Wednesday, 8. January 2020¶
To Do¶
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Look into qcp - Read up on SAPT
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Figure out why SSH boots me when I try to transfer files - Figure out how to automate genmer script
- Write molclus slurm script
- Psi4 run script
Note!¶
Don’t forget your first year chem!!
In Boltzmann distributions, a \(10\:kj\cdot mol^{-1}\) is a kind of cutoff of significance, sine it’s going to have an incredibly small contribution to the expectation value.
What I did¶
Today I spent a lot of time scripting and wrote some beautiful tools to generate initial structures and optimise them using molclus/genmer, through gaussian. The recursive folder generations script worked a treat, and genmer is doing some really cool things in producing these structures.
I submitted all of the ions agains alkene but need to look into basis sets for the transition metals. I was suggested to look at ECP rather than all electron basis sets, but someone else just suggested using a dunning basis set from the basis set exchange.
It will likely take a while to get all my jobs through
I got an email from Simon that put me in the partner QOS pool, so I get that now… does mean that I had to resubmit though… again… only a little bit annoying
I found a paper that suggests to stick with dunning basis sets for my transition metals, I guess it’s just up to which ones to use, and whether to go full electron or ECP and for which metals
In the evening¶
OMFG so many issues… I think i’ve fixed them though? A few things to remeber:
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DO NOT USE PATH AS A VARIABLE WITHIN A SCRIPT
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Just let the scripts run
bash -l
find a better way to check for an interactive shell… like:if [ -n "$PS1" ]; then exec -l zsh -l fi