[WIP]

[ml-evs]

Summary

This PR adds some optimizations and shortcuts for periodic image site detection that can be used in certain applications.

The optimizations are two-fold:

• Currently, the periodic image check checks the lattice vectors of parent cell, species and position of a site and its potential image. For situations where the image checker is working with a fixed lattice, no overlapping sites, i.e., when performing a voronoi decomposition of a given cell, then these checks can be made optional. As these checks are wrapped in Python object niceties there can be quite a significant overhead from performing them, the composition check in particular (my benchmarks indicated ~30% of time when looping over a structure is just checking these compositions).

• Secondly, the actual fractional coordinate diff can be optimized by replacing the element-wise tolerance check with a tolerance on an L1 norm (or L2, if desired). The default tolerance could be tweaked slightly to adjust for this.

Todo (if any)

Report back with a proper benchmark

Checklist

Work-in-progress pull requests are encouraged, but please put [WIP] in the pull request title.

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

• Doc strings have been added in the Google docstring format. Run pydocstyle on your code.
• Type annotations are highly encouraged. Run mypy path/to/file.py to type check your code.
• Tests have been added for any new functionality or bug fixes.
• All linting and tests pass.