AtmosphericChemistry 0.1.0

Tools for creating and managing atmospheric chemistry mechanisms.

This collection of python classes and routines facilitates the exploration, construction, and conversion of (gas-phase) chemical mechanisms (the system of differential equations that are solved in numerical models of atmospheric chemistry and transport). It consists of the following key elements:

1. The Compound class describing various physical and chemical properties of individual molecules or lumped substances and defining their names in various common chemistry schemes.

2. The speciesTable class which collects the compound information from all molecules and handles reading and writing this information from or to csv files.

3. The Reaction class describing gas-phase chemical reactants, products, product yields, the rate coefficient term(s) and optional tags, comments, and reaction labels.

4. The Mechanism class which contains a list of reactions and additional variables, comments, and other information and handles in- and output from and to various file formats (mech, csv, kpp, mozpp, racm).

Additional utilities allow computation of molecular weights based on the elemental composition of a molecule and queries of the Pubchem and Master Chemical Mechanism databases to obtain additional information about a compound (e.g. SMILES code, IUPAC name, etc.). There is even a rudimentary algebra class (mathTree) included, which allows scanning of mathematical expressions and factorisation.

The main purpose of this package is the interconversion of chemical mechanisms from one format to another, including the translation of species names from the namespace of one model to that of another model. It has been developed originally because of the author’s need to perform an intercomparison of various mechanisms with the help of a specific chemical boxmodel (CAABA/MECCA, see http://www.mecca.messy-interface.org/), but it may also be useful for other purposes, and the author will be grateful for feedback on various use cases as well as suggestions for improvement.

Conversion of a chemical mechanism is possible in only 4 lines of code:

from ac.gasphase.mechanism import Mechanism
    m = Mechanism.from_mech(inputfilename)
    m.translate_to_model('tm5')
    m.write_kpp_mecca(outputfilename)

This will read a mechanism in the ‘mech’ format, translate all species names to the TM5 namespace and write out species and equations files for the Kinetic Preprocessor (KPP, see http://people.cs.vt.edu/~asandu/Software/Kpp/).

It is also easily possible to test all reactions for mass conservation:

m.check_mass_balance()

or to find out which reactions involve a specific reactant, say HO2:

rlist = m.find_reactions(['HO2'])
    for r in rlist:
        print r.to_mech()

A number of applications of the ac package are provided in the bin directory of this distribution.

Requirements

Most of the functionality of the AtmosphericChemistry package requires only python standard libraries and numpy. However, if you want to use the pubchem or mcm_query routines to access compound information from internet databases, you will also need urllib, urllib2, lxml.html, json, time.

Author

Martin G. Schultz, IEK-8, Forschungszentrum Juelich, Germany

A Acknowledgements

Matt Swain for providing the PubChemPy module which is included in this package for cross-referencing compound information in the master species table. Snehal Waychal for providing the mcm_query module and for packaging this up.