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1c8cebb321 Jeff* .. _sub_global_oce_biogeo:
                 
                 Biogeochemistry Simulation
                 ==========================
d67096e55c Jeff* 
                 (in directory: :filelink:`verification/tutorial_global_oce_biogeo/`)
                 
                 Overview
                 --------
                 
                 This model overlays the dissolved inorganic carbon biogeochemistry model
                 (:filelink:`pkg/dic`) over a 2.8\ :sup:`o` global physical model. The
                 physical model has 15 levels, and is forced with a climatological annual
                 cycle of surface wind stresses (Trenberth et al. 1989 :cite:`trenberth:89`,
                 surface heat and freshwater fluxes (Jiang et al. 1999 :cite:`jiang:99`) with
                 additional relaxation toward climatological sea surface temperature and
                 salinity (Levitus and Boyer (1994a,b) :cite:`levitus:94a,levitus:94b`). It uses the Gent and
                 McWilliams (1990) :cite:`gen-mcw:90` eddy parameterization scheme,
                 has an implicit free-surface, implicit vertical diffusion and uses the
                 convective adjustment scheme.
                 
                 The biogeochemical model considers the coupled cycles of carbon, oxygen,
                 phosphorus and alkalinity. A simplified parameterization of biological
                 production is used, limited by the availability of light and phosphate.
                 A fraction of this productivity enters the dissolved organic pool pool,
                 which has an e-folding timescale for remineralization of 6 months
                 (following Yamanaka and Tajika 1997 :cite:`yamanaka:97`). The remaining fraction of this
                 productivity is instantaneously exported as particulate to depth
                 (Yamanaka and Tajika 1997 :cite:`yamanaka:97`) where it is remineralized according to the
                 empirical power law relationship determined by Martin et al. (1987]) :cite:`martin:87`. The
                 fate of carbon is linked to that of phosphorus by the Redfield ratio.
                 Carbonate chemistry is explicitly solved (see Follow et al. 2006)
                 :cite:`follows:06`) and the air-sea exchange of
1c8cebb321 Jeff* CO\ :sub:`2` is parameterized with a uniform gas transfer coefficient
d67096e55c Jeff* following Wanninkhof (1992) :cite:`wannink:92`. Oxygen is also linked to
                 phosphorus by the Redfield ratio, and oxygen air-sea exchange also
                 follows Wanninkhof (1992) :cite:`wannink:92`. For more details see
                 Dutkiewicz et al. (2005) :cite:`dutkiewicz:05`.
                 
                 The example setup described here shows the physical model after 5900
                 years of spin-up and the biogeochemistry after 2900 years of spin-up.
                 The biogeochemistry is at a pre-industrial steady-state (atmospheric
                 ppmv is kept at 278). Five tracers are resolved: dissolved inorganic
                 carbon (:math:`DIC`), alkalinity (:math:`ALK`), phosphate (:math:`PO4`),
                 dissolved organic phosphorus (:math:`DOP`) and dissolved oxygen
                 (:math:`O2`).
                 
                    .. figure:: figs/co2flux.png
                        :width: 80%
                        :align: center
                        :alt: Modeled annual mean air-sea CO2
                        :name: tut_biogeochem_co2flux
                 
                        Modeled annual mean air-sea CO\ :sub:`2` flux (mol C m\ :sup:`-2` y\ :sup:`-1`) for pre-industrial steady-state. Positive indicates flux of CO\ :sub:`2` from ocean to the atmosphere (out-gassing), contour interval is 1 mol C m\ :sup:`-2` y\ :sup:`-1`.
                 
                 Equations Solved
                 ----------------
                 
                 The physical ocean model velocity and diffusivities are used to
                 redistribute the 5 tracers within the ocean. Additional redistribution
                 comes from chemical and biological sources and sinks. For any tracer
                 :math:`A`:
                 
                 .. math::
                 
0bad585a21 Navi*    \frac{\partial A}{\partial t}=- \nabla  \cdot (\vec{u^{*}} A)+ \nabla  \cdot
d67096e55c Jeff*      (\mathbf{K}\nabla A)+S_A \nonumber
                 
                 where :math:`\vec{u^{*}}` is the transformed Eulerian mean circulation
                 (which includes Eulerian and eddy-induced advection), :math:`\mathbf{K}`
                 is the mixing tensor, and :math:`S_A` are the sources and sinks due to
                 biological and chemical processes.
                 
                 The sources and sinks are:
                 
                 .. math::
                    \begin{aligned}
0bad585a21 Navi*    S_{DIC} & =  F_{CO_2} + V_{CO_2} + r_{C:P} S_{PO_4}  + J_{Ca} \\
                    S_{ALK} & =  V_{ALK}-r_{N:P} S_{PO_4}  + 2 J_{Ca}  \\
                    S_{PO_4}& =  -f_{DOP} J_{prod} - \frac{\partial F_P}{\partial z} + \kappa_{remin} [DOP]\\
                    S_{DOP} & =  f_{DOP} J_{prod} -\kappa_{remin} [DOP] \\
                    S_{O_2} & = \left\{ \begin{array}{ll}
d67096e55c Jeff*                   -r_{O:P} S_{PO_4} & \mbox{if $O_2>O_{2crit}$} \\
                                    0  & \mbox{if $O_2<O_{2crit}$}
                                          \end{array}
                                  \right. \end{aligned}
                 
                 where:
                 
                 -  :math:`F_{CO_2}` is the flux of CO\ :sup:`2` from the ocean to the
                    atmosphere
                 
                
** Warning **
Wide character in print at /usr/local/share/lxr/source line 1030, <$git> line 94.


 -  :math:`V_{CO_2}` is “virtual flux” due to changes in :math:`DIC` due
                    to the surface freshwater fluxes
                 
                 -  :math:`r_{C:P}` is Redfield ratio of carbon to phosphorus
                 
                 -  :math:`J_{Ca}` includes carbon removed from surface due to calcium
                    carbonate formation and subsequent cumulation of the downward flux of
                    CaCO\ :math:`_3`
                 
                
** Warning **
Wide character in print at /usr/local/share/lxr/source line 1030, <$git> line 103.


 -  :math:`V_{ALK}` is “virtual flux” due to changes in alkalinity due to
                    the surface freshwater fluxes
                 
                 -  :math:`r_{N:P}` Redfield ratio is nitrogen to phosphorus
                 
                 -  :math:`f_{DOP}` is fraction of productivity that remains suspended in
                    the water column as dissolved organic phosphorus
                 
                 -  :math:`J_{prod}` is the net community productivity
                 
                 -  :math:`\frac{\partial F_P}{\partial z}` is the accumulation of
                    remineralized phosphorus with depth
                 
                 -  :math:`\kappa_{remin}` is rate with which :math:`DOP` remineralizes
                    back to :math:`PO_4`
                 
                 -  :math:`F_{O_2}` is air-sea flux of oxygen
                 
                 -  :math:`r_{O:P}` is Redfield ratio of oxygen to phosphorus
                 
                 -  :math:`O_{2crit}` is a critical level below which oxygen consumption
                    if halted
                 
                 These terms (for the first four tracers) are described more in
                 Dutkiewicz et al. (2005) :cite:`dutkiewicz:05` and by
                 McKinley et al. (2004) :cite:`mckinley:04` for the terms relating to oxygen.
                 
                 Code configuration
                 ------------------
                 
                 The modifications to the code (in
                 :filelink:`verification/tutorial_global_oce_biogeo/code`) are:
                 
                 -  :filelink:`code/SIZE.h <verification/tutorial_global_oce_biogeo/code/SIZE.h>`: which dictates the size of the model domain (128x64x15).
                 
                 -  :filelink:`code/PTRACERS_SIZE.h <verification/tutorial_global_oce_biogeo/code/PTRACERS_SIZE.h>`: which dictates how many tracers to assign how
                    many tracers will be used (here, 5).
                 
                 -  :filelink:`code/DIAGNOSTICS_SIZE.h <verification/tutorial_global_oce_biogeo/code/DIAGNOSTICS_SIZE.h>`: assigns size information for the diagnostics
                    package.
                 
                 -  :filelink:`code/packages.conf <verification/tutorial_global_oce_biogeo/code/packages.conf>`: which dictates which packages will be compiled in
                    this version of the model - among the many that are used for the
                    physical part of the model, this also includes :filelink:`pkg/ptracers`,  :filelink:`pkg/gchem`,
                    and :filelink:`pkg/dic` which allow the biogeochemical part of this setup to
                    function.
                 
                 The input fields needed for this run (in
                 :filelink:`verification/tutorial_global_oce_biogeo/input`) are:
                 
                 -  :filelink:`input/data <verification/tutorial_global_oce_biogeo/input/data>`: specifies the main parameters for the experiment. Some
                    parameters that may be useful to know: :varlink:`nTimeSteps` number timesteps
                    model will run, change to 720 to run for a year :varlink:`taveFreq` frequency
                    with which time averages are done, change to 31104000 for annual
                    averages.
                 
                 -  :filelink:`input/data.diagnostics <verification/tutorial_global_oce_biogeo/input/data.diagnostics>`: specifies details of diagnostic pkg output
                 
                 -  :filelink:`input/data.gchem <verification/tutorial_global_oce_biogeo/input/data.gchem>`: specifies details needed in the
                    biogeochemistry model run
                 
                 -  :filelink:`input/data.gmredi <verification/tutorial_global_oce_biogeo/input/data.gmredi>`: specifies details for the GM parameterization
                 
                 -  :filelink:`input/data.pkg <verification/tutorial_global_oce_biogeo/input/data.pkg>`: set true or false for various packages to be used
                 
                 -  :filelink:`input/data.ptracers <verification/tutorial_global_oce_biogeo/input/data.ptracers>`: details of the tracers to be used, including
                    makes, diffusivity information and (if needed) initial files. Of
                    particular importance is the :varlink:`PTRACERS_numInUse` which states how
                    many tracers are used, and :varlink:`PTRACERS_Iter0` which states at which
                    timestep the biogeochemistry model tracers were initialized.
                 
5197f5318e Dust* -  ``bathy.bin``: bathymetry data file
d67096e55c Jeff* 
                 -  :filelink:`input/eedata <verification/tutorial_global_oce_biogeo/input/eedata>`: This file uses standard default values and does not
                    contain customizations for this experiment.
                 
                 -  ``fice.bin``: ice data file, needed for the biogeochemistry
                 
                 -  ``lev_monthly_salt.bin``: SSS values which model relaxes toward
                 
                 -  ``lev_monthly_temp.bin``: SST values which model relaxes toward
                 
                 -  ``pickup.0005184000.data``: variable and tendency values need to
                    restart the physical part of the model
                 
                 -  ``pickup_cd.0005184000.data``: variable and tendency values need to
                    restart the cd pkg
                 
                 -  ``pickup_ptracers.0005184000.data``: variable and tendency values
                    need to restart the the biogeochemistry part of the model
                 
                 -  ``shi_empmr_year.bin``: freshwater forcing data file
                 
                 -  ``shi_qnet.bin``: heat flux forcing data file
                 
                 -  ``sillev1.bin``: silica data file, need for the biogeochemistry
                 
                 -  ``tren_speed.bin``: wind speed data file, needed for the
                    biogeochemistry
                 
                 -  ``tren_taux.bin``: meridional wind stress data file
                 
                 -  ``tren_tauy.bin``: zonal wind stress data file
                 
                 Running the example
                 -------------------
                 
                 As the model is set up to run in the verification experiment, it only
                 runs for 4 timesteps (2 days) and outputs data at the end of this short
                 run. For a more informative run, you will need to run longer. As set up,
                 this model starts from a pre-spun up state and initializes physical
                 fields and the biogeochemical tracers from the pickup files.
                 
                 Physical data (e.g., S,T, velocities etc) will be output as for any
                 regular ocean run. The biogeochemical output are:
                 
                 -  tracer snapshots: look in :filelink:`input/data.ptracers <verification/tutorial_global_oce_biogeo/input/data.ptracers>` to see which
                    number matches which type of tracer (e.g., ptracer01 is DIC).
                 
                 -  tracer time averages
                 
                 -  specific DIC diagnostics: these are averaged over :varlink:`taveFreq` (set in
                    :filelink:`input/data <verification/tutorial_global_oce_biogeo/input/data>`) and are specific to :filelink:`pkg/dic` (currently are only
                    available in binary format):
                 
                    -  ``DIC_Biotave``: 3-D biological community productivity (mol P
                       m\ :sup:`-3` s\ :sup:`-1`)
                 
                    -  ``DIC_Cartave``: 3-D tendencies due to calcium carbonate cycle
                       (mol C m\ :sup:`-3` s\ :sup:`-1`)
                 
                    -  ``DIC_fluxCO2ave``: 2-D air-sea flux of CO\ :sub:`2` (mol C
                       m\ :sup:`-2` s\ :sup:`-1`)
                 
                    -  ``DIC_pCO2tave``: 2-D partial pressure of CO\ :sub:`2` in
                       surface layer
                 
                    -  ``DIC_pHtave``: 2-D pH in surface layer
                 
                    -  ``DIC_SurOtave``: 2-D tendency due to air-sea flux of
                       O\ :sub:`2` (mol O m\ :sup:`-3` s\ :sup:`-1`)
                 
                    -  ``DIC_Surtave``: 2-D surface tendency of DIC due to air-sea flux
                       and virtual flux (mol C m\ :sup:`-3` s\ :sup:`-1`)

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