JAX-MD Neighbourlists in Non-Orthorhombic Systems
I've written a quick colab notebook to point out that in non-orthorhombic systems, one needs to be slightly careful when using the
jax-md neighbourlist implementation. The implementation works in fractional coordinates, and in systems where the lattice vectors are not orthogonal, the corresponding bins in real space are not rectangular, but rather skewed. So the bin sizes must take the distance between boundaries of the real space bins, rather then edge lengths, into account...
This is just a preliminary consideration -- the real fun part is thinking about this when both positions and cell can change between steps.