Changeset 6436 for branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Biblio/Biblio.bib

-                      r5120
+                      r6436
   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},
+}
 …
   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}
+}
 …
+}
+@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},
 …
   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}
+}
 …
+}
+@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},
 …
+}
+@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,
 …
   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}
 …
   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 =   {}
+}
 …
+}
+@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},
 …
   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}
+}
 …
+}
+@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
 …
+}
+@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},
 …
+}
+@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},
 …
+}
+@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}},
 …
   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}
+}
 …
+}
+@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},
 …
   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}
 …
   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}
+}
 …
   journal = JC,
   year = {2003},
+  volume = {16},  number = {20},
+  pages = {3330--3343}
+  volume = {16},  number = {20}, pages = {3330--3343}
+}
 …
+}
+@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},
 …
   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}
+}
 …
   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}
+}
 …
+}
+@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},
 …
   title = {Estimates of the local rate of vertical diﬀusion from dissipation measurements},
   journal = JPO,
+  year = {1980},
   volume = {10},
   pages = {83--89}
 …
+}
+@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},
 …
   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"
+}
 …
+}
+@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},
 …
   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},
+}
 …
+}
+@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},
 …
   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},
+}
 …
+}
+@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},
 …
   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},
+}

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Chapters/Abstracts_Foreword.tex

-                      r3294
+                      r6436
 be a flexible tool for studying the ocean and its interactions with the others components of
 the earth climate system over a wide range of space and time scales.
 Prognostic variables are the three-dimensional velocity field, a linear
 or non-linear sea surface height, the temperature and the salinity. In the horizontal direction,
 the model uses a curvilinear orthogonal grid and in the vertical direction, a full or partial step
 $z$-coordinate, or $s$-coordinate, or a mixture of the two. The distribution of variables is a
 three-dimensional Arakawa C-type grid. Various physical choices are available to describe
 ocean physics, including TKE, GLS and KPP vertical physics. Within NEMO, the ocean is
 interfaced with a sea-ice model (LIM v2 and v3), passive tracer and biogeochemical models (TOP)
 and, via the OASIS coupler, with several atmospheric general circulation models. It also
 support two-way grid embedding via the AGRIF software.
+Prognostic variables are the three-dimensional velocity field, a non-linear sea surface height,
+the \textit{Conservative} Temperature and the \textit{Absolute} Salinity.
+In the horizontal direction, the model uses a curvilinear orthogonal grid and in the vertical direction,
+a full or partial step $z$-coordinate, or $s$-coordinate, or a mixture of the two.
+The distribution of variables is a three-dimensional Arakawa C-type grid.
+Various physical choices are available to describe ocean physics, including TKE, and GLS vertical physics.
+Within NEMO, the ocean is interfaced with a sea-ice model (LIM or CICE), passive tracer and
+biogeochemical models (TOP) and, via the OASIS coupler, with several atmospheric general circulation models.
+It also support two-way grid embedding via the AGRIF software.
 % ================================================================
 …
 interactions avec les autres composantes du syst\`{e}me climatique terrestre.
 Les variables pronostiques sont le champ tridimensionnel de vitesse, une hauteur de la mer
 lin\'{e}aire ou non, la temperature et la salinit\'{e}.
+lin\'{e}aire, la Temp\'{e}rature Conservative et la Salinit\'{e} Absolue.
 La distribution des variables se fait sur une grille C d'Arakawa tridimensionnelle utilisant une
 coordonn\'{e}e verticale $z$ \`{a} niveaux entiers ou partiels, ou une coordonn\'{e}e s, ou encore
 une combinaison des deux. Diff\'{e}rents choix sont propos\'{e}s pour d\'{e}crire la physique
 oc\'{e}anique, incluant notamment des physiques verticales TKE, GLS et KPP. A travers l'infrastructure
 NEMO, l'oc\'{e}an est interfac\'{e} avec des mod\`{e}les de glace de mer, de biog\'{e}ochimie
 et de traceurs passifs, et, via le coupleur OASIS, \`{a} plusieurs mod\`{e}les de circulation
 g\'{e}n\'{e}rale atmosph\'{e}rique. Il supporte \'{e}galement l'embo\^{i}tement interactif de
 maillages via le logiciel AGRIF.
+oc\'{e}anique, incluant notamment des physiques verticales TKE et GLS. A travers l'infrastructure
+NEMO, l'oc\'{e}an est interfac\'{e} avec des mod\`{e}les de glace de mer (LIM ou CICE),
+de biog\'{e}ochimie marine et de traceurs passifs, et, via le coupleur OASIS, \`{a} plusieurs
+mod\`{e}les de circulation g\'{e}n\'{e}rale atmosph\'{e}rique.
+Il supporte \'{e}galement l'embo\^{i}tement interactif de maillages via le logiciel AGRIF.
+}

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Chapters/Annex_C.tex

-                      r3294
+                      r6436
 \end{aligned}   } \right.
 \end{equation}
 where the indices $i_p$ and $k_p$ take the following value:
+where the indices $i_p$ and $j_p$ take the following value:
 $i_p = -1/2$ or $1/2$ and $j_p = -1/2$ or $1/2$,
 and the vorticity triads, ${^i_j}\mathbb{Q}^{i_p}_{j_p}$, defined at $T$-point, are given by:
 …
 The discrete formulation of the horizontal diffusion of momentum ensures the
 conservation of potential vorticity and the horizontal divergence, and the
 dissipation of the square of these quantities (i.e. enstrophy and the
+dissipation of the square of these quantities ($i.e.$ enstrophy and the
 variance of the horizontal divergence) as well as the dissipation of the
 horizontal kinetic energy. In particular, when the eddy coefficients are
 …
 &\int \limits_D \frac{1} {e_3 } \textbf{k} \cdot \nabla \times
    \Bigl[    \nabla_h  \left( A^{\,lm}\;\chi  \right)
              - \nabla_h \times \left( A^{\,lm}\;\zeta \; \textbf{k} \right)    \Bigr]\;dv  = 0
 \end{flalign*}
+           - \nabla_h \times \left( A^{\,lm}\;\zeta \; \textbf{k} \right)    \Bigr]\;dv   \\
+%\end{flalign*}
 %%%%%%%%%%  recheck here....  (gm)
 \begin{flalign*}
 = \int \limits_D  -\frac{1} {e_3 } \textbf{k} \cdot \nabla \times
    \Bigl[ \nabla_h \times \left( A^{\,lm}\;\zeta \; \textbf{k} \right)  \Bigr]\;dv &&& \\
 \end{flalign*}
 \begin{flalign*}
+%\begin{flalign*}
+=& \int \limits_D  -\frac{1} {e_3 } \textbf{k} \cdot \nabla \times
+   \Bigl[ \nabla_h \times \left( A^{\,lm}\;\zeta \; \textbf{k} \right)  \Bigr]\;dv  \\
+%\end{flalign*}
+%\begin{flalign*}
 \equiv& \sum\limits_{i,j}
    \left\{
+   \delta_{i+1/2}
+   \left[
+   \frac {e_{2v}} {e_{1v}\,e_{3v}}  \delta_i
+      \left[ A_f^{\,lm} e_{3f} \zeta  \right]
+    \right]
+   + \delta_{j+1/2}
+   \left[
+   \frac {e_{1u}} {e_{2u}\,e_{3u}} \delta_j
+      \left[ A_f^{\,lm} e_{3f} \zeta  \right]
+   \right]
+   \right\}
+   && \\
+     \delta_{i+1/2} \left[  \frac {e_{2v}} {e_{1v}\,e_{3v}}  \delta_i \left[ A_f^{\,lm} e_{3f} \zeta  \right]  \right]
+   + \delta_{j+1/2} \left[  \frac {e_{1u}} {e_{2u}\,e_{3u}}  \delta_j \left[ A_f^{\,lm} e_{3f} \zeta  \right]  \right]
+   \right\}     \\
+%
 \intertext{Using \eqref{DOM_di_adj}, it follows:}
 …
 \equiv& \sum\limits_{i,j,k}
    -\,\left\{
+      \frac{e_{2v}} {e_{1v}\,e_{3v}}  \delta_i
+      \left[ A_f^{\,lm} e_{3f} \zeta  \right]\;\delta_i \left[ 1\right]
+   + \frac{e_{1u}} {e_{2u}\,e_{3u}} \delta_j
+      \left[ A_f^{\,lm} e_{3f} \zeta  \right]\;\delta_j \left[ 1\right]
+      \frac{e_{2v}} {e_{1v}\,e_{3v}}  \delta_i  \left[ A_f^{\,lm} e_{3f} \zeta  \right]\;\delta_i \left[ 1\right]
+    + \frac{e_{1u}} {e_{2u}\,e_{3u}}  \delta_j  \left[ A_f^{\,lm} e_{3f} \zeta  \right]\;\delta_j \left[ 1\right]
    \right\} \quad \equiv 0
    && \\
+    \\
 \end{flalign*}
 …
 \subsection{Dissipation of Horizontal Kinetic Energy}
 \label{Apdx_C.3.2}
 The lateral momentum diffusion term dissipates the horizontal kinetic energy:
 …
 \label{Apdx_C.3.3}
 The lateral momentum diffusion term dissipates the enstrophy when the eddy
 coefficients are horizontally uniform:
 …
    \left[   \nabla_h \left( A^{\,lm}\;\chi  \right)
           - \nabla_h \times \left( A^{\,lm}\;\zeta \; \textbf{k} \right)   \right]\;dv &&&\\
 &= A^{\,lm} \int \limits_D \zeta \textbf{k} \cdot \nabla \times
+&\quad = A^{\,lm} \int \limits_D \zeta \textbf{k} \cdot \nabla \times
    \left[    \nabla_h \times \left( \zeta \; \textbf{k} \right)   \right]\;dv &&&\\
 &\equiv A^{\,lm} \sum\limits_{i,j,k}  \zeta \;e_{3f}
+&\quad \equiv A^{\,lm} \sum\limits_{i,j,k}  \zeta \;e_{3f}
    \left\{     \delta_{i+1/2} \left[  \frac{e_{2v}} {e_{1v}\,e_{3v}} \delta_i \left[ e_{3f} \zeta  \right]   \right]
              + \delta_{j+1/2} \left[  \frac{e_{1u}} {e_{2u}\,e_{3u}} \delta_j \left[ e_{3f} \zeta  \right]   \right]      \right\}   &&&\\
 …
 \intertext{Using \eqref{DOM_di_adj}, it follows:}
+%
 &\equiv  - A^{\,lm} \sum\limits_{i,j,k}
+&\quad \equiv  - A^{\,lm} \sum\limits_{i,j,k}
    \left\{    \left(  \frac{1} {e_{1v}\,e_{3v}}  \delta_i \left[ e_{3f} \zeta  \right]  \right)^2   b_v
+            + \left(  \frac{1} {e_{2u}\,e_{3u}}  \delta_j \left[ e_{3f} \zeta  \right] \right)^2   b_u  \right\}      &&&\\
+& \leq \;0       &&&\\
+            + \left(  \frac{1} {e_{2u}\,e_{3u}}  \delta_j \left[ e_{3f} \zeta  \right] \right)^2   b_u  \right\}  \quad \leq \;0    &&&\\
 \end{flalign*}
 …
 When the horizontal divergence of the horizontal diffusion of momentum
 (discrete sense) is taken, the term associated with the vertical curl of the
 vorticity is zero locally, due to (!!! II.1.8  !!!!!). The resulting term conserves the
 $\chi$ and dissipates $\chi^2$ when the eddy coefficients are
 horizontally uniform.
+vorticity is zero locally, due to \eqref{Eq_DOM_div_curl}.
+The resulting term conserves the $\chi$ and dissipates $\chi^2$
+when the eddy coefficients are horizontally uniform.
 \begin{flalign*}
 & \int\limits_D  \nabla_h \cdot
    \Bigl[     \nabla_h \left( A^{\,lm}\;\chi \right)
              - \nabla_h \times \left( A^{\,lm}\;\zeta \;\textbf{k} \right)    \Bigr]  dv
 = \int\limits_D  \nabla_h \cdot \nabla_h \left( A^{\,lm}\;\chi  \right)   dv   &&&\\
+= \int\limits_D  \nabla_h \cdot \nabla_h \left( A^{\,lm}\;\chi  \right)   dv   \\
+%
 &\equiv \sum\limits_{i,j,k}
    \left\{   \delta_i \left[ A_u^{\,lm} \frac{e_{2u}\,e_{3u}} {e_{1u}}  \delta_{i+1/2} \left[ \chi \right]  \right]
            + \delta_j \left[ A_v^{\,lm} \frac{e_{1v}\,e_{3v}} {e_{2v}}  \delta_{j+1/2} \left[ \chi \right]  \right]    \right\}    &&&\\
+           + \delta_j \left[ A_v^{\,lm} \frac{e_{1v}\,e_{3v}} {e_{2v}}  \delta_{j+1/2} \left[ \chi \right]  \right]    \right\}    \\
+%
 \intertext{Using \eqref{DOM_di_adj}, it follows:}
 …
 &\equiv \sum\limits_{i,j,k}
    - \left\{   \frac{e_{2u}\,e_{3u}} {e_{1u}}  A_u^{\,lm} \delta_{i+1/2} \left[ \chi \right] \delta_{i+1/2} \left[ 1 \right]
              + \frac{e_{1v}\,e_{3v}}  {e_{2v}}  A_v^{\,lm} \delta_{j+1/2} \left[ \chi \right] \delta_{j+1/2} \left[ 1 \right]    \right\}
    \qquad \equiv 0     &&& \\
+             + \frac{e_{1v}\,e_{3v}} {e_{2v}}  A_v^{\,lm} \delta_{j+1/2} \left[ \chi \right] \delta_{j+1/2} \left[ 1 \right]    \right\}
+   \quad \equiv 0      \\
 \end{flalign*}
 …
    \left[    \nabla_h              \left( A^{\,lm}\;\chi                    \right)
            - \nabla_h   \times  \left( A^{\,lm}\;\zeta \;\textbf{k} \right)    \right]\;  dv
  = A^{\,lm}   \int\limits_D \chi \;\nabla_h \cdot \nabla_h \left( \chi \right)\;  dv    &&&\\
+ = A^{\,lm}   \int\limits_D \chi \;\nabla_h \cdot \nabla_h \left( \chi \right)\;  dv    \\
+%
 &\equiv A^{\,lm}  \sum\limits_{i,j,k}  \frac{1} {e_{1t}\,e_{2t}\,e_{3t}}  \chi
 …
       \delta_i  \left[   \frac{e_{2u}\,e_{3u}} {e_{1u}}  \delta_{i+1/2} \left[ \chi \right]   \right]
    + \delta_j  \left[   \frac{e_{1v}\,e_{3v}} {e_{2v}}   \delta_{j+1/2} \left[ \chi \right]   \right]
    \right\} \;   e_{1t}\,e_{2t}\,e_{3t}    &&&\\
+   \right\} \;   e_{1t}\,e_{2t}\,e_{3t}    \\
+%
 \intertext{Using \eqref{DOM_di_adj}, it turns out to be:}
 …
 &\equiv - A^{\,lm} \sum\limits_{i,j,k}
    \left\{    \left(  \frac{1} {e_{1u}}  \delta_{i+1/2}  \left[ \chi \right]  \right)^2  b_u
+                 + \left(  \frac{1} {e_{2v}}  \delta_{j+1/2}  \left[ \chi \right]  \right)^2  b_v    \right\} \;    &&&\\
+%
+&\leq 0              &&&\\
+            + \left(  \frac{1} {e_{2v}}  \delta_{j+1/2}  \left[ \chi \right]  \right)^2  b_v    \right\}
+\quad \leq 0             \\
 \end{flalign*}
 …
 \section{Conservation Properties on Vertical Momentum Physics}
 \label{Apdx_C_4}
 As for the lateral momentum physics, the continuous form of the vertical diffusion
 …
    \left(   \frac{A^{\,vm}} {e_3 }\; \frac{\partial \textbf{U}_h } {\partial k}   \right)\; dv    \quad &\leq 0     \\
 \end{align*}
 The first property is obvious. The second results from:
 \begin{flalign*}
 \int\limits_D
 …
    e_{1f}\,e_{2f}\,e_{3f} \; \equiv 0   && \\
 \end{flalign*}
 If the vertical diffusion coefficient is uniform over the whole domain, the
 enstrophy is dissipated, $i.e.$
 …
       \left( \frac{A^{\,vm}} {e_3 }\; \frac{\partial \textbf{U}_h } {\partial k}   \right)   \right)\; dv = 0   &&&\\
 \end{flalign*}
 This property is only satisfied in $z$-coordinates:
 \begin{flalign*}
 \int\limits_D \zeta \, \textbf{k} \cdot \nabla \times
 …
 The numerical schemes used for tracer subgridscale physics are written such
+that the heat and salt contents are conserved (equations in flux form, second
+order centered finite differences). Since a flux form is used to compute the
+temperature and salinity, the quadratic form of these quantities (i.e. their variance)
+globally tends to diminish. As for the advection term, there is generally no strict
+conservation of mass, even if in practice the mass is conserved to a very high
+accuracy.
+that the heat and salt contents are conserved (equations in flux form).
+Since a flux form is used to compute the temperature and salinity,
+the quadratic form of these quantities ($i.e.$ their variance) globally tends to diminish.
+As for the advection term, there is conservation of mass only if the Equation Of Seawater is linear.
 % -------------------------------------------------------------------------------------------------------------

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Chapters/Annex_D.tex

-                      r3294
+                      r6436
 \hline
 public  \par or  \par module variable&
 \textbf{m n} \par \textit{but not} \par \textbf{nn\_}&
+\textbf{m n} \par \textit{but not} \par \textbf{nn\_ np\_}&
 \textbf{a b e f g h o q r} \par \textbf{t} \textit{to} \textbf{x} \par but not \par \textbf{fs rn\_}&
 \textbf{l} \par \textit{but not} \par \textbf{lp ld} \par \textbf{ ll ln\_}&
 …
 \hline
 parameter&
 \textbf{jp}&
+\textbf{jp np\_}&
 \textbf{pp}&
 \textbf{lp}&
 …
 %--------------------------------------------------------------------------------------------------------------
+N.B.   Parameter here, in not only parameter in the \textsc{Fortran} acceptation, it is also used for code variables
+that are read in namelist and should never been modified during a simulation.
+It is the case, for example, for the size of a domain (jpi,jpj,jpk).
 \newpage
 % ================================================================

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Chapters/Chap_DIA.tex

-                      r5515
+                      r6436
 % Chapter I/O & Diagnostics
 % ================================================================
 \chapter{Ouput and Diagnostics (IOM, DIA, TRD, FLO)}
+\chapter{Output and Diagnostics (IOM, DIA, TRD, FLO)}
 \label{DIA}
 \minitoc
 \newpage
 $\ $\newline    % force a new ligne
+$\ $\newline    % force a new line
 % ================================================================
 …
+Since version 3.2, iomput is the NEMO output interface of choice. It has been designed to be simple to use, flexible and efficient. The two main purposes of iomput are:
+Since version 3.2, iomput is the NEMO output interface of choice.
+It has been designed to be simple to use, flexible and efficient.
+The two main purposes of iomput are:
 \begin{enumerate}
 \item The complete and flexible control of the output files through external XML files adapted by the user from standard templates.
 …
 % -------------------------------------------------------------------------------------------------------------
 \section[Tracer/Dynamics Trends (TRD)]
+                  {Tracer/Dynamics Trends  (\key{trdtra}, \key{trddyn},    \\
+                                                             \key{trddvor}, \key{trdmld})}
+                  {Tracer/Dynamics Trends  (\ngn{namtrd})}
 \label{DIA_trd}
 …
 %-------------------------------------------------------------------------------------------------------------
+When \key{trddyn} and/or \key{trddyn} CPP variables are defined, each
+trend of the dynamics and/or temperature and salinity time evolution equations
+is stored in three-dimensional arrays just after their computation ($i.e.$ at the end
+of each $dyn\cdots.F90$ and/or $tra\cdots.F90$ routines). Options are defined by
+\ngn{namtrd} namelist variables. These trends are then
+used in \mdl{trdmod} (see TRD directory) every \textit{nn\_trd } time-steps.
+What is done depends on the CPP keys defined:
+Each trend of the dynamics and/or temperature and salinity time evolution equations
+can be send to \mdl{trddyn} and/or \mdl{trdtra} modules (see TRD directory) just after their computation
+($i.e.$ at the end of each $dyn\cdots.F90$ and/or $tra\cdots.F90$ routines).
+This capability is controlled by options offered in \ngn{namtrd} namelist.
+Note that the output are done with xIOS, and therefore the \key{IOM} is required.
+What is done depends on the \ngn{namtrd} logical set to \textit{true}:
 \begin{description}
+\item[\key{trddyn}, \key{trdtra}] : a check of the basin averaged properties of the momentum
+and/or tracer equations is performed ;
+\item[\key{trdvor}] : a vertical summation of the moment tendencies is performed,
+then the curl is computed to obtain the barotropic vorticity tendencies which are output ;
+\item[\key{trdmld}] : output of the tracer tendencies averaged vertically
+either over the mixed layer (\np{nn\_ctls}=0),
+or       over a fixed number of model levels (\np{nn\_ctls}$>$1 provides the number of level),
+or       over a spatially varying but temporally fixed number of levels (typically the base
+of the winter mixed layer) read in \ifile{ctlsurf\_idx} (\np{nn\_ctls}=1) ;
+\item[\np{ln\_glo\_trd}] : at each \np{nn\_trd} time-step a check of the basin averaged properties
+of the momentum and tracer equations is performed. This also includes a check of $T^2$, $S^2$,
+$\tfrac{1}{2} (u^2+v2)$, and potential energy time evolution equations properties ;
+\item[\np{ln\_dyn\_trd}] : each 3D trend of the evolution of the two momentum components is output ;
+\item[\np{ln\_dyn\_mxl}] : each 3D trend of the evolution of the two momentum components averaged
+                           over the mixed layer is output  ;
+\item[\np{ln\_vor\_trd}] : a vertical summation of the moment tendencies is performed,
+                           then the curl is computed to obtain the barotropic vorticity tendencies which are output ;
+\item[\np{ln\_KE\_trd}]  : each 3D trend of the Kinetic Energy equation is output ;
+\item[\np{ln\_tra\_trd}] : each 3D trend of the evolution of temperature and salinity is output ;
+\item[\np{ln\_tra\_mxl}] : each 2D trend of the evolution of temperature and salinity averaged
+                           over the mixed layer is output ;
 \end{description}
-The units in the output file can be changed using the \np{nn\_ucf} namelist parameter.
-For example, in case of salinity tendency the units are given by PSU/s/\np{nn\_ucf}.
-Setting \np{nn\_ucf}=86400 ($i.e.$ the number of second in a day) provides the tendencies in PSU/d.
-When \key{trdmld} is defined, two time averaging procedure are proposed.
-Setting \np{ln\_trdmld\_instant} to \textit{true}, a simple time averaging is performed,
-so that the resulting tendency is the contribution to the change of a quantity between
-the two instantaneous values taken at the extremities of the time averaging period.
-Setting \np{ln\_trdmld\_instant} to \textit{false}, a double time averaging is performed,
-so that the resulting tendency is the contribution to the change of a quantity between
-two \textit{time mean} values. The later option requires the use of an extra file, \ifile{restart\_mld}
-(\np{ln\_trdmld\_restart}=true), to restart a run.
 Note that the mixed layer tendency diagnostic can also be used on biogeochemical models
 via the \key{trdtrc} and \key{trdmld\_trc} CPP keys.
+\textbf{Note that} in the current version (v3.6), many changes has been introduced but not fully tested.
+In particular, options associated with \np{ln\_dyn\_mxl}, \np{ln\_vor\_trd}, and \np{ln\_tra\_mxl}
+are not working, and none of the option have been tested with variable volume ($i.e.$ \key{vvl} defined).
 % -------------------------------------------------------------------------------------------------------------
 …
 \label{DIA_diag_harm}
-A module is available to compute the amplitude and phase for tidal waves.
-This diagnostic is actived with \key{diaharm}.
 %------------------------------------------namdia_harm----------------------------------------------------
 \namdisplay{namdia_harm}
 %----------------------------------------------------------------------------------------------------------
+Concerning the on-line Harmonic analysis, some parameters are available in namelist
+\ngn{namdia\_harm} :
+- \texttt{nit000\_han} is the first time step used for harmonic analysis
+- \texttt{nitend\_han} is the last time step used for harmonic analysis
+- \texttt{nstep\_han} is the time step frequency for harmonic analysis
+- \texttt{nb\_ana} is the number of harmonics to analyse
+- \texttt{tname} is an array with names of tidal constituents to analyse
+\texttt{nit000\_han} and \texttt{nitend\_han} must be between \texttt{nit000} and \texttt{nitend} of the simulation.
+A module is available to compute the amplitude and phase of tidal waves.
+This on-line Harmonic analysis is actived with \key{diaharm}.
+Some parameters are available in namelist \ngn{namdia\_harm} :
+- \np{nit000\_han} is the first time step used for harmonic analysis
+- \np{nitend\_han} is the last time step used for harmonic analysis
+- \np{nstep\_han} is the time step frequency for harmonic analysis
+- \np{nb\_ana} is the number of harmonics to analyse
+- \np{tname} is an array with names of tidal constituents to analyse
+\np{nit000\_han} and \np{nitend\_han} must be between \np{nit000} and \np{nitend} of the simulation.
 The restart capability is not implemented.
 The Harmonic analysis solve this equation:
+The Harmonic analysis solve the following equation:
 \begin{equation}
 h_{i} - A_{0} + \sum^{nb\_ana}_{j=1}[A_{j}cos(\nu_{j}t_{j}-\phi_{j})] = e_{i}
 …
 \label{DIA_diag_dct}
 A module is available to compute the transport of volume, heat and salt through sections. This diagnostic
 is actived with \key{diadct}.
+A module is available to compute the transport of volume, heat and salt through sections.
+This diagnostic is actived with \key{diadct}.
 Each section is defined by the coordinates of its 2 extremities. The pathways between them are contructed
 …
 %-------------------------------------------------------------------------------------------------------------
 \texttt{nn\_dct}: frequency of instantaneous transports computing
 \texttt{nn\_dctwri}: frequency of writing ( mean of instantaneous transports )
 \texttt{nn\_debug}: debugging of the section
+\np{nn\_dct}: frequency of instantaneous transports computing
+\np{nn\_dctwri}: frequency of writing ( mean of instantaneous transports )
+\np{nn\_debug}: debugging of the section
 \subsubsection{ To create a binary file containing the pathway of each section }
 …
 the \key{diahth} CPP key:
 - the mixed layer depth (based on a density criterion, \citet{de_Boyer_Montegut_al_JGR04}) (\mdl{diahth})
+- the mixed layer depth (based on a density criterion \citep{de_Boyer_Montegut_al_JGR04}) (\mdl{diahth})
 - the turbocline depth (based on a turbulent mixing coefficient criterion) (\mdl{diahth})

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Chapters/Chap_DOM.tex

-                      r5120
+                      r6436
 % ================================================================
 % Chapter 2 � Space and Time Domain (DOM)
+% Chapter 2 ——— Space and Time Domain (DOM)
 % ================================================================
 \chapter{Space Domain (DOM) }
 …
 and $f$-points, and its divergence defined at $t$-points:
 \begin{eqnarray}  \label{Eq_DOM_curl}
  \nabla \times {\rm {\bf A}}\equiv &
+ \nabla \times {\rm{\bf A}}\equiv &
       \frac{1}{e_{2v}\,e_{3vw} } \ \left( \delta_{j +1/2} \left[e_{3w}\,a_3 \right] -\delta_{k+1/2} \left[e_{2v} \,a_2 \right] \right)  &\ \mathbf{i} \\
  +& \frac{1}{e_{2u}\,e_{3uw}} \ \left( \delta_{k+1/2} \left[e_{1u}\,a_1  \right] -\delta_{i +1/2} \left[e_{3w}\,a_3 \right] \right)  &\ \mathbf{j} \\
 …
 Let $a$ and $b$ be two fields defined on the mesh, with value zero inside
 continental area. Using integration by parts it can be shown that the differencing
 operators ($\delta_i$, $\delta_j$ and $\delta_k$) are anti-symmetric linear
 operators, and further that the averaging operators $\overline{\,\cdot\,}^{\,i}$,
+operators ($\delta_i$, $\delta_j$ and $\delta_k$) are skew-symmetric linear operators,
+and further that the averaging operators $\overline{\,\cdot\,}^{\,i}$,
 $\overline{\,\cdot\,}^{\,k}$ and $\overline{\,\cdot\,}^{\,k}$) are symmetric linear
 operators, $i.e.$
 …
 For both grids here,  the same $w$-point depth has been chosen but in (a) the
 $t$-points are set half way between $w$-points while in (b) they are defined from
 an analytical function: $z(k)=5\,(i-1/2)^3 - 45\,(i-1/2)^2 + 140\,(i-1/2) - 150$.
+an analytical function: $z(k)=5\,(k-1/2)^3 - 45\,(k-1/2)^2 + 140\,(k-1/2) - 150$.
 Note the resulting difference between the value of the grid-size $\Delta_k$ and
 those of the scale factor $e_k$. }
 …
 The choice of the grid must be consistent with the boundary conditions specified
 by the parameter \np{jperio} (see {\S\ref{LBC}).
+by \np{jperio}, a parameter found in \ngn{namcfg} namelist (see {\S\ref{LBC}).
 % -------------------------------------------------------------------------------------------------------------
 …
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 The choice of a vertical coordinate, even if it is made through a namelist parameter,
+The choice of a vertical coordinate, even if it is made through \ngn{namzgr} namelist parameters,
 must be done once of all at the beginning of an experiment. It is not intended as an
 option which can be enabled or disabled in the middle of an experiment. Three main
 …
 bathymetry or $s$-coordinate (hybrid and partial step coordinates have not
 yet been tested in NEMO v2.3). If using $z$-coordinate with partial step bathymetry
+(\np{ln\_zps}~=~true), ocean cavity beneath ice shelves can be open (\np{ln\_isfcav}~=~true).
+(\np{ln\_zps}~=~true), ocean cavity beneath ice shelves can be open (\np{ln\_isfcav}~=~true)
+and partial step are also applied at the ocean/ice shelf interface.
 Contrary to the horizontal grid, the vertical grid is computed in the code and no
 provision is made for reading it from a file. The only input file is the bathymetry
 (in meters) (\ifile{bathy\_meter})
+(in meters) (\ifile{bathy\_meter}).
 \footnote{N.B. in full step $z$-coordinate, a \ifile{bathy\_level} file can replace the
 \ifile{bathy\_meter} file, so that the computation of the number of wet ocean point
 …
 Three options are possible for defining the bathymetry, according to the
 namelist variable \np{nn\_bathy}:
+namelist variable \np{nn\_bathy} (found in \ngn{namdom} namelist):
 \begin{description}
 \item[\np{nn\_bathy} = 0] a flat-bottom domain is defined. The total depth $z_w (jpk)$
 …
 domain width at the central latitude. This is meant for the "EEL-R5" configuration,
 a periodic or open boundary channel with a seamount.
 \item[\np{nn\_bathy} = 1] read a bathymetry. The \ifile{bathy\_meter} file (Netcdf format)
+provides the ocean depth (positive, in meters) at each grid point of the model grid.
 The bathymetry is usually built by interpolating a standard bathymetry product
+\item[\np{nn\_bathy} = 1] read a bathymetry and ice shelf draft (if needed).
+ The \ifile{bathy\_meter} file (Netcdf format) provides the ocean depth (positive, in meters)
+ at each grid point of the model grid. The bathymetry is usually built by interpolating a standard bathymetry product
 ($e.g.$ ETOPO2) onto the horizontal ocean mesh. Defining the bathymetry also
 defines the coastline: where the bathymetry is zero, no model levels are defined
 (all levels are masked).
+The \ifile{isfdraft\_meter} file (Netcdf format) provides the ice shelf draft (positive, in meters)
+ at each grid point of the model grid. This file is only needed if \np{ln\_isfcav}~=~true.
+Defining the ice shelf draft will also define the ice shelf edge and the grounding line position.
 \end{description}
 …
 (Fig.~\ref{Fig_zgr}).
+If the ice shelf cavities are opened (\np{ln\_isfcav}=~true~}), the definition of $z_0$ is the same.
+However, definition of $e_3^0$ at $t$- and $w$-points is respectively changed to:
+\begin{equation} \label{DOM_zgr_ana}
+\begin{split}
+ e_3^T(k) &= z_W (k+1) - z_W (k)   \\
+ e_3^W(k) &= z_T (k)   - z_T (k-1) \\
+\end{split}
+\end{equation}
+This formulation decrease the self-generated circulation into the ice shelf cavity
+(which can, in extreme case, leads to blow up).\\
 The most used vertical grid for ORCA2 has $10~m$ ($500~m)$ resolution in the
 surface (bottom) layers and a depth which varies from 0 at the sea surface to a
 …
 usually 10\%, of the default thickness $e_{3t}(jk)$).
  \colorbox{yellow}{Add a figure here of pstep especially at last ocean level }
+\gmcomment{ \colorbox{yellow}{Add a figure here of pstep especially at last ocean level }  }
 % -------------------------------------------------------------------------------------------------------------
 …
 gives the number of ocean levels ($i.e.$ those that are not masked) at each
 $t$-point. mbathy is computed from the meter bathymetry using the definiton of
 gdept as the number of $t$-points which gdept $\leq$ bathy.
+gdept as the number of $t$-points which gdept $\leq$ bathy.
 Modifications of the model bathymetry are performed in the \textit{bat\_ctl}
 routine (see \mdl{domzgr} module) after mbathy is computed. Isolated grid points
+that do not communicate with another ocean point at the same level are eliminated.
+that do not communicate with another ocean point at the same level are eliminated.\\
+As for the representation of bathymetry, a 2D integer array, misfdep, is created.
+misfdep defines the level of the first wet $t$-point. All the cells between $k=1$ and $misfdep(i,j)-1$ are masked.
+By default, misfdep(:,:)=1 and no cells are masked.
+In case of ice shelf cavities (\np{ln\_isfcav}~=~true), modifications of the model bathymetry and ice shelf draft in
+the cavities are performed through the \textit{zgr\_isf} routine. The compatibility between ice shelf draft and bathymetry is checked:
+if only one cell on the water column is opened at $t$-, $u$- or $v$-points, the bathymetry or the ice shelf draft is dug to have a 2-level water column
+(i.e. two unmasked levels). If the incompatibility is too strong (i.e. need to dig more than one cell), the entire water column is masked.\\
 From the \textit{mbathy} array, the mask fields are defined as follows:
 \begin{align*}
+tmask(i,j,k) &= \begin{cases}   \; 1&   \text{ if $k\leq mbathy(i,j)$  }    \\
+                                                \; 0&   \text{ if $k\leq mbathy(i,j)$  }    \end{cases}     \\
+tmask(i,j,k) &= \begin{cases}   \; 0&   \text{ if $k < misfdep(i,j) $ } \\
+                                \; 1&   \text{ if $misfdep(i,j) \leq k\leq mbathy(i,j)$  }    \\
+                                \; 0&   \text{ if $k > mbathy(i,j)$  }    \end{cases}     \\
 umask(i,j,k) &=         \; tmask(i,j,k) \ * \ tmask(i+1,j,k)   \\
 vmask(i,j,k) &=         \; tmask(i,j,k) \ * \ tmask(i,j+1,k)   \\
 fmask(i,j,k) &=         \; tmask(i,j,k) \ * \ tmask(i+1,j,k)   \\
+                   & \ \ \, * tmask(i,j,k) \ * \ tmask(i+1,j,k)
+                   & \ \ \, * tmask(i,j,k) \ * \ tmask(i+1,j,k) \\
+wmask(i,j,k) &=         \; tmask(i,j,k) \ * \ tmask(i,j,k-1) \text{ with } wmask(i,j,1) = tmask(i,j,1)
 \end{align*}
+Note that \textit{wmask} is not defined as it is exactly equal to \textit{tmask} with
+the numerical indexing used (\S~\ref{DOM_Num_Index}). Moreover, the
+specification of closed lateral boundaries requires that at least the first and last
+Note, wmask is now defined. It allows, in case of ice shelves,
+to deal with the top boundary (ice shelf/ocean interface) exactly in the same way as for the bottom boundary.
+The specification of closed lateral boundaries requires that at least the first and last
 rows and columns of the \textit{mbathy} array are set to zero. In the particular
 case of an east-west cyclical boundary condition, \textit{mbathy} has its last

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Chapters/Chap_DYN.tex

-                      r5120
+                      r6436
 % ================================================================
 % Chapter � Ocean Dynamics (DYN)
+% Chapter ——— Ocean Dynamics (DYN)
 % ================================================================
 \chapter{Ocean Dynamics (DYN)}
 \label{DYN}
 \minitoc
-% add a figure for  dynvor ens, ene latices
 %\vspace{2.cm}
 …
 %-------------------------------------------------------------------------------------------------------------
+The vector invariant form of the momentum equations is the one most
+often used in applications of the \NEMO ocean model. The flux form option
+(see next section) has been present since version $2$. Options are defined
+through the \ngn{namdyn\_adv} namelist variables
+Coriolis and momentum advection terms are evaluated using a leapfrog
+scheme, $i.e.$ the velocity appearing in these expressions is centred in
+time (\textit{now} velocity).
+The vector invariant form of the momentum equations (\np{ln\_dynhpg\_vec}~=~true) is the one most
+often used in applications of the \NEMO ocean model. The flux form option (\np{ln\_dynhpg\_vec}~=false)
+(see next section) has been present since version $2$.
+Options are defined through the \ngn{namdyn\_adv} namelist variables.
+Coriolis and momentum advection terms are evaluated using a leapfrog scheme,
+$i.e.$ the velocity appearing in these expressions is centred in time (\textit{now} velocity).
 At the lateral boundaries either free slip, no slip or partial slip boundary
 conditions are applied following Chap.\ref{LBC}.
 …
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+Note that a key point in \eqref{Eq_een_e3f} is that the averaging in the \textbf{i}- and
+\textbf{j}- directions uses the masked vertical scale factor but is always divided by
+$4$, not by the sum of the masks at the four $T$-points. This preserves the continuity of
+$e_{3f}$ when one or more of the neighbouring $e_{3t}$ tends to zero and
+extends by continuity the value of $e_{3f}$ into the land areas. This feature is essential for
+the $z$-coordinate with partial steps.
+A key point in \eqref{Eq_een_e3f} is how the averaging in the \textbf{i}- and \textbf{j}- directions is made.
+It uses the sum of masked t-point vertical scale factor divided either
+by the sum of the four t-point masks (\np{ln\_dynvor\_een\_old}~=~false),
+or  just by $4$ (\np{ln\_dynvor\_een\_old}~=~true).
+The latter case preserves the continuity of $e_{3f}$ when one or more of the neighbouring $e_{3t}$
+tends to zero and extends by continuity the value of $e_{3f}$ into the land areas.
+This case introduces a sub-grid-scale topography at f-points (with a systematic reduction of $e_{3f}$
+when a model level intercept the bathymetry) that tends to reinforce the topostrophy of the flow
+($i.e.$ the tendency of the flow to follow the isobaths) \citep{Penduff_al_OS07}.
 Next, the vorticity triads, $ {^i_j}\mathbb{Q}^{i_p}_{j_p}$ can be defined at a $T$-point as
 …
 \end{aligned}         \right.
 \end{equation}
+When \np{ln\_dynzad\_zts}~=~\textit{true}, a split-explicit time stepping with 5 sub-timesteps is used
+on the vertical advection term.
+This option can be useful when the value of the timestep is limited by vertical advection \citep{Lemarie_OM2015}.
+Note that in this case, a similar split-explicit time stepping should be used on
+vertical advection of tracer to ensure a better stability,
+an option which is only available with a TVD scheme (see \np{ln\_traadv\_tvd\_zts} in \S\ref{TRA_adv_tvd}).
 % ================================================================
 …
 those in the centred second order method. As the scheme already includes
 a diffusion component, it can be used without explicit  lateral diffusion on momentum
+($i.e.$ \np{ln\_dynldf\_lap}=\np{ln\_dynldf\_bilap}=false), and it is recommended to do so.
+($i.e.$ setting both \np{ln\_dynldf\_lap} and \np{ln\_dynldf\_bilap} to \textit{false}),
+and it is recommended to do so.
 The UBS scheme is not used in all directions. In the vertical, the centred $2^{nd}$
 …
 ($e_{3w}$).
-$\bullet$ Traditional coding with adaptation for ice shelf cavities (\np{ln\_dynhpg\_isf}=true).
-This scheme need the activation of ice shelf cavities (\np{ln\_isfcav}=true).
 $\bullet$ Pressure Jacobian scheme (prj) (a research paper in preparation) (\np{ln\_dynhpg\_prj}=true)
 …
 pressure Jacobian method is used to solve the horizontal pressure gradient. This method can provide
 a more accurate calculation of the horizontal pressure gradient than the standard scheme.
+\subsection{Ice shelf cavity}
+\label{DYN_hpg_isf}
+Beneath an ice shelf, the total pressure gradient is the sum of the pressure gradient due to the ice shelf load and
+ the pressure gradient due to the ocean load. If cavities are present (\np{ln\_isfcav}~=~true) these two terms can be
+ calculated by setting \np{ln\_dynhpg\_isf}~=~true. No other scheme is working with ice shelves.\\
+$\bullet$ The main hypothesis to compute the ice shelf load is that the ice shelf is in isostatic equilibrium.
+ The top pressure is computed integrating a reference density profile (prescribed as density of a water at 34.4
+PSU and -1.9$\degres C$) from the sea surface to the ice shelf base, which corresponds to the load of the water
+column in which the ice shelf is floatting. This top pressure is constant over time. A detailed description of
+this method is described in \citet{Losch2008}.\\
+$\bullet$ The ocean load is computed using the expression \eqref{Eq_dynhpg_sco} described in \ref{DYN_hpg_sco}.
+A treatment of the top and bottom partial cells similar to the one described in \ref{DYN_hpg_zps} is done
+to reduce the residual circulation generated by the top partial cell.
 %--------------------------------------------------------------------------------------------------------------
 …
 $\ $\newline      %force an empty line
-%%%
 Options are defined through the \ngn{namdyn\_spg} namelist variables.
+The surface pressure gradient term is related to the representation of the free surface (\S\ref{PE_hor_pg}). The main distinction is between the fixed volume case (linear free surface) and the variable volume case (nonlinear free surface, \key{vvl} is defined). In the linear free surface case (\S\ref{PE_free_surface}) the vertical scale factors $e_{3}$ are fixed in time, while they are time-dependent in the nonlinear case (\S\ref{PE_free_surface}). With both linear and nonlinear free surface, external gravity waves are allowed in the equations, which imposes a very small time step when an explicit time stepping is used. Two methods are proposed to allow a longer time step for the three-dimensional equations: the filtered free surface, which is a modification of the continuous equations (see \eqref{Eq_PE_flt}), and the split-explicit free surface described below. The extra term introduced in the filtered method is calculated implicitly, so that the update of the next velocities is done in module \mdl{dynspg\_flt} and not in \mdl{dynnxt}.
+%%%
+The surface pressure gradient term is related to the representation of the free surface (\S\ref{PE_hor_pg}).
+The main distinction is between the fixed volume case (linear free surface) and the variable volume case
+(nonlinear free surface, \key{vvl} is defined). In the linear free surface case (\S\ref{PE_free_surface})
+the vertical scale factors $e_{3}$ are fixed in time, while they are time-dependent in the nonlinear case
+(\S\ref{PE_free_surface}).
+With both linear and nonlinear free surface, external gravity waves are allowed in the equations,
+which imposes a very small time step when an explicit time stepping is used.
+Two methods are proposed to allow a longer time step for the three-dimensional equations:
+the filtered free surface, which is a modification of the continuous equations (see \eqref{Eq_PE_flt}),
+and the split-explicit free surface described below.
+The extra term introduced in the filtered method is calculated implicitly,
+so that the update of the next velocities is done in module \mdl{dynspg\_flt} and not in \mdl{dynnxt}.
 …
 implicitly, so that a solver is used to compute it. As a consequence the update of the $next$
 velocities is done in module \mdl{dynspg\_flt} and not in \mdl{dynnxt}.
 …
 $\rdt_e = \rdt / nn\_baro$. This parameter can be optionally defined automatically (\np{ln\_bt\_nn\_auto}=true)
 considering that the stability of the barotropic system is essentially controled by external waves propagation.
+Maximum allowed Courant number is in that case time independent, and easily computed online from the input bathymetry.
+Maximum Courant number is in that case time independent, and easily computed online from the input bathymetry.
+Therefore, $\rdt_e$ is adjusted so that the Maximum allowed Courant number is smaller than \np{rn\_bt\_cmax}.
 %%%
 …
 Schematic of the split-explicit time stepping scheme for the external
 and internal modes. Time increases to the right. In this particular exemple,
 a boxcar averaging window over $nn\_baro$ barotropic time steps is used ($nn\_bt\_filt=1$) and $nn\_baro=5$.
+a boxcar averaging window over $nn\_baro$ barotropic time steps is used ($nn\_bt\_flt=1$) and $nn\_baro=5$.
 Internal mode time steps (which are also the model time steps) are denoted
 by $t-\rdt$, $t$ and $t+\rdt$. Variables with $k$ superscript refer to instantaneous barotropic variables,
 …
 The former are used to obtain time filtered quantities at $t+\rdt$ while the latter are used to obtain time averaged
 transports to advect tracers.
 a) Forward time integration: \np{ln\_bt\_fw}=true, \np{ln\_bt\_ave}=true.
 b) Centred time integration: \np{ln\_bt\_fw}=false, \np{ln\_bt\_ave}=true.
 c) Forward time integration with no time filtering (POM-like scheme): \np{ln\_bt\_fw}=true, \np{ln\_bt\_ave}=false. }
+a) Forward time integration: \np{ln\_bt\_fw}=true, \np{ln\_bt\_av}=true.
+b) Centred time integration: \np{ln\_bt\_fw}=false, \np{ln\_bt\_av}=true.
+c) Forward time integration with no time filtering (POM-like scheme): \np{ln\_bt\_fw}=true, \np{ln\_bt\_av}=false. }
 \end{center}    \end{figure}
 %>   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >   >
 …
 In the default case (\np{ln\_bt\_fw}=true), the external mode is integrated
 between \textit{now} and  \textit{after} baroclinic time-steps (Fig.~\ref{Fig_DYN_dynspg_ts}a). To avoid aliasing of fast barotropic motions into three dimensional equations, time filtering is eventually applied on barotropic
 quantities (\np{ln\_bt\_ave}=true). In that case, the integration is extended slightly beyond  \textit{after} time step to provide time filtered quantities.
+quantities (\np{ln\_bt\_av}=true). In that case, the integration is extended slightly beyond  \textit{after} time step to provide time filtered quantities.
 These are used for the subsequent initialization of the barotropic mode in the following baroclinic step.
 Since external mode equations written at baroclinic time steps finally follow a forward time stepping scheme,
 …
 %%%
 One can eventually choose to feedback instantaneous values by not using any time filter (\np{ln\_bt\_ave}=false).
+One can eventually choose to feedback instantaneous values by not using any time filter (\np{ln\_bt\_av}=false).
 In that case, external mode equations are continuous in time, ie they are not re-initialized when starting a new
 sub-stepping sequence. This is the method used so far in the POM model, the stability being maintained by refreshing at (almost)
 …
 Besides the surface and bottom stresses (see the above section) which are
+introduced as boundary conditions on the vertical mixing, two other forcings
+enter the dynamical equations.
+One is the effect of atmospheric pressure on the ocean dynamics.
+Another forcing term is the tidal potential.
+Both of which will be introduced into the reference version soon.
+\gmcomment{atmospheric pressure is there!!!!    include its description }
+introduced as boundary conditions on the vertical mixing, three other forcings
+may enter the dynamical equations by affecting the surface pressure gradient.
+(1) When \np{ln\_apr\_dyn}~=~true (see \S\ref{SBC_apr}), the atmospheric pressure is taken
+into account when computing the surface pressure gradient.
+(2) When \np{ln\_tide\_pot}~=~true and \key{tide} is defined (see \S\ref{SBC_tide}),
+the tidal potential is taken into account when computing the surface pressure gradient.
+(3) When \np{nn\_ice\_embd}~=~2 and LIM or CICE is used ($i.e.$ when the sea-ice is embedded in the ocean),
+the snow-ice mass is taken into account when computing the surface pressure gradient.
+\gmcomment{ missing : the lateral boundary condition !!!   another external forcing
+ }
 % ================================================================

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Chapters/Chap_LBC.tex

-                      r4147
+                      r6436
 % ================================================================
 % Chapter � Lateral Boundary Condition (LBC)
+% Chapter — Lateral Boundary Condition (LBC)
 % ================================================================
 \chapter{Lateral Boundary Condition (LBC) }
 …
 %        North fold (\textit{jperio = 3 }to $6)$
 % -------------------------------------------------------------------------------------------------------------
 \subsection{North-fold (\textit{jperio = 3 }to $6)$ }
+\subsection{North-fold (\textit{jperio = 3 }to $6$) }
 \label{LBC_north_fold}
 The north fold boundary condition has been introduced in order to handle the north
+boundary of a three-polar ORCA grid. Such a grid has two poles in the northern hemisphere.
+\colorbox{yellow}{to be completed...}
+boundary of a three-polar ORCA grid. Such a grid has two poles in the northern hemisphere
+(Fig.\ref{Fig_MISC_ORCA_msh}, and thus requires a specific treatment illustrated in Fig.\ref{Fig_North_Fold_T}.
+Further information can be found in \mdl{lbcnfd} module which applies the north fold boundary condition.
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 …
 ocean model. Second order finite difference schemes lead to local discrete
 operators that depend at the very most on one neighbouring point. The only
 non-local computations concern the vertical physics (implicit diffusion, 1.5
+non-local computations concern the vertical physics (implicit diffusion,
 turbulent closure scheme, ...) (delocalization over the whole water column),
 and the solving of the elliptic equation associated with the surface pressure
 gradient computation (delocalization over the whole horizontal domain).
 Therefore, a pencil strategy is used for the data sub-structuration
-\gmcomment{no idea what this means!}
 : the 3D initial domain is laid out on local processor
 memories following a 2D horizontal topological splitting. Each sub-domain
 …
 phase starts: each processor sends to its neighbouring processors the update
 values of the points corresponding to the interior overlapping area to its
+neighbouring sub-domain (i.e. the innermost of the two overlapping rows).
+The communication is done through message passing. Usually the parallel virtual
+language, PVM, is used as it is a standard language available on  nearly  all
+MPP computers. More specific languages (i.e. computer dependant languages)
+can be easily used to speed up the communication, such as SHEM on a T3E
+computer. The data exchanges between processors are required at the very
+neighbouring sub-domain ($i.e.$ the innermost of the two overlapping rows).
+The communication is done through the Message Passing Interface (MPI).
+The data exchanges between processors are required at the very
 place where lateral domain boundary conditions are set in the mono-domain
+computation (\S III.10-c): the lbc\_lnk routine which manages such conditions
+is substituted by mpplnk.F or mpplnk2.F routine when running on an MPP
+computer (\key{mpp\_mpi} defined). It has to be pointed out that when using
+the MPP version of the model, the east-west cyclic boundary condition is done
+implicitly, whilst the south-symmetric boundary condition option is not available.
+computation : the \rou{lbc\_lnk} routine (found in \mdl{lbclnk} module)
+which manages such conditions is interfaced with routines found in \mdl{lib\_mpp} module
+when running on an MPP computer ($i.e.$ when \key{mpp\_mpi} defined).
+It has to be pointed out that when using the MPP version of the model,
+the east-west cyclic boundary condition is done implicitly,
+whilst the south-symmetric boundary condition option is not available.
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 …
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+In the standard version of the OPA model, the splitting is regular and arithmetic.
+ the i-axis is divided by \jp{jpni} and the j-axis by \jp{jpnj} for a number of processors
+ \jp{jpnij} most often equal to $jpni \times jpnj$ (model parameters set in
+ \mdl{par\_oce}). Each processor is independent and without message passing
+ or synchronous process
+ \gmcomment{how does a synchronous process relate to this?},
+ programs run alone and access just its own local memory. For this reason, the
+ main model dimensions are now the local dimensions of the subdomain (pencil)
+In the standard version of \NEMO, the splitting is regular and arithmetic.
+The i-axis is divided by \jp{jpni} and the j-axis by \jp{jpnj} for a number of processors
+\jp{jpnij} most often equal to $jpni \times jpnj$ (parameters set in
+ \ngn{nammpp} namelist). Each processor is independent and without message passing
+ or synchronous process, programs run alone and access just its own local memory.
+ For this reason, the main model dimensions are now the local dimensions of the subdomain (pencil)
  that are named \jp{jpi}, \jp{jpj}, \jp{jpk}. These dimensions include the internal
  domain and the overlapping rows. The number of rows to exchange (known as
 …
 where \jp{jpni}, \jp{jpnj} are the number of processors following the i- and j-axis.
+\colorbox{yellow}{Figure IV.3: example of a domain splitting with 9 processors and
+no east-west cyclic boundary conditions.}
+One also defines variables nldi and nlei which correspond to the internal
+domain bounds, and the variables nimpp and njmpp which are the position
+of the (1,1) grid-point in the global domain. An element of $T_{l}$, a local array
+(subdomain) corresponds to an element of $T_{g}$, a global array
+(whole domain) by the relationship:
+One also defines variables nldi and nlei which correspond to the internal domain bounds,
+and the variables nimpp and njmpp which are the position of the (1,1) grid-point in the global domain.
+An element of $T_{l}$, a local array (subdomain) corresponds to an element of $T_{g}$,
+a global array (whole domain) by the relationship:
 \begin{equation} \label{Eq_lbc_nimpp}
 T_{g} (i+nimpp-1,j+njmpp-1,k) = T_{l} (i,j,k),
 …
 nproc. In the standard version, a processor has no more than four neighbouring
 processors named nono (for north), noea (east), noso (south) and nowe (west)
+and two variables, nbondi and nbondj, indicate the relative position of the processor
+\colorbox{yellow}{(see Fig.IV.3)}:
+and two variables, nbondi and nbondj, indicate the relative position of the processor :
 \begin{itemize}
 \item       nbondi = -1    an east neighbour, no west processor,
 …
 processor on its overlapping row, and sends the data issued from internal
 domain corresponding to the overlapping row of the other processor.
-\colorbox{yellow}{Figure IV.4: pencil splitting with the additional outer halos }
 …
 global ocean where more than 50 \% of points are land points. For this reason, a
 pre-processing tool can be used to choose the mpp domain decomposition with a
 maximum number of only land points processors, which can then be eliminated.
 (For example, the mpp\_optimiz tools, available from the DRAKKAR web site.)
+maximum number of only land points processors, which can then be eliminated (Fig. \ref{Fig_mppini2})
+(For example, the mpp\_optimiz tools, available from the DRAKKAR web site).
 This optimisation is dependent on the specific bathymetry employed. The user
 then chooses optimal parameters \jp{jpni}, \jp{jpnj} and \jp{jpnij} with
 $jpnij < jpni \times jpnj$, leading to the elimination of $jpni \times jpnj - jpnij$
 land processors. When those parameters are specified in module \mdl{par\_oce},
+land processors. When those parameters are specified in \ngn{nammpp} namelist,
 the algorithm in the \rou{inimpp2} routine sets each processor's parameters (nbound,
 nono, noea,...) so that the land-only processors are not taken into account.
 \colorbox{yellow}{Note that the inimpp2 routine is general so that the original inimpp
+\gmcomment{Note that the inimpp2 routine is general so that the original inimpp
 routine should be suppressed from the code.}
 When land processors are eliminated, the value corresponding to these locations in
+the model output files is zero. Note that this is a problem for a mesh output file written
+by such a model configuration, because model users often divide by the scale factors
+($e1t$, $e2t$, etc) and do not expect the grid size to be zero, even on land. It may be
+best not to eliminate land processors when running the model especially to write the
+mesh files as outputs (when \np{nn\_msh} namelist parameter differs from 0).
+%%
+\gmcomment{Steven : dont understand this, no land processor means no output file
+covering this part of globe; its only when files are stitched together into one that you
+can leave a hole}
+%%
+the model output files is undefined. Note that this is a problem for the meshmask file
+which requires to be defined over the whole domain. Therefore, user should not eliminate
+land processors when creating a meshmask file ($i.e.$ when setting a non-zero value to \np{nn\_msh}).
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 …
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-% ================================================================
-% Open Boundary Conditions
-% ================================================================
-\section{Open Boundary Conditions (\key{obc}) (OBC)}
-\label{LBC_obc}
-%-----------------------------------------nam_obc  -------------------------------------------
-%-    nobc_dta    =    0     !  = 0 the obc data are equal to the initial state
-%-                           !  = 1 the obc data are read in 'obc   .dta' files
-%-    rn_dpein      =    1.    !  ???
-%-    rn_dpwin      =    1.    !  ???
-%-    rn_dpnin      =   30.    !  ???
-%-    rn_dpsin      =    1.    !  ???
-%-    rn_dpeob      = 1500.    !  time relaxation (days) for the east  open boundary
-%-    rn_dpwob      =   15.    !    "        "           for the west  open boundary
-%-    rn_dpnob      =  150.    !    "        "           for the north open boundary
-%-    rn_dpsob      =   15.    !    "        "           for the south open boundary
-%-    ln_obc_clim = .true.   !  climatological obc data files (default T)
-%-    ln_vol_cst  = .true.   !  total volume conserved
-\namdisplay{namobc}
-It is often necessary to implement a model configuration limited to an oceanic
-region or a basin, which communicates with the rest of the global ocean through
-''open boundaries''. As stated by \citet{Roed1986}, an open boundary is a
-computational border where the aim of the calculations is to allow the perturbations
-generated inside the computational domain to leave it without deterioration of the
-inner model solution. However, an open boundary also has to let information from
-the outer ocean enter the model and should support inflow and outflow conditions.
-The open boundary package OBC is the first open boundary option developed in
-NEMO (originally in OPA8.2). It allows the user to
-\begin{itemize}
-\item tell the model that a boundary is ''open'' and not closed by a wall, for example
-by modifying the calculation of the divergence of velocity there;
-\item impose values of tracers and velocities at that boundary (values which may
-be taken from a climatology): this is the``fixed OBC'' option.
-\item calculate boundary values by a sophisticated algorithm combining radiation
-and relaxation (``radiative OBC'' option)
-\end{itemize}
-Options are defined through the \ngn{namobc} namelist variables.
-The package resides in the OBC directory. It is described here in four parts: the
-boundary geometry (parameters to be set in \mdl{obc\_par}), the forcing data at
-the boundaries (module \mdl{obcdta}),  the radiation algorithm involving the
-namelist and module \mdl{obcrad}, and a brief presentation of boundary update
-and restart files.
-%----------------------------------------------
-\subsection{Boundary geometry}
-\label{OBC_geom}
+%
-First one has to realize that open boundaries may not necessarily be located
-at the extremities of the computational domain. They may exist in the middle
-of the domain, for example at Gibraltar Straits if one wants to avoid including
-the Mediterranean in an Atlantic domain. This flexibility has been found necessary
-for the CLIPPER project \citep{Treguier_al_JGR01}. Because of the complexity of the
-geometry of ocean basins, it may even be necessary to have more than one
-''west'' open boundary, more than one ''north'', etc. This is not possible with
-the OBC option: only one open boundary of each kind, west, east, south and
-north is allowed; these names refer to the grid geometry (not to the direction
-of the geographical ''west'', ''east'', etc).
-The open boundary geometry is set by a series of parameters in the module
-\mdl{obc\_par}. For an eastern open boundary, parameters are \jp{lp\_obc\_east}
-(true if an east open boundary exists), \jp{jpieob} the $i$-index along which
-the eastern open boundary (eob) is located, \jp{jpjed} the $j$-index at which
-it starts, and \jp{jpjef} the $j$-index where it ends (note $d$ is for ''d\'{e}but''
-and $f$ for ''fin'' in French). Similar parameters exist for the west, south and
-north cases (Table~\ref{Tab_obc_param}).
-%--------------------------------------------------TABLE--------------------------------------------------
-\begin{table}[htbp]     \begin{center}    \begin{tabular}{|l|c|c|c|}
-\hline
-Boundary and  & Constant index  & Starting index (d\'{e}but) & Ending index (fin) \\
-Logical flag  &                 &                            &                     \\
-\hline
-West          & \jp{jpiwob} $>= 2$         &  \jp{jpjwd}$>= 2$          &  \jp{jpjwf}<= \np{jpjglo}-1 \\
-lp\_obc\_west & $i$-index of a $u$ point   & $j$ of a $T$ point   &$j$ of a $T$ point \\
-\hline
-East            & \jp{jpieob}$<=$\np{jpiglo}-2&\jp{jpjed} $>= 2$         & \jp{jpjef}$<=$ \np{jpjglo}-1 \\
- lp\_obc\_east  & $i$-index of a $u$ point    & $j$ of a $T$ point & $j$ of a $T$ point \\
-\hline
-South           & \jp{jpjsob} $>= 2$         & \jp{jpisd} $>= 2$          & \jp{jpisf}$<=$\np{jpiglo}-1 \\
-lp\_obc\_south  & $j$-index of a $v$ point   & $i$ of a $T$ point   & $i$ of a $T$ point \\
-\hline
-North           & \jp{jpjnob} $<=$ \np{jpjglo}-2& \jp{jpind} $>= 2$        & \jp{jpinf}$<=$\np{jpiglo}-1 \\
-lp\_obc\_north  & $j$-index of a $v$ point      & $i$  of a $T$ point & $i$ of a $T$ point \\
-\hline
-\end{tabular}    \end{center}
-\caption{     \label{Tab_obc_param}
-Names of different indices relating to the open boundaries. In the case
-of a completely open ocean domain with four ocean boundaries, the parameters
-take exactly the values indicated.}
-\end{table}
-%------------------------------------------------------------------------------------------------------------
-The open boundaries must be along coordinate lines. On the C-grid, the boundary
-itself is along a line of normal velocity points: $v$ points for a zonal open boundary
-(the south or north one), and $u$ points for a meridional open boundary (the west
-or east one). Another constraint is that there still must be a row of masked points
-all around the domain, as if the domain were a closed basin (unless periodic conditions
-are used together with open boundary conditions). Therefore, an open boundary
-cannot be located at the first/last index, namely, 1, \jp{jpiglo} or \jp{jpjglo}. Also,
-the open boundary algorithm involves calculating the normal velocity points situated
-just on the boundary, as well as the tangential velocity and temperature and salinity
-just outside the boundary. This means that for a west/south boundary, normal
-velocities and temperature are calculated at the same index \jp{jpiwob} and
-\jp{jpjsob}, respectively. For an east/north boundary, the normal velocity is
-calculated at index \jp{jpieob} and \jp{jpjnob}, but the ``outside'' temperature is
-at index \jp{jpieob}+1 and \jp{jpjnob}+1. This means that \jp{jpieob}, \jp{jpjnob}
-cannot be bigger than \jp{jpiglo}-2, \jp{jpjglo}-2.
-The starting and ending indices are to be thought of as $T$ point indices: in many
-cases they indicate the first land $T$-point, at the extremity of an open boundary
-(the coast line follows the $f$ grid points, see Fig.~\ref{Fig_obc_north} for an example
-of a northern open boundary). All indices are relative to the global domain. In the
-free surface case it is possible to have ``ocean corners'', that is, an open boundary
-starting and ending in the ocean.
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-\begin{figure}[!t]     \begin{center}
-\includegraphics[width=0.70\textwidth]{./TexFiles/Figures/Fig_obc_north.pdf}
-\caption{    \label{Fig_obc_north}
-Localization of the North open boundary points.}
-\end{center}     \end{figure}
-%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
-Although not compulsory, it is highly recommended that the bathymetry in the
-vicinity of an open boundary follows the following rule: in the direction perpendicular
-to the open line, the water depth should be constant for 4 grid points. This is in
-order to ensure that the radiation condition, which involves model variables next
-to the boundary, is calculated in a consistent way. On Fig.\ref{Fig_obc_north} we
-indicate by an $=$ symbol, the points which should have the same depth. It means
-that at the 4 points near the boundary, the bathymetry is cylindrical \gmcomment{not sure
-why cylindrical}. The line behind the open $T$-line must be 0 in the bathymetry file
-(as shown on Fig.\ref{Fig_obc_north} for example).
-%----------------------------------------------
-\subsection{Boundary data}
-\label{OBC_data}
-It is necessary to provide information at the boundaries. The simplest case is
-when this information does not change in time and is equal to the initial conditions
-(namelist variable \np{nn\_obcdta}=0). This is the case for the standard configuration
-EEL5 with open boundaries. When (\np{nn\_obcdta}=1), open boundary information
-is read from netcdf files. For convenience the input files are supposed to be similar
-to the ''history'' NEMO output files, for dimension names and variable names.
-Open boundary arrays must be dimensioned according to the parameters of table~
-\ref{Tab_obc_param}: for example, at the western boundary, arrays have a
-dimension of \jp{jpwf}-\jp{jpwd}+1 in the horizontal and \jp{jpk} in the vertical.
-When ocean observations are used to generate the boundary data (a hydrographic
-section for example, as in \citet{Treguier_al_JGR01}) it happens often that only the velocity
-normal to the boundary is known, which is the reason why the initial OBC code
-assumes that only $T$, $S$, and the normal velocity ($u$ or $v$) needs to be
-specified. As more and more global model solutions and ocean analysis products
-become available, it will be possible to provide information about all the variables
-(including the tangential velocity) so that the specification of four variables at each
-boundaries will become standard. For the sea surface height, one must distinguish
-between the filtered free surface case and the time-splitting or explicit treatment of
-the free surface.
- In the first case, it is assumed that the user does not wish to represent high
- frequency motions such as tides. The boundary condition is thus one of zero
- normal gradient of sea surface height at the open boundaries, following \citet{Marchesiello2001}.
-No information other than the total velocity needs to be provided at the open
-boundaries in that case. In the other two cases (time splitting or explicit free surface),
-the user must provide barotropic information (sea surface height and barotropic
-velocities) and the use of the Flather algorithm for barotropic variables is
-recommanded. However, this algorithm has not yet been fully tested and bugs
-remain in NEMO v2.3. Users should read the code carefully before using it. Finally,
-in the case of the rigid lid approximation the barotropic streamfunction must be
-provided, as documented in \citet{Treguier_al_JGR01}). This option is no longer
-recommended but remains in NEMO V2.3.
-One frequently encountered case is when an open boundary domain is constructed
-from a global or larger scale NEMO configuration. Assuming the domain corresponds
-to indices $ib:ie$, $jb:je$ of the global domain, the bathymetry and forcing of the
-small domain can be created by using the following netcdf utility on the global files:
-ncks -F $-d\;x,ib,ie$ $-d\;y,jb,je$ (part of the nco series of utilities,
-see their \href{http://nco.sourceforge.net}{website}).
-The open boundary files can be constructed using ncks
-commands, following table~\ref{Tab_obc_ind}.
-%--------------------------------------------------TABLE--------------------------------------------------
-\begin{table}[htbp]     \begin{center}      \begin{tabular}{|l|c|c|c|c|c|}
-\hline
-OBC  & Variable   & file name      & Index  & Start  & end  \\
-West &  T,S       &   obcwest\_TS.nc &  $ib$+1     &   $jb$+1 &  $je-1$  \\
-     &    U       &   obcwest\_U.nc  &  $ib$+1     &   $jb$+1 &  $je-1$  \\
-     &    V       &   obcwest\_V.nc  &  $ib$+1     &   $jb$+1 &  $je-1$  \\
-\hline
-East &  T,S       &   obceast\_TS.nc &  $ie$-1     &   $jb$+1 &  $je-1$  \\
-     &    U       &   obceast\_U.nc  &  $ie$-2     &   $jb$+1 &  $je-1$  \\
-     &    V       &   obceast\_V.nc  &  $ie$-1     &   $jb$+1 &  $je-1$  \\
-\hline
-South &  T,S      &   obcsouth\_TS.nc &  $jb$+1     &  $ib$+1 &  $ie-1$  \\
-      &    U      &   obcsouth\_U.nc  &  $jb$+1     &  $ib$+1 &  $ie-1$  \\
-      &    V      &   obcsouth\_V.nc  &  $jb$+1     &  $ib$+1 &  $ie-1$  \\
-\hline
-North &  T,S      &   obcnorth\_TS.nc &  $je$-1     &  $ib$+1 &  $ie-1$  \\
-      &    U      &   obcnorth\_U.nc  &  $je$-1     &  $ib$+1 &  $ie-1$  \\
-      &    V      &   obcnorth\_V.nc  &  $je$-2     &  $ib$+1 &  $ie-1$  \\
-\hline
-\end{tabular}     \end{center}
-\caption{    \label{Tab_obc_ind}
-Requirements for creating open boundary files from a global configuration,
-appropriate for the subdomain of indices $ib:ie$, $jb:je$. ``Index'' designates the
-$i$ or $j$ index along which the $u$ of $v$ boundary point is situated in the global
-configuration, starting and ending with the $j$ or $i$ indices indicated.
-For example, to generate file obcnorth\_V.nc, use the command ncks
-$-F$ $-d\;y,je-2$  $-d\;x,ib+1,ie-1$ }
-\end{table}
-%-----------------------------------------------------------------------------------------------------------
-It is assumed that the open boundary files contain the variables for the period of
-the model integration. If the boundary files contain one time frame, the boundary
-data is held fixed in time. If the files contain 12 values, it is assumed that the input
-is a climatology for a repeated annual cycle (corresponding to the case \np{ln\_obc\_clim}
-=true). The case of an arbitrary number of time frames is not yet implemented
-correctly; the user is required to write his own code in the module \mdl{obc\_dta}
-to deal with this situation.
-\subsection{Radiation algorithm}
-\label{OBC_rad}
-The art of open boundary management consists in applying a constraint strong
-enough that the inner domain "feels" the rest of the ocean, but weak enough
-that perturbations are allowed to leave the domain with minimum false reflections
-of energy. The constraints are specified separately at each boundary as time
-scales for ''inflow'' and ''outflow'' as defined below. The time scales are set (in days)
-by namelist parameters such as \np{rn\_dpein}, \np{rn\_dpeob} for the eastern open
-boundary for example. When both time scales are zero for a given boundary
-($e.g.$ for the western boundary, \jp{lp\_obc\_west}=true, \np{rn\_dpwob}=0 and
-\np{rn\_dpwin}=0) this means that the boundary in question is a ''fixed '' boundary
-where the solution is set exactly by the boundary data. This is not recommended,
-except in combination with increased viscosity in a ''sponge'' layer next to the
-boundary in order to avoid spurious reflections.
-The radiation\/relaxation \gmcomment{the / doesnt seem to appear in the output}
-algorithm is applied when either relaxation time (for ''inflow'' or ''outflow'') is
-non-zero. It has been developed and tested in the SPEM model and its
-successor ROMS \citep{Barnier1996, Marchesiello2001}, which is an
-$s$-coordinate model on an Arakawa C-grid. Although the algorithm has
-been numerically successful in the CLIPPER Atlantic models, the physics
-do not work as expected \citep{Treguier_al_JGR01}. Users are invited to consider
-open boundary conditions (OBC hereafter) with some scepticism
-\citep{Durran2001, Blayo2005}.
-The first part of the algorithm calculates a phase velocity to determine
-whether perturbations tend to propagate toward, or away from, the
-boundary. Let us consider a model variable $\phi$.
-The phase velocities ($C_{\phi x}$,$C_{\phi y}$) for the variable $\phi$,
-in the directions normal and tangential to the boundary are
-\begin{equation} \label{Eq_obc_cphi}
-C_{\phi x} = \frac{ -\phi_{t} }{ ( \phi_{x}^{2} + \phi_{y}^{2}) } \phi_{x}
-\;\;\;\;\; \;\;\;
-C_{\phi y} = \frac{ -\phi_{t} }{ ( \phi_{x}^{2} + \phi_{y}^{2}) } \phi_{y}.
-\end{equation}
-Following \citet{Treguier_al_JGR01} and \citet{Marchesiello2001} we retain only
-the normal component of the velocity, $C_{\phi x}$, setting $C_{\phi y} =0$
-(but unlike the original Orlanski radiation algorithm we retain $\phi_{y}$ in
-the expression for $C_{\phi x}$).
-The discrete form of (\ref{Eq_obc_cphi}), described by \citet{Barnier1998},
-takes into account the two rows of grid points situated inside the domain
-next to the boundary, and the three previous time steps ($n$, $n-1$,
-and $n-2$). The same equation can then be discretized at the boundary at
-time steps $n-1$, $n$ and $n+1$ \gmcomment{since the original was three time-level}
-in order to extrapolate for the new boundary value $\phi^{n+1}$.
-In the open boundary algorithm as implemented in NEMO v2.3, the new boundary
-values are updated differently depending on the sign of $C_{\phi x}$. Let us take
-an eastern boundary as an example. The solution for variable $\phi$ at the
-boundary is given by a generalized wave equation with phase velocity $C_{\phi}$,
-with the addition of a relaxation term, as:
-\begin{eqnarray}
-\phi_{t} &  =  & -C_{\phi x} \phi_{x} + \frac{1}{\tau_{o}} (\phi_{c}-\phi)
-                        \;\;\; \;\;\; \;\;\; (C_{\phi x} > 0), \label{Eq_obc_rado} \\
-\phi_{t} &  =  & \frac{1}{\tau_{i}} (\phi_{c}-\phi)
-\;\;\; \;\;\; \;\;\;\;\;\; (C_{\phi x} < 0), \label{Eq_obc_radi}
-\end{eqnarray}
-where $\phi_{c}$ is the estimate of $\phi$ at the boundary, provided as boundary
-data. Note that in (\ref{Eq_obc_rado}), $C_{\phi x}$ is bounded by the ratio
-$\delta x/\delta t$ for stability reasons. When $C_{\phi x}$ is eastward (outward
-propagation), the radiation condition (\ref{Eq_obc_rado}) is used.
-When  $C_{\phi x}$ is westward (inward propagation), (\ref{Eq_obc_radi}) is
-used with a strong relaxation to climatology (usually $\tau_{i}=\np{rn\_dpein}=$1~day).
-Equation (\ref{Eq_obc_radi}) is solved with a Euler time-stepping scheme. As a
-consequence, setting $\tau_{i}$ smaller than, or equal to the time step is equivalent
-to a fixed boundary condition. A time scale of one day is usually a good compromise
-which guarantees that the inflow conditions remain close to climatology while ensuring
-numerical stability.
-In  the case of a western boundary located in the Eastern Atlantic, \citet{Penduff_al_JGR00}
-have been able to implement the radiation algorithm without any boundary data,
-using persistence from the previous time step instead. This solution has not worked
-in other cases \citep{Treguier_al_JGR01}, so that the use of boundary data is recommended.
-Even in the outflow condition (\ref{Eq_obc_rado}), we have found it desirable to
-maintain a weak relaxation to climatology. The time step is usually chosen so as to
-be larger than typical turbulent scales (of order 1000~days \gmcomment{or maybe seconds?}).
-The radiation condition is applied to the model variables: temperature, salinity,
-tangential and normal velocities. For normal and tangential velocities, $u$ and $v$,
-radiation is applied with phase velocities calculated from $u$ and $v$ respectively.
-For the radiation of tracers, we use the phase velocity calculated from the tangential
-velocity in order to avoid calculating too many independent radiation velocities and
-because tangential velocities and tracers have the same position along the boundary
-on a C-grid.
-\subsection{Domain decomposition (\key{mpp\_mpi})}
-\label{OBC_mpp}
-When \key{mpp\_mpi} is active in the code, the computational domain is divided
-into rectangles that are attributed each to a different processor. The open boundary
-code is ``mpp-compatible'' up to a certain point. The radiation algorithm will not
-work if there is an mpp subdomain boundary parallel to the open boundary at the
-index of the boundary, or the grid point after (outside), or three grid points before
-(inside). On the other hand, there is no problem if an mpp subdomain boundary
-cuts the open boundary perpendicularly. These geometrical limitations must be
-checked for by the user (there is no safeguard in the code).
-The general principle for the open boundary mpp code is that loops over the open
-boundaries {not sure what this means} are performed on local indices (nie0,
-nie1, nje0, nje1 for an eastern boundary for instance) that are initialized in module
-\mdl{obc\_ini}. Those indices have relevant values on the processors that contain
-a segment of an open boundary. For processors that do not include an open
-boundary segment, the indices are such that the calculations within the loops are
-not performed.
-\gmcomment{I dont understand most of the last few sentences}
-Arrays of climatological data that are read from files are seen by all processors
-and have the same dimensions for all (for instance, for the eastern boundary,
-uedta(jpjglo,jpk,2)). On the other hand, the arrays for the calculation of radiation
-are local to each processor (uebnd(jpj,jpk,3,3) for instance).  This allowed the
-CLIPPER model for example, to save on memory where the eastern boundary
-crossed 8 processors so that \jp{jpj} was much smaller than (\jp{jpjef}-\jp{jpjed}+1).
-\subsection{Volume conservation}
-\label{OBC_vol}
-It is necessary to control the volume inside a domain when using open boundaries.
-With fixed boundaries, it is enough to ensure that the total inflow/outflow has
-reasonable values (either zero or a value compatible with an observed volume
-balance). When using radiative boundary conditions it is necessary to have a
-volume constraint because each open boundary works independently from the
-others. The methodology used to control this volume is identical to the one
-coded in the ROMS model \citep{Marchesiello2001}.
-%---------------------------------------- EXTRAS
-\colorbox{yellow}{Explain obc\_vol{\ldots}}
-\colorbox{yellow}{OBC algorithm for update, OBC restart, list of routines where obc key appears{\ldots}}
-\colorbox{yellow}{OBC rigid lid? {\ldots}}
 % ====================================================================

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Chapters/Chap_LDF.tex

-                      r4147
+                      r6436
 % ================================================================
 % Chapter � Lateral Ocean Physics (LDF)
+% Chapter ———  Lateral Ocean Physics (LDF)
 % ================================================================
 \chapter{Lateral Ocean Physics (LDF)}
 …
 When none of the \textbf{key\_dynldf\_...} and \textbf{key\_traldf\_...} keys are
 defined, a constant value is used over the whole ocean for momentum and
 tracers, which is specified through the \np{rn\_ahm0} and \np{rn\_aht0} namelist
+tracers, which is specified through the \np{rn\_ahm\_0\_lap} and \np{rn\_aht\_0} namelist
 parameters.
 …
 mixing coefficients will require 3D arrays. In the 1D option, a hyperbolic variation
 of the lateral mixing coefficient is introduced in which the surface value is
 \np{rn\_aht0} (\np{rn\_ahm0}), the bottom value is 1/4 of the surface value,
+\np{rn\_aht\_0} (\np{rn\_ahm\_0\_lap}), the bottom value is 1/4 of the surface value,
 and the transition takes place around z=300~m with a width of 300~m
 ($i.e.$ both the depth and the width of the inflection point are set to 300~m).
 …
 \end{equation}
 where $e_{max}$ is the maximum of $e_1$ and $e_2$ taken over the whole masked
 ocean domain, and $A_o^l$ is the \np{rn\_ahm0} (momentum) or \np{rn\_aht0} (tracer)
+ocean domain, and $A_o^l$ is the \np{rn\_ahm\_0\_lap} (momentum) or \np{rn\_aht\_0} (tracer)
 namelist parameter. This variation is intended to reflect the lesser need for subgrid
 scale eddy mixing where the grid size is smaller in the domain. It was introduced in
 …
 Other formulations can be introduced by the user for a given configuration.
 For example, in the ORCA2 global ocean model (see Configurations), the laplacian
 viscosity operator uses \np{rn\_ahm0}~= 4.10$^4$ m$^2$/s poleward of 20$^{\circ}$
 north and south and decreases linearly to \np{rn\_aht0}~= 2.10$^3$ m$^2$/s
+viscosity operator uses \np{rn\_ahm\_0\_lap}~= 4.10$^4$ m$^2$/s poleward of 20$^{\circ}$
+north and south and decreases linearly to \np{rn\_aht\_0}~= 2.10$^3$ m$^2$/s
 at the equator \citep{Madec_al_JPO96, Delecluse_Madec_Bk00}. This modification
 can be found in routine \rou{ldf\_dyn\_c2d\_orca} defined in \mdl{ldfdyn\_c2d}.
 …
 \subsubsection{Space and Time Varying Mixing Coefficients}
+There is no default specification of space and time varying mixing coefficient.
+The only case available is specific to the ORCA2 and ORCA05 global ocean
+configurations. It provides only a tracer
+mixing coefficient for eddy induced velocity (ORCA2) or both iso-neutral and
+eddy induced velocity (ORCA05) that depends on the local growth rate of
+baroclinic instability. This specification is actually used when an ORCA key
+There are no default specifications of space and time varying mixing coefficient.  One
+available case is specific to the ORCA2 and ORCA05 global ocean configurations. It
+provides only a tracer mixing coefficient for eddy induced velocity (ORCA2) or both
+iso-neutral and eddy induced velocity (ORCA05) that depends on the local growth rate of
+baroclinic instability. This specification is actually used when an ORCA key
 and both \key{traldf\_eiv} and \key{traldf\_c2d} are defined.
+\subsubsection{Smagorinsky viscosity (\key{dynldf\_c3d} and \key{dynldf\_smag})}
+The \key{dynldf\_smag} key activates a 3D, time-varying viscosity that depends on the
+resolved motions. Following \citep{Smagorinsky_93} the viscosity coefficient is set
+proportional to a local deformation rate based on the horizontal shear and tension,
+namely:
+\begin{equation}
+A_{m_{Smag}} = \left(\frac{{\sf CM_{Smag}}}{\pi}\right)^2L^2\vert{D}\vert
+\end{equation}
+\noindent where the deformation rate $\vert{D}\vert$ is given by
+\begin{equation}
+\vert{D}\vert=\sqrt{\left({\frac{\partial{u}} {\partial{x}}}
+                         -{\frac{\partial{v}} {\partial{y}}}\right)^2
+                 +  \left({\frac{\partial{u}} {\partial{y}}}
+                         +{\frac{\partial{v}} {\partial{x}}}\right)^2}
+\end{equation}
+\noindent and $L$ is the local gridscale given by:
+\begin{equation}
+L^2 = \frac{2{e_1}^2 {e_2}^2}{\left ( {e_1}^2 + {e_2}^2 \right )}
+\end{equation}
+\citep{Griffies_Hallberg_MWR00} suggest values in the range 2.2 to 4.0 of the coefficient
+$\sf CM_{Smag}$ for oceanic flows. This value is set via the \np{rn\_cmsmag\_1} namelist
+parameter. An additional parameter: \np{rn\_cmsh} is included in NEMO for experimenting
+with the contribution of the shear term. A value of 1.0 (the default) calculates the
+deformation rate as above; a value of 0.0 will discard the shear term entirely.
+For numerical stability, the calculated viscosity is bounded according to the following:
+\begin{equation}
+{\rm MIN}\left ({ L^2\over {8\Delta{t}}}, rn\_ahm\_m\_lap\right ) \geq A_{m_{Smag}}
+                                                                  \geq rn\_ahm\_0\_lap
+\end{equation}
+\noindent with both parameters for the upper and lower bounds being provided via the
+indicated namelist parameters.
+\bigskip When $ln\_dynldf\_bilap = .true.$, a biharmonic version of the Smagorinsky
+viscosity is also available which sets a coefficient for the biharmonic viscosity as:
+\begin{equation}
+B_{m_{Smag}} = - \left(\frac{{\sf CM_{bSmag}}}{\pi}\right)^2 {L^4\over 8}\vert{D}\vert
+\end{equation}
+\noindent which is bounded according to:
+\begin{equation}
+{\rm MAX}\left (-{ L^4\over {64\Delta{t}}}, rn\_ahm\_m\_blp\right ) \leq B_{m_{Smag}}
+                                                                    \leq rn\_ahm\_0\_blp
+\end{equation}
+\noindent Note the reversal of the inequalities here because NEMO requires the biharmonic
+coefficients as negative numbers. $\sf CM_{bSmag}$ is set via the \np{rn\_cmsmag\_2}
+namelist parameter and the bounding values have corresponding entries in the namelist too.
+\bigskip The current implementation in NEMO also allows for 3D, time-varying diffusivities
+to be set using the Smagorinsky approach. Users should note that this option is not
+recommended for many applications since diffusivities will tend to be largest near
+boundaries (where shears are greatest) leading to spurious upwellings
+(\citep{Griffies_Bk04}, chapter 18.3.4). Nevertheless the option is there for those
+wishing to experiment. This choice requires both \key{traldf\_c3d} and \key{traldf\_smag}
+and uses the \np{rn\_chsmag} (${\sf CH_{Smag}}$), \np{rn\_smsh} and \np{rn\_aht\_m}
+namelist parameters in an analogous way to \np{rn\_cmsmag\_1}, \np{rn\_cmsh} and
+\np{rn\_ahm\_m\_lap} (see above) to set the diffusion coefficient:
+\begin{equation}
+A_{h_{Smag}} = \left(\frac{{\sf CH_{Smag}}}{\pi}\right)^2L^2\vert{D}\vert
+\end{equation}
+For numerical stability, the calculated diffusivity is bounded according to the following:
+\begin{equation}
+{\rm MIN}\left ({ L^2\over {8\Delta{t}}}, rn\_aht\_m\right ) \geq A_{h_{Smag}}
+                                                             \geq rn\_aht\_0
+\end{equation}
 $\ $\newline    % force a new ligne
 …
 (3) for isopycnal diffusion on momentum or tracers, an additional purely
 horizontal background diffusion with uniform coefficient can be added by
 setting a non zero value of \np{rn\_ahmb0} or \np{rn\_ahtb0}, a background horizontal
+setting a non zero value of \np{rn\_ahmb\_0} or \np{rn\_ahtb\_0}, a background horizontal
 eddy viscosity or diffusivity coefficient (namelist parameters whose default
 values are $0$). However, the technique used to compute the isopycnal

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-                      r5118
+                      r6436
 has been made to set them in a generic way. However, examples of how
 they can be set up is given in the ORCA 2\deg and 0.5\deg configurations. For example,
+for details of implementation in ORCA2, search:
+\vspace{-10pt}
+\begin{alltt}
+\tiny
+\begin{verbatim}
+IF( cp_cfg == "orca" .AND. jp_cfg == 2 )
+\end{verbatim}
+\end{alltt}
+for details of implementation in ORCA2, search:
+\texttt{ IF( cp\_cfg == "orca" .AND. jp\_cfg == 2 ) }
 % -------------------------------------------------------------------------------------------------------------
 …
 %--------------------------------------------------------------------------------------------------------------
-\colorbox{yellow}{Add a short description of CLA staff here or in lateral boundary condition chapter?}
 Options are defined through the  \ngn{namcla} namelist variables.
+This option is an obsolescent feature that will be removed in version 3.7 and followings.
 %The problem is resolved here by allowing the mixing of tracers and mass/volume between non-adjacent water columns at nominated regions within the model. Momentum is not mixed. The scheme conserves total tracer content, and total volume (the latter in $z*$- or $s*$-coordinate), and maintains compatibility between the tracer and mass/volume budgets.

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-                      r3294
+                      r6436
 sufficient to solve a linearized version of (\ref{Eq_PE_ssh}), which still allows
 to take into account freshwater fluxes applied at the ocean surface \citep{Roullet_Madec_JGR00}.
+Nevertheless, with the linearization, an exact conservation of heat and salt contents is lost.
 The filtering of EGWs in models with a free surface is usually a matter of discretisation
+of the temporal derivatives, using the time splitting method \citep{Killworth_al_JPO91, Zhang_Endoh_JGR92}
+or the implicit scheme \citep{Dukowicz1994}. In \NEMO, we use a slightly different approach
+developed by \citet{Roullet_Madec_JGR00}: the damping of EGWs is ensured by introducing an
+additional force in the momentum equation. \eqref{Eq_PE_dyn} becomes:
+\begin{equation} \label{Eq_PE_flt}
+\frac{\partial {\rm {\bf U}}_h }{\partial t}= {\rm {\bf M}}
+- g \nabla \left( \tilde{\rho} \ \eta \right)
+- g \ T_c \nabla \left( \widetilde{\rho} \ \partial_t \eta \right)
+\end{equation}
+where $T_c$, is a parameter with dimensions of time which characterizes the force,
+$\widetilde{\rho} = \rho / \rho_o$ is the dimensionless density, and $\rm {\bf M}$
+represents the collected contributions of the Coriolis, hydrostatic pressure gradient,
+non-linear and viscous terms in \eqref{Eq_PE_dyn}.
+The new force can be interpreted as a diffusion of vertically integrated volume flux divergence.
+The time evolution of $D$ is thus governed by a balance of two terms, $-g$ \textbf{A} $\eta$
+and $g \, T_c \,$ \textbf{A} $D$, associated with a propagative regime and a diffusive regime
+in the temporal spectrum, respectively. In the diffusive regime, the EGWs no longer propagate,
+$i.e.$ they are stationary and damped. The diffusion regime applies to the modes shorter than
+$T_c$. For longer ones, the diffusion term vanishes. Hence, the temporally unresolved EGWs
+can be damped by choosing $T_c > \rdt$. \citet{Roullet_Madec_JGR00} demonstrate that
+(\ref{Eq_PE_flt}) can be integrated with a leap frog scheme except the additional term which
+has to be computed implicitly. This is not surprising since the use of a large time step has a
+necessarily numerical cost. Two gains arise in comparison with the previous formulations.
+Firstly, the damping of EGWs can be quantified through the magnitude of the additional term.
+Secondly, the numerical scheme does not need any tuning. Numerical stability is ensured as
+soon as $T_c > \rdt$.
+When the variations of free surface elevation are small compared to the thickness of the first
+model layer, the free surface equation (\ref{Eq_PE_ssh}) can be linearized. As emphasized
+by \citet{Roullet_Madec_JGR00} the linearization of (\ref{Eq_PE_ssh}) has consequences on the
+conservation of salt in the model. With the nonlinear free surface equation, the time evolution
+of the total salt content is
+\begin{equation} \label{Eq_PE_salt_content}
+    \frac{\partial }{\partial t}\int\limits_{D\eta } {S\;dv}
+                        =\int\limits_S {S\;(-\frac{\partial \eta }{\partial t}-D+P-E)\;ds}
+\end{equation}
+where $S$ is the salinity, and the total salt is integrated over the whole ocean volume
+$D_\eta$ bounded by the time-dependent free surface. The right hand side (which is an
+integral over the free surface) vanishes when the nonlinear equation (\ref{Eq_PE_ssh})
+is satisfied, so that the salt is perfectly conserved. When the free surface equation is
+linearized, \citet{Roullet_Madec_JGR00} show that the total salt content integrated in the fixed
+volume $D$ (bounded by the surface $z=0$) is no longer conserved:
+\begin{equation} \label{Eq_PE_salt_content_linear}
+         \frac{\partial }{\partial t}\int\limits_D {S\;dv}
+               = - \int\limits_S {S\;\frac{\partial \eta }{\partial t}ds}
+\end{equation}
+The right hand side of (\ref{Eq_PE_salt_content_linear}) is small in equilibrium solutions
+\citep{Roullet_Madec_JGR00}. It can be significant when the freshwater forcing is not balanced and
+the globally averaged free surface is drifting. An increase in sea surface height \textit{$\eta $}
+results in a decrease of the salinity in the fixed volume $D$. Even in that case though,
+the total salt integrated in the variable volume $D_{\eta}$ varies much less, since
+(\ref{Eq_PE_salt_content_linear}) can be rewritten as
+\begin{equation} \label{Eq_PE_salt_content_corrected}
+\frac{\partial }{\partial t}\int\limits_{D\eta } {S\;dv}
+=\frac{\partial}{\partial t} \left[ \;{\int\limits_D {S\;dv} +\int\limits_S {S\eta \;ds} } \right]
+=\int\limits_S {\eta \;\frac{\partial S}{\partial t}ds}
+\end{equation}
+Although the total salt content is not exactly conserved with the linearized free surface,
+its variations are driven by correlations of the time variation of surface salinity with the
+sea surface height, which is a negligible term. This situation contrasts with the case of
+the rigid lid approximation in which case freshwater forcing is represented by a virtual
+salt flux, leading to a spurious source of salt at the ocean surface
+\citep{Huang_JPO93, Roullet_Madec_JGR00}.
+\newpage
+$\ $\newline    % force a new ligne
+of the temporal derivatives, using a split-explicit method \citep{Killworth_al_JPO91, Zhang_Endoh_JGR92}
+or the implicit scheme \citep{Dukowicz1994} or the addition of a filtering force in the momentum equation
+\citep{Roullet_Madec_JGR00}. With the present release, \NEMO offers the choice between
+an explicit free surface (see \S\ref{DYN_spg_exp}) or a split-explicit scheme strongly
+inspired the one proposed by \citet{Shchepetkin_McWilliams_OM05} (see \S\ref{DYN_spg_ts}).
+%\newpage
+%$\ $\newline    % force a new line
 % ================================================================
 …
 \end{equation}
 The equations solved by the ocean model \eqref{Eq_PE} in $s-$coordinate can be written as follows:
+The equations solved by the ocean model \eqref{Eq_PE} in $s-$coordinate can be written as follows (see Appendix~\ref{Apdx_A_momentum}):
  \vspace{0.5cm}
 * momentum equation:
+$\bullet$ Vector invariant form of the momentum equation :
 \begin{multline} \label{Eq_PE_sco_u}
 \frac{1}{e_3} \frac{\partial \left(  e_3\,u  \right) }{\partial t}=
+\frac{\partial  u   }{\partial t}=
    +   \left( {\zeta +f} \right)\,v
    -   \frac{1}{2\,e_1} \frac{\partial}{\partial i} \left(  u^2+v^2   \right)
 …
 \end{multline}
 \begin{multline} \label{Eq_PE_sco_v}
 \frac{1}{e_3} \frac{\partial \left(  e_3\,v  \right) }{\partial t}=
+\frac{\partial v }{\partial t}=
    -   \left( {\zeta +f} \right)\,u
    -   \frac{1}{2\,e_2 }\frac{\partial }{\partial j}\left(  u^2+v^2  \right)
 …
    +  D_v^{\vect{U}}  +   F_v^{\vect{U}} \quad
 \end{multline}
+ \vspace{0.5cm}
+$\bullet$ Vector invariant form of the momentum equation :
+\begin{multline} \label{Eq_PE_sco_u}
+\frac{1}{e_3} \frac{\partial \left(  e_3\,u  \right) }{\partial t}=
+   +   \left( { f + \frac{1}{e_1 \; e_2 }
+               \left(    v \frac{\partial e_2}{\partial i}
+                  -u \frac{\partial e_1}{\partial j}  \right)}    \right) \, v    \\
+   - \frac{1}{e_1 \; e_2 \; e_3 }   \left(
+               \frac{\partial \left( {e_2 \, e_3 \, u\,u} \right)}{\partial i}
+      +        \frac{\partial \left( {e_1 \, e_3 \, v\,u} \right)}{\partial j}   \right)
+   - \frac{1}{e_3 }\frac{\partial \left( { \omega\,u} \right)}{\partial k}    \\
+   - \frac{1}{e_1} \frac{\partial}{\partial i} \left( \frac{p_s + p_h}{\rho _o}    \right)
+   +  g\frac{\rho }{\rho _o}\sigma _1
+   +   D_u^{\vect{U}}  +   F_u^{\vect{U}} \quad
+\end{multline}
+\begin{multline} \label{Eq_PE_sco_v}
+\frac{1}{e_3} \frac{\partial \left(  e_3\,v  \right) }{\partial t}=
+   -   \left( { f + \frac{1}{e_1 \; e_2}
+               \left(    v \frac{\partial e_2}{\partial i}
+                  -u \frac{\partial e_1}{\partial j}  \right)}    \right) \, u   \\
+   - \frac{1}{e_1 \; e_2 \; e_3 }   \left(
+               \frac{\partial \left( {e_2 \; e_3  \,u\,v} \right)}{\partial i}
+      +        \frac{\partial \left( {e_1 \; e_3  \,v\,v} \right)}{\partial j}   \right)
+                 - \frac{1}{e_3 } \frac{\partial \left( { \omega\,v} \right)}{\partial k}    \\
+   -   \frac{1}{e_2 }\frac{\partial }{\partial j}\left( \frac{p_s+p_h }{\rho _o}  \right)
+    +  g\frac{\rho }{\rho _o }\sigma _2
+   +  D_v^{\vect{U}}  +   F_v^{\vect{U}} \quad
+\end{multline}
 where the relative vorticity, \textit{$\zeta $}, the surface pressure gradient, and the hydrostatic
 pressure have the same expressions as in $z$-coordinates although they do not represent
 exactly the same quantities. $\omega$ is provided by the continuity equation
 (see Appendix~\ref{Apdx_A}):
 \begin{equation} \label{Eq_PE_sco_continuity}
 \frac{\partial e_3}{\partial t} + e_3 \; \chi + \frac{\partial \omega }{\partial s} = 0
 …
  \vspace{0.5cm}
 * tracer equations:
+$\bullet$ tracer equations:
 \begin{multline} \label{Eq_PE_sco_t}
 \frac{1}{e_3} \frac{\partial \left(  e_3\,T  \right) }{\partial t}=
 …
 \label{PE_zco_tilde}
+The $\tilde{z}$-coordinate has been developed by \citet{Leclair_Madec_OM10s}.
+It is not available in the current version of \NEMO.
+The $\tilde{z}$-coordinate has been developed by \citet{Leclair_Madec_OM11}.
+It is available in \NEMO since the version 3.4. Nevertheless, it is currently not robust enough
+to be used in all possible configurations. Its use is therefore not recommended.
 \newpage
 …
 operator acting along $s-$surfaces (see \S\ref{LDF}).
 \subsubsection{Lateral second order tracer diffusive operator}
 The lateral second order tracer diffusive operator is defined by (see Appendix~\ref{Apdx_B}):
+\subsubsection{Lateral Laplacian tracer diffusive operator}
+The lateral Laplacian tracer diffusive operator is defined by (see Appendix~\ref{Apdx_B}):
 \begin{equation} \label{Eq_PE_iso_tensor}
 D^{lT}=\nabla {\rm {\bf .}}\left( {A^{lT}\;\Re \;\nabla T} \right) \qquad
 …
 ocean (see Appendix~\ref{Apdx_B}).
+For \textit{iso-level} diffusion, $r_1$ and $r_2 $ are zero. $\Re $ reduces to the identity
+in the horizontal direction, no rotation is applied.
 For \textit{geopotential} diffusion, $r_1$ and $r_2 $ are the slopes between the
+geopotential and computational surfaces: in $z$-coordinates they are zero
+($r_1 = r_2 = 0$) while in $s$-coordinate (including $\textit{z*}$ case) they are
+equal to $\sigma _1$ and $\sigma _2$, respectively (see \eqref{Eq_PE_sco_slope} ).
+geopotential and computational surfaces: they are equal to $\sigma _1$ and $\sigma _2$,
+respectively (see \eqref{Eq_PE_sco_slope} ).
 For \textit{isoneutral} diffusion $r_1$ and $r_2$ are the slopes between the isoneutral
 …
 to zero in the vicinity of the boundaries. The latter strategy is used in \NEMO (cf. Chap.~\ref{LDF}).
 \subsubsection{Lateral fourth order tracer diffusive operator}
 The lateral fourth order tracer diffusive operator is defined by:
+\subsubsection{Lateral bilaplacian tracer diffusive operator}
+The lateral bilaplacian tracer diffusive operator is defined by:
 \begin{equation} \label{Eq_PE_bilapT}
 D^{lT}=\Delta \left( {A^{lT}\;\Delta T} \right)
 \qquad \text{where} \  D^{lT}=\Delta \left( {A^{lT}\;\Delta T} \right)
  \end{equation}
 It is the second order operator given by \eqref{Eq_PE_iso_tensor} applied twice with
 the eddy diffusion coefficient correctly placed.
+\subsubsection{Lateral second order momentum diffusive operator}
+The second order momentum diffusive operator along $z$- or $s$-surfaces is found by
+\subsubsection{Lateral Laplacian momentum diffusive operator}
+The Laplacian momentum diffusive operator along $z$- or $s$-surfaces is found by
 applying \eqref{Eq_PE_lap_vector} to the horizontal velocity vector (see Appendix~\ref{Apdx_B}):
 \begin{equation} \label{Eq_PE_lapU}
 …
 of the Equator in a geographical coordinate system \citep{Lengaigne_al_JGR03}.
 \subsubsection{lateral fourth order momentum diffusive operator}
+\subsubsection{lateral bilaplacian momentum diffusive operator}
 As for tracers, the fourth order momentum diffusive operator along $z$ or $s$-surfaces

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1	1	% ================================================================
2		% Chapter 1 � Model Basics
	2	% Chapter 1 ——— Model Basics
3	3	% ================================================================
4	4	% ================================================================

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-                      r5120
+                      r6436
 % ================================================================
 % Chapter � Surface Boundary Condition (SBC, ISF, ICB)
+% Chapter —— Surface Boundary Condition (SBC, ISF, ICB)
 % ================================================================
 \chapter{Surface Boundary Condition (SBC, ISF, ICB) }
 …
    \item the two components of the surface ocean stress $\left( {\tau _u \;,\;\tau _v} \right)$
    \item the incoming solar and non solar heat fluxes $\left( {Q_{ns} \;,\;Q_{sr} } \right)$
+   \item the surface freshwater budget $\left( {\textit{emp},\;\textit{emp}_S } \right)$
+   \item the surface freshwater budget $\left( {\textit{emp}} \right)$
+   \item the surface salt flux associated with freezing/melting of seawater $\left( {\textit{sfx}} \right)$
 \end{itemize}
 plus an optional field:
 …
 are controlled by namelist \ngn{namsbc} variables: an analytical formulation (\np{ln\_ana}~=~true),
 a flux formulation (\np{ln\_flx}~=~true), a bulk formulae formulation (CORE
 (\np{ln\_core}~=~true), CLIO (\np{ln\_clio}~=~true) or MFS
+(\np{ln\_blk\_core}~=~true), CLIO (\np{ln\_blk\_clio}~=~true) or MFS
 \footnote { Note that MFS bulk formulae compute fluxes only for the ocean component}
+(\np{ln\_mfs}~=~true) bulk formulae) and a coupled
+formulation (exchanges with a atmospheric model via the OASIS coupler)
+(\np{ln\_cpl}~=~true). When used, the atmospheric pressure forces both
+ocean and ice dynamics (\np{ln\_apr\_dyn}~=~true).
+The frequency at which the six or seven fields have to be updated is the \np{nn\_fsbc}
+namelist parameter.
+(\np{ln\_blk\_mfs}~=~true) bulk formulae) and a coupled or mixed forced/coupled formulation
+(exchanges with a atmospheric model via the OASIS coupler) (\np{ln\_cpl} or \np{ln\_mixcpl}~=~true).
+When used ($i.e.$ \np{ln\_apr\_dyn}~=~true), the atmospheric pressure forces both ocean and ice dynamics.
+The frequency at which the forcing fields have to be updated is given by the \np{nn\_fsbc} namelist parameter.
 When the fields are supplied from data files (flux and bulk formulations), the input fields
 need not be supplied on the model grid.  Instead a file of coordinates and weights can
+need not be supplied on the model grid. Instead a file of coordinates and weights can
 be supplied which maps the data from the supplied grid to the model points
 (so called "Interpolation on the Fly", see \S\ref{SBC_iof}).
 …
 can be masked to avoid spurious results in proximity of the coasts  as large sea-land gradients characterize
 most of the atmospheric variables.
 In addition, the resulting fields can be further modified using several namelist options.
+These options control  the rotation of vector components supplied relative to an east-north
+coordinate system onto the local grid directions in the model; the addition of a surface
+restoring term to observed SST and/or SSS (\np{ln\_ssr}~=~true); the modification of fluxes
+below ice-covered areas (using observed ice-cover or a sea-ice model)
+(\np{nn\_ice}~=~0,1, 2 or 3); the addition of river runoffs as surface freshwater
+fluxes or lateral inflow (\np{ln\_rnf}~=~true); the addition of isf melting as lateral inflow (parameterisation)
+(\np{nn\_isf}~=~2 or 3 and \np{ln\_isfcav}~=~false) or as surface flux at the land-ice ocean interface
+(\np{nn\_isf}~=~1 or 4 and \np{ln\_isfcav}~=~true);
+the addition of a freshwater flux adjustment in order to avoid a mean sea-level drift (\np{nn\_fwb}~=~0,~1~or~2); the
+transformation of the solar radiation (if provided as daily mean) into a diurnal
+cycle (\np{ln\_dm2dc}~=~true); and a neutral drag coefficient can be read from an external wave
+model (\np{ln\_cdgw}~=~true). The latter option is possible only in case core or mfs bulk formulas are selected.
+These options control
+\begin{itemize}
+\item the rotation of vector components supplied relative to an east-north
+coordinate system onto the local grid directions in the model ;
+\item the addition of a surface restoring term to observed SST and/or SSS (\np{ln\_ssr}~=~true) ;
+\item the modification of fluxes below ice-covered areas (using observed ice-cover or a sea-ice model) (\np{nn\_ice}~=~0,1, 2 or 3) ;
+\item the addition of river runoffs as surface freshwater fluxes or lateral inflow (\np{ln\_rnf}~=~true) ;
+\item the addition of isf melting as lateral inflow (parameterisation) (\np{nn\_isf}~=~2 or 3 and \np{ln\_isfcav}~=~false)
+or as fluxes applied at the land-ice ocean interface (\np{nn\_isf}~=~1 or 4 and \np{ln\_isfcav}~=~true) ;
+\item the addition of a freshwater flux adjustment in order to avoid a mean sea-level drift (\np{nn\_fwb}~=~0,~1~or~2) ;
+\item the transformation of the solar radiation (if provided as daily mean) into a diurnal cycle (\np{ln\_dm2dc}~=~true) ;
+and a neutral drag coefficient can be read from an external wave model (\np{ln\_cdgw}~=~true).
+\end{itemize}
+The latter option is possible only in case core or mfs bulk formulas are selected.
 In this chapter, we first discuss where the surface boundary condition appears in the
 …
 The surface ocean stress is the stress exerted by the wind and the sea-ice
+on the ocean. The two components of stress are assumed to be interpolated
+onto the ocean mesh, $i.e.$ resolved onto the model (\textbf{i},\textbf{j}) direction
+at $u$- and $v$-points They are applied as a surface boundary condition of the
+computation of the momentum vertical mixing trend (\mdl{dynzdf} module) :
+\begin{equation} \label{Eq_sbc_dynzdf}
+\left.{\left( {\frac{A^{vm} }{e_3 }\ \frac{\partial \textbf{U}_h}{\partial k}} \right)} \right|_{z=1}
+    = \frac{1}{\rho _o} \binom{\tau _u}{\tau _v }
+\end{equation}
+where $(\tau _u ,\;\tau _v )=(utau,vtau)$ are the two components of the wind
+stress vector in the $(\textbf{i},\textbf{j})$ coordinate system.
+on the ocean. It is applied in \mdl{dynzdf} module as a surface boundary condition of the
+computation of the momentum vertical mixing trend (see \eqref{Eq_dynzdf_sbc} in \S\ref{DYN_zdf}).
+As such, it has to be provided as a 2D vector interpolated
+onto the horizontal velocity ocean mesh, $i.e.$ resolved onto the model
+(\textbf{i},\textbf{j}) direction at $u$- and $v$-points.
 The surface heat flux is decomposed into two parts, a non solar and a solar heat
 flux, $Q_{ns}$ and $Q_{sr}$, respectively. The former is the non penetrative part
+of the heat flux ($i.e.$ the sum of sensible, latent and long wave heat fluxes).
+It is applied as a surface boundary condition trend of the first level temperature
+time evolution equation (\mdl{trasbc} module).
+\begin{equation} \label{Eq_sbc_trasbc_q}
+\frac{\partial T}{\partial t}\equiv \cdots \;+\;\left. {\frac{Q_{ns} }{\rho
+_o \;C_p \;e_{3t} }} \right|_{k=1} \quad
+\end{equation}
+$Q_{sr}$ is the penetrative part of the heat flux. It is applied as a 3D
+trends of the temperature equation (\mdl{traqsr} module) when \np{ln\_traqsr}=True.
+\begin{equation} \label{Eq_sbc_traqsr}
+\frac{\partial T}{\partial t}\equiv \cdots \;+\frac{Q_{sr} }{\rho_o C_p \,e_{3t} }\delta _k \left[ {I_w } \right]
+\end{equation}
+where $I_w$ is a non-dimensional function that describes the way the light
+penetrates inside the water column. It is generally a sum of decreasing
+exponentials (see \S\ref{TRA_qsr}).
+The surface freshwater budget is provided by fields: \textit{emp} and $\textit{emp}_S$ which
+may or may not be identical. Indeed, a surface freshwater flux has two effects:
+it changes the volume of the ocean and it changes the surface concentration of
+salt (and other tracers). Therefore it appears in the sea surface height as a volume
+flux, \textit{emp} (\textit{dynspg\_xxx} modules), and in the salinity time evolution equations
+as a concentration/dilution effect,
+$\textit{emp}_{S}$ (\mdl{trasbc} module).
+\begin{equation} \label{Eq_trasbc_emp}
+\begin{aligned}
+&\frac{\partial \eta }{\partial t}\equiv \cdots \;+\;\textit{emp}\quad  \\
+\\
+ &\frac{\partial S}{\partial t}\equiv \cdots \;+\left. {\frac{\textit{emp}_S \;S}{e_{3t} }} \right|_{k=1} \\
+ \end{aligned}
+\end{equation}
+In the real ocean, $\textit{emp}=\textit{emp}_S$ and the ocean salt content is conserved,
+but it exist several numerical reasons why this equality should be broken.
+For example, when the ocean is coupled to a sea-ice model, the water exchanged between
+ice and ocean is slightly salty (mean sea-ice salinity is $\sim $\textit{4 psu}). In this case,
+$\textit{emp}_{S}$ take into account both concentration/dilution effect associated with
+freezing/melting and the salt flux between ice and ocean, while \textit{emp} is
+only the volume flux. In addition, in the current version of \NEMO, the sea-ice is
+assumed to be above the ocean (the so-called levitating sea-ice). Freezing/melting does
+not change the ocean volume (no impact on \textit{emp}) but it modifies the SSS.
+%gm  \colorbox{yellow}{(see {\S} on LIM sea-ice model)}.
+Note that SST can also be modified by a freshwater flux. Precipitation (in
+particular solid precipitation) may have a temperature significantly different from
+the SST. Due to the lack of information about the temperature of
+precipitation, we assume it is equal to the SST. Therefore, no
+concentration/dilution term appears in the temperature equation. It has to
+be emphasised that this absence does not mean that there is no heat flux
+associated with precipitation! Precipitation can change the ocean volume and thus the
+ocean heat content. It is therefore associated with a heat flux (not yet
+diagnosed in the model) \citep{Roullet_Madec_JGR00}).
+of the heat flux ($i.e.$ the sum of sensible, latent and long wave heat fluxes
+plus the heat content of the mass exchange with the atmosphere and sea-ice).
+It is applied in \mdl{trasbc} module as a surface boundary condition trend of
+the first level temperature time evolution equation (see \eqref{Eq_tra_sbc}
+and \eqref{Eq_tra_sbc_lin} in \S\ref{TRA_sbc}).
+The latter is the penetrative part of the heat flux. It is applied as a 3D
+trends of the temperature equation (\mdl{traqsr} module) when \np{ln\_traqsr}=\textit{true}.
+The way the light penetrates inside the water column is generally a sum of decreasing
+exponentials (see \S\ref{TRA_qsr}).
+The surface freshwater budget is provided by the \textit{emp} field.
+It represents the mass flux exchanged with the atmosphere (evaporation minus precipitation)
+and possibly with the sea-ice and ice shelves (freezing minus melting of ice).
+It affects both the ocean in two different ways:
+$(i)$   it changes the volume of the ocean and therefore appears in the sea surface height
+equation as a volume flux, and
+$(ii)$  it changes the surface temperature and salinity through the heat and salt contents
+of the mass exchanged with the atmosphere, the sea-ice and the ice shelves.
 %\colorbox{yellow}{Miss: }
 …
 %Sbcmod manage the ``providing'' (fourniture) to the ocean the 7 fields
+%
 %Fluxes update only each nf{\_}sbc time step (namsbc) explain relation
 %between nf{\_}sbc and nf{\_}ice, do we define nf{\_}blk??? ? only one
 %nf{\_}sbc
+%Fluxes update only each nn{\_}fsbc time step (namsbc) explain relation
+%between nn{\_}fsbc and nf{\_}ice, do we define nf{\_}blk??? ? only one
+%nn{\_}fsbc
+%
 %Explain here all the namlist namsbc variable{\ldots}.
+%
+% explain : use or not of surface currents
+%
 %\colorbox{yellow}{End Miss }
+The ocean model provides the surface currents, temperature and salinity
+averaged over \np{nf\_sbc} time-step (\ref{Tab_ssm}).The computation of the
+mean is done in \mdl{sbcmod} module.
+The ocean model provides, at each time step, to the surface module (\mdl{sbcmod})
+the surface currents, temperature and salinity.
+These variables are averaged over \np{nn\_fsbc} time-step (\ref{Tab_ssm}),
+and it is these averaged fields which are used to computes the surface fluxes
+at a frequency of \np{nn\_fsbc} time-step.
 %-------------------------------------------------TABLE---------------------------------------------------
 …
 \caption{  \label{Tab_ssm}
 Ocean variables provided by the ocean to the surface module (SBC).
 The variable are averaged over nf{\_}sbc time step, $i.e.$ the frequency of
+The variable are averaged over nn{\_}fsbc time step, $i.e.$ the frequency of
 computation of surface fluxes.}
 \end{center}   \end{table}
 …
 %--------------------------------------------------------------------------------------------------------------
 In some circumstances it may be useful to avoid calculating the 3D temperature, salinity and velocity fields and simply read them in from  a previous run.
+Options are defined through the  \ngn{namsbc\_sas} namelist variables.
+In some circumstances it may be useful to avoid calculating the 3D temperature, salinity and velocity fields
+and simply read them in from a previous run or receive them from OASIS.
 For example:
 \begin{enumerate}
 \item  Multiple runs of the model are required in code development to see the affect of different algorithms in
+\begin{itemize}
+\item  Multiple runs of the model are required in code development to see the effect of different algorithms in
        the bulk formulae.
 \item  The effect of different parameter sets in the ice model is to be examined.
+\end{enumerate}
+\item  Development of sea-ice algorithms or parameterizations.
+\item  spinup of the iceberg floats
+\item  ocean/sea-ice simulation with both media running in parallel (\np{ln\_mixcpl}~=~\textit{true})
+\end{itemize}
 The StandAlone Surface scheme provides this utility.
+Its options are defined through the \ngn{namsbc\_sas} namelist variables.
 A new copy of the model has to be compiled with a configuration based on ORCA2\_SAS\_LIM.
 However no namelist parameters need be changed from the settings of the previous run (except perhaps nn{\_}date0)
 …
 Routines replaced are:
+\begin{enumerate}
+\item  \mdl{nemogcm}
+       This routine initialises the rest of the model and repeatedly calls the stp time stepping routine (step.F90)
+\begin{itemize}
+\item \mdl{nemogcm} : This routine initialises the rest of the model and repeatedly calls the stp time stepping routine (step.F90)
        Since the ocean state is not calculated all associated initialisations have been removed.
+\item  \mdl{step}
+       The main time stepping routine now only needs to call the sbc routine (and a few utility functions).
+\item  \mdl{sbcmod}
+       This has been cut down and now only calculates surface forcing and the ice model required.  New surface modules
+\item  \mdl{step} : The main time stepping routine now only needs to call the sbc routine (and a few utility functions).
+\item  \mdl{sbcmod} : This has been cut down and now only calculates surface forcing and the ice model required.  New surface modules
        that can function when only the surface level of the ocean state is defined can also be added (e.g. icebergs).
+\item  \mdl{daymod}
+       No ocean restarts are read or written (though the ice model restarts are retained), so calls to restart functions
+\item  \mdl{daymod} : No ocean restarts are read or written (though the ice model restarts are retained), so calls to restart functions
        have been removed.  This also means that the calendar cannot be controlled by time in a restart file, so the user
        must make sure that nn{\_}date0 in the model namelist is correct for his or her purposes.
+\item  \mdl{stpctl}
+       Since there is no free surface solver, references to it have been removed from \rou{stp\_ctl} module.
+\item  \mdl{diawri}
+       All 3D data have been removed from the output.  The surface temperature, salinity and velocity components (which
+\item  \mdl{stpctl} : Since there is no free surface solver, references to it have been removed from \rou{stp\_ctl} module.
+\item  \mdl{diawri} : All 3D data have been removed from the output.  The surface temperature, salinity and velocity components (which
        have been read in) are written along with relevant forcing and ice data.
 \end{enumerate}
+\end{itemize}
 One new routine has been added:
+\begin{enumerate}
+\item  \mdl{sbcsas}
+       This module initialises the input files needed for reading temperature, salinity and velocity arrays at the surface.
+\begin{itemize}
+\item  \mdl{sbcsas} : This module initialises the input files needed for reading temperature, salinity and velocity arrays at the surface.
        These filenames are supplied in namelist namsbc{\_}sas.  Unfortunately because of limitations with the \mdl{iom} module,
        the full 3D fields from the mean files have to be read in and interpolated in time, before using just the top level.
        Since fldread is used to read in the data, Interpolation on the Fly may be used to change input data resolution.
+\end{enumerate}
+\end{itemize}
+% Missing the description of the 2 following variables:
+%   ln_3d_uve   = .true.    !  specify whether we are supplying a 3D u,v and e3 field
+%   ln_read_frq = .false.    !  specify whether we must read frq or not
 % ================================================================
 …
 reanalysis and satellite data. They use an inertial dissipative method to compute
 the turbulent transfer coefficients (momentum, sensible heat and evaporation)
 from the 10 metre wind speed, air temperature and specific humidity.
+from the 10 meters wind speed, air temperature and specific humidity.
 This \citet{Large_Yeager_Rep04} dataset is available through the
 \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}.
 …
 or larger than the one of the input atmospheric fields.
+The  \np{sn\_wndi}, \np{sn\_wndj}, \np{sn\_qsr}, \np{sn\_qlw}, \np{sn\_tair},\np{sn\_humi},\np{sn\_prec}, \np{sn\_snow}, \np{sn\_tdif} parameters describe the fields and the way they have to be used (spatial and temporal interpolations).
+\np{cn\_dir} is the directory of location of bulk files
+\np{ln\_taudif} is the flag to specify if we use Hight Frequency (HF) tau information (.true.) or not (.false.)
+\np{rn\_zqt}: is the height of humidity and temperature measurements (m)
+\np{rn\_zu}: is the height of wind measurements (m)
+The multiplicative factors to activate (value is 1) or deactivate (value is 0) :
+\np{rn\_pfac} for precipitations (total and snow)
+\np{rn\_efac} for evaporation
+\np{rn\_vfac} for for ice/ocean velocities in the calculation of wind stress
 % -------------------------------------------------------------------------------------------------------------
 %        CLIO Bulk formulea
 …
 are sent to the atmospheric component.
+A generalised coupled interface has been developed. It is currently interfaced with OASIS 3
+(\key{oasis3}) and does not support OASIS 4
+\footnote{The \key{oasis4} exist. It activates portion of the code that are still under development.}.
+A generalised coupled interface has been developed.
+It is currently interfaced with OASIS-3-MCT (\key{oasis3}).
 It has been successfully used to interface \NEMO to most of the European atmospheric
 GCM (ARPEGE, ECHAM, ECMWF, HadAM, HadGAM, LMDz),
 …
 \label{SBC_tide}
+A module is available to use the tidal potential forcing and is activated with with \key{tide}.
+%------------------------------------------nam_tide----------------------------------------------------
+%------------------------------------------nam_tide---------------------------------------
 \namdisplay{nam_tide}
+%-------------------------------------------------------------------------------------------------------------
+Concerning the tidal potential, some parameters are available in namelist \ngn{nam\_tide}:
+%-----------------------------------------------------------------------------------------
+A module is available to compute the tidal potential and use it in the momentum equation.
+This option is activated when \key{tide} is defined.
+Some parameters are available in namelist \ngn{nam\_tide}:
 - \np{ln\_tide\_pot} activate the tidal potential forcing
 …
 - \np{clname} is the name of constituent
 The tide is generated by the forces of gravity ot the Earth-Moon and Earth-Sun sytem;
 …
 lowest box the river water is being added to (i.e. the total depth that river water is being added to in the model).
+%Christian:
+If the depth information is not provide in the NetCDF file, it can be estimate from the runoff input file at the initial time-step, by setting the namelist parameter \np{ln\_rnf\_depth\_ini} to true.
+This estimation is a simple linear relation between the runoff and a given depth :
+\begin{equation}
+h\_dep  = \frac{rn\_dep\_max} {rn\_rnf\_max}  rnf
+\end{equation}
+where  \np{rn\_dep\_max} is the given maximum depth over which the runoffs is spread,
+ \np{rn\_rnf\_max} is the maximum value of the runoff climatologie over the global domain
+and rnf is the maximum value in time of the runoff climatology at each grid cell (computed online).
+The estimated depth array can be output if needed in a NetCDF file by setting the namelist parameter \np{nn\_rnf\_depth\_file} to 1.
 The mass/volume addition due to the river runoff is, at each relevant depth level, added to the horizontal divergence
 (\textit{hdivn}) in the subroutine \rou{sbc\_rnf\_div} (called from \mdl{divcur}).
 …
 \namdisplay{namsbc_isf}
 %--------------------------------------------------------------------------------------------------------
+Namelist variable in \ngn{namsbc}, \np{nn\_isf},  control the kind of ice shelf representation used.
+Namelist variable in \ngn{namsbc}, \np{nn\_isf}, controls the ice shelf representation used (Fig. \ref{Fig_SBC_isf}):
+%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+\begin{figure}[!h]    \begin{center}
+\includegraphics[width=0.8\textwidth]{./TexFiles/Figures/Fig_SBC_isf.pdf}
+\caption{ \label{Fig_SBC_isf}
+Schematic for all the options available trough \np{nn\_isf}.}
+\end{center}   \end{figure}
+%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 \begin{description}
+\item[\np{nn\_isf}~=~0]
+The ice shelf routines are not used. The ice shelf melting is not computed or prescribed, the cavity have to be closed.
+If needed, the ice shelf melting should be added to the runoff or the precipitation file.
 \item[\np{nn\_isf}~=~1]
+The ice shelf cavity is represented. The fwf and heat flux are computed.
+Full description, sensitivity and validation in preparation.
+The ice shelf cavity is represented. The fwf and heat flux are computed. Two different bulk formula are available:
+   \begin{description}
+   \item[\np{nn\_isfblk}~=~1]
+   The bulk formula used to compute the melt is based the one described in \citet{Hunter2006}.
+        This formulation is based on a balance between the upward ocean heat flux and the latent heat flux at the ice shelf base.
+   \item[\np{nn\_isfblk}~=~2]
+   The bulk formula used to compute the melt is based the one described in \citet{Jenkins1991}.
+        This formulation is based on a 3 equations formulation (a heat flux budget, a salt flux budget and a linearised freezing point temperature equation).
+   \end{description}
+For this 2 bulk formulations, there are 3 different ways to compute the exchange coeficient:
+   \begin{description}
+        \item[\np{nn\_gammablk~=~0~}]
+   The salt and heat exchange coefficients are constant and defined by \np{rn\_gammas0} and \np{rn\_gammat0}
+   \item[\np{nn\_gammablk~=~1~}]
+   The salt and heat exchange coefficients are velocity dependent and defined as $\np{rn\_gammas0} \times u_{*}$ and $\np{rn\_gammat0} \times u_{*}$
+        where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn\_hisf\_tbl} meters).
+        See \citet{Jenkins2010} for all the details on this formulation.
+   \item[\np{nn\_gammablk~=~2~}]
+   The salt and heat exchange coefficients are velocity and stability dependent and defined as
+        $\gamma_{T,S} = \frac{u_{*}}{\Gamma_{Turb} + \Gamma^{T,S}_{Mole}}$
+        where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn\_hisf\_tbl} meters),
+        $\Gamma_{Turb}$ the contribution of the ocean stability and
+        $\Gamma^{T,S}_{Mole}$ the contribution of the molecular diffusion.
+        See \citet{Holland1999} for all the details on this formulation.
+        \end{description}
 \item[\np{nn\_isf}~=~2]
 …
 The fwf is distributed along the ice shelf edge between the depth of the average grounding line (GL)
 (\np{sn\_depmax\_isf}) and the base of the ice shelf along the calving front (\np{sn\_depmin\_isf}) as in (\np{nn\_isf}~=~3).
 Furthermore the fwf is computed using the \citet{Beckmann2003} parameterisation of isf melting.
+Furthermore the fwf and heat flux are computed using the \citet{Beckmann2003} parameterisation of isf melting.
 The effective melting length (\np{sn\_Leff\_isf}) is read from a file.
 \item[\np{nn\_isf}~=~3]
 A simple parameterisation of isf is used. The ice shelf cavity is not represented.
 The fwf (\np{sn\_rnfisf}) is distributed along the ice shelf edge between the depth of the average grounding line (GL)
 (\np{sn\_depmax\_isf}) and the base of the ice shelf along the calving front (\np{sn\_depmin\_isf}).
 Full description, sensitivity and validation in preparation.
+The fwf (\np{sn\_rnfisf}) is prescribed and distributed along the ice shelf edge between the depth of the average grounding line (GL)
+(\np{sn\_depmax\_isf}) and the base of the ice shelf along the calving front (\np{sn\_depmin\_isf}).
+The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$.
 \item[\np{nn\_isf}~=~4]
 The ice shelf cavity is represented. However, the fwf (\np{sn\_fwfisf}) and heat flux (\np{sn\_qisf}) are
+not computed but specified from file.
+The ice shelf cavity is opened. However, the fwf is not computed but specified from file \np{sn\_fwfisf}).
+The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$.\\
 \end{description}
+\np{nn\_isf}~=~1 and \np{nn\_isf}~=~2 compute a melt rate based on the water masse properties, ocean velocities and depth.
+ This flux is thus highly dependent of the model resolution (horizontal and vertical), realism of the water masse onto the shelf ...
+\np{nn\_isf}~=~3 and \np{nn\_isf}~=~4 read the melt rate and heat flux from a file. You have total control of the fwf scenario.
+ This can be usefull if the water masses on the shelf are not realistic or the resolution (horizontal/vertical) are too
+coarse to have realistic melting or for sensitivity studies where you want to control your input.
+Full description, sensitivity and validation in preparation.
+There is 2 ways to apply the fwf to NEMO. The first possibility (\np{ln\_divisf}~=~false) applied the fwf
+ and heat flux directly on the salinity and temperature tendancy. The second possibility (\np{ln\_divisf}~=~true)
+ apply the fwf as for the runoff fwf (see \S\ref{SBC_rnf}). The mass/volume addition due to the ice shelf melting is,
+ at each relevant depth level, added to the horizontal divergence (\textit{hdivn}) in the subroutine \rou{sbc\_isf\_div}
+(called from \mdl{divcur}).
+$\bullet$ \np{nn\_isf}~=~1 and \np{nn\_isf}~=~2 compute a melt rate based on the water mass properties, ocean velocities and depth.
+ This flux is thus highly dependent of the model resolution (horizontal and vertical), realism of the water masses onto the shelf ...\\
+$\bullet$ \np{nn\_isf}~=~3 and \np{nn\_isf}~=~4 read the melt rate from a file. You have total control of the fwf forcing.
+This can be usefull if the water masses on the shelf are not realistic or the resolution (horizontal/vertical) are too
+coarse to have realistic melting or for studies where you need to control your heat and fw input.\\
+Two namelist parameters control how the heat and fw fluxes are passed to NEMO: \np{rn\_hisf\_tbl} and \np{ln\_divisf}
+\begin{description}
+\item[\np{rn\_hisf\_tbl}] is the top boundary layer thickness as defined in \citet{Losch2008}.
+This parameter is only used if \np{nn\_isf}~=~1 or \np{nn\_isf}~=~4
+It allows you to control over which depth you want to spread the heat and fw fluxes.
+If \np{rn\_hisf\_tbl} = 0.0, the fluxes are put in the top level whatever is its tickness.
+If \np{rn\_hisf\_tbl} $>$ 0.0, the fluxes are spread over the first \np{rn\_hisf\_tbl} m (ie over one or several cells).
+\item[\np{ln\_divisf}] is a flag to apply the fw flux as a volume flux or as a salt flux.
+\np{ln\_divisf}~=~true applies the fwf as a volume flux. This volume flux is implemented with in the same way as for the runoff.
+The fw addition due to the ice shelf melting is, at each relevant depth level, added to the horizontal divergence
+(\textit{hdivn}) in the subroutine \rou{sbc\_isf\_div}, called from \mdl{divcur}.
+See the runoff section \ref{SBC_rnf} for all the details about the divergence correction.
+\np{ln\_divisf}~=~false applies the fwf and heat flux directly on the salinity and temperature tendancy.
+\item[\np{ln\_conserve}] is a flag for \np{nn\_isf}~=~1. A conservative boundary layer scheme as described in \citet{Jenkins2001}
+is used if \np{ln\_conserve}=true. It takes into account the fact that the melt water is at freezing T and needs to be warm up to ocean temperature.
+It is only relevant for \np{ln\_divisf}~=~false.
+If \np{ln\_divisf}~=~true, \np{ln\_conserve} has to be set to false to avoid a double counting of the contribution.
+\end{description}
+%
 % ================================================================
 %        Handling of icebergs
 % ================================================================
 \section{ Handling of icebergs (ICB) }
+\section{Handling of icebergs (ICB)}
 \label{ICB_icebergs}
 %------------------------------------------namberg----------------------------------------------------
 …
 %-------------------------------------------------------------------------------------------------------------
+Icebergs are modelled as lagrangian particles in NEMO.
+Their physical behaviour is controlled by equations as described in  \citet{Martin_Adcroft_OM10} ).
+(Note that the authors kindly provided a copy of their code to act as a basis for implementation in NEMO.)
+Icebergs are initially spawned into one of ten classes which have specific mass and thickness as described in the \ngn{namberg} namelist:
+Icebergs are modelled as lagrangian particles in NEMO \citep{Marsh_GMD2015}.
+Their physical behaviour is controlled by equations as described in \citet{Martin_Adcroft_OM10} ).
+(Note that the authors kindly provided a copy of their code to act as a basis for implementation in NEMO).
+Icebergs are initially spawned into one of ten classes which have specific mass and thickness as described
+in the \ngn{namberg} namelist:
 \np{rn\_initial\_mass} and \np{rn\_initial\_thickness}.
 Each class has an associated scaling (\np{rn\_mass\_scaling}), which is an integer representing how many icebergs
 …
 The presence at the sea surface of an ice covered area modifies all the fluxes
 transmitted to the ocean. There are several way to handle sea-ice in the system
 depending on the value of the \np{nn{\_}ice} namelist parameter.
+depending on the value of the \np{nn\_ice} namelist parameter found in \ngn{namsbc} namelist.
 \begin{description}
 \item[nn{\_}ice = 0]  there will never be sea-ice in the computational domain.
 …
 % -------------------------------------------------------------------------------------------------------------
 \subsection   [Neutral drag coefficient from external wave model (\textit{sbcwave})]
                         {Neutral drag coefficient from external wave model (\mdl{sbcwave})}
+              {Neutral drag coefficient from external wave model (\mdl{sbcwave})}
 \label{SBC_wave}
 %------------------------------------------namwave----------------------------------------------------
 \namdisplay{namsbc_wave}
 %-------------------------------------------------------------------------------------------------------------
+\begin{description}
+\item [??] In order to read a neutral drag coeff, from an external data source (i.e. a wave model), the
+logical variable \np{ln\_cdgw}
+ in $namsbc$ namelist must be defined ${.true.}$.
+In order to read a neutral drag coeff, from an external data source ($i.e.$ a wave model), the
+logical variable \np{ln\_cdgw} in \ngn{namsbc} namelist must be set to \textit{true}.
 The \mdl{sbcwave} module containing the routine \np{sbc\_wave} reads the
 namelist \ngn{namsbc\_wave} (for external data names, locations, frequency, interpolation and all
 the miscellanous options allowed by Input Data generic Interface see \S\ref{SBC_input})
+and a 2D field of neutral drag coefficient. Then using the routine
+TURB\_CORE\_1Z or TURB\_CORE\_2Z, and starting from the neutral drag coefficent provided, the drag coefficient is computed according
+to stable/unstable conditions of the air-sea interface following \citet{Large_Yeager_Rep04}.
+\end{description}
+and a 2D field of neutral drag coefficient.
+Then using the routine TURB\_CORE\_1Z or TURB\_CORE\_2Z, and starting from the neutral drag coefficent provided,
+the drag coefficient is computed according to stable/unstable conditions of the air-sea interface following \citet{Large_Yeager_Rep04}.
 % Griffies doc:
+% When running ocean-ice simulations, we are not explicitly representing land processes, such as rivers, catchment areas, snow accumulation, etc. However, to reduce model drift, it is important to balance the hydrological cycle in ocean-ice models. We thus need to prescribe some form of global normalization to the precipitation minus evaporation plus river runoff. The result of the normalization should be a global integrated zero net water input to the ocean-ice system over a chosen time scale.
+%How often the normalization is done is a matter of choice. In mom4p1, we choose to do so at each model time step, so that there is always a zero net input of water to the ocean-ice system. Others choose to normalize over an annual cycle, in which case the net imbalance over an annual cycle is used to alter the subsequent year�s water budget in an attempt to damp the annual water imbalance. Note that the annual budget approach may be inappropriate with interannually varying precipitation forcing.
+%When running ocean-ice coupled models, it is incorrect to include the water transport between the ocean and ice models when aiming to balance the hydrological cycle. The reason is that it is the sum of the water in the ocean plus ice that should be balanced when running ocean-ice models, not the water in any one sub-component. As an extreme example to illustrate the issue, consider an ocean-ice model with zero initial sea ice. As the ocean-ice model spins up, there should be a net accumulation of water in the growing sea ice, and thus a net loss of water from the ocean. The total water contained in the ocean plus ice system is constant, but there is an exchange of water between the subcomponents. This exchange should not be part of the normalization used to balance the hydrological cycle in ocean-ice models.
+% When running ocean-ice simulations, we are not explicitly representing land processes,
+% such as rivers, catchment areas, snow accumulation, etc. However, to reduce model drift,
+% it is important to balance the hydrological cycle in ocean-ice models.
+% We thus need to prescribe some form of global normalization to the precipitation minus evaporation plus river runoff.
+% The result of the normalization should be a global integrated zero net water input to the ocean-ice system over
+% a chosen time scale.
+%How often the normalization is done is a matter of choice. In mom4p1, we choose to do so at each model time step,
+% so that there is always a zero net input of water to the ocean-ice system.
+% Others choose to normalize over an annual cycle, in which case the net imbalance over an annual cycle is used
+% to alter the subsequent year�s water budget in an attempt to damp the annual water imbalance.
+% Note that the annual budget approach may be inappropriate with interannually varying precipitation forcing.
+% When running ocean-ice coupled models, it is incorrect to include the water transport between the ocean
+% and ice models when aiming to balance the hydrological cycle.
+% The reason is that it is the sum of the water in the ocean plus ice that should be balanced when running ocean-ice models,
+% not the water in any one sub-component. As an extreme example to illustrate the issue,
+% consider an ocean-ice model with zero initial sea ice. As the ocean-ice model spins up,
+% there should be a net accumulation of water in the growing sea ice, and thus a net loss of water from the ocean.
+% The total water contained in the ocean plus ice system is constant, but there is an exchange of water between
+% the subcomponents. This exchange should not be part of the normalization used to balance the hydrological cycle
+% in ocean-ice models.

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Chapters/Chap_STO.tex

-                      r5404
+                      r6436
 \label{STO}
+Authors: P.-A. Bouttier
 \minitoc
 \newpage
 $\ $\newline    % force a new line
+The stochastic parametrization module aims to explicitly simulate uncertainties in the model. More particularly, \cite{Brankart_OM2013} has shown that, because of the nonlinearity of the seawater equation of state, unresolved scales represent a major source of uncertainties in the computation of the large scale horizontal density gradient (from T/S large scale fields), and that the impact of these uncertainties can be simulated by random processes representing unresolved T/S fluctuations.
+The stochastic formulation of the equation of state can be written as:
+\begin{equation}
+ \label{eq:eos_sto}
+  \rho = \frac{1}{2} \sum_{i=1}^m\{ \rho[T+\Delta T_i,S+\Delta S_i,p_o(z)] + \rho[T-\Delta T_i,S-\Delta S_i,p_o(z)] \}
+\end{equation}
+where $p_o(z)$ is the reference pressure depending on the depth and $\Delta T_i$ and $\Delta S_i$ are a set of T/S perturbations defined as the scalar product of the respective local T/S gradients with random walks $\mathbf{\xi}$:
+\begin{equation}
+ \label{eq:sto_pert}
+ \Delta T_i = \mathbf{\xi}_i \cdot \nabla T \qquad \hbox{and} \qquad \Delta S_i = \mathbf{\xi}_i \cdot \nabla S
+\end{equation}
+$\mathbf{\xi}_i$ are produced by a first-order autoregressive processes (AR-1) with a parametrized decorrelation time scale, and horizontal and vertical standard deviations $\sigma_s$. $\mathbf{\xi}$ are uncorrelated over the horizontal and fully correlated along the vertical.
+\section{Stochastic processes}
+\label{STO_the_details}
+The starting point of our implementation of stochastic parameterizations
+in NEMO is to observe that many existing parameterizations are based
+on autoregressive processes, which are used as a basic source of randomness
+to transform a deterministic model into a probabilistic model.
+A generic approach is thus to add one single new module in NEMO,
+generating processes with appropriate statistics
+to simulate each kind of uncertainty in the model
+(see \cite{Brankart_al_GMD2015} for more details).
+In practice, at every model grid point, independent Gaussian autoregressive
+processes~$\xi^{(i)},\,i=1,\ldots,m$ are first generated
+using the same basic equation:
+\begin{equation}
+\label{eq:autoreg}
+\xi^{(i)}_{k+1} = a^{(i)} \xi^{(i)}_k + b^{(i)} w^{(i)} + c^{(i)}
+\end{equation}
+\noindent
+where $k$ is the index of the model timestep; and
+$a^{(i)}$, $b^{(i)}$, $c^{(i)}$ are parameters defining
+the mean ($\mu^{(i)}$) standard deviation ($\sigma^{(i)}$)
+and correlation timescale ($\tau^{(i)}$) of each process:
+\begin{itemize}
+\item for order~1 processes, $w^{(i)}$ is a Gaussian white noise,
+with zero mean and standard deviation equal to~1, and the parameters
+$a^{(i)}$, $b^{(i)}$, $c^{(i)}$ are given by:
+\begin{equation}
+\label{eq:ord1}
+\left\{
+\begin{array}{l}
+a^{(i)} = \varphi \\
+b^{(i)} = \sigma^{(i)} \sqrt{ 1 - \varphi^2 }
+ \qquad\qquad\mbox{with}\qquad\qquad
+\varphi = \exp \left( - 1 / \tau^{(i)} \right) \\
+c^{(i)} = \mu^{(i)} \left( 1 - \varphi \right) \\
+\end{array}
+\right.
+\end{equation}
+\item for order~$n>1$ processes, $w^{(i)}$ is an order~$n-1$ autoregressive process,
+with zero mean, standard deviation equal to~$\sigma^{(i)}$; correlation timescale
+equal to~$\tau^{(i)}$; and the parameters
+$a^{(i)}$, $b^{(i)}$, $c^{(i)}$ are given by:
+\begin{equation}
+\label{eq:ord2}
+\left\{
+\begin{array}{l}
+a^{(i)} = \varphi \\
+b^{(i)} = \frac{n-1}{2(4n-3)} \sqrt{ 1 - \varphi^2 }
+ \qquad\qquad\mbox{with}\qquad\qquad
+\varphi = \exp \left( - 1 / \tau^{(i)} \right) \\
+c^{(i)} = \mu^{(i)} \left( 1 - \varphi \right) \\
+\end{array}
+\right.
+\end{equation}
+\end{itemize}
+\noindent
+In this way, higher order processes can be easily generated recursively using the same piece of code implementing Eq.~(\ref{eq:autoreg}), and using succesively processes from order $0$ to~$n-1$ as~$w^{(i)}$.
+The parameters in Eq.~(\ref{eq:ord2}) are computed so that this recursive application
+of Eq.~(\ref{eq:autoreg}) leads to processes with the required standard deviation
+and correlation timescale, with the additional condition that
+the $n-1$ first derivatives of the autocorrelation function
+are equal to zero at~$t=0$, so that the resulting processes
+become smoother and smoother as $n$ is increased.
+Overall, this method provides quite a simple and generic way of generating a wide class of stochastic processes. However, this also means that new model parameters are needed to specify each of these stochastic processes. As in any parameterization of lacking physics, a very important issues then to tune these new parameters using either first principles, model simulations, or real-world observations.
+\section{Implementation details}
+\label{STO_thech_details}
+The computer code implementing stochastic parametrisations is made of one single FORTRAN module,
+with 3 public routines to be called by the model (in our case, NEMO):
+The first routine ({sto\_par}) is a direct implementation of Eq.~(\ref{eq:autoreg}),
+applied at each model grid point (in 2D or 3D),
+and called at each model time step ($k$) to update
+every autoregressive process ($i=1,\ldots,m$).
+This routine also includes a filtering operator, applied to $w^{(i)}$,
+to introduce a spatial correlation between the stochastic processes.
+The second routine ({sto\_par\_init})
+is an initialization routine mainly dedicated
+to the computation of parameters $a^{(i)}, b^{(i)}, c^{(i)}$
+for each autoregressive process, as a function of the statistical properties
+required by the model user (mean, standard deviation, time correlation,
+order of the process,\ldots). Parameters for the processes can be specified through the following namelist parameters:
+\begin{alltt}
+\tiny
+\begin{verbatim}
+   nn_sto_eos = 1                ! number of independent random walks
+   rn_eos_stdxy = 1.4            ! random walk horz. standard deviation (in grid points)
+   rn_eos_stdz  = 0.7            ! random walk vert. standard deviation (in grid points)
+   rn_eos_tcor  = 1440.0         ! random walk time correlation (in timesteps)
+   nn_eos_ord  = 1               ! order of autoregressive processes
+   nn_eos_flt  = 0               ! passes of Laplacian filter
+   rn_eos_lim  = 2.0             ! limitation factor (default = 3.0)
+\end{verbatim}
+\end{alltt}
+This routine also includes the initialization (seeding)
+of the random number generator.
+The third routine ({sto\_rst\_write}) writes a ``restart file''
+with the current value of all autoregressive processes
+to allow restarting a simulation from where it has been interrupted.
+This file also contains the current state of the random number generator.
+In case of a restart, this file is then read by the initialization routine
+({sto\_par\_init}), so that the simulation can continue exactly
+as if it was not interrupted.
+Restart capabilities of the module are driven by the following namelist parameters:
+\begin{alltt}
+\tiny
+\begin{verbatim}
+   ln_rststo = .false.           ! start from mean parameter (F) or from restart file (T)
+   ln_rstseed = .true.           ! read seed of RNG from restart file
+   cn_storst_in  = "restart_sto" !  suffix of stochastic parameter restart file (input)
+   cn_storst_out = "restart_sto" !  suffix of stochastic parameter restart file (output)
+\end{verbatim}
+\end{alltt}
+In the particular case of the stochastic equation of state, there is also an additional module ({sto\_pts}) implementing Eq~\ref{eq:sto_pert} and specific piece of code in the equation of state implementing Eq~\ref{eq:eos_sto}.

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Chapters/Chap_TRA.tex

-                      r5102
+                      r6436
 % ================================================================
 % Chapter 1 � Ocean Tracers (TRA)
+% Chapter 1 ——— Ocean Tracers (TRA)
 % ================================================================
 \chapter{Ocean Tracers (TRA)}
 …
 (BBL) parametrisation, and an internal damping (DMP) term. The terms QSR,
 BBC, BBL and DMP are optional. The external forcings and parameterisations
 require complex inputs and complex calculations (e.g. bulk formulae, estimation
+require complex inputs and complex calculations ($e.g.$ bulk formulae, estimation
 of mixing coefficients) that are carried out in the SBC, LDF and ZDF modules and
 described in chapters \S\ref{SBC}, \S\ref{LDF} and  \S\ref{ZDF}, respectively.
+Note that \mdl{tranpc}, the non-penetrative convection module,  although
+(temporarily) located in the NEMO/OPA/TRA directory, is described with the
+model vertical physics (ZDF).
+%%%
+\gmcomment{change the position of eosbn2 in the reference code}
+%%%
+Note that \mdl{tranpc}, the non-penetrative convection module, although
+located in the NEMO/OPA/TRA directory as it directly modifies the tracer fields,
+is described with the model vertical physics (ZDF) together with other available
+parameterization of convection.
 In the present chapter we also describe the diagnostic equations used to compute
 the sea-water properties (density, Brunt-Vais\"{a}l\"{a} frequency, specific heat and
+the sea-water properties (density, Brunt-V\"{a}is\"{a}l\"{a} frequency, specific heat and
 freezing point with associated modules \mdl{eosbn2} and \mdl{phycst}).
 …
 found in the \textit{trattt} or \textit{trattt\_xxx} module, in the NEMO/OPA/TRA directory.
 The user has the option of extracting each tendency term on the rhs of the tracer
 equation for output (\key{trdtra} is defined), as described in Chap.~\ref{MISC}.
+The user has the option of extracting each tendency term on the RHS of the tracer
+equation for output (\np{ln\_tra\_trd} or \np{ln\_tra\_mxl}~=~true), as described in Chap.~\ref{DIA}.
 $\ $\newline    % force a new ligne
 …
 \end{description}
 In all cases, this boundary condition retains local conservation of tracer.
 Global conservation is obtained in both rigid-lid and non-linear free surface
+cases, but not in the linear free surface case. Nevertheless, in the latter
 case, it is achieved to a good approximation since the non-conservative
+Global conservation is obtained in non-linear free surface case,
+but \textit{not} in the linear free surface case. Nevertheless, in the latter case,
+it is achieved to a good approximation since the non-conservative
 term is the product of the time derivative of the tracer and the free surface
 height, two quantities that are not correlated (see \S\ref{PE_free_surface},
 …
 The velocity field that appears in (\ref{Eq_tra_adv}) and (\ref{Eq_tra_adv_zco})
+is the centred (\textit{now}) \textit{eulerian} ocean velocity (see Chap.~\ref{DYN}).
+When eddy induced velocity (\textit{eiv}) parameterisation is used it is the \textit{now}
+\textit{effective} velocity ($i.e.$ the sum of the eulerian and eiv velocities) which is used.
+is the centred (\textit{now}) \textit{effective} ocean velocity, $i.e.$ the \textit{eulerian} velocity
+(see Chap.~\ref{DYN}) plus the eddy induced velocity (\textit{eiv})
+and/or the mixed layer eddy induced velocity (\textit{eiv})
+when those parameterisations are used (see Chap.~\ref{LDF}).
 The choice of an advection scheme is made in the \textit{\ngn{nam\_traadv}} namelist, by
 …
 Note that
 (1) cen2, cen4 and TVD schemes require an explicit diffusion
+(1) cen2 and TVD schemes require an explicit diffusion
 operator while the other schemes are diffusive enough so that they do not
 require additional diffusion ;
 (2) cen2, cen4, MUSCL2, and UBS are not \textit{positive} schemes
+(2) cen2, MUSCL2, and UBS are not \textit{positive} schemes
 \footnote{negative values can appear in an initially strictly positive tracer field
 which is advected}
 …
 temperature is close to the freezing point).
 This combined scheme has been included for specific grid points in the ORCA2
 and ORCA4 configurations only. This is an obsolescent feature as the recommended
+configuration only. This is an obsolescent feature as the recommended
 advection scheme for the ORCA configuration is TVD (see  \S\ref{TRA_adv_tvd}).
 …
 have this order of accuracy. \gmcomment{Note also that ... blah, blah}
-% -------------------------------------------------------------------------------------------------------------
-%        4nd order centred scheme
-% -------------------------------------------------------------------------------------------------------------
-\subsection   [$4^{nd}$ order centred scheme (cen4) (\np{ln\_traadv\_cen4})]
-           {$4^{nd}$ order centred scheme (cen4) (\np{ln\_traadv\_cen4}=true)}
-\label{TRA_adv_cen4}
-In the $4^{th}$ order formulation (to be implemented), tracer values are
-evaluated at velocity points as a $4^{th}$ order interpolation, and thus depend on
-the four neighbouring $T$-points. For example, in the $i$-direction:
-\begin{equation} \label{Eq_tra_adv_cen4}
-\tau _u^{cen4}
-=\overline{   T - \frac{1}{6}\,\delta _i \left[ \delta_{i+1/2}[T] \,\right]   }^{\,i+1/2}
-\end{equation}
-Strictly speaking, the cen4 scheme is not a $4^{th}$ order advection scheme
-but a $4^{th}$ order evaluation of advective fluxes, since the divergence of
-advective fluxes \eqref{Eq_tra_adv} is kept at $2^{nd}$ order. The phrase ``$4^{th}$
-order scheme'' used in oceanographic literature is usually associated
-with the scheme presented here. Introducing a \textit{true} $4^{th}$ order advection
-scheme is feasible but, for consistency reasons, it requires changes in the
-discretisation of the tracer advection together with changes in both the
-continuity equation and the momentum advection terms.
-A direct consequence of the pseudo-fourth order nature of the scheme is that
-it is not non-diffusive, i.e. the global variance of a tracer is not preserved using
-\textit{cen4}. Furthermore, it must be used in conjunction with an explicit
-diffusion operator to produce a sensible solution. The time-stepping is also
-performed using a leapfrog scheme in conjunction with an Asselin time-filter,
-so $T$ in (\ref{Eq_tra_adv_cen4}) is the \textit{now} tracer.
-At a $T$-grid cell adjacent to a boundary (coastline, bottom and surface), an
-additional hypothesis must be made to evaluate $\tau _u^{cen4}$. This
-hypothesis usually reduces the order of the scheme. Here we choose to set
-the gradient of $T$ across the boundary to zero. Alternative conditions can be
-specified, such as a reduction to a second order scheme for these near boundary
-grid points.
 % -------------------------------------------------------------------------------------------------------------
 …
 used for the diffusive part.
+An additional option has been added controlled by \np{ln\_traadv\_tvd\_zts}.
+By setting this logical to true, a TVD scheme is used on both horizontal and vertical direction,
+but on the latter, a split-explicit time stepping is used, with 5 sub-timesteps.
+This option can be useful when the value of the timestep is limited by vertical advection \citep{Lemarie_OM2015}.
+Note that in this case, a similar split-explicit time stepping should be used on
+vertical advection of momentum to ensure a better stability (see \np{ln\_dynzad\_zts} in \S\ref{DYN_zad}).
 % -------------------------------------------------------------------------------------------------------------
 %        MUSCL scheme
 …
 For an ocean grid point adjacent to land and where the ocean velocity is
+directed toward land, two choices are available: an upstream flux
+(\np{ln\_traadv\_muscl}=true) or a second order flux
+(\np{ln\_traadv\_muscl2}=true). Note that the latter choice does not ensure
+the \textit{positive} character of the scheme. Only the former can be used
+on both active and passive tracers. The two MUSCL schemes are implemented
+in the \mdl{traadv\_tvd} and \mdl{traadv\_tvd2} modules.
+directed toward land, two choices are available: an upstream flux (\np{ln\_traadv\_muscl}=true)
+or a second order flux (\np{ln\_traadv\_muscl2}=true).
+Note that the latter choice does not ensure the \textit{positive} character of the scheme.
+Only the former can be used on both active and passive tracers.
+The two MUSCL schemes are implemented in the \mdl{traadv\_tvd} and \mdl{traadv\_tvd2} modules.
+Note that when using np{ln\_traadv\_msc\_ups}~=~true in addition to \np{ln\_traadv\_muscl}=true,
+the MUSCL fluxes are replaced by upstream fluxes in vicinity of river mouths.
 % -------------------------------------------------------------------------------------------------------------
 …
 direction (as for the UBS case) should be implemented to restore this property.
-% -------------------------------------------------------------------------------------------------------------
-%        PPM scheme
-% -------------------------------------------------------------------------------------------------------------
-\subsection   [Piecewise Parabolic Method (PPM) (\np{ln\_traadv\_ppm})]
-         {Piecewise Parabolic Method (PPM) (\np{ln\_traadv\_ppm}=true)}
-\label{TRA_adv_ppm}
-The Piecewise Parabolic Method (PPM) proposed by Colella and Woodward (1984)
-\sgacomment{reference?}
-is based on a quadradic piecewise construction. Like the QCK scheme, it is associated
-with the ULTIMATE QUICKEST limiter \citep{Leonard1991}. It has been implemented
-in \NEMO by G. Reffray (MERCATOR-ocean) but is not yet offered in the reference
-version 3.3.
 % ================================================================
 …
 surfaces is given by:
 \begin{equation} \label{Eq_tra_ldf_lap}
 D_T^{lT} =\frac{1}{b_tT} \left( \;
+D_T^{lT} =\frac{1}{b_t} \left( \;
    \delta _{i}\left[ A_u^{lT} \; \frac{e_{2u}\,e_{3u}}{e_{1u}} \;\delta _{i+1/2} [T] \right]
 + \delta _{j}\left[ A_v^{lT} \;  \frac{e_{1v}\,e_{3v}}{e_{2v}} \;\delta _{j+1/2} [T] \right]  \;\right)
 …
 the thickness of the top model layer.
+Due to interactions and mass exchange of water ($F_{mass}$) with other Earth system components ($i.e.$ atmosphere, sea-ice, land),
+the change in the heat and salt content of the surface layer of the ocean is due both
+to the heat and salt fluxes crossing the sea surface (not linked with $F_{mass}$)
+ and to the heat and salt content of the mass exchange.
+\sgacomment{ the following does not apply to the release to which this documentation is
+attached and so should not be included ....
+In a forthcoming release, these two parts, computed in the surface module (SBC), will be included directly
+in $Q_{ns}$, the surface heat flux and $F_{salt}$, the surface salt flux.
+The specification of these fluxes is further detailed in the SBC chapter (see \S\ref{SBC}).
+This change will provide a forcing formulation which is the same for any tracer (including temperature and salinity).
+In the current version, the situation is a little bit more complicated. }
+Due to interactions and mass exchange of water ($F_{mass}$) with other Earth system components
+($i.e.$ atmosphere, sea-ice, land), the change in the heat and salt content of the surface layer
+of the ocean is due both to the heat and salt fluxes crossing the sea surface (not linked with $F_{mass}$)
+and to the heat and salt content of the mass exchange. They are both included directly in $Q_{ns}$,
+the surface heat flux, and $F_{salt}$, the surface salt flux (see \S\ref{SBC} for further details).
+By doing this, the forcing formulation is the same for any tracer (including temperature and salinity).
 The surface module (\mdl{sbcmod}, see \S\ref{SBC}) provides the following
 …
 $\bullet$ $Q_{ns}$, the non-solar part of the net surface heat flux that crosses the sea surface
 (i.e. the difference between the total surface heat flux and the fraction of the short wave flux that
+penetrates into the water column, see \S\ref{TRA_qsr})
+$\bullet$ \textit{emp}, the mass flux exchanged with the atmosphere (evaporation minus precipitation)
+$\bullet$ $\textit{emp}_S$, an equivalent mass flux taking into account the effect of ice-ocean mass exchange
+$\bullet$ \textit{rnf}, the mass flux associated with runoff (see \S\ref{SBC_rnf} for further detail of how it acts on temperature and salinity tendencies)
+The $\textit{emp}_S$ field is not simply the budget of evaporation-precipitation+freezing-melting because
+the sea-ice is not currently embedded in the ocean but levitates above it. There is no mass
+exchanged between the sea-ice and the ocean. Instead we only take into account the salt
+flux associated with the non-zero salinity of sea-ice, and the concentration/dilution effect
+due to the freezing/melting (F/M) process. These two parts of the forcing are then converted into
+an equivalent mass flux given by $\textit{emp}_S - \textit{emp}$. As a result of this mess,
+the surface boundary condition on temperature and salinity is applied as follows:
+In the nonlinear free surface case (\key{vvl} is defined):
+penetrates into the water column, see \S\ref{TRA_qsr}) plus the heat content associated with
+of the mass exchange with the atmosphere and lands.
+$\bullet$ $\textit{sfx}$, the salt flux resulting from ice-ocean mass exchange (freezing, melting, ridging...)
+$\bullet$ \textit{emp}, the mass flux exchanged with the atmosphere (evaporation minus precipitation)
+ and possibly with the sea-ice and ice-shelves.
+$\bullet$ \textit{rnf}, the mass flux associated with runoff
+(see \S\ref{SBC_rnf} for further detail of how it acts on temperature and salinity tendencies)
+$\bullet$ \textit{fwfisf}, the mass flux associated with ice shelf melt, (see \S\ref{SBC_isf} for further details
+on how the ice shelf melt is computed and applied).\\
+In the non-linear free surface case (\key{vvl} is defined), the surface boundary condition
+on temperature and salinity is applied as follows:
 \begin{equation} \label{Eq_tra_sbc}
+\begin{aligned}
+ &F^T = \frac{ 1 }{\rho _o \;C_p \,\left. e_{3t} \right|_{k=1} }  &\overline{ Q_{ns}       }^t  & \\
+& F^S =\frac{ 1 }{\rho _o  \,      \left. e_{3t} \right|_{k=1} }  &\overline{ \textit{sfx} }^t   & \\
+ \end{aligned}
+\end{equation}
+where $\overline{x }^t$ means that $x$ is averaged over two consecutive time steps
+($t-\rdt/2$ and $t+\rdt/2$). Such time averaging prevents the
+divergence of odd and even time step (see \S\ref{STP}).
+In the linear free surface case (\key{vvl} is \textit{not} defined),
+an additional term has to be added on both temperature and salinity.
+On temperature, this term remove the heat content associated with mass exchange
+that has been added to $Q_{ns}$. On salinity, this term mimics the concentration/dilution effect that
+would have resulted from a change in the volume of the first level.
+The resulting surface boundary condition is applied as follows:
+\begin{equation} \label{Eq_tra_sbc_lin}
 \begin{aligned}
  &F^T = \frac{ 1 }{\rho _o \;C_p \,\left. e_{3t} \right|_{k=1} }
 …
+%
 & F^S =\frac{ 1 }{\rho _o \,\left. e_{3t} \right|_{k=1} }
            &\overline{ \left( (\textit{emp}_S - \textit{emp})\;\left. S \right|_{k=1}  \right) }^t   & \\
+           &\overline{ \left( \;\textit{sfx} - \textit{emp} \;\left. S \right|_{k=1}  \right) }^t   & \\
  \end{aligned}
 \end{equation}
+In the linear free surface case (\key{vvl} not defined):
+\begin{equation} \label{Eq_tra_sbc_lin}
+\begin{aligned}
+ &F^T = \frac{ 1 }{\rho _o \;C_p \,\left. e_{3t} \right|_{k=1} }  &\overline{ Q_{ns} }^t  & \\
+%
+& F^S =\frac{ 1 }{\rho _o \,\left. e_{3t} \right|_{k=1} }
+           &\overline{ \left( \textit{emp}_S\;\left. S \right|_{k=1}  \right) }^t   & \\
+ \end{aligned}
+\end{equation}
+where $\overline{x }^t$ means that $x$ is averaged over two consecutive time steps
+($t-\rdt/2$ and $t+\rdt/2$). Such time averaging prevents the
+divergence of odd and even time step (see \S\ref{STP}).
+The two set of equations, \eqref{Eq_tra_sbc} and \eqref{Eq_tra_sbc_lin}, are obtained
+by assuming that the temperature of precipitation and evaporation are equal to
+the ocean surface temperature and that their salinity is zero. Therefore, the heat content
+of the \textit{emp} budget must be added to the temperature equation in the variable volume case,
+while it does not appear in the constant volume case. Similarly, the \textit{emp} budget affects
+the ocean surface salinity in the constant volume case (through the concentration dilution effect)
+while it does not appears explicitly in the variable volume case since salinity change will be
+induced by volume change. In both constant and variable volume cases, surface salinity
+will change with ice-ocean salt flux and F/M flux (both contained in $\textit{emp}_S - \textit{emp}$) without mass exchanges.
+Note that the concentration/dilution effect due to F/M is computed using
+a constant ice salinity as well as a constant ocean salinity.
+This approximation suppresses the correlation between \textit{SSS}
+and F/M flux, allowing the ice-ocean salt exchanges to be conservative.
+Indeed, if this approximation is not made, even if the F/M budget is zero
+on average over the whole ocean domain and over the seasonal cycle,
+the associated salt flux is not zero, since sea-surface salinity and F/M flux are
+intrinsically correlated (high \textit{SSS} are found where freezing is
+strong whilst low \textit{SSS} is usually associated with high melting areas).
+Even using this approximation, an exact conservation of heat and salt content
+is only achieved in the variable volume case. In the constant volume case,
+there is a small imbalance associated with the product $(\partial_t\eta - \textit{emp}) * \textit{SSS}$.
+Nevertheless, the salt content variation is quite small and will not induce
+a long term drift as there is no physical reason for $(\partial_t\eta - \textit{emp})$
+and \textit{SSS} to be correlated \citep{Roullet_Madec_JGR00}.
+Note that, while quite small, the imbalance in the constant volume case is larger
+Note that an exact conservation of heat and salt content is only achieved with non-linear free surface.
+In the linear free surface case, there is a small imbalance. The imbalance is larger
 than the imbalance associated with the Asselin time filter \citep{Leclair_Madec_OM09}.
 This is the reason why the modified filter is not applied in the constant volume case.
+This is the reason why the modified filter is not applied in the linear free surface case (see \S\ref{STP}).
 % -------------------------------------------------------------------------------------------------------------
 …
 ($i.e.$ the inverses of the extinction length scales) are tabulated over 61 nonuniform
 chlorophyll classes ranging from 0.01 to 10 g.Chl/L (see the routine \rou{trc\_oce\_rgb}
+in \mdl{trc\_oce} module). Three types of chlorophyll can be chosen in the RGB formulation:
+(1) a constant 0.05 g.Chl/L value everywhere (\np{nn\_chdta}=0) ; (2) an observed
+time varying chlorophyll (\np{nn\_chdta}=1) ; (3) simulated time varying chlorophyll
+by TOP biogeochemical model (\np{ln\_qsr\_bio}=true). In the latter case, the RGB
+formulation is used to calculate both the phytoplankton light limitation in PISCES
+or LOBSTER and the oceanic heating rate.
+in \mdl{trc\_oce} module). Four types of chlorophyll can be chosen in the RGB formulation:
+\begin{description}
+\item[\np{nn\_chdta}=0]
+a constant 0.05 g.Chl/L value everywhere ;
+\item[\np{nn\_chdta}=1]
+an observed time varying chlorophyll deduced from satellite surface ocean color measurement
+spread uniformly in the vertical direction ;
+\item[\np{nn\_chdta}=2]
+same as previous case except that a vertical profile of chlorophyl is used.
+Following \cite{Morel_Berthon_LO89}, the profile is computed from the local surface chlorophyll value ;
+\item[\np{ln\_qsr\_bio}=true]
+simulated time varying chlorophyll by TOP biogeochemical model.
+In this case, the RGB formulation is used to calculate both the phytoplankton
+light limitation in PISCES or LOBSTER and the oceanic heating rate.
+\end{description}
 The trend in \eqref{Eq_tra_qsr} associated with the penetration of the solar radiation
 is added to the temperature trend, and the surface heat flux is modified in routine \mdl{traqsr}.
 …
 \label{TRA_bbc}
 %--------------------------------------------nambbc--------------------------------------------------------
 \namdisplay{namtra_bbc}
+\namdisplay{nambbc}
 %--------------------------------------------------------------------------------------------------------------
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 …
 \subsection[DMP\_TOOLS]{Generating resto.nc using DMP\_TOOLS}
+DMP\_TOOLS can be used to generate a netcdf file containing the restoration coefficient $\gamma$. Note that in order to maintain bit comparison with previous NEMO versions DMP\_TOOLS must be compiled and run on the same machine as the NEMO model. A mesh\_mask.nc file for the model configuration is required as an input. This can be generated by carrying out a short model run with the namelist parameter \np{nn\_msh} set to 1. The namelist parameter \np{ln\_tradmp} will also need to be set to .false. for this to work. The \nl{nam\_dmp\_create} namelist in the DMP\_TOOLS directory is used to specify options for the restoration coefficient.
+DMP\_TOOLS can be used to generate a netcdf file containing the restoration coefficient $\gamma$.
+Note that in order to maintain bit comparison with previous NEMO versions DMP\_TOOLS must be compiled
+and run on the same machine as the NEMO model. A mesh\_mask.nc file for the model configuration is required as an input.
+This can be generated by carrying out a short model run with the namelist parameter \np{nn\_msh} set to 1.
+The namelist parameter \np{ln\_tradmp} will also need to be set to .false. for this to work.
+The \nl{nam\_dmp\_create} namelist in the DMP\_TOOLS directory is used to specify options for the restoration coefficient.
 %--------------------------------------------nam_dmp_create-------------------------------------------------
 …
 \np{cp\_cfg}, \np{cp\_cpz}, \np{jp\_cfg} and \np{jperio} specify the model configuration being used and should be the same as specified in \nl{namcfg}. The variable \nl{lzoom} is used to specify that the damping is being used as in case \textit{a} above to provide boundary conditions to a zoom configuration. In the case of the arctic or antarctic zoom configurations this includes some specific treatment. Otherwise damping is applied to the 6 grid points along the ocean boundaries. The open boundaries are specified by the variables \np{lzoom\_n}, \np{lzoom\_e}, \np{lzoom\_s}, \np{lzoom\_w} in the \nl{nam\_zoom\_dmp} name list.
+The remaining switch namelist variables determine the spatial variation of the restoration coefficient in non-zoom configurations. \np{ln\_full\_field} specifies that newtonian damping should be applied to the whole model domain. \np{ln\_med\_red\_seas} specifies grid specific restoration coefficients in the Mediterranean Sea for the ORCA4, ORCA2 and ORCA05 configurations. If \np{ln\_old\_31\_lev\_code} is set then the depth variation of the coeffients will be specified as a function of the model number. This option is included to allow backwards compatability of the ORCA2 reference configurations with previous model versions. \np{ln\_coast} specifies that the restoration coefficient should be reduced near to coastlines. This option only has an effect if \np{ln\_full\_field} is true. \np{ln\_zero\_top\_layer} specifies that the restoration coefficient should be zero in the surface layer. Finally \np{ln\_custom} specifies that the custom module will be called. This module is contained in the file custom.F90 and can be edited by users. For example damping could be applied in a specific region.
+The restoration coefficient can be set to zero in equatorial regions by specifying a positive value of \np{nn\_hdmp}. Equatorward of this latitude the restoration coefficient will be zero with a smooth transition to the full values of a 10$^{\circ}$ latitud band. This is often used because of the short adjustment time scale in the equatorial region \citep{Reverdin1991, Fujio1991, Marti_PhD92}. The time scale associated with the damping depends on the depth as a hyperbolic tangent, with \np{rn\_surf} as surface value, \np{rn\_bot} as bottom value and a transition depth of \np{rn\_dep}.
+The remaining switch namelist variables determine the spatial variation of the restoration coefficient in non-zoom configurations.
+\np{ln\_full\_field} specifies that newtonian damping should be applied to the whole model domain.
+\np{ln\_med\_red\_seas} specifies grid specific restoration coefficients in the Mediterranean Sea
+for the ORCA4, ORCA2 and ORCA05 configurations.
+If \np{ln\_old\_31\_lev\_code} is set then the depth variation of the coeffients will be specified as
+a function of the model number. This option is included to allow backwards compatability of the ORCA2 reference
+configurations with previous model versions.
+\np{ln\_coast} specifies that the restoration coefficient should be reduced near to coastlines.
+This option only has an effect if \np{ln\_full\_field} is true.
+\np{ln\_zero\_top\_layer} specifies that the restoration coefficient should be zero in the surface layer.
+Finally \np{ln\_custom} specifies that the custom module will be called.
+This module is contained in the file custom.F90 and can be edited by users. For example damping could be applied in a specific region.
+The restoration coefficient can be set to zero in equatorial regions by specifying a positive value of \np{nn\_hdmp}.
+Equatorward of this latitude the restoration coefficient will be zero with a smooth transition to
+the full values of a 10$^{\circ}$ latitud band.
+This is often used because of the short adjustment time scale in the equatorial region
+\citep{Reverdin1991, Fujio1991, Marti_PhD92}. The time scale associated with the damping depends on the depth as a
+hyperbolic tangent, with \np{rn\_surf} as surface value, \np{rn\_bot} as bottom value and a transition depth of \np{rn\_dep}.
 % ================================================================
 …
 %        Equation of State
 % -------------------------------------------------------------------------------------------------------------
 \subsection{Equation of State (\np{nn\_eos} = 0, 1 or 2)}
+\subsection{Equation Of Seawater (\np{nn\_eos} = -1, 0, or 1)}
 \label{TRA_eos}
+It is necessary to know the equation of state for the ocean very accurately
+to determine stability properties (especially the Brunt-Vais\"{a}l\"{a} frequency),
+particularly in the deep ocean. The ocean seawater volumic mass, $\rho$,
+abusively called density, is a non linear empirical function of \textit{in situ}
+temperature, salinity and pressure. The reference equation of state is that
+defined by the Joint Panel on Oceanographic Tables and Standards
+\citep{UNESCO1983}. It was the standard equation of state used in early
+releases of OPA. However, even though this computation is fully vectorised,
+it is quite time consuming ($15$ to $20${\%} of the total CPU time) since
+it requires the prior computation of the \textit{in situ} temperature from the
+model \textit{potential} temperature using the \citep{Bryden1973} polynomial
+for adiabatic lapse rate and a $4^th$ order Runge-Kutta integration scheme.
+Since OPA6, we have used the \citet{JackMcD1995} equation of state for
+seawater instead. It allows the computation of the \textit{in situ} ocean density
+directly as a function of \textit{potential} temperature relative to the surface
+(an \NEMO variable), the practical salinity (another \NEMO variable) and the
+pressure (assuming no pressure variation along geopotential surfaces, $i.e.$
+the pressure in decibars is approximated by the depth in meters).
+Both the \citet{UNESCO1983} and \citet{JackMcD1995} equations of state
+have exactly the same except that the values of the various coefficients have
+been adjusted by \citet{JackMcD1995} in order to directly use the \textit{potential}
+temperature instead of the \textit{in situ} one. This reduces the CPU time of the
+\textit{in situ} density computation to about $3${\%} of the total CPU time,
+while maintaining a quite accurate equation of state.
+In the computer code, a \textit{true} density anomaly, $d_a= \rho / \rho_o - 1$,
+is computed, with $\rho_o$ a reference volumic mass. Called \textit{rau0}
+in the code, $\rho_o$ is defined in \mdl{phycst}, and a value of $1,035~Kg/m^3$.
+The Equation Of Seawater (EOS) is an empirical nonlinear thermodynamic relationship
+linking seawater density, $\rho$, to a number of state variables,
+most typically temperature, salinity and pressure.
+Because density gradients control the pressure gradient force through the hydrostatic balance,
+the equation of state provides a fundamental bridge between the distribution of active tracers
+and the fluid dynamics. Nonlinearities of the EOS are of major importance, in particular
+influencing the circulation through determination of the static stability below the mixed layer,
+thus controlling rates of exchange between the atmosphere  and the ocean interior \citep{Roquet_JPO2015}.
+Therefore an accurate EOS based on either the 1980 equation of state (EOS-80, \cite{UNESCO1983})
+or TEOS-10 \citep{TEOS10} standards should be used anytime a simulation of the real
+ocean circulation is attempted \citep{Roquet_JPO2015}.
+The use of TEOS-10 is highly recommended because
+\textit{(i)} it is the new official EOS,
+\textit{(ii)} it is more accurate, being based on an updated database of laboratory measurements, and
+\textit{(iii)} it uses Conservative Temperature and Absolute Salinity (instead of potential temperature
+and practical salinity for EOS-980, both variables being more suitable for use as model variables
+\citep{TEOS10, Graham_McDougall_JPO13}.
+EOS-80 is an obsolescent feature of the NEMO system, kept only for backward compatibility.
+For process studies, it is often convenient to use an approximation of the EOS. To that purposed,
+a simplified EOS (S-EOS) inspired by \citet{Vallis06} is also available.
+In the computer code, a density anomaly, $d_a= \rho / \rho_o - 1$,
+is computed, with $\rho_o$ a reference density. Called \textit{rau0}
+in the code, $\rho_o$ is set in \mdl{phycst} to a value of $1,026~Kg/m^3$.
 This is a sensible choice for the reference density used in a Boussinesq ocean
 climate model, as, with the exception of only a small percentage of the ocean,
+density in the World Ocean varies by no more than 2$\%$ from $1,035~kg/m^3$
+\citep{Gill1982}.
+Options are defined through the  \ngn{nameos} namelist variables.
+The default option (namelist parameter \np{nn\_eos}=0) is the \citet{JackMcD1995}
+equation of state. Its use is highly recommended. However, for process studies,
+it is often convenient to use a linear approximation of the density.
+density in the World Ocean varies by no more than 2$\%$ from that value \citep{Gill1982}.
+Options are defined through the  \ngn{nameos} namelist variables, and in particular \np{nn\_eos}
+which controls the EOS used (=-1 for TEOS10 ; =0 for EOS-80 ; =1 for S-EOS).
+\begin{description}
+\item[\np{nn\_eos}$=-1$] the polyTEOS10-bsq equation of seawater \citep{Roquet_OM2015} is used.
+The accuracy of this approximation is comparable to the TEOS-10 rational function approximation,
+but it is optimized for a boussinesq fluid and the polynomial expressions have simpler
+and more computationally efficient expressions for their derived quantities
+which make them more adapted for use in ocean models.
+Note that a slightly higher precision polynomial form is now used replacement of the TEOS-10
+rational function approximation for hydrographic data analysis  \citep{TEOS10}.
+A key point is that conservative state variables are used:
+Absolute Salinity (unit: g/kg, notation: $S_A$) and Conservative Temperature (unit: $\degres C$, notation: $\Theta$).
+The pressure in decibars is approximated by the depth in meters.
+With TEOS10, the specific heat capacity of sea water, $C_p$, is a constant. It is set to
+$C_p=3991.86795711963~J\,Kg^{-1}\,\degres K^{-1}$, according to \citet{TEOS10}.
+Choosing polyTEOS10-bsq implies that the state variables used by the model are
+$\Theta$ and $S_A$. In particular, the initial state deined by the user have to be given as
+\textit{Conservative} Temperature and \textit{Absolute} Salinity.
+In addition, setting \np{ln\_useCT} to \textit{true} convert the Conservative SST to potential SST
+prior to either computing the air-sea and ice-sea fluxes (forced mode)
+or sending the SST field to the atmosphere (coupled mode).
+\item[\np{nn\_eos}$=0$] the polyEOS80-bsq equation of seawater is used.
+It takes the same polynomial form as the polyTEOS10, but the coefficients have been optimized
+to accurately fit EOS80 (Roquet, personal comm.). The state variables used in both the EOS80
+and the ocean model are:
+the Practical Salinity ((unit: psu, notation: $S_p$)) and Potential Temperature (unit: $\degres C$, notation: $\theta$).
+The pressure in decibars is approximated by the depth in meters.
+With thsi EOS, the specific heat capacity of sea water, $C_p$, is a function of temperature,
+salinity and pressure \citep{UNESCO1983}. Nevertheless, a severe assumption is made in order to
+have a heat content ($C_p T_p$) which is conserved by the model: $C_p$ is set to a constant
+value, the TEOS10 value.
+\item[\np{nn\_eos}$=1$] a simplified EOS (S-EOS) inspired by \citet{Vallis06} is chosen,
+the coefficients of which has been optimized to fit the behavior of TEOS10 (Roquet, personal comm.)
+(see also \citet{Roquet_JPO2015}). It provides a simplistic linear representation of both
+cabbeling and thermobaricity effects which is enough for a proper treatment of the EOS
+in theoretical studies \citep{Roquet_JPO2015}.
 With such an equation of state there is no longer a distinction between
+\textit{in situ} and \textit{potential} density and both cabbeling and thermobaric
+effects are removed.
+Two linear formulations are available: a function of $T$ only (\np{nn\_eos}=1)
+and a function of both $T$ and $S$ (\np{nn\_eos}=2):
+\begin{equation} \label{Eq_tra_eos_linear}
+\textit{conservative} and \textit{potential} temperature, as well as between \textit{absolute}
+and \textit{practical} salinity.
+S-EOS takes the following expression:
+\begin{equation} \label{Eq_tra_S-EOS}
 \begin{split}
+  d_a(T)       &=  \rho (T)      /  \rho_o   - 1     =  \  0.0285         -  \alpha   \;T     \\
+  d_a(T,S)    &=  \rho (T,S)   /  \rho_o   - 1     =  \  \beta \; S       -  \alpha   \;T
+  d_a(T,S,z)  =  ( & - a_0 \; ( 1 + 0.5 \; \lambda_1 \; T_a + \mu_1 \; z ) * T_a  \\
+                                & + b_0 \; ( 1 - 0.5 \; \lambda_2 \; S_a - \mu_2 \; z ) * S_a  \\
+                                & - \nu \; T_a \; S_a \;  ) \; / \; \rho_o                     \\
+  with \ \  T_a = T-10  \; ;  & \;  S_a = S-35  \; ;\;  \rho_o = 1026~Kg/m^3
 \end{split}
 \end{equation}
+where $\alpha$ and $\beta$ are the thermal and haline expansion
+coefficients, and $\rho_o$, the reference volumic mass, $rau0$.
+($\alpha$ and $\beta$ can be modified through the \np{rn\_alpha} and
+\np{rn\_beta} namelist variables). Note that when $d_a$ is a function
+of $T$ only (\np{nn\_eos}=1), the salinity is a passive tracer and can be
+used as such.
+% -------------------------------------------------------------------------------------------------------------
+%        Brunt-Vais\"{a}l\"{a} Frequency
+% -------------------------------------------------------------------------------------------------------------
+\subsection{Brunt-Vais\"{a}l\"{a} Frequency (\np{nn\_eos} = 0, 1 or 2)}
+where the computer name of the coefficients as well as their standard value are given in \ref{Tab_SEOS}.
+In fact, when choosing S-EOS, various approximation of EOS can be specified simply by changing
+the associated coefficients.
+Setting to zero the two thermobaric coefficients ($\mu_1$, $\mu_2$) remove thermobaric effect from S-EOS.
+setting to zero the three cabbeling coefficients ($\lambda_1$, $\lambda_2$, $\nu$) remove cabbeling effect from S-EOS.
+Keeping non-zero value to $a_0$ and $b_0$ provide a linear EOS function of T and S.
+\end{description}
+%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+\begin{table}[!tb]
+\begin{center} \begin{tabular}{|p{26pt}|p{72pt}|p{56pt}|p{136pt}|}
+\hline
+coeff.   & computer name   & S-EOS     &  description                      \\ \hline
+$a_0$       & \np{rn\_a0}     & 1.6550 $10^{-1}$ &  linear thermal expansion coeff.    \\ \hline
+$b_0$       & \np{rn\_b0}     & 7.6554 $10^{-1}$ &  linear haline  expansion coeff.    \\ \hline
+$\lambda_1$ & \np{rn\_lambda1}& 5.9520 $10^{-2}$ &  cabbeling coeff. in $T^2$          \\ \hline
+$\lambda_2$ & \np{rn\_lambda2}& 5.4914 $10^{-4}$ &  cabbeling coeff. in $S^2$       \\ \hline
+$\nu$       & \np{rn\_nu}     & 2.4341 $10^{-3}$ &  cabbeling coeff. in $T \, S$       \\ \hline
+$\mu_1$     & \np{rn\_mu1}    & 1.4970 $10^{-4}$ &  thermobaric coeff. in T         \\ \hline
+$\mu_2$     & \np{rn\_mu2}    & 1.1090 $10^{-5}$ &  thermobaric coeff. in S            \\ \hline
+\end{tabular}
+\caption{ \label{Tab_SEOS}
+Standard value of S-EOS coefficients. }
+\end{center}
+\end{table}
+%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+% -------------------------------------------------------------------------------------------------------------
+%        Brunt-V\"{a}is\"{a}l\"{a} Frequency
+% -------------------------------------------------------------------------------------------------------------
+\subsection{Brunt-V\"{a}is\"{a}l\"{a} Frequency (\np{nn\_eos} = 0, 1 or 2)}
 \label{TRA_bn2}
+An accurate computation of the ocean stability (i.e. of $N$, the brunt-Vais\"{a}l\"{a}
+ frequency) is of paramount importance as it is used in several ocean
+ parameterisations (namely TKE, KPP, Richardson number dependent
+ vertical diffusion, enhanced vertical diffusion, non-penetrative convection,
+ iso-neutral diffusion). In particular, one must be aware that $N^2$ has to
+ be computed with an \textit{in situ} reference. The expression for $N^2$
+ depends on the type of equation of state used (\np{nn\_eos} namelist parameter).
+For \np{nn\_eos}=0 (\citet{JackMcD1995} equation of state), the \citet{McDougall1987}
+polynomial expression is used (with the pressure in decibar approximated by
+the depth in meters):
+An accurate computation of the ocean stability (i.e. of $N$, the brunt-V\"{a}is\"{a}l\"{a}
+ frequency) is of paramount importance as determine the ocean stratification and
+ is used in several ocean parameterisations (namely TKE, GLS, Richardson number dependent
+ vertical diffusion, enhanced vertical diffusion, non-penetrative convection, tidal mixing
+ parameterisation, iso-neutral diffusion). In particular, $N^2$ has to be computed at the local pressure
+ (pressure in decibar being approximated by the depth in meters). The expression for $N^2$
+ is given by:
 \begin{equation} \label{Eq_tra_bn2}
-N^2 = \frac{g}{e_{3w}} \; \beta   \
-      \left(  \alpha / \beta \ \delta_{k+1/2}[T]     - \delta_{k+1/2}[S]   \right)
-\end{equation}
-where $\alpha$ and $\beta$ are the thermal and haline expansion coefficients.
-They are a function of  $\overline{T}^{\,k+1/2},\widetilde{S}=\overline{S}^{\,k+1/2} - 35.$,
-and  $z_w$, with $T$ the \textit{potential} temperature and $\widetilde{S}$ a salinity anomaly.
-Note that both $\alpha$ and $\beta$ depend on \textit{potential}
-temperature and salinity which are averaged at $w$-points prior
-to the computation instead of being computed at $T$-points and
-then averaged to $w$-points.
-When a linear equation of state is used (\np{nn\_eos}=1 or 2,
-\eqref{Eq_tra_bn2} reduces to:
-\begin{equation} \label{Eq_tra_bn2_linear}
 N^2 = \frac{g}{e_{3w}} \left(   \beta \;\delta_{k+1/2}[S] - \alpha \;\delta_{k+1/2}[T]   \right)
 \end{equation}
+where $\alpha$ and $\beta $ are the constant coefficients used to
+defined the linear equation of state \eqref{Eq_tra_eos_linear}.
+% -------------------------------------------------------------------------------------------------------------
+%        Specific Heat
+% -------------------------------------------------------------------------------------------------------------
+\subsection    [Specific Heat (\textit{phycst})]
+         {Specific Heat (\mdl{phycst})}
+\label{TRA_adv_ldf}
+The specific heat of sea water, $C_p$, is a function of temperature, salinity
+and pressure \citep{UNESCO1983}. It is only used in the model to convert
+surface heat fluxes into surface temperature increase and so the pressure
+dependence is neglected. The dependence on $T$ and $S$ is weak.
+For example, with $S=35~psu$, $C_p$ increases from $3989$ to $4002$
+when $T$ varies from -2~\degres C to 31~\degres C. Therefore, $C_p$ has
+been chosen as a constant: $C_p=4.10^3~J\,Kg^{-1}\,\degres K^{-1}$.
+Its value is set in \mdl{phycst} module.
+where $(T,S) = (\Theta, S_A)$ for TEOS10, $= (\theta, S_p)$ for TEOS-80, or $=(T,S)$ for S-EOS,
+and, $\alpha$ and $\beta$ are the thermal and haline expansion coefficients.
+The coefficients are a polynomial function of temperature, salinity and depth which expression
+depends on the chosen EOS. They are computed through \textit{eos\_rab}, a \textsc{Fortran}
+function that can be found in \mdl{eosbn2}.
 % -------------------------------------------------------------------------------------------------------------
 …
 sea water ($i.e.$ referenced to the surface $p=0$), thus the pressure dependent
 terms in \eqref{Eq_tra_eos_fzp} (last term) have been dropped. The freezing
 point is computed through \textit{tfreez}, a \textsc{Fortran} function that can be found
+point is computed through \textit{eos\_fzp}, a \textsc{Fortran} function that can be found
 in \mdl{eosbn2}.
 …
 \label{TRA_zpshde}
+\gmcomment{STEVEN: to be consistent with earlier discussion of differencing and averaging operators, I've changed "derivative" to "difference" and "mean" to "average"}
+With partial bottom cells (\np{ln\_zps}=true), in general, tracers in horizontally
+\gmcomment{STEVEN: to be consistent with earlier discussion of differencing and averaging operators,
+                   I've changed "derivative" to "difference" and "mean" to "average"}
+With partial cells (\np{ln\_zps}=true) at bottom and top (\np{ln\_isfcav}=true), in general, tracers in horizontally
 adjacent cells live at different depths. Horizontal gradients of tracers are needed
 for horizontal diffusion (\mdl{traldf} module) and for the hydrostatic pressure
 gradient (\mdl{dynhpg} module) to be active.
 \gmcomment{STEVEN from gm : question: not sure of  what -to be active- means}
 Before taking horizontal gradients between the tracers next to the bottom, a linear
 interpolation in the vertical is used to approximate the deeper tracer as if it actually
 …
 \gmcomment{gm :   this last remark has to be done}
 %%%
+If under ice shelf seas opened (\np{ln\_isfcav}=true), the partial cell properties
+at the top are computed in the same way as for the bottom. Some extra variables are,
+however, computed to reduce the flow generated at the top and bottom if $z*$ coordinates activated.
+The extra variables calculated and used by \S\ref{DYN_hpg_isf} are:
+$\bullet$ $\overline{T}_k^{\,i+1/2}$ as described in \eqref{Eq_zps_hde}
+$\bullet$ $\delta _{i+1/2} Z_{T_k} = \widetilde {Z}^{\,i}_{T_k}-Z^{\,i}_{T_k}$ to compute
+the pressure gradient correction term used by \eqref{Eq_dynhpg_sco} in \S\ref{DYN_hpg_isf},
+ with $\widetilde {Z}_{T_k}$ the depth of the point $\widetilde {T}_{k}$ in case of $z^*$ coordinates
+(this term = 0 in z-coordinates)

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Chapters/Chap_ZDF.tex

-                      r5120
+                      r6436
 points, respectively (see \S\ref{TRA_zdf} and \S\ref{DYN_zdf}). These
 coefficients can be assumed to be either constant, or a function of the local
+Richardson number, or computed from a turbulent closure model (either
+TKE or KPP formulation). The computation of these coefficients is initialized
+in the \mdl{zdfini} module and performed in the \mdl{zdfric}, \mdl{zdftke} or
+\mdl{zdfkpp} modules. The trends due to the vertical momentum and tracer
+diffusion, including the surface forcing, are computed and added to the
+general trend in the \mdl{dynzdf} and \mdl{trazdf} modules, respectively.
+Richardson number, or computed from a turbulent closure model (TKE, GLS or KPP formulation).
+The computation of these coefficients is initialized in the \mdl{zdfini} module
+and performed in the \mdl{zdfric}, \mdl{zdftke}, \mdl{zdfgls} or \mdl{zdfkpp} modules.
+The trends due to the vertical momentum and tracer diffusion, including the surface forcing,
+are computed and added to the general trend in the \mdl{dynzdf} and \mdl{trazdf} modules, respectively.
 These trends can be computed using either a forward time stepping scheme
 (namelist parameter \np{ln\_zdfexp}=true) or a backward time stepping
 …
 \end{equation}
 At the ocean surface, a non zero length scale is set through the  \np{rn\_lmin0} namelist
+At the ocean surface, a non zero length scale is set through the  \np{rn\_mxl0} namelist
 parameter. Usually the surface scale is given by $l_o = \kappa \,z_o$
 where $\kappa = 0.4$ is von Karman's constant and $z_o$ the roughness
 parameter of the surface. Assuming $z_o=0.1$~m \citep{Craig_Banner_JPO94}
 leads to a 0.04~m, the default value of \np{rn\_lsurf}. In the ocean interior
+leads to a 0.04~m, the default value of \np{rn\_mxl0}. In the ocean interior
 a minimum length scale is set to recover the molecular viscosity when $\bar{e}$
 reach its minimum value ($1.10^{-6}= C_k\, l_{min} \,\sqrt{\bar{e}_{min}}$ ).
 …
 As the surface boundary condition on TKE is prescribed through $\bar{e}_o = e_{bb} |\tau| / \rho_o$,
 with $e_{bb}$ the \np{rn\_ebb} namelist parameter, setting \np{rn\_ebb}~=~67.83 corresponds
 to $\alpha_{CB} = 100$. further setting  \np{ln\_lsurf} to true applies \eqref{ZDF_Lsbc}
 as surface boundary condition on length scale, with $\beta$ hard coded to the Stacet's value.
+to $\alpha_{CB} = 100$. Further setting  \np{ln\_mxl0} to true applies \eqref{ZDF_Lsbc}
+as surface boundary condition on length scale, with $\beta$ hard coded to the Stacey's value.
 Note that a minimal threshold of \np{rn\_emin0}$=10^{-4}~m^2.s^{-2}$ (namelist parameters)
 is applied on surface $\bar{e}$ value.
 …
 %--------------------------------------------------------------%
+To be add here a description of "penetration of TKE" and the associated namelist parameters
+ \np{nn\_etau}, \np{rn\_efr} and \np{nn\_htau}.
+Vertical mixing parameterizations commonly used in ocean general circulation models
+tend to produce mixed-layer depths that are too shallow during summer months and windy conditions.
+This bias is particularly acute over the Southern Ocean.
+To overcome this systematic bias, an ad hoc parameterization is introduced into the TKE scheme  \cite{Rodgers_2014}.
+The parameterization is an empirical one, $i.e.$ not derived from theoretical considerations,
+but rather is meant to account for observed processes that affect the density structure of
+the ocean’s planetary boundary layer that are not explicitly captured by default in the TKE scheme
+($i.e.$ near-inertial oscillations and ocean swells and waves).
+When using this parameterization ($i.e.$ when \np{nn\_etau}~=~1), the TKE input to the ocean ($S$)
+imposed by the winds in the form of near-inertial oscillations, swell and waves is parameterized
+by \eqref{ZDF_Esbc} the standard TKE surface boundary condition, plus a depth depend one given by:
+\begin{equation}  \label{ZDF_Ehtau}
+S = (1-f_i) \; f_r \; e_s \; e^{-z / h_\tau}
+\end{equation}
+where
+$z$ is the depth,
+$e_s$ is TKE surface boundary condition,
+$f_r$ is the fraction of the surface TKE that penetrate in the ocean,
+$h_\tau$ is a vertical mixing length scale that controls exponential shape of the penetration,
+and $f_i$ is the ice concentration (no penetration if $f_i=1$, that is if the ocean is entirely
+covered by sea-ice).
+The value of $f_r$, usually a few percents, is specified through \np{rn\_efr} namelist parameter.
+The vertical mixing length scale, $h_\tau$, can be set as a 10~m uniform value (\np{nn\_etau}~=~0)
+or a latitude dependent value (varying from 0.5~m at the Equator to a maximum value of 30~m
+at high latitudes (\np{nn\_etau}~=~1).
+Note that two other option existe, \np{nn\_etau}~=~2, or 3. They correspond to applying
+\eqref{ZDF_Ehtau} only at the base of the mixed layer, or to using the high frequency part
+of the stress to evaluate the fraction of TKE that penetrate the ocean.
+Those two options are obsolescent features introduced for test purposes.
+They will be removed in the next release.
 % from Burchard et al OM 2008 :
+% the most critical process not reproduced by statistical turbulence models is the activity of internal waves and their interaction with turbulence. After the Reynolds decomposition, internal waves are in principle included in the RANS equations, but later partially excluded by the hydrostatic assumption and the model resolution. Thus far, the representation of internal wave mixing in ocean models has been relatively crude (e.g. Mellor, 1989; Large et al., 1994; Meier, 2001; Axell, 2002; St. Laurent and Garrett, 2002).
+% the most critical process not reproduced by statistical turbulence models is the activity of
+% internal waves and their interaction with turbulence. After the Reynolds decomposition,
+% internal waves are in principle included in the RANS equations, but later partially
+% excluded by the hydrostatic assumption and the model resolution.
+% Thus far, the representation of internal wave mixing in ocean models has been relatively crude
+% (e.g. Mellor, 1989; Large et al., 1994; Meier, 2001; Axell, 2002; St. Laurent and Garrett, 2002).
 …
 Options are defined through the  \ngn{namzdf\_kpp} namelist variables.
+\colorbox{yellow}{Add a description of KPP here.}
+Note that KPP is an obsolescent feature of the \NEMO system.
+It will be removed in the next release (v3.7 and followings).
 …
 Options are defined through the  \ngn{namzdf} namelist variables.
 The non-penetrative convective adjustment is used when \np{ln\_zdfnpc}=true.
+The non-penetrative convective adjustment is used when \np{ln\_zdfnpc}~=~\textit{true}.
 It is applied at each \np{nn\_npc} time step and mixes downwards instantaneously
 the statically unstable portion of the water column, but only until the density
 …
 (Fig. \ref{Fig_npc}): starting from the top of the ocean, the first instability is
 found. Assume in the following that the instability is located between levels
 $k$ and $k+1$. The potential temperature and salinity in the two levels are
+$k$ and $k+1$. The temperature and salinity in the two levels are
 vertically mixed, conserving the heat and salt contents of the water column.
 The new density is then computed by a linear approximation. If the new
 …
 \citep{Madec_al_JPO91, Madec_al_DAO91, Madec_Crepon_Bk91}.
+Note that in the current implementation of this algorithm presents several
+limitations. First, potential density referenced to the sea surface is used to
+check whether the density profile is stable or not. This is a strong
+simplification which leads to large errors for realistic ocean simulations.
+Indeed, many water masses of the world ocean, especially Antarctic Bottom
+Water, are unstable when represented in surface-referenced potential density.
+The scheme will erroneously mix them up. Second, the mixing of potential
+density is assumed to be linear. This assures the convergence of the algorithm
+even when the equation of state is non-linear. Small static instabilities can thus
+persist due to cabbeling: they will be treated at the next time step.
+Third, temperature and salinity, and thus density, are mixed, but the
+corresponding velocity fields remain unchanged. When using a Richardson
+Number dependent eddy viscosity, the mixing of momentum is done through
+the vertical diffusion: after a static adjustment, the Richardson Number is zero
+and thus the eddy viscosity coefficient is at a maximum. When this convective
+adjustment algorithm is used with constant vertical eddy viscosity, spurious
+solutions can occur since the vertical momentum diffusion remains small even
+after a static adjustment. In that case, we recommend the addition of momentum
+mixing in a manner that mimics the mixing in temperature and salinity
+\citep{Speich_PhD92, Speich_al_JPO96}.
+The current implementation has been modified in order to deal with any non linear
+equation of seawater (L. Brodeau, personnal communication).
+Two main differences have been introduced compared to the original algorithm:
+$(i)$ the stability is now checked using the Brunt-V\"{a}is\"{a}l\"{a} frequency
+(not the the difference in potential density) ;
+$(ii)$ when two levels are found unstable, their thermal and haline expansion coefficients
+are vertically mixed in the same way their temperature and salinity has been mixed.
+These two modifications allow the algorithm to perform properly and accurately
+with TEOS10 or EOS-80 without having to recompute the expansion coefficients at each
+mixing iteration.
 % -------------------------------------------------------------------------------------------------------------
 …
 % -------------------------------------------------------------------------------------------------------------
 \subsection   [Enhanced Vertical Diffusion (\np{ln\_zdfevd})]
          {Enhanced Vertical Diffusion (\np{ln\_zdfevd}=true)}
+              {Enhanced Vertical Diffusion (\np{ln\_zdfevd}=true)}
 \label{ZDF_evd}
 …
 % Bottom Friction
 % ================================================================
 \section  [Bottom and top Friction (\textit{zdfbfr})]   {Bottom Friction (\mdl{zdfbfr} module)}
+\section  [Bottom and Top Friction (\textit{zdfbfr})]   {Bottom and Top Friction (\mdl{zdfbfr} module)}
 \label{ZDF_bfr}
 …
 Options to define the top and bottom friction are defined through the  \ngn{nambfr} namelist variables.
+The top friction is activated only if the ice shelf cavities are opened (\np{ln\_isfcav}~=~true).
+As the friction processes at the top and bottom are the represented similarly, only the bottom friction is described in detail.
+The bottom friction represents the friction generated by the bathymetry.
+The top friction represents the friction generated by the ice shelf/ocean interface.
+As the friction processes at the top and bottom are represented similarly, only the bottom friction is described in detail below.\\
 Both the surface momentum flux (wind stress) and the bottom momentum
 …
 $H = 4000$~m, the resulting friction coefficient is $r = 4\;10^{-4}$~m\;s$^{-1}$.
 This is the default value used in \NEMO. It corresponds to a decay time scale
 of 115~days. It can be changed by specifying \np{rn\_bfric1} (namelist parameter).
+of 115~days. It can be changed by specifying \np{rn\_bfri1} (namelist parameter).
 For the linear friction case the coefficients defined in the general
 …
 \end{split}
 \end{equation}
 When \np{nn\_botfr}=1, the value of $r$ used is \np{rn\_bfric1}.
+When \np{nn\_botfr}=1, the value of $r$ used is \np{rn\_bfri1}.
 Setting \np{nn\_botfr}=0 is equivalent to setting $r=0$ and leads to a free-slip
 bottom boundary condition. These values are assigned in \mdl{zdfbfr}.
 …
 in the \ifile{bfr\_coef} input NetCDF file. The mask values should vary from 0 to 1.
 Locations with a non-zero mask value will have the friction coefficient increased
 by $mask\_value$*\np{rn\_bfrien}*\np{rn\_bfric1}.
+by $mask\_value$*\np{rn\_bfrien}*\np{rn\_bfri1}.
 % -------------------------------------------------------------------------------------------------------------
 …
 $e_b = 2.5\;10^{-3}$m$^2$\;s$^{-2}$, while the FRAM experiment \citep{Killworth1992}
 uses $C_D = 1.4\;10^{-3}$ and $e_b =2.5\;\;10^{-3}$m$^2$\;s$^{-2}$.
 The CME choices have been set as default values (\np{rn\_bfric2} and \np{rn\_bfeb2}
+The CME choices have been set as default values (\np{rn\_bfri2} and \np{rn\_bfeb2}
 namelist parameters).
 …
 \end{equation}
+The coefficients that control the strength of the non-linear bottom friction are
+initialised as namelist parameters: $C_D$= \np{rn\_bfri2}, and $e_b$ =\np{rn\_bfeb2}.
+Note for applications which treat tides explicitly a low or even zero value of
+\np{rn\_bfeb2} is recommended. From v3.2 onwards a local enhancement of $C_D$
+is possible via an externally defined 2D mask array (\np{ln\_bfr2d}=true).
+See previous section for details.
+The coefficients that control the strength of the non-linear bottom friction are
+initialised as namelist parameters: $C_D$= \np{rn\_bfri2}, and $e_b$ =\np{rn\_bfeb2}.
+Note for applications which treat tides explicitly a low or even zero value of
+\np{rn\_bfeb2} is recommended. From v3.2 onwards a local enhancement of $C_D$ is possible
+via an externally defined 2D mask array (\np{ln\_bfr2d}=true).  This works in the same way
+as for the linear bottom friction case with non-zero masked locations increased by
+$mask\_value$*\np{rn\_bfrien}*\np{rn\_bfri2}.
+% -------------------------------------------------------------------------------------------------------------
+%       Bottom Friction Log-layer
+% -------------------------------------------------------------------------------------------------------------
+\subsection{Log-layer Bottom Friction enhancement (\np{nn\_botfr} = 2, \np{ln\_loglayer} = .true.)}
+\label{ZDF_bfr_loglayer}
+In the non-linear bottom friction case, the drag coefficient, $C_D$, can be optionally
+enhanced using a "law of the wall" scaling. If  \np{ln\_loglayer} = .true., $C_D$ is no
+longer constant but is related to the thickness of the last wet layer in each column by:
+\begin{equation}
+C_D = \left ( {\kappa \over {\rm log}\left ( 0.5e_{3t}/rn\_bfrz0 \right ) } \right )^2
+\end{equation}
+\noindent where $\kappa$ is the von-Karman constant and \np{rn\_bfrz0} is a roughness
+length provided via the namelist.
+For stability, the drag coefficient is bounded such that it is kept greater or equal to
+the base \np{rn\_bfri2} value and it is not allowed to exceed the value of an additional
+namelist parameter: \np{rn\_bfri2\_max}, i.e.:
+\begin{equation}
+rn\_bfri2 \leq C_D \leq rn\_bfri2\_max
+\end{equation}
+\noindent Note also that a log-layer enhancement can also be applied to the top boundary
+friction if under ice-shelf cavities are in use (\np{ln\_isfcav}=.true.).  In this case, the
+relevant namelist parameters are \np{rn\_tfrz0}, \np{rn\_tfri2}
+and \np{rn\_tfri2\_max}.
 % -------------------------------------------------------------------------------------------------------------
 …
 % ================================================================
+% Internal wave-driven mixing
+% ================================================================
+\section{Internal wave-driven mixing (\key{zdftmx\_new})}
+\label{ZDF_tmx_new}
+%--------------------------------------------namzdf_tmx_new------------------------------------------
+\namdisplay{namzdf_tmx_new}
+%--------------------------------------------------------------------------------------------------------------
+The parameterization of mixing induced by breaking internal waves is a generalization
+of the approach originally proposed by \citet{St_Laurent_al_GRL02}.
+A three-dimensional field of internal wave energy dissipation $\epsilon(x,y,z)$ is first constructed,
+and the resulting diffusivity is obtained as
+\begin{equation} \label{Eq_Kwave}
+A^{vT}_{wave} =  R_f \,\frac{ \epsilon }{ \rho \, N^2 }
+\end{equation}
+where $R_f$ is the mixing efficiency and $\epsilon$ is a specified three dimensional distribution
+of the energy available for mixing. If the \np{ln\_mevar} namelist parameter is set to false,
+the mixing efficiency is taken as constant and equal to 1/6 \citep{Osborn_JPO80}.
+In the opposite (recommended) case, $R_f$ is instead a function of the turbulence intensity parameter
+$Re_b = \frac{ \epsilon}{\nu \, N^2}$, with $\nu$ the molecular viscosity of seawater,
+following the model of \cite{Bouffard_Boegman_DAO2013}
+and the implementation of \cite{de_lavergne_JPO2016_efficiency}.
+Note that $A^{vT}_{wave}$ is bounded by $10^{-2}\,m^2/s$, a limit that is often reached when the mixing efficiency is constant.
+In addition to the mixing efficiency, the ratio of salt to heat diffusivities can chosen to vary
+as a function of $Re_b$ by setting the \np{ln\_tsdiff} parameter to true, a recommended choice).
+This parameterization of differential mixing, due to \cite{Jackson_Rehmann_JPO2014},
+is implemented as in \cite{de_lavergne_JPO2016_efficiency}.
+The three-dimensional distribution of the energy available for mixing, $\epsilon(i,j,k)$, is constructed
+from three static maps of column-integrated internal wave energy dissipation, $E_{cri}(i,j)$,
+$E_{pyc}(i,j)$, and $E_{bot}(i,j)$, combined to three corresponding vertical structures
+(de Lavergne et al., in prep):
+\begin{align*}
+F_{cri}(i,j,k) &\propto e^{-h_{ab} / h_{cri} }\\
+F_{pyc}(i,j,k) &\propto N^{n\_p}\\
+F_{bot}(i,j,k) &\propto N^2 \, e^{- h_{wkb} / h_{bot} }
+\end{align*}
+In the above formula, $h_{ab}$ denotes the height above bottom,
+$h_{wkb}$ denotes the WKB-stretched height above bottom, defined by
+\begin{equation*}
+h_{wkb} = H \, \frac{ \int_{-H}^{z} N \, dz' } { \int_{-H}^{\eta} N \, dz'  } \; ,
+\end{equation*}
+The $n_p$ parameter (given by \np{nn\_zpyc} in \ngn{namzdf\_tmx\_new} namelist)  controls the stratification-dependence of the pycnocline-intensified dissipation.
+It can take values of 1 (recommended) or 2.
+Finally, the vertical structures $F_{cri}$ and $F_{bot}$ require the specification of
+the decay scales $h_{cri}(i,j)$ and $h_{bot}(i,j)$, which are defined by two additional input maps.
+$h_{cri}$ is related to the large-scale topography of the ocean (etopo2)
+and $h_{bot}$ is a function of the energy flux $E_{bot}$, the characteristic horizontal scale of
+the abyssal hill topography \citep{Goff_JGR2010} and the latitude.
+% ================================================================

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Chapters/Introduction.tex

-                      r4661
+                      r6436
 release 8.2, described in \citet{Madec1998}. This model has been used for a wide
 range of applications, both regional or global, as a forced ocean model and as a
+model coupled with the atmosphere. A complete list of references is found on the
+\NEMO web site.
+model coupled with the sea-ice and/or the atmosphere.
 This manual is organised in as follows. Chapter~\ref{PE} presents the model basics,
 $i.e.$ the equations and their assumptions, the vertical coordinates used, and the
 subgrid scale physics. This part deals with the continuous equations of the model
 (primitive equations, with potential temperature, salinity and an equation of state).
+(primitive equations, with temperature, salinity and an equation of seawater).
 The equations are written in a curvilinear coordinate system, with a choice of vertical
 coordinates ($z$ or $s$, with the rescaled height coordinate formulation \textit{z*}, or
 …
 space and time variable coefficient \citet{Treguier1997}. The model has vertical harmonic
 viscosity and diffusion with a space and time variable coefficient, with options to compute
 the coefficients with \citet{Blanke1993}, \citet{Large_al_RG94}, \citet{Pacanowski_Philander_JPO81},
+the coefficients with \citet{Blanke1993}, \citet{Pacanowski_Philander_JPO81},
 or \citet{Umlauf_Burchard_JMS03} mixing schemes.
  \vspace{1cm}
+%%gm    To be put somewhere else ....
 \noindent CPP keys and namelists are used for inputs to the code.  \newline
 …
  \vspace{1cm}
+%%gm  end
 Model outputs management and specific online diagnostics are described in chapters~\ref{DIA}.
 …
 \item a deep re-writting and simplification of the off-line tracer component (OFF\_SRC) ;
 \item the merge of passive and active advection and diffusion modules ;
 \item  Use of the Flexible Configuration Manager (FCM) to build configurations, generate the Makefile and produce the executable ;
+\item Use of the Flexible Configuration Manager (FCM) to build configurations, generate the Makefile and produce the executable ;
 \item Linear-tangent and Adjoint component (TAM) added, phased with v3.0
 \end{enumerate}
 …
+ \vspace{1cm}
+$\bullet$ The main modifications from NEMO/OPA v3.4 and  v3.6 are :\\
+\begin{enumerate}
+\item I/O management: NEMO in now interfaced with XIOS, a Input/Output server having a versatile xml user interface, and
+allowing I/O to be performed on dedicated processors thus improving scalability and performance on massively parallel platforms.
+\item ICB module \citep{Marsh_GMD2015}: icebergs as lagrangian floats ;
+\item SAS: Stand Alone Surface module allowing testing of forcing set with bulk formulae, to run sea-ice models without ocean, to run ICB icebergs module alone, and to test AGRIF with sea-ice
+\item ISF : Under ice-selves cavities (parametrisation and/or explicit representation)
+\item Coupled interface for next IPCC requirements (multi category sea-ice, calving and iceberg module)
+\item Ocean and ice allowed to be explicitly coupled through OASIS, using StandAlone Surface module)
+\item On line coarsening of ocean I/O
+\item Major evolution of LIM3 sea-ice model \citep{Rousset_GMD2015}
+\item Open boundaries: completion of BDY/OBC merge : BDY is now the only Open boundary module available
+\item re-visit of the specification of heat/salt(tracers)/mass fluxes ;
+\item levitating or fully embedded sea-ice (for LIM and CICE) ;
+\item a new parameterization of mixing induced by breaking internal waves (de Lavergne et al. in prep.)
+And also:
+\item update of AGRIF package and AGRIF compatibility with LIM2 sea-ice model ;
+\item A new vertical sigma coordinate stretching function \citep{Siddorn_Furner_OM12} ;
+\item Smagorinsky eddy coefficients: the \cite{Griffies_Hallberg_MWR00} Smagorinsky type diffusivity/viscosity for lateral mixing has been introduced ;
+\item Standard Fox Kemper parametrisation
+\item Analytical tropical cyclones taken in account using track and magnitude observations (Vincent et al. JGR 2012a,b) ;
+\item OBS: observation operators improved and now available in Standalone mode ;
+\item Log layer option for bottom friction
+\item Faster split-explicit time stepping ;
+\item Z-tilde ALE coordinates \citep{Leclair_Madec_OM11} ;
+\item implicit bottom friction ;
+\item Runoff improved and SBC with BGC
+\item MPP assessment and optimisation
+\item First steps of wave coupling
+Features becoming obsolete: LIM2 (replaced by LIM3 monocategory) ; IOIPSL (replaced by XIOS) ;
+Features that has been removed : LOBSTER (now included in PISCES) ; OBC, replaced by BDY ;
+\end{enumerate}

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/nam_tide

-                      r4147
+                      r6436
 !-----------------------------------------------------------------------
    ln_tide_pot   = .true.   !  use tidal potential forcing
+   clname(1)     =   'M2'   !  name of constituent
+   clname(2)     =   'S2'
+   clname(3)     =   'N2'
+   clname(4)     =   'K1'
+   clname(5)     =   'O1'
+   clname(6)     =   'Q1'
+   clname(7)     =   'M4'
+   clname(8)     =   'K2'
+   clname(9)     =   'P1'
+   clname(10)    =   'Mf'
+   clname(11)    =   'Mm'
+   ln_tide_ramp  = .false.  !
+   rdttideramp   =    0.    !
+   clname(1)     = 'DUMMY'  !  name of constituent - all tidal components must be set in namelist_cfg
+/

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/nambdy

-                      r4147
+                      r6436
 &nambdy        !  unstructured open boundaries                          ("key_bdy")
 !-----------------------------------------------------------------------
+    nb_bdy = 1                            !  number of open boundary sets
+    ln_coords_file = .true.               !  =T : read bdy coordinates from file
+    cn_coords_file = 'coordinates.bdy.nc' !  bdy coordinates files
+    ln_mask_file = .false.                !  =T : read mask from file
+    cn_mask_file = ''                     !  name of mask file (if ln_mask_file=.TRUE.)
+    nn_dyn2d      =  2                    !  boundary conditions for barotropic fields
+    nn_dyn2d_dta  =  3                    !  = 0, bdy data are equal to the initial state
+                                          !  = 1, bdy data are read in 'bdydata   .nc' files
+                                          !  = 2, use tidal harmonic forcing data from files
+                                          !  = 3, use external data AND tidal harmonic forcing
+    nn_dyn3d      =  0                    !  boundary conditions for baroclinic velocities
+    nn_dyn3d_dta  =  0                    !  = 0, bdy data are equal to the initial state
+                           !  = 1, bdy data are read in 'bdydata   .nc' files
+    nn_tra        =  1                    !  boundary conditions for T and S
+    nn_tra_dta    =  1                    !  = 0, bdy data are equal to the initial state
+                           !  = 1, bdy data are read in 'bdydata   .nc' files
+    nn_rimwidth  = 10                      !  width of the relaxation zone
+    ln_vol     = .false.                  !  total volume correction (see nn_volctl parameter)
+    nn_volctl  = 1                        !  = 0, the total water flux across open boundaries is zero
+    nb_bdy = 2                               !  number of open boundary sets
+    ln_coords_file = .true.,.false.          !  =T : read bdy coordinates from file
+    cn_coords_file = 'coordinates.bdy.nc','' !  bdy coordinates files
+    ln_mask_file = .false.                   !  =T : read mask from file
+    cn_mask_file = ''                        !  name of mask file (if ln_mask_file=.TRUE.)
+    cn_dyn2d       = 'none','none'           !
+    nn_dyn2d      =  2, 0                    !  boundary conditions for barotropic fields
+    nn_dyn2d_dta  =  3, 0                    !  = 0, bdy data are equal to the initial state
+                                             !  = 1, bdy data are read in 'bdydata   .nc' files
+                                             !  = 2, use tidal harmonic forcing data from files
+                                             !  = 3, use external data AND tidal harmonic forcing
+    cn_dyn3d      =  'none',' none'          !
+    nn_dyn3d      =  0, 0                    !  boundary conditions for baroclinic velocities
+    nn_dyn3d_dta  =  0, 0                    !  = 0, bdy data are equal to the initial state
+                                             !  = 1, bdy data are read in 'bdydata   .nc' files
+    cn_tra        =  'none', 'none'          !
+    nn_tra_dta    =  1, 1                    !  = 0, bdy data are equal to the initial state
+                                             !  = 1, bdy data are read in 'bdydata   .nc' files
+    cn_ice_lim      =  'none','none'         !
+    nn_ice_lim_dta  =  0, 0                  !  = 0, bdy data are equal to the initial state
+                                             !  = 1, bdy data are read in 'bdydata   .nc' files
+    rn_ice_tem      = 270., 270.             !  lim3 only: arbitrary temperature of incoming sea ice
+    rn_ice_sal      = 10.,  10.              !  lim3 only:      --   salinity           --
+    rn_ice_age      = 30., 30.               !  lim3 only:      --   age                --
+    ln_tra_dmp    = .false.,.false.          !  open boudaries conditions for tracers
+    ln_dyn3d_dmp  = .false.,.false.          !  open boundary condition for baroclinic velocities
+    rn_time_dmp   =  1., 1.                  ! Damping time scale in days
+    rn_time_dmp_out =  1., 1.                ! Outflow damping time scale
+    nn_rimwidth  = 10, 5                     !  width of the relaxation zone
+    ln_vol     = .false.                     !  total volume correction (see nn_volctl parameter)
+    nn_volctl  = 1                           !  = 0, the total water flux across open boundaries is zero
+/

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/nambdy_dta

-                      r4230
+                      r6436
 &nambdy_dta      !  open boundaries - external data           ("key_bdy")
 !-----------------------------------------------------------------------
+!              !   file name    ! frequency (hours) !  variable  ! time interpol. !  clim   ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
+!              !                !  (if <0  months)  !    name    !    (logical)   !  (T/F)  ! 'monthly' ! filename ! pairing  ! filename      !
+   bn_ssh =     'amm12_bdyT_u2d' ,         24        , 'sossheig' ,     .true.     , .false. ,  'daily'  ,    ''    ,   ''    , ''
+   bn_u2d =     'amm12_bdyU_u2d' ,         24        , 'vobtcrtx' ,     .true.     , .false. ,  'daily'  ,    ''    ,   ''    , ''
+   bn_v2d =     'amm12_bdyV_u2d' ,         24        , 'vobtcrty' ,     .true.     , .false. ,  'daily'  ,    ''    ,   ''    , ''
+   bn_u3d  =    'amm12_bdyU_u3d' ,         24        , 'vozocrtx' ,     .true.     , .false. ,  'daily'  ,    ''    ,   ''    , ''
+   bn_v3d  =    'amm12_bdyV_u3d' ,         24        , 'vomecrty' ,     .true.     , .false. ,  'daily'  ,    ''    ,   ''    , ''
+   bn_tem  =    'amm12_bdyT_tra' ,         24        , 'votemper' ,     .true.     , .false. ,  'daily'  ,    ''    ,   ''    , ''
+   bn_sal  =    'amm12_bdyT_tra' ,         24        , 'vosaline' ,     .true.     , .false. ,  'daily'  ,    ''    ,   ''    , ''
+!              !  file name      ! frequency (hours) ! variable   ! time interp.   !  clim   ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
+!              !                 !  (if <0  months)  !   name     !   (logical)    !  (T/F ) ! 'monthly' ! filename ! pairing  ! filename      !
+   bn_ssh =     'amm12_bdyT_u2d' ,         24        , 'sossheig' ,     .true.     , .false. ,  'daily'  ,    ''    ,   ''     , ''
+   bn_u2d =     'amm12_bdyU_u2d' ,         24        , 'vobtcrtx' ,     .true.     , .false. ,  'daily'  ,    ''    ,   ''     , ''
+   bn_v2d =     'amm12_bdyV_u2d' ,         24        , 'vobtcrty' ,     .true.     , .false. ,  'daily'  ,    ''    ,   ''     , ''
+   bn_u3d  =    'amm12_bdyU_u3d' ,         24        , 'vozocrtx' ,     .true.     , .false. ,  'daily'  ,    ''    ,   ''     , ''
+   bn_v3d  =    'amm12_bdyV_u3d' ,         24        , 'vomecrty' ,     .true.     , .false. ,  'daily'  ,    ''    ,   ''     , ''
+   bn_tem  =    'amm12_bdyT_tra' ,         24        , 'votemper' ,     .true.     , .false. ,  'daily'  ,    ''    ,   ''     , ''
+   bn_sal  =    'amm12_bdyT_tra' ,         24        , 'vosaline' ,     .true.     , .false. ,  'daily'  ,    ''    ,   ''     , ''
+! for lim2
+!   bn_frld  =    'amm12_bdyT_ice' ,         24        , 'ileadfra' ,     .true.     , .false. ,  'daily'  ,    ''    ,   ''     , ''
+!   bn_hicif =    'amm12_bdyT_ice' ,         24        , 'iicethic' ,     .true.     , .false. ,  'daily'  ,    ''    ,   ''     , ''
+!   bn_hsnif =    'amm12_bdyT_ice' ,         24        , 'isnowthi' ,     .true.     , .false. ,  'daily'  ,    ''    ,   ''     , ''
+! for lim3
+!   bn_a_i  =    'amm12_bdyT_ice' ,         24        , 'ileadfra' ,     .true.     , .false. ,  'daily'  ,    ''    ,   ''     , ''
+!   bn_ht_i =    'amm12_bdyT_ice' ,         24        , 'iicethic' ,     .true.     , .false. ,  'daily'  ,    ''    ,   ''     , ''
+!   bn_ht_s =    'amm12_bdyT_ice' ,         24        , 'isnowthi' ,     .true.     , .false. ,  'daily'  ,    ''    ,   ''     , ''
    cn_dir  =    'bdydta/'
    ln_full_vel = .false.

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/namberg

-                      r4230
+                      r6436
                                                       ! Initial mass required for an iceberg of each class
       rn_initial_mass          = 8.8e7, 4.1e8, 3.3e9, 1.8e10, 3.8e10, 7.5e10, 1.2e11, 2.2e11, 3.9e11, 7.4e11
                                                       ! Proportion of calving mass to apportion to each class
+                                                      ! Proportion of calving mass to apportion to each class
       rn_distribution          = 0.24, 0.12, 0.15, 0.18, 0.12, 0.07, 0.03, 0.03, 0.03, 0.02
                                                       ! Ratio between effective and real iceberg mass (non-dim)
                                                       ! i.e. number of icebergs represented at a point
+                                                      ! i.e. number of icebergs represented at a point
       rn_mass_scaling          = 2000, 200, 50, 20, 10, 5, 2, 1, 1, 1
                                                       ! thickness of newly calved bergs (m)
 …
       rn_bits_erosion_fraction = 0.                   ! Fraction of erosion melt flux to divert to bergy bits
       rn_sicn_shift            = 0.                   ! Shift of sea-ice concn in erosion flux (0<sicn_shift<1)
       ln_passive_mode          = .false.              ! iceberg - ocean decoupling
+      ln_passive_mode          = .false.              ! iceberg - ocean decoupling
       nn_test_icebergs         =  10                  ! Create test icebergs of this class (-1 = no)
                                                       ! Put a test iceberg at each gridpoint in box (lon1,lon2,lat1,lat2)
       rn_test_box              = 108.0,  116.0, -66.0, -58.0
       rn_speed_limit           = 0.                   ! CFL speed limit for a berg
+      rn_speed_limit           = 0.                   ! CFL speed limit for a berg
                ! filename ! freq (hours) ! variable ! time interp. ! clim  !'yearly' or ! weights  ! rotation ! land/sea mask !
                !          ! (<0  months) !   name   !  (logical)   ! (T/F) ! 'monthly'  ! filename ! pairing  ! filename      !
       sn_icb =  'calving' ,     -1       , 'calvingmask',  .true.      , .true., 'yearly'   , ' '      , ' '  , ''
       cn_dir = './'
+!              ! file name ! frequency (hours) !   variable   ! time interp.   !  clim   ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
+!              !           !  (if <0  months)  !     name     !   (logical)    !  (T/F ) ! 'monthly' ! filename ! pairing  ! filename      !
+      sn_icb =  'calving' ,       -1           , 'calvingmask',  .true.        , .true.  , 'yearly'  , ''       , ''       , ''
+      cn_dir = './'
+/

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/namdom

-                      r4560
+                      r6436
 !-----------------------------------------------------------------------
    nn_bathy    =    1      !  compute (=0) or read (=1) the bathymetry file
+   nn_closea    =   0      !  remove (=0) or keep (=1) closed seas and lakes (ORCA)
+   nn_msh      =    0      !  create (=1) a mesh file or not (=0)
+   rn_bathy    =    0.     !  value of the bathymetry. if (=0) bottom flat at jpkm1
+   nn_closea   =    0      !  remove (=0) or keep (=1) closed seas and lakes (ORCA)
+   nn_msh      =    1      !  create (=1) a mesh file or not (=0)
    rn_hmin     =   -3.     !  min depth of the ocean (>0) or min number of ocean level (<0)
    rn_e3zps_min=   20.     !  partial step thickness is set larger than the minimum of
 …
    rn_rdtmax   = 28800.          !  maximum time step on tracers (used if nn_acc=1)
    rn_rdth     =  800.           !  depth variation of tracer time step  (used if nn_acc=1)
+   ln_crs      = .false.      !  Logical switch for coarsening module
    jphgr_msh   =       0               !  type of horizontal mesh
                                        !  = 0 curvilinear coordinate on the sphere read in coordinate.nc

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/namdyn_adv

-                      r3294
+                      r6436
 &namdyn_adv    !   formulation of the momentum advection
 !-----------------------------------------------------------------------
+   ln_dynadv_vec = .true.  !  vector form (T) or flux form (F)
+   ln_dynadv_vec = .true.  !  vector form (T) or flux form (F)
+   nn_dynkeg     = 0       ! scheme for grad(KE): =0   C2  ;  =1   Hollingsworth correction
    ln_dynadv_cen2= .false. !  flux form - 2nd order centered scheme
+   ln_dynadv_ubs = .false. !  flux form - 3rd order UBS      scheme
+/
+   ln_dynadv_ubs = .false. !  flux form - 3rd order UBS      scheme
+   ln_dynzad_zts = .false. !  Use (T) sub timestepping for vertical momentum advection
+/

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/namdyn_hpg

r5120	r6436
5	5	ln_hpg_zps = .true. ! z-coordinate - partial steps (interpolation)
6	6	ln_hpg_sco = .false. ! s-coordinate (standard jacobian formulation)
7		ln_hpg_isf = .false. ! s-coordinate (sco ) adapted to i~~ce shelf cavity~~
	7	ln_hpg_isf = .false. ! s-coordinate (sco ) adapted to isf
8	8	ln_hpg_djc = .false. ! s-coordinate (Density Jacobian with Cubic polynomial)
9	9	ln_hpg_prj = .false. ! s-coordinate (Pressure Jacobian scheme)

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/namdyn_vor

r4147	r6436
6	6	ln_dynvor_mix = .false. ! mixed scheme
7	7	ln_dynvor_een = .true. ! energy & enstrophy scheme
	8	ln_dynvor_een_old = .false. ! energy & enstrophy scheme - original formulation
8	9	/

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/nameos

-                      r3294
+                      r6436
 &nameos        !   ocean physical parameters
 !-----------------------------------------------------------------------
+   nn_eos      =   0       !  type of equation of state and Brunt-Vaisala frequency
+                           !     = 0, UNESCO (formulation of Jackett and McDougall (1994) and of McDougall (1987) )
+                           !     = 1, linear: rho(T)   = rau0 * ( 1.028 - ralpha * T )
+                           !     = 2, linear: rho(T,S) = rau0 * ( rbeta * S - ralpha * T )
+   rn_alpha    =   2.0e-4  !  thermal expension coefficient (nn_eos= 1 or 2)
+   rn_beta     =   7.7e-4  !  saline  expension coefficient (nn_eos= 2)
+   nn_eos      =  -1     !  type of equation of state and Brunt-Vaisala frequency
+                                 !  =-1, TEOS-10
+                                 !  = 0, EOS-80
+                                 !  = 1, S-EOS   (simplified eos)
+   ln_useCT    = .true.  ! use of Conservative Temp. ==> surface CT converted in Pot. Temp. in sbcssm
+   !                             !
+   !                     ! S-EOS coefficients :
+   !                             !  rd(T,S,Z)*rau0 = -a0*(1+.5*lambda*dT+mu*Z+nu*dS)*dT+b0*dS
+   rn_a0       =  1.6550e-1      !  thermal expension coefficient (nn_eos= 1)
+   rn_b0       =  7.6554e-1      !  saline  expension coefficient (nn_eos= 1)
+   rn_lambda1  =  5.9520e-2      !  cabbeling coeff in T^2  (=0 for linear eos)
+   rn_lambda2  =  7.4914e-4      !  cabbeling coeff in S^2  (=0 for linear eos)
+   rn_mu1      =  1.4970e-4      !  thermobaric coeff. in T (=0 for linear eos)
+   rn_mu2      =  1.1090e-5      !  thermobaric coeff. in S (=0 for linear eos)
+   rn_nu       =  2.4341e-3      !  cabbeling coeff in T*S  (=0 for linear eos)
+/

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/namhsb

r2540	r6436
1	1	!-----------------------------------------------------------------------
2		&namhsb ! Heat and salt budgets
	2	&namhsb ! Heat and salt budgets
3	3	!-----------------------------------------------------------------------
4	4	ln_diahsb = .false. ! check the heat and salt budgets (T) or not (F)

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/namobs

-                      r4147
+                      r6436
    ln_s3d     = .false.    ! Logical switch for S profile observations
    ln_ena     = .false.    ! Logical switch for ENACT insitu data set
    !                       !     ln_cor                  Logical switch for Coriolis insitu data set
+   ln_cor     = .false.    ! Logical switch for Coriolis insitu data set
    ln_profb   = .false.    ! Logical switch for feedback insitu data set
    ln_sla     = .false.    ! Logical switch for SLA observations
    ln_sladt   = .false.    ! Logical switch for AVISO SLA data
    ln_slafb   = .false.    ! Logical switch for feedback SLA data
+                           !     ln_ssh                  Logical switch for SSH observations
+   ln_sst     = .true.     ! Logical switch for SST observations
+   ln_reysst  = .true.     !     ln_reysst               Logical switch for Reynolds observations
+   ln_ghrsst  = .false.    !     ln_ghrsst               Logical switch for GHRSST observations
+   ln_ssh     = .false.    ! Logical switch for SSH observations
+   ln_sst     = .false.    ! Logical switch for SST observations
+   ln_reysst  = .false.    ! Logical switch for Reynolds observations
+   ln_ghrsst  = .false.    ! Logical switch for GHRSST observations
    ln_sstfb   = .false.    ! Logical switch for feedback SST data
+                           !     ln_sss                  Logical switch for SSS observations
+                           !     ln_seaice               Logical switch for Sea Ice observations
+                           !     ln_vel3d                Logical switch for velocity observations
+                           !     ln_velavcur             Logical switch for velocity daily av. cur.
+                           !     ln_velhrcur             Logical switch for velocity high freq. cur.
+                           !     ln_velavadcp            Logical switch for velocity daily av. ADCP
+                           !     ln_velhradcp            Logical switch for velocity high freq. ADCP
+                           !     ln_velfb                Logical switch for feedback velocity data
+                           !     ln_grid_global          Global distribtion of observations
+                           !     ln_grid_search_lookup   Logical switch for obs grid search w/lookup table
+                           !     grid_search_file        Grid search lookup file header
+                           !     enactfiles              ENACT input observation file names
+                           !     coriofiles              Coriolis input observation file name
+   !                       ! profbfiles: Profile feedback input observation file name
+   profbfiles = 'profiles_01.nc'
+                           !     ln_profb_enatim         Enact feedback input time setting switch
+                           !     slafilesact             Active SLA input observation file name
+                           !     slafilespas             Passive SLA input observation file name
+   !                       ! slafbfiles: Feedback SLA input observation file name
+   slafbfiles = 'sla_01.nc'
+                           !     sstfiles                GHRSST input observation file name
+   !                       ! sstfbfiles: Feedback SST input observation file name
+   sstfbfiles = 'sst_01.nc' 'sst_02.nc' 'sst_03.nc' 'sst_04.nc' 'sst_05.nc'
+                           !     seaicefiles             Sea Ice input observation file name
+                           !     velavcurfiles           Vel. cur. daily av. input file name
+                           !     velhvcurfiles           Vel. cur. high freq. input file name
+                           !     velavadcpfiles          Vel. ADCP daily av. input file name
+                           !     velhvadcpfiles          Vel. ADCP high freq. input file name
+                           !     velfbfiles              Vel. feedback input observation file name
+                           !     dobsini                 Initial date in window YYYYMMDD.HHMMSS
+                           !     dobsend                 Final date in window YYYYMMDD.HHMMSS
+                           !     n1dint                  Type of vertical interpolation method
+                           !     n2dint                  Type of horizontal interpolation method
+                           !     ln_nea                  Rejection of observations near land switch
+   nmsshc     = 0          ! MSSH correction scheme
+                           !     mdtcorr                 MDT  correction
+                           !     mdtcutoff               MDT cutoff for computed correction
+   ln_sss     = .false.    ! Logical switch for SSS observations
+   ln_seaice  = .false.    ! Logical switch for Sea Ice observations
+   ln_vel3d   = .false.    ! Logical switch for velocity observations
+   ln_velavcur= .false     ! Logical switch for velocity daily av. cur.
+   ln_velhrcur= .false     ! Logical switch for velocity high freq. cur.
+   ln_velavadcp = .false.  ! Logical switch for velocity daily av. ADCP
+   ln_velhradcp = .false.  ! Logical switch for velocity high freq. ADCP
+   ln_velfb   = .false.    ! Logical switch for feedback velocity data
+   ln_grid_global = .false. ! Global distribtion of observations
+   ln_grid_search_lookup = .false. !  Logical switch for obs grid search w/lookup table
+   grid_search_file = 'grid_search'  !  Grid search lookup file header
+! All of the *files* variables below are arrays. Use namelist_cfg to add more files
+   enactfiles = 'enact.nc' !  ENACT input observation file names (specify full array in namelist_cfg)
+   coriofiles = 'corio.nc' !  Coriolis input observation file name
+   profbfiles = 'profiles_01.nc' ! Profile feedback input observation file name
+   ln_profb_enatim = .false !        Enact feedback input time setting switch
+   slafilesact = 'sla_act.nc' !  Active SLA input observation file names
+   slafilespas = 'sla_pass.nc' ! Passive SLA input observation file names
+   slafbfiles = 'sla_01.nc' ! slafbfiles: Feedback SLA input observation file names
+   sstfiles = 'ghrsst.nc'   ! GHRSST input observation file names
+   sstfbfiles = 'sst_01.nc' ! Feedback SST input observation file names
+   seaicefiles = 'seaice_01.nc' ! Sea Ice input observation file names
+   velavcurfiles = 'velavcurfile.nc'  ! Vel. cur. daily av. input file name
+   velhrcurfiles = 'velhrcurfile.nc'  ! Vel. cur. high freq. input file name
+   velavadcpfiles = 'velavadcpfile.nc' ! Vel. ADCP daily av. input file name
+   velhradcpfiles = 'velhradcpfile.nc' ! Vel. ADCP high freq. input file name
+   velfbfiles = 'velfbfile.nc' ! Vel. feedback input observation file name
+   dobsini = 20000101.000000  !  Initial date in window YYYYMMDD.HHMMSS
+   dobsend = 20010101.000000  !  Final date in window YYYYMMDD.HHMMSS
+   n1dint = 0  !               Type of vertical interpolation method
+   n2dint = 0  !               Type of horizontal interpolation method
+   ln_nea = .false.   !        Rejection of observations near land switch
+   nmsshc     = 0     !        MSSH correction scheme
+   mdtcorr = 1.61     !        MDT  correction
+   mdtcutoff = 65.0   !        MDT cutoff for computed correction
    ln_altbias = .false.    ! Logical switch for alt bias
    ln_ignmis  = .true.     ! Logical switch for ignoring missing files
                            !     endailyavtypes   ENACT daily average types
+   endailyavtypes = 820    ! ENACT daily average types - array (use namelist_cfg to set more values)
    ln_grid_global = .true.
    ln_grid_search_lookup = .false.

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/namptr

-                      r4147
+                      r6436
 !-----------------------------------------------------------------------
    ln_diaptr  = .false.    !  Poleward heat and salt transport (T) or not (F)
+   ln_diaznl  = .true.     !  Add zonal means and meridional stream functions
+   ln_subbas  = .true.     !  Atlantic/Pacific/Indian basins computation (T) or not
+                           !  (orca configuration only, need input basins mask file named "subbasins.nc"
+   ln_ptrcomp = .true.     !  Add decomposition : overturning
+   nn_fptr    =  1         !  Frequency of ptr computation [time step]
+   nn_fwri    =  15        !  Frequency of ptr outputs [time step]
+   ln_subbas  = .false.     !  Atlantic/Pacific/Indian basins computation (T) or not
+/

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/namrun

-                      r4147
+                      r6436
    nn_leapy    =       0   !  Leap year calendar (1) or not (0)
    ln_rstart   = .false.   !  start from rest (F) or from a restart file (T)
+   nn_rstctl   =       0   !  restart control => activated only if ln_rstart = T
+   nn_euler    =       1   !  = 0 : start with forward time step if ln_rstart=T
+   nn_rstctl   =       0   !  restart control ==> activated only if ln_rstart=T
                            !    = 0 nn_date0 read in namelist ; nn_it000 : read in namelist
                            !    = 1 nn_date0 read in namelist ; nn_it000 : check consistancy between namelist and restart
                            !    = 2 nn_date0 read in restart  ; nn_it000 : check consistancy between namelist and restart
    cn_ocerst_in  = "restart"   !  suffix of ocean restart name (input)
+   cn_ocerst_indir = "."       !  directory from which to read input ocean restarts
    cn_ocerst_out = "restart"   !  suffix of ocean restart name (output)
+   cn_ocerst_outdir = "."      !  directory in which to write output ocean restarts
    nn_istate   =       0   !  output the initial state (1) or not (0)
+   ln_rst_list = .false.   !  output restarts at list of times using nn_stocklist (T) or at set frequency with nn_stock (F)
    nn_stock    =    5475   !  frequency of creation of a restart file (modulo referenced to 1)
+   nn_stocklist = 0,0,0,0,0,0,0,0,0,0 ! List of timesteps when a restart file is to be written
    nn_write    =    5475   !  frequency of write in the output file   (modulo referenced to nn_it000)
    ln_dimgnnn  = .false.   !  DIMG file format: 1 file for all processors (F) or by processor (T)
    ln_mskland  = .false.   !  mask land points in NetCDF outputs (costly: + ~15%)
+   ln_cfmeta   = .false.   !  output additional data to netCDF files required for compliance with the CF metadata standard
    ln_clobber  = .false.   !  clobber (overwrite) an existing file
    nn_chunksz  =       0   !  chunksize (bytes) for NetCDF file (works only with iom_nf90 routines)

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/namsbc

-                      r5120
+                      r6436
    ln_blk_core = .true.    !  CORE bulk formulation                     (T => fill namsbc_core)
    ln_blk_mfs  = .false.   !  MFS bulk formulation                      (T => fill namsbc_mfs )
+   ln_cpl      = .false.   !  Coupled formulation                       (T => fill namsbc_cpl )
+   ln_cpl      = .false.   !  atmosphere coupled   formulation          ( requires key_oasis3 )
+   ln_mixcpl   = .false.   !  forced-coupled mixed formulation          ( requires key_oasis3 )
+   nn_components = 0       !  configuration of the opa-sas OASIS coupling
+                           !  =0 no opa-sas OASIS coupling: default single executable configuration
+                           !  =1 opa-sas OASIS coupling: multi executable configuration, OPA component
+                           !  =2 opa-sas OASIS coupling: multi executable configuration, SAS component
    ln_apr_dyn  = .false.   !  Patm gradient added in ocean & ice Eqs.   (T => fill namsbc_apr )
    nn_ice      = 2         !  =0 no ice boundary condition   ,
                            !  =1 use observed ice-cover      ,
                            !  =2 ice-model used                         ("key_lim3" or "key_lim2)
    nn_ice_embd = 0         !  =0 levitating ice (no mass exchange, concentration/dilution effect)
+                           !  =2 ice-model used                         ("key_lim3" or "key_lim2")
+   nn_ice_embd = 1         !  =0 levitating ice (no mass exchange, concentration/dilution effect)
                            !  =1 levitating ice with mass and salt exchange but no presure effect
                            !  =2 embedded sea-ice (full salt and mass exchanges and pressure)
    ln_dm2dc    = .false.   !  daily mean to diurnal cycle on short wave
    ln_rnf      = .true.    !  runoffs                                   (T => fill namsbc_rnf)
+   ln_rnf      = .true.    !  runoffs                                   (T   => fill namsbc_rnf)
    nn_isf      = 0         !  ice shelf melting/freezing                (/=0 => fill namsbc_isf)
                            !  0 =no isf                  1 = presence of ISF
 …
                            !  option 1 and 4 need ln_isfcav = .true. (domzgr)
    ln_ssr      = .true.    !  Sea Surface Restoring on T and/or S       (T => fill namsbc_ssr)
    nn_fwb      = 3         !  FreshWater Budget: =0 unchecked
+   nn_fwb      = 2         !  FreshWater Budget: =0 unchecked
                            !     =1 global mean of e-p-r set to zero at each time step
                            !     =2 annual global mean of e-p-r set to zero
-                           !     =3 global emp set to zero and spread out over erp area
    ln_wave = .false.       !  Activate coupling with wave (either Stokes Drift or Drag coefficient, or both)  (T => fill namsbc_wave)
    ln_cdgw = .false.       !  Neutral drag coefficient read from wave model (T => fill namsbc_wave)
    ln_sdw  = .false.       !  Computation of 3D stokes drift                (T => fill namsbc_wave)
+   nn_lsm  = 0             !  =0   land/sea mask for input fields is not applied (the field land/sea mask filename
+                           !       is left empty in namelist)  ,
+                           !  =1:n number of iterations of land/sea mask application for input fields
+   nn_lsm  = 0             !  =0 land/sea mask for input fields is not applied (keep empty land/sea mask filename field) ,
+                           !  =1:n number of iterations of land/sea mask application for input fields (fill land/sea mask filename field)
+   nn_limflx = -1          !  LIM3 Multi-category heat flux formulation (use -1 if LIM3 is not used)
+                           !  =-1  Use per-category fluxes, bypass redistributor, forced mode only, not yet implemented coupled
+                           !  = 0  Average per-category fluxes (forced and coupled mode)
+                           !  = 1  Average and redistribute per-category fluxes, forced mode only, not yet implemented coupled
+                           !  = 2  Redistribute a single flux over categories (coupled mode only)
+/

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/namsbc_alb

-                      r4147
+                      r6436
 &namsbc_alb    !   albedo parameters
 !-----------------------------------------------------------------------
+   rn_cloud    =    0.06   !  cloud correction to snow and ice albedo
+   rn_albice   =    0.53   !  albedo of melting ice in the arctic and antarctic
+   rn_alphd    =    0.80   !  coefficients for linear interpolation used to
+   rn_alphc    =    0.65   !  compute albedo between two extremes values
+   rn_alphdi   =    0.72   !  (Pyane, 1972)
+   nn_ice_alb  =    0   !  parameterization of ice/snow albedo
+                        !     0: Shine & Henderson-Sellers (JGR 1985)
+                        !     1: "home made" based on Brandt et al. (J. Climate 2005)
+                        !                         and Grenfell & Perovich (JGR 2004)
+   rn_albice   =  0.53  !  albedo of bare puddled ice (values from 0.49 to 0.58)
+                        !     0.53 (default) => if nn_ice_alb=0
+                        !     0.50 (default) => if nn_ice_alb=1
+/

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/namsbc_apr

-                      r4230
+                      r6436
 &namsbc_apr    !   Atmospheric pressure used as ocean forcing or in bulk
 !-----------------------------------------------------------------------
 !              ! file name ! frequency (hours) ! variable ! time interpol. !  clim   ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
 !              !           !  (if <0  months)  !   name   !    (logical)   !  (T/F)  ! 'monthly' ! filename ! pairing  ! filename      !
    sn_apr      = 'patm'    ,         -1        ,'somslpre',    .true.      , .true.  , 'yearly'  ,  ''      ,   ''     , ''
+!              !  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
+!              !             !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
+   sn_apr      = 'patm'      ,         -1        ,'somslpre',    .true.     , .true. , 'yearly'  ,  ''      ,   ''     , ''
    cn_dir      = './'       !  root directory for the location of the bulk files
    rn_pref     = 101000._wp !  reference atmospheric pressure   [N/m2]/
+   rn_pref     = 101000.    !  reference atmospheric pressure   [N/m2]/
    ln_ref_apr  = .false.    !  ref. pressure: global mean Patm (T) or a constant (F)
    ln_apr_obc  = .false.    !  inverse barometer added to OBC ssh data

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/namsbc_core

-                      r4230
+                      r6436
 &namsbc_core   !   namsbc_core  CORE bulk formulae
 !-----------------------------------------------------------------------
 !              !  file name                    ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
 !              !                               !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  !  filename     !
    sn_wndi     = 'u_10.15JUNE2009_orca2'       ,         6         , 'U_10_MOD',   .false.    , .true. , 'yearly'  , ''       , 'Uwnd'   , ''
    sn_wndj     = 'v_10.15JUNE2009_orca2'       ,         6         , 'V_10_MOD',   .false.    , .true. , 'yearly'  , ''       , 'Vwnd'   , ''
    sn_qsr      = 'ncar_rad.15JUNE2009_orca2'   ,        24         , 'SWDN_MOD',   .false.    , .true. , 'yearly'  , ''       , ''       , ''
    sn_qlw      = 'ncar_rad.15JUNE2009_orca2'   ,        24         , 'LWDN_MOD',   .false.    , .true. , 'yearly'  , ''       , ''       , ''
    sn_tair     = 't_10.15JUNE2009_orca2'       ,         6         , 'T_10_MOD',   .false.    , .true. , 'yearly'  , ''       , ''       , ''
    sn_humi     = 'q_10.15JUNE2009_orca2'       ,         6         , 'Q_10_MOD',   .false.    , .true. , 'yearly'  , ''       , ''       , ''
    sn_prec     = 'ncar_precip.15JUNE2009_orca2',        -1         , 'PRC_MOD1',   .false.    , .true. , 'yearly'  , ''       , ''       , ''
    sn_snow     = 'ncar_precip.15JUNE2009_orca2',        -1         , 'SNOW'    ,   .false.    , .true. , 'yearly'  , ''       , ''       , ''
    sn_tdif     = 'taudif_core'                 ,        24         , 'taudif'  ,   .false.    , .true. , 'yearly'  , ''       , ''       , ''
+!
+!              !  file name                    ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights                               ! rotation ! land/sea mask !
+!              !                               !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename                              ! pairing  ! filename      !
+   sn_wndi     = 'u_10.15JUNE2009_fill'        ,         6         , 'U_10_MOD',   .false.    , .true. , 'yearly'  , 'weights_core_orca2_bicubic_noc.nc'   , 'Uwnd'   , ''
+   sn_wndj     = 'v_10.15JUNE2009_fill'        ,         6         , 'V_10_MOD',   .false.    , .true. , 'yearly'  , 'weights_core_orca2_bicubic_noc.nc'   , 'Vwnd'   , ''
+   sn_qsr      = 'ncar_rad.15JUNE2009_fill'    ,        24         , 'SWDN_MOD',   .false.    , .true. , 'yearly'  , 'weights_core_orca2_bilinear_noc.nc'  , ''       , ''
+   sn_qlw      = 'ncar_rad.15JUNE2009_fill'    ,        24         , 'LWDN_MOD',   .false.    , .true. , 'yearly'  , 'weights_core_orca2_bilinear_noc.nc'  , ''       , ''
+   sn_tair     = 't_10.15JUNE2009_fill'        ,         6         , 'T_10_MOD',   .false.    , .true. , 'yearly'  , 'weights_core_orca2_bilinear_noc.nc'  , ''       , ''
+   sn_humi     = 'q_10.15JUNE2009_fill'        ,         6         , 'Q_10_MOD',   .false.    , .true. , 'yearly'  , 'weights_core_orca2_bilinear_noc.nc'  , ''       , ''
+   sn_prec     = 'ncar_precip.15JUNE2009_fill' ,        -1         , 'PRC_MOD1',   .false.    , .true. , 'yearly'  , 'weights_core_orca2_bilinear_noc.nc'  , ''       , ''
+   sn_snow     = 'ncar_precip.15JUNE2009_fill' ,        -1         , 'SNOW'    ,   .false.    , .true. , 'yearly'  , 'weights_core_orca2_bilinear_noc.nc'  , ''       , ''
+   sn_tdif     = 'taudif_core'                 ,        24         , 'taudif'  ,   .false.    , .true. , 'yearly'  , 'weights_core_orca2_bilinear_noc.nc'  , ''       , ''
    cn_dir      = './'      !  root directory for the location of the bulk files
-   ln_2m       = .false.   !  air temperature and humidity referenced at 2m (T) instead 10m (F)
    ln_taudif   = .false.   !  HF tau contribution: use "mean of stress module - module of the mean stress" data
+   rn_zqt      = 10.        !  Air temperature and humidity reference height (m)
+   rn_zu       = 10.        !  Wind vector reference height (m)
    rn_pfac     = 1.        !  multiplicative factor for precipitation (total & snow)
+   rn_efac     = 1.        !  multiplicative factor for evaporation (0. or 1.)
+   rn_vfac     = 0.        !  multiplicative factor for ocean/ice velocity
+                           !  in the calculation of the wind stress (0.=absolute winds or 1.=relative winds)
+/

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/namsbc_cpl

-                      r4147
+                      r6436
 !-----------------------------------------------------------------------
 &namsbc_cpl    !   coupled ocean/atmosphere model                       ("key_coupled")
+&namsbc_cpl    !   coupled ocean/atmosphere model                       ("key_oasis3")
 !-----------------------------------------------------------------------
 !                    !     description       !  multiple  !    vector   !      vector          ! vector !
 !                    !                       ! categories !  reference  !    orientation       ! grids  !
 ! send
 sn_snd_temp   =       'weighted oce and ice' ,    'no'    ,     ''      ,         ''           ,   ''
 sn_snd_alb    =       'weighted ice'         ,    'no'    ,     ''      ,         ''           ,   ''
 sn_snd_thick  =       'none'                 ,    'no'   ,     ''      ,         ''           ,   ''
 sn_snd_crt    =       'none'                 ,    'no'    , 'spherical' , 'eastward-northward' ,  'T'
 sn_snd_co2    =       'coupled'              ,    'no'    ,     ''      ,         ''           ,   ''
+   sn_snd_temp   =       'weighted oce and ice' ,    'no'    ,     ''      ,         ''           ,   ''
+   sn_snd_alb    =       'weighted ice'         ,    'no'    ,     ''      ,         ''           ,   ''
+   sn_snd_thick  =       'none'                 ,    'no'   ,     ''      ,         ''           ,   ''
+   sn_snd_crt    =       'none'                 ,    'no'    , 'spherical' , 'eastward-northward' ,  'T'
+   sn_snd_co2    =       'coupled'              ,    'no'    ,     ''      ,         ''           ,   ''
 ! receive
+sn_rcv_w10m   =       'none'                 ,    'no'    ,     ''      ,         ''          ,   ''
+sn_rcv_taumod =       'coupled'              ,    'no'    ,     ''      ,         ''          ,   ''
+sn_rcv_tau    =       'oce only'             ,    'no'    , 'cartesian' , 'eastward-northward',  'U,V'
+sn_rcv_dqnsdt =       'coupled'              ,    'no'    ,     ''      ,         ''          ,   ''
+sn_rcv_qsr    =       'oce and ice'          ,    'no'    ,     ''      ,         ''          ,   ''
+sn_rcv_qns    =       'oce and ice'          ,    'no'    ,     ''      ,         ''          ,   ''
+sn_rcv_emp    =       'conservative'         ,    'no'    ,     ''      ,         ''          ,   ''
+sn_rcv_rnf    =       'coupled'              ,    'no'    ,     ''      ,         ''          ,   ''
+sn_rcv_cal    =       'coupled'              ,    'no'    ,     ''      ,         ''          ,   ''
+sn_rcv_co2    =       'coupled'              ,    'no'    ,     ''      ,         ''          ,   ''
+   sn_rcv_w10m   =       'none'                 ,    'no'    ,     ''      ,         ''          ,   ''
+   sn_rcv_taumod =       'coupled'              ,    'no'    ,     ''      ,         ''          ,   ''
+   sn_rcv_tau    =       'oce only'             ,    'no'    , 'cartesian' , 'eastward-northward',  'U,V'
+   sn_rcv_dqnsdt =       'coupled'              ,    'no'    ,     ''      ,         ''          ,   ''
+   sn_rcv_qsr    =       'oce and ice'          ,    'no'    ,     ''      ,         ''          ,   ''
+   sn_rcv_qns    =       'oce and ice'          ,    'no'    ,     ''      ,         ''          ,   ''
+   sn_rcv_emp    =       'conservative'         ,    'no'    ,     ''      ,         ''          ,   ''
+   sn_rcv_rnf    =       'coupled'              ,    'no'    ,     ''      ,         ''          ,   ''
+   sn_rcv_cal    =       'coupled'              ,    'no'    ,     ''      ,         ''          ,   ''
+   sn_rcv_co2    =       'coupled'              ,    'no'    ,     ''      ,         ''          ,   ''
+!
+   nn_cplmodel   =     1     !  Maximum number of models to/from which NEMO is potentialy sending/receiving data
+   ln_usecplmask = .false.   !  use a coupling mask file to merge data received from several models
+                             !   -> file cplmask.nc with the float variable called cplmask (jpi,jpj,nn_cplmodel)
+/

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/namsbc_mfs

-                      r4230
+                      r6436
 &namsbc_mfs   !   namsbc_mfs  MFS bulk formulae
 !-----------------------------------------------------------------------
+!              !  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
+!              !             !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
+   sn_wndi     =   'ecmwf'   ,        6          , 'u10'     ,    .true.    , .false. , 'daily'  ,'bicubic.nc' , ''    , ''
+   sn_wndj     =   'ecmwf'   ,        6          , 'v10'     ,    .true.    , .false. , 'daily'  ,'bicubic.nc' , ''    , ''
+   sn_clc      =   'ecmwf'   ,        6          , 'clc'     ,    .true.    , .false. , 'daily'  ,'bilinear.nc', ''    , ''
+   sn_msl      =   'ecmwf'   ,        6          , 'msl'     ,    .true.    , .false. , 'daily'  ,'bicubic.nc' , ''    , ''
+   sn_tair     =   'ecmwf'   ,        6          , 't2'      ,    .true.    , .false. , 'daily'  ,'bicubic.nc' , ''    , ''
+   sn_rhm      =   'ecmwf'   ,        6          , 'rh'      ,    .true.    , .false. , 'daily'  ,'bilinear.nc', ''    , ''
+   sn_prec     =   'precip'  ,        6          , 'precip'  ,    .true.    , .false. , 'daily'  ,'bicubic'    , ''    , ''
+   cn_dir      =   './'      !  root directory for the location of the bulk files
+!              !  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights     ! rotation ! land/sea mask !
+!              !             !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename    ! pairing  ! filename      !
+   sn_wndi     =   'ecmwf'   ,        6          , 'u10'     ,    .true.    , .false. , 'daily'  ,'bicubic.nc' , ''       , ''
+   sn_wndj     =   'ecmwf'   ,        6          , 'v10'     ,    .true.    , .false. , 'daily'  ,'bicubic.nc' , ''       , ''
+   sn_clc      =   'ecmwf'   ,        6          , 'clc'     ,    .true.    , .false. , 'daily'  ,'bilinear.nc', ''       , ''
+   sn_msl      =   'ecmwf'   ,        6          , 'msl'     ,    .true.    , .false. , 'daily'  ,'bicubic.nc' , ''       , ''
+   sn_tair     =   'ecmwf'   ,        6          , 't2'      ,    .true.    , .false. , 'daily'  ,'bicubic.nc' , ''       , ''
+   sn_rhm      =   'ecmwf'   ,        6          , 'rh'      ,    .true.    , .false. , 'daily'  ,'bilinear.nc', ''       , ''
+   sn_prec     =   'ecmwf'   ,        6          , 'precip'  ,    .true.    , .true.  , 'daily'  ,'bicubic.nc' , ''       , ''
+   cn_dir      = './ECMWF/'      !  root directory for the location of the bulk files
+/

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/namsbc_rnf

-                      r4230
+                      r6436
 &namsbc_rnf    !   runoffs namelist surface boundary condition
 !-----------------------------------------------------------------------
 !              !  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
 !              !             !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
    sn_rnf      = 'runoff_core_monthly',    -1    , 'sorunoff',   .true.     , .true. , 'yearly'  , ''       , ''       , ''
    sn_cnf      = 'runoff_core_monthly',     0    , 'socoefr0',   .false.    , .true. , 'yearly'  , ''       , ''       , ''
    sn_s_rnf    = 'runoffs'            ,    24    , 'rosaline',   .true.     , .true. , 'yearly'  , ''       , ''       , ''
    sn_t_rnf    = 'runoffs'            ,    24    , 'rotemper',   .true.     , .true. , 'yearly'  , ''       , ''       , ''
    sn_dep_rnf  = 'runoffs'            ,     0    , 'rodepth' ,   .false.    , .true. , 'yearly'  , ''       , ''       , ''
+!              !  file name           ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
+!              !                      !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
+   sn_rnf      = 'runoff_core_monthly',        -1         , 'sorunoff',   .true.     , .true. , 'yearly'  , ''       , ''       , ''
+   sn_cnf      = 'runoff_core_monthly',         0         , 'socoefr0',   .false.    , .true. , 'yearly'  , ''       , ''       , ''
+   sn_s_rnf    = 'runoffs'            ,        24         , 'rosaline',   .true.     , .true. , 'yearly'  , ''       , ''       , ''
+   sn_t_rnf    = 'runoffs'            ,        24         , 'rotemper',   .true.     , .true. , 'yearly'  , ''       , ''       , ''
+   sn_dep_rnf  = 'runoffs'            ,         0         , 'rodepth' ,   .false.    , .true. , 'yearly'  , ''       , ''       , ''
    cn_dir       = './'      !  root directory for the location of the runoff files
-   ln_rnf_emp   = .false.   !  runoffs included into precipitation field (T) or into a file (F)
    ln_rnf_mouth = .true.    !  specific treatment at rivers mouths
    rn_hrnf      =  15.e0    !  depth over which enhanced vertical mixing is used
 …
    ln_rnf_tem   = .false.   !  read in temperature information for runoff
    ln_rnf_sal   = .false.   !  read in salinity information for runoff
+   ln_rnf_depth_ini = .false.  ! compute depth at initialisation from runoff file
+   rn_rnf_max   = 5.735e-4  !  max value of the runoff climatologie over global domain ( ln_rnf_depth_ini = .true )
+   rn_dep_max   = 150.      !  depth over which runoffs is spread ( ln_rnf_depth_ini = .true )
+   nn_rnf_depth_file = 0    !  create (=1) a runoff depth file or not (=0)
+/

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/namsbc_sas

-                      r4230
+                      r6436
 !              !  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
 !              !             !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
+   sn_usp      = 'sas_grid_U' ,    120    , 'vozocrtx' ,  .true.    , .true. ,   'yearly'  , ''       , ''             , ''
+   sn_vsp      = 'sas_grid_V' ,    120    , 'vomecrty' ,  .true.    , .true. ,   'yearly'  , ''       , ''             , ''
+   sn_tem      = 'sas_grid_T' ,    120    , 'sosstsst' ,  .true.    , .true. ,   'yearly'  , ''       , ''             , ''
+   sn_sal      = 'sas_grid_T' ,    120    , 'sosaline' ,  .true.    , .true. ,   'yearly'  , ''       , ''             , ''
+   sn_ssh      = 'sas_grid_T' ,    120    , 'sossheig' ,  .true.    , .true. ,   'yearly'  , ''       , ''             , ''
+   sn_usp      = 'sas_grid_U' ,    120           , 'vozocrtx' ,  .true.    , .true. ,   'yearly'  , ''       , ''             , ''
+   sn_vsp      = 'sas_grid_V' ,    120           , 'vomecrty' ,  .true.    , .true. ,   'yearly'  , ''       , ''             , ''
+   sn_tem      = 'sas_grid_T' ,    120           , 'sosstsst' ,  .true.    , .true. ,   'yearly'  , ''       , ''             , ''
+   sn_sal      = 'sas_grid_T' ,    120           , 'sosaline' ,  .true.    , .true. ,   'yearly'  , ''       , ''             , ''
+   sn_ssh      = 'sas_grid_T' ,    120           , 'sossheig' ,  .true.    , .true. ,   'yearly'  , ''       , ''             , ''
+   sn_e3t      = 'sas_grid_T' ,    120           , 'e3t_m'    ,  .true.    , .true. ,   'yearly'  , ''       , ''             , ''
+   sn_frq      = 'sas_grid_T' ,    120           , 'frq_m'    ,  .true.    , .true. ,   'yearly'  , ''       , ''             , ''
+   ln_3d_uv    = .true.    !  specify whether we are supplying a 3D u,v field
+   ln_3d_uve   = .true.    !  specify whether we are supplying a 3D u,v and e3 field
+   ln_read_frq = .false.    !  specify whether we must read frq or not
    cn_dir      = './'      !  root directory for the location of the bulk files are
+/

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/namsbc_wave

-                      r4230
+                      r6436
 &namsbc_wave   ! External fields from wave model
 !-----------------------------------------------------------------------
 !              !  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
 !              !             !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
    sn_cdg      =  'cdg_wave' ,        1          , 'drag_coeff' , .true.    , .false. , 'daily'  , ''       , ''       , ''
    sn_usd      =  'sdw_wave' ,        1          , 'u_sd2d'     , .true.   , .false. , 'daily'  ,''         , ''       , ''
    sn_vsd      =  'sdw_wave' ,        1          , 'v_sd2d'     , .true.   , .false. , 'daily'  ,''         , ''       , ''
    sn_wn       =  'sdw_wave' ,        1          , 'wave_num'   , .true.   , .false. , 'daily'  ,''         , ''       , ''
+!              !  file name  ! frequency (hours) ! variable     ! time interp. !  clim   ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
+!              !             !  (if <0  months)  !   name       !   (logical)  !  (T/F)  ! 'monthly' ! filename ! pairing  ! filename      !
+   sn_cdg      =  'cdg_wave' ,        1          , 'drag_coeff' ,     .true.   , .false. , 'daily'   ,  ''      , ''       , ''
+   sn_usd      =  'sdw_wave' ,        1          , 'u_sd2d'     ,     .true.   , .false. , 'daily'   ,  ''      , ''       , ''
+   sn_vsd      =  'sdw_wave' ,        1          , 'v_sd2d'     ,     .true.   , .false. , 'daily'   ,  ''      , ''       , ''
+   sn_wn       =  'sdw_wave' ,        1          , 'wave_num'   ,     .true.   , .false. , 'daily'   ,  ''      , ''       , ''
+!
    cn_dir_cdg  = './'  !  root directory for the location of drag coefficient files

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/namtra_adv

-                      r4147
+                      r6436
 &namtra_adv    !   advection scheme for tracer
 !-----------------------------------------------------------------------
+   ln_traadv_cen2   =  .false.  !  2nd order centered scheme
+   ln_traadv_tvd    =  .true.   !  TVD scheme
+   ln_traadv_muscl  =  .false.  !  MUSCL scheme
+   ln_traadv_muscl2 =  .false.  !  MUSCL2 scheme + cen2 at boundaries
+   ln_traadv_ubs    =  .false.  !  UBS scheme
+   ln_traadv_qck    =  .false.  !  QUICKEST scheme
+   ln_traadv_msc_ups=  .false.  !  use upstream scheme within muscl
+   ln_traadv_cen2   =  .false.   !  2nd order centered scheme
+   ln_traadv_tvd    =  .true.    !  TVD scheme
+   ln_traadv_muscl  =  .false.   !  MUSCL scheme
+   ln_traadv_muscl2 =  .false.   !  MUSCL2 scheme + cen2 at boundaries
+   ln_traadv_ubs    =  .false.   !  UBS scheme
+   ln_traadv_qck    =  .false.   !  QUICKEST scheme
+   ln_traadv_msc_ups=  .false.   !  use upstream scheme within muscl
+   ln_traadv_tvd_zts=  .false.  !  TVD scheme with sub-timestepping of vertical tracer advection
+/

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/namtra_dmp

-                      r5102
+                      r6436
 &namtra_dmp    !   tracer: T & S newtonian damping
 !-----------------------------------------------------------------------
+   ln_tradmp   =  .true.     !  add a damping termn (T) or not (F)
+   nn_zdmp     =    0        !  vertical   shape =0    damping throughout the water column
+                             !                   =1 no damping in the mixing layer (kz  criteria)
+                             !                   =2 no damping in the mixed  layer (rho crieria)
+   cn_resto    = 'resto.nc'  ! Name of file containing restoration coefficient field (use dmp_tools to create this)
+   ln_tradmp   =  .true.   !  add a damping termn (T) or not (F)
+   nn_zdmp     =    0      !  vertical   shape =0    damping throughout the water column
+                           !                   =1 no damping in the mixing layer (kz  criteria)
+                           !                   =2 no damping in the mixed  layer (rho crieria)
+   cn_resto    = 'resto.nc' ! Name of file containing restoration coefficient field (use dmp_tools to create this)
+/

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/namtra_qsr

-                      r4230
+                      r6436
    ln_qsr_2bd  = .false.   !  2 bands              light penetration
    ln_qsr_bio  = .false.   !  bio-model light penetration
    nn_chldta   =      1    !  RGB : Chl data (=1) or cst value (=0)
+   nn_chldta   =      1    !  RGB : 2D Chl data (=1), 3D Chl data (=2) or cst value (=0)
    rn_abs      =   0.58    !  RGB & 2 bands: fraction of light (rn_si1)
    rn_si0      =   0.35    !  RGB & 2 bands: shortess depth of extinction
    rn_si1      =   23.0    !  2 bands: longest depth of extinction
+   ln_qsr_ice  = .true.    !  light penetration for ice-model LIM3
+/

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/namtrd

-                      r3294
+                      r6436
 !-----------------------------------------------------------------------
 &namtrd        !   diagnostics on dynamics and/or tracer trends         ("key_trddyn" and/or "key_trdtra")
 !              !       or mixed-layer trends or barotropic vorticity    ("key_trdmld" or     "key_trdvor")
+&namtrd        !   diagnostics on dynamics and/or tracer trends
+!              !       and/or mixed-layer trends and/or barotropic vorticity
 !-----------------------------------------------------------------------
+   nn_trd      = 365       !  time step frequency dynamics and tracers trends
+   nn_ctls     =   0       !  control surface type in mixed-layer trends (0,1 or n<jpk)
+   rn_ucf      =   1.      !  unit conversion factor (=1 -> /seconds ; =86400. -> /day)
+   cn_trdrst_in      = "restart_mld"   ! suffix of ocean restart name (input)
+   cn_trdrst_out     = "restart_mld"   ! suffix of ocean restart name (output)
+   ln_trdmld_restart = .false.         !  restart for ML diagnostics
+   ln_trdmld_instant = .false.         !  flag to diagnose trends of instantantaneous or mean ML T/S
+   ln_glo_trd  = .false.   ! (T) global domain averaged diag for T, T^2, KE, and PE
+   ln_dyn_trd  = .false.   ! (T) 3D momentum trend output
+   ln_dyn_mxl  = .FALSE.   ! (T) 2D momentum trends averaged over the mixed layer (not coded yet)
+   ln_vor_trd  = .FALSE.   ! (T) 2D barotropic vorticity trends (not coded yet)
+   ln_KE_trd   = .false.   ! (T) 3D Kinetic   Energy     trends
+   ln_PE_trd   = .false.   ! (T) 3D Potential Energy     trends
+   ln_tra_trd  = .FALSE.   ! (T) 3D tracer trend output
+   ln_tra_mxl  = .false.   ! (T) 2D tracer trends averaged over the mixed layer (not coded yet)
+   nn_trd      = 365       !  print frequency (ln_glo_trd=T) (unit=time step)
+/

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/namtsd

-                      r4230
+                      r6436
 &namtsd    !   data : Temperature  & Salinity
 !-----------------------------------------------------------------------
+!          ! file name ! frequency (hours)         ! variable     ! time interp. ! clim  !'yearly' or ! weights  ! rotation ! land/sea mask !
+!          !           !  (if <0  months)          !   name       !  (logical)   ! (T/F) ! 'monthly'  ! filename ! pairing  ! filename      !
+   sn_tem  = 'data_1m_potential_temperature_nomask', -1,'votemper',  .true.      , .true., 'yearly'   , ' '      , ' '      , ''
+   sn_sal  = 'data_1m_salinity_nomask'             , -1,'vosaline',  .true.      , .true., 'yearly'   , ''       , ' '      , ''
+!-----------------------------------------------------------------------
+!          !  file name                            ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
+!          !                                       !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
+   sn_tem  = 'data_1m_potential_temperature_nomask',         -1        ,'votemper' ,    .true.    , .true. , 'yearly'   , ''       ,   ''    ,    ''
+   sn_sal  = 'data_1m_salinity_nomask'             ,         -1        ,'vosaline' ,    .true.    , .true. , 'yearly'   , ''       ,   ''    ,    ''
+   !
    cn_dir        = './'     !  root directory for the location of the runoff files

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/namzdf_gls

-                      r3294
+                      r6436
 &namzdf_gls                !   GLS vertical diffusion                   ("key_zdfgls")
 !-----------------------------------------------------------------------
    rn_emin       = 1.e-6   !  minimum value of e   [m2/s2]
+   rn_emin       = 1.e-7   !  minimum value of e   [m2/s2]
    rn_epsmin     = 1.e-12  !  minimum value of eps [m2/s3]
    ln_length_lim = .true.  !  limit on the dissipation rate under stable stratification (Galperin et al., 1988)
+   rn_clim_galp  = 0.53    !  galperin limit
+   ln_crban      = .true.  !  Use Craig & Banner (1994) surface wave mixing parametrisation
+   rn_clim_galp  = 0.267   !  galperin limit
    ln_sigpsi     = .true.  !  Activate or not Burchard 2001 mods on psi schmidt number in the wb case
    rn_crban      = 100.    !  Craig and Banner 1994 constant for wb tke flux
    rn_charn      = 70000.  !  Charnock constant for wb induced roughness length
+   nn_tkebc_surf =   1     !  surface tke condition (0/1/2=Dir/Neum/Dir Mellor-Blumberg)
+   nn_tkebc_bot  =   1     !  bottom tke condition (0/1=Dir/Neum)
+   nn_psibc_surf =   1     !  surface psi condition (0/1/2=Dir/Neum/Dir Mellor-Blumberg)
+   nn_psibc_bot  =   1     !  bottom psi condition (0/1=Dir/Neum)
+   nn_stab_func  =   2     !  stability function (0=Galp, 1= KC94, 2=CanutoA, 3=CanutoB)
+   nn_clos       =   1     !  predefined closure type (0=MY82, 1=k-eps, 2=k-w, 3=Gen)
+   rn_hsro       =  0.02   !  Minimum surface roughness
+   rn_frac_hs    =   1.3   !  Fraction of wave height as roughness (if nn_z0_met=2)
+   nn_z0_met     =     2   !  Method for surface roughness computation (0/1/2)
+   nn_bc_surf    =     1   !  surface condition (0/1=Dir/Neum)
+   nn_bc_bot     =     1   !  bottom condition (0/1=Dir/Neum)
+   nn_stab_func  =     2   !  stability function (0=Galp, 1= KC94, 2=CanutoA, 3=CanutoB)
+   nn_clos       =     1   !  predefined closure type (0=MY82, 1=k-eps, 2=k-w, 3=Gen)
+/

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/namzdf_tke

r4147	r6436
21	21	! = 1 add a tke source below the ML
22	22	! = 2 add a tke source just at the base of the ML
23		! = 3 as = 1 applied on HF part of the stress ("key_~~coupled~~")
	23	! = 3 as = 1 applied on HF part of the stress ("key_oasis3")
24	24	rn_efr = 0.05 ! fraction of surface tke value which penetrates below the ML (nn_etau=1 or 2)
25	25	nn_htau = 1 ! type of exponential decrease of tke penetration below the ML

branches/UKMO/nemo_v3_6_STABLE_copy/DOC/TexFiles/Namelist/namzgr_sco

-                      r3680
+                      r6436
                         !!!!!!!  SH94 stretching coefficients  (ln_s_sh94 = .true.)
    rn_theta    =    6.0    !  surface control parameter (0<=theta<=20)
    rn_bb       =    0.8    !  stretching with SH94 s-sigma
+   rn_bb       =    0.8    !  stretching with SH94 s-sigma
                         !!!!!!!  SF12 stretching coefficient  (ln_s_sf12 = .true.)
    rn_alpha    =    4.4    !  stretching with SF12 s-sigma
 …
    rn_zb_b     =   -0.2    !  offset for calculating Zb
                         !!!!!!!! Other stretching (not SH94 or SF12) [also uses rn_theta above]
    rn_thetb    =    1.0    !  bottom control parameter  (0<=thetb<= 1)
+   rn_thetb    =    1.0    !  bottom control parameter  (0<=thetb<= 1)
+/

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