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Messages - Anders Blom

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Google is kind of nice for these types of questions.

General Questions and Answers / Re: BSSE & Possible ATK Bug
« on: October 3, 2022, 19:28 »
Yes, this works, and it's not even really a serious approximation because you are not interested in how the atoms rearrange in the XY-plane or relative each other, they should be bound by symmetry. In fact, you can even do it simpler by computing the BSSE-corrected total energy for a series of interface layer distances and find the energy minimum by fitting a parabola. That way are you not reliant on the optimization convergence criterion.

General Questions and Answers / Re: BSSE & Possible ATK Bug
« on: October 3, 2022, 07:46 »
I have no idea why this is happening but for sure I will report it, thanks for letting us know.
Note that the Script Generator will probably look a bit different in the next release!

General Questions and Answers / Re: BSSE & Possible ATK Bug
« on: September 30, 2022, 22:33 »
I confirm the bug.

Btw, what else did you change to end up with the message that it cannot preview the number of k-points? I don't see that but it indicates a potential additional problem

General Questions and Answers / Re: BSSE & Possible ATK Bug
« on: September 30, 2022, 19:43 »
I can't reproduce the problem in Q2, see attached. What version do you use? I am on T-2022.03-SP1

For Q1, I have not tried thus myself but according to the tutorial and manual the way you suggested originally should work. I did not however mean that A and C interact, in fact the opposite. My idea was to group them together and letting them interact collectively with B. If you think about what the BSSE does, it will then compute B where AC are ghost, and AC where B is ghost, and I think that should work. It would not work, however if A and C interact.

General Questions and Answers / Re: Graphene Mobility
« on: September 29, 2022, 09:28 »
The results are quite sensitive to details, so it might be that some parameter changed its default value in newer versions compared to the one used when the tutorial was written. Or, you might have forgotten to change perhaps one parameter, like force tolerance or basis set. Anyway your numbers seem reasonable, at least.

The last point is interesting and sounds like maybe a bug, could you share the full error message shown?

General Questions and Answers / Re: BSSE & Possible ATK Bug
« on: September 28, 2022, 23:48 »
A1. If A and C are not interacting much, maybe you can just do B as one part and AC as the other?
A2: Are you sure you are not looking at the sampling density?

It's basically just a smearing parameter for the Fermi distribution function. Although the temperature can affect convergence, it usually not the main reason why something does not converge. Things like k-point sampling and in general how the system was set up geometrically are often more important.

General Questions and Answers / Re: Optimization issue
« on: September 28, 2022, 23:40 »
I took a look at your script and problem in general, and I think you need to divide it up into smaller pieces. When designing a car, you don't make a whole working car and then put it in a wind tunnel to see if it's aerodynamic enough, you test and improve each component separately first. Same here - instead of putting the whole device together and optimizing it, which is a huge task, it's a lost faster, easier and simply better to build the device from optimized parts.

So, first you should make sure the 2D sheet itself has an optimal lattice constant and atomic coordinates. This can be done for what constitutes the electrodes, and better yet on just the primitive cell of the 2D material. That is, you optimize the size and positions of the cell with 2 atoms, I guess.

From that optimized unit, you build the 2D ribbon by repeating in A or B whichever makes sense (do not repeat in C yet), passivate it and (optionally, I would say) optimize again for edge reconstruction. I imagine this has negligible effect on the overall results, but for completeness I mention it here.

Now you can make a small repetition, maybe 2 or 3x in the C-direction and add the extra atom over the surface. To find its optimal position you can run a regular geometry optimization on this relatively small system, which is periodic in C (and A and B too). It is highly unlikely that the ad-atom has any influence on the lattice constant, so just a force optimization will be enough. Make sure the outer layers in C of the 2D material are fixed, for later use!

Finally, repeat the ribbon in C as much as needed. In the middle, remove a portion corresponding to the small repeated system with the ad-atom you looked at in the previous step but leave the atoms corresponding to the ones you fixed. Drop in the optimized structure - if you do it right, the fixed atoms will exactly overlap existing atoms in the structure, but that is easy to fix using the selection tools.

Now create the device and run it - there is no need to relax the whole device since each part is already optimized.

Not true excited states, no. But the Kohn-Sham orbitals above the Fermi level do provide some estimate of the excited levels, even if not formally correct...

MD is very short-sighted, it basically only knows what happened in the previous step. So if you read positions and velocities from the last step, it's really  the same as if the previous run had continued from that point, and there will be no need for a new equilibration.

General Questions and Answers / Re: class STM
« on: September 20, 2022, 21:41 »
Yes they should. I will locate someone who can provide an example

Did you remove all hdf5 files, like state.hdf5 also? Maybe also try removing machines.hdf5

You could grep for "not converge" or "warning" instead to check. Yeah unless your energies or MD temperature go crazy, I would not worry much if a single calculation here and there don't converge or behave strange.

Temperature, depends on whether it's a metal or semiconductor. 1000 K is high for insulators but ok for metals.
Other convergence tricks are usually problem-specific so I cannot say without knowing the system. Vacuum? Magnetic?

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