Author Topic: Filtering defects by time or frame sequence  (Read 128 times)

qjli

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Filtering defects by time or frame sequence
« on: November 21, 2017, 10:43:39 PM »
Hi Alex,

I have a system that initially populated with some dislocations and interstitials and this system evolves under external load. With increasing simulation time, there are more and more point defects generated by the dislocation-interstitial interactions. I used DXA to analyze the defects, but all the defects (initial defects and new defects) are mixing together and hard to distinguish visually. Are there good ways to visualize such a system by highlighting the newly generated point defects? In other words, is it possible to color the new defects with different colors or just show the new defects? BTW, the newly generated defects are largely interstitial and vacancies. 

Thanks,
qjli

Alexander Stukowski

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Re: Filtering defects by time or frame sequence
« Reply #1 on: November 21, 2017, 11:22:44 PM »
Hi,

If we focus on the point defects for the moment, I suggest to use Freeze Property modifier for that. Here is what I have in mind:

First, you identify the atoms that form point defects in the very first simulation frame and select them. You then apply the Freeze Property modifier to "freeze in" the Selection particle property so that it doesn't change anymore even if new defects are created at later frames. You can now highlight this static selection of atoms using the Assign Color modifier. It might make sense to insert a Compute Property to dynamically modify the atom selection and restrict it to just those atoms which were selected in the first frame and which are still defects in the current frame.

Dislocation line defects identified via DXA are a different story. I'm not sure how to do it here. It is possible, at least in principle, to save the dislocations found in the first frame and overlay them with the defects dynamically identified in later frames. However, those dislocation will then appear twice. The problem is that dislocations do not have a unique identity and unlike atoms they cannot be tracked over time.

-Alex

qjli

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Re: Filtering defects by time or frame sequence
« Reply #2 on: November 23, 2017, 05:34:48 AM »
Thanks, Alex, for the nice suggestions. Following your method, I used selection, freeze and compute property to filter out the initial defects. Then the transparency of these initial defects were set to 0.8 and the new defects are thus highlighted. This works well; however, there is a minor issue, i.e., there are also many sparsely distributed individual atoms identified as new point defects (they are actually belonging to the deformed initial defects but not identified in the first step). It will be much better if these atoms were not displayed. Do you have any suggestions to eliminate these 'noise' atoms?

thanks,
qjli

Alexander Stukowski

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Re: Filtering defects by time or frame sequence
« Reply #3 on: November 23, 2017, 09:48:10 AM »
I don't have a clear picture of situation and can give you only general advice..

Typically, one would use a coordination-based criterion to filter out such spurious atoms. For example, you can employ the Compute Property modifier to count how many neighbors within given cutoff range of each new defect atom belonged to the initial defects. This information can then be used to select certain atoms, e.g. those which are close one of the initial defects, with the Expression Select modifier and remove them.

qjli

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Re: Filtering defects by time or frame sequence
« Reply #4 on: November 23, 2017, 06:26:30 PM »
Thanks, Alex.  Let me take a one dimensional example to show the situation.

Suppose we have a one dimensional atomic structure:

...---0---1---2---3---4---5---6---...

Initially, 2---3---4 are the defect atoms forming a point defect (let's denote these atoms as set I).

After some deformation, atoms 1---2---3---4---5 become defect atoms (i.e, the number of atoms belonging to a point defect may fluctuate by deformation or local distortion).  Of course, there are also completely new point defects formed on this chain. Let's denote all these defect atoms in this deformed configuration as set N.

By the previous discussed procedure (select, freeze and compute property), we can only identify 2---3---4 as the initial point defect (i.e., the intersection of set I and N), thus atom 1 and atom 5 stand out as individual defect atoms (they are not new point defect but still related to the initial point defect). 

My question is how to assign these individual atoms such as  1 and 5 to the initial point defect, thus reducing the 'noise' of true new point defects.

My thought was to perform a cluster analysis on the atom set N-I, then those 'noise' atoms should have very small cluster size and the true new point defects should have relatively large cluster size. This may allow us to filter out the 'noise' atoms. But I am not sure if/how this could be done.

In your last reply, did you mean the coordination of atoms 2---3---4 can be directly obtained using 'Compute Property' modifier?

Thanks,
qjli

Alexander Stukowski

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Re: Filtering defects by time or frame sequence
« Reply #5 on: November 29, 2017, 02:32:30 PM »
I'm sorry for the delay.

Here is what I had in mind:

Let's say the 'Selection' particle property indicates whether an atom belongs to set 'I' or not, i.e. being an initial defect or not. You can then use the Compute Property modifier to determine for every atom in the system whether it is close to one of the atoms from that set 'I' or not. In order to do that, you need to activate the 'include neighbor terms' option in the Compute Property modifier. You simply enter 'Selection' in the neighbor expression field and choose an appropriate cutoff. You can name the output property 'IsCloseToInitialDefect' to similar. Enter '0' as expression for the center atom.

The new property 'IsCloseToInitialDefect' will be zero for atoms that do not have any selected neighbors and non-zero for atoms which have at least one selected neighbor.

In a final step you can now restrict your set 'N' to atoms having IsCloseToInitialDefect==0.

qjli

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Re: Filtering defects by time or frame sequence
« Reply #6 on: December 11, 2017, 06:31:23 PM »
Thanks a lot, Alex. This works for most of the noise defect atoms (a minor issue is that new point defects very close to the initial point defects were also excluded).