AtmosphericChemistry 0.1.0

Description:

AtmosphericChemistry 0.1.0

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.