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University of LeedsDepartment of Chemistry
The New MCM Website
Stephen Pascoe, Louise Whitehouse and Andrew Rickard
Overview
Using the new MCMv3.1 website Andrew
• Features (Mark List, Browse, Search, Extract)
• Other updates (Feedback)
Extraction into different formats Louise
• FORTRAN and XML
Under the hood: Technical detail Stephen
• IT perspective
• Design decisions
• MCM development platform (access/accord database - MySQL database)
• Contextual information - reaction categories
The New MCM Website: Improvements
• Updated to McMv3.1 (including Box and PTM models)
• Improve User Experience:
• Better navigation• Search/Extract tools
• Simplify update and maintenance:
• More integrated data representation
• Facilitate inclusion of contextual information:
• Protocol methodology• Reaction source• Rate uncertainty
• Provide base for future development
www.chem.leeds.ac.uk/Atmospheric/MCM/mcmproj
www.mcm.leeds.ac.uk/MCM
Navigational Features: Homepage
● Menu Bar
● Mark species for later processing
● Three main functions– Browse– Search– Extract
Navigational Features: Browse
Navigational Features: Search
● Enter SMILES string
– e.g. isoprene: C=C(C)C=C
● Enter a MCM species name
– e.g. n-butane: NC4H10
Navigational Features: Search Results
● Structure image linked to reaction listing.
Navigational Features: Reaction Listing
● Reaction source information
● Add species to Mark List
Navigational Features: Source information
● Information based on Protocol papers
● Hyperlinked citations
Reaction categories
KEY
Initial reactionsIntermediate reactionsRO
2reactions
Product reactions
VOC
h OH NO3 O3
R
RO
RO2
[Criegee]*Criegee
Cl Removal
Carbonyls RONO2 ROONO2
Rxns of unsaturated degradation products
ROOH RC(O)OOH
RC(O)OONO2
RC(O)OH
ROH Multi-functional h
RO2 + NORO2 + NO2 (acyl and CH3O2)RO2 + NO3
RO2 + HO2
RO2 + RO2 (permutation)
further degradation
paper-sectionS - Saunders 2003J - Jenkin 1997
S-4.1.1S-4.4.1
S-4.5.1
S-4.2.1S-4.3.1
S-4.8.1
S-4.6.2
S-4.7.1
S-4.6.1
S-4.7.2
S-4.6.3
S-4.6.4
S-4.6.5
J-3.10.2 J-3.10.3
J-3.9.1
J-3.10.1 J-3.10.4 J-3.10.5 J-3.10.6
J-3.10.7 J-3.10.8 J-3.10.9S-4.9.1
paper-sectionS - Saunders 2003J - Jenkin 1997
S-4.1.1S-4.4.1
S-4.5.1
S-4.2.1S-4.3.1
S-4.8.1
S-4.6.2
S-4.7.1
S-4.6.1
S-4.7.2
S-4.6.3
S-4.6.4
S-4.6.5
J-3.10.2 J-3.10.3
J-3.9.1
J-3.10.1 J-3.10.4 J-3.10.5 J-3.10.6
J-3.10.7 J-3.10.8 J-3.10.9S-4.9.1
Future and Ongoing WorkKinetic Database
• In the future it is hoped that the MCM can also be used as comprehensive up-to-date kinetic database.
• Ideally, this large database will include literature citations for all rate constants and branching ratios for ALL reactions in MCMv3.1.
• An estimation of a degree of uncertainty associated with the quoted rate parameters will also be evaluated.
• This facility will provide an extremely useful reference tool for the user and subject the MCM to a broader audience.
• This fits in well with the PrIMe initiative currently being put together in the US.
Process InforMatics Model (PrIMe)
• The PrIMe initiative is a community based effort to generate data libraries, analysis software and supporting IT infrastructure that will enable a collaborative approach to the development of predictive models.
• New site at NIST, Washington (http://www.me.berkeley.edu/prime/) to coordinate the development of kinetic and thermodynamic databases for combustion.
• Has potential applications for atmospheric chemistry.
• MJP is involved and will investigate potential for wider dissemination of the MCM and development of methods to enhance the reaction database.
• DIAC will provide some funding, to augment that from DEFRA, to support the maintenance of the database associated with the MCM.
Navigational Features: Extract
● Use Mark List as primary species
● Choose output format– HTML– FACSIMILE– FORTRAN– XML
Navigational Features: Extract Listing
Feedback: Mailing List
• Keep up-to-date with
updates and improvements
to the MCM and website
• Provides a forum for
suggestions and error
reporting
Alternative formats for subset data (1)
• Numerical Fortran compatible format.– Species number allocation– Reactions represented in numerical format– FORTRAN subroutine detailing rate coefficients– Routine includes all expressions for the calculation of the
complex rate coefficients and photolysis rates. – FORTRAN subroutine for calculation of rate equations.– Reactions represented in this form can easily be input into
numerical integrators.• A converter which will allow users to convert their own
mechanisms from a standard FACSIMILE format to FORTRAN format is in the final developmental stages and will shortly be available on the website.– This will allow the user to generate all the data files described
above for any existing FACSIMILE file. – This code only extracts the reaction structure from the file, it is
then up to the user to adapt the output files to allow simulation of the required conditions.
Fortran format
Alternative formats for subset data (2)
XML• XML stands for Extensible Markup Language. • XML is similar to HTML but all tags are user defined. • XML is based around the concept that every piece of
information is tagged. – This allows easier and more flexible storage, retrieval, and
exchange of data.
• A tree structure is designed for easy representation of the subset in a set of tables.– This is called a schema and defines the way in which data is
represented and applies constraints to data in certain fields.– e.g. A species appearing in a reaction must be present in the
species table.
XML Format
XML Schema Design
species definitions
species species number
species name
RO2 speciesspecies name
reaction definitions
reactionreaction number
ratereaction number
rate name
reactantsreaction numberspecies name
productsreaction numberspecies name
•There are 2 sets of nested tables one representing species and the other the reactions contained in the subset.
•The underlined coloured entries are table keys.•Other table entries represented in this colour must hold a value of an
entry in the corresponding key column.
Continuing work on subset formats
• Numerical Fortran compatible format.– Feed back on style of Fortran output with relevance
to its practicality for users.– Finalisation of Fortran converter which can be
downloaded to convert existing Facsimile subsets to the numerical Fortran style.
• XML– Continuing development of XML schema design.– Comparison with existing XML designs used within
chemistry.– Aim to achieve a flexible and robust format for data
storage, display and use.