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