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1c8cebb321 Jeff* .. _sub_pkg_dic:
                 
9ce7d74115 Jeff* DIC Package
                 -----------
                 
                 Introduction
                 ~~~~~~~~~~~~
                 
                 This is one of the biogeochemical packages handled from the pkg gchem.
                 The main purpose of this package is to consider the cycling of carbon in
                 the ocean. It also looks at the cycling of phosphorous and potentially
                 oxygen and iron. There are four standard tracers :math:`DIC`,
                 :math:`ALK`, :math:`PO4`, :math:`DOP` and also possibly :math:`O2` and
                 :math:`Fe`. The air-sea exchange of CO\ :math:`_2` and O\ :math:`_2` are
                 handled as in the OCMIP experiments (reference). The export of
                 biological matter is computed as a function of available light and
                 PO\ :math:`_4` (and Fe). This export is remineralized at depth according
                 to a Martin curve (again, this is the same as in the OCMIP experiments).
                 There is also a representation of the carbonate flux handled as in the
                 OCMIP experiments. The air-sea exchange on CO\ :math:`_2` is affected by
                 temperature, salinity and the pH of the surface waters. The pH is
                 determined following the method of Follows et al. For more details of
c89c701cfc Jean* the equations see :numref:`sub_global_oce_biogeo`.
9ce7d74115 Jeff* 
                 Key subroutines and parameters
                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 
                 | **INITIALIZATION**
                 | *DIC\_ABIOTIC.h* contains the common block for the parameters and
                   fields needed to calculate the air-sea flux of :math:`CO_2` and
                   :math:`O_2`. The fixed parameters are set in *dic\_abiotic\_param*
                   which is called from *gchem\_init\_fixed.F*. The parameters needed for
                   the biotic part of the calculations are initialized in
                   *dic\_biotic\_param* and are stored in *DIC\_BIOTIC.h*. The first
                   guess of pH is calculated in *dic\_surfforcing\_init.F*.
b02408d40c Bria* |
9ce7d74115 Jeff* | **LOADING FIELDS**
                 | The air-sea exchange of :math:`CO_2` and :math:`O_2` need wind,
                   atmospheric pressure (although the current version has this hardwired
                   to 1), and sea-ice coverage. The calculation of pH needs silica
                   fields. These fields are read in in *dic\_fields\_load.F*. These
                   fields are initialized to zero in *dic\_ini\_forcing.F*. The fields
                   for interpolating are in common block in *DIC\_LOAD.h*.
b02408d40c Bria* |
9ce7d74115 Jeff* | **FORCING**
                 | The tracers are advected-diffused in *ptracers\_integrate.F*. The
                   updated tracers are passed to *dic\_biotic\_forcing.F* where the
                   effects of the air-sea exchange and biological activity and
                   remineralization are calculated and the tracers are updated for a
                   second time. Below we discuss the subroutines called from
                   *dic\_biotic\_forcing.F*.
                 
                 | Air-sea exchange of :math:`CO_2` is calculated in *dic\_surfforcing*.
                   Air-Sea Exchange of :math:`CO_2` depends on T,S and pH. The
                   determination of pH is done in *carbon\_chem.F*. There are three
                   subroutines in this file: *carbon\_coeffs* which determines the
                   coefficients for the carbon chemistry equations; *calc\_pco2* which
                   calculates the pH using a Newton-Raphson method; and
                   *calc\_pco2\_approx* which uses the much more efficient method of
                   Follows et al. The latter is hard-wired into this package, the former is
                   kept here for completeness.
                 
                 | Biological productivity is determined following Dutkiewicz et al. (2005)
                   and is calculated in *bio\_export.F* The light in each latitude band is
                   calculate in *insol.F*, unless using one of the flags listed below. The
                   formation of hard tissue (carbonate) is linked to the biological
                   productivity and has an effect on the alkalinity - the flux of carbonate
                   is calculated in *car\_flux.F*, unless using the flag listed below for
                   the Friis et al (2006) scheme. The flux of phosphate to depth where it
                   instantly remineralized is calculated in *phos\_flux.F*.
                 
                 | The dilution or concentration of carbon and alkalinity by the addition
                   or subtraction of freshwater is important to their surface patterns.
                
** Warning **
Wide character in print at /usr/local/share/lxr/source line 1030, <$git> line 75.


   These “virtual” fluxes can be calculated by the model in several ways.
                   The older scheme is done following OCMIP protocols (see more in
                   Dutkiewicz et al 2005), in the subroutines *dic\_surfforcing.F* and
                   *alk\_surfforcing.F*. To use this you need to set in
b02408d40c Bria*   GCHEM\_OPTIONS.h: #define ALLOW\_OLD\_VIRTUALFLUX. But this can also
9ce7d74115 Jeff*   be done by the ptracers pkg if this is undefined.
                   You will then need to set the concentration of the tracer in rainwater
                   and potentially a reference tracer value in data.ptracer
                   (PTRACERS_EvPrRn, and PTRACERS_ref respectively).
                 
                 | Oxygen air-sea exchange is calculated in *o2\_surfforcing.F*.
                 
                 | Iron chemistry (the amount of free iron) is taken care of in
                   *fe\_chem.F*.
b02408d40c Bria* |
9ce7d74115 Jeff* | **DIAGNOSTICS**
                 | Averages of air-sea exchanges, biological productivity, carbonate
                   activity and pH are calculated. These are initialized to zero in
                   *dic\_biotic\_init* and are stored in common block in *DIC\_BIOTIC.h*.
b02408d40c Bria* |
9ce7d74115 Jeff* | **COMPILE TIME FLAGS**
                 | These are set in GCHEM\_OPTIONS.h:
                 | DIC\_BIOTIC: needs to be set for dic to work properly (should be fixed
                   sometime).
                 | ALLOW\_O2: include the tracer oxygen.
                 | ALLOW\_FE: include the tracer iron. Note you will need an iron dust
                   file set in data.gchem in this case.
                 | MINFE: limit the iron, assuming precpitation of any excess free iron.
                 | CAR\_DISS: use the calcium carbonate scheme of Friis et al 2006.
                 | ALLOW\_OLD\_VIRTUALFLUX: use the old OCMIP style virtual flux for
                   alklinity adn carbon (rather than doing it through pkg/ptracers).
                 | READ\_PAR: read the light (photosynthetically available radiation)
                   from a file set in data.gchem.
                 | USE\_QSW: use the numbers from QSW to be the PAR. Note that a file for
                   Qsw must be supplied in data, or Qsw must be supplied by an
                   atmospheric model.
                 | If the above two flags are not set, the model calculates PAR in
                   insol.F as a function of latitude and year day.
                 | USE\_QSW\_UNDERICE: if using a sea ice model, or if the Qsw variable
                   has the seaice fraction already taken into account, this flag must be
                   set.
                 | AD\_SAFE: will use a tanh function instead of a max function - this is
                   better if using the adjoint
                 | DIC\_NO\_NEG: will include some failsafes in case any of the variables
                   become negative. (This is advicable). ALLOW\_DIC\_COST: was used for
                
** Warning **
Wide character in print at /usr/local/share/lxr/source line 1030, <$git> line 120.


   calculating cost function (but hasn’t been updated or maintained, so
                   not sure if it works still)
b02408d40c Bria* |
9ce7d74115 Jeff* 
                
** Warning **
Wide character in print at /usr/local/share/lxr/source line 1030, <$git> line 124.


 Do’s and Don’ts
                 ~~~~~~~~~~~~~~~
                 
                 This package must be run with both ptracers and gchem enabled. It is set
                 up for at least 4 tracers, but there is the provision for oxygen and
                 iron. Note the flags above.
                 
                 Reference Material
                 ~~~~~~~~~~~~~~~~~~
                 
                 | Dutkiewicz. S., A. Sokolov, J. Scott and P. Stone, 2005: A
                   Three-Dimensional Ocean-Seaice-Carbon Cycle Model and its Coupling to
                   a Two-Dimensional Atmospheric Model: Uses in Climate Change Studies,
                   Report 122, Joint Program of the Science and Policy of Global Change,
                   M.I.T., Cambridge, MA.
b02408d40c Bria* | Follows, M., T. Ito and S. Dutkiewicz, 2006: On the solution of the carbonate
                   chemistry system in ocean biogeochemistry models, *Ocean Modeling*, 12,
                   290-301, doi:10.1016/j.ocemod.2005.05.004
9ce7d74115 Jeff* | Friis, K., R. Najjar, M.J. Follows, and S. Dutkiewicz, 2006: Possible
                   overestimation of shallow-depth calcium carbonate dissolution in the
                   ocean, *Global Biogeochemical Cycles*, 20, GB4019,
                   doi:10.1029/2006GB002727.
                 
                 Experiments and tutorials that use dic
                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 
                 -  Global Ocean tutorial, in tutorial\_global\_oce\_biogeo verification
c89c701cfc Jean*    directory, described in :numref:`sub_global_oce_biogeo`.

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