Author Topic: atomic strain calculation during the shear process  (Read 241 times)

June

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atomic strain calculation during the shear process
« on: December 19, 2018, 02:26:38 PM »
Dear Ovito users,

I am running an interface shear simulation and want to calculate the atomic strain at different frames during the shear process. Since after relaxation the interface reconstructs,  the initial atomic structure before relaxation is taken as a reference. The simulation box is periodic in directions parallel to the interface and I outputted unwrapped atomic positions in lammps.

I think the shear displacements should not contribute to atomic strain calculation and I only care about the relative displacements between atoms. Then the reference configuration need to move rigidly as interface shears. Could Ovito set different reference configurations for each frame? Or is there a better method to calculate the atomic strain during the shear process?

I attatched one output file for your reference.

Thank you in advance.

Sincerely,
June

Alexander Stukowski

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Re: atomic strain calculation during the shear process
« Reply #1 on: December 19, 2018, 04:20:33 PM »
Dear June,

Yes, Ovito can compute atomic strains with respect to a varying reference configuration. In this case, the reference series of configurations should contain the same number of frames as the series of fully relaxed interface configurations. You can load the reference series in the Atomic Strain modifier and select the "Reference frame - Relative to current frame" option and set the "Frame offset" to 0. When the modifier calculates the atomic strains for a frame of the shear simulation, it will use the corresponding frame from the reference series.

You didn't mention how the shearing of the interface was performed. If it was done by shearing the periodic simulation cell boundaries (in contrast to moving the atoms inside the cell), then it would suffice to simply use the "Eliminate homogeneous cell deformation" option of Ovito 2.9.0 (or the equivalent "Affine mapping: To reference" option of Ovito 3.0.0-dev). The modifier will then apply an affine shear deformation to all atomic positions prior to calculating the atomic strains, basically reverting the overall shear of the interface and retaining only the internal motion of atoms due to relaxations. In this case you would not need to create and use an explicitly varying reference configuration as described above.

A third option is for you to simply work with a static reference configuration and focus on the "non-affine squared displacements" computed by the Atomic Strain modifier instead of the atomic shear strains. The non-affine squared displacement value calculated for each atom quantifies how irregular the local displacements around a central atom are, i.e. how much the neighboring displacements deviate from a perfectly affine shear deformation.

-Alex

June

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Re: atomic strain calculation during the shear process
« Reply #2 on: December 20, 2018, 02:19:11 AM »
Dear Alex,

OK, I will try these methods. Thank you for your help.

Best wishes
June