Metadata-Version: 1.1
Name: AtmosphericChemistry
Version: 0.1.0
Summary: Tools for creating and managing atmospheric chemistry mechanisms.
Home-page: http://pypi.python.org/pypi/AtmosphericChemistry/
Author: M. G. Schultz
Author-email: m.schultz@fz-juelich.de
License: LICENSE.txt
Description: =============================
        Atmospheric Chemistry Package
        =============================
        
        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.
        
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Scientific/Engineering :: Atmospheric Science
Classifier: Operating System :: MacOS
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: Unix
