Index: /NEMO/trunk/doc/latex/NEMO/main/definitions.tex
===================================================================
--- /NEMO/trunk/doc/latex/NEMO/main/definitions.tex	(revision 11170)
+++ /NEMO/trunk/doc/latex/NEMO/main/definitions.tex	(revision 11171)
@@ -3,13 +3,13 @@
 
 %% Title (variable name already use by 'titling' pkg)
-\def \heading{NEMO ocean engine~}
+\def \heading{NEMO ocean engine}
 
-%% Authors
+%% Authors (thanks will apply to the second author)
 \def \1stauthor{Gurvan Madec~}
-\def \2ndauthor{NEMO System Team~}
+\def \2ndauthor{NEMO System Team}
 
 %% IPSL publication number
 \def \ipslnum{27}
 
-%% Zenodo ID, i.e. doi:10.5281/zenodo.[0-9]*
+%% Zenodo ID, i.e. doi:10.5281/zenodo.\([0-9]*\)
 \def \zid{1464816}
Index: MO/trunk/doc/latex/SI3/main/SI3_manual.bib
===================================================================
--- /NEMO/trunk/doc/latex/SI3/main/SI3_manual.bib	(revision 11170)
+++ 	(revision )
@@ -1,677 +1,0 @@
-
-@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},
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-  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{	  hoyland_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)}
-}
-
-@techreport{	  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{	  lepparanta_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},
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-  url		= {http://dx.doi.org/10.1016/0165-232x(94)00019-t},
-  journal	= {Cold Regions Science and Technology},
-  publisher	= {Elsevier BV}
-}
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-@Article{	  lepparanta_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},
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-  url		= {http://dx.doi.org/10.1029/2005JC003355},
-  journal	= {Journal of Geophysical Research},
-  publisher	= {American Geophysical Union (AGU)}
-}
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-@Article{	  massonnet_2018,
-  author	= {Massonnet, F. and Barth\'el\'emy, A. and Worou, K. and
-		  Fichefet, T. and Vancoppenolle, M. and Rousset, C.},
-  title		= {Insights on the discretization of the ice thickness
-		  distribution in large-scale sea ice models},
-  journal	= {submitted},
-  year		= {2018}
-}
-
-@Article{	  maykut_1971,
-  author	= {Maykut, Gary A. and Untersteiner, Norbert},
-  title		= {Some results from a time-dependent thermodynamic model of
-		  sea ice},
-  year		= 1971,
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-  journal	= {Journal of Geophysical Research},
-  publisher	= {American Geophysical Union (AGU)}
-}
-
-@Article{	  maykut_1973,
-  author	= {Maykut, G. A. and Thorndike, A. S.},
-  title		= {An approach to coupling the dynamics and thermodynamics of
-		  Arctic sea ice},
-  journal	= {AIDJEX Bulletin},
-  year		= {1973},
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-  author	= {Maykut, Gary A.},
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-  isbn		= 9781489953520,
-  journal	= {The Geophysics of Sea Ice},
-  publisher	= {Springer US}
-}
-
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-  author	= {Maykut, G. A. and McPhee, Miles G.},
-  title		= {Solar heating of the Arctic mixed layer},
-  year		= 1995,
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-  author	= {McPhee, Miles G.},
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-  author	= {Mellor, George L. and Kantha, Lakshmi},
-  title		= {An ice-ocean coupled model},
-  year		= 1989,
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-@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},
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-}
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-  author	= {Parmerter, R. Reid},
-  title		= {A model of simple rafting in sea ice},
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-}
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-  volume	= 107,
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-  journal	= {Journal of Geophysical Research},
-  publisher	= {American Geophysical Union (AGU)}
-}
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-  author	= {Prather, Michael J.},
-  title		= {Numerical advection by conservation of second-order
-		  moments},
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-  title		= {Thermal conductivity of landfast Antarctic and Arctic sea
-		  ice},
-  year		= 2007,
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-  author	= {Schmidt, Gavin A. and Bitz, Cecilia M. and Mikolajewicz,
-		  Uwe and Tremblay, L.-Bruno},
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-  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)}
-}
-
-@Book{		  teos-10_2010,
-  title		= {{The international thermodynamic equation of seawater -
-		  2010: Calculation and use of thermodynamic properties}},
-  publisher	= {UNESCO (English)},
-  year		= {2010},
-  author	= {{IOC, SCOR and IAPSO}},
-  series	= {Intergovernmental Oceanographic Commission, Manuals and
-		  Guides No. 56},
-  url =          {http://www.teos-10.org/pubs/TEOS-10_Manual.pdf}
-}
-
-@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: MO/trunk/doc/latex/SI3/main/SI3_manual.tex
===================================================================
--- /NEMO/trunk/doc/latex/SI3/main/SI3_manual.tex	(revision 11170)
+++ 	(revision )
@@ -1,125 +1,0 @@
-%% ==============================================================================
-%% SI3 Reference Manual
-%% ==============================================================================
-
-
-%% Preamble
-%% ==============================================================================
-
-%% Document layout
-\documentclass[draft]{scrreport}
-
-%% Custom style (.sty)
-\usepackage{../../global/packages}
-\hypersetup{
-  pdftitle={Sea Ice modelling Integrated Initiative (SI³) -- The NEMO sea ice engine},
-  pdfauthor={NEMO Sea Ice Working Group},
-  colorlinks
-}
-
-%% 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}
-\pagenumbering{gobble}
-
-%% Override custom cmds for full manual compilation
-\renewcommand{\biblio}{}
-\renewcommand{\pindex}{}
-
-
-%% Frontmatter
-%% ==============================================================================
-
-\title{Sea Ice modelling Integrated Initiative (SI$^3$) \\ The NEMO sea ice engine
-%  \small{\textcolor{red}{First draft documentation. Needs completion and rewriting.}}
-}
-\author{NEMO Sea Ice Working Group\thanks{
-    TBD
-  }
-}
-\date{\today}
-
-%% Title and information pages
-\input{../../global/frontpages}
-
-%% Citation embedded
-\textsf{
-``{\bfseries Sea Ice modelling Integrated Initiative (SI$^3$) -- The NEMO sea ice engine}'', 
-NEMO Sea Ice Working Group, 
-{\em Scientific Notes of Climate Modelling Center (31)} -- ISSN 1288-1619, 
-Institut Pierre-Simon Laplace (IPSL), 
-\href{http://doi.org/10.5281/zenodo.1471689}{doi:10.5281/zenodo.1471689}
-}
-
-\newpage
-%\frontmatter   %% Chapter numbering off and Roman numerals for page numbers
-\pagenumbering{roman}
-
-%\subfile{../subfiles/foreword}            %% Foreword
-
-
-%% ToC i.e. Table of Contents
-\newpage
-\dominitoc
-\tableofcontents
-
-\clearpage
-
-%% Mainmatter
-%% ==============================================================================
-
-%\mainmatter   %% Chapter numbering on, page numbering is reset with Arabic numerals
-\pagenumbering{arabic}
-
-\graphicspath{{../../figures/SI3/}}
-
-\subfile{../subfiles/todolist}
-
-% 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   % Chapter numbering is reset with letters now
-
-
-%% Backmatter
-%% ==============================================================================
-
-%\backmatter   %% Chapter numbering off
-
-%% Bibliography
-\phantomsection
-\addcontentsline{toc}{chapter}{Bibliography}
-\bibliography{../main/SI3_manual}
-%\bibliography{/Users/ioulianikolskaia/Boulot/LIBRARY/BIBTEX/Martin_biblio.bib} 
-
-%% Index
-\clearpage
-\phantomsection
-\addcontentsline{toc}{chapter}{Index}
-\printindex
-
-\end{document}
Index: /NEMO/trunk/doc/latex/SI3/main/bibliography.bib
===================================================================
--- /NEMO/trunk/doc/latex/SI3/main/bibliography.bib	(revision 11171)
+++ /NEMO/trunk/doc/latex/SI3/main/bibliography.bib	(revision 11171)
@@ -0,0 +1,677 @@
+
+@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{	  hoyland_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)}
+}
+
+@techreport{	  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{	  lepparanta_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{	  lepparanta_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{	  massonnet_2018,
+  author	= {Massonnet, F. and Barth\'el\'emy, A. and Worou, K. and
+		  Fichefet, T. and Vancoppenolle, M. and Rousset, C.},
+  title		= {Insights on the discretization of the ice thickness
+		  distribution in large-scale sea ice models},
+  journal	= {submitted},
+  year		= {2018}
+}
+
+@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_1973,
+  author	= {Maykut, G. A. and Thorndike, A. S.},
+  title		= {An approach to coupling the dynamics and thermodynamics of
+		  Arctic sea ice},
+  journal	= {AIDJEX Bulletin},
+  year		= {1973},
+  volume	= {21},
+  pages		= {23--29}
+}
+
+@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)}
+}
+
+@Book{		  teos-10_2010,
+  title		= {{The international thermodynamic equation of seawater -
+		  2010: Calculation and use of thermodynamic properties}},
+  publisher	= {UNESCO (English)},
+  year		= {2010},
+  author	= {{IOC, SCOR and IAPSO}},
+  series	= {Intergovernmental Oceanographic Commission, Manuals and
+		  Guides No. 56},
+  url =          {http://www.teos-10.org/pubs/TEOS-10_Manual.pdf}
+}
+
+@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/trunk/doc/latex/SI3/main/chapters.tex
===================================================================
--- /NEMO/trunk/doc/latex/SI3/main/chapters.tex	(revision 11171)
+++ /NEMO/trunk/doc/latex/SI3/main/chapters.tex	(revision 11171)
@@ -0,0 +1,16 @@
+\subfile{../subfiles/todolist}
+
+\subfile{../subfiles/introduction}               % Introduction
+
+\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}
Index: /NEMO/trunk/doc/latex/SI3/main/definitions.tex
===================================================================
--- /NEMO/trunk/doc/latex/SI3/main/definitions.tex	(revision 11171)
+++ /NEMO/trunk/doc/latex/SI3/main/definitions.tex	(revision 11171)
@@ -0,0 +1,15 @@
+%% Engine (folder name)
+\def \engine{SI3}
+
+%% Title (variable name already use by 'titling' pkg)
+\def \heading{Sea Ice modelling Integrated Initiative (SI$^3$) \\ The NEMO sea ice engine}
+
+%% Authors (thanks will apply to the second author)
+\def \1stauthor{}
+\def \2ndauthor{NEMO Sea Ice Working Group}
+
+%% IPSL publication number
+\def \ipslnum{31}
+
+%% Zenodo ID, i.e. doi:10.5281/zenodo.\([0-9]*\)
+\def \zid{1471689}
Index: /NEMO/trunk/doc/latex/SI3/main/thanks.tex
===================================================================
--- /NEMO/trunk/doc/latex/SI3/main/thanks.tex	(revision 11171)
+++ /NEMO/trunk/doc/latex/SI3/main/thanks.tex	(revision 11171)
@@ -0,0 +1,1 @@
+TBD
Index: MO/trunk/doc/latex/TOP/main/TOP_manual.bib
===================================================================
--- /NEMO/trunk/doc/latex/TOP/main/TOP_manual.bib	(revision 11170)
+++ 	(revision )
@@ -1,619 +1,0 @@
-
-@Article{	  ahn_2007,
-  author	= {Ahn, Jinho and Brook, Edward J.},
-  title		= {Atmospheric CO2and climate from 65 to 30 ka B.P.},
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-  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,
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-  month		= {Oct},
-  pages		= {83–85},
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-  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.
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-}
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-  journal	= {Trends in Ecology \& Evolution},
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Index: MO/trunk/doc/latex/TOP/main/TOP_manual.tex
===================================================================
--- /NEMO/trunk/doc/latex/TOP/main/TOP_manual.tex	(revision 11170)
+++ 	(revision )
@@ -1,109 +1,0 @@
-%% ==============================================================================
-%% TOP Reference Manual
-%% ==============================================================================
-
-
-%% Preamble
-%% ==============================================================================
-
-%% Document layout
-\documentclass[draft]{scrreport}
-
-%% Custom style (.sty)
-\usepackage{../../global/packages}
-\hypersetup{
-  pdftitle={Tracers in Ocean Paradigm (TOP) -- The NEMO passive tracers engine},
-  pdfauthor={NEMO TOP Working Group},
-  colorlinks
-}
-
-%% 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}
-\pagenumbering{gobble}
-
-%% Override custom cmds for full manual compilation
-\renewcommand{\biblio}{}
-\renewcommand{\pindex}{}
-
-
-%% Frontmatter
-%% ==============================================================================
-
-\title{Tracer in Ocean Paradigm (TOP) \\ The NEMO passive tracer engine
-%  \small{\textcolor{red}{First draft documentation. Needs completion and rewriting.}}
-}
-\author{NEMO TOP Working Group\thanks{
-    \'{E}th\'{e} Christian, Lovato Tomas, Aumont Olivier, Palmi\'{e}ri Julien,
-    Mouchet Anne, Nurser Georges, Yool Andrew
-  }
-}
-\date{\today}
-
-%% Title and information pages
-\input{../../global/frontpages}
-
-%% Citation embedded
-\textsf{
-``{\bfseries Tracer in Ocean Paradigm (TOP) -- The NEMO passive tracer engine}'', 
-NEMO TOP Working Group, 
-{\em Scientific Notes of Climate Modelling Center (28)} -- ISSN 1288-1619, 
-Institut Pierre-Simon Laplace (IPSL), 
-\href{http://doi.org/10.5281/zenodo.1471700}{doi:10.5281/zenodo.1471700}
-}
-
-\newpage
-%\frontmatter   %% Chapter numbering off and Roman numerals for page numbers
-\pagenumbering{roman}
-
-%\subfile{../subfiles/foreword}            %% Foreword
-
-
-%% ToC i.e. Table of Contents
-\newpage
-\dominitoc
-\tableofcontents
-
-\clearpage
-
-%% Mainmatter
-%% ==============================================================================
-
-%\mainmatter   %% Chapter numbering on, page numbering is reset with Arabic numerals
-\pagenumbering{arabic}
-
-\graphicspath{{../../figures/TOP/}}
-
-\subfile{../subfiles/introduction}
-\subfile{../subfiles/model_description}
-\subfile{../subfiles/model_setup}
-\subfile{../subfiles/miscellaneous}
-
-%% Appendix
-%% ==============================================================================
-
-%\appendix   % Chapter numbering is reset with letters now
-
-
-%% Backmatter
-%% ==============================================================================
-
-%\backmatter   %% Chapter numbering off
-
-%% Bibliography
-\phantomsection
-\addcontentsline{toc}{chapter}{Bibliography}
-\bibliography{../main/TOP_manual}
-
-%% Index
-\clearpage
-\phantomsection
-\addcontentsline{toc}{chapter}{Index}
-\printindex
-
-\end{document}
Index: /NEMO/trunk/doc/latex/TOP/main/bibliography.bib
===================================================================
--- /NEMO/trunk/doc/latex/TOP/main/bibliography.bib	(revision 11171)
+++ /NEMO/trunk/doc/latex/TOP/main/bibliography.bib	(revision 11171)
@@ -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.},
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+  year		= 2002,
+  volume	= 4,
+  number	= 2,
+  month		= {Jan},
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+  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}
+}
+
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+  author	= {G Enting, I and M L Wigley, T and Heimann, Martin},
+  year		= {1994},
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+}
+
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+  author	= {Fiadeiro, M.E.},
+  year		= {1982},
+  month		= {01},
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+  journal	= {J. Mar. Res.}
+}
+
+@Article{	  fluckiger_2002,
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+		  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,
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+  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.},
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+  year		= 2006,
+  volume	= 111,
+  number	= {C5},
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+  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}
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+
+@Article{	  joos_1997,
+  author	= {Joos, Fortunat and Orr, James C. and Siegenthaler,
+		  Ulrich},
+  title		= {Ocean carbon transport in a box-diffusion versus a general
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+  volume	= 102,
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+  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},
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+  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,
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+  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$_{2}$ 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.},
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+  issn		= {1945-5755},
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+  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
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+  volume	= 90,
+  number	= {C4},
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+  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_1989a,
+  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_1989b,
+  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},
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+  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,
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+  number	= 4,
+  month		= {Jun},
+  pages		= {689–697},
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+  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},
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+  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},
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+  volume	= 32,
+  number	= 12,
+  month		= {Dec},
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+  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/trunk/doc/latex/TOP/main/chapters.tex
===================================================================
--- /NEMO/trunk/doc/latex/TOP/main/chapters.tex	(revision 11171)
+++ /NEMO/trunk/doc/latex/TOP/main/chapters.tex	(revision 11171)
@@ -0,0 +1,4 @@
+\subfile{../subfiles/introduction}
+\subfile{../subfiles/model_description}
+\subfile{../subfiles/model_setup}
+\subfile{../subfiles/miscellaneous}
Index: /NEMO/trunk/doc/latex/TOP/main/definitions.tex
===================================================================
--- /NEMO/trunk/doc/latex/TOP/main/definitions.tex	(revision 11171)
+++ /NEMO/trunk/doc/latex/TOP/main/definitions.tex	(revision 11171)
@@ -0,0 +1,15 @@
+%% Engine (folder name)
+\def \engine{TOP}
+
+%% Title (variable name already use by 'titling' pkg)
+\def \heading{Tracers in Ocean Paradigm (TOP) \\ The NEMO passive tracers engine}
+
+%% Authors (thanks will apply to the second author)
+\def \1stauthor{}
+\def \2ndauthor{NEMO TOP Working Group}
+
+%% IPSL publication number
+\def \ipslnum{28}
+
+%% Zenodo ID, i.e. doi:10.5281/zenodo.\([0-9]*\)
+\def \zid{1471700}
Index: /NEMO/trunk/doc/latex/TOP/main/thanks.tex
===================================================================
--- /NEMO/trunk/doc/latex/TOP/main/thanks.tex	(revision 11171)
+++ /NEMO/trunk/doc/latex/TOP/main/thanks.tex	(revision 11171)
@@ -0,0 +1,8 @@
+\'{E}th\'{e} Christian, 
+Lovato Tomas, 
+Aumont Olivier, 
+Palmi\'{e}ri Julien, 
+Mouchet Anne, 
+Nurser Georges, 
+Yool Andrew
+
Index: /NEMO/trunk/doc/latex/global/document.tex
===================================================================
--- /NEMO/trunk/doc/latex/global/document.tex	(revision 11170)
+++ /NEMO/trunk/doc/latex/global/document.tex	(revision 11171)
@@ -12,9 +12,9 @@
 \documentclass[draft]{scrreport}
 
+%% Engine name and Zenodo DOI
+\input{definitions}
+
 %% Custom style (.sty)
 \usepackage{../../global/packages}
-
-%% Engine name and Zenodo DOI
-\input{definitions}
 
 %% Include references and index for single subfile compilation
@@ -50,5 +50,6 @@
 %% ToC i.e. Table of Contents
 \newpage
-\dominitoc\tableofcontents
+\dominitoc
+\tableofcontents
 
 \clearpage
@@ -81,10 +82,12 @@
 
 %% Bibliography
-\phantomsection\addcontentsline{toc}{chapter}{Bibliography}
+\phantomsection
+\addcontentsline{toc}{chapter}{Bibliography}
 \bibliography{../main/bibliography}
 
 %% Index
 \clearpage
-\phantomsection\addcontentsline{toc}{chapter}{Index}
+\phantomsection
+\addcontentsline{toc}{chapter}{Index}
 \printindex
 
Index: /NEMO/trunk/doc/latex/global/styles.sty
===================================================================
--- /NEMO/trunk/doc/latex/global/styles.sty	(revision 11170)
+++ /NEMO/trunk/doc/latex/global/styles.sty	(revision 11171)
@@ -10,4 +10,6 @@
 %% Hyperref
 \hypersetup{
+%  pdftitle={\heading},
+%  pdfauthor={\1stauthor and \2ndauthor},
   colorlinks
 }
