Add functions to plot radial distributions and angular distributions

stfc / janus

collection of scripts to train and generate data for machine learnt interatomic potentials

BSD 3-Clause "New" or "Revised" License

0 stars 0 forks source link

Add functions to plot radial distributions and angular distributions #50

Closed dave452 closed 1 year ago

dave452 commented 1 year ago

Added function to read parameters of symmetry functions from input.nn file and plot them.

ElliottKasoar commented 1 year ago

A few initial thoughts:

Should we add pandas e.g. using this commit (or equivalent) to the dependencies?
- Do we not also need import pandas as pd?
It might be better to use circular coordinates for the angular plots, or if that makes it more complicated, maybe scale the axes equally?
- A (optional) contour plot might be nice too
Some of the lines are very long, which makes it quite hard to follow in places
- It'd add a few lines, but temporally storing variables e.g. zeta = self.sym_functions.iloc[i]['zeta'] might make things a little easier to read
We should consider whether to add these plots into one of the notebooks

dave452 commented 1 year ago

We do need import pandas, its on the working version on the cluster but not here, I will correct this. I agree with placing the zeta = self.sym_functions.iloc[i]['zeta'] seperating things out a bit would be useful.

dave452 commented 1 year ago

It's probably also worthwhile adding the elements as an input. So you can plot symmetry functions for given element combinations.

ElliottKasoar commented 1 year ago

Are the only real changes to visualise.ipynb the addition of the final four cells?

It doesn't always work, but sometimes doing git add <file> -p allows you to only select the specific changes you want. (You may well have tried this, and even if not, from the number of changes that git picked up, it probably wouldn't have made a difference in this case, but worth being aware of either way)

dave452 commented 1 year ago

Do i also need to be the only other change the .ipynb_checkpoints/? because that seems to be the only change

ElliottKasoar commented 1 year ago

Do i also need to be the only other change the .ipynb_checkpoints/? because that seems to be the only change

We don't want those, they're just checkpoints that are made when you manually save a notebook (we could potentially add it to the .gitignore, but that doesn't need to be part of this PR).

I mostly just wanted to check I wasn't missing anything because there are apparently 20,000+ changes to the notebook.