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.