Author Topic: Regarding atomic strain modification  (Read 66 times)

bahmanpbamp

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Regarding atomic strain modification
« on: June 05, 2018, 01:11:24 PM »
Dear OVITO experts,

I am going to compute "atomic strain" by OVITO from a 2D dump file(as per attached). However I face with this error:

"Simulation cell is degenerate in the deformed configuration."

Actually, I checked the box Adjust the simulation size box in the show periodic image box. But, the result is the same!

 The reference file including initial positions of atoms has also been attached.

Any help is highly appreciated.

Yours Sincerely,
Bahman

Alexander Stukowski

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Re: Regarding atomic strain modification
« Reply #1 on: June 05, 2018, 01:39:08 PM »
Dear Bahman,

The error message occurs because the strain calculation function thinks that the simulation cell has no (3d) volume.
When loading a XYZ file, OVITO cannot automatically detect whether it is a 3d or 2d domain. For 2d systems, you may have to explicitly activate 2d mode as indicated in the attached screenshot to avoid the error message.

-Alex

bahmanpbamp

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Re: Regarding atomic strain modification
« Reply #2 on: June 05, 2018, 03:29:58 PM »
Dear Alex,

Thank you very much for your response. Actually, I did what you suggested. But, I have still problem when I activated the strain analysis checkbox during playing the dump movie. Actually OVITO reports  that:

"waiting for input data to become ready"?!

By the way, I have also inserted an initial atomic configuration file as the refrence

Yours Sincerely,
Bahman

Alexander Stukowski

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Re: Regarding atomic strain modification
« Reply #3 on: June 05, 2018, 03:34:10 PM »
I didn't really check if the atomic strain calculation works, because you did attach only a single dump file ("dump_initial positions.dat") in your first post. Is there a deformed configuration that you can upload as well?

And please let us know which OVITO program release you are using. There are some subtle differences between the versions.

bahmanpbamp

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Re: Regarding atomic strain modification
« Reply #4 on: June 05, 2018, 04:35:39 PM »
Thank you very much for your response. Actually I am using OVITO rev.2.9.0 on WIN 7.0. Please find attached the dump file from history of model deformation.
« Last Edit: June 05, 2018, 04:38:13 PM by bahmanpbamp »

Alexander Stukowski

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Re: Regarding atomic strain modification
« Reply #5 on: June 05, 2018, 05:14:17 PM »
Thanks. I tested it myself and it worked as expected. Here is what I did:

1. Load the file dumpf.dat in OVITO.
2. In the "XYZ" panel, activate the option "File contains time series"
3. Go to the 'Simulation cell' panel and activate the 2D mode.
4. Insert Atomic Strain modifier, set "cutoff radius" parameter to a value of 3.0
5. Scroll down to "Reference: External file" panel and use the "Pick new file" tool button to load the reference configuration (dump_initial positions.dat).

bahmanpbamp

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Re: Regarding atomic strain modification
« Reply #6 on: June 05, 2018, 05:22:21 PM »
thank  you very much for your email. yes it works. I was doing the same but did not going to the color coding to observe the results!
thank you Alex.

bahmanpbamp

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Re: Regarding atomic strain modification
« Reply #7 on: June 06, 2018, 10:41:29 AM »
When I apply the larger model, it still calculates the strain tensors but it seems that the STRAIN TENSORS are not activated inside the Color coding/particle property.So, I cannot access to the strain tensors!

Alexander Stukowski

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Re: Regarding atomic strain modification
« Reply #8 on: June 06, 2018, 11:20:35 AM »
With "strain tensors" you mean the 6 individual components of the atomic strain tensor (in 3d), right?

OVITO should have computed those tensor components given that you did not disable the Atomic Strain modifier, the "Output strain tensors" option of the modifier has been activated, and there is no error message being displayed by the modifier. Note that the Stress Tensor particle property may not be visible in selection box of the Color Coding panel while the Atomic Strain modifier is still computing its results.

Also note that, by default, the Atomic Strain modifier outputs only the Shear Strain property for each atom. You need to activate the "Output strain tensors" option in order to get all 6 strain components (3 of which will be zero in case of a 2d system).