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NEMO/trunk/doc/latex/TOP/subfiles/model_description.tex
r14375 r14929 17 17 \label{sec:Bas} 18 18 19 The time evolution of any passive tracer $C$ followsthe transport equation, which is similar to that of active tracer - temperature or salinity :19 The time evolution of any passive tracer $C$ is given by the transport equation, which is similar to that of active tracer - temperature or salinity : 20 20 21 21 \begin{equation} … … 24 24 \end{equation} 25 25 26 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}27 28 {S(C)} , the first term on the right hand side of \autoref{Eq_tracer}; is the SMS - Source Minus Sink- inherent to the tracer.29 In the case of biological tracer such as phytoplankton, {S(C)} is the balance between phytoplankton growth and its decaythrough mortality and grazing.30 In the case of a tracer comprising carbon, {S(C)} accounts for gas exchange, river discharge, flux to the sediments, gravitational sinking and other bio logical processes.31 In the case of a radioactive tracer, {S(C)} is simply loss due to radioactive decay.26 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 \cite{nemo_manual}). 27 28 {S(C)}, the first term on the right hand side of \autoref{Eq_tracer}, is the SMS - Sources Minus Sinks - inherent to the tracer. 29 In the case of a biological tracer such as phytoplankton, {S(C)} is the balance between phytoplankton growth and its loss through mortality and grazing. 30 In the case of a tracer comprising carbon, {S(C)} accounts for gas exchange, river discharge, flux to the sediments, gravitational sinking and other biogeochemical processes. 31 In the case of a radioactive tracer, {S(C)} is simply the loss due to radioactive decay. 32 32 33 33 The second term (within brackets) represents the advection of the tracer in the three directions. … … 36 36 The third term represents the change due to lateral diffusion. 37 37 38 The fourth term ischange due to vertical diffusion, parameterized as eddy diffusion to represent vertical turbulent fluxes :38 The fourth term denotes the change due to vertical diffusion, parameterized as eddy diffusion to represent vertical turbulent fluxes : 39 39 40 40 \begin{equation} … … 43 43 \end{equation} 44 44 45 where $A^{vT}$ is the vertical eddy diffusivity coefficient of active tracers 45 where $A^{vT}$ is the vertical eddy diffusivity coefficient of active tracers. 46 46 47 47 \section{The NEMO-TOP interface} 48 48 \label{sec:TopInt} 49 49 50 TOP is the NEMO hardwired interface toward biogeochemical models and providethe physical constraints/boundaries for oceanic tracers.50 TOP is the NEMO hardwired interface toward biogeochemical models, which provides the physical constraints/boundaries for oceanic tracers. 51 51 It consists of a modular framework to handle multiple ocean tracers, including also a variety of built-in modules. 52 52 53 This component of the NEMO framework allows one to exploit available modules and further develop a range of applications, spanning from the implementation of a dye passive tracer to evaluate dispersion processes (by means of MY\_TRC), track water masses age (AGE module), assess the ocean interior penetration of persistent chemical compounds (e.g., gases like CFC or even PCBs), up to the full set of equations involvingmarine biogeochemical cycles.53 This component of the NEMO framework allows one to exploit available modules and further develop a range of applications, spanning from the implementation of a dye passive tracer to evaluate dispersion processes (by means of MY\_TRC), track water masses age (AGE module), assess the ocean interior penetration of persistent chemical compounds (e.g., gases like CFC or even PCBs), up to the full set of equations to simulate marine biogeochemical cycles. 54 54 55 55 TOP interface has the following location in the code repository : \path{<repository>/src/TOP/} … … 60 60 \begin{itemize} 61 61 \item \textbf{TRP} : Interface to NEMO physical core for computing tracers transport 62 \item \textbf{CFC} : Inert carbontracers (CFC11,CFC12, SF6)62 \item \textbf{CFC} : Inert tracers (CFC11,CFC12, SF6) 63 63 \item \textbf{C14} : Radiocarbon passive tracer 64 64 \item \textbf{AGE} : Water age tracking 65 65 \item \textbf{MY\_TRC} : Template for creation of new modules and external BGC models coupling 66 \item \textbf{PISCES} : Built in BGC model. 67 See \citep{aumont_2015} for a throughout description. 66 \item \textbf{PISCES} : Built in BGC model. See \cite{aumont_2015} for a complete description 68 67 \end{itemize} 69 68 % ---------------------------------------------------------- … … 71 70 \section{The transport component : TRP} 72 71 73 The passive tracer transport component 72 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. 74 73 75 74 \subsection{Advection} 75 76 The advection schemes used for the passive tracers are the same as those used for $T$ and $S$. They are described in section 5.1 of \cite{nemo_manual}. 77 The choice of an advection scheme can be selected independently and can differ from the ones used for active tracers. 78 This choice is made in \textit{namelist\_to}p (ref or cfg) in the namelist block \textit{namtrc\_adv}, 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. 79 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 artificial extrema are permitted. Their use is not recommended for passive tracers. 80 76 81 %------------------------------------------namtrc_adv---------------------------------------------------- 77 82 \nlst{namtrc_adv} 78 %------------------------------------------------------------------------------------------------------------- 79 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}. 80 The choice of an advection scheme can be selected independently and can differ from the ones used for active tracers. 81 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. 82 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. 83 Their use is not recommended on passive tracers 83 %---------------------------------------------------------------------------------------------------------- 84 84 85 85 \subsection{Lateral diffusion} 86 87 In NEMO v4.0, diffusion of passive tracers has necessarily the same form as the active tracer diffusion, meaning that the numerical scheme must be the same. 88 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}. 89 The choice of the numerical scheme is then set in the \forcode{&namtra_ldf} namelist section for the dynamic described in section 5.2 of \cite{nemo_manual}. 90 91 rn\_fact\_lap is a factor used to increase zonal equatorial diffusion for depths beyond 200 m. It can be useful to achieve a better representation of Oxygen Minimum Zone (OMZ) in some biogeochemical models, especially at coarse resolution \citep{getzlaff_2013}. 92 86 93 %------------------------------------------namtrc_ldf---------------------------------------------------- 87 94 \nlst{namtrc_ldf} 88 %------------------------------------------------------------------------------------------------------------- 89 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. 90 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}. 91 The choice of numerical scheme is then set in the \forcode{&namtra_ldf} namelist for the dynamic described in section 5.2 of \citep{nemo_manual}. 95 %--------------------------------------------------------------------------------------------------------- 92 96 93 97 %-----------------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 : … … 98 102 \subsection{Tracer damping} 99 103 104 The use of newtonian damping to climatological fields or observations is also coded, sharing the same routine as that of active tracers. 105 Boolean variables are defined in the namelist\_top\_ref to select the tracers on which restoring is applied. 106 Options are defined through the \textit{\&namtrc\_dmp} namelist variables. 107 The restoring term is added when the namelist parameter \textit{ln\_trcdmp} is set to \textit{true}. 108 The restoring coefficient is a three-dimensional array read in a file, whose name is specified by the namelist variable \textit{cn\_resto\_tr}. 109 This netcdf file can be generated using the DMP\_TOOLS tool. 110 100 111 %------------------------------------------namtrc_dmp---------------------------------------------------- 101 112 \nlst{namtrc_dmp} 102 %------------------------------------------------------------------------------------------------------------- 103 104 The use of newtonian damping to climatological fields or observations is also coded, sharing the same routine dans active tracers. 105 Boolean variables are defined in the namelist\_top\_ref to select the tracers on which restoring is applied 106 Options are defined through the \nam{trc_dmp}{trc\_dmp} namelist variables. 107 The restoring term is added when the namelist parameter \np{ln\_trcdmp} is set to true. 108 The restoring coefficient is a three-dimensional array read in a file, which name is specified by the namelist variable \np{cn\_resto\_tr}. 109 This netcdf file can be generated using the DMP\_TOOLS tool. 113 %----------------------------------------------------------------------------------------------------------- 110 114 111 115 \subsection{Tracer positivity} 116 117 Some numerical schemes can generate negative values of passive tracers concentration, which is obviously unrealistic. 118 For example, isopycnal diffusion can created local extrema, meaning that negative concentrations can be generated. 119 The trcrad routine artificially corrects negative concentrations with a very crude solution that either sets negative concentrations to zero without adjusting the tracer budget (CFCs or C14 chemical coumpounds), or by removing negative concentrations while computing the corresponding tracer content that is added and then, adjusting the tracer concentration using a multiplicative factor so that the total tracer concentration is preserved (PISCES model). 120 The treatment of negative concentrations is an option and can be selected in the namelist \textit{\&namtrc\_rad} by setting the parameter \textit{ln\_trcrad} to true. 112 121 113 122 %------------------------------------------namtrc_rad---------------------------------------------------- 114 123 \nlst{namtrc_rad} 115 %------------------------------------------------------------------------------------------------------------- 116 117 Sometimes, numerical scheme can generates negative values of passive tracers concentration that must be positive. 118 For exemple, isopycnal diffusion can created extrema. 119 The trcrad routine artificially corrects negative concentrations with a very crude solution that either sets negative concentration to zero without adjusting the tracer budget, or by removing negative concentration and keeping mass conservation. 120 The treatment of negative concentrations is an option and can be selected in the namelist \nam{trc_rad}{trc\_rad} by setting the parameter \np{ln\_trcrad} to true. 124 %---------------------------------------------------------------------------------------------------------- 125 126 \subsection{Tracer boundary conditions} 127 128 In NEMO, different types of boundary conditions can be specified for biogeochemical tracers. For every single variable, it is possible to define a field of surface boundary conditions, such as deposition of dust or nitrogen, which is then interpolated to the grid and timestep using the fld\_read function. The same facility is available to include river inputs or coastal erosion (coastal boundary conditions) and the treatment of open boundary conditions. For lateral boundary conditions, spatial interpolation should not be activated. 129 130 %------------------------------------------namtrc_bc---------------------------------------------------- 131 \nlst{namtrc_cfg} 132 %--------------------------------------------------------------------------------------------------------- 133 134 \subsubsection{Surface and lateral boundaries} 135 136 The namelist \textit{\&namtrc\_bc} is in file \textit{namelist\_top\_cfg} and allows to specify the name of the files, the frequency of the input and the time and space interpolation as done for any other field using the fld\_read interface. 137 138 %------------------------------------------namtrc_bc---------------------------------------------------- 139 \nlst{namtrc_bc} 140 %--------------------------------------------------------------------------------------------------------- 141 \subsubsection{Open boundaries} 142 143 The BDY for passive tracer are set together with the physical oceanic variables (lnbdy =.true.). Boundary conditions are set in the structure used to define the passive tracer properties in the « cbc » column. These boundary conditions are applied on the segments defined for the physical core of NEMO (see BDY description in the User Manual). 144 \begin{itemize} 145 \item cn\_trc\_dflt : the type of OBC applied to all the tracers 146 \item cn\_trc : the boundary condition used for tracers with data file 147 \end{itemize} 148 149 %------------------------------------------namtrc_bdy---------------------------------------------------- 150 \nlst{namtrc_bdy} 151 %---------------------------------------------------------------------------------------------------------- 152 153 \subsubsection{Sedimentation of particles} 154 155 This module computes the vertical flux of particulate matter due to gravitational sinking. It also offers a temporary solution for the problem that may arise in specific situation where the CFL criterion is broken for vertical sedimentation of particles. To avoid this, a time splitting algorithm has been coded. The number of iterations niter necessary to respect the CFL criterion is dynamically computed. A specific maximum number of iterations nitermax may be specified in the namelist. This is to avoid a very large number of iterations when explicit free surface is used, for instance. If niter is larger than the prescribed nitermax, sinking speeds are clipped so that the CFL criterion is respected. The numerical scheme used to compute sedimentation is based on the MUSCL advection scheme. 156 157 %------------------------------------------namtrc_bdy---------------------------------------------------- 158 \nlst{namtrc_snk} 159 %---------------------------------------------------------------------------------------------------------- 160 161 \subsubsection{Sea-ice growth and melt effect} 162 163 NEMO provides three options for the specification of tracer concentrations in sea ice: (-1) identical tracer concentrations in sea ice and ocean, which corresponds to no concentration/dilution effect upon ice growth and melt; (0) zero concentrations in sea ice, which gives the largest concentration-dilution effect upon ice growth and melt; (1) specified concentrations in sea ice, which gives a possibly more realistic effect of sea ice on tracers. Option (-1) and (0) work for all tracers, but (1) is currently only available for PISCES. 164 165 %------------------------------------------namtrc_ice---------------------------------------------------- 166 \nlst{namtrc_ice} 167 %--------------------------------------------------------------------------------------------------------- 168 169 \subsubsection{Antartic Ice Sheet tracer supply} 170 171 The external input of biogeochemical tracers from the Antarctic Ice Sheet (AIS) is represented by associating a tracer content with the freshwater flux from icebergs and ice shelves \citep{person_sensitivity_2019}. This supply is currently implemented only for dissolved Fe (\autoref{img_icbisf}) and is effective in model configurations with south-extended grids (eORCA1 and eORCA025). As the ORCA2 grid does not extend south into Antarctica, the external source of tracers from the AIS cannot be enabled in this configuration. 172 173 For icebergs, a homogeneous distribution of biogeochemical tracers is applied from the surface to a depth that can be defined in \textit{\&namtrc\_ais}, currently set at 120 m. It should be noted that the freshwater flux from icebergs affects only the ocean properties at the surface. For ice shelves, biogeochemical tracers follow the explicit or parameterized representation of freshwater flux distribution modeled in NEMO. The AIS tracer supply is activated by setting \textit{ln\_trcais} to \textit{true} in the \textit{\&namtrc} section. 174 175 \begin{figure}[!h] 176 \centering 177 \includegraphics[width=0.80\textwidth]{ICB-ISF-Feflx} 178 \caption{Annual Fe fluxes from icebergs and ice shelves in the Southern Ocean.} 179 \label{img_icbisf} 180 \end{figure} 181 182 %------------------------------------------namtrc_ais---------------------------------------------------- 183 \nlst{namtrc_ais} 184 %--------------------------------------------------------------------------------------------------------- 121 185 122 186 \section{The SMS modules} … … 129 193 \subsection{Ideal Age} 130 194 %------------------------------------------namage---------------------------------------------------- 131 %132 195 \nlst{namage} 133 196 %---------------------------------------------------------------------------------------------------------- 134 197 135 198 An `ideal age' tracer is integrated online in TOP when \textit{ln\_age} = \texttt{.true.} in namelist \textit{namtrc}. 136 This tracer marks the length of time in units of years that fluid has spent in the interior of the ocean, insulated from exposure to the atmosphere. 199 This tracer marks the duration in units of years that fluid has spent in the interior of the ocean, insulated from exposure to the atmosphere (\autoref{img_ageatl} and \autoref{img_age200}). 200 201 \begin{figure}[!h] 202 \centering 203 \includegraphics[width=0.80\textwidth]{Age_Atl} 204 \caption{Vertical distribution of the Age tracer in the Atlantic Ocean at 35°W from a 62-year simulation.} 205 \label{img_ageatl} 206 \end{figure} 207 208 \begin{figure}[!h] 209 \centering 210 \includegraphics[width=0.80\textwidth]{Age_200m} 211 \caption{Age tracer at 200 m depth from a 62-year simulation.} 212 \label{img_age200} 213 \end{figure} 214 137 215 Thus, away from the surface for $z<-H_{\mathrm{Age}}$ where $H_{\mathrm{Age}}$ is specified by the \textit{namage} namelist variable \textit{rn\_age\_depth}, whose default value is 10~m, there is a source $\mathrm{SMS_{\mathrm{Age}}}$ of the age tracer $A$: 138 216 … … 151 229 152 230 where the relaxation rate $\lambda_{\mathrm{Age}}$ (units $\mathrm{s}\;^{-1}$) is specified by the \textit{namage} namelist variable \textit{rn\_age\_kill\_rate} and has a default value of 1/7200~s. 153 Since this relaxation is applied explicitly, th is relaxation rate in principle shouldnot exceed $1/\Delta t$, where $\Delta t$ is the time step used to step forward passive tracers (2 * \textit{nn\_dttrc * rn\_rdt} when the default leapfrog time-stepping scheme is employed).231 Since this relaxation is applied explicitly, the relaxation rate should in principle not exceed $1/\Delta t$, where $\Delta t$ is the time step used to step forward passive tracers (2 * \textit{nn\_dttrc * rn\_rdt} when the default leapfrog time-stepping scheme is employed). 154 232 155 233 Currently the 1-dimensional reference depth of the grid boxes is used rather than the dynamically evolving depth to determine whether the age tracer is incremented or relaxed to zero. 156 This means that the traceronly works correctly in z-coordinates.157 To ensure that the forcing is independent of the level thicknesses, where the tracer cell at level $k$ has its upper face $z=-depw(k)$ above the depth $-H_{\mathrm{Age}}$, but its lower face $z=-depw(k+1)$ below that depth, then the age source 234 This means that the age tracer module only works correctly in z-coordinates. 235 To ensure that the forcing is independent of the level thicknesses, where the tracer cell at level $k$ has its upper face $z=-depw(k)$ above the depth $-H_{\mathrm{Age}}$, but its lower face $z=-depw(k+1)$ below that depth, then the age source is computed as: 158 236 159 237 \begin{equation} … … 169 247 \end{align} 170 248 171 172 This implementation was first used in the CORE-II intercomparison runs described e.g.\ in \citet{danabasoglu_2014}. 249 This implementation was first used in the CORE-II intercomparison runs described in \citet{danabasoglu_2014}. 173 250 174 251 \subsection{Inert carbons tracer} … … 184 261 and additionally as an aerosol propellant. 185 262 SF6 (SF$_{6}$) is also a gas at room temperature, with a range of applications based around its property as an excellent electrical insulator (often replacing more toxic alternatives). 186 All three are relatively inert chemicals that are both non-toxic and non-flammable, and their wide use has led to their accumulation within the Earth'satmosphere.187 Large-scale production of CFC-11 and CFC-12 began in the 1930s, while production of SF6 began in the 1950s, and the ir atmospheric concentration time-histories are shown in Figure \autoref{img_cfcatm}.188 As can be seen in the figure, while the concentration of SF6 continues to rise to the present day, theconcentrations of both CFC-11 and CFC-12 have levelled off and declined since around the 1990s.263 All three gases are relatively inert chemicals that are both non-toxic and non-flammable, and their wide use has led to their accumulation in the atmosphere. 264 Large-scale production of CFC-11 and CFC-12 began in the 1930s, while production of SF6 began in the 1950s, and the time-histories of their atmospheric concentrations are shown in Figure \autoref{img_cfcatm}. 265 As can be seen in the figure, while the concentration of SF6 continues to rise to the present day, concentrations of both CFC-11 and CFC-12 have levelled off and declined since around the 1990s. 189 266 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 190 stratospheric ozone (O$_{3}$), critical in decreasing the flux of ultraviolet radiation to the Earth's surface. 191 Separate to this role in ozone-depletion, all three chemicals are significantly more potent greenhouse gases 267 stratospheric ozone (O$_{3}$), critical in decreasing the flux of ultraviolet radiation to the Earth's surface. All three chemicals are also significantly more potent greenhouse gases 192 268 than CO$_{2}$ (especially SF6), although their relatively low atmospheric concentrations limit their role in climate change. \\ 193 269 … … 204 280 The ocean is a notable sink for all three gases, and their relatively recent occurrence in the atmosphere, coupled to the ease of making high precision measurements of their dissolved concentrations, has made them 205 281 valuable in oceanography. % for tracking interior ventilation and mixing. 206 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 ventilationvia transport and mixing.207 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 lastcontact with the282 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 ventilation of the latter via transport and mixing. 283 Measuring the dissolved concentrations of these 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 has been last in contact with the 208 284 atmosphere). 209 This feature of the gaseshas made them valuable across a wide range of oceanographic problems.210 One use lies in ocean modelling, where they can be used to evaluate the realism of thecirculation and211 ventilation of models, key for understanding the behaviour of widermodelled marine biogeochemistry (e.g. \citep{dutay_2002,palmieri_2015}). \\285 This feature has made them valuable across a wide range of oceanographic problems. 286 In ocean modelling, they can be used to evaluate the realism of the simulated circulation and 287 ventilation patterns, which is key for understanding the behaviour of modelled marine biogeochemistry (e.g. \citep{dutay_2002,palmieri_2015}). \\ 212 288 213 289 Modelling these gases (henceforth CFCs) in NEMO is done within the passive tracer transport module, TOP, using the conservation state equation \autoref{Eq_tracer} 214 290 215 Advection and diffusion of the CFCs in NEMO are calculated by the physical module, OPA,291 Advection and diffusion of the CFCs in NEMO are calculated by the physical module, TRP, 216 292 whereas sources and sinks are done by the CFC module within TOP. 217 The only source for CFCs inthe ocean is via air-sea gas exchange at its surface, and since CFCs are generally293 The only source of CFCs to the ocean is via air-sea gas exchange at its surface, and since CFCs are generally 218 294 stable within the ocean, we assume that there are no sinks (i.e. no loss processes) within the ocean interior. 219 295 Consequently, the sinks-minus-sources term for CFCs consists only of their air-sea fluxes, $F_{cfc}$, as … … 233 309 $C_{surf}$ is the local surface concentration of the CFC tracer within the model (in mol~m$^{-3}$); 234 310 and $f_{i}$ is the fractional sea-ice cover of the local ocean (ranging between 0.0 for ice-free ocean, 235 throughto 1.0 for completely ice-covered ocean with no air-sea exchange).311 to 1.0 for completely ice-covered ocean with no air-sea exchange). 236 312 237 313 The saturation concentration of the CFC, $C_{sat}$, is calculated as follows: … … 312 388 % AXY: consider an itemized list here if you've got a list of differences 313 389 314 For instance, C$_{sat}$ is calculated for a fixed surface pressure of 1atm , what could be corrected in a furtherversion of the module.390 For instance, C$_{sat}$ is calculated for a fixed surface pressure of 1atm. This may be corrected in a future version of the module. 315 391 316 392 … … 333 409 334 410 \begin{table}[!t] 335 \caption{Coefficients for fit of the CFCs Schmidt number (Eq. \autoref{equ_Sc}). 411 \caption{Coefficients for fit of the CFCs Schmidt number (Eq. \autoref{equ_Sc}).} 336 412 \vskip4mm 337 413 \centering … … 384 460 %---------------------------------------------------------------------------------------------------------- 385 461 386 The C14 package implemented in NEMO by Anne Mouchet models ocean$\Dcq$.462 The C14 package has been implemented in NEMO by Anne Mouchet $\Dcq$. 387 463 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. 388 464 … … 390 466 391 467 Let $\Rq$ represent the ratio of $\cq$ atoms to the total number of carbon atoms in the sample, i.e. $\cq/\mathrm{C}$. 392 Then, radiocarbon anomalies are reported as 468 Then, radiocarbon anomalies are reported as: 393 469 394 470 \begin{equation} … … 397 473 398 474 where $\Rq_{\textrm{ref}}$ is a reference ratio. 399 For the purpose of ocean ventilation studies $\Rq_{\textrm{ref}}$ is set to one.475 For the purpose of ocean ventilation studies, $\Rq_{\textrm{ref}}$ is set to one. 400 476 401 477 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 $\cq$. … … 464 540 The radiocarbon decay rate (\forcode{rlam14}; in \texttt{trcnam\_c14} module) is set to $\lambda=(1/8267)$ yr$^{-1}$ \citep{stuiver_1977}, which corresponds to a half-life of 5730 yr.\\[1pt] 465 541 % 466 The Schmidt number $Sc$, Eq. \autoref{eq:wanc14}, is calculated with the help ofthe formulation of \cite{wanninkhof_2014}.542 The Schmidt number $Sc$, Eq. \autoref{eq:wanc14}, is calculated using the formulation of \cite{wanninkhof_2014}. 467 543 The $\cd$ solubility $K_0$ in \autoref{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] 468 544 % … … 522 598 \end{figure} 523 599 524 Performing this type of experiment requires that a pre-industrial equilibrium run beperformed beforehand (\forcode{ln\_rsttr} should be set to \texttt{.TRUE.}).525 526 An exception to this rule is when wishing to performa perturbation bomb experiment as was possible with the package \texttt{C14b}.600 Performing this type of experiment requires that a pre-industrial equilibrium run has been performed beforehand (\forcode{ln\_rsttr} should be set to \texttt{.TRUE.}). 601 602 An exception to this rule is when performing a perturbation bomb experiment as was possible with the package \texttt{C14b}. 527 603 It is still possible to easily set-up that type of transient experiment for which no previous run is needed. 528 In addition to the instructions as given in this sectionit 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).604 In addition to the instructions 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). 529 605 530 606 The model is integrated from a given initial date following the observed records provided from 1765 AD on ( Fig. \autoref{fig:bomb}). … … 535 611 Dates in these forcing files are expressed as yr AD. 536 612 537 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:613 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: 538 614 539 615 \begin{itemize} … … 543 619 \end{itemize} 544 620 545 If the experiment date is outside the data time span then the first or last atmospheric concentrations areprescribed depending on whether the date is earlier or later.546 Note that \forcode{tyrc14\_beg} (\texttt{namelist\_c14}) is not used in this context.621 If the experiment date is outside the data time span, the first or last atmospheric concentrations are then prescribed depending on whether the date is earlier or later. 622 Note that \forcode{tyrc14\_beg} (\texttt{namelist\_c14}) is not used in this context. 547 623 548 624 % … … 582 658 583 659 All output fields in Table \autoref{tab:out} are routinely computed. 584 It depends on the actual settings in \texttt{iodef.xml} whether they are s tored or not.660 It depends on the actual settings in \texttt{iodef.xml} whether they are saved or not. 585 661 % 586 662 \begin{table}[!h] … … 645 721 \subsection{PISCES biogeochemical model} 646 722 647 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). 648 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. 723 PISCES is a biogeochemical model that simulates the lower trophic levels of marine ecosystem (phytoplankton, microzooplankton, and mesozooplankton) and the biogeochemical cycles of carbon and of the main nutrients (P, N, Si, and Fe) (\autoref{img_piscesdesign} and \autoref{img_pisces}). 724 725 \begin{figure}[ht] 726 \begin{center} 727 \vspace{0cm} 728 \includegraphics[width=0.80\textwidth]{Fig_PISCES_model} 729 \caption{Schematic view of the PISCES-v2 model (figure by Jorge Martinez-Rey).} 730 \label{img_piscesdesign} 731 \end{center} 732 \end{figure} 733 734 \begin{figure}[!h] 735 \centering 736 \includegraphics[width=0.80\textwidth]{PISCES_tracers} 737 \caption{Surface concentrations of NO$_{3}$, PO$_{4}$, total chlorophyll, and air-sea CO$_{2}$ flux from the last year of a 62-year simulation.} 738 \label{img_pisces} 739 \end{figure} 740 741 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. 742 649 743 Two versions of PISCES are available in NEMO v4.0 : 650 744 651 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}. 652 It assumes a constant Redfield ratio and phytoplankton growth depends on the external concentration in nutrients. 653 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. 654 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. 655 On the other hand, the iron and silicium quotas are variable and growth rate of phytoplankton is limited by the internal availability in Fe. 656 Various parameterizations can be activated in PISCES-v2, setting for instance the complexity of iron chemistry or the description of particulate organic materials. 657 658 PISCES-QUOTA has been built on the PISCES-v2 model described in \citet{aumont_2015}. 659 PISCES-QUOTA has thirty-nine prognostic compartments. 660 Phytoplankton growth can be controlled by five modeled limiting nutrients: Nitrate and Ammonium, Phosphate, Silicate and Iron. 661 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. 662 For phytoplankton, the prognostic variables are the carbon, nitrogen, phosphorus, iron, chlorophyll and silicon biomasses (the latter only for diatoms). 663 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. 664 Zooplankton are assumed to be strictly homeostatic \citep[e.g.,][]{sterner_2003,woods_2013,meunier_2014}. 665 As a consequence, the C/N/P/Fe ratios of these groups are maintained constant and are not allowed to vary. 666 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}. 667 No silicified zooplankton is assumed. 668 The bacterial pool is not yet explicitly modeled. 745 \begin{itemize} 746 \item PISCES-v2, by setting \textit{ln\_p4z} = \texttt{.true.} in \textit{namelist\_pisces\_ref}. This version 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. 747 748 \item PISCES-QUOTA, by setting \textit{ln\_p5z} = \texttt{.true.} in \textit{namelist\_pisces\_ref}. This version has been built on the PISCES-v2 model described in \citet{aumont_2015}. PISCES-QUOTA has thirty-nine prognostic compartments. Phytoplankton growth is 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 the three 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. 749 \end{itemize} 669 750 670 751 There are three non-living compartments: Semi-labile dissolved organic matter, small sinking particles, and large sinking particles. 671 752 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. 672 Indeed, the nitrogen, phosphorus, iron, silicon and calcite pools of the particles are now all explicitly modeled.753 Indeed, the nitrogen, phosphorus, iron, silicon, and calcite pools of the particles are now all explicitly modeled. 673 754 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}). 674 755 The latter particles are assumed to sink at the same speed as the large organic matter particles. … … 678 759 \label{Mytrc} 679 760 680 The NEMO-TOP has only one built-in biogeochemical model - PISCES - but there are several BGC models - MEDUSA, ERSEM, BFM or ECO3M - which are meant to be coupled with the NEMO dynamics.681 Therefore it was necessary to provide to the users a framework for easily add their own BGCM model, that can be a single passive tracer.761 NEMO-TOP has one built-in biogeochemical model - PISCES - but there are several BGC models - MEDUSA, ERSEM, BFM or ECO3M - which are meant to be used within the NEMO plateform. 762 Therefore it was necessary to provide to the users a framework to easily add their own BGCM model. 682 763 The generalized interface is pivoted on MY\_TRC module that contains template files to build the coupling between NEMO and any external BGC model. 683 The call to MY\_TRC is activated by setting \textit{ln\_my\_trc} = \texttt{.true.} in namelist \textit{namtrc} 764 Call to MY\_TRC is activated by setting \textit{ln\_my\_trc} = \texttt{.true.} in namelist \textit{namtrc}.\\ 684 765 685 766 The following 6 fortran files are available in MY\_TRC with the specific purposes here described. … … 692 773 \item \textit{trcsms\_my\_trc.F90} : The routine performs the call to Boundary Conditions and its main purpose is to contain the Source-Minus-Sinks terms due to the biogeochemical processes of the external model. 693 774 Be aware that lateral boundary conditions are applied in trcnxt routine. 694 IMPORTANT: the routines to compute thelight penetration along the water column and the tracer vertical sinking should be defined/called in here, as generalized modules are still missing in the code.695 \item \textit{trcice\_my\_trc.F90} : Here it is possible to prescribe the tracers concentrations in the seaice that will be used as boundary conditions when icemelting occurs (nn\_ice\_tr =1 in namtrc\_ice).775 IMPORTANT: the routines to compute light penetration along the water column and the tracer vertical sinking should be defined/called in here, as generalized modules are still missing in the code. 776 \item \textit{trcice\_my\_trc.F90} : Here it is possible to prescribe the tracers concentrations in sea ice that will be used as boundary conditions when ice formation and melting occurs (nn\_ice\_tr =1 in namtrc\_ice). 696 777 See e.g. the correspondent PISCES subroutine. 697 778 \item \textit{trcwri\_my\_trc.F90} : This routine performs the output of the model tracers using IOM module (see Manual Chapter Output and Diagnostics). … … 702 783 \label{Offline} 703 784 704 %------------------------------------------namtrc_sms---------------------------------------------------- 705 \nlst{namdta_dyn} 706 %------------------------------------------------------------------------------------------------------------- 707 708 Coupling passive tracers offline with NEMO requires precomputed physical fields from OGCM. 709 Those fields are read from files and interpolated on-the-fly at each model time step 710 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). 711 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. 712 713 The offline interface is located in the code repository : \path{<repository>/src/OFF/}. 714 It is activated by adding the CPP key \textit{key\_offline} to the CPP keys list. 715 There are two specifics routines for the Offline code : 785 Coupling passive tracers offline with NEMO requires precomputed physical fields 786 from OGCM. Those fields are read in files and interpolated on-the-fly at each model 787 time step. There are two sets of fields to perform offline simulations : 716 788 717 789 \begin{itemize} 718 \item \textit{dtadyn.F90} : this module allows to read and compute the dynamical fields at each model time-step 719 \item \textit{nemogcm.F90} : a degraded version of the main nemogcm.F90 code of NEMO to manage the time-stepping 790 \item linear free surface ( ln\_linssh = .true. ) where the vertical scale factor is constant with time. At least, the following dynamical parameters should be absolutely passed 791 to transport : the effective ocean transport velocities (eulerian plus the eddy induced plus all others parameterizations), vertical diffusion coefficient and the freshwater flux 792 . 793 %------------------------------------------namtrc_sms---------------------------------------------------- 794 \nlst{namdta_dyn_linssh} 795 %----------------------------------------------------------------------------------------------------------- 796 \item non linear free surface ( ln\_linssh = .false. or key\_qco ) : the same fields than the ones in the linear free surface case. In addition, the horizontal divergence transport is needed to recompute the time evolution of the sea surface heigth and the vertical scale factor and depth, and thus the time evolution of the vertical transport velocity. 797 %------------------------------------------namtrc_sms---------------------------------------------------- 798 \nlst{namdta_dyn_nolinssh} 799 %----------------------------------------------------------------------------------------------------------- 720 800 \end{itemize} 721 801 722 %- 723 %- 724 %- 725 %- Describes here the specifities of oflline : At least the dynamical variables needed - u/v/w transport T/S for isopycnal MLD for biogeo models etc ... 726 %- the specfities of vvl - ssh + runoffs and how to 727 %- 802 Additionally, temperature, salinity, and mixed layer depth are needed to compute slopes for isopycnal diffusion. Some ecosystem models like PISCES need sea ice concentration, short-wave radiation at the ocean surface, and wind speed (or at least, wind stress). 803 804 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 CO$_{2}$ sinks for climate-carbon studies. 805 806 The offline interface is located in the code repository : <repository>/src/OFF/. It is activated by adding the\textit{ key\_offline} CPP key to the CPP keys list. 807 There are 808 two specifics routines for the offline code : 809 \begin{itemize} 810 \item dtadyn.F90 : this module reads and computes the dynamical fields at 811 each model time-step 812 \item nemogcm.F90 : a degraded version of the main nemogcm.F90 code of NEMO to 813 manage the time-stepping 814 \end{itemize} 815 816 728 817 \end{document}
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