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Simulating 2D materials #156

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jmunshi1990 opened this issue Jan 11, 2022 · 4 comments
Open

Simulating 2D materials #156

jmunshi1990 opened this issue Jan 11, 2022 · 4 comments

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@jmunshi1990
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Hello,

I am trying to simulate EBSD pattern for 2D structures with EMsoft. I have a question about basic geometry.

  1. Is there any way to control/change the size of the geometry (such as the thickness, and lateral in-plane dimensions)? Also how do we make sure that the EBSD simulations are being performed in the thickness (vertical) direction?
  2. Additionally, does it have any implications on the simulated pattern (theoretically).
  3. Our purpose is to compare these with experimental EBSD which will be performed for 2-20 nm thickness (i.e., typically 3-30 layers of MoS2)
  4. One more question on top of this, is there any way to simulate 2D heterostructures (for example MoS2 with hBN as substrate)?

I think the all answers to my question lies in the xtal creation step but your elaborations are much appreciated. Thanks and look forward to your response.

Joydeep

@marcdegraef
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marcdegraef commented Jan 11, 2022 via email

@jmunshi1990
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Hello professor Graef,

Thank you very much for your elaborated explanation. For the heterostructure, initially I was not aware of the EMEBSDoverlap and what I did was actually superimpose images with some weights (to the intensity) to EBSD pattern of each phase (Considering there is no interfacial effect/dynamical effect between two phases). Usually in experiments as well hBN phase has a very weak signal and poor SNR compared to say MoS2. So for our machine learning problem, we wanted that to be the case to simulate/mimic real experiments. I will try the overlap code and check the results. Thanks for the suggestions.

Couple of questions related to the sample orientation (as I found these details a bit confusing in the Wiki page as probably I am new to EBSD field):

  1. while defining the unit cell, the c direction (mentioned in the commandline input) is always the thickness direction for the sample - is that right? meaning c direction defined through the xtal file is always going to be the back scatter direction. is that right?
  2. The last question is about some more clarifications on the euler.txt file at the very end. what we want is to simulate patterns for multiple orientations with different relative orientation between the two phases. for example, keeping hBN and MoS2 layers stacked on top of each other we want to rotate the MoS2 layer relative to hBN layer. How do we vary the euler angles in the file? so if the c direction of the unit cell for both of them are in normal directions (thickness) then we are rotating MoS2 in the a-b plane...
  3. also, can we tilt the sample (i.e. rotate the c-axis) by changing the euler angle? As per my understanding if the master simulation considers electrons scattering from the sample keeping c-direction as normal, is it possible to tilt c-axis after the master simulation is done?

Thanks again and please correct me if I am wrong in any case.

Joydeep

@marcdegraef
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marcdegraef commented Jan 11, 2022 via email

@jmunshi1990
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Thank you very much professor.

I have one quick question about high throughput simulations. I am trying to simulate 100s of structures in automated manner whose initial unit cell structures will be extracted from a data repository through python program. Is there any way to use a input file for the crystal structure through the EMmkxtal command. Currently the way it is implemented it is difficult to use a script to run this command. Thanks

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