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The linked question(s) below describes a DIY project to simulate how Xenes (honeycomb nets of atoms like graphehe) behave on single crystal surfaces. Behaviors include rotation, strain, and heigh modulations (moires, bucklings, etc.) and will in the future include defects.

The simplest implementation could just use a Lennard-Jones potential for Xene bond lengths, ignore bond angles and use a sinusoidal-like periodic potential for interaction with an unperturbed crystal surface as shown below.

But now I am considering get my feet wet in classical molecular dynamics proper, and starting to incorporate some open source molecular dynamics force fields by using parameterizations in my script.

My guess is that open source force fields are likely to be in a form that is easy to plug in to open source MD software, and someone might comment "Why don't you just run program X instead of writing something likely to be less powerful and slower?" and the answer to that is because that's just my modus operandi I always try to calculate things first myself before running someone else's program for reasons of fun and insight.

Question: DIY molecular dynamics for Xenes on crystal surfaces; where can I get applicable open-source force field parameters that I can use in my scripts?

Here are the types of atoms I'm interested in; I certainly don't need all of them, so any place to start will already be helpful.

  • Xenes of interest include honeycombs of C, Pb, Si, Ge, Sn, BN, SiC, (graphene, plumbene, silicene, germanene, stanene, 2D boron nitride and silicon carbide)...
  • Crystal surfaces of interest include Pb, Au, Ag, hexagonal BN, hexagonal SiC, epitaxial graphene

Related:


My nascent DIY model, from here (click for larger)

enter image description here

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    $\begingroup$ What does open-source force field mean? Force field is not a code, it is a mathematical function + parameter. have you tried OpenKim? $\endgroup$
    – Greg
    Mar 12, 2022 at 1:36
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    $\begingroup$ @Greg Yes you are right, I need a better word for this. Let me try to explain what I mean. If I had a set of parameters, but there is no openly available explanation how to write an expression using those parameters exactly as they are intended to be used, I'd call that "closed" in the sense that I'd have to run someone else's code to use those parameters; I couldn't use them myself. However if they came with a complete explanation, or if their use was standardized and a reference was available, I'd call it "open". $\endgroup$
    – uhoh
    Mar 12, 2022 at 1:45
  • $\begingroup$ @Greg Thanks very much for OpenKim! If I look at (just for exampe) this parameter set I see lots of parameters, and they are likely ready to go for any OpenKim compliant simulator. However if I want to write a simple MD simulator myself for instructional purposes, I haven't a clue how to use them. $\endgroup$
    – uhoh
    Mar 12, 2022 at 1:48
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    $\begingroup$ AFAK all algorithm in OpenKIM is published and you can read the papers. Your unfamiliarity with the field and the literature doesn’t mean it was “closed” “or secret”. Eg. you can read the EDIP papers (the Ga data should have something similar): openkim.org/id/EDIP__MD_506186535567_002 $\endgroup$
    – Greg
    Mar 12, 2022 at 15:20
  • $\begingroup$ @Greg my "closed" would be there is no openly available explanation how to write an expression using those parameters exactly as they are intended to be used Since there is, then of course it isn't. However, I may have to refactor this question now. I may temporarily delete it if I can't rewrite it by tomorrow. $\endgroup$
    – uhoh
    Mar 12, 2022 at 15:33

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