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Re: [lammps-users] Moire potential implementation
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Re: [lammps-users] Moire potential implementation


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Tue, 27 Jun 2017 08:25:44 -0400



On Tue, Jun 27, 2017 at 5:07 AM, Nicolas Leconte <lecontenicolas@...24...> wrote:
Axel, I've looked at the Kolmogorov Crespi implementation. It helped me get some better understanding of my rather vague question. 

So, to rephrase, my question is if there already exists an implementation where the potential is given based on the relative position of the top 2D layer with respect to the bottom 2D layer (relative position of the top atoms with respect to the substrate)? That would greatly help me implementing my own _expression_ (creating my own .cpp file) without having to understand all the inner workings of LAMMPS.

​no, there isn't. as far as i can tell, this pair style and the two fixes i mentioned are conceptionally the closest​ to what you seem to be after.
there are a number of challenges in your description, e.g. how would you identify the top/bottom layer, are they dynamic or static?

​you do not have to understand *all* the inner workings, but you need to study LAMMPS more closely than if you were planning to implement a simple pairwise additive potential. you also need to get use to considering, that in LAMMPS ​everything has to be implemented in parallel and that LAMMPS uses domain decomposition, so that each processor only "owns" a subset of the system and a "halo" of so-called ghost atoms around it.

i suggest, that before digging into the source, you should write down a detailed, step-by-step description of how you would want to implement the interaction you would like to implement (ideally in some simple pseudo-code) and post it here, to get some suggestions about how to actually realize this from within LAMMPS.

​axel.​

 

However, from what I've seen in the list of available user contributions, everything is based on the distance (and possibly angle) of two (three) atoms, leading to pairwise interactions.

Regards,
Nicolas

On Tue, Jun 27, 2017 at 3:30 PM, Nicolas Leconte <lecontenicolas@...24...> wrote:
@Steve. Thanks for this clarification.

@Axel, thanks for the references. I may help me to implement by own potential.

On Mon, Jun 26, 2017 at 10:01 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:


On Mon, Jun 26, 2017 at 6:00 AM, Nicolas Leconte <lecontenicolas@...24...> wrote:
Hi,

Not a regular LAMMPS user for now, but I was wondering if there is an easy, or not-so easy, way to implement a non-pairwise potential in LAMMPS. The model I have describes accurately the potential felt by one layer deposited on another bilayer. 

Its parameters are the interlayer distance as well as the displacement given by x and y coordinates of an atom in the top layer with respect to the bottom layer, thus providing information for any stacking possible stacking configuration encountered in a moire system.

I have looked into the manual as well as existing threads, but I have not found much beyond the implementation of simple pairwise potentials (or simple improvements thereupon).


​structural biases have also been implemented as fixes, e.g. these:



​axel.​

 

Any suggestion or reference to existing attempts to do this before I dive into the source code?

Thank you.

Regards,
Nicolas

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--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.





--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.