ReactionMechanismGenerator/RMG-Py

📋 What's Changed

• Update Jupyter Notebooks to call RMS using juliacall by @mjohnson541 in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2829
• Merge 3.3.0 release from stable back into main by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2830
• Dockerfile: use miniforge instead of miniconda to avoid `defaults` by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2834
• Avoid Accidental `conda` Uploads by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2839
• More helpful debugging for PDep networks, and option to always generatePESDiagrams. by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2825
• Fix Li atom type defs by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2845
• Explicitly Forbid Default `conda` Channels by @JacksonBurns in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2846
• Expanding the unit testing of ring decomposition features. by @rwest in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2852
• + 83 more

✨ New Contributors

• @12Chao made their first contribution in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2646
• @djlucey made their first contribution in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2947
• Full Changelog: https://github.com/ReactionMechanismGenerator/RMG-Py/compare/3.3.0...4.0.0

📦 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`

📦 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
• + 11 more

🐛 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
• + 15 more

📦 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 'e_electronic_with_corrections' referenced before assignment by @alongd in https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2756
• + 4 more

🗑️ 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
• + 14 more

✨ 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
• + 5 more

📋 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 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
• + 156 more

📋 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
• + 164 more

✨ 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

📋 Changes

• 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
• + 52 more

📋 Changes

• 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
• + 52 more

📋 Changes

• 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
• + 9 more

📋 Changes

• 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
• + 43 more

📋 Changes

• 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
• + 19 more

📋 Changes

• 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

📋 Changes

• 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:
• + 21 more

📋 Changes

• 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
• + 4 more

📋 Changes

• 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**
• + 9 more

📋 Changes

• 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
• + 11 more

📋 Changes

• 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
• + 8 more

📋 Changes

• 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:
• + 5 more

📋 Changes

• 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:
• + 16 more

📋 Changes

• 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
• + 21 more

📋 Changes

• 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:
• + 2 more

📋 Changes

• 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]

📋 Changes

• 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
• + 6 more

📋 Changes

• 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`](https://github.com/ReactionMechanismGenerator/RMG-Py/wiki/Running-RMG-in-parallel-with-a-SLURM-scheduler) and [`here for SGE scheduler`](https://github.com/ReactionMechanismGenerator/RMG-Py/wiki/Running-RMG-in-parallel-with-a-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
• + 11 more

📋 Changes

• IPython notebooks now found in the `ipython` folder and contains useful illustrative examples. Requires the installation of jupyter via the command `conda install jupyter`
• Cantera support in RMG:
• New module found in `rmgpy.tools.canteraModel`, which provides functions to help simulate RMG models using Cantera instead of native RMG solvers.
• 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
• This new module is found at `rmgpy.tools.observableRegression` and helps identify differences between different versions of models generated by RMG, using the "observables" that the user cares about (i.e. main species mole fractions). Runs simulations via cantera.
• Automatic plotting of simulations and sensitivities when generating models
• + 21 more

📋 Changes

• 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 the RMG log file.

📋 Changes

• 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](http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/index.html#installation) 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](http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/input.html#filterreactions). Learn more about the theory and algorithm on the [Rate-based Model Enlarging Algorithm](http://reactionmechanismgenerator.github.io/RMG-Py/theory/rmg/enlarger.html) page.
• The RMG [native scripts](http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/modules/index.html) 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](http://rmg.mit.edu/simulate/chemkin)