# Changeset 11591 for NEMO/trunk/doc/latex/TOP/subfiles

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Timestamp:
2019-09-25T13:52:24+02:00 (22 months ago)
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NEMO/trunk/doc/latex/TOP/subfiles
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• ## NEMO/trunk/doc/latex/TOP/subfiles

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• ## NEMO/trunk/doc/latex/TOP/subfiles/miscellaneous.tex

 r10896 \documentclass[../../NEMO/main/NEMO_manual]{subfiles} \documentclass[../main/TOP_manual]{subfiles} \begin{document} \begin{minted}{bash} bld::tool::fppkeys   key_iomput key_mpp_mpi key_top src::MYBGC::initialization         /initialization src::MYBGC::pelagic                /pelagic
• ## NEMO/trunk/doc/latex/TOP/subfiles/model_description.tex

 r11043 \documentclass[../../NEMO/main/NEMO_manual]{subfiles} \documentclass[../main/TOP_manual]{subfiles} \newcommand{\cd}{\mathrm{CO_2}} 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} where expressions of $D^{lC}$ and $D^{vC}$ depend on the choice for the lateral and vertical subgrid scale parameterizations, see equations 5.10 and 5.11 in \citep{nemo_manual} {S(C)} , the first term on the right hand side of \ref{Eq_tracer}; is the SMS - Source Minus Sink - inherent to the tracer.  In the case of biological tracer such as phytoplankton, {S(C)} is the balance between phytoplankton growth and its decay through mortality and grazing. In the case of a tracer comprising carbon,  {S(C)} accounts for gas exchange, river discharge, flux to the sediments, gravitational sinking and other biological processes. In the case of a radioactive tracer, {S(C)} is simply loss due to radioactive decay. The second term (within brackets) represents the advection of the tracer in the three directions. It can be interpreted as the budget between the incoming and outgoing tracer fluxes in a volume $T$-cells $b_t= e_{1t}\,e_{2t}\,e_{3t}$ The third term  represents the change due to lateral diffusion. The second term (within brackets) represents the advection of the tracer in the three directions. It can be interpreted as the budget between the incoming and outgoing tracer fluxes in a volume $T$-cells $b_t= e_{1t}\,e_{2t}\,e_{3t}$ The third term  represents the change due to lateral diffusion. The fourth term is change due to vertical diffusion, parameterized as eddy diffusion to represent vertical turbulent fluxes : The passive tracer transport component  shares the same advection/diffusion routines with the dynamics, with specific treatment of some features like the surface boundary conditions, or the positivity of passive tracers concentrations. \subsection{ Advection} %------------------------------------------namtrc_adv---------------------------------------------------- \nlst{namtrc_ldf} %------------------------------------------------------------------------------------------------------------- In NEMO v4.0, the passive tracer diffusion has necessarily the same form as the active tracer diffusion, meaning that the numerical scheme must be the same. However the passive tracer mixing coefficient can be chosen as a multiple of the active ones by changing the value of \textit{rn\_ldf\_multi} in namelist \textit{namtrc\_ldf}. The choice of numerical scheme is then set  in the \ngn{namtra\_ldf} namelist for the dynamic described in section 5.2 of \citep{nemo_manual}. In NEMO v4.0, the passive tracer diffusion has necessarily the same form as the active tracer diffusion, meaning that the numerical scheme must be the same. However the passive tracer mixing coefficient can be chosen as a multiple of the active ones by changing the value of \textit{rn\_ldf\_multi} in namelist \textit{namtrc\_ldf}. The choice of numerical scheme is then set  in the \ngn{namtra\_ldf} namelist for the dynamic described in section 5.2 of \citep{nemo_manual}. %-----------------We also offers the possibility to increase zonal equatorial diffusion for passive tracers by introducing an enhanced zonal diffusivity coefficent in the equatorial domain which can be defined by the equation below : %----------------- \label{eq:traqsr_iradiance} %-----------------Aht  = Aht *  rn_fact_lap * \exp( - \max( 0., z -1000  ) / 1000}  \quad \text{for $L=1$ to $N$} %-----------------Aht  = Aht *  rn_fact_lap * \exp( - \max( 0., z -1000  ) / 1000}  \quad \text{for $L=1$ to $N$} %----------------- \subsection{ Tracer damping} %------------------------------------------namtrc_dmp---------------------------------------------------- \nlst{namtrc_dmp} \subsection{ Tracer positivity} %------------------------------------------namtrc_rad---------------------------------------------------- \nlst{namtrc_rad} As can be seen in the figure, while the concentration of SF6 continues to rise to the present  day, the concentrations of both CFC-11 and CFC-12 have levelled off and declined since around the 1990s. These declines have been driven by the Montreal Protocol (effective since August 1989), which has banned the production of CFC-11 and CFC-12 (as well as other CFCs) because of their role in the depletion of stratospheric ozone (O$_{3}$), critical in decreasing the flux of ultraviolet radiation to the Earth's surface. Separate to this role in ozone-depletion, all three chemicals are significantly more potent greenhouse gases stratospheric ozone (O$_{3}$), critical in decreasing the flux of ultraviolet radiation to the Earth's surface. Separate to this role in ozone-depletion, all three chemicals are significantly more potent greenhouse gases than CO$_{2}$ (especially SF6), although their relatively low atmospheric concentrations limit their role in climate change. \\ % concentrations increased until around the late 1990s afterwhich they began to decline in % response to the Montreal Protocol. % In the case of SF6, release began in the 1950s % In the case of SF6, release began in the 1950s % This release began in the 1930s for CFC-11 and CFC-12, and the 1950s for SF6, and % regularly increasing their atmospheric concentration until the 1090s, 2000s for respectively CFC11, CFC12, % regularly increasing their atmospheric concentration until the 1090s, 2000s for respectively CFC11, CFC12, % and is still increasing, and SF6 (see Figure \ref{img_cfcatm}).  \\ Because they only enter the ocean via surface air-sea exchange, and are almost completely chemically and biologically inert, their distribution within the ocean interior reveals its ventilation via transport and mixing. Measuring the dissolved concentrations of the gases -- as well as the mixing ratios between them -- shows circulation pathways within the ocean as well as water mass ages (i.e. the time since last contact with the atmosphere). This feature of the gases has made them valuable across a wide range of oceanographic problems. One use lies in ocean modelling, where they can be used to evaluate the realism of the circulation and atmosphere). This feature of the gases has made them valuable across a wide range of oceanographic problems. One use lies in ocean modelling, where they can be used to evaluate the realism of the circulation and ventilation of models, key for understanding the behaviour of wider modelled marine biogeochemistry (e.g. \citep{dutay_2002,palmieri_2015}). \\ Advection and diffusion of the CFCs in NEMO are calculated by the physical module, OPA, whereas sources and sinks are done by the CFC module within TOP. The only source for CFCs in the ocean is via air-sea gas exchange at its surface, and since CFCs are generally stable within the ocean, we assume that there are no sinks (i.e. no loss processes) within the ocean interior. whereas sources and sinks are done by the CFC module within TOP. The only source for CFCs in the ocean is via air-sea gas exchange at its surface, and since CFCs are generally stable within the ocean, we assume that there are no sinks (i.e. no loss processes) within the ocean interior. Consequently, the sinks-minus-sources term for CFCs consists only of their air-sea fluxes, $F_{cfc}$, as described in the Ocean Model Inter-comparison Project (OMIP) protocol \citep{orr_2017}: F_{cfc} = K_{w} \, \cdot \, (C_{sat} - C_{surf}) \, \cdot  \, (1 - f_{i}) \label{equ_CFC_flux} \end{eqnarray} Where $K_{w}$ is the piston velocity (in m~s$^{-1}$), as defined in Equation \ref{equ_Kw}; $C_{sat}$ is the saturation concentration of the CFC tracer, as defined in Equation \ref{equ_C_sat}; $C_{surf}$ is the local surface concentration of the CFC tracer within the model (in mol~m$^{-3}$); \end{eqnarray} Where $K_{w}$ is the piston velocity (in m~s$^{-1}$), as defined in Equation \ref{equ_Kw}; $C_{sat}$ is the saturation concentration of the CFC tracer, as defined in Equation \ref{equ_C_sat}; $C_{surf}$ is the local surface concentration of the CFC tracer within the model (in mol~m$^{-3}$); and $f_{i}$ is the fractional sea-ice cover of the local ocean (ranging between 0.0 for ice-free ocean, through to 1.0 for completely ice-covered ocean with no air-sea exchange). C_{sat} = Sol \, \cdot \, P_{cfc} \label{equ_C_sat} \end{eqnarray} Where $Sol$ is the gas solubility in mol~m$^{-3}$~pptv$^{-1}$, as defined in Equation \ref{equ_Sol_CFC}; \end{eqnarray} Where $Sol$ is the gas solubility in mol~m$^{-3}$~pptv$^{-1}$, as defined in Equation \ref{equ_Sol_CFC}; and $P_{cfc}$ is the atmosphere concentration of the CFC (in parts per trillion by volume, pptv). This latter concentration is provided to the model by the historical time-series of \citet{bullister_2017}. This includes bulk atmospheric concentrations of the CFCs for both hemispheres -- this is necessary because of the geographical asymmetry in the production and release of CFCs to the atmosphere. Within the model, hemispheric concentrations are uniform, with the exception of the region between This includes bulk atmospheric concentrations of the CFCs for both hemispheres -- this is necessary because of the geographical asymmetry in the production and release of CFCs to the atmosphere. Within the model, hemispheric concentrations are uniform, with the exception of the region between 10$^{\circ}$N and 10$^{\circ}$ in which they are linearly interpolated. The piston velocity $K_{w}$ is a function of 10~m wind speed (in m~s$^{-1}$) and sea surface temperature, The piston velocity $K_{w}$ is a function of 10~m wind speed (in m~s$^{-1}$) and sea surface temperature, $T$ (in $^{\circ}$C), and is calculated here following \citet{wanninkhof_1992}: K_{w} = X_{conv} \, \cdot \, a \, \cdot \, u^2 \, \cdot \, \sqrt{ \frac{Sc(T)}{660} } \label{equ_Kw} \end{eqnarray} Where $X_{conv}$ = $\frac{0.01}{3600}$, a conversion factor that changes the piston velocity from cm~h$^{-1}$ to m~s$^{-1}$; \end{eqnarray} Where $X_{conv}$ = $\frac{0.01}{3600}$, a conversion factor that changes the piston velocity from cm~h$^{-1}$ to m~s$^{-1}$; $a$ is a constant re-estimated by \citet{wanninkhof_2014} to 0.251 (in $\frac{cm~h^{-1}}{(m~s^{-1})^{2}}$); and $u$ is the 10~m wind speed in m~s$^{-1}$ from either an atmosphere model or reanalysis atmospheric forcing. Sc =  a0 + (a1 \, \cdot \, T) + (a2  \, \cdot \, T^2) + (a3 \, \cdot \, T^3) + (a4 \, \cdot \, T^4) \label{equ_Sc} \end{eqnarray} The solubility, $Sol$, used in Equation \ref{equ_C_sat} is calculated in mol~l$^{-1}$~atm$^{-1}$, and is specific for each gas. It has been experimentally estimated by \citet{warner_1985} as a function of temperature \end{eqnarray} The solubility, $Sol$, used in Equation \ref{equ_C_sat} is calculated in mol~l$^{-1}$~atm$^{-1}$, and is specific for each gas. It has been experimentally estimated by \citet{warner_1985} as a function of temperature and salinity: % code version that I have to hand, although this might be out of date; in any case, I'dag % strongly suggest avoiding the use of the \frac{}{100}, and instead substitute a term that is % "degrees Kelvin divided by 100" (which is weird in itself); and make this term use Celcius % "degrees Kelvin divided by 100" (which is weird in itself); and make this term use Celcius % so that you're not using T twice in different ways \ln{(Sol)} = a_1 + \frac{a_2}{ T_{X}} + a_3 \, \cdot \, \ln{ T_{X} } + a_4 \, \cdot \, T_{X}^2 + S \, \cdot \, ( b_1 + b_2 \, \cdot \, T_{X} + b_3 \, \cdot \, T_{X}^2 ) \label{equ_Sol_CFC} \end{eqnarray} \end{eqnarray} % \begin{eqnarray} % \ln{(Sol)} = a1 + a2 \, \frac{100}{T} + a3 \, \ln{ (\frac{T}{100}) } + a4 \, \frac{T}{100}^2 + S \, ( b1 + b2 \, \frac{T}{100} + b3 \, \frac{T}{100}^2 ) % \label{equ_Sol_CFC} % \end{eqnarray} Where $T_{X}$ is $\frac{T + 273.16}{100}$, a function of temperature; % \end{eqnarray} Where $T_{X}$ is $\frac{T + 273.16}{100}$, a function of temperature; and the $a_{x}$ and $b_{x}$ coefficients are specific for each gas (see Table \ref{tab_ref_CFC}). This is then converted to mol~m$^{-3}$~pptv$^{-1}$ assuming a constant atmospheric surface pressure of 1~atm. The solubility of CFCs thus decreases with rising $T$ while being relatively insensitive to salinity changes. The solubility of CFCs thus decreases with rising $T$ while being relatively insensitive to salinity changes. Consequently, this translates to a pattern of solubility where it is greatest in cold, polar regions (see Figure \ref{img_cfcsol}). \centering \begin{tabular}{l l l l l l l l l} \hline Gas   & & a1 & a2 & a3 & a4 & b1 & b2 & b3 \\ \hline Gas   & & a1 & a2 & a3 & a4 & b1 & b2 & b3 \\ \hline CFC-11 & & -218.0971 & 298.9702 & 113.8049 & -1.39165 & -0.143566  & 0.091015   & -0.0153924 \\ SF6    & & -80.0343  & 117.232  & 29.5817  & 0.0      & 0.0335183  & -0.0373942 & 0.00774862 \\ \hline \end{tabular} \end{tabular} \label{tab_ref_CFC} \end{table} \centering \begin{tabular}{l l l l l l l } \hline Gas  & & a0 & a1 & a2 & a3 & a4 \\ \hline Gas  & & a0 & a1 & a2 & a3 & a4 \\ \hline CFC-11 & & 3579.2  & -222.63 & 7.5749 & -0.14595 & 0.0011874   \\ SF6    & & 3177.5  & -200.57 & 6.8865 & -0.13335 & 0.0010877   \\ \hline \end{tabular} \end{tabular} \label{tab_Sc} \end{table} %---------------------------------------------------------------------------------------------------------- The C14 package implemented in NEMO by Anne Mouchet models ocean $\Dcq$. It offers several possibilities: $\Dcq$ as a physical tracer of the ocean ventilation (natural $\cq$), assessment of bomb radiocarbon uptake, as well as transient studies of paleo-historical ocean radiocarbon distributions. The C14 package implemented in NEMO by Anne Mouchet models ocean $\Dcq$. It offers several possibilities: $\Dcq$ as a physical tracer of the ocean ventilation (natural $\cq$), assessment of bomb radiocarbon uptake, as well as transient studies of paleo-historical ocean radiocarbon distributions. \subsubsection{Method} This simplified approach also neglects the effects of fractionation (e.g.,  air-sea exchange) and of biological processes. Previous studies by \cite{bacastow_1990} and \cite{joos_1997} resulted in nearly identical $\Dcq$ distributions among experiments considering biology or not. Since observed $\Rq$ ratios are corrected for the isotopic fractionation when converted to the standard $\Dcq$ notation \citep{stuiver_1977} the model results are directly comparable to observations. Since observed $\Rq$ ratios are corrected for the isotopic fractionation when converted to the standard $\Dcq$ notation \citep{stuiver_1977} the model results are directly comparable to observations. Therefore the simplified approach is justified for the purpose of assessing the circulation and ventilation of OGCMs. %The sensitivity to this parametrization is discussed in section \ref{sec:result}. % \item Chemical enhancement (term $b$  in Eq. \ref{eq:wanchem}) may be set on/off by means of the logical variable \CODE{ln\_chemh}. \item Chemical enhancement (term $b$  in Eq. \ref{eq:wanchem}) may be set on/off by means of the logical variable \CODE{ln\_chemh}. \end{itemize} \end{figure} Performing this type of experiment requires that a pre-industrial equilibrium run be performed beforehand (\CODE{ln\_rsttr} should be set to \texttt{.TRUE.}). Performing this type of experiment requires that a pre-industrial equilibrium run be performed beforehand (\CODE{ln\_rsttr} should be set to \texttt{.TRUE.}). An exception to this rule is when wishing to perform a perturbation bomb experiment as was possible with the package \texttt{C14b}. It is still possible to easily set-up that type of transient experiment for which no previous run is needed.  In addition to the instructions as given in this section it is however necessary to adapt the \texttt{atmc14.dat} file so that it does no longer contain any negative $\Dcq$ values (Suess effect in the pre-bomb period). \begin{itemize} \item Specify the starting date of the experiment: \CODE{nn\_date0} in \texttt{namelist}.  \CODE{nn\_date0} is written as Year0101 where Year may take any positive value (AD). \item Then the parameters \CODE{nn\_rstctl} in  \texttt{namelist} (on-line) and \CODE{nn\_rsttr} in \texttt{namelist\_top} (off-line)  must be \textbf{set to 0} at the start of the experiment (force the date to \CODE{nn\_date0} for the \textbf{first} experiment year). \item Then the parameters \CODE{nn\_rstctl} in  \texttt{namelist} (on-line) and \CODE{nn\_rsttr} in \texttt{namelist\_top} (off-line)  must be \textbf{set to 0} at the start of the experiment (force the date to \CODE{nn\_date0} for the \textbf{first} experiment year). \item These two parameters (\CODE{nn\_rstctl} and \CODE{nn\_rsttr}) have then to be \textbf{set to 2} for the following years (the date must be read in the restart file). \end{itemize} The file \texttt{intcal13.14c} \citep{reimer_2013} contains atmospheric $\Dcq$ from 0 to 50 kyr cal BP\footnote{cal BP: number of years before 1950 AD}. The $\cd$ forcing is provided in file \texttt{ByrdEdcCO2.txt}. The content of this file is based on  the high resolution record from EPICA Dome C \citep{monnin_2004} for the Holocene and the Transition, and on Byrd Ice Core CO2 Data for 20--90 kyr BP  \citep{ahn_2008}. These atmospheric values are reproduced in Fig. \ref{fig:paleo}. Dates in these files are expressed as yr BP. The $\cd$ forcing is provided in file \texttt{ByrdEdcCO2.txt}. The content of this file is based on  the high resolution record from EPICA Dome C \citep{monnin_2004} for the Holocene and the Transition, and on Byrd Ice Core CO2 Data for 20--90 kyr BP  \citep{ahn_2008}. These atmospheric values are reproduced in Fig. \ref{fig:paleo}. Dates in these files are expressed as yr BP. To ensure that the atmospheric forcing is applied properly as well as that output files contain consistent dates and inventories the experiment should be set up carefully. Field & Type & Dim & Units & Description \\ \hline RC14 & ptrc & 3-D & -        & Radiocarbon ratio \\ DeltaC14 & diad & 3-D & \textperthousand & $\Dcq$\\ DeltaC14 & diad & 3-D & \textperthousand & $\Dcq$\\ C14Age & diad & 3-D & yr &   Radiocarbon age \\ RAge & diad & 2-D & yr & Reservoir age\\ qtr\_c14 &  diad & 2-D & m$^{-2}$ yr$^{-1}$ & Air-to-sea net $\Rq$ flux\\ qint\_c14 & diad & 2-D &   m$^{-2}$ &  Cumulative air-to-sea $\Rq$ flux \\ AtmCO2 & scalar & 0-D & ppm & Global atmospheric $\cd$ \\ AtmC14 & scalar & 0-D & \textperthousand  & Global atmospheric $\Dcq$\\ K\_CO2 & scalar & 0-D & cm h$^{-1}$  & Global $\cd$ piston velocity ($\overline{\kappa_{\cd}}$) \\ K\_C14 & scalar & 0-D &m yr$^{-1}$ & Global $\Rq$ transfer velocity  ($\overline{\kappa_R}$)\\ AtmCO2 & scalar & 0-D & ppm & Global atmospheric $\cd$ \\ AtmC14 & scalar & 0-D & \textperthousand  & Global atmospheric $\Dcq$\\ K\_CO2 & scalar & 0-D & cm h$^{-1}$  & Global $\cd$ piston velocity ($\overline{\kappa_{\cd}}$) \\ K\_C14 & scalar & 0-D &m yr$^{-1}$ & Global $\Rq$ transfer velocity  ($\overline{\kappa_R}$)\\ C14Inv & scalar & 0-D & $10^{26}$ atoms & Ocean radiocarbon inventory \\ \hline \end{tabular} \end{table} %!   Standard ratio: 1.176E-12 ; Avogadro's nbr = 6.022E+23 at/mol ; bomb C14 traditionally reported as 1.E+26 atoms %   REAL(wp), PARAMETER            :: atomc14=1.176*6.022E-15   ! conversion factor %   REAL(wp), PARAMETER            :: atomc14=1.176*6.022E-15   ! conversion factor % atomc14 * xdicsur * zdum The radiocarbon age is computed as  $(-1/\lambda) \ln{ \left( \Rq \right)}$, with zero age corresponding to $\Rq=1$. The radiocarbon age is computed as  $(-1/\lambda) \ln{ \left( \Rq \right)}$, with zero age corresponding to $\Rq=1$. The reservoir age is the age difference between the ocean uppermost layer and the atmosphere. It is usually reported as conventional radiocarbon age; i.e., computed by means of the Libby radiocarbon mean life \cite[8033 yr;][]{stuiver_1977} \subsection{PISCES biogeochemical model} PISCES is a biogeochemical model which simulates the lower trophic levels of marine ecosystem (phytoplankton, microzooplankton and mesozooplankton) and the biogeochemical cycles of carbonand of the main nutrients (P, N, Fe, and Si). The  model is intended to be used for both regional and global configurations at high or low spatial resolutions as well as for  short-term (seasonal, interannual) and long-term (climate change, paleoceanography) analyses. PISCES is a biogeochemical model which simulates the lower trophic levels of marine ecosystem (phytoplankton, microzooplankton and mesozooplankton) and the biogeochemical cycles of carbonand of the main nutrients (P, N, Fe, and Si). The  model is intended to be used for both regional and global configurations at high or low spatial resolutions as well as for  short-term (seasonal, interannual) and long-term (climate change, paleoceanography) analyses. Two versions of PISCES are available in NEMO v4.0 : PISCES-v2, by setting in namelist\_pisces\_ref  \np{ln\_p4z} to true,  can be seen as one of the many Monod models \citep{monod_1958}. It assumes a constant Redfield ratio and phytoplankton growth depends on the external concentration in nutrients. There are twenty-four prognostic variables (tracers) including two phytoplankton compartments  (diatoms and nanophytoplankton), two zooplankton size-classes (microzooplankton and  mesozooplankton) and a description of the carbonate chemistry. Formulations in PISCES-v2 are based on a mixed Monod/Quota formalism: On one hand, stoichiometry of C/N/P is fixed and growth rate of phytoplankton is limited by the external availability in N, P and Si. On the other hand, the iron and silicium quotas are variable and growth rate of phytoplankton is limited by the internal availability in Fe. Various parameterizations can be activated in PISCES-v2, setting for instance the complexity of iron chemistry or the description of particulate organic materials. PISCES-v2, by setting in namelist\_pisces\_ref  \np{ln\_p4z} to true,  can be seen as one of the many Monod models \citep{monod_1958}. It assumes a constant Redfield ratio and phytoplankton growth depends on the external concentration in nutrients. There are twenty-four prognostic variables (tracers) including two phytoplankton compartments  (diatoms and nanophytoplankton), two zooplankton size-classes (microzooplankton and  mesozooplankton) and a description of the carbonate chemistry. Formulations in PISCES-v2 are based on a mixed Monod/Quota formalism: On one hand, stoichiometry of C/N/P is fixed and growth rate of phytoplankton is limited by the external availability in N, P and Si. On the other hand, the iron and silicium quotas are variable and growth rate of phytoplankton is limited by the internal availability in Fe. Various parameterizations can be activated in PISCES-v2, setting for instance the complexity of iron chemistry or the description of particulate organic materials. PISCES-QUOTA has been built on the PISCES-v2 model described in \citet{aumont_2015}. PISCES-QUOTA has thirty-nine prognostic compartments. Phytoplankton growth can be controlled by five modeled limiting nutrients: Nitrate and Ammonium, Phosphate, Silicate and Iron. Five living compartments are represented: Three phytoplankton size classes/groups corresponding to picophytoplankton, nanophytoplankton and diatoms, and two zooplankton size classes which are microzooplankton and mesozooplankton. For phytoplankton, the prognostic variables are the carbon, nitrogen, phosphorus,  iron, chlorophyll and silicon biomasses (the latter only for diatoms). This means that the N/C, P/C, Fe/C and Chl/C ratios of both phytoplankton groups as well as the Si/C ratio of diatoms are prognostically predicted  by the model. Zooplankton are assumed to be strictly homeostatic \citep[e.g.,][]{sterner_2003,woods_2013,meunier_2014}. As a consequence, the C/N/P/Fe ratios of these groups are maintained constant and are not allowed to vary. In PISCES, the Redfield ratios C/N/P are set to 122/16/1 \citep{takahashi_1985} and the -O/C ratio is set to 1.34 \citep{kortzinger_2001}. No silicified zooplankton is assumed. The bacterial pool is not yet explicitly modeled. There are three non-living compartments: Semi-labile dissolved organic matter, small sinking particles, and large sinking particles. As a consequence of the variable stoichiometric ratios of phytoplankton and of the stoichiometric regulation of zooplankton, elemental ratios in organic matter cannot be supposed constant anymore as that was the case in PISCES-v2. Indeed, the nitrogen, phosphorus, iron, silicon and calcite pools of the particles are now all explicitly modeled. The sinking speed of the particles is not altered by their content in calcite and biogenic silicate (''The ballast effect'', \citep{honjo_1996,armstrong_2001}). The latter particles are assumed to sink at the same speed as the large organic matter particles. All the non-living compartments experience aggregation due to turbulence and differential settling as well as Brownian coagulation for DOM. \subsection{MY\_TRC interface for coupling external BGC models} \label{Mytrc} Coupling passive tracers offline with NEMO requires precomputed  physical fields from OGCM. Those fields are read from files and interpolated on-the-fly at each model time step At least the following dynamical parameters should be absolutely passed to the transport : ocean velocities, temperature, salinity, mixed layer depth and for ecosystem models like PISCES, sea ice concentration, short wave radiation at the ocean surface, wind speed (or at least, wind stress). At least the following dynamical parameters should be absolutely passed to the transport : ocean velocities, temperature, salinity, mixed layer depth and for ecosystem models like PISCES, sea ice concentration, short wave radiation at the ocean surface, wind speed (or at least, wind stress). The so-called offline mode is useful since it has lower computational costs for example to perform very longer simulations - about 3000 years - to reach equilibrium of CO2 sinks for climate-carbon studies. \begin{itemize} \item \textit{dtadyn.F90} :  this module allows to read and compute the dynamical fields at each model time-step \item \textit{dtadyn.F90} :  this module allows to read and compute the dynamical fields at each model time-step \item \textit{nemogcm.F90} :  a degraded version of the main nemogcm.F90 code of NEMO to manage the time-stepping \end{itemize}
• ## NEMO/trunk/doc/latex/TOP/subfiles/model_setup.tex

 r11019 \documentclass[../../NEMO/main/NEMO_manual]{subfiles} \documentclass[../main/TOP_manual]{subfiles} \begin{document} %------------------------------------------------------------------------------------------------------------- The usage of TOP is activated The usage of TOP is activated \begin{itemize} As an example, the user can refer to already available configurations in the code, GYRE\_PISCES being the NEMO biogeochemical demonstrator and GYRE\_BFM to see the required configuration elements to couple with an external biogeochemical model (see also section \S\ref{SMS_models}) . Note that, since version 4.0, TOP interface core functionalities are activated by means of logical keys and all submodules preprocessing macros from previous versions were removed. Note that, since version 4.0, TOP interface core functionalities are activated by means of logical keys and all submodules preprocessing macros from previous versions were removed. There are only three specific keys remaining in TOP \end{itemize} For a remind, the revisited structure of TOP interface now counts for five different modules handled in namelist\_top : For a remind, the revisited structure of TOP interface now counts for five different modules handled in namelist\_top : \begin{itemize}
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