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Visualizing spheres representing LES

I have a porous material framework (.lmps file format) for which I have calculated the largest empty spheres (LES) to represent the pore distribution. Essentially the LES coordinate centers are stored in a file with a size (the sphere radius). I would like to be able to visualize these pores inside the framework. I do not believe this is easily doable without creating an xyz file of the LES coordinates, overlaying them onto to porous framework, and manually setting each particle radius. However, I wanted to make sure that I am not missing something or that there is not some sort of duct tape solution.

 

I appreciate any help or thoughts.

Hi Dylan,

there's no need to manually set each particle radius. I think the easiest would be to create an extended xyz-file that contains the LES coordinates and then an extra column with the radii (and any other property you would like to import). During file import OVITO lets you specify which particle properties you would like to map to each individual column (see attached screenshot).

As an example, let's say your porous structure has a cell size of 10x10x10, the origin of the cell lies at -5, -5, -5 and there are two pores, one located at (0,0,0) with a radius of 2 and another one at (2.5, 2.5, 2.5) with a radius of 1. In addition you would like your "pores" to have a transparency of 0.5. Then your xyz-file containing the pores would look like this:

2
Lattice="10 0.0 0.0 0.0 10 0.0 0.0 0.0 10", cell_origin="-5 -5 -5"
0.0 0.0 0.0 2 0.5
2.5 2.5 2.5 1 0.5


where the first three columns are the xyz-coordinates, the fourth is the radius and the fifth the transparency. Moreover, if you add the names of the particle properties to the header of the xyz-file, you can skip the manual column mapping during file import.

Properties=pos:R:3:radius:R:1:transparency:R:1

In order to overlay these two datasets, you can first import your porous structure into the GUI. Then add a second pipeline by choosing "Add to scene" during the second file import, see second screenshot.

Hope that helps,

Constanze

Uploaded files:
  • column_mapping.png
  • pores.png

Hi!

I just wanted to follow up and say thank you for the help. The problem was on my end with the way that I wrote my xyz file format. I was able to accomplish this task nicely after fixing the error. I meant to follow up sooner.

 

Best,

Dylan

Hi Dylan,

great to hear that this issue is resolved. Don't hesitate to get back to us should you have any further questions.

-Constanze

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