fix npt_langevin

[jla-gardner]

Summary

• I found that the npt_langevin integrator appears to be broken in NPT bug #152
• I think this is arising because the kinetic energy term currently being used is per-atom, whereas it needs to be per-structure
• this fix now allows npt_langevin to reproduce the expected volume of a perfect-gas:

## Checklist

Before a pull request can be merged, the following items must be checked:

• Doc strings have been added in the Google docstring format.
  Run ruff on your code.
• Tests have been added for any new functionality or bug fixes.
• All linting and tests pass.

Note that the CI system will run all the above checks. But it will be much more
efficient if you already fix most errors prior to submitting the PR. It is highly
recommended that you use the pre-commit hook provided in the repository. Simply run
pre-commit install and a check will be run prior to allowing commits.

[jla-gardner]

tests/test_neighbors.py::test_neighbor_lists_time_and_memory is failing, but I am unsure if this is caused by my changes or is a known flaky test (#133 ?)

[janosh]

thanks a lot for catching this and submitting a fix! 🙏

but I am unsure if this is caused by my changes or is a known flaky test (#133 ?)

most likely not caused by your changes. i just added that test yesterday. the thresholds still need to be tweaked based on CI variance. feel free to increase the threshold to match observed time and/or mem usage

[janosh]

thanks @jla-gardner 👍