18. Release Notes

18.1. RMG-Py Version 3.2.0

Date: August 2, 2023

• RMG-Py

  • Transport: Added halogens transport corrections to boiling point when estimating critical properties using group additivity

  • Updated solvation thermo GAV method to use more groups

  • Made it optional to generate_resonance_structures when loading species dicts

  • Added filter so radical/lone pair/formal charge is not added to surface site when generating resonance structures

  • Forbid surface bidentate vdW species

  • Add Transitory Edge Analysis species selection algorithm

  • Added get_react_thermo function to avoid deepcopy

  • Added decay framework for handling species RMG templates think exist, but really aren’t wells

  • Added check to prevent multiple surface bonds from forming through a single adatom

  • Added multidentate adsorption correction for thermo estimation

  • Added error checks to make MOPAC calculations more robust

  • Added features to preserve atom order and template labels when generating reactions

  • Added coverage dependent effects to surface kinetics

  • Added support for halogen families in autogen tree script

  • Enabled pyrms for RMG Simulations and Edge Analysis

  • Added Liquid-Surface Reactor for RMG Electrocat

  • Added support for forbidden structures, more general than forbidden molecules

  • Removed hard-coded template matching code for Bimolec hydroperoxide decomposition

  • Added support for 2-parameter Troe reactions, only had 3-parameter Troe before

  • Included noncyclic long distance GAV correction for halogen regardless of its existence in the cycle

  • Added support for pdep networks with halogens

  • Added atom labels to molecule to_group method in order to keep the atom labels during conversion

  • Moved rmgrc to template file so user’s settings won’t be overwritten every pull from RMG-Py

  • Implemented two backup conformer embedding algorithms for robustness

  • Added Nitrogen groups to transport

  • Removed check for adsorbate getting adsorbed again which prevents Surface_Dissociation_to_Bidentate family

  • Modified the liquid reactor to be able to simulate as CSTR, semi-batch, and/or vapor liquid mass transfer interface

  • Added fragment code to rmgpy/molecule

  • Added PDEP improvements: simulation least squares methods and the Georgievskii et al. 2013 CSE variant to Arkane

  • Allow users to load thermo or kinetic libraries from a user-specified location

  • Add radical flux tolerance

  • Improved kH estimation code for solute

  • Allow irreversible PDEP reactions by setting Keq=inf

  • only calculate frequency and x in get_partition_function if semiclassical correction is needed

  • Implemented deadend radical species selection algorithm

  • Enable Metal, Facet, site and terrace specification in Molecule

  • Increase species label max length for chemkin to avoid S(14567) style species

  • Don’t replace PDep kinetics of a library reaction

  • Added solvation to surfaces

  • Added some charge transfer reactions

  • Added lithium

• Auto Generated Trees

  • Enabled estimator to ascend autogenerated rate tree if uncertainty is too high in a lower node

  • Made some major improvements to automated tree extension generation and the cascade algorithm

  • Added support for quadruple bonds in auto tree generation

  • Added binding energies for N-S and C#S

  • Removed hard-coded special treatment for Peroxyl Disproportionation family during template matching

  • Increased ArrheniusBM fitting temperature upper limit to 2000K for RMG-database rate trees

  • Skipped number of products check for ATG tree generation of Intra_R_Add_Endocyclic and Intra_R_Add_Exocyclic

• RMS

  • Add Transitory Edge Analysis

  • Added surface reactions to RMS yaml format

  • Updated developer installation instructions to use main RMS branch

  • Add comment as input to to_rms() function

  • Change RMS to use keyword variables to avoid twin PR with RMG whenever RMG changes struct

• Arkane

  • Added check for convergence and other common errors in QM parsers

  • Updated the documentation that tabulates which levels of theory are supported by Arkane

  • Read actual scan angles for rotor calculations

  • Corrected Fourier fitting in torsion.pyx

  • Added Psi4 ESS adapter to Arkane

  • Added commit strings for RMG-Py and RMG-database to Arkane logs

  • Added BAC confidence interval estimates to Arkane logs

  • Added leave-one-out cross-validation for evaluating BAC fits

  • Enabled parsing of scan log files with linear bend (something like L 1 2 3 B)

  • Enabled assignment of PES (angles vs energies) directly in the Arkane input file

  • Added a readme file for Arkane

  • Updated QChem parser to only return the negative frequency from the last frequency block instead of the first

  • Added more unit tests

  • Save meaningful reaction label for PDEP reactions when creating RMG library

  • Added more examples

  • Added Arkane citation info: https://doi.org/10.1002/kin.21637, https://doi.org/10.1021/acs.jcim.2c00965

  • Allow RMG to read Arkane YAML files through the RMGObject even if they have mol or aux keywords

• Bugfixes

  • Added check for multiplicity of reverse products if the family template reactants have multiplicity constraints

  • Added check for vdW multiplicity constraints in forward direction

  • Added check to see that empty surface site template group only matches empty surface site structure (and not vdW species with empty site)

  • Fixed regex bug in checking multiplicity of adjacency list

  • Fixed bug where RMG can output mechanisms in which two species have the same name

  • Added QM fallback to ML or GAV in case of bad conformer ID error from rdkit

  • Fixed many broken links in documentation

  • Fixed species missing metal attribute error

  • Fixed some automated tree generation parallelization bugs

  • Changed tree generation get_training_set method to use deepcopy to clear atom labels and to parse out the metal from the entry

  • Added a save_order attribute to some methods to preserve atom order in cases that need it

  • Fixed load chemkin function to allow extended elements and species that start with digits

  • Handle string data properly when averaging children solute

  • Fixed bug in get_w0 where a_dict didn’t match the molecule because it was made before the molecule was deepcopied

  • Added check for pdep net reactions when removing species to prevent forbidden species from ending up in net reactions

  • Fixed bug where add_atom_labels_for_reaction mislabels reactants if family is its own reverse

  • Fixed bug where save_training_reactions occasionally mixes up atom labels

  • Added Ctc atom type to prevent RMG from crashing when trying to make [C+]#[C-] molecule, which was then added to the forbidden structures

  • Fixed bug where generate_resonance_structure does not preserve atom when keep_isomorphic=False and save_order=True

  • Fixed bugs related to RMS object construction, particularly Multi/Pdep/Arrhenius and falloff

  • Added check to always draw CO as ‘CO’ instead of ‘OC’

  • Converted ThermoData object to a NASA object for compatibility with RMS

  • Corrected pyrms core/edge species/reaction handling for phase systems

  • Fixed incorrect reading in load_chemkin_file for surface species with site density specified

  • Added properties so group can be pickled without losing important information like ring membership

  • Fixed bug where atom map changes even if save_order=True

  • PDEP networks update before writing/filtering to avoid differences in barrier energy corrections between networks

  • Check for debug mode so rms can be imported in debug mode

  • Fixed group property has_wildcards to avoid AttributeError

  • Fixed several calls missing the ‘r’ at the start of regex pattern string

  • Fixed Fragment count_internal_rotors and is_atom_in_cycle attribute errors

  • Added missing term in Troe kinetics formula

  • Fixed some broken links in documentation

  • Change cython variables from cpdef to cdef to avoid warnings

  • Updated load_transport_file to skip any species in the transport file that’s not in the species dictionary instead of crashing

  • Fixed CI error “Unable to dlopen(cxxpath) in parent! cannot open shared object file: File name too long”

• Testing

  • Updated reference number of reactions for Arkane test_reactions unit test

  • Changed molecule for rmgpy/data/thermoTest.py test_identifying_missing_group test because group is no longer missing

  • Added continuous integration test for links in documentation

  • Changed kinetics database tests to look for auto_generated tag instead of the hardcoded family list

  • Updated rmg test data with new 2+2 cycloaddition species and reactions

  • Remove cti file generation from regression tests to avoid Cantera IO error

  • Added tests to check number of reactants and products defined in ATG rate rules

  • CI is now done with mamba to drastically reduce runtime

  • Move regression testing into main CI.yaml

  • Simplify condition checking for scheduled vs pushed CI

  • Remove redundant step creating stable_regression_results dir for running on a schedule or push to main because it already is the stable result

  • Update CI.yml to allow CI tests on forks

  • Added “phony” target so make test will always remake when run (instead of checking whether the test folder is up to date)

  • Add a unit test to make a sample molecule for every atom type

  • Update CI.yml and environment.yml to allow CI to run on MacOS

  • Add regression testing for RMS’s CSTR and constant V ideal gas reactors

  • Bugfix on CI documentation testing so errors are reported as failures

  • Relax tolerance on HinderedRotor.get_enthalpy() test to accomodate slightly different answer likely due to numerical issues

  • Regression tests report failure if a model changes significantly

  • Allow CI testing to be called from other repos

  • Regression tests pass by default and the user must look at the report to see details of comparison

  • Generate summary of regression test results to be displayed on annotation of PR results

• Miscellaneous

  • Added Docker install

  • Added check to only publish documentation documentation from RMG official fork

  • Fixed RMG-Py 3.1.0 release note bullet formatting

  • Changed installation instructions for WSL users to install graphviz system wide to include all dependencies

  • Changed get_all_solute_data function for RMG-website use in order to apply halogen or radical correction on top of library or GAV

  • Added openSUSE installation instructions

  • Changed default branch to main

  • Changed rmg.py shebang to use python-jl instead of python3 for compatibility with RMS/pyrms

  • Updated ketoenol template image to 1,3 sigmatropic rearrangement

  • Updated 2+2_cycloaddition images in documentation

  • Added licensing information to the README file

  • Updated installation instructions with main instead of master branch, latest Anaconda link, and ssh instead of https clone from github

  • Added support for Sticking Reactions in HTML reports

  • Added reminder in documentation to activate rmg_env before making tests

  • Check that family tree is not autogenerated before calling add_rules_from_training and fill_rules_by_averaging_up

  • Added warning to not to call add_rules_from_training and fill_rules_by_averaging_up on ATG trees, and return statement before error

  • Replaced BurkeH2O2 library with PrimaryH2O2 in relevant RMG examples

  • Added instructions to Documentation for fixing libmkl_ts.so.2 ImportError

  • Added new RMG-database paper to cite https://pubs.acs.org/doi/10.1021/acs.jcim.2c00965

  • Added .bib file for easy citation

  • Updated RMG-Py install instructions to remove old Julia instructions and to use mamba solver

  • Use conda-forge ncurses for compatibility with docker

  • Use conda-forge pyjulia instead of customized RMG channel version for better standardization

  • Update Cantera version requirement to 2.6

  • Upgrade to OpenMOPAC to fix license issues

  • Updated list of developers

  • Added Jupyter Notebook example for simulating and analyzing superminimal model

  • Robot automatically marks issues and PR’s as stale after 90 days of inactivity and closes them after 30 more days of inactivity

18.2. RMG-Database Version 3.2.0

Date: August 2, 2023

• Thermochemistry

  • Identified and fitted thermo for missing groups using the following libraries:

    ‘Klippenstein_Glarborg2016’, ‘BurkeH2O2’, ‘thermo_DFT_CCSDTF12_BAC’, ‘DFT_QCI_thermo’, ‘primaryThermoLibrary’, ‘primaryNS’, ‘NitrogenCurran’, ‘NOx2018’, ‘FFCM1(-)’, ‘SulfurLibrary’, ‘SulfurGlarborgH2S’, ‘SABIC_aromatics’

  • Added more solutes and solvents to the solvent library

  • Updated GAV method for solvation thermo to use more groups

  • Added the following new halogen thermo libraries:

    • CHOF_G4

    • CHOCl_G4

    • CHOBr_G4

    • CHOFCl_G4

    • CHOClBr_G4

    • CHOFBr_G4

    • CHOFClBr_G4

    • Chlorination

    • halogens

    • 2-BTP

    • 2-BTP_G4

  • Added new halogens group entries for group.py, radical.py nonring.py, and longDistanceInteraction_noncyclic.py

  • Added the following species to the primaryThermoLibrary: F, HF, F2, Br, HBr, Br2, NO, NO2, CO, OCCCO

  • Updated halogen group entries with molecule symmetry number correction

  • Added corrections for overestimation of triplet and multidentate adsorbates

  • Added CO2, COOH, and HCOO to the Pt(111) thermo database

  • Added halogens statmech library

  • Added F/Cl/Br-benzene group additivity values

  • Added “heavy halogen interaction” long distance thermo group

  • Added thermo library with 1D rotor scans for species in ketoenol, retroene, and 1,3 sigmatropic rearrangement training reactions

  • Added more Pt(111) thermo data

  • Added correction to S6ddd thermo group

• Kinetics

  • Added coverage-dependent kinetics for surface reactions

  • Added new halogens kinetics families and libraries

  • Added the following new families:

    • 1,3 sigmatropic rearrangement

    • Intra halogen migration family

    • Surface_Abstraction_Beta

    • Surface_Abstraction_Beta_double_vdW

    • Surface_Adsorption_Dissociative_Double

    • Surface_Dissociation_to_Bidentate

    • XY_elimination_hydroxy

  • Autogenerated the following family trees:

    • 1,3_Insertion_CO2

    • 1,3_NH3_elimination

    • 1,3_sigmatropic_rearrangement

    • 2+2_cycloaddition

    • Bimolec_Hydroperoxide_Decomposition

    • Birad_recombination

    • CO Disproportionation

    • Cyclopentadiene_scission

    • Diels alder addition

    • Disproportionation

    • Ketoenol

    • Peroxyl Disproportionation

    • Retroene

    • Substitution_O

  • Added new rates and refit the following family trees:

    • 1,3_Insertion CO2

    • 1,3 sigmatropic rate tree

    • Diels Alder Addition

    • Intra_R_Add_Endo/Exocyclic

    • retroene

    • ketoenol

    • aromatic_H_abstraction (new rates from Hou et al.)

    • Surface_Adsorption_Bidentate

    • Surface_Adsorption_Double

    • Surface_Adsorption_Single

    • Surface_Adsorption_vdW

    • Surface_Bidentate_Dissociation

    • Surface_Dissociation

    • Surface_Dissociation_Beta

    • Surface_vdW_to_Bidentate

  • Added PrimaryH2O2 library with rates by Konnov

  • Updated reactions for PrimaryNitrogenLibrary

  • Added surface library reactions for ammonia

  • Merged all 2+2_cycloaddition families in to one 2+2_cycloaddition family

  • Generate Intra R Add Endo/Exocyclic rate trees from the ring opening direction to help distinguish between endo/exo

  • Added training reactions and groups related to PAH formation

  • Save additional DFT settings information for metal binding energy calculations

  • Added corrections to primaryH2O2 library

  • Added corrections to Klippenstein_Glarborg2016 library related to singlet/triplet carbene reactions and other incorrectly imported reactions

• Transport

  • Added NIST transport library for fluorines

  • Added new halogen transport groups

  • Added Nitrogen groups to transport

• QM Corrections

  • Added frequency scaling factors AEC and BAC for wB97X-D3/def2-TZVP and B97-D3/def2-mSVP

  • Added notebooks demonstrating how to update AEC and BAC

  • Updated AECs for CCSD(T)-F12/cc-pVXZ-F12 st X = D, T

  • Added frequency factors for b2plypd3/def2tzvp, b2plypd3/aug-cc-pvtz, b2plypd3/cc-pvtz

  • Updated BAC using correct frequency scaling factor for:

    • wB97X-D3/def2-TZVP

    • B97-D3/def2-mSVP

    • CCSD(T)-F12/cc-pVTZ-F12//wB97X-D3/def2-TZVP

    • CCSD(T)-F12/cc-pVDZ-F12//wB97X-D3/def2-TZVP

• Bugfixes

  • Fixed the number of unpaired radicals in surface vdW families

  • Fixed typos in training reactions field names

  • Fixed enthalpy errors in adsorption corrections for O-containing species on Pt(111)

  • Fixed some errors in surface training reaction rates

  • Fixed some minor errors in the solvent library

  • Fixed typos in coverage dependent kinetics parameters

  • Used forbidden group to fix error where unsymmetric head node leads to Undeterminable Kinetics Error

  • Removed duplicates in XY_addition_multiplebond

  • Fixed typo in R_Recombination training reaction units

  • Fixed incorrectly imported species H2CCC and C3H2 in the CurranPentane library

  • Fixed master to main in trigger script

  • Added the missing reactant and product number in the intra_R_Add families

  • Fixed Intra_R_Add_Endocyclic/Exocyclic families by generating from the ring opening direction and enumerating backbones

• Miscellaneous

  • Updated Github Actions workflow for better handling of dual RMG-Py and RMG-database pull requests

  • Added the Blowers-Masel tree generation notebook

  • Added [C-]#[C+] to forbidden structures

  • Added thermally forbidden 2pi + 2pi cycloaddition to forbidden structures

  • Changed Github Actions to run on main branch instead of master

  • Updated 2+2_cycloaddition reaction family images

18.3. RMG-Py Version 3.1.0

Date: April 23, 2021

We recommend creating a new conda environment using the latest environment.yml as many dependencies have changed, and upgrading an existing environment is always troublesome.

• RMG-Py

  • Added support for Bromine

  • Added improved method to calculate temperature dependent solvation free energy

  • Made Rank 1 accuracy correspond to 0.2 kcal/mol instead of 0 kcal/mol

  • Improvements to Group Additivity comments, in particular adding missing group comments

  • Added support for trimolecular units in ArrheniusBM fits

  • Improvements to profiling

  • Use kekulized structures for transport estimation

  • Automatic tree generation script improvements

  • Properly short circuit is_isomorphic when strict=False

  • Added block for specifying species tuples to react when starting an RMG run

  • Improve ArrheniusBM fitting to a single reaction

  • Improvements in bidentate thermochemistry estimation

  • Added new surface attributes for metals and facets

  • Added support for Phosphorus

  • Enable use LSRs to scale thermo from different metals and enable proper use of training reactions from different metals

  • Added maximumSurfaceSites constraint

• Arkane

  • Added frequency scaling factors for apfd/deef2tzvp and wb97xd/def2svp

  • Kinetics and pdep sensitivities additionally saved in YAML format

  • Enable automatic isodesmic reaction generation

  • AECs, BACs and frequency scaling factors moved from Arkane to RMG-database

  • Added functionality for Petersson and Melius BAC fitting using Arkane and the reference database

  • Enabled two parameter Arrhenius fit option

  • Added functionality for fitting AECs

  • Added classes to standardize model chemistry definitions

  • Use adjlists instead of smiles when saving

• Bugfixes

  • QMTP updated to work with g16 executable

  • Fixed various Sticking Coefficient bugs

  • Fixed issues with Surface Arrhenius reactions written in the reverse being converted to ArrheniusEP instead of SurfaceArrheniusBEP

  • Fixed NaN handling in the explorer tool’s steady state solve

  • Fixed determine_qm_software for Orca

  • Fixed bug where elementary_high_p library reactions with more than the maximum number of atoms for pdep never entered the edge

  • Fixed bug related to pdep networks having sources not contained in the core

  • Fixed various profiling bugs

  • Fixed issue with indexing when merging models

  • Fixed bug with ranged liquid reactors

  • Fixed bug with loading of autogenerated trees in Arkane

  • Fixed bug related to collision limit violation checks in LiquidReactor

  • Fixed bug related to Pmin and Pmax definition in SurfaceReactor

  • Fixed bugs in global uncertainty analysis for LiquidReactor

  • Fixed bug related to the units of reverse rate constants for reactions involving surface species

  • Fixed bug in Molecule isomorphism where it would simply assume the given initial map was correct

  • Remove deprecated matplotlib warn keyword

  • Fixed bug related to reading Chebyshev forms in Chemkin files

  • Fixed reference concentration for surface species when calculating Kc

  • Fixed issue with the reaction generation using the reversee of Surface_ElleyRideal_Addition_MultipleBond

  • Fixed bug with adjlist multiplicitly line being mistaken as the species name

  • Fixed bug with the library to training notebook

  • Remove temporary seed mechanisms if they exist from a previous run

• Miscellaneous

  • Modified find_parameter_sources_and_assign_uncertainties to regenerate chem.inp as needed

  • Added option to save atom order when labeling template reactions

  • Added option to ignore atom type errors when creating molecule objects

  • Enable use of critical_distance_factor in from_xyz

  • Improved SIGINT handling when calling lpsolve

  • Enable H-bond drawing

  • Improvements to debug messages

  • Updated dependencies cclib and OpenBabel

Note that the upgrade to OpenBabel v3+ will change the interpretation of some ambiguous SMILES strings that use the lower-case aromatics notation. Although we think the new interpretation is not wrong, it might be different from previous versions, so take care.

18.4. RMG-Database Version 3.1.0

Date: April 23, 2021

• Thermochemistry

  • Added groups and library for Iodine

  • Added additional solvent parameters

  • Updated SABIC_aromatics thermo library added s3_5_7_ane thermo library and updated polycyclic groups

  • Renaming of adsorption libraries

• Kinetics

  • Added kinetic library and training reactions for Iodine

  • Added training reactions for peroxy families

  • Prevent forbidden [2pi+2pi] thermal cycloaddition for C=C + C=C

  • Removed incorrectly transcribed training reaction for CH3OH+O2=>CH3O+HO2

  • Added H_Abstraction training reactions

  • Creation of the retroene family uses automatic tree generation

  • Added Surface Dissociation Double vdW, Surface Dissociation vdW, Surface Migration and Eley-Rideal, Surface Addition Single vdW, Surface Abstraction vdW, Surface Dual adsorption vdW, Surface Dissociation Beta, Surface Adsorption Abstraction vdW and Surface_DoubleBond_to_Bidentate families

  • Updated Surface Dissociation, Surface Abstraction, Surface Adsorption Dissociative, Surface Adsorption Single and Surface Bidentate Dissociation families

  • Added assorted Nitrogen catalysis training reactions

  • Allow CO insertion to H–C(R)=O

• QM Corrections

  • Updated AECs and added frequency scaling factor for wB97M-V/def2-TZVPD

  • Standardized level of theory specifications

• Bug fixes

  • Fixed Cds-CdSH node reference

  • Fixed typos causing thermo discontinuities for H2_ads and O-NH2-ads

  • Fixed enthalpy error for O-NH2_ads

  • Corrected structure of H2CC in JetSurF2.0, Klippenstein_Glarborg2016, and Narayanaswamy

  • Fixed Ni211 binding energies

• Miscellaneous

  • Fix indexing of importChemkinLibrary.py script

  • Moved AEC, BAC and frequency scale factor data from RMG-Py into RMG-database

  • Added notebook for fitting polycyclic thermo groups

  • New surface attributes

18.5. RMG-Py Version 3.0.0

Date: December 16, 2019

This release represents a major milestone in RMG development and includes many backwards-incompatible changes, most notably Python 3 compatibility and major API changes. Users switching to RMG 3 will need to create new conda environments and update any scripts which access the API. We recommend using the futurize script from python-future for updating scripts for Python 3 and the provided rmg2to3.py script for updating scripts for RMG 3.

• Python 3 #1724

  • RMG is now compatible with Python 3.7 and newer

  • RMG v2.x versions will no longer be supported

  • API changes

    • Method, function, and argument names have been standardized to use snake_case across RMG and Arkane

    • Input file related code was not changed, in order to continue support for existing syntax

    • Conversion script has been provided to aid transition (scripts/rmg2to3.py)

    • Standardized submodule names in the rmgpy.tools module #1794

  • Accompanying changes

    • Reduction and scoop_framework modules have been removed

    • New/updated hash and comparison methods for Species/Molecule/Atom/Bond classes

    • DDE thermochemistry estimator has been replaced by chemprop

    • Update example IPython notebooks #1735

    • Update global uncertainty module to work with MUQ 2 and Python 3 #1738

  • Miscellaneous clean up and bug fixes following transition #1741, #1744, #1752, #1759, #1785, #1802, #1798, #1799, #1808

• Arkane

  • Improvements and refactoring of job output file creation and content #1607

  • Fix kinetics fitting bug #1672

  • Improvements to automatic network exploration tool #1647

  • Support for ND classical and semi-classical rotor calculations #1640, #1849

  • Support for 2D quantum mechanical rotor calculations using Q2DTor #1640

  • Support for providing absolute file paths #1685

  • Output RMG-style libraries #1769

  • Check for error termination in Gaussian log files #1766

  • Support for parsing Orca log files #1749

  • Support for parsing MP2, double hybrid DFT, CCSD, and CCSD(T) energies from Gaussian log files #1815

  • Support for TeraChem log files #1788

  • Miscellaneous bug fixes #1810

• New features and other additions

  • Additional options for heterocycles in MLEstimator #1621

  • Automatic tree generation algorithm implementation completed #1486, #1675, #1848

  • New simulation restart approach using seed mechanisms (old pickle-based method removed) #1641

  • Added new MBSampledReactor type for simulating molecular beam experiments (does not support model generation) #1669

  • Improvements to group additivity thermo estimates for aromatics and sulfur species #1731, #1751

  • Improvements to solvation correction determination with multiple resonance structures #1832

  • Add support for reading and writing extended element syntax in Chemkin NASA polynomials #1636

  • Add support for fitting negative Arrhenius rates (found in MultiArrhenius data) #1834

• Bug fixes

  • Fix numpy rcond usage to restore support for older numpy versions #1670

  • Fix bug with duplicate library reactions when using RMG generated seed mechanisms #1676

  • Move parse_command_line_arguments to facilitate importing in binary package #1717

  • Fix issues with is_identical_to methods of kinetics models #1705

  • Fix cython issue with make_object definitions #1817

  • Fix issue with estimating solvation corrections for radicals #1773

  • Fix parsing of certain types of RMG generated reaction comments #1842

  • Fix identifier generation for surface species using OpenBabel #1842

  • Fix mole fraction normalization for SimpleReactor #1809

  • Fix permissions error when writing seed mechanisms in WSL #1796

  • Fix issue with restarting from job without reaction filters #1847

• Other

  • Improvements to mergeModels.py script #1649

  • Miscellaneous performance improvements #1677, #1765,

  • Raise errors when NaN is encountered in solver #1679

  • Allow sulfur species to have valence 12 in resonance algorithm #1751

  • Add support for maxproc argument to generate_reactions module #1780

  • Display atom index when drawing groups #1758

  • Update sensitivity example #1805

  • Update commented input file #1806

  • Generate reverse reaction recipes in reverse order of the forward recipe #1829

  • Add iodine to Chemkin elements list #1825

  • Remove unnecessary duplicate checking for seed mechanisms #1824

  • Organize examples for running RMG scripts #1840

  • Increase RDKit version requirement to avoid memory leak #1851

  • Logging changes #1721, #1755

  • Documentation updates #1680, #1709, #1767, #1781, #1784, #1807, #1845

Thanks to all contributors: ajocher, alongd, amarkpayne, cgrambow, dranasinghe, hwpang, kspieks, goldmanm, mazeau, mjohnson541, mliu49, oscarwumit, rwest, rgillis8, sarakha, sudoursa, xiaoruiDong, yunsiechung, zjburas

18.6. RMG-database Version 3.0.0

Date: December 16, 2019

• Thermochemistry

  • Add new models for chemprop estimator to replace dde models #351

  • Revamp GAVs for oxygenated sulfur species #360

  • Add polycyclic GAVs for various strained molecules #333

• Kinetics

  • New automatically generated tree for R_Recombination #334, #369

  • Refine root template for 1,2_NH3_elimination #350

  • New DMSOxy kinetics family #360

  • Add DMS related training reactions to H_abstraction #360

• Bug fixes

  • Fix drawing for 2+2_cycloaddition_Cd #345

  • Fix incorrect SMILES in solute database #348

  • Fix incorrect adjacency list for HON in kinetics libraries #350

  • Fix typo in solvent parameters #357

• Miscellaneous

  • Update scripts and IPython notebooks for Python 3 #364

18.7. RMG-Py Version 2.4.1

Date: July 23, 2019

• Bugfixes

  • Improve error handling in NASA as_dict method #1630

  • Fixes to Fluorine atomtypes #1656

  • Fix pressure dependent network generation #1658

  • Add support for reversing PDepArrhenius with MultiArrhenius rates #1659

• Arkane

  • Implement ZPE scaling factor #1619

  • Refactor infrastructure for bond additivity corrections #1605

  • Add frequency scale factors for wb97xd/def2tzvp and apfd/def2tzvpp #1653

  • Fix frequency scale factors in example files #1657

  • Get element counts from conformers #1651

• Miscellaneous

  • Update conda environment files #1623, #1644

  • Output RMS (Reaction Mechanism Simulator) format mechanism files #1629

  • Properly clean up files after running tests #1645

  • Documentation fixes #1650

  • Improve as_dict and make_object by making them recursive #1643

18.8. RMG-Py Version 2.4.0

Date: June 14, 2019

• Heterogeneous catalysis!

  • RMG-cat fork has been merged #1573

    • Introduce SurfaceReactor

    • Thermo estimation for adsorbed species

    • Surface reaction generation and kinetics estimation

  • Introduce Van der Waals bonds (order 0) and quadruple bonds (order 4) #1542

• Arkane

  • Automatically detect rotor symmetry #1526

  • Introduce new YAML files for storing and loading species statmech data #1402, #1551

  • Don’t create species dictionary file if there are no structures #1528

  • Improvements to network explorer tool #1545

  • Improved class inheritance for quantum log file classes #1571

  • Automatic determination of optical isomers and symmetry using symmetry package #1571

  • Parse CCSD(T) energies from Molpro output #1592

  • Automatically determine molecule linearity #1601

  • Determine frequency scaling factor based on geom/freq method rather than sp method #1612

  • Improve logging related to energy barriers #1575

  • Ensure that translational mode is calculated for atoms #1620

• Miscellaneous features

  • New enumerate_bonds method of Molecule to generate dictionary of bond types #1525

  • Introduce RMGObject parent class to support YAML dumping and loading #1402, #1540

  • Add support for fluorine atomtypes #1543

  • Introduce ArrheniusBM class for Blower-Masel kinetics #1461

  • Allow defining and using co-solvents for solvent libraries #1558

  • Introduce strict option to perform isomorphism between species/molecules while ignoring electrons and bond orders #1329

  • Molecule and Species objects can be instantiated by providing SMILES or InChI argument directly, and the identifiers can be accessed via the SMILES and InChI attributes #1329

  • Parallelization has been completely refactored using Python multiprocessing module in replacement of scoop, currently supports parallel reaction generation and QMTP #1459

  • Improvements to usability of uncertainty analysis functionality #1593

• Bug fixes

  • Various fixes for supporting mono-atomic molecules in Arkane #1513, #1521

  • Ensure keras_backend is set consistently #1535

  • Fix handling of disconnected graphs in VF2 isomorphism algorithm #1538

  • Ignore hydrogen bonds when converting to RDKit molecule #1552

  • Other miscellaneous bugs #1546, #1556, #1593, #1600, #1622

• Backward incompatible changes

  • Hydrogen bonds are now order 0.1 (instead of 0) #1542

• New dependencies

  • pyyaml (required) #1402

  • scikit-learn (required) #1461

  • textgenrnn (optional) #1573

• Other

  • Windows binaries are no longer officially supported. The new recommended way to use RMG on Windows computers is via a virtual machine or through the Linux subsystem. See documentation for updated installation instructions. #1531, #1534

  • Documentation updates #1544, #1567

  • Logging/exception improvements #1538, #1562

  • PEP-8 improvements #1566, #1592, #1596

  • Solver output files (png/csv) now report moles instead of mole fractions #1542

  • Replace global RMGDatabase object if the database is reloaded #1565

  • Print ML generated quote upon completion of RMG jobs #1573

  • Infrastructure for automatically generated reaction rate trees #1461

  • Testing related changes #1597, #1599

  • Updates to example Jupyter notebooks #1541, #1593

18.9. RMG-database Version 2.4.0

Date: June 14, 2019

• Heterogeneous catalysis!

  • RMG-cat fork has been merged #309

  • New kinetics families

    • Surface_Adsorption_Single

    • Surface_Adsorption_vdW

    • Surface_Adsorption_Dissociative

    • Surface_Dissociation

    • Surface_Abstraction

    • Surface_Adsorption_Double

    • Surface_Dissociation_vdW

    • Surface_Adsorption_Bidentate

    • Surface_Bidentate_Dissociation

    • Surface_Recombination (deprecated, use Surface_Dissociation instead)

  • New thermo group types

    • adsorptionNi

    • adsorptionPt

  • New thermo libraries

    • surfaceThermoNi

    • surfaceThermoPt

• New kinetics families

  • 1,2_NH3_elimination #326

  • 1,3_NH3_elimination #326

• New kinetics libraries

  • HydrazinePDep #326

• New transport libraries

  • OneDMinN2 #326

• Kinetics training reaction additions

  • 1,2_shiftC #306

  • Intra_R_Add_Endocyclic #306, #258

  • Intra_R_Add_Exocyclic #306, #258, #331

  • Intra_ene_reaction #306

  • R_Addition_COm #306

  • R_Addition_MultipleBond #306, #258

  • R_Recombination #306, #326

  • Intra_H_migration #306

  • H_Abstraction #326

• Kinetics library additions

  • primaryNitrogenLibrary #326

  • Lai_Hexylbenzene #258

• Thermo library additions

  • CBS_QB3_1dHR, thermo_DFT_CCSDTF12_BAC #319

  • primaryNS #326

  • Lai_Hexylbenzene #258

• Thermo group additions

  • ring, polycyclic, radical #258

• Changes

  • [adjlist] kinetics/libraries/Klippenstein_Glarborg2016 #308

  • [labels] thermo/libraries/CBS_QB3_1dHR, Narayanaswamy #306

  • [units] kinetics/libraries/Sulfur/GlarborgMarhsall, Nitrogen_Dean_and_Bozzelli, primaryNitrogenLibrary, primarySulfurLibrary #311

  • [units] R_Addition_MultipleBond/training, R_Recombination/training #312

  • [adjlist] kinetics/libraries/GRI-Mech3.0-N #313

  • [adjlist] thermo/libraries/GRI-Mech3.0-N, GRI-Mech3.0 #313

  • [rates] Disproportionation/training, R_Addition_MultipleBond/training #326

  • [labels] kinetics/libraries/NOx2018 #326

  • [labels, attributes] kinetics/libraries/Nitrogen_Dean_and_Bozelli #326

  • [labels] kinetics/librariesNitrogen_Glarbog_Gimenez_et_al, Nitrogen_Glarborg_Zhang_et_al #326

  • [labels, adjlist] thermo/libraries/BurcatNS #326

  • [labels] thermo/libraries/NOx2018, NitrogenCurran #326

  • [labels] transport/libraries/NOx2018 #326

  • [adjlist] Intra_R_Add_Endocyclic/training #332

  • [value] thermo/groups/ring/12dioxetane #327

  • [adjlist] thermo/libraries/GRI-Mech3.0 #336

  • [value] thermo/libraries/primaryThermoLibrary #338

18.10. RMG-Py Version 2.3.0

Date: Dec 20, 2018

• Arkane (formerly CanTherm):

  • CanTherm had been renamed to Arkane (Automated Reaction Kinetics And Network Exploration)

  • New network exploration functionality using RMG-database

  • Support for all elements has been added for reading quantum output files

  • New supporting information output file with rotational constants and frequencies

  • Known thermo and kinetics can be provided in addition to quantum information

  • Improve general user experience and error handling

• New machine learning thermo estimator

  • Estimate species thermochemistry using a graph convolutional neural network

  • Estimator trained on quantum calculations at B3LYP and CCSD(T)-F12 levels

  • Currently supports C/H/O/N, with an emphasis on cyclic molecules

• Resonance:

  • New pathways added for lone-pair multiple-bond resonance, replacing two pathways which were more specific

  • New pathways added for aryne resonance

  • Aromatic resonance pathways simplified and refactored to use filtration

  • Kekule structures are now considered unreactive structures

• Miscellaneous changes:

  • Isotope support added for reading and writing InChI strings

  • New branching algorithm for picking up feedback loops implemented (beta)

  • Global forbidden structure checking is now only done for core species for efficiency, which may lead to forbidden species existing in the edge

  • Minor improvements to symmetry algorithm to fix a few incorrect cases

• Bug fixes:

  • Fixed issue where react flags were being reset when filterReactions was used with multiple reactors, resulting in no reactions generated

  • File paths for collision violators log changed to output directory

  • Fixed bug in local uncertainty introduced by ranged reactor changes

  • Fixed bug with diffusion limitation calculations for multi-molecular reactions

  • Various other minor fixes

18.11. RMG-database Version 2.3.0

Date: Dec 20, 2018

• Kinetics rules to training reactions

  • All kinetics rules have been converted into training reactions by converting each group to the smallest molecule that matches it

  • Training reactions are preferred over rules because they correspond to a specific reaction and are therefore easier to update

  • This conversion is in anticipation of upcoming changes to trees in kinetics families

• Additions:

  • R_Addition_MultipleBond training reactions

  • intra_NO2_ONO_conversion training reactions

  • SABIC_aromatics thermo library (CBS-QB3, RRHO)

  • McGowan volumes for noble gases

  • More entries added to Lai_Hexylbenzene libraries

  • Architecture and weights for neural network thermo estimator

18.12. RMG-Py Version 2.2.1

Date July 23, 2018

This release is minor patch which fixes a number of issues discovered after 2.2.0.

• Collision limit checking:

  • RMG will now output a list of collision limit violations for the generated model

• Fixes:

  • Ambiguous chemical formulas in SMILES lookup leading to incorrect SMILES generation

  • Fixed issue with reading geometries from QChem output files

  • React flags for reaction filter were not properly updated on each iteration

  • Fixed issue with inconsistent symmetry number calculation

18.13. RMG-Py Version 2.2.0

Date: July 5, 2018

• New features:

  • New ring membership attribute added to atoms. Can be specified in group adjacency lists in order to enforce ring membership of atoms during subgraph matching.

  • Reactors now support specification of T, P, X ranges. Different conditions are sampled on each iteration to optimally capture the full parameter space.

  • New termination type! Termination rate ratio stops the simulation when the characteristic rate falls to the specified fraction of the maximum characteristic rate. Currently not recommended for systems with two-stage ignition.

  • New resonance transitions implemented for species with lone pairs (particularly N and S containing species). A filtration algorithm was also added to select only the most representative structures.

  • Formal support for trimolecular reaction families.

  • New isotopes module allows post-processing of RMG mechanisms to generate a mechanism with isotopic labeling.

• Changes:

  • Library reactions can now be integrated into RMG pdep networks if the new elementary_high_p attribute is True

  • Library reactions may be duplicated by pdep reactions if the new allow_pdep_route attribute is True

  • Jupyter notebook for adding new training reactions has been revamped and is now located at ipython/kinetics_library_to_training.ipynb

  • Syntax for recommended families has changed to set notation instead of dictionaries, old style still compatible

  • Ranking system for database entries expanded to new 0-11 system from the old 0-5 system

  • Collision limit checking has been added for database entries

• Cantherm:

  • Improved support for MolPro output files

  • Added iodine support

  • Automatically read spin multiplicity from quantum output

  • Automatically assign frequency scale factor for supported model chemistries

  • Plot calculated rates and thermo by default

  • New sensitivity analysis feature analyzes sensitivity of reaction rates to isomer/TS energies in pdep networks

• Fixes:

  • Properly update charges when creating product templates in reaction families

  • Excessive duplicate reactions from different resonance structures has been fixed (bug introduced in 2.1.3)

  • Fixed rate calculation for MultiPdepArrhenius objects when member rates have different plists

• A more formal deprecation process is now being trialed. Deprecation warnings have been added to functions to be removed in version 2.3.0:

  • All methods related to saving or reading RMG-Java databases and old-style adjacency lists

  • The group additivity method for kinetics estimation (unrelated to thermo group additivity)

  • The saveRestartPeriod option and the old method of saving restart files

18.14. RMG-database Version 2.2.0

Date: July 5, 2018

• Additions:

  • New Intra_R_Add_Exo_Scission reaction family

  • New 1,2_ShiftC reaction family

  • New reaction families for peroxide chemistry in liquid systems

    • Korcek_step1_cat

    • Bimolec_Hydroperoxide_Decomposition

    • Peroxyl_Termination

    • Peroxyl_Disproportionation

    • Baeyer-Villiger_step1_cat

    • Baeyer-Villiger_step2

    • Baeyer-Villiger_step2_cat

  • Numerous new training reactions added to many families

• Changes:

  • New tree structure for Intra_R_Add_Endocyclic with consideration for cyclic species

  • Multiple bond on ring is no longer allowed in Intra_R_Add_Exocyclic and should react in Intra_R_Add_Endocyclic instead

  • Entry ranks rescaled to new 0-11 ranking system

  • Global forbidden structures has been cleaned up, leading to significant performance improvement

• Fixes:

  • Corrected shape indices in NOx2018 transport library

  • Removed or corrected some kinetics entries based on collision limit check

18.15. RMG-Py Version 2.1.9

Date: May 1, 2018

• Cantherm:

  • Atom counts are no longer necessary in input files and are automatically determined from geometries

  • Custom atom energies can now be specified in input files

  • Removed atom energies for a few ambiguous model chemistries

  • Add atom energies for B3LYP/6-311+g(3df,2p)

• Changes:

  • Refactored molecule.parser and molecule.generator modules into molecule.converter and molecule.translator to improve code organization

  • SMILES generation now outputs canonical SMILES

  • Molecule.sortAtoms method restored for deterministic atom order

  • PDep reactions which match an existing library reaction are no longer added to the model

• Fixes:

  • Fix issue with reaction filter initiation when using seed mechanisms

18.16. RMG-database Version 2.1.9

Date: May 1, 2018

• Chlorine:

  • New Chlorinated_Hydrocarbons thermo library

  • Added group additivity values and long distance corrections for chlorinated species

  • Added chlorine groups and training reactions to H_Abstraction

• Additions:

  • New NOx2018 kinetics, thermo, and transport libraries

  • New N-S_interactions kinetics library

  • New SulfurHaynes thermo library

  • Added species to SOxNOx thermo library from quantum calculations

• Other changes:

  • Renamed NOx and SOx kinetics libraries to PrimaryNitrogenLibrary and PrimarySulfurLibrary

  • S2O2, SOO2, SO2O2, and N2SH were globally forbidden due to inability to optimize geometries

• Fixes:

  • Corrected some A-factor units in Nitrogen_Dean_and_Bozzelli kinetics library

18.17. RMG-Py Version 2.1.8

Date: March 22, 2018

• 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

18.18. RMG-database Version 2.1.8

Date: March 22, 2018

• Changes:

  • Corrected name of JetSurf2.0 kinetics and thermo libraries to JetSurf1.0

  • Added actual JetSurf2.0 kinetics and thermo libraries

  • Updated thermo groups for near-aromatic radicals, including radical and polycyclic corrections

18.19. RMG-Py Version 2.1.7

Date: February 12, 2018

• 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

18.20. RMG-database Version 2.1.7

Date: February 12, 2018

• Charged atom types:

  • Update adjlists with new atom types across the entire database

  • Added sulfur groups to all relevant kinetics families

  • New thermo group additivity values for sulfur/oxygen species

• Additions:

  • Benzene bonds can now react in in R_Addition_MultipleBond

  • Many new training reactions and groups added in R_Addition_MultipleBond

  • New Singlet_Val6_to_triplet kinetics family

  • New Sulfur GlarborgBozzelli kinetics and thermo libraries

  • New Sulfur GlarborgMarshall kinetics and thermo libraries

  • New Sulfur GlarborgH2S kinetics and thermo libraries

  • New Sulfur GlarborgNS kinetics and thermo libraries

  • New NOx and NOx/LowT kinetics libraries

  • New SOx kinetics library

  • New BurcatNS thermo library

  • New SOxNOx thermo library

  • New 2+2_cycloaddition_CS kinetics family

  • New Cyclic_Thioether_Formation kinetics family

  • New Lai_Hexylbenzene kinetics and thermo libraries

• Changes:

  • 1,2-Birad_to_alkene family is now irreversible

  • OxygenSingTrip kinetics library removed (replaced by Singlet_Val6_to_triplet family)

  • Ozone is no longer forbidden

• Fixes:

  • Corrected adjlist for phenyl radical in JetSurf2.0 and USC-Mech-ii

  • Some singlet thermo groups relocated from radical.py to group.py

18.21. RMG-Py Version 2.1.6

Date: December 21, 2017

• 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

18.22. RMG-database Version 2.1.6

Date: December 21, 2017

• Additions:

  • New training reactions added for [NH2] related H_Abstractions

  • 14 new kinetics libraries related to aromatics formation (see RMG-database #222 for details)

• Other changes:

  • Removed some global forbidden groups which are no longer needed

  • Forbid CO and CS biradicals

  • Updated lone_electron_pair_bond family and removed from recommended list

• Fixes:

  • Fixed unit errors in some H_Abstraction and R_Addition_MultipleBond depositories

18.23. RMG-Py Version 2.1.5

Date: October 18, 2017

• 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

18.24. RMG-database Version 2.1.5

Date: October 18, 2017

• Additions:

  • New thermo groups added for species relevant in cyclopentadiene and natural gas pyrolysis

  • Added C2H4+O_Klipp2017 kinetics library

• Fixes:

  • Prevent charged carbenes from reacting in Singlet_Carbene_Intra_Disproportionation

  • Updated H_Abstraction rates in ethylamine library and corresponding training reactions

18.25. RMG-Py Version 2.1.4

Date: September 08, 2017

• 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

18.26. RMG-database Version 2.1.4

Date: September 08, 2017

• New kinetics families for propargyl recombination route to benzene:

  • Singlet_Carbene_Intra_Disproportionation

  • Intra_5_membered_conjugated_C=C_C=C_addition

  • Intra_Diels_alder_monocyclic

  • Concerted_Intra_Diels_alder_monocyclic_1,2_shift

  • Intra_2+2_cycloaddition_Cd

  • Cyclopentadiene_scission

  • 6_membered_central_C-C_shift

• Renamed kinetics families:

  • Intra_Diels_Alder –> Intra_Retro_Diels_alder_bicyclic

  • H_shift_cyclopentadiene –> Intra_ene_reaction

• Other additions:

  • Klippenstein_Glarborg2016 kinetics and thermo libraries

  • Group additivity values added for singlet carbenes, which are no longer forbidden

18.27. RMG-Py Version 2.1.3

Date: July 27, 2017

• 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

18.28. RMG-database Version 2.1.3

Date: July 27, 2017

• Long-distance interaction thermo corrections:

  • The gauche and int15 group files have been replaced by longDistanceInteraction_noncyclic

  • New corrections for cyclic ortho/meta/para interactions are now available in longDistanceInteraction_cyclic

• Changes:

  • Oa_R_Recombination family renamed to Birad_R_Recombination

  • More training reactions added for sulfur species in H_Abstraction

  • RMG-database tests have been moved to RMG-Py

18.29. RMG-Py Version 2.1.2

Date: May 18, 2017

• 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

18.30. RMG-database Version 2.1.2

Date: May 18, 2017

• Nitrogen improvements:

  • Added ethylamine kinetics library

  • Updated group additivity values for nitrogen species

  • Added rate rules and training reactions for nitrogen species

• Additions:

  • New CO_Disproportionation family

  • Added CurranPentane kinetics and thermo libraries

• Fixes:

  • Corrected some rates in FFCM1(-) to use MultiArrhenius kinetics

  • Corrected a few adjlists in FFCM1(-)

18.31. RMG-Py Version 2.1.1

Date: April 07, 2017

• 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]

18.32. RMG-database Version 2.1.1

Date: April 07, 2017

• Additions:

  • More species added to FFCM1(-) thermo library

• Changes:

  • Improved handling of excited species in FFCM1(-) kinetics library

  • Replaced Klippenstein H2O2 kinetics and thermo libraries with BurkeH2O2inN2 and BurkeH2O2inArHe

• Fixes:

  • Corrected adjlists for some species in JetSurf2.0 kinetics and thermo libraries (also renamed from JetSurf0.2)

  • Correct multiplicities for [C] and [CH] in multiple libraries ([C] from 5 to 3, [CH] from 4 to 2)

18.33. RMG-Py Version 2.1.0

Date: March 07, 2017

• 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

18.34. RMG-database Version 2.1.0

Date: March 07, 2017

• Several new kinetics libraries added

  • FFCM-1

  • JetSurF 0.2

  • Chernov_aromatic_only

  • Narayanaswamy_aromatic_only

  • 1989_Stewart_2CH3_to_C2H5_H

  • 2005_Senosiain_OH_C2H2

  • 2006_Joshi_OH_CO

  • C6H5_C4H4_Mebel

  • c-C5H5_CH3_Sharma

• Several new thermochemistry libraries added

  • FFCM-1

  • JetSurF 0.2

  • Chernov_aromatic_only

  • Narayanaswamy_aromatic_only

• Improved kinetics tree accessibility

  • adds database tests ensuring groups in the tree to be accessible

  • improves definitions of group structures in the kinetics trees to ensure accessibility

• New oxygenates thermo groups are added based Paraskeva et al.

• Improved database tools

  • convertKineticsLibraryToTrainingReactions.ipynb now can visualize groups of matched rate rules that training reactions hit

  • exportKineticsLibrarytoChemkin.py and importChemkinLibrary.py add more logging information on reaction sources

18.35. RMG-Py Version 2.0.0

Date: September 16, 2016

This release includes several milestones of RMG project:

• 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

18.36. RMG-database Version 2.0.0

Date: September 16, 2016

In conjunction with the release of RMG-Py v2.0.0, an updated package for the RMG-database has also been released. This release brings some new additions and fixes:

• Polycyclic thermochemistry estimation improved:

  • polycyclic database reorganized and more entries added in systematic way (input.thermo.groups.polycyclic)

• Database entry accessibility tests:

  • Fixes existing inaccessible entries in solvation/statmech/thermo of RMG-database

18.37. RMG-Py Version 1.0.4

Date: March 28, 2016

• Cantera support in RMG (rmgpy.tools.canteraModel):

  • Provides functions to help simulate RMG models using Cantera.

  • Has capability to generate cantera conditions and convert CHEMKIN files to cantera models, or use RMG to directly convert species and reactions objects to Cantera objects.

  • Demonstrative example found in ipython/canteraSimulation.ipynb

• Module for regression testing of models generated by RMG (rmgpy.tools.observableRegression):

  • Helps identify differences between two versions of models generated by RMG, using the “observables” that the user cares about.

• Automatic plotting of simulations and sensitivities when generating models (rmgpy.tools.plot):

  • Contains plotting classes useful for plotting simulations, sensitivities, and other data

  • Automatic plotting of simulations in the job’s solver folder when saveSimulationProfiles is set to True in the input file.

  • Sensitivities for top 10 most sensitivie reactions and thermo now plotted automatically and stored in the solver folder.

• Improved thermochemistry estimation (mostly for cyclics and polycyclics)

  • Add rank as an additional attribute in thermo database entries to determine trustworthiness

• Bug fixes:

  • Training reactions now load successfully regardless of generateSpeciesConstraints parameters

  • Transport data is now saved correctly to CHEMKIN tran.dat file and also imports successfully

  • Fixes appending of reactions to CHEMKIN file when reaction libraries are desired to be appended to output

  • Fixes writing of csv files for simulation and sensitivity results in Windows

  • Fixes Reaction.draw() function to draw the entire reaction rather than a single species

18.38. RMG-Py Version 1.0.3

Date: February 4, 2016

This mini release contains the following updates:

• Pdep convergence issues in RMG-Py v1.0.2 are now fixed.

• RMG-database version information and anaconda binary version information is now recorded in RMG log file.

18.39. RMG-Py Version 1.0.2

Date: January 29, 2016

This new release adds several new features and bug fixes.

• Windows users can rejoice: RMG is now available in binary format on the Anaconda platform. Building by source is also much easier now through the Anaconda managed python environment for dependencies. See the updated Installation Page for more details

• Reaction filtering for speeding up model generation has now been added. It has been shown to speed up model convergence by 7-10x. See more details about how to use it in your RMG job here. Learn more about the theory and algorithm on the Rate-based Model Enlarging Algorithm page.

• The RMG native scripts are now organized under the rmgpy.tools submodule for developer ease and better extensibility in external scripts.

• InChI conversion is now more robust for singlets and triplets, and augmented InChIs and InChI keys are now possible with new radical electron, lone pair, and multiplicity flags.

• Output HTML for visualizing models are now cleaned up and also more functional, including features to display thermo comments, display enthalpy, entropy, and free energy of reaction, as well as filter reactions by species. You can use this new visualization format either by running a job in RMG v1.0.2 or revisualizing your CHEMKIN file and species dictionary using the visualization web tool.

18.40. RMG-database Version 1.0.2

Date: January 29, 2016

In conjunction with the release of RMG-Py v1.0.2, an updated package for the RMG-database has also been released. This release brings some new additions and fixes:

• New group additivity values for oxitene, oxerene, oexpane, and furan ring groups

• Improvements to sulfur chemistry:

  • Restructuring of radical trees in the kinetics families SubstitutionS and intra_substitutionCS_cyclization

  • A reaction library for di-tert-butyl sulfide

• Improvements for the R_Addition_Multiple_Bond kinetics family through new rate rules for the addition of allyl radical to double bonds in ethene, propene, and butene-like compounds, based on CBS-QB3 estimates from K. Wang, S.M. Villano, A.M. Dean, “Reactions of allylic radicals that impact molecular weight growth kinetics”, PCCP, 6255-6273 (2015).

• Several new thermodynamic and kinetics libraries for molecules associated with the pyrolysis of cyclopentadiene in the presence of ethene, based off of calculations from the paper A.G. Vandeputte, S.S. Merchant, M.R. Djokic, K.M. Van Geem, G.B. Marin, W. H. Green, “Detailed study of cyclopentadiene pyrolysis in the presence of ethene: realistic pathways from C5H5 to naphthalene” (2016)