Changeset 11043
 Timestamp:
 20190523T15:51:08+02:00 (3 years ago)
 Location:
 NEMO/trunk/doc
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NEMO/trunk/doc/latex/NEMO/main/NEMO_manual.sty
r11022 r11043 6 6 %% LaTeX packages 7 7 %% ============================================================================== 8 9 8 \usepackage{natbib} %% bib 10 9 \usepackage{caption} %% caption … … 24 23 25 24 %% Extensions in bundle package 26 27 25 \usepackage{amssymb, graphicx, makeidx, tabularx} 28 26 29 30 27 %% Configuration 31 32 28 \captionsetup{margin=10pt, font={small}, labelsep=colon, labelfont={bf}} 33 \hypersetup{34 pdftitle={NEMO ocean engine}, pdfauthor={Gurvan Madec, and NEMO System Team},35 colorlinks36 }37 29 \idxlayout{font=footnotesize, columns=3} 38 30 \renewcommand{\bibfont}{\footnotesize} … … 42 34 %% Styles 43 35 %% ============================================================================== 44 45 36 \pagestyle{fancy} 46 37 \bibliographystyle{../../NEMO/main/ametsoc} 47 38 48 39 %% Additionnal fonts 49 50 40 \DeclareMathAlphabet{\mathpzc}{OT1}{pzc}{m}{it} 51 41 52 42 53 43 %% Page layout 54 55 44 \fancyhf{} 56 45 \fancyhead[LE,RO]{\bfseries\thepage} … … 65 54 66 55 %% Catcodes 67 68 56 \makeatletter 69 57 \def\LigneVerticale{\vrule height 5cm depth 2cm\hspace{0.1cm}\relax} 
NEMO/trunk/doc/latex/NEMO/main/NEMO_manual.tex
r11013 r11043 12 12 %% Custom style (.sty) 13 13 \usepackage{../main/NEMO_manual} 14 \hypersetup{ 15 pdftitle={NEMO ocean engine}, pdfauthor={Gurvan Madec, and NEMO System Team}, 16 colorlinks 17 } 14 18 15 19 %% Include references and index for single subfile compilation … … 47 51 % 48 52 % } \\ 49 % \\50 53 \textit{Issue 27, Notes du P\^{o}le de mod\'{e}lisation} \\ 51 54 \textit{Institut PierreSimon Laplace (IPSL)} \\ … … 56 59 \maketitle 57 60 \frontmatter 58 59 61 60 62 %% ToC i.e. Table of Contents … … 123 125 \printindex 124 126 125 126 127 \end{document} 
NEMO/trunk/doc/latex/SI3/main/SI3_manual.bib
r11030 r11043 1 1 2 @Article{ 3 author 4 year 5 month 6 pages 7 title 8 volume 9 journal 2 @Article{ assur_1958, 3 author = {Assur, A}, 4 year = {1958}, 5 month = {01}, 6 pages = {106138}, 7 title = {Composition of sea ice and its tensile strength}, 8 volume = {598}, 9 journal = {Arctic Sea Ice} 10 10 } 11 11 … … 234 234 } 235 235 236 @Article{ h _yland_2002,236 @Article{ hoyland_2002, 237 237 author = {Høyland, Knut V.}, 238 238 title = {Consolidation of firstyear sea ice ridges}, … … 308 308 } 309 309 310 @Article{ lepp _ranta_1995,310 @Article{ lepparanta_1995, 311 311 author = {Leppäranta, Matti and Lensu, Mikko and Kosloff, Pekka and 312 312 Veitch, Brian}, … … 324 324 } 325 325 326 @Article{ lepp _ranta_2011,326 @Article{ lepparanta_2011, 327 327 author = {Leppäranta, Matti}, 328 328 title = {Drift ice material}, 329 329 year = 2011, 330 330 pages = {11–63}, 331 doi = {10.1007/9783642046834 _2},332 url = {http://dx.doi.org/10.1007/9783642046834 _2},331 doi = {10.1007/9783642046834\_2}, 332 url = {http://dx.doi.org/10.1007/9783642046834\_2}, 333 333 isbn = 9783642046834, 334 334 journal = {The Drift of Sea Ice}, … … 367 367 } 368 368 369 @Article{ massonnet_2018, 370 author = {Massonnet, F. and Barth\'el\'emy, A. and Worou, K. and 371 Fichefet, T. and Vancoppenolle, M. and Rousset, C.}, 372 title = {Insights on the discretization of the ice thickness 373 distribution in largescale sea ice models}, 374 journal = {submitted}, 375 year = {2018} 376 } 377 369 378 @Article{ maykut_1971, 370 379 author = {Maykut, Gary A. and Untersteiner, Norbert}, … … 383 392 } 384 393 394 @Article{ maykut_1973, 395 author = {Maykut, G. A. and Thorndike, A. S.}, 396 title = {An approach to coupling the dynamics and thermodynamics of 397 Arctic sea ice}, 398 journal = {AIDJEX Bulletin}, 399 year = {1973}, 400 volume = {21}, 401 pages = {2329} 402 } 403 385 404 @Article{ maykut_1986, 386 405 author = {Maykut, Gary A.}, … … 388 407 year = 1986, 389 408 pages = {395–463}, 390 doi = {10.1007/9781489953520 _6},391 url = {http://dx.doi.org/10.1007/9781489953520 _6},409 doi = {10.1007/9781489953520\_6}, 410 url = {http://dx.doi.org/10.1007/9781489953520\_6}, 392 411 isbn = 9781489953520, 393 412 journal = {The Geophysics of Sea Ice}, … … 546 565 } 547 566 567 @Book{ teos10_2010, 568 title = {{The international thermodynamic equation of seawater  569 2010: Calculation and use of thermodynamic properties}}, 570 publisher = {UNESCO (English)}, 571 year = {2010}, 572 author = {{IOC, SCOR and IAPSO}}, 573 series = {Intergovernmental Oceanographic Commission, Manuals and 574 Guides No. 56} 575 } 576 548 577 @Article{ thorndike_1975, 549 578 author = {Thorndike, A. S. and Rothrock, D. A. and Maykut, G. A. and … … 610 639 year = 1992, 611 640 pages = {113–138}, 612 doi = {10.1007/9789401128094 _20},613 url = {http://dx.doi.org/10.1007/9789401128094 _20},641 doi = {10.1007/9789401128094\_20}, 642 url = {http://dx.doi.org/10.1007/9789401128094\_20}, 614 643 isbn = 9789401128094, 615 644 journal = {Interactive Dynamics of Convection and Solidification}, 
NEMO/trunk/doc/latex/SI3/main/SI3_manual.tex
r11030 r11043 12 12 %% Custom style (.sty) 13 13 \usepackage{../../NEMO/main/NEMO_manual} 14 \hypersetup{ 15 pdftitle={SI³ – Sea Ice modelling Integrated Initiative – The NEMO Sea Ice engine}, 16 pdfauthor={NEMO Sea Ice Working Group}, 17 colorlinks 18 } 14 19 15 20 %% Include references and index for single subfile compilation 
NEMO/trunk/doc/latex/SI3/subfiles/chap_model_basics.tex
r11031 r11043 28 28 29 29 \subsection{Scales, thermodynamics and dynamics} 30 Because sea ice is much wider  $\mathcal{O}$(1001000 km)  than thick  $\mathcal{O}$(1 m)  ice drift can be considered as purely horizontal: vertical motions around the hydrostatic equilibrium position are negligible. The same scaling argument justifies the assumption that heat exchanges are purely vertical\footnote{The latter assumption is probably less valid, because the horizontal scales of temperature variations are $\mathcal{O}$(10100 m)}. It is on this basis that thermodynamics and dynamics are separated and rely upon different frameworks and sets of hypotheses: thermodynamics use the ice thickness distribution \citep{thorndike_1975} and the mushylayer \citep{worster_1992} frameworks, whereas dynamics assume continuum mechanics \citep[e.g.,][]{lepp _ranta_2011}. Thermodynamics and dynamics interact by two means: first, advection impacts state variables; second, the horizontal momentum equation depends, among other things, on the ice state.30 Because sea ice is much wider  $\mathcal{O}$(1001000 km)  than thick  $\mathcal{O}$(1 m)  ice drift can be considered as purely horizontal: vertical motions around the hydrostatic equilibrium position are negligible. The same scaling argument justifies the assumption that heat exchanges are purely vertical\footnote{The latter assumption is probably less valid, because the horizontal scales of temperature variations are $\mathcal{O}$(10100 m)}. It is on this basis that thermodynamics and dynamics are separated and rely upon different frameworks and sets of hypotheses: thermodynamics use the ice thickness distribution \citep{thorndike_1975} and the mushylayer \citep{worster_1992} frameworks, whereas dynamics assume continuum mechanics \citep[e.g.,][]{lepparanta_2011}. Thermodynamics and dynamics interact by two means: first, advection impacts state variables; second, the horizontal momentum equation depends, among other things, on the ice state. 31 31 32 32 \subsection{Subgrid scale variations} … … 70 70 & Description & Value & Units & Ref \\ \hline 71 71 $c_i$ (cpic) & Pure ice specific heat & 2067 & J/kg/K & ? \\ 72 $c_w$ (rcp) & Seawater specific heat & 3991 & J/kg/K & \cite{ TEOS_2010} \\72 $c_w$ (rcp) & Seawater specific heat & 3991 & J/kg/K & \cite{teos10_2010} \\ 73 73 $L$ (lfus) & Latent heat of fusion (0$^\circ$C) & 334000 & J/kg/K & \cite{bitz_1999} \\ 74 74 $\rho_i$ (rhoic) & Sea ice density & 917 & kg/m$^3$ & \cite{bitz_1999} \\ … … 154 154 \subsection{Dynamic formulation} 155 155 156 The formulation of ice dynamics is based on the continuum approach. The latter holds provided the drift ice particles are much larger than single ice floes, and much smaller than typical gradient scales. This compromise is rarely achieved in practice \citep{lepp _ranta_2011}. Yet the continuum approach generates a convenient momentum equation for the horizontal ice velocity vector $\mathbf{u}=(u,v)$, which can be solved with classical numerical methods (here, finite differences on the NEMO Cgrid). The most important term in the momentum equation is internal stress. We follow the viscousplastic (VP) rheological framework \citep{hibler_1979}, assuming that sea ice has no tensile strength but responds to compressive and shear deformations in a plastic way. In practice, the elasticviscousplastic (EVP) technique of \citep{bouillon_2013} is used, more convient numerically than VP. It is well accepted that the VP rheology and its relatives are the minimum complexity to get reasonable ice drift patterns \citep{kreyscher_2000}, but fail at generating the observed deformation patterns \citep{girard_2009}. This is a longlasting problem: what is the ideal rheological model for sea ice and how it should be applied are still being debated \citep[see, e.g.][]{weiss_2013}.156 The formulation of ice dynamics is based on the continuum approach. The latter holds provided the drift ice particles are much larger than single ice floes, and much smaller than typical gradient scales. This compromise is rarely achieved in practice \citep{lepparanta_2011}. Yet the continuum approach generates a convenient momentum equation for the horizontal ice velocity vector $\mathbf{u}=(u,v)$, which can be solved with classical numerical methods (here, finite differences on the NEMO Cgrid). The most important term in the momentum equation is internal stress. We follow the viscousplastic (VP) rheological framework \citep{hibler_1979}, assuming that sea ice has no tensile strength but responds to compressive and shear deformations in a plastic way. In practice, the elasticviscousplastic (EVP) technique of \citep{bouillon_2013} is used, more convient numerically than VP. It is well accepted that the VP rheology and its relatives are the minimum complexity to get reasonable ice drift patterns \citep{kreyscher_2000}, but fail at generating the observed deformation patterns \citep{girard_2009}. This is a longlasting problem: what is the ideal rheological model for sea ice and how it should be applied are still being debated \citep[see, e.g.][]{weiss_2013}. 157 157 158 158 % … … 296 296 $C$ (rn\_crhg) & ice strength concentration param. & 20 &  & \citep{hibler_1979} \\ 297 297 $H^*$ (rn\_hstar) & maximum ridged ice thickness param. & 25 & m & \citep{lipscomb_2007} \\ 298 $p$ (rn\_por\_rdg) & porosity of new ridges & 0.3 &  & \citep{lepp _ranta_1995} \\298 $p$ (rn\_por\_rdg) & porosity of new ridges & 0.3 &  & \citep{lepparanta_1995} \\ 299 299 $amax$ (rn\_amax) & maximum ice concentration & 0.999 &  & \\ 300 300 $h_0$ (rn\_hnewice) & thickness of newly formed ice & 0.1 & m &  \\ … … 313 313 Transport connects the horizontal velocity fields and the rest of the ice properties. LIM assumes that the ice properties in the different thickness categories are transported at the same velocity. The scheme of \cite{prather_1986}, based on the conservation of 0, 1$^{st}$ and 2$^{nd}$ order moments in $x$ and $y$directions, is used, with some numerical diffusion if desired. Whereas this scheme is accurate, nearly conservative, it is also quite expensive since, for each advected field, five moments need to be advected, which proves CPU consuming, in particular when multiple categories are used. Other solutions are currently explored. 314 314 315 The dissipation of energy associated with plastic failure under convergence and shear is accomplished by rafting (overriding of two ice plates) and ridging (breaking of an ice plate and subsequent piling of the broken ice blocks into pressure ridges). Thin ice preferentially rafts whereas thick ice preferentially ridges \citep{tuhkuri_2002}. Because observations of these processes are limited, their representation in LIM is rather heuristic. The amount of ice that rafts/ridges depends on the strain rate tensor invariants (shear and divergence) as in \citep{flato_1995}, while the ice categories involved are determined by a participation function favouring thin ice \citep{lipscomb_2007}. The thickness of ice being deformed ($h'$) determines whether ice rafts ($h'<$ 0.75 m) or ridges ($h'>$ 0.75 m), following \cite{haapala_2000}. The deformed ice thickness is $2h'$ after rafting, and is distributed between $2h'$ and $2 \sqrt{H^*h'}$ after ridging, where $H^* = 25$ m \citep{lipscomb_2007}. Newly ridged ice is highly porous, effectively trapping seawater. To represent this, a prescribed volume fraction (30\%) of newly ridged ice \citep{lepp _ranta_1995} incorporates mass, salt and heat are extracted from the ocean. Hence, in contrast with other models, the net thermodynamic ice production during convergence is not zero in LIM, since mass is added to sea ice during ridging. Consequently, simulated new ridges have high temperature and salinity as observed \citep{h_yland_2002}. A fraction of snow (50 \%) falls into the ocean during deformation.315 The dissipation of energy associated with plastic failure under convergence and shear is accomplished by rafting (overriding of two ice plates) and ridging (breaking of an ice plate and subsequent piling of the broken ice blocks into pressure ridges). Thin ice preferentially rafts whereas thick ice preferentially ridges \citep{tuhkuri_2002}. Because observations of these processes are limited, their representation in LIM is rather heuristic. The amount of ice that rafts/ridges depends on the strain rate tensor invariants (shear and divergence) as in \citep{flato_1995}, while the ice categories involved are determined by a participation function favouring thin ice \citep{lipscomb_2007}. The thickness of ice being deformed ($h'$) determines whether ice rafts ($h'<$ 0.75 m) or ridges ($h'>$ 0.75 m), following \cite{haapala_2000}. The deformed ice thickness is $2h'$ after rafting, and is distributed between $2h'$ and $2 \sqrt{H^*h'}$ after ridging, where $H^* = 25$ m \citep{lipscomb_2007}. Newly ridged ice is highly porous, effectively trapping seawater. To represent this, a prescribed volume fraction (30\%) of newly ridged ice \citep{lepparanta_1995} incorporates mass, salt and heat are extracted from the ocean. Hence, in contrast with other models, the net thermodynamic ice production during convergence is not zero in LIM, since mass is added to sea ice during ridging. Consequently, simulated new ridges have high temperature and salinity as observed \citep{hoyland_2002}. A fraction of snow (50 \%) falls into the ocean during deformation. 316 316 317 317 \section{Ice thermodynamics} 
NEMO/trunk/doc/latex/SI3/subfiles/chap_ridging_rafting.tex
r11031 r11043 70 70 \textbf{Rafting} is the piling of two ice sheets on top of each other. Rafting doubles the participating ice thickness and is a volumeconserving process. \cite{babko_2002} concluded that rafting plays a significant role during initial ice growth in fall, therefore we included it into the model. 71 71 72 \textbf{Ridging} is the piling of a series of broken ice blocks into pressure ridges. Ridging redistributes participating ice on a various range of thicknesses. Ridging does not conserve ice volume, as pressure ridges are porous. Therefore, the volume of ridged ice is larger than the volume of new ice being ridged. In the model, newly ridged is has a prescribed porosity $p=30\%$ (\textit{ridge\_por} in \textit{namelist\_ice}), following observations \citep{lepp _ranta_1995,h_yland_2002}. The importance of ridging is now since the early works of \citep{thorndike_1975}.72 \textbf{Ridging} is the piling of a series of broken ice blocks into pressure ridges. Ridging redistributes participating ice on a various range of thicknesses. Ridging does not conserve ice volume, as pressure ridges are porous. Therefore, the volume of ridged ice is larger than the volume of new ice being ridged. In the model, newly ridged is has a prescribed porosity $p=30\%$ (\textit{ridge\_por} in \textit{namelist\_ice}), following observations \citep{lepparanta_1995,hoyland_2002}. The importance of ridging is now since the early works of \citep{thorndike_1975}. 73 73 74 74 The deformation modes are formulated using \textbf{participation} and \textbf{transfer} functions with specific contributions from ridging and rafting: … … 115 115 \label{eq:nri} 116 116 \end{equation} 117 The redistributor $\gamma(h',h)$ specifies how area of thickness $h'$ is redistributed on area of thickness $h$. We follow \citep{hibler_1980} who constructed a rule, based on observations, that forces all ice participating in ridging with thickness $h'$ to be linearly distributed between ice that is between $2h'$ and $2\sqrt{H^*h'}$ thick, where $H^\star=100$ m (\textit{Hstar} in \textit{namelist\_ice}). This in turn determines how to construct the ice volume redistribution function $\Psi^v$. Volumes equal to participating area times thickness are removed from thin ice. They are redistributed following Hibler's rule. The factor $(1+p)$ accounts for initial ridge porosity $p$ (\textit{ridge\_por} in \textit{namelist\_ice}, defined as the fractional volume of seawater initially included into ridges. In many previous models, the initial ridge porosity has been assumed to be 0, which is not the case in reality since newly formed ridges are porous, as indicated by insitu observations \citep{lepp _ranta_1995,h_yland_2002}. In other words, LIM3 creates a higher volume of ridged ice with the same participating ice.117 The redistributor $\gamma(h',h)$ specifies how area of thickness $h'$ is redistributed on area of thickness $h$. We follow \citep{hibler_1980} who constructed a rule, based on observations, that forces all ice participating in ridging with thickness $h'$ to be linearly distributed between ice that is between $2h'$ and $2\sqrt{H^*h'}$ thick, where $H^\star=100$ m (\textit{Hstar} in \textit{namelist\_ice}). This in turn determines how to construct the ice volume redistribution function $\Psi^v$. Volumes equal to participating area times thickness are removed from thin ice. They are redistributed following Hibler's rule. The factor $(1+p)$ accounts for initial ridge porosity $p$ (\textit{ridge\_por} in \textit{namelist\_ice}, defined as the fractional volume of seawater initially included into ridges. In many previous models, the initial ridge porosity has been assumed to be 0, which is not the case in reality since newly formed ridges are porous, as indicated by insitu observations \citep{lepparanta_1995,hoyland_2002}. In other words, LIM3 creates a higher volume of ridged ice with the same participating ice. 118 118 119 119 For the numerical computation of the integrals, we have to compute several temporary values: … … 152 152 \section{Mechanical redistribution for other global ice variables} 153 153 154 The other global ice state variables redistribution functions $\Psi^X$ are computed based on $\Psi^g$ for the ice age content and on $\Psi^{v^i}$ for the remainder (ice enthalpy and salt content, snow volume and enthalpy). The general principles behind this derivation are described in Appendix A of \cite{bitz_2001}. A fraction $f_s=0.5$ (\textit{fsnowrdg} and \textit{fsnowrft} in \textit{namelist\_ice}) of the snow volume and enthalpy is assumed to be lost during ridging and rafting and transferred to the ocean. The contribution of the seawater trapped into the porous ridges is included in the computation of the redistribution of ice enthalpy and salt content (i.e., $\Psi^{e^i}$ and $\Psi^{M^s}$). During this computation, seawater is supposed to be in thermal equilibrium with the surrounding ice blocks. Ridged ice desalination induces an implicit decrease in internal brine volume, and heat supply to the ocean, which accounts for ridge consolidation as described by \cite{h _yland_2002}. The inclusion of seawater in ridges does not imply any net change in ocean salinity. The energy used to cool down the seawater trapped in porous ridges until the seawater freezing point is rejected into the ocean.154 The other global ice state variables redistribution functions $\Psi^X$ are computed based on $\Psi^g$ for the ice age content and on $\Psi^{v^i}$ for the remainder (ice enthalpy and salt content, snow volume and enthalpy). The general principles behind this derivation are described in Appendix A of \cite{bitz_2001}. A fraction $f_s=0.5$ (\textit{fsnowrdg} and \textit{fsnowrft} in \textit{namelist\_ice}) of the snow volume and enthalpy is assumed to be lost during ridging and rafting and transferred to the ocean. The contribution of the seawater trapped into the porous ridges is included in the computation of the redistribution of ice enthalpy and salt content (i.e., $\Psi^{e^i}$ and $\Psi^{M^s}$). During this computation, seawater is supposed to be in thermal equilibrium with the surrounding ice blocks. Ridged ice desalination induces an implicit decrease in internal brine volume, and heat supply to the ocean, which accounts for ridge consolidation as described by \cite{hoyland_2002}. The inclusion of seawater in ridges does not imply any net change in ocean salinity. The energy used to cool down the seawater trapped in porous ridges until the seawater freezing point is rejected into the ocean. 155 155 156 156 \end{document} 
NEMO/trunk/doc/latex/SI3/subfiles/introduction.tex
r11031 r11043 15 15 16 16 % Limitations & scope 17 %There are limitations to the applicability of models such as SI$^3$. The continuum approach is not invalid for grid cell size above at least 1 km, below which sea ice particles may include just a few floes, which is not sufficient \citep{lepp _ranta_2011}. Second, one must remember that our current knowledge of sea ice is not as complete as for the ocean: there are no fundamental equations such as Navier Stokes equations for sea ice. Besides, important features and processes span widely different scales, such as brine inclusions (1 $\mu$m1 mm) \citep{perovich_1996}, horizontal thickness variations (1 m100 km) \citep{percival_2008}, deformation and fracturing (10 m1000 km) \citep{marsan_2004}. These impose complicated and often subjective subgridscale treatments. All in all, there is more empirism in sea ice models than in ocean models.17 %There are limitations to the applicability of models such as SI$^3$. The continuum approach is not invalid for grid cell size above at least 1 km, below which sea ice particles may include just a few floes, which is not sufficient \citep{lepparanta_2011}. Second, one must remember that our current knowledge of sea ice is not as complete as for the ocean: there are no fundamental equations such as Navier Stokes equations for sea ice. Besides, important features and processes span widely different scales, such as brine inclusions (1 $\mu$m1 mm) \citep{perovich_1996}, horizontal thickness variations (1 m100 km) \citep{percival_2008}, deformation and fracturing (10 m1000 km) \citep{marsan_2004}. These impose complicated and often subjective subgridscale treatments. All in all, there is more empirism in sea ice models than in ocean models. 18 18 19 19 In order to handle all the subsequent required subjective choices, we applied the following guidelines or principles: 
NEMO/trunk/doc/latex/TOP/main/TOP_manual.bib
r11037 r11043 87 87 CFC113, CCl4, SF6 and N2O (NCEI Accession 0164584)}, 88 88 year = 2017, 89 doi = {10.3334/cdiac/otg.cfc _atm_hist_2015},89 doi = {10.3334/cdiac/otg.cfc\_atm\_hist\_2015}, 90 90 url = {https://accession.nodc.noaa.gov/0164584}, 91 91 publisher = {NOAA National Centers for Environmental Information} … … 349 349 number = {3–4}, 350 350 issn = {00338222}, 351 doi = {10.2458/azu _js_rc.55.16402},352 url = {http://dx.doi.org/10.2458/azu _js_rc.55.16402},351 doi = {10.2458/azu\_js\_rc.55.16402}, 352 url = {http://dx.doi.org/10.2458/azu\_js\_rc.55.16402}, 353 353 journal = {Radiocarbon}, 354 354 publisher = {Cambridge University Press (CUP)} … … 422 422 Béranger, K. and Schneider, A. and Beuvier, J. and Somot, 423 423 S.}, 424 title = {Simulated anthropogenic CO <sub>2</sub>storage424 title = {Simulated anthropogenic CO$_{2}$ storage 425 425 and acidification of the Mediterranean Sea}, 426 426 year = 2015, … … 448 448 pages = {1869–1887}, 449 449 issn = {19455755}, 450 doi = {10.2458/azu _js_rc.55.16947},451 url = {http://dx.doi.org/10.2458/azu _js_rc.55.16947},450 doi = {10.2458/azu\_js\_rc.55.16947}, 451 url = {http://dx.doi.org/10.2458/azu\_js\_rc.55.16947}, 452 452 journal = {Radiocarbon}, 453 453 publisher = {Cambridge University Press (CUP)} … … 495 495 } 496 496 497 @Article{ toggweiler_1989 ,497 @Article{ toggweiler_1989a, 498 498 author = {Toggweiler, J. R. and Dixon, K. and Bryan, K.}, 499 499 title = {Simulations of radiocarbon in a coarseresolution world … … 510 510 } 511 511 512 @Article{ toggweiler_1989 ,512 @Article{ toggweiler_1989b, 513 513 author = {Toggweiler, J. R. and Dixon, K. and Bryan, K.}, 514 514 title = {Simulations of radiocarbon in a coarseresolution world … … 615 615 doi = {10.1016/j.tree.2012.10.021}, 616 616 url = {http://dx.doi.org/10.1016/j.tree.2012.10.021}, 617 journal = {Trends in Ecology & Evolution},618 publisher = {Elsevier BV} 619 } 617 journal = {Trends in Ecology \& Evolution}, 618 publisher = {Elsevier BV} 619 } 
NEMO/trunk/doc/latex/TOP/main/TOP_manual.tex
r11019 r11043 12 12 %% Custom style (.sty) 13 13 \usepackage{../../NEMO/main/NEMO_manual} 14 \hypersetup{ 15 pdftitle={TOP – Tracers in Ocean Paradigm – The NEMO Tracers engine}, 16 pdfauthor={NEMO TOP Working Group}, 17 colorlinks 18 } 14 19 15 20 %% Include references and index for single subfile compilation 
NEMO/trunk/doc/latex/TOP/subfiles/model_description.tex
r11032 r11043 26 26 \end{equation} 27 27 28 where expressions of $D^{lC}$ and $D^{vC}$ depend on the choice for the lateral and vertical subgrid scale parameterizations, see equations 5.10 and 5.11 in \citep{ Madec_Bk2008}28 where expressions of $D^{lC}$ and $D^{vC}$ depend on the choice for the lateral and vertical subgrid scale parameterizations, see equations 5.10 and 5.11 in \citep{nemo_manual} 29 29 30 30 {S(C)} , the first term on the right hand side of \ref{Eq_tracer}; is the SMS  Source Minus Sink  inherent to the tracer. In the case of biological tracer such as phytoplankton, {S(C)} is the balance between phytoplankton growth and its decay through mortality and grazing. In the case of a tracer comprising carbon, {S(C)} accounts for gas exchange, river discharge, flux to the sediments, gravitational sinking and other biological processes. In the case of a radioactive tracer, {S(C)} is simply loss due to radioactive decay. … … 61 61 \item \textbf{AGE} : Water age tracking 62 62 \item \textbf{MY\_TRC} : Template for creation of new modules and external BGC models coupling 63 \item \textbf{PISCES} : Built in BGC model. See \citep{ Aumont_al_2015} for a throughout description.63 \item \textbf{PISCES} : Built in BGC model. See \citep{aumont_2015} for a throughout description. 64 64 \end{itemize} 65 65 %  … … 73 73 \nlst{namtrc_adv} 74 74 % 75 The advection schemes used for the passive tracers are the same than the ones for $T$ and $S$ and described in section 5.1 of \citep{ Madec_Bk2008}. The choice of an advection scheme can be selected independently and can differ from the ones used for active tracers. This choice is made in the \textit{namtrc\_adv} namelist, by setting to \textit{true} one and only one of the logicals \textit{ln\_trcadv\_xxx}, the same way of what is done for dynamics.75 The advection schemes used for the passive tracers are the same than the ones for $T$ and $S$ and described in section 5.1 of \citep{nemo_manual}. The choice of an advection scheme can be selected independently and can differ from the ones used for active tracers. This choice is made in the \textit{namtrc\_adv} namelist, by setting to \textit{true} one and only one of the logicals \textit{ln\_trcadv\_xxx}, the same way of what is done for dynamics. 76 76 cen2, MUSCL2, and UBS are not \textit{positive} schemes meaning that negative values can appear in an initially strictly positive tracer field which is advected, implying that false extrema are permitted. Their use is not recommended on passive tracers 77 77 … … 80 80 \nlst{namtrc_ldf} 81 81 % 82 In NEMO v4.0, the passive tracer diffusion has necessarily the same form as the active tracer diffusion, meaning that the numerical scheme must be the same. However the passive tracer mixing coefficient can be chosen as a multiple of the active ones by changing the value of \textit{rn\_ldf\_multi} in namelist \textit{namtrc\_ldf}. The choice of numerical scheme is then set in the \ngn{namtra\_ldf} namelist for the dynamic described in section 5.2 of \citep{ Madec_Bk2008}.82 In NEMO v4.0, the passive tracer diffusion has necessarily the same form as the active tracer diffusion, meaning that the numerical scheme must be the same. However the passive tracer mixing coefficient can be chosen as a multiple of the active ones by changing the value of \textit{rn\_ldf\_multi} in namelist \textit{namtrc\_ldf}. The choice of numerical scheme is then set in the \ngn{namtra\_ldf} namelist for the dynamic described in section 5.2 of \citep{nemo_manual}. 83 83 84 84 … … 145 145 146 146 147 This implementation was first used in the COREII intercomparison runs described e.g.\ in \citet{ Danabasoglu_al_2014}.147 This implementation was first used in the COREII intercomparison runs described e.g.\ in \citet{danabasoglu_2014}. 148 148 149 149 \subsection{Inert carbons tracer} … … 178 178 Measuring the dissolved concentrations of the gases  as well as the mixing ratios between them  shows circulation pathways within the ocean as well as water mass ages (i.e. the time since last contact with the 179 179 atmosphere). This feature of the gases has made them valuable across a wide range of oceanographic problems. One use lies in ocean modelling, where they can be used to evaluate the realism of the circulation and 180 ventilation of models, key for understanding the behaviour of wider modelled marine biogeochemistry (e.g. \citep{ Dutay_al_2002,Palmieri_2015}). \\180 ventilation of models, key for understanding the behaviour of wider modelled marine biogeochemistry (e.g. \citep{dutay_2002,palmieri_2015}). \\ 181 181 182 182 Modelling these gases (henceforth CFCs) in NEMO is done within the passive tracer transport module, TOP, using the conservation state equation \ref{Eq_tracer} … … 187 187 stable within the ocean, we assume that there are no sinks (i.e. no loss processes) within the ocean interior. 188 188 Consequently, the sinksminussources term for CFCs consists only of their airsea fluxes, $F_{cfc}$, as 189 described in the Ocean Model Intercomparison Project (OMIP) protocol \citep{ Orr_al_2017}:189 described in the Ocean Model Intercomparison Project (OMIP) protocol \citep{orr_2017}: 190 190 191 191 % Because CFCs being stable in the ocean, we consider that there is no CFCs sink. … … 213 213 Where $Sol$ is the gas solubility in mol~m$^{3}$~pptv$^{1}$, as defined in Equation \ref{equ_Sol_CFC}; 214 214 and $P_{cfc}$ is the atmosphere concentration of the CFC (in parts per trillion by volume, pptv). 215 This latter concentration is provided to the model by the historical timeseries of \citet{ Bullister_2015}.215 This latter concentration is provided to the model by the historical timeseries of \citet{bullister_2017}. 216 216 This includes bulk atmospheric concentrations of the CFCs for both hemispheres  this is necessary because of 217 217 the geographical asymmetry in the production and release of CFCs to the atmosphere. … … 220 220 221 221 The piston velocity $K_{w}$ is a function of 10~m wind speed (in m~s$^{1}$) and sea surface temperature, 222 $T$ (in $^{\circ}$C), and is calculated here following \citet{ Wanninkhof_1992}:222 $T$ (in $^{\circ}$C), and is calculated here following \citet{wanninkhof_1992}: 223 223 224 224 \begin{eqnarray} … … 229 229 Where $X_{conv}$ = $\frac{0.01}{3600}$, a conversion factor that changes the piston velocity 230 230 from cm~h$^{1}$ to m~s$^{1}$; 231 $a$ is a constant reestimated by \citet{ Wanninkhof_2014} to 0.251 (in $\frac{cm~h^{1}}{(m~s^{1})^{2}}$);231 $a$ is a constant reestimated by \citet{wanninkhof_2014} to 0.251 (in $\frac{cm~h^{1}}{(m~s^{1})^{2}}$); 232 232 and $u$ is the 10~m wind speed in m~s$^{1}$ from either an atmosphere model or reanalysis atmospheric forcing. 233 $Sc$ is the Schmidt number, and is calculated as follow, using coefficients from \citet{ Wanninkhof_2014} (see Table \ref{tab_Sc}).233 $Sc$ is the Schmidt number, and is calculated as follow, using coefficients from \citet{wanninkhof_2014} (see Table \ref{tab_Sc}). 234 234 235 235 \begin{eqnarray} … … 240 240 The solubility, $Sol$, used in Equation \ref{equ_C_sat} is calculated in mol~l$^{1}$~atm$^{1}$, 241 241 and is specific for each gas. 242 It has been experimentally estimated by \citet{ Warner_Weiss_1985} as a function of temperature242 It has been experimentally estimated by \citet{warner_1985} as a function of temperature 243 243 and salinity: 244 244 … … 363 363 where $\Rq_{\textrm{ref}}$ is a reference ratio. For the purpose of ocean ventilation studies $\Rq_{\textrm{ref}}$ is set to one. 364 364 365 Here we adopt the approach of \cite{ Fiadeiro_1982} and \cite{Toggweiler_al_1989a,Toggweiler_al_1989b} in which the ratio $\Rq$ is transported rather than the individual concentrations C and $\cq$.366 This approach calls for a strong assumption, i.e., that of a homogeneous and constant dissolved inorganic carbon (DIC) field \citep{ Toggweiler_al_1989a,Mouchet_2013}. While in terms of367 oceanic $\Dcq$, it yields similar results to approaches involving carbonate chemistry, it underestimates the bomb radiocarbon inventory because it assumes a constant airsea $\cd$ disequilibrium (Mouchet, 2013). Yet, field reconstructions of the ocean bomb $\cq$ inventory are also biased low \citep{ Naegler_2009} since they assume that the anthropogenic perturbation did not affect ocean DIC since the prebomb epoch. For these reasons, bomb $\cq$ inventories obtained with the present method are directly comparable to reconstructions based on field measurements.368 369 This simplified approach also neglects the effects of fractionation (e.g., airsea exchange) and of biological processes. Previous studies by \cite{ Bacastow_MaierReimer_1990} and \cite{Joos_al_1997} resulted in nearly identical $\Dcq$ distributions among experiments considering biology or not.370 Since observed $\Rq$ ratios are corrected for the isotopic fractionation when converted to the standard $\Dcq$ notation \citep{ Stuiver_Polach_1977} the model results are directly comparable to observations.365 Here we adopt the approach of \cite{fiadeiro_1982} and \cite{toggweiler_1989a,toggweiler_1989b} in which the ratio $\Rq$ is transported rather than the individual concentrations C and $\cq$. 366 This approach calls for a strong assumption, i.e., that of a homogeneous and constant dissolved inorganic carbon (DIC) field \citep{toggweiler_1989a,mouchet_2013}. While in terms of 367 oceanic $\Dcq$, it yields similar results to approaches involving carbonate chemistry, it underestimates the bomb radiocarbon inventory because it assumes a constant airsea $\cd$ disequilibrium (Mouchet, 2013). Yet, field reconstructions of the ocean bomb $\cq$ inventory are also biased low \citep{naegler_2009} since they assume that the anthropogenic perturbation did not affect ocean DIC since the prebomb epoch. For these reasons, bomb $\cq$ inventories obtained with the present method are directly comparable to reconstructions based on field measurements. 368 369 This simplified approach also neglects the effects of fractionation (e.g., airsea exchange) and of biological processes. Previous studies by \cite{bacastow_1990} and \cite{joos_1997} resulted in nearly identical $\Dcq$ distributions among experiments considering biology or not. 370 Since observed $\Rq$ ratios are corrected for the isotopic fractionation when converted to the standard $\Dcq$ notation \citep{stuiver_1977} the model results are directly comparable to observations. 371 371 372 372 Therefore the simplified approach is justified for the purpose of assessing the circulation and ventilation of OGCMs. … … 378 378 where $\lambda$ is the radiocarbon decay rate, ${\mathbf{u}}$ the 3D velocity field, and $\mathbf{K}$ the diffusivity tensor. 379 379 380 At the airsea interface a Robin boundary condition \citep{ Haine_2006} is applied to \eqref{eq:quick}, i.e., the flux380 At the airsea interface a Robin boundary condition \citep{haine_2006} is applied to \eqref{eq:quick}, i.e., the flux 381 381 through the interface is proportional to the difference in the ratios between 382 382 the ocean and the atmosphere … … 391 391 392 392 393 The $\cd$ transfer velocity is based on the empirical formulation of \cite{ Wanninkhof_1992} with chemical enhancement \citep{Wanninkhof_Knox_1996,Wanninkhof_2014}. The original formulation is modified to account for the reduction of the airsea exchange rate in the presence of sea ice. Hence393 The $\cd$ transfer velocity is based on the empirical formulation of \cite{wanninkhof_1992} with chemical enhancement \citep{wanninkhof_1996,wanninkhof_2014}. The original formulation is modified to account for the reduction of the airsea exchange rate in the presence of sea ice. Hence 394 394 \begin{equation} 395 395 \kappa_\cd=\left( K_W\,\mathrm{w}^2 + b \right)\, (1f_\mathrm{ice})\,\sqrt{660/Sc}, \label{eq:wanc14} … … 397 397 with $\mathrm{w}$ the wind magnitude, $f_\mathrm{ice}$ the fractional ice cover, and $Sc$ the Schmidt number. 398 398 $K_W$ in \eqref{eq:wanc14} is an empirical coefficient with dimension of an inverse velocity. 399 The chemical enhancement term $b$ is represented as a function of temperature $T$ \citep{ Wanninkhof_1992}399 The chemical enhancement term $b$ is represented as a function of temperature $T$ \citep{wanninkhof_1992} 400 400 \begin{equation} 401 401 b=2.5 ( 0.5246 + 0.016256 T+ 0.00049946 * T^2 ). \label{eq:wanchem} … … 413 413 \label{sec:param} 414 414 % 415 The radiocarbon decay rate (\CODE{rlam14}; in \texttt{trcnam\_c14} module) is set to $\lambda=(1/8267)$ yr$^{1}$ \citep{ Stuiver_Polach_1977}, which corresponds to a halflife of 5730 yr.\\[1pt]416 % 417 The Schmidt number $Sc$, Eq. \eqref{eq:wanc14}, is calculated with the help of the formulation of \cite{ Wanninkhof_2014}. The $\cd$ solubility $K_0$ in \eqref{eq:Rspeed} is taken from \cite{Weiss_1974}. $K_0$ and $Sc$ are computed with the OGCM temperature and salinity fields (\texttt{trcsms\_c14} module).\\[1pt]415 The radiocarbon decay rate (\CODE{rlam14}; in \texttt{trcnam\_c14} module) is set to $\lambda=(1/8267)$ yr$^{1}$ \citep{stuiver_1977}, which corresponds to a halflife of 5730 yr.\\[1pt] 416 % 417 The Schmidt number $Sc$, Eq. \eqref{eq:wanc14}, is calculated with the help of the formulation of \cite{wanninkhof_2014}. The $\cd$ solubility $K_0$ in \eqref{eq:Rspeed} is taken from \cite{weiss_1974}. $K_0$ and $Sc$ are computed with the OGCM temperature and salinity fields (\texttt{trcsms\_c14} module).\\[1pt] 418 418 % 419 419 The following parameters intervening in the airsea exchange rate are set in \texttt{namelist\_c14}: 420 420 \begin{itemize} 421 \item The reference DIC concentration $\overline{\Ct}$ (\CODE{xdicsur}) intervening in \eqref{eq:Rspeed} is classically set to 2 mol m$^{3}$ \citep{ Toggweiler_al_1989a,Orr_al_2001,Butzin_al_2005}.422 % 423 \item The value of the empirical coefficient $K_W$ (\CODE{xkwind}) in \eqref{eq:wanc14} depends on the wind field and on the model upper ocean mixing rate \citep{ Toggweiler_al_1989a,Wanninkhof_1992,Naegler_2009,Wanninkhof_2014}.424 It should be adjusted so that the globally averaged $\cd$ piston velocity is $\kappa_\cd = 16.5\pm 3.2$ cm/h \citep{ Naegler_2009}.421 \item The reference DIC concentration $\overline{\Ct}$ (\CODE{xdicsur}) intervening in \eqref{eq:Rspeed} is classically set to 2 mol m$^{3}$ \citep{toggweiler_1989a,orr_2001,butzin_2005}. 422 % 423 \item The value of the empirical coefficient $K_W$ (\CODE{xkwind}) in \eqref{eq:wanc14} depends on the wind field and on the model upper ocean mixing rate \citep{toggweiler_1989a,wanninkhof_1992,naegler_2009,wanninkhof_2014}. 424 It should be adjusted so that the globally averaged $\cd$ piston velocity is $\kappa_\cd = 16.5\pm 3.2$ cm/h \citep{naegler_2009}. 425 425 %The sensitivity to this parametrization is discussed in section \ref{sec:result}. 426 426 % … … 440 440 \CODE{kc14typ}=0 441 441 442 Unless otherwise specified in \texttt{namelist\_c14}, the atmospheric $\Rq_a$ (\CODE{rc14at}) is set to one, the atmospheric $\cd$ (\CODE{pco2at}) to 280 ppm, and the ocean $\Rq$ is initialized with \CODE{rc14init=0.85}, i.e., $\Dcq=$150\textperthousand \cite[typical for deepocean, Fig 6 in][]{ Key_al_2004}.443 444 Equilibrium experiment should last until 98\% of the ocean volume exhibit a drift of less than 0.001\textperthousand/year \citep{ Orr_al_2000}; this is usually achieved after few kyr (Fig. \ref{fig:drift}).442 Unless otherwise specified in \texttt{namelist\_c14}, the atmospheric $\Rq_a$ (\CODE{rc14at}) is set to one, the atmospheric $\cd$ (\CODE{pco2at}) to 280 ppm, and the ocean $\Rq$ is initialized with \CODE{rc14init=0.85}, i.e., $\Dcq=$150\textperthousand \cite[typical for deepocean, Fig 6 in][]{key_2004}. 443 444 Equilibrium experiment should last until 98\% of the ocean volume exhibit a drift of less than 0.001\textperthousand/year \citep{orr_2000}; this is usually achieved after few kyr (Fig. \ref{fig:drift}). 445 445 % 446 446 \begin{figure}[!h] … … 469 469 470 470 The model is integrated from a given initial date following the observed records provided from 1765 AD on ( Fig. \ref{fig:bomb}). 471 The file \texttt{atmc14.dat} \cite[][\& I. Levin, personal comm.]{ Enting_al_1994} provides atmospheric $\Dcq$ for three latitudinal bands: 90S20S, 20S20N \& 20N90N.472 Atmospheric $\cd$ in the file \texttt{splco2.dat} is obtained from a spline fit through ice core data and direct atmospheric measurements \cite[][\& J. Orr, personal comm.]{ Orr_al_2000}.471 The file \texttt{atmc14.dat} \cite[][\& I. Levin, personal comm.]{enting_1994} provides atmospheric $\Dcq$ for three latitudinal bands: 90S20S, 20S20N \& 20N90N. 472 Atmospheric $\cd$ in the file \texttt{splco2.dat} is obtained from a spline fit through ice core data and direct atmospheric measurements \cite[][\& J. Orr, personal comm.]{orr_2000}. 473 473 Dates in these forcing files are expressed as yr AD. 474 474 … … 496 496 Atmospheric $\Rq_a$ and $\cd$ are prescribed from forcing files. The ocean $\Rq$ is initialized with the value attributed to \CODE{rc14init} in \texttt{namelist\_c14}. 497 497 498 The file \texttt{intcal13.14c} \citep{ Reimer_al_2013} contains atmospheric $\Dcq$ from 0 to 50 kyr cal BP\footnote{cal BP: number of years before 1950 AD}.499 The $\cd$ forcing is provided in file \texttt{ByrdEdcCO2.txt}. The content of this file is based on the high resolution record from EPICA Dome C \citep{ Monnin_al_2004} for the Holocene and the Transition, and on Byrd Ice Core CO2 Data for 2090 kyr BP \citep{Ahn_Brook_2008}. These atmospheric values are reproduced in Fig. \ref{fig:paleo}. Dates in these files are expressed as yr BP.498 The file \texttt{intcal13.14c} \citep{reimer_2013} contains atmospheric $\Dcq$ from 0 to 50 kyr cal BP\footnote{cal BP: number of years before 1950 AD}. 499 The $\cd$ forcing is provided in file \texttt{ByrdEdcCO2.txt}. The content of this file is based on the high resolution record from EPICA Dome C \citep{monnin_2004} for the Holocene and the Transition, and on Byrd Ice Core CO2 Data for 2090 kyr BP \citep{ahn_2008}. These atmospheric values are reproduced in Fig. \ref{fig:paleo}. Dates in these files are expressed as yr BP. 500 500 501 501 To ensure that the atmospheric forcing is applied properly as well as that output files contain consistent dates and inventories the experiment should be set up carefully. … … 539 539 The radiocarbon age is computed as $(1/\lambda) \ln{ \left( \Rq \right)}$, with zero age corresponding to $\Rq=1$. 540 540 541 The reservoir age is the age difference between the ocean uppermost layer and the atmosphere. It is usually reported as conventional radiocarbon age; i.e., computed by means of the Libby radiocarbon mean life \cite[8033 yr;][]{ Stuiver_Polach_1977}541 The reservoir age is the age difference between the ocean uppermost layer and the atmosphere. It is usually reported as conventional radiocarbon age; i.e., computed by means of the Libby radiocarbon mean life \cite[8033 yr;][]{stuiver_1977} 542 542 \begin{align} 543 543 {^{14}\tau_\mathrm{c}}= 8033 \; \ln \left(1 + \frac{\Dcq}{10^3}\right), \label{eq:convage} … … 549 549 N_A \Rq_\mathrm{oxa} \overline{\Ct} \left( \int_\Omega \Rq d\Omega \right) /10^{26}, \label{eq:inv} 550 550 \end{equation} 551 where $N_A$ is the Avogadro's number ($N_A=6.022\times10^{23}$ at/mol), $\Rq_\mathrm{oxa}$ is the oxalic acid radiocarbon standard \cite[$\Rq_\mathrm{oxa}=1.176\times10^{12}$;][]{ Stuiver_Polach_1977}, and $\Omega$ is the ocean volume. Bomb $\cq$ inventories are traditionally reported in units of $10^{26}$ atoms, hence the denominator in \eqref{eq:inv}.551 where $N_A$ is the Avogadro's number ($N_A=6.022\times10^{23}$ at/mol), $\Rq_\mathrm{oxa}$ is the oxalic acid radiocarbon standard \cite[$\Rq_\mathrm{oxa}=1.176\times10^{12}$;][]{stuiver_1977}, and $\Omega$ is the ocean volume. Bomb $\cq$ inventories are traditionally reported in units of $10^{26}$ atoms, hence the denominator in \eqref{eq:inv}. 552 552 553 553 All transformations from second to year, and inversely, are performed with the help of the physical constant \CODE{rsiyea} the sideral year length expressed in seconds\footnote{The variable (\CODE{nyear\_len}) which reports the length in days of the previous/current/future year (see \textrm{oce\_trc.F90}) is not a constant. }. … … 564 564 Two versions of PISCES are available in NEMO v4.0 : 565 565 566 PISCESv2, by setting in namelist\_pisces\_ref \np{ln\_p4z} to true, can be seen as one of the many Monod models \citep{ Monod_1942}. It assumes a constant Redfield ratio and phytoplankton growth depends on the external concentration in nutrients. There are twentyfour prognostic variables (tracers) including two phytoplankton compartments (diatoms and nanophytoplankton), two zooplankton sizeclasses (microzooplankton and mesozooplankton) and a description of the carbonate chemistry. Formulations in PISCESv2 are based on a mixed Monod/Quota formalism: On one hand, stoichiometry of C/N/P is fixed and growth rate of phytoplankton is limited by the external availability in N, P and Si. On the other hand, the iron and silicium quotas are variable and growth rate of phytoplankton is limited by the internal availability in Fe. Various parameterizations can be activated in PISCESv2, setting for instance the complexity of iron chemistry or the description of particulate organic materials.567 568 PISCESQUOTA has been built on the PISCESv2 model described in \citet{ Aumont_al_2015}. PISCESQUOTA has thirtynine prognostic compartments. Phytoplankton growth can be controlled by five modeled limiting nutrients: Nitrate and Ammonium, Phosphate, Silicate and Iron. Five living compartments are represented: Three phytoplankton size classes/groups corresponding to picophytoplankton, nanophytoplankton and diatoms, and two zooplankton size classes which are microzooplankton and mesozooplankton. For phytoplankton, the prognostic variables are the carbon, nitrogen, phosphorus, iron, chlorophyll and silicon biomasses (the latter only for diatoms). This means that the N/C, P/C, Fe/C and Chl/C ratios of both phytoplankton groups as well as the Si/C ratio of diatoms are prognostically predicted by the model. Zooplankton are assumed to be strictly homeostatic \citep[e.g.,][]{Sterner_2002,Woods_Wilson_2013,Meunier_al_2014}. As a consequence, the C/N/P/Fe ratios of these groups are maintained constant and are not allowed to vary. In PISCES, the Redfield ratios C/N/P are set to 122/16/1 \citep{Takahashi_al_1985} and the O/C ratio is set to 1.34 \citep{Kortzinger_al_2001}. No silicified zooplankton is assumed. The bacterial pool is not yet explicitly modeled.569 570 There are three nonliving compartments: Semilabile dissolved organic matter, small sinking particles, and large sinking particles. As a consequence of the variable stoichiometric ratios of phytoplankton and of the stoichiometric regulation of zooplankton, elemental ratios in organic matter cannot be supposed constant anymore as that was the case in PISCESv2. Indeed, the nitrogen, phosphorus, iron, silicon and calcite pools of the particles are now all explicitly modeled. The sinking speed of the particles is not altered by their content in calcite and biogenic silicate (''The ballast effect'', \citep{ Honjo_1996,Armstrong_al_2002}). The latter particles are assumed to sink at the same speed as the large organic matter particles. All the nonliving compartments experience aggregation due to turbulence and differential settling as well as Brownian coagulation for DOM.566 PISCESv2, by setting in namelist\_pisces\_ref \np{ln\_p4z} to true, can be seen as one of the many Monod models \citep{monod_1958}. It assumes a constant Redfield ratio and phytoplankton growth depends on the external concentration in nutrients. There are twentyfour prognostic variables (tracers) including two phytoplankton compartments (diatoms and nanophytoplankton), two zooplankton sizeclasses (microzooplankton and mesozooplankton) and a description of the carbonate chemistry. Formulations in PISCESv2 are based on a mixed Monod/Quota formalism: On one hand, stoichiometry of C/N/P is fixed and growth rate of phytoplankton is limited by the external availability in N, P and Si. On the other hand, the iron and silicium quotas are variable and growth rate of phytoplankton is limited by the internal availability in Fe. Various parameterizations can be activated in PISCESv2, setting for instance the complexity of iron chemistry or the description of particulate organic materials. 567 568 PISCESQUOTA has been built on the PISCESv2 model described in \citet{aumont_2015}. PISCESQUOTA has thirtynine prognostic compartments. Phytoplankton growth can be controlled by five modeled limiting nutrients: Nitrate and Ammonium, Phosphate, Silicate and Iron. Five living compartments are represented: Three phytoplankton size classes/groups corresponding to picophytoplankton, nanophytoplankton and diatoms, and two zooplankton size classes which are microzooplankton and mesozooplankton. For phytoplankton, the prognostic variables are the carbon, nitrogen, phosphorus, iron, chlorophyll and silicon biomasses (the latter only for diatoms). This means that the N/C, P/C, Fe/C and Chl/C ratios of both phytoplankton groups as well as the Si/C ratio of diatoms are prognostically predicted by the model. Zooplankton are assumed to be strictly homeostatic \citep[e.g.,][]{sterner_2003,woods_2013,meunier_2014}. As a consequence, the C/N/P/Fe ratios of these groups are maintained constant and are not allowed to vary. In PISCES, the Redfield ratios C/N/P are set to 122/16/1 \citep{takahashi_1985} and the O/C ratio is set to 1.34 \citep{kortzinger_2001}. No silicified zooplankton is assumed. The bacterial pool is not yet explicitly modeled. 569 570 There are three nonliving compartments: Semilabile dissolved organic matter, small sinking particles, and large sinking particles. As a consequence of the variable stoichiometric ratios of phytoplankton and of the stoichiometric regulation of zooplankton, elemental ratios in organic matter cannot be supposed constant anymore as that was the case in PISCESv2. Indeed, the nitrogen, phosphorus, iron, silicon and calcite pools of the particles are now all explicitly modeled. The sinking speed of the particles is not altered by their content in calcite and biogenic silicate (''The ballast effect'', \citep{honjo_1996,armstrong_2001}). The latter particles are assumed to sink at the same speed as the large organic matter particles. All the nonliving compartments experience aggregation due to turbulence and differential settling as well as Brownian coagulation for DOM. 571 571 572 572 
NEMO/trunk/doc/manual_build.sh
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