Author Topic: DisplacementMagnitude  (Read 49 times)

lcosta

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DisplacementMagnitude
« on: May 09, 2019, 06:22:45 PM »
Please see the screenshot below:
https://imgur.com/a/YfRXnpu

This is a 2 nm radius x 8 nm long cylinder. A uniaxial tension simulation was performed in LAMMPS using metal units so I assume the distance units Ovito is using are Angstroms. At timestep 1000 (0.0001 strain), Ovito is displaying 0.4% of the atoms have a DisplacementMagnitude > 100. If that is 10 nm this is impossible.

What is going on here? Thank you.

Constanze Kalcher

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Re: DisplacementMagnitude
« Reply #1 on: May 09, 2019, 07:04:48 PM »
Hello,

please upload your screenshot here in the forum, using the "Attachments" function below the text editor.  The link you posted here shows a black image, so I can't see what you did.

-Constanze

lcosta

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Re: DisplacementMagnitude
« Reply #2 on: May 09, 2019, 07:29:16 PM »
Sorry about that. Please see attached.

Constanze Kalcher

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Re: DisplacementMagnitude
« Reply #3 on: May 09, 2019, 07:37:07 PM »
Hello,

it seems that there is an issue with your input data. Can you upload the two cfg files here, e.g. the current file and the reference you used? Than I can look into this further tomorrow.

-Constanze
« Last Edit: May 09, 2019, 07:41:03 PM by Constanze Kalcher »

lcosta

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Re: DisplacementMagnitude
« Reply #4 on: May 09, 2019, 07:43:11 PM »
They're a bit too large for an attachment. I placed them in my Public Dropbox.

https://www.dropbox.com/sh/n5x64nen0w8bjao/AAAXEXZXTiccVZDlb_g_DpCZa?dl=0


lcosta

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Re: DisplacementMagnitude
« Reply #5 on: May 09, 2019, 10:49:46 PM »
Here I am attaching a smaller simulation with the same problem.

c_displace_4 is the LAMMPS supplied displacement magnitude; the fourth element of the vector computed by compute displace/atom.
DisplacementMagnitude is the OVITO displacement magnitude.

Both are at the same timestep and use the same reference configuration.

Constanze Kalcher

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Re: DisplacementMagnitude
« Reply #6 on: May 10, 2019, 10:54:35 AM »
Hello Icosta,

thanks for uploading the files. So the problem is that you didn't dump the atom ID's along with the positions etc. And unless you didn't specifically make sure that the atoms in the different snapshots are still sorted by their atom ID's there is no way you can calculate displacements in post-processing. Let me give you an example: Let's call the atom that is in the fifth line of the cfg file atom 5. If there is no particle property "Particle Identifier"-  OVITO then calculates the displacement vector of atom 5 by taking the reference position of the atom in the 5th line in the reference file. However, in your case it is very likely not the same particle. So you're really comparing positions of different particles that's why the displacements you calculated are so large.
So for the future, either dump the ID's or turn on sorting by atom ID's when dumping to avoid these problems.

-Constanze