RMG-Py v2.0.0

This release includes several milestones of RMG project (see installation here):

• 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 and here for 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
  • Implements Euclidean distance algorithm for the selection of the best rate rules to use in estimateKinetics
  • Streamlines storage of kinetics comments for averaged rules, which can be analyzed by extractSourceFromComments
• Database entry accessibility tests:
  • Adds entry accessibility tests for future entries (testing.databaseTest)
• Fixes bugs
  • fluxdiagram generation is now fixed, one can use it to generate short video of fluxdigram evolution
  • mac environment yml file is introduced to make sure smooth RMG-Py installation and jobs on mac
  • fixes failure of checkForExistingSpecies for polyaromatics species
  • fixes execution failure when both pruning and pDep are turned on
  • fixes pDep irreversible reactions
  • fixes issue of valency of Cbf atom by dynamic benzene bond order assignment