Non periodic neighbors error

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jude vishnu

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Jan 25, 2022, 5:07:02 AM1/25/22

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Dear all,

I was using freud to calculate the neighbors of my particles. Since I did not want o get periodic neighbors I used

box.periodic_x=False

box.periodic_y=False
box.periodic_z=False

and then did

aq = freud.locality.AABBQuery(box,poly_pos)
query_result = aq.query(poly_pos, dict(r_max = 0.89, exclude_ii = True))
nlist = query_result.toNeighborList().

This was working fine in our local cluster. But in our university cluster the same code shows an error as follows.

" nlist = query_result.toNeighborList()

File "locality.pyx", line 218, in freud.locality.NeighborQueryResult.toNeighborList"

Do you guys know what could cause it? Is it the freud version in these two clusters?

Regards,
Jude

Tommy Waltmann

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Jan 25, 2022, 10:02:37 AM1/25/22

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Hi Jude,

I need some more information before I can be of help here.

1) Please indicate the version of freud you used as well as how you installed freud in both cases.

2) Please post the entire error output.

3) If possible, it would also help to see a minimal script which reproduces the problem.

Best,

Tommy

jude vishnu

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Feb 21, 2022, 4:27:01 AM2/21/22

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Sorry for the late response. I used large values of Lx,Ly,Lz to prevent periodic boundary conditions while calculating neighbors.

Regards,

Jude

Tommy Waltmann

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Feb 21, 2022, 10:10:27 AM2/21/22

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Hi Jude,

It's great that you were able to identify a workaround so your code is working in both places now! Because I am still curious, did you end up determining what the source of the error was?

Best,

Tommy

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