dump cluster coordinates

[Shuai Jiang]

Hi, I am dealing with gas phase clusters under periodic boundary conditions with freud. And after I wrap the coordinates into the cell and dump them, it shows that the clusters are separate as parts of them are on the boundary. So I am wondering how to dump cluster coordinates with avoiding molecules splitting across boundaries. Thank you very much!

[Tommy Waltmann]

Hi,

I don't completely understand the problem. Do you perceive there is a bug in freud's clustering algorithms, or are you simply asking how to render your system so that no single clusters are visually split in two by the box's periodic boundary conditions after wrapping?

If the problem is the latter, trying wrapping the coordinates into larger boxes until your clusters are not longer split across the periodic boundary conditions after wrapping.

- Tommy