Messages

31

General Questions and Answers / Re: The r_13 parameter in Stiwe3Potential

« on: February 9, 2018, 11:17 »

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.

32

General 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.

33

General Questions and Answers / 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.

34

General 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.

35

General Questions and Answers / Re: Double counting in combined sw and tersoff potential

« on: September 21, 2017, 13:04 »

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 http://www.sciencedirect.com/science/article/pii/S0927025606002023).
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 https://docs.quantumwise.com/manuals/Types/TersoffTriplePotential/TersoffTriplePotential.html#tersofftriplepotential-c  for more details.
Finally, the SW potential classes need to be added to the potential set.

36

General 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.

37

General Questions and Answers / Re: interface thermal resistance(or conductance)

« on: August 4, 2017, 09:31 »

If you are talking about an interface system that looks like copper-substrate / graphene layer / copper substrate (i.e. something like in https://journals.aps.org/prb/abstract/10.1103/PhysRevB.88.045444) 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.

38

General Questions and Answers / Re: Young’s modulus of graphene

« on: August 3, 2017, 22:18 »

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

39

General Questions and Answers / Re: Questions about Geometry Optimization of Defective Graphene with Al atoms

« on: July 28, 2017, 11:58 »

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 (http://docs.quantumwise.com/manuals/Types/MorsePotential/MorsePotential.html#morsepotential-) 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.

40

Future Releases / Re: Combining potentials of classical

« on: July 24, 2017, 16:34 »

You cannot select particle types when you set up a ReaxFF potential (see http://docs.quantumwise.com/manuals/Types/ReaxFFPotential/ReaxFFPotential.html#reaxffpotential-c). It automatically acts on all particles in the system, meaning that the reax parameter file must contain parameters for at least all elements in the configuration.
If you wanted the potential not to act on some of the elements, you would have to add these as dummy elements with zero interaction to the reax parameter file.

Once you have set up a ReaxFF potential for your entire system, you can add (almost) any other potential on top of the ReaxFF potential to extend the potential if necessary.

41

Future Releases / Re: Combining potentials of classical

« on: July 22, 2017, 12:09 »

In principle you can combine all potentials, not only Lennard Jones and Tersoff.
There are some limitations for EAM and ReaxFF, which means that a ReaxFF or EAM potential cannot be used for only a part of the configuration, but they must be defined for all atoms in the system (for EAM one can make a workaround, if necessary).
Still, other potentials, such as Lennard Jones, can be added to a ReaxFF or EAM potential, as well.

42

General Questions and Answers / Re: how to analyse lammps trajectory file in ATK

« on: July 20, 2017, 17:24 »

With these settings you should in principle be able to import your trajectory in the labfloor in VNL.
VNL looks for the log file that has been generated by lammps,  make sure that this file ends with ".lammps", otherwise VNL will not detect it as lammps file. Rename the file if it has a different extension.
From this log file, VNL will read the name of the lammps trajectory file and import the trajectory.
The trajectory should show up under the name "xxx" if "xxx.lammps" is the name of the lammps log file.
You can treat it as a normal VNL MD-Trajectory. i.e. open it in the Viewer / MovieTool / MD-Analyzer, etc.
 If you want to send a snapshot of the trajectory to the Script Generator, open the lammps trajectory with the MovieTool, play the movie until you have reached the desired snapshot, and then use the blue "Send To" arrow in the lower right-hand corner to send the configuration to the ScriptGenerator.
If you haven't done so already, you should read the tutorial http://docs.quantumwise.com/tutorials/lammps_trajectories/lammps_trajectories.html, everything should be explained there.

43

General Questions and Answers / Re: Stress Error

« on: July 12, 2017, 13:58 »

If you use the ScriptGenerator:
You will only do a stress optimization if you uncheck the "Constrain Lattice Vectors" box, no matter what stress error tolerance value you give.

If you set up the calculation in a script:
Whether you do a stress optimization or not, depends on if you set the parameter

Code

disable_stress

to True (no stress optimization) or False (so a stress optimization).
If you don't set this keyword, the default is False, that means by default you do a stress optimization (see http://docs.quantumwise.com/manuals/Types/OptimizeGeometry/OptimizeGeometry.html#optimizegeometry-f).
That also means you will perform a stress optimization, even if you don't explicitly give the stress error tolerance (i.e. via the

Code

max_stress

keyword). In that case the default stress tolerance of 0.1*GPa will be used.
Same with the

Code

target_stress

, here the default is 0.0*GPa, unless you specify something else.

44

General Questions and Answers / Re: Stress Error

« on: July 10, 2017, 12:49 »

The stress error tells you by how much the current stress deviates from the given target stress. The stress error must be below the given stress tolerance to consider the stress optimization converged.

45

General Questions and Answers / Re: Phonon transmission sprectrum

« on: July 2, 2017, 14:12 »

I would guess the problem comes from the fact that the Tersoff-potential only describes the local bonded interactions within the graphene-layers, but does not account for the longer-ranged dispersion interactions between adjacent layers. This is  a known short-coming of Tersoff- and similar potentials. If there is no interactions between adjacent layers, then phonons cannot be transmitted across different layers.
This is typically corrected by adding a Lennard-Jones potential between Carbon-atoms, that accounts for the dispersion interactions, as e.g. in http://dx.doi.org/10.1103/PhysRevB.88.045444 .