--- manual/s_phys_pkgs/text/gchem.tex 2006/06/28 15:35:07 1.8 +++ manual/s_phys_pkgs/text/gchem.tex 2008/01/15 18:03:30 1.9 @@ -17,8 +17,9 @@ the subroutines used by specific biogeochemical experiments, and does not "do" anything on its own. -There are two examples: cfc which looks at 2 tracers with a -simple external forcing and dic with 5 tracers whose tendency terms +There are two examples: {\bf cfc} which looks at 2 tracers with a +simple external forcing and {\bf dic} with 4,5 or 6 tracers +whose tendency terms are related to one another. We will discuss these here only as how they provide examples to use this package. @@ -27,22 +28,24 @@ \noindent {{\bf FRAMEWORK}} \\ +The different biogeochemistry frameworks (e.g. cfc of dic) +are specified in the packages\_conf file. {\it GCHEM\_OPTIONS.h} includes the compiler options to be used -in any experiment. For instance \#define ALLOW\_CFC allows -the CFC code to be run. An important compiler option is +in any experiment. +An important compiler option is \#define GCHEM\_SEPARATE\_FORCING which determined how and when the tracer forcing is applied (see discussion -on Forcing below). +on Forcing below). See section on dic for some additional +flags that can be set for that experiment. There are further runtime parameters set in {\it data.gchem} and kept in common block {\it GCHEM.h}. These runtime options include:\\ -$\bullet$ {\bf tIter0} which is the integer timestep when the tracer experiment - is initialized. If {\bf nIter0} $=$ {\bf tIter0} then the tracers - are initialized to zero or from initial files. If {\bf nIter0} $>$ - {\bf tIter0} then tracers (and previous timestep tendency terms) - are read in from a the ptracers pickup file. Note that tracers - of zeros will be carried around if {\bf nIter0} $<$ {\bf tIter0}. -\\ +$\bullet$ Parameters to set the timing for periodic forcing files to +be loaded are: {\it gchem\_ForcingPeriod}, {\it gchem\_ForcingCycle}. +The former is how often to load, the latter is how often to cycle +through those fields (eg. period couple be monthly and cycle one year). +This is used in {\it dic} and {\it cfc}, with gchem\_ForcingPeriod=0 +meaning no periodic forcing. $\bullet$ {\bf nsubtime} is the integer number of extra timesteps required by the tracer experiment. This will give a timestep of {\bf deltaTtracer}$/${\bf nsubtime} for the dependencies @@ -53,6 +56,12 @@ wind speed is needed in both DIC and CFC packages to calculate the air-sea exchange of gases. Not all file names will be used for every tracer experiment. +\\ +$\bullet$ {\bf gchem\_int\_*} are variable names for run-time set integer numbers. (Currently 1 through 5). +\\ +$\bullet$ {\bf gchem\_rl\_*} are variable names for run-time set real numbers. (Currently 1 through 5). +$\bullet$ Note that the old {\bf tIter0} has been replaced by {\bf PTRACERS\_Iter0} which is +set in data.ptracers instead. \vspace{.5cm} @@ -125,6 +134,8 @@ \subsubsection{GCHEM Diagnostics} \label{sec:pkg:gchem:diagnostics} +These diagnostics are particularly for the {\bf dic} package. + {\footnotesize \begin{verbatim} @@ -156,7 +167,16 @@ \label{sec:pkg:gchem:experiments} \begin{itemize} -\item{Global Ocean tutorial, in tutorial\_global\_oce\_biogeo verification directory, -described in section \ref{sect:eg-biogeochem_tutorial} } +\item{Global Ocean biogeochemical tutorial, in tutorial\_global\_oce\_biogeo verification directory, +described in section \ref{sect:eg-biogeochem_tutorial} uses gchem and dic } + +\item{Global Ocean cfc tutorial, in tutorial\_cfc\_offline verification directory, +uses gchem and cfc (and offline) described in \ref{sect:eg-cfc_offline} } + +\item{Global Ocean online cfc example in cfc\_example verification directory, +uses gchem and cfc} + + + \end{itemize}