getting neighbour list from a list of bonds in freud

[mubisk]

Hi. I am new to Freud and would like to calculate cluster properties. I have ring polymeric system and would like to form cluster only based on the bonds. However I a stuck with the following command:
cl = freud.cluster.Cluster()
cl.compute(system, neighbors)

I tried converting my array of bonds into a dictionary and using as neighbors in the above command but I am getting the following error: "ValueError: An invalid value was provided for neighbors, which must be a dict or NeighborList object."

The bonds array in my code is [[1,2], [2,3], [3,4], .......].

Can someone please help me in formatting the neighbors correctly?

[tommy-waltmann]

Hi @mubisk,

For the purpose of organization, please ask this question on the freud discussion board.

[joaander]

I transferred the discussion from hoomd-blue to freud.

[tommy-waltmann]

To create a neighbor list for which the neighbors are already known, use the factory method from_arrays of the NeighborList class. There is an example and further description in the documentation here

If you have any further questions, don't hesistate to ask!