topic Re: 3D plot of crystal structure in Discussions

3D plot of crystal structure

Georg — Sun, 11 Jun 2023 11:03:24 GMT

Has anyone done this, is there any example?

I would like to use JMP's 3D plotting capabilities to understand Location of Atoms in a Crystal lattice, to plot some crystallographic planes etc.

Re: 3D plot of crystal structure

martindemel — Fri, 10 Jul 2020 11:08:42 GMT

Hmm, I don't think this is easily to be done. The knots (aka molecules) could be represented by dots, using color by column (for the element). However the tough part would be the correct connection and possible free arms.

I'd be happy if someone knows a solution or has implemented one already, I'd love to see this working.

my2cents

Re: 3D plot of crystal structure

MikeD_Anderson — Fri, 10 Jul 2020 14:18:48 GMT

If you have the coordinates of the unit cell, you could just plot it in Scatterplot 3D. You'd have to do the translations yourself to flesh out the unit cell from the basis set you get in the CIF files, though. Coloring the atoms should be easy enough in Scatterplot 3D

best,

M

Re: 3D plot of crystal structure

Craige_Hales — Fri, 10 Jul 2020 20:52:56 GMT

If you are thinking of writing your own JSL using the 3D SceneBox, might give you some ideas about what is feasible. Also check out the examples in the sampledata/scene3d directory.

Also, checkout the Graph3DBox in the scripting index. It doesn't do much more than the example, but it doesn't require learning OpenGL commands either.

Graph3DBox in scripting index

Re: 3D plot of crystal structure

gzmorgan0 — Fri, 10 Jul 2020 21:26:33 GMT

Thank you, Craig, @Craige_Hales . I missed this.

Re: 3D plot of crystal structure

lwx228 — Sat, 11 Jul 2020 00:50:02 GMT

Thanks Craige!

It looks like this video can be done with JSL?

https://www.youtube.com/watch?v=KKr91v7yLcM

Re: 3D plot of crystal structure

Craige_Hales — Sat, 11 Jul 2020 03:07:03 GMT

the green pea parts should be straight forward; shadows are not something JMP's use of OpenGL does except by trickery, like

@Paul_Nelson

Re: 3D plot of crystal structure

Georg — Wed, 22 Jul 2020 15:42:43 GMT

@Craige_Hales unfortunately I was not able to figure out how to do simple shapes as Spheres, planes and lines in the Scene.

The Vector in the example is very impressive, but I Need simple shapes also. The Show properties command gives only three possibilities for adding markers, Ellipsoids and vectors.

The platform is experimental, so would you recommend me to do Scenes with many spheres, some planes and lines in OpenGL or is there a way to do it in Graph 3D Box? Thanks!

  Add Markers [Action] [Scripting Only] (Draws n markers on the plot.)
  Add Ellipsoid [Action] [Scripting Only] (Draws an ellipsoid on the plot.)
  Add Vector [Action] [Scripting Only] (Draws a vector or arrow on the plot.)

Re: 3D plot of crystal structure

Craige_Hales — Wed, 22 Jul 2020 16:43:55 GMT

Good use of show properties to discover the limited set of capabilities in the Graph3D box! If you need general drawing, you'll have to go with the SceneBox OpenGL code.

@Paul_Nelson