RMG v3.0.0 Release Planning

[mliu49]

It's time to start preparing for the RMG v3.0.0 release. This is a major release, with the biggest changes being Python 3 support and API naming style changes.

There will be an accompanying paper highlighting some of the major changes since RMG v1.0, and I assume that the ongoing Arkane paper will most likely be updated to reference this release as well.

There are still a number of PR's which need to be merged, which are tagged with For Next Release.

This issue is for any release related discussion. Draft release notes will also be prepared here.

[mliu49]

RMG-Py v3.0.0 Release Notes (draft)

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

Python 3 #1724

• RMG is now compatible with Python 3.7 and newer
• RMG v2.x versions will no longer be supported
• API changes
  • Method, function, and argument names have been standardized to use snake_case across RMG and Arkane
  • Input file related code was not changed, in order to continue support for existing syntax
  • Conversion script has been provided to aid transition (scripts/rmg2to3.py)
  • Standardized submodule names in the rmgpy.tools module Rename submodules in rmgpy.tools #1794
• Accompanying changes
  • Reduction and scoop_framework modules have been removed
  • New/updated hash and comparison methods for Species/Molecule/Atom/Bond classes
  • DDE thermochemistry estimator has been replaced by chemprop
  • Update example IPython notebooks Update IPython notebooks #1735
  • Update global uncertainty module to work with MUQ 2 and Python 3 Update global uncertainty module to work with MUQ 2 #1738
• Miscellaneous clean up and bug fixes following transition Fix inconsistent molecule fingerprint generation #1741, Prettify #1744, Fix two calls to Exception.message, which no longer exists #1752, Fix variable name in FluxDiagram script #1759, Several small Pdep bug fixes #1785, Fix PES figure generation in png format #1802, Revert 'spin_multiplicity' to 'spinMultiplicity' in Arkane pdep #1798, Test and fix Molecule.remove_van_der_waals_bonds #1799, Arkane pdep py3 fixes #1808

Arkane

• Improvements and refactoring of job output file creation and content Arkane output fixes #1607
• Fix kinetics fitting bug Fix kinetics fitting with Tmin & Tmax in Arakne #1672
• Improvements to automatic network exploration tool Automatic Network Generation 3 #1647
• Support for ND classical and semi-classical rotor calculations Multi-Dimensional Rotors #1640, ND Hindered Rotor Improvements #1849
• Support for 2D quantum mechanical rotor calculations using Q2DTor Multi-Dimensional Rotors #1640
• Support for providing absolute file paths Allow relative paths in Arkane statmech #1685
• Output RMG-style libraries Output RMG libraries in Arkane #1769
• Check for error termination in Gaussian log files Add LogError to raise LogError for unconverged gaussian log file #1766
• Support for parsing Orca log files added orca parser to arkane #1749
• Support for parsing MP2, double hybrid DFT, CCSD, and CCSD(T) energies from Gaussian log files Gaussian energies #1815
• Support for TeraChem log files Terachem #1788
• Miscellaneous bug fixes Arkane bugfixes #1810

New features and other additions

• Additional options for heterocycles in MLEstimator onlyHeterocyclics option for Machine Leaning Estimator Settings #1621
• Automatic tree generation algorithm implementation completed Automatic Tree Generation Part 4 #1486, skip generation when # tree reactants != # given reactants #1675, Tree generation improvements #1848
• New simulation restart approach using seed mechanisms (old pickle-based method removed) Enable Restarting RMG Jobs from a Seed Mechanism #1641
• Added new MBSampledReactor type for simulating molecular beam experiments (does not support model generation) Created a new reactor type MBSampledReactor for modeling laser lab Mass-Spec experiments #1669
• Improvements to group additivity thermo estimates for aromatics and sulfur species Improve group additivity ranking for aromatic species #1731, Dms oxy changes #1751
• Improvements to solvation correction determination with multiple resonance structures fixed the solvation GAV heuristic #1832
• Add support for reading and writing extended element syntax in Chemkin NASA polynomials Fix bugs in Chemkin thermo entry element reading/writing #1636
• Add support for fitting negative Arrhenius rates (found in MultiArrhenius data) Enable fitting and reversing of negative reaction rates. #1834

Bug fixes

• Fix numpy rcond usage to restore support for older numpy versions Check numpy version before passing rcond to numpy.linalg.lstsq #1670
• Fix bug with duplicate library reactions when using RMG generated seed mechanisms fix bug with duplicate library reactions #1676
• Move parse_command_line_arguments to facilitate importing in binary package Move parse_command_line_arguments to util.py #1717
• Fix issues with is_identical_to methods of kinetics models Fix a few bugs and add tests: KineticsModel and uncertainty handling. #1705
• Fix cython issue with make_object definitions Overriding cdef method with def method warning for make_object #1817
• Fix issue with estimating solvation corrections for radicals Fix solvaion radical bug #1773
• Fix parsing of certain types of RMG generated reaction comments Collection of small fixes #1842
• Fix identifier generation for surface species using OpenBabel Collection of small fixes #1842
• Fix mole fraction normalization for SimpleReactor Allow mole fractions to be normalized if they do not sum to one #1809
• Fix permissions error when writing seed mechanisms in WSL Fix WSL permisson bug for renaming directories #1796
• Fix issue with restarting from job without reaction filters Restart attribute error #1847

Other

• Improvements to mergeModels.py script Merge model improvements #1649
• Miscellaneous performance improvements Reduce species copying and resonance structure generation when reacting #1677, Performance improvements to pdep logging #1765,
• Raise errors when NaN is encountered in solver raise a DASxError if nan found in moles #1679
• Allow sulfur species to have valence 12 in resonance algorithm Dms oxy changes #1751
• Add support for maxproc argument to generate_reactions module Allow generate_reactions.py script to accept number of processors  #1780
• Display atom index when drawing groups Add atom index to Group()._repr_png_ #1758
• Update sensitivity example Update sensitivity example for py3 #1805
• Update commented input file Minor: updated parts of the commented input.py file #1806
• Generate reverse reaction recipes in reverse order of the forward recipe Reverse recipes should be in reverse order #1829
• Add iodine to Chemkin elements list Added Iodine as element in Chemkin input file #1825
• Remove unnecessary duplicate checking for seed mechanisms Remove unnecessary duplicate check #1824
• Organize examples for running RMG scripts Python3 Script check #1840
• Increase RDKit version requirement to avoid memory leak Update required version of rdkit to avoid severe memory leaks #1851
• Logging changes Reduce the amount of logging messages that get too frequently printed during debug #1721, Reduced print statement frequency for exceeded max number of objects.… #1755
• Documentation updates Make page titles contain current release number instead of 2.1.0 #1680, Corrected the instructions for running in parallel #1709, Update documentation from py2 to py3 #1767, Title underline too short. #1781, Docs: Corrections to Arkane's Multidimensional Hindered Rotors docs #1784, Update isotope documentation #1807, API documentation updates #1845

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

[mliu49]

RMG-database v3.0.0 Release Notes (Draft)

Thermochemistry

• Add new models for chemprop estimator to replace dde models Add chemprop models RMG-database#351
• Revamp GAVs for oxygenated sulfur species Dms oxy changes RMG-database#360
• Add polycyclic GAVs for various strained molecules Add polycyclic corrections for some strained cyclic species RMG-database#333

Kinetics

• New automatically generated tree for R_Recombination Automatic Tree generation for R_Recombination RMG-database#334, Improve R_Recombination Generated Tree RMG-database#369
• Refine root template for 1,2_NH3_elimination Modified the 1,2_NH3_elimination root group RMG-database#350
• New DMSOxy kinetics family Dms oxy changes RMG-database#360
• Add DMS related training reactions to H_abstraction Dms oxy changes RMG-database#360

Bug fixes

• Fix drawing for 2+2_cycloaddition_Cd Fix drawing for 2+2_cycloaddition_Cd RMG-database#345
• Fix incorrect SMILES in solute database Fixed typo and wrong SMILES in solute library RMG-database#348
• Fix incorrect adjacency list for HON in kinetics libraries Modified the 1,2_NH3_elimination root group RMG-database#350
• Fix typo in solvent parameters Corrected typo with one of the solvent abraham parameter RMG-database#357

Miscellaneous

• Update scripts and IPython notebooks for Python 3 Update RMG-database scripts and notebooks to Python 3 RMG-database#364

[goldmanm]

I am not sure how to get this in the binary for 3.0.0, but the isotopes script, located in scripts/isotopes.py was not in the 2.4.1 binary in the bin folder. Let me know if there's anything I can do to help with that.

[mliu49]

Good catch! It should be added to the list of scripts in setup.py: https://github.com/ReactionMechanismGenerator/RMG-Py/blob/master/setup.py#L203