Feature decouple somd

[Roy-Haolin-Du]

This PR includes the following changes:

Refactored SystemPreparationConfig into the configuration module.
Added and updated SlurmConfig for better modularity.
Updated and passed all relevant pytest cases.
ruff format and check for standard files format

[fjclark]

This file gets automatically updated according to the git tag. You can list git tags with git tag -l. 0.2.0 should be the most recent one - if it's not, please pull changes from the main branch.

As this gets auto-updated and isn't a deliberate code change, please revert this change. Thanks!

[fjclark]

Hi Roy. Thanks very much for this!

I've cancelled the CI for the moment as there are a few changes it would be good to make before running all the tests.

It's a bit hard to see the relevant changes because there are 204 files changed. Most of these are in the data directory. Please could you revert all changes to the a3fe/data directory? These files aren't related to this PR and shouldn't be changed. After that I'll have a closer look at your changes.

Thanks!

[fjclark]

These changes aren't directly related to this PR, so please revert them.

We should probably make the plotting more flexible so you don't have to make manual changes like this, but let's save this for another PR! Thanks.