Obtaining the delta vectors of the distance

[Bart Bruininks]

Hi Freudians,

I am using the AABBQuery in Freud for a project and I was wondering if it is possible to return the difference vector instead of returning the the length of the difference vector. 

I could not find this in the documentation and it also does not seem to be an optional kwarg like num_neighbors etc. It would be great if there is a nice solution possible, which would not require a custom Freud version, as I would like to flag Freud as a dependency and creating installers would become messy with custom versions.

I need such vectors for treatment of aggregates to classify their containment hierarchy. I have been using a voxel based paradigm in the past, but I am trying out Freud to replace and enhance my distance/PBC logic.

A project I want to use it for is MDVContainment (github link)

Cheers,

Bart

PS

If anyone turns out to be interested in inside and outside classification (containment) in Periodic Spaces and want to know how it works, feel free to send me an email. It is pretty wild, but can be really useful!

[Joshua Anderson]

Bart,

This is already implemented and will be in freud 3.0: https://github.com/glotzerlab/freud/pull/738

You can test it now by checking out the `next` branch and installing from source.

------

Joshua A. Anderson, Ph.D.

Research Area Specialist, Chemical Engineering, University of Michigan

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[Bart Bruininks]

Nice that is excellent news and I guess I will have to keep an eye out for the final 3.0 API but that is something I can certainly accept. 

So far I really enjoyed using Freud :D

Cheers,

Bart

Op woensdag 4 oktober 2023 om 18:02:22 UTC+2 schreef Josh Anderson:

[Tommy Waltmann]

Hi Bart,

Great to hear you're enjoying using freud!

If you don't want to wait for the version 3 release, there is quick way to get the neighbor vectors with some numpy indexing. The example in the documentation for the neighborlist class demonstrates this: https://freud.readthedocs.io/en/latest/modules/locality.html#freud.locality.NeighborList

Let me know if you have any more questions,

- Tommy

[Bart Bruininks]

Hoi Tommy,

Thanks even more, I think this is roughly what I was doing (I was performing the minimum distance convention myself). However, it just felt wrong for I presumed you would have that vector to calculate the distance in the first place.

Cheers,

Bart

Op do 5 okt 2023 om 17:23 schreef Tommy Waltmann <tom...@umich.edu>:

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