Changeset 6322
- Timestamp:
- 2016-02-18T08:38:04+01:00 (8 years ago)
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- branches/2015/nemo_v3_6_STABLE/DOC/TexFiles
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branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Biblio/Biblio.bib
r6317 r6322 472 472 } 473 473 474 @article{bouffard_Boegman_DAO2013, 475 author = {D. Bouffard and L. Boegman}, 476 title = {A diapycnal diffusivity model for stratified environmental flows}, 477 volume = {61-62}, 478 issn = {03770265}, 479 url = {http://dx.doi.org/10.1016/j.dynatmoce.2013.02.002}, 480 doi = {10.1016/j.dynatmoce.2013.02.002}, 481 journal = DAO, 482 year = {2013}, 483 pages = {14--34}, 484 } 485 474 486 @ARTICLE{Bougeault1989, 475 487 author = {P. Bougeault and P. Lacarrere}, … … 787 799 volume = {34}, 788 800 pages = {8--13} 801 } 802 803 @article{de_lavergne_JPO2016_efficiency, 804 title = {The impact of a variable mixing efficiency on the abyssal overturning}, 805 issn = {0022-3670}, 806 url = {http://dx.doi.org//10.1175/JPO-D-14-0259.1}, 807 doi = {10.1175/JPO-D-14-0259.1}, 808 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.}, 809 journal = {Journal of Physical Oceanography}, 810 author = {C. de Lavergne and G. Madec and J. Le Sommer and A. J. G. Nurser and A. C. Naveira Garabato }, 811 year = {2016}, 812 volume = {46}, pages = {663-–681} 789 813 } 790 814 … … 1160 1184 } 1161 1185 1186 @article{goff_JGR2010, 1187 author = {J. A. Goff}, 1188 title = {Global prediction of abyssal hill root-mean-square heights from small-scale altimetric gravity variability}, 1189 issn = {2156-2202}, 1190 url = {http://dx.doi.org/10.1029/2010JB007867}, 1191 doi = {10.1029/2010JB007867}, 1192 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.}, 1193 volume = {115}, 1194 number = {B12}, 1195 journal = {Journal of Geophysical Research: Solid Earth}, 1196 year = {2010}, 1197 pages = {B12104}, 1198 } 1199 1162 1200 @ARTICLE{Goosse_al_JGR99, 1163 1201 author = {H. Goosse and E. Deleersnijder and T. Fichefet and M. England}, … … 1264 1302 1265 1303 @ARTICLE{Griffies_Hallberg_MWR00, 1266 author = {S.M. Griffies and R. Hallberg},1304 author = {S.M. Griffies and R.H. Hallberg}, 1267 1305 title = {Biharmonic friction with a Smagorinsky-like viscosity for use in large-scale eddy-permitting ocean models}, 1268 1306 journal = MWR, 1269 1307 year = {2000}, 1270 volume = {128(8)}, 1271 pages = {2935--2946} 1308 volume = {128}, 1309 pages = {2935–-2946}, 1310 url = {http://dx.doi.org/10.1175/1520-0493(2000)128} 1272 1311 } 1273 1312 … … 1585 1624 volume = {12}, 1586 1625 pages = {381--389} 1626 } 1627 1628 @article{Jackson_Rehmann_JPO2014, 1629 author = {P. R. Jackson and C. R. Rehmann}, 1630 title = {Experiments on differential scalar mixing in turbulence in a sheared, stratified flow}, 1631 journal = JPO, 1632 volume = {44}, 1633 issn = {0022-3670}, 1634 url = {http://dx.doi.org/10.1175/JPO-D-14-0027.1}, 1635 doi = {10.1175/JPO-D-14-0027.1}, 1636 number = {10}, 1637 year = {2014}, 1638 pages = {2661--2680}, 1587 1639 } 1588 1640 … … 1935 1987 year = {2009}, 1936 1988 volume = {30}, number = {2-3}, 1937 pages = {88- 94},1989 pages = {88--94}, 1938 1990 doi = {10.1016/j.ocemod.2009.06.006}, 1939 url = {http://dx.doi.org/ }1940 } 1941 1942 @ARTICLE{Leclair_Madec_OM1 0s,1991 url = {http://dx.doi.org/10.1016/j.ocemod.2009.06.006} 1992 } 1993 1994 @ARTICLE{Leclair_Madec_OM11, 1943 1995 author = {M. Leclair and G. Madec}, 1944 1996 title = {$\tilde{z}$-coordinate, an Arbitrary Lagrangian-Eulerian coordinate separating high and low frequency}, 1945 1997 journal = OM, 1946 year = {2010}, 1947 pages = {submitted}, 1998 year = {2011}, 1999 volume = {37}, pages = {139--152}, 2000 doi = {10.1016/j.ocemod.2011.02.001}, 2001 url = {http://dx.doi.org/10.1016/j.ocemod.2011.02.001} 1948 2002 } 1949 2003 … … 2427 2481 } 2428 2482 2483 2484 @ARTICLE{Morel_Berthon_LO89, 2485 author = {A. Morel and J.-F. Berthon}, 2486 title = {Surface pigments, algal biomass profiles, and potential production of the euphotic layer: 2487 Relationships reinvestigated in view of remote-sensing applications}, 2488 journal = {Limnol. Oceanogr.}, 2489 year = {1989}, 2490 volume = {34(8)}, 2491 pages = {1545--1562} 2492 } 2493 2429 2494 @ARTICLE{Morel_Maritorena_JGR01, 2430 2495 author = {A. Morel and S. Maritorena}, … … 2475 2540 title = {Estimates of the local rate of vertical diffusion from dissipation measurements}, 2476 2541 journal = JPO, 2542 year = {1980}, 2477 2543 volume = {10}, 2478 2544 pages = {83--89} … … 2709 2775 volume = {105}, 2710 2776 pages = {23,927--23,942} 2777 } 2778 2779 @ARTICLE{Rousset_GMD2015, 2780 author = {C. Rousset and M. Vancoppenolle and G. Madec and T. Fichefet and S. Flavoni 2781 and A. Barth\'{e}lemy and R. Benshila and J. Chanut and C. L\'{e}vy and S. Masson and F. Vivier }, 2782 title = {The Louvain-La-Neuve sea-ice model LIM3.6: Global and regional capabilities}, 2783 journal= {Geoscientific Model Development}, 2784 year = {2015}, 2785 volume = {8}, pages={2991--3005}, 2786 doi = {10.5194/gmd-8-2991-2015}, 2787 url = {http://dx.doi.org/10.5194/gmd-8-2991-2015} 2711 2788 } 2712 2789 -
branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_Model_Basics.tex
r6275 r6322 992 992 \label{PE_zco_tilde} 993 993 994 The $\tilde{z}$-coordinate has been developed by \citet{Leclair_Madec_OM1 0s}.994 The $\tilde{z}$-coordinate has been developed by \citet{Leclair_Madec_OM11}. 995 995 It is available in \NEMO since the version 3.4. Nevertheless, it is currently not robust enough 996 996 to be used in all possible configurations. Its use is therefore not recommended. -
branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_TRA.tex
r6317 r6322 749 749 ($i.e.$ the inverses of the extinction length scales) are tabulated over 61 nonuniform 750 750 chlorophyll classes ranging from 0.01 to 10 g.Chl/L (see the routine \rou{trc\_oce\_rgb} 751 in \mdl{trc\_oce} module). Three types of chlorophyll can be chosen in the RGB formulation: 752 (1) a constant 0.05 g.Chl/L value everywhere (\np{nn\_chdta}=0) ; (2) an observed 753 time varying chlorophyll (\np{nn\_chdta}=1) ; (3) simulated time varying chlorophyll 754 by TOP biogeochemical model (\np{ln\_qsr\_bio}=true). In the latter case, the RGB 755 formulation is used to calculate both the phytoplankton light limitation in PISCES 756 or LOBSTER and the oceanic heating rate. 757 751 in \mdl{trc\_oce} module). Four types of chlorophyll can be chosen in the RGB formulation: 752 \begin{description} 753 \item[\np{nn\_chdta}=0] 754 a constant 0.05 g.Chl/L value everywhere ; 755 \item[\np{nn\_chdta}=1] 756 an observed time varying chlorophyll deduced from satellite surface ocean color measurement 757 spread uniformly in the vertical direction ; 758 \item[\np{nn\_chdta}=2] 759 same as previous case except that a vertical profile of chlorophyl is used. 760 Following \cite{Morel_Berthon_LO89}, the profile is computed from the local surface chlorophyll value ; 761 \item[\np{ln\_qsr\_bio}=true] 762 simulated time varying chlorophyll by TOP biogeochemical model. 763 In this case, the RGB formulation is used to calculate both the phytoplankton 764 light limitation in PISCES or LOBSTER and the oceanic heating rate. 765 \end{description} 758 766 The trend in \eqref{Eq_tra_qsr} associated with the penetration of the solar radiation 759 767 is added to the temperature trend, and the surface heat flux is modified in routine \mdl{traqsr}. -
branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_ZDF.tex
r6317 r6322 1313 1313 1314 1314 % ================================================================ 1315 % Internal wave-driven mixing 1316 % ================================================================ 1317 \section{Internal wave-driven mixing (\key{zdftmx\_new})} 1318 \label{ZDF_tmx_new} 1319 1320 %--------------------------------------------namzdf_tmx_new------------------------------------------ 1321 \namdisplay{namzdf_tmx_new} 1322 %-------------------------------------------------------------------------------------------------------------- 1323 1324 The parameterization of mixing induced by breaking internal waves is a generalization 1325 of the approach originally proposed by \citet{St_Laurent_al_GRL02}. 1326 A three-dimensional field of internal wave energy dissipation $\epsilon(x,y,z)$ is first constructed, 1327 and the resulting diffusivity is obtained as 1328 \begin{equation} \label{Eq_Kwave} 1329 A^{vT}_{wave} = R_f \,\frac{ \epsilon }{ \rho \, N^2 } 1330 \end{equation} 1331 where $R_f$ is the mixing efficiency and $\epsilon$ is a specified three dimensional distribution 1332 of the energy available for mixing. If the \np{ln\_mevar} namelist parameter is set to false, 1333 the mixing efficiency is taken as constant and equal to 1/6 \citep{Osborn_JPO80}. 1334 In the opposite (recommended) case, $R_f$ is instead a function of the turbulence intensity parameter 1335 $Re_b = \frac{ \epsilon}{\nu \, N^2}$, with $\nu$ the molecular viscosity of seawater, 1336 following the model of \cite{Bouffard_Boegman_DAO2013} 1337 and the implementation of \cite{de_lavergne_JPO2016_efficiency}. 1338 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. 1339 1340 In addition to the mixing efficiency, the ratio of salt to heat diffusivities can chosen to vary 1341 as a function of $Re_b$ by setting the \np{ln\_tsdiff} parameter to true, a recommended choice). 1342 This parameterization of differential mixing, due to \cite{Jackson_Rehmann_JPO2014}, 1343 is implemented as in \cite{de_lavergne_JPO2016_efficiency}. 1344 1345 The three-dimensional distribution of the energy available for mixing, $\epsilon(i,j,k)$, is constructed 1346 from three static maps of column-integrated internal wave energy dissipation, $E_{cri}(i,j)$, 1347 $E_{pyc}(i,j)$, and $E_{bot}(i,j)$, combined to three corresponding vertical structures 1348 (de Lavergne et al., in prep): 1349 \begin{align*} 1350 F_{cri}(i,j,k) &\propto e^{-h_{ab} / h_{cri} }\\ 1351 F_{pyc}(i,j,k) &\propto N^{n\_p}\\ 1352 F_{bot}(i,j,k) &\propto N^2 \, e^{- h_{wkb} / h_{bot} } 1353 \end{align*} 1354 In the above formula, $h_{ab}$ denotes the height above bottom, 1355 $h_{wkb}$ denotes the WKB-stretched height above bottom, defined by 1356 \begin{equation*} 1357 h_{wkb} = H \, \frac{ \int_{-H}^{z} N \, dz' } { \int_{-H}^{\eta} N \, dz' } \; , 1358 \end{equation*} 1359 The $n_p$ parameter (given by \np{nn\_zpyc} in \ngn{namzdf\_tmx\_new} namelist) controls the stratification-dependence of the pycnocline-intensified dissipation. 1360 It can take values of 1 (recommended) or 2. 1361 Finally, the vertical structures $F_{cri}$ and $F_{bot}$ require the specification of 1362 the decay scales $h_{cri}(i,j)$ and $h_{bot}(i,j)$, which are defined by two additional input maps. 1363 $h_{cri}$ is related to the large-scale topography of the ocean (etopo2) 1364 and $h_{bot}$ is a function of the energy flux $E_{bot}$, the characteristic horizontal scale of 1365 the abyssal hill topography \citep{Goff_JGR2010} and the latitude. 1366 1367 % ================================================================ 1368 1369 1370 -
branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Introduction.tex
r6275 r6322 228 228 \item a deep re-writting and simplification of the off-line tracer component (OFF\_SRC) ; 229 229 \item the merge of passive and active advection and diffusion modules ; 230 \item 230 \item Use of the Flexible Configuration Manager (FCM) to build configurations, generate the Makefile and produce the executable ; 231 231 \item Linear-tangent and Adjoint component (TAM) added, phased with v3.0 232 232 \end{enumerate} … … 253 253 $\bullet$ The main modifications from NEMO/OPA v3.4 and v3.6 are :\\ 254 254 \begin{enumerate} 255 \item ... ; 256 \end{enumerate} 257 258 255 \item I/O management: NEMO in now interfaced with XIOS, a Input/Output server having a versatile xml user interface, and 256 allowing I/O to be performed on dedicated processors thus improving scalability and performance on massively parallel platforms. 257 \item ICB module \citep{Marsh_GMD2015}: icebergs as lagrangian floats ; 258 \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 259 \item ISF : Under ice-selves cavities (parametrisation and/or explicit representation) 260 \item Coupled interface for next IPCC requirements (multi category sea-ice, calving and iceberg module) 261 \item Ocean and ice allowed to be explicitly coupled through OASIS, using StandAlone Surface module) 262 \item On line coarsening of ocean I/O 263 \item Major evolution of LIM3 sea-ice model \citep{Rousset_GMD2015} 264 \item Open boundaries: completion of BDY/OBC merge : BDY is now the only Open boundary module available 265 \item re-visit of the specification of heat/salt(tracers)/mass fluxes ; 266 \item levitating or fully embedded sea-ice (for LIM and CICE) ; 267 \item a new parameterization of mixing induced by breaking internal waves (de Lavergne et al. in prep.) 268 And also: 269 \item update of AGRIF package and AGRIF compatibility with LIM2 sea-ice model ; 270 \item A new vertical sigma coordinate stretching function \citep{Siddorn_Furner_OM12} ; 271 \item Smagorinsky eddy coefficients: the \cite{Griffies_Hallberg_MWR00} Smagorinsky type diffusivity/viscosity for lateral mixing has been introduced ; 272 \item Standard Fox Kemper parametrisation 273 \item Analytical tropical cyclones taken in account using track and magnitude observations (Vincent et al. JGR 2012a,b) ; 274 \item OBS: observation operators improved and now available in Standalone mode ; 275 \item Log layer option for bottom friction 276 \item Faster split-explicit time stepping ; 277 \item Z-tilde ALE coordinates \citep{Leclair_Madec_OM11} ; 278 \item implicit bottom friction ; 279 \item Runoff improved and SBC with BGC 280 \item MPP assessment and optimisation 281 \item First steps of wave coupling 282 283 Features becoming obsolete: LIM2 (replaced by LIM3 monocategory) ; IOIPSL (replaced by XIOS) ; 284 285 Features that has been removed : LOBSTER (now included in PISCES) ; OBC, replaced by BDY ; 286 287 288 289 \end{enumerate} 290 291 -
branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Namelist/namsbc_alb
r4147 r6322 2 2 &namsbc_alb ! albedo parameters 3 3 !----------------------------------------------------------------------- 4 rn_cloud = 0.06 ! cloud correction to snow and ice albedo 5 rn_albice = 0.53 ! albedo of melting ice in the arctic and antarctic 6 rn_alphd = 0.80 ! coefficients for linear interpolation used to 7 rn_alphc = 0.65 ! compute albedo between two extremes values 8 rn_alphdi = 0.72 ! (Pyane, 1972) 4 nn_ice_alb = 0 ! parameterization of ice/snow albedo 5 ! 0: Shine & Henderson-Sellers (JGR 1985) 6 ! 1: "home made" based on Brandt et al. (J. Climate 2005) 7 ! and Grenfell & Perovich (JGR 2004) 8 rn_albice = 0.53 ! albedo of bare puddled ice (values from 0.49 to 0.58) 9 ! 0.53 (default) => if nn_ice_alb=0 10 ! 0.50 (default) => if nn_ice_alb=1 9 11 / -
branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Namelist/namtra_qsr
r5890 r6322 11 11 ln_qsr_2bd = .false. ! 2 bands light penetration 12 12 ln_qsr_bio = .false. ! bio-model light penetration 13 nn_chldta = 1 ! RGB : Chl data (=1) or cst value (=0)13 nn_chldta = 1 ! RGB : 2D Chl data (=1), 3D Chl data (=2) or cst value (=0) 14 14 rn_abs = 0.58 ! RGB & 2 bands: fraction of light (rn_si1) 15 15 rn_si0 = 0.35 ! RGB & 2 bands: shortess depth of extinction
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