Recent Releases of reactionmechanismgenerator

reactionmechanismgenerator - RMG-Py v3.3.0

Releases:

Source code on GitHub. git clone --branch v3.3.0 --depth 1 https://github.com/ReactionMechanismGenerator/RMG-Py.git
Conda binaries on CondaForge. conda create --name rmg_330 'rmg::rmg==3.3.0'
Docker on DockerHub docker pull reactionmechanismgenerator/rmg:3.3.0

What's Changed

Software Improvements

RMG-Py Itself

Python 3.9 by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2741
Removing the excessive debug comment by @MichaelGeuking in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2102
Conversion from nose to pytest by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2516
Modified main.py script to include TROE reactions in the violators log by @PoojaNem in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2614
Replace a few packages maintained by us to their conda-forge version by @xiaoruiDong in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2624
Switch muq, lpsolve55, and RingDecomposerLib from rmg to conda-forge by @jonwzheng in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2671
environment.yml Unblocking Python 3.11 - rdkit to conda-forge channel, remove chemprop for now by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2553
Make chemkin read of transport and thermo files more robust by @sevyharris in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2643
Add documentation about speciesCuttingThreshold by @donerancl in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2601
Fix Failing Joback Method Unit Test by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2682
Load a kinetic library not in the RMG database by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2663
Draw reversible arrow if reaction is reversible by @sevyharris in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2693
Ignore more example output files in git. by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2822
Make RMG-Py conda Work Again :tada: by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2820
fix typos by @KnathanM in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2670
update user and developer installation instructions to point towards miniforge by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2719
Add and improve to_cantera methods for conversion to in-memory Cantera objects by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2700
Add details to thermo comments. by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2788
A note about installing developer version from Docker. by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2806

Bug Fixes

When loading all reaction libraries, only process "reactions.py" files. by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2513
Fix pytest Discovery Bug (FooTest vs. TestFoo), Add Missing Tests, Fix Generator Tests by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2525
Minor: Added quotation marks to Pt111 in the docs by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2529
Fix Failing CI because of cclib by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2535
Update RMSE/MAE average formula for BAC cross validation by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2538
Fix a logical short circuit in a test expression by @munahaf in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2542
FIX: Updated logical expression to remove short circuit by @fazledyn-or in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2555
Fix CC smiles by @xiaoruiDong in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2545
changing forbidden groups documentation by @Nora-Khalil in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2561
exempt announcements from being closed as stale by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2565
Update uncertainty SI when averaging ThermoData by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2589
Julia restriction by @calvinp0 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2609
changed typo from pydas.daspk to pydas.dassl #2070 by @Julian-Ufert in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2615
restrict newer versions of cclib by @ChrisBNEU in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2638
Remove duplicated test data directory by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2644
FIx Handling of Initial Species with Seed Mechanisms by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2653
add check for all zeros in thermo comparison by @sevyharris in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2658
Better debugging messages for database errors. by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2661
Send P in SI units to Chebyshev.fittodata() when reversing a rate by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2662
Draw Hydrogen bonds (again) by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2734
Fix library reaction barrier heights for linear scaling by @sevyharris in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2729
Fix database issues with loading new kinetic libraries by @jonwzheng in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2753
Update comment parser for autogen trees by @sevyharris in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2787

New Features (and their fixes)

Electrochemistry :tada:

Electrochemistry! (finally) a.k.a. RMG-electrocat by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2598
Fix bug in electrons initialization for depository reaction data by @jonwzheng in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2775

Automated Fragment Modeling

Remove label in adjlist before detecting cutting label by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2519
Add regression input file for fragment + simple reactor and regression test for fragment + RMS reactor by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2571
Compatibility of regression.py with fragment by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2574
fragment.py: refactoring, patches, and compatibility with RMS by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2413
Add Fragment Reattachment Example Notebook by @donerancl in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2585
Fix Fragment Resonance Structure Bug by @donerancl in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2647
Fix AFM fragment crash in LiquidReactor by @Kyamaguchi16 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2813

Surface Catalysis

Doc surf rxns by @ChrisBNEU in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2497
correcting bidentate adsorption rate constant by @bjkreitz in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2533
fix Kc for bidentate rxns by @bjkreitz in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2554
Group Structures for Complex Surface Representations by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2618
Patch for surface regression diffmodels by @sevyharris in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2656
Add surface combustion example for regression testing by @sevyharris in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2514
adding resonance for adsorbates by @bjkreitz in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2511

AECs and BACs

Allow user to plot correlation matrix for AECs by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2550

Arkane

Add keyword "HF=" to parse electronic energy by @JintaoWu98 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2586
resolved issue #2266 by @Julian-Ufert in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2651
Allow scratch dir as input for arkane symmetry calculation by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2691
Change method for loading energies from Gaussian log files to regex search to avoid errors by @donerancl in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2595
updating 'rotconsts' ref to be compatible with cclib v1.8+ by @ChrisBNEU in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2639
Process monoatomic molecules in Arkane's Orca ESS adapter by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2709
Parse RS2C (CASPT2) energy in Molpro by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2711
Fxi UnboundLocalError: local variable 'eelectronicwith_corrections' referenced before assignment by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2756
Fix rotational constants in Gaussian files listing ****s by @sevyharris in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2761
Orca parser fixup by @kfir4444 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2739
Molpro f12a by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2771
Fix CCSD(T)-F12 energy parsing by @shihchengli in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2816

Deprecations

Remove kinetic group additivity methods from code and documentation by @jonwzheng in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2612
Clean up some code for calculating degeneracy in kinetics codebase by @jonwzheng in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2632
Remove Wiki and gitter from README by @jonwzheng in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2762
[Docs] Update outdated docs, wiki, and contributor guidelines by @jonwzheng in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2703

Continuous Integration

Fix CI workflow to function on forked pushes. by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2515
Tweak annotation workflow name. by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2517
Instruct Docker, Github Actions, and users to use 'for_rmg' branch of RMS by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2523
update docker usage instructions to point to v3.2.0 by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2522
Switch back to RMS main in CI by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2552
Change Documentation Build Action to use github-actions bot instead of RMG_dev by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2599
fix checkout command for docs building action by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2602
Continuous Integration, Documentation Build, and Dockerfile Fixes by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2608
Continued docs build fixes by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2610
documentation builder bug fixes and general overhaul by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2621
GitHub Actions Maintenance by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2628
github actions CI maintainence by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2669
Remove default Channel from environment.yml by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2712
Patch minimal_surface Regression Test by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2674
Change CI to use Miniforge3 instead of Mambaforge by @ssun30 in https://github.com/
Deprecate the nomkl mutex metapackage by @ssun30 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2723
Changed Dockerfile to use Miniforge3 by @ssun30 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2724ReactionMechanismGenerator/RMG-Py/pull/2718
Update CI artifact actions to v4 and fix runner glitch by @jonwzheng in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2748
require a more recent version of mkl for Cantera by @sevyharris in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2766
Fix the CI regression logging; make Julia optional via environment and module variables. by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2802
Lazy loading of Julia things by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2804
Docker build updates by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2808

New Contributors

@munahaf made their first contribution in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2542
@MichaelGeuking made their first contribution in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2102
@fazledyn-or made their first contribution in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2555
@bjkreitz made their first contribution in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2554
@JintaoWu98 made their first contribution in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2586
@donerancl made their first contribution in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2585
@PoojaNem made their first contribution in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2614
@Julian-Ufert made their first contribution in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2615
@KnathanM made their first contribution in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2670
@ssun30 made their first contribution in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2718
@Kyamaguchi16 made their first contribution in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2813
@shihchengli made their first contribution in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2816

Full Changelog: https://github.com/ReactionMechanismGenerator/RMG-Py/compare/3.2.0...3.3.0

- Python
Published by JacksonBurns 7 months ago

reactionmechanismgenerator - RMG-Py v3.2.0

A note about timing and binaries: Release 3.2.0 was tagged in commit e60d3467f444f12f7b6d5bbca43d724f895d112b on August 8, 2023. Conda binaries were never built for it (we couldn't) but it was released via DockerHub and can be accessed by docker pull reactionmechanismgenerator/rmg:3.2.0. The corresponding "release" was not made on the GitHub platform until July 15, 2025, almost 2 years later.

What's changed

Release notes written manually in 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 generateresonancestructures 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 getreactthermo 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 togroup 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 SurfaceDissociationtoBidentate 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 getpartitionfunction 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 IntraRAddEndocyclic and IntraRAddExocyclic
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 gettrainingset 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 getw0 where adict 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 addatomlabelsforreaction mislabels reactants if family is its own reverse
- Fixed bug where savetrainingreactions 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 generateresonancestructure does not preserve atom when keepisomorphic=False and saveorder=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 loadchemkinfile 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 countinternalrotors and isatomin_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 loadtransportfile 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 testidentifyingmissing_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 stableregressionresults 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 getallsolute_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 addrulesfromtraining and fillrulesbyaveraging_up
- Added warning to not to call addrulesfromtraining and fillrulesbyaveraging_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

What's Changed

Summary of pull requests generated automatically by GitHub. * halogen additions (simultaneous update with DB) by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/1997 * Halogens transport by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2114 * Primary thermo library - unit test change by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2123 * Only publish documentation from official fork by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2111 * Halogens thermo - missing group test by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2120 * fix RMG-Py 3.1.0 release note bullet formatting by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2127 * Upgrade solvation thermo GAV by @yunsiechung in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2112 * Catch Bad Conformer ID error from rdkit by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2130 * check multiplicity of reverse products if the family template reactants have multiplicity constraints (vdW groups) by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2131 * an empty surface site template group should only match an empty surface site by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2129 * optionally generate_resonance_structures when loading species dicts by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2126 * Allow RMS to output surface mechanisms and bugfixes by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2075 * Remove fileformat kwarg from plt.savefig by @amarkpayne in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2143 * Have WSL users install graphviz system wide by @amarkpayne in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2144 * Automatic Tree Generation part 5 by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2139 * Cat fixes - vdw radicals, bidentates, resonance by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2136 * Some fixes to documentation (and a CI test) by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2132 * Fix QM Parsers by @kspieks in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2137 * fixups in `gettrainingset` family method by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2153 * Assorted Tree Generation Support by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2155 * Fix spc doesn't have metal attribute error by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2156 * Use autoGenerated tag instead of the hardcoded family list by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2157 * Added a saveorder attribute to some methods, and make sure it is properly being passed around by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2162 * Twin RP for merged all 2+2 cycloaddition families by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/1974 * Decay Framework by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2076 * Forming surface bonds by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2173 * Adsorption corrections multidentate by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2169 * Some miscellaneous fixes by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2168 * Making Mopac calculations more robust by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2177 * Minor change to get_all_solute_data function. by @yunsiechung in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2174 * Load chemkin bug fix - extended elements and digits by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2181 * Added additional features to preserve atom order and template labels when generating reactions by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2182 * Adding in coverage dependent effects to surface kinetics by @mazeau in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2090 * Update documentation to reflect additions in RMG-database by @kspieks in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2175 * change to the documentation, added openSUSE installation instructions by @kfir4444 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2192 * Handle string data properly when averaging children solute by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2193 * autogen trees with halogens by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2178 * a_dict bugfix in get_w0 by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2186 * Enabling use of pyrms for RMG Simulations and Edge Analysis by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2164 * Pyrms Reactor Bugfixes and Liquid-Surface Reactor for RMG Electrocat by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2197 * Pdep bugfix - removing edge species by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2200 * Use python-jl for running RMG-Py by @amarkpayne in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2212 * Update ketoenol template image to 1,3 sigmatropic rearrangement by @kspieks in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2219 * Fixing the link to Gri-mesh by @ProfLeao in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2209 * Changes related to ATG Peroxyl Disproportionation family by @xiaoruiDong in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2220 * Forbidden structs in input by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2185 * Family atom labels by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2216 * Ctc atomtype by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2170 * Minor changes to rotor related functions by @xiaoruiDong in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/1980 * Update reaction family images to reflect the merged 2+2cycloaddition by @kspieks in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2226 * Fix RMS Object Construction by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2208 * Fix atom order issue in generateresonancestructure by @xiaoruiDong in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2229 * Remove stale template matching for Bimolec hydroperoxide decomposition by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2232 * Check for two-parameter Troe reaction when converting to Cantera by @sevyharris in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2231 * Add licensing information to the README file by @yunsiechung in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2234 * Documentation updates for developer install and update by @mefuller in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2224 * halogen longdistancenoncyclic in cycle interaction by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2235 * Halogens pdep by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2195 * Allow ArrheniusBM Fitting up to 2000K for RMG-database Rate Trees by @kspieks in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2243 * Psi4 is back by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2257 * Update missing group test now that data is added for the original missing group by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2255 * BugFix: Draw CO as 'CO' by @xiaoruiDong in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2260 * give integer num of points to linspace by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2263 * Add commit strings for RMG-Py and RMG-database by @kspieks in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2269 * Convert a ThermoData object to a NASA object instance for RMS by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2258 * Mol to group with atom labels by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2158 * added method to write rate const to HTML for sticking rxns by @ChrisBNEU in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2140 * BAC parameter confidence intervals by @cgrambow in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/1969 * Change rmgrc to a template file by @amarkpayne in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2273 * BAC cross-validation by @cgrambow in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/1968 * More robust conformer embed in QM module by @xiaoruiDong in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2272 * Handle core/edge species/reactions for phase system correctly by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2252 * Cantera issue in regression testing by @ChrisBNEU in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2271 * Add Nitrogen groups to transport by @yunsiechung in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2274 * Several Arkane Torsion (Rotor) related changes by @xiaoruiDong in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2268 * reminder to activate env before making tests by @kfir4444 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2281 * remove check for adsorbate getting adsorbed again by @ChrisBNEU in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2285 * CSTR with vapor liquid mass transfer by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2194 * Add tests to check num of reactant and product defined in ATG rate rules by @xiaoruiDong in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2297 * Correct ATG rate rules initialization by @xiaoruiDong in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2299 * Fix loadchemkinfile read of surface species by @sevyharris in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2276 * merge AFM code into RMG-Py by @lily90502 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2060 * Skip number of products check for ATG tree by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2306 * Add atom props to _reduce__ by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2308 * Primary H2O2 by @josemvdh in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2291 * Fix neg freq qchem parser by @kspieks in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2319 * Added a readme file for Arkane by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2320 * Pressure Dependence Improvements by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2315 * Added an instruction on how to fix ImportError for rmg binary by @yunsiechung in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2327 * Fix resonance save order by @xiaoruiDong in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2329 * Add Arkane unit tests by @kspieks in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2330 * update developer installation instructions to use the main rms branch by @ChrisBNEU in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2305 * Allow RMG to load thermo or kinetic libraries from a file by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2340 * Save the actual reaction label when creating a reaction library in Arkane by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2345 * Added Arkane examples by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2349 * Add the RMG-database paper to the citation info by @yunsiechung in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2351 * Transitory Edge Analysis by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2317 * Add bib file by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2357 * Pdep Explorer Multinetwork fixes by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2358 * importing pyrms and diffeqpy during a debug session by @calvinp0 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2364 * Ci with mamba by @kfir4444 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2377 * Minor: Update group attribute name to py3 by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/1979 * update doc workflow, was failing bc 'uses' was incorrect by @ChrisBNEU in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2387 * Added 'r' at the start of regex pattern strings where it was missing by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2396 * Solving the 'Fragment' object has no attribute 'countinternalrotors' error by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2395 * 'Fragment' object has no attribute 'isatomincycle' error by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2400 * Add radical flux tolerance by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2368 * add comment as input to RMS reaction and species object by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2403 * Improve kH estimation code by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2389 * Adapt change in RMS to use keyword variables by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2408 * Should be name, not label by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2409 * Move Regression Testing in to the CI by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2390 * accidentally used changes from an experimental local branch, revert by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2410 * simplify condition checking for scheduled vs pushes CI by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2411 * Correct Troe kinetics formula by @xiaoruiDong in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2398 * CI: don't make destination directory for reference results when generating reference results by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2412 * Set Keq=inf for irreversible reactions. by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2399 * Updates to RMG-Py installation instructions documentation by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2414 * Fix Incorrect Rendering in RMG-Py Installation Documentation by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2416 * Added Arkane citation info by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2418 * Modified assertion in thermodata.pyx by @NellyMitnik in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2420 * use conda-forge ncurses instead of default by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2421 * fix typo in reactors.py by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2422 * [Move to Docker]: Add Dockerfile, update installation instructions, add automatic image builds to CI by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2424 * fix typo in updated docker installation docs by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2426 * Calculate x only when semiclassical corrections are needed by @kfir4444 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2425 * Cantera version 2.6 by @ChrisBNEU in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2288 * Upgrade to OpenMOPAC by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2417 * Fix documentation View Source links by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2430 * [Regression Testing]: Small changes to CI.yml to allow testing on Forks by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2431 * Make 'test' a phony target in Makefile by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2433 * Update list of developers by @kspieks in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2419 * Add jupyter notebook to simulate and analyze superminimal & change docker instruction by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2434 * [Documentation]: point users to a specific version of RMG rather than latest by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2432 * Fix Documentation Build by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2436 * Change variables from cpdef to cdef in cython. by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2438 * Deadend radical species selection RMG-RMS Twin PR by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2388 * Test that we can make a sample molecule for every atom type. by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/1661 * transport warning for undefined species in loadtransportfile by @Nora-Khalil in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2427 * CI.yml and environment.yml updates to run CI on MacOS and Ubuntu by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2415 * Update/Add example notebooks based on RMG Training updates by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2439 * Fix our use of pyjulia so we can use the conda-forge version. by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2444 * Allow auxilary keywords in an Arkane species YAML file by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2447 * Fix documentation errors (and CI testing) by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2448 * Improve conda installation instructions by @mefuller in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2246 * Adding halogens kinetics (twin with DB) by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2135 * Trying to fix CI see issue #2455 by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2456 * Relax tolerances when testing HinderedRotor.getenthalpy() by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2457 * [Docker]: add linux patch step for libstdcxx-ng<13 by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2458 * Add regression test for RMS reactor by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2446 * Regression testing updates by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2459 * Enable Metal, Facet, site and terrace specification in Molecule by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2452 * Revert libstdcxx-ng Patches in CI, Docs, and Dockerfile by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2469 * Fix docker instruction by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2471 * Reducing Docker Size by @calvinp0 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2437 * allow the CI to be called from other repos in the organization by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2472 * Getting the regression tests to work by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2473 * Cleaning up the RMG-Py GitHub with a robot by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2474 * Surface diff fixup by @ChrisBNEU in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2335 * Small fix for explorer tool by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2374 * Allow colons and periods in chemkin species names by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/1923 * Increase allowed length of species labels for chemkin output. by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2454 * minor changes to CI to fix reusable workflow by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2494 * A collection of Matt and David's commits from #2316 by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2491 * Make the Continuous Integration Pass by Default by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2500 * Limit aromaticity perception for strained polycyclics by @mliu49 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/1732 * Expand the regression test annotations. by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2501 * Fix a bug in the CI workflow by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2505 * More github workflow improvements by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2506 * Don't replace PDep kinetics of a library reaction by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2466 * remove reusable workflow logic, make RMGDATABSEBRANCH file-scoped by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2512

New Contributors

@ProfLeao made their first contribution in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2209
@josemvdh made their first contribution in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2291
@NellyMitnik made their first contribution in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2420

Full Changelog: https://github.com/ReactionMechanismGenerator/RMG-Py/compare/3.1.0...3.2.0

- Python
Published by rwest 7 months ago

reactionmechanismgenerator - RMG-Py v3.1.1

`RMG-Py` v3.1.1

This release of RMG contains a number of changes (listed below) and coincides with a switch to Docker for deployment. Check the update installation instructions here.

What's Changed

halogen additions (simultaneous update with DB) by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/1997
Halogens transport by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2114
Primary thermo library - unit test change by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2123
Only publish documentation from official fork by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2111
Halogens thermo - missing group test by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2120
fix RMG-Py 3.1.0 release note bullet formatting by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2127
Upgrade solvation thermo GAV by @yunsiechung in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2112
Catch Bad Conformer ID error from rdkit by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2130
check multiplicity of reverse products if the family template reactants have multiplicity constraints (vdW groups) by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2131
an empty surface site template group should only match an empty surface site by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2129
optionally generate_resonance_structures when loading species dicts by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2126
Allow RMS to output surface mechanisms and bugfixes by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2075
Remove file_format kwarg from plt.savefig by @amarkpayne in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2143
Have WSL users install graphviz system wide by @amarkpayne in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2144
Automatic Tree Generation part 5 by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2139
Cat fixes - vdw radicals, bidentates, resonance by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2136
Some fixes to documentation (and a CI test) by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2132
Fix QM Parsers by @kspieks in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2137
fixups in get_training_set family method by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2153
Assorted Tree Generation Support by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2155
Fix spc doesn't have metal attribute error by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2156
Use autoGenerated tag instead of the hardcoded family list by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2157
Added a save_order attribute to some methods, and make sure it is properly being passed around by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2162
Twin RP for merged all 2+2 cycloaddition families by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/1974
Decay Framework by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2076
Forming surface bonds by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2173
Adsorption corrections multidentate by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2169
Some miscellaneous fixes by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2168
Making Mopac calculations more robust by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2177
Minor change to get_all_solute_data function. by @yunsiechung in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2174
Load chemkin bug fix - extended elements and digits by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2181
Added additional features to preserve atom order and template labels when generating reactions by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2182
Adding in coverage dependent effects to surface kinetics by @mazeau in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2090
Update documentation to reflect additions in RMG-database by @kspieks in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2175
change to the documentation, added openSUSE installation instructions by @kfir4444 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2192
Handle string data properly when averaging children solute by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2193
autogen trees with halogens by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2178
a_dict bugfix in get_w0 by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2186
Enabling use of pyrms for RMG Simulations and Edge Analysis by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2164
Pyrms Reactor Bugfixes and Liquid-Surface Reactor for RMG Electrocat by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2197
Pdep bugfix - removing edge species by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2200
Use python-jl for running RMG-Py by @amarkpayne in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2212
Update ketoenol template image to 1,3 sigmatropic rearrangement by @kspieks in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2219
Fixing the link to Gri-mesh by @ProfLeao in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2209
Changes related to ATG Peroxyl Disproportionation family by @xiaoruiDong in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2220
Forbidden structs in input by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2185
Family atom labels by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2216
Ctc atomtype by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2170
Minor changes to rotor related functions by @xiaoruiDong in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/1980
Update reaction family images to reflect the merged 2+2_cycloaddition by @kspieks in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2226
Fix RMS Object Construction by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2208
Fix atom order issue in generateresonancestructure by @xiaoruiDong in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2229
Remove stale template matching for Bimolec hydroperoxide decomposition by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2232
Check for two-parameter Troe reaction when converting to Cantera by @sevyharris in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2231
Add licensing information to the README file by @yunsiechung in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2234
Documentation updates for developer install and update by @mefuller in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2224
halogen longdistancenoncyclic in cycle interaction by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2235
Halogens pdep by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2195
Allow ArrheniusBM Fitting up to 2000K for RMG-database Rate Trees by @kspieks in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2243
Psi4 is back by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2257
Update missing group test now that data is added for the original missing group by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2255
BugFix: Draw CO as 'CO' by @xiaoruiDong in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2260
give integer num of points to linspace by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2263
Add commit strings for RMG-Py and RMG-database by @kspieks in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2269
Convert a ThermoData object to a NASA object instance for RMS by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2258
Mol to group with atom labels by @davidfarinajr in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2158
added method to write rate const to HTML for sticking rxns by @ChrisBNEU in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2140
BAC parameter confidence intervals by @cgrambow in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/1969
Change rmgrc to a template file by @amarkpayne in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2273
BAC cross-validation by @cgrambow in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/1968
More robust conformer embed in QM module by @xiaoruiDong in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2272
Handle core/edge species/reactions for phase system correctly by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2252
Cantera issue in regression testing by @ChrisBNEU in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2271
Add Nitrogen groups to transport by @yunsiechung in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2274
Several Arkane Torsion (Rotor) related changes by @xiaoruiDong in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2268
reminder to activate env before making tests by @kfir4444 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2281
remove check for adsorbate getting adsorbed again by @ChrisBNEU in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2285
CSTR with vapor liquid mass transfer by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2194
Add tests to check num of reactant and product defined in ATG rate rules by @xiaoruiDong in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2297
Correct ATG rate rules initialization by @xiaoruiDong in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2299
Fix loadchemkinfile read of surface species by @sevyharris in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2276
merge AFM code into RMG-Py by @lily90502 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2060
Skip number of products check for ATG tree by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2306
Add atom props to reduce by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2308
Primary H2O2 by @josemvdh in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2291
Fix neg freq qchem parser by @kspieks in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2319
Added a readme file for Arkane by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2320
Pressure Dependence Improvements by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2315
Added an instruction on how to fix ImportError for rmg binary by @yunsiechung in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2327
Fix resonance save order by @xiaoruiDong in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2329
Add Arkane unit tests by @kspieks in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2330
update developer installation instructions to use the main rms branch by @ChrisBNEU in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2305
Allow RMG to load thermo or kinetic libraries from a file by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2340
Save the actual reaction label when creating a reaction library in Arkane by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2345
Added Arkane examples by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2349
Add the RMG-database paper to the citation info by @yunsiechung in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2351
Transitory Edge Analysis by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2317
Add bib file by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2357
Pdep Explorer Multinetwork fixes by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2358
importing pyrms and diffeqpy during a debug session by @calvinp0 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2364
Ci with mamba by @kfir4444 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2377
Minor: Update group attribute name to py3 by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/1979
update doc workflow, was failing bc 'uses' was incorrect by @ChrisBNEU in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2387
Added 'r' at the start of regex pattern strings where it was missing by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2396
Solving the 'Fragment' object has no attribute 'countinternalrotors' error by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2395
'Fragment' object has no attribute 'isatomin_cycle' error by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2400
Add radical flux tolerance by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2368
add comment as input to RMS reaction and species object by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2403
Improve kH estimation code by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2389
Adapt change in RMS to use keyword variables by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2408
Should be name, not label by @hwpang in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2409
Move Regression Testing in to the CI by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2390
accidentally used changes from an experimental local branch, revert by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2410
simplify condition checking for scheduled vs pushes CI by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2411
Correct Troe kinetics formula by @xiaoruiDong in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2398
CI: don't make destination directory for reference results when generating reference results by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2412
Set Keq=inf for irreversible reactions. by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2399
Updates to RMG-Py installation instructions documentation by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2414
Fix Incorrect Rendering in RMG-Py Installation Documentation by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2416
Added Arkane citation info by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2418
Modified assertion in thermodata.pyx by @NellyMitnik in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2420

New Contributors

@kfir4444 made their first contribution in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2192
@ProfLeao made their first contribution in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2209
@josemvdh made their first contribution in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2291
@JacksonBurns made their first contribution in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2357
@calvinp0 made their first contribution in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2364
@NellyMitnik made their first contribution in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2420

Full Changelog: https://github.com/ReactionMechanismGenerator/RMG-Py/compare/3.1.0...3.1.1

- Python
Published by JacksonBurns 8 months ago

reactionmechanismgenerator - RMG-Py v3.1.0

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 determineqmsoftware for Orca
- Fixed bug where elementaryhighp 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 SurfaceElleyRidealAddition_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 findparametersourcesandassign_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 criticaldistancefactor 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.

- Python
Published by mjohnson541 almost 5 years ago

reactionmechanismgenerator - RMG-Py v3.0.0

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 snakecase 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 scoopframework 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 parsecommandlinearguments to facilitate importing in binary package #1717 - Fix issues with isidenticalto methods of kinetics models #1705 - Fix cython issue with makeobject 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

- Python
Published by mliu49 about 6 years ago

reactionmechanismgenerator - RMG-Py v2.4.1

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 asdict and makeobject by making them recursive #1643

- Python
Published by mliu49 over 6 years ago

reactionmechanismgenerator - RMG-Py v2.4.0

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

- Python
Published by mliu49 over 6 years ago

reactionmechanismgenerator - RMG-Py v2.3.0

Arkane (formerly CanTherm):
- CanTherm has 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

- Python
Published by mliu49 about 7 years ago

reactionmechanismgenerator - RMG-Py v2.2.1

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

- Python
Published by mliu49 over 7 years ago

reactionmechanismgenerator - RMG-Py v2.2.0

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 elementaryhighp attribute is True
- Library reactions may be duplicated by pdep reactions if the new allowpdeproute attribute is True
- Jupyter notebook for adding new training reactions has been revamped and is now located at ipython/kineticslibraryto_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

- Python
Published by mliu49 over 7 years ago