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71

General Questions and Answers / Re: Bias direction for different electrodes

« Last post by Anders Blom on October 9, 2024, 19:46 »

No matter how the bias is applied, the current is computed according to the formula in https://docs.quantumatk.com/manual/Types/TransmissionSpectrum/TransmissionSpectrum.html#current. In principle the integral is from -inf to +inf, but in practice of course we can only carry it out for the energy points included in the transmission spectrum calculation.

72

General Questions and Answers / Re: Error in MoS2 forcefield implementation in QuantumATK

« Last post by Anders Blom on October 9, 2024, 19:43 »

MoS2 2D material would be a nice candidate to fit an MTP for, and then one can add additional atoms as needed. Not trivial, but probably a lot better than this potential, yes. The article makes references to a few other existing ReaxFFs for MoS2 (and, notably, claims to improve on them: Ostadhossein et al., 2017; Hong et al., 2017; Chen et al., 2020) - perhaps you can test those, provided they supply the parameters.

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General Questions and Answers / Re: Error in MoS2 forcefield implementation in QuantumATK

« Last post by AsifShah on October 9, 2024, 12:03 »

Dear Anders Blom,

Thanks a lot for your response.
Yes, the Mo-S bonds are overestimated. Also, though there is O2 molecule but the distortion is high than what is obtained from DFT.

I tested the script u shared on Gold and the results do not make sense. The Au atom does not bond at S vacancy which is clearly in contrast with DFT. (See attached pic)

I think you are right the authors perhaps do not want to share the real forcefield. This one looks useless.

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General Questions and Answers / Re: Bias direction for different electrodes

« Last post by lohy on October 9, 2024, 11:00 »

What confuses me a bit when you say that is that when I calculate the current from the transmission spectrums I can only reproduce the IV curve when I have the bias window from -0.5 to 0.5. In the transmission analyzer the left electrode is at 0 and the right is then moved from -1 to 1. So I would assume, based on what you say, that the bias window that is integrated in the code would be e.g. at one point from 0 to 1.  Is this how I should understand it?

75

General Questions and Answers / Re: DOS vs TS

« Last post by Anders Blom on October 9, 2024, 00:19 »

I didn't say use more k-points for the transmission, you should use more energy points.

76

General Questions and Answers / Re: Error in MoS2 forcefield implementation in QuantumATK

« Last post by Anders Blom on October 9, 2024, 00:17 »

Some of these are comparing the wrong lines with each other, there are two different lines in the file starting with "4 4 7", and the other one matches. And the "4 4 4 4" line is correct, just has truncated decimal zeroes in one case. I can't even see a line with "1 3 1 2" in the current version of QuantumATK, so it seems this was partly fixed after your release (I checked in W-2024.09), but I do agree on the 48th torsion still missing even in W.

However, now things get interesting. To use the original file in QuantumATK, just save it as a text file and use file="reaxff.txt" instead. If you do this, however, we discover that the file is not correct. The missing torsion angle "0 4 9 0" cannot be used because there is no particle 9. Maybe it should be 8, but trying to "fix" a ReaxFF potential like that is most likely not going to work.

So, we now have 3 potentials, all slightly different:
1) The one shipped with whichever version of QuantumATK you use
2) The original from the paper
3) The one shipped with QuantumATK W-2024.09

You say that 1 gives weird structures, but we also cannot use 2 (someone should maybe notify the authors...). So hopefully 3 is actually the correct one, I have attached it to this post and shown how to use it in the Python script.

Finally, I ran your script, and yes it does bend the structure, but you have an oxygen molecule there, so I am not too surprised. I am also somewhat skeptical to the quality of the potential as it makes very long Mo-S bonds, 2.65 Å compared to 2.42 Å in databases for MoS2. Maybe this is an effect of the fact that the potential they publish is invalid, and in reality they used a different one for the paper (which they don't want to share...?), but clearly the forcefield as published does not appear to work well for MoS2, and the paper also never checks this (they have a few other bond comparisons with DFT, but not Mo-S). I would also ask the authors why they state that they build on the "force field based on ReaxFF Mo/S/O/H (Islam et al., 2014)" when the paper by Islam has nothing to with Mo/S...

77

General Questions and Answers / Re: Charged vacancy in a device configuration for transmission

« Last post by Anders Blom on October 8, 2024, 23:33 »

Whether a vacancy is charged in a device or not depends on the location of the defect level in relation to the band edges. In an atomistic first-principles simulation we don't preassume any of that, you would just enter the vacancy as is, and then look for the charge around it in the converged state of the calculation.

78

General Questions and Answers / Re: Error in MoS2 forcefield implementation in QuantumATK

« Last post by AsifShah on October 8, 2024, 22:43 »

Dear Anders Blom,

Sure. Please find the attached pics highlighting errors. The yellow lines indicate places where mismatch is found between Reax parameters from article (left side) and QATK implementation (Right side). Also, torsion has one missing line and Angles also misplaced or missing line.
I am also attaching a original reactive forcefield (with parameters from article) file but unfortunately it gives some runtime error. Please help fix it if possible.

PS: This is a quick manual check I did. There might be other errors as well.

Thanks
regards
Asif Altaf Shah

79

General Questions and Answers / Re: DOS vs TS

« Last post by Jahanzaib on October 8, 2024, 21:49 »

Thank you Dr Blom.

The reason for using only a few k-points for the TS calculation in my case is that I have a very long stanene nanoribbon, which generally requires only a few k-points. In some cases, I observed a bigger peak in the DOS, but when I examined the transmission spectrum (TS) at zero bias for the same system, that peak was not present. To my understanding, the transmission function T(E), which can be considered a density of states (DOS) weighted by the probability of electron transfer from the device region to the left or right electrodes.

I think if I increase the number of k-points in the B direction only in stanene nanoribbon, I might observe similar peaks. For a 1D system like this, I assume that increasing k-points in the B direction should be fine??

80

General Questions and Answers / Re: Error in MoS2 forcefield implementation in QuantumATK

« Last post by Anders Blom on October 8, 2024, 21:29 »

Ok, I can confirm there is a difference, but to me it looks like it's only one line difference, viz. one of the torsions is left out (we have 47, the article has 48). Perhaps the article was updated after it was published. But you said multiple lines, I don't see that, so please share your differences.

Note that you can easily use the ReaxFF version from the article in QuantumATK, by downloading and saving it as a text file, and then use the ReaxFFPotential class (https://docs.quantumatk.com/manual/Types/ReaxFFPotential/ReaxFFPotential.html) to define the potential set. Then you can also directly compare if the article version gives stable structures.

It would also be helpful for us if you can share some scripts that show that the QuantumATK version give these distortions, and then we can verify if the article version works better.