Having trouble with setup

[xiaoruiDong]

Hi, I was trying to run Kinbot but got some issues.

Environment: Python 3.6 Queue: Slurm

What I have done:

• I have cloned Kinbot and ASE under zadorlab and installed pybel, rdkit and other necessary packages. I have added both ~/kinbot and ~/ase to my PYTHONPATH and ~/kinbot/ and ~ase/bin to my PATH.
• I created an input file (input.json, according to the documentation from your literature) for a calculation by g09, and that input file seemed to work. But the job soon terminated due to errors in Gaussian calculation.
• I checked the Gaussian job log file, and the error was due to force, opt and freq are in the arguments in the meantime.
• I looked into the code, and I think in your ase code, you tried to remove force when freq is added. So the case ideally should not happen.
• Then, I thought that I might use a wrong ase version. I redo the setup and find that when I run python setup.py install (or other lines you recommended), it will search for ase 3.19.1 from pypi and use as kinbot's default ase, which might be the problem.

Can you please provide any suggestions on this? Thanks.

Followup:

• I run the python setup.py install --user inside ~/ase as suggested by ASE. It seems to overwrite some of the settings by Kinbot, and it eventually works. Thanks

[juditzador]

Yes, right now you have to use the ~/ase version to run with KinBot. We recently merged some changes into the official ASE project which will enable us to get away from this special version of ASE, but we need to do some work to allow that version, and we haven't gotten there yet. I'm glad you were able to figure this out.