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compute D2min for 2D models

Dear OVITO users,

Could you teach me how to tell ovitos my configurations are just 2 dimensions in input scripts when using ovitos 3.0 to compute D2min Falk et al defined? Thanks.

Best,

Zhao

Dear Zhao,

the Simulation Cell object has an attribute is2D which you can set, see also https://www.ovito.org/docs/current/python/modules/ovito_data.php#ovito.data.SimulationCell.

pipeline.source.data.cell_.is2D = True

-Constanze

Dear Constanze,

Thanks a lot for your answer. It worked.

Best,

Zhao

Dear Constanze,

Could you teach me how to set the "is2D" in Ovito 2.9 ?

I found that the D2min calculated with Ovitio 3.0.0 for sheared 2D models may not be correct. Thus I want to check it with Ovito 2.9. Thanks.

Zhao

Hi,

I'm not sure if the calculation of the non-affine squared displacements has been possible for 2 dimensional systems in OVITO 2.9 https://www.ovito.org/about/version-history/, but the attribute of the Simulation Cell Data object is also called is2D in OVITO 2.9.

Could you explain what makes you suspect that the result might not be correct?

-Constanze

I tried to set "is2D" in ovito 2.9 as below:

from ovito.io import *

node = import_file(fn_input)

node.source.load(fn_input)

node.source.data.cell_.is2D = True

But got the error: AttributeError: DataCollection does not have an attribute named 'data'.

For non-triclinic 2D models, the calculation of D2min by Ovito 3.0.0 looks reasonable.

But for triclinic 2D models, the atoms close to both top and bottom boundaries always have larger D2min compared to atoms at other regions. This phenomenon is more obvious at large strain. I tried many different samples and always observed this phenomenon, which is inconsistent with my expectation, as all these models are with PBCs in all dimensions. So I suspect if the D2min got with Ovito is correct, as the stress-strain curves I got are consistent with our expectation and I didn't find other bugs.

And I also tried 3D samples and everything looks normal.

Zhao

 

 

Thanks for the detailed explanation Zhao, we would like to investigate this further. Could you please send us an example snapshot and the corresponding reference configuration through the official mail support? That will make it easier for us to help.

 

 

Hi Constanze, today I wrote code by myself to compute D2min for sheared 2D model and I got very similar value as that obtained with Ovito, which seems to suggest that the problem is not due to Ovito.

Ok that's good to hear, let us know if you need further help.

Best,
Constanze