Finish implementation for crystals

[jhrmnn]

• [x] Prune internal coordinates for periodic images.
• [ ] Calculate elements of the B matrix corresponding to unit cell vectors.

Relevant publications:

• https://aip.scitation.org/doi/10.1063/1.1340578
• https://aip.scitation.org/doi/full/10.1063/1.1864932

[jhrmnn]

Coordinate pruning added in 1916a45562