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\section{Biogeochemistry Tutorial} |
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\label{www:tutorials} |
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\label{sect:eg-biogeochem_tutorial} |
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\begin{rawhtml} |
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<!-- CMIREDIR:eg-biogeochem_tutorial: --> |
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\end{rawhtml} |
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\subsection{Overview} |
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This model overlays the dissolved inorganic carbon biogeochemistry |
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model (the ``dic'' package) over a 2.8$^o$ global physical model. The |
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physical model has 15 levels, and is forced with a climatological |
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1.2 |
annual cycle of surface wind stresses \cite{Trenberth_etal_89}, |
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1.3 |
surface heat and freshwater fluxes \cite{jiang99} with additional |
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1.2 |
relaxation toward climatological sea surface temperature and salinity |
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\cite{lev:94a,Levitus94}. It uses the Gent and and McWilliams |
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\cite{gen-mcw:90} eddy parameterization scheme, has an implicit |
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free-surface, implicit vertical diffusion and uses the convective |
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adjustment scheme. |
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1.1 |
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The biogeochemical model considers the coupled cycles of carbon, |
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oxygen, phosphorus and alkalinity. A simplified parameterization of |
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biological production is used, limited by the availability of light |
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and phosphate. A fraction of this productivity enters the dissolved |
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organic pool pool, which has an e-folding timescale for |
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remineralization of 6 months [following Yamanaka and Tajika, 1997]. |
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The remaining fraction of this productivity is instantaneously |
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exported as particulate to depth [Yamanaka and Tajika, 1997] where it |
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is remineralized according to the empirical power law relationship |
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determined by Martin et al [1987]. The fate of carbon is linked to |
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that of phosphorus by the Redfield ratio. Carbonate chemistry is |
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1.2 |
explicitly solved \cite{Follows_etal_05} and the air-sea exchange of |
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CO$_2$ is parameterized with a uniform gas transfer coefficient |
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following \cite{Wanninkhof_92}. Oxygen is also linked to phosphorus by |
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the Redfield ratio, and oxygen air-sea exchange also follows |
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\cite{Wanninkhof_92}. For more details see \cite{Dutkiewicz_etal_05}. |
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1.1 |
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The example setup described here shows the physical model after 5900 |
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years of spin-up and the biogeochemistry after 2900 years of spin-up. |
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The biogeochemistry is at a pre-industrial steady-state (atmospheric |
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ppmv is kept at 278). Five tracers are resolved: dissolved inorganic |
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carbon ($DIC$), alkalinity ($ALK$), phosphate ($PO4$), dissolved |
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organic phosphorus ($DOP$) and dissolved oxygen ($O2$). |
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\begin{figure} [tpb] |
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\begin{center} |
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\includegraphics[width=\textwidth,height=.3\textheight]{part3/case_studies/biogeochem_tutorial/co2flux.eps} |
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\caption{Modelled annual mean air-sea CO$_2$ flux (mol C m$^{-2}$ y$^{-1}$) |
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for pre-industrial steady-state. Positive indicates flux of CO$_2$ |
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from ocean to the atmosphere (out-gassing), |
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contour interval is 1 mol C m$^{-2}$ y$^{-1}$.} |
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\label{lFcarflux} |
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\end{center} |
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\end{figure} |
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\subsection{Equations Solved} |
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The physical ocean model velocity and diffusivities are used to |
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redistribute the 5 tracers within the ocean. Additional redistribution |
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comes from chemical and biological sources and sinks. For any tracer |
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$A$: |
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\begin{equation} |
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\frac{\partial A}{\partial t}=-\nabla \cdot (\vec{u^{*}} A)+\nabla \cdot |
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(\mathbf{K}\nabla A)+S_A \nonumber \label{lEtrac} |
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\end{equation} |
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where $\vec{u^{*}}$ is the transformed Eulerian mean circulation |
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(which includes Eulerian and eddy-induced advection), $\mathbf{K}$ is |
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the mixing tensor, and $S_A$ are the sources and sinks due to |
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biological and chemical processes. |
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The sources and sinks are: |
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\begin{eqnarray} |
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S_{DIC} & = & F_{CO_2} + V_{CO_2} + r_{C:P} S_{PO_4} + J_{Ca} \label{lEsdic} \\ |
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S_{ALK} & = & V_{ALK}-r_{N:P} S_{PO_4} + 2 J_{Ca} \label{lEsalk} \\ |
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S_{PO_4}& = & -f_{DOP} J_{prod} - \frac{\partial F_P}{\partial z} + \kappa_{remin} [DOP]\\ |
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S_{DOP} & = & f_{DOP} J_{prod} -\kappa_{remin} [DOP] \\ |
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S_{O_2} & = & \left\{ \begin{array}{ll} |
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-r_{O:P} S_{PO_4} & \mbox{if $O_2>O_{2crit}$} \\ |
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0 & \mbox{if $O_2<O_{2crit}$} |
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\end{array} |
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\right. |
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\end{eqnarray} |
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where: |
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\begin{itemize} |
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\item $F_{CO_2}$ is the flux of CO$_2$ from the ocean to the |
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atmosphere |
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\item $V_{CO_2}$ is ``virtual flux'' due to changes in $DIC$ due to |
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the surface freshwater fluxes |
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\item $r_{C:P}$ is Redfield ratio of carbon to phosphorus |
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\item $J_{Ca}$ includes carbon removed from surface due to calcium |
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carbonate formation and subsequent cumulation of the downward flux |
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of CaCO$_3$ |
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\item $V_{ALK}$ is ``virtual flux'' due to changes in alkalinity due |
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to the surface freshwater fluxes |
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\item $r_{N:P}$ Redfield ratio is nitrogen to phosphorus |
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\item $f_{DOP}$ is fraction of productivity that remains suspended in |
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the water column as dissolved organic phosphorus |
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\item $J_{prod}$ is the net community productivity |
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\item $\frac{\partial F_P}{\partial z}$ is the accumulation of |
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remineralized phosphorus with depth |
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\item $\kappa_{remin}$ is rate with which $DOP$ remineralizes back to |
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$PO_4$ |
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\item $F_{O_2}$ is air-sea flux of oxygen |
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\item $r_{O:P}$ is Redfield ratio of oxygen to phosphorus |
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\item $O_{2crit}$ is a critical level below which oxygen consumption |
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if halted |
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\end{itemize} |
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These terms (for the first four tracers) are described more in |
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\cite{Dutkiewicz_etal_05} and by \cite{McKinley_etal_04} for the terms |
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relating to oxygen. |
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1.1 |
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\subsection{Code configuration} |
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The model configuration for this experiment resides in |
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verification/dic\_example. The modifications to the code (in {\it |
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verification/dic\_example/code}) are: |
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\begin{itemize} |
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\item{{\bf SIZE.h}: which dictates the size of the model domain |
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(128x64x15).} |
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\item{\bf PTRACERS\_SIZE.h}: which dictates how many tracers to assign |
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how many tracers will be used (5). |
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\item{\bf GCHEM\_OPTIONS.h}: provides some compiler time options for |
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the {\it /pkg/gchem}. In particular this example requires that {\it |
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DIC\_BIOTIC} and {\it GCHEM\_SEPARATE\_FORCING} be defined. |
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\item{\bf GMREDI\_OPTIONS.h}: assigns the Gent-McWilliam eddy |
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parameterization options. |
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\item{\bf DIAGNOSTICS\_SIZE.h}: assigns size information for the |
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diagnostics package. |
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\item{\bf packages.conf}: which dictates which packages will be |
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compiled in this version of the model - among the many that are used |
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for the physical part of the model, this also includes {\it |
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ptracers}, {\it gchem}, and {\it dic} which allow the |
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biogeochemical part of this setup to function. |
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\end{itemize} |
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\vspace{1cm} |
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\noindent |
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The input fields needed for this run (in {\it |
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verification/dic\_example/input}) are: |
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\begin{itemize} |
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\item {\bf data}: specifies the main parameters for the experiment, |
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some parameters that may be useful to know: {\it nTimeSteps} number |
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timesteps model will run, change to 720 to run for a year {\it |
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taveFreq} frequency with which time averages are done, change to |
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31104000 for annual averages. |
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\item {\bf data.diagnostics}: species details of diagnostic pkg output |
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\item {\bf data.gchem}: specifics files and other details needed in |
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the biogeochemistry model run |
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\item {\bf data.gmredi}: species details for the GM parameterization |
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\item {\bf data.mnc}: specifies details for types of output, netcdf or |
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binary |
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\item {\bf data.pkg}: set true or false for various packages to be |
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used |
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\item {\bf data.ptracers}: details of the tracers to be used, |
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including makes, diffusivity information and (if needed) initial |
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files. Of particular importance is the {\it PTRACERS\_numInUse} |
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which states how many tracers are used, and {\it PTRACERS\_Iter0} |
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which states at which timestep the biogeochemistry model tracers |
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were initialized. |
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\item {\bf depth\_g77.bin}: bathymetry data file |
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\item {\bf eedata}: This file uses standard default values and does |
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not contain customizations for this experiment. |
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\item {\bf fice.bin}: ice data file, needed for the biogeochemistry |
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\item {\bf lev\_monthly\_salt.bin}: SSS values which model relaxes |
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toward |
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\item {\bf lev\_monthly\_temp.bin}: SST values which model relaxes |
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toward |
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\item {\bf pickup.0004248000.data}: variable and tendency values need |
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to restart the physical part of the model |
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\item {\bf pickup\_cd.0004248000.data}: variable and tendency values |
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need to restart the cd pkg |
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\item {\bf pickup\_ptracers.0004248000.data}: variable and tendency |
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values need to restart the the biogeochemistry part of the model |
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\item {\bf POLY3.COEFFS}: coefficient for the non-linear equation of |
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state |
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\item {\bf shi\_empmr\_year.bin}: freshwater forcing data file |
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\item {\bf shi\_qnet.bin}: heat flux forcing data file |
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\item {\bf sillev1.bin}: silica data file, need for the |
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biogeochemistry |
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\item {\bf tren\_speed.bin}: wind speed data file, needed for the |
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biogeochemistry |
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\item {\bf tren\_taux.bin}: meridional wind stress data file |
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\item {\bf tren\_tauy.bin}: zonal wind stress data file |
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\end{itemize} |
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\subsection{Running the example} |
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You will first need to download the MITgcm code. Instructions for |
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downloading the code can be found in section 3.2. |
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\begin{enumerate} |
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\item{go to the build directory in verification/dic\_example:\\ |
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\hspace{1cm} $>$ {\it cd verification/dic\_example/build}} |
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\item{create the Makefile:\\ |
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\hspace{1cm} $>$ {\it ../../../tools/genmake2 -mods=code}} |
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\item{create all the links:\\ |
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\hspace{1cm} $>$ {\it make depend}} |
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\item{compile (the executable will be called mitgcmuv):\\ |
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\hspace{1cm} $>$ {\it make}} |
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\item{move the executable to the directory with all the inputs:\\ |
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\hspace{1cm} $>$ {\it mv mitgcmuv ../input/}} |
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\item{go to the input directory and run the model:\\ |
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\hspace{1cm} $>$ {\it cd ../input}\\ |
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\hspace{1cm} $>$ {\it ./mitgcmuv}} |
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\end{enumerate} |
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As the model is set up to run in the verification experiment, it only |
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runs for 4 timestep (2 days) and outputs data at the end of this short |
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run. For a more informative run, you will need to run longer. As set |
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up, this model starts from a pre-spun up state and initializes |
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physical fields and the biogeochemical tracers from the {\it pickup} |
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files. |
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Physical data (e.g. S,T, velocities etc) will be output as for any |
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regular ocean run. The biogeochemical output are: |
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\begin{itemize} |
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\item tracer snap shots: either netcdf, or older-style binary |
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(depending on how {\it data.mnc} is set up). Look in {\it |
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data.ptracers} to see which number matches which type of tracer |
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(e.g. ptracer01 is DIC). |
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\item tracer time averages: either netcdf, or older-style binary |
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(depending on how {\it data.mnc} is set up) |
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\item specific DIC diagnostics: these are averaged over {\it taveFreq} |
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(set in {\it data}) and are specific to the dic package, and |
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currently are only available in binary format: |
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\begin{itemize} |
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\item{\bf DIC\_Biotave}: 3-D biological community productivity (mol |
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P m$^{-3}$ s$^{-1}$) |
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\item{\bf DIC\_Cartave}: 3-D tendencies due to calcium carbonate |
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cycle (mol C m$^{-3}$ s$^{-1}$) |
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\item{\bf DIC\_fluxCO2ave}: 2-D air-sea flux of CO$_2$ (mol C |
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m$^{-2}$ s$^{-1}$) |
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\item{\bf DIC\_pCO2tave}: 2-D partial pressure of CO$_2$ in surface |
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layer |
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\item{\bf DIC\_pHtave}: 2-D pH in surface layer |
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\item{\bf DIC\_SurOtave}: 2-D tendency due to air-sea flux of O$_2$ |
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(mol O m$^{-3}$ s$^{-1}$) |
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\item{\bf DIC\_Surtave}: 2-D surface tendency of DIC due to air-sea |
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flux and virtual flux (mol C m$^{-3}$ s$^{-1}$) |
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\end{itemize} |
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\end{itemize} |
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%% \subsection{Reference Material} |
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%% \Hpar |
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%% Dutkiewicz. S., A. Sokolov, J.Scott and P. Stone, 2005: |
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%% A Three-Dimensional Ocean-Seaice-Carbon Cycle Model and its Coupling |
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%% to a Two-Dimensional Atmospheric Model: Uses in Climate Change Studies, |
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%% Report 122, Joint Program of the Science and Policy of Global Change, |
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%% M.I.T., Cambridge, MA.\\ |
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%% (http://web.mit.edu/globalchange/www/MITJPSPGC\_Rpt122.pdf) |
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%% \Hpar |
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%% Follows, M., T. Ito and S. Dutkiewicz, 2005: |
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%% A Compact and Accurate Carbonate Chemistry Solver for Ocean |
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%% Biogeochemistry Models. {\it Ocean Modeling}, in press. |
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%% \Hpar |
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%% Gent, P. and J. McWilliams, 1990: |
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%% Isopycnal mixing in ocean circulation models. |
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%% {\it Journal of Physical Oceanography}, 20, 150 -- 155. |
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%% \Hpar |
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%% Jiang, S., P.H. Stone, and P. Malanotte-Rizzoli, |
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%% An assessment of the Geophysical Fluid Dynamics Laboratory |
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%% ocean model with coarse resolution: Annual-mean climatology, |
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%% {\it Journal of Geophysical Research}, 104, 25623 -- 25645, 1999. |
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%% \Hpar |
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%% Levitus, S. and T.P. Boyer, 1994: |
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%% {\it World Ocean Atlas 1994 Volume 4: Temperature}, |
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%% NOAA Atlas NESDIS 4, U.S. Department of Commerce, |
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%% Washington, D.C., 117pp. |
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%% \Hpar |
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%% Levitus, S., R. Burgett, and T.P. Boyer, 1994: |
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%% {\it World Ocean Atlas 1994 Volume 3: Salinity}, |
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%% NOAA Atlas NESDIS 3, U.S. Department of Commerce, |
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%% Washington, D.C., 99pp. |
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%% \Hpar |
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%% McKinley, G., M.J. Follows and J.C. Marshall, 2004: |
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%% Mechanisms of air-sea CO$_2$ flux variability in the Equatorial Pacific |
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%% and the North Atlantic. |
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%% {\it Global Biogeochemical Cycles}, 18, doi:10.1029/2003GB002179. |
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%% \Hpar |
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%% Trenberth, K., J. Olson, and W. Large, 1989: |
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%% {\it A global wind stress climatology based on ECMWF analyses, |
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%% Tech. Rep. NCAR/TN-338+STR}, |
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%% National Center for Atmospheric Research, Boulder, Colorado. |
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%% \Hpar |
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%% Wanninkhof, R., 1992: |
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%% Relationship between wind speed and gas exchange over the ocean, |
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%% {\it Journal of Geophysical Research}, 97, 7373 -- 7382. |
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