Running ARC

From the terminal

Running ARC from the terminal requires an input file (see example input files under the examples folder).

The input files are in a YAML format, and a (very) simple input file might look like this:

   project: demo

   species:
     - label: OH
       smiles: '[OH]'

To run, make sure to first activate the RMG environment with the additional dependencies (see Installation-instructions). Then simply type:

python <path_to_the_ARC_folder>/ARC.py input.yml

replacing <path_to_the_ARC_folder> with your actual local path to ARC. It might be more convenient to add the following lines to your .bashrc:

export arc_path=$HOME'<path_to_the_ARC_folder>'
alias arc='source activate rmg_env && python $arc_path/ARC.py input.yml'
alias arcrestart='source activate rmg_env && python $arc_path/ARC.py restart.yml'

then, simply typing arc in any folder with a valid input.yml file in it will execute ARC.

ARC automatically creates restart files in the same format as its input files. If ARC crashes, e.g. due to connectivity issues or shutting down your machine, simply typing arcrestart will cause ARC to restart. 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.

Using Jupyter Notebook

When run using a Jupyter notebook, interactive 3D geometries are presented after final geometry optimizations (as opposed to running from the terminal). However, restarting ARC can currently only be done via a terminal (see above).

To run, make sure to first activate the RMG environment with the additional dependencies (see Installation-instructions).

Call jupyter notebook and edit a copy of the ARC Demo notebook.