RMG News and Updates

2010-06-DD: RMG 3.2 Released!

RMG version 3.2 has been released. The new release includes a number of improvements and bug fixes, including the following:

Features:

• The RMG_Database folder has been restructured more logically. (PrimaryReactionLibrary and Seed Mechanism specifications in condition files will need updating)
• More accurate thermodynamic quantities from PM3 calculations for cyclic species based on explicit 3D molecule geometries (provided the user has access to GAUSSIAN03 or MOPAC2009)
• Transport property estimation
• New Reaction Library option for considering (but not forcing) reactions not automatically identified by RMG’s reaction templates (The old Primary Reaction Library has been renamed to Primary Kinetic Library.)
• New reaction model pruning option to reduce number of edge species and ease memory limitations.
• New non-negativity option for DASSL simulations. This offers a new way of dealing with NegativeConcentrationException cases.
• New reaction family, 1,2-Birad_to_alkene, for interconversion of alkene (triplet) biradicals and singlet alkenes
• It is possible to specify forbidden structures in the input file.
• Various error messages have been improved to give more helpful information to the user.
• RMG_Dictionary.txt will now be written at every iteration, rather than just the final iteration.
• CHEMKIN input files from each iteration are saved to separate folders
• RMG output file includes timestamp and code revision information.
• RMG stores Restart files. The reading-in of these files allows RMG to restore the conditions (species, reactions, pressure-dependent networks, etc.) of a converged mechanism without having to re-run the entire simulation from scratch.

Bug fixes and performance improvements:

• Treatment of molecular oxygen has changed significantly, including support for both triplet ground state and singlet; oxygen should now be specified in biradical form rather than the O=O form used previously; see “Representing oxygen” for details
• Various improvements to pressure-dependent network enlargement algorithm
• Fixed writing of reactions with Evans-Polanyi parameters to CHEMKIN input file
• Refinements to values in the database based on literature review.
• No longer falls into infinite loop when the simulation results in an invalid model but RMG cannot identify a suitable action to take to enlarge the model.
• Reservoir state method for evaluating pressure-dependent rate coefficients has been vetted and is now the recommended method for publication-quality models. The modified strong collision method remains available for preliminary exploration of reaction models.
• Pressure-dependence algorithm now defaults to an appropriate grid of temperatures and pressures based on the chosen interpolation model (e.g. Gauss-Chebyshev grid for Chebyshev polynomial model).
• Fixed several bugs relating to enlarging of partial pressure-dependent networks.
• Addressed issues that could lead to trying to simulate an empty reaction model in pressure-dependent cases.
• Fixed IWORK/RWORK renaming on Linux platforms.
• Fixed bug producing unneccessary error message (when using AUTO option) suggesting that the ODE solver failed when an edge flux exceeds user-specified tolerances at t=0.
• Fixed DASPK issues, including variables.dat renaming for multiple reaction systems, ability to use constant concentration, reaction flux evaluation for Lindemann reactions, and sensitivity coefficient calculation.
• Improved robustness for frequency estimation code (“frankie”).
• Changed ODE Solver input file writing to use BufferedWriter to ease memory usage issues when using AUTO with large reaction models.
• Fixed a bug in counting pressure-dependent edge reactions with the AUTO method.
• Fixed calculation of Cp(T=0) and Cp(T=Infinity) for monoatomic and linear species.
• Addressed collider issues, including an ArrayOutOfBoundsException associated with colliders and a collider identification issue.
• Addressed infinite recursion error in getToEndOfAxis that could occur with cyclic cumulenic species.
• Fixed syntax for helium thermochemistry in CHEMKIN input file written by RMG.
• Fixed bugs in counting of core and edge reactions caused by pressure-dependent reactions and irreversible reactions.
• Primary Kinetics Library now correctly identifies matches for molecules with multiple resonance forms
• Updated how RMG internally stores kinetics. In particular, RMG can now recognize and store kinetics for a given structure (e.g. A –> B + C) from multiple reaction families (i.e. different Transition States).

2009-08-05: RMG 3.1 Released!

RMG version 3.1 has been released. The new release includes a number of improvements and bug fixes, including the following:

• PrimaryReactionLibrary and PrimaryThermoLibrary now both behave as reference libraries from which data are taken (in preference to group additivity estimates), when and if the data are needed.

• Seed Mechanism allows the mechanism building to start from a seed mechanism, which is included in its entirety before the simulation starts. (This is how PrimaryReactionLibrary behaved in previous releases.)

• New databases: GRIMech 3.0 (PrIMe recommended) thermodynamic and kinetic values are included

• Support for Chemkin’s P-Log format for k(T,P) reporting (in addition to Chebyshev format).

• Added additional options for the input file, including:

  • User-specified limits for number of carbon / oxygen / radical per species
  • User-specified Chebyshev fitting options

• Changed many dependent Fortran codes to use standard input and output, rather than writing temporary files to disk.

• Reduced run-to-run variations by standardizing the order of averaging of values in the kinetics trees.

• Corrected inconsistencies in edge flux evaluation for pressure-dependent reactions.

• Corrected an error in inert gas normalization for runs with multiple temperatures/pressures

• Fixed DASPK interface

• Fixed bugs in peroxide (ROOR) frequency estimation

• Fixed a bug in the gauche correction database for alkenes

• Fixed issues with duplicate reactions and with Chebyshev fitting in writing CHEMKIN input files

• More frequent garbage collection

Special thanks to Dr. Seyed-Abdolreza Seyed-Reihani and Jeffrey Mo for identifying many of the bugs.

2009-03-05: RMG 3.0 Released!

After nearly two years of development, the RMG team is proud to present the release of RMG version 3.0. New features include:

• Cocurrent generation of a reaction mechanism over multiple temperature and pressure conditions
• Automatic time and conversion stepping when no intermediate points specified
• A new open-source module for handling pressure-dependent reaction networks
• On-the-fly generation of InChI strings for species
• A new graphical user interface for easier RMG input file generation
• Updated RMG Viewer and Editor (RMGVE), including database editing tools
• Thermodynamics estimates for non-cyclic species incorporate certain steric effects (1,5-interactions and gauche interactions)
• Simplified Windows installation

Also including a number of bug fixes, RMG 3.0 is a marked improvement over RMG 2. Find out how to download RMG.

2007-03-25: RMG 2 Release

RMG 2 has been released. The source code of the software, the manual, and sample initialization files are provided with this release.