Author Topic: Void in amorphous material  (Read 962 times)

jhart

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Void in amorphous material
« on: November 13, 2017, 07:46:43 PM »
How can I identify void formation in an amorphous material using OVITO? Is there a computation that can identify regions that are much less dense than others?


Alexander Stukowski

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Re: Void in amorphous material
« Reply #1 on: November 17, 2017, 11:41:52 AM »
Hi,

there are two approaches that come to my mind:

(1) You can use OVITO's Voronoi Analysis function to compute the atomic volume. The volume per atom can be taken as a local measure of the density. Note that it might be necessary to flatten out local fluctuations. This can be done using the Compute Property modifier or the Bin and Reduce modifier.

(2) The Construct Surface Mesh modifier allows you to reconstruct the outer and inner surfaces of a solid. Hence, it can be used to identify pores in a material. Here, the probe sphere radius parameter of the modifier controls the minimum size of the pores to be identified.

jhart

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Re: Void in amorphous material
« Reply #2 on: December 06, 2017, 06:22:53 PM »
If I use the Voronoi analysis modifier, I see that it outputs atomic volume, which gives a local measure of the density. You said that I can use the bin and reduce modifier to flatten out local fluctuations. Once I go to Bin and Reduce, and select Atomic Volume under particle property, Which Reduction operation should I use, and which binning direction should I use?

Will this output something new that I Can use under particle selection? How specifically can I determine the less-dense regions and thus a void?

Thanks for your help!

Alexander Stukowski

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Re: Void in amorphous material
« Reply #3 on: December 10, 2017, 06:20:19 PM »
The Bin and Reduce function can map the per-atom volumes only to a two-dimensional grid of bins, not a three-dimensional one. So averaging will be performed within each bin and along the third axis. I don't know, this may not be the best choice for you problem at hand. It makes most sense for situations that are quasi-two-dimensional.

With the Compute Property modifier you can do a three-dimensional spatial averaging around each atom. Imagine a sphere with a user-defined radius around each atom. The value at every central site is computed as the sum over the values of all atoms contained within the sphere. In a second step, you can divide the summed values by the number of atoms in each sphere, giving you average values.

zhen

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Re: Void in amorphous material
« Reply #4 on: August 09, 2018, 11:21:26 AM »
Hi Alex,

I am also interested in the void size distribution of amorphous material under tension. I noticed that the " Construct Surface Mesh" modifier seems promising because with this modifier I will be able to output a set of point coordinates that defines the outer and inner surfaces. So if I consider the volumes enclosed by the inner surfaces as voids, I should also be able to estimate the voids size use the coordinates of points on the surface, right? Is this can be realized using the latest version of OVITO?

Thank you very much.

Regards,
Zhen

Alexander Stukowski

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Re: Void in amorphous material
« Reply #5 on: August 09, 2018, 01:31:53 PM »
Hi Zhen,

Since you are interested in the void size distribution, you want to identify the individual voids in the material and determine their sizes, right?

Yes, in principle you can do this by taking the triangle mesh generated by the Construct Surface Mesh modifier, decompose it into disconnected components, one component (polyhedron) per void. For each mesh component, you would then have to calculate the volume it encloses. That is probably the hardest part, because the voids may be non-convex, and calculating the volume of a general non-convex polyhedron is not trivial.

The SurfaceMesh class of the OVITO 3.0 Python interface gives you programmatic access to the vertices and triangles of the surface mesh. From here on you are on your own though. OVITO doesn't provide any built-in functions for calculating the volumes, and I am not working on any such functionality at the moment.

Best regards,
-Alex

zhen

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Re: Void in amorphous material
« Reply #6 on: August 09, 2018, 02:18:00 PM »
Hi Alex,

Thank you for your reply. Yes one of my goals is to know the sizes of the individual voids in the material.

I'll take a closer look to the Python interface of the SurfaceMesh class see if I make something out of it.

with best regards,
Zhen