RMG-Py v2.1.8

• New features:

  • Chlorine and iodine atom types have been added, bringing support for these elements to RMG-database
  • Forbidden structures now support Molecule and Species definitions in addition to Group definitions

• Changes:

  • Reaction pair generation will now fall back to generic method instead of raising an exception
  • Removed sensitivity.py script since it was effectively a duplicate of simulate.py
  • Thermo jobs in Cantherm now output a species dictionary
  • Fitted atom energy corrections added for B3LYP/6-31g**
  • Initial framework added for hydrogen bonding
  • Renamed molepro module and associated classes to molpro (MolPro) to match actual spelling of the program
  • Chemkin module is now cythonized to improve performance

• Fixes:

  • Allow delocalization of triradicals to prevent hysteresis in resonance structure generation
  • Fix reaction comment parsing issue with uncertainty analysis
  • Fix numerical issue causing a number of pressure dependent RMG jobs to crash
  • Template reactions from seed mechanisms are now loaded as library reactions if the original family is not loaded
  • Fix issues with degeneracy calculation for identical reactants

RMG-Py v2.1.7

• Charged atom types:

  • Atom types now have a charge attribute to cover a wider range of species
  • New atom types added for nitrogen and sulfur groups
  • Carbon and oxygen atom types renamed following new valence based naming scheme

• Ring perception:

  • Ring perception methods in the Graph class now use RingDecomposerLib
  • This includes the getSmallestSetOfSmallestRings methods and a newly added getRelevantCycles method
  • The set of relevant cycles is unique and generally more useful for chemical graphs
  • This also fixes inaccuracies with the original SSSR method

• Other changes:

  • Automatically load reaction libraries when using a seed mechanism
  • Default kinetics estimator has been changed to rate rules instead of group additivity
  • Kinetics families can now be set to be irreversible
  • Model enlargement now occurs after each reactor simulation rather than after all of them
  • Updated bond additivity corrections for CBS-QB3 in Cantherm

• Fixes:

  • Do not print SMILES when raising AtomTypeError to avoid further exceptions
  • Do not recalculate thermo if a species already has it
  • Fixes to parsing of family names in seed mechanisms

RMG-Py v2.1.6

• Model resurrection:

  • Automatically attempts to save simulation after encountering a DASPK error
  • Adds species and reactions in order to modify model dynamics and fix the error

• New features:

  • Add functionality to read RCCSD(T)-F12 energies from MolPro log files
  • Add liquidReactor support to flux diagram generation

• Other changes:

  • Removed rmgpy.rmg.model.Species class and merged functionality into main rmgpy.species.Species class
  • Refactored parsing of RMG-generated kinetics comments from Chemkin files and fixed related issues
  • Refactored framework for generating reactions to reduce code duplication
  • Resonance methods renamed from generateResonanceIsomers to generate_resonance_structures across all modules
  • Raise CpInf to Cphigh for entropy calculations to prevent invalid results

• Fixes:

  • Update sensitivity analysis to use ModelSettings and SimulatorSettings classes introduced in v2.1.5
  • Fixed generate_reactions methods in KineticsDatabase to be directly usable again
  • Fixed issues with aromaticity perception and generation of aromatic resonance structures

RMG-Py v2.1.5

• New bicyclic formula:

  • Estimates polycyclic corrections for unsaturated bicyclics by adjusting the correction for the saturated version
  • Can provide a decent estimate in many cases where there is not an exact match

• Other changes:

  • Refactored simulation algorithm to properly add multiple objects per iteration
  • Print equilibrium constant and reverse rate coefficient values when using Cantherm to calculate kinetics
  • Speed up degeneracy calculation by reducing unnecessary operations

• Fixes:

  • Loosen tolerance for bond order identification to account for floating point error
  • Fixed uncertainty analysis to allow floats as bond orders
  • Fixed some comment parsing issues in uncertainty analysis
  • Added product structure atom relabeling for families added in RMG-database v2.1.5
  • Fixed issue with automatic debugging of kinetics errors due to forbidden structures

RMG-Py v2.1.4

• Accelerator tools:

  • Dynamics criterion provides another method to expand the mechanism by adding reactions to the core
  • Surface algorithm enables better control of species movement to the core when using the dynamics criterion
  • Multiple sets of model parameters can now be specified in a input file to allow different stages of model generation
  • A species number termination criterion can now be set to limit model size
  • Multiple items can now be added per iteration to speed up model construction
  • New ModelSettings and SimulatorSettings classes for storing input parameters

• New features:

  • Kinetics libraries can now be automatically generated during RMG runs to be used as seeds for subsequent runs
  • Loading automatically generated seed mechanisms recreates the original template reaction objects to allow restarting runs from the seed mechanism
  • Carbene constraints can now be set in the species constraint block using maxSingletCarbenes and maxCarbeneRadicals
  • Chirality is now considered for determining symmetry numbers
  • Thermodynamic pruning has been added to allow removal of edge species with unfavorable free energy (beta)

• Other changes:

  • RMG-Py exception classes have been consolidated in the rmgpy.exceptions module
  • Species labels will now inherit the label from a matched thermo library entry
  • Sensitivity analysis is now available for LiquidReactor

• Fixes:

  • Fixed sensitivity analysis following changes to the simulate method
  • Add memory handling when generating collision matrix for pressure dependence
  • Improved error checking for MOPAC
  • Prevent infinite loops when retrieving thermo groups

• Known issues:

  • Seed mechanisms cannot be loaded if the database settings are different from the original ones used to generate the seed

RMG-Py v2.1.3

• Thermo central database:

  • Framework for tracking and submitting species to a central database have been added
  • Following species submission, the central database will queue and submit quantum chemistry jobs for thermochemistry calculation
  • This is an initial step towards self-improving thermochemistry prediction

• Rotor handling in Cantherm:

  • Free rotors can now be specified
  • Limit number of terms used when fitting hinder rotor scans
  • Fixed bug with ZPE calculation when using hindered rotors

• New reaction degeneracy algorithm:

  • Use atom ID's to distinguish degenerate reactions from duplicates due to other factors
  • Degeneracy calculation now operates across all families rather than within each separately
  • Multiple transition states are now identified based on template comparisons and kept as duplicate reactions

• Nodal distances:

  • Distances can now be assigned to trees in reaction families
  • This enables better rate averages with multiple trees
  • Fixed bug with finding the closest rate rule in the tree

• New features:

  • Added methods for automatically writing RMG-database files
  • New symmetry algorithm improves symmetry number calculations for resonant and cyclic species
  • Group additivity algorithm updated to apply new long distance corrections
  • Specific colliders can now be specified for pressure-dependent rates
  • Very short superminimal example added (hydrogen oxidation) for checking basic RMG operation
  • Cantera now outputs a Chemkin file which can be directly imported into Chemkin

• Fixes:

  • Fixed bug with negative activation energies when using Evans-Polanyi rates
  • Fixed walltime specification from command line when running RMG
  • Fixes and unit tests added for diffusionLimited module

• Known issues:

  • The multiple transition state algorithm can result in undesired duplicate reactions for reactants with multiple resonance structures

RMG-Py v2.1.2

• Improvements:

  • New nitrogen atom types
  • Kinetics libraries can now be specified as a list of strings in the input file
  • New script to generate output HTML locally: generateChemkinHTML.py
  • New kekulization module replaces RDKit for generating Kekule structures
  • Benzene bonds can now be reacted in reaction families
  • Removed cantherm.geometry module due to redundancy with statmech.conformer

• Fixes:

  • Reaction direction is now more deterministic after accounting for floating point error
  • Multiple bugs with resonance structure generation for aromatics have been addressed

RMG-Py v2.1.1

• Uncertainty analysis:

  • Local and global uncertainty analysis now available for RMG-generated models
  • Global uncertainty analysis uses MIT Uncertainty Quantification library, currently only supported on Linux systems
  • Examples for each module are available in localUncertainty.ipynb and globalUncertainty.ipynb

• Fixes:

  • Clar structure generation no longer intercepts signals
  • Fixes to SMILES generation
  • Fix default spin state of [CH]

RMG-Py v2.1.0

This release contains several new features and bug-fixes.

• Clar structure generation

  • optimizes the aromatic isomer representations in RMG
  • lays the foundations for future development of poly-aromatic kinetics reaction families

• Flux pathway analysis

  • introduces an ipython notebook for post-generatation pathway analysis (ipython.mechanism_analyzer.ipynb)
  • visualizes reactions and provides flux statistics in a more transparent way

• Cantera mechanism

  • automatically writes cantera version of RMG-generated mechanism at the end of RMG jobs

• Fixes bugs

  • upgrades pruning to fix new memory leaks introduced by recent functionalities
  • fixes the bug of duplicated species creation caused by getThermoData removing isomers unexpectedly
  • fixes restart file generation and parsing problems and users can choose restart mode again
  • upgrades bicyclic decomposition method such that more deterministic behaviors are ensured
  • change bond order type to float from string to improve RMG's symmetry calculation for species with multiple resonance structures

RMG-Py v2.0.0

This release includes several milestones of RMG project (see installation here):

• Parallelization finally introduced in RMG:
  • Generates reactions during enlarge step in parallel fashion (rmgpy.rmg.react)
  • Enables concurrent computing for QMTP thermochemistry calculations (rmgpy.thermo.thermoengine)
  • Instructions of running RMG parallel mode can be found here for SLURM scheduler and here for SGE scheduler.
• Polycyclic thermochemistry estimation improved:
  • Extends group additivity method for polycyclics and estimates polycyclics of any large sizes by a heuristic method (bicyclics decomposition)
• New tree averaging for kinetics:
  • Fixes previous issue of imcomplete generation of cross-level rate rules
  • Implements Euclidean distance algorithm for the selection of the best rate rules to use in estimateKinetics
  • Streamlines storage of kinetics comments for averaged rules, which can be analyzed by extractSourceFromComments
• Database entry accessibility tests:
  • Adds entry accessibility tests for future entries (testing.databaseTest)
• Fixes bugs
  • fluxdiagram generation is now fixed, one can use it to generate short video of fluxdigram evolution
  • mac environment yml file is introduced to make sure smooth RMG-Py installation and jobs on mac
  • fixes failure of checkForExistingSpecies for polyaromatics species
  • fixes execution failure when both pruning and pDep are turned on
  • fixes pDep irreversible reactions
  • fixes issue of valency of Cbf atom by dynamic benzene bond order assignment