File structure

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 files:

• 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.

The local Project folder contains the following directory tree:

• 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 output.py: The Arkane output file for the Species
      • species_dictionary.txt: The adjacency list for the Species
  • Reactions (soon to be implemented)