Index: MO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/PDF_creation.sh
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/PDF_creation.sh	(revision 11041)
+++ 	(revision )
@@ -1,47 +1,0 @@
-#!/bin/sh
-
-export opts='-shell-escape -pdf -quiet'
-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() {
-    ## Delete latex build files
-    find latex -regextype posix-extended                                              \
-         -regex ".*\.(aux|bbl|blg|dvi|fdb|fls|idx|ilg|ind|log|maf|mtc|out|pdf|toc).*" \
-         -exec rm {} \;
-
-    ## Remove 'minted' directories
-    find latex -type d -name '_minted*' -exec rm -r {} \;
-
-    ## HTML exports
-    find latex -type d -name 'html*'    -exec rm -r {} \;
-}
-
-build() {
-    cd latex/$1/main
-    latexmk $opts $1'_manual' > /dev/null
-    mv            $1'_manual'.pdf ../../..
-    cd -
-}
-
-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
-
-[ ! -d figures ] && svn co http://forge.ipsl.jussieu.fr/nemo/svn/utils/figures
-
-build $model
-
-exit 0
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/guide_build.sh
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/guide_build.sh	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/guide_build.sh	(revision 11042)
@@ -0,0 +1,29 @@
+#!/bin/sh
+
+## Avoid the use of shell builtin echo (for -e option)
+alias echo='/bin/echo -e'
+
+## Check dependancies
+##-------------------
+
+## Sphinx, BibTeX extension and "Read The Docs" theme
+if [ -n "$( ./tools/check_pkg.py sphinx sphinxcontrib.bibtex sphinx_rtd_theme )" ]; then
+    echo 'One of the Python dependencies is missing => QUIT'
+    exit 2
+fi
+
+cd rst
+
+echo "\t¤ Clean previous build"
+make clean
+echo
+
+echo "\t¤ Generation of the guide"
+make html > /dev/null
+echo
+
+echo "\t¤ End of building run"
+echo "Open ./rst/build/html/NEMO_guide.html"
+cd - > /dev/null
+
+exit 0
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/DEPS
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/DEPS	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/DEPS	(revision 11042)
@@ -0,0 +1,53 @@
+amsmath
+babel
+caption
+capt-of
+carlisle
+cmap
+courier
+draftwatermark
+ec
+enumitem
+epstopdf
+etoolbox
+everypage
+fancyhdr
+fancyvrb
+float
+fncychap
+framed
+fvextra
+geometry
+graphics
+graphics-cfg
+helvetic
+hyperref
+idxlayout
+ifplatform
+latex
+latex-bin
+latexconfig
+latex-fonts
+latexmk
+lineno
+lm
+marvosym
+minitoc
+minted
+natbib
+needspace
+oberdiek
+parskip
+psnfss
+subfiles
+tabulary
+times
+titlesec
+tools
+upquote
+url
+varwidth
+wrapfig
+xcolor
+xstring
+zapfchan
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/NEMO/main/NEMO_manual.sty
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/NEMO/main/NEMO_manual.sty	(revision 11041)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/NEMO/main/NEMO_manual.sty	(revision 11042)
@@ -31,5 +31,4 @@
 
 \captionsetup{margin=10pt, font={small}, labelsep=colon, labelfont={bf}}
-\graphicspath{{../../../figures/}}
 \hypersetup{
 	pdftitle={NEMO ocean engine}, pdfauthor={Gurvan Madec, and NEMO System Team},
@@ -45,5 +44,5 @@
 
 \pagestyle{fancy}
-\bibliographystyle{../main/ametsoc}
+\bibliographystyle{../../NEMO/main/ametsoc}
 
 %% Additionnal fonts
@@ -128,11 +127,11 @@
 
 %% Index entries (italic font for files, preformat for code)
-\newcommand{\hf}[1]{\textit{#1.h90}            \index{h90 file!#1}}
+\newcommand{\hf}[1]{\textit{#1.h90}            \index{h90 files!#1}}
 \newcommand{\ifile}[1]{\textit{#1.nc}          \index{Input NetCDF files!#1.nc}}
 \newcommand{\jp}[1]{\texttt{#1}                \index{Model parameters!#1}}
 \newcommand{\key}[1]{\texttt{\textbf{key\_#1}} \index{CPP keys!key\_#1}}
 \newcommand{\mdl}[1]{\textit{#1.F90}           \index{Modules!#1}}
-\newcommand{\ngn}[1]{\texttt{#1}               \index{Namelist Group Name!#1}}
-\newcommand{\np}[1]{\texttt{#1}                \index{Namelist variables!#1}}
+\newcommand{\ngn}[1]{\texttt{#1}               \index{Namelist Group Names!#1}}
+\newcommand{\np}[1]{\texttt{#1}                \index{Namelist parameters!#1}}
 \newcommand{\rou}[1]{\texttt{#1}               \index{Routines!#1}}
 
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/NEMO/main/NEMO_manual.tex
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/NEMO/main/NEMO_manual.tex	(revision 11041)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/NEMO/main/NEMO_manual.tex	(revision 11042)
@@ -2,7 +2,4 @@
 %% NEMO Reference Manual
 %% ==============================================================================
-
-
-%% Run ./PDF_creation.sh to generate the manual with latexmk
 
 
@@ -33,4 +30,6 @@
 %% ==============================================================================
 
+\graphicspath{{../../figures/logos/}}
+
 %% Frontpage
 \title{
@@ -41,23 +40,17 @@
   \includegraphics[height=0.05\textheight]{NERC}       \\
   \includegraphics[ width=0.8\textwidth  ]{NEMO_grey}  \\
-  {\Huge NEMO ocean engine}                            \\
+  {\Huge NEMO ocean engine}                                     \\
 }
 \author{
   \Large Gurvan Madec and NEMO System Team
-  \thanks{
-    Yevgeny Aksenov, Mirek Andrejczuk, Mike Bell, Romain Bourdalle-Badie, Cl\'{e}ment Bricaud,
-    J\'{e}r\^{o}me Chanut, Stefania Ciliberti, Emanuela Clementi, Andrew Coward, Damiano Delrosso,
-    Massimiliano Drudi, Christian Eth\'{e}, Simona Flavoni, Doroteaciro Iovino, Claire L\'{e}vy, Tomas Lovato,
-    Nicolas Martin, S\'{e}bastien Masson, Pierre Mathiot, Gelsomina Mattia, Francesca Mele, Silvia Mocavero,
-    Simon M\"{u}ller, George Nurser, Enda O'Dea, Julien Paul, Cl\'{e}ment Rousset, Dave Storkey,
-    Martin Vancoppenolle
-  }                                                        \\
-                                                           \\
+%  \thanks{
+%
+%  }                                                        \\
+%                                                           \\
   \textit{Issue 27, Notes du P\^{o}le de mod\'{e}lisation} \\
   \textit{Institut Pierre-Simon Laplace (IPSL)}            \\
   \textit{ISSN 1288-1619}
 }
-\date{Version 4.0 -- January 2019}
-%\date{\today}
+\date{\today}
 
 \maketitle
@@ -74,4 +67,6 @@
 
 \mainmatter
+
+\graphicspath{{../../figures/NEMO/}}
 
 %% Foreword
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/main/SI3_manual.bib
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/main/SI3_manual.bib	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/main/SI3_manual.bib	(revision 11042)
@@ -0,0 +1,647 @@
+
+@Article{         assur_1958,
+  author        = {Assur, A},
+  year          = {1958},
+  month         = {01},
+  pages         = {106-138},
+  title         = {Composition of sea ice and its tensile strength},
+  volume        = {598},
+  journal       = {Arctic Sea Ice}
+}
+
+@Article{	  babko_2002,
+  author	= {Babko, O.},
+  title		= {Role of rafting in the mechanical redistribution of sea
+		  ice thickness},
+  year		= 2002,
+  volume	= 107,
+  number	= {C8},
+  issn		= {0148-0227},
+  doi		= {10.1029/1999jc000190},
+  url		= {http://dx.doi.org/10.1029/1999JC000190},
+  journal	= {Journal of Geophysical Research},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  bitz_1999,
+  author	= {Bitz, C. M. and Lipscomb, William H.},
+  title		= {An energy-conserving thermodynamic model of sea ice},
+  year		= 1999,
+  volume	= 104,
+  number	= {C7},
+  month		= {Jul},
+  pages		= {15669–15677},
+  issn		= {0148-0227},
+  doi		= {10.1029/1999jc900100},
+  url		= {http://dx.doi.org/10.1029/1999jc900100},
+  journal	= {Journal of Geophysical Research: Oceans},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  bitz_2001,
+  author	= {Bitz, C. M. and Holland, M. M. and Weaver, A. J. and Eby,
+		  M.},
+  title		= {Simulating the ice-thickness distribution in a coupled
+		  climate model},
+  year		= 2001,
+  volume	= 106,
+  number	= {C2},
+  month		= {Feb},
+  pages		= {2441–2463},
+  issn		= {0148-0227},
+  doi		= {10.1029/1999jc000113},
+  url		= {http://dx.doi.org/10.1029/1999jc000113},
+  journal	= {Journal of Geophysical Research: Oceans},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  bouillon_2013,
+  author	= {Bouillon, Sylvain and Fichefet, Thierry and Legat, Vincent
+		  and Madec, Gurvan},
+  title		= {The elastic–viscous–plastic method revisited},
+  year		= 2013,
+  volume	= 71,
+  month		= {Nov},
+  pages		= {2–12},
+  issn		= {1463-5003},
+  doi		= {10.1016/j.ocemod.2013.05.013},
+  url		= {http://dx.doi.org/10.1016/j.ocemod.2013.05.013},
+  journal	= {Ocean Modelling},
+  publisher	= {Elsevier BV}
+}
+
+@Article{	  brandt_2005,
+  author	= {Brandt, Richard E. and Warren, Stephen G. and Worby,
+		  Anthony P. and Grenfell, Thomas C.},
+  title		= {Surface Albedo of the Antarctic Sea Ice Zone},
+  year		= 2005,
+  volume	= 18,
+  number	= 17,
+  month		= {Sep},
+  pages		= {3606–3622},
+  issn		= {1520-0442},
+  doi		= {10.1175/jcli3489.1},
+  url		= {http://dx.doi.org/10.1175/jcli3489.1},
+  journal	= {Journal of Climate},
+  publisher	= {American Meteorological Society}
+}
+
+@Article{	  coon_1974,
+  author	= {Coon, M.D. and Maykut, G.A. and Pritchard, R.S. and
+		  Rothrock, D.A. and Thorndike, A.S.},
+  year		= {1974},
+  month		= {01},
+  pages		= {1-106},
+  title		= {Modeling the pack ice as an elastic-plastic material},
+  volume	= {24},
+  journal	= {AIDJEX Bull.}
+}
+
+@Article{	  ebert_1993,
+  author	= {Ebert, Elizabeth E. and Curry, Judith A.},
+  title		= {An intermediate one-dimensional thermodynamic sea ice
+		  model for investigating ice-atmosphere interactions},
+  year		= 1993,
+  volume	= 98,
+  number	= {C6},
+  pages		= 10085,
+  issn		= {0148-0227},
+  doi		= {10.1029/93jc00656},
+  url		= {http://dx.doi.org/10.1029/93jc00656},
+  journal	= {Journal of Geophysical Research},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  fichefet_1997,
+  author	= {Fichefet, T. and Maqueda, M. A. Morales},
+  title		= {Sensitivity of a global sea ice model to the treatment of
+		  ice thermodynamics and dynamics},
+  year		= 1997,
+  volume	= 102,
+  number	= {C6},
+  month		= {Jun},
+  pages		= {12609–12646},
+  issn		= {0148-0227},
+  doi		= {10.1029/97jc00480},
+  url		= {http://dx.doi.org/10.1029/97jc00480},
+  journal	= {Journal of Geophysical Research: Oceans},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  flato_1995,
+  author	= {Flato, Gregory M. and Hibler, William D.},
+  title		= {Ridging and strength in modeling the thickness
+		  distribution of Arctic sea ice},
+  year		= 1995,
+  volume	= 100,
+  number	= {C9},
+  pages		= 18611,
+  issn		= {0148-0227},
+  doi		= {10.1029/95jc02091},
+  url		= {http://dx.doi.org/10.1029/95jc02091},
+  journal	= {Journal of Geophysical Research},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  girard_2009,
+  author	= {Girard, L. and Weiss, J. and Molines, J. M. and Barnier,
+		  B. and Bouillon, S.},
+  title		= {Evaluation of high-resolution sea ice models on the basis
+		  of statistical and scaling properties of Arctic sea ice
+		  drift and deformation},
+  year		= 2009,
+  volume	= 114,
+  number	= {C8},
+  month		= {Aug},
+  issn		= {0148-0227},
+  doi		= {10.1029/2008jc005182},
+  url		= {http://dx.doi.org/10.1029/2008JC005182},
+  journal	= {Journal of Geophysical Research},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  grenfell_1977,
+  author	= {Grenfell, Thomas C. and Maykut, Gary A.},
+  title		= {The Optical Properties of Ice and Snow in the Arctic
+		  Basin},
+  year		= 1977,
+  volume	= 18,
+  number	= 80,
+  pages		= {445–463},
+  issn		= {1727-5652},
+  doi		= {10.3189/s0022143000021122},
+  url		= {http://dx.doi.org/10.3189/s0022143000021122},
+  journal	= {Journal of Glaciology},
+  publisher	= {Cambridge University Press (CUP)}
+}
+
+@Article{	  grenfell_2004,
+  author	= {Grenfell, Thomas C.},
+  title		= {Seasonal and spatial evolution of albedo in a
+		  snow-ice-land-ocean environment},
+  year		= 2004,
+  volume	= 109,
+  number	= {C1},
+  issn		= {0148-0227},
+  doi		= {10.1029/2003jc001866},
+  url		= {http://dx.doi.org/10.1029/2003JC001866},
+  journal	= {Journal of Geophysical Research},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  haapala_2000,
+  author	= {Haapala, Jari},
+  title		= {On the modelling of ice-thickness redistribution},
+  year		= 2000,
+  volume	= 46,
+  number	= 154,
+  pages		= {427–437},
+  issn		= {1727-5652},
+  doi		= {10.3189/172756500781833106},
+  url		= {http://dx.doi.org/10.3189/172756500781833106},
+  journal	= {Journal of Glaciology},
+  publisher	= {Cambridge University Press (CUP)}
+}
+
+@Article{	  hibler_1979,
+  author	= {Hibler, W. D.},
+  title		= {A Dynamic Thermodynamic Sea Ice Model},
+  year		= 1979,
+  volume	= 9,
+  number	= 4,
+  month		= {Jul},
+  pages		= {815–846},
+  issn		= {1520-0485},
+  doi		= {10.1175/1520-0485(1979)009<0815:adtsim>2.0.co;2},
+  url		= {http://dx.doi.org/10.1175/1520-0485(1979)009<0815:adtsim>2.0.co;2},
+  journal	= {Journal of Physical Oceanography},
+  publisher	= {American Meteorological Society}
+}
+
+@Article{	  hibler_1980,
+  author	= {Hibler, W. D.},
+  title		= {Modeling a Variable Thickness Sea Ice Cover},
+  year		= 1980,
+  volume	= 108,
+  number	= 12,
+  month		= {Dec},
+  pages		= {1943–1973},
+  issn		= {1520-0493},
+  doi		= {10.1175/1520-0493(1980)108<1943:mavtsi>2.0.co;2},
+  url		= {http://dx.doi.org/10.1175/1520-0493(1980)108<1943:mavtsi>2.0.co;2},
+  journal	= {Monthly Weather Review},
+  publisher	= {American Meteorological Society}
+}
+
+@Article{	  h_yland_2002,
+  author	= {Høyland, Knut V.},
+  title		= {Consolidation of first-year sea ice ridges},
+  year		= 2002,
+  volume	= 107,
+  number	= {C6},
+  issn		= {0148-0227},
+  doi		= {10.1029/2000jc000526},
+  url		= {http://dx.doi.org/10.1029/2000JC000526},
+  journal	= {Journal of Geophysical Research},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  kovacs_1996,
+  author	= {Kovacs, Austin},
+  title		= {Sea Ice. Part 1. Bulk Salinity Versus Ice Floe
+		  Thickness,},
+  year		= 1996,
+  month		= {Jun},
+  doi		= {10.21236/ada312027},
+  url		= {http://dx.doi.org/10.21236/ada312027},
+  publisher	= {Defense Technical Information Center}
+}
+
+@Article{	  kreyscher_2000,
+  author	= {Kreyscher, Martin and Harder, Markus and Lemke, Peter and
+		  Flato, Gregory M.},
+  title		= {Results of the Sea Ice Model Intercomparison Project:
+		  Evaluation of sea ice rheology schemes for use in climate
+		  simulations},
+  year		= 2000,
+  volume	= 105,
+  number	= {C5},
+  month		= {May},
+  pages		= {11299–11320},
+  issn		= {0148-0227},
+  doi		= {10.1029/1999jc000016},
+  url		= {http://dx.doi.org/10.1029/1999jc000016},
+  journal	= {Journal of Geophysical Research: Oceans},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  lecomte_2011,
+  author	= {Lecomte, Olivier and Fichefet, Thierry and Vancoppenolle,
+		  Martin and Nicolaus, Marcel},
+  title		= {A new snow thermodynamic scheme for large-scale sea-ice
+		  models},
+  year		= 2011,
+  volume	= 52,
+  number	= 57,
+  pages		= {337–346},
+  issn		= {1727-5644},
+  doi		= {10.3189/172756411795931453},
+  url		= {http://dx.doi.org/10.3189/172756411795931453},
+  journal	= {Annals of Glaciology},
+  publisher	= {Cambridge University Press (CUP)}
+}
+
+@Article{	  lecomte_2015,
+  author	= {Lecomte, Olivier and Fichefet, Thierry and Flocco, Daniela
+		  and Schroeder, David and Vancoppenolle, Martin},
+  title		= {Interactions between wind-blown snow redistribution and
+		  melt ponds in a coupled ocean–sea ice model},
+  year		= 2015,
+  volume	= 87,
+  month		= {Mar},
+  pages		= {67–80},
+  issn		= {1463-5003},
+  doi		= {10.1016/j.ocemod.2014.12.003},
+  url		= {http://dx.doi.org/10.1016/j.ocemod.2014.12.003},
+  journal	= {Ocean Modelling},
+  publisher	= {Elsevier BV}
+}
+
+@Article{	  lepp_ranta_1995,
+  author	= {Leppäranta, Matti and Lensu, Mikko and Kosloff, Pekka and
+		  Veitch, Brian},
+  title		= {The life story of a first-year sea ice ridge},
+  year		= 1995,
+  volume	= 23,
+  number	= 3,
+  month		= {May},
+  pages		= {279–290},
+  issn		= {0165-232X},
+  doi		= {10.1016/0165-232x(94)00019-t},
+  url		= {http://dx.doi.org/10.1016/0165-232x(94)00019-t},
+  journal	= {Cold Regions Science and Technology},
+  publisher	= {Elsevier BV}
+}
+
+@Article{	  lepp_ranta_2011,
+  author	= {Leppäranta, Matti},
+  title		= {Drift ice material},
+  year		= 2011,
+  pages		= {11–63},
+  doi		= {10.1007/978-3-642-04683-4_2},
+  url		= {http://dx.doi.org/10.1007/978-3-642-04683-4_2},
+  isbn		= 9783642046834,
+  journal	= {The Drift of Sea Ice},
+  publisher	= {Springer Berlin Heidelberg}
+}
+
+@Article{	  lipscomb_2001,
+  author	= {Lipscomb, William H.},
+  title		= {Remapping the thickness distribution in sea ice models},
+  year		= 2001,
+  volume	= 106,
+  number	= {C7},
+  month		= {Jul},
+  pages		= {13989–14000},
+  issn		= {0148-0227},
+  doi		= {10.1029/2000jc000518},
+  url		= {http://dx.doi.org/10.1029/2000jc000518},
+  journal	= {Journal of Geophysical Research: Oceans},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  lipscomb_2007,
+  author	= {Lipscomb, William H. and Hunke, Elizabeth C. and
+		  Maslowski, Wieslaw and Jakacki, Jaromir},
+  title		= {Ridging, strength, and stability in high-resolution sea
+		  ice models},
+  year		= 2007,
+  volume	= 112,
+  number	= {C3},
+  month		= {Mar},
+  issn		= {0148-0227},
+  doi		= {10.1029/2005jc003355},
+  url		= {http://dx.doi.org/10.1029/2005JC003355},
+  journal	= {Journal of Geophysical Research},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  maykut_1971,
+  author	= {Maykut, Gary A. and Untersteiner, Norbert},
+  title		= {Some results from a time-dependent thermodynamic model of
+		  sea ice},
+  year		= 1971,
+  volume	= 76,
+  number	= 6,
+  month		= {Feb},
+  pages		= {1550–1575},
+  issn		= {0148-0227},
+  doi		= {10.1029/jc076i006p01550},
+  url		= {http://dx.doi.org/10.1029/jc076i006p01550},
+  journal	= {Journal of Geophysical Research},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  maykut_1986,
+  author	= {Maykut, Gary A.},
+  title		= {The Surface Heat and Mass Balance},
+  year		= 1986,
+  pages		= {395–463},
+  doi		= {10.1007/978-1-4899-5352-0_6},
+  url		= {http://dx.doi.org/10.1007/978-1-4899-5352-0_6},
+  isbn		= 9781489953520,
+  journal	= {The Geophysics of Sea Ice},
+  publisher	= {Springer US}
+}
+
+@Article{	  maykut_1995,
+  author	= {Maykut, G. A. and McPhee, Miles G.},
+  title		= {Solar heating of the Arctic mixed layer},
+  year		= 1995,
+  volume	= 100,
+  number	= {C12},
+  pages		= 24691,
+  issn		= {0148-0227},
+  doi		= {10.1029/95jc02554},
+  url		= {http://dx.doi.org/10.1029/95jc02554},
+  journal	= {Journal of Geophysical Research},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  mcphee_1992,
+  author	= {McPhee, Miles G.},
+  title		= {Turbulent heat flux in the upper ocean under sea ice},
+  year		= 1992,
+  volume	= 97,
+  number	= {C4},
+  pages		= 5365,
+  issn		= {0148-0227},
+  doi		= {10.1029/92jc00239},
+  url		= {http://dx.doi.org/10.1029/92jc00239},
+  journal	= {Journal of Geophysical Research},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  mellor_1989,
+  author	= {Mellor, George L. and Kantha, Lakshmi},
+  title		= {An ice-ocean coupled model},
+  year		= 1989,
+  volume	= 94,
+  number	= {C8},
+  pages		= 10937,
+  issn		= {0148-0227},
+  doi		= {10.1029/jc094ic08p10937},
+  url		= {http://dx.doi.org/10.1029/jc094ic08p10937},
+  journal	= {Journal of Geophysical Research},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  notz_2016,
+  author	= {Notz, Dirk and Jahn, Alexandra and Holland, Marika and
+		  Hunke, Elizabeth and Massonnet, François and Stroeve,
+		  Julienne and Tremblay, Bruno and Vancoppenolle, Martin},
+  title		= {The CMIP6 Sea-Ice Model Intercomparison Project (SIMIP):
+		  understanding sea ice through climate-model simulations},
+  year		= 2016,
+  volume	= 9,
+  number	= 9,
+  month		= {Sep},
+  pages		= {3427–3446},
+  issn		= {1991-9603},
+  doi		= {10.5194/gmd-9-3427-2016},
+  url		= {http://dx.doi.org/10.5194/gmd-9-3427-2016},
+  journal	= {Geoscientific Model Development},
+  publisher	= {Copernicus GmbH}
+}
+
+@Article{	  parmerter_1975,
+  author	= {Parmerter, R. Reid},
+  title		= {A model of simple rafting in sea ice},
+  year		= 1975,
+  volume	= 80,
+  number	= 15,
+  month		= {May},
+  pages		= {1948–1952},
+  issn		= {0148-0227},
+  doi		= {10.1029/jc080i015p01948},
+  url		= {http://dx.doi.org/10.1029/jc080i015p01948},
+  journal	= {Journal of Geophysical Research},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  perovich_2002,
+  author	= {Perovich, D. K.},
+  title		= {Seasonal evolution of the albedo of multiyear Arctic sea
+		  ice},
+  year		= 2002,
+  volume	= 107,
+  number	= {C10},
+  issn		= {0148-0227},
+  doi		= {10.1029/2000jc000438},
+  url		= {http://dx.doi.org/10.1029/2000JC000438},
+  journal	= {Journal of Geophysical Research},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  prather_1986,
+  author	= {Prather, Michael J.},
+  title		= {Numerical advection by conservation of second-order
+		  moments},
+  year		= 1986,
+  volume	= 91,
+  number	= {D6},
+  pages		= 6671,
+  issn		= {0148-0227},
+  doi		= {10.1029/jd091id06p06671},
+  url		= {http://dx.doi.org/10.1029/jd091id06p06671},
+  journal	= {Journal of Geophysical Research},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  pringle_2007,
+  author	= {Pringle, D. J. and Eicken, H. and Trodahl, H. J. and
+		  Backstrom, L. G. E.},
+  title		= {Thermal conductivity of landfast Antarctic and Arctic sea
+		  ice},
+  year		= 2007,
+  volume	= 112,
+  number	= {C4},
+  month		= {Apr},
+  issn		= {0148-0227},
+  doi		= {10.1029/2006jc003641},
+  url		= {http://dx.doi.org/10.1029/2006JC003641},
+  journal	= {Journal of Geophysical Research},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  schmidt_2004,
+  author	= {Schmidt, Gavin A. and Bitz, Cecilia M. and Mikolajewicz,
+		  Uwe and Tremblay, L.-Bruno},
+  title		= {Ice–ocean boundary conditions for coupled models},
+  year		= 2004,
+  volume	= 7,
+  number	= {1-2},
+  month		= {Jan},
+  pages		= {59–74},
+  issn		= {1463-5003},
+  doi		= {10.1016/s1463-5003(03)00030-1},
+  url		= {http://dx.doi.org/10.1016/S1463-5003(03)00030-1},
+  journal	= {Ocean Modelling},
+  publisher	= {Elsevier BV}
+}
+
+@Article{	  shine_1985,
+  author	= {Shine, K. P. and Henderson-Sellers, A.},
+  title		= {The sensitivity of a thermodynamic sea ice model to
+		  changes in surface albedo parameterization},
+  year		= 1985,
+  volume	= 90,
+  number	= {D1},
+  pages		= 2243,
+  issn		= {0148-0227},
+  doi		= {10.1029/jd090id01p02243},
+  url		= {http://dx.doi.org/10.1029/jd090id01p02243},
+  journal	= {Journal of Geophysical Research},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  thorndike_1975,
+  author	= {Thorndike, A. S. and Rothrock, D. A. and Maykut, G. A. and
+		  Colony, R.},
+  title		= {The thickness distribution of sea ice},
+  year		= 1975,
+  volume	= 80,
+  number	= 33,
+  month		= {Nov},
+  pages		= {4501–4513},
+  issn		= {0148-0227},
+  doi		= {10.1029/jc080i033p04501},
+  url		= {http://dx.doi.org/10.1029/JC080i033p04501},
+  journal	= {Journal of Geophysical Research},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  tuhkuri_2002,
+  author	= {Tuhkuri, Jukka},
+  title		= {Laboratory tests on ridging and rafting of ice sheets},
+  year		= 2002,
+  volume	= 107,
+  number	= {C9},
+  issn		= {0148-0227},
+  doi		= {10.1029/2001jc000848},
+  url		= {http://dx.doi.org/10.1029/2001JC000848},
+  journal	= {Journal of Geophysical Research},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  vancoppenolle_2009,
+  author	= {Vancoppenolle, Martin and Fichefet, Thierry and Goosse,
+		  Hugues},
+  title		= {Simulating the mass balance and salinity of Arctic and
+		  Antarctic sea ice. 2. Importance of sea ice salinity
+		  variations},
+  year		= 2009,
+  volume	= 27,
+  number	= {1-2},
+  month		= {Jan},
+  pages		= {54–69},
+  issn		= {1463-5003},
+  doi		= {10.1016/j.ocemod.2008.11.003},
+  url		= {http://dx.doi.org/10.1016/j.ocemod.2008.11.003},
+  journal	= {Ocean Modelling},
+  publisher	= {Elsevier BV}
+}
+
+@Article{	  weiss_2013,
+  author	= {Weiss, Jérôme},
+  title		= {Drift, Deformation, and Fracture of Sea Ice},
+  year		= 2013,
+  issn		= {2191-5377},
+  doi		= {10.1007/978-94-007-6202-2},
+  url		= {http://dx.doi.org/10.1007/978-94-007-6202-2},
+  isbn		= 9789400762022,
+  journal	= {SpringerBriefs in Earth Sciences},
+  publisher	= {Springer Netherlands}
+}
+
+@Article{	  worster_1992,
+  author	= {Worster, M. G.},
+  title		= {The Dynamics of Mushy Layers},
+  year		= 1992,
+  pages		= {113–138},
+  doi		= {10.1007/978-94-011-2809-4_20},
+  url		= {http://dx.doi.org/10.1007/978-94-011-2809-4_20},
+  isbn		= 9789401128094,
+  journal	= {Interactive Dynamics of Convection and Solidification},
+  publisher	= {Springer Netherlands}
+}
+
+@Article{	  zhang_2001,
+  author	= {Zhang, Jinlun and Rothrock, Drew},
+  title		= {A Thickness and Enthalpy Distribution Sea-Ice Model},
+  year		= 2001,
+  volume	= 31,
+  number	= 10,
+  month		= {Oct},
+  pages		= {2986–3001},
+  issn		= {1520-0485},
+  doi		= {10.1175/1520-0485(2001)031<2986:ataeds>2.0.co;2},
+  url		= {http://dx.doi.org/10.1175/1520-0485(2001)031<2986:ataeds>2.0.co;2},
+  journal	= {Journal of Physical Oceanography},
+  publisher	= {American Meteorological Society}
+}
+
+@Article{	  zuo_1996,
+  author	= {Zuo, Z. and Oerlemans, J.},
+  title		= {Modelling albedo and specific balance of the Greenland ice
+		  sheet: calculations for the Søndre Strømfjord transect},
+  year		= 1996,
+  volume	= 42,
+  number	= 141,
+  pages		= {305–317},
+  issn		= {1727-5652},
+  doi		= {10.1017/s0022143000004160},
+  url		= {http://dx.doi.org/10.1017/s0022143000004160},
+  journal	= {Journal of Glaciology},
+  publisher	= {Cambridge University Press (CUP)}
+}
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/main/SI3_manual.tex
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/main/SI3_manual.tex	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/main/SI3_manual.tex	(revision 11042)
@@ -0,0 +1,127 @@
+%% ==============================================================================
+%% SI3 Reference Manual
+%% ==============================================================================
+
+
+%% Preamble
+%% ==============================================================================
+
+%% Document layout
+\documentclass{book}
+
+%% Custom style (.sty)
+\usepackage{../../NEMO/main/NEMO_manual}
+
+%% Include references and index for single subfile compilation
+\newcommand{\biblio}{\bibliography{../main/SI3_manual}}
+\newcommand{\pindex}{\printindex}
+
+\makeindex
+
+%% End of common preamble between main and sub-files
+\begin{document}
+
+%% Override custom cmds for full manual compilation
+\renewcommand{\biblio}{}
+\renewcommand{\pindex}{}
+
+
+%% Frontmatter
+%% ==============================================================================
+
+\graphicspath{{../../figures/logos/}}
+
+%% Frontpage
+\title{
+  \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}       \\
+  {\Huge SI$^3$ \\}
+  {\Large Sea Ice modelling Integrated Initiative -- The NEMO Sea Ice engine}\\ 
+  {\small \textcolor{red}{First draft documentation. Needs completion and rewriting}.}
+}
+\author{The NEMO Sea Ice Working Group
+%  \thanks{
+%
+%  }                                                        \\
+  \textit{Issue 27, Notes du P\^{o}le de mod\'{e}lisation} \\
+  \textit{Institut Pierre-Simon Laplace (IPSL)}            \\
+  \textit{ISSN 1288-1619}
+}
+\date{\today}
+
+\maketitle
+\frontmatter
+
+%% ToC i.e. Table of Contents
+\dominitoc
+\tableofcontents
+
+
+%% Mainmatter
+%% ==============================================================================
+
+\mainmatter
+
+\graphicspath{{../../figures/SI3/}}
+
+\subfile{../subfiles/todolist}
+
+%% Abstract - Foreword
+
+\subfile{../subfiles/abstract_foreword}
+
+% Introduction
+
+\subfile{../subfiles/introduction}
+
+% Chapters
+
+\subfile{../subfiles/chap_model_basics}
+
+\subfile{../subfiles/chap_domain}
+
+\subfile{../subfiles/chap_dynamics}
+
+\subfile{../subfiles/chap_transport}
+
+\subfile{../subfiles/chap_ridging_rafting}
+
+\subfile{../subfiles/chap_radiative_transfer}
+
+\subfile{../subfiles/chap_thermo}
+
+\subfile{../subfiles/chap_interfaces}
+
+\subfile{../subfiles/chap_output_diagnostics}
+
+\subfile{../subfiles/chap_single_category_use}
+
+\subfile{../subfiles/chap_bdy_agrif}
+
+\subfile{../subfiles/chap_miscellaneous}
+
+%% Appendix
+
+%\appendix
+%% Backmatter
+%% ==============================================================================
+
+\backmatter
+
+%% Bibliography
+\cleardoublepage
+\phantomsection
+\addcontentsline{toc}{chapter}{Bibliography}
+\bibliography{../main/SI3_manual}
+%\bibliography{/Users/ioulianikolskaia/Boulot/LIBRARY/BIBTEX/Martin_biblio.bib} 
+
+%% Index
+\cleardoublepage
+\phantomsection
+\addcontentsline{toc}{chapter}{Index}
+\printindex
+
+\end{document}
Index: MO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namalb
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namalb	(revision 11041)
+++ 	(revision )
@@ -1,10 +1,0 @@
-!------------------------------------------------------------------------------
-&namalb         !   albedo parameters
-!------------------------------------------------------------------------------
-   !                                  !                          !  obs range (cloud-sky)
-   rn_alb_sdry      =   0.85          !  dry snow albedo         :  0.85 -- 0.87
-   rn_alb_smlt      =   0.75          !  melting snow albedo     :  0.72 -- 0.82
-   rn_alb_idry      =   0.60          !  dry ice albedo          :  0.54 -- 0.65
-   rn_alb_imlt      =   0.50          !  bare puddled ice albedo :  0.49 -- 0.58
-   rn_alb_dpnd      =   0.27          !  ponded ice albedo       :  0.10 -- 0.30 
-/
Index: MO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namdia
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namdia	(revision 11041)
+++ 	(revision )
@@ -1,9 +1,0 @@
-!------------------------------------------------------------------------------
-&namdia         !   Diagnostics
-!------------------------------------------------------------------------------
-   ln_icediachk     = .false.         !  check online the heat, mass & salt budgets (T) or not (F)
-   ln_icediahsb     = .false.         !  output the heat, mass & salt budgets (T) or not (F)
-   ln_icectl        = .false.         !  ice points output for debug (T or F)
-   iiceprt          =  10             !  i-index for debug
-   jiceprt          =  10             !  j-index for debug
-/
Index: MO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namdyn
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namdyn	(revision 11041)
+++ 	(revision )
@@ -1,17 +1,0 @@
-!------------------------------------------------------------------------------
-&namdyn         !   Ice dynamics
-!------------------------------------------------------------------------------
-   ln_dynFULL       = .true.          !  dyn.: full ice dynamics               (rheology + advection + ridging/rafting + correction)
-   ln_dynRHGADV     = .false.         !  dyn.: no ridge/raft & no corrections  (rheology + advection)
-   ln_dynADV        = .false.         !  dyn.: only advection w prescribed vel.(rn_uvice + advection)
-      rn_uice       =   0.00001       !        prescribed ice u-velocity
-      rn_vice       =   0.            !        prescribed ice v-velocity
-   rn_ishlat        =   2.            !  free slip (0) ; partial slip (0-2) ; no slip (2) ; strong slip (>2)
-   ln_landfast      = .false.         !  landfast ice parameterization (T or F)                           
-      rn_gamma      =   0.15          !     fraction of ocean depth that ice must reach to initiate landfast
-                                      !        recommended range: [0.1 ; 0.25]
-      rn_icebfr     =  10.            !     maximum bottom stress per unit area of contact [N/m2]                 
-                                      !        a very large value ensures ice velocity=0 even with a small contact area
-                                      !        recommended range: ?? (should be greater than atm-ice stress => >0.1 N/m2)
-      rn_lfrelax    =   1.e-5         !     relaxation time scale to reach static friction [s-1]
-/
Index: MO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namdyn_rdgrft
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namdyn_rdgrft	(revision 11041)
+++ 	(revision )
@@ -1,25 +1,0 @@
-!------------------------------------------------------------------------------
-&namdyn_rdgrft  !   Ice ridging/rafting
-!------------------------------------------------------------------------------
-          ! -- ice_rdgrft_strength -- !
-   ln_str_H79       = .true.          !  ice strength param.: Hibler_79   => P = pstar*<h>*exp(-c_rhg*A)                      
-      rn_pstar      =   2.0e+04       !     ice strength thickness parameter [N/m2]
-      rn_crhg       =   20.0          !     ice strength conc. parameter (-)
-                   ! -- ice_rdgrft -- !
-   rn_csrdg         =   0.5           !  fraction of shearing energy contributing to ridging
-              ! -- ice_rdgrft_prep -- !
-   ln_partf_lin     = .false.         !  Linear ridging participation function (Thorndike et al, 1975)
-      rn_gstar      =   0.15          !     fractional area of thin ice being ridged 
-   ln_partf_exp     = .true.          !  Exponential ridging participation function (Lipscomb, 2007)
-      rn_astar      =   0.03          !     exponential measure of ridging ice fraction [set to 0.05 if hstar=100]
-   ln_ridging       = .true.          !  ridging activated (T) or not (F)
-      rn_hstar      =  25.0           !     determines the maximum thickness of ridged ice [m] (Hibler, 1980)
-      rn_porordg    =   0.3           !     porosity of newly ridged ice (Lepparanta et al., 1995)
-      rn_fsnwrdg    =   0.5           !     snow volume fraction that survives in ridging
-      rn_fpndrdg    =   1.0           !     pond fraction that survives in ridging (small a priori)
-   ln_rafting       = .true.          !  rafting activated (T) or not (F)
-      rn_hraft      =   0.75          !     threshold thickness for rafting [m]
-      rn_craft      =   5.0           !     squeezing coefficient used in the rafting function
-      rn_fsnwrft    =   0.5           !     snow volume fraction that survives in rafting
-      rn_fpndrft    =   1.0           !     pond fraction that survives in rafting (0.5 a priori)
-/
Index: MO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namdyn_rhg
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namdyn_rhg	(revision 11041)
+++ 	(revision )
@@ -1,11 +1,0 @@
-!------------------------------------------------------------------------------
-&namdyn_rhg     !   Ice rheology
-!------------------------------------------------------------------------------
-   ln_rhg_EVP       = .true.          !  EVP rheology
-      ln_aEVP       = .true.          !     adaptive rheology (Kimmritz et al. 2016 & 2017)
-      rn_creepl     =   2.0e-9        !     creep limit [1/s]
-      rn_ecc        =   2.0           !     eccentricity of the elliptical yield curve          
-      nn_nevp       = 120             !     number of EVP subcycles                             
-      rn_relast     =   0.333         !     ratio of elastic timescale to ice time step: Telast = dt_ice * rn_relast 
-                                      !        advised value: 1/3 (rn_nevp=120) or 1/9 (rn_nevp=300)
-/
Index: MO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namforcing
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namforcing	(revision 11041)
+++ 	(revision )
@@ -1,13 +1,0 @@
-!------------------------------------------------------------------------------
-&namforcing     !   Ice surface forcing
-!------------------------------------------------------------------------------
-   rn_cio           =   5.0e-03       !  ice-ocean drag coefficient (-)
-   rn_blow_s        =   0.66          !  mesure of snow blowing into the leads
-                                      !     = 1 => no snow blowing, < 1 => some snow blowing
-   nn_flxdist       =  -1             !  Redistribute heat flux over ice categories
-                                      !     =-1  Do nothing (needs N(cat) fluxes)
-                                      !     = 0  Average N(cat) fluxes then apply the average over the N(cat) ice
-                                      !     = 1  Average N(cat) fluxes then redistribute over the N(cat) ice using T-ice and albedo sensitivity
-                                      !     = 2  Redistribute a single flux over categories
-   nice_jules       = 0               !  Jules coupling (0=OFF, 1=EMULATED, 2=ACTIVE)
-/
Index: MO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namini
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namini	(revision 11041)
+++ 	(revision )
@@ -1,25 +1,0 @@
-!------------------------------------------------------------------------------
-&namini         !   Ice initialization
-!------------------------------------------------------------------------------
-   ln_iceini        = .true.          !  activate ice initialization (T) or not (F)
-   ln_iceini_file   = .false.         !  netcdf file provided for initialization (T) or not (F)
-   rn_thres_sst     =   2.0           !  max delta temp. above Tfreeze with initial ice = (sst - tfreeze)
-   rn_hts_ini_n     =   0.3           !  initial real snow thickness (m), North
-   rn_hts_ini_s     =   0.3           !        "            "             South
-   rn_hti_ini_n     =   3.0           !  initial real ice thickness  (m), North
-   rn_hti_ini_s     =   1.0           !        "            "             South
-   rn_ati_ini_n     =   0.9           !  initial ice concentration   (-), North
-   rn_ati_ini_s     =   0.9           !        "            "             South
-   rn_smi_ini_n     =   6.3           !  initial ice salinity     (g/kg), North
-   rn_smi_ini_s     =   6.3           !        "            "             South
-   rn_tmi_ini_n     = 270.            !  initial ice/snw temperature (K), North
-   rn_tmi_ini_s     = 270.            !        "            "             South
-
-   sn_hti = 'Ice_initialization'    , -12 ,'hti'   ,  .false.  , .true., 'yearly'  , '' , '', ''
-   sn_hts = 'Ice_initialization'    , -12 ,'hts'   ,  .false.  , .true., 'yearly'  , '' , '', ''
-   sn_ati = 'Ice_initialization'    , -12 ,'ati'   ,  .false.  , .true., 'yearly'  , '' , '', ''
-   sn_tsu = 'Ice_initialization'    , -12 ,'tsu'   ,  .false.  , .true., 'yearly'  , '' , '', ''
-   sn_tmi = 'Ice_initialization'    , -12 ,'tmi'   ,  .false.  , .true., 'yearly'  , '' , '', ''
-   sn_smi = 'Ice_initialization'    , -12 ,'smi'   ,  .false.  , .true., 'yearly'  , '' , '', ''
-   cn_dir='./'
-/
Index: MO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namitd
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namitd	(revision 11041)
+++ 	(revision )
@@ -1,9 +1,0 @@
-!------------------------------------------------------------------------------
-&namitd         !   Ice discretization
-!------------------------------------------------------------------------------
-   ln_cat_hfn       = .true.          !  ice categories are defined by a function following rn_himean**(-0.05)
-      rn_himean     =   2.0           !  expected domain-average ice thickness (m)
-   ln_cat_usr       = .false.         !  ice categories are defined by rn_catbnd below (m)
-      rn_catbnd     =   0.,0.45,1.1,2.1,3.7,6.0  
-   rn_himin         =   0.1           !  minimum ice thickness (m) used in remapping
-/
Index: MO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/nampar
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/nampar	(revision 11041)
+++ 	(revision )
@@ -1,10 +1,0 @@
-!------------------------------------------------------------------------------
-&nampar         !   Generic parameters
-!------------------------------------------------------------------------------
-   jpl              =   5             !  number of ice  categories
-   nlay_i           =   2             !  number of ice  layers
-   nlay_s           =   1             !  number of snow layers (only 1 is working)
-   nn_virtual_itd   =   0             !  virtual ITD mono-category parameterizations (1-3 => jpl = 1 only) or not (0)
-                                      !     2: activate enhanced thermal conductivity only --- temporary option
-                                      !     3: activate virtual thin ice melting only      ---  temporary option
-/
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namsbc
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namsbc	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namsbc	(revision 11042)
@@ -0,0 +1,14 @@
+!------------------------------------------------------------------------------
+&namsbc         !   Ice surface boundary conditions
+!------------------------------------------------------------------------------
+   rn_cio           =   5.0e-03       !  ice-ocean drag coefficient (-)
+   rn_blow_s        =   0.66          !  mesure of snow blowing into the leads
+                                      !     = 1 => no snow blowing, < 1 => some snow blowing
+   nn_flxdist       =  -1             !  Redistribute heat flux over ice categories
+                                      !     =-1  Do nothing (needs N(cat) fluxes)
+                                      !     = 0  Average N(cat) fluxes then apply the average over the N(cat) ice
+                                      !     = 1  Average N(cat) fluxes then redistribute over the N(cat) ice using T-ice and albedo sensitivity
+                                      !     = 2  Redistribute a single flux over categories
+   ln_cndflx        = .false.         !  Use conduction flux as surface boundary conditions (i.e. for Jules coupling)
+      ln_cndemulate = .false.         !     emulate conduction flux (if not provided in the inputs)
+/
Index: MO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namthd
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namthd	(revision 11041)
+++ 	(revision )
@@ -1,8 +1,0 @@
-!------------------------------------------------------------------------------
-&namthd         !   Ice thermodynamics
-!------------------------------------------------------------------------------
-   ln_icedH         = .true.          !  activate ice thickness change from growing/melting (T) or not (F)
-   ln_icedA         = .true.          !  activate lateral melting param. (T) or not (F)
-   ln_icedO         = .true.          !  activate ice growth in open-water (T) or not (F)
-   ln_icedS         = .true.          !  activate brine drainage (T) or not (F)
-/
Index: MO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namthd_da
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namthd_da	(revision 11041)
+++ 	(revision )
@@ -1,11 +1,0 @@
-!------------------------------------------------------------------------------
-&namthd_da      !   Ice lateral melting
-!------------------------------------------------------------------------------
-   rn_beta          =   1.0           !  coef. beta for lateral melting param. Recommended range=[0.8-1.2]
-                                      !   => decrease = more melt and melt peaks toward higher concentration (A~0.5 for beta=1 ; A~0.8 for beta=0.2)
-                                      !      0.3 = best fit for western Fram Strait and Antarctica
-                                      !      1.4 = best fit for eastern Fram Strait      
-   rn_dmin          =   8.            !  minimum floe diameter for lateral melting param. Recommended range=[6-10]
-                                      !   => 6  vs 8m = +40% melting at the peak (A~0.5)
-                                      !      10 vs 8m = -20% melting
-/
Index: MO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namthd_do
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namthd_do	(revision 11041)
+++ 	(revision )
@@ -1,9 +1,0 @@
-!------------------------------------------------------------------------------
-&namthd_do      !   Ice growth in open water
-!------------------------------------------------------------------------------
-   rn_hinew         =   0.1           !  thickness for new ice formation in open water (m), must be larger than rn_hnewice
-   ln_frazil        = .false.         !  Frazil ice parameterization (ice collection as a function of wind)
-      rn_maxfraz    =   1.0           !     maximum fraction of frazil ice collecting at the ice base
-      rn_vfraz      =   0.417         !     thresold drift speed for frazil ice collecting at the ice bottom (m/s)
-      rn_Cfraz      =   5.0           !     squeezing coefficient for frazil ice collecting at the ice bottom
-/
Index: MO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namthd_pnd
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namthd_pnd	(revision 11041)
+++ 	(revision )
@@ -1,10 +1,0 @@
-!------------------------------------------------------------------------------
-&namthd_pnd     !   Melt ponds
-!------------------------------------------------------------------------------
-   ln_pnd_H12       = .false.         !  activate evolutive melt ponds (from Holland et al 2012)
-      ln_pnd_fwb    = .false.         !     melt ponds store freshwater or not
-   ln_pnd_CST       = .false.         !  activate constant melt ponds
-      rn_apnd       =   0.2           !     prescribed pond fraction, at Tsu=0
-      rn_hpnd       =   0.05          !     prescribed pond depth, at Tsu=0
-   ln_pnd_alb       = .false.         !  melt ponds affect albedo or not
-/
Index: MO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namthd_sal
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namthd_sal	(revision 11041)
+++ 	(revision )
@@ -1,15 +1,0 @@
-!------------------------------------------------------------------------------
-&namthd_sal     !   Ice salinity
-!------------------------------------------------------------------------------
-   nn_icesal        =   2             !  ice salinity option
-                                      !     1: constant ice salinity (S=rn_icesal)
-                                      !     2: varying salinity parameterization S(z,t)
-                                      !     3: prescribed salinity profile S(z), Schwarzacher, 1959
-   rn_icesal        =   4.            !    (nn_icesal=1) ice salinity (g/kg)
-   rn_sal_gd        =   5.            !  restoring ice salinity, gravity drainage (g/kg)
-   rn_time_gd       =   1.73e+6       !  restoring time scale, gravity drainage  (s)
-   rn_sal_fl        =   2.            !  restoring ice salinity, flushing (g/kg)
-   rn_time_fl       =   8.64e+5       !  restoring time scale, flushing (s)
-   rn_simax         =  20.            !  maximum tolerated ice salinity (g/kg)
-   rn_simin         =   0.1           !  minimum tolerated ice salinity (g/kg)
-/
Index: MO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namthd_zdf
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/namelists/namthd_zdf	(revision 11041)
+++ 	(revision )
@@ -1,10 +1,0 @@
-!------------------------------------------------------------------------------
-&namthd_zdf     !   Ice heat diffusion
-!------------------------------------------------------------------------------
-   ln_zdf_BL99      = .true.          !  Heat diffusion follows Bitz and Lipscomb 1999
-   ln_cndi_U64      = .false.         !  sea ice thermal conductivity: k = k0 + beta.S/T            (Untersteiner, 1964)
-   ln_cndi_P07      = .true.          !  sea ice thermal conductivity: k = k0 + beta1.S/T - beta2.T (Pringle et al., 2007)
-   rn_cnd_s         =   0.31          !  thermal conductivity of the snow (0.31 W/m/K, Maykut and Untersteiner, 1971)
-                                      !     Obs: 0.1-0.5 (Lecomte et al, JAMES 2013)
-   rn_kappa_i       =   1.0           !  radiation attenuation coefficient in sea ice [1/m]
-/
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/abstract_foreword.tex
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/abstract_foreword.tex	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/abstract_foreword.tex	(revision 11042)
@@ -0,0 +1,44 @@
+
+\documentclass[../main/SI3_manual]{subfiles}
+
+\begin{document}
+
+% ================================================================
+% Abstract
+% ================================================================
+
+\chapter*{Abstract}
+
+SI$^3$ (Sea Ice modelling Integrated Initiative) is the sea ice engine of NEMO (Nucleus for European Modelling of the Ocean). It is adapted to regional and global sea ice and climate problems. 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 based on the Arctic Ice Dynamics Joint EXperiment (AIDJEX) framework \citep{coon_1974}, combining the ice thickness distribution framework, the conservation of horizontal momentum, an elastic-viscous plastic rheology, and energy-conserving halo-thermodynamics. Prognostic variables are the two-dimensional horizontal velocity field, ice volume, area, enthalpy, salt content, snow volume and enthalpy. In the horizontal direction, the model uses a curvilinear orthogonal grid. In the vertical direction, the model uses equally-spaced layers. In thickness space, the model uses thickness categories with prescribed boundaries. Various physical and numerical choices are available to describe sea ice physics. SI$^3$ is interfaced with the NEMO ocean engine, and, via the OASIS coupler, with several atmospheric general circulation models. It also supports two-way grid embedding via the AGRIF software.
+
+%\vspace{-40pt}
+
+{\small
+} 
+
+% ================================================================
+% Disclaimer
+% ================================================================
+\chapter*{Disclaimer}
+
+Like all components of NEMO, the sea ice 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 authors assume no responsibility 
+for problems, errors, or incorrect usage of NEMO.
+
+\vspace{1cm}
+SI3 reference in papers and other publications is as follows:
+\vspace{0.5cm}
+
+The NEMO Sea Ice Working Group, 2018: SI$^3$ -- Sea Ice modelling Integrated Initiative -- The NEMO Sea Ice Engine, \textit{Note du P\^ole de mod\'{e}lisation}, Institut Pierre-Simon Laplace (IPSL), France, 
+No XX, ISSN No 1288-1619.\\
+
+\vspace{0.5cm}
+Additional information can be found on \href{http://www.nemo-ocean.eu/}{www.nemo-ocean.eu}.
+\vspace{0.5cm}
+
+\end{document}
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_bdy_agrif.tex
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_bdy_agrif.tex	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_bdy_agrif.tex	(revision 11042)
@@ -0,0 +1,16 @@
+\documentclass[../main/SI3_manual]{subfiles}
+
+\begin{document}
+
+% ================================================================
+% Chapter 11 - BDY and AGRIF with SI$^3$
+% ================================================================
+
+\chapter{BDY and AGRIF with SI$^3$}
+\label{chap:REG}
+\minitoc
+
+\newpage
+$\ $\newline    % force a new line
+
+\end{document}
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_domain.tex
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_domain.tex	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_domain.tex	(revision 11042)
@@ -0,0 +1,106 @@
+
+\documentclass[../main/SI3_manual]{subfiles}
+
+\begin{document}
+
+% ================================================================
+% Chapter 2 Ñ Domain
+% ================================================================
+
+\chapter{Time, space and thickness space domain}
+\label{chap:DOM}
+\minitoc
+
+\newpage
+$\ $\newline    % force a new line
+
+Having defined the model equations in previous Chapter, we need now to choose the numerical discretization.  In the present chapter, we provide a general description of the SI$^3$ discretization strategy, in terms of time, space and thickness, which is considered as an extra independent variable. 
+
+Sea ice state variables are typically expressed as:
+\begin{equation}
+X(ji,jj,\textcolor{gray}{jk},jl).
+\end{equation}
+$ji$ and $jj$ are x-y spatial indices, as in the ocean. $jk=1, ..., nlay\_i$ corresponds to the vertical coordinate system in sea ice (ice layers), and only applies to vertically-resolved quantities (ice enthalpy and salinity). $jl=1, ..., jpl$ corresponds to the ice categories, discretizing thickness space.
+
+\section{Time domain}
+
+%--------------------------------------------------------------------------------------------------------------------
+%
+% FIG x : Time Stepping
+%
+\begin{figure}[ht]
+\begin{center}
+\vspace{0cm}
+\includegraphics[height=6cm,angle=-00]{time_stepping}
+\caption{Schematic representation of time stepping in SI$^3$, assuming $nn\_fsbc=5$.}
+\label{ice_scheme}
+\end{center}
+\end{figure}
+%
+%--------------------------------------------------------------------------------------------------------------------
+
+The sea ice time stepping is synchronized with that of the ocean. Because of the potentially large numerical cost of sea ice physics, in particular rheology, SI$^3$ can be called every nn\_fsbc time steps (namsbc in \textit{namelist\_ref}). The sea ice time step is therefore $rdt\_ice = rdt * nn\_fsbc$. In terms of quality, the best value for \textit{nn\_fsbc} is 1, providing full consistency between sea ice and oceanic fields. Larger values (typically 2 to 5) can be used but numerical instabilities can appear because of the progressive decoupling between the state of sea ice and that of the ocean, hence changing $nn\_fsbc$ must be done carefully.
+
+Ice dynamics (rheology, advection, ridging/rafting) and thermodynamics are called successively. To avoid pathological situations, thermodynamics were chosen to be applied on fields that have been updated by dynamics, in a somehow semi-implicit procedure.
+
+There are a few iterative / subcycling procedures throughout the code, notably for rheology, advection, ridging/ rafting and the diffusion of heat. In some cases, the arrays at the beginning of the sea ice time step are required. Those are referred to as $X\_b$.
+
+\section{Spatial domain}
+
+%--------------------------------------------------------------------------------------------------------------------
+%
+% FIGx : Vertical grid
+%
+%
+\begin{figure}[!ht]
+\begin{center}
+\vspace{0cm}
+\includegraphics[height=10cm,angle=-00]{thermogrid.eps}
+\caption{\footnotesize{Vertical grid of the model, used to resolve vertical temperature and salinity profiles}}\label{fig_dom_icelayers}
+\end{center}
+\end{figure}
+%
+%--------------------------------------------------------------------------------------------------------------------
+
+The horizontal indices $ji$ and $jj$ are handled as for the ocean in NEMO, assuming C-grid discretization and in most cases a finite difference expression for scale factors.
+
+The vertical index $jk=1, ..., nlay\_i$ is used for enthalpy (temperature) and salinity. In each ice category, the temperature and salinity profiles are vertically resolved over $nlay\_i$ equally-spaced layers. The number of snow layers can currently only be set to $nlay\_s=1$ (Fig. \ref{fig_dom_icelayers}).
+
+To increase numerical efficiency of the code, the two horizontal dimensions of an array $X(ji,jj,jk,jl)$ are collapsed into one (array $X\_1d(ji,jk,jl)$) for thermodynamic computations, and re-expanded afterwards.
+
+\nlst{nampar}
+
+\section{Thickness space domain}
+
+\nlst{namitd}
+
+Thickness space is discretized using $jl=1, ..., jpl$ thickness categories, with prescribed boundaries $hi\_max(jl-1),hi\_max(jl)$. Following \cite{lipscomb_2001}, ice thickness can freely evolve between these boundaries. The number of ice categories $jpl$ can be adjusted from the namelist ($nampar$).
+
+There are two means to specify the position of the thickness boundaries of ice categories. The first option (ln\_cat\_hfn) is to use a fitting function that places the category boundaries between 0 and 3$\overline h$, with $\overline h$ the expected mean ice thickness over the domain (namelist parameter rn\_himean), and with a greater resolution for thin ice (Fig. \ref{fig_dom_icecats}). More specifically, the upper limits for ice in category $jl=1, ..., jpl-1$ are:
+\begin{eqnarray} 
+hi\_max(jl) = \biggr ( \frac{jl \cdot (3\overline h + 1 )^{\alpha}}{ (jpl-jl)(3 \overline h + 1)^{\alpha} + jl }\biggr )^{\alpha^{-1}} - 1,
+\end{eqnarray}
+with $hi\_max(0)$=0 m and $\alpha = 0.05$. The last category has no upper boundary, so that it can contain arbitrarily thick ice.
+
+%--------------------------------------------------------------------------------------------------------------------
+%
+% FIGx : Ice categories
+%
+%
+\begin{figure}[!ht]
+\begin{center}
+\vspace{0cm}
+\includegraphics[height=6cm,angle=-00]{ice_cats.eps}
+\caption{\footnotesize{Boundaries of the model ice thickness categories (m) for varying number of categories and prescribed mean thickness ($\overline h$). The formerly used $tanh$ formulation is also depicted.}}\label{fig_dom_icecats}
+\end{center}
+\end{figure}
+%
+%--------------------------------------------------------------------------------------------------------------------
+
+The other option (ln\_cat\_usr) is to specify category boundaries by hand using rn\_catbnd. The first category must always be thickner than rn\_himin (0.1 m by default).
+
+The choice of ice categories is important, because it constraints the ability of the model to resolve the ice thickness distribution. The latest study \citep{massonnet_2018} recommends to use at least 5 categories, which should include one thick ice with lower bounds at $\sim$4 m and $\sim$2 m for the Arctic and Antarctic, respectively, for allowing the storage of deformed ice.
+
+With a fixed number of cores, the cost of the model linearly increases with the number of ice categories. Using $jpl=1$ single ice category is also much cheaper than with 5 categories, but seriously deteriorates the ability of the model to grow and melt ice. Indeed, thin ice thicknes faster than thick ice, and shrinks more rapidly as well. When nn\_virtual\_itd=1 ($jpl$ = 1 only), two parameterizations are activated to compensate for these shortcomings. Heat conduction and areal decay of melting ice are adjusted to closely approach the 5 categories case.
+
+\end{document}
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_dynamics.tex
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_dynamics.tex	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_dynamics.tex	(revision 11042)
@@ -0,0 +1,35 @@
+
+\documentclass[../main/SI3_manual]{subfiles}
+
+\begin{document}
+
+% ================================================================
+% Chapter 3 Ñ Ice dynamics
+% ================================================================
+
+\chapter{Ice dynamics}
+\label{chap:DYN}
+\minitoc
+
+\newpage
+$\ $\newline    % force a new line
+
+In this chapter, we describe how the momentum equation is solved.
+
+I guess we could be brief. Gurvan and Clem should take the lead to write this.
+
+1) aEVP approach, revisited by Bouillon et al (2013).
+
+2) Short description of the numerical method. NEMO scale factors.
+
+3) Landfast ice option
+
+4) Boundary conditions (free-slip, no-slip, ...)
+
+4) Practical use of namelist parameters (nevp, telast, ...).
+
+\end{document}
+
+
+
+
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_interfaces.tex
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_interfaces.tex	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_interfaces.tex	(revision 11042)
@@ -0,0 +1,30 @@
+\documentclass[../main/SI3_manual]{subfiles}
+
+\begin{document}
+
+% ================================================================
+% Chapter 8 Ñ Interfaces
+% ================================================================
+
+\chapter{Ice-atmosphere and ice-ocean interfaces}
+\label{chap:INT}
+\minitoc
+
+\newpage
+$\ $\newline    % force a new line
+
+In this chapter, we give information on the representation of interfaces.
+
+\section{Ice-ocean interface}
+
+\section{Ice-atmosphere interface}
+
+Drags?
+
+Blowing snow parameter
+
+Flux redistributor
+
+Jules coupling
+
+\end{document}
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_miscellaneous.tex
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_miscellaneous.tex	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_miscellaneous.tex	(revision 11042)
@@ -0,0 +1,18 @@
+\documentclass[../main/SI3_manual]{subfiles}
+
+\begin{document}
+
+% ================================================================
+% Chapter 12 -Miscellaneous
+% ================================================================
+
+\chapter{Miscellaneous topics}
+\label{chap:MIS}
+\minitoc
+
+\newpage
+$\ $\newline    % force a new line
+
+getting started, namelists, configs, ...
+
+\end{document}
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_model_basics.tex
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_model_basics.tex	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_model_basics.tex	(revision 11042)
@@ -0,0 +1,457 @@
+
+\documentclass[../main/SI3_manual]{subfiles}
+
+\begin{document}
+% ================================================================
+% Chapter 1 Ñ Model Basics
+% ================================================================
+
+\chapter{Model Basics}
+\label{chap:MB}
+\minitoc
+
+\newpage
+$\ $\newline    % force a new line
+
+%-------------------------------------------------------------------------------------------------------------------------
+%
+% 2.1 Assumptions
+\section{Rationale and assumptions}
+%
+%-------------------------------------------------------------------------------------------------------------------------
+\begin{itemize}
+\item Separation of horizontal dynamics and vertical thermodynamics;
+\item Dynamics: sea ice is a viscous-plastic continuum;
+\item Thermodynamics: sea ice is a mushy layer covered by snow
+\item Subgrid-scale physics
+\end{itemize}
+
+\subsection{Scales, thermodynamics and dynamics}
+Because sea ice is much wider -- $\mathcal{O}$(100-1000 km) -- than thick -- $\mathcal{O}$(1 m) -- ice drift can be considered as purely horizontal: vertical motions around the hydrostatic equilibrium position are negligible. The same scaling argument justifies the assumption that heat exchanges are purely vertical\footnote{The latter assumption is probably less valid, because the horizontal scales of temperature variations are $\mathcal{O}$(10-100 m)}. It is on this basis that thermodynamics and dynamics are separated and rely upon different frameworks and sets of hypotheses: thermodynamics use the ice thickness distribution \citep{thorndike_1975} and the mushy-layer \citep{worster_1992} frameworks, whereas dynamics assume continuum mechanics \citep[e.g.,][]{lepp_ranta_2011}. Thermodynamics and dynamics interact by two means: first, advection impacts state variables; second, the horizontal momentum equation depends, among other things, on the ice state.
+
+\subsection{Subgrid scale variations}
+
+Sea ice properties -- in particular ice thickness -- feature important changes at horizontal scales $\mathcal{O}$(1m) \citep{thorndike_1975}. An explicit representation of these variations is not and will not be -- at least in the next twenty years or so -- accessible to large-scale sea ice models. Yet important features, such as energy exchanges through the ice, quite non-linearly depend on ice thickness \citep{maykut_1986}; whereas ice motion depends on the presence of open water, thin and thick ice at the very least, suggesting that subgrid-scale variations in ice properties must be accounted for, at least in a statistical fashion \citep{maykut_1973}. 
+
+%--------------------------------------------------------------------------------------------------------------------
+%
+% FIG x : Ice scheme
+%
+\begin{figure}[ht]
+\begin{center}
+\vspace{0cm}
+\includegraphics[height=10cm,angle=-00]{ice_scheme}
+\caption{Representation of the ice pack, using multiple categories with specific ice concentration ($a_l, l=1, 2, ..., L$), thickness ($h^i_l$), snow depth ($h^s_l$), vertical temperature and salinity profiles ($T^i_{kl}$, $S^{*}_{kl}$) and a single ice velocity vector ($\mathbf{u}$).}
+\label{ice_scheme}
+\end{center}
+\end{figure}
+%
+%--------------------------------------------------------------------------------------------------------------------
+
+The \textit{multi-category} framework \citep{maykut_1973} addresses this issue by treating the ice thickness as an independent variable next to spatial coordinates and time, and introducing a thickness distribution\footnote{$g(h)$, termed the \textit{ice thickness distribution} is the density of probability of ice thickness \citep{thorndike_1975}.} $g(h)$ as the main prognostic model field. In the discrete world, the thickness distribution is converted into $L$ thickness categories. Ice thickness categories occupy a fraction of each grid cell, termed ice concentration ($a_l, l=1, 2, ..., L$), with specific thickness and properties. 
+
+The \textit{single-category} framework \citep{hibler_1979} tackles the subgrid-scale issue by drastically simplifying the ice thickness distribution. The grid cell is divided into open water and sea ice characterized by a single ice concentration $A$ and mean thickness $H$. Single-category models (in particular LIM2) typically add parameterizations to represent the effects of unresolved ice thickness distribution on ice growth and melt \citep[see, e.g.][]{mellor_1989,fichefet_1997}.
+
+SI$^3$ provides the choice between either a multi- or a single-category framework. The default mode is multi-category. The single-category mode can be activated by setting the number of categories ($jpl=1$) and by activating the virtual thickness distribution parameterizations (nn\_monocat=1).
+
+\subsection{Thermodynamic formulation}
+
+%
+%--------------------------------------------------------------------------------------------------------------------
+%
+% TABLE x Physical constants
+%
+%
+\begin{table}[ht]
+\begin{footnotesize}
+\caption{Thermodynamic constants of the model.}
+\begin{center}
+\begin{tabular}{@{}llccl}\hline
+ & Description & Value & Units & Ref \\ \hline
+$c_i$ (cpic) & Pure ice specific heat & 2067 & J/kg/K & ? \\
+$c_w$ (rcp) & Seawater specific heat & 3991 & J/kg/K & \cite{TEOS_2010} \\
+$L$ (lfus) & Latent heat of fusion (0$^\circ$C) & 334000 & J/kg/K & \cite{bitz_1999} \\
+$\rho_i$ (rhoic) & Sea ice density & 917 & kg/m$^3$ & \cite{bitz_1999} \\
+$\rho_s$ (rhosn) & Snow density & 330 & kg/m$^3$ & \cite{maykut_1971} \\
+$\mu$ (tmut) & Linear liquidus coefficient & 0.054 & $^\circ$C/(g/kg) & \cite{assur_1958} \\
+\hline
+\end{tabular}
+\end{center}
+\label{PhysicalConstants_table}
+\end{footnotesize}
+\end{table}
+%
+%--------------------------------------------------------------------------------------------------------------------
+%
+
+Ice thermodynamics are formulated assuming that sea ice is covered by snow. Within each thickness category, both snow and sea ice are horizontally uniform, hence each thickness category has a specific ice thickness ($h_i^l$) and snow depth ($h_s^l$). Snow is assumed to be fresh, with constant density and thermal conductivity. Sea ice is assumed to be a \textit{mushy layer}\footnote{Mushy layers are two-phase, two-component porous media.} \citep{worster_1992} of constant density, made of pure ice and brine in thermal equilibrium, related by a linear liquidus relationship \citep{bitz_1999}. A vertically-averaged bulk salinity $S_l$ uniquely characterizes brine fraction for each thickness category, and changes through  time from a simple parametrization of brine drainage. The linear vertical salinity profile ($S^*_{kl}$) is reconstructed from the vertical mean \citep{vancoppenolle_2009}. The diffusion of heat affects the vertical temperature profile, discretized on a unique layer of snow and multiple ice layers (typically 2-5) for each category, whereas thermal properties depend on local brine fraction. Growth and melt rates are computed, also for each ice category. The choice of the main thermodynamic constants  is described in Tab. \ref{PhysicalConstants_table}.
+
+
+
+%
+%--------------------------------------------------------------------------------------------------------------------
+%
+% TABLE x Global variables
+%
+%
+\begin{table}[ht]
+\begin{footnotesize}
+\caption{LIM global variables.}
+\begin{center}
+\begin{tabular}{@{}llcc}\hline
+Symbol   & Description & Units & Code name \\ \hline
+$\mathbf{u}$ & Sea ice velocity & [$m.s^{-1}$] & \textit{u\_ice, v\_ice (ji,jj)} \\
+$\mathbf{\sigma}$ & Stress tensor & [$Pa.m$] & \textit{stress1\_i, stress2\_i} \\
+ & & & \textit{stress12\_i (ji,jj)} \\
+$a_l$ & Concentration of sea ice in category $l$ & [-] & \textit{a\_i(ji,jj,jl)} \\
+$v^i_l$ & Volume of sea ice per unit area in category $l$ & [$m$] & \textit{v\_i(ji,jj,jl)} \\
+$v^s_l$ & Volume of snow per unit area in category $l$ & [$m$] & \textit{v\_s(ji,jj,jl)} \\
+$e^i_{kl}$ & Sea ice enthalpy per unit area in layer $k$ and category $l$ & [$J.m^{-2}$] & \textit{e\_i(ji,jj,jk,jl)} \\
+$e^s_{l}$ & Snow enthalpy per unit area in category $l$ & [$J.m^{-2}$] & \textit{e\_s(ji,jj,jl)} \\
+$M^s_l$ & Sea ice salt content in category $l$ & [$g/kg.m$] & \textit{smv\_i(ji,jj,jl)}\\
+%$O_l$ & Sea ice age content in category $l$ & $[days.m]$ \\
+\hline
+\end{tabular}
+\end{center}
+\label{GVariables_table}
+\end{footnotesize}
+\end{table}
+%
+%--------------------------------------------------------------------------------------------------------------------
+
+ Temperature, salinity, ice thickness, and snow depth are not extensive variables and therefore not conservative. Hence, conservative, extensive variables, must be introduced to ensure mass, salt and energy conservation. There are several back-and-forth conversions from extensive (conservative) state variables (see Table \ref{GVariables_table}) to intensive state variables of practical use (Table \ref{IVariables_table}).
+ 
+ %--------------------------------------------------------------------------------------------------------------------
+%
+% TABLE x Equivalent variables
+%
+%
+\begin{table}[ht]
+\begin{footnotesize}
+\caption{Intensive variables of practical use.}
+\begin{center}
+\begin{tabular}{@{}llcc}\hline
+Symbol   & Description & Units \\ \hline
+$h^i_l=v^i_l/g^i_l$ & Ice thickness & [$m$] \\
+$h^s_l=v^s_l/g^i_l$ & Snow depth & [$m$] \\
+$q^i_{m,kl}=e^i_{l,k}/(h^i_l/N)$ & Ice specific enthalpy & [$J.kg^{-1}$]\\
+$q^s_{m,l}=e^s_{l}/h^s_l$ & Snow specific enthalpy & [$J.kg^{-1}$] \\
+$T^i_{kl}=T(q^i_{kl})$ & Ice temperature & [$K$] \\
+$T^s_{l} =T(q^s_{l}) $ & Snow temperature & [$K$] \\
+$\overline S^i_{l}=M^s_l / v^i_l$ & Vertically-averaged bulk ice salinity & [g/kg] \\
+$S^*_{kl}$ & Depth-dependent ice salinity & [g/kg] \\
+$\phi_{kl}$ & Brine fraction & [-] \\
+%$o^i_{l}=O_l / g^i_l $ & Ice age & [$days$] \\
+\hline
+\end{tabular}
+\end{center}
+\label{IVariables_table}
+\end{footnotesize}
+\end{table}
+%
+%--------------------------------------------------------------------------------------------------------------------
+
+\subsection{Dynamic formulation}
+
+The formulation of ice dynamics is based on the continuum approach. The latter holds provided the drift ice particles are much larger than single ice floes, and much smaller than typical gradient scales. This compromise is rarely achieved in practice \citep{lepp_ranta_2011}. Yet the continuum approach generates a convenient momentum equation for the horizontal ice velocity vector $\mathbf{u}=(u,v)$, which can be solved with classical numerical methods (here, finite differences on the NEMO C-grid). The most important term in the momentum equation is internal stress. We follow the viscous-plastic (VP) rheological framework \citep{hibler_1979}, assuming that sea ice has no tensile strength but responds to compressive and shear deformations in a plastic way. In practice, the elastic-viscous-plastic (EVP) technique of  \citep{bouillon_2013} is used, more convient numerically than VP.  It is well accepted that the VP rheology and its relatives are the minimum complexity to get reasonable ice drift patterns \citep{kreyscher_2000}, but fail at generating the observed deformation patterns \citep{girard_2009}. This is a long-lasting problem: what is the ideal rheological model for sea ice and how it should be applied are still being debated \citep[see, e.g.][]{weiss_2013}. 
+
+%-------------------------------------------------------------------------------------------------------------------------
+%
+\section{Thickness distribution framework}
+%
+%-------------------------------------------------------------------------------------------------------------------------
+
+We first present the essentials of the thickness distribution framework \citep{thorndike_1975}. Consider a given region of area $R$ centered at spatial coordinates $(\mathbf{x})$ at a given time $t$. $R$ could be e.g. a model grid cell. The ice thickness distribution $g(\mathbf{x},t, h)$ is introduced as follows:
+\begin{linenomath}
+\begin{align}
+g(h) &= \lim_{dh \to 0} \frac{dA(h,h+dh)}{dh},
+\end{align}
+\end{linenomath}
+where $dA(h,h+dh)$ is the surface fraction of all parts of $R$ with ice thickness between $h$ and $h+dh$. Using this definition, the spatial structure of ice thickness is lost (see Fig. \ref{fig_g_h}), and $h$ becomes an extra independent variable, next to spatial coordinates and time, that can be thought as random. $g$ is by definition normalized to 1. The conservation of area, expressed in terms of $g(h)$, is given by \citep{thorndike_1975}: 
+\begin{linenomath}
+\begin{align}
+\frac{\partial g}{\partial t} = - \nabla .(g \mathbf{u}) - \frac{\partial}{\partial h} (f g) + \psi,
+\label{eq:gt}
+\end{align}
+\end{linenomath}
+where the terms on the right hand side refer to horizontal transport, thermodynamic transport in thickness space ($f$, m/s is the growth/melt rate), and mechanical redistribution rate, e.g. by ridging and rafting, where $\psi$ must conserve ice area and volume by construction.
+
+%--------------------------------------------------------------------------------------------------------------------
+%
+% FIG x : Ice thickness distribution
+%
+\begin{figure}[ht]
+\begin{center}
+\vspace{0cm}
+\includegraphics[height=6cm,angle=-00]{g_h}
+\caption{Representation of the relation between real thickness profiles and the ice thickness distribution function $g(h)$}
+\label{fig_g_h}
+\end{center}
+\end{figure}
+%
+%--------------------------------------------------------------------------------------------------------------------
+
+In numerical implementations, the thickness distribution is discretized into several thickness categories, with specific ice concentration $a_l$ and ice volume per area $v_l^i$:
+\begin{linenomath}
+\begin{align}
+a_l &= \int _{H^*_{l-1}}^{H^*_l} dh \cdot g(h) , \\
+v_l^i &= \int _{H^*_{l-1}}^{H^*_l} dh \cdot h \cdot g(h).
+\end{align}
+\end{linenomath}
+Ice volume per area is the extensive counterpart for ice thickness, connected with volume through $h_l^i = v_l^i / a_l$. Evolution equations for extensive variables can be readily derived from equation \ref{eq:gt} by integration between thickness boundaries of the $l^{th}$ category \citep{bitz_2001}. This applies to all model extensive variables (see Table \ref{GVariables_table}). For ice area, this reads:
+\begin{linenomath}
+\begin{align}
+\frac{\partial a_l}{\partial t} = - \mathbf{\nabla} \cdot (a_l \mathbf{u}) + \Theta^a_l + \int_{H^*_{l-1}}^{H^*_l} dh \psi.
+\label{eq:gt}
+\end{align}
+\end{linenomath}
+wher $\Theta^a_l$ refers to the effect of thermodynamics. Enthalpy is a particular case because it also has a vertical depth dependence $z$, which corresponds to $K$ vertical layers of equal thickness. The solution adopted here, following from \cite{zhang_2001}, is that enthalpy from the individual layers are conserved separately. This is a practical solution, for lack of better.
+
+One of the major actions of LIM is to resolve conservation equations for all extensive variables that characterize the ice state.  Let us now connect this detailed information with classical sea ice fields. The ice concentration $A$ and the ice volume per area\footnote{Ice volume per area is equivalent to the grid-cell averaged ice thickness.} $V_i$ (m) directly derive from $g$: 
+\begin{linenomath}
+\begin{align}
+ A(\mathbf{x},t) &=\int_{0^+}^{\infty} dh \cdot g(h,\mathbf{x},t) \sim A_{ij} = \sum_{l=1}^L a_{ijl}, & \\
+ V_i(\mathbf{x},t)&=\int_{0}^{\infty} dh \cdot g(h,\mathbf{x},t) \cdot h \sim V^i_{ij} = \sum_{l=1}^L v^i_{ijl}. & \\
+\end{align}
+\end{linenomath}
+where the $0^+$ boundary implies that the means exclude open water. The mean ice thicknesses $H_i$ (m) is:
+\begin{linenomath}
+\begin{align}
+H_i = V_i/A,
+\end{align}
+\end{linenomath}
+whereas the open water fraction is simply $1-A$.
+
+\section{Governing equations}
+
+Let us now readily present the set of the LIM "governing" equations in the framework of the assumptions developed above. The conservation of horizontal momentum reads:
+\begin{linenomath}
+\begin{align}
+m \frac{\partial \mathbf{u}} {\partial t} & = \mathbf{\nabla}\cdot\mathbf{\sigma} +A \left(\mathbf{\tau}_{a}+\mathbf{\tau}_{w}\right) - m f \mathbf{k} \times \mathbf{u} - m g \mathbf{\nabla}{\eta},
+\label{a}
+\end{align}
+\end{linenomath}
+where $m=\rho_i V_i + \rho_s V_s $ is the ice and snow mass per unit area, $\mathbf{u}$ is the ice velocity, $\mathbf{\sigma}$ is the internal stress tensor, $\mathbf{\tau}_a$ and $\mathbf{\tau}_w$ are the air and ocean stresses, respectively, $f$ is the Coriolis parameter, $\mathbf{k}$ is a unit vector pointing upwards, $g$ is the gravity acceleration and $\eta$ is the ocean surface elevation. The EVP approach used in LIM \citep{bouillon_2013} gives the stress tensor as a function of the strain rate tensor $\dot{\mathbf{\epsilon}}$ and some of the sea ice state variables:
+\begin{linenomath}
+\begin{align}
+\mathbf{\sigma} & = \mathbf{\sigma} (\dot{ \mathbf{\epsilon}}, \text{ice state}).
+\end{align}
+\end{linenomath}
+To the exception of velocity and internal stress, all extensive variables in Table \ref{GVariables_table} follow a conservation equation of the form:
+\begin{linenomath}
+\begin{align}
+\frac{\partial X}{\partial t} & = - \nabla .(\mathbf{u}X) + \Theta^X + \Psi^X,
+\label{eq:Xt}
+\end{align}
+\end{linenomath}
+including the effets of transport, thermodynamics ($\Theta^X$) and mechanical redistribution ($\Psi^X$). Solving these $jpl.(4+2.jpk)$ equations gives the temporal evolution of $\mathbf{u}$, $\mathbf{\sigma}$ and the rest of the global (extensive) variables listed in Table \ref{GVariables_table}.
+
+\section{Ice Dynamics}
+
+Dynamical processes include the conservation of momentum, rheology, transport and mechanical redistribution.
+To resolve the momentum equation, atmospheric stress is taken either as forcing or from an atmospheric model, oceanic stress and sea surface elevation from the ocean model, the Coriolis term is trivial. The last term, the divergence of the internal stress tensor $\sigma$, is the most critical term in the momentum equation and requires a rheological formulation. The EVP approach used in LIM gives the stress tensor components as \citep{bouillon_2013}:
+\begin{linenomath}
+\begin{align}
+\sigma_{ij} & = \frac{P}{2(\Delta + \Delta_{min}) }
+\biggr [ ( \dot{\epsilon}_{kk} - \Delta) \delta_{ij} + \frac{1}{e^2} ( 2 \dot{\epsilon}_{ij} - \dot{\epsilon}_{kk} \delta_{ij} ) \biggr ],
+\end{align}
+\end{linenomath}
+where $\Delta$ is a particular measure of the deformation rate, $\Delta_{min}$ a parameter determining a smooth transition from pure viscous vlow ($\Delta<<\Delta_{min}$) to pure plastic flow ($\Delta >> \Delta_{min}$), and $e$ is a parameter giving the ratio between the maximum compressive stress and twice the maximum shear stress. In the pure plastic regime, the stress principal components should lie on the edge of an elliptical yield curve (Fig. \ref{fig_yield}). In the viscous regime, they are within the ellipse. The ice strength $P$ determines the plastic failure criterion and connects the momentum equation with the state of the sea ice. $P$ is not well constrained and must be parameterized. The heuristic option of \cite{hibler_1979} was here adopted as a reference formulation:
+\begin{linenomath}
+\begin{align}
+P & = P^* V_i e^{-C(1-A)},
+\end{align}
+\end{linenomath}
+where $P^*$ and $C$ are empirical constants (see Table \ref{Modelparameters_table} for the values of the main model parameters).
+
+%--------------------------------------------------------------------------------------------------------------------
+%
+% FIG x : Ice thickness distribution
+%
+\begin{figure}[ht]
+\begin{center}
+\vspace{0cm}
+\includegraphics[height=6cm,angle=-00]{yield_curve}
+\caption{Elliptical yield curve used in the VP rheologies, drawn in the space of the principal components of the stress tensor ($\sigma_1$ and $\sigma_2$).}
+\label{fig_yield}
+\end{center}
+\end{figure}
+%
+%--------------------------------------------------------------------------------------------------------------------
+
+%
+%--------------------------------------------------------------------------------------------------------------------
+%
+% TABLE x Model parameters %
+%
+\begin{table}[ht]
+\begin{footnotesize}
+\caption{Main model parameters.}
+\begin{center}
+\begin{tabular}{@{}llccl}\hline
+ & Description & Value & Units & Ref \\ \hline
+ 
+% Parameters
+$P*$ (rn\_pstar) & ice strength thickness param. & 20000 & N/m2 & - \\
+$C$ (rn\_crhg) & ice strength concentration param. & 20 & - & \citep{hibler_1979} \\
+$H^*$ (rn\_hstar) & maximum ridged ice thickness param. & 25 & m & \citep{lipscomb_2007} \\
+$p$ (rn\_por\_rdg) & porosity of new ridges & 0.3 & - & \citep{lepp_ranta_1995} \\
+$amax$ (rn\_amax) & maximum ice concentration & 0.999 & - & -\\
+$h_0$ (rn\_hnewice) & thickness of newly formed ice & 0.1 & m & - \\
+ 
+\hline
+\end{tabular}
+\end{center}
+\label{Modelparameters_table}
+\end{footnotesize}
+\end{table}
+%
+%--------------------------------------------------------------------------------------------------------------------
+%
+
+
+Transport connects the horizontal velocity fields and the rest of the ice properties. LIM assumes that the ice properties in the different thickness categories are transported at the same velocity. The scheme of \cite{prather_1986}, based on the conservation of 0, 1$^{st}$ and 2$^{nd}$ order moments in $x-$ and $y-$directions,  is used, with some numerical diffusion if desired. Whereas this scheme is accurate, nearly conservative, it is also quite expensive since, for each advected field, five moments need to be advected, which proves CPU consuming, in particular when multiple categories are used. Other solutions are currently explored.
+
+The dissipation of energy associated with plastic failure under convergence and shear is accomplished by rafting (overriding of two ice plates) and ridging (breaking of an ice plate and subsequent piling of the broken ice blocks into pressure ridges). Thin ice preferentially rafts whereas thick ice preferentially ridges \citep{tuhkuri_2002}. Because observations of these processes are limited, their representation in LIM is rather heuristic. The amount of ice that rafts/ridges depends on the strain rate tensor invariants (shear and divergence) as in \citep{flato_1995}, while the ice categories involved are determined by a participation function favouring thin ice \citep{lipscomb_2007}. The thickness of ice being deformed ($h'$) determines whether ice rafts ($h'<$ 0.75 m) or ridges ($h'>$ 0.75 m), following \cite{haapala_2000}. The deformed ice thickness is $2h'$ after rafting, and is distributed between $2h'$ and $2 \sqrt{H^*h'}$ after ridging, where $H^* = 25$ m \citep{lipscomb_2007}. Newly ridged ice is highly porous, effectively trapping seawater. To represent this, a prescribed volume fraction (30\%) of newly ridged ice \citep{lepp_ranta_1995} incorporates mass, salt and heat are extracted from the ocean. Hence, in contrast with other models, the net thermodynamic ice production during convergence is not zero in LIM, since mass is added to sea ice during ridging. Consequently, simulated new ridges have high temperature and salinity as observed \citep{h_yland_2002}. A fraction of snow (50 \%) falls into the ocean during deformation.
+
+\section{Ice thermodynamics}
+In this section, we develop the underlying principles of the thermodynamic formulation, summarized in the term $\Theta^X$, where $X$ refers to all extensive state variables. $\Theta^X$ includes the contributions of transport in thickness space and thermodynamic source and sink terms.
+
+\subsection{Transport in thickness space}
+Transport in thickness space describes how vertical growth and melt moves ice state variables among the different thicknesses at a velocity $f(h)$, the net ice growth/melt rate, which needs to be first computed.  In discretized form, this term moves ice properties between neighbouring categories. The linear remapping scheme of \cite{lipscomb_2001} is used. This scheme is semi-lagrangian, second-order, is less diffusive and converges faster than other options.
+
+\subsection{Thermodynamic source and sink terms}
+
+Since heat, salt and mass are strongly inter-dependent for sea ice, the thermodynamic source and sink terms are treated together. They include the changes in extensive sea ice state associated with thermodynamic processes. The latter are separated in two main parts: (i) open water fraction processes, where atmosphere and ocean are in direct interaction; and (ii) vertical ice thermodynamic processes, driven by surface snow/ice-atmosphere and basal ice-ocean exchanges, for each thickness category. For each part, first, the energy available or lost is specified. Then the impact on mass exchanges is evaluated. The latter part requires to specify how sea ice and snow responds to energy supply or loss, which is achieved through the enthalpy formulation.
+
+%\subsubsection{Atmosphere-ice-ocean heat and mass exchanges}
+%
+%The atmosphere-ice heat exchanges are either specified in external files (forcing) or computed from an atmospheric model. The following heat and mass fluxes should be specified:
+%\begin{itemize}
+%\item Net solar flux, for open water ($Q^{sol}$) and ice categories ($Q^{sol,ice}_{l}$);
+%\item Net non-solar flux, for open water ($Q^{nsol}$) and ice categories ($Q^{nsol,ice}_{l}$);
+%\item Solid and liquid precipitation (kg/m$^2$/s).
+%\end{itemize}
+%
+%In terms of mass (freshwater), the ocean gets:
+%\begin{itemize}
+%\item All liquid precipitation;
+%\item The part of solid precipitation that is not intercepted by the ice, accounting for the part that is blown off the sea ice by winds;
+%\item The net melting minus freezing mass flux, as diagnosed from thermodynamic sea ice calculations.
+%\end{itemize}
+%
+%In terms of energy, the ocean gets:
+%\begin{itemize}
+%\item The net atmospheric solar flux, minus what is intercepted by the ice; plus what is transmitted below the ice; 
+%\item The net atmospheric non-solar heat flux, minus what is used by the sea ice; 
+%\item The sensible heat exchange associated with ice-ocean and atmosphere-ocean mass fluxes. 
+%\end{itemize}
+%
+%In terms of salt, the ocean gets the net salt release minus uptake associated with sea ice growth, melt and brine drainage. There is no atmosphere-ocean salt flux.
+
+\subsubsection{Enthalpy formulation}
+
+% Add snow and water
+
+A first overarching aspect of the thermodynamic calculations is the specification of the response of sea ice to energy supply. This is achieved by defining the internal energy (or enthalpy\footnote{Wording it internal energy or enthalpy is equivalent since pressure effects are not considered.}). This ultimately relies on the response of the phase composition to salinity and temperature changes. The enthalpy formulation used in LIM is based on the following assumptions:
+\begin{itemize}
+\item Sea ice is gas-free, composed solely of pure ice and saline brine, characterized by brine fraction $\phi$;
+\item brine and pure ice are in thermodynamic equilibrium;
+\item the salinity-dependence of the freezing point is linear (linear liquidus);
+\item the density of the sea ice (ice+brine) medium is constant ($\rho_i$).
+\end{itemize}
+%In this context, the bulk salinity of a small control sea ice volume is related to the salinity of brine ($S_{br}$):
+%\begin{linenomath}
+%\begin{align}
+%S = \phi S_{br}
+%\label{eq_S_Sbr}
+%\end{align}
+%\end{linenomath}
+%Because of thermal equilibrium and linear liquidus, brine salinity directly depends on local temperature: $T=-\mu S_{br}$. Hence, brine fraction is given by
+%\begin{linenomath}
+%\begin{align}
+%\phi = -\frac{\mu S}{T}.
+%\end{align}
+%\end{linenomath}
+%This equation relates brine fraction to bulk salinity and temperature, which therefore can be seen as the two main state variables in this linear mushy layer formulation for sea ice thermodynamics. 
+
+%--------------------------------------------------------------------------------------------------------------------
+%
+% FIG x : Thermal properties
+%
+\begin{figure}[ht]
+\begin{center}
+\vspace{0cm}
+\includegraphics[height=8cm,angle=-00]{Thermal_properties}
+\caption{Thermal properties of sea ice vs temperature for different bulk salinities: brine fraction, specific enthalpy, thermal conductivity, and effective specific heat.}
+\label{fig_thermal_properties}
+\end{center}
+\end{figure}
+%
+%--------------------------------------------------------------------------------------------------------------------
+
+Based on these, brine fraction reduces to $\phi = -\mu S/T$ (see Fig. \ref{fig_thermal_properties}), where $\mu$ relates the freezing point of brine to salinity, and one can derive the specific enthalpy $q_m(S,T)$, defined as the energy required to warm and melt a unit control volume of sea ice at temperature $T$ (in Celsius) and salinity $S$ until 0$^\circ$ C, taken as a reference zero-energy level \citep{bitz_1999,schmidt_2004}:
+\begin{linenomath}
+\begin{align}
+q_m(S,T) = \biggr [ c_i ( T + \mu S) - L \biggr ( 1 + \frac{\mu S}{T} \biggr ) - c_w \mu S \biggr ]
+\end{align}
+\end{linenomath}
+where $c_i$ is pure ice specific heat, $L$ is latent heat of fusion at 0$^\circ$C, and $c_w$ is water specific heat. The first term expresses the warming of solid ice. The second term expresses internal change in brine fraction, which is often the largest because the Stefan number  ($c_i T/L$) is generally small. The last term gives the warming of the remaining water from $T_{fr} = -\mu S$ until 0$^\circ$C. Similar, but simpler and linear expressions for snow and water can be derived.
+
+The second overarching aspect is that all growth and melt processes must be calculated consistently with the enthalpy formulation. Energetics of phase transitions are handled using the formalism of \cite{schmidt_2004}. For each phase transition, initial and final states (temperature and salinity) are defined, and the ice-to-ocean mass flux to the ice $F_m$ (kg/s) relates to the energy gain or loss $\Delta Q$ through:
+\begin{linenomath}
+\begin{align}
+\Delta Q / \Delta q_m = F_m,
+\label{eq_phasechange}
+\end{align}
+\end{linenomath}
+where $\Delta q_m$ is the change in specific enthalpy involved in the considered phase transition, from initial to final state.
+
+
+\subsubsection{Open water processes}
+
+As part of the sea ice thermodynamic calculations, a heat budget estimate for the uppermost ocean level ($B^{opw}$) must be included, to compute the rate of new ice formation or the contribution of sensible heat to bottom melting. $B^{opw}$ includes:
+\begin{itemize}
+\item the absorption of a fraction $f_1^{qsr}$ of solar radiation (given by radiative transfer component of the ocean model);
+\item the non-solar heat flux absorbed at the surface;
+\item the sensible heat content of precipitation
+\item the sensible heat flux from the ocean to the sea ice ($A.F_w$)
+\end{itemize}
+Other contributions are not assumed not to contribute. The ocean-to-ice sensible heat flux is formulated the bulk formula of \citep{mcphee_1992}.
+
+% Ice growth
+If $B^{opw}$ is such that the SST would decrease below the freezing point, the remainder of the heat is used to form new ice. The heat loss is converted into a volume of new ice $v_0$. The thickness $h_0$ of the new ice grown during a sea ice time step depends on unresolved small-scale currents and waves and is prescribed. The fraction $a_0=v_0/h_0$ is computed accordingly. The salinity of this new ice $S_0$ is given by the salinity-thickness empirical relationship of \cite{kovacs_1996}. The temperature assumed for this new ice is the local freezing point. If by contrast $B^{opw}$ is positive and there still is ice in the grid cell, then $B^{opw}$ is directly redirected to bottom melting. This argument follows from \cite{maykut_1995}, who found that most of solar heat absorbed in the surface waters is converted into melting. In practise, this prevents the SST to be above freezing as long ice is present.
+
+$B^{opw}$ can be seen as a predictor of the heat budget of the first ocean level. As such, it only helps to compute new ice formation and the extra bottom melt in summer, but is not part of the conservation of heat in the model. To ensure heat conservation, the heat effectively contributing to changing sea ice is removed from the non-solar flux sent to the ocean. This includes: (i) the heat loss used for ice formation, (ii) the heat gain used to melt ice, and (iii) the sensible heat given by the ocean to the ice. Finally, because ice dynamics are not able to maintain the small amount of open water that is observed, a maximum ice fraction ($amax, <1$) is prescribed.
+
+\subsubsection{Vertical ice thermodynamic processes}
+
+The second part of the computations regard the computation of purerly vertical processes in the ice-covered part of the grid cell, similarly for each ice category. 
+
+\textbf{Surface melt, basal growth and melt and diffusion of heat}. The surface melt rate, as well as the basal growth / melt rate depend on the energy budget at the upper and lower interfaces, respectively, between the external fluxes either from the atmosphere or the ocean, and the internal conduction fluxes. The internal conduction fluxes depend on the internal temperature profile, which is determined by solving the enthalpy equation:
+\begin{linenomath}
+\begin{align}
+\rho \frac{\partial q_m}{\partial t} = - \frac{\partial}{\partial z} (F_c + F_r ).
+\end{align}
+\end{linenomath}
+which state that the local change in enthalpy is given by the divergence of the vertical conduction ($F_c=-k(S,T) \partial T / \partial z$) and radiation ($F_r$) fluxes. $\rho$ is the density of ice or snow. Re-expressed as a function of temperature, this becomes the heat diffusion equation.  This equation is non-linear in $T$, because of $q$ and $k$, and its main specificity is that internal melting requires large amounts of energy near the freezing point. The thermal conductivity is formulated following \cite{pringle_2007}, empirically accounting for the reduction of thermal conductivity at large brine fractions. 
+
+At the ice base, we assume that the temperature is at the local freezing point.  Ice grows or melt if the heat balance between the oceanic sensible heat flux ($F_w$) and internal conduction is negative or positive.
+
+At the ice surface, the boundary condition on the heat diffusion equation is:
+\begin{linenomath}
+\begin{align}
+Q^{sr}  + Q^{ns}(T_{su})= F_c + Q^{sum}.
+\end{align}
+\end{linenomath}
+where $Q^{sr}$ and $Q^{ns}$ are the net downwelling atmospheric solar and non-solar flux components. If the solution of this equation without melting gives a surface temperature ($T_{su}$) below 0$^\circ$ C, then there is no melting and the heat available for surface melting $Q_{sum}=0$.  Otherwise $T_{su}$ is capped at 0$^\circ$ C and $Q_{sum}$ is calculated as a residual.
+
+\textbf{Radiation}. Radiation contributes to the surface and internal heat budget. The radiative transfer scheme is currently basic, composed of surface albedo, transmission through the ice interior and attenuation with vertical depth. The albedo is computed empirically as a function of ice thickness, snow depth and surface temperature, using a reformulation of the parameterization of \cite{shine_1985}. When snow is present, all the absorbed radiation is transformed into sensible heat available for conduction or melting. Over snow-free ice, a fraction of solar radiation is transmitted below the surface and attenuates exponentially with depth, until it reaches the base of the ice.
+
+\textbf{Growth and melt processes}.  Snow grows from precipitation and loses mass from melting and snow-ice conversion once the snow base is below sea level. Sea ice grows and melts by various means. Ice forms by congelation or melt at the base, can melt at the surface and form from snow-to-ice conversion at the snow-ice interface if the latter is below sea level. Some new ice is also added to the system when seawater is trapped into newly formed pressure ridges.
+
+\textbf{Salt dynamics}. Bulk salinity is empirically parameterized, as a function of salt uptake during growth, gravity drainage and flushing. The shape of the vertical profile depends on the bulk salinity \citep{vancoppenolle_2009}.
+
+\textbf{Single-category parameterizations}. If the single-category representation is adopted, then two parameterizations can be activated, following \citep{fichefet_1997}. First, the thermal conductivity of both ice and snow is multiplied by a factor $>1$ accounting for the unresolved thin ice, effectively increasing the ice growth rate. Second, to account for the loss of thin ice in summer, the ice concentration is reduced in proportion to the loss of ice thickness. Both parameterizations have been tuned to match the results in multi-category mode.
+
+\end{document}
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_output_diagnostics.tex
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_output_diagnostics.tex	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_output_diagnostics.tex	(revision 11042)
@@ -0,0 +1,65 @@
+\documentclass[../main/SI3_manual]{subfiles}
+
+\begin{document}
+
+% ================================================================
+% Chapter 9 - Outputs and diagnostics
+% ================================================================
+
+\chapter{Output and diagnostics}
+\label{chap:DIA}
+\minitoc
+
+\newpage
+$\ $\newline    % force a new line
+
+\section{SIMIP diagnostics}
+
+The SIMIP protocol \citep{notz_2016} was designed for CMIP6, to standardize sea ice model outputs in climate simulations. We tried to follow the data request as closely as possible. Outputs are in most cases directly managed with XIOS2 in \textbf{limwri.F90}, but not always. In the code, output fields keep their native LIM reference name. 
+
+A corresponding entry exists in \textbf{field\_def\_nemo-lim.xml}, where fields are given their SIMIP specifications (standard name, long name, units). At the end of the file the fields are gathered in the field groups \textbf{SIday\_fields}, \textbf{SImon\_fields} and \textbf{SImon\_scalar} for separation of the daily (SIday) and monthly (SImon) requests. 
+
+In \textbf{file\_def\_nemo-lim.xml}, the daily, monthly and scalar output files are created.
+
+In the reference xml files, the largest possible SIMIP-based diagnostics with LIM are distributed among the field groups. If some fields are to be discarded, the best way to do so is to remove them from the field groups in  field\_def\_nemo-lim.xml.
+
+\subsection{Missing SIMIP fields}
+
+About 90\% of the SIMIP fields can be output. Below is the list of the missing fields and why they are missing. \\
+
+\textbf{1. Fields that are not part of the sea ice representation in LIM3.6}
+\begin{itemize}
+\item sisnconc (snow area fraction), siitdsnconc (snow area fractions in thickness categories);
+\item simpconc (meltpond area fraction), simpmass (melt pond mass per area), simprefrozen (thickness of refrozen ice on ponds);
+\item sirdgconc (ridged ice area fraction), sirdgmass (ridged ice thickness);
+\item sidmasslat (lateral sea ice melt rate);
+\item sndmasswindrif (snow mass change through wind drift of snow);
+\end{itemize}
+
+\textbf{2. Fields which value is trivial}
+\begin{itemize}
+\item sipr (rainfall over sea ice): all rain falls in open water;
+\item sidragtop (atmospheric drag over sea ice): namelist parameter;
+\item sidragbot (oceanic drag over sea ice): namelist parameter
+\end{itemize}
+
+\textbf{3. Fields that belong to the atmospheric component}
+\begin{itemize}
+\item siflswdtop, siflswutop, siflswdbot, sifllwdtop, sifllwutop, siflsenstop, sifllatstop (surface energy budget components)
+\end{itemize}
+
+Ice thickness and snow depth were masked below 5\% ice concentration, because below this value, they become meaninglessly large in LIM. This is notably because of the Prather advection scheme. We hope to fix these issues for our next release. For similar reasons, the ice age is masked below 15\% concentration.
+
+Fluxes through straits and passages were not directly implemented. Instead, ice mass, snow mass, and ice area transports were implemented as 2D arrays, for x- and y- directions. A python script is available to derive the fluxes through straits and passages from full 2D arrays for ORCA2 and eORCA1 grids.
+
+\subsection{Links}
+
+\begin{itemize}
+\item \textcolor{blue}{\href{http://www.geosci-model-dev.net/9/3427/2016/}{Paper of Notz et al}};
+\item \textcolor{blue}{\href{http://clipc-services.ceda.ac.uk/dreq/u/SIMIP.html}{SIMIP CMIP6 data request page}};
+\item \textcolor{blue}{\href{http://www.climate-cryosphere.org/activities/targeted/simip}{SIMIP description on CliC website}}.
+\end{itemize}
+
+\section{Conservation checks}
+
+\end{document}
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_radiative_transfer.tex
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_radiative_transfer.tex	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_radiative_transfer.tex	(revision 11042)
@@ -0,0 +1,210 @@
+
+\documentclass[../main/SI3_manual]{subfiles}
+
+\begin{document}
+
+
+
+
+% ================================================================
+% Chapter 6 Ñ Radiative transfer
+% ================================================================
+
+\chapter{Radiative transfer}
+\label{chap:RAD}
+\minitoc
+
+\newpage
+$\ $\newline    % force a new line
+
+Radiative transfer in SI$^3$ currently reduces to the parameterization of solar radiation partitionning through the snow/ice/open water system, treated using a single wavelength band. This will likely be improved in future versions of the code. In this chapter, we first explain how solar radiation is partionned in the snow-ice system, then describe how, solar radiation-wise, the snow-ice system is framed in the context of the atmosphere-ice-ocean boundary.
+
+\section{Solar radiation partitionning in the snow-ice system}
+
+%--------------------------------------------------------------------------------------------------------------------
+%
+% FIG x : Radiation balance %
+\begin{figure}[!ht]
+\begin{center}
+\vspace{0cm}
+\includegraphics[height=6cm,angle=-00]{radiative_transfer}
+\caption{Partitionning of solar radiation in the snow-ice system, as represented in SI$^3$.}
+\label{fig_radiative_transfer}
+\end{center}
+\end{figure}
+%
+%--------------------------------------------------------------------------------------------------------------------
+
+Solar radiation in the snow-ice system is represented following the principles of \cite{maykut_1971}, see Fig.\ref{fig_radiative_transfer}, using a unique band of solar radiation. Incident solar radiation (W/m$^2$, counted per unit ice area - not per grid cell area) is specified in the SBC routines and is a priori category dependent, because multiple atmosphere-surface reflexions are frequent in polar regions imply that incident radiation depends on the surface albedo and therefore surface state. 
+
+Net solar radiation qsr\_ice(i,j,l) is obtained by substracting the reflected part of the incident radiation using the surface albedo $\alpha(i,j,l)$, parameterized as a function of environmental conditions. 
+
+The subsequent attenuation of solar radiation through the snow-ice system is represented assuming the presence of a highly diffusive surface scattering layer, absorbing a fraction $i_o$ of net solar radiation, which is transformed into sensible heat, contributing to the surface energy balance. 
+
+The remainder of solar radiation, qtr\_ice\_top(i,j,l), is transmitted below the surface and attenuates following Beer-Lambert law. The part of solar radiation that is absorbed on its path to the base of the ice is given as sensible heat to the snow/ice system, via a source term in the heat diffusion equation. The rest of solar radiation that reaches the ice base, qtr\_ice\_bot(i,j,l), is transmitted to the ocean. 
+
+In the rest of this section, we describe how the albedo, the surface transmission parameter $i_o$ and the attenuation of solar radiation are parameterized.
+
+\subsection{Surface albedo}
+
+The surface albedo determines the amount of solar radiation that is reflected by the ice surface, hence also net solar radiation. The philosophy of the parameterization of surface albedo is the following: each ice category has its own albedo value $\alpha(i,j,l)$, determined as a function of cloud fraction, ice thickness, snow depth, melt pond fraction and depth, using observation-based empirical fits. 
+
+The original \cite{shine_1985} parameterization had a few inconsistencies and flaws that the revisited parameterization described hereafter fixes. In particular, the dependencies of albedos on ice thickness, snow depth and cloud fraction have been revised in the light of recent observational constraints \citep{brandt_2005,grenfell_2004}. In addition, the asymptotic properties of albedo are better specified and now fully consistent with oceanic values. Finally, the effect of melt ponds has been included \citep{lecomte_2015}.
+
+The user has control on 5 reference namelist values, which describe the asymptotic values of albedo of snow and ice for dry and wet conditions, as well as the deep ponded-ice albedo. Observational surveys, in particular during SHEBA in the Arctic \citep{perovich_2002} and further additional experiments \citep{grenfell_2004}, as well as by \cite{brandt_2005} in the Antarctic, have provided relatively strong constraints on the surface albedo. In this context, the albedo can hardly be used as the main model tuning parameter, at least outside of these observation-based bounds (see namalb for reference values).
+
+\nlst{namalb}
+
+%--------------------------------------------------------------------------------------------------------------------
+%
+% FIG x : cloud correction
+%
+\begin{figure}[ht]
+\begin{center}
+\vspace{0cm}
+\includegraphics[height=10cm,angle=-00]{albedo_cloud_correction}
+\caption{Albedo correction $\Delta \alpha$ as a function of overcast sky (diffuse light) albedo $\alpha_os$, from field observations \cite[][their Table 3]{grenfell_2004} (squares) and 2nd-order fit (Eq. \ref{eq_albedo_cloud_correction}). Red squares represent the irrelevant data points excluded from the fit. For indication, the amplitude of the correction used in the ocean component is also depicted (blue circle).}
+% ocean uses 0.06 for overcast sky (Payne 74) and Briegleb and Ramanathan parameterization
+\label{fig_albedo_cloud_correction}
+\end{center}
+\end{figure}
+%
+%--------------------------------------------------------------------------------------------------------------------
+
+Because the albedo is not an intrinsic optical property, it depends on the type of light (diffuse of direct), which is practically handled by weighting the clear (cs) and overcast (os) skies values by cloud fraction $c(i,j)$ \citep{fichefet_1997}:
+\begin{equation}
+\alpha(i,j,l) = [ 1 - c(i,j) ] \cdot \alpha_{cs} (i,j,l) + c (i,j) \cdot \alpha_{os}(i,j,l).
+\end{equation}
+For concision, we drop the spatial and category indices hereafter. \cite{grenfell_2004} observations at Point Barrow, on the Alaskan Coast, suggest that clear and overcast sky albedos are directly related through
+\begin{equation}
+\alpha_{cs} = \alpha_{os} - \Delta \alpha(\alpha_{os}).
+\end{equation}
+The relation between $\Delta \alpha$ and $ \alpha_{os}$ can well be handled using a 2$^{nd}$-order polynomial fit (Fig. \ref{fig_albedo_cloud_correction}):
+\begin{equation}
+\Delta \alpha =  ( -0.1010 \cdot \alpha_{os}^2 + 0.1933 \cdot \alpha_{os} - 0.0148 ).
+\label{eq_albedo_cloud_correction}
+\end{equation}
+Overcast sky surface albedo is used as a reference, from which the clear-sky value is derived.
+
+%--------------------------------------------------------------------------------------------------------------------
+%
+% FIG x : thickness, snow depth, pond depth dependencies
+%
+\begin{figure}[ht]
+\begin{center}
+\vspace{0cm}
+\includegraphics[height=4cm,angle=-00]{albedo_dependencies}
+\caption{Example albedo dependencies on ice thickness, snow depth and pond depth, as parameterized in SI$^3$.}
+\label{fig_albedo_dependencies}
+\end{center}
+\end{figure}
+%
+%--------------------------------------------------------------------------------------------------------------------
+
+The second important parameter that controls surface albedo is surface type. In each category, we assume that three types of surfaces can coexist (bare, snow-covered and ponded ice), with respective fractions $f_{ice}$, $f_{snw}$ and $f_{pnd}$ summing to 1. Then the overcast albedo is expressed as
+\begin{equation}
+\alpha_{os}(i,j,l) = f_{ice} \cdot \alpha_{ice} + f_{snw} \cdot \alpha_{snw} + f_{pnd}\cdot \alpha_{pnd}
+\end{equation}
+with a specific albedo value for each surface type. 
+
+The surface fractions $f_{ice}$, $f_{snw}$ and $f_{pnd}$ are currently crudely parameterized: if snow is present ($h_s>0$), then $f_{snw}=1$ and $f_{ice}=f_{pnd}=0$. In the absence of snow, $f_{pnd}$ is either specified or calculated (depending on melt pond options in nampnd), and $f_{ice}=1.-f_{pnd}$. Admittedly, more refined parameterizations of $f_{snw}$ could improve the realism of the model. Note finally that the dependence of surface albedo on the presence of melt ponds can be included or not (namelist parameter ln\_pnd\_alb). If the latter is set to false, $f_{pnd}$ is always assumed zero in the albedo computations.
+
+Works by \cite{brandt_2005} and references therein, indicate that the dependence of the albedo of bare ice on ice thickness depends is linear/logarithmic/constant from thin to thick ice. Hence, the following expressions capture  the essence of their works:
+\begin{eqnarray}
+\alpha_{ice} = 
+\begin{cases}
+\alpha_{ice}^{\infty} & \text{ if } h_i > 1.5, \\
+\alpha_{ice}^{\infty} + ( 0.18 - \alpha_{ice}^{\infty} ) \cdot \frac{ln(1.5) - ln(h_i)}{ln(1.5) - ln(0.05)} & \text{ if } 0.05 < h_i ,<= 1.5 \\
+\alpha_{oce}  + ( 0.18 - \alpha_{oce} ) h_i /0.05 & \text{ if } h_i < 0.05.
+\end{cases}
+\end{eqnarray}
+The thick-ice constant albedo value depends on whether the surface is dry or melting:
+\begin{eqnarray}
+\alpha_{ice}^{\infty} =
+\begin{cases}
+\alpha_{i,dry} & \text{ if } T_{su} < T_{fr} \\
+\alpha_{i,mlt} & \text{ if } T_{su} = T_{fr},
+\end{cases}
+\end{eqnarray}
+values that are to be specified from the namelist.
+
+\cite{grenfell_2004} suggest that the dependence of surface albedo on snow depth is exponential,
+\begin{eqnarray}
+\alpha_{snw} = \alpha_{snw}^{\infty} - ( \alpha_{snw}^{\infty} - \alpha_{ice} ) * exp( -h_s / h_s^{ref} ),
+\end{eqnarray}
+where $h_s^{ref} = 0.02$ $(0.03)$ m for dry (wet) snow. As for bare ice, the deep-snow asymptotic albedo also depends on whether the surface is dry or melting:
+\begin{eqnarray}
+\alpha_{snw}^{\infty} =
+\begin{cases}
+\alpha_{s,dry} & \text{ if } T_{su} < T_{fr} \\
+\alpha_{s,mlt} & \text{ if } T_{su} = T_{fr},
+\end{cases}
+\end{eqnarray}
+values that are to be specified from the namelist.
+
+Based on ideas developed from melt ponds on continental ice \citep{zuo_1996}, the albedo of ponded ice was proposed to follow \citep{lecomte_2011}:
+\begin{eqnarray}
+\alpha_{pnd} = \alpha_{dpnd} - ( \alpha_{dpnd} -\alpha_{ice} ) \cdot exp( -h_{pnd} / 0.05 )
+\end{eqnarray}
+$\alpha_{dpnd}$ is a namelist parameter. \cite{ebert_1993} also use such dependency for their multi-spectral albedo.
+
+The dependencies of surface albedo on ice thickness, snow depth and pond depth are illustrated in Fig. \ref{fig_albedo_dependencies}.
+
+\subsection{Transmission below the snow/ice surface}
+
+The transmitted solar radiation below the surface is represented following \cite{fichefet_1997} and \cite{maykut_1971}:
+\begin{eqnarray}
+qtr\_ice\_top(i,j,l) = i_o(i,j) qsr\_ice(i,j,l),
+\end{eqnarray}
+where $i_o=0$ in presence of snow, and depends on cloud fraction otherwise, based on works of \cite{grenfell_1977}. This parameterization needs to be re-evaluated and likely updated.
+
+\subsection{Attenuation and transmission below the ice/ocean interface}
+
+Attenuation of solar radiation through the ice follows Beer-Lambert law. In practise, we assume that irradiance below layer $k$ is given by
+
+\begin{eqnarray}
+radtr\_i(i,j,k,l) = qtr\_ice\_top(i,j,l) \cdot exp(-\kappa_i z),
+\end{eqnarray}
+where $\kappa_i = 1$ m$^{-1}$ is the exponential attenuation coefficient (namelist parameter rn\_kappa\_i). Hence, at the ice base, remains below the $l^{th}$ category a transmitted flux: 
+\begin{eqnarray}
+qtr\_ice\_bot(i,j,l) = qtr\_ice\_top(i,j,l) \cdot exp(-\kappa_i h_i).
+\end{eqnarray}
+
+\section{Solar radiation: framing sea ice at the ocean-atmosphere boundary}
+
+How solar radiation transfer through sea ice is framed into the atmosphere-ice-ocean is nearly identical but not exactly the same in forced and coupled mode (see Fig. \ref{fig_radiative_transfer}.
+
+The basic principle of the computation is that the irradiant flux given to the ocean model (qsr) is computed as the average flux per grid cell area (qsr\_tot) minus what is given to the sea ice ($\sum a(l) qsr\_ice(l)$), plus what is transmitted below sea ice $\sum$ qtr\_ice\_bot(jl) (see at the base of Fig. \ref{fig_radiative_transfer}). Such formulation ensures heat conservation by construction.
+
+%--------------------------------------------------------------------------------------------------------------------
+%
+% FIG x : Radiation balance %
+\begin{figure}[!ht]
+\begin{center}
+\vspace{0cm}
+\includegraphics[height=8cm,angle=-00]{radiation_atm_ice_oce}
+\caption{Framing solar radiation transfer through sea ice into the atmosphere-ice-ocean context.}
+% ocean uses 0.06 for overcast sky (Payne 74) and Briegleb and Ramanathan parameterization
+\label{fig_radiative_transfer}
+\end{center}
+\end{figure}
+%
+%--------------------------------------------------------------------------------------------------------------------
+
+\subsection{Forced mode}
+
+In forced-atmosphere mode, it is the incoming solar irradiance fluxes above the ocean and sea ice (categories) that are specified (from files) or computed (from bulk formulae), and constitute the basis of solar radiation transfer computations. Then the net solar fluxes above open water (qsr\_oce) and ice categories (qsr\_ice) are obtained by multiplication by $1-\alpha$. qsr\_tot is then diagnosed as a weighted sum of qsr\_oce and the qsr\_ice(jl)'s.
+
+\subsection{Coupled mode}
+
+In coupled-atmosphere mode, qsr\_tot and qsr\_ice have to be provided by the atmospheric model, whereas qsr\_oce is diagnosed from qsr\_ice and qsr\_tot.
+
+Some atmospheric models enable \textit{tiling} and can provide solar fluxes over individual ice categories. For such atmospheric models, net solar radiation fluxes are directly useable by SI$^3$ (nn\_flxdist =  -1). Other models cannot do tiling, being only able to provide a net solar flux above all ice categories, seen as a single surface type. For such models a first option is to give the net solar flux above sea ice identically to all sea ice categories (nn\_flxdist = 0). Yet a better option is to redistribute the mean solar flux above sea ice $< qsr_ice >$ above categories (nn\_flxdist = 2) using the following scaling, conserving heat by construction:
+
+\begin{eqnarray}
+qsr\_ice(jl) = < qsr\_ice > \frac{1 - \alpha(jl)}{1 - < \alpha >}
+\end{eqnarray}
+
+where $ < \alpha >$ is the albedo averaged over the ice categories. Note that for testing, the flux redistributor can be emulated in forced mode (nn\_flxdist = 1).
+
+\end{document}
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_ridging_rafting.tex
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_ridging_rafting.tex	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_ridging_rafting.tex	(revision 11042)
@@ -0,0 +1,156 @@
+
+\documentclass[../main/SI3_manual]{subfiles}
+
+\begin{document}
+
+% ================================================================
+% Chapter 5 Ñ Ridging and rafting
+% ================================================================
+
+\chapter{Ridging and rafting}
+\label{chap:RDG}
+\minitoc
+
+\newpage
+$\ $\newline    % force a new line
+
+This chapter focuses on how LIM solves the red part of the general equation:
+\begin{equation}
+\frac{\partial X}{\partial t} = - \nabla .(\mathbf{u} X)  \color{black} \Theta^X  + \color{red} \Psi^X,
+\label{eq:Xt}
+\end{equation}
+where $X$ refers to any global sea ice state variable.
+
+Divergence and shear open the ice pack and create ice of zero thickness. Convergence and shear consumes thin ice and create thicker ice by mechanical deformation. The redistribution functions $\Psi^X$ describe how opening and mechanical deformation redistribute the global ice state variables into the various ice thickness categories. 
+
+The fundamental redistribution function is $\Psi^g$, which accounts for area redistribution. The other redistribution functions $\Psi^X$ associated with other state variables will derive naturally. The redistribution function $\Psi^g$ should first ensure area conservation. By integrating the evolution equation for $g(h)$ over all thicknesses, recalling that $\int_0^\infty g(h) = 1$, and that the total areal change due to thermodynamics must be zero, e.g. $\int_0^\infty \partial (fg) / \partial h=0$, then the area conservation reads: 
+\begin{equation}
+\int_0^\infty h \Psi^g dh = \nabla \cdot \mathbf{u}.
+\end{equation}
+
+Second, we must say something about volume conservation, and this will be done more specifically later. Following \cite{thorndike_1975}, we separate the $\Psi^X$'s into \textbf{(i)} \textit{dynamical inputs}, \textbf{(ii)} \textit{participation functions}, i.e., how much area of ice with a given thickness participates to mechanical deformation \textbf{(iii)} \textit{transfer functions}, i.e., where in thickness space the ice is transferred after deformation.
+
+\section{Dynamical inputs}
+
+A general expression of $\Psi^g$, the mechanical redistribution function associated to the ice concentration, was proposed by \cite{thorndike_1975}:
+\begin{equation}
+\Psi^g = \vert \dot{\epsilon} \vert [ \alpha_o(\theta) \delta(h) + \alpha_d(\theta) w_d(h,g) ],
+\label{eq:psi}
+\end{equation}
+which is convenient to separate the dependence in $\mathbf{u}$ from those in $g$ and $h$. The first and second terms on the right-hand side correspond to opening and deformation, respectively. $\vert \dot{\epsilon} \vert = (\dot{\epsilon}_{I}^2+ \dot{\epsilon}_{II}^2)^{1/2}$, where $\dot{\epsilon}_{I}=\nabla \cdot \mathbf{u}$ and $\dot{ \epsilon}_{II}$ are the strain rate tensor invariants; $\theta=\textrm{atan}(\dot{\epsilon_{II}} / \dot{\epsilon_{I}} )$. $w_d(h,g)$, the deformation mode will be discussed in the next section. $\vert \dot{\epsilon} \vert \alpha_o$ and $\vert \dot{\epsilon} \vert \alpha_d$ are called the lead opening and closing rates, respectively.
+
+The \textbf{dynamical} inputs of the mechanical redistribution in LIM are:
+\begin{itemize}
+\item $\vert \dot{\epsilon} \vert \alpha_o$, the opening rate,
+\item $\vert \dot{\epsilon} \vert \alpha_d$, the net closing rate.
+\end{itemize}
+Following \cite{thorndike_1975}, we choose $\int_0^\infty w_d(h,g) = - 1$. In order to satisfy area conservation, the relation $\vert \dot{\epsilon} \vert \alpha_o - \vert \dot{\epsilon} \vert \alpha_d = \nabla \cdot \mathbf{u}$ must be verified. In the model, there are two ways to compute the divergence of the velocity field. A first way is to use the velocity components ($\dot{\epsilon}_I = \nabla \cdot \mathbf{u}\vert^{rhg}$) as computed after the rheology (superscript $rhg$). Another way is to derive it from the horizontal transport of ice concentration and open water fraction. In principle, the equality $A^o + \sum_{l=1}^L g^i_L = 1$ should always be verified. However, after ice transport (superscript $trp$), this is not the case, and one can diagnose a velocity divergence using the departure from this equality: $\nabla \cdot \mathbf{u}\vert^{trp} = ( 1 - A^o - \sum_{l=1}^L g^i_L )/ \Delta t$. In general, we will use $\dot{\epsilon}_I$ unless otherwise stated.
+
+The \textbf{net closing rate} is written as a sum of two terms representing the energy dissipation by shear and convergence \citep{flato_1995}:
+\begin{equation}
+\vert \dot{\epsilon} \vert \alpha_d (\theta) = C_s \frac{1}{2} ( \Delta - \vert \dot{\epsilon}_I \vert) - \textrm{min} (\dot{\epsilon}_I,0),
+\end{equation}
+where $\Delta$ is a measure of deformation (defined in the rheology section). The factor $C_s=0.5$ (\textit{Cs} in \textit{namelist\_ice}) is added to allow for energy sinks other than ridge building (e.g., sliding friction) during shear. In case of convergence, the closing rate must be large enough to satisfy area conservation after ridging, so we take:
+\begin{equation}
+\vert \dot{\epsilon} \vert \alpha_d (\theta) = \text{max}(\vert \dot{\epsilon} \vert \alpha_d (\theta), - \nabla \cdot \mathbf{u} \vert^{trp}) \quad \text{if } \nabla \cdot \mathbf{u} < 0.
+\end{equation}
+
+The \textbf{opening rate} is obtained by taking the difference:
+\begin{equation}
+\vert \dot{\epsilon} \vert \alpha_o = \vert \dot{\epsilon} \vert \alpha_d = \nabla \cdot \mathbf{u}\vert^{trp}
+\end{equation}
+
+\section{The two deformation modes: ridging and rafting}
+
+The deformation mode is separated into ridging $w^{ri}$ and rafting $w^{ra}$ modes:
+\begin{equation}
+w^d(h,g) = w^{ri}(g,h) + w^{ra}(g,h).
+\end{equation}
+
+\textbf{Rafting} is the piling of two ice sheets on top of each other. Rafting doubles the participating ice thickness and is a volume-conserving process. \cite{babko_2002} concluded that rafting plays a significant role during initial ice growth in fall, therefore we included it into the model. 
+
+\textbf{Ridging} is the piling of a series of broken ice blocks into pressure ridges. Ridging redistributes participating ice on a various range of thicknesses. Ridging does not conserve ice volume, as pressure ridges are porous. Therefore, the volume of ridged ice is larger than the volume of new ice being ridged. In the model, newly ridged is has a prescribed porosity $p=30\%$ (\textit{ridge\_por} in \textit{namelist\_ice}), following observations \citep{lepp_ranta_1995,h_yland_2002}. The importance of ridging is now since the early works of \citep{thorndike_1975}.
+
+The deformation modes are formulated using \textbf{participation} and \textbf{transfer} functions with specific contributions from ridging and rafting:
+\begin{equation}
+w_d(h,g) = - [ b^{ra}(h) + b^{ri}(h) ] g(h) + n^{ra}(h)+n^{ri}(h).
+\label{eq:wd}
+\end{equation}
+$b^{ra}(h)$ and $b^{ri}(h)$ are the rafting and ridging participation functions. They determine which regions of the ice thickness space participate in the redistribution. $n^{ra}(h)$ and $n^{ri}(h)$, called transfer functions, specify how thin, deformation ice is redistributed onto thick, deformed ice. Participation and transfer functions are normalized in order to conserve area.
+
+\section{Participation functions}
+
+We assume that the participation of ice in redistribution does not depend upon whether the deformation process is rafting or ridging. Therefore, the participation functions can be written as follows:
+\begin{equation}
+b^{ra}(h)= \beta(h) b(h),
+\label{eq:bra}
+\end{equation}
+\begin{equation}
+b^{ri}(h) = [1-\beta(h)] b(h),
+\label{eq:bri}
+\end{equation}
+where $b(h)$ is an exponential weighting function with an e-folding scale $a*$ \citep{lipscomb_2007} (\textit{astar} in \textit{namelist\_ice}) which preferentially apportions the thinnest available ice to ice deformation:
+\begin{equation}
+b(h) = \frac{\text{exp} [ - G(h) / a^\star ]}{a^\star[1-\text{exp}(-1/a^\star)]} ,
+\end{equation}
+It is numerically more stable than the original version of \cite{thorndike_1975}. This scheme is still present in the code and can be activated using \textit{partfun\_swi} from \textit{namelist\_ice}, with the associated parameter \textit{Gstar}.
+
+$\beta(h)$ partitions deformation ice between rafted and ridged ice. $\beta(h)$ is formulated following \cite{haapala_2000}, using the \cite{parmerter_1975} law, which states that, under a critical participating ice thickness $h_P$, ice rafts, otherwise it ridges:
+\begin{equation}
+\beta(h)= \frac{ \textrm{tanh} [ -C_{ra} (h-h_P) ] + 1 } {2},
+\end{equation}
+where $C_{ra}=5$ m$^{-1}$ (\textit{Craft} in \textit{namelist\_ice})  and $h_P=0.75$ m (\textit{hparmeter} in \textit{namelist\_ice}) \citep{haapala_2000,babko_2002}. The $tanh$ function is used to smooth the transition between ridging and rafting.  If namelist parameter \textit{raftswi} is set to 0, ice only ridges and does not raft. 
+
+\section{Transfer functions}
+
+The rafting transfer function assumes a doubling of ice thickness :
+\begin{equation}
+n^{ra}(h)=\frac{1}{2}\int_0^\infty \delta(h-2h') b(h') g(h') dh,
+\end{equation}
+where $\delta$ is the Dirac delta function. 
+
+The ridging transfer function is :
+\begin{equation}
+n^{ri}(h)=\int_0^\infty \gamma(h',h) (1+p) b(h') g(h') dh.
+\label{eq:nri}
+\end{equation}
+The redistributor $\gamma(h',h)$ specifies how area of thickness $h'$ is redistributed on area of thickness $h$. We follow \citep{hibler_1980} who constructed a rule, based on observations, that forces all ice participating in ridging with thickness $h'$ to be linearly distributed between ice that is between $2h'$ and $2\sqrt{H^*h'}$ thick, where $H^\star=100$ m (\textit{Hstar} in \textit{namelist\_ice}). This in turn determines how to construct the ice volume redistribution function $\Psi^v$. Volumes equal to participating area times thickness are removed from thin ice. They are redistributed following Hibler's rule. The factor $(1+p)$ accounts for initial ridge porosity $p$ (\textit{ridge\_por} in \textit{namelist\_ice}, defined as the fractional volume of seawater initially included into ridges. In many previous models, the initial ridge porosity has been assumed to be 0, which is not the case in reality since newly formed ridges are porous, as indicated by in-situ observations \citep{lepp_ranta_1995,h_yland_2002}. In other words, LIM3 creates a higher volume of ridged ice with the same participating ice.
+
+For the numerical computation of the integrals, we have to compute several temporary values:
+\begin{itemize}
+\item The thickness of rafted ice $h^{ra}_l = 2 h^i_l$
+\item The mean thickness of ridged ice $h^{ri,mean}_l=\text{max} ( \sqrt{H^\star h^i_l} , h^i_l \cdot 1.1 )$
+\item The minimum thickness of ridged ice $h^{ri,min}_l = \text{min} [ 2*h^i_l, 0.5\cdot(h^{ri,mean}_l+h^i_l) ]$
+\item The maximum thickness of ridged ice $h^{ri,min}_l = 2 h^{ri,mean}_l - h^{ri,min}_l$
+\item The mean rate of thickening of ridged ice $k^{ri}_l = h^{ri,mean}_l / h^{i}_l$
+\end{itemize}
+
+\section{Ridging shift}
+
+%\textit{Subroutine}: \textbf{lim\_itd\_ridgeshift}
+
+The numerical computation of the impact of mechanical redistribution on ice concentration involves:
+\begin{itemize}
+\item A normalization factor that ensures volume conservation (\textit{aksum})
+\item The removal of ice participating in deformation (including the closing of open water)
+\item The addition of deformed ice
+\end{itemize}
+
+For ice concentrations, the numerical procedure reads:
+\begin{equation}
+\Delta g^i_l = C^{net} \Delta t \biggr [ - ( b^{ri}_l + b^{ra}_l) + \sum_{l_2=1}^L \biggr ( f^{ra}_{l,l_2}  \frac{b^{ra}_{l_2}}{k^{ra}} + f^{ri}_{l,l_2} \frac{ b^{ri}_{l_2} }{k^{ri}_{l_2}} \biggr ) \biggr ]
+\end{equation}
+\begin{itemize}
+\item $C^{net}$ is the normalized closing rate ($\vert \dot{\epsilon} \vert \alpha^d/\textit{aksum}$)
+\item $b^{ri}_l$ and $b^{ra}_l$ are the area participating into redistribution for category $l$
+\item $f^{ra}_{l,l_2}$ and $f^{ri}_{l,l_2}$ are the fractions of are of category $l$ being redistributed into category $l_2$
+\item $k^{ra}$ is the rate of thickening of rafted ice (=2)
+\end{itemize}
+
+Because of the nonlinearities involved in the integrals, the ridging procedure has to be iterated until $A^\star = A^{ow} + \sum_{l=1}^L g^i_l = 1$.
+
+\section{Mechanical redistribution for other global ice variables}
+
+The other global ice state variables redistribution functions $\Psi^X$ are computed based on $\Psi^g$ for the ice age content and on $\Psi^{v^i}$ for the remainder (ice enthalpy and salt content, snow volume and enthalpy). The general principles behind this derivation are described in Appendix A of \cite{bitz_2001}. A fraction $f_s=0.5$ (\textit{fsnowrdg} and \textit{fsnowrft} in \textit{namelist\_ice}) of the snow volume and enthalpy is assumed to be lost during ridging and rafting and transferred to the ocean. The contribution of the seawater trapped into the porous ridges is included in the computation of the redistribution of ice enthalpy and salt content (i.e., $\Psi^{e^i}$ and $\Psi^{M^s}$). During this computation, seawater is supposed to be in thermal equilibrium with the surrounding ice blocks. Ridged ice desalination induces an implicit decrease in internal brine volume, and heat supply to the ocean, which accounts for ridge consolidation as described by \cite{h_yland_2002}. The inclusion of seawater in ridges does not imply any net change in ocean salinity. The energy used to cool down the seawater trapped in porous ridges until the seawater freezing point is rejected into the ocean.
+
+\end{document}
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_single_category_use.tex
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_single_category_use.tex	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_single_category_use.tex	(revision 11042)
@@ -0,0 +1,22 @@
+
+\documentclass[../main/SI3_manual]{subfiles}
+
+\begin{document}
+
+% ================================================================
+% Chapter 10 Ñ Single-category use
+% ================================================================
+
+\chapter{Using SI$^3$ with a single category}
+
+\label{chap:INT}
+\minitoc
+
+\newpage
+$\ $\newline    % force a new line
+
+\section{Enhanced conduction}
+\section{Virtual thin ice melting (fake lateral melting)}
+\section{Ridging and rafting with a single ice category}
+
+\end{document}
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_thermo.tex
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_thermo.tex	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_thermo.tex	(revision 11042)
@@ -0,0 +1,88 @@
+\documentclass[../main/SI3_manual]{subfiles}
+
+\begin{document}
+
+% ================================================================
+% Chapter 7 Ñ Ice thermodynamics
+% ================================================================
+
+\chapter{Ice thermodynamics}
+\label{chap:THD}
+\minitoc
+
+\newpage
+$\ $\newline    % force a new line
+
+
+% ================================================================
+% Thermodynamics % ================================================================
+
+Mass, energy and salt are intertwined for sea ice. Referred to as thermodynamics, or more exactly halo-thermodynamics. Mushy-layer theory.
+
+\section{Open water and new ice formation}
+
+% There is everything in here, but there are too much details.
+% Move things around into chapters and summarize.
+
+As part of the sea ice computations, a heat budget of the uppermost oceanic level is estimated. This heat budget is used if negative to compute the production of new ice or, if positive, for bottom melting. 
+
+%--------------------------------------------------------------------------------------------------------------------
+%
+% FIG x : Open water energy budget
+%
+\begin{figure}[ht]
+\begin{center}
+\vspace{0cm}
+\includegraphics[height=10cm,angle=-00]{Openwater_eb}
+\caption{Scheme of the estimate of the heat budget of the first ocean level.}
+\label{fig_yield}
+\end{center}
+\end{figure}
+%
+%--------------------------------------------------------------------------------------------------------------------
+
+We estimate the heat budget of the first ocean level ($B^{opw}$) assuming four contributions, namely:
+\begin{itemize}
+\item The absorption of a fraction $f_1^{qsr}$ of solar radiation (given by radiative transfer component of the ocean model);
+\item The non-solar heat flux absorbed at the surface;
+\item The sensible heat content of precipitation
+\item The sensible heat loss to the sea ice
+\end{itemize}
+The estimated heat budget thus reads:
+\begin{linenomath}
+\begin{align}
+B^{opw} = Q^{sr} ( 1 - A ) f_1^{qsr} + Q^{ns} ( 1 - A ) + Q^{emp} - A F_w,
+\end{align}
+\end{linenomath}
+Hence there is no consideration of the entrainment of heat at the base of the first ocean level, or of solar radiation transmitted below the ice. The ocean-to-ice turbulent sensible heat flux is formulated following \citep{mcphee_1992}
+\begin{linenomath}
+\begin{align}
+F_w = \rho_0 c_w C_h u^* ( SST - T_b )
+\end{align}
+\end{linenomath}
+where $\rho_0$ is the reference ocean density, $c_w$ is the seawater specific heat, $C_h = 7.5 \times 10^{-3}$ is a heat transfer coefficient, and $u^*=\sqrt{\tau_{iw}/\rho_0}$. There are two additional conditions, the oceanic heat flux cannot be negative. Second, $F_w$ cannot exceed the heat content of the first ocean level.
+
+% Ice growth
+If the $B^{opw}$ is such that the SST would decrease below the freezing point, the remainder of the heat is used to form new ice. The heat loss is converted into mass through [\ref{eq_phasechange}], giving by multiplication by density a volume of new ice $v_0$. The thickness $h_0$ of the new ice grown during a sea ice time step depends on unresolved small currents and waves and is prescribed. The fraction $a_0=v_0/h_0$ is computed accordingly. The salinity of this new ice $S_0$ is given by the S-h empirical relationship of \cite{kovacs_1996}. The temperature assumed for this new ice is the local freezing point.
+
+% Ice melt
+If there is ice in the grid cell and that the $B^{opw}$ is positive, it is directly given attributed to the heat available for bottom melting. This argument follows from \cite{maykut_1995}, who found that most of solar heat absorbed in the surface waters is converted into melting. In practise, this means that the SST cannot go above freezing as long ice is present.
+
+The heat loss used for ice formation, heat gain used to melt ice and the sensible heat given by the ocean to the ice, are all removed from the non-solar heat flux transmitted to the ocean.
+
+Because ice dynamics are not able to maintain the small amount of open water that is observed, a maximum ice fraction ($amax, <1$) is prescribed.
+
+\section{Diffusion of heat}
+
+\section{Vertical growth and melt}
+
+\section{Desalination}
+
+\section{Remapping}
+
+\section{Transport in thickness space}
+
+\section{True lateral melting}
+
+\end{document}
+
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_transport.tex
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_transport.tex	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/chap_transport.tex	(revision 11042)
@@ -0,0 +1,27 @@
+
+\documentclass[../main/SI3_manual]{subfiles}
+
+\begin{document}
+
+% ================================================================
+% Chapter 4 Ñ Ice transport
+% ================================================================
+
+\chapter{Ice transport}
+\label{chap:TRP}
+\minitoc
+
+\newpage
+$\ $\newline    % force a new line
+
+As soon as ice dynamics are activated (\textit{ln\_dyn\_xxx}), all extensive state variables are to be advected following the horizontal velocity field.
+
+\section{Second order moments conserving (Prather 1986) scheme (\textit{ln\_adv\_Pra})}
+
+The scheme of  \cite{prather_1986} explicitly computes the conservation of second-order moments of the spatial distribution of global sea ice state variables. This scheme preserves positivity of the transported variables and is practically non-diffusive. It is also computationally expensive, however it allows to localize the ice edge quite accurately. As the scheme is conditionally stable, the time step is split into two parts if the ice drift is too fast, based on the CFL criterion. 
+
+State variables per unit grid cell area are first multiplied by grid cell area. Then, for each state variable, the 0$^{th}$ (mean), 1$^{st}$ (x, y) and 2$^{nd}$ (xx, xy, yy) order moments of the spatial distribution are transported. At 1st time step, all moments are zero (if prescribed initial state); or read from a restart file, and then evolve through the course of the run. Therefore, for each global variable, 5 additional tracers have to be kept into memory and written in the restart file, which significantly increases the required memory. Advection following x and y are computed independently. The succession order of x- and y- advection is reversed every day.
+
+\section{5$^{th}$ order flux-corrected transport scheme (UM5)}
+
+\end{document}
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/introduction.tex
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/introduction.tex	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/introduction.tex	(revision 11042)
@@ -0,0 +1,59 @@
+
+% ================================================================
+% INTRODUCTION
+% ================================================================
+
+\chapter*{Introduction}
+
+\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.
+
+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). 
+
+% 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{lepp_ranta_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. 
+
+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 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 Energy, mass and salt must be conserved as much as possible.
+\end{itemize}
+
+This manual is organised as follows. \\
+
+List of chapters... \\
+
+There are no more CPP keys in the code. \\
+
+Namelists and output management follow NEMO guidelines. \\
+
+Changes between releases. \\
+
+The list of people that should be acknowledged is too long, but a great number of people or more exactly a number of great people contributed to the code and should be gratefully acknowledged. As for today,
+the SIWG members are \textit{(July 2018)}.
+
+\begin{itemize}
+\begin{footnotesize}
+\item Yevgeny Aksenov (NOCS, Southampton, UK)
+\item Ed Blockley (Met Office, Exeter, UK, co-chair)
+\item Matthieu Chevallier (CNRM-GAME, M\'et\'eo France, Toulouse)
+\item Danny Feltham (CPOM, Reading, UK)
+\item Thierry Fichefet (UCL, Louvain-la-Neuve, Belgium)
+\item Gilles Garric (Mercator-Oc\'ean, Toulouse, France)
+\item Paul Holland (BAS, Cambridge, UK)
+\item Dorotea Iovino (CMCC, Bologna, Italy)
+\item Gurvan Madec (LOCEAN, CNRS, Paris, France)
+\item Fran\c cois Massonnet (UCL, Louain-la-Neuve, Belgium)
+\item Jeff Ridley (Met Office, Exeter, UK)
+\item Cl\'ement Rousset (LOCEAN, CNRS, Paris, France)
+\item David Salas (CNRM-GAME, M\'et\'eo France, Toulouse)
+\item David Schroeder (CPOM, Reading, UK)
+\item Steffen Tietsche (ECMWF, Reading, UK)
+\item Martin Vancoppenolle (LOCEAN, CNRS, Paris, France, co-chair) 
+\end{footnotesize}
+\end{itemize}
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/todolist.tex
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/todolist.tex	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/SI3/subfiles/todolist.tex	(revision 11042)
@@ -0,0 +1,56 @@
+\documentclass[../main/SI3_manual]{subfiles}
+
+\begin{document}
+
+% ================================================================
+% Dummy Chapter - To do list
+% ================================================================
+
+\chapter*{To-do-list for documentation}
+\label{chap:TDL}
+
+\begin{itemize}
+
+\item \textcolor{gray}{Documentation infrastructure ready by Jul 19, 2018.}
+
+\item \textcolor{gray}{Abstract: v1 written.}
+
+\item \textcolor{gray}{Disclaimer: v1 written.}
+
+\item Introduction: list of chapters and change between realeases to be written (1h)
+
+\item \textcolor{gray}{1. Model basics: v1 written.}
+
+\item \textcolor{gray}{Add namelist infrastructure as in NEMO doc (done)}
+
+\item \textcolor{gray}{2. Time, space and thickness space domain}
+
+\item 3. Ice dynamics: to be written (Clem \& Martin, 3h)
+
+\item 4. Ice transport: UM5 description to be written (Clem, 3h)
+
+\item 5. Ridging and rafting: V1 from previous doc. Should be refreshed. A bit too long. All namelist parameters are not explained (namdyn\_rdgrft).
+
+\item \textcolor{gray}{6. Radiative transfer: Full rewriting required (Martin \& Clem, 3-6h). Available elements from previous documentation, but mostly obsolete.}
+
+\item 7. Thermodynamics: Lots of rewriting required. Available elements from previous documentation, but mostly obsolete (Martin, 6h)
+
+\item 8. Interfaces: Full writing required 
+
+\item 9. Output and diagnostics: Full writing required
+
+\item 10. Single category (Martin, 3h). Full writing required.
+
+\item 11. BDY-AGRIF (Clem, 3h). Full writing required.
+
+\item 12. Miscellaneous. Full writing required.
+
+\item Melt ponds are not currently considered in the plan.
+
+\item Make sure all namelist parameters are properly described.
+
+\item Peer-review by SIWG members.
+
+\end{itemize}
+
+\end{document}
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/TOP/main/TOP_manual.bib
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/TOP/main/TOP_manual.bib	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/TOP/main/TOP_manual.bib	(revision 11042)
@@ -0,0 +1,619 @@
+
+@Article{	  ahn_2007,
+  author	= {Ahn, Jinho and Brook, Edward J.},
+  title		= {Atmospheric CO2and climate from 65 to 30 ka B.P.},
+  year		= 2007,
+  volume	= 34,
+  number	= 10,
+  month		= {May},
+  issn		= {0094-8276},
+  doi		= {10.1029/2007gl029551},
+  url		= {http://dx.doi.org/10.1029/2007GL029551},
+  journal	= {Geophysical Research Letters},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  ahn_2008,
+  author	= {Ahn, J. and Brook, E. J.},
+  title		= {Atmospheric CO2 and Climate on Millennial Time Scales
+		  During the Last Glacial Period},
+  year		= 2008,
+  volume	= 322,
+  number	= 5898,
+  month		= {Oct},
+  pages		= {83–85},
+  issn		= {1095-9203},
+  doi		= {10.1126/science.1160832},
+  url		= {http://dx.doi.org/10.1126/science.1160832},
+  journal	= {Science},
+  publisher	= {American Association for the Advancement of Science
+		  (AAAS)}
+}
+
+@Article{	  armstrong_2001,
+  author	= {Armstrong, Robert A. and Lee, Cindy and Hedges, John I.
+		  and Honjo, Susumu and Wakeham, Stuart G.},
+  title		= {A new, mechanistic model for organic carbon fluxes in the
+		  ocean based on the quantitative association of POC with
+		  ballast minerals},
+  year		= 2001,
+  volume	= 49,
+  number	= {1-3},
+  month		= {Jan},
+  pages		= {219–236},
+  issn		= {0967-0645},
+  doi		= {10.1016/s0967-0645(01)00101-1},
+  url		= {http://dx.doi.org/10.1016/S0967-0645(01)00101-1},
+  journal	= {Deep Sea Research Part II: Topical Studies in
+		  Oceanography},
+  publisher	= {Elsevier BV}
+}
+
+@Article{	  aumont_2015,
+  author	= {Aumont, O. and Ethé, C. and Tagliabue, A. and Bopp, L.
+		  and Gehlen, M.},
+  title		= {PISCES-v2: an ocean biogeochemical model for carbon and
+		  ecosystem studies},
+  year		= 2015,
+  volume	= 8,
+  number	= 8,
+  month		= {Aug},
+  pages		= {2465–2513},
+  issn		= {1991-9603},
+  doi		= {10.5194/gmd-8-2465-2015},
+  url		= {http://dx.doi.org/10.5194/gmd-8-2465-2015},
+  journal	= {Geoscientific Model Development},
+  publisher	= {Copernicus GmbH}
+}
+
+@Article{	  bacastow_1990,
+  author	= {Bacastow, R and Maier-Reimer, E},
+  title		= {Ocean-circulation model of the carbon cycle},
+  year		= 1990,
+  volume	= 4,
+  number	= 2,
+  month		= {Apr},
+  pages		= {95–125},
+  issn		= {1432-0894},
+  doi		= {10.1007/bf00208905},
+  url		= {http://dx.doi.org/10.1007/bf00208905},
+  journal	= {Climate Dynamics},
+  publisher	= {Springer Nature}
+}
+
+@Misc{		  bullister_2017,
+  author	= {Bullister, J.L.},
+  title		= {Atmospheric Histories (1765-2015) for CFC-11, CFC-12,
+		  CFC-113, CCl4, SF6 and N2O (NCEI Accession 0164584)},
+  year		= 2017,
+  doi		= {10.3334/cdiac/otg.cfc_atm_hist_2015},
+  url		= {https://accession.nodc.noaa.gov/0164584},
+  publisher	= {NOAA National Centers for Environmental Information}
+}
+
+@Article{	  butzin_2005,
+  author	= {BUTZIN, M and PRANGE, M and LOHMANN, G},
+  title		= {Radiocarbon simulations for the glacial ocean: The effects
+		  of wind stress, Southern Ocean sea ice and Heinrich
+		  events},
+  year		= 2005,
+  volume	= 235,
+  number	= {1-2},
+  month		= {Jun},
+  pages		= {45–61},
+  issn		= {0012-821X},
+  doi		= {10.1016/j.epsl.2005.03.003},
+  url		= {http://dx.doi.org/10.1016/j.epsl.2005.03.003},
+  journal	= {Earth and Planetary Science Letters},
+  publisher	= {Elsevier BV}
+}
+
+@Article{	  danabasoglu_2014,
+  author	= {Danabasoglu, Gokhan and Yeager, Steve G. and Bailey, David
+		  and Behrens, Erik and Bentsen, Mats and Bi, Daohua and
+		  Biastoch, Arne and Böning, Claus and Bozec, Alexandra and
+		  Canuto, Vittorio M. and et al.},
+  title		= {North Atlantic simulations in Coordinated Ocean-ice
+		  Reference Experiments phase II (CORE-II). Part I: Mean
+		  states},
+  year		= 2014,
+  volume	= 73,
+  month		= {Jan},
+  pages		= {76–107},
+  issn		= {1463-5003},
+  doi		= {10.1016/j.ocemod.2013.10.005},
+  url		= {http://dx.doi.org/10.1016/j.ocemod.2013.10.005},
+  journal	= {Ocean Modelling},
+  publisher	= {Elsevier BV}
+}
+
+@Article{	  dutay_2002,
+  author	= {Dutay, J.-C and Bullister, J.L and Doney, S.C and Orr, J.C
+		  and Najjar, R and Caldeira, K and Campin, J.-M and Drange,
+		  H and Follows, M and Gao, Y and et al.},
+  title		= {Evaluation of ocean model ventilation with CFC-11:
+		  comparison of 13 global ocean models},
+  year		= 2002,
+  volume	= 4,
+  number	= 2,
+  month		= {Jan},
+  pages		= {89–120},
+  issn		= {1463-5003},
+  doi		= {10.1016/s1463-5003(01)00013-0},
+  url		= {http://dx.doi.org/10.1016/S1463-5003(01)00013-0},
+  journal	= {Ocean Modelling},
+  publisher	= {Elsevier BV}
+}
+
+@Article{	  enting_1994,
+  author	= {G Enting, I and M L Wigley, T and Heimann, Martin},
+  year		= {1994},
+  month		= {01},
+  pages		= {},
+  title		= {Future Emissions and Concentrations of Carbon Dioxide: Key
+		  Ocean/Atmosphere/Land Analyses},
+  volume	= {31},
+  journal	= {CSIRO Division Atmospheric Research Technical Paper}
+}
+
+@Article{	  fiadeiro_1982,
+  author	= {Fiadeiro, M.E.},
+  year		= {1982},
+  month		= {01},
+  pages		= {537-550},
+  title		= {Three-dimensional modeling of tracers in the deep Pacific
+		  Ocean II. Radiocarbon and the circulation},
+  volume	= {40},
+  journal	= {J. Mar. Res.}
+}
+
+@Article{	  fluckiger_2002,
+  author	= {Flückiger, Jacqueline and Monnin, Eric and Stauffer,
+		  Bernhard and Schwander, Jakob and Stocker, Thomas F. and
+		  Chappellaz, Jérôme and Raynaud, Dominique and Barnola,
+		  Jean-Marc},
+  title		= {High-resolution Holocene N2O ice core record and its
+		  relationship with CH4and CO2},
+  year		= 2002,
+  volume	= 16,
+  number	= 1,
+  month		= {Feb},
+  pages		= {10–1–10–8},
+  issn		= {0886-6236},
+  doi		= {10.1029/2001gb001417},
+  url		= {http://dx.doi.org/10.1029/2001GB001417},
+  journal	= {Global Biogeochemical Cycles},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  haine_2006,
+  author	= {Haine, T. W. N.},
+  title		= {On tracer boundary conditions for geophysical reservoirs:
+		  How to find the boundary concentration from a mixed
+		  condition},
+  year		= 2006,
+  volume	= 111,
+  number	= {C5},
+  issn		= {0148-0227},
+  doi		= {10.1029/2005jc003215},
+  url		= {http://dx.doi.org/10.1029/2005JC003215},
+  journal	= {Journal of Geophysical Research},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Book{		  honjo_1996,
+  title		= {Fluxes of Particles to the Interior of the Open Oceans},
+  author	= {Honjo, S.},
+  url		= {https://books.google.fr/books?id=FwA6cgAACAAJ},
+  year		= {1996},
+  publisher	= {John Wiley \& Sons}
+}
+
+@Article{	  joos_1997,
+  author	= {Joos, Fortunat and Orr, James C. and Siegenthaler,
+		  Ulrich},
+  title		= {Ocean carbon transport in a box-diffusion versus a general
+		  circulation model},
+  year		= 1997,
+  volume	= 102,
+  number	= {C6},
+  month		= {Jun},
+  pages		= {12367–12388},
+  issn		= {0148-0227},
+  doi		= {10.1029/97jc00470},
+  url		= {http://dx.doi.org/10.1029/97JC00470},
+  journal	= {Journal of Geophysical Research: Oceans},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  key_2004,
+  author	= {Key, R. M. and Kozyr, A. and Sabine, C. L. and Lee, K. and
+		  Wanninkhof, R. and Bullister, J. L. and Feely, R. A. and
+		  Millero, F. J. and Mordy, C. and Peng, T.-H.},
+  title		= {A global ocean carbon climatology: Results from Global
+		  Data Analysis Project (GLODAP)},
+  year		= 2004,
+  volume	= 18,
+  number	= 4,
+  month		= {Dec},
+  pages		= {n/a–n/a},
+  issn		= {0886-6236},
+  doi		= {10.1029/2004gb002247},
+  url		= {http://dx.doi.org/10.1029/2004gb002247},
+  journal	= {Global Biogeochemical Cycles},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  kortzinger_2001,
+  author	= {Körtzinger, Arne and Hedges, John I. and Quay, Paul D.},
+  title		= {Redfield ratios revisited: Removing the biasing effect of
+		  anthropogenic CO2},
+  year		= 2001,
+  volume	= 46,
+  number	= 4,
+  month		= {Jun},
+  pages		= {964–970},
+  issn		= {0024-3590},
+  doi		= {10.4319/lo.2001.46.4.0964},
+  url		= {http://dx.doi.org/10.4319/lo.2001.46.4.0964},
+  journal	= {Limnology and Oceanography},
+  publisher	= {Wiley}
+}
+
+@Manual{	  nemo_manual,
+  author	= {Madec Gurvan and NEMO System Team},
+  title		= {NEMO ocean engine},
+  organization	= {NEMO Consortium},
+  journal	= {Notes du Pôle de modélisation de l\'Institut
+		  Pierre-Simon Laplace (IPSL)},
+  issn		= {1288-1619},
+  number	= {27},
+  publisher	= {Zenodo},
+  doi		= {10.5281/zenodo.1464816},
+  url		= {https://zenodo.org/record/1464816},
+  edition	= {TBD},
+  year		= {TBD}
+}
+
+@Article{	  meunier_2014,
+  author	= {Meunier, Cédric L. and Malzahn, Arne M. and Boersma,
+		  Maarten},
+  title		= {A New Approach to Homeostatic Regulation: Towards a
+		  Unified View of Physiological and Ecological Concepts},
+  year		= 2014,
+  editor	= {Munn, Adam J.Editor},
+  volume	= 9,
+  number	= 9,
+  month		= {Sep},
+  pages		= {e107737},
+  issn		= {1932-6203},
+  doi		= {10.1371/journal.pone.0107737},
+  url		= {http://dx.doi.org/10.1371/journal.pone.0107737},
+  journal	= {PLoS ONE},
+  publisher	= {Public Library of Science (PLoS)}
+}
+
+@Article{	  monnin_2001,
+  author	= {Monnin, E.},
+  title		= {Atmospheric CO2 Concentrations over the Last Glacial
+		  Termination},
+  year		= 2001,
+  volume	= 291,
+  number	= 5501,
+  month		= {Jan},
+  pages		= {112–114},
+  issn		= {1095-9203},
+  doi		= {10.1126/science.291.5501.112},
+  url		= {http://dx.doi.org/10.1126/science.291.5501.112},
+  journal	= {Science},
+  publisher	= {American Association for the Advancement of Science
+		  (AAAS)}
+}
+
+@Article{	  monnin_2004,
+  author	= {Monnin, Eric and Steig, Eric J and Siegenthaler, Urs and
+		  Kawamura, Kenji and Schwander, Jakob and Stauffer, Bernhard
+		  and Stocker, Thomas F and Morse, David L and Barnola,
+		  Jean-Marc and Bellier, Blandine and et al.},
+  title		= {Evidence for substantial accumulation rate variability in
+		  Antarctica during the Holocene, through synchronization of
+		  CO 2 in the Taylor Dome, Dome C and DML ice cores},
+  year		= 2004,
+  volume	= 224,
+  number	= {1-2},
+  month		= {Jul},
+  pages		= {45–54},
+  issn		= {0012-821X},
+  doi		= {10.1016/j.epsl.2004.05.007},
+  url		= {http://dx.doi.org/10.1016/j.epsl.2004.05.007},
+  journal	= {Earth and Planetary Science Letters},
+  publisher	= {Elsevier BV}
+}
+
+@Book{		  monod_1958,
+  title		= {Recherches sur la croissance des cultures
+		  bact{\'e}riennes},
+  author	= {Monod, J.},
+  lccn		= {nlm11031168},
+  series	= {Actualit{\'e}s scientifiques et industrielles},
+  url		= {https://books.google.fr/books?id=yhy6AAAAIAAJ},
+  year		= {1958},
+  publisher	= {Hermann}
+}
+
+@Article{	  mouchet_2013,
+  author	= {Mouchet, Anne},
+  title		= {The Ocean Bomb Radiocarbon Inventory Revisited},
+  year		= 2013,
+  volume	= 55,
+  number	= {3–4},
+  issn		= {0033-8222},
+  doi		= {10.2458/azu_js_rc.55.16402},
+  url		= {http://dx.doi.org/10.2458/azu_js_rc.55.16402},
+  journal	= {Radiocarbon},
+  publisher	= {Cambridge University Press (CUP)}
+}
+
+@Article{	  naegler_2009,
+  author	= {Naegler, Tobias},
+  title		= {Reconciliation of excess14C-constrained global CO2piston
+		  velocity estimates},
+  year		= 2009,
+  volume	= 61,
+  number	= 2,
+  month		= {Jan},
+  pages		= {372–384},
+  issn		= {1600-0889},
+  doi		= {10.1111/j.1600-0889.2008.00408.x},
+  url		= {http://dx.doi.org/10.1111/j.1600-0889.2008.00408.x},
+  journal	= {Tellus B: Chemical and Physical Meteorology},
+  publisher	= {Informa UK Limited}
+}
+
+@TechReport{	  orr_2000,
+  author	= {Orr, J. and Najjar, R. and Sabine, C. and Joos, F.},
+  title		= {Abiotic-HOWTO. Ocean-Carbon Cycle Model Intercomparison
+		  Project (OCMIP)},
+  url		= {http://ocmip5.ipsl.jussieu.fr/OCMIP/},
+  year		= {2000}
+}
+
+@Article{	  orr_2001,
+  author	= {Orr, James C. and Maier-Reimer, Ernst and Mikolajewicz,
+		  Uwe and Monfray, Patrick and Sarmiento, Jorge L. and
+		  Toggweiler, J. R. and Taylor, Nicholas K. and Palmer,
+		  Jonathan and Gruber, Nicolas and Sabine, Christopher L. and
+		  et al.},
+  title		= {Estimates of anthropogenic carbon uptake from four
+		  three-dimensional global ocean models},
+  year		= 2001,
+  volume	= 15,
+  number	= 1,
+  month		= {Mar},
+  pages		= {43–60},
+  issn		= {0886-6236},
+  doi		= {10.1029/2000gb001273},
+  url		= {http://dx.doi.org/10.1029/2000GB001273},
+  journal	= {Global Biogeochemical Cycles},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  orr_2017,
+  author	= {Orr, James C. and Najjar, Raymond G. and Aumont, Olivier
+		  and Bopp, Laurent and Bullister, John L. and Danabasoglu,
+		  Gokhan and Doney, Scott C. and Dunne, John P. and Dutay,
+		  Jean-Claude and Graven, Heather and et al.},
+  title		= {Biogeochemical protocols and diagnostics for the CMIP6
+		  Ocean Model Intercomparison Project (OMIP)},
+  year		= 2017,
+  volume	= 10,
+  number	= 6,
+  month		= {Jun},
+  pages		= {2169–2199},
+  issn		= {1991-9603},
+  doi		= {10.5194/gmd-10-2169-2017},
+  url		= {http://dx.doi.org/10.5194/gmd-10-2169-2017},
+  journal	= {Geoscientific Model Development},
+  publisher	= {Copernicus GmbH}
+}
+
+@Article{	  palmieri_2015,
+  author	= {Palmiéri, J. and Orr, J. C. and Dutay, J.-C. and
+		  Béranger, K. and Schneider, A. and Beuvier, J. and Somot,
+		  S.},
+  title		= {Simulated anthropogenic CO&lt;sub&gt;2&lt;/sub&gt; storage
+		  and acidification of the Mediterranean Sea},
+  year		= 2015,
+  volume	= 12,
+  number	= 3,
+  month		= {Feb},
+  pages		= {781–802},
+  issn		= {1726-4189},
+  doi		= {10.5194/bg-12-781-2015},
+  url		= {http://dx.doi.org/10.5194/bg-12-781-2015},
+  journal	= {Biogeosciences},
+  publisher	= {Copernicus GmbH}
+}
+
+@Article{	  reimer_2013,
+  author	= {Reimer, Paula J and Bard, Edouard and Bayliss, Alex and
+		  Beck, J Warren and Blackwell, Paul G and Ramsey,
+		  Christopher Bronk and Buck, Caitlin E and Cheng, Hai and
+		  Edwards, R Lawrence and Friedrich, Michael and et al.},
+  title		= {IntCal13 and Marine13 Radiocarbon Age Calibration Curves
+		  0–50,000 Years cal BP},
+  year		= 2013,
+  volume	= 55,
+  number	= 4,
+  pages		= {1869–1887},
+  issn		= {1945-5755},
+  doi		= {10.2458/azu_js_rc.55.16947},
+  url		= {http://dx.doi.org/10.2458/azu_js_rc.55.16947},
+  journal	= {Radiocarbon},
+  publisher	= {Cambridge University Press (CUP)}
+}
+
+@Article{	  sterner_2003,
+  author	= {Sterner, Robert W. and Elser, James J.},
+  title		= {Ecological Stoichiometry},
+  year		= 2003,
+  month		= {Dec},
+  doi		= {10.1515/9781400885695},
+  url		= {http://dx.doi.org/10.1515/9781400885695},
+  isbn		= 9781400885695,
+  publisher	= {Princeton University Press}
+}
+
+@Article{	  stuiver_1977,
+  author	= {Stuiver, Minze and Polach, Henry A},
+  title		= {Discussion Reporting of 14C Data},
+  year		= 1977,
+  volume	= 19,
+  number	= 03,
+  pages		= {355–363},
+  issn		= {1945-5755},
+  doi		= {10.1017/s0033822200003672},
+  url		= {http://dx.doi.org/10.1017/s0033822200003672},
+  journal	= {Radiocarbon},
+  publisher	= {Cambridge University Press (CUP)}
+}
+
+@Article{	  takahashi_1985,
+  author	= {Takahashi, Taro and Broecker, Wallace S. and Langer,
+		  Sara},
+  title		= {Redfield ratio based on chemical data from isopycnal
+		  surfaces},
+  year		= 1985,
+  volume	= 90,
+  number	= {C4},
+  pages		= 6907,
+  issn		= {0148-0227},
+  doi		= {10.1029/jc090ic04p06907},
+  url		= {http://dx.doi.org/10.1029/jc090ic04p06907},
+  journal	= {Journal of Geophysical Research},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  toggweiler_1989,
+  author	= {Toggweiler, J. R. and Dixon, K. and Bryan, K.},
+  title		= {Simulations of radiocarbon in a coarse-resolution world
+		  ocean model: 1. Steady state prebomb distributions},
+  year		= 1989,
+  volume	= 94,
+  number	= {C6},
+  pages		= 8217,
+  issn		= {0148-0227},
+  doi		= {10.1029/jc094ic06p08217},
+  url		= {http://dx.doi.org/10.1029/JC094iC06p08217},
+  journal	= {Journal of Geophysical Research},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  toggweiler_1989,
+  author	= {Toggweiler, J. R. and Dixon, K. and Bryan, K.},
+  title		= {Simulations of radiocarbon in a coarse-resolution world
+		  ocean model: 2. Distributions of bomb-produced carbon 14},
+  year		= 1989,
+  volume	= 94,
+  number	= {C6},
+  pages		= 8243,
+  issn		= {0148-0227},
+  doi		= {10.1029/jc094ic06p08243},
+  url		= {http://dx.doi.org/10.1029/JC094iC06p08243},
+  journal	= {Journal of Geophysical Research},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  wanninkhof_1992,
+  author	= {Wanninkhof, Rik},
+  title		= {Relationship between wind speed and gas exchange over the
+		  ocean},
+  year		= 1992,
+  volume	= 97,
+  number	= {C5},
+  pages		= 7373,
+  issn		= {0148-0227},
+  doi		= {10.1029/92jc00188},
+  url		= {http://dx.doi.org/10.1029/92jc00188},
+  journal	= {Journal of Geophysical Research},
+  publisher	= {American Geophysical Union (AGU)}
+}
+
+@Article{	  wanninkhof_1996,
+  author	= {Wanninkhof, Rik and Knox, Molly},
+  title		= {Chemical enhancement of CO2exchange in natural waters},
+  year		= 1996,
+  volume	= 41,
+  number	= 4,
+  month		= {Jun},
+  pages		= {689–697},
+  issn		= {0024-3590},
+  doi		= {10.4319/lo.1996.41.4.0689},
+  url		= {http://dx.doi.org/10.4319/lo.1996.41.4.0689},
+  journal	= {Limnology and Oceanography},
+  publisher	= {Wiley}
+}
+
+@Article{	  wanninkhof_2014,
+  author	= {Wanninkhof, Rik},
+  title		= {Relationship between wind speed and gas exchange over the
+		  ocean revisited},
+  year		= 2014,
+  volume	= 12,
+  number	= 6,
+  month		= {Jun},
+  pages		= {351–362},
+  issn		= {1541-5856},
+  doi		= {10.4319/lom.2014.12.351},
+  url		= {http://dx.doi.org/10.4319/lom.2014.12.351},
+  journal	= {Limnology and Oceanography: Methods},
+  publisher	= {Wiley}
+}
+
+@Article{	  warner_1985,
+  author	= {Warner, M.J. and Weiss, R.F.},
+  title		= {Solubilities of chlorofluorocarbons 11 and 12 in water and
+		  seawater},
+  year		= 1985,
+  volume	= 32,
+  number	= 12,
+  month		= {Dec},
+  pages		= {1485–1497},
+  issn		= {0198-0149},
+  doi		= {10.1016/0198-0149(85)90099-8},
+  url		= {http://dx.doi.org/10.1016/0198-0149(85)90099-8},
+  journal	= {Deep Sea Research Part A. Oceanographic Research Papers},
+  publisher	= {Elsevier BV}
+}
+
+@Article{	  weiss_1974,
+  author	= {Weiss, R.F.},
+  title		= {Carbon dioxide in water and seawater: the solubility of a
+		  non-ideal gas},
+  year		= 1974,
+  volume	= 2,
+  number	= 3,
+  month		= {Nov},
+  pages		= {203–215},
+  issn		= {0304-4203},
+  doi		= {10.1016/0304-4203(74)90015-2},
+  url		= {http://dx.doi.org/10.1016/0304-4203(74)90015-2},
+  journal	= {Marine Chemistry},
+  publisher	= {Elsevier BV}
+}
+
+@Article{	  woods_2013,
+  author	= {Woods, H. Arthur and Wilson, J. Keaton},
+  title		= {An information hypothesis for the evolution of
+		  homeostasis},
+  year		= 2013,
+  volume	= 28,
+  number	= 5,
+  month		= {May},
+  pages		= {283–289},
+  issn		= {0169-5347},
+  doi		= {10.1016/j.tree.2012.10.021},
+  url		= {http://dx.doi.org/10.1016/j.tree.2012.10.021},
+  journal	= {Trends in Ecology & Evolution},
+  publisher	= {Elsevier BV}
+}
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/TOP/main/TOP_manual.tex
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/TOP/main/TOP_manual.tex	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/TOP/main/TOP_manual.tex	(revision 11042)
@@ -0,0 +1,97 @@
+%% ==============================================================================
+%% TOP Reference Manual
+%% ==============================================================================
+
+
+%% Preamble
+%% ==============================================================================
+
+%% Document layout
+\documentclass{book}
+
+%% Custom style (.sty)
+\usepackage{../../NEMO/main/NEMO_manual}
+
+%% Include references and index for single subfile compilation
+\newcommand{\biblio}{\bibliography{../main/TOP_manual}}
+\newcommand{\pindex}{\printindex}
+
+\makeindex
+
+%% End of common preamble between main and sub-files
+\begin{document}
+
+%% Override custom cmds for full manual compilation
+\renewcommand{\biblio}{}
+\renewcommand{\pindex}{}
+
+
+%% Frontmatter
+%% ==============================================================================
+
+\graphicspath{{../../figures/logos/}}
+
+%% Frontpage
+\title{
+  \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}       \\
+  {\Huge TOP \\}
+  {\Large Tracer in Ocean Paradigm -- The NEMO Passive Tracer engine}\\
+  \small \textcolor{red}{First draft documentation. Needs completion and rewriting}. \\
+}
+\author{The NEMO-TOP Group
+  \thanks{
+    Eth\'{e} Christian, Lovato Thomas, Aumont Olivier, Palmi\'{e}ri Julien,
+    Mouchet Anne, Nurser Georges, Yool Andrew
+  }\\
+  \textit{Issue 27, Notes du P\^{o}le de mod\'{e}lisation} \\
+  \textit{Institut Pierre-Simon Laplace (IPSL)}            \\
+  \textit{ISSN 1288-1619}
+}
+\date{\today}
+
+\maketitle
+\frontmatter
+
+%% ToC i.e. Table of Contents
+
+\dominitoc
+\tableofcontents
+
+
+%% Mainmatter
+%% ==============================================================================
+
+\mainmatter
+
+\graphicspath{{../../figures/TOP/}}
+
+\subfile{../subfiles/introduction}
+\subfile{../subfiles/model_description}
+\subfile{../subfiles/model_setup}
+\subfile{../subfiles/miscellaneous}
+
+%% Appendix
+
+%\appendix
+%% Backmatter
+%% ==============================================================================
+
+\backmatter
+
+%% Bibliography
+\cleardoublepage
+\phantomsection
+\addcontentsline{toc}{chapter}{Bibliography}
+\bibliography{../main/TOP_manual}
+
+%% Index
+\cleardoublepage
+\phantomsection
+\addcontentsline{toc}{chapter}{Index}
+\printindex
+
+\end{document}
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/TOP/main/byrd-co2-2008.txt
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/TOP/main/byrd-co2-2008.txt	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/TOP/main/byrd-co2-2008.txt	(revision 11042)
@@ -0,0 +1,273 @@
+Byrd Ice Core CO2 Data for 20-90 KYrBP
+-----------------------------------------------------------------------
+               World Data Center for Paleoclimatology, Boulder
+                                  and
+                     NOAA Paleoclimatology Program
+-----------------------------------------------------------------------
+NOTE: PLEASE CITE ORIGINAL REFERENCE WHEN USING THIS DATA!!!!!
+
+
+NAME OF DATA SET: Byrd Ice Core CO2 Data for 20-90 KYrBP
+
+LAST UPDATE: 10/2008 (Original receipt by WDC Paleo)
+CONTRIBUTORS: Jinho Ahn and Edward J. Brook
+IGBP PAGES/WDCA CONTRIBUTION SERIES NUMBER: 2008-095
+
+WDC PALEO CONTRIBUTION SERIES CITATION: 
+Ahn, J. and E.J. Brook. 2008.
+Byrd Ice Core CO2 Data for 20-90 KYrBP. 
+IGBP PAGES/World Data Center for Paleoclimatology 
+Data Contribution Series # 2008-095. 
+NOAA/NCDC Paleoclimatology Program, Boulder CO, USA.
+
+
+ORIGINAL REFERENCES: 
+References for CO2 data: 
+ 
+Ahn, J. and E.J. Brook. 2008.
+Atmospheric CO2 and Climate on Millennial Time Scales During 
+the Last Glacial Period. 
+Science, 322, 83-85, doi: 10.1126/science.1160832.
+
+Ahn, J. and Brook, E.J.  2007.  
+Atmospheric CO2 and climate from 65 to 30 ka B.P.. 
+Geophysical Research Letters, 34, L10703, doi:10.1029/2007GL029551.
+
+ 
+References for CO2 age:	 
+  
+Blunier-01 age: 
+Blunier, T., and Brook, E.J.  2001. 
+Timing of millennial-scale climate change in Antarctica and Greenland 
+during the last glacial period.  
+Science, 291, 109-112.  
+	   
+Ahn-08 age: 
+Ahn, J. and E.J. Brook. 2008.
+Atmospheric CO2 and Climate on Millennial Time Scales During 
+the Last Glacial Period. 
+Science, 322, 83-85, doi: 10.1126/science.1160832.
+
+
+ABSTRACT (Ahn and Brook 2008):
+Reconstructions of ancient atmospheric carbon dioxide (CO2) variations 
+help us better understand how the global carbon cycle and climate are 
+linked.  We compared CO2 variations on millennial time scales between 
+20,000 and 90,000 years ago with an Antarctic temperature proxy and 
+records of abrupt climate change in the Northern Hemisphere. CO2 
+concentration and Antarctic temperature were positively correlated 
+over millennial-scale climate cycles, implying a strong connection 
+to Southern Ocean processes. Evidence from marine sediment proxies 
+indicates that CO2 concentration rose most rapidly when North Atlantic 
+Deep Water shoaled and stratification in the Southern Ocean was reduced. 
+These increases in CO2 concentration occurred during stadial (cold) 
+periods in the Northern Hemisphere, several thousand years before 
+abrupt warming events in Greenland.
+
+
+
+GEOGRAPHIC REGION: Antarctica
+PERIOD OF RECORD:  90 - 20 KYrBP
+
+FUNDING SOURCES: 
+Gary Comer Science and Education Foundation, and
+US National Science Foundation  grants OPP 0337891 and ATM 0602395.
+
+
+
+DESCRIPTION:  
+Byrd ice core carbon dioxide data for 20-90 KYrBP, analyzed at 
+Oregon State University.  
+
+Byrd Ice Core location: 
+80.01°S , 119.51°W; 1530 m elev. 
+  
+
+
+
+DATA:
+Byrd Ice Core CO2 Data for 20-90 KYrBP
+
+Column 1: Depth (m) 
+Column 2: Blunier 2001 Age (ka before 1950 AD)
+Column 3: Ahn 2008 Age (ka before 1950 AD)
+Column 4: Mean CO2 (ppm)
+Column 5: Number of replicates
+Column 6: Uncertainty (ppm)*
+Column 7: Reference
+
+*Uncertainty is estimated from the standard deviation of the mean for 2~5 ice samples
+
+Depth       Age Bl01  Age Ahn08   Mean CO2    Repl.  Uncert.    Ref.
+1315.91       19.460     19.286     194.36      2     0.97     AB-08
+1332.34       20.061     19.887     191.14      2     0.19     AB-08
+1334.20       20.152     19.978     192.54      2     0.09     AB-08
+1346.28       20.578     20.404     204.27      2     0.48     AB-08
+1353.02       20.759     20.585     195.37      2     0.02     AB-08
+1363.17       21.065     20.891     197.12      2     1.04     AB-08
+1381.14       21.731     21.557     195.81      2     1.66     AB-08
+1401.95       22.399     22.225     199.75      3     4.49     AB-08
+1410.30       22.729     22.555     194.62      2     0.31     AB-08
+1420.27       23.530     23.356     195.97      2     1.88     AB-08
+1430.78       24.824     24.650     194.74      2     1.94     AB-08
+1441.45       26.002     25.828     189.76      2     1.30     AB-08
+1460.20       26.711     26.537     192.21      2     1.28     AB-08
+1470.77       27.148     26.974     184.40      2     1.42     AB-08
+1480.48       27.619     27.445     188.07      2     1.48     AB-08
+1490.87       27.989     27.815     201.96      2     0.46     AB-08
+1496.52       28.135     27.961     204.98      2     1.71     AB-08
+1503.54       28.395     28.221     205.91      3     2.43     AB-08
+1512.46       28.660     28.486     207.48      2     1.73     AB-08
+1523.46       29.147     28.973     205.54      2     0.40     AB-08
+1533.76       29.568     29.396     201.49      2     1.84     AB-08
+1543.63       30.013     29.843     197.51      2     3.18     AB-08
+1552.76       30.412     30.245     195.36      2     0.89     AB-08
+1573.34       31.216     31.053     195.09      3     2.37     AB-08
+1581.93       31.738     31.577     202.29      2     0.38     AB-08
+1594.06       32.328     32.170     203.67      2     0.40     AB-08
+1615.15       33.450     33.297     208.11      2     0.11     AB-08
+1620.38       33.692     33.541     205.25      2     0.53     AB-08
+1631.11       34.183     34.033     201.53      2     1.67     AB-08
+1640.90       34.630     34.484     213.08      2     0.47     AB-08
+1650.56       35.097     34.953     206.62      2     1.72     AB-08
+1658.96       35.428     35.286     209.93      2     1.10     AB-08
+1677.79       36.249     36.111     207.76      2     0.00     AB-08
+1688.63       36.840     36.704     212.63      2     0.99     AB-08
+1693.68       37.167     37.033     213.98      2     1.37     AB-08
+1699.73       37.621     37.488     217.48      2     1.16     AB-08
+1708.70       38.122     37.992     216.21      2     1.03     AB-08
+1714.20       38.428     38.298     216.52      2     2.21     AB-08
+1717.20       38.545     38.415     212.50      2     1.51     AB-08
+1719.47       38.655     38.520     211.09      2     1.83     AB-08
+1723.22       38.850     38.708     214.78      2     2.64     AB-08
+1730.78       39.163     39.006     207.63      2     0.18     AB-08
+1740.51       39.539     39.364     214.06      2     0.14     AB-08
+1743.27       39.651     39.470     213.84      2     1.23     AB-08
+1747.69       39.811     39.621     203.03      2     1.03     AB-08
+1755.15       40.038     39.834     202.11      2     0.45     AB-08
+1760.29       40.172     39.958     203.78      2     2.59     AB-08
+1770.24       40.544     40.311     203.40      2     1.56     AB-08
+1779.99       40.966     40.714     201.30      2     1.46     AB-08
+1790.29       41.585     41.313     202.69      2     2.43     AB-08
+1802.03       42.320     42.025     204.64      2     0.56     AB-08
+1811.74       42.851     42.537     207.18      2     1.53     AB-08
+1821.19       43.591     43.259     210.31      2     0.60     AB-08
+1830.63       44.137     43.786     214.57      2     0.51     AB-08
+1840.93       44.598     44.228     216.83      3     2.50     AB-08
+1844.41       44.760     44.383     215.54      2     1.26     AB-08
+1847.46       44.899     44.516     219.62      2     0.94     AB-08
+1855.09       45.229     44.831     221.00      2     0.60     AB-08
+1859.57       45.526     45.120     217.56      2     0.82     AB-08
+1861.17       45.633     45.223     219.39      2     0.53     AB-08
+1862.59       45.725     45.313     218.62      2     2.56     AB-08
+1864.56       45.852     45.436     217.23      2     2.04     AB-08
+1867.90       46.075     45.654     211.58      2     0.64     AB-08
+1871.26       46.298     45.872     206.99      2     0.29     AB-08
+1873.26       46.431     46.002     209.25      2     1.24     AB-08
+1880.36       46.889     46.448     205.61      2     1.63     AB-08
+1884.88       47.187     46.740     204.28      2     1.02     AB-08
+1892.21       47.687     47.228     205.36      2     1.00     AB-08
+1894.8        47.865     47.402     205.51      2     1.63     AB-07
+1903.72       48.450     47.973     201.79      2     2.79     AB-07
+1909.75       48.874     48.388     211.47      4     1.09     AB-07
+1911.29       48.984     48.495     207.15      4     1.93     AB-07
+1914.31       49.191     48.697     212.35      2     0.57     AB-07
+1920.25       49.596     49.092     213.91      4     2.43     AB-07
+1929.4        50.230     49.712     216.76      2     0.28     AB-07
+1938.5        50.857     50.325     215.07      2     0.30     AB-07
+1943.09       51.175     50.636     218.12      5     2.35     AB-07
+1945.98       51.394     50.850     221.08      3     0.35     AB-07
+1953.17       51.894     51.339     216.69      4     2.96     AB-07
+1956.34       52.193     51.633     217.93      2     2.81     AB-07
+1959.23       52.505     51.941     218.83      2     1.55     AB-07
+1962.18       52.812     52.259     219.08      4     2.10     AB-07
+1963.62       52.963     52.423     215.70      2     1.94     AB-07
+1968.07       53.422     52.923     212.28      2     2.52     AB-07
+1972.66       53.926     53.470     213.25      2     0.74     AB-07
+1978.74       54.577     54.177     205.57      2     0.58     AB-07
+1981.61       54.859     54.486     212.48      4     2.46     AB-07
+1988.98       55.644     55.339     215.94      2     0.96     AB-07
+1995.01       56.317     56.068     215.25      2     0.38     AB-07
+2001.46       57.022     56.833     218.27      2     3.65     AB-07
+2003.23       57.222     57.049     223.09      2     0.30     AB-07
+2013.21       58.096     58.016     222.69      3     2.59     AB-07
+2017.71       58.467     58.421     224.99      2     0.97     AB-07
+2022.42       59.125     59.072     220.11      2     1.49     AB-07
+2026.9        59.806     59.746     224.21      3     1.18     AB-07
+2028.47       60.039     59.976     217.96      2     1.39     AB-07
+2031.5        60.526     60.459     218.85      2     3.26     AB-07
+2037.68       61.451     61.374     210.28      2     1.65     AB-07
+2042.43       62.186     62.102     212.26      2     0.85     AB-07
+2048.32       63.079     62.986     204.65      2     0.39     AB-07
+2051.4        63.526     63.429     206.76      2     2.20     AB-07
+2055.9        64.152     64.048     204.06      2     0.84     AB-07
+2066.85       65.565     65.444     208.22      2     2.01     AB-08
+2069.64       65.938     65.813     207.08      2     2.09     AB-08
+2072.65       66.333     66.204     217.67      2     2.07     AB-08
+2075.59       66.779     66.644     211.79      2     0.25     AB-08
+2075.745      66.818    66.6833     219.64      3     1.17     AB-08
+2076.02       66.890     66.755     222.40      2     0.47     AB-08
+2076.43       66.997     66.861     223.63      2     0.27     AB-08
+2077.02       67.151     67.014     220.43      2     3.79     AB-08
+2080.12       67.959     67.818     244.03      2     5.52     AB-08
+2080.61       68.086     67.944     240.28      2     0.28     AB-08
+2081.10       68.213     68.071     246.47      2     0.93     AB-08
+2081.59       68.340     68.197     247.22      2     2.42     AB-08
+2082.54       68.582     68.435     249.96      3     3.97     AB-08
+2082.64       68.608     68.460     248.32      2     2.08     AB-08
+2083.085      68.721    68.5708     238.70      4     4.19     AB-08
+2083.54       68.837     68.685     238.61      2     0.33     AB-08
+2083.82       68.908     68.755     238.78      2     1.42     AB-08
+2084.14       68.989     68.834     238.84      2     0.02     AB-08
+2084.52       69.086     68.929     231.99      3     4.59     AB-08
+2085.44       69.314     69.149     237.98      2     0.97     AB-08
+2087.02       69.706     69.527     237.26      3     0.40     AB-08
+2087.75       69.886     69.700     233.74      2     0.93     AB-08
+2089.24       70.246     70.048     234.85      2     0.19     AB-08
+2090.16       70.469     70.262     234.35      2     3.03     AB-08
+2093.50       71.337     71.101     237.17      2     0.49     AB-08
+2093.71       71.395     71.158     236.62      3     1.43     AB-08
+2095.46       71.875     71.622     240.58      2     3.79     AB-08
+2097.91       72.515     72.240     246.81      3     2.23     AB-08
+2099.29       72.885     72.598     244.19      1              AB-08
+2100.05       73.073     72.783     246.30      2     0.85     AB-08
+2100.69       73.230     72.937     236.93      2     0.88     AB-08
+2101.27       73.369     73.079     242.80      2     3.41     AB-08
+2101.80       73.492     73.209     241.26      2     0.14     AB-08
+2101.97       73.531     73.251     237.79      4     2.31     AB-08
+2103.15       73.805     73.542     240.63      3     0.85     AB-08
+2103.60       73.909     73.653     235.11      2     0.58     AB-08
+2104.68       74.184     73.944     231.11      2     0.89     AB-08
+2105.52       74.410     74.182     228.82      2     2.08     AB-08
+2106.32       74.656     74.440     223.79      2     1.22     AB-08
+2107.63       75.055     74.858     230.49      2     0.28     AB-08
+2109.17       75.518     75.343     228.85      2     0.25     AB-08
+2110.06       75.783     75.621     226.25      1              AB-08
+2111.20       76.120     75.975     229.45      2     2.14     AB-08
+2113.37       76.765     76.651     229.56      2     1.56     AB-08
+2116.08       77.586     77.513     232.82      3     1.97     AB-08
+2116.73       77.785     77.721     240.83      3     1.24     AB-08
+2120.16       78.809     78.795     235.51      2     0.11     AB-08
+2122.78       79.604     79.628     238.65      2     4.76     AB-08
+2125.62       80.449     80.515     240.08      3     1.03     AB-08
+2126.13       80.635     80.708     233.00      3     1.69     AB-08
+2130.20       82.116     82.248     250.22      2     4.72     AB-08
+2130.67       82.399     82.539     246.47      2     0.04     AB-08
+2130.78       82.466     82.607     244.08      2     2.06     AB-08
+2131.99       83.195     83.354     250.70      2     0.33     AB-08
+2132.50       83.503     83.669     248.75      2     2.37     AB-08
+2132.66       83.600     83.766     237.44      2     2.38     AB-08
+2134.46       84.687     84.855     240.19      2     1.00     AB-08
+2134.70       84.828     84.996     240.36      2     1.19     AB-08
+2135.22       85.133     85.301     233.84      2     0.20     AB-08
+2135.97       85.572     85.740     241.73      2     1.76     AB-08
+2136.25       85.734     85.902     220.23      2     5.01     AB-08
+2136.93       86.127     86.295     225.72      2     1.15     AB-08
+2137.57       86.498     86.666     228.99      3     1.73     AB-08
+2138.02       86.764     86.932     229.26      2     1.58     AB-08
+2138.32       86.942     87.110     218.37      2     0.94     AB-08
+2138.79       87.221     87.389     222.25      2     1.43     AB-08
+2143.57       90.075     90.266     236.19      5     2.31     AB-08
+2144.02       90.342     90.534     235.65      2     2.86     AB-08
+2144.72       90.759     90.953     242.07      3     4.54     AB-08
+
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/TOP/main/edc-co2.txt
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/TOP/main/edc-co2.txt	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/TOP/main/edc-co2.txt	(revision 11042)
@@ -0,0 +1,620 @@
+EPICA Dome C Ice Core High Resolution Holocene and Transition CO2 Data
+-----------------------------------------------------------------------
+               World Data Center for Paleoclimatology, Boulder
+                                  and
+                     NOAA Paleoclimatology Program
+-----------------------------------------------------------------------
+NOTE: PLEASE CITE CONTRIBUTORS WHEN USING THIS DATA!!!!!
+
+
+NAME OF DATA SET: 
+EPICA Dome C Ice Core High Resolution Holocene and Transition CO2 Data
+LAST UPDATE: 9/2004 (Original receipt by WDC Paleo)
+CONTRIBUTOR:  Eric Monnin, University of Bern
+IGBP PAGES/WDCA CONTRIBUTION SERIES NUMBER: 2004-055
+
+
+SUGGESTED DATA CITATION: Monnin, E., et al.. 2004. 
+EPICA Dome C Ice Core High Resolution Holocene and Transition CO2 Data. 
+IGBP PAGES/World Data Center for Paleoclimatology 
+Data Contribution Series # 2004-055.
+NOAA/NGDC Paleoclimatology Program, Boulder CO, USA.
+
+
+ORIGINAL REFERENCE:  
+Monnin, E., E.J. Steig, U. Siegenthaler, K. Kawamura, J. Schwander, B. Stauffer, 
+T.F. Stocker, D.L. Morse, J.-M. Barnola, B. Bellier, D. Raynaud, and H. Fischer. 2004.  
+Evidence for substantial accumulation rate variability in Antarctica during the Holocene, 
+through synchronization of CO2 in the Taylor Dome, Dome C and DML ice cores. 
+Earth and Planetary Science Letters, 224, 45-54, doi: 10.1016/j.epsl.2004.05.007. 
+
+
+ADDITIONAL REFERENCES FOR DATA:
+Flückiger, J.,  E. Monnin, B. Stauffer, J. Schwander, T. F. Stocker, J. Chappellaz, 
+D. Raynaud and J.-M. Barnola.  2002.
+High resolution Holocene N2O ice core record and its relationship with CH4 and CO2. 
+Global Biogeochemical Cycles, 16 (1), 1010, doi:10.1029/2001GB001417.
+
+Monnin, E., A. Indermühle, A. Dällenbach, J. Flückiger, B. Stauffer, T. F. Stocker, 
+D. Raynaud, and J.-M. Barnola.  2001. 
+Atmospheric CO2 concentrations over the last glacial termination. 
+Science 291, 112-114.
+
+ 
+ADDITIONAL REFERENCE FOR DATING:
+Schwander, J., J. Jouzel, C. U. Hammer, J.-R. Petit, R. Udisti, and E. Wolff. 2001.
+A tentative chronology for the EPICA Dome Concordia ice core. 
+Geophys. Res. Lett. Vol. 28, No. 22, p. 4243.
+
+
+ABSTRACT (Monnin et al. 2004):
+High resolution records of atmospheric CO2 concentration during the Holocene 
+are obtained from the Dome Concordia and Dronning Maud Land (Antarctica) ice cores. 
+These records confirm that the CO2 concentration varied between 260 and 280 ppmv in 
+the Holocene as measured in the Taylor Dome ice core. However, there are differences 
+in the CO2 records most likely caused by mismatches in timescales. Matching the 
+Taylor Dome timescale to the Dome C timescale by synchronization of CO2 indicates that 
+the accumulation rate at Taylor Dome increased through the Holocene by a factor of two 
+and bears little resemblance to the stable isotope record used as a proxy for temperature. 
+This result shows that different locations experienced substantially different 
+accumulation changes, and casts doubt on the often-used assumption that accumulation 
+rate scales with the saturation vapor pressure as a function of temperature, at least 
+for coastal locations. 
+
+
+GEOGRAPHIC REGION: Antarctica
+PERIOD OF RECORD:  22 KYrBP - present
+
+
+DESCRIPTION: High Resolution CO2 Data for the EPICA Dome C ice core, 
+and derived timescale for Taylor Dome Ice Core. 
+
+
+Core locations: 
+EPICA Dome C:  75° 06'S, 123° 21'E 
+Dronning Maud Land (DML): 75° 00'S, 00° 04'E 
+Taylor Dome:  77° 47'47" S,  158° 43'26" E
+
+
+
+
+Data:
+1. High-resolution EDC CO2 data
+
+Column 1: Depth (m)
+Column 2: Age (Years before 1950 AD, EDC1 Timescale)
+Column 3: CO2 mean (ppmv)
+Column 4: CO2 sigma mean (ppmv) sigma mean is one sigma of the mean value 
+          (of 6 neighboring samples)
+
+
+  Depth      Age    CO2      sigma
+  102.83     173   280.4     1.8
+ 106.885     311   274.9     0.7
+ 107.195     322   277.9     0.7
+ 110.245     427   279.1     1.3
+   110.5     435   281.9     1.1
+ 113.265     530   277.7     0.7
+  115.48     604   281.1     1.1
+ 118.615     709   282.2     0.5
+   121.5     806   280.1     0.6
+ 124.815     917   278.4     1.5
+ 127.015     991   276.6     1.4
+ 129.745    1083   279.1       1
+   132.5    1175   277.7     1.2
+ 134.715    1249   278.7     1.2
+ 138.015    1362   277.4     0.8
+ 141.295    1477   279.2     0.9
+  144.05    1574     280     0.8
+ 146.265    1653   278.9     0.8
+ 149.015    1751   278.7     0.7
+ 151.195    1830     278     1.2
+   154.5    1948   276.9     0.7
+ 157.815    2069   276.7     0.8
+  160.03    2150   276.7     0.8
+ 162.165    2228   277.6     1.3
+ 165.515    2352   277.9     0.5
+  168.28    2453   273.9     1.1
+     171    2550   278.9     0.6
+ 173.135    2625   275.3     1.6
+ 176.515    2743   274.7     1.2
+ 178.715    2820   276.3     0.9
+ 181.445    2918   274.6     0.8
+ 185.845    3078   276.3     1.5
+ 187.515    3138   273.1     1.1
+ 189.715    3219     274     0.3
+     193    3337     275     0.6
+ 196.295    3454   273.4     1.3
+ 198.515    3531     273     0.8
+  201.28    3628   271.5       1
+     204    3724   275.4     0.5
+ 206.195    3802   274.9     1.3
+ 209.515    3921   271.7       1
+ 212.265    4019   271.6     0.7
+     215    4117   272.8     0.8
+ 216.645    4176   271.5     0.9
+  221.05    4335   271.1     0.8
+ 222.715    4395   269.1     0.6
+  225.48    4496   269.8       1
+ 228.195    4596   271.5     0.8
+  232.05    4737   270.7     0.5
+ 233.715    4797   269.3       1
+ 236.465    4895   268.6     1.1
+ 240.265    5033   269.8     1.2
+   242.5    5114   267.6     0.6
+ 244.715    5196   265.3     1.7
+ 248.015    5318   265.2     0.8
+ 250.715    5419   267.6       2
+   253.5    5521   265.9     0.9
+ 256.265    5621   265.5     0.8
+ 259.015    5721   260.7     1.6
+ 260.645    5780   266.7     0.9
+   264.5    5921   265.5     0.8
+ 268.365    6064   263.2     0.6
+ 269.415    6102   262.7     0.9
+ 272.195    6205   261.2     0.7
+ 276.065    6349   261.1     0.4
+ 278.265    6430   259.4     0.6
+  280.53    6514   262.1     0.9
+ 283.715    6631   262.9     0.5
+ 285.965    6713   258.1     1.4
+ 288.165    6792   257.6     0.9
+     292    6930   262.3     0.9
+ 294.745    7031     263     0.7
+ 297.515    7132   260.7     0.6
+ 299.715    7211   258.4     0.8
+     303    7328   260.1     0.6
+ 305.745    7424   260.4     0.4
+ 308.515    7521   259.7     0.9
+  311.26    7617   259.2     0.7
+ 313.995    7714   260.8     1.4
+ 316.745    7813   259.6     0.5
+ 319.515    7915   259.3     0.9
+ 322.265    8017   258.3     1.2
+     325    8118   261.3     0.9
+ 326.545    8174   260.7     0.4
+   330.5    8315   261.8       1
+ 333.265    8412     259     1.1
+ 336.015    8508   260.9     0.7
+ 338.645    8599   260.4     0.6
+   341.5    8697   259.3       1
+ 343.715    8772     262     0.8
+ 347.015    8883   263.7     1.2
+ 349.745    8974   263.8     0.8
+  352.58    9067   265.2     0.9
+ 355.815    9171   260.6     1.7
+ 357.465    9224   260.9     0.6
+ 360.195    9310     263     0.4
+  362.98    9399   263.8     1.2
+ 369.545    9604   264.4     0.4
+  371.23    9657   264.2     0.9
+ 375.045    9776     264     0.3
+ 377.265    9846   263.4     0.1
+ 379.995    9931   265.7     0.5
+ 382.215   10001   264.9     0.4
+ 385.125   10093   267.5     0.4
+ 388.225   10192   266.9     0.6
+ 390.445   10263     266     1.1
+  393.78   10370   265.1     1.6
+ 396.495   10458   267.6     0.7
+  399.28   10550   264.8     0.6
+ 401.995   10640   264.8     0.4
+ 404.185   10712     265     0.8
+  404.78   10732   265.3     0.4
+ 406.385   10785   264.4     1.5
+ 407.495   10822   264.1     0.7
+   409.7   10896   264.2     1.1
+  411.38   10952   264.5     0.4
+  413.03   11008     264     0.5
+  414.75   11066     263     1.3
+  415.73   11099   265.2     0.8
+ 417.065   11144   258.8     0.7
+  418.53   11195   260.8     0.5
+ 420.485   11263   255.4     0.3
+ 421.795   11310   253.9     0.6
+   422.9   11349   253.8     0.8
+   426.1   11468   250.7     1.1
+  427.33   11515   249.7     0.4
+   428.3   11554   251.1     0.3
+ 429.495   11602   250.7     0.9
+  431.73   11695   245.3     1.1
+ 433.785   11784   245.3     0.6
+ 434.995   11838   246.6     0.5
+  437.23   11941   243.2     0.4
+  438.85   12017   240.3     0.3
+ 443.795   12258   237.5     0.5
+  446.03   12372   237.6     0.6
+ 448.745   12511   234.2     0.3
+  450.98   12625   238.3     1.1
+ 454.245   12789   237.3     0.5
+  457.03   12927   237.9     0.2
+ 459.895   13068   237.6     0.6
+  463.63   13252   236.4     0.9
+ 465.245   13332   239.2     0.5
+  467.45   13440   238.6     0.6
+ 470.195   13574   238.6     0.3
+ 473.055   13711   239.1     0.4
+ 479.705   14022   228.5     0.6
+   484.1   14230   228.4     0.7
+ 487.245   14387   226.1     0.6
+  490.03   14532   225.2     0.5
+ 492.195   14647   224.5     0.6
+  496.07   14855     222     0.8
+ 499.345   15037     221     0.8
+  501.58   15166   220.9     0.5
+ 504.195   15323   219.4     0.6
+  506.53   15466     214     0.8
+ 509.245   15637   207.5     0.9
+  512.03   15818   207.7     0.5
+ 514.745   16002   202.9     0.7
+  517.53   16199   200.8       1
+ 520.245   16400   195.2     0.3
+  523.03   16616   193.9     0.5
+ 526.295   16883     191     0.5
+  528.53   17073   188.5     0.7
+ 531.245   17311   188.5     0.7
+  532.93   17463   189.2     0.4
+ 536.745   17815     187     0.2
+  539.53   18074   188.6     0.5
+   542.9   18391   189.4     0.4
+ 543.345   18433   192.3     0.6
+  543.93   18487   188.3     0.6
+ 548.845   18948   188.7     0.2
+  550.51   19104   188.8     0.5
+ 553.245   19360     190     0.8
+  556.03   19621     188     0.9
+  557.89   19795   188.2     0.7
+ 558.195   19824     195     0.7
+  561.53   20137   187.8     0.4
+  564.26   20390   186.9     0.3
+  567.03   20646   186.5     0.3
+ 569.745   20897   184.7     1.2
+  572.53   21156   186.1     0.4
+ 576.325   21511   185.7     1.3
+ 578.105   21676   184.4     0.8
+
+
+2.  CO2 synchronization timescale for Taylor Dome Ice Core
+
+A. Gas age:
+
+ depth(m)    gas age (yr BP 1950)
+      86       94.5
+      90      149.2
+      94      205.2
+      98      260.9
+     102      316.2
+     106        372
+     110      427.9
+     114      483.7
+     118      540.1
+     122      598.1
+     126      658.4
+     130      722.7
+     134      790.3
+     138      860.5
+   142.1      929.8
+   146.1      995.5
+   150.1     1058.1
+   154.1     1119.4
+   158.1     1180.7
+   162.1     1243.2
+   166.1       1308
+   170.1     1377.6
+   174.1     1454.7
+   178.1     1539.6
+   182.1       1633
+   186.1     1731.9
+   190.1     1835.6
+   194.1       1940
+   198.1     2045.1
+   202.1       2150
+   206.1     2254.5
+   210.1     2361.9
+   214.1     2475.5
+   218.1     2594.6
+   222.1     2715.6
+   226.1     2835.7
+   230.1     2954.2
+   234.1     3070.8
+   238.1     3188.2
+   242.1       3308
+   246.1     3429.6
+   250.1     3550.6
+   254.2     3670.1
+   258.2     3787.9
+   262.2     3905.9
+   266.2     4026.1
+   270.2     4153.3
+   274.2     4295.3
+   278.2     4454.1
+   282.2     4629.4
+   286.2       4814
+   290.2     4998.6
+   294.2     5174.8
+   298.2     5342.8
+   302.2     5507.9
+   306.2     5674.9
+   310.2     5846.8
+   314.2     6031.1
+   318.2     6242.5
+   322.2       6502
+   326.2     6830.5
+   330.2     7238.7
+   334.2     7710.2
+   338.2     8215.9
+   342.2     8735.9
+   346.2     9226.8
+   350.2     9762.8
+   354.2    10289.2
+   358.2    10720.5
+   362.3    11224.1
+
+
+
+B. Ice age:
+
+ depth(m)    ice age (yr BP 1950)
+      86     730.1
+    87.3     746.9
+    88.5     763.6
+    89.7     780.4
+    90.9     797.2
+      92     813.9
+    93.2     830.5
+    94.4       847
+    95.5     863.4
+    96.7     879.7
+    97.8     895.9
+    98.9     912.1
+     100     928.3
+   101.2     944.6
+   102.3     961.1
+   103.4     977.6
+   104.6     994.2
+   105.7    1010.5
+   106.8    1026.6
+   107.9    1042.7
+     109      1059
+   110.1    1075.2
+   111.1    1091.5
+   112.2    1107.9
+   113.3    1124.3
+   114.4    1140.8
+   115.5    1157.4
+   116.5      1174
+   117.6    1190.8
+   118.6    1207.9
+   119.7      1225
+   120.8    1242.2
+   121.8    1259.8
+   122.9    1277.8
+   123.9    1295.9
+     125    1314.1
+     126    1332.7
+   127.1    1351.4
+   128.1      1370
+   129.2    1388.5
+   130.2    1407.3
+   131.2    1426.3
+   132.3      1445
+   133.3    1463.6
+   134.4    1482.2
+   135.4    1500.9
+   136.5    1519.5
+   137.5    1537.9
+   138.5      1556
+   139.6    1573.9
+   140.6    1591.7
+   141.6    1609.4
+   142.7    1626.8
+   143.7    1644.1
+   144.7    1661.2
+   145.7    1678.1
+   146.8    1694.6
+   147.8      1711
+   148.8    1727.5
+   149.8    1743.9
+   150.9    1760.3
+   151.9    1776.6
+   152.9    1793.1
+   153.9    1809.6
+   154.9    1826.2
+     156    1842.9
+     157    1859.6
+     158    1876.5
+     159    1893.5
+     160    1910.6
+     161    1927.7
+   162.1    1945.1
+   163.1    1962.8
+   164.1    1980.5
+   165.1    1998.3
+   166.1      2017
+   167.1    2036.8
+   168.1    2056.8
+   169.1    2077.2
+   170.2    2098.8
+   171.2    2121.7
+   172.2      2145
+   173.2    2168.6
+   174.2    2193.2
+   175.2      2219
+   176.2    2244.7
+   177.2    2270.3
+   178.2    2296.7
+   179.3    2323.9
+   180.3      2351
+   181.3    2378.2
+   182.3      2406
+   183.3    2434.1
+   184.3    2462.3
+   185.3    2490.5
+   186.3    2519.3
+   187.3    2548.5
+   188.3    2577.7
+   189.3    2606.7
+   190.4    2635.8
+   191.4      2665
+   192.4    2694.1
+   193.4    2723.2
+   194.4    2752.3
+   195.4    2781.6
+   196.4    2810.8
+   197.4    2839.9
+   198.4    2868.9
+   199.4    2897.8
+   200.4    2926.4
+   201.4    2954.9
+   202.4      2983
+   203.5    3010.9
+   204.5    3038.5
+   205.5      3066
+   206.5    3093.6
+   207.5    3121.2
+   208.5    3148.4
+   209.5    3175.7
+   210.5    3203.4
+   211.5    3231.3
+   212.5      3259
+   213.5    3286.9
+   214.5    3315.4
+   215.5    3344.4
+   216.5    3373.3
+   217.5    3402.5
+   218.6    3431.9
+   219.6    3461.4
+   220.6    3490.9
+   221.6    3520.3
+   222.6    3549.6
+   223.6      3579
+   224.6    3608.4
+   225.6    3637.6
+   226.6    3666.2
+   227.6    3694.6
+   228.6      3723
+   229.6      3751
+   230.6    3778.4
+   231.6    3805.5
+   232.6    3832.5
+   233.6    3859.3
+   234.6      3886
+   235.7    3912.7
+   236.7    3939.3
+   237.7      3966
+   238.7    3992.9
+   239.7    4020.1
+   240.7    4047.4
+   241.7    4074.9
+   242.7    4102.9
+   243.7    4130.9
+   244.7    4158.9
+   245.7    4186.9
+   246.7    4215.2
+   247.7    4243.7
+   248.7    4272.2
+   249.7    4300.6
+   250.8    4328.8
+   251.8    4357.3
+   252.8    4385.9
+   253.8    4414.9
+   254.8    4444.3
+   255.8    4474.3
+   256.8    4504.4
+   257.8    4534.8
+   258.8    4565.6
+   259.8    4596.7
+   260.8      4628
+   261.8    4659.4
+   262.8    4691.3
+   263.8    4723.4
+   264.8    4755.4
+   265.8    4788.2
+   266.8    4821.8
+   267.9    4855.7
+   268.9    4889.6
+   269.9    4924.9
+   270.9    4961.8
+   271.9    4999.1
+   272.9    5036.2
+   273.9    5074.7
+   274.9      5115
+   275.9    5155.8
+   276.9    5196.5
+   277.9    5238.6
+   278.9    5282.7
+   279.9    5327.3
+   280.9    5371.8
+   281.9    5417.1
+   282.9    5463.7
+   283.9    5510.6
+   284.9    5557.4
+   285.9    5604.1
+   286.9    5650.6
+     288    5697.3
+     289    5743.8
+     290    5789.3
+     291    5833.8
+     292    5878.1
+     293    5922.3
+     294    5965.5
+     295    6007.8
+     296    6050.3
+     297      6093
+     298    6135.2
+     299    6177.2
+     300    6219.5
+     301    6262.3
+     302    6305.5
+     303    6349.4
+     304    6393.8
+     305    6438.7
+     306    6484.6
+     307    6531.7
+     308    6579.1
+     309    6626.8
+     310    6676.5
+     311    6728.2
+     312    6780.3
+   313.1    6832.7
+   314.1    6888.4
+   315.1    6947.6
+   316.1    7007.4
+   317.1    7067.1
+   318.1    7132.1
+   319.1    7203.1
+   320.1    7274.9
+   321.1    7346.6
+   322.1      7426
+   323.1    7514.1
+   324.1    7603.5
+   325.1    7693.4
+   326.1    7792.7
+   327.1    7902.5
+   328.1    8013.9
+   329.1    8125.8
+   330.1    8245.7
+   331.1    8373.8
+   332.1    8502.4
+   333.1    8630.8
+   334.1    8761.6
+   335.1    8894.5
+   336.1    9026.4
+   337.1    9157.7
+   338.1    9290.6
+   339.1    9425.8
+   340.1    9561.1
+   341.2    9695.7
+   342.2    9826.2
+   343.2    9951.2
+   344.2   10075.6
+   345.2   10201.2
+   346.2   10331.7
+   347.2   10467.7
+   348.2   10603.6
+   349.2   10739.5
+   350.2   10873.8
+   351.2   11006.9
+   352.2   11139.9
+   353.2     11273
+
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/TOP/subfiles/introduction.tex
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/TOP/subfiles/introduction.tex	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/TOP/subfiles/introduction.tex	(revision 11042)
@@ -0,0 +1,47 @@
+\documentclass[../../NEMO/main/NEMO_manual]{subfiles}
+\begin{document}
+% ================================================================
+% INTRODUCTION
+% ================================================================
+
+\chapter*{Introduction}
+
+TOP (Tracers in the Ocean Paradigm) handles oceanic passive tracers in NEMO. At present, 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.
+
+It includes three independent components :  
+
+\begin{itemize}
+        \item a transport code TRP sharing the same advection/diffusion routines with the dynamics, with specific treatment of some features like the surface boundary
+conditions, or the positivity of passive tracers concentrations
+        \item sources and sinks - SMS - models that can be typically biogeochemical, biological or radioactive
+        \item an offline option which is a simplified OPA 9 model using fields of physics variables that are previously stored to disk
+\end{itemize}
+
+There is two ways of coupling TOP to the dynamics :
+
+\begin{itemize}
+        \item \textit{online coupling} : the evolution of passive tracers is computed along with the dynamics
+        \item \textit{offline coupling} : the fields of physics variables are read from files and interpolated at each model time step, with no constraints on the time sampling in the input files
+\end{itemize}
+
+TOP is designed to handle multiple oceanic tracers through a modular approach and it includes different sub-modules :
+
+\begin{itemize}
+        \item the ocean water age module (AGE) tracks down the time-dependent spread of surface waters into the ocean interior
+        \item inorganic carbon (e.g. CFCs, SF6) and radiocarbon (C14) passive tracers can be modeled to assess ocean absorption timescales of anthropogenic emissions and further address water masses ventilation
+        \item a built-in biogeochemical model (PISCES) to simulate lower trophic levels ecosystem dynamics in the global ocean
+        \item a prototype tracer module (MY\_TRC) to enable user-defined cases or the coupling with alternative biogeochemical models ( e.g. BFM, MEDUSA, ERSEM, BFM, ECO3M)
+\end{itemize}
+
+\begin{figure}[ht]        
+\begin{center}
+\vspace{0cm}
+\includegraphics[width=0.80\textwidth]{Fig_TOP_design}
+%\includegraphics[height=6cm,angle=-00]{Fig_TOP_design}
+\caption{A schematic view of NEMO-TOP component}
+\label{topdesign}
+\end{center}   
+\end{figure}
+
+\end{document}
+
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/TOP/subfiles/miscellaneous.tex
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/TOP/subfiles/miscellaneous.tex	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/TOP/subfiles/miscellaneous.tex	(revision 11042)
@@ -0,0 +1,70 @@
+\documentclass[../../NEMO/main/NEMO_manual]{subfiles}
+
+\begin{document}
+
+\chapter{Miscellaneous}
+
+\section{TOP synthetic Workflow}
+
+\subsection{Model initialization}
+
+\subsection{Time marching procedure}
+
+\section{Coupling an external BGC model using NEMO framework}
+
+The coupling with an external BGC model through the NEMO compilation framework can be achieved in different ways according to the degree of coding complexity of the Biogeochemical model, like e.g., the whole code is made only by one file or it has multiple modules and interfaces spread across several subfolders.\\ \\
+Beside the 6 core files of MY\_TRC module, see (see \label{Mytrc}, let's assume an external BGC model named \textit{"MYBGC"} and constituted by a rather essential coding structure, likely few Fortran files. The new coupled configuration name is NEMO\_MYBGC. \\ \\
+The best solution is to have all files (the modified MY\_TRC routines and the BGC model ones) placed in a unique folder with root \path{<MYBGCPATH>} and to use the \textit{makenemo} external readdressing of MY\_SRC folder. \\ \\
+The coupled configuration listed in \textbf{cfg.txt}  will look like
+
+\begin{minted}{bash}
+   NEMO_MYBGC OPA_SRC TOP_SRC
+\end{minted}
+and the related cpp\_MYBGC.fcm content will be
+%
+\begin{minted}{bash}
+    bld::tool::fppkeys   key_iomput key_mpp_mpi key_top
+\end{minted}
+
+the compilation with \textit{makenemo} will be executed through the following syntax
+
+\begin{minted}{bash}
+   makenemo -n NEMO_MYBGC -m <arch_my_machine> -j 8 -e <MYBGCPATH>
+\end{minted}
+%The makenemo feature ?-e? was introduced to readdress at compilation time the standard MY_SRC folder (usually found in NEMO configurations) with a user defined external one.
+%
+%
+%The compilation of more articulated BGC model code & infrastructure, like in the case of BFM (?BFM-NEMO coupling manual), requires some additional features.
+%
+%As before, let?s assume a coupled configuration name NEMO_MYBGC, but in this case MYBGC model root becomes <MYBGCPATH> that contains 4 different subfolders for biogeochemistry, named initialization, pelagic, and benthic, and a separate one named nemo_coupling including the modified MY_SRC routines. The latter folder containing the modified NEMO coupling interface will be still linked using the makenemo ?-e? option.
+%
+%In order to include the BGC model subfolders in the compilation of NEMO code, it will be necessary to extend the configuration cpp_NEMO_MYBGC.fcm file to include the specific paths of MYBGC folders, as in the following example
+%
+\begin{minted}{bash}
+   bld::tool::fppkeys   key_iomput key_mpp_mpi key_top
+   
+   src::MYBGC::initialization         <MYBGCPATH>/initialization
+   src::MYBGC::pelagic                <MYBGCPATH>/pelagic
+   src::MYBGC::benthic                <MYBGCPATH>/benthic
+
+   bld::pp::MYBGC      1
+   bld::tool::fppflags::MYBGC   %FPPFLAGS
+   bld::tool::fppkeys   %bld::tool::fppkeys MYBGC_MACROS
+\end{minted}
+
+%where MYBGC_MACROS is the space delimited list of macros used in MYBGC model for selecting/excluding specific parts of the code. The BGC model code will be preprocessed in the configuration BLD folder as for NEMO, but with an independent path, like NEMO_MYBGC/BLD/MYBGC/<subforlders>.
+%
+%The compilation will be performed similarly to in the previous case with the following
+%
+%makenemo -n NEMO_MYBGC -m <arch_my_machine> -j 8 -e <MYBGCPATH>/nemo_coupling
+%Note that, the additional lines specific for the BGC model source and build paths, can be written into a separate file, e.g. named MYBGC.fcm, and then simply included in the cpp_NEMO_MYBGC.fcm as follow
+%
+%bld::tool::fppkeys  key_zdftke key_dynspg_ts key_iomput key_mpp_mpi key_top
+%inc <MYBGCPATH>/MYBGC.fcm
+%This will enable a more portable compilation structure for all MYBGC related configurations.
+%
+%Important: the coupling interface contained in nemo_coupling cannot be added using the FCM syntax, as the same files already exists in NEMO and they are overridden only with the readdressing of MY_SRC contents to avoid compilation conflicts due to duplicate routines.
+%
+%All modifications illustrated above, can be easily implemented using shell or python scripting to edit the NEMO configuration cpp.fcm file and to create the BGC model specific FCM compilation file with code paths.
+
+\end{document}
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/TOP/subfiles/model_description.tex
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/TOP/subfiles/model_description.tex	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/TOP/subfiles/model_description.tex	(revision 11042)
@@ -0,0 +1,616 @@
+\documentclass[../../NEMO/main/NEMO_manual]{subfiles}
+
+\newcommand{\cd}{\mathrm{CO_2}}
+\newcommand{\Ct}{\mathrm{C_T}}
+\newcommand{\pacd}{\mathrm{p^a_{CO_2}}}
+\newcommand{\cq}{\mathrm{^{14}C}}
+\newcommand{\Dcq}{\Delta ^{14}\mathrm{C}}
+\newcommand{\Rq}{\mathrm{^{14}{R}}}
+\newcommand{\CODE}[1]{\textsc{#1}}
+%\newcommand{\CODE}[1]{\textcolor{black}{\textsc{#1}}\xspace}
+
+\begin{document}
+
+\chapter{Model Description}
+\label{chap:ModDes}
+\minitoc
+
+\section{Basics}
+\label{sec:Bas}
+
+The time evolution of any passive tracer $C$ follows the transport equation, which is similar to that of active tracer - temperature or salinity :
+
+\begin{equation}
+\frac{\partial C}{\partial t} = {S(C)} -  \frac{1}{b_t} \left[   \frac{\partial e_{2u}\,e_{3u} \;  u\, C}{\partial i} +   \frac{\partial e_{1v}\,e_{3v} \;  uv, C}{\partial i}  \right] + \frac{1}{e_{3t}} \frac{\partial w\, C}{\partial k} + D^{lC} + D^{vC}
+\label{Eq_tracer}
+\end{equation}
+
+where expressions of $D^{lC}$ and $D^{vC}$ depend on the choice for the lateral and vertical subgrid scale parameterizations, see equations 5.10 and 5.11 in \citep{Madec_Bk2008} 
+
+{S(C)} , the first term on the right hand side of \ref{Eq_tracer}; is the SMS - Source Minus Sink - inherent to the tracer.  In the case of biological tracer such as phytoplankton, {S(C)} is the balance between phytoplankton growth and its decay through mortality and grazing. In the case of a tracer comprising carbon,  {S(C)} accounts for gas exchange, river discharge, flux to the sediments, gravitational sinking and other biological processes. In the case of a radioactive tracer, {S(C)} is simply loss due to radioactive decay.
+
+The second term (within brackets) represents the advection of the tracer in the three directions. It can be interpreted as the budget between the incoming and outgoing tracer fluxes in a volume $T$-cells $b_t= e_{1t}\,e_{2t}\,e_{3t}$ 
+
+The third term  represents the change due to lateral diffusion. 
+
+The fourth term is change due to vertical diffusion, parameterized as eddy diffusion to represent vertical turbulent fluxes :
+
+\begin{equation}
+D^{vC} =  \frac{1}{e_{3t}} \frac{\partial}{\partial k} \left[  A^{vT} \frac{\partial C}{\partial k} \right]
+\label{Eq_trczdf}
+\end{equation}
+
+where $A^{vT}$ is the vertical eddy diffusivity coefficient of active tracers
+
+\section{The NEMO-TOP interface}
+\label{sec:TopInt}
+
+TOP is the NEMO hardwired interface toward biogeochemical models and provide the physical constraints/boundaries for oceanic tracers. It consists of a modular framework to handle multiple ocean tracers, including also a variety of built-in modules.
+
+This component of the NEMO framework allows one to exploit available modules  and further develop a range of applications, spanning from the implementation of a dye passive tracer to evaluate dispersion processes (by means of MY\_TRC), track water masses age (AGE module), assess the ocean interior penetration of persistent chemical compounds (e.g., gases like CFC or even PCBs), up to the full set of equations involving marine biogeochemical cycles.
+
+TOP interface has the following location in the code repository : \path{<repository>/src/TOP/}
+
+and the following modules are available:
+
+% -----------  tableau  ------------------------------------
+\begin{itemize}
+        \item \textbf{TRP}    	    :    Interface to NEMO physical core for computing tracers transport
+        \item \textbf{CFC}	    :    Inert carbon tracers (CFC11,CFC12, SF6)
+        \item \textbf{C14}	    :    Radiocarbon passive tracer
+        \item \textbf{AGE}	    :    Water age tracking
+        \item \textbf{MY\_TRC}  :	Template for creation of new modules and external BGC models coupling
+        \item \textbf{PISCES}    :	 Built in BGC model. See \citep{Aumont_al_2015} for a throughout description.
+\end{itemize}
+%  ----------------------------------------------------------
+
+\section{The transport component : TRP}
+
+The passive tracer transport component  shares the same advection/diffusion routines with the dynamics, with specific treatment of some features like the surface boundary conditions, or the positivity of passive tracers concentrations.
+ 
+ \subsection{ Advection}
+%------------------------------------------namtrc_adv----------------------------------------------------
+\nlst{namtrc_adv}
+%-------------------------------------------------------------------------------------------------------------
+The advection schemes used for the passive tracers are the same than the ones for $T$ and $S$ and described in section 5.1 of \citep{Madec_Bk2008}. The choice of an advection scheme  can be selected independently and  can differ from the ones used for active tracers. This choice is made in the \textit{namtrc\_adv} namelist, by  setting to \textit{true} one and only one of the logicals \textit{ln\_trcadv\_xxx}, the same way of what is done for dynamics.
+cen2, MUSCL2, and UBS are not \textit{positive} schemes meaning that negative values can appear in an initially strictly positive tracer field which is advected, implying that false extrema are permitted. Their use is not recommended on passive tracers
+
+ \subsection{ Lateral diffusion}
+%------------------------------------------namtrc_ldf----------------------------------------------------
+\nlst{namtrc_ldf}
+%-------------------------------------------------------------------------------------------------------------
+In NEMO v4.0, the passive tracer diffusion has necessarily the same form as the active tracer diffusion, meaning that the numerical scheme must be the same. However the passive tracer mixing coefficient can be chosen as a multiple of the active ones by changing the value of \textit{rn\_ldf\_multi} in namelist \textit{namtrc\_ldf}. The choice of numerical scheme is then set  in the \ngn{namtra\_ldf} namelist for the dynamic described in section 5.2 of \citep{Madec_Bk2008}. 
+
+
+%-----------------We also offers the possibility to increase zonal equatorial diffusion for passive tracers by introducing an enhanced zonal diffusivity coefficent in the equatorial domain which can be defined by the equation below :
+%-----------------\begin{equation} \label{eq:traqsr_iradiance}
+%-----------------Aht  = Aht *  rn_fact_lap * \exp( - \max( 0., z -1000  ) / 1000}  \quad \text{for $L=1$ to $N$}  
+%-----------------\end{equation}
+
+ \subsection{ Tracer damping}
+ 
+%------------------------------------------namtrc_dmp----------------------------------------------------
+\nlst{namtrc_dmp}
+%-------------------------------------------------------------------------------------------------------------
+
+The use of newtonian damping  to climatological fields or observations is also coded, sharing the same routine dans active tracers. Boolean variables are defined in the namelist\_top\_ref to select the tracers on which restoring is applied
+Options are defined through the  \ngn{namtrc\_dmp} namelist variables. The restoring term is added when the namelist parameter \np{ln\_trcdmp} is set to true. The restoring coefficient is a three-dimensional array read in a file, which name is specified by the namelist variable \np{cn\_resto\_tr}. This netcdf file can be generated using the DMP\_TOOLS tool.
+
+ \subsection{ Tracer positivity}
+ 
+%------------------------------------------namtrc_rad----------------------------------------------------
+\nlst{namtrc_rad}
+%-------------------------------------------------------------------------------------------------------------
+
+Sometimes, numerical scheme can generates negative values of passive tracers concentration that must be positive. For exemple,  isopycnal diffusion can created extrema. The trcrad routine artificially corrects negative concentrations with a very crude solution that either sets negative concentration to zero without adjusting the tracer budget, or by removing negative concentration and keeping mass conservation.
+The treatment of negative concentrations is an option and can be selected in the namelist \ngn{namtrc\_rad} by setting the parameter \np{ln\_trcrad}  to true.
+
+\section{The SMS modules}
+
+\label{SMS_models}
+%------------------------------------------namtrc_sms----------------------------------------------------
+%\nlst{namtrc}
+%-------------------------------------------------------------------------------------------------------------
+
+\subsection{Ideal Age}
+%------------------------------------------namage----------------------------------------------------
+%
+\nlst{namage}
+%----------------------------------------------------------------------------------------------------------
+
+
+ An `ideal age' tracer is integrated online in TOP when \textit{ln\_age} = \texttt{.true.} in namelist \textit{namtrc}. This tracer marks the length of time in units of years that fluid has spent in the interior of the ocean, insulated from exposure to the atmosphere. Thus, away from the surface for $z<-H_{\mathrm{Age}}$ where $H_{\mathrm{Age}}$ is specified by the \textit{namage} namelist variable \textit{rn\_age\_depth}, whose default value is 10~m, there is a source $\mathrm{SMS_{\mathrm{Age}}}$ of the age tracer $A$:
+\begin{equation}
+  \label{eq:TOP-age-interior}
+  \mathrm{SMS_{\mathrm{Age}}} = 1 \mathrm{yr}\;^{-1} = 1/T_{\mathrm{year}},
+ \end{equation}
+ where the length of the current year $T_{\mathrm{year}} = 86400*N_{\mathrm{days\;in\;current\; year}}\;\mathrm{s}$, where $N_{\mathrm{days\;in\;current\; year}}$ may be 366 or 365 depending on whether the current year is a leap year or not.
+ Near the surface, for $z>-H_{\mathrm{Age}}$, ideal age is relaxed back to zero:
+\begin{equation}
+  \label{eq:TOP-age-surface}
+   \mathrm{SMS_{\mathrm{Age}}} = -\lambda_{\mathrm{Age}}A,
+ \end{equation}
+ where the relaxation rate $\lambda_{\mathrm{Age}}$  (units $\mathrm{s}\;^{-1}$) is specified by the \textit{namage} namelist variable \textit{rn\_age\_kill\_rate} and has a default value of 1/7200~s. Since this relaxation is applied explicitly, this relaxation rate in principle should not exceed $1/\Delta t$, where $\Delta t$ is the time step used to step forward passive tracers (2 * \textit{nn\_dttrc * rn\_rdt} when the default  leapfrog time-stepping scheme is employed).
+
+ Currently the 1-dimensional reference depth of the grid boxes is used rather than the dynamically evolving depth to determine whether the age tracer is incremented or relaxed to zero. This means that the tracer only works correctly in z-coordinates. To ensure that the forcing is independent of the level thicknesses, where the tracer cell at level $k$ has its upper face $z=-depw(k)$ above the depth $-H_{\mathrm{Age}}$, but its lower face $z=-depw(k+1)$ below that depth, then the age source
+ \begin{equation}
+  \label{eq:TOP-age-mixed}
+   \mathrm{SMS_{\mathrm{Age}}} = -f_{\mathrm{kill}}\lambda_{\mathrm{Age}}A +f_{\mathrm{add}}/T_{\mathrm{year}} ,
+ \end{equation}
+ where
+ \begin{align}
+    f_{\mathrm{kill}} &= e3t_k^{-1}(H_{\mathrm{Age}} - depw(k)) , \\
+    f_{\mathrm{add}} &= 1 - f_{\mathrm{kill}}.
+ \end{align}
+
+
+ This implementation was first used in the CORE-II intercomparison runs described e.g.\ in \citet{Danabasoglu_al_2014}.
+
+\subsection{Inert carbons tracer}
+
+%------------------------------------------namage----------------------------------------------------
+%
+\nlst{namcfc}
+%----------------------------------------------------------------------------------------------------------
+
+Chlorofluorocarbons 11 and 12 (CFC-11 and CFC-12), and sulfur hexafluoride (SF6), are synthetic chemicals manufactured for industrial and domestic applications from the early 20th century onwards.
+CFC-11 (CCl$_{3}$F) is a volatile liquid at room temperature, and was widely used in refrigeration. CFC-12 (CCl$_{2}$F$_{2}$) is a gas at room temperature, and, like CFC-11, was widely used as a refrigerant,
+and additionally as an aerosol propellant. SF6 (SF$_{6}$) is also a gas at room temperature, with a range of applications based around its property as an excellent electrical insulator (often replacing more toxic alternatives).
+All three are relatively inert chemicals that are both non-toxic and non-flammable, and their wide use has led to their accumulation within the Earth's atmosphere. Large-scale production of CFC-11 and CFC-12 began in the 1930s, while production of SF6 began in the 1950s, and their atmospheric concentration time-histories are shown in Figure \ref{img_cfcatm}.
+As can be seen in the figure, while the concentration of SF6 continues to rise to the present  day, the concentrations of both CFC-11 and CFC-12 have levelled off and declined since around the 1990s.
+These declines have been driven by the Montreal Protocol (effective since August 1989), which has banned the production of CFC-11 and CFC-12 (as well as other CFCs) because of their role in the depletion of
+stratospheric ozone (O$_{3}$), critical in decreasing the flux of ultraviolet radiation to the Earth's surface. Separate to this role in ozone-depletion, all three chemicals are significantly more potent greenhouse gases 
+than CO$_{2}$ (especially SF6), although their relatively low atmospheric concentrations limit their role in climate change. \\
+
+% Chlorofluorocarbons 11 and 12 (CFC-11 and CFC-12), and sulfur hexafluoride (SF6),
+% are greenhouse gases that have been released into the atmosphere by human activities.
+% In the case of CFC-11 and CFC-12, this release began in the 1930s, and atmospheric
+% concentrations increased until around the late 1990s afterwhich they began to decline in
+% response to the Montreal Protocol.
+% In the case of SF6, release began in the 1950s 
+% This release began in the 1930s for CFC-11 and CFC-12, and the 1950s for SF6, and
+% regularly increasing their atmospheric concentration until the 1090s, 2000s for respectively CFC11, CFC12, 
+% and is still increasing, and SF6 (see Figure \ref{img_cfcatm}).  \\
+
+The ocean is a notable sink for all three gases, and their relatively recent occurrence in the atmosphere, coupled to the ease of making high precision measurements of their dissolved concentrations, has made them
+valuable in oceanography. % for tracking interior ventilation and mixing.
+Because they only enter the ocean via surface air-sea exchange, and are almost completely chemically and biologically inert, their distribution within the ocean interior reveals its ventilation via transport and mixing.
+Measuring the dissolved concentrations of the gases -- as well as the mixing ratios between them -- shows circulation pathways within the ocean as well as water mass ages (i.e. the time since last contact with the
+atmosphere). This feature of the gases has made them valuable across a wide range of oceanographic problems. One use lies in ocean modelling, where they can be used to evaluate the realism of the circulation and 
+ventilation of models, key for understanding the behaviour of wider modelled marine biogeochemistry (e.g. \citep{Dutay_al_2002,Palmieri_2015}). \\
+
+Modelling these gases (henceforth CFCs) in NEMO is done within the passive tracer transport module, TOP, using the conservation state equation \ref{Eq_tracer}
+
+Advection and diffusion of the CFCs in NEMO are calculated by the physical module, OPA,
+whereas sources and sinks are done by the CFC module within TOP. 
+The only source for CFCs in the ocean is via air-sea gas exchange at its surface, and since CFCs are generally 
+stable within the ocean, we assume that there are no sinks (i.e. no loss processes) within the ocean interior. 
+Consequently, the sinks-minus-sources term for CFCs consists only of their air-sea fluxes, $F_{cfc}$, as
+described in the Ocean Model Inter-comparison Project (OMIP) protocol \citep{Orr_al_2017}:
+
+% Because CFCs being stable in the ocean, we consider that there is no CFCs sink.
+% The only CFC source in the ocean is through the Air-Sea gas exchange at the surface.
+% These are calculated as air-sea fluxes (F$_{cfc}$), as described in the OMIP6 protocol \citep{artOMIP6}:
+
+\begin{eqnarray}
+F_{cfc} = K_{w} \, \cdot \, (C_{sat} - C_{surf}) \, \cdot  \, (1 - f_{i})
+\label{equ_CFC_flux}
+\end{eqnarray}  
+
+Where $K_{w}$ is the piston velocity (in m~s$^{-1}$), as defined in Equation \ref{equ_Kw}; 
+$C_{sat}$ is the saturation concentration of the CFC tracer, as defined in Equation \ref{equ_C_sat}; 
+$C_{surf}$ is the local surface concentration of the CFC tracer within the model (in mol~m$^{-3}$); 
+and $f_{i}$ is the fractional sea-ice cover of the local ocean (ranging between 0.0 for ice-free ocean,
+through to 1.0 for completely ice-covered ocean with no air-sea exchange).
+
+The saturation concentration of the CFC, $C_{sat}$, is calculated as follows:
+
+\begin{eqnarray}
+C_{sat} = Sol \, \cdot \, P_{cfc}
+\label{equ_C_sat}
+\end{eqnarray}  
+
+Where $Sol$ is the gas solubility in mol~m$^{-3}$~pptv$^{-1}$, as defined in Equation \ref{equ_Sol_CFC}; 
+and $P_{cfc}$ is the atmosphere concentration of the CFC (in parts per trillion by volume, pptv).
+This latter concentration is provided to the model by the historical time-series of \citet{Bullister_2015}.
+This includes bulk atmospheric concentrations of the CFCs for both hemispheres -- this is necessary because of 
+the geographical asymmetry in the production and release of CFCs to the atmosphere. 
+Within the model, hemispheric concentrations are uniform, with the exception of the region between 
+10$^{\circ}$N and 10$^{\circ}$ in which they are linearly interpolated.
+
+The piston velocity $K_{w}$ is a function of 10~m wind speed (in m~s$^{-1}$) and sea surface temperature, 
+$T$ (in $^{\circ}$C), and is calculated here following \citet{Wanninkhof_1992}:
+
+\begin{eqnarray}
+K_{w} = X_{conv} \, \cdot \, a \, \cdot \, u^2 \, \cdot \, \sqrt{ \frac{Sc(T)}{660} }
+\label{equ_Kw}
+\end{eqnarray} 
+
+Where $X_{conv}$ = $\frac{0.01}{3600}$, a conversion factor that changes the piston velocity 
+from cm~h$^{-1}$ to m~s$^{-1}$; 
+$a$ is a constant re-estimated by \citet{Wanninkhof_2014} to 0.251 (in $\frac{cm~h^{-1}}{(m~s^{-1})^{2}}$);
+and $u$ is the 10~m wind speed in m~s$^{-1}$ from either an atmosphere model or reanalysis atmospheric forcing.
+$Sc$ is the Schmidt number, and is calculated as follow, using coefficients from \citet{Wanninkhof_2014} (see Table \ref{tab_Sc}).
+
+\begin{eqnarray}
+Sc =  a0 + (a1 \, \cdot \, T) + (a2  \, \cdot \, T^2) + (a3 \, \cdot \, T^3) + (a4 \, \cdot \, T^4)
+\label{equ_Sc}
+\end{eqnarray} 
+
+The solubility, $Sol$, used in Equation \ref{equ_C_sat} is calculated in mol~l$^{-1}$~atm$^{-1}$, 
+and is specific for each gas. 
+It has been experimentally estimated by \citet{Warner_Weiss_1985} as a function of temperature 
+and salinity:
+
+% AXY: this equation looks both weird and possibly wrong; it doesn't look like the one in the
+% code version that I have to hand, although this might be out of date; in any case, I'dag
+% strongly suggest avoiding the use of the \frac{}{100}, and instead substitute a term that is
+% "degrees Kelvin divided by 100" (which is weird in itself); and make this term use Celcius 
+% so that you're not using T twice in different ways
+
+\begin{eqnarray}
+\ln{(Sol)} = a_1 + \frac{a_2}{ T_{X}} + a_3 \, \cdot \, \ln{ T_{X} } + a_4 \, \cdot \, T_{X}^2 + S \, \cdot \, ( b_1 + b_2 \, \cdot \, T_{X} + b_3 \, \cdot \, T_{X}^2 )
+\label{equ_Sol_CFC}
+\end{eqnarray}  
+
+% \begin{eqnarray}
+% \ln{(Sol)} = a1 + a2 \, \frac{100}{T} + a3 \, \ln{ (\frac{T}{100}) } + a4 \, \frac{T}{100}^2 + S \, ( b1 + b2 \, \frac{T}{100} + b3 \, \frac{T}{100}^2 )
+% \label{equ_Sol_CFC}
+% \end{eqnarray}  
+
+Where $T_{X}$ is $\frac{T + 273.16}{100}$, a function of temperature; 
+and the $a_{x}$ and $b_{x}$ coefficients are specific for each gas (see Table \ref{tab_ref_CFC}).
+This is then converted to mol~m$^{-3}$~pptv$^{-1}$ assuming a constant atmospheric surface pressure of 1~atm.
+The solubility of CFCs thus decreases with rising $T$ while being relatively insensitive to salinity changes. 
+Consequently, this translates to a pattern of solubility where it is greatest in cold, polar regions (see Figure \ref{img_cfcsol}).
+
+% AXY: not 100% sure about the units below; they might be in nanomol, or in seconds or years
+
+The standard outputs of the CFC module are seawater CFC concentrations (in mol~m$^{-3}$), the net air-sea flux (in mol~m$^{-2}$~d$^{-1}$) and the cumulative net air-sea flux (in mol~m$^{-2}$).
+Using XIOS, it is possible to obtain outputs such as the vertical integral of CFC concentrations (in mol~m$^{-2}$; see Figure \ref{img_cfcinv}).
+This property, when divided by the surface CFC concentration, estimates the local penetration depth (in m) of the CFC.
+
+% AXY: not sure what's meant by some of the below; I've tried to reword it above
+% The standard outputs of the CFC module are the CFCs concentration in the sea water, and the records of the outputs-frequency-averaged as well as the total air-sea fluxes.
+% Using XIOS, it is also possible to ask for the CFCs vertical inventory in the output file (see Figure cfc inventory example ?).
+
+\subsubsection{Notes}
+
+In comparison to the OMIP protocol, the CFC module in NEMO has several differences:
+
+% AXY: consider an itemized list here if you've got a list of differences
+
+For instance, C$_{sat}$ is calculated for a fixed surface pressure of 1atm, what could be corrected in a further version of the module.
+
+
+\begin{table}[!t]
+\caption{Coefficients for fit of the CFCs solubility (Eq. \ref{equ_Sol_CFC}).}
+\vskip4mm
+\centering
+\begin{tabular}{l l l l l l l l l}
+\hline 
+Gas   & & a1 & a2 & a3 & a4 & b1 & b2 & b3 \\          
+\hline
+CFC-11 & & -218.0971 & 298.9702 & 113.8049 & -1.39165 & -0.143566  & 0.091015   & -0.0153924 \\
+CFC-12 & & -229.9261 & 319.6552 & 119.4471 & -1.39165 & -0.142382  & 0.091459   & -0.0157274 \\
+SF6    & & -80.0343  & 117.232  & 29.5817  & 0.0      & 0.0335183  & -0.0373942 & 0.00774862 \\
+\hline
+\end{tabular} 
+\label{tab_ref_CFC}
+\end{table}
+
+
+\begin{table}[!t]
+\caption{Coefficients for fit of the CFCs Schmidt number (Eq. \ref{equ_Sc}). }
+\vskip4mm
+\centering
+\begin{tabular}{l l l l l l l }
+\hline 
+Gas  & & a0 & a1 & a2 & a3 & a4 \\          
+\hline
+CFC-11 & & 3579.2  & -222.63 & 7.5749 & -0.14595 & 0.0011874   \\
+CFC-12 & & 3828.1  & -249.86 & 8.7603 & -0.1716  & 0.001408    \\
+SF6    & & 3177.5  & -200.57 & 6.8865 & -0.13335 & 0.0010877   \\
+\hline
+\end{tabular} 
+\label{tab_Sc}
+\end{table}
+
+%% -----------------------------------
+%% -----------------------------------
+%% Figures %%
+
+
+\begin{figure}[!h]
+\centering
+\includegraphics[width=0.80\textwidth]{CFC-atm-evol}
+  \caption{Atmospheric CFC11, CFC12 and SF6 partial pressure evolution in both hemispheres.}
+\label{img_cfcatm}
+\end{figure}
+
+\begin{figure}[!h]
+\centering
+\includegraphics[width=0.80\textwidth]{CFC_solub}
+  \caption{CFC11 solubility in mol m$^{-3}$ pptv$^{-1}$, calculated from the World Ocean Atlas 2013 temperature and salinity annual climatology.}
+\label{img_cfcsol}
+\end{figure}
+
+\begin{figure}[!h]
+\centering
+\includegraphics[width=0.80\textwidth]{CFC_inventory}
+  \caption{CFC11 vertical inventory in $\mu$mol m$^{-2}$, from one of the UK Earth System Model 1 model (UKESM1 - which uses NEMO as ocean component, with TOP for the passive tracers) historical run at year 2000.}
+\label{img_cfcinv}
+\end{figure}
+
+
+\subsection{Radiocarbon}
+
+%------------------------------------------namage----------------------------------------------------
+%
+\nlst{namc14_fcg}
+\nlst{namc14_typ}
+\nlst{namc14_sbc}
+%----------------------------------------------------------------------------------------------------------
+
+The C14 package implemented in NEMO by Anne Mouchet models ocean $\Dcq$. It offers several possibilities: $\Dcq$ as a physical tracer of the ocean ventilation (natural $\cq$), assessment of bomb radiocarbon uptake, as well as transient studies of paleo-historical ocean radiocarbon distributions. 
+
+\subsubsection{Method}
+
+ Let  $\Rq$ represent the ratio of $\cq$ atoms to the total number of carbon atoms in the sample, i.e. $\cq/\mathrm{C}$. Then, radiocarbon anomalies are reported as
+\begin{equation}
+\Dcq = \left( \frac{\Rq}{\Rq_\mathrm{ref}} - 1 \right) 10^3, \label{eq:c14dcq}
+\end{equation}
+where $\Rq_{\textrm{ref}}$ is a reference ratio. For the purpose of ocean ventilation studies $\Rq_{\textrm{ref}}$ is set to one.
+
+Here we adopt the approach of \cite{Fiadeiro_1982} and \cite{Toggweiler_al_1989a,Toggweiler_al_1989b} in which  the ratio $\Rq$ is transported rather than the individual concentrations C and $\cq$.
+This approach calls for a strong assumption, i.e., that of a homogeneous and constant dissolved inorganic carbon (DIC) field \citep{Toggweiler_al_1989a,Mouchet_2013}. While in terms of
+oceanic $\Dcq$, it yields similar results to approaches involving carbonate chemistry, it underestimates the bomb radiocarbon inventory because it assumes a constant air-sea $\cd$ disequilibrium (Mouchet, 2013). Yet, field reconstructions of the ocean bomb $\cq$ inventory are also biased low \citep{Naegler_2009} since they assume that the anthropogenic perturbation did not affect ocean DIC since the pre-bomb epoch. For these reasons, bomb $\cq$ inventories obtained with the present method are directly comparable to reconstructions based on field measurements.
+
+This simplified approach also neglects the effects of fractionation (e.g.,  air-sea exchange) and of biological processes. Previous studies by \cite{Bacastow_MaierReimer_1990} and \cite{Joos_al_1997} resulted in nearly identical $\Dcq$ distributions among experiments considering biology or not.
+Since observed $\Rq$ ratios are corrected for the isotopic fractionation when converted to the standard $\Dcq$ notation \citep{Stuiver_Polach_1977} the model results are directly comparable to observations. 
+
+Therefore the simplified approach is justified for the purpose of assessing the circulation and ventilation of OGCMs.
+
+The equation governing the transport of $\Rq$  in the ocean is
+\begin{equation}
+\frac{\partial}{\partial t} {\Rq} =  - \bigtriangledown \cdot ( \mathbf{u} \Rq - \mathbf{K} \cdot \bigtriangledown \Rq )  - \lambda \Rq, \label{eq:quick}
+\end{equation}
+where $\lambda$ is the radiocarbon decay rate, ${\mathbf{u}}$ the 3-D velocity field, and $\mathbf{K}$ the diffusivity tensor.
+
+At the air-sea interface a Robin boundary condition \citep{Haine_2006} is applied to \eqref{eq:quick}, i.e., the flux
+through the interface is proportional to the difference in the ratios between
+the ocean and the atmosphere
+\begin{equation}
+\mathcal{\!F} =  \kappa_{R}  (\Rq  - \Rq_{a} ), \label{eq:BCR}
+\end{equation}
+where $\mathcal{\!F}$ is the flux out of the ocean, and $\Rq_{a}$ is the atmospheric $\cq/\mathrm{C}$ ratio. The transfer velocity $ \kappa_{R} $ for the radiocarbon ratio in \eqref{eq:BCR} is computed as
+\begin{equation}
+ \kappa_{R} =  \frac{\kappa_{\cd} K_0}{\overline{\Ct}} \, \pacd   \label{eq:Rspeed}
+\end{equation}
+with $\kappa_{\cd}$ the carbon dioxide transfer or piston velocity, $K_0$ the $\cd$ solubility in seawater, $\pacd$ the atmospheric $\cd$ pressure at sea level, and $\overline{\Ct}$ the average sea-surface dissolved inorganic carbon concentration.
+
+
+The $\cd$ transfer velocity is based on the empirical formulation of \cite{Wanninkhof_1992} with chemical enhancement \citep{Wanninkhof_Knox_1996,Wanninkhof_2014}. The original formulation is modified to account for the reduction of the  air-sea exchange rate in the presence of sea ice. Hence
+\begin{equation}
+\kappa_\cd=\left( K_W\,\mathrm{w}^2 + b  \right)\, (1-f_\mathrm{ice})\,\sqrt{660/Sc}, \label{eq:wanc14}
+\end{equation}
+with $\mathrm{w}$ the wind magnitude, $f_\mathrm{ice}$ the fractional ice cover, and $Sc$ the Schmidt number.
+$K_W$ in \eqref{eq:wanc14} is an empirical coefficient with dimension of an inverse velocity.
+The chemical enhancement term $b$ is represented as a function of temperature $T$ \citep{Wanninkhof_1992}
+\begin{equation}
+b=2.5 ( 0.5246 + 0.016256 T+ 0.00049946  * T^2 ). \label{eq:wanchem}
+\end{equation}
+
+%We compare the results of equilibrium and transient experiments obtained with both methods in section \ref{sec:UNDEU}.
+
+%
+\subsubsection{Model setup}
+\label{sec:setup}
+
+To activate the \texttt{C14} package, set the parameter \textit{ln\_c14} = \texttt{.true.} in namelist \textit{namtrc}.
+
+\paragraph{Parameters and formulations}
+\label{sec:param}
+ %
+The radiocarbon decay rate (\CODE{rlam14}; in \texttt{trcnam\_c14} module) is set to $\lambda=(1/8267)$ yr$^{-1}$ \citep{Stuiver_Polach_1977}, which corresponds to a half-life of 5730 yr.\\[1pt]
+%
+The Schmidt number $Sc$, Eq. \eqref{eq:wanc14}, is calculated with the help of the formulation of \cite{Wanninkhof_2014}. The $\cd$ solubility $K_0$ in \eqref{eq:Rspeed} is taken from \cite{Weiss_1974}. $K_0$ and $Sc$ are computed with the OGCM temperature and salinity fields (\texttt{trcsms\_c14} module).\\[1pt]
+%
+The following parameters intervening in the air-sea exchange rate are set in \texttt{namelist\_c14}:
+\begin{itemize}
+\item The reference DIC concentration $\overline{\Ct}$ (\CODE{xdicsur}) intervening in \eqref{eq:Rspeed} is classically set to 2 mol m$^{-3}$ \citep{Toggweiler_al_1989a,Orr_al_2001,Butzin_al_2005}.
+%
+\item The value of the empirical coefficient $K_W$ (\CODE{xkwind}) in \eqref{eq:wanc14} depends on the wind field and on the model upper ocean mixing rate \citep{Toggweiler_al_1989a,Wanninkhof_1992,Naegler_2009,Wanninkhof_2014}.
+It should be adjusted so that the globally averaged $\cd$ piston velocity is $\kappa_\cd = 16.5\pm 3.2$ cm/h \citep{Naegler_2009}.
+%The sensitivity to this parametrization is discussed in section \ref{sec:result}.
+%
+\item Chemical enhancement (term $b$  in Eq. \ref{eq:wanchem}) may be set on/off by means of the logical variable \CODE{ln\_chemh}. 
+\end{itemize}
+
+%
+\paragraph{Experiment type}
+The type of experiment is determined by the value given to \CODE{kc14typ} in \texttt{namelist\_c14}. There are three possibilities:
+\begin{enumerate}
+\item natural $\Dcq$: \CODE{kc14typ}=0
+\item bomb $\Dcq$: \CODE{kc14typ}=1
+\item transient paleo-historical $\Dcq$: \CODE{kc14typ}=2
+\end{enumerate}
+%
+\textbf{Natural or Equilibrium radiocarbon}
+\CODE{kc14typ}=0
+
+Unless otherwise specified in \texttt{namelist\_c14}, the atmospheric $\Rq_a$ (\CODE{rc14at}) is set to one, the atmospheric $\cd$ (\CODE{pco2at}) to 280 ppm, and the ocean $\Rq$ is initialized with \CODE{rc14init=0.85}, i.e., $\Dcq=$-150\textperthousand  \cite[typical for deep-ocean, Fig 6 in][]{Key_al_2004}.
+
+Equilibrium experiment should last until 98\% of the ocean volume exhibit a drift of less than 0.001\textperthousand/year \citep{Orr_al_2000}; this is usually achieved after few kyr (Fig. \ref{fig:drift}).
+%
+\begin{figure}[!h]
+\begin{center}
+\includegraphics[width=0.9\hsize]{drift-EXP06}
+\end{center}
+\vspace{-4ex}
+\caption{ Time evolution of $\Rq$ inventory anomaly for equilibrium run with homogeneous ocean initial state. The anomaly (or drift) is given in \%  change in total ocean inventory per 50 years. Time on x-axis is in simulation year.\label{fig:drift} }
+\end{figure}
+
+\textbf{Transient: Bomb}
+\label{sec:bomb}
+\CODE{kc14typ}=1
+
+\begin{figure}[!h]
+\begin{center}
+\includegraphics[width=0.9\hsize]{C14bombCO2-NB}
+\end{center}
+\vspace{-4ex}
+\caption{Atmospheric $\Dcq$ (solid; left axis) and $\cd$ (dashed; right axis)  forcing for the $\cq$-bomb experiments. The $\Dcq$ is illustrated for the three zonal bands (upper, middle, and lower curves correspond to latitudes $> 20$N, $\in [20\mathrm{S},20\mathrm{N}]$, and $< 20$S, respectively.} \label{fig:bomb}
+\end{figure}
+
+Performing this type of experiment requires that a pre-industrial equilibrium run be performed beforehand (\CODE{ln\_rsttr} should be set to \texttt{.TRUE.}). 
+
+An exception to this rule is when wishing to perform a perturbation bomb experiment as was possible with the package \texttt{C14b}. It is still possible to easily set-up that type of transient experiment for which no previous run is needed.  In addition to the instructions as given in this section it is however necessary to adapt the \texttt{atmc14.dat} file so that it does no longer contain any negative $\Dcq$ values (Suess effect in the pre-bomb period).
+
+The model  is integrated from a given initial date following the observed records provided from 1765 AD on ( Fig. \ref{fig:bomb}).
+The file \texttt{atmc14.dat}  \cite[][\& I. Levin, personal comm.]{Enting_al_1994} provides atmospheric $\Dcq$ for three latitudinal bands: 90S-20S,    20S-20N \&    20N-90N.
+Atmospheric $\cd$ in the file \texttt{splco2.dat} is obtained from a spline fit through ice core data and direct atmospheric measurements \cite[][\& J. Orr, personal comm.]{Orr_al_2000}.
+Dates in these forcing files are expressed as yr AD.
+
+To ensure that the atmospheric forcing is applied properly as well as that output files contain consistent dates and inventories the experiment should be set up carefully:
+\begin{itemize}
+\item Specify the starting date of the experiment: \CODE{nn\_date0} in \texttt{namelist}.  \CODE{nn\_date0} is written as Year0101 where Year may take any positive value (AD).
+\item Then the parameters \CODE{nn\_rstctl} in  \texttt{namelist} (on-line) and \CODE{nn\_rsttr} in \texttt{namelist\_top} (off-line)  must be \textbf{set to 0} at the start of the experiment (force the date to \CODE{nn\_date0} for the \textbf{first} experiment year). 
+\item These two parameters (\CODE{nn\_rstctl} and \CODE{nn\_rsttr}) have then to be \textbf{set to 2} for the following years (the date must be read in the restart file).
+\end{itemize}
+ If the experiment date is outside the data time span then the first or last atmospheric concentrations are prescribed depending on whether the date is earlier or later. Note that \CODE{tyrc14\_beg} (\texttt{namelist\_c14}) is not used in this context.
+
+%
+\textbf{Transient: Past}
+\CODE{kc14typ}=2
+%
+\begin{figure}[!h]
+\begin{center}
+\includegraphics[width=0.9\hsize]{PaleoCO2C14-NB}
+\end{center}
+\vspace{-4ex}
+\caption{Atmospheric $\Dcq$ (solid) and $\cd$ (dashed)  forcing for the Paleo experiments. The $\cd$ scale is given on the right axis.} \label{fig:paleo}
+\end{figure}
+
+This experiment type does not need a previous equilibrium run. It should start 5--6 kyr earlier than the period to be analyzed.
+Atmospheric $\Rq_a$ and $\cd$ are prescribed from forcing files. The ocean $\Rq$ is initialized with the value attributed to \CODE{rc14init} in \texttt{namelist\_c14}.
+
+The file \texttt{intcal13.14c} \citep{Reimer_al_2013} contains atmospheric $\Dcq$ from 0 to 50 kyr cal BP\footnote{cal BP: number of years before 1950 AD}.
+The $\cd$ forcing is provided in file \texttt{ByrdEdcCO2.txt}. The content of this file is based on  the high resolution record from EPICA Dome C \citep{Monnin_al_2004} for the Holocene and the Transition, and on Byrd Ice Core CO2 Data for 20--90 kyr BP  \citep{Ahn_Brook_2008}. These atmospheric values are reproduced in Fig. \ref{fig:paleo}. Dates in these files are expressed as yr BP. 
+
+To ensure that the atmospheric forcing is applied properly as well as that output files contain consistent dates and inventories the experiment should be set up carefully.
+The true experiment starting date is given by \CODE{tyrc14\_beg} (in yr BP) in \texttt{namelist\_c14}. In consequence, \CODE{nn\_date0} in \texttt{namelist} MUST be set to 00010101.\\
+Then the parameters \CODE{nn\_rstctl} in  \texttt{namelist} (on-line) and \CODE{nn\_rsttr} in \texttt{namelist\_top} (off-line)  must be set to 0 at the start of the experiment (force the date to \CODE{nn\_date0} for the first experiment year). These two parameters have then to be set to 2 for the following years (read the date in the restart file). \\
+ If the experiment date is outside the data time span then the first or last atmospheric concentrations are prescribed depending on whether the date is earlier or later.
+
+%
+\paragraph{Model output}
+\label{sec:output}
+All output fields in Table \ref{tab:out} are routinely computed. It depends on the actual settings in \texttt{iodef.xml} whether they are stored or not.
+%
+\begin{table}[!h]
+\begin{center}
+\caption{Standard output fields for the C14 package \label{tab:out}.
+}
+%\begin{small}
+\renewcommand{\arraystretch}{1.3}%
+\begin{tabular}[h]{|l*{3}{|c}|l|}
+\hline
+Field & Type & Dim & Units & Description \\ \hline
+RC14 & ptrc & 3-D & -        & Radiocarbon ratio \\
+DeltaC14 & diad & 3-D & \textperthousand & $\Dcq$\\ 
+C14Age & diad & 3-D & yr &   Radiocarbon age \\
+RAge & diad & 2-D & yr & Reservoir age\\
+qtr\_c14 &  diad & 2-D & m$^{-2}$ yr$^{-1}$ & Air-to-sea net $\Rq$ flux\\
+qint\_c14 & diad & 2-D &   m$^{-2}$ &  Cumulative air-to-sea $\Rq$ flux \\
+AtmCO2 & scalar & 0-D & ppm & Global atmospheric $\cd$ \\ 
+AtmC14 & scalar & 0-D & \textperthousand  & Global atmospheric $\Dcq$\\ 
+K\_CO2 & scalar & 0-D & cm h$^{-1}$  & Global $\cd$ piston velocity ($ \overline{\kappa_{\cd}}$) \\ 
+K\_C14 & scalar & 0-D &m yr$^{-1}$ & Global $\Rq$ transfer velocity  ($ \overline{\kappa_R}$)\\ 
+C14Inv & scalar & 0-D & $10^{26}$ atoms & Ocean radiocarbon inventory \\ \hline
+\end{tabular}
+%\end{small}
+\end{center}
+\end{table}
+%!   Standard ratio: 1.176E-12 ; Avogadro's nbr = 6.022E+23 at/mol ; bomb C14 traditionally reported as 1.E+26 atoms
+%   REAL(wp), PARAMETER            :: atomc14=1.176*6.022E-15   ! conversion factor 
+% atomc14 * xdicsur * zdum
+
+The radiocarbon age is computed as  $(-1/\lambda) \ln{ \left( \Rq \right)}$, with zero age corresponding to $\Rq=1$. 
+
+The reservoir age is the age difference between the ocean uppermost layer and the atmosphere. It is usually reported as conventional radiocarbon age; i.e., computed by means of the Libby radiocarbon mean life \cite[8033 yr;][]{Stuiver_Polach_1977}
+\begin{align}
+{^{14}\tau_\mathrm{c}}= -8033 \; \ln \left(1 + \frac{\Dcq}{10^3}\right), \label{eq:convage}
+\end{align}
+where ${^{14}\tau_\mathrm{c}}$ is expressed in years B.P. Here we do not use that convention and compute reservoir ages with the mean lifetime $1/\lambda$. Conversion from one scale to the other is readily performed. The conventional radiocarbon age is lower than the radiocarbon age by $\simeq3\%$.
+
+The ocean radiocarbon  inventory is computed as
+\begin{equation}
+N_A \Rq_\mathrm{oxa} \overline{\Ct} \left( \int_\Omega \Rq d\Omega \right) /10^{26}, \label{eq:inv}
+\end{equation}
+where $N_A$ is the Avogadro's number ($N_A=6.022\times10^{23}$ at/mol), $\Rq_\mathrm{oxa}$ is the oxalic acid radiocarbon standard \cite[$\Rq_\mathrm{oxa}=1.176\times10^{-12}$;][]{Stuiver_Polach_1977}, and $\Omega$ is the ocean volume.  Bomb $\cq$ inventories are traditionally reported in units of $10^{26}$ atoms, hence the denominator in \eqref{eq:inv}.
+
+All transformations from second to year, and inversely, are performed with the help of the physical constant \CODE{rsiyea} the sideral year length expressed in seconds\footnote{The variable (\CODE{nyear\_len}) which reports the length in days of the previous/current/future year (see \textrm{oce\_trc.F90}) is not a constant. }.
+
+The global transfer velocities represent time-averaged\footnote{the actual duration is set in \texttt{iodef.xml}} global integrals of the transfer rates:
+ \begin{equation}
+ \overline{\kappa_{\cd}}= \int_\mathcal{S} \kappa_{\cd} d\mathcal{S}  \text{ and } \overline{\kappa_R}= \int_\mathcal{S} \kappa_R d\mathcal{S}
+\end{equation}
+
+
+\subsection{PISCES biogeochemical model}
+
+PISCES is a biogeochemical model which simulates the lower trophic levels of marine ecosystem (phytoplankton, microzooplankton and mesozooplankton) and the biogeochemical cycles of carbonand of the main nutrients (P, N, Fe, and Si). The  model is intended to be used for both regional and global configurations at high or low spatial resolutions as well as for  short-term (seasonal, interannual) and long-term (climate change, paleoceanography) analyses. 
+Two versions of PISCES are available in NEMO v4.0 :
+
+PISCES-v2, by setting in namelist\_pisces\_ref  \np{ln\_p4z} to true,  can be seen as one of the many Monod models \citep{Monod_1942}. It assumes a constant Redfield ratio and phytoplankton growth depends on the external concentration in nutrients. There are twenty-four prognostic variables (tracers) including two phytoplankton compartments  (diatoms and nanophytoplankton), two zooplankton size-classes (microzooplankton and  mesozooplankton) and a description of the carbonate chemistry. Formulations in PISCES-v2 are based on a mixed Monod/Quota formalism: On one hand, stoichiometry of C/N/P is fixed and growth rate of phytoplankton is limited by the external availability in N, P and Si. On the other hand, the iron and silicium quotas are variable and growth rate of phytoplankton is limited by the internal availability in Fe. Various parameterizations can be activated in PISCES-v2, setting for instance the complexity of iron chemistry or the description of particulate organic materials. 
+
+PISCES-QUOTA has been built on the PISCES-v2 model described in \citet{Aumont_al_2015}. PISCES-QUOTA has thirty-nine prognostic compartments. Phytoplankton growth can be controlled by five modeled limiting nutrients: Nitrate and Ammonium, Phosphate, Silicate and Iron. Five living compartments are represented: Three phytoplankton size classes/groups corresponding to picophytoplankton, nanophytoplankton and diatoms, and two zooplankton size classes which are microzooplankton and mesozooplankton. For phytoplankton, the prognostic variables are the carbon, nitrogen, phosphorus,  iron, chlorophyll and silicon biomasses (the latter only for diatoms). This means that the N/C, P/C, Fe/C and Chl/C ratios of both phytoplankton groups as well as the Si/C ratio of diatoms are prognostically predicted  by the model. Zooplankton are assumed to be strictly homeostatic \citep[e.g.,][]{Sterner_2002,Woods_Wilson_2013,Meunier_al_2014}. As a consequence, the C/N/P/Fe ratios of these groups are maintained constant and are not allowed to vary. In PISCES, the Redfield ratios C/N/P are set to 122/16/1 \citep{Takahashi_al_1985} and the -O/C ratio is set to 1.34 \citep{Kortzinger_al_2001}. No silicified zooplankton is assumed. The bacterial pool is not yet explicitly modeled.
+
+There are three non-living compartments: Semi-labile dissolved organic matter, small sinking particles, and large sinking particles. As a consequence of the variable stoichiometric ratios of phytoplankton and of the stoichiometric regulation of zooplankton, elemental ratios in organic matter cannot be supposed constant anymore as that was the case in PISCES-v2. Indeed, the nitrogen, phosphorus, iron, silicon and calcite pools of the particles are now all explicitly modeled. The sinking speed of the particles is not altered by their content in calcite and biogenic silicate (''The ballast effect'', \citep{Honjo_1996,Armstrong_al_2002}). The latter particles are assumed to sink at the same speed as the large organic matter particles. All the non-living compartments experience aggregation due to turbulence and differential settling as well as Brownian coagulation for DOM.
+
+ 
+\subsection{MY\_TRC interface for coupling external BGC models}
+\label{Mytrc}
+
+The NEMO-TOP has only one built-in biogeochemical model - PISCES - but there are several BGC models - MEDUSA, ERSEM, BFM or ECO3M - which are meant to be coupled with the NEMO dynamics. Therefore it was necessary to provide to the users a framework for easily add their own BGCM model, that can be a single passive tracer.
+The generalized interface is pivoted on MY\_TRC module that contains template files to build the coupling between NEMO and any external BGC model. The call to MY\_TRC is activated by setting  \textit{ln\_my\_trc} = \texttt{.true.} in namelist \textit{namtrc}
+
+The following 6 fortran files are available in MY\_TRC with the specific purposes here described.
+
+\begin{itemize}
+   \item \textit{par\_my\_trc.F90} :  This module allows to define additional arrays and public variables to be used within the MY\_TRC interface
+   \item \textit{trcini\_my\_trc.F90} :  Here are initialized user defined namelists and the call to the external BGC model initialization procedures to populate general tracer array (trn and trb). Here are also likely to be defined suport arrays related to system metrics that could be needed by the BGC model.
+  \item \textit{trcnam\_my\_trc.F90} :  This routine is called at the beginning of trcini\_my\_trc and should contain the initialization of additional namelists for the BGC model or user-defined code.
+  \item \textit{trcsms\_my\_trc.F90} :  The routine performs the call to Boundary Conditions and its main purpose is to contain the Source-Minus-Sinks terms due to the biogeochemical processes of the external model. Be aware that lateral boundary conditions are applied in trcnxt routine. IMPORTANT: the routines to compute the light penetration along the water column and the tracer vertical sinking should be defined/called in here, as generalized modules are still missing in the code.
+ \item \textit{trcice\_my\_trc.F90} : Here it is possible to prescribe the tracers concentrations in the seaice that will be used as boundary conditions when ice melting occurs (nn\_ice\_tr =1 in namtrc\_ice). See e.g. the correspondent PISCES subroutine.
+ \item \textit{trcwri\_my\_trc.F90} : This routine performs the output of the model tracers using IOM module (see Manual Chapter Output and Diagnostics). It is possible to place here the output of additional variables produced by the model, if not done elsewhere in the code, using the call to \textit{iom\_put}.
+\end{itemize}
+
+
+\section{The Offline Option}
+\label{Offline}
+
+%------------------------------------------namtrc_sms----------------------------------------------------
+\nlst{namdta_dyn}
+%-------------------------------------------------------------------------------------------------------------
+
+Coupling passive tracers offline with NEMO requires precomputed  physical fields from OGCM. Those fields are read from files and interpolated on-the-fly at each model time step
+At least the following dynamical parameters should be absolutely passed to the transport : ocean velocities, temperature, salinity, mixed layer depth and for ecosystem models like PISCES, sea ice concentration, short wave radiation at the ocean surface, wind speed (or at least, wind stress). 
+The so-called offline mode is useful since it has lower computational costs for example to perform very longer simulations - about 3000 years - to reach equilibrium of CO2 sinks for climate-carbon studies.
+
+The offline interface is located in the code repository : \path{<repository>/src/OFF/}. It is activated by adding the CPP key  \textit{key\_offline} to the CPP keys list. There are two specifics routines for the Offline code :
+
+\begin{itemize}
+   \item \textit{dtadyn.F90} :  this module allows to read and compute the dynamical fields at each model time-step 
+   \item \textit{nemogcm.F90} :  a degraded version of the main nemogcm.F90 code of NEMO to manage the time-stepping
+\end{itemize}
+
+
+%-
+%-
+%-
+%-  Describes here the specifities of oflline : At least the dynamical variables needed - u/v/w transport T/S for isopycnal MLD for biogeo models etc ...
+%-  the specfities of vvl - ssh + runoffs and how to
+%-
+\end{document}
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/TOP/subfiles/model_setup.tex
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/TOP/subfiles/model_setup.tex	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/latex/TOP/subfiles/model_setup.tex	(revision 11042)
@@ -0,0 +1,46 @@
+\documentclass[../../NEMO/main/NEMO_manual]{subfiles}
+
+\begin{document}
+
+\chapter{ Model Setup}
+
+\section{ Setting up a passive tracer configuration}
+%------------------------------------------namtrc_int----------------------------------------------------
+\nlst{namtrc}
+%-------------------------------------------------------------------------------------------------------------
+
+The usage of TOP is activated 
+
+\begin{itemize}
+         \item by including in the configuration definition the component TOP\_SRC
+         \item by adding the macro \textit{key\_top} in the configuration cpp file
+\end{itemize}
+
+As an example, the user can refer to already available configurations in the code, GYRE\_PISCES being the NEMO biogeochemical demonstrator and GYRE\_BFM to see the required configuration elements to couple with an external biogeochemical model (see also section \S\ref{SMS_models}) .
+
+Note that, since version 4.0, TOP interface core functionalities are activated by means of logical keys and all submodules preprocessing macros from previous versions were removed. 
+
+There are only three specific keys remaining in TOP
+
+\begin{itemize}
+        \item \textit{key\_top} : to enables passive tracer module
+        \item \textit{key\_trdtrc} and \textit{key\_trdmxl\_trc} : trend computation for tracers
+\end{itemize}
+
+For a remind, the revisited structure of TOP interface now counts for five different modules handled in namelist\_top : 
+
+\begin{itemize}
+        \item \textbf{PISCES}, default BGC model
+        \item \textbf{MY\_TRC}, template for creation of new modules couplings (maybe run a single passive tracer)
+        \item \textbf{CFC}, inert carbon tracers dynamics (CFC11,CFC12,SF6) Updated with OMIP-BGC guidelines (Orr et al, 2016)
+        \item \textbf{C14}, radiocarbon passive tracer
+        \item \textbf{AGE}, water age tracking revised implementation
+\end{itemize}
+
+The modular approach was implemented also in the definition of the total number of passive tracers (jptra). This results from to user setting from the namelist \textit{namtrc}
+
+\section{ TOP Tracer Initialisation}
+
+\section{ TOP Boundaries Conditions}
+
+\end{document}
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/manual_build.sh
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/manual_build.sh	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/manual_build.sh	(revision 11042)
@@ -0,0 +1,49 @@
+#!/bin/sh
+
+## Initialisation
+##---------------
+
+## latekmk options
+opts='-shell-escape -quiet -pdf'
+
+## Default selection for models
+if   [ "$1" = 'all' ]; then
+	models='NEMO SI3 TOP'
+elif [ "$1" =    '' ]; then
+	models='NEMO'
+else
+	models=$*
+fi
+
+# Source shared functions
+. tools/shr_func.sh
+
+
+## Check dependancies
+##-------------------
+
+## LaTeX installation, find latexmk should be enough
+[ -z $( which latexmk ) ] && { echo 'latexmk binary is not present => QUIT'; exit 2; }
+
+## Retrieve figures if not already there
+if [ ! -d latex/figures ]; then
+	printf "Downloading of shared figures and logos\n\n"
+	svn co https://forge.ipsl.jussieu.fr/nemo/svn/utils/figures latex/figures > /dev/null
+fi
+
+## Pygments package for syntax highlighting of source code (namelists & snippets)
+[ -n "$( ./tools/check_pkg.py pygments )" ] && { exit 2; }
+
+
+## Loop on the models
+##-------------------
+
+for model in $models; do
+	echo $model
+	clean $model; build $model
+	printf "\t¤ End of building run\n"
+	printf "\t  The export should be available at root\n"
+	printf "\t  If not check LaTeX log in ./latex/$model/main/${model}_manual.log\n"
+done
+
+exit 0
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/nambdy
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/nambdy	(revision 11041)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/nambdy	(revision 11042)
@@ -3,42 +3,34 @@
 !-----------------------------------------------------------------------
    ln_bdy         = .false.   !  Use unstructured open boundaries
-   nb_bdy         = 2         !  number of open boundary sets
-   ln_coords_file = .true. , .false.    !  =T : read bdy coordinates from file
+   nb_bdy         = 0         !  number of open boundary sets
+   ln_coords_file = .true.    !  =T : read bdy coordinates from file
       cn_coords_file = 'coordinates.bdy.nc'  !  bdy coordinates files
    ln_mask_file   = .false.   !  =T : read mask from file
-      cn_mask_file = ''       !  name of mask file (if ln_mask_file=.TRUE.)
-   cn_dyn2d    = 'flather', 'none'       !
-   nn_dyn2d_dta   =  3 , 0    !  = 0, bdy data are equal to the initial state
+      cn_mask_file = ''        !  name of mask file (if ln_mask_file=.TRUE.)
+   cn_dyn2d    = 'none'       !
+   nn_dyn2d_dta   =  0        !  = 0, bdy data are equal to the initial state
       !                       !  = 1, bdy data are read in 'bdydata   .nc' files
       !                       !  = 2, use tidal harmonic forcing data from files
       !                       !  = 3, use external data AND tidal harmonic forcing
-   cn_dyn3d      =  'none' , 'none'
-   nn_dyn3d_dta  =  0 , 0     !  = 0, bdy data are equal to the initial state
+   cn_dyn3d      =  'none'    !
+   nn_dyn3d_dta  =  0         !  = 0, bdy data are equal to the initial state
    !                          !  = 1, bdy data are read in 'bdydata   .nc' files
-   cn_tra        =  'frs' , 'frs'
-   nn_tra_dta    =  1 , 0     !  = 0, bdy data are equal to the initial state
+   cn_tra        =  'none'    !
+   nn_tra_dta    =  0         !  = 0, bdy data are equal to the initial state
    !                          !  = 1, bdy data are read in 'bdydata   .nc' files
-   cn_ice        =  'none' , 'none'
-   nn_ice_dta    =  0, 0      !  = 0, bdy data are equal to the initial state
+   cn_ice        =  'none'    !
+   nn_ice_dta    =  0         !  = 0, bdy data are equal to the initial state
    !                          !  = 1, bdy data are read in 'bdydata   .nc' files
-   rn_ice_tem    = 270., 270. !  si3 only: arbitrary temperature of incoming sea ice
-   rn_ice_sal    = 10. ,  10. !  si3 only:      --   salinity           --
-   rn_ice_age    = 30. ,  30. !  si3 only:      --   age                --
+   rn_ice_tem    = 270.       !  si3 only: arbitrary temperature of incoming sea ice
+   rn_ice_sal    = 10.        !  si3 only:      --   salinity           --
+   rn_ice_age    = 30.        !  si3 only:      --   age                --
    !
-   ln_tra_dmp    =.false., .false.  !  open boudaries conditions for tracers
-   ln_dyn3d_dmp  =.false., .false.  !  open boundary condition for baroclinic velocities
-   rn_time_dmp   =  1., 1.    !  Damping time scale in days
-   rn_time_dmp_out = 1., 1.    !  Outflow damping time scale
-   nn_rimwidth   = 10, 5      !  width of the relaxation zone
+   ln_tra_dmp    =.false.     !  open boudaries conditions for tracers
+   ln_dyn3d_dmp  =.false.     !  open boundary condition for baroclinic velocities
+   rn_time_dmp   =  1.        !  Damping time scale in days
+   rn_time_dmp_out = 1.        !  Outflow damping time scale
+   nn_rimwidth   = 10         !  width of the relaxation zone
    ln_vol        = .false.    !  total volume correction (see nn_volctl parameter)
    nn_volctl     =  1         !  = 0, the total water flux across open boundaries is zero
    nb_jpk_bdy    = -1         ! number of levels in the bdy data (set < 0 if consistent with planned run)
 /
-!-----------------------------------------------------------------------
-&nambdy_index     ! index definition of bdy
-!-----------------------------------------------------------------------
-    ctypebdy = 'S'
-    nbdyind  =  2
-    nbdybeg  = 2
-    nbdyend  = 273
-/
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namberg
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namberg	(revision 11041)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namberg	(revision 11042)
@@ -5,31 +5,31 @@
    !
    !                          ! diagnostics:
-   ln_bergdia        = .true.       ! Calculate budgets
-   nn_verbose_level  = 1            ! Turn on more verbose output if level > 0
-   nn_verbose_write  = 15           ! Timesteps between verbose messages
-   nn_sample_rate    = 1            ! Timesteps between sampling for trajectory storage
+   ln_bergdia        = .true.        ! Calculate budgets
+   nn_verbose_level  = 0             ! Turn on more verbose output if level > 0
+   nn_verbose_write  = 15            ! Timesteps between verbose messages
+   nn_sample_rate    = 1             ! Timesteps between sampling for trajectory storage
    !
    !                          ! iceberg setting:
-   !                                ! Initial mass required for an iceberg of each class
+   !                                 ! Initial mass required for an iceberg of each class
    rn_initial_mass   = 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
-   !                                ! Proportion of calving mass to apportion to each class
+   !                                 ! Proportion of calving mass to apportion to each class
    rn_distribution   = 0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02
-   !                                ! Ratio between effective and real iceberg mass (non-dim)
-   !                                ! i.e. number of icebergs represented at a point
-   rn_mass_scaling   = 2000, 200, 50, 20, 10, 5, 2, 1, 1, 1
-                                    ! thickness of newly calved bergs (m)
+   !                                 ! Ratio between effective and real iceberg mass (non-dim)
+   !                                 ! i.e. number of icebergs represented at a point
+   rn_mass_scaling   = 2000., 200., 50., 20., 10., 5., 2., 1., 1., 1.
+                                     ! thickness of newly calved bergs (m)
    rn_initial_thickness     = 40., 67., 133., 175., 250., 250., 250., 250., 250., 250.
    !
-   rn_rho_bergs            = 850.   ! Density of icebergs
-   rn_LoW_ratio            = 1.5    ! Initial ratio L/W for newly calved icebergs
-   ln_operator_splitting   = .true. ! Use first order operator splitting for thermodynamics
-   rn_bits_erosion_fraction = 0.    ! Fraction of erosion melt flux to divert to bergy bits
-   rn_sicn_shift           = 0.     ! Shift of sea-ice concn in erosion flux (0<sicn_shift<1)
-   ln_passive_mode         = .false.! iceberg - ocean decoupling
-   nn_test_icebergs        =  10    ! Create test icebergs of this class (-1 = no)
-   !                                ! Put a test iceberg at each gridpoint in box (lon1,lon2,lat1,lat2)
+   rn_rho_bergs            = 850.    ! Density of icebergs
+   rn_LoW_ratio            = 1.5     ! Initial ratio L/W for newly calved icebergs
+   ln_operator_splitting   = .true.  ! Use first order operator splitting for thermodynamics
+   rn_bits_erosion_fraction = 0.     ! Fraction of erosion melt flux to divert to bergy bits
+   rn_sicn_shift           = 0.      ! Shift of sea-ice concn in erosion flux (0<sicn_shift<1)
+   ln_passive_mode         = .false. ! iceberg - ocean decoupling
+   nn_test_icebergs        =  10     ! Create test icebergs of this class (-1 = no)
+   !                                 ! Put a test iceberg at each gridpoint in box (lon1,lon2,lat1,lat2)
    rn_test_box             = 108.0,  116.0, -66.0, -58.0
-   ln_use_calving          = .false.! Use calving data even when nn_test_icebergs > 0
-   rn_speed_limit          = 0.     ! CFL speed limit for a berg
+   ln_use_calving          = .false. ! Use calving data even when nn_test_icebergs > 0
+   rn_speed_limit          = 0.      ! CFL speed limit for a berg
 
    cn_dir      = './'      !  root directory for the calving data location
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namdom
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namdom	(revision 11041)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namdom	(revision 11042)
@@ -5,5 +5,5 @@
    rn_isfhmin  =    1.00   !  treshold [m] to discriminate grounding ice from floating ice
    !
-   rn_rdt      = 5760.     !  time step for the dynamics and tracer
+   rn_rdt      = 5400.     !  time step for the dynamics and tracer
    rn_atfp     =    0.1    !  asselin time filter parameter
    !
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namdyn
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namdyn	(revision 11041)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namdyn	(revision 11042)
@@ -17,4 +17,4 @@
                                       !          recommended range: ?? L16=15 - home=10
       rn_lfrelax    =   1.e-5         !        relaxation time scale to reach static friction [s-1]
-      rn_tensile    =   0.2           !        isotropic tensile strength
+      rn_tensile    =   0.2           !        ln_landfast_L16: isotropic tensile strength
 /
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namdyn_rhg
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namdyn_rhg	(revision 11041)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namdyn_rhg	(revision 11042)
@@ -3,5 +3,5 @@
 !------------------------------------------------------------------------------
    ln_rhg_EVP       = .true.          !  EVP rheology
-      ln_aEVP       = .true.          !     adaptive rheology (Kimmritz et al. 2016 & 2017)
+      ln_aEVP       = .false.         !     adaptive rheology (Kimmritz et al. 2016 & 2017)
       rn_creepl     =   2.0e-9        !     creep limit [1/s]
       rn_ecc        =   2.0           !     eccentricity of the elliptical yield curve          
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namdyn_vor
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namdyn_vor	(revision 11041)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namdyn_vor	(revision 11042)
@@ -8,5 +8,5 @@
    ln_dynvor_eeT = .false. !  energy conserving scheme (een using e3t)
    ln_dynvor_een = .false. !  energy & enstrophy scheme
-      nn_een_e3f = 1          ! =0  e3f = mi(mj(e3t))/4 
+      nn_een_e3f = 0          ! =0  e3f = mi(mj(e3t))/4 
       !                       ! =1  e3f = mi(mj(e3t))/mi(mj( tmask))
    ln_dynvor_msk = .false. !  vorticity multiplied by fmask (=T)        ==>>> PLEASE DO NOT ACTIVATE
Index: MO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namforcing
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namforcing	(revision 11041)
+++ 	(revision )
@@ -1,13 +1,0 @@
-!------------------------------------------------------------------------------
-&namforcing     !   Ice surface forcing
-!------------------------------------------------------------------------------
-   rn_cio           =   5.0e-03       !  ice-ocean drag coefficient (-)
-   rn_blow_s        =   0.66          !  mesure of snow blowing into the leads
-                                      !     = 1 => no snow blowing, < 1 => some snow blowing
-   nn_flxdist       =  -1             !  Redistribute heat flux over ice categories
-                                      !     =-1  Do nothing (needs N(cat) fluxes)
-                                      !     = 0  Average N(cat) fluxes then apply the average over the N(cat) ice
-                                      !     = 1  Average N(cat) fluxes then redistribute over the N(cat) ice using T-ice and albedo sensitivity
-                                      !     = 2  Redistribute a single flux over categories
-   nice_jules       = 0               !  Jules coupling (0=OFF, 1=EMULATED, 2=ACTIVE)
-/
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namobs
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namobs	(revision 11041)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namobs	(revision 11042)
@@ -19,4 +19,5 @@
    ln_s_at_t   = .false.             ! Logical switch for computing model S at T obs if not there
    ln_sstnight = .false.             ! Logical switch for calculating night-time average for SST obs
+   ln_bound_reject  = .false.        ! Logical to remove obs near boundaries in LAMs.
    ln_sla_fp_indegs = .true.         ! Logical for SLA: T=> averaging footprint is in degrees, F=> in metres
    ln_sst_fp_indegs = .true.         ! Logical for SST: T=> averaging footprint is in degrees, F=> in metres
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/nampar
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/nampar	(revision 11041)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/nampar	(revision 11042)
@@ -5,7 +5,6 @@
    nlay_i           =   2             !  number of ice  layers
    nlay_s           =   1             !  number of snow layers (only 1 is working)
-   nn_virtual_itd   =   0             !  virtual ITD mono-category parameterizations (1-3 => jpl = 1 only) or not (0)
-                                      !     2: activate enhanced thermal conductivity only --- temporary option
-                                      !     3: activate virtual thin ice melting only      ---  temporary option
+   ln_virtual_itd   =   .false.       !  virtual ITD mono-category parameterization (jpl=1 only)
+                                      !     i.e. enhanced thermal conductivity & virtual thin ice melting
    ln_icedyn        = .true.          !  ice dynamics (T) or not (F)
    ln_icethd        = .true.          !  ice thermo   (T) or not (F)
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/nampisfer
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/nampisfer	(revision 11041)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/nampisfer	(revision 11042)
@@ -2,5 +2,5 @@
 &nampisfer     !   parameters for iron chemistry
 !-----------------------------------------------------------------------
-   ln_ligvar =  .true.    ! variable ligand concentration
+   ln_ligvar =  .false.    ! variable ligand concentration
    xlam1     =  0.005     ! scavenging rate of Iron
    xlamdust  =  150.0     ! Scavenging rate of dust
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namrun
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namrun	(revision 11041)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namrun	(revision 11042)
@@ -5,5 +5,5 @@
    cn_exp      =  "ORCA2"  !  experience name
    nn_it000    =       1   !  first time step
-   nn_itend    =    5475   !  last  time step (std 5475)
+   nn_itend    =    5840   !  last  time step (std 5840)
    nn_date0    =  010101   !  date at nit_0000 (format yyyymmdd) used if ln_rstart=F or (ln_rstart=T and nn_rstctl=0 or 1)
    nn_time0    =       0   !  initial time of day in hhmm
@@ -22,7 +22,7 @@
    nn_istate   =       0   !  output the initial state (1) or not (0)
    ln_rst_list = .false.   !  output restarts at list of times using nn_stocklist (T) or at set frequency with nn_stock (F)
-   nn_stock    =    5475   !  frequency of creation of a restart file (modulo referenced to 1)
+   nn_stock    =    5840   !  frequency of creation of a restart file (modulo referenced to 1)
    nn_stocklist = 0,0,0,0,0,0,0,0,0,0 ! List of timesteps when a restart file is to be written
-   nn_write    =    5475   !  frequency of write in the output file   (modulo referenced to nn_it000)
+   nn_write    =    5840   !  frequency of write in the output file   (modulo referenced to nn_it000)
    ln_mskland  = .false.   !  mask land points in NetCDF outputs (costly: + ~15%)
    ln_cfmeta   = .false.   !  output additional data to netCDF files required for compliance with the CF metadata standard
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namsbc
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namsbc	(revision 11041)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namsbc	(revision 11042)
@@ -2,5 +2,5 @@
 &namsbc        !   Surface Boundary Condition manager                   (default: NO selection)
 !-----------------------------------------------------------------------
-   nn_fsbc     = 5         !  frequency of SBC module call
+   nn_fsbc     = 2         !  frequency of SBC module call
       !                    !  (control sea-ice & iceberg model call)
                      ! Type of air-sea fluxes 
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namthd_do
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namthd_do	(revision 11041)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namthd_do	(revision 11042)
@@ -2,5 +2,5 @@
 &namthd_do      !   Ice growth in open water
 !------------------------------------------------------------------------------
-   rn_hinew         =   0.1           !  thickness for new ice formation in open water (m), must be larger than rn_hnewice
+   rn_hinew         =   0.1           !  thickness for new ice formation in open water (m), must be larger than rn_himin
    ln_frazil        = .false.         !  Frazil ice parameterization (ice collection as a function of wind)
       rn_maxfraz    =   1.0           !     maximum fraction of frazil ice collecting at the ice base
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namthd_pnd
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namthd_pnd	(revision 11041)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namthd_pnd	(revision 11042)
@@ -3,8 +3,7 @@
 !------------------------------------------------------------------------------
    ln_pnd_H12       = .false.         !  activate evolutive melt ponds (from Holland et al 2012)
-      ln_pnd_fwb    = .false.         !     melt ponds store freshwater or not
-   ln_pnd_CST       = .false.         !  activate constant melt ponds
-      rn_apnd       =   0.2           !     prescribed pond fraction, at Tsu=0
-      rn_hpnd       =   0.05          !     prescribed pond depth, at Tsu=0
+   ln_pnd_CST       = .false.         !  activate constant  melt ponds
+      rn_apnd       =   0.2           !     prescribed pond fraction, at Tsu=0 degC
+      rn_hpnd       =   0.05          !     prescribed pond depth,    at Tsu=0 degC
    ln_pnd_alb       = .false.         !  melt ponds affect albedo or not
 /
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namthd_sal
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namthd_sal	(revision 11041)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namthd_sal	(revision 11042)
@@ -5,10 +5,10 @@
                                       !     1: constant ice salinity (S=rn_icesal)
                                       !     2: varying salinity parameterization S(z,t)
-                                      !     3: prescribed salinity profile S(z), Schwarzacher, 1959
-   rn_icesal        =   4.            !    (nn_icesal=1) ice salinity (g/kg)
-   rn_sal_gd        =   5.            !  restoring ice salinity, gravity drainage (g/kg)
-   rn_time_gd       =   1.73e+6       !  restoring time scale, gravity drainage  (s)
-   rn_sal_fl        =   2.            !  restoring ice salinity, flushing (g/kg)
-   rn_time_fl       =   8.64e+5       !  restoring time scale, flushing (s)
+                                      !     3: prescribed salinity profile S(z) (Schwarzacher 1959)
+   rn_icesal        =   4.            !      (nn_icesal=1) ice salinity (g/kg)
+   rn_sal_gd        =   5.            !      (nn_icesal=2) restoring ice salinity, gravity drainage (g/kg)
+   rn_time_gd       =   1.73e+6       !      (nn_icesal=2) restoring time scale,   gravity drainage  (s)
+   rn_sal_fl        =   2.            !      (nn_icesal=2) restoring ice salinity, flushing (g/kg)
+   rn_time_fl       =   8.64e+5       !      (nn_icesal=2) restoring time scale,   flushing (s)
    rn_simax         =  20.            !  maximum tolerated ice salinity (g/kg)
    rn_simin         =   0.1           !  minimum tolerated ice salinity (g/kg)
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namwad
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namwad	(revision 11041)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/namelists/namwad	(revision 11042)
@@ -1,15 +1,15 @@
 !-----------------------------------------------------------------------
-&namwad  !   Wetting and drying
+&namwad        !   Wetting and Drying (WaD)                             (default: OFF)
 !-----------------------------------------------------------------------
-   ln_wd_il          = .false   ! T/F activation of iterative limiter for  wetting and drying scheme
-   ln_wd_dl          = .true.   ! T/F activation of directional llimiter for wetting drying scheme
-   ln_wd_dl_bc       = .true.   ! T/F Directional limiteer Baroclinic option
-   ln_wd_dl_rmp      = .true.   ! T/F Turn on directional limiter ramp
-   rn_wdmin0         =  0.30    ! dpoth at which wetting/drying starts
-   rn_wdmin1         =  0.2     ! Minimum wet depth on dried cells
-   rn_wdmin2         =  0.0001  ! Tolerance of min wet depth on dried cells
-   rn_wdld           =  2.5     ! Land elevation below which wetting/drying is allowed
-   nn_wdit           =   20     ! Max iterations for W/D limiter
-   rn_wd_sbcdep      =  5.0     ! Depth at which to taper sbc fluxes
-   rn_wd_sbcfra      =  0.999   ! Fraction of SBC fluxes at taper depth (Must be <1)
+   ln_wd_il    = .false.   !  T/F activation of iterative   limiter
+   ln_wd_dl    = .false.   !  T/F activation of directional limiter
+   ln_wd_dl_bc = .false.   !  T/F Directional limiteer Baroclinic option
+   ln_wd_dl_rmp = .false.  !  T/F Turn on directional limiter ramp
+   rn_wdmin0   =  0.30     !  depth at which WaD starts
+   rn_wdmin1   =  0.2      !  Minimum wet depth on dried cells
+   rn_wdmin2   =  0.0001   !  Tolerance of min wet depth on dried cells
+   rn_wdld     =  2.5      !  Land elevation below which WaD is allowed
+   nn_wdit     =   20      !  Max iterations for WaD limiter
+   rn_wd_sbcdep =  5.0     !  Depth at which to taper sbc fluxes
+   rn_wd_sbcfra =  0.999   !  Fraction of SBC fluxes at taper depth (Must be <1)
 /
Index: MO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/requirements_latex.txt
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/requirements_latex.txt	(revision 11041)
+++ 	(revision )
@@ -1,53 +1,0 @@
-amsmath
-babel
-caption
-capt-of
-carlisle
-cmap
-courier
-draftwatermark
-ec
-enumitem
-epstopdf
-etoolbox
-everypage
-fancyhdr
-fancyvrb
-float
-fncychap
-framed
-fvextra
-geometry
-graphics
-graphics-cfg
-helvetic
-hyperref
-idxlayout
-ifplatform
-latex
-latex-bin
-latexconfig
-latex-fonts
-latexmk
-lineno
-lm
-marvosym
-minitoc
-minted
-natbib
-needspace
-oberdiek
-parskip
-psnfss
-subfiles
-tabulary
-times
-titlesec
-tools
-upquote
-url
-varwidth
-wrapfig
-xcolor
-xstring
-zapfchan
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/tools/check_pkg.py
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/tools/check_pkg.py	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/tools/check_pkg.py	(revision 11042)
@@ -0,0 +1,10 @@
+#!/usr/bin/env python
+
+import sys, importlib
+
+for argv in sys.argv[1:]:
+	try:
+		importlib.import_module(argv)
+	except ImportError:
+		print("Package %s is missing in Python" % argv)
+
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/tools/manuals_checking.sh
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/tools/manuals_checking.sh	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/tools/manuals_checking.sh	(revision 11042)
@@ -0,0 +1,80 @@
+#!/bin/sh
+
+#set -evx
+
+if [[ $* != '' ]]; then
+	 if [[ $1 = 'all' ]]; then models='NEMO SI3 TOP'; else models=$1; fi
+else
+	 models='NEMO'
+fi
+
+for model in $models; do
+	 [[ $model =~ ^(SI3|TOP)$ ]] && continue
+
+    files=$( find latex/$model -type f -name *.tex )
+
+	 echo '¤ Missing namelist groups in '$model' manual'
+
+	 for nlst in $( ls namelists ); do
+        [[ ! $( grep \\nlst{$nlst} $files ) ]] && printf '%s ' $nlst
+	 done
+
+    echo; echo
+	 echo '¤ Vanished index entries in '$model' manual (\{hf,jp,key,mdl,ngn,nlst,np,rou}{...})'
+
+    for file in $files; do
+
+        items=$( grep -Eho "(hf|jp|key|mdl|ngn|nlst|np|rou){[a-zA-Z0-9_\]*}" $file | sort -u )
+
+        if [[ $items == '' ]]; then
+            continue
+        else
+            printf ${file/latex\/*\/subfiles\/}': '
+        fi
+
+        for item in $items; do
+
+            arg=$( echo $item | sed 's/.*{\([^}]*\)}/\1/' | tr -d '\\' )
+
+		      if [[ ( $item =~ ^hf   && ! $( find ../src -type f -name   $arg.h90               ) ) || \
+                  ( $item =~ ^jp   && ! $( grep ":: *$arg"             ../src/OCE/par_oce.F90 ) ) || \
+                  ( $item =~ ^key  && ! $( grep -ri "#if .* $arg"      ../src                 ) ) || \
+		            ( $item =~ ^mdl  && ! $( find ../src -type f -name   $arg.[Ff]90            ) ) || \
+                  ( $item =~ ^ngn  && ! $( grep \&$arg                 namelists/*            ) ) || \
+                  ( $item =~ ^nlst && ! -f namelists/$arg                                       ) || \
+                  ( $item =~ ^np   && ! $( grep " $arg *="             namelists/*            ) ) || \
+                  ( $item =~ ^rou  && ! $( grep -ri "SUBROUTINE *$arg" ../src                 ) )      ]]; then
+                printf $item' '
+            fi
+
+        done
+
+        echo
+
+    done
+
+done
+
+echo
+echo '¤ Namelist parameters unfollowing naming conventions (^[cdlnr]n_* or uppercase somewhere)'
+
+for nlst in $( ls namelists ); do
+    np_list=$( sed '/^ *[!/&]/d; s|[!/&].*||' namelists/$nlst | tr -d ' ' | cut -d= -f1 )
+    array=()
+
+    for np in ${np_list}; do
+
+        if [[ ! ${np:0:3} =~ ^[cdlnr]n_$ || $( echo $np | grep [A-Z] ) ]]; then
+            array+=$np' '
+        fi
+
+    done
+
+	 if (( ${#array[@]} != 0 )); then
+        printf '%15s: ' $nlst
+        echo ${array[@]}
+    fi
+
+done
+
+exit 0
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/tools/nlsts_releases.sh
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/tools/nlsts_releases.sh	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/tools/nlsts_releases.sh	(revision 11042)
@@ -0,0 +1,26 @@
+#!/bin/sh
+
+## Estimate changes in namelists between two releases
+#####################################################
+
+## Prerequisites: f90nml to parse Fortran namelists (http://f90nml.readthedocs.org)
+## Launch under ./doc, edit the path to previous namelists accordingly
+
+for nlst in ../../releases/release-3.6/DOC/Namelists/*; do
+
+    if [ -f namelists/$( basename $nlst ) ]; then
+        printf "%s: " $( basename $nlst )
+        f90nml namelists/$( basename $nlst ) | awk '/=/ { print $0 }' | sort > nlst_new.txt
+        f90nml                       $nlst   | awk '/=/ { print $0 }' | sort > nlst_old.txt
+
+        if [[ $( diff -q nlst_*.txt ) ]]; then
+            diff -y --suppress-common-lines nlst_*.txt | wc -l
+        else
+            echo 0
+        fi
+
+    fi
+
+done | sort -k2rn
+
+\rm nlst_*.txt
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/tools/nlsts_update.sh
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/tools/nlsts_update.sh	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/tools/nlsts_update.sh	(revision 11042)
@@ -0,0 +1,247 @@
+#! /bin/sh
+#
+#       usage for NEMO doc to create an update of the Namelists directory :
+# 1- delete the existing directory (You can also choose to save it somewhere) 
+#    rm -rf Namelists
+# 2- create the updated Namelists directory from the SHARED/namelist_ref :
+#    ./namelist_split.sh -i ../NEMOGCM/CONFIG/SHARED/namelist_ref -o Namelists
+#
+# .. _namelist_split.sh:
+#
+# =================
+# namelist_split.sh
+# =================
+#
+# ----------------
+# split a namelist
+# ----------------
+#
+# SYNOPSIS
+# ========
+#
+# .. code-block:: bash
+#
+#    namelist_split.sh -i namelist -o dirout [-n]
+#
+# DESCRIPTION
+# ===========
+#
+# Split a namelist file (NEMO convention syntax) given in parameter
+# into files in a given output directory.
+#
+# .. option:: -i <input file (namelist)>
+# .. option:: -o <output directory>
+# .. option:: -n <numbered output files>
+#
+# Each file of the output directory is named after the *block* it contains.
+#
+# We assume here that the input file is written with this pattern of block:
+#
+# .. parsed-literal::
+#
+#    !---------------
+#    &nameblock
+#    !---------------
+#    var1 = val1
+#    ...
+#    varn = valn
+#    /
+#
+# If ``-n`` option is used, files in the directory output are named after
+# the number of the block it contains and the name of this block. This might
+# be useful to recombine blocks in the same order.
+#
+# EXAMPLES
+# ========
+#
+# To split the namelist NEMO ORCA2_LIM experiment 00 if you are in NEMO
+# working space :
+#
+# .. code-block:: bash
+#
+#    namelist_split.sh -i CONFIG/ORCA2_LIM/EXP00/namelist -o /tmp/EXP00_namelist_split/
+#
+# To split the namelist under data directory with numbered files:
+#
+# .. code-block:: bash
+#
+#    namelist_split.sh -i ./data/namelist -o /tmp/EXP00_namelist_split/ -n
+#
+# Check can be made by concatenation of files in output directory if ``-n``
+# option have been used and comparison with original file :
+#
+# .. code-block:: bash
+#
+#    cat /tmp/EXP00_namelist_split/b???_* > /tmp/EXP00_namelist_rebuild
+#    sdiff -w80 ./data/namelist /tmp/EXP00_namelist_rebuild
+#
+# Output contains lines which are before the first block, after the last
+# block and lines between blocks.
+#
+# EVOLUTIONS
+# ==========
+#
+# $Id$
+#
+# - fplod 2008-08-11T08:56:44Z aedon.locean-ipsl.upmc.fr (Darwin)
+#
+#   * commentaires dans ce fichier en reStructuredText
+#     cf. reStructuredText_ and Docutils_
+#
+# .. _reStructuredText: http://docutils.sourceforge.net/rst.html
+# .. _Docutils: http://docutils.sourceforge.net/
+#
+# - fplod 2008-07-22T12:41:04Z aedon.locean-ipsl.upmc.fr (Darwin)
+#
+#   * creation with test on
+#     http://forge.ipsl.jussieu.fr/nemo/browser/trunk/CONFIG/ORCA2_LIM/EXP00/namelist revision 1151
+#-
+#
+system=$(uname)
+case "${system}" in
+    AIX|IRIX64)
+        echo " www : no specific posix checking"
+    ;;
+    *)
+        #set -o posix
+    ;;
+esac
+unset system
+#
+command=$(basename ${0})
+log_date=$(date -u +"%Y%m%dT%H%M%SZ")
+#
+usage=" Usage : ${command} -i namelist -o dirout [-n]"
+#
+# default
+blocknum=0
+#
+minargcount=4
+if [ ${#} -lt ${minargcount} ]
+then
+    echo "eee : not enough arguments"
+    echo "${usage}"
+    exit 1
+fi
+#
+while [ ${#} -gt 0 ]
+do
+    case ${1} in
+        -i)
+            filein=${2}
+            shift
+        ;;
+        -o)
+            dirout=${2}
+            shift
+        ;;
+        -h)
+            echo "${usage}"
+            exit 0
+        ;;
+        -n)
+            blocknum=1
+        ;;
+        *)
+            # anything else
+            echo "eee : unknown option ${1}"
+            echo "eee : ${usage}"
+            exit 1
+        ;;
+    esac
+    # next flag
+    shift
+done
+unset usage
+#
+set -u
+#
+# check for filein
+if [ ! -r ${filein} ]
+then
+    echo "eee : ${filein} not accessible"
+    exit 1
+fi
+#
+# check for dirout
+# the idea is to prevent unwanted overwrite
+if [ -d ${dirout} ]
+then
+    echo "eee : ${dirout} already exist"
+    exit 1
+else
+    mkdir -p ${dirout}
+    if [ ${?} -ne 0 ]
+    then
+        echo "eee : cannot create ${dirout}"
+        exit 1
+    fi
+fi
+#
+# loop on each line of ${filein} ie the namelist to be split
+fileout=/dev/null
+begin=0
+if [ ${blocknum} -eq 1 ]
+then
+    iblock=0
+fi
+nbline=$(wc -l ${filein} | awk '{print $1}')
+il=1
+while [ ${il} -le ${nbline} ]
+do
+    line=$(sed -ne "${il},${il}p" ${filein})
+    # if current line start with "&", we can establish the name of output file
+    echo ${line} | grep -q "^&"
+    if [ ${?} -eq 0 ]
+    then
+        begin=1
+        # the form of this line is "&block   !"
+        block=${line#&}
+        block=${block%% *}
+        echo "iii : detection of the beginning of ${block}"
+        if [ ${blocknum} -eq 1 ]
+        then
+            iblock=$(( ${iblock} + 1))
+            fileout=${dirout}/b$(echo ${iblock} | awk '{printf "%3.3d", $1}')_${block}
+        else
+            fileout="${dirout}/${block}"
+        fi
+        # check for ${fileout}
+        if [ -f ${fileout} ]
+        then
+            echo "eee : ${fileout} already exists"
+            exit 1
+        fi
+        # write the previous line and the current line
+        echo "${memoline}" > ${fileout}
+        echo "${line}" >> ${fileout}
+    fi
+    # if current line contains "/" there will be no more lines to put in fileout
+    echo ${line} | grep -q "^/$"
+    if [ ${?} -eq 0 ]
+    then
+        echo "iii : detection of the end of ${block}"
+        echo "${line}" >> ${fileout}
+        fileout="/dev/null"
+    fi
+    # if current line is between "&" and "/", it should be written in fileout
+    # if current line is before the first &, it won't be written
+    if [ "${fileout}" != "/dev/null" ]
+    then
+        if [ ${begin} -eq 0 ]
+        then
+            echo "${line}" >> ${fileout}
+        fi
+    fi
+    # keep memory of this current line to use it if the next one is the
+    # beginning of a block
+    memoline=${line}
+    begin=0
+    # next line
+    il=$(( ${il} + 1 ))
+done
+#
+echo "iii : ${filein} is split in ${dirout}"
+#
+# end
+exit 0
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/tools/shr_func.sh
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/tools/shr_func.sh	(revision 11042)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/doc/tools/shr_func.sh	(revision 11042)
@@ -0,0 +1,38 @@
+#!/bin/sh
+
+
+## Default options for GNU find (Linux OS)
+find_pre=''; find_suf='-regextype posix-extended'
+
+## Test OS to tweak the options in find command for working in extended mode everywhere
+[ '$( uname )' = 'Darwin' ] && { find_pre='-E'; find_suf=''; }
+
+clean() {
+    ## Not sure if this step is needed, guess latexmk should be able to detect a change
+    printf "\t¤ Clean previous build\n"
+
+    ## Delete temp files from previous build
+    printf "\t  - delete all temporary files (.aux, .bbl, ...)\n"
+    find ${find_pre} latex/$1 ${find_suf}                                                                \
+	                      -regex ".*\.(aux|bbl|blg|dvi|fdb|fls|idx|ilg|ind|log|maf|mtc|out|pdf|toc)" \
+                              -exec rm {} \;
+
+    ## Remove minted folders
+    printf "\t  - remove pygments input hash files (\"_minted\" folders)\n"
+    find latex/$1 -type d -name '_minted*' -exec rm -r {} \; 2> /dev/null
+
+    ## HTML exports
+    #printf '   - possible HTML export'
+    #find latex/$1 -type d -name 'html*'    -exec rm -r {} \;
+
+    echo
+}
+
+build() {
+    printf "\t¤ Generation of the PDF format\n"
+    cd latex/$1/main
+    latexmk $opts $1'_manual' 1> /dev/null
+    [ -f $1'_manual'.pdf ] && mv $1'_manual'.pdf ../../..
+    cd - > /dev/null
+    echo
+}
Index: /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/src/OCE/BDY/bdyice.F90
===================================================================
--- /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/src/OCE/BDY/bdyice.F90	(revision 11041)
+++ /NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/src/OCE/BDY/bdyice.F90	(revision 11042)
@@ -57,6 +57,7 @@
       INTEGER ::   jbdy   ! BDY set index
       !!----------------------------------------------------------------------
-      !
-      IF( ln_timing )   CALL timing_start('bdy_ice_thd')
+      ! controls
+      IF( ln_timing    )   CALL timing_start('bdy_ice_thd')                                                            ! timing
+      IF( ln_icediachk )   CALL ice_cons_hsm(0,'bdy_ice_thd', rdiag_v, rdiag_s, rdiag_t, rdiag_fv, rdiag_fs, rdiag_ft) ! conservation
       !
       CALL ice_var_glo2eqv
@@ -78,6 +79,8 @@
       CALL ice_var_agg(1)
       !
-      IF( ln_icectl )   CALL ice_prt( kt, iiceprt, jiceprt, 1, ' - ice thermo bdy - ' )
-      IF( ln_timing )   CALL timing_stop('bdy_ice_thd')
+      ! controls
+      IF( ln_icediachk )   CALL ice_cons_hsm(1,'bdy_ice_thd', rdiag_v, rdiag_s, rdiag_t, rdiag_fv, rdiag_fs, rdiag_ft) ! conservation
+      IF( ln_icectl    )   CALL ice_prt     ( kt, iiceprt, jiceprt, 1, ' - ice thermo bdy - ' )                        ! prints
+      IF( ln_timing    )   CALL timing_stop ('bdy_ice_thd')                                                            ! timing
       !
    END SUBROUTINE bdy_ice
@@ -148,8 +151,8 @@
             jpbound = 0   ;   ib = ji   ;   jb = jj
             !
-            IF( u_ice(ji+1,jj  ) < 0. .AND. umask(ji-1,jj  ,1) == 0. )   jpbound = 1 ; ib = ji+1 ; jb = jj
-            IF( u_ice(ji-1,jj  ) > 0. .AND. umask(ji+1,jj  ,1) == 0. )   jpbound = 1 ; ib = ji-1 ; jb = jj
-            IF( v_ice(ji  ,jj+1) < 0. .AND. vmask(ji  ,jj-1,1) == 0. )   jpbound = 1 ; ib = ji   ; jb = jj+1
-            IF( v_ice(ji  ,jj-1) > 0. .AND. vmask(ji  ,jj+1,1) == 0. )   jpbound = 1 ; ib = ji   ; jb = jj-1
+            IF( u_ice(ji  ,jj  ) < 0. .AND. umask(ji-1,jj  ,1) == 0. )   jpbound = 1 ; ib = ji+1
+            IF( u_ice(ji-1,jj  ) > 0. .AND. umask(ji  ,jj  ,1) == 0. )   jpbound = 1 ; ib = ji-1
+            IF( v_ice(ji  ,jj  ) < 0. .AND. vmask(ji  ,jj-1,1) == 0. )   jpbound = 1 ; jb = jj+1
+            IF( v_ice(ji  ,jj-1) > 0. .AND. vmask(ji  ,jj  ,1) == 0. )   jpbound = 1 ; jb = jj-1
             !
             IF( nn_ice_dta(jbdy) == 0 )   jpbound = 0 ; ib = ji ; jb = jj   ! case ice boundaries = initial conditions
