ReactionMechanismGenerator/ARC: ARC 1.1.0

ARC Version 1.1.0

ARC - Automated Rate Calculator is a software for automating electronic structure calculations relevant for chemical kinetic modeling. ARC has many advanced options, yet at its core it is simple: it accepts 2D graph representations of chemical species (e.g., SMILES or adjacency lists), and automatically executes, tracks, and processes relevant electronic structure jobs on user-defined servers. The principal outputs of ARC are thermodynamic properties (H, S, Cp) and high-pressure limit kinetic rate coefficients for the defined species and reactions. (Note that automating transition states is still in progress).

  • New features:

    • Project name validity check #58
    • Added Free Rotors #59
    • Report the git head in the log file #63
    • Determine rotor symmetry using a cyclic energy scan list #66
    • Improve SGE submit file #68
    • Improved restart #64
    • Parse xyz for a species from file #70
    • Troubleshoot conformer jobs if they all fail #77
    • Changed rotor inconsistency_ab #78
    • Don't crush ARC if it couldn't troubleshoot a job #79
    • Make xyz to 2D more robust (catch errors) #80
    • Check isomorphism for conformers #84
    • Improve submit files #81
    • Troubleshoot rotor scans #85
    • Generate resonance structures before checking molecule isomorphism #87
    • Standardize xyz #88
    • Copy the frequency output file for a TS #89
    • Save the generated conformers in the species geometry folder #90
    • Allow nonisomorphic 2d #91
    • Improved management and report of job time #94
    • Don't use applyAtomEnergyCorrections for kinetics #95
    • Fix to xyz/2D loading and atom reordering in ARCSpecies #96
    • Preserve multiplicity throughout Species representations #99
    • Archive log and restart files #97
    • Run and save molecular orbitals #102
    • Allow ARCSpecies to be initialized with a conformer list file #104
    • Set default max stepsize for optimization in Gaussian #108
    • Save unconverged species (labels) #98
    • Use the Gaussian check file #100
    • Allow birad singlet to be defined and run as unrestricted #114
    • Update determine_qm_software to new Arkane #111
    • Calculating Lennard-Jones coefficients #117
    • Allow the user to define adaptive levels of theory (by heavy atoms) #119
    • Set the 1d_rotors settings directive to True by default #121
    • Updated submit scripts #123
    • Allow defining a TS species simply with .xyz guesses #124
    • Save conformer jobs in the restart file #125
    • Parse Molpro frequencies #127
    • Run ARC on a server #128
    • Activate the job_types flags for opt, freq, and sp #132
    • Modifications to how the model chemistry is treated to be consistent with Arkane #134
    • Organized job memory handling #137
    • Consider the requested job types for species already defined with xyz #139
    • Added a ZPE/freq scaling factor script to utils #136
    • Added a function to save an input file (and not run ARC on spot) #140
    • Added some Job methods and reorganized init #142
    • Added NIST to kinetics plots (off by default) #146
    • A new way of thinking about conformers #143
    • Improved ESS troubleshooting #147
    • Adapt Processor to the new Arkane output #148
  • Documentation:

    • Added ARC's documentation #152
  • Bug fixes:

    • Plot kinetics even if no RMG reaction matches #62
    • Treat same scan point at 0 and 360 deg correctly #67
    • Fix bug with loading molecule statmech during Rate jobs #73
    • If statement in model chemistry #101
    • Don't lose track of jobs in 'qw' status on SGE #103
    • Don't overwrite self.mol if self.mol_from_xyz is None #106
    • Remove extra parentheses in gaussian input file #120
    • Don't run a fine opt in Molpro #122
    • Set the memory per cpu slightly higher than the ESS memory #144
    • File compatibility with MAC OS (skip .DS_Store files) #145
    • Improved ARC's sleeping habits when experiencing connection errors #149
    • Minor conformers/xyz files fixes #150
    • Correcly move the Arkane YAML file #151
  • Miscellaneous:

    • #109:
      • Added examples to .gitignore
      • Allow users to specify the number of cpu's to use per server
      • Download additional info re failed jobs (out.txt, err.txt, slurm.out)
      • Don't run orbitals jobs by default
      • Make servers in ess_settings a list
      • Allow users to specify a levels_ess dictionary associating levels of theory (or partial phrases of methods or basis sets) with an ESS
      • Added ess_settings to settings.py instead of the API
      • Tests: functions in main
      • Additional minor fixes
    • #112:
      • Load ess_settings correctly from dict
      • Improved species logging in project info file
      • Don't plot kinetics if it is None
      • Improved error message if rxn energetics are problematic
      • Added min_list() to Scheduler
      • Improve converter xyz functions
      • Improved xyz handeling in Species (xyz can now be a list)
    • #133:
      • Updated isomorphic species check method name in rmgdb
      • Corrected local server check
      • Updated ESS check function name in iPython notebook
    • #141:
      • Added an iPy notebook with an xyz to SMILES script
      • Don't load the RMG database if not necessary
  • New dependencies:

    • scikit-learn #116