/[MITgcm]/manual/s_phys_pkgs/text/gchem.tex
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revision 1.5 by molod, Wed Apr 5 03:35:15 2006 UTC revision 1.10 by stephd, Tue Jan 15 22:03:22 2008 UTC
# Line 17  Note that the gchem package itself is on Line 17  Note that the gchem package itself is on
17  the subroutines used by specific biogeochemical experiments,  the subroutines used by specific biogeochemical experiments,
18  and does not "do" anything on its own.  and does not "do" anything on its own.
19    
20  There are two examples: cfc which looks at 2 tracers with a  There are two examples: {\bf cfc} which looks at 2 tracers with a
21  simple external forcing and dic with 5 tracers whose tendency terms  simple external forcing and {\bf dic} with 4,5 or 6 tracers
22    whose tendency terms
23  are related to one another. We will discuss these here only as  are related to one another. We will discuss these here only as
24  how they provide examples to use this package.  how they provide examples to use this package.
25    
# Line 27  how they provide examples to use this pa Line 28  how they provide examples to use this pa
28    
29  \noindent  \noindent
30  {{\bf FRAMEWORK}} \\  {{\bf FRAMEWORK}} \\
31    The different biogeochemistry frameworks (e.g. cfc of dic)
32    are specified in the packages\_conf file.
33  {\it GCHEM\_OPTIONS.h} includes the compiler options to be used  {\it GCHEM\_OPTIONS.h} includes the compiler options to be used
34  in any experiment. For instance \#define ALLOW\_CFC allows  in any experiment.
35  the CFC code to be run. An important compiler option is  An important compiler option is
36   \#define GCHEM\_SEPARATE\_FORCING which determined   \#define GCHEM\_SEPARATE\_FORCING which determined
37  how and when the tracer forcing is applied (see discussion  how and when the tracer forcing is applied (see discussion
38  on Forcing below).  on Forcing below). See section on dic for some additional
39    flags that can be set for that experiment.
40   There are further runtime parameters   There are further runtime parameters
41  set in {\it data.gchem} and kept in common block {\it GCHEM.h}.  set in {\it data.gchem} and kept in common block {\it GCHEM.h}.
42  These runtime options include:\\  These runtime options include:\\
43  $\bullet$ {\bf tIter0} which is the integer timestep when the tracer experiment  $\bullet$ Parameters to set the timing for periodic forcing files to
44   is initialized. If {\bf nIter0} $=$ {\bf tIter0} then the tracers  be loaded are: {\it gchem\_ForcingPeriod}, {\it gchem\_ForcingCycle}.
45   are initialized to zero or from initial files. If {\bf nIter0} $>$  The former is how often to load, the latter is how often to cycle
46   {\bf tIter0} then tracers (and previous timestep tendency terms)  through those fields (eg. period couple be monthly and cycle one year).
47    are read in from a the ptracers pickup file. Note that tracers  This is used in {\it dic} and {\it cfc}, with gchem\_ForcingPeriod=0
48    of zeros will be carried around if {\bf nIter0} $<$ {\bf tIter0}.  meaning no periodic forcing.
49  \\  \\
50  $\bullet$ {\bf nsubtime} is the integer number of extra timesteps  $\bullet$ {\bf nsubtime} is the integer number of extra timesteps
51   required by the tracer experiment. This will give a timestep   required by the tracer experiment. This will give a timestep
# Line 53  $\bullet$ File names - these are several Line 57  $\bullet$ File names - these are several
57   wind speed is needed in both DIC and CFC packages to calculate   wind speed is needed in both DIC and CFC packages to calculate
58   the air-sea exchange of gases. Not all file names will be used   the air-sea exchange of gases. Not all file names will be used
59   for every tracer experiment.   for every tracer experiment.
60    \\
61    $\bullet$ {\bf gchem\_int\_*} are variable names for run-time set integer numbers. (Currently 1 through 5).
62    \\
63    $\bullet$ {\bf gchem\_rl\_*} are variable names for run-time set real numbers. (Currently 1 through 5).
64    \\
65    $\bullet$ Note that the old {\bf tIter0} has been replaced by {\bf PTRACERS\_Iter0} which is
66    set in data.ptracers instead.
67    
68  \vspace{.5cm}  \vspace{.5cm}
69    
# Line 122  This is done in {\it gchem\_diags.F}. Fo Line 133  This is done in {\it gchem\_diags.F}. Fo
133  air-sea fluxes, and sea surface pH (among others) are written  air-sea fluxes, and sea surface pH (among others) are written
134  out by {\it dic\_biotic\_diags.F} which is called from {\it gchem\_diags.F}.  out by {\it dic\_biotic\_diags.F} which is called from {\it gchem\_diags.F}.
135    
136  \subsubsection{GCHEM Diagnostics  \subsubsection{GCHEM Diagnostics}
137  \label{sec:pkg:gchem:diagnostics}  \label{sec:pkg:gchem:diagnostics}
138    
139    These diagnostics are particularly for the {\bf dic} package.
140    
141    {\footnotesize
142  \begin{verbatim}  \begin{verbatim}
143    
144  ------------------------------------------------------------------------  ------------------------------------------------------------------------
# Line 138  DICCFLX |  1 |SM P    L1      |mol/m2/se Line 152  DICCFLX |  1 |SM P    L1      |mol/m2/se
152  DICPCO2 |  1 |SM P    M1      |atm             |Partial Pressure of CO2 (atm)  DICPCO2 |  1 |SM P    M1      |atm             |Partial Pressure of CO2 (atm)
153  DICPHAV |  1 |SM P    M1      |dimensionless   |pH (dimensionless)  DICPHAV |  1 |SM P    M1      |dimensionless   |pH (dimensionless)
154  \end{verbatim}  \end{verbatim}
155    }
156    
157  \subsubsection{Do's and Don'ts}  \subsubsection{Do's and Don'ts}
158    
# Line 150  to dic and cfc pkgs). Line 165  to dic and cfc pkgs).
165    
166  \subsubsection{Reference Material}  \subsubsection{Reference Material}
167    
168    \subsubsection{Experiments and tutorials that use gchem}
169    \label{sec:pkg:gchem:experiments}
170    
171    \begin{itemize}
172    \item{Global Ocean biogeochemical tutorial, in tutorial\_global\_oce\_biogeo verification directory,  
173    described in section \ref{sect:eg-biogeochem_tutorial} uses gchem and dic }
174    
175    \item{Global Ocean cfc tutorial, in tutorial\_cfc\_offline verification directory,  
176    uses gchem and cfc (and offline) described in \ref{sect:eg-cfc_offline} }
177    
178    \item{Global Ocean online cfc example in cfc\_example verification directory,  
179    uses gchem and cfc}
180    
181    
182    
183    \end{itemize}
184    
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