Having trouble with setup
xiaoruiDong opened this issue · 1 comments
xiaoruiDong commented
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
andASE
underzadorlab
and installedpybel
,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
andfreq
are in the arguments in the meantime. - I looked into the code, and I think in your ase code, you tried to remove
force
whenfreq
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 forase 3.19.1
frompypi
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 commented
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.