Enhancement: Include `zi` in the `ParticleSet.populate_indices()` method

[michaeldenes]

Currently the ParticleSet.populate_indices only populates the xi and yi indices. For 3D simulations, a nice-to-have addition to the ParticleSet.populate_indices method is to include the zi index, and not just xi, and yi. While it's fairly easy to determine the grid index in the vertical direction by a simple comparison of the particle depth with the grid depths in physical space, removing this post-processing step would be nice!