Running ARC

Using an input file

To run ARC, make sure to first activate the ARC environment (see the installation instructions). Then simply type:

python <path_to_the_ARC_folder>/ARC.py input.yml

replacing <path_to_the_ARC_folder> in the above command with the actual path to ARC. You could of course name the input file whatever you like. However, if you’re using the recommended aliases, then simply typing:

arc

in any folder with a valid input.yml file will execute ARC using that file.

ARC automatically creates restart files, which have the same format as an input file. If ARC crashes (e.g., due to a bug which was later fixed, or due to connectivity issues), typing:

arcrestart

in a folder containing an ARC restart.yml file (assuming you’re using the recommended aliases) will cause ARC to execute, considering all previously spawned jobs specified in the restart file. In restart mode, ARC is aware of all past submitted jobs and collects their output files or waits for them to terminate if they are still running.

ARC’s adopts the YAML format for its input/restart files. In fact, a restart file is nothing but a very detailed input file, and internally ARC treats them the same. Other than the file name, the difference is that the restart file was automatically generated.

A (very) simple input file might look like this:

project: example1

species:
  - label: ethanol
    smiles: CCO

All the parameters of arc.main.ARC class are legal input file keywords. Specifying species and reactions lists define ARCSpecies and ARCReaction object. See ARC’s API for a complete and updated list of keywords along with their allowed types.

Additional input file examples are available in ARC’s examples folder (ARC/examples). Another convenient way to see a valid and detailed input file is to run an ARC job and peak at the automatically generated restart.yml file.

A sample reaction input file with a user-supplied TS geometry guess is:

project: example2

species:
  - label: N2H4
    smiles: NN

  - label: NH
    smiles: '[NH]'

  - label: N2H3
    smiles: N[NH]

  - label: NH2
    smiles: '[NH2]'

reactions:
  - label: N2H4 + NH <=> N2H3 + NH2
    ts_xyz_guess:
    - |
      N      -0.4465194713     0.6830090994    -0.0932618217
      H      -0.4573825998     1.1483344874     0.8104886823
      H       0.6773598975     0.3820642106    -0.2197000290
      N      -1.2239012380    -0.4695695875    -0.0069891203
      H      -1.8039356973    -0.5112019151     0.8166872835
      H      -1.7837217777    -0.5685801608    -0.8405154279
      N       1.9039017235    -0.1568337145    -0.0766247796
      H       1.7333130781    -0.8468572038     0.6711695415

Using the API

To run ARC, make sure to first activate the ARC environment (see the installation instructions).

ARC’s API can be reached from any python platform, if ARC was added to the PYTHONPATH (see the installation instructions).

Running ARC using Jupyter notebooks (comes pre-installed with Anaconda) has the benefit of displaying “live” and interactive 3D geometries for the species of interest.

Example iPython notebooks are available in the ipython/Demo folder. Various standalone tools in an iPython format are also available, demonstrating different utilizations of the API. Users are of course directed to read ARC’s API.