamics and thermodynamics,
+brine inclusions and subgrid-scale thickness variations (``white ocean''),
+as well as its interactions with the other components of the Earth climate system over
+a wide range of space and time scales.
+\SIcube\ is interfaced with the \NEMO\ ocean engine, and,
+via the \href{http://portal.enes.org/oasis}{OASIS} coupler,
+with several atmospheric general circulation models.
+It also supports two-way grid embedding by means of the \href{http://agrif.imag.fr}{AGRIF} software.
+
+%% Specific part
+Designed for global to regional applications up to $~$10 km of effective resolution,
+\SIcube\ is a curvilinear grid, finite-difference implementation of the classical AIDJEX model
+(Arctic Ice Dynamics Joint EXperiment),
+combining the conservation of momentum for viscous-plastic continuum,
+energy and salt-conserving halo-thermodynamics,
+an explicit representation of subgrid-scale ice thickness variations, snow and melt ponds.
+An option to switch back to the \textit{single-category} (or \textit{2-level}) framework provides
+a cheap sea ice modelling solution.
Index: /NEMO/trunk/doc/latex/SI3/main/thanks.tex
===================================================================
--- /NEMO/trunk/doc/latex/SI3/main/thanks.tex	(revision 11432)
+++ /NEMO/trunk/doc/latex/SI3/main/thanks.tex	(revision 11433)
@@ -1,1 +1,16 @@
-TBD
+Yevgeny Aksenov       \\
+Ed Blockley           \\
+Matthieu Chevallier   \\
+Danny Feltham         \\
+Thierry Fichefet      \\
+Gilles Garric         \\
+Paul Holland          \\
+Dorotea Iovino        \\
+Gurvan Madec          \\
+Fran\c cois Massonnet \\
+Jeff Ridley           \\
+Cl\'ement Rousset     \\
+David Salas           \\
+David Schroeder       \\
+Steffen Tietsche      \\
+Martin Vancoppenolle
Index: /NEMO/trunk/doc/latex/SI3/subfiles/introduction.tex
===================================================================
--- /NEMO/trunk/doc/latex/SI3/subfiles/introduction.tex	(revision 11432)
+++ /NEMO/trunk/doc/latex/SI3/subfiles/introduction.tex	(revision 11433)
@@ -8,18 +8,22 @@
 \textcolor{red}{[ \textit{July 2018} ]} \\
 
-%Near the poles of the Earth, the seas and oceans freeze when seawater at the freezing point loses heat. The resulting forms of saline ice are collectively called \textit{sea ice} \citep{WMO70}, reaching up to a few meters in thickness, where as sea ice coverage is about 5\% of the global ocean, about 30 million square kilometers. All sea ice characteristics vary over a wide range of spatio-temporal scales, reflecting changes in heat, mass and momentum exchanges with the atmosphere and the ocean; the clearest temporal signal being an ample seasonal cycle. Sea ice formation and melting affects water mass formation in the ocean \citep{goosse_1999}. It not only impacts, but also reflects the state of the climate system \citep{budyko_1969,notz_2016}.  Sea ice also affects marine life, water chemistry and human activities in polar regions. Local populations use sea ice for travelling and hunting, whereas navigation and resource exploitation are dependent on sea ice conditions. For such reasons, ocean modelling systems, including NEMO, must include a sea ice component.
+%Near the poles of the Earth, the seas and oceans freeze when seawater at the freezing point loses heat. The resulting forms of saline ice are collectively called \textit{sea ice} \citep{WMO70}, reaching up to a few meters in thickness, where as sea ice coverage is about 5\% of the global ocean, about 30 million square kilometers. All sea ice characteristics vary over a wide range of spatio-temporal scales, reflecting changes in heat, mass and momentum exchanges with the atmosphere and the ocean; the clearest temporal signal being an ample seasonal cycle. Sea ice formation and melting affects water mass formation in the ocean \citep{goosse_1999}. It not only impacts, but also reflects the state of the climate system \citep{budyko_1969,notz_2016}.  Sea ice also affects marine life, water chemistry and human activities in polar regions. Local populations use sea ice for travelling and hunting, whereas navigation and resource exploitation are dependent on sea ice conditions. For such reasons, ocean modelling systems, including \NEMO, must include a sea ice component.
 
-The sea Ice Modelling Integrated Initiative (SI$^3$) is the sea ice engine of the Nucleus for European Modelling of the Ocean (NEMO). It is intended to be a flexible tool for studying sea ice and its interactions with the other components of the Earth System over a wide range of space and time scales. SI$^3$ is a curvilinear grid, finite-difference implementation of the classical AIDJEX\footnote{AIDJEX=\textbf{A}rctic \textbf{I}ce \textbf{D}ynamics \textbf{J}oint \textbf{EX}periment} model \citep{coon_1974}, combining the conservation of momentum for viscous-plastic continuum, energy and salt-conserving halo-thermodynamics, an explicit representation of subgrid-scale ice thickness variations, snow and melt ponds. An option to switch back to the \textit{single-category} (or \textit{2-level}) framework of \cite{hibler_1979} provides a cheap sea ice modelling solution.
-
-SI$^3$ is the result of the recommendation of the Sea Ice Working Group (SIWG) to reduce duplication and better use development resources. SI$^3$ merges the capabilities of the 3 formerly used NEMO sea ice models (CICE, GELATO and LIM). The \textbf{3} in SI$^3$ refers to the three formerly used sea ice models. It also refers to linkages between 3 different media (ocean, ice, snow). The model can be spelt 'SI3' in situations where the superscript could be problematic (i.e., within code and svn repository etc.) The model name would be pronounced as 'si-cube' for short (or 'sea ice cubed' for slightly longer). 
+\SIcube\ is the result of the recommendation of the Sea Ice Working Group (SIWG) to
+reduce duplication and better use development resources.
+\SIcube\ merges the capabilities of the 3 formerly sea ice models used in \NEMO\ (CICE, GELATO and LIM).
+The \textbf{3} in \SIcube\ refers either to the three formerly used sea ice models and
+linkages between 3 different media (ocean-ice-snow).
+The model would be pronounced as ``SI cube'' for short (or ``Sea Ice cubed'' for slightly longer),
+otherwise it can be spelt ``SI three'' in situations where the superscript could be problematic.
 
 % Limitations & scope
-%There are limitations to the applicability of models such as SI$^3$. The continuum approach is not invalid for grid cell size above at least 1 km, below which sea ice particles may include just a few floes, which is not sufficient \citep{lepparanta_2011}. Second, one must remember that our current knowledge of sea ice is not as complete as for the ocean: there are no fundamental equations such as Navier Stokes equations for sea ice. Besides, important features and processes span widely different scales, such as brine inclusions (1 $\mu$m-1 mm) \citep{perovich_1996}, horizontal thickness variations (1 m-100 km) \citep{percival_2008}, deformation and fracturing (10 m-1000 km) \citep{marsan_2004}. These impose complicated and often subjective subgrid-scale treatments. All in all, there is more empirism in sea ice models than in ocean models. 
+%There are limitations to the applicability of models such as \SIcube. The continuum approach is not invalid for grid cell size above at least 1 km, below which sea ice particles may include just a few floes, which is not sufficient \citep{lepparanta_2011}. Second, one must remember that our current knowledge of sea ice is not as complete as for the ocean: there are no fundamental equations such as Navier Stokes equations for sea ice. Besides, important features and processes span widely different scales, such as brine inclusions (1 $\mu$m-1 mm) \citep{perovich_1996}, horizontal thickness variations (1 m-100 km) \citep{percival_2008}, deformation and fracturing (10 m-1000 km) \citep{marsan_2004}. These impose complicated and often subjective subgrid-scale treatments. All in all, there is more empiricism in sea ice models than in ocean models.
 
 In order to handle all the subsequent required subjective choices, we applied the following guidelines or principles:
 \begin{itemize}
-\item Sea ice is frozen seawater that is in tight interaction with the underlying ocean. This close connexion suggests that the sea ice and ocean model components must be as consistent as possible. In practice, this is materialized by the close match between LIM and NEMO, in terms of numerical choices, regarding the grid (Arakawa C-type) and the numerical discretization (finite differences with NEMO scale factors).
+\item Sea ice is frozen seawater that is in tight interaction with the underlying ocean. This close connexion suggests that the sea ice and ocean model components must be as consistent as possible. In practice, this is materialized by the close match between LIM and \NEMO, in terms of numerical choices, regarding the grid (Arakawa C-type) and the numerical discretization (finite differences with \NEMO\ scale factors).
 \item It is useful to be able to either prescribe the atmospheric state or to use an atmospheric model. For consistency and simplicity of the code, we choose to use formulations as close as possible in both cases.
-\item Different resolutions and time steps can be used. There are parameters that depend on such choices. We thrieved to achieve a resolution and time-step independent code, by imposing a priori scaling on the resolution / time step dependence of such parameters.
+\item Different resolutions and time steps can be used. There are parameters that depend on such choices. We thrived to achieve a resolution and time-step independent code, by imposing a priori scaling on the resolution / time step dependence of such parameters.
 \item Energy, mass and salt must be conserved as much as possible.
 \end{itemize}
@@ -31,5 +35,5 @@
 There are no more CPP keys in the code. \\
 
-Namelists and output management follow NEMO guidelines. \\
+Namelists and output management follow \NEMO\ guidelines. \\
 
 Changes between releases. \\
@@ -55,5 +59,5 @@
 \item David Schroeder (CPOM, Reading, UK)
 \item Steffen Tietsche (ECMWF, Reading, UK)
-\item Martin Vancoppenolle (LOCEAN, CNRS, Paris, France, co-chair) 
+\item Martin Vancoppenolle (LOCEAN, CNRS, Paris, France, co-chair)
 \end{footnotesize}
 \end{itemize}
Index: /NEMO/trunk/doc/latex/TOP/main/definitions.tex
===================================================================
--- /NEMO/trunk/doc/latex/TOP/main/definitions.tex	(revision 11432)
+++ /NEMO/trunk/doc/latex/TOP/main/definitions.tex	(revision 11433)
@@ -2,10 +2,15 @@
 \def \engine{TOP}
 
-%% Title (variable name already use by 'titling' pkg)
-\def \heading{Tracers in Ocean Paradigm (TOP) \\ The NEMO passive tracers engine}
+%% Title and cover page settings
+\def \spacetop{  \vspace*{1.3cm} }
+\def \heading{Tracers in Ocean Paradigm (TOP)
+\def \subheading{The NEMO passive tracers engine}
+\def \spacedown{ \vspace*{1cm  } }
+\def \authorswidth{0.15\linewidth}
+\def \rulelenght{110pt}
+\def \abstractwidth{0.7\linewidth}
 
-%% Authors (thanks will apply to the second author)
-\def \firstauthor{}
-\def \secondauthor{NEMO TOP Working Group}
+%% Color for document (frontpage banner, links and chapter boxes)
+\def \setcolor{ \definecolor{manualcolor}{cmyk}{1, 0, 1, 0.4} }
 
 %% IPSL publication number
Index: /NEMO/trunk/doc/latex/TOP/main/foreword.tex
===================================================================
--- /NEMO/trunk/doc/latex/TOP/main/foreword.tex	(revision 11432)
+++ /NEMO/trunk/doc/latex/TOP/main/foreword.tex	(revision 11433)
@@ -0,0 +1,26 @@
+%% ================================================================
+%% Abstract
+%% ================================================================
+
+%% Common part between NEMO-SI3-TOP
+``Tracers in Ocean Paradigm'' (\TOP) is the passive tracers engine of
+the \NEMO\ ocean model (``Nucleus for European Modelling of the Ocean'').
+It is intended to be a flexible tool for studying the on/offline oceanic tracers transport and
+the biogeochemical processes (``green ocean''),
+as well as its interactions with the other components of the Earth climate system over
+a wide range of space and time scales.
+\TOP\ is interfaced with the \NEMO\ ocean engine, and,
+via the \href{http://portal.enes.org/oasis}{OASIS} coupler,
+with several atmospheric general circulation models.
+%It also supports two-way grid embedding by means of the \href{http://agrif.imag.fr}{AGRIF} software.
+
+%% Specific part
+This component provides the physical constraints and boundaries conditions for
+oceanic tracers transport and represents a generalized, hardwired interface toward
+biogeochemical models to enable a seamless coupling.
+In particular, transport dynamics are supplied by the ocean dynamical core thus
+enabling the use of all available advection and diffusion schemes in both on- and off-line modes.
+\TOP\ is designed to handle multiple oceanic tracers through a modular approach and
+it includes different sub-modules: ocean water age, inorganic carbon (CFCs) \& radiocarbon (C14b),
+built-in biogeochemical model (PISCES), and prototype for user-defined cases or
+coupling with alternative biogeochemical models (\eg \href{http://www.bfm-community.eu}{BFM}).
Index: /NEMO/trunk/doc/latex/TOP/main/thanks.tex
===================================================================
--- /NEMO/trunk/doc/latex/TOP/main/thanks.tex	(revision 11432)
+++ /NEMO/trunk/doc/latex/TOP/main/thanks.tex	(revision 11433)
@@ -1,8 +1,7 @@
-\'{E}th\'{e} Christian, 
-Lovato Tomas, 
-Aumont Olivier, 
-Palmi\'{e}ri Julien, 
-Mouchet Anne, 
-Nurser Georges, 
-Yool Andrew
-
+Olivier Aumont         \\
+Christian \'{E}th\'{e} \\
+Tomas Lovato           \\
+Anne Mouchet           \\
+Georges Nurser         \\
+Julien Palmi\'{e}ri    \\
+Andrew Yool
Index: /NEMO/trunk/doc/latex/global/coding_rules.tex
===================================================================
--- /NEMO/trunk/doc/latex/global/coding_rules.tex	(revision 11432)
+++ /NEMO/trunk/doc/latex/global/coding_rules.tex	(revision 11433)
@@ -1,50 +1,3 @@
-%\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}
-
-%\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}
-
-%\maketitle
-
-%\newpage
-
-%\tableofcontents
-
-%\newpage
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
 \chapter{Coding Rules}
 \label{apdx:coding}
@@ -60,25 +13,21 @@
 produces fewer bugs and is easier to maintain.
 Therefore, it is essential that the model development follows some rules:
-
-- well planned and designed
-
-- well written
-
-- well documented (both on- and off-line)
-
-- maintainable
-
-- easily portable
-
-- flexible.
+\begin{itemize}
+	\item well planned and designed
+	\item well written
+	\item well documented (both on- and off-line)
+	\item maintainable
+	\item easily portable
+	\item flexible.
+\end{itemize}
 
 To satisfy part of these aims, \NEMO is written with a coding standard which is close to the ECMWF rules,
 named DOCTOR \citep{gibson_rpt86}. 
 These rules present some advantages like:
-
-- to provide a well presented program
-
-- to use rules for variable names which allow recognition of their type
-(integer, real, parameter, local or shared variables, etc. ). 
+\begin{itemize}
+	\item to provide a well presented program
+	\item to use rules for variable names which allow recognition of their type
+	(integer, real, parameter, local or shared variables, etc. ). 
+\end{itemize}
 
 This facilitates both the understanding and the debugging of an algorithm.
@@ -86,8 +35,8 @@
 \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
+This document describes 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.
+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
@@ -98,21 +47,17 @@
 \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.
+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.
+	\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 3 major components: ocean dynamics (\path{./src/OCE}), sea-ice (\path{./src/ICE}) and
+\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.
@@ -126,20 +71,19 @@
 See \path{.src/OCE/DOM/phycst.F90} files for conversions.
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \section{Architecture}
 
-Within each directory, organisation of files is driven by orthogonality\index{orthogonality},
+Within each directory, organisation of files is driven by 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:
+The functional modules are:
 
 \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{...}
+	\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}
 
@@ -147,11 +91,9 @@
 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,
+Routine argument lists will contain a maximum 5 variables 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.
@@ -164,5 +106,4 @@
 \end{forlines}
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Array syntax}
 
@@ -198,11 +139,9 @@
 \end{forlines}
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{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.
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\forcode{NAMELIST}, ... All other parts of the \NEMO code will be written in lower case.
+
 \subsection{Comments}
 
@@ -248,5 +187,4 @@
 \end{enumerate}
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Continuation lines}
 
@@ -265,5 +203,4 @@
 use a ``\&'' as first character of the continuing lines to maintain the alignment.
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Declaration of arguments and local variables}
 
@@ -277,12 +214,9 @@
 \end{forlines}
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{F90 Standard}
 
-NEMO software adheres to the FORTRAN 95 language standard and does not rely on any specific language or
+\NEMO software adheres to the \fninety language standard and does not rely on any specific language or
 vendor extensions.
 
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Free-Form Source}
 
@@ -292,5 +226,4 @@
 Multi-line comments that extend to column 100 are unacceptable.
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Indentation}
 
@@ -310,5 +243,4 @@
 \end{forlines}
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Loops}
 
@@ -317,5 +249,4 @@
 In the case of a long loop, a self-descriptive label can be used ($i.e.$ not just a number).
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Naming Conventions: files}
 
@@ -331,5 +262,4 @@
 }
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Naming Conventions: modules}
 
@@ -338,15 +268,14 @@
 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.
+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. \\
-Never use a FORTRAN keyword as a routine or variable name. \\
+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--------------------------------------------------
@@ -355,19 +284,67 @@
     \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 & & & & \\
+      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}                                                                                 &
+                                                                                                  &
+                                                                                                  &
+                                                                                                  &
+                                                                                                  \\
       \hline
     \end{tabular}
@@ -377,5 +354,4 @@
 %--------------------------------------------------------------------------------------------------------------
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Operators}
 
@@ -385,5 +361,5 @@
 In general use the notation: \\
 $<Blank><Operator><Blank>$
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
 \subsection{Pre processor}
 
@@ -412,5 +388,5 @@
 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:
+Tests on cpp keys included in \NEMO at compilation step:
 
 \begin{itemize}
@@ -421,12 +397,11 @@
   If a change occurs in the CPP keys used for a given experiment, the whole compilation phase is done again.
 \end{itemize}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
 \section{Content rules}
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \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 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
@@ -438,10 +413,9 @@
 \end{forlines}
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Constants}
 
-Physical constants ($e.g.$ $\pi$, gas constants) must never be hardwired into the executable portion of a code.
+Physical constants ($e.g.$ $\pi$, gas constants) must never be hard-wired 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}.
+in the setup routine for the package.
 We realize than many parameterizations rely on empirically derived constants or fudge factors,
 which are not easy to name.
@@ -450,5 +424,4 @@
 Hard-coded numbers should never be passed through argument lists.
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Declaration for variables and constants}
 
@@ -512,13 +485,11 @@
 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
+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}
 
@@ -528,5 +499,4 @@
 FORTRAN 95 compilers can automatically provide explicit interface blocks for routines contained in a module.
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{I/O Error Conditions}
 
@@ -536,5 +506,4 @@
 a negative value means the end of record or end of file was encountered.
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{PRINT - ASCII output files}
 
@@ -551,5 +520,4 @@
 \end{forlines}
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Precision}
 
@@ -570,8 +538,7 @@
 \end{forlines}
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Structures}
 
-The \forcode{TYPE} structure allowing to declare some variables is more often used in NEMO,
+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:
@@ -592,11 +559,9 @@
 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
+\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:
@@ -610,5 +575,4 @@
 it effectively disables array bounds checking.
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Communication}
 
@@ -624,5 +588,4 @@
 }
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Error conditions}
 
@@ -634,9 +597,8 @@
 see \textit{stpctl.F90}.
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \subsection{Memory management}
 
 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.
+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.
@@ -644,7 +606,7 @@
 the \texttt{stat=<integer\ variable>} optional argument. \\
 
-In addition to arrays contained within modules, many routines in NEMO require local, ``workspace'' arrays to
+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
+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:
@@ -735,5 +697,5 @@
 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
+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. \\
 
@@ -748,19 +710,17 @@
 This should enable the developer to choose alternatives for use in the subroutine being worked on. \\
 
-When compiling NEMO for production runs,
+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
+These stubs may then be in-lined (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.
+In \NEMO, portability is a priority, before any too specific optimisation.
 
 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}}
 
@@ -770,17 +730,15 @@
 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
+\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).
+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
+However, this may be overriden by specifying the number of sub-domains in latitude and longitude in
 the \texttt{nammpp} section of the namelist file.
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \section{Features to be avoided}
 
@@ -804,6 +762,6 @@
   \forcode{SELECT CASE} construct instead)
 \item
-  Labeled \forcode{DO} construct
-  (use unlabeled \forcode{END DO} instead)
+  Labelled \forcode{DO} construct
+  (use unlabelled \forcode{END DO} instead)
 \item
   \forcode{FORMAT} statement
@@ -817,5 +775,5 @@
   \forcode{PAUSE}
 \item
-  \forcode{ENTRY} statement: a subprogram must only have one entry point.
+  \forcode{ENTRY} statement: a sub-program must only have one entry point.
 \item
   \forcode{RETURN} is obsolete and so not necessary at the end of program units
@@ -837,8 +795,2 @@
 \end{itemize}
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-% \printindex
-% \input NEMO_coding.conv.ind
-
-%\end{document}
Index: /NEMO/trunk/doc/latex/global/document.tex
===================================================================
--- /NEMO/trunk/doc/latex/global/document.tex	(revision 11432)
+++ /NEMO/trunk/doc/latex/global/document.tex	(revision 11433)
@@ -5,5 +5,5 @@
 
 %% NEMO release version
-\def \version{4.0rc~}
+\def \version{trunk}
 
 %% Preamble
@@ -11,17 +11,10 @@
 
 %% Document layout
-\documentclass[draft]{scrreprt}
+\documentclass[twoside = semi, abstract = on]{scrreprt}
 
-%% Load the configuration of the manual
-\input{../main/definitions}
-
-%% Load global *.tex files
+%% Load configurations
 \input{../../global/preamble}
 
 \dominitoc
-
-%% Launch the creation of the indexes
-\input{../../global/indexes}
-
 
 %% End of common preamble between main and sub-files
@@ -42,28 +35,31 @@
 %% ==============================================================================
 
+%% Disable page numbering temporarily
 \pagenumbering{gobble}
 
 %% Title page
-\input{../../global/frontpage}
+%\input{../../global/frontpage}
+\input{../../global/frontpage_new}
 
-\maketitle
-\emptythanks
+%\maketitle
+%\emptythanks
 
 %% Information page (2nd page)
 \input{../../global/info_page}
 
+%% Headings for introductory parts (no header, simple footer)
+\ofoot{\engine\ Reference Manual}\ifoot{\pagemark}
+\pagenumbering{roman}
+
 %% Foreword
-%\frontmatter   %% Chapter numbering off and Roman numerals for page numbers
-\pagenumbering{roman}
-\input{foreword}
+%\input{foreword}
 
 %% Table of Contents
 \tableofcontents
-\listoffigures
-\listoftables
-\listoflistings
+%\listoffigures
+%\listoftables
+%\listoflistings
 
 \clearpage
-%\end{document}
 
 
@@ -71,5 +67,7 @@
 %% ==============================================================================
 
-%\mainmatter   %% Chapter numbering on, page numbering is reset with Arabic numerals
+%% Headings for document body
+\lohead{Chap.\ \thechapter\ \leftmark}\rehead{Sect.\ \thesection\ \rightmark}
+\ifoot{Page\ \pagemark\ of \pageref*{LastPage}}
 \pagenumbering{arabic}
 
@@ -81,5 +79,5 @@
 
 %% Chapter numbering is reset with letters now
-\appendix   
+\appendix
 
 \include{appendices}
@@ -110,3 +108,2 @@
 
 \end{document}
-
Index: /NEMO/trunk/doc/latex/global/frontpage.tex
===================================================================
--- /NEMO/trunk/doc/latex/global/frontpage.tex	(revision 11432)
+++ /NEMO/trunk/doc/latex/global/frontpage.tex	(revision 11433)
@@ -1,25 +1,27 @@
 
 \title{\heading}
-\author{\firstauthor \and \secondauthor\thanks{\protect\input{thanks}}}
 \date{\today}
+\author{\protect\input{thanks}}
 
 \pretitle{
   \begin{center}
-\begin{figure}[H]
-  \begin{minipage}[c]{0.35\textwidth}
-    \href{http://www.nemo-ocean.eu}{\includegraphics[width=0.7\textwidth]{logos/NEMO_grey}}
-  \end{minipage}
-  \hfill
-  \begin{minipage}[c]{0.65\textwidth}
-    \centering
-    \large{\em{{N}ucleus for {E}uropean {M}odelling of the {O}cean}}
-  \end{minipage}
-\end{figure}
-\vfill
+    \begin{figure}[H]
+      \begin{minipage}[c]{0.35\textwidth}
+        \href{http://www.nemo-ocean.eu}{\includegraphics[width=0.7\textwidth]{logos/NEMO_grey}}
+      \end{minipage}
+      \hfill
+      \begin{minipage}[c]{0.65\textwidth}
+        \centering
+        \large{\em{{N}ucleus for {E}uropean {M}odelling of the {O}cean}}
+      \end{minipage}
+    \end{figure}
+    \vfill
     \Huge
 }
-\posttitle{\par\end{center}\vskip 0.5em}
-\preauthor{\begin{center}\Large\lineskip0.5em\begin{tabular}[t]{c}}
-\postauthor{\end{tabular}\par\end{center}}
+\posttitle{
+  \par
+  \end{center}
+  \vskip 0.5em
+}
 \predate{
   \vfill
@@ -46,4 +48,15 @@
 }
 
+\preauthor{
+  \begin{center}
+    \Large
+    \lineskip 0.5em
+    \begin{tabular}[t]{c c c}
+}
+\postauthor{
+    \end{tabular}
+    \par
+  \end{center}
+}
+
 \thanksmarkseries{fnsymbol}
-
Index: /NEMO/trunk/doc/latex/global/frontpage_new.tex
===================================================================
--- /NEMO/trunk/doc/latex/global/frontpage_new.tex	(revision 11433)
+++ /NEMO/trunk/doc/latex/global/frontpage_new.tex	(revision 11433)
@@ -0,0 +1,72 @@
+
+\begin{titlepage}
+  \newgeometry{hmargin = 1.5cm, vmargin = 2cm}
+
+  \begin{center}
+    \begin{minipage}{0.3\textwidth}
+      \includegraphics[height=1.5cm]{logos/NEMO_grey}
+    \end{minipage}
+    \begin{minipage}{0.6\textwidth}
+      \begin{center}
+      \Large
+      \textbf{N}ucleus for \textbf{E}uropean \textbf{M}odelling of the \textbf{O}cean \\[0.25cm]
+        \href{http://www.nemo-ocean.eu                        }{\textcolor{black} \faWordpress    }
+        \hspace{1cm}
+        \href{http://forge.ipsl.jussieu.fr/nemo               }{\textcolor{black} \faCodeFork     }
+        \hspace{1cm}
+        \href{http://github.com/NEMO-ocean                    }{\textcolor{black} \faGithub       }
+        \hspace{1cm}
+        \href{http://zenodo.org/communities/nemo-ocean        }{\textcolor{black} \faCloudDownload}
+        \hspace{1cm}
+        \href{http://listes.ipsl.fr/sympa/info/nemo-newsletter}{\textcolor{black} \faEnvelope     }
+      \end{center}
+    \end{minipage}
+  \end{center}
+
+  \spacetop
+  \noindent
+  \textcolor{white}{\fontsize{1cm}{1cm} \selectfont \heading   }\\[0.25cm]
+  \noindent
+  \textcolor{white}{\Huge \subheading}
+  \spacedown
+
+  \begin{center}
+    \LARGE Version \version\ -\ \today \\[0.25cm]
+    \href{http://doi.org/10.5281/zenodo.\zid}{ \includegraphics{{badges/zenodo.\zid}.pdf} }
+  \end{center}
+
+  \vfill
+
+  \begin{minipage}{\authorswidth}
+    \begin{flushright}
+      \input{thanks}
+    \end{flushright}
+  \end{minipage}
+  \hspace{15pt}
+  \begin{minipage}{0.02\linewidth}
+    \rule{1pt}{\rulelenght}
+  \end{minipage}
+  \hspace{5pt}
+  \begin{minipage}{\abstractwidth}
+    \begin{abstract}
+      \input{foreword}
+    \end{abstract}
+  \end{minipage}
+
+  \vfill
+
+  \begin{center}
+    \Large
+    {C}ommunity \hspace{1.5em} {O}cean \hspace{1.5em} {M}odel \\[0.25cm]
+    \href{http://www.cmcc.it          }{ \includegraphics[height=1cm]{logos/CMCC} } \hspace{0.25cm}
+    \href{http://www.cnrs.fr          }{ \includegraphics[height=1cm]{logos/CNRS} } \hspace{0.25cm}
+    \href{http://www.mercator-ocean.fr}{ \includegraphics[height=1cm]{logos/MOI}  } \hspace{0.25cm}
+    \href{http://www.metoffice.gov.uk }{ \includegraphics[height=1cm]{logos/UKMO} } \hspace{0.25cm}
+    \href{http://nerc.ukri.org        }{ \includegraphics[height=1cm]{logos/NERC} } \\
+  \end{center}
+
+\end{titlepage}
+
+\restoregeometry
+
+%\end{document}
Index: /NEMO/trunk/doc/latex/global/indexes.tex
===================================================================
--- /NEMO/trunk/doc/latex/global/indexes.tex	(revision 11432)
+++ /NEMO/trunk/doc/latex/global/indexes.tex	(revision 11433)
@@ -8,5 +8,5 @@
 \newcommand{\key}[1]{\index[keys]{#1}        \texttt{\textbf{key\_#1}}}
 \newcommand{\mdl}[1]{\index[modules]{#1}     \textit{#1.F90}          }
-\newcommand{\ngn}[1]{\index[blocks]{#1}      \texttt{#1}              }
+\newcommand{\nam}[1]{\index[blocks]{#1}      \texttt{nam#1}           }
 \newcommand{\np}[1]{ \index[parameters]{#1}  \texttt{#1}              }
 \newcommand{\rou}[1]{\index[subroutines]{#1} \texttt{#1}              }
@@ -14,19 +14,7 @@
 \indexsetup{toclevel=section, othercode=\small}
 
-\makeindex[intoc=true, name=keys       , title=CPP keys                      ]
-\makeindex[intoc=true, name=modules    , title=Modules                       ]
-\makeindex[intoc=true, name=blocks     , title=Namelist blocks               ]
-\makeindex[intoc=true, name=parameters , title=Namelist parameters, columns=3]
-\makeindex[intoc=true, name=subroutines, title=Subroutines                   ]
-
-
-%% Load hyperref at the end of the preamble to make it work with other pkgs
-\usepackage{hyperref}                    %% hyper
-\hypersetup{
-%  pdftitle={\heading},
-%  pdfauthor={\firstauthor and \secondauthor},
-  colorlinks,
-  citecolor=olive,
-  linkcolor=blue,
-  urlcolor=gray
-}
+\makeindex[intoc=true, name=keys       , title=CPP keys            ({\em key\_     } prefix)           ]
+\makeindex[intoc=true, name=modules    , title=\fortran modules                                        ]
+\makeindex[intoc=true, name=blocks     , title=Namelist blocks     ({\em nam       } prefix), columns=3]
+\makeindex[intoc=true, name=parameters , title=Namelist parameters ({\em [cdlnr]n\_}       ), columns=3]
+\makeindex[intoc=true, name=subroutines, title=Subroutines                                             ]
Index: /NEMO/trunk/doc/latex/global/info_page.tex
===================================================================
--- /NEMO/trunk/doc/latex/global/info_page.tex	(revision 11432)
+++ /NEMO/trunk/doc/latex/global/info_page.tex	(revision 11433)
@@ -8,8 +8,8 @@
 
 Like all components of the modelling framework,
-the \engine~core engine is developed under the \href{http://www.cecill.info}{CECILL license},
-which is a French adaptation of the GNU GPL (General Public License).
+the \engine\ core engine is developed under the \href{http://www.cecill.info}{CECILL license},
+which is a French adaptation of the GNU GPL (\textbf{G}eneral \textbf{P}ublic \textbf{L}icense).
 Anyone may use it freely for research purposes, and is encouraged to
-communicate back to the NEMO team its own developments and improvements.
+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.
@@ -27,11 +27,14 @@
 Additional information can be found on:
 \begin{itemize}
-\item the \href{http://www.nemo-ocean.eu}{website} of the project detailing several
+\item \faWordpress\ the \href{http://www.nemo-ocean.eu}{website} of the project detailing several
   associated applications and an exhaustive users bibliography
-\item the \href{http://forge.ipsl.jussieu.fr/nemo}{development platform} of the model with
-  the code repository and some main resources (wiki, ticket system, forums, \ldots)
-\item the \href{http://zenodo.org/communities/nemo-ocean}{online archive}
-  delivering the publications issued by the consortium
-\item two mailing lists:
+\item \faCodeFork\ the \href{http://forge.ipsl.jussieu.fr/nemo}{development platform} of
+  the model with the code repository for the shared reference and some main resources
+  (wiki, ticket system, forums, \ldots) \\
+  \faGithub\ the \href{http://github.com/NEMO-ocean/NEMO-examples}
+  {repository of the demonstration cases} for research or training
+\item \faCloudDownload\ the \href{http://zenodo.org/communities/nemo-ocean}{online archive}
+  delivering the publications issued by the consortium (manuals, reports, datasets, \ldots)
+\item \faEnvelope\ two mailing lists:
   the \href{http://listes.ipsl.fr/sympa/info/nemo-newsletter}{newsletter} for
   top-down communications from the project
@@ -48,18 +51,16 @@
 Reference for papers and other publications is as follows:
 
-\vspace{0.5cm}
-
-%% \sloppy: workaround for breaking DOI URL
-\sloppy
-``{\bfseries \heading}'', 
-\firstauthor and \secondauthor, 
-{\em Scientific Notes of Climate Modelling Center}, \textbf{\ipslnum} --- ISSN 1288-1619, 
-Institut Pierre-Simon Laplace (IPSL), 
+``{\bfseries \heading}'',
+%\firstauthor and \secondauthor,
+{\em Scientific Notes of Climate Modelling Center}, \textbf{\ipslnum} --- ISSN 1288-1619,
+Institut Pierre-Simon Laplace (IPSL),
 \href{https://doi.org/10.5281/zenodo.\zid}{doi:10.5281/zenodo.\zid}
 
 \begin{figure}[b]
-  \begin{minipage}[c]{0.72\textwidth}
-    \small\ttfamily{Scientific Notes of Climate Modelling Center \\
-      ISSN 1288-1619                                             \\
+  \begin{minipage}[c]{0.7\textwidth}
+    \small
+    \ttfamily{
+      Scientific Notes of Climate Modelling Center \\
+      ISSN 1288-1619                               \\
       Institut Pierre-Simon Laplace (IPSL)
     }
@@ -71,2 +72,3 @@
 \end{figure}
 
+\end{document}
Index: /NEMO/trunk/doc/latex/global/latexmkrc
===================================================================
--- /NEMO/trunk/doc/latex/global/latexmkrc	(revision 11432)
+++ /NEMO/trunk/doc/latex/global/latexmkrc	(revision 11433)
@@ -10,8 +10,8 @@
 ## Custom cmds
 $makeindex = 'makeindex -s %R.ist %O -o %D %S';
-$pdflatex  = 'pdflatex -shell-escape %O %S';
+#$pdflatex  = 'pdflatex -shell-escape %O %S';
+$pdflatex  = 'xelatex -shell-escape %O %S';
 
 #@BIBINPUTS=('.', '../main');
 #$bibtex    = 'bibtex %O ../main/bibliography.bib';
 #$kpsewhich = 'kpsewhich bibliography.bib'
-
Index: /NEMO/trunk/doc/latex/global/new_cmds.tex
===================================================================
--- /NEMO/trunk/doc/latex/global/new_cmds.tex	(revision 11432)
+++ /NEMO/trunk/doc/latex/global/new_cmds.tex	(revision 11433)
@@ -2,13 +2,15 @@
 %% ==============================================================================
 
-%% Include references and index for compilation of single subfile 
+%% Include references and index for compilation of single subfile
 \newcommand{\mtoc}{\minitoc}
-\newcommand{\biblio}{\bibliography{../main/bibliography}}
+\newcommand{\biblio}{ \bibliography{../main/bibliography} }
 \newcommand{\pindex}{\printindex}
 
 %% NEMO and Fortran in small capitals
-\newcommand{\NEMO}{\textsc{nemo}~}
-\newcommand{\fortran}{\textsc{Fortran}~}
-\newcommand{\fninety}{\textsc{Fortran 90}~}
+\newcommand{\NEMO   }{\textsc{nemo}}
+\newcommand{\SIcube }{\textsc{si$^3$}}
+\newcommand{\TOP    }{\textsc{top}}
+\newcommand{\fortran}{\textsc{Fortran}}
+\newcommand{\fninety}{\textsc{Fortran 90}}
 
 %% Common aliases
@@ -18,6 +20,6 @@
 \newcommand{\ztilde}{\ensuremath{\tilde z}}
 \newcommand{\stilde}{\ensuremath{\tilde s}}
-\newcommand{\ie}{\ensuremath{i.e.}~}
-\newcommand{\eg}{\ensuremath{e.g.}~}
+\newcommand{\ie}{\ensuremath{i.e.}}
+\newcommand{\eg}{\ensuremath{e.g.}}
 
 %% Inline maths
@@ -25,5 +27,5 @@
 \newcommand{\rdt}{\Delta t}
 
-%% Text env. for Gurvan
+%% Gurvan's comments
 \newcommand{\gmcomment}[1]{}
 
@@ -31,7 +33,23 @@
 \newcommand{\lt}{\left}
 \newcommand{\rt}{\right}
-\newcommand{\vect}[1]{\ensuremath{\mathbf{#1}}}
+\newcommand{\vect}[1]{\ensuremath{ \mathbf{#1} }}
 \newcommand{\pd}[2][]{\ensuremath{\frac{\partial #1}{\partial #2}}}
 
+%% Convert chapter/section headings to lowercase
+\renewcommand{\chaptermark}[1]{\markboth{#1}{}}
+\renewcommand{\sectionmark}[1]{\markright{#1}{}}
+
+%% Retrieve month name
+\renewcommand{\today}{
+  \ifcase \month\or January\or February\or March\or
+                    April\or   May\or      June\or
+                    July\or    August\or   September\or
+                    October\or November\or December
+  \fi, \number \year
+}
+
+%% Macro for link to orcid profile
+\newcommand{\orcid}[1]{ \href{http://orcid.org/#1}{\textcolor{orcidcolor} \aiOrcidSquare} }
+
 %% Workaround for issue with \listoffigures
-\DeclareRobustCommand{\triad}[6][]{\ensuremath{{}_{#2}^{#3}{\mathbb{#4}_{#1}}_{#5}^{\,#6}}}
+\DeclareRobustCommand{\triad}[6][]{\ensuremath{ {}_{#2}^{#3} { \mathbb{#4}_{#1} }_{#5}^{\,#6} }}
Index: /NEMO/trunk/doc/latex/global/packages.tex
===================================================================
--- /NEMO/trunk/doc/latex/global/packages.tex	(revision 11432)
+++ /NEMO/trunk/doc/latex/global/packages.tex	(revision 11433)
@@ -3,24 +3,34 @@
 %% ==============================================================================
 
-\usepackage{natbib}                      %% bib
-\usepackage{caption}                     %% caption
-\usepackage{xcolor}                      %% color
-\usepackage{times}                       %% font
-\usepackage{enumitem}                    %% list
-\usepackage{amsmath}                     %% maths
-%\usepackage{fancyhdr}                    %% page
-\usepackage{minitoc}                     %% toc
-\usepackage{subfiles}                    %% subdocs
-\usepackage{draftwatermark}              %% watermark
-\usepackage{titling}                     %% titlepage
+%% 'hyperref' pkg is loaded at the end of the preamble
+\usepackage{natbib}                 %% bibtex
+\usepackage{caption}                %% caption
+\usepackage{xcolor}                 %% colour
+\usepackage{times}                  %% font
+\usepackage{enumitem}               %% list
+\usepackage{amsmath}                %% maths
+\usepackage{minitoc}                %% toc
+\usepackage{subfiles}               %% subdocs
+\usepackage{draftwatermark}         %% watermark
+\usepackage[Bjornstrup]{fncychap}   %% headings
+\usepackage{fontspec}
+%\setmainfont[Ligatures=TeX]{Georgia}
+%\setsansfont[Ligatures=TeX]{Arial}
+\defaultfontfeatures{
+    Path = /home/ntmlod/.local/texlive2019/texmf-dist/fonts/opentype/public/fontawesome/
+}
+\usepackage{academicons}            %% font
+\usepackage{fontawesome}            %% font
+\usepackage{lastpage}               %% label
+\usepackage[pages = some]{background}             %% decoration
+\usepackage{geometry}               %% margin
 
 %% Extensions in bundle package
 \usepackage{amssymb, graphicx, tabularx, textcomp}
-\usepackage[utf8]{inputenc}              %% input encoding
+%\usepackage[utf8]{inputenc}         %% encoding
+\usepackage[footsepline=0.25pt,
+headsepline=0.25pt]{scrlayer-scrpage}   %% page layout
 
 %% Configuration
 \graphicspath{ {../../figures/} {../../figures/\engine/} }
-%\captionsetup{margin=10pt, font={small}, labelsep=colon, labelfont={bf}}
-\renewcommand{\bibfont}{\small}
-%\renewcommand{\bibsep}{3pt}
-
+\geometry{showframe}
Index: /NEMO/trunk/doc/latex/global/preamble.tex
===================================================================
--- /NEMO/trunk/doc/latex/global/preamble.tex	(revision 11432)
+++ /NEMO/trunk/doc/latex/global/preamble.tex	(revision 11433)
@@ -1,7 +1,28 @@
 
+%% Specific configuration
+\input{../main/definitions}
+
+%% Global configuration
 \input{../../global/packages}
 \input{../../global/highlighting}
+\input{../../global/indexes}
+\input{../../global/styles}
+\backgroundsetup{
+  firstpage = true,
+  scale = 1, angle = 0, opacity = 1,
+  contents = {
+    \begin{tikzpicture}[remember picture, overlay]
+      \path [fill = manualcolor] (-0.5\paperwidth, 7) rectangle (0.5\paperwidth, 10);
+    \end{tikzpicture}
+  }
+}
 \input{../../global/new_cmds}
-\input{../../global/styles}
 %\input{../../global/todonotes}
 
+%% Load hyperref at the end of the preamble to make it work with other pkgs
+\usepackage{hyperref}   %% links
+\hypersetup{
+  colorlinks,
+  citecolor = manualcolor, linkcolor = manualcolor, urlcolor = manualcolor,
+  final   %% Links even with draft building
+}
Index: /NEMO/trunk/doc/latex/global/styles.tex
===================================================================
--- /NEMO/trunk/doc/latex/global/styles.tex	(revision 11432)
+++ /NEMO/trunk/doc/latex/global/styles.tex	(revision 11433)
@@ -3,59 +3,42 @@
 %% ==============================================================================
 
-%\pagestyle{fancy}
-\bibliographystyle{../../global/ametsoc}
-\renewcommand{\bibpreamble}{\begin{multicols}{2}}
-\renewcommand{\bibpostamble}{\end{multicols}}
+\setcolor
+%\definecolor{ghcolor}{HTML}{000333}
+\definecolor{orcidcolor}{HTML}{A6CE39}
+%\definecolor{wpcolor}{HTML}{464646}
+
+%% Page layout
+\pagestyle{scrheadings}
+\addtokomafont{pagehead}{  \sffamily              }
+\addtokomafont{pagefoot}{  \sffamily \footnotesize}
+\addtokomafont{pagenumber}{\sffamily \slshape     }
+\ohead{} \ofoot{}   %% Clear defaults
+
+%% Caption
+\captionsetup{font = footnotesize, justification = justified}
 
 %% Additional fonts
 \DeclareMathAlphabet{\mathpzc}{OT1}{pzc}{m}{it}
 
-%% Page layout
-%\fancyhf{}
-%\fancyhead[LE,RO]{\bfseries\thepage}
-%\fancyhead[LO]{\bfseries\hspace{-0em}\rightmark}
-%\renewcommand{\sectionmark}[1]{\markright{\thesection.\ #1}}
-%\fancyhead[RE]{\bfseries\leftmark}
-%\renewcommand{\chaptermark}[1]{\markboth{#1}{}}
-%\renewcommand{\headrulewidth}{0.5pt}
-%\renewcommand{\footrulewidth}{0pt  }
-%\addtolength{\headheight}{2.6pt}
-
+%% Bibliography
+\bibliographystyle{../../global/ametsoc}
+\renewcommand{\bibfont}{\small}
+\renewcommand{\bibpreamble }{\begin{multicols}{2}}
+\renewcommand{\bibpostamble}{  \end{multicols}   }
 
 %% Catcodes
-%\makeatletter
-%\def\LigneVerticale{\vrule height 5cm depth 2cm\hspace{0.1cm}\relax}
-%\def\LignesVerticales{\let\LV\LigneVerticale\LV\LV\LV\LV\LV\LV\LV\LV\LV\LV}
-%\def\GrosCarreAvecUnChiffre#1{
-%	\rlap{\vrule height 0.8cm width 1cm depth 0.2cm}
-%	\rlap{\hbox to 1cm{\hss\mbox{\color{white} #1}\hss}}
-% 	\vrule height 0pt width 1cm depth 0pt
+\makeatletter
+
+%% Prevent error with tikz and namelist inclusion
+\global\let\tikz@ensure@dollar@catcode=\relax
+
+%% Apply engine color for chapter boxes (code from fncychap.sty)
+%\renewcommand{\DOTI}[1]{
+%  \nointerlineskip\raggedright
+%  \fboxsep=\myhi
+%  \vskip-1ex
+%  \colorbox[manualcolor]{.85}{\parbox[t]{\mylen}{\CTV\FmTi{#1}}}\par\nobreak
+%  \vskip 40\p@
 %}
-%\def\@makechapterhead#1{
-%	\hbox{
-%		\huge\LignesVerticales\hspace{-0.5cm}
-%		\GrosCarreAvecUnChiffre{\thechapter}\hspace{0.2cm}
-%		\hbox{#1}
-%	}
-%	\par\vskip
-%1cm
-%}
-%\def\@makeschapterhead#1{
-%	\hbox{
-%		\huge\LignesVerticales
-%		\hbox{#1}
-%	}
-%	\par\vskip
-%2cm
-%}
-%\def\cleardoublepage{\clearpage\if@twoside \ifodd\c@page\else
-%  \hbox{}
-%  \vspace*{\fill}
-%  \vspace{\fill}
-%  \thispagestyle{empty}
-%  \newpage
-%  \if@twocolumn\hbox{}\newpage\fi\fi\fi}
-%\def\@seccntformat#1{\protect\makebox[0pt][r]{\csname the#1\endcsname\quad}}
-%\makeatother
 
-
+\makeatother
