Index: branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Biblio/Biblio.bib
===================================================================
--- branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Biblio/Biblio.bib	(revision 5780)
+++ branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Biblio/Biblio.bib	(revision 6436)
@@ -149,4 +149,17 @@
   volume = {36},
   pages = {1502--1522}
+}
+
+@ARTICLE{Artale_al_JGR02,
+  author={V. Artale and D. Iudicone and R. Santoleri and V. Rupolo and S. Marullo
+          and F. {D'O}rtenzio},
+  title={Role of surface fluxes in ocean general circulation models using satellite
+          sea surface temperature: Validation of and sensitivity to the forcing
+          frequency of the Mediterranean thermohaline circulation},
+  journal=JGR,
+  year={2002},
+  volume={107},
+  pages={1978-2012},
+  doi = {10.1029/2000JC000452},
 }
 
@@ -276,7 +289,7 @@
   author = {A. Beckmann and H. Goosse},
   title = {A parameterization of ice shelf-ocean interaction for climate models},
-  journal = OM
-  year = {2003}
-  volume = {5}
+  journal = OM,
+  year = {2003},
+  volume = {5},
   pages = {157--170}
 }
@@ -459,4 +472,16 @@
 }
 
+@article{bouffard_Boegman_DAO2013,
+	author = {D. Bouffard and L. Boegman},
+	title = {A diapycnal diffusivity model for stratified environmental flows},
+	volume = {61-62},
+	issn = {03770265},
+	url = {http://dx.doi.org/10.1016/j.dynatmoce.2013.02.002},
+	doi = {10.1016/j.dynatmoce.2013.02.002},
+	journal = DAO,
+	year = {2013},
+	pages = {14--34},
+}
+
 @ARTICLE{Bougeault1989,
   author = {P. Bougeault and P. Lacarrere},
@@ -489,4 +514,27 @@
   volume = {28},  number = {8},
   pages = {1603--1606}
+}
+
+@article{Brankart_OM2013,
+author = "J.-M. Brankart",
+title = "Impact of uncertainties in the horizontal density gradient upon low resolution global ocean modelling ",
+journal = OM,
+year = "2013",
+volume = "66", pages = "64--76",
+issn = "1463-5003",
+doi = "http://dx.doi.org/10.1016/j.ocemod.2013.02.004",
+url = "http://www.sciencedirect.com/science/article/pii/S1463500313000309",
+}
+
+@Article{Brankart_al_GMD2015,
+AUTHOR = {Brankart, J.-M. and Candille, G. and Garnier, F. and Calone, C. and Melet, A. and Bouttier, P.-A. and Brasseur, P. and Verron, J.},
+TITLE = {A generic approach to explicit simulation of uncertainty in the NEMO ocean model},
+JOURNAL = {Geoscientific Model Development},
+VOLUME = {8},
+YEAR = {2015},
+NUMBER = {5},
+PAGES = {1285--1297},
+URL = {http://www.geosci-model-dev.net/8/1285/2015/},
+DOI = {10.5194/gmd-8-1285-2015}
 }
 
@@ -753,4 +801,16 @@
 }
 
+@article{de_lavergne_JPO2016_efficiency,
+	title = {The impact of a variable mixing efficiency on the abyssal overturning},
+	issn = {0022-3670},
+	url = {http://dx.doi.org//10.1175/JPO-D-14-0259.1},
+	doi = {10.1175/JPO-D-14-0259.1},
+	abstract = {In studies of ocean mixing, it is generally assumed that small-scale turbulent overturns lose 15-20 \% of their energy in eroding the background stratification. Accumulating evidence that this energy fraction, or mixing efficiency Rf, significantly varies depending on flow properties challenges this assumption, however. Here, we examine the implications of a varying mixing efficiency for ocean energetics and deep water mass transformation. Combining current parameterizations of internal wave-driven mixing with a recent model expressing Rf as a function of a turbulence intensity parameter Reb = εν/νN2, we show that accounting for reduced mixing efficiencies in regions of weak stratification or energetic turbulence (high Reb) strongly limits the ability of breaking internal waves to supply oceanic potential energy and drive abyssal upwelling. Moving from a fixed Rf = 1/6 to a variable efficiency Rf(Reb) causes Antarctic Bottom Water upwelling induced by locally-dissipating internal tides and lee waves to fall from 9 to 4 Sv, and the corresponding potential energy source to plunge from 97 to 44 GW. When adding the contribution of remotely-dissipating internal tides under idealized distributions of energy dissipation, the total rate of Antarctic Bottom Water upwelling is reduced by about a factor of 2, reaching 5-15 Sv compared to 10-33 Sv for a fixed efficiency. Our results suggest that distributed mixing, overflow-related boundary processes and geothermal heating are more effective in consuming abyssal waters than topographically-enhanced mixing by breaking internal waves. Our calculations also point to the importance of accurately constraining Rf(Reb) and including the effect in ocean models.},
+	journal = {Journal of Physical Oceanography},
+	author = {C. de Lavergne and G. Madec and J. Le Sommer and A. J. G. Nurser and A. C. Naveira Garabato },
+	year = {2016},
+	volume = {46},  pages = {663-–681}
+}
+
 @ARTICLE{Delecluse_Madec_Bk00,
   author = {P. Delecluse and G. Madec},
@@ -763,4 +823,12 @@
 }
 
+@PHDTHESIS{Demange_PhD2014,
+  author = {J. Demange},
+  title = {Sch\'{e}́mas num\'{e}́riques d'advection et de propagation d’ondes de gravit\'{e}́ 
+           dans les mod\`{e}les de circulation oc\'{e}́anique.},
+  school = {Doctorat es Applied Mathematiques, Grenoble University, France},
+  year = {2014},
+  pages = {138pp}
+}
 
 @ARTICLE{Dobricic_al_OS07,
@@ -983,5 +1051,5 @@
   author = {M. Farge},
   title = {Dynamique non lineaire des ondes et des tourbillons dans les equations de Saint Venant},
-  school = {Doctorat es Mathematiques, Paris VI University},
+  school = {Doctorat es Mathematiques, Paris VI University, France},
   year = {1987},
   pages = {401pp}
@@ -1059,4 +1127,16 @@
   volume = {20},  number = {1},
   pages = {150--155},
+}
+
+@Article{Gentemann_al_JGR09,
+  author = 	 {C. L. Gentemann  and P. J. Minnett and B. Ward},
+  title =        {Profiles of Ocean Surface heating ({POSH}): A new model 
+                  of upper ocean diurnal warming},
+  journal = 	 JGR,
+  year = 	 {2009},
+  Volume = 	 {114},
+  Pages = 	 {C07017},
+  doi = 	 {10.1029/2008JC004825},
+  OPTannote = 	 {}
 }
 
@@ -1104,4 +1184,18 @@
 }
 
+@article{goff_JGR2010,
+	author = {J. A. Goff},
+	title = {Global prediction of abyssal hill root-mean-square heights from small-scale altimetric gravity variability},
+	issn = {2156-2202},
+	url = {http://dx.doi.org/10.1029/2010JB007867},
+	doi = {10.1029/2010JB007867},
+	abstract = {Abyssal hills, which are pervasive landforms on the seafloor of the Earth's oceans, represent a potential tectonic record of the history of mid-ocean ridge spreading. However, the most detailed global maps of the seafloor, derived from the satellite altimetry-based gravity field, cannot be used to deterministically characterize such small-scale ({\textless}10 km) morphology. Nevertheless, the small-scale variability of the gravity field can be related to the statistical properties of abyssal hill morphology using the upward continuation formulation. In this paper, I construct a global prediction of abyssal hill root-mean-square (rms) heights from the small-scale variability of the altimetric gravity field. The abyssal hill-related component of the gravity field is derived by first masking distinct features, such as seamounts, mid-ocean ridges, and continental margins, and then applying a newly designed adaptive directional filter algorithm to remove fracture zone/discontinuity fabric. A noise field is derived empirically by correlating the rms variability of the small-scale gravity field to the altimetric noise field in regions of very low relief, and the noise variance is subtracted from the small-scale gravity variance. Suites of synthetically derived, abyssal hill formed gravity fields are generated as a function of water depth, basement rms heights, and sediment thickness and used to predict abyssal hill seafloor rms heights from corrected small-scale gravity rms height. The resulting global prediction of abyssal hill rms heights is validated qualitatively by comparing against expected variations in abyssal hill morphology and quantitatively by comparing against actual measurements of rms heights. Although there is scatter, the prediction appears unbiased.},
+	volume = {115},
+	number = {B12},
+	journal = {Journal of Geophysical Research: Solid Earth},
+	year = {2010},
+	pages = {B12104},
+}
+
 @ARTICLE{Goosse_al_JGR99,
   author = {H. Goosse and E. Deleersnijder and T. Fichefet and M. England},
@@ -1122,4 +1216,14 @@
   doi = {10.1029/2006GL028210},
   url = {http://dx.doi.org/10.1029/2006GL028210}
+}
+
+@ARTICLE{Graham_McDougall_JPO13,
+  author = {F.S. Graham and T.J. McDougall},
+  title = {Quantifying the nonconservative production of conservative temperature, potential temperature, and entropy},
+  journal = JPO,
+  year = {2013},
+  volume = {43},
+  pages = {838--862},
+  url ={http://dx.doi.org/10.1175/JPO-D-11-0188.1}
 }
 
@@ -1197,4 +1301,14 @@
 }
 
+@ARTICLE{Griffies_Hallberg_MWR00,
+  author = {S.M. Griffies and R.H. Hallberg},
+  title = {Biharmonic friction with a Smagorinsky-like viscosity for use in large-scale eddy-permitting ocean models},
+  journal = MWR,
+  year = {2000},
+  volume = {128},  
+  pages = {2935–-2946},
+ url = {http://dx.doi.org/10.1175/1520-0493(2000)128}
+}
+
 @ARTICLE{Guilyardi_al_JC04,
   author = {E. Guilyardi and S. Gualdi and J. M. Slingo and A. Navarra and P. Delecluse 
@@ -1347,4 +1461,13 @@
 }
 
+@ARTICLE{Holland1999, 
+  author = {D. Holland and A. Jenkins},
+  title = {Modeling Thermodynamic Ice-Ocean Interactions at the Base of an Ice Shelf},
+  journal = JPO,
+  year = {1999},
+  volume = {29},  
+  pages = {1787--1800},
+}
+
 @ARTICLE{HollowayOM86,
   author = {Greg Holloway},
@@ -1430,4 +1553,21 @@
 }
 
+@TechReport{Hunter2006,
+  Title                    = {Specification for Test Models of Ice Shelf Cavities},
+  Author                   = {J. R. Hunter},
+  Institution              = {Antarctic Climate \& Ecosystems Cooperative Research Centre Private Bag 80, Hobart, Tasmania 7001},
+  Year                     = {2006},
+}
+
+@TECHREPORT{TEOS10,
+  author = {IOC and SCOR and IAPSO},
+  title = {The international thermodynamic equation of seawater - 2010: Calculation and use of thermodynamic properties},
+  institution = {Intergovernmental Oceanographic Commission},
+  publisher = {Manuals and Guides No. 56, UNESCO (English)},
+  year = {2010},
+  pages = {196pp},
+  url = {http://www.teos-10.org/pubs/TEOS-10_Manual.pdf}
+}
+
 @ARTICLE{Iudicone_al_JPO08b,
   author = {D. Iudicone and G. Madec and B. Blanke and S. Speich},
@@ -1486,4 +1626,17 @@
 }
 
+@article{Jackson_Rehmann_JPO2014,
+	author = {P. R. Jackson and C. R. Rehmann},
+	title = {Experiments on differential scalar mixing in turbulence in a sheared, stratified flow},
+	journal = JPO,
+	volume = {44},
+	issn = {0022-3670},
+	url = {http://dx.doi.org/10.1175/JPO-D-14-0027.1},
+	doi = {10.1175/JPO-D-14-0027.1},
+	number = {10},
+	year = {2014},
+	pages = {2661--2680},
+}
+
 @ARTICLE{Jayne_St_Laurent_GRL01,
   author = {S.R. Jayne and L.C. {St. Laurent}},
@@ -1491,4 +1644,31 @@
   journal = GRL,
   pages = {811--814}
+}
+
+@ARTICLE{Jenkins1991,
+  author = {A. Jenkins},
+  title = {A one-dimensional model of ice shelf-ocean interaction},
+  journal = JGR,
+  year = {1991},
+  volume = {96},  number = {C11},
+  pages = {2298--2312}
+}
+
+@ARTICLE{Jenkins2001,
+  author = {A. Jenkins},
+  title = {The Role of Meltwater Advection in the Formulation of Conservative Boundary Conditions at an Ice-Ocean Interface},
+  journal = JPO,
+  year = {2001},
+  volume = {31},
+  pages = {285--296}
+}
+
+@ARTICLE{Jenkins2010,
+  author = {A. Jenkins},
+  title = {observation and parameterization of ablation at the base of Ronne Ice Shelf, Antarctica},
+  journal = JPO,
+  year = {2010},
+  volume = {40},  number = {10},
+  pages = {2298--2312}
 }
 
@@ -1643,4 +1823,28 @@
 }
 
+@article{Lemarie_OM2012,
+author = "F. Lemari\'{e} and L. Debreu and A.F. Shchepetkin and J.C. McWilliams",
+title = "On the stability and accuracy of the harmonic and biharmonic isoneutral mixing operators in ocean models ",
+journal = OM,
+year = "2012",
+volume = "52–53", pages = "9--35",
+issn = "1463-5003",
+doi = "http://dx.doi.org/10.1016/j.ocemod.2012.04.007",
+url = "http://www.sciencedirect.com/science/article/pii/S1463500312000674",
+}
+
+
+@ARTICLE{Lemarie_OM2015,
+  author = {F. Lemari\'{e} and L. Debreu and J. Demange and  G. Madec and J.M. Molines and M. Honnorat},
+  title = {Stability Constraints for Oceanic Numerical Models: 
+           Implications for the Formulation of time and space Discretizations},
+  journal = OM,
+  year = {2015},
+  volume = {92}, 
+  pages = {124--148},
+  doi = {10.1016/j.ocemod.2015.06.006},
+  url = {http://dx.doi.org/10.1016/j.ocemod.2015.06.006}
+}
+
 @ARTICLE{Lermusiaux2001,
   author = {P. F. J. Lermusiaux},
@@ -1655,5 +1859,5 @@
   author = {M. L\'{e}vy},
   title = {Mod\'{e}lisation des processus biog\'{e}ochimiques en M\'{e}diterran\'{e}e
-	nord-occidentale. Cycle saisonnier et variabilit\'{e} m\'{e}so\'{e}chelle},
+	        nord-occidentale. Cycle saisonnier et variabilit\'{e} m\'{e}so\'{e}chelle},
   school = {Universit\'{e} Pierre et Marie Curie, Paris, France, 207pp},
   year = {1996}
@@ -1783,15 +1987,25 @@
   year = {2009},
   volume = {30},  number = {2-3},
-  pages = {88-94},
+  pages = {88--94},
   doi = {10.1016/j.ocemod.2009.06.006},
-  url = {http://dx.doi.org/}
-}
-
-@ARTICLE{Leclair_Madec_OM10s,
+  url = {http://dx.doi.org/10.1016/j.ocemod.2009.06.006}
+}
+
+@ARTICLE{Leclair_Madec_OM11,
   author = {M. Leclair and G. Madec},
   title = {$\tilde{z}$-coordinate, an Arbitrary Lagrangian-Eulerian coordinate separating high and low frequency},
   journal = OM,
-  year = {2010},
-  pages = {submitted},
+  year = {2011},
+  volume = {37},  pages = {139--152}, 
+  doi = {10.1016/j.ocemod.2011.02.001},
+  url = {http://dx.doi.org/10.1016/j.ocemod.2011.02.001}
+}
+
+@ARTICLE{Lele_JCP1992,
+  author = {S.K. Lele},
+  title = {Compact finite difference schemes with spectral-like resolution},
+  journal = JCP,
+  year = {1992},
+  volume = {103}, pages = {16--42}
 }
 
@@ -1803,6 +2017,5 @@
   journal = JC,
   year = {2003},
-  volume = {16},  number = {20},
-  pages = {3330--3343}
+  volume = {16},  number = {20}, pages = {3330--3343}
 }
 
@@ -1900,4 +2113,12 @@
 }
 
+@ARTICLE{Losch2008,
+  author = {M. Losch},
+  title = {Modeling ice shelf cavities in a z coordinate ocean general circulation model},
+  journal = JGR,
+  year = {2008},
+  volume = {113},  number = {C13},
+}
+
 @TECHREPORT{Lott1989,
   author = {F. Lott and G. Madec},
@@ -2074,17 +2295,4 @@
   volume = {3},
   pages = {1--20}
-}
-
-
-@article{Martin_Adcroft_OM10,
-author = {T. Martin and A. Adcroft},
-title = {Parameterizing the fresh-water flux from land ice to ocean with interactive icebergs in a coupled climate model},
-journal = OM,
-year = {2010},
-volume = {34}, number = {3--4},
-pages = {111--124},
-issn = {1463-5003},
-doi = {10.1016/j.ocemod.2010.05.001},
-url = {http://dx.doi.org/10.1016/j.ocemod.2010.05.001}
 }
 
@@ -2100,4 +2308,28 @@
   doi = {10.1016/j.ocemod.2007.07.005},
   url = {http://dx.doi.org/10.1016/j.ocemod.2007.07.005}
+}
+
+@Article{Marsh_GMD2015,
+AUTHOR = {R. Marsh and V. O. Ivchenko and N. Skliris and S. Alderson and G. R. Bigg and G. Madec and A. T. Blaker and Y. Aksenov and B. Sinha and A. C. Coward and J. Le Sommer and N. Merino and V. B. Zalesny},
+TITLE = {NEMO-ICB (v1.0): interactive icebergs in the NEMO ocean model globally configured at eddy-permitting resolution},
+JOURNAL = {Geoscientific Model Development},
+VOLUME = {8},
+YEAR = {2015},
+NUMBER = {5},
+PAGES = {1547--1562},
+url = {HTTP://www.geosci-model-dev.net/8/1547/2015/},
+DOI = {10.5194/gmd-8-1547-2015}
+}
+
+@article{Martin_Adcroft_OM10,
+author = {T. Martin and A. Adcroft},
+title = {Parameterizing the fresh-water flux from land ice to ocean with interactive icebergs in a coupled climate model},
+journal = OM,
+year = {2010},
+volume = {34}, number = {3--4},
+pages = {111--124},
+issn = {1463-5003},
+doi = {10.1016/j.ocemod.2010.05.001},
+url = {http://dx.doi.org/10.1016/j.ocemod.2010.05.001}
 }
 
@@ -2249,4 +2481,15 @@
 }
 
+
+@ARTICLE{Morel_Berthon_LO89,
+  author = {A. Morel and J.-F. Berthon},
+  title = {Surface pigments, algal biomass profiles, and potential production of the euphotic layer: 
+           Relationships reinvestigated in view of remote-sensing applications},
+  journal = {Limnol. Oceanogr.},
+  year = {1989},
+  volume = {34(8)},
+  pages = {1545--1562}
+}
+
 @ARTICLE{Morel_Maritorena_JGR01,
   author = {A. Morel and S. Maritorena},
@@ -2297,4 +2540,5 @@
   title = {Estimates of the local rate of vertical diﬀusion from dissipation measurements},
   journal = JPO,
+  year = {1980},
   volume = {10},
   pages = {83--89}
@@ -2470,4 +2714,16 @@
 }
 
+@Article{Rodgers_2014,
+AUTHOR = {Rodgers, K. B. and Aumont, O. and Mikaloff Fletcher, S. E. and Plancherel, Y. and Bopp, L. and de Boyer Mont\'egut, C. and Iudicone, D. and Keeling, R. F. and Madec, G. and Wanninkhof, R.},
+TITLE = {Strong sensitivity of Southern Ocean carbon uptake and nutrient cycling to wind stirring},
+JOURNAL = {Biogeosciences},
+VOLUME = {11},
+YEAR = {2014},
+NUMBER = {15},
+PAGES = {4077--4098},
+URL = {HTTP://www.biogeosciences.net/11/4077/2014/},
+DOI = {10.5194/bg-11-4077-2014}
+}
+
 @ARTICLE{Rodi_1987,
   author = {W. Rodi},
@@ -2486,4 +2742,27 @@
   year = {1986},
   editor = {J.J. O'Brien}
+}
+
+@article{Roquet_OM2015,
+author = "F. Roquet and G. Madec and T.J. McDougall and P.M. Barker",
+title = "Accurate polynomial expressions for the density and specific volume of seawater using the TEOS-10 standard ",
+journal = OM,
+volume = "90",
+pages = "29--43",
+year = "2015",
+issn = "1463-5003",
+doi = "10.1016/j.ocemod.2015.04.002",
+url = "http://dx.doi.org/10.1016/j.ocemod.2015.04.002"
+}
+
+@article{Roquet_JPO2015,
+author = "F. Roquet and G. Madec and L. Brodeau and J. Nycander",
+title = "Defining a Simplified Yet Realistic Equation of State for Seawater",
+journal = JPO,
+volume = "45",
+pages = "2564--2579",
+year = "2015",
+doi = "10.1175/JPO-D-15-0080.1",
+url = "http://dx.doi.org/10.1175/JPO-D-15-0080.1"
 }
 
@@ -2498,4 +2777,15 @@
 }
 
+@ARTICLE{Rousset_GMD2015,
+  author = {C. Rousset and M. Vancoppenolle and G. Madec and T. Fichefet and S. Flavoni 
+            and A. Barth\'{e}lemy and R. Benshila and J. Chanut and C. L\'{e}vy and S. Masson and F. Vivier },
+  title  = {The Louvain-La-Neuve sea-ice model LIM3.6: Global and regional capabilities},
+  journal= {Geoscientific Model Development},
+  year = {2015},
+  volume = {8}, pages={2991--3005},
+  doi = {10.5194/gmd-8-2991-2015},
+  url = {http://dx.doi.org/10.5194/gmd-8-2991-2015}
+}
+
 @ARTICLE{Sadourny1975,
   author = {R. Sadourny},
@@ -2514,4 +2804,14 @@
   volume = {87},
   pages = {394--409}
+}
+
+@ARTICLE{Saunders_JAS82,
+  author={P. M. Saunders},
+  title={{The Temperature at the Ocean-air Interface}},
+  journal=JAS,
+  year={1967},
+  volume={24},
+  pages={269-273},
+  doi = {10.1175/1520-0469(1967)024<0269:TTATOA>2.0.CO;2},
 }
 
@@ -2570,4 +2870,13 @@
 }
 
+@INBOOK{Smagorinsky_93,
+  author = {Smagorinsky, J.},
+  chapter = {Some historical remarks on the use of non-linear viscosities},
+  title = {Large Eddy Simulation of Complex Engineering and Geophysical Flows},
+  pages = {3--36},
+  year = {1993},
+  publisher = {Cambridge University Press, B. Galperin and S. A. Orszag (eds.)},
+}
+
 @ARTICLE{Song_Haidvogel_JCP94,
   author = {Y. Song and D. Haidvogel},
@@ -2688,4 +2997,15 @@
   volume = {359},
   pages = {123--129}
+}
+
+@ARTICLE{Takaya_al_JGR10,
+  author = {Y. Takaya and J-R. Bidlot and A. C. M. Beljaars and 
+                  P. A. E. M. Janssen},
+  title = {Refinements to a prognostic scheme of sea surface skin temperature},
+  journal = JGR,
+  year   = 	 {2010},
+  Volume = 	 {115},
+  Pages  = 	 {C06009},
+  doi    = {10.1029/2009JC005985},
 }
 
@@ -2793,4 +3113,14 @@
 }
 
+@ARTICLE{Tu_Tsuang_GRL05,
+  title={{Cool-skin simulation by a one-column ocean model}},
+  author={{C-Y}. Tu  and {B-J}. Tsuang},
+  journal=GRL,
+  year={2005},
+  volume={32},
+  pages={L22602},
+  doi = {10.1029/2005GL024252},
+}
+
 @ARTICLE{Umlauf_Burchard_JMS03,
   author = {L. Umlauf and H. Burchard},
@@ -2842,4 +3172,13 @@
   volume = {27},
   pages = {54--69}
+}
+
+@book{Vallis06,
+author = {Vallis, G. K.},
+title = {Atmospheric and Oceanic Fluid Dynamics},
+publisher = {Cambridge University Press},
+address = {Cambridge, U.K.},
+year = {2006},
+pages = {745},
 }
 
