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Simulating 2D materials #156
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Hi Joydeep,
1. you can set the film thickness in the EMMCOpenCL Monte Carlo program
simply by limiting the total thickness with the depthmax parameter; that
will then determine the maximum integration depth for the dynamical
simulations in the EMEBSDmaster program. So, if you have a 5 nm film,
set depthmax to 5.0, and depthstep to 0.5 to have a sufficient number of
energy bins.
2. Not sure what "implications" you are referring to here...
3. Typically, the EBSD signal comes from the top 10-20 nm of the sample
so you should be able to incorporate that in your simulations.
4. There is no direct way to simulate a two-phase stack of layers.
However, if your stack is epitaxial, you can in principle define a long
(but low symmetry) unit cell that has both phases in it with the long
axis normal to the film. In your case though, keep in mind that most of
the signal will come from Mo and S... EBSD signal is roughly
proportional to Z^2 (Rutherford scattering cross section), so if you
take two layers of equal thickness, one MoS2 and the other hBN, then the
total scattering cross section (ignoring relative atom positions and
such) is 42^2 + 2*16^2 = 2,276 for MoS2, and 5^2 + 7^2 = 74 for hBN...
so in this case only about 3% of the BSEs will come from the hBN layer.
This of course ignores the actual geometry and beam direction, but I
think you will not see much pattern due to the hBN, except perhaps for
very thin MoS2 layers on hBN bulk.
I would start by computing the master patterns for both phases and then
adding them together; in the EMEBSDmaster HDF5 output files, the
relative intensities of the two phases will be preserved, so as a first
approximation you can add the two patterns in the correct orientation
relationship. The EMEBSDoverlap program will do that for you... I have
an illustration of how that works in the following paper:
W. Lenthe, L. Germain, M.R. Chini, N. Gey, and M. De Graef, "Spherical
indexing of overlap EBSD patterns for orientation-related phases --
application to titanium", Acta Materialia 188:579-590 (2020) DOI:
<https://doi.org/10.1016/j.actamat.2020.02.025>
Let me know if this helps...
Regards,
Marc.
…On 1/10/22 9:38 PM, Joydeep Munshi wrote:
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
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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):
Thanks again and please correct me if I am wrong in any case. Joydeep |
Hi Joydeep,
see responses below.
Regards, Marc.
On 1/11/22 8:52 AM, Joydeep Munshi wrote:
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?
No that's not always the case. In EMsoft, we use the International
Tables of Crystallography convention that the z-axis of the cartesian
reference frame is normal to the a-b plane, i.e., parallel to the
reciprocal c* axis. The doesn't matter for the Monte Carlo simulations
which treat the structure as amorphous, but it does matter for the
EMEBSDmaster simulation; the c* axis is always at the center of the
master pattern.
1. 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...
Take a look at the template file for the EMEBSDoverlap program... I
think you can do this by varying the orientation relations.
1. 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?
The master pattern does not consider a specific sample orientation at
all. Think of the master pattern simulation as the following thought
experiment: take your crystal structure and align it with a Cartesian
reference frame; assume that the crystal forms a sphere and that there
is a uniform electron source at the center of the sphere. The electrons
channel in all directions through the spherical crystal and then hit a
spherical detector (the Kikuchi sphere) surrounding the crystal. The
pattern of intensity on that sphere is the master pattern. It has
nothing to do with sample orientation which is defined afterwards in the
EMEBSD program.
… Thanks again and please correct me if I am wrong in any case.
Joydeep
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Marc De Graef
Professor
Department of Materials Science and Engineering
130 Roberts Engineering Hall
Carnegie Mellon University
5000 Forbes Avenue
Pittsburgh, PA 15213-3890
USA
Ph: (412) 268-8527
Fx: (412) 268-7596
***@***.***
web:http://materials.cmu.edu/degraef
Admin. Asst.: Marygrace Antkowski
Phone: (412) 268-7240
|
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 |
Hello,
I am trying to simulate EBSD pattern for 2D structures with EMsoft. I have a question about basic geometry.
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
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