Hello Martin,
We need to remember that CF will be used for both observational and model data in both atmospheric and oceanographic domains and so we shouldn't place functionality limits based on the domain interests of ane particular community. From my experience dealing with ocean biogeochemical data I know there is a need for chemical entities that represent groups of compounds, but there is also a need for having a catalogue at the CAS-level of detail. Otherwise it is impossible to develop automated comparisons between models that tend to lump compounds together and field data where the objective seems to be to push analytical technology to split things up as much as possible.
The types of system I am working on can store the discrete compounds, compound groups and the relationships between them as a simple bottom-up ontology. What I think we need to do for CF is to identify the chemical terms that are being used in chemical models, define them in terms of their component compounds and agree their nomenclature. If the domain experts can gather this information together then we have the basis for populating an ontology.
Cheers, Roy.
>>> "Schultz, Martin" <m.schultz at fz-juelich.de> 8/6/2007 9:40 am >>>
Hi,
first of all, I am very pleased to see this topic getting more and more attention in this newsgroup and also in the community of (atmospheric) chemistry modellers. It is good to have people like Christiane and Philip involved in this and I hope that we will be more in the future when more people realize the advantages of some standards for exchanging and assessing multiple output.
Concerning the list of chemical names, I don't think that CAS or any list with similar level of detail is the way forward. While most models treat a certain number of species (typically 40-60) explicitely, they always group organic species into compound classes in order to make the problem solvable (you just cannot imagine a global or regional 3D model with several million chemical variables). Yes - there are box models which go a certain way to treat individual compounds and radical species (for example the Master Chemical Mechanism in the UK or NCAR's master mechanism), but even these don't resolve everything after a certain point.
Luckily, the community is usually interested in a small subset of species only. Presumably the list compiled by Christiane covers quite a bit of that already. However, it is unavoidable to also consider "lumped" compounds in for example intercomparison studies. Then the difficulty is to find an unambiguous definition which nevertheless encompasses a sufficiently large number of models so that the "standard" is not only a private convention which could even interfere with other similar definitions. Let me give two examples here:
(1) pentanes: chemically, one distinguishes between n-pentane and i-pentane (one is linear the other molecule "T"-shaped). Both react through different pathways and form different compounds in the end. Nevertheless, the two molecules are practically always grouped together in modelling applications and the different reaction pathways are described via stochiometric factors
pentane + OH -> 0.7 * X + 0.3 * Y + 0.235 * Z + ...
In this example, defining a standard name for pentane would pose no major problem, I suppose.
(2) alkanes: Many models treat alkanes explicitly up to a certain C-number (usually 3, 4, or 5) and then lump everything else together. Practically, one could of course define standard names such as
mixing_ratio_of_alkanes_with_at_least_three_c_atoms_in_air
mixing_ratio_of_alkanes_with_at_least_four_c_atoms_in_air
mixing_ratio_of_alkanes_with_at_least_five_c_atoms_in_air
mixing_ratio_of_alkanes_with_at_least_six_c_atoms_in_air
...
However, the rule to make use of these would be quite complex. Say, you want to compute the total amount of hydrocarbons in an air mass, then this would be either
ethane + alkanes(C3) + "aromatics" + ...
or
ethane + propane + alkanes(C4) + "aromatics" + ...
or
ethane + propane + butane + alkanes(C5) + "aromatics" + ...
...
And the same complications (if not worse) appear with unsaturated species, oxygenated species, etc.
I don't know an easy way out of this, but it is good that these things are discussed here and now.
Best regards,
Martin
< Dr. Martin G. Schultz, ICG-II, Forschungszentrum J?lich >
< D-52425 J?lich, Germany >
< ph: +49 (0)2461 61 2831, fax: +49 (0)2461 61 8131 >
< email: m.schultz at fz-juelich.de >
< web:
http://www.fz-juelich.de/icg/icg-2/m_schultz >
Forschungszentrum J?lich GmbH
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Vorstand: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv.
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Received on Mon Aug 06 2007 - 03:31:49 BST
