In response to the JOSS review.
Running the executable with:
_build/app/s-dftd3 --bj pbe0 --atm --json --noedisp --grad app/example.xyz
didn't work for me. I had to specify a file name for the output of the gradient evaluation. I assume the CLI can't have the input file name follow an an option with an optional file name arg, as this is ambiguous. For example, if I change the order to:
_build/app/s-dftd3 --bj pbe0 --atm --json --grad --noedisp app/example.xyz
then the defaults for the JSON and gradient file outputs are picked up. If however I follow either of them with the input structure, it gives an error.
One could note this in the docs, or modify the CLI to do some extra checking as JSON, gradient and input files can be distinguished from their extensions.
In response to the JOSS review.
Running the executable with:
didn't work for me. I had to specify a file name for the output of the gradient evaluation. I assume the CLI can't have the input file name follow an an option with an optional file name arg, as this is ambiguous. For example, if I change the order to:
then the defaults for the JSON and gradient file outputs are picked up. If however I follow either of them with the input structure, it gives an error.
One could note this in the docs, or modify the CLI to do some extra checking as JSON, gradient and input files can be distinguished from their extensions.