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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...
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...