Index: NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/build/TOP_manual.ist
===================================================================
--- NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/build/TOP_manual.ist	(revision 11564)
+++ NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/build/TOP_manual.ist	(revision 11564)
@@ -0,0 +1,1 @@
+link ../../global/index.ist
Index: NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/TOP_manual.ist
===================================================================
--- NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/TOP_manual.ist	(revision 11564)
+++ NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/TOP_manual.ist	(revision 11564)
@@ -0,0 +1,1 @@
+link ../../global/index.ist
Index: NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/TOP_manual.tex
===================================================================
--- NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/TOP_manual.tex	(revision 11564)
+++ NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/TOP_manual.tex	(revision 11564)
@@ -0,0 +1,1 @@
+link ../../global/document.tex
Index: NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/bibliography.bib
===================================================================
--- NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/bibliography.bib	(revision 11564)
+++ NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/bibliography.bib	(revision 11564)
@@ -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$_{2}$ 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.},
+  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_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},
+  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_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/blocks.idx
===================================================================
--- NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/blocks.idx	(revision 11564)
+++ NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/blocks.idx	(revision 11564)
@@ -0,0 +1,1 @@
+link ../build/blocks.idx
Index: NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/byrd-co2-2008.txt
===================================================================
--- NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/byrd-co2-2008.txt	(revision 11564)
+++ NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/byrd-co2-2008.txt	(revision 11564)
@@ -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_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/chapters.tex
===================================================================
--- NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/chapters.tex	(revision 11564)
+++ NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/chapters.tex	(revision 11564)
@@ -0,0 +1,4 @@
+\subfile{../subfiles/introduction}
+\subfile{../subfiles/model_description}
+\subfile{../subfiles/model_setup}
+\subfile{../subfiles/miscellaneous}
Index: NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/definitions.tex
===================================================================
--- NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/definitions.tex	(revision 11564)
+++ NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/definitions.tex	(revision 11564)
@@ -0,0 +1,20 @@
+%% Engine (folder name)
+\def \engine{TOP}
+
+%% Title and cover page settings
+\def \spacetop{  \vspace*{1.3cm} }
+\def \heading{Tracers in Ocean Paradigm (TOP)
+\def \subheading{The NEMO passive tracers engine}
+\def \spacedown{ \vspace*{1cm  } }
+\def \authorswidth{0.15\linewidth}
+\def \rulelenght{110pt}
+\def \abstractwidth{0.7\linewidth}
+
+%% Color for document (frontpage banner, links and chapter boxes)
+\def \setcolor{ \definecolor{manualcolor}{cmyk}{1, 0, 1, 0.4} }
+
+%% IPSL publication number
+\def \ipslnum{28}
+
+%% Zenodo ID, i.e. doi:10.5281/zenodo.\([0-9]*\)
+\def \zid{1471700}
Index: NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/edc-co2.txt
===================================================================
--- NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/edc-co2.txt	(revision 11564)
+++ NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/edc-co2.txt	(revision 11564)
@@ -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_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/foreword.tex
===================================================================
--- NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/foreword.tex	(revision 11564)
+++ NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/foreword.tex	(revision 11564)
@@ -0,0 +1,26 @@
+%% ================================================================
+%% Abstract
+%% ================================================================
+
+%% Common part between NEMO-SI3-TOP
+``Tracers in Ocean Paradigm'' (\TOP) is the passive tracers engine of
+the \NEMO\ ocean model (``Nucleus for European Modelling of the Ocean'').
+It is intended to be a flexible tool for studying the on/offline oceanic tracers transport and
+the biogeochemical processes (``green ocean''),
+as well as its interactions with the other components of the Earth climate system over
+a wide range of space and time scales.
+\TOP\ is interfaced with the \NEMO\ ocean engine, and,
+via the \href{http://portal.enes.org/oasis}{OASIS} coupler,
+with several atmospheric general circulation models.
+%It also supports two-way grid embedding by means of the \href{http://agrif.imag.fr}{AGRIF} software.
+
+%% Specific part
+This component provides the physical constraints and boundaries conditions for
+oceanic tracers transport and represents a generalized, hardwired interface toward
+biogeochemical models to enable a seamless coupling.
+In particular, transport dynamics are supplied by the ocean dynamical core thus
+enabling the use of all available advection and diffusion schemes in both on- and off-line modes.
+\TOP\ is designed to handle multiple oceanic tracers through a modular approach and
+it includes different sub-modules: ocean water age, inorganic carbon (CFCs) \& radiocarbon (C14b),
+built-in biogeochemical model (PISCES), and prototype for user-defined cases or
+coupling with alternative biogeochemical models (\eg \href{http://www.bfm-community.eu}{BFM}).
Index: NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/keys.idx
===================================================================
--- NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/keys.idx	(revision 11564)
+++ NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/keys.idx	(revision 11564)
@@ -0,0 +1,1 @@
+link ../build/keys.idx
Index: NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/modules.idx
===================================================================
--- NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/modules.idx	(revision 11564)
+++ NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/modules.idx	(revision 11564)
@@ -0,0 +1,1 @@
+link ../build/modules.idx
Index: NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/parameters.idx
===================================================================
--- NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/parameters.idx	(revision 11564)
+++ NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/parameters.idx	(revision 11564)
@@ -0,0 +1,1 @@
+link ../build/parameters.idx
Index: NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/subroutines.idx
===================================================================
--- NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/subroutines.idx	(revision 11564)
+++ NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/subroutines.idx	(revision 11564)
@@ -0,0 +1,1 @@
+link ../build/subroutines.idx
Index: NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/thanks.tex
===================================================================
--- NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/thanks.tex	(revision 11564)
+++ NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/main/thanks.tex	(revision 11564)
@@ -0,0 +1,7 @@
+Olivier Aumont         \\
+Christian \'{E}th\'{e} \\
+Tomas Lovato           \\
+Anne Mouchet           \\
+Georges Nurser         \\
+Julien Palmi\'{e}ri    \\
+Andrew Yool
Index: NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/subfiles/introduction.tex
===================================================================
--- NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/subfiles/introduction.tex	(revision 11564)
+++ NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/subfiles/introduction.tex	(revision 11564)
@@ -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_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/subfiles/miscellaneous.tex
===================================================================
--- NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/subfiles/miscellaneous.tex	(revision 11564)
+++ NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/subfiles/miscellaneous.tex	(revision 11564)
@@ -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_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/subfiles/model_description.tex
===================================================================
--- NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/subfiles/model_description.tex	(revision 11564)
+++ NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/subfiles/model_description.tex	(revision 11564)
@@ -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{nemo_manual} 
+
+{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_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{nemo_manual}. 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{nemo_manual}. 
+
+
+%-----------------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_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_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_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_2017}.
+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_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_1989a,toggweiler_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_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_1990} and \cite{joos_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_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_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_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_1989a,orr_2001,butzin_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_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_2004}.
+
+Equilibrium experiment should last until 98\% of the ocean volume exhibit a drift of less than 0.001\textperthousand/year \citep{orr_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_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_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_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_2004} for the Holocene and the Transition, and on Byrd Ice Core CO2 Data for 20--90 kyr BP  \citep{ahn_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_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_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_1958}. 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_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_2003,woods_2013,meunier_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_1985} and the -O/C ratio is set to 1.34 \citep{kortzinger_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_2001}). 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_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/subfiles/model_setup.tex
===================================================================
--- NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/subfiles/model_setup.tex	(revision 11564)
+++ NEMO/branches/2019/dev_r10973_AGRIF-01_jchanut_small_jpi_jpj/doc/latex/TOP/subfiles/model_setup.tex	(revision 11564)
@@ -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}
