Changeset 11591 for NEMO/trunk/doc/latex/TOP/subfiles
 Timestamp:
 20190925T13:52:24+02:00 (22 months ago)
 Location:
 NEMO/trunk/doc/latex/TOP/subfiles
 Files:

 5 added
 4 edited
 2 moved
Legend:
 Unmodified
 Added
 Removed

NEMO/trunk/doc/latex/TOP/subfiles
 Property svn:ignore deleted

NEMO/trunk/doc/latex/TOP/subfiles/miscellaneous.tex
r10896 r11591 1 \documentclass[../ ../NEMO/main/NEMO_manual]{subfiles}1 \documentclass[../main/TOP_manual]{subfiles} 2 2 3 3 \begin{document} … … 43 43 \begin{minted}{bash} 44 44 bld::tool::fppkeys key_iomput key_mpp_mpi key_top 45 45 46 46 src::MYBGC::initialization <MYBGCPATH>/initialization 47 47 src::MYBGC::pelagic <MYBGCPATH>/pelagic 
NEMO/trunk/doc/latex/TOP/subfiles/model_description.tex
r11043 r11591 1 \documentclass[../ ../NEMO/main/NEMO_manual]{subfiles}1 \documentclass[../main/TOP_manual]{subfiles} 2 2 3 3 \newcommand{\cd}{\mathrm{CO_2}} … … 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{nemo_manual} 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. 31 31 32 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 $b_t= e_{1t}\,e_{2t}\,e_{3t}$ 33 34 The third term represents the change due to lateral diffusion. 32 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 $b_t= e_{1t}\,e_{2t}\,e_{3t}$ 33 34 The third term represents the change due to lateral diffusion. 35 35 36 36 The fourth term is change due to vertical diffusion, parameterized as eddy diffusion to represent vertical turbulent fluxes : … … 68 68 69 69 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. 70 70 71 71 \subsection{ Advection} 72 72 %namtrc_adv … … 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{nemo_manual}. 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 85 85 %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 : 86 86 %\begin{equation} \label{eq:traqsr_iradiance} 87 %Aht = Aht * rn_fact_lap * \exp(  \max( 0., z 1000 ) / 1000} \quad \text{for $L=1$ to $N$} 87 %Aht = Aht * rn_fact_lap * \exp(  \max( 0., z 1000 ) / 1000} \quad \text{for $L=1$ to $N$} 88 88 %\end{equation} 89 89 90 90 \subsection{ Tracer damping} 91 91 92 92 %namtrc_dmp 93 93 \nlst{namtrc_dmp} … … 98 98 99 99 \subsection{ Tracer positivity} 100 100 101 101 %namtrc_rad 102 102 \nlst{namtrc_rad} … … 160 160 As can be seen in the figure, while the concentration of SF6 continues to rise to the present day, the concentrations of both CFC11 and CFC12 have levelled off and declined since around the 1990s. 161 161 These declines have been driven by the Montreal Protocol (effective since August 1989), which has banned the production of CFC11 and CFC12 (as well as other CFCs) because of their role in the depletion of 162 stratospheric ozone (O$_{3}$), critical in decreasing the flux of ultraviolet radiation to the Earth's surface. Separate to this role in ozonedepletion, all three chemicals are significantly more potent greenhouse gases 162 stratospheric ozone (O$_{3}$), critical in decreasing the flux of ultraviolet radiation to the Earth's surface. Separate to this role in ozonedepletion, all three chemicals are significantly more potent greenhouse gases 163 163 than CO$_{2}$ (especially SF6), although their relatively low atmospheric concentrations limit their role in climate change. \\ 164 164 … … 168 168 % concentrations increased until around the late 1990s afterwhich they began to decline in 169 169 % response to the Montreal Protocol. 170 % In the case of SF6, release began in the 1950s 170 % In the case of SF6, release began in the 1950s 171 171 % This release began in the 1930s for CFC11 and CFC12, and the 1950s for SF6, and 172 % regularly increasing their atmospheric concentration until the 1090s, 2000s for respectively CFC11, CFC12, 172 % regularly increasing their atmospheric concentration until the 1090s, 2000s for respectively CFC11, CFC12, 173 173 % and is still increasing, and SF6 (see Figure \ref{img_cfcatm}). \\ 174 174 … … 177 177 Because they only enter the ocean via surface airsea exchange, and are almost completely chemically and biologically inert, their distribution within the ocean interior reveals its ventilation via transport and mixing. 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 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 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 180 180 ventilation of models, key for understanding the behaviour of wider modelled marine biogeochemistry (e.g. \citep{dutay_2002,palmieri_2015}). \\ 181 181 … … 183 183 184 184 Advection and diffusion of the CFCs in NEMO are calculated by the physical module, OPA, 185 whereas sources and sinks are done by the CFC module within TOP. 186 The only source for CFCs in the ocean is via airsea gas exchange at its surface, and since CFCs are generally 187 stable within the ocean, we assume that there are no sinks (i.e. no loss processes) within the ocean interior. 185 whereas sources and sinks are done by the CFC module within TOP. 186 The only source for CFCs in the ocean is via airsea gas exchange at its surface, and since CFCs are generally 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 189 189 described in the Ocean Model Intercomparison Project (OMIP) protocol \citep{orr_2017}: … … 196 196 F_{cfc} = K_{w} \, \cdot \, (C_{sat}  C_{surf}) \, \cdot \, (1  f_{i}) 197 197 \label{equ_CFC_flux} 198 \end{eqnarray} 199 200 Where $K_{w}$ is the piston velocity (in m~s$^{1}$), as defined in Equation \ref{equ_Kw}; 201 $C_{sat}$ is the saturation concentration of the CFC tracer, as defined in Equation \ref{equ_C_sat}; 202 $C_{surf}$ is the local surface concentration of the CFC tracer within the model (in mol~m$^{3}$); 198 \end{eqnarray} 199 200 Where $K_{w}$ is the piston velocity (in m~s$^{1}$), as defined in Equation \ref{equ_Kw}; 201 $C_{sat}$ is the saturation concentration of the CFC tracer, as defined in Equation \ref{equ_C_sat}; 202 $C_{surf}$ is the local surface concentration of the CFC tracer within the model (in mol~m$^{3}$); 203 203 and $f_{i}$ is the fractional seaice cover of the local ocean (ranging between 0.0 for icefree ocean, 204 204 through to 1.0 for completely icecovered ocean with no airsea exchange). … … 209 209 C_{sat} = Sol \, \cdot \, P_{cfc} 210 210 \label{equ_C_sat} 211 \end{eqnarray} 212 213 Where $Sol$ is the gas solubility in mol~m$^{3}$~pptv$^{1}$, as defined in Equation \ref{equ_Sol_CFC}; 211 \end{eqnarray} 212 213 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). 215 215 This latter concentration is provided to the model by the historical timeseries of \citet{bullister_2017}. 216 This includes bulk atmospheric concentrations of the CFCs for both hemispheres  this is necessary because of 217 the geographical asymmetry in the production and release of CFCs to the atmosphere. 218 Within the model, hemispheric concentrations are uniform, with the exception of the region between 216 This includes bulk atmospheric concentrations of the CFCs for both hemispheres  this is necessary because of 217 the geographical asymmetry in the production and release of CFCs to the atmosphere. 218 Within the model, hemispheric concentrations are uniform, with the exception of the region between 219 219 10$^{\circ}$N and 10$^{\circ}$ in which they are linearly interpolated. 220 220 221 The piston velocity $K_{w}$ is a function of 10~m wind speed (in m~s$^{1}$) and sea surface temperature, 221 The piston velocity $K_{w}$ is a function of 10~m wind speed (in m~s$^{1}$) and sea surface temperature, 222 222 $T$ (in $^{\circ}$C), and is calculated here following \citet{wanninkhof_1992}: 223 223 … … 225 225 K_{w} = X_{conv} \, \cdot \, a \, \cdot \, u^2 \, \cdot \, \sqrt{ \frac{Sc(T)}{660} } 226 226 \label{equ_Kw} 227 \end{eqnarray} 228 229 Where $X_{conv}$ = $\frac{0.01}{3600}$, a conversion factor that changes the piston velocity 230 from cm~h$^{1}$ to m~s$^{1}$; 227 \end{eqnarray} 228 229 Where $X_{conv}$ = $\frac{0.01}{3600}$, a conversion factor that changes the piston velocity 230 from cm~h$^{1}$ to m~s$^{1}$; 231 231 $a$ 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. … … 236 236 Sc = a0 + (a1 \, \cdot \, T) + (a2 \, \cdot \, T^2) + (a3 \, \cdot \, T^3) + (a4 \, \cdot \, T^4) 237 237 \label{equ_Sc} 238 \end{eqnarray} 239 240 The solubility, $Sol$, used in Equation \ref{equ_C_sat} is calculated in mol~l$^{1}$~atm$^{1}$, 241 and is specific for each gas. 242 It has been experimentally estimated by \citet{warner_1985} as a function of temperature 238 \end{eqnarray} 239 240 The solubility, $Sol$, used in Equation \ref{equ_C_sat} is calculated in mol~l$^{1}$~atm$^{1}$, 241 and is specific for each gas. 242 It has been experimentally estimated by \citet{warner_1985} as a function of temperature 243 243 and salinity: 244 244 … … 246 246 % code version that I have to hand, although this might be out of date; in any case, I'dag 247 247 % strongly suggest avoiding the use of the \frac{}{100}, and instead substitute a term that is 248 % "degrees Kelvin divided by 100" (which is weird in itself); and make this term use Celcius 248 % "degrees Kelvin divided by 100" (which is weird in itself); and make this term use Celcius 249 249 % so that you're not using T twice in different ways 250 250 … … 252 252 \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 ) 253 253 \label{equ_Sol_CFC} 254 \end{eqnarray} 254 \end{eqnarray} 255 255 256 256 % \begin{eqnarray} 257 257 % \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 ) 258 258 % \label{equ_Sol_CFC} 259 % \end{eqnarray} 260 261 Where $T_{X}$ is $\frac{T + 273.16}{100}$, a function of temperature; 259 % \end{eqnarray} 260 261 Where $T_{X}$ is $\frac{T + 273.16}{100}$, a function of temperature; 262 262 and the $a_{x}$ and $b_{x}$ coefficients are specific for each gas (see Table \ref{tab_ref_CFC}). 263 263 This is then converted to mol~m$^{3}$~pptv$^{1}$ assuming a constant atmospheric surface pressure of 1~atm. 264 The solubility of CFCs thus decreases with rising $T$ while being relatively insensitive to salinity changes. 264 The solubility of CFCs thus decreases with rising $T$ while being relatively insensitive to salinity changes. 265 265 Consequently, this translates to a pattern of solubility where it is greatest in cold, polar regions (see Figure \ref{img_cfcsol}). 266 266 … … 289 289 \centering 290 290 \begin{tabular}{l l l l l l l l l} 291 \hline 292 Gas & & a1 & a2 & a3 & a4 & b1 & b2 & b3 \\ 291 \hline 292 Gas & & a1 & a2 & a3 & a4 & b1 & b2 & b3 \\ 293 293 \hline 294 294 CFC11 & & 218.0971 & 298.9702 & 113.8049 & 1.39165 & 0.143566 & 0.091015 & 0.0153924 \\ … … 296 296 SF6 & & 80.0343 & 117.232 & 29.5817 & 0.0 & 0.0335183 & 0.0373942 & 0.00774862 \\ 297 297 \hline 298 \end{tabular} 298 \end{tabular} 299 299 \label{tab_ref_CFC} 300 300 \end{table} … … 306 306 \centering 307 307 \begin{tabular}{l l l l l l l } 308 \hline 309 Gas & & a0 & a1 & a2 & a3 & a4 \\ 308 \hline 309 Gas & & a0 & a1 & a2 & a3 & a4 \\ 310 310 \hline 311 311 CFC11 & & 3579.2 & 222.63 & 7.5749 & 0.14595 & 0.0011874 \\ … … 313 313 SF6 & & 3177.5 & 200.57 & 6.8865 & 0.13335 & 0.0010877 \\ 314 314 \hline 315 \end{tabular} 315 \end{tabular} 316 316 \label{tab_Sc} 317 317 \end{table} … … 353 353 % 354 354 355 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 paleohistorical ocean radiocarbon distributions. 355 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 paleohistorical ocean radiocarbon distributions. 356 356 357 357 \subsubsection{Method} … … 368 368 369 369 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. 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. … … 425 425 %The sensitivity to this parametrization is discussed in section \ref{sec:result}. 426 426 % 427 \item Chemical enhancement (term $b$ in Eq. \ref{eq:wanchem}) may be set on/off by means of the logical variable \CODE{ln\_chemh}. 427 \item Chemical enhancement (term $b$ in Eq. \ref{eq:wanchem}) may be set on/off by means of the logical variable \CODE{ln\_chemh}. 428 428 \end{itemize} 429 429 … … 464 464 \end{figure} 465 465 466 Performing this type of experiment requires that a preindustrial equilibrium run be performed beforehand (\CODE{ln\_rsttr} should be set to \texttt{.TRUE.}). 466 Performing this type of experiment requires that a preindustrial equilibrium run be performed beforehand (\CODE{ln\_rsttr} should be set to \texttt{.TRUE.}). 467 467 468 468 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 setup 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 prebomb period). … … 476 476 \begin{itemize} 477 477 \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). 478 \item Then the parameters \CODE{nn\_rstctl} in \texttt{namelist} (online) and \CODE{nn\_rsttr} in \texttt{namelist\_top} (offline) 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). 478 \item Then the parameters \CODE{nn\_rstctl} in \texttt{namelist} (online) and \CODE{nn\_rsttr} in \texttt{namelist\_top} (offline) 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). 479 479 \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). 480 480 \end{itemize} … … 497 497 498 498 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. 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. … … 519 519 Field & Type & Dim & Units & Description \\ \hline 520 520 RC14 & ptrc & 3D &  & Radiocarbon ratio \\ 521 DeltaC14 & diad & 3D & \textperthousand & $\Dcq$\\ 521 DeltaC14 & diad & 3D & \textperthousand & $\Dcq$\\ 522 522 C14Age & diad & 3D & yr & Radiocarbon age \\ 523 523 RAge & diad & 2D & yr & Reservoir age\\ 524 524 qtr\_c14 & diad & 2D & m$^{2}$ yr$^{1}$ & Airtosea net $\Rq$ flux\\ 525 525 qint\_c14 & diad & 2D & m$^{2}$ & Cumulative airtosea $\Rq$ flux \\ 526 AtmCO2 & scalar & 0D & ppm & Global atmospheric $\cd$ \\ 527 AtmC14 & scalar & 0D & \textperthousand & Global atmospheric $\Dcq$\\ 528 K\_CO2 & scalar & 0D & cm h$^{1}$ & Global $\cd$ piston velocity ($ \overline{\kappa_{\cd}}$) \\ 529 K\_C14 & scalar & 0D &m yr$^{1}$ & Global $\Rq$ transfer velocity ($ \overline{\kappa_R}$)\\ 526 AtmCO2 & scalar & 0D & ppm & Global atmospheric $\cd$ \\ 527 AtmC14 & scalar & 0D & \textperthousand & Global atmospheric $\Dcq$\\ 528 K\_CO2 & scalar & 0D & cm h$^{1}$ & Global $\cd$ piston velocity ($ \overline{\kappa_{\cd}}$) \\ 529 K\_C14 & scalar & 0D &m yr$^{1}$ & Global $\Rq$ transfer velocity ($ \overline{\kappa_R}$)\\ 530 530 C14Inv & scalar & 0D & $10^{26}$ atoms & Ocean radiocarbon inventory \\ \hline 531 531 \end{tabular} … … 534 534 \end{table} 535 535 %! Standard ratio: 1.176E12 ; Avogadro's nbr = 6.022E+23 at/mol ; bomb C14 traditionally reported as 1.E+26 atoms 536 % REAL(wp), PARAMETER :: atomc14=1.176*6.022E15 ! conversion factor 536 % REAL(wp), PARAMETER :: atomc14=1.176*6.022E15 ! conversion factor 537 537 % atomc14 * xdicsur * zdum 538 538 539 The radiocarbon age is computed as $(1/\lambda) \ln{ \left( \Rq \right)}$, with zero age corresponding to $\Rq=1$. 539 The radiocarbon age is computed as $(1/\lambda) \ln{ \left( \Rq \right)}$, with zero age corresponding to $\Rq=1$. 540 540 541 541 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} … … 561 561 \subsection{PISCES biogeochemical model} 562 562 563 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 shortterm (seasonal, interannual) and longterm (climate change, paleoceanography) analyses. 563 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 shortterm (seasonal, interannual) and longterm (climate change, paleoceanography) analyses. 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_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. 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. 567 567 568 568 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. … … 570 570 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. 571 571 572 572 573 573 \subsection{MY\_TRC interface for coupling external BGC models} 574 574 \label{Mytrc} … … 597 597 598 598 Coupling passive tracers offline with NEMO requires precomputed physical fields from OGCM. Those fields are read from files and interpolated onthefly at each model time step 599 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). 599 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). 600 600 The socalled 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 climatecarbon studies. 601 601 … … 603 603 604 604 \begin{itemize} 605 \item \textit{dtadyn.F90} : this module allows to read and compute the dynamical fields at each model timestep 605 \item \textit{dtadyn.F90} : this module allows to read and compute the dynamical fields at each model timestep 606 606 \item \textit{nemogcm.F90} : a degraded version of the main nemogcm.F90 code of NEMO to manage the timestepping 607 607 \end{itemize} 
NEMO/trunk/doc/latex/TOP/subfiles/model_setup.tex
r11019 r11591 1 \documentclass[../ ../NEMO/main/NEMO_manual]{subfiles}1 \documentclass[../main/TOP_manual]{subfiles} 2 2 3 3 \begin{document} … … 10 10 % 11 11 12 The usage of TOP is activated 12 The usage of TOP is activated 13 13 14 14 \begin{itemize} … … 19 19 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}) . 20 20 21 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. 21 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. 22 22 23 23 There are only three specific keys remaining in TOP … … 28 28 \end{itemize} 29 29 30 For a remind, the revisited structure of TOP interface now counts for five different modules handled in namelist\_top : 30 For a remind, the revisited structure of TOP interface now counts for five different modules handled in namelist\_top : 31 31 32 32 \begin{itemize}
Note: See TracChangeset
for help on using the changeset viewer.