File structure - ReactionMechanismGenerator/ARC GitHub Wiki

Each ARC Project has a library of its own. If ARC is run from the terminal with an input file (whether an input or a restart file) then the folder in which the input file is located becomes the Project's folder. If ARC is run from Jupyter Notebook, a folder with the Project's name is created under ARC/Projects/. A respective Project folder is also created on each of the servers ARC uses for a Project under ~/runs/ARC_Projects/.

After running a Project, the local Project folder will contain the following directory tree:

  • arc.log: Details of the project execution procedure and troubleshootings
  • <Project_name>.info: A quick record of the levels of theory used for the project, the servers used and the Species / TSs / Reactions calculated with respective execution times, where <Project_name> is the actual Project name. Note that ARC periodically check the servers for terminated Jobs, hence execution time is only an estimate and isn't parsed from the Job's output file; also note that restarting ARC causes inaccuracies in the reported execution times, and the actual times might be significantly shorter.
  • restart.yml: A restart file for restarting the Project, constantly updates while ARC is running and the Project is in progress.
  • Any additional backup files (i.e., arc.old.log and restart.old.yml), if relevant
  • calcs:
    • Species
      • Species label
        • Job name
          • The Job's input, submit and final output files
    • TSs
      • TS label
        • Job name
          • The Job's input, submit and final output files
  • output:
    • A thermo parity plot PDF file with comparisons of H298 and S298 between ARC's calculations and RMG's best estimation
    • RMG libraries
      • thermo
        • An RMG thermo library of Species calculated in the project
      • kinetics
        • An RMG kinetics library of Reactions calculated in the project (soon to be implemented)
    • Species
      • ArkaneSpecies
        • A YAML file for the Species to be used independently in further Arkane computations if desired
      • geometry
        • Species label.gjf: A dummy Gaussian input file with the Species' geometry for further geometry manipulations in GaussView
        • Species label.xyz: An XYZ file with the Species' geometry for further geometry manipulations in other software such as Avogadro
      • chem.inp: A Chemkin format NASA polynomial of the thermo data for the Species
      • Species label arkane input.py: An Arkane species file to be used independently in further Arkane computations if desired (note that the YAML file generated will function the same, and is probably preferable since it has no absolute paths for QM output files)
      • Species label arkane output.py: The Arkane output file for the Species
      • species_dictionary.txt: The adjacency list for the Species
    • TSs (with a similar structure as described for Species above)
    • Reactions (soon to be implemented)