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\section {GCHEM Package} |
\subsection {GCHEM Package} |
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\label{sec:pkg:gchem} |
\label{sec:pkg:gchem} |
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<!-- CMIREDIR:package_gchem: --> |
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\subsection {Introduction} |
\subsubsection {Introduction} |
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This package has been developed as interface to the PTRACERS package. |
This package has been developed as interface to the PTRACERS package. |
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The purpose is to provide a structure where various (any) |
The purpose is to provide a structure where various (any) |
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tracer experiments can be added to the code. |
tracer experiments can be added to the code. |
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the subroutines used by specific biogeochemical experiments, |
the subroutines used by specific biogeochemical experiments, |
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and does not "do" anything on its own. |
and does not "do" anything on its own. |
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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 |
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simple external forcing and dic with 5 tracers whose tendency terms |
simple external forcing and {\bf dic} with 4,5 or 6 tracers |
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whose tendency terms |
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are related to one another. We will discuss these here only as |
are related to one another. We will discuss these here only as |
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how they provide examples to use this package. |
how they provide examples to use this package. |
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\subsection {Key subroutines and parameters} |
\subsubsection {Key subroutines and parameters} |
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\noindent |
\noindent |
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{{\bf FRAMEWORK}} \\ |
{{\bf FRAMEWORK}} \\ |
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The different biogeochemistry frameworks (e.g. cfc of dic) |
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are specified in the packages\_conf file. |
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{\it GCHEM\_OPTIONS.h} includes the compiler options to be used |
{\it GCHEM\_OPTIONS.h} includes the compiler options to be used |
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in any experiment. For instance \#define ALLOW\_CFC allows |
in any experiment. |
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the CFC code to be run. An important compiler option is |
An important compiler option is |
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\#define GCHEM\_SEPARATE\_FORCING which determined |
\#define GCHEM\_SEPARATE\_FORCING which determined |
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how and when the tracer forcing is applied (see discussion |
how and when the tracer forcing is applied (see discussion |
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on Forcing below). |
on Forcing below). See section on dic for some additional |
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flags that can be set for that experiment. |
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\\ |
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There are further runtime parameters |
There are further runtime parameters |
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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}. |
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These runtime options include:\\ |
These runtime options include:\\ |
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$\bullet$ {\bf tIter0} which is the integer timestep when the tracer experiment |
$\bullet$ Parameters to set the timing for periodic forcing files to |
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is initialized. If {\bf nIter0} $=$ {\bf tIter0} then the tracers |
be loaded are: {\it gchem\_ForcingPeriod}, {\it gchem\_ForcingCycle}. |
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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 |
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{\bf tIter0} then tracers (and previous timestep tendency terms) |
through those fields (eg. period couple be monthly and cycle one year). |
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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 |
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of zeros will be carried around if {\bf nIter0} $<$ {\bf tIter0}. |
meaning no periodic forcing. |
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\\ |
\\ |
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$\bullet$ {\bf nsubtime} is the integer number of extra timesteps |
$\bullet$ {\bf nsubtime} is the integer number of extra timesteps |
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required by the tracer experiment. This will give a timestep |
required by the tracer experiment. This will give a timestep |
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wind speed is needed in both DIC and CFC packages to calculate |
wind speed is needed in both DIC and CFC packages to calculate |
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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 |
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for every tracer experiment. |
for every tracer experiment. |
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$\bullet$ {\bf gchem\_int\_*} are variable names for run-time set integer numbers. (Currently 1 through 5). |
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$\bullet$ {\bf gchem\_rl\_*} are variable names for run-time set real numbers. (Currently 1 through 5). |
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\\ |
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$\bullet$ Note that the old {\bf tIter0} has been replaced by {\bf PTRACERS\_Iter0} which is |
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set in data.ptracers instead. |
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\vspace{.5cm} |
\vspace{.5cm} |
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air-sea fluxes, and sea surface pH (among others) are written |
air-sea fluxes, and sea surface pH (among others) are written |
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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}. |
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\subsection{Do's and Don'ts} |
\subsubsection{GCHEM Diagnostics} |
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\label{sec:pkg:gchem:diagnostics} |
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These diagnostics are particularly for the {\bf dic} package. |
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{\footnotesize |
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\begin{verbatim} |
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------------------------------------------------------------------------ |
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<-Name->|Levs|<-parsing code->|<-- Units -->|<- Tile (max=80c) |
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------------------------------------------------------------------------ |
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DICBIOA | 15 |SM P MR |mol/m3/sec |Biological Productivity (mol/m3/s) |
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DICCARB | 15 |SM P MR |mol eq/m3/sec |Carbonate chg-biol prod and remin (mol eq/m3/s) |
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DICTFLX | 1 |SM P L1 |mol/m3/sec |Tendency of DIC due to air-sea exch (mol/m3/s) |
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DICOFLX | 1 |SM P L1 |mol/m3/sec |Tendency of O2 due to air-sea exch (mol/m3/s) |
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DICCFLX | 1 |SM P L1 |mol/m2/sec |Flux of CO2 - air-sea exch (mol/m2/s) |
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DICPCO2 | 1 |SM P M1 |atm |Partial Pressure of CO2 (atm) |
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DICPHAV | 1 |SM P M1 |dimensionless |pH (dimensionless) |
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\end{verbatim} |
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} |
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\subsubsection{Do's and Don'ts} |
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The pkg ptracer is required with use with this pkg. Also, as usual, the |
The pkg ptracer is required with use with this pkg. Also, as usual, the |
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runtime flag \textbf{useGCHEM} must be set to \textbf{.TRUE.} in \textbf{data.pkg}. |
runtime flag \textbf{useGCHEM} must be set to \textbf{.TRUE.} in \textbf{data.pkg}. |
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specific calls to do anything else (for instance the calls |
specific calls to do anything else (for instance the calls |
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to dic and cfc pkgs). |
to dic and cfc pkgs). |
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\subsection{Reference Material} |
\subsubsection{Reference Material} |
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\subsubsection{Experiments and tutorials that use gchem} |
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\label{sec:pkg:gchem:experiments} |
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\begin{itemize} |
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\item{Global Ocean biogeochemical tutorial, in tutorial\_global\_oce\_biogeo verification directory, |
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described in section \ref{sect:eg-biogeochem_tutorial} uses gchem and dic } |
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\item{Global Ocean cfc tutorial, in tutorial\_cfc\_offline verification directory, |
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uses gchem and cfc (and offline) described in \ref{sect:eg-cfc_offline} } |
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\item{Global Ocean online cfc example in cfc\_example verification directory, |
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uses gchem and cfc} |
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\end{itemize} |
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