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revision 1.4 by molod, Wed Jun 28 15:35:06 2006 UTC revision 1.5 by stephd, Tue Jan 15 22:01:46 2008 UTC
# Line 8  Line 8 
8  This is one of the biogeochemical packages handled from the  This is one of the biogeochemical packages handled from the
9  pkg gchem. The main purpose of this package is to consider  pkg gchem. The main purpose of this package is to consider
10  the cycling of carbon in the ocean. It also looks at the  the cycling of carbon in the ocean. It also looks at the
11  cycling of phosphorous and oxygen. There are five tracers  cycling of phosphorous and potentially oxygen and iron.
12  $DIC$, $ALK$, $PO4$, $DOP$ and $O2$. The air-sea exchange  There are four standard tracers
13    $DIC$, $ALK$, $PO4$, $DOP$ and also possibly $O2$ and $Fe$.
14    The air-sea exchange
15  of CO$_2$ and O$_2$ are handled as in the OCMIP experiments  of CO$_2$ and O$_2$ are handled as in the OCMIP experiments
16  (reference). The export of biological matter is computed  (reference). The export of biological matter is computed
17  as a function of available light and PO$_4$. This export is  as a function of available light and PO$_4$ (and Fe). This export is
18  remineralized at depth according to a Martin curve (again,  remineralized at depth according to a Martin curve (again,
19  this is the same as in the OCMIP experiments). There is  this is the same as in the OCMIP experiments). There is
20  also a representation of the carbonate flux handled as in  also a representation of the carbonate flux handled as in
# Line 20  the OCMIP experiments. The air-sea excha Line 22  the OCMIP experiments. The air-sea excha
22  is affected by temperature, salinity and the pH of the  is affected by temperature, salinity and the pH of the
23  surface waters. The pH is determined following the  surface waters. The pH is determined following the
24  method of Follows et al.  method of Follows et al.
25    For more details of the equations see section
26    \ref{sect:eg-biogeochem_tutorial}.
27    
28  \subsubsection {Key subroutines and parameters}  \subsubsection {Key subroutines and parameters}
29    
# Line 69  The latter is hard-wired into this packa Line 73  The latter is hard-wired into this packa
73  here for completeness.  here for completeness.
74    
75  Biological productivity is determined following  Biological productivity is determined following
76  McKinely et al. and is calculated in {\it bio\_export.F}  Dutkiewicz et al. (2005) and is calculated in {\it bio\_export.F}
77  The light in each latitude band is calculate in {\it insol.F}.  The light in each latitude band is calculate in {\it insol.F},
78    unless using one of the flags listed below.
79  The formation of hard tissue (carbonate) is linked to  The formation of hard tissue (carbonate) is linked to
80  the biological productivity and has an effect on the  the biological productivity and has an effect on the
81  alkalinity - the flux of carbonate is calculated in  alkalinity - the flux of carbonate is calculated in
82  {\it car\_flux.F}. The flux of phosphate to depth where  {\it car\_flux.F}, unless using the flag listed below
83    for the Friis et al (2006) scheme. The flux of phosphate to depth where
84  it instantly remineralized is calculated in {\it phos\_flux.F}.  it instantly remineralized is calculated in {\it phos\_flux.F}.
85    
86  Alkalinity tendency comes from changes to the salinity from  The dilution or concentration of  carbon and alkalinity by
87  addition/subtraction of freshwater in the surface. This  the addition  or subtraction of freshwater is important to
88  is handled in {\it alk\_surfforcing.F}.  their surface patterns. These "virtual" fluxes can be calculated
89    by the model in several ways.
90    The older scheme is done following OCMIP protocols (see
91    more in Dutkiewicz et al 2005), in the subroutines
92    {\it dic\_surfforcing.F} and {\it alk\_surfforcing.F}.
93    To use this you need to set in GCHEM\_OPTIONS.h:\\
94    \#define ALLOW\_OLD\_VIRTUALFLUX\\
95    But this can also be done by the ptracers pkg if this
96    is undefined. You will then need to set the concentration
97    of the tracer in rainwater and potentially a reference
98    tracer value in data.ptracer
99    (PTRACERS\_EvPrRn, and PTRACERS\_ref respectively).
100    
101  Oxygen air-sea exchange is calculated in {\it o2\_surfforcing.F}.  Oxygen air-sea exchange is calculated in {\it o2\_surfforcing.F}.
102    
103    Iron chemistry (the amount of free iron) is taken care of in
104    {\it fe\_chem.F}.
105    
106  \vspace{.5cm}  \vspace{.5cm}
107    
# Line 92  carbonate activity and pH are calculated Line 112  carbonate activity and pH are calculated
112  initialized to zero in {\it dic\_biotic\_init} and  initialized to zero in {\it dic\_biotic\_init} and
113  are stored in common block in {\it DIC\_BIOTIC.h}.  are stored in common block in {\it DIC\_BIOTIC.h}.
114    
115    \vspace{.5cm}
116    
117    \noindent
118    {{\bf COMPILE TIME FLAGS}}\\
119    These are set in GCHEM\_OPTIONS.h: \\
120    
121    DIC\_BIOTIC: needs to be set for dic to work properly
122    (should be fixed sometime).\\
123    ALLOW\_O2: include the tracer oxygen.\\
124    ALLOW\_FE: include the tracer iron. Note you will need an
125    iron dust file set in data.gchem in this case.\\
126    MINFE: limit the iron, assuming precpitation of any
127    excess free iron.\\
128    CAR\_DISS: use the calcium carbonate scheme of Friis et al 2006.\\
129    ALLOW\_OLD\_VIRTUALFLUX: use the old OCMIP style virtual flux
130    for alklinity adn carbon (rather than doing it through pkg/ptracers).
131    \\
132    READ\_PAR: read the light (photosynthetically available
133    radiation) from a file set in data.gchem.\\
134    USE\_QSW: use the numbers from QSW to be the PAR. Note that
135    a file for Qsw must be supplied in data, or Qsw must be
136    supplied by an atmospheric model.\\
137    If the above two flags are not set, the model calculates
138    PAR in insol.F as a function of latitude and year day.\\
139    USE\_QSW\_UNDERICE: if using a sea ice model, or if the
140    Qsw variable has the seaice fraction already taken into
141    account, this flag must be set.\\
142    \\
143    AD\_SAFE: will use a tanh function instead of a
144    max function - this is better if using the adjoint\\
145    DIC\_NO\_NEG: will include some failsafes in case any
146    of the variables become negative. (This is advicable).
147    ALLOW\_DIC\_COST: was used for calculating cost function
148    (but hasn't been updated or maintained, so not sure if it works still)
149    
150    
151    
152  \subsubsection{Do's and Don'ts}  \subsubsection{Do's and Don'ts}
153    
154  This package must be run with both ptracers and gchem enabled.  This package must be run with both ptracers and gchem enabled.
155  It is set up for 5 tracers, but there is the provision of  It is set up for at least 4 tracers, but there is the provision for
156  a 6th tracer (iron) that is not discussed here.  oxygen and iron. Note the flags above.
157    
158  \subsubsection{Reference Material}  \subsubsection{Reference Material}
159    
160    Dutkiewicz. S., A. Sokolov, J. Scott and P. Stone, 2005:
161    A Three-Dimensional Ocean-Seaice-Carbon Cycle Model and its Coupling
162    to a Two-Dimensional Atmospheric Model: Uses in Climate Change Studies,
163    Report 122, Joint Program of the Science and Policy of Global Change,
164    M.I.T., Cambridge, MA.
165    \\
166    
167    Follows, M., T. Ito and S. Dutkiewicz, 2006:
168    A Compact and Accurate Carbonate Chemistry Solver for Ocean
169    Biogeochemistry Models. {\it Ocean Modeling}, 12, 290-301.
170    \\
171    
172    Friis, K.,  R. Najjar, M.J. Follows, and S. Dutkiewicz, 2006:
173    Possible overestimation of shallow-depth calcium carbonate
174    dissolution in the ocean,
175    {\it Global Biogeochemical Cycles}, 20, GB4019, doi:10.1029/2006GB002727.
176    \\
177    
178    
179  \subsubsection{Experiments and tutorials that use dic}  \subsubsection{Experiments and tutorials that use dic}
180  \label{sec:pkg:dic:experiments}  \label{sec:pkg:dic:experiments}
181    
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