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RMG-Py v3.0.0
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@mliu49 mliu49 released this 17 Dec 05:00
· 1505 commits to stable since this release
3.0.0
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This release represents a major milestone in RMG development and includes many backwards-incompatible changes, most notably Python 3 compatibility and major API changes. Users switching to RMG 3 will need to create new conda environments and update any scripts which access the API. We recommend using the futurize script from python-future for updating scripts for Python 3 and the provided rmg2to3.py script for updating scripts for RMG 3.

Python 3 #1724

  • RMG is now compatible with Python 3.7 and newer
  • RMG v2.x versions will no longer be supported
  • API changes
    • Method, function, and argument names have been standardized to use snake_case across RMG and Arkane
    • Input file related code was not changed, in order to continue support for existing syntax
    • Conversion script has been provided to aid transition (scripts/rmg2to3.py)
    • Standardized submodule names in the rmgpy.tools module #1794
  • Accompanying changes
    • Reduction and scoop_framework modules have been removed
    • New/updated hash and comparison methods for Species/Molecule/Atom/Bond classes
    • DDE thermochemistry estimator has been replaced by chemprop
    • Update example IPython notebooks #1735
    • Update global uncertainty module to work with MUQ 2 and Python 3 #1738
  • Miscellaneous clean up and bug fixes following transition #1741, #1744, #1752, #1759, #1785, #1802, #1798, #1799, #1808

Arkane

  • Improvements and refactoring of job output file creation and content #1607
  • Fix kinetics fitting bug #1672
  • Improvements to automatic network exploration tool #1647
  • Support for ND classical and semi-classical rotor calculations #1640, #1849
  • Support for 2D quantum mechanical rotor calculations using Q2DTor #1640
  • Support for providing absolute file paths #1685
  • Output RMG-style libraries #1769
  • Check for error termination in Gaussian log files #1766
  • Support for parsing Orca log files #1749
  • Support for parsing MP2, double hybrid DFT, CCSD, and CCSD(T) energies from Gaussian log files #1815
  • Support for TeraChem log files #1788
  • Miscellaneous bug fixes #1810

New features and other additions

  • Additional options for heterocycles in MLEstimator #1621
  • Automatic tree generation algorithm implementation completed #1486, #1675, #1848
  • New simulation restart approach using seed mechanisms (old pickle-based method removed) #1641
  • Added new MBSampledReactor type for simulating molecular beam experiments (does not support model generation) #1669
  • Improvements to group additivity thermo estimates for aromatics and sulfur species #1731, #1751
  • Improvements to solvation correction determination with multiple resonance structures #1832
  • Add support for reading and writing extended element syntax in Chemkin NASA polynomials #1636
  • Add support for fitting negative Arrhenius rates (found in MultiArrhenius data) #1834

Bug fixes

  • Fix numpy rcond usage to restore support for older numpy versions #1670
  • Fix bug with duplicate library reactions when using RMG generated seed mechanisms #1676
  • Move parse_command_line_arguments to facilitate importing in binary package #1717
  • Fix issues with is_identical_to methods of kinetics models #1705
  • Fix cython issue with make_object definitions #1817
  • Fix issue with estimating solvation corrections for radicals #1773
  • Fix parsing of certain types of RMG generated reaction comments #1842
  • Fix identifier generation for surface species using OpenBabel #1842
  • Fix mole fraction normalization for SimpleReactor #1809
  • Fix permissions error when writing seed mechanisms in WSL #1796
  • Fix issue with restarting from job without reaction filters #1847

Other

  • Improvements to mergeModels.py script #1649
  • Miscellaneous performance improvements #1677, #1765,
  • Raise errors when NaN is encountered in solver #1679
  • Allow sulfur species to have valence 12 in resonance algorithm #1751
  • Add support for maxproc argument to generate_reactions module #1780
  • Display atom index when drawing groups #1758
  • Update sensitivity example #1805
  • Update commented input file #1806
  • Generate reverse reaction recipes in reverse order of the forward recipe #1829
  • Add iodine to Chemkin elements list #1825
  • Remove unnecessary duplicate checking for seed mechanisms #1824
  • Organize examples for running RMG scripts #1840
  • Increase RDKit version requirement to avoid memory leak #1851
  • Logging changes #1721, #1755
  • Documentation updates #1680, #1709, #1767, #1781, #1784, #1807, #1845

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

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