# Wednesday, 8. January 2020¶

## To Do¶

• Look into qcp
• 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!!

$\text{Formal charge}=\text{<valence electrons>}-\text{<lone pair electrons>}-\text{<bonds>}$

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:

1. DO NOT USE PATH AS A VARIABLE WITHIN A SCRIPT

2. 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