Error in rdf plot of 2d system.

[Jenis Thongam]

Hello,

I have a system of 2d ellipsoids built using lammps. As lammps does not particularly allow building of 2d system, I include z axis value of (0 to 1) and the define the system as 2d using "fix 3 all enforce2d". Now from the output dump file, I am trying to calculate the rdf of the frames.

I am getting the rdf curve when I set "box = freud.box.Box.cube(76.7495)". Since my system is 2d, I am confused as to why the the box has to be a cube.

Further I tried setting the z component to 0 ( "box.Lz = 0, box.xz = 0, box.yz = 0") but I get the error of "The AABBQuery r_max is too large for this box."

Can someone please help me out in this?

Thank you for your time,

Regards,

Jenis.

[Tommy Waltmann]

Hi Jenis,

Boxes in freud can be constructed in a variety of ways, boxes don't need to be constructed as cubes. Please see the box documentation for more details on this: https://freud.readthedocs.io/en/latest/modules/box.html . Additionally, to do the RDF calculation on a 2D system, please set the `is2D` property of the box to be True and pass positions of the form [x, y, 0]. This is also mentioned in the documentation for the RDF class here: https://freud.readthedocs.io/en/latest/modules/density.html#freud.density.RDF

Hope this clarifies how to do the calculation properly!

Best,

Tommy

[Jenis Thongam]

Dear Tommy,

Thank you so much for the clarification. I can now implement the 2d rdf plot of my system without any error.

Regards,

Jenis

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