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Messages - Julian Schneider

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This problem was known to appear in very rare cases, but should have been fixed in the QATK-Q-2019.12 version.
Which QATK version are you using?


Questions and Answers / Re: Phonon DOS
« on: September 2, 2020, 10:05 »

these fluctuations are not uncommon for Nose-Hoover-like thermostats, especially for small systems like yours. One could try to increase the thermostat timescale or the Nose-Hoover chain length (in script), but this would probably only decrease the fluctuations a bit and with DFT-MD it is probably not so easy to run a few test simulations.

If it is only about the stability of the system at the given temperature, then you could use NVT-Berendsen instead. This should give a much more constant temperature than Nose-Hoover.
Berendsen is a bit more approximate in how exactly the canonical ensemble is reproduced, but just for qualitatively checking the thermal stability it should be ok.



The NEB Builder plugin requires atoms to have the exact same position before constraints can be applied, so this would probably not help in your case.

I think the most straightforward way to fix your problem would be to manually (e.g. in  Coordinate Tools > Coordinate List plugin, see attached image) change the problematic atom positions so that they match in the first and last image.

The potential you selected uses a polarization energy term in which the dipole moments on each atom needs to be computed self-consistently via optimization at each MD step
(see e.g. or ).

In your case the optimization of the dipoles did not meet the convergence criteria, which results in this error message.
Without knowing what system you are looking at I can only speculate that this could be due to that you have an unstable system which is tricky to optimize (i.e. atoms too close,) or not suited for this type of potential.
You could try to pre-optimize it with a simpler potential or use a simpler potential alltogether (if available).

An advanced possibility would be to change the optimization options in the Madden potential by adding a MaddenOptimizationOption to the potential set (see example in
Here the parameters to play around with would be to increase the polMaxIterations (i.e. the max number of optimization iterations, default 200), or to increase the polFTol or polGradTol values (tolerance to stop the optimization, default values 10**-10 and 10**-4)

Questions and Answers / Re: Repetition score/ Electrode lengths
« on: October 1, 2018, 13:59 »
The repetition score is a measure for how many of the atoms in the electrode candidate can be repeated beyond the electrode extension in the central region by translating them by a multiple of the electrode length, minus the number of atoms in the electrode candidate itself.

    As an example: If we have 8 atoms in the electrode candidate, and we find 2 complete
    repetitions of these atoms beyond the electrode extension (translating them by 1*electrode_length, and by 2*electrode_length)
    then the score for this candidate would be 8.
    If we find exactly one complete repetition, the score would be zero.
    If only 4 of the 8 atoms are repeated, the score would be -4.

So, a negative score can still mean that the electrode candidate is suitable, but it is not always guaranteed.

Note that, all this applies to "full" (i.e. not minimal) electrodes.

If I want to make the interface with 3A between two materials, is it correct to put -24.0 as z value as the first picture?
Yes, that should do it.

With this structure having negative B-Y value, LAMMPS input file showed an error because it yhi value is smaller than ylo value as shown the 2nd.
I think this would be fixed if you edit the LAMMPS file to use ylo -211 and yhi 0, or, if that does not work, to ylo 0 and yhi 211. This would shift the origin of the cell, but then you'd probably also need to change the sign of the xy value in the LAMMPS file  from -121 to 121.. But please double check that the structure in LAMMPS is still the correct one. after this change.

The parameter r_13 can be used to set an additional cutoff, i.e. if r_13 is set greater or equal than zero and if the distance between particle_type1 and particle_type3 is greater than r_13 , then the three body interaction term V_3 is neglected. By default r_13 is set to a negative value, which means it is ignored.

Questions and Answers / Re: pH value - molecular dynamics
« on: December 15, 2017, 09:24 »
Modelling a given pH value explicitly, i.e. via introducing a certain number of H3O+ ions is normally difficult because, unless you go to very extreme pH values, the H3O+ concentration is so low that you'd have to use a huge number of water molecules. That also requires that you'd need to use DFT or at least a very good reactive force field, to correctly model proton transfer.

Another more implicit approach is, if you know what effect the pH has on your system (e.g. if you have acidic groups) , to manually fix the protonation state of these groups according to the given pH, e.g. if you have an acidic group and you want to simulate neutral pH, the acidic group would most likely be present in the deprotonated state.

A good thing to start with  could be to try and find out what the effect of pH is on the components of your system, for example if water molecules might dissociate at the edges of your graphene flake, leading to adsorbed OH groups, whose behavior might then be pH dependent.

General Questions / Re: LAMMPS plugins
« on: November 13, 2017, 17:34 »
The LAMMPS exporter plugin is only available in newer VNL versions.
You need to upgrade to a newer VNL version if you want to use the LAMMPS exporter.
In VNL-2014 the LAMMPS plugin only contains the LabFloor importer plugin to read the output of LAMMPS simulations.

Questions and Answers / Re: Questions about potentials
« on: September 22, 2017, 09:21 »
Regarding the potentials for C-O systems:
Currently, we only provide ReaxFF potentials, for such systems. The first one in the list sounds as if it may be close to what you are looking for ("ReaxFF reactive force field for molecular dynamics simulations of hydrocarbon oxidation"), however, you'd need to check if it works for graphene, as well. And it might be that it hasn't been parameterized to reproduce the dynamical matrix.
We are working on implementing REBO potentials at the moment, I'll check whether that can be extended to AIREBO potentials.

Bonds and potentials only depend on the elements, they are not influenced by the changing the masses of an element.

You can switch off the Si-Si interaction in  the Tersoff potential, but I would not recommend it, because, since the Tersoff potential is a manybody potential, it is not really made for disentangling the two and three body parts, meaning that removing the Si-Si interactions might have unpredictable consequences on the Si-O interactions.
Instead I would suggest to use the Tersoff Si-O potential for the entire system, as the Si-Si interaction in that potential are very similar to the original Tersoff potential for Silicon (Tersoff_Si_1988), with only slight modifications to few parameters (see the paper
You could test the potential for a silicon system alone to see if it reproduces the desired properties for silicon sufficiently well.

If you really want to use the SW potential for Si-Si, you have to follow the genral procedure to modify potentials, as outlined in the tutorial above, in your case you specifically have to remove the TersoffSingleTypePotential for Si and instead of the TersoffMixitPotential for Si-O you have to use the TersoffTriplePotential and specifiy all Si-O pair parameters manually using the combination rules given in the paper.
See also  for more details.
Finally, the SW potential classes need to be added to the potential set.

Questions and Answers / Re: Questions about potentials
« on: September 18, 2017, 14:54 »
i) If there are possible to obtain the phonon dispersion using reaxFF, please let me know.
In principle there should be no problem calculating the Phonon dispersion with ReaxFF, but phonons are probably not the primary type of property that ReaxFF potentials are fitted to.
Moreover, many ReaxFF potentials only give good results for the context they are parameterized for.  E.g. a potential that is parameterized primarily for SP3 Carbon atoms, might not give good results when applied to graphene. You should check the publication for that potential to find out if its the purpose it has been designed for, matches your application.

ii) Is it possible to use airebo potential? Actually, I know the parameter about the airebo potential.
Unfortunately Airebo potentials are currently not implemented in ATK. I'll check if there is a workaround, but I don't think so.

iii) If possible, I want you to recommend some potentials that can support C-O bonding.
I'll check if I can find a suitable potential.

If you are talking about an interface system that looks like copper-substrate / graphene layer / copper substrate (i.e. something like in or copper substrate / bulk-like graphene layers then yes we can simulate it.
Just one copper substrate and a single layer of graphene on top, bounded by vacuum, would probably be difficult, it depends how one would define thermal conductance in a meaningful way for that case.

To calculate the intrefacial thermal conductance via MD (as in the tutorial) one would probably have to use a classical potential (e.g. EAM for copper and Tersoff for graphene) and couple the interactions between copper and graphene via Lennard Jones-potentials (as in the paper mentioned above).

Phonon transmission via NEMD would also be possible, here one could even try using DFT.

We don't have a tutorial on that particular case interface but the main challenge here is primarily setting up the classical potentials, the rest should be more or less analogue to the tutorial and the paper mentioned above.

The elastic constants analysis object is primarily suited for bulk materials, not for 2D- or 1D-systems, so the script should be more correct.

The Lennard-Jones potential is probably not a suitable potential to model bonding between atoms, as it is a non-bonded potential which only accounts for dispersion interactions (plus a repulsive part).
The best potential and parameters depends on what you want to simulate.
If you already know that the atoms will bond and how they will bond and you want to maintain the bonding in an MD simulation, a Morse-potential ( might be a better choice than LJ to keep the bonds stable.
If you don't know if and how the atoms are bonding then it is more difficult to select a  suitable potential. In this case it might make more sense to run a DFT calculation (at least on a small part of the system that contains your C-Pt-O2 group) to understand how that part behaves.

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