Hi,
There are two key points I want to add:
1) One of the current problems with chemistry output is that there is
currently NO agreed upon list of species names: many species have various
common names, and those names are often abbreviated in codes, which can
lead to confusion and incompatible files (eg ACET could refer to acetone
or acetaldehyde)
It would be really good if an agreed upon list of names could be agreed
upon bf CF.
2) The internal structure containing chemicals in models does NOT have to
be the same as that used in the NetCDF output, and my preference is to
have them be different.
Jonathan is correct that in all the models I have worked with the species
are all in the same array with an additional dimension for specie, and
sometimes an additional dimension for aerosol size. There are a couple of
problems with copying this into the netCDF file: first, it means 5 and 6
dimensional arrays (lat,lon,alt,time,specie,size), which some plotting
programs don't handle. The large arrays can also be unwieldy (both memory
and file-size constraints can be a problem).
Second, and more importantly, chemical mechanisms often change. If the
netCDF structure just uses a dimension for species, it is a pain to create
new input files: I often find myself needing to add or remove species, or
scale some of the species. For analysis, I also usually find myself
wanting to extract a long time history of just one or two species (out of
a hundred), which is also a real nuisance with a single array for all
species, and the process is prone to error. There is also a minor
nuisance that if a single specie is extracted, the degenerate dimension
needs to be handled.
Lastly, it is usually sufficient to output a small subset of species
(saving a lot of file-space), in which case the output array will not
match the internal array anyway.
The alternative is to have each specie as a different variable in the
NetCDF file. The pain here is that the code needs to know the names of
all the variables, and needs to read them in one by one.
I have used codes that handled this situation both ways. Personally, I
prefer to have each specie separate in the netCDF: the ease and accuracy
of post-processing easily outweighs the disadvantages.
In conclusion, I would like to see:
A) A list of specie names agreed upon by CF,
B) Species stored separately in CF compliant netCDF files.
Best wishes,
Philip
On Mon, 30 Jul 2007, Jonathan Gregory wrote:
> Dear Stephen
>
> When dealing with 5600 chemical species in a model, I guess that you must
> have arrays in which the chemical species is one of the dimensions, do you?
> In that case, allowing a dimension for chemical species in CF would be
> an obvious generalisation, as with surface cover types.
>
> Cheers
>
> Jonathan
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>
------------------------------------------------------------------------
Dr Philip Cameron-Smith Energy & Environment Directorate
pjc at llnl.gov Lawrence Livermore National Laboratory
+1 925 4236634 7000 East Avenue, Livermore, CA94550, USA
------------------------------------------------------------------------
Received on Mon Jul 30 2007 - 11:13:39 BST
