[BUG] Out of Memory Issue During Neighbor List Generation about dmff HOT 2 CLOSED

Try to use NeighborListFreud, instead of NeighborList. The latter one relies on the neighbor list module of jax-md, which is slow and memory consuming. On the other hand, the Freud neighbor list runs on CPU, which does not have the memory issue for large systems, and, surprisingly, often runs faster.

Nevertheless, the performances of both modules are unsatisfactory. We are working on more efficient implementations of neighbor list. And hopefully can get it done in next few months.

from dmff.

It seems like this does the trick. Comparing with some larger systems at reasonable cutoffs (8-10 Angstrom), the results scale somewhat better with NeighborListFreud although still run into bottlenecks on especially large systems from the benchmark suites of other packages. In regards to my other issue, it looks like there were also some issues with box vector input format that would cause the generation of some large n^2 arrays. This behavior seems to no longer be an issue in the development branch mentioned in that issue though.

from dmff.