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\subsection {GCHEM Package} |
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\label{sec:pkg:gchem} |
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<!-- CMIREDIR:package_gchem: --> |
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\subsubsection {Introduction} |
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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) |
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tracer experiments can be added to the code. |
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For instance there are placeholders for routines |
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to read in parameters needed for any tracer experiments, a routine |
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to read in extra fields required for the tracer code, routines |
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for either external forcing or internal interactions between tracers |
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and routines for additional diagnostics relating to the tracers. |
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Note that the gchem package itself is only a means to call |
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the subroutines used by specific biogeochemical experiments, |
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and does not "do" anything on its own. |
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There are two examples: cfc which looks at 2 tracers with a |
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simple external forcing and dic with 5 tracers whose tendency terms |
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are related to one another. We will discuss these here only as |
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how they provide examples to use this package. |
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\subsubsection {Key subroutines and parameters} |
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\noindent |
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{{\bf FRAMEWORK}} \\ |
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{\it GCHEM\_OPTIONS.h} includes the compiler options to be used |
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in any experiment. For instance \#define ALLOW\_CFC allows |
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the CFC code to be run. An important compiler option is |
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\#define GCHEM\_SEPARATE\_FORCING which determined |
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how and when the tracer forcing is applied (see discussion |
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on Forcing below). |
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There are further runtime parameters |
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set in {\it data.gchem} and kept in common block {\it GCHEM.h}. |
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These runtime options include:\\ |
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$\bullet$ {\bf tIter0} which is the integer timestep when the tracer experiment |
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is initialized. If {\bf nIter0} $=$ {\bf tIter0} then the tracers |
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are initialized to zero or from initial files. If {\bf nIter0} $>$ |
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{\bf tIter0} then tracers (and previous timestep tendency terms) |
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are read in from a the ptracers pickup file. Note that tracers |
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of zeros will be carried around if {\bf nIter0} $<$ {\bf tIter0}. |
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\\ |
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$\bullet$ {\bf nsubtime} is the integer number of extra timesteps |
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required by the tracer experiment. This will give a timestep |
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of {\bf deltaTtracer}$/${\bf nsubtime} for the dependencies |
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between tracers. The default is one. |
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\\ |
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$\bullet$ File names - these are several filenames than can be read in |
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for external fields needed in the tracer forcing - for instance |
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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 |
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for every tracer experiment. |
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\vspace{.5cm} |
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\noindent |
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{{\bf INITIALIZATION}}\\ |
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The values set at runtime in data.gchem are read in |
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using {\it gchem\_readparms.F} which is called from |
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packages\_readparms.F. This will include any external |
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forcing files that will be needed by the tracer experiment. |
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There are two routine used to initialize parameters and fields |
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needed by the experiment packages. These are |
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{\it gchem\_init\_fixed.F} which is called from \textit{packages\_init\_fixed.F}, and |
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{\it gchem\_init\_vari.F} called from |
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packages\_init\_variable.F. The first should |
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be used to call a subroutine specific to the tracer experiment |
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which sets fixed parameters, the second should call a subroutine |
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specific to the tracer experiment |
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which sets (or initializes) time fields that will vary with time. |
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\vspace{.5cm} |
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\noindent |
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{{\bf LOADING FIELDS}}\\ |
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External forcing fields used by the tracer experiment are read |
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in by a subroutine (specific to the tracer experiment) called from |
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{\it gchem\_fields\_load.F}. This latter is called from \textit{forward\_step.F}. |
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\vspace{.5cm} |
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\noindent |
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{{\bf FORCING}}\\ |
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Tracer fields are advected-and-diffused by the ptracer package. |
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Additional changes (e.g. surface forcing or interactions |
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between tracers) to these fields are taken care of by the gchem |
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interface. For tracers that are essentially passive (e.g. CFC's) |
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but may have some surface boundary conditions |
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this can easily be done within the regular tracer timestep. In this case |
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{\it gchem\_calc\_tendency.F} is called from {\it forward\_step.F}, where the |
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reactive (as opposed to the advective diffusive) tendencies are computed. |
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These tendencies, stored on the 3D field \textbf{gchemTendency}, are added to |
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the passive tracer tendencies \textbf{gPtr} in {\it gchem\_add\_tendency.F}, |
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which is called from {\it ptracers\_forcing.F}. |
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For tracers with more complicated dependencies on each other, |
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and especially tracers which require a smaller timestep than |
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deltaTtracer, it will be easier to use {\it gchem\_forcing\_sep.F} |
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which is called from forward\_step.F. There is a |
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compiler option set in {\it GCHEM\_OPTIONS.h} that determines |
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which method is used: \#define GCHEM\_SEPARATE\_FORCING |
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does the latter where tracers are forced separately from the |
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advection-diffusion code, and \#undef GCHEM\_SEPARATE\_FORCING |
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includes the forcing in the regular timestepping. |
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\vspace{.5cm} |
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\noindent |
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{{\bf DIAGNOSTICS}}\\ |
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This package also also used the passive tracer routine {\it ptracers\_monitor.F} |
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which prints out tracer statistics |
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as often as the model dynamic statistic diagnostics (dynsys) are written (or |
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as prescribed by the runtime flag \textbf{PTRACERS\_monitorFreq}, set in {\it data.ptracers}). |
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There is also a placeholder for any tracer experiment |
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specific diagnostics to be calculated and printed to files. |
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This is done in {\it gchem\_diags.F}. For instance the time average CO2 |
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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}. |
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\subsubsection{GCHEM Diagnostics} |
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\label{sec:pkg:gchem:diagnostics} |
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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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\subsubsection{Do's and Don'ts} |
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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}. |
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By itself, gchem pkg will read in \textbf{data.gchem} and will |
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write out gchem diagnostics. It requires tracer experiment |
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specific calls to do anything else (for instance the calls |
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to dic and cfc pkgs). |
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\subsubsection{Reference Material} |
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